diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/cmake-local/gcc.cmake b/methods/ring/utils/fast_gicp/thirdparty/nvbio/cmake-local/gcc.cmake new file mode 100644 index 0000000000000000000000000000000000000000..6898f652b480c36e1cd9be8e99b83eaae7419fef --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/cmake-local/gcc.cmake @@ -0,0 +1,25 @@ +if (CMAKE_COMPILER_IS_GNUCC) + # common GCC compiler flags + # we add -Wno-unknown-pragmas because of nvcc's #pragma unroll + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -Wno-unknown-pragmas -Wstrict-aliasing=0") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-unknown-pragmas -Wstrict-aliasing=0") + if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 4.8 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 4.8) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-local-typedefs -Wno-unused-result") + endif() + + set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG") + if (CMAKE_SYSTEM_PROCESSOR MATCHES "Intel" OR CMAKE_SYSTEM_PROCESSOR MATCHES "x86") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -msse4.2 -mpopcnt -funroll-loops") + endif() + + if(WERROR) + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Werror") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Werror") + endif() + + if(PROFILING) + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pg") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") + endif() +endif() + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/cmake-local/nvbio.cmake b/methods/ring/utils/fast_gicp/thirdparty/nvbio/cmake-local/nvbio.cmake new file mode 100644 index 0000000000000000000000000000000000000000..d2d22f7fe95fa74f8112db05be7dd1196f2d27bd --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/cmake-local/nvbio.cmake @@ -0,0 +1,84 @@ +# this keeps track of the targets that are generated for doxygen, +# used to set up the doc target later on +# unfortunately, this has to be a property instead of a variable due to cmake's +# weird scoping rules +set_property(GLOBAL PROPERTY _nvbio_doxygen_target_list "") + +# set up doxygen for a given nvbio module +# checks if there's a Doxyfile.in in the module directory +# and sets up build rules to generate documentation for this module +macro(_nvbio_doxygen_module name) + if (DOXYGEN_FOUND) + # set up paths + set(doxy_in_directory "${CMAKE_CURRENT_SOURCE_DIR}/doxy") + set(doxy_out_directory "${CMAKE_CURRENT_BINARY_DIR}/doxy") + # set up the path to the Doxyfile.in for the current module + set(doxyfile_in "${doxy_in_directory}/Doxyfile.in") + # set up the path to the Doxyfile that we'll generate from Doxyfile.in + set(doxyfile_out "${doxy_out_directory}/Doxyfile") + + # test if the current module has a Doxyfile.in + if (EXISTS ${doxyfile_in}) + message("==> Found Doxygen file for module ${name}") + # parse the Doxyfile.in with cmake to substitute build variables and generate the Doxyfile + configure_file(${doxyfile_in} ${doxyfile_out} @ONLY) + add_custom_target(doc_${name}_copy + ${CMAKE_COMMAND} -E copy_directory ${doxy_in_directory} ${doxy_out_directory}) + add_custom_target(doc_${name} + DEPENDS doc_${name}_copy + COMMAND ${DOXYGEN_EXECUTABLE} ${doxyfile} + WORKING_DIRECTORY ${doxy_out_directory} + COMMENT "Generating API documentation for ${name} with Doxygen" VERBATIM) + set_property(GLOBAL APPEND PROPERTY _nvbio_doxygen_target_list doc_${name}) + endif() + endif() +endmacro(_nvbio_doxygen_module) + +# generate the doc target +# doc will depend on all doc_* targets generated for any modules with doxygen.in files +macro(nvbio_doxygen) + if (DOXYGEN_FOUND) + get_property(_targets GLOBAL PROPERTY _nvbio_doxygen_target_list) + add_custom_target(doc DEPENDS ${_targets}) + endif() +endmacro(nvbio_doxygen) + +# start a new nvbio module (library or executable) +# this will match a MSVC project +macro(nvbio_module name) + set(_current_nvbio_module ${name}) + set(_current_nvbio_module_srcs "") + set(_current_nvbio_directory "") + + _nvbio_doxygen_module(${name}) +endmacro(nvbio_module) + +# add sources to the current module or directory +macro(addsources) + set(_src_list_TMP "") + # add the directory path + foreach(l ${ARGN}) + list(APPEND _src_list_TMP ${_current_nvbio_directory}${l}) + endforeach() + + if (NOT "${_current_nvbio_directory}" STREQUAL "") + # chop the trailing '/' off the group name + string(REGEX REPLACE "/$" "" _tmp_group ${_current_nvbio_directory}) + # convert '/' into '\\' + string(REGEX REPLACE "/" "\\\\" _tmp_group ${_tmp_group}) + source_group(${_tmp_group} FILES ${_src_list_TMP}) + unset(_tmp_group) + else() + source_group("" FILES ${_src_list_TMP}) + endif() + + list(APPEND ${_current_nvbio_module}_srcs ${_src_list_TMP}) + unset(_src_list_TMP) +endmacro(addsources) + +# add a module directory +macro(nvbio_add_module_directory directory) + set(_current_nvbio_directory "${directory}/") + include(${directory}/CMakeLists.txt) +endmacro(nvbio_add_module_directory) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BGZF.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BGZF.cpp new file mode 100644 index 0000000000000000000000000000000000000000..dda5f8b1c7c8d9357f4802f8d5341b4d4b336354 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BGZF.cpp @@ -0,0 +1,441 @@ +// *************************************************************************** +// BGZF.cpp (c) 2009 Derek Barnett, Michael Str�mberg +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 8 December 2009 (DB) +// --------------------------------------------------------------------------- +// BGZF routines were adapted from the bgzf.c code developed at the Broad +// Institute. +// --------------------------------------------------------------------------- +// Provides the basic functionality for reading & writing BGZF files +// *************************************************************************** + +#include "BGZF.h" +#include +#include +#include + +using namespace BamTools; +using namespace nvbio; +using std::string; +using std::min; + +namespace BamTools { + +struct BgzfThread : public Thread +{ + void set_data(BgzfData* data) { m_data = data; } + + void run() + { + const uint32 tid = ++m_data->BackgroundThreads; + log_verbose( stderr, "starting BAM output thread %u\n", tid ); + + while (m_data->BackgroundThreads != 0) + { + if (m_data->WorkCounter > 0u) + { + const int32 id = --m_data->WorkCounter; + + if (id >= 0) + { + m_data->BlockLengths[id] = m_data->DeflateBlock( id, m_data->CurrentBlockSize ); + + --m_data->ActiveThreads; + } + } + } + } + + BgzfData* m_data; +}; + +BgzfData::BgzfData(const uint32_t threads) + : UncompressedBlockSize(DEFAULT_BLOCK_SIZE) + , CompressedBlockSize(MAX_BLOCK_SIZE) + , BlockLength(0) + , BlockOffset(0) + , BlockAddress(0) + , IsOpen(false) + , IsWriteOnly(false) + , Stream(NULL) + , UncompressedBlock(NULL) + , CompressedBlock(NULL) + , BackgroundThreads( 0 ) + , ActiveThreads( 0 ) + , WorkCounter( 0 ) + , ThreadCount( threads == uint32(-1) ? nvbio::num_physical_cores() : 4 ) +{ + try { + CompressedBlock = new char[CompressedBlockSize * ThreadCount * 4]; + UncompressedBlock = new char[UncompressedBlockSize * ThreadCount]; + BlockLengths = new int [ThreadCount]; + ThreadPool = new BgzfThread[ThreadCount]; + + // launch background threads + for (uint32_t i = 0; i < ThreadCount; ++i) + { + ThreadPool[i].set_data( this ); + ThreadPool[i].create(); + } + + // poll until all background threads are ready + while (BackgroundThreads < ThreadCount) {} + } + catch( std::bad_alloc& ) { + printf("ERROR: Unable to allocate memory for our BGZF object.\n"); + exit(1); + } +} + +// destructor +BgzfData::~BgzfData(void) +{ + // stop background threads + BackgroundThreads = 0; + + for (uint32_t i = 0; i < ThreadCount; ++i) + ThreadPool[i].join(); + + if(CompressedBlock) delete [] CompressedBlock; + if(UncompressedBlock) delete [] UncompressedBlock; + if(BlockLengths) delete [] BlockLengths; + if(ThreadPool) delete [] ThreadPool; +} + +// closes BGZF file +void BgzfData::Close(void) { + + if (!IsOpen) { return; } + IsOpen = false; + + // flush the BGZF block + if ( IsWriteOnly ) { FlushBlocks(); } + + // flush and close + fflush(Stream); + fclose(Stream); +} + +// compresses the current block +int BgzfData::DeflateBlocks(void) +{ + // count the number of blocks to deflate + int32_t blockSize = UncompressedBlockSize; + while (1) + { + const int n_blocks = (BlockOffset + blockSize-1) / blockSize; + + #if 0 + // single threaded implementation + for (int i = 0; i < n_blocks; ++i) + BlockLengths[i] = DeflateBlock( i, blockSize ); + #else + CurrentBlockSize = blockSize; // set current block size + WorkCounter = n_blocks; // set number of blocks to process + ActiveThreads = n_blocks; // activate background threads + + // poll until the blocks are being processed + while (ActiveThreads > 0) {} + #endif + + // check whether compression failed for any of the blocks + bool ok = true; + for (int i = 0; i < n_blocks; ++i) + { + if (BlockLengths[i] < 0) + ok = false; + } + + if (ok) + return n_blocks; + + // compression failed: reduce block size + blockSize -= 1024; + if (blockSize <= 0) + { + printf("ERROR: input reduction failed.\n"); + exit(1); + } + } + return 0; +} + +// compresses the current block +int BgzfData::DeflateBlock(int32_t id, const unsigned int uncompressedBlockSize) +{ + // check if the block is within the proper range + if (uncompressedBlockSize * id >= BlockOffset) + return 0; + + // initialize the gzip header + char* buffer = CompressedBlock + id * CompressedBlockSize; + unsigned int bufferSize = CompressedBlockSize; + + memset(buffer, 0, 18); + buffer[0] = GZIP_ID1; + buffer[1] = (char)GZIP_ID2; + buffer[2] = CM_DEFLATE; + buffer[3] = FLG_FEXTRA; + buffer[9] = (char)OS_UNKNOWN; + buffer[10] = BGZF_XLEN; + buffer[12] = BGZF_ID1; + buffer[13] = BGZF_ID2; + buffer[14] = BGZF_LEN; + + // loop to retry for blocks that do not compress enough + int inputLength = std::min( uncompressedBlockSize, BlockOffset - uncompressedBlockSize * id ); + int compressedLength = 0; + + z_stream zs; + zs.zalloc = NULL; + zs.zfree = NULL; + zs.next_in = (Bytef*)UncompressedBlock + id * uncompressedBlockSize; + zs.avail_in = inputLength; + zs.next_out = (Bytef*)&buffer[BLOCK_HEADER_LENGTH]; + zs.avail_out = bufferSize - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH; + + // initialize the zlib compression algorithm + if(deflateInit2(&zs, Z_DEFAULT_COMPRESSION, Z_DEFLATED, GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY) != Z_OK) { + printf("ERROR: zlib deflate initialization failed.\n"); + exit(1); + } + + // compress the data + int status = deflate(&zs, Z_FINISH); + if(status != Z_STREAM_END) { + + deflateEnd(&zs); + + // reduce the input length and try again + if(status == Z_OK) + return -1; + } + + // finalize the compression routine + if(deflateEnd(&zs) != Z_OK) { + printf("ERROR: deflate end failed.\n"); + exit(1); + } + + compressedLength = zs.total_out; + compressedLength += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH; + + if(compressedLength > MAX_BLOCK_SIZE) { + printf("ERROR: deflate overflow.\n"); + exit(1); + } + + // store the compressed length + BgzfData::PackUnsignedShort(&buffer[16], (unsigned short)(compressedLength - 1)); + + // store the CRC32 checksum + unsigned int crc = crc32(0, NULL, 0); + crc = crc32(crc, (Bytef*)UncompressedBlock + id * uncompressedBlockSize, inputLength); + BgzfData::PackUnsignedInt(&buffer[compressedLength - 8], crc); + BgzfData::PackUnsignedInt(&buffer[compressedLength - 4], inputLength); + + return compressedLength; +} + +// flushes the data in the BGZF block +void BgzfData::FlushBlocks(void) { + + // compress the data block + int n_blocks = DeflateBlocks(); + + // flush the data to our output stream + for (int i = 0; i < n_blocks; ++i) + { + int blockLength = BlockLengths[i]; + + int numBytesWritten = (int)fwrite(CompressedBlock + i * CompressedBlockSize, 1, blockLength, Stream); + + if(numBytesWritten != blockLength) { + printf("ERROR: Expected to write %u bytes during flushing, but wrote %u bytes.\n", blockLength, numBytesWritten); + exit(1); + } + + BlockAddress += blockLength; + } + BlockOffset = 0; +} + +// de-compresses the current block +int BgzfData::InflateBlock(const int& blockLength) { + + // Inflate the block in m_BGZF.CompressedBlock into m_BGZF.UncompressedBlock + z_stream zs; + zs.zalloc = NULL; + zs.zfree = NULL; + zs.next_in = (Bytef*)CompressedBlock + 18; + zs.avail_in = blockLength - 16; + zs.next_out = (Bytef*)UncompressedBlock; + zs.avail_out = UncompressedBlockSize; + + int status = inflateInit2(&zs, GZIP_WINDOW_BITS); + if (status != Z_OK) { + printf("inflateInit failed\n"); + exit(1); + } + + status = inflate(&zs, Z_FINISH); + if (status != Z_STREAM_END) { + inflateEnd(&zs); + printf("inflate failed\n"); + exit(1); + } + + status = inflateEnd(&zs); + if (status != Z_OK) { + printf("inflateEnd failed\n"); + exit(1); + } + + return zs.total_out; +} + +void BgzfData::Open(const string& filename, const char* mode) { + + if ( strcmp(mode, "rb") == 0 ) { + IsWriteOnly = false; + } else if ( strcmp(mode, "wb") == 0) { + IsWriteOnly = true; + } else { + printf("ERROR: Unknown file mode: %s\n", mode); + exit(1); + } + + Stream = fopen(filename.c_str(), mode); + if(!Stream) { + printf("ERROR: Unable to open the BAM file %s\n", filename.c_str() ); + exit(1); + } + IsOpen = true; +} + +int BgzfData::Read(char* data, const unsigned int dataLength) { + + if (dataLength == 0) { return 0; } + + char* output = data; + unsigned int numBytesRead = 0; + while (numBytesRead < dataLength) { + + int bytesAvailable = BlockLength - BlockOffset; + if (bytesAvailable <= 0) { + if ( ReadBlock() != 0 ) { return -1; } + bytesAvailable = BlockLength - BlockOffset; + if ( bytesAvailable <= 0 ) { break; } + } + + char* buffer = UncompressedBlock; + int copyLength = min( (int)(dataLength-numBytesRead), bytesAvailable ); + memcpy(output, buffer + BlockOffset, copyLength); + + BlockOffset += copyLength; + output += copyLength; + numBytesRead += copyLength; + } + + if ( BlockOffset == BlockLength ) { + BlockAddress = ftell(Stream); + BlockOffset = 0; + BlockLength = 0; + } + + return numBytesRead; +} + +int BgzfData::ReadBlock(void) { + + char header[BLOCK_HEADER_LENGTH]; + int64_t blockAddress = ftell(Stream); + + int count = (int)fread(header, 1, sizeof(header), Stream); + if (count == 0) { + BlockLength = 0; + return 0; + } + + if (count != sizeof(header)) { + printf("read block failed - count != sizeof(header)\n"); + return -1; + } + + if (!BgzfData::CheckBlockHeader(header)) { + printf("read block failed - CheckBlockHeader() returned false\n"); + return -1; + } + + int blockLength = BgzfData::UnpackUnsignedShort(&header[16]) + 1; + char* compressedBlock = CompressedBlock; + memcpy(compressedBlock, header, BLOCK_HEADER_LENGTH); + int remaining = blockLength - BLOCK_HEADER_LENGTH; + + count = (int)fread(&compressedBlock[BLOCK_HEADER_LENGTH], 1, remaining, Stream); + if (count != remaining) { + printf("read block failed - count != remaining\n"); + return -1; + } + + count = InflateBlock(blockLength); + if (count < 0) { return -1; } + + if ( BlockLength != 0 ) { + BlockOffset = 0; + } + + BlockAddress = blockAddress; + BlockLength = count; + return 0; +} + +bool BgzfData::Seek(int64_t position) { + + int blockOffset = (position & 0xFFFF); + int64_t blockAddress = (position >> 16) & 0xFFFFFFFFFFFFLL; + + if (fseek(Stream, (long)blockAddress, SEEK_SET) != 0) { + printf("ERROR: Unable to seek in BAM file\n"); + exit(1); + } + + BlockLength = 0; + BlockAddress = blockAddress; + BlockOffset = blockOffset; + return true; +} + +int64_t BgzfData::Tell(void) { + return ( (BlockAddress << 16) | (BlockOffset & 0xFFFF) ); +} + +// writes the supplied data into the BGZF buffer +unsigned int BgzfData::Write(const char* data, const unsigned int dataLen) { + + // initialize + unsigned int numBytesWritten = 0; + const char* input = data; + unsigned int blockLength = UncompressedBlockSize * ThreadCount; + + // copy the data to the buffer + while(numBytesWritten < dataLen) { + unsigned int copyLength = min(blockLength - BlockOffset, dataLen - numBytesWritten); + char* buffer = UncompressedBlock; + memcpy(buffer + BlockOffset, input, copyLength); + + BlockOffset += copyLength; + input += copyLength; + numBytesWritten += copyLength; + + if(BlockOffset == blockLength) { + FlushBlocks(); + } + } + + return numBytesWritten; +} + +} // namespace BamTools \ No newline at end of file diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BGZF.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BGZF.h new file mode 100644 index 0000000000000000000000000000000000000000..04969d462a8851c2e9c8dfff665caef818cf10a7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BGZF.h @@ -0,0 +1,198 @@ +// *************************************************************************** +// BGZF.h (c) 2009 Derek Barnett, Michael Str�mberg +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 8 December 2009 (DB) +// --------------------------------------------------------------------------- +// BGZF routines were adapted from the bgzf.c code developed at the Broad +// Institute. +// --------------------------------------------------------------------------- +// Provides the basic functionality for reading & writing BGZF files +// *************************************************************************** + +#ifndef BGZF_H +#define BGZF_H + +#include + +// 'C' includes +#include +#include +#include + +// C++ includes +#include + +// zlib includes +#include + +// Platform-specific type definitions +#ifdef _MSC_VER + typedef char int8_t; + typedef unsigned char uint8_t; + typedef short int16_t; + typedef unsigned short uint16_t; + typedef int int32_t; + typedef unsigned int uint32_t; + typedef long long int64_t; + typedef unsigned long long uint64_t; +#else + #include +#endif + +namespace BamTools { + +// zlib constants +const int GZIP_ID1 = 31; +const int GZIP_ID2 = 139; +const int CM_DEFLATE = 8; +const int FLG_FEXTRA = 4; +const int OS_UNKNOWN = 255; +const int BGZF_XLEN = 6; +const int BGZF_ID1 = 66; +const int BGZF_ID2 = 67; +const int BGZF_LEN = 2; +const int GZIP_WINDOW_BITS = -15; +const int Z_DEFAULT_MEM_LEVEL = 8; + +// BZGF constants +const int BLOCK_HEADER_LENGTH = 18; +const int BLOCK_FOOTER_LENGTH = 8; +const int MAX_BLOCK_SIZE = 65536; +const int DEFAULT_BLOCK_SIZE = 65536; + +struct BgzfThread; + +struct BgzfData { + + // data members + unsigned int UncompressedBlockSize; + unsigned int CompressedBlockSize; + unsigned int BlockLength; + unsigned int BlockOffset; + uint64_t BlockAddress; + bool IsOpen; + bool IsWriteOnly; + FILE* Stream; + char* UncompressedBlock; + char* CompressedBlock; + + nvbio::AtomicInt32 BackgroundThreads; + nvbio::AtomicInt32 ActiveThreads; + volatile unsigned int CurrentBlockSize; + nvbio::AtomicInt32 WorkCounter; + uint32_t ThreadCount; + int volatile* BlockLengths; + BgzfThread* ThreadPool; + + // constructor & destructor + BgzfData(const uint32_t threads = uint32_t(-1)); + ~BgzfData(void); + + // closes BGZF file + void Close(void); + // opens the BGZF file for reading (mode is either "rb" for reading, or "wb" for writing + void Open(const std::string& filename, const char* mode); + // reads BGZF data into a byte buffer + int Read(char* data, const unsigned int dataLength); + // reads BGZF block + int ReadBlock(void); + // seek to position in BAM file + bool Seek(int64_t position); + // get file position in BAM file + int64_t Tell(void); + // writes the supplied data into the BGZF buffer + unsigned int Write(const char* data, const unsigned int dataLen); + + // checks BGZF block header + static inline bool CheckBlockHeader(char* header); + // packs an unsigned integer into the specified buffer + static inline void PackUnsignedInt(char* buffer, unsigned int value); + // packs an unsigned short into the specified buffer + static inline void PackUnsignedShort(char* buffer, unsigned short value); + // unpacks a buffer into a signed int + static inline signed int UnpackSignedInt(char* buffer); + // unpacks a buffer into a unsigned int + static inline unsigned int UnpackUnsignedInt(char* buffer); + // unpacks a buffer into a unsigned short + static inline unsigned short UnpackUnsignedShort(char* buffer); + + // compresses the given block + int DeflateBlock(int32_t id, const unsigned int blockSize); + // compresses the current block + int DeflateBlocks(void); + // flushes the data in the BGZF block + void FlushBlocks(void); + // de-compresses the current block + int InflateBlock(const int& blockLength); +}; + +// ------------------------------------------------------------- + +inline +bool BgzfData::CheckBlockHeader(char* header) { + + return (header[0] == GZIP_ID1 && + header[1] == (char)GZIP_ID2 && + header[2] == Z_DEFLATED && + (header[3] & FLG_FEXTRA) != 0 && + BgzfData::UnpackUnsignedShort(&header[10]) == BGZF_XLEN && + header[12] == BGZF_ID1 && + header[13] == BGZF_ID2 && + BgzfData::UnpackUnsignedShort(&header[14]) == BGZF_LEN ); +} + +// packs an unsigned integer into the specified buffer +inline +void BgzfData::PackUnsignedInt(char* buffer, unsigned int value) { + buffer[0] = (char)value; + buffer[1] = (char)(value >> 8); + buffer[2] = (char)(value >> 16); + buffer[3] = (char)(value >> 24); +} + +// packs an unsigned short into the specified buffer +inline +void BgzfData::PackUnsignedShort(char* buffer, unsigned short value) { + buffer[0] = (char)value; + buffer[1] = (char)(value >> 8); +} + +// unpacks a buffer into a signed int +inline +signed int BgzfData::UnpackSignedInt(char* buffer) { + union { signed int value; unsigned char valueBuffer[sizeof(signed int)]; } un; + un.value = 0; + un.valueBuffer[0] = buffer[0]; + un.valueBuffer[1] = buffer[1]; + un.valueBuffer[2] = buffer[2]; + un.valueBuffer[3] = buffer[3]; + return un.value; +} + +// unpacks a buffer into an unsigned int +inline +unsigned int BgzfData::UnpackUnsignedInt(char* buffer) { + union { unsigned int value; unsigned char valueBuffer[sizeof(unsigned int)]; } un; + un.value = 0; + un.valueBuffer[0] = buffer[0]; + un.valueBuffer[1] = buffer[1]; + un.valueBuffer[2] = buffer[2]; + un.valueBuffer[3] = buffer[3]; + return un.value; +} + +// unpacks a buffer into an unsigned short +inline +unsigned short BgzfData::UnpackUnsignedShort(char* buffer) { + union { unsigned short value; unsigned char valueBuffer[sizeof(unsigned short)];} un; + un.value = 0; + un.valueBuffer[0] = buffer[0]; + un.valueBuffer[1] = buffer[1]; + return un.value; +} + +} // namespace BamTools + +#endif // BGZF_H diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamAux.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamAux.h new file mode 100644 index 0000000000000000000000000000000000000000..fa468523dd3485efa58fb7815a36cf67ff575d13 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamAux.h @@ -0,0 +1,485 @@ +// *************************************************************************** +// BamAux.h (c) 2009 Derek Barnett, Michael Str�mberg +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 8 December 2009 (DB) +// --------------------------------------------------------------------------- +// Provides the basic constants, data structures, etc. for using BAM files +// *************************************************************************** + +#ifndef BAMAUX_H +#define BAMAUX_H + +#include "BGZF.h" + +// C inclues +#include +#include + +// C++ includes +#include +#include +#include +#include +#include + +namespace BamTools { + +// BAM constants +const int BAM_CORE_SIZE = 32; +const int BAM_CMATCH = 0; +const int BAM_CINS = 1; +const int BAM_CDEL = 2; +const int BAM_CREF_SKIP = 3; +const int BAM_CSOFT_CLIP = 4; +const int BAM_CHARD_CLIP = 5; +const int BAM_CPAD = 6; +const int BAM_CIGAR_SHIFT = 4; +const int BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1); + +// BAM index constants +const int MAX_BIN = 37450; // =(8^6-1)/7+1 +const int BAM_MIN_CHUNK_GAP = 32768; +const int BAM_LIDX_SHIFT = 14; + +// Explicit variable sizes +const int BT_SIZEOF_INT = 4; + +struct CigarOp; +struct RefEdit; + +struct BamAlignment { + + // Queries against alignment flag + public: + // Returns true if this read is a PCR duplicate (determined by external app) + bool IsDuplicate(void) const { return ( (AlignmentFlag & DUPLICATE) != 0 ); } + // Returns true if this read failed quality control (determined by external app) + bool IsFailedQC(void) const { return ( (AlignmentFlag & QC_FAILED) != 0 ); } + // Returns true if alignment is first mate on read + bool IsFirstMate(void) const { return ( (AlignmentFlag & READ_1) != 0 ); } + // Returns true if alignment is mapped + bool IsMapped(void) const { return ( (AlignmentFlag & UNMAPPED) == 0 ); } + // Returns true if alignment's mate is mapped + bool IsMateMapped(void) const { return ( (AlignmentFlag & MATE_UNMAPPED) == 0 ); } + // Returns true if alignment's mate mapped to reverse strand + bool IsMateReverseStrand(void) const { return ( (AlignmentFlag & MATE_REVERSE) != 0 ); } + // Returns true if alignment part of paired-end read + bool IsPaired(void) const { return ( (AlignmentFlag & PAIRED) != 0 ); } + // Returns true if this position is primary alignment (determined by external app) + bool IsPrimaryAlignment(void) const { return ( (AlignmentFlag & SECONDARY) == 0 ); } + // Returns true if alignment is part of read that satisfied paired-end resolution (determined by external app) + bool IsProperPair(void) const { return ( (AlignmentFlag & PROPER_PAIR) != 0 ); } + // Returns true if alignment mapped to reverse strand + bool IsReverseStrand(void) const { return ( (AlignmentFlag & REVERSE) != 0 ); } + // Returns true if alignment is second mate on read + bool IsSecondMate(void) const { return ( (AlignmentFlag & READ_2) != 0 ); } + + public: + + // get "RG" tag data + bool GetReadGroup(std::string& readGroup) const + { + const char* rg = GetTag("RG"); + if (rg==NULL || !rg) + { + return false; + } + // assign the read group + const unsigned int readGroupLen = (unsigned int)std::strlen(rg); + readGroup = std::string(rg, readGroupLen); + //readGroup.resize(readGroupLen); + //std::memcpy((char*)readGroup.data, rg, readGroupLen ); + return true; + } + + // get "NM" tag data - contributed by Aaron Quinlan + bool GetEditDistance(uint8_t& editDistance) const { return GetTag( "NM", editDistance ); } + + // get generic tag data - NVBIO + template + bool GetTag(const char* tagName, T& tagVal) const + { + if ( TagData.empty() ) { return false; } + + // localize the tag data + const char* pTagData = (const char*)TagData.c_str(); + const char* pTagStorageType = NULL; + const unsigned int tagDataLen = (unsigned int)TagData.size() + 1; + unsigned int numBytesParsed = 0; + + bool foundTag = false; + while( numBytesParsed < tagDataLen ) + { + // skip white spaces + while ( (*pTagData == ' ' || *pTagData == '\n') && numBytesParsed < tagDataLen) + { + ++numBytesParsed; + ++pTagData; + } + if (*pTagData == '\0' || numBytesParsed == tagDataLen) + break; + + const char* pTagType = pTagData; + pTagStorageType = pTagData + 2; + pTagData += 3; + numBytesParsed += 3; + + // check the current tag + if (strncmp(pTagType, tagName, 2) == 0) { + foundTag = true; + break; + } + + // get the storage class and find the next tag + SkipToNextTag( pTagType, *pTagStorageType, pTagData, numBytesParsed ); + } + // return if the edit distance tag was not present + if ( !foundTag ) { return false; } + + // assign the tag value + return GetTagValue( tagName, pTagData, *pTagStorageType, &tagVal ); + } + + // get generic tag data - NVBIO + const char* GetTag(const char* tagName) const + { + if ( TagData.empty() ) { return NULL; } + + // localize the tag data + const char* pTagData = (const char*)TagData.c_str(); + const unsigned int tagDataLen = (unsigned int)TagData.size() + 1; + unsigned int numBytesParsed = 0; + + while( numBytesParsed < tagDataLen ) + { + // skip white spaces + while ( (*pTagData == ' ' || *pTagData == '\n') && numBytesParsed < tagDataLen) + { + ++numBytesParsed; + ++pTagData; + } + if (*pTagData == '\0' || numBytesParsed == tagDataLen) + break; + + const char* pTagType = pTagData; + const char* pTagStorageType = pTagData + 2; + pTagData += 3; + numBytesParsed += 3; + + // check the current tag + if (strncmp(pTagType, tagName, 2) == 0) + return pTagData; + + // get the storage class and find the next tag + SkipToNextTag( pTagType, *pTagStorageType, pTagData, numBytesParsed ); + } + // return if the edit distance tag was not present + return NULL; + } + + private: + static bool CheckType(const char storageType, int8_t) { return (storageType == 'A') || (storageType == 'c'); } + static bool CheckType(const char storageType, uint8_t) { return (storageType == 'C'); } + static bool CheckType(const char storageType, int16_t) { return (storageType == 's') || (storageType == 'c') || (storageType == 'C'); } + static bool CheckType(const char storageType, uint16_t) { return (storageType == 'S') || (storageType == 'C'); } + static bool CheckType(const char storageType, int32_t) { return (storageType == 'i') || (storageType == 'c') || (storageType == 'C') || (storageType == 's') || (storageType == 'S'); } + static bool CheckType(const char storageType, uint32_t) { return (storageType == 'I') || (storageType == 'C') || (storageType == 'S'); } + static bool CheckType(const char storageType, float) { return (storageType == 'f'); } + + template + static bool GetTagValue(const char* tagName, const char *pTagData, const char storageType, T* tagVal) + { + switch(storageType) { + case 'A': + if (CheckType(storageType,T()) == false) + return false; + + *tagVal = T( *(const char*)(pTagData) ); + break; + case 'c': + if (CheckType(storageType,T()) == false) + return false; + + *tagVal = T( *(const int8_t*)(pTagData) ); + break; + case 'C': + if (CheckType(storageType,T()) == false) + return false; + + *tagVal = T( *(const uint8_t*)(pTagData) ); + break; + case 's': + if (CheckType(storageType,T()) == false) + return false; + + *tagVal = T( *(const int16_t*)(pTagData) ); + break; + case 'S': + if (CheckType(storageType,T()) == false) + return false; + + *tagVal = T( *(const uint16_t*)(pTagData) ); + break; + + case 'i': + case 'f': + case 'I': + if (CheckType(storageType,T()) == false) + return false; + + *tagVal = T( *(const T*)(pTagData) ); + break; + + case 'B': + { + const char type = *pTagData++; + const uint8_t len0 = *pTagData++; + const uint8_t len1 = *pTagData++; + const uint8_t len2 = *pTagData++; + const uint8_t len3 = *pTagData++; + const uint32_t len = len0 | (len1 << 8) | (len2 << 16) | (len3 << 24); + + if (CheckType(type,T()) == false) + return false; + + const T* tagData = (const T*)pTagData; + + switch (type) + { + case 'c': + case 'C': + for (uint32_t i = 0; i < len; ++i) + *tagVal++ = *(const T*)(tagData++); + break; + case 's': + case 'S': + for (uint32_t i = 0; i < len; ++i) + *tagVal++ = *(const T*)(tagData++); + break; + case 'i': + case 'I': + case 'f': + for (uint32_t i = 0; i < len; ++i) + *tagVal++ = *(const T*)(tagData++); + break; + } + } + + case 'Z': + if (CheckType(storageType,T()) == false) + return false; + + while(*pTagData != '\0') + *tagVal++ = *pTagData++; + + break; + + case 'H': + // TODO! + { + char tagString[3]; + tagString[0] = tagName[0]; + tagString[1] = tagName[1]; + tagString[2] = '\0'; + + fprintf(stderr,"WARNING: tag storage class 'H' is not yet supported, tag[%s:H]\n", tagString); + return false; + } + //break; + + default: + { + //char tagString[3]; + //tagString[0] = tagName[0]; + //tagString[1] = tagName[1]; + //tagString[2] = '\0'; + + //fprintf(stderr,"ERROR: Unknown tag storage class encountered, tag[%s:%c]\n", tagString, storageType); + //exit(1); + } + } + return true; + } + + static void SkipToNextTag(const char* tagName, const char storageType, const char* &pTagData, unsigned int& numBytesParsed) + { + switch(storageType) { + case 'A': + case 'c': + case 'C': + ++numBytesParsed; + ++pTagData; + break; + + case 'B': + { + const char type = *pTagData++; + const uint8_t len0 = *pTagData++; + const uint8_t len1 = *pTagData++; + const uint8_t len2 = *pTagData++; + const uint8_t len3 = *pTagData++; + const uint32_t len = len0 | (len1 << 8) | (len2 << 16) | (len3 << 24); + + switch (type) + { + case 'c': + case 'C': + pTagData += len; + break; + case 's': + case 'S': + pTagData += len * 2; + break; + case 'i': + case 'I': + case 'f': + pTagData += len * 4; + break; + } + break; + } + + case 's': + case 'S': + numBytesParsed += 2; + pTagData += 2; + break; + + case 'i': + case 'f': + case 'I': + numBytesParsed += 4; + pTagData += 4; + break; + + case 'Z': + case 'H': + while(*pTagData != '\0') { + ++numBytesParsed; + ++pTagData; + } + if(*pTagData == '\0') + { + ++numBytesParsed; + ++pTagData; + } + break; + + default: + { + //char tagString[3]; + //tagString[0] = tagName[0]; + //tagString[1] = tagName[1]; + //tagString[2] = '\0'; + + //fprintf(stderr,"ERROR: Unknown tag storage class encountered: [%s:%c]\n", tagString, storageType); + //exit(1); + } + } + } + + // Data members + public: + std::string Name; // Read name + int32_t Length; // Query length + std::string QueryBases; // 'Original' sequence (as reported from sequencing machine) + std::string AlignedBases; // 'Aligned' sequence (includes any indels, padding, clipping) + std::string Qualities; // FASTQ qualities (ASCII characters, not numeric values) + std::string TagData; // Tag data (accessor methods will pull the requested information out) + int32_t RefID; // ID number for reference sequence + int32_t Position; // Position (0-based) where alignment starts + uint16_t Bin; // Bin in BAM file where this alignment resides + uint16_t MapQuality; // Mapping quality score + uint32_t AlignmentFlag; // Alignment bit-flag - see Is() methods for available queries + std::vector CigarData; // CIGAR operations for this alignment + std::vector DeltaData; // Delta operations from reference to the query sequence + int32_t MateRefID; // ID number for reference sequence where alignment's mate was aligned + int32_t MatePosition; // Position (0-based) where alignment's mate starts + int32_t InsertSize; // Mate-pair insert size + + // Alignment flag query constants + enum { PAIRED = 1, + PROPER_PAIR = 2, + UNMAPPED = 4, + MATE_UNMAPPED = 8, + REVERSE = 16, + MATE_REVERSE = 32, + READ_1 = 64, + READ_2 = 128, + SECONDARY = 256, + QC_FAILED = 512, + DUPLICATE = 1024 + }; +}; + +// ---------------------------------------------------------------- +// Auxiliary data structs & typedefs + +struct CigarOp { + char Type; // Operation type (MIDNSHP) + uint32_t Length; // Operation length (number of bases) +}; + +struct RefEdit +{ + char Type; //Op type (MID etc.) + uint32_t L; //parameter - length for ID, Sub Code for X + uint32_t pos; //position in the query sequence +}; +struct RefData { + // data members + std::string RefName; // Name of reference sequence + uint32_t RefLength; // Length of reference sequence + bool RefHasAlignments; // True if BAM file contains alignments mapped to reference sequence + // constructor + RefData(void) + : RefLength(0) + , RefHasAlignments(false) + { } +}; + +typedef std::vector RefVector; +typedef std::vector BamAlignmentVector; + +// ---------------------------------------------------------------- +// Indexing structs & typedefs + +struct Chunk { + // data members + uint64_t Start; + uint64_t Stop; + // constructor + Chunk(const uint64_t& start = 0, const uint64_t& stop = 0) + : Start(start) + , Stop(stop) + { } +}; + +inline +bool ChunkLessThan(const Chunk& lhs, const Chunk& rhs) { + return lhs.Start < rhs.Start; +} + +typedef std::vector ChunkVector; +typedef std::map BamBinMap; +typedef std::vector LinearOffsetVector; + +struct ReferenceIndex { + // data members + BamBinMap Bins; + LinearOffsetVector Offsets; + // constructor + ReferenceIndex(const BamBinMap& binMap = BamBinMap(), + const LinearOffsetVector& offsets = LinearOffsetVector()) + : Bins(binMap) + , Offsets(offsets) + { } +}; + +typedef std::vector BamIndex; + +} // namespace BamTools + +#endif // BAMAUX_H diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamReader.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamReader.cpp new file mode 100644 index 0000000000000000000000000000000000000000..670210ac525241a481b490a5ef44a62e3af6e6ae --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamReader.cpp @@ -0,0 +1,1041 @@ +// *************************************************************************** +// BamReader.cpp (c) 2009 Derek Barnett, Michael Str�mberg +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 8 December 2009 (DB) +// --------------------------------------------------------------------------- +// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad +// Institute. +// --------------------------------------------------------------------------- +// Provides the basic functionality for reading BAM files +// *************************************************************************** + +// C++ includes +#include +#include +#include +#include + +// BamTools includes +#include "BGZF.h" +#include "BamReader.h" +using namespace BamTools; +using namespace std; + +struct BamReader::BamReaderPrivate { + + // ------------------------------- + // data members + // ------------------------------- + + // general data + BgzfData mBGZF; + string HeaderText; + BamIndex Index; + RefVector References; + bool IsIndexLoaded; + int64_t AlignmentsBeginOffset; + string Filename; + string IndexFilename; + + // user-specified region values + bool IsRegionSpecified; + int CurrentRefID; + int CurrentLeft; + + // BAM character constants + const char* DNA_LOOKUP; + const char* CIGAR_LOOKUP; + + // ------------------------------- + // constructor & destructor + // ------------------------------- + BamReaderPrivate(void); + ~BamReaderPrivate(void); + + // ------------------------------- + // "public" interface + // ------------------------------- + + // flie operations + void Close(void); + bool Jump(int refID, int position = 0); + void Open(const string& filename, const string& indexFilename = ""); + bool Rewind(void); + + // access alignment data + bool GetNextAlignment(BamAlignment& bAlignment); + + // access auxiliary data + const string GetHeaderText(void) const; + const int GetReferenceCount(void) const; + const RefVector GetReferenceData(void) const; + const int GetReferenceID(const string& refName) const; + + // index operations + bool CreateIndex(void); + + // ------------------------------- + // internal methods + // ------------------------------- + + // *** reading alignments and auxiliary data *** // + + // calculate bins that overlap region ( left to reference end for now ) + int BinsFromRegion(int refID, int left, uint16_t[MAX_BIN]); + // calculates alignment end position based on starting position and provided CIGAR operations + int CalculateAlignmentEnd(const int& position, const std::vector& cigarData); + // calculate file offset for first alignment chunk overlapping 'left' + int64_t GetOffset(int refID, int left); + // checks to see if alignment overlaps current region + bool IsOverlap(BamAlignment& bAlignment); + // retrieves header text from BAM file + void LoadHeaderData(void); + // retrieves BAM alignment under file pointer + bool LoadNextAlignment(BamAlignment& bAlignment); + // builds reference data structure from BAM file + void LoadReferenceData(void); + + // *** index file handling *** // + + // calculates index for BAM file + bool BuildIndex(void); + // clear out inernal index data structure + void ClearIndex(void); + // saves BAM bin entry for index + void InsertBinEntry(BamBinMap& binMap, const uint32_t& saveBin, const uint64_t& saveOffset, const uint64_t& lastOffset); + // saves linear offset entry for index + void InsertLinearOffset(LinearOffsetVector& offsets, const BamAlignment& bAlignment, const uint64_t& lastOffset); + // loads index from BAM index file + bool LoadIndex(void); + // simplifies index by merging 'chunks' + void MergeChunks(void); + // round-up 32-bit integer to next power-of-2 + void Roundup32(int& value); + // saves index to BAM index file + bool WriteIndex(void); +}; + +// ----------------------------------------------------- +// BamReader implementation (wrapper around BRPrivate) +// ----------------------------------------------------- + +// constructor +BamReader::BamReader(void) { + d = new BamReaderPrivate; +} + +// destructor +BamReader::~BamReader(void) { + delete d; + d = 0; +} + +// file operations +void BamReader::Close(void) { d->Close(); } +bool BamReader::Jump(int refID, int position) { return d->Jump(refID, position); } +void BamReader::Open(const string& filename, const string& indexFilename) { d->Open(filename, indexFilename); } +bool BamReader::Rewind(void) { return d->Rewind(); } + +// access alignment data +bool BamReader::GetNextAlignment(BamAlignment& bAlignment) { return d->GetNextAlignment(bAlignment); } + +// access auxiliary data +const string BamReader::GetHeaderText(void) const { return d->HeaderText; } +const int BamReader::GetReferenceCount(void) const { return (int)d->References.size(); } +const RefVector BamReader::GetReferenceData(void) const { return d->References; } +const int BamReader::GetReferenceID(const string& refName) const { return d->GetReferenceID(refName); } + +// index operations +bool BamReader::CreateIndex(void) { return d->CreateIndex(); } + +// ----------------------------------------------------- +// BamReaderPrivate implementation +// ----------------------------------------------------- + +// constructor +BamReader::BamReaderPrivate::BamReaderPrivate(void) + : IsIndexLoaded(false) + , AlignmentsBeginOffset(0) + , IsRegionSpecified(false) + , CurrentRefID(0) + , CurrentLeft(0) + , DNA_LOOKUP("=ACMGRSVTWYHKDBN") + , CIGAR_LOOKUP("MIDNSHP") +{ } + +// destructor +BamReader::BamReaderPrivate::~BamReaderPrivate(void) { + Close(); +} + +// calculate bins that overlap region ( left to reference end for now ) +int BamReader::BamReaderPrivate::BinsFromRegion(int refID, int left, uint16_t list[MAX_BIN]) { + + // get region boundaries + uint32_t begin = (unsigned int)left; + uint32_t end = (unsigned int)References.at(refID).RefLength - 1; + + // initialize list, bin '0' always a valid bin + int i = 0; + list[i++] = 0; + + // get rest of bins that contain this region + unsigned int k; + for (k = 1 + (begin>>26); k <= 1 + (end>>26); ++k) { list[i++] = k; } + for (k = 9 + (begin>>23); k <= 9 + (end>>23); ++k) { list[i++] = k; } + for (k = 73 + (begin>>20); k <= 73 + (end>>20); ++k) { list[i++] = k; } + for (k = 585 + (begin>>17); k <= 585 + (end>>17); ++k) { list[i++] = k; } + for (k = 4681 + (begin>>14); k <= 4681 + (end>>14); ++k) { list[i++] = k; } + + // return number of bins stored + return i; +} + +// populates BAM index data structure from BAM file data +bool BamReader::BamReaderPrivate::BuildIndex(void) { + + // check to be sure file is open + if (!mBGZF.IsOpen) { return false; } + + // move file pointer to beginning of alignments + Rewind(); + + // get reference count, reserve index space + int numReferences = (int)References.size(); + for ( int i = 0; i < numReferences; ++i ) { + Index.push_back(ReferenceIndex()); + } + + // sets default constant for bin, ID, offset, coordinate variables + const uint32_t defaultValue = 0xffffffffu; + + // bin data + uint32_t saveBin(defaultValue); + uint32_t lastBin(defaultValue); + + // reference ID data + int32_t saveRefID(defaultValue); + int32_t lastRefID(defaultValue); + + // offset data + uint64_t saveOffset = mBGZF.Tell(); + uint64_t lastOffset = saveOffset; + + // coordinate data + int32_t lastCoordinate = defaultValue; + + BamAlignment bAlignment; + while( GetNextAlignment(bAlignment) ) { + + // change of chromosome, save ID, reset bin + if ( lastRefID != bAlignment.RefID ) { + lastRefID = bAlignment.RefID; + lastBin = defaultValue; + } + + // if lastCoordinate greater than BAM position - file not sorted properly + else if ( lastCoordinate > bAlignment.Position ) { + printf("BAM file not properly sorted:\n"); + printf("Alignment %s : %d > %d on reference (id = %d)", bAlignment.Name.c_str(), lastCoordinate, bAlignment.Position, bAlignment.RefID); + exit(1); + } + + // if valid reference && BAM bin spans some minimum cutoff (smaller bin ids span larger regions) + if ( (bAlignment.RefID >= 0) && (bAlignment.Bin < 4681) ) { + + // save linear offset entry (matched to BAM entry refID) + ReferenceIndex& refIndex = Index.at(bAlignment.RefID); + LinearOffsetVector& offsets = refIndex.Offsets; + InsertLinearOffset(offsets, bAlignment, lastOffset); + } + + // if current BamAlignment bin != lastBin, "then possibly write the binning index" + if ( bAlignment.Bin != lastBin ) { + + // if not first time through + if ( saveBin != defaultValue ) { + + // save Bam bin entry + ReferenceIndex& refIndex = Index.at(saveRefID); + BamBinMap& binMap = refIndex.Bins; + InsertBinEntry(binMap, saveBin, saveOffset, lastOffset); + } + + // update saveOffset + saveOffset = lastOffset; + + // update bin values + saveBin = bAlignment.Bin; + lastBin = bAlignment.Bin; + + // update saveRefID + saveRefID = bAlignment.RefID; + + // if invalid RefID, break out (why?) + if ( saveRefID < 0 ) { break; } + } + + // make sure that current file pointer is beyond lastOffset + if ( mBGZF.Tell() <= (int64_t)lastOffset ) { + printf("Error in BGZF offsets.\n"); + exit(1); + } + + // update lastOffset + lastOffset = mBGZF.Tell(); + + // update lastCoordinate + lastCoordinate = bAlignment.Position; + } + + // save any leftover BAM data (as long as refID is valid) + if ( saveRefID >= 0 ) { + // save Bam bin entry + ReferenceIndex& refIndex = Index.at(saveRefID); + BamBinMap& binMap = refIndex.Bins; + InsertBinEntry(binMap, saveBin, saveOffset, lastOffset); + } + + // simplify index by merging chunks + MergeChunks(); + + // iterate over references + BamIndex::iterator indexIter = Index.begin(); + BamIndex::iterator indexEnd = Index.end(); + for ( int i = 0; indexIter != indexEnd; ++indexIter, ++i ) { + + // get reference index data + ReferenceIndex& refIndex = (*indexIter); + BamBinMap& binMap = refIndex.Bins; + LinearOffsetVector& offsets = refIndex.Offsets; + + // store whether reference has alignments or no + References[i].RefHasAlignments = ( binMap.size() > 0 ); + + // sort linear offsets + sort(offsets.begin(), offsets.end()); + } + + + // rewind file pointer to beginning of alignments, return success/fail + return Rewind(); +} + +// calculates alignment end position based on starting position and provided CIGAR operations +int BamReader::BamReaderPrivate::CalculateAlignmentEnd(const int& position, const vector& cigarData) { + + // initialize alignment end to starting position + int alignEnd = position; + + // iterate over cigar operations + vector::const_iterator cigarIter = cigarData.begin(); + vector::const_iterator cigarEnd = cigarData.end(); + for ( ; cigarIter != cigarEnd; ++cigarIter) { + char cigarType = (*cigarIter).Type; + if ( cigarType == 'M' || cigarType == 'D' || cigarType == 'N' ) { + alignEnd += (*cigarIter).Length; + } + } + return alignEnd; +} + + +// clear index data structure +void BamReader::BamReaderPrivate::ClearIndex(void) { + Index.clear(); // sufficient ?? +} + +// closes the BAM file +void BamReader::BamReaderPrivate::Close(void) { + mBGZF.Close(); + ClearIndex(); + HeaderText.clear(); + IsRegionSpecified = false; +} + +// create BAM index from BAM file (keep structure in memory) and write to default index output file +bool BamReader::BamReaderPrivate::CreateIndex(void) { + + // clear out index + ClearIndex(); + + // build (& save) index from BAM file + bool ok = true; + ok &= BuildIndex(); + ok &= WriteIndex(); + + // return success/fail + return ok; +} + +// returns RefID for given RefName (returns References.size() if not found) +const int BamReader::BamReaderPrivate::GetReferenceID(const string& refName) const { + + // retrieve names from reference data + vector refNames; + RefVector::const_iterator refIter = References.begin(); + RefVector::const_iterator refEnd = References.end(); + for ( ; refIter != refEnd; ++refIter) { + refNames.push_back( (*refIter).RefName ); + } + + // return 'index-of' refName ( if not found, returns refNames.size() ) + return (int)distance(refNames.begin(), find(refNames.begin(), refNames.end(), refName)); +} + +// get next alignment (from specified region, if given) +bool BamReader::BamReaderPrivate::GetNextAlignment(BamAlignment& bAlignment) { + + // if valid alignment available + if ( LoadNextAlignment(bAlignment) ) { + + // if region not specified, return success + if ( !IsRegionSpecified ) { return true; } + + // load next alignment until region overlap is found + while ( !IsOverlap(bAlignment) ) { + // if no valid alignment available (likely EOF) return failure + if ( !LoadNextAlignment(bAlignment) ) { return false; } + } + + // return success (alignment found that overlaps region) + return true; + } + + // no valid alignment + else { return false; } +} + +// calculate closest indexed file offset for region specified +int64_t BamReader::BamReaderPrivate::GetOffset(int refID, int left) { + + // calculate which bins overlap this region + uint16_t* bins = (uint16_t*)calloc(MAX_BIN, 2); + int numBins = BinsFromRegion(refID, left, bins); + + // get bins for this reference + const ReferenceIndex& refIndex = Index.at(refID); + const BamBinMap& binMap = refIndex.Bins; + + // get minimum offset to consider + const LinearOffsetVector& offsets = refIndex.Offsets; + uint64_t minOffset = ( (unsigned int)(left>>BAM_LIDX_SHIFT) >= offsets.size() ) ? 0 : offsets.at(left>>BAM_LIDX_SHIFT); + + // store offsets to beginning of alignment 'chunks' + std::vector chunkStarts; + + // store all alignment 'chunk' starts for bins in this region + for (int i = 0; i < numBins; ++i ) { + uint16_t binKey = bins[i]; + + map::const_iterator binIter = binMap.find(binKey); + if ( (binIter != binMap.end()) && ((*binIter).first == binKey) ) { + + const ChunkVector& chunks = (*binIter).second; + std::vector::const_iterator chunksIter = chunks.begin(); + std::vector::const_iterator chunksEnd = chunks.end(); + for ( ; chunksIter != chunksEnd; ++chunksIter) { + const Chunk& chunk = (*chunksIter); + if ( chunk.Stop > minOffset ) { + chunkStarts.push_back( chunk.Start ); + } + } + } + } + + // clean up memory + free(bins); + + // if no alignments found, else return smallest offset for alignment starts + if ( chunkStarts.size() == 0 ) { return -1; } + else { return *min_element(chunkStarts.begin(), chunkStarts.end()); } +} + +// saves BAM bin entry for index +void BamReader::BamReaderPrivate::InsertBinEntry(BamBinMap& binMap, + const uint32_t& saveBin, + const uint64_t& saveOffset, + const uint64_t& lastOffset) +{ + // look up saveBin + BamBinMap::iterator binIter = binMap.find(saveBin); + + // create new chunk + Chunk newChunk(saveOffset, lastOffset); + + // if entry doesn't exist + if ( binIter == binMap.end() ) { + ChunkVector newChunks; + newChunks.push_back(newChunk); + binMap.insert( pair(saveBin, newChunks)); + } + + // otherwise + else { + ChunkVector& binChunks = (*binIter).second; + binChunks.push_back( newChunk ); + } +} + +// saves linear offset entry for index +void BamReader::BamReaderPrivate::InsertLinearOffset(LinearOffsetVector& offsets, + const BamAlignment& bAlignment, + const uint64_t& lastOffset) +{ + // get converted offsets + int beginOffset = bAlignment.Position >> BAM_LIDX_SHIFT; + int endOffset = ( CalculateAlignmentEnd(bAlignment.Position, bAlignment.CigarData) - 1) >> BAM_LIDX_SHIFT; + + // resize vector if necessary + int oldSize = (int)offsets.size(); + int newSize = endOffset + 1; + if ( oldSize < newSize ) { + Roundup32(newSize); + offsets.resize(newSize, 0); + } + + // store offset + for(int i = beginOffset + 1; i <= endOffset ; ++i) { + if ( offsets[i] == 0) { + offsets[i] = lastOffset; + } + } +} + +// returns whether alignment overlaps currently specified region (refID, leftBound) +bool BamReader::BamReaderPrivate::IsOverlap(BamAlignment& bAlignment) { + + // if on different reference sequence, quit + if ( bAlignment.RefID != CurrentRefID ) { return false; } + + // read starts after left boundary + if ( bAlignment.Position >= CurrentLeft) { return true; } + + // return whether alignment end overlaps left boundary + return ( CalculateAlignmentEnd(bAlignment.Position, bAlignment.CigarData) >= CurrentLeft ); +} + +// jumps to specified region(refID, leftBound) in BAM file, returns success/fail +bool BamReader::BamReaderPrivate::Jump(int refID, int position) { + + // if data exists for this reference and position is valid + if ( References.at(refID).RefHasAlignments && ((unsigned int)position <= References.at(refID).RefLength) ) { + + // set current region + CurrentRefID = refID; + CurrentLeft = position; + IsRegionSpecified = true; + + // calculate offset + int64_t offset = GetOffset(CurrentRefID, CurrentLeft); + + // if in valid offset, return failure + if ( offset == -1 ) { return false; } + + // otherwise return success of seek operation + else { return mBGZF.Seek(offset); } + } + + // invalid jump request parameters, return failure + return false; +} + +// load BAM header data +void BamReader::BamReaderPrivate::LoadHeaderData(void) { + + // check to see if proper BAM header + char buffer[4]; + if (mBGZF.Read(buffer, 4) != 4) { + printf("Could not read header type\n"); + exit(1); + } + + if (strncmp(buffer, "BAM\001", 4)) { + printf("wrong header type!\n"); + exit(1); + } + + // get BAM header text length + mBGZF.Read(buffer, 4); + const unsigned int headerTextLength = BgzfData::UnpackUnsignedInt(buffer); + + // get BAM header text + char* headerText = (char*)calloc(headerTextLength + 1, 1); + mBGZF.Read(headerText, headerTextLength); + HeaderText = (string)((const char*)headerText); + + // clean up calloc-ed temp variable + free(headerText); +} + +// load existing index data from BAM index file (".bai"), return success/fail +bool BamReader::BamReaderPrivate::LoadIndex(void) { + + // clear out index data + ClearIndex(); + + // skip if index file empty + if ( IndexFilename.empty() ) { return false; } + + // open index file, abort on error + FILE* indexStream = fopen(IndexFilename.c_str(), "rb"); + if(!indexStream) { + printf("ERROR: Unable to open the BAM index file %s for reading.\n", IndexFilename.c_str() ); + return false; + } + + // see if index is valid BAM index + char magic[4]; + fread(magic, 1, 4, indexStream); + if (strncmp(magic, "BAI\1", 4)) { + printf("Problem with index file - invalid format.\n"); + fclose(indexStream); + return false; + } + + // get number of reference sequences + uint32_t numRefSeqs; + fread(&numRefSeqs, 4, 1, indexStream); + + // intialize space for BamIndex data structure + Index.reserve(numRefSeqs); + + // iterate over reference sequences + for (unsigned int i = 0; i < numRefSeqs; ++i) { + + // get number of bins for this reference sequence + int32_t numBins; + fread(&numBins, 4, 1, indexStream); + + if (numBins > 0) { + RefData& refEntry = References[i]; + refEntry.RefHasAlignments = true; + } + + // intialize BinVector + BamBinMap binMap; + + // iterate over bins for that reference sequence + for (int j = 0; j < numBins; ++j) { + + // get binID + uint32_t binID; + fread(&binID, 4, 1, indexStream); + + // get number of regionChunks in this bin + uint32_t numChunks; + fread(&numChunks, 4, 1, indexStream); + + // intialize ChunkVector + ChunkVector regionChunks; + regionChunks.reserve(numChunks); + + // iterate over regionChunks in this bin + for (unsigned int k = 0; k < numChunks; ++k) { + + // get chunk boundaries (left, right) + uint64_t left; + uint64_t right; + fread(&left, 8, 1, indexStream); + fread(&right, 8, 1, indexStream); + + // save ChunkPair + regionChunks.push_back( Chunk(left, right) ); + } + + // sort chunks for this bin + sort( regionChunks.begin(), regionChunks.end(), ChunkLessThan ); + + // save binID, chunkVector for this bin + binMap.insert( pair(binID, regionChunks) ); + } + + // load linear index for this reference sequence + + // get number of linear offsets + int32_t numLinearOffsets; + fread(&numLinearOffsets, 4, 1, indexStream); + + // intialize LinearOffsetVector + LinearOffsetVector offsets; + offsets.reserve(numLinearOffsets); + + // iterate over linear offsets for this reference sequeence + uint64_t linearOffset; + for (int j = 0; j < numLinearOffsets; ++j) { + // read a linear offset & store + fread(&linearOffset, 8, 1, indexStream); + offsets.push_back(linearOffset); + } + + // sort linear offsets + sort( offsets.begin(), offsets.end() ); + + // store index data for that reference sequence + Index.push_back( ReferenceIndex(binMap, offsets) ); + } + + // close index file (.bai) and return + fclose(indexStream); + return true; +} + +// populates BamAlignment with alignment data under file pointer, returns success/fail +bool BamReader::BamReaderPrivate::LoadNextAlignment(BamAlignment& bAlignment) { + + // read in the 'block length' value, make sure it's not zero + char buffer[4]; + mBGZF.Read(buffer, 4); + const unsigned int blockLength = BgzfData::UnpackUnsignedInt(buffer); + if ( blockLength == 0 ) { return false; } + + // keep track of bytes read as method progresses + int bytesRead = 4; + + // read in core alignment data, make sure the right size of data was read + char x[BAM_CORE_SIZE]; + if ( mBGZF.Read(x, BAM_CORE_SIZE) != BAM_CORE_SIZE ) { return false; } + bytesRead += BAM_CORE_SIZE; + + // set BamAlignment 'core' data and character data lengths + unsigned int tempValue; + unsigned int queryNameLength; + unsigned int numCigarOperations; + unsigned int querySequenceLength; + + bAlignment.RefID = BgzfData::UnpackSignedInt(&x[0]); + bAlignment.Position = BgzfData::UnpackSignedInt(&x[4]); + + tempValue = BgzfData::UnpackUnsignedInt(&x[8]); + bAlignment.Bin = tempValue >> 16; + bAlignment.MapQuality = tempValue >> 8 & 0xff; + queryNameLength = tempValue & 0xff; + + tempValue = BgzfData::UnpackUnsignedInt(&x[12]); + bAlignment.AlignmentFlag = tempValue >> 16; + numCigarOperations = tempValue & 0xffff; + + querySequenceLength = BgzfData::UnpackUnsignedInt(&x[16]); + bAlignment.MateRefID = BgzfData::UnpackSignedInt(&x[20]); + bAlignment.MatePosition = BgzfData::UnpackSignedInt(&x[24]); + bAlignment.InsertSize = BgzfData::UnpackSignedInt(&x[28]); + + // calculate lengths/offsets + const unsigned int dataLength = blockLength - BAM_CORE_SIZE; + const unsigned int cigarDataOffset = queryNameLength; + const unsigned int seqDataOffset = cigarDataOffset + (numCigarOperations * 4); + const unsigned int qualDataOffset = seqDataOffset + (querySequenceLength+1)/2; + const unsigned int tagDataOffset = qualDataOffset + querySequenceLength; + const unsigned int tagDataLen = dataLength - tagDataOffset; + + // set up destination buffers for character data + char* allCharData = (char*)calloc(sizeof(char), dataLength); + uint32_t* cigarData = (uint32_t*)(allCharData + cigarDataOffset); + char* seqData = ((char*)allCharData) + seqDataOffset; + char* qualData = ((char*)allCharData) + qualDataOffset; + char* tagData = ((char*)allCharData) + tagDataOffset; + + // get character data - make sure proper data size was read + if ( mBGZF.Read(allCharData, dataLength) != (signed int)dataLength) { return false; } + else { + + bytesRead += dataLength; + + // clear out any previous string data + bAlignment.Name.clear(); + bAlignment.QueryBases.clear(); + bAlignment.Qualities.clear(); + bAlignment.AlignedBases.clear(); + bAlignment.CigarData.clear(); + bAlignment.TagData.clear(); + + // save name + bAlignment.Name = (string)((const char*)(allCharData)); + + // save query sequence + for (unsigned int i = 0; i < querySequenceLength; ++i) { + char singleBase = DNA_LOOKUP[ ( ( seqData[(i/2)] >> (4*(1-(i%2)))) & 0xf ) ]; + bAlignment.QueryBases.append( 1, singleBase ); + } + + // save sequence length + bAlignment.Length = (int)bAlignment.QueryBases.length(); + + // save qualities, convert from numeric QV to FASTQ character + for (unsigned int i = 0; i < querySequenceLength; ++i) { + char singleQuality = (char)(qualData[i]+33); + bAlignment.Qualities.append( 1, singleQuality ); + } + + // save CIGAR-related data; + int k = 0; + for (unsigned int i = 0; i < numCigarOperations; ++i) { + + // build CigarOp struct + CigarOp op; + op.Length = (cigarData[i] >> BAM_CIGAR_SHIFT); + op.Type = CIGAR_LOOKUP[ (cigarData[i] & BAM_CIGAR_MASK) ]; + + // save CigarOp + bAlignment.CigarData.push_back(op); + + // build AlignedBases string + switch (op.Type) { + + case ('M') : + case ('I') : bAlignment.AlignedBases.append( bAlignment.QueryBases.substr(k, op.Length) ); // for 'M', 'I' - write bases + case ('S') : k += op.Length; // for 'S' - skip over query bases + break; + + case ('D') : bAlignment.AlignedBases.append( op.Length, '-' ); // for 'D' - write gap character + break; + + case ('P') : bAlignment.AlignedBases.append( op.Length, '*' ); // for 'P' - write padding character; + break; + + case ('N') : bAlignment.AlignedBases.append( op.Length, 'N' ); // for 'N' - write N's, skip bases in query sequence + k += op.Length; + break; + + case ('H') : break; // for 'H' - do nothing, move to next op + + default : printf("ERROR: Invalid Cigar op type\n"); // shouldn't get here + exit(1); + } + } + + // read in the tag data + bAlignment.TagData.resize(tagDataLen); + memcpy((char*)bAlignment.TagData.data(), tagData, tagDataLen); + } + + free(allCharData); + return true; +} + +// loads reference data from BAM file +void BamReader::BamReaderPrivate::LoadReferenceData(void) { + + // get number of reference sequences + char buffer[4]; + mBGZF.Read(buffer, 4); + const unsigned int numberRefSeqs = BgzfData::UnpackUnsignedInt(buffer); + if (numberRefSeqs == 0) { return; } + References.reserve((int)numberRefSeqs); + + // iterate over all references in header + for (unsigned int i = 0; i != numberRefSeqs; ++i) { + + // get length of reference name + mBGZF.Read(buffer, 4); + const unsigned int refNameLength = BgzfData::UnpackUnsignedInt(buffer); + char* refName = (char*)calloc(refNameLength, 1); + + // get reference name and reference sequence length + mBGZF.Read(refName, refNameLength); + mBGZF.Read(buffer, 4); + const int refLength = BgzfData::UnpackSignedInt(buffer); + + // store data for reference + RefData aReference; + aReference.RefName = (string)((const char*)refName); + aReference.RefLength = refLength; + References.push_back(aReference); + + // clean up calloc-ed temp variable + free(refName); + } +} + +// merges 'alignment chunks' in BAM bin (used for index building) +void BamReader::BamReaderPrivate::MergeChunks(void) { + + // iterate over reference enties + BamIndex::iterator indexIter = Index.begin(); + BamIndex::iterator indexEnd = Index.end(); + for ( ; indexIter != indexEnd; ++indexIter ) { + + // get BAM bin map for this reference + ReferenceIndex& refIndex = (*indexIter); + BamBinMap& bamBinMap = refIndex.Bins; + + // iterate over BAM bins + BamBinMap::iterator binIter = bamBinMap.begin(); + BamBinMap::iterator binEnd = bamBinMap.end(); + for ( ; binIter != binEnd; ++binIter ) { + + // get chunk vector for this bin + ChunkVector& binChunks = (*binIter).second; + if ( binChunks.size() == 0 ) { continue; } + + ChunkVector mergedChunks; + mergedChunks.push_back( binChunks[0] ); + + // iterate over chunks + int i = 0; + ChunkVector::iterator chunkIter = binChunks.begin(); + ChunkVector::iterator chunkEnd = binChunks.end(); + for ( ++chunkIter; chunkIter != chunkEnd; ++chunkIter) { + + // get 'currentChunk' based on numeric index + Chunk& currentChunk = mergedChunks[i]; + + // get iteratorChunk based on vector iterator + Chunk& iteratorChunk = (*chunkIter); + + // if currentChunk.Stop(shifted) == iterator Chunk.Start(shifted) + if ( currentChunk.Stop>>16 == iteratorChunk.Start>>16 ) { + + // set currentChunk.Stop to iteratorChunk.Stop + currentChunk.Stop = iteratorChunk.Stop; + } + + // otherwise + else { + // set currentChunk + 1 to iteratorChunk + mergedChunks.push_back(iteratorChunk); + ++i; + } + } + + // saved merged chunk vector + (*binIter).second = mergedChunks; + } + } +} + +// opens BAM file (and index) +void BamReader::BamReaderPrivate::Open(const string& filename, const string& indexFilename) { + + Filename = filename; + IndexFilename = indexFilename; + + // open the BGZF file for reading, retrieve header text & reference data + mBGZF.Open(filename, "rb"); + LoadHeaderData(); + LoadReferenceData(); + + // store file offset of first alignment + AlignmentsBeginOffset = mBGZF.Tell(); + + // open index file & load index data (if exists) + if ( !IndexFilename.empty() ) { + LoadIndex(); + } +} + +// returns BAM file pointer to beginning of alignment data +bool BamReader::BamReaderPrivate::Rewind(void) { + + // find first reference that has alignments in the BAM file + int refID = 0; + int refCount = (int)References.size(); + for ( ; refID < refCount; ++refID ) { + if ( References.at(refID).RefHasAlignments ) { break; } + } + + // store default bounds for first alignment + CurrentRefID = refID; + CurrentLeft = 0; + IsRegionSpecified = false; + + // return success/failure of seek + return mBGZF.Seek(AlignmentsBeginOffset); +} + +// rounds value up to next power-of-2 (used in index building) +void BamReader::BamReaderPrivate::Roundup32(int& value) { + --value; + value |= value >> 1; + value |= value >> 2; + value |= value >> 4; + value |= value >> 8; + value |= value >> 16; + ++value; +} + +// saves index data to BAM index file (".bai"), returns success/fail +bool BamReader::BamReaderPrivate::WriteIndex(void) { + + IndexFilename = Filename + ".bai"; + FILE* indexStream = fopen(IndexFilename.c_str(), "wb"); + if ( indexStream == 0 ) { + printf("ERROR: Could not open file to save index\n"); + return false; + } + + // write BAM index header + fwrite("BAI\1", 1, 4, indexStream); + + // write number of reference sequences + int32_t numReferenceSeqs = (int32_t)Index.size(); + fwrite(&numReferenceSeqs, 4, 1, indexStream); + + // iterate over reference sequences + BamIndex::const_iterator indexIter = Index.begin(); + BamIndex::const_iterator indexEnd = Index.end(); + for ( ; indexIter != indexEnd; ++ indexIter ) { + + // get reference index data + const ReferenceIndex& refIndex = (*indexIter); + const BamBinMap& binMap = refIndex.Bins; + const LinearOffsetVector& offsets = refIndex.Offsets; + + // write number of bins + int32_t binCount = (int32_t)binMap.size(); + fwrite(&binCount, 4, 1, indexStream); + + // iterate over bins + BamBinMap::const_iterator binIter = binMap.begin(); + BamBinMap::const_iterator binEnd = binMap.end(); + for ( ; binIter != binEnd; ++binIter ) { + + // get bin data (key and chunk vector) + const uint32_t& binKey = (*binIter).first; + const ChunkVector& binChunks = (*binIter).second; + + // save BAM bin key + fwrite(&binKey, 4, 1, indexStream); + + // save chunk count + int32_t chunkCount = (int32_t)binChunks.size(); + fwrite(&chunkCount, 4, 1, indexStream); + + // iterate over chunks + ChunkVector::const_iterator chunkIter = binChunks.begin(); + ChunkVector::const_iterator chunkEnd = binChunks.end(); + for ( ; chunkIter != chunkEnd; ++chunkIter ) { + + // get current chunk data + const Chunk& chunk = (*chunkIter); + const uint64_t& start = chunk.Start; + const uint64_t& stop = chunk.Stop; + + // save chunk offsets + fwrite(&start, 8, 1, indexStream); + fwrite(&stop, 8, 1, indexStream); + } + } + + // write linear offsets size + int32_t offsetSize = (int32_t)offsets.size(); + fwrite(&offsetSize, 4, 1, indexStream); + + // iterate over linear offsets + LinearOffsetVector::const_iterator offsetIter = offsets.begin(); + LinearOffsetVector::const_iterator offsetEnd = offsets.end(); + for ( ; offsetIter != offsetEnd; ++offsetIter ) { + + // write linear offset value + const uint64_t& linearOffset = (*offsetIter); + fwrite(&linearOffset, 8, 1, indexStream); + } + } + + // flush buffer, close file, and return success + fflush(indexStream); + fclose(indexStream); + return true; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamReader.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamReader.h new file mode 100644 index 0000000000000000000000000000000000000000..a6435097c73a9508c129ff34df1f6c1713b318e7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamReader.h @@ -0,0 +1,83 @@ +// *************************************************************************** +// BamReader.h (c) 2009 Derek Barnett, Michael Strmberg +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 8 December 2009 (DB) +// --------------------------------------------------------------------------- +// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad +// Institute. +// --------------------------------------------------------------------------- +// Provides the basic functionality for reading BAM files +// *************************************************************************** + +#ifndef BAMREADER_H +#define BAMREADER_H + +// C++ includes +#include + +// BamTools includes +#include "BamAux.h" + +namespace BamTools { + +class BamReader { + + // constructor / destructor + public: + BamReader(void); + ~BamReader(void); + + // public interface + public: + + // ---------------------- + // BAM file operations + // ---------------------- + + // close BAM file + void Close(void); + // performs random-access jump to reference, position + bool Jump(int refID, int position = 0); + // opens BAM file (and optional BAM index file, if provided) + void Open(const std::string& filename, const std::string& indexFilename = ""); + // returns file pointer to beginning of alignments + bool Rewind(void); + + // ---------------------- + // access alignment data + // ---------------------- + + // retrieves next available alignment (returns success/fail) + bool GetNextAlignment(BamAlignment& bAlignment); + + // ---------------------- + // access auxiliary data + // ---------------------- + + // returns SAM header text + const std::string GetHeaderText(void) const; + // returns number of reference sequences + const int GetReferenceCount(void) const; + // returns vector of reference objects + const BamTools::RefVector GetReferenceData(void) const; + // returns reference id (used for BamReader::Jump()) for the given reference name + const int GetReferenceID(const std::string& refName) const; + + // ---------------------- + // BAM index operations + // ---------------------- + + // creates index for BAM file, saves to file (default = bamFilename + ".bai") + bool CreateIndex(void); + + // private implementation + private: + struct BamReaderPrivate; + BamReaderPrivate* d; +}; + +} // namespace BamTools + +#endif // BAMREADER_H diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamWriter.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamWriter.cpp new file mode 100644 index 0000000000000000000000000000000000000000..2252dbe63612b7baee700fecc37668c71076c710 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamWriter.cpp @@ -0,0 +1,290 @@ +// *************************************************************************** +// BamWriter.cpp (c) 2009 Michael Strmberg, Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 8 December 2009 (DB) +// --------------------------------------------------------------------------- +// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad +// Institute. +// --------------------------------------------------------------------------- +// Provides the basic functionality for producing BAM files +// *************************************************************************** + +// BGZF includes +#include "BGZF.h" +#include "BamWriter.h" +using namespace BamTools; +using namespace std; + +struct BamWriter::BamWriterPrivate { + + // data members + BgzfData mBGZF; + + string mpackedCigar; + string mencodedQuery; + string mbaseQualities; + + // constructor / destructor + BamWriterPrivate(void) { } + ~BamWriterPrivate(void) { + mBGZF.Close(); + } + + // "public" interface + void Close(void); + void Open(const std::string& filename, const std::string& samHeader, const BamTools::RefVector& referenceSequences); + void SaveAlignment(const BamTools::BamAlignment& al); + + // internal methods + void CreatePackedCigar(const std::vector& cigarOperations, std::string& packedCigar); + void EncodeQuerySequence(const std::string& query, std::string& encodedQuery); +}; + +// ----------------------------------------------------- +// BamWriter implementation +// ----------------------------------------------------- + +// constructor +BamWriter::BamWriter(void) { + d = new BamWriterPrivate; +} + +// destructor +BamWriter::~BamWriter(void) { + delete d; + d = 0; +} + +// closes the alignment archive +void BamWriter::Close(void) { + d->Close(); +} + +// opens the alignment archive +void BamWriter::Open(const string& filename, const string& samHeader, const RefVector& referenceSequences) { + d->Open(filename, samHeader, referenceSequences); +} + +// saves the alignment to the alignment archive +void BamWriter::SaveAlignment(const BamAlignment& al) { + d->SaveAlignment(al); +} + +// ----------------------------------------------------- +// BamWriterPrivate implementation +// ----------------------------------------------------- + +// closes the alignment archive +void BamWriter::BamWriterPrivate::Close(void) { + mBGZF.Close(); +} + +// creates a cigar string from the supplied alignment +void BamWriter::BamWriterPrivate::CreatePackedCigar(const vector& cigarOperations, string& packedCigar) { + + // initialize + const unsigned int numCigarOperations = (unsigned int)cigarOperations.size(); + packedCigar.resize(numCigarOperations * BT_SIZEOF_INT); + + // pack the cigar data into the string + unsigned int* pPackedCigar = (unsigned int*)packedCigar.data(); + + unsigned int cigarOp; + vector::const_iterator coIter; + for(coIter = cigarOperations.begin(); coIter != cigarOperations.end(); coIter++) { + + switch(coIter->Type) { + case 'M': + cigarOp = BAM_CMATCH; + break; + case 'I': + cigarOp = BAM_CINS; + break; + case 'D': + cigarOp = BAM_CDEL; + break; + case 'N': + cigarOp = BAM_CREF_SKIP; + break; + case 'S': + cigarOp = BAM_CSOFT_CLIP; + break; + case 'H': + cigarOp = BAM_CHARD_CLIP; + break; + case 'P': + cigarOp = BAM_CPAD; + break; + default: + printf("ERROR: Unknown cigar operation found: %c\n", coIter->Type); + exit(1); + } + + *pPackedCigar = coIter->Length << BAM_CIGAR_SHIFT | cigarOp; + pPackedCigar++; + } +} + +// encodes the supplied query sequence into 4-bit notation +void BamWriter::BamWriterPrivate::EncodeQuerySequence(const string& query, string& encodedQuery) { + + // prepare the encoded query string + const unsigned int queryLen = (unsigned int)query.size(); + const unsigned int encodedQueryLen = (unsigned int)((queryLen / 2.0) + 0.5); + encodedQuery.resize(encodedQueryLen); + char* pEncodedQuery = (char*)encodedQuery.data(); + const char* pQuery = (const char*)query.data(); + + unsigned char nucleotideCode; + bool useHighWord = true; + + while(*pQuery) { + + switch(*pQuery) { + case '=': + nucleotideCode = 0; + break; + case 'A': + nucleotideCode = 1; + break; + case 'C': + nucleotideCode = 2; + break; + case 'G': + nucleotideCode = 4; + break; + case 'T': + nucleotideCode = 8; + break; + case 'N': + nucleotideCode = 15; + break; + default: + printf("ERROR: Only the following bases are supported in the BAM format: {=, A, C, G, T, N}. Found [%c]\n", *pQuery); + exit(1); + } + + // pack the nucleotide code + if(useHighWord) { + *pEncodedQuery = nucleotideCode << 4; + useHighWord = false; + } else { + *pEncodedQuery |= nucleotideCode; + pEncodedQuery++; + useHighWord = true; + } + + // increment the query position + pQuery++; + } +} + +// opens the alignment archive +void BamWriter::BamWriterPrivate::Open(const string& filename, const string& samHeader, const RefVector& referenceSequences) { + + // open the BGZF file for writing + mBGZF.Open(filename, "wb"); + + // ================ + // write the header + // ================ + + // write the BAM signature + const unsigned char SIGNATURE_LENGTH = 4; + const char* BAM_SIGNATURE = "BAM\1"; + mBGZF.Write(BAM_SIGNATURE, SIGNATURE_LENGTH); + + // write the SAM header text length + const unsigned int samHeaderLen = (unsigned int)samHeader.size(); + mBGZF.Write((char*)&samHeaderLen, BT_SIZEOF_INT); + + // write the SAM header text + if(samHeaderLen > 0) { + mBGZF.Write(samHeader.data(), samHeaderLen); + } + + // write the number of reference sequences + const unsigned int numReferenceSequences = (unsigned int)referenceSequences.size(); + mBGZF.Write((char*)&numReferenceSequences, BT_SIZEOF_INT); + + // ============================= + // write the sequence dictionary + // ============================= + + RefVector::const_iterator rsIter; + for(rsIter = referenceSequences.begin(); rsIter != referenceSequences.end(); rsIter++) { + + // write the reference sequence name length + const unsigned int referenceSequenceNameLen = (unsigned int)rsIter->RefName.size() + 1; + mBGZF.Write((char*)&referenceSequenceNameLen, BT_SIZEOF_INT); + + // write the reference sequence name + mBGZF.Write(rsIter->RefName.c_str(), referenceSequenceNameLen); + + // write the reference sequence length + mBGZF.Write((char*)&rsIter->RefLength, BT_SIZEOF_INT); + } +} + +// saves the alignment to the alignment archive +void BamWriter::BamWriterPrivate::SaveAlignment(const BamAlignment& al) { + + // initialize + const unsigned int nameLen = (unsigned int)al.Name.size() + 1; + const unsigned int queryLen = (unsigned int)al.QueryBases.size(); + const unsigned int numCigarOperations = (unsigned int)al.CigarData.size(); + + // create our packed cigar string + string& packedCigar = mpackedCigar; + packedCigar.erase( packedCigar.begin(), packedCigar.end() ); + CreatePackedCigar(al.CigarData, packedCigar); + const unsigned int packedCigarLen = (unsigned int)packedCigar.size(); + + // encode the query + string& encodedQuery = mencodedQuery; + encodedQuery.erase( encodedQuery.begin(), encodedQuery.end() ); + EncodeQuerySequence(al.QueryBases, encodedQuery); + const unsigned int encodedQueryLen = (unsigned int)encodedQuery.size(); + + // store the tag data length + const unsigned int tagDataLength = (unsigned int)al.TagData.size() + 1; + + // assign the BAM core data + unsigned int buffer[8]; + buffer[0] = al.RefID; + buffer[1] = al.Position; + buffer[2] = (al.Bin << 16) | (al.MapQuality << 8) | nameLen; + buffer[3] = (al.AlignmentFlag << 16) | numCigarOperations; + buffer[4] = queryLen; + buffer[5] = al.MateRefID; + buffer[6] = al.MatePosition; + buffer[7] = al.InsertSize; + + // write the block size + const unsigned int dataBlockSize = nameLen + packedCigarLen + encodedQueryLen + queryLen + tagDataLength; + const unsigned int blockSize = BAM_CORE_SIZE + dataBlockSize; + mBGZF.Write((char*)&blockSize, BT_SIZEOF_INT); + + // write the BAM core + mBGZF.Write((char*)&buffer, BAM_CORE_SIZE); + + // write the query name + mBGZF.Write(al.Name.c_str(), nameLen); + + // write the packed cigar + mBGZF.Write(packedCigar.data(), packedCigarLen); + + // write the encoded query sequence + mBGZF.Write(encodedQuery.data(), encodedQueryLen); + + // write the base qualities + mbaseQualities = al.Qualities; + char* pBaseQualities = (char*)mbaseQualities.data(); + for(unsigned int i = 0; i < queryLen; i++) { pBaseQualities[i] -= 33; } + mBGZF.Write(pBaseQualities, queryLen); + + // write the read group tag + mBGZF.Write(al.TagData.data(), tagDataLength); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamWriter.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamWriter.h new file mode 100644 index 0000000000000000000000000000000000000000..11622a08f00b7e6c2bbfcd8a46cd6b357bee388f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/BamWriter.h @@ -0,0 +1,49 @@ +// *************************************************************************** +// BamWriter.h (c) 2009 Michael Strmberg, Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 8 December 2009 (DB) +// --------------------------------------------------------------------------- +// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad +// Institute. +// --------------------------------------------------------------------------- +// Provides the basic functionality for producing BAM files +// *************************************************************************** + +#ifndef BAMWRITER_H +#define BAMWRITER_H + +// C++ includes +#include + +// BamTools includes +#include "BamAux.h" + +namespace BamTools { + +class BamWriter { + + // constructor/destructor + public: + BamWriter(void); + ~BamWriter(void); + + // public interface + public: + // closes the alignment archive + void Close(void); + // opens the alignment archive + void Open(const std::string& filename, const std::string& samHeader, const BamTools::RefVector& referenceSequences); + // saves the alignment to the alignment archive + void SaveAlignment(const BamTools::BamAlignment& al); + + // private implementation + private: + struct BamWriterPrivate; + BamWriterPrivate* d; +}; + +} // namespace BamTools + +#endif // BAMWRITER_H diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..b9d24b0e71da8ae7700e531128b4f5225a9cce65 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/bamtools/CMakeLists.txt @@ -0,0 +1,20 @@ +project(bamtools) + +cmake_minimum_required(VERSION 2.8) + +find_package(CUDA) + +include_directories(${CMAKE_CURRENT_BINARY_DIR} ${NVBIO_SOURCE_ROOT}/nvbio) + +set(BAMTOOLS_SRCS + BamAux.h + BamReader.cpp + BamReader.h + BamWriter.cpp + BamWriter.h + BGZF.cpp + BGZF.h +) + +cuda_add_library(bamtools STATIC ${BAMTOOLS_SRCS}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/crc/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/crc/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..4f86ff14a20df8c0fc7366d9fb4fa8b6e9fb5d6e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/crc/CMakeLists.txt @@ -0,0 +1,42 @@ +cmake_minimum_required(VERSION 2.4.4) +set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON) + +project(crc CXX) + +set(INSTALL_BIN_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory for executables") +set(INSTALL_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib" CACHE PATH "Installation directory for libraries") +set(INSTALL_INC_DIR "${CMAKE_INSTALL_PREFIX}/include" CACHE PATH "Installation directory for headers") +set(INSTALL_MAN_DIR "${CMAKE_INSTALL_PREFIX}/share/man" CACHE PATH "Installation directory for manual pages") +set(INSTALL_PKGCONFIG_DIR "${CMAKE_INSTALL_PREFIX}/share/pkgconfig" CACHE PATH "Installation directory for pkgconfig (.pc) files") + +include(CheckTypeSize) +include(CheckFunctionExists) +include(CheckIncludeFile) +include(CheckCSourceCompiles) +enable_testing() + +check_include_file(sys/types.h HAVE_SYS_TYPES_H) +check_include_file(stdint.h HAVE_STDINT_H) +check_include_file(stddef.h HAVE_STDDEF_H) + +if(MSVC) + set(CMAKE_DEBUG_POSTFIX "d") + add_definitions(-D_CRT_SECURE_NO_DEPRECATE) + add_definitions(-D_CRT_NONSTDC_NO_DEPRECATE) + include_directories(${CMAKE_CURRENT_SOURCE_DIR}) +endif() + + +include_directories(${CMAKE_CURRENT_BINARY_DIR} ${NVBIO_SOURCE_ROOT}) + +#============================================================================ +# crc +#============================================================================ + +set(CRC_SRCS + crc.cpp + crc.h +) + +add_library(crcstatic STATIC ${CRC_SRCS}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/crc/crc.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/crc/crc.cpp new file mode 100644 index 0000000000000000000000000000000000000000..d0710263265cac828eb1bd3e54f08ca9fd512479 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/crc/crc.cpp @@ -0,0 +1,140 @@ +/********************************************************************** + * + * Filename: crc.c + * + * Description: Slow and fast implementations of the CRC standards. + * + * Notes: The parameters for each supported CRC standard are + * defined in the header file crc.h. The implementations + * here should stand up to further additions to that list. + * + * + * Copyright (c) 2000 by Michael Barr. This software is placed into + * the public domain and may be used for any purpose. However, this + * notice must not be changed or removed and no warranty is either + * expressed or implied by its publication or distribution. + **********************************************************************/ + +#include "crc.h" + + +/* + * Derive parameters from the standard-specific parameters in crc.h. + */ +#define WIDTH (8 * sizeof(crc)) +#define TOPBIT (1 << (WIDTH - 1)) + +#if (REFLECT_DATA == CRC_TRUE) +#undef REFLECT_DATA +#define REFLECT_DATA(X) ((unsigned char) reflect((X), 8)) +#else +#undef REFLECT_DATA +#define REFLECT_DATA(X) (X) +#endif + +#if (REFLECT_REMAINDER == CRC_TRUE) +#undef REFLECT_REMAINDER +#define REFLECT_REMAINDER(X) ((crc) reflect((X), WIDTH)) +#else +#undef REFLECT_REMAINDER +#define REFLECT_REMAINDER(X) (X) +#endif + + +/********************************************************************* + * + * Function: reflect() + * + * Description: Reorder the bits of a binary sequence, by reflecting + * them about the middle position. + * + * Notes: No checking is done that nBits <= 32. + * + * Returns: The reflection of the original data. + * + *********************************************************************/ +unsigned long +reflect(unsigned long data, unsigned char nBits) +{ + unsigned long reflection = 0x00000000; + unsigned char bit; + + /* + * Reflect the data about the center bit. + */ + for (bit = 0; bit < nBits; ++bit) + { + /* + * If the LSB bit is set, set the reflection of it. + */ + if (data & 0x01) + { + reflection |= (1 << ((nBits - 1) - bit)); + } + + data = (data >> 1); + } + + return (reflection); + +} /* reflect() */ + +crc crcTable[256]; + + +/********************************************************************* + * + * Function: crcInit() + * + * Description: Populate the partial CRC lookup table. + * + * Notes: This function must be rerun any time the CRC standard + * is changed. If desired, it can be run "offline" and + * the table results stored in an embedded system's ROM. + * + * Returns: None defined. + * + *********************************************************************/ +void +crcInit(void) +{ + crc remainder; + int dividend; + unsigned char bit; + + + /* + * Compute the remainder of each possible dividend. + */ + for (dividend = 0; dividend < 256; ++dividend) + { + /* + * Start with the dividend followed by zeros. + */ + remainder = dividend << (WIDTH - 8); + + /* + * Perform modulo-2 division, a bit at a time. + */ + for (bit = 8; bit > 0; --bit) + { + /* + * Try to divide the current data bit. + */ + if (remainder & TOPBIT) + { + remainder = (remainder << 1) ^ POLYNOMIAL; + } + else + { + remainder = (remainder << 1); + } + } + + /* + * Store the result into the table. + */ + crcTable[dividend] = remainder; + } + +} /* crcInit() */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/crc/crc.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/crc/crc.h new file mode 100644 index 0000000000000000000000000000000000000000..be46379f2578a6798f5deedfe0351aa353b7b0b3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/crc/crc.h @@ -0,0 +1,137 @@ +/********************************************************************** + * + * Filename: crc.h + * + * Description: A header file describing the various CRC standards. + * + * Notes: + * + * + * Copyright (c) 2000 by Michael Barr. This software is placed into + * the public domain and may be used for any purpose. However, this + * notice must not be changed or removed and no warranty is either + * expressed or implied by its publication or distribution. + **********************************************************************/ + +#ifndef _crc_h +#define _crc_h + +#if !defined(CRC_FALSE) +#define CRC_FALSE 0 +#endif +#if !defined(CRC_TRUE) +#define CRC_TRUE !CRC_FALSE +#endif + +/* + * Select the CRC standard from the list that follows. + */ +#define CRC32 + + +#if defined(CRC_CCITT) + +typedef unsigned short crc; + +#define CRC_NAME "CRC-CCITT" +#define POLYNOMIAL 0x1021 +#define INITIAL_REMAINDER 0xFFFF +#define FINAL_XOR_VALUE 0x0000 +#define REFLECT_DATA CRC_FALSE +#define REFLECT_REMAINDER CRC_FALSE +#define CHECK_VALUE 0x29B1 + +#elif defined(CRC16) + +typedef unsigned short crc; + +#define CRC_NAME "CRC-16" +#define POLYNOMIAL 0x8005 +#define INITIAL_REMAINDER 0x0000 +#define FINAL_XOR_VALUE 0x0000 +#define REFLECT_DATA CRC_TRUE +#define REFLECT_REMAINDER CRC_TRUE +#define CHECK_VALUE 0xBB3D + +#elif defined(CRC32) + +// xxxnsubtil: unsigned long was a 64-bit type for us! switched to nvbio's uint32 instead +// xxxjpantaleoni: removed dependeny on nvbio and switched to unsigned int +typedef unsigned int crc; + +#define CRC_NAME "CRC-32" +#define POLYNOMIAL 0x04C11DB7 +#define INITIAL_REMAINDER 0xFFFFFFFF +#define FINAL_XOR_VALUE 0xFFFFFFFF +#define REFLECT_DATA CRC_TRUE +#define REFLECT_REMAINDER CRC_TRUE +#define CHECK_VALUE 0xCBF43926 + +#else + +#error "One of CRC_CCITT, CRC16, or CRC32 must be #define'd." + +#endif + +/* + * Derive parameters from the standard-specific parameters in crc.h. + */ +#define WIDTH (8 * sizeof(crc)) +#define TOPBIT (1 << (WIDTH - 1)) + +#if (REFLECT_DATA == CRC_TRUE) +#undef REFLECT_DATA +#define REFLECT_DATA(X) ((unsigned char) reflect((X), 8)) +#else +#undef REFLECT_DATA +#define REFLECT_DATA(X) (X) +#endif + +#if (REFLECT_REMAINDER == CRC_TRUE) +#undef REFLECT_REMAINDER +#define REFLECT_REMAINDER(X) ((crc) reflect((X), WIDTH)) +#else +#undef REFLECT_REMAINDER +#define REFLECT_REMAINDER(X) (X) +#endif + +unsigned long reflect(unsigned long data, unsigned char nBits); + +extern crc crcTable[256]; + +void crcInit(void); + +/********************************************************************* + * + * Function: crcCalc() + * + * Description: Compute the CRC of a given message. + * + * Notes: crcInit() must be called first. + * + * Returns: The CRC of the message. + * + *********************************************************************/ +template +crc crcCalc(const CharIterator message, unsigned int nBytes) +{ + crc remainder = INITIAL_REMAINDER; + unsigned char data; + unsigned int byte; + + /* + * Divide the message by the polynomial, a byte at a time. + */ + for (byte = 0; byte < nBytes; ++byte) + { + data = REFLECT_DATA(message[byte]) ^ (remainder >> (WIDTH - 8)); + remainder = crcTable[data] ^ (remainder << 8); + } + + /* + * The final remainder is the CRC. + */ + return (REFLECT_REMAINDER(remainder) ^ FINAL_XOR_VALUE); +} + +#endif /* _crc_h */ \ No newline at end of file diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_discontinuity.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_discontinuity.cuh new file mode 100644 index 0000000000000000000000000000000000000000..ff6836c847b99d5695376398d160e427282a4882 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_discontinuity.cuh @@ -0,0 +1,601 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * The cub::BlockDiscontinuity class provides [collective](index.html#sec0) methods for flagging discontinuities within an ordered set of items partitioned across a CUDA thread block. + */ + +#pragma once + +#include "../util_type.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/** + * \brief The BlockDiscontinuity class provides [collective](index.html#sec0) methods for flagging discontinuities within an ordered set of items partitioned across a CUDA thread block. ![](discont_logo.png) + * \ingroup BlockModule + * + * \tparam T The data type to be flagged. + * \tparam BLOCK_THREADS The thread block size in threads. + * + * \par Overview + * - A set of "head flags" (or "tail flags") is often used to indicate corresponding items + * that differ from their predecessors (or successors). For example, head flags are convenient + * for demarcating disjoint data segments as part of a segmented scan or reduction. + * + * \par Performance Considerations + * - \granularity + * + * \par A Simple Example + * \blockcollective{BlockDiscontinuity} + * \par + * The code snippet below illustrates the head flagging of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockDiscontinuity for 128 threads on type int + * typedef cub::BlockDiscontinuity BlockDiscontinuity; + * + * // Allocate shared memory for BlockDiscontinuity + * __shared__ typename BlockDiscontinuity::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Collectively compute head flags for discontinuities in the segment + * int head_flags[4]; + * BlockDiscontinuity(temp_storage).FlagHeads(head_flags, thread_data, cub::Inequality()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is + * { [0,0,1,1], [1,1,1,1], [2,3,3,3], [3,4,4,4], ... }. + * The corresponding output \p head_flags in those threads will be + * { [1,0,1,0], [0,0,0,0], [1,1,0,0], [0,1,0,0], ... }. + * + * \par Performance Considerations + * - Incurs zero bank conflicts for most types + * + */ +template < + typename T, + int BLOCK_THREADS> +class BlockDiscontinuity +{ +private: + + /****************************************************************************** + * Type definitions + ******************************************************************************/ + + /// Shared memory storage layout type (last element from each thread's input) + typedef T _TempStorage[BLOCK_THREADS]; + + + /****************************************************************************** + * Utility methods + ******************************************************************************/ + + /// Internal storage allocator + __device__ __forceinline__ _TempStorage& PrivateStorage() + { + __shared__ _TempStorage private_storage; + return private_storage; + } + + + /// Specialization for when FlagOp has third index param + template ::HAS_PARAM> + struct ApplyOp + { + // Apply flag operator + static __device__ __forceinline__ bool Flag(FlagOp flag_op, const T &a, const T &b, int idx) + { + return flag_op(a, b, idx); + } + }; + + /// Specialization for when FlagOp does not have a third index param + template + struct ApplyOp + { + // Apply flag operator + static __device__ __forceinline__ bool Flag(FlagOp flag_op, const T &a, const T &b, int idx) + { + return flag_op(a, b); + } + }; + + /// Templated unrolling of item comparison (inductive case) + template + struct Iterate + { + template < + int ITEMS_PER_THREAD, + typename FlagT, + typename FlagOp> + static __device__ __forceinline__ void FlagItems( + int linear_tid, + FlagT (&flags)[ITEMS_PER_THREAD], ///< [out] Calling thread's discontinuity head_flags + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + FlagOp flag_op) ///< [in] Binary boolean flag predicate + { + flags[ITERATION] = ApplyOp::Flag( + flag_op, + input[ITERATION - 1], + input[ITERATION], + (linear_tid * ITEMS_PER_THREAD) + ITERATION); + + Iterate::FlagItems(linear_tid, flags, input, flag_op); + } + }; + + /// Templated unrolling of item comparison (termination case) + template + struct Iterate + { + template < + int ITEMS_PER_THREAD, + typename FlagT, + typename FlagOp> + static __device__ __forceinline__ void FlagItems( + int linear_tid, + FlagT (&flags)[ITEMS_PER_THREAD], ///< [out] Calling thread's discontinuity head_flags + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + FlagOp flag_op) ///< [in] Binary boolean flag predicate + {} + }; + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + /// Shared storage reference + _TempStorage &temp_storage; + + /// Linear thread-id + int linear_tid; + + +public: + + /// \smemstorage{BlockDiscontinuity} + struct TempStorage : Uninitialized<_TempStorage> {}; + + + /******************************************************************//** + * \name Collective constructors + *********************************************************************/ + //@{ + + /** + * \brief Collective constructor for 1D thread blocks using a private static allocation of shared memory as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockDiscontinuity() + : + temp_storage(PrivateStorage()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor for 1D thread blocks using the specified memory allocation as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockDiscontinuity( + TempStorage &temp_storage) ///< [in] Reference to memory allocation having layout type TempStorage + : + temp_storage(temp_storage.Alias()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor using a private static allocation of shared memory as temporary storage. Each thread is identified using the supplied linear thread identifier + */ + __device__ __forceinline__ BlockDiscontinuity( + int linear_tid) ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(PrivateStorage()), + linear_tid(linear_tid) + {} + + + /** + * \brief Collective constructor using the specified memory allocation as temporary storage. Each thread is identified using the supplied linear thread identifier. + */ + __device__ __forceinline__ BlockDiscontinuity( + TempStorage &temp_storage, ///< [in] Reference to memory allocation having layout type TempStorage + int linear_tid) ///< [in] [optional] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + + + //@} end member group + /******************************************************************//** + * \name Head flag operations + *********************************************************************/ + //@{ + + + /** + * \brief Sets head flags indicating discontinuities between items partitioned across the thread block, for which the first item has no reference and is always flagged. + * + * \par + * - The flag head_flagsi is set for item + * inputi when + * flag_op(previous-item, inputi) + * returns \p true (where previous-item is either the preceding item + * in the same thread or the last item in the previous thread). + * - For thread0, item input0 is always flagged. + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates the head-flagging of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockDiscontinuity for 128 threads on type int + * typedef cub::BlockDiscontinuity BlockDiscontinuity; + * + * // Allocate shared memory for BlockDiscontinuity + * __shared__ typename BlockDiscontinuity::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Collectively compute head flags for discontinuities in the segment + * int head_flags[4]; + * BlockDiscontinuity(temp_storage).FlagHeads(head_flags, thread_data, cub::Inequality()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is + * { [0,0,1,1], [1,1,1,1], [2,3,3,3], [3,4,4,4], ... }. + * The corresponding output \p head_flags in those threads will be + * { [1,0,1,0], [0,0,0,0], [1,1,0,0], [0,1,0,0], ... }. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam FlagT [inferred] The flag type (must be an integer type) + * \tparam FlagOp [inferred] Binary predicate functor type having member T operator()(const T &a, const T &b) or member T operator()(const T &a, const T &b, unsigned int b_index), and returning \p true if a discontinuity exists between \p a and \p b, otherwise \p false. \p b_index is the rank of b in the aggregate tile of data. + */ + template < + int ITEMS_PER_THREAD, + typename FlagT, + typename FlagOp> + __device__ __forceinline__ void FlagHeads( + FlagT (&head_flags)[ITEMS_PER_THREAD], ///< [out] Calling thread's discontinuity head_flags + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + FlagOp flag_op) ///< [in] Binary boolean flag predicate + { + // Share last item + temp_storage[linear_tid] = input[ITEMS_PER_THREAD - 1]; + + __syncthreads(); + + // Set flag for first item + head_flags[0] = (linear_tid == 0) ? + 1 : // First thread + ApplyOp::Flag( + flag_op, + temp_storage[linear_tid - 1], + input[0], + linear_tid * ITEMS_PER_THREAD); + + // Set head_flags for remaining items + Iterate<1, ITEMS_PER_THREAD>::FlagItems(linear_tid, head_flags, input, flag_op); + } + + + /** + * \brief Sets head flags indicating discontinuities between items partitioned across the thread block. + * + * \par + * - The flag head_flagsi is set for item + * inputi when + * flag_op(previous-item, inputi) + * returns \p true (where previous-item is either the preceding item + * in the same thread or the last item in the previous thread). + * - For thread0, item input0 is compared + * against \p tile_predecessor_item. + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates the head-flagging of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockDiscontinuity for 128 threads on type int + * typedef cub::BlockDiscontinuity BlockDiscontinuity; + * + * // Allocate shared memory for BlockDiscontinuity + * __shared__ typename BlockDiscontinuity::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Have thread0 obtain the predecessor item for the entire tile + * int tile_predecessor_item; + * if (threadIdx.x == 0) tile_predecessor_item == ... + * + * // Collectively compute head flags for discontinuities in the segment + * int head_flags[4]; + * BlockDiscontinuity(temp_storage).FlagHeads( + * head_flags, thread_data, cub::Inequality(), tile_predecessor_item); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is + * { [0,0,1,1], [1,1,1,1], [2,3,3,3], [3,4,4,4], ... }, + * and that \p tile_predecessor_item is \p 0. The corresponding output \p head_flags in those threads will be + * { [0,0,1,0], [0,0,0,0], [1,1,0,0], [0,1,0,0], ... }. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam FlagT [inferred] The flag type (must be an integer type) + * \tparam FlagOp [inferred] Binary predicate functor type having member T operator()(const T &a, const T &b) or member T operator()(const T &a, const T &b, unsigned int b_index), and returning \p true if a discontinuity exists between \p a and \p b, otherwise \p false. \p b_index is the rank of b in the aggregate tile of data. + */ + template < + int ITEMS_PER_THREAD, + typename FlagT, + typename FlagOp> + __device__ __forceinline__ void FlagHeads( + FlagT (&head_flags)[ITEMS_PER_THREAD], ///< [out] Calling thread's discontinuity head_flags + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + FlagOp flag_op, ///< [in] Binary boolean flag predicate + T tile_predecessor_item) ///< [in] [thread0 only] Item with which to compare the first tile item (input0 from thread0). + { + // Share last item + temp_storage[linear_tid] = input[ITEMS_PER_THREAD - 1]; + + __syncthreads(); + + // Set flag for first item + T predecessor_item = (linear_tid == 0) ? + tile_predecessor_item : // First thread + temp_storage[linear_tid - 1]; + + head_flags[0] = ApplyOp::Flag( + flag_op, + predecessor_item, + input[0], + linear_tid * ITEMS_PER_THREAD); + + // Set head_flags for remaining items + Iterate<1, ITEMS_PER_THREAD>::FlagItems(linear_tid, head_flags, input, flag_op); + } + + + //@} end member group + /******************************************************************//** + * \name Tail flag operations + *********************************************************************/ + //@{ + + + /** + * \brief Sets tail flags indicating discontinuities between items partitioned across the thread block, for which the last item has no reference and is always flagged. + * + * \par + * - The flag tail_flagsi is set for item + * inputi when + * flag_op(inputi, next-item) + * returns \p true (where next-item is either the next item + * in the same thread or the first item in the next thread). + * - For threadBLOCK_THREADS-1, item + * inputITEMS_PER_THREAD-1 is always flagged. + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates the tail-flagging of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockDiscontinuity for 128 threads on type int + * typedef cub::BlockDiscontinuity BlockDiscontinuity; + * + * // Allocate shared memory for BlockDiscontinuity + * __shared__ typename BlockDiscontinuity::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Collectively compute tail flags for discontinuities in the segment + * int tail_flags[4]; + * BlockDiscontinuity(temp_storage).FlagTails(tail_flags, thread_data, cub::Inequality()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is + * { [0,0,1,1], [1,1,1,1], [2,3,3,3], ..., [124,125,125,125] }. + * The corresponding output \p tail_flags in those threads will be + * { [0,1,0,0], [0,0,0,1], [1,0,0,...], ..., [1,0,0,1] }. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam FlagT [inferred] The flag type (must be an integer type) + * \tparam FlagOp [inferred] Binary predicate functor type having member T operator()(const T &a, const T &b) or member T operator()(const T &a, const T &b, unsigned int b_index), and returning \p true if a discontinuity exists between \p a and \p b, otherwise \p false. \p b_index is the rank of b in the aggregate tile of data. + */ + template < + int ITEMS_PER_THREAD, + typename FlagT, + typename FlagOp> + __device__ __forceinline__ void FlagTails( + FlagT (&tail_flags)[ITEMS_PER_THREAD], ///< [out] Calling thread's discontinuity tail_flags + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + FlagOp flag_op) ///< [in] Binary boolean flag predicate + { + // Share first item + temp_storage[linear_tid] = input[0]; + + __syncthreads(); + + // Set flag for last item + tail_flags[ITEMS_PER_THREAD - 1] = (linear_tid == BLOCK_THREADS - 1) ? + 1 : // Last thread + ApplyOp::Flag( + flag_op, + input[ITEMS_PER_THREAD - 1], + temp_storage[linear_tid + 1], + (linear_tid * ITEMS_PER_THREAD) + (ITEMS_PER_THREAD - 1)); + + // Set tail_flags for remaining items + Iterate<0, ITEMS_PER_THREAD - 1>::FlagItems(linear_tid, tail_flags, input, flag_op); + } + + + /** + * \brief Sets tail flags indicating discontinuities between items partitioned across the thread block. + * + * \par + * - The flag tail_flagsi is set for item + * inputi when + * flag_op(inputi, next-item) + * returns \p true (where next-item is either the next item + * in the same thread or the first item in the next thread). + * - For threadBLOCK_THREADS-1, item + * inputITEMS_PER_THREAD-1 is compared + * against \p tile_predecessor_item. + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates the tail-flagging of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockDiscontinuity for 128 threads on type int + * typedef cub::BlockDiscontinuity BlockDiscontinuity; + * + * // Allocate shared memory for BlockDiscontinuity + * __shared__ typename BlockDiscontinuity::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Have thread127 obtain the successor item for the entire tile + * int tile_successor_item; + * if (threadIdx.x == 127) tile_successor_item == ... + * + * // Collectively compute tail flags for discontinuities in the segment + * int tail_flags[4]; + * BlockDiscontinuity(temp_storage).FlagTails( + * tail_flags, thread_data, cub::Inequality(), tile_successor_item); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is + * { [0,0,1,1], [1,1,1,1], [2,3,3,3], ..., [124,125,125,125] } + * and that \p tile_successor_item is \p 125. The corresponding output \p tail_flags in those threads will be + * { [0,1,0,0], [0,0,0,1], [1,0,0,...], ..., [1,0,0,0] }. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam FlagT [inferred] The flag type (must be an integer type) + * \tparam FlagOp [inferred] Binary predicate functor type having member T operator()(const T &a, const T &b) or member T operator()(const T &a, const T &b, unsigned int b_index), and returning \p true if a discontinuity exists between \p a and \p b, otherwise \p false. \p b_index is the rank of b in the aggregate tile of data. + */ + template < + int ITEMS_PER_THREAD, + typename FlagT, + typename FlagOp> + __device__ __forceinline__ void FlagTails( + FlagT (&tail_flags)[ITEMS_PER_THREAD], ///< [out] Calling thread's discontinuity tail_flags + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + FlagOp flag_op, ///< [in] Binary boolean flag predicate + T tile_successor_item) ///< [in] [threadBLOCK_THREADS-1 only] Item with which to compare the last tile item (inputITEMS_PER_THREAD-1 from threadBLOCK_THREADS-1). + { + // Share first item + temp_storage[linear_tid] = input[0]; + + __syncthreads(); + + // Set flag for last item + T successor_item = (linear_tid == BLOCK_THREADS - 1) ? + tile_successor_item : // Last thread + temp_storage[linear_tid + 1]; + + tail_flags[ITEMS_PER_THREAD - 1] = ApplyOp::Flag( + flag_op, + input[ITEMS_PER_THREAD - 1], + successor_item, + (linear_tid * ITEMS_PER_THREAD) + (ITEMS_PER_THREAD - 1)); + + // Set tail_flags for remaining items + Iterate<0, ITEMS_PER_THREAD - 1>::FlagItems(linear_tid, tail_flags, input, flag_op); + } + + //@} end member group + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_exchange.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_exchange.cuh new file mode 100644 index 0000000000000000000000000000000000000000..4f2645ace8c834373b6a78f31fc14b072eb363d2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_exchange.cuh @@ -0,0 +1,1005 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * The cub::BlockExchange class provides [collective](index.html#sec0) methods for rearranging data partitioned across a CUDA thread block. + */ + +#pragma once + +#include "../util_arch.cuh" +#include "../util_macro.cuh" +#include "../util_type.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/** + * \brief The BlockExchange class provides [collective](index.html#sec0) methods for rearranging data partitioned across a CUDA thread block. ![](transpose_logo.png) + * \ingroup BlockModule + * + * \tparam T The data type to be exchanged. + * \tparam BLOCK_THREADS The thread block size in threads. + * \tparam ITEMS_PER_THREAD The number of items partitioned onto each thread. + * \tparam WARP_TIME_SLICING [optional] When \p true, only use enough shared memory for a single warp's worth of tile data, time-slicing the block-wide exchange over multiple synchronized rounds. Yields a smaller memory footprint at the expense of decreased parallelism. (Default: false) + * + * \par Overview + * - It is commonplace for blocks of threads to rearrange data items between + * threads. For example, the global memory subsystem prefers access patterns + * where data items are "striped" across threads (where consecutive threads access consecutive items), + * yet most block-wide operations prefer a "blocked" partitioning of items across threads + * (where consecutive items belong to a single thread). + * - BlockExchange supports the following types of data exchanges: + * - Transposing between [blocked](index.html#sec5sec3) and [striped](index.html#sec5sec3) arrangements + * - Transposing between [blocked](index.html#sec5sec3) and [warp-striped](index.html#sec5sec3) arrangements + * - Scattering ranked items to a [blocked arrangement](index.html#sec5sec3) + * - Scattering ranked items to a [striped arrangement](index.html#sec5sec3) + * + * \par A Simple Example + * \blockcollective{BlockExchange} + * \par + * The code snippet below illustrates the conversion from a "blocked" to a "striped" arrangement + * of 512 integer items partitioned across 128 threads where each thread owns 4 items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(int *d_data, ...) + * { + * // Specialize BlockExchange for 128 threads owning 4 integer items each + * typedef cub::BlockExchange BlockExchange; + * + * // Allocate shared memory for BlockExchange + * __shared__ typename BlockExchange::TempStorage temp_storage; + * + * // Load a tile of data striped across threads + * int thread_data[4]; + * cub::LoadDirectStriped<128>(threadIdx.x, d_data, thread_data); + * + * // Collectively exchange data into a blocked arrangement across threads + * BlockExchange(temp_storage).StripedToBlocked(thread_data); + * + * \endcode + * \par + * Suppose the set of striped input \p thread_data across the block of threads is + * { [0,128,256,384], [1,129,257,385], ..., [127,255,383,511] }. + * The corresponding output \p thread_data in those threads will be + * { [0,1,2,3], [4,5,6,7], [8,9,10,11], ..., [508,509,510,511] }. + * + * \par Performance Considerations + * - Proper device-specific padding ensures zero bank conflicts for most types. + * + */ +template < + typename T, + int BLOCK_THREADS, + int ITEMS_PER_THREAD, + bool WARP_TIME_SLICING = false> +class BlockExchange +{ +private: + + /****************************************************************************** + * Constants + ******************************************************************************/ + + enum + { + LOG_WARP_THREADS = CUB_PTX_LOG_WARP_THREADS, + WARP_THREADS = 1 << LOG_WARP_THREADS, + WARPS = (BLOCK_THREADS + CUB_PTX_WARP_THREADS - 1) / CUB_PTX_WARP_THREADS, + + LOG_SMEM_BANKS = CUB_PTX_LOG_SMEM_BANKS, + SMEM_BANKS = 1 << LOG_SMEM_BANKS, + + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + + TIME_SLICES = (WARP_TIME_SLICING) ? WARPS : 1, + + TIME_SLICED_THREADS = (WARP_TIME_SLICING) ? CUB_MIN(BLOCK_THREADS, WARP_THREADS) : BLOCK_THREADS, + TIME_SLICED_ITEMS = TIME_SLICED_THREADS * ITEMS_PER_THREAD, + + WARP_TIME_SLICED_THREADS = CUB_MIN(BLOCK_THREADS, WARP_THREADS), + WARP_TIME_SLICED_ITEMS = WARP_TIME_SLICED_THREADS * ITEMS_PER_THREAD, + + // Insert padding if the number of items per thread is a power of two + INSERT_PADDING = 0, //PowerOfTwo::VALUE, + PADDING_ITEMS = (INSERT_PADDING) ? (TIME_SLICED_ITEMS >> LOG_SMEM_BANKS) : 0, + }; + + /****************************************************************************** + * Type definitions + ******************************************************************************/ + + /// Shared memory storage layout type + typedef T _TempStorage[TIME_SLICED_ITEMS + PADDING_ITEMS]; + +public: + + /// \smemstorage{BlockExchange} + struct TempStorage : Uninitialized<_TempStorage> {}; + +private: + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + /// Shared storage reference + _TempStorage &temp_storage; + + /// Linear thread-id + int linear_tid; + int warp_lane; + int warp_id; + int warp_offset; + + + /****************************************************************************** + * Utility methods + ******************************************************************************/ + + /// Internal storage allocator + __device__ __forceinline__ _TempStorage& PrivateStorage() + { + __shared__ _TempStorage private_storage; + return private_storage; + } + + + /** + * Transposes data items from blocked arrangement to striped arrangement. Specialized for no timeslicing. + */ + __device__ __forceinline__ void BlockedToStriped( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange, converting between blocked and striped arrangements. + Int2Type time_slicing) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = (linear_tid * ITEMS_PER_THREAD) + ITEM; + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + temp_storage[item_offset] = items[ITEM]; + } + + __syncthreads(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = int(ITEM * BLOCK_THREADS) + linear_tid; + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + items[ITEM] = temp_storage[item_offset]; + } + } + + + /** + * Transposes data items from blocked arrangement to striped arrangement. Specialized for warp-timeslicing. + */ + __device__ __forceinline__ void BlockedToStriped( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange, converting between blocked and striped arrangements. + Int2Type time_slicing) + { + T temp_items[ITEMS_PER_THREAD]; + + #pragma unroll + for (int SLICE = 0; SLICE < TIME_SLICES; SLICE++) + { + const int SLICE_OFFSET = SLICE * TIME_SLICED_ITEMS; + const int SLICE_OOB = SLICE_OFFSET + TIME_SLICED_ITEMS; + + __syncthreads(); + + if (warp_id == SLICE) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = (warp_lane * ITEMS_PER_THREAD) + ITEM; + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + temp_storage[item_offset] = items[ITEM]; + } + } + + __syncthreads(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + // Read a strip of items + const int STRIP_OFFSET = ITEM * BLOCK_THREADS; + const int STRIP_OOB = STRIP_OFFSET + BLOCK_THREADS; + + if ((SLICE_OFFSET < STRIP_OOB) && (SLICE_OOB > STRIP_OFFSET)) + { + int item_offset = STRIP_OFFSET + linear_tid - SLICE_OFFSET; + if ((item_offset >= 0) && (item_offset < TIME_SLICED_ITEMS)) + { + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + temp_items[ITEM] = temp_storage[item_offset]; + } + } + } + } + + // Copy + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = temp_items[ITEM]; + } + } + + + /** + * Transposes data items from blocked arrangement to warp-striped arrangement. Specialized for no timeslicing + */ + __device__ __forceinline__ void BlockedToWarpStriped( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange, converting between blocked and warp-striped arrangements. + Int2Type time_slicing) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = warp_offset + ITEM + (warp_lane * ITEMS_PER_THREAD); + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + temp_storage[item_offset] = items[ITEM]; + } + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = warp_offset + (ITEM * WARP_TIME_SLICED_THREADS) + warp_lane; + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + items[ITEM] = temp_storage[item_offset]; + } + } + + /** + * Transposes data items from blocked arrangement to warp-striped arrangement. Specialized for warp-timeslicing + */ + __device__ __forceinline__ void BlockedToWarpStriped( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange, converting between blocked and warp-striped arrangements. + Int2Type time_slicing) + { + #pragma unroll + for (int SLICE = 0; SLICE < TIME_SLICES; ++SLICE) + { + __syncthreads(); + + if (warp_id == SLICE) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = ITEM + (warp_lane * ITEMS_PER_THREAD); + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + temp_storage[item_offset] = items[ITEM]; + } + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = (ITEM * WARP_TIME_SLICED_THREADS) + warp_lane; + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + items[ITEM] = temp_storage[item_offset]; + } + } + } + } + + + /** + * Transposes data items from striped arrangement to blocked arrangement. Specialized for no timeslicing. + */ + __device__ __forceinline__ void StripedToBlocked( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange, converting between striped and blocked arrangements. + Int2Type time_slicing) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = int(ITEM * BLOCK_THREADS) + linear_tid; + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + temp_storage[item_offset] = items[ITEM]; + } + + __syncthreads(); + + // No timeslicing + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = (linear_tid * ITEMS_PER_THREAD) + ITEM; + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + items[ITEM] = temp_storage[item_offset]; + } + } + + + /** + * Transposes data items from striped arrangement to blocked arrangement. Specialized for warp-timeslicing. + */ + __device__ __forceinline__ void StripedToBlocked( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange, converting between striped and blocked arrangements. + Int2Type time_slicing) + { + // Warp time-slicing + T temp_items[ITEMS_PER_THREAD]; + + #pragma unroll + for (int SLICE = 0; SLICE < TIME_SLICES; SLICE++) + { + const int SLICE_OFFSET = SLICE * TIME_SLICED_ITEMS; + const int SLICE_OOB = SLICE_OFFSET + TIME_SLICED_ITEMS; + + __syncthreads(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + // Write a strip of items + const int STRIP_OFFSET = ITEM * BLOCK_THREADS; + const int STRIP_OOB = STRIP_OFFSET + BLOCK_THREADS; + + if ((SLICE_OFFSET < STRIP_OOB) && (SLICE_OOB > STRIP_OFFSET)) + { + int item_offset = STRIP_OFFSET + linear_tid - SLICE_OFFSET; + if ((item_offset >= 0) && (item_offset < TIME_SLICED_ITEMS)) + { + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + temp_storage[item_offset] = items[ITEM]; + } + } + } + + __syncthreads(); + + if (warp_id == SLICE) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = (warp_lane * ITEMS_PER_THREAD) + ITEM; + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + temp_items[ITEM] = temp_storage[item_offset]; + } + } + } + + // Copy + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = temp_items[ITEM]; + } + } + + + /** + * Transposes data items from warp-striped arrangement to blocked arrangement. Specialized for no timeslicing + */ + __device__ __forceinline__ void WarpStripedToBlocked( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange, converting between warp-striped and blocked arrangements. + Int2Type time_slicing) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = warp_offset + (ITEM * WARP_TIME_SLICED_THREADS) + warp_lane; + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + temp_storage[item_offset] = items[ITEM]; + } + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = warp_offset + ITEM + (warp_lane * ITEMS_PER_THREAD); + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + items[ITEM] = temp_storage[item_offset]; + } + } + + + /** + * Transposes data items from warp-striped arrangement to blocked arrangement. Specialized for warp-timeslicing + */ + __device__ __forceinline__ void WarpStripedToBlocked( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange, converting between warp-striped and blocked arrangements. + Int2Type time_slicing) + { + #pragma unroll + for (int SLICE = 0; SLICE < TIME_SLICES; ++SLICE) + { + __syncthreads(); + + if (warp_id == SLICE) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = (ITEM * WARP_TIME_SLICED_THREADS) + warp_lane; + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + temp_storage[item_offset] = items[ITEM]; + } + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = ITEM + (warp_lane * ITEMS_PER_THREAD); + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + items[ITEM] = temp_storage[item_offset]; + } + } + } + } + + + /** + * Exchanges data items annotated by rank into blocked arrangement. Specialized for no timeslicing. + */ + template + __device__ __forceinline__ void ScatterToBlocked( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange + Offset ranks[ITEMS_PER_THREAD], ///< [in] Corresponding scatter ranks + Int2Type time_slicing) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = ranks[ITEM]; + if (INSERT_PADDING) item_offset = SHR_ADD(item_offset, LOG_SMEM_BANKS, item_offset); + temp_storage[item_offset] = items[ITEM]; + } + + __syncthreads(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = (linear_tid * ITEMS_PER_THREAD) + ITEM; + if (INSERT_PADDING) item_offset = SHR_ADD(item_offset, LOG_SMEM_BANKS, item_offset); + items[ITEM] = temp_storage[item_offset]; + } + } + + /** + * Exchanges data items annotated by rank into blocked arrangement. Specialized for warp-timeslicing. + */ + template + __device__ __forceinline__ void ScatterToBlocked( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange + Offset ranks[ITEMS_PER_THREAD], ///< [in] Corresponding scatter ranks + Int2Type time_slicing) + { + T temp_items[ITEMS_PER_THREAD]; + + #pragma unroll + for (int SLICE = 0; SLICE < TIME_SLICES; SLICE++) + { + __syncthreads(); + + const int SLICE_OFFSET = TIME_SLICED_ITEMS * SLICE; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = ranks[ITEM] - SLICE_OFFSET; + if ((item_offset >= 0) && (item_offset < WARP_TIME_SLICED_ITEMS)) + { + if (INSERT_PADDING) item_offset = SHR_ADD(item_offset, LOG_SMEM_BANKS, item_offset); + temp_storage[item_offset] = items[ITEM]; + } + } + + __syncthreads(); + + if (warp_id == SLICE) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = (warp_lane * ITEMS_PER_THREAD) + ITEM; + if (INSERT_PADDING) item_offset = SHR_ADD(item_offset, LOG_SMEM_BANKS, item_offset); + temp_items[ITEM] = temp_storage[item_offset]; + } + } + } + + // Copy + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = temp_items[ITEM]; + } + } + + + /** + * Exchanges data items annotated by rank into striped arrangement. Specialized for no timeslicing. + */ + template + __device__ __forceinline__ void ScatterToStriped( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange + Offset ranks[ITEMS_PER_THREAD], ///< [in] Corresponding scatter ranks + Int2Type time_slicing) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = ranks[ITEM]; + if (INSERT_PADDING) item_offset = SHR_ADD(item_offset, LOG_SMEM_BANKS, item_offset); + temp_storage[item_offset] = items[ITEM]; + } + + __syncthreads(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = int(ITEM * BLOCK_THREADS) + linear_tid; + if (INSERT_PADDING) item_offset = SHR_ADD(item_offset, LOG_SMEM_BANKS, item_offset); + items[ITEM] = temp_storage[item_offset]; + } + } + + + /** + * Exchanges data items annotated by rank into striped arrangement. Specialized for warp-timeslicing. + */ + template + __device__ __forceinline__ void ScatterToStriped( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange + Offset ranks[ITEMS_PER_THREAD], ///< [in] Corresponding scatter ranks + Int2Type time_slicing) + { + T temp_items[ITEMS_PER_THREAD]; + + #pragma unroll + for (int SLICE = 0; SLICE < TIME_SLICES; SLICE++) + { + const int SLICE_OFFSET = SLICE * TIME_SLICED_ITEMS; + const int SLICE_OOB = SLICE_OFFSET + TIME_SLICED_ITEMS; + + __syncthreads(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = ranks[ITEM] - SLICE_OFFSET; + if ((item_offset >= 0) && (item_offset < WARP_TIME_SLICED_ITEMS)) + { + if (INSERT_PADDING) item_offset = SHR_ADD(item_offset, LOG_SMEM_BANKS, item_offset); + temp_storage[item_offset] = items[ITEM]; + } + } + + __syncthreads(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + // Read a strip of items + const int STRIP_OFFSET = ITEM * BLOCK_THREADS; + const int STRIP_OOB = STRIP_OFFSET + BLOCK_THREADS; + + if ((SLICE_OFFSET < STRIP_OOB) && (SLICE_OOB > STRIP_OFFSET)) + { + int item_offset = STRIP_OFFSET + linear_tid - SLICE_OFFSET; + if ((item_offset >= 0) && (item_offset < TIME_SLICED_ITEMS)) + { + if (INSERT_PADDING) item_offset += item_offset >> LOG_SMEM_BANKS; + temp_items[ITEM] = temp_storage[item_offset]; + } + } + } + } + + // Copy + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = temp_items[ITEM]; + } + } + + +public: + + /******************************************************************//** + * \name Collective constructors + *********************************************************************/ + //@{ + + /** + * \brief Collective constructor for 1D thread blocks using a private static allocation of shared memory as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockExchange() + : + temp_storage(PrivateStorage()), + linear_tid(threadIdx.x), + warp_lane(linear_tid & (WARP_THREADS - 1)), + warp_id(linear_tid >> LOG_WARP_THREADS), + warp_offset(warp_id * WARP_TIME_SLICED_ITEMS) + {} + + + /** + * \brief Collective constructor for 1D thread blocks using the specified memory allocation as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockExchange( + TempStorage &temp_storage) ///< [in] Reference to memory allocation having layout type TempStorage + : + temp_storage(temp_storage.Alias()), + linear_tid(threadIdx.x), + warp_lane(linear_tid & (WARP_THREADS - 1)), + warp_id(linear_tid >> LOG_WARP_THREADS), + warp_offset(warp_id * WARP_TIME_SLICED_ITEMS) + {} + + + /** + * \brief Collective constructor using a private static allocation of shared memory as temporary storage. Each thread is identified using the supplied linear thread identifier + */ + __device__ __forceinline__ BlockExchange( + int linear_tid) ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(PrivateStorage()), + linear_tid(linear_tid), + warp_lane(linear_tid & (WARP_THREADS - 1)), + warp_id(linear_tid >> LOG_WARP_THREADS), + warp_offset(warp_id * WARP_TIME_SLICED_ITEMS) + {} + + + /** + * \brief Collective constructor using the specified memory allocation as temporary storage. Each thread is identified using the supplied linear thread identifier. + */ + __device__ __forceinline__ BlockExchange( + TempStorage &temp_storage, ///< [in] Reference to memory allocation having layout type TempStorage + int linear_tid) ///< [in] [optional] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid), + warp_lane(linear_tid & (WARP_THREADS - 1)), + warp_id(linear_tid >> LOG_WARP_THREADS), + warp_offset(warp_id * WARP_TIME_SLICED_ITEMS) + {} + + + //@} end member group + /******************************************************************//** + * \name Structured exchanges + *********************************************************************/ + //@{ + + /** + * \brief Transposes data items from striped arrangement to blocked arrangement. + * + * \par + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates the conversion from a "striped" to a "blocked" arrangement + * of 512 integer items partitioned across 128 threads where each thread owns 4 items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(int *d_data, ...) + * { + * // Specialize BlockExchange for 128 threads owning 4 integer items each + * typedef cub::BlockExchange BlockExchange; + * + * // Allocate shared memory for BlockExchange + * __shared__ typename BlockExchange::TempStorage temp_storage; + * + * // Load a tile of ordered data into a striped arrangement across block threads + * int thread_data[4]; + * cub::LoadDirectStriped<128>(threadIdx.x, d_data, thread_data); + * + * // Collectively exchange data into a blocked arrangement across threads + * BlockExchange(temp_storage).StripedToBlocked(thread_data); + * + * \endcode + * \par + * Suppose the set of striped input \p thread_data across the block of threads is + * { [0,128,256,384], [1,129,257,385], ..., [127,255,383,511] } after loading from global memory. + * The corresponding output \p thread_data in those threads will be + * { [0,1,2,3], [4,5,6,7], [8,9,10,11], ..., [508,509,510,511] }. + * + */ + __device__ __forceinline__ void StripedToBlocked( + T items[ITEMS_PER_THREAD]) ///< [in-out] Items to exchange, converting between striped and blocked arrangements. + { + StripedToBlocked(items, Int2Type()); + } + + /** + * \brief Transposes data items from blocked arrangement to striped arrangement. + * + * \par + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates the conversion from a "blocked" to a "striped" arrangement + * of 512 integer items partitioned across 128 threads where each thread owns 4 items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(int *d_data, ...) + * { + * // Specialize BlockExchange for 128 threads owning 4 integer items each + * typedef cub::BlockExchange BlockExchange; + * + * // Allocate shared memory for BlockExchange + * __shared__ typename BlockExchange::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Collectively exchange data into a striped arrangement across threads + * BlockExchange(temp_storage).BlockedToStriped(thread_data); + * + * // Store data striped across block threads into an ordered tile + * cub::StoreDirectStriped(threadIdx.x, d_data, thread_data); + * + * \endcode + * \par + * Suppose the set of blocked input \p thread_data across the block of threads is + * { [0,1,2,3], [4,5,6,7], [8,9,10,11], ..., [508,509,510,511] }. + * The corresponding output \p thread_data in those threads will be + * { [0,128,256,384], [1,129,257,385], ..., [127,255,383,511] } in + * preparation for storing to global memory. + * + */ + __device__ __forceinline__ void BlockedToStriped( + T items[ITEMS_PER_THREAD]) ///< [in-out] Items to exchange, converting between blocked and striped arrangements. + { + BlockedToStriped(items, Int2Type()); + } + + + /** + * \brief Transposes data items from warp-striped arrangement to blocked arrangement. + * + * \par + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates the conversion from a "warp-striped" to a "blocked" arrangement + * of 512 integer items partitioned across 128 threads where each thread owns 4 items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(int *d_data, ...) + * { + * // Specialize BlockExchange for 128 threads owning 4 integer items each + * typedef cub::BlockExchange BlockExchange; + * + * // Allocate shared memory for BlockExchange + * __shared__ typename BlockExchange::TempStorage temp_storage; + * + * // Load a tile of ordered data into a warp-striped arrangement across warp threads + * int thread_data[4]; + * cub::LoadSWarptriped(threadIdx.x, d_data, thread_data); + * + * // Collectively exchange data into a blocked arrangement across threads + * BlockExchange(temp_storage).WarpStripedToBlocked(thread_data); + * + * \endcode + * \par + * Suppose the set of warp-striped input \p thread_data across the block of threads is + * { [0,32,64,96], [1,33,65,97], [2,34,66,98], ..., [415,447,479,511] } + * after loading from global memory. (The first 128 items are striped across + * the first warp of 32 threads, the second 128 items are striped across the second warp, etc.) + * The corresponding output \p thread_data in those threads will be + * { [0,1,2,3], [4,5,6,7], [8,9,10,11], ..., [508,509,510,511] }. + * + */ + __device__ __forceinline__ void WarpStripedToBlocked( + T items[ITEMS_PER_THREAD]) ///< [in-out] Items to exchange, converting between warp-striped and blocked arrangements. + { + WarpStripedToBlocked(items, Int2Type()); + } + + /** + * \brief Transposes data items from blocked arrangement to warp-striped arrangement. + * + * \par + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates the conversion from a "blocked" to a "warp-striped" arrangement + * of 512 integer items partitioned across 128 threads where each thread owns 4 items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(int *d_data, ...) + * { + * // Specialize BlockExchange for 128 threads owning 4 integer items each + * typedef cub::BlockExchange BlockExchange; + * + * // Allocate shared memory for BlockExchange + * __shared__ typename BlockExchange::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Collectively exchange data into a warp-striped arrangement across threads + * BlockExchange(temp_storage).BlockedToWarpStriped(thread_data); + * + * // Store data striped across warp threads into an ordered tile + * cub::StoreDirectStriped(threadIdx.x, d_data, thread_data); + * + * \endcode + * \par + * Suppose the set of blocked input \p thread_data across the block of threads is + * { [0,1,2,3], [4,5,6,7], [8,9,10,11], ..., [508,509,510,511] }. + * The corresponding output \p thread_data in those threads will be + * { [0,32,64,96], [1,33,65,97], [2,34,66,98], ..., [415,447,479,511] } + * in preparation for storing to global memory. (The first 128 items are striped across + * the first warp of 32 threads, the second 128 items are striped across the second warp, etc.) + * + */ + __device__ __forceinline__ void BlockedToWarpStriped( + T items[ITEMS_PER_THREAD]) ///< [in-out] Items to exchange, converting between blocked and warp-striped arrangements. + { + BlockedToWarpStriped(items, Int2Type()); + } + + + //@} end member group + /******************************************************************//** + * \name Scatter exchanges + *********************************************************************/ + //@{ + + + /** + * \brief Exchanges data items annotated by rank into blocked arrangement. + * + * \par + * - \smemreuse + * + * \tparam Offset [inferred] Signed integer type for local offsets + */ + template + __device__ __forceinline__ void ScatterToBlocked( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange + Offset ranks[ITEMS_PER_THREAD]) ///< [in] Corresponding scatter ranks + { + ScatterToBlocked(items, ranks, Int2Type()); + } + + + /** + * \brief Exchanges data items annotated by rank into striped arrangement. + * + * \par + * - \smemreuse + * + * \tparam Offset [inferred] Signed integer type for local offsets + */ + template + __device__ __forceinline__ void ScatterToStriped( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange + Offset ranks[ITEMS_PER_THREAD]) ///< [in] Corresponding scatter ranks + { + ScatterToStriped(items, ranks, Int2Type()); + } + + + /** + * \brief Exchanges data items annotated by rank into striped arrangement. Items with rank -1 are not exchanged. + * + * \par + * - \smemreuse + * + * \tparam Offset [inferred] Signed integer type for local offsets + */ + template + __device__ __forceinline__ void ScatterToStripedGuarded( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange + Offset ranks[ITEMS_PER_THREAD]) ///< [in] Corresponding scatter ranks + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = ranks[ITEM]; + if (INSERT_PADDING) item_offset = SHR_ADD(item_offset, LOG_SMEM_BANKS, item_offset); + if (ranks[ITEM] >= 0) + temp_storage[item_offset] = items[ITEM]; + } + + __syncthreads(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = int(ITEM * BLOCK_THREADS) + linear_tid; + if (INSERT_PADDING) item_offset = SHR_ADD(item_offset, LOG_SMEM_BANKS, item_offset); + items[ITEM] = temp_storage[item_offset]; + } + } + + /** + * \brief Exchanges valid data items annotated by rank into striped arrangement. + * + * \par + * - \smemreuse + * + * \tparam Offset [inferred] Signed integer type for local offsets + * \tparam ValidFlag [inferred] Flag type denoting which items are valid + */ + template + __device__ __forceinline__ void ScatterToStriped( + T items[ITEMS_PER_THREAD], ///< [in-out] Items to exchange + Offset ranks[ITEMS_PER_THREAD], ///< [in] Corresponding scatter ranks + ValidFlag is_valid[ITEMS_PER_THREAD]) ///< [in] Corresponding flag denoting item validity + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = ranks[ITEM]; + if (INSERT_PADDING) item_offset = SHR_ADD(item_offset, LOG_SMEM_BANKS, item_offset); + if (is_valid[ITEM]) + temp_storage[item_offset] = items[ITEM]; + } + + __syncthreads(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + int item_offset = int(ITEM * BLOCK_THREADS) + linear_tid; + if (INSERT_PADDING) item_offset = SHR_ADD(item_offset, LOG_SMEM_BANKS, item_offset); + items[ITEM] = temp_storage[item_offset]; + } + } + + //@} end member group + + +}; + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_histo_256.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_histo_256.cuh new file mode 100644 index 0000000000000000000000000000000000000000..9c33921c36c17a7bb8ebedefb09c8ab5ab6f3e48 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_histo_256.cuh @@ -0,0 +1,446 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockHisto256 provides methods for constructing (and compositing into) 256-bin histograms from 8b data partitioned across threads within a CUDA thread block. + */ + +#pragma once + +#include "../util_arch.cuh" +#include "../block/block_radix_sort.cuh" +#include "../block/block_discontinuity.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Algorithmic variants + ******************************************************************************/ + +/** + * \brief BlockHisto256Algorithm enumerates alternative algorithms for the parallel construction of 8b histograms. + */ +enum BlockHisto256Algorithm +{ + + /** + * \par Overview + * Sorting followed by differentiation. Execution is comprised of two phases: + * -# Sort the 8b data using efficient radix sort + * -# Look for "runs" of same-valued 8b keys by detecting discontinuities; the run-lengths are histogram bin counts. + * + * \par Performance Considerations + * Delivers consistent throughput regardless of sample bin distribution. + */ + BLOCK_HISTO_256_SORT, + + + /** + * \par Overview + * Use atomic addition to update byte counts directly + * + * \par Performance Considerations + * Performance is strongly tied to the hardware implementation of atomic + * addition, and may be significantly degraded for non uniformly-random + * input distributions where many concurrent updates are likely to be + * made to the same bin counter. + */ + BLOCK_HISTO_256_ATOMIC, +}; + + + +/****************************************************************************** + * Block histogram + ******************************************************************************/ + + +/** + * \addtogroup BlockModule + * @{ + */ + +/** + * \brief BlockHisto256 provides methods for constructing (and compositing into) 256-bin histograms from 8b data partitioned across threads within a CUDA thread block. ![](histogram_logo.png) + * + * \par Overview + * A histogram + * counts the number of observations that fall into each of the disjoint categories (known as bins). + * + * \par + * For convenience, BlockHisto256 provides alternative entrypoints that differ by: + * - Complete/incremental composition (compute a new histogram vs. update existing histogram data) + * + * \tparam BLOCK_THREADS The threadblock size in threads + * \tparam ITEMS_PER_THREAD The number of items per thread + * \tparam ALGORITHM [optional] cub::BlockHisto256Algorithm enumerator specifying the underlying algorithm to use (default = cub::BLOCK_HISTO_256_SORT) + * + * \par Algorithm + * BlockHisto256 can be (optionally) configured to use different algorithms: + * -# cub::BLOCK_HISTO_256_SORT. Sorting followed by differentiation. [More...](\ref cub::BlockHisto256Algorithm) + * -# cub::BLOCK_HISTO_256_ATOMIC. Use atomic addition to update byte counts directly. [More...](\ref cub::BlockHisto256Algorithm) + * + * \par Usage Considerations + * - The histogram output can be constructed in shared or global memory + * - Supports partially-full threadblocks (i.e., the most-significant thread ranks having undefined values). + * - \smemreuse{BlockHisto256::SmemStorage} + * + * \par Performance Considerations + * - Computation is slightly more efficient (i.e., having lower instruction overhead) for: + * - \p BLOCK_THREADS is a multiple of the architecture's warp size + * - Every thread has a valid input (i.e., full vs. partial-tiles) + * - See cub::BlockHisto256Algorithm for performance details regarding algorithmic alternatives + * + * \par Examples + * \par + * Example 1. Compute a simple 8b histogram in shared memory from 512 byte values that + * are partitioned across a 128-thread threadblock (where each thread holds 4 values). + * \code + * #include + * + * __global__ void SomeKernel(...) + * { + * // Parameterize BlockHisto256 for 128 threads + * typedef cub::BlockHisto256<128> BlockHisto256; + * + * // Declare shared memory for BlockHisto256 + * __shared__ typename BlockHisto256::SmemStorage smem_storage; + * + * // Declare shared memory for histogram bins + * __shared__ unsigned int smem_histogram[256]; + * + * // Input items per thread + * unsigned char data[4]; + * + * // Obtain items + * ... + * + * // Compute the threadblock-wide histogram + * BlockHisto256::Histogram(smem_storage, smem_histogram, data); + * + * ... + * \endcode + * + * \par + * Example 2: Composite an incremental round of 8b histogram data onto + * an existing histogram in global memory. + * \code + * #include + * + * template + * __global__ void SomeKernel(..., int *d_histogram) + * { + * // Parameterize BlockHisto256 + * typedef cub::BlockHisto256 BlockHisto256; + * + * // Declare shared memory for BlockHisto256 + * __shared__ typename BlockHisto256::SmemStorage smem_storage; + * + * // Guarded load of input item + * int data; + * if (threadIdx.x < num_items) data = ...; + * + * // Compute the threadblock-wide sum of valid elements in thread0 + * BlockHisto256::Composite(smem_storage, d_histogram, data); + * + * ... + * \endcode + * + */ +template < + int BLOCK_THREADS, + int ITEMS_PER_THREAD, + BlockHisto256Algorithm ALGORITHM = BLOCK_HISTO_256_SORT> +class BlockHisto256 +{ +private: + + /****************************************************************************** + * Constants + ******************************************************************************/ + + /** + * Ensure the template parameterization meets the requirements of the + * targeted device architecture. BLOCK_HISTO_256_ATOMIC can only be used + * on version SM120 or later. Otherwise BLOCK_HISTO_256_SORT is used + * regardless. + */ + static const BlockHisto256Algorithm SAFE_ALGORITHM = + ((ALGORITHM == BLOCK_HISTO_256_ATOMIC) && (CUB_PTX_ARCH < 120)) ? + BLOCK_HISTO_256_SORT : + ALGORITHM; + + #ifndef DOXYGEN_SHOULD_SKIP_THIS // Do not document + + + /****************************************************************************** + * Algorithmic variants + ******************************************************************************/ + + /** + * BLOCK_HISTO_256_SORT algorithmic variant + */ + template + struct BlockHisto256Internal + { + // Parameterize BlockRadixSort type for our thread block + typedef BlockRadixSort BlockRadixSortT; + + // Parameterize BlockDiscontinuity type for our thread block + typedef BlockDiscontinuity BlockDiscontinuityT; + + // Shared memory + union SmemStorage + { + // Storage for sorting bin values + typename BlockRadixSortT::SmemStorage sort_storage; + + struct + { + // Storage for detecting discontinuities in the tile of sorted bin values + typename BlockDiscontinuityT::SmemStorage discont_storage; + + // Storage for noting begin/end offsets of bin runs in the tile of sorted bin values + unsigned int run_begin[256]; + unsigned int run_end[256]; + }; + }; + + + // Discontinuity functor + struct DiscontinuityOp + { + // Reference to smem_storage + SmemStorage &smem_storage; + + // Constructor + __device__ __forceinline__ DiscontinuityOp(SmemStorage &smem_storage) : smem_storage(smem_storage) {} + + // Discontinuity predicate + __device__ __forceinline__ bool operator()(const unsigned char &a, const unsigned char &b, unsigned int b_index) + { + if (a != b) + { + // Note the begin/end offsets in shared storage + smem_storage.run_begin[b] = b_index; + smem_storage.run_end[a] = b_index; + + return true; + } + else + { + return false; + } + } + }; + + + // Composite data onto an existing histogram + template < + typename HistoCounter> + static __device__ __forceinline__ void Composite( + SmemStorage &smem_storage, ///< [in] Reference to shared memory allocation having layout type SmemStorage + unsigned char (&items)[ITEMS_PER_THREAD], ///< [in] Calling thread's 8b input values to histogram + HistoCounter histogram[256]) ///< [out] Reference to shared/global memory 256-bin histogram + { + enum { TILE_SIZE = BLOCK_THREADS * ITEMS_PER_THREAD }; + + // Sort bytes in blocked arrangement + BlockRadixSortT::SortBlocked(smem_storage.sort_storage, items); + + __syncthreads(); + + // Initialize the shared memory's run_begin and run_end for each bin + int histo_offset = 0; + + #pragma unroll + for(; histo_offset + BLOCK_THREADS <= 256; histo_offset += BLOCK_THREADS) + { + smem_storage.run_begin[histo_offset + threadIdx.x] = TILE_SIZE; + smem_storage.run_end[histo_offset + threadIdx.x] = TILE_SIZE; + } + // Finish up with guarded initialization if necessary + if ((histo_offset < BLOCK_THREADS) && (histo_offset + threadIdx.x < 256)) + { + smem_storage.run_begin[histo_offset + threadIdx.x] = TILE_SIZE; + smem_storage.run_end[histo_offset + threadIdx.x] = TILE_SIZE; + } + + __syncthreads(); + + int flags[ITEMS_PER_THREAD]; // unused + + // Note the begin/end run offsets of bin runs in the sorted tile + DiscontinuityOp flag_op(smem_storage); + BlockDiscontinuityT::Flag(smem_storage.discont_storage, items, flag_op, flags); + + // Update begin for first item + if (threadIdx.x == 0) smem_storage.run_begin[items[0]] = 0; + + __syncthreads(); + + // Composite into histogram + histo_offset = 0; + + #pragma unroll + for(; histo_offset + BLOCK_THREADS <= 256; histo_offset += BLOCK_THREADS) + { + int thread_offset = histo_offset + threadIdx.x; + HistoCounter count = smem_storage.run_end[thread_offset] - smem_storage.run_begin[thread_offset]; + histogram[thread_offset] += count; + } + // Finish up with guarded composition if necessary + if ((histo_offset < BLOCK_THREADS) && (histo_offset + threadIdx.x < 256)) + { + int thread_offset = histo_offset + threadIdx.x; + HistoCounter count = smem_storage.run_end[thread_offset] - smem_storage.run_begin[thread_offset]; + histogram[thread_offset] += count; + } + } + + }; + + + /** + * BLOCK_HISTO_256_ATOMIC algorithmic variant + */ + template + struct BlockHisto256Internal + { + /// Shared memory storage layout type + struct SmemStorage {}; + + /// Composite data onto an existing histogram + template < + typename HistoCounter> + static __device__ __forceinline__ void Composite( + SmemStorage &smem_storage, ///< [in] Reference to shared memory allocation having layout type SmemStorage + unsigned char (&items)[ITEMS_PER_THREAD], ///< [in] Calling thread's 8b input values to histogram + HistoCounter histogram[256]) ///< [out] Reference to shared/global memory 256-bin histogram + { + // Update histogram + #pragma unroll + for (int i = 0; i < ITEMS_PER_THREAD; ++i) + { + atomicAdd(histogram + items[i], 1); + } + } + + }; + + + #endif // DOXYGEN_SHOULD_SKIP_THIS + + + /// Shared memory storage layout type for BlockHisto256 + typedef typename BlockHisto256Internal::SmemStorage _SmemStorage; + + +public: + + /// \smemstorage{BlockHisto256} + typedef _SmemStorage SmemStorage; + + + /** + * Initialize shared histogram + */ + template + static __device__ __forceinline__ void InitHistogram(HistoCounter histogram[256]) + { + // Initialize histogram bin counts to zeros + int histo_offset = 0; + + #pragma unroll + for(; histo_offset + BLOCK_THREADS <= 256; histo_offset += BLOCK_THREADS) + { + histogram[histo_offset + threadIdx.x] = 0; + } + // Finish up with guarded initialization if necessary + if ((histo_offset < BLOCK_THREADS) && (histo_offset + threadIdx.x < 256)) + { + histogram[histo_offset + threadIdx.x] = 0; + } + } + + + /** + * \brief Constructs a threadblock-wide histogram in shared/global memory. Each thread contributes an array of 8b input elements. + * + * \smemreuse + * + * \tparam ITEMS_PER_THREAD [inferred] The number of 8b values per thread + * \tparam HistoCounter [inferred] Histogram counter type + */ + template < + typename HistoCounter> + static __device__ __forceinline__ void Histogram( + SmemStorage &smem_storage, ///< [in] Reference to shared memory allocation having layout type SmemStorage + unsigned char (&items)[ITEMS_PER_THREAD], ///< [in] Calling thread's 8b input values to histogram + HistoCounter histogram[256]) ///< [out] Reference to shared/global memory 256-bin histogram + { + // Initialize histogram bin counts to zeros + InitHistogram(histogram); + + // Composite the histogram + BlockHisto256Internal::Composite(smem_storage, items, histogram); + } + + + + /** + * \brief Updates an existing threadblock-wide histogram in shared/global memory. Each thread composites an array of 8b input elements. + * + * \smemreuse + * + * \tparam HistoCounter [inferred] Histogram counter type + */ + template < + typename HistoCounter> + static __device__ __forceinline__ void Composite( + SmemStorage &smem_storage, ///< [in] Reference to shared memory allocation having layout type SmemStorage + unsigned char (&items)[ITEMS_PER_THREAD], ///< [in] Calling thread's 8b input values to histogram + HistoCounter histogram[256]) ///< [out] Reference to shared/global memory 256-bin histogram + { + BlockHisto256Internal::Composite(smem_storage, items, histogram); + } + +}; + +/** @} */ // end group BlockModule + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_histogram.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_histogram.cuh new file mode 100644 index 0000000000000000000000000000000000000000..61194546b92e4e566adc808745183ebdc5fbebb5 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_histogram.cuh @@ -0,0 +1,424 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * The cub::BlockHistogram class provides [collective](index.html#sec0) methods for constructing block-wide histograms from data samples partitioned across a CUDA thread block. + */ + +#pragma once + +#include "specializations/block_histogram_sort.cuh" +#include "specializations/block_histogram_atomic.cuh" +#include "../util_arch.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Algorithmic variants + ******************************************************************************/ + +/** + * \brief BlockHistogramAlgorithm enumerates alternative algorithms for the parallel construction of block-wide histograms. + */ +enum BlockHistogramAlgorithm +{ + + /** + * \par Overview + * Sorting followed by differentiation. Execution is comprised of two phases: + * -# Sort the data using efficient radix sort + * -# Look for "runs" of same-valued keys by detecting discontinuities; the run-lengths are histogram bin counts. + * + * \par Performance Considerations + * Delivers consistent throughput regardless of sample bin distribution. + */ + BLOCK_HISTO_SORT, + + + /** + * \par Overview + * Use atomic addition to update byte counts directly + * + * \par Performance Considerations + * Performance is strongly tied to the hardware implementation of atomic + * addition, and may be significantly degraded for non uniformly-random + * input distributions where many concurrent updates are likely to be + * made to the same bin counter. + */ + BLOCK_HISTO_ATOMIC, +}; + + + +/****************************************************************************** + * Block histogram + ******************************************************************************/ + + +/** + * \brief The BlockHistogram class provides [collective](index.html#sec0) methods for constructing block-wide histograms from data samples partitioned across a CUDA thread block. ![](histogram_logo.png) + * \ingroup BlockModule + * + * \tparam T The sample type being histogrammed (must be castable to an integer bin identifier) + * \tparam BLOCK_THREADS The thread block size in threads + * \tparam ITEMS_PER_THREAD The number of items per thread + * \tparam BINS The number bins within the histogram + * \tparam ALGORITHM [optional] cub::BlockHistogramAlgorithm enumerator specifying the underlying algorithm to use (default: cub::BLOCK_HISTO_SORT) + * + * \par Overview + * - A histogram + * counts the number of observations that fall into each of the disjoint categories (known as bins). + * - BlockHistogram can be optionally specialized to use different algorithms: + * -# cub::BLOCK_HISTO_SORT. Sorting followed by differentiation. [More...](\ref cub::BlockHistogramAlgorithm) + * -# cub::BLOCK_HISTO_ATOMIC. Use atomic addition to update byte counts directly. [More...](\ref cub::BlockHistogramAlgorithm) + * + * \par Performance Considerations + * - \granularity + * + * \par A Simple Example + * \blockcollective{BlockHistogram} + * \par + * The code snippet below illustrates a 256-bin histogram of 512 integer samples that + * are partitioned across 128 threads where each thread owns 4 samples. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize a 256-bin BlockHistogram type for 128 threads having 4 character samples each + * typedef cub::BlockHistogram BlockHistogram; + * + * // Allocate shared memory for BlockHistogram + * __shared__ typename BlockHistogram::TempStorage temp_storage; + * + * // Allocate shared memory for block-wide histogram bin counts + * __shared__ unsigned int smem_histogram[256]; + * + * // Obtain input samples per thread + * unsigned char data[4]; + * ... + * + * // Compute the block-wide histogram + * BlockHistogram(temp_storage).Histogram(data, smem_histogram); + * + * \endcode + * + * \par Performance and Usage Considerations + * - The histogram output can be constructed in shared or global memory + * - See cub::BlockHistogramAlgorithm for performance details regarding algorithmic alternatives + * + */ +template < + typename T, + int BLOCK_THREADS, + int ITEMS_PER_THREAD, + int BINS, + BlockHistogramAlgorithm ALGORITHM = BLOCK_HISTO_SORT> +class BlockHistogram +{ +private: + + /****************************************************************************** + * Constants and type definitions + ******************************************************************************/ + + /** + * Ensure the template parameterization meets the requirements of the + * targeted device architecture. BLOCK_HISTO_ATOMIC can only be used + * on version SM120 or later. Otherwise BLOCK_HISTO_SORT is used + * regardless. + */ + static const BlockHistogramAlgorithm SAFE_ALGORITHM = + ((ALGORITHM == BLOCK_HISTO_ATOMIC) && (CUB_PTX_VERSION < 120)) ? + BLOCK_HISTO_SORT : + ALGORITHM; + + /// Internal specialization. + typedef typename If<(SAFE_ALGORITHM == BLOCK_HISTO_SORT), + BlockHistogramSort, + BlockHistogramAtomic >::Type InternalBlockHistogram; + + /// Shared memory storage layout type for BlockHistogram + typedef typename InternalBlockHistogram::TempStorage _TempStorage; + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + /// Shared storage reference + _TempStorage &temp_storage; + + /// Linear thread-id + int linear_tid; + + + /****************************************************************************** + * Utility methods + ******************************************************************************/ + + /// Internal storage allocator + __device__ __forceinline__ _TempStorage& PrivateStorage() + { + __shared__ _TempStorage private_storage; + return private_storage; + } + + +public: + + /// \smemstorage{BlockHistogram} + struct TempStorage : Uninitialized<_TempStorage> {}; + + + /******************************************************************//** + * \name Collective constructors + *********************************************************************/ + //@{ + + /** + * \brief Collective constructor for 1D thread blocks using a private static allocation of shared memory as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockHistogram() + : + temp_storage(PrivateStorage()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor for 1D thread blocks using the specified memory allocation as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockHistogram( + TempStorage &temp_storage) ///< [in] Reference to memory allocation having layout type TempStorage + : + temp_storage(temp_storage.Alias()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor using a private static allocation of shared memory as temporary storage. Each thread is identified using the supplied linear thread identifier + */ + __device__ __forceinline__ BlockHistogram( + int linear_tid) ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(PrivateStorage()), + linear_tid(linear_tid) + {} + + + /** + * \brief Collective constructor using the specified memory allocation as temporary storage. Each thread is identified using the supplied linear thread identifier. + */ + __device__ __forceinline__ BlockHistogram( + TempStorage &temp_storage, ///< [in] Reference to memory allocation having layout type TempStorage + int linear_tid) ///< [in] [optional] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + + //@} end member group + /******************************************************************//** + * \name Histogram operations + *********************************************************************/ + //@{ + + + /** + * \brief Initialize the shared histogram counters to zero. + * + * \par Snippet + * The code snippet below illustrates a the initialization and update of a + * histogram of 512 integer samples that are partitioned across 128 threads + * where each thread owns 4 samples. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize a 256-bin BlockHistogram type for 128 threads having 4 character samples each + * typedef cub::BlockHistogram BlockHistogram; + * + * // Allocate shared memory for BlockHistogram + * __shared__ typename BlockHistogram::TempStorage temp_storage; + * + * // Allocate shared memory for block-wide histogram bin counts + * __shared__ unsigned int smem_histogram[256]; + * + * // Obtain input samples per thread + * unsigned char thread_samples[4]; + * ... + * + * // Initialize the block-wide histogram + * BlockHistogram(temp_storage).InitHistogram(smem_histogram); + * + * // Update the block-wide histogram + * BlockHistogram(temp_storage).Composite(thread_samples, smem_histogram); + * + * \endcode + * + * \tparam HistoCounter [inferred] Histogram counter type + */ + template + __device__ __forceinline__ void InitHistogram(HistoCounter histogram[BINS]) + { + // Initialize histogram bin counts to zeros + int histo_offset = 0; + + #pragma unroll + for(; histo_offset + BLOCK_THREADS <= BINS; histo_offset += BLOCK_THREADS) + { + histogram[histo_offset + linear_tid] = 0; + } + // Finish up with guarded initialization if necessary + if ((BINS % BLOCK_THREADS != 0) && (histo_offset + linear_tid < BINS)) + { + histogram[histo_offset + linear_tid] = 0; + } + } + + + /** + * \brief Constructs a block-wide histogram in shared/global memory. Each thread contributes an array of input elements. + * + * \par + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a 256-bin histogram of 512 integer samples that + * are partitioned across 128 threads where each thread owns 4 samples. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize a 256-bin BlockHistogram type for 128 threads having 4 character samples each + * typedef cub::BlockHistogram BlockHistogram; + * + * // Allocate shared memory for BlockHistogram + * __shared__ typename BlockHistogram::TempStorage temp_storage; + * + * // Allocate shared memory for block-wide histogram bin counts + * __shared__ unsigned int smem_histogram[256]; + * + * // Obtain input samples per thread + * unsigned char thread_samples[4]; + * ... + * + * // Compute the block-wide histogram + * BlockHistogram(temp_storage).Histogram(thread_samples, smem_histogram); + * + * \endcode + * + * \tparam HistoCounter [inferred] Histogram counter type + */ + template < + typename HistoCounter> + __device__ __forceinline__ void Histogram( + T (&items)[ITEMS_PER_THREAD], ///< [in] Calling thread's input values to histogram + HistoCounter histogram[BINS]) ///< [out] Reference to shared/global memory histogram + { + // Initialize histogram bin counts to zeros + InitHistogram(histogram); + + __syncthreads(); + + // Composite the histogram + InternalBlockHistogram(temp_storage, linear_tid).Composite(items, histogram); + } + + + + /** + * \brief Updates an existing block-wide histogram in shared/global memory. Each thread composites an array of input elements. + * + * \par + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a the initialization and update of a + * histogram of 512 integer samples that are partitioned across 128 threads + * where each thread owns 4 samples. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize a 256-bin BlockHistogram type for 128 threads having 4 character samples each + * typedef cub::BlockHistogram BlockHistogram; + * + * // Allocate shared memory for BlockHistogram + * __shared__ typename BlockHistogram::TempStorage temp_storage; + * + * // Allocate shared memory for block-wide histogram bin counts + * __shared__ unsigned int smem_histogram[256]; + * + * // Obtain input samples per thread + * unsigned char thread_samples[4]; + * ... + * + * // Initialize the block-wide histogram + * BlockHistogram(temp_storage).InitHistogram(smem_histogram); + * + * // Update the block-wide histogram + * BlockHistogram(temp_storage).Composite(thread_samples, smem_histogram); + * + * \endcode + * + * \tparam HistoCounter [inferred] Histogram counter type + */ + template < + typename HistoCounter> + __device__ __forceinline__ void Composite( + T (&items)[ITEMS_PER_THREAD], ///< [in] Calling thread's input values to histogram + HistoCounter histogram[BINS]) ///< [out] Reference to shared/global memory histogram + { + InternalBlockHistogram(temp_storage, linear_tid).Composite(items, histogram); + } + +}; + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_load.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_load.cuh new file mode 100644 index 0000000000000000000000000000000000000000..710bb296c53d494b73737c726399ce24f62f1fb3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_load.cuh @@ -0,0 +1,1093 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * Operations for reading linear tiles of data into the CUDA thread block. + */ + +#pragma once + +#include + +#include "../util_namespace.cuh" +#include "../util_macro.cuh" +#include "../util_type.cuh" +#include "block_exchange.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/** + * \addtogroup UtilIo + * @{ + */ + + +/******************************************************************//** + * \name Blocked arrangement I/O (direct) + *********************************************************************/ +//@{ + + +/** + * \brief Load a linear segment of items into a blocked arrangement across the thread block. + * + * \blocked + * + * \tparam T [inferred] The data type to load. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam InputIterator [inferred] The random-access iterator type for input \iterator. + */ +template < + typename T, + int ITEMS_PER_THREAD, + typename InputIterator> +__device__ __forceinline__ void LoadDirectBlocked( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD]) ///< [out] Data to load +{ + // Load directly in thread-blocked order + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = block_itr[(linear_tid * ITEMS_PER_THREAD) + ITEM]; + } +} + + +/** + * \brief Load a linear segment of items into a blocked arrangement across the thread block, guarded by range. + * + * \blocked + * + * \tparam T [inferred] The data type to load. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam InputIterator [inferred] The random-access iterator type for input \iterator. + */ +template < + typename T, + int ITEMS_PER_THREAD, + typename InputIterator> +__device__ __forceinline__ void LoadDirectBlocked( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items) ///< [in] Number of valid items to load +{ + int bounds = valid_items - (linear_tid * ITEMS_PER_THREAD); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + if (ITEM < bounds) + { + items[ITEM] = block_itr[(linear_tid * ITEMS_PER_THREAD) + ITEM]; + } + } +} + + +/** + * \brief Load a linear segment of items into a blocked arrangement across the thread block, guarded by range, with a fall-back assignment of out-of-bound elements.. + * + * \blocked + * + * \tparam T [inferred] The data type to load. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam InputIterator [inferred] The random-access iterator type for input \iterator. + */ +template < + typename T, + int ITEMS_PER_THREAD, + typename InputIterator> +__device__ __forceinline__ void LoadDirectBlocked( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items, ///< [in] Number of valid items to load + T oob_default) ///< [in] Default value to assign out-of-bound items +{ + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = oob_default; + } + + LoadDirectBlocked(linear_tid, block_itr, items, valid_items); +} + + +/** + * \brief Load a linear segment of items into a blocked arrangement across the thread block. + * + * \blocked + * + * The input offset (\p block_ptr + \p block_offset) must be quad-item aligned + * + * The following conditions will prevent vectorization and loading will fall back to cub::BLOCK_LOAD_DIRECT: + * - \p ITEMS_PER_THREAD is odd + * - The data type \p T is not a built-in primitive or CUDA vector type (e.g., \p short, \p int2, \p double, \p float2, etc.) + * + * \tparam T [inferred] The data type to load. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + */ +template < + typename T, + int ITEMS_PER_THREAD> +__device__ __forceinline__ void LoadDirectBlockedVectorized( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + T *block_ptr, ///< [in] Input pointer for loading from + T (&items)[ITEMS_PER_THREAD]) ///< [out] Data to load +{ + enum + { + // Maximum CUDA vector size is 4 elements + MAX_VEC_SIZE = CUB_MIN(4, ITEMS_PER_THREAD), + + // Vector size must be a power of two and an even divisor of the items per thread + VEC_SIZE = ((((MAX_VEC_SIZE - 1) & MAX_VEC_SIZE) == 0) && ((ITEMS_PER_THREAD % MAX_VEC_SIZE) == 0)) ? + MAX_VEC_SIZE : + 1, + + VECTORS_PER_THREAD = ITEMS_PER_THREAD / VEC_SIZE, + }; + + // Vector type + typedef typename CubVector::Type Vector; + + // Vector items + Vector vec_items[VECTORS_PER_THREAD]; + + // Aliased input ptr + Vector *ptr = reinterpret_cast(block_ptr + (linear_tid * VEC_SIZE * VECTORS_PER_THREAD)); + + // Load directly in thread-blocked order + #pragma unroll + for (int ITEM = 0; ITEM < VECTORS_PER_THREAD; ITEM++) + { + vec_items[ITEM] = ptr[ITEM]; + } + + // Copy + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = reinterpret_cast(vec_items)[ITEM]; + } +} + + + +//@} end member group +/******************************************************************//** + * \name Striped arrangement I/O (direct) + *********************************************************************/ +//@{ + + +/** + * \brief Load a linear segment of items into a striped arrangement across the thread block. + * + * \striped + * + * \tparam BLOCK_THREADS The thread block size in threads + * \tparam T [inferred] The data type to load. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam InputIterator [inferred] The random-access iterator type for input \iterator. + */ +template < + int BLOCK_THREADS, + typename T, + int ITEMS_PER_THREAD, + typename InputIterator> +__device__ __forceinline__ void LoadDirectStriped( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD]) ///< [out] Data to load +{ + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = block_itr[(ITEM * BLOCK_THREADS) + linear_tid]; + } +} + + +/** + * \brief Load a linear segment of items into a striped arrangement across the thread block, guarded by range + * + * \striped + * + * \tparam BLOCK_THREADS The thread block size in threads + * \tparam T [inferred] The data type to load. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam InputIterator [inferred] The random-access iterator type for input \iterator. + */ +template < + int BLOCK_THREADS, + typename T, + int ITEMS_PER_THREAD, + typename InputIterator> +__device__ __forceinline__ void LoadDirectStriped( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items) ///< [in] Number of valid items to load +{ + int bounds = valid_items - linear_tid; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + if (ITEM * BLOCK_THREADS < bounds) + { + items[ITEM] = block_itr[linear_tid + (ITEM * BLOCK_THREADS)]; + } + } +} + + +/** + * \brief Load a linear segment of items into a striped arrangement across the thread block, guarded by range, with a fall-back assignment of out-of-bound elements. + * + * \striped + * + * \tparam BLOCK_THREADS The thread block size in threads + * \tparam T [inferred] The data type to load. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam InputIterator [inferred] The random-access iterator type for input \iterator. + */ +template < + int BLOCK_THREADS, + typename T, + int ITEMS_PER_THREAD, + typename InputIterator> +__device__ __forceinline__ void LoadDirectStriped( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items, ///< [in] Number of valid items to load + T oob_default) ///< [in] Default value to assign out-of-bound items +{ + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = oob_default; + } + + LoadDirectStriped(linear_tid, block_itr, items, valid_items); +} + + + +//@} end member group +/******************************************************************//** + * \name Warp-striped arrangement I/O (direct) + *********************************************************************/ +//@{ + + +/** + * \brief Load a linear segment of items into a warp-striped arrangement across the thread block. + * + * \warpstriped + * + * \par Usage Considerations + * The number of threads in the thread block must be a multiple of the architecture's warp size. + * + * \tparam T [inferred] The data type to load. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam InputIterator [inferred] The random-access iterator type for input \iterator. + */ +template < + typename T, + int ITEMS_PER_THREAD, + typename InputIterator> +__device__ __forceinline__ void LoadDirectWarpStriped( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD]) ///< [out] Data to load +{ + int tid = linear_tid & (CUB_PTX_WARP_THREADS - 1); + int wid = linear_tid >> CUB_PTX_LOG_WARP_THREADS; + int warp_offset = wid * CUB_PTX_WARP_THREADS * ITEMS_PER_THREAD; + + // Load directly in warp-striped order + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = block_itr[warp_offset + tid + (ITEM * CUB_PTX_WARP_THREADS)]; + } +} + + +/** + * \brief Load a linear segment of items into a warp-striped arrangement across the thread block, guarded by range + * + * \warpstriped + * + * \par Usage Considerations + * The number of threads in the thread block must be a multiple of the architecture's warp size. + * + * \tparam T [inferred] The data type to load. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam InputIterator [inferred] The random-access iterator type for input \iterator. + */ +template < + typename T, + int ITEMS_PER_THREAD, + typename InputIterator> +__device__ __forceinline__ void LoadDirectWarpStriped( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items) ///< [in] Number of valid items to load +{ + int tid = linear_tid & (CUB_PTX_WARP_THREADS - 1); + int wid = linear_tid >> CUB_PTX_LOG_WARP_THREADS; + int warp_offset = wid * CUB_PTX_WARP_THREADS * ITEMS_PER_THREAD; + int bounds = valid_items - warp_offset - tid; + + // Load directly in warp-striped order + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + if ((ITEM * CUB_PTX_WARP_THREADS) < bounds) + { + items[ITEM] = block_itr[warp_offset + tid + (ITEM * CUB_PTX_WARP_THREADS)]; + } + } +} + + +/** + * \brief Load a linear segment of items into a warp-striped arrangement across the thread block, guarded by range, with a fall-back assignment of out-of-bound elements. + * + * \warpstriped + * + * \par Usage Considerations + * The number of threads in the thread block must be a multiple of the architecture's warp size. + * + * \tparam T [inferred] The data type to load. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam InputIterator [inferred] The random-access iterator type for input \iterator. + */ +template < + typename T, + int ITEMS_PER_THREAD, + typename InputIterator> +__device__ __forceinline__ void LoadDirectWarpStriped( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items, ///< [in] Number of valid items to load + T oob_default) ///< [in] Default value to assign out-of-bound items +{ + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = oob_default; + } + + LoadDirectWarpStriped(linear_tid, block_itr, items, valid_items); +} + + +//@} end member group + +/** @} */ // end group UtilIo + + + +//----------------------------------------------------------------------------- +// Generic BlockLoad abstraction +//----------------------------------------------------------------------------- + +/** + * \brief cub::BlockLoadAlgorithm enumerates alternative algorithms for cub::BlockLoad to read a linear segment of data from memory into a blocked arrangement across a CUDA thread block. + */ +enum BlockLoadAlgorithm +{ + /** + * \par Overview + * + * A [blocked arrangement](index.html#sec5sec3) of data is read + * directly from memory. The thread block reads items in a parallel "raking" fashion: threadi + * reads the ith segment of consecutive elements. + * + * \par Performance Considerations + * - The utilization of memory transactions (coalescing) decreases as the + * access stride between threads increases (i.e., the number items per thread). + */ + BLOCK_LOAD_DIRECT, + + /** + * \par Overview + * + * A [blocked arrangement](index.html#sec5sec3) of data is read directly + * from memory using CUDA's built-in vectorized loads as a coalescing optimization. + * The thread block reads items in a parallel "raking" fashion: threadi uses vector loads to + * read the ith segment of consecutive elements. + * + * For example, ld.global.v4.s32 instructions will be generated when \p T = \p int and \p ITEMS_PER_THREAD > 4. + * + * \par Performance Considerations + * - The utilization of memory transactions (coalescing) remains high until the the + * access stride between threads (i.e., the number items per thread) exceeds the + * maximum vector load width (typically 4 items or 64B, whichever is lower). + * - The following conditions will prevent vectorization and loading will fall back to cub::BLOCK_LOAD_DIRECT: + * - \p ITEMS_PER_THREAD is odd + * - The \p InputIterator is not a simple pointer type + * - The block input offset is not quadword-aligned + * - The data type \p T is not a built-in primitive or CUDA vector type (e.g., \p short, \p int2, \p double, \p float2, etc.) + */ + BLOCK_LOAD_VECTORIZE, + + /** + * \par Overview + * + * A [striped arrangement](index.html#sec5sec3) of data is read + * directly from memory and then is locally transposed into a + * [blocked arrangement](index.html#sec5sec3). The thread block + * reads items in a parallel "strip-mining" fashion: + * threadi reads items having stride \p BLOCK_THREADS + * between them. cub::BlockExchange is then used to locally reorder the items + * into a [blocked arrangement](index.html#sec5sec3). + * + * \par Performance Considerations + * - The utilization of memory transactions (coalescing) remains high regardless + * of items loaded per thread. + * - The local reordering incurs slightly longer latencies and throughput than the + * direct cub::BLOCK_LOAD_DIRECT and cub::BLOCK_LOAD_VECTORIZE alternatives. + */ + BLOCK_LOAD_TRANSPOSE, + + + /** + * \par Overview + * + * A [warp-striped arrangement](index.html#sec5sec3) of data is read + * directly from memory and then is locally transposed into a + * [blocked arrangement](index.html#sec5sec3). Each warp reads its own + * contiguous segment in a parallel "strip-mining" fashion: lanei + * reads items having stride \p WARP_THREADS between them. cub::BlockExchange + * is then used to locally reorder the items into a + * [blocked arrangement](index.html#sec5sec3). + * + * \par Usage Considerations + * - BLOCK_THREADS must be a multiple of WARP_THREADS + * + * \par Performance Considerations + * - The utilization of memory transactions (coalescing) remains high regardless + * of items loaded per thread. + * - The local reordering incurs slightly longer latencies and throughput than the + * direct cub::BLOCK_LOAD_DIRECT and cub::BLOCK_LOAD_VECTORIZE alternatives. + */ + BLOCK_LOAD_WARP_TRANSPOSE, +}; + + +/** + * \brief The BlockLoad class provides [collective](index.html#sec0) data movement methods for loading a linear segment of items from memory into a [blocked arrangement](index.html#sec5sec3) across a CUDA thread block. ![](block_load_logo.png) + * \ingroup BlockModule + * \ingroup UtilIo + * + * \tparam InputIterator The input iterator type \iterator. + * \tparam BLOCK_THREADS The thread block size in threads. + * \tparam ITEMS_PER_THREAD The number of consecutive items partitioned onto each thread. + * \tparam ALGORITHM [optional] cub::BlockLoadAlgorithm tuning policy. default: cub::BLOCK_LOAD_DIRECT. + * \tparam WARP_TIME_SLICING [optional] Whether or not only one warp's worth of shared memory should be allocated and time-sliced among block-warps during any load-related data transpositions (versus each warp having its own storage). (default: false) + * + * \par Overview + * - The BlockLoad class provides a single data movement abstraction that can be specialized + * to implement different cub::BlockLoadAlgorithm strategies. This facilitates different + * performance policies for different architectures, data types, granularity sizes, etc. + * - BlockLoad can be optionally specialized by different data movement strategies: + * -# cub::BLOCK_LOAD_DIRECT. A [blocked arrangement](index.html#sec5sec3) + * of data is read directly from memory. [More...](\ref cub::BlockLoadAlgorithm) + * -# cub::BLOCK_LOAD_VECTORIZE. A [blocked arrangement](index.html#sec5sec3) + * of data is read directly from memory using CUDA's built-in vectorized loads as a + * coalescing optimization. [More...](\ref cub::BlockLoadAlgorithm) + * -# cub::BLOCK_LOAD_TRANSPOSE. A [striped arrangement](index.html#sec5sec3) + * of data is read directly from memory and is then locally transposed into a + * [blocked arrangement](index.html#sec5sec3). [More...](\ref cub::BlockLoadAlgorithm) + * -# cub::BLOCK_LOAD_WARP_TRANSPOSE. A [warp-striped arrangement](index.html#sec5sec3) + * of data is read directly from memory and is then locally transposed into a + * [blocked arrangement](index.html#sec5sec3). [More...](\ref cub::BlockLoadAlgorithm) + * + * \par A Simple Example + * \blockcollective{BlockLoad} + * \par + * The code snippet below illustrates the loading of a linear + * segment of 512 integers into a "blocked" arrangement across 128 threads where each + * thread owns 4 consecutive items. The load is specialized for \p BLOCK_LOAD_WARP_TRANSPOSE, + * meaning memory references are efficiently coalesced using a warp-striped access + * pattern (after which items are locally reordered among threads). + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(int *d_data, ...) + * { + * // Specialize BlockLoad for 128 threads owning 4 integer items each + * typedef cub::BlockLoad BlockLoad; + * + * // Allocate shared memory for BlockLoad + * __shared__ typename BlockLoad::TempStorage temp_storage; + * + * // Load a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * BlockLoad(temp_storage).Load(d_data, thread_data); + * + * \endcode + * \par + * Suppose the input \p d_data is 0, 1, 2, 3, 4, 5, .... + * The set of \p thread_data across the block of threads in those threads will be + * { [0,1,2,3], [4,5,6,7], ..., [508,509,510,511] }. + * + */ +template < + typename InputIterator, + int BLOCK_THREADS, + int ITEMS_PER_THREAD, + BlockLoadAlgorithm ALGORITHM = BLOCK_LOAD_DIRECT, + bool WARP_TIME_SLICING = false> +class BlockLoad +{ +private: + + /****************************************************************************** + * Constants and typed definitions + ******************************************************************************/ + + // Data type of input iterator + typedef typename std::iterator_traits::value_type T; + + + /****************************************************************************** + * Algorithmic variants + ******************************************************************************/ + + /// Load helper + template + struct LoadInternal; + + + /** + * BLOCK_LOAD_DIRECT specialization of load helper + */ + template + struct LoadInternal + { + /// Shared memory storage layout type + typedef NullType TempStorage; + + /// Linear thread-id + int linear_tid; + + /// Constructor + __device__ __forceinline__ LoadInternal( + TempStorage &temp_storage, + int linear_tid) + : + linear_tid(linear_tid) + {} + + /// Load a linear segment of items from memory + __device__ __forceinline__ void Load( + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD]) ///< [out] Data to load + { + LoadDirectBlocked(linear_tid, block_itr, items); + } + + /// Load a linear segment of items from memory, guarded by range + __device__ __forceinline__ void Load( + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items) ///< [in] Number of valid items to load + { + LoadDirectBlocked(linear_tid, block_itr, items, valid_items); + } + + /// Load a linear segment of items from memory, guarded by range, with a fall-back assignment of out-of-bound elements + __device__ __forceinline__ void Load( + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items, ///< [in] Number of valid items to load + T oob_default) ///< [in] Default value to assign out-of-bound items + { + LoadDirectBlocked(linear_tid, block_itr, items, valid_items, oob_default); + } + + }; + + + /** + * BLOCK_LOAD_VECTORIZE specialization of load helper + */ + template + struct LoadInternal + { + /// Shared memory storage layout type + typedef NullType TempStorage; + + /// Linear thread-id + int linear_tid; + + /// Constructor + __device__ __forceinline__ LoadInternal( + TempStorage &temp_storage, + int linear_tid) + : + linear_tid(linear_tid) + {} + + /// Load a linear segment of items from memory, specialized for native pointer types (attempts vectorization) + __device__ __forceinline__ void Load( + T *block_ptr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD]) ///< [out] Data to load + { + LoadDirectBlockedVectorized(linear_tid, block_ptr, items); + } + + /// Load a linear segment of items from memory, specialized for opaque input iterators (skips vectorization) + template < + typename T, + typename _InputIterator> + __device__ __forceinline__ void Load( + _InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD]) ///< [out] Data to load + { + LoadDirectBlocked(linear_tid, block_itr, items); + } + + /// Load a linear segment of items from memory, guarded by range (skips vectorization) + __device__ __forceinline__ void Load( + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items) ///< [in] Number of valid items to load + { + LoadDirectBlocked(linear_tid, block_itr, items, valid_items); + } + + /// Load a linear segment of items from memory, guarded by range, with a fall-back assignment of out-of-bound elements (skips vectorization) + __device__ __forceinline__ void Load( + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items, ///< [in] Number of valid items to load + T oob_default) ///< [in] Default value to assign out-of-bound items + { + LoadDirectBlocked(linear_tid, block_itr, items, valid_items, oob_default); + } + + }; + + + /** + * BLOCK_LOAD_TRANSPOSE specialization of load helper + */ + template + struct LoadInternal + { + // BlockExchange utility type for keys + typedef BlockExchange BlockExchange; + + /// Shared memory storage layout type + typedef typename BlockExchange::TempStorage _TempStorage; + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + /// Thread reference to shared storage + _TempStorage &temp_storage; + + /// Linear thread-id + int linear_tid; + + /// Constructor + __device__ __forceinline__ LoadInternal( + TempStorage &temp_storage, + int linear_tid) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + /// Load a linear segment of items from memory + __device__ __forceinline__ void Load( + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD]) ///< [out] Data to load{ + { + LoadDirectStriped(linear_tid, block_itr, items); + BlockExchange(temp_storage, linear_tid).StripedToBlocked(items); + } + + /// Load a linear segment of items from memory, guarded by range + __device__ __forceinline__ void Load( + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items) ///< [in] Number of valid items to load + { + LoadDirectStriped(linear_tid, block_itr, items, valid_items); + BlockExchange(temp_storage, linear_tid).StripedToBlocked(items); + } + + /// Load a linear segment of items from memory, guarded by range, with a fall-back assignment of out-of-bound elements + __device__ __forceinline__ void Load( + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items, ///< [in] Number of valid items to load + T oob_default) ///< [in] Default value to assign out-of-bound items + { + LoadDirectStriped(linear_tid, block_itr, items, valid_items, oob_default); + BlockExchange(temp_storage, linear_tid).StripedToBlocked(items); + } + + }; + + + /** + * BLOCK_LOAD_WARP_TRANSPOSE specialization of load helper + */ + template + struct LoadInternal + { + enum + { + WARP_THREADS = CUB_PTX_WARP_THREADS + }; + + // Assert BLOCK_THREADS must be a multiple of WARP_THREADS + CUB_STATIC_ASSERT((BLOCK_THREADS % WARP_THREADS == 0), "BLOCK_THREADS must be a multiple of WARP_THREADS"); + + // BlockExchange utility type for keys + typedef BlockExchange BlockExchange; + + /// Shared memory storage layout type + typedef typename BlockExchange::TempStorage _TempStorage; + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + /// Thread reference to shared storage + _TempStorage &temp_storage; + + /// Linear thread-id + int linear_tid; + + /// Constructor + __device__ __forceinline__ LoadInternal( + TempStorage &temp_storage, + int linear_tid) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + /// Load a linear segment of items from memory + __device__ __forceinline__ void Load( + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD]) ///< [out] Data to load{ + { + LoadDirectWarpStriped(linear_tid, block_itr, items); + BlockExchange(temp_storage, linear_tid).WarpStripedToBlocked(items); + } + + /// Load a linear segment of items from memory, guarded by range + __device__ __forceinline__ void Load( + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items) ///< [in] Number of valid items to load + { + LoadDirectWarpStriped(linear_tid, block_itr, items, valid_items); + BlockExchange(temp_storage, linear_tid).WarpStripedToBlocked(items); + } + + + /// Load a linear segment of items from memory, guarded by range, with a fall-back assignment of out-of-bound elements + __device__ __forceinline__ void Load( + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items, ///< [in] Number of valid items to load + T oob_default) ///< [in] Default value to assign out-of-bound items + { + LoadDirectWarpStriped(linear_tid, block_itr, items, valid_items, oob_default); + BlockExchange(temp_storage, linear_tid).WarpStripedToBlocked(items); + } + }; + + + /****************************************************************************** + * Type definitions + ******************************************************************************/ + + /// Internal load implementation to use + typedef LoadInternal InternalLoad; + + + /// Shared memory storage layout type + typedef typename InternalLoad::TempStorage _TempStorage; + + + /****************************************************************************** + * Utility methods + ******************************************************************************/ + + /// Internal storage allocator + __device__ __forceinline__ _TempStorage& PrivateStorage() + { + __shared__ _TempStorage private_storage; + return private_storage; + } + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + /// Thread reference to shared storage + _TempStorage &temp_storage; + + /// Linear thread-id + int linear_tid; + +public: + + /// \smemstorage{BlockLoad} + struct TempStorage : Uninitialized<_TempStorage> {}; + + + /******************************************************************//** + * \name Collective constructors + *********************************************************************/ + //@{ + + /** + * \brief Collective constructor for 1D thread blocks using a private static allocation of shared memory as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockLoad() + : + temp_storage(PrivateStorage()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor for 1D thread blocks using the specified memory allocation as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockLoad( + TempStorage &temp_storage) ///< [in] Reference to memory allocation having layout type TempStorage + : + temp_storage(temp_storage.Alias()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor using a private static allocation of shared memory as temporary storage. Each thread is identified using the supplied linear thread identifier + */ + __device__ __forceinline__ BlockLoad( + int linear_tid) ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(PrivateStorage()), + linear_tid(linear_tid) + {} + + + /** + * \brief Collective constructor using the specified memory allocation as temporary storage. Each thread is identified using the supplied linear thread identifier. + */ + __device__ __forceinline__ BlockLoad( + TempStorage &temp_storage, ///< [in] Reference to memory allocation having layout type TempStorage + int linear_tid) ///< [in] [optional] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + + + //@} end member group + /******************************************************************//** + * \name Data movement + *********************************************************************/ + //@{ + + + /** + * \brief Load a linear segment of items from memory. + * + * \par + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates the loading of a linear + * segment of 512 integers into a "blocked" arrangement across 128 threads where each + * thread owns 4 consecutive items. The load is specialized for \p BLOCK_LOAD_WARP_TRANSPOSE, + * meaning memory references are efficiently coalesced using a warp-striped access + * pattern (after which items are locally reordered among threads). + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(int *d_data, ...) + * { + * // Specialize BlockLoad for 128 threads owning 4 integer items each + * typedef cub::BlockLoad BlockLoad; + * + * // Allocate shared memory for BlockLoad + * __shared__ typename BlockLoad::TempStorage temp_storage; + * + * // Load a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * BlockLoad(temp_storage).Load(d_data, thread_data); + * + * \endcode + * \par + * Suppose the input \p d_data is 0, 1, 2, 3, 4, 5, .... + * The set of \p thread_data across the block of threads in those threads will be + * { [0,1,2,3], [4,5,6,7], ..., [508,509,510,511] }. + * + */ + __device__ __forceinline__ void Load( + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD]) ///< [out] Data to load + { + InternalLoad(temp_storage, linear_tid).Load(block_itr, items); + } + + + /** + * \brief Load a linear segment of items from memory, guarded by range. + * + * \par + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates the guarded loading of a linear + * segment of 512 integers into a "blocked" arrangement across 128 threads where each + * thread owns 4 consecutive items. The load is specialized for \p BLOCK_LOAD_WARP_TRANSPOSE, + * meaning memory references are efficiently coalesced using a warp-striped access + * pattern (after which items are locally reordered among threads). + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(int *d_data, int valid_items, ...) + * { + * // Specialize BlockLoad for 128 threads owning 4 integer items each + * typedef cub::BlockLoad BlockLoad; + * + * // Allocate shared memory for BlockLoad + * __shared__ typename BlockLoad::TempStorage temp_storage; + * + * // Load a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * BlockLoad(temp_storage).Load(d_data, thread_data, valid_items); + * + * \endcode + * \par + * Suppose the input \p d_data is 0, 1, 2, 3, 4, 5, 6... and \p valid_items is \p 5. + * The set of \p thread_data across the block of threads in those threads will be + * { [0,1,2,3], [4,?,?,?], ..., [?,?,?,?] }, with only the first two threads + * being unmasked to load portions of valid data (and other items remaining unassigned). + * + */ + __device__ __forceinline__ void Load( + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items) ///< [in] Number of valid items to load + { + InternalLoad(temp_storage, linear_tid).Load(block_itr, items, valid_items); + } + + + /** + * \brief Load a linear segment of items from memory, guarded by range, with a fall-back assignment of out-of-bound elements + * + * \par + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates the guarded loading of a linear + * segment of 512 integers into a "blocked" arrangement across 128 threads where each + * thread owns 4 consecutive items. The load is specialized for \p BLOCK_LOAD_WARP_TRANSPOSE, + * meaning memory references are efficiently coalesced using a warp-striped access + * pattern (after which items are locally reordered among threads). + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(int *d_data, int valid_items, ...) + * { + * // Specialize BlockLoad for 128 threads owning 4 integer items each + * typedef cub::BlockLoad BlockLoad; + * + * // Allocate shared memory for BlockLoad + * __shared__ typename BlockLoad::TempStorage temp_storage; + * + * // Load a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * BlockLoad(temp_storage).Load(d_data, thread_data, valid_items, -1); + * + * \endcode + * \par + * Suppose the input \p d_data is 0, 1, 2, 3, 4, 5, 6..., + * \p valid_items is \p 5, and the out-of-bounds default is \p -1. + * The set of \p thread_data across the block of threads in those threads will be + * { [0,1,2,3], [4,-1,-1,-1], ..., [-1,-1,-1,-1] }, with only the first two threads + * being unmasked to load portions of valid data (and other items are assigned \p -1) + * + */ + __device__ __forceinline__ void Load( + InputIterator block_itr, ///< [in] The thread block's base input iterator for loading from + T (&items)[ITEMS_PER_THREAD], ///< [out] Data to load + int valid_items, ///< [in] Number of valid items to load + T oob_default) ///< [in] Default value to assign out-of-bound items + { + InternalLoad(temp_storage, linear_tid).Load(block_itr, items, valid_items, oob_default); + } + + + //@} end member group + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_radix_rank.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_radix_rank.cuh new file mode 100644 index 0000000000000000000000000000000000000000..126c2d27399c8b82e4e647fdac2f480094c05423 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_radix_rank.cuh @@ -0,0 +1,490 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockRadixRank provides operations for ranking unsigned integer types within a CUDA threadblock + */ + +#pragma once + +#include "../util_arch.cuh" +#include "../util_type.cuh" +#include "../thread/thread_reduce.cuh" +#include "../thread/thread_scan.cuh" +#include "../block/block_scan.cuh" +#include "../util_namespace.cuh" + + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/** + * \brief BlockRadixRank provides operations for ranking unsigned integer types within a CUDA threadblock. + * \ingroup BlockModule + * + * \par Overview + * Blah... + * + * \tparam BLOCK_THREADS The thread block size in threads + * \tparam RADIX_BITS The number of radix bits per digit place + * \tparam DESCENDING Whether or not the sorted-order is high-to-low + * \tparam MEMOIZE_OUTER_SCAN [optional] Whether or not to buffer outer raking scan partials to incur fewer shared memory reads at the expense of higher register pressure (default: true for architectures SM35 and newer, false otherwise). See BlockScanAlgorithm::BLOCK_SCAN_RAKING_MEMOIZE for more details. + * \tparam INNER_SCAN_ALGORITHM [optional] The cub::BlockScanAlgorithm algorithm to use (default: cub::BLOCK_SCAN_WARP_SCANS) + * \tparam SMEM_CONFIG [optional] Shared memory bank mode (default: \p cudaSharedMemBankSizeFourByte) + * + * \par Usage Considerations + * - Keys must be in a form suitable for radix ranking (i.e., unsigned bits). + * - Assumes a [blocked arrangement](index.html#sec5sec3) of elements across threads + * - \smemreuse{BlockRadixRank::TempStorage} + * + * \par Performance Considerations + * + * \par Algorithm + * These parallel radix ranking variants have O(n) work complexity and are implemented in XXX phases: + * -# blah + * -# blah + * + * \par Examples + * \par + * - Example 1: Simple radix rank of 32-bit integer keys + * \code + * #include + * + * template + * __global__ void ExampleKernel(...) + * { + * + * \endcode + */ +template < + int BLOCK_THREADS, + int RADIX_BITS, + bool DESCENDING, + bool MEMOIZE_OUTER_SCAN = (CUB_PTX_VERSION >= 350) ? true : false, + BlockScanAlgorithm INNER_SCAN_ALGORITHM = BLOCK_SCAN_WARP_SCANS, + cudaSharedMemConfig SMEM_CONFIG = cudaSharedMemBankSizeFourByte> +class BlockRadixRank +{ +private: + + /****************************************************************************** + * Type definitions and constants + ******************************************************************************/ + + // Integer type for digit counters (to be packed into words of type PackedCounters) + typedef unsigned short DigitCounter; + + // Integer type for packing DigitCounters into columns of shared memory banks + typedef typename If<(SMEM_CONFIG == cudaSharedMemBankSizeEightByte), + unsigned long long, + unsigned int>::Type PackedCounter; + + enum + { + RADIX_DIGITS = 1 << RADIX_BITS, + + LOG_WARP_THREADS = CUB_PTX_LOG_WARP_THREADS, + WARP_THREADS = 1 << LOG_WARP_THREADS, + WARPS = (BLOCK_THREADS + WARP_THREADS - 1) / WARP_THREADS, + + BYTES_PER_COUNTER = sizeof(DigitCounter), + LOG_BYTES_PER_COUNTER = Log2::VALUE, + + PACKING_RATIO = sizeof(PackedCounter) / sizeof(DigitCounter), + LOG_PACKING_RATIO = Log2::VALUE, + + LOG_COUNTER_LANES = CUB_MAX((RADIX_BITS - LOG_PACKING_RATIO), 0), // Always at least one lane + COUNTER_LANES = 1 << LOG_COUNTER_LANES, + + // The number of packed counters per thread (plus one for padding) + RAKING_SEGMENT = COUNTER_LANES + 1, + + LOG_SMEM_BANKS = CUB_PTX_LOG_SMEM_BANKS, + SMEM_BANKS = 1 << LOG_SMEM_BANKS, + }; + + + /// BlockScan type + typedef BlockScan BlockScan; + + + /// Shared memory storage layout type for BlockRadixRank + struct _TempStorage + { + // Storage for scanning local ranks + typename BlockScan::TempStorage block_scan; + + union + { + DigitCounter digit_counters[COUNTER_LANES + 1][BLOCK_THREADS][PACKING_RATIO]; + PackedCounter raking_grid[BLOCK_THREADS][RAKING_SEGMENT]; + }; + }; + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + /// Shared storage reference + _TempStorage &temp_storage; + + /// Linear thread-id + int linear_tid; + + /// Copy of raking segment, promoted to registers + PackedCounter cached_segment[RAKING_SEGMENT]; + + + /****************************************************************************** + * Templated iteration + ******************************************************************************/ + + // General template iteration + template + struct Iterate + { + /** + * Decode keys. Decodes the radix digit from the current digit place + * and increments the thread's corresponding counter in shared + * memory for that digit. + * + * Saves both (1) the prior value of that counter (the key's + * thread-local exclusive prefix sum for that digit), and (2) the shared + * memory offset of the counter (for later use). + */ + template + static __device__ __forceinline__ void DecodeKeys( + BlockRadixRank &cta, // BlockRadixRank instance + UnsignedBits (&keys)[KEYS_PER_THREAD], // Key to decode + DigitCounter (&thread_prefixes)[KEYS_PER_THREAD], // Prefix counter value (out parameter) + DigitCounter* (&digit_counters)[KEYS_PER_THREAD], // Counter smem offset (out parameter) + int current_bit) // The least-significant bit position of the current digit to extract + { + // Get sub-counter + UnsignedBits sub_counter = BFE(keys[COUNT], current_bit + LOG_COUNTER_LANES, LOG_PACKING_RATIO); + + // Get counter lane + UnsignedBits counter_lane = BFE(keys[COUNT], current_bit, LOG_COUNTER_LANES); + + if (DESCENDING) + { + sub_counter = PACKING_RATIO - 1 - sub_counter; + counter_lane = COUNTER_LANES - 1 - counter_lane; + } + + // Pointer to smem digit counter + digit_counters[COUNT] = &cta.temp_storage.digit_counters[counter_lane][cta.linear_tid][sub_counter]; + + // Load thread-exclusive prefix + thread_prefixes[COUNT] = *digit_counters[COUNT]; + + // Store inclusive prefix + *digit_counters[COUNT] = thread_prefixes[COUNT] + 1; + + // Iterate next key + Iterate::DecodeKeys(cta, keys, thread_prefixes, digit_counters, current_bit); + } + + + // Termination + template + static __device__ __forceinline__ void UpdateRanks( + int (&ranks)[KEYS_PER_THREAD], // Local ranks (out parameter) + DigitCounter (&thread_prefixes)[KEYS_PER_THREAD], // Prefix counter value + DigitCounter* (&digit_counters)[KEYS_PER_THREAD]) // Counter smem offset + { + // Add in threadblock exclusive prefix + ranks[COUNT] = thread_prefixes[COUNT] + *digit_counters[COUNT]; + + // Iterate next key + Iterate::UpdateRanks(ranks, thread_prefixes, digit_counters); + } + }; + + + // Termination + template + struct Iterate + { + // DecodeKeys + template + static __device__ __forceinline__ void DecodeKeys( + BlockRadixRank &cta, + UnsignedBits (&keys)[KEYS_PER_THREAD], + DigitCounter (&thread_prefixes)[KEYS_PER_THREAD], + DigitCounter* (&digit_counters)[KEYS_PER_THREAD], + int current_bit) {} + + + // UpdateRanks + template + static __device__ __forceinline__ void UpdateRanks( + int (&ranks)[KEYS_PER_THREAD], + DigitCounter (&thread_prefixes)[KEYS_PER_THREAD], + DigitCounter *(&digit_counters)[KEYS_PER_THREAD]) {} + }; + + + /****************************************************************************** + * Utility methods + ******************************************************************************/ + + /** + * Internal storage allocator + */ + __device__ __forceinline__ _TempStorage& PrivateStorage() + { + __shared__ _TempStorage private_storage; + return private_storage; + } + + + /** + * Performs upsweep raking reduction, returning the aggregate + */ + __device__ __forceinline__ PackedCounter Upsweep() + { + PackedCounter *smem_raking_ptr = temp_storage.raking_grid[linear_tid]; + PackedCounter *raking_ptr; + + if (MEMOIZE_OUTER_SCAN) + { + // Copy data into registers + #pragma unroll + for (int i = 0; i < RAKING_SEGMENT; i++) + { + cached_segment[i] = smem_raking_ptr[i]; + } + raking_ptr = cached_segment; + } + else + { + raking_ptr = smem_raking_ptr; + } + + return ThreadReduce(raking_ptr, Sum()); + } + + + /// Performs exclusive downsweep raking scan + __device__ __forceinline__ void ExclusiveDownsweep( + PackedCounter raking_partial) + { + PackedCounter *smem_raking_ptr = temp_storage.raking_grid[linear_tid]; + + PackedCounter *raking_ptr = (MEMOIZE_OUTER_SCAN) ? + cached_segment : + smem_raking_ptr; + + // Exclusive raking downsweep scan + ThreadScanExclusive(raking_ptr, raking_ptr, Sum(), raking_partial); + + if (MEMOIZE_OUTER_SCAN) + { + // Copy data back to smem + #pragma unroll + for (int i = 0; i < RAKING_SEGMENT; i++) + { + smem_raking_ptr[i] = cached_segment[i]; + } + } + } + + + /** + * Reset shared memory digit counters + */ + __device__ __forceinline__ void ResetCounters() + { + // Reset shared memory digit counters + #pragma unroll + for (int LANE = 0; LANE < COUNTER_LANES + 1; LANE++) + { + *((PackedCounter*) temp_storage.digit_counters[LANE][linear_tid]) = 0; + } + } + + + /** + * Scan shared memory digit counters. + */ + __device__ __forceinline__ void ScanCounters() + { + // Upsweep scan + PackedCounter raking_partial = Upsweep(); + + // Compute exclusive sum + PackedCounter exclusive_partial; + PackedCounter packed_aggregate; + BlockScan(temp_storage.block_scan, linear_tid).ExclusiveSum(raking_partial, exclusive_partial, packed_aggregate); + + // Propagate totals in packed fields + #pragma unroll + for (int PACKED = 1; PACKED < PACKING_RATIO; PACKED++) + { + exclusive_partial += packed_aggregate << (sizeof(DigitCounter) * 8 * PACKED); + } + + // Downsweep scan with exclusive partial + ExclusiveDownsweep(exclusive_partial); + } + +public: + + /// \smemstorage{BlockScan} + struct TempStorage : Uninitialized<_TempStorage> {}; + + + /******************************************************************//** + * \name Collective constructors + *********************************************************************/ + //@{ + + /** + * \brief Collective constructor for 1D thread blocks using a private static allocation of shared memory as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockRadixRank() + : + temp_storage(PrivateStorage()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor for 1D thread blocks using the specified memory allocation as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockRadixRank( + TempStorage &temp_storage) ///< [in] Reference to memory allocation having layout type TempStorage + : + temp_storage(temp_storage.Alias()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor using a private static allocation of shared memory as temporary storage. Each thread is identified using the supplied linear thread identifier + */ + __device__ __forceinline__ BlockRadixRank( + int linear_tid) ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(PrivateStorage()), + linear_tid(linear_tid) + {} + + + /** + * \brief Collective constructor using the specified memory allocation as temporary storage. Each thread is identified using the supplied linear thread identifier. + */ + __device__ __forceinline__ BlockRadixRank( + TempStorage &temp_storage, ///< [in] Reference to memory allocation having layout type TempStorage + int linear_tid) ///< [in] [optional] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + + + //@} end member group + /******************************************************************//** + * \name Raking + *********************************************************************/ + //@{ + + /** + * \brief Rank keys. + */ + template < + typename UnsignedBits, + int KEYS_PER_THREAD> + __device__ __forceinline__ void RankKeys( + UnsignedBits (&keys)[KEYS_PER_THREAD], ///< [in] Keys for this tile + int (&ranks)[KEYS_PER_THREAD], ///< [out] For each key, the local rank within the tile + int current_bit) ///< [in] The least-significant bit position of the current digit to extract + { + DigitCounter thread_prefixes[KEYS_PER_THREAD]; // For each key, the count of previous keys in this tile having the same digit + DigitCounter* digit_counters[KEYS_PER_THREAD]; // For each key, the byte-offset of its corresponding digit counter in smem + + // Reset shared memory digit counters + ResetCounters(); + + // Decode keys and update digit counters + Iterate<0, KEYS_PER_THREAD>::DecodeKeys(*this, keys, thread_prefixes, digit_counters, current_bit); + + __syncthreads(); + + // Scan shared memory counters + ScanCounters(); + + __syncthreads(); + + // Extract the local ranks of each key + Iterate<0, KEYS_PER_THREAD>::UpdateRanks(ranks, thread_prefixes, digit_counters); + } + + + /** + * \brief Rank keys. For the lower \p RADIX_DIGITS threads, digit counts for each digit are provided for the corresponding thread. + */ + template < + typename UnsignedBits, + int KEYS_PER_THREAD> + __device__ __forceinline__ void RankKeys( + UnsignedBits (&keys)[KEYS_PER_THREAD], ///< [in] Keys for this tile + int (&ranks)[KEYS_PER_THREAD], ///< [out] For each key, the local rank within the tile (out parameter) + int current_bit, ///< [in] The least-significant bit position of the current digit to extract + int &inclusive_digit_prefix) ///< [out] The incluisve prefix sum for the digit threadIdx.x + { + // Rank keys + RankKeys(keys, ranks, current_bit); + + // Get the inclusive and exclusive digit totals corresponding to the calling thread. + if ((BLOCK_THREADS == RADIX_DIGITS) || (linear_tid < RADIX_DIGITS)) + { + int bin_idx = (DESCENDING) ? + RADIX_DIGITS - linear_tid - 1 : + linear_tid; + + // Obtain ex/inclusive digit counts. (Unfortunately these all reside in the + // first counter column, resulting in unavoidable bank conflicts.) + int counter_lane = (bin_idx & (COUNTER_LANES - 1)); + int sub_counter = bin_idx >> (LOG_COUNTER_LANES); + inclusive_digit_prefix = temp_storage.digit_counters[counter_lane + 1][0][sub_counter]; + } + } +}; + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_radix_sort.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_radix_sort.cuh new file mode 100644 index 0000000000000000000000000000000000000000..b48591b5f031e9e3f39a81e9d752a2d6077d7137 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_radix_sort.cuh @@ -0,0 +1,861 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * The cub::BlockRadixSort class provides [collective](index.html#sec0) methods for radix sorting of items partitioned across a CUDA thread block. + */ + + +#pragma once + +#include "../util_namespace.cuh" +#include "../util_arch.cuh" +#include "../util_type.cuh" +#include "block_exchange.cuh" +#include "block_radix_rank.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/** + * \brief The BlockRadixSort class provides [collective](index.html#sec0) methods for sorting items partitioned across a CUDA thread block using a radix sorting method. ![](sorting_logo.png) + * \ingroup BlockModule + * + * \tparam Key Key type + * \tparam BLOCK_THREADS The thread block size in threads + * \tparam ITEMS_PER_THREAD The number of items per thread + * \tparam Value [optional] Value type (default: cub::NullType, which indicates a keys-only sort) + * \tparam RADIX_BITS [optional] The number of radix bits per digit place (default: 4 bits) + * \tparam MEMOIZE_OUTER_SCAN [optional] Whether or not to buffer outer raking scan partials to incur fewer shared memory reads at the expense of higher register pressure (default: true for architectures SM35 and newer, false otherwise). + * \tparam INNER_SCAN_ALGORITHM [optional] The cub::BlockScanAlgorithm algorithm to use (default: cub::BLOCK_SCAN_WARP_SCANS) + * \tparam SMEM_CONFIG [optional] Shared memory bank mode (default: \p cudaSharedMemBankSizeFourByte) + * + * \par Overview + * - The [radix sorting method](http://en.wikipedia.org/wiki/Radix_sort) arranges + * items into ascending order. It relies upon a positional representation for + * keys, i.e., each key is comprised of an ordered sequence of symbols (e.g., digits, + * characters, etc.) specified from least-significant to most-significant. For a + * given input sequence of keys and a set of rules specifying a total ordering + * of the symbolic alphabet, the radix sorting method produces a lexicographic + * ordering of those keys. + * - BlockRadixSort can sort all of the built-in C++ numeric primitive types, e.g.: + * unsigned char, \p int, \p double, etc. Within each key, the implementation treats fixed-length + * bit-sequences of \p RADIX_BITS as radix digit places. Although the direct radix sorting + * method can only be applied to unsigned integral types, BlockRadixSort + * is able to sort signed and floating-point types via simple bit-wise transformations + * that ensure lexicographic key ordering. + * + * \par Performance Considerations + * - \granularity + * + * \par A Simple Example + * \blockcollective{BlockRadixSort} + * \par + * The code snippet below illustrates a sort of 512 integer keys that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockRadixSort for 128 threads owning 4 integer items each + * typedef cub::BlockRadixSort BlockRadixSort; + * + * // Allocate shared memory for BlockRadixSort + * __shared__ typename BlockRadixSort::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_keys[4]; + * ... + * + * // Collectively sort the keys + * BlockRadixSort(temp_storage).Sort(thread_keys); + * + * ... + * \endcode + * \par + * Suppose the set of input \p thread_keys across the block of threads is + * { [0,511,1,510], [2,509,3,508], [4,507,5,506], ..., [254,257,255,256] }. The + * corresponding output \p thread_keys in those threads will be + * { [0,1,2,3], [4,5,6,7], [8,9,10,11], ..., [508,509,510,511] }. + * + */ +template < + typename Key, + int BLOCK_THREADS, + int ITEMS_PER_THREAD, + typename Value = NullType, + int RADIX_BITS = 4, + bool MEMOIZE_OUTER_SCAN = (CUB_PTX_VERSION >= 350) ? true : false, + BlockScanAlgorithm INNER_SCAN_ALGORITHM = BLOCK_SCAN_WARP_SCANS, + cudaSharedMemConfig SMEM_CONFIG = cudaSharedMemBankSizeFourByte> +class BlockRadixSort +{ +private: + + /****************************************************************************** + * Constants and type definitions + ******************************************************************************/ + + enum + { + KEYS_ONLY = Equals::VALUE, + }; + + // Key traits and unsigned bits type + typedef NumericTraits KeyTraits; + typedef typename KeyTraits::UnsignedBits UnsignedBits; + + /// Ascending BlockRadixRank utility type + typedef BlockRadixRank< + BLOCK_THREADS, + RADIX_BITS, + false, + MEMOIZE_OUTER_SCAN, + INNER_SCAN_ALGORITHM, + SMEM_CONFIG> + AscendingBlockRadixRank; + + /// Descending BlockRadixRank utility type + typedef BlockRadixRank< + BLOCK_THREADS, + RADIX_BITS, + true, + MEMOIZE_OUTER_SCAN, + INNER_SCAN_ALGORITHM, + SMEM_CONFIG> + DescendingBlockRadixRank; + + /// BlockExchange utility type for keys + typedef BlockExchange BlockExchangeKeys; + + /// BlockExchange utility type for values + typedef BlockExchange BlockExchangeValues; + + /// Shared memory storage layout type + struct _TempStorage + { + union + { + typename AscendingBlockRadixRank::TempStorage asending_ranking_storage; + typename DescendingBlockRadixRank::TempStorage descending_ranking_storage; + typename BlockExchangeKeys::TempStorage exchange_keys; + typename BlockExchangeValues::TempStorage exchange_values; + }; + }; + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + /// Shared storage reference + _TempStorage &temp_storage; + + /// Linear thread-id + int linear_tid; + + /****************************************************************************** + * Utility methods + ******************************************************************************/ + + /// Internal storage allocator + __device__ __forceinline__ _TempStorage& PrivateStorage() + { + __shared__ _TempStorage private_storage; + return private_storage; + } + + /// Rank keys (specialized for ascending sort) + __device__ __forceinline__ void RankKeys( + UnsignedBits (&unsigned_keys)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + int begin_bit, + Int2Type is_descending) + { + AscendingBlockRadixRank(temp_storage.asending_ranking_storage, linear_tid).RankKeys( + unsigned_keys, + ranks, + begin_bit); + } + + /// Rank keys (specialized for descending sort) + __device__ __forceinline__ void RankKeys( + UnsignedBits (&unsigned_keys)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + int begin_bit, + Int2Type is_descending) + { + DescendingBlockRadixRank(temp_storage.descending_ranking_storage, linear_tid).RankKeys( + unsigned_keys, + ranks, + begin_bit); + } + + /// ExchangeValues (specialized for key-value sort, to-blocked arrangement) + __device__ __forceinline__ void ExchangeValues( + Value (&values)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Int2Type is_keys_only, + Int2Type is_blocked) + { + __syncthreads(); + + // Exchange values through shared memory in blocked arrangement + BlockExchangeValues(temp_storage.exchange_values, linear_tid).ScatterToBlocked(values, ranks); + } + + /// ExchangeValues (specialized for key-value sort, to-striped arrangement) + __device__ __forceinline__ void ExchangeValues( + Value (&values)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Int2Type is_keys_only, + Int2Type is_blocked) + { + __syncthreads(); + + // Exchange values through shared memory in blocked arrangement + BlockExchangeValues(temp_storage.exchange_values, linear_tid).ScatterToStriped(values, ranks); + } + + /// ExchangeValues (specialized for keys-only sort) + template + __device__ __forceinline__ void ExchangeValues( + Value (&values)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Int2Type is_keys_only, + Int2Type is_blocked) + {} + + /// Sort blocked arrangement + template + __device__ __forceinline__ void SortBlocked( + Key (&keys)[ITEMS_PER_THREAD], ///< Keys to sort + Value (&values)[ITEMS_PER_THREAD], ///< Values to sort + int begin_bit, ///< The beginning (least-significant) bit index needed for key comparison + int end_bit, ///< The past-the-end (most-significant) bit index needed for key comparison + Int2Type is_descending, ///< Tag whether is a descending-order sort + Int2Type is_keys_only) ///< Tag whether is keys-only sort + { + UnsignedBits (&unsigned_keys)[ITEMS_PER_THREAD] = + reinterpret_cast(keys); + + // Twiddle bits if necessary + #pragma unroll + for (int KEY = 0; KEY < ITEMS_PER_THREAD; KEY++) + { + unsigned_keys[KEY] = KeyTraits::TwiddleIn(unsigned_keys[KEY]); + } + + // Radix sorting passes + while (true) + { + // Rank the blocked keys + int ranks[ITEMS_PER_THREAD]; + RankKeys(unsigned_keys, ranks, begin_bit, is_descending); + begin_bit += RADIX_BITS; + + __syncthreads(); + + // Exchange keys through shared memory in blocked arrangement + BlockExchangeKeys(temp_storage.exchange_keys, linear_tid).ScatterToBlocked(keys, ranks); + + // Exchange values through shared memory in blocked arrangement + ExchangeValues(values, ranks, is_keys_only, Int2Type()); + + // Quit if done + if (begin_bit >= end_bit) break; + + __syncthreads(); + } + + // Untwiddle bits if necessary + #pragma unroll + for (int KEY = 0; KEY < ITEMS_PER_THREAD; KEY++) + { + unsigned_keys[KEY] = KeyTraits::TwiddleOut(unsigned_keys[KEY]); + } + } + + /// Sort blocked -> striped arrangement + template + __device__ __forceinline__ void SortBlockedToStriped( + Key (&keys)[ITEMS_PER_THREAD], ///< Keys to sort + Value (&values)[ITEMS_PER_THREAD], ///< Values to sort + int begin_bit, ///< The beginning (least-significant) bit index needed for key comparison + int end_bit, ///< The past-the-end (most-significant) bit index needed for key comparison + Int2Type is_descending, ///< Tag whether is a descending-order sort + Int2Type is_keys_only) ///< Tag whether is keys-only sort + { + UnsignedBits (&unsigned_keys)[ITEMS_PER_THREAD] = + reinterpret_cast(keys); + + // Twiddle bits if necessary + #pragma unroll + for (int KEY = 0; KEY < ITEMS_PER_THREAD; KEY++) + { + unsigned_keys[KEY] = KeyTraits::TwiddleIn(unsigned_keys[KEY]); + } + + // Radix sorting passes + while (true) + { + // Rank the blocked keys + int ranks[ITEMS_PER_THREAD]; + RankKeys(unsigned_keys, ranks, begin_bit, is_descending); + begin_bit += RADIX_BITS; + + __syncthreads(); + + // Check if this is the last pass + if (begin_bit >= end_bit) + { + // Last pass exchanges keys through shared memory in striped arrangement + BlockExchangeKeys(temp_storage.exchange_keys, linear_tid).ScatterToStriped(keys, ranks); + + // Last pass exchanges through shared memory in striped arrangement + ExchangeValues(values, ranks, is_keys_only, Int2Type()); + + // Quit + break; + } + + // Exchange keys through shared memory in blocked arrangement + BlockExchangeKeys(temp_storage.exchange_keys, linear_tid).ScatterToBlocked(keys, ranks); + + // Exchange values through shared memory in blocked arrangement + ExchangeValues(values, ranks, is_keys_only, Int2Type()); + + __syncthreads(); + } + + // Untwiddle bits if necessary + #pragma unroll + for (int KEY = 0; KEY < ITEMS_PER_THREAD; KEY++) + { + unsigned_keys[KEY] = KeyTraits::TwiddleOut(unsigned_keys[KEY]); + } + } + + + +public: + + /// \smemstorage{BlockScan} + struct TempStorage : Uninitialized<_TempStorage> {}; + + + /******************************************************************//** + * \name Collective constructors + *********************************************************************/ + //@{ + + /** + * \brief Collective constructor for 1D thread blocks using a private static allocation of shared memory as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockRadixSort() + : + temp_storage(PrivateStorage()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor for 1D thread blocks using the specified memory allocation as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockRadixSort( + TempStorage &temp_storage) ///< [in] Reference to memory allocation having layout type TempStorage + : + temp_storage(temp_storage.Alias()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor using a private static allocation of shared memory as temporary storage. Each thread is identified using the supplied linear thread identifier + */ + __device__ __forceinline__ BlockRadixSort( + int linear_tid) ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(PrivateStorage()), + linear_tid(linear_tid) + {} + + + /** + * \brief Collective constructor using the specified memory allocation as temporary storage. Each thread is identified using the supplied linear thread identifier. + */ + __device__ __forceinline__ BlockRadixSort( + TempStorage &temp_storage, ///< [in] Reference to memory allocation having layout type TempStorage + int linear_tid) ///< [in] [optional] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + + + //@} end member group + /******************************************************************//** + * \name Sorting (blocked arrangements) + *********************************************************************/ + //@{ + + /** + * \brief Performs an ascending block-wide radix sort over a [blocked arrangement](index.html#sec5sec3) of keys. + * + * \par + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a sort of 512 integer keys that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive keys. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockRadixSort for 128 threads owning 4 integer keys each + * typedef cub::BlockRadixSort BlockRadixSort; + * + * // Allocate shared memory for BlockRadixSort + * __shared__ typename BlockRadixSort::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_keys[4]; + * ... + * + * // Collectively sort the keys + * BlockRadixSort(temp_storage).Sort(thread_keys); + * + * \endcode + * \par + * Suppose the set of input \p thread_keys across the block of threads is + * { [0,511,1,510], [2,509,3,508], [4,507,5,506], ..., [254,257,255,256] }. + * The corresponding output \p thread_keys in those threads will be + * { [0,1,2,3], [4,5,6,7], [8,9,10,11], ..., [508,509,510,511] }. + */ + __device__ __forceinline__ void Sort( + Key (&keys)[ITEMS_PER_THREAD], ///< [in-out] Keys to sort + int begin_bit = 0, ///< [in] [optional] The beginning (least-significant) bit index needed for key comparison + int end_bit = sizeof(Key) * 8) ///< [in] [optional] The past-the-end (most-significant) bit index needed for key comparison + { + NullType values[ITEMS_PER_THREAD]; + + SortBlocked(keys, values, begin_bit, end_bit, Int2Type(), Int2Type()); + } + + + /** + * \brief Performs an ascending block-wide radix sort across a [blocked arrangement](index.html#sec5sec3) of keys and values. + * + * \par + * - BlockRadixSort can only accommodate one associated tile of values. To "truck along" + * more than one tile of values, simply perform a key-value sort of the keys paired + * with a temporary value array that enumerates the key indices. The reordered indices + * can then be used as a gather-vector for exchanging other associated tile data through + * shared memory. + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a sort of 512 integer keys and values that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive pairs. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockRadixSort for 128 threads owning 4 integer keys and values each + * typedef cub::BlockRadixSort BlockRadixSort; + * + * // Allocate shared memory for BlockRadixSort + * __shared__ typename BlockRadixSort::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_keys[4]; + * int thread_values[4]; + * ... + * + * // Collectively sort the keys and values among block threads + * BlockRadixSort(temp_storage).Sort(thread_keys, thread_values); + * + * \endcode + * \par + * Suppose the set of input \p thread_keys across the block of threads is + * { [0,511,1,510], [2,509,3,508], [4,507,5,506], ..., [254,257,255,256] }. The + * corresponding output \p thread_keys in those threads will be + * { [0,1,2,3], [4,5,6,7], [8,9,10,11], ..., [508,509,510,511] }. + * + */ + __device__ __forceinline__ void Sort( + Key (&keys)[ITEMS_PER_THREAD], ///< [in-out] Keys to sort + Value (&values)[ITEMS_PER_THREAD], ///< [in-out] Values to sort + int begin_bit = 0, ///< [in] [optional] The beginning (least-significant) bit index needed for key comparison + int end_bit = sizeof(Key) * 8) ///< [in] [optional] The past-the-end (most-significant) bit index needed for key comparison + { + SortBlocked(keys, values, begin_bit, end_bit, Int2Type(), Int2Type()); + } + + /** + * \brief Performs a descending block-wide radix sort over a [blocked arrangement](index.html#sec5sec3) of keys. + * + * \par + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a sort of 512 integer keys that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive keys. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockRadixSort for 128 threads owning 4 integer keys each + * typedef cub::BlockRadixSort BlockRadixSort; + * + * // Allocate shared memory for BlockRadixSort + * __shared__ typename BlockRadixSort::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_keys[4]; + * ... + * + * // Collectively sort the keys + * BlockRadixSort(temp_storage).Sort(thread_keys); + * + * \endcode + * \par + * Suppose the set of input \p thread_keys across the block of threads is + * { [0,511,1,510], [2,509,3,508], [4,507,5,506], ..., [254,257,255,256] }. + * The corresponding output \p thread_keys in those threads will be + * { [511,510,509,508], [11,10,9,8], [7,6,5,4], ..., [3,2,1,0] }. + */ + __device__ __forceinline__ void SortDescending( + Key (&keys)[ITEMS_PER_THREAD], ///< [in-out] Keys to sort + int begin_bit = 0, ///< [in] [optional] The beginning (least-significant) bit index needed for key comparison + int end_bit = sizeof(Key) * 8) ///< [in] [optional] The past-the-end (most-significant) bit index needed for key comparison + { + NullType values[ITEMS_PER_THREAD]; + + SortBlocked(keys, values, begin_bit, end_bit, Int2Type(), Int2Type()); + } + + + /** + * \brief Performs a descending block-wide radix sort across a [blocked arrangement](index.html#sec5sec3) of keys and values. + * + * \par + * - BlockRadixSort can only accommodate one associated tile of values. To "truck along" + * more than one tile of values, simply perform a key-value sort of the keys paired + * with a temporary value array that enumerates the key indices. The reordered indices + * can then be used as a gather-vector for exchanging other associated tile data through + * shared memory. + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a sort of 512 integer keys and values that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive pairs. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockRadixSort for 128 threads owning 4 integer keys and values each + * typedef cub::BlockRadixSort BlockRadixSort; + * + * // Allocate shared memory for BlockRadixSort + * __shared__ typename BlockRadixSort::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_keys[4]; + * int thread_values[4]; + * ... + * + * // Collectively sort the keys and values among block threads + * BlockRadixSort(temp_storage).Sort(thread_keys, thread_values); + * + * \endcode + * \par + * Suppose the set of input \p thread_keys across the block of threads is + * { [0,511,1,510], [2,509,3,508], [4,507,5,506], ..., [254,257,255,256] }. The + * corresponding output \p thread_keys in those threads will be + * { [511,510,509,508], [11,10,9,8], [7,6,5,4], ..., [3,2,1,0] }. + * + */ + __device__ __forceinline__ void SortDescending( + Key (&keys)[ITEMS_PER_THREAD], ///< [in-out] Keys to sort + Value (&values)[ITEMS_PER_THREAD], ///< [in-out] Values to sort + int begin_bit = 0, ///< [in] [optional] The beginning (least-significant) bit index needed for key comparison + int end_bit = sizeof(Key) * 8) ///< [in] [optional] The past-the-end (most-significant) bit index needed for key comparison + { + SortBlocked(keys, values, begin_bit, end_bit, Int2Type(), Int2Type()); + } + + + //@} end member group + /******************************************************************//** + * \name Sorting (blocked arrangement -> striped arrangement) + *********************************************************************/ + //@{ + + + /** + * \brief Performs an ascending radix sort across a [blocked arrangement](index.html#sec5sec3) of keys, leaving them in a [striped arrangement](index.html#sec5sec3). + * + * \par + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a sort of 512 integer keys that + * are initially partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive keys. The final partitioning is striped. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockRadixSort for 128 threads owning 4 integer keys each + * typedef cub::BlockRadixSort BlockRadixSort; + * + * // Allocate shared memory for BlockRadixSort + * __shared__ typename BlockRadixSort::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_keys[4]; + * ... + * + * // Collectively sort the keys + * BlockRadixSort(temp_storage).SortBlockedToStriped(thread_keys); + * + * \endcode + * \par + * Suppose the set of input \p thread_keys across the block of threads is + * { [0,511,1,510], [2,509,3,508], [4,507,5,506], ..., [254,257,255,256] }. The + * corresponding output \p thread_keys in those threads will be + * { [0,128,256,384], [1,129,257,385], [2,130,258,386], ..., [127,255,383,511] }. + * + */ + __device__ __forceinline__ void SortBlockedToStriped( + Key (&keys)[ITEMS_PER_THREAD], ///< [in-out] Keys to sort + int begin_bit = 0, ///< [in] [optional] The beginning (least-significant) bit index needed for key comparison + int end_bit = sizeof(Key) * 8) ///< [in] [optional] The past-the-end (most-significant) bit index needed for key comparison + { + NullType values[ITEMS_PER_THREAD]; + + SortBlockedToStriped(keys, values, begin_bit, end_bit, Int2Type(), Int2Type()); + } + + + /** + * \brief Performs an ascending radix sort across a [blocked arrangement](index.html#sec5sec3) of keys and values, leaving them in a [striped arrangement](index.html#sec5sec3). + * + * \par + * - BlockRadixSort can only accommodate one associated tile of values. To "truck along" + * more than one tile of values, simply perform a key-value sort of the keys paired + * with a temporary value array that enumerates the key indices. The reordered indices + * can then be used as a gather-vector for exchanging other associated tile data through + * shared memory. + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a sort of 512 integer keys and values that + * are initially partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive pairs. The final partitioning is striped. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockRadixSort for 128 threads owning 4 integer keys and values each + * typedef cub::BlockRadixSort BlockRadixSort; + * + * // Allocate shared memory for BlockRadixSort + * __shared__ typename BlockRadixSort::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_keys[4]; + * int thread_values[4]; + * ... + * + * // Collectively sort the keys and values among block threads + * BlockRadixSort(temp_storage).SortBlockedToStriped(thread_keys, thread_values); + * + * \endcode + * \par + * Suppose the set of input \p thread_keys across the block of threads is + * { [0,511,1,510], [2,509,3,508], [4,507,5,506], ..., [254,257,255,256] }. The + * corresponding output \p thread_keys in those threads will be + * { [0,128,256,384], [1,129,257,385], [2,130,258,386], ..., [127,255,383,511] }. + * + */ + __device__ __forceinline__ void SortBlockedToStriped( + Key (&keys)[ITEMS_PER_THREAD], ///< [in-out] Keys to sort + Value (&values)[ITEMS_PER_THREAD], ///< [in-out] Values to sort + int begin_bit = 0, ///< [in] [optional] The beginning (least-significant) bit index needed for key comparison + int end_bit = sizeof(Key) * 8) ///< [in] [optional] The past-the-end (most-significant) bit index needed for key comparison + { + SortBlockedToStriped(keys, values, begin_bit, end_bit, Int2Type(), Int2Type()); + } + + + /** + * \brief Performs a descending radix sort across a [blocked arrangement](index.html#sec5sec3) of keys, leaving them in a [striped arrangement](index.html#sec5sec3). + * + * \par + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a sort of 512 integer keys that + * are initially partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive keys. The final partitioning is striped. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockRadixSort for 128 threads owning 4 integer keys each + * typedef cub::BlockRadixSort BlockRadixSort; + * + * // Allocate shared memory for BlockRadixSort + * __shared__ typename BlockRadixSort::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_keys[4]; + * ... + * + * // Collectively sort the keys + * BlockRadixSort(temp_storage).SortBlockedToStriped(thread_keys); + * + * \endcode + * \par + * Suppose the set of input \p thread_keys across the block of threads is + * { [0,511,1,510], [2,509,3,508], [4,507,5,506], ..., [254,257,255,256] }. The + * corresponding output \p thread_keys in those threads will be + * { [511,383,255,127], [386,258,130,2], [385,257,128,1], ..., [384,256,128,0] }. + * + */ + __device__ __forceinline__ void SortDescendingBlockedToStriped( + Key (&keys)[ITEMS_PER_THREAD], ///< [in-out] Keys to sort + int begin_bit = 0, ///< [in] [optional] The beginning (least-significant) bit index needed for key comparison + int end_bit = sizeof(Key) * 8) ///< [in] [optional] The past-the-end (most-significant) bit index needed for key comparison + { + NullType values[ITEMS_PER_THREAD]; + + SortBlockedToStriped(keys, values, begin_bit, end_bit, Int2Type(), Int2Type()); + } + + + /** + * \brief Performs a descending radix sort across a [blocked arrangement](index.html#sec5sec3) of keys and values, leaving them in a [striped arrangement](index.html#sec5sec3). + * + * \par + * - BlockRadixSort can only accommodate one associated tile of values. To "truck along" + * more than one tile of values, simply perform a key-value sort of the keys paired + * with a temporary value array that enumerates the key indices. The reordered indices + * can then be used as a gather-vector for exchanging other associated tile data through + * shared memory. + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a sort of 512 integer keys and values that + * are initially partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive pairs. The final partitioning is striped. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockRadixSort for 128 threads owning 4 integer keys and values each + * typedef cub::BlockRadixSort BlockRadixSort; + * + * // Allocate shared memory for BlockRadixSort + * __shared__ typename BlockRadixSort::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_keys[4]; + * int thread_values[4]; + * ... + * + * // Collectively sort the keys and values among block threads + * BlockRadixSort(temp_storage).SortBlockedToStriped(thread_keys, thread_values); + * + * \endcode + * \par + * Suppose the set of input \p thread_keys across the block of threads is + * { [0,511,1,510], [2,509,3,508], [4,507,5,506], ..., [254,257,255,256] }. The + * corresponding output \p thread_keys in those threads will be + * { [511,383,255,127], [386,258,130,2], [385,257,128,1], ..., [384,256,128,0] }. + * + */ + __device__ __forceinline__ void SortDescendingBlockedToStriped( + Key (&keys)[ITEMS_PER_THREAD], ///< [in-out] Keys to sort + Value (&values)[ITEMS_PER_THREAD], ///< [in-out] Values to sort + int begin_bit = 0, ///< [in] [optional] The beginning (least-significant) bit index needed for key comparison + int end_bit = sizeof(Key) * 8) ///< [in] [optional] The past-the-end (most-significant) bit index needed for key comparison + { + SortBlockedToStriped(keys, values, begin_bit, end_bit, Int2Type(), Int2Type()); + } + + + //@} end member group + +}; + +/** + * \example example_block_radix_sort.cu + */ + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_raking_layout.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_raking_layout.cuh new file mode 100644 index 0000000000000000000000000000000000000000..582253705efe4e7912a7157a9d58f5efd70af6bc --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_raking_layout.cuh @@ -0,0 +1,144 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockRakingLayout provides a conflict-free shared memory layout abstraction for warp-raking across thread block data. + */ + + +#pragma once + +#include "../util_macro.cuh" +#include "../util_arch.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/** + * \brief BlockRakingLayout provides a conflict-free shared memory layout abstraction for raking across thread block data. ![](raking.png) + * \ingroup BlockModule + * + * \par Overview + * This type facilitates a shared memory usage pattern where a block of CUDA + * threads places elements into shared memory and then reduces the active + * parallelism to one "raking" warp of threads for serially aggregating consecutive + * sequences of shared items. Padding is inserted to eliminate bank conflicts + * (for most data types). + * + * \tparam T The data type to be exchanged. + * \tparam BLOCK_THREADS The thread block size in threads. + */ +template < + typename T, + int BLOCK_THREADS> +struct BlockRakingLayout +{ + //--------------------------------------------------------------------- + // Constants and type definitions + //--------------------------------------------------------------------- + + enum + { + /// The total number of elements that need to be cooperatively reduced + SHARED_ELEMENTS = BLOCK_THREADS, + + /// Maximum number of warp-synchronous raking threads + MAX_RAKING_THREADS = CUB_MIN(BLOCK_THREADS, CUB_PTX_WARP_THREADS), + + /// Number of raking elements per warp-synchronous raking thread (rounded up) + SEGMENT_LENGTH = (SHARED_ELEMENTS + MAX_RAKING_THREADS - 1) / MAX_RAKING_THREADS, + + /// Never use a raking thread that will have no valid data (e.g., when BLOCK_THREADS is 62 and SEGMENT_LENGTH is 2, we should only use 31 raking threads) + RAKING_THREADS = (SHARED_ELEMENTS + SEGMENT_LENGTH - 1) / SEGMENT_LENGTH, + + /// Whether we will have bank conflicts + HAS_CONFLICTS = (CUB_PTX_SMEM_BANKS % SEGMENT_LENGTH == 0), + + /// Degree of bank conflicts (e.g., 4-way) + CONFLICT_DEGREE = (HAS_CONFLICTS) ? + (MAX_RAKING_THREADS / (CUB_PTX_SMEM_BANKS / SEGMENT_LENGTH)) : + 0, + + /// Pad each segment length with one element if degree of bank conflicts is greater than 4-way (heuristic) + SEGMENT_PADDING = (CONFLICT_DEGREE <= CUB_PTX_PREFER_CONFLICT_OVER_PADDING) ? 0 : 1, +// SEGMENT_PADDING = (HAS_CONFLICTS) ? 1 : 0, + + /// Total number of elements in the raking grid + GRID_ELEMENTS = RAKING_THREADS * (SEGMENT_LENGTH + SEGMENT_PADDING), + + /// Whether or not we need bounds checking during raking (the number of reduction elements is not a multiple of the number of raking threads) + UNGUARDED = (SHARED_ELEMENTS % RAKING_THREADS == 0), + }; + + + /** + * \brief Shared memory storage type + */ + typedef T TempStorage[BlockRakingLayout::GRID_ELEMENTS]; + + + /** + * \brief Returns the location for the calling thread to place data into the grid + */ + static __device__ __forceinline__ T* PlacementPtr( + TempStorage &temp_storage, + int linear_tid) + { + // Offset for partial + unsigned int offset = linear_tid; + + // Add in one padding element for every segment + if (SEGMENT_PADDING > 0) + { + offset += offset / SEGMENT_LENGTH; + } + + // Incorporating a block of padding partials every shared memory segment + return temp_storage + offset; + } + + + /** + * \brief Returns the location for the calling thread to begin sequential raking + */ + static __device__ __forceinline__ T* RakingPtr( + TempStorage &temp_storage, + int linear_tid) + { + return temp_storage + (linear_tid * (SEGMENT_LENGTH + SEGMENT_PADDING)); + } +}; + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_reduce.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_reduce.cuh new file mode 100644 index 0000000000000000000000000000000000000000..528512bb77c4546e6369f818976a0107d21db25f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_reduce.cuh @@ -0,0 +1,610 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * The cub::BlockReduce class provides [collective](index.html#sec0) methods for computing a parallel reduction of items partitioned across a CUDA thread block. + */ + +#pragma once + +#include "specializations/block_reduce_raking.cuh" +#include "specializations/block_reduce_raking_commutative_only.cuh" +#include "specializations/block_reduce_warp_reductions.cuh" +#include "../util_type.cuh" +#include "../thread/thread_operators.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + + +/****************************************************************************** + * Algorithmic variants + ******************************************************************************/ + +/** + * BlockReduceAlgorithm enumerates alternative algorithms for parallel + * reduction across a CUDA threadblock. + */ +enum BlockReduceAlgorithm +{ + + /** + * \par Overview + * An efficient "raking" reduction algorithm that only supports commutative + * reduction operators (e.g., addition). + * + * \par + * Execution is comprised of three phases: + * -# Upsweep sequential reduction in registers (if threads contribute more + * than one input each). Threads in warps other than the first warp place + * their partial reductions into shared memory. + * -# Upsweep sequential reduction in shared memory. Threads within the first + * warp continue to accumulate by raking across segments of shared partial reductions + * -# A warp-synchronous Kogge-Stone style reduction within the raking warp. + * + * \par + * \image html block_reduce.png + *
\p BLOCK_REDUCE_RAKING data flow for a hypothetical 16-thread threadblock and 4-thread raking warp.
+ * + * \par Performance Considerations + * - This variant performs less communication than BLOCK_REDUCE_RAKING_NON_COMMUTATIVE + * and is preferable when the reduction operator is commutative. This variant + * applies fewer reduction operators than BLOCK_REDUCE_WARP_REDUCTIONS, and can provide higher overall + * throughput across the GPU when suitably occupied. However, turn-around latency may be + * higher than to BLOCK_REDUCE_WARP_REDUCTIONS and thus less-desirable + * when the GPU is under-occupied. + */ + BLOCK_REDUCE_RAKING_COMMUTATIVE_ONLY, + + + /** + * \par Overview + * An efficient "raking" reduction algorithm that supports commutative + * (e.g., addition) and non-commutative (e.g., string concatenation) reduction + * operators. + * + * \par + * Execution is comprised of three phases: + * -# Upsweep sequential reduction in registers (if threads contribute more + * than one input each). Each thread then places the partial reduction + * of its item(s) into shared memory. + * -# Upsweep sequential reduction in shared memory. Threads within a + * single warp rake across segments of shared partial reductions. + * -# A warp-synchronous Kogge-Stone style reduction within the raking warp. + * + * \par + * \image html block_reduce.png + *
\p BLOCK_REDUCE_RAKING data flow for a hypothetical 16-thread threadblock and 4-thread raking warp.
+ * + * \par Performance Considerations + * - This variant performs more communication than BLOCK_REDUCE_RAKING + * and is only preferable when the reduction operator is non-commutative. This variant + * applies fewer reduction operators than BLOCK_REDUCE_WARP_REDUCTIONS, and can provide higher overall + * throughput across the GPU when suitably occupied. However, turn-around latency may be + * higher than to BLOCK_REDUCE_WARP_REDUCTIONS and thus less-desirable + * when the GPU is under-occupied. + */ + BLOCK_REDUCE_RAKING, + + + /** + * \par Overview + * A quick "tiled warp-reductions" reduction algorithm that supports commutative + * (e.g., addition) and non-commutative (e.g., string concatenation) reduction + * operators. + * + * \par + * Execution is comprised of four phases: + * -# Upsweep sequential reduction in registers (if threads contribute more + * than one input each). Each thread then places the partial reduction + * of its item(s) into shared memory. + * -# Compute a shallow, but inefficient warp-synchronous Kogge-Stone style + * reduction within each warp. + * -# A propagation phase where the warp reduction outputs in each warp are + * updated with the aggregate from each preceding warp. + * + * \par + * \image html block_scan_warpscans.png + *
\p BLOCK_REDUCE_WARP_REDUCTIONS data flow for a hypothetical 16-thread threadblock and 4-thread raking warp.
+ * + * \par Performance Considerations + * - This variant applies more reduction operators than BLOCK_REDUCE_RAKING + * or BLOCK_REDUCE_RAKING_NON_COMMUTATIVE, which may result in lower overall + * throughput across the GPU. However turn-around latency may be lower and + * thus useful when the GPU is under-occupied. + */ + BLOCK_REDUCE_WARP_REDUCTIONS, +}; + + +/****************************************************************************** + * Block reduce + ******************************************************************************/ + +/** + * \brief The BlockReduce class provides [collective](index.html#sec0) methods for computing a parallel reduction of items partitioned across a CUDA thread block. ![](reduce_logo.png) + * \ingroup BlockModule + * + * \tparam T Data type being reduced + * \tparam BLOCK_THREADS The thread block size in threads + * \tparam ALGORITHM [optional] cub::BlockReduceAlgorithm enumerator specifying the underlying algorithm to use (default: cub::BLOCK_REDUCE_WARP_REDUCTIONS) + * + * \par Overview + * - A reduction (or fold) + * uses a binary combining operator to compute a single aggregate from a list of input elements. + * - BlockReduce can be optionally specialized by algorithm to accommodate different latency/throughput workload profiles: + * -# cub::BLOCK_REDUCE_RAKING_COMMUTATIVE_ONLY. An efficient "raking" reduction algorithm that only supports commutative reduction operators. [More...](\ref cub::BlockReduceAlgorithm) + * -# cub::BLOCK_REDUCE_RAKING. An efficient "raking" reduction algorithm that supports commutative and non-commutative reduction operators. [More...](\ref cub::BlockReduceAlgorithm) + * -# cub::BLOCK_REDUCE_WARP_REDUCTIONS. A quick "tiled warp-reductions" reduction algorithm that supports commutative and non-commutative reduction operators. [More...](\ref cub::BlockReduceAlgorithm) + * + * \par Performance Considerations + * - \granularity + * - Very efficient (only one synchronization barrier). + * - Incurs zero bank conflicts for most types + * - Computation is slightly more efficient (i.e., having lower instruction overhead) for: + * - Summation (vs. generic reduction) + * - \p BLOCK_THREADS is a multiple of the architecture's warp size + * - Every thread has a valid input (i.e., full vs. partial-tiles) + * - See cub::BlockReduceAlgorithm for performance details regarding algorithmic alternatives + * + * \par A Simple Example + * \blockcollective{BlockReduce} + * \par + * The code snippet below illustrates a sum reduction of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockReduce for 128 threads on type int + * typedef cub::BlockReduce BlockReduce; + * + * // Allocate shared memory for BlockReduce + * __shared__ typename BlockReduce::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Compute the block-wide sum for thread0 + * int aggregate = BlockReduce(temp_storage).Sum(thread_data); + * + * \endcode + * + */ +template < + typename T, + int BLOCK_THREADS, + BlockReduceAlgorithm ALGORITHM = BLOCK_REDUCE_WARP_REDUCTIONS> +class BlockReduce +{ +private: + + /****************************************************************************** + * Constants and type definitions + ******************************************************************************/ + + /// Internal specialization type + typedef typename If<(ALGORITHM == BLOCK_REDUCE_WARP_REDUCTIONS), + BlockReduceWarpReductions, // BlockReduceWarpReductions + typename If<(ALGORITHM == BLOCK_REDUCE_RAKING_COMMUTATIVE_ONLY), + BlockReduceRakingCommutativeOnly, // BlockReduceRakingCommutativeOnly + BlockReduceRaking >::Type>::Type InternalBlockReduce; // BlockReduceRaking + + /// Shared memory storage layout type for BlockReduce + typedef typename InternalBlockReduce::TempStorage _TempStorage; + + + /****************************************************************************** + * Utility methods + ******************************************************************************/ + + /// Internal storage allocator + __device__ __forceinline__ _TempStorage& PrivateStorage() + { + __shared__ _TempStorage private_storage; + return private_storage; + } + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + /// Shared storage reference + _TempStorage &temp_storage; + + /// Linear thread-id + int linear_tid; + + +public: + + /// \smemstorage{BlockReduce} + struct TempStorage : Uninitialized<_TempStorage> {}; + + + /******************************************************************//** + * \name Collective constructors + *********************************************************************/ + //@{ + + /** + * \brief Collective constructor for 1D thread blocks using a private static allocation of shared memory as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockReduce() + : + temp_storage(PrivateStorage()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor for 1D thread blocks using the specified memory allocation as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockReduce( + TempStorage &temp_storage) ///< [in] Reference to memory allocation having layout type TempStorage + : + temp_storage(temp_storage.Alias()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor using a private static allocation of shared memory as temporary storage. Each thread is identified using the supplied linear thread identifier + */ + __device__ __forceinline__ BlockReduce( + int linear_tid) ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(PrivateStorage()), + linear_tid(linear_tid) + {} + + + /** + * \brief Collective constructor using the specified memory allocation as temporary storage. Each thread is identified using the supplied linear thread identifier. + */ + __device__ __forceinline__ BlockReduce( + TempStorage &temp_storage, ///< [in] Reference to memory allocation having layout type TempStorage + int linear_tid) ///< [in] [optional] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + + + //@} end member group + /******************************************************************//** + * \name Generic reductions + *********************************************************************/ + //@{ + + + /** + * \brief Computes a block-wide reduction for thread0 using the specified binary reduction functor. Each thread contributes one input element. + * + * \par + * - The return value is undefined in threads other than thread0. + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a max reduction of 128 integer items that + * are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockReduce for 128 threads on type int + * typedef cub::BlockReduce BlockReduce; + * + * // Allocate shared memory for BlockReduce + * __shared__ typename BlockReduce::TempStorage temp_storage; + * + * // Each thread obtains an input item + * int thread_data; + * ... + * + * // Compute the block-wide max for thread0 + * int aggregate = BlockReduce(temp_storage).Reduce(thread_data, cub::Max()); + * + * \endcode + * + * \tparam ReductionOp [inferred] Binary reduction functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ T Reduce( + T input, ///< [in] Calling thread's input + ReductionOp reduction_op) ///< [in] Binary reduction functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + { + return InternalBlockReduce(temp_storage, linear_tid).template Reduce(input, BLOCK_THREADS, reduction_op); + } + + + /** + * \brief Computes a block-wide reduction for thread0 using the specified binary reduction functor. Each thread contributes an array of consecutive input elements. + * + * \par + * - The return value is undefined in threads other than thread0. + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a max reduction of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockReduce for 128 threads on type int + * typedef cub::BlockReduce BlockReduce; + * + * // Allocate shared memory for BlockReduce + * __shared__ typename BlockReduce::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Compute the block-wide max for thread0 + * int aggregate = BlockReduce(temp_storage).Reduce(thread_data, cub::Max()); + * + * \endcode + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam ReductionOp [inferred] Binary reduction functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template < + int ITEMS_PER_THREAD, + typename ReductionOp> + __device__ __forceinline__ T Reduce( + T (&inputs)[ITEMS_PER_THREAD], ///< [in] Calling thread's input segment + ReductionOp reduction_op) ///< [in] Binary reduction functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + { + // Reduce partials + T partial = ThreadReduce(inputs, reduction_op); + return Reduce(partial, reduction_op); + } + + + /** + * \brief Computes a block-wide reduction for thread0 using the specified binary reduction functor. The first \p num_valid threads each contribute one input element. + * + * \par + * - The return value is undefined in threads other than thread0. + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a max reduction of a partially-full tile of integer items that + * are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(int num_valid, ...) + * { + * // Specialize BlockReduce for 128 threads on type int + * typedef cub::BlockReduce BlockReduce; + * + * // Allocate shared memory for BlockReduce + * __shared__ typename BlockReduce::TempStorage temp_storage; + * + * // Each thread obtains an input item + * int thread_data; + * if (threadIdx.x < num_valid) thread_data = ... + * + * // Compute the block-wide max for thread0 + * int aggregate = BlockReduce(temp_storage).Reduce(thread_data, cub::Max(), num_valid); + * + * \endcode + * + * \tparam ReductionOp [inferred] Binary reduction functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ T Reduce( + T input, ///< [in] Calling thread's input + ReductionOp reduction_op, ///< [in] Binary reduction functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + int num_valid) ///< [in] Number of threads containing valid elements (may be less than BLOCK_THREADS) + { + // Determine if we scan skip bounds checking + if (num_valid >= BLOCK_THREADS) + { + return InternalBlockReduce(temp_storage, linear_tid).template Reduce(input, num_valid, reduction_op); + } + else + { + return InternalBlockReduce(temp_storage, linear_tid).template Reduce(input, num_valid, reduction_op); + } + } + + + //@} end member group + /******************************************************************//** + * \name Summation reductions + *********************************************************************/ + //@{ + + + /** + * \brief Computes a block-wide reduction for thread0 using addition (+) as the reduction operator. Each thread contributes one input element. + * + * \par + * - The return value is undefined in threads other than thread0. + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a sum reduction of 128 integer items that + * are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockReduce for 128 threads on type int + * typedef cub::BlockReduce BlockReduce; + * + * // Allocate shared memory for BlockReduce + * __shared__ typename BlockReduce::TempStorage temp_storage; + * + * // Each thread obtains an input item + * int thread_data; + * ... + * + * // Compute the block-wide sum for thread0 + * int aggregate = BlockReduce(temp_storage).Sum(thread_data); + * + * \endcode + * + */ + __device__ __forceinline__ T Sum( + T input) ///< [in] Calling thread's input + { + return InternalBlockReduce(temp_storage, linear_tid).template Sum(input, BLOCK_THREADS); + } + + /** + * \brief Computes a block-wide reduction for thread0 using addition (+) as the reduction operator. Each thread contributes an array of consecutive input elements. + * + * \par + * - The return value is undefined in threads other than thread0. + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a sum reduction of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockReduce for 128 threads on type int + * typedef cub::BlockReduce BlockReduce; + * + * // Allocate shared memory for BlockReduce + * __shared__ typename BlockReduce::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Compute the block-wide sum for thread0 + * int aggregate = BlockReduce(temp_storage).Sum(thread_data); + * + * \endcode + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + */ + template + __device__ __forceinline__ T Sum( + T (&inputs)[ITEMS_PER_THREAD]) ///< [in] Calling thread's input segment + { + // Reduce partials + T partial = ThreadReduce(inputs, cub::Sum()); + return Sum(partial); + } + + + /** + * \brief Computes a block-wide reduction for thread0 using addition (+) as the reduction operator. The first \p num_valid threads each contribute one input element. + * + * \par + * - The return value is undefined in threads other than thread0. + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a sum reduction of a partially-full tile of integer items that + * are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(int num_valid, ...) + * { + * // Specialize BlockReduce for 128 threads on type int + * typedef cub::BlockReduce BlockReduce; + * + * // Allocate shared memory for BlockReduce + * __shared__ typename BlockReduce::TempStorage temp_storage; + * + * // Each thread obtains an input item (up to num_items) + * int thread_data; + * if (threadIdx.x < num_valid) + * thread_data = ... + * + * // Compute the block-wide sum for thread0 + * int aggregate = BlockReduce(temp_storage).Sum(thread_data, num_valid); + * + * \endcode + * + */ + __device__ __forceinline__ T Sum( + T input, ///< [in] Calling thread's input + int num_valid) ///< [in] Number of threads containing valid elements (may be less than BLOCK_THREADS) + { + // Determine if we scan skip bounds checking + if (num_valid >= BLOCK_THREADS) + { + return InternalBlockReduce(temp_storage, linear_tid).template Sum(input, num_valid); + } + else + { + return InternalBlockReduce(temp_storage, linear_tid).template Sum(input, num_valid); + } + } + + + //@} end member group +}; + +/** + * \example example_block_reduce.cu + */ + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_scan.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_scan.cuh new file mode 100644 index 0000000000000000000000000000000000000000..380e7f318d32dbf3e7bde34dfc86b4d73b0c9579 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_scan.cuh @@ -0,0 +1,2322 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * The cub::BlockScan class provides [collective](index.html#sec0) methods for computing a parallel prefix sum/scan of items partitioned across a CUDA thread block. + */ + +#pragma once + +#include "specializations/block_scan_raking.cuh" +#include "specializations/block_scan_warp_scans.cuh" +#include "../util_arch.cuh" +#include "../util_type.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + + +/****************************************************************************** + * Scan utility types + ******************************************************************************/ + +#ifndef DOXYGEN_SHOULD_SKIP_THIS // Do not document + +/** + * Reduce-value-by-ID scan operator + */ +template ///< Wrapped reduction operator type +struct ReduceByKeyOp +{ + ReductionOp op; ///< Wrapped reduction operator + + /// Constructor + __device__ __forceinline__ ReduceByKeyOp(ReductionOp op) : op(op) {} + + /// Scan operator + template + __device__ __forceinline__ KeyValuePair operator()( + const KeyValuePair &first, + const KeyValuePair &second) + { + KeyValuePair retval; + + retval.value = (second.key != first.key) ? + second.value : // The second value is for a different ID, return only that value + op(first.value, second.value); // The values are for the same ID so reduce them + + retval.key = second.key; + return retval; + } +}; + + + +/** + * Segmented scan operator + */ +template ///< Wrapped reduction operator type +struct SegmentedOp +{ + ReductionOp op; ///< Wrapped reduction operator + + /// Constructor + __device__ __forceinline__ SegmentedOp(ReductionOp op) : op(op) {} + + /// Scan operator + template + __device__ __forceinline__ KeyValuePair operator()( + const KeyValuePair &first, + const KeyValuePair &second) + { + if (second.key) { + KeyValuePair retval; + retval.value = second.value; + retval.key = first.key + second.key; + return retval; + } else { + KeyValuePair retval; + retval.value = op(first.value, second.value); + retval.key = first.key + second.key; + return ; + } + } +}; + +#endif // DOXYGEN_SHOULD_SKIP_THIS + + + +/****************************************************************************** + * Algorithmic variants + ******************************************************************************/ + +/** + * \brief BlockScanAlgorithm enumerates alternative algorithms for cub::BlockScan to compute a parallel prefix scan across a CUDA thread block. + */ +enum BlockScanAlgorithm +{ + + /** + * \par Overview + * An efficient "raking reduce-then-scan" prefix scan algorithm. Execution is comprised of five phases: + * -# Upsweep sequential reduction in registers (if threads contribute more than one input each). Each thread then places the partial reduction of its item(s) into shared memory. + * -# Upsweep sequential reduction in shared memory. Threads within a single warp rake across segments of shared partial reductions. + * -# A warp-synchronous Kogge-Stone style exclusive scan within the raking warp. + * -# Downsweep sequential exclusive scan in shared memory. Threads within a single warp rake across segments of shared partial reductions, seeded with the warp-scan output. + * -# Downsweep sequential scan in registers (if threads contribute more than one input), seeded with the raking scan output. + * + * \par + * \image html block_scan_raking.png + *
\p BLOCK_SCAN_RAKING data flow for a hypothetical 16-thread threadblock and 4-thread raking warp.
+ * + * \par Performance Considerations + * - Although this variant may suffer longer turnaround latencies when the + * GPU is under-occupied, it can often provide higher overall throughput + * across the GPU when suitably occupied. + */ + BLOCK_SCAN_RAKING, + + + /** + * \par Overview + * Similar to cub::BLOCK_SCAN_RAKING, but with fewer shared memory reads at + * the expense of higher register pressure. Raking threads preserve their + * "upsweep" segment of values in registers while performing warp-synchronous + * scan, allowing the "downsweep" not to re-read them from shared memory. + */ + BLOCK_SCAN_RAKING_MEMOIZE, + + + /** + * \par Overview + * A quick "tiled warpscans" prefix scan algorithm. Execution is comprised of four phases: + * -# Upsweep sequential reduction in registers (if threads contribute more than one input each). Each thread then places the partial reduction of its item(s) into shared memory. + * -# Compute a shallow, but inefficient warp-synchronous Kogge-Stone style scan within each warp. + * -# A propagation phase where the warp scan outputs in each warp are updated with the aggregate from each preceding warp. + * -# Downsweep sequential scan in registers (if threads contribute more than one input), seeded with the raking scan output. + * + * \par + * \image html block_scan_warpscans.png + *
\p BLOCK_SCAN_WARP_SCANS data flow for a hypothetical 16-thread threadblock and 4-thread raking warp.
+ * + * \par Performance Considerations + * - Although this variant may suffer lower overall throughput across the + * GPU because due to a heavy reliance on inefficient warpscans, it can + * often provide lower turnaround latencies when the GPU is under-occupied. + */ + BLOCK_SCAN_WARP_SCANS, +}; + + +/****************************************************************************** + * Block scan + ******************************************************************************/ + +/** + * \brief The BlockScan class provides [collective](index.html#sec0) methods for computing a parallel prefix sum/scan of items partitioned across a CUDA thread block. ![](block_scan_logo.png) + * \ingroup BlockModule + * + * \tparam T Data type being scanned + * \tparam BLOCK_THREADS The thread block size in threads + * \tparam ALGORITHM [optional] cub::BlockScanAlgorithm enumerator specifying the underlying algorithm to use (default: cub::BLOCK_SCAN_RAKING) + * + * \par Overview + * - Given a list of input elements and a binary reduction operator, a [prefix scan](http://en.wikipedia.org/wiki/Prefix_sum) + * produces an output list where each element is computed to be the reduction + * of the elements occurring earlier in the input list. Prefix sum + * connotes a prefix scan with the addition operator. The term \em inclusive indicates + * that the ith output reduction incorporates the ith input. + * The term \em exclusive indicates the ith input is not incorporated into + * the ith output reduction. + * - BlockScan can be optionally specialized by algorithm to accommodate different workload profiles: + * -# cub::BLOCK_SCAN_RAKING. An efficient (high throughput) "raking reduce-then-scan" prefix scan algorithm. [More...](\ref cub::BlockScanAlgorithm) + * -# cub::BLOCK_SCAN_RAKING_MEMOIZE. Similar to cub::BLOCK_SCAN_RAKING, but having higher throughput at the expense of additional register pressure for intermediate storage. [More...](\ref cub::BlockScanAlgorithm) + * -# cub::BLOCK_SCAN_WARP_SCANS. A quick (low latency) "tiled warpscans" prefix scan algorithm. [More...](\ref cub::BlockScanAlgorithm) + * + * \par Performance Considerations + * - \granularity + * - Uses special instructions when applicable (e.g., warp \p SHFL) + * - Uses synchronization-free communication between warp lanes when applicable + * - Uses only one or two block-wide synchronization barriers (depending on + * algorithm selection) + * - Incurs zero bank conflicts for most types + * - Computation is slightly more efficient (i.e., having lower instruction overhead) for: + * - Prefix sum variants (vs. generic scan) + * - Exclusive variants (vs. inclusive) + * - \p BLOCK_THREADS is a multiple of the architecture's warp size + * - See cub::BlockScanAlgorithm for performance details regarding algorithmic alternatives + * + * \par A Simple Example + * \blockcollective{BlockScan} + * \par + * The code snippet below illustrates an exclusive prefix sum of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Collectively compute the block-wide exclusive prefix sum + * BlockScan(temp_storage).ExclusiveSum(thread_data, thread_data); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is + * {[1,1,1,1], [1,1,1,1], ..., [1,1,1,1]}. + * The corresponding output \p thread_data in those threads will be + * {[0,1,2,3], [4,5,6,7], ..., [508,509,510,511]}. + * + */ +template < + typename T, + int BLOCK_THREADS, + BlockScanAlgorithm ALGORITHM = BLOCK_SCAN_RAKING> +class BlockScan +{ +private: + + /****************************************************************************** + * Constants and type definitions + ******************************************************************************/ + + /** + * Ensure the template parameterization meets the requirements of the + * specified algorithm. Currently, the BLOCK_SCAN_WARP_SCANS policy + * cannot be used with threadblock sizes not a multiple of the + * architectural warp size. + */ + static const BlockScanAlgorithm SAFE_ALGORITHM = + ((ALGORITHM == BLOCK_SCAN_WARP_SCANS) && (BLOCK_THREADS % CUB_PTX_WARP_THREADS != 0)) ? + BLOCK_SCAN_RAKING : + ALGORITHM; + + /// Internal specialization. + typedef typename If<(SAFE_ALGORITHM == BLOCK_SCAN_WARP_SCANS), + BlockScanWarpScans, + BlockScanRaking >::Type InternalBlockScan; + + + /// Shared memory storage layout type for BlockScan + typedef typename InternalBlockScan::TempStorage _TempStorage; + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + /// Shared storage reference + _TempStorage &temp_storage; + + /// Linear thread-id + int linear_tid; + + + /****************************************************************************** + * Utility methods + ******************************************************************************/ + + /// Internal storage allocator + __device__ __forceinline__ _TempStorage& PrivateStorage() + { + __shared__ _TempStorage private_storage; + return private_storage; + } + + +public: + + /// \smemstorage{BlockScan} + struct TempStorage : Uninitialized<_TempStorage> {}; + + + /******************************************************************//** + * \name Collective constructors + *********************************************************************/ + //@{ + + /** + * \brief Collective constructor for 1D thread blocks using a private static allocation of shared memory as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockScan() + : + temp_storage(PrivateStorage()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor for 1D thread blocks using the specified memory allocation as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockScan( + TempStorage &temp_storage) ///< [in] Reference to memory allocation having layout type TempStorage + : + temp_storage(temp_storage.Alias()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor using a private static allocation of shared memory as temporary storage. Each thread is identified using the supplied linear thread identifier + */ + __device__ __forceinline__ BlockScan( + int linear_tid) ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(PrivateStorage()), + linear_tid(linear_tid) + {} + + + /** + * \brief Collective constructor using the specified memory allocation as temporary storage. Each thread is identified using the supplied linear thread identifier. + */ + __device__ __forceinline__ BlockScan( + TempStorage &temp_storage, ///< [in] Reference to memory allocation having layout type TempStorage + int linear_tid) ///< [in] [optional] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + + + //@} end member group + /******************************************************************//** + * \name Exclusive prefix sum operations + *********************************************************************/ + //@{ + + + /** + * \brief Computes an exclusive block-wide prefix scan using addition (+) as the scan operator. Each thread contributes one input element. + * + * \par + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an exclusive prefix sum of 128 integer items that + * are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain input item for each thread + * int thread_data; + * ... + * + * // Collectively compute the block-wide exclusive prefix sum + * BlockScan(temp_storage).ExclusiveSum(thread_data, thread_data); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is 1, 1, ..., 1. The + * corresponding output \p thread_data in those threads will be 0, 1, ..., 127. + * + */ + __device__ __forceinline__ void ExclusiveSum( + T input, ///< [in] Calling thread's input item + T &output) ///< [out] Calling thread's output item (may be aliased to \p input) + { + T block_aggregate; + InternalBlockScan(temp_storage, linear_tid).ExclusiveSum(input, output, block_aggregate); + } + + + /** + * \brief Computes an exclusive block-wide prefix scan using addition (+) as the scan operator. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an exclusive prefix sum of 128 integer items that + * are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain input item for each thread + * int thread_data; + * ... + * + * // Collectively compute the block-wide exclusive prefix sum + * int block_aggregate; + * BlockScan(temp_storage).ExclusiveSum(thread_data, thread_data, block_aggregate); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is 1, 1, ..., 1. The + * corresponding output \p thread_data in those threads will be 0, 1, ..., 127. + * Furthermore the value \p 128 will be stored in \p block_aggregate for all threads. + * + */ + __device__ __forceinline__ void ExclusiveSum( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T &block_aggregate) ///< [out] block-wide aggregate reduction of input items + { + InternalBlockScan(temp_storage, linear_tid).ExclusiveSum(input, output, block_aggregate); + } + + + /** + * \brief Computes an exclusive block-wide prefix scan using addition (+) as the scan operator. Each thread contributes one input element. Instead of using 0 as the block-wide prefix, the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - The \p block_prefix_callback_op functor must implement a member function T operator()(T block_aggregate). + * The functor's input parameter \p block_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the first warp of threads in the block, however only the return value from + * lane0 is applied as the block-wide prefix. Can be stateful. + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a single thread block that progressively + * computes an exclusive prefix sum over multiple "tiles" of input using a + * prefix functor to maintain a running total between block-wide scans. Each tile consists + * of 128 integer items that are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * // A stateful callback functor that maintains a running prefix to be applied + * // during consecutive scan operations. + * struct BlockPrefixCallbackOp + * { + * // Running prefix + * int running_total; + * + * // Constructor + * __device__ BlockPrefixCallbackOp(int running_total) : running_total(running_total) {} + * + * // Callback operator to be entered by the first warp of threads in the block. + * // Thread-0 is responsible for returning a value for seeding the block-wide scan. + * __device__ int operator()(int block_aggregate) + * { + * int old_prefix = running_total; + * running_total += block_aggregate; + * return old_prefix; + * } + * }; + * + * __global__ void ExampleKernel(int *d_data, int num_items, ...) + * { + * // Specialize BlockScan for 128 threads + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Initialize running total + * BlockPrefixCallbackOp prefix_op(0); + * + * // Have the block iterate over segments of items + * for (int block_offset = 0; block_offset < num_items; block_offset += 128) + * { + * // Load a segment of consecutive items that are blocked across threads + * int thread_data = d_data[block_offset]; + * + * // Collectively compute the block-wide exclusive prefix sum + * int block_aggregate; + * BlockScan(temp_storage).ExclusiveSum( + * thread_data, thread_data, block_aggregate, prefix_op); + * __syncthreads(); + * + * // Store scanned items to output segment + * d_data[block_offset] = thread_data; + * } + * \endcode + * \par + * Suppose the input \p d_data is 1, 1, 1, 1, 1, 1, 1, 1, .... + * The corresponding output for the first segment will be 0, 1, ..., 127. + * The output for the second segment will be 128, 129, ..., 255. Furthermore, + * the value \p 128 will be stored in \p block_aggregate for all threads after each scan. + * + * \tparam BlockPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T block_aggregate) + */ + template + __device__ __forceinline__ void ExclusiveSum( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T &block_aggregate, ///< [out] block-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a block-wide prefix to be applied to all inputs. + { + InternalBlockScan(temp_storage, linear_tid).ExclusiveSum(input, output, block_aggregate, block_prefix_callback_op); + } + + + //@} end member group + /******************************************************************//** + * \name Exclusive prefix sum operations (multiple data per thread) + *********************************************************************/ + //@{ + + + /** + * \brief Computes an exclusive block-wide prefix scan using addition (+) as the scan operator. Each thread contributes an array of consecutive input elements. + * + * \par + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an exclusive prefix sum of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Collectively compute the block-wide exclusive prefix sum + * BlockScan(temp_storage).ExclusiveSum(thread_data, thread_data); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is { [1,1,1,1], [1,1,1,1], ..., [1,1,1,1] }. The + * corresponding output \p thread_data in those threads will be { [0,1,2,3], [4,5,6,7], ..., [508,509,510,511] }. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + */ + template + __device__ __forceinline__ void ExclusiveSum( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD]) ///< [out] Calling thread's output items (may be aliased to \p input) + { + // Reduce consecutive thread items in registers + Sum scan_op; + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveSum(thread_partial, thread_partial); + + // Exclusive scan in registers with prefix + ThreadScanExclusive(input, output, scan_op, thread_partial); + } + + + /** + * \brief Computes an exclusive block-wide prefix scan using addition (+) as the scan operator. Each thread contributes an array of consecutive input elements. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an exclusive prefix sum of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Collectively compute the block-wide exclusive prefix sum + * int block_aggregate; + * BlockScan(temp_storage).ExclusiveSum(thread_data, thread_data, block_aggregate); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is { [1,1,1,1], [1,1,1,1], ..., [1,1,1,1] }. The + * corresponding output \p thread_data in those threads will be { [0,1,2,3], [4,5,6,7], ..., [508,509,510,511] }. + * Furthermore the value \p 512 will be stored in \p block_aggregate for all threads. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + */ + template + __device__ __forceinline__ void ExclusiveSum( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD], ///< [out] Calling thread's output items (may be aliased to \p input) + T &block_aggregate) ///< [out] block-wide aggregate reduction of input items + { + // Reduce consecutive thread items in registers + Sum scan_op; + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveSum(thread_partial, thread_partial, block_aggregate); + + // Exclusive scan in registers with prefix + ThreadScanExclusive(input, output, scan_op, thread_partial); + } + + + /** + * \brief Computes an exclusive block-wide prefix scan using addition (+) as the scan operator. Each thread contributes an array of consecutive input elements. Instead of using 0 as the block-wide prefix, the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - The \p block_prefix_callback_op functor must implement a member function T operator()(T block_aggregate). + * The functor's input parameter \p block_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the first warp of threads in the block, however only the return value from + * lane0 is applied as the block-wide prefix. Can be stateful. + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a single thread block that progressively + * computes an exclusive prefix sum over multiple "tiles" of input using a + * prefix functor to maintain a running total between block-wide scans. Each tile consists + * of 512 integer items that are partitioned in a [blocked arrangement](index.html#sec5sec3) + * across 128 threads where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * // A stateful callback functor that maintains a running prefix to be applied + * // during consecutive scan operations. + * struct BlockPrefixCallbackOp + * { + * // Running prefix + * int running_total; + * + * // Constructor + * __device__ BlockPrefixCallbackOp(int running_total) : running_total(running_total) {} + * + * // Callback operator to be entered by the first warp of threads in the block. + * // Thread-0 is responsible for returning a value for seeding the block-wide scan. + * __device__ int operator()(int block_aggregate) + * { + * int old_prefix = running_total; + * running_total += block_aggregate; + * return old_prefix; + * } + * }; + * + * __global__ void ExampleKernel(int *d_data, int num_items, ...) + * { + * // Specialize BlockLoad, BlockStore, and BlockScan for 128 threads, 4 ints per thread + * typedef cub::BlockLoad BlockLoad; + * typedef cub::BlockStore BlockStore; + * typedef cub::BlockScan BlockScan; + * + * // Allocate aliased shared memory for BlockLoad, BlockStore, and BlockScan + * __shared__ union { + * typename BlockLoad::TempStorage load; + * typename BlockScan::TempStorage scan; + * typename BlockStore::TempStorage store; + * } temp_storage; + * + * // Initialize running total + * BlockPrefixCallbackOp prefix_op(0); + * + * // Have the block iterate over segments of items + * for (int block_offset = 0; block_offset < num_items; block_offset += 128 * 4) + * { + * // Load a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * BlockLoad(temp_storage.load).Load(d_data + block_offset, thread_data); + * __syncthreads(); + * + * // Collectively compute the block-wide exclusive prefix sum + * int block_aggregate; + * BlockScan(temp_storage.scan).ExclusiveSum( + * thread_data, thread_data, block_aggregate, prefix_op); + * __syncthreads(); + * + * // Store scanned items to output segment + * BlockStore(temp_storage.store).Store(d_data + block_offset, thread_data); + * __syncthreads(); + * } + * \endcode + * \par + * Suppose the input \p d_data is 1, 1, 1, 1, 1, 1, 1, 1, .... + * The corresponding output for the first segment will be 0, 1, 2, 3, ..., 510, 511. + * The output for the second segment will be 512, 513, 514, 515, ..., 1022, 1023. Furthermore, + * the value \p 512 will be stored in \p block_aggregate for all threads after each scan. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam BlockPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T block_aggregate) + */ + template < + int ITEMS_PER_THREAD, + typename BlockPrefixCallbackOp> + __device__ __forceinline__ void ExclusiveSum( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD], ///< [out] Calling thread's output items (may be aliased to \p input) + T &block_aggregate, ///< [out] block-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a block-wide prefix to be applied to all inputs. + { + // Reduce consecutive thread items in registers + Sum scan_op; + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveSum(thread_partial, thread_partial, block_aggregate, block_prefix_callback_op); + + // Exclusive scan in registers with prefix + ThreadScanExclusive(input, output, scan_op, thread_partial); + } + + + + //@} end member group // Inclusive prefix sums + /******************************************************************//** + * \name Exclusive prefix scan operations + *********************************************************************/ + //@{ + + + /** + * \brief Computes an exclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. + * + * \par + * - Supports non-commutative scan operators. + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an exclusive prefix max scan of 128 integer items that + * are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain input item for each thread + * int thread_data; + * ... + * + * // Collectively compute the block-wide exclusive prefix max scan + * BlockScan(temp_storage).ExclusiveScan(thread_data, thread_data, INT_MIN, cub::Max()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is 0, -1, 2, -3, ..., 126, -127. The + * corresponding output \p thread_data in those threads will be INT_MIN, 0, 0, 2, ..., 124, 126. + * + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T identity, ///< [in] Identity value + ScanOp scan_op) ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + { + T block_aggregate; + InternalBlockScan(temp_storage, linear_tid).ExclusiveScan(input, output, identity, scan_op, block_aggregate); + } + + + /** + * \brief Computes an exclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - Supports non-commutative scan operators. + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an exclusive prefix max scan of 128 integer items that + * are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain input item for each thread + * int thread_data; + * ... + * + * // Collectively compute the block-wide exclusive prefix max scan + * int block_aggregate; + * BlockScan(temp_storage).ExclusiveScan(thread_data, thread_data, INT_MIN, cub::Max(), block_aggregate); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is 0, -1, 2, -3, ..., 126, -127. The + * corresponding output \p thread_data in those threads will be INT_MIN, 0, 0, 2, ..., 124, 126. + * Furthermore the value \p 126 will be stored in \p block_aggregate for all threads. + * + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input items + T &output, ///< [out] Calling thread's output items (may be aliased to \p input) + T identity, ///< [in] Identity value + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + T &block_aggregate) ///< [out] block-wide aggregate reduction of input items + { + InternalBlockScan(temp_storage, linear_tid).ExclusiveScan(input, output, identity, scan_op, block_aggregate); + } + + + /** + * \brief Computes an exclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - The \p block_prefix_callback_op functor must implement a member function T operator()(T block_aggregate). + * The functor's input parameter \p block_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the first warp of threads in the block, however only the return value from + * lane0 is applied as the block-wide prefix. Can be stateful. + * - Supports non-commutative scan operators. + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a single thread block that progressively + * computes an exclusive prefix max scan over multiple "tiles" of input using a + * prefix functor to maintain a running total between block-wide scans. Each tile consists + * of 128 integer items that are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * // A stateful callback functor that maintains a running prefix to be applied + * // during consecutive scan operations. + * struct BlockPrefixCallbackOp + * { + * // Running prefix + * int running_total; + * + * // Constructor + * __device__ BlockPrefixCallbackOp(int running_total) : running_total(running_total) {} + * + * // Callback operator to be entered by the first warp of threads in the block. + * // Thread-0 is responsible for returning a value for seeding the block-wide scan. + * __device__ int operator()(int block_aggregate) + * { + * int old_prefix = running_total; + * running_total = (block_aggregate > old_prefix) ? block_aggregate : old_prefix; + * return old_prefix; + * } + * }; + * + * __global__ void ExampleKernel(int *d_data, int num_items, ...) + * { + * // Specialize BlockScan for 128 threads + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Initialize running total + * BlockPrefixCallbackOp prefix_op(INT_MIN); + * + * // Have the block iterate over segments of items + * for (int block_offset = 0; block_offset < num_items; block_offset += 128) + * { + * // Load a segment of consecutive items that are blocked across threads + * int thread_data = d_data[block_offset]; + * + * // Collectively compute the block-wide exclusive prefix max scan + * int block_aggregate; + * BlockScan(temp_storage).ExclusiveScan( + * thread_data, thread_data, INT_MIN, cub::Max(), block_aggregate, prefix_op); + * __syncthreads(); + * + * // Store scanned items to output segment + * d_data[block_offset] = thread_data; + * } + * \endcode + * \par + * Suppose the input \p d_data is 0, -1, 2, -3, 4, -5, .... + * The corresponding output for the first segment will be INT_MIN, 0, 0, 2, ..., 124, 126. + * The output for the second segment will be 126, 128, 128, 130, ..., 252, 254. Furthermore, + * \p block_aggregate will be assigned \p 126 in all threads after the first scan, assigned \p 254 after the second + * scan, etc. + * + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + * \tparam BlockPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T block_aggregate) + */ + template < + typename ScanOp, + typename BlockPrefixCallbackOp> + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T identity, ///< [in] Identity value + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + T &block_aggregate, ///< [out] block-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a block-wide prefix to be applied to all inputs. + { + InternalBlockScan(temp_storage, linear_tid).ExclusiveScan(input, output, identity, scan_op, block_aggregate, block_prefix_callback_op); + } + + + //@} end member group // Inclusive prefix sums + /******************************************************************//** + * \name Exclusive prefix scan operations (multiple data per thread) + *********************************************************************/ + //@{ + + + /** + * \brief Computes an exclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes an array of consecutive input elements. + * + * \par + * - Supports non-commutative scan operators. + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an exclusive prefix max scan of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Collectively compute the block-wide exclusive prefix max scan + * BlockScan(temp_storage).ExclusiveScan(thread_data, thread_data, INT_MIN, cub::Max()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is + * { [0,-1,2,-3], [4,-5,6,-7], ..., [508,-509,510,-511] }. + * The corresponding output \p thread_data in those threads will be + * { [INT_MIN,0,0,2], [2,4,4,6], ..., [506,508,508,510] }. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template < + int ITEMS_PER_THREAD, + typename ScanOp> + __device__ __forceinline__ void ExclusiveScan( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD], ///< [out] Calling thread's output items (may be aliased to \p input) + T identity, ///< [in] Identity value + ScanOp scan_op) ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + { + // Reduce consecutive thread items in registers + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveScan(thread_partial, thread_partial, identity, scan_op); + + // Exclusive scan in registers with prefix + ThreadScanExclusive(input, output, scan_op, thread_partial); + } + + + /** + * \brief Computes an exclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes an array of consecutive input elements. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - Supports non-commutative scan operators. + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an exclusive prefix max scan of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Collectively compute the block-wide exclusive prefix max scan + * int block_aggregate; + * BlockScan(temp_storage).ExclusiveScan(thread_data, thread_data, INT_MIN, cub::Max(), block_aggregate); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is { [0,-1,2,-3], [4,-5,6,-7], ..., [508,-509,510,-511] }. The + * corresponding output \p thread_data in those threads will be { [INT_MIN,0,0,2], [2,4,4,6], ..., [506,508,508,510] }. + * Furthermore the value \p 510 will be stored in \p block_aggregate for all threads. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template < + int ITEMS_PER_THREAD, + typename ScanOp> + __device__ __forceinline__ void ExclusiveScan( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD], ///< [out] Calling thread's output items (may be aliased to \p input) + T identity, ///< [in] Identity value + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + T &block_aggregate) ///< [out] block-wide aggregate reduction of input items + { + // Reduce consecutive thread items in registers + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveScan(thread_partial, thread_partial, identity, scan_op, block_aggregate); + + // Exclusive scan in registers with prefix + ThreadScanExclusive(input, output, scan_op, thread_partial); + } + + + /** + * \brief Computes an exclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes an array of consecutive input elements. the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - The \p block_prefix_callback_op functor must implement a member function T operator()(T block_aggregate). + * The functor's input parameter \p block_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the first warp of threads in the block, however only the return value from + * lane0 is applied as the block-wide prefix. Can be stateful. + * - Supports non-commutative scan operators. + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a single thread block that progressively + * computes an exclusive prefix max scan over multiple "tiles" of input using a + * prefix functor to maintain a running total between block-wide scans. Each tile consists + * of 128 integer items that are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * // A stateful callback functor that maintains a running prefix to be applied + * // during consecutive scan operations. + * struct BlockPrefixCallbackOp + * { + * // Running prefix + * int running_total; + * + * // Constructor + * __device__ BlockPrefixCallbackOp(int running_total) : running_total(running_total) {} + * + * // Callback operator to be entered by the first warp of threads in the block. + * // Thread-0 is responsible for returning a value for seeding the block-wide scan. + * __device__ int operator()(int block_aggregate) + * { + * int old_prefix = running_total; + * running_total = (block_aggregate > old_prefix) ? block_aggregate : old_prefix; + * return old_prefix; + * } + * }; + * + * __global__ void ExampleKernel(int *d_data, int num_items, ...) + * { + * // Specialize BlockLoad, BlockStore, and BlockScan for 128 threads, 4 ints per thread + * typedef cub::BlockLoad BlockLoad; + * typedef cub::BlockStore BlockStore; + * typedef cub::BlockScan BlockScan; + * + * // Allocate aliased shared memory for BlockLoad, BlockStore, and BlockScan + * __shared__ union { + * typename BlockLoad::TempStorage load; + * typename BlockScan::TempStorage scan; + * typename BlockStore::TempStorage store; + * } temp_storage; + * + * // Initialize running total + * BlockPrefixCallbackOp prefix_op(0); + * + * // Have the block iterate over segments of items + * for (int block_offset = 0; block_offset < num_items; block_offset += 128 * 4) + * { + * // Load a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * BlockLoad(temp_storage.load).Load(d_data + block_offset, thread_data); + * __syncthreads(); + * + * // Collectively compute the block-wide exclusive prefix max scan + * int block_aggregate; + * BlockScan(temp_storage.scan).ExclusiveScan( + * thread_data, thread_data, INT_MIN, cub::Max(), block_aggregate, prefix_op); + * __syncthreads(); + * + * // Store scanned items to output segment + * BlockStore(temp_storage.store).Store(d_data + block_offset, thread_data); + * __syncthreads(); + * } + * \endcode + * \par + * Suppose the input \p d_data is 0, -1, 2, -3, 4, -5, .... + * The corresponding output for the first segment will be INT_MIN, 0, 0, 2, 2, 4, ..., 508, 510. + * The output for the second segment will be 510, 512, 512, 514, 514, 516, ..., 1020, 1022. Furthermore, + * \p block_aggregate will be assigned \p 510 in all threads after the first scan, assigned \p 1022 after the second + * scan, etc. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + * \tparam BlockPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T block_aggregate) + */ + template < + int ITEMS_PER_THREAD, + typename ScanOp, + typename BlockPrefixCallbackOp> + __device__ __forceinline__ void ExclusiveScan( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD], ///< [out] Calling thread's output items (may be aliased to \p input) + T identity, ///< [in] Identity value + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + T &block_aggregate, ///< [out] block-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a block-wide prefix to be applied to all inputs. + { + // Reduce consecutive thread items in registers + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveScan(thread_partial, thread_partial, identity, scan_op, block_aggregate, block_prefix_callback_op); + + // Exclusive scan in registers with prefix + ThreadScanExclusive(input, output, scan_op, thread_partial); + } + + + //@} end member group + +#ifndef DOXYGEN_SHOULD_SKIP_THIS // Do not document + + /******************************************************************//** + * \name Exclusive prefix scan operations (identityless, single datum per thread) + *********************************************************************/ + //@{ + + + /** + * \brief Computes an exclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. With no identity value, the output computed for thread0 is undefined. + * + * \par + * - Supports non-commutative scan operators. + * - \blocked + * - \smemreuse + * + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + ScanOp scan_op) ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + { + T block_aggregate; + InternalBlockScan(temp_storage, linear_tid).ExclusiveScan(input, output, scan_op, block_aggregate); + } + + + /** + * \brief Computes an exclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. With no identity value, the output computed for thread0 is undefined. + * + * \par + * - Supports non-commutative scan operators. + * - \blocked + * - \smemreuse + * + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + T &block_aggregate) ///< [out] block-wide aggregate reduction of input items + { + InternalBlockScan(temp_storage, linear_tid).ExclusiveScan(input, output, scan_op, block_aggregate); + } + + + /** + * \brief Computes an exclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * The \p block_prefix_callback_op functor must implement a member function T operator()(T block_aggregate). + * The functor's input parameter \p block_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the first warp of threads in the block, however only the return value from + * lane0 is applied as the block-wide prefix. Can be stateful. + * + * \par + * - Supports non-commutative scan operators. + * - \blocked + * - \smemreuse + * + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + * \tparam BlockPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T block_aggregate) + */ + template < + typename ScanOp, + typename BlockPrefixCallbackOp> + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + T &block_aggregate, ///< [out] block-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a block-wide prefix to be applied to all inputs. + { + InternalBlockScan(temp_storage, linear_tid).ExclusiveScan(input, output, scan_op, block_aggregate, block_prefix_callback_op); + } + + + //@} end member group + /******************************************************************//** + * \name Exclusive prefix scan operations (identityless, multiple data per thread) + *********************************************************************/ + //@{ + + + /** + * \brief Computes an exclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes an array of consecutive input elements. With no identity value, the output computed for thread0 is undefined. + * + * \par + * - Supports non-commutative scan operators. + * - \blocked + * - \granularity + * - \smemreuse + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template < + int ITEMS_PER_THREAD, + typename ScanOp> + __device__ __forceinline__ void ExclusiveScan( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD], ///< [out] Calling thread's output items (may be aliased to \p input) + ScanOp scan_op) ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + { + // Reduce consecutive thread items in registers + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveScan(thread_partial, thread_partial, scan_op); + + // Exclusive scan in registers with prefix + ThreadScanExclusive(input, output, scan_op, thread_partial, (linear_tid != 0)); + } + + + /** + * \brief Computes an exclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes an array of consecutive input elements. Also provides every thread with the block-wide \p block_aggregate of all inputs. With no identity value, the output computed for thread0 is undefined. + * + * \par + * - Supports non-commutative scan operators. + * - \blocked + * - \granularity + * - \smemreuse + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template < + int ITEMS_PER_THREAD, + typename ScanOp> + __device__ __forceinline__ void ExclusiveScan( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD], ///< [out] Calling thread's output items (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + T &block_aggregate) ///< [out] block-wide aggregate reduction of input items + { + // Reduce consecutive thread items in registers + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveScan(thread_partial, thread_partial, scan_op, block_aggregate); + + // Exclusive scan in registers with prefix + ThreadScanExclusive(input, output, scan_op, thread_partial, (linear_tid != 0)); + } + + + /** + * \brief Computes an exclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes an array of consecutive input elements. the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * The \p block_prefix_callback_op functor must implement a member function T operator()(T block_aggregate). + * The functor's input parameter \p block_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the first warp of threads in the block, however only the return value from + * lane0 is applied as the block-wide prefix. Can be stateful. + * + * \par + * - Supports non-commutative scan operators. + * - \blocked + * - \granularity + * - \smemreuse + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + * \tparam BlockPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T block_aggregate) + */ + template < + int ITEMS_PER_THREAD, + typename ScanOp, + typename BlockPrefixCallbackOp> + __device__ __forceinline__ void ExclusiveScan( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD], ///< [out] Calling thread's output items (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + T &block_aggregate, ///< [out] block-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a block-wide prefix to be applied to all inputs. + { + // Reduce consecutive thread items in registers + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveScan(thread_partial, thread_partial, scan_op, block_aggregate, block_prefix_callback_op); + + // Exclusive scan in registers with prefix + ThreadScanExclusive(input, output, scan_op, thread_partial); + } + + + //@} end member group + +#endif // DOXYGEN_SHOULD_SKIP_THIS + + /******************************************************************//** + * \name Inclusive prefix sum operations + *********************************************************************/ + //@{ + + + /** + * \brief Computes an inclusive block-wide prefix scan using addition (+) as the scan operator. Each thread contributes one input element. + * + * \par + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an inclusive prefix sum of 128 integer items that + * are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain input item for each thread + * int thread_data; + * ... + * + * // Collectively compute the block-wide inclusive prefix sum + * BlockScan(temp_storage).InclusiveSum(thread_data, thread_data); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is 1, 1, ..., 1. The + * corresponding output \p thread_data in those threads will be 1, 2, ..., 128. + * + */ + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item + T &output) ///< [out] Calling thread's output item (may be aliased to \p input) + { + T block_aggregate; + InternalBlockScan(temp_storage, linear_tid).InclusiveSum(input, output, block_aggregate); + } + + + /** + * \brief Computes an inclusive block-wide prefix scan using addition (+) as the scan operator. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an inclusive prefix sum of 128 integer items that + * are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain input item for each thread + * int thread_data; + * ... + * + * // Collectively compute the block-wide inclusive prefix sum + * int block_aggregate; + * BlockScan(temp_storage).InclusiveSum(thread_data, thread_data, block_aggregate); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is 1, 1, ..., 1. The + * corresponding output \p thread_data in those threads will be 1, 2, ..., 128. + * Furthermore the value \p 128 will be stored in \p block_aggregate for all threads. + * + */ + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T &block_aggregate) ///< [out] block-wide aggregate reduction of input items + { + InternalBlockScan(temp_storage, linear_tid).InclusiveSum(input, output, block_aggregate); + } + + + + /** + * \brief Computes an inclusive block-wide prefix scan using addition (+) as the scan operator. Each thread contributes one input element. Instead of using 0 as the block-wide prefix, the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - The \p block_prefix_callback_op functor must implement a member function T operator()(T block_aggregate). + * The functor's input parameter \p block_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the first warp of threads in the block, however only the return value from + * lane0 is applied as the block-wide prefix. Can be stateful. + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a single thread block that progressively + * computes an inclusive prefix sum over multiple "tiles" of input using a + * prefix functor to maintain a running total between block-wide scans. Each tile consists + * of 128 integer items that are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * // A stateful callback functor that maintains a running prefix to be applied + * // during consecutive scan operations. + * struct BlockPrefixCallbackOp + * { + * // Running prefix + * int running_total; + * + * // Constructor + * __device__ BlockPrefixCallbackOp(int running_total) : running_total(running_total) {} + * + * // Callback operator to be entered by the first warp of threads in the block. + * // Thread-0 is responsible for returning a value for seeding the block-wide scan. + * __device__ int operator()(int block_aggregate) + * { + * int old_prefix = running_total; + * running_total += block_aggregate; + * return old_prefix; + * } + * }; + * + * __global__ void ExampleKernel(int *d_data, int num_items, ...) + * { + * // Specialize BlockScan for 128 threads + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Initialize running total + * BlockPrefixCallbackOp prefix_op(0); + * + * // Have the block iterate over segments of items + * for (int block_offset = 0; block_offset < num_items; block_offset += 128) + * { + * // Load a segment of consecutive items that are blocked across threads + * int thread_data = d_data[block_offset]; + * + * // Collectively compute the block-wide inclusive prefix sum + * int block_aggregate; + * BlockScan(temp_storage).InclusiveSum( + * thread_data, thread_data, block_aggregate, prefix_op); + * __syncthreads(); + * + * // Store scanned items to output segment + * d_data[block_offset] = thread_data; + * } + * \endcode + * \par + * Suppose the input \p d_data is 1, 1, 1, 1, 1, 1, 1, 1, .... + * The corresponding output for the first segment will be 1, 2, ..., 128. + * The output for the second segment will be 129, 130, ..., 256. Furthermore, + * the value \p 128 will be stored in \p block_aggregate for all threads after each scan. + * + * \tparam BlockPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T block_aggregate) + */ + template + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T &block_aggregate, ///< [out] block-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a block-wide prefix to be applied to all inputs. + { + InternalBlockScan(temp_storage, linear_tid).InclusiveSum(input, output, block_aggregate, block_prefix_callback_op); + } + + + //@} end member group + /******************************************************************//** + * \name Inclusive prefix sum operations (multiple data per thread) + *********************************************************************/ + //@{ + + + /** + * \brief Computes an inclusive block-wide prefix scan using addition (+) as the scan operator. Each thread contributes an array of consecutive input elements. + * + * \par + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an inclusive prefix sum of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Collectively compute the block-wide inclusive prefix sum + * BlockScan(temp_storage).InclusiveSum(thread_data, thread_data); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is { [1,1,1,1], [1,1,1,1], ..., [1,1,1,1] }. The + * corresponding output \p thread_data in those threads will be { [1,2,3,4], [5,6,7,8], ..., [509,510,511,512] }. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + */ + template + __device__ __forceinline__ void InclusiveSum( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD]) ///< [out] Calling thread's output items (may be aliased to \p input) + { + if (ITEMS_PER_THREAD == 1) + { + InclusiveSum(input[0], output[0]); + } + else + { + // Reduce consecutive thread items in registers + Sum scan_op; + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveSum(thread_partial, thread_partial); + + // Inclusive scan in registers with prefix + ThreadScanInclusive(input, output, scan_op, thread_partial, (linear_tid != 0)); + } + } + + + /** + * \brief Computes an inclusive block-wide prefix scan using addition (+) as the scan operator. Each thread contributes an array of consecutive input elements. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an inclusive prefix sum of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Collectively compute the block-wide inclusive prefix sum + * int block_aggregate; + * BlockScan(temp_storage).InclusiveSum(thread_data, thread_data, block_aggregate); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is + * { [1,1,1,1], [1,1,1,1], ..., [1,1,1,1] }. The + * corresponding output \p thread_data in those threads will be + * { [1,2,3,4], [5,6,7,8], ..., [509,510,511,512] }. + * Furthermore the value \p 512 will be stored in \p block_aggregate for all threads. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ void InclusiveSum( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD], ///< [out] Calling thread's output items (may be aliased to \p input) + T &block_aggregate) ///< [out] block-wide aggregate reduction of input items + { + if (ITEMS_PER_THREAD == 1) + { + InclusiveSum(input[0], output[0], block_aggregate); + } + else + { + // Reduce consecutive thread items in registers + Sum scan_op; + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveSum(thread_partial, thread_partial, block_aggregate); + + // Inclusive scan in registers with prefix + ThreadScanInclusive(input, output, scan_op, thread_partial, (linear_tid != 0)); + } + } + + + /** + * \brief Computes an inclusive block-wide prefix scan using addition (+) as the scan operator. Each thread contributes an array of consecutive input elements. Instead of using 0 as the block-wide prefix, the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - The \p block_prefix_callback_op functor must implement a member function T operator()(T block_aggregate). + * The functor's input parameter \p block_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the first warp of threads in the block, however only the return value from + * lane0 is applied as the block-wide prefix. Can be stateful. + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a single thread block that progressively + * computes an inclusive prefix sum over multiple "tiles" of input using a + * prefix functor to maintain a running total between block-wide scans. Each tile consists + * of 512 integer items that are partitioned in a [blocked arrangement](index.html#sec5sec3) + * across 128 threads where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * // A stateful callback functor that maintains a running prefix to be applied + * // during consecutive scan operations. + * struct BlockPrefixCallbackOp + * { + * // Running prefix + * int running_total; + * + * // Constructor + * __device__ BlockPrefixCallbackOp(int running_total) : running_total(running_total) {} + * + * // Callback operator to be entered by the first warp of threads in the block. + * // Thread-0 is responsible for returning a value for seeding the block-wide scan. + * __device__ int operator()(int block_aggregate) + * { + * int old_prefix = running_total; + * running_total += block_aggregate; + * return old_prefix; + * } + * }; + * + * __global__ void ExampleKernel(int *d_data, int num_items, ...) + * { + * // Specialize BlockLoad, BlockStore, and BlockScan for 128 threads, 4 ints per thread + * typedef cub::BlockLoad BlockLoad; + * typedef cub::BlockStore BlockStore; + * typedef cub::BlockScan BlockScan; + * + * // Allocate aliased shared memory for BlockLoad, BlockStore, and BlockScan + * __shared__ union { + * typename BlockLoad::TempStorage load; + * typename BlockScan::TempStorage scan; + * typename BlockStore::TempStorage store; + * } temp_storage; + * + * // Initialize running total + * BlockPrefixCallbackOp prefix_op(0); + * + * // Have the block iterate over segments of items + * for (int block_offset = 0; block_offset < num_items; block_offset += 128 * 4) + * { + * // Load a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * BlockLoad(temp_storage.load).Load(d_data + block_offset, thread_data); + * __syncthreads(); + * + * // Collectively compute the block-wide inclusive prefix sum + * int block_aggregate; + * BlockScan(temp_storage.scan).IncluisveSum( + * thread_data, thread_data, block_aggregate, prefix_op); + * __syncthreads(); + * + * // Store scanned items to output segment + * BlockStore(temp_storage.store).Store(d_data + block_offset, thread_data); + * __syncthreads(); + * } + * \endcode + * \par + * Suppose the input \p d_data is 1, 1, 1, 1, 1, 1, 1, 1, .... + * The corresponding output for the first segment will be 1, 2, 3, 4, ..., 511, 512. + * The output for the second segment will be 513, 514, 515, 516, ..., 1023, 1024. Furthermore, + * the value \p 512 will be stored in \p block_aggregate for all threads after each scan. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam BlockPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T block_aggregate) + */ + template < + int ITEMS_PER_THREAD, + typename BlockPrefixCallbackOp> + __device__ __forceinline__ void InclusiveSum( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD], ///< [out] Calling thread's output items (may be aliased to \p input) + T &block_aggregate, ///< [out] block-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a block-wide prefix to be applied to all inputs. + { + if (ITEMS_PER_THREAD == 1) + { + InclusiveSum(input[0], output[0], block_aggregate, block_prefix_callback_op); + } + else + { + // Reduce consecutive thread items in registers + Sum scan_op; + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveSum(thread_partial, thread_partial, block_aggregate, block_prefix_callback_op); + + // Inclusive scan in registers with prefix + ThreadScanInclusive(input, output, scan_op, thread_partial); + } + } + + + //@} end member group + /******************************************************************//** + * \name Inclusive prefix scan operations + *********************************************************************/ + //@{ + + + /** + * \brief Computes an inclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. + * + * \par + * - Supports non-commutative scan operators. + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an inclusive prefix max scan of 128 integer items that + * are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain input item for each thread + * int thread_data; + * ... + * + * // Collectively compute the block-wide inclusive prefix max scan + * BlockScan(temp_storage).InclusiveScan(thread_data, thread_data, cub::Max()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is 0, -1, 2, -3, ..., 126, -127. The + * corresponding output \p thread_data in those threads will be 0, 0, 2, 2, ..., 126, 126. + * + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ void InclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + ScanOp scan_op) ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + { + T block_aggregate; + InclusiveScan(input, output, scan_op, block_aggregate); + } + + + /** + * \brief Computes an inclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - Supports non-commutative scan operators. + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an inclusive prefix max scan of 128 integer items that + * are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain input item for each thread + * int thread_data; + * ... + * + * // Collectively compute the block-wide inclusive prefix max scan + * int block_aggregate; + * BlockScan(temp_storage).InclusiveScan(thread_data, thread_data, cub::Max(), block_aggregate); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is 0, -1, 2, -3, ..., 126, -127. The + * corresponding output \p thread_data in those threads will be 0, 0, 2, 2, ..., 126, 126. + * Furthermore the value \p 126 will be stored in \p block_aggregate for all threads. + * + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ void InclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + T &block_aggregate) ///< [out] block-wide aggregate reduction of input items + { + InternalBlockScan(temp_storage, linear_tid).InclusiveScan(input, output, scan_op, block_aggregate); + } + + + /** + * \brief Computes an inclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - The \p block_prefix_callback_op functor must implement a member function T operator()(T block_aggregate). + * The functor's input parameter \p block_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the first warp of threads in the block, however only the return value from + * lane0 is applied as the block-wide prefix. Can be stateful. + * - Supports non-commutative scan operators. + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a single thread block that progressively + * computes an inclusive prefix max scan over multiple "tiles" of input using a + * prefix functor to maintain a running total between block-wide scans. Each tile consists + * of 128 integer items that are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * // A stateful callback functor that maintains a running prefix to be applied + * // during consecutive scan operations. + * struct BlockPrefixCallbackOp + * { + * // Running prefix + * int running_total; + * + * // Constructor + * __device__ BlockPrefixCallbackOp(int running_total) : running_total(running_total) {} + * + * // Callback operator to be entered by the first warp of threads in the block. + * // Thread-0 is responsible for returning a value for seeding the block-wide scan. + * __device__ int operator()(int block_aggregate) + * { + * int old_prefix = running_total; + * running_total = (block_aggregate > old_prefix) ? block_aggregate : old_prefix; + * return old_prefix; + * } + * }; + * + * __global__ void ExampleKernel(int *d_data, int num_items, ...) + * { + * // Specialize BlockScan for 128 threads + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Initialize running total + * BlockPrefixCallbackOp prefix_op(INT_MIN); + * + * // Have the block iterate over segments of items + * for (int block_offset = 0; block_offset < num_items; block_offset += 128) + * { + * // Load a segment of consecutive items that are blocked across threads + * int thread_data = d_data[block_offset]; + * + * // Collectively compute the block-wide inclusive prefix max scan + * int block_aggregate; + * BlockScan(temp_storage).InclusiveScan( + * thread_data, thread_data, cub::Max(), block_aggregate, prefix_op); + * __syncthreads(); + * + * // Store scanned items to output segment + * d_data[block_offset] = thread_data; + * } + * \endcode + * \par + * Suppose the input \p d_data is 0, -1, 2, -3, 4, -5, .... + * The corresponding output for the first segment will be 0, 0, 2, 2, ..., 126, 126. + * The output for the second segment will be 128, 128, 130, 130, ..., 254, 254. Furthermore, + * \p block_aggregate will be assigned \p 126 in all threads after the first scan, assigned \p 254 after the second + * scan, etc. + * + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + * \tparam BlockPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T block_aggregate) + */ + template < + typename ScanOp, + typename BlockPrefixCallbackOp> + __device__ __forceinline__ void InclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + T &block_aggregate, ///< [out] block-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a block-wide prefix to be applied to all inputs. + { + InternalBlockScan(temp_storage, linear_tid).InclusiveScan(input, output, scan_op, block_aggregate, block_prefix_callback_op); + } + + + //@} end member group + /******************************************************************//** + * \name Inclusive prefix scan operations (multiple data per thread) + *********************************************************************/ + //@{ + + + /** + * \brief Computes an inclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes an array of consecutive input elements. + * + * \par + * - Supports non-commutative scan operators. + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an inclusive prefix max scan of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Collectively compute the block-wide inclusive prefix max scan + * BlockScan(temp_storage).InclusiveScan(thread_data, thread_data, cub::Max()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is { [0,-1,2,-3], [4,-5,6,-7], ..., [508,-509,510,-511] }. The + * corresponding output \p thread_data in those threads will be { [0,0,2,2], [4,4,6,6], ..., [508,508,510,510] }. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template < + int ITEMS_PER_THREAD, + typename ScanOp> + __device__ __forceinline__ void InclusiveScan( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD], ///< [out] Calling thread's output items (may be aliased to \p input) + ScanOp scan_op) ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + { + if (ITEMS_PER_THREAD == 1) + { + InclusiveScan(input[0], output[0], scan_op); + } + else + { + // Reduce consecutive thread items in registers + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveScan(thread_partial, thread_partial, scan_op); + + // Inclusive scan in registers with prefix + ThreadScanInclusive(input, output, scan_op, thread_partial, (linear_tid != 0)); + } + } + + + /** + * \brief Computes an inclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes an array of consecutive input elements. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - Supports non-commutative scan operators. + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates an inclusive prefix max scan of 512 integer items that + * are partitioned in a [blocked arrangement](index.html#sec5sec3) across 128 threads + * where each thread owns 4 consecutive items. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(...) + * { + * // Specialize BlockScan for 128 threads on type int + * typedef cub::BlockScan BlockScan; + * + * // Allocate shared memory for BlockScan + * __shared__ typename BlockScan::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Collectively compute the block-wide inclusive prefix max scan + * int block_aggregate; + * BlockScan(temp_storage).InclusiveScan(thread_data, thread_data, cub::Max(), block_aggregate); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is + * { [0,-1,2,-3], [4,-5,6,-7], ..., [508,-509,510,-511] }. + * The corresponding output \p thread_data in those threads will be + * { [0,0,2,2], [4,4,6,6], ..., [508,508,510,510] }. + * Furthermore the value \p 510 will be stored in \p block_aggregate for all threads. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + */ + template < + int ITEMS_PER_THREAD, + typename ScanOp> + __device__ __forceinline__ void InclusiveScan( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD], ///< [out] Calling thread's output items (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + T &block_aggregate) ///< [out] block-wide aggregate reduction of input items + { + if (ITEMS_PER_THREAD == 1) + { + InclusiveScan(input[0], output[0], scan_op, block_aggregate); + } + else + { + // Reduce consecutive thread items in registers + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveScan(thread_partial, thread_partial, scan_op, block_aggregate); + + // Inclusive scan in registers with prefix + ThreadScanInclusive(input, output, scan_op, thread_partial, (linear_tid != 0)); + } + } + + + /** + * \brief Computes an inclusive block-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes an array of consecutive input elements. the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + * + * \par + * - The \p block_prefix_callback_op functor must implement a member function T operator()(T block_aggregate). + * The functor's input parameter \p block_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the first warp of threads in the block, however only the return value from + * lane0 is applied as the block-wide prefix. Can be stateful. + * - Supports non-commutative scan operators. + * - \blocked + * - \granularity + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates a single thread block that progressively + * computes an inclusive prefix max scan over multiple "tiles" of input using a + * prefix functor to maintain a running total between block-wide scans. Each tile consists + * of 128 integer items that are partitioned across 128 threads. + * \par + * \code + * #include // or equivalently + * + * // A stateful callback functor that maintains a running prefix to be applied + * // during consecutive scan operations. + * struct BlockPrefixCallbackOp + * { + * // Running prefix + * int running_total; + * + * // Constructor + * __device__ BlockPrefixCallbackOp(int running_total) : running_total(running_total) {} + * + * // Callback operator to be entered by the first warp of threads in the block. + * // Thread-0 is responsible for returning a value for seeding the block-wide scan. + * __device__ int operator()(int block_aggregate) + * { + * int old_prefix = running_total; + * running_total = (block_aggregate > old_prefix) ? block_aggregate : old_prefix; + * return old_prefix; + * } + * }; + * + * __global__ void ExampleKernel(int *d_data, int num_items, ...) + * { + * // Specialize BlockLoad, BlockStore, and BlockScan for 128 threads, 4 ints per thread + * typedef cub::BlockLoad BlockLoad; + * typedef cub::BlockStore BlockStore; + * typedef cub::BlockScan BlockScan; + * + * // Allocate aliased shared memory for BlockLoad, BlockStore, and BlockScan + * __shared__ union { + * typename BlockLoad::TempStorage load; + * typename BlockScan::TempStorage scan; + * typename BlockStore::TempStorage store; + * } temp_storage; + * + * // Initialize running total + * BlockPrefixCallbackOp prefix_op(0); + * + * // Have the block iterate over segments of items + * for (int block_offset = 0; block_offset < num_items; block_offset += 128 * 4) + * { + * // Load a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * BlockLoad(temp_storage.load).Load(d_data + block_offset, thread_data); + * __syncthreads(); + * + * // Collectively compute the block-wide inclusive prefix max scan + * int block_aggregate; + * BlockScan(temp_storage.scan).InclusiveScan( + * thread_data, thread_data, cub::Max(), block_aggregate, prefix_op); + * __syncthreads(); + * + * // Store scanned items to output segment + * BlockStore(temp_storage.store).Store(d_data + block_offset, thread_data); + * __syncthreads(); + * } + * \endcode + * \par + * Suppose the input \p d_data is 0, -1, 2, -3, 4, -5, .... + * The corresponding output for the first segment will be 0, 0, 2, 2, 4, 4, ..., 510, 510. + * The output for the second segment will be 512, 512, 514, 514, 516, 516, ..., 1022, 1022. Furthermore, + * \p block_aggregate will be assigned \p 510 in all threads after the first scan, assigned \p 1022 after the second + * scan, etc. + * + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam ScanOp [inferred] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) type having member T operator()(const T &a, const T &b) + * \tparam BlockPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T block_aggregate) + */ + template < + int ITEMS_PER_THREAD, + typename ScanOp, + typename BlockPrefixCallbackOp> + __device__ __forceinline__ void InclusiveScan( + T (&input)[ITEMS_PER_THREAD], ///< [in] Calling thread's input items + T (&output)[ITEMS_PER_THREAD], ///< [out] Calling thread's output items (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + T &block_aggregate, ///< [out] block-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a block-wide prefix to be applied to all inputs. + { + if (ITEMS_PER_THREAD == 1) + { + InclusiveScan(input[0], output[0], scan_op, block_aggregate, block_prefix_callback_op); + } + else + { + // Reduce consecutive thread items in registers + T thread_partial = ThreadReduce(input, scan_op); + + // Exclusive threadblock-scan + ExclusiveScan(thread_partial, thread_partial, scan_op, block_aggregate, block_prefix_callback_op); + + // Inclusive scan in registers with prefix + ThreadScanInclusive(input, output, scan_op, thread_partial); + } + } + + //@} end member group + + +}; + +/** + * \example example_block_scan.cu + */ + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_shift.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_shift.cuh new file mode 100644 index 0000000000000000000000000000000000000000..69089e98bde8505d06d70452675dc85971bd88f9 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_shift.cuh @@ -0,0 +1,345 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * The cub::BlockShift class provides [collective](index.html#sec0) methods for rearranging data partitioned across a CUDA thread block. + */ + +#pragma once + +#include "../util_arch.cuh" +#include "../util_macro.cuh" +#include "../util_type.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/** + * \brief The BlockShift class provides [collective](index.html#sec0) methods for shifting data partitioned across a CUDA thread block. ![](transpose_logo.png) + * \ingroup BlockModule + * + * \tparam T The data type to be exchanged. + * \tparam BLOCK_THREADS The thread block size in threads. + * + * \par Overview + * It is commonplace for blocks of threads to rearrange data items between + * threads. The BlockShift abstraction allows threads to efficiently shift items + * either (a) up to their successor or (b) down to their predecessor. + * + */ +template < + typename T, + int BLOCK_THREADS> +class BlockShift +{ +private: + + /****************************************************************************** + * Constants + ******************************************************************************/ + + enum + { + LOG_WARP_THREADS = CUB_PTX_LOG_WARP_THREADS, + WARP_THREADS = 1 << LOG_WARP_THREADS, + WARPS = (BLOCK_THREADS + CUB_PTX_WARP_THREADS - 1) / CUB_PTX_WARP_THREADS, + }; + + /****************************************************************************** + * Type definitions + ******************************************************************************/ + + /// Shared memory storage layout type +#if CUB_PTX_VERSION >= 300 + typedef T _TempStorage[WARPS]; // Kepler+ only needs smem to share between warps +#else + typedef T _TempStorage[BLOCK_THREADS]; +#endif + +public: + + /// \smemstorage{BlockShift} + struct TempStorage : Uninitialized<_TempStorage> {}; + +private: + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + /// Shared storage reference + _TempStorage &temp_storage; + + /// Linear thread-id + int linear_tid; + int warp_lane; + int warp_id; + + + /****************************************************************************** + * Utility methods + ******************************************************************************/ + + /// Internal storage allocator + __device__ __forceinline__ _TempStorage& PrivateStorage() + { + __shared__ _TempStorage private_storage; + return private_storage; + } + + +public: + + /******************************************************************//** + * \name Collective constructors + *********************************************************************/ + //@{ + + /** + * \brief Collective constructor for 1D thread blocks using a private static allocation of shared memory as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockShift() + : + temp_storage(PrivateStorage()), + linear_tid(threadIdx.x), + warp_lane(linear_tid & (WARP_THREADS - 1)), + warp_id(linear_tid >> LOG_WARP_THREADS) + {} + + + /** + * \brief Collective constructor for 1D thread blocks using the specified memory allocation as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockShift( + TempStorage &temp_storage) ///< [in] Reference to memory allocation having layout type TempStorage + : + temp_storage(temp_storage.Alias()), + linear_tid(threadIdx.x), + warp_lane(linear_tid & (WARP_THREADS - 1)), + warp_id(linear_tid >> LOG_WARP_THREADS) + {} + + + /** + * \brief Collective constructor using a private static allocation of shared memory as temporary storage. Each thread is identified using the supplied linear thread identifier + */ + __device__ __forceinline__ BlockShift( + int linear_tid) ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(PrivateStorage()), + linear_tid(linear_tid), + warp_lane(linear_tid & (WARP_THREADS - 1)), + warp_id(linear_tid >> LOG_WARP_THREADS) + {} + + + /** + * \brief Collective constructor using the specified memory allocation as temporary storage. Each thread is identified using the supplied linear thread identifier. + */ + __device__ __forceinline__ BlockShift( + TempStorage &temp_storage, ///< [in] Reference to memory allocation having layout type TempStorage + int linear_tid) ///< [in] [optional] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid), + warp_lane(linear_tid & (WARP_THREADS - 1)), + warp_id(linear_tid >> LOG_WARP_THREADS) + {} + + + //@} end member group + /******************************************************************//** + * \name Shift exchanges + *********************************************************************/ + //@{ + + + /** + * \brief Each thread obtains the \p input provided by its predecessor. The first thread receives \p block_prefix. + * + * \par + * - \smemreuse + */ + __device__ __forceinline__ void Up( + T input, ///< [in] Input item + T &output, ///< [out] Output item + T block_prefix) ///< [in] Prefix item to be provided to thread0 + { +#if CUB_PTX_VERSION >= 300 + if (warp_lane == WARP_THREADS - 1) + temp_storage[warp_id] = input; + + __syncthreads(); + + output = ShuffleUp(input, 1); + if (warp_lane == 0) + { + output = (linear_tid == 0) ? + block_prefix : + temp_storage[warp_id - 1]; + } +#else + temp_storage[linear_tid] = input; + + __syncthreads(); + + output = (linear_tid == 0) ? + block_prefix : + temp_storage[linear_tid - 1]; +#endif + } + + + /** + * \brief Each thread receives the \p input provided by its predecessor. The first thread receives \p block_prefix. All threads receive the \p input provided by threadBLOCK_THREADS-1. + * + * \par + * - \smemreuse + */ + __device__ __forceinline__ void Up( + T input, ///< [in] Input item + T &output, ///< [out] Output item + T block_prefix, ///< [in] Prefix item to be provided to thread0 + T &block_suffix) ///< [out] Suffix item shifted out by the threadBLOCK_THREADS-1 to be provided to all threads + { +#if CUB_PTX_VERSION >= 300 + if (warp_lane == WARP_THREADS - 1) + temp_storage[warp_id] = input; + + __syncthreads(); + + output = ShuffleUp(input, 1); + if (warp_lane == 0) + { + output = (linear_tid == 0) ? + block_prefix : + temp_storage[warp_id - 1]; + } + block_suffix = temp_storage[WARPS - 1]; +#else + temp_storage[linear_tid] = input; + + __syncthreads(); + + output = (linear_tid == 0) ? + block_prefix : + temp_storage[linear_tid - 1]; + + block_suffix = temp_storage[BLOCK_THREADS - 1]; +#endif + } + + + /** + * \brief Each thread obtains the \p input provided by its successor. The last thread receives \p block_suffix. + * + * \par + * - \smemreuse + */ + __device__ __forceinline__ void Down( + T input, ///< [in] Input item + T &output, ///< [out] Output item + T block_suffix) ///< [in] Suffix item to be provided to threadBLOCK_THREADS-1 + { +#if CUB_PTX_VERSION >= 300 + if (warp_lane == 0) + temp_storage[warp_id] = input; + + __syncthreads(); + + output = ShuffleDown(input, 1); + if (warp_lane == WARP_THREADS - 1) + { + output = (linear_tid == BLOCK_THREADS - 1) ? + block_suffix : + temp_storage[warp_id + 1]; + } +#else + temp_storage[linear_tid] = input; + + __syncthreads(); + + output = (linear_tid == BLOCK_THREADS - 1) ? + block_suffix : + temp_storage[linear_tid + 1]; +#endif + } + + + /** + * \brief Each thread obtains the \p input provided by its successor. The last thread receives \p block_suffix. All threads receive the \p input provided by thread0. + * + * \par + * - \smemreuse + */ + __device__ __forceinline__ void Down( + T input, ///< [in] Input item + T &output, ///< [out] Output item + T block_suffix, ///< [in] Suffix item to be provided to threadBLOCK_THREADS-1 + T &block_prefix) ///< [out] Prefix item shifted out by the thread0 to be provided to all threads + { +#if CUB_PTX_VERSION >= 300 + if (warp_lane == 0) + temp_storage[warp_id] = input; + + __syncthreads(); + + output = ShuffleDown(input, 1); + if (warp_lane == WARP_THREADS - 1) + { + output = (linear_tid == BLOCK_THREADS - 1) ? + block_suffix : + temp_storage[warp_id + 1]; + } +#else + temp_storage[linear_tid] = input; + + __syncthreads(); + + output = (linear_tid == BLOCK_THREADS - 1) ? + block_suffix : + temp_storage[linear_tid + 1]; +#endif + + block_prefix = temp_storage[0]; + } + + //@} end member group + + +}; + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_store.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_store.cuh new file mode 100644 index 0000000000000000000000000000000000000000..bfcee2e29fddd9dcba85551b31c400dc12759bfa --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/block_store.cuh @@ -0,0 +1,900 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * Operations for writing linear segments of data from the CUDA thread block + */ + +#pragma once + +#include + +#include "../util_namespace.cuh" +#include "../util_macro.cuh" +#include "../util_type.cuh" +#include "block_exchange.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/** + * \addtogroup UtilIo + * @{ + */ + + +/******************************************************************//** + * \name Blocked arrangement I/O (direct) + *********************************************************************/ +//@{ + +/** + * \brief Store a blocked arrangement of items across a thread block into a linear segment of items. + * + * \blocked + * + * \tparam T [inferred] The data type to store. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam OutputIterator [inferred] The random-access iterator type for output \iterator. + */ +template < + typename T, + int ITEMS_PER_THREAD, + typename OutputIterator> +__device__ __forceinline__ void StoreDirectBlocked( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD]) ///< [in] Data to store +{ + // Store directly in thread-blocked order + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + block_itr[(linear_tid * ITEMS_PER_THREAD) + ITEM] = items[ITEM]; + } +} + + +/** + * \brief Store a blocked arrangement of items across a thread block into a linear segment of items, guarded by range + * + * \blocked + * + * \tparam T [inferred] The data type to store. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam OutputIterator [inferred] The random-access iterator type for output \iterator. + */ +template < + typename T, + int ITEMS_PER_THREAD, + typename OutputIterator> +__device__ __forceinline__ void StoreDirectBlocked( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD], ///< [in] Data to store + int valid_items) ///< [in] Number of valid items to write +{ + // Store directly in thread-blocked order + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + if (ITEM + (linear_tid * ITEMS_PER_THREAD) < valid_items) + { + block_itr[(linear_tid * ITEMS_PER_THREAD) + ITEM] = items[ITEM]; + } + } +} + + +/** + * \brief Store a blocked arrangement of items across a thread block into a linear segment of items. + * + * \blocked + * + * The output offset (\p block_ptr + \p block_offset) must be quad-item aligned, + * which is the default starting offset returned by \p cudaMalloc() + * + * \par + * The following conditions will prevent vectorization and storing will fall back to cub::BLOCK_STORE_DIRECT: + * - \p ITEMS_PER_THREAD is odd + * - The data type \p T is not a built-in primitive or CUDA vector type (e.g., \p short, \p int2, \p double, \p float2, etc.) + * + * \tparam T [inferred] The data type to store. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * + */ +template < + typename T, + int ITEMS_PER_THREAD> +__device__ __forceinline__ void StoreDirectBlockedVectorized( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + T *block_ptr, ///< [in] Input pointer for storing from + T (&items)[ITEMS_PER_THREAD]) ///< [in] Data to store +{ + enum + { + // Maximum CUDA vector size is 4 elements + MAX_VEC_SIZE = CUB_MIN(4, ITEMS_PER_THREAD), + + // Vector size must be a power of two and an even divisor of the items per thread + VEC_SIZE = ((((MAX_VEC_SIZE - 1) & MAX_VEC_SIZE) == 0) && ((ITEMS_PER_THREAD % MAX_VEC_SIZE) == 0)) ? + MAX_VEC_SIZE : + 1, + + VECTORS_PER_THREAD = ITEMS_PER_THREAD / VEC_SIZE, + }; + + // Vector type + typedef typename CubVector::Type Vector; + + // Alias global pointer + Vector *block_ptr_vectors = reinterpret_cast(block_ptr); + + // Alias pointers (use "raw" array here which should get optimized away to prevent conservative PTXAS lmem spilling) + Vector raw_vector[VECTORS_PER_THREAD]; + T *raw_items = reinterpret_cast(raw_vector); + + // Copy + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + raw_items[ITEM] = items[ITEM]; + } + + // Direct-store using vector types + StoreDirectBlocked(linear_tid, block_ptr_vectors, raw_vector); +} + + + +//@} end member group +/******************************************************************//** + * \name Striped arrangement I/O (direct) + *********************************************************************/ +//@{ + + +/** + * \brief Store a striped arrangement of data across the thread block into a linear segment of items. + * + * \striped + * + * \tparam BLOCK_THREADS The thread block size in threads + * \tparam T [inferred] The data type to store. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam OutputIterator [inferred] The random-access iterator type for output \iterator. + */ +template < + int BLOCK_THREADS, + typename T, + int ITEMS_PER_THREAD, + typename OutputIterator> +__device__ __forceinline__ void StoreDirectStriped( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD]) ///< [in] Data to store +{ + // Store directly in striped order + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + block_itr[(ITEM * BLOCK_THREADS) + linear_tid] = items[ITEM]; + } +} + + +/** + * \brief Store a striped arrangement of data across the thread block into a linear segment of items, guarded by range + * + * \striped + * + * \tparam BLOCK_THREADS The thread block size in threads + * \tparam T [inferred] The data type to store. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam OutputIterator [inferred] The random-access iterator type for output \iterator. + */ +template < + int BLOCK_THREADS, + typename T, + int ITEMS_PER_THREAD, + typename OutputIterator> +__device__ __forceinline__ void StoreDirectStriped( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD], ///< [in] Data to store + int valid_items) ///< [in] Number of valid items to write +{ + // Store directly in striped order + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + if ((ITEM * BLOCK_THREADS) + linear_tid < valid_items) + { + block_itr[(ITEM * BLOCK_THREADS) + linear_tid] = items[ITEM]; + } + } +} + + + +//@} end member group +/******************************************************************//** + * \name Warp-striped arrangement I/O (direct) + *********************************************************************/ +//@{ + + +/** + * \brief Store a warp-striped arrangement of data across the thread block into a linear segment of items. + * + * \warpstriped + * + * \par Usage Considerations + * The number of threads in the thread block must be a multiple of the architecture's warp size. + * + * \tparam T [inferred] The data type to store. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam OutputIterator [inferred] The random-access iterator type for output \iterator. + */ +template < + typename T, + int ITEMS_PER_THREAD, + typename OutputIterator> +__device__ __forceinline__ void StoreDirectWarpStriped( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD]) ///< [out] Data to load +{ + int tid = linear_tid & (CUB_PTX_WARP_THREADS - 1); + int wid = linear_tid >> CUB_PTX_LOG_WARP_THREADS; + int warp_offset = wid * CUB_PTX_WARP_THREADS * ITEMS_PER_THREAD; + + // Store directly in warp-striped order + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + block_itr[warp_offset + tid + (ITEM * CUB_PTX_WARP_THREADS)] = items[ITEM]; + } +} + + +/** + * \brief Store a warp-striped arrangement of data across the thread block into a linear segment of items, guarded by range + * + * \warpstriped + * + * \par Usage Considerations + * The number of threads in the thread block must be a multiple of the architecture's warp size. + * + * \tparam T [inferred] The data type to store. + * \tparam ITEMS_PER_THREAD [inferred] The number of consecutive items partitioned onto each thread. + * \tparam OutputIterator [inferred] The random-access iterator type for output \iterator. + */ +template < + typename T, + int ITEMS_PER_THREAD, + typename OutputIterator> +__device__ __forceinline__ void StoreDirectWarpStriped( + int linear_tid, ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD], ///< [in] Data to store + int valid_items) ///< [in] Number of valid items to write +{ + int tid = linear_tid & (CUB_PTX_WARP_THREADS - 1); + int wid = linear_tid >> CUB_PTX_LOG_WARP_THREADS; + int warp_offset = wid * CUB_PTX_WARP_THREADS * ITEMS_PER_THREAD; + + // Store directly in warp-striped order + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + if (warp_offset + tid + (ITEM * CUB_PTX_WARP_THREADS) < valid_items) + { + block_itr[warp_offset + tid + (ITEM * CUB_PTX_WARP_THREADS)] = items[ITEM]; + } + } +} + + +//@} end member group + + +/** @} */ // end group UtilIo + + +//----------------------------------------------------------------------------- +// Generic BlockStore abstraction +//----------------------------------------------------------------------------- + +/** + * \brief cub::BlockStoreAlgorithm enumerates alternative algorithms for cub::BlockStore to write a blocked arrangement of items across a CUDA thread block to a linear segment of memory. + */ +enum BlockStoreAlgorithm +{ + /** + * \par Overview + * + * A [blocked arrangement](index.html#sec5sec3) of data is written + * directly to memory. The thread block writes items in a parallel "raking" fashion: + * threadi writes the ith segment of consecutive elements. + * + * \par Performance Considerations + * - The utilization of memory transactions (coalescing) decreases as the + * access stride between threads increases (i.e., the number items per thread). + */ + BLOCK_STORE_DIRECT, + + /** + * \par Overview + * + * A [blocked arrangement](index.html#sec5sec3) of data is written directly + * to memory using CUDA's built-in vectorized stores as a coalescing optimization. + * The thread block writes items in a parallel "raking" fashion: threadi uses vector stores to + * write the ith segment of consecutive elements. + * + * For example, st.global.v4.s32 instructions will be generated when \p T = \p int and \p ITEMS_PER_THREAD > 4. + * + * \par Performance Considerations + * - The utilization of memory transactions (coalescing) remains high until the the + * access stride between threads (i.e., the number items per thread) exceeds the + * maximum vector store width (typically 4 items or 64B, whichever is lower). + * - The following conditions will prevent vectorization and writing will fall back to cub::BLOCK_STORE_DIRECT: + * - \p ITEMS_PER_THREAD is odd + * - The \p OutputIterator is not a simple pointer type + * - The block output offset is not quadword-aligned + * - The data type \p T is not a built-in primitive or CUDA vector type (e.g., \p short, \p int2, \p double, \p float2, etc.) + */ + BLOCK_STORE_VECTORIZE, + + /** + * \par Overview + * A [blocked arrangement](index.html#sec5sec3) is locally + * transposed into a [striped arrangement](index.html#sec5sec3) + * which is then written to memory. More specifically, cub::BlockExchange + * used to locally reorder the items into a + * [striped arrangement](index.html#sec5sec3), after which the + * thread block writes items in a parallel "strip-mining" fashion: consecutive + * items owned by threadi are written to memory with + * stride \p BLOCK_THREADS between them. + * + * \par Performance Considerations + * - The utilization of memory transactions (coalescing) remains high regardless + * of items written per thread. + * - The local reordering incurs slightly longer latencies and throughput than the + * direct cub::BLOCK_STORE_DIRECT and cub::BLOCK_STORE_VECTORIZE alternatives. + */ + BLOCK_STORE_TRANSPOSE, + + /** + * \par Overview + * A [blocked arrangement](index.html#sec5sec3) is locally + * transposed into a [warp-striped arrangement](index.html#sec5sec3) + * which is then written to memory. More specifically, cub::BlockExchange used + * to locally reorder the items into a + * [warp-striped arrangement](index.html#sec5sec3), after which + * each warp writes its own contiguous segment in a parallel "strip-mining" fashion: + * consecutive items owned by lanei are written to memory + * with stride \p WARP_THREADS between them. + * + * \par Performance Considerations + * - The utilization of memory transactions (coalescing) remains high regardless + * of items written per thread. + * - The local reordering incurs slightly longer latencies and throughput than the + * direct cub::BLOCK_STORE_DIRECT and cub::BLOCK_STORE_VECTORIZE alternatives. + */ + BLOCK_STORE_WARP_TRANSPOSE, +}; + + +/** + * \brief The BlockStore class provides [collective](index.html#sec0) data movement methods for writing a [blocked arrangement](index.html#sec5sec3) of items partitioned across a CUDA thread block to a linear segment of memory. ![](block_store_logo.png) + * \ingroup BlockModule + * \ingroup UtilIo + * + * \tparam OutputIterator The input iterator type \iterator. + * \tparam BLOCK_THREADS The thread block size in threads. + * \tparam ITEMS_PER_THREAD The number of consecutive items partitioned onto each thread. + * \tparam ALGORITHM [optional] cub::BlockStoreAlgorithm tuning policy enumeration. default: cub::BLOCK_STORE_DIRECT. + * \tparam WARP_TIME_SLICING [optional] Whether or not only one warp's worth of shared memory should be allocated and time-sliced among block-warps during any load-related data transpositions (versus each warp having its own storage). (default: false) + * + * \par Overview + * - The BlockStore class provides a single data movement abstraction that can be specialized + * to implement different cub::BlockStoreAlgorithm strategies. This facilitates different + * performance policies for different architectures, data types, granularity sizes, etc. + * - BlockStore can be optionally specialized by different data movement strategies: + * -# cub::BLOCK_STORE_DIRECT. A [blocked arrangement](index.html#sec5sec3) of data is written + * directly to memory. [More...](\ref cub::BlockStoreAlgorithm) + * -# cub::BLOCK_STORE_VECTORIZE. A [blocked arrangement](index.html#sec5sec3) + * of data is written directly to memory using CUDA's built-in vectorized stores as a + * coalescing optimization. [More...](\ref cub::BlockStoreAlgorithm) + * -# cub::BLOCK_STORE_TRANSPOSE. A [blocked arrangement](index.html#sec5sec3) + * is locally transposed into a [striped arrangement](index.html#sec5sec3) which is + * then written to memory. [More...](\ref cub::BlockStoreAlgorithm) + * -# cub::BLOCK_STORE_WARP_TRANSPOSE. A [blocked arrangement](index.html#sec5sec3) + * is locally transposed into a [warp-striped arrangement](index.html#sec5sec3) which is + * then written to memory. [More...](\ref cub::BlockStoreAlgorithm) + * + * \par A Simple Example + * \blockcollective{BlockStore} + * \par + * The code snippet below illustrates the storing of a "blocked" arrangement + * of 512 integers across 128 threads (where each thread owns 4 consecutive items) + * into a linear segment of memory. The store is specialized for \p BLOCK_STORE_WARP_TRANSPOSE, + * meaning items are locally reordered among threads so that memory references will be + * efficiently coalesced using a warp-striped access pattern. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(int *d_data, ...) + * { + * // Specialize BlockStore for 128 threads owning 4 integer items each + * typedef cub::BlockStore BlockStore; + * + * // Allocate shared memory for BlockStore + * __shared__ typename BlockStore::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Store items to linear memory + * int thread_data[4]; + * BlockStore(temp_storage).Store(d_data, thread_data); + * + * \endcode + * \par + * Suppose the set of \p thread_data across the block of threads is + * { [0,1,2,3], [4,5,6,7], ..., [508,509,510,511] }. + * The output \p d_data will be 0, 1, 2, 3, 4, 5, .... + * + */ +template < + typename OutputIterator, + int BLOCK_THREADS, + int ITEMS_PER_THREAD, + BlockStoreAlgorithm ALGORITHM = BLOCK_STORE_DIRECT, + bool WARP_TIME_SLICING = false> +class BlockStore +{ +private: + /****************************************************************************** + * Constants and typed definitions + ******************************************************************************/ + + // Data type of input iterator + typedef typename std::iterator_traits::value_type T; + + + /****************************************************************************** + * Algorithmic variants + ******************************************************************************/ + + /// Store helper + template + struct StoreInternal; + + + /** + * BLOCK_STORE_DIRECT specialization of store helper + */ + template + struct StoreInternal + { + /// Shared memory storage layout type + typedef NullType TempStorage; + + /// Linear thread-id + int linear_tid; + + /// Constructor + __device__ __forceinline__ StoreInternal( + TempStorage &temp_storage, + int linear_tid) + : + linear_tid(linear_tid) + {} + + /// Store items into a linear segment of memory + __device__ __forceinline__ void Store( + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD]) ///< [in] Data to store + { + StoreDirectBlocked(linear_tid, block_itr, items); + } + + /// Store items into a linear segment of memory, guarded by range + __device__ __forceinline__ void Store( + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD], ///< [in] Data to store + int valid_items) ///< [in] Number of valid items to write + { + StoreDirectBlocked(linear_tid, block_itr, items, valid_items); + } + }; + + + /** + * BLOCK_STORE_VECTORIZE specialization of store helper + */ + template + struct StoreInternal + { + /// Shared memory storage layout type + typedef NullType TempStorage; + + /// Linear thread-id + int linear_tid; + + /// Constructor + __device__ __forceinline__ StoreInternal( + TempStorage &temp_storage, + int linear_tid) + : + linear_tid(linear_tid) + {} + + /// Store items into a linear segment of memory, specialized for native pointer types (attempts vectorization) + __device__ __forceinline__ void Store( + T *block_ptr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD]) ///< [in] Data to store + { + StoreDirectBlockedVectorized(linear_tid, block_ptr, items); + } + + /// Store items into a linear segment of memory, specialized for opaque input iterators (skips vectorization) + template + __device__ __forceinline__ void Store( + _OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD]) ///< [in] Data to store + { + StoreDirectBlocked(linear_tid, block_itr, items); + } + + /// Store items into a linear segment of memory, guarded by range + __device__ __forceinline__ void Store( + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD], ///< [in] Data to store + int valid_items) ///< [in] Number of valid items to write + { + StoreDirectBlocked(linear_tid, block_itr, items, valid_items); + } + }; + + + /** + * BLOCK_STORE_TRANSPOSE specialization of store helper + */ + template + struct StoreInternal + { + // BlockExchange utility type for keys + typedef BlockExchange BlockExchange; + + /// Shared memory storage layout type + typedef typename BlockExchange::TempStorage _TempStorage; + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + /// Thread reference to shared storage + _TempStorage &temp_storage; + + /// Linear thread-id + int linear_tid; + + /// Constructor + __device__ __forceinline__ StoreInternal( + TempStorage &temp_storage, + int linear_tid) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + /// Store items into a linear segment of memory + __device__ __forceinline__ void Store( + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD]) ///< [in] Data to store + { + BlockExchange(temp_storage).BlockedToStriped(items); + StoreDirectStriped(linear_tid, block_itr, items); + } + + /// Store items into a linear segment of memory, guarded by range + __device__ __forceinline__ void Store( + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD], ///< [in] Data to store + int valid_items) ///< [in] Number of valid items to write + { + BlockExchange(temp_storage).BlockedToStriped(items); + StoreDirectStriped(linear_tid, block_itr, items, valid_items); + } + }; + + + /** + * BLOCK_STORE_WARP_TRANSPOSE specialization of store helper + */ + template + struct StoreInternal + { + enum + { + WARP_THREADS = CUB_PTX_WARP_THREADS + }; + + // Assert BLOCK_THREADS must be a multiple of WARP_THREADS + CUB_STATIC_ASSERT((BLOCK_THREADS % WARP_THREADS == 0), "BLOCK_THREADS must be a multiple of WARP_THREADS"); + + // BlockExchange utility type for keys + typedef BlockExchange BlockExchange; + + /// Shared memory storage layout type + typedef typename BlockExchange::TempStorage _TempStorage; + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + /// Thread reference to shared storage + _TempStorage &temp_storage; + + /// Linear thread-id + int linear_tid; + + /// Constructor + __device__ __forceinline__ StoreInternal( + TempStorage &temp_storage, + int linear_tid) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + /// Store items into a linear segment of memory + __device__ __forceinline__ void Store( + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD]) ///< [in] Data to store + { + BlockExchange(temp_storage).BlockedToWarpStriped(items); + StoreDirectWarpStriped(linear_tid, block_itr, items); + } + + /// Store items into a linear segment of memory, guarded by range + __device__ __forceinline__ void Store( + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD], ///< [in] Data to store + int valid_items) ///< [in] Number of valid items to write + { + BlockExchange(temp_storage).BlockedToWarpStriped(items); + StoreDirectWarpStriped(linear_tid, block_itr, items, valid_items); + } + }; + + /****************************************************************************** + * Type definitions + ******************************************************************************/ + + /// Internal load implementation to use + typedef StoreInternal InternalStore; + + + /// Shared memory storage layout type + typedef typename InternalStore::TempStorage _TempStorage; + + + /****************************************************************************** + * Utility methods + ******************************************************************************/ + + /// Internal storage allocator + __device__ __forceinline__ _TempStorage& PrivateStorage() + { + __shared__ _TempStorage private_storage; + return private_storage; + } + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + /// Thread reference to shared storage + _TempStorage &temp_storage; + + /// Linear thread-id + int linear_tid; + +public: + + + /// \smemstorage{BlockStore} + struct TempStorage : Uninitialized<_TempStorage> {}; + + + /******************************************************************//** + * \name Collective constructors + *********************************************************************/ + //@{ + + /** + * \brief Collective constructor for 1D thread blocks using a private static allocation of shared memory as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockStore() + : + temp_storage(PrivateStorage()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor for 1D thread blocks using the specified memory allocation as temporary storage. Threads are identified using threadIdx.x. + */ + __device__ __forceinline__ BlockStore( + TempStorage &temp_storage) ///< [in] Reference to memory allocation having layout type TempStorage + : + temp_storage(temp_storage.Alias()), + linear_tid(threadIdx.x) + {} + + + /** + * \brief Collective constructor using a private static allocation of shared memory as temporary storage. Each thread is identified using the supplied linear thread identifier + */ + __device__ __forceinline__ BlockStore( + int linear_tid) ///< [in] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(PrivateStorage()), + linear_tid(linear_tid) + {} + + + /** + * \brief Collective constructor using the specified memory allocation as temporary storage. Each thread is identified using the supplied linear thread identifier. + */ + __device__ __forceinline__ BlockStore( + TempStorage &temp_storage, ///< [in] Reference to memory allocation having layout type TempStorage + int linear_tid) ///< [in] [optional] A suitable 1D thread-identifier for the calling thread (e.g., (threadIdx.y * blockDim.x) + linear_tid for 2D thread blocks) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + + //@} end member group + /******************************************************************//** + * \name Data movement + *********************************************************************/ + //@{ + + + /** + * \brief Store items into a linear segment of memory. + * + * \par + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates the storing of a "blocked" arrangement + * of 512 integers across 128 threads (where each thread owns 4 consecutive items) + * into a linear segment of memory. The store is specialized for \p BLOCK_STORE_WARP_TRANSPOSE, + * meaning items are locally reordered among threads so that memory references will be + * efficiently coalesced using a warp-striped access pattern. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(int *d_data, ...) + * { + * // Specialize BlockStore for 128 threads owning 4 integer items each + * typedef cub::BlockStore BlockStore; + * + * // Allocate shared memory for BlockStore + * __shared__ typename BlockStore::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Store items to linear memory + * int thread_data[4]; + * BlockStore(temp_storage).Store(d_data, thread_data); + * + * \endcode + * \par + * Suppose the set of \p thread_data across the block of threads is + * { [0,1,2,3], [4,5,6,7], ..., [508,509,510,511] }. + * The output \p d_data will be 0, 1, 2, 3, 4, 5, .... + * + */ + __device__ __forceinline__ void Store( + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD]) ///< [in] Data to store + { + InternalStore(temp_storage, linear_tid).Store(block_itr, items); + } + + /** + * \brief Store items into a linear segment of memory, guarded by range. + * + * \par + * - \blocked + * - \smemreuse + * + * \par Snippet + * The code snippet below illustrates the guarded storing of a "blocked" arrangement + * of 512 integers across 128 threads (where each thread owns 4 consecutive items) + * into a linear segment of memory. The store is specialized for \p BLOCK_STORE_WARP_TRANSPOSE, + * meaning items are locally reordered among threads so that memory references will be + * efficiently coalesced using a warp-striped access pattern. + * \par + * \code + * #include // or equivalently + * + * __global__ void ExampleKernel(int *d_data, int valid_items, ...) + * { + * // Specialize BlockStore for 128 threads owning 4 integer items each + * typedef cub::BlockStore BlockStore; + * + * // Allocate shared memory for BlockStore + * __shared__ typename BlockStore::TempStorage temp_storage; + * + * // Obtain a segment of consecutive items that are blocked across threads + * int thread_data[4]; + * ... + * + * // Store items to linear memory + * int thread_data[4]; + * BlockStore(temp_storage).Store(d_data, thread_data, valid_items); + * + * \endcode + * \par + * Suppose the set of \p thread_data across the block of threads is + * { [0,1,2,3], [4,5,6,7], ..., [508,509,510,511] } and \p valid_items is \p 5. + * The output \p d_data will be 0, 1, 2, 3, 4, ?, ?, ?, ..., with + * only the first two threads being unmasked to store portions of valid data. + * + */ + __device__ __forceinline__ void Store( + OutputIterator block_itr, ///< [in] The thread block's base output iterator for storing to + T (&items)[ITEMS_PER_THREAD], ///< [in] Data to store + int valid_items) ///< [in] Number of valid items to write + { + InternalStore(temp_storage, linear_tid).Store(block_itr, items, valid_items); + } +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_histogram_atomic.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_histogram_atomic.cuh new file mode 100644 index 0000000000000000000000000000000000000000..3e18ddd6de89ba49c885a70b5d3ae97237f5108d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_histogram_atomic.cuh @@ -0,0 +1,85 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * The cub::BlockHistogramAtomic class provides atomic-based methods for constructing block-wide histograms from data samples partitioned across a CUDA thread block. + */ + +#pragma once + +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \brief The BlockHistogramAtomic class provides atomic-based methods for constructing block-wide histograms from data samples partitioned across a CUDA thread block. + */ +template < + typename T, + int BLOCK_THREADS, + int ITEMS_PER_THREAD, + int BINS> +struct BlockHistogramAtomic +{ + /// Shared memory storage layout type + struct TempStorage {}; + + + /// Constructor + __device__ __forceinline__ BlockHistogramAtomic( + TempStorage &temp_storage, + int linear_tid) + {} + + + /// Composite data onto an existing histogram + template < + typename HistoCounter> + __device__ __forceinline__ void Composite( + T (&items)[ITEMS_PER_THREAD], ///< [in] Calling thread's input values to histogram + HistoCounter histogram[BINS]) ///< [out] Reference to shared/global memory histogram + { + // Update histogram + #pragma unroll + for (int i = 0; i < ITEMS_PER_THREAD; ++i) + { + atomicAdd(histogram + items[i], 1); + } + } + +}; + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_histogram_sort.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_histogram_sort.cuh new file mode 100644 index 0000000000000000000000000000000000000000..d380cdb9ba4d5795d8944190ecb02d4ff6b2c525 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_histogram_sort.cuh @@ -0,0 +1,197 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * The cub::BlockHistogramSort class provides sorting-based methods for constructing block-wide histograms from data samples partitioned across a CUDA thread block. + */ + +#pragma once + +#include "../../block/block_radix_sort.cuh" +#include "../../block/block_discontinuity.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + + +/** + * \brief The BlockHistogramSort class provides sorting-based methods for constructing block-wide histograms from data samples partitioned across a CUDA thread block. + */ +template < + typename T, + int BLOCK_THREADS, + int ITEMS_PER_THREAD, + int BINS> +struct BlockHistogramSort +{ + // Parameterize BlockRadixSort type for our thread block + typedef BlockRadixSort BlockRadixSortT; + + // Parameterize BlockDiscontinuity type for our thread block + typedef BlockDiscontinuity BlockDiscontinuityT; + + // Shared memory + union _TempStorage + { + // Storage for sorting bin values + typename BlockRadixSortT::TempStorage sort; + + struct + { + // Storage for detecting discontinuities in the tile of sorted bin values + typename BlockDiscontinuityT::TempStorage flag; + + // Storage for noting begin/end offsets of bin runs in the tile of sorted bin values + unsigned int run_begin[BINS]; + unsigned int run_end[BINS]; + }; + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + // Thread fields + _TempStorage &temp_storage; + int linear_tid; + + + /// Constructor + __device__ __forceinline__ BlockHistogramSort( + TempStorage &temp_storage, + int linear_tid) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + + // Discontinuity functor + struct DiscontinuityOp + { + // Reference to temp_storage + _TempStorage &temp_storage; + + // Constructor + __device__ __forceinline__ DiscontinuityOp(_TempStorage &temp_storage) : + temp_storage(temp_storage) + {} + + // Discontinuity predicate + __device__ __forceinline__ bool operator()(const T &a, const T &b, unsigned int b_index) + { + if (a != b) + { + // Note the begin/end offsets in shared storage + temp_storage.run_begin[b] = b_index; + temp_storage.run_end[a] = b_index; + + return true; + } + else + { + return false; + } + } + }; + + + // Composite data onto an existing histogram + template < + typename HistoCounter> + __device__ __forceinline__ void Composite( + T (&items)[ITEMS_PER_THREAD], ///< [in] Calling thread's input values to histogram + HistoCounter histogram[BINS]) ///< [out] Reference to shared/global memory histogram + { + enum { TILE_SIZE = BLOCK_THREADS * ITEMS_PER_THREAD }; + + // Sort bytes in blocked arrangement + BlockRadixSortT(temp_storage.sort, linear_tid).Sort(items); + + __syncthreads(); + + // Initialize the shared memory's run_begin and run_end for each bin + int histo_offset = 0; + + #pragma unroll + for(; histo_offset + BLOCK_THREADS <= BINS; histo_offset += BLOCK_THREADS) + { + temp_storage.run_begin[histo_offset + linear_tid] = TILE_SIZE; + temp_storage.run_end[histo_offset + linear_tid] = TILE_SIZE; + } + // Finish up with guarded initialization if necessary + if ((BINS % BLOCK_THREADS != 0) && (histo_offset + linear_tid < BINS)) + { + temp_storage.run_begin[histo_offset + linear_tid] = TILE_SIZE; + temp_storage.run_end[histo_offset + linear_tid] = TILE_SIZE; + } + + __syncthreads(); + + int flags[ITEMS_PER_THREAD]; // unused + + // Compute head flags to demarcate contiguous runs of the same bin in the sorted tile + DiscontinuityOp flag_op(temp_storage); + BlockDiscontinuityT(temp_storage.flag, linear_tid).FlagHeads(flags, items, flag_op); + + // Update begin for first item + if (linear_tid == 0) temp_storage.run_begin[items[0]] = 0; + + __syncthreads(); + + // Composite into histogram + histo_offset = 0; + + #pragma unroll + for(; histo_offset + BLOCK_THREADS <= BINS; histo_offset += BLOCK_THREADS) + { + int thread_offset = histo_offset + linear_tid; + HistoCounter count = temp_storage.run_end[thread_offset] - temp_storage.run_begin[thread_offset]; + histogram[thread_offset] += count; + } + // Finish up with guarded composition if necessary + if ((BINS % BLOCK_THREADS != 0) && (histo_offset + linear_tid < BINS)) + { + int thread_offset = histo_offset + linear_tid; + HistoCounter count = temp_storage.run_end[thread_offset] - temp_storage.run_begin[thread_offset]; + histogram[thread_offset] += count; + } + } + +}; + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_reduce_raking.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_reduce_raking.cuh new file mode 100644 index 0000000000000000000000000000000000000000..c739b6d90b563a9753090f5f84efe5309a3643b3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_reduce_raking.cuh @@ -0,0 +1,237 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockReduceRaking provides raking-based methods of parallel reduction across a CUDA thread block. Supports non-commutative reduction operators. + */ + +#pragma once + +#include "../../block/block_raking_layout.cuh" +#include "../../warp/warp_reduce.cuh" +#include "../../thread/thread_reduce.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \brief BlockReduceRaking provides raking-based methods of parallel reduction across a CUDA thread block. Supports non-commutative reduction operators. + * + * Supports non-commutative binary reduction operators. Unlike commutative + * reduction operators (e.g., addition), the application of a non-commutative + * reduction operator (e.g, string concatenation) across a sequence of inputs must + * honor the relative ordering of items and partial reductions when applying the + * reduction operator. + * + * Compared to the implementation of BlockReduceRaking (which does not support + * non-commutative operators), this implementation requires a few extra + * rounds of inter-thread communication. + */ +template < + typename T, ///< Data type being reduced + int BLOCK_THREADS> ///< The thread block size in threads +struct BlockReduceRaking +{ + /// Layout type for padded thread block raking grid + typedef BlockRakingLayout BlockRakingLayout; + + /// WarpReduce utility type + typedef typename WarpReduce::InternalWarpReduce WarpReduce; + + /// Constants + enum + { + /// Number of raking threads + RAKING_THREADS = BlockRakingLayout::RAKING_THREADS, + + /// Number of raking elements per warp synchronous raking thread + SEGMENT_LENGTH = BlockRakingLayout::SEGMENT_LENGTH, + + /// Cooperative work can be entirely warp synchronous + WARP_SYNCHRONOUS = (RAKING_THREADS == BLOCK_THREADS), + + /// Whether or not warp-synchronous reduction should be unguarded (i.e., the warp-reduction elements is a power of two + WARP_SYNCHRONOUS_UNGUARDED = PowerOfTwo::VALUE, + + /// Whether or not accesses into smem are unguarded + RAKING_UNGUARDED = BlockRakingLayout::UNGUARDED, + + }; + + + /// Shared memory storage layout type + struct _TempStorage + { + typename WarpReduce::TempStorage warp_storage; ///< Storage for warp-synchronous reduction + typename BlockRakingLayout::TempStorage raking_grid; ///< Padded threadblock raking grid + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + // Thread fields + _TempStorage &temp_storage; + int linear_tid; + + + /// Constructor + __device__ __forceinline__ BlockReduceRaking( + TempStorage &temp_storage, + int linear_tid) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + + template + __device__ __forceinline__ T RakingReduction( + ReductionOp reduction_op, ///< [in] Binary scan operator + T *raking_segment, + T partial, ///< [in] [lane0s only] Warp-wide aggregate reduction of input items + int num_valid, ///< [in] Number of valid elements (may be less than BLOCK_THREADS) + Int2Type iteration) + { + // Update partial if addend is in range + if ((FULL_TILE && RAKING_UNGUARDED) || ((linear_tid * SEGMENT_LENGTH) + ITERATION < num_valid)) + { + T addend = raking_segment[ITERATION]; + partial = reduction_op(partial, addend); + } + return RakingReduction(reduction_op, raking_segment, partial, num_valid, Int2Type()); + } + + template + __device__ __forceinline__ T RakingReduction( + ReductionOp reduction_op, ///< [in] Binary scan operator + T *raking_segment, + T partial, ///< [in] [lane0s only] Warp-wide aggregate reduction of input items + int num_valid, ///< [in] Number of valid elements (may be less than BLOCK_THREADS) + Int2Type iteration) + { + return partial; + } + + + /// Computes a threadblock-wide reduction using addition (+) as the reduction operator. The first num_valid threads each contribute one reduction partial. The return value is only valid for thread0. + template + __device__ __forceinline__ T Sum( + T partial, ///< [in] Calling thread's input partial reductions + int num_valid) ///< [in] Number of valid elements (may be less than BLOCK_THREADS) + { + cub::Sum reduction_op; + + if (WARP_SYNCHRONOUS) + { + // Short-circuit directly to warp synchronous reduction (unguarded if active threads is a power-of-two) + partial = WarpReduce(temp_storage.warp_storage, 0, linear_tid).template Sum( + partial, + num_valid); + } + else + { + // Place partial into shared memory grid. + *BlockRakingLayout::PlacementPtr(temp_storage.raking_grid, linear_tid) = partial; + + __syncthreads(); + + // Reduce parallelism to one warp + if (linear_tid < RAKING_THREADS) + { + // Raking reduction in grid + T *raking_segment = BlockRakingLayout::RakingPtr(temp_storage.raking_grid, linear_tid); + partial = raking_segment[0]; + + partial = RakingReduction(reduction_op, raking_segment, partial, num_valid, Int2Type<1>()); + + partial = WarpReduce(temp_storage.warp_storage, 0, linear_tid).template Sum( + partial, + num_valid); + } + } + + return partial; + } + + + /// Computes a threadblock-wide reduction using the specified reduction operator. The first num_valid threads each contribute one reduction partial. The return value is only valid for thread0. + template < + bool FULL_TILE, + typename ReductionOp> + __device__ __forceinline__ T Reduce( + T partial, ///< [in] Calling thread's input partial reductions + int num_valid, ///< [in] Number of valid elements (may be less than BLOCK_THREADS) + ReductionOp reduction_op) ///< [in] Binary reduction operator + { + if (WARP_SYNCHRONOUS) + { + // Short-circuit directly to warp synchronous reduction (unguarded if active threads is a power-of-two) + partial = WarpReduce(temp_storage.warp_storage, 0, linear_tid).template Reduce( + partial, + num_valid, + reduction_op); + } + else + { + // Place partial into shared memory grid. + *BlockRakingLayout::PlacementPtr(temp_storage.raking_grid, linear_tid) = partial; + + __syncthreads(); + + // Reduce parallelism to one warp + if (linear_tid < RAKING_THREADS) + { + // Raking reduction in grid + T *raking_segment = BlockRakingLayout::RakingPtr(temp_storage.raking_grid, linear_tid); + partial = raking_segment[0]; + + partial = RakingReduction(reduction_op, raking_segment, partial, num_valid, Int2Type<1>()); + + partial = WarpReduce(temp_storage.warp_storage, 0, linear_tid).template Reduce( + partial, + num_valid, + reduction_op); + } + } + + return partial; + } + +}; + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_reduce_raking_commutative_only.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_reduce_raking_commutative_only.cuh new file mode 100644 index 0000000000000000000000000000000000000000..6ab79e828172be3e93709462996d5cfdf60b89df --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_reduce_raking_commutative_only.cuh @@ -0,0 +1,189 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockReduceRakingCommutativeOnly provides raking-based methods of parallel reduction across a CUDA thread block. Does not support non-commutative reduction operators. + */ + +#pragma once + +#include "block_reduce_raking.cuh" +#include "../../warp/warp_reduce.cuh" +#include "../../thread/thread_reduce.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \brief BlockReduceRakingCommutativeOnly provides raking-based methods of parallel reduction across a CUDA thread block. Does not support non-commutative reduction operators. Does not support block sizes that are not a multiple of the warp size. + */ +template < + typename T, ///< Data type being reduced + int BLOCK_THREADS> ///< The thread block size in threads +struct BlockReduceRakingCommutativeOnly +{ + // The fall-back implementation to use when BLOCK_THREADS is not a multiple of the warp size or not all threads have valid values + typedef BlockReduceRaking FallBack; + + /// Constants + enum + { + /// Whether or not to use fall-back + USE_FALLBACK = ((BLOCK_THREADS % CUB_PTX_WARP_THREADS != 0) || (BLOCK_THREADS <= CUB_PTX_WARP_THREADS)), + + /// Number of raking threads + RAKING_THREADS = CUB_PTX_WARP_THREADS, + + /// Number of threads actually sharing items with the raking threads + SHARING_THREADS = CUB_MAX(1, BLOCK_THREADS - RAKING_THREADS), + + /// Number of raking elements per warp synchronous raking thread + SEGMENT_LENGTH = SHARING_THREADS / CUB_PTX_WARP_THREADS, + }; + + /// WarpReduce utility type + typedef WarpReduce WarpReduce; + + /// Layout type for padded thread block raking grid + typedef BlockRakingLayout BlockRakingLayout; + + /// Shared memory storage layout type + struct _TempStorage + { + union + { + struct + { + typename WarpReduce::TempStorage warp_storage; ///< Storage for warp-synchronous reduction + typename BlockRakingLayout::TempStorage raking_grid; ///< Padded threadblock raking grid + }; + typename FallBack::TempStorage fallback_storage; ///< Fall-back storage for non-commutative block scan + }; + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + // Thread fields + _TempStorage &temp_storage; + int linear_tid; + + + /// Constructor + __device__ __forceinline__ BlockReduceRakingCommutativeOnly( + TempStorage &temp_storage, + int linear_tid) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + + /// Computes a threadblock-wide reduction using addition (+) as the reduction operator. The first num_valid threads each contribute one reduction partial. The return value is only valid for thread0. + template + __device__ __forceinline__ T Sum( + T partial, ///< [in] Calling thread's input partial reductions + int num_valid) ///< [in] Number of valid elements (may be less than BLOCK_THREADS) + { + if (USE_FALLBACK || !FULL_TILE) + { + return FallBack(temp_storage.fallback_storage, linear_tid).template Sum(partial, num_valid); + } + else + { + // Place partial into shared memory grid + if (linear_tid >= RAKING_THREADS) + *BlockRakingLayout::PlacementPtr(temp_storage.raking_grid, linear_tid - RAKING_THREADS) = partial; + + __syncthreads(); + + // Reduce parallelism to one warp + if (linear_tid < RAKING_THREADS) + { + // Raking reduction in grid + T *raking_segment = BlockRakingLayout::RakingPtr(temp_storage.raking_grid, linear_tid); + partial = ThreadReduce(raking_segment, cub::Sum(), partial); + + // Warpscan + partial = WarpReduce(temp_storage.warp_storage, 0, linear_tid).Sum(partial); + } + } + + return partial; + } + + + /// Computes a threadblock-wide reduction using the specified reduction operator. The first num_valid threads each contribute one reduction partial. The return value is only valid for thread0. + template < + bool FULL_TILE, + typename ReductionOp> + __device__ __forceinline__ T Reduce( + T partial, ///< [in] Calling thread's input partial reductions + int num_valid, ///< [in] Number of valid elements (may be less than BLOCK_THREADS) + ReductionOp reduction_op) ///< [in] Binary reduction operator + { + if (USE_FALLBACK || !FULL_TILE) + { + return FallBack(temp_storage.fallback_storage, linear_tid).template Reduce(partial, num_valid, reduction_op); + } + else + { + // Place partial into shared memory grid + if (linear_tid >= RAKING_THREADS) + *BlockRakingLayout::PlacementPtr(temp_storage.raking_grid, linear_tid - RAKING_THREADS) = partial; + + __syncthreads(); + + // Reduce parallelism to one warp + if (linear_tid < RAKING_THREADS) + { + // Raking reduction in grid + T *raking_segment = BlockRakingLayout::RakingPtr(temp_storage.raking_grid, linear_tid); + partial = ThreadReduce(raking_segment, reduction_op, partial); + + // Warpscan + partial = WarpReduce(temp_storage.warp_storage, 0, linear_tid).Reduce(partial, reduction_op); + } + } + + return partial; + } + +}; + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_reduce_warp_reductions.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_reduce_warp_reductions.cuh new file mode 100644 index 0000000000000000000000000000000000000000..8e36436b5b1c58b55ec777fa7e0f7e0799606f8c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_reduce_warp_reductions.cuh @@ -0,0 +1,217 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockReduceWarpReductions provides variants of warp-reduction-based parallel reduction across a CUDA threadblock. Supports non-commutative reduction operators. + */ + +#pragma once + +#include "../../warp/warp_reduce.cuh" +#include "../../util_arch.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \brief BlockReduceWarpReductions provides variants of warp-reduction-based parallel reduction across a CUDA threadblock. Supports non-commutative reduction operators. + */ +template < + typename T, ///< Data type being reduced + int BLOCK_THREADS> ///< The thread block size in threads +struct BlockReduceWarpReductions +{ + /// Constants + enum + { + /// Number of active warps + WARPS = (BLOCK_THREADS + CUB_PTX_WARP_THREADS - 1) / CUB_PTX_WARP_THREADS, + + /// The logical warp size for warp reductions + LOGICAL_WARP_SIZE = CUB_MIN(BLOCK_THREADS, CUB_PTX_WARP_THREADS), + + /// Whether or not the logical warp size evenly divides the threadblock size + EVEN_WARP_MULTIPLE = (BLOCK_THREADS % LOGICAL_WARP_SIZE == 0) + }; + + + /// WarpReduce utility type + typedef typename WarpReduce::InternalWarpReduce WarpReduce; + + + /// Shared memory storage layout type + struct _TempStorage + { + typename WarpReduce::TempStorage warp_reduce; ///< Buffer for warp-synchronous scan + T warp_aggregates[WARPS]; ///< Shared totals from each warp-synchronous scan + T block_prefix; ///< Shared prefix for the entire threadblock + }; + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + // Thread fields + _TempStorage &temp_storage; + int linear_tid; + int warp_id; + int lane_id; + + + /// Constructor + __device__ __forceinline__ BlockReduceWarpReductions( + TempStorage &temp_storage, + int linear_tid) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid), + warp_id((BLOCK_THREADS <= CUB_PTX_WARP_THREADS) ? + 0 : + linear_tid / CUB_PTX_WARP_THREADS), + lane_id((BLOCK_THREADS <= CUB_PTX_WARP_THREADS) ? + linear_tid : + linear_tid % CUB_PTX_WARP_THREADS) + {} + + + template + __device__ __forceinline__ T ApplyWarpAggregates( + ReductionOp reduction_op, ///< [in] Binary scan operator + T warp_aggregate, ///< [in] [lane0s only] Warp-wide aggregate reduction of input items + int num_valid, ///< [in] Number of valid elements (may be less than BLOCK_THREADS) + Int2Type successor_warp) + { + if (FULL_TILE || (SUCCESSOR_WARP * LOGICAL_WARP_SIZE < num_valid)) + { + T addend = temp_storage.warp_aggregates[SUCCESSOR_WARP]; + warp_aggregate = reduction_op(warp_aggregate, addend); + } + return ApplyWarpAggregates(reduction_op, warp_aggregate, num_valid, Int2Type()); + } + + template + __device__ __forceinline__ T ApplyWarpAggregates( + ReductionOp reduction_op, ///< [in] Binary scan operator + T warp_aggregate, ///< [in] [lane0s only] Warp-wide aggregate reduction of input items + int num_valid, ///< [in] Number of valid elements (may be less than BLOCK_THREADS) + Int2Type successor_warp) + { + return warp_aggregate; + } + + + /// Returns block-wide aggregate in thread0. + template < + bool FULL_TILE, + typename ReductionOp> + __device__ __forceinline__ T ApplyWarpAggregates( + ReductionOp reduction_op, ///< [in] Binary scan operator + T warp_aggregate, ///< [in] [lane0s only] Warp-wide aggregate reduction of input items + int num_valid) ///< [in] Number of valid elements (may be less than BLOCK_THREADS) + { + // Share lane aggregates + if (lane_id == 0) + { + temp_storage.warp_aggregates[warp_id] = warp_aggregate; + } + + __syncthreads(); + + // Update total aggregate in warp 0, lane 0 + if (linear_tid == 0) + { + warp_aggregate = ApplyWarpAggregates(reduction_op, warp_aggregate, num_valid, Int2Type<1>()); + } + + return warp_aggregate; + } + + + /// Computes a threadblock-wide reduction using addition (+) as the reduction operator. The first num_valid threads each contribute one reduction partial. The return value is only valid for thread0. + template + __device__ __forceinline__ T Sum( + T input, ///< [in] Calling thread's input partial reductions + int num_valid) ///< [in] Number of valid elements (may be less than BLOCK_THREADS) + { + cub::Sum reduction_op; + unsigned int warp_offset = warp_id * LOGICAL_WARP_SIZE; + unsigned int warp_num_valid = (FULL_TILE && EVEN_WARP_MULTIPLE) ? + LOGICAL_WARP_SIZE : + (warp_offset < num_valid) ? + num_valid - warp_offset : + 0; + + // Warp reduction in every warp + T warp_aggregate = WarpReduce(temp_storage.warp_reduce, warp_id, lane_id).template Sum<(FULL_TILE && EVEN_WARP_MULTIPLE), 1>( + input, + warp_num_valid); + + // Update outputs and block_aggregate with warp-wide aggregates from lane-0s + return ApplyWarpAggregates(reduction_op, warp_aggregate, num_valid); + } + + + /// Computes a threadblock-wide reduction using the specified reduction operator. The first num_valid threads each contribute one reduction partial. The return value is only valid for thread0. + template < + bool FULL_TILE, + typename ReductionOp> + __device__ __forceinline__ T Reduce( + T input, ///< [in] Calling thread's input partial reductions + int num_valid, ///< [in] Number of valid elements (may be less than BLOCK_THREADS) + ReductionOp reduction_op) ///< [in] Binary reduction operator + { + unsigned int warp_id = (WARPS == 1) ? 0 : (linear_tid / LOGICAL_WARP_SIZE); + unsigned int warp_offset = warp_id * LOGICAL_WARP_SIZE; + unsigned int warp_num_valid = (FULL_TILE && EVEN_WARP_MULTIPLE) ? + LOGICAL_WARP_SIZE : + (warp_offset < num_valid) ? + num_valid - warp_offset : + 0; + + // Warp reduction in every warp + T warp_aggregate = WarpReduce(temp_storage.warp_reduce, warp_id, lane_id).template Reduce<(FULL_TILE && EVEN_WARP_MULTIPLE), 1>( + input, + warp_num_valid, + reduction_op); + + // Update outputs and block_aggregate with warp-wide aggregates from lane-0s + return ApplyWarpAggregates(reduction_op, warp_aggregate, num_valid); + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_scan_raking.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_scan_raking.cuh new file mode 100644 index 0000000000000000000000000000000000000000..8870015a9d1324b28d7cb6f2dcbaa42a00b8257a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_scan_raking.cuh @@ -0,0 +1,780 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + + +/** + * \file + * cub::BlockScanRaking provides variants of raking-based parallel prefix scan across a CUDA threadblock. + */ + +#pragma once + +#include "../../util_arch.cuh" +#include "../../block/block_raking_layout.cuh" +#include "../../thread/thread_reduce.cuh" +#include "../../thread/thread_scan.cuh" +#include "../../warp/warp_scan.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \brief BlockScanRaking provides variants of raking-based parallel prefix scan across a CUDA threadblock. + */ +template < + typename T, ///< Data type being scanned + int BLOCK_THREADS, ///< The thread block size in threads + bool MEMOIZE> ///< Whether or not to buffer outer raking scan partials to incur fewer shared memory reads at the expense of higher register pressure +struct BlockScanRaking +{ + /// Layout type for padded threadblock raking grid + typedef BlockRakingLayout BlockRakingLayout; + + /// Constants + enum + { + /// Number of active warps + WARPS = (BLOCK_THREADS + CUB_PTX_WARP_THREADS - 1) / CUB_PTX_WARP_THREADS, + + /// Number of raking threads + RAKING_THREADS = BlockRakingLayout::RAKING_THREADS, + + /// Number of raking elements per warp synchronous raking thread + SEGMENT_LENGTH = BlockRakingLayout::SEGMENT_LENGTH, + + /// Cooperative work can be entirely warp synchronous + WARP_SYNCHRONOUS = (BLOCK_THREADS == RAKING_THREADS), + }; + + /// WarpScan utility type + typedef WarpScan WarpScan; + + /// Shared memory storage layout type + struct _TempStorage + { + typename WarpScan::TempStorage warp_scan; ///< Buffer for warp-synchronous scan + typename BlockRakingLayout::TempStorage raking_grid; ///< Padded threadblock raking grid + T block_aggregate; ///< Block aggregate + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + // Thread fields + _TempStorage &temp_storage; + int linear_tid; + T cached_segment[SEGMENT_LENGTH]; + + + /// Constructor + __device__ __forceinline__ BlockScanRaking( + TempStorage &temp_storage, + int linear_tid) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid) + {} + + /// Templated reduction + template + __device__ __forceinline__ T GuardedReduce( + T* raking_ptr, ///< [in] Input array + ScanOp scan_op, ///< [in] Binary reduction operator + T raking_partial, ///< [in] Prefix to seed reduction with + Int2Type iteration) + { + if ((BlockRakingLayout::UNGUARDED) || (((linear_tid * SEGMENT_LENGTH) + ITERATION) < BLOCK_THREADS)) + { + T addend = raking_ptr[ITERATION]; + raking_partial = scan_op(raking_partial, addend); + } + + return GuardedReduce(raking_ptr, scan_op, raking_partial, Int2Type()); + } + + + /// Templated reduction (base case) + template + __device__ __forceinline__ T GuardedReduce( + T* raking_ptr, ///< [in] Input array + ScanOp scan_op, ///< [in] Binary reduction operator + T raking_partial, ///< [in] Prefix to seed reduction with + Int2Type iteration) + { + return raking_partial; + } + + + /// Performs upsweep raking reduction, returning the aggregate + template + __device__ __forceinline__ T Upsweep( + ScanOp scan_op) + { + T *smem_raking_ptr = BlockRakingLayout::RakingPtr(temp_storage.raking_grid, linear_tid); + + // Read data into registers + #pragma unroll + for (int i = 0; i < SEGMENT_LENGTH; i++) + { + cached_segment[i] = smem_raking_ptr[i]; + } + + T raking_partial = cached_segment[0]; + + return GuardedReduce(cached_segment, scan_op, raking_partial, Int2Type<1>()); + } + + + /// Performs exclusive downsweep raking scan + template + __device__ __forceinline__ void ExclusiveDownsweep( + ScanOp scan_op, + T raking_partial, + bool apply_prefix = true) + { + T *smem_raking_ptr = BlockRakingLayout::RakingPtr(temp_storage.raking_grid, linear_tid); + + // Read data back into registers + if (!MEMOIZE) + { + #pragma unroll + for (int i = 0; i < SEGMENT_LENGTH; i++) + { + cached_segment[i] = smem_raking_ptr[i]; + } + } + + ThreadScanExclusive(cached_segment, cached_segment, scan_op, raking_partial, apply_prefix); + + // Write data back to smem + #pragma unroll + for (int i = 0; i < SEGMENT_LENGTH; i++) + { + smem_raking_ptr[i] = cached_segment[i]; + } + } + + + /// Performs inclusive downsweep raking scan + template + __device__ __forceinline__ void InclusiveDownsweep( + ScanOp scan_op, + T raking_partial, + bool apply_prefix = true) + { + T *smem_raking_ptr = BlockRakingLayout::RakingPtr(temp_storage.raking_grid, linear_tid); + + // Read data back into registers + if (!MEMOIZE) + { + #pragma unroll + for (int i = 0; i < SEGMENT_LENGTH; i++) + { + cached_segment[i] = smem_raking_ptr[i]; + } + } + + ThreadScanInclusive(cached_segment, cached_segment, scan_op, raking_partial, apply_prefix); + + // Write data back to smem + #pragma unroll + for (int i = 0; i < SEGMENT_LENGTH; i++) + { + smem_raking_ptr[i] = cached_segment[i]; + } + } + + + /// Computes an exclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input items + T &output, ///< [out] Calling thread's output items (may be aliased to \p input) + const T &identity, ///< [in] Identity value + ScanOp scan_op, ///< [in] Binary scan operator + T &block_aggregate) ///< [out] Threadblock-wide aggregate reduction of input items + { + + if (WARP_SYNCHRONOUS) + { + // Short-circuit directly to warp scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveScan( + input, + output, + identity, + scan_op, + block_aggregate); + } + else + { + // Place thread partial into shared memory raking grid + T *placement_ptr = BlockRakingLayout::PlacementPtr(temp_storage.raking_grid, linear_tid); + *placement_ptr = input; + + __syncthreads(); + + // Reduce parallelism down to just raking threads + if (linear_tid < RAKING_THREADS) + { + // Raking upsweep reduction in grid + T raking_partial = Upsweep(scan_op); + + // Exclusive warp synchronous scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveScan( + raking_partial, + raking_partial, + identity, + scan_op, + temp_storage.block_aggregate); + + // Exclusive raking downsweep scan + ExclusiveDownsweep(scan_op, raking_partial); + } + + __syncthreads(); + + // Grab thread prefix from shared memory + output = *placement_ptr; + + // Retrieve block aggregate + block_aggregate = temp_storage.block_aggregate; + } + } + + + /// Computes an exclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + template < + typename ScanOp, + typename BlockPrefixCallbackOp> + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T identity, ///< [in] Identity value + ScanOp scan_op, ///< [in] Binary scan operator + T &block_aggregate, ///< [out] Threadblock-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a threadblock-wide prefix to be applied to all inputs. + { + if (WARP_SYNCHRONOUS) + { + // Short-circuit directly to warp scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveScan( + input, + output, + identity, + scan_op, + block_aggregate, + block_prefix_callback_op); + } + else + { + // Place thread partial into shared memory raking grid + T *placement_ptr = BlockRakingLayout::PlacementPtr(temp_storage.raking_grid, linear_tid); + *placement_ptr = input; + + __syncthreads(); + + // Reduce parallelism down to just raking threads + if (linear_tid < RAKING_THREADS) + { + // Raking upsweep reduction in grid + T raking_partial = Upsweep(scan_op); + + // Exclusive warp synchronous scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveScan( + raking_partial, + raking_partial, + identity, + scan_op, + temp_storage.block_aggregate, + block_prefix_callback_op); + + // Exclusive raking downsweep scan + ExclusiveDownsweep(scan_op, raking_partial); + } + + __syncthreads(); + + // Grab thread prefix from shared memory + output = *placement_ptr; + + // Retrieve block aggregate + block_aggregate = temp_storage.block_aggregate; + } + } + + + /// Computes an exclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. With no identity value, the output computed for thread0 is undefined. + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan operator + T &block_aggregate) ///< [out] Threadblock-wide aggregate reduction of input items + { + if (WARP_SYNCHRONOUS) + { + // Short-circuit directly to warp scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveScan( + input, + output, + scan_op, + block_aggregate); + } + else + { + // Place thread partial into shared memory raking grid + T *placement_ptr = BlockRakingLayout::PlacementPtr(temp_storage.raking_grid, linear_tid); + *placement_ptr = input; + + __syncthreads(); + + // Reduce parallelism down to just raking threads + if (linear_tid < RAKING_THREADS) + { + // Raking upsweep reduction in grid + T raking_partial = Upsweep(scan_op); + + // Exclusive warp synchronous scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveScan( + raking_partial, + raking_partial, + scan_op, + temp_storage.block_aggregate); + + // Exclusive raking downsweep scan + ExclusiveDownsweep(scan_op, raking_partial, (linear_tid != 0)); + } + + __syncthreads(); + + // Grab thread prefix from shared memory + output = *placement_ptr; + + // Retrieve block aggregate + block_aggregate = temp_storage.block_aggregate; + } + } + + + /// Computes an exclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + template < + typename ScanOp, + typename BlockPrefixCallbackOp> + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan operator + T &block_aggregate, ///< [out] Threadblock-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a threadblock-wide prefix to be applied to all inputs. + { + if (WARP_SYNCHRONOUS) + { + // Short-circuit directly to warp scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveScan( + input, + output, + scan_op, + block_aggregate, + block_prefix_callback_op); + } + else + { + // Place thread partial into shared memory raking grid + T *placement_ptr = BlockRakingLayout::PlacementPtr(temp_storage.raking_grid, linear_tid); + *placement_ptr = input; + + __syncthreads(); + + // Reduce parallelism down to just raking threads + if (linear_tid < RAKING_THREADS) + { + // Raking upsweep reduction in grid + T raking_partial = Upsweep(scan_op); + + // Exclusive warp synchronous scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveScan( + raking_partial, + raking_partial, + scan_op, + temp_storage.block_aggregate, + block_prefix_callback_op); + + // Exclusive raking downsweep scan + ExclusiveDownsweep(scan_op, raking_partial); + } + + __syncthreads(); + + // Grab thread prefix from shared memory + output = *placement_ptr; + + // Retrieve block aggregate + block_aggregate = temp_storage.block_aggregate; + } + } + + + /// Computes an exclusive threadblock-wide prefix scan using addition (+) as the scan operator. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. + __device__ __forceinline__ void ExclusiveSum( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T &block_aggregate) ///< [out] Threadblock-wide aggregate reduction of input items + { + if (WARP_SYNCHRONOUS) + { + // Short-circuit directly to warp scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveSum( + input, + output, + block_aggregate); + } + else + { + // Raking scan + Sum scan_op; + + // Place thread partial into shared memory raking grid + T *placement_ptr = BlockRakingLayout::PlacementPtr(temp_storage.raking_grid, linear_tid); + *placement_ptr = input; + + __syncthreads(); + + // Reduce parallelism down to just raking threads + if (linear_tid < RAKING_THREADS) + { + // Raking upsweep reduction in grid + T raking_partial = Upsweep(scan_op); + + // Exclusive warp synchronous scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveSum( + raking_partial, + raking_partial, + temp_storage.block_aggregate); + + // Exclusive raking downsweep scan + ExclusiveDownsweep(scan_op, raking_partial); + } + + __syncthreads(); + + // Grab thread prefix from shared memory + output = *placement_ptr; + + // Retrieve block aggregate + block_aggregate = temp_storage.block_aggregate; + } + } + + + /// Computes an exclusive threadblock-wide prefix scan using addition (+) as the scan operator. Each thread contributes one input element. Instead of using 0 as the threadblock-wide prefix, the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + template + __device__ __forceinline__ void ExclusiveSum( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T &block_aggregate, ///< [out] Threadblock-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a threadblock-wide prefix to be applied to all inputs. + { + if (WARP_SYNCHRONOUS) + { + // Short-circuit directly to warp scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveSum( + input, + output, + block_aggregate, + block_prefix_callback_op); + } + else + { + // Raking scan + Sum scan_op; + + // Place thread partial into shared memory raking grid + T *placement_ptr = BlockRakingLayout::PlacementPtr(temp_storage.raking_grid, linear_tid); + *placement_ptr = input; + + __syncthreads(); + + // Reduce parallelism down to just raking threads + if (linear_tid < RAKING_THREADS) + { + // Raking upsweep reduction in grid + T raking_partial = Upsweep(scan_op); + + // Exclusive warp synchronous scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveSum( + raking_partial, + raking_partial, + temp_storage.block_aggregate, + block_prefix_callback_op); + + // Exclusive raking downsweep scan + ExclusiveDownsweep(scan_op, raking_partial); + } + + __syncthreads(); + + // Grab thread prefix from shared memory + output = *placement_ptr; + + // Retrieve block aggregate + block_aggregate = temp_storage.block_aggregate; + } + } + + + /// Computes an inclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. + template + __device__ __forceinline__ void InclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan operator + T &block_aggregate) ///< [out] Threadblock-wide aggregate reduction of input items + { + if (WARP_SYNCHRONOUS) + { + // Short-circuit directly to warp scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).InclusiveScan( + input, + output, + scan_op, + block_aggregate); + } + else + { + // Place thread partial into shared memory raking grid + T *placement_ptr = BlockRakingLayout::PlacementPtr(temp_storage.raking_grid, linear_tid); + *placement_ptr = input; + + __syncthreads(); + + // Reduce parallelism down to just raking threads + if (linear_tid < RAKING_THREADS) + { + // Raking upsweep reduction in grid + T raking_partial = Upsweep(scan_op); + + // Exclusive warp synchronous scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveScan( + raking_partial, + raking_partial, + scan_op, + temp_storage.block_aggregate); + + // Inclusive raking downsweep scan + InclusiveDownsweep(scan_op, raking_partial, (linear_tid != 0)); + } + + __syncthreads(); + + // Grab thread prefix from shared memory + output = *placement_ptr; + + // Retrieve block aggregate + block_aggregate = temp_storage.block_aggregate; + } + } + + + /// Computes an inclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + template < + typename ScanOp, + typename BlockPrefixCallbackOp> + __device__ __forceinline__ void InclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan operator + T &block_aggregate, ///< [out] Threadblock-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a threadblock-wide prefix to be applied to all inputs. + { + if (WARP_SYNCHRONOUS) + { + // Short-circuit directly to warp scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).InclusiveScan( + input, + output, + scan_op, + block_aggregate, + block_prefix_callback_op); + } + else + { + // Place thread partial into shared memory raking grid + T *placement_ptr = BlockRakingLayout::PlacementPtr(temp_storage.raking_grid, linear_tid); + *placement_ptr = input; + + __syncthreads(); + + // Reduce parallelism down to just raking threads + if (linear_tid < RAKING_THREADS) + { + // Raking upsweep reduction in grid + T raking_partial = Upsweep(scan_op); + + // Warp synchronous scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveScan( + raking_partial, + raking_partial, + scan_op, + temp_storage.block_aggregate, + block_prefix_callback_op); + + // Inclusive raking downsweep scan + InclusiveDownsweep(scan_op, raking_partial); + } + + __syncthreads(); + + // Grab thread prefix from shared memory + output = *placement_ptr; + + // Retrieve block aggregate + block_aggregate = temp_storage.block_aggregate; + } + } + + + /// Computes an inclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T &block_aggregate) ///< [out] Threadblock-wide aggregate reduction of input items + { + if (WARP_SYNCHRONOUS) + { + // Short-circuit directly to warp scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).InclusiveSum( + input, + output, + block_aggregate); + } + else + { + // Raking scan + Sum scan_op; + + // Place thread partial into shared memory raking grid + T *placement_ptr = BlockRakingLayout::PlacementPtr(temp_storage.raking_grid, linear_tid); + *placement_ptr = input; + + __syncthreads(); + + // Reduce parallelism down to just raking threads + if (linear_tid < RAKING_THREADS) + { + // Raking upsweep reduction in grid + T raking_partial = Upsweep(scan_op); + + // Exclusive warp synchronous scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveSum( + raking_partial, + raking_partial, + temp_storage.block_aggregate); + + // Inclusive raking downsweep scan + InclusiveDownsweep(scan_op, raking_partial, (linear_tid != 0)); + } + + __syncthreads(); + + // Grab thread prefix from shared memory + output = *placement_ptr; + + // Retrieve block aggregate + block_aggregate = temp_storage.block_aggregate; + } + } + + + /// Computes an inclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. Instead of using 0 as the threadblock-wide prefix, the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + template + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T &block_aggregate, ///< [out] Threadblock-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a threadblock-wide prefix to be applied to all inputs. + { + if (WARP_SYNCHRONOUS) + { + // Short-circuit directly to warp scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).InclusiveSum( + input, + output, + block_aggregate, + block_prefix_callback_op); + } + else + { + // Raking scan + Sum scan_op; + + // Place thread partial into shared memory raking grid + T *placement_ptr = BlockRakingLayout::PlacementPtr(temp_storage.raking_grid, linear_tid); + *placement_ptr = input; + + __syncthreads(); + + // Reduce parallelism down to just raking threads + if (linear_tid < RAKING_THREADS) + { + // Raking upsweep reduction in grid + T raking_partial = Upsweep(scan_op); + + // Warp synchronous scan + WarpScan(temp_storage.warp_scan, 0, linear_tid).ExclusiveSum( + raking_partial, + raking_partial, + temp_storage.block_aggregate, + block_prefix_callback_op); + + // Inclusive raking downsweep scan + InclusiveDownsweep(scan_op, raking_partial); + } + + __syncthreads(); + + // Grab thread prefix from shared memory + output = *placement_ptr; + + // Retrieve block aggregate + block_aggregate = temp_storage.block_aggregate; + } + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_scan_warp_scans.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_scan_warp_scans.cuh new file mode 100644 index 0000000000000000000000000000000000000000..aed114c690b118c893f3ac965c3f08d51b7b177d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/block/specializations/block_scan_warp_scans.cuh @@ -0,0 +1,363 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockScanWarpscans provides warpscan-based variants of parallel prefix scan across a CUDA threadblock. + */ + +#pragma once + +#include "../../util_arch.cuh" +#include "../../warp/warp_scan.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/** + * \brief BlockScanWarpScans provides warpscan-based variants of parallel prefix scan across a CUDA threadblock. + */ +template < + typename T, + int BLOCK_THREADS> +struct BlockScanWarpScans +{ + /// Constants + enum + { + /// Number of active warps + WARPS = (BLOCK_THREADS + CUB_PTX_WARP_THREADS - 1) / CUB_PTX_WARP_THREADS, + }; + + /// WarpScan utility type + typedef WarpScan WarpScan; + + /// Shared memory storage layout type + struct _TempStorage + { + typename WarpScan::TempStorage warp_scan; ///< Buffer for warp-synchronous scan + T warp_aggregates[WARPS]; ///< Shared totals from each warp-synchronous scan + T block_prefix; ///< Shared prefix for the entire threadblock + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + // Thread fields + _TempStorage &temp_storage; + int linear_tid; + int warp_id; + int lane_id; + + + /// Constructor + __device__ __forceinline__ BlockScanWarpScans( + TempStorage &temp_storage, + int linear_tid) + : + temp_storage(temp_storage.Alias()), + linear_tid(linear_tid), + warp_id((BLOCK_THREADS <= CUB_PTX_WARP_THREADS) ? + 0 : + linear_tid / CUB_PTX_WARP_THREADS), + lane_id((BLOCK_THREADS <= CUB_PTX_WARP_THREADS) ? + linear_tid : + linear_tid % CUB_PTX_WARP_THREADS) + {} + + + /// Update the calling thread's partial reduction with the warp-wide aggregates from preceding warps. Also returns block-wide aggregate in thread0. + template + __device__ __forceinline__ void ApplyWarpAggregates( + T &partial, ///< [out] The calling thread's partial reduction + ScanOp scan_op, ///< [in] Binary scan operator + T warp_aggregate, ///< [in] [lane0s only] Warp-wide aggregate reduction of input items + T &block_aggregate, ///< [out] Threadblock-wide aggregate reduction of input items + bool lane_valid = true) ///< [in] Whether or not the partial belonging to the current thread is valid + { + // Share lane aggregates + temp_storage.warp_aggregates[warp_id] = warp_aggregate; + + __syncthreads(); + + block_aggregate = temp_storage.warp_aggregates[0]; + + #pragma unroll + for (int WARP = 1; WARP < WARPS; WARP++) + { + T inclusive = scan_op(block_aggregate, partial); + if (warp_id == WARP) + { + partial = (lane_valid) ? + inclusive : + block_aggregate; + } + + block_aggregate = scan_op(block_aggregate, temp_storage.warp_aggregates[WARP]); + } + } + + + /// Computes an exclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input items + T &output, ///< [out] Calling thread's output items (may be aliased to \p input) + const T &identity, ///< [in] Identity value + ScanOp scan_op, ///< [in] Binary scan operator + T &block_aggregate) ///< [out] Threadblock-wide aggregate reduction of input items + { + T warp_aggregate; + WarpScan(temp_storage.warp_scan, warp_id, lane_id).ExclusiveScan(input, output, identity, scan_op, warp_aggregate); + + // Update outputs and block_aggregate with warp-wide aggregates + ApplyWarpAggregates(output, scan_op, warp_aggregate, block_aggregate); + } + + + /// Computes an exclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + template < + typename ScanOp, + typename BlockPrefixCallbackOp> + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T identity, ///< [in] Identity value + ScanOp scan_op, ///< [in] Binary scan operator + T &block_aggregate, ///< [out] Threadblock-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a threadblock-wide prefix to be applied to all inputs. + { + ExclusiveScan(input, output, identity, scan_op, block_aggregate); + + // Compute and share threadblock prefix + if (warp_id == 0) + { + T block_prefix = block_prefix_callback_op(block_aggregate); + if (lane_id == 0) + { + temp_storage.block_prefix = block_prefix; + } + } + + __syncthreads(); + + // Incorporate threadblock prefix into outputs + output = scan_op(temp_storage.block_prefix, output); + } + + + /// Computes an exclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. With no identity value, the output computed for thread0 is undefined. + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan operator + T &block_aggregate) ///< [out] Threadblock-wide aggregate reduction of input items + { + T warp_aggregate; + WarpScan(temp_storage.warp_scan, warp_id, lane_id).ExclusiveScan(input, output, scan_op, warp_aggregate); + + // Update outputs and block_aggregate with warp-wide aggregates + ApplyWarpAggregates(output, scan_op, warp_aggregate, block_aggregate, (lane_id > 0)); + } + + + /// Computes an exclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + template < + typename ScanOp, + typename BlockPrefixCallbackOp> + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan operator + T &block_aggregate, ///< [out] Threadblock-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a threadblock-wide prefix to be applied to all inputs. + { + ExclusiveScan(input, output, scan_op, block_aggregate); + + // Compute and share threadblock prefix + if (warp_id == 0) + { + T block_prefix = block_prefix_callback_op(block_aggregate); + if (lane_id == 0) + { + temp_storage.block_prefix = block_prefix; + } + } + + __syncthreads(); + + // Incorporate threadblock prefix into outputs + output = (linear_tid == 0) ? + temp_storage.block_prefix : + scan_op(temp_storage.block_prefix, output); + } + + + /// Computes an exclusive threadblock-wide prefix scan using addition (+) as the scan operator. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. + __device__ __forceinline__ void ExclusiveSum( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T &block_aggregate) ///< [out] Threadblock-wide aggregate reduction of input items + { + T warp_aggregate; + WarpScan(temp_storage.warp_scan, warp_id, lane_id).ExclusiveSum(input, output, warp_aggregate); + + // Update outputs and block_aggregate with warp-wide aggregates from lane-0s + ApplyWarpAggregates(output, Sum(), warp_aggregate, block_aggregate); + } + + + /// Computes an exclusive threadblock-wide prefix scan using addition (+) as the scan operator. Each thread contributes one input element. Instead of using 0 as the threadblock-wide prefix, the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + template + __device__ __forceinline__ void ExclusiveSum( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T &block_aggregate, ///< [out] Threadblock-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a threadblock-wide prefix to be applied to all inputs. + { + ExclusiveSum(input, output, block_aggregate); + + // Compute and share threadblock prefix + if (warp_id == 0) + { + T block_prefix = block_prefix_callback_op(block_aggregate); + if (lane_id == 0) + { + temp_storage.block_prefix = block_prefix; + } + } + + __syncthreads(); + + // Incorporate threadblock prefix into outputs + Sum scan_op; + output = scan_op(temp_storage.block_prefix, output); + } + + + /// Computes an inclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. + template + __device__ __forceinline__ void InclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan operator + T &block_aggregate) ///< [out] Threadblock-wide aggregate reduction of input items + { + T warp_aggregate; + WarpScan(temp_storage.warp_scan, warp_id, lane_id).InclusiveScan(input, output, scan_op, warp_aggregate); + + // Update outputs and block_aggregate with warp-wide aggregates from lane-0s + ApplyWarpAggregates(output, scan_op, warp_aggregate, block_aggregate); + + } + + + /// Computes an inclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + template < + typename ScanOp, + typename BlockPrefixCallbackOp> + __device__ __forceinline__ void InclusiveScan( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + ScanOp scan_op, ///< [in] Binary scan operator + T &block_aggregate, ///< [out] Threadblock-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a threadblock-wide prefix to be applied to all inputs. + { + InclusiveScan(input, output, scan_op, block_aggregate); + + // Compute and share threadblock prefix + if (warp_id == 0) + { + T block_prefix = block_prefix_callback_op(block_aggregate); + if (lane_id == 0) + { + temp_storage.block_prefix = block_prefix; + } + } + + __syncthreads(); + + // Incorporate threadblock prefix into outputs + output = scan_op(temp_storage.block_prefix, output); + } + + + /// Computes an inclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. Also provides every thread with the block-wide \p block_aggregate of all inputs. + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T &block_aggregate) ///< [out] Threadblock-wide aggregate reduction of input items + { + T warp_aggregate; + WarpScan(temp_storage.warp_scan, warp_id, lane_id).InclusiveSum(input, output, warp_aggregate); + + // Update outputs and block_aggregate with warp-wide aggregates from lane-0s + ApplyWarpAggregates(output, Sum(), warp_aggregate, block_aggregate); + } + + + /// Computes an inclusive threadblock-wide prefix scan using the specified binary \p scan_op functor. Each thread contributes one input element. Instead of using 0 as the threadblock-wide prefix, the call-back functor \p block_prefix_callback_op is invoked by the first warp in the block, and the value returned by lane0 in that warp is used as the "seed" value that logically prefixes the threadblock's scan inputs. Also provides every thread with the block-wide \p block_aggregate of all inputs. + template + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item + T &output, ///< [out] Calling thread's output item (may be aliased to \p input) + T &block_aggregate, ///< [out] Threadblock-wide aggregate reduction of input items (exclusive of the \p block_prefix_callback_op value) + BlockPrefixCallbackOp &block_prefix_callback_op) ///< [in-out] [warp0 only] Call-back functor for specifying a threadblock-wide prefix to be applied to all inputs. + { + InclusiveSum(input, output, block_aggregate); + + // Compute and share threadblock prefix + if (warp_id == 0) + { + T block_prefix = block_prefix_callback_op(block_aggregate); + if (lane_id == 0) + { + temp_storage.block_prefix = block_prefix; + } + } + + __syncthreads(); + + // Incorporate threadblock prefix into outputs + Sum scan_op; + output = scan_op(temp_storage.block_prefix, output); + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_histo_tiles.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_histo_tiles.cuh new file mode 100644 index 0000000000000000000000000000000000000000..e1165d60c3d1d70066fe4414420bc9af2f170eca --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_histo_tiles.cuh @@ -0,0 +1,322 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockHistogramTiles implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram. + */ + +#pragma once + +#include + +#include "specializations/block_histo_tiles_gatomic.cuh" +#include "specializations/block_histo_tiles_satomic.cuh" +#include "specializations/block_histo_tiles_sort.cuh" +#include "../../util_type.cuh" +#include "../../grid/grid_mapping.cuh" +#include "../../grid/grid_even_share.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Algorithmic variants + ******************************************************************************/ + + +/** + * \brief BlockHistogramTilesAlgorithm enumerates alternative algorithms for BlockHistogramTiles. + */ +enum BlockHistogramTilesAlgorithm +{ + + /** + * \par Overview + * A two-kernel approach in which: + * -# Thread blocks in the first kernel aggregate their own privatized + * histograms using block-wide sorting (see BlockHistogramAlgorithm::BLOCK_HISTO_SORT). + * -# A single thread block in the second kernel reduces them into the output histogram(s). + * + * \par Performance Considerations + * Delivers consistent throughput regardless of sample bin distribution. + * + * However, because histograms are privatized in shared memory, a large + * number of bins (e.g., thousands) may adversely affect occupancy and + * performance (or even the ability to launch). + */ + GRID_HISTO_SORT, + + + /** + * \par Overview + * A two-kernel approach in which: + * -# Thread blocks in the first kernel aggregate their own privatized + * histograms using shared-memory \p atomicAdd(). + * -# A single thread block in the second kernel reduces them into the + * output histogram(s). + * + * \par Performance Considerations + * Performance is strongly tied to the hardware implementation of atomic + * addition, and may be significantly degraded for non uniformly-random + * input distributions where many concurrent updates are likely to be + * made to the same bin counter. + * + * However, because histograms are privatized in shared memory, a large + * number of bins (e.g., thousands) may adversely affect occupancy and + * performance (or even the ability to launch). + */ + GRID_HISTO_SHARED_ATOMIC, + + + /** + * \par Overview + * A single-kernel approach in which thread blocks update the output histogram(s) directly + * using global-memory \p atomicAdd(). + * + * \par Performance Considerations + * Performance is strongly tied to the hardware implementation of atomic + * addition, and may be significantly degraded for non uniformly-random + * input distributions where many concurrent updates are likely to be + * made to the same bin counter. + * + * Performance is not significantly impacted when computing histograms having large + * numbers of bins (e.g., thousands). + */ + GRID_HISTO_GLOBAL_ATOMIC, + +}; + + +/****************************************************************************** + * Tuning policy + ******************************************************************************/ + +/** + * Tuning policy for BlockHistogramTiles + */ +template < + int _BLOCK_THREADS, + int _ITEMS_PER_THREAD, + BlockHistogramTilesAlgorithm _GRID_ALGORITHM, + GridMappingStrategy _GRID_MAPPING, + int _SM_OCCUPANCY> +struct BlockHistogramTilesPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, + SM_OCCUPANCY = _SM_OCCUPANCY, + }; + + static const BlockHistogramTilesAlgorithm GRID_ALGORITHM = _GRID_ALGORITHM; + static const GridMappingStrategy GRID_MAPPING = _GRID_MAPPING; +}; + + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + + +/** + * Implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using global atomics + */ +template < + typename BlockHistogramTilesPolicy, ///< Tuning policy + int BINS, ///< Number of histogram bins per channel + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIteratorRA, ///< The input iterator type (may be a simple pointer type). Must have a value type that can be cast as an integer in the range [0..BINS-1] + typename HistoCounter, ///< Integral type for counting sample occurrences per histogram bin + typename SizeT> ///< Integer type for offsets +struct BlockHistogramTiles +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Histogram grid algorithm + static const BlockHistogramTilesAlgorithm GRID_ALGORITHM = BlockHistogramTilesPolicy::GRID_ALGORITHM; + + // Alternative internal implementation types + typedef BlockHistogramTilesSort< BlockHistogramTilesPolicy, BINS, CHANNELS, ACTIVE_CHANNELS, InputIteratorRA, HistoCounter, SizeT> BlockHistogramTilesSortT; + typedef BlockHistogramTilesSharedAtomic< BlockHistogramTilesPolicy, BINS, CHANNELS, ACTIVE_CHANNELS, InputIteratorRA, HistoCounter, SizeT> BlockHistogramTilesSharedAtomicT; + typedef BlockHistogramTilesGlobalAtomic< BlockHistogramTilesPolicy, BINS, CHANNELS, ACTIVE_CHANNELS, InputIteratorRA, HistoCounter, SizeT> BlockHistogramTilesGlobalAtomicT; + + // Internal block sweep histogram type + typedef typename If<(GRID_ALGORITHM == GRID_HISTO_SORT), + BlockHistogramTilesSortT, + typename If<(GRID_ALGORITHM == GRID_HISTO_SHARED_ATOMIC), + BlockHistogramTilesSharedAtomicT, + BlockHistogramTilesGlobalAtomicT>::Type>::Type InternalBlockDelegate; + + enum + { + TILE_ITEMS = InternalBlockDelegate::TILE_ITEMS, + }; + + + // Temporary storage type + typedef typename InternalBlockDelegate::TempStorage TempStorage; + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + // Internal block delegate + InternalBlockDelegate internal_delegate; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockHistogramTiles( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIteratorRA d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) ///< Reference to output histograms + : + internal_delegate(temp_storage, d_in, d_out_histograms) + {} + + + /** + * \brief Reduce a consecutive segment of input tiles + */ + __device__ __forceinline__ void ConsumeTiles( + SizeT block_offset, ///< [in] Threadblock begin offset (inclusive) + SizeT block_oob) ///< [in] Threadblock end offset (exclusive) + { + // Consume subsequent full tiles of input + while (block_offset + TILE_ITEMS <= block_oob) + { + internal_delegate.ConsumeTile(block_offset); + block_offset += TILE_ITEMS; + } + + // Consume a partially-full tile + if (block_offset < block_oob) + { + int valid_items = block_oob - block_offset; + internal_delegate.ConsumeTile(block_offset, valid_items); + } + + // Aggregate output + internal_delegate.AggregateOutput(); + } + + + /** + * Reduce a consecutive segment of input tiles + */ + __device__ __forceinline__ void ConsumeTiles( + SizeT num_items, ///< [in] Total number of global input items + GridEvenShare &even_share, ///< [in] GridEvenShare descriptor + GridQueue &queue, ///< [in,out] GridQueue descriptor + Int2Type is_even_share) ///< [in] Marker type indicating this is an even-share mapping + { + even_share.BlockInit(); + ConsumeTiles(even_share.block_offset, even_share.block_oob); + } + + + /** + * Dequeue and reduce tiles of items as part of a inter-block scan + */ + __device__ __forceinline__ void ConsumeTiles( + int num_items, ///< Total number of input items + GridQueue queue) ///< Queue descriptor for assigning tiles of work to thread blocks + { + // Shared block offset + __shared__ SizeT shared_block_offset; + + // We give each thread block at least one tile of input. + SizeT block_offset = blockIdx.x * TILE_ITEMS; + SizeT even_share_base = gridDim.x * TILE_ITEMS; + + // Process full tiles of input + while (block_offset + TILE_ITEMS <= num_items) + { + internal_delegate.ConsumeTile(block_offset); + + // Dequeue up to TILE_ITEMS + if (threadIdx.x == 0) + shared_block_offset = queue.Drain(TILE_ITEMS) + even_share_base; + + __syncthreads(); + + block_offset = shared_block_offset; + + __syncthreads(); + } + + // Consume a partially-full tile + if (block_offset < num_items) + { + int valid_items = num_items - block_offset; + internal_delegate.ConsumeTile(block_offset, valid_items); + } + + // Aggregate output + internal_delegate.AggregateOutput(); + } + + + /** + * Dequeue and reduce tiles of items as part of a inter-block scan + */ + __device__ __forceinline__ void ConsumeTiles( + SizeT num_items, ///< [in] Total number of global input items + GridEvenShare &even_share, ///< [in] GridEvenShare descriptor + GridQueue &queue, ///< [in,out] GridQueue descriptor + Int2Type is_dynamic) ///< [in] Marker type indicating this is a dynamic mapping + { + ConsumeTiles(num_items, queue); + } + + +}; + + + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_partition_tiles.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_partition_tiles.cuh new file mode 100644 index 0000000000000000000000000000000000000000..4597773af6382012d6771a7f7ee82d9af57c3147 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_partition_tiles.cuh @@ -0,0 +1,381 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockPartitionTiles implements a stateful abstraction of CUDA thread blocks for participating in device-wide list partitioning. + */ + +#pragma once + +#include + +#include "scan_tiles_types.cuh" +#include "../../thread/thread_operators.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_store.cuh" +#include "../../block/block_scan.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../util_vector.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Tuning policy for BlockPartitionTiles + */ +template < + int _PARTITIONS, + int _BLOCK_THREADS, + int _ITEMS_PER_THREAD, + PtxLoadModifier _LOAD_MODIFIER, + BlockScanAlgorithm _SCAN_ALGORITHM> +struct BlockPartitionTilesPolicy +{ + enum + { + PARTITIONS = _PARTITIONS, + BLOCK_THREADS = _BLOCK_THREADS, + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, + }; + + static const PtxLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; + static const BlockScanAlgorithm SCAN_ALGORITHM = _SCAN_ALGORITHM; +}; + + + +/** + * Tuple type for scanning partition membership flags + */ +template < + typename SizeT, + int PARTITIONS> +struct PartitionScanTuple; + + +/** + * Tuple type for scanning partition membership flags (specialized for 1 output partition) + */ +template +struct PartitionScanTuple : VectorHelper::Type +{ + __device__ __forceinline__ PartitionScanTuple operator+(const PartitionScanTuple &other) + { + PartitionScanTuple retval; + retval.x = x + other.x; + return retval; + } + + template + __device__ __forceinline__ void SetFlags(PredicateOp pred_op, T val) + { + this->x = pred_op(val); + } + + template + __device__ __forceinline__ void Scatter(PredicateOp pred_op, T val, OutputIteratorRA d_out, SizeT num_items) + { + if (pred_op(val)) + d_out[this->x - 1] = val; + } + +}; + + +/** + * Tuple type for scanning partition membership flags (specialized for 2 output partitions) + */ +template +struct PartitionScanTuple : VectorHelper::Type +{ + __device__ __forceinline__ PartitionScanTuple operator+(const PartitionScanTuple &other) + { + PartitionScanTuple retval; + retval.x = x + other.x; + retval.y = y + other.y; + return retval; + } + + template + __device__ __forceinline__ void SetFlags(PredicateOp pred_op, T val) + { + bool pred = pred_op(val); + this->x = pred; + this->y = !pred; + } + + template + __device__ __forceinline__ void Scatter(PredicateOp pred_op, T val, OutputIteratorRA d_out, SizeT num_items) + { + SizeT scatter_offset = (pred_op(val)) ? + this->x - 1 : + num_items - this->y; + + d_out[scatter_offset] = val; + } +}; + + + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockPartitionTiles implements a stateful abstraction of CUDA thread blocks for participating in device-wide list partitioning. + * + * Implements a single-pass "domino" strategy with adaptive prefix lookback. + */ +template < + typename BlockPartitionTilesPolicy, ///< Tuning policy + typename InputIteratorRA, ///< Input iterator type + typename OutputIteratorRA, ///< Output iterator type + typename PredicateOp, ///< Partition predicate functor type + typename SizeT> ///< Offset integer type +struct BlockPartitionTiles +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Constants + enum + { + PARTITIONS = BlockPartitionTilesPolicy::PARTITIONS, + BLOCK_THREADS = BlockPartitionTilesPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockPartitionTilesPolicy::ITEMS_PER_THREAD, + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + }; + + // Load modifier + static const PtxLoadModifier LOAD_MODIFIER = BlockPartitionTilesPolicy::LOAD_MODIFIER; + + // Data type of input iterator + typedef typename std::iterator_traits::value_type T; + + // Tuple type for scanning partition membership flags + typedef PartitionScanTuple PartitionScanTuple; + + // Tile status descriptor type + typedef ScanTileDescriptor ScanTileDescriptorT; + + // Block scan type for scanning membership flag scan_tuples + typedef BlockScan< + PartitionScanTuple, + BlockPartitionTilesPolicy::BLOCK_THREADS, + BlockPartitionTilesPolicy::SCAN_ALGORITHM> BlockScanT; + + // Callback type for obtaining inter-tile prefix during block scan + typedef DeviceScanBlockPrefixOp InterblockPrefixOp; + + // Shared memory type for this threadblock + struct TempStorage + { + typename InterblockPrefixOp::TempStorage prefix; // Smem needed for cooperative prefix callback + typename BlockScanT::TempStorage scan; // Smem needed for tile scanning + SizeT tile_idx; // Shared tile index + }; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + TempStorage &temp_storage; ///< Reference to temp_storage + InputIteratorRA d_in; ///< Input data + OutputIteratorRA d_out; ///< Output data + ScanTileDescriptorT *d_tile_status; ///< Global list of tile status + PredicateOp pred_op; ///< Unary predicate operator indicating membership in the first partition + SizeT num_items; ///< Total number of input items + + + //--------------------------------------------------------------------- + // Constructor + //--------------------------------------------------------------------- + + // Constructor + __device__ __forceinline__ + BlockPartitionTiles( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIteratorRA d_in, ///< Input data + OutputIteratorRA d_out, ///< Output data + ScanTileDescriptorT *d_tile_status, ///< Global list of tile status + PredicateOp pred_op, ///< Unary predicate operator indicating membership in the first partition + SizeT num_items) ///< Total number of input items + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + d_out(d_out), + d_tile_status(d_tile_status), + pred_op(pred_op), + num_items(num_items) + {} + + + //--------------------------------------------------------------------- + // Domino scan + //--------------------------------------------------------------------- + + /** + * Process a tile of input + */ + template + __device__ __forceinline__ void ConsumeTile( + int tile_idx, ///< Tile index + SizeT block_offset, ///< Tile offset + PartitionScanTuple &partition_ends) ///< Running total + { + T items[ITEMS_PER_THREAD]; + PartitionScanTuple scan_tuples[ITEMS_PER_THREAD]; + + // Load items + int valid_items = num_items - block_offset; + if (FULL_TILE) + LoadStriped(threadIdx.x, d_in + block_offset, items); + else + LoadStriped(threadIdx.x, d_in + block_offset, items, valid_items); + + // Prevent hoisting +// __syncthreads(); +// __threadfence_block(); + + // Set partition membership flags in scan scan_tuples + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + scan_tuples[ITEM].SetFlags(pred_op, items[ITEM]); + } + + // Perform inclusive scan over scan scan_tuples + PartitionScanTuple block_aggregate; + if (tile_idx == 0) + { + BlockScanT(temp_storage.scan).InclusiveScan(scan_tuples, scan_tuples, Sum(), block_aggregate); + partition_ends = block_aggregate; + + // Update tile status if there are successor tiles + if (FULL_TILE && (threadIdx.x == 0)) + ScanTileDescriptorT::SetPrefix(d_tile_status, block_aggregate); + } + else + { + InterblockPrefixOp prefix_op(d_tile_status, temp_storage.prefix, Sum(), tile_idx); + BlockScanT(temp_storage.scan).InclusiveScan(scan_tuples, scan_tuples, Sum(), block_aggregate, prefix_op); + partition_ends = prefix_op.inclusive_prefix; + } + + // Scatter items + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + // Scatter if not out-of-bounds + if (FULL_TILE || (threadIdx.x + (ITEM * BLOCK_THREADS) < valid_items)) + { + scan_tuples[ITEM].Scatter(pred_op, items[ITEM], d_out, num_items); + } + } + } + + + /** + * Dequeue and scan tiles of items as part of a domino scan + */ + __device__ __forceinline__ void ConsumeTiles( + GridQueue queue, ///< [in] Queue descriptor for assigning tiles of work to thread blocks + SizeT num_tiles, ///< [in] Total number of input tiles + PartitionScanTuple &partition_ends, ///< [out] Running partition end offsets + bool &is_last_tile) ///< [out] Whether or not this block handled the last tile (i.e., partition_ends is valid for the entire input) + { +#if CUB_PTX_ARCH < 200 + + // No concurrent kernels allowed and blocks are launched in increasing order, so just assign one tile per block (up to 65K blocks) + int tile_idx = blockIdx.x; + SizeT block_offset = SizeT(TILE_ITEMS) * tile_idx; + + if (block_offset + TILE_ITEMS <= num_items) + { + ConsumeTile(tile_idx, block_offset, partition_ends); + } + else if (block_offset < num_items) + { + ConsumeTile(tile_idx, block_offset, partition_ends); + } + is_last_tile = (tile_idx == num_tiles - 1); + +#else + + // Get first tile + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + int tile_idx = temp_storage.tile_idx; + SizeT block_offset = SizeT(TILE_ITEMS) * tile_idx; + + while (block_offset + TILE_ITEMS <= num_items) + { + // Consume full tile + ConsumeTile(tile_idx, block_offset, partition_ends); + is_last_tile = (tile_idx == num_tiles - 1); + + // Get next tile + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + tile_idx = temp_storage.tile_idx; + block_offset = SizeT(TILE_ITEMS) * tile_idx; + } + + // Consume a partially-full tile + if (block_offset < num_items) + { + ConsumeTile(tile_idx, block_offset, partition_ends); + is_last_tile = (tile_idx == num_tiles - 1); + } +#endif + } +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_radix_sort_downsweep_tiles.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_radix_sort_downsweep_tiles.cuh new file mode 100644 index 0000000000000000000000000000000000000000..91d628e000cc4aea06c3ee408fb1706112524529 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_radix_sort_downsweep_tiles.cuh @@ -0,0 +1,713 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * BlockRadixSortDownsweepTiles implements a stateful abstraction of CUDA thread blocks for participating in device-wide radix sort downsweep. + */ + + +#pragma once + +#include "../../thread/thread_load.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_store.cuh" +#include "../../block/block_radix_rank.cuh" +#include "../../block/block_exchange.cuh" +#include "../../util_type.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Types of scattering strategies + */ +enum RadixSortScatterAlgorithm +{ + RADIX_SORT_SCATTER_DIRECT, ///< Scatter directly from registers to global bins + RADIX_SORT_SCATTER_TWO_PHASE, ///< First scatter from registers into shared memory bins, then into global bins +}; + + +/** + * Tuning policy for BlockRadixSortDownsweepTiles + */ +template < + int _BLOCK_THREADS, ///< The number of threads per CTA + int _ITEMS_PER_THREAD, ///< The number of consecutive downsweep keys to process per thread + BlockLoadAlgorithm _LOAD_ALGORITHM, ///< The BlockLoad algorithm to use + PtxLoadModifier _LOAD_MODIFIER, ///< The PTX cache-modifier to use for loads + bool _EXCHANGE_TIME_SLICING, ///< Whether or not to time-slice key/value exchanges through shared memory to lower shared memory pressure + bool _MEMOIZE_OUTER_SCAN, ///< Whether or not to buffer outer raking scan partials to incur fewer shared memory reads at the expense of higher register pressure. See BlockScanAlgorithm::BLOCK_SCAN_RAKING_MEMOIZE for more details. + BlockScanAlgorithm _INNER_SCAN_ALGORITHM, ///< The cub::BlockScanAlgorithm algorithm to use + RadixSortScatterAlgorithm _SCATTER_ALGORITHM, ///< The scattering strategy to use + cudaSharedMemConfig _SMEM_CONFIG, ///< Shared memory bank mode (default: \p cudaSharedMemBankSizeFourByte) + int _RADIX_BITS> ///< The number of radix bits, i.e., log2(bins) +struct BlockRadixSortDownsweepTilesPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, + EXCHANGE_TIME_SLICING = _EXCHANGE_TIME_SLICING, + RADIX_BITS = _RADIX_BITS, + MEMOIZE_OUTER_SCAN = _MEMOIZE_OUTER_SCAN, + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + }; + + static const BlockLoadAlgorithm LOAD_ALGORITHM = _LOAD_ALGORITHM; + static const PtxLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; + static const BlockScanAlgorithm INNER_SCAN_ALGORITHM = _INNER_SCAN_ALGORITHM; + static const RadixSortScatterAlgorithm SCATTER_ALGORITHM = _SCATTER_ALGORITHM; + static const cudaSharedMemConfig SMEM_CONFIG = _SMEM_CONFIG; + + typedef BlockRadixSortDownsweepTilesPolicy< + BLOCK_THREADS, + ITEMS_PER_THREAD, + LOAD_ALGORITHM, + LOAD_MODIFIER, + EXCHANGE_TIME_SLICING, + MEMOIZE_OUTER_SCAN, + INNER_SCAN_ALGORITHM, + SCATTER_ALGORITHM, + SMEM_CONFIG, + CUB_MAX(1, RADIX_BITS - 1)> AltPolicy; +}; + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * CTA-wide "downsweep" abstraction for distributing keys from + * a range of input tiles. + */ +template < + typename BlockRadixSortDownsweepTilesPolicy, + typename Key, + typename Value, + typename SizeT> +struct BlockRadixSortDownsweepTiles +{ + //--------------------------------------------------------------------- + // Type definitions and constants + //--------------------------------------------------------------------- + + // Appropriate unsigned-bits representation of Key + typedef typename Traits::UnsignedBits UnsignedBits; + + static const UnsignedBits MIN_KEY = Traits::MIN_KEY; + static const UnsignedBits MAX_KEY = Traits::MAX_KEY; + + static const BlockLoadAlgorithm LOAD_ALGORITHM = BlockRadixSortDownsweepTilesPolicy::LOAD_ALGORITHM; + static const PtxLoadModifier LOAD_MODIFIER = BlockRadixSortDownsweepTilesPolicy::LOAD_MODIFIER; + static const BlockScanAlgorithm INNER_SCAN_ALGORITHM = BlockRadixSortDownsweepTilesPolicy::INNER_SCAN_ALGORITHM; + static const RadixSortScatterAlgorithm SCATTER_ALGORITHM = BlockRadixSortDownsweepTilesPolicy::SCATTER_ALGORITHM; + static const cudaSharedMemConfig SMEM_CONFIG = BlockRadixSortDownsweepTilesPolicy::SMEM_CONFIG; + + enum + { + BLOCK_THREADS = BlockRadixSortDownsweepTilesPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockRadixSortDownsweepTilesPolicy::ITEMS_PER_THREAD, + EXCHANGE_TIME_SLICING = BlockRadixSortDownsweepTilesPolicy::EXCHANGE_TIME_SLICING, + RADIX_BITS = BlockRadixSortDownsweepTilesPolicy::RADIX_BITS, + MEMOIZE_OUTER_SCAN = BlockRadixSortDownsweepTilesPolicy::MEMOIZE_OUTER_SCAN, + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + + RADIX_DIGITS = 1 << RADIX_BITS, + KEYS_ONLY = Equals::VALUE, + + WARP_THREADS = PtxArchProps::LOG_WARP_THREADS, + WARPS = (BLOCK_THREADS + WARP_THREADS - 1) / WARP_THREADS, + + BYTES_PER_SIZET = sizeof(SizeT), + LOG_BYTES_PER_SIZET = Log2::VALUE, + + LOG_SMEM_BANKS = PtxArchProps::LOG_SMEM_BANKS, + SMEM_BANKS = 1 << LOG_SMEM_BANKS, + + DIGITS_PER_SCATTER_PASS = BLOCK_THREADS / SMEM_BANKS, + SCATTER_PASSES = RADIX_DIGITS / DIGITS_PER_SCATTER_PASS, + + LOG_STORE_TXN_THREADS = LOG_SMEM_BANKS, + STORE_TXN_THREADS = 1 << LOG_STORE_TXN_THREADS, + }; + + // BlockRadixRank type + typedef BlockRadixRank< + BLOCK_THREADS, + RADIX_BITS, + MEMOIZE_OUTER_SCAN, + INNER_SCAN_ALGORITHM, + SMEM_CONFIG> BlockRadixRank; + + // BlockLoad type (keys) + typedef BlockLoad< + UnsignedBits*, + BLOCK_THREADS, + ITEMS_PER_THREAD, + LOAD_ALGORITHM, + LOAD_MODIFIER, + EXCHANGE_TIME_SLICING> BlockLoadKeys; + + // BlockLoad type (values) + typedef BlockLoad< + Value*, + BLOCK_THREADS, + ITEMS_PER_THREAD, + LOAD_ALGORITHM, + LOAD_MODIFIER, + EXCHANGE_TIME_SLICING> BlockLoadValues; + + // BlockExchange type (keys) + typedef BlockExchange< + UnsignedBits, + BLOCK_THREADS, + ITEMS_PER_THREAD, + EXCHANGE_TIME_SLICING> BlockExchangeKeys; + + // BlockExchange type (values) + typedef BlockExchange< + Value, + BLOCK_THREADS, + ITEMS_PER_THREAD, + EXCHANGE_TIME_SLICING> BlockExchangeValues; + + + /** + * Shared memory storage layout + */ + struct _TempStorage + { + SizeT relative_bin_offsets[RADIX_DIGITS + 1]; + bool short_circuit; + + union + { + typename BlockRadixRank::TempStorage ranking; + typename BlockLoadKeys::TempStorage load_keys; + typename BlockLoadValues::TempStorage load_values; + typename BlockExchangeKeys::TempStorage exchange_keys; + typename BlockExchangeValues::TempStorage exchange_values; + }; + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Thread fields + //--------------------------------------------------------------------- + + // Shared storage for this CTA + _TempStorage &temp_storage; + + // Input and output device pointers + UnsignedBits *d_keys_in; + UnsignedBits *d_keys_out; + Value *d_values_in; + Value *d_values_out; + + // The global scatter base offset for each digit (valid in the first RADIX_DIGITS threads) + SizeT bin_offset; + + // The least-significant bit position of the current digit to extract + int current_bit; + + // Whether to short-ciruit + bool short_circuit; + + + + //--------------------------------------------------------------------- + // Utility methods + //--------------------------------------------------------------------- + + /** + * Decodes given keys to lookup digit offsets in shared memory + */ + __device__ __forceinline__ void DecodeRelativeBinOffsets( + UnsignedBits (&twiddled_keys)[ITEMS_PER_THREAD], + SizeT (&relative_bin_offsets)[ITEMS_PER_THREAD]) + { + #pragma unroll + for (int KEY = 0; KEY < ITEMS_PER_THREAD; KEY++) + { + UnsignedBits digit = BFE(twiddled_keys[KEY], current_bit, RADIX_BITS); + + // Lookup base digit offset from shared memory + relative_bin_offsets[KEY] = temp_storage.relative_bin_offsets[digit]; + } + } + + + /** + * Scatter ranked items to global memory + */ + template + __device__ __forceinline__ void ScatterItems( + T (&items)[ITEMS_PER_THREAD], + int (&local_ranks)[ITEMS_PER_THREAD], + SizeT (&relative_bin_offsets)[ITEMS_PER_THREAD], + T *d_out, + SizeT valid_items) + { + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + // Scatter if not out-of-bounds + if (FULL_TILE || (local_ranks[ITEM] < valid_items)) + { + d_out[relative_bin_offsets[ITEM] + local_ranks[ITEM]] = items[ITEM]; + } + } + } + + + /** + * Scatter ranked keys directly to global memory + */ + template + __device__ __forceinline__ void ScatterKeys( + UnsignedBits (&twiddled_keys)[ITEMS_PER_THREAD], + SizeT (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + SizeT valid_items, + Int2Type scatter_algorithm) + { + // Compute scatter offsets + DecodeRelativeBinOffsets(twiddled_keys, relative_bin_offsets); + + // Untwiddle keys before outputting + UnsignedBits keys[ITEMS_PER_THREAD]; + + #pragma unroll + for (int KEY = 0; KEY < ITEMS_PER_THREAD; KEY++) + { + keys[KEY] = Traits::TwiddleOut(twiddled_keys[KEY]); + } + + // Scatter to global + ScatterItems(keys, ranks, relative_bin_offsets, d_keys_out, valid_items); + } + + + /** + * Scatter ranked keys through shared memory, then to global memory + */ + template + __device__ __forceinline__ void ScatterKeys( + UnsignedBits (&twiddled_keys)[ITEMS_PER_THREAD], + SizeT (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + SizeT valid_items, + Int2Type scatter_algorithm) + { + // Exchange keys through shared memory + BlockExchangeKeys(temp_storage.exchange_keys).ScatterToStriped(twiddled_keys, ranks); + + // Compute striped local ranks + int local_ranks[ITEMS_PER_THREAD]; + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + local_ranks[ITEM] = threadIdx.x + (ITEM * BLOCK_THREADS); + } + + // Scatter directly + ScatterKeys( + twiddled_keys, + relative_bin_offsets, + local_ranks, + valid_items, + Int2Type()); + } + + + /** + * Scatter ranked values directly to global memory + */ + template + __device__ __forceinline__ void ScatterValues( + Value (&values)[ITEMS_PER_THREAD], + SizeT (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + SizeT valid_items, + Int2Type scatter_algorithm) + { + // Scatter to global + ScatterItems(values, ranks, relative_bin_offsets, d_values_out, valid_items); + } + + + /** + * Scatter ranked values through shared memory, then to global memory + */ + template + __device__ __forceinline__ void ScatterValues( + Value (&values)[ITEMS_PER_THREAD], + SizeT (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + SizeT valid_items, + Int2Type scatter_algorithm) + { + __syncthreads(); + + // Exchange keys through shared memory + BlockExchangeValues(temp_storage.exchange_values).ScatterToStriped(values, ranks); + + // Compute striped local ranks + int local_ranks[ITEMS_PER_THREAD]; + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + local_ranks[ITEM] = threadIdx.x + (ITEM * BLOCK_THREADS); + } + + // Scatter directly + ScatterValues( + values, + relative_bin_offsets, + local_ranks, + valid_items, + Int2Type()); + } + + + /** + * Load a tile of items (specialized for full tile) + */ + template + __device__ __forceinline__ void LoadItems( + BlockLoadT &block_loader, + T (&items)[ITEMS_PER_THREAD], + T *d_in, + SizeT valid_items, + Int2Type is_full_tile) + { + block_loader.Load(d_in, items); + } + + + /** + * Load a tile of items (specialized for partial tile) + */ + template + __device__ __forceinline__ void LoadItems( + BlockLoadT &block_loader, + T (&items)[ITEMS_PER_THREAD], + T *d_in, + SizeT valid_items, + Int2Type is_full_tile) + { + block_loader.Load(d_in, items, valid_items); + } + + + /** + * Truck along associated values + */ + template + __device__ __forceinline__ void GatherScatterValues( + _Value (&values)[ITEMS_PER_THREAD], + SizeT (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + SizeT block_offset, + SizeT valid_items) + { + BlockLoadValues loader(temp_storage.load_values); + LoadItems( + loader, + values, + d_values_in + block_offset, + valid_items, + Int2Type()); + + ScatterValues( + values, + relative_bin_offsets, + ranks, + valid_items, + Int2Type()); + } + + + /** + * Truck along associated values (specialized for key-only sorting) + */ + template + __device__ __forceinline__ void GatherScatterValues( + NullType (&values)[ITEMS_PER_THREAD], + SizeT (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + SizeT block_offset, + SizeT valid_items) + {} + + + /** + * Process tile + */ + template + __device__ __forceinline__ void ProcessTile( + SizeT block_offset, + const SizeT &valid_items = TILE_ITEMS) + { + // Per-thread tile data + UnsignedBits keys[ITEMS_PER_THREAD]; // Keys + UnsignedBits twiddled_keys[ITEMS_PER_THREAD]; // Twiddled keys + int ranks[ITEMS_PER_THREAD]; // For each key, the local rank within the CTA + SizeT relative_bin_offsets[ITEMS_PER_THREAD]; // For each key, the global scatter base offset of the corresponding digit + + if (LOAD_ALGORITHM != BLOCK_LOAD_DIRECT) __syncthreads(); + + // Assign max-key to all keys + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + keys[ITEM] = MAX_KEY; + } + + // Load tile of keys + BlockLoadKeys loader(temp_storage.load_keys); + LoadItems( + loader, + keys, + d_keys_in + block_offset, + valid_items, + Int2Type()); + + __syncthreads(); + + // Twiddle key bits if necessary + #pragma unroll + for (int KEY = 0; KEY < ITEMS_PER_THREAD; KEY++) + { + twiddled_keys[KEY] = Traits::TwiddleIn(keys[KEY]); + } + + // Rank the twiddled keys + int inclusive_digit_prefix; + BlockRadixRank(temp_storage.ranking).RankKeys( + twiddled_keys, + ranks, + current_bit, + inclusive_digit_prefix); + + // Update global scatter base offsets for each digit + if ((BLOCK_THREADS == RADIX_DIGITS) || (threadIdx.x < RADIX_DIGITS)) + { + int exclusive_digit_prefix; + + // Get exclusive digit prefix from inclusive prefix +#if CUB_PTX_ARCH >= 300 + exclusive_digit_prefix = ShuffleUp(inclusive_digit_prefix, 1); + if (threadIdx.x == 0) + exclusive_digit_prefix = 0; +#else + volatile int* exchange = reinterpret_cast(temp_storage.relative_bin_offsets); + exchange[threadIdx.x] = 0; + exchange[threadIdx.x + 1] = inclusive_digit_prefix; + exclusive_digit_prefix = exchange[threadIdx.x]; +#endif + + bin_offset -= exclusive_digit_prefix; + temp_storage.relative_bin_offsets[threadIdx.x] = bin_offset; + bin_offset += inclusive_digit_prefix; + } + + __syncthreads(); + + // Scatter keys + ScatterKeys(twiddled_keys, relative_bin_offsets, ranks, valid_items, Int2Type()); + + // Gather/scatter values + Value values[ITEMS_PER_THREAD]; + GatherScatterValues(values, relative_bin_offsets, ranks, block_offset, valid_items); + } + + + /** + * Copy tiles within the range of input + */ + template + __device__ __forceinline__ void Copy( + T *d_in, + T *d_out, + SizeT block_offset, + SizeT block_oob) + { + // Simply copy the input + while (block_offset + TILE_ITEMS <= block_oob) + { + T items[ITEMS_PER_THREAD]; + + LoadStriped(threadIdx.x, d_in + block_offset, items); + __syncthreads(); + StoreStriped(threadIdx.x, d_out + block_offset, items); + + block_offset += TILE_ITEMS; + } + + // Clean up last partial tile with guarded-I/O + if (block_offset < block_oob) + { + SizeT valid_items = block_oob - block_offset; + + T items[ITEMS_PER_THREAD]; + + LoadStriped(threadIdx.x, d_in + block_offset, items, valid_items); + __syncthreads(); + StoreStriped(threadIdx.x, d_out + block_offset, items, valid_items); + } + } + + + /** + * Copy tiles within the range of input (specialized for NullType) + */ + __device__ __forceinline__ void Copy( + NullType *d_in, + NullType *d_out, + SizeT block_offset, + SizeT block_oob) + {} + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockRadixSortDownsweepTiles( + TempStorage &temp_storage, + SizeT bin_offset, + Key *d_keys_in, + Key *d_keys_out, + Value *d_values_in, + Value *d_values_out, + int current_bit) + : + temp_storage(temp_storage.Alias()), + bin_offset(bin_offset), + d_keys_in(reinterpret_cast(d_keys_in)), + d_keys_out(reinterpret_cast(d_keys_out)), + d_values_in(d_values_in), + d_values_out(d_values_out), + current_bit(current_bit), + short_circuit(false) + {} + + + /** + * Constructor + */ + __device__ __forceinline__ BlockRadixSortDownsweepTiles( + TempStorage &temp_storage, + SizeT num_items, + SizeT *d_spine, + Key *d_keys_in, + Key *d_keys_out, + Value *d_values_in, + Value *d_values_out, + int current_bit) + : + temp_storage(temp_storage.Alias()), + d_keys_in(reinterpret_cast(d_keys_in)), + d_keys_out(reinterpret_cast(d_keys_out)), + d_values_in(d_values_in), + d_values_out(d_values_out), + current_bit(current_bit) + { + // Load digit bin offsets (each of the first RADIX_DIGITS threads will load an offset for that digit) + if (threadIdx.x < RADIX_DIGITS) + { + // Short circuit if the first block's histogram has only bin counts of only zeros or problem-size + SizeT first_block_bin_offset = d_spine[gridDim.x * threadIdx.x]; + int predicate = ((first_block_bin_offset == 0) || (first_block_bin_offset == num_items)); + this->temp_storage.short_circuit = WarpAll(predicate); + + // Load my block's bin offset for my bin + bin_offset = d_spine[(gridDim.x * threadIdx.x) + blockIdx.x]; + } + + __syncthreads(); + + short_circuit = this->temp_storage.short_circuit; + } + + + /** + * Distribute keys from a segment of input tiles. + */ + __device__ __forceinline__ void ProcessTiles( + SizeT block_offset, + const SizeT &block_oob) + { + if (short_circuit) + { + // Copy keys + Copy(d_keys_in, d_keys_out, block_offset, block_oob); + + // Copy values + Copy(d_values_in, d_values_out, block_offset, block_oob); + } + else + { + // Process full tiles of tile_items + while (block_offset + TILE_ITEMS <= block_oob) + { + ProcessTile(block_offset); + block_offset += TILE_ITEMS; + } + + // Clean up last partial tile with guarded-I/O + if (block_offset < block_oob) + { + ProcessTile(block_offset, block_oob - block_offset); + } + } + } +}; + + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_radix_sort_upsweep_tiles.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_radix_sort_upsweep_tiles.cuh new file mode 100644 index 0000000000000000000000000000000000000000..22f8c9c75eb1458933d34672996bad066b130e44 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_radix_sort_upsweep_tiles.cuh @@ -0,0 +1,464 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * BlockRadixSortUpsweepTiles implements a stateful abstraction of CUDA thread blocks for participating in device-wide radix sort upsweep. + */ + +#pragma once + +#include "../../thread/thread_reduce.cuh" +#include "../../thread/thread_load.cuh" +#include "../../block/block_load.cuh" +#include "../../util_type.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Tuning policy for BlockRadixSortUpsweepTiles + */ +template < + int _BLOCK_THREADS, ///< The number of threads per CTA + int _ITEMS_PER_THREAD, ///< The number of items to load per thread per tile + PtxLoadModifier _LOAD_MODIFIER, ///< Load cache-modifier + int _RADIX_BITS> ///< The number of radix bits, i.e., log2(bins) +struct BlockRadixSortUpsweepTilesPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, + RADIX_BITS = _RADIX_BITS, + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + }; + + static const PtxLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; + + typedef BlockRadixSortUpsweepTilesPolicy< + BLOCK_THREADS, + ITEMS_PER_THREAD, + LOAD_MODIFIER, + CUB_MAX(1, RADIX_BITS - 1)> AltPolicy; +}; + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockRadixSortUpsweepTiles implements a stateful abstraction of CUDA thread blocks for participating in device-wide radix sort upsweep. + * + * Computes radix digit histograms over a range of input tiles. + */ +template < + typename BlockRadixSortUpsweepTilesPolicy, + typename Key, + typename SizeT> +struct BlockRadixSortUpsweepTiles +{ + + //--------------------------------------------------------------------- + // Type definitions and constants + //--------------------------------------------------------------------- + + typedef typename Traits::UnsignedBits UnsignedBits; + + // Integer type for digit counters (to be packed into words of PackedCounters) + typedef unsigned char DigitCounter; + + // Integer type for packing DigitCounters into columns of shared memory banks + typedef unsigned int PackedCounter; + + static const PtxLoadModifier LOAD_MODIFIER = BlockRadixSortUpsweepTilesPolicy::LOAD_MODIFIER; + + enum + { + RADIX_BITS = BlockRadixSortUpsweepTilesPolicy::RADIX_BITS, + BLOCK_THREADS = BlockRadixSortUpsweepTilesPolicy::BLOCK_THREADS, + KEYS_PER_THREAD = BlockRadixSortUpsweepTilesPolicy::ITEMS_PER_THREAD, + + RADIX_DIGITS = 1 << RADIX_BITS, + + LOG_WARP_THREADS = PtxArchProps::LOG_WARP_THREADS, + WARP_THREADS = 1 << LOG_WARP_THREADS, + WARPS = (BLOCK_THREADS + WARP_THREADS - 1) / WARP_THREADS, + + TILE_ITEMS = BLOCK_THREADS * KEYS_PER_THREAD, + + BYTES_PER_COUNTER = sizeof(DigitCounter), + LOG_BYTES_PER_COUNTER = Log2::VALUE, + + PACKING_RATIO = sizeof(PackedCounter) / sizeof(DigitCounter), + LOG_PACKING_RATIO = Log2::VALUE, + + LOG_COUNTER_LANES = CUB_MAX(0, RADIX_BITS - LOG_PACKING_RATIO), + COUNTER_LANES = 1 << LOG_COUNTER_LANES, + + // To prevent counter overflow, we must periodically unpack and aggregate the + // digit counters back into registers. Each counter lane is assigned to a + // warp for aggregation. + + LANES_PER_WARP = CUB_MAX(1, (COUNTER_LANES + WARPS - 1) / WARPS), + + // Unroll tiles in batches without risk of counter overflow + UNROLL_COUNT = CUB_MIN(64, 255 / KEYS_PER_THREAD), + UNROLLED_ELEMENTS = UNROLL_COUNT * TILE_ITEMS, + }; + + + + /** + * Shared memory storage layout + */ + struct _TempStorage + { + union + { + DigitCounter digit_counters[COUNTER_LANES][BLOCK_THREADS][PACKING_RATIO]; + PackedCounter packed_counters[COUNTER_LANES][BLOCK_THREADS]; + SizeT digit_partials[RADIX_DIGITS][WARP_THREADS + 1]; + }; + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Thread fields (aggregate state bundle) + //--------------------------------------------------------------------- + + // Shared storage for this CTA + _TempStorage &temp_storage; + + // Thread-local counters for periodically aggregating composite-counter lanes + SizeT local_counts[LANES_PER_WARP][PACKING_RATIO]; + + // Input and output device pointers + UnsignedBits *d_keys_in; + + // The least-significant bit position of the current digit to extract + int current_bit; + + + + //--------------------------------------------------------------------- + // Helper structure for templated iteration + //--------------------------------------------------------------------- + + // Iterate + template + struct Iterate + { + enum { + HALF = (MAX / 2), + }; + + // BucketKeys + static __device__ __forceinline__ void BucketKeys( + BlockRadixSortUpsweepTiles &cta, + UnsignedBits keys[KEYS_PER_THREAD]) + { + cta.Bucket(keys[COUNT]); + + // Next + Iterate::BucketKeys(cta, keys); + } + + // ProcessTiles + static __device__ __forceinline__ void ProcessTiles(BlockRadixSortUpsweepTiles &cta, SizeT block_offset) + { + // Next + Iterate<1, HALF>::ProcessTiles(cta, block_offset); + Iterate<1, MAX - HALF>::ProcessTiles(cta, block_offset + (HALF * TILE_ITEMS)); + } + }; + + // Terminate + template + struct Iterate + { + // BucketKeys + static __device__ __forceinline__ void BucketKeys(BlockRadixSortUpsweepTiles &cta, UnsignedBits keys[KEYS_PER_THREAD]) {} + + // ProcessTiles + static __device__ __forceinline__ void ProcessTiles(BlockRadixSortUpsweepTiles &cta, SizeT block_offset) + { + cta.ProcessFullTile(block_offset); + } + }; + + + //--------------------------------------------------------------------- + // Utility methods + //--------------------------------------------------------------------- + + /** + * Decode a key and increment corresponding smem digit counter + */ + __device__ __forceinline__ void Bucket(UnsignedBits key) + { + // Perform transform op + UnsignedBits converted_key = Traits::TwiddleIn(key); + + // Add in sub-counter offset + UnsignedBits sub_counter = BFE(converted_key, current_bit, LOG_PACKING_RATIO); + + // Add in row offset + UnsignedBits row_offset = BFE(converted_key, current_bit + LOG_PACKING_RATIO, LOG_COUNTER_LANES); + + // Increment counter + temp_storage.digit_counters[row_offset][threadIdx.x][sub_counter]++; + + } + + + /** + * Reset composite counters + */ + __device__ __forceinline__ void ResetDigitCounters() + { + #pragma unroll + for (int LANE = 0; LANE < COUNTER_LANES; LANE++) + { + temp_storage.packed_counters[LANE][threadIdx.x] = 0; + } + } + + + /** + * Reset the unpacked counters in each thread + */ + __device__ __forceinline__ void ResetUnpackedCounters() + { + #pragma unroll + for (int LANE = 0; LANE < LANES_PER_WARP; LANE++) + { + #pragma unroll + for (int UNPACKED_COUNTER = 0; UNPACKED_COUNTER < PACKING_RATIO; UNPACKED_COUNTER++) + { + local_counts[LANE][UNPACKED_COUNTER] = 0; + } + } + } + + + /** + * Extracts and aggregates the digit counters for each counter lane + * owned by this warp + */ + __device__ __forceinline__ void UnpackDigitCounts() + { + unsigned int warp_id = threadIdx.x >> LOG_WARP_THREADS; + unsigned int warp_tid = threadIdx.x & (WARP_THREADS - 1); + + #pragma unroll + for (int LANE = 0; LANE < LANES_PER_WARP; LANE++) + { + const int counter_lane = (LANE * WARPS) + warp_id; + if (counter_lane < COUNTER_LANES) + { + #pragma unroll + for (int PACKED_COUNTER = 0; PACKED_COUNTER < BLOCK_THREADS; PACKED_COUNTER += WARP_THREADS) + { + #pragma unroll + for (int UNPACKED_COUNTER = 0; UNPACKED_COUNTER < PACKING_RATIO; UNPACKED_COUNTER++) + { + SizeT counter = temp_storage.digit_counters[counter_lane][warp_tid + PACKED_COUNTER][UNPACKED_COUNTER]; + local_counts[LANE][UNPACKED_COUNTER] += counter; + } + } + } + } + } + + + /** + * Places unpacked counters into smem for final digit reduction + */ + __device__ __forceinline__ void ReduceUnpackedCounts(SizeT &bin_count) + { + unsigned int warp_id = threadIdx.x >> LOG_WARP_THREADS; + unsigned int warp_tid = threadIdx.x & (WARP_THREADS - 1); + + // Place unpacked digit counters in shared memory + #pragma unroll + for (int LANE = 0; LANE < LANES_PER_WARP; LANE++) + { + int counter_lane = (LANE * WARPS) + warp_id; + if (counter_lane < COUNTER_LANES) + { + int digit_row = counter_lane << LOG_PACKING_RATIO; + + #pragma unroll + for (int UNPACKED_COUNTER = 0; UNPACKED_COUNTER < PACKING_RATIO; UNPACKED_COUNTER++) + { + temp_storage.digit_partials[digit_row + UNPACKED_COUNTER][warp_tid] = + local_counts[LANE][UNPACKED_COUNTER]; + } + } + } + + __syncthreads(); + + // Rake-reduce bin_count reductions + if (threadIdx.x < RADIX_DIGITS) + { + bin_count = ThreadReduce( + temp_storage.digit_partials[threadIdx.x], + Sum()); + } + } + + + /** + * Processes a single, full tile + */ + __device__ __forceinline__ void ProcessFullTile(SizeT block_offset) + { + // Tile of keys + UnsignedBits keys[KEYS_PER_THREAD]; + + LoadStriped(threadIdx.x, d_keys_in + block_offset, keys); + + // Prevent hoisting +// __threadfence_block(); +// __syncthreads(); + + // Bucket tile of keys + Iterate<0, KEYS_PER_THREAD>::BucketKeys(*this, keys); + } + + + /** + * Processes a single load (may have some threads masked off) + */ + __device__ __forceinline__ void ProcessPartialTile( + SizeT block_offset, + const SizeT &block_oob) + { + // Process partial tile if necessary using single loads + block_offset += threadIdx.x; + while (block_offset < block_oob) + { + // Load and bucket key + UnsignedBits key = ThreadLoad(d_keys_in + block_offset); + Bucket(key); + block_offset += BLOCK_THREADS; + } + } + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockRadixSortUpsweepTiles( + TempStorage &temp_storage, + Key *d_keys_in, + int current_bit) + : + temp_storage(temp_storage.Alias()), + d_keys_in(reinterpret_cast(d_keys_in)), + current_bit(current_bit) + {} + + + /** + * Compute radix digit histograms from a segment of input tiles. + */ + __device__ __forceinline__ void ProcessTiles( + SizeT block_offset, + const SizeT &block_oob, + SizeT &bin_count) ///< [out] The digit count for tid'th bin (output param, valid in the first RADIX_DIGITS threads) + { + // Reset digit counters in smem and unpacked counters in registers + ResetDigitCounters(); + ResetUnpackedCounters(); + + // Unroll batches of full tiles + while (block_offset + UNROLLED_ELEMENTS <= block_oob) + { + Iterate<0, UNROLL_COUNT>::ProcessTiles(*this, block_offset); + block_offset += UNROLLED_ELEMENTS; + + __syncthreads(); + + // Aggregate back into local_count registers to prevent overflow + UnpackDigitCounts(); + + __syncthreads(); + + // Reset composite counters in lanes + ResetDigitCounters(); + } + + // Unroll single full tiles + while (block_offset + TILE_ITEMS <= block_oob) + { + ProcessFullTile(block_offset); + block_offset += TILE_ITEMS; + } + + // Process partial tile if necessary + ProcessPartialTile( + block_offset, + block_oob); + + __syncthreads(); + + // Aggregate back into local_count registers + UnpackDigitCounts(); + + __syncthreads(); + + // Final raking reduction of counts by bin + ReduceUnpackedCounts(bin_count); + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_reduce_by_key_tiles.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_reduce_by_key_tiles.cuh new file mode 100644 index 0000000000000000000000000000000000000000..99e1980b6fdbe123d9bc6fe7a7ec99dff8a6bc80 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_reduce_by_key_tiles.cuh @@ -0,0 +1,399 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockReduceByKeyiles implements a stateful abstraction of CUDA thread blocks for participating in device-wide reduce-value-by-key. + */ + +#pragma once + +#include + +#include "scan_tiles_types.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_discontinuity.cuh" +#include "../../block/block_scan.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Utility data types + ******************************************************************************/ + +/// Scan tuple data type for reduce-value-by-key +template +struct ReduceByKeyuple +{ + Value value; // Initially set as value, contains segment aggregate after prefix scan + SizeT flag; // Initially set as a tail flag, contains scatter offset after prefix scan +}; + + +/// Binary reduce-by-key scan operator +template +struct ReduceByKeyScanOp +{ + /// Reduction functor + ReductionOp reduction_op; + + /// Constructor + ReduceByKeyScanOp(ReductionOp reduction_op) : reduction_op(reduction_op) + {} + + /// Binary scan operator + template + __device__ __forceinline__ ReduceByKeyuple operator()( + const ReduceByKeyuple &first, + const ReduceByKeyuple &second) + { + ReduceByKeyuple retval; + retval.val = (second.flag) ? second.val : reduction_op(first.val, second.val); + retval.flag = first.flag + second.flag; + return retval; + } +}; + + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Tuning policy for BlockReduceByKeyiles + */ +template < + int _BLOCK_THREADS, + int _ITEMS_PER_THREAD, + BlockLoadAlgorithm _LOAD_ALGORITHM, + bool _LOAD_WARP_TIME_SLICING, + PtxLoadModifier _LOAD_MODIFIER, + BlockScanAlgorithm _SCAN_ALGORITHM> +struct BlockReduceByKeyilesPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, + LOAD_WARP_TIME_SLICING = _LOAD_WARP_TIME_SLICING, + }; + + static const BlockLoadAlgorithm LOAD_ALGORITHM = _LOAD_ALGORITHM; + static const PtxLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; + static const BlockScanAlgorithm SCAN_ALGORITHM = _SCAN_ALGORITHM; +}; + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockReduceByKeyiles implements a stateful abstraction of CUDA thread blocks for participating in device-wide prefix scan. + */ +template < + typename BlockReduceByKeyilesPolicy, ///< Tuning policy + typename KeyInputIteratorRA, ///< Random-access input iterator type for keys + typename KeyOutputIteratorRA, ///< Random-access output iterator type for keys + typename ValueInputIteratorRA, ///< Random-access input iterator type for values + typename ValueOutputIteratorRA, ///< Random-access output iterator type for values + typename ReductionOp, ///< Reduction functor type + typename SizeT> ///< Offset integer type +struct BlockReduceByKeyiles +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Data types of input iterators + typedef typename std::iterator_traits::value_type Key; // Key data type + typedef typename std::iterator_traits::value_type Value; // Value data type + + // Constants + enum + { + BLOCK_THREADS = BlockReduceByKeyilesPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockReduceByKeyilesPolicy::ITEMS_PER_THREAD, + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + STATUS_PADDING = PtxArchProps::WARP_THREADS, + }; + + // Block load type for keys + typedef BlockLoad< + KeyInputIteratorRA, + BlockReduceByKeyilesPolicy::BLOCK_THREADS, + BlockReduceByKeyilesPolicy::ITEMS_PER_THREAD, + BlockReduceByKeyilesPolicy::LOAD_ALGORITHM, + BlockReduceByKeyilesPolicy::LOAD_MODIFIER, + BlockReduceByKeyilesPolicy::LOAD_WARP_TIME_SLICING> BlockLoadKeys; + + // Block load type for values + typedef BlockLoad< + ValueInputIteratorRA, + BlockReduceByKeyilesPolicy::BLOCK_THREADS, + BlockReduceByKeyilesPolicy::ITEMS_PER_THREAD, + BlockReduceByKeyilesPolicy::LOAD_ALGORITHM, + BlockReduceByKeyilesPolicy::LOAD_MODIFIER, + BlockReduceByKeyilesPolicy::LOAD_WARP_TIME_SLICING> BlockLoadValues; + + // Block discontinuity type for setting tail flags + typedef BlockDiscontinuity BlockDiscontinuityKeys; + + // Scan tuple type + typedef ReduceByKeyuple ScanTuple; + + // Tile status descriptor type + typedef ScanTileDescriptor ScanTileDescriptorT; + + // Block scan functor type + typedef ReduceByKeyScanOp ScanOp; + + // Block scan prefix callback type + typedef DeviceScanBlockPrefixOp PrefixCallback; + + // Block scan type + typedef BlockScan< + ScanTuple, + BlockReduceByKeyilesPolicy::BLOCK_THREADS, + BlockReduceByKeyilesPolicy::SCAN_ALGORITHM> BlockScanT; + + /// Shared memory type for this threadblock + struct _TempStorage + { + union + { + typename BlockLoadKeys::TempStorage load_keys; // Smem needed for loading tiles of keys + typename BlockLoadValues::TempStorage load_values; // Smem needed for loading tiles of values + struct + { + typename BlockScanT::TempStorage scan; // Smem needed for tile scanning + typename PrefixCallback::TempStorage prefix; // Smem needed for cooperative prefix callback + }; + }; + + typename BlockDiscontinuityKeys::TempStorage flagging; // Smem needed for tile scanning + SizeT tile_idx; // Shared tile index + }; + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + _TempStorage &temp_storage; ///< Reference to temp_storage + KeyInputIteratorRA d_keys_in; ///< Key input data + KeyOutputIteratorRA d_keys_out; ///< Key output data + ValueInputIteratorRA d_values_in; ///< Value input data + ValueOutputIteratorRA d_values_out; ///< Value output data + ScanTileDescriptorT *d_tile_status; ///< Global list of tile status + ScanOp scan_op; ///< Binary scan operator + int num_tiles; ///< Total number of input tiles for the entire problem + SizeT num_items; ///< Total number of scan items for the entire problem + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + // Constructor + __device__ __forceinline__ + BlockReduceByKeyiles( + TempStorage &temp_storage, ///< Reference to temp_storage + KeyInputIteratorRA d_keys_in, ///< Key input data + KeyOutputIteratorRA d_keys_out, ///< Key output data + ValueInputIteratorRA d_values_in, ///< Value input data + ValueOutputIteratorRA d_values_out, ///< Value output data + ScanTileDescriptorT *d_tile_status, ///< Global list of tile status + ReductionOp reduction_op, ///< Binary scan operator + int num_tiles, ///< Total number of input tiles for the entire problem + SizeT num_items) ///< Total number of scan items for the entire problem + : + temp_storage(temp_storage.Alias()), + d_keys_in(d_keys_in), + d_keys_out(d_keys_out), + d_values_in(d_values_in), + d_values_out(d_values_out), + d_tile_status(d_tile_status), + scan_op(reduction_op), + num_tiles(num_tiles), + num_items(num_items) + {} + + + /** + * Process a tile of input + */ + template + __device__ __forceinline__ void ConsumeTile( + int tile_idx, ///< Tile index + SizeT block_offset, ///< Tile offset + int valid_items = TILE_ITEMS) ///< Number of valid items in the tile + { + Key keys[ITEMS_PER_THREAD]; + Value values[ITEMS_PER_THREAD]; + int tail_flags[ITEMS_PER_THREAD]; + ScanTuple scan_tuples[ITEMS_PER_THREAD]; + + // Load keys + if (FULL_TILE) + BlockLoadKeys(temp_storage.load_keys).Load(d_keys_in + block_offset, keys); + else + BlockLoadKeys(temp_storage.load_keys).Load(d_keys_in + block_offset, keys, valid_items); + + // Set tail flags + if (tile_idx == num_tiles - 1) + { + // Last tile + BlockDiscontinuityKeys(temp_storage.flagging).FlagTails(tail_flags, keys, Equality()); + } + else + { + // Preceding tiles require the first element of the next tile + Key tile_suffix_item; + if (threadIdx.x == 0) + tile_suffix_item = d_keys_in[block_offset + TILE_ITEMS]; + + BlockDiscontinuityKeys(temp_storage.flagging).FlagTails(tail_flags, keys, Equality(), tile_suffix_item); + } + + __syncthreads(); + + // Load values + if (FULL_TILE) + BlockLoadValues(temp_storage.load_values).Load(d_values_in + block_offset, values); + else + BlockLoadValues(temp_storage.load_values).Load(d_values_in + block_offset, values, valid_items); + + // Assemble scan tuples + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + scan_tuples[ITEM].value = values[ITEM]; + scan_tuples[ITEM].flag = tail_flags[ITEM]; + } + + __syncthreads(); + + // Perform inclusive prefix scan + ScanTuple block_aggregate; + if (tile_idx == 0) + { + // Without prefix callback + BlockScanT(temp_storage.scan).InclusiveScan(scan_tuples, scan_tuples, scan_op, block_aggregate); + + // Update tile status + if (threadIdx.x == 0) + ScanTileDescriptorT::SetPrefix(d_tile_status, block_aggregate); + } + else + { + // With prefix callback + PrefixCallback prefix_op(d_tile_status, temp_storage.prefix, scan_op, tile_idx); + BlockScanT(temp_storage.scan).InclusiveScan(scan_tuples, scan_tuples, scan_op, block_aggregate, prefix_op); + } + + // Scatter flagged keys and values to output + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + int tile_item = (threadIdx.x * ITEMS_PER_THREAD) + ITEM; + + // Set the head flag on the last item in a partially-full tile + if (!FULL_TILE && (tile_item == valid_items - 1)) + tail_flags[ITEM] = 1; + + // Decrement scatter offset + scan_tuples[ITEM].flag--; + + // Scatter key and aggregate value if flagged and in range + if ((FULL_TILE || (tile_item < valid_items)) && (tail_flags[ITEM])) + { + d_keys_out[scan_tuples[ITEM].flag] = keys[ITEM]; + d_values_out[scan_tuples[ITEM].flag] = scan_tuples[ITEM].value; + } + } + } + + + + /** + * Dequeue and scan tiles of elements + */ + __device__ __forceinline__ void ProcessTiles(GridQueue queue) ///< Queue descriptor for assigning tiles of work to thread blocks + { + // We give each thread block at least one tile of input + int tile_idx = blockIdx.x; + + // Consume full tiles of input + SizeT block_offset = SizeT(TILE_ITEMS) * tile_idx; + while (block_offset + TILE_ITEMS <= num_items) + { + ConsumeTile(tile_idx, block_offset); + + // Get next tile +#if CUB_PTX_ARCH < 200 + // No concurrent kernels allowed, so just stripe tiles + tile_idx += gridDim.x; +#else + // Concurrent kernels are allowed, so we must only use active blocks to dequeue tile indices + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1) + gridDim.x; + + __syncthreads(); + + tile_idx = temp_storage.tile_idx; +#endif + block_offset = SizeT(TILE_ITEMS) * tile_idx; + } + + // Consume a partially-full tile + if (block_offset < num_items) + { + // Consume a partially-full tile + int valid_items = num_items - block_offset; + ConsumeTile(tile_idx, block_offset, valid_items); + } + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_reduce_tiles.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_reduce_tiles.cuh new file mode 100644 index 0000000000000000000000000000000000000000..a83c098aeb2f13a80654e7424ddee422b1e33352 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_reduce_tiles.cuh @@ -0,0 +1,375 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockReduceTiles implements a stateful abstraction of CUDA thread blocks for participating in device-wide reduction. + */ + +#pragma once + +#include + +#include "../../block/block_load.cuh" +#include "../../block/block_reduce.cuh" +#include "../../grid/grid_mapping.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../grid/grid_even_share.cuh" +#include "../../util_vector.cuh" +#include "../../util_namespace.cuh" + + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Tuning policy for BlockReduceTiles + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread per tile of input + int _VECTOR_LOAD_LENGTH, ///< Number of items per vectorized load + BlockReduceAlgorithm _BLOCK_ALGORITHM, ///< Cooperative block-wide reduction algorithm to use + PtxLoadModifier _LOAD_MODIFIER, ///< PTX load modifier + GridMappingStrategy _GRID_MAPPING> ///< How to map tiles of input onto thread blocks +struct BlockReduceTilesPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, + VECTOR_LOAD_LENGTH = _VECTOR_LOAD_LENGTH, + }; + + static const BlockReduceAlgorithm BLOCK_ALGORITHM = _BLOCK_ALGORITHM; + static const GridMappingStrategy GRID_MAPPING = _GRID_MAPPING; + static const PtxLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; +}; + + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockReduceTiles implements a stateful abstraction of CUDA thread blocks for participating in device-wide reduction. + * + * Each thread reduces only the values it loads. If \p FIRST_TILE, this + * partial reduction is stored into \p thread_aggregate. Otherwise it is + * accumulated into \p thread_aggregate. + */ +template < + typename BlockReduceTilesPolicy, + typename InputIteratorRA, + typename SizeT, + typename ReductionOp> +struct BlockReduceTiles +{ + + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + typedef typename std::iterator_traits::value_type T; // Type of input iterator + typedef VectorHelper VecHelper; // Helper type for vectorizing loads of T + typedef typename VecHelper::Type VectorT; // Vector of T + + // Constants + enum + { + BLOCK_THREADS = BlockReduceTilesPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockReduceTilesPolicy::ITEMS_PER_THREAD, + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + VECTOR_LOAD_LENGTH = BlockReduceTilesPolicy::VECTOR_LOAD_LENGTH, + + // Can vectorize according to the policy if the input iterator is a native pointer to a built-in primitive + CAN_VECTORIZE = (BlockReduceTilesPolicy::VECTOR_LOAD_LENGTH > 1) && + (IsPointer::VALUE) && + (VecHelper::BUILT_IN), + + }; + + static const PtxLoadModifier LOAD_MODIFIER = BlockReduceTilesPolicy::LOAD_MODIFIER; + static const BlockReduceAlgorithm BLOCK_ALGORITHM = BlockReduceTilesPolicy::BLOCK_ALGORITHM; + + // Parameterized BlockReduce primitive + typedef BlockReduce BlockReduceT; + + /// Shared memory type required by this thread block + typedef typename BlockReduceT::TempStorage _TempStorage; + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + T thread_aggregate; ///< Each thread's partial reduction + _TempStorage& temp_storage; ///< Reference to temp_storage + InputIteratorRA d_in; ///< Input data to reduce + ReductionOp reduction_op; ///< Binary reduction operator + int first_tile_size; ///< Size of first tile consumed + bool input_aligned; ///< Whether or not input is vector-aligned + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockReduceTiles( + TempStorage& temp_storage, ///< Reference to temp_storage + InputIteratorRA d_in, ///< Input data to reduce + ReductionOp reduction_op) ///< Binary reduction operator + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + reduction_op(reduction_op), + first_tile_size(0), + input_aligned(CAN_VECTORIZE && ((size_t(d_in) & (sizeof(VectorT) - 1)) == 0)) + {} + + + /** + * Process a single tile of input + */ + template + __device__ __forceinline__ void ConsumeTile( + SizeT block_offset, ///< The offset the tile to consume + int valid_items = TILE_ITEMS) ///< The number of valid items in the tile + { + if (FULL_TILE) + { + T stripe_partial; + + // Load full tile + if (input_aligned) + { + // Alias items as an array of VectorT and load it in striped fashion + enum { WORDS = ITEMS_PER_THREAD / VECTOR_LOAD_LENGTH }; + + VectorT vec_items[WORDS]; + + // Load striped into vec items + VectorT* alias_ptr = reinterpret_cast(d_in + block_offset + (threadIdx.x * VECTOR_LOAD_LENGTH)); + + #pragma unroll + for (int i = 0; i < WORDS; ++i) + vec_items[i] = alias_ptr[BLOCK_THREADS * i]; + + // Reduce items within each thread stripe + stripe_partial = ThreadReduce( + reinterpret_cast(vec_items), + reduction_op); + } + else + { + T items[ITEMS_PER_THREAD]; + + // Load items in striped fashion + LoadStriped(threadIdx.x, d_in + block_offset, items); + + // Reduce items within each thread stripe + stripe_partial = ThreadReduce(items, reduction_op); + } + + // Update running thread aggregate + thread_aggregate = (first_tile_size) ? + reduction_op(thread_aggregate, stripe_partial) : // Update + stripe_partial; // Assign + } + else + { + + // Partial tile + int thread_offset = threadIdx.x; + + if (!first_tile_size && (thread_offset < valid_items)) + { + // Assign thread_aggregate + thread_aggregate = ThreadLoad(d_in + block_offset + thread_offset); + thread_offset += BLOCK_THREADS; + } + + while (thread_offset < valid_items) + { + // Update thread aggregate + T item = ThreadLoad(d_in + block_offset + thread_offset); + thread_aggregate = reduction_op(thread_aggregate, item); + thread_offset += BLOCK_THREADS; + } + } + + // Set first tile size if necessary + if (!first_tile_size) + first_tile_size = valid_items; + } + + + //--------------------------------------------------------------------- + // Consume a contiguous segment of tiles + //--------------------------------------------------------------------- + + /** + * \brief Reduce a contiguous segment of input tiles + */ + __device__ __forceinline__ void ConsumeTiles( + SizeT block_offset, ///< [in] Threadblock begin offset (inclusive) + SizeT block_oob, ///< [in] Threadblock end offset (exclusive) + T &block_aggregate) ///< [out] Running total + { + // Consume subsequent full tiles of input + while (block_offset + TILE_ITEMS <= block_oob) + { + ConsumeTile(block_offset); + block_offset += TILE_ITEMS; + } + + // Consume a partially-full tile + if (block_offset < block_oob) + { + int valid_items = block_oob - block_offset; + ConsumeTile(block_offset, valid_items); + } + + // Compute block-wide reduction + block_aggregate = (first_tile_size < TILE_ITEMS) ? + BlockReduceT(temp_storage).Reduce(thread_aggregate, reduction_op, first_tile_size) : + BlockReduceT(temp_storage).Reduce(thread_aggregate, reduction_op); + } + + + /** + * Reduce a contiguous segment of input tiles + */ + __device__ __forceinline__ void ConsumeTiles( + SizeT num_items, ///< [in] Total number of global input items + GridEvenShare &even_share, ///< [in] GridEvenShare descriptor + GridQueue &queue, ///< [in,out] GridQueue descriptor + T &block_aggregate, ///< [out] Running total + Int2Type is_even_share) ///< [in] Marker type indicating this is an even-share mapping + { + // Initialize even-share descriptor for this thread block + even_share.BlockInit(); + + // Consume input tiles + ConsumeTiles(even_share.block_offset, even_share.block_oob, block_aggregate); + } + + + //--------------------------------------------------------------------- + // Dynamically consume tiles + //--------------------------------------------------------------------- + + /** + * Dequeue and reduce tiles of items as part of a inter-block scan + */ + __device__ __forceinline__ void ConsumeTiles( + int num_items, ///< Total number of input items + GridQueue queue, ///< Queue descriptor for assigning tiles of work to thread blocks + T &block_aggregate) ///< [out] Running total + { + // Shared dequeue offset + __shared__ SizeT dequeue_offset; + + // We give each thread block at least one tile of input. + SizeT block_offset = blockIdx.x * TILE_ITEMS; + SizeT even_share_base = gridDim.x * TILE_ITEMS; + + if (block_offset + TILE_ITEMS <= num_items) + { + // Consume full tile of input + ConsumeTile(block_offset); + + // Dequeue more tiles + while (true) + { + // Dequeue a tile of items + if (threadIdx.x == 0) + dequeue_offset = queue.Drain(TILE_ITEMS) + even_share_base; + + __syncthreads(); + + // Grab tile offset and check if we're done with full tiles + block_offset = dequeue_offset; + + __syncthreads(); + + if (block_offset + TILE_ITEMS > num_items) + break; + + // Consume a full tile + ConsumeTile(block_offset); + } + } + + if (block_offset < num_items) + { + int valid_items = num_items - block_offset; + ConsumeTile(block_offset, valid_items); + } + + // Compute block-wide reduction + block_aggregate = (first_tile_size < TILE_ITEMS) ? + BlockReduceT(temp_storage).Reduce(thread_aggregate, reduction_op, first_tile_size) : + BlockReduceT(temp_storage).Reduce(thread_aggregate, reduction_op); + } + + + /** + * Dequeue and reduce tiles of items as part of a inter-block scan + */ + __device__ __forceinline__ void ConsumeTiles( + SizeT num_items, ///< [in] Total number of global input items + GridEvenShare &even_share, ///< [in] GridEvenShare descriptor + GridQueue &queue, ///< [in,out] GridQueue descriptor + T &block_aggregate, ///< [out] Running total + Int2Type is_dynamic) ///< [in] Marker type indicating this is a dynamic mapping + { + ConsumeTiles(num_items, queue, block_aggregate); + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_scan_tiles.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_scan_tiles.cuh new file mode 100644 index 0000000000000000000000000000000000000000..980220480e0e95c5e8cc4fc2030a7d5a278cc220 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/block_scan_tiles.cuh @@ -0,0 +1,509 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockScanTiles implements a stateful abstraction of CUDA thread blocks for participating in device-wide prefix scan. + */ + +#pragma once + +#include + +#include "scan_tiles_types.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_store.cuh" +#include "../../block/block_scan.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Tuning policy for BlockScanTiles + */ +template < + int _BLOCK_THREADS, + int _ITEMS_PER_THREAD, + BlockLoadAlgorithm _LOAD_ALGORITHM, + bool _LOAD_WARP_TIME_SLICING, + PtxLoadModifier _LOAD_MODIFIER, + BlockStoreAlgorithm _STORE_ALGORITHM, + bool _STORE_WARP_TIME_SLICING, + BlockScanAlgorithm _SCAN_ALGORITHM> +struct BlockScanTilesPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, + LOAD_WARP_TIME_SLICING = _LOAD_WARP_TIME_SLICING, + STORE_WARP_TIME_SLICING = _STORE_WARP_TIME_SLICING, + }; + + static const BlockLoadAlgorithm LOAD_ALGORITHM = _LOAD_ALGORITHM; + static const PtxLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; + static const BlockStoreAlgorithm STORE_ALGORITHM = _STORE_ALGORITHM; + static const BlockScanAlgorithm SCAN_ALGORITHM = _SCAN_ALGORITHM; +}; + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockScanTiles implements a stateful abstraction of CUDA thread blocks for participating in device-wide prefix scan. + * + * Implements a single-pass "domino" strategy with adaptive prefix lookback. + */ +template < + typename BlockScanTilesPolicy, ///< Tuning policy + typename InputIteratorRA, ///< Input iterator type + typename OutputIteratorRA, ///< Output iterator type + typename ScanOp, ///< Scan functor type + typename Identity, ///< Identity element type (cub::NullType for inclusive scan) + typename SizeT> ///< Offset integer type +struct BlockScanTiles +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Data type of input iterator + typedef typename std::iterator_traits::value_type T; + + // Constants + enum + { + INCLUSIVE = Equals::VALUE, // Inclusive scan if no identity type is provided + BLOCK_THREADS = BlockScanTilesPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockScanTilesPolicy::ITEMS_PER_THREAD, + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + }; + + // Block load type + typedef BlockLoad< + InputIteratorRA, + BlockScanTilesPolicy::BLOCK_THREADS, + BlockScanTilesPolicy::ITEMS_PER_THREAD, + BlockScanTilesPolicy::LOAD_ALGORITHM, + BlockScanTilesPolicy::LOAD_MODIFIER, + BlockScanTilesPolicy::LOAD_WARP_TIME_SLICING> BlockLoadT; + + // Block store type + typedef BlockStore< + OutputIteratorRA, + BlockScanTilesPolicy::BLOCK_THREADS, + BlockScanTilesPolicy::ITEMS_PER_THREAD, + BlockScanTilesPolicy::STORE_ALGORITHM, + STORE_DEFAULT, + BlockScanTilesPolicy::STORE_WARP_TIME_SLICING> BlockStoreT; + + // Tile status descriptor type + typedef ScanTileDescriptor ScanTileDescriptorT; + + // Block scan type + typedef BlockScan< + T, + BlockScanTilesPolicy::BLOCK_THREADS, + BlockScanTilesPolicy::SCAN_ALGORITHM> BlockScanT; + + // Callback type for obtaining inter-tile prefix during block scan + typedef DeviceScanBlockPrefixOp InterblockPrefixOp; + + // Shared memory type for this threadblock + struct _TempStorage + { + union + { + typename BlockLoadT::TempStorage load; // Smem needed for tile loading + typename BlockStoreT::TempStorage store; // Smem needed for tile storing + struct + { + typename InterblockPrefixOp::TempStorage prefix; // Smem needed for cooperative prefix callback + typename BlockScanT::TempStorage scan; // Smem needed for tile scanning + }; + }; + + SizeT tile_idx; // Shared tile index + }; + + // Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + _TempStorage &temp_storage; ///< Reference to temp_storage + InputIteratorRA d_in; ///< Input data + OutputIteratorRA d_out; ///< Output data + ScanOp scan_op; ///< Binary scan operator + Identity identity; ///< Identity element + + + + //--------------------------------------------------------------------- + // Block scan utility methods (first tile) + //--------------------------------------------------------------------- + + /** + * Exclusive scan specialization + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], _ScanOp scan_op, _Identity identity, T& block_aggregate) + { + BlockScanT(temp_storage.scan).ExclusiveScan(items, items, identity, scan_op, block_aggregate); + } + + /** + * Exclusive sum specialization + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], Sum scan_op, _Identity identity, T& block_aggregate) + { + BlockScanT(temp_storage.scan).ExclusiveSum(items, items, block_aggregate); + } + + /** + * Inclusive scan specialization + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], _ScanOp scan_op, NullType identity, T& block_aggregate) + { + BlockScanT(temp_storage.scan).InclusiveScan(items, items, scan_op, block_aggregate); + } + + /** + * Inclusive sum specialization + */ + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], Sum scan_op, NullType identity, T& block_aggregate) + { + BlockScanT(temp_storage.scan).InclusiveSum(items, items, block_aggregate); + } + + //--------------------------------------------------------------------- + // Block scan utility methods (subsequent tiles) + //--------------------------------------------------------------------- + + /** + * Exclusive scan specialization (with prefix from predecessors) + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], _ScanOp scan_op, _Identity identity, T& block_aggregate, PrefixCallback &prefix_op) + { + BlockScanT(temp_storage.scan).ExclusiveScan(items, items, identity, scan_op, block_aggregate, prefix_op); + } + + /** + * Exclusive sum specialization (with prefix from predecessors) + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], Sum scan_op, _Identity identity, T& block_aggregate, PrefixCallback &prefix_op) + { + BlockScanT(temp_storage.scan).ExclusiveSum(items, items, block_aggregate, prefix_op); + } + + /** + * Inclusive scan specialization (with prefix from predecessors) + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], _ScanOp scan_op, NullType identity, T& block_aggregate, PrefixCallback &prefix_op) + { + BlockScanT(temp_storage.scan).InclusiveScan(items, items, scan_op, block_aggregate, prefix_op); + } + + /** + * Inclusive sum specialization (with prefix from predecessors) + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], Sum scan_op, NullType identity, T& block_aggregate, PrefixCallback &prefix_op) + { + BlockScanT(temp_storage.scan).InclusiveSum(items, items, block_aggregate, prefix_op); + } + + //--------------------------------------------------------------------- + // Constructor + //--------------------------------------------------------------------- + + // Constructor + __device__ __forceinline__ + BlockScanTiles( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIteratorRA d_in, ///< Input data + OutputIteratorRA d_out, ///< Output data + ScanOp scan_op, ///< Binary scan operator + Identity identity) ///< Identity element + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + d_out(d_out), + scan_op(scan_op), + identity(identity) + {} + + + //--------------------------------------------------------------------- + // Domino scan + //--------------------------------------------------------------------- + + /** + * Process a tile of input (domino scan) + */ + template + __device__ __forceinline__ void ConsumeTile( + SizeT num_items, ///< Total number of input items + int tile_idx, ///< Tile index + SizeT block_offset, ///< Tile offset + ScanTileDescriptorT *d_tile_status) ///< Global list of tile status + { + // Load items + T items[ITEMS_PER_THREAD]; + + if (FULL_TILE) + BlockLoadT(temp_storage.load).Load(d_in + block_offset, items); + else + BlockLoadT(temp_storage.load).Load(d_in + block_offset, items, num_items - block_offset); + + __syncthreads(); + + T block_aggregate; + if (tile_idx == 0) + { + ScanBlock(items, scan_op, identity, block_aggregate); + + // Update tile status if there are successor tiles + if (FULL_TILE && (threadIdx.x == 0)) + ScanTileDescriptorT::SetPrefix(d_tile_status, block_aggregate); + } + else + { + InterblockPrefixOp prefix_op(d_tile_status, temp_storage.prefix, scan_op, tile_idx); + ScanBlock(items, scan_op, identity, block_aggregate, prefix_op); + } + + __syncthreads(); + + // Store items + if (FULL_TILE) + BlockStoreT(temp_storage.store).Store(d_out + block_offset, items); + else + BlockStoreT(temp_storage.store).Store(d_out + block_offset, items, num_items - block_offset); + } + + /** + * Dequeue and scan tiles of items as part of a domino scan + */ + __device__ __forceinline__ void ConsumeTiles( + int num_items, ///< Total number of input items + GridQueue queue, ///< Queue descriptor for assigning tiles of work to thread blocks + ScanTileDescriptorT *d_tile_status) ///< Global list of tile status + { +#if CUB_PTX_ARCH < 200 + + // No concurrent kernels allowed and blocks are launched in increasing order, so just assign one tile per block (up to 65K blocks) + int tile_idx = blockIdx.x; + SizeT block_offset = SizeT(TILE_ITEMS) * tile_idx; + + if (block_offset + TILE_ITEMS <= num_items) + ConsumeTile(num_items, tile_idx, block_offset, d_tile_status); + else if (block_offset < num_items) + ConsumeTile(num_items, tile_idx, block_offset, d_tile_status); + +#else + + // Get first tile + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + int tile_idx = temp_storage.tile_idx; + SizeT block_offset = SizeT(TILE_ITEMS) * tile_idx; + + while (block_offset + TILE_ITEMS <= num_items) + { + // Consume full tile + ConsumeTile(num_items, tile_idx, block_offset, d_tile_status); + + // Get next tile + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + tile_idx = temp_storage.tile_idx; + block_offset = SizeT(TILE_ITEMS) * tile_idx; + } + + // Consume a partially-full tile + if (block_offset < num_items) + { + ConsumeTile(num_items, tile_idx, block_offset, d_tile_status); + } +#endif + + } + + + //--------------------------------------------------------------------- + // Even-share scan + //--------------------------------------------------------------------- + + /** + * Process a tile of input + */ + template < + bool FULL_TILE, + bool FIRST_TILE> + __device__ __forceinline__ void ConsumeTile( + SizeT block_offset, ///< Tile offset + RunningBlockPrefixOp &prefix_op, ///< Running prefix operator + int valid_items = TILE_ITEMS) ///< Number of valid items in the tile + { + // Load items + T items[ITEMS_PER_THREAD]; + + if (FULL_TILE) + BlockLoadT(temp_storage.load).Load(d_in + block_offset, items); + else + BlockLoadT(temp_storage.load).Load(d_in + block_offset, items, valid_items); + + __syncthreads(); + + // Block scan + T block_aggregate; + if (FIRST_TILE) + { + ScanBlock(items, scan_op, identity, block_aggregate); + prefix_op.running_total = block_aggregate; + } + else + { + ScanBlock(items, scan_op, identity, block_aggregate, prefix_op); + } + + __syncthreads(); + + // Store items + if (FULL_TILE) + BlockStoreT(temp_storage.store).Store(d_out + block_offset, items); + else + BlockStoreT(temp_storage.store).Store(d_out + block_offset, items, valid_items); + } + + + /** + * Scan a consecutive share of input tiles + */ + __device__ __forceinline__ void ConsumeTiles( + SizeT block_offset, ///< [in] Threadblock begin offset (inclusive) + SizeT block_oob) ///< [in] Threadblock end offset (exclusive) + { + RunningBlockPrefixOp prefix_op; + + if (block_offset + TILE_ITEMS <= block_oob) + { + // Consume first tile of input (full) + ConsumeTile(block_offset, prefix_op); + block_offset += TILE_ITEMS; + + // Consume subsequent full tiles of input + while (block_offset + TILE_ITEMS <= block_oob) + { + ConsumeTile(block_offset, prefix_op); + block_offset += TILE_ITEMS; + } + + // Consume a partially-full tile + if (block_offset < block_oob) + { + int valid_items = block_oob - block_offset; + ConsumeTile(block_offset, prefix_op, valid_items); + } + } + else + { + // Consume the first tile of input (partially-full) + int valid_items = block_oob - block_offset; + ConsumeTile(block_offset, prefix_op, valid_items); + } + } + + + /** + * Scan a consecutive share of input tiles, seeded with the specified prefix value + */ + __device__ __forceinline__ void ConsumeTiles( + SizeT block_offset, ///< [in] Threadblock begin offset (inclusive) + SizeT block_oob, ///< [in] Threadblock end offset (exclusive) + T prefix) ///< [in] The prefix to apply to the scan segment + { + RunningBlockPrefixOp prefix_op; + prefix_op.running_total = prefix; + + // Consume full tiles of input + while (block_offset + TILE_ITEMS <= block_oob) + { + ConsumeTile(block_offset, prefix_op); + block_offset += TILE_ITEMS; + } + + // Consume a partially-full tile + if (block_offset < block_oob) + { + int valid_items = block_oob - block_offset; + ConsumeTile(block_offset, prefix_op, valid_items); + } + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/scan_tiles_types.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/scan_tiles_types.cuh new file mode 100644 index 0000000000000000000000000000000000000000..2b933d0af2d0c10e0e3c9d88629da767861e8e27 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/scan_tiles_types.cuh @@ -0,0 +1,318 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * Utility types for device-wide scan + */ + +#pragma once + +#include + +#include "../../thread/thread_load.cuh" +#include "../../thread/thread_store.cuh" +#include "../../warp/warp_reduce.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * Enumerations of tile status + */ +enum ScanTileStatus +{ + SCAN_TILE_OOB, // Out-of-bounds (e.g., padding) + SCAN_TILE_INVALID, // Not yet processed + SCAN_TILE_PARTIAL, // Tile aggregate is available + SCAN_TILE_PREFIX, // Inclusive tile prefix is available +}; + + +/** + * Data type of tile status descriptor. + * + * Specialized for scan status and value types that can be combined into the same + * machine word that can be read/written coherently in a single access. + */ +template < + typename T, + bool SINGLE_WORD = (PowerOfTwo::VALUE && (sizeof(T) <= 8))> +struct ScanTileDescriptor +{ + // Status word type + typedef typename If<(sizeof(T) == 8), + long long, + typename If<(sizeof(T) == 4), + int, + typename If<(sizeof(T) == 2), + short, + char>::Type>::Type>::Type StatusWord; + + // Vector word type + typedef typename If<(sizeof(T) == 8), + longlong2, + typename If<(sizeof(T) == 4), + int2, + typename If<(sizeof(T) == 2), + int, + short>::Type>::Type>::Type VectorWord; + + T value; + StatusWord status; + + static __device__ __forceinline__ void SetPrefix(ScanTileDescriptor *ptr, T prefix) + { + ScanTileDescriptor tile_descriptor; + tile_descriptor.status = SCAN_TILE_PREFIX; + tile_descriptor.value = prefix; + + VectorWord alias; + *reinterpret_cast(&alias) = tile_descriptor; + ThreadStore(reinterpret_cast(ptr), alias); + } + + static __device__ __forceinline__ void SetPartial(ScanTileDescriptor *ptr, T partial) + { + ScanTileDescriptor tile_descriptor; + tile_descriptor.status = SCAN_TILE_PARTIAL; + tile_descriptor.value = partial; + + VectorWord alias; + *reinterpret_cast(&alias) = tile_descriptor; + ThreadStore(reinterpret_cast(ptr), alias); + } + + static __device__ __forceinline__ void WaitForValid( + ScanTileDescriptor *ptr, + int &status, + T &value) + { + ScanTileDescriptor tile_descriptor; + while (true) + { + VectorWord alias = ThreadLoad(reinterpret_cast(ptr)); + + tile_descriptor = *reinterpret_cast(&alias); + if (tile_descriptor.status != SCAN_TILE_INVALID) break; + + __threadfence_block(); + } + + status = tile_descriptor.status; + value = tile_descriptor.value; + } + +}; + + +/** + * Data type of tile status descriptor. + * + * Specialized for scan status and value types that cannot fused into + * the same machine word. + */ +template +struct ScanTileDescriptor +{ + T prefix_value; + T partial_value; + + /// Workaround for the fact that win32 doesn't guarantee 16B alignment 16B values of T + union + { + int status; + Uninitialized padding; + }; + + static __device__ __forceinline__ void SetPrefix(ScanTileDescriptor *ptr, T prefix) + { + ThreadStore(&ptr->prefix_value, prefix); + __threadfence_block(); +// __threadfence(); // __threadfence_block seems sufficient on current architectures to prevent reordeing + ThreadStore(&ptr->status, (int) SCAN_TILE_PREFIX); + + } + + static __device__ __forceinline__ void SetPartial(ScanTileDescriptor *ptr, T partial) + { + ThreadStore(&ptr->partial_value, partial); + __threadfence_block(); +// __threadfence(); // __threadfence_block seems sufficient on current architectures to prevent reordeing + ThreadStore(&ptr->status, (int) SCAN_TILE_PARTIAL); + } + + static __device__ __forceinline__ void WaitForValid( + ScanTileDescriptor *ptr, + int &status, + T &value) + { + while (true) + { + status = ThreadLoad(&ptr->status); + if (status != SCAN_TILE_INVALID) break; + + __threadfence_block(); + } + + value = (status == SCAN_TILE_PARTIAL) ? + ThreadLoad(&ptr->partial_value) : + ThreadLoad(&ptr->prefix_value); + } +}; + + +/** + * Stateful prefix functor that provides the the running prefix for + * the current tile by using the callback warp to wait on on + * aggregates/prefixes from predecessor tiles to become available + */ +template < + typename T, + typename ScanOp> +struct DeviceScanBlockPrefixOp +{ + // Parameterized warp reduce + typedef WarpReduce WarpReduceT; + + // Storage type + typedef typename WarpReduceT::TempStorage _TempStorage; + + // Alias wrapper allowing storage to be unioned + typedef Uninitialized<_TempStorage> TempStorage; + + // Tile status descriptor type + typedef ScanTileDescriptor ScanTileDescriptorT; + + // Fields + ScanTileDescriptorT *d_tile_status; ///< Pointer to array of tile status + _TempStorage &temp_storage; ///< Reference to a warp-reduction instance + ScanOp scan_op; ///< Binary scan operator + int tile_idx; ///< The current tile index + T inclusive_prefix; ///< Inclusive prefix for the tile + + // Constructor + __device__ __forceinline__ + DeviceScanBlockPrefixOp( + ScanTileDescriptorT *d_tile_status, + TempStorage &temp_storage, + ScanOp scan_op, + int tile_idx) : + d_tile_status(d_tile_status), + temp_storage(temp_storage.Alias()), + scan_op(scan_op), + tile_idx(tile_idx) {} + + + // Block until all predecessors within the specified window have non-invalid status + __device__ __forceinline__ + void ProcessWindow( + int predecessor_idx, + int &predecessor_status, + T &window_aggregate) + { + T value; + ScanTileDescriptorT::WaitForValid(d_tile_status + predecessor_idx, predecessor_status, value); + + // Perform a segmented reduction to get the prefix for the current window + int flag = (predecessor_status != SCAN_TILE_PARTIAL); + window_aggregate = WarpReduceT(temp_storage).TailSegmentedReduce(value, flag, scan_op); + } + + + // Prefix functor (called by the first warp) + __device__ __forceinline__ + T operator()(T block_aggregate) + { + // Update our status with our tile-aggregate + if (threadIdx.x == 0) + { + ScanTileDescriptorT::SetPartial(d_tile_status + tile_idx, block_aggregate); + } + + // Wait for the window of predecessor tiles to become valid + int predecessor_idx = tile_idx - threadIdx.x - 1; + int predecessor_status; + T window_aggregate; + ProcessWindow(predecessor_idx, predecessor_status, window_aggregate); + + // The exclusive tile prefix starts out as the current window aggregate + T exclusive_prefix = window_aggregate; + + // Keep sliding the window back until we come across a tile whose inclusive prefix is known + while (WarpAll(predecessor_status != SCAN_TILE_PREFIX)) + { + predecessor_idx -= PtxArchProps::WARP_THREADS; + + // Update exclusive tile prefix with the window prefix + ProcessWindow(predecessor_idx, predecessor_status, window_aggregate); + exclusive_prefix = scan_op(window_aggregate, exclusive_prefix); + } + + // Compute the inclusive tile prefix and update the status for this tile + if (threadIdx.x == 0) + { + inclusive_prefix = scan_op(exclusive_prefix, block_aggregate); + ScanTileDescriptorT::SetPrefix( + d_tile_status + tile_idx, + inclusive_prefix); + } + + // Return exclusive_prefix + return exclusive_prefix; + } +}; + + +// Running scan prefix callback type for single-block scans. +// Maintains a running prefix that can be applied to consecutive +// scan operations. +template +struct RunningBlockPrefixOp +{ + // Running prefix + T running_total; + + // Callback operator. + __device__ T operator()(T block_aggregate) + { + T old_prefix = running_total; + running_total += block_aggregate; + return old_prefix; + } +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/specializations/block_histo_tiles_gatomic.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/specializations/block_histo_tiles_gatomic.cuh new file mode 100644 index 0000000000000000000000000000000000000000..5896dbcf63583703ad7a0a1b43bf5ff04ba68e88 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/specializations/block_histo_tiles_gatomic.cuh @@ -0,0 +1,184 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockHistogramTilesGlobalAtomic implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram. + */ + +#pragma once + +#include + +#include "../../../util_type.cuh" +#include "../../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + + +/** + * BlockHistogramTilesGlobalAtomic implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using global atomics + */ +template < + typename BlockHistogramTilesPolicy, ///< Tuning policy + int BINS, ///< Number of histogram bins per channel + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIteratorRA, ///< The input iterator type (may be a simple pointer type). Must have a value type that can be cast as an integer in the range [0..BINS-1] + typename HistoCounter, ///< Integral type for counting sample occurrences per histogram bin + typename SizeT> ///< Integer type for offsets +struct BlockHistogramTilesGlobalAtomic +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Sample type + typedef typename std::iterator_traits::value_type SampleT; + + // Constants + enum + { + BLOCK_THREADS = BlockHistogramTilesPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockHistogramTilesPolicy::ITEMS_PER_THREAD, + TILE_CHANNEL_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + TILE_ITEMS = TILE_CHANNEL_ITEMS * CHANNELS, + }; + + // Shared memory type required by this thread block + typedef NullType TempStorage; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + /// Reference to output histograms + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]; + + /// Input data to reduce + InputIteratorRA d_in; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockHistogramTilesGlobalAtomic( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIteratorRA d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) ///< Reference to output histograms + : + d_in(d_in), + d_out_histograms(d_out_histograms) + {} + + + /** + * Process a single tile of input + */ + template + __device__ __forceinline__ void ConsumeTile( + SizeT block_offset, ///< The offset the tile to consume + int valid_items = TILE_ITEMS) ///< The number of valid items in the tile + { + if (FULL_TILE) + { + // Full tile of samples to read and composite + SampleT items[ITEMS_PER_THREAD][CHANNELS]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + items[ITEM][CHANNEL] = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + } + } + } + + __threadfence_block(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + atomicAdd(d_out_histograms[CHANNEL] + items[ITEM][CHANNEL], 1); + } + } + } + } + else + { + // Only a partially-full tile of samples to read and composite + int bounds = valid_items - (threadIdx.x * CHANNELS); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (((ACTIVE_CHANNELS == CHANNELS) || (CHANNEL < ACTIVE_CHANNELS)) && ((ITEM * BLOCK_THREADS * CHANNELS) + CHANNEL < bounds)) + { + SampleT item = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + atomicAdd(d_out_histograms[CHANNEL] + item, 1); + } + } + } + + } + } + + + /** + * Aggregate results into output + */ + __device__ __forceinline__ void AggregateOutput() + {} +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/specializations/block_histo_tiles_satomic.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/specializations/block_histo_tiles_satomic.cuh new file mode 100644 index 0000000000000000000000000000000000000000..c55d78953c943e4bd490948d613399d3d30479db --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/specializations/block_histo_tiles_satomic.cuh @@ -0,0 +1,237 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockHistogramTilesSharedAtomic implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using shared atomics + */ + +#pragma once + +#include + +#include "../../../util_type.cuh" +#include "../../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * BlockHistogramTilesSharedAtomic implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using shared atomics + */ +template < + typename BlockHistogramTilesPolicy, ///< Tuning policy + int BINS, ///< Number of histogram bins + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIteratorRA, ///< The input iterator type (may be a simple pointer type). Must have a value type that can be cast as an integer in the range [0..BINS-1] + typename HistoCounter, ///< Integral type for counting sample occurrences per histogram bin + typename SizeT> ///< Integer type for offsets +struct BlockHistogramTilesSharedAtomic +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Sample type + typedef typename std::iterator_traits::value_type SampleT; + + // Constants + enum + { + BLOCK_THREADS = BlockHistogramTilesPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockHistogramTilesPolicy::ITEMS_PER_THREAD, + TILE_CHANNEL_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + TILE_ITEMS = TILE_CHANNEL_ITEMS * CHANNELS, + }; + + /// Shared memory type required by this thread block + struct _TempStorage + { + HistoCounter histograms[ACTIVE_CHANNELS][BINS + 1]; // One word of padding between channel histograms to prevent warps working on different histograms from hammering on the same bank + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + /// Reference to temp_storage + _TempStorage &temp_storage; + + /// Reference to output histograms + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]; + + /// Input data to reduce + InputIteratorRA d_in; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockHistogramTilesSharedAtomic( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIteratorRA d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) ///< Reference to output histograms + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + d_out_histograms(d_out_histograms) + { + // Initialize histogram bin counts to zeros + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + int histo_offset = 0; + + #pragma unroll + for(; histo_offset + BLOCK_THREADS <= BINS; histo_offset += BLOCK_THREADS) + { + this->temp_storage.histograms[CHANNEL][histo_offset + threadIdx.x] = 0; + } + // Finish up with guarded initialization if necessary + if ((BINS % BLOCK_THREADS != 0) && (histo_offset + threadIdx.x < BINS)) + { + this->temp_storage.histograms[CHANNEL][histo_offset + threadIdx.x] = 0; + } + } + } + + + /** + * Process a single tile of input + */ + template + __device__ __forceinline__ void ConsumeTile( + SizeT block_offset, ///< The offset the tile to consume + int valid_items = TILE_ITEMS) ///< The number of valid items in the tile + { + if (FULL_TILE) + { + // Full tile of samples to read and composite + SampleT items[ITEMS_PER_THREAD][CHANNELS]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + items[ITEM][CHANNEL] = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + } + } + } + + __threadfence_block(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + atomicAdd(temp_storage.histograms[CHANNEL] + items[ITEM][CHANNEL], 1); + } + } + } + + __threadfence_block(); + } + else + { + // Only a partially-full tile of samples to read and composite + int bounds = valid_items - (threadIdx.x * CHANNELS); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (((ACTIVE_CHANNELS == CHANNELS) || (CHANNEL < ACTIVE_CHANNELS)) && ((ITEM * BLOCK_THREADS * CHANNELS) + CHANNEL < bounds)) + { + SampleT item = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + atomicAdd(temp_storage.histograms[CHANNEL] + item, 1); + } + } + } + + } + } + + + /** + * Aggregate results into output + */ + __device__ __forceinline__ void AggregateOutput() + { + // Barrier to ensure shared memory histograms are coherent + __syncthreads(); + + // Copy shared memory histograms to output + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + int channel_offset = (blockIdx.x * BINS); + int histo_offset = 0; + + #pragma unroll + for(; histo_offset + BLOCK_THREADS <= BINS; histo_offset += BLOCK_THREADS) + { + d_out_histograms[CHANNEL][channel_offset + histo_offset + threadIdx.x] = temp_storage.histograms[CHANNEL][histo_offset + threadIdx.x]; + } + // Finish up with guarded initialization if necessary + if ((BINS % BLOCK_THREADS != 0) && (histo_offset + threadIdx.x < BINS)) + { + d_out_histograms[CHANNEL][channel_offset + histo_offset + threadIdx.x] = temp_storage.histograms[CHANNEL][histo_offset + threadIdx.x]; + } + } + } +}; + + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/specializations/block_histo_tiles_sort.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/specializations/block_histo_tiles_sort.cuh new file mode 100644 index 0000000000000000000000000000000000000000..0f821309cb4b15c736473713319fd9f665315035 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block/specializations/block_histo_tiles_sort.cuh @@ -0,0 +1,364 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockHistogramTilesSort implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using local sorting + */ + +#pragma once + +#include + +#include "../../../block/block_radix_sort.cuh" +#include "../../../block/block_discontinuity.cuh" +#include "../../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * BlockHistogramTilesSort implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using local sorting + */ +template < + typename BlockHistogramTilesPolicy, ///< Tuning policy + int BINS, ///< Number of histogram bins per channel + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIteratorRA, ///< The input iterator type (may be a simple pointer type). Must have a value type that can be cast as an integer in the range [0..BINS-1] + typename HistoCounter, ///< Integral type for counting sample occurrences per histogram bin + typename SizeT> ///< Integer type for offsets +struct BlockHistogramTilesSort +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Sample type + typedef typename std::iterator_traits::value_type SampleT; + + // Constants + enum + { + BLOCK_THREADS = BlockHistogramTilesPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockHistogramTilesPolicy::ITEMS_PER_THREAD, + TILE_CHANNEL_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + TILE_ITEMS = TILE_CHANNEL_ITEMS * CHANNELS, + + STRIPED_COUNTERS_PER_THREAD = (BINS + BLOCK_THREADS - 1) / BLOCK_THREADS, + }; + + // Parameterize BlockRadixSort type for our thread block + typedef BlockRadixSort BlockRadixSortT; + + // Parameterize BlockDiscontinuity type for our thread block + typedef BlockDiscontinuity BlockDiscontinuityT; + + /// Shared memory type required by this thread block + union _TempStorage + { + // Storage for sorting bin values + typename BlockRadixSortT::TempStorage sort; + + struct + { + // Storage for detecting discontinuities in the tile of sorted bin values + typename BlockDiscontinuityT::TempStorage flag; + + // Storage for noting begin/end offsets of bin runs in the tile of sorted bin values + int run_begin[BLOCK_THREADS * STRIPED_COUNTERS_PER_THREAD]; + int run_end[BLOCK_THREADS * STRIPED_COUNTERS_PER_THREAD]; + }; + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + // Discontinuity functor + struct DiscontinuityOp + { + // Reference to temp_storage + _TempStorage &temp_storage; + + // Constructor + __device__ __forceinline__ DiscontinuityOp(_TempStorage &temp_storage) : + temp_storage(temp_storage) + {} + + // Discontinuity predicate + __device__ __forceinline__ bool operator()(const SampleT &a, const SampleT &b, int b_index) + { + if (a != b) + { + // Note the begin/end offsets in shared storage + temp_storage.run_begin[b] = b_index; + temp_storage.run_end[a] = b_index; + + return true; + } + else + { + return false; + } + } + }; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + /// Reference to temp_storage + _TempStorage &temp_storage; + + /// Histogram counters striped across threads + HistoCounter thread_counters[ACTIVE_CHANNELS][STRIPED_COUNTERS_PER_THREAD]; + + /// Reference to output histograms + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]; + + /// Input data to reduce + InputIteratorRA d_in; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockHistogramTilesSort( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIteratorRA d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) ///< Reference to output histograms + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + d_out_histograms(d_out_histograms) + { + // Initialize histogram counters striped across threads + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + thread_counters[CHANNEL][COUNTER] = 0; + } + } + } + + + /** + * Composite a tile of input items + */ + __device__ __forceinline__ void Composite( + SampleT (&items)[ITEMS_PER_THREAD], ///< Tile of samples + HistoCounter thread_counters[STRIPED_COUNTERS_PER_THREAD]) ///< Histogram counters striped across threads + { + // Sort bytes in blocked arrangement + BlockRadixSortT(temp_storage.sort).Sort(items); + + __syncthreads(); + + // Initialize the shared memory's run_begin and run_end for each bin + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + temp_storage.run_begin[(COUNTER * BLOCK_THREADS) + threadIdx.x] = TILE_CHANNEL_ITEMS; + temp_storage.run_end[(COUNTER * BLOCK_THREADS) + threadIdx.x] = TILE_CHANNEL_ITEMS; + } + + __syncthreads(); + + // Note the begin/end run offsets of bin runs in the sorted tile + int flags[ITEMS_PER_THREAD]; // unused + DiscontinuityOp flag_op(temp_storage); + BlockDiscontinuityT(temp_storage.flag).FlagHeads(flags, items, flag_op); + + // Update begin for first item + if (threadIdx.x == 0) temp_storage.run_begin[items[0]] = 0; + + __syncthreads(); + + // Composite into histogram + // Initialize the shared memory's run_begin and run_end for each bin + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + int bin = (COUNTER * BLOCK_THREADS) + threadIdx.x; + HistoCounter run_length = temp_storage.run_end[bin] - temp_storage.run_begin[bin]; + + thread_counters[COUNTER] += run_length; + } + } + + + /** + * Process one channel within a tile. + */ + template + __device__ __forceinline__ void ConsumeTileChannel( + int channel, + SizeT block_offset, + int valid_items) + { + // Load items in striped fashion + if (FULL_TILE) + { + // Full tile of samples to read and composite + SampleT items[ITEMS_PER_THREAD]; + + // Unguarded loads + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = d_in[channel + block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS)]; + } + + // Composite our histogram data + Composite(items, thread_counters[channel]); + } + else + { + // Only a partially-full tile of samples to read and composite + SampleT items[ITEMS_PER_THREAD]; + + // Assign our tid as the bin for out-of-bounds items (to give an even distribution), and keep track of how oob items to subtract out later + int bounds = (valid_items - (threadIdx.x * CHANNELS)); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = ((ITEM * BLOCK_THREADS * CHANNELS) < bounds) ? + d_in[channel + block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS)] : + 0; + } + + // Composite our histogram data + Composite(items, thread_counters[channel]); + + __syncthreads(); + + // Correct the overcounting in the zero-bin from invalid (out-of-bounds) items + if (threadIdx.x == 0) + { + int extra = (TILE_ITEMS - valid_items) / CHANNELS; + thread_counters[channel][0] -= extra; + } + } + } + + + /** + * Template iteration over channels (to silence not-unrolled warnings for SM10-13). Inductive step. + */ + template + struct IterateChannels + { + /** + * Process one channel within a tile. + */ + static __device__ __forceinline__ void ConsumeTileChannel( + BlockHistogramTilesSort *cta, + SizeT block_offset, + int valid_items) + { + __syncthreads(); + + cta->ConsumeTileChannel(CHANNEL, block_offset, valid_items); + + IterateChannels::ConsumeTileChannel(cta, block_offset, valid_items); + } + }; + + + /** + * Template iteration over channels (to silence not-unrolled warnings for SM10-13). Base step. + */ + template + struct IterateChannels + { + static __device__ __forceinline__ void ConsumeTileChannel(BlockHistogramTilesSort *cta, SizeT block_offset, int valid_items) {} + }; + + + /** + * Process a single tile of input + */ + template + __device__ __forceinline__ void ConsumeTile( + SizeT block_offset, ///< The offset the tile to consume + int valid_items = TILE_ITEMS) ///< The number of valid items in the tile + { + // First channel + ConsumeTileChannel(0, block_offset, valid_items); + + // Iterate through remaining channels + IterateChannels::ConsumeTileChannel(this, block_offset, valid_items); + } + + + /** + * Aggregate results into output + */ + __device__ __forceinline__ void AggregateOutput() + { + // Copy counters striped across threads into the histogram output + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + int channel_offset = (blockIdx.x * BINS); + + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + int bin = (COUNTER * BLOCK_THREADS) + threadIdx.x; + + if ((STRIPED_COUNTERS_PER_THREAD * BLOCK_THREADS == BINS) || (bin < BINS)) + { + d_out_histograms[CHANNEL][channel_offset + bin] = thread_counters[CHANNEL][COUNTER]; + } + } + } + } +}; + + + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_histo.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_histo.cuh new file mode 100644 index 0000000000000000000000000000000000000000..d26e338bed9dfb8f4eb2899692c1e18f3d16cc1f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_histo.cuh @@ -0,0 +1,319 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockRegionHistogram implements a stateful abstraction of CUDA thread blocks for participating in device-wide selection across a region of tiles. + */ + +#pragma once + +#include + +#include "specializations/block_region_histo_gatomic.cuh" +#include "specializations/block_region_histo_satomic.cuh" +#include "specializations/block_region_histo_sort.cuh" +#include "../../util_type.cuh" +#include "../../grid/grid_mapping.cuh" +#include "../../grid/grid_even_share.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Algorithmic variants + ******************************************************************************/ + + +/** + * \brief DeviceHistogramAlgorithm enumerates alternative algorithms for BlockRegionHistogram. + */ +enum DeviceHistogramAlgorithm +{ + + /** + * \par Overview + * A two-kernel approach in which: + * -# Thread blocks in the first kernel aggregate their own privatized + * histograms using block-wide sorting (see BlockHistogramAlgorithm::BLOCK_HISTO_SORT). + * -# A single thread block in the second kernel reduces them into the output histogram(s). + * + * \par Performance Considerations + * Delivers consistent throughput regardless of sample bin distribution. + * + * However, because histograms are privatized in shared memory, a large + * number of bins (e.g., thousands) may adversely affect occupancy and + * performance (or even the ability to launch). + */ + DEVICE_HISTO_SORT, + + + /** + * \par Overview + * A two-kernel approach in which: + * -# Thread blocks in the first kernel aggregate their own privatized + * histograms using shared-memory \p atomicAdd(). + * -# A single thread block in the second kernel reduces them into the + * output histogram(s). + * + * \par Performance Considerations + * Performance is strongly tied to the hardware implementation of atomic + * addition, and may be significantly degraded for non uniformly-random + * input distributions where many concurrent updates are likely to be + * made to the same bin counter. + * + * However, because histograms are privatized in shared memory, a large + * number of bins (e.g., thousands) may adversely affect occupancy and + * performance (or even the ability to launch). + */ + DEVICE_HISTO_SHARED_ATOMIC, + + + /** + * \par Overview + * A single-kernel approach in which thread blocks update the output histogram(s) directly + * using global-memory \p atomicAdd(). + * + * \par Performance Considerations + * Performance is strongly tied to the hardware implementation of atomic + * addition, and may be significantly degraded for non uniformly-random + * input distributions where many concurrent updates are likely to be + * made to the same bin counter. + * + * Performance is not significantly impacted when computing histograms having large + * numbers of bins (e.g., thousands). + */ + DEVICE_HISTO_GLOBAL_ATOMIC, + +}; + + +/****************************************************************************** + * Tuning policy + ******************************************************************************/ + +/** + * Parameterizable tuning policy type for BlockRegionHistogram + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + DeviceHistogramAlgorithm _HISTO_ALGORITHM, ///< Cooperative histogram algorithm to use + GridMappingStrategy _GRID_MAPPING> ///< How to map tiles of input onto thread blocks +struct BlockRegionHistogramPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, ///< Threads per thread block + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + }; + + static const DeviceHistogramAlgorithm HISTO_ALGORITHM = _HISTO_ALGORITHM; ///< Cooperative histogram algorithm to use + static const GridMappingStrategy GRID_MAPPING = _GRID_MAPPING; ///< How to map tiles of input onto thread blocks +}; + + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockRegionHistogram implements a stateful abstraction of CUDA thread blocks for participating in device-wide selection across a region of tiles. + */ +template < + typename BlockRegionHistogramPolicy, ///< Parameterized BlockRegionHistogramPolicy tuning policy type + int BINS, ///< Number of histogram bins per channel + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIterator, ///< Random-access input iterator type for reading samples. Must have an an InputIterator::value_type that, when cast as an integer, falls in the range [0..BINS-1] + typename HistoCounter, ///< Integer type for counting sample occurrences per histogram bin + typename Offset> ///< Signed integer type for global offsets +struct BlockRegionHistogram +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Histogram grid algorithm + static const DeviceHistogramAlgorithm HISTO_ALGORITHM = BlockRegionHistogramPolicy::HISTO_ALGORITHM; + + // Alternative internal implementation types + typedef BlockRegionHistogramSort< BlockRegionHistogramPolicy, BINS, CHANNELS, ACTIVE_CHANNELS, InputIterator, HistoCounter, Offset> BlockRegionHistogramSortT; + typedef BlockRegionHistogramSharedAtomic< BlockRegionHistogramPolicy, BINS, CHANNELS, ACTIVE_CHANNELS, InputIterator, HistoCounter, Offset> BlockRegionHistogramSharedAtomicT; + typedef BlockRegionHistogramGlobalAtomic< BlockRegionHistogramPolicy, BINS, CHANNELS, ACTIVE_CHANNELS, InputIterator, HistoCounter, Offset> BlockRegionHistogramGlobalAtomicT; + + // Internal block sweep histogram type + typedef typename If<(HISTO_ALGORITHM == DEVICE_HISTO_SORT), + BlockRegionHistogramSortT, + typename If<(HISTO_ALGORITHM == DEVICE_HISTO_SHARED_ATOMIC), + BlockRegionHistogramSharedAtomicT, + BlockRegionHistogramGlobalAtomicT>::Type>::Type InternalBlockDelegate; + + enum + { + TILE_ITEMS = InternalBlockDelegate::TILE_ITEMS, + }; + + + // Temporary storage type + typedef typename InternalBlockDelegate::TempStorage TempStorage; + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + // Internal block delegate + InternalBlockDelegate internal_delegate; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockRegionHistogram( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIterator d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) ///< Reference to output histograms + : + internal_delegate(temp_storage, d_in, d_out_histograms) + {} + + + /** + * \brief Reduce a consecutive segment of input tiles + */ + __device__ __forceinline__ void ConsumeRegion( + Offset block_offset, ///< [in] Threadblock begin offset (inclusive) + Offset block_end) ///< [in] Threadblock end offset (exclusive) + { + // Consume subsequent full tiles of input + while (block_offset + TILE_ITEMS <= block_end) + { + internal_delegate.ConsumeTile(block_offset); + block_offset += TILE_ITEMS; + } + + // Consume a partially-full tile + if (block_offset < block_end) + { + int valid_items = block_end - block_offset; + internal_delegate.ConsumeTile(block_offset, valid_items); + } + + // Aggregate output + internal_delegate.AggregateOutput(); + } + + + /** + * Reduce a consecutive segment of input tiles + */ + __device__ __forceinline__ void ConsumeRegion( + Offset num_items, ///< [in] Total number of global input items + GridEvenShare &even_share, ///< [in] GridEvenShare descriptor + GridQueue &queue, ///< [in,out] GridQueue descriptor + Int2Type is_even_share) ///< [in] Marker type indicating this is an even-share mapping + { + even_share.BlockInit(); + ConsumeRegion(even_share.block_offset, even_share.block_end); + } + + + /** + * Dequeue and reduce tiles of items as part of a inter-block scan + */ + __device__ __forceinline__ void ConsumeRegion( + int num_items, ///< Total number of input items + GridQueue queue) ///< Queue descriptor for assigning tiles of work to thread blocks + { + // Shared block offset + __shared__ Offset shared_block_offset; + + // We give each thread block at least one tile of input. + Offset block_offset = blockIdx.x * TILE_ITEMS; + Offset even_share_base = gridDim.x * TILE_ITEMS; + + // Process full tiles of input + while (block_offset + TILE_ITEMS <= num_items) + { + internal_delegate.ConsumeTile(block_offset); + + // Dequeue up to TILE_ITEMS + if (threadIdx.x == 0) + shared_block_offset = queue.Drain(TILE_ITEMS) + even_share_base; + + __syncthreads(); + + block_offset = shared_block_offset; + + __syncthreads(); + } + + // Consume a partially-full tile + if (block_offset < num_items) + { + int valid_items = num_items - block_offset; + internal_delegate.ConsumeTile(block_offset, valid_items); + } + + // Aggregate output + internal_delegate.AggregateOutput(); + } + + + /** + * Dequeue and reduce tiles of items as part of a inter-block scan + */ + __device__ __forceinline__ void ConsumeRegion( + Offset num_items, ///< [in] Total number of global input items + GridEvenShare &even_share, ///< [in] GridEvenShare descriptor + GridQueue &queue, ///< [in,out] GridQueue descriptor + Int2Type is_dynamic) ///< [in] Marker type indicating this is a dynamic mapping + { + ConsumeRegion(num_items, queue); + } + + +}; + + + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_radix_sort_downsweep.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_radix_sort_downsweep.cuh new file mode 100644 index 0000000000000000000000000000000000000000..5e8f6e3531b67dc69c2f56a3a94bf992da849fbb --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_radix_sort_downsweep.cuh @@ -0,0 +1,736 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * BlockRegionRadixSortDownsweep implements a stateful abstraction of CUDA thread blocks for participating in device-wide radix sort downsweep across a region of tiles. + */ + + +#pragma once + +#include "../../thread/thread_load.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_store.cuh" +#include "../../block/block_radix_rank.cuh" +#include "../../block/block_exchange.cuh" +#include "../../util_type.cuh" +#include "../../iterator/cache_modified_input_iterator.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Types of scattering strategies + */ +enum RadixSortScatterAlgorithm +{ + RADIX_SORT_SCATTER_DIRECT, ///< Scatter directly from registers to global bins + RADIX_SORT_SCATTER_TWO_PHASE, ///< First scatter from registers into shared memory bins, then into global bins +}; + + +/** + * Parameterizable tuning policy type for BlockRegionRadixSortDownsweep + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + BlockLoadAlgorithm _LOAD_ALGORITHM, ///< The BlockLoad algorithm to use + CacheLoadModifier _LOAD_MODIFIER, ///< Cache load modifier for reading keys (and values) + bool _EXCHANGE_TIME_SLICING, ///< Whether or not to time-slice key/value exchanges through shared memory to lower shared memory pressure + bool _MEMOIZE_OUTER_SCAN, ///< Whether or not to buffer outer raking scan partials to incur fewer shared memory reads at the expense of higher register pressure. See BlockScanAlgorithm::BLOCK_SCAN_RAKING_MEMOIZE for more details. + BlockScanAlgorithm _INNER_SCAN_ALGORITHM, ///< The BlockScan algorithm algorithm to use + RadixSortScatterAlgorithm _SCATTER_ALGORITHM, ///< The scattering strategy to use + cudaSharedMemConfig _SMEM_CONFIG, ///< Shared memory bank mode + int _RADIX_BITS> ///< The number of radix bits, i.e., log2(bins) +struct BlockRegionRadixSortDownsweepPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, ///< Threads per thread block + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + EXCHANGE_TIME_SLICING = _EXCHANGE_TIME_SLICING, ///< Whether or not to time-slice key/value exchanges through shared memory to lower shared memory pressure + RADIX_BITS = _RADIX_BITS, ///< The number of radix bits, i.e., log2(bins) + MEMOIZE_OUTER_SCAN = _MEMOIZE_OUTER_SCAN, ///< Whether or not to buffer outer raking scan partials to incur fewer shared memory reads at the expense of higher register pressure. See BlockScanAlgorithm::BLOCK_SCAN_RAKING_MEMOIZE for more details. + }; + + static const BlockLoadAlgorithm LOAD_ALGORITHM = _LOAD_ALGORITHM; ///< The BlockLoad algorithm to use + static const CacheLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; ///< Cache load modifier for reading keys (and values) + static const BlockScanAlgorithm INNER_SCAN_ALGORITHM = _INNER_SCAN_ALGORITHM; ///< The BlockScan algorithm algorithm to use + static const RadixSortScatterAlgorithm SCATTER_ALGORITHM = _SCATTER_ALGORITHM; ///< The scattering strategy to use + static const cudaSharedMemConfig SMEM_CONFIG = _SMEM_CONFIG; ///< Shared memory bank mode +}; + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockRegionRadixSortDownsweep implements a stateful abstraction of CUDA thread blocks for participating in device-wide radix sort downsweep across a region of tiles. + */ +template < + typename BlockRegionRadixSortDownsweepPolicy, ///< Parameterized BlockRegionRadixSortDownsweepPolicy tuning policy type + bool DESCENDING, ///< Whether or not the sorted-order is high-to-low + typename Key, ///< Key type + typename Value, ///< Value type + typename Offset> ///< Signed integer type for global offsets +struct BlockRegionRadixSortDownsweep +{ + //--------------------------------------------------------------------- + // Type definitions and constants + //--------------------------------------------------------------------- + + // Appropriate unsigned-bits representation of Key + typedef typename Traits::UnsignedBits UnsignedBits; + + static const UnsignedBits MIN_KEY = Traits::MIN_KEY; + static const UnsignedBits MAX_KEY = Traits::MAX_KEY; + + static const BlockLoadAlgorithm LOAD_ALGORITHM = BlockRegionRadixSortDownsweepPolicy::LOAD_ALGORITHM; + static const CacheLoadModifier LOAD_MODIFIER = BlockRegionRadixSortDownsweepPolicy::LOAD_MODIFIER; + static const BlockScanAlgorithm INNER_SCAN_ALGORITHM = BlockRegionRadixSortDownsweepPolicy::INNER_SCAN_ALGORITHM; + static const RadixSortScatterAlgorithm SCATTER_ALGORITHM = BlockRegionRadixSortDownsweepPolicy::SCATTER_ALGORITHM; + static const cudaSharedMemConfig SMEM_CONFIG = BlockRegionRadixSortDownsweepPolicy::SMEM_CONFIG; + + enum + { + BLOCK_THREADS = BlockRegionRadixSortDownsweepPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockRegionRadixSortDownsweepPolicy::ITEMS_PER_THREAD, + EXCHANGE_TIME_SLICING = BlockRegionRadixSortDownsweepPolicy::EXCHANGE_TIME_SLICING, + RADIX_BITS = BlockRegionRadixSortDownsweepPolicy::RADIX_BITS, + MEMOIZE_OUTER_SCAN = BlockRegionRadixSortDownsweepPolicy::MEMOIZE_OUTER_SCAN, + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + + RADIX_DIGITS = 1 << RADIX_BITS, + KEYS_ONLY = Equals::VALUE, + + WARP_THREADS = CUB_PTX_LOG_WARP_THREADS, + WARPS = (BLOCK_THREADS + WARP_THREADS - 1) / WARP_THREADS, + + BYTES_PER_SIZET = sizeof(Offset), + LOG_BYTES_PER_SIZET = Log2::VALUE, + + LOG_SMEM_BANKS = CUB_PTX_LOG_SMEM_BANKS, + SMEM_BANKS = 1 << LOG_SMEM_BANKS, + + DIGITS_PER_SCATTER_PASS = BLOCK_THREADS / SMEM_BANKS, + SCATTER_PASSES = RADIX_DIGITS / DIGITS_PER_SCATTER_PASS, + + LOG_STORE_TXN_THREADS = LOG_SMEM_BANKS, + STORE_TXN_THREADS = 1 << LOG_STORE_TXN_THREADS, + }; + + // Input iterator wrapper types + typedef CacheModifiedInputIterator KeysItr; + typedef CacheModifiedInputIterator ValuesItr; + + // BlockRadixRank type + typedef BlockRadixRank< + BLOCK_THREADS, + RADIX_BITS, + DESCENDING, + MEMOIZE_OUTER_SCAN, + INNER_SCAN_ALGORITHM, + SMEM_CONFIG> BlockRadixRank; + + // BlockLoad type (keys) + typedef BlockLoad< + KeysItr, + BLOCK_THREADS, + ITEMS_PER_THREAD, + LOAD_ALGORITHM, + EXCHANGE_TIME_SLICING> BlockLoadKeys; + + // BlockLoad type (values) + typedef BlockLoad< + ValuesItr, + BLOCK_THREADS, + ITEMS_PER_THREAD, + LOAD_ALGORITHM, + EXCHANGE_TIME_SLICING> BlockLoadValues; + + // BlockExchange type (keys) + typedef BlockExchange< + UnsignedBits, + BLOCK_THREADS, + ITEMS_PER_THREAD, + EXCHANGE_TIME_SLICING> BlockExchangeKeys; + + // BlockExchange type (values) + typedef BlockExchange< + Value, + BLOCK_THREADS, + ITEMS_PER_THREAD, + EXCHANGE_TIME_SLICING> BlockExchangeValues; + + + /** + * Shared memory storage layout + */ + struct _TempStorage + { + Offset relative_bin_offsets[RADIX_DIGITS + 1]; + bool short_circuit; + + union + { + typename BlockRadixRank::TempStorage ranking; + typename BlockLoadKeys::TempStorage load_keys; + typename BlockLoadValues::TempStorage load_values; + typename BlockExchangeKeys::TempStorage exchange_keys; + typename BlockExchangeValues::TempStorage exchange_values; + }; + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Thread fields + //--------------------------------------------------------------------- + + // Shared storage for this CTA + _TempStorage &temp_storage; + + // Input and output device pointers + KeysItr d_keys_in; + ValuesItr d_values_in; + UnsignedBits *d_keys_out; + Value *d_values_out; + + // The global scatter base offset for each digit (valid in the first RADIX_DIGITS threads) + Offset bin_offset; + + // The least-significant bit position of the current digit to extract + int current_bit; + + // Whether to short-ciruit + bool short_circuit; + + + + //--------------------------------------------------------------------- + // Utility methods + //--------------------------------------------------------------------- + + /** + * Decodes given keys to lookup digit offsets in shared memory + */ + __device__ __forceinline__ void DecodeRelativeBinOffsets( + UnsignedBits (&twiddled_keys)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD]) + { + #pragma unroll + for (int KEY = 0; KEY < ITEMS_PER_THREAD; KEY++) + { + UnsignedBits digit = BFE(twiddled_keys[KEY], current_bit, RADIX_BITS); + + // Lookup base digit offset from shared memory + relative_bin_offsets[KEY] = temp_storage.relative_bin_offsets[digit]; + } + } + + + /** + * Scatter ranked items to global memory + */ + template + __device__ __forceinline__ void ScatterItems( + T (&items)[ITEMS_PER_THREAD], + int (&local_ranks)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD], + T *d_out, + Offset valid_items) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + // Scatter if not out-of-bounds + if (FULL_TILE || (local_ranks[ITEM] < valid_items)) + { + d_out[relative_bin_offsets[ITEM] + local_ranks[ITEM]] = items[ITEM]; + } + } + } + + + /** + * Scatter ranked keys directly to global memory + */ + template + __device__ __forceinline__ void ScatterKeys( + UnsignedBits (&twiddled_keys)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Offset valid_items, + Int2Type scatter_algorithm) + { + // Compute scatter offsets + DecodeRelativeBinOffsets(twiddled_keys, relative_bin_offsets); + + // Untwiddle keys before outputting + UnsignedBits keys[ITEMS_PER_THREAD]; + + #pragma unroll + for (int KEY = 0; KEY < ITEMS_PER_THREAD; KEY++) + { + keys[KEY] = Traits::TwiddleOut(twiddled_keys[KEY]); + } + + // Scatter to global + ScatterItems(keys, ranks, relative_bin_offsets, d_keys_out, valid_items); + } + + + /** + * Scatter ranked keys through shared memory, then to global memory + */ + template + __device__ __forceinline__ void ScatterKeys( + UnsignedBits (&twiddled_keys)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Offset valid_items, + Int2Type scatter_algorithm) + { + // Exchange keys through shared memory + BlockExchangeKeys(temp_storage.exchange_keys).ScatterToStriped(twiddled_keys, ranks); + + // Compute striped local ranks + int local_ranks[ITEMS_PER_THREAD]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + local_ranks[ITEM] = threadIdx.x + (ITEM * BLOCK_THREADS); + } + + // Scatter directly + ScatterKeys( + twiddled_keys, + relative_bin_offsets, + local_ranks, + valid_items, + Int2Type()); + } + + + /** + * Scatter ranked values directly to global memory + */ + template + __device__ __forceinline__ void ScatterValues( + Value (&values)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Offset valid_items, + Int2Type scatter_algorithm) + { + // Scatter to global + ScatterItems(values, ranks, relative_bin_offsets, d_values_out, valid_items); + } + + + /** + * Scatter ranked values through shared memory, then to global memory + */ + template + __device__ __forceinline__ void ScatterValues( + Value (&values)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Offset valid_items, + Int2Type scatter_algorithm) + { + __syncthreads(); + + // Exchange keys through shared memory + BlockExchangeValues(temp_storage.exchange_values).ScatterToStriped(values, ranks); + + // Compute striped local ranks + int local_ranks[ITEMS_PER_THREAD]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + local_ranks[ITEM] = threadIdx.x + (ITEM * BLOCK_THREADS); + } + + // Scatter directly + ScatterValues( + values, + relative_bin_offsets, + local_ranks, + valid_items, + Int2Type()); + } + + + /** + * Load a tile of items (specialized for full tile) + */ + template + __device__ __forceinline__ void LoadItems( + BlockLoadT &block_loader, + T (&items)[ITEMS_PER_THREAD], + InputIterator d_in, + Offset valid_items, + Int2Type is_full_tile) + { + block_loader.Load(d_in, items); + } + + + /** + * Load a tile of items (specialized for partial tile) + */ + template + __device__ __forceinline__ void LoadItems( + BlockLoadT &block_loader, + T (&items)[ITEMS_PER_THREAD], + InputIterator d_in, + Offset valid_items, + Int2Type is_full_tile) + { + block_loader.Load(d_in, items, valid_items); + } + + + /** + * Truck along associated values + */ + template + __device__ __forceinline__ void GatherScatterValues( + _Value (&values)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Offset block_offset, + Offset valid_items) + { + __syncthreads(); + + BlockLoadValues loader(temp_storage.load_values); + LoadItems( + loader, + values, + d_values_in + block_offset, + valid_items, + Int2Type()); + + ScatterValues( + values, + relative_bin_offsets, + ranks, + valid_items, + Int2Type()); + } + + + /** + * Truck along associated values (specialized for key-only sorting) + */ + template + __device__ __forceinline__ void GatherScatterValues( + NullType (&values)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Offset block_offset, + Offset valid_items) + {} + + + /** + * Process tile + */ + template + __device__ __forceinline__ void ProcessTile( + Offset block_offset, + const Offset &valid_items = TILE_ITEMS) + { + // Per-thread tile data + UnsignedBits keys[ITEMS_PER_THREAD]; // Keys + UnsignedBits twiddled_keys[ITEMS_PER_THREAD]; // Twiddled keys + int ranks[ITEMS_PER_THREAD]; // For each key, the local rank within the CTA + Offset relative_bin_offsets[ITEMS_PER_THREAD]; // For each key, the global scatter base offset of the corresponding digit + + // Assign max-key to all keys + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + keys[ITEM] = (DESCENDING) ? MIN_KEY : MAX_KEY; + } + + // Load tile of keys + BlockLoadKeys loader(temp_storage.load_keys); + LoadItems( + loader, + keys, + d_keys_in + block_offset, + valid_items, + Int2Type()); + + __syncthreads(); + + // Twiddle key bits if necessary + #pragma unroll + for (int KEY = 0; KEY < ITEMS_PER_THREAD; KEY++) + { + twiddled_keys[KEY] = Traits::TwiddleIn(keys[KEY]); + } + + // Rank the twiddled keys + int inclusive_digit_prefix; + BlockRadixRank(temp_storage.ranking).RankKeys( + twiddled_keys, + ranks, + current_bit, + inclusive_digit_prefix); + + // Update global scatter base offsets for each digit + if ((BLOCK_THREADS == RADIX_DIGITS) || (threadIdx.x < RADIX_DIGITS)) + { + int exclusive_digit_prefix; + + // Get exclusive digit prefix from inclusive prefix + if (DESCENDING) + { + // Get the prefix from the next thread (higher bins come first) +#if CUB_PTX_VERSION >= 300 + exclusive_digit_prefix = ShuffleDown(inclusive_digit_prefix, 1); + if (threadIdx.x == RADIX_DIGITS - 1) + exclusive_digit_prefix = 0; +#else + volatile int* exchange = reinterpret_cast(temp_storage.relative_bin_offsets); + exchange[threadIdx.x + 1] = 0; + exchange[threadIdx.x] = inclusive_digit_prefix; + exclusive_digit_prefix = exchange[threadIdx.x + 1]; +#endif + } + else + { + // Get the prefix from the previous thread (lower bins come first) +#if CUB_PTX_VERSION >= 300 + exclusive_digit_prefix = ShuffleUp(inclusive_digit_prefix, 1); + if (threadIdx.x == 0) + exclusive_digit_prefix = 0; +#else + volatile int* exchange = reinterpret_cast(temp_storage.relative_bin_offsets); + exchange[threadIdx.x] = 0; + exchange[threadIdx.x + 1] = inclusive_digit_prefix; + exclusive_digit_prefix = exchange[threadIdx.x]; +#endif + } + + bin_offset -= exclusive_digit_prefix; + temp_storage.relative_bin_offsets[threadIdx.x] = bin_offset; + bin_offset += inclusive_digit_prefix; + } + + __syncthreads(); + + // Scatter keys + ScatterKeys(twiddled_keys, relative_bin_offsets, ranks, valid_items, Int2Type()); + + // Gather/scatter values + Value values[ITEMS_PER_THREAD]; + GatherScatterValues(values, relative_bin_offsets, ranks, block_offset, valid_items); + } + + + /** + * Copy tiles within the range of input + */ + template < + typename InputIterator, + typename T> + __device__ __forceinline__ void Copy( + InputIterator d_in, + T *d_out, + Offset block_offset, + Offset block_end) + { + // Simply copy the input + while (block_offset + TILE_ITEMS <= block_end) + { + T items[ITEMS_PER_THREAD]; + + LoadDirectStriped(threadIdx.x, d_in + block_offset, items); + __syncthreads(); + StoreDirectStriped(threadIdx.x, d_out + block_offset, items); + + block_offset += TILE_ITEMS; + } + + // Clean up last partial tile with guarded-I/O + if (block_offset < block_end) + { + Offset valid_items = block_end - block_offset; + + T items[ITEMS_PER_THREAD]; + + LoadDirectStriped(threadIdx.x, d_in + block_offset, items, valid_items); + __syncthreads(); + StoreDirectStriped(threadIdx.x, d_out + block_offset, items, valid_items); + } + } + + + /** + * Copy tiles within the range of input (specialized for NullType) + */ + template + __device__ __forceinline__ void Copy( + InputIterator d_in, + NullType *d_out, + Offset block_offset, + Offset block_end) + {} + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockRegionRadixSortDownsweep( + TempStorage &temp_storage, + Offset bin_offset, + Key *d_keys_in, + Key *d_keys_out, + Value *d_values_in, + Value *d_values_out, + int current_bit) + : + temp_storage(temp_storage.Alias()), + bin_offset(bin_offset), + d_keys_in(reinterpret_cast(d_keys_in)), + d_keys_out(reinterpret_cast(d_keys_out)), + d_values_in(d_values_in), + d_values_out(d_values_out), + current_bit(current_bit), + short_circuit(false) + {} + + + /** + * Constructor + */ + __device__ __forceinline__ BlockRegionRadixSortDownsweep( + TempStorage &temp_storage, + Offset num_items, + Offset *d_spine, + Key *d_keys_in, + Key *d_keys_out, + Value *d_values_in, + Value *d_values_out, + int current_bit) + : + temp_storage(temp_storage.Alias()), + d_keys_in(reinterpret_cast(d_keys_in)), + d_keys_out(reinterpret_cast(d_keys_out)), + d_values_in(d_values_in), + d_values_out(d_values_out), + current_bit(current_bit) + { + // Load digit bin offsets (each of the first RADIX_DIGITS threads will load an offset for that digit) + if (threadIdx.x < RADIX_DIGITS) + { + int bin_idx = (DESCENDING) ? + RADIX_DIGITS - threadIdx.x - 1 : + threadIdx.x; + + // Short circuit if the first block's histogram has only bin counts of only zeros or problem-size + Offset first_block_bin_offset = d_spine[gridDim.x * bin_idx]; + int predicate = ((first_block_bin_offset == 0) || (first_block_bin_offset == num_items)); + this->temp_storage.short_circuit = WarpAll(predicate); + + // Load my block's bin offset for my bin + bin_offset = d_spine[(gridDim.x * bin_idx) + blockIdx.x]; + } + + __syncthreads(); + + short_circuit = this->temp_storage.short_circuit; + } + + + /** + * Distribute keys from a segment of input tiles. + */ + __device__ __forceinline__ void ProcessRegion( + Offset block_offset, + const Offset &block_end) + { + if (short_circuit) + { + // Copy keys + Copy(d_keys_in, d_keys_out, block_offset, block_end); + + // Copy values + Copy(d_values_in, d_values_out, block_offset, block_end); + } + else + { + // Process full tiles of tile_items + while (block_offset + TILE_ITEMS <= block_end) + { + ProcessTile(block_offset); + block_offset += TILE_ITEMS; + + __syncthreads(); + } + + // Clean up last partial tile with guarded-I/O + if (block_offset < block_end) + { + ProcessTile(block_offset, block_end - block_offset); + } + } + } +}; + + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_radix_sort_upsweep.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_radix_sort_upsweep.cuh new file mode 100644 index 0000000000000000000000000000000000000000..d8adee02ee89266d329605a8d7d7cdbd5f4136c5 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_radix_sort_upsweep.cuh @@ -0,0 +1,443 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * BlockRegionRadixSortUpsweep implements a stateful abstraction of CUDA thread blocks for participating in device-wide radix sort upsweep across a region of tiles. + */ + +#pragma once + +#include "../../thread/thread_reduce.cuh" +#include "../../thread/thread_load.cuh" +#include "../../block/block_load.cuh" +#include "../../util_type.cuh" +#include "../../iterator/cache_modified_input_iterator.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Parameterizable tuning policy type for BlockRegionRadixSortUpsweep + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + CacheLoadModifier _LOAD_MODIFIER, ///< Cache load modifier for reading keys + int _RADIX_BITS> ///< The number of radix bits, i.e., log2(bins) +struct BlockRegionRadixSortUpsweepPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, ///< Threads per thread block + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + RADIX_BITS = _RADIX_BITS, ///< The number of radix bits, i.e., log2(bins) + }; + + static const CacheLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; ///< Cache load modifier for reading keys +}; + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockRegionRadixSortUpsweep implements a stateful abstraction of CUDA thread blocks for participating in device-wide radix sort upsweep across a region of tiles. + */ +template < + typename BlockRegionRadixSortUpsweepPolicy, ///< Parameterized BlockRegionRadixSortUpsweepPolicy tuning policy type + typename Key, ///< Key type + typename Offset> ///< Signed integer type for global offsets +struct BlockRegionRadixSortUpsweep +{ + + //--------------------------------------------------------------------- + // Type definitions and constants + //--------------------------------------------------------------------- + + typedef typename Traits::UnsignedBits UnsignedBits; + + // Integer type for digit counters (to be packed into words of PackedCounters) + typedef unsigned char DigitCounter; + + // Integer type for packing DigitCounters into columns of shared memory banks + typedef unsigned int PackedCounter; + + static const CacheLoadModifier LOAD_MODIFIER = BlockRegionRadixSortUpsweepPolicy::LOAD_MODIFIER; + + enum + { + RADIX_BITS = BlockRegionRadixSortUpsweepPolicy::RADIX_BITS, + BLOCK_THREADS = BlockRegionRadixSortUpsweepPolicy::BLOCK_THREADS, + KEYS_PER_THREAD = BlockRegionRadixSortUpsweepPolicy::ITEMS_PER_THREAD, + + RADIX_DIGITS = 1 << RADIX_BITS, + + LOG_WARP_THREADS = CUB_PTX_LOG_WARP_THREADS, + WARP_THREADS = 1 << LOG_WARP_THREADS, + WARPS = (BLOCK_THREADS + WARP_THREADS - 1) / WARP_THREADS, + + TILE_ITEMS = BLOCK_THREADS * KEYS_PER_THREAD, + + BYTES_PER_COUNTER = sizeof(DigitCounter), + LOG_BYTES_PER_COUNTER = Log2::VALUE, + + PACKING_RATIO = sizeof(PackedCounter) / sizeof(DigitCounter), + LOG_PACKING_RATIO = Log2::VALUE, + + LOG_COUNTER_LANES = CUB_MAX(0, RADIX_BITS - LOG_PACKING_RATIO), + COUNTER_LANES = 1 << LOG_COUNTER_LANES, + + // To prevent counter overflow, we must periodically unpack and aggregate the + // digit counters back into registers. Each counter lane is assigned to a + // warp for aggregation. + + LANES_PER_WARP = CUB_MAX(1, (COUNTER_LANES + WARPS - 1) / WARPS), + + // Unroll tiles in batches without risk of counter overflow + UNROLL_COUNT = CUB_MIN(64, 255 / KEYS_PER_THREAD), + UNROLLED_ELEMENTS = UNROLL_COUNT * TILE_ITEMS, + }; + + + // Input iterator wrapper types + typedef CacheModifiedInputIterator KeysItr; + + /** + * Shared memory storage layout + */ + struct _TempStorage + { + union + { + DigitCounter digit_counters[COUNTER_LANES][BLOCK_THREADS][PACKING_RATIO]; + PackedCounter packed_counters[COUNTER_LANES][BLOCK_THREADS]; + Offset digit_partials[RADIX_DIGITS][WARP_THREADS + 1]; + }; + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Thread fields (aggregate state bundle) + //--------------------------------------------------------------------- + + // Shared storage for this CTA + _TempStorage &temp_storage; + + // Thread-local counters for periodically aggregating composite-counter lanes + Offset local_counts[LANES_PER_WARP][PACKING_RATIO]; + + // Input and output device pointers + KeysItr d_keys_in; + + // The least-significant bit position of the current digit to extract + int current_bit; + + + + //--------------------------------------------------------------------- + // Helper structure for templated iteration + //--------------------------------------------------------------------- + + // Iterate + template + struct Iterate + { + // BucketKeys + static __device__ __forceinline__ void BucketKeys( + BlockRegionRadixSortUpsweep &cta, + UnsignedBits keys[KEYS_PER_THREAD]) + { + cta.Bucket(keys[COUNT]); + + // Next + Iterate::BucketKeys(cta, keys); + } + }; + + // Terminate + template + struct Iterate + { + // BucketKeys + static __device__ __forceinline__ void BucketKeys(BlockRegionRadixSortUpsweep &cta, UnsignedBits keys[KEYS_PER_THREAD]) {} + }; + + + //--------------------------------------------------------------------- + // Utility methods + //--------------------------------------------------------------------- + + /** + * Decode a key and increment corresponding smem digit counter + */ + __device__ __forceinline__ void Bucket(UnsignedBits key) + { + // Perform transform op + UnsignedBits converted_key = Traits::TwiddleIn(key); + + // Add in sub-counter offset + UnsignedBits sub_counter = BFE(converted_key, current_bit, LOG_PACKING_RATIO); + + // Add in row offset + UnsignedBits row_offset = BFE(converted_key, current_bit + LOG_PACKING_RATIO, LOG_COUNTER_LANES); + + // Increment counter + temp_storage.digit_counters[row_offset][threadIdx.x][sub_counter]++; + + } + + + /** + * Reset composite counters + */ + __device__ __forceinline__ void ResetDigitCounters() + { + #pragma unroll + for (int LANE = 0; LANE < COUNTER_LANES; LANE++) + { + temp_storage.packed_counters[LANE][threadIdx.x] = 0; + } + } + + + /** + * Reset the unpacked counters in each thread + */ + __device__ __forceinline__ void ResetUnpackedCounters() + { + #pragma unroll + for (int LANE = 0; LANE < LANES_PER_WARP; LANE++) + { + #pragma unroll + for (int UNPACKED_COUNTER = 0; UNPACKED_COUNTER < PACKING_RATIO; UNPACKED_COUNTER++) + { + local_counts[LANE][UNPACKED_COUNTER] = 0; + } + } + } + + + /** + * Extracts and aggregates the digit counters for each counter lane + * owned by this warp + */ + __device__ __forceinline__ void UnpackDigitCounts() + { + unsigned int warp_id = threadIdx.x >> LOG_WARP_THREADS; + unsigned int warp_tid = threadIdx.x & (WARP_THREADS - 1); + + #pragma unroll + for (int LANE = 0; LANE < LANES_PER_WARP; LANE++) + { + const int counter_lane = (LANE * WARPS) + warp_id; + if (counter_lane < COUNTER_LANES) + { + #pragma unroll + for (int PACKED_COUNTER = 0; PACKED_COUNTER < BLOCK_THREADS; PACKED_COUNTER += WARP_THREADS) + { + #pragma unroll + for (int UNPACKED_COUNTER = 0; UNPACKED_COUNTER < PACKING_RATIO; UNPACKED_COUNTER++) + { + Offset counter = temp_storage.digit_counters[counter_lane][warp_tid + PACKED_COUNTER][UNPACKED_COUNTER]; + local_counts[LANE][UNPACKED_COUNTER] += counter; + } + } + } + } + } + + + /** + * Places unpacked counters into smem for final digit reduction + */ + __device__ __forceinline__ void ReduceUnpackedCounts(Offset &bin_count) + { + unsigned int warp_id = threadIdx.x >> LOG_WARP_THREADS; + unsigned int warp_tid = threadIdx.x & (WARP_THREADS - 1); + + // Place unpacked digit counters in shared memory + #pragma unroll + for (int LANE = 0; LANE < LANES_PER_WARP; LANE++) + { + int counter_lane = (LANE * WARPS) + warp_id; + if (counter_lane < COUNTER_LANES) + { + int digit_row = counter_lane << LOG_PACKING_RATIO; + + #pragma unroll + for (int UNPACKED_COUNTER = 0; UNPACKED_COUNTER < PACKING_RATIO; UNPACKED_COUNTER++) + { + temp_storage.digit_partials[digit_row + UNPACKED_COUNTER][warp_tid] = + local_counts[LANE][UNPACKED_COUNTER]; + } + } + } + + __syncthreads(); + + // Rake-reduce bin_count reductions + if (threadIdx.x < RADIX_DIGITS) + { + bin_count = ThreadReduce( + temp_storage.digit_partials[threadIdx.x], + Sum()); + } + } + + + /** + * Processes a single, full tile + */ + __device__ __forceinline__ void ProcessFullTile(Offset block_offset) + { + // Tile of keys + UnsignedBits keys[KEYS_PER_THREAD]; + + LoadDirectStriped(threadIdx.x, d_keys_in + block_offset, keys); + + // Prevent hoisting +// __threadfence_block(); +// __syncthreads(); + + // Bucket tile of keys + Iterate<0, KEYS_PER_THREAD>::BucketKeys(*this, keys); + } + + + /** + * Processes a single load (may have some threads masked off) + */ + __device__ __forceinline__ void ProcessPartialTile( + Offset block_offset, + const Offset &block_end) + { + // Process partial tile if necessary using single loads + block_offset += threadIdx.x; + while (block_offset < block_end) + { + // Load and bucket key + UnsignedBits key = d_keys_in[block_offset]; + Bucket(key); + block_offset += BLOCK_THREADS; + } + } + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockRegionRadixSortUpsweep( + TempStorage &temp_storage, + Key *d_keys_in, + int current_bit) + : + temp_storage(temp_storage.Alias()), + d_keys_in(reinterpret_cast(d_keys_in)), + current_bit(current_bit) + {} + + + /** + * Compute radix digit histograms from a segment of input tiles. + */ + __device__ __forceinline__ void ProcessRegion( + Offset block_offset, + const Offset &block_end, + Offset &bin_count) ///< [out] The digit count for tid'th bin (output param, valid in the first RADIX_DIGITS threads) + { + // Reset digit counters in smem and unpacked counters in registers + ResetDigitCounters(); + ResetUnpackedCounters(); + + // Unroll batches of full tiles + while (block_offset + UNROLLED_ELEMENTS <= block_end) + { + for (int i = 0; i < UNROLL_COUNT; ++i) + { + ProcessFullTile(block_offset); + block_offset += TILE_ITEMS; + } + + __syncthreads(); + + // Aggregate back into local_count registers to prevent overflow + UnpackDigitCounts(); + + __syncthreads(); + + // Reset composite counters in lanes + ResetDigitCounters(); + } + + // Unroll single full tiles + while (block_offset + TILE_ITEMS <= block_end) + { + ProcessFullTile(block_offset); + block_offset += TILE_ITEMS; + } + + // Process partial tile if necessary + ProcessPartialTile( + block_offset, + block_end); + + __syncthreads(); + + // Aggregate back into local_count registers + UnpackDigitCounts(); + + __syncthreads(); + + // Final raking reduction of counts by bin + ReduceUnpackedCounts(bin_count); + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_reduce.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_reduce.cuh new file mode 100644 index 0000000000000000000000000000000000000000..14a80bb407b3927259b2612289611d68c946573f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_reduce.cuh @@ -0,0 +1,430 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockRegionReduce implements a stateful abstraction of CUDA thread blocks for participating in device-wide reduction across a region of tiles. + */ + +#pragma once + +#include + +#include "../../block/block_load.cuh" +#include "../../block/block_reduce.cuh" +#include "../../grid/grid_mapping.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../grid/grid_even_share.cuh" +#include "../../util_type.cuh" +#include "../../iterator/cache_modified_input_iterator.cuh" +#include "../../util_namespace.cuh" + + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Parameterizable tuning policy type for BlockRegionReduce + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + int _VECTOR_LOAD_LENGTH, ///< Number of items per vectorized load + BlockReduceAlgorithm _BLOCK_ALGORITHM, ///< Cooperative block-wide reduction algorithm to use + CacheLoadModifier _LOAD_MODIFIER, ///< Cache load modifier for reading input elements + GridMappingStrategy _GRID_MAPPING> ///< How to map tiles of input onto thread blocks +struct BlockRegionReducePolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, ///< Threads per thread block + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + VECTOR_LOAD_LENGTH = _VECTOR_LOAD_LENGTH, ///< Number of items per vectorized load + }; + + static const BlockReduceAlgorithm BLOCK_ALGORITHM = _BLOCK_ALGORITHM; ///< Cooperative block-wide reduction algorithm to use + static const CacheLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; ///< Cache load modifier for reading input elements + static const GridMappingStrategy GRID_MAPPING = _GRID_MAPPING; ///< How to map tiles of input onto thread blocks +}; + + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockRegionReduce implements a stateful abstraction of CUDA thread blocks for participating in device-wide reduction across a region of tiles. + * + * Each thread reduces only the values it loads. If \p FIRST_TILE, this + * partial reduction is stored into \p thread_aggregate. Otherwise it is + * accumulated into \p thread_aggregate. + */ +template < + typename BlockRegionReducePolicy, ///< Parameterized BlockRegionReducePolicy tuning policy type + typename InputIterator, ///< Random-access iterator type for input + typename Offset, ///< Signed integer type for global offsets + typename ReductionOp> ///< Binary reduction operator type having member T operator()(const T &a, const T &b) +struct BlockRegionReduce +{ + + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // The value type of the input iterator + typedef typename std::iterator_traits::value_type T; + + // Vector type of T for data movement + typedef typename CubVector::Type VectorT; + + // Input iterator wrapper type + typedef typename If::VALUE, + CacheModifiedInputIterator, // Wrap the native input pointer with CacheModifiedInputIterator + InputIterator>::Type // Directly use the supplied input iterator type + WrappedInputIterator; + + // Constants + enum + { + BLOCK_THREADS = BlockRegionReducePolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockRegionReducePolicy::ITEMS_PER_THREAD, + VECTOR_LOAD_LENGTH = CUB_MIN(ITEMS_PER_THREAD, BlockRegionReducePolicy::VECTOR_LOAD_LENGTH), + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + + // Can vectorize according to the policy if the input iterator is a native pointer to a primitive type + CAN_VECTORIZE = (VECTOR_LOAD_LENGTH > 1) && + (IsPointer::VALUE) && + Traits::PRIMITIVE, + + }; + + static const CacheLoadModifier LOAD_MODIFIER = BlockRegionReducePolicy::LOAD_MODIFIER; + static const BlockReduceAlgorithm BLOCK_ALGORITHM = BlockRegionReducePolicy::BLOCK_ALGORITHM; + + // Parameterized BlockReduce primitive + typedef BlockReduce BlockReduceT; + + /// Shared memory type required by this thread block + typedef typename BlockReduceT::TempStorage _TempStorage; + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + T thread_aggregate; ///< Each thread's partial reduction + _TempStorage& temp_storage; ///< Reference to temp_storage + InputIterator d_in; ///< Input data to reduce + WrappedInputIterator d_wrapped_in; ///< Wrapped input data to reduce + ReductionOp reduction_op; ///< Binary reduction operator + int first_tile_size; ///< Size of first tile consumed + bool is_aligned; ///< Whether or not input is vector-aligned + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + + // Whether or not the input is aligned with the vector type (specialized for types we can vectorize) + template + static __device__ __forceinline__ bool IsAligned( + Iterator d_in, + Int2Type can_vectorize) + { + return (size_t(d_in) & (sizeof(VectorT) - 1)) == 0; + } + + // Whether or not the input is aligned with the vector type (specialized for types we cannot vectorize) + template + static __device__ __forceinline__ bool IsAligned( + Iterator d_in, + Int2Type can_vectorize) + { + return false; + } + + + /** + * Constructor + */ + __device__ __forceinline__ BlockRegionReduce( + TempStorage& temp_storage, ///< Reference to temp_storage + InputIterator d_in, ///< Input data to reduce + ReductionOp reduction_op) ///< Binary reduction operator + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + d_wrapped_in(d_in), + reduction_op(reduction_op), + first_tile_size(0), + is_aligned(IsAligned(d_in, Int2Type())) + {} + + + /** + * Consume a full tile of input (specialized for cases where we cannot vectorize) + */ + template + __device__ __forceinline__ T ConsumeFullTile( + _Offset block_offset, ///< The offset the tile to consume + Int2Type can_vectorize) ///< Whether or not we can vectorize loads + { + T items[ITEMS_PER_THREAD]; + + // Load items in striped fashion + LoadDirectStriped(threadIdx.x, d_wrapped_in + block_offset, items); + + // Reduce items within each thread stripe + return ThreadReduce(items, reduction_op); + } + + + /** + * Consume a full tile of input (specialized for cases where we can vectorize) + */ + template + __device__ __forceinline__ T ConsumeFullTile( + _Offset block_offset, ///< The offset the tile to consume + Int2Type can_vectorize) ///< Whether or not we can vectorize loads + { + if (!is_aligned) + { + // Not aligned + return ConsumeFullTile(block_offset, Int2Type()); + } + else + { + // Alias items as an array of VectorT and load it in striped fashion + enum { WORDS = ITEMS_PER_THREAD / VECTOR_LOAD_LENGTH }; + + T items[ITEMS_PER_THREAD]; + + VectorT *vec_items = reinterpret_cast(items); + + // Vector input iterator wrapper type + CacheModifiedInputIterator d_vec_in( + reinterpret_cast(d_in + block_offset + (threadIdx.x * VECTOR_LOAD_LENGTH))); + + #pragma unroll + for (int i = 0; i < WORDS; ++i) + vec_items[i] = d_vec_in[BLOCK_THREADS * i]; + + // Reduce items within each thread stripe + return ThreadReduce(items, reduction_op); + } + } + + + + /** + * Process a single tile of input + */ + template + __device__ __forceinline__ void ConsumeTile( + Offset block_offset, ///< The offset the tile to consume + int valid_items = TILE_ITEMS) ///< The number of valid items in the tile + { + if (FULL_TILE) + { + // Full tile + T partial = ConsumeFullTile(block_offset, Int2Type()); + + // Update running thread aggregate + thread_aggregate = (first_tile_size) ? + reduction_op(thread_aggregate, partial) : // Update + partial; // Assign + } + else + { + // Partial tile + int thread_offset = threadIdx.x; + + if (!first_tile_size && (thread_offset < valid_items)) + { + // Assign thread_aggregate + thread_aggregate = d_wrapped_in[block_offset + thread_offset]; + thread_offset += BLOCK_THREADS; + } + + while (thread_offset < valid_items) + { + // Update thread aggregate + T item = d_wrapped_in[block_offset + thread_offset]; + thread_aggregate = reduction_op(thread_aggregate, item); + thread_offset += BLOCK_THREADS; + } + } + + // Set first tile size if necessary + if (!first_tile_size) + first_tile_size = valid_items; + } + + + //--------------------------------------------------------------- + // Consume a contiguous segment of tiles + //--------------------------------------------------------------------- + + /** + * \brief Reduce a contiguous segment of input tiles + */ + __device__ __forceinline__ void ConsumeRegion( + Offset block_offset, ///< [in] Threadblock begin offset (inclusive) + Offset block_end, ///< [in] Threadblock end offset (exclusive) + T &block_aggregate) ///< [out] Running total + { + // Consume subsequent full tiles of input + while (block_offset + TILE_ITEMS <= block_end) + { + ConsumeTile(block_offset); + block_offset += TILE_ITEMS; + } + + // Consume a partially-full tile + if (block_offset < block_end) + { + int valid_items = block_end - block_offset; + ConsumeTile(block_offset, valid_items); + } + + // Compute block-wide reduction + block_aggregate = (first_tile_size < TILE_ITEMS) ? + BlockReduceT(temp_storage).Reduce(thread_aggregate, reduction_op, first_tile_size) : + BlockReduceT(temp_storage).Reduce(thread_aggregate, reduction_op); + } + + + /** + * Reduce a contiguous segment of input tiles + */ + __device__ __forceinline__ void ConsumeRegion( + Offset num_items, ///< [in] Total number of global input items + GridEvenShare &even_share, ///< [in] GridEvenShare descriptor + GridQueue &queue, ///< [in,out] GridQueue descriptor + T &block_aggregate, ///< [out] Running total + Int2Type is_even_share) ///< [in] Marker type indicating this is an even-share mapping + { + // Initialize even-share descriptor for this thread block + even_share.BlockInit(); + + // Consume input tiles + ConsumeRegion(even_share.block_offset, even_share.block_end, block_aggregate); + } + + + //--------------------------------------------------------------------- + // Dynamically consume tiles + //--------------------------------------------------------------------- + + /** + * Dequeue and reduce tiles of items as part of a inter-block scan + */ + __device__ __forceinline__ void ConsumeRegion( + int num_items, ///< Total number of input items + GridQueue queue, ///< Queue descriptor for assigning tiles of work to thread blocks + T &block_aggregate) ///< [out] Running total + { + // Shared dequeue offset + __shared__ Offset dequeue_offset; + + // We give each thread block at least one tile of input. + Offset block_offset = blockIdx.x * TILE_ITEMS; + Offset even_share_base = gridDim.x * TILE_ITEMS; + + if (block_offset + TILE_ITEMS <= num_items) + { + // Consume full tile of input + ConsumeTile(block_offset); + + // Dequeue more tiles + while (true) + { + // Dequeue a tile of items + if (threadIdx.x == 0) + dequeue_offset = queue.Drain(TILE_ITEMS) + even_share_base; + + __syncthreads(); + + // Grab tile offset and check if we're done with full tiles + block_offset = dequeue_offset; + + __syncthreads(); + + if (block_offset + TILE_ITEMS > num_items) + break; + + // Consume a full tile + ConsumeTile(block_offset); + } + } + + if (block_offset < num_items) + { + int valid_items = num_items - block_offset; + ConsumeTile(block_offset, valid_items); + } + + // Compute block-wide reduction + block_aggregate = (first_tile_size < TILE_ITEMS) ? + BlockReduceT(temp_storage).Reduce(thread_aggregate, reduction_op, first_tile_size) : + BlockReduceT(temp_storage).Reduce(thread_aggregate, reduction_op); + } + + + /** + * Dequeue and reduce tiles of items as part of a inter-block scan + */ + __device__ __forceinline__ void ConsumeRegion( + Offset num_items, ///< [in] Total number of global input items + GridEvenShare &even_share, ///< [in] GridEvenShare descriptor + GridQueue &queue, ///< [in,out] GridQueue descriptor + T &block_aggregate, ///< [out] Running total + Int2Type is_dynamic) ///< [in] Marker type indicating this is a dynamic mapping + { + ConsumeRegion(num_items, queue, block_aggregate); + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_reduce_by_key.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_reduce_by_key.cuh new file mode 100644 index 0000000000000000000000000000000000000000..8eb5a33794718782734e86dc2bdca6253b7725ea --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_reduce_by_key.cuh @@ -0,0 +1,1010 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockRegionReduceByKey implements a stateful abstraction of CUDA thread blocks for participating in device-wide reduce-value-by-key. + */ + +#pragma once + +#include + +#include "device_scan_types.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_store.cuh" +#include "../../block/block_scan.cuh" +#include "../../block/block_exchange.cuh" +#include "../../block/block_discontinuity.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../iterator/cache_modified_input_iterator.cuh" +#include "../../iterator/constant_input_iterator.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Parameterizable tuning policy type for BlockRegionReduceByKey + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + BlockLoadAlgorithm _LOAD_ALGORITHM, ///< The BlockLoad algorithm to use + CacheLoadModifier _LOAD_MODIFIER, ///< Cache load modifier for reading input elements + bool _TWO_PHASE_SCATTER, ///< Whether or not to coalesce output values in shared memory before scattering them to global + BlockScanAlgorithm _SCAN_ALGORITHM> ///< The BlockScan algorithm to use +struct BlockRegionReduceByKeyPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, ///< Threads per thread block + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + TWO_PHASE_SCATTER = _TWO_PHASE_SCATTER, ///< Whether or not to coalesce output values in shared memory before scattering them to global + }; + + static const BlockLoadAlgorithm LOAD_ALGORITHM = _LOAD_ALGORITHM; ///< The BlockLoad algorithm to use + static const CacheLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; ///< Cache load modifier for reading input elements + static const BlockScanAlgorithm SCAN_ALGORITHM = _SCAN_ALGORITHM; ///< The BlockScan algorithm to use +}; + + +/****************************************************************************** + * Tile status interface types + ******************************************************************************/ + +/** + * Tile status interface for reduction by key. + * + */ +template < + typename Value, + typename Offset, + bool SINGLE_WORD = (Traits::PRIMITIVE) && (sizeof(Value) + sizeof(Offset) < 16)> +struct ReduceByKeyTileLookbackStatus; + + +/** + * Tile status interface for reduction by key, specialized for scan status and value types that + * cannot be combined into one machine word. + */ +template < + typename Value, + typename Offset> +struct ReduceByKeyTileLookbackStatus : + TileLookbackStatus > +{ + typedef TileLookbackStatus > SuperClass; + + /// Constructor + __host__ __device__ __forceinline__ + ReduceByKeyTileLookbackStatus() : SuperClass() {} +}; + + +/** + * Tile status interface for reduction by key, specialized for scan status and value types that + * can be combined into one machine word that can be read/written coherently in a single access. + */ +template < + typename Value, + typename Offset> +struct ReduceByKeyTileLookbackStatus +{ + typedef ItemOffsetPair ItemOffsetPair; + + // Constants + enum + { + PAIR_SIZE = sizeof(Value) + sizeof(Offset), + TXN_WORD_SIZE = 1 << Log2::VALUE, + STATUS_WORD_SIZE = TXN_WORD_SIZE - PAIR_SIZE, + + TILE_STATUS_PADDING = CUB_PTX_WARP_THREADS, + }; + + // Status word type + typedef typename If<(STATUS_WORD_SIZE == 8), + long long, + typename If<(STATUS_WORD_SIZE == 4), + int, + typename If<(STATUS_WORD_SIZE == 2), + short, + char>::Type>::Type>::Type StatusWord; + + // Status word type + typedef typename If<(TXN_WORD_SIZE == 16), + longlong2, + typename If<(TXN_WORD_SIZE == 8), + long long, + int>::Type>::Type TxnWord; + + // Device word type (for when sizeof(Value) == sizeof(Offset)) + struct TileDescriptorBigStatus + { + Offset offset; + Value value; + StatusWord status; + }; + + // Device word type (for when sizeof(Value) != sizeof(Offset)) + struct TileDescriptorLittleStatus + { + Value value; + StatusWord status; + Offset offset; + }; + + // Device word type + typedef typename If< + (sizeof(Value) == sizeof(Offset)), + TileDescriptorBigStatus, + TileDescriptorLittleStatus>::Type + TileDescriptor; + + + // Device storage + TileDescriptor *d_tile_status; + + + /// Constructor + __host__ __device__ __forceinline__ + ReduceByKeyTileLookbackStatus() + : + d_tile_status(NULL) + {} + + + /// Initializer + __host__ __device__ __forceinline__ + cudaError_t Init( + int num_tiles, ///< [in] Number of tiles + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t temp_storage_bytes) ///< [in] Size in bytes of \t d_temp_storage allocation + { + d_tile_status = reinterpret_cast(d_temp_storage); + return cudaSuccess; + } + + + /** + * Compute device memory needed for tile status + */ + __host__ __device__ __forceinline__ + static cudaError_t AllocationSize( + int num_tiles, ///< [in] Number of tiles + size_t &temp_storage_bytes) ///< [out] Size in bytes of \t d_temp_storage allocation + { + temp_storage_bytes = (num_tiles + TILE_STATUS_PADDING) * sizeof(TileDescriptor); // bytes needed for tile status descriptors + return cudaSuccess; + } + + + /** + * Initialize (from device) + */ + __device__ __forceinline__ void InitializeStatus(int num_tiles) + { + int tile_idx = (blockIdx.x * blockDim.x) + threadIdx.x; + if (tile_idx < num_tiles) + { + // Not-yet-set + d_tile_status[TILE_STATUS_PADDING + tile_idx].status = StatusWord(LOOKBACK_TILE_INVALID); + } + + if ((blockIdx.x == 0) && (threadIdx.x < TILE_STATUS_PADDING)) + { + // Padding + d_tile_status[threadIdx.x].status = StatusWord(LOOKBACK_TILE_OOB); + } + } + + + /** + * Update the specified tile's inclusive value and corresponding status + */ + __device__ __forceinline__ void SetInclusive(int tile_idx, ItemOffsetPair tile_inclusive) + { + TileDescriptor tile_descriptor; + tile_descriptor.status = LOOKBACK_TILE_INCLUSIVE; + tile_descriptor.value = tile_inclusive.value; + tile_descriptor.offset = tile_inclusive.offset; + + TxnWord alias; + *reinterpret_cast(&alias) = tile_descriptor; + ThreadStore(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx), alias); + } + + + /** + * Update the specified tile's partial value and corresponding status + */ + __device__ __forceinline__ void SetPartial(int tile_idx, ItemOffsetPair tile_partial) + { + TileDescriptor tile_descriptor; + tile_descriptor.status = LOOKBACK_TILE_PARTIAL; + tile_descriptor.value = tile_partial.value; + tile_descriptor.offset = tile_partial.offset; + + TxnWord alias; + *reinterpret_cast(&alias) = tile_descriptor; + ThreadStore(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx), alias); + } + + /** + * Wait for the corresponding tile to become non-invalid + */ + __device__ __forceinline__ void WaitForValid( + int tile_idx, + StatusWord &status, + ItemOffsetPair &value) + { + // Use warp-any to determine when all threads have valid status + TxnWord alias = ThreadLoad(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx)); + TileDescriptor tile_descriptor = reinterpret_cast(alias); + + while ((tile_descriptor.status == LOOKBACK_TILE_INVALID)) + { + alias = ThreadLoad(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx)); + tile_descriptor = reinterpret_cast(alias); + } + + status = tile_descriptor.status; + value.value = tile_descriptor.value; + value.offset = tile_descriptor.offset; + } + +}; + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockRegionReduceByKey implements a stateful abstraction of CUDA thread blocks for participating in device-wide reduce-value-by-key across a region of tiles + */ +template < + typename BlockRegionReduceByKeyPolicy, ///< Parameterized BlockRegionReduceByKeyPolicy tuning policy type + typename KeyInputIterator, ///< Random-access input iterator type for keys + typename KeyOutputIterator, ///< Random-access output iterator type for keys + typename ValueInputIterator, ///< Random-access input iterator type for values + typename ValueOutputIterator, ///< Random-access output iterator type for values + typename EqualityOp, ///< Key equality operator type + typename ReductionOp, ///< Value reduction operator type + typename Offset> ///< Signed integer type for global offsets +struct BlockRegionReduceByKey +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Data type of key iterator + typedef typename std::iterator_traits::value_type Key; + + // Data type of value iterator + typedef typename std::iterator_traits::value_type Value; + + // Tile status descriptor interface type + typedef ReduceByKeyTileLookbackStatus TileLookbackStatus; + + // Constants + enum + { + BLOCK_THREADS = BlockRegionReduceByKeyPolicy::BLOCK_THREADS, + WARPS = BLOCK_THREADS / CUB_PTX_WARP_THREADS, + ITEMS_PER_THREAD = BlockRegionReduceByKeyPolicy::ITEMS_PER_THREAD, + TWO_PHASE_SCATTER = (BlockRegionReduceByKeyPolicy::TWO_PHASE_SCATTER) && (ITEMS_PER_THREAD > 1), + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + + // Whether or not the scan operation has a zero-valued identity value (true if we're performing addition on a primitive type) + HAS_IDENTITY_ZERO = (Equals::VALUE) && (Traits::PRIMITIVE), + + // Whether or not to sync after loading data + SYNC_AFTER_LOAD = (BlockRegionReduceByKeyPolicy::LOAD_ALGORITHM != BLOCK_LOAD_DIRECT), + + // Whether or not this is run-length-encoding with a constant iterator as values + IS_RUN_LENGTH_ENCODE = (Equals >::VALUE) || (Equals >::VALUE) || (Equals >::VALUE), + + }; + + // Cache-modified input iterator wrapper type for keys + typedef typename If::VALUE, + CacheModifiedInputIterator, // Wrap the native input pointer with CacheModifiedValueInputIterator + KeyInputIterator>::Type // Directly use the supplied input iterator type + WrappedKeyInputIterator; + + // Cache-modified input iterator wrapper type for values + typedef typename If::VALUE, + CacheModifiedInputIterator, // Wrap the native input pointer with CacheModifiedValueInputIterator + ValueInputIterator>::Type // Directly use the supplied input iterator type + WrappedValueInputIterator; + + // Value-offset tuple type for scanning (maps accumulated values to segment index) + typedef ItemOffsetPair ValueOffsetPair; + + // Reduce-value-by-segment scan operator + struct ReduceByKeyOp + { + ReductionOp op; ///< Wrapped reduction operator + + /// Constructor + __device__ __forceinline__ ReduceByKeyOp(ReductionOp op) : op(op) {} + + /// Scan operator (specialized for sum on primitive types) + __device__ __forceinline__ ValueOffsetPair operator()( + const ValueOffsetPair &first, ///< First partial reduction + const ValueOffsetPair &second, ///< Second partial reduction + Int2Type has_identity_zero) ///< Whether the operation has a zero-valued identity + { + Value select = (second.offset) ? 0 : first.value; + + ValueOffsetPair retval; + retval.offset = first.offset + second.offset; + retval.value = op(select, second.value); + return retval; + } + + /// Scan operator (specialized for reductions without zero-valued identity) + __device__ __forceinline__ ValueOffsetPair operator()( + const ValueOffsetPair &first, ///< First partial reduction + const ValueOffsetPair &second, ///< Second partial reduction + Int2Type has_identity_zero) ///< Whether the operation has a zero-valued identity + { + ValueOffsetPair retval; + retval.offset = first.offset + second.offset; + if (second.offset) + { + retval.value = second.value; + return retval; + } + else + { + retval.value = op(first.value, second.value); + return retval; + } +/* + // Alternate expression below uses more registers, slower + ValueOffsetPair retval; + retval.offset = first.offset + second.offset; + retval.value = (second.offset) ? + second.value : // The second partial reduction spans a segment reset, so it's value aggregate becomes the running aggregate + op(first.value, second.value); // The second partial reduction does not span a reset, so accumulate both into the running aggregate + return retval; +*/ + } + + /// Scan operator + __device__ __forceinline__ ValueOffsetPair operator()( + const ValueOffsetPair &first, ///< First partial reduction + const ValueOffsetPair &second) ///< Second partial reduction + { + return (*this)(first, second, Int2Type()); + } + }; + + // Parameterized BlockLoad type for keys + typedef BlockLoad< + WrappedKeyInputIterator, + BlockRegionReduceByKeyPolicy::BLOCK_THREADS, + BlockRegionReduceByKeyPolicy::ITEMS_PER_THREAD, + BlockRegionReduceByKeyPolicy::LOAD_ALGORITHM> + BlockLoadKeys; + + // Parameterized BlockLoad type for values + typedef BlockLoad< + WrappedValueInputIterator, + BlockRegionReduceByKeyPolicy::BLOCK_THREADS, + BlockRegionReduceByKeyPolicy::ITEMS_PER_THREAD, + (IS_RUN_LENGTH_ENCODE) ? + BLOCK_LOAD_DIRECT : + (BlockLoadAlgorithm) BlockRegionReduceByKeyPolicy::LOAD_ALGORITHM> + BlockLoadValues; + + // Parameterized BlockExchange type for locally compacting items as part of a two-phase scatter + typedef BlockExchange< + Key, + BLOCK_THREADS, + ITEMS_PER_THREAD> + BlockExchangeKeys; + + // Parameterized BlockExchange type for locally compacting items as part of a two-phase scatter + typedef BlockExchange< + Value, + BLOCK_THREADS, + ITEMS_PER_THREAD> + BlockExchangeValues; + + // Parameterized BlockDiscontinuity type for keys + typedef BlockDiscontinuity BlockDiscontinuityKeys; + + // Parameterized BlockScan type + typedef BlockScan< + ValueOffsetPair, + BlockRegionReduceByKeyPolicy::BLOCK_THREADS, + BlockRegionReduceByKeyPolicy::SCAN_ALGORITHM> + BlockScanAllocations; + + // Callback type for obtaining tile prefix during block scan + typedef LookbackBlockPrefixCallbackOp< + ValueOffsetPair, + ReduceByKeyOp, + TileLookbackStatus> + LookbackPrefixCallbackOp; + + // Shared memory type for this threadblock + struct _TempStorage + { + + union + { + struct + { + typename BlockScanAllocations::TempStorage scan; // Smem needed for tile scanning + typename LookbackPrefixCallbackOp::TempStorage prefix; // Smem needed for cooperative prefix callback + typename BlockDiscontinuityKeys::TempStorage discontinuity; // Smem needed for discontinuity detection + typename BlockLoadKeys::TempStorage load_keys; // Smem needed for loading keys + + Offset tile_idx; // Shared tile index + Offset tile_num_flags_prefix; // Exclusive tile prefix + }; + + // Smem needed for loading values + typename BlockLoadValues::TempStorage load_values; + + // Smem needed for compacting values + typename BlockExchangeValues::TempStorage exchange_values; + + // Smem needed for compacting keys + typename BlockExchangeKeys::TempStorage exchange_keys; + }; + + }; + + // Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + _TempStorage &temp_storage; ///< Reference to temp_storage + + WrappedKeyInputIterator d_keys_in; ///< Input keys + KeyOutputIterator d_keys_out; ///< Output keys + + WrappedValueInputIterator d_values_in; ///< Input values + ValueOutputIterator d_values_out; ///< Output values + + InequalityWrapper inequality_op; ///< Key inequality operator + ReduceByKeyOp scan_op; ///< Reduce-value-by flag scan operator + Offset num_items; ///< Total number of input items + + + //--------------------------------------------------------------------- + // Constructor + //--------------------------------------------------------------------- + + // Constructor + __device__ __forceinline__ + BlockRegionReduceByKey( + TempStorage &temp_storage, ///< Reference to temp_storage + KeyInputIterator d_keys_in, ///< Input keys + KeyOutputIterator d_keys_out, ///< Output keys + ValueInputIterator d_values_in, ///< Input values + ValueOutputIterator d_values_out, ///< Output values + EqualityOp equality_op, ///< Key equality operator + ReductionOp reduction_op, ///< Value reduction operator + Offset num_items) ///< Total number of input items + : + temp_storage(temp_storage.Alias()), + d_keys_in(d_keys_in), + d_keys_out(d_keys_out), + d_values_in(d_values_in), + d_values_out(d_values_out), + inequality_op(equality_op), + scan_op(reduction_op), + num_items(num_items) + {} + + + //--------------------------------------------------------------------- + // Block scan utility methods + //--------------------------------------------------------------------- + + /** + * Scan with identity (first tile) + */ + __device__ __forceinline__ + void ScanBlock( + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + ValueOffsetPair &block_aggregate, + Int2Type has_identity) + { + ValueOffsetPair identity; + identity.value = 0; + identity.offset = 0; + BlockScanAllocations(temp_storage.scan).ExclusiveScan(values_and_segments, values_and_segments, identity, scan_op, block_aggregate); + } + + /** + * Scan without identity (first tile). Without an identity, the first output item is undefined. + * + */ + __device__ __forceinline__ + void ScanBlock( + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + ValueOffsetPair &block_aggregate, + Int2Type has_identity) + { + BlockScanAllocations(temp_storage.scan).ExclusiveScan(values_and_segments, values_and_segments, scan_op, block_aggregate); + } + + /** + * Scan with identity (subsequent tile) + */ + __device__ __forceinline__ + void ScanBlock( + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + ValueOffsetPair &block_aggregate, + LookbackPrefixCallbackOp &prefix_op, + Int2Type has_identity) + { + ValueOffsetPair identity; + identity.value = 0; + identity.offset = 0; + BlockScanAllocations(temp_storage.scan).ExclusiveScan(values_and_segments, values_and_segments, identity, scan_op, block_aggregate, prefix_op); + } + + /** + * Scan without identity (subsequent tile). Without an identity, the first output item is undefined. + */ + __device__ __forceinline__ + void ScanBlock( + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + ValueOffsetPair &block_aggregate, + LookbackPrefixCallbackOp &prefix_op, + Int2Type has_identity) + { + BlockScanAllocations(temp_storage.scan).ExclusiveScan(values_and_segments, values_and_segments, scan_op, block_aggregate, prefix_op); + } + + + //--------------------------------------------------------------------- + // Zip utility methods + //--------------------------------------------------------------------- + + template + __device__ __forceinline__ void ZipValuesAndFlags( + Offset num_remaining, + Value (&values)[ITEMS_PER_THREAD], + Offset (&flags)[ITEMS_PER_THREAD], + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD]) + { + // Zip values and flags + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + // Unset flags for out-of-bounds keys + if ((LAST_TILE) && (Offset(threadIdx.x * ITEMS_PER_THREAD) + ITEM >= num_remaining)) + flags[ITEM] = 0; + + values_and_segments[ITEM].value = values[ITEM]; + values_and_segments[ITEM].offset = flags[ITEM]; + } + } + + //--------------------------------------------------------------------- + // Scatter utility methods + //--------------------------------------------------------------------- + + + + /** + * Scatter flagged items to output offsets (specialized for direct scattering) + * + * The exclusive scan causes each head flag to be paired with the previous + * value aggregate. As such: + * - The scatter offsets must be decremented for value value aggregates + * - The first tile does not scatter the first flagged value (it is undefined from the exclusive scan) + * - If the tile is partially-full, we need to scatter the first out-of-bounds value (which aggregates all valid values in the last segment) + * + */ + template + __device__ __forceinline__ void ScatterDirect( + Offset num_remaining, + Key (&keys)[ITEMS_PER_THREAD], + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + Offset (&flags)[ITEMS_PER_THREAD], + Offset tile_num_flags, + Int2Type iteration) + { + // Scatter key + if (flags[ITEM]) + { + d_keys_out[values_and_segments[ITEM].offset] = keys[ITEM]; + } + + bool is_first_flag = FIRST_TILE && (ITEM == 0) && (threadIdx.x == 0); + bool is_oob_value = (LAST_TILE) && (Offset(threadIdx.x * ITEMS_PER_THREAD) + ITEM == num_remaining); + + // Scatter value reduction + if (((flags[ITEM] || is_oob_value)) && (!is_first_flag)) + { + d_values_out[values_and_segments[ITEM].offset - 1] = values_and_segments[ITEM].value; + } + + ScatterDirect(num_remaining, keys, values_and_segments, flags, tile_num_flags, Int2Type()); + } + + template + __device__ __forceinline__ void ScatterDirect( + Offset num_remaining, + Key (&keys)[ITEMS_PER_THREAD], + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + Offset (&flags)[ITEMS_PER_THREAD], + Offset tile_num_flags, + Int2Type iteration) + {} + + /** + * Scatter flagged items to output offsets (specialized for two-phase scattering) + * + * The exclusive scan causes each head flag to be paired with the previous + * value aggregate. As such: + * - The scatter offsets must be decremented for value value aggregates + * - The first tile does not scatter the first flagged value (it is undefined from the exclusive scan) + * - If the tile is partially-full, we need to scatter the first out-of-bounds value (which aggregates all valid values in the last segment) + * + */ + template + __device__ __forceinline__ void ScatterTwoPhase( + Offset num_remaining, + Key (&keys)[ITEMS_PER_THREAD], + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + Offset (&flags)[ITEMS_PER_THREAD], + Offset tile_num_flags, + Offset tile_num_flags_prefix) + { + int local_ranks[ITEMS_PER_THREAD]; + Value values[ITEMS_PER_THREAD]; + + // Share exclusive tile prefix + if (threadIdx.x == 0) + { + temp_storage.tile_num_flags_prefix = tile_num_flags_prefix; + } + + __syncthreads(); + + // Load exclusive tile prefix in all threads + tile_num_flags_prefix = temp_storage.tile_num_flags_prefix; + + __syncthreads(); + + // Compute local scatter ranks + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + local_ranks[ITEM] = values_and_segments[ITEM].offset - tile_num_flags_prefix; + } + + // Compact keys in shared memory + BlockExchangeKeys(temp_storage.exchange_keys).ScatterToStriped(keys, local_ranks, flags); + + // Scatter keys + StoreDirectStriped(threadIdx.x, d_keys_out + tile_num_flags_prefix, keys, tile_num_flags); + + // Unzip values and set flag for first oob item in last tile + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + values[ITEM] = values_and_segments[ITEM].value; + + if (FIRST_TILE) + local_ranks[ITEM]--; + + if (LAST_TILE && (Offset(threadIdx.x * ITEMS_PER_THREAD) + ITEM == num_remaining)) + flags[ITEM] = 1; + } + + // Unset first flag in first tile + if (FIRST_TILE && (threadIdx.x == 0)) + flags[0] = 0; + + __syncthreads(); + + // Compact values in shared memory + BlockExchangeValues(temp_storage.exchange_values).ScatterToStriped(values, local_ranks, flags); + + // Number to output + Offset exchange_count = tile_num_flags; + + if (LAST_TILE && (num_remaining < TILE_ITEMS)) + exchange_count++; + + if (FIRST_TILE) + { + exchange_count--; + } + else + { + tile_num_flags_prefix--; + } + + // Scatter values + StoreDirectStriped(threadIdx.x, d_values_out + tile_num_flags_prefix, values, exchange_count); + + __syncthreads(); + } + + + /** + * Scatter flagged items + */ + template + __device__ __forceinline__ void Scatter( + Offset num_remaining, + Key (&keys)[ITEMS_PER_THREAD], + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + Offset (&flags)[ITEMS_PER_THREAD], + Offset tile_num_flags, + Offset tile_num_flags_prefix) + { + // Do a one-phase scatter if (a) two-phase is disabled or (b) the average number of selected items per thread is less than one + if ((TWO_PHASE_SCATTER) && ((tile_num_flags >> Log2::VALUE) > 0)) + { + ScatterTwoPhase( + num_remaining, + keys, + values_and_segments, + flags, + tile_num_flags, + tile_num_flags_prefix); + } + else + { + ScatterDirect( + num_remaining, + keys, + values_and_segments, + flags, + tile_num_flags, + Int2Type<0>()); + } + } + + + //--------------------------------------------------------------------- + // Cooperatively scan a device-wide sequence of tiles with other CTAs + //--------------------------------------------------------------------- + + /** + * Process a tile of input (dynamic domino scan) + */ + template < + bool LAST_TILE> + __device__ __forceinline__ ValueOffsetPair ConsumeTile( + Offset num_items, ///< Total number of global input items + Offset num_remaining, ///< Number of global input items remaining (including this tile) + int tile_idx, ///< Tile index + Offset block_offset, ///< Tile offset + TileLookbackStatus &tile_status) ///< Global list of tile status + { + Key keys[ITEMS_PER_THREAD]; // Tile keys + Value values[ITEMS_PER_THREAD]; // Tile values + Offset flags[ITEMS_PER_THREAD]; // Segment head flags + ValueOffsetPair values_and_segments[ITEMS_PER_THREAD]; // Zipped values and segment flags|indices + + ValueOffsetPair running_total; // Running count of segments and current value aggregate (including this tile) + + // Load keys and values + if (LAST_TILE) + { + BlockLoadKeys(temp_storage.load_keys).Load(d_keys_in + block_offset, keys, num_remaining); + } + else + { + BlockLoadKeys(temp_storage.load_keys).Load(d_keys_in + block_offset, keys); + } + + if (SYNC_AFTER_LOAD) + __syncthreads(); + + // Load values + if (LAST_TILE) + BlockLoadValues(temp_storage.load_values).Load(d_values_in + block_offset, values, num_remaining); + else + BlockLoadValues(temp_storage.load_values).Load(d_values_in + block_offset, values); + + if (SYNC_AFTER_LOAD) + __syncthreads(); + + if (tile_idx == 0) + { + // First tile + + // Set head flags. First tile sets the first flag for the first item + BlockDiscontinuityKeys(temp_storage.discontinuity).FlagHeads(flags, keys, inequality_op); + + // Zip values and flags + ZipValuesAndFlags(num_remaining, values, flags, values_and_segments); + + // Exclusive scan of values and flags + ValueOffsetPair block_aggregate; + ScanBlock(values_and_segments, block_aggregate, Int2Type()); + + // Update tile status if this is not the last tile + if (!LAST_TILE && (threadIdx.x == 0)) + tile_status.SetInclusive(0, block_aggregate); + + // Set offset for first scan output + if (!HAS_IDENTITY_ZERO && (threadIdx.x == 0)) + values_and_segments[0].offset = 0; + + running_total = block_aggregate; + + // Scatter flagged items + Scatter(num_remaining, keys, values_and_segments, flags, block_aggregate.offset, 0); + } + else + { + // Not first tile + + // Obtain the last key in the previous tile to compare with + Key tile_predecessor_key = (threadIdx.x == 0) ? + d_keys_in[block_offset - 1] : + ZeroInitialize(); + + // Set head flags + BlockDiscontinuityKeys(temp_storage.discontinuity).FlagHeads(flags, keys, inequality_op, tile_predecessor_key); + + // Zip values and flags + ZipValuesAndFlags(num_remaining, values, flags, values_and_segments); + + // Exclusive scan of values and flags + ValueOffsetPair block_aggregate; + LookbackPrefixCallbackOp prefix_op(tile_status, temp_storage.prefix, scan_op, tile_idx); + ScanBlock(values_and_segments, block_aggregate, prefix_op, Int2Type()); + + running_total = prefix_op.inclusive_prefix; + + // Scatter flagged items + Scatter(num_remaining, keys, values_and_segments, flags, block_aggregate.offset, prefix_op.exclusive_prefix.offset); + } + + return running_total; + } + + + /** + * Dequeue and scan tiles of items as part of a dynamic domino scan + */ + template ///< Output iterator type for recording number of items selected + __device__ __forceinline__ void ConsumeRegion( + int num_tiles, ///< Total number of input tiles + GridQueue queue, ///< Queue descriptor for assigning tiles of work to thread blocks + TileLookbackStatus &tile_status, ///< Global list of tile status + NumSegmentsIterator d_num_segments) ///< Output pointer for total number of segments identified + { +#if (CUB_PTX_VERSION <= 130) + // Blocks are launched in increasing order, so just assign one tile per block + + int tile_idx = (blockIdx.y * 32 * 1024) + blockIdx.x; // Current tile index + Offset block_offset = Offset(TILE_ITEMS) * tile_idx; // Global offset for the current tile + Offset num_remaining = num_items - block_offset; // Remaining items (including this tile) + + if (num_remaining > TILE_ITEMS) + { + // Full tile + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + } + else if (num_remaining > 0) + { + // Last tile + ValueOffsetPair running_total = ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + + // Output the total number of items selected + if (threadIdx.x == 0) + { + *d_num_segments = running_total.offset; + + // If the last tile is a whole tile, the inclusive prefix contains accumulated value reduction for the last segment + if (num_remaining == TILE_ITEMS) + { + d_values_out[running_total.offset - 1] = running_total.value; + } + } + } +#else + // Blocks may not be launched in increasing order, so work-steal tiles + + // Get first tile index + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + int tile_idx = temp_storage.tile_idx; + Offset block_offset = Offset(TILE_ITEMS) * tile_idx; // Global offset for the current tile + Offset num_remaining = num_items - block_offset; // Remaining items (including this tile) + + while (num_remaining > TILE_ITEMS) + { + if (SYNC_AFTER_LOAD) + __syncthreads(); + + // Consume full tile + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + + // Get tile index + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + tile_idx = temp_storage.tile_idx; + block_offset = Offset(TILE_ITEMS) * tile_idx; + num_remaining = num_items - block_offset; + } + + if (num_remaining > 0) + { + // Consume last tile (treat as partially-full) + ValueOffsetPair running_total = ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + + if ((threadIdx.x == 0)) + { + // Output the total number of items selected + *d_num_segments = running_total.offset; + + // If the last tile is a whole tile, the inclusive prefix contains accumulated value reduction for the last segment + if (num_remaining == TILE_ITEMS) + { + d_values_out[running_total.offset - 1] = running_total.value; + } + } + } +#endif + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_scan.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_scan.cuh new file mode 100644 index 0000000000000000000000000000000000000000..26020d8f6e95f9efcaff6928033279c6157de966 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_scan.cuh @@ -0,0 +1,536 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockRegionScan implements a stateful abstraction of CUDA thread blocks for participating in device-wide prefix scan across a region of tiles. + */ + +#pragma once + +#include + +#include "device_scan_types.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_store.cuh" +#include "../../block/block_scan.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../iterator/cache_modified_input_iterator.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Parameterizable tuning policy type for BlockRegionScan + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + BlockLoadAlgorithm _LOAD_ALGORITHM, ///< The BlockLoad algorithm to use + bool _LOAD_WARP_TIME_SLICING, ///< Whether or not only one warp's worth of shared memory should be allocated and time-sliced among block-warps during any load-related data transpositions (versus each warp having its own storage) + CacheLoadModifier _LOAD_MODIFIER, ///< Cache load modifier for reading input elements + BlockStoreAlgorithm _STORE_ALGORITHM, ///< The BlockStore algorithm to use + bool _STORE_WARP_TIME_SLICING, ///< Whether or not only one warp's worth of shared memory should be allocated and time-sliced among block-warps during any store-related data transpositions (versus each warp having its own storage) + BlockScanAlgorithm _SCAN_ALGORITHM> ///< The BlockScan algorithm to use +struct BlockRegionScanPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, ///< Threads per thread block + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + LOAD_WARP_TIME_SLICING = _LOAD_WARP_TIME_SLICING, ///< Whether or not only one warp's worth of shared memory should be allocated and time-sliced among block-warps during any load-related data transpositions (versus each warp having its own storage) + STORE_WARP_TIME_SLICING = _STORE_WARP_TIME_SLICING, ///< Whether or not only one warp's worth of shared memory should be allocated and time-sliced among block-warps during any store-related data transpositions (versus each warp having its own storage) + }; + + static const BlockLoadAlgorithm LOAD_ALGORITHM = _LOAD_ALGORITHM; ///< The BlockLoad algorithm to use + static const CacheLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; ///< Cache load modifier for reading input elements + static const BlockStoreAlgorithm STORE_ALGORITHM = _STORE_ALGORITHM; ///< The BlockStore algorithm to use + static const BlockScanAlgorithm SCAN_ALGORITHM = _SCAN_ALGORITHM; ///< The BlockScan algorithm to use +}; + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockRegionScan implements a stateful abstraction of CUDA thread blocks for participating in device-wide prefix scan across a region of tiles. + */ +template < + typename BlockRegionScanPolicy, ///< Parameterized BlockRegionScanPolicy tuning policy type + typename InputIterator, ///< Random-access input iterator type + typename OutputIterator, ///< Random-access output iterator type + typename ScanOp, ///< Scan functor type + typename Identity, ///< Identity element type (cub::NullType for inclusive scan) + typename Offset> ///< Signed integer type for global offsets +struct BlockRegionScan +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Data type of input iterator + typedef typename std::iterator_traits::value_type T; + + // Tile status descriptor interface type + typedef TileLookbackStatus TileLookbackStatus; + + // Input iterator wrapper type + typedef typename If::VALUE, + CacheModifiedInputIterator, // Wrap the native input pointer with CacheModifiedInputIterator + InputIterator>::Type // Directly use the supplied input iterator type + WrappedInputIterator; + + // Constants + enum + { + INCLUSIVE = Equals::VALUE, // Inclusive scan if no identity type is provided + BLOCK_THREADS = BlockRegionScanPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockRegionScanPolicy::ITEMS_PER_THREAD, + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + }; + + // Parameterized BlockLoad type + typedef BlockLoad< + WrappedInputIterator, + BlockRegionScanPolicy::BLOCK_THREADS, + BlockRegionScanPolicy::ITEMS_PER_THREAD, + BlockRegionScanPolicy::LOAD_ALGORITHM, + BlockRegionScanPolicy::LOAD_WARP_TIME_SLICING> + BlockLoadT; + + // Parameterized BlockStore type + typedef BlockStore< + OutputIterator, + BlockRegionScanPolicy::BLOCK_THREADS, + BlockRegionScanPolicy::ITEMS_PER_THREAD, + BlockRegionScanPolicy::STORE_ALGORITHM, + BlockRegionScanPolicy::STORE_WARP_TIME_SLICING> + BlockStoreT; + + // Parameterized BlockScan type + typedef BlockScan< + T, + BlockRegionScanPolicy::BLOCK_THREADS, + BlockRegionScanPolicy::SCAN_ALGORITHM> + BlockScanT; + + // Callback type for obtaining tile prefix during block scan + typedef LookbackBlockPrefixCallbackOp< + T, + ScanOp, + TileLookbackStatus> + LookbackPrefixCallbackOp; + + // Stateful BlockScan prefix callback type for managing a running total while scanning consecutive tiles + typedef RunningBlockPrefixCallbackOp< + T, + ScanOp> + RunningPrefixCallbackOp; + + // Shared memory type for this threadblock + struct _TempStorage + { + union + { + typename BlockLoadT::TempStorage load; // Smem needed for tile loading + typename BlockStoreT::TempStorage store; // Smem needed for tile storing + struct + { + typename LookbackPrefixCallbackOp::TempStorage prefix; // Smem needed for cooperative prefix callback + typename BlockScanT::TempStorage scan; // Smem needed for tile scanning + }; + }; + + Offset tile_idx; // Shared tile index + }; + + // Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + _TempStorage &temp_storage; ///< Reference to temp_storage + WrappedInputIterator d_in; ///< Input data + OutputIterator d_out; ///< Output data + ScanOp scan_op; ///< Binary scan operator + Identity identity; ///< Identity element + + + + //--------------------------------------------------------------------- + // Block scan utility methods (first tile) + //--------------------------------------------------------------------- + + /** + * Exclusive scan specialization + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], _ScanOp scan_op, _Identity identity, T& block_aggregate) + { + BlockScanT(temp_storage.scan).ExclusiveScan(items, items, identity, scan_op, block_aggregate); + } + + /** + * Exclusive sum specialization + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], Sum scan_op, _Identity identity, T& block_aggregate) + { + BlockScanT(temp_storage.scan).ExclusiveSum(items, items, block_aggregate); + } + + /** + * Inclusive scan specialization + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], _ScanOp scan_op, NullType identity, T& block_aggregate) + { + BlockScanT(temp_storage.scan).InclusiveScan(items, items, scan_op, block_aggregate); + } + + /** + * Inclusive sum specialization + */ + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], Sum scan_op, NullType identity, T& block_aggregate) + { + BlockScanT(temp_storage.scan).InclusiveSum(items, items, block_aggregate); + } + + //--------------------------------------------------------------------- + // Block scan utility methods (subsequent tiles) + //--------------------------------------------------------------------- + + /** + * Exclusive scan specialization (with prefix from predecessors) + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], _ScanOp scan_op, _Identity identity, T& block_aggregate, PrefixCallback &prefix_op) + { + BlockScanT(temp_storage.scan).ExclusiveScan(items, items, identity, scan_op, block_aggregate, prefix_op); + } + + /** + * Exclusive sum specialization (with prefix from predecessors) + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], Sum scan_op, _Identity identity, T& block_aggregate, PrefixCallback &prefix_op) + { + BlockScanT(temp_storage.scan).ExclusiveSum(items, items, block_aggregate, prefix_op); + } + + /** + * Inclusive scan specialization (with prefix from predecessors) + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], _ScanOp scan_op, NullType identity, T& block_aggregate, PrefixCallback &prefix_op) + { + BlockScanT(temp_storage.scan).InclusiveScan(items, items, scan_op, block_aggregate, prefix_op); + } + + /** + * Inclusive sum specialization (with prefix from predecessors) + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], Sum scan_op, NullType identity, T& block_aggregate, PrefixCallback &prefix_op) + { + BlockScanT(temp_storage.scan).InclusiveSum(items, items, block_aggregate, prefix_op); + } + + + //--------------------------------------------------------------------- + // Constructor + //--------------------------------------------------------------------- + + // Constructor + __device__ __forceinline__ + BlockRegionScan( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIterator d_in, ///< Input data + OutputIterator d_out, ///< Output data + ScanOp scan_op, ///< Binary scan operator + Identity identity) ///< Identity element + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + d_out(d_out), + scan_op(scan_op), + identity(identity) + {} + + + //--------------------------------------------------------------------- + // Cooperatively scan a device-wide sequence of tiles with other CTAs + //--------------------------------------------------------------------- + + /** + * Process a tile of input (dynamic domino scan) + */ + template + __device__ __forceinline__ void ConsumeTile( + Offset num_items, ///< Total number of input items + Offset num_remaining, ///< Total number of items remaining to be processed (including this tile) + int tile_idx, ///< Tile index + Offset block_offset, ///< Tile offset + TileLookbackStatus &tile_status) ///< Global list of tile status + { + // Load items + T items[ITEMS_PER_THREAD]; + + if (LAST_TILE) + BlockLoadT(temp_storage.load).Load(d_in + block_offset, items, num_remaining); + else + BlockLoadT(temp_storage.load).Load(d_in + block_offset, items); + + __syncthreads(); + + // Perform tile scan + if (tile_idx == 0) + { + // Scan first tile + T block_aggregate; + ScanBlock(items, scan_op, identity, block_aggregate); + + // Update tile status if there may be successor tiles (i.e., this tile is full) + if (!LAST_TILE && (threadIdx.x == 0)) + tile_status.SetInclusive(0, block_aggregate); + } + else + { + // Scan non-first tile + T block_aggregate; + LookbackPrefixCallbackOp prefix_op(tile_status, temp_storage.prefix, scan_op, tile_idx); + ScanBlock(items, scan_op, identity, block_aggregate, prefix_op); + } + + __syncthreads(); + + // Store items + if (LAST_TILE) + BlockStoreT(temp_storage.store).Store(d_out + block_offset, items, num_remaining); + else + BlockStoreT(temp_storage.store).Store(d_out + block_offset, items); + } + + + /** + * Dequeue and scan tiles of items as part of a dynamic domino scan + */ + __device__ __forceinline__ void ConsumeRegion( + int num_items, ///< Total number of input items + GridQueue queue, ///< Queue descriptor for assigning tiles of work to thread blocks + TileLookbackStatus &tile_status) ///< Global list of tile status + { +#if (CUB_PTX_VERSION <= 130) + // Blocks are launched in increasing order, so just assign one tile per block + + int tile_idx = (blockIdx.y * 32 * 1024) + blockIdx.x; // Current tile index + Offset block_offset = Offset(TILE_ITEMS) * tile_idx; // Global offset for the current tile + Offset num_remaining = num_items - block_offset; // Remaining items (including this tile) + + if (block_offset + TILE_ITEMS <= num_items) + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + else if (block_offset < num_items) + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + +#else + // Blocks may not be launched in increasing order, so work-steal tiles + + // Get first tile index + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + int tile_idx = temp_storage.tile_idx; + Offset block_offset = TILE_ITEMS * tile_idx; + Offset num_remaining = num_items - block_offset; + + while (num_remaining >= TILE_ITEMS) + { + // Consume full tile + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + + // Get next tile + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + tile_idx = temp_storage.tile_idx; + block_offset = TILE_ITEMS * tile_idx; + num_remaining = num_items - block_offset; + } + + // Consume the last (and potentially partially-full) tile + if (num_remaining > 0) + { + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + } + +#endif + } + + + //--------------------------------------------------------------------- + // Scan an sequence of consecutive tiles (independent of other thread blocks) + //--------------------------------------------------------------------- + + /** + * Process a tile of input + */ + template < + bool FULL_TILE, + bool FIRST_TILE> + __device__ __forceinline__ void ConsumeTile( + Offset block_offset, ///< Tile offset + RunningPrefixCallbackOp &prefix_op, ///< Running prefix operator + int valid_items = TILE_ITEMS) ///< Number of valid items in the tile + { + // Load items + T items[ITEMS_PER_THREAD]; + + if (FULL_TILE) + BlockLoadT(temp_storage.load).Load(d_in + block_offset, items); + else + BlockLoadT(temp_storage.load).Load(d_in + block_offset, items, valid_items); + + __syncthreads(); + + // Block scan + if (FIRST_TILE) + { + T block_aggregate; + ScanBlock(items, scan_op, identity, block_aggregate); + prefix_op.running_total = block_aggregate; + } + else + { + T block_aggregate; + ScanBlock(items, scan_op, identity, block_aggregate, prefix_op); + } + + __syncthreads(); + + // Store items + if (FULL_TILE) + BlockStoreT(temp_storage.store).Store(d_out + block_offset, items); + else + BlockStoreT(temp_storage.store).Store(d_out + block_offset, items, valid_items); + } + + + /** + * Scan a consecutive share of input tiles + */ + __device__ __forceinline__ void ConsumeRegion( + Offset block_offset, ///< [in] Threadblock begin offset (inclusive) + Offset block_end) ///< [in] Threadblock end offset (exclusive) + { + RunningBlockPrefixCallbackOp prefix_op(scan_op); + + if (block_offset + TILE_ITEMS <= block_end) + { + // Consume first tile of input (full) + ConsumeTile(block_offset, prefix_op); + block_offset += TILE_ITEMS; + + // Consume subsequent full tiles of input + while (block_offset + TILE_ITEMS <= block_end) + { + ConsumeTile(block_offset, prefix_op); + block_offset += TILE_ITEMS; + } + + // Consume a partially-full tile + if (block_offset < block_end) + { + int valid_items = block_end - block_offset; + ConsumeTile(block_offset, prefix_op, valid_items); + } + } + else + { + // Consume the first tile of input (partially-full) + int valid_items = block_end - block_offset; + ConsumeTile(block_offset, prefix_op, valid_items); + } + } + + + /** + * Scan a consecutive share of input tiles, seeded with the specified prefix value + */ + __device__ __forceinline__ void ConsumeRegion( + Offset block_offset, ///< [in] Threadblock begin offset (inclusive) + Offset block_end, ///< [in] Threadblock end offset (exclusive) + T prefix) ///< [in] The prefix to apply to the scan segment + { + RunningBlockPrefixCallbackOp prefix_op(prefix, scan_op); + + // Consume full tiles of input + while (block_offset + TILE_ITEMS <= block_end) + { + ConsumeTile(block_offset, prefix_op); + block_offset += TILE_ITEMS; + } + + // Consume a partially-full tile + if (block_offset < block_end) + { + int valid_items = block_end - block_offset; + ConsumeTile(block_offset, prefix_op, valid_items); + } + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_select.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_select.cuh new file mode 100644 index 0000000000000000000000000000000000000000..df7aa578076a57d735caf8ebfc5ffb436d1bd296 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/block_region_select.cuh @@ -0,0 +1,735 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockRegionSelect implements a stateful abstraction of CUDA thread blocks for participating in device-wide select. + */ + +#pragma once + +#include + +#include "device_scan_types.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_store.cuh" +#include "../../block/block_scan.cuh" +#include "../../block/block_exchange.cuh" +#include "../../block/block_discontinuity.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../iterator/cache_modified_input_iterator.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Parameterizable tuning policy type for BlockRegionSelect + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + BlockLoadAlgorithm _LOAD_ALGORITHM, ///< The BlockLoad algorithm to use + CacheLoadModifier _LOAD_MODIFIER, ///< Cache load modifier for reading input elements + bool _TWO_PHASE_SCATTER, ///< Whether or not to coalesce output values in shared memory before scattering them to global + BlockScanAlgorithm _SCAN_ALGORITHM> ///< The BlockScan algorithm to use +struct BlockRegionSelectPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, ///< Threads per thread block + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + TWO_PHASE_SCATTER = _TWO_PHASE_SCATTER, ///< Whether or not to coalesce output values in shared memory before scattering them to global + }; + + static const BlockLoadAlgorithm LOAD_ALGORITHM = _LOAD_ALGORITHM; ///< The BlockLoad algorithm to use + static const CacheLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; ///< Cache load modifier for reading input elements + static const BlockScanAlgorithm SCAN_ALGORITHM = _SCAN_ALGORITHM; ///< The BlockScan algorithm to use +}; + + + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockRegionSelect implements a stateful abstraction of CUDA thread blocks for participating in device-wide selection across a region of tiles + * + * Performs functor-based selection if SelectOp functor type != NullType + * Otherwise performs flag-based selection if FlagIterator's value type != NullType + * Otherwise performs discontinuity selection (keep unique) + */ +template < + typename BlockRegionSelectPolicy, ///< Parameterized BlockRegionSelectPolicy tuning policy type + typename InputIterator, ///< Random-access input iterator type for selection items + typename FlagIterator, ///< Random-access input iterator type for selections (NullType* if a selection functor or discontinuity flagging is to be used for selection) + typename OutputIterator, ///< Random-access input iterator type for selected items + typename SelectOp, ///< Selection operator type (NullType if selections or discontinuity flagging is to be used for selection) + typename EqualityOp, ///< Equality operator type (NullType if selection functor or selections is to be used for selection) + typename Offset, ///< Signed integer type for global offsets + bool KEEP_REJECTS> ///< Whether or not we push rejected items to the back of the output +struct BlockRegionSelect +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Data type of input iterator + typedef typename std::iterator_traits::value_type T; + + // Data type of flag iterator + typedef typename std::iterator_traits::value_type Flag; + + // Tile status descriptor interface type + typedef TileLookbackStatus TileLookbackStatus; + + // Constants + enum + { + USE_SELECT_OP, + USE_SELECT_FLAGS, + USE_DISCONTINUITY, + + BLOCK_THREADS = BlockRegionSelectPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockRegionSelectPolicy::ITEMS_PER_THREAD, + TWO_PHASE_SCATTER = (BlockRegionSelectPolicy::TWO_PHASE_SCATTER) && (ITEMS_PER_THREAD > 1), + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + + // Whether or not to sync after loading data + SYNC_AFTER_LOAD = (BlockRegionSelectPolicy::LOAD_ALGORITHM != BLOCK_LOAD_DIRECT), + + SELECT_METHOD = (!Equals::VALUE) ? + USE_SELECT_OP : + (!Equals::VALUE) ? + USE_SELECT_FLAGS : + USE_DISCONTINUITY + }; + + // Input iterator wrapper type + typedef typename If::VALUE, + CacheModifiedInputIterator, // Wrap the native input pointer with CacheModifiedInputIterator + InputIterator>::Type // Directly use the supplied input iterator type + WrappedInputIterator; + + // Flag iterator wrapper type + typedef typename If::VALUE, + CacheModifiedInputIterator, // Wrap the native input pointer with CacheModifiedInputIterator + FlagIterator>::Type // Directly use the supplied input iterator type + WrappedFlagIterator; + + // Parameterized BlockLoad type for input items + typedef BlockLoad< + WrappedInputIterator, + BlockRegionSelectPolicy::BLOCK_THREADS, + BlockRegionSelectPolicy::ITEMS_PER_THREAD, + BlockRegionSelectPolicy::LOAD_ALGORITHM> + BlockLoadT; + + // Parameterized BlockLoad type for flags + typedef BlockLoad< + WrappedFlagIterator, + BlockRegionSelectPolicy::BLOCK_THREADS, + BlockRegionSelectPolicy::ITEMS_PER_THREAD, + BlockRegionSelectPolicy::LOAD_ALGORITHM> + BlockLoadFlags; + + // Parameterized BlockExchange type for input items + typedef BlockExchange< + T, + BLOCK_THREADS, + ITEMS_PER_THREAD> + BlockExchangeT; + + // Parameterized BlockDiscontinuity type for input items + typedef BlockDiscontinuity BlockDiscontinuityT; + + // Parameterized BlockScan type + typedef BlockScan< + Offset, + BlockRegionSelectPolicy::BLOCK_THREADS, + BlockRegionSelectPolicy::SCAN_ALGORITHM> + BlockScanAllocations; + + // Callback type for obtaining tile prefix during block scan + typedef LookbackBlockPrefixCallbackOp< + Offset, + Sum, + TileLookbackStatus> + LookbackPrefixCallbackOp; + + // Shared memory type for this threadblock + struct _TempStorage + { + union + { + struct + { + typename LookbackPrefixCallbackOp::TempStorage prefix; // Smem needed for cooperative prefix callback + typename BlockScanAllocations::TempStorage scan; // Smem needed for tile scanning + typename BlockDiscontinuityT::TempStorage discontinuity; // Smem needed for discontinuity detection + }; + + // Smem needed for input loading + typename BlockLoadT::TempStorage load_items; + + // Smem needed for flag loading + typename BlockLoadFlags::TempStorage load_flags; + + // Smem needed for two-phase scatter + typename If::Type exchange; + }; + + Offset tile_idx; // Shared tile index + Offset tile_num_selected_prefix; // Exclusive tile prefix + }; + + // Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + _TempStorage &temp_storage; ///< Reference to temp_storage + WrappedInputIterator d_in; ///< Input data + WrappedFlagIterator d_flags; ///< Input flags + OutputIterator d_out; ///< Output data + SelectOp select_op; ///< Selection operator + InequalityWrapper inequality_op; ///< Inequality operator + Offset num_items; ///< Total number of input items + + + //--------------------------------------------------------------------- + // Constructor + //--------------------------------------------------------------------- + + // Constructor + __device__ __forceinline__ + BlockRegionSelect( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIterator d_in, ///< Input data + FlagIterator d_flags, ///< Input flags + OutputIterator d_out, ///< Output data + SelectOp select_op, ///< Selection operator + EqualityOp equality_op, ///< Equality operator + Offset num_items) ///< Total number of input items + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + d_flags(d_flags), + d_out(d_out), + select_op(select_op), + inequality_op(equality_op), + num_items(num_items) + {} + + + //--------------------------------------------------------------------- + // Utility methods for initializing the selections + //--------------------------------------------------------------------- + + /** + * Template unrolled selection via selection operator + */ + template + __device__ __forceinline__ void ApplySelectionOp( + Offset block_offset, + Offset num_remaining, + T (&items)[ITEMS_PER_THREAD], + Offset (&selected)[ITEMS_PER_THREAD], + Int2Type iteration) + { + selected[ITERATION] = 0; + if (!LAST_TILE || (Offset(threadIdx.x * ITEMS_PER_THREAD) + ITERATION < num_remaining)) + selected[ITERATION] = select_op(items[ITERATION]); + + ApplySelectionOp(block_offset, num_remaining, items, selected, Int2Type()); + } + + /** + * Template unrolled selection via selection operator + */ + template + __device__ __forceinline__ void ApplySelectionOp( + Offset block_offset, + Offset num_remaining, + T (&items)[ITEMS_PER_THREAD], + Offset (&selected)[ITEMS_PER_THREAD], + Int2Type iteration) + {} + + /** + * Initialize selections (specialized for selection operator) + */ + template + __device__ __forceinline__ void InitializeSelections( + Offset block_offset, + Offset num_remaining, + T (&items)[ITEMS_PER_THREAD], + Offset (&selected)[ITEMS_PER_THREAD], + Int2Type select_method) + { + ApplySelectionOp(block_offset, num_remaining, items, selected, Int2Type<0>()); + } + + + /** + * Initialize selections (specialized for valid flags) + */ + template + __device__ __forceinline__ void InitializeSelections( + Offset block_offset, + Offset num_remaining, + T (&items)[ITEMS_PER_THREAD], + Offset (&selected)[ITEMS_PER_THREAD], + Int2Type select_method) + { + Flag flags[ITEMS_PER_THREAD]; + + if (LAST_TILE) + BlockLoadFlags(temp_storage.load_flags).Load(d_flags + block_offset, flags, num_remaining, 0); + else + BlockLoadFlags(temp_storage.load_flags).Load(d_flags + block_offset, flags); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + selected[ITEM] = flags[ITEM]; + } + + if (SYNC_AFTER_LOAD) + __syncthreads(); + } + + + /** + * Initialize selections (specialized for discontinuity detection) + */ + template + __device__ __forceinline__ void InitializeSelections( + Offset block_offset, + Offset num_remaining, + T (&items)[ITEMS_PER_THREAD], + Offset (&selected)[ITEMS_PER_THREAD], + Int2Type select_method) + { + if (FIRST_TILE) + { + // First tile always flags the first item + BlockDiscontinuityT(temp_storage.discontinuity).FlagHeads(selected, items, inequality_op); + } + else + { + // Subsequent tiles require the last item from the previous tile + T tile_predecessor_item; + if (threadIdx.x == 0) + tile_predecessor_item = d_in[block_offset - 1]; + + BlockDiscontinuityT(temp_storage.discontinuity).FlagHeads(selected, items, inequality_op, tile_predecessor_item); + } + } + + + //--------------------------------------------------------------------- + // Utility methods for scattering selections + //--------------------------------------------------------------------- + + /** + * Scatter data items to select offsets (specialized for direct scattering and for discarding rejected items) + */ + template + __device__ __forceinline__ void Scatter( + Offset block_offset, + T (&items)[ITEMS_PER_THREAD], + Offset selected[ITEMS_PER_THREAD], + Offset scatter_offsets[ITEMS_PER_THREAD], + Offset tile_num_selected_prefix, + Offset tile_num_selected, + Offset num_remaining, + Int2Type keep_rejects, + Int2Type two_phase_scatter) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + if (selected[ITEM]) + { + // Selected items are placed front-to-back + d_out[scatter_offsets[ITEM]] = items[ITEM]; + } + } + } + + + /** + * Scatter data items to select offsets (specialized for direct scattering and for partitioning rejected items after selected items) + */ + template + __device__ __forceinline__ void Scatter( + Offset block_offset, + T (&items)[ITEMS_PER_THREAD], + Offset selected[ITEMS_PER_THREAD], + Offset scatter_offsets[ITEMS_PER_THREAD], + Offset tile_num_selected_prefix, + Offset tile_num_selected, + Offset num_remaining, + Int2Type keep_rejects, + Int2Type two_phase_scatter) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + if (selected[ITEM]) + { + // Selected items are placed front-to-back + d_out[scatter_offsets[ITEM]] = items[ITEM]; + } + else if (!LAST_TILE || (Offset(threadIdx.x * ITEMS_PER_THREAD) + ITEM < num_remaining)) + { + Offset global_idx = block_offset + (threadIdx.x * ITEMS_PER_THREAD) + ITEM; + Offset reject_idx = global_idx - scatter_offsets[ITEM]; + + // Rejected items are placed back-to-front + d_out[num_items - reject_idx - 1] = items[ITEM]; + } + } + } + + + /** + * Scatter data items to select offsets (specialized for two-phase scattering and for discarding rejected items) + */ + template + __device__ __forceinline__ void Scatter( + Offset block_offset, + T (&items)[ITEMS_PER_THREAD], + Offset selected[ITEMS_PER_THREAD], + Offset scatter_offsets[ITEMS_PER_THREAD], + Offset tile_num_selected_prefix, + Offset tile_num_selected, + Offset num_remaining, + Int2Type keep_rejects, + Int2Type two_phase_scatter) + { + if ((tile_num_selected >> Log2::VALUE) == 0) + { + // Average number of selected items per thread is less than one, so just do a one-phase scatter + Scatter( + block_offset, + items, + selected, + scatter_offsets, + tile_num_selected_prefix, + tile_num_selected, + num_remaining, + keep_rejects, + Int2Type()); + } + else + { + // Share exclusive tile prefix + if (threadIdx.x == 0) + { + temp_storage.tile_num_selected_prefix = tile_num_selected_prefix; + } + + __syncthreads(); + + // Load exclusive tile prefix in all threads + tile_num_selected_prefix = temp_storage.tile_num_selected_prefix; + + int local_ranks[ITEMS_PER_THREAD]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + local_ranks[ITEM] = scatter_offsets[ITEM] - tile_num_selected_prefix; + } + + BlockExchangeT(temp_storage.exchange).ScatterToStriped(items, local_ranks, selected); + + // Selected items are placed front-to-back + StoreDirectStriped(threadIdx.x, d_out + tile_num_selected_prefix, items, tile_num_selected); + } + } + + + /** + * Scatter data items to select offsets (specialized for two-phase scattering and for partitioning rejected items after selected items) + */ + template + __device__ __forceinline__ void Scatter( + Offset block_offset, + T (&items)[ITEMS_PER_THREAD], + Offset selected[ITEMS_PER_THREAD], + Offset scatter_offsets[ITEMS_PER_THREAD], + Offset tile_num_selected_prefix, + Offset tile_num_selected, + Offset num_remaining, + Int2Type keep_rejects, + Int2Type two_phase_scatter) + { + // Share exclusive tile prefix + if (threadIdx.x == 0) + { + temp_storage.tile_num_selected_prefix = tile_num_selected_prefix; + } + + __syncthreads(); + + // Load the exclusive tile prefix in all threads + tile_num_selected_prefix = temp_storage.tile_num_selected_prefix; + + // Determine the exclusive prefix for rejects + Offset tile_rejected_exclusive_prefix = block_offset - tile_num_selected_prefix; + + // Determine local scatter offsets + int local_ranks[ITEMS_PER_THREAD]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + local_ranks[ITEM] = -1; + Offset global_idx = block_offset + (threadIdx.x * ITEMS_PER_THREAD) + ITEM; + Offset reject_idx = global_idx - scatter_offsets[ITEM]; + + if (selected[ITEM]) + { + // Selected items + local_ranks[ITEM] = scatter_offsets[ITEM] - tile_num_selected_prefix; + } + else if (!LAST_TILE || (Offset(threadIdx.x * ITEMS_PER_THREAD) + ITEM < num_remaining)) + { + // Rejected items + local_ranks[ITEM] = (reject_idx - tile_rejected_exclusive_prefix) + tile_num_selected; + } + } + + // Coalesce selected and rejected items in shared memory, gathering in striped arrangements + if (LAST_TILE) + BlockExchangeT(temp_storage.exchange).ScatterToStripedGuarded(items, local_ranks); + else + BlockExchangeT(temp_storage.exchange).ScatterToStriped(items, local_ranks); + + // Store in striped order + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + Offset local_idx = (ITEM * BLOCK_THREADS) + threadIdx.x; + Offset scatter_offset = tile_num_selected_prefix + local_idx; + if (local_idx >= tile_num_selected) + scatter_offset = num_items - (tile_rejected_exclusive_prefix + (local_idx - tile_num_selected)) - 1; + + if (!LAST_TILE || (local_idx < num_remaining)) + { + d_out[scatter_offset] = items[ITEM]; + } + } + } + + + //--------------------------------------------------------------------- + // Cooperatively scan a device-wide sequence of tiles with other CTAs + //--------------------------------------------------------------------- + + /** + * Process a tile of input (dynamic domino scan) + */ + template + __device__ __forceinline__ Offset ConsumeTile( + Offset num_items, ///< Total number of input items + Offset num_remaining, ///< Total number of items remaining to be processed (including this tile) + int tile_idx, ///< Tile index + Offset block_offset, ///< Tile offset + TileLookbackStatus &tile_status) ///< Global list of tile status + { + T items[ITEMS_PER_THREAD]; + Offset selected[ITEMS_PER_THREAD]; // Selection flags + Offset scatter_offsets[ITEMS_PER_THREAD]; // Scatter offsets + Offset tile_num_selected_prefix; // Total number of selected items prior to this tile + Offset tile_num_selected; // Total number of selected items within this tile + Offset num_selected; // + + // Load items + if (LAST_TILE) + BlockLoadT(temp_storage.load_items).Load(d_in + block_offset, items, num_remaining, d_in[num_items - 1]); // Repeat last item + else + BlockLoadT(temp_storage.load_items).Load(d_in + block_offset, items); + + if (SYNC_AFTER_LOAD) + __syncthreads(); + + if (tile_idx == 0) + { + // Initialize selected/rejected output flags for first tile + InitializeSelections( + block_offset, + num_remaining, + items, + selected, + Int2Type()); + + // Compute scatter offsets by scanning the flags + BlockScanAllocations(temp_storage.scan).ExclusiveSum(selected, scatter_offsets, tile_num_selected); + + // Update tile status if there may be successor tiles + if (!LAST_TILE && (threadIdx.x == 0)) + tile_status.SetInclusive(0, tile_num_selected); + + tile_num_selected_prefix = 0; + num_selected = tile_num_selected; + } + else + { + // Initialize selected/rejected output flags for non-first tile + InitializeSelections( + block_offset, + num_remaining, + items, + selected, + Int2Type()); + + // Compute scatter offsets by scanning the flags + LookbackPrefixCallbackOp prefix_op(tile_status, temp_storage.prefix, Sum(), tile_idx); + BlockScanAllocations(temp_storage.scan).ExclusiveSum(selected, scatter_offsets, tile_num_selected, prefix_op); + + tile_num_selected_prefix = prefix_op.exclusive_prefix; + num_selected = prefix_op.inclusive_prefix; + } + + // Store selected items + Scatter( + block_offset, + items, + selected, + scatter_offsets, + tile_num_selected_prefix, + tile_num_selected, + num_remaining, + Int2Type(), + Int2Type()); + + // Return total number of items selected (inclusive of this tile) + return num_selected; + } + + + /** + * Dequeue and scan tiles of items as part of a dynamic domino scan + */ + template ///< Output iterator type for recording number of items selected + __device__ __forceinline__ void ConsumeRegion( + int num_tiles, ///< Total number of input tiles + GridQueue queue, ///< Queue descriptor for assigning tiles of work to thread blocks + TileLookbackStatus &tile_status, ///< Global list of tile status + NumSelectedIterator d_num_selected) ///< Output total number selected + { +#if (CUB_PTX_VERSION <= 130) + // Blocks are launched in increasing order, so just assign one tile per block + + int tile_idx = (blockIdx.y * 32 * 1024) + blockIdx.x; // Current tile index + Offset block_offset = Offset(TILE_ITEMS) * tile_idx; // Global offset for the current tile + Offset num_remaining = num_items - block_offset; // Remaining items (including this tile) + + if (num_remaining > TILE_ITEMS) + { + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + } + else if (num_remaining > 0) + { + Offset total_selected = ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + + // Output the total number of items selected + if (threadIdx.x == 0) + { + *d_num_selected = total_selected; + } + } + +#else + // Blocks may not be launched in increasing order, so work-steal tiles + + // Get first tile index + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + int tile_idx = temp_storage.tile_idx; + Offset block_offset = Offset(TILE_ITEMS) * tile_idx; + Offset num_remaining = num_items - block_offset; + + while (num_remaining > TILE_ITEMS) + { + // Consume full tile + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + + // Get next tile + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + tile_idx = temp_storage.tile_idx; + block_offset = Offset(TILE_ITEMS) * tile_idx; + num_remaining = num_items - block_offset; + } + + // Consume the last (and potentially partially-full) tile + if (num_remaining > 0) + { + Offset total_selected = ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + + // Output the total number of items selected + if (threadIdx.x == 0) + { + *d_num_selected = total_selected; + } + } + +#endif + + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/device_scan_types.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/device_scan_types.cuh new file mode 100644 index 0000000000000000000000000000000000000000..95889f6001a33674fd9d9ab22714adcfe3afa233 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/device_scan_types.cuh @@ -0,0 +1,561 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * Utility types for device-wide scan and similar primitives + */ + +#pragma once + +#include + +#include "../../thread/thread_load.cuh" +#include "../../thread/thread_store.cuh" +#include "../../warp/warp_reduce.cuh" +#include "../../util_arch.cuh" +#include "../../util_device.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Callback operator types for supplying BlockScan prefixes + ******************************************************************************/ + +/** + * Stateful callback operator type for supplying BlockScan prefixes. + * Maintains a running prefix that can be applied to consecutive + * BlockScan operations. + */ +template < + typename T, ///< BlockScan value type + typename ScanOp> ///< Wrapped scan operator type +struct RunningBlockPrefixCallbackOp +{ + ScanOp op; ///< Wrapped scan operator + T running_total; ///< Running block-wide prefix + + /// Constructor + __device__ __forceinline__ RunningBlockPrefixCallbackOp(ScanOp op) + : + op(op) + {} + + /// Constructor + __device__ __forceinline__ RunningBlockPrefixCallbackOp( + T starting_prefix, + ScanOp op) + : + op(op), + running_total(starting_prefix) + {} + + /** + * Prefix callback operator. Returns the block-wide running_total in thread-0. + */ + __device__ __forceinline__ T operator()( + const T &block_aggregate) ///< The aggregate sum of the BlockScan inputs + { + T retval = running_total; + running_total = op(running_total, block_aggregate); + return retval; + } +}; + + +/****************************************************************************** + * Bookkeeping types for single-pass device-wide scan with dynamic lookback + ******************************************************************************/ + +/** + * Enumerations of tile status + */ +enum LookbackTileStatus +{ + LOOKBACK_TILE_OOB, // Out-of-bounds (e.g., padding) + LOOKBACK_TILE_INVALID, // Not yet processed + LOOKBACK_TILE_PARTIAL, // Tile aggregate is available + LOOKBACK_TILE_INCLUSIVE, // Inclusive tile prefix is available +}; + + +/** + * Tile status interface. + */ +template < + typename T, + bool SINGLE_WORD = Traits::PRIMITIVE> +struct TileLookbackStatus; + + +/** + * Tile status interface specialized for scan status and value types + * that can be combined into one machine word that can be + * read/written coherently in a single access. + */ +template +struct TileLookbackStatus +{ + // Status word type + typedef typename If<(sizeof(T) == 8), + long long, + typename If<(sizeof(T) == 4), + int, + typename If<(sizeof(T) == 2), + short, + char>::Type>::Type>::Type StatusWord; + + + // Unit word type + typedef typename If<(sizeof(T) == 8), + longlong2, + typename If<(sizeof(T) == 4), + int2, + typename If<(sizeof(T) == 2), + int, + uchar2>::Type>::Type>::Type TxnWord; + + + // Device word type + struct TileDescriptor + { + StatusWord status; + T value; + }; + + + // Constants + enum + { + TILE_STATUS_PADDING = CUB_PTX_WARP_THREADS, + }; + + + // Device storage + TileDescriptor *d_tile_status; + + + /// Constructor + __host__ __device__ __forceinline__ + TileLookbackStatus() + : + d_tile_status(NULL) + {} + + + /// Initializer + __host__ __device__ __forceinline__ + cudaError_t Init( + int num_tiles, ///< [in] Number of tiles + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t temp_storage_bytes) ///< [in] Size in bytes of \t d_temp_storage allocation + { + d_tile_status = reinterpret_cast(d_temp_storage); + return cudaSuccess; + } + + + /** + * Compute device memory needed for tile status + */ + __host__ __device__ __forceinline__ + static cudaError_t AllocationSize( + int num_tiles, ///< [in] Number of tiles + size_t &temp_storage_bytes) ///< [out] Size in bytes of \t d_temp_storage allocation + { + temp_storage_bytes = (num_tiles + TILE_STATUS_PADDING) * sizeof(TileDescriptor); // bytes needed for tile status descriptors + return cudaSuccess; + } + + + /** + * Initialize (from device) + */ + __device__ __forceinline__ void InitializeStatus(int num_tiles) + { + int tile_idx = (blockIdx.x * blockDim.x) + threadIdx.x; + if (tile_idx < num_tiles) + { + // Not-yet-set + d_tile_status[TILE_STATUS_PADDING + tile_idx].status = StatusWord(LOOKBACK_TILE_INVALID); + } + + if ((blockIdx.x == 0) && (threadIdx.x < TILE_STATUS_PADDING)) + { + // Padding + d_tile_status[threadIdx.x].status = StatusWord(LOOKBACK_TILE_OOB); + } + } + + + /** + * Update the specified tile's inclusive value and corresponding status + */ + __device__ __forceinline__ void SetInclusive(int tile_idx, T tile_inclusive) + { + TileDescriptor tile_descriptor; + tile_descriptor.status = LOOKBACK_TILE_INCLUSIVE; + tile_descriptor.value = tile_inclusive; + + TxnWord alias; + *reinterpret_cast(&alias) = tile_descriptor; + ThreadStore(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx), alias); + } + + + /** + * Update the specified tile's partial value and corresponding status + */ + __device__ __forceinline__ void SetPartial(int tile_idx, T tile_partial) + { + TileDescriptor tile_descriptor; + tile_descriptor.status = LOOKBACK_TILE_PARTIAL; + tile_descriptor.value = tile_partial; + + TxnWord alias; + *reinterpret_cast(&alias) = tile_descriptor; + ThreadStore(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx), alias); + } + + /** + * Wait for the corresponding tile to become non-invalid + */ + __device__ __forceinline__ void WaitForValid( + int tile_idx, + StatusWord &status, + T &value) + { + // Use warp-any to determine when all threads have valid status + TxnWord alias = ThreadLoad(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx)); + TileDescriptor tile_descriptor = reinterpret_cast(alias); + + while ((tile_descriptor.status == LOOKBACK_TILE_INVALID)) + { + alias = ThreadLoad(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx)); + tile_descriptor = reinterpret_cast(alias); + } + + status = tile_descriptor.status; + value = tile_descriptor.value; + } + +}; + + + +/** + * Tile status interface specialized for scan status and value types that + * cannot be combined into one machine word. + */ +template +struct TileLookbackStatus +{ + // Status word type + typedef char StatusWord; + + // Constants + enum + { + TILE_STATUS_PADDING = CUB_PTX_WARP_THREADS, + }; + + // Device storage + StatusWord *d_tile_status; + T *d_tile_partial; + T *d_tile_inclusive; + + /// Constructor + __host__ __device__ __forceinline__ + TileLookbackStatus() + : + d_tile_status(NULL), + d_tile_partial(NULL), + d_tile_inclusive(NULL) + {} + + + /// Initializer + __host__ __device__ __forceinline__ + cudaError_t Init( + int num_tiles, ///< [in] Number of tiles + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t temp_storage_bytes) ///< [in] Size in bytes of \t d_temp_storage allocation + { + cudaError_t error = cudaSuccess; + do + { + void* allocations[3]; + size_t allocation_sizes[3]; + + allocation_sizes[0] = (num_tiles + TILE_STATUS_PADDING) * sizeof(StatusWord); // bytes needed for tile status descriptors + allocation_sizes[1] = num_tiles * sizeof(Uninitialized); // bytes needed for partials + allocation_sizes[2] = num_tiles * sizeof(Uninitialized); // bytes needed for inclusives + + // Compute allocation pointers into the single storage blob + if (CubDebug(error = AliasTemporaries(d_temp_storage, temp_storage_bytes, allocations, allocation_sizes))) break; + + // Alias the offsets + d_tile_status = reinterpret_cast(allocations[0]); + d_tile_partial = reinterpret_cast(allocations[1]); + d_tile_inclusive = reinterpret_cast(allocations[2]); + } + while (0); + + return error; + } + + + /** + * Compute device memory needed for tile status + */ + __host__ __device__ __forceinline__ + static cudaError_t AllocationSize( + int num_tiles, ///< [in] Number of tiles + size_t &temp_storage_bytes) ///< [out] Size in bytes of \t d_temp_storage allocation + { + // Specify storage allocation requirements + size_t allocation_sizes[3]; + allocation_sizes[0] = (num_tiles + TILE_STATUS_PADDING) * sizeof(StatusWord); // bytes needed for tile status descriptors + allocation_sizes[1] = num_tiles * sizeof(Uninitialized); // bytes needed for partials + allocation_sizes[2] = num_tiles * sizeof(Uninitialized); // bytes needed for inclusives + + // Set the necessary size of the blob + void* allocations[3]; + return CubDebug(AliasTemporaries(NULL, temp_storage_bytes, allocations, allocation_sizes)); + } + + + /** + * Initialize (from device) + */ + __device__ __forceinline__ void InitializeStatus(int num_tiles) + { + int tile_idx = (blockIdx.x * blockDim.x) + threadIdx.x; + if (tile_idx < num_tiles) + { + // Not-yet-set + d_tile_status[TILE_STATUS_PADDING + tile_idx] = StatusWord(LOOKBACK_TILE_INVALID); + } + + if ((blockIdx.x == 0) && (threadIdx.x < TILE_STATUS_PADDING)) + { + // Padding + d_tile_status[threadIdx.x] = StatusWord(LOOKBACK_TILE_OOB); + } + } + + + /** + * Update the specified tile's inclusive value and corresponding status + */ + __device__ __forceinline__ void SetInclusive(int tile_idx, T tile_inclusive) + { + // Update tile inclusive value + ThreadStore(d_tile_inclusive + tile_idx, tile_inclusive); + + // Fence + __threadfence(); + + // Update tile status + ThreadStore(d_tile_status + TILE_STATUS_PADDING + tile_idx, StatusWord(LOOKBACK_TILE_INCLUSIVE)); + } + + + /** + * Update the specified tile's partial value and corresponding status + */ + __device__ __forceinline__ void SetPartial(int tile_idx, T tile_partial) + { + // Update tile partial value + ThreadStore(d_tile_partial + tile_idx, tile_partial); + + // Fence + __threadfence(); + + // Update tile status + ThreadStore(d_tile_status + TILE_STATUS_PADDING + tile_idx, StatusWord(LOOKBACK_TILE_PARTIAL)); + } + + /** + * Wait for the corresponding tile to become non-invalid + */ + __device__ __forceinline__ void WaitForValid( + int tile_idx, + StatusWord &status, + T &value) + { + status = ThreadLoad(d_tile_status + TILE_STATUS_PADDING + tile_idx); + while (status == LOOKBACK_TILE_INVALID) + { + status = ThreadLoad(d_tile_status + TILE_STATUS_PADDING + tile_idx); + } + + T partial = ThreadLoad(d_tile_partial + tile_idx); + T inclusive = ThreadLoad(d_tile_inclusive + tile_idx); + + value = (status == StatusWord(LOOKBACK_TILE_PARTIAL)) ? + partial : + inclusive; + + } +}; + + + +/** + * Stateful block-scan prefix functor. Provides the the running prefix for + * the current tile by using the call-back warp to wait on on + * aggregates/prefixes from predecessor tiles to become available. + */ +template < + typename T, + typename ScanOp, + typename TileLookbackStatus> +struct LookbackBlockPrefixCallbackOp +{ + // Parameterized warp reduce + typedef WarpReduce WarpReduceT; + + // Temporary storage type + typedef typename WarpReduceT::TempStorage _TempStorage; + + // Alias wrapper allowing temporary storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + // Type of status word + typedef typename TileLookbackStatus::StatusWord StatusWord; + + // Scan operator for switching the scan arguments + struct SwizzleScanOp + { + ScanOp scan_op; + + // Constructor + __host__ __device__ __forceinline__ + SwizzleScanOp(ScanOp scan_op) : scan_op(scan_op) {} + + // Switch the scan arguments + __host__ __device__ __forceinline__ + T operator()(const T &a, const T &b) + { + return scan_op(b, a); + } + }; + + // Fields + TileLookbackStatus &tile_status; ///< Interface to tile status + _TempStorage &temp_storage; ///< Reference to a warp-reduction instance + ScanOp scan_op; ///< Binary scan operator + int tile_idx; ///< The current tile index + T exclusive_prefix; ///< Exclusive prefix for the tile + T inclusive_prefix; ///< Inclusive prefix for the tile + + // Constructor + __device__ __forceinline__ + LookbackBlockPrefixCallbackOp( + TileLookbackStatus &tile_status, + TempStorage &temp_storage, + ScanOp scan_op, + int tile_idx) + : + tile_status(tile_status), + temp_storage(temp_storage.Alias()), + scan_op(scan_op), + tile_idx(tile_idx) {} + + + // Block until all predecessors within the warp-wide window have non-invalid status + __device__ __forceinline__ + void ProcessWindow( + int predecessor_idx, ///< Preceding tile index to inspect + StatusWord &predecessor_status, ///< [out] Preceding tile status + T &window_aggregate) ///< [out] Relevant partial reduction from this window of preceding tiles + { + T value; + tile_status.WaitForValid(predecessor_idx, predecessor_status, value); + + // Perform a segmented reduction to get the prefix for the current window. + // Use the swizzled scan operator because we are now scanning *down* towards thread0. + + int tail_flag = (predecessor_status == StatusWord(LOOKBACK_TILE_INCLUSIVE)); + window_aggregate = WarpReduceT(temp_storage).TailSegmentedReduce(value, tail_flag, SwizzleScanOp(scan_op)); + } + + + // BlockScan prefix callback functor (called by the first warp) + __device__ __forceinline__ + T operator()(T block_aggregate) + { + // Update our status with our tile-aggregate + if (threadIdx.x == 0) + { + tile_status.SetPartial(tile_idx, block_aggregate); + } + + int predecessor_idx = tile_idx - threadIdx.x - 1; + StatusWord predecessor_status; + T window_aggregate; + + // Wait for the warp-wide window of predecessor tiles to become valid + ProcessWindow(predecessor_idx, predecessor_status, window_aggregate); + + // The exclusive tile prefix starts out as the current window aggregate + exclusive_prefix = window_aggregate; + + // Keep sliding the window back until we come across a tile whose inclusive prefix is known + while (WarpAll(predecessor_status != StatusWord(LOOKBACK_TILE_INCLUSIVE))) + { + predecessor_idx -= CUB_PTX_WARP_THREADS; + + // Update exclusive tile prefix with the window prefix + ProcessWindow(predecessor_idx, predecessor_status, window_aggregate); + exclusive_prefix = scan_op(window_aggregate, exclusive_prefix); + } + + // Compute the inclusive tile prefix and update the status for this tile + if (threadIdx.x == 0) + { + inclusive_prefix = scan_op(exclusive_prefix, block_aggregate); + tile_status.SetInclusive(tile_idx, inclusive_prefix); + } + + // Return exclusive_prefix + return exclusive_prefix; + } +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/specializations/block_region_histo_gatomic.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/specializations/block_region_histo_gatomic.cuh new file mode 100644 index 0000000000000000000000000000000000000000..7aa278407577a936f4cae270e3245c6e2a5e9fb4 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/specializations/block_region_histo_gatomic.cuh @@ -0,0 +1,184 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockRegionHistogramGlobalAtomic implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram. + */ + +#pragma once + +#include + +#include "../../../util_type.cuh" +#include "../../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + + +/** + * BlockRegionHistogramGlobalAtomic implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using global atomics + */ +template < + typename BlockRegionHistogramPolicy, ///< Tuning policy + int BINS, ///< Number of histogram bins per channel + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIterator, ///< The input iterator type \iterator. Must have an an InputIterator::value_type that, when cast as an integer, falls in the range [0..BINS-1] + typename HistoCounter, ///< Integer type for counting sample occurrences per histogram bin + typename Offset> ///< Signed integer type for global offsets +struct BlockRegionHistogramGlobalAtomic +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Sample type + typedef typename std::iterator_traits::value_type SampleT; + + // Constants + enum + { + BLOCK_THREADS = BlockRegionHistogramPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockRegionHistogramPolicy::ITEMS_PER_THREAD, + TILE_CHANNEL_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + TILE_ITEMS = TILE_CHANNEL_ITEMS * CHANNELS, + }; + + // Shared memory type required by this thread block + typedef NullType TempStorage; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + /// Reference to output histograms + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]; + + /// Input data to reduce + InputIterator d_in; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockRegionHistogramGlobalAtomic( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIterator d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) ///< Reference to output histograms + : + d_in(d_in), + d_out_histograms(d_out_histograms) + {} + + + /** + * Process a single tile of input + */ + template + __device__ __forceinline__ void ConsumeTile( + Offset block_offset, ///< The offset the tile to consume + int valid_items = TILE_ITEMS) ///< The number of valid items in the tile + { + if (FULL_TILE) + { + // Full tile of samples to read and composite + SampleT items[ITEMS_PER_THREAD][CHANNELS]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + items[ITEM][CHANNEL] = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + } + } + } + + __threadfence_block(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + atomicAdd(d_out_histograms[CHANNEL] + items[ITEM][CHANNEL], 1); + } + } + } + } + else + { + // Only a partially-full tile of samples to read and composite + int bounds = valid_items - (threadIdx.x * CHANNELS); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (((ACTIVE_CHANNELS == CHANNELS) || (CHANNEL < ACTIVE_CHANNELS)) && ((ITEM * BLOCK_THREADS * CHANNELS) + CHANNEL < bounds)) + { + SampleT item = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + atomicAdd(d_out_histograms[CHANNEL] + item, 1); + } + } + } + + } + } + + + /** + * Aggregate results into output + */ + __device__ __forceinline__ void AggregateOutput() + {} +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/specializations/block_region_histo_satomic.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/specializations/block_region_histo_satomic.cuh new file mode 100644 index 0000000000000000000000000000000000000000..3e6f7d9841972bce0e9513c0f786e23b90c605fb --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/specializations/block_region_histo_satomic.cuh @@ -0,0 +1,245 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockRegionHistogramSharedAtomic implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using shared atomics + */ + +#pragma once + +#include + +#include "../../../util_type.cuh" +#include "../../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * BlockRegionHistogramSharedAtomic implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using shared atomics + */ +template < + typename BlockRegionHistogramPolicy, ///< Tuning policy + int BINS, ///< Number of histogram bins + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIterator, ///< The input iterator type \iterator. Must have an an InputIterator::value_type that, when cast as an integer, falls in the range [0..BINS-1] + typename HistoCounter, ///< Integer type for counting sample occurrences per histogram bin + typename Offset> ///< Signed integer type for global offsets +struct BlockRegionHistogramSharedAtomic +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Sample type + typedef typename std::iterator_traits::value_type SampleT; + + // Constants + enum + { + BLOCK_THREADS = BlockRegionHistogramPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockRegionHistogramPolicy::ITEMS_PER_THREAD, + TILE_CHANNEL_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + TILE_ITEMS = TILE_CHANNEL_ITEMS * CHANNELS, + }; + + /// Shared memory type required by this thread block + struct _TempStorage + { + HistoCounter histograms[ACTIVE_CHANNELS][BINS + 1]; // One word of padding between channel histograms to prevent warps working on different histograms from hammering on the same bank + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + /// Reference to temp_storage + _TempStorage &temp_storage; + + /// Reference to output histograms + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]; + + /// Input data to reduce + InputIterator d_in; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockRegionHistogramSharedAtomic( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIterator d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) ///< Reference to output histograms + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + d_out_histograms(d_out_histograms) + { + // Initialize histogram bin counts to zeros + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + int histo_offset = 0; + + #pragma unroll + for(; histo_offset + BLOCK_THREADS <= BINS; histo_offset += BLOCK_THREADS) + { + this->temp_storage.histograms[CHANNEL][histo_offset + threadIdx.x] = 0; + } + // Finish up with guarded initialization if necessary + if ((BINS % BLOCK_THREADS != 0) && (histo_offset + threadIdx.x < BINS)) + { + this->temp_storage.histograms[CHANNEL][histo_offset + threadIdx.x] = 0; + } + } + + __syncthreads(); + } + + + /** + * Process a single tile of input + */ + template + __device__ __forceinline__ void ConsumeTile( + Offset block_offset, ///< The offset the tile to consume + int valid_items = TILE_ITEMS) ///< The number of valid items in the tile + { + if (FULL_TILE) + { + // Full tile of samples to read and composite + SampleT items[ITEMS_PER_THREAD][CHANNELS]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + items[ITEM][CHANNEL] = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + } + } + } + + __threadfence_block(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + atomicAdd(temp_storage.histograms[CHANNEL] + items[ITEM][CHANNEL], 1); + } + } + } + + __threadfence_block(); + } + else + { + // Only a partially-full tile of samples to read and composite + int bounds = valid_items - (threadIdx.x * CHANNELS); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (((ACTIVE_CHANNELS == CHANNELS) || (CHANNEL < ACTIVE_CHANNELS)) && ((ITEM * BLOCK_THREADS * CHANNELS) + CHANNEL < bounds)) + { + SampleT item = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + atomicAdd(temp_storage.histograms[CHANNEL] + item, 1); + } + } + } + + } + } + + + /** + * Aggregate results into output + */ + __device__ __forceinline__ void AggregateOutput() + { + // Barrier to ensure shared memory histograms are coherent + __syncthreads(); + + // Copy shared memory histograms to output + int channel_offset = (blockIdx.x * BINS); + + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + int histo_offset = 0; + + #pragma unroll + for(; histo_offset + BLOCK_THREADS <= BINS; histo_offset += BLOCK_THREADS) + { + HistoCounter count = temp_storage.histograms[CHANNEL][histo_offset + threadIdx.x]; + + d_out_histograms[CHANNEL][channel_offset + histo_offset + threadIdx.x] = count; + } + + // Finish up with guarded initialization if necessary + if ((BINS % BLOCK_THREADS != 0) && (histo_offset + threadIdx.x < BINS)) + { + HistoCounter count = temp_storage.histograms[CHANNEL][histo_offset + threadIdx.x]; + + d_out_histograms[CHANNEL][channel_offset + histo_offset + threadIdx.x] = count; + } + } + } +}; + + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/specializations/block_region_histo_sort.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/specializations/block_region_histo_sort.cuh new file mode 100644 index 0000000000000000000000000000000000000000..a9105bc3c1f542dc01be5e7d3d30043ff54f45fd --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/block_region/specializations/block_region_histo_sort.cuh @@ -0,0 +1,364 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockRegionHistogramSort implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using local sorting + */ + +#pragma once + +#include + +#include "../../../block/block_radix_sort.cuh" +#include "../../../block/block_discontinuity.cuh" +#include "../../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * BlockRegionHistogramSort implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using local sorting + */ +template < + typename BlockRegionHistogramPolicy, ///< Tuning policy + int BINS, ///< Number of histogram bins per channel + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIterator, ///< The input iterator type \iterator. Must have an an InputIterator::value_type that, when cast as an integer, falls in the range [0..BINS-1] + typename HistoCounter, ///< Integer type for counting sample occurrences per histogram bin + typename Offset> ///< Signed integer type for global offsets +struct BlockRegionHistogramSort +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Sample type + typedef typename std::iterator_traits::value_type SampleT; + + // Constants + enum + { + BLOCK_THREADS = BlockRegionHistogramPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockRegionHistogramPolicy::ITEMS_PER_THREAD, + TILE_CHANNEL_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + TILE_ITEMS = TILE_CHANNEL_ITEMS * CHANNELS, + + STRIPED_COUNTERS_PER_THREAD = (BINS + BLOCK_THREADS - 1) / BLOCK_THREADS, + }; + + // Parameterize BlockRadixSort type for our thread block + typedef BlockRadixSort BlockRadixSortT; + + // Parameterize BlockDiscontinuity type for our thread block + typedef BlockDiscontinuity BlockDiscontinuityT; + + /// Shared memory type required by this thread block + union _TempStorage + { + // Storage for sorting bin values + typename BlockRadixSortT::TempStorage sort; + + struct + { + // Storage for detecting discontinuities in the tile of sorted bin values + typename BlockDiscontinuityT::TempStorage flag; + + // Storage for noting begin/end offsets of bin runs in the tile of sorted bin values + int run_begin[BLOCK_THREADS * STRIPED_COUNTERS_PER_THREAD]; + int run_end[BLOCK_THREADS * STRIPED_COUNTERS_PER_THREAD]; + }; + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + // Discontinuity functor + struct DiscontinuityOp + { + // Reference to temp_storage + _TempStorage &temp_storage; + + // Constructor + __device__ __forceinline__ DiscontinuityOp(_TempStorage &temp_storage) : + temp_storage(temp_storage) + {} + + // Discontinuity predicate + __device__ __forceinline__ bool operator()(const SampleT &a, const SampleT &b, int b_index) + { + if (a != b) + { + // Note the begin/end offsets in shared storage + temp_storage.run_begin[b] = b_index; + temp_storage.run_end[a] = b_index; + + return true; + } + else + { + return false; + } + } + }; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + /// Reference to temp_storage + _TempStorage &temp_storage; + + /// Histogram counters striped across threads + HistoCounter thread_counters[ACTIVE_CHANNELS][STRIPED_COUNTERS_PER_THREAD]; + + /// Reference to output histograms + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]; + + /// Input data to reduce + InputIterator d_in; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockRegionHistogramSort( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIterator d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) ///< Reference to output histograms + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + d_out_histograms(d_out_histograms) + { + // Initialize histogram counters striped across threads + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + thread_counters[CHANNEL][COUNTER] = 0; + } + } + } + + + /** + * Composite a tile of input items + */ + __device__ __forceinline__ void Composite( + SampleT (&items)[ITEMS_PER_THREAD], ///< Tile of samples + HistoCounter thread_counters[STRIPED_COUNTERS_PER_THREAD]) ///< Histogram counters striped across threads + { + // Sort bytes in blocked arrangement + BlockRadixSortT(temp_storage.sort).Sort(items); + + __syncthreads(); + + // Initialize the shared memory's run_begin and run_end for each bin + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + temp_storage.run_begin[(COUNTER * BLOCK_THREADS) + threadIdx.x] = TILE_CHANNEL_ITEMS; + temp_storage.run_end[(COUNTER * BLOCK_THREADS) + threadIdx.x] = TILE_CHANNEL_ITEMS; + } + + __syncthreads(); + + // Note the begin/end run offsets of bin runs in the sorted tile + int flags[ITEMS_PER_THREAD]; // unused + DiscontinuityOp flag_op(temp_storage); + BlockDiscontinuityT(temp_storage.flag).FlagHeads(flags, items, flag_op); + + // Update begin for first item + if (threadIdx.x == 0) temp_storage.run_begin[items[0]] = 0; + + __syncthreads(); + + // Composite into histogram + // Initialize the shared memory's run_begin and run_end for each bin + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + int bin = (COUNTER * BLOCK_THREADS) + threadIdx.x; + HistoCounter run_length = temp_storage.run_end[bin] - temp_storage.run_begin[bin]; + + thread_counters[COUNTER] += run_length; + } + } + + + /** + * Process one channel within a tile. + */ + template + __device__ __forceinline__ void ConsumeTileChannel( + int channel, + Offset block_offset, + int valid_items) + { + // Load items in striped fashion + if (FULL_TILE) + { + // Full tile of samples to read and composite + SampleT items[ITEMS_PER_THREAD]; + + // Unguarded loads + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = d_in[channel + block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS)]; + } + + // Composite our histogram data + Composite(items, thread_counters[channel]); + } + else + { + // Only a partially-full tile of samples to read and composite + SampleT items[ITEMS_PER_THREAD]; + + // Assign our tid as the bin for out-of-bounds items (to give an even distribution), and keep track of how oob items to subtract out later + int bounds = (valid_items - (threadIdx.x * CHANNELS)); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = ((ITEM * BLOCK_THREADS * CHANNELS) < bounds) ? + d_in[channel + block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS)] : + 0; + } + + // Composite our histogram data + Composite(items, thread_counters[channel]); + + __syncthreads(); + + // Correct the overcounting in the zero-bin from invalid (out-of-bounds) items + if (threadIdx.x == 0) + { + int extra = (TILE_ITEMS - valid_items) / CHANNELS; + thread_counters[channel][0] -= extra; + } + } + } + + + /** + * Template iteration over channels (to silence not-unrolled warnings for SM10-13). Inductive step. + */ + template + struct IterateChannels + { + /** + * Process one channel within a tile. + */ + static __device__ __forceinline__ void ConsumeTileChannel( + BlockRegionHistogramSort *cta, + Offset block_offset, + int valid_items) + { + __syncthreads(); + + cta->ConsumeTileChannel(CHANNEL, block_offset, valid_items); + + IterateChannels::ConsumeTileChannel(cta, block_offset, valid_items); + } + }; + + + /** + * Template iteration over channels (to silence not-unrolled warnings for SM10-13). Base step. + */ + template + struct IterateChannels + { + static __device__ __forceinline__ void ConsumeTileChannel(BlockRegionHistogramSort *cta, Offset block_offset, int valid_items) {} + }; + + + /** + * Process a single tile of input + */ + template + __device__ __forceinline__ void ConsumeTile( + Offset block_offset, ///< The offset the tile to consume + int valid_items = TILE_ITEMS) ///< The number of valid items in the tile + { + // First channel + ConsumeTileChannel(0, block_offset, valid_items); + + // Iterate through remaining channels + IterateChannels::ConsumeTileChannel(this, block_offset, valid_items); + } + + + /** + * Aggregate results into output + */ + __device__ __forceinline__ void AggregateOutput() + { + // Copy counters striped across threads into the histogram output + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + int channel_offset = (blockIdx.x * BINS); + + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + int bin = (COUNTER * BLOCK_THREADS) + threadIdx.x; + + if ((STRIPED_COUNTERS_PER_THREAD * BLOCK_THREADS == BINS) || (bin < BINS)) + { + d_out_histograms[CHANNEL][channel_offset + bin] = thread_counters[CHANNEL][COUNTER]; + } + } + } + } +}; + + + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_histo_256.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_histo_256.cuh new file mode 100644 index 0000000000000000000000000000000000000000..9dabd1ec44697618726929e563aa7ea8bf45c8fd --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_histo_256.cuh @@ -0,0 +1,792 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DeviceHisto256 provides device-wide parallel operations for constructing 256-bin histogram(s) over data samples residing within global memory. + */ + +#pragma once + +#include +#include + +#include "persistent_block/persistent_block_histo_256.cuh" +#include "../block/block_load.cuh" +#include "../thread/thread_reduce.cuh" +#include "../util_allocator.cuh" +#include "../grid/grid_even_share.cuh" +#include "../grid/grid_queue.cuh" +#include "../util_debug.cuh" +#include "../util_iterator.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Kernel entry points + *****************************************************************************/ + +#ifndef DOXYGEN_SHOULD_SKIP_THIS // Do not document + + +/** + * Initialization kernel for queue descriptor preparation and for zeroing global counters + */ +template < + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename SizeT, ///< Integral type used for global array indexing + typename HistoCounter> ///< Integral type for counting sample occurrences per histogram bin +__launch_bounds__ (256, 1) +__global__ void InitHisto256Kernel( + GridQueue grid_queue, ///< [in] Descriptor for performing dynamic mapping of tile data to thread blocks + ArrayWrapper d_out_histograms, ///< [out] Histogram counter data having logical dimensions HistoCounter[ACTIVE_CHANNELS][256] + SizeT num_samples) ///< [in] Total number of samples \p d_samples for all channels +{ + d_out_histograms.array[blockIdx.x][threadIdx.x] = 0; + if (threadIdx.x == 0) grid_queue.ResetDrain(num_samples); +} + + +/** + * Multi-block histogram kernel entry point. Computes privatized histograms, one per thread block. + */ +template < + typename PersistentBlockHisto256Policy, ///< Tuning policy for cub::PersistentBlockHisto256 abstraction + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of channels being actively histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIteratorRA, ///< The input iterator type (may be a simple pointer type). Must have a value type that is assignable to unsigned char + typename HistoCounter, ///< Integral type for counting sample occurrences per histogram bin + typename SizeT> ///< Integral type used for global array indexing +__launch_bounds__ (int(PersistentBlockHisto256Policy::BLOCK_THREADS), PersistentBlockHisto256Policy::SM_OCCUPANCY) +__global__ void MultiBlockHisto256Kernel( + InputIteratorRA d_samples, ///< [in] Array of sample data. (Channels, if any, are interleaved in "AOS" format) + ArrayWrapper d_out_histograms, ///< [out] Histogram counter data having logical dimensions HistoCounter[ACTIVE_CHANNELS][gridDim.x][256] + SizeT num_samples, ///< [in] Total number of samples \p d_samples for all channels + GridEvenShare even_share, ///< [in] Descriptor for how to map an even-share of tiles across thread blocks + GridQueue queue) ///< [in] Descriptor for performing dynamic mapping of tile data to thread blocks +{ + // Constants + enum + { + BLOCK_THREADS = PersistentBlockHisto256Policy::BLOCK_THREADS, + ITEMS_PER_THREAD = PersistentBlockHisto256Policy::ITEMS_PER_THREAD, + TILE_SIZE = BLOCK_THREADS * ITEMS_PER_THREAD, + }; + + // Thread block type for compositing input tiles + typedef PersistentBlockHisto256 PersistentBlockHisto256T; + + // Shared memory for PersistentBlockHisto256 + __shared__ typename PersistentBlockHisto256T::SmemStorage smem_storage; + + // Thread block instance + PersistentBlockHisto256T tiles(smem_storage, d_samples, d_out_histograms.array); + + // Consume tiles using thread block instance + int dummy_result; + GridMapping::ConsumeTiles( + tiles, num_samples, even_share, queue, dummy_result); +} + + +/** + * Aggregation kernel for aggregating privatized threadblock histograms from a previous kernel invocation. + */ +template < + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename HistoCounter> ///< Integral type for counting sample occurrences per histogram bin +__launch_bounds__ (256, 1) +__global__ void AggregateHisto256Kernel( + HistoCounter* d_block_histograms_linear, ///< [in] Histogram counter data having logical dimensions HistoCounter[ACTIVE_CHANNELS][num_threadblocks][256] + ArrayWrapper d_out_histograms, ///< [out] Histogram counter data having logical dimensions HistoCounter[ACTIVE_CHANNELS][256] + int num_threadblocks) ///< [in] Number of threadblock histograms per channel in \p d_block_histograms +{ + // Accumulate threadblock-histograms from the channel + HistoCounter bin_aggregate = 0; + + int block_offset = blockIdx.x * (num_threadblocks * 256); + int block_oob = block_offset + (num_threadblocks * 256); + +#if CUB_PTX_ARCH >= 200 + #pragma unroll 32 +#endif + while (block_offset < block_oob) + { + bin_aggregate += d_block_histograms_linear[block_offset + threadIdx.x]; + block_offset += 256; + } + + // Output + d_out_histograms.array[blockIdx.x][threadIdx.x] = bin_aggregate; +} + +#endif // DOXYGEN_SHOULD_SKIP_THIS + + + +/****************************************************************************** + * DeviceHisto256 + *****************************************************************************/ + +/** + * \addtogroup DeviceModule + * @{ + */ + +/** + * \brief DeviceHisto256 provides device-wide parallel operations for constructing 256-bin histogram(s) over samples data residing within global memory. ![](histogram_logo.png) + */ +struct DeviceHisto256 +{ +#ifndef DOXYGEN_SHOULD_SKIP_THIS // Do not document + + + /// Generic structure for encapsulating dispatch properties. Mirrors the constants within PersistentBlockHisto256Policy. + struct KernelDispachParams + { + // Policy fields + int block_threads; + int items_per_thread; + PersistentBlockHisto256Algorithm block_algorithm; + GridMappingStrategy grid_mapping; + int subscription_factor; + + // Derived fields + int tile_size; + + template + __host__ __device__ __forceinline__ + void Init(int subscription_factor = 1) + { + block_threads = PersistentBlockHisto256Policy::BLOCK_THREADS; + items_per_thread = PersistentBlockHisto256Policy::ITEMS_PER_THREAD; + block_algorithm = PersistentBlockHisto256Policy::GRID_ALGORITHM; + grid_mapping = PersistentBlockHisto256Policy::GRID_MAPPING; + this->subscription_factor = subscription_factor; + + tile_size = block_threads * items_per_thread; + } + + __host__ __device__ __forceinline__ + void Print() + { + printf("%d, %d, %d, %d, %d", + block_threads, + items_per_thread, + block_algorithm, + grid_mapping, + subscription_factor); + } + + }; + + + /// Specializations of tuned policy types for different PTX architectures + template < + int CHANNELS, + int ACTIVE_CHANNELS, + PersistentBlockHisto256Algorithm GRID_ALGORITHM, + int ARCH> + struct TunedPolicies; + + /// SM35 tune + template + struct TunedPolicies + { + typedef PersistentBlockHisto256Policy< + (GRID_ALGORITHM == GRID_HISTO_256_SORT) ? 128 : 256, + (GRID_ALGORITHM == GRID_HISTO_256_SORT) ? 12 : (30 / ACTIVE_CHANNELS), + GRID_ALGORITHM, + (GRID_ALGORITHM == GRID_HISTO_256_SORT) ? GRID_MAPPING_DYNAMIC : GRID_MAPPING_EVEN_SHARE, + (GRID_ALGORITHM == GRID_HISTO_256_SORT) ? 8 : 1> MultiBlockPolicy; + enum { SUBSCRIPTION_FACTOR = 7 }; + }; + + /// SM30 tune + template + struct TunedPolicies + { + typedef PersistentBlockHisto256Policy< + 128, + (GRID_ALGORITHM == GRID_HISTO_256_SORT) ? 20 : (22 / ACTIVE_CHANNELS), + GRID_ALGORITHM, + (GRID_ALGORITHM == GRID_HISTO_256_SORT) ? GRID_MAPPING_DYNAMIC : GRID_MAPPING_EVEN_SHARE, + 1> MultiBlockPolicy; + enum { SUBSCRIPTION_FACTOR = 1 }; + }; + + /// SM20 tune + template + struct TunedPolicies + { + typedef PersistentBlockHisto256Policy< + 128, + (GRID_ALGORITHM == GRID_HISTO_256_SORT) ? 21 : (23 / ACTIVE_CHANNELS), + GRID_ALGORITHM, + GRID_MAPPING_DYNAMIC, + 1> MultiBlockPolicy; + enum { SUBSCRIPTION_FACTOR = 1 }; + }; + + /// SM10 tune + template + struct TunedPolicies + { + typedef PersistentBlockHisto256Policy< + 128, + 7, + GRID_HISTO_256_SORT, // (use sort regardless because atomics are perf-useless) + GRID_MAPPING_EVEN_SHARE, + 1> MultiBlockPolicy; + enum { SUBSCRIPTION_FACTOR = 1 }; + }; + + + /// Tuning policy(ies) for the PTX architecture that DeviceHisto256 operations will get dispatched to + template < + int CHANNELS, + int ACTIVE_CHANNELS, + PersistentBlockHisto256Algorithm GRID_ALGORITHM> + struct PtxDefaultPolicies + { + static const int PTX_TUNE_ARCH = (CUB_PTX_ARCH >= 350) ? + 350 : + (CUB_PTX_ARCH >= 300) ? + 300 : + (CUB_PTX_ARCH >= 200) ? + 200 : + 100; + + // Tuned policy set for the current PTX compiler pass + typedef TunedPolicies PtxPassTunedPolicies; + + // Subscription factor for the current PTX compiler pass + static const int SUBSCRIPTION_FACTOR = PtxPassTunedPolicies::SUBSCRIPTION_FACTOR; + + // MultiBlockPolicy that opaquely derives from the specialization corresponding to the current PTX compiler pass + struct MultiBlockPolicy : PtxPassTunedPolicies::MultiBlockPolicy {}; + + /** + * Initialize dispatch params with the policies corresponding to the PTX assembly we will use + */ + static void InitDispatchParams(int ptx_version, KernelDispachParams &multi_block_dispatch_params) + { + if (ptx_version >= 350) + { + typedef TunedPolicies TunedPolicies; + multi_block_dispatch_params.Init(TunedPolicies::SUBSCRIPTION_FACTOR); + } + else if (ptx_version >= 300) + { + typedef TunedPolicies TunedPolicies; + multi_block_dispatch_params.Init(TunedPolicies::SUBSCRIPTION_FACTOR); + } + else if (ptx_version >= 200) + { + typedef TunedPolicies TunedPolicies; + multi_block_dispatch_params.Init(TunedPolicies::SUBSCRIPTION_FACTOR); + } + else + { + typedef TunedPolicies TunedPolicies; + multi_block_dispatch_params.Init(TunedPolicies::SUBSCRIPTION_FACTOR); + } + } + }; + + + + + + /** + * Internal dispatch routine for invoking device-wide, multi-channel, 256-bin histogram + */ + template < + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of channels being actively histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InitHisto256KernelPtr, ///< Function type of cub::InitHisto256Kernel + typename MultiBlockHisto256KernelPtr, ///< Function type of cub::MultiBlockHisto256Kernel + typename AggregateHisto256KernelPtr, ///< Function type of cub::AggregateHisto256Kernel + typename InputIteratorRA, ///< The input iterator type (may be a simple pointer type). Must have a value type that is assignable to unsigned char + typename HistoCounter, ///< Integral type for counting sample occurrences per histogram bin + typename SizeT> ///< Integral type used for global array indexing + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + InitHisto256KernelPtr init_kernel_ptr, ///< [in] Kernel function pointer to parameterization of cub::InitHisto256Kernel + MultiBlockHisto256KernelPtr multi_block_kernel_ptr, ///< [in] Kernel function pointer to parameterization of cub::MultiBlockHisto256Kernel + AggregateHisto256KernelPtr aggregate_kernel_ptr, ///< [in] Kernel function pointer to parameterization of cub::AggregateHisto256Kernel + KernelDispachParams &multi_block_dispatch_params, ///< [in] Dispatch parameters that match the policy that \p multi_block_kernel_ptr was compiled for + InputIteratorRA d_samples, ///< [in] Input samples to histogram + HistoCounter *(&d_histograms)[ACTIVE_CHANNELS], ///< [out] Array of channel histograms, each having 256 counters of integral type \p HistoCounter. + SizeT num_samples, ///< [in] Number of samples to process + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream-0. + bool stream_synchronous = false, ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Default is \p false. + DeviceAllocator *device_allocator = DefaultDeviceAllocator()) ///< [in] [optional] Allocator for allocating and freeing device memory. Default is provided by DefaultDeviceAllocator. + { + #ifndef CUB_RUNTIME_ENABLED + + // Kernel launch not supported from this device + return CubDebug(cudaErrorInvalidConfiguration); + + #else + + HistoCounter *d_block_histograms_linear = NULL; // Temporary storage + GridEvenShare even_share; // Even-share work distribution + GridQueue queue; // Dynamic, queue-based work distribution + + cudaError error = cudaSuccess; + do + { + // Setup array wrapper for histogram channel output because we can't pass static arrays as kernel parameters + ArrayWrapper d_histo_wrapper; + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + d_histo_wrapper.array[CHANNEL] = d_histograms[CHANNEL]; + } + + // Initialize counters and queue descriptor if necessary + if ((multi_block_dispatch_params.grid_mapping == GRID_MAPPING_DYNAMIC) || + (multi_block_dispatch_params.block_algorithm == GRID_HISTO_256_GLOBAL_ATOMIC)) + { + queue.Allocate(device_allocator); + + if (stream_synchronous) CubLog("Invoking init_kernel_ptr<<<%d, 256, 0, %ul>>>()\n", ACTIVE_CHANNELS, (unsigned long) stream); + + init_kernel_ptr<<>>(queue, d_histo_wrapper, num_samples); + + #ifndef __CUDA_ARCH__ + // Sync the stream on the host + if (stream_synchronous && CubDebug(error = cudaStreamSynchronize(stream))) break; + #else + // Sync the entire device on the device (cudaStreamSynchronize doesn't exist on device) + if (stream_synchronous && CubDebug(error = cudaDeviceSynchronize())) break; + #endif + } + + // Determine grid size for the multi-block kernel + + int device_ordinal; + if (CubDebug(error = cudaGetDevice(&device_ordinal))) break; + + int sm_count; + if (CubDebug(error = cudaDeviceGetAttribute (&sm_count, cudaDevAttrMultiProcessorCount, device_ordinal))) break; + + // Rough estimate of SM occupancies based upon the maximum SM occupancy of the targeted PTX architecture + int multi_sm_occupancy = CUB_MIN( + ArchProps::MAX_SM_THREADBLOCKS, + ArchProps::MAX_SM_THREADS / multi_block_dispatch_params.block_threads); + + #ifndef __CUDA_ARCH__ + + // We're on the host, so come up with a more accurate estimate of SM occupancies from actual device properties + Device device_props; + if (CubDebug(error = device_props.Init(device_ordinal))) break; + + if (CubDebug(error = device_props.MaxSmOccupancy( + multi_sm_occupancy, + multi_block_kernel_ptr, + multi_block_dispatch_params.block_threads))) break; + + #endif + + int multi_occupancy = multi_sm_occupancy * sm_count; + int multi_tile_size = multi_block_dispatch_params.block_threads * multi_block_dispatch_params.items_per_thread; + int multi_grid_size; + + switch (multi_block_dispatch_params.grid_mapping) + { + case GRID_MAPPING_EVEN_SHARE: + + // Work is distributed evenly + even_share.GridInit( + num_samples, + multi_occupancy * multi_block_dispatch_params.subscription_factor, + multi_tile_size); + + // Set MultiBlock grid size + multi_grid_size = even_share.grid_size; + break; + + case GRID_MAPPING_DYNAMIC: + + // Prepare queue to distribute work dynamically + int num_tiles = (num_samples + multi_tile_size - 1) / multi_tile_size; + + // Set MultiBlock grid size + multi_grid_size = (num_tiles < multi_occupancy) ? + num_tiles : // Not enough to fill the device with threadblocks + multi_occupancy; // Fill the device with threadblocks + + break; + }; + + // Bind textures if the iterator supports it + #ifndef __CUDA_ARCH__ + if (CubDebug(error = BindIteratorTexture(d_samples))) break; + #endif // __CUDA_ARCH__ + + // Invoke MultiBlockHisto256 + if (stream_synchronous) CubLog("Invoking multi_block_kernel_ptr<<<%d, %d, 0, %ul>>>(), %d items per thread, %d SM occupancy\n", + multi_grid_size, multi_block_dispatch_params.block_threads, (unsigned long) stream, multi_block_dispatch_params.items_per_thread, multi_sm_occupancy); + + if ((multi_grid_size == 1) || (multi_block_dispatch_params.block_algorithm == GRID_HISTO_256_GLOBAL_ATOMIC)) + { + // A single pass will do + multi_block_kernel_ptr<<>>( + d_samples, + d_histo_wrapper, + num_samples, + even_share, + queue); + } + else + { + // Use two-pass approach to compute and reduce privatized block histograms + + // Allocate temporary storage for privatized thread block histograms in each channel + if (CubDebug(error = DeviceAllocate( + (void**) &d_block_histograms_linear, + ACTIVE_CHANNELS * multi_grid_size * sizeof(HistoCounter) * 256, + device_allocator))) break; + + // Setup array wrapper for temporary histogram channel output because we can't pass static arrays as kernel parameters + ArrayWrapper d_temp_histo_wrapper; + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + d_temp_histo_wrapper.array[CHANNEL] = d_block_histograms_linear + (CHANNEL * multi_grid_size * 256); + } + + multi_block_kernel_ptr<<>>( + d_samples, + d_temp_histo_wrapper, + num_samples, + even_share, + queue); + + #ifndef __CUDA_ARCH__ + // Sync the stream on the host + if (stream_synchronous && CubDebug(error = cudaStreamSynchronize(stream))) break; + #else + // Sync the entire device on the device (cudaStreamSynchronize doesn't exist on device) + if (stream_synchronous && CubDebug(error = cudaDeviceSynchronize())) break; + #endif + + if (stream_synchronous) CubLog("Invoking aggregate_kernel_ptr<<<%d, %d, 0, %ul>>>()\n", + ACTIVE_CHANNELS, 256, (unsigned long) stream); + + aggregate_kernel_ptr<<>>( + d_block_histograms_linear, + d_histo_wrapper, + multi_grid_size); + } + + #ifndef __CUDA_ARCH__ + // Sync the stream on the host + if (stream_synchronous && CubDebug(error = cudaStreamSynchronize(stream))) break; + #else + // Sync the entire device on the device (cudaStreamSynchronize doesn't exist on device) + if (stream_synchronous && CubDebug(error = cudaDeviceSynchronize())) break; + #endif + } + while (0); + + // Free temporary storage allocation + if (d_block_histograms_linear) + error = CubDebug(DeviceFree(d_block_histograms_linear, device_allocator)); + + // Free queue allocation + if ((multi_block_dispatch_params.grid_mapping == GRID_MAPPING_DYNAMIC) || + (multi_block_dispatch_params.block_algorithm == GRID_HISTO_256_GLOBAL_ATOMIC)) + { + error = CubDebug(queue.Free(device_allocator)); + } + + // Unbind texture + #ifndef __CUDA_ARCH__ + error = CubDebug(UnbindIteratorTexture(d_samples)); + #endif // __CUDA_ARCH__ + + return error; + + #endif + } + + + /** + * \brief Computes a 256-bin device-wide histogram + * + * \tparam GRID_ALGORITHM cub::PersistentBlockHisto256Algorithm enumerator specifying the underlying algorithm to use + * \tparam CHANNELS Number of channels interleaved in the input data (may be greater than the number of channels being actively histogrammed) + * \tparam ACTIVE_CHANNELS [inferred] Number of channels actively being histogrammed + * \tparam InputIteratorRA [inferred] The random-access iterator type for input (may be a simple pointer type). Must have a value type that is assignable to unsigned char + * \tparam HistoCounter [inferred] Integral type for counting sample occurrences per histogram bin + */ + template < + PersistentBlockHisto256Algorithm GRID_ALGORITHM, + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of channels being actively histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIteratorRA, + typename HistoCounter> + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + InputIteratorRA d_samples, ///< [in] Input samples to histogram + HistoCounter *(&d_histograms)[ACTIVE_CHANNELS], ///< [out] Array of channel histograms, each having 256 counters of integral type \p HistoCounter. + int num_samples, ///< [in] Number of samples to process + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream-0. + bool stream_synchronous = false, ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Default is \p false. + DeviceAllocator* device_allocator = DefaultDeviceAllocator()) ///< [in] [optional] Allocator for allocating and freeing device memory. Default is provided by DefaultDeviceAllocator. + { + // Type used for array indexing + typedef int SizeT; + + // Tuning polices for the PTX architecture that will get dispatched to + typedef PtxDefaultPolicies PtxDefaultPolicies; + typedef typename PtxDefaultPolicies::MultiBlockPolicy MultiBlockPolicy; + + cudaError error = cudaSuccess; + do + { + // Declare dispatch parameters + KernelDispachParams multi_block_dispatch_params; + + #ifdef __CUDA_ARCH__ + + // We're on the device, so initialize the dispatch parameters with the PtxDefaultPolicies directly + multi_block_dispatch_params.Init(PtxDefaultPolicies::SUBSCRIPTION_FACTOR); + + #else + + // We're on the host, so lookup and initialize the dispatch parameters with the policies that match the device's PTX version + int ptx_version; + if (CubDebug(error = PtxVersion(ptx_version))) break; + PtxDefaultPolicies::InitDispatchParams(ptx_version, multi_block_dispatch_params); + + #endif + + Dispatch( + InitHisto256Kernel, + MultiBlockHisto256Kernel, + AggregateHisto256Kernel, + multi_block_dispatch_params, + d_samples, + d_histograms, + num_samples, + stream, + stream_synchronous, + device_allocator); + + if (CubDebug(error)) break; + } + while (0); + + return error; + } + + #endif // DOXYGEN_SHOULD_SKIP_THIS + + + //--------------------------------------------------------------------- + // Public interface + //--------------------------------------------------------------------- + + /** + * \brief Computes a 256-bin device-wide histogram. Uses fast block-sorting to compute the histogram. + * + * Delivers consistent throughput regardless of sample diversity. + * + * \tparam InputIteratorRA [inferred] The random-access iterator type for input (may be a simple pointer type). Must have a value type that is assignable to unsigned char + * \tparam HistoCounter [inferred] Integral type for counting sample occurrences per histogram bin + */ + template < + typename InputIteratorRA, + typename HistoCounter> + __host__ __device__ __forceinline__ + static cudaError_t SingleChannel( + InputIteratorRA d_samples, ///< [in] Input samples + HistoCounter* d_histogram, ///< [out] Array of 256 counters of integral type \p HistoCounter. + int num_samples, ///< [in] Number of samples to process + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream-0. + bool stream_synchronous = false, ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Default is \p false. + DeviceAllocator* device_allocator = DefaultDeviceAllocator()) ///< [in] [optional] Allocator for allocating and freeing device memory. Default is provided by DefaultDeviceAllocator. + { + return Dispatch( + d_samples, &d_histogram, num_samples, stream, stream_synchronous, device_allocator); + } + + /** + * \brief Computes a 256-bin device-wide histogram. Uses shared-memory atomic read-modify-write operations to compute the histogram. + * + * Sample input having lower diversity cause performance to be degraded. + * + * \tparam InputIteratorRA [inferred] The random-access iterator type for input (may be a simple pointer type). Must have a value type that is assignable to unsigned char + * \tparam HistoCounter [inferred] Integral type for counting sample occurrences per histogram bin + */ + template < + typename InputIteratorRA, + typename HistoCounter> + __host__ __device__ __forceinline__ + static cudaError_t SingleChannelAtomic( + InputIteratorRA d_samples, ///< [in] Input samples + HistoCounter* d_histogram, ///< [out] Array of 256 counters of integral type \p HistoCounter. + int num_samples, ///< [in] Number of samples to process + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream-0. + bool stream_synchronous = false, ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Default is \p false. + DeviceAllocator* device_allocator = DefaultDeviceAllocator()) ///< [in] [optional] Allocator for allocating and freeing device memory. Default is provided by DefaultDeviceAllocator. + { + return Dispatch( + d_samples, &d_histogram, num_samples, stream, stream_synchronous, device_allocator); + } + + + /** + * \brief Computes a 256-bin device-wide histogram. Uses global-memory atomic read-modify-write operations to compute the histogram. + * + * Sample input having lower diversity cause performance to be degraded. + * + * \tparam InputIteratorRA [inferred] The random-access iterator type for input (may be a simple pointer type). Must have a value type that is assignable to unsigned char + * \tparam HistoCounter [inferred] Integral type for counting sample occurrences per histogram bin + */ + template < + typename InputIteratorRA, + typename HistoCounter> + __host__ __device__ __forceinline__ + static cudaError_t SingleChannelGlobalAtomic( + InputIteratorRA d_samples, ///< [in] Input samples + HistoCounter* d_histogram, ///< [out] Array of 256 counters of integral type \p HistoCounter. + int num_samples, ///< [in] Number of samples to process + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream-0. + bool stream_synchronous = false, ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Default is \p false. + DeviceAllocator* device_allocator = DefaultDeviceAllocator()) ///< [in] [optional] Allocator for allocating and freeing device memory. Default is provided by DefaultDeviceAllocator. + { + return Dispatch( + d_samples, &d_histogram, num_samples, stream, stream_synchronous, device_allocator); + } + + + /** + * \brief Computes a 256-bin device-wide histogram from multi-channel data. Uses fast block-sorting to compute the histogram. + * + * Delivers consistent throughput regardless of sample diversity. + * + * \tparam CHANNELS Number of channels interleaved in the input data (may be greater than the number of channels being actively histogrammed) + * \tparam ACTIVE_CHANNELS [inferred] Number of channels actively being histogrammed + * \tparam InputIteratorRA [inferred] The random-access iterator type for input (may be a simple pointer type). Must have a value type that is assignable to unsigned char + * \tparam HistoCounter [inferred] Integral type for counting sample occurrences per histogram bin + */ + template < + int CHANNELS, + int ACTIVE_CHANNELS, + typename InputIteratorRA, + typename HistoCounter> + __host__ __device__ __forceinline__ + static cudaError_t MultiChannel( + InputIteratorRA d_samples, ///< [in] Input samples. (Channels, if any, are interleaved in "AOS" format) + HistoCounter *(&d_histograms)[ACTIVE_CHANNELS], ///< [out] Array of channel histograms, each having 256 counters of integral type \p HistoCounter. + int num_samples, ///< [in] Number of samples to process + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream-0. + bool stream_synchronous = false, ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Default is \p false. + DeviceAllocator* device_allocator = DefaultDeviceAllocator()) ///< [in] [optional] Allocator for allocating and freeing device memory. Default is provided by DefaultDeviceAllocator. + { + return Dispatch( + d_samples, d_histograms, num_samples, stream, stream_synchronous, device_allocator); + } + + + /** + * \brief Computes a 256-bin device-wide histogram from multi-channel data. Uses shared-memory atomic read-modify-write operations to compute the histogram. + * + * Sample input having lower diversity cause performance to be degraded. + * + * \tparam CHANNELS Number of channels interleaved in the input data (may be greater than the number of channels being actively histogrammed) + * \tparam ACTIVE_CHANNELS [inferred] Number of channels actively being histogrammed + * \tparam InputIteratorRA [inferred] The random-access iterator type for input (may be a simple pointer type). Must have a value type that is assignable to unsigned char + * \tparam HistoCounter [inferred] Integral type for counting sample occurrences per histogram bin + */ + template < + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of channels being actively histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIteratorRA, + typename HistoCounter> + __host__ __device__ __forceinline__ + static cudaError_t MultiChannelAtomic( + InputIteratorRA d_samples, ///< [in] Input samples. (Channels, if any, are interleaved in "AOS" format) + HistoCounter *(&d_histograms)[ACTIVE_CHANNELS], ///< [out] Array of channel histograms, each having 256 counters of integral type \p HistoCounter. + int num_samples, ///< [in] Number of samples to process + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream-0. + bool stream_synchronous = false, ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Default is \p false. + DeviceAllocator* device_allocator = DefaultDeviceAllocator()) ///< [in] [optional] Allocator for allocating and freeing device memory. Default is provided by DefaultDeviceAllocator. + { + return Dispatch( + d_samples, d_histograms, num_samples, stream, stream_synchronous, device_allocator); + } + + + /** + * \brief Computes a 256-bin device-wide histogram from multi-channel data. Uses global-memory atomic read-modify-write operations to compute the histogram. + * + * Sample input having lower diversity cause performance to be degraded. + * + * \tparam CHANNELS Number of channels interleaved in the input data (may be greater than the number of channels being actively histogrammed) + * \tparam ACTIVE_CHANNELS [inferred] Number of channels actively being histogrammed + * \tparam InputIteratorRA [inferred] The random-access iterator type for input (may be a simple pointer type). Must have a value type that is assignable to unsigned char + * \tparam HistoCounter [inferred] Integral type for counting sample occurrences per histogram bin + */ + template < + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of channels being actively histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIteratorRA, + typename HistoCounter> + __host__ __device__ __forceinline__ + static cudaError_t MultiChannelGlobalAtomic( + InputIteratorRA d_samples, ///< [in] Input samples. (Channels, if any, are interleaved in "AOS" format) + HistoCounter *(&d_histograms)[ACTIVE_CHANNELS], ///< [out] Array of channel histograms, each having 256 counters of integral type \p HistoCounter. + int num_samples, ///< [in] Number of samples to process + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream-0. + bool stream_synchronous = false, ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Default is \p false. + DeviceAllocator* device_allocator = DefaultDeviceAllocator()) ///< [in] [optional] Allocator for allocating and freeing device memory. Default is provided by DefaultDeviceAllocator. + { + return Dispatch( + d_samples, d_histograms, num_samples, stream, stream_synchronous, device_allocator); + } + + +}; + + +/** @} */ // DeviceModule + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_histogram.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_histogram.cuh new file mode 100644 index 0000000000000000000000000000000000000000..b070ad0da15bc4138785cfa72b3f65b3cc646b6e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_histogram.cuh @@ -0,0 +1,653 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DeviceHistogram provides device-wide parallel operations for constructing histogram(s) from a sequence of samples data residing within global memory. + */ + +#pragma once + +#include +#include + +#include "dispatch/device_histogram_dispatch.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \brief DeviceHistogram provides device-wide parallel operations for constructing histogram(s) from a sequence of samples data residing within global memory. ![](histogram_logo.png) + * \ingroup DeviceModule + * + * \par Overview + * A histogram + * counts the number of observations that fall into each of the disjoint categories (known as bins). + * + * \par Usage Considerations + * \cdp_class{DeviceHistogram} + * + * \par Performance + * + * \image html histo_perf.png + * + */ +struct DeviceHistogram +{ + /******************************************************************//** + * \name Single-channel samples + *********************************************************************/ + //@{ + + + /** + * \brief Computes a device-wide histogram using fast block-wide sorting. + * + * \par + * - The total number of samples across all channels (\p num_samples) must be a whole multiple of \p CHANNELS. + * - Delivers consistent throughput regardless of sample diversity + * - Histograms having a large number of bins (e.g., thousands) may adversely affect shared memory occupancy and performance (or even the ability to launch). + * - Performance is often improved when referencing input samples through a texture-caching iterator (e.g., cub::TexObjInputIterator). + * - \devicestorage + * - \cdp + * + * \par Snippet + * The code snippet below illustrates the computation of a 8-bin histogram of + * single-channel unsigned char samples. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and histogram + * int num_samples; // e.g., 12 + * unsigned char *d_samples; // e.g., [2, 6, 7, 5, 3, 0, 2, 1, 7, 0, 6, 2] + * unsigned int *d_histogram; // e.g., [ , , , , , , , ] + * ... + * + * // Wrap d_samples device pointer in a random-access texture iterator + * cub::TexObjInputIterator d_samples_tex_itr; + * d_samples_tex_itr.BindTexture(d_samples, num_samples * sizeof(unsigned char)); + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceHistogram::SingleChannelSorting<8>(d_temp_storage, temp_storage_bytes, d_samples_tex_itr, d_histogram, num_samples); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Compute histogram + * cub::DeviceHistogram::SingleChannelSorting<8>(d_temp_storage, temp_storage_bytes, d_samples_tex_itr, d_histogram, num_samples); + * + * // Unbind texture iterator + * d_samples_tex_itr.UnbindTexture(); + * + * // d_histogram <-- [2, 1, 3, 1, 0, 1, 2, 2] + * + * \endcode + * + * \tparam BINS Number of histogram bins per channel + * \tparam InputIterator [inferred] Random-access input iterator type for reading input samples. (Must have an InputIterator::value_type that, when cast as an integer, falls in the range [0..BINS-1]) \iterator + * \tparam HistoCounter [inferred] Integer type for counting sample occurrences per histogram bin + */ + template < + int BINS, + typename InputIterator, + typename HistoCounter> + __host__ __device__ + static cudaError_t SingleChannelSorting( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_samples, ///< [in] Input samples + HistoCounter* d_histogram, ///< [out] Array of BINS counters of integral type \p HistoCounter. + int num_samples, ///< [in] Number of samples to process + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Dispatch type + typedef DeviceHistogramDispatch< + DEVICE_HISTO_SORT, + BINS, + 1, + 1, + InputIterator, + HistoCounter, + Offset> + DeviceHistogramDispatch; + + return DeviceHistogramDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_samples, + &d_histogram, + num_samples, + stream, + debug_synchronous); + } + + + /** + * \brief Computes a device-wide histogram using shared-memory atomic read-modify-write operations. + * + * \par + * - Input samples having lower diversity can cause performance to be degraded due to serializations from bin-collisions. + * - Histograms having a large number of bins (e.g., thousands) may adversely affect shared memory occupancy and performance (or even the ability to launch). + * - Performance is often improved when referencing input samples through a texture-caching iterator (e.g., cub::TexObjInputIterator). + * - \devicestorage + * - \cdp + * + * \par Snippet + * The code snippet below illustrates the computation of a 8-bin histogram of + * single-channel unsigned char samples. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and histogram + * int num_samples; // e.g., 12 + * unsigned char *d_samples; // e.g., [2, 6, 7, 5, 3, 0, 2, 1, 7, 0, 6, 2] + * unsigned int *d_histogram; // e.g., [ , , , , , , , ] + * ... + * + * // Wrap d_samples device pointer in a random-access texture iterator + * cub::TexObjInputIterator d_samples_tex_itr; + * d_samples_tex_itr.BindTexture(d_samples, num_samples * sizeof(unsigned char)); + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceHistogram::SingleChannelSorting<8>(d_temp_storage, temp_storage_bytes, d_samples_tex_itr, d_histogram, num_samples); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Compute histogram + * cub::DeviceHistogram::SingleChannelSharedAtomic<8>(d_temp_storage, temp_storage_bytes, d_samples_tex_itr, d_histogram, num_samples); + * + * // Unbind texture iterator + * d_samples_tex_itr.UnbindTexture(); + * + * // d_histogram <-- [2, 1, 3, 1, 0, 1, 2, 2] + * + * \endcode + * + * \tparam BINS Number of histogram bins per channel + * \tparam InputIterator [inferred] Random-access input iterator type for reading input samples. (Must have an InputIterator::value_type that, when cast as an integer, falls in the range [0..BINS-1]) \iterator + * \tparam HistoCounter [inferred] Integer type for counting sample occurrences per histogram bin + */ + template < + int BINS, + typename InputIterator, + typename HistoCounter> + __host__ __device__ + static cudaError_t SingleChannelSharedAtomic( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_samples, ///< [in] Input samples + HistoCounter* d_histogram, ///< [out] Array of BINS counters of integral type \p HistoCounter. + int num_samples, ///< [in] Number of samples to process + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Dispatch type + typedef DeviceHistogramDispatch< + DEVICE_HISTO_SHARED_ATOMIC, + BINS, + 1, + 1, + InputIterator, + HistoCounter, + Offset> + DeviceHistogramDispatch; + + return DeviceHistogramDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_samples, + &d_histogram, + num_samples, + stream, + debug_synchronous); + } + + + /** + * \brief Computes a device-wide histogram using global-memory atomic read-modify-write operations. + * + * \par + * - Input samples having lower diversity can cause performance to be degraded due to serializations from bin-collisions. + * - Performance is not significantly impacted when computing histograms having large numbers of bins (e.g., thousands). + * - Performance is often improved when referencing input samples through a texture-caching iterator (e.g., cub::TexObjInputIterator). + * - \devicestorage + * - \cdp + * + * \par Snippet + * The code snippet below illustrates the computation of a 8-bin histogram of + * single-channel unsigned char samples. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and histogram + * int num_samples; // e.g., 12 + * unsigned char *d_samples; // e.g., [2, 6, 7, 5, 3, 0, 2, 1, 7, 0, 6, 2] + * unsigned int *d_histogram; // e.g., [ , , , , , , , ] + * ... + * + * // Wrap d_samples device pointer in a random-access texture iterator + * cub::TexObjInputIterator d_samples_tex_itr; + * d_samples_tex_itr.BindTexture(d_samples, num_samples * sizeof(unsigned char)); + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceHistogram::SingleChannelSorting<8>(d_temp_storage, temp_storage_bytes, d_samples_tex_itr, d_histogram, num_samples); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Compute histogram + * cub::DeviceHistogram::SingleChannelGlobalAtomic<8>(d_temp_storage, temp_storage_bytes, d_samples_tex_itr, d_histogram, num_samples); + * + * // Unbind texture iterator + * d_samples_tex_itr.UnbindTexture(); + * + * // d_histogram <-- [2, 1, 3, 1, 0, 1, 2, 2] + * + * \endcode + * + * \tparam BINS Number of histogram bins per channel + * \tparam InputIterator [inferred] Random-access input iterator type for reading input samples. (Must have an InputIterator::value_type that, when cast as an integer, falls in the range [0..BINS-1]) \iterator + * \tparam HistoCounter [inferred] Integer type for counting sample occurrences per histogram bin + */ + template < + int BINS, + typename InputIterator, + typename HistoCounter> + __host__ __device__ + static cudaError_t SingleChannelGlobalAtomic( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_samples, ///< [in] Input samples + HistoCounter* d_histogram, ///< [out] Array of BINS counters of integral type \p HistoCounter. + int num_samples, ///< [in] Number of samples to process + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Dispatch type + typedef DeviceHistogramDispatch< + DEVICE_HISTO_GLOBAL_ATOMIC, + BINS, + 1, + 1, + InputIterator, + HistoCounter, + Offset> + DeviceHistogramDispatch; + + return DeviceHistogramDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_samples, + &d_histogram, + num_samples, + stream, + debug_synchronous); + } + + + //@} end member group + /******************************************************************//** + * \name Interleaved multi-channel samples + *********************************************************************/ + //@{ + + + /** + * \brief Computes a device-wide histogram from multi-channel data using fast block-sorting. + * + * \par + * - The total number of samples across all channels (\p num_samples) must be a whole multiple of \p CHANNELS. + * - Delivers consistent throughput regardless of sample diversity + * - Histograms having a large number of bins (e.g., thousands) may adversely affect shared memory occupancy and performance (or even the ability to launch). + * - Performance is often improved when referencing input samples through a texture-caching iterator (e.g., cub::TexObjInputIterator). + * - \devicestorage + * - \cdp + * + * \par Snippet + * The code snippet below illustrates the computation of three 256-bin histograms from + * an input sequence of quad-channel (interleaved) unsigned char samples. + * (E.g., RGB histograms from RGBA pixel samples.) + * + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and histograms + * int num_samples; // e.g., 20 (five pixels with four channels each) + * unsigned char *d_samples; // e.g., [(2, 6, 7, 5), (3, 0, 2, 1), (7, 0, 6, 2), + * // (0, 6, 7, 5), (3, 0, 2, 6)] + * unsigned int *d_histogram[3]; // e.g., [ [ , , , , , , , ]; + * // [ , , , , , , , ]; + * // [ , , , , , , , ] ] + * ... + * + * // Wrap d_samples device pointer in a random-access texture iterator + * cub::TexObjInputIterator d_samples_tex_itr; + * d_samples_tex_itr.BindTexture(d_samples, num_samples * sizeof(unsigned char)); + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceHistogram::MultiChannelSorting<8, 4, 3>(d_temp_storage, temp_storage_bytes, d_samples_tex_itr, d_histograms, num_samples); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Compute histograms + * cub::DeviceHistogram::MultiChannelSorting<8, 4, 3>(d_temp_storage, temp_storage_bytes, d_samples_tex_itr, d_histograms, num_samples); + * + * // Unbind texture iterator + * d_samples_tex_itr.UnbindTexture(); + * + * // d_histogram <-- [ [1, 0, 1, 2, 0, 0, 0, 1]; + * // [0, 3, 0, 0, 0, 0, 2, 0]; + * // [0, 0, 2, 0, 0, 0, 1, 2] ] + * + * \endcode + * + * \tparam BINS Number of histogram bins per channel + * \tparam CHANNELS Number of channels interleaved in the input data (may be greater than the number of channels being actively histogrammed) + * \tparam ACTIVE_CHANNELS [inferred] Number of channels actively being histogrammed + * \tparam InputIterator [inferred] Random-access input iterator type for reading input samples. (Must have an InputIterator::value_type that, when cast as an integer, falls in the range [0..BINS-1]) \iterator + * \tparam HistoCounter [inferred] Integer type for counting sample occurrences per histogram bin + */ + template < + int BINS, + int CHANNELS, + int ACTIVE_CHANNELS, + typename InputIterator, + typename HistoCounter> + __host__ __device__ + static cudaError_t MultiChannelSorting( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_samples, ///< [in] Pointer to the input sequence of sample items. The samples from different channels are assumed to be interleaved (e.g., an array of 32b pixels where each pixel consists of four RGBA 8b samples). + HistoCounter *d_histograms[ACTIVE_CHANNELS], ///< [out] Array of active channel histogram pointers, each pointing to an output array having BINS counters of integral type \p HistoCounter. + int num_samples, ///< [in] Total number of samples to process in all channels, including non-active channels + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Dispatch type + typedef DeviceHistogramDispatch< + DEVICE_HISTO_SORT, + BINS, + CHANNELS, + ACTIVE_CHANNELS, + InputIterator, + HistoCounter, + Offset> DeviceHistogramDispatch; + + return DeviceHistogramDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_samples, + d_histograms, + num_samples, + stream, + debug_synchronous); + } + + + /** + * \brief Computes a device-wide histogram from multi-channel data using shared-memory atomic read-modify-write operations. + * + * \par + * - The total number of samples across all channels (\p num_samples) must be a whole multiple of \p CHANNELS. + * - Input samples having lower diversity can cause performance to be degraded due to serializations from bin-collisions. + * - Histograms having a large number of bins (e.g., thousands) may adversely affect shared memory occupancy and performance (or even the ability to launch). + * - Performance is often improved when referencing input samples through a texture-caching iterator (e.g., cub::TexObjInputIterator). + * - \devicestorage + * - \cdp + * + * \par Snippet + * The code snippet below illustrates the computation of three 256-bin histograms from + * an input sequence of quad-channel (interleaved) unsigned char samples. + * (E.g., RGB histograms from RGBA pixel samples.) + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and histograms + * int num_samples; // e.g., 20 (five pixels with four channels each) + * unsigned char *d_samples; // e.g., [(2, 6, 7, 5), (3, 0, 2, 1), (7, 0, 6, 2), + * // (0, 6, 7, 5), (3, 0, 2, 6)] + * unsigned int *d_histogram[3]; // e.g., [ [ , , , , , , , ]; + * // [ , , , , , , , ]; + * // [ , , , , , , , ] ] + * ... + * + * // Wrap d_samples device pointer in a random-access texture iterator + * cub::TexObjInputIterator d_samples_tex_itr; + * d_samples_tex_itr.BindTexture(d_samples, num_samples * sizeof(unsigned char)); + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceHistogram::MultiChannelSharedAtomic<8, 4, 3>(d_temp_storage, temp_storage_bytes, d_samples_tex_itr, d_histograms, num_samples); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Compute histograms + * cub::DeviceHistogram::MultiChannelSharedAtomic<8, 4, 3>(d_temp_storage, temp_storage_bytes, d_samples_tex_itr, d_histograms, num_samples); + * + * // Unbind texture iterator + * d_samples_tex_itr.UnbindTexture(); + * + * // d_histogram <-- [ [1, 0, 1, 2, 0, 0, 0, 1]; + * // [0, 3, 0, 0, 0, 0, 2, 0]; + * // [0, 0, 2, 0, 0, 0, 1, 2] ] + * + * \endcode + * + * \tparam BINS Number of histogram bins per channel + * \tparam CHANNELS Number of channels interleaved in the input data (may be greater than the number of channels being actively histogrammed) + * \tparam ACTIVE_CHANNELS [inferred] Number of channels actively being histogrammed + * \tparam InputIterator [inferred] Random-access input iterator type for reading input samples. (Must have an InputIterator::value_type that, when cast as an integer, falls in the range [0..BINS-1]) \iterator + * \tparam HistoCounter [inferred] Integer type for counting sample occurrences per histogram bin + */ + template < + int BINS, + int CHANNELS, + int ACTIVE_CHANNELS, + typename InputIterator, + typename HistoCounter> + __host__ __device__ + static cudaError_t MultiChannelSharedAtomic( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_samples, ///< [in] Pointer to the input sequence of sample items. The samples from different channels are assumed to be interleaved (e.g., an array of 32b pixels where each pixel consists of four RGBA 8b samples). + HistoCounter *d_histograms[ACTIVE_CHANNELS], ///< [out] Array of active channel histogram pointers, each pointing to an output array having BINS counters of integral type \p HistoCounter. + int num_samples, ///< [in] Total number of samples to process in all channels, including non-active channels + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Dispatch type + typedef DeviceHistogramDispatch< + DEVICE_HISTO_SHARED_ATOMIC, + BINS, + CHANNELS, + ACTIVE_CHANNELS, + InputIterator, + HistoCounter, + Offset> DeviceHistogramDispatch; + + return DeviceHistogramDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_samples, + d_histograms, + num_samples, + stream, + debug_synchronous); + } + + + /** + * \brief Computes a device-wide histogram from multi-channel data using global-memory atomic read-modify-write operations. + * + * \par + * - The total number of samples across all channels (\p num_samples) must be a whole multiple of \p CHANNELS. + * - Input samples having lower diversity can cause performance to be degraded due to serializations from bin-collisions. + * - Performance is not significantly impacted when computing histograms having large numbers of bins (e.g., thousands). + * - Performance is often improved when referencing input samples through a texture-caching iterator (e.g., cub::TexObjInputIterator). + * - \devicestorage + * - \cdp + * + * \par Snippet + * The code snippet below illustrates the computation of three 256-bin histograms from + * an input sequence of quad-channel (interleaved) unsigned char samples. + * (E.g., RGB histograms from RGBA pixel samples.) + * + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and histograms + * int num_samples; // e.g., 20 (five pixels with four channels each) + * unsigned char *d_samples; // e.g., [(2, 6, 7, 5), (3, 0, 2, 1), (7, 0, 6, 2), + * // (0, 6, 7, 5), (3, 0, 2, 6)] + * unsigned int *d_histogram[3]; // e.g., [ [ , , , , , , , ]; + * // [ , , , , , , , ]; + * // [ , , , , , , , ] ] + * ... + * + * // Wrap d_samples device pointer in a random-access texture iterator + * cub::TexObjInputIterator d_samples_tex_itr; + * d_samples_tex_itr.BindTexture(d_samples, num_samples * sizeof(unsigned char)); + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceHistogram::MultiChannelGlobalAtomic<8, 4, 3>(d_temp_storage, temp_storage_bytes, d_samples_tex_itr, d_histograms, num_samples); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Compute histograms + * cub::DeviceHistogram::MultiChannelGlobalAtomic<8, 4, 3>(d_temp_storage, temp_storage_bytes, d_samples_tex_itr, d_histograms, num_samples); + * + * // Unbind texture iterator + * d_samples_tex_itr.UnbindTexture(); + * + * // d_histogram <-- [ [1, 0, 1, 2, 0, 0, 0, 1]; + * // [0, 3, 0, 0, 0, 0, 2, 0]; + * // [0, 0, 2, 0, 0, 0, 1, 2] ] + * + * \endcode + * + * \tparam BINS Number of histogram bins per channel + * \tparam CHANNELS Number of channels interleaved in the input data (may be greater than the number of channels being actively histogrammed) + * \tparam ACTIVE_CHANNELS [inferred] Number of channels actively being histogrammed + * \tparam InputIterator [inferred] Random-access input iterator type for reading input samples. (Must have an InputIterator::value_type that, when cast as an integer, falls in the range [0..BINS-1]) \iterator + * \tparam HistoCounter [inferred] Integer type for counting sample occurrences per histogram bin + */ + template < + int BINS, + int CHANNELS, + int ACTIVE_CHANNELS, + typename InputIterator, + typename HistoCounter> + __host__ __device__ + static cudaError_t MultiChannelGlobalAtomic( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_samples, ///< [in] Pointer to the input sequence of sample items. The samples from different channels are assumed to be interleaved (e.g., an array of 32b pixels where each pixel consists of four RGBA 8b samples). + HistoCounter *d_histograms[ACTIVE_CHANNELS], ///< [out] Array of active channel histogram pointers, each pointing to an output array having BINS counters of integral type \p HistoCounter. + int num_samples, ///< [in] Total number of samples to process in all channels, including non-active channels + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Dispatch type + typedef DeviceHistogramDispatch< + DEVICE_HISTO_GLOBAL_ATOMIC, + BINS, + CHANNELS, + ACTIVE_CHANNELS, + InputIterator, + HistoCounter, + Offset> + DeviceHistogramDispatch; + + return DeviceHistogramDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_samples, + d_histograms, + num_samples, + stream, + debug_synchronous); + } + + //@} end member group + +}; + +/** + * \example example_device_histogram.cu + */ + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_partition.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_partition.cuh new file mode 100644 index 0000000000000000000000000000000000000000..b2f8ed32ef864a2d7139ffb266a018bf43e628ee --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_partition.cuh @@ -0,0 +1,275 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DevicePartition provides device-wide, parallel operations for partitioning sequences of data items residing within global memory. + */ + +#pragma once + +#include +#include + +#include "dispatch/device_select_dispatch.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \brief DevicePartition provides device-wide, parallel operations for partitioning sequences of data items residing within global memory. ![](partition_logo.png) + * \ingroup DeviceModule + * + * \par Overview + * These operations apply a selection criterion to construct a partitioned output sequence from items selected/unselected from + * a specified input sequence. + * + * \par Usage Considerations + * \cdp_class{DevicePartition} + * + * \par Performance + * \linear_performance{partition} + * + * \par + * The following chart illustrates DevicePartition::If + * performance across different CUDA architectures for \p int32 items, + * where 50% of the items are randomly selected for the first partition. + * \plots_below + * + * \image html partition_if_int32_50_percent.png + * + */ +struct DevicePartition +{ + /** + * \brief Uses the \p d_flags sequence to split the corresponding items from \p d_in into a partitioned sequence \p d_out. The total number of items copied into the first partition is written to \p d_num_selected. ![](partition_flags_logo.png) + * + * \par + * - The value type of \p d_flags must be castable to \p bool (e.g., \p bool, \p char, \p int, etc.). + * - Copies of the selected items are compacted into \p d_out and maintain their original + * relative ordering, however copies of the unselected items are compacted into the + * rear of \p d_out in reverse order. + * - \devicestorage + * - \cdp + * + * \par Snippet + * The code snippet below illustrates the compaction of items selected from an \p int device vector. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input, flags, and output + * int num_items; // e.g., 8 + * int *d_in; // e.g., [1, 2, 3, 4, 5, 6, 7, 8] + * char *d_flags; // e.g., [1, 0, 0, 1, 0, 1, 1, 0] + * int *d_out; // e.g., [ , , , , , , , ] + * int *d_num_selected; // e.g., [ ] + * ... + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DevicePartition::Flagged(d_temp_storage, temp_storage_bytes, d_in, d_flags, d_out, d_num_selected, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run selection + * cub::DevicePartition::Flagged(d_temp_storage, temp_storage_bytes, d_in, d_flags, d_out, d_num_selected, num_items); + * + * // d_out <-- [1, 4, 6, 7, 8, 5, 3, 2] + * // d_num_selected <-- [4] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading input items \iterator + * \tparam FlagIterator [inferred] Random-access input iterator type for reading selection flags \iterator + * \tparam OutputIterator [inferred] Random-access output iterator type for writing output items \iterator + * \tparam NumSelectedIterator [inferred] Output iterator type for recording the number of items selected \iterator + */ + template < + typename InputIterator, + typename FlagIterator, + typename OutputIterator, + typename NumSelectedIterator> + __host__ __device__ __forceinline__ + static cudaError_t Flagged( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + FlagIterator d_flags, ///< [in] Pointer to the input sequence of selection flags + OutputIterator d_out, ///< [out] Pointer to the output sequence of partitioned data items + NumSelectedIterator d_num_selected, ///< [out] Pointer to the output total number of items selected (i.e., the offset of the unselected partition) + int num_items, ///< [in] Total number of items to select from + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + typedef int Offset; // Signed integer type for global offsets + typedef NullType SelectOp; // Selection op (not used) + typedef NullType EqualityOp; // Equality operator (not used) + + return DeviceSelectDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + d_flags, + d_out, + d_num_selected, + SelectOp(), + EqualityOp(), + num_items, + stream, + debug_synchronous); + } + + + /** + * \brief Uses the \p select_op functor to split the corresponding items from \p d_in into a partitioned sequence \p d_out. The total number of items copied into the first partition is written to \p d_num_selected. ![](partition_logo.png) + * + * \par + * - Copies of the selected items are compacted into \p d_out and maintain their original + * relative ordering, however copies of the unselected items are compacted into the + * rear of \p d_out in reverse order. + * - \devicestorage + * - \cdp + * + * \par Performance + * The following charts illustrate saturated partition-if performance across different + * CUDA architectures for \p int32 and \p int64 items, respectively. Items are + * selected for the first partition with 50% probability. + * + * \image html partition_if_int32_50_percent.png + * \image html partition_if_int64_50_percent.png + * + * \par + * The following charts are similar, but 5% selection probability for the first partition: + * + * \image html partition_if_int32_5_percent.png + * \image html partition_if_int64_5_percent.png + * + * \par Snippet + * The code snippet below illustrates the compaction of items selected from an \p int device vector. + * \par + * \code + * #include // or equivalently + * + * // Functor type for selecting values less than some criteria + * struct LessThan + * { + * int compare; + * + * __host__ __device__ __forceinline__ + * LessThan(int compare) : compare(compare) {} + * + * __host__ __device__ __forceinline__ + * bool operator()(const int &a) const { + * return (a < compare); + * } + * }; + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 8 + * int *d_in; // e.g., [0, 2, 3, 9, 5, 2, 81, 8] + * int *d_out; // e.g., [ , , , , , , , ] + * int *d_num_selected; // e.g., [ ] + * LessThan select_op(7); + * ... + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceSelect::If(d_temp_storage, temp_storage_bytes, d_in, d_out, d_num_selected, num_items, select_op); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run selection + * cub::DeviceSelect::If(d_temp_storage, temp_storage_bytes, d_in, d_out, d_num_selected, num_items, select_op); + * + * // d_out <-- [0, 2, 3, 5, 2, 8, 81, 9] + * // d_num_selected <-- [5] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading input items \iterator + * \tparam OutputIterator [inferred] Random-access output iterator type for writing output items \iterator + * \tparam NumSelectedIterator [inferred] Output iterator type for recording the number of items selected \iterator + * \tparam SelectOp [inferred] Selection functor type having member bool operator()(const T &a) + */ + template < + typename InputIterator, + typename OutputIterator, + typename NumSelectedIterator, + typename SelectOp> + __host__ __device__ __forceinline__ + static cudaError_t If( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output sequence of partitioned data items + NumSelectedIterator d_num_selected, ///< [out] Pointer to the output total number of items selected (i.e., the offset of the unselected partition) + int num_items, ///< [in] Total number of items to select from + SelectOp select_op, ///< [in] Unary selection operator + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + typedef int Offset; // Signed integer type for global offsets + typedef NullType* FlagIterator; // Flag iterator type (not used) + typedef NullType EqualityOp; // Equality operator (not used) + + return DeviceSelectDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + NULL, + d_out, + d_num_selected, + select_op, + EqualityOp(), + num_items, + stream, + debug_synchronous); + } + +}; + +/** + * \example example_device_partition_flagged.cu + * \example example_device_partition_if.cu + */ + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_radix_sort.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_radix_sort.cuh new file mode 100644 index 0000000000000000000000000000000000000000..a1cd30570dbe440e9a68af17c16c96c474e3d737 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_radix_sort.cuh @@ -0,0 +1,420 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DeviceRadixSort provides device-wide, parallel operations for computing a radix sort across a sequence of data items residing within global memory. + */ + +#pragma once + +#include +#include + +#include "dispatch/device_radix_sort_dispatch.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \brief DeviceRadixSort provides device-wide, parallel operations for computing a radix sort across a sequence of data items residing within global memory. ![](sorting_logo.png) + * \ingroup DeviceModule + * + * \par Overview + * The [radix sorting method](http://en.wikipedia.org/wiki/Radix_sort) arranges + * items into ascending order. It relies upon a positional representation for + * keys, i.e., each key is comprised of an ordered sequence of symbols (e.g., digits, + * characters, etc.) specified from least-significant to most-significant. For a + * given input sequence of keys and a set of rules specifying a total ordering + * of the symbolic alphabet, the radix sorting method produces a lexicographic + * ordering of those keys. + * + * \par + * DeviceRadixSort can sort all of the built-in C++ numeric primitive types, e.g.: + * unsigned char, \p int, \p double, etc. Although the direct radix sorting + * method can only be applied to unsigned integral types, BlockRadixSort + * is able to sort signed and floating-point types via simple bit-wise transformations + * that ensure lexicographic key ordering. + * + * \par Usage Considerations + * \cdp_class{DeviceRadixSort} + * + * \par Performance + * \linear_performance{radix sort} The following chart illustrates DeviceRadixSort::SortKeys + * performance across different CUDA architectures for uniform-random \p uint32 keys. + * \plots_below + * + * \image html lsb_radix_sort_int32_keys.png + * + */ +struct DeviceRadixSort +{ + /** + * \brief Sorts key-value pairs into ascending order. + * + * \par + * - The sorting operation requires a pair of key buffers and a pair of value + * buffers. Each pair is wrapped in a DoubleBuffer structure whose member + * DoubleBuffer::Current() references the active buffer. The currently-active + * buffer may be changed by the sorting operation. + * - \devicestorage + * - \cdp + * + * \par Performance + * The following charts illustrate saturated sorting performance across different + * CUDA architectures for uniform-random uint32,uint32 and + * uint64,uint64 pairs, respectively. + * + * \image html lsb_radix_sort_int32_pairs.png + * \image html lsb_radix_sort_int64_pairs.png + * + * \par Snippet + * The code snippet below illustrates the sorting of a device vector of \p int keys + * with associated vector of \p int values. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for sorting data + * int num_items; // e.g., 7 + * int *d_key_buf; // e.g., [8, 6, 7, 5, 3, 0, 9] + * int *d_key_alt_buf; // e.g., [ ... ] + * int *d_value_buf; // e.g., [0, 1, 2, 3, 4, 5, 6] + * int *d_value_alt_buf; // e.g., [ ... ] + * ... + * + * // Create a set of DoubleBuffers to wrap pairs of device pointers + * cub::DoubleBuffer d_keys(d_key_buf, d_key_alt_buf); + * cub::DoubleBuffer d_values(d_value_buf, d_value_alt_buf); + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceRadixSort::SortPairs(d_temp_storage, temp_storage_bytes, d_keys, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run sorting operation + * cub::DeviceRadixSort::SortPairs(d_temp_storage, temp_storage_bytes, d_keys, num_items); + * + * // d_keys.Current() <-- [0, 3, 5, 6, 7, 8, 9] + * // d_values.Current() <-- [5, 4, 3, 1, 2, 0, 6] + * + * \endcode + * + * \tparam Key [inferred] Key type + * \tparam Value [inferred] Value type + */ + template < + typename Key, + typename Value> + __host__ __device__ + static cudaError_t SortPairs( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + DoubleBuffer &d_keys, ///< [in,out] Reference to the double-buffer of keys whose current buffer contains the unsorted input keys and, upon return, is updated to point to the sorted output keys + DoubleBuffer &d_values, ///< [in,out] Double-buffer of values whose current buffer contains the unsorted input values and, upon return, is updated to point to the sorted output values + int num_items, ///< [in] Number of items to reduce + int begin_bit = 0, ///< [in] [optional] The first (least-significant) bit index needed for key comparison + int end_bit = sizeof(Key) * 8, ///< [in] [optional] The past-the-end (most-significant) bit index needed for key comparison + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + return DeviceRadixSortDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_keys, + d_values, + num_items, + begin_bit, + end_bit, + stream, + debug_synchronous); + } + + + /** + * \brief Sorts key-value pairs into descending order. + * + * \par + * - The sorting operation requires a pair of key buffers and a pair of value + * buffers. Each pair is wrapped in a DoubleBuffer structure whose member + * DoubleBuffer::Current() references the active buffer. The currently-active + * buffer may be changed by the sorting operation. + * - \devicestorage + * - \cdp + * + * \par Performance + * Performance is similar to DeviceRadixSort::SortPairs. + * + * \par Snippet + * The code snippet below illustrates the sorting of a device vector of \p int keys + * with associated vector of \p int values. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for sorting data + * int num_items; // e.g., 7 + * int *d_key_buf; // e.g., [8, 6, 7, 5, 3, 0, 9] + * int *d_key_alt_buf; // e.g., [ ... ] + * int *d_value_buf; // e.g., [0, 1, 2, 3, 4, 5, 6] + * int *d_value_alt_buf; // e.g., [ ... ] + * ... + * + * // Create a set of DoubleBuffers to wrap pairs of device pointers + * cub::DoubleBuffer d_keys(d_key_buf, d_key_alt_buf); + * cub::DoubleBuffer d_values(d_value_buf, d_value_alt_buf); + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceRadixSort::SortPairsDescending(d_temp_storage, temp_storage_bytes, d_keys, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run sorting operation + * cub::DeviceRadixSort::SortPairsDescending(d_temp_storage, temp_storage_bytes, d_keys, num_items); + * + * // d_keys.Current() <-- [9, 8, 7, 6, 5, 3, 0] + * // d_values.Current() <-- [6, 0, 2, 1, 3, 4, 5] + * + * \endcode + * + * \tparam Key [inferred] Key type + * \tparam Value [inferred] Value type + */ + template < + typename Key, + typename Value> + __host__ __device__ + static cudaError_t SortPairsDescending( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + DoubleBuffer &d_keys, ///< [in,out] Reference to the double-buffer of keys whose current buffer contains the unsorted input keys and, upon return, is updated to point to the sorted output keys + DoubleBuffer &d_values, ///< [in,out] Double-buffer of values whose current buffer contains the unsorted input values and, upon return, is updated to point to the sorted output values + int num_items, ///< [in] Number of items to reduce + int begin_bit = 0, ///< [in] [optional] The first (least-significant) bit index needed for key comparison + int end_bit = sizeof(Key) * 8, ///< [in] [optional] The past-the-end (most-significant) bit index needed for key comparison + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + return DeviceRadixSortDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_keys, + d_values, + num_items, + begin_bit, + end_bit, + stream, + debug_synchronous); + } + + + /** + * \brief Sorts keys into ascending order + * + * \par + * - The sorting operation requires a pair of key buffers. The pair is + * wrapped in a DoubleBuffer structure whose member DoubleBuffer::Current() + * references the active buffer. The currently-active buffer may be changed + * by the sorting operation. + * - \devicestorage + * - \cdp + * + * \par Performance + * The following charts illustrate saturated sorting performance across different + * CUDA architectures for uniform-random \p uint32 and \p uint64 keys, respectively. + * + * \image html lsb_radix_sort_int32_keys.png + * \image html lsb_radix_sort_int64_keys.png + * + * \par Snippet + * The code snippet below illustrates the sorting of a device vector of \p int keys. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for sorting data + * int num_items; // e.g., 7 + * int *d_key_buf; // e.g., [8, 6, 7, 5, 3, 0, 9] + * int *d_key_alt_buf; // e.g., [ ... ] + * ... + * + * // Create a DoubleBuffer to wrap the pair of device pointers + * cub::DoubleBuffer d_keys(d_key_buf, d_key_alt_buf); + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceRadixSort::SortKeys(d_temp_storage, temp_storage_bytes, d_keys, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run sorting operation + * cub::DeviceRadixSort::SortKeys(d_temp_storage, temp_storage_bytes, d_keys, num_items); + * + * // d_keys.Current() <-- [0, 3, 5, 6, 7, 8, 9] + * + * \endcode + * + * \tparam Key [inferred] Key type + */ + template + __host__ __device__ + static cudaError_t SortKeys( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + DoubleBuffer &d_keys, ///< [in,out] Reference to the double-buffer of keys whose current buffer contains the unsorted input keys and, upon return, is updated to point to the sorted output keys + int num_items, ///< [in] Number of items to reduce + int begin_bit = 0, ///< [in] [optional] The first (least-significant) bit index needed for key comparison + int end_bit = sizeof(Key) * 8, ///< [in] [optional] The past-the-end (most-significant) bit index needed for key comparison + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Null value type + DoubleBuffer d_values; + + return DeviceRadixSortDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_keys, + d_values, + num_items, + begin_bit, + end_bit, + stream, + debug_synchronous); + } + + + /** + * \brief Sorts keys into ascending order + * + * \par + * - The sorting operation requires a pair of key buffers. The pair is + * wrapped in a DoubleBuffer structure whose member DoubleBuffer::Current() + * references the active buffer. The currently-active buffer may be changed + * by the sorting operation. + * - \devicestorage + * - \cdp + * + * \par Performance + * Performance is similar to DeviceRadixSort::SortKeys. + * + * \par Snippet + * The code snippet below illustrates the sorting of a device vector of \p int keys. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for sorting data + * int num_items; // e.g., 7 + * int *d_key_buf; // e.g., [8, 6, 7, 5, 3, 0, 9] + * int *d_key_alt_buf; // e.g., [ ... ] + * ... + * + * // Create a DoubleBuffer to wrap the pair of device pointers + * cub::DoubleBuffer d_keys(d_key_buf, d_key_alt_buf); + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceRadixSort::SortKeysDescending(d_temp_storage, temp_storage_bytes, d_keys, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run sorting operation + * cub::DeviceRadixSort::SortKeysDescending(d_temp_storage, temp_storage_bytes, d_keys, num_items); + * + * // d_keys.Current() <-- [9, 8, 7, 6, 5, 3, 0] + * + * \endcode + * + * \tparam Key [inferred] Key type + */ + template + __host__ __device__ + static cudaError_t SortKeysDescending( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + DoubleBuffer &d_keys, ///< [in,out] Reference to the double-buffer of keys whose current buffer contains the unsorted input keys and, upon return, is updated to point to the sorted output keys + int num_items, ///< [in] Number of items to reduce + int begin_bit = 0, ///< [in] [optional] The first (least-significant) bit index needed for key comparison + int end_bit = sizeof(Key) * 8, ///< [in] [optional] The past-the-end (most-significant) bit index needed for key comparison + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Null value type + DoubleBuffer d_values; + + return DeviceRadixSortDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_keys, + d_values, + num_items, + begin_bit, + end_bit, + stream, + debug_synchronous); + } + +}; + +/** + * \example example_device_radix_sort.cu + */ + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_reduce.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_reduce.cuh new file mode 100644 index 0000000000000000000000000000000000000000..42b2b08c5fb79a3b3f253faa0349be1ca76a5691 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_reduce.cuh @@ -0,0 +1,804 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DeviceReduce provides device-wide, parallel operations for computing a reduction across a sequence of data items residing within global memory. + */ + +#pragma once + +#include +#include + +#include "dispatch/device_reduce_dispatch.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \brief DeviceReduce provides device-wide, parallel operations for computing a reduction across a sequence of data items residing within global memory. ![](reduce_logo.png) + * \ingroup DeviceModule + * + * \par Overview + * A reduction (or fold) + * uses a binary combining operator to compute a single aggregate from a sequence of input elements. + * + * \par Usage Considerations + * \cdp_class{DeviceReduce} + * + * \par Performance + * \linear_performance{reduction, reduce-by-key, and run-length encode} + * + * \par + * The following chart illustrates DeviceReduce::Sum + * performance across different CUDA architectures for \p int32 keys. + * + * \image html reduce_int32.png + * + * \par + * The following chart illustrates DeviceReduce::ReduceByKey (summation) + * performance across different CUDA architectures for \p fp32 + * values. Segments are identified by \p int32 keys, and have lengths uniformly sampled from [1,1000]. + * + * \image html reduce_by_key_fp32_len_500.png + * + * \par + * The following chart illustrates DeviceReduce::RunLengthEncode performance across + * different CUDA architectures for \p int32 items. + * Segments have lengths uniformly sampled from [1,1000]. + * + * \image html rle_int32_len_500.png + * + * \par + * \plots_below + * + * + */ +struct DeviceReduce +{ + /** + * \brief Computes a device-wide reduction using the specified binary \p reduction_op functor. + * + * \par + * - Does not support non-commutative reduction operators. + * - \devicestorage + * - \cdp + * + * \par Performance + * Performance is typically similar to DeviceReduce::Sum. + * + * \par Snippet + * The code snippet below illustrates a custom min reduction of a device vector of \p int items. + * \par + * \code + * #include // or equivalently + * + * // CustomMin functor + * struct CustomMin + * { + * template + * __host__ __device__ __forceinline__ + * T operator()(const T &a, const T &b) const { + * return (b < a) ? b : a; + * } + * }; + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 7 + * int *d_in; // e.g., [8, 6, 7, 5, 3, 0, 9] + * int *d_out; // e.g., [ ] + * CustomMin min_op; + * ... + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceReduce::Reduce(d_temp_storage, temp_storage_bytes, d_in, d_out, num_items, min_op); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run reduction + * cub::DeviceReduce::Reduce(d_temp_storage, temp_storage_bytes, d_in, d_out, num_items, min_op); + * + * // d_out <-- [0] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading input items \iterator + * \tparam OutputIterator [inferred] Output iterator type for recording the reduced aggregate \iterator + * \tparam ReductionOp [inferred] Binary reduction functor type having member T operator()(const T &a, const T &b) + */ + template < + typename InputIterator, + typename OutputIterator, + typename ReductionOp> + __host__ __device__ + static cudaError_t Reduce( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output aggregate + int num_items, ///< [in] Total number of input items (i.e., length of \p d_in) + ReductionOp reduction_op, ///< [in] Binary reduction functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Dispatch type + typedef DeviceReduceDispatch DeviceReduceDispatch; + + return DeviceReduceDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + d_out, + num_items, + reduction_op, + stream, + debug_synchronous); + } + + + /** + * \brief Computes a device-wide sum using the addition ('+') operator. + * + * \par + * - Does not support non-commutative reduction operators. + * - \devicestorage + * - \cdp + * + * \par Performance + * The following charts illustrate saturated reduction (sum) performance across different + * CUDA architectures for \p int32 and \p int64 items, respectively. + * + * \image html reduce_int32.png + * \image html reduce_int64.png + * + * \par Snippet + * The code snippet below illustrates the sum reduction of a device vector of \p int items. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 7 + * int *d_in; // e.g., [8, 6, 7, 5, 3, 0, 9] + * int *d_out; // e.g., [ ] + * ... + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceReduce::Sum(d_temp_storage, temp_storage_bytes, d_in, d_sum, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run sum-reduction + * cub::DeviceReduce::Sum(d_temp_storage, temp_storage_bytes, d_in, d_sum, num_items); + * + * // d_out <-- [38] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading input items \iterator + * \tparam OutputIterator [inferred] Output iterator type for recording the reduced aggregate \iterator + */ + template < + typename InputIterator, + typename OutputIterator> + __host__ __device__ + static cudaError_t Sum( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output aggregate + int num_items, ///< [in] Total number of input items (i.e., length of \p d_in) + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Dispatch type + typedef DeviceReduceDispatch DeviceReduceDispatch; + + return DeviceReduceDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + d_out, + num_items, + cub::Sum(), + stream, + debug_synchronous); + } + + + /** + * \brief Computes a device-wide minimum using the less-than ('<') operator. + * + * \par + * - Does not support non-commutative minimum operators. + * - \devicestorage + * - \cdp + * + * \par Performance + * Performance is typically similar to DeviceReduce::Sum. + * + * \par Snippet + * The code snippet below illustrates the min-reduction of a device vector of \p int items. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 7 + * int *d_in; // e.g., [8, 6, 7, 5, 3, 0, 9] + * int *d_out; // e.g., [ ] + * ... + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceReduce::Min(d_temp_storage, temp_storage_bytes, d_in, d_min, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run min-reduction + * cub::DeviceReduce::Min(d_temp_storage, temp_storage_bytes, d_in, d_min, num_items); + * + * // d_out <-- [0] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading input items \iterator + * \tparam OutputIterator [inferred] Output iterator type for recording the reduced aggregate \iterator + */ + template < + typename InputIterator, + typename OutputIterator> + __host__ __device__ + static cudaError_t Min( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output aggregate + int num_items, ///< [in] Total number of input items (i.e., length of \p d_in) + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Dispatch type + typedef DeviceReduceDispatch DeviceReduceDispatch; + + return DeviceReduceDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + d_out, + num_items, + cub::Min(), + stream, + debug_synchronous); + } + + + /** + * \brief Finds the first device-wide minimum using the less-than ('<') operator, also returning the index of that item. + * + * \par + * Assuming the input \p d_in has value type \p T, the output \p d_out must have value type + * ItemOffsetPair. The minimum value is written to d_out.value and its + * location in the input array is written to d_out.offset. + * + * \par + * - Does not support non-commutative minimum operators. + * - \devicestorage + * - \cdp + * + * \par Performance + * Performance is typically similar to DeviceReduce::Sum. + * + * \par Snippet + * The code snippet below illustrates the argmin-reduction of a device vector of \p int items. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 7 + * int *d_in; // e.g., [8, 6, 7, 5, 3, 0, 9] + * ItemOffsetPair *d_out; // e.g., [{ , }] + * ... + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceReduce::ArgMin(d_temp_storage, temp_storage_bytes, d_in, d_argmin, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run argmin-reduction + * cub::DeviceReduce::ArgMin(d_temp_storage, temp_storage_bytes, d_in, d_argmin, num_items); + * + * // d_out <-- [{0, 5}] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading input items (of some type \p T) \iterator + * \tparam OutputIterator [inferred] Output iterator type for recording the reduced aggregate (having value type ItemOffsetPair) \iterator + */ + template < + typename InputIterator, + typename OutputIterator> + __host__ __device__ + static cudaError_t ArgMin( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output aggregate + int num_items, ///< [in] Total number of input items (i.e., length of \p d_in) + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Wrapped input iterator + typedef ArgIndexInputIterator ArgIndexInputIterator; + ArgIndexInputIterator d_argmin_in(d_in, 0); + + // Dispatch type + typedef DeviceReduceDispatch DeviceReduceDispatch; + + return DeviceReduceDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_argmin_in, + d_out, + num_items, + cub::ArgMin(), + stream, + debug_synchronous); + } + + + /** + * \brief Computes a device-wide maximum using the greater-than ('>') operator. + * + * \par + * - Does not support non-commutative maximum operators. + * - \devicestorage + * - \cdp + * + * \par Performance + * Performance is typically similar to DeviceReduce::Sum. + * + * \par Snippet + * The code snippet below illustrates the max-reduction of a device vector of \p int items. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 7 + * int *d_in; // e.g., [8, 6, 7, 5, 3, 0, 9] + * int *d_out; // e.g., [ ] + * ... + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceReduce::Max(d_temp_storage, temp_storage_bytes, d_in, d_max, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run max-reduction + * cub::DeviceReduce::Max(d_temp_storage, temp_storage_bytes, d_in, d_max, num_items); + * + * // d_out <-- [9] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading input items \iterator + * \tparam OutputIterator [inferred] Output iterator type for recording the reduced aggregate \iterator + */ + template < + typename InputIterator, + typename OutputIterator> + __host__ __device__ + static cudaError_t Max( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output aggregate + int num_items, ///< [in] Total number of input items (i.e., length of \p d_in) + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Dispatch type + typedef DeviceReduceDispatch DeviceReduceDispatch; + + return DeviceReduceDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + d_out, + num_items, + cub::Max(), + stream, + debug_synchronous); + } + + + /** + * \brief Finds the first device-wide maximum using the greater-than ('>') operator, also returning the index of that item + * + * \par + * Assuming the input \p d_in has value type \p T, the output \p d_out must have value type + * ItemOffsetPair. The maximum value is written to d_out.value and its + * location in the input array is written to d_out.offset. + * + * \par + * - Does not support non-commutative maximum operators. + * - \devicestorage + * - \cdp + * + * \par Performance + * Performance is typically similar to DeviceReduce::Sum. + * + * \par Snippet + * The code snippet below illustrates the argmax-reduction of a device vector of \p int items. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 7 + * int *d_in; // e.g., [8, 6, 7, 5, 3, 0, 9] + * ItemOffsetPair *d_out; // e.g., [{ , }] + * ... + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceReduce::ArgMax(d_temp_storage, temp_storage_bytes, d_in, d_argmax, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run argmax-reduction + * cub::DeviceReduce::ArgMax(d_temp_storage, temp_storage_bytes, d_in, d_argmax, num_items); + * + * // d_out <-- [{9, 6}] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading input items (of some type \p T) \iterator + * \tparam OutputIterator [inferred] Output iterator type for recording the reduced aggregate (having value type ItemOffsetPair) \iterator + */ + template < + typename InputIterator, + typename OutputIterator> + __host__ __device__ + static cudaError_t ArgMax( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output aggregate + int num_items, ///< [in] Total number of input items (i.e., length of \p d_in) + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Wrapped input iterator + typedef ArgIndexInputIterator ArgIndexInputIterator; + ArgIndexInputIterator d_argmax_in(d_in, 0); + + // Dispatch type + typedef DeviceReduceDispatch DeviceReduceDispatch; + + return DeviceReduceDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_argmax_in, + d_out, + num_items, + cub::ArgMax(), + stream, + debug_synchronous); + } + + + /** + * \brief Reduces segments of values, where segments are demarcated by corresponding runs of identical keys. + * + * \par + * This operation computes segmented reductions using the specified binary + * \p reduction_op functor. Each "run" of consecutive, identical keys in \p d_keys_in + * is used to identify a corresponding segment of values in \p d_values_in. The first key in + * the ith segment is copied to d_keys_out[i], and + * the value aggregate for that segment is written to d_values_out[i]. + * The total number of segments discovered is written to \p d_num_segments. + * + * \par + * - The == equality operator is used to determine whether keys are equivalent + * - \devicestorage + * - \cdp + * + * \par Performance + * The following chart illustrates reduction-by-key (sum) performance across + * different CUDA architectures for \p fp32 and \p fp64 values, respectively. Segments + * are identified by \p int32 keys, and have lengths uniformly sampled from [1,1000]. + * + * \image html reduce_by_key_fp32_len_500.png + * \image html reduce_by_key_fp64_len_500.png + * + * \par + * The following charts are similar, but with segment lengths uniformly sampled from [1,10]: + * + * \image html reduce_by_key_fp32_len_5.png + * \image html reduce_by_key_fp64_len_5.png + * + * \par Snippet + * The code snippet below illustrates the segmented reduction of \p int values grouped + * by runs of associated \p int keys. + * \par + * \code + * #include // or equivalently + * + * // CustomMin functor + * struct CustomMin + * { + * template + * __host__ __device__ __forceinline__ + * T operator()(const T &a, const T &b) const { + * return (b < a) ? b : a; + * } + * }; + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 8 + * int *d_keys_in; // e.g., [0, 2, 2, 9, 5, 5, 5, 8] + * int *d_values_in; // e.g., [0, 7, 1, 6, 2, 5, 3, 4] + * int *d_keys_out; // e.g., [ , , , , , , , ] + * int *d_values_out; // e.g., [ , , , , , , , ] + * int *d_num_segments; // e.g., [ ] + * CustomMin reduction_op; + * ... + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceSelect::ReduceByKey(d_temp_storage, temp_storage_bytes, d_keys_in, d_keys_out, d_values_in, d_values_out, d_num_segments, reduction_op, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run reduce-by-key + * cub::DeviceSelect::ReduceByKey(d_temp_storage, temp_storage_bytes, d_keys_in, d_keys_out, d_values_in, d_values_out, d_num_segments, reduction_op, num_items); + * + * // d_keys_out <-- [0, 2, 9, 5, 8] + * // d_values_out <-- [0, 1, 6, 2, 4] + * // d_num_segments <-- [5] + * + * \endcode + * + * \tparam KeyInputIterator [inferred] Random-access input iterator type for reading input keys \iterator + * \tparam KeyOutputIterator [inferred] Random-access output iterator type for writing output keys \iterator + * \tparam ValueInputIterator [inferred] Random-access input iterator type for reading input values \iterator + * \tparam ValueOutputIterator [inferred] Random-access output iterator type for writing output values \iterator + * \tparam NumSegmentsIterator [inferred] Output iterator type for recording the number of segments encountered \iterator + * \tparam ReductionOp [inferred] Binary reduction functor type having member T operator()(const T &a, const T &b) + */ + template < + typename KeyInputIterator, + typename KeyOutputIterator, + typename ValueInputIterator, + typename ValueOutputIterator, + typename NumSegmentsIterator, + typename ReductionOp> + __host__ __device__ __forceinline__ + static cudaError_t ReduceByKey( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + KeyInputIterator d_keys_in, ///< [in] Pointer to consecutive runs of input keys + KeyOutputIterator d_keys_out, ///< [out] Pointer to output keys (one key per run) + ValueInputIterator d_values_in, ///< [in] Pointer to consecutive runs of input values + ValueOutputIterator d_values_out, ///< [out] Pointer to output value aggregates (one aggregate per run) + NumSegmentsIterator d_num_segments, ///< [out] Pointer to total number of segments + ReductionOp reduction_op, ///< [in] Binary reduction functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + int num_items, ///< [in] Total number of associated key+value pairs (i.e., the length of \p d_in_keys and \p d_in_values) + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + typedef int Offset; // Signed integer type for global offsets + typedef NullType* FlagIterator; // Flag iterator type (not used) + typedef NullType SelectOp; // Selection op (not used) + typedef Equality EqualityOp; // Default == operator + + return DeviceReduceByKeyDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_keys_in, + d_keys_out, + d_values_in, + d_values_out, + d_num_segments, + EqualityOp(), + reduction_op, + num_items, + stream, + debug_synchronous); + } + + + /** + * \brief Counts the segment lengths in the sequence \p d_in, where segments are demarcated by runs of identical values. + * + * \par + * This operation computes a run-length encoding of \p d_in, where segments are identified + * by "runs" of consecutive, identical values. The length of the ith segment + * is written to d_counts_out[i]. The unique values are also compacted, + * i.e., the first value in the ith segment is copied to + * d_compacted_out[i]. The total number of segments discovered is written + * to \p d_num_segments. + * + * \par + * - The == equality operator is used to determine whether values are equivalent + * - \devicestorage + * - \cdp + * + * \par Performance + * The following charts illustrate saturated encode performance across different + * CUDA architectures for \p int32 and \p int64 items, respectively. Segments have + * lengths uniformly sampled from [1,1000]. + * + * \image html rle_int32_len_500.png + * \image html rle_int64_len_500.png + * + * \par + * The following charts are similar, but with segment lengths uniformly sampled from [1,10]: + * + * \image html rle_int32_len_5.png + * \image html rle_int64_len_5.png + * + * \par Snippet + * The code snippet below illustrates the run-length encoding of a sequence of \p int values. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 8 + * int *d_in; // e.g., [0, 2, 2, 9, 5, 5, 5, 8] + * int *d_compacted_out; // e.g., [ , , , , , , , ] + * int *d_counts_out; // e.g., [ , , , , , , , ] + * int *d_num_segments; // e.g., [ ] + * ... + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceSelect::RunLengthEncode(d_temp_storage, temp_storage_bytes, d_in, d_compacted_out, d_counts_out, d_num_segments, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run encoding + * cub::DeviceSelect::RunLengthEncode(d_temp_storage, temp_storage_bytes, d_in, d_compacted_out, d_counts_out, d_num_segments, num_items); + * + * // d_keys_out <-- [0, 2, 9, 5, 8] + * // d_values_out <-- [1, 2, 1, 3, 1] + * // d_num_segments <-- [5] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading input items \iterator + * \tparam OutputIterator [inferred] Random-access output iterator type for writing compacted output items \iterator + * \tparam CountsOutputIterator [inferred] Random-access output iterator type for writing output counts \iterator + * \tparam NumSegmentsIterator [inferred] Output iterator type for recording the number of segments encountered \iterator + */ + template < + typename InputIterator, + typename OutputIterator, + typename CountsOutputIterator, + typename NumSegmentsIterator> + __host__ __device__ __forceinline__ + static cudaError_t RunLengthEncode( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to consecutive runs of input keys + OutputIterator d_compacted_out, ///< [out] Pointer to output keys (one key per run) + CountsOutputIterator d_counts_out, ///< [out] Pointer to output value aggregates (one aggregate per run) + NumSegmentsIterator d_num_segments, ///< [out] Pointer to total number of segments + int num_items, ///< [in] Total number of associated key+value pairs (i.e., the length of \p d_in_keys and \p d_in_values) + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + // Data type of value iterator + typedef typename std::iterator_traits::value_type Value; + + typedef int Offset; // Signed integer type for global offsets + typedef NullType* FlagIterator; // Flag iterator type (not used) + typedef NullType SelectOp; // Selection op (not used) + typedef Equality EqualityOp; // Default == operator + typedef cub::Sum ReductionOp; // Value reduction operator + + // Generator type for providing 1s values for run-length reduction + typedef ConstantInputIterator CountsInputIterator; + + Value one_val; + one_val = 1; + + return DeviceReduceByKeyDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + d_compacted_out, + CountsInputIterator(one_val), + d_counts_out, + d_num_segments, + EqualityOp(), + ReductionOp(), + num_items, + stream, + debug_synchronous); + } + +}; + +/** + * \example example_device_reduce.cu + */ + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_reduce_by_key.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_reduce_by_key.cuh new file mode 100644 index 0000000000000000000000000000000000000000..bb86b5347aa5118589c0cdeb9bd647719540bb24 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_reduce_by_key.cuh @@ -0,0 +1,597 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DeviceReduceByKey provides device-wide, parallel operations for reducing segments of values residing within global memory. + */ + +#pragma once + +#include +#include + +#include "device_scan.cuh" +#include "region/block_reduce_by_key_region.cuh" +#include "../thread/thread_operators.cuh" +#include "../grid/grid_queue.cuh" +#include "../util_device.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Kernel entry points + *****************************************************************************/ + +#ifndef DOXYGEN_SHOULD_SKIP_THIS // Do not document + + +/** + * Reduce-by-key kernel entry point (multi-block) + */ +template < + typename BlockReduceByKeyRegionPolicy, ///< Parameterized BlockReduceByKeyRegionPolicy tuning policy type + typename KeyInputIterator, ///< Random-access input iterator type for keys + typename KeyOutputIterator, ///< Random-access output iterator type for keys + typename ValueInputIterator, ///< Random-access input iterator type for values + typename ValueOutputIterator, ///< Random-access output iterator type for values + typename NumSegmentsIterator, ///< Output iterator type for recording number of segments encountered + typename TileLookbackStatus, ///< Tile status interface type + typename EqualityOp, ///< Key equality operator type + typename ReductionOp, ///< Value reduction operator type + typename Offset> ///< Signed integer type for global offsets +__launch_bounds__ (int(BlockReduceByKeyRegionPolicy::BLOCK_THREADS)) +__global__ void ReduceByKeyRegionKernel( + KeyInputIterator d_keys_in, ///< [in] Pointer to consecutive runs of input keys + KeyOutputIterator d_keys_out, ///< [in] Pointer to output keys (one key per run) + ValueInputIterator d_values_in, ///< [in] Pointer to consecutive runs of input values + ValueOutputIterator d_values_out, ///< [in] Pointer to output value aggregates (one aggregate per run) + NumSegmentsIterator d_num_segments, ///< [in] Pointer to total number of runs + TileLookbackStatus tile_status, ///< [in] Tile status interface + EqualityOp equality_op, ///< [in] Key equality operator + ReductionOp reduction_op, ///< [in] Value reduction operator + Offset num_items, ///< [in] Total number of items to select from + int num_tiles, ///< [in] Total number of tiles for the entire problem + GridQueue queue) ///< [in] Drain queue descriptor for dynamically mapping tile data onto thread blocks +{ + // Thread block type for reducing tiles of value segments + typedef BlockReduceByKeyRegion< + BlockReduceByKeyRegionPolicy, + KeyInputIterator, + KeyOutputIterator, + ValueInputIterator, + ValueOutputIterator, + EqualityOp, + ReductionOp, + Offset> BlockReduceByKeyRegionT; + + // Shared memory for BlockReduceByKeyRegion + __shared__ typename BlockReduceByKeyRegionT::TempStorage temp_storage; + + // Process tiles + BlockReduceByKeyRegionT(temp_storage, d_keys_in, d_keys_out, d_values_in, d_values_out, equality_op, reduction_op, num_items).ConsumeRegion( + num_tiles, + queue, + tile_status, + d_num_segments); +} + + + + +/****************************************************************************** + * Dispatch + ******************************************************************************/ + +/** + * Utility class for dispatching the appropriately-tuned kernels for DeviceReduceByKey + */ +template < + typename KeyInputIterator, ///< Random-access input iterator type for keys + typename KeyOutputIterator, ///< Random-access output iterator type for keys + typename ValueInputIterator, ///< Random-access input iterator type for values + typename ValueOutputIterator, ///< Random-access output iterator type for values + typename NumSegmentsIterator, ///< Output iterator type for recording number of segments encountered + typename EqualityOp, ///< Key equality operator type + typename ReductionOp, ///< Value reduction operator type + typename Offset> ///< Signed integer type for global offsets +struct DeviceReduceByKeyDispatch +{ + /****************************************************************************** + * Types and constants + ******************************************************************************/ + + // Data type of key input iterator + typedef typename std::iterator_traits::value_type Key; + + // Data type of value input iterator + typedef typename std::iterator_traits::value_type Value; + + enum + { + INIT_KERNEL_THREADS = 128, + MAX_INPUT_BYTES = CUB_MAX(sizeof(Key), sizeof(Value)), + COMBINED_INPUT_BYTES = sizeof(Key) + sizeof(Value), + }; + + // Value-offset tuple type for scanning (maps accumulated values to segment index) + typedef ItemOffsetPair ValueOffsetPair; + + // Tile status descriptor interface type + typedef ReduceByKeyTileLookbackStatus TileLookbackStatus; + + + /****************************************************************************** + * Tuning policies + ******************************************************************************/ + + /// SM35 + struct Policy350 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 8, + ITEMS_PER_THREAD = (MAX_INPUT_BYTES <= 8) ? 8 : CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, ((NOMINAL_4B_ITEMS_PER_THREAD * 8) + COMBINED_INPUT_BYTES - 1) / COMBINED_INPUT_BYTES)), + }; + + typedef BlockReduceByKeyRegionPolicy< + 128, + ITEMS_PER_THREAD, + BLOCK_LOAD_DIRECT, + LOAD_LDG, + true, + BLOCK_SCAN_WARP_SCANS> + ReduceByKeyPolicy; + }; + + /// SM30 + struct Policy300 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 6, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, ((NOMINAL_4B_ITEMS_PER_THREAD * 8) + COMBINED_INPUT_BYTES - 1) / COMBINED_INPUT_BYTES)), + }; + + typedef BlockReduceByKeyRegionPolicy< + 128, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + LOAD_DEFAULT, + true, + BLOCK_SCAN_WARP_SCANS> + ReduceByKeyPolicy; + }; + + /// SM20 + struct Policy200 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 13, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, ((NOMINAL_4B_ITEMS_PER_THREAD * 8) + COMBINED_INPUT_BYTES - 1) / COMBINED_INPUT_BYTES)), + }; + + typedef BlockReduceByKeyRegionPolicy< + 128, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + LOAD_DEFAULT, + true, + BLOCK_SCAN_WARP_SCANS> + ReduceByKeyPolicy; + }; + + /// SM13 + struct Policy130 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 7, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, ((NOMINAL_4B_ITEMS_PER_THREAD * 8) + COMBINED_INPUT_BYTES - 1) / COMBINED_INPUT_BYTES)), + }; + + typedef BlockReduceByKeyRegionPolicy< + 128, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + LOAD_DEFAULT, + true, + BLOCK_SCAN_WARP_SCANS> + ReduceByKeyPolicy; + }; + + /// SM10 + struct Policy100 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 5, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 8) / COMBINED_INPUT_BYTES)), + }; + + typedef BlockReduceByKeyRegionPolicy< + 64, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + LOAD_DEFAULT, + true, + BLOCK_SCAN_RAKING> + ReduceByKeyPolicy; + }; + + + /****************************************************************************** + * Tuning policies of current PTX compiler pass + ******************************************************************************/ + +#if (CUB_PTX_VERSION >= 350) + typedef Policy350 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 300) + typedef Policy300 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 200) + typedef Policy200 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 130) + typedef Policy130 PtxPolicy; + +#else + typedef Policy100 PtxPolicy; + +#endif + + // "Opaque" policies (whose parameterizations aren't reflected in the type signature) + struct PtxReduceByKeyPolicy : PtxPolicy::ReduceByKeyPolicy {}; + + + /****************************************************************************** + * Utilities + ******************************************************************************/ + + /** + * Initialize kernel dispatch configurations with the policies corresponding to the PTX assembly we will use + */ + template + __host__ __device__ __forceinline__ + static void InitConfigs( + int ptx_version, + KernelConfig &reduce_by_key_region_config) + { + #if (CUB_PTX_VERSION > 0) + + // We're on the device, so initialize the kernel dispatch configurations with the current PTX policy + reduce_by_key_region_config.template Init(); + + #else + + // We're on the host, so lookup and initialize the kernel dispatch configurations with the policies that match the device's PTX version + if (ptx_version >= 350) + { + reduce_by_key_region_config.template Init(); + } + else if (ptx_version >= 300) + { + reduce_by_key_region_config.template Init(); + } + else if (ptx_version >= 200) + { + reduce_by_key_region_config.template Init(); + } + else if (ptx_version >= 130) + { + reduce_by_key_region_config.template Init(); + } + else + { + reduce_by_key_region_config.template Init(); + } + + #endif + } + + + /** + * Kernel kernel dispatch configuration. Mirrors the constants within BlockReduceByKeyRegionPolicy. + */ + struct KernelConfig + { + int block_threads; + int items_per_thread; + BlockLoadAlgorithm load_policy; + bool two_phase_scatter; + BlockScanAlgorithm scan_algorithm; + cudaSharedMemConfig smem_config; + + template + __host__ __device__ __forceinline__ + void Init() + { + block_threads = BlockReduceByKeyRegionPolicy::BLOCK_THREADS; + items_per_thread = BlockReduceByKeyRegionPolicy::ITEMS_PER_THREAD; + load_policy = BlockReduceByKeyRegionPolicy::LOAD_ALGORITHM; + two_phase_scatter = BlockReduceByKeyRegionPolicy::TWO_PHASE_SCATTER; + scan_algorithm = BlockReduceByKeyRegionPolicy::SCAN_ALGORITHM; + smem_config = cudaSharedMemBankSizeEightByte; + } + + __host__ __device__ __forceinline__ + void Print() + { + printf("%d, %d, %d, %d, %d", + block_threads, + items_per_thread, + load_policy, + two_phase_scatter, + scan_algorithm); + } + }; + + + /****************************************************************************** + * Dispatch entrypoints + ******************************************************************************/ + + /** + * Internal dispatch routine for computing a device-wide prefix scan using the + * specified kernel functions. + */ + template < + typename ScanInitKernelPtr, ///< Function type of cub::ScanInitKernel + typename ReduceByKeyRegionKernelPtr> ///< Function type of cub::ReduceByKeyRegionKernelPtr + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + KeyInputIterator d_keys_in, ///< [in] Pointer to consecutive runs of input keys + KeyOutputIterator d_keys_out, ///< [in] Pointer to output keys (one key per run) + ValueInputIterator d_values_in, ///< [in] Pointer to consecutive runs of input values + ValueOutputIterator d_values_out, ///< [in] Pointer to output value aggregates (one aggregate per run) + NumSegmentsIterator d_num_segments, ///< [in] Pointer to total number of runs + EqualityOp equality_op, ///< [in] Key equality operator + ReductionOp reduction_op, ///< [in] Value reduction operator + Offset num_items, ///< [in] Total number of items to select from + cudaStream_t stream, ///< [in] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous, ///< [in] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + int ptx_version, ///< [in] PTX version of dispatch kernels + ScanInitKernelPtr init_kernel, ///< [in] Kernel function pointer to parameterization of cub::ScanInitKernel + ReduceByKeyRegionKernelPtr reduce_by_key_region_kernel, ///< [in] Kernel function pointer to parameterization of cub::ReduceByKeyRegionKernel + KernelConfig reduce_by_key_region_config) ///< [in] Dispatch parameters that match the policy that \p reduce_by_key_region_kernel was compiled for + { + +#ifndef CUB_RUNTIME_ENABLED + + // Kernel launch not supported from this device + return CubDebug(cudaErrorNotSupported); + +#else + + cudaError error = cudaSuccess; + do + { + // Get device ordinal + int device_ordinal; + if (CubDebug(error = cudaGetDevice(&device_ordinal))) break; + + // Get device SM version + int sm_version; + if (CubDebug(error = SmVersion(sm_version, device_ordinal))) break; + + // Get SM count + int sm_count; + if (CubDebug(error = cudaDeviceGetAttribute (&sm_count, cudaDevAttrMultiProcessorCount, device_ordinal))) break; + + // Number of input tiles + int tile_size = reduce_by_key_region_config.block_threads * reduce_by_key_region_config.items_per_thread; + int num_tiles = (num_items + tile_size - 1) / tile_size; + + // Specify temporary storage allocation requirements + size_t allocation_sizes[2]; + if (CubDebug(error = TileLookbackStatus::AllocationSize(num_tiles, allocation_sizes[0]))) break; // bytes needed for tile status descriptors + allocation_sizes[1] = GridQueue::AllocationSize(); // bytes needed for grid queue descriptor + + // Compute allocation pointers into the single storage blob (or set the necessary size of the blob) + void* allocations[2]; + if (CubDebug(error = AliasTemporaries(d_temp_storage, temp_storage_bytes, allocations, allocation_sizes))) break; + if (d_temp_storage == NULL) + { + // Return if the caller is simply requesting the size of the storage allocation + return cudaSuccess; + } + + // Construct the tile status interface + TileLookbackStatus tile_status; + if (CubDebug(error = tile_status.Init(num_tiles, allocations[0], allocation_sizes[0]))) break; + + // Construct the grid queue descriptor + GridQueue queue(allocations[1]); + + // Log init_kernel configuration + int init_grid_size = (num_tiles + INIT_KERNEL_THREADS - 1) / INIT_KERNEL_THREADS; + if (debug_synchronous) CubLog("Invoking init_kernel<<<%d, %d, 0, %lld>>>()\n", init_grid_size, INIT_KERNEL_THREADS, (long long) stream); + + // Invoke init_kernel to initialize tile descriptors and queue descriptors + init_kernel<<>>( + queue, + tile_status, + num_tiles); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + + // Get SM occupancy for reduce_by_key_region_kernel + int reduce_by_key_region_sm_occupancy; + if (CubDebug(error = MaxSmOccupancy( + reduce_by_key_region_sm_occupancy, // out + sm_version, + reduce_by_key_region_kernel, + reduce_by_key_region_config.block_threads))) break; + + // Get grid size for scanning tiles + dim3 reduce_by_key_grid_size; + if (ptx_version <= 130) + { + // Blocks are launched in order, so just assign one block per tile + int max_dim_x = 32 * 1024; + reduce_by_key_grid_size.z = 1; + reduce_by_key_grid_size.y = (num_tiles + max_dim_x - 1) / max_dim_x; + reduce_by_key_grid_size.x = CUB_MIN(num_tiles, max_dim_x); + } + else + { + // Blocks may not be launched in order, so use atomics + int reduce_by_key_region_occupancy = reduce_by_key_region_sm_occupancy * sm_count; // Whole-device occupancy for reduce_by_key_region_kernel + reduce_by_key_grid_size.z = 1; + reduce_by_key_grid_size.y = 1; + reduce_by_key_grid_size.x = (num_tiles < reduce_by_key_region_occupancy) ? + num_tiles : // Not enough to fill the device with threadblocks + reduce_by_key_region_occupancy; // Fill the device with threadblocks + } + +#if (CUB_PTX_VERSION == 0) + // Get current smem bank configuration + cudaSharedMemConfig original_smem_config; + if (CubDebug(error = cudaDeviceGetSharedMemConfig(&original_smem_config))) break; + cudaSharedMemConfig current_smem_config = original_smem_config; + + // Update smem config if necessary + if (current_smem_config != reduce_by_key_region_config.smem_config) + { + if (CubDebug(error = cudaDeviceSetSharedMemConfig(reduce_by_key_region_config.smem_config))) break; + current_smem_config = reduce_by_key_region_config.smem_config; + } +#endif + + // Log reduce_by_key_region_kernel configuration + if (debug_synchronous) CubLog("Invoking reduce_by_key_region_kernel<<<{%d,%d,%d}, %d, 0, %lld>>>(), %d items per thread, %d SM occupancy\n", + reduce_by_key_grid_size.x, reduce_by_key_grid_size.y, reduce_by_key_grid_size.z, reduce_by_key_region_config.block_threads, (long long) stream, reduce_by_key_region_config.items_per_thread, reduce_by_key_region_sm_occupancy); + + // Invoke reduce_by_key_region_kernel + reduce_by_key_region_kernel<<>>( + d_keys_in, + d_keys_out, + d_values_in, + d_values_out, + d_num_segments, + tile_status, + equality_op, + reduction_op, + num_items, + num_tiles, + queue); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + +#if (CUB_PTX_VERSION == 0) + // Reset smem config if necessary + if (current_smem_config != original_smem_config) + { + if (CubDebug(error = cudaDeviceSetSharedMemConfig(original_smem_config))) break; + } +#endif + + } + while (0); + + return error; + +#endif // CUB_RUNTIME_ENABLED + } + + + /** + * Internal dispatch routine + */ + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + KeyInputIterator d_keys_in, ///< [in] Pointer to consecutive runs of input keys + KeyOutputIterator d_keys_out, ///< [in] Pointer to output keys (one key per run) + ValueInputIterator d_values_in, ///< [in] Pointer to consecutive runs of input values + ValueOutputIterator d_values_out, ///< [in] Pointer to output value aggregates (one aggregate per run) + NumSegmentsIterator d_num_segments, ///< [in] Pointer to total number of runs + EqualityOp equality_op, ///< [in] Key equality operator + ReductionOp reduction_op, ///< [in] Value reduction operator + Offset num_items, ///< [in] Total number of items to select from + cudaStream_t stream, ///< [in] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous) ///< [in] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + cudaError error = cudaSuccess; + do + { + // Get PTX version + int ptx_version; + #if (CUB_PTX_VERSION == 0) + if (CubDebug(error = PtxVersion(ptx_version))) break; + #else + ptx_version = CUB_PTX_VERSION; + #endif + + // Get kernel kernel dispatch configurations + KernelConfig reduce_by_key_region_config; + InitConfigs(ptx_version, reduce_by_key_region_config); + + // Dispatch + if (CubDebug(error = Dispatch( + d_temp_storage, + temp_storage_bytes, + d_keys_in, + d_keys_out, + d_values_in, + d_values_out, + d_num_segments, + equality_op, + reduction_op, + num_items, + stream, + debug_synchronous, + ptx_version, + ScanInitKernel, + ReduceByKeyRegionKernel, + reduce_by_key_region_config))) break; + } + while (0); + + return error; + } +}; + + + +#endif // DOXYGEN_SHOULD_SKIP_THIS + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_reorder.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_reorder.cuh new file mode 100644 index 0000000000000000000000000000000000000000..cba3bb48f1ca3c2e6e7399f07c27867549feb6ce --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_reorder.cuh @@ -0,0 +1,550 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DeviceReorder provides device-wide operations for partitioning and filtering lists of items residing within global memory. + */ + +#pragma once + +#include +#include + +#include "device_scan.cuh" +#include "block/block_partition_tiles.cuh" +#include "../grid/grid_queue.cuh" +#include "../util_debug.cuh" +#include "../util_device.cuh" +#include "../util_vector.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Kernel entry points + *****************************************************************************/ + +#ifndef DOXYGEN_SHOULD_SKIP_THIS // Do not document + +/** + * Partition kernel entry point (multi-block) + */ +template < + typename BlockPartitionTilesPolicy, ///< Tuning policy for cub::BlockPartitionTiles abstraction + typename InputIteratorRA, ///< Random-access iterator type for input (may be a simple pointer type) + typename OutputIteratorRA, ///< Random-access iterator type for output (may be a simple pointer type) + typename LengthOutputIterator, ///< Output iterator type for recording the length of the first partition (may be a simple pointer type) + typename PredicateOp, ///< Unary predicate operator indicating membership in the first partition type having member bool operator()(const T &val) + typename SizeT> ///< Integer type used for global array indexing +__launch_bounds__ (int(BlockPartitionTilesPolicy::BLOCK_THREADS)) +__global__ void PartitionKernel( + InputIteratorRA d_in, ///< Input data + OutputIteratorRA d_out, ///< Output data + LengthOutputIterator d_partition_length, ///< Number of items in the first partition + ScanTileDescriptor > *d_tile_status, ///< Global list of tile status + PredicateOp pred_op, ///< Unary predicate operator indicating membership in the first partition + SizeT num_items, ///< Total number of input items for the entire problem + int num_tiles, ///< Totla number of intut tiles for the entire problem + GridQueue queue) ///< Descriptor for performing dynamic mapping of tile data to thread blocks +{ + enum + { + TILE_STATUS_PADDING = PtxArchProps::WARP_THREADS, + }; + + typedef PartitionScanTuple PartitionScanTuple; + + // Thread block type for scanning input tiles + typedef BlockPartitionTiles< + BlockPartitionTilesPolicy, + InputIteratorRA, + OutputIteratorRA, + PredicateOp, + SizeT> BlockPartitionTilesT; + + // Shared memory for BlockPartitionTiles + __shared__ typename BlockPartitionTilesT::TempStorage temp_storage; + + // Process tiles + PartitionScanTuple partition_ends; // Ending offsets for partitions (one-after) + bool is_last_tile; // Whether or not this block handled the last tile (i.e., partition_ends is valid for the entire input) + BlockPartitionTilesT(temp_storage, d_in, d_out, d_tile_status + TILE_STATUS_PADDING, pred_op, num_items).ConsumeTiles( + queue, + num_tiles, + partition_ends, + is_last_tile); + + // Record the length of the first partition + if (is_last_tile && (threadIdx.x == 0)) + { + *d_partition_length = partition_ends.x; + } +} + + +#endif // DOXYGEN_SHOULD_SKIP_THIS + + + +/****************************************************************************** + * DeviceReorder + *****************************************************************************/ + +/** + * \addtogroup DeviceModule + * @{ + */ + +/** + * \brief DeviceReorder provides device-wide operations for partitioning and filtering lists of items residing within global memory + */ +struct DeviceReorder +{ +#ifndef DOXYGEN_SHOULD_SKIP_THIS // Do not document + + /****************************************************************************** + * Constants and typedefs + ******************************************************************************/ + + /// Generic structure for encapsulating dispatch properties. Mirrors the constants within BlockPartitionTilesPolicy. + struct KernelDispachParams + { + int block_threads; + int items_per_thread; + BlockScanAlgorithm scan_algorithm; + int tile_size; + + template + __host__ __device__ __forceinline__ + void Init() + { + block_threads = BlockPartitionTilesPolicy::BLOCK_THREADS; + items_per_thread = BlockPartitionTilesPolicy::ITEMS_PER_THREAD; + scan_algorithm = BlockPartitionTilesPolicy::SCAN_ALGORITHM; + tile_size = block_threads * items_per_thread; + } + }; + + + /****************************************************************************** + * Tuning policies + ******************************************************************************/ + + + /// Specializations of tuned policy types for different PTX architectures + template < + int PARTITIONS, + typename T, + typename SizeT, + int ARCH> + struct TunedPolicies; + + /// SM35 tune + template + struct TunedPolicies + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 16, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + typedef BlockPartitionTilesPolicy PartitionPolicy; + }; + + /// SM30 tune + template + struct TunedPolicies + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 9, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + typedef BlockPartitionTilesPolicy PartitionPolicy; + }; + + /// SM20 tune + template + struct TunedPolicies + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 15, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + typedef BlockPartitionTilesPolicy PartitionPolicy; + }; + + /// SM10 tune + template + struct TunedPolicies + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 7, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + typedef BlockPartitionTilesPolicy PartitionPolicy; + }; + + + /// Tuning policy for the PTX architecture that DevicePartition operations will get dispatched to + template + struct PtxDefaultPolicies + { + static const int PTX_TUNE_ARCH = (CUB_PTX_ARCH >= 350) ? + 350 : + (CUB_PTX_ARCH >= 300) ? + 300 : + (CUB_PTX_ARCH >= 200) ? + 200 : + 100; + + // Tuned policy set for the current PTX compiler pass + typedef TunedPolicies PtxTunedPolicies; + + // PartitionPolicy that opaquely derives from the specialization corresponding to the current PTX compiler pass + struct PartitionPolicy : PtxTunedPolicies::PartitionPolicy {}; + + /** + * Initialize dispatch params with the policies corresponding to the PTX assembly we will use + */ + static void InitDispatchParams(int ptx_version, KernelDispachParams &scan_dispatch_params) + { + if (ptx_version >= 350) + { + typedef TunedPolicies TunedPolicies; + scan_dispatch_params.Init(); + } + else if (ptx_version >= 300) + { + typedef TunedPolicies TunedPolicies; + scan_dispatch_params.Init(); + } + else if (ptx_version >= 200) + { + typedef TunedPolicies TunedPolicies; + scan_dispatch_params.Init(); + } + else + { + typedef TunedPolicies TunedPolicies; + scan_dispatch_params.Init(); + } + } + }; + + + /****************************************************************************** + * Utility methods + ******************************************************************************/ + + /** + * Internal dispatch routine + */ + template < + typename ScanInitKernelPtr, ///< Function type of cub::ScanInitKernel + typename PartitionKernelPtr, ///< Function type of cub::PartitionKernel + typename InputIteratorRA, ///< Random-access iterator type for input (may be a simple pointer type) + typename OutputIteratorRA, ///< Random-access iterator type for output (may be a simple pointer type) + typename LengthOutputIterator, ///< Output iterator type for recording the length of the first partition (may be a simple pointer type) + typename PredicateOp, ///< Unary predicate operator indicating membership in the first partition type having member bool operator()(const T &val) + typename SizeT> ///< Integer type used for global array indexing + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + int ptx_version, ///< [in] PTX version + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is returned in \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Size in bytes of \p d_temp_storage allocation. + ScanInitKernelPtr init_kernel, ///< [in] Kernel function pointer to parameterization of cub::PartitionInitKernel + PartitionKernelPtr partition_kernel, ///< [in] Kernel function pointer to parameterization of cub::PartitionKernel + KernelDispachParams &scan_dispatch_params, ///< [in] Dispatch parameters that match the policy that \p partition_kernel was compiled for + InputIteratorRA d_in, ///< [in] Iterator pointing to scan input + OutputIteratorRA d_out, ///< [in] Iterator pointing to scan output + LengthOutputIterator d_partition_length, ///< [out] Output iterator referencing the location where the pivot offset (i.e., the length of the first partition) is to be recorded + PredicateOp pred_op, ///< [in] Unary predicate operator indicating membership in the first partition + SizeT num_items, ///< [in] Total number of items to partition + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool stream_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Default is \p false. + { + +#ifndef CUB_RUNTIME_ENABLED + + // Kernel launch not supported from this device + return CubDebug(cudaErrorNotSupported); + +#else + + enum + { + TILE_STATUS_PADDING = 32, + }; + + // Data type + typedef typename std::iterator_traits::value_type T; + + // Scan tuple type and tile status descriptor type + typedef typename VectorHelper::Type ScanTuple; + typedef ScanTileDescriptor ScanTileDescriptorT; + + cudaError error = cudaSuccess; + do + { + // Number of input tiles + int num_tiles = (num_items + scan_dispatch_params.tile_size - 1) / scan_dispatch_params.tile_size; + + // Temporary storage allocation requirements + void* allocations[2]; + size_t allocation_sizes[2] = + { + (num_tiles + TILE_STATUS_PADDING) * sizeof(ScanTileDescriptorT), // bytes needed for tile status descriptors + GridQueue::AllocationSize() // bytes needed for grid queue descriptor + }; + + // Alias temporaries (or set the necessary size of the storage allocation) + if (CubDebug(error = AliasTemporaries(d_temp_storage, temp_storage_bytes, allocations, allocation_sizes))) break; + + // Return if the caller is simply requesting the size of the storage allocation + if (d_temp_storage == NULL) + return cudaSuccess; + + // Global list of tile status + ScanTileDescriptorT *d_tile_status = (ScanTileDescriptorT*) allocations[0]; + + // Grid queue descriptor + GridQueue queue(allocations[1]); + + // Log init_kernel configuration + int init_kernel_threads = 128; + int init_grid_size = (num_tiles + init_kernel_threads - 1) / init_kernel_threads; + if (stream_synchronous) CubLog("Invoking init_kernel<<<%d, %d, 0, %lld>>>()\n", init_grid_size, init_kernel_threads, (long long) stream); + + // Invoke init_kernel to initialize tile descriptors and queue descriptors + init_kernel<<>>( + queue, + d_tile_status, + num_tiles); + + // Sync the stream if specified + if (stream_synchronous && (CubDebug(error = SyncStream(stream)))) break; + + // Get grid size for multi-block kernel + int scan_grid_size; + int multi_sm_occupancy = -1; + if (ptx_version < 200) + { + // We don't have atomics (or don't have fast ones), so just assign one + // block per tile (limited to 65K tiles) + scan_grid_size = num_tiles; + } + else + { + // We have atomics and can thus reuse blocks across multiple tiles using a queue descriptor. + // Get GPU id + int device_ordinal; + if (CubDebug(error = cudaGetDevice(&device_ordinal))) break; + + // Get SM count + int sm_count; + if (CubDebug(error = cudaDeviceGetAttribute (&sm_count, cudaDevAttrMultiProcessorCount, device_ordinal))) break; + + // Get a rough estimate of partition_kernel SM occupancy based upon the maximum SM occupancy of the targeted PTX architecture + multi_sm_occupancy = CUB_MIN( + ArchProps::MAX_SM_THREADBLOCKS, + ArchProps::MAX_SM_THREADS / scan_dispatch_params.block_threads); + +#ifndef __CUDA_ARCH__ + // We're on the host, so come up with a + Device device_props; + if (CubDebug(error = device_props.Init(device_ordinal))) break; + + if (CubDebug(error = device_props.MaxSmOccupancy( + multi_sm_occupancy, + partition_kernel, + scan_dispatch_params.block_threads))) break; +#endif + // Get device occupancy for partition_kernel + int scan_occupancy = multi_sm_occupancy * sm_count; + + // Get grid size for partition_kernel + scan_grid_size = (num_tiles < scan_occupancy) ? + num_tiles : // Not enough to fill the device with threadblocks + scan_occupancy; // Fill the device with threadblocks + } + + // Log partition_kernel configuration + if (stream_synchronous) CubLog("Invoking partition_kernel<<<%d, %d, 0, %lld>>>(), %d items per thread, %d SM occupancy\n", + scan_grid_size, scan_dispatch_params.block_threads, (long long) stream, scan_dispatch_params.items_per_thread, multi_sm_occupancy); + + // Invoke partition_kernel + partition_kernel<<>>( + d_in, + d_out, + d_partition_length, + d_tile_status, + pred_op, + num_items, + num_tiles, + queue); + + // Sync the stream if specified + if (stream_synchronous && (CubDebug(error = SyncStream(stream)))) break; + } + while (0); + + return error; + +#endif // CUB_RUNTIME_ENABLED + } + + + + /** + * Internal partition dispatch routine for using default tuning policies + */ + template < + typename PARTITIONS, ///< Number of partitions we are keeping + typename InputIteratorRA, ///< Random-access iterator type for input (may be a simple pointer type) + typename OutputIteratorRA, ///< Random-access iterator type for output (may be a simple pointer type) + typename LengthOutputIterator, ///< Output iterator type for recording the length of the first partition (may be a simple pointer type) + typename PredicateOp, ///< Unary predicate operator indicating membership in the first partition type having member bool operator()(const T &val) + typename SizeT> ///< Integer type used for global array indexing + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is returned in \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Size in bytes of \p d_temp_storage allocation. + InputIteratorRA d_in, ///< [in] Iterator pointing to input items + OutputIteratorRA d_out, ///< [in] Iterator pointing to output items + LengthOutputIterator d_partition_length, ///< [out] Output iterator referencing the location where the pivot offset (i.e., the length of the first partition) is to be recorded + PredicateOp pred_op, ///< [in] Unary predicate operator indicating membership in the first partition + SizeT num_items, ///< [in] Total number of items to partition + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool stream_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Default is \p false. + { + // Data type + typedef typename std::iterator_traits::value_type T; + + // Tuning polices + typedef PtxDefaultPolicies PtxDefaultPolicies; // Wrapper of default kernel policies + typedef typename PtxDefaultPolicies::PartitionPolicy PartitionPolicy; // Partition kernel policy + + cudaError error = cudaSuccess; + do + { + // Declare dispatch parameters + KernelDispachParams scan_dispatch_params; + + int ptx_version; +#ifdef __CUDA_ARCH__ + // We're on the device, so initialize the dispatch parameters with the PtxDefaultPolicies directly + scan_dispatch_params.Init(); + ptx_version = CUB_PTX_ARCH; +#else + // We're on the host, so lookup and initialize the dispatch parameters with the policies that match the device's PTX version + if (CubDebug(error = PtxVersion(ptx_version))) break; + PtxDefaultPolicies::InitDispatchParams(ptx_version, scan_dispatch_params); +#endif + + Dispatch( + ptx_version, + d_temp_storage, + temp_storage_bytes, + ScanInitKernel, + PartitionKernel, + scan_dispatch_params, + d_in, + d_out, + d_partition_length, + pred_op, + num_items, + stream, + stream_synchronous); + + if (CubDebug(error)) break; + } + while (0); + + return error; + } + + #endif // DOXYGEN_SHOULD_SKIP_THIS + + + /** + * \brief Splits a list of input items into two partitions within the given output list using the specified predicate. The relative ordering of inputs is not necessarily preserved. + * + * An item \p val is placed in the first partition if pred_op(val) == true, otherwise + * it is placed in the second partition. The offset of the partitioning pivot (equivalent to + * the total length of the first partition as well as the starting offset of the second), is + * recorded to \p d_partition_length. + * + * The length of the output referenced by \p d_out is assumed to be the same as that of \p d_in. + * + * \devicestorage + * + * \tparam InputIteratorRA [inferred] Random-access iterator type for input (may be a simple pointer type) + * \tparam OutputIteratorRA [inferred] Random-access iterator type for output (may be a simple pointer type) + * \tparam LengthOutputIterator [inferred] Random-access iterator type for output (may be a simple pointer type) + * \tparam PredicateOp [inferred] Unary predicate operator indicating membership in the first partition type having member bool operator()(const T &val) + */ + template < + typename InputIteratorRA, + typename OutputIteratorRA, + typename LengthOutputIterator, + typename PredicateOp> + __host__ __device__ __forceinline__ + static cudaError_t Partition( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is returned in \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Size in bytes of \p d_temp_storage allocation. + InputIteratorRA d_in, ///< [in] Iterator pointing to input items + OutputIteratorRA d_out, ///< [in] Iterator pointing to output items + LengthOutputIterator d_pivot_offset, ///< [out] Output iterator referencing the location where the pivot offset is to be recorded + PredicateOp pred_op, ///< [in] Unary predicate operator indicating membership in the first partition + int num_items, ///< [in] Total number of items to partition + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool stream_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + typedef typename std::iterator_traits::value_type T; + return Dispatch(d_temp_storage, temp_storage_bytes, d_in, d_out, Sum(), T(), num_items, stream, stream_synchronous); + } + + +}; + + +/** @} */ // DeviceModule + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_scan.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_scan.cuh new file mode 100644 index 0000000000000000000000000000000000000000..3ead95740ffc28aa9565deb889f9a9083017e081 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_scan.cuh @@ -0,0 +1,419 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DeviceScan provides device-wide, parallel operations for computing a prefix scan across a sequence of data items residing within global memory. + */ + +#pragma once + +#include +#include + +#include "dispatch/device_scan_dispatch.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \brief DeviceScan provides device-wide, parallel operations for computing a prefix scan across a sequence of data items residing within global memory. ![](device_scan.png) + * \ingroup DeviceModule + * + * \par Overview + * Given a sequence of input elements and a binary reduction operator, a [prefix scan](http://en.wikipedia.org/wiki/Prefix_sum) + * produces an output sequence where each element is computed to be the reduction + * of the elements occurring earlier in the input sequence. Prefix sum + * connotes a prefix scan with the addition operator. The term \em inclusive indicates + * that the ith output reduction incorporates the ith input. + * The term \em exclusive indicates the ith input is not incorporated into + * the ith output reduction. + * + * \par Usage Considerations + * \cdp_class{DeviceScan} + * + * \par Performance + * \linear_performance{prefix scan} + * + * \par + * The following chart illustrates DeviceScan::ExclusiveSum + * performance across different CUDA architectures for \p int32 keys. + * \plots_below + * + * \image html scan_int32.png + * + */ +struct DeviceScan +{ + /******************************************************************//** + * \name Exclusive scans + *********************************************************************/ + //@{ + + /** + * \brief Computes a device-wide exclusive prefix sum. + * + * \par + * - Supports non-commutative sum operators. + * - \devicestorage + * - \cdp + * + * \par Performance + * The following charts illustrate saturated exclusive sum performance across different + * CUDA architectures for \p int32 and \p int64 items, respectively. + * + * \image html scan_int32.png + * \image html scan_int64.png + * + * \par Snippet + * The code snippet below illustrates the exclusive prefix sum of an \p int device vector. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 7 + * int *d_in; // e.g., [8, 6, 7, 5, 3, 0, 9] + * int *d_out; // e.g., [ , , , , , , ] + * ... + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceScan::ExclusiveSum(d_temp_storage, temp_storage_bytes, d_in, d_out, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run exclusive prefix sum + * cub::DeviceScan::ExclusiveSum(d_temp_storage, temp_storage_bytes, d_in, d_out, num_items); + * + * // d_out s<-- [0, 8, 14, 21, 26, 29, 29] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading scan input data \iterator + * \tparam OutputIterator [inferred] Random-access output iterator type for writing scan output data \iterator + */ + template < + typename InputIterator, + typename OutputIterator> + __host__ __device__ + static cudaError_t ExclusiveSum( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output sequence of data items + int num_items, ///< [in] Total number of input items (i.e., the length of \p d_in) + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + // Scan data type + typedef typename std::iterator_traits::value_type T; + + return DeviceScanDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + d_out, + Sum(), + T(), + num_items, + stream, + debug_synchronous); + } + + + /** + * \brief Computes a device-wide exclusive prefix scan using the specified binary \p scan_op functor. + * + * \par + * - Supports non-commutative scan operators. + * - \devicestorage + * - \cdp + * + * \par Performance + * Performance is typically similar to DeviceScan::ExclusiveSum. + * + * \par Snippet + * The code snippet below illustrates the exclusive prefix min-scan of an \p int device vector + * \par + * \code + * #include // or equivalently + * + * // CustomMin functor + * struct CustomMin + * { + * template + * __host__ __device__ __forceinline__ + * T operator()(const T &a, const T &b) const { + * return (b < a) ? b : a; + * } + * }; + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 7 + * int *d_in; // e.g., [8, 6, 7, 5, 3, 0, 9] + * int *d_out; // e.g., [ , , , , , , ] + * CustomMin min_op + * ... + * + * // Determine temporary device storage requirements for exclusive prefix scan + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceScan::ExclusiveScan(d_temp_storage, temp_storage_bytes, d_in, d_out, min_op, (int) MAX_INT, num_items); + * + * // Allocate temporary storage for exclusive prefix scan + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run exclusive prefix min-scan + * cub::DeviceScan::ExclusiveScan(d_temp_storage, temp_storage_bytes, d_in, d_out, min_op, (int) MAX_INT, num_items); + * + * // d_out <-- [2147483647, 8, 6, 6, 5, 3, 0] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading scan input data \iterator + * \tparam OutputIterator [inferred] Random-access output iterator type for writing scan output data \iterator + * \tparam ScanOp [inferred] Binary scan functor type having member T operator()(const T &a, const T &b) + * \tparam Identity [inferred] Type of the \p identity value used Binary scan functor type having member T operator()(const T &a, const T &b) + */ + template < + typename InputIterator, + typename OutputIterator, + typename ScanOp, + typename Identity> + __host__ __device__ + static cudaError_t ExclusiveScan( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output sequence of data items + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + Identity identity, ///< [in] Identity element + int num_items, ///< [in] Total number of input items (i.e., the length of \p d_in) + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + return DeviceScanDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + d_out, + scan_op, + identity, + num_items, + stream, + debug_synchronous); + } + + + //@} end member group + /******************************************************************//** + * \name Inclusive scans + *********************************************************************/ + //@{ + + + /** + * \brief Computes a device-wide inclusive prefix sum. + * + * \par + * - Supports non-commutative sum operators. + * - \devicestorage + * - \cdp + * + * \par Performance + * Performance is typically similar to DeviceScan::ExclusiveSum. + * + * \par Snippet + * The code snippet below illustrates the inclusive prefix sum of an \p int device vector. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 7 + * int *d_in; // e.g., [8, 6, 7, 5, 3, 0, 9] + * int *d_out; // e.g., [ , , , , , , ] + * ... + * + * // Determine temporary device storage requirements for inclusive prefix sum + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceScan::InclusiveSum(d_temp_storage, temp_storage_bytes, d_in, d_out, num_items); + * + * // Allocate temporary storage for inclusive prefix sum + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run inclusive prefix sum + * cub::DeviceScan::InclusiveSum(d_temp_storage, temp_storage_bytes, d_in, d_out, num_items); + * + * // d_out <-- [8, 14, 21, 26, 29, 29, 38] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading scan input data \iterator + * \tparam OutputIterator [inferred] Random-access output iterator type for writing scan output data \iterator + */ + template < + typename InputIterator, + typename OutputIterator> + __host__ __device__ + static cudaError_t InclusiveSum( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output sequence of data items + int num_items, ///< [in] Total number of input items (i.e., the length of \p d_in) + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + return DeviceScanDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + d_out, + Sum(), + NullType(), + num_items, + stream, + debug_synchronous); + } + + + /** + * \brief Computes a device-wide inclusive prefix scan using the specified binary \p scan_op functor. + * + * \par + * - Supports non-commutative scan operators. + * - \devicestorage + * - \cdp + * + * \par Performance + * Performance is typically similar to DeviceScan::ExclusiveSum. + * + * \par Snippet + * The code snippet below illustrates the inclusive prefix min-scan of an \p int device vector. + * \par + * \code + * #include // or equivalently + * + * // CustomMin functor + * struct CustomMin + * { + * template + * __host__ __device__ __forceinline__ + * T operator()(const T &a, const T &b) const { + * return (b < a) ? b : a; + * } + * }; + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 7 + * int *d_in; // e.g., [8, 6, 7, 5, 3, 0, 9] + * int *d_out; // e.g., [ , , , , , , ] + * CustomMin min_op; + * ... + * + * // Determine temporary device storage requirements for inclusive prefix scan + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceScan::InclusiveScan(d_temp_storage, temp_storage_bytes, d_in, d_out, min_op, num_items); + * + * // Allocate temporary storage for inclusive prefix scan + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run inclusive prefix min-scan + * cub::DeviceScan::InclusiveScan(d_temp_storage, temp_storage_bytes, d_in, d_out, min_op, num_items); + * + * // d_out <-- [8, 6, 6, 5, 3, 0, 0] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading scan input data \iterator + * \tparam OutputIterator [inferred] Random-access output iterator type for writing scan output data \iterator + * \tparam ScanOp [inferred] Binary scan functor type having member T operator()(const T &a, const T &b) + */ + template < + typename InputIterator, + typename OutputIterator, + typename ScanOp> + __host__ __device__ + static cudaError_t InclusiveScan( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output sequence of data items + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + int num_items, ///< [in] Total number of input items (i.e., the length of \p d_in) + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + // Signed integer type for global offsets + typedef int Offset; + + return DeviceScanDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + d_out, + scan_op, + NullType(), + num_items, + stream, + debug_synchronous); + } + + //@} end member group + +}; + +/** + * \example example_device_scan.cu + */ + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_select.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_select.cuh new file mode 100644 index 0000000000000000000000000000000000000000..c485cad731febe550e6958aeb5ee081fdd1dc0de --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/device_select.cuh @@ -0,0 +1,372 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DeviceSelect provides device-wide, parallel operations for selecting items from sequences of data items residing within global memory. + */ + +#pragma once + +#include +#include + +#include "dispatch/device_select_dispatch.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \brief DeviceSelect provides device-wide, parallel operations for compacting selected items from sequences of data items residing within global memory. ![](select_logo.png) + * \ingroup DeviceModule + * + * \par Overview + * These operations apply a selection criterion to selectively copy + * items from a specified input sequence to a compact output sequence. + * + * \par Usage Considerations + * \cdp_class{DeviceSelect} + * + * \par Performance + * \linear_performance{select-flagged, select-if, and select-unique} + * + * \par + * The following chart illustrates DeviceSelect::If + * performance across different CUDA architectures for \p int32 items, + * where 50% of the items are randomly selected. + * + * \image html select_if_int32_50_percent.png + * + * \par + * The following chart illustrates DeviceSelect::Unique + * performance across different CUDA architectures for \p int32 items + * where segments have lengths uniformly sampled from [1,1000]. + * + * \image html select_unique_int32_len_500.png + * + * \par + * \plots_below + * + */ +struct DeviceSelect +{ + /** + * \brief Uses the \p d_flags sequence to selectively copy the corresponding items from \p d_in into \p d_out. The total number of items selected is written to \p d_num_selected. ![](select_flags_logo.png) + * + * \par + * - The value type of \p d_flags must be castable to \p bool (e.g., \p bool, \p char, \p int, etc.). + * - Copies of the selected items are compacted into \p d_out and maintain their original relative ordering. + * - \devicestorage + * - \cdp + * + * \par Snippet + * The code snippet below illustrates the compaction of items selected from an \p int device vector. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input, flags, and output + * int num_items; // e.g., 8 + * int *d_in; // e.g., [1, 2, 3, 4, 5, 6, 7, 8] + * char *d_flags; // e.g., [1, 0, 0, 1, 0, 1, 1, 0] + * int *d_out; // e.g., [ , , , , , , , ] + * int *d_num_selected; // e.g., [ ] + * ... + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceSelect::Flagged(d_temp_storage, temp_storage_bytes, d_in, d_flags, d_out, d_num_selected, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run selection + * cub::DeviceSelect::Flagged(d_temp_storage, temp_storage_bytes, d_in, d_flags, d_out, d_num_selected, num_items); + * + * // d_out <-- [1, 4, 6, 7] + * // d_num_selected <-- [4] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading input items \iterator + * \tparam FlagIterator [inferred] Random-access input iterator type for reading selection flags \iterator + * \tparam OutputIterator [inferred] Random-access output iterator type for writing selected items \iterator + * \tparam NumSelectedIterator [inferred] Output iterator type for recording the number of items selected \iterator + */ + template < + typename InputIterator, + typename FlagIterator, + typename OutputIterator, + typename NumSelectedIterator> + __host__ __device__ __forceinline__ + static cudaError_t Flagged( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + FlagIterator d_flags, ///< [in] Pointer to the input sequence of selection flags + OutputIterator d_out, ///< [out] Pointer to the output sequence of selected data items + NumSelectedIterator d_num_selected, ///< [out] Pointer to the output total number of items selected (i.e., length of \p d_out) + int num_items, ///< [in] Total number of input items (i.e., length of \p d_in) + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + typedef int Offset; // Signed integer type for global offsets + typedef NullType SelectOp; // Selection op (not used) + typedef NullType EqualityOp; // Equality operator (not used) + + return DeviceSelectDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + d_flags, + d_out, + d_num_selected, + SelectOp(), + EqualityOp(), + num_items, + stream, + debug_synchronous); + } + + + /** + * \brief Uses the \p select_op functor to selectively copy items from \p d_in into \p d_out. The total number of items selected is written to \p d_num_selected. ![](select_logo.png) + * + * \par + * - Copies of the selected items are compacted into \p d_out and maintain their original relative ordering. + * - \devicestorage + * - \cdp + * + * \par Performance + * The following charts illustrate saturated select-if performance across different + * CUDA architectures for \p int32 and \p int64 items, respectively. Items are + * selected with 50% probability. + * + * \image html select_if_int32_50_percent.png + * \image html select_if_int64_50_percent.png + * + * \par + * The following charts are similar, but 5% selection probability: + * + * \image html select_if_int32_5_percent.png + * \image html select_if_int64_5_percent.png + * + * \par Snippet + * The code snippet below illustrates the compaction of items selected from an \p int device vector. + * \par + * \code + * #include // or equivalently + * + * // Functor type for selecting values less than some criteria + * struct LessThan + * { + * int compare; + * + * __host__ __device__ __forceinline__ + * LessThan(int compare) : compare(compare) {} + * + * __host__ __device__ __forceinline__ + * bool operator()(const int &a) const { + * return (a < compare); + * } + * }; + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 8 + * int *d_in; // e.g., [0, 2, 3, 9, 5, 2, 81, 8] + * int *d_out; // e.g., [ , , , , , , , ] + * int *d_num_selected; // e.g., [ ] + * LessThan select_op(7); + * ... + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceSelect::If(d_temp_storage, temp_storage_bytes, d_in, d_out, d_num_selected, num_items, select_op); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run selection + * cub::DeviceSelect::If(d_temp_storage, temp_storage_bytes, d_in, d_out, d_num_selected, num_items, select_op); + * + * // d_out <-- [0, 2, 3, 5, 2] + * // d_num_selected <-- [5] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading input items \iterator + * \tparam OutputIterator [inferred] Random-access output iterator type for writing selected items \iterator + * \tparam NumSelectedIterator [inferred] Output iterator type for recording the number of items selected \iterator + * \tparam SelectOp [inferred] Selection operator type having member bool operator()(const T &a) + */ + template < + typename InputIterator, + typename OutputIterator, + typename NumSelectedIterator, + typename SelectOp> + __host__ __device__ __forceinline__ + static cudaError_t If( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output sequence of selected data items + NumSelectedIterator d_num_selected, ///< [out] Pointer to the output total number of items selected (i.e., length of \p d_out) + int num_items, ///< [in] Total number of input items (i.e., length of \p d_in) + SelectOp select_op, ///< [in] Unary selection operator + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + typedef int Offset; // Signed integer type for global offsets + typedef NullType* FlagIterator; // Flag iterator type (not used) + typedef NullType EqualityOp; // Equality operator (not used) + + return DeviceSelectDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + NULL, + d_out, + d_num_selected, + select_op, + EqualityOp(), + num_items, + stream, + debug_synchronous); + } + + + /** + * \brief Given an input sequence \p d_in having runs of consecutive equal-valued keys, only the first key from each run is selectively copied to \p d_out. The total number of items selected is written to \p d_num_selected. ![](unique_logo.png) + * + * \par + * - The == equality operator is used to determine whether keys are equivalent + * - Copies of the selected items are compacted into \p d_out and maintain their original relative ordering. + * - \devicestorage + * - \cdp + * + * \par Performance + * The following charts illustrate saturated select-unique performance across different + * CUDA architectures for \p int32 and \p int64 items, respectively. Segments have + * lengths uniformly sampled from [1,1000]. + * + * \image html select_unique_int32_len_500.png + * \image html select_unique_int64_len_500.png + * + * \par + * The following charts are similar, but with segment lengths uniformly sampled from [1,10]: + * + * \image html select_unique_int32_len_5.png + * \image html select_unique_int64_len_5.png + * + * \par Snippet + * The code snippet below illustrates the compaction of items selected from an \p int device vector. + * \par + * \code + * #include // or equivalently + * + * // Declare, allocate, and initialize device pointers for input and output + * int num_items; // e.g., 8 + * int *d_in; // e.g., [0, 2, 2, 9, 5, 5, 5, 8] + * int *d_out; // e.g., [ , , , , , , , ] + * int *d_num_selected; // e.g., [ ] + * ... + * + * // Determine temporary device storage requirements + * void *d_temp_storage = NULL; + * size_t temp_storage_bytes = 0; + * cub::DeviceSelect::Unique(d_temp_storage, temp_storage_bytes, d_in, d_out, d_num_selected, num_items); + * + * // Allocate temporary storage + * cudaMalloc(&d_temp_storage, temp_storage_bytes); + * + * // Run selection + * cub::DeviceSelect::Unique(d_temp_storage, temp_storage_bytes, d_in, d_out, d_num_selected, num_items); + * + * // d_out <-- [0, 2, 9, 5, 8] + * // d_num_selected <-- [5] + * + * \endcode + * + * \tparam InputIterator [inferred] Random-access input iterator type for reading input items \iterator + * \tparam OutputIterator [inferred] Random-access output iterator type for writing selected items \iterator + * \tparam NumSelectedIterator [inferred] Output iterator type for recording the number of items selected \iterator + */ + template < + typename InputIterator, + typename OutputIterator, + typename NumSelectedIterator> + __host__ __device__ __forceinline__ + static cudaError_t Unique( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output sequence of selected data items + NumSelectedIterator d_num_selected, ///< [out] Pointer to the output total number of items selected (i.e., length of \p d_out) + int num_items, ///< [in] Total number of input items (i.e., length of \p d_in) + cudaStream_t stream = 0, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous = false) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. May cause significant slowdown. Default is \p false. + { + typedef int Offset; // Signed integer type for global offsets + typedef NullType* FlagIterator; // Flag iterator type (not used) + typedef NullType SelectOp; // Selection op (not used) + typedef Equality EqualityOp; // Default == operator + + return DeviceSelectDispatch::Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + NULL, + d_out, + d_num_selected, + SelectOp(), + EqualityOp(), + num_items, + stream, + debug_synchronous); + } + +}; + +/** + * \example example_device_select_flagged.cu + * \example example_device_select_if.cu + * \example example_device_select_unique.cu + */ + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_histogram_dispatch.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_histogram_dispatch.cuh new file mode 100644 index 0000000000000000000000000000000000000000..8022902caeca69d94b09dbb08563a4fe86c8a35b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_histogram_dispatch.cuh @@ -0,0 +1,545 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DeviceHistogram provides device-wide parallel operations for constructing histogram(s) from a sequence of samples data residing within global memory. + */ + +#pragma once + +#include +#include + +#include "../block_region/block_region_histo.cuh" +#include "../../grid/grid_even_share.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../util_debug.cuh" +#include "../../util_device.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/****************************************************************************** + * Kernel entry points + *****************************************************************************/ + +/** + * Initialization kernel entry point (multi-block). Prepares queue descriptors and zeroes global counters. + */ +template < + int BINS, ///< Number of histogram bins per channel + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename Offset, ///< Signed integer type for global offsets + typename HistoCounter> ///< Integer type for counting sample occurrences per histogram bin +__launch_bounds__ (BINS, 1) +__global__ void HistoInitKernel( + GridQueue grid_queue, ///< [in] Drain queue descriptor for dynamically mapping tile data onto thread blocks + ArrayWrapper d_out_histograms, ///< [out] Histogram counter data having logical dimensions HistoCounter[ACTIVE_CHANNELS][BINS] + Offset num_samples) ///< [in] Total number of samples \p d_samples for all channels +{ + d_out_histograms.array[blockIdx.x][threadIdx.x] = 0; + if (threadIdx.x == 0) grid_queue.FillAndResetDrain(num_samples); +} + + +/** + * Histogram tiles kernel entry point (multi-block). Computes privatized histograms, one per thread block. + */ +template < + typename BlockRegionHistogramPolicy, ///< Parameterized BlockRegionHistogramPolicy tuning policy type + int BINS, ///< Number of histogram bins per channel + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of channels being actively histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIterator, ///< The input iterator type \iterator. Must have a value type that is assignable to unsigned char + typename HistoCounter, ///< Integer type for counting sample occurrences per histogram bin + typename Offset> ///< Signed integer type for global offsets +__launch_bounds__ (int(BlockRegionHistogramPolicy::BLOCK_THREADS)) +__global__ void HistoRegionKernel( + InputIterator d_samples, ///< [in] Array of sample data. The samples from different channels are assumed to be interleaved (e.g., an array of 32b pixels where each pixel consists of four RGBA 8b samples). + ArrayWrapper d_out_histograms, ///< [out] Histogram counter data having logical dimensions HistoCounter[ACTIVE_CHANNELS][gridDim.x][BINS] + Offset num_samples, ///< [in] Total number of samples \p d_samples for all channels + GridEvenShare even_share, ///< [in] Even-share descriptor for mapping an equal number of tiles onto each thread block + GridQueue queue) ///< [in] Drain queue descriptor for dynamically mapping tile data onto thread blocks +{ + // Constants + enum + { + BLOCK_THREADS = BlockRegionHistogramPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockRegionHistogramPolicy::ITEMS_PER_THREAD, + TILE_SIZE = BLOCK_THREADS * ITEMS_PER_THREAD, + }; + + // Thread block type for compositing input tiles + typedef BlockRegionHistogram BlockRegionHistogramT; + + // Shared memory for BlockRegionHistogram + __shared__ typename BlockRegionHistogramT::TempStorage temp_storage; + + // Consume input tiles + BlockRegionHistogramT(temp_storage, d_samples, d_out_histograms.array).ConsumeRegion( + num_samples, + even_share, + queue, + Int2Type()); +} + + +/** + * Aggregation kernel entry point (single-block). Aggregates privatized threadblock histograms from a previous multi-block histogram pass. + */ +template < + int BINS, ///< Number of histogram bins per channel + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename HistoCounter> ///< Integer type for counting sample occurrences per histogram bin +__launch_bounds__ (BINS, 1) +__global__ void HistoAggregateKernel( + HistoCounter* d_block_histograms, ///< [in] Histogram counter data having logical dimensions HistoCounter[ACTIVE_CHANNELS][num_threadblocks][BINS] + ArrayWrapper d_out_histograms, ///< [out] Histogram counter data having logical dimensions HistoCounter[ACTIVE_CHANNELS][BINS] + int num_threadblocks) ///< [in] Number of threadblock histograms per channel in \p d_block_histograms +{ + // Accumulate threadblock-histograms from the channel + HistoCounter bin_aggregate = 0; + + int block_offset = blockIdx.x * (num_threadblocks * BINS); + int block_end = block_offset + (num_threadblocks * BINS); + +#if CUB_PTX_VERSION >= 200 + #pragma unroll 32 +#endif + while (block_offset < block_end) + { + HistoCounter block_bin_count = d_block_histograms[block_offset + threadIdx.x]; + + bin_aggregate += block_bin_count; + block_offset += BINS; + } + + // Output + d_out_histograms.array[blockIdx.x][threadIdx.x] = bin_aggregate; +} + + + +/****************************************************************************** + * Dispatch + ******************************************************************************/ + +/** + * Utility class for dispatching the appropriately-tuned kernels for DeviceHistogram + */ +template < + DeviceHistogramAlgorithm HISTO_ALGORITHM, ///< Cooperative histogram algorithm to use + int BINS, ///< Number of histogram bins per channel + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of channels being actively histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIterator, ///< The input iterator type \iterator. Must have a value type that is assignable to unsigned char + typename HistoCounter, ///< Integer type for counting sample occurrences per histogram bin + typename Offset> ///< Signed integer type for global offsets +struct DeviceHistogramDispatch +{ + /****************************************************************************** + * Tuning policies + ******************************************************************************/ + + /// SM35 + struct Policy350 + { + // HistoRegionPolicy + typedef BlockRegionHistogramPolicy< + (HISTO_ALGORITHM == DEVICE_HISTO_SORT) ? 128 : 256, + (HISTO_ALGORITHM == DEVICE_HISTO_SORT) ? 12 : (30 / ACTIVE_CHANNELS), + HISTO_ALGORITHM, + (HISTO_ALGORITHM == DEVICE_HISTO_SORT) ? GRID_MAPPING_DYNAMIC : GRID_MAPPING_EVEN_SHARE> + HistoRegionPolicy; + }; + + /// SM30 + struct Policy300 + { + // HistoRegionPolicy + typedef BlockRegionHistogramPolicy< + 128, + (HISTO_ALGORITHM == DEVICE_HISTO_SORT) ? 20 : (22 / ACTIVE_CHANNELS), + HISTO_ALGORITHM, + (HISTO_ALGORITHM == DEVICE_HISTO_SORT) ? GRID_MAPPING_DYNAMIC : GRID_MAPPING_EVEN_SHARE> + HistoRegionPolicy; + }; + + /// SM20 + struct Policy200 + { + // HistoRegionPolicy + typedef BlockRegionHistogramPolicy< + 128, + (HISTO_ALGORITHM == DEVICE_HISTO_SORT) ? 21 : (23 / ACTIVE_CHANNELS), + HISTO_ALGORITHM, + GRID_MAPPING_DYNAMIC> + HistoRegionPolicy; + }; + + /// SM10 + struct Policy100 + { + // HistoRegionPolicy + typedef BlockRegionHistogramPolicy< + 128, + 7, + DEVICE_HISTO_SORT, // (use sort regardless because g-atomics are unsupported and s-atomics are perf-useless) + GRID_MAPPING_EVEN_SHARE> + HistoRegionPolicy; + }; + + + /****************************************************************************** + * Tuning policies of current PTX compiler pass + ******************************************************************************/ + +#if (CUB_PTX_VERSION >= 350) + typedef Policy350 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 300) + typedef Policy300 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 200) + typedef Policy200 PtxPolicy; + +#else + typedef Policy100 PtxPolicy; + +#endif + + // "Opaque" policies (whose parameterizations aren't reflected in the type signature) + struct PtxHistoRegionPolicy : PtxPolicy::HistoRegionPolicy {}; + + + /****************************************************************************** + * Utilities + ******************************************************************************/ + + /** + * Initialize kernel dispatch configurations with the policies corresponding to the PTX assembly we will use + */ + template + __host__ __device__ __forceinline__ + static void InitConfigs( + int ptx_version, + KernelConfig &histo_region_config) + { + #if (CUB_PTX_VERSION > 0) + + // We're on the device, so initialize the kernel dispatch configurations with the current PTX policy + histo_region_config.template Init(); + + #else + + // We're on the host, so lookup and initialize the kernel dispatch configurations with the policies that match the device's PTX version + if (ptx_version >= 350) + { + histo_region_config.template Init(); + } + else if (ptx_version >= 300) + { + histo_region_config.template Init(); + } + else if (ptx_version >= 200) + { + histo_region_config.template Init(); + } + else + { + histo_region_config.template Init(); + } + + #endif + } + + + /** + * Kernel kernel dispatch configuration + */ + struct KernelConfig + { + int block_threads; + int items_per_thread; + DeviceHistogramAlgorithm block_algorithm; + GridMappingStrategy grid_mapping; + + template + __host__ __device__ __forceinline__ + void Init() + { + block_threads = BlockPolicy::BLOCK_THREADS; + items_per_thread = BlockPolicy::ITEMS_PER_THREAD; + block_algorithm = BlockPolicy::HISTO_ALGORITHM; + grid_mapping = BlockPolicy::GRID_MAPPING; + } + + __host__ __device__ __forceinline__ + void Print() + { + printf("%d, %d, %d, %d", block_threads, items_per_thread, block_algorithm, grid_mapping); + } + + }; + + + /****************************************************************************** + * Dispatch entrypoints + ******************************************************************************/ + + + /** + * Internal dispatch routine + */ + template < + typename InitHistoKernelPtr, ///< Function type of cub::HistoInitKernel + typename HistoRegionKernelPtr, ///< Function type of cub::HistoRegionKernel + typename AggregateHistoKernelPtr> ///< Function type of cub::HistoAggregateKernel + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_samples, ///< [in] Input samples to histogram + HistoCounter *d_histograms[ACTIVE_CHANNELS], ///< [out] Array of channel histograms, each having BINS counters of integral type \p HistoCounter. + Offset num_samples, ///< [in] Number of samples to process + cudaStream_t stream, ///< [in] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous, ///< [in] Whether or not to synchronize the stream after every kernel launch to check for errors. Default is \p false. + InitHistoKernelPtr init_kernel, ///< [in] Kernel function pointer to parameterization of cub::HistoInitKernel + HistoRegionKernelPtr histo_region_kernel, ///< [in] Kernel function pointer to parameterization of cub::HistoRegionKernel + AggregateHistoKernelPtr aggregate_kernel, ///< [in] Kernel function pointer to parameterization of cub::HistoAggregateKernel + KernelConfig histo_region_config) ///< [in] Dispatch parameters that match the policy that \p histo_region_kernel was compiled for + { + #ifndef CUB_RUNTIME_ENABLED + + // Kernel launch not supported from this device + return CubDebug(cudaErrorNotSupported); + + #else + + cudaError error = cudaSuccess; + do + { + // Get device ordinal + int device_ordinal; + if (CubDebug(error = cudaGetDevice(&device_ordinal))) break; + + // Get device SM version + int sm_version; + if (CubDebug(error = SmVersion(sm_version, device_ordinal))) break; + + // Get SM count + int sm_count; + if (CubDebug(error = cudaDeviceGetAttribute (&sm_count, cudaDevAttrMultiProcessorCount, device_ordinal))) break; + + // Get SM occupancy for histo_region_kernel + int histo_region_sm_occupancy; + if (CubDebug(error = MaxSmOccupancy( + histo_region_sm_occupancy, + sm_version, + histo_region_kernel, + histo_region_config.block_threads))) break; + + // Get device occupancy for histo_region_kernel + int histo_region_occupancy = histo_region_sm_occupancy * sm_count; + + // Get tile size for histo_region_kernel + int channel_tile_size = histo_region_config.block_threads * histo_region_config.items_per_thread; + int tile_size = channel_tile_size * CHANNELS; + + // Even-share work distribution + int subscription_factor = histo_region_sm_occupancy; // Amount of CTAs to oversubscribe the device beyond actively-resident (heuristic) + GridEvenShare even_share( + num_samples, + histo_region_occupancy * subscription_factor, + tile_size); + + // Get grid size for histo_region_kernel + int histo_region_grid_size; + switch (histo_region_config.grid_mapping) + { + case GRID_MAPPING_EVEN_SHARE: + + // Work is distributed evenly + histo_region_grid_size = even_share.grid_size; + break; + + case GRID_MAPPING_DYNAMIC: + + // Work is distributed dynamically + int num_tiles = (num_samples + tile_size - 1) / tile_size; + histo_region_grid_size = (num_tiles < histo_region_occupancy) ? + num_tiles : // Not enough to fill the device with threadblocks + histo_region_occupancy; // Fill the device with threadblocks + break; + }; + + // Temporary storage allocation requirements + void* allocations[2]; + size_t allocation_sizes[2] = + { + ACTIVE_CHANNELS * histo_region_grid_size * sizeof(HistoCounter) * BINS, // bytes needed for privatized histograms + GridQueue::AllocationSize() // bytes needed for grid queue descriptor + }; + + // Alias the temporary allocations from the single storage blob (or set the necessary size of the blob) + if (CubDebug(error = AliasTemporaries(d_temp_storage, temp_storage_bytes, allocations, allocation_sizes))) break; + if (d_temp_storage == NULL) + { + // Return if the caller is simply requesting the size of the storage allocation + return cudaSuccess; + } + + // Alias the allocation for the privatized per-block reductions + HistoCounter *d_block_histograms = (HistoCounter*) allocations[0]; + + // Alias the allocation for the grid queue descriptor + GridQueue queue(allocations[1]); + + // Setup array wrapper for histogram channel output (because we can't pass static arrays as kernel parameters) + ArrayWrapper d_histo_wrapper; + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + d_histo_wrapper.array[CHANNEL] = d_histograms[CHANNEL]; + + // Setup array wrapper for temporary histogram channel output (because we can't pass static arrays as kernel parameters) + ArrayWrapper d_temp_histo_wrapper; + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + d_temp_histo_wrapper.array[CHANNEL] = d_block_histograms + (CHANNEL * histo_region_grid_size * BINS); + + // Log init_kernel configuration + if (debug_synchronous) CubLog("Invoking init_kernel<<<%d, %d, 0, %lld>>>()\n", ACTIVE_CHANNELS, BINS, (long long) stream); + + // Invoke init_kernel to initialize counters and queue descriptor + init_kernel<<>>(queue, d_histo_wrapper, num_samples); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + + // Whether we need privatized histograms (i.e., non-global atomics and multi-block) + bool privatized_temporaries = (histo_region_grid_size > 1) && (histo_region_config.block_algorithm != DEVICE_HISTO_GLOBAL_ATOMIC); + + // Log histo_region_kernel configuration + if (debug_synchronous) CubLog("Invoking histo_region_kernel<<<%d, %d, 0, %lld>>>(), %d items per thread, %d SM occupancy\n", + histo_region_grid_size, histo_region_config.block_threads, (long long) stream, histo_region_config.items_per_thread, histo_region_sm_occupancy); + + // Invoke histo_region_kernel + histo_region_kernel<<>>( + d_samples, + (privatized_temporaries) ? + d_temp_histo_wrapper : + d_histo_wrapper, + num_samples, + even_share, + queue); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + + // Aggregate privatized block histograms if necessary + if (privatized_temporaries) + { + // Log aggregate_kernel configuration + if (debug_synchronous) CubLog("Invoking aggregate_kernel<<<%d, %d, 0, %lld>>>()\n", + ACTIVE_CHANNELS, BINS, (long long) stream); + + // Invoke aggregate_kernel + aggregate_kernel<<>>( + d_block_histograms, + d_histo_wrapper, + histo_region_grid_size); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + } + } + while (0); + + return error; + + #endif // CUB_RUNTIME_ENABLED + } + + + /** + * Internal dispatch routine + */ + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_samples, ///< [in] Input samples to histogram + HistoCounter *d_histograms[ACTIVE_CHANNELS], ///< [out] Array of channel histograms, each having BINS counters of integral type \p HistoCounter. + int num_samples, ///< [in] Number of samples to process + cudaStream_t stream, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + cudaError error = cudaSuccess; + do + { + // Get PTX version + int ptx_version; + #if (CUB_PTX_VERSION == 0) + if (CubDebug(error = PtxVersion(ptx_version))) break; + #else + ptx_version = CUB_PTX_VERSION; + #endif + + // Get kernel kernel dispatch configurations + KernelConfig histo_region_config; + InitConfigs(ptx_version, histo_region_config); + + // Dispatch + if (CubDebug(error = Dispatch( + d_temp_storage, + temp_storage_bytes, + d_samples, + d_histograms, + num_samples, + stream, + debug_synchronous, + HistoInitKernel, + HistoRegionKernel, + HistoAggregateKernel, + histo_region_config))) break; + } + while (0); + + return error; + } +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_radix_sort_dispatch.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_radix_sort_dispatch.cuh new file mode 100644 index 0000000000000000000000000000000000000000..e3472e7fd1725c54bcfe4919ff938b4bb23c9d25 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_radix_sort_dispatch.cuh @@ -0,0 +1,924 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DeviceRadixSort provides device-wide, parallel operations for computing a radix sort across a sequence of data items residing within global memory. + */ + +#pragma once + +#include +#include + +#include "../block_region/block_region_radix_sort_upsweep.cuh" +#include "../block_region/block_region_radix_sort_downsweep.cuh" +#include "../block_region/block_region_scan.cuh" +#include "../../grid/grid_even_share.cuh" +#include "../../util_debug.cuh" +#include "../../util_device.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/****************************************************************************** + * Kernel entry points + *****************************************************************************/ + +/** + * Upsweep pass kernel entry point (multi-block). Computes privatized digit histograms, one per block. + */ +template < + typename BlockRegionRadixSortUpsweepPolicy, ///< Parameterized BlockRegionRadixSortUpsweepPolicy tuning policy type + bool DESCENDING, ///< Whether or not the sorted-order is high-to-low + typename Key, ///< Key type + typename Offset> ///< Signed integer type for global offsets +__launch_bounds__ (int(BlockRegionRadixSortUpsweepPolicy::BLOCK_THREADS), 1) +__global__ void RadixSortUpsweepKernel( + Key *d_keys, ///< [in] Input keys buffer + Offset *d_spine, ///< [out] Privatized (per block) digit histograms (striped, i.e., 0s counts from each block, then 1s counts from each block, etc.) + Offset num_items, ///< [in] Total number of input data items + int current_bit, ///< [in] Bit position of current radix digit + bool first_pass, ///< [in] Whether this is the first digit pass + GridEvenShare even_share) ///< [in] Even-share descriptor for mapping an equal number of tiles onto each thread block +{ + // Parameterize BlockRegionRadixSortUpsweep type for the current configuration + typedef BlockRegionRadixSortUpsweep BlockRegionRadixSortUpsweepT; // Primary + + // Shared memory storage + __shared__ typename BlockRegionRadixSortUpsweepT::TempStorage temp_storage; + + // Initialize even-share descriptor for this thread block + even_share.BlockInit(); + + Offset bin_count; + BlockRegionRadixSortUpsweepT(temp_storage, d_keys, current_bit).ProcessRegion( + even_share.block_offset, + even_share.block_end, + bin_count); + + // Write out digit counts (striped) + if (threadIdx.x < BlockRegionRadixSortUpsweepT::RADIX_DIGITS) + { + int bin_idx = (DESCENDING) ? + BlockRegionRadixSortUpsweepT::RADIX_DIGITS - threadIdx.x - 1 : + threadIdx.x; + + d_spine[(gridDim.x * bin_idx) + blockIdx.x] = bin_count; + } +} + + +/** + * Spine scan kernel entry point (single-block). Computes an exclusive prefix sum over the privatized digit histograms + */ +template < + typename BlockRegionScanPolicy, ///< Parameterizable tuning policy type for cub::BlockRegionScan abstraction + typename Offset> ///< Signed integer type for global offsets +__launch_bounds__ (int(BlockRegionScanPolicy::BLOCK_THREADS), 1) +__global__ void RadixSortScanKernel( + Offset *d_spine, ///< [in,out] Privatized (per block) digit histograms (striped, i.e., 0s counts from each block, then 1s counts from each block, etc.) + int num_counts) ///< [in] Total number of bin-counts +{ + // Parameterize the BlockRegionScan type for the current configuration + typedef BlockRegionScan BlockRegionScanT; + + // Shared memory storage + __shared__ typename BlockRegionScanT::TempStorage temp_storage; + + if (blockIdx.x > 0) return; + + // Block scan instance + BlockRegionScanT block_scan(temp_storage, d_spine, d_spine, cub::Sum(), Offset(0)) ; + + // Process full input tiles + int block_offset = 0; + RunningBlockPrefixCallbackOp prefix_op(0, Sum()); + while (block_offset + BlockRegionScanT::TILE_ITEMS <= num_counts) + { + block_scan.ConsumeTile(block_offset, prefix_op); + block_offset += BlockRegionScanT::TILE_ITEMS; + } +} + + +/** + * Downsweep pass kernel entry point (multi-block). Scatters keys (and values) into corresponding bins for the current digit place. + */ +template < + typename BlockRegionRadixSortDownsweepPolicy, ///< Parameterizable tuning policy type for cub::BlockRegionRadixSortUpsweep abstraction + bool DESCENDING, ///< Whether or not the sorted-order is high-to-low + typename Key, ///< Key type + typename Value, ///< Value type + typename Offset> ///< Signed integer type for global offsets +__launch_bounds__ (int(BlockRegionRadixSortDownsweepPolicy::BLOCK_THREADS)) +__global__ void RadixSortDownsweepKernel( + Key *d_keys_in, ///< [in] Input keys ping buffer + Key *d_keys_out, ///< [in] Output keys pong buffer + Value *d_values_in, ///< [in] Input values ping buffer + Value *d_values_out, ///< [in] Output values pong buffer + Offset *d_spine, ///< [in] Scan of privatized (per block) digit histograms (striped, i.e., 0s counts from each block, then 1s counts from each block, etc.) + Offset num_items, ///< [in] Total number of input data items + int current_bit, ///< [in] Bit position of current radix digit + bool first_pass, ///< [in] Whether this is the first digit pass + bool last_pass, ///< [in] Whether this is the last digit pass + GridEvenShare even_share) ///< [in] Even-share descriptor for mapping an equal number of tiles onto each thread block +{ + // Parameterize BlockRegionRadixSortDownsweep type for the current configuration + typedef BlockRegionRadixSortDownsweep BlockRegionRadixSortDownsweepT; + + // Shared memory storage + __shared__ typename BlockRegionRadixSortDownsweepT::TempStorage temp_storage; + + // Initialize even-share descriptor for this thread block + even_share.BlockInit(); + + // Process input tiles + BlockRegionRadixSortDownsweepT(temp_storage, num_items, d_spine, d_keys_in, d_keys_out, d_values_in, d_values_out, current_bit).ProcessRegion( + even_share.block_offset, + even_share.block_end); +} + + + +/****************************************************************************** + * Dispatch + ******************************************************************************/ + +/** + * Utility class for dispatching the appropriately-tuned kernels for DeviceRadixSort + */ +template < + bool DESCENDING, ///< Whether or not the sorted-order is high-to-low + typename Key, ///< Key type + typename Value, ///< Value type + typename Offset> ///< Signed integer type for global offsets +struct DeviceRadixSortDispatch +{ + /****************************************************************************** + * Tuning policies + ******************************************************************************/ + + /// SM35 + struct Policy350 + { + enum { + KEYS_ONLY = (Equals::VALUE), + SCALE_FACTOR = (CUB_MAX(sizeof(Key), sizeof(Value)) + 3) / 4, + RADIX_BITS = 5, + }; + + // Primary UpsweepPolicy + typedef BlockRegionRadixSortUpsweepPolicy <64, CUB_MAX(1, 18 / SCALE_FACTOR), LOAD_LDG, RADIX_BITS> UpsweepPolicyKeys; + typedef BlockRegionRadixSortUpsweepPolicy <128, CUB_MAX(1, 15 / SCALE_FACTOR), LOAD_LDG, RADIX_BITS> UpsweepPolicyPairs; + typedef typename If::Type UpsweepPolicy; + + // Alternate UpsweepPolicy for (RADIX_BITS-1)-bit passes + typedef BlockRegionRadixSortUpsweepPolicy <64, CUB_MAX(1, 22 / SCALE_FACTOR), LOAD_LDG, RADIX_BITS - 1> AltUpsweepPolicyKeys; + typedef BlockRegionRadixSortUpsweepPolicy <128, CUB_MAX(1, 15 / SCALE_FACTOR), LOAD_LDG, RADIX_BITS - 1> AltUpsweepPolicyPairs; + typedef typename If::Type AltUpsweepPolicy; + + // ScanPolicy + typedef BlockRegionScanPolicy <1024, 4, BLOCK_LOAD_VECTORIZE, false, LOAD_DEFAULT, BLOCK_STORE_VECTORIZE, false, BLOCK_SCAN_RAKING_MEMOIZE> ScanPolicy; + + // Primary DownsweepPolicy + typedef BlockRegionRadixSortDownsweepPolicy <64, CUB_MAX(1, 18 / SCALE_FACTOR), BLOCK_LOAD_DIRECT, LOAD_LDG, false, true, BLOCK_SCAN_WARP_SCANS, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeEightByte, RADIX_BITS> DownsweepPolicyKeys; + typedef BlockRegionRadixSortDownsweepPolicy <128, CUB_MAX(1, 15 / SCALE_FACTOR), BLOCK_LOAD_DIRECT, LOAD_LDG, false, true, BLOCK_SCAN_WARP_SCANS, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeEightByte, RADIX_BITS> DownsweepPolicyPairs; + typedef typename If::Type DownsweepPolicy; + + // Alternate DownsweepPolicy for (RADIX_BITS-1)-bit passes + typedef BlockRegionRadixSortDownsweepPolicy <128, CUB_MAX(1, 11 / SCALE_FACTOR), BLOCK_LOAD_DIRECT, LOAD_LDG, false, true, BLOCK_SCAN_WARP_SCANS, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeEightByte, RADIX_BITS - 1> AltDownsweepPolicyKeys; + typedef BlockRegionRadixSortDownsweepPolicy <128, CUB_MAX(1, 15 / SCALE_FACTOR), BLOCK_LOAD_DIRECT, LOAD_LDG, false, true, BLOCK_SCAN_WARP_SCANS, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeEightByte, RADIX_BITS - 1> AltDownsweepPolicyPairs; + typedef typename If::Type AltDownsweepPolicy; + }; + + + /// SM30 + struct Policy300 + { + enum { + KEYS_ONLY = (Equals::VALUE), + SCALE_FACTOR = (CUB_MAX(sizeof(Key), sizeof(Value)) + 3) / 4, + RADIX_BITS = 5, + }; + + // UpsweepPolicy + typedef BlockRegionRadixSortUpsweepPolicy <256, CUB_MAX(1, 7 / SCALE_FACTOR), LOAD_DEFAULT, RADIX_BITS> UpsweepPolicyKeys; + typedef BlockRegionRadixSortUpsweepPolicy <256, CUB_MAX(1, 5 / SCALE_FACTOR), LOAD_DEFAULT, RADIX_BITS> UpsweepPolicyPairs; + typedef typename If::Type UpsweepPolicy; + + // Alternate UpsweepPolicy for (RADIX_BITS-1)-bit passes + typedef BlockRegionRadixSortUpsweepPolicy <256, CUB_MAX(1, 7 / SCALE_FACTOR), LOAD_DEFAULT, RADIX_BITS - 1> AltUpsweepPolicyKeys; + typedef BlockRegionRadixSortUpsweepPolicy <256, CUB_MAX(1, 5 / SCALE_FACTOR), LOAD_DEFAULT, RADIX_BITS - 1> AltUpsweepPolicyPairs; + typedef typename If::Type AltUpsweepPolicy; + + // ScanPolicy + typedef BlockRegionScanPolicy <1024, 4, BLOCK_LOAD_VECTORIZE, false, LOAD_DEFAULT, BLOCK_STORE_VECTORIZE, false, BLOCK_SCAN_RAKING_MEMOIZE> ScanPolicy; + + // DownsweepPolicy + typedef BlockRegionRadixSortDownsweepPolicy <128, CUB_MAX(1, 14 / SCALE_FACTOR), BLOCK_LOAD_WARP_TRANSPOSE, LOAD_DEFAULT, false, false, BLOCK_SCAN_WARP_SCANS, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeEightByte, RADIX_BITS> DownsweepPolicyKeys; + typedef BlockRegionRadixSortDownsweepPolicy <128, CUB_MAX(1, 10 / SCALE_FACTOR), BLOCK_LOAD_TRANSPOSE, LOAD_DEFAULT, false, false, BLOCK_SCAN_WARP_SCANS, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeEightByte, RADIX_BITS> DownsweepPolicyPairs; + typedef typename If::Type DownsweepPolicy; + + // Alternate DownsweepPolicy for (RADIX_BITS-1)-bit passes + typedef BlockRegionRadixSortDownsweepPolicy <128, CUB_MAX(1, 14 / SCALE_FACTOR), BLOCK_LOAD_WARP_TRANSPOSE, LOAD_DEFAULT, false, false, BLOCK_SCAN_WARP_SCANS, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeEightByte, RADIX_BITS - 1> AltDownsweepPolicyKeys; + typedef BlockRegionRadixSortDownsweepPolicy <128, CUB_MAX(1, 10 / SCALE_FACTOR), BLOCK_LOAD_TRANSPOSE, LOAD_DEFAULT, false, false, BLOCK_SCAN_WARP_SCANS, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeEightByte, RADIX_BITS - 1> AltDownsweepPolicyPairs; + typedef typename If::Type AltDownsweepPolicy; + }; + + + /// SM20 + struct Policy200 + { + enum { + KEYS_ONLY = (Equals::VALUE), + SCALE_FACTOR = (CUB_MAX(sizeof(Key), sizeof(Value)) + 3) / 4, + RADIX_BITS = 5, + }; + + // UpsweepPolicy + typedef BlockRegionRadixSortUpsweepPolicy <64, CUB_MAX(1, 18 / SCALE_FACTOR), LOAD_DEFAULT, RADIX_BITS> UpsweepPolicyKeys; + typedef BlockRegionRadixSortUpsweepPolicy <128, CUB_MAX(1, 13 / SCALE_FACTOR), LOAD_DEFAULT, RADIX_BITS> UpsweepPolicyPairs; + typedef typename If::Type UpsweepPolicy; + + // Alternate UpsweepPolicy for (RADIX_BITS-1)-bit passes + typedef BlockRegionRadixSortUpsweepPolicy <64, CUB_MAX(1, 18 / SCALE_FACTOR), LOAD_DEFAULT, RADIX_BITS - 1> AltUpsweepPolicyKeys; + typedef BlockRegionRadixSortUpsweepPolicy <128, CUB_MAX(1, 13 / SCALE_FACTOR), LOAD_DEFAULT, RADIX_BITS - 1> AltUpsweepPolicyPairs; + typedef typename If::Type AltUpsweepPolicy; + + // ScanPolicy + typedef BlockRegionScanPolicy <512, 4, BLOCK_LOAD_VECTORIZE, false, LOAD_DEFAULT, BLOCK_STORE_VECTORIZE, false, BLOCK_SCAN_RAKING_MEMOIZE> ScanPolicy; + + // DownsweepPolicy + typedef BlockRegionRadixSortDownsweepPolicy <64, CUB_MAX(1, 18 / SCALE_FACTOR), BLOCK_LOAD_WARP_TRANSPOSE, LOAD_DEFAULT, false, false, BLOCK_SCAN_RAKING_MEMOIZE, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeFourByte, RADIX_BITS> DownsweepPolicyKeys; + typedef BlockRegionRadixSortDownsweepPolicy <128, CUB_MAX(1, 13 / SCALE_FACTOR), BLOCK_LOAD_WARP_TRANSPOSE, LOAD_DEFAULT, false, false, BLOCK_SCAN_RAKING_MEMOIZE, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeFourByte, RADIX_BITS> DownsweepPolicyPairs; + typedef typename If::Type DownsweepPolicy; + + // Alternate DownsweepPolicy for (RADIX_BITS-1)-bit passes + typedef BlockRegionRadixSortDownsweepPolicy <64, CUB_MAX(1, 18 / SCALE_FACTOR), BLOCK_LOAD_WARP_TRANSPOSE, LOAD_DEFAULT, false, false, BLOCK_SCAN_RAKING_MEMOIZE, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeFourByte, RADIX_BITS - 1> AltDownsweepPolicyKeys; + typedef BlockRegionRadixSortDownsweepPolicy <128, CUB_MAX(1, 13 / SCALE_FACTOR), BLOCK_LOAD_WARP_TRANSPOSE, LOAD_DEFAULT, false, false, BLOCK_SCAN_RAKING_MEMOIZE, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeFourByte, RADIX_BITS - 1> AltDownsweepPolicyPairs; + typedef typename If::Type AltDownsweepPolicy; + }; + + + /// SM13 + struct Policy130 + { + enum { + KEYS_ONLY = (Equals::VALUE), + SCALE_FACTOR = (CUB_MAX(sizeof(Key), sizeof(Value)) + 3) / 4, + RADIX_BITS = 5, + }; + + // UpsweepPolicy + typedef BlockRegionRadixSortUpsweepPolicy <128, CUB_MAX(1, 19 / SCALE_FACTOR), LOAD_DEFAULT, RADIX_BITS> UpsweepPolicyKeys; + typedef BlockRegionRadixSortUpsweepPolicy <128, CUB_MAX(1, 19 / SCALE_FACTOR), LOAD_DEFAULT, RADIX_BITS> UpsweepPolicyPairs; + typedef typename If::Type UpsweepPolicy; + + // Alternate UpsweepPolicy for (RADIX_BITS-1)-bit passes + typedef BlockRegionRadixSortUpsweepPolicy <128, CUB_MAX(1, 15 / SCALE_FACTOR), LOAD_DEFAULT, RADIX_BITS - 1> AltUpsweepPolicyKeys; + typedef BlockRegionRadixSortUpsweepPolicy <128, CUB_MAX(1, 15 / SCALE_FACTOR), LOAD_DEFAULT, RADIX_BITS - 1> AltUpsweepPolicyPairs; + typedef typename If::Type AltUpsweepPolicy; + + // ScanPolicy + typedef BlockRegionScanPolicy <256, 4, BLOCK_LOAD_VECTORIZE, false, LOAD_DEFAULT, BLOCK_STORE_VECTORIZE, false, BLOCK_SCAN_WARP_SCANS> ScanPolicy; + + // DownsweepPolicy + typedef BlockRegionRadixSortDownsweepPolicy <64, CUB_MAX(1, 19 / SCALE_FACTOR), BLOCK_LOAD_WARP_TRANSPOSE, LOAD_DEFAULT, false, false, BLOCK_SCAN_WARP_SCANS, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeFourByte, RADIX_BITS> DownsweepPolicyKeys; + typedef BlockRegionRadixSortDownsweepPolicy <64, CUB_MAX(1, 19 / SCALE_FACTOR), BLOCK_LOAD_WARP_TRANSPOSE, LOAD_DEFAULT, false, false, BLOCK_SCAN_WARP_SCANS, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeFourByte, RADIX_BITS> DownsweepPolicyPairs; + typedef typename If::Type DownsweepPolicy; + + // Alternate DownsweepPolicy for (RADIX_BITS-1)-bit passes + typedef BlockRegionRadixSortDownsweepPolicy <128, CUB_MAX(1, 15 / SCALE_FACTOR), BLOCK_LOAD_WARP_TRANSPOSE, LOAD_DEFAULT, false, false, BLOCK_SCAN_WARP_SCANS, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeFourByte, RADIX_BITS - 1> AltDownsweepPolicyKeys; + typedef BlockRegionRadixSortDownsweepPolicy <128, CUB_MAX(1, 15 / SCALE_FACTOR), BLOCK_LOAD_WARP_TRANSPOSE, LOAD_DEFAULT, false, false, BLOCK_SCAN_WARP_SCANS, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeFourByte, RADIX_BITS - 1> AltDownsweepPolicyPairs; + typedef typename If::Type AltDownsweepPolicy; + }; + + + /// SM10 + struct Policy100 + { + enum { + RADIX_BITS = 4, + }; + + // UpsweepPolicy + typedef BlockRegionRadixSortUpsweepPolicy <64, 9, LOAD_DEFAULT, RADIX_BITS> UpsweepPolicy; + + // Alternate UpsweepPolicy for (RADIX_BITS-1)-bit passes + typedef BlockRegionRadixSortUpsweepPolicy <64, 9, LOAD_DEFAULT, RADIX_BITS - 1> AltUpsweepPolicy; + + // ScanPolicy + typedef BlockRegionScanPolicy <256, 4, BLOCK_LOAD_VECTORIZE, false, LOAD_DEFAULT, BLOCK_STORE_VECTORIZE, false, BLOCK_SCAN_RAKING_MEMOIZE> ScanPolicy; + + // DownsweepPolicy + typedef BlockRegionRadixSortDownsweepPolicy <64, 9, BLOCK_LOAD_WARP_TRANSPOSE, LOAD_DEFAULT, false, false, BLOCK_SCAN_WARP_SCANS, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeFourByte, RADIX_BITS> DownsweepPolicy; + + // Alternate DownsweepPolicy for (RADIX_BITS-1)-bit passes + typedef BlockRegionRadixSortDownsweepPolicy <64, 9, BLOCK_LOAD_WARP_TRANSPOSE, LOAD_DEFAULT, false, false, BLOCK_SCAN_WARP_SCANS, RADIX_SORT_SCATTER_TWO_PHASE, cudaSharedMemBankSizeFourByte, RADIX_BITS - 1> AltDownsweepPolicy; + }; + + + /****************************************************************************** + * Tuning policies of current PTX compiler pass + ******************************************************************************/ + +#if (CUB_PTX_VERSION >= 350) + typedef Policy350 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 300) + typedef Policy300 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 200) + typedef Policy200 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 130) + typedef Policy130 PtxPolicy; + +#else + typedef Policy100 PtxPolicy; + +#endif + + // "Opaque" policies (whose parameterizations aren't reflected in the type signature) + struct PtxUpsweepPolicy : PtxPolicy::UpsweepPolicy {}; + struct PtxAltUpsweepPolicy : PtxPolicy::AltUpsweepPolicy {}; + struct PtxScanPolicy : PtxPolicy::ScanPolicy {}; + struct PtxDownsweepPolicy : PtxPolicy::DownsweepPolicy {}; + struct PtxAltDownsweepPolicy : PtxPolicy::AltDownsweepPolicy {}; + + + /****************************************************************************** + * Utilities + ******************************************************************************/ + + /** + * Initialize kernel dispatch configurations with the policies corresponding to the PTX assembly we will use + */ + template < + typename Policy, + typename KernelConfig, + typename UpsweepKernelPtr, ///< Function type of cub::RadixSortUpsweepKernel + typename ScanKernelPtr, ///< Function type of cub::SpineScanKernel + typename DownsweepKernelPtr> ///< Function type of cub::RadixSortUpsweepKernel + __host__ __device__ __forceinline__ + static cudaError_t InitConfigs( + int sm_version, + int sm_count, + KernelConfig &upsweep_config, + KernelConfig &alt_upsweep_config, + KernelConfig &scan_config, + KernelConfig &downsweep_config, + KernelConfig &alt_downsweep_config, + UpsweepKernelPtr upsweep_kernel, + UpsweepKernelPtr alt_upsweep_kernel, + ScanKernelPtr scan_kernel, + DownsweepKernelPtr downsweep_kernel, + DownsweepKernelPtr alt_downsweep_kernel) + { + cudaError_t error; + do { + if (CubDebug(error = upsweep_config.template InitUpsweepPolicy( sm_version, sm_count, upsweep_kernel))) break; + if (CubDebug(error = alt_upsweep_config.template InitUpsweepPolicy( sm_version, sm_count, alt_upsweep_kernel))) break; + if (CubDebug(error = scan_config.template InitScanPolicy( sm_version, sm_count, scan_kernel))) break; + if (CubDebug(error = downsweep_config.template InitDownsweepPolicy( sm_version, sm_count, downsweep_kernel))) break; + if (CubDebug(error = alt_downsweep_config.template InitDownsweepPolicy( sm_version, sm_count, alt_downsweep_kernel))) break; + + } while (0); + + return error; + } + + + /** + * Initialize kernel dispatch configurations with the policies corresponding to the PTX assembly we will use + */ + template < + typename KernelConfig, + typename UpsweepKernelPtr, ///< Function type of cub::RadixSortUpsweepKernel + typename ScanKernelPtr, ///< Function type of cub::SpineScanKernel + typename DownsweepKernelPtr> ///< Function type of cub::RadixSortUpsweepKernel + __host__ __device__ __forceinline__ + static cudaError_t InitConfigs( + int ptx_version, + int sm_version, + int sm_count, + KernelConfig &upsweep_config, + KernelConfig &alt_upsweep_config, + KernelConfig &scan_config, + KernelConfig &downsweep_config, + KernelConfig &alt_downsweep_config, + UpsweepKernelPtr upsweep_kernel, + UpsweepKernelPtr alt_upsweep_kernel, + ScanKernelPtr scan_kernel, + DownsweepKernelPtr downsweep_kernel, + DownsweepKernelPtr alt_downsweep_kernel) + { + #if (CUB_PTX_VERSION > 0) + + // We're on the device, so initialize the kernel dispatch configurations with the current PTX policy + cudaError_t error; + do { + + if (CubDebug(error = upsweep_config.template InitUpsweepPolicy( sm_version, sm_count, upsweep_kernel))) break; + if (CubDebug(error = alt_upsweep_config.template InitUpsweepPolicy( sm_version, sm_count, alt_upsweep_kernel))) break; + if (CubDebug(error = scan_config.template InitScanPolicy( sm_version, sm_count, scan_kernel))) break; + if (CubDebug(error = downsweep_config.template InitDownsweepPolicy( sm_version, sm_count, downsweep_kernel))) break; + if (CubDebug(error = alt_downsweep_config.template InitDownsweepPolicy( sm_version, sm_count, alt_downsweep_kernel))) break; + + } while (0); + + return error; + + #else + + // We're on the host, so lookup and initialize the kernel dispatch configurations with the policies that match the device's PTX version + cudaError_t error; + if (ptx_version >= 350) + { + error = InitConfigs(sm_version, sm_count, upsweep_config, alt_upsweep_config, scan_config, downsweep_config, alt_downsweep_config, upsweep_kernel, alt_upsweep_kernel, scan_kernel, downsweep_kernel, alt_downsweep_kernel); + } + else if (ptx_version >= 300) + { + error = InitConfigs(sm_version, sm_count, upsweep_config, alt_upsweep_config, scan_config, downsweep_config, alt_downsweep_config, upsweep_kernel, alt_upsweep_kernel, scan_kernel, downsweep_kernel, alt_downsweep_kernel); + } + else if (ptx_version >= 200) + { + error = InitConfigs(sm_version, sm_count, upsweep_config, alt_upsweep_config, scan_config, downsweep_config, alt_downsweep_config, upsweep_kernel, alt_upsweep_kernel, scan_kernel, downsweep_kernel, alt_downsweep_kernel); + } + else if (ptx_version >= 130) + { + error = InitConfigs(sm_version, sm_count, upsweep_config, alt_upsweep_config, scan_config, downsweep_config, alt_downsweep_config, upsweep_kernel, alt_upsweep_kernel, scan_kernel, downsweep_kernel, alt_downsweep_kernel); + } + else + { + error = InitConfigs(sm_version, sm_count, upsweep_config, alt_upsweep_config, scan_config, downsweep_config, alt_downsweep_config, upsweep_kernel, alt_upsweep_kernel, scan_kernel, downsweep_kernel, alt_downsweep_kernel); + } + + return error; + + #endif + } + + + + /** + * Kernel kernel dispatch configurations + */ + struct KernelConfig + { + int block_threads; + int items_per_thread; + int tile_size; + cudaSharedMemConfig smem_config; + int radix_bits; + int sm_occupancy; // Amount of CTAs to oversubscribe the device beyond actively-resident (heuristic) + int max_grid_size; + int subscription_factor; + + template + __host__ __device__ __forceinline__ cudaError_t InitUpsweepPolicy( + int sm_version, int sm_count, UpsweepKernelPtr upsweep_kernel) + { + block_threads = UpsweepPolicy::BLOCK_THREADS; + items_per_thread = UpsweepPolicy::ITEMS_PER_THREAD; + radix_bits = UpsweepPolicy::RADIX_BITS; + smem_config = cudaSharedMemBankSizeFourByte; + tile_size = block_threads * items_per_thread; + cudaError_t retval = MaxSmOccupancy(sm_occupancy, sm_version, upsweep_kernel, block_threads); + subscription_factor = CUB_SUBSCRIPTION_FACTOR(sm_version); + max_grid_size = (sm_occupancy * sm_count) * subscription_factor; + + return retval; + } + + template + __host__ __device__ __forceinline__ cudaError_t InitScanPolicy( + int sm_version, int sm_count, ScanKernelPtr scan_kernel) + { + block_threads = ScanPolicy::BLOCK_THREADS; + items_per_thread = ScanPolicy::ITEMS_PER_THREAD; + radix_bits = 0; + smem_config = cudaSharedMemBankSizeFourByte; + tile_size = block_threads * items_per_thread; + sm_occupancy = 1; + subscription_factor = 1; + max_grid_size = 1; + + return cudaSuccess; + } + + template + __host__ __device__ __forceinline__ cudaError_t InitDownsweepPolicy( + int sm_version, int sm_count, DownsweepKernelPtr downsweep_kernel) + { + block_threads = DownsweepPolicy::BLOCK_THREADS; + items_per_thread = DownsweepPolicy::ITEMS_PER_THREAD; + radix_bits = DownsweepPolicy::RADIX_BITS; + smem_config = DownsweepPolicy::SMEM_CONFIG; + tile_size = block_threads * items_per_thread; + cudaError_t retval = MaxSmOccupancy(sm_occupancy, sm_version, downsweep_kernel, block_threads); + subscription_factor = CUB_SUBSCRIPTION_FACTOR(sm_version); + max_grid_size = (sm_occupancy * sm_count) * subscription_factor; + + return retval; + } + }; + + + /****************************************************************************** + * Allocation of device temporaries + ******************************************************************************/ + + __host__ __device__ __forceinline__ + static cudaError_t AllocateTemporaries( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + Offset* &d_spine, ///< [out] Digit count histograms per thread block + KernelConfig &scan_config, ///< [in] Dispatch parameters that match the policy that \p scan_kernel was compiled for + KernelConfig &downsweep_config) ///< [in] Dispatch parameters that match the policy that \p downsweep_kernel was compiled for + { + cudaError error = cudaSuccess; + do + { + // Get spine size (conservative) + int spine_size = (downsweep_config.max_grid_size * (1 << downsweep_config.radix_bits)) + scan_config.tile_size; + + // Temporary storage allocation requirements + void* allocations[1]; + size_t allocation_sizes[1] = + { + spine_size * sizeof(Offset), // bytes needed for privatized block digit histograms + }; + + // Alias the temporary allocations from the single storage blob (or set the necessary size of the blob) + if (CubDebug(error = AliasTemporaries(d_temp_storage, temp_storage_bytes, allocations, allocation_sizes))) break; + + // Return if the caller is simply requesting the size of the storage allocation + if (d_temp_storage == NULL) + return cudaSuccess; + + // Alias the allocation for the privatized per-block digit histograms + d_spine = (Offset*) allocations[0]; + + } while(0); + + return error; + } + + + /****************************************************************************** + * Dispatch entrypoints + ******************************************************************************/ + + /** + * Internal dispatch routine for computing a device-wide radix sort using the + * specified kernel functions. + */ + template < + typename UpsweepKernelPtr, ///< Function type of cub::RadixSortUpsweepKernel + typename ScanKernelPtr, ///< Function type of cub::SpineScanKernel + typename DownsweepKernelPtr> ///< Function type of cub::RadixSortUpsweepKernel + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + DoubleBuffer &d_keys, ///< [in,out] Double-buffer whose current buffer contains the unsorted input keys and, upon return, is updated to point to the sorted output keys + DoubleBuffer &d_values, ///< [in,out] Double-buffer whose current buffer contains the unsorted input values and, upon return, is updated to point to the sorted output values + Offset *d_spine, ///< [in] Digit count histograms per thread block + int spine_size, ///< [in] Number of histogram counters + Offset num_items, ///< [in] Number of items to reduce + int begin_bit, ///< [in] The beginning (least-significant) bit index needed for key comparison + int end_bit, ///< [in] The past-the-end (most-significant) bit index needed for key comparison + cudaStream_t stream, ///< [in] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous, ///< [in] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + KernelConfig &upsweep_config, ///< [in] Dispatch parameters that match the policy that \p upsweep_kernel was compiled for + KernelConfig &scan_config, ///< [in] Dispatch parameters that match the policy that \p scan_kernel was compiled for + KernelConfig &downsweep_config, ///< [in] Dispatch parameters that match the policy that \p downsweep_kernel was compiled for + UpsweepKernelPtr upsweep_kernel, ///< [in] Kernel function pointer to parameterization of cub::RadixSortUpsweepKernel + ScanKernelPtr scan_kernel, ///< [in] Kernel function pointer to parameterization of cub::SpineScanKernel + DownsweepKernelPtr downsweep_kernel) ///< [in] Kernel function pointer to parameterization of cub::RadixSortUpsweepKernel + { +#ifndef CUB_RUNTIME_ENABLED + + // Kernel launch not supported from this device + return CubDebug(cudaErrorNotSupported ); + +#else + + cudaError error = cudaSuccess; + do + { + // Get even-share work distribution descriptor + GridEvenShare even_share(num_items, downsweep_config.max_grid_size, CUB_MAX(downsweep_config.tile_size, upsweep_config.tile_size)); + +#if (CUB_PTX_VERSION == 0) + // Get current smem bank configuration + cudaSharedMemConfig original_smem_config; + if (CubDebug(error = cudaDeviceGetSharedMemConfig(&original_smem_config))) break; + cudaSharedMemConfig current_smem_config = original_smem_config; +#endif + // Iterate over digit places + int current_bit = begin_bit; + while (current_bit < end_bit) + { +#if (CUB_PTX_VERSION == 0) + // Update smem config if necessary + if (current_smem_config != upsweep_config.smem_config) + { + if (CubDebug(error = cudaDeviceSetSharedMemConfig(upsweep_config.smem_config))) break; + current_smem_config = upsweep_config.smem_config; + } +#endif + + // Log upsweep_kernel configuration + if (debug_synchronous) + CubLog("Invoking upsweep_kernel<<<%d, %d, 0, %lld>>>(), %d smem config, %d items per thread, %d SM occupancy, selector %d, current bit %d, bit_grain %d\n", + even_share.grid_size, upsweep_config.block_threads, (long long) stream, upsweep_config.smem_config, upsweep_config.items_per_thread, upsweep_config.sm_occupancy, d_keys.selector, current_bit, downsweep_config.radix_bits); + + // Invoke upsweep_kernel with same grid size as downsweep_kernel + upsweep_kernel<<>>( + d_keys.d_buffers[d_keys.selector], + d_spine, + num_items, + current_bit, + (current_bit == begin_bit), + even_share); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + + // Log scan_kernel configuration + if (debug_synchronous) CubLog("Invoking scan_kernel<<<%d, %d, 0, %lld>>>(), %d items per thread\n", + 1, scan_config.block_threads, (long long) stream, scan_config.items_per_thread); + + // Invoke scan_kernel + scan_kernel<<<1, scan_config.block_threads, 0, stream>>>( + d_spine, + spine_size); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + + +#if (CUB_PTX_VERSION == 0) + // Update smem config if necessary + if (current_smem_config != downsweep_config.smem_config) + { + if (CubDebug(error = cudaDeviceSetSharedMemConfig(downsweep_config.smem_config))) break; + current_smem_config = downsweep_config.smem_config; + } +#endif + // Log downsweep_kernel configuration + if (debug_synchronous) CubLog("Invoking downsweep_kernel<<<%d, %d, 0, %lld>>>(), %d smem config, %d items per thread, %d SM occupancy\n", + even_share.grid_size, downsweep_config.block_threads, (long long) stream, downsweep_config.smem_config, downsweep_config.items_per_thread, downsweep_config.sm_occupancy); + + // Invoke downsweep_kernel + downsweep_kernel<<>>( + d_keys.d_buffers[d_keys.selector], + d_keys.d_buffers[d_keys.selector ^ 1], + d_values.d_buffers[d_values.selector], + d_values.d_buffers[d_values.selector ^ 1], + d_spine, + num_items, + current_bit, + (current_bit == begin_bit), + (current_bit + downsweep_config.radix_bits >= end_bit), + even_share); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + + // Invert selectors + d_keys.selector ^= 1; + d_values.selector ^= 1; + + // Update current bit position + current_bit += downsweep_config.radix_bits; + } + +#if (CUB_PTX_VERSION == 0) + // Reset smem config if necessary + if (current_smem_config != original_smem_config) + { + if (CubDebug(error = cudaDeviceSetSharedMemConfig(original_smem_config))) break; + } +#endif + + } + while (0); + + return error; + +#endif // CUB_RUNTIME_ENABLED + } + + + /** + * Internal dispatch routine + */ + template < + typename UpsweepKernelPtr, ///< Function type of cub::RadixSortUpsweepKernel + typename ScanKernelPtr, ///< Function type of cub::SpineScanKernel + typename DownsweepKernelPtr> ///< Function type of cub::RadixSortUpsweepKernel + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + DoubleBuffer &d_keys, ///< [in,out] Double-buffer whose current buffer contains the unsorted input keys and, upon return, is updated to point to the sorted output keys + DoubleBuffer &d_values, ///< [in,out] Double-buffer whose current buffer contains the unsorted input values and, upon return, is updated to point to the sorted output values + Offset num_items, ///< [in] Number of items to reduce + int begin_bit, ///< [in] The beginning (least-significant) bit index needed for key comparison + int end_bit, ///< [in] The past-the-end (most-significant) bit index needed for key comparison + cudaStream_t stream, ///< [in] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous, ///< [in] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + UpsweepKernelPtr upsweep_kernel, ///< [in] Kernel function pointer to parameterization of cub::RadixSortUpsweepKernel + UpsweepKernelPtr alt_upsweep_kernel, ///< [in] Alternate kernel function pointer to parameterization of cub::RadixSortUpsweepKernel + ScanKernelPtr scan_kernel, ///< [in] Kernel function pointer to parameterization of cub::SpineScanKernel + DownsweepKernelPtr downsweep_kernel, ///< [in] Kernel function pointer to parameterization of cub::RadixSortUpsweepKernel + DownsweepKernelPtr alt_downsweep_kernel) ///< [in] Alternate kernel function pointer to parameterization of cub::RadixSortUpsweepKernel + { +#ifndef CUB_RUNTIME_ENABLED + + // Kernel launch not supported from this device + return CubDebug(cudaErrorNotSupported ); + +#else + + cudaError error = cudaSuccess; + + do + { + // Get PTX version + int ptx_version; + #if (CUB_PTX_VERSION == 0) + if (CubDebug(error = PtxVersion(ptx_version))) break; + #else + ptx_version = CUB_PTX_VERSION; + #endif + + // Get device ordinal + int device_ordinal; + if (CubDebug(error = cudaGetDevice(&device_ordinal))) break; + + // Get device SM version + int sm_version; + if (CubDebug(error = SmVersion(sm_version, device_ordinal))) break; + + // Get SM count + int sm_count; + if (CubDebug(error = cudaDeviceGetAttribute (&sm_count, cudaDevAttrMultiProcessorCount, device_ordinal))) break; + + // Get kernel kernel dispatch configurations + KernelConfig upsweep_config; + KernelConfig alt_upsweep_config; + KernelConfig scan_config; + KernelConfig downsweep_config; + KernelConfig alt_downsweep_config; + + if (CubDebug(error = InitConfigs(ptx_version, sm_version, sm_count, + upsweep_config, alt_upsweep_config, scan_config, downsweep_config, alt_downsweep_config, + upsweep_kernel, alt_upsweep_kernel, scan_kernel, downsweep_kernel, alt_downsweep_kernel))) break; + + // Get spine sizes (conservative) + int spine_size = (downsweep_config.max_grid_size * (1 << downsweep_config.radix_bits)) + scan_config.tile_size; + int alt_spine_size = (alt_downsweep_config.max_grid_size * (1 << alt_downsweep_config.radix_bits)) + scan_config.tile_size; + + // Allocate temporaries + Offset *d_spine = NULL; + if (spine_size > alt_spine_size) + { + if (CubDebug(error = AllocateTemporaries(d_temp_storage, temp_storage_bytes, d_spine, scan_config, downsweep_config))) break; + } + else + { + if (CubDebug(error = AllocateTemporaries(d_temp_storage, temp_storage_bytes, d_spine, scan_config, alt_downsweep_config))) break; + } + + // Return if the caller is simply requesting the size of the storage allocation + if (d_temp_storage == NULL) + return cudaSuccess; + + // Run radix sorting passes + int num_bits = end_bit - begin_bit; + int remaining_bits = num_bits % downsweep_config.radix_bits; + + if (remaining_bits != 0) + { + // Run passes of alternate configuration + int max_alt_passes = downsweep_config.radix_bits - remaining_bits; + int alt_end_bit = CUB_MIN(end_bit, begin_bit + (max_alt_passes * alt_downsweep_config.radix_bits)); + + if (CubDebug(error = Dispatch( + d_keys, + d_values, + d_spine, + alt_spine_size, + num_items, + begin_bit, + alt_end_bit, + stream, + debug_synchronous, + alt_upsweep_config, + scan_config, + alt_downsweep_config, + alt_upsweep_kernel, + scan_kernel, + alt_downsweep_kernel))) break; + + begin_bit = alt_end_bit; + } + + // Run passes of primary configuration + if (CubDebug(error = Dispatch( + d_keys, + d_values, + d_spine, + spine_size, + num_items, + begin_bit, + end_bit, + stream, + debug_synchronous, + upsweep_config, + scan_config, + downsweep_config, + upsweep_kernel, + scan_kernel, + downsweep_kernel))) break; + } + while (0); + + return error; + +#endif // CUB_RUNTIME_ENABLED + } + + + /** + * Internal dispatch routine + */ + + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + DoubleBuffer &d_keys, ///< [in,out] Double-buffer whose current buffer contains the unsorted input keys and, upon return, is updated to point to the sorted output keys + DoubleBuffer &d_values, ///< [in,out] Double-buffer whose current buffer contains the unsorted input values and, upon return, is updated to point to the sorted output values + Offset num_items, ///< [in] Number of items to reduce + int begin_bit, ///< [in] The beginning (least-significant) bit index needed for key comparison + int end_bit, ///< [in] The past-the-end (most-significant) bit index needed for key comparison + cudaStream_t stream, ///< [in] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous) ///< [in] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + return Dispatch( + d_temp_storage, + temp_storage_bytes, + d_keys, + d_values, + num_items, + begin_bit, + end_bit, + stream, + debug_synchronous, + RadixSortUpsweepKernel, + RadixSortUpsweepKernel, + RadixSortScanKernel, + RadixSortDownsweepKernel, + RadixSortDownsweepKernel); + } + +}; + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_reduce_by_key_dispatch.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_reduce_by_key_dispatch.cuh new file mode 100644 index 0000000000000000000000000000000000000000..7849e7f23a93b8beeb549f3b860813e021e7af5f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_reduce_by_key_dispatch.cuh @@ -0,0 +1,588 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DeviceReduceByKey provides device-wide, parallel operations for reducing segments of values residing within global memory. + */ + +#pragma once + +#include +#include + +#include "device_scan_dispatch.cuh" +#include "../block_region/block_region_reduce_by_key.cuh" +#include "../../thread/thread_operators.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../util_device.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/****************************************************************************** + * Kernel entry points + *****************************************************************************/ + +/** + * Reduce-by-key kernel entry point (multi-block) + */ +template < + typename BlockRegionReduceByKeyPolicy, ///< Parameterized BlockRegionReduceByKeyPolicy tuning policy type + typename KeyInputIterator, ///< Random-access input iterator type for keys + typename KeyOutputIterator, ///< Random-access output iterator type for keys + typename ValueInputIterator, ///< Random-access input iterator type for values + typename ValueOutputIterator, ///< Random-access output iterator type for values + typename NumSegmentsIterator, ///< Output iterator type for recording number of segments encountered + typename TileLookbackStatus, ///< Tile status interface type + typename EqualityOp, ///< Key equality operator type + typename ReductionOp, ///< Value reduction operator type + typename Offset> ///< Signed integer type for global offsets +__launch_bounds__ (int(BlockRegionReduceByKeyPolicy::BLOCK_THREADS)) +__global__ void ReduceByKeyRegionKernel( + KeyInputIterator d_keys_in, ///< [in] Pointer to consecutive runs of input keys + KeyOutputIterator d_keys_out, ///< [in] Pointer to output keys (one key per run) + ValueInputIterator d_values_in, ///< [in] Pointer to consecutive runs of input values + ValueOutputIterator d_values_out, ///< [in] Pointer to output value aggregates (one aggregate per run) + NumSegmentsIterator d_num_segments, ///< [in] Pointer to total number of runs + TileLookbackStatus tile_status, ///< [in] Tile status interface + EqualityOp equality_op, ///< [in] Key equality operator + ReductionOp reduction_op, ///< [in] Value reduction operator + Offset num_items, ///< [in] Total number of items to select from + int num_tiles, ///< [in] Total number of tiles for the entire problem + GridQueue queue) ///< [in] Drain queue descriptor for dynamically mapping tile data onto thread blocks +{ + // Thread block type for reducing tiles of value segments + typedef BlockRegionReduceByKey< + BlockRegionReduceByKeyPolicy, + KeyInputIterator, + KeyOutputIterator, + ValueInputIterator, + ValueOutputIterator, + EqualityOp, + ReductionOp, + Offset> BlockRegionReduceByKeyT; + + // Shared memory for BlockRegionReduceByKey + __shared__ typename BlockRegionReduceByKeyT::TempStorage temp_storage; + + // Process tiles + BlockRegionReduceByKeyT(temp_storage, d_keys_in, d_keys_out, d_values_in, d_values_out, equality_op, reduction_op, num_items).ConsumeRegion( + num_tiles, + queue, + tile_status, + d_num_segments); +} + + + + +/****************************************************************************** + * Dispatch + ******************************************************************************/ + +/** + * Utility class for dispatching the appropriately-tuned kernels for DeviceReduceByKey + */ +template < + typename KeyInputIterator, ///< Random-access input iterator type for keys + typename KeyOutputIterator, ///< Random-access output iterator type for keys + typename ValueInputIterator, ///< Random-access input iterator type for values + typename ValueOutputIterator, ///< Random-access output iterator type for values + typename NumSegmentsIterator, ///< Output iterator type for recording number of segments encountered + typename EqualityOp, ///< Key equality operator type + typename ReductionOp, ///< Value reduction operator type + typename Offset> ///< Signed integer type for global offsets +struct DeviceReduceByKeyDispatch +{ + /****************************************************************************** + * Types and constants + ******************************************************************************/ + + // Data type of key input iterator + typedef typename std::iterator_traits::value_type Key; + + // Data type of value input iterator + typedef typename std::iterator_traits::value_type Value; + + enum + { + INIT_KERNEL_THREADS = 128, + MAX_INPUT_BYTES = CUB_MAX(sizeof(Key), sizeof(Value)), + COMBINED_INPUT_BYTES = sizeof(Key) + sizeof(Value), + }; + + // Value-offset tuple type for scanning (maps accumulated values to segment index) + typedef ItemOffsetPair ValueOffsetPair; + + // Tile status descriptor interface type + typedef ReduceByKeyTileLookbackStatus TileLookbackStatus; + + + /****************************************************************************** + * Tuning policies + ******************************************************************************/ + + /// SM35 + struct Policy350 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 8, + ITEMS_PER_THREAD = (MAX_INPUT_BYTES <= 8) ? 8 : CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, ((NOMINAL_4B_ITEMS_PER_THREAD * 8) + COMBINED_INPUT_BYTES - 1) / COMBINED_INPUT_BYTES)), + }; + + typedef BlockRegionReduceByKeyPolicy< + 128, + ITEMS_PER_THREAD, + BLOCK_LOAD_DIRECT, + LOAD_LDG, + true, + BLOCK_SCAN_WARP_SCANS> + ReduceByKeyPolicy; + }; + + /// SM30 + struct Policy300 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 6, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, ((NOMINAL_4B_ITEMS_PER_THREAD * 8) + COMBINED_INPUT_BYTES - 1) / COMBINED_INPUT_BYTES)), + }; + + typedef BlockRegionReduceByKeyPolicy< + 128, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + LOAD_DEFAULT, + true, + BLOCK_SCAN_WARP_SCANS> + ReduceByKeyPolicy; + }; + + /// SM20 + struct Policy200 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 13, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, ((NOMINAL_4B_ITEMS_PER_THREAD * 8) + COMBINED_INPUT_BYTES - 1) / COMBINED_INPUT_BYTES)), + }; + + typedef BlockRegionReduceByKeyPolicy< + 128, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + LOAD_DEFAULT, + true, + BLOCK_SCAN_WARP_SCANS> + ReduceByKeyPolicy; + }; + + /// SM13 + struct Policy130 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 7, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, ((NOMINAL_4B_ITEMS_PER_THREAD * 8) + COMBINED_INPUT_BYTES - 1) / COMBINED_INPUT_BYTES)), + }; + + typedef BlockRegionReduceByKeyPolicy< + 128, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + LOAD_DEFAULT, + true, + BLOCK_SCAN_WARP_SCANS> + ReduceByKeyPolicy; + }; + + /// SM10 + struct Policy100 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 5, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 8) / COMBINED_INPUT_BYTES)), + }; + + typedef BlockRegionReduceByKeyPolicy< + 64, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + LOAD_DEFAULT, + true, + BLOCK_SCAN_RAKING> + ReduceByKeyPolicy; + }; + + + /****************************************************************************** + * Tuning policies of current PTX compiler pass + ******************************************************************************/ + +#if (CUB_PTX_VERSION >= 350) + typedef Policy350 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 300) + typedef Policy300 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 200) + typedef Policy200 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 130) + typedef Policy130 PtxPolicy; + +#else + typedef Policy100 PtxPolicy; + +#endif + + // "Opaque" policies (whose parameterizations aren't reflected in the type signature) + struct PtxReduceByKeyPolicy : PtxPolicy::ReduceByKeyPolicy {}; + + + /****************************************************************************** + * Utilities + ******************************************************************************/ + + /** + * Initialize kernel dispatch configurations with the policies corresponding to the PTX assembly we will use + */ + template + __host__ __device__ __forceinline__ + static void InitConfigs( + int ptx_version, + KernelConfig &reduce_by_key_region_config) + { + #if (CUB_PTX_VERSION > 0) + + // We're on the device, so initialize the kernel dispatch configurations with the current PTX policy + reduce_by_key_region_config.template Init(); + + #else + + // We're on the host, so lookup and initialize the kernel dispatch configurations with the policies that match the device's PTX version + if (ptx_version >= 350) + { + reduce_by_key_region_config.template Init(); + } + else if (ptx_version >= 300) + { + reduce_by_key_region_config.template Init(); + } + else if (ptx_version >= 200) + { + reduce_by_key_region_config.template Init(); + } + else if (ptx_version >= 130) + { + reduce_by_key_region_config.template Init(); + } + else + { + reduce_by_key_region_config.template Init(); + } + + #endif + } + + + /** + * Kernel kernel dispatch configuration. Mirrors the constants within BlockRegionReduceByKeyPolicy. + */ + struct KernelConfig + { + int block_threads; + int items_per_thread; + BlockLoadAlgorithm load_policy; + bool two_phase_scatter; + BlockScanAlgorithm scan_algorithm; + cudaSharedMemConfig smem_config; + + template + __host__ __device__ __forceinline__ + void Init() + { + block_threads = BlockRegionReduceByKeyPolicy::BLOCK_THREADS; + items_per_thread = BlockRegionReduceByKeyPolicy::ITEMS_PER_THREAD; + load_policy = BlockRegionReduceByKeyPolicy::LOAD_ALGORITHM; + two_phase_scatter = BlockRegionReduceByKeyPolicy::TWO_PHASE_SCATTER; + scan_algorithm = BlockRegionReduceByKeyPolicy::SCAN_ALGORITHM; + smem_config = cudaSharedMemBankSizeEightByte; + } + + __host__ __device__ __forceinline__ + void Print() + { + printf("%d, %d, %d, %d, %d", + block_threads, + items_per_thread, + load_policy, + two_phase_scatter, + scan_algorithm); + } + }; + + + /****************************************************************************** + * Dispatch entrypoints + ******************************************************************************/ + + /** + * Internal dispatch routine for computing a device-wide prefix scan using the + * specified kernel functions. + */ + template < + typename ScanInitKernelPtr, ///< Function type of cub::ScanInitKernel + typename ReduceByKeyRegionKernelPtr> ///< Function type of cub::ReduceByKeyRegionKernelPtr + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + KeyInputIterator d_keys_in, ///< [in] Pointer to consecutive runs of input keys + KeyOutputIterator d_keys_out, ///< [in] Pointer to output keys (one key per run) + ValueInputIterator d_values_in, ///< [in] Pointer to consecutive runs of input values + ValueOutputIterator d_values_out, ///< [in] Pointer to output value aggregates (one aggregate per run) + NumSegmentsIterator d_num_segments, ///< [in] Pointer to total number of runs + EqualityOp equality_op, ///< [in] Key equality operator + ReductionOp reduction_op, ///< [in] Value reduction operator + Offset num_items, ///< [in] Total number of items to select from + cudaStream_t stream, ///< [in] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous, ///< [in] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + int ptx_version, ///< [in] PTX version of dispatch kernels + ScanInitKernelPtr init_kernel, ///< [in] Kernel function pointer to parameterization of cub::ScanInitKernel + ReduceByKeyRegionKernelPtr reduce_by_key_region_kernel, ///< [in] Kernel function pointer to parameterization of cub::ReduceByKeyRegionKernel + KernelConfig reduce_by_key_region_config) ///< [in] Dispatch parameters that match the policy that \p reduce_by_key_region_kernel was compiled for + { + +#ifndef CUB_RUNTIME_ENABLED + + // Kernel launch not supported from this device + return CubDebug(cudaErrorNotSupported); + +#else + + cudaError error = cudaSuccess; + do + { + // Get device ordinal + int device_ordinal; + if (CubDebug(error = cudaGetDevice(&device_ordinal))) break; + + // Get device SM version + int sm_version; + if (CubDebug(error = SmVersion(sm_version, device_ordinal))) break; + + // Get SM count + int sm_count; + if (CubDebug(error = cudaDeviceGetAttribute (&sm_count, cudaDevAttrMultiProcessorCount, device_ordinal))) break; + + // Number of input tiles + int tile_size = reduce_by_key_region_config.block_threads * reduce_by_key_region_config.items_per_thread; + int num_tiles = (num_items + tile_size - 1) / tile_size; + + // Specify temporary storage allocation requirements + size_t allocation_sizes[2]; + if (CubDebug(error = TileLookbackStatus::AllocationSize(num_tiles, allocation_sizes[0]))) break; // bytes needed for tile status descriptors + allocation_sizes[1] = GridQueue::AllocationSize(); // bytes needed for grid queue descriptor + + // Compute allocation pointers into the single storage blob (or set the necessary size of the blob) + void* allocations[2]; + if (CubDebug(error = AliasTemporaries(d_temp_storage, temp_storage_bytes, allocations, allocation_sizes))) break; + if (d_temp_storage == NULL) + { + // Return if the caller is simply requesting the size of the storage allocation + return cudaSuccess; + } + + // Construct the tile status interface + TileLookbackStatus tile_status; + if (CubDebug(error = tile_status.Init(num_tiles, allocations[0], allocation_sizes[0]))) break; + + // Construct the grid queue descriptor + GridQueue queue(allocations[1]); + + // Log init_kernel configuration + int init_grid_size = (num_tiles + INIT_KERNEL_THREADS - 1) / INIT_KERNEL_THREADS; + if (debug_synchronous) CubLog("Invoking init_kernel<<<%d, %d, 0, %lld>>>()\n", init_grid_size, INIT_KERNEL_THREADS, (long long) stream); + + // Invoke init_kernel to initialize tile descriptors and queue descriptors + init_kernel<<>>( + queue, + tile_status, + num_tiles); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + + // Get SM occupancy for reduce_by_key_region_kernel + int reduce_by_key_region_sm_occupancy; + if (CubDebug(error = MaxSmOccupancy( + reduce_by_key_region_sm_occupancy, // out + sm_version, + reduce_by_key_region_kernel, + reduce_by_key_region_config.block_threads))) break; + + // Get grid size for scanning tiles + dim3 reduce_by_key_grid_size; + if (ptx_version <= 130) + { + // Blocks are launched in order, so just assign one block per tile + int max_dim_x = 32 * 1024; + reduce_by_key_grid_size.z = 1; + reduce_by_key_grid_size.y = (num_tiles + max_dim_x - 1) / max_dim_x; + reduce_by_key_grid_size.x = CUB_MIN(num_tiles, max_dim_x); + } + else + { + // Blocks may not be launched in order, so use atomics + int reduce_by_key_region_occupancy = reduce_by_key_region_sm_occupancy * sm_count; // Whole-device occupancy for reduce_by_key_region_kernel + reduce_by_key_grid_size.z = 1; + reduce_by_key_grid_size.y = 1; + reduce_by_key_grid_size.x = (num_tiles < reduce_by_key_region_occupancy) ? + num_tiles : // Not enough to fill the device with threadblocks + reduce_by_key_region_occupancy; // Fill the device with threadblocks + } + +#if (CUB_PTX_VERSION == 0) + // Get current smem bank configuration + cudaSharedMemConfig original_smem_config; + if (CubDebug(error = cudaDeviceGetSharedMemConfig(&original_smem_config))) break; + cudaSharedMemConfig current_smem_config = original_smem_config; + + // Update smem config if necessary + if (current_smem_config != reduce_by_key_region_config.smem_config) + { + if (CubDebug(error = cudaDeviceSetSharedMemConfig(reduce_by_key_region_config.smem_config))) break; + current_smem_config = reduce_by_key_region_config.smem_config; + } +#endif + + // Log reduce_by_key_region_kernel configuration + if (debug_synchronous) CubLog("Invoking reduce_by_key_region_kernel<<<{%d,%d,%d}, %d, 0, %lld>>>(), %d items per thread, %d SM occupancy\n", + reduce_by_key_grid_size.x, reduce_by_key_grid_size.y, reduce_by_key_grid_size.z, reduce_by_key_region_config.block_threads, (long long) stream, reduce_by_key_region_config.items_per_thread, reduce_by_key_region_sm_occupancy); + + // Invoke reduce_by_key_region_kernel + reduce_by_key_region_kernel<<>>( + d_keys_in, + d_keys_out, + d_values_in, + d_values_out, + d_num_segments, + tile_status, + equality_op, + reduction_op, + num_items, + num_tiles, + queue); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + +#if (CUB_PTX_VERSION == 0) + // Reset smem config if necessary + if (current_smem_config != original_smem_config) + { + if (CubDebug(error = cudaDeviceSetSharedMemConfig(original_smem_config))) break; + } +#endif + + } + while (0); + + return error; + +#endif // CUB_RUNTIME_ENABLED + } + + + /** + * Internal dispatch routine + */ + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + KeyInputIterator d_keys_in, ///< [in] Pointer to consecutive runs of input keys + KeyOutputIterator d_keys_out, ///< [in] Pointer to output keys (one key per run) + ValueInputIterator d_values_in, ///< [in] Pointer to consecutive runs of input values + ValueOutputIterator d_values_out, ///< [in] Pointer to output value aggregates (one aggregate per run) + NumSegmentsIterator d_num_segments, ///< [in] Pointer to total number of runs + EqualityOp equality_op, ///< [in] Key equality operator + ReductionOp reduction_op, ///< [in] Value reduction operator + Offset num_items, ///< [in] Total number of items to select from + cudaStream_t stream, ///< [in] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous) ///< [in] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + cudaError error = cudaSuccess; + do + { + // Get PTX version + int ptx_version; + #if (CUB_PTX_VERSION == 0) + if (CubDebug(error = PtxVersion(ptx_version))) break; + #else + ptx_version = CUB_PTX_VERSION; + #endif + + // Get kernel kernel dispatch configurations + KernelConfig reduce_by_key_region_config; + InitConfigs(ptx_version, reduce_by_key_region_config); + + // Dispatch + if (CubDebug(error = Dispatch( + d_temp_storage, + temp_storage_bytes, + d_keys_in, + d_keys_out, + d_values_in, + d_values_out, + d_num_segments, + equality_op, + reduction_op, + num_items, + stream, + debug_synchronous, + ptx_version, + ScanInitKernel, + ReduceByKeyRegionKernel, + reduce_by_key_region_config))) break; + } + while (0); + + return error; + } +}; + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_reduce_dispatch.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_reduce_dispatch.cuh new file mode 100644 index 0000000000000000000000000000000000000000..062cad9b226030c9116c117f28b593dc13ada7df --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_reduce_dispatch.cuh @@ -0,0 +1,731 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DeviceReduce provides device-wide, parallel operations for computing a reduction across a sequence of data items residing within global memory. + */ + +#pragma once + +#include +#include + +#include "device_reduce_by_key_dispatch.cuh" +#include "../block_region/block_region_reduce.cuh" +#include "../../iterator/constant_input_iterator.cuh" +#include "../../thread/thread_operators.cuh" +#include "../../grid/grid_even_share.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../iterator/arg_index_input_iterator.cuh" +#include "../../util_debug.cuh" +#include "../../util_device.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/****************************************************************************** + * Kernel entry points + *****************************************************************************/ + +/** + * Reduce region kernel entry point (multi-block). Computes privatized reductions, one per thread block. + */ +template < + typename BlockRegionReducePolicy, ///< Parameterized BlockRegionReducePolicy tuning policy type + typename InputIterator, ///< Random-access input iterator type for reading input items \iterator + typename OutputIterator, ///< Output iterator type for recording the reduced aggregate \iterator + typename Offset, ///< Signed integer type for global offsets + typename ReductionOp> ///< Binary reduction functor type having member T operator()(const T &a, const T &b) +__launch_bounds__ (int(BlockRegionReducePolicy::BLOCK_THREADS)) +__global__ void ReduceRegionKernel( + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output aggregate + Offset num_items, ///< [in] Total number of input data items + GridEvenShare even_share, ///< [in] Even-share descriptor for mapping an equal number of tiles onto each thread block + GridQueue queue, ///< [in] Drain queue descriptor for dynamically mapping tile data onto thread blocks + ReductionOp reduction_op) ///< [in] Binary reduction functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) +{ + // Data type + typedef typename std::iterator_traits::value_type T; + + // Thread block type for reducing input tiles + typedef BlockRegionReduce BlockRegionReduceT; + + // Block-wide aggregate + T block_aggregate; + + // Shared memory storage + __shared__ typename BlockRegionReduceT::TempStorage temp_storage; + + // Consume input tiles + BlockRegionReduceT(temp_storage, d_in, reduction_op).ConsumeRegion( + num_items, + even_share, + queue, + block_aggregate, + Int2Type()); + + // Output result + if (threadIdx.x == 0) + { + d_out[blockIdx.x] = block_aggregate; + } +} + + +/** + * Reduce a single tile kernel entry point (single-block). Can be used to aggregate privatized threadblock reductions from a previous multi-block reduction pass. + */ +template < + typename BlockRegionReducePolicy, ///< Parameterized BlockRegionReducePolicy tuning policy type + typename InputIterator, ///< Random-access input iterator type for reading input items \iterator + typename OutputIterator, ///< Output iterator type for recording the reduced aggregate \iterator + typename Offset, ///< Signed integer type for global offsets + typename ReductionOp> ///< Binary reduction functor type having member T operator()(const T &a, const T &b) +__launch_bounds__ (int(BlockRegionReducePolicy::BLOCK_THREADS), 1) +__global__ void SingleTileKernel( + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output aggregate + Offset num_items, ///< [in] Total number of input data items + ReductionOp reduction_op) ///< [in] Binary reduction functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) +{ + // Data type + typedef typename std::iterator_traits::value_type T; + + // Thread block type for reducing input tiles + typedef BlockRegionReduce BlockRegionReduceT; + + // Block-wide aggregate + T block_aggregate; + + // Shared memory storage + __shared__ typename BlockRegionReduceT::TempStorage temp_storage; + + // Consume input tiles + BlockRegionReduceT(temp_storage, d_in, reduction_op).ConsumeRegion( + Offset(0), + Offset(num_items), + block_aggregate); + + // Output result + if (threadIdx.x == 0) + { + d_out[blockIdx.x] = block_aggregate; + } +} + + + + +/****************************************************************************** + * Dispatch + ******************************************************************************/ + +/** + * Utility class for dispatching the appropriately-tuned kernels for DeviceReduce + */ +template < + typename InputIterator, ///< Random-access input iterator type for reading input items \iterator + typename OutputIterator, ///< Output iterator type for recording the reduced aggregate \iterator + typename Offset, ///< Signed integer type for global offsets + typename ReductionOp> ///< Binary reduction functor type having member T operator()(const T &a, const T &b) +struct DeviceReduceDispatch +{ + // Data type of input iterator + typedef typename std::iterator_traits::value_type T; + + + /****************************************************************************** + * Tuning policies + ******************************************************************************/ + + /// SM35 + struct Policy350 + { + // ReduceRegionPolicy1B (GTX Titan: 228.7 GB/s @ 192M 1B items) + typedef BlockRegionReducePolicy< + 128, ///< Threads per thread block + 24, ///< Items per thread per tile of input + 4, ///< Number of items per vectorized load + BLOCK_REDUCE_RAKING, ///< Cooperative block-wide reduction algorithm to use + LOAD_LDG, ///< Cache load modifier + GRID_MAPPING_DYNAMIC> ///< How to map tiles of input onto thread blocks + ReduceRegionPolicy1B; + + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 20, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + // ReduceRegionPolicy4B (GTX Titan: 255.1 GB/s @ 48M 4B items) + typedef BlockRegionReducePolicy< + 256, ///< Threads per thread block + ITEMS_PER_THREAD, ///< Items per thread per tile of input + 2, ///< Number of items per vectorized load + BLOCK_REDUCE_RAKING, ///< Cooperative block-wide reduction algorithm to use + LOAD_LDG, ///< Cache load modifier + GRID_MAPPING_DYNAMIC> ///< How to map tiles of input onto thread blocks + ReduceRegionPolicy4B; + + // ReduceRegionPolicy + typedef typename If<(sizeof(T) >= 4), + ReduceRegionPolicy4B, + ReduceRegionPolicy1B>::Type ReduceRegionPolicy; + + // SingleTilePolicy + typedef BlockRegionReducePolicy< + 256, ///< Threads per thread block + 8, ///< Items per thread per tile of input + 1, ///< Number of items per vectorized load + BLOCK_REDUCE_WARP_REDUCTIONS, ///< Cooperative block-wide reduction algorithm to use + LOAD_DEFAULT, ///< Cache load modifier + GRID_MAPPING_EVEN_SHARE> ///< How to map tiles of input onto thread blocks + SingleTilePolicy; + }; + + /// SM30 + struct Policy300 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 2, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + // ReduceRegionPolicy (GTX670: 154.0 @ 48M 4B items) + typedef BlockRegionReducePolicy< + 256, ///< Threads per thread block + ITEMS_PER_THREAD, ///< Items per thread per tile of input + 1, ///< Number of items per vectorized load + BLOCK_REDUCE_WARP_REDUCTIONS, ///< Cooperative block-wide reduction algorithm to use + LOAD_DEFAULT, ///< Cache load modifier + GRID_MAPPING_EVEN_SHARE> ///< How to map tiles of input onto thread blocks + ReduceRegionPolicy; + + // SingleTilePolicy + typedef BlockRegionReducePolicy< + 256, ///< Threads per thread block + 24, ///< Items per thread per tile of input + 4, ///< Number of items per vectorized load + BLOCK_REDUCE_WARP_REDUCTIONS, ///< Cooperative block-wide reduction algorithm to use + LOAD_DEFAULT, ///< Cache load modifier + GRID_MAPPING_EVEN_SHARE> ///< How to map tiles of input onto thread blocks + SingleTilePolicy; + }; + + /// SM20 + struct Policy200 + { + // ReduceRegionPolicy1B (GTX 580: 158.1 GB/s @ 192M 1B items) + typedef BlockRegionReducePolicy< + 192, ///< Threads per thread block + 24, ///< Items per thread per tile of input + 4, ///< Number of items per vectorized load + BLOCK_REDUCE_RAKING, ///< Cooperative block-wide reduction algorithm to use + LOAD_DEFAULT, ///< Cache load modifier + (sizeof(T) == 1) ? ///< How to map tiles of input onto thread blocks + GRID_MAPPING_EVEN_SHARE : + GRID_MAPPING_DYNAMIC> + ReduceRegionPolicy1B; + + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 8, + NOMINAL_4B_VEC_ITEMS = 4, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + VEC_ITEMS = CUB_MIN(NOMINAL_4B_VEC_ITEMS, CUB_MAX(1, (NOMINAL_4B_VEC_ITEMS * 4 / sizeof(T)))), + }; + + // ReduceRegionPolicy4B (GTX 580: 178.9 GB/s @ 48M 4B items) + typedef BlockRegionReducePolicy< + 128, ///< Threads per thread block + ITEMS_PER_THREAD, ///< Items per thread per tile of input + VEC_ITEMS, ///< Number of items per vectorized load + BLOCK_REDUCE_RAKING, ///< Cooperative block-wide reduction algorithm to use + LOAD_DEFAULT, ///< Cache load modifier + GRID_MAPPING_DYNAMIC> ///< How to map tiles of input onto thread blocks + ReduceRegionPolicy4B; + + // ReduceRegionPolicy + typedef typename If<(sizeof(T) < 4), + ReduceRegionPolicy1B, + ReduceRegionPolicy4B>::Type ReduceRegionPolicy; + + // SingleTilePolicy + typedef BlockRegionReducePolicy< + 192, ///< Threads per thread block + 7, ///< Items per thread per tile of input + 1, ///< Number of items per vectorized load + BLOCK_REDUCE_RAKING, ///< Cooperative block-wide reduction algorithm to use + LOAD_DEFAULT, ///< Cache load modifier + GRID_MAPPING_EVEN_SHARE> ///< How to map tiles of input onto thread blocks + SingleTilePolicy; + }; + + /// SM13 + struct Policy130 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 8, + NOMINAL_4B_VEC_ITEMS = 2, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + VEC_ITEMS = CUB_MIN(NOMINAL_4B_VEC_ITEMS, CUB_MAX(1, (NOMINAL_4B_VEC_ITEMS * 4 / sizeof(T)))), + }; + + // ReduceRegionPolicy + typedef BlockRegionReducePolicy< + 128, ///< Threads per thread block + ITEMS_PER_THREAD, ///< Items per thread per tile of input + VEC_ITEMS, ///< Number of items per vectorized load + BLOCK_REDUCE_RAKING, ///< Cooperative block-wide reduction algorithm to use + LOAD_DEFAULT, ///< Cache load modifier + GRID_MAPPING_EVEN_SHARE> ///< How to map tiles of input onto thread blocks + ReduceRegionPolicy; + + // SingleTilePolicy + typedef BlockRegionReducePolicy< + 32, ///< Threads per thread block + 4, ///< Items per thread per tile of input + VEC_ITEMS, ///< Number of items per vectorized load + BLOCK_REDUCE_RAKING, ///< Cooperative block-wide reduction algorithm to use + LOAD_DEFAULT, ///< Cache load modifier + GRID_MAPPING_EVEN_SHARE> ///< How to map tiles of input onto thread blocks + SingleTilePolicy; + }; + + /// SM10 + struct Policy100 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 8, + NOMINAL_4B_VEC_ITEMS = 2, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + VEC_ITEMS = CUB_MIN(NOMINAL_4B_VEC_ITEMS, CUB_MAX(1, (NOMINAL_4B_VEC_ITEMS * 4 / sizeof(T)))), + }; + + // ReduceRegionPolicy + typedef BlockRegionReducePolicy< + 128, ///< Threads per thread block + ITEMS_PER_THREAD, ///< Items per thread per tile of input + VEC_ITEMS, ///< Number of items per vectorized load + BLOCK_REDUCE_RAKING, ///< Cooperative block-wide reduction algorithm to use + LOAD_DEFAULT, ///< Cache load modifier + GRID_MAPPING_EVEN_SHARE> ///< How to map tiles of input onto thread blocks + ReduceRegionPolicy; + + // SingleTilePolicy + typedef BlockRegionReducePolicy< + 32, ///< Threads per thread block + 4, ///< Items per thread per tile of input + 4, ///< Number of items per vectorized load + BLOCK_REDUCE_RAKING, ///< Cooperative block-wide reduction algorithm to use + LOAD_DEFAULT, ///< Cache load modifier + GRID_MAPPING_EVEN_SHARE> ///< How to map tiles of input onto thread blocks + SingleTilePolicy; + }; + + + /****************************************************************************** + * Tuning policies of current PTX compiler pass + ******************************************************************************/ + +#if (CUB_PTX_VERSION >= 350) + typedef Policy350 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 300) + typedef Policy300 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 200) + typedef Policy200 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 130) + typedef Policy130 PtxPolicy; + +#else + typedef Policy100 PtxPolicy; + +#endif + + // "Opaque" policies (whose parameterizations aren't reflected in the type signature) + struct PtxReduceRegionPolicy : PtxPolicy::ReduceRegionPolicy {}; + struct PtxSingleTilePolicy : PtxPolicy::SingleTilePolicy {}; + + + /****************************************************************************** + * Utilities + ******************************************************************************/ + + /** + * Initialize kernel dispatch configurations with the policies corresponding to the PTX assembly we will use + */ + template + __host__ __device__ __forceinline__ + static void InitConfigs( + int ptx_version, + KernelConfig &reduce_region_config, + KernelConfig &single_tile_config) + { + #if (CUB_PTX_VERSION > 0) + + // We're on the device, so initialize the kernel dispatch configurations with the current PTX policy + reduce_region_config.template Init(); + single_tile_config.template Init(); + + #else + + // We're on the host, so lookup and initialize the kernel dispatch configurations with the policies that match the device's PTX version + if (ptx_version >= 350) + { + reduce_region_config.template Init(); + single_tile_config.template Init(); + } + else if (ptx_version >= 300) + { + reduce_region_config.template Init(); + single_tile_config.template Init(); + } + else if (ptx_version >= 200) + { + reduce_region_config.template Init(); + single_tile_config.template Init(); + } + else if (ptx_version >= 130) + { + reduce_region_config.template Init(); + single_tile_config.template Init(); + } + else + { + reduce_region_config.template Init(); + single_tile_config.template Init(); + } + + #endif + } + + + /** + * Kernel kernel dispatch configuration + */ + struct KernelConfig + { + int block_threads; + int items_per_thread; + int vector_load_length; + BlockReduceAlgorithm block_algorithm; + CacheLoadModifier load_modifier; + GridMappingStrategy grid_mapping; + + template + __host__ __device__ __forceinline__ + void Init() + { + block_threads = BlockPolicy::BLOCK_THREADS; + items_per_thread = BlockPolicy::ITEMS_PER_THREAD; + vector_load_length = BlockPolicy::VECTOR_LOAD_LENGTH; + block_algorithm = BlockPolicy::BLOCK_ALGORITHM; + load_modifier = BlockPolicy::LOAD_MODIFIER; + grid_mapping = BlockPolicy::GRID_MAPPING; + } + + __host__ __device__ __forceinline__ + void Print() + { + printf("%d threads, %d per thread, %d veclen, %d algo, %d loadmod, %d mapping", + block_threads, + items_per_thread, + vector_load_length, + block_algorithm, + load_modifier, + grid_mapping); + } + }; + + /****************************************************************************** + * Dispatch entrypoints + ******************************************************************************/ + + /** + * Internal dispatch routine for computing a device-wide reduction using the + * specified kernel functions. + * + * If the input is larger than a single tile, this method uses two-passes of + * kernel invocations. + */ + template < + typename ReduceRegionKernelPtr, ///< Function type of cub::ReduceRegionKernel + typename AggregateTileKernelPtr, ///< Function type of cub::SingleTileKernel for consuming partial reductions (T*) + typename SingleTileKernelPtr, ///< Function type of cub::SingleTileKernel for consuming input (InputIterator) + typename FillAndResetDrainKernelPtr> ///< Function type of cub::FillAndResetDrainKernel + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output aggregate + Offset num_items, ///< [in] Total number of input items (i.e., length of \p d_in) + ReductionOp reduction_op, ///< [in] Binary reduction functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + cudaStream_t stream, ///< [in] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous, ///< [in] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + FillAndResetDrainKernelPtr prepare_drain_kernel, ///< [in] Kernel function pointer to parameterization of cub::FillAndResetDrainKernel + ReduceRegionKernelPtr reduce_region_kernel, ///< [in] Kernel function pointer to parameterization of cub::ReduceRegionKernel + AggregateTileKernelPtr aggregate_kernel, ///< [in] Kernel function pointer to parameterization of cub::SingleTileKernel for consuming partial reductions (T*) + SingleTileKernelPtr single_kernel, ///< [in] Kernel function pointer to parameterization of cub::SingleTileKernel for consuming input (InputIterator) + KernelConfig &reduce_region_config, ///< [in] Dispatch parameters that match the policy that \p reduce_region_kernel_ptr was compiled for + KernelConfig &single_tile_config) ///< [in] Dispatch parameters that match the policy that \p single_kernel was compiled for + { +#ifndef CUB_RUNTIME_ENABLED + + // Kernel launch not supported from this device + return CubDebug(cudaErrorNotSupported ); + +#else + cudaError error = cudaSuccess; + do + { + // Get device ordinal + int device_ordinal; + if (CubDebug(error = cudaGetDevice(&device_ordinal))) break; + + // Get device SM version + int sm_version; + if (CubDebug(error = SmVersion(sm_version, device_ordinal))) break; + + // Get SM count + int sm_count; + if (CubDebug(error = cudaDeviceGetAttribute (&sm_count, cudaDevAttrMultiProcessorCount, device_ordinal))) break; + + // Tile size of reduce_region_kernel + int tile_size = reduce_region_config.block_threads * reduce_region_config.items_per_thread; + + if ((reduce_region_kernel == NULL) || (num_items <= tile_size)) + { + // Dispatch a single-block reduction kernel + + // Return if the caller is simply requesting the size of the storage allocation + if (d_temp_storage == NULL) + { + temp_storage_bytes = 1; + return cudaSuccess; + } + + // Log single_kernel configuration + if (debug_synchronous) CubLog("Invoking ReduceSingle<<<1, %d, 0, %lld>>>(), %d items per thread\n", + single_tile_config.block_threads, (long long) stream, single_tile_config.items_per_thread); + + // Invoke single_kernel + single_kernel<<<1, single_tile_config.block_threads>>>( + d_in, + d_out, + num_items, + reduction_op); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + + } + else + { + // Dispatch two kernels: (1) a multi-block kernel to compute + // privatized per-block reductions, and (2) a single-block + // to reduce those partial reductions + + // Get SM occupancy for reduce_region_kernel + int reduce_region_sm_occupancy; + if (CubDebug(error = MaxSmOccupancy( + reduce_region_sm_occupancy, + sm_version, + reduce_region_kernel, + reduce_region_config.block_threads))) break; + + // Get device occupancy for reduce_region_kernel + int reduce_region_occupancy = reduce_region_sm_occupancy * sm_count; + + // Even-share work distribution + int subscription_factor = reduce_region_sm_occupancy; // Amount of CTAs to oversubscribe the device beyond actively-resident (heuristic) + GridEvenShare even_share( + num_items, + reduce_region_occupancy * subscription_factor, + tile_size); + + // Get grid size for reduce_region_kernel + int reduce_region_grid_size; + switch (reduce_region_config.grid_mapping) + { + case GRID_MAPPING_EVEN_SHARE: + + // Work is distributed evenly + reduce_region_grid_size = even_share.grid_size; + break; + + case GRID_MAPPING_DYNAMIC: + + // Work is distributed dynamically + int num_tiles = (num_items + tile_size - 1) / tile_size; + reduce_region_grid_size = (num_tiles < reduce_region_occupancy) ? + num_tiles : // Not enough to fill the device with threadblocks + reduce_region_occupancy; // Fill the device with threadblocks + break; + }; + + // Temporary storage allocation requirements + void* allocations[2]; + size_t allocation_sizes[2] = + { + reduce_region_grid_size * sizeof(T), // bytes needed for privatized block reductions + GridQueue::AllocationSize() // bytes needed for grid queue descriptor + }; + + // Alias the temporary allocations from the single storage blob (or set the necessary size of the blob) + if (CubDebug(error = AliasTemporaries(d_temp_storage, temp_storage_bytes, allocations, allocation_sizes))) break; + if (d_temp_storage == NULL) + { + // Return if the caller is simply requesting the size of the storage allocation + return cudaSuccess; + } + + // Alias the allocation for the privatized per-block reductions + T *d_block_reductions = (T*) allocations[0]; + + // Alias the allocation for the grid queue descriptor + GridQueue queue(allocations[1]); + + // Prepare the dynamic queue descriptor if necessary + if (reduce_region_config.grid_mapping == GRID_MAPPING_DYNAMIC) + { + // Prepare queue using a kernel so we know it gets prepared once per operation + if (debug_synchronous) CubLog("Invoking prepare_drain_kernel<<<1, 1, 0, %lld>>>()\n", (long long) stream); + + // Invoke prepare_drain_kernel + prepare_drain_kernel<<<1, 1, 0, stream>>>(queue, num_items); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + } + + // Log reduce_region_kernel configuration + if (debug_synchronous) CubLog("Invoking reduce_region_kernel<<<%d, %d, 0, %lld>>>(), %d items per thread, %d SM occupancy\n", + reduce_region_grid_size, reduce_region_config.block_threads, (long long) stream, reduce_region_config.items_per_thread, reduce_region_sm_occupancy); + + // Invoke reduce_region_kernel + reduce_region_kernel<<>>( + d_in, + d_block_reductions, + num_items, + even_share, + queue, + reduction_op); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + + // Log single_kernel configuration + if (debug_synchronous) CubLog("Invoking single_kernel<<<%d, %d, 0, %lld>>>(), %d items per thread\n", + 1, single_tile_config.block_threads, (long long) stream, single_tile_config.items_per_thread); + + // Invoke single_kernel + aggregate_kernel<<<1, single_tile_config.block_threads, 0, stream>>>( + d_block_reductions, + d_out, + reduce_region_grid_size, + reduction_op); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + } + } + while (0); + + return error; + +#endif // CUB_RUNTIME_ENABLED + } + + + /** + * Internal dispatch routine for computing a device-wide reduction + */ + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output aggregate + Offset num_items, ///< [in] Total number of input items (i.e., length of \p d_in) + ReductionOp reduction_op, ///< [in] Binary reduction functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + cudaStream_t stream, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + cudaError error = cudaSuccess; + do + { + // Get PTX version + int ptx_version; + #if (CUB_PTX_VERSION == 0) + if (CubDebug(error = PtxVersion(ptx_version))) break; + #else + ptx_version = CUB_PTX_VERSION; + #endif + + // Get kernel kernel dispatch configurations + KernelConfig reduce_region_config; + KernelConfig single_tile_config; + InitConfigs(ptx_version, reduce_region_config, single_tile_config); + + // Dispatch + if (CubDebug(error = Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + d_out, + num_items, + reduction_op, + stream, + debug_synchronous, + FillAndResetDrainKernel, + ReduceRegionKernel, + SingleTileKernel, + SingleTileKernel, + reduce_region_config, + single_tile_config))) break; + } + while (0); + + return error; + } +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_scan_dispatch.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_scan_dispatch.cuh new file mode 100644 index 0000000000000000000000000000000000000000..db7ddd45b2b891371b2e582456d8dc5348d631ae --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_scan_dispatch.cuh @@ -0,0 +1,559 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DeviceScan provides device-wide, parallel operations for computing a prefix scan across a sequence of data items residing within global memory. + */ + +#pragma once + +#include +#include + +#include "../block_region/block_region_scan.cuh" +#include "../../thread/thread_operators.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../util_debug.cuh" +#include "../../util_device.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Kernel entry points + *****************************************************************************/ + +/** + * Initialization kernel for tile status initialization (multi-block) + */ +template < + typename Offset, ///< Signed integer type for global offsets + typename TileLookbackStatus> ///< Tile status interface type +__global__ void ScanInitKernel( + GridQueue grid_queue, ///< [in] Descriptor for performing dynamic mapping of input tiles to thread blocks + TileLookbackStatus tile_status, ///< [in] Tile status interface + int num_tiles) ///< [in] Number of tiles +{ + // Reset queue descriptor + if ((blockIdx.x == 0) && (threadIdx.x == 0)) + grid_queue.FillAndResetDrain(num_tiles); + + // Initialize tile status + tile_status.InitializeStatus(num_tiles); +} + + +/** + * Scan kernel entry point (multi-block) + */ +template < + typename BlockRegionScanPolicy, ///< Parameterized BlockRegionScanPolicy tuning policy type + typename InputIterator, ///< Random-access input iterator type for reading scan input data \iterator + typename OutputIterator, ///< Random-access output iterator type for writing scan output data \iterator + typename TileLookbackStatus, ///< Tile status interface type + typename ScanOp, ///< Binary scan functor type having member T operator()(const T &a, const T &b) + typename Identity, ///< Identity value type (cub::NullType for inclusive scans) + typename Offset> ///< Signed integer type for global offsets +__launch_bounds__ (int(BlockRegionScanPolicy::BLOCK_THREADS)) +__global__ void ScanRegionKernel( + InputIterator d_in, ///< Input data + OutputIterator d_out, ///< Output data + TileLookbackStatus tile_status, ///< [in] Tile status interface + ScanOp scan_op, ///< Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + Identity identity, ///< Identity element + Offset num_items, ///< Total number of scan items for the entire problem + GridQueue queue) ///< Drain queue descriptor for dynamically mapping tile data onto thread blocks +{ + // Thread block type for scanning input tiles + typedef BlockRegionScan< + BlockRegionScanPolicy, + InputIterator, + OutputIterator, + ScanOp, + Identity, + Offset> BlockRegionScanT; + + // Shared memory for BlockRegionScan + __shared__ typename BlockRegionScanT::TempStorage temp_storage; + + // Process tiles + BlockRegionScanT(temp_storage, d_in, d_out, scan_op, identity).ConsumeRegion( + num_items, + queue, + tile_status); +} + + + + +/****************************************************************************** + * Dispatch + ******************************************************************************/ + +/** + * Utility class for dispatching the appropriately-tuned kernels for DeviceScan + */ +template < + typename InputIterator, ///< Random-access input iterator type for reading scan input data \iterator + typename OutputIterator, ///< Random-access output iterator type for writing scan output data \iterator + typename ScanOp, ///< Binary scan functor type having member T operator()(const T &a, const T &b) + typename Identity, ///< Identity value type (cub::NullType for inclusive scans) + typename Offset> ///< Signed integer type for global offsets +struct DeviceScanDispatch +{ + enum + { + INIT_KERNEL_THREADS = 128 + }; + + // Data type + typedef typename std::iterator_traits::value_type T; + + // Tile status descriptor interface type + typedef TileLookbackStatus TileLookbackStatus; + + + /****************************************************************************** + * Tuning policies + ******************************************************************************/ + + /// SM35 + struct Policy350 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 12, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + // GTX Titan: 29.5B items/s (232.4 GB/s) @ 48M 32-bit T + typedef BlockRegionScanPolicy< + 128, + ITEMS_PER_THREAD, + BLOCK_LOAD_DIRECT, + false, + LOAD_LDG, + BLOCK_STORE_WARP_TRANSPOSE, + true, + BLOCK_SCAN_RAKING_MEMOIZE> + ScanRegionPolicy; + }; + + /// SM30 + struct Policy300 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 9, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + typedef BlockRegionScanPolicy< + 256, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + false, + LOAD_DEFAULT, + BLOCK_STORE_WARP_TRANSPOSE, + false, + BLOCK_SCAN_RAKING_MEMOIZE> + ScanRegionPolicy; + }; + + /// SM20 + struct Policy200 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 15, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + // GTX 580: 20.3B items/s (162.3 GB/s) @ 48M 32-bit T + typedef BlockRegionScanPolicy< + 128, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + false, + LOAD_DEFAULT, + BLOCK_STORE_WARP_TRANSPOSE, + false, + BLOCK_SCAN_RAKING_MEMOIZE> + ScanRegionPolicy; + }; + + /// SM13 + struct Policy130 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 21, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + typedef BlockRegionScanPolicy< + 96, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + false, + LOAD_DEFAULT, + BLOCK_STORE_WARP_TRANSPOSE, + false, + BLOCK_SCAN_RAKING_MEMOIZE> + ScanRegionPolicy; + }; + + /// SM10 + struct Policy100 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 9, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + typedef BlockRegionScanPolicy< + 64, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + true, + LOAD_DEFAULT, + BLOCK_STORE_WARP_TRANSPOSE, + true, + BLOCK_SCAN_WARP_SCANS> + ScanRegionPolicy; + }; + + + /****************************************************************************** + * Tuning policies of current PTX compiler pass + ******************************************************************************/ + +#if (CUB_PTX_VERSION >= 350) + typedef Policy350 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 300) + typedef Policy300 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 200) + typedef Policy200 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 130) + typedef Policy130 PtxPolicy; + +#else + typedef Policy100 PtxPolicy; + +#endif + + // "Opaque" policies (whose parameterizations aren't reflected in the type signature) + struct PtxScanRegionPolicy : PtxPolicy::ScanRegionPolicy {}; + + + /****************************************************************************** + * Utilities + ******************************************************************************/ + + /** + * Initialize kernel dispatch configurations with the policies corresponding to the PTX assembly we will use + */ + template + __host__ __device__ __forceinline__ + static void InitConfigs( + int ptx_version, + KernelConfig &scan_region_config) + { + #if (CUB_PTX_VERSION > 0) + + // We're on the device, so initialize the kernel dispatch configurations with the current PTX policy + scan_region_config.template Init(); + + #else + + // We're on the host, so lookup and initialize the kernel dispatch configurations with the policies that match the device's PTX version + if (ptx_version >= 350) + { + scan_region_config.template Init(); + } + else if (ptx_version >= 300) + { + scan_region_config.template Init(); + } + else if (ptx_version >= 200) + { + scan_region_config.template Init(); + } + else if (ptx_version >= 130) + { + scan_region_config.template Init(); + } + else + { + scan_region_config.template Init(); + } + + #endif + } + + + /** + * Kernel kernel dispatch configuration. Mirrors the constants within BlockRegionScanPolicy. + */ + struct KernelConfig + { + int block_threads; + int items_per_thread; + BlockLoadAlgorithm load_policy; + BlockStoreAlgorithm store_policy; + BlockScanAlgorithm scan_algorithm; + + template + __host__ __device__ __forceinline__ + void Init() + { + block_threads = BlockRegionScanPolicy::BLOCK_THREADS; + items_per_thread = BlockRegionScanPolicy::ITEMS_PER_THREAD; + load_policy = BlockRegionScanPolicy::LOAD_ALGORITHM; + store_policy = BlockRegionScanPolicy::STORE_ALGORITHM; + scan_algorithm = BlockRegionScanPolicy::SCAN_ALGORITHM; + } + + __host__ __device__ __forceinline__ + void Print() + { + printf("%d, %d, %d, %d, %d", + block_threads, + items_per_thread, + load_policy, + store_policy, + scan_algorithm); + } + }; + + + /****************************************************************************** + * Dispatch entrypoints + ******************************************************************************/ + + /** + * Internal dispatch routine for computing a device-wide prefix scan using the + * specified kernel functions. + */ + template < + typename ScanInitKernelPtr, ///< Function type of cub::ScanInitKernel + typename ScanRegionKernelPtr> ///< Function type of cub::ScanRegionKernelPtr + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output sequence of data items + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + Identity identity, ///< [in] Identity element + Offset num_items, ///< [in] Total number of input items (i.e., the length of \p d_in) + cudaStream_t stream, ///< [in] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous, ///< [in] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + int ptx_version, ///< [in] PTX version of dispatch kernels + ScanInitKernelPtr init_kernel, ///< [in] Kernel function pointer to parameterization of cub::ScanInitKernel + ScanRegionKernelPtr scan_region_kernel, ///< [in] Kernel function pointer to parameterization of cub::ScanRegionKernel + KernelConfig scan_region_config) ///< [in] Dispatch parameters that match the policy that \p scan_region_kernel was compiled for + { + +#ifndef CUB_RUNTIME_ENABLED + + // Kernel launch not supported from this device + return CubDebug(cudaErrorNotSupported); + +#else + cudaError error = cudaSuccess; + do + { + // Get device ordinal + int device_ordinal; + if (CubDebug(error = cudaGetDevice(&device_ordinal))) break; + + // Get device SM version + int sm_version; + if (CubDebug(error = SmVersion(sm_version, device_ordinal))) break; + + // Get SM count + int sm_count; + if (CubDebug(error = cudaDeviceGetAttribute (&sm_count, cudaDevAttrMultiProcessorCount, device_ordinal))) break; + + // Number of input tiles + int tile_size = scan_region_config.block_threads * scan_region_config.items_per_thread; + int num_tiles = (num_items + tile_size - 1) / tile_size; + + // Specify temporary storage allocation requirements + size_t allocation_sizes[2]; + if (CubDebug(error = TileLookbackStatus::AllocationSize(num_tiles, allocation_sizes[0]))) break; // bytes needed for tile status descriptors + allocation_sizes[1] = GridQueue::AllocationSize(); // bytes needed for grid queue descriptor + + // Compute allocation pointers into the single storage blob (or set the necessary size of the blob) + void* allocations[2]; + if (CubDebug(error = AliasTemporaries(d_temp_storage, temp_storage_bytes, allocations, allocation_sizes))) break; + if (d_temp_storage == NULL) + { + // Return if the caller is simply requesting the size of the storage allocation + return cudaSuccess; + } + + // Construct the tile status interface + TileLookbackStatus tile_status; + if (CubDebug(error = tile_status.Init(num_tiles, allocations[0], allocation_sizes[0]))) break; + + // Construct the grid queue descriptor + GridQueue queue(allocations[1]); + + // Log init_kernel configuration + int init_grid_size = (num_tiles + INIT_KERNEL_THREADS - 1) / INIT_KERNEL_THREADS; + if (debug_synchronous) CubLog("Invoking init_kernel<<<%d, %d, 0, %lld>>>()\n", init_grid_size, INIT_KERNEL_THREADS, (long long) stream); + + // Invoke init_kernel to initialize tile descriptors and queue descriptors + init_kernel<<>>( + queue, + tile_status, + num_tiles); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + + // Get SM occupancy for scan_region_kernel + int scan_region_sm_occupancy; + if (CubDebug(error = MaxSmOccupancy( + scan_region_sm_occupancy, // out + sm_version, + scan_region_kernel, + scan_region_config.block_threads))) break; + + // Get grid size for scanning tiles + dim3 scan_grid_size; + if (ptx_version <= 130) + { + // Blocks are launched in order, so just assign one block per tile + int max_dim_x = 32 * 1024; + scan_grid_size.z = 1; + scan_grid_size.y = (num_tiles + max_dim_x - 1) / max_dim_x; + scan_grid_size.x = CUB_MIN(num_tiles, max_dim_x); + } + else + { + // Blocks may not be launched in order, so use atomics + int scan_region_occupancy = scan_region_sm_occupancy * sm_count; // Whole-device occupancy for scan_region_kernel + scan_grid_size.z = 1; + scan_grid_size.y = 1; + scan_grid_size.x = (num_tiles < scan_region_occupancy) ? + num_tiles : // Not enough to fill the device with threadblocks + scan_region_occupancy; // Fill the device with threadblocks + } + + // Log scan_region_kernel configuration + if (debug_synchronous) CubLog("Invoking scan_region_kernel<<<{%d,%d,%d}, %d, 0, %lld>>>(), %d items per thread, %d SM occupancy\n", + scan_grid_size.x, scan_grid_size.y, scan_grid_size.z, scan_region_config.block_threads, (long long) stream, scan_region_config.items_per_thread, scan_region_sm_occupancy); + + // Invoke scan_region_kernel + scan_region_kernel<<>>( + d_in, + d_out, + tile_status, + scan_op, + identity, + num_items, + queue); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + } + while (0); + + return error; + +#endif // CUB_RUNTIME_ENABLED + } + + + /** + * Internal dispatch routine + */ + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to the input sequence of data items + OutputIterator d_out, ///< [out] Pointer to the output sequence of data items + ScanOp scan_op, ///< [in] Binary scan functor (e.g., an instance of cub::Sum, cub::Min, cub::Max, etc.) + Identity identity, ///< [in] Identity element + Offset num_items, ///< [in] Total number of input items (i.e., the length of \p d_in) + cudaStream_t stream, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + cudaError error = cudaSuccess; + do + { + // Get PTX version + int ptx_version; + #if (CUB_PTX_VERSION == 0) + if (CubDebug(error = PtxVersion(ptx_version))) break; + #else + ptx_version = CUB_PTX_VERSION; + #endif + + // Get kernel kernel dispatch configurations + KernelConfig scan_region_config; + InitConfigs(ptx_version, scan_region_config); + + // Dispatch + if (CubDebug(error = Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + d_out, + scan_op, + identity, + num_items, + stream, + debug_synchronous, + ptx_version, + ScanInitKernel, + ScanRegionKernel, + scan_region_config))) break; + } + while (0); + + return error; + } +}; + + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_select_dispatch.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_select_dispatch.cuh new file mode 100644 index 0000000000000000000000000000000000000000..22b47dd2f1a07d2963ebeb2434d434f2b2bf7552 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/dispatch/device_select_dispatch.cuh @@ -0,0 +1,558 @@ + +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::DeviceSelect provides device-wide, parallel operations for selecting items from sequences of data items residing within global memory. + */ + +#pragma once + +#include +#include + +#include "device_scan_dispatch.cuh" +#include "../block_region/block_region_select.cuh" +#include "../../thread/thread_operators.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../util_device.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/****************************************************************************** + * Kernel entry points + *****************************************************************************/ + +/** + * Select kernel entry point (multi-block) + * + * Performs functor-based selection if SelectOp functor type != NullType + * Otherwise performs flag-based selection if FlagIterator's value type != NullType + * Otherwise performs discontinuity selection (keep unique) + */ +template < + typename BlockRegionSelectPolicy, ///< Parameterized BlockRegionSelectPolicy tuning policy type + typename InputIterator, ///< Random-access input iterator type for reading input items + typename FlagIterator, ///< Random-access input iterator type for reading selection flags (NullType* if a selection functor or discontinuity flagging is to be used for selection) + typename OutputIterator, ///< Random-access output iterator type for writing selected items + typename NumSelectedIterator, ///< Output iterator type for recording the number of items selected + typename TileLookbackStatus, ///< Tile status interface type + typename SelectOp, ///< Selection operator type (NullType if selection flags or discontinuity flagging is to be used for selection) + typename EqualityOp, ///< Equality operator type (NullType if selection functor or selection flags is to be used for selection) + typename Offset, ///< Signed integer type for global offsets + bool KEEP_REJECTS> ///< Whether or not we push rejected items to the back of the output +__launch_bounds__ (int(BlockRegionSelectPolicy::BLOCK_THREADS)) +__global__ void SelectRegionKernel( + InputIterator d_in, ///< [in] Pointer to input sequence of data items + FlagIterator d_flags, ///< [in] Pointer to the input sequence of selection flags + OutputIterator d_out, ///< [in] Pointer to output sequence of selected data items + NumSelectedIterator d_num_selected, ///< [in] Pointer to total number of items selected (i.e., length of \p d_out) + TileLookbackStatus tile_status, ///< [in] Tile status interface + SelectOp select_op, ///< [in] Selection operator + EqualityOp equality_op, ///< [in] Equality operator + Offset num_items, ///< [in] Total number of input items (i.e., length of \p d_in) + int num_tiles, ///< [in] Total number of tiles for the entire problem + GridQueue queue) ///< [in] Drain queue descriptor for dynamically mapping tile data onto thread blocks +{ + // Thread block type for selecting data from input tiles + typedef BlockRegionSelect< + BlockRegionSelectPolicy, + InputIterator, + FlagIterator, + OutputIterator, + SelectOp, + EqualityOp, + Offset, + KEEP_REJECTS> BlockRegionSelectT; + + // Shared memory for BlockRegionSelect + __shared__ typename BlockRegionSelectT::TempStorage temp_storage; + + // Process tiles + BlockRegionSelectT(temp_storage, d_in, d_flags, d_out, select_op, equality_op, num_items).ConsumeRegion( + num_tiles, + queue, + tile_status, + d_num_selected); +} + + + + +/****************************************************************************** + * Dispatch + ******************************************************************************/ + +/** + * Utility class for dispatching the appropriately-tuned kernels for DeviceSelect + */ +template < + typename InputIterator, ///< Random-access input iterator type for reading input items + typename FlagIterator, ///< Random-access input iterator type for reading selection flags (NullType* if a selection functor or discontinuity flagging is to be used for selection) + typename OutputIterator, ///< Random-access output iterator type for writing selected items + typename NumSelectedIterator, ///< Output iterator type for recording the number of items selected + typename SelectOp, ///< Selection operator type (NullType if selection flags or discontinuity flagging is to be used for selection) + typename EqualityOp, ///< Equality operator type (NullType if selection functor or selection flags is to be used for selection) + typename Offset, ///< Signed integer type for global offsets + bool KEEP_REJECTS> ///< Whether or not we push rejected items to the back of the output +struct DeviceSelectDispatch +{ + /****************************************************************************** + * Types and constants + ******************************************************************************/ + + // Data type of input iterator + typedef typename std::iterator_traits::value_type T; + + // Data type of flag iterator + typedef typename std::iterator_traits::value_type Flag; + + enum + { + INIT_KERNEL_THREADS = 128, + }; + + // Tile status descriptor interface type + typedef TileLookbackStatus TileLookbackStatus; + + + /****************************************************************************** + * Tuning policies + ******************************************************************************/ + + /// SM35 + struct Policy350 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 11, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + typedef BlockRegionSelectPolicy< + 128, + ITEMS_PER_THREAD, + BLOCK_LOAD_DIRECT, + LOAD_LDG, + true, + BLOCK_SCAN_WARP_SCANS> + SelectRegionPolicy; + }; + + /// SM30 + struct Policy300 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 5, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + typedef BlockRegionSelectPolicy< + 256, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + LOAD_DEFAULT, + true, + BLOCK_SCAN_RAKING_MEMOIZE> + SelectRegionPolicy; + }; + + /// SM20 + struct Policy200 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = (KEEP_REJECTS) ? 7 : 17, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + typedef BlockRegionSelectPolicy< + 128, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + LOAD_DEFAULT, + true, + BLOCK_SCAN_WARP_SCANS> + SelectRegionPolicy; + }; + + /// SM13 + struct Policy130 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 9, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + typedef BlockRegionSelectPolicy< + 64, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + LOAD_DEFAULT, + true, + BLOCK_SCAN_RAKING_MEMOIZE> + SelectRegionPolicy; + }; + + /// SM10 + struct Policy100 + { + enum { + NOMINAL_4B_ITEMS_PER_THREAD = 9, + ITEMS_PER_THREAD = CUB_MIN(NOMINAL_4B_ITEMS_PER_THREAD, CUB_MAX(1, (NOMINAL_4B_ITEMS_PER_THREAD * 4 / sizeof(T)))), + }; + + typedef BlockRegionSelectPolicy< + 256, + ITEMS_PER_THREAD, + BLOCK_LOAD_WARP_TRANSPOSE, + LOAD_DEFAULT, + true, + BLOCK_SCAN_RAKING_MEMOIZE> + SelectRegionPolicy; + }; + + + /****************************************************************************** + * Tuning policies of current PTX compiler pass + ******************************************************************************/ + +#if (CUB_PTX_VERSION >= 350) + typedef Policy350 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 300) + typedef Policy300 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 200) + typedef Policy200 PtxPolicy; + +#elif (CUB_PTX_VERSION >= 130) + typedef Policy130 PtxPolicy; + +#else + typedef Policy100 PtxPolicy; + +#endif + + // "Opaque" policies (whose parameterizations aren't reflected in the type signature) + struct PtxSelectRegionPolicy : PtxPolicy::SelectRegionPolicy {}; + + + /****************************************************************************** + * Utilities + ******************************************************************************/ + + /** + * Initialize kernel dispatch configurations with the policies corresponding to the PTX assembly we will use + */ + template + __host__ __device__ __forceinline__ + static void InitConfigs( + int ptx_version, + KernelConfig &select_region_config) + { + #if (CUB_PTX_VERSION > 0) + + // We're on the device, so initialize the kernel dispatch configurations with the current PTX policy + select_region_config.template Init(); + + #else + + // We're on the host, so lookup and initialize the kernel dispatch configurations with the policies that match the device's PTX version + if (ptx_version >= 350) + { + select_region_config.template Init(); + } + else if (ptx_version >= 300) + { + select_region_config.template Init(); + } + else if (ptx_version >= 200) + { + select_region_config.template Init(); + } + else if (ptx_version >= 130) + { + select_region_config.template Init(); + } + else + { + select_region_config.template Init(); + } + + #endif + } + + + /** + * Kernel kernel dispatch configuration. Mirrors the constants within BlockRegionSelectPolicy. + */ + struct KernelConfig + { + int block_threads; + int items_per_thread; + BlockLoadAlgorithm load_policy; + bool two_phase_scatter; + BlockScanAlgorithm scan_algorithm; + + template + __host__ __device__ __forceinline__ + void Init() + { + block_threads = BlockRegionSelectPolicy::BLOCK_THREADS; + items_per_thread = BlockRegionSelectPolicy::ITEMS_PER_THREAD; + load_policy = BlockRegionSelectPolicy::LOAD_ALGORITHM; + two_phase_scatter = BlockRegionSelectPolicy::TWO_PHASE_SCATTER; + scan_algorithm = BlockRegionSelectPolicy::SCAN_ALGORITHM; + } + + __host__ __device__ __forceinline__ + void Print() + { + printf("%d, %d, %d, %d, %d", + block_threads, + items_per_thread, + load_policy, + two_phase_scatter, + scan_algorithm); + } + }; + + + /****************************************************************************** + * Dispatch entrypoints + ******************************************************************************/ + + /** + * Internal dispatch routine for computing a device-wide prefix scan using the + * specified kernel functions. + */ + template < + typename ScanInitKernelPtr, ///< Function type of cub::ScanInitKernel + typename SelectRegionKernelPtr> ///< Function type of cub::SelectRegionKernelPtr + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to input sequence of data items + FlagIterator d_flags, ///< [in] Pointer to the input sequence of selection flags + OutputIterator d_out, ///< [in] Pointer to output sequence of selected data items + NumSelectedIterator d_num_selected, ///< [in] Pointer to total number of items selected (i.e., length of \p d_out) + SelectOp select_op, ///< [in] Selection operator + EqualityOp equality_op, ///< [in] Equality operator + Offset num_items, ///< [in] Total number of input items (i.e., length of \p d_in) + cudaStream_t stream, ///< [in] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous, ///< [in] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + int ptx_version, ///< [in] PTX version of dispatch kernels + ScanInitKernelPtr init_kernel, ///< [in] Kernel function pointer to parameterization of cub::ScanInitKernel + SelectRegionKernelPtr select_region_kernel, ///< [in] Kernel function pointer to parameterization of cub::SelectRegionKernel + KernelConfig select_region_config) ///< [in] Dispatch parameters that match the policy that \p select_region_kernel was compiled for + { + +#ifndef CUB_RUNTIME_ENABLED + + // Kernel launch not supported from this device + return CubDebug(cudaErrorNotSupported); + +#else + + cudaError error = cudaSuccess; + do + { + // Get device ordinal + int device_ordinal; + if (CubDebug(error = cudaGetDevice(&device_ordinal))) break; + + // Get device SM version + int sm_version; + if (CubDebug(error = SmVersion(sm_version, device_ordinal))) break; + + // Get SM count + int sm_count; + if (CubDebug(error = cudaDeviceGetAttribute (&sm_count, cudaDevAttrMultiProcessorCount, device_ordinal))) break; + + // Number of input tiles + int tile_size = select_region_config.block_threads * select_region_config.items_per_thread; + int num_tiles = (num_items + tile_size - 1) / tile_size; + + // Specify temporary storage allocation requirements + size_t allocation_sizes[2]; + if (CubDebug(error = TileLookbackStatus::AllocationSize(num_tiles, allocation_sizes[0]))) break; // bytes needed for tile status descriptors + allocation_sizes[1] = GridQueue::AllocationSize(); // bytes needed for grid queue descriptor + + // Compute allocation pointers into the single storage blob (or set the necessary size of the blob) + void* allocations[2]; + if (CubDebug(error = AliasTemporaries(d_temp_storage, temp_storage_bytes, allocations, allocation_sizes))) break; + if (d_temp_storage == NULL) + { + // Return if the caller is simply requesting the size of the storage allocation + return cudaSuccess; + } + + // Construct the tile status interface + TileLookbackStatus tile_status; + if (CubDebug(error = tile_status.Init(num_tiles, allocations[0], allocation_sizes[0]))) break; + + // Construct the grid queue descriptor + GridQueue queue(allocations[1]); + + // Log init_kernel configuration + int init_grid_size = (num_tiles + INIT_KERNEL_THREADS - 1) / INIT_KERNEL_THREADS; + if (debug_synchronous) CubLog("Invoking init_kernel<<<%d, %d, 0, %lld>>>()\n", init_grid_size, INIT_KERNEL_THREADS, (long long) stream); + + // Invoke init_kernel to initialize tile descriptors and queue descriptors + init_kernel<<>>( + queue, + tile_status, + num_tiles); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + + // Get SM occupancy for select_region_kernel + int select_region_sm_occupancy; + if (CubDebug(error = MaxSmOccupancy( + select_region_sm_occupancy, // out + sm_version, + select_region_kernel, + select_region_config.block_threads))) break; + + // Get grid size for scanning tiles + dim3 select_grid_size; + if (ptx_version <= 130) + { + // Blocks are launched in order, so just assign one block per tile + int max_dim_x = 32 * 1024; + select_grid_size.z = 1; + select_grid_size.y = (num_tiles + max_dim_x - 1) / max_dim_x; + select_grid_size.x = CUB_MIN(num_tiles, max_dim_x); + } + else + { + // Blocks may not be launched in order, so use atomics + int select_region_occupancy = select_region_sm_occupancy * sm_count; // Whole-device occupancy for select_region_kernel + select_grid_size.z = 1; + select_grid_size.y = 1; + select_grid_size.x = (num_tiles < select_region_occupancy) ? + num_tiles : // Not enough to fill the device with threadblocks + select_region_occupancy; // Fill the device with threadblocks + } + + // Log select_region_kernel configuration + if (debug_synchronous) CubLog("Invoking select_region_kernel<<<{%d,%d,%d}, %d, 0, %lld>>>(), %d items per thread, %d SM occupancy\n", + select_grid_size.x, select_grid_size.y, select_grid_size.z, select_region_config.block_threads, (long long) stream, select_region_config.items_per_thread, select_region_sm_occupancy); + + // Invoke select_region_kernel + select_region_kernel<<>>( + d_in, + d_flags, + d_out, + d_num_selected, + tile_status, + select_op, + equality_op, + num_items, + num_tiles, + queue); + + // Sync the stream if specified + if (debug_synchronous && (CubDebug(error = SyncStream(stream)))) break; + } + while (0); + + return error; + +#endif // CUB_RUNTIME_ENABLED + } + + + /** + * Internal dispatch routine + */ + __host__ __device__ __forceinline__ + static cudaError_t Dispatch( + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t &temp_storage_bytes, ///< [in,out] Reference to size in bytes of \p d_temp_storage allocation + InputIterator d_in, ///< [in] Pointer to input sequence of data items + FlagIterator d_flags, ///< [in] Pointer to the input sequence of selection flags + OutputIterator d_out, ///< [in] Pointer to output sequence of selected data items + NumSelectedIterator d_num_selected, ///< [in] Pointer to total number of items selected (i.e., length of \p d_out) + SelectOp select_op, ///< [in] Selection operator + EqualityOp equality_op, ///< [in] Equality operator + Offset num_items, ///< [in] Total number of input items (i.e., length of \p d_in) + cudaStream_t stream, ///< [in] [optional] CUDA stream to launch kernels within. Default is stream0. + bool debug_synchronous) ///< [in] [optional] Whether or not to synchronize the stream after every kernel launch to check for errors. Also causes launch configurations to be printed to the console. Default is \p false. + { + cudaError error = cudaSuccess; + do + { + // Get PTX version + int ptx_version; + #if (CUB_PTX_VERSION == 0) + if (CubDebug(error = PtxVersion(ptx_version))) break; + #else + ptx_version = CUB_PTX_VERSION; + #endif + + // Get kernel kernel dispatch configurations + KernelConfig select_region_config; + InitConfigs(ptx_version, select_region_config); + + // Dispatch + if (CubDebug(error = Dispatch( + d_temp_storage, + temp_storage_bytes, + d_in, + d_flags, + d_out, + d_num_selected, + select_op, + equality_op, + num_items, + stream, + debug_synchronous, + ptx_version, + ScanInitKernel, + SelectRegionKernel, + select_region_config))) break; + } + while (0); + + return error; + } +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/persistent_block/persistent_block_histo_256.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/persistent_block/persistent_block_histo_256.cuh new file mode 100644 index 0000000000000000000000000000000000000000..8c4d93a1d1581eebc1ed7d447918d6507708145e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/persistent_block/persistent_block_histo_256.cuh @@ -0,0 +1,810 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::PersistentBlockHisto256 implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide 256-bin histogram. + */ + +#pragma once + +#include + +#include "../../util_arch.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_histo_256.cuh" +#include "../../block/block_radix_sort.cuh" +#include "../../block/block_discontinuity.cuh" +#include "../../grid/grid_mapping.cuh" +#include "../../grid/grid_even_share.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../util_vector.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Algorithmic variants + ******************************************************************************/ + + +/** + * \brief PersistentBlockHisto256Algorithm enumerates alternative algorithms for the parallel construction of 8b histograms. + */ +enum PersistentBlockHisto256Algorithm +{ + + /** + * \par Overview + * A two-kernel approach in which: + * -# Thread blocks in the first kernel aggregate their own privatized + * histograms using block-wide sorting (see BlockHisto256Algorithm::BLOCK_HISTO_256_SORT). + * -# A single thread block in the second kernel reduces them into the output histogram(s). + * + * \par Performance Considerations + * Delivers consistent throughput regardless of sample bin distribution. + */ + GRID_HISTO_256_SORT, + + + /** + * \par Overview + * A two-kernel approach in which: + * -# Thread blocks in the first kernel aggregate their own privatized + * histograms using shared-memory \p atomicAdd(). + * -# A single thread block in the second kernel reduces them into the + * output histogram(s). + * + * \par Performance Considerations + * Performance is strongly tied to the hardware implementation of atomic + * addition, and may be significantly degraded for non uniformly-random + * input distributions where many concurrent updates are likely to be + * made to the same bin counter. + */ + GRID_HISTO_256_SHARED_ATOMIC, + + + /** + * \par Overview + * A single-kernel approach in which thread blocks update the output histogram(s) directly + * using global-memory \p atomicAdd(). + * + * \par Performance Considerations + * Performance is strongly tied to the hardware implementation of atomic + * addition, and may be significantly degraded for non uniformly-random + * input distributions where many concurrent updates are likely to be + * made to the same bin counter. + */ + GRID_HISTO_256_GLOBAL_ATOMIC, + +}; + + +/****************************************************************************** + * Tuning policy + ******************************************************************************/ + +/** + * Tuning policy for PersistentBlockHisto256 + */ +template < + int _BLOCK_THREADS, + int _ITEMS_PER_THREAD, + PersistentBlockHisto256Algorithm _GRID_ALGORITHM, + GridMappingStrategy _GRID_MAPPING, + int _SM_OCCUPANCY> +struct PersistentBlockHisto256Policy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, + SM_OCCUPANCY = _SM_OCCUPANCY, + }; + + static const PersistentBlockHisto256Algorithm GRID_ALGORITHM = _GRID_ALGORITHM; + static const GridMappingStrategy GRID_MAPPING = _GRID_MAPPING; +}; + + + +/****************************************************************************** + * PersistentBlockHisto256 + ******************************************************************************/ + +/** + * \brief implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide 256-bin histogram. + */ +template < + typename PersistentBlockHisto256Policy, ///< Tuning policy + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIteratorRA, ///< The input iterator type (may be a simple pointer type). Must have a value type that is assignable to unsigned char + typename HistoCounter, ///< Integral type for counting sample occurrences per histogram bin + typename SizeT, ///< Integer type for offsets + PersistentBlockHisto256Algorithm GRID_ALGORITHM = PersistentBlockHisto256Policy::GRID_ALGORITHM> +struct PersistentBlockHisto256; + + +/** + * Specialized for GRID_HISTO_256_GLOBAL_ATOMIC + */ +template < + typename PersistentBlockHisto256Policy, ///< Tuning policy + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIteratorRA, ///< The input iterator type (may be a simple pointer type). Must have a value type that is assignable to unsigned char + typename HistoCounter, ///< Integral type for counting sample occurrences per histogram bin + typename SizeT> ///< Integer type for offsets +struct PersistentBlockHisto256 +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Constants + enum + { + BLOCK_THREADS = PersistentBlockHisto256Policy::BLOCK_THREADS, + ITEMS_PER_THREAD = PersistentBlockHisto256Policy::ITEMS_PER_THREAD, + TILE_CHANNEL_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + TILE_ITEMS = TILE_CHANNEL_ITEMS * CHANNELS, + }; + + // Shared memory type required by this thread block + struct SmemStorage {}; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + /// Reference to smem_storage + SmemStorage &smem_storage; + + /// Reference to output histograms + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]; + + /// Input data to reduce + InputIteratorRA d_in; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ PersistentBlockHisto256( + SmemStorage &smem_storage, ///< Reference to smem_storage + InputIteratorRA d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) : ///< Reference to output histograms + smem_storage(smem_storage), + d_in(d_in), + d_out_histograms(d_out_histograms) + {} + + + /** + * The number of items processed per "tile" + */ + __device__ __forceinline__ int TileItems() + { + return TILE_ITEMS; + } + + + /** + * Process a single tile. + */ + __device__ __forceinline__ void ConsumeTile( + bool &sync_after, + SizeT block_offset, + int num_valid) + { + if (num_valid < TILE_ITEMS) + { + // Only a partially-full tile of samples to read and composite + int bounds = num_valid - (threadIdx.x * CHANNELS); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (((ACTIVE_CHANNELS == CHANNELS) || (CHANNEL < ACTIVE_CHANNELS)) && ((ITEM * BLOCK_THREADS * CHANNELS) + CHANNEL < bounds)) + { + unsigned char item = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + atomicAdd(d_out_histograms[CHANNEL] + item, 1); + } + } + } + + } + else + { + // Full tile of samples to read and composite + unsigned char items[ITEMS_PER_THREAD][CHANNELS]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + items[ITEM][CHANNEL] = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + } + } + } + + __threadfence_block(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + atomicAdd(d_out_histograms[CHANNEL] + items[ITEM][CHANNEL], 1); + } + } + } + } + + // No need to sync after processing this tile to ensure smem coherence + sync_after = false; + } + + + /** + * Finalize the computation. + */ + __device__ __forceinline__ void Finalize( + int dummy_result) + {} +}; + + + + +/** + * Specialized for GRID_HISTO_256_SHARED_ATOMIC + */ +template < + typename PersistentBlockHisto256Policy, ///< Tuning policy + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIteratorRA, ///< The input iterator type (may be a simple pointer type). Must have a value type that is assignable to unsigned char + typename HistoCounter, ///< Integral type for counting sample occurrences per histogram bin + typename SizeT> ///< Integer type for offsets +struct PersistentBlockHisto256 +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Constants + enum + { + BLOCK_THREADS = PersistentBlockHisto256Policy::BLOCK_THREADS, + ITEMS_PER_THREAD = PersistentBlockHisto256Policy::ITEMS_PER_THREAD, + TILE_CHANNEL_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + TILE_ITEMS = TILE_CHANNEL_ITEMS * CHANNELS, + }; + + // Shared memory type required by this thread block + struct SmemStorage + { + HistoCounter histograms[ACTIVE_CHANNELS][256]; + }; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + /// Reference to smem_storage + SmemStorage &smem_storage; + + /// Reference to output histograms + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]; + + /// Input data to reduce + InputIteratorRA d_in; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ PersistentBlockHisto256( + SmemStorage &smem_storage, ///< Reference to smem_storage + InputIteratorRA d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) : ///< Reference to output histograms + smem_storage(smem_storage), + d_in(d_in), + d_out_histograms(d_out_histograms) + { + // Initialize histogram bin counts to zeros + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + int histo_offset = 0; + + #pragma unroll + for(; histo_offset + BLOCK_THREADS <= 256; histo_offset += BLOCK_THREADS) + { + smem_storage.histograms[CHANNEL][histo_offset + threadIdx.x] = 0; + } + // Finish up with guarded initialization if necessary + if ((histo_offset < BLOCK_THREADS) && (histo_offset + threadIdx.x < 256)) + { + smem_storage.histograms[CHANNEL][histo_offset + threadIdx.x] = 0; + } + } + } + + + /** + * The number of items processed per "tile" + */ + __device__ __forceinline__ int TileItems() + { + return TILE_ITEMS; + } + + + /** + * Process a single tile. + */ + __device__ __forceinline__ void ConsumeTile( + bool &sync_after, + SizeT block_offset, + int num_valid) + { + if (num_valid < TILE_ITEMS) + { + // Only a partially-full tile of samples to read and composite + int bounds = num_valid - (threadIdx.x * CHANNELS); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (((ACTIVE_CHANNELS == CHANNELS) || (CHANNEL < ACTIVE_CHANNELS)) && ((ITEM * BLOCK_THREADS * CHANNELS) + CHANNEL < bounds)) + { + unsigned char item = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + atomicAdd(smem_storage.histograms[CHANNEL] + item, 1); + } + } + } + + } + else + { + // Full tile of samples to read and composite + unsigned char items[ITEMS_PER_THREAD][CHANNELS]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + items[ITEM][CHANNEL] = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + } + } + } + + __threadfence_block(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + atomicAdd(smem_storage.histograms[CHANNEL] + items[ITEM][CHANNEL], 1); + } + } + } + } + + // No need to sync after processing this tile to ensure smem coherence + sync_after = false; + } + + + /** + * Finalize the computation. + */ + __device__ __forceinline__ void Finalize( + int dummy_result) + { + // Barrier to ensure shared memory histograms are coherent + __syncthreads(); + + // Copy shared memory histograms to output + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + int channel_offset = (blockIdx.x * 256); + int histo_offset = 0; + + #pragma unroll + for(; histo_offset + BLOCK_THREADS <= 256; histo_offset += BLOCK_THREADS) + { + d_out_histograms[CHANNEL][channel_offset + histo_offset + threadIdx.x] = smem_storage.histograms[CHANNEL][histo_offset + threadIdx.x]; + } + // Finish up with guarded initialization if necessary + if ((histo_offset < BLOCK_THREADS) && (histo_offset + threadIdx.x < 256)) + { + d_out_histograms[CHANNEL][channel_offset + histo_offset + threadIdx.x] = smem_storage.histograms[CHANNEL][histo_offset + threadIdx.x]; + } + } + } +}; + + +/** + * Specialized for GRID_HISTO_256_SORT + */ +template < + typename PersistentBlockHisto256Policy, ///< Tuning policy + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIteratorRA, ///< The input iterator type (may be a simple pointer type). Must have a value type that is assignable to unsigned char + typename HistoCounter, ///< Integral type for counting sample occurrences per histogram bin + typename SizeT> ///< Integer type for offsets +struct PersistentBlockHisto256 +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Constants + enum + { + BLOCK_THREADS = PersistentBlockHisto256Policy::BLOCK_THREADS, + ITEMS_PER_THREAD = PersistentBlockHisto256Policy::ITEMS_PER_THREAD, + TILE_CHANNEL_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + TILE_ITEMS = TILE_CHANNEL_ITEMS * CHANNELS, + + STRIPED_COUNTERS_PER_THREAD = (256 + BLOCK_THREADS - 1) / BLOCK_THREADS, + }; + + // Parameterize BlockRadixSort type for our thread block + typedef BlockRadixSort BlockRadixSortT; + + // Parameterize BlockDiscontinuity type for our thread block + typedef BlockDiscontinuity BlockDiscontinuityT; + + // Shared memory type required by this thread block + union SmemStorage + { + // Storage for sorting bin values + typename BlockRadixSortT::SmemStorage sort_storage; + + struct + { + // Storage for detecting discontinuities in the tile of sorted bin values + typename BlockDiscontinuityT::SmemStorage discont_storage; + + // Storage for noting begin/end offsets of bin runs in the tile of sorted bin values + unsigned int run_begin[BLOCK_THREADS * STRIPED_COUNTERS_PER_THREAD]; + unsigned int run_end[BLOCK_THREADS * STRIPED_COUNTERS_PER_THREAD]; + }; + }; + + + // Discontinuity functor + struct DiscontinuityOp + { + // Reference to smem_storage + SmemStorage &smem_storage; + + // Constructor + __device__ __forceinline__ DiscontinuityOp(SmemStorage &smem_storage) : smem_storage(smem_storage) {} + + // Discontinuity predicate + __device__ __forceinline__ bool operator()(const unsigned char &a, const unsigned char &b, unsigned int b_index) + { + if (a != b) + { + // Note the begin/end offsets in shared storage + smem_storage.run_begin[b] = b_index; + smem_storage.run_end[a] = b_index; + + return true; + } + else + { + return false; + } + } + }; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + /// Reference to smem_storage + SmemStorage &smem_storage; + + /// Histogram counters striped across threads + HistoCounter thread_counters[ACTIVE_CHANNELS][STRIPED_COUNTERS_PER_THREAD]; + + /// Reference to output histograms + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]; + + /// Input data to reduce + InputIteratorRA d_in; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ PersistentBlockHisto256( + SmemStorage &smem_storage, ///< Reference to smem_storage + InputIteratorRA d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) : ///< Reference to output histograms + smem_storage(smem_storage), + d_in(d_in), + d_out_histograms(d_out_histograms) + { + // Initialize histogram counters striped across threads + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + thread_counters[CHANNEL][COUNTER] = 0; + } + } + } + + + /** + * The number of items processed per "tile" + */ + __device__ __forceinline__ int TileItems() + { + return TILE_ITEMS; + } + + + /** + * Composite a tile of input items + */ + __device__ __forceinline__ void Composite( + unsigned char (&items)[ITEMS_PER_THREAD], ///< Tile of samples + HistoCounter thread_counters[STRIPED_COUNTERS_PER_THREAD]) ///< Histogram counters striped across threads + { + // Sort bytes in blocked arrangement + BlockRadixSortT::SortBlocked(smem_storage.sort_storage, items); + + __syncthreads(); + + // Initialize the shared memory's run_begin and run_end for each bin + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + smem_storage.run_begin[(COUNTER * BLOCK_THREADS) + threadIdx.x] = TILE_CHANNEL_ITEMS; + smem_storage.run_end[(COUNTER * BLOCK_THREADS) + threadIdx.x] = TILE_CHANNEL_ITEMS; + } + + __syncthreads(); + + // Note the begin/end run offsets of bin runs in the sorted tile + int flags[ITEMS_PER_THREAD]; // unused + DiscontinuityOp flag_op(smem_storage); + BlockDiscontinuityT::Flag(smem_storage.discont_storage, items, flag_op, flags); + + // Update begin for first item + if (threadIdx.x == 0) smem_storage.run_begin[items[0]] = 0; + + __syncthreads(); + + // Composite into histogram + // Initialize the shared memory's run_begin and run_end for each bin + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + int bin = (COUNTER * BLOCK_THREADS) + threadIdx.x; + thread_counters[COUNTER] += smem_storage.run_end[bin] - smem_storage.run_begin[bin]; + } + } + + + /** + * Process one channel within a tile. + */ + __device__ __forceinline__ void ConsumeTileChannel( + int channel, + SizeT block_offset, + int num_valid) + { + // Load items in striped fashion + if (num_valid < TILE_ITEMS) + { + // Only a partially-full tile of samples to read and composite + unsigned char items[ITEMS_PER_THREAD]; + + // Assign our tid as the bin for out-of-bounds items (to give an even distribution), and keep track of how oob items to subtract out later + int bounds = (num_valid - (threadIdx.x * CHANNELS)); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = ((ITEM * BLOCK_THREADS * CHANNELS) < bounds) ? + d_in[channel + block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS)] : + 0; + } + + // Composite our histogram data + Composite(items, thread_counters[channel]); + + __syncthreads(); + + // Correct the overcounting in the zero-bin from invalid (out-of-bounds) items + if (threadIdx.x == 0) + { + int extra = (TILE_ITEMS - num_valid) / CHANNELS; + thread_counters[channel][0] -= extra; + } + } + else + { + // Full tile of samples to read and composite + unsigned char items[ITEMS_PER_THREAD]; + + // Unguarded loads + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = d_in[channel + block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS)]; + } + + // Composite our histogram data + Composite(items, thread_counters[channel]); + } + } + + + /** + * Template iteration over channels (to silence not-unrolled warnings for SM10-13). Inductive step. + */ + template + struct IterateChannels + { + /** + * Process one channel within a tile. + */ + static __device__ __forceinline__ void ConsumeTileChannel( + PersistentBlockHisto256 *persistent_block_histo, + SizeT block_offset, + int num_valid) + { + __syncthreads(); + + persistent_block_histo->ConsumeTileChannel(CHANNEL, block_offset, num_valid); + + IterateChannels::ConsumeTileChannel(persistent_block_histo, block_offset, num_valid); + } + }; + + + /** + * Template iteration over channels (to silence not-unrolled warnings for SM10-13). Base step. + */ + template + struct IterateChannels + { + static __device__ __forceinline__ void ConsumeTileChannel(PersistentBlockHisto256 *persistent_block_histo, SizeT block_offset, int num_valid) {} + }; + + + /** + * Process a single tile. + * + * We take several passes through the tile in this variant, extracting the samples for one channel at a time + */ + __device__ __forceinline__ void ConsumeTile( + bool &sync_after, + SizeT block_offset, + int num_valid) + { + // First channel + ConsumeTileChannel(0, block_offset, num_valid); + + // Iterate through remaining channels + IterateChannels<1, ACTIVE_CHANNELS>::ConsumeTileChannel(this, block_offset, num_valid); + + // Need to sync after processing this tile to ensure smem coherence + sync_after = true; + } + + + /** + * Finalize the computation. + */ + __device__ __forceinline__ void Finalize( + int dummy_result) + { + // Copy counters striped across threads into the histogram output + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + int channel_offset = (blockIdx.x * 256); + + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + int bin = (COUNTER * BLOCK_THREADS) + threadIdx.x; + + if ((STRIPED_COUNTERS_PER_THREAD * BLOCK_THREADS == 256) || (bin < 256)) + { + d_out_histograms[CHANNEL][channel_offset + bin] = thread_counters[CHANNEL][COUNTER]; + } + } + } + } +}; + + + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/persistent_block/persistent_block_reduce.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/persistent_block/persistent_block_reduce.cuh new file mode 100644 index 0000000000000000000000000000000000000000..9dbc7a3f15edc89df2ccf9ce3bb6712d1b0a1125 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/persistent_block/persistent_block_reduce.cuh @@ -0,0 +1,247 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::PersistentBlockReduce implements a stateful abstraction of CUDA thread blocks for participating in device-wide reduction. + + */ + +#pragma once + +#include + +#include "../../grid/grid_mapping.cuh" +#include "../../grid/grid_even_share.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_reduce.cuh" +#include "../../util_vector.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * Tuning policy for PersistentBlockReduce + */ +template < + int _BLOCK_THREADS, + int _ITEMS_PER_THREAD, + int _VECTOR_LOAD_LENGTH, + BlockReduceAlgorithm _BLOCK_ALGORITHM, + PtxLoadModifier _LOAD_MODIFIER, + GridMappingStrategy _GRID_MAPPING> +struct PersistentBlockReducePolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, + VECTOR_LOAD_LENGTH = _VECTOR_LOAD_LENGTH, + }; + + static const BlockReduceAlgorithm BLOCK_ALGORITHM = _BLOCK_ALGORITHM; + static const GridMappingStrategy GRID_MAPPING = _GRID_MAPPING; + static const PtxLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; +}; + + +/** + * \brief PersistentBlockReduce implements a stateful abstraction of CUDA thread blocks for participating in device-wide reduction. + */ +template < + typename PersistentBlockReducePolicy, + typename InputIteratorRA, + typename SizeT, + typename ReductionOp> +struct PersistentBlockReduce +{ + + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + typedef typename std::iterator_traits::value_type T; // Type of input iterator + typedef VectorHelper VecHelper; // Helper type for vectorizing loads of T + typedef typename VecHelper::Type VectorT; // Vector of T + + // Constants + enum + { + BLOCK_THREADS = PersistentBlockReducePolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = PersistentBlockReducePolicy::ITEMS_PER_THREAD, + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + VECTOR_LOAD_LENGTH = PersistentBlockReducePolicy::VECTOR_LOAD_LENGTH, + + // Can vectorize according to the policy if the input iterator is a native pointer to a built-in primitive + CAN_VECTORIZE = (PersistentBlockReducePolicy::VECTOR_LOAD_LENGTH > 1) && + (IsPointer::VALUE) && + (VecHelper::BUILT_IN), + + }; + + static const BlockReduceAlgorithm BLOCK_ALGORITHM = PersistentBlockReducePolicy::BLOCK_ALGORITHM; + + // Parameterized BlockReduce primitive + typedef BlockReduce BlockReduceT; + + // Shared memory type required by this thread block + typedef typename BlockReduceT::SmemStorage SmemStorage; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + T thread_aggregate; ///< Each thread's partial reduction + SmemStorage& smem_storage; ///< Reference to smem_storage + InputIteratorRA d_in; ///< Input data to reduce + ReductionOp reduction_op; ///< Binary reduction operator + int first_tile_size; ///< Size of first tile consumed + bool input_aligned; ///< Whether or not input is vector-aligned + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ PersistentBlockReduce( + SmemStorage& smem_storage, ///< Reference to smem_storage + InputIteratorRA d_in, ///< Input data to reduce + ReductionOp reduction_op) : ///< Binary reduction operator + smem_storage(smem_storage), + d_in(d_in), + reduction_op(reduction_op), + first_tile_size(TILE_ITEMS), + input_aligned(CAN_VECTORIZE && ((size_t(d_in) & (sizeof(VectorT) - 1)) == 0)){} + + + /** + * The number of items processed per "tile" + */ + __device__ __forceinline__ int TileItems() + { + return TILE_ITEMS; + } + + + /** + * Process a single tile. + * + * Each thread reduces only the values it loads. If \p FIRST_TILE, this + * partial reduction is stored into \p thread_aggregate. Otherwise it is + * accumulated into \p thread_aggregate. + */ + __device__ __forceinline__ void ConsumeTile( + bool &sync_after, + SizeT block_offset, + int num_valid, + bool first_tile) + { + if (num_valid < TILE_ITEMS) + { + // Our first tile is a partial tile size + if (first_tile) first_tile_size = num_valid; + + // Partial tile + int thread_offset = threadIdx.x; + + if ((first_tile) && (thread_offset < num_valid)) + { + thread_aggregate = ThreadLoad(d_in + block_offset + thread_offset); + thread_offset += BLOCK_THREADS; + } + + while (thread_offset < num_valid) + { + T item = ThreadLoad(d_in + block_offset + thread_offset); + thread_aggregate = reduction_op(thread_aggregate, item); + thread_offset += BLOCK_THREADS; + } + } + else + { + T items[ITEMS_PER_THREAD]; + + // Load full tile + if (input_aligned) + { + // Alias items as an array of VectorT and load it in striped fashion + BlockLoadDirectStriped( + reinterpret_cast(d_in + block_offset), + reinterpret_cast(items)); + } + else + { + // Load items in striped fashion + BlockLoadDirectStriped(d_in + block_offset, items); + } + + // Prevent hoisting + __threadfence_block(); + + // Reduce items within each thread + T partial = ThreadReduce(items, reduction_op); + + // Update|assign the thread's running aggregate + thread_aggregate = (first_tile) ? + partial : + reduction_op(thread_aggregate, partial); + } + + // No synchronization needed after tile processing + sync_after = false; + } + + + /** + * Finalize the computation. + */ + __device__ __forceinline__ void Finalize( + T& block_aggregate) + { + // Cooperative reduction across the thread block (guarded reduction if our first tile was a partial tile) + block_aggregate = (first_tile_size < TILE_ITEMS) ? + BlockReduceT::Reduce(smem_storage, thread_aggregate, reduction_op, first_tile_size) : + BlockReduceT::Reduce(smem_storage, thread_aggregate, reduction_op); + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/persistent_block/persistent_block_scan.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/persistent_block/persistent_block_scan.cuh new file mode 100644 index 0000000000000000000000000000000000000000..a6ff67798344e888fb9b4a03078f3dd24faea0be --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/persistent_block/persistent_block_scan.cuh @@ -0,0 +1,513 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::PersistentBlockScan implements an abstraction of CUDA thread blocks for + * participating in device-wide prefix scan. + */ + +#pragma once + +#include + +#include "../grid/grid_mapping.cuh" +#include "../grid/grid_even_share.cuh" +#include "../grid/grid_queue.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_reduce.cuh" +#include "../../util_vector.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +enum +{ + BLOCK_SCAN_OOB, + BLOCK_SCAN_INVALID, + BLOCK_SCAN_PARTIAL, + BLOCK_SCAN_PREFIX, +}; + + +/** + * Tuning policy for PersistentBlockScan + */ +template < + int _BLOCK_THREADS, + int _ITEMS_PER_THREAD, + BlockLoadPolicy _LOAD_POLICY, + BlockStorePolicy _STORE_POLICY, + BlockScanAlgorithm _SCAN_ALGORITHM> +struct PersistentBlockScanPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, + }; + + static const BlockLoadPolicy LOAD_POLICY = _LOAD_POLICY; + static const BlockStorePolicy STORE_POLICY = _STORE_POLICY; + static const BlockScanAlgorithm SCAN_ALGORITHM = _SCAN_ALGORITHM; + + // Data type of block-signaling flag + typedef int BlockFlag; +}; + + +/** + * \brief PersistentBlockScan implements an abstraction of CUDA thread blocks for + * participating in device-wide reduction. + */ +template < + typename PersistentBlockScanPolicy, + typename InputIteratorRA, + typename OutputIteratorRA, + typename SizeT> +class PersistentBlockScan +{ +public: + + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Data type of input iterator + typedef typename std::iterator_traits::value_type T; + + // Data type of block-signaling flag + typedef typename PersistentBlockScanPolicy::BlockFlag BlockFlag; + + // Constants + enum + { + TILE_ITEMS = PersistentBlockScanPolicy::BLOCK_THREADS * PersistentBlockScanPolicy::ITEMS_PER_THREAD, + }; + + struct Signal + { + BlockFlag flag; + T value; + }; + + template + struct SignalReduceOp + { + ScanOp scan_op; + + // Constructor + __device__ __forceinline__ + SignalReduceOp(ScanOp scan_op) : scan_op(scan_op) {} + + __device__ __forceinline__ + Signal operator()(const Signal& first, const Signal& second) + { + if ((first.flag == BLOCK_SCAN_OOB) || (second.flag == BLOCK_SCAN_PREFIX)) + return second; + + Signal retval; + retval.flag = first.flag; + retval.value = scan_op(first.value, second.value); + return retval; + } + }; + + // Parameterized block load + typedef BlockLoad< + InputIteratorRA, + PersistentBlockScanPolicy::BLOCK_THREADS, + PersistentBlockScanPolicy::ITEMS_PER_THREAD, + PersistentBlockScanPolicy::LOAD_POLICY> BlockLoadT; + + // Parameterized block store + typedef BlockStore< + OutputIteratorRA, + PersistentBlockScanPolicy::BLOCK_THREADS, + PersistentBlockScanPolicy::ITEMS_PER_THREAD, + PersistentBlockScanPolicy::STORE_POLICY> BlockStoreT; + + // Parameterized block scan + typedef BlockScan< + T, + PersistentBlockScanPolicy::BLOCK_THREADS, + PersistentBlockScanPolicy::SCAN_ALGORITHM> BlockScanT; + + // Parameterized warp reduce + typedef WarpReduce WarpReduceT; + + // Shared memory type for this threadblock + struct SmemStorage + { + union + { + typename BlockLoadT::SmemStorage load; // Smem needed for tile loading + typename BlockStoreT::SmemStorage store; // Smem needed for tile storing + typename BlockScanT::SmemStorage scan; // Smem needed for tile scanning + }; + + typename WarpReduceT::SmemStorage warp_reduce; // Smem needed for warp reduction + }; + + + // Stateful prefix functor + template + struct BlockPrefixOp + { + T* d_partials; + T* d_prefixes; + BlockFlag* d_flags; + ScanOp scan_op; + SmemStorage& smem_storage; + + // Constructor + __device__ __forceinline__ + BlockPrefixOp( + T* d_partials, + T* d_prefixes, + BlockFlag* d_flags, + ScanOp scan_op, + SmemStorage& smem_storage) : + d_partials(d_partials), d_prefixes(d_prefixes), d_flags(d_flags), scan_op(scan_op), smem_storage(smem_storage) {} + + // Prefix functor (called by the first warp) + __device__ __forceinline__ + T operator()(T block_aggregate) + { + // Update our partial + if (threadIdx.x == 0) + { + d_partials[PtxArchProps::WARP_THREADS + blockIdx.x] = block_aggregate; + __threadfence(); + d_flags[PtxArchProps::WARP_THREADS + blockIdx.x] = BLOCK_SCAN_PARTIAL; + } + + // Wait for predecessor blocks to become valid and at least one prefix to show up. + Signal predecessor_signal; + unsigned int predecessor_idx = PtxArchProps::WARP_THREADS + blockIdx.x - threadIdx.x; + do + { + predecessor_signal.flag = ThreadLoad(d_flags + predecessor_idx); + } + while (__any(predecessor_signal.flag == BLOCK_SCAN_INVALID) || __all(predecessor_signal.flag != BLOCK_SCAN_PREFIX)); + + // Grab predecessor block's corresponding partial/prefix + predecessor_signal.value = (predecessor_signal.flag == BLOCK_SCAN_PREFIX) ? + d_prefixes[predecessor_idx] : + d_partials[predecessor_idx]; + + // Reduce predecessor partials/prefixes to get our block-wide exclusive prefix + Signal prefix_signal = WarpReduceT::Reduce( + smem_storage.warp_reduce, + predecessor_signal, + SignalReduceOp(scan_op)); + + // Update the signals with our inclusive prefix + if (threadIdx.x == 0) + { + T inclusive_prefix = scan_op(prefix_signal.value, block_aggregate); + + d_prefixes[PtxArchProps::WARP_THREADS + blockIdx.x] = inclusive_prefix; + __threadfence(); + d_flags[PtxArchProps::WARP_THREADS + blockIdx.x] = BLOCK_SCAN_PREFIX; + } + + // Return block-wide exclusive prefix + return prefix_signal.value; + } + }; + + + //--------------------------------------------------------------------- + // Utility operations + //--------------------------------------------------------------------- + + /** + * Process a single, full tile. Specialized for d_in is an iterator (not a native pointer) + * + * Each thread reduces only the values it loads. If \p FIRST_TILE, + * this partial reduction is stored into \p thread_aggregate. Otherwise + * it is accumulated into \p thread_aggregate. + */ + template < + typename SizeT, + typename ScanOp> + static __device__ __forceinline__ void ConsumeFullTile( + SmemStorage &smem_storage, + InputIteratorRA d_in, + OutputIteratorRA d_out, + SizeT block_offset, + ScanOp &scan_op, + T &thread_aggregate) + { + T items[PersistentBlockScanPolicy::ITEMS_PER_THREAD]; + + BlockLoadT::Load(smem_storage.load, d_in + block_offset, items); + + __syncthreads(); + + BlockScanT::Load(smem_storage.load, d_in + block_offset, items); + + __syncthreads(); + + BlockStoreT::Store(smem_storage.load, d_in + block_offset, items); + } + + + /** + * Process a single, full tile. Specialized for native pointers + * + * Each thread reduces only the values it loads. If \p FIRST_TILE, + * this partial reduction is stored into \p thread_aggregate. Otherwise + * it is accumulated into \p thread_aggregate. + * + * Performs a block-wide barrier synchronization + */ + template < + bool FIRST_TILE, + typename SizeT, + typename ScanOp> + static __device__ __forceinline__ void ConsumeFullTile( + SmemStorage &smem_storage, + T *d_in, + SizeT block_offset, + ScanOp &scan_op, + T &thread_aggregate) + { + if ((size_t(d_in) & (VECTOR_LOAD_LENGTH - 1)) == 0) + { + T items[ITEMS_PER_THREAD]; + + typedef typename VectorHelper::Type VectorT; + + // Alias items as an array of VectorT and load it in striped fashion + BlockLoadDirectStriped( + reinterpret_cast(d_in + block_offset), + reinterpret_cast(items)); + + // Prevent hoisting + __syncthreads(); + + T partial = ThreadReduce(items, scan_op); + + thread_aggregate = (FIRST_TILE) ? + partial : + scan_op(thread_aggregate, partial); + } + else + { + T items[ITEMS_PER_THREAD]; + + BlockLoadDirectStriped( + d_in + block_offset, + items); + + // Prevent hoisting + __syncthreads(); + + T partial = ThreadReduce(items, scan_op); + + thread_aggregate = (FIRST_TILE) ? + partial : + scan_op(thread_aggregate, partial); + } + + } + + + /** + * Process a single, partial tile. + * + * Each thread reduces only the values it loads. If \p FIRST_TILE, + * this partial reduction is stored into \p thread_aggregate. Otherwise + * it is accumulated into \p thread_aggregate. + */ + template < + bool FIRST_TILE, + typename SizeT, + typename ScanOp> + static __device__ __forceinline__ void ConsumePartialTile( + SmemStorage &smem_storage, + InputIteratorRA d_in, + SizeT block_offset, + const SizeT &block_oob, + ScanOp &scan_op, + T &thread_aggregate) + { + SizeT thread_offset = block_offset + threadIdx.x; + + if ((FIRST_TILE) && (thread_offset < block_oob)) + { + thread_aggregate = ThreadLoad(d_in + thread_offset); + thread_offset += BLOCK_THREADS; + } + + while (thread_offset < block_oob) + { + T item = ThreadLoad(d_in + thread_offset); + thread_aggregate = scan_op(thread_aggregate, item); + thread_offset += BLOCK_THREADS; + } + } + +public: + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * \brief Consumes input tiles using an even-share policy, computing a threadblock-wide reduction for thread0 using the specified binary reduction functor. + * + * The return value is undefined in threads other than thread0. + */ + template + static __device__ __forceinline__ T ProcessPersistentBlockEvenShare( + SmemStorage &smem_storage, + InputIteratorRA d_in, + SizeT block_offset, + const SizeT &block_oob, + ScanOp &scan_op) + { + if (block_offset + TILE_ITEMS <= block_oob) + { + // We have at least one full tile to consume + T thread_aggregate; + ConsumeFullTile(smem_storage, d_in, block_offset, scan_op, thread_aggregate); + block_offset += TILE_ITEMS; + + // Consume any other full tiles + while (block_offset + TILE_ITEMS <= block_oob) + { + ConsumeFullTile(smem_storage, d_in, block_offset, scan_op, thread_aggregate); + block_offset += TILE_ITEMS; + } + + // Consume any remaining input + ConsumePartialTile(smem_storage, d_in, block_offset, block_oob, scan_op, thread_aggregate); + + // Compute the block-wide reduction (every thread has a valid input) + return BlockReduceT::Reduce(smem_storage.reduce, thread_aggregate, scan_op); + } + else + { + // We have less than a full tile to consume + T thread_aggregate; + ConsumePartialTile(smem_storage, d_in, block_offset, block_oob, scan_op, thread_aggregate); + + // Compute the block-wide reduction (up to block_items threads have valid inputs) + SizeT block_items = block_oob - block_offset; + return BlockReduceT::Reduce(smem_storage.reduce, thread_aggregate, scan_op, block_items); + } + } + + + /** + * \brief Consumes input tiles using a dynamic queue policy, computing a threadblock-wide reduction for thread0 using the specified binary reduction functor. + * + * The return value is undefined in threads other than thread0. + */ + template + static __device__ __forceinline__ T ProcessPersistentBlockDynamic( + SmemStorage &smem_storage, + InputIteratorRA d_in, + SizeT num_items, + GridQueue &queue, + ScanOp &scan_op) + { + // Each thread block is statically assigned at some input, otherwise its + // block_aggregate will be undefined. + SizeT block_offset = blockIdx.x * TILE_ITEMS; + + if (block_offset + TILE_ITEMS <= num_items) + { + // We have a full tile to consume + T thread_aggregate; + ConsumeFullTile(smem_storage, d_in, block_offset, scan_op, thread_aggregate); + + // Dynamically consume other tiles + SizeT even_share_base = gridDim.x * TILE_ITEMS; + + if (even_share_base < num_items) + { + // There are tiles left to consume + while (true) + { + // Dequeue up to TILE_ITEMS + if (threadIdx.x == 0) + { + smem_storage.block_offset = queue.Drain(TILE_ITEMS) + even_share_base; + } + + __syncthreads(); + + block_offset = smem_storage.block_offset; + + if (block_offset + TILE_ITEMS > num_items) + { + if (block_offset < num_items) + { + // We have less than a full tile to consume + ConsumePartialTile(smem_storage, d_in, block_offset, num_items, scan_op, thread_aggregate); + } + + // No more work to do + break; + } + + // We have a full tile to consume (which performs a barrier to protect smem_storage.block_offset WARs) + ConsumeFullTile(smem_storage, d_in, block_offset, scan_op, thread_aggregate); + } + } + + // Compute the block-wide reduction (every thread has a valid input) + return BlockReduceT::Reduce(smem_storage.reduce, thread_aggregate, scan_op); + } + else + { + // We have less than a full tile to consume + T thread_aggregate; + SizeT block_items = num_items - block_offset; + ConsumePartialTile(smem_storage, d_in, block_offset, num_items, scan_op, thread_aggregate); + + // Compute the block-wide reduction (up to block_items threads have valid inputs) + return BlockReduceT::Reduce(smem_storage.reduce, thread_aggregate, scan_op, block_items); + } + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_histo_region.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_histo_region.cuh new file mode 100644 index 0000000000000000000000000000000000000000..64e3b20e4f571ceb29a33bbd2f021afc1966de90 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_histo_region.cuh @@ -0,0 +1,319 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockHistogramRegion implements a stateful abstraction of CUDA thread blocks for participating in device-wide selection across a region of tiles. + */ + +#pragma once + +#include + +#include "specializations/block_histo_region_gatomic.cuh" +#include "specializations/block_histo_region_satomic.cuh" +#include "specializations/block_histo_region_sort.cuh" +#include "../../util_type.cuh" +#include "../../grid/grid_mapping.cuh" +#include "../../grid/grid_even_share.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Algorithmic variants + ******************************************************************************/ + + +/** + * \brief DeviceHistogramAlgorithm enumerates alternative algorithms for BlockHistogramRegion. + */ +enum DeviceHistogramAlgorithm +{ + + /** + * \par Overview + * A two-kernel approach in which: + * -# Thread blocks in the first kernel aggregate their own privatized + * histograms using block-wide sorting (see BlockHistogramAlgorithm::BLOCK_HISTO_SORT). + * -# A single thread block in the second kernel reduces them into the output histogram(s). + * + * \par Performance Considerations + * Delivers consistent throughput regardless of sample bin distribution. + * + * However, because histograms are privatized in shared memory, a large + * number of bins (e.g., thousands) may adversely affect occupancy and + * performance (or even the ability to launch). + */ + DEVICE_HISTO_SORT, + + + /** + * \par Overview + * A two-kernel approach in which: + * -# Thread blocks in the first kernel aggregate their own privatized + * histograms using shared-memory \p atomicAdd(). + * -# A single thread block in the second kernel reduces them into the + * output histogram(s). + * + * \par Performance Considerations + * Performance is strongly tied to the hardware implementation of atomic + * addition, and may be significantly degraded for non uniformly-random + * input distributions where many concurrent updates are likely to be + * made to the same bin counter. + * + * However, because histograms are privatized in shared memory, a large + * number of bins (e.g., thousands) may adversely affect occupancy and + * performance (or even the ability to launch). + */ + DEVICE_HISTO_SHARED_ATOMIC, + + + /** + * \par Overview + * A single-kernel approach in which thread blocks update the output histogram(s) directly + * using global-memory \p atomicAdd(). + * + * \par Performance Considerations + * Performance is strongly tied to the hardware implementation of atomic + * addition, and may be significantly degraded for non uniformly-random + * input distributions where many concurrent updates are likely to be + * made to the same bin counter. + * + * Performance is not significantly impacted when computing histograms having large + * numbers of bins (e.g., thousands). + */ + DEVICE_HISTO_GLOBAL_ATOMIC, + +}; + + +/****************************************************************************** + * Tuning policy + ******************************************************************************/ + +/** + * Parameterizable tuning policy type for BlockHistogramRegion + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + DeviceHistogramAlgorithm _HISTO_ALGORITHM, ///< Cooperative histogram algorithm to use + GridMappingStrategy _GRID_MAPPING> ///< How to map tiles of input onto thread blocks +struct BlockHistogramRegionPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, ///< Threads per thread block + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + }; + + static const DeviceHistogramAlgorithm HISTO_ALGORITHM = _HISTO_ALGORITHM; ///< Cooperative histogram algorithm to use + static const GridMappingStrategy GRID_MAPPING = _GRID_MAPPING; ///< How to map tiles of input onto thread blocks +}; + + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockHistogramRegion implements a stateful abstraction of CUDA thread blocks for participating in device-wide selection across a region of tiles. + */ +template < + typename BlockHistogramRegionPolicy, ///< Parameterized BlockHistogramRegionPolicy tuning policy type + int BINS, ///< Number of histogram bins per channel + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIterator, ///< Random-access input iterator type for reading samples. Must have an an InputIterator::value_type that, when cast as an integer, falls in the range [0..BINS-1] + typename HistoCounter, ///< Integer type for counting sample occurrences per histogram bin + typename Offset> ///< Signed integer type for global offsets +struct BlockHistogramRegion +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Histogram grid algorithm + static const DeviceHistogramAlgorithm HISTO_ALGORITHM = BlockHistogramRegionPolicy::HISTO_ALGORITHM; + + // Alternative internal implementation types + typedef BlockHistogramRegionSort< BlockHistogramRegionPolicy, BINS, CHANNELS, ACTIVE_CHANNELS, InputIterator, HistoCounter, Offset> BlockHistogramRegionSortT; + typedef BlockHistogramRegionSharedAtomic< BlockHistogramRegionPolicy, BINS, CHANNELS, ACTIVE_CHANNELS, InputIterator, HistoCounter, Offset> BlockHistogramRegionSharedAtomicT; + typedef BlockHistogramRegionGlobalAtomic< BlockHistogramRegionPolicy, BINS, CHANNELS, ACTIVE_CHANNELS, InputIterator, HistoCounter, Offset> BlockHistogramRegionGlobalAtomicT; + + // Internal block sweep histogram type + typedef typename If<(HISTO_ALGORITHM == DEVICE_HISTO_SORT), + BlockHistogramRegionSortT, + typename If<(HISTO_ALGORITHM == DEVICE_HISTO_SHARED_ATOMIC), + BlockHistogramRegionSharedAtomicT, + BlockHistogramRegionGlobalAtomicT>::Type>::Type InternalBlockDelegate; + + enum + { + TILE_ITEMS = InternalBlockDelegate::TILE_ITEMS, + }; + + + // Temporary storage type + typedef typename InternalBlockDelegate::TempStorage TempStorage; + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + // Internal block delegate + InternalBlockDelegate internal_delegate; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockHistogramRegion( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIterator d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) ///< Reference to output histograms + : + internal_delegate(temp_storage, d_in, d_out_histograms) + {} + + + /** + * \brief Reduce a consecutive segment of input tiles + */ + __device__ __forceinline__ void ConsumeRegion( + Offset block_offset, ///< [in] Threadblock begin offset (inclusive) + Offset block_end) ///< [in] Threadblock end offset (exclusive) + { + // Consume subsequent full tiles of input + while (block_offset + TILE_ITEMS <= block_end) + { + internal_delegate.ConsumeTile(block_offset); + block_offset += TILE_ITEMS; + } + + // Consume a partially-full tile + if (block_offset < block_end) + { + int valid_items = block_end - block_offset; + internal_delegate.ConsumeTile(block_offset, valid_items); + } + + // Aggregate output + internal_delegate.AggregateOutput(); + } + + + /** + * Reduce a consecutive segment of input tiles + */ + __device__ __forceinline__ void ConsumeRegion( + Offset num_items, ///< [in] Total number of global input items + GridEvenShare &even_share, ///< [in] GridEvenShare descriptor + GridQueue &queue, ///< [in,out] GridQueue descriptor + Int2Type is_even_share) ///< [in] Marker type indicating this is an even-share mapping + { + even_share.BlockInit(); + ConsumeRegion(even_share.block_offset, even_share.block_end); + } + + + /** + * Dequeue and reduce tiles of items as part of a inter-block scan + */ + __device__ __forceinline__ void ConsumeRegion( + int num_items, ///< Total number of input items + GridQueue queue) ///< Queue descriptor for assigning tiles of work to thread blocks + { + // Shared block offset + __shared__ Offset shared_block_offset; + + // We give each thread block at least one tile of input. + Offset block_offset = blockIdx.x * TILE_ITEMS; + Offset even_share_base = gridDim.x * TILE_ITEMS; + + // Process full tiles of input + while (block_offset + TILE_ITEMS <= num_items) + { + internal_delegate.ConsumeTile(block_offset); + + // Dequeue up to TILE_ITEMS + if (threadIdx.x == 0) + shared_block_offset = queue.Drain(TILE_ITEMS) + even_share_base; + + __syncthreads(); + + block_offset = shared_block_offset; + + __syncthreads(); + } + + // Consume a partially-full tile + if (block_offset < num_items) + { + int valid_items = num_items - block_offset; + internal_delegate.ConsumeTile(block_offset, valid_items); + } + + // Aggregate output + internal_delegate.AggregateOutput(); + } + + + /** + * Dequeue and reduce tiles of items as part of a inter-block scan + */ + __device__ __forceinline__ void ConsumeRegion( + Offset num_items, ///< [in] Total number of global input items + GridEvenShare &even_share, ///< [in] GridEvenShare descriptor + GridQueue &queue, ///< [in,out] GridQueue descriptor + Int2Type is_dynamic) ///< [in] Marker type indicating this is a dynamic mapping + { + ConsumeRegion(num_items, queue); + } + + +}; + + + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_radix_sort_downsweep_region.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_radix_sort_downsweep_region.cuh new file mode 100644 index 0000000000000000000000000000000000000000..89c4c69c0c710b76d0f10ce69f23416eebd927ca --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_radix_sort_downsweep_region.cuh @@ -0,0 +1,736 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * BlockRadixSortDownsweepRegion implements a stateful abstraction of CUDA thread blocks for participating in device-wide radix sort downsweep across a region of tiles. + */ + + +#pragma once + +#include "../../thread/thread_load.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_store.cuh" +#include "../../block/block_radix_rank.cuh" +#include "../../block/block_exchange.cuh" +#include "../../util_type.cuh" +#include "../../iterator/cache_modified_input_iterator.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Types of scattering strategies + */ +enum RadixSortScatterAlgorithm +{ + RADIX_SORT_SCATTER_DIRECT, ///< Scatter directly from registers to global bins + RADIX_SORT_SCATTER_TWO_PHASE, ///< First scatter from registers into shared memory bins, then into global bins +}; + + +/** + * Parameterizable tuning policy type for BlockRadixSortDownsweepRegion + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + BlockLoadAlgorithm _LOAD_ALGORITHM, ///< The BlockLoad algorithm to use + CacheLoadModifier _LOAD_MODIFIER, ///< Cache load modifier for reading keys (and values) + bool _EXCHANGE_TIME_SLICING, ///< Whether or not to time-slice key/value exchanges through shared memory to lower shared memory pressure + bool _MEMOIZE_OUTER_SCAN, ///< Whether or not to buffer outer raking scan partials to incur fewer shared memory reads at the expense of higher register pressure. See BlockScanAlgorithm::BLOCK_SCAN_RAKING_MEMOIZE for more details. + BlockScanAlgorithm _INNER_SCAN_ALGORITHM, ///< The BlockScan algorithm algorithm to use + RadixSortScatterAlgorithm _SCATTER_ALGORITHM, ///< The scattering strategy to use + cudaSharedMemConfig _SMEM_CONFIG, ///< Shared memory bank mode + int _RADIX_BITS> ///< The number of radix bits, i.e., log2(bins) +struct BlockRadixSortDownsweepRegionPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, ///< Threads per thread block + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + EXCHANGE_TIME_SLICING = _EXCHANGE_TIME_SLICING, ///< Whether or not to time-slice key/value exchanges through shared memory to lower shared memory pressure + RADIX_BITS = _RADIX_BITS, ///< The number of radix bits, i.e., log2(bins) + MEMOIZE_OUTER_SCAN = _MEMOIZE_OUTER_SCAN, ///< Whether or not to buffer outer raking scan partials to incur fewer shared memory reads at the expense of higher register pressure. See BlockScanAlgorithm::BLOCK_SCAN_RAKING_MEMOIZE for more details. + }; + + static const BlockLoadAlgorithm LOAD_ALGORITHM = _LOAD_ALGORITHM; ///< The BlockLoad algorithm to use + static const CacheLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; ///< Cache load modifier for reading keys (and values) + static const BlockScanAlgorithm INNER_SCAN_ALGORITHM = _INNER_SCAN_ALGORITHM; ///< The BlockScan algorithm algorithm to use + static const RadixSortScatterAlgorithm SCATTER_ALGORITHM = _SCATTER_ALGORITHM; ///< The scattering strategy to use + static const cudaSharedMemConfig SMEM_CONFIG = _SMEM_CONFIG; ///< Shared memory bank mode +}; + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockRadixSortDownsweepRegion implements a stateful abstraction of CUDA thread blocks for participating in device-wide radix sort downsweep across a region of tiles. + */ +template < + typename BlockRadixSortDownsweepRegionPolicy, ///< Parameterized BlockRadixSortDownsweepRegionPolicy tuning policy type + bool DESCENDING, ///< Whether or not the sorted-order is high-to-low + typename Key, ///< Key type + typename Value, ///< Value type + typename Offset> ///< Signed integer type for global offsets +struct BlockRadixSortDownsweepRegion +{ + //--------------------------------------------------------------------- + // Type definitions and constants + //--------------------------------------------------------------------- + + // Appropriate unsigned-bits representation of Key + typedef typename Traits::UnsignedBits UnsignedBits; + + static const UnsignedBits MIN_KEY = Traits::MIN_KEY; + static const UnsignedBits MAX_KEY = Traits::MAX_KEY; + + static const BlockLoadAlgorithm LOAD_ALGORITHM = BlockRadixSortDownsweepRegionPolicy::LOAD_ALGORITHM; + static const CacheLoadModifier LOAD_MODIFIER = BlockRadixSortDownsweepRegionPolicy::LOAD_MODIFIER; + static const BlockScanAlgorithm INNER_SCAN_ALGORITHM = BlockRadixSortDownsweepRegionPolicy::INNER_SCAN_ALGORITHM; + static const RadixSortScatterAlgorithm SCATTER_ALGORITHM = BlockRadixSortDownsweepRegionPolicy::SCATTER_ALGORITHM; + static const cudaSharedMemConfig SMEM_CONFIG = BlockRadixSortDownsweepRegionPolicy::SMEM_CONFIG; + + enum + { + BLOCK_THREADS = BlockRadixSortDownsweepRegionPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockRadixSortDownsweepRegionPolicy::ITEMS_PER_THREAD, + EXCHANGE_TIME_SLICING = BlockRadixSortDownsweepRegionPolicy::EXCHANGE_TIME_SLICING, + RADIX_BITS = BlockRadixSortDownsweepRegionPolicy::RADIX_BITS, + MEMOIZE_OUTER_SCAN = BlockRadixSortDownsweepRegionPolicy::MEMOIZE_OUTER_SCAN, + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + + RADIX_DIGITS = 1 << RADIX_BITS, + KEYS_ONLY = Equals::VALUE, + + WARP_THREADS = CUB_PTX_LOG_WARP_THREADS, + WARPS = (BLOCK_THREADS + WARP_THREADS - 1) / WARP_THREADS, + + BYTES_PER_SIZET = sizeof(Offset), + LOG_BYTES_PER_SIZET = Log2::VALUE, + + LOG_SMEM_BANKS = CUB_PTX_LOG_SMEM_BANKS, + SMEM_BANKS = 1 << LOG_SMEM_BANKS, + + DIGITS_PER_SCATTER_PASS = BLOCK_THREADS / SMEM_BANKS, + SCATTER_PASSES = RADIX_DIGITS / DIGITS_PER_SCATTER_PASS, + + LOG_STORE_TXN_THREADS = LOG_SMEM_BANKS, + STORE_TXN_THREADS = 1 << LOG_STORE_TXN_THREADS, + }; + + // Input iterator wrapper types + typedef CacheModifiedInputIterator KeysItr; + typedef CacheModifiedInputIterator ValuesItr; + + // BlockRadixRank type + typedef BlockRadixRank< + BLOCK_THREADS, + RADIX_BITS, + DESCENDING, + MEMOIZE_OUTER_SCAN, + INNER_SCAN_ALGORITHM, + SMEM_CONFIG> BlockRadixRank; + + // BlockLoad type (keys) + typedef BlockLoad< + KeysItr, + BLOCK_THREADS, + ITEMS_PER_THREAD, + LOAD_ALGORITHM, + EXCHANGE_TIME_SLICING> BlockLoadKeys; + + // BlockLoad type (values) + typedef BlockLoad< + ValuesItr, + BLOCK_THREADS, + ITEMS_PER_THREAD, + LOAD_ALGORITHM, + EXCHANGE_TIME_SLICING> BlockLoadValues; + + // BlockExchange type (keys) + typedef BlockExchange< + UnsignedBits, + BLOCK_THREADS, + ITEMS_PER_THREAD, + EXCHANGE_TIME_SLICING> BlockExchangeKeys; + + // BlockExchange type (values) + typedef BlockExchange< + Value, + BLOCK_THREADS, + ITEMS_PER_THREAD, + EXCHANGE_TIME_SLICING> BlockExchangeValues; + + + /** + * Shared memory storage layout + */ + struct _TempStorage + { + Offset relative_bin_offsets[RADIX_DIGITS + 1]; + bool short_circuit; + + union + { + typename BlockRadixRank::TempStorage ranking; + typename BlockLoadKeys::TempStorage load_keys; + typename BlockLoadValues::TempStorage load_values; + typename BlockExchangeKeys::TempStorage exchange_keys; + typename BlockExchangeValues::TempStorage exchange_values; + }; + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Thread fields + //--------------------------------------------------------------------- + + // Shared storage for this CTA + _TempStorage &temp_storage; + + // Input and output device pointers + KeysItr d_keys_in; + ValuesItr d_values_in; + UnsignedBits *d_keys_out; + Value *d_values_out; + + // The global scatter base offset for each digit (valid in the first RADIX_DIGITS threads) + Offset bin_offset; + + // The least-significant bit position of the current digit to extract + int current_bit; + + // Whether to short-ciruit + bool short_circuit; + + + + //--------------------------------------------------------------------- + // Utility methods + //--------------------------------------------------------------------- + + /** + * Decodes given keys to lookup digit offsets in shared memory + */ + __device__ __forceinline__ void DecodeRelativeBinOffsets( + UnsignedBits (&twiddled_keys)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD]) + { + #pragma unroll + for (int KEY = 0; KEY < ITEMS_PER_THREAD; KEY++) + { + UnsignedBits digit = BFE(twiddled_keys[KEY], current_bit, RADIX_BITS); + + // Lookup base digit offset from shared memory + relative_bin_offsets[KEY] = temp_storage.relative_bin_offsets[digit]; + } + } + + + /** + * Scatter ranked items to global memory + */ + template + __device__ __forceinline__ void ScatterItems( + T (&items)[ITEMS_PER_THREAD], + int (&local_ranks)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD], + T *d_out, + Offset valid_items) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + // Scatter if not out-of-bounds + if (FULL_TILE || (local_ranks[ITEM] < valid_items)) + { + d_out[relative_bin_offsets[ITEM] + local_ranks[ITEM]] = items[ITEM]; + } + } + } + + + /** + * Scatter ranked keys directly to global memory + */ + template + __device__ __forceinline__ void ScatterKeys( + UnsignedBits (&twiddled_keys)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Offset valid_items, + Int2Type scatter_algorithm) + { + // Compute scatter offsets + DecodeRelativeBinOffsets(twiddled_keys, relative_bin_offsets); + + // Untwiddle keys before outputting + UnsignedBits keys[ITEMS_PER_THREAD]; + + #pragma unroll + for (int KEY = 0; KEY < ITEMS_PER_THREAD; KEY++) + { + keys[KEY] = Traits::TwiddleOut(twiddled_keys[KEY]); + } + + // Scatter to global + ScatterItems(keys, ranks, relative_bin_offsets, d_keys_out, valid_items); + } + + + /** + * Scatter ranked keys through shared memory, then to global memory + */ + template + __device__ __forceinline__ void ScatterKeys( + UnsignedBits (&twiddled_keys)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Offset valid_items, + Int2Type scatter_algorithm) + { + // Exchange keys through shared memory + BlockExchangeKeys(temp_storage.exchange_keys).ScatterToStriped(twiddled_keys, ranks); + + // Compute striped local ranks + int local_ranks[ITEMS_PER_THREAD]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + local_ranks[ITEM] = threadIdx.x + (ITEM * BLOCK_THREADS); + } + + // Scatter directly + ScatterKeys( + twiddled_keys, + relative_bin_offsets, + local_ranks, + valid_items, + Int2Type()); + } + + + /** + * Scatter ranked values directly to global memory + */ + template + __device__ __forceinline__ void ScatterValues( + Value (&values)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Offset valid_items, + Int2Type scatter_algorithm) + { + // Scatter to global + ScatterItems(values, ranks, relative_bin_offsets, d_values_out, valid_items); + } + + + /** + * Scatter ranked values through shared memory, then to global memory + */ + template + __device__ __forceinline__ void ScatterValues( + Value (&values)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Offset valid_items, + Int2Type scatter_algorithm) + { + __syncthreads(); + + // Exchange keys through shared memory + BlockExchangeValues(temp_storage.exchange_values).ScatterToStriped(values, ranks); + + // Compute striped local ranks + int local_ranks[ITEMS_PER_THREAD]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + local_ranks[ITEM] = threadIdx.x + (ITEM * BLOCK_THREADS); + } + + // Scatter directly + ScatterValues( + values, + relative_bin_offsets, + local_ranks, + valid_items, + Int2Type()); + } + + + /** + * Load a tile of items (specialized for full tile) + */ + template + __device__ __forceinline__ void LoadItems( + BlockLoadT &block_loader, + T (&items)[ITEMS_PER_THREAD], + InputIterator d_in, + Offset valid_items, + Int2Type is_full_tile) + { + block_loader.Load(d_in, items); + } + + + /** + * Load a tile of items (specialized for partial tile) + */ + template + __device__ __forceinline__ void LoadItems( + BlockLoadT &block_loader, + T (&items)[ITEMS_PER_THREAD], + InputIterator d_in, + Offset valid_items, + Int2Type is_full_tile) + { + block_loader.Load(d_in, items, valid_items); + } + + + /** + * Truck along associated values + */ + template + __device__ __forceinline__ void GatherScatterValues( + _Value (&values)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Offset block_offset, + Offset valid_items) + { + __syncthreads(); + + BlockLoadValues loader(temp_storage.load_values); + LoadItems( + loader, + values, + d_values_in + block_offset, + valid_items, + Int2Type()); + + ScatterValues( + values, + relative_bin_offsets, + ranks, + valid_items, + Int2Type()); + } + + + /** + * Truck along associated values (specialized for key-only sorting) + */ + template + __device__ __forceinline__ void GatherScatterValues( + NullType (&values)[ITEMS_PER_THREAD], + Offset (&relative_bin_offsets)[ITEMS_PER_THREAD], + int (&ranks)[ITEMS_PER_THREAD], + Offset block_offset, + Offset valid_items) + {} + + + /** + * Process tile + */ + template + __device__ __forceinline__ void ProcessTile( + Offset block_offset, + const Offset &valid_items = TILE_ITEMS) + { + // Per-thread tile data + UnsignedBits keys[ITEMS_PER_THREAD]; // Keys + UnsignedBits twiddled_keys[ITEMS_PER_THREAD]; // Twiddled keys + int ranks[ITEMS_PER_THREAD]; // For each key, the local rank within the CTA + Offset relative_bin_offsets[ITEMS_PER_THREAD]; // For each key, the global scatter base offset of the corresponding digit + + // Assign max-key to all keys + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + keys[ITEM] = (DESCENDING) ? MIN_KEY : MAX_KEY; + } + + // Load tile of keys + BlockLoadKeys loader(temp_storage.load_keys); + LoadItems( + loader, + keys, + d_keys_in + block_offset, + valid_items, + Int2Type()); + + __syncthreads(); + + // Twiddle key bits if necessary + #pragma unroll + for (int KEY = 0; KEY < ITEMS_PER_THREAD; KEY++) + { + twiddled_keys[KEY] = Traits::TwiddleIn(keys[KEY]); + } + + // Rank the twiddled keys + int inclusive_digit_prefix; + BlockRadixRank(temp_storage.ranking).RankKeys( + twiddled_keys, + ranks, + current_bit, + inclusive_digit_prefix); + + // Update global scatter base offsets for each digit + if ((BLOCK_THREADS == RADIX_DIGITS) || (threadIdx.x < RADIX_DIGITS)) + { + int exclusive_digit_prefix; + + // Get exclusive digit prefix from inclusive prefix + if (DESCENDING) + { + // Get the prefix from the next thread (higher bins come first) +#if CUB_PTX_VERSION >= 300 + exclusive_digit_prefix = ShuffleDown(inclusive_digit_prefix, 1); + if (threadIdx.x == RADIX_DIGITS - 1) + exclusive_digit_prefix = 0; +#else + volatile int* exchange = reinterpret_cast(temp_storage.relative_bin_offsets); + exchange[threadIdx.x + 1] = 0; + exchange[threadIdx.x] = inclusive_digit_prefix; + exclusive_digit_prefix = exchange[threadIdx.x + 1]; +#endif + } + else + { + // Get the prefix from the previous thread (lower bins come first) +#if CUB_PTX_VERSION >= 300 + exclusive_digit_prefix = ShuffleUp(inclusive_digit_prefix, 1); + if (threadIdx.x == 0) + exclusive_digit_prefix = 0; +#else + volatile int* exchange = reinterpret_cast(temp_storage.relative_bin_offsets); + exchange[threadIdx.x] = 0; + exchange[threadIdx.x + 1] = inclusive_digit_prefix; + exclusive_digit_prefix = exchange[threadIdx.x]; +#endif + } + + bin_offset -= exclusive_digit_prefix; + temp_storage.relative_bin_offsets[threadIdx.x] = bin_offset; + bin_offset += inclusive_digit_prefix; + } + + __syncthreads(); + + // Scatter keys + ScatterKeys(twiddled_keys, relative_bin_offsets, ranks, valid_items, Int2Type()); + + // Gather/scatter values + Value values[ITEMS_PER_THREAD]; + GatherScatterValues(values, relative_bin_offsets, ranks, block_offset, valid_items); + } + + + /** + * Copy tiles within the range of input + */ + template < + typename InputIterator, + typename T> + __device__ __forceinline__ void Copy( + InputIterator d_in, + T *d_out, + Offset block_offset, + Offset block_end) + { + // Simply copy the input + while (block_offset + TILE_ITEMS <= block_end) + { + T items[ITEMS_PER_THREAD]; + + LoadDirectStriped(threadIdx.x, d_in + block_offset, items); + __syncthreads(); + StoreDirectStriped(threadIdx.x, d_out + block_offset, items); + + block_offset += TILE_ITEMS; + } + + // Clean up last partial tile with guarded-I/O + if (block_offset < block_end) + { + Offset valid_items = block_end - block_offset; + + T items[ITEMS_PER_THREAD]; + + LoadDirectStriped(threadIdx.x, d_in + block_offset, items, valid_items); + __syncthreads(); + StoreDirectStriped(threadIdx.x, d_out + block_offset, items, valid_items); + } + } + + + /** + * Copy tiles within the range of input (specialized for NullType) + */ + template + __device__ __forceinline__ void Copy( + InputIterator d_in, + NullType *d_out, + Offset block_offset, + Offset block_end) + {} + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockRadixSortDownsweepRegion( + TempStorage &temp_storage, + Offset bin_offset, + Key *d_keys_in, + Key *d_keys_out, + Value *d_values_in, + Value *d_values_out, + int current_bit) + : + temp_storage(temp_storage.Alias()), + bin_offset(bin_offset), + d_keys_in(reinterpret_cast(d_keys_in)), + d_keys_out(reinterpret_cast(d_keys_out)), + d_values_in(d_values_in), + d_values_out(d_values_out), + current_bit(current_bit), + short_circuit(false) + {} + + + /** + * Constructor + */ + __device__ __forceinline__ BlockRadixSortDownsweepRegion( + TempStorage &temp_storage, + Offset num_items, + Offset *d_spine, + Key *d_keys_in, + Key *d_keys_out, + Value *d_values_in, + Value *d_values_out, + int current_bit) + : + temp_storage(temp_storage.Alias()), + d_keys_in(reinterpret_cast(d_keys_in)), + d_keys_out(reinterpret_cast(d_keys_out)), + d_values_in(d_values_in), + d_values_out(d_values_out), + current_bit(current_bit) + { + // Load digit bin offsets (each of the first RADIX_DIGITS threads will load an offset for that digit) + if (threadIdx.x < RADIX_DIGITS) + { + int bin_idx = (DESCENDING) ? + RADIX_DIGITS - threadIdx.x - 1 : + threadIdx.x; + + // Short circuit if the first block's histogram has only bin counts of only zeros or problem-size + Offset first_block_bin_offset = d_spine[gridDim.x * bin_idx]; + int predicate = ((first_block_bin_offset == 0) || (first_block_bin_offset == num_items)); + this->temp_storage.short_circuit = WarpAll(predicate); + + // Load my block's bin offset for my bin + bin_offset = d_spine[(gridDim.x * bin_idx) + blockIdx.x]; + } + + __syncthreads(); + + short_circuit = this->temp_storage.short_circuit; + } + + + /** + * Distribute keys from a segment of input tiles. + */ + __device__ __forceinline__ void ProcessRegion( + Offset block_offset, + const Offset &block_end) + { + if (short_circuit) + { + // Copy keys + Copy(d_keys_in, d_keys_out, block_offset, block_end); + + // Copy values + Copy(d_values_in, d_values_out, block_offset, block_end); + } + else + { + // Process full tiles of tile_items + while (block_offset + TILE_ITEMS <= block_end) + { + ProcessTile(block_offset); + block_offset += TILE_ITEMS; + + __syncthreads(); + } + + // Clean up last partial tile with guarded-I/O + if (block_offset < block_end) + { + ProcessTile(block_offset, block_end - block_offset); + } + } + } +}; + + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_radix_sort_upsweep_region.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_radix_sort_upsweep_region.cuh new file mode 100644 index 0000000000000000000000000000000000000000..7f1e92ed413ebcdd17d445ad7d7e5cd1fa1bf4b2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_radix_sort_upsweep_region.cuh @@ -0,0 +1,443 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * BlockRadixSortUpsweepRegion implements a stateful abstraction of CUDA thread blocks for participating in device-wide radix sort upsweep across a region of tiles. + */ + +#pragma once + +#include "../../thread/thread_reduce.cuh" +#include "../../thread/thread_load.cuh" +#include "../../block/block_load.cuh" +#include "../../util_type.cuh" +#include "../../iterator/cache_modified_input_iterator.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Parameterizable tuning policy type for BlockRadixSortUpsweepRegion + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + CacheLoadModifier _LOAD_MODIFIER, ///< Cache load modifier for reading keys + int _RADIX_BITS> ///< The number of radix bits, i.e., log2(bins) +struct BlockRadixSortUpsweepRegionPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, ///< Threads per thread block + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + RADIX_BITS = _RADIX_BITS, ///< The number of radix bits, i.e., log2(bins) + }; + + static const CacheLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; ///< Cache load modifier for reading keys +}; + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockRadixSortUpsweepRegion implements a stateful abstraction of CUDA thread blocks for participating in device-wide radix sort upsweep across a region of tiles. + */ +template < + typename BlockRadixSortUpsweepRegionPolicy, ///< Parameterized BlockRadixSortUpsweepRegionPolicy tuning policy type + typename Key, ///< Key type + typename Offset> ///< Signed integer type for global offsets +struct BlockRadixSortUpsweepRegion +{ + + //--------------------------------------------------------------------- + // Type definitions and constants + //--------------------------------------------------------------------- + + typedef typename Traits::UnsignedBits UnsignedBits; + + // Integer type for digit counters (to be packed into words of PackedCounters) + typedef unsigned char DigitCounter; + + // Integer type for packing DigitCounters into columns of shared memory banks + typedef unsigned int PackedCounter; + + static const CacheLoadModifier LOAD_MODIFIER = BlockRadixSortUpsweepRegionPolicy::LOAD_MODIFIER; + + enum + { + RADIX_BITS = BlockRadixSortUpsweepRegionPolicy::RADIX_BITS, + BLOCK_THREADS = BlockRadixSortUpsweepRegionPolicy::BLOCK_THREADS, + KEYS_PER_THREAD = BlockRadixSortUpsweepRegionPolicy::ITEMS_PER_THREAD, + + RADIX_DIGITS = 1 << RADIX_BITS, + + LOG_WARP_THREADS = CUB_PTX_LOG_WARP_THREADS, + WARP_THREADS = 1 << LOG_WARP_THREADS, + WARPS = (BLOCK_THREADS + WARP_THREADS - 1) / WARP_THREADS, + + TILE_ITEMS = BLOCK_THREADS * KEYS_PER_THREAD, + + BYTES_PER_COUNTER = sizeof(DigitCounter), + LOG_BYTES_PER_COUNTER = Log2::VALUE, + + PACKING_RATIO = sizeof(PackedCounter) / sizeof(DigitCounter), + LOG_PACKING_RATIO = Log2::VALUE, + + LOG_COUNTER_LANES = CUB_MAX(0, RADIX_BITS - LOG_PACKING_RATIO), + COUNTER_LANES = 1 << LOG_COUNTER_LANES, + + // To prevent counter overflow, we must periodically unpack and aggregate the + // digit counters back into registers. Each counter lane is assigned to a + // warp for aggregation. + + LANES_PER_WARP = CUB_MAX(1, (COUNTER_LANES + WARPS - 1) / WARPS), + + // Unroll tiles in batches without risk of counter overflow + UNROLL_COUNT = CUB_MIN(64, 255 / KEYS_PER_THREAD), + UNROLLED_ELEMENTS = UNROLL_COUNT * TILE_ITEMS, + }; + + + // Input iterator wrapper types + typedef CacheModifiedInputIterator KeysItr; + + /** + * Shared memory storage layout + */ + struct _TempStorage + { + union + { + DigitCounter digit_counters[COUNTER_LANES][BLOCK_THREADS][PACKING_RATIO]; + PackedCounter packed_counters[COUNTER_LANES][BLOCK_THREADS]; + Offset digit_partials[RADIX_DIGITS][WARP_THREADS + 1]; + }; + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Thread fields (aggregate state bundle) + //--------------------------------------------------------------------- + + // Shared storage for this CTA + _TempStorage &temp_storage; + + // Thread-local counters for periodically aggregating composite-counter lanes + Offset local_counts[LANES_PER_WARP][PACKING_RATIO]; + + // Input and output device pointers + KeysItr d_keys_in; + + // The least-significant bit position of the current digit to extract + int current_bit; + + + + //--------------------------------------------------------------------- + // Helper structure for templated iteration + //--------------------------------------------------------------------- + + // Iterate + template + struct Iterate + { + // BucketKeys + static __device__ __forceinline__ void BucketKeys( + BlockRadixSortUpsweepRegion &cta, + UnsignedBits keys[KEYS_PER_THREAD]) + { + cta.Bucket(keys[COUNT]); + + // Next + Iterate::BucketKeys(cta, keys); + } + }; + + // Terminate + template + struct Iterate + { + // BucketKeys + static __device__ __forceinline__ void BucketKeys(BlockRadixSortUpsweepRegion &cta, UnsignedBits keys[KEYS_PER_THREAD]) {} + }; + + + //--------------------------------------------------------------------- + // Utility methods + //--------------------------------------------------------------------- + + /** + * Decode a key and increment corresponding smem digit counter + */ + __device__ __forceinline__ void Bucket(UnsignedBits key) + { + // Perform transform op + UnsignedBits converted_key = Traits::TwiddleIn(key); + + // Add in sub-counter offset + UnsignedBits sub_counter = BFE(converted_key, current_bit, LOG_PACKING_RATIO); + + // Add in row offset + UnsignedBits row_offset = BFE(converted_key, current_bit + LOG_PACKING_RATIO, LOG_COUNTER_LANES); + + // Increment counter + temp_storage.digit_counters[row_offset][threadIdx.x][sub_counter]++; + + } + + + /** + * Reset composite counters + */ + __device__ __forceinline__ void ResetDigitCounters() + { + #pragma unroll + for (int LANE = 0; LANE < COUNTER_LANES; LANE++) + { + temp_storage.packed_counters[LANE][threadIdx.x] = 0; + } + } + + + /** + * Reset the unpacked counters in each thread + */ + __device__ __forceinline__ void ResetUnpackedCounters() + { + #pragma unroll + for (int LANE = 0; LANE < LANES_PER_WARP; LANE++) + { + #pragma unroll + for (int UNPACKED_COUNTER = 0; UNPACKED_COUNTER < PACKING_RATIO; UNPACKED_COUNTER++) + { + local_counts[LANE][UNPACKED_COUNTER] = 0; + } + } + } + + + /** + * Extracts and aggregates the digit counters for each counter lane + * owned by this warp + */ + __device__ __forceinline__ void UnpackDigitCounts() + { + unsigned int warp_id = threadIdx.x >> LOG_WARP_THREADS; + unsigned int warp_tid = threadIdx.x & (WARP_THREADS - 1); + + #pragma unroll + for (int LANE = 0; LANE < LANES_PER_WARP; LANE++) + { + const int counter_lane = (LANE * WARPS) + warp_id; + if (counter_lane < COUNTER_LANES) + { + #pragma unroll + for (int PACKED_COUNTER = 0; PACKED_COUNTER < BLOCK_THREADS; PACKED_COUNTER += WARP_THREADS) + { + #pragma unroll + for (int UNPACKED_COUNTER = 0; UNPACKED_COUNTER < PACKING_RATIO; UNPACKED_COUNTER++) + { + Offset counter = temp_storage.digit_counters[counter_lane][warp_tid + PACKED_COUNTER][UNPACKED_COUNTER]; + local_counts[LANE][UNPACKED_COUNTER] += counter; + } + } + } + } + } + + + /** + * Places unpacked counters into smem for final digit reduction + */ + __device__ __forceinline__ void ReduceUnpackedCounts(Offset &bin_count) + { + unsigned int warp_id = threadIdx.x >> LOG_WARP_THREADS; + unsigned int warp_tid = threadIdx.x & (WARP_THREADS - 1); + + // Place unpacked digit counters in shared memory + #pragma unroll + for (int LANE = 0; LANE < LANES_PER_WARP; LANE++) + { + int counter_lane = (LANE * WARPS) + warp_id; + if (counter_lane < COUNTER_LANES) + { + int digit_row = counter_lane << LOG_PACKING_RATIO; + + #pragma unroll + for (int UNPACKED_COUNTER = 0; UNPACKED_COUNTER < PACKING_RATIO; UNPACKED_COUNTER++) + { + temp_storage.digit_partials[digit_row + UNPACKED_COUNTER][warp_tid] = + local_counts[LANE][UNPACKED_COUNTER]; + } + } + } + + __syncthreads(); + + // Rake-reduce bin_count reductions + if (threadIdx.x < RADIX_DIGITS) + { + bin_count = ThreadReduce( + temp_storage.digit_partials[threadIdx.x], + Sum()); + } + } + + + /** + * Processes a single, full tile + */ + __device__ __forceinline__ void ProcessFullTile(Offset block_offset) + { + // Tile of keys + UnsignedBits keys[KEYS_PER_THREAD]; + + LoadDirectStriped(threadIdx.x, d_keys_in + block_offset, keys); + + // Prevent hoisting +// __threadfence_block(); +// __syncthreads(); + + // Bucket tile of keys + Iterate<0, KEYS_PER_THREAD>::BucketKeys(*this, keys); + } + + + /** + * Processes a single load (may have some threads masked off) + */ + __device__ __forceinline__ void ProcessPartialTile( + Offset block_offset, + const Offset &block_end) + { + // Process partial tile if necessary using single loads + block_offset += threadIdx.x; + while (block_offset < block_end) + { + // Load and bucket key + UnsignedBits key = d_keys_in[block_offset]; + Bucket(key); + block_offset += BLOCK_THREADS; + } + } + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockRadixSortUpsweepRegion( + TempStorage &temp_storage, + Key *d_keys_in, + int current_bit) + : + temp_storage(temp_storage.Alias()), + d_keys_in(reinterpret_cast(d_keys_in)), + current_bit(current_bit) + {} + + + /** + * Compute radix digit histograms from a segment of input tiles. + */ + __device__ __forceinline__ void ProcessRegion( + Offset block_offset, + const Offset &block_end, + Offset &bin_count) ///< [out] The digit count for tid'th bin (output param, valid in the first RADIX_DIGITS threads) + { + // Reset digit counters in smem and unpacked counters in registers + ResetDigitCounters(); + ResetUnpackedCounters(); + + // Unroll batches of full tiles + while (block_offset + UNROLLED_ELEMENTS <= block_end) + { + for (int i = 0; i < UNROLL_COUNT; ++i) + { + ProcessFullTile(block_offset); + block_offset += TILE_ITEMS; + } + + __syncthreads(); + + // Aggregate back into local_count registers to prevent overflow + UnpackDigitCounts(); + + __syncthreads(); + + // Reset composite counters in lanes + ResetDigitCounters(); + } + + // Unroll single full tiles + while (block_offset + TILE_ITEMS <= block_end) + { + ProcessFullTile(block_offset); + block_offset += TILE_ITEMS; + } + + // Process partial tile if necessary + ProcessPartialTile( + block_offset, + block_end); + + __syncthreads(); + + // Aggregate back into local_count registers + UnpackDigitCounts(); + + __syncthreads(); + + // Final raking reduction of counts by bin + ReduceUnpackedCounts(bin_count); + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_reduce_by_key_region.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_reduce_by_key_region.cuh new file mode 100644 index 0000000000000000000000000000000000000000..247db193e04c4b7e0dc5970fc4b72b6b6d3d61d5 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_reduce_by_key_region.cuh @@ -0,0 +1,1010 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockReduceByKeyRegion implements a stateful abstraction of CUDA thread blocks for participating in device-wide reduce-value-by-key. + */ + +#pragma once + +#include + +#include "device_scan_types.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_store.cuh" +#include "../../block/block_scan.cuh" +#include "../../block/block_exchange.cuh" +#include "../../block/block_discontinuity.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../iterator/cache_modified_input_iterator.cuh" +#include "../../iterator/constant_input_iterator.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Parameterizable tuning policy type for BlockReduceByKeyRegion + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + BlockLoadAlgorithm _LOAD_ALGORITHM, ///< The BlockLoad algorithm to use + CacheLoadModifier _LOAD_MODIFIER, ///< Cache load modifier for reading input elements + bool _TWO_PHASE_SCATTER, ///< Whether or not to coalesce output values in shared memory before scattering them to global + BlockScanAlgorithm _SCAN_ALGORITHM> ///< The BlockScan algorithm to use +struct BlockReduceByKeyRegionPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, ///< Threads per thread block + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + TWO_PHASE_SCATTER = _TWO_PHASE_SCATTER, ///< Whether or not to coalesce output values in shared memory before scattering them to global + }; + + static const BlockLoadAlgorithm LOAD_ALGORITHM = _LOAD_ALGORITHM; ///< The BlockLoad algorithm to use + static const CacheLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; ///< Cache load modifier for reading input elements + static const BlockScanAlgorithm SCAN_ALGORITHM = _SCAN_ALGORITHM; ///< The BlockScan algorithm to use +}; + + +/****************************************************************************** + * Tile status interface types + ******************************************************************************/ + +/** + * Tile status interface for reduction by key. + * + */ +template < + typename Value, + typename Offset, + bool SINGLE_WORD = (Traits::PRIMITIVE) && (sizeof(Value) + sizeof(Offset) < 16)> +struct ReduceByKeyTileLookbackStatus; + + +/** + * Tile status interface for reduction by key, specialized for scan status and value types that + * cannot be combined into one machine word. + */ +template < + typename Value, + typename Offset> +struct ReduceByKeyTileLookbackStatus : + TileLookbackStatus > +{ + typedef TileLookbackStatus > SuperClass; + + /// Constructor + __host__ __device__ __forceinline__ + ReduceByKeyTileLookbackStatus() : SuperClass() {} +}; + + +/** + * Tile status interface for reduction by key, specialized for scan status and value types that + * can be combined into one machine word that can be read/written coherently in a single access. + */ +template < + typename Value, + typename Offset> +struct ReduceByKeyTileLookbackStatus +{ + typedef ItemOffsetPair ItemOffsetPair; + + // Constants + enum + { + PAIR_SIZE = sizeof(Value) + sizeof(Offset), + TXN_WORD_SIZE = 1 << Log2::VALUE, + STATUS_WORD_SIZE = TXN_WORD_SIZE - PAIR_SIZE, + + TILE_STATUS_PADDING = CUB_PTX_WARP_THREADS, + }; + + // Status word type + typedef typename If<(STATUS_WORD_SIZE == 8), + long long, + typename If<(STATUS_WORD_SIZE == 4), + int, + typename If<(STATUS_WORD_SIZE == 2), + short, + char>::Type>::Type>::Type StatusWord; + + // Status word type + typedef typename If<(TXN_WORD_SIZE == 16), + longlong2, + typename If<(TXN_WORD_SIZE == 8), + long long, + int>::Type>::Type TxnWord; + + // Device word type (for when sizeof(Value) == sizeof(Offset)) + struct TileDescriptorBigStatus + { + Offset offset; + Value value; + StatusWord status; + }; + + // Device word type (for when sizeof(Value) != sizeof(Offset)) + struct TileDescriptorLittleStatus + { + Value value; + StatusWord status; + Offset offset; + }; + + // Device word type + typedef typename If< + (sizeof(Value) == sizeof(Offset)), + TileDescriptorBigStatus, + TileDescriptorLittleStatus>::Type + TileDescriptor; + + + // Device storage + TileDescriptor *d_tile_status; + + + /// Constructor + __host__ __device__ __forceinline__ + ReduceByKeyTileLookbackStatus() + : + d_tile_status(NULL) + {} + + + /// Initializer + __host__ __device__ __forceinline__ + cudaError_t Init( + int num_tiles, ///< [in] Number of tiles + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t temp_storage_bytes) ///< [in] Size in bytes of \t d_temp_storage allocation + { + d_tile_status = reinterpret_cast(d_temp_storage); + return cudaSuccess; + } + + + /** + * Compute device memory needed for tile status + */ + __host__ __device__ __forceinline__ + static cudaError_t AllocationSize( + int num_tiles, ///< [in] Number of tiles + size_t &temp_storage_bytes) ///< [out] Size in bytes of \t d_temp_storage allocation + { + temp_storage_bytes = (num_tiles + TILE_STATUS_PADDING) * sizeof(TileDescriptor); // bytes needed for tile status descriptors + return cudaSuccess; + } + + + /** + * Initialize (from device) + */ + __device__ __forceinline__ void InitializeStatus(int num_tiles) + { + int tile_idx = (blockIdx.x * blockDim.x) + threadIdx.x; + if (tile_idx < num_tiles) + { + // Not-yet-set + d_tile_status[TILE_STATUS_PADDING + tile_idx].status = StatusWord(LOOKBACK_TILE_INVALID); + } + + if ((blockIdx.x == 0) && (threadIdx.x < TILE_STATUS_PADDING)) + { + // Padding + d_tile_status[threadIdx.x].status = StatusWord(LOOKBACK_TILE_OOB); + } + } + + + /** + * Update the specified tile's inclusive value and corresponding status + */ + __device__ __forceinline__ void SetInclusive(int tile_idx, ItemOffsetPair tile_inclusive) + { + TileDescriptor tile_descriptor; + tile_descriptor.status = LOOKBACK_TILE_INCLUSIVE; + tile_descriptor.value = tile_inclusive.value; + tile_descriptor.offset = tile_inclusive.offset; + + TxnWord alias; + *reinterpret_cast(&alias) = tile_descriptor; + ThreadStore(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx), alias); + } + + + /** + * Update the specified tile's partial value and corresponding status + */ + __device__ __forceinline__ void SetPartial(int tile_idx, ItemOffsetPair tile_partial) + { + TileDescriptor tile_descriptor; + tile_descriptor.status = LOOKBACK_TILE_PARTIAL; + tile_descriptor.value = tile_partial.value; + tile_descriptor.offset = tile_partial.offset; + + TxnWord alias; + *reinterpret_cast(&alias) = tile_descriptor; + ThreadStore(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx), alias); + } + + /** + * Wait for the corresponding tile to become non-invalid + */ + __device__ __forceinline__ void WaitForValid( + int tile_idx, + StatusWord &status, + ItemOffsetPair &value) + { + // Use warp-any to determine when all threads have valid status + TxnWord alias = ThreadLoad(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx)); + TileDescriptor tile_descriptor = reinterpret_cast(alias); + + while ((tile_descriptor.status == LOOKBACK_TILE_INVALID)) + { + alias = ThreadLoad(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx)); + tile_descriptor = reinterpret_cast(alias); + } + + status = tile_descriptor.status; + value.value = tile_descriptor.value; + value.offset = tile_descriptor.offset; + } + +}; + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockReduceByKeyRegion implements a stateful abstraction of CUDA thread blocks for participating in device-wide reduce-value-by-key across a region of tiles + */ +template < + typename BlockReduceByKeyRegionPolicy, ///< Parameterized BlockReduceByKeyRegionPolicy tuning policy type + typename KeyInputIterator, ///< Random-access input iterator type for keys + typename KeyOutputIterator, ///< Random-access output iterator type for keys + typename ValueInputIterator, ///< Random-access input iterator type for values + typename ValueOutputIterator, ///< Random-access output iterator type for values + typename EqualityOp, ///< Key equality operator type + typename ReductionOp, ///< Value reduction operator type + typename Offset> ///< Signed integer type for global offsets +struct BlockReduceByKeyRegion +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Data type of key iterator + typedef typename std::iterator_traits::value_type Key; + + // Data type of value iterator + typedef typename std::iterator_traits::value_type Value; + + // Tile status descriptor interface type + typedef ReduceByKeyTileLookbackStatus TileLookbackStatus; + + // Constants + enum + { + BLOCK_THREADS = BlockReduceByKeyRegionPolicy::BLOCK_THREADS, + WARPS = BLOCK_THREADS / CUB_PTX_WARP_THREADS, + ITEMS_PER_THREAD = BlockReduceByKeyRegionPolicy::ITEMS_PER_THREAD, + TWO_PHASE_SCATTER = (BlockReduceByKeyRegionPolicy::TWO_PHASE_SCATTER) && (ITEMS_PER_THREAD > 1), + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + + // Whether or not the scan operation has a zero-valued identity value (true if we're performing addition on a primitive type) + HAS_IDENTITY_ZERO = (Equals::VALUE) && (Traits::PRIMITIVE), + + // Whether or not to sync after loading data + SYNC_AFTER_LOAD = (BlockReduceByKeyRegionPolicy::LOAD_ALGORITHM != BLOCK_LOAD_DIRECT), + + // Whether or not this is run-length-encoding with a constant iterator as values + IS_RUN_LENGTH_ENCODE = (Equals >::VALUE) || (Equals >::VALUE) || (Equals >::VALUE), + + }; + + // Cache-modified input iterator wrapper type for keys + typedef typename If::VALUE, + CacheModifiedInputIterator, // Wrap the native input pointer with CacheModifiedValueInputIterator + KeyInputIterator>::Type // Directly use the supplied input iterator type + WrappedKeyInputIterator; + + // Cache-modified input iterator wrapper type for values + typedef typename If::VALUE, + CacheModifiedInputIterator, // Wrap the native input pointer with CacheModifiedValueInputIterator + ValueInputIterator>::Type // Directly use the supplied input iterator type + WrappedValueInputIterator; + + // Value-offset tuple type for scanning (maps accumulated values to segment index) + typedef ItemOffsetPair ValueOffsetPair; + + // Reduce-value-by-segment scan operator + struct ReduceByKeyOp + { + ReductionOp op; ///< Wrapped reduction operator + + /// Constructor + __device__ __forceinline__ ReduceByKeyOp(ReductionOp op) : op(op) {} + + /// Scan operator (specialized for sum on primitive types) + __device__ __forceinline__ ValueOffsetPair operator()( + const ValueOffsetPair &first, ///< First partial reduction + const ValueOffsetPair &second, ///< Second partial reduction + Int2Type has_identity_zero) ///< Whether the operation has a zero-valued identity + { + Value select = (second.offset) ? 0 : first.value; + + ValueOffsetPair retval; + retval.offset = first.offset + second.offset; + retval.value = op(select, second.value); + return retval; + } + + /// Scan operator (specialized for reductions without zero-valued identity) + __device__ __forceinline__ ValueOffsetPair operator()( + const ValueOffsetPair &first, ///< First partial reduction + const ValueOffsetPair &second, ///< Second partial reduction + Int2Type has_identity_zero) ///< Whether the operation has a zero-valued identity + { + ValueOffsetPair retval; + retval.offset = first.offset + second.offset; + if (second.offset) + { + retval.value = second.value; + return retval; + } + else + { + retval.value = op(first.value, second.value); + return retval; + } +/* + // Alternate expression below uses more registers, slower + ValueOffsetPair retval; + retval.offset = first.offset + second.offset; + retval.value = (second.offset) ? + second.value : // The second partial reduction spans a segment reset, so it's value aggregate becomes the running aggregate + op(first.value, second.value); // The second partial reduction does not span a reset, so accumulate both into the running aggregate + return retval; +*/ + } + + /// Scan operator + __device__ __forceinline__ ValueOffsetPair operator()( + const ValueOffsetPair &first, ///< First partial reduction + const ValueOffsetPair &second) ///< Second partial reduction + { + return (*this)(first, second, Int2Type()); + } + }; + + // Parameterized BlockLoad type for keys + typedef BlockLoad< + WrappedKeyInputIterator, + BlockReduceByKeyRegionPolicy::BLOCK_THREADS, + BlockReduceByKeyRegionPolicy::ITEMS_PER_THREAD, + BlockReduceByKeyRegionPolicy::LOAD_ALGORITHM> + BlockLoadKeys; + + // Parameterized BlockLoad type for values + typedef BlockLoad< + WrappedValueInputIterator, + BlockReduceByKeyRegionPolicy::BLOCK_THREADS, + BlockReduceByKeyRegionPolicy::ITEMS_PER_THREAD, + (IS_RUN_LENGTH_ENCODE) ? + BLOCK_LOAD_DIRECT : + (BlockLoadAlgorithm) BlockReduceByKeyRegionPolicy::LOAD_ALGORITHM> + BlockLoadValues; + + // Parameterized BlockExchange type for locally compacting items as part of a two-phase scatter + typedef BlockExchange< + Key, + BLOCK_THREADS, + ITEMS_PER_THREAD> + BlockExchangeKeys; + + // Parameterized BlockExchange type for locally compacting items as part of a two-phase scatter + typedef BlockExchange< + Value, + BLOCK_THREADS, + ITEMS_PER_THREAD> + BlockExchangeValues; + + // Parameterized BlockDiscontinuity type for keys + typedef BlockDiscontinuity BlockDiscontinuityKeys; + + // Parameterized BlockScan type + typedef BlockScan< + ValueOffsetPair, + BlockReduceByKeyRegionPolicy::BLOCK_THREADS, + BlockReduceByKeyRegionPolicy::SCAN_ALGORITHM> + BlockScanAllocations; + + // Callback type for obtaining tile prefix during block scan + typedef LookbackBlockPrefixCallbackOp< + ValueOffsetPair, + ReduceByKeyOp, + TileLookbackStatus> + LookbackPrefixCallbackOp; + + // Shared memory type for this threadblock + struct _TempStorage + { + + union + { + struct + { + typename BlockScanAllocations::TempStorage scan; // Smem needed for tile scanning + typename LookbackPrefixCallbackOp::TempStorage prefix; // Smem needed for cooperative prefix callback + typename BlockDiscontinuityKeys::TempStorage discontinuity; // Smem needed for discontinuity detection + typename BlockLoadKeys::TempStorage load_keys; // Smem needed for loading keys + + Offset tile_idx; // Shared tile index + Offset tile_num_flags_prefix; // Exclusive tile prefix + }; + + // Smem needed for loading values + typename BlockLoadValues::TempStorage load_values; + + // Smem needed for compacting values + typename BlockExchangeValues::TempStorage exchange_values; + + // Smem needed for compacting keys + typename BlockExchangeKeys::TempStorage exchange_keys; + }; + + }; + + // Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + _TempStorage &temp_storage; ///< Reference to temp_storage + + WrappedKeyInputIterator d_keys_in; ///< Input keys + KeyOutputIterator d_keys_out; ///< Output keys + + WrappedValueInputIterator d_values_in; ///< Input values + ValueOutputIterator d_values_out; ///< Output values + + InequalityWrapper inequality_op; ///< Key inequality operator + ReduceByKeyOp scan_op; ///< Reduce-value-by flag scan operator + Offset num_items; ///< Total number of input items + + + //--------------------------------------------------------------------- + // Constructor + //--------------------------------------------------------------------- + + // Constructor + __device__ __forceinline__ + BlockReduceByKeyRegion( + TempStorage &temp_storage, ///< Reference to temp_storage + KeyInputIterator d_keys_in, ///< Input keys + KeyOutputIterator d_keys_out, ///< Output keys + ValueInputIterator d_values_in, ///< Input values + ValueOutputIterator d_values_out, ///< Output values + EqualityOp equality_op, ///< Key equality operator + ReductionOp reduction_op, ///< Value reduction operator + Offset num_items) ///< Total number of input items + : + temp_storage(temp_storage.Alias()), + d_keys_in(d_keys_in), + d_keys_out(d_keys_out), + d_values_in(d_values_in), + d_values_out(d_values_out), + inequality_op(equality_op), + scan_op(reduction_op), + num_items(num_items) + {} + + + //--------------------------------------------------------------------- + // Block scan utility methods + //--------------------------------------------------------------------- + + /** + * Scan with identity (first tile) + */ + __device__ __forceinline__ + void ScanBlock( + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + ValueOffsetPair &block_aggregate, + Int2Type has_identity) + { + ValueOffsetPair identity; + identity.value = 0; + identity.offset = 0; + BlockScanAllocations(temp_storage.scan).ExclusiveScan(values_and_segments, values_and_segments, identity, scan_op, block_aggregate); + } + + /** + * Scan without identity (first tile). Without an identity, the first output item is undefined. + * + */ + __device__ __forceinline__ + void ScanBlock( + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + ValueOffsetPair &block_aggregate, + Int2Type has_identity) + { + BlockScanAllocations(temp_storage.scan).ExclusiveScan(values_and_segments, values_and_segments, scan_op, block_aggregate); + } + + /** + * Scan with identity (subsequent tile) + */ + __device__ __forceinline__ + void ScanBlock( + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + ValueOffsetPair &block_aggregate, + LookbackPrefixCallbackOp &prefix_op, + Int2Type has_identity) + { + ValueOffsetPair identity; + identity.value = 0; + identity.offset = 0; + BlockScanAllocations(temp_storage.scan).ExclusiveScan(values_and_segments, values_and_segments, identity, scan_op, block_aggregate, prefix_op); + } + + /** + * Scan without identity (subsequent tile). Without an identity, the first output item is undefined. + */ + __device__ __forceinline__ + void ScanBlock( + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + ValueOffsetPair &block_aggregate, + LookbackPrefixCallbackOp &prefix_op, + Int2Type has_identity) + { + BlockScanAllocations(temp_storage.scan).ExclusiveScan(values_and_segments, values_and_segments, scan_op, block_aggregate, prefix_op); + } + + + //--------------------------------------------------------------------- + // Zip utility methods + //--------------------------------------------------------------------- + + template + __device__ __forceinline__ void ZipValuesAndFlags( + Offset num_remaining, + Value (&values)[ITEMS_PER_THREAD], + Offset (&flags)[ITEMS_PER_THREAD], + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD]) + { + // Zip values and flags + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + // Unset flags for out-of-bounds keys + if ((LAST_TILE) && (Offset(threadIdx.x * ITEMS_PER_THREAD) + ITEM >= num_remaining)) + flags[ITEM] = 0; + + values_and_segments[ITEM].value = values[ITEM]; + values_and_segments[ITEM].offset = flags[ITEM]; + } + } + + //--------------------------------------------------------------------- + // Scatter utility methods + //--------------------------------------------------------------------- + + + + /** + * Scatter flagged items to output offsets (specialized for direct scattering) + * + * The exclusive scan causes each head flag to be paired with the previous + * value aggregate. As such: + * - The scatter offsets must be decremented for value value aggregates + * - The first tile does not scatter the first flagged value (it is undefined from the exclusive scan) + * - If the tile is partially-full, we need to scatter the first out-of-bounds value (which aggregates all valid values in the last segment) + * + */ + template + __device__ __forceinline__ void ScatterDirect( + Offset num_remaining, + Key (&keys)[ITEMS_PER_THREAD], + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + Offset (&flags)[ITEMS_PER_THREAD], + Offset tile_num_flags, + Int2Type iteration) + { + // Scatter key + if (flags[ITEM]) + { + d_keys_out[values_and_segments[ITEM].offset] = keys[ITEM]; + } + + bool is_first_flag = FIRST_TILE && (ITEM == 0) && (threadIdx.x == 0); + bool is_oob_value = (LAST_TILE) && (Offset(threadIdx.x * ITEMS_PER_THREAD) + ITEM == num_remaining); + + // Scatter value reduction + if (((flags[ITEM] || is_oob_value)) && (!is_first_flag)) + { + d_values_out[values_and_segments[ITEM].offset - 1] = values_and_segments[ITEM].value; + } + + ScatterDirect(num_remaining, keys, values_and_segments, flags, tile_num_flags, Int2Type()); + } + + template + __device__ __forceinline__ void ScatterDirect( + Offset num_remaining, + Key (&keys)[ITEMS_PER_THREAD], + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + Offset (&flags)[ITEMS_PER_THREAD], + Offset tile_num_flags, + Int2Type iteration) + {} + + /** + * Scatter flagged items to output offsets (specialized for two-phase scattering) + * + * The exclusive scan causes each head flag to be paired with the previous + * value aggregate. As such: + * - The scatter offsets must be decremented for value value aggregates + * - The first tile does not scatter the first flagged value (it is undefined from the exclusive scan) + * - If the tile is partially-full, we need to scatter the first out-of-bounds value (which aggregates all valid values in the last segment) + * + */ + template + __device__ __forceinline__ void ScatterTwoPhase( + Offset num_remaining, + Key (&keys)[ITEMS_PER_THREAD], + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + Offset (&flags)[ITEMS_PER_THREAD], + Offset tile_num_flags, + Offset tile_num_flags_prefix) + { + int local_ranks[ITEMS_PER_THREAD]; + Value values[ITEMS_PER_THREAD]; + + // Share exclusive tile prefix + if (threadIdx.x == 0) + { + temp_storage.tile_num_flags_prefix = tile_num_flags_prefix; + } + + __syncthreads(); + + // Load exclusive tile prefix in all threads + tile_num_flags_prefix = temp_storage.tile_num_flags_prefix; + + __syncthreads(); + + // Compute local scatter ranks + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + local_ranks[ITEM] = values_and_segments[ITEM].offset - tile_num_flags_prefix; + } + + // Compact keys in shared memory + BlockExchangeKeys(temp_storage.exchange_keys).ScatterToStriped(keys, local_ranks, flags); + + // Scatter keys + StoreDirectStriped(threadIdx.x, d_keys_out + tile_num_flags_prefix, keys, tile_num_flags); + + // Unzip values and set flag for first oob item in last tile + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + values[ITEM] = values_and_segments[ITEM].value; + + if (FIRST_TILE) + local_ranks[ITEM]--; + + if (LAST_TILE && (Offset(threadIdx.x * ITEMS_PER_THREAD) + ITEM == num_remaining)) + flags[ITEM] = 1; + } + + // Unset first flag in first tile + if (FIRST_TILE && (threadIdx.x == 0)) + flags[0] = 0; + + __syncthreads(); + + // Compact values in shared memory + BlockExchangeValues(temp_storage.exchange_values).ScatterToStriped(values, local_ranks, flags); + + // Number to output + Offset exchange_count = tile_num_flags; + + if (LAST_TILE && (num_remaining < TILE_ITEMS)) + exchange_count++; + + if (FIRST_TILE) + { + exchange_count--; + } + else + { + tile_num_flags_prefix--; + } + + // Scatter values + StoreDirectStriped(threadIdx.x, d_values_out + tile_num_flags_prefix, values, exchange_count); + + __syncthreads(); + } + + + /** + * Scatter flagged items + */ + template + __device__ __forceinline__ void Scatter( + Offset num_remaining, + Key (&keys)[ITEMS_PER_THREAD], + ValueOffsetPair (&values_and_segments)[ITEMS_PER_THREAD], + Offset (&flags)[ITEMS_PER_THREAD], + Offset tile_num_flags, + Offset tile_num_flags_prefix) + { + // Do a one-phase scatter if (a) two-phase is disabled or (b) the average number of selected items per thread is less than one + if ((TWO_PHASE_SCATTER) && ((tile_num_flags >> Log2::VALUE) > 0)) + { + ScatterTwoPhase( + num_remaining, + keys, + values_and_segments, + flags, + tile_num_flags, + tile_num_flags_prefix); + } + else + { + ScatterDirect( + num_remaining, + keys, + values_and_segments, + flags, + tile_num_flags, + Int2Type<0>()); + } + } + + + //--------------------------------------------------------------------- + // Cooperatively scan a device-wide sequence of tiles with other CTAs + //--------------------------------------------------------------------- + + /** + * Process a tile of input (dynamic domino scan) + */ + template < + bool LAST_TILE> + __device__ __forceinline__ ValueOffsetPair ConsumeTile( + Offset num_items, ///< Total number of global input items + Offset num_remaining, ///< Number of global input items remaining (including this tile) + int tile_idx, ///< Tile index + Offset block_offset, ///< Tile offset + TileLookbackStatus &tile_status) ///< Global list of tile status + { + Key keys[ITEMS_PER_THREAD]; // Tile keys + Value values[ITEMS_PER_THREAD]; // Tile values + Offset flags[ITEMS_PER_THREAD]; // Segment head flags + ValueOffsetPair values_and_segments[ITEMS_PER_THREAD]; // Zipped values and segment flags|indices + + ValueOffsetPair running_total; // Running count of segments and current value aggregate (including this tile) + + // Load keys and values + if (LAST_TILE) + { + BlockLoadKeys(temp_storage.load_keys).Load(d_keys_in + block_offset, keys, num_remaining); + } + else + { + BlockLoadKeys(temp_storage.load_keys).Load(d_keys_in + block_offset, keys); + } + + if (SYNC_AFTER_LOAD) + __syncthreads(); + + // Load values + if (LAST_TILE) + BlockLoadValues(temp_storage.load_values).Load(d_values_in + block_offset, values, num_remaining); + else + BlockLoadValues(temp_storage.load_values).Load(d_values_in + block_offset, values); + + if (SYNC_AFTER_LOAD) + __syncthreads(); + + if (tile_idx == 0) + { + // First tile + + // Set head flags. First tile sets the first flag for the first item + BlockDiscontinuityKeys(temp_storage.discontinuity).FlagHeads(flags, keys, inequality_op); + + // Zip values and flags + ZipValuesAndFlags(num_remaining, values, flags, values_and_segments); + + // Exclusive scan of values and flags + ValueOffsetPair block_aggregate; + ScanBlock(values_and_segments, block_aggregate, Int2Type()); + + // Update tile status if this is not the last tile + if (!LAST_TILE && (threadIdx.x == 0)) + tile_status.SetInclusive(0, block_aggregate); + + // Set offset for first scan output + if (!HAS_IDENTITY_ZERO && (threadIdx.x == 0)) + values_and_segments[0].offset = 0; + + running_total = block_aggregate; + + // Scatter flagged items + Scatter(num_remaining, keys, values_and_segments, flags, block_aggregate.offset, 0); + } + else + { + // Not first tile + + // Obtain the last key in the previous tile to compare with + Key tile_predecessor_key = (threadIdx.x == 0) ? + d_keys_in[block_offset - 1] : + ZeroInitialize(); + + // Set head flags + BlockDiscontinuityKeys(temp_storage.discontinuity).FlagHeads(flags, keys, inequality_op, tile_predecessor_key); + + // Zip values and flags + ZipValuesAndFlags(num_remaining, values, flags, values_and_segments); + + // Exclusive scan of values and flags + ValueOffsetPair block_aggregate; + LookbackPrefixCallbackOp prefix_op(tile_status, temp_storage.prefix, scan_op, tile_idx); + ScanBlock(values_and_segments, block_aggregate, prefix_op, Int2Type()); + + running_total = prefix_op.inclusive_prefix; + + // Scatter flagged items + Scatter(num_remaining, keys, values_and_segments, flags, block_aggregate.offset, prefix_op.exclusive_prefix.offset); + } + + return running_total; + } + + + /** + * Dequeue and scan tiles of items as part of a dynamic domino scan + */ + template ///< Output iterator type for recording number of items selected + __device__ __forceinline__ void ConsumeRegion( + int num_tiles, ///< Total number of input tiles + GridQueue queue, ///< Queue descriptor for assigning tiles of work to thread blocks + TileLookbackStatus &tile_status, ///< Global list of tile status + NumSegmentsIterator d_num_segments) ///< Output pointer for total number of segments identified + { +#if (CUB_PTX_VERSION <= 130) + // Blocks are launched in increasing order, so just assign one tile per block + + int tile_idx = (blockIdx.y * 32 * 1024) + blockIdx.x; // Current tile index + Offset block_offset = Offset(TILE_ITEMS) * tile_idx; // Global offset for the current tile + Offset num_remaining = num_items - block_offset; // Remaining items (including this tile) + + if (num_remaining > TILE_ITEMS) + { + // Full tile + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + } + else if (num_remaining > 0) + { + // Last tile + ValueOffsetPair running_total = ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + + // Output the total number of items selected + if (threadIdx.x == 0) + { + *d_num_segments = running_total.offset; + + // If the last tile is a whole tile, the inclusive prefix contains accumulated value reduction for the last segment + if (num_remaining == TILE_ITEMS) + { + d_values_out[running_total.offset - 1] = running_total.value; + } + } + } +#else + // Blocks may not be launched in increasing order, so work-steal tiles + + // Get first tile index + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + int tile_idx = temp_storage.tile_idx; + Offset block_offset = Offset(TILE_ITEMS) * tile_idx; // Global offset for the current tile + Offset num_remaining = num_items - block_offset; // Remaining items (including this tile) + + while (num_remaining > TILE_ITEMS) + { + if (SYNC_AFTER_LOAD) + __syncthreads(); + + // Consume full tile + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + + // Get tile index + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + tile_idx = temp_storage.tile_idx; + block_offset = Offset(TILE_ITEMS) * tile_idx; + num_remaining = num_items - block_offset; + } + + if (num_remaining > 0) + { + // Consume last tile (treat as partially-full) + ValueOffsetPair running_total = ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + + if ((threadIdx.x == 0)) + { + // Output the total number of items selected + *d_num_segments = running_total.offset; + + // If the last tile is a whole tile, the inclusive prefix contains accumulated value reduction for the last segment + if (num_remaining == TILE_ITEMS) + { + d_values_out[running_total.offset - 1] = running_total.value; + } + } + } +#endif + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_reduce_region.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_reduce_region.cuh new file mode 100644 index 0000000000000000000000000000000000000000..a5cf89d38a1e804ca5bd91639944dc6092e91c90 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_reduce_region.cuh @@ -0,0 +1,430 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockReduceRegion implements a stateful abstraction of CUDA thread blocks for participating in device-wide reduction across a region of tiles. + */ + +#pragma once + +#include + +#include "../../block/block_load.cuh" +#include "../../block/block_reduce.cuh" +#include "../../grid/grid_mapping.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../grid/grid_even_share.cuh" +#include "../../util_type.cuh" +#include "../../iterator/cache_modified_input_iterator.cuh" +#include "../../util_namespace.cuh" + + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Parameterizable tuning policy type for BlockReduceRegion + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + int _VECTOR_LOAD_LENGTH, ///< Number of items per vectorized load + BlockReduceAlgorithm _BLOCK_ALGORITHM, ///< Cooperative block-wide reduction algorithm to use + CacheLoadModifier _LOAD_MODIFIER, ///< Cache load modifier for reading input elements + GridMappingStrategy _GRID_MAPPING> ///< How to map tiles of input onto thread blocks +struct BlockReduceRegionPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, ///< Threads per thread block + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + VECTOR_LOAD_LENGTH = _VECTOR_LOAD_LENGTH, ///< Number of items per vectorized load + }; + + static const BlockReduceAlgorithm BLOCK_ALGORITHM = _BLOCK_ALGORITHM; ///< Cooperative block-wide reduction algorithm to use + static const CacheLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; ///< Cache load modifier for reading input elements + static const GridMappingStrategy GRID_MAPPING = _GRID_MAPPING; ///< How to map tiles of input onto thread blocks +}; + + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockReduceRegion implements a stateful abstraction of CUDA thread blocks for participating in device-wide reduction across a region of tiles. + * + * Each thread reduces only the values it loads. If \p FIRST_TILE, this + * partial reduction is stored into \p thread_aggregate. Otherwise it is + * accumulated into \p thread_aggregate. + */ +template < + typename BlockReduceRegionPolicy, ///< Parameterized BlockReduceRegionPolicy tuning policy type + typename InputIterator, ///< Random-access iterator type for input + typename Offset, ///< Signed integer type for global offsets + typename ReductionOp> ///< Binary reduction operator type having member T operator()(const T &a, const T &b) +struct BlockReduceRegion +{ + + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // The value type of the input iterator + typedef typename std::iterator_traits::value_type T; + + // Vector type of T for data movement + typedef typename CubVector::Type VectorT; + + // Input iterator wrapper type + typedef typename If::VALUE, + CacheModifiedInputIterator, // Wrap the native input pointer with CacheModifiedInputIterator + InputIterator>::Type // Directly use the supplied input iterator type + WrappedInputIterator; + + // Constants + enum + { + BLOCK_THREADS = BlockReduceRegionPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockReduceRegionPolicy::ITEMS_PER_THREAD, + VECTOR_LOAD_LENGTH = CUB_MIN(ITEMS_PER_THREAD, BlockReduceRegionPolicy::VECTOR_LOAD_LENGTH), + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + + // Can vectorize according to the policy if the input iterator is a native pointer to a primitive type + CAN_VECTORIZE = (VECTOR_LOAD_LENGTH > 1) && + (IsPointer::VALUE) && + Traits::PRIMITIVE, + + }; + + static const CacheLoadModifier LOAD_MODIFIER = BlockReduceRegionPolicy::LOAD_MODIFIER; + static const BlockReduceAlgorithm BLOCK_ALGORITHM = BlockReduceRegionPolicy::BLOCK_ALGORITHM; + + // Parameterized BlockReduce primitive + typedef BlockReduce BlockReduceT; + + /// Shared memory type required by this thread block + typedef typename BlockReduceT::TempStorage _TempStorage; + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + T thread_aggregate; ///< Each thread's partial reduction + _TempStorage& temp_storage; ///< Reference to temp_storage + InputIterator d_in; ///< Input data to reduce + WrappedInputIterator d_wrapped_in; ///< Wrapped input data to reduce + ReductionOp reduction_op; ///< Binary reduction operator + int first_tile_size; ///< Size of first tile consumed + bool is_aligned; ///< Whether or not input is vector-aligned + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + + // Whether or not the input is aligned with the vector type (specialized for types we can vectorize) + template + static __device__ __forceinline__ bool IsAligned( + Iterator d_in, + Int2Type can_vectorize) + { + return (size_t(d_in) & (sizeof(VectorT) - 1)) == 0; + } + + // Whether or not the input is aligned with the vector type (specialized for types we cannot vectorize) + template + static __device__ __forceinline__ bool IsAligned( + Iterator d_in, + Int2Type can_vectorize) + { + return false; + } + + + /** + * Constructor + */ + __device__ __forceinline__ BlockReduceRegion( + TempStorage& temp_storage, ///< Reference to temp_storage + InputIterator d_in, ///< Input data to reduce + ReductionOp reduction_op) ///< Binary reduction operator + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + d_wrapped_in(d_in), + reduction_op(reduction_op), + first_tile_size(0), + is_aligned(IsAligned(d_in, Int2Type())) + {} + + + /** + * Consume a full tile of input (specialized for cases where we cannot vectorize) + */ + template + __device__ __forceinline__ T ConsumeFullTile( + _Offset block_offset, ///< The offset the tile to consume + Int2Type can_vectorize) ///< Whether or not we can vectorize loads + { + T items[ITEMS_PER_THREAD]; + + // Load items in striped fashion + LoadDirectStriped(threadIdx.x, d_wrapped_in + block_offset, items); + + // Reduce items within each thread stripe + return ThreadReduce(items, reduction_op); + } + + + /** + * Consume a full tile of input (specialized for cases where we can vectorize) + */ + template + __device__ __forceinline__ T ConsumeFullTile( + _Offset block_offset, ///< The offset the tile to consume + Int2Type can_vectorize) ///< Whether or not we can vectorize loads + { + if (!is_aligned) + { + // Not aligned + return ConsumeFullTile(block_offset, Int2Type()); + } + else + { + // Alias items as an array of VectorT and load it in striped fashion + enum { WORDS = ITEMS_PER_THREAD / VECTOR_LOAD_LENGTH }; + + T items[ITEMS_PER_THREAD]; + + VectorT *vec_items = reinterpret_cast(items); + + // Vector input iterator wrapper type + CacheModifiedInputIterator d_vec_in( + reinterpret_cast(d_in + block_offset + (threadIdx.x * VECTOR_LOAD_LENGTH))); + + #pragma unroll + for (int i = 0; i < WORDS; ++i) + vec_items[i] = d_vec_in[BLOCK_THREADS * i]; + + // Reduce items within each thread stripe + return ThreadReduce(items, reduction_op); + } + } + + + + /** + * Process a single tile of input + */ + template + __device__ __forceinline__ void ConsumeTile( + Offset block_offset, ///< The offset the tile to consume + int valid_items = TILE_ITEMS) ///< The number of valid items in the tile + { + if (FULL_TILE) + { + // Full tile + T partial = ConsumeFullTile(block_offset, Int2Type()); + + // Update running thread aggregate + thread_aggregate = (first_tile_size) ? + reduction_op(thread_aggregate, partial) : // Update + partial; // Assign + } + else + { + // Partial tile + int thread_offset = threadIdx.x; + + if (!first_tile_size && (thread_offset < valid_items)) + { + // Assign thread_aggregate + thread_aggregate = d_wrapped_in[block_offset + thread_offset]; + thread_offset += BLOCK_THREADS; + } + + while (thread_offset < valid_items) + { + // Update thread aggregate + T item = d_wrapped_in[block_offset + thread_offset]; + thread_aggregate = reduction_op(thread_aggregate, item); + thread_offset += BLOCK_THREADS; + } + } + + // Set first tile size if necessary + if (!first_tile_size) + first_tile_size = valid_items; + } + + + //--------------------------------------------------------------- + // Consume a contiguous segment of tiles + //--------------------------------------------------------------------- + + /** + * \brief Reduce a contiguous segment of input tiles + */ + __device__ __forceinline__ void ConsumeRegion( + Offset block_offset, ///< [in] Threadblock begin offset (inclusive) + Offset block_end, ///< [in] Threadblock end offset (exclusive) + T &block_aggregate) ///< [out] Running total + { + // Consume subsequent full tiles of input + while (block_offset + TILE_ITEMS <= block_end) + { + ConsumeTile(block_offset); + block_offset += TILE_ITEMS; + } + + // Consume a partially-full tile + if (block_offset < block_end) + { + int valid_items = block_end - block_offset; + ConsumeTile(block_offset, valid_items); + } + + // Compute block-wide reduction + block_aggregate = (first_tile_size < TILE_ITEMS) ? + BlockReduceT(temp_storage).Reduce(thread_aggregate, reduction_op, first_tile_size) : + BlockReduceT(temp_storage).Reduce(thread_aggregate, reduction_op); + } + + + /** + * Reduce a contiguous segment of input tiles + */ + __device__ __forceinline__ void ConsumeRegion( + Offset num_items, ///< [in] Total number of global input items + GridEvenShare &even_share, ///< [in] GridEvenShare descriptor + GridQueue &queue, ///< [in,out] GridQueue descriptor + T &block_aggregate, ///< [out] Running total + Int2Type is_even_share) ///< [in] Marker type indicating this is an even-share mapping + { + // Initialize even-share descriptor for this thread block + even_share.BlockInit(); + + // Consume input tiles + ConsumeRegion(even_share.block_offset, even_share.block_end, block_aggregate); + } + + + //--------------------------------------------------------------------- + // Dynamically consume tiles + //--------------------------------------------------------------------- + + /** + * Dequeue and reduce tiles of items as part of a inter-block scan + */ + __device__ __forceinline__ void ConsumeRegion( + int num_items, ///< Total number of input items + GridQueue queue, ///< Queue descriptor for assigning tiles of work to thread blocks + T &block_aggregate) ///< [out] Running total + { + // Shared dequeue offset + __shared__ Offset dequeue_offset; + + // We give each thread block at least one tile of input. + Offset block_offset = blockIdx.x * TILE_ITEMS; + Offset even_share_base = gridDim.x * TILE_ITEMS; + + if (block_offset + TILE_ITEMS <= num_items) + { + // Consume full tile of input + ConsumeTile(block_offset); + + // Dequeue more tiles + while (true) + { + // Dequeue a tile of items + if (threadIdx.x == 0) + dequeue_offset = queue.Drain(TILE_ITEMS) + even_share_base; + + __syncthreads(); + + // Grab tile offset and check if we're done with full tiles + block_offset = dequeue_offset; + + __syncthreads(); + + if (block_offset + TILE_ITEMS > num_items) + break; + + // Consume a full tile + ConsumeTile(block_offset); + } + } + + if (block_offset < num_items) + { + int valid_items = num_items - block_offset; + ConsumeTile(block_offset, valid_items); + } + + // Compute block-wide reduction + block_aggregate = (first_tile_size < TILE_ITEMS) ? + BlockReduceT(temp_storage).Reduce(thread_aggregate, reduction_op, first_tile_size) : + BlockReduceT(temp_storage).Reduce(thread_aggregate, reduction_op); + } + + + /** + * Dequeue and reduce tiles of items as part of a inter-block scan + */ + __device__ __forceinline__ void ConsumeRegion( + Offset num_items, ///< [in] Total number of global input items + GridEvenShare &even_share, ///< [in] GridEvenShare descriptor + GridQueue &queue, ///< [in,out] GridQueue descriptor + T &block_aggregate, ///< [out] Running total + Int2Type is_dynamic) ///< [in] Marker type indicating this is a dynamic mapping + { + ConsumeRegion(num_items, queue, block_aggregate); + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_scan_region.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_scan_region.cuh new file mode 100644 index 0000000000000000000000000000000000000000..308f7c29204aaae7ab4280389befd9020f5cf8f5 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_scan_region.cuh @@ -0,0 +1,536 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockScanRegion implements a stateful abstraction of CUDA thread blocks for participating in device-wide prefix scan across a region of tiles. + */ + +#pragma once + +#include + +#include "device_scan_types.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_store.cuh" +#include "../../block/block_scan.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../iterator/cache_modified_input_iterator.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Parameterizable tuning policy type for BlockScanRegion + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + BlockLoadAlgorithm _LOAD_ALGORITHM, ///< The BlockLoad algorithm to use + bool _LOAD_WARP_TIME_SLICING, ///< Whether or not only one warp's worth of shared memory should be allocated and time-sliced among block-warps during any load-related data transpositions (versus each warp having its own storage) + CacheLoadModifier _LOAD_MODIFIER, ///< Cache load modifier for reading input elements + BlockStoreAlgorithm _STORE_ALGORITHM, ///< The BlockStore algorithm to use + bool _STORE_WARP_TIME_SLICING, ///< Whether or not only one warp's worth of shared memory should be allocated and time-sliced among block-warps during any store-related data transpositions (versus each warp having its own storage) + BlockScanAlgorithm _SCAN_ALGORITHM> ///< The BlockScan algorithm to use +struct BlockScanRegionPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, ///< Threads per thread block + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + LOAD_WARP_TIME_SLICING = _LOAD_WARP_TIME_SLICING, ///< Whether or not only one warp's worth of shared memory should be allocated and time-sliced among block-warps during any load-related data transpositions (versus each warp having its own storage) + STORE_WARP_TIME_SLICING = _STORE_WARP_TIME_SLICING, ///< Whether or not only one warp's worth of shared memory should be allocated and time-sliced among block-warps during any store-related data transpositions (versus each warp having its own storage) + }; + + static const BlockLoadAlgorithm LOAD_ALGORITHM = _LOAD_ALGORITHM; ///< The BlockLoad algorithm to use + static const CacheLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; ///< Cache load modifier for reading input elements + static const BlockStoreAlgorithm STORE_ALGORITHM = _STORE_ALGORITHM; ///< The BlockStore algorithm to use + static const BlockScanAlgorithm SCAN_ALGORITHM = _SCAN_ALGORITHM; ///< The BlockScan algorithm to use +}; + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockScanRegion implements a stateful abstraction of CUDA thread blocks for participating in device-wide prefix scan across a region of tiles. + */ +template < + typename BlockScanRegionPolicy, ///< Parameterized BlockScanRegionPolicy tuning policy type + typename InputIterator, ///< Random-access input iterator type + typename OutputIterator, ///< Random-access output iterator type + typename ScanOp, ///< Scan functor type + typename Identity, ///< Identity element type (cub::NullType for inclusive scan) + typename Offset> ///< Signed integer type for global offsets +struct BlockScanRegion +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Data type of input iterator + typedef typename std::iterator_traits::value_type T; + + // Tile status descriptor interface type + typedef TileLookbackStatus TileLookbackStatus; + + // Input iterator wrapper type + typedef typename If::VALUE, + CacheModifiedInputIterator, // Wrap the native input pointer with CacheModifiedInputIterator + InputIterator>::Type // Directly use the supplied input iterator type + WrappedInputIterator; + + // Constants + enum + { + INCLUSIVE = Equals::VALUE, // Inclusive scan if no identity type is provided + BLOCK_THREADS = BlockScanRegionPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockScanRegionPolicy::ITEMS_PER_THREAD, + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + }; + + // Parameterized BlockLoad type + typedef BlockLoad< + WrappedInputIterator, + BlockScanRegionPolicy::BLOCK_THREADS, + BlockScanRegionPolicy::ITEMS_PER_THREAD, + BlockScanRegionPolicy::LOAD_ALGORITHM, + BlockScanRegionPolicy::LOAD_WARP_TIME_SLICING> + BlockLoadT; + + // Parameterized BlockStore type + typedef BlockStore< + OutputIterator, + BlockScanRegionPolicy::BLOCK_THREADS, + BlockScanRegionPolicy::ITEMS_PER_THREAD, + BlockScanRegionPolicy::STORE_ALGORITHM, + BlockScanRegionPolicy::STORE_WARP_TIME_SLICING> + BlockStoreT; + + // Parameterized BlockScan type + typedef BlockScan< + T, + BlockScanRegionPolicy::BLOCK_THREADS, + BlockScanRegionPolicy::SCAN_ALGORITHM> + BlockScanT; + + // Callback type for obtaining tile prefix during block scan + typedef LookbackBlockPrefixCallbackOp< + T, + ScanOp, + TileLookbackStatus> + LookbackPrefixCallbackOp; + + // Stateful BlockScan prefix callback type for managing a running total while scanning consecutive tiles + typedef RunningBlockPrefixCallbackOp< + T, + ScanOp> + RunningPrefixCallbackOp; + + // Shared memory type for this threadblock + struct _TempStorage + { + union + { + typename BlockLoadT::TempStorage load; // Smem needed for tile loading + typename BlockStoreT::TempStorage store; // Smem needed for tile storing + struct + { + typename LookbackPrefixCallbackOp::TempStorage prefix; // Smem needed for cooperative prefix callback + typename BlockScanT::TempStorage scan; // Smem needed for tile scanning + }; + }; + + Offset tile_idx; // Shared tile index + }; + + // Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + _TempStorage &temp_storage; ///< Reference to temp_storage + WrappedInputIterator d_in; ///< Input data + OutputIterator d_out; ///< Output data + ScanOp scan_op; ///< Binary scan operator + Identity identity; ///< Identity element + + + + //--------------------------------------------------------------------- + // Block scan utility methods (first tile) + //--------------------------------------------------------------------- + + /** + * Exclusive scan specialization + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], _ScanOp scan_op, _Identity identity, T& block_aggregate) + { + BlockScanT(temp_storage.scan).ExclusiveScan(items, items, identity, scan_op, block_aggregate); + } + + /** + * Exclusive sum specialization + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], Sum scan_op, _Identity identity, T& block_aggregate) + { + BlockScanT(temp_storage.scan).ExclusiveSum(items, items, block_aggregate); + } + + /** + * Inclusive scan specialization + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], _ScanOp scan_op, NullType identity, T& block_aggregate) + { + BlockScanT(temp_storage.scan).InclusiveScan(items, items, scan_op, block_aggregate); + } + + /** + * Inclusive sum specialization + */ + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], Sum scan_op, NullType identity, T& block_aggregate) + { + BlockScanT(temp_storage.scan).InclusiveSum(items, items, block_aggregate); + } + + //--------------------------------------------------------------------- + // Block scan utility methods (subsequent tiles) + //--------------------------------------------------------------------- + + /** + * Exclusive scan specialization (with prefix from predecessors) + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], _ScanOp scan_op, _Identity identity, T& block_aggregate, PrefixCallback &prefix_op) + { + BlockScanT(temp_storage.scan).ExclusiveScan(items, items, identity, scan_op, block_aggregate, prefix_op); + } + + /** + * Exclusive sum specialization (with prefix from predecessors) + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], Sum scan_op, _Identity identity, T& block_aggregate, PrefixCallback &prefix_op) + { + BlockScanT(temp_storage.scan).ExclusiveSum(items, items, block_aggregate, prefix_op); + } + + /** + * Inclusive scan specialization (with prefix from predecessors) + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], _ScanOp scan_op, NullType identity, T& block_aggregate, PrefixCallback &prefix_op) + { + BlockScanT(temp_storage.scan).InclusiveScan(items, items, scan_op, block_aggregate, prefix_op); + } + + /** + * Inclusive sum specialization (with prefix from predecessors) + */ + template + __device__ __forceinline__ + void ScanBlock(T (&items)[ITEMS_PER_THREAD], Sum scan_op, NullType identity, T& block_aggregate, PrefixCallback &prefix_op) + { + BlockScanT(temp_storage.scan).InclusiveSum(items, items, block_aggregate, prefix_op); + } + + + //--------------------------------------------------------------------- + // Constructor + //--------------------------------------------------------------------- + + // Constructor + __device__ __forceinline__ + BlockScanRegion( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIterator d_in, ///< Input data + OutputIterator d_out, ///< Output data + ScanOp scan_op, ///< Binary scan operator + Identity identity) ///< Identity element + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + d_out(d_out), + scan_op(scan_op), + identity(identity) + {} + + + //--------------------------------------------------------------------- + // Cooperatively scan a device-wide sequence of tiles with other CTAs + //--------------------------------------------------------------------- + + /** + * Process a tile of input (dynamic domino scan) + */ + template + __device__ __forceinline__ void ConsumeTile( + Offset num_items, ///< Total number of input items + Offset num_remaining, ///< Total number of items remaining to be processed (including this tile) + int tile_idx, ///< Tile index + Offset block_offset, ///< Tile offset + TileLookbackStatus &tile_status) ///< Global list of tile status + { + // Load items + T items[ITEMS_PER_THREAD]; + + if (LAST_TILE) + BlockLoadT(temp_storage.load).Load(d_in + block_offset, items, num_remaining); + else + BlockLoadT(temp_storage.load).Load(d_in + block_offset, items); + + __syncthreads(); + + // Perform tile scan + if (tile_idx == 0) + { + // Scan first tile + T block_aggregate; + ScanBlock(items, scan_op, identity, block_aggregate); + + // Update tile status if there may be successor tiles (i.e., this tile is full) + if (!LAST_TILE && (threadIdx.x == 0)) + tile_status.SetInclusive(0, block_aggregate); + } + else + { + // Scan non-first tile + T block_aggregate; + LookbackPrefixCallbackOp prefix_op(tile_status, temp_storage.prefix, scan_op, tile_idx); + ScanBlock(items, scan_op, identity, block_aggregate, prefix_op); + } + + __syncthreads(); + + // Store items + if (LAST_TILE) + BlockStoreT(temp_storage.store).Store(d_out + block_offset, items, num_remaining); + else + BlockStoreT(temp_storage.store).Store(d_out + block_offset, items); + } + + + /** + * Dequeue and scan tiles of items as part of a dynamic domino scan + */ + __device__ __forceinline__ void ConsumeRegion( + int num_items, ///< Total number of input items + GridQueue queue, ///< Queue descriptor for assigning tiles of work to thread blocks + TileLookbackStatus &tile_status) ///< Global list of tile status + { +#if (CUB_PTX_VERSION <= 130) + // Blocks are launched in increasing order, so just assign one tile per block + + int tile_idx = (blockIdx.y * 32 * 1024) + blockIdx.x; // Current tile index + Offset block_offset = Offset(TILE_ITEMS) * tile_idx; // Global offset for the current tile + Offset num_remaining = num_items - block_offset; // Remaining items (including this tile) + + if (block_offset + TILE_ITEMS <= num_items) + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + else if (block_offset < num_items) + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + +#else + // Blocks may not be launched in increasing order, so work-steal tiles + + // Get first tile index + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + int tile_idx = temp_storage.tile_idx; + Offset block_offset = TILE_ITEMS * tile_idx; + Offset num_remaining = num_items - block_offset; + + while (num_remaining >= TILE_ITEMS) + { + // Consume full tile + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + + // Get next tile + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + tile_idx = temp_storage.tile_idx; + block_offset = TILE_ITEMS * tile_idx; + num_remaining = num_items - block_offset; + } + + // Consume the last (and potentially partially-full) tile + if (num_remaining > 0) + { + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + } + +#endif + } + + + //--------------------------------------------------------------------- + // Scan an sequence of consecutive tiles (independent of other thread blocks) + //--------------------------------------------------------------------- + + /** + * Process a tile of input + */ + template < + bool FULL_TILE, + bool FIRST_TILE> + __device__ __forceinline__ void ConsumeTile( + Offset block_offset, ///< Tile offset + RunningPrefixCallbackOp &prefix_op, ///< Running prefix operator + int valid_items = TILE_ITEMS) ///< Number of valid items in the tile + { + // Load items + T items[ITEMS_PER_THREAD]; + + if (FULL_TILE) + BlockLoadT(temp_storage.load).Load(d_in + block_offset, items); + else + BlockLoadT(temp_storage.load).Load(d_in + block_offset, items, valid_items); + + __syncthreads(); + + // Block scan + if (FIRST_TILE) + { + T block_aggregate; + ScanBlock(items, scan_op, identity, block_aggregate); + prefix_op.running_total = block_aggregate; + } + else + { + T block_aggregate; + ScanBlock(items, scan_op, identity, block_aggregate, prefix_op); + } + + __syncthreads(); + + // Store items + if (FULL_TILE) + BlockStoreT(temp_storage.store).Store(d_out + block_offset, items); + else + BlockStoreT(temp_storage.store).Store(d_out + block_offset, items, valid_items); + } + + + /** + * Scan a consecutive share of input tiles + */ + __device__ __forceinline__ void ConsumeRegion( + Offset block_offset, ///< [in] Threadblock begin offset (inclusive) + Offset block_end) ///< [in] Threadblock end offset (exclusive) + { + RunningBlockPrefixCallbackOp prefix_op(scan_op); + + if (block_offset + TILE_ITEMS <= block_end) + { + // Consume first tile of input (full) + ConsumeTile(block_offset, prefix_op); + block_offset += TILE_ITEMS; + + // Consume subsequent full tiles of input + while (block_offset + TILE_ITEMS <= block_end) + { + ConsumeTile(block_offset, prefix_op); + block_offset += TILE_ITEMS; + } + + // Consume a partially-full tile + if (block_offset < block_end) + { + int valid_items = block_end - block_offset; + ConsumeTile(block_offset, prefix_op, valid_items); + } + } + else + { + // Consume the first tile of input (partially-full) + int valid_items = block_end - block_offset; + ConsumeTile(block_offset, prefix_op, valid_items); + } + } + + + /** + * Scan a consecutive share of input tiles, seeded with the specified prefix value + */ + __device__ __forceinline__ void ConsumeRegion( + Offset block_offset, ///< [in] Threadblock begin offset (inclusive) + Offset block_end, ///< [in] Threadblock end offset (exclusive) + T prefix) ///< [in] The prefix to apply to the scan segment + { + RunningBlockPrefixCallbackOp prefix_op(prefix, scan_op); + + // Consume full tiles of input + while (block_offset + TILE_ITEMS <= block_end) + { + ConsumeTile(block_offset, prefix_op); + block_offset += TILE_ITEMS; + } + + // Consume a partially-full tile + if (block_offset < block_end) + { + int valid_items = block_end - block_offset; + ConsumeTile(block_offset, prefix_op, valid_items); + } + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_select_region.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_select_region.cuh new file mode 100644 index 0000000000000000000000000000000000000000..6bbf430a96928b6a7afa2bfa3198db669b0b07fe --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/block_select_region.cuh @@ -0,0 +1,735 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockSelectRegion implements a stateful abstraction of CUDA thread blocks for participating in device-wide select. + */ + +#pragma once + +#include + +#include "device_scan_types.cuh" +#include "../../block/block_load.cuh" +#include "../../block/block_store.cuh" +#include "../../block/block_scan.cuh" +#include "../../block/block_exchange.cuh" +#include "../../block/block_discontinuity.cuh" +#include "../../grid/grid_queue.cuh" +#include "../../iterator/cache_modified_input_iterator.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Tuning policy types + ******************************************************************************/ + +/** + * Parameterizable tuning policy type for BlockSelectRegion + */ +template < + int _BLOCK_THREADS, ///< Threads per thread block + int _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + BlockLoadAlgorithm _LOAD_ALGORITHM, ///< The BlockLoad algorithm to use + CacheLoadModifier _LOAD_MODIFIER, ///< Cache load modifier for reading input elements + bool _TWO_PHASE_SCATTER, ///< Whether or not to coalesce output values in shared memory before scattering them to global + BlockScanAlgorithm _SCAN_ALGORITHM> ///< The BlockScan algorithm to use +struct BlockSelectRegionPolicy +{ + enum + { + BLOCK_THREADS = _BLOCK_THREADS, ///< Threads per thread block + ITEMS_PER_THREAD = _ITEMS_PER_THREAD, ///< Items per thread (per tile of input) + TWO_PHASE_SCATTER = _TWO_PHASE_SCATTER, ///< Whether or not to coalesce output values in shared memory before scattering them to global + }; + + static const BlockLoadAlgorithm LOAD_ALGORITHM = _LOAD_ALGORITHM; ///< The BlockLoad algorithm to use + static const CacheLoadModifier LOAD_MODIFIER = _LOAD_MODIFIER; ///< Cache load modifier for reading input elements + static const BlockScanAlgorithm SCAN_ALGORITHM = _SCAN_ALGORITHM; ///< The BlockScan algorithm to use +}; + + + + +/****************************************************************************** + * Thread block abstractions + ******************************************************************************/ + +/** + * \brief BlockSelectRegion implements a stateful abstraction of CUDA thread blocks for participating in device-wide selection across a region of tiles + * + * Performs functor-based selection if SelectOp functor type != NullType + * Otherwise performs flag-based selection if FlagIterator's value type != NullType + * Otherwise performs discontinuity selection (keep unique) + */ +template < + typename BlockSelectRegionPolicy, ///< Parameterized BlockSelectRegionPolicy tuning policy type + typename InputIterator, ///< Random-access input iterator type for selection items + typename FlagIterator, ///< Random-access input iterator type for selections (NullType* if a selection functor or discontinuity flagging is to be used for selection) + typename OutputIterator, ///< Random-access input iterator type for selected items + typename SelectOp, ///< Selection operator type (NullType if selections or discontinuity flagging is to be used for selection) + typename EqualityOp, ///< Equality operator type (NullType if selection functor or selections is to be used for selection) + typename Offset, ///< Signed integer type for global offsets + bool KEEP_REJECTS> ///< Whether or not we push rejected items to the back of the output +struct BlockSelectRegion +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Data type of input iterator + typedef typename std::iterator_traits::value_type T; + + // Data type of flag iterator + typedef typename std::iterator_traits::value_type Flag; + + // Tile status descriptor interface type + typedef TileLookbackStatus TileLookbackStatus; + + // Constants + enum + { + USE_SELECT_OP, + USE_SELECT_FLAGS, + USE_DISCONTINUITY, + + BLOCK_THREADS = BlockSelectRegionPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockSelectRegionPolicy::ITEMS_PER_THREAD, + TWO_PHASE_SCATTER = (BlockSelectRegionPolicy::TWO_PHASE_SCATTER) && (ITEMS_PER_THREAD > 1), + TILE_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + + // Whether or not to sync after loading data + SYNC_AFTER_LOAD = (BlockSelectRegionPolicy::LOAD_ALGORITHM != BLOCK_LOAD_DIRECT), + + SELECT_METHOD = (!Equals::VALUE) ? + USE_SELECT_OP : + (!Equals::VALUE) ? + USE_SELECT_FLAGS : + USE_DISCONTINUITY + }; + + // Input iterator wrapper type + typedef typename If::VALUE, + CacheModifiedInputIterator, // Wrap the native input pointer with CacheModifiedInputIterator + InputIterator>::Type // Directly use the supplied input iterator type + WrappedInputIterator; + + // Flag iterator wrapper type + typedef typename If::VALUE, + CacheModifiedInputIterator, // Wrap the native input pointer with CacheModifiedInputIterator + FlagIterator>::Type // Directly use the supplied input iterator type + WrappedFlagIterator; + + // Parameterized BlockLoad type for input items + typedef BlockLoad< + WrappedInputIterator, + BlockSelectRegionPolicy::BLOCK_THREADS, + BlockSelectRegionPolicy::ITEMS_PER_THREAD, + BlockSelectRegionPolicy::LOAD_ALGORITHM> + BlockLoadT; + + // Parameterized BlockLoad type for flags + typedef BlockLoad< + WrappedFlagIterator, + BlockSelectRegionPolicy::BLOCK_THREADS, + BlockSelectRegionPolicy::ITEMS_PER_THREAD, + BlockSelectRegionPolicy::LOAD_ALGORITHM> + BlockLoadFlags; + + // Parameterized BlockExchange type for input items + typedef BlockExchange< + T, + BLOCK_THREADS, + ITEMS_PER_THREAD> + BlockExchangeT; + + // Parameterized BlockDiscontinuity type for input items + typedef BlockDiscontinuity BlockDiscontinuityT; + + // Parameterized BlockScan type + typedef BlockScan< + Offset, + BlockSelectRegionPolicy::BLOCK_THREADS, + BlockSelectRegionPolicy::SCAN_ALGORITHM> + BlockScanAllocations; + + // Callback type for obtaining tile prefix during block scan + typedef LookbackBlockPrefixCallbackOp< + Offset, + Sum, + TileLookbackStatus> + LookbackPrefixCallbackOp; + + // Shared memory type for this threadblock + struct _TempStorage + { + union + { + struct + { + typename LookbackPrefixCallbackOp::TempStorage prefix; // Smem needed for cooperative prefix callback + typename BlockScanAllocations::TempStorage scan; // Smem needed for tile scanning + typename BlockDiscontinuityT::TempStorage discontinuity; // Smem needed for discontinuity detection + }; + + // Smem needed for input loading + typename BlockLoadT::TempStorage load_items; + + // Smem needed for flag loading + typename BlockLoadFlags::TempStorage load_flags; + + // Smem needed for two-phase scatter + typename If::Type exchange; + }; + + Offset tile_idx; // Shared tile index + Offset tile_num_selected_prefix; // Exclusive tile prefix + }; + + // Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + _TempStorage &temp_storage; ///< Reference to temp_storage + WrappedInputIterator d_in; ///< Input data + WrappedFlagIterator d_flags; ///< Input flags + OutputIterator d_out; ///< Output data + SelectOp select_op; ///< Selection operator + InequalityWrapper inequality_op; ///< Inequality operator + Offset num_items; ///< Total number of input items + + + //--------------------------------------------------------------------- + // Constructor + //--------------------------------------------------------------------- + + // Constructor + __device__ __forceinline__ + BlockSelectRegion( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIterator d_in, ///< Input data + FlagIterator d_flags, ///< Input flags + OutputIterator d_out, ///< Output data + SelectOp select_op, ///< Selection operator + EqualityOp equality_op, ///< Equality operator + Offset num_items) ///< Total number of input items + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + d_flags(d_flags), + d_out(d_out), + select_op(select_op), + inequality_op(equality_op), + num_items(num_items) + {} + + + //--------------------------------------------------------------------- + // Utility methods for initializing the selections + //--------------------------------------------------------------------- + + /** + * Template unrolled selection via selection operator + */ + template + __device__ __forceinline__ void ApplySelectionOp( + Offset block_offset, + Offset num_remaining, + T (&items)[ITEMS_PER_THREAD], + Offset (&selected)[ITEMS_PER_THREAD], + Int2Type iteration) + { + selected[ITERATION] = 0; + if (!LAST_TILE || (Offset(threadIdx.x * ITEMS_PER_THREAD) + ITERATION < num_remaining)) + selected[ITERATION] = select_op(items[ITERATION]); + + ApplySelectionOp(block_offset, num_remaining, items, selected, Int2Type()); + } + + /** + * Template unrolled selection via selection operator + */ + template + __device__ __forceinline__ void ApplySelectionOp( + Offset block_offset, + Offset num_remaining, + T (&items)[ITEMS_PER_THREAD], + Offset (&selected)[ITEMS_PER_THREAD], + Int2Type iteration) + {} + + /** + * Initialize selections (specialized for selection operator) + */ + template + __device__ __forceinline__ void InitializeSelections( + Offset block_offset, + Offset num_remaining, + T (&items)[ITEMS_PER_THREAD], + Offset (&selected)[ITEMS_PER_THREAD], + Int2Type select_method) + { + ApplySelectionOp(block_offset, num_remaining, items, selected, Int2Type<0>()); + } + + + /** + * Initialize selections (specialized for valid flags) + */ + template + __device__ __forceinline__ void InitializeSelections( + Offset block_offset, + Offset num_remaining, + T (&items)[ITEMS_PER_THREAD], + Offset (&selected)[ITEMS_PER_THREAD], + Int2Type select_method) + { + Flag flags[ITEMS_PER_THREAD]; + + if (LAST_TILE) + BlockLoadFlags(temp_storage.load_flags).Load(d_flags + block_offset, flags, num_remaining, 0); + else + BlockLoadFlags(temp_storage.load_flags).Load(d_flags + block_offset, flags); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + selected[ITEM] = flags[ITEM]; + } + + if (SYNC_AFTER_LOAD) + __syncthreads(); + } + + + /** + * Initialize selections (specialized for discontinuity detection) + */ + template + __device__ __forceinline__ void InitializeSelections( + Offset block_offset, + Offset num_remaining, + T (&items)[ITEMS_PER_THREAD], + Offset (&selected)[ITEMS_PER_THREAD], + Int2Type select_method) + { + if (FIRST_TILE) + { + // First tile always flags the first item + BlockDiscontinuityT(temp_storage.discontinuity).FlagHeads(selected, items, inequality_op); + } + else + { + // Subsequent tiles require the last item from the previous tile + T tile_predecessor_item; + if (threadIdx.x == 0) + tile_predecessor_item = d_in[block_offset - 1]; + + BlockDiscontinuityT(temp_storage.discontinuity).FlagHeads(selected, items, inequality_op, tile_predecessor_item); + } + } + + + //--------------------------------------------------------------------- + // Utility methods for scattering selections + //--------------------------------------------------------------------- + + /** + * Scatter data items to select offsets (specialized for direct scattering and for discarding rejected items) + */ + template + __device__ __forceinline__ void Scatter( + Offset block_offset, + T (&items)[ITEMS_PER_THREAD], + Offset selected[ITEMS_PER_THREAD], + Offset scatter_offsets[ITEMS_PER_THREAD], + Offset tile_num_selected_prefix, + Offset tile_num_selected, + Offset num_remaining, + Int2Type keep_rejects, + Int2Type two_phase_scatter) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + if (selected[ITEM]) + { + // Selected items are placed front-to-back + d_out[scatter_offsets[ITEM]] = items[ITEM]; + } + } + } + + + /** + * Scatter data items to select offsets (specialized for direct scattering and for partitioning rejected items after selected items) + */ + template + __device__ __forceinline__ void Scatter( + Offset block_offset, + T (&items)[ITEMS_PER_THREAD], + Offset selected[ITEMS_PER_THREAD], + Offset scatter_offsets[ITEMS_PER_THREAD], + Offset tile_num_selected_prefix, + Offset tile_num_selected, + Offset num_remaining, + Int2Type keep_rejects, + Int2Type two_phase_scatter) + { + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + if (selected[ITEM]) + { + // Selected items are placed front-to-back + d_out[scatter_offsets[ITEM]] = items[ITEM]; + } + else if (!LAST_TILE || (Offset(threadIdx.x * ITEMS_PER_THREAD) + ITEM < num_remaining)) + { + Offset global_idx = block_offset + (threadIdx.x * ITEMS_PER_THREAD) + ITEM; + Offset reject_idx = global_idx - scatter_offsets[ITEM]; + + // Rejected items are placed back-to-front + d_out[num_items - reject_idx - 1] = items[ITEM]; + } + } + } + + + /** + * Scatter data items to select offsets (specialized for two-phase scattering and for discarding rejected items) + */ + template + __device__ __forceinline__ void Scatter( + Offset block_offset, + T (&items)[ITEMS_PER_THREAD], + Offset selected[ITEMS_PER_THREAD], + Offset scatter_offsets[ITEMS_PER_THREAD], + Offset tile_num_selected_prefix, + Offset tile_num_selected, + Offset num_remaining, + Int2Type keep_rejects, + Int2Type two_phase_scatter) + { + if ((tile_num_selected >> Log2::VALUE) == 0) + { + // Average number of selected items per thread is less than one, so just do a one-phase scatter + Scatter( + block_offset, + items, + selected, + scatter_offsets, + tile_num_selected_prefix, + tile_num_selected, + num_remaining, + keep_rejects, + Int2Type()); + } + else + { + // Share exclusive tile prefix + if (threadIdx.x == 0) + { + temp_storage.tile_num_selected_prefix = tile_num_selected_prefix; + } + + __syncthreads(); + + // Load exclusive tile prefix in all threads + tile_num_selected_prefix = temp_storage.tile_num_selected_prefix; + + int local_ranks[ITEMS_PER_THREAD]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + local_ranks[ITEM] = scatter_offsets[ITEM] - tile_num_selected_prefix; + } + + BlockExchangeT(temp_storage.exchange).ScatterToStriped(items, local_ranks, selected); + + // Selected items are placed front-to-back + StoreDirectStriped(threadIdx.x, d_out + tile_num_selected_prefix, items, tile_num_selected); + } + } + + + /** + * Scatter data items to select offsets (specialized for two-phase scattering and for partitioning rejected items after selected items) + */ + template + __device__ __forceinline__ void Scatter( + Offset block_offset, + T (&items)[ITEMS_PER_THREAD], + Offset selected[ITEMS_PER_THREAD], + Offset scatter_offsets[ITEMS_PER_THREAD], + Offset tile_num_selected_prefix, + Offset tile_num_selected, + Offset num_remaining, + Int2Type keep_rejects, + Int2Type two_phase_scatter) + { + // Share exclusive tile prefix + if (threadIdx.x == 0) + { + temp_storage.tile_num_selected_prefix = tile_num_selected_prefix; + } + + __syncthreads(); + + // Load the exclusive tile prefix in all threads + tile_num_selected_prefix = temp_storage.tile_num_selected_prefix; + + // Determine the exclusive prefix for rejects + Offset tile_rejected_exclusive_prefix = block_offset - tile_num_selected_prefix; + + // Determine local scatter offsets + int local_ranks[ITEMS_PER_THREAD]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + local_ranks[ITEM] = -1; + Offset global_idx = block_offset + (threadIdx.x * ITEMS_PER_THREAD) + ITEM; + Offset reject_idx = global_idx - scatter_offsets[ITEM]; + + if (selected[ITEM]) + { + // Selected items + local_ranks[ITEM] = scatter_offsets[ITEM] - tile_num_selected_prefix; + } + else if (!LAST_TILE || (Offset(threadIdx.x * ITEMS_PER_THREAD) + ITEM < num_remaining)) + { + // Rejected items + local_ranks[ITEM] = (reject_idx - tile_rejected_exclusive_prefix) + tile_num_selected; + } + } + + // Coalesce selected and rejected items in shared memory, gathering in striped arrangements + if (LAST_TILE) + BlockExchangeT(temp_storage.exchange).ScatterToStripedGuarded(items, local_ranks); + else + BlockExchangeT(temp_storage.exchange).ScatterToStriped(items, local_ranks); + + // Store in striped order + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + Offset local_idx = (ITEM * BLOCK_THREADS) + threadIdx.x; + Offset scatter_offset = tile_num_selected_prefix + local_idx; + if (local_idx >= tile_num_selected) + scatter_offset = num_items - (tile_rejected_exclusive_prefix + (local_idx - tile_num_selected)) - 1; + + if (!LAST_TILE || (local_idx < num_remaining)) + { + d_out[scatter_offset] = items[ITEM]; + } + } + } + + + //--------------------------------------------------------------------- + // Cooperatively scan a device-wide sequence of tiles with other CTAs + //--------------------------------------------------------------------- + + /** + * Process a tile of input (dynamic domino scan) + */ + template + __device__ __forceinline__ Offset ConsumeTile( + Offset num_items, ///< Total number of input items + Offset num_remaining, ///< Total number of items remaining to be processed (including this tile) + int tile_idx, ///< Tile index + Offset block_offset, ///< Tile offset + TileLookbackStatus &tile_status) ///< Global list of tile status + { + T items[ITEMS_PER_THREAD]; + Offset selected[ITEMS_PER_THREAD]; // Selection flags + Offset scatter_offsets[ITEMS_PER_THREAD]; // Scatter offsets + Offset tile_num_selected_prefix; // Total number of selected items prior to this tile + Offset tile_num_selected; // Total number of selected items within this tile + Offset num_selected; // + + // Load items + if (LAST_TILE) + BlockLoadT(temp_storage.load_items).Load(d_in + block_offset, items, num_remaining, d_in[num_items - 1]); // Repeat last item + else + BlockLoadT(temp_storage.load_items).Load(d_in + block_offset, items); + + if (SYNC_AFTER_LOAD) + __syncthreads(); + + if (tile_idx == 0) + { + // Initialize selected/rejected output flags for first tile + InitializeSelections( + block_offset, + num_remaining, + items, + selected, + Int2Type()); + + // Compute scatter offsets by scanning the flags + BlockScanAllocations(temp_storage.scan).ExclusiveSum(selected, scatter_offsets, tile_num_selected); + + // Update tile status if there may be successor tiles + if (!LAST_TILE && (threadIdx.x == 0)) + tile_status.SetInclusive(0, tile_num_selected); + + tile_num_selected_prefix = 0; + num_selected = tile_num_selected; + } + else + { + // Initialize selected/rejected output flags for non-first tile + InitializeSelections( + block_offset, + num_remaining, + items, + selected, + Int2Type()); + + // Compute scatter offsets by scanning the flags + LookbackPrefixCallbackOp prefix_op(tile_status, temp_storage.prefix, Sum(), tile_idx); + BlockScanAllocations(temp_storage.scan).ExclusiveSum(selected, scatter_offsets, tile_num_selected, prefix_op); + + tile_num_selected_prefix = prefix_op.exclusive_prefix; + num_selected = prefix_op.inclusive_prefix; + } + + // Store selected items + Scatter( + block_offset, + items, + selected, + scatter_offsets, + tile_num_selected_prefix, + tile_num_selected, + num_remaining, + Int2Type(), + Int2Type()); + + // Return total number of items selected (inclusive of this tile) + return num_selected; + } + + + /** + * Dequeue and scan tiles of items as part of a dynamic domino scan + */ + template ///< Output iterator type for recording number of items selected + __device__ __forceinline__ void ConsumeRegion( + int num_tiles, ///< Total number of input tiles + GridQueue queue, ///< Queue descriptor for assigning tiles of work to thread blocks + TileLookbackStatus &tile_status, ///< Global list of tile status + NumSelectedIterator d_num_selected) ///< Output total number selected + { +#if (CUB_PTX_VERSION <= 130) + // Blocks are launched in increasing order, so just assign one tile per block + + int tile_idx = (blockIdx.y * 32 * 1024) + blockIdx.x; // Current tile index + Offset block_offset = Offset(TILE_ITEMS) * tile_idx; // Global offset for the current tile + Offset num_remaining = num_items - block_offset; // Remaining items (including this tile) + + if (num_remaining > TILE_ITEMS) + { + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + } + else if (num_remaining > 0) + { + Offset total_selected = ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + + // Output the total number of items selected + if (threadIdx.x == 0) + { + *d_num_selected = total_selected; + } + } + +#else + // Blocks may not be launched in increasing order, so work-steal tiles + + // Get first tile index + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + int tile_idx = temp_storage.tile_idx; + Offset block_offset = Offset(TILE_ITEMS) * tile_idx; + Offset num_remaining = num_items - block_offset; + + while (num_remaining > TILE_ITEMS) + { + // Consume full tile + ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + + // Get next tile + if (threadIdx.x == 0) + temp_storage.tile_idx = queue.Drain(1); + + __syncthreads(); + + tile_idx = temp_storage.tile_idx; + block_offset = Offset(TILE_ITEMS) * tile_idx; + num_remaining = num_items - block_offset; + } + + // Consume the last (and potentially partially-full) tile + if (num_remaining > 0) + { + Offset total_selected = ConsumeTile(num_items, num_remaining, tile_idx, block_offset, tile_status); + + // Output the total number of items selected + if (threadIdx.x == 0) + { + *d_num_selected = total_selected; + } + } + +#endif + + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/device_scan_types.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/device_scan_types.cuh new file mode 100644 index 0000000000000000000000000000000000000000..95889f6001a33674fd9d9ab22714adcfe3afa233 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/device_scan_types.cuh @@ -0,0 +1,561 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * Utility types for device-wide scan and similar primitives + */ + +#pragma once + +#include + +#include "../../thread/thread_load.cuh" +#include "../../thread/thread_store.cuh" +#include "../../warp/warp_reduce.cuh" +#include "../../util_arch.cuh" +#include "../../util_device.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/****************************************************************************** + * Callback operator types for supplying BlockScan prefixes + ******************************************************************************/ + +/** + * Stateful callback operator type for supplying BlockScan prefixes. + * Maintains a running prefix that can be applied to consecutive + * BlockScan operations. + */ +template < + typename T, ///< BlockScan value type + typename ScanOp> ///< Wrapped scan operator type +struct RunningBlockPrefixCallbackOp +{ + ScanOp op; ///< Wrapped scan operator + T running_total; ///< Running block-wide prefix + + /// Constructor + __device__ __forceinline__ RunningBlockPrefixCallbackOp(ScanOp op) + : + op(op) + {} + + /// Constructor + __device__ __forceinline__ RunningBlockPrefixCallbackOp( + T starting_prefix, + ScanOp op) + : + op(op), + running_total(starting_prefix) + {} + + /** + * Prefix callback operator. Returns the block-wide running_total in thread-0. + */ + __device__ __forceinline__ T operator()( + const T &block_aggregate) ///< The aggregate sum of the BlockScan inputs + { + T retval = running_total; + running_total = op(running_total, block_aggregate); + return retval; + } +}; + + +/****************************************************************************** + * Bookkeeping types for single-pass device-wide scan with dynamic lookback + ******************************************************************************/ + +/** + * Enumerations of tile status + */ +enum LookbackTileStatus +{ + LOOKBACK_TILE_OOB, // Out-of-bounds (e.g., padding) + LOOKBACK_TILE_INVALID, // Not yet processed + LOOKBACK_TILE_PARTIAL, // Tile aggregate is available + LOOKBACK_TILE_INCLUSIVE, // Inclusive tile prefix is available +}; + + +/** + * Tile status interface. + */ +template < + typename T, + bool SINGLE_WORD = Traits::PRIMITIVE> +struct TileLookbackStatus; + + +/** + * Tile status interface specialized for scan status and value types + * that can be combined into one machine word that can be + * read/written coherently in a single access. + */ +template +struct TileLookbackStatus +{ + // Status word type + typedef typename If<(sizeof(T) == 8), + long long, + typename If<(sizeof(T) == 4), + int, + typename If<(sizeof(T) == 2), + short, + char>::Type>::Type>::Type StatusWord; + + + // Unit word type + typedef typename If<(sizeof(T) == 8), + longlong2, + typename If<(sizeof(T) == 4), + int2, + typename If<(sizeof(T) == 2), + int, + uchar2>::Type>::Type>::Type TxnWord; + + + // Device word type + struct TileDescriptor + { + StatusWord status; + T value; + }; + + + // Constants + enum + { + TILE_STATUS_PADDING = CUB_PTX_WARP_THREADS, + }; + + + // Device storage + TileDescriptor *d_tile_status; + + + /// Constructor + __host__ __device__ __forceinline__ + TileLookbackStatus() + : + d_tile_status(NULL) + {} + + + /// Initializer + __host__ __device__ __forceinline__ + cudaError_t Init( + int num_tiles, ///< [in] Number of tiles + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t temp_storage_bytes) ///< [in] Size in bytes of \t d_temp_storage allocation + { + d_tile_status = reinterpret_cast(d_temp_storage); + return cudaSuccess; + } + + + /** + * Compute device memory needed for tile status + */ + __host__ __device__ __forceinline__ + static cudaError_t AllocationSize( + int num_tiles, ///< [in] Number of tiles + size_t &temp_storage_bytes) ///< [out] Size in bytes of \t d_temp_storage allocation + { + temp_storage_bytes = (num_tiles + TILE_STATUS_PADDING) * sizeof(TileDescriptor); // bytes needed for tile status descriptors + return cudaSuccess; + } + + + /** + * Initialize (from device) + */ + __device__ __forceinline__ void InitializeStatus(int num_tiles) + { + int tile_idx = (blockIdx.x * blockDim.x) + threadIdx.x; + if (tile_idx < num_tiles) + { + // Not-yet-set + d_tile_status[TILE_STATUS_PADDING + tile_idx].status = StatusWord(LOOKBACK_TILE_INVALID); + } + + if ((blockIdx.x == 0) && (threadIdx.x < TILE_STATUS_PADDING)) + { + // Padding + d_tile_status[threadIdx.x].status = StatusWord(LOOKBACK_TILE_OOB); + } + } + + + /** + * Update the specified tile's inclusive value and corresponding status + */ + __device__ __forceinline__ void SetInclusive(int tile_idx, T tile_inclusive) + { + TileDescriptor tile_descriptor; + tile_descriptor.status = LOOKBACK_TILE_INCLUSIVE; + tile_descriptor.value = tile_inclusive; + + TxnWord alias; + *reinterpret_cast(&alias) = tile_descriptor; + ThreadStore(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx), alias); + } + + + /** + * Update the specified tile's partial value and corresponding status + */ + __device__ __forceinline__ void SetPartial(int tile_idx, T tile_partial) + { + TileDescriptor tile_descriptor; + tile_descriptor.status = LOOKBACK_TILE_PARTIAL; + tile_descriptor.value = tile_partial; + + TxnWord alias; + *reinterpret_cast(&alias) = tile_descriptor; + ThreadStore(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx), alias); + } + + /** + * Wait for the corresponding tile to become non-invalid + */ + __device__ __forceinline__ void WaitForValid( + int tile_idx, + StatusWord &status, + T &value) + { + // Use warp-any to determine when all threads have valid status + TxnWord alias = ThreadLoad(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx)); + TileDescriptor tile_descriptor = reinterpret_cast(alias); + + while ((tile_descriptor.status == LOOKBACK_TILE_INVALID)) + { + alias = ThreadLoad(reinterpret_cast(d_tile_status + TILE_STATUS_PADDING + tile_idx)); + tile_descriptor = reinterpret_cast(alias); + } + + status = tile_descriptor.status; + value = tile_descriptor.value; + } + +}; + + + +/** + * Tile status interface specialized for scan status and value types that + * cannot be combined into one machine word. + */ +template +struct TileLookbackStatus +{ + // Status word type + typedef char StatusWord; + + // Constants + enum + { + TILE_STATUS_PADDING = CUB_PTX_WARP_THREADS, + }; + + // Device storage + StatusWord *d_tile_status; + T *d_tile_partial; + T *d_tile_inclusive; + + /// Constructor + __host__ __device__ __forceinline__ + TileLookbackStatus() + : + d_tile_status(NULL), + d_tile_partial(NULL), + d_tile_inclusive(NULL) + {} + + + /// Initializer + __host__ __device__ __forceinline__ + cudaError_t Init( + int num_tiles, ///< [in] Number of tiles + void *d_temp_storage, ///< [in] %Device allocation of temporary storage. When NULL, the required allocation size is written to \p temp_storage_bytes and no work is done. + size_t temp_storage_bytes) ///< [in] Size in bytes of \t d_temp_storage allocation + { + cudaError_t error = cudaSuccess; + do + { + void* allocations[3]; + size_t allocation_sizes[3]; + + allocation_sizes[0] = (num_tiles + TILE_STATUS_PADDING) * sizeof(StatusWord); // bytes needed for tile status descriptors + allocation_sizes[1] = num_tiles * sizeof(Uninitialized); // bytes needed for partials + allocation_sizes[2] = num_tiles * sizeof(Uninitialized); // bytes needed for inclusives + + // Compute allocation pointers into the single storage blob + if (CubDebug(error = AliasTemporaries(d_temp_storage, temp_storage_bytes, allocations, allocation_sizes))) break; + + // Alias the offsets + d_tile_status = reinterpret_cast(allocations[0]); + d_tile_partial = reinterpret_cast(allocations[1]); + d_tile_inclusive = reinterpret_cast(allocations[2]); + } + while (0); + + return error; + } + + + /** + * Compute device memory needed for tile status + */ + __host__ __device__ __forceinline__ + static cudaError_t AllocationSize( + int num_tiles, ///< [in] Number of tiles + size_t &temp_storage_bytes) ///< [out] Size in bytes of \t d_temp_storage allocation + { + // Specify storage allocation requirements + size_t allocation_sizes[3]; + allocation_sizes[0] = (num_tiles + TILE_STATUS_PADDING) * sizeof(StatusWord); // bytes needed for tile status descriptors + allocation_sizes[1] = num_tiles * sizeof(Uninitialized); // bytes needed for partials + allocation_sizes[2] = num_tiles * sizeof(Uninitialized); // bytes needed for inclusives + + // Set the necessary size of the blob + void* allocations[3]; + return CubDebug(AliasTemporaries(NULL, temp_storage_bytes, allocations, allocation_sizes)); + } + + + /** + * Initialize (from device) + */ + __device__ __forceinline__ void InitializeStatus(int num_tiles) + { + int tile_idx = (blockIdx.x * blockDim.x) + threadIdx.x; + if (tile_idx < num_tiles) + { + // Not-yet-set + d_tile_status[TILE_STATUS_PADDING + tile_idx] = StatusWord(LOOKBACK_TILE_INVALID); + } + + if ((blockIdx.x == 0) && (threadIdx.x < TILE_STATUS_PADDING)) + { + // Padding + d_tile_status[threadIdx.x] = StatusWord(LOOKBACK_TILE_OOB); + } + } + + + /** + * Update the specified tile's inclusive value and corresponding status + */ + __device__ __forceinline__ void SetInclusive(int tile_idx, T tile_inclusive) + { + // Update tile inclusive value + ThreadStore(d_tile_inclusive + tile_idx, tile_inclusive); + + // Fence + __threadfence(); + + // Update tile status + ThreadStore(d_tile_status + TILE_STATUS_PADDING + tile_idx, StatusWord(LOOKBACK_TILE_INCLUSIVE)); + } + + + /** + * Update the specified tile's partial value and corresponding status + */ + __device__ __forceinline__ void SetPartial(int tile_idx, T tile_partial) + { + // Update tile partial value + ThreadStore(d_tile_partial + tile_idx, tile_partial); + + // Fence + __threadfence(); + + // Update tile status + ThreadStore(d_tile_status + TILE_STATUS_PADDING + tile_idx, StatusWord(LOOKBACK_TILE_PARTIAL)); + } + + /** + * Wait for the corresponding tile to become non-invalid + */ + __device__ __forceinline__ void WaitForValid( + int tile_idx, + StatusWord &status, + T &value) + { + status = ThreadLoad(d_tile_status + TILE_STATUS_PADDING + tile_idx); + while (status == LOOKBACK_TILE_INVALID) + { + status = ThreadLoad(d_tile_status + TILE_STATUS_PADDING + tile_idx); + } + + T partial = ThreadLoad(d_tile_partial + tile_idx); + T inclusive = ThreadLoad(d_tile_inclusive + tile_idx); + + value = (status == StatusWord(LOOKBACK_TILE_PARTIAL)) ? + partial : + inclusive; + + } +}; + + + +/** + * Stateful block-scan prefix functor. Provides the the running prefix for + * the current tile by using the call-back warp to wait on on + * aggregates/prefixes from predecessor tiles to become available. + */ +template < + typename T, + typename ScanOp, + typename TileLookbackStatus> +struct LookbackBlockPrefixCallbackOp +{ + // Parameterized warp reduce + typedef WarpReduce WarpReduceT; + + // Temporary storage type + typedef typename WarpReduceT::TempStorage _TempStorage; + + // Alias wrapper allowing temporary storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + // Type of status word + typedef typename TileLookbackStatus::StatusWord StatusWord; + + // Scan operator for switching the scan arguments + struct SwizzleScanOp + { + ScanOp scan_op; + + // Constructor + __host__ __device__ __forceinline__ + SwizzleScanOp(ScanOp scan_op) : scan_op(scan_op) {} + + // Switch the scan arguments + __host__ __device__ __forceinline__ + T operator()(const T &a, const T &b) + { + return scan_op(b, a); + } + }; + + // Fields + TileLookbackStatus &tile_status; ///< Interface to tile status + _TempStorage &temp_storage; ///< Reference to a warp-reduction instance + ScanOp scan_op; ///< Binary scan operator + int tile_idx; ///< The current tile index + T exclusive_prefix; ///< Exclusive prefix for the tile + T inclusive_prefix; ///< Inclusive prefix for the tile + + // Constructor + __device__ __forceinline__ + LookbackBlockPrefixCallbackOp( + TileLookbackStatus &tile_status, + TempStorage &temp_storage, + ScanOp scan_op, + int tile_idx) + : + tile_status(tile_status), + temp_storage(temp_storage.Alias()), + scan_op(scan_op), + tile_idx(tile_idx) {} + + + // Block until all predecessors within the warp-wide window have non-invalid status + __device__ __forceinline__ + void ProcessWindow( + int predecessor_idx, ///< Preceding tile index to inspect + StatusWord &predecessor_status, ///< [out] Preceding tile status + T &window_aggregate) ///< [out] Relevant partial reduction from this window of preceding tiles + { + T value; + tile_status.WaitForValid(predecessor_idx, predecessor_status, value); + + // Perform a segmented reduction to get the prefix for the current window. + // Use the swizzled scan operator because we are now scanning *down* towards thread0. + + int tail_flag = (predecessor_status == StatusWord(LOOKBACK_TILE_INCLUSIVE)); + window_aggregate = WarpReduceT(temp_storage).TailSegmentedReduce(value, tail_flag, SwizzleScanOp(scan_op)); + } + + + // BlockScan prefix callback functor (called by the first warp) + __device__ __forceinline__ + T operator()(T block_aggregate) + { + // Update our status with our tile-aggregate + if (threadIdx.x == 0) + { + tile_status.SetPartial(tile_idx, block_aggregate); + } + + int predecessor_idx = tile_idx - threadIdx.x - 1; + StatusWord predecessor_status; + T window_aggregate; + + // Wait for the warp-wide window of predecessor tiles to become valid + ProcessWindow(predecessor_idx, predecessor_status, window_aggregate); + + // The exclusive tile prefix starts out as the current window aggregate + exclusive_prefix = window_aggregate; + + // Keep sliding the window back until we come across a tile whose inclusive prefix is known + while (WarpAll(predecessor_status != StatusWord(LOOKBACK_TILE_INCLUSIVE))) + { + predecessor_idx -= CUB_PTX_WARP_THREADS; + + // Update exclusive tile prefix with the window prefix + ProcessWindow(predecessor_idx, predecessor_status, window_aggregate); + exclusive_prefix = scan_op(window_aggregate, exclusive_prefix); + } + + // Compute the inclusive tile prefix and update the status for this tile + if (threadIdx.x == 0) + { + inclusive_prefix = scan_op(exclusive_prefix, block_aggregate); + tile_status.SetInclusive(tile_idx, inclusive_prefix); + } + + // Return exclusive_prefix + return exclusive_prefix; + } +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/specializations/block_histo_region_gatomic.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/specializations/block_histo_region_gatomic.cuh new file mode 100644 index 0000000000000000000000000000000000000000..fdffb872bf3430b23fa1b11e4ccd8708b68e8d39 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/specializations/block_histo_region_gatomic.cuh @@ -0,0 +1,184 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockHistogramRegionGlobalAtomic implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram. + */ + +#pragma once + +#include + +#include "../../../util_type.cuh" +#include "../../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + + +/** + * BlockHistogramRegionGlobalAtomic implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using global atomics + */ +template < + typename BlockHistogramRegionPolicy, ///< Tuning policy + int BINS, ///< Number of histogram bins per channel + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIterator, ///< The input iterator type \iterator. Must have an an InputIterator::value_type that, when cast as an integer, falls in the range [0..BINS-1] + typename HistoCounter, ///< Integer type for counting sample occurrences per histogram bin + typename Offset> ///< Signed integer type for global offsets +struct BlockHistogramRegionGlobalAtomic +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Sample type + typedef typename std::iterator_traits::value_type SampleT; + + // Constants + enum + { + BLOCK_THREADS = BlockHistogramRegionPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockHistogramRegionPolicy::ITEMS_PER_THREAD, + TILE_CHANNEL_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + TILE_ITEMS = TILE_CHANNEL_ITEMS * CHANNELS, + }; + + // Shared memory type required by this thread block + typedef NullType TempStorage; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + /// Reference to output histograms + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]; + + /// Input data to reduce + InputIterator d_in; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockHistogramRegionGlobalAtomic( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIterator d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) ///< Reference to output histograms + : + d_in(d_in), + d_out_histograms(d_out_histograms) + {} + + + /** + * Process a single tile of input + */ + template + __device__ __forceinline__ void ConsumeTile( + Offset block_offset, ///< The offset the tile to consume + int valid_items = TILE_ITEMS) ///< The number of valid items in the tile + { + if (FULL_TILE) + { + // Full tile of samples to read and composite + SampleT items[ITEMS_PER_THREAD][CHANNELS]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + items[ITEM][CHANNEL] = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + } + } + } + + __threadfence_block(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + atomicAdd(d_out_histograms[CHANNEL] + items[ITEM][CHANNEL], 1); + } + } + } + } + else + { + // Only a partially-full tile of samples to read and composite + int bounds = valid_items - (threadIdx.x * CHANNELS); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (((ACTIVE_CHANNELS == CHANNELS) || (CHANNEL < ACTIVE_CHANNELS)) && ((ITEM * BLOCK_THREADS * CHANNELS) + CHANNEL < bounds)) + { + SampleT item = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + atomicAdd(d_out_histograms[CHANNEL] + item, 1); + } + } + } + + } + } + + + /** + * Aggregate results into output + */ + __device__ __forceinline__ void AggregateOutput() + {} +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/specializations/block_histo_region_satomic.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/specializations/block_histo_region_satomic.cuh new file mode 100644 index 0000000000000000000000000000000000000000..d496e7dcba405a674744da05d7075a0f539e6dc4 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/specializations/block_histo_region_satomic.cuh @@ -0,0 +1,245 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockHistogramRegionSharedAtomic implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using shared atomics + */ + +#pragma once + +#include + +#include "../../../util_type.cuh" +#include "../../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * BlockHistogramRegionSharedAtomic implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using shared atomics + */ +template < + typename BlockHistogramRegionPolicy, ///< Tuning policy + int BINS, ///< Number of histogram bins + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIterator, ///< The input iterator type \iterator. Must have an an InputIterator::value_type that, when cast as an integer, falls in the range [0..BINS-1] + typename HistoCounter, ///< Integer type for counting sample occurrences per histogram bin + typename Offset> ///< Signed integer type for global offsets +struct BlockHistogramRegionSharedAtomic +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Sample type + typedef typename std::iterator_traits::value_type SampleT; + + // Constants + enum + { + BLOCK_THREADS = BlockHistogramRegionPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockHistogramRegionPolicy::ITEMS_PER_THREAD, + TILE_CHANNEL_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + TILE_ITEMS = TILE_CHANNEL_ITEMS * CHANNELS, + }; + + /// Shared memory type required by this thread block + struct _TempStorage + { + HistoCounter histograms[ACTIVE_CHANNELS][BINS + 1]; // One word of padding between channel histograms to prevent warps working on different histograms from hammering on the same bank + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + /// Reference to temp_storage + _TempStorage &temp_storage; + + /// Reference to output histograms + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]; + + /// Input data to reduce + InputIterator d_in; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockHistogramRegionSharedAtomic( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIterator d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) ///< Reference to output histograms + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + d_out_histograms(d_out_histograms) + { + // Initialize histogram bin counts to zeros + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + int histo_offset = 0; + + #pragma unroll + for(; histo_offset + BLOCK_THREADS <= BINS; histo_offset += BLOCK_THREADS) + { + this->temp_storage.histograms[CHANNEL][histo_offset + threadIdx.x] = 0; + } + // Finish up with guarded initialization if necessary + if ((BINS % BLOCK_THREADS != 0) && (histo_offset + threadIdx.x < BINS)) + { + this->temp_storage.histograms[CHANNEL][histo_offset + threadIdx.x] = 0; + } + } + + __syncthreads(); + } + + + /** + * Process a single tile of input + */ + template + __device__ __forceinline__ void ConsumeTile( + Offset block_offset, ///< The offset the tile to consume + int valid_items = TILE_ITEMS) ///< The number of valid items in the tile + { + if (FULL_TILE) + { + // Full tile of samples to read and composite + SampleT items[ITEMS_PER_THREAD][CHANNELS]; + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + items[ITEM][CHANNEL] = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + } + } + } + + __threadfence_block(); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (CHANNEL < ACTIVE_CHANNELS) + { + atomicAdd(temp_storage.histograms[CHANNEL] + items[ITEM][CHANNEL], 1); + } + } + } + + __threadfence_block(); + } + else + { + // Only a partially-full tile of samples to read and composite + int bounds = valid_items - (threadIdx.x * CHANNELS); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ++ITEM) + { + #pragma unroll + for (int CHANNEL = 0; CHANNEL < CHANNELS; ++CHANNEL) + { + if (((ACTIVE_CHANNELS == CHANNELS) || (CHANNEL < ACTIVE_CHANNELS)) && ((ITEM * BLOCK_THREADS * CHANNELS) + CHANNEL < bounds)) + { + SampleT item = d_in[block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS) + CHANNEL]; + atomicAdd(temp_storage.histograms[CHANNEL] + item, 1); + } + } + } + + } + } + + + /** + * Aggregate results into output + */ + __device__ __forceinline__ void AggregateOutput() + { + // Barrier to ensure shared memory histograms are coherent + __syncthreads(); + + // Copy shared memory histograms to output + int channel_offset = (blockIdx.x * BINS); + + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + int histo_offset = 0; + + #pragma unroll + for(; histo_offset + BLOCK_THREADS <= BINS; histo_offset += BLOCK_THREADS) + { + HistoCounter count = temp_storage.histograms[CHANNEL][histo_offset + threadIdx.x]; + + d_out_histograms[CHANNEL][channel_offset + histo_offset + threadIdx.x] = count; + } + + // Finish up with guarded initialization if necessary + if ((BINS % BLOCK_THREADS != 0) && (histo_offset + threadIdx.x < BINS)) + { + HistoCounter count = temp_storage.histograms[CHANNEL][histo_offset + threadIdx.x]; + + d_out_histograms[CHANNEL][channel_offset + histo_offset + threadIdx.x] = count; + } + } + } +}; + + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/specializations/block_histo_region_sort.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/specializations/block_histo_region_sort.cuh new file mode 100644 index 0000000000000000000000000000000000000000..ab8bd03424860dbcd96cfc1334ffd3be495350d2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/device/region/specializations/block_histo_region_sort.cuh @@ -0,0 +1,364 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::BlockHistogramRegionSort implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using local sorting + */ + +#pragma once + +#include + +#include "../../../block/block_radix_sort.cuh" +#include "../../../block/block_discontinuity.cuh" +#include "../../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * BlockHistogramRegionSort implements a stateful abstraction of CUDA thread blocks for histogramming multiple tiles as part of device-wide histogram using local sorting + */ +template < + typename BlockHistogramRegionPolicy, ///< Tuning policy + int BINS, ///< Number of histogram bins per channel + int CHANNELS, ///< Number of channels interleaved in the input data (may be greater than the number of active channels being histogrammed) + int ACTIVE_CHANNELS, ///< Number of channels actively being histogrammed + typename InputIterator, ///< The input iterator type \iterator. Must have an an InputIterator::value_type that, when cast as an integer, falls in the range [0..BINS-1] + typename HistoCounter, ///< Integer type for counting sample occurrences per histogram bin + typename Offset> ///< Signed integer type for global offsets +struct BlockHistogramRegionSort +{ + //--------------------------------------------------------------------- + // Types and constants + //--------------------------------------------------------------------- + + // Sample type + typedef typename std::iterator_traits::value_type SampleT; + + // Constants + enum + { + BLOCK_THREADS = BlockHistogramRegionPolicy::BLOCK_THREADS, + ITEMS_PER_THREAD = BlockHistogramRegionPolicy::ITEMS_PER_THREAD, + TILE_CHANNEL_ITEMS = BLOCK_THREADS * ITEMS_PER_THREAD, + TILE_ITEMS = TILE_CHANNEL_ITEMS * CHANNELS, + + STRIPED_COUNTERS_PER_THREAD = (BINS + BLOCK_THREADS - 1) / BLOCK_THREADS, + }; + + // Parameterize BlockRadixSort type for our thread block + typedef BlockRadixSort BlockRadixSortT; + + // Parameterize BlockDiscontinuity type for our thread block + typedef BlockDiscontinuity BlockDiscontinuityT; + + /// Shared memory type required by this thread block + union _TempStorage + { + // Storage for sorting bin values + typename BlockRadixSortT::TempStorage sort; + + struct + { + // Storage for detecting discontinuities in the tile of sorted bin values + typename BlockDiscontinuityT::TempStorage flag; + + // Storage for noting begin/end offsets of bin runs in the tile of sorted bin values + int run_begin[BLOCK_THREADS * STRIPED_COUNTERS_PER_THREAD]; + int run_end[BLOCK_THREADS * STRIPED_COUNTERS_PER_THREAD]; + }; + }; + + + /// Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + // Discontinuity functor + struct DiscontinuityOp + { + // Reference to temp_storage + _TempStorage &temp_storage; + + // Constructor + __device__ __forceinline__ DiscontinuityOp(_TempStorage &temp_storage) : + temp_storage(temp_storage) + {} + + // Discontinuity predicate + __device__ __forceinline__ bool operator()(const SampleT &a, const SampleT &b, int b_index) + { + if (a != b) + { + // Note the begin/end offsets in shared storage + temp_storage.run_begin[b] = b_index; + temp_storage.run_end[a] = b_index; + + return true; + } + else + { + return false; + } + } + }; + + + //--------------------------------------------------------------------- + // Per-thread fields + //--------------------------------------------------------------------- + + /// Reference to temp_storage + _TempStorage &temp_storage; + + /// Histogram counters striped across threads + HistoCounter thread_counters[ACTIVE_CHANNELS][STRIPED_COUNTERS_PER_THREAD]; + + /// Reference to output histograms + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]; + + /// Input data to reduce + InputIterator d_in; + + + //--------------------------------------------------------------------- + // Interface + //--------------------------------------------------------------------- + + /** + * Constructor + */ + __device__ __forceinline__ BlockHistogramRegionSort( + TempStorage &temp_storage, ///< Reference to temp_storage + InputIterator d_in, ///< Input data to reduce + HistoCounter* (&d_out_histograms)[ACTIVE_CHANNELS]) ///< Reference to output histograms + : + temp_storage(temp_storage.Alias()), + d_in(d_in), + d_out_histograms(d_out_histograms) + { + // Initialize histogram counters striped across threads + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + thread_counters[CHANNEL][COUNTER] = 0; + } + } + } + + + /** + * Composite a tile of input items + */ + __device__ __forceinline__ void Composite( + SampleT (&items)[ITEMS_PER_THREAD], ///< Tile of samples + HistoCounter thread_counters[STRIPED_COUNTERS_PER_THREAD]) ///< Histogram counters striped across threads + { + // Sort bytes in blocked arrangement + BlockRadixSortT(temp_storage.sort).Sort(items); + + __syncthreads(); + + // Initialize the shared memory's run_begin and run_end for each bin + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + temp_storage.run_begin[(COUNTER * BLOCK_THREADS) + threadIdx.x] = TILE_CHANNEL_ITEMS; + temp_storage.run_end[(COUNTER * BLOCK_THREADS) + threadIdx.x] = TILE_CHANNEL_ITEMS; + } + + __syncthreads(); + + // Note the begin/end run offsets of bin runs in the sorted tile + int flags[ITEMS_PER_THREAD]; // unused + DiscontinuityOp flag_op(temp_storage); + BlockDiscontinuityT(temp_storage.flag).FlagHeads(flags, items, flag_op); + + // Update begin for first item + if (threadIdx.x == 0) temp_storage.run_begin[items[0]] = 0; + + __syncthreads(); + + // Composite into histogram + // Initialize the shared memory's run_begin and run_end for each bin + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + int bin = (COUNTER * BLOCK_THREADS) + threadIdx.x; + HistoCounter run_length = temp_storage.run_end[bin] - temp_storage.run_begin[bin]; + + thread_counters[COUNTER] += run_length; + } + } + + + /** + * Process one channel within a tile. + */ + template + __device__ __forceinline__ void ConsumeTileChannel( + int channel, + Offset block_offset, + int valid_items) + { + // Load items in striped fashion + if (FULL_TILE) + { + // Full tile of samples to read and composite + SampleT items[ITEMS_PER_THREAD]; + + // Unguarded loads + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = d_in[channel + block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS)]; + } + + // Composite our histogram data + Composite(items, thread_counters[channel]); + } + else + { + // Only a partially-full tile of samples to read and composite + SampleT items[ITEMS_PER_THREAD]; + + // Assign our tid as the bin for out-of-bounds items (to give an even distribution), and keep track of how oob items to subtract out later + int bounds = (valid_items - (threadIdx.x * CHANNELS)); + + #pragma unroll + for (int ITEM = 0; ITEM < ITEMS_PER_THREAD; ITEM++) + { + items[ITEM] = ((ITEM * BLOCK_THREADS * CHANNELS) < bounds) ? + d_in[channel + block_offset + (ITEM * BLOCK_THREADS * CHANNELS) + (threadIdx.x * CHANNELS)] : + 0; + } + + // Composite our histogram data + Composite(items, thread_counters[channel]); + + __syncthreads(); + + // Correct the overcounting in the zero-bin from invalid (out-of-bounds) items + if (threadIdx.x == 0) + { + int extra = (TILE_ITEMS - valid_items) / CHANNELS; + thread_counters[channel][0] -= extra; + } + } + } + + + /** + * Template iteration over channels (to silence not-unrolled warnings for SM10-13). Inductive step. + */ + template + struct IterateChannels + { + /** + * Process one channel within a tile. + */ + static __device__ __forceinline__ void ConsumeTileChannel( + BlockHistogramRegionSort *cta, + Offset block_offset, + int valid_items) + { + __syncthreads(); + + cta->ConsumeTileChannel(CHANNEL, block_offset, valid_items); + + IterateChannels::ConsumeTileChannel(cta, block_offset, valid_items); + } + }; + + + /** + * Template iteration over channels (to silence not-unrolled warnings for SM10-13). Base step. + */ + template + struct IterateChannels + { + static __device__ __forceinline__ void ConsumeTileChannel(BlockHistogramRegionSort *cta, Offset block_offset, int valid_items) {} + }; + + + /** + * Process a single tile of input + */ + template + __device__ __forceinline__ void ConsumeTile( + Offset block_offset, ///< The offset the tile to consume + int valid_items = TILE_ITEMS) ///< The number of valid items in the tile + { + // First channel + ConsumeTileChannel(0, block_offset, valid_items); + + // Iterate through remaining channels + IterateChannels::ConsumeTileChannel(this, block_offset, valid_items); + } + + + /** + * Aggregate results into output + */ + __device__ __forceinline__ void AggregateOutput() + { + // Copy counters striped across threads into the histogram output + #pragma unroll + for (int CHANNEL = 0; CHANNEL < ACTIVE_CHANNELS; ++CHANNEL) + { + int channel_offset = (blockIdx.x * BINS); + + #pragma unroll + for (int COUNTER = 0; COUNTER < STRIPED_COUNTERS_PER_THREAD; ++COUNTER) + { + int bin = (COUNTER * BLOCK_THREADS) + threadIdx.x; + + if ((STRIPED_COUNTERS_PER_THREAD * BLOCK_THREADS == BINS) || (bin < BINS)) + { + d_out_histograms[CHANNEL][channel_offset + bin] = thread_counters[CHANNEL][COUNTER]; + } + } + } + } +}; + + + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/grid/grid_even_share.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/grid/grid_even_share.cuh new file mode 100644 index 0000000000000000000000000000000000000000..e331d0d86a23e85970e873c309f2d5abbd5f0582 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/grid/grid_even_share.cuh @@ -0,0 +1,185 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::GridEvenShare is a descriptor utility for distributing input among CUDA threadblocks in an "even-share" fashion. Each threadblock gets roughly the same number of fixed-size work units (grains). + */ + + +#pragma once + +#include "../util_namespace.cuh" +#include "../util_macro.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \addtogroup GridModule + * @{ + */ + + +/** + * \brief GridEvenShare is a descriptor utility for distributing input among CUDA threadblocks in an "even-share" fashion. Each threadblock gets roughly the same number of fixed-size work units (grains). + * + * \par Overview + * GridEvenShare indicates which sections of input are to be mapped onto which threadblocks. + * Threadblocks may receive one of three different amounts of work: "big", "normal", + * and "last". The "big" workloads are one scheduling grain larger than "normal". The "last" work unit + * for the last threadblock may be partially-full if the input is not an even multiple of + * the scheduling grain size. + * + * \par + * Before invoking a child grid, a parent thread will typically construct an instance of + * GridEvenShare. The instance can be passed to child threadblocks which can + * initialize their per-threadblock offsets using \p BlockInit(). + * + * \tparam Offset Signed integer type for global offsets + */ +template +struct GridEvenShare +{ + Offset total_grains; + int big_blocks; + Offset big_share; + Offset normal_share; + Offset normal_base_offset; + + /// Total number of input items + Offset num_items; + + /// Grid size in threadblocks + int grid_size; + + /// Offset into input marking the beginning of the owning thread block's segment of input tiles + Offset block_offset; + + /// Offset into input of marking the end (one-past) of the owning thread block's segment of input tiles + Offset block_end; + + /** + * \brief Default constructor. Zero-initializes block-specific fields. + */ + __host__ __device__ __forceinline__ GridEvenShare() : + num_items(0), + grid_size(0), + block_offset(0), + block_end(0) {} + + /** + * \brief Constructor. Initializes the grid-specific members \p num_items and \p grid_size. To be called prior prior to kernel launch) + */ + __host__ __device__ __forceinline__ GridEvenShare( + Offset num_items, ///< Total number of input items + int max_grid_size, ///< Maximum grid size allowable (actual grid size may be less if not warranted by the the number of input items) + int schedule_granularity) ///< Granularity by which the input can be parcelled into and distributed among threablocks. Usually the thread block's native tile size (or a multiple thereof. + { + this->num_items = num_items; + this->block_offset = num_items; + this->block_end = num_items; + this->total_grains = (num_items + schedule_granularity - 1) / schedule_granularity; + this->grid_size = CUB_MIN(total_grains, max_grid_size); + Offset grains_per_block = total_grains / grid_size; + this->big_blocks = total_grains - (grains_per_block * grid_size); // leftover grains go to big blocks + this->normal_share = grains_per_block * schedule_granularity; + this->normal_base_offset = big_blocks * schedule_granularity; + this->big_share = normal_share + schedule_granularity; + } + + + + /** + * \brief Initializes ranges for the specified partition index + */ + __device__ __forceinline__ void Init(int partition_id) + { + if (partition_id < big_blocks) + { + // This threadblock gets a big share of grains (grains_per_block + 1) + block_offset = (partition_id * big_share); + block_end = block_offset + big_share; + } + else if (partition_id < total_grains) + { + // This threadblock gets a normal share of grains (grains_per_block) + block_offset = normal_base_offset + (partition_id * normal_share); + block_end = CUB_MIN(num_items, block_offset + normal_share); + } + } + + + /** + * \brief Initializes ranges for the current thread block (e.g., to be called by each threadblock after startup) + */ + __device__ __forceinline__ void BlockInit() + { + Init(blockIdx.x); + } + + + /** + * Print to stdout + */ + __host__ __device__ __forceinline__ void Print() + { + printf( +#if (CUB_PTX_VERSION > 0) + "\tthreadblock(%d) " + "block_offset(%lu) " + "block_end(%lu) " +#endif + "num_items(%lu) " + "total_grains(%lu) " + "big_blocks(%lu) " + "big_share(%lu) " + "normal_share(%lu)\n", +#if (CUB_PTX_VERSION > 0) + blockIdx.x, + (unsigned long) block_offset, + (unsigned long) block_end, +#endif + (unsigned long) num_items, + (unsigned long) total_grains, + (unsigned long) big_blocks, + (unsigned long) big_share, + (unsigned long) normal_share); + } +}; + + + +/** @} */ // end group GridModule + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/grid/grid_mapping.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/grid/grid_mapping.cuh new file mode 100644 index 0000000000000000000000000000000000000000..ff6679b9b74cec40c78725b58432d92e903a9255 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/grid/grid_mapping.cuh @@ -0,0 +1,95 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::GridMappingStrategy enumerates alternative strategies for mapping constant-sized tiles of device-wide data onto a grid of CUDA thread blocks. + */ + +#pragma once + +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \addtogroup GridModule + * @{ + */ + + +/****************************************************************************** + * Mapping policies + *****************************************************************************/ + + +/** + * \brief cub::GridMappingStrategy enumerates alternative strategies for mapping constant-sized tiles of device-wide data onto a grid of CUDA thread blocks. + */ +enum GridMappingStrategy +{ + /** + * \brief An "even-share" strategy for assigning input tiles to thread blocks. + * + * \par Overview + * The input is evenly partitioned into \p p segments, where \p p is + * constant and corresponds loosely to the number of thread blocks that may + * actively reside on the target device. Each segment is comprised of + * consecutive tiles, where a tile is a small, constant-sized unit of input + * to be processed to completion before the thread block terminates or + * obtains more work. The kernel invokes \p p thread blocks, each + * of which iteratively consumes a segment of n/p elements + * in tile-size increments. + */ + GRID_MAPPING_EVEN_SHARE, + + /** + * \brief A dynamic "queue-based" strategy for assigning input tiles to thread blocks. + * + * \par Overview + * The input is treated as a queue to be dynamically consumed by a grid of + * thread blocks. Work is atomically dequeued in tiles, where a tile is a + * unit of input to be processed to completion before the thread block + * terminates or obtains more work. The grid size \p p is constant, + * loosely corresponding to the number of thread blocks that may actively + * reside on the target device. + */ + GRID_MAPPING_DYNAMIC, +}; + + +/** @} */ // end group GridModule + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/grid/grid_multi_buffer.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/grid/grid_multi_buffer.cuh new file mode 100644 index 0000000000000000000000000000000000000000..fc15366af52ac58862ee3393b35cd96e7f964256 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/grid/grid_multi_buffer.cuh @@ -0,0 +1,152 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * Storage wrapper for multi-pass stream transformations that require a + * secondary problem storage array to stream results back and forth from. + ******************************************************************************/ + +#pragma once + +#include "../util_type.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \addtogroup GridModule + * @{ + */ + + +/** + * Storage wrapper for multi-pass stream transformations that require a + * more than one problem storage array to stream results back and forth from. + * + * This wrapper provides maximum flexibility for re-using device allocations + * for subsequent transformations. As such, it is the caller's responsibility + * to free any non-NULL storage arrays when no longer needed. + * + * Many multi-pass stream computations require at least two problem storage + * arrays, e.g., one for reading in from, the other for writing out to. + * (And their roles can be reversed for each subsequent pass.) This structure + * tracks two sets of device vectors (a keys and a values sets), and a "selector" + * member to index which vector in each set is "currently valid". I.e., the + * valid data within "MultiBuffer<2, int, int> b" is accessible by: + * + * b.d_keys[b.selector]; + * + */ +template < + int BUFFER_COUNT, + typename _KeyType, + typename _ValueType = NullType> +struct MultiBuffer +{ + typedef _KeyType KeyType; + typedef _ValueType ValueType; + + // Set of device vector pointers for keys + KeyType* d_keys[BUFFER_COUNT]; + + // Set of device vector pointers for values + ValueType* d_values[BUFFER_COUNT]; + + // Selector into the set of device vector pointers (i.e., where the results are) + int selector; + + // Constructor + MultiBuffer() + { + selector = 0; + for (int i = 0; i < BUFFER_COUNT; i++) + { + d_keys[i] = NULL; + d_values[i] = NULL; + } + } +}; + + + +/** + * Double buffer (a.k.a. page-flip, ping-pong, etc.) version of the + * multi-buffer storage abstraction above. + * + * Many of the B40C primitives are templated upon the DoubleBuffer type: they + * are compiled differently depending upon whether the declared type contains + * keys-only versus key-value pairs (i.e., whether ValueType is NullType + * or some real type). + * + * Declaring keys-only storage wrapper: + * + * DoubleBuffer key_storage; + * + * Declaring key-value storage wrapper: + * + * DoubleBuffer key_value_storage; + * + */ +template < + typename KeyType, + typename ValueType = NullType> +struct DoubleBuffer : MultiBuffer<2, KeyType, ValueType> +{ + typedef MultiBuffer<2, KeyType, ValueType> ParentType; + + // Constructor + DoubleBuffer() : ParentType() {} + +}; + + +/** + * Triple buffer version of the multi-buffer storage abstraction above. + */ +template < + typename KeyType, + typename ValueType = NullType> +struct TripleBuffer : MultiBuffer<3, KeyType, ValueType> +{ + typedef MultiBuffer<3, KeyType, ValueType> ParentType; + + // Constructor + TripleBuffer() : ParentType() {} +}; + + +/** @} */ // end group GridModule + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/specializations/warp_reduce_shfl.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/specializations/warp_reduce_shfl.cuh new file mode 100644 index 0000000000000000000000000000000000000000..2e30ffc89dc2f87a0b3d5e0c35a461e760959f3e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/specializations/warp_reduce_shfl.cuh @@ -0,0 +1,327 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::WarpReduceShfl provides SHFL-based variants of parallel reduction across CUDA warps. + */ + +#pragma once + +#include "../../thread/thread_operators.cuh" +#include "../../util_ptx.cuh" +#include "../../util_type.cuh" +#include "../../util_macro.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \brief WarpReduceShfl provides SHFL-based variants of parallel reduction across CUDA warps. + */ +template < + typename T, ///< Data type being reduced + int LOGICAL_WARPS, ///< Number of logical warps entrant + int LOGICAL_WARP_THREADS> ///< Number of threads per logical warp +struct WarpReduceShfl +{ + /****************************************************************************** + * Constants and type definitions + ******************************************************************************/ + + enum + { + /// The number of warp reduction steps + STEPS = Log2::VALUE, + + // The 5-bit SHFL mask for logically splitting warps into sub-segments + SHFL_MASK = (-1 << STEPS) & 31, + + // The 5-bit SFHL clamp + SHFL_CLAMP = LOGICAL_WARP_THREADS - 1, + + // The packed C argument (mask starts 8 bits up) + SHFL_C = (SHFL_MASK << 8) | SHFL_CLAMP, + }; + + + /// Shared memory storage layout type + typedef NullType TempStorage; + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + int warp_id; + int lane_id; + + + /****************************************************************************** + * Construction + ******************************************************************************/ + + /// Constructor + __device__ __forceinline__ WarpReduceShfl( + TempStorage &temp_storage, + int warp_id, + int lane_id) + : + warp_id(warp_id), + lane_id(lane_id) + {} + + + /****************************************************************************** + * Operation + ******************************************************************************/ + + /// Summation (single-SHFL) + template < + bool FULL_WARPS, ///< Whether all lanes in each warp are contributing a valid fold of items + int FOLDED_ITEMS_PER_LANE> ///< Number of items folded into each lane + __device__ __forceinline__ T Sum( + T input, ///< [in] Calling thread's input + int folded_items_per_warp, ///< [in] Total number of valid items folded into each logical warp + Int2Type single_shfl) ///< [in] Marker type indicating whether only one SHFL instruction is required + { + unsigned int output = reinterpret_cast(input); + + // Iterate reduction steps + #pragma unroll + for (int STEP = 0; STEP < STEPS; STEP++) + { + const int OFFSET = 1 << STEP; + + if (FULL_WARPS) + { + // Use predicate set from SHFL to guard against invalid peers + asm( + "{" + " .reg .u32 r0;" + " .reg .pred p;" + " shfl.down.b32 r0|p, %1, %2, %3;" + " @p add.u32 r0, r0, %4;" + " mov.u32 %0, r0;" + "}" + : "=r"(output) : "r"(output), "r"(OFFSET), "r"(SHFL_C), "r"(output)); + } + else + { + // Set range predicate to guard against invalid peers + asm( + "{" + " .reg .u32 r0;" + " .reg .pred p;" + " shfl.down.b32 r0, %1, %2, %3;" + " setp.lt.u32 p, %5, %6;" + " mov.u32 %0, %1;" + " @p add.u32 %0, %1, r0;" + "}" + : "=r"(output) : "r"(output), "r"(OFFSET), "r"(SHFL_C), "r"(output), "r"((lane_id + OFFSET) * FOLDED_ITEMS_PER_LANE), "r"(folded_items_per_warp)); + } + } + + return output; + } + + + /// Summation (multi-SHFL) + template < + bool FULL_WARPS, ///< Whether all lanes in each warp are contributing a valid fold of items + int FOLDED_ITEMS_PER_LANE> ///< Number of items folded into each lane + __device__ __forceinline__ T Sum( + T input, ///< [in] Calling thread's input + int folded_items_per_warp, ///< [in] Total number of valid items folded into each logical warp + Int2Type single_shfl) ///< [in] Marker type indicating whether only one SHFL instruction is required + { + // Delegate to generic reduce + return Reduce(input, folded_items_per_warp, cub::Sum()); + } + + + /// Summation (float) + template < + bool FULL_WARPS, ///< Whether all lanes in each warp are contributing a valid fold of items + int FOLDED_ITEMS_PER_LANE> ///< Number of items folded into each lane + __device__ __forceinline__ float Sum( + float input, ///< [in] Calling thread's input + int folded_items_per_warp) ///< [in] Total number of valid items folded into each logical warp + { + T output = input; + + // Iterate reduction steps + #pragma unroll + for (int STEP = 0; STEP < STEPS; STEP++) + { + const int OFFSET = 1 << STEP; + + if (FULL_WARPS) + { + // Use predicate set from SHFL to guard against invalid peers + asm( + "{" + " .reg .f32 r0;" + " .reg .pred p;" + " shfl.down.b32 r0|p, %1, %2, %3;" + " @p add.f32 r0, r0, %4;" + " mov.f32 %0, r0;" + "}" + : "=f"(output) : "f"(output), "r"(OFFSET), "r"(SHFL_C), "f"(output)); + } + else + { + // Set range predicate to guard against invalid peers + asm( + "{" + " .reg .f32 r0;" + " .reg .pred p;" + " shfl.down.b32 r0, %1, %2, %3;" + " setp.lt.u32 p, %5, %6;" + " mov.f32 %0, %1;" + " @p add.f32 %0, %0, r0;" + "}" + : "=f"(output) : "f"(output), "r"(OFFSET), "r"(SHFL_C), "f"(output), "r"((lane_id + OFFSET) * FOLDED_ITEMS_PER_LANE), "r"(folded_items_per_warp)); + } + } + + return output; + } + + /// Summation (generic) + template < + bool FULL_WARPS, ///< Whether all lanes in each warp are contributing a valid fold of items + int FOLDED_ITEMS_PER_LANE, ///< Number of items folded into each lane + typename _T> + __device__ __forceinline__ _T Sum( + _T input, ///< [in] Calling thread's input + int folded_items_per_warp) ///< [in] Total number of valid items folded into each logical warp + { + // Whether sharing can be done with a single SHFL instruction (vs multiple SFHL instructions) + Int2Type<(Traits<_T>::PRIMITIVE) && (sizeof(_T) <= sizeof(unsigned int))> single_shfl; + + return Sum(input, folded_items_per_warp, single_shfl); + } + + + /// Reduction + template < + bool FULL_WARPS, ///< Whether all lanes in each warp are contributing a valid fold of items + int FOLDED_ITEMS_PER_LANE, ///< Number of items folded into each lane + typename ReductionOp> + __device__ __forceinline__ T Reduce( + T input, ///< [in] Calling thread's input + int folded_items_per_warp, ///< [in] Total number of valid items folded into each logical warp + ReductionOp reduction_op) ///< [in] Binary reduction operator + { + T output = input; + + // Iterate scan steps + #pragma unroll + for (int STEP = 0; STEP < STEPS; STEP++) + { + // Grab addend from peer + const int OFFSET = 1 << STEP; + + T temp = ShuffleDown(output, OFFSET); + + // Perform reduction op if from a valid peer + if (FULL_WARPS) + { + if (lane_id < LOGICAL_WARP_THREADS - OFFSET) + output = reduction_op(output, temp); + } + else + { + if (((lane_id + OFFSET) * FOLDED_ITEMS_PER_LANE) < folded_items_per_warp) + output = reduction_op(output, temp); + } + } + + return output; + } + + + /// Segmented reduction + template < + bool HEAD_SEGMENTED, ///< Whether flags indicate a segment-head or a segment-tail + typename Flag, + typename ReductionOp> + __device__ __forceinline__ T SegmentedReduce( + T input, ///< [in] Calling thread's input + Flag flag, ///< [in] Whether or not the current lane is a segment head/tail + ReductionOp reduction_op) ///< [in] Binary reduction operator + { + T output = input; + + // Get the start flags for each thread in the warp. + int warp_flags = __ballot(flag); + + if (!HEAD_SEGMENTED) + warp_flags <<= 1; + + // Keep bits above the current thread. + warp_flags &= LaneMaskGt(); + + // Accommodate packing of multiple logical warps in a single physical warp + if ((LOGICAL_WARPS > 1) && (LOGICAL_WARP_THREADS < 32)) + warp_flags >>= (warp_id * LOGICAL_WARP_THREADS); + + // Find next flag + int next_flag = __clz(__brev(warp_flags)); + + // Clip the next segment at the warp boundary if necessary + if (LOGICAL_WARP_THREADS != 32) + next_flag = CUB_MIN(next_flag, LOGICAL_WARP_THREADS); + + // Iterate scan steps + #pragma unroll + for (int STEP = 0; STEP < STEPS; STEP++) + { + // Grab addend from peer + const int OFFSET = 1 << STEP; + + T temp = ShuffleDown(output, OFFSET); + + // Perform reduction op if valid + if (OFFSET < next_flag - lane_id) + output = reduction_op(output, temp); + } + + return output; + } +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/specializations/warp_reduce_smem.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/specializations/warp_reduce_smem.cuh new file mode 100644 index 0000000000000000000000000000000000000000..0639aca3f9d3749c4e9115e311489dac6ba2b433 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/specializations/warp_reduce_smem.cuh @@ -0,0 +1,291 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::WarpReduceSmem provides smem-based variants of parallel reduction across CUDA warps. + */ + +#pragma once + +#include "../../thread/thread_operators.cuh" +#include "../../thread/thread_load.cuh" +#include "../../thread/thread_store.cuh" +#include "../../util_type.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/** + * \brief WarpReduceSmem provides smem-based variants of parallel reduction across CUDA warps. + */ +template < + typename T, ///< Data type being reduced + int LOGICAL_WARPS, ///< Number of logical warps entrant + int LOGICAL_WARP_THREADS> ///< Number of threads per logical warp +struct WarpReduceSmem +{ + /****************************************************************************** + * Constants and type definitions + ******************************************************************************/ + + enum + { + /// Whether the logical warp size is a power-of-two + POW_OF_TWO = ((LOGICAL_WARP_THREADS & (LOGICAL_WARP_THREADS - 1)) == 0), + + /// The number of warp scan steps + STEPS = Log2::VALUE, + + /// The number of threads in half a warp + HALF_WARP_THREADS = 1 << (STEPS - 1), + + /// The number of shared memory elements per warp + WARP_SMEM_ELEMENTS = LOGICAL_WARP_THREADS + HALF_WARP_THREADS, + }; + + /// Shared memory flag type + typedef unsigned char SmemFlag; + + /// Shared memory storage layout type (1.5 warps-worth of elements for each warp) + typedef T _TempStorage[LOGICAL_WARPS][WARP_SMEM_ELEMENTS]; + + // Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + _TempStorage &temp_storage; + int warp_id; + int lane_id; + + + /****************************************************************************** + * Construction + ******************************************************************************/ + + /// Constructor + __device__ __forceinline__ WarpReduceSmem( + TempStorage &temp_storage, + int warp_id, + int lane_id) + : + temp_storage(temp_storage.Alias()), + warp_id(warp_id), + lane_id(lane_id) + {} + + + /****************************************************************************** + * Operation + ******************************************************************************/ + + /** + * Reduction + */ + template < + bool FULL_WARPS, ///< Whether all lanes in each warp are contributing a valid fold of items + int FOLDED_ITEMS_PER_LANE, ///< Number of items folded into each lane + typename ReductionOp> + __device__ __forceinline__ T Reduce( + T input, ///< [in] Calling thread's input + int folded_items_per_warp, ///< [in] Total number of valid items folded into each logical warp + ReductionOp reduction_op) ///< [in] Reduction operator + { + for (int STEP = 0; STEP < STEPS; STEP++) + { + const int OFFSET = 1 << STEP; + + // Share input through buffer + ThreadStore(&temp_storage[warp_id][lane_id], input); + + // Update input if peer_addend is in range + if ((FULL_WARPS && POW_OF_TWO) || ((lane_id + OFFSET) * FOLDED_ITEMS_PER_LANE < folded_items_per_warp)) + { + T peer_addend = ThreadLoad(&temp_storage[warp_id][lane_id + OFFSET]); + input = reduction_op(input, peer_addend); + } + } + + return input; + } + + + /** + * Segmented reduction + */ + template < + bool HEAD_SEGMENTED, ///< Whether flags indicate a segment-head or a segment-tail + typename Flag, + typename ReductionOp> + __device__ __forceinline__ T SegmentedReduce( + T input, ///< [in] Calling thread's input + Flag flag, ///< [in] Whether or not the current lane is a segment head/tail + ReductionOp reduction_op) ///< [in] Reduction operator + { + #if CUB_PTX_VERSION >= 200 + + // Ballot-based segmented reduce + + // Get the start flags for each thread in the warp. + int warp_flags = __ballot(flag); + + if (!HEAD_SEGMENTED) + warp_flags <<= 1; + + // Keep bits above the current thread. + warp_flags &= LaneMaskGt(); + + // Accommodate packing of multiple logical warps in a single physical warp + if ((LOGICAL_WARPS > 1) && (LOGICAL_WARP_THREADS < 32)) + warp_flags >>= (warp_id * LOGICAL_WARP_THREADS); + + // Find next flag + int next_flag = __clz(__brev(warp_flags)); + + // Clip the next segment at the warp boundary if necessary + if (LOGICAL_WARP_THREADS != 32) + next_flag = CUB_MIN(next_flag, LOGICAL_WARP_THREADS); + + for (int STEP = 0; STEP < STEPS; STEP++) + { + const int OFFSET = 1 << STEP; + + // Share input into buffer + ThreadStore(&temp_storage[warp_id][lane_id], input); + + // Update input if peer_addend is in range + if (OFFSET < next_flag - lane_id) + { + T peer_addend = ThreadLoad(&temp_storage[warp_id][lane_id + OFFSET]); + input = reduction_op(input, peer_addend); + } + } + + return input; + + #else + + // Smem-based segmented reduce + + enum + { + UNSET = 0x0, // Is initially unset + SET = 0x1, // Is initially set + SEEN = 0x2, // Has seen another head flag from a successor peer + }; + + // Alias flags onto shared data storage + volatile SmemFlag *flag_storage = reinterpret_cast(temp_storage[warp_id]); + + SmemFlag flag_status = (flag) ? SET : UNSET; + + for (int STEP = 0; STEP < STEPS; STEP++) + { + const int OFFSET = 1 << STEP; + + // Share input through buffer + ThreadStore(&temp_storage[warp_id][lane_id], input); + + // Get peer from buffer + T peer_addend = ThreadLoad(&temp_storage[warp_id][lane_id + OFFSET]); + + // Share flag through buffer + flag_storage[lane_id] = flag_status; + + // Get peer flag from buffer + SmemFlag peer_flag_status = flag_storage[lane_id + OFFSET]; + + // Update input if peer was in range + if (lane_id < LOGICAL_WARP_THREADS - OFFSET) + { + if (HEAD_SEGMENTED) + { + // Head-segmented + if ((flag_status & SEEN) == 0) + { + // Has not seen a more distant head flag + if (peer_flag_status & SET) + { + // Has now seen a head flag + flag_status |= SEEN; + } + else + { + // Peer is not a head flag: grab its count + input = reduction_op(input, peer_addend); + } + + // Update seen status to include that of peer + flag_status |= (peer_flag_status & SEEN); + } + } + else + { + // Tail-segmented. Simply propagate flag status + if (!flag_status) + { + input = reduction_op(input, peer_addend); + flag_status |= peer_flag_status; + } + + } + } + } + + return input; + + #endif + } + + + /** + * Summation + */ + template < + bool FULL_WARPS, ///< Whether all lanes in each warp are contributing a valid fold of items + int FOLDED_ITEMS_PER_LANE> ///< Number of items folded into each lane + __device__ __forceinline__ T Sum( + T input, ///< [in] Calling thread's input + int folded_items_per_warp) ///< [in] Total number of valid items folded into each logical warp + { + return Reduce(input, folded_items_per_warp, cub::Sum()); + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/specializations/warp_scan_shfl.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/specializations/warp_scan_shfl.cuh new file mode 100644 index 0000000000000000000000000000000000000000..91a57f7c244423411a1a41e80b7653ca00dd31df --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/specializations/warp_scan_shfl.cuh @@ -0,0 +1,355 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::WarpScanShfl provides SHFL-based variants of parallel prefix scan across CUDA warps. + */ + +#pragma once + +#include "../../thread/thread_operators.cuh" +#include "../../util_type.cuh" +#include "../../util_ptx.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/** + * \brief WarpScanShfl provides SHFL-based variants of parallel prefix scan across CUDA warps. + */ +template < + typename T, ///< Data type being scanned + int LOGICAL_WARPS, ///< Number of logical warps entrant + int LOGICAL_WARP_THREADS> ///< Number of threads per logical warp +struct WarpScanShfl +{ + + /****************************************************************************** + * Constants and type definitions + ******************************************************************************/ + + enum + { + /// The number of warp scan steps + STEPS = Log2::VALUE, + + // The 5-bit SHFL mask for logically splitting warps into sub-segments starts 8-bits up + SHFL_C = ((-1 << STEPS) & 31) << 8, + }; + + /// Shared memory storage layout type + typedef NullType TempStorage; + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + int warp_id; + int lane_id; + + /****************************************************************************** + * Construction + ******************************************************************************/ + + /// Constructor + __device__ __forceinline__ WarpScanShfl( + TempStorage &temp_storage, + int warp_id, + int lane_id) + : + warp_id(warp_id), + lane_id(lane_id) + {} + + + /****************************************************************************** + * Operation + ******************************************************************************/ + + /// Broadcast + __device__ __forceinline__ T Broadcast( + T input, ///< [in] The value to broadcast + int src_lane) ///< [in] Which warp lane is to do the broadcasting + { + return ShuffleBroadcast(input, src_lane, LOGICAL_WARP_THREADS); + } + + + //--------------------------------------------------------------------- + // Inclusive operations + //--------------------------------------------------------------------- + + /// Inclusive prefix sum with aggregate (single-SHFL) + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + T &warp_aggregate, ///< [out] Warp-wide aggregate reduction of input items. + Int2Type single_shfl) + { + unsigned int temp = reinterpret_cast(input); + + // Iterate scan steps + #pragma unroll + for (int STEP = 0; STEP < STEPS; STEP++) + { + // Use predicate set from SHFL to guard against invalid peers + asm( + "{" + " .reg .u32 r0;" + " .reg .pred p;" + " shfl.up.b32 r0|p, %1, %2, %3;" + " @p add.u32 r0, r0, %4;" + " mov.u32 %0, r0;" + "}" + : "=r"(temp) : "r"(temp), "r"(1 << STEP), "r"(SHFL_C), "r"(temp)); + } + + output = temp; + + // Grab aggregate from last warp lane + warp_aggregate = Broadcast(output, LOGICAL_WARP_THREADS - 1); + } + + + /// Inclusive prefix sum with aggregate (multi-SHFL) + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + T &warp_aggregate, ///< [out] Warp-wide aggregate reduction of input items. + Int2Type single_shfl) ///< [in] Marker type indicating whether only one SHFL instruction is required + { + // Delegate to generic scan + InclusiveScan(input, output, Sum(), warp_aggregate); + } + + + /// Inclusive prefix sum with aggregate (specialized for float) + __device__ __forceinline__ void InclusiveSum( + float input, ///< [in] Calling thread's input item. + float &output, ///< [out] Calling thread's output item. May be aliased with \p input. + float &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + output = input; + + // Iterate scan steps + #pragma unroll + for (int STEP = 0; STEP < STEPS; STEP++) + { + // Use predicate set from SHFL to guard against invalid peers + asm( + "{" + " .reg .f32 r0;" + " .reg .pred p;" + " shfl.up.b32 r0|p, %1, %2, %3;" + " @p add.f32 r0, r0, %4;" + " mov.f32 %0, r0;" + "}" + : "=f"(output) : "f"(output), "r"(1 << STEP), "r"(SHFL_C), "f"(output)); + } + + // Grab aggregate from last warp lane + warp_aggregate = Broadcast(output, LOGICAL_WARP_THREADS - 1); + } + + + /// Inclusive prefix sum with aggregate (specialized for unsigned long long) + __device__ __forceinline__ void InclusiveSum( + unsigned long long input, ///< [in] Calling thread's input item. + unsigned long long &output, ///< [out] Calling thread's output item. May be aliased with \p input. + unsigned long long &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + output = input; + + // Iterate scan steps + #pragma unroll + for (int STEP = 0; STEP < STEPS; STEP++) + { + // Use predicate set from SHFL to guard against invalid peers + asm( + "{" + " .reg .u32 r0;" + " .reg .u32 r1;" + " .reg .u32 lo;" + " .reg .u32 hi;" + " .reg .pred p;" + " mov.b64 {lo, hi}, %1;" + " shfl.up.b32 r0|p, lo, %2, %3;" + " shfl.up.b32 r1|p, hi, %2, %3;" + " @p add.cc.u32 r0, r0, lo;" + " @p addc.u32 r1, r1, hi;" + " mov.b64 %0, {r0, r1};" + "}" + : "=l"(output) : "l"(output), "r"(1 << STEP), "r"(SHFL_C)); + } + + // Grab aggregate from last warp lane + warp_aggregate = Broadcast(output, LOGICAL_WARP_THREADS - 1); + } + + + /// Inclusive prefix sum with aggregate (generic) + template + __device__ __forceinline__ void InclusiveSum( + _T input, ///< [in] Calling thread's input item. + _T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + _T &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + // Whether sharing can be done with a single SHFL instruction (vs multiple SFHL instructions) + Int2Type<(Traits<_T>::PRIMITIVE) && (sizeof(_T) <= sizeof(unsigned int))> single_shfl; + + InclusiveSum(input, output, warp_aggregate, single_shfl); + } + + + /// Inclusive prefix sum + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item. + T &output) ///< [out] Calling thread's output item. May be aliased with \p input. + { + T warp_aggregate; + InclusiveSum(input, output, warp_aggregate); + } + + + /// Inclusive scan with aggregate + template + __device__ __forceinline__ void InclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + ScanOp scan_op, ///< [in] Binary scan operator + T &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + output = input; + + // Iterate scan steps + #pragma unroll + for (int STEP = 0; STEP < STEPS; STEP++) + { + // Grab addend from peer + const int OFFSET = 1 << STEP; + T temp = ShuffleUp(output, OFFSET); + + // Perform scan op if from a valid peer + if (lane_id >= OFFSET) + output = scan_op(temp, output); + } + + // Grab aggregate from last warp lane + warp_aggregate = Broadcast(output, LOGICAL_WARP_THREADS - 1); + } + + + /// Inclusive scan + template + __device__ __forceinline__ void InclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + ScanOp scan_op) ///< [in] Binary scan operator + { + T warp_aggregate; + InclusiveScan(input, output, scan_op, warp_aggregate); + } + + + //--------------------------------------------------------------------- + // Exclusive operations + //--------------------------------------------------------------------- + + /// Exclusive scan with aggregate + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + T identity, ///< [in] Identity value + ScanOp scan_op, ///< [in] Binary scan operator + T &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + // Compute inclusive scan + T inclusive; + InclusiveScan(input, inclusive, scan_op, warp_aggregate); + + // Grab result from predecessor + T exclusive = ShuffleUp(inclusive, 1); + + output = (lane_id == 0) ? + identity : + exclusive; + } + + + /// Exclusive scan + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + T identity, ///< [in] Identity value + ScanOp scan_op) ///< [in] Binary scan operator + { + T warp_aggregate; + ExclusiveScan(input, output, identity, scan_op, warp_aggregate); + } + + + /// Exclusive scan with aggregate, without identity + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + ScanOp scan_op, ///< [in] Binary scan operator + T &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + // Compute inclusive scan + T inclusive; + InclusiveScan(input, inclusive, scan_op, warp_aggregate); + + // Grab result from predecessor + output = ShuffleUp(inclusive, 1); + } + + + /// Exclusive scan without identity + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + ScanOp scan_op) ///< [in] Binary scan operator + { + T warp_aggregate; + ExclusiveScan(input, output, scan_op, warp_aggregate); + } +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/specializations/warp_scan_smem.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/specializations/warp_scan_smem.cuh new file mode 100644 index 0000000000000000000000000000000000000000..4fdd541a6ab86c51b930e52d417617be2a0911f2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/specializations/warp_scan_smem.cuh @@ -0,0 +1,327 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * cub::WarpScanSmem provides smem-based variants of parallel prefix scan across CUDA warps. + */ + +#pragma once + +#include "../../thread/thread_operators.cuh" +#include "../../thread/thread_load.cuh" +#include "../../thread/thread_store.cuh" +#include "../../util_type.cuh" +#include "../../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/** + * \brief WarpScanSmem provides smem-based variants of parallel prefix scan across CUDA warps. + */ +template < + typename T, ///< Data type being scanned + int LOGICAL_WARPS, ///< Number of logical warps entrant + int LOGICAL_WARP_THREADS> ///< Number of threads per logical warp +struct WarpScanSmem +{ + /****************************************************************************** + * Constants and type definitions + ******************************************************************************/ + + enum + { + /// The number of warp scan steps + STEPS = Log2::VALUE, + + /// The number of threads in half a warp + HALF_WARP_THREADS = 1 << (STEPS - 1), + + /// The number of shared memory elements per warp + WARP_SMEM_ELEMENTS = LOGICAL_WARP_THREADS + HALF_WARP_THREADS, + }; + + + /// Shared memory storage layout type (1.5 warps-worth of elements for each warp) + typedef T _TempStorage[LOGICAL_WARPS][WARP_SMEM_ELEMENTS]; + + // Alias wrapper allowing storage to be unioned + struct TempStorage : Uninitialized<_TempStorage> {}; + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + _TempStorage &temp_storage; + unsigned int warp_id; + unsigned int lane_id; + + + /****************************************************************************** + * Construction + ******************************************************************************/ + + /// Constructor + __device__ __forceinline__ WarpScanSmem( + TempStorage &temp_storage, + int warp_id, + int lane_id) + : + temp_storage(temp_storage.Alias()), + warp_id(warp_id), + lane_id(lane_id) + {} + + + /****************************************************************************** + * Operation + ******************************************************************************/ + + /// Initialize identity padding (specialized for operations that have identity) + __device__ __forceinline__ void InitIdentity(Int2Type has_identity) + { + T identity = ZeroInitialize(); + ThreadStore(&temp_storage[warp_id][lane_id], identity); + } + + + /// Initialize identity padding (specialized for operations without identity) + __device__ __forceinline__ void InitIdentity(Int2Type has_identity) + {} + + + /// Basic inclusive scan iteration(template unrolled, base-case specialization) + template < + bool HAS_IDENTITY, + typename ScanOp> + __device__ __forceinline__ void ScanStep( + T &partial, + ScanOp scan_op, + Int2Type step) + {} + + + /// Basic inclusive scan iteration (template unrolled, inductive-case specialization) + template < + bool HAS_IDENTITY, + int STEP, + typename ScanOp> + __device__ __forceinline__ void ScanStep( + T &partial, + ScanOp scan_op, + Int2Type step) + { + const int OFFSET = 1 << STEP; + + // Share partial into buffer + ThreadStore(&temp_storage[warp_id][HALF_WARP_THREADS + lane_id], partial); + + // Update partial if addend is in range + if (HAS_IDENTITY || (lane_id >= OFFSET)) + { + T addend = ThreadLoad(&temp_storage[warp_id][HALF_WARP_THREADS + lane_id - OFFSET]); + partial = scan_op(addend, partial); + } + + ScanStep(partial, scan_op, Int2Type()); + } + + + /// Broadcast + __device__ __forceinline__ T Broadcast( + T input, ///< [in] The value to broadcast + unsigned int src_lane) ///< [in] Which warp lane is to do the broadcasting + { + if (lane_id == src_lane) + { + ThreadStore(temp_storage[warp_id], input); + } + + return ThreadLoad(temp_storage[warp_id]); + } + + + /// Basic inclusive scan + template < + bool HAS_IDENTITY, + bool SHARE_FINAL, + typename ScanOp> + __device__ __forceinline__ T BasicScan( + T partial, ///< Calling thread's input partial reduction + ScanOp scan_op) ///< Binary associative scan functor + { + // Iterate scan steps + ScanStep(partial, scan_op, Int2Type<0>()); + + if (SHARE_FINAL) + { + // Share partial into buffer + ThreadStore(&temp_storage[warp_id][HALF_WARP_THREADS + lane_id], partial); + } + + return partial; + } + + + /// Inclusive prefix sum + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item. + T &output) ///< [out] Calling thread's output item. May be aliased with \p input. + { + const bool HAS_IDENTITY = Traits::PRIMITIVE; + + // Initialize identity region + InitIdentity(Int2Type()); + + // Compute inclusive warp scan (has identity, don't share final) + output = BasicScan(input, Sum()); + } + + + /// Inclusive prefix sum with aggregate + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + T &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + const bool HAS_IDENTITY = Traits::PRIMITIVE; + + // Initialize identity region + InitIdentity(Int2Type()); + + // Compute inclusive warp scan (has identity, share final) + output = BasicScan(input, Sum()); + + // Retrieve aggregate in warp-lane0 + warp_aggregate = ThreadLoad(&temp_storage[warp_id][WARP_SMEM_ELEMENTS - 1]); + } + + + /// Inclusive scan + template + __device__ __forceinline__ void InclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + ScanOp scan_op) ///< [in] Binary scan operator + { + // Compute inclusive warp scan (no identity, don't share final) + output = BasicScan(input, scan_op); + } + + + /// Inclusive scan with aggregate + template + __device__ __forceinline__ void InclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + ScanOp scan_op, ///< [in] Binary scan operator + T &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + // Compute inclusive warp scan (no identity, share final) + output = BasicScan(input, scan_op); + + // Retrieve aggregate + warp_aggregate = ThreadLoad(&temp_storage[warp_id][WARP_SMEM_ELEMENTS - 1]); + } + + /// Exclusive scan + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + T identity, ///< [in] Identity value + ScanOp scan_op) ///< [in] Binary scan operator + { + // Initialize identity region + ThreadStore(&temp_storage[warp_id][lane_id], identity); + + // Compute inclusive warp scan (identity, share final) + T inclusive = BasicScan(input, scan_op); + + // Retrieve exclusive scan + output = ThreadLoad(&temp_storage[warp_id][HALF_WARP_THREADS + lane_id - 1]); + } + + + /// Exclusive scan with aggregate + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + T identity, ///< [in] Identity value + ScanOp scan_op, ///< [in] Binary scan operator + T &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + // Exclusive warp scan (which does share final) + ExclusiveScan(input, output, identity, scan_op); + + // Retrieve aggregate + warp_aggregate = ThreadLoad(&temp_storage[warp_id][WARP_SMEM_ELEMENTS - 1]); + } + + + /// Exclusive scan without identity + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + ScanOp scan_op) ///< [in] Binary scan operator + { + // Compute inclusive warp scan (no identity, share final) + T inclusive = BasicScan(input, scan_op); + + // Retrieve exclusive scan + output = ThreadLoad(&temp_storage[warp_id][HALF_WARP_THREADS + lane_id - 1]); + } + + + /// Exclusive scan with aggregate, without identity + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + ScanOp scan_op, ///< [in] Binary scan operator + T &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + // Exclusive warp scan (which does share final) + ExclusiveScan(input, output, scan_op); + + // Retrieve aggregate + warp_aggregate = ThreadLoad(&temp_storage[warp_id][WARP_SMEM_ELEMENTS - 1]); + } + +}; + + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/warp_reduce.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/warp_reduce.cuh new file mode 100644 index 0000000000000000000000000000000000000000..3adde54686ca9d91de06bd7a5436131897270839 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/warp_reduce.cuh @@ -0,0 +1,685 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * The cub::WarpReduce class provides [collective](index.html#sec0) methods for computing a parallel reduction of items partitioned across CUDA warp threads. + */ + +#pragma once + +#include "specializations/warp_reduce_shfl.cuh" +#include "specializations/warp_reduce_smem.cuh" +#include "../thread/thread_operators.cuh" +#include "../util_arch.cuh" +#include "../util_type.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + + +/** + * \addtogroup WarpModule + * @{ + */ + +/** + * \brief The WarpReduce class provides [collective](index.html#sec0) methods for computing a parallel reduction of items partitioned across CUDA warp threads. ![](warp_reduce_logo.png) + * + * \tparam T The reduction input/output element type + * \tparam LOGICAL_WARPS [optional] The number of entrant "logical" warps performing concurrent warp reductions. Default is 1. + * \tparam LOGICAL_WARP_THREADS [optional] The number of threads per "logical" warp (may be less than the number of hardware warp threads). Default is the warp size of the targeted CUDA compute-capability (e.g., 32 threads for SM20). + * + * \par Overview + * - A reduction (or fold) + * uses a binary combining operator to compute a single aggregate from a list of input elements. + * - Supports "logical" warps smaller than the physical warp size (e.g., logical warps of 8 threads) + * - The number of entrant threads must be an multiple of \p LOGICAL_WARP_THREADS + * + * \par Performance Considerations + * - Warp reductions are concurrent if more than one logical warp is participating + * - Uses special instructions when applicable (e.g., warp \p SHFL instructions) + * - Uses synchronization-free communication between warp lanes when applicable + * - Incurs zero bank conflicts for most types + * - Computation is slightly more efficient (i.e., having lower instruction overhead) for: + * - Summation (vs. generic reduction) + * - The architecture's warp size is a whole multiple of \p LOGICAL_WARP_THREADS + * + * \par Simple Examples + * \warpcollective{WarpReduce} + * \par + * The code snippet below illustrates four concurrent warp sum reductions within a block of + * 128 threads (one per each of the 32-thread warps). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpReduce for 4 warps on type int + * typedef cub::WarpReduce WarpReduce; + * + * // Allocate shared memory for WarpReduce + * __shared__ typename WarpReduce::TempStorage temp_storage; + * + * // Obtain one input item per thread + * int thread_data = ... + * + * // Return the warp-wide sums to each lane0 (threads 0, 32, 64, and 96) + * int aggregate = WarpReduce(temp_storage).Sum(thread_data); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is {0, 1, 2, 3, ..., 127}. + * The corresponding output \p aggregate in threads 0, 32, 64, and 96 will \p 496, \p 1520, + * \p 2544, and \p 3568, respectively (and is undefined in other threads). + * + * \par + * The code snippet below illustrates a single warp sum reduction within a block of + * 128 threads. + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpReduce for one warp on type int + * typedef cub::WarpReduce WarpReduce; + * + * // Allocate shared memory for WarpReduce + * __shared__ typename WarpReduce::TempStorage temp_storage; + * ... + * + * // Only the first warp performs a reduction + * if (threadIdx.x < 32) + * { + * // Obtain one input item per thread + * int thread_data = ... + * + * // Return the warp-wide sum to lane0 + * int aggregate = WarpReduce(temp_storage).Sum(thread_data); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the warp of threads is {0, 1, 2, 3, ..., 31}. + * The corresponding output \p aggregate in thread0 will be \p 496 (and is undefined in other threads). + * + */ +template < + typename T, + int LOGICAL_WARPS = 1, + int LOGICAL_WARP_THREADS = CUB_PTX_WARP_THREADS> +class WarpReduce +{ +private: + + /****************************************************************************** + * Constants and type definitions + ******************************************************************************/ + + enum + { + POW_OF_TWO = ((LOGICAL_WARP_THREADS & (LOGICAL_WARP_THREADS - 1)) == 0), + }; + +public: + + #ifndef DOXYGEN_SHOULD_SKIP_THIS // Do not document + + /// Internal specialization. Use SHFL-based reduction if (architecture is >= SM30) and ((only one logical warp) or (LOGICAL_WARP_THREADS is a power-of-two)) + typedef typename If<(CUB_PTX_VERSION >= 300) && ((LOGICAL_WARPS == 1) || POW_OF_TWO), + WarpReduceShfl, + WarpReduceSmem >::Type InternalWarpReduce; + + #endif // DOXYGEN_SHOULD_SKIP_THIS + + +private: + + /// Shared memory storage layout type for WarpReduce + typedef typename InternalWarpReduce::TempStorage _TempStorage; + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + /// Shared storage reference + _TempStorage &temp_storage; + + /// Warp ID + int warp_id; + + /// Lane ID + int lane_id; + + + /****************************************************************************** + * Utility methods + ******************************************************************************/ + + /// Internal storage allocator + __device__ __forceinline__ _TempStorage& PrivateStorage() + { + __shared__ TempStorage private_storage; + return private_storage; + } + + +public: + + /// \smemstorage{WarpReduce} + struct TempStorage : Uninitialized<_TempStorage> {}; + + + /******************************************************************//** + * \name Collective constructors + *********************************************************************/ + //@{ + + + /** + * \brief Collective constructor for 1D thread blocks using a private static allocation of shared memory as temporary storage. Logical warp and lane identifiers are constructed from threadIdx.x. + * + */ + __device__ __forceinline__ WarpReduce() + : + temp_storage(PrivateStorage()), + warp_id((LOGICAL_WARPS == 1) ? + 0 : + threadIdx.x / LOGICAL_WARP_THREADS), + lane_id(((LOGICAL_WARPS == 1) || (LOGICAL_WARP_THREADS == CUB_PTX_WARP_THREADS)) ? + LaneId() : + threadIdx.x % LOGICAL_WARP_THREADS) + {} + + + /** + * \brief Collective constructor for 1D thread blocks using the specified memory allocation as temporary storage. Logical warp and lane identifiers are constructed from threadIdx.x. + */ + __device__ __forceinline__ WarpReduce( + TempStorage &temp_storage) ///< [in] Reference to memory allocation having layout type TempStorage + : + temp_storage(temp_storage.Alias()), + warp_id((LOGICAL_WARPS == 1) ? + 0 : + threadIdx.x / LOGICAL_WARP_THREADS), + lane_id(((LOGICAL_WARPS == 1) || (LOGICAL_WARP_THREADS == CUB_PTX_WARP_THREADS)) ? + LaneId() : + threadIdx.x % LOGICAL_WARP_THREADS) + {} + + + /** + * \brief Collective constructor using a private static allocation of shared memory as temporary storage. Threads are identified using the given warp and lane identifiers. + */ + __device__ __forceinline__ WarpReduce( + int warp_id, ///< [in] A suitable warp membership identifier + int lane_id) ///< [in] A lane identifier within the warp + : + temp_storage(PrivateStorage()), + warp_id(warp_id), + lane_id(lane_id) + {} + + + /** + * \brief Collective constructor using the specified memory allocation as temporary storage. Threads are identified using the given warp and lane identifiers. + */ + __device__ __forceinline__ WarpReduce( + TempStorage &temp_storage, ///< [in] Reference to memory allocation having layout type TempStorage + int warp_id, ///< [in] A suitable warp membership identifier + int lane_id) ///< [in] A lane identifier within the warp + : + temp_storage(temp_storage.Alias()), + warp_id(warp_id), + lane_id(lane_id) + {} + + + + //@} end member group + /******************************************************************//** + * \name Summation reductions + *********************************************************************/ + //@{ + + + /** + * \brief Computes a warp-wide sum in each active warp. The output is valid in warp lane0. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates four concurrent warp sum reductions within a block of + * 128 threads (one per each of the 32-thread warps). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpReduce for 4 warps on type int + * typedef cub::WarpReduce WarpReduce; + * + * // Allocate shared memory for WarpReduce + * __shared__ typename WarpReduce::TempStorage temp_storage; + * + * // Obtain one input item per thread + * int thread_data = ... + * + * // Return the warp-wide sums to each lane0 + * int aggregate = WarpReduce(temp_storage).Sum(thread_data); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is {0, 1, 2, 3, ..., 127}. + * The corresponding output \p aggregate in threads 0, 32, 64, and 96 will \p 496, \p 1520, + * \p 2544, and \p 3568, respectively (and is undefined in other threads). + * + */ + __device__ __forceinline__ T Sum( + T input) ///< [in] Calling thread's input + { + return InternalWarpReduce(temp_storage, warp_id, lane_id).Sum(input, LOGICAL_WARP_THREADS); + } + + /** + * \brief Computes a partially-full warp-wide sum in each active warp. The output is valid in warp lane0. + * + * All threads in each logical warp must agree on the same value for \p valid_items. Otherwise the result is undefined. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates a sum reduction within a single, partially-full + * block of 32 threads (one warp). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(int *d_data, int valid_items) + * { + * // Specialize WarpReduce for a single warp on type int + * typedef cub::WarpReduce WarpReduce; + * + * // Allocate shared memory for WarpReduce + * __shared__ typename WarpReduce::TempStorage temp_storage; + * + * // Obtain one input item per thread if in range + * int thread_data; + * if (threadIdx.x < valid_items) + * thread_data = d_data[threadIdx.x]; + * + * // Return the warp-wide sums to each lane0 + * int aggregate = WarpReduce(temp_storage).Sum( + * thread_data, valid_items); + * + * \endcode + * \par + * Suppose the input \p d_data is {0, 1, 2, 3, 4, ... and \p valid_items + * is \p 4. The corresponding output \p aggregate in thread0 is \p 6 (and is + * undefined in other threads). + * + */ + __device__ __forceinline__ T Sum( + T input, ///< [in] Calling thread's input + int valid_items) ///< [in] Total number of valid items in the calling thread's logical warp (may be less than \p LOGICAL_WARP_THREADS) + { + // Determine if we don't need bounds checking + if (valid_items >= LOGICAL_WARP_THREADS) + { + return InternalWarpReduce(temp_storage, warp_id, lane_id).Sum(input, valid_items); + } + else + { + return InternalWarpReduce(temp_storage, warp_id, lane_id).Sum(input, valid_items); + } + } + + + /** + * \brief Computes a segmented sum in each active warp where segments are defined by head-flags. The sum of each segment is returned to the first lane in that segment (which always includes lane0). + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates a head-segmented warp sum + * reduction within a block of 32 threads (one warp). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpReduce for a single warp on type int + * typedef cub::WarpReduce WarpReduce; + * + * // Allocate shared memory for WarpReduce + * __shared__ typename WarpReduce::TempStorage temp_storage; + * + * // Obtain one input item and flag per thread + * int thread_data = ... + * int head_flag = ... + * + * // Return the warp-wide sums to each lane0 + * int aggregate = WarpReduce(temp_storage).HeadSegmentedSum( + * thread_data, head_flag); + * + * \endcode + * \par + * Suppose the set of input \p thread_data and \p head_flag across the block of threads + * is {0, 1, 2, 3, ..., 31 and is {1, 0, 0, 0, 1, 0, 0, 0, ..., 1, 0, 0, 0, + * respectively. The corresponding output \p aggregate in threads 0, 4, 8, etc. will be + * \p 6, \p 22, \p 38, etc. (and is undefined in other threads). + * + * \tparam ReductionOp [inferred] Binary reduction operator type having member T operator()(const T &a, const T &b) + * + */ + template < + typename Flag> + __device__ __forceinline__ T HeadSegmentedSum( + T input, ///< [in] Calling thread's input + Flag head_flag) ///< [in] Head flag denoting whether or not \p input is the start of a new segment + { + return HeadSegmentedReduce(input, head_flag, cub::Sum()); + } + + + /** + * \brief Computes a segmented sum in each active warp where segments are defined by tail-flags. The sum of each segment is returned to the first lane in that segment (which always includes lane0). + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates a tail-segmented warp sum + * reduction within a block of 32 threads (one warp). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpReduce for a single warp on type int + * typedef cub::WarpReduce WarpReduce; + * + * // Allocate shared memory for WarpReduce + * __shared__ typename WarpReduce::TempStorage temp_storage; + * + * // Obtain one input item and flag per thread + * int thread_data = ... + * int tail_flag = ... + * + * // Return the warp-wide sums to each lane0 + * int aggregate = WarpReduce(temp_storage).TailSegmentedSum( + * thread_data, tail_flag); + * + * \endcode + * \par + * Suppose the set of input \p thread_data and \p tail_flag across the block of threads + * is {0, 1, 2, 3, ..., 31 and is {0, 0, 0, 1, 0, 0, 0, 1, ..., 0, 0, 0, 1, + * respectively. The corresponding output \p aggregate in threads 0, 4, 8, etc. will be + * \p 6, \p 22, \p 38, etc. (and is undefined in other threads). + * + * \tparam ReductionOp [inferred] Binary reduction operator type having member T operator()(const T &a, const T &b) + */ + template < + typename Flag> + __device__ __forceinline__ T TailSegmentedSum( + T input, ///< [in] Calling thread's input + Flag tail_flag) ///< [in] Head flag denoting whether or not \p input is the start of a new segment + { + return TailSegmentedReduce(input, tail_flag, cub::Sum()); + } + + + + //@} end member group + /******************************************************************//** + * \name Generic reductions + *********************************************************************/ + //@{ + + /** + * \brief Computes a warp-wide reduction in each active warp using the specified binary reduction functor. The output is valid in warp lane0. + * + * Supports non-commutative reduction operators + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates four concurrent warp max reductions within a block of + * 128 threads (one per each of the 32-thread warps). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpReduce for 4 warps on type int + * typedef cub::WarpReduce WarpReduce; + * + * // Allocate shared memory for WarpReduce + * __shared__ typename WarpReduce::TempStorage temp_storage; + * + * // Obtain one input item per thread + * int thread_data = ... + * + * // Return the warp-wide reductions to each lane0 + * int aggregate = WarpReduce(temp_storage).Reduce( + * thread_data, cub::Max()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is {0, 1, 2, 3, ..., 127}. + * The corresponding output \p aggregate in threads 0, 32, 64, and 96 will \p 31, \p 63, + * \p 95, and \p 127, respectively (and is undefined in other threads). + * + * \tparam ReductionOp [inferred] Binary reduction operator type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ T Reduce( + T input, ///< [in] Calling thread's input + ReductionOp reduction_op) ///< [in] Binary reduction operator + { + return InternalWarpReduce(temp_storage, warp_id, lane_id).Reduce(input, LOGICAL_WARP_THREADS, reduction_op); + } + + /** + * \brief Computes a partially-full warp-wide reduction in each active warp using the specified binary reduction functor. The output is valid in warp lane0. + * + * All threads in each logical warp must agree on the same value for \p valid_items. Otherwise the result is undefined. + * + * Supports non-commutative reduction operators + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates a max reduction within a single, partially-full + * block of 32 threads (one warp). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(int *d_data, int valid_items) + * { + * // Specialize WarpReduce for a single warp on type int + * typedef cub::WarpReduce WarpReduce; + * + * // Allocate shared memory for WarpReduce + * __shared__ typename WarpReduce::TempStorage temp_storage; + * + * // Obtain one input item per thread if in range + * int thread_data; + * if (threadIdx.x < valid_items) + * thread_data = d_data[threadIdx.x]; + * + * // Return the warp-wide reductions to each lane0 + * int aggregate = WarpReduce(temp_storage).Reduce( + * thread_data, cub::Max(), valid_items); + * + * \endcode + * \par + * Suppose the input \p d_data is {0, 1, 2, 3, 4, ... and \p valid_items + * is \p 4. The corresponding output \p aggregate in thread0 is \p 3 (and is + * undefined in other threads). + * + * \tparam ReductionOp [inferred] Binary reduction operator type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ T Reduce( + T input, ///< [in] Calling thread's input + ReductionOp reduction_op, ///< [in] Binary reduction operator + int valid_items) ///< [in] Total number of valid items in the calling thread's logical warp (may be less than \p LOGICAL_WARP_THREADS) + { + // Determine if we don't need bounds checking + if (valid_items >= LOGICAL_WARP_THREADS) + { + return InternalWarpReduce(temp_storage, warp_id, lane_id).Reduce(input, valid_items, reduction_op); + } + else + { + return InternalWarpReduce(temp_storage, warp_id, lane_id).Reduce(input, valid_items, reduction_op); + } + } + + + /** + * \brief Computes a segmented reduction in each active warp where segments are defined by head-flags. The reduction of each segment is returned to the first lane in that segment (which always includes lane0). + * + * Supports non-commutative reduction operators + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates a head-segmented warp max + * reduction within a block of 32 threads (one warp). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpReduce for a single warp on type int + * typedef cub::WarpReduce WarpReduce; + * + * // Allocate shared memory for WarpReduce + * __shared__ typename WarpReduce::TempStorage temp_storage; + * + * // Obtain one input item and flag per thread + * int thread_data = ... + * int head_flag = ... + * + * // Return the warp-wide reductions to each lane0 + * int aggregate = WarpReduce(temp_storage).HeadSegmentedReduce( + * thread_data, head_flag, cub::Max()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data and \p head_flag across the block of threads + * is {0, 1, 2, 3, ..., 31 and is {1, 0, 0, 0, 1, 0, 0, 0, ..., 1, 0, 0, 0, + * respectively. The corresponding output \p aggregate in threads 0, 4, 8, etc. will be + * \p 3, \p 7, \p 11, etc. (and is undefined in other threads). + * + * \tparam ReductionOp [inferred] Binary reduction operator type having member T operator()(const T &a, const T &b) + */ + template < + typename ReductionOp, + typename Flag> + __device__ __forceinline__ T HeadSegmentedReduce( + T input, ///< [in] Calling thread's input + Flag head_flag, ///< [in] Head flag denoting whether or not \p input is the start of a new segment + ReductionOp reduction_op) ///< [in] Reduction operator + { + return InternalWarpReduce(temp_storage, warp_id, lane_id).template SegmentedReduce(input, head_flag, reduction_op); + } + + + /** + * \brief Computes a segmented reduction in each active warp where segments are defined by tail-flags. The reduction of each segment is returned to the first lane in that segment (which always includes lane0). + * + * Supports non-commutative reduction operators + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates a tail-segmented warp max + * reduction within a block of 32 threads (one warp). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpReduce for a single warp on type int + * typedef cub::WarpReduce WarpReduce; + * + * // Allocate shared memory for WarpReduce + * __shared__ typename WarpReduce::TempStorage temp_storage; + * + * // Obtain one input item and flag per thread + * int thread_data = ... + * int tail_flag = ... + * + * // Return the warp-wide reductions to each lane0 + * int aggregate = WarpReduce(temp_storage).TailSegmentedReduce( + * thread_data, tail_flag, cub::Max()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data and \p tail_flag across the block of threads + * is {0, 1, 2, 3, ..., 31 and is {0, 0, 0, 1, 0, 0, 0, 1, ..., 0, 0, 0, 1, + * respectively. The corresponding output \p aggregate in threads 0, 4, 8, etc. will be + * \p 3, \p 7, \p 11, etc. (and is undefined in other threads). + * + * \tparam ReductionOp [inferred] Binary reduction operator type having member T operator()(const T &a, const T &b) + */ + template < + typename ReductionOp, + typename Flag> + __device__ __forceinline__ T TailSegmentedReduce( + T input, ///< [in] Calling thread's input + Flag tail_flag, ///< [in] Tail flag denoting whether or not \p input is the end of the current segment + ReductionOp reduction_op) ///< [in] Reduction operator + { + return InternalWarpReduce(temp_storage, warp_id, lane_id).template SegmentedReduce(input, tail_flag, reduction_op); + } + + + + //@} end member group +}; + +/** @} */ // end group WarpModule + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/warp_scan.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/warp_scan.cuh new file mode 100644 index 0000000000000000000000000000000000000000..142c8a877b94488643684d30fd89c11fe47a797b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/cub/warp/warp_scan.cuh @@ -0,0 +1,1312 @@ +/****************************************************************************** + * Copyright (c) 2011, Duane Merrill. All rights reserved. + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/** + * \file + * The cub::WarpScan class provides [collective](index.html#sec0) methods for computing a parallel prefix scan of items partitioned across CUDA warp threads. + */ + +#pragma once + +#include "specializations/warp_scan_shfl.cuh" +#include "specializations/warp_scan_smem.cuh" +#include "../thread/thread_operators.cuh" +#include "../util_arch.cuh" +#include "../util_type.cuh" +#include "../util_namespace.cuh" + +/// Optional outer namespace(s) +CUB_NS_PREFIX + +/// CUB namespace +namespace cub { + +/** + * \addtogroup WarpModule + * @{ + */ + +/** + * \brief The WarpScan class provides [collective](index.html#sec0) methods for computing a parallel prefix scan of items partitioned across CUDA warp threads. ![](warp_scan_logo.png) + * + * \tparam T The scan input/output element type + * \tparam LOGICAL_WARPS [optional] The number of "logical" warps performing concurrent warp scans. Default is 1. + * \tparam LOGICAL_WARP_THREADS [optional] The number of threads per "logical" warp (may be less than the number of hardware warp threads). Default is the warp size associated with the CUDA Compute Capability targeted by the compiler (e.g., 32 threads for SM20). + * + * \par Overview + * - Given a list of input elements and a binary reduction operator, a [prefix scan](http://en.wikipedia.org/wiki/Prefix_sum) + * produces an output list where each element is computed to be the reduction + * of the elements occurring earlier in the input list. Prefix sum + * connotes a prefix scan with the addition operator. The term \em inclusive indicates + * that the ith output reduction incorporates the ith input. + * The term \em exclusive indicates the ith input is not incorporated into + * the ith output reduction. + * - Supports "logical" warps smaller than the physical warp size (e.g., a logical warp of 8 threads) + * - The number of entrant threads must be an multiple of \p LOGICAL_WARP_THREADS + * + * \par Performance Considerations + * - Warp scans are concurrent if more than one warp is participating + * - Uses special instructions when applicable (e.g., warp \p SHFL) + * - Uses synchronization-free communication between warp lanes when applicable + * - Incurs zero bank conflicts for most types + * - Computation is slightly more efficient (i.e., having lower instruction overhead) for: + * - Summation (vs. generic scan) + * - The architecture's warp size is a whole multiple of \p LOGICAL_WARP_THREADS + * + * \par Simple Examples + * \warpcollective{WarpScan} + * \par + * The code snippet below illustrates four concurrent warp prefix sums within a block of + * 128 threads (one per each of the 32-thread warps). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpScan for 4 warps on type int + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Obtain one input item per thread + * int thread_data = ... + * + * // Compute warp-wide prefix sums + * WarpScan(temp_storage).ExclusiveSum(thread_data, thread_data); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is {1, 1, 1, 1, ...}. + * The corresponding output \p thread_data in each of the four warps of threads will be + * 0, 1, 2, 3, ..., 31}. + * + * \par + * The code snippet below illustrates a single warp prefix sum within a block of + * 128 threads. + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpScan for one warp on type int + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * ... + * + * // Only the first warp performs a prefix sum + * if (threadIdx.x < 32) + * { + * // Obtain one input item per thread + * int thread_data = ... + * + * // Compute warp-wide prefix sums + * WarpScan(temp_storage).ExclusiveSum(thread_data, thread_data); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the warp of threads is {1, 1, 1, 1, ...}. + * The corresponding output \p thread_data will be {0, 1, 2, 3, ..., 31}. + * + */ +template < + typename T, + int LOGICAL_WARPS = 1, + int LOGICAL_WARP_THREADS = CUB_PTX_WARP_THREADS> +class WarpScan +{ +private: + + /****************************************************************************** + * Constants and type definitions + ******************************************************************************/ + + enum + { + POW_OF_TWO = ((LOGICAL_WARP_THREADS & (LOGICAL_WARP_THREADS - 1)) == 0), + }; + + /// Internal specialization. Use SHFL-based reduction if (architecture is >= SM30) and ((only one logical warp) or (LOGICAL_WARP_THREADS is a power-of-two)) + typedef typename If<(CUB_PTX_VERSION >= 300) && ((LOGICAL_WARPS == 1) || POW_OF_TWO), + WarpScanShfl, + WarpScanSmem >::Type InternalWarpScan; + + /// Shared memory storage layout type for WarpScan + typedef typename InternalWarpScan::TempStorage _TempStorage; + + + /****************************************************************************** + * Thread fields + ******************************************************************************/ + + /// Shared storage reference + _TempStorage &temp_storage; + + /// Warp ID + int warp_id; + + /// Lane ID + int lane_id; + + + /****************************************************************************** + * Utility methods + ******************************************************************************/ + + /// Internal storage allocator + __device__ __forceinline__ _TempStorage& PrivateStorage() + { + __shared__ TempStorage private_storage; + return private_storage; + } + + +public: + + /// \smemstorage{WarpScan} + struct TempStorage : Uninitialized<_TempStorage> {}; + + + /******************************************************************//** + * \name Collective constructors + *********************************************************************/ + //@{ + + /** + * \brief Collective constructor for 1D thread blocks using a private static allocation of shared memory as temporary storage. Logical warp and lane identifiers are constructed from threadIdx.x. + */ + __device__ __forceinline__ WarpScan() + : + temp_storage(PrivateStorage()), + warp_id((LOGICAL_WARPS == 1) ? + 0 : + threadIdx.x / LOGICAL_WARP_THREADS), + lane_id(((LOGICAL_WARPS == 1) || (LOGICAL_WARP_THREADS == CUB_PTX_WARP_THREADS)) ? + LaneId() : + threadIdx.x % LOGICAL_WARP_THREADS) + {} + + + /** + * \brief Collective constructor for 1D thread blocks using the specified memory allocation as temporary storage. Logical warp and lane identifiers are constructed from threadIdx.x. + */ + __device__ __forceinline__ WarpScan( + TempStorage &temp_storage) ///< [in] Reference to memory allocation having layout type TempStorage + : + temp_storage(temp_storage.Alias()), + warp_id((LOGICAL_WARPS == 1) ? + 0 : + threadIdx.x / LOGICAL_WARP_THREADS), + lane_id(((LOGICAL_WARPS == 1) || (LOGICAL_WARP_THREADS == CUB_PTX_WARP_THREADS)) ? + LaneId() : + threadIdx.x % LOGICAL_WARP_THREADS) + {} + + + /** + * \brief Collective constructor using a private static allocation of shared memory as temporary storage. Threads are identified using the given warp and lane identifiers. + */ + __device__ __forceinline__ WarpScan( + int warp_id, ///< [in] A suitable warp membership identifier + int lane_id) ///< [in] A lane identifier within the warp + : + temp_storage(PrivateStorage()), + warp_id(warp_id), + lane_id(lane_id) + {} + + + /** + * \brief Collective constructor using the specified memory allocation as temporary storage. Threads are identified using the given warp and lane identifiers. + */ + __device__ __forceinline__ WarpScan( + TempStorage &temp_storage, ///< [in] Reference to memory allocation having layout type TempStorage + int warp_id, ///< [in] A suitable warp membership identifier + int lane_id) ///< [in] A lane identifier within the warp + : + temp_storage(temp_storage.Alias()), + warp_id(warp_id), + lane_id(lane_id) + {} + + + //@} end member group + /******************************************************************//** + * \name Inclusive prefix sums + *********************************************************************/ + //@{ + + + /** + * \brief Computes an inclusive prefix sum in each logical warp. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates four concurrent warp-wide inclusive prefix sums within a block of + * 128 threads (one per each of the 32-thread warps). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpScan for 4 warps on type int + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Obtain one input item per thread + * int thread_data = ... + * + * // Compute inclusive warp-wide prefix sums + * WarpScan(temp_storage).InclusiveSum(thread_data, thread_data); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is {1, 1, 1, 1, ...}. + * The corresponding output \p thread_data in each of the four warps of threads will be + * 1, 2, 3, ..., 32}. + */ + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item. + T &output) ///< [out] Calling thread's output item. May be aliased with \p input. + { + InternalWarpScan(temp_storage, warp_id, lane_id).InclusiveSum(input, output); + } + + + /** + * \brief Computes an inclusive prefix sum in each logical warp. Also provides every thread with the warp-wide \p warp_aggregate of all inputs. + * + * The \p warp_aggregate is undefined in threads other than warp-lane0. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates four concurrent warp-wide inclusive prefix sums within a block of + * 128 threads (one per each of the 32-thread warps). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpScan for 4 warps on type int + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Obtain one input item per thread + * int thread_data = ... + * + * // Compute inclusive warp-wide prefix sums + * int warp_aggregate; + * WarpScan(temp_storage).InclusiveSum(thread_data, thread_data, warp_aggregate); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is {1, 1, 1, 1, ...}. + * The corresponding output \p thread_data in each of the four warps of threads will be + * 1, 2, 3, ..., 32}. Furthermore, \p warp_aggregate for all threads in all warps will be \p 32. + */ + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + T &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + InternalWarpScan(temp_storage, warp_id, lane_id).InclusiveSum(input, output, warp_aggregate); + } + + + /** + * \brief Computes an inclusive prefix sum in each logical warp. Instead of using 0 as the warp-wide prefix, the call-back functor \p warp_prefix_op is invoked to provide the "seed" value that logically prefixes the warp's scan inputs. Also provides every thread with the warp-wide \p warp_aggregate of all inputs. + * + * The \p warp_aggregate is undefined in threads other than warp-lane0. + * + * The \p warp_prefix_op functor must implement a member function T operator()(T warp_aggregate). + * The functor's input parameter \p warp_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the entire warp of threads, however only the return value from + * lane0 is applied as the threadblock-wide prefix. Can be stateful. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates a single thread block of 32 threads (one warp) that progressively + * computes an inclusive prefix sum over multiple "tiles" of input using a + * prefix functor to maintain a running total between block-wide scans. Each tile consists + * of 32 integer items that are partitioned across the warp. + * \par + * \code + * #include + * + * // A stateful callback functor that maintains a running prefix to be applied + * // during consecutive scan operations. + * struct WarpPrefixCallbackOp + * { + * // Running prefix + * int running_total; + * + * // Constructor + * __device__ WarpPrefixCallbackOp(int running_total) : running_total(running_total) {} + * + * // Callback operator to be entered by the entire warp. Lane-0 is responsible + * // for returning a value for seeding the warp-wide scan. + * __device__ int operator()(int warp_aggregate) + * { + * int old_prefix = running_total; + * running_total += warp_aggregate; + * return old_prefix; + * } + * }; + * + * __global__ void ExampleKernel(int *d_data, int num_items, ...) + * { + * // Specialize WarpScan for one warp + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Initialize running total + * WarpPrefixCallbackOp prefix_op(0); + * + * // Have the warp iterate over segments of items + * for (int block_offset = 0; block_offset < num_items; block_offset += 32) + * { + * // Load a segment of consecutive items + * int thread_data = d_data[block_offset]; + * + * // Collectively compute the warp-wide inclusive prefix sum + * int warp_aggregate; + * WarpScan(temp_storage).InclusiveSum( + * thread_data, thread_data, warp_aggregate, prefix_op); + * + * // Store scanned items to output segment + * d_data[block_offset] = thread_data; + * } + * \endcode + * \par + * Suppose the input \p d_data is {1, 1, 1, 1, 1, 1, 1, 1, ...}. + * The corresponding output for the first segment will be {1, 2, 3, ..., 32}. + * The output for the second segment will be {33, 34, 35, ..., 64}. Furthermore, + * the value \p 32 will be stored in \p warp_aggregate for all threads after each scan. + * + * \tparam WarpPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T warp_aggregate) + */ + template + __device__ __forceinline__ void InclusiveSum( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + T &warp_aggregate, ///< [out] [warp-lane0 only] Warp-wide aggregate reduction of input items, exclusive of the \p warp_prefix_op value + WarpPrefixCallbackOp &warp_prefix_op) ///< [in-out] [warp-lane0 only] Call-back functor for specifying a warp-wide prefix to be applied to all inputs. + { + // Compute inclusive warp scan + InclusiveSum(input, output, warp_aggregate); + + // Compute warp-wide prefix from aggregate, then broadcast to other lanes + T prefix; + prefix = warp_prefix_op(warp_aggregate); + prefix = InternalWarpScan(temp_storage, warp_id, lane_id).Broadcast(prefix, 0); + + // Update output + output = prefix + output; + } + + //@} end member group + +private: + + /// Computes an exclusive prefix sum in each logical warp. + __device__ __forceinline__ void ExclusiveSum(T input, T &output, Int2Type is_primitive) + { + // Compute exclusive warp scan from inclusive warp scan + T inclusive; + InclusiveSum(input, inclusive); + output = inclusive - input; + } + + /// Computes an exclusive prefix sum in each logical warp. Specialized for non-primitive types. + __device__ __forceinline__ void ExclusiveSum(T input, T &output, Int2Type is_primitive) + { + // Delegate to regular scan for non-primitive types (because we won't be able to use subtraction) + T identity = ZeroInitialize(); + ExclusiveScan(input, output, identity, Sum()); + } + + /// Computes an exclusive prefix sum in each logical warp. Also provides every thread with the warp-wide \p warp_aggregate of all inputs. + __device__ __forceinline__ void ExclusiveSum(T input, T &output, T &warp_aggregate, Int2Type is_primitive) + { + // Compute exclusive warp scan from inclusive warp scan + T inclusive; + InclusiveSum(input, inclusive, warp_aggregate); + output = inclusive - input; + } + + /// Computes an exclusive prefix sum in each logical warp. Also provides every thread with the warp-wide \p warp_aggregate of all inputs. Specialized for non-primitive types. + __device__ __forceinline__ void ExclusiveSum(T input, T &output, T &warp_aggregate, Int2Type is_primitive) + { + // Delegate to regular scan for non-primitive types (because we won't be able to use subtraction) + T identity = ZeroInitialize(); + ExclusiveScan(input, output, identity, Sum(), warp_aggregate); + } + + /// Computes an exclusive prefix sum in each logical warp. Instead of using 0 as the warp-wide prefix, the call-back functor \p warp_prefix_op is invoked to provide the "seed" value that logically prefixes the warp's scan inputs. Also provides every thread with the warp-wide \p warp_aggregate of all inputs. + template + __device__ __forceinline__ void ExclusiveSum(T input, T &output, T &warp_aggregate, WarpPrefixCallbackOp &warp_prefix_op, Int2Type is_primitive) + { + // Compute exclusive warp scan from inclusive warp scan + T inclusive; + InclusiveSum(input, inclusive, warp_aggregate, warp_prefix_op); + output = inclusive - input; + } + + /// Computes an exclusive prefix sum in each logical warp. Instead of using 0 as the warp-wide prefix, the call-back functor \p warp_prefix_op is invoked to provide the "seed" value that logically prefixes the warp's scan inputs. Also provides every thread with the warp-wide \p warp_aggregate of all inputs. Specialized for non-primitive types. + template + __device__ __forceinline__ void ExclusiveSum(T input, T &output, T &warp_aggregate, WarpPrefixCallbackOp &warp_prefix_op, Int2Type is_primitive) + { + // Delegate to regular scan for non-primitive types (because we won't be able to use subtraction) + T identity = ZeroInitialize(); + ExclusiveScan(input, output, identity, Sum(), warp_aggregate, warp_prefix_op); + } + +public: + + + /******************************************************************//** + * \name Exclusive prefix sums + *********************************************************************/ + //@{ + + + /** + * \brief Computes an exclusive prefix sum in each logical warp. + * + * This operation assumes the value of obtained by the T's default + * constructor (or by zero-initialization if no user-defined default + * constructor exists) is suitable as the identity value "zero" for + * addition. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates four concurrent warp-wide exclusive prefix sums within a block of + * 128 threads (one per each of the 32-thread warps). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpScan for 4 warps on type int + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Obtain one input item per thread + * int thread_data = ... + * + * // Compute exclusive warp-wide prefix sums + * WarpScan(temp_storage).ExclusiveSum(thread_data, thread_data); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is {1, 1, 1, 1, ...}. + * The corresponding output \p thread_data in each of the four warps of threads will be + * 0, 1, 2, ..., 31}. + * + */ + __device__ __forceinline__ void ExclusiveSum( + T input, ///< [in] Calling thread's input item. + T &output) ///< [out] Calling thread's output item. May be aliased with \p input. + { + ExclusiveSum(input, output, Int2Type::PRIMITIVE>()); + } + + + /** + * \brief Computes an exclusive prefix sum in each logical warp. Also provides every thread with the warp-wide \p warp_aggregate of all inputs. + * + * This operation assumes the value of obtained by the T's default + * constructor (or by zero-initialization if no user-defined default + * constructor exists) is suitable as the identity value "zero" for + * addition. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates four concurrent warp-wide exclusive prefix sums within a block of + * 128 threads (one per each of the 32-thread warps). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpScan for 4 warps on type int + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Obtain one input item per thread + * int thread_data = ... + * + * // Compute exclusive warp-wide prefix sums + * int warp_aggregate; + * WarpScan(temp_storage).ExclusiveSum(thread_data, thread_data, warp_aggregate); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is {1, 1, 1, 1, ...}. + * The corresponding output \p thread_data in each of the four warps of threads will be + * 0, 1, 2, ..., 31}. Furthermore, \p warp_aggregate for all threads in all warps will be \p 32. + */ + __device__ __forceinline__ void ExclusiveSum( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + T &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + ExclusiveSum(input, output, warp_aggregate, Int2Type::PRIMITIVE>()); + } + + + /** + * \brief Computes an exclusive prefix sum in each logical warp. Instead of using 0 as the warp-wide prefix, the call-back functor \p warp_prefix_op is invoked to provide the "seed" value that logically prefixes the warp's scan inputs. Also provides every thread with the warp-wide \p warp_aggregate of all inputs. + * + * This operation assumes the value of obtained by the T's default + * constructor (or by zero-initialization if no user-defined default + * constructor exists) is suitable as the identity value "zero" for + * addition. + * + * The \p warp_prefix_op functor must implement a member function T operator()(T warp_aggregate). + * The functor's input parameter \p warp_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the entire warp of threads, however only the return value from + * lane0 is applied as the threadblock-wide prefix. Can be stateful. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates a single thread block of 32 threads (one warp) that progressively + * computes an exclusive prefix sum over multiple "tiles" of input using a + * prefix functor to maintain a running total between block-wide scans. Each tile consists + * of 32 integer items that are partitioned across the warp. + * \par + * \code + * #include + * + * // A stateful callback functor that maintains a running prefix to be applied + * // during consecutive scan operations. + * struct WarpPrefixCallbackOp + * { + * // Running prefix + * int running_total; + * + * // Constructor + * __device__ WarpPrefixCallbackOp(int running_total) : running_total(running_total) {} + * + * // Callback operator to be entered by the entire warp. Lane-0 is responsible + * // for returning a value for seeding the warp-wide scan. + * __device__ int operator()(int warp_aggregate) + * { + * int old_prefix = running_total; + * running_total += warp_aggregate; + * return old_prefix; + * } + * }; + * + * __global__ void ExampleKernel(int *d_data, int num_items, ...) + * { + * // Specialize WarpScan for one warp + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Initialize running total + * WarpPrefixCallbackOp prefix_op(0); + * + * // Have the warp iterate over segments of items + * for (int block_offset = 0; block_offset < num_items; block_offset += 32) + * { + * // Load a segment of consecutive items + * int thread_data = d_data[block_offset]; + * + * // Collectively compute the warp-wide exclusive prefix sum + * int warp_aggregate; + * WarpScan(temp_storage).ExclusiveSum( + * thread_data, thread_data, warp_aggregate, prefix_op); + * + * // Store scanned items to output segment + * d_data[block_offset] = thread_data; + * } + * \endcode + * \par + * Suppose the input \p d_data is {1, 1, 1, 1, 1, 1, 1, 1, ...}. + * The corresponding output for the first segment will be {0, 1, 2, ..., 31}. + * The output for the second segment will be {32, 33, 34, ..., 63}. Furthermore, + * the value \p 32 will be stored in \p warp_aggregate for all threads after each scan. + * + * \tparam WarpPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T warp_aggregate) + */ + template + __device__ __forceinline__ void ExclusiveSum( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + T &warp_aggregate, ///< [out] [warp-lane0 only] Warp-wide aggregate reduction of input items (exclusive of the \p warp_prefix_op value). + WarpPrefixCallbackOp &warp_prefix_op) ///< [in-out] [warp-lane0 only] Call-back functor for specifying a warp-wide prefix to be applied to all inputs. + { + ExclusiveSum(input, output, warp_aggregate, warp_prefix_op, Int2Type::PRIMITIVE>()); + } + + + //@} end member group + /******************************************************************//** + * \name Inclusive prefix scans + *********************************************************************/ + //@{ + + /** + * \brief Computes an inclusive prefix sum using the specified binary scan functor in each logical warp. + * + * Supports non-commutative scan operators. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates four concurrent warp-wide inclusive prefix max scans within a block of + * 128 threads (one per each of the 32-thread warps). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpScan for 4 warps on type int + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Obtain one input item per thread + * int thread_data = ... + * + * // Compute inclusive warp-wide prefix max scans + * WarpScan(temp_storage).InclusiveScan(thread_data, thread_data, cub::Max()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is {0, -1, 2, -3, ..., 126, -127}. + * The corresponding output \p thread_data in the first warp would be + * 0, 0, 2, 2, ..., 30, 30, the output for the second warp would be 32, 32, 34, 34, ..., 62, 62, etc. + * + * \tparam ScanOp [inferred] Binary scan operator type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ void InclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + ScanOp scan_op) ///< [in] Binary scan operator + { + InternalWarpScan(temp_storage, warp_id, lane_id).InclusiveScan(input, output, scan_op); + } + + + /** + * \brief Computes an inclusive prefix sum using the specified binary scan functor in each logical warp. Also provides every thread with the warp-wide \p warp_aggregate of all inputs. + * + * Supports non-commutative scan operators. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates four concurrent warp-wide inclusive prefix max scans within a block of + * 128 threads (one per each of the 32-thread warps). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpScan for 4 warps on type int + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Obtain one input item per thread + * int thread_data = ... + * + * // Compute inclusive warp-wide prefix max scans + * int warp_aggregate; + * WarpScan(temp_storage).InclusiveScan( + * thread_data, thread_data, cub::Max(), warp_aggregate); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is {0, -1, 2, -3, ..., 126, -127}. + * The corresponding output \p thread_data in the first warp would be + * 0, 0, 2, 2, ..., 30, 30, the output for the second warp would be 32, 32, 34, 34, ..., 62, 62, etc. + * Furthermore, \p warp_aggregate would be assigned \p 30 for threads in the first warp, \p 62 for threads + * in the second warp, etc. + * + * \tparam ScanOp [inferred] Binary scan operator type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ void InclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + ScanOp scan_op, ///< [in] Binary scan operator + T &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + InternalWarpScan(temp_storage, warp_id, lane_id).InclusiveScan(input, output, scan_op, warp_aggregate); + } + + + /** + * \brief Computes an inclusive prefix sum using the specified binary scan functor in each logical warp. The call-back functor \p warp_prefix_op is invoked to provide the "seed" value that logically prefixes the warp's scan inputs. Also provides every thread with the warp-wide \p warp_aggregate of all inputs. + * + * The \p warp_prefix_op functor must implement a member function T operator()(T warp_aggregate). + * The functor's input parameter \p warp_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the entire warp of threads, however only the return value from + * lane0 is applied as the threadblock-wide prefix. Can be stateful. + * + * Supports non-commutative scan operators. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates a single thread block of 32 threads (one warp) that progressively + * computes an inclusive prefix max scan over multiple "tiles" of input using a + * prefix functor to maintain a running total between block-wide scans. Each tile consists + * of 32 integer items that are partitioned across the warp. + * \par + * \code + * #include + * + * // A stateful callback functor that maintains a running prefix to be applied + * // during consecutive scan operations. + * struct WarpPrefixCallbackOp + * { + * // Running prefix + * int running_total; + * + * // Constructor + * __device__ WarpPrefixCallbackOp(int running_total) : running_total(running_total) {} + * + * // Callback operator to be entered by the entire warp. Lane-0 is responsible + * // for returning a value for seeding the warp-wide scan. + * __device__ int operator()(int warp_aggregate) + * { + * int old_prefix = running_total; + * running_total = (warp_aggregate > old_prefix) ? warp_aggregate : old_prefix; + * return old_prefix; + * } + * }; + * + * __global__ void ExampleKernel(int *d_data, int num_items, ...) + * { + * // Specialize WarpScan for one warp + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Initialize running total + * WarpPrefixCallbackOp prefix_op(0); + * + * // Have the warp iterate over segments of items + * for (int block_offset = 0; block_offset < num_items; block_offset += 32) + * { + * // Load a segment of consecutive items + * int thread_data = d_data[block_offset]; + * + * // Collectively compute the warp-wide inclusive prefix max scan + * int warp_aggregate; + * WarpScan(temp_storage).InclusiveScan( + * thread_data, thread_data, cub::Max(), warp_aggregate, prefix_op); + * + * // Store scanned items to output segment + * d_data[block_offset] = thread_data; + * } + * \endcode + * \par + * Suppose the input \p d_data is {0, -1, 2, -3, 4, -5, ...}. + * The corresponding output for the first segment will be {0, 0, 2, 2, ..., 30, 30}. + * The output for the second segment will be {32, 32, 34, 34, ..., 62, 62}. Furthermore, + * \p block_aggregate will be assigned \p 30 in all threads after the first scan, assigned \p 62 after the second + * scan, etc. + * + * \tparam ScanOp [inferred] Binary scan operator type having member T operator()(const T &a, const T &b) + * \tparam WarpPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T warp_aggregate) + */ + template < + typename ScanOp, + typename WarpPrefixCallbackOp> + __device__ __forceinline__ void InclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + ScanOp scan_op, ///< [in] Binary scan operator + T &warp_aggregate, ///< [out] [warp-lane0 only] Warp-wide aggregate reduction of input items (exclusive of the \p warp_prefix_op value). + WarpPrefixCallbackOp &warp_prefix_op) ///< [in-out] [warp-lane0 only] Call-back functor for specifying a warp-wide prefix to be applied to all inputs. + { + // Compute inclusive warp scan + InclusiveScan(input, output, scan_op, warp_aggregate); + + // Compute warp-wide prefix from aggregate, then broadcast to other lanes + T prefix; + prefix = warp_prefix_op(warp_aggregate); + prefix = InternalWarpScan(temp_storage, warp_id, lane_id).Broadcast(prefix, 0); + + // Update output + output = scan_op(prefix, output); + } + + + //@} end member group + /******************************************************************//** + * \name Exclusive prefix scans + *********************************************************************/ + //@{ + + /** + * \brief Computes an exclusive prefix scan using the specified binary scan functor in each logical warp. + * + * Supports non-commutative scan operators. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates four concurrent warp-wide exclusive prefix max scans within a block of + * 128 threads (one per each of the 32-thread warps). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpScan for 4 warps on type int + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Obtain one input item per thread + * int thread_data = ... + * + * // Compute exclusive warp-wide prefix max scans + * WarpScan(temp_storage).ExclusiveScan(thread_data, thread_data, INT_MIN, cub::Max()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is {0, -1, 2, -3, ..., 126, -127}. + * The corresponding output \p thread_data in the first warp would be + * INT_MIN, 0, 0, 2, ..., 28, 30, the output for the second warp would be 30, 32, 32, 34, ..., 60, 62, etc. + * + * \tparam ScanOp [inferred] Binary scan operator type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + T identity, ///< [in] Identity value + ScanOp scan_op) ///< [in] Binary scan operator + { + InternalWarpScan(temp_storage, warp_id, lane_id).ExclusiveScan(input, output, identity, scan_op); + } + + + /** + * \brief Computes an exclusive prefix scan using the specified binary scan functor in each logical warp. Also provides every thread with the warp-wide \p warp_aggregate of all inputs. + * + * Supports non-commutative scan operators. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates four concurrent warp-wide exclusive prefix max scans within a block of + * 128 threads (one per each of the 32-thread warps). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpScan for 4 warps on type int + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Obtain one input item per thread + * int thread_data = ... + * + * // Compute exclusive warp-wide prefix max scans + * WarpScan(temp_storage).ExclusiveScan(thread_data, thread_data, INT_MIN, cub::Max()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is {0, -1, 2, -3, ..., 126, -127}. + * The corresponding output \p thread_data in the first warp would be + * INT_MIN, 0, 0, 2, ..., 28, 30, the output for the second warp would be 30, 32, 32, 34, ..., 60, 62, etc. + * Furthermore, \p warp_aggregate would be assigned \p 30 for threads in the first warp, \p 62 for threads + * in the second warp, etc. + * + * \tparam ScanOp [inferred] Binary scan operator type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + T identity, ///< [in] Identity value + ScanOp scan_op, ///< [in] Binary scan operator + T &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + InternalWarpScan(temp_storage, warp_id, lane_id).ExclusiveScan(input, output, identity, scan_op, warp_aggregate); + } + + + /** + * \brief Computes an exclusive prefix scan using the specified binary scan functor in each logical warp. The call-back functor \p warp_prefix_op is invoked to provide the "seed" value that logically prefixes the warp's scan inputs. Also provides every thread with the warp-wide \p warp_aggregate of all inputs. + * + * The \p warp_prefix_op functor must implement a member function T operator()(T warp_aggregate). + * The functor's input parameter \p warp_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the entire warp of threads, however only the return value from + * lane0 is applied as the threadblock-wide prefix. Can be stateful. + * + * Supports non-commutative scan operators. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates a single thread block of 32 threads (one warp) that progressively + * computes an exclusive prefix max scan over multiple "tiles" of input using a + * prefix functor to maintain a running total between block-wide scans. Each tile consists + * of 32 integer items that are partitioned across the warp. + * \par + * \code + * #include + * + * // A stateful callback functor that maintains a running prefix to be applied + * // during consecutive scan operations. + * struct WarpPrefixCallbackOp + * { + * // Running prefix + * int running_total; + * + * // Constructor + * __device__ WarpPrefixCallbackOp(int running_total) : running_total(running_total) {} + * + * // Callback operator to be entered by the entire warp. Lane-0 is responsible + * // for returning a value for seeding the warp-wide scan. + * __device__ int operator()(int warp_aggregate) + * { + * int old_prefix = running_total; + * running_total = (warp_aggregate > old_prefix) ? warp_aggregate : old_prefix; + * return old_prefix; + * } + * }; + * + * __global__ void ExampleKernel(int *d_data, int num_items, ...) + * { + * // Specialize WarpScan for one warp + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Initialize running total + * WarpPrefixCallbackOp prefix_op(INT_MIN); + * + * // Have the warp iterate over segments of items + * for (int block_offset = 0; block_offset < num_items; block_offset += 32) + * { + * // Load a segment of consecutive items + * int thread_data = d_data[block_offset]; + * + * // Collectively compute the warp-wide exclusive prefix max scan + * int warp_aggregate; + * WarpScan(temp_storage).ExclusiveScan( + * thread_data, thread_data, INT_MIN, cub::Max(), warp_aggregate, prefix_op); + * + * // Store scanned items to output segment + * d_data[block_offset] = thread_data; + * } + * \endcode + * \par + * Suppose the input \p d_data is {0, -1, 2, -3, 4, -5, ...}. + * The corresponding output for the first segment will be {INT_MIN, 0, 0, 2, ..., 28, 30}. + * The output for the second segment will be {30, 32, 32, 34, ..., 60, 62}. Furthermore, + * \p block_aggregate will be assigned \p 30 in all threads after the first scan, assigned \p 62 after the second + * scan, etc. + * + * \tparam ScanOp [inferred] Binary scan operator type having member T operator()(const T &a, const T &b) + * \tparam WarpPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T warp_aggregate) + */ + template < + typename ScanOp, + typename WarpPrefixCallbackOp> + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + T identity, ///< [in] Identity value + ScanOp scan_op, ///< [in] Binary scan operator + T &warp_aggregate, ///< [out] [warp-lane0 only] Warp-wide aggregate reduction of input items (exclusive of the \p warp_prefix_op value). + WarpPrefixCallbackOp &warp_prefix_op) ///< [in-out] [warp-lane0 only] Call-back functor for specifying a warp-wide prefix to be applied to all inputs. + { + // Exclusive warp scan + ExclusiveScan(input, output, identity, scan_op, warp_aggregate); + + // Compute warp-wide prefix from aggregate, then broadcast to other lanes + T prefix = warp_prefix_op(warp_aggregate); + prefix = InternalWarpScan(temp_storage, warp_id, lane_id).Broadcast(prefix, 0); + + // Update output + output = (lane_id == 0) ? + prefix : + scan_op(prefix, output); + } + + + //@} end member group + /******************************************************************//** + * \name Identityless exclusive prefix scans + *********************************************************************/ + //@{ + + + /** + * \brief Computes an exclusive prefix scan using the specified binary scan functor in each logical warp. Because no identity value is supplied, the \p output computed for warp-lane0 is undefined. + * + * Supports non-commutative scan operators. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates four concurrent warp-wide exclusive prefix max scans within a block of + * 128 threads (one per each of the 32-thread warps). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpScan for 4 warps on type int + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Obtain one input item per thread + * int thread_data = ... + * + * // Compute exclusive warp-wide prefix max scans + * WarpScan(temp_storage).ExclusiveScan(thread_data, thread_data, cub::Max()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is {0, -1, 2, -3, ..., 126, -127}. + * The corresponding output \p thread_data in the first warp would be + * ?, 0, 0, 2, ..., 28, 30, the output for the second warp would be ?, 32, 32, 34, ..., 60, 62, etc. + * (The output \p thread_data in each warp lane0 is undefined.) + * + * \tparam ScanOp [inferred] Binary scan operator type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + ScanOp scan_op) ///< [in] Binary scan operator + { + InternalWarpScan(temp_storage, warp_id, lane_id).ExclusiveScan(input, output, scan_op); + } + + + /** + * \brief Computes an exclusive prefix scan using the specified binary scan functor in each logical warp. Because no identity value is supplied, the \p output computed for warp-lane0 is undefined. Also provides every thread with the warp-wide \p warp_aggregate of all inputs. + * + * Supports non-commutative scan operators. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates four concurrent warp-wide exclusive prefix max scans within a block of + * 128 threads (one per each of the 32-thread warps). + * \par + * \code + * #include + * + * __global__ void ExampleKernel(...) + * { + * // Specialize WarpScan for 4 warps on type int + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Obtain one input item per thread + * int thread_data = ... + * + * // Compute exclusive warp-wide prefix max scans + * WarpScan(temp_storage).ExclusiveScan(thread_data, thread_data, cub::Max()); + * + * \endcode + * \par + * Suppose the set of input \p thread_data across the block of threads is {0, -1, 2, -3, ..., 126, -127}. + * The corresponding output \p thread_data in the first warp would be + * ?, 0, 0, 2, ..., 28, 30, the output for the second warp would be ?, 32, 32, 34, ..., 60, 62, etc. + * (The output \p thread_data in each warp lane0 is undefined.) Furthermore, \p warp_aggregate would be assigned \p 30 for threads in the first warp, \p 62 for threads + * in the second warp, etc. + * + * \tparam ScanOp [inferred] Binary scan operator type having member T operator()(const T &a, const T &b) + */ + template + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + ScanOp scan_op, ///< [in] Binary scan operator + T &warp_aggregate) ///< [out] Warp-wide aggregate reduction of input items. + { + InternalWarpScan(temp_storage, warp_id, lane_id).ExclusiveScan(input, output, scan_op, warp_aggregate); + } + + + /** + * \brief Computes an exclusive prefix scan using the specified binary scan functor in each logical warp. The \p warp_prefix_op value from thread-thread-lane0 is applied to all scan outputs. Also computes the warp-wide \p warp_aggregate of all inputs for thread-thread-lane0. + * + * The \p warp_prefix_op functor must implement a member function T operator()(T warp_aggregate)}. + * The functor's input parameter \p warp_aggregate is the same value also returned by the scan operation. + * The functor will be invoked by the entire warp of threads, however only the return value from + * lane0 is applied as the threadblock-wide prefix. Can be stateful. + * + * Supports non-commutative scan operators. + * + * \smemreuse + * + * \par Snippet + * The code snippet below illustrates a single thread block of 32 threads (one warp) that progressively + * computes an exclusive prefix max scan over multiple "tiles" of input using a + * prefix functor to maintain a running total between block-wide scans. Each tile consists + * of 32 integer items that are partitioned across the warp. + * \par + * \code + * #include + * + * // A stateful callback functor that maintains a running prefix to be applied + * // during consecutive scan operations. + * struct WarpPrefixCallbackOp + * { + * // Running prefix + * int running_total; + * + * // Constructor + * __device__ WarpPrefixCallbackOp(int running_total) : running_total(running_total) {} + * + * // Callback operator to be entered by the entire warp. Lane-0 is responsible + * // for returning a value for seeding the warp-wide scan. + * __device__ int operator()(int warp_aggregate) + * { + * int old_prefix = running_total; + * running_total = (warp_aggregate > old_prefix) ? warp_aggregate : old_prefix; + * return old_prefix; + * } + * }; + * + * __global__ void ExampleKernel(int *d_data, int num_items, ...) + * { + * // Specialize WarpScan for one warp + * typedef cub::WarpScan WarpScan; + * + * // Allocate shared memory for WarpScan + * __shared__ typename WarpScan::TempStorage temp_storage; + * + * // Initialize running total + * WarpPrefixCallbackOp prefix_op(INT_MIN); + * + * // Have the warp iterate over segments of items + * for (int block_offset = 0; block_offset < num_items; block_offset += 32) + * { + * // Load a segment of consecutive items + * int thread_data = d_data[block_offset]; + * + * // Collectively compute the warp-wide exclusive prefix max scan + * int warp_aggregate; + * WarpScan(temp_storage).ExclusiveScan( + * thread_data, thread_data, INT_MIN, cub::Max(), warp_aggregate, prefix_op); + * + * // Store scanned items to output segment + * d_data[block_offset] = thread_data; + * } + * \endcode + * \par + * Suppose the input \p d_data is {0, -1, 2, -3, 4, -5, ...}. + * The corresponding output for the first segment will be {INT_MIN, 0, 0, 2, ..., 28, 30}. + * The output for the second segment will be {30, 32, 32, 34, ..., 60, 62}. Furthermore, + * \p block_aggregate will be assigned \p 30 in all threads after the first scan, assigned \p 62 after the second + * scan, etc. + * + * \tparam ScanOp [inferred] Binary scan operator type having member T operator()(const T &a, const T &b) + * \tparam WarpPrefixCallbackOp [inferred] Call-back functor type having member T operator()(T warp_aggregate) + */ + template < + typename ScanOp, + typename WarpPrefixCallbackOp> + __device__ __forceinline__ void ExclusiveScan( + T input, ///< [in] Calling thread's input item. + T &output, ///< [out] Calling thread's output item. May be aliased with \p input. + ScanOp scan_op, ///< [in] Binary scan operator + T &warp_aggregate, ///< [out] [warp-lane0 only] Warp-wide aggregate reduction of input items (exclusive of the \p warp_prefix_op value). + WarpPrefixCallbackOp &warp_prefix_op) ///< [in-out] [warp-lane0 only] Call-back functor for specifying a warp-wide prefix to be applied to all inputs. + { + // Exclusive warp scan + ExclusiveScan(input, output, scan_op, warp_aggregate); + + // Compute warp-wide prefix from aggregate, then broadcast to other lanes + T prefix = warp_prefix_op(warp_aggregate); + prefix = InternalWarpScan(temp_storage, warp_id, lane_id).Broadcast(prefix, 0); + + // Update output with prefix + output = (lane_id == 0) ? + prefix : + scan_op(prefix, output); + } + + //@} end member group +}; + +/** @} */ // end group WarpModule + +} // CUB namespace +CUB_NS_POSTFIX // Optional outer namespace(s) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/.travis.yml b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/.travis.yml new file mode 100644 index 0000000000000000000000000000000000000000..3e1c43adf6477aa491c9314d25dec128eb77d607 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/.travis.yml @@ -0,0 +1,8 @@ +# Control file for continuous integration testing at http://travis-ci.org/ + +language: c +compiler: + - clang + - gcc + +script: make -e && make test diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..d167fcbd06db0704d3fb88f08e497526bec24a31 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/CMakeLists.txt @@ -0,0 +1,87 @@ +project(htslib) +cmake_minimum_required(VERSION 2.8) + +include_directories(${CMAKE_CURRENT_BINARY_DIR} ${NVBIO_SOURCE_ROOT}/nvbio) +include_directories(${CMAKE_CURRENT_SOURCE_DIR} ${NVBIO_SOURCE_ROOT}/contrib/zlib) +add_definitions(-DSAMTOOLS) + +set(HTSLIB_SRCS + bgzf.c + hfile.c + hts.c + kstring.c + vcfutils.c + bgzip.c + hfile_internal.h + kfunc.c + sam.c + tabix.c + vcf.c + config.h + faidx.c + hfile_net.c + knetfile.c + synced_bcf_reader.c + tbx.c + vcf_sweep.c + version.h + htslib/bgzf.h + htslib/hfile.h + htslib/hts.h + htslib/khash.h + htslib/klist.h + htslib/kseq.h + htslib/kstdint.h + htslib/sam.h + htslib/tbx.h + htslib/vcf_sweep.h + htslib/faidx.h + htslib/hts_defs.h + htslib/kfunc.h + htslib/khash_str2int.h + htslib/knetfile.h + htslib/ksort.h + htslib/kstring.h + htslib/synced_bcf_reader.h + htslib/vcf.h + htslib/vcfutils.h + cram/cram_codecs.c + cram/cram_encode.c + cram/cram_index.h + cram/cram_samtools.h + cram/files.c + cram/mFILE.h + cram/os.h + cram/sam_header.h + cram/thread_pool.h + cram/zfio.h + cram/cram_codecs.h + cram/cram_encode.h + cram/cram_io.c + cram/cram_stats.c + cram/md5.c + cram/misc.h + cram/pooled_alloc.c + cram/string_alloc.c + cram/vlen.c + cram/cram_decode.c + cram/cram.h + cram/cram_io.h + cram/cram_stats.h + cram/md5.h + cram/open_trace_file.c + cram/pooled_alloc.h + cram/string_alloc.h + cram/vlen.h + cram/cram_decode.h + cram/cram_index.c + cram/cram_samtools.c + cram/cram_structs.h + cram/mFILE.c + cram/open_trace_file.h + cram/sam_header.c + cram/thread_pool.c + cram/zfio.c +) + +add_library(htslib STATIC ${HTSLIB_SRCS}) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/Makefile b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..1087528fb9e30f40f7228ec25559a57a99968d79 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/Makefile @@ -0,0 +1,303 @@ +# Makefile for htslib, a C library for high-throughput sequencing data formats. +# +# Copyright (C) 2013-2014 Genome Research Ltd. +# +# Author: John Marshall + +CC = gcc +AR = ar +RANLIB = ranlib + +# TODO: edit cram code to remove need for -DSAMTOOLS +CPPFLAGS = -I. -DSAMTOOLS=1 +# TODO: probably update cram code to make it compile cleanly with -Wc++-compat +CFLAGS = -g -Wall -O2 +EXTRA_CFLAGS_PIC = -fpic +LDFLAGS = +LDLIBS = + +prefix = /usr/local +exec_prefix = $(prefix) +bindir = $(exec_prefix)/bin +includedir = $(prefix)/include +libdir = $(exec_prefix)/lib +mandir = $(prefix)/share/man +man1dir = $(mandir)/man1 +man5dir = $(mandir)/man5 + +INSTALL = install -p +INSTALL_PROGRAM = $(INSTALL) +INSTALL_DATA = $(INSTALL) -m 644 + +BUILT_PROGRAMS = \ + bgzip \ + tabix + +BUILT_TEST_PROGRAMS = \ + test/fieldarith \ + test/hfile \ + test/sam \ + test/test_view \ + test/test-vcf-api \ + test/test-vcf-sweep + +all: lib-static lib-shared $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS) + +HTSPREFIX = +include htslib_vars.mk + +lib-static: libhts.a + +# $(shell), :=, and ifeq/.../endif are GNU Make-specific. If you don't have +# GNU Make, comment out the parts of this conditional that don't apply. +PLATFORM := $(shell uname -s) +ifeq "$(PLATFORM)" "Darwin" +SHLIB_FLAVOUR = dylib +lib-shared: libhts.dylib +else +SHLIB_FLAVOUR = so +lib-shared: libhts.so +endif + + +PACKAGE_VERSION = 0.0.1 +LIBHTS_SOVERSION = 0 + + +# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string +# even if this is a dirty or untagged Git working tree. +NUMERIC_VERSION = $(PACKAGE_VERSION) + +# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git +# description of the working tree: either a release tag with the same value +# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. +# Much of this is also GNU Make-specific. If you don't have GNU Make and/or +# are not building from a Git repository, comment out this conditional. +ifneq "$(wildcard .git)" "" +original_version := $(PACKAGE_VERSION) +PACKAGE_VERSION := $(shell git describe --always --dirty) + +# Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag +# with a numeric name, revert $(NUMERIC_VERSION) to the original version number +# written above, but with the patchlevel field bumped to 255. +ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "." +empty := +NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255) +endif + +# Force version.h to be remade if $(PACKAGE_VERSION) has changed. +version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) +endif + +version.h: + echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@ + + +.SUFFIXES: .c .o .pico + +.c.o: + $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< + +.c.pico: + $(CC) $(CFLAGS) $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $< + + +LIBHTS_OBJS = \ + kfunc.o \ + knetfile.o \ + kstring.o \ + bgzf.o \ + faidx.o \ + hfile.o \ + hfile_net.o \ + hts.o \ + sam.o \ + synced_bcf_reader.o \ + vcf_sweep.o \ + tbx.o \ + vcf.o \ + vcfutils.o \ + cram/cram_codecs.o \ + cram/cram_decode.o \ + cram/cram_encode.o \ + cram/cram_index.o \ + cram/cram_io.o \ + cram/cram_samtools.o \ + cram/cram_stats.o \ + cram/files.o \ + cram/mFILE.o \ + cram/md5.o \ + cram/open_trace_file.o \ + cram/pooled_alloc.o \ + cram/sam_header.o \ + cram/string_alloc.o \ + cram/thread_pool.o \ + cram/vlen.o \ + cram/zfio.o + + +libhts.a: $(LIBHTS_OBJS) + @-rm -f $@ + $(AR) -rc $@ $(LIBHTS_OBJS) + -$(RANLIB) $@ + + +# The target here is libhts.so, as that is the built file that other rules +# depend upon and that is used when -lhts appears in other program's recipes. +# As a byproduct invisible to make, libhts.so.NN is also created, as it is the +# file used at runtime (when $LD_LIBRARY_PATH includes the build directory). + +libhts.so: $(LIBHTS_OBJS:.o=.pico) + $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LDLIBS) -lz + ln -sf $@ libhts.so.$(LIBHTS_SOVERSION) + +# Similarly this also creates libhts.NN.dylib as a byproduct, so that programs +# when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH +# includes this project's build directory). + +libhts.dylib: $(LIBHTS_OBJS) + $(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) $(LDLIBS) -lz + ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib + + +cram_h = cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h +cram_io_h = cram/cram_io.h $(cram_misc_h) +cram_misc_h = cram/misc.h cram/os.h +cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h htslib/khash.h htslib/kstring.h +cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h) +cram_structs_h = cram/cram_structs.h cram/thread_pool.h cram/string_alloc.h htslib/khash.h +cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h +hfile_internal_h = hfile_internal.h $(htslib_hfile_h) + +bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) htslib/khash.h +kstring.o kstring.pico: kstring.c htslib/kstring.h +knetfile.o knetfile.pico: knetfile.c htslib/knetfile.h +hfile.o hfile.pico: hfile.c $(htslib_hfile_h) $(hfile_internal_h) +hfile_net.o hfile_net.pico: hfile_net.c $(hfile_internal_h) htslib/knetfile.h +hts.o hts.pico: hts.c version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) htslib/khash.h htslib/kseq.h htslib/ksort.h +vcf.o vcf.pico: vcf.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) htslib/khash.h htslib/kseq.h htslib/kstring.h +sam.o sam.pico: sam.c $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) htslib/khash.h htslib/kseq.h htslib/kstring.h +tbx.o tbx.pico: tbx.c $(htslib_tbx_h) $(htslib_bgzf_h) htslib/khash.h +faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) htslib/khash.h htslib/knetfile.h +synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c $(htslib_synced_bcf_reader_h) htslib/kseq.h htslib/khash_str2int.h +vcf_sweep.o vcf_sweep.pico: vcf_sweep.c $(htslib_vcf_sweep_h) $(htslib_bgzf_h) +vcfutils.o vcfutils.pico: vcfutils.c $(htslib_vcfutils_h) +kfunc.o kfunc.pico: kfunc.c htslib/kfunc.h + +cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c $(cram_h) +cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c $(cram_h) cram/os.h cram/md5.h +cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c $(cram_h) cram/os.h cram/md5.h +cram/cram_index.o cram/cram_index.pico: cram/cram_index.c $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h +cram/cram_io.o cram/cram_io.pico: cram/cram_io.c $(cram_h) cram/os.h cram/md5.h $(cram_open_trace_file_h) $(htslib_hfile_h) +cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c $(cram_h) $(htslib_sam_h) +cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c $(cram_h) cram/os.h +cram/files.o cram/files.pico: cram/files.c $(cram_misc_h) +cram/mFILE.o cram/mFILE.pico: cram/mFILE.c cram/os.h cram/mFILE.h cram/vlen.h +cram/md5.o cram/md5.pico: cram/md5.c cram/md5.h +cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c $(cram_open_trace_file_h) $(cram_misc_h) +cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c cram/pooled_alloc.h +cram/sam_header.o cram/sam_header.pico: cram/sam_header.c $(cram_sam_header_h) cram/string_alloc.h +cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c cram/string_alloc.h +cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c cram/thread_pool.h +cram/vlen.o cram/vlen.pico: cram/vlen.c cram/vlen.h cram/os.h +cram/zfio.o cram/zfio.pico: cram/zfio.c cram/os.h cram/zfio.h + + +bgzip: bgzip.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a $(LDLIBS) -lz + +tabix: tabix.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a $(LDLIBS) -lz + +bgzip.o: bgzip.c $(htslib_bgzf_h) $(htslib_hts_h) +tabix.o: tabix.c $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) htslib/kseq.h $(htslib_bgzf_h) $(htslib_hts_h) + + +check test: $(BUILT_TEST_PROGRAMS) + test/fieldarith test/fieldarith.sam + test/hfile + test/sam + cd test && ./test_view.pl + cd test && ./test.pl + +test/fieldarith: test/fieldarith.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a $(LDLIBS) -lz + +test/hfile: test/hfile.o libhts.a + $(CC) $(LDFLAGS) -o $@ test/hfile.o libhts.a $(LDLIBS) -lz + +test/sam: test/sam.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a $(LDLIBS) -lz + +test/test_view: test/test_view.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a $(LDLIBS) -lz + +test/test-vcf-api: test/test-vcf-api.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a $(LDLIBS) -lz + +test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a $(LDLIBS) -lz + +test/fieldarith.o: test/fieldarith.c $(htslib_sam_h) +test/hfile.o: test/hfile.c $(htslib_hfile_h) $(htslib_hts_defs_h) +test/sam.o: test/sam.c $(htslib_sam_h) htslib/kstring.h +test/test_view.o: test/test_view.c $(cram_h) $(htslib_sam_h) +test/test-vcf-api.o: test/test-vcf-api.c $(htslib_hts_h) $(htslib_vcf_h) htslib/kstring.h +test/test-vcf-sweep.o: test/test-vcf-sweep.c $(htslib_vcf_sweep_h) + + +install: installdirs install-$(SHLIB_FLAVOUR) + $(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir) + $(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib + $(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a + $(INSTALL_DATA) *.1 $(DESTDIR)$(man1dir) + $(INSTALL_DATA) *.5 $(DESTDIR)$(man5dir) + +installdirs: + mkdir -p $(DESTDIR)$(bindir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) + +# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z, +# with symlinks libhts.so (used via -lhts during linking of client programs) +# and libhts.so.NN (used by client executables at runtime). + +install-so: libhts.so installdirs + $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION) + ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so + ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION) + +install-dylib: libhts.dylib installdirs + $(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib + ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib + ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib + + +testclean: + -rm -f test/*.tmp test/*.tmp.* + +mostlyclean: testclean + -rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h + +clean: mostlyclean clean-$(SHLIB_FLAVOUR) + -rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS) + +distclean: clean + -rm -f TAGS + +clean-so: + -rm -f libhts.so libhts.so.* + +clean-dylib: + -rm -f libhts.dylib libhts.*.dylib + + +tags: + ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h + + +force: + + +.PHONY: all check clean distclean force install installdirs +.PHONY: lib-shared lib-static mostlyclean tags test testclean +.PHONY: clean-so install-so +.PHONY: clean-dylib install-dylib diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/README.md b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/README.md new file mode 100644 index 0000000000000000000000000000000000000000..4afb1123c5e0f17de366da7846d8bdb070305405 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/README.md @@ -0,0 +1,17 @@ +HTSlib is an implementation of a unified C library for accessing common file +formats, such as [SAM, CRAM and VCF][1], used for high-throughput sequencing +data, and is the core library used by [samtools][2] and [bcftools][3]. +HTSlib only depends on [zlib][4]. +It is known to be compatible with gcc, g++ and clang. + +HTSlib implements a generalized BAM index, with file extension `.csi` +(coordinate-sorted index). The HTSlib file reader first looks for the new index +and then for the old if the new index is absent. + +This project also includes the popular tabix indexer, which indexes both `.tbi` +and `.csi` formats, and the bgzip compression utility. + +[1]: http://samtools.github.io/hts-specs/ +[2]: http://samtools.github.io/bcftools/ +[3]: http://github.com/samtools/samtools +[4]: http://zlib.net/ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/README.nvbio b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/README.nvbio new file mode 100644 index 0000000000000000000000000000000000000000..8d154e1ed46cfd77a8e3a767450a0b0a8d81ff16 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/README.nvbio @@ -0,0 +1,7 @@ +htslib source obtained from: +https://github.com/samtools/htslib.git +commit 049f877de780bf72c4b12a7d9f05b6ae984715be + +note that the 'test' subdirectory in htslib was removed due to file name +conflicts with perforce + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/bgzf.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/bgzf.c new file mode 100644 index 0000000000000000000000000000000000000000..ec64111b69d849b17fde8b450d411021b240ac6a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/bgzf.c @@ -0,0 +1,1086 @@ +/* The MIT License + + Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology + 2011 Attractive Chaos + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + THE SOFTWARE. +*/ + +#include "config.h" + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "htslib/hts.h" +#include "htslib/bgzf.h" +#include "htslib/hfile.h" + +#define BLOCK_HEADER_LENGTH 18 +#define BLOCK_FOOTER_LENGTH 8 + + +/* BGZF/GZIP header (speciallized from RFC 1952; little endian): + +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+ + | 31|139| 8| 4| 0| 0|255| 6| 66| 67| 2|BLK_LEN| + +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+ + BGZF extension: + ^ ^ ^ ^ + | | | | + FLG.EXTRA XLEN B C + + BGZF format is compatible with GZIP. It limits the size of each compressed + block to 2^16 bytes and adds and an extra "BC" field in the gzip header which + records the size. + +*/ +static const uint8_t g_magic[19] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\0\0"; + +#ifdef BGZF_CACHE +typedef struct { + int size; + uint8_t *block; + int64_t end_offset; +} cache_t; +#include "htslib/khash.h" +KHASH_MAP_INIT_INT64(cache, cache_t) +#endif + +typedef struct +{ + uint64_t uaddr; // offset w.r.t. uncompressed data + uint64_t caddr; // offset w.r.t. compressed data +} +bgzidx1_t; + +struct __bgzidx_t +{ + int noffs, moffs; // the size of the index, n:used, m:allocated + bgzidx1_t *offs; // offsets + uint64_t ublock_addr; // offset of the current block (uncompressed data) +}; + +void bgzf_index_destroy(BGZF *fp); +int bgzf_index_add_block(BGZF *fp); + +static inline void packInt16(uint8_t *buffer, uint16_t value) +{ + buffer[0] = value; + buffer[1] = value >> 8; +} + +static inline int unpackInt16(const uint8_t *buffer) +{ + return buffer[0] | buffer[1] << 8; +} + +static inline void packInt32(uint8_t *buffer, uint32_t value) +{ + buffer[0] = value; + buffer[1] = value >> 8; + buffer[2] = value >> 16; + buffer[3] = value >> 24; +} + +static BGZF *bgzf_read_init(hFILE *hfpr) +{ + BGZF *fp; + uint8_t magic[2]; + ssize_t n = hpeek(hfpr, magic, 2); + if (n < 0) return NULL; + + fp = (BGZF*)calloc(1, sizeof(BGZF)); + if (fp == NULL) return NULL; + + fp->is_write = 0; + fp->is_compressed = (n==2 && magic[0]==0x1f && magic[1]==0x8b); + fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE); + fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE); +#ifdef BGZF_CACHE + fp->cache = kh_init(cache); +#endif + return fp; +} + +static BGZF *bgzf_write_init(int compress_level) // compress_level==-1 for the default level, -2 plain uncompressed +{ + BGZF *fp; + fp = (BGZF*)calloc(1, sizeof(BGZF)); + fp->is_write = 1; + if ( compress_level==-2 ) + { + fp->is_compressed = 0; + return fp; + } + fp->is_compressed = 1; + fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE); + fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE); + fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1 + if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION; + return fp; +} +// get the compress level from the mode string +static int mode2level(const char *__restrict mode) +{ + int i, compress_level = -1; + for (i = 0; mode[i]; ++i) + if (mode[i] >= '0' && mode[i] <= '9') break; + if (mode[i]) compress_level = (int)mode[i] - '0'; + if (strchr(mode, 'u')) compress_level = -2; + return compress_level; +} + +BGZF *bgzf_open(const char *path, const char *mode) +{ + BGZF *fp = 0; + assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE); + if (strchr(mode, 'r')) { + hFILE *fpr; + if ((fpr = hopen(path, mode)) == 0) return 0; + fp = bgzf_read_init(fpr); + if (fp == 0) { hclose_abruptly(fpr); return NULL; } + fp->fp = fpr; + } else if (strchr(mode, 'w') || strchr(mode, 'a')) { + hFILE *fpw; + if ((fpw = hopen(path, mode)) == 0) return 0; + fp = bgzf_write_init(mode2level(mode)); + fp->fp = fpw; + } + else { errno = EINVAL; return 0; } + + fp->is_be = ed_is_big(); + return fp; +} + +BGZF *bgzf_dopen(int fd, const char *mode) +{ + BGZF *fp = 0; + assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE); + if (strchr(mode, 'r')) { + hFILE *fpr; + if ((fpr = hdopen(fd, mode)) == 0) return 0; + fp = bgzf_read_init(fpr); + if (fp == 0) { hclose_abruptly(fpr); return NULL; } // FIXME this closes fd + fp->fp = fpr; + } else if (strchr(mode, 'w') || strchr(mode, 'a')) { + hFILE *fpw; + if ((fpw = hdopen(fd, mode)) == 0) return 0; + fp = bgzf_write_init(mode2level(mode)); + fp->fp = fpw; + } + else { errno = EINVAL; return 0; } + + fp->is_be = ed_is_big(); + return fp; +} + +BGZF *bgzf_hopen(hFILE *hfp, const char *mode) +{ + BGZF *fp = NULL; + assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE); + if (strchr(mode, 'r')) { + fp = bgzf_read_init(hfp); + if (fp == NULL) return NULL; + } else if (strchr(mode, 'w') || strchr(mode, 'a')) { + fp = bgzf_write_init(mode2level(mode)); + } + else { errno = EINVAL; return 0; } + + fp->fp = hfp; + fp->is_be = ed_is_big(); + return fp; +} + +static int bgzf_compress(void *_dst, int *dlen, void *src, int slen, int level) +{ + uint32_t crc; + z_stream zs; + uint8_t *dst = (uint8_t*)_dst; + + // compress the body + zs.zalloc = NULL; zs.zfree = NULL; + zs.next_in = (Bytef*)src; + zs.avail_in = slen; + zs.next_out = dst + BLOCK_HEADER_LENGTH; + zs.avail_out = *dlen - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH; + if (deflateInit2(&zs, level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY) != Z_OK) return -1; // -15 to disable zlib header/footer + if (deflate(&zs, Z_FINISH) != Z_STREAM_END) return -1; + if (deflateEnd(&zs) != Z_OK) return -1; + *dlen = zs.total_out + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH; + // write the header + memcpy(dst, g_magic, BLOCK_HEADER_LENGTH); // the last two bytes are a place holder for the length of the block + packInt16(&dst[16], *dlen - 1); // write the compressed length; -1 to fit 2 bytes + // write the footer + crc = crc32(crc32(0L, NULL, 0L), (Bytef*)src, slen); + packInt32((uint8_t*)&dst[*dlen - 8], crc); + packInt32((uint8_t*)&dst[*dlen - 4], slen); + return 0; +} + +// Deflate the block in fp->uncompressed_block into fp->compressed_block. Also adds an extra field that stores the compressed block length. +static int deflate_block(BGZF *fp, int block_length) +{ + int comp_size = BGZF_MAX_BLOCK_SIZE; + if (bgzf_compress(fp->compressed_block, &comp_size, fp->uncompressed_block, block_length, fp->compress_level) != 0) { + fp->errcode |= BGZF_ERR_ZLIB; + return -1; + } + fp->block_offset = 0; + return comp_size; +} + +// Inflate the block in fp->compressed_block into fp->uncompressed_block +static int inflate_block(BGZF* fp, int block_length) +{ + z_stream zs; + zs.zalloc = NULL; + zs.zfree = NULL; + zs.next_in = (Bytef*)fp->compressed_block + 18; + zs.avail_in = block_length - 16; + zs.next_out = (Bytef*)fp->uncompressed_block; + zs.avail_out = BGZF_MAX_BLOCK_SIZE; + + if (inflateInit2(&zs, -15) != Z_OK) { + fp->errcode |= BGZF_ERR_ZLIB; + return -1; + } + if (inflate(&zs, Z_FINISH) != Z_STREAM_END) { + inflateEnd(&zs); + fp->errcode |= BGZF_ERR_ZLIB; + return -1; + } + if (inflateEnd(&zs) != Z_OK) { + fp->errcode |= BGZF_ERR_ZLIB; + return -1; + } + return zs.total_out; +} + +static int inflate_gzip_block(BGZF *fp, int cached) +{ + int ret = Z_OK; + do + { + if ( !cached && fp->gz_stream->avail_out!=0 ) + { + fp->gz_stream->avail_in = hread(fp->fp, fp->compressed_block, BGZF_BLOCK_SIZE); + if ( fp->gz_stream->avail_in<=0 ) return fp->gz_stream->avail_in; + if ( fp->gz_stream->avail_in==0 ) break; + fp->gz_stream->next_in = fp->compressed_block; + } + else cached = 0; + do + { + fp->gz_stream->next_out = (Bytef*)fp->uncompressed_block + fp->block_offset; + fp->gz_stream->avail_out = BGZF_MAX_BLOCK_SIZE - fp->block_offset; + ret = inflate(fp->gz_stream, Z_NO_FLUSH); + if ( ret==Z_BUF_ERROR ) continue; // non-critical error + if ( ret<0 ) return -1; + unsigned int have = BGZF_MAX_BLOCK_SIZE - fp->gz_stream->avail_out; + if ( have ) return have; + } + while ( fp->gz_stream->avail_out == 0 ); + } + while (ret != Z_STREAM_END); + return BGZF_MAX_BLOCK_SIZE - fp->gz_stream->avail_out; +} + +// Returns: 0 on success (BGZF header); -1 on non-BGZF GZIP header; -2 on error +static int check_header(const uint8_t *header) +{ + if ( header[0] != 31 || header[1] != 139 || header[2] != 8 ) return -2; + return ((header[3] & 4) != 0 + && unpackInt16((uint8_t*)&header[10]) == 6 + && header[12] == 'B' && header[13] == 'C' + && unpackInt16((uint8_t*)&header[14]) == 2) ? 0 : -1; +} + +#ifdef BGZF_CACHE +static void free_cache(BGZF *fp) +{ + khint_t k; + khash_t(cache) *h = (khash_t(cache)*)fp->cache; + if (fp->is_write) return; + for (k = kh_begin(h); k < kh_end(h); ++k) + if (kh_exist(h, k)) free(kh_val(h, k).block); + kh_destroy(cache, h); +} + +static int load_block_from_cache(BGZF *fp, int64_t block_address) +{ + khint_t k; + cache_t *p; + khash_t(cache) *h = (khash_t(cache)*)fp->cache; + k = kh_get(cache, h, block_address); + if (k == kh_end(h)) return 0; + p = &kh_val(h, k); + if (fp->block_length != 0) fp->block_offset = 0; + fp->block_address = block_address; + fp->block_length = p->size; + memcpy(fp->uncompressed_block, p->block, BGZF_MAX_BLOCK_SIZE); + if ( hseek(fp->fp, p->end_offset, SEEK_SET) < 0 ) + { + // todo: move the error up + fprintf(stderr,"Could not hseek to %"PRId64"\n", p->end_offset); + exit(1); + } + return p->size; +} + +static void cache_block(BGZF *fp, int size) +{ + int ret; + khint_t k; + cache_t *p; + khash_t(cache) *h = (khash_t(cache)*)fp->cache; + if (BGZF_MAX_BLOCK_SIZE >= fp->cache_size) return; + if ((kh_size(h) + 1) * BGZF_MAX_BLOCK_SIZE > (uint32_t)fp->cache_size) { + /* A better way would be to remove the oldest block in the + * cache, but here we remove a random one for simplicity. This + * should not have a big impact on performance. */ + for (k = kh_begin(h); k < kh_end(h); ++k) + if (kh_exist(h, k)) break; + if (k < kh_end(h)) { + free(kh_val(h, k).block); + kh_del(cache, h, k); + } + } + k = kh_put(cache, h, fp->block_address, &ret); + if (ret == 0) return; // if this happens, a bug! + p = &kh_val(h, k); + p->size = fp->block_length; + p->end_offset = fp->block_address + size; + p->block = (uint8_t*)malloc(BGZF_MAX_BLOCK_SIZE); + memcpy(kh_val(h, k).block, fp->uncompressed_block, BGZF_MAX_BLOCK_SIZE); +} +#else +static void free_cache(BGZF *fp) {} +static int load_block_from_cache(BGZF *fp, int64_t block_address) {return 0;} +static void cache_block(BGZF *fp, int size) {} +#endif + +int bgzf_read_block(BGZF *fp) +{ + uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block; + int count, size = 0, block_length, remaining; + + // Reading an uncompressed file + if ( !fp->is_compressed ) + { + count = hread(fp->fp, fp->uncompressed_block, BGZF_MAX_BLOCK_SIZE); + if ( count==0 ) + { + fp->block_length = 0; + return 0; + } + if (fp->block_length != 0) fp->block_offset = 0; + fp->block_address += count; + fp->block_length = count; + return 0; + } + + // Reading compressed file + int64_t block_address; + block_address = htell(fp->fp); + if ( fp->is_gzip ) + { + count = inflate_gzip_block(fp, 0); + if ( count<0 ) + { + fp->errcode |= BGZF_ERR_ZLIB; + return -1; + } + fp->block_length = count; + fp->block_address = block_address; + return 0; + } + if (fp->cache_size && load_block_from_cache(fp, block_address)) return 0; + count = hread(fp->fp, header, sizeof(header)); + if (count == 0) { // no data read + fp->block_length = 0; + return 0; + } + int ret; + if ( count != sizeof(header) || (ret=check_header(header))==-2 ) + { + fp->errcode |= BGZF_ERR_HEADER; + return -1; + } + if ( ret==-1 ) + { + // GZIP, not BGZF + uint8_t *cblock = (uint8_t*)fp->compressed_block; + memcpy(cblock, header, sizeof(header)); + count = hread(fp->fp, cblock+sizeof(header), BGZF_BLOCK_SIZE - sizeof(header)) + sizeof(header); + int nskip = 10; + + // Check optional fields to skip: FLG.FNAME,FLG.FCOMMENT,FLG.FHCRC,FLG.FEXTRA + // Note: Some of these fields are untested, I did not have appropriate data available + if ( header[3] & 0x4 ) // FLG.FEXTRA + { + nskip += unpackInt16(&cblock[nskip]) + 2; + } + if ( header[3] & 0x8 ) // FLG.FNAME + { + while ( nskiperrcode |= BGZF_ERR_HEADER; + return -1; + } + nskip++; + } + if ( header[3] & 0x10 ) // FLG.FCOMMENT + { + while ( nskiperrcode |= BGZF_ERR_HEADER; + return -1; + } + nskip++; + } + if ( header[3] & 0x2 ) nskip += 2; // FLG.FHCRC + + fp->is_gzip = 1; + fp->gz_stream = (z_stream*) calloc(1,sizeof(z_stream)); + int ret = inflateInit2(fp->gz_stream, -15); + if (ret != Z_OK) + { + fp->errcode |= BGZF_ERR_ZLIB; + return -1; + } + fp->gz_stream->avail_in = count - nskip; + fp->gz_stream->next_in = cblock + nskip; + count = inflate_gzip_block(fp, 1); + if ( count<0 ) + { + fp->errcode |= BGZF_ERR_ZLIB; + return -1; + } + fp->block_length = count; + fp->block_address = block_address; + return 0; + } + size = count; + block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1" + compressed_block = (uint8_t*)fp->compressed_block; + memcpy(compressed_block, header, BLOCK_HEADER_LENGTH); + remaining = block_length - BLOCK_HEADER_LENGTH; + count = hread(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining); + if (count != remaining) { + fp->errcode |= BGZF_ERR_IO; + return -1; + } + size += count; + if ((count = inflate_block(fp, block_length)) < 0) return -1; + if (fp->block_length != 0) fp->block_offset = 0; // Do not reset offset if this read follows a seek. + fp->block_address = block_address; + fp->block_length = count; + if ( fp->idx_build_otf ) + { + bgzf_index_add_block(fp); + fp->idx->ublock_addr += count; + } + cache_block(fp, size); + return 0; +} + +ssize_t bgzf_read(BGZF *fp, void *data, size_t length) +{ + ssize_t bytes_read = 0; + uint8_t *output = (uint8_t*)data; + if (length <= 0) return 0; + assert(fp->is_write == 0); + while (bytes_read < length) { + int copy_length, available = fp->block_length - fp->block_offset; + uint8_t *buffer; + if (available <= 0) { + if (bgzf_read_block(fp) != 0) return -1; + available = fp->block_length - fp->block_offset; + if (available <= 0) break; + } + copy_length = length - bytes_read < available? length - bytes_read : available; + buffer = (uint8_t*)fp->uncompressed_block; + memcpy(output, buffer + fp->block_offset, copy_length); + fp->block_offset += copy_length; + output += copy_length; + bytes_read += copy_length; + } + if (fp->block_offset == fp->block_length) { + fp->block_address = htell(fp->fp); + fp->block_offset = fp->block_length = 0; + } + fp->uncompressed_address += bytes_read; + return bytes_read; +} + +ssize_t bgzf_raw_read(BGZF *fp, void *data, size_t length) +{ + return hread(fp->fp, data, length); +} + +#ifdef BGZF_MT + +typedef struct { + struct bgzf_mtaux_t *mt; + void *buf; + int i, errcode, toproc, compress_level; +} worker_t; + +typedef struct bgzf_mtaux_t { + int n_threads, n_blks, curr, done; + volatile int proc_cnt; + void **blk; + int *len; + worker_t *w; + pthread_t *tid; + pthread_mutex_t lock; + pthread_cond_t cv; +} mtaux_t; + +static int worker_aux(worker_t *w) +{ + int i, stop = 0; + // wait for condition: to process or all done + pthread_mutex_lock(&w->mt->lock); + while (!w->toproc && !w->mt->done) + pthread_cond_wait(&w->mt->cv, &w->mt->lock); + if (w->mt->done) stop = 1; + w->toproc = 0; + pthread_mutex_unlock(&w->mt->lock); + if (stop) return 1; // to quit the thread + w->errcode = 0; + for (i = w->i; i < w->mt->curr; i += w->mt->n_threads) { + int clen = BGZF_MAX_BLOCK_SIZE; + if (bgzf_compress(w->buf, &clen, w->mt->blk[i], w->mt->len[i], w->compress_level) != 0) + w->errcode |= BGZF_ERR_ZLIB; + memcpy(w->mt->blk[i], w->buf, clen); + w->mt->len[i] = clen; + } + __sync_fetch_and_add(&w->mt->proc_cnt, 1); + return 0; +} + +static void *mt_worker(void *data) +{ + while (worker_aux((worker_t*)data) == 0); + return 0; +} + +int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks) +{ + int i; + mtaux_t *mt; + pthread_attr_t attr; + if (!fp->is_write || fp->mt || n_threads <= 1) return -1; + mt = (mtaux_t*)calloc(1, sizeof(mtaux_t)); + mt->n_threads = n_threads; + mt->n_blks = n_threads * n_sub_blks; + mt->len = (int*)calloc(mt->n_blks, sizeof(int)); + mt->blk = (void**)calloc(mt->n_blks, sizeof(void*)); + for (i = 0; i < mt->n_blks; ++i) + mt->blk[i] = malloc(BGZF_MAX_BLOCK_SIZE); + mt->tid = (pthread_t*)calloc(mt->n_threads, sizeof(pthread_t)); // tid[0] is not used, as the worker 0 is launched by the master + mt->w = (worker_t*)calloc(mt->n_threads, sizeof(worker_t)); + for (i = 0; i < mt->n_threads; ++i) { + mt->w[i].i = i; + mt->w[i].mt = mt; + mt->w[i].compress_level = fp->compress_level; + mt->w[i].buf = malloc(BGZF_MAX_BLOCK_SIZE); + } + pthread_attr_init(&attr); + pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE); + pthread_mutex_init(&mt->lock, 0); + pthread_cond_init(&mt->cv, 0); + for (i = 1; i < mt->n_threads; ++i) // worker 0 is effectively launched by the master thread + pthread_create(&mt->tid[i], &attr, mt_worker, &mt->w[i]); + fp->mt = mt; + return 0; +} + +static void mt_destroy(mtaux_t *mt) +{ + int i; + // signal all workers to quit + pthread_mutex_lock(&mt->lock); + mt->done = 1; mt->proc_cnt = 0; + pthread_cond_broadcast(&mt->cv); + pthread_mutex_unlock(&mt->lock); + for (i = 1; i < mt->n_threads; ++i) pthread_join(mt->tid[i], 0); // worker 0 is effectively launched by the master thread + // free other data allocated on heap + for (i = 0; i < mt->n_blks; ++i) free(mt->blk[i]); + for (i = 0; i < mt->n_threads; ++i) free(mt->w[i].buf); + free(mt->blk); free(mt->len); free(mt->w); free(mt->tid); + pthread_cond_destroy(&mt->cv); + pthread_mutex_destroy(&mt->lock); + free(mt); +} + +static void mt_queue(BGZF *fp) +{ + mtaux_t *mt = fp->mt; + assert(mt->curr < mt->n_blks); // guaranteed by the caller + memcpy(mt->blk[mt->curr], fp->uncompressed_block, fp->block_offset); + mt->len[mt->curr] = fp->block_offset; + fp->block_offset = 0; + ++mt->curr; +} + +static int mt_flush_queue(BGZF *fp) +{ + int i; + mtaux_t *mt = fp->mt; + // signal all the workers to compress + pthread_mutex_lock(&mt->lock); + for (i = 0; i < mt->n_threads; ++i) mt->w[i].toproc = 1; + mt->proc_cnt = 0; + pthread_cond_broadcast(&mt->cv); + pthread_mutex_unlock(&mt->lock); + // worker 0 is doing things here + worker_aux(&mt->w[0]); + // wait for all the threads to complete + while (mt->proc_cnt < mt->n_threads); + // dump data to disk + for (i = 0; i < mt->n_threads; ++i) fp->errcode |= mt->w[i].errcode; + for (i = 0; i < mt->curr; ++i) + if (hwrite(fp->fp, mt->blk[i], mt->len[i]) != mt->len[i]) { + fp->errcode |= BGZF_ERR_IO; + break; + } + mt->curr = 0; + return (fp->errcode == 0)? 0 : -1; +} + +static int lazy_flush(BGZF *fp) +{ + if (fp->mt) { + if (fp->block_offset) mt_queue(fp); + return (fp->mt->curr < fp->mt->n_blks)? 0 : mt_flush_queue(fp); + } + else return bgzf_flush(fp); +} + +#else // ~ #ifdef BGZF_MT + +int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks) +{ + return 0; +} + +static inline int lazy_flush(BGZF *fp) +{ + return bgzf_flush(fp); +} + +#endif // ~ #ifdef BGZF_MT + +int bgzf_flush(BGZF *fp) +{ + if (!fp->is_write) return 0; +#ifdef BGZF_MT + if (fp->mt) { + if (fp->block_offset) mt_queue(fp); // guaranteed that assertion does not fail + return mt_flush_queue(fp); + } +#endif + while (fp->block_offset > 0) { + if ( fp->idx_build_otf ) + { + bgzf_index_add_block(fp); + fp->idx->ublock_addr += fp->block_offset; + } + int block_length = deflate_block(fp, fp->block_offset); + if (block_length < 0) return -1; + if (hwrite(fp->fp, fp->compressed_block, block_length) != block_length) { + fp->errcode |= BGZF_ERR_IO; // possibly truncated file + return -1; + } + fp->block_address += block_length; + } + return 0; +} + +int bgzf_flush_try(BGZF *fp, ssize_t size) +{ + if (fp->block_offset + size > BGZF_BLOCK_SIZE) return lazy_flush(fp); + return 0; +} + +ssize_t bgzf_write(BGZF *fp, const void *data, size_t length) +{ + if ( !fp->is_compressed ) + return hwrite(fp->fp, data, length); + + const uint8_t *input = (const uint8_t*)data; + ssize_t remaining = length; + assert(fp->is_write); + while (remaining > 0) { + uint8_t* buffer = (uint8_t*)fp->uncompressed_block; + int copy_length = BGZF_BLOCK_SIZE - fp->block_offset; + if (copy_length > remaining) copy_length = remaining; + memcpy(buffer + fp->block_offset, input, copy_length); + fp->block_offset += copy_length; + input += copy_length; + remaining -= copy_length; + if (fp->block_offset == BGZF_BLOCK_SIZE) { + if (lazy_flush(fp) != 0) return -1; + } + } + return length - remaining; +} + +ssize_t bgzf_raw_write(BGZF *fp, const void *data, size_t length) +{ + return hwrite(fp->fp, data, length); +} + +int bgzf_close(BGZF* fp) +{ + int ret, block_length; + if (fp == 0) return -1; + if (fp->is_write && fp->is_compressed) { + if (bgzf_flush(fp) != 0) return -1; + fp->compress_level = -1; + block_length = deflate_block(fp, 0); // write an empty block + if (hwrite(fp->fp, fp->compressed_block, block_length) < 0 + || hflush(fp->fp) != 0) { + fp->errcode |= BGZF_ERR_IO; + return -1; + } +#ifdef BGZF_MT + if (fp->mt) mt_destroy(fp->mt); +#endif + } + if ( fp->is_gzip ) + { + (void)inflateEnd(fp->gz_stream); + free(fp->gz_stream); + } + ret = hclose(fp->fp); + if (ret != 0) return -1; + bgzf_index_destroy(fp); + free(fp->uncompressed_block); + free(fp->compressed_block); + free_cache(fp); + free(fp); + return 0; +} + +void bgzf_set_cache_size(BGZF *fp, int cache_size) +{ + if (fp) fp->cache_size = cache_size; +} + +int bgzf_check_EOF(BGZF *fp) +{ + uint8_t buf[28]; + off_t offset = htell(fp->fp); + if (hseek(fp->fp, -28, SEEK_END) < 0) { + if (errno == ESPIPE) { hclearerr(fp->fp); return 2; } + else return -1; + } + if ( hread(fp->fp, buf, 28) != 28 ) return -1; + if ( hseek(fp->fp, offset, SEEK_SET) < 0 ) return -1; + return (memcmp("\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0", buf, 28) == 0)? 1 : 0; +} + +int64_t bgzf_seek(BGZF* fp, int64_t pos, int where) +{ + int block_offset; + int64_t block_address; + + if (fp->is_write || where != SEEK_SET) { + fp->errcode |= BGZF_ERR_MISUSE; + return -1; + } + block_offset = pos & 0xFFFF; + block_address = pos >> 16; + if (hseek(fp->fp, block_address, SEEK_SET) < 0) { + fp->errcode |= BGZF_ERR_IO; + return -1; + } + fp->block_length = 0; // indicates current block has not been loaded + fp->block_address = block_address << 16; + fp->block_offset = block_offset; + return 0; +} + +int bgzf_is_bgzf(const char *fn) +{ + uint8_t buf[16]; + int n; + hFILE *fp; + if ((fp = hopen(fn, "r")) == 0) return 0; + n = hread(fp, buf, 16); + if ( hclose(fp) < 0 ) return -1; + if (n != 16) return 0; + return memcmp(g_magic, buf, 16) == 0? 1 : 0; +} + +int bgzf_getc(BGZF *fp) +{ + int c; + if (fp->block_offset >= fp->block_length) { + if (bgzf_read_block(fp) != 0) return -2; /* error */ + if (fp->block_length == 0) return -1; /* end-of-file */ + } + c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++]; + if (fp->block_offset == fp->block_length) { + fp->block_address = htell(fp->fp); + fp->block_offset = 0; + fp->block_length = 0; + } + fp->uncompressed_address++; + return c; +} + +#ifndef kroundup32 +#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) +#endif + +int bgzf_getline(BGZF *fp, int delim, kstring_t *str) +{ + int l, state = 0; + unsigned char *buf = (unsigned char*)fp->uncompressed_block; + str->l = 0; + do { + if (fp->block_offset >= fp->block_length) { + if (bgzf_read_block(fp) != 0) { state = -2; break; } + if (fp->block_length == 0) { state = -1; break; } + } + for (l = fp->block_offset; l < fp->block_length && buf[l] != delim; ++l); + if (l < fp->block_length) state = 1; + l -= fp->block_offset; + if (str->l + l + 1 >= str->m) { + str->m = str->l + l + 2; + kroundup32(str->m); + str->s = (char*)realloc(str->s, str->m); + } + memcpy(str->s + str->l, buf + fp->block_offset, l); + str->l += l; + fp->block_offset += l + 1; + if (fp->block_offset >= fp->block_length) { + fp->block_address = htell(fp->fp); + fp->block_offset = 0; + fp->block_length = 0; + } + } while (state == 0); + if (str->l == 0 && state < 0) return state; + fp->uncompressed_address += str->l; + str->s[str->l] = 0; + return str->l; +} + +void bgzf_index_destroy(BGZF *fp) +{ + if ( !fp->idx ) return; + free(fp->idx->offs); + free(fp->idx); + fp->idx = NULL; + fp->idx_build_otf = 0; +} + +int bgzf_index_build_init(BGZF *fp) +{ + bgzf_index_destroy(fp); + fp->idx = (bgzidx_t*) calloc(1,sizeof(bgzidx_t)); + if ( !fp->idx ) return -1; + fp->idx_build_otf = 1; // build index on the fly + return 0; +} + +int bgzf_index_add_block(BGZF *fp) +{ + fp->idx->noffs++; + if ( fp->idx->noffs > fp->idx->moffs ) + { + fp->idx->moffs = fp->idx->noffs; + kroundup32(fp->idx->moffs); + fp->idx->offs = (bgzidx1_t*) realloc(fp->idx->offs, fp->idx->moffs*sizeof(bgzidx1_t)); + if ( !fp->idx->offs ) return -1; + } + fp->idx->offs[ fp->idx->noffs-1 ].uaddr = fp->idx->ublock_addr; + fp->idx->offs[ fp->idx->noffs-1 ].caddr = fp->block_address; + return 0; +} + +int bgzf_index_dump(BGZF *fp, const char *bname, const char *suffix) +{ + if (bgzf_flush(fp) != 0) return -1; + + assert(fp->idx); + char *tmp = NULL; + if ( suffix ) + { + int blen = strlen(bname); + int slen = strlen(suffix); + tmp = (char*) malloc(blen + slen + 1); + if ( !tmp ) return -1; + memcpy(tmp,bname,blen); + memcpy(tmp+blen,suffix,slen+1); + } + + FILE *idx = fopen(tmp?tmp:bname,"wb"); + if ( tmp ) free(tmp); + if ( !idx ) return -1; + + // Note that the index contains one extra record when indexing files opened + // for reading. The terminating record is not present when opened for writing. + // This is not a bug. + + int i; + if ( fp->is_be ) + { + uint64_t x = fp->idx->noffs - 1; + fwrite(ed_swap_8p(&x), 1, sizeof(x), idx); + for (i=1; iidx->noffs; i++) + { + x = fp->idx->offs[i].caddr; fwrite(ed_swap_8p(&x), 1, sizeof(x), idx); + x = fp->idx->offs[i].uaddr; fwrite(ed_swap_8p(&x), 1, sizeof(x), idx); + } + } + else + { + uint64_t x = fp->idx->noffs - 1; + fwrite(&x, 1, sizeof(x), idx); + for (i=1; iidx->noffs; i++) + { + fwrite(&fp->idx->offs[i].caddr, 1, sizeof(fp->idx->offs[i].caddr), idx); + fwrite(&fp->idx->offs[i].uaddr, 1, sizeof(fp->idx->offs[i].uaddr), idx); + } + } + fclose(idx); + return 0; +} + + +int bgzf_index_load(BGZF *fp, const char *bname, const char *suffix) +{ + char *tmp = NULL; + if ( suffix ) + { + int blen = strlen(bname); + int slen = strlen(suffix); + tmp = (char*) malloc(blen + slen + 1); + if ( !tmp ) return -1; + memcpy(tmp,bname,blen); + memcpy(tmp+blen,suffix,slen+1); + } + + FILE *idx = fopen(tmp?tmp:bname,"rb"); + if ( tmp ) free(tmp); + if ( !idx ) return -1; + + fp->idx = (bgzidx_t*) calloc(1,sizeof(bgzidx_t)); + uint64_t x; + if ( fread(&x, 1, sizeof(x), idx) != sizeof(x) ) return -1; + + fp->idx->noffs = fp->idx->moffs = 1 + (fp->is_be ? ed_swap_8(x) : x); + fp->idx->offs = (bgzidx1_t*) malloc(fp->idx->moffs*sizeof(bgzidx1_t)); + fp->idx->offs[0].caddr = fp->idx->offs[0].uaddr = 0; + + int i; + if ( fp->is_be ) + { + int ret = 0; + for (i=1; iidx->noffs; i++) + { + ret += fread(&x, 1, sizeof(x), idx); fp->idx->offs[i].caddr = ed_swap_8(x); + ret += fread(&x, 1, sizeof(x), idx); fp->idx->offs[i].uaddr = ed_swap_8(x); + } + if ( ret != sizeof(x)*2*(fp->idx->noffs-1) ) return -1; + } + else + { + int ret = 0; + for (i=1; iidx->noffs; i++) + { + ret += fread(&x, 1, sizeof(x), idx); fp->idx->offs[i].caddr = x; + ret += fread(&x, 1, sizeof(x), idx); fp->idx->offs[i].uaddr = x; + } + if ( ret != sizeof(x)*2*(fp->idx->noffs-1) ) return -1; + } + fclose(idx); + return 0; + +} + +int bgzf_useek(BGZF *fp, long uoffset, int where) +{ + if ( !fp->is_compressed ) + { + if (hseek(fp->fp, uoffset, SEEK_SET) < 0) + { + fp->errcode |= BGZF_ERR_IO; + return -1; + } + fp->block_length = 0; // indicates current block has not been loaded + fp->block_address = uoffset; + fp->block_offset = 0; + bgzf_read_block(fp); + fp->uncompressed_address = uoffset; + return 0; + } + + if ( !fp->idx ) + { + fp->errcode |= BGZF_ERR_IO; + return -1; + } + + // binary search + int ilo = 0, ihi = fp->idx->noffs - 1; + while ( ilo<=ihi ) + { + int i = (ilo+ihi)*0.5; + if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1; + else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1; + else break; + } + int i = ilo-1; + if (hseek(fp->fp, fp->idx->offs[i].caddr, SEEK_SET) < 0) + { + fp->errcode |= BGZF_ERR_IO; + return -1; + } + fp->block_length = 0; // indicates current block has not been loaded + fp->block_address = fp->idx->offs[i].caddr; + fp->block_offset = 0; + if ( bgzf_read_block(fp) < 0 ) return -1; + if ( uoffset - fp->idx->offs[i].uaddr > 0 ) + { + fp->block_offset = uoffset - fp->idx->offs[i].uaddr; + assert( fp->block_offset <= fp->block_length ); // todo: skipped, unindexed, blocks + } + fp->uncompressed_address = uoffset; + return 0; +} + +long bgzf_utell(BGZF *fp) +{ + return fp->uncompressed_address; // currently maintained only when reading +} + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/bgzip.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/bgzip.c new file mode 100644 index 0000000000000000000000000000000000000000..bcd81f8cd8e7f24a2b4bf8fdde99b69c6d04cea1 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/bgzip.c @@ -0,0 +1,283 @@ +/* The MIT License + + Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + THE SOFTWARE. +*/ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include "htslib/bgzf.h" +#include "htslib/hts.h" + +static const int WINDOW_SIZE = 64 * 1024; + +static void error(const char *format, ...) +{ + va_list ap; + va_start(ap, format); + vfprintf(stderr, format, ap); + va_end(ap); + exit(EXIT_FAILURE); +} + +static int write_open(const char *fn, int is_forced) +{ + int fd = -1; + char c; + if (!is_forced) { + if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) { + fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn); + if ( scanf("%c", &c) != 1 ) c = 'n'; + if (c != 'Y' && c != 'y') { + fprintf(stderr, "[bgzip] not overwritten\n"); + exit(EXIT_FAILURE); + } + } + } + if (fd < 0) { + if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) { + fprintf(stderr, "[bgzip] %s: Fail to write\n", fn); + exit(EXIT_FAILURE); + } + } + return fd; +} + +static int bgzip_main_usage(void) +{ + fprintf(stderr, "\n"); + fprintf(stderr, "Version: %s\n", hts_version()); + fprintf(stderr, "Usage: bgzip [OPTIONS] [FILE] ...\n"); + fprintf(stderr, "Options:\n"); + fprintf(stderr, " -b, --offset INT decompress at virtual file pointer (0-based uncompressed offset)\n"); + fprintf(stderr, " -c, --stdout write on standard output, keep original files unchanged\n"); + fprintf(stderr, " -d, --decompress decompress\n"); + fprintf(stderr, " -f, --force overwrite files without asking\n"); + fprintf(stderr, " -h, --help give this help\n"); + fprintf(stderr, " -i, --index compress and create BGZF index\n"); + fprintf(stderr, " -I, --index-name FILE name of BGZF index file [file.gz.gzi]\n"); + fprintf(stderr, " -r, --reindex (re)index compressed file\n"); + fprintf(stderr, " -s, --size INT decompress INT bytes (uncompressed size)\n"); + fprintf(stderr, "\n"); + return 1; +} + +int main(int argc, char **argv) +{ + int c, compress, pstdout, is_forced, index = 0, reindex = 0; + BGZF *fp; + void *buffer; + long start, end, size; + char *index_fname = NULL; + + static struct option loptions[] = + { + {"help",0,0,'h'}, + {"offset",1,0,'b'}, + {"stdout",0,0,'c'}, + {"decompress",0,0,'d'}, + {"force",0,0,'f'}, + {"index",0,0,'i'}, + {"index-name",1,0,'I'}, + {"reindex",0,0,'r'}, + {"size",1,0,'s'}, + {0,0,0,0} + }; + + compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0; + while((c = getopt_long(argc, argv, "cdh?fb:s:iI:r",loptions,NULL)) >= 0){ + switch(c){ + case 'd': compress = 0; break; + case 'c': pstdout = 1; break; + case 'b': start = atol(optarg); compress = 0; pstdout = 1; break; + case 's': size = atol(optarg); pstdout = 1; break; + case 'f': is_forced = 1; break; + case 'i': index = 1; break; + case 'I': index_fname = optarg; break; + case 'r': reindex = 1; compress = 0; break; + case 'h': + case '?': return bgzip_main_usage(); + } + } + if (size >= 0) end = start + size; + if (end >= 0 && end < start) { + fprintf(stderr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end); + return 1; + } + if (compress == 1) { + struct stat sbuf; + int f_src = fileno(stdin); + int f_dst = fileno(stdout); + + if ( argc>optind ) + { + if ( stat(argv[optind],&sbuf)<0 ) + { + fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); + return 1; + } + + if ((f_src = open(argv[optind], O_RDONLY)) < 0) { + fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); + return 1; + } + + if (pstdout) + f_dst = fileno(stdout); + else + { + char *name = malloc(strlen(argv[optind]) + 5); + strcpy(name, argv[optind]); + strcat(name, ".gz"); + f_dst = write_open(name, is_forced); + if (f_dst < 0) return 1; + free(name); + } + } + else if (!pstdout && isatty(fileno((FILE *)stdout)) ) + return bgzip_main_usage(); + else if ( index && !index_fname ) + { + fprintf(stderr, "[bgzip] Index file name expected when writing to stdout\n"); + return 1; + } + + fp = bgzf_fdopen(f_dst, "w"); + if ( index ) bgzf_index_build_init(fp); + buffer = malloc(WINDOW_SIZE); + while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0) + if (bgzf_write(fp, buffer, c) < 0) error("Could not write %d bytes: Error %d\n", c, fp->errcode); + // f_dst will be closed here + if ( index ) + { + if ( index_fname ) bgzf_index_dump(fp, index_fname, NULL); + else bgzf_index_dump(fp, argv[optind], ".gz.gzi"); + } + if (bgzf_close(fp) < 0) error("Close failed: Error %d", fp->errcode); + if (argc > optind && !pstdout) unlink(argv[optind]); + free(buffer); + close(f_src); + return 0; + } + else if ( reindex ) + { + if ( argc>optind ) + { + fp = bgzf_open(argv[optind], "r"); + if ( !fp ) error("[bgzip] Could not open file: %s\n", argv[optind]); + } + else + { + if ( !index_fname ) error("[bgzip] Index file name expected when reading from stdin\n"); + fp = bgzf_fdopen(fileno(stdin), "r"); + if ( !fp ) error("[bgzip] Could not read from stdin: %s\n", strerror(errno)); + } + + buffer = malloc(BGZF_BLOCK_SIZE); + bgzf_index_build_init(fp); + int ret; + while ( (ret=bgzf_read(fp, buffer, BGZF_BLOCK_SIZE))>0 ) ; + free(buffer); + if ( ret<0 ) error("Is the file gzipped or bgzipped? The latter is required for indexing.\n"); + + if ( index_fname ) + bgzf_index_dump(fp, index_fname, NULL); + else + bgzf_index_dump(fp, argv[optind], ".gzi"); + + if ( bgzf_close(fp)<0 ) error("Close failed: Error %d\n",fp->errcode); + return 0; + } + else + { + struct stat sbuf; + int f_dst; + + if ( argc>optind ) + { + if ( stat(argv[optind],&sbuf)<0 ) + { + fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); + return 1; + } + char *name; + int len = strlen(argv[optind]); + if ( strcmp(argv[optind]+len-3,".gz") ) + { + fprintf(stderr, "[bgzip] %s: unknown suffix -- ignored\n", argv[optind]); + return 1; + } + fp = bgzf_open(argv[optind], "r"); + if (fp == NULL) { + fprintf(stderr, "[bgzip] Could not open file: %s\n", argv[optind]); + return 1; + } + + if (pstdout) { + f_dst = fileno(stdout); + } + else { + name = strdup(argv[optind]); + name[strlen(name) - 3] = '\0'; + f_dst = write_open(name, is_forced); + free(name); + } + } + else if (!pstdout && isatty(fileno((FILE *)stdin)) ) + return bgzip_main_usage(); + else + { + f_dst = fileno(stdout); + fp = bgzf_fdopen(fileno(stdin), "r"); + if (fp == NULL) { + fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno)); + return 1; + } + } + buffer = malloc(WINDOW_SIZE); + if ( start>0 ) + { + if ( bgzf_index_load(fp, argv[optind], ".gzi") < 0 ) error("Could not load index: %s.gzi\n", argv[optind]); + if ( bgzf_useek(fp, start, SEEK_SET) < 0 ) error("Could not seek to %d-th (uncompressd) byte\n", start); + } + while (1) { + if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE); + else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start)); + if (c == 0) break; + if (c < 0) error("Could not read %d bytes: Error %d\n", (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start), fp->errcode); + start += c; + if ( write(f_dst, buffer, c) != c ) error("Could not write %d bytes\n", c); + if (end >= 0 && start >= end) break; + } + free(buffer); + if (bgzf_close(fp) < 0) error("Close failed: Error %d\n",fp->errcode); + if (!pstdout) unlink(argv[optind]); + return 0; + } + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/config.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/config.h new file mode 100644 index 0000000000000000000000000000000000000000..6d32bf5fd0046c875b3424c30c6804187519e179 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/config.h @@ -0,0 +1,3 @@ +#define _USE_KNETFILE +#define BGZF_CACHE +#define BGZF_MT diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram.h new file mode 100644 index 0000000000000000000000000000000000000000..0b8b2916ddefd91c97176a7450c79e384c9c3444 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram.h @@ -0,0 +1,66 @@ +/* +Copyright (c) 2012-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +/*! \file + * CRAM interface. + * + * Consider using the higher level scram_*() API for programs that wish to + * be file format agnostic. + * + * This API should be used for CRAM specific code. The specifics of the + * public API are implemented in cram_io.h, cram_encode.h and cram_decode.h + * although these should not be included directly (use this file instead). + */ + +#ifdef __cplusplus +extern "C" { +#endif + +#ifdef SAMTOOLS +# include "cram/cram_samtools.h" +#endif + +#ifndef _CRAM_H_ +#define _CRAM_H_ + +#include "cram/sam_header.h" +#include "cram_structs.h" +#include "cram_io.h" +#include "cram_encode.h" +#include "cram_decode.h" +#include "cram_stats.h" +#include "cram_codecs.h" +#include "cram_index.h" + +#endif + +#ifdef __cplusplus +} +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_codecs.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_codecs.c new file mode 100644 index 0000000000000000000000000000000000000000..3c3d13f9763811704524192e4e11517f21827954 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_codecs.c @@ -0,0 +1,1764 @@ +/* +Copyright (c) 2012-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +/* + * FIXME: add checking of cram_external_type to return NULL on unsupported + * {codec,type} tuples. + */ + +#ifdef HAVE_CONFIG_H +#include "io_lib_config.h" +#endif + +#include +#include +#include +#include + +#include "cram/cram.h" + +static char *codec2str(enum cram_encoding codec) { + switch (codec) { + case E_NULL: return "NULL"; + case E_EXTERNAL: return "EXTERNAL"; + case E_GOLOMB: return "GOLOMB"; + case E_HUFFMAN: return "HUFFMAN"; + case E_BYTE_ARRAY_LEN: return "BYTE_ARRAY_LEN"; + case E_BYTE_ARRAY_STOP: return "BYTE_ARRAY_STOP"; + case E_BETA: return "BETA"; + case E_SUBEXP: return "SUBEXP"; + case E_GOLOMB_RICE: return "GOLOMB_RICE"; + case E_GAMMA: return "GAMMA"; + } + + return "(unknown)"; +} + +/* + * --------------------------------------------------------------------------- + * Block bit-level I/O functions. + * All defined static here to promote easy inlining by the compiler. + */ + +#if 0 +/* Get a single bit, MSB first */ +static signed int get_bit_MSB(cram_block *block) { + unsigned int val; + + if (block->byte > block->alloc) + return -1; + + val = block->data[block->byte] >> block->bit; + if (--block->bit == -1) { + block->bit = 7; + block->byte++; + //printf("(%02X)", block->data[block->byte]); + } + + //printf("-B%d-", val&1); + + return val & 1; +} +#endif + +/* + * Count number of successive 0 and 1 bits + */ +static int get_one_bits_MSB(cram_block *block) { + int n = 0, b; + do { + b = block->data[block->byte] >> block->bit; + if (--block->bit == -1) { + block->bit = 7; + block->byte++; + } + n++; + } while (b&1); + + return n-1; +} + +static int get_zero_bits_MSB(cram_block *block) { + int n = 0, b; + do { + b = block->data[block->byte] >> block->bit; + if (--block->bit == -1) { + block->bit = 7; + block->byte++; + } + n++; + } while (!(b&1)); + + return n-1; +} + +#if 0 +/* Stores a single bit */ +static void store_bit_MSB(cram_block *block, unsigned int bit) { + if (block->byte >= block->alloc) { + block->alloc = block->alloc ? block->alloc*2 : 1024; + block->data = realloc(block->data, block->alloc); + } + + if (bit) + block->data[block->byte] |= (1 << block->bit); + + if (--block->bit == -1) { + block->bit = 7; + block->byte++; + block->data[block->byte] = 0; + } +} +#endif + +#if 0 +/* Rounds to the next whole byte boundary first */ +static void store_bytes_MSB(cram_block *block, char *bytes, int len) { + if (block->bit != 7) { + block->bit = 7; + block->byte++; + } + + while (block->byte + len >= block->alloc) { + block->alloc = block->alloc ? block->alloc*2 : 1024; + block->data = realloc(block->data, block->alloc); + } + + memcpy(&block->data[block->byte], bytes, len); + block->byte += len; +} +#endif + +/* Local optimised copy for inlining */ +static inline unsigned int get_bits_MSB(cram_block *block, int nbits) { + unsigned int val = 0; + int i; + +#if 0 + // Fits within the current byte */ + if (nbits <= block->bit+1) { + val = (block->data[block->byte]>>(block->bit-(nbits-1))) & ((1<bit -= nbits) == -1) { + block->bit = 7; + block->byte++; + } + return val; + } + + // partial first byte + val = block->data[block->byte] & ((1<<(block->bit+1))-1); + nbits -= block->bit+1; + block->bit = 7; + block->byte++; + + // whole middle bytes + while (nbits >= 8) { + val = (val << 8) | block->data[block->byte++]; + nbits -= 8; + } + + val <<= nbits; + val |= (block->data[block->byte]>>(block->bit-(nbits-1))) & ((1<bit -= nbits; + return val; +#endif + +#if 0 + /* Inefficient implementation! */ + //printf("{"); + for (i = 0; i < nbits; i++) + //val = (val << 1) | get_bit_MSB(block); + GET_BIT_MSB(block, val); +#endif + +#if 1 + /* Combination of 1st two methods */ + if (nbits <= block->bit+1) { + val = (block->data[block->byte]>>(block->bit-(nbits-1))) & ((1<bit -= nbits) == -1) { + block->bit = 7; + block->byte++; + } + return val; + } + + switch(nbits) { +// case 15: GET_BIT_MSB(block, val); +// case 14: GET_BIT_MSB(block, val); +// case 13: GET_BIT_MSB(block, val); +// case 12: GET_BIT_MSB(block, val); +// case 11: GET_BIT_MSB(block, val); +// case 10: GET_BIT_MSB(block, val); +// case 9: GET_BIT_MSB(block, val); + case 8: GET_BIT_MSB(block, val); + case 7: GET_BIT_MSB(block, val); + case 6: GET_BIT_MSB(block, val); + case 5: GET_BIT_MSB(block, val); + case 4: GET_BIT_MSB(block, val); + case 3: GET_BIT_MSB(block, val); + case 2: GET_BIT_MSB(block, val); + case 1: GET_BIT_MSB(block, val); + break; + + default: + for (i = 0; i < nbits; i++) + //val = (val << 1) | get_bit_MSB(block); + GET_BIT_MSB(block, val); + } +#endif + + //printf("=0x%x}", val); + + return val; +} + +/* + * Can store up to 24-bits worth of data encoded in an integer value + * Possibly we'd want to have a less optimal store_bits function when dealing + * with nbits > 24, but for now we assume the codes generated are never + * that big. (Given this is only possible with 121392 or more + * characters with exactly the correct frequency distribution we check + * for it elsewhere.) + */ +static int store_bits_MSB(cram_block *block, unsigned int val, int nbits) { + /* fprintf(stderr, " store_bits: %02x %d\n", val, nbits); */ + + /* + * Use slow mode until we tweak the huffman generator to never generate + * codes longer than 24-bits. + */ + unsigned int mask; + + if (block->byte+4 >= block->alloc) { + if (block->byte) { + block->alloc *= 2; + block->data = realloc(block->data, block->alloc + 4); + if (!block->data) + return -1; + } else { + block->alloc = 1024; + block->data = realloc(block->data, block->alloc + 4); + if (!block->data) + return -1; + block->data[0] = 0; // initialise first byte of buffer + } + } + + + + if (nbits <= block->bit+1) { + block->data[block->byte] |= (val << (block->bit+1-nbits)); + if ((block->bit-=nbits) == -1) { + block->bit = 7; + block->byte++; + block->data[block->byte] = 0; + } + return 0; + } + + block->data[block->byte] |= (val >> (nbits -= block->bit+1)); + block->bit = 7; + block->byte++; + block->data[block->byte] = 0; + + mask = 1<<(nbits-1); + do { + if (val & mask) + block->data[block->byte] |= (1 << block->bit); + if (--block->bit == -1) { + block->bit = 7; + block->byte++; + block->data[block->byte] = 0; + } + mask >>= 1; + } while(--nbits); + + return 0; +} + +/* + * Returns the next 'size' bytes from a block, or NULL if insufficient + * data left.This is just a pointer into the block data and not an + * allocated object, so do not free the result. + */ +static char *cram_extract_block(cram_block *b, int size) { + char *cp = (char *)b->data + b->idx; + b->idx += size; + if (b->idx > b->uncomp_size) + return NULL; + + return cp; +} + +/* + * --------------------------------------------------------------------------- + * EXTERNAL + */ +int cram_external_decode_int(cram_slice *slice, cram_codec *c, + cram_block *in, char *out, int *out_size) { + int i; + char *cp; + cram_block *b = NULL; + + /* Find the external block */ + if (slice->block_by_id) { + if (!(b = slice->block_by_id[c->external.content_id])) + return -1; + } else { + for (i = 0; i < slice->hdr->num_blocks; i++) { + b = slice->block[i]; + if (b->content_type == EXTERNAL && + b->content_id == c->external.content_id) { + break; + } + } + if (i == slice->hdr->num_blocks || !b) + return -1; + } + + cp = (char *)b->data + b->idx; + // E_INT and E_LONG are guaranteed single item queries + b->idx += itf8_get(cp, (int32_t *)out); + *out_size = 1; + + return 0; +} + +int cram_external_decode_char(cram_slice *slice, cram_codec *c, + cram_block *in, char *out, + int *out_size) { + int i; + char *cp; + cram_block *b = NULL; + + /* Find the external block */ + if (slice->block_by_id) { + if (!(b = slice->block_by_id[c->external.content_id])) + return -1; + } else { + for (i = 0; i < slice->hdr->num_blocks; i++) { + b = slice->block[i]; + if (b->content_type == EXTERNAL && + b->content_id == c->external.content_id) { + break; + } + } + if (i == slice->hdr->num_blocks || !b) + return -1; + } + + cp = cram_extract_block(b, *out_size); + if (!cp) + return -1; + + memcpy(out, cp, *out_size); + return 0; +} + +int cram_external_decode_block(cram_slice *slice, cram_codec *c, + cram_block *in, char *out_, + int *out_size) { + int i; + char *cp; + cram_block *b = NULL; + cram_block *out = (cram_block *)out_; + + /* Find the external block */ + if (slice->block_by_id) { + if (!(b = slice->block_by_id[c->external.content_id])) + return -1; + } else { + for (i = 0; i < slice->hdr->num_blocks; i++) { + b = slice->block[i]; + if (b->content_type == EXTERNAL && + b->content_id == c->external.content_id) { + break; + } + } + if (i == slice->hdr->num_blocks || !b) + return -1; + } + + cp = cram_extract_block(b, *out_size); + if (!cp) + return -1; + + BLOCK_APPEND(out, cp, *out_size); + return 0; +} + +void cram_external_decode_free(cram_codec *c) { + if (c) + free(c); +} + +cram_codec *cram_external_decode_init(char *data, int size, + enum cram_external_type option, + int version) { + cram_codec *c; + char *cp = data; + + if (!(c = malloc(sizeof(*c)))) + return NULL; + + c->codec = E_EXTERNAL; + if (option == E_INT || option == E_LONG) + c->decode = cram_external_decode_int; + else if (option == E_BYTE_ARRAY || option == E_BYTE) + c->decode = cram_external_decode_char; + else + c->decode = cram_external_decode_block; + c->free = cram_external_decode_free; + + cp += itf8_get(cp, &c->external.content_id); + + if (cp - data != size) { + fprintf(stderr, "Malformed external header stream\n"); + free(c); + return NULL; + } + + c->external.type = option; + + return c; +} + +int cram_external_encode(cram_slice *slice, cram_codec *c, + cram_block *out, char *in, int in_size) { + uint32_t *i32 = (uint32_t *)in; + + itf8_put_blk(out, *i32); + return 0; +} + +void cram_external_encode_free(cram_codec *c) { + if (!c) + return; + free(c); +} + +int cram_external_encode_store(cram_codec *c, cram_block *b, char *prefix, + int version) { + char tmp[99], *tp = tmp; + int len = 0; + + if (prefix) { + size_t l = strlen(prefix); + BLOCK_APPEND(b, prefix, l); + len += l; + } + + tp += itf8_put(tp, c->e_external.content_id); + len += itf8_put_blk(b, c->codec); + len += itf8_put_blk(b, tp-tmp); + BLOCK_APPEND(b, tmp, tp-tmp); + len += tp-tmp; + + return len; +} + +cram_codec *cram_external_encode_init(cram_stats *st, + enum cram_external_type option, + void *dat, + int version) { + cram_codec *c; + + c = malloc(sizeof(*c)); + if (!c) + return NULL; + c->codec = E_EXTERNAL; + c->free = cram_external_encode_free; + c->encode = cram_external_encode; + c->store = cram_external_encode_store; + + c->e_external.content_id = (size_t)dat; + + return c; +} + +/* + * --------------------------------------------------------------------------- + * BETA + */ +int cram_beta_decode_int(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { + int32_t *out_i = (int32_t *)out; + int i, n; + + if (c->beta.nbits) { + for (i = 0, n = *out_size; i < n; i++) + out_i[i] = get_bits_MSB(in, c->beta.nbits) - c->beta.offset; + } else { + for (i = 0, n = *out_size; i < n; i++) + out_i[i] = 0; + } + + return 0; +} + +int cram_beta_decode_char(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { + int i, n; + + if (c->beta.nbits) { + for (i = 0, n = *out_size; i < n; i++) + out[i] = get_bits_MSB(in, c->beta.nbits) - c->beta.offset; + } else { + for (i = 0, n = *out_size; i < n; i++) + out[i] = 0; + } + + return 0; +} + +void cram_beta_decode_free(cram_codec *c) { + if (c) + free(c); +} + +cram_codec *cram_beta_decode_init(char *data, int size, + enum cram_external_type option, + int version) { + cram_codec *c; + char *cp = data; + + if (!(c = malloc(sizeof(*c)))) + return NULL; + + c->codec = E_BETA; + if (option == E_INT || option == E_LONG) + c->decode = cram_beta_decode_int; + else if (option == E_BYTE_ARRAY || option == E_BYTE) + c->decode = cram_beta_decode_char; + else + abort(); + c->free = cram_beta_decode_free; + + cp += itf8_get(cp, &c->beta.offset); + cp += itf8_get(cp, &c->beta.nbits); + + if (cp - data != size) { + fprintf(stderr, "Malformed beta header stream\n"); + free(c); + return NULL; + } + + return c; +} + +int cram_beta_encode_store(cram_codec *c, cram_block *b, + char *prefix, int version) { + int len = 0; + + if (prefix) { + size_t l = strlen(prefix); + BLOCK_APPEND(b, prefix, l); + len += l; + } + + len += itf8_put_blk(b, c->codec); + len += itf8_put_blk(b, itf8_size(c->e_beta.offset) + + itf8_size(c->e_beta.nbits)); // codec length + len += itf8_put_blk(b, c->e_beta.offset); + len += itf8_put_blk(b, c->e_beta.nbits); + + return len; +} + +int cram_beta_encode_int(cram_slice *slice, cram_codec *c, + cram_block *out, char *in, int in_size) { + int *syms = (int *)in; + int i, r = 0; + + for (i = 0; i < in_size; i++) + r |= store_bits_MSB(out, syms[i] + c->e_beta.offset, c->e_beta.nbits); + + return r; +} + +int cram_beta_encode_char(cram_slice *slice, cram_codec *c, + cram_block *out, char *in, int in_size) { + unsigned char *syms = (unsigned char *)in; + int i, r = 0; + + for (i = 0; i < in_size; i++) + r |= store_bits_MSB(out, syms[i] + c->e_beta.offset, c->e_beta.nbits); + + return r; +} + +void cram_beta_encode_free(cram_codec *c) { + if (c) free(c); +} + +cram_codec *cram_beta_encode_init(cram_stats *st, + enum cram_external_type option, + void *dat, + int version) { + cram_codec *c; + int min_val, max_val, len = 0; + + c = malloc(sizeof(*c)); + if (!c) + return NULL; + c->codec = E_BETA; + c->free = cram_beta_encode_free; + if (option == E_INT) + c->encode = cram_beta_encode_int; + else + c->encode = cram_beta_encode_char; + c->store = cram_beta_encode_store; + + if (dat) { + min_val = ((int *)dat)[0]; + max_val = ((int *)dat)[1]; + } else { + min_val = INT_MAX; + max_val = INT_MIN; + int i; + for (i = 0; i < MAX_STAT_VAL; i++) { + if (!st->freqs[i]) + continue; + if (min_val > i) + min_val = i; + max_val = i; + } + if (st->h) { + khint_t k; + + for (k = kh_begin(st->h); k != kh_end(st->h); k++) { + if (!kh_exist(st->h, k)) + continue; + + i = kh_key(st->h, k); + if (min_val > i) + min_val = i; + if (max_val < i) + max_val = i; + } + } + } + + assert(max_val >= min_val); + c->e_beta.offset = -min_val; + max_val -= min_val; + while (max_val) { + len++; + max_val >>= 1; + } + c->e_beta.nbits = len; + + return c; +} + +/* + * --------------------------------------------------------------------------- + * SUBEXP + */ +int cram_subexp_decode(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { + int32_t *out_i = (int32_t *)out; + int n, count; + int k = c->subexp.k; + + for (count = 0, n = *out_size; count < n; count++) { + int i = 0, tail; + int val; + + /* Get number of 1s */ + //while (get_bit_MSB(in) == 1) i++; + i = get_one_bits_MSB(in); + + /* + * Val is + * i > 0: 2^(k+i-1) + k+i-1 bits + * i = 0: k bits + */ + if (i) { + tail = i + k-1; + val = 0; + while (tail) { + //val = val<<1; val |= get_bit_MSB(in); + GET_BIT_MSB(in, val); + tail--; + } + val += 1 << (i + k-1); + } else { + tail = k; + val = 0; + while (tail) { + //val = val<<1; val |= get_bit_MSB(in); + GET_BIT_MSB(in, val); + tail--; + } + } + + out_i[count] = val - c->subexp.offset; + } + + return 0; +} + +void cram_subexp_decode_free(cram_codec *c) { + if (c) + free(c); +} + +cram_codec *cram_subexp_decode_init(char *data, int size, + enum cram_external_type option, + int version) { + cram_codec *c; + char *cp = data; + + if (!(c = malloc(sizeof(*c)))) + return NULL; + + c->codec = E_SUBEXP; + c->decode = cram_subexp_decode; + c->free = cram_subexp_decode_free; + + cp += itf8_get(cp, &c->subexp.offset); + cp += itf8_get(cp, &c->subexp.k); + + if (cp - data != size) { + fprintf(stderr, "Malformed subexp header stream\n"); + free(c); + return NULL; + } + + return c; +} + +/* + * --------------------------------------------------------------------------- + * GAMMA + */ +int cram_gamma_decode(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { + int32_t *out_i = (int32_t *)out; + int i, n; + + for (i = 0, n = *out_size; i < n; i++) { + int nz = 0; + int val; + //while (get_bit_MSB(in) == 0) nz++; + nz = get_zero_bits_MSB(in); + val = 1; + while (nz > 0) { + //val <<= 1; val |= get_bit_MSB(in); + GET_BIT_MSB(in, val); + nz--; + } + + out_i[i] = val - c->gamma.offset; + } + + return 0; +} + +void cram_gamma_decode_free(cram_codec *c) { + if (c) + free(c); +} + +cram_codec *cram_gamma_decode_init(char *data, int size, + enum cram_external_type option, + int version) { + cram_codec *c; + char *cp = data; + + if (!(c = malloc(sizeof(*c)))) + return NULL; + + c->codec = E_GAMMA; + c->decode = cram_gamma_decode; + c->free = cram_gamma_decode_free; + + cp += itf8_get(cp, &c->gamma.offset); + + if (cp - data != size) { + fprintf(stderr, "Malformed gamma header stream\n"); + free(c); + return NULL; + } + + return c; +} + +/* + * --------------------------------------------------------------------------- + * HUFFMAN + */ + +static int code_sort(const void *vp1, const void *vp2) { + const cram_huffman_code *c1 = (const cram_huffman_code *)vp1; + const cram_huffman_code *c2 = (const cram_huffman_code *)vp2; + + if (c1->len != c2->len) + return c1->len - c2->len; + else + return c1->symbol - c2->symbol; +} + +void cram_huffman_decode_free(cram_codec *c) { + if (!c) + return; + + if (c->huffman.codes) + free(c->huffman.codes); + free(c); +} + +int cram_huffman_decode_char0(cram_slice *slice, cram_codec *c, + cram_block *in, char *out, int *out_size) { + int i, n; + + /* Special case of 0 length codes */ + for (i = 0, n = *out_size; i < n; i++) { + out[i] = c->huffman.codes[0].symbol; + } + return 0; +} + +int cram_huffman_decode_char(cram_slice *slice, cram_codec *c, + cram_block *in, char *out, int *out_size) { + int i, n, ncodes = c->huffman.ncodes; + const cram_huffman_code * const codes = c->huffman.codes; + + for (i = 0, n = *out_size; i < n; i++) { + int idx = 0; + int val = 0, len = 0, last_len = 0; + + for (;;) { + int dlen = codes[idx].len - last_len; + if (dlen <= 0 || (in->alloc - in->byte)*8 + in->bit + 7 < dlen) + return -1; + + //val <<= dlen; + //val |= get_bits_MSB(in, dlen); + //last_len = (len += dlen); + + last_len = (len += dlen); + for (; dlen; dlen--) GET_BIT_MSB(in, val); + + idx = val - codes[idx].p; + if (idx >= ncodes || idx < 0) + return -1; + + if (codes[idx].code == val && codes[idx].len == len) { + out[i] = codes[idx].symbol; + break; + } + } + } + + return 0; +} + +int cram_huffman_decode_int0(cram_slice *slice, cram_codec *c, + cram_block *in, char *out, int *out_size) { + int32_t *out_i = (int32_t *)out; + int i, n; + const cram_huffman_code * const codes = c->huffman.codes; + + /* Special case of 0 length codes */ + for (i = 0, n = *out_size; i < n; i++) { + out_i[i] = codes[0].symbol; + } + return 0; +} + +int cram_huffman_decode_int(cram_slice *slice, cram_codec *c, + cram_block *in, char *out, int *out_size) { + int32_t *out_i = (int32_t *)out; + int i, n, ncodes = c->huffman.ncodes; + const cram_huffman_code * const codes = c->huffman.codes; + + for (i = 0, n = *out_size; i < n; i++) { + int idx = 0; + int val = 0, len = 0, last_len = 0; + + // Now one bit at a time for remaining checks + for (;;) { + int dlen = codes[idx].len - last_len; + if (dlen <= 0 || (in->alloc - in->byte)*8 + in->bit + 7 < dlen) + return -1; + + //val <<= dlen; + //val |= get_bits_MSB(in, dlen); + //last_len = (len += dlen); + + last_len = (len += dlen); + for (; dlen; dlen--) GET_BIT_MSB(in, val); + + idx = val - codes[idx].p; + if (idx >= ncodes || idx < 0) + return -1; + + if (codes[idx].code == val && codes[idx].len == len) { + out_i[i] = codes[idx].symbol; + break; + } + } + } + + return 0; +} + +/* + * Initialises a huffman decoder from an encoding data stream. + */ +cram_codec *cram_huffman_decode_init(char *data, int size, + enum cram_external_type option, + int version) { + int32_t ncodes, i, j; + char *cp = data, *data_end = &data[size]; + cram_codec *h; + cram_huffman_code *codes; + int32_t val, last_len, max_len = 0; + + cp += itf8_get(cp, &ncodes); + h = calloc(1, sizeof(*h)); + if (!h) + return NULL; + + h->free = cram_huffman_decode_free; + + h->huffman.ncodes = ncodes; + codes = h->huffman.codes = malloc(ncodes * sizeof(*codes)); + if (!codes) { + free(h); + return NULL; + } + + /* Read symbols and bit-lengths */ + for (i = 0; i < ncodes && cp < data_end; i++) { + cp += itf8_get(cp, &codes[i].symbol); + } + + if (cp >= data_end) { + fprintf(stderr, "Malformed huffman header stream\n"); + free(h); + return NULL; + } + cp += itf8_get(cp, &i); + if (i != ncodes) { + fprintf(stderr, "Malformed huffman header stream\n"); + free(h); + return NULL; + } + + if (ncodes == 0) { + /* NULL huffman stream */ + return h; + } + + for (i = 0; i < ncodes && cp < data_end; i++) { + cp += itf8_get(cp, &codes[i].len); + if (max_len < codes[i].len) + max_len = codes[i].len; + } + if (cp - data != size || max_len >= ncodes) { + fprintf(stderr, "Malformed huffman header stream\n"); + free(h); + return NULL; + } + + /* Sort by bit length and then by symbol value */ + qsort(codes, ncodes, sizeof(*codes), code_sort); + + /* Assign canonical codes */ + val = -1, last_len = 0; + for (i = 0; i < ncodes; i++) { + val++; + if (codes[i].len > last_len) { + while (codes[i].len > last_len) { + val <<= 1; + last_len++; + } + } + codes[i].code = val; + } + + /* + * Compute the next starting point, offset by the i'th value. + * For example if codes 10, 11, 12, 13 are 30, 31, 32, 33 then + * codes[10..13].p = 30 - 10. + */ + last_len = 0; + for (i = j = 0; i < ncodes; i++) { + if (codes[i].len > last_len) { + j = codes[i].code - i; + last_len = codes[i].len; + } + codes[i].p = j; + } + +// puts("==HUFF LEN=="); +// for (i = 0; i <= last_len+1; i++) { +// printf("len %d=%d prefix %d\n", i, h->huffman.lengths[i], h->huffman.prefix[i]); +// } +// puts("===HUFFMAN CODES==="); +// for (i = 0; i < ncodes; i++) { +// int j; +// printf("%d: %d %d %d ", i, codes[i].symbol, codes[i].len, codes[i].code); +// j = codes[i].len; +// while (j) { +// putchar(codes[i].code & (1 << --j) ? '1' : '0'); +// } +// printf(" %d\n", codes[i].code); +// } + + h->codec = E_HUFFMAN; + if (option == E_BYTE || option == E_BYTE_ARRAY) { + if (h->huffman.codes[0].len == 0) + h->decode = cram_huffman_decode_char0; + else + h->decode = cram_huffman_decode_char; + } else if (option == E_BYTE_ARRAY_BLOCK) { + abort(); + } else { + if (h->huffman.codes[0].len == 0) + h->decode = cram_huffman_decode_int0; + else + h->decode = cram_huffman_decode_int; + } + + return (cram_codec *)h; +} + +int cram_huffman_encode_char0(cram_slice *slice, cram_codec *c, + cram_block *out, char *in, int in_size) { + return 0; +} + +int cram_huffman_encode_char(cram_slice *slice, cram_codec *c, + cram_block *out, char *in, int in_size) { + int i, code, len, r = 0; + unsigned char *syms = (unsigned char *)in; + + do { + int sym = *syms++; + if (sym >= -1 && sym < MAX_HUFF) { + i = c->e_huffman.val2code[sym+1]; + assert(c->e_huffman.codes[i].symbol == sym); + code = c->e_huffman.codes[i].code; + len = c->e_huffman.codes[i].len; + } else { + /* Slow - use a lookup table for when sym < MAX_HUFF? */ + for (i = 0; i < c->e_huffman.nvals; i++) { + if (c->e_huffman.codes[i].symbol == sym) + break; + } + if (i == c->e_huffman.nvals) + return -1; + + code = c->e_huffman.codes[i].code; + len = c->e_huffman.codes[i].len; + } + + r |= store_bits_MSB(out, code, len); + } while (--in_size); + + return r; +} + +int cram_huffman_encode_int0(cram_slice *slice, cram_codec *c, + cram_block *out, char *in, int in_size) { + return 0; +} + +int cram_huffman_encode_int(cram_slice *slice, cram_codec *c, + cram_block *out, char *in, int in_size) { + int i, code, len, r = 0; + int *syms = (int *)in; + + do { + int sym = *syms++; + + if (sym >= -1 && sym < MAX_HUFF) { + i = c->e_huffman.val2code[sym+1]; + assert(c->e_huffman.codes[i].symbol == sym); + code = c->e_huffman.codes[i].code; + len = c->e_huffman.codes[i].len; + } else { + /* Slow - use a lookup table for when sym < MAX_HUFFMAN_SYM? */ + for (i = 0; i < c->e_huffman.nvals; i++) { + if (c->e_huffman.codes[i].symbol == sym) + break; + } + if (i == c->e_huffman.nvals) + return -1; + + code = c->e_huffman.codes[i].code; + len = c->e_huffman.codes[i].len; + } + + r |= store_bits_MSB(out, code, len); + } while (--in_size); + + return r; +} + +void cram_huffman_encode_free(cram_codec *c) { + if (!c) + return; + + if (c->e_huffman.codes) + free(c->e_huffman.codes); + free(c); +} + +/* + * Encodes a huffman tree. + * Returns number of bytes written. + */ +int cram_huffman_encode_store(cram_codec *c, cram_block *b, char *prefix, + int version) { + int i, len = 0; + cram_huffman_code *codes = c->e_huffman.codes; + /* + * Up to code length 127 means 2.5e+26 bytes of data required (worst + * case huffman tree needs symbols with freqs matching the Fibonacci + * series). So guaranteed 1 byte per code. + * + * Symbols themselves could be 5 bytes (eg -1 is 5 bytes in itf8). + * + * Therefore 6*ncodes + 5 + 5 + 1 + 5 is max memory + */ + char *tmp = malloc(6*c->e_huffman.nvals+16); + char *tp = tmp; + + if (!tmp) + return -1; + + if (prefix) { + size_t l = strlen(prefix); + BLOCK_APPEND(b, prefix, l); + len += l; + } + + tp += itf8_put(tp, c->e_huffman.nvals); + for (i = 0; i < c->e_huffman.nvals; i++) { + tp += itf8_put(tp, codes[i].symbol); + } + + tp += itf8_put(tp, c->e_huffman.nvals); + for (i = 0; i < c->e_huffman.nvals; i++) { + tp += itf8_put(tp, codes[i].len); + } + + len += itf8_put_blk(b, c->codec); + len += itf8_put_blk(b, tp-tmp); + BLOCK_APPEND(b, tmp, tp-tmp); + len += tp-tmp; + + free(tmp); + + return len; +} + +cram_codec *cram_huffman_encode_init(cram_stats *st, + enum cram_external_type option, + void *dat, + int version) { + int *vals = NULL, *freqs = NULL, vals_alloc = 0, *lens, code, len; + int nvals, i, ntot = 0, max_val = 0, min_val = INT_MAX, k; + cram_codec *c; + cram_huffman_code *codes; + + c = malloc(sizeof(*c)); + if (!c) + return NULL; + c->codec = E_HUFFMAN; + + /* Count number of unique symbols */ + for (nvals = i = 0; i < MAX_STAT_VAL; i++) { + if (!st->freqs[i]) + continue; + if (nvals >= vals_alloc) { + vals_alloc = vals_alloc ? vals_alloc*2 : 1024; + vals = realloc(vals, vals_alloc * sizeof(int)); + freqs = realloc(freqs, vals_alloc * sizeof(int)); + if (!vals || !freqs) { + if (vals) free(vals); + if (freqs) free(freqs); + free(c); + return NULL; + } + } + vals[nvals] = i; + freqs[nvals] = st->freqs[i]; + assert(st->freqs[i] > 0); + ntot += freqs[nvals]; + if (max_val < i) max_val = i; + if (min_val > i) min_val = i; + nvals++; + } + if (st->h) { + khint_t k; + + for (k = kh_begin(st->h); k != kh_end(st->h); k++) { + if (!kh_exist(st->h, k)) + continue; + if (nvals >= vals_alloc) { + vals_alloc = vals_alloc ? vals_alloc*2 : 1024; + vals = realloc(vals, vals_alloc * sizeof(int)); + freqs = realloc(freqs, vals_alloc * sizeof(int)); + if (!vals || !freqs) + return NULL; + } + vals[nvals]= kh_key(st->h, k); + freqs[nvals] = kh_val(st->h, k); + assert(freqs[nvals] > 0); + ntot += freqs[nvals]; + if (max_val < i) max_val = i; + if (min_val > i) min_val = i; + nvals++; + } + } + + assert(nvals > 0); + + freqs = realloc(freqs, 2*nvals*sizeof(*freqs)); + lens = calloc(2*nvals, sizeof(*lens)); + if (!lens || !freqs) + return NULL; + + /* Inefficient, use pointers to form chain so we can insert and maintain + * a sorted list? This is currently O(nvals^2) complexity. + */ + for (;;) { + int low1 = INT_MAX, low2 = INT_MAX; + int ind1 = 0, ind2 = 0; + for (i = 0; i < nvals; i++) { + if (freqs[i] < 0) + continue; + if (low1 > freqs[i]) + low2 = low1, ind2 = ind1, low1 = freqs[i], ind1 = i; + else if (low2 > freqs[i]) + low2 = freqs[i], ind2 = i; + } + if (low2 == INT_MAX) + break; + + freqs[nvals] = low1 + low2; + lens[ind1] = nvals; + lens[ind2] = nvals; + freqs[ind1] *= -1; + freqs[ind2] *= -1; + nvals++; + } + nvals = nvals/2+1; + + /* Assign lengths */ + for (i = 0; i < nvals; i++) { + int code_len = 0; + for (k = lens[i]; k; k = lens[k]) + code_len++; + lens[i] = code_len; + freqs[i] *= -1; + //fprintf(stderr, "%d / %d => %d\n", vals[i], freqs[i], lens[i]); + } + + + /* Sort, need in a struct */ + if (!(codes = malloc(nvals * sizeof(*codes)))) + return NULL; + for (i = 0; i < nvals; i++) { + codes[i].symbol = vals[i]; + codes[i].len = lens[i]; + } + qsort(codes, nvals, sizeof(*codes), code_sort); + + /* + * Generate canonical codes from lengths. + * Sort by length. + * Start with 0. + * Every new code of same length is +1. + * Every new code of new length is +1 then <<1 per extra length. + * + * /\ + * a/\ + * /\/\ + * bcd/\ + * ef + * + * a 1 0 + * b 3 4 (0+1)<<2 + * c 3 5 + * d 3 6 + * e 4 14 (6+1)<<1 + * f 5 15 + */ + code = 0; len = codes[0].len; + for (i = 0; i < nvals; i++) { + while (len != codes[i].len) { + code<<=1; + len++; + } + codes[i].code = code++; + + if (codes[i].symbol >= -1 && codes[i].symbol < MAX_HUFF) + c->e_huffman.val2code[codes[i].symbol+1] = i; + + //fprintf(stderr, "sym %d, code %d, len %d\n", + // codes[i].symbol, codes[i].code, codes[i].len); + } + + free(lens); + free(vals); + free(freqs); + + c->e_huffman.codes = codes; + c->e_huffman.nvals = nvals; + + c->free = cram_huffman_encode_free; + if (option == E_BYTE || option == E_BYTE_ARRAY) { + if (c->e_huffman.codes[0].len == 0) + c->encode = cram_huffman_encode_char0; + else + c->encode = cram_huffman_encode_char; + } else { + if (c->e_huffman.codes[0].len == 0) + c->encode = cram_huffman_encode_int0; + else + c->encode = cram_huffman_encode_int; + } + c->store = cram_huffman_encode_store; + + return c; +} + +/* + * --------------------------------------------------------------------------- + * BYTE_ARRAY_LEN + */ +int cram_byte_array_len_decode(cram_slice *slice, cram_codec *c, + cram_block *in, char *out, + int *out_size) { + /* Fetch length */ + int32_t len, one = 1; + + c->byte_array_len.len_codec->decode(slice, c->byte_array_len.len_codec, in, (char *)&len, &one); + //printf("ByteArray Len=%d\n", len); + + if (c->byte_array_len.value_codec) { + c->byte_array_len.value_codec->decode(slice, + c->byte_array_len.value_codec, + in, out, &len); + } else { + return -1; + } + + *out_size = len; + + return 0; +} + +void cram_byte_array_len_decode_free(cram_codec *c) { + if (!c) return; + + if (c->byte_array_len.len_codec) + c->byte_array_len.len_codec->free(c->byte_array_len.len_codec); + + if (c->byte_array_len.value_codec) + c->byte_array_len.value_codec->free(c->byte_array_len.value_codec); + + free(c); +} + +cram_codec *cram_byte_array_len_decode_init(char *data, int size, + enum cram_external_type option, + int version) { + cram_codec *c; + char *cp = data; + int32_t encoding; + int32_t sub_size; + + if (!(c = malloc(sizeof(*c)))) + return NULL; + + c->codec = E_BYTE_ARRAY_LEN; + c->decode = cram_byte_array_len_decode; + c->free = cram_byte_array_len_decode_free; + + cp += itf8_get(cp, &encoding); + cp += itf8_get(cp, &sub_size); + c->byte_array_len.len_codec = cram_decoder_init(encoding, cp, sub_size, + E_INT, version); + cp += sub_size; + + cp += itf8_get(cp, &encoding); + cp += itf8_get(cp, &sub_size); + c->byte_array_len.value_codec = cram_decoder_init(encoding, cp, sub_size, + option, version); + cp += sub_size; + + if (cp - data != size) { + fprintf(stderr, "Malformed byte_array_len header stream\n"); + free(c); + return NULL; + } + + return c; +} + +int cram_byte_array_len_encode(cram_slice *slice, cram_codec *c, + cram_block *out, char *in, int in_size) { + return -1; // not imp. +} + +void cram_byte_array_len_encode_free(cram_codec *c) { + if (!c) + return; + free(c); +} + +int cram_byte_array_len_encode_store(cram_codec *c, cram_block *b, + char *prefix, int version) { + int len = 0; + + if (prefix) { + size_t l = strlen(prefix); + BLOCK_APPEND(b, prefix, l); + len += l; + } + + len += itf8_put_blk(b, c->codec); + len += itf8_put_blk(b, c->e_byte_array_len.len_len + + c->e_byte_array_len.val_len); + BLOCK_APPEND(b, c->e_byte_array_len.len_dat, c->e_byte_array_len.len_len); + len += c->e_byte_array_len.len_len; + + BLOCK_APPEND(b, c->e_byte_array_len.val_dat, c->e_byte_array_len.val_len); + len += c->e_byte_array_len.val_len; + + return len; +} + +cram_codec *cram_byte_array_len_encode_init(cram_stats *st, + enum cram_external_type option, + void *dat, + int version) { + cram_codec *c; + cram_byte_array_len_encoder *e = (cram_byte_array_len_encoder *)dat; + + c = malloc(sizeof(*c)); + if (!c) + return NULL; + c->codec = E_BYTE_ARRAY_LEN; + c->free = cram_byte_array_len_encode_free; + c->encode = cram_byte_array_len_encode; + c->store = cram_byte_array_len_encode_store; + + c->e_byte_array_len.len_len = e->len_len; + c->e_byte_array_len.len_dat = e->len_dat; + c->e_byte_array_len.val_len = e->val_len; + c->e_byte_array_len.val_dat = e->val_dat; + + return c; +} + +/* + * --------------------------------------------------------------------------- + * BYTE_ARRAY_STOP + */ +int cram_byte_array_stop_decode_char(cram_slice *slice, cram_codec *c, + cram_block *in, char *out, + int *out_size) { + int i; + cram_block *b = NULL; + char *cp, ch; + + if (slice->block_by_id) { + if (!(b = slice->block_by_id[c->byte_array_stop.content_id])) + return -1; + } else { + for (i = 0; i < slice->hdr->num_blocks; i++) { + b = slice->block[i]; + if (b->content_type == EXTERNAL && + b->content_id == c->byte_array_stop.content_id) { + break; + } + } + if (i == slice->hdr->num_blocks || !b) + return -1; + } + + if (b->idx >= b->uncomp_size) + return -1; + + cp = (char *)b->data + b->idx; + while ((ch = *cp) != (char)c->byte_array_stop.stop) { + if (cp - (char *)b->data >= b->uncomp_size) + return -1; + *out++ = ch; + cp++; + } + + *out_size = cp - (char *)(b->data + b->idx); + b->idx = cp - (char *)b->data + 1; + + return 0; +} + +int cram_byte_array_stop_decode_block(cram_slice *slice, cram_codec *c, + cram_block *in, char *out_, + int *out_size) { + int space = 256; + cram_block *b = NULL; + cram_block *out = (cram_block *)out_; + char *cp, ch, *out_cp, *cp_end, *out_end; + char stop; + + if (slice->block_by_id) { + if (!(b = slice->block_by_id[c->byte_array_stop.content_id])) + return -1; + } else { + int i; + for (i = 0; i < slice->hdr->num_blocks; i++) { + b = slice->block[i]; + if (b->content_type == EXTERNAL && + b->content_id == c->byte_array_stop.content_id) { + break; + } + } + if (i == slice->hdr->num_blocks || !b) + return -1; + } + + if (b->idx >= b->uncomp_size) + return -1; + cp = (char *)b->data + b->idx; + cp_end = (char *)b->data + b->uncomp_size; + BLOCK_GROW(out, space); + out_cp = (char *)BLOCK_END(out); + out_end = out_cp + space; + + stop = c->byte_array_stop.stop; + while ((ch = *cp) != stop) { + if (cp++ == cp_end) + return -1; + *out_cp++ = ch; + + if (out_cp == out_end) { + BLOCK_SIZE(out) = out_cp - (char *)BLOCK_DATA(out); + space *= 2; + BLOCK_GROW(out, space); + out_cp = (char *)BLOCK_END(out); + out_end = out_cp + space; + } + } + BLOCK_SIZE(out) = out_cp - (char *)BLOCK_DATA(out); + + *out_size = cp - (char *)(b->data + b->idx); + b->idx = cp - (char *)b->data + 1; + + return 0; +} + +void cram_byte_array_stop_decode_free(cram_codec *c) { + if (!c) return; + + free(c); +} + +cram_codec *cram_byte_array_stop_decode_init(char *data, int size, + enum cram_external_type option, + int version) { + cram_codec *c; + unsigned char *cp = (unsigned char *)data; + + if (!(c = malloc(sizeof(*c)))) + return NULL; + + c->codec = E_BYTE_ARRAY_STOP; + c->decode = (option == E_BYTE_ARRAY_BLOCK) + ? cram_byte_array_stop_decode_block + : cram_byte_array_stop_decode_char; + c->free = cram_byte_array_stop_decode_free; + + c->byte_array_stop.stop = *cp++; + if (version == CRAM_1_VERS) { + c->byte_array_stop.content_id = cp[0] + (cp[1]<<8) + (cp[2]<<16) + + (cp[3]<<24); + cp += 4; + } else { + cp += itf8_get(cp, &c->byte_array_stop.content_id); + } + + if ((char *)cp - data != size) { + fprintf(stderr, "Malformed byte_array_stop header stream\n"); + free(c); + return NULL; + } + + return c; +} + +int cram_byte_array_stop_encode(cram_slice *slice, cram_codec *c, + cram_block *out, char *in, int in_size) { + return -1; // not imp. +} + +void cram_byte_array_stop_encode_free(cram_codec *c) { + if (!c) + return; + free(c); +} + +int cram_byte_array_stop_encode_store(cram_codec *c, cram_block *b, + char *prefix, int version) { + int len = 0; + char buf[20], *cp = buf; + + if (prefix) { + size_t l = strlen(prefix); + BLOCK_APPEND(b, prefix, l); + len += l; + } + + cp += itf8_put(cp, c->codec); + + if (version == CRAM_1_VERS) { + cp += itf8_put(cp, 5); + *cp++ = c->e_byte_array_stop.stop; + *cp++ = (c->e_byte_array_stop.content_id >> 0) & 0xff; + *cp++ = (c->e_byte_array_stop.content_id >> 8) & 0xff; + *cp++ = (c->e_byte_array_stop.content_id >> 16) & 0xff; + *cp++ = (c->e_byte_array_stop.content_id >> 24) & 0xff; + } else { + cp += itf8_put(cp, 1 + itf8_size(c->e_byte_array_stop.content_id)); + *cp++ = c->e_byte_array_stop.stop; + cp += itf8_put(cp, c->e_byte_array_stop.content_id); + } + + BLOCK_APPEND(b, buf, cp-buf); + len += cp-buf; + + return len; +} + +cram_codec *cram_byte_array_stop_encode_init(cram_stats *st, + enum cram_external_type option, + void *dat, + int version) { + cram_codec *c; + + c = malloc(sizeof(*c)); + if (!c) + return NULL; + c->codec = E_BYTE_ARRAY_STOP; + c->free = cram_byte_array_stop_encode_free; + c->encode = cram_byte_array_stop_encode; + c->store = cram_byte_array_stop_encode_store; + + c->e_byte_array_stop.stop = ((int *)dat)[0]; + c->e_byte_array_stop.content_id = ((int *)dat)[1]; + + return c; +} + +/* + * --------------------------------------------------------------------------- + */ + +char *cram_encoding2str(enum cram_encoding t) { + switch (t) { + case E_NULL: return "NULL"; + case E_EXTERNAL: return "EXTERNAL"; + case E_GOLOMB: return "GOLOMB"; + case E_HUFFMAN: return "HUFFMAN"; + case E_BYTE_ARRAY_LEN: return "BYTE_ARRAY_LEN"; + case E_BYTE_ARRAY_STOP: return "BYTE_ARRAY_STOP"; + case E_BETA: return "BETA"; + case E_SUBEXP: return "SUBEXP"; + case E_GOLOMB_RICE: return "GOLOMB_RICE"; + case E_GAMMA: return "GAMMA"; + } + return "?"; +} + +static cram_codec *(*decode_init[])(char *data, + int size, + enum cram_external_type option, + int version) = { + NULL, + cram_external_decode_init, + NULL, + cram_huffman_decode_init, + cram_byte_array_len_decode_init, + cram_byte_array_stop_decode_init, + cram_beta_decode_init, + cram_subexp_decode_init, + NULL, + cram_gamma_decode_init, +}; + +cram_codec *cram_decoder_init(enum cram_encoding codec, + char *data, int size, + enum cram_external_type option, + int version) { + if (decode_init[codec]) { + return decode_init[codec](data, size, option, version); + } else { + fprintf(stderr, "Unimplemented codec of type %s\n", codec2str(codec)); + return NULL; + } +} + +static cram_codec *(*encode_init[])(cram_stats *stx, + enum cram_external_type option, + void *opt, + int version) = { + NULL, + cram_external_encode_init, + NULL, + cram_huffman_encode_init, + cram_byte_array_len_encode_init, + cram_byte_array_stop_encode_init, + cram_beta_encode_init, + NULL, //cram_subexp_encode_init, + NULL, + NULL, //cram_gamma_encode_init, +}; + +cram_codec *cram_encoder_init(enum cram_encoding codec, + cram_stats *st, + enum cram_external_type option, + void *dat, + int version) { + if (st && !st->nvals) + return NULL; + + if (encode_init[codec]) { + return encode_init[codec](st, option, dat, version); + } else { + fprintf(stderr, "Unimplemented codec of type %s\n", codec2str(codec)); + abort(); + } +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_codecs.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_codecs.h new file mode 100644 index 0000000000000000000000000000000000000000..7037814c116842914307953102b727a9160d7679 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_codecs.h @@ -0,0 +1,155 @@ +/* +Copyright (c) 2012-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifndef _CRAM_ENCODINGS_H_ +#define _CRAM_ENCODINGS_H_ + +#ifdef __cplusplus +extern "C" { +#endif + +#include + +struct cram_codec; + +/* + * Slow but simple huffman decoder to start with. + * Read a bit at a time, keeping track of {length, value} + * eg. 1 1 0 1 => {1,1}, {2,3}, {3,6}, {4,13} + * + * Keep track of this through the huffman code table. + * For fast scanning we have an index of where the first code of length X + * appears. + */ +typedef struct { + int32_t symbol; + int32_t p; // next code start value, minus index to codes[] + int32_t code; + int32_t len; +} cram_huffman_code; + +typedef struct { + int ncodes; + cram_huffman_code *codes; +} cram_huffman_decoder; + +#define MAX_HUFF 128 +typedef struct { + cram_huffman_code *codes; + int nvals; + int val2code[MAX_HUFF+1]; // value to code lookup for small values +} cram_huffman_encoder; + +typedef struct { + int32_t offset; + int32_t nbits; +} cram_beta_decoder; + +typedef struct { + int32_t offset; +} cram_gamma_decoder; + +typedef struct { + int32_t offset; + int32_t k; +} cram_subexp_decoder; + +typedef struct { + int32_t content_id; + enum cram_external_type type; +} cram_external_decoder; + +typedef struct { + struct cram_codec *len_codec; + struct cram_codec *value_codec; +} cram_byte_array_len_decoder; + +typedef struct { + unsigned char stop; + int32_t content_id; +} cram_byte_array_stop_decoder; + +typedef struct { + uint32_t len_len; + unsigned char *len_dat; + uint32_t val_len; + unsigned char *val_dat; +} cram_byte_array_len_encoder; + +/* + * A generic codec structure. + */ +typedef struct cram_codec { + enum cram_encoding codec; + void (*free)(struct cram_codec *codec); + int (*decode)(cram_slice *slice, struct cram_codec *codec, + cram_block *in, char *out, int *out_size); + int (*encode)(cram_slice *slice, struct cram_codec *codec, + cram_block *out, char *in, int in_size); + int (*store)(struct cram_codec *codec, cram_block *b, char *prefix, + int version); + union { + cram_huffman_decoder huffman; + cram_external_decoder external; + cram_beta_decoder beta; + cram_gamma_decoder gamma; + cram_subexp_decoder subexp; + cram_byte_array_len_decoder byte_array_len; + cram_byte_array_stop_decoder byte_array_stop; + + cram_huffman_encoder e_huffman; + cram_external_decoder e_external; + cram_byte_array_stop_decoder e_byte_array_stop; + cram_byte_array_len_encoder e_byte_array_len; + cram_beta_decoder e_beta; + }; +} cram_codec; + +char *cram_encoding2str(enum cram_encoding t); + +cram_codec *cram_decoder_init(enum cram_encoding codec, char *data, int size, + enum cram_external_type option, + int version); +cram_codec *cram_encoder_init(enum cram_encoding codec, cram_stats *st, + enum cram_external_type option, void *dat, + int version); + +//int cram_decode(void *codes, char *in, int in_size, char *out, int *out_size); +//void cram_decoder_free(void *codes); + +//#define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, (--b->bit == -1) && (b->bit = 7, b->byte++)) + +#define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, b->byte += (b->bit==0), b->bit+=(b->bit==0)*8-1) + +#ifdef __cplusplus +} +#endif + +#endif /* _CRAM_ENCODINGS_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_decode.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_decode.c new file mode 100644 index 0000000000000000000000000000000000000000..83fdaeea6ef52958d531826be0d89032be29739d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_decode.c @@ -0,0 +1,2138 @@ +/* +Copyright (c) 2012-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +/* + * - In-memory decoding of CRAM data structures. + * - Iterator for reading CRAM record by record. + */ + +#ifdef HAVE_CONFIG_H +#include "io_lib_config.h" +#endif + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "cram/cram.h" +#include "cram/os.h" +#include "cram/md5.h" + +//Whether CIGAR has just M or uses = and X to indicate match and mismatch +//#define USE_X + +/* ---------------------------------------------------------------------- + * CRAM compression headers + */ + +/* + * Decodes the Tag Dictionary record in the preservation map + * Updates the cram compression header. + * + * Returns number of bytes decoded on success + * -1 on failure + */ +int cram_decode_TD(char *cp, cram_block_compression_hdr *h) { + char *op = cp; + unsigned char *dat; + cram_block *b; + int32_t blk_size; + int nTL, i, sz; + + if (!(b = cram_new_block(0, 0))) + return -1; + h->TD_blk = b; + + /* Decode */ + cp += itf8_get(cp, &blk_size); + if (!blk_size) { + h->nTL = 0; + h->TL = NULL; + cram_free_block(b); + return cp - op; + } + + BLOCK_APPEND(b, cp, blk_size); + cp += blk_size; + sz = cp - op; + + // Force nul termination if missing + if (BLOCK_DATA(b)[BLOCK_SIZE(b)-1]) + BLOCK_APPEND_CHAR(b, '\0'); + + /* Set up TL lookup table */ + dat = BLOCK_DATA(b); + + // Count + for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { + nTL++; + while (dat[i]) + i++; + } + + // Copy + h->nTL = nTL; + if (!(h->TL = calloc(h->nTL, sizeof(unsigned char *)))) + return -1; + for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { + h->TL[nTL++] = &dat[i]; + while (dat[i]) + i++; + } + + return sz; +} + +/* + * Decodes a CRAM block compression header. + * Returns header ptr on success + * NULL on failure + */ +cram_block_compression_hdr *cram_decode_compression_header(cram_fd *fd, + cram_block *b) { + char *cp, *cp_copy; + cram_block_compression_hdr *hdr = calloc(1, sizeof(*hdr)); + int i; + int32_t map_size, map_count; + + if (!hdr) + return NULL; + + if (b->method != RAW) { + if (cram_uncompress_block(b)) + return NULL; + } + + cp = (char *)b->data; + + if (fd->version == CRAM_1_VERS) { + cp += itf8_get(cp, &hdr->ref_seq_id); + cp += itf8_get(cp, &hdr->ref_seq_start); + cp += itf8_get(cp, &hdr->ref_seq_span); + cp += itf8_get(cp, &hdr->num_records); + cp += itf8_get(cp, &hdr->num_landmarks); + if (!(hdr->landmark = malloc(hdr->num_landmarks * sizeof(int32_t)))) { + free(hdr); + return NULL; + } + for (i = 0; i < hdr->num_landmarks; i++) { + cp += itf8_get(cp, &hdr->landmark[i]); + } + } + + hdr->preservation_map = kh_init(map); + + memset(hdr->rec_encoding_map, 0, + CRAM_MAP_HASH * sizeof(hdr->rec_encoding_map[0])); + memset(hdr->tag_encoding_map, 0, + CRAM_MAP_HASH * sizeof(hdr->tag_encoding_map[0])); + + if (!hdr->preservation_map) { + cram_free_compression_header(hdr); + return NULL; + } + + /* Initialise defaults for preservation map */ + hdr->mapped_qs_included = 0; + hdr->unmapped_qs_included = 0; + hdr->unmapped_placed = 0; + hdr->qs_included = 0; + hdr->read_names_included = 0; + hdr->AP_delta = 1; + memcpy(hdr->substitution_matrix, "CGTNAGTNACTNACGNACGT", 20); + + /* Preservation map */ + cp += itf8_get(cp, &map_size); cp_copy = cp; + cp += itf8_get(cp, &map_count); + for (i = 0; i < map_count; i++) { + pmap_t hd; + khint_t k; + int r; + + cp += 2; + switch(CRAM_KEY(cp[-2],cp[-1])) { + case CRAM_KEY('M','I'): + hd.i = *cp++; + k = kh_put(map, hdr->preservation_map, "MI", &r); + if (-1 == r) { + cram_free_compression_header(hdr); + return NULL; + } + + kh_val(hdr->preservation_map, k) = hd; + hdr->mapped_qs_included = hd.i; + break; + + case CRAM_KEY('U','I'): + hd.i = *cp++; + k = kh_put(map, hdr->preservation_map, "UI", &r); + if (-1 == r) { + cram_free_compression_header(hdr); + return NULL; + } + + kh_val(hdr->preservation_map, k) = hd; + hdr->unmapped_qs_included = hd.i; + break; + + case CRAM_KEY('P','I'): + hd.i = *cp++; + k = kh_put(map, hdr->preservation_map, "PI", &r); + if (-1 == r) { + cram_free_compression_header(hdr); + return NULL; + } + + kh_val(hdr->preservation_map, k) = hd; + hdr->unmapped_placed = hd.i; + break; + + case CRAM_KEY('R','N'): + hd.i = *cp++; + k = kh_put(map, hdr->preservation_map, "RN", &r); + if (-1 == r) { + cram_free_compression_header(hdr); + return NULL; + } + + kh_val(hdr->preservation_map, k) = hd; + hdr->read_names_included = hd.i; + break; + + case CRAM_KEY('A','P'): + hd.i = *cp++; + k = kh_put(map, hdr->preservation_map, "AP", &r); + if (-1 == r) { + cram_free_compression_header(hdr); + return NULL; + } + + kh_val(hdr->preservation_map, k) = hd; + hdr->AP_delta = hd.i; + break; + + case CRAM_KEY('R','R'): + hd.i = *cp++; + k = kh_put(map, hdr->preservation_map, "RR", &r); + if (-1 == r) { + cram_free_compression_header(hdr); + return NULL; + } + + kh_val(hdr->preservation_map, k) = hd; + fd->no_ref = !hd.i; + break; + + case CRAM_KEY('S','M'): + hdr->substitution_matrix[0][(cp[0]>>6)&3] = 'C'; + hdr->substitution_matrix[0][(cp[0]>>4)&3] = 'G'; + hdr->substitution_matrix[0][(cp[0]>>2)&3] = 'T'; + hdr->substitution_matrix[0][(cp[0]>>0)&3] = 'N'; + + hdr->substitution_matrix[1][(cp[1]>>6)&3] = 'A'; + hdr->substitution_matrix[1][(cp[1]>>4)&3] = 'G'; + hdr->substitution_matrix[1][(cp[1]>>2)&3] = 'T'; + hdr->substitution_matrix[1][(cp[1]>>0)&3] = 'N'; + + hdr->substitution_matrix[2][(cp[2]>>6)&3] = 'A'; + hdr->substitution_matrix[2][(cp[2]>>4)&3] = 'C'; + hdr->substitution_matrix[2][(cp[2]>>2)&3] = 'T'; + hdr->substitution_matrix[2][(cp[2]>>0)&3] = 'N'; + + hdr->substitution_matrix[3][(cp[3]>>6)&3] = 'A'; + hdr->substitution_matrix[3][(cp[3]>>4)&3] = 'C'; + hdr->substitution_matrix[3][(cp[3]>>2)&3] = 'G'; + hdr->substitution_matrix[3][(cp[3]>>0)&3] = 'N'; + + hdr->substitution_matrix[4][(cp[4]>>6)&3] = 'A'; + hdr->substitution_matrix[4][(cp[4]>>4)&3] = 'C'; + hdr->substitution_matrix[4][(cp[4]>>2)&3] = 'G'; + hdr->substitution_matrix[4][(cp[4]>>0)&3] = 'T'; + + hd.p = cp; + cp += 5; + + k = kh_put(map, hdr->preservation_map, "SM", &r); + if (-1 == r) { + cram_free_compression_header(hdr); + return NULL; + } + kh_val(hdr->preservation_map, k) = hd; + break; + + case CRAM_KEY('T','D'): { + int sz = cram_decode_TD(cp, hdr); // tag dictionary + if (sz < 0) { + cram_free_compression_header(hdr); + return NULL; + } + + hd.p = cp; + cp += sz; + + k = kh_put(map, hdr->preservation_map, "TD", &r); + if (-1 == r) { + cram_free_compression_header(hdr); + return NULL; + } + kh_val(hdr->preservation_map, k) = hd; + break; + } + + default: + fprintf(stderr, "Unrecognised preservation map key %c%c\n", + cp[-2], cp[-1]); + // guess byte; + cp++; + break; + } + } + if (cp - cp_copy != map_size) { + cram_free_compression_header(hdr); + return NULL; + } + + /* Record encoding map */ + cp += itf8_get(cp, &map_size); cp_copy = cp; + cp += itf8_get(cp, &map_count); + for (i = 0; i < map_count; i++) { + char *key = cp; + int32_t encoding; + int32_t size; + cram_map *m = malloc(sizeof(*m)); // FIXME: use pooled_alloc + + if (!m) { + cram_free_compression_header(hdr); + return NULL; + } + + cp += 2; + cp += itf8_get(cp, &encoding); + cp += itf8_get(cp, &size); + + // Fill out cram_map purely for cram_dump to dump out. + m->key = (key[0]<<8)|key[1]; + m->encoding = encoding; + m->size = size; + m->offset = cp - (char *)b->data; + m->codec = NULL; + + if (m->encoding == E_NULL) + continue; + + //printf("%s codes for %.2s\n", cram_encoding2str(encoding), key); + + /* + * For CRAM1.0 CF and BF are Byte and not Int. + * Practically speaking it makes no difference unless we have a + * 1.0 format file that stores these in EXTERNAL as only then + * does Byte vs Int matter. + * + * Neither this C code nor Java reference implementations did this, + * so we gloss over it and treat them as int. + */ + + if (key[0] == 'B' && key[1] == 'F') { + if (!(hdr->BF_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'C' && key[1] == 'F') { + if (!(hdr->CF_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'R' && key[1] == 'I') { + if (!(hdr->RI_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'R' && key[1] == 'L') { + if (!(hdr->RL_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'A' && key[1] == 'P') { + if (!(hdr->AP_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'R' && key[1] == 'G') { + if (!(hdr->RG_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'M' && key[1] == 'F') { + if (!(hdr->MF_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'N' && key[1] == 'S') { + if (!(hdr->NS_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'N' && key[1] == 'P') { + if (!(hdr->NP_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'T' && key[1] == 'S') { + if (!(hdr->TS_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'N' && key[1] == 'F') { + if (!(hdr->NF_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'T' && key[1] == 'C') { + if (!(hdr->TC_codec = cram_decoder_init(encoding, cp, size, E_BYTE, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'T' && key[1] == 'N') { + if (!(hdr->TN_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'F' && key[1] == 'N') { + if (!(hdr->FN_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'F' && key[1] == 'C') { + if (!(hdr->FC_codec = cram_decoder_init(encoding, cp, size, E_BYTE, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'F' && key[1] == 'P') { + if (!(hdr->FP_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'B' && key[1] == 'S') { + if (!(hdr->BS_codec = cram_decoder_init(encoding, cp, size, E_BYTE, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'I' && key[1] == 'N') { + if (!(hdr->IN_codec = cram_decoder_init(encoding, cp, size, + E_BYTE_ARRAY, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'S' && key[1] == 'C') { + if (!(hdr->SC_codec = cram_decoder_init(encoding, cp, size, + E_BYTE_ARRAY, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'D' && key[1] == 'L') { + if (!(hdr->DL_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'B' && key[1] == 'A') { + if (!(hdr->BA_codec = cram_decoder_init(encoding, cp, size, E_BYTE, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'R' && key[1] == 'S') { + if (!(hdr->RS_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'P' && key[1] == 'D') { + if (!(hdr->PD_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'H' && key[1] == 'C') { + if (!(hdr->HC_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'M' && key[1] == 'Q') { + if (!(hdr->MQ_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'R' && key[1] == 'N') { + if (!(hdr->RN_codec = cram_decoder_init(encoding, cp, size, + E_BYTE_ARRAY_BLOCK, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'Q' && key[1] == 'S') { + if (!(hdr->QS_codec = cram_decoder_init(encoding, cp, size, E_BYTE, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + if (!(hdr->Qs_codec = cram_decoder_init(encoding, cp, size, + E_BYTE_ARRAY, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'T' && key[1] == 'L') { + if (!(hdr->TL_codec = cram_decoder_init(encoding, cp, size, E_INT, + fd->version))) { + cram_free_compression_header(hdr); + return NULL; + } + } else if (key[0] == 'T' && key[1] == 'M') { + } else if (key[0] == 'T' && key[1] == 'V') { + } else + fprintf(stderr, "Unrecognised key: %.2s\n", key); + + cp += size; + + m->next = hdr->rec_encoding_map[CRAM_MAP(key[0], key[1])]; + hdr->rec_encoding_map[CRAM_MAP(key[0], key[1])] = m; + } + if (cp - cp_copy != map_size) { + cram_free_compression_header(hdr); + return NULL; + } + + /* Tag encoding map */ + cp += itf8_get(cp, &map_size); cp_copy = cp; + cp += itf8_get(cp, &map_count); + for (i = 0; i < map_count; i++) { + int32_t encoding; + int32_t size; + cram_map *m = malloc(sizeof(*m)); // FIXME: use pooled_alloc + char *key = cp+1; + + if (!m) { + cram_free_compression_header(hdr); + return NULL; + } + + m->key = (key[0]<<16)|(key[1]<<8)|key[2]; + + cp += 4; // Strictly ITF8, but this suffices + cp += itf8_get(cp, &encoding); + cp += itf8_get(cp, &size); + + m->encoding = encoding; + m->size = size; + m->offset = cp - (char *)b->data; + if (!(m->codec = cram_decoder_init(encoding, cp, size, + E_BYTE_ARRAY_BLOCK, fd->version))) { + cram_free_compression_header(hdr); + free(m); + return NULL; + } + + cp += size; + + m->next = hdr->tag_encoding_map[CRAM_MAP(key[0],key[1])]; + hdr->tag_encoding_map[CRAM_MAP(key[0],key[1])] = m; + } + if (cp - cp_copy != map_size) { + cram_free_compression_header(hdr); + return NULL; + } + + return hdr; +} + +/* ---------------------------------------------------------------------- + * CRAM slices + */ + +/* + * Decodes a CRAM (un)mapped slice header block. + * Returns slice header ptr on success + * NULL on failure + */ +cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b) { + cram_block_slice_hdr *hdr; + char *cp = (char *)b->data; + int i; + + if (b->content_type != MAPPED_SLICE && + b->content_type != UNMAPPED_SLICE) + return NULL; + + if (!(hdr = calloc(1, sizeof(*hdr)))) + return NULL; + + hdr->content_type = b->content_type; + + if (b->content_type == MAPPED_SLICE) { + cp += itf8_get(cp, &hdr->ref_seq_id); + cp += itf8_get(cp, &hdr->ref_seq_start); + cp += itf8_get(cp, &hdr->ref_seq_span); + } + cp += itf8_get(cp, &hdr->num_records); + if (fd->version != CRAM_1_VERS) + cp += itf8_get(cp, &hdr->record_counter); + cp += itf8_get(cp, &hdr->num_blocks); + + cp += itf8_get(cp, &hdr->num_content_ids); + hdr->block_content_ids = malloc(hdr->num_content_ids * sizeof(int32_t)); + if (!hdr->block_content_ids) { + free(hdr); + return NULL; + } + + for (i = 0; i < hdr->num_content_ids; i++) { + cp += itf8_get(cp, &hdr->block_content_ids[i]); + } + + if (b->content_type == MAPPED_SLICE) { + cp += itf8_get(cp, &hdr->ref_base_id); + } + + if (fd->version != CRAM_1_VERS) { + memcpy(hdr->md5, cp, 16); + } else { + memset(hdr->md5, 0, 16); + } + + return hdr; +} + + +#if 0 +/* Returns the number of bits set in val; it the highest bit used */ +static int nbits(int v) { + static const int MultiplyDeBruijnBitPosition[32] = { + 1, 10, 2, 11, 14, 22, 3, 30, 12, 15, 17, 19, 23, 26, 4, 31, + 9, 13, 21, 29, 16, 18, 25, 8, 20, 28, 24, 7, 27, 6, 5, 32 + }; + + v |= v >> 1; // first up to set all bits 1 after the first 1 */ + v |= v >> 2; + v |= v >> 4; + v |= v >> 8; + v |= v >> 16; + + // DeBruijn magic to find top bit + return MultiplyDeBruijnBitPosition[(uint32_t)(v * 0x07C4ACDDU) >> 27]; +} +#endif + +#if 0 +static int sort_freqs(const void *vp1, const void *vp2) { + const int i1 = *(const int *)vp1; + const int i2 = *(const int *)vp2; + return i1-i2; +} +#endif + +/* ---------------------------------------------------------------------- + * Primary CRAM sequence decoder + */ + +/* + * Internal part of cram_decode_slice(). + * Generates the sequence, quality and cigar components. + */ +static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s, + cram_block *blk, cram_record *cr, SAM_hdr *bfd, + int cf, char *seq, char *qual) { + int prev_pos = 0, f, r = 0, out_sz = 1; + int seq_pos = 1; + int cig_len = 0, ref_pos = cr->apos; + int32_t fn, i32; + enum cigar_op cig_op = BAM_CMATCH; + uint32_t *cigar = s->cigar; + uint32_t ncigar = s->ncigar; + uint32_t cigar_alloc = s->cigar_alloc; + uint32_t nm = 0, md_dist = 0; + int orig_aux = 0; + int decode_md = fd->decode_md; + char buf[20]; + + if (!(cf & CRAM_FLAG_PRESERVE_QUAL_SCORES)) { + memset(qual, 30, cr->len); + } + + if (decode_md) { + orig_aux = BLOCK_SIZE(s->aux_blk); + BLOCK_APPEND(s->aux_blk, "MDZ", 3); + } + + if (!c->comp_hdr->FN_codec) return -1; + r |= c->comp_hdr->FN_codec->decode(s,c->comp_hdr->FN_codec, blk, + (char *)&fn, &out_sz); + + ref_pos--; // count from 0 + cr->cigar = ncigar; + for (f = 0; f < fn; f++) { + int32_t pos; + char op; + + if (ncigar+2 >= cigar_alloc) { + cigar_alloc = cigar_alloc ? cigar_alloc*2 : 1024; + s->cigar = cigar; + if (!(cigar = realloc(cigar, cigar_alloc * sizeof(*cigar)))) + return -1; + } + + if (!c->comp_hdr->FC_codec) return -1; + r |= c->comp_hdr->FC_codec->decode(s, c->comp_hdr->FC_codec, blk, + &op, &out_sz); + if (!c->comp_hdr->FP_codec) return -1; + r |= c->comp_hdr->FP_codec->decode(s, c->comp_hdr->FP_codec, blk, + (char *)&pos, &out_sz); + pos += prev_pos; + + if (pos > seq_pos) { + if (pos > cr->len+1) + return -1; + + if (s->ref && cr->ref_id >= 0) { + if (ref_pos + pos - seq_pos > bfd->ref[cr->ref_id].len) { + static int whinged = 0; + if (!whinged) + fprintf(stderr, "Ref pos outside of ref " + "sequence boundary\n"); + whinged = 1; + } else { + memcpy(&seq[seq_pos-1], &s->ref[ref_pos - s->ref_start +1], + pos - seq_pos); + } + } +#ifdef USE_X + if (cig_len && cig_op != BAM_CBASE_MATCH) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } + cig_op = BAM_CBASE_MATCH; +#else + if (cig_len && cig_op != BAM_CMATCH) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } + cig_op = BAM_CMATCH; +#endif + cig_len += pos - seq_pos; + ref_pos += pos - seq_pos; + md_dist += pos - seq_pos; + seq_pos = pos; + } + + prev_pos = pos; + + switch(op) { + case 'S': { // soft clip: IN + int32_t out_sz2 = 1; + + if (cig_len) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } + if (fd->version == CRAM_1_VERS) { + r |= c->comp_hdr->IN_codec + ? c->comp_hdr->IN_codec->decode(s, c->comp_hdr->IN_codec, + blk, &seq[pos-1], &out_sz2) + : (seq[pos-1] = 'N', out_sz2 = 1, 0); + } else { + r |= c->comp_hdr->SC_codec + ? c->comp_hdr->SC_codec->decode(s, c->comp_hdr->SC_codec, + blk, &seq[pos-1], &out_sz2) + : (seq[pos-1] = 'N', out_sz2 = 1, 0); + } + cigar[ncigar++] = (out_sz2<<4) + BAM_CSOFT_CLIP; + cig_op = BAM_CSOFT_CLIP; + seq_pos += out_sz2; + break; + } + + case 'X': { // Substitution; BS + unsigned char base; +#ifdef USE_X + if (cig_len && cig_op != BAM_CBASE_MISMATCH) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } + if (!c->comp_hdr->BS_codec) return -1; + r |= c->comp_hdr->BS_codec->decode(s, c->comp_hdr->BS_codec, blk, + (char *)&base, &out_sz); + seq[pos-1] = 'N'; // FIXME look up BS=base value + cig_op = BAM_CBASE_MISMATCH; +#else + int ref_base; + if (cig_len && cig_op != BAM_CMATCH) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } + if (!c->comp_hdr->BS_codec) return -1; + r |= c->comp_hdr->BS_codec->decode(s, c->comp_hdr->BS_codec, blk, + (char *)&base, &out_sz); + if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { + seq[pos-1] = 'N'; + } else { + ref_base = fd->L1[(uc)s->ref[ref_pos - s->ref_start +1]]; + seq[pos-1] = c->comp_hdr->substitution_matrix[ref_base][base]; + if (decode_md) { + BLOCK_APPENDF_2(s->aux_blk, buf, "%d%c", + md_dist, s->ref[ref_pos-s->ref_start +1]); + md_dist = 0; + } + } + cig_op = BAM_CMATCH; +#endif + nm++; + cig_len++; + seq_pos++; + ref_pos++; + break; + } + + case 'D': { // Deletion; DL + if (cig_len && cig_op != BAM_CDEL) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } + if (!c->comp_hdr->DL_codec) return -1; + r |= c->comp_hdr->DL_codec->decode(s, c->comp_hdr->DL_codec, blk, + (char *)&i32, &out_sz); + if (decode_md) { + BLOCK_APPENDF_1(s->aux_blk, buf, "%d^", md_dist); + BLOCK_APPEND(s->aux_blk, &s->ref[ref_pos - s->ref_start +1], + i32); + md_dist = 0; + } + cig_op = BAM_CDEL; + cig_len += i32; + ref_pos += i32; + nm += i32; + //printf(" %d: DL = %d (ret %d)\n", f, i32, r); + break; + } + + case 'I': { // Insertion (several bases); IN + int32_t out_sz2 = 1; + + if (cig_len && cig_op != BAM_CINS) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } + + if (!c->comp_hdr->IN_codec) return -1; + r |= c->comp_hdr->IN_codec->decode(s, c->comp_hdr->IN_codec, blk, + &seq[pos-1], &out_sz2); + cig_op = BAM_CINS; + cig_len += out_sz2; + seq_pos += out_sz2; + nm += out_sz2; + //printf(" %d: IN(I) = %.*s (ret %d, out_sz %d)\n", f, out_sz2, dat, r, out_sz2); + break; + } + + case 'i': { // Insertion (single base); BA + if (cig_len && cig_op != BAM_CINS) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } + if (!c->comp_hdr->BA_codec) return -1; + r |= c->comp_hdr->BA_codec->decode(s, c->comp_hdr->BA_codec, blk, + (char *)&seq[pos-1], &out_sz); + cig_op = BAM_CINS; + cig_len++; + seq_pos++; + nm++; + //printf(" %d: BA = %c (ret %d)\n", f, seq[pos-1], r); + break; + } + + case 'B': { // Read base; BA, QS +#ifdef USE_X + if (cig_len && cig_op != BAM_CBASE_MISMATCH) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } +#else + if (cig_len && cig_op != BAM_CMATCH) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } +#endif + if (!c->comp_hdr->BA_codec) return -1; + r |= c->comp_hdr->BA_codec->decode(s, c->comp_hdr->BA_codec, blk, + (char *)&seq[pos-1], &out_sz); + if (!c->comp_hdr->QS_codec) return -1; + r |= c->comp_hdr->QS_codec->decode(s, c->comp_hdr->QS_codec, blk, + (char *)&qual[pos-1], &out_sz); +#ifdef USE_X + cig_op = BAM_CBASE_MISMATCH; +#else + cig_op = BAM_CMATCH; +#endif + cig_len++; + seq_pos++; + ref_pos++; + //printf(" %d: BA/QS(B) = %c/%d (ret %d)\n", f, i32, qc, r); + break; + } + + case 'Q': { // Quality score; QS + if (!c->comp_hdr->QS_codec) return -1; + r |= c->comp_hdr->QS_codec->decode(s, c->comp_hdr->QS_codec, blk, + (char *)&qual[pos-1], &out_sz); + //printf(" %d: QS = %d (ret %d)\n", f, qc, r); + break; + } + + case 'H': { // hard clip; HC + if (cig_len && cig_op != BAM_CHARD_CLIP) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } + if (!c->comp_hdr->HC_codec) return -1; + r |= c->comp_hdr->HC_codec->decode(s, c->comp_hdr->HC_codec, blk, + (char *)&i32, &out_sz); + cig_op = BAM_CHARD_CLIP; + cig_len += i32; + nm += i32; + break; + } + + case 'P': { // padding; PD + if (cig_len && cig_op != BAM_CPAD) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } + if (!c->comp_hdr->PD_codec) return -1; + r |= c->comp_hdr->PD_codec->decode(s, c->comp_hdr->PD_codec, blk, + (char *)&i32, &out_sz); + cig_op = BAM_CPAD; + cig_len += i32; + nm += i32; + break; + } + + case 'N': { // Ref skip; RS + if (cig_len && cig_op != BAM_CREF_SKIP) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } + if (!c->comp_hdr->RS_codec) return -1; + r |= c->comp_hdr->RS_codec->decode(s, c->comp_hdr->RS_codec, blk, + (char *)&i32, &out_sz); + cig_op = BAM_CREF_SKIP; + cig_len += i32; + ref_pos += i32; + nm += i32; + break; + } + + default: + abort(); + } + } + + /* An implement match op for any unaccounted for bases */ + if (cr->len >= seq_pos) { + if (s->ref) { + if (ref_pos + cr->len - seq_pos + 1 > bfd->ref[cr->ref_id].len) { + static int whinged = 0; + if (!whinged) + fprintf(stderr, "Ref pos outside of ref sequence boundary\n"); + whinged = 1; + } else { + memcpy(&seq[seq_pos-1], &s->ref[ref_pos - s->ref_start +1], + cr->len - seq_pos + 1); + ref_pos += cr->len - seq_pos + 1; + md_dist += cr->len - seq_pos + 1; + } + } + + if (ncigar+1 >= cigar_alloc) { + cigar_alloc = cigar_alloc ? cigar_alloc*2 : 1024; + s->cigar = cigar; + if (!(cigar = realloc(cigar, cigar_alloc * sizeof(*cigar)))) + return -1; + } +#ifdef USE_X + if (cig_len && cig_op != BAM_CBASE_MATCH) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } + cig_op = BAM_CBASE_MATCH; +#else + if (cig_len && cig_op != BAM_CMATCH) { + cigar[ncigar++] = (cig_len<<4) + cig_op; + cig_len = 0; + } + cig_op = BAM_CMATCH; +#endif + cig_len += cr->len - seq_pos+1; + } + if (decode_md) { + BLOCK_APPENDF_1(s->aux_blk, buf, "%d", md_dist); + } + + if (cig_len) { + if (ncigar >= cigar_alloc) { + cigar_alloc = cigar_alloc ? cigar_alloc*2 : 1024; + s->cigar = cigar; + if (!(cigar = realloc(cigar, cigar_alloc * sizeof(*cigar)))) + return -1; + } + + cigar[ncigar++] = (cig_len<<4) + cig_op; + } + + cr->ncigar = ncigar - cr->cigar; + cr->aend = ref_pos; + + //printf("2: %.*s %d .. %d\n", cr->name_len, DSTRING_STR(name_ds) + cr->name, cr->apos, ref_pos); + + if (!c->comp_hdr->MQ_codec) return -1; + r |= c->comp_hdr->MQ_codec->decode(s, c->comp_hdr->MQ_codec, blk, + (char *)&cr->mqual, &out_sz); + + if (cf & CRAM_FLAG_PRESERVE_QUAL_SCORES) { + int32_t out_sz2 = cr->len; + + if (!c->comp_hdr->Qs_codec) return -1; + r |= c->comp_hdr->Qs_codec->decode(s, c->comp_hdr->Qs_codec, blk, + qual, &out_sz2); + } + + s->cigar = cigar; + s->cigar_alloc = cigar_alloc; + s->ncigar = ncigar; + + if (decode_md) { + char buf[7]; + BLOCK_APPEND_CHAR(s->aux_blk, '\0'); // null terminate MD:Z: + cr->aux_size += BLOCK_SIZE(s->aux_blk) - orig_aux; + buf[0] = 'N'; buf[1] = 'M'; buf[2] = 'I'; + buf[3] = (nm>> 0) & 0xff; + buf[4] = (nm>> 8) & 0xff; + buf[5] = (nm>>16) & 0xff; + buf[6] = (nm>>24) & 0xff; + BLOCK_APPEND(s->aux_blk, buf, 7); + cr->aux_size += 7; + } + + return r; +} + +/* + * Quick and simple hash lookup for cram_map arrays + */ +static cram_map *map_find(cram_map **map, unsigned char *key, int id) { + cram_map *m; + + m = map[CRAM_MAP(key[0],key[1])]; + while (m && m->key != id) + m= m->next; + + return m; +} + +//#define map_find(M,K,I) M[CRAM_MAP(K[0],K[1])];while (m && m->key != I);m= m->next + + +static int cram_decode_aux_1_0(cram_container *c, cram_slice *s, + cram_block *blk, cram_record *cr) { + int i, r = 0, out_sz = 1; + unsigned char ntags; + + if (!c->comp_hdr->TC_codec) return -1; + r |= c->comp_hdr->TC_codec->decode(s, c->comp_hdr->TC_codec, blk, + (char *)&ntags, &out_sz); + cr->ntags = ntags; + + //printf("TC=%d\n", cr->ntags); + cr->aux_size = 0; + cr->aux = BLOCK_SIZE(s->aux_blk); + + for (i = 0; i < cr->ntags; i++) { + int32_t id, out_sz = 1; + unsigned char tag_data[3]; + cram_map *m; + + //printf("Tag %d/%d\n", i+1, cr->ntags); + if (!c->comp_hdr->TN_codec) return -1; + r |= c->comp_hdr->TN_codec->decode(s, c->comp_hdr->TN_codec, + blk, (char *)&id, &out_sz); + if (out_sz == 3) { + tag_data[0] = ((char *)&id)[0]; + tag_data[1] = ((char *)&id)[1]; + tag_data[2] = ((char *)&id)[2]; + } else { + tag_data[0] = (id>>16) & 0xff; + tag_data[1] = (id>>8) & 0xff; + tag_data[2] = id & 0xff; + } + + m = map_find(c->comp_hdr->tag_encoding_map, tag_data, id); + if (!m) + return -1; + BLOCK_APPEND(s->aux_blk, (char *)tag_data, 3); + + if (!m->codec) return -1; + r |= m->codec->decode(s, m->codec, blk, (char *)s->aux_blk, &out_sz); + + cr->aux_size += out_sz + 3; + } + + return r; +} + +static int cram_decode_aux(cram_container *c, cram_slice *s, + cram_block *blk, cram_record *cr) { + int i, r = 0, out_sz = 1; + int32_t TL; + unsigned char *TN; + + if (!c->comp_hdr->TL_codec) return -1; + r |= c->comp_hdr->TL_codec->decode(s, c->comp_hdr->TL_codec, blk, + (char *)&TL, &out_sz); + if (r || TL < 0 || TL >= c->comp_hdr->nTL) + return -1; + + TN = c->comp_hdr->TL[TL]; + cr->ntags = strlen((char *)TN)/3; // optimise to remove strlen + + //printf("TC=%d\n", cr->ntags); + cr->aux_size = 0; + cr->aux = BLOCK_SIZE(s->aux_blk); + + for (i = 0; i < cr->ntags; i++) { + int32_t id, out_sz = 1; + unsigned char tag_data[3]; + cram_map *m; + + //printf("Tag %d/%d\n", i+1, cr->ntags); + tag_data[0] = *TN++; + tag_data[1] = *TN++; + tag_data[2] = *TN++; + id = (tag_data[0]<<16) | (tag_data[1]<<8) | tag_data[2]; + + m = map_find(c->comp_hdr->tag_encoding_map, tag_data, id); + if (!m) + return -1; + BLOCK_APPEND(s->aux_blk, (char *)tag_data, 3); + + if (!m->codec) return -1; + r |= m->codec->decode(s, m->codec, blk, (char *)s->aux_blk, &out_sz); + cr->aux_size += out_sz + 3; + } + + return r; +} + +/* Resolve mate pair cross-references between recs within this slice */ +static void cram_decode_slice_xref(cram_slice *s) { + int rec; + + for (rec = 0; rec < s->hdr->num_records; rec++) { + cram_record *cr = &s->crecs[rec]; + + if (cr->mate_line >= 0) { + if (cr->mate_line < s->hdr->num_records) { + /* + * On the first read, loop through computing lengths. + * It's not perfect as we have one slice per reference so we + * cannot detect when TLEN should be zero due to seqs that + * map to multiple references. + * + * We also cannot set tlen correct when it spans a slice for + * other reasons. This may make tlen too small. Should we + * fix this by forcing TLEN to be stored verbatim in such cases? + * + * Or do we just admit defeat and output 0 for tlen? It's the + * safe option... + */ + if (cr->tlen == INT_MIN) { + int id1 = rec, id2 = rec; + int aleft = cr->apos, aright = cr->aend; + int tlen; + int ref = cr->ref_id; + + do { + if (aleft > s->crecs[id2].apos) + aleft = s->crecs[id2].apos; + if (aright < s->crecs[id2].aend) + aright = s->crecs[id2].aend; + if (s->crecs[id2].mate_line == -1) { + s->crecs[id2].mate_line = rec; + break; + } + assert(s->crecs[id2].mate_line > id2); + id2 = s->crecs[id2].mate_line; + + if (s->crecs[id2].ref_id != ref) + ref = -1; + } while (id2 != id1); + + if (ref != -1) { + tlen = aright - aleft + 1; + id1 = id2 = rec; + + /* + * When we have two seqs with identical start and + * end coordinates, set +/- tlen based on 1st/last + * bit flags instead, as a tie breaker. + */ + if (s->crecs[id2].apos == aleft) { + if (s->crecs[id2].aend != aright) + s->crecs[id2].tlen = tlen; + else if (s->crecs[id2].flags & BAM_FREAD1) + s->crecs[id2].tlen = tlen; + else + s->crecs[id2].tlen = -tlen; + } else { + s->crecs[id2].tlen = -tlen; + } + + id2 = s->crecs[id2].mate_line; + while (id2 != id1) { + if (s->crecs[id2].apos == aleft) { + if (s->crecs[id2].aend != aright) + s->crecs[id2].tlen = tlen; + else if (s->crecs[id2].flags & BAM_FREAD1) + s->crecs[id2].tlen = tlen; + else + s->crecs[id2].tlen = -tlen; + } else { + s->crecs[id2].tlen = -tlen; + } + id2 = s->crecs[id2].mate_line; + } + } else { + id1 = id2 = rec; + + s->crecs[id2].tlen = 0; + id2 = s->crecs[id2].mate_line; + while (id2 != id1) { + s->crecs[id2].tlen = 0; + id2 = s->crecs[id2].mate_line; + } + } + } + + cr->mate_pos = s->crecs[cr->mate_line].apos; + cr->mate_ref_id = s->crecs[cr->mate_line].ref_id; + + // paired + cr->flags |= BAM_FPAIRED; + + // set mate unmapped if needed + if (s->crecs[cr->mate_line].flags & BAM_FUNMAP) { + cr->flags |= BAM_FMUNMAP; + cr->tlen = 0; + } + if (cr->flags & BAM_FUNMAP) { + cr->tlen = 0; + } + + // set mate reversed if needed + if (s->crecs[cr->mate_line].flags & BAM_FREVERSE) + cr->flags |= BAM_FMREVERSE; + } else { + fprintf(stderr, "Mate line out of bounds: %d vs [0, %d]\n", + cr->mate_line, s->hdr->num_records-1); + } + + /* FIXME: construct read names here too if needed */ + } else { + if (cr->mate_flags & CRAM_M_REVERSE) { + cr->flags |= BAM_FPAIRED | BAM_FMREVERSE; + } + if (cr->mate_flags & CRAM_M_UNMAP) { + cr->flags |= BAM_FMUNMAP; + //cr->mate_ref_id = -1; + } + if (!(cr->flags & BAM_FPAIRED)) + cr->mate_ref_id = -1; + } + + if (cr->tlen == INT_MIN) + cr->tlen = 0; // Just incase + } +} + +static char *md5_print(unsigned char *md5, char *out) { + int i; + for (i = 0; i < 16; i++) { + out[i*2+0] = "0123456789abcdef"[md5[i]>>4]; + out[i*2+1] = "0123456789abcdef"[md5[i]&15]; + } + out[32] = 0; + + return out; +} + +/* + * Decode an entire slice from container blocks. Fills out s->crecs[] array. + * Returns 0 on success + * -1 on failure + */ +int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s, + SAM_hdr *bfd) { + cram_block *blk = s->block[0]; + int32_t bf, ref_id; + unsigned char cf; + int out_sz, r = 0; + int rec; + char *seq, *qual; + int unknown_rg = -1; + int id, embed_ref; + char **refs = NULL; + + for (id = 0; id < s->hdr->num_blocks; id++) { + if (cram_uncompress_block(s->block[id])) + return -1; + } + + blk->bit = 7; // MSB first + + /* Look for unknown RG, added as last by Java CRAM? */ + if (bfd->nrg > 0 && + !strcmp(bfd->rg[bfd->nrg-1].name, "UNKNOWN")) + unknown_rg = bfd->nrg-1; + + if (blk->content_type != CORE) + return -1; + + if (s->crecs) + free(s->crecs); + if (!(s->crecs = malloc(s->hdr->num_records * sizeof(*s->crecs)))) + return -1; + + ref_id = s->hdr->ref_seq_id; + embed_ref = s->hdr->ref_base_id >= 0 ? 1 : 0; + + if (ref_id >= 0) { + if (embed_ref) { + cram_block *b; + if (s->hdr->ref_base_id < 0) { + fprintf(stderr, "No reference specified and " + "no embedded reference is available.\n"); + return -1; + } + if (!s->block_by_id || + !(b = s->block_by_id[s->hdr->ref_base_id])) + return -1; + s->ref = (char *)BLOCK_DATA(b); + s->ref_start = s->hdr->ref_seq_start; + s->ref_end = s->hdr->ref_seq_start + s->hdr->ref_seq_span-1; + } else if (!fd->no_ref) { + //// Avoid Java cramtools bug by loading entire reference seq + //s->ref = cram_get_ref(fd, s->hdr->ref_seq_id, 1, 0); + //s->ref_start = 1; + + s->ref = + cram_get_ref(fd, s->hdr->ref_seq_id, + s->hdr->ref_seq_start, + s->hdr->ref_seq_start + s->hdr->ref_seq_span -1); + s->ref_start = s->hdr->ref_seq_start; + s->ref_end = s->hdr->ref_seq_start + s->hdr->ref_seq_span-1; + + /* Sanity check */ + if (s->ref_start < 0) { + fprintf(stderr, "Slice starts before base 1.\n"); + s->ref_start = 0; + } + pthread_mutex_lock(&fd->ref_lock); + pthread_mutex_lock(&fd->refs->lock); + if (s->ref_end > fd->refs->ref_id[ref_id]->length) { + fprintf(stderr, "Slice ends beyond reference end.\n"); + s->ref_end = fd->refs->ref_id[ref_id]->length; + } + pthread_mutex_unlock(&fd->refs->lock); + pthread_mutex_unlock(&fd->ref_lock); + } + } + + if (s->ref == NULL && s->hdr->ref_seq_id >= 0 && !fd->no_ref) { + fprintf(stderr, "Unable to fetch reference #%d %d..%d\n", + s->hdr->ref_seq_id, s->hdr->ref_seq_start, + s->hdr->ref_seq_start + s->hdr->ref_seq_span-1); + return -1; + } + + if (fd->version != CRAM_1_VERS && s->hdr->ref_seq_id >= 0 + && !fd->ignore_md5 + && memcmp(s->hdr->md5, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0", 16)) { + MD5_CTX md5; + unsigned char digest[16]; + + if (s->ref && s->hdr->ref_seq_id >= 0) { + int start, len; + + if (s->hdr->ref_seq_start >= s->ref_start) { + start = s->hdr->ref_seq_start - s->ref_start; + } else { + fprintf(stderr, "Slice starts before base 1.\n"); + start = 0; + } + + if (s->hdr->ref_seq_span <= s->ref_end - s->ref_start + 1) { + len = s->hdr->ref_seq_span; + } else { + fprintf(stderr, "Slice ends beyond reference end.\n"); + len = s->ref_end - s->ref_start + 1; + } + + MD5_Init(&md5); + if (start + len > s->ref_end - s->ref_start + 1) + len = s->ref_end - s->ref_start + 1 - start; + if (len >= 0) + MD5_Update(&md5, s->ref + start, len); + MD5_Final(digest, &md5); + } else if (!s->ref && s->hdr->ref_base_id >= 0) { + cram_block *b; + if (s->block_by_id && (b = s->block_by_id[s->hdr->ref_base_id])) { + MD5_Init(&md5); + MD5_Update(&md5, b->data, b->uncomp_size); + MD5_Final(digest, &md5); + } + } + + if ((!s->ref && s->hdr->ref_base_id < 0) + || memcmp(digest, s->hdr->md5, 16) != 0) { + char M[33]; + fprintf(stderr, "ERROR: md5sum reference mismatch for ref " + "%d pos %d..%d\n", ref_id, s->ref_start, s->ref_end); + fprintf(stderr, "CRAM: %s\n", md5_print(s->hdr->md5, M)); + fprintf(stderr, "Ref : %s\n", md5_print(digest, M)); + return -1; + } + } + + if (ref_id == -2) { + pthread_mutex_lock(&fd->ref_lock); + pthread_mutex_lock(&fd->refs->lock); + refs = calloc(fd->refs->nref, sizeof(char *)); + pthread_mutex_unlock(&fd->refs->lock); + pthread_mutex_unlock(&fd->ref_lock); + if (!refs) + return -1; + } + + for (rec = 0; rec < s->hdr->num_records; rec++) { + cram_record *cr = &s->crecs[rec]; + + //fprintf(stderr, "Decode seq %d, %d/%d\n", rec, blk->byte, blk->bit); + + cr->s = s; + + out_sz = 1; /* decode 1 item */ + if (!c->comp_hdr->BF_codec) return -1; + r |= c->comp_hdr->BF_codec->decode(s, c->comp_hdr->BF_codec, blk, + (char *)&bf, &out_sz); + if (bf < 0 || + bf >= sizeof(fd->bam_flag_swap)/sizeof(*fd->bam_flag_swap)) + return -1; + bf = fd->bam_flag_swap[bf]; + cr->flags = bf; + + if (fd->version == CRAM_1_VERS) { + /* CF is byte in 1.0, int32 in 2.0 */ + if (!c->comp_hdr->CF_codec) return -1; + r |= c->comp_hdr->CF_codec->decode(s, c->comp_hdr->CF_codec, blk, + (char *)&cf, &out_sz); + cr->cram_flags = cf; + } else { + if (!c->comp_hdr->CF_codec) return -1; + r |= c->comp_hdr->CF_codec->decode(s, c->comp_hdr->CF_codec, blk, + (char *)&cr->cram_flags, + &out_sz); + cf = cr->cram_flags; + } + + if (fd->version != CRAM_1_VERS && ref_id == -2) { + if (!c->comp_hdr->RI_codec) return -1; + r |= c->comp_hdr->RI_codec->decode(s, c->comp_hdr->RI_codec, blk, + (char *)&cr->ref_id, &out_sz); + if (cr->ref_id >= 0) { + if (!fd->no_ref) { + if (!refs[cr->ref_id]) + refs[cr->ref_id] = cram_get_ref(fd, cr->ref_id, 1, 0); + s->ref = refs[cr->ref_id]; + } + s->ref_start = 1; + pthread_mutex_lock(&fd->ref_lock); + pthread_mutex_lock(&fd->refs->lock); + s->ref_end = fd->refs->ref_id[cr->ref_id]->length; + pthread_mutex_unlock(&fd->refs->lock); + pthread_mutex_unlock(&fd->ref_lock); + } + } else { + cr->ref_id = ref_id; // Forced constant in CRAM 1.0 + } + + + if (!c->comp_hdr->RL_codec) return -1; + r |= c->comp_hdr->RL_codec->decode(s, c->comp_hdr->RL_codec, blk, + (char *)&cr->len, &out_sz); + + if (!c->comp_hdr->AP_codec) return -1; + r |= c->comp_hdr->AP_codec->decode(s, c->comp_hdr->AP_codec, blk, + (char *)&cr->apos, &out_sz); + if (c->comp_hdr->AP_delta) + cr->apos += s->last_apos; + s->last_apos= cr->apos; + + if (!c->comp_hdr->RG_codec) return -1; + r |= c->comp_hdr->RG_codec->decode(s, c->comp_hdr->RG_codec, blk, + (char *)&cr->rg, &out_sz); + if (cr->rg == unknown_rg) + cr->rg = -1; + + cr->name_len = 0; + + if (c->comp_hdr->read_names_included) { + int32_t out_sz2 = 1; + + // Read directly into name cram_block + cr->name = BLOCK_SIZE(s->name_blk); + if (!c->comp_hdr->RN_codec) return -1; + r |= c->comp_hdr->RN_codec->decode(s, c->comp_hdr->RN_codec, blk, + (char *)s->name_blk, &out_sz2); + cr->name_len = out_sz2; + } + + cr->mate_line = -1; + cr->mate_ref_id = -1; + if (cf & CRAM_FLAG_DETACHED) { + if (fd->version == CRAM_1_VERS) { + /* MF is byte in 1.0, int32 in 2.0 */ + unsigned char mf; + if (!c->comp_hdr->MF_codec) return -1; + r |= c->comp_hdr->MF_codec->decode(s, c->comp_hdr->MF_codec, + blk, (char *)&mf, &out_sz); + cr->mate_flags = mf; + } else { + if (!c->comp_hdr->MF_codec) return -1; + r |= c->comp_hdr->MF_codec->decode(s, c->comp_hdr->MF_codec, + blk, + (char *)&cr->mate_flags, + &out_sz); + } + + if (!c->comp_hdr->read_names_included) { + int32_t out_sz2 = 1; + + // Read directly into name cram_block + cr->name = BLOCK_SIZE(s->name_blk); + if (!c->comp_hdr->RN_codec) return -1; + r |= c->comp_hdr->RN_codec->decode(s, c->comp_hdr->RN_codec, + blk, (char *)s->name_blk, + &out_sz2); + cr->name_len = out_sz2; + } + + if (!c->comp_hdr->NS_codec) return -1; + r |= c->comp_hdr->NS_codec->decode(s, c->comp_hdr->NS_codec, blk, + (char *)&cr->mate_ref_id, &out_sz); + +// Skip as mate_ref of "*" is legit. It doesn't mean unmapped, just unknown. +// if (cr->mate_ref_id == -1 && cr->flags & 0x01) { +// /* Paired, but unmapped */ +// cr->flags |= BAM_FMUNMAP; +// } + + if (!c->comp_hdr->NP_codec) return -1; + r |= c->comp_hdr->NP_codec->decode(s, c->comp_hdr->NP_codec, blk, + (char *)&cr->mate_pos, &out_sz); + if (!c->comp_hdr->TS_codec) return -1; + r |= c->comp_hdr->TS_codec->decode(s, c->comp_hdr->TS_codec, blk, + (char *)&cr->tlen, &out_sz); + } else if (cf & CRAM_FLAG_MATE_DOWNSTREAM) { + if (!c->comp_hdr->NF_codec) return -1; + r |= c->comp_hdr->NF_codec->decode(s, c->comp_hdr->NF_codec, blk, + (char *)&cr->mate_line, &out_sz); + cr->mate_line += rec + 1; + + //cr->name_len = sprintf(name, "%d", name_id++); + //cr->name = DSTRING_LEN(name_ds); + //dstring_nappend(name_ds, name, cr->name_len); + + cr->mate_ref_id = -1; + cr->tlen = INT_MIN; + cr->mate_pos = 0; + } else { + cr->mate_flags = 0; + cr->tlen = INT_MIN; + } + /* + else if (!name[0]) { + //name[0] = '?'; name[1] = 0; + //cr->name_len = 1; + //cr->name= DSTRING_LEN(s->name_ds); + //dstring_nappend(s->name_ds, "?", 1); + + cr->mate_ref_id = -1; + cr->tlen = 0; + cr->mate_pos = 0; + } + */ + + /* Auxiliary tags */ + if (fd->version == CRAM_1_VERS) + r |= cram_decode_aux_1_0(c, s, blk, cr); + else + r |= cram_decode_aux(c, s, blk, cr); + + /* Fake up dynamic string growth and appending */ + cr->seq = BLOCK_SIZE(s->seqs_blk); + BLOCK_GROW(s->seqs_blk, cr->len); + seq = (char *)BLOCK_END(s->seqs_blk); + BLOCK_SIZE(s->seqs_blk) += cr->len; + + if (!seq) + return -1; + + cr->qual = BLOCK_SIZE(s->qual_blk); + BLOCK_GROW(s->qual_blk, cr->len); + qual = (char *)BLOCK_END(s->qual_blk); + BLOCK_SIZE(s->qual_blk) += cr->len; + + if (!s->ref) + memset(seq, '=', cr->len); + + if (!(bf & BAM_FUNMAP)) { + /* Decode sequence and generate CIGAR */ + r |= cram_decode_seq(fd, c, s, blk, cr, bfd, cf, seq, qual); + } else { + int out_sz2 = cr->len; + + //puts("Unmapped"); + cr->cigar = 0; + cr->ncigar = 0; + cr->aend = cr->apos; + cr->mqual = 0; + + if (!c->comp_hdr->BA_codec) return -1; + r |= c->comp_hdr->BA_codec->decode(s, c->comp_hdr->BA_codec, blk, + (char *)seq, &out_sz2); + + if (cf & CRAM_FLAG_PRESERVE_QUAL_SCORES) { + out_sz2 = cr->len; + if (!c->comp_hdr->Qs_codec) return -1; + r |= c->comp_hdr->Qs_codec->decode(s, c->comp_hdr->Qs_codec, + blk, qual, &out_sz2); + } else { + memset(qual, 30, cr->len); + } + } + } + + pthread_mutex_lock(&fd->ref_lock); + if (refs) { + int i; + for (i = 0; i < fd->refs->nref; i++) { + if (refs[i]) + cram_ref_decr(fd->refs, i); + } + free(refs); + } else if (ref_id >= 0 && s->ref != fd->ref_free) { + cram_ref_decr(fd->refs, ref_id); + } + pthread_mutex_unlock(&fd->ref_lock); + + /* Resolve mate pair cross-references between recs within this slice */ + cram_decode_slice_xref(s); + + return r; +} + +typedef struct { + cram_fd *fd; + cram_container *c; + cram_slice *s; + SAM_hdr *h; + int exit_code; +} cram_decode_job; + +void *cram_decode_slice_thread(void *arg) { + cram_decode_job *j = (cram_decode_job *)arg; + + j->exit_code = cram_decode_slice(j->fd, j->c, j->s, j->h); + + return j; +} + +/* + * Spawn a multi-threaded version of cram_decode_slice(). + */ +int cram_decode_slice_mt(cram_fd *fd, cram_container *c, cram_slice *s, + SAM_hdr *bfd) { + cram_decode_job *j; + int nonblock; + + if (!fd->pool) + return cram_decode_slice(fd, c, s, bfd); + + if (!(j = malloc(sizeof(*j)))) + return -1; + + j->fd = fd; + j->c = c; + j->s = s; + j->h = bfd; + + nonblock = t_pool_results_queue_len(fd->rqueue) ? 0 : 1; + + if (-1 == t_pool_dispatch2(fd->pool, fd->rqueue, cram_decode_slice_thread, + j, nonblock)) { + /* Would block */ + fd->job_pending = j; + } else { + fd->job_pending = NULL; + } + + // flush too + return 0; +} + + +/* ---------------------------------------------------------------------- + * CRAM sequence iterators. + */ + +/* + * Converts a cram in-memory record into a bam in-memory record. We + * pass a pointer to a bam_seq_t pointer along with the a pointer to + * the allocated size. These can initially be pointers to NULL and zero. + * + * This function will reallocate the bam buffer as required and update + * (*bam)->alloc accordingly, allowing it to be used within a loop + * efficiently without needing to allocate new bam objects over and + * over again. + * + * Returns the used size of the bam record on success + * -1 on failure. + */ +static int cram_to_bam(SAM_hdr *bfd, cram_fd *fd, cram_slice *s, + cram_record *cr, int rec, bam_seq_t **bam) { + int bam_idx, rg_len; + char name_a[1024], *name; + int name_len; + char *aux, *aux_orig; + + /* Assign names if not explicitly set */ + if (cr->name_len) { + name = (char *)BLOCK_DATA(s->name_blk) + cr->name; + name_len = cr->name_len; + } else { + // FIXME: add prefix, container number, slice number, etc + name = name_a; + + if (cr->mate_line >= 0 && cr->mate_line < rec) + name_len = sprintf(name_a, "%s:%"PRId64":%d", + fd->prefix, s->id, cr->mate_line); + else + name_len = sprintf(name_a, "%s:%"PRId64":%d", + fd->prefix, s->id, rec); + } + + /* Generate BAM record */ + if (cr->rg < -1 || cr->rg >= bfd->nrg) + return -1; + rg_len = (cr->rg != -1) ? bfd->rg[cr->rg].name_len + 4 : 0; + + if (!BLOCK_DATA(s->seqs_blk)) + return -1; + if (!BLOCK_DATA(s->qual_blk)) + return -1; + + bam_idx = bam_construct_seq(bam, cr->aux_size + rg_len, + name, name_len, + cr->flags, + cr->ref_id, + cr->apos, + cr->aend, + cr->mqual, + cr->ncigar, &s->cigar[cr->cigar], + cr->mate_ref_id, + cr->mate_pos, + cr->tlen, + cr->len, + (char *)BLOCK_DATA(s->seqs_blk) + cr->seq, + (char *)BLOCK_DATA(s->qual_blk) + cr->qual); + if (bam_idx == -1) + return -1; + + aux = aux_orig = (char *)bam_aux(*bam); + + /* Auxiliary strings */ + if (cr->aux_size != 0) { + memcpy(aux, BLOCK_DATA(s->aux_blk) + cr->aux, cr->aux_size); + aux += cr->aux_size; + } + + /* RG:Z: */ + if (cr->rg != -1) { + int len = bfd->rg[cr->rg].name_len; + *aux++ = 'R'; *aux++ = 'G'; *aux++ = 'Z'; + memcpy(aux, bfd->rg[cr->rg].name, len); + aux += len; + *aux++ = 0; + } + +#ifndef SAMTOOLS + bam_set_blk_size(*bam, bam_blk_size(*bam) + (aux - aux_orig)); +#endif + + *aux++ = 0; + + return bam_idx + (aux - aux_orig); +} + +/* + * Here be dragons! The multi-threading code in this is crufty beyond belief. + */ +static cram_slice *cram_next_slice(cram_fd *fd, cram_container **cp) { + cram_container *c; + cram_slice *s = NULL; + + fd->eof = 0; + + if (!(c = fd->ctr)) { + // Load first container. + do { + if (!(c = fd->ctr = cram_read_container(fd))) + return NULL; + } while (c->length == 0); + + /* + * The first container may be a result of a sub-range query. + * In which case it may still not be the optimal starting point + * due to skipped containers/slices in the index. + */ + if (fd->range.refid != -2) { + while (c->ref_seq_id != -2 && + (c->ref_seq_id < fd->range.refid || + c->ref_seq_start + c->ref_seq_span-1 < fd->range.start)) { + if (0 != cram_seek(fd, c->length, SEEK_CUR)) + return NULL; + cram_free_container(fd->ctr); + do { + if (!(c = fd->ctr = cram_read_container(fd))) + return NULL; + } while (c->length == 0); + } + + if (c->ref_seq_id != -2 && c->ref_seq_id != fd->range.refid) + return NULL; + } + + if (!(c->comp_hdr_block = cram_read_block(fd))) + return NULL; + if (c->comp_hdr_block->content_type != COMPRESSION_HEADER) + return NULL; + + c->comp_hdr = cram_decode_compression_header(fd, c->comp_hdr_block); + if (!c->comp_hdr) + return NULL; + if (!c->comp_hdr->AP_delta) { + pthread_mutex_lock(&fd->ref_lock); + fd->unsorted = 1; + pthread_mutex_unlock(&fd->ref_lock); + } + } + + if ((s = c->slice)) + cram_free_slice(s); + + if (c->curr_slice == c->max_slice) { + cram_free_container(c); + c = NULL; + } + + /* Sorry this is so contorted! */ + for (;;) { + if (fd->job_pending) { + cram_decode_job *j = (cram_decode_job *)fd->job_pending; + c = j->c; + s = j->s; + free(fd->job_pending); + fd->job_pending = NULL; + } else if (!fd->ooc) { + empty_container: + if (!c || c->curr_slice == c->max_slice) { + // new container + do { + if (!(c = fd->ctr = cram_read_container(fd))) { + if (fd->pool) { + fd->ooc = 1; + break; + } + + return NULL; + } + } while (c->length == 0); + if (fd->ooc) + break; + + /* Skip containers not yet spanning our range */ + if (fd->range.refid != -2 && c->ref_seq_id != -2) { + if (c->ref_seq_id != fd->range.refid) { + fd->eof = 1; + return NULL; + } + + if (c->ref_seq_start > fd->range.end) { + fd->eof = 1; + return NULL; + } + + if (c->ref_seq_start + c->ref_seq_span-1 < + fd->range.start) { + c->curr_rec = c->max_rec; + c->curr_slice = c->max_slice; + cram_seek(fd, c->length, SEEK_CUR); + cram_free_container(c); + c = NULL; + continue; + } + } + + if (!(c->comp_hdr_block = cram_read_block(fd))) + return NULL; + if (c->comp_hdr_block->content_type != COMPRESSION_HEADER) + return NULL; + + c->comp_hdr = + cram_decode_compression_header(fd, c->comp_hdr_block); + if (!c->comp_hdr) + return NULL; + + if (!c->comp_hdr->AP_delta) { + pthread_mutex_lock(&fd->ref_lock); + fd->unsorted = 1; + pthread_mutex_unlock(&fd->ref_lock); + } + } + + if (c->num_records == 0) { + cram_free_container(c); c = NULL; + goto empty_container; + } + + + if (!(s = c->slice = cram_read_slice(fd))) + return NULL; + c->curr_slice++; + c->curr_rec = 0; + c->max_rec = s->hdr->num_records; + + s->last_apos = s->hdr->ref_seq_start; + + /* Skip slices not yet spanning our range */ + if (fd->range.refid != -2 && s->hdr->ref_seq_id != -2) { + if (s->hdr->ref_seq_id != fd->range.refid) { + fd->eof = 1; + cram_free_slice(s); + c->slice = NULL; + return NULL; + } + + if (s->hdr->ref_seq_start > fd->range.end) { + fd->eof = 1; + cram_free_slice(s); + c->slice = NULL; + return NULL; + } + + if (s->hdr->ref_seq_start + s->hdr->ref_seq_span-1 < + fd->range.start) { + cram_free_slice(s); + c->slice = NULL; + cram_free_container(c); + c = NULL; + continue; + } + } + } + + /* Test decoding of 1st seq */ + if (!c || !s) + break; + + if (cram_decode_slice_mt(fd, c, s, fd->header) != 0) { + // if (cram_decode_slice(fd, c, s, fd->header) != 0) { + fprintf(stderr, "Failure to decode slice\n"); + cram_free_slice(s); + c->slice = NULL; + return NULL; + } + + if (!fd->pool || fd->job_pending) + break; + + if (t_pool_results_queue_sz(fd->rqueue) > fd->pool->qsize) + break; + } + + if (fd->pool) { + t_pool_result *res; + cram_decode_job *j; + +// fprintf(stderr, "Thread pool len = %d, %d\n", +// t_pool_results_queue_len(fd->rqueue), +// t_pool_results_queue_sz(fd->rqueue)); + + if (fd->ooc && t_pool_results_queue_empty(fd->rqueue)) + return NULL; + + res = t_pool_next_result_wait(fd->rqueue); + + if (!res || !res->data) { + fprintf(stderr, "t_pool_next_result failure\n"); + return NULL; + } + + j = (cram_decode_job *)res->data; + c = j->c; + s = j->s; + + t_pool_delete_result(res, 1); + } + + *cp = c; + return s; +} + +/* + * Read the next cram record and return it. + * Note that to decode cram_record the caller will need to look up some data + * in the current slice, pointed to by fd->ctr->slice. This is valid until + * the next call to cram_get_seq (which may invalidate it). + * + * Returns record pointer on success (do not free) + * NULL on failure + */ +cram_record *cram_get_seq(cram_fd *fd) { + cram_container *c; + cram_slice *s; + + for (;;) { + c = fd->ctr; + if (c && c->slice && c->curr_rec < c->max_rec) { + s = c->slice; + } else { + if (!(s = cram_next_slice(fd, &c))) + return NULL; + } + + if (fd->range.refid != -2) { + if (s->crecs[c->curr_rec].ref_id < fd->range.refid) { + c->curr_rec++; + continue; + } + + if (s->crecs[c->curr_rec].ref_id != fd->range.refid) { + fd->eof = 1; + cram_free_slice(s); + c->slice = NULL; + return NULL; + } + + if (s->crecs[c->curr_rec].apos > fd->range.end) { + fd->eof = 1; + cram_free_slice(s); + c->slice = NULL; + return NULL; + } + + if (s->crecs[c->curr_rec].aend < fd->range.start) { + c->curr_rec++; + continue; + } + } + + break; + } + + fd->ctr = c; + c->slice = s; + return &s->crecs[c->curr_rec++]; +} + +/* + * Read the next cram record and convert it to a bam_seq_t struct. + * + * Returns 0 on success + * -1 on EOF or failure (check fd->err) + */ +int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam) { + cram_record *cr; + cram_container *c; + cram_slice *s; + + if (!(cr = cram_get_seq(fd))) + return -1; + + c = fd->ctr; + s = c->slice; + + return cram_to_bam(fd->header, fd, s, cr, c->curr_rec-1, bam); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_decode.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_decode.h new file mode 100644 index 0000000000000000000000000000000000000000..64b188e25c24fab4cede98ac6242dc8b01727b85 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_decode.h @@ -0,0 +1,112 @@ +/* +Copyright (c) 2012-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +/*! \file + * Include cram.h instead. + * + * This is an internal part of the CRAM system and is automatically included + * when you #include cram.h. + * + * Implements the decoding portion of CRAM I/O. Also see + * cram_codecs.[ch] for the actual encoding functions themselves. + */ + +#ifndef _CRAM_READ_H_ +#define _CRAM_READ_H_ + +#ifdef __cplusplus +extern "C" { +#endif + +/* ---------------------------------------------------------------------- + * CRAM sequence iterators. + */ + +/*! Read the next cram record and return it as a cram_record. + * + * Note that to decode cram_record the caller will need to look up some data + * in the current slice, pointed to by fd->ctr->slice. This is valid until + * the next call to cram_get_seq (which may invalidate it). + * + * @return + * Returns record pointer on success (do not free); + * NULL on failure + */ +cram_record *cram_get_seq(cram_fd *fd); + +/*! Read the next cram record and convert it to a bam_seq_t struct. + * + * @return + * Returns 0 on success; + * -1 on EOF or failure (check fd->err) + */ +int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam); + + +/* ---------------------------------------------------------------------- + * Internal functions + */ + +/*! INTERNAL: + * Decodes a CRAM block compression header. + * + * @return + * Returns header ptr on success; + * NULL on failure + */ +cram_block_compression_hdr *cram_decode_compression_header(cram_fd *fd, + cram_block *b); + +/*! INTERNAL: + * Decodes a CRAM (un)mapped slice header block. + * + * @return + * Returns slice header ptr on success; + * NULL on failure + */ +cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b); + + +/*! INTERNAL: + * Decode an entire slice from container blocks. Fills out s->crecs[] array. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s, + SAM_hdr *hdr); + + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_encode.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_encode.c new file mode 100644 index 0000000000000000000000000000000000000000..94c2cebecbd63d981fe0771c54a3a0c3607ca8e7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_encode.c @@ -0,0 +1,2630 @@ +/* +Copyright (c) 2012-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifdef HAVE_CONFIG_H +#include "io_lib_config.h" +#endif + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "cram/cram.h" +#include "cram/os.h" +#include "cram/md5.h" + +#ifdef SAMTOOLS +# define bam_copy(dst, src) bam_copy1(*(dst), (src)) +#else +void bam_copy(bam_seq_t **bt, bam_seq_t *bf) { + size_t a; + + if (bf->alloc > (*bt)->alloc) { + a = ((int)((bf->alloc+15)/16))*16; + *bt = realloc(*bt, a); + memcpy(*bt, bf, bf->alloc); + } else { + a = (*bt)->alloc; + memcpy(*bt, bf, bf->alloc); + } + + (*bt)->alloc = a; +} +#endif + +#define Z_CRAM_STRAT Z_FILTERED +//#define Z_CRAM_STRAT Z_RLE +//#define Z_CRAM_STRAT Z_HUFFMAN_ONLY +//#define Z_CRAM_STRAT Z_DEFAULT_STRATEGY + +static int process_one_read(cram_fd *fd, cram_container *c, + cram_slice *s, cram_record *cr, + bam_seq_t *b, int rnum); + +/* + * Returns index of val into key. + * Basically strchr(key, val)-key; + */ +static int sub_idx(char *key, char val) { + int i; + + for (i = 0; *key && *key++ != val; i++); + return i; +} + +/* + * Encodes a compression header block into a generic cram_block structure. + * + * Returns cram_block ptr on success + * NULL on failure + */ +cram_block *cram_encode_compression_header(cram_fd *fd, cram_container *c, + cram_block_compression_hdr *h) { + cram_block *cb = cram_new_block(COMPRESSION_HEADER, 0); + cram_block *map = cram_new_block(COMPRESSION_HEADER, 0); + int i, mc; + + if (!cb || !map) + return NULL; + + /* + * This is a concatenation of several blocks of data: + * header + landmarks, preservation map, read encoding map, and the tag + * encoding map. + * All 4 are variable sized and we need to know how large these are + * before creating the compression header itself as this starts with + * the total size (stored as a variable length string). + */ + + // Duplicated from container itself, and removed in 1.1 + if (fd->version == CRAM_1_VERS) { + itf8_put_blk(cb, h->ref_seq_id); + itf8_put_blk(cb, h->ref_seq_start); + itf8_put_blk(cb, h->ref_seq_span); + itf8_put_blk(cb, h->num_records); + itf8_put_blk(cb, h->num_landmarks); + for (i = 0; i < h->num_landmarks; i++) { + itf8_put_blk(cb, h->landmark[i]); + } + } + + /* Create in-memory preservation map */ + /* FIXME: should create this when we create the container */ + { + khint_t k; + int r; + + if (!(h->preservation_map = kh_init(map))) + return NULL; + + k = kh_put(map, h->preservation_map, "RN", &r); + if (-1 == r) return NULL; + kh_val(h->preservation_map, k).i = 1; + + if (fd->version == CRAM_1_VERS) { + k = kh_put(map, h->preservation_map, "PI", &r); + if (-1 == r) return NULL; + kh_val(h->preservation_map, k).i = 0; + + k = kh_put(map, h->preservation_map, "UI", &r); + if (-1 == r) return NULL; + kh_val(h->preservation_map, k).i = 1; + + k = kh_put(map, h->preservation_map, "MI", &r); + if (-1 == r) return NULL; + kh_val(h->preservation_map, k).i = 1; + + } else { + // Technically SM was in 1.0, but wasn't in Java impl. + k = kh_put(map, h->preservation_map, "SM", &r); + if (-1 == r) return NULL; + kh_val(h->preservation_map, k).i = 0; + + k = kh_put(map, h->preservation_map, "TD", &r); + if (-1 == r) return NULL; + kh_val(h->preservation_map, k).i = 0; + + k = kh_put(map, h->preservation_map, "AP", &r); + if (-1 == r) return NULL; + kh_val(h->preservation_map, k).i = c->pos_sorted; + + if (fd->no_ref || fd->embed_ref) { + // Reference Required == No + k = kh_put(map, h->preservation_map, "RR", &r); + if (-1 == r) return NULL; + kh_val(h->preservation_map, k).i = 0; + } + } + } + + /* Encode preservation map; could collapse this and above into one */ + mc = 0; + BLOCK_SIZE(map) = 0; + if (h->preservation_map) { + khint_t k; + + for (k = kh_begin(h->preservation_map); + k != kh_end(h->preservation_map); + k++) { + const char *key; + khash_t(map) *pmap = h->preservation_map; + + + if (!kh_exist(pmap, k)) + continue; + + key = kh_key(pmap, k); + BLOCK_APPEND(map, key, 2); + + switch(CRAM_KEY(key[0], key[1])) { + case CRAM_KEY('M','I'): + BLOCK_APPEND_CHAR(map, kh_val(pmap, k).i); + break; + + case CRAM_KEY('U','I'): + BLOCK_APPEND_CHAR(map, kh_val(pmap, k).i); + break; + + case CRAM_KEY('P','I'): + BLOCK_APPEND_CHAR(map, kh_val(pmap, k).i); + break; + + case CRAM_KEY('A','P'): + BLOCK_APPEND_CHAR(map, kh_val(pmap, k).i); + break; + + case CRAM_KEY('R','N'): + BLOCK_APPEND_CHAR(map, kh_val(pmap, k).i); + break; + + case CRAM_KEY('R','R'): + BLOCK_APPEND_CHAR(map, kh_val(pmap, k).i); + break; + + case CRAM_KEY('S','M'): { + char smat[5], *mp = smat; + *mp++ = + (sub_idx("CGTN", h->substitution_matrix[0][0]) << 6) | + (sub_idx("CGTN", h->substitution_matrix[0][1]) << 4) | + (sub_idx("CGTN", h->substitution_matrix[0][2]) << 2) | + (sub_idx("CGTN", h->substitution_matrix[0][3]) << 0); + *mp++ = + (sub_idx("AGTN", h->substitution_matrix[1][0]) << 6) | + (sub_idx("AGTN", h->substitution_matrix[1][1]) << 4) | + (sub_idx("AGTN", h->substitution_matrix[1][2]) << 2) | + (sub_idx("AGTN", h->substitution_matrix[1][3]) << 0); + *mp++ = + (sub_idx("ACTN", h->substitution_matrix[2][0]) << 6) | + (sub_idx("ACTN", h->substitution_matrix[2][1]) << 4) | + (sub_idx("ACTN", h->substitution_matrix[2][2]) << 2) | + (sub_idx("ACTN", h->substitution_matrix[2][3]) << 0); + *mp++ = + (sub_idx("ACGN", h->substitution_matrix[3][0]) << 6) | + (sub_idx("ACGN", h->substitution_matrix[3][1]) << 4) | + (sub_idx("ACGN", h->substitution_matrix[3][2]) << 2) | + (sub_idx("ACGN", h->substitution_matrix[3][3]) << 0); + *mp++ = + (sub_idx("ACGT", h->substitution_matrix[4][0]) << 6) | + (sub_idx("ACGT", h->substitution_matrix[4][1]) << 4) | + (sub_idx("ACGT", h->substitution_matrix[4][2]) << 2) | + (sub_idx("ACGT", h->substitution_matrix[4][3]) << 0); + BLOCK_APPEND(map, smat, 5); + break; + } + + case CRAM_KEY('T','D'): { + itf8_put_blk(map, BLOCK_SIZE(h->TD_blk)); + BLOCK_APPEND(map, + BLOCK_DATA(h->TD_blk), + BLOCK_SIZE(h->TD_blk)); + break; + } + + default: + fprintf(stderr, "Unknown preservation key '%.2s'\n", key); + break; + } + + mc++; + } + } + itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); + itf8_put_blk(cb, mc); + BLOCK_APPEND(cb, BLOCK_DATA(map), BLOCK_SIZE(map)); + + /* rec encoding map */ + mc = 0; + BLOCK_SIZE(map) = 0; + if (h->BF_codec) { + if (-1 == h->BF_codec->store(h->BF_codec, map, "BF", fd->version)) + return NULL; + mc++; + } + if (h->CF_codec) { + if (-1 == h->CF_codec->store(h->CF_codec, map, "CF", fd->version)) + return NULL; + mc++; + } + if (h->RL_codec) { + if (-1 == h->RL_codec->store(h->RL_codec, map, "RL", fd->version)) + return NULL; + mc++; + } + if (h->AP_codec) { + if (-1 == h->AP_codec->store(h->AP_codec, map, "AP", fd->version)) + return NULL; + mc++; + } + if (h->RG_codec) { + if (-1 == h->RG_codec->store(h->RG_codec, map, "RG", fd->version)) + return NULL; + mc++; + } + if (h->MF_codec) { + if (-1 == h->MF_codec->store(h->MF_codec, map, "MF", fd->version)) + return NULL; + mc++; + } + if (h->NS_codec) { + if (-1 == h->NS_codec->store(h->NS_codec, map, "NS", fd->version)) + return NULL; + mc++; + } + if (h->NP_codec) { + if (-1 == h->NP_codec->store(h->NP_codec, map, "NP", fd->version)) + return NULL; + mc++; + } + if (h->TS_codec) { + if (-1 == h->TS_codec->store(h->TS_codec, map, "TS", fd->version)) + return NULL; + mc++; + } + if (h->NF_codec) { + if (-1 == h->NF_codec->store(h->NF_codec, map, "NF", fd->version)) + return NULL; + mc++; + } + if (h->TC_codec) { + if (-1 == h->TC_codec->store(h->TC_codec, map, "TC", fd->version)) + return NULL; + mc++; + } + if (h->TN_codec) { + if (-1 == h->TN_codec->store(h->TN_codec, map, "TN", fd->version)) + return NULL; + mc++; + } + if (h->TL_codec) { + if (-1 == h->TL_codec->store(h->TL_codec, map, "TL", fd->version)) + return NULL; + mc++; + } + if (h->FN_codec) { + if (-1 == h->FN_codec->store(h->FN_codec, map, "FN", fd->version)) + return NULL; + mc++; + } + if (h->FC_codec) { + if (-1 == h->FC_codec->store(h->FC_codec, map, "FC", fd->version)) + return NULL; + mc++; + } + if (h->FP_codec) { + if (-1 == h->FP_codec->store(h->FP_codec, map, "FP", fd->version)) + return NULL; + mc++; + } + if (h->BS_codec) { + if (-1 == h->BS_codec->store(h->BS_codec, map, "BS", fd->version)) + return NULL; + mc++; + } + if (h->IN_codec) { + if (-1 == h->IN_codec->store(h->IN_codec, map, "IN", fd->version)) + return NULL; + mc++; + } + if (h->DL_codec) { + if (-1 == h->DL_codec->store(h->DL_codec, map, "DL", fd->version)) + return NULL; + mc++; + } + if (h->BA_codec) { + if (-1 == h->BA_codec->store(h->BA_codec, map, "BA", fd->version)) + return NULL; + mc++; + } + if (h->MQ_codec) { + if (-1 == h->MQ_codec->store(h->MQ_codec, map, "MQ", fd->version)) + return NULL; + mc++; + } + if (h->RN_codec) { + if (-1 == h->RN_codec->store(h->RN_codec, map, "RN", fd->version)) + return NULL; + mc++; + } + if (h->QS_codec) { + if (-1 == h->QS_codec->store(h->QS_codec, map, "QS", fd->version)) + return NULL; + mc++; + } + if (h->Qs_codec) { + if (-1 == h->Qs_codec->store(h->Qs_codec, map, "Qs", fd->version)) + return NULL; + mc++; + } + if (h->RI_codec) { + if (-1 == h->RI_codec->store(h->RI_codec, map, "RI", fd->version)) + return NULL; + mc++; + } + if (fd->version != CRAM_1_VERS) { + if (h->SC_codec) { + if (-1 == h->SC_codec->store(h->SC_codec, map, "SC", fd->version)) + return NULL; + mc++; + } + if (h->RS_codec) { + if (-1 == h->RS_codec->store(h->RS_codec, map, "RS", fd->version)) + return NULL; + mc++; + } + if (h->PD_codec) { + if (-1 == h->PD_codec->store(h->PD_codec, map, "PD", fd->version)) + return NULL; + mc++; + } + if (h->HC_codec) { + if (-1 == h->HC_codec->store(h->HC_codec, map, "HC", fd->version)) + return NULL; + mc++; + } + } + if (h->TM_codec) { + if (-1 == h->TM_codec->store(h->TM_codec, map, "TM", fd->version)) + return NULL; + mc++; + } + if (h->TV_codec) { + if (-1 == h->TV_codec->store(h->TV_codec, map, "TV", fd->version)) + return NULL; + mc++; + } + itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); + itf8_put_blk(cb, mc); + BLOCK_APPEND(cb, BLOCK_DATA(map), BLOCK_SIZE(map)); + + /* tag encoding map */ +#if 0 + mp = map; mc = 0; + if (h->tag_encoding_map) { + HashItem *hi; + HashIter *iter = HashTableIterCreate(); + if (!iter) + return NULL; + + while ((hi = HashTableIterNext(h->tag_encoding_map, iter))) { + cram_map *m = hi->data.p; + int sz; + + mp += itf8_put(mp, (hi->key[0]<<16)|(hi->key[1]<<8)|hi->key[2]); + if (-1 == (sz = m->codec->store(m->codec, mp, NULL, fd->version))) + return NULL; + mp += sz; + mc++; + } + + HashTableIterDestroy(iter); + } +#else + mc = 0; + BLOCK_SIZE(map) = 0; + if (c->tags_used) { + khint_t k; + + for (k = kh_begin(c->tags_used); k != kh_end(c->tags_used); k++) { + if (!kh_exist(c->tags_used, k)) + continue; + + mc++; + itf8_put_blk(map, kh_key(c->tags_used, k)); + + // use block content id 4 + switch(kh_key(c->tags_used, k) & 0xff) { + case 'Z': case 'H': + // string as byte_array_stop + if (fd->version == CRAM_1_VERS) { + BLOCK_APPEND(map, + "\005" // BYTE_ARRAY_STOP + "\005" // len + "\t" // stop-byte is also SAM separator + CRAM_EXT_TAG_S "\000\000\000", + 7); + } else { + BLOCK_APPEND(map, + "\005" // BYTE_ARRAY_STOP + "\002" // len + "\t" // stop-byte is also SAM separator + CRAM_EXT_TAG_S, + 4); + } + break; + + case 'A': case 'c': case 'C': + // byte array len, 1 byte + BLOCK_APPEND(map, + "\004" // BYTE_ARRAY_LEN + "\011" // length + "\003" // HUFFMAN (len) + "\004" // huffman-len + "\001" // 1 symbol + "\001" // symbol=1 byte value + "\001" // 1 length + "\000" // length=0 + "\001" // EXTERNAL (val) + "\001" // external-len + CRAM_EXT_TAG_S,// content-id + 11); + break; + + case 's': case 'S': + // byte array len, 2 byte + BLOCK_APPEND(map, + "\004" // BYTE_ARRAY_LEN + "\011" // length + "\003" // HUFFMAN (len) + "\004" // huffman-len + "\001" // 1 symbol + "\002" // symbol=2 byte value + "\001" // 1 length + "\000" // length=0 + "\001" // EXTERNAL (val) + "\001" // external-len + CRAM_EXT_TAG_S,// content-id + 11); + break; + + case 'i': case 'I': case 'f': + // byte array len, 4 byte + BLOCK_APPEND(map, + "\004" // BYTE_ARRAY_LEN + "\011" // length + "\003" // HUFFMAN (len) + "\004" // huffman-len + "\001" // 1 symbol + "\004" // symbol=4 byte value + "\001" // 1 length + "\000" // length=0 + "\001" // EXTERNAL (val) + "\001" // external-len + CRAM_EXT_TAG_S,// content-id + 11); + break; + + case 'B': + // Byte array of variable size, but we generate our tag + // byte stream at the wrong stage (during reading and not + // after slice header construction). So we use + // BYTE_ARRAY_LEN with the length codec being external + // too. + BLOCK_APPEND(map, + "\004" // BYTE_ARRAY_LEN + "\006" // length + "\001" // EXTERNAL (len) + "\001" // external-len + "\004" // content-id + "\001" // EXTERNAL (val) + "\001" // external-len + CRAM_EXT_TAG_S,// content-id + 8); + break; + + default: + fprintf(stderr, "Unsupported SAM aux type '%c'\n", + kh_key(c->tags_used, k) & 0xff); + } + //mp += m->codec->store(m->codec, mp, NULL, fd->version); + } + } +#endif + itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); + itf8_put_blk(cb, mc); + BLOCK_APPEND(cb, BLOCK_DATA(map), BLOCK_SIZE(map)); + + if (fd->verbose) + fprintf(stderr, "Wrote compression block header in %d bytes\n", + (int)BLOCK_SIZE(cb)); + + BLOCK_UPLEN(cb); + + cram_free_block(map); + + return cb; +} + + +/* + * Encodes a slice compression header. + * + * Returns cram_block on success + * NULL on failure + */ +cram_block *cram_encode_slice_header(cram_fd *fd, cram_slice *s) { + char *buf; + char *cp; + cram_block *b = cram_new_block(MAPPED_SLICE, 0); + int j; + + if (!b) + return NULL; + + if (NULL == (cp = buf = malloc(16+5*(8+s->hdr->num_blocks)))) { + cram_free_block(b); + return NULL; + } + + cp += itf8_put(cp, s->hdr->ref_seq_id); + cp += itf8_put(cp, s->hdr->ref_seq_start); + cp += itf8_put(cp, s->hdr->ref_seq_span); + cp += itf8_put(cp, s->hdr->num_records); + if (fd->version != CRAM_1_VERS) + cp += itf8_put(cp, s->hdr->record_counter); + cp += itf8_put(cp, s->hdr->num_blocks); + cp += itf8_put(cp, s->hdr->num_content_ids); + for (j = 0; j < s->hdr->num_content_ids; j++) { + cp += itf8_put(cp, s->hdr->block_content_ids[j]); + } + if (s->hdr->content_type == MAPPED_SLICE) + cp += itf8_put(cp, s->hdr->ref_base_id); + + if (fd->version != CRAM_1_VERS) { + memcpy(cp, s->hdr->md5, 16); cp += 16; + } + + assert(cp-buf <= 16+5*(8+s->hdr->num_blocks)); + + b->data = (unsigned char *)buf; + b->comp_size = b->uncomp_size = cp-buf; + + return b; +} + + +/* + * Encodes a single slice from a container + * FIXME: break into smaller components. + * + * Returns 0 on success + * -1 on failure + */ +static int cram_encode_slice(cram_fd *fd, cram_container *c, + cram_block_compression_hdr *h, cram_slice *s) { + int rec, r = 0, last_pos; + cram_block *core; + int nblk, embed_ref; + + embed_ref = fd->embed_ref && s->hdr->ref_seq_id != -1 ? 1 : 0; + + /* + * Slice external blocks: + * ID 0 => base calls (insertions, soft-clip) + * ID 1 => qualities + * ID 2 => names + * ID 3 => TS (insert size), NP (next frag) + * ID 4 => tag values + * ID 5 => BA, ifdef BA_external + * ID 6 => tag IDs (TN), ifdef TN_external and CRAM_1_VERS + * ID 7 => TD tag dictionary, if !CRAM_1_VERS + */ + + /* Create cram slice header, num_blocks etc */ + s->hdr->ref_base_id = embed_ref ? CRAM_EXT_REF : -1; + s->hdr->record_counter = c->num_records + c->record_counter; + c->num_records += s->hdr->num_records; + nblk = (fd->version == CRAM_1_VERS) ? 5 : 6; +#ifdef BA_external + nblk++; +#endif +#ifdef TN_external + if (fd->version == CRAM_1_VERS) { + nblk++; + } +#endif + if (embed_ref) + nblk++; + + s->hdr->num_content_ids = nblk; + s->hdr->num_blocks = s->hdr->num_content_ids+1; + s->block = calloc(s->hdr->num_blocks, sizeof(s->block[0])); + s->hdr->block_content_ids = malloc(s->hdr->num_content_ids * + sizeof(int32_t)); + if (!s->block || !s->hdr->block_content_ids) + return -1; + s->hdr->block_content_ids[0] = 0; // core + s->hdr->block_content_ids[1] = CRAM_EXT_QUAL; + s->hdr->block_content_ids[2] = CRAM_EXT_NAME; + s->hdr->block_content_ids[3] = CRAM_EXT_TS_NP; + s->hdr->block_content_ids[4] = CRAM_EXT_TAG; + s->hdr->block_content_ids[5] = CRAM_EXT_SC; + nblk = (fd->version == CRAM_1_VERS) ? 5 : 6; +#ifdef BA_external + s->hdr->block_content_ids[(s->ba_id = ++nblk)-1] = CRAM_EXT_BA; +#endif +#ifdef TN_external + if (fd->version == CRAM_1_VERS) { + s->hdr->block_content_ids[(s->tn_id = ++nblk)-1] = CRAM_EXT_TN; + } +#endif + if (embed_ref) + s->hdr->block_content_ids[(s->ref_id = ++nblk)-1] = CRAM_EXT_REF; + + if (!(s->block[0] = cram_new_block(CORE, 0))) return -1; + if (!(s->block[1] = cram_new_block(EXTERNAL, CRAM_EXT_IN))) return -1; + if (!(s->block[2] = cram_new_block(EXTERNAL, CRAM_EXT_QUAL))) return -1; + if (!(s->block[3] = cram_new_block(EXTERNAL, CRAM_EXT_NAME))) return -1; + if (!(s->block[4] = cram_new_block(EXTERNAL, CRAM_EXT_TS_NP))) return -1; + if (!(s->block[5] = cram_new_block(EXTERNAL, CRAM_EXT_TAG))) return -1; + if (fd->version != CRAM_1_VERS) { + if (!(s->block[6] = cram_new_block(EXTERNAL, CRAM_EXT_SC))) + return -1; + } +#ifdef BA_external + if (!(s->block[s->ba_id] = cram_new_block(EXTERNAL, CRAM_EXT_BA))) + return -1; +#endif +#ifdef TN_external + if (fd->version == CRAM_1_VERS) { + if (!(s->block[s->tn_id] = cram_new_block(EXTERNAL, CRAM_EXT_TN))) + return -1; + } +#endif + if (embed_ref) { + if (!(s->block[s->ref_id] = cram_new_block(EXTERNAL, CRAM_EXT_REF))) + return -1; + BLOCK_APPEND(s->block[s->ref_id], + c->ref + c->first_base - c->ref_start, + c->last_base - c->first_base + 1); + } + + core = s->block[0]; + + /* Create a formal method for stealing from dstrings! */ + s->block[4]->data = calloc(10, s->hdr->num_records); // NP TS + if (!s->block[4]->data) + return -1; + s->block[4]->comp_size = s->block[4]->uncomp_size = 0; + +#ifdef BA_external + s->block[s->ba_id]->data = calloc(1, s->BA_len); + if (!s->block[s->ba_id]->data) + return -1; + s->block[s->ba_id]->comp_size = s->block[s->ba_id]->uncomp_size = 0; +#endif + + /* Generate core block */ + if (!(s->hdr_block = cram_encode_slice_header(fd, s))) + return -1; + + last_pos = s->hdr->ref_seq_start; + for (rec = 0; rec < s->hdr->num_records; rec++) { + cram_record *cr = &s->crecs[rec]; + int32_t i32; + unsigned char uc; + + //fprintf(stderr, "Encode seq %d, %d/%d FN=%d, %s\n", rec, core->byte, core->bit, cr->nfeature, s->name_ds->str + cr->name); + + //printf("BF=0x%x\n", cr->flags); + // bf = cram_flag_swap[cr->flags]; + i32 = fd->cram_flag_swap[cr->flags & 0xfff]; + r |= h->BF_codec->encode(s, h->BF_codec, core, (char *)&i32, 1); + + i32 = cr->cram_flags; + r |= h->CF_codec->encode(s, h->CF_codec, core, + (char *)&i32, 1); + + if (fd->version != CRAM_1_VERS) + r |= h->RI_codec->encode(s, h->RI_codec, core, + (char *)&cr->ref_id, 1); + + r |= h->RL_codec->encode(s, h->RL_codec, core, + (char *)&cr->len, 1); + + if (c->pos_sorted) { + i32 = cr->apos - last_pos; + r |= h->AP_codec->encode(s, h->AP_codec, core, (char *)&i32, 1); + last_pos = cr->apos; + } else { + i32 = cr->apos; + r |= h->AP_codec->encode(s, h->AP_codec, core, (char *)&i32, 1); + } + + r |= h->RG_codec->encode(s, h->RG_codec, core, + (char *)&cr->rg, 1); + + if (c->comp_hdr->read_names_included) { + // RN codec: Already stored in block[3]. + } + + if (cr->cram_flags & CRAM_FLAG_DETACHED) { + i32 = cr->mate_flags; + r |= h->MF_codec->encode(s, h->MF_codec, core, (char *)&i32, 1); + + if (!c->comp_hdr->read_names_included) { + // RN codec: Already stored in block[3]. + } + +#ifndef NS_external + r |= h->NS_codec->encode(s, h->NS_codec, core, + (char *)&cr->mate_ref_id, 1); +#else + s->block[4]->uncomp_size += + itf8_put(&s->block[4]->data[s->block[4]->uncomp_size], + cr->mate_ref_id); +#endif + +#ifndef TS_external + r |= h->NP_codec->encode(s, h->NP_codec, core, + (char *)&cr->mate_pos, 1); + + r |= h->TS_codec->encode(s, h->TS_codec, core, + (char *)&cr->tlen, 1); +#else + s->block[4]->uncomp_size += + itf8_put((char *)&s->block[4]->data[s->block[4]->uncomp_size], + cr->mate_pos); + s->block[4]->uncomp_size += + itf8_put((char *)&s->block[4]->data[s->block[4]->uncomp_size], + cr->tlen); +#endif + } else if (cr->cram_flags & CRAM_FLAG_MATE_DOWNSTREAM) { + r |= h->NF_codec->encode(s, h->NF_codec, core, + (char *)&cr->mate_line, 1); + } + + /* Aux tags */ + if (fd->version == CRAM_1_VERS) { + uc = cr->ntags; + r |= h->TC_codec->encode(s, h->TC_codec, core, (char *)&uc, 1); +#ifndef TN_external + { + int j; + for (j = 0; j < cr->ntags; j++) { + uint32_t i32 = s->TN[cr->TN_idx + j]; // id + r |= h->TN_codec->encode(s, h->TN_codec, core, + (char *)&i32, 1); + } + } +#endif + } else { + r |= h->TL_codec->encode(s, h->TL_codec, core, (char *)&cr->TL, 1); + } + + // qual + // QS codec : Already stored in block[2]. + + // features (diffs) + if (!(cr->flags & BAM_FUNMAP)) { + int prev_pos = 0, j; + + r |= h->FN_codec->encode(s, h->FN_codec, core, + (char *)&cr->nfeature, 1); + for (j = 0; j < cr->nfeature; j++) { + cram_feature *f = &s->features[cr->feature + j]; + + uc = f->X.code; + r |= h->FC_codec->encode(s, h->FC_codec, core, + (char *)&uc, 1); + i32 = f->X.pos - prev_pos; + r |= h->FP_codec->encode(s, h->FP_codec, core, + (char *)&i32, 1); + prev_pos = f->X.pos; + + switch(f->X.code) { + //char *seq; + + case 'X': + //fprintf(stderr, " FC=%c FP=%d base=%d\n", f->X.code, i32, f->X.base); + + uc = f->X.base; + r |= h->BS_codec->encode(s, h->BS_codec, core, + (char *)&uc, 1); + break; + case 'S': + //seq = DSTRING_STR(s->seqs_ds) + f->S.seq_idx; + //r |= h->SC_codec->encode(s, h->SC_codec, core, + // seq, f->S.len); + break; + case 'I': + //seq = DSTRING_STR(s->seqs_ds) + f->S.seq_idx; + //r |= h->IN_codec->encode(s, h->IN_codec, core, + // seq, f->S.len); + break; + case 'i': + uc = f->i.base; +#ifdef BA_external + s->block[s->ba_id]->data[s->block[s->ba_id]->uncomp_size++] = uc; +#else + r |= h->BA_codec->encode(s, h->BA_codec, core, + (char *)&uc, 1); +#endif + //seq = DSTRING_STR(s->seqs_ds) + f->S.seq_idx; + //r |= h->IN_codec->encode(s, h->IN_codec, core, + // seq, 1); + break; + case 'D': + i32 = f->D.len; + r |= h->DL_codec->encode(s, h->DL_codec, core, + (char *)&i32, 1); + break; + + case 'B': +// // Used when we try to store a non ACGTN base or an N +// // that aligns against a non ACGTN reference + + uc = f->B.base; +#ifdef BA_external + s->block[s->ba_id]->data[s->block[s->ba_id]->uncomp_size++] = uc; +#else + r |= h->BA_codec->encode(s, h->BA_codec, core, + (char *)&uc, 1); +#endif + +// Already added +// uc = f->B.qual; +// r |= h->QS_codec->encode(s, h->QS_codec, core, +// (char *)&uc, 1); + break; + + case 'Q': +// Already added +// uc = f->B.qual; +// r |= h->QS_codec->encode(s, h->QS_codec, core, +// (char *)&uc, 1); + break; + + case 'N': + i32 = f->N.len; + r |= h->RS_codec->encode(s, h->RS_codec, core, + (char *)&i32, 1); + break; + + case 'P': + i32 = f->P.len; + r |= h->PD_codec->encode(s, h->PD_codec, core, + (char *)&i32, 1); + break; + + case 'H': + i32 = f->H.len; + r |= h->HC_codec->encode(s, h->HC_codec, core, + (char *)&i32, 1); + break; + + + default: + fprintf(stderr, "unhandled feature code %c\n", + f->X.code); + return -1; + } + } + + r |= h->MQ_codec->encode(s, h->MQ_codec, core, + (char *)&cr->mqual, 1); + } else { + char *seq = (char *)BLOCK_DATA(s->seqs_blk) + cr->seq; +#ifdef BA_external + memcpy(&s->block[s->ba_id]->data[s->block[s->ba_id]->uncomp_size], + seq, cr->len); + s->block[s->ba_id]->uncomp_size += cr->len; +#else + r |= h->BA_codec->encode(s, h->BA_codec, core, seq, cr->len); +#endif + } + + if (r) + return -1; + } + s->block[0]->uncomp_size = s->block[0]->byte + (s->block[0]->bit < 7); + s->block[0]->comp_size = s->block[0]->uncomp_size; + + // FIXME: we should avoid creating these in the first place and just + // point them to s->base_blk et al. + cram_free_block(s->block[1]); + cram_free_block(s->block[2]); + cram_free_block(s->block[3]); + cram_free_block(s->block[5]); + if (fd->version != CRAM_1_VERS) { + cram_free_block(s->block[6]); + BLOCK_UPLEN(s->soft_blk); + s->block[6] = s->soft_blk; + s->soft_blk = NULL; + } + BLOCK_UPLEN(s->base_blk); s->block[1] = s->base_blk; s->base_blk = NULL; + BLOCK_UPLEN(s->qual_blk); s->block[2] = s->qual_blk; s->qual_blk = NULL; + BLOCK_UPLEN(s->name_blk); s->block[3] = s->name_blk; s->name_blk = NULL; + BLOCK_UPLEN(s->aux_blk); s->block[5] = s->aux_blk; s->aux_blk = NULL; + +#ifdef TN_external + if (fd->version == CRAM_1_VERS) { + cram_free_block(s->block[s->tn_id]); + BLOCK_UPLEN(s->tn_blk); s->block[s->tn_id] = s->tn_blk; + s->tn_blk = NULL; + } +#endif + + s->block[4]->comp_size = s->block[4]->uncomp_size; + +#ifdef BA_external + s->block[s->ba_id]->comp_size = s->block[s->ba_id]->uncomp_size; +#endif + + /* Compress the CORE Block too, with minimal zlib level */ + if (fd->level > 5) + cram_compress_block(fd, s->block[0], NULL, 1, Z_CRAM_STRAT, -1, -1); + +#define USE_METRICS + +#ifdef USE_METRICS +# define LEVEL2 1 +# define STRAT2 Z_RLE +#else +# define LEVEL2 -1 +# define STRAT2 -1 +#endif + + /* Compress the other blocks */ + if (cram_compress_block(fd, s->block[1], NULL, //IN (seq) + fd->level, Z_CRAM_STRAT, + -1, -1)) + return -1; + + if (fd->level == 0) { + /* Do nothing */ + } else if (fd->level == 1) { + if (cram_compress_block(fd, s->block[2], fd->m[1], //qual + 1, Z_RLE, -1, -1)) + return -1; + if (cram_compress_block(fd, s->block[5], fd->m[4], //Tags + 1, Z_RLE, -1, -1)) + return -1; + } else if (fd->level < 3) { + if (cram_compress_block(fd, s->block[2], fd->m[1], //qual + 1, Z_RLE, + 1, Z_HUFFMAN_ONLY)) + return -1; + if (cram_compress_block(fd, s->block[5], fd->m[4], //Tags + 1, Z_RLE, + 1, Z_HUFFMAN_ONLY)) + return -1; + } else { + if (cram_compress_block(fd, s->block[2], fd->m[1], //qual + fd->level, Z_CRAM_STRAT, + LEVEL2, STRAT2)) + return -1; + if (cram_compress_block(fd, s->block[5], fd->m[4], //Tags + fd->level, Z_CRAM_STRAT, + LEVEL2, STRAT2)) + return -1; + } + if (cram_compress_block(fd, s->block[3], NULL, //Name + fd->level, Z_CRAM_STRAT, + -1, -1)) + return -1; + if (cram_compress_block(fd, s->block[4], NULL, //TS, NP + fd->level, Z_CRAM_STRAT, + -1, -1)) + return -1; + if (fd->version != CRAM_1_VERS) { + if (cram_compress_block(fd, s->block[6], NULL, //SC (seq) + fd->level, Z_CRAM_STRAT, + -1, -1)) + return -1; + } +#ifdef BA_external + if (cram_compress_block(fd, s->block[s->ba_id], NULL, + fd->level, Z_CRAM_STRAT, -1, -1)) + return -1; +#endif +#ifdef TN_external + if (fd->version == CRAM_1_VERS) { + if (cram_compress_block(fd, s->block[s->tn_id], NULL, + fd->level, Z_DEFAULT_STRATEGY, -1, -1)) + return -1; + } +#endif + if (embed_ref) { + BLOCK_UPLEN(s->block[s->ref_id]); + if (cram_compress_block(fd, s->block[s->ref_id], NULL, + fd->level, Z_DEFAULT_STRATEGY, -1, -1)) + return -1; + } + + return r ? -1 : 0; +} + +/* + * Encodes all slices in a container into blocks. + * Returns 0 on success + * -1 on failure + */ +int cram_encode_container(cram_fd *fd, cram_container *c) { + int i, j, slice_offset; + cram_block_compression_hdr *h = c->comp_hdr; + cram_block *c_hdr; + int multi_ref = 0; + int r1, r2, sn, nref; + spare_bams *spares; + + /* Cache references up-front if we have unsorted access patterns */ + pthread_mutex_lock(&fd->ref_lock); + nref = fd->refs->nref; + pthread_mutex_unlock(&fd->ref_lock); + + if (c->refs_used) { + for (i = 0; i < nref; i++) { + if (c->refs_used[i]) { + cram_get_ref(fd, i, 1, 0); + } + } + } + + /* Fetch reference sequence */ + if (!fd->no_ref) { + bam_seq_t *b = c->bams[0]; + char *ref; + + ref = cram_get_ref(fd, bam_ref(b), 1, 0); + if (!ref && bam_ref(b) >= 0) { + fprintf(stderr, "Failed to load reference #%d\n", bam_ref(b)); + return -1; + } + if ((c->ref_id = bam_ref(b)) >= 0) { + c->ref_seq_id = c->ref_id; + c->ref = fd->refs->ref_id[c->ref_seq_id]->seq; + c->ref_start = 1; + c->ref_end = fd->refs->ref_id[c->ref_seq_id]->length; + } else { + c->ref_seq_id = c->ref_id; // FIXME remove one var! + } + } else { + c->ref_seq_id = c->ref_id; // FIXME remove one var! + } + + /* Turn bams into cram_records and gather basic stats */ + for (r1 = sn = 0; r1 < c->curr_c_rec; sn++) { + cram_slice *s = c->slices[sn]; + int first_base = INT_MAX, last_base = INT_MIN; + + assert(sn < c->curr_slice); + + /* FIXME: we could create our slice objects here too instead of + * in cram_put_bam_seq. It's more natural here and also this is + * bit is threaded so it's less work in the main thread. + */ + + for (r2 = 0; r1 < c->curr_c_rec && r2 < c->max_rec; r1++, r2++) { + cram_record *cr = &s->crecs[r2]; + bam_seq_t *b = c->bams[r1]; + + /* If multi-ref we need to cope with changing reference per seq */ + if (c->multi_seq && !fd->no_ref) { + if (bam_ref(b) != c->ref_seq_id && bam_ref(b) >= 0) { + if (c->ref_seq_id >= 0) + cram_ref_decr(fd->refs, c->ref_seq_id); + + if (!cram_get_ref(fd, bam_ref(b), 1, 0)) { + fprintf(stderr, "Failed to load reference #%d\n", + bam_ref(b)); + return -1; + } + + c->ref_seq_id = bam_ref(b); // overwritten later by -2 + assert(fd->refs->ref_id[c->ref_seq_id]->seq); + c->ref = fd->refs->ref_id[c->ref_seq_id]->seq; + c->ref_start = 1; + c->ref_end = fd->refs->ref_id[c->ref_seq_id]->length; + } + } + + process_one_read(fd, c, s, cr, b, r2); + + if (first_base > cr->apos) + first_base = cr->apos; + + if (last_base < cr->aend) + last_base = cr->aend; + } + + if (c->multi_seq) { + s->hdr->ref_seq_id = -2; + s->hdr->ref_seq_start = 0; + s->hdr->ref_seq_span = 0; + } else { + s->hdr->ref_seq_id = c->ref_id; + s->hdr->ref_seq_start = first_base; + s->hdr->ref_seq_span = last_base - first_base + 1; + } + s->hdr->num_records = r2; + } + + /* Link our bams[] array onto the spare bam list for reuse */ + spares = malloc(sizeof(*spares)); + pthread_mutex_lock(&fd->bam_list_lock); + spares->bams = c->bams; + spares->next = fd->bl; + fd->bl = spares; + pthread_mutex_unlock(&fd->bam_list_lock); + c->bams = NULL; + + /* Detect if a multi-seq container */ + cram_stats_encoding(fd, c->RI_stats); + multi_ref = c->RI_stats->nvals > 1; + + if (multi_ref) { + if (fd->verbose) + fprintf(stderr, "Multi-ref container\n"); + c->ref_seq_id = -2; + c->ref_seq_start = 0; + c->ref_seq_span = 0; + } + + + /* Compute MD5s */ + for (i = 0; i < c->curr_slice; i++) { + cram_slice *s = c->slices[i]; + + if (fd->version != CRAM_1_VERS) { + if (s->hdr->ref_seq_id >= 0 && c->multi_seq == 0 && !fd->no_ref) { + MD5_CTX md5; + MD5_Init(&md5); + MD5_Update(&md5, + c->ref + s->hdr->ref_seq_start - c->ref_start, + s->hdr->ref_seq_span); + MD5_Final(s->hdr->md5, &md5); + } else { + memset(s->hdr->md5, 0, 16); + } + } + } + + c->num_records = 0; + c->num_blocks = 0; + c->length = 0; + + //fprintf(stderr, "=== BF ===\n"); + h->BF_codec = cram_encoder_init(cram_stats_encoding(fd, c->BF_stats), + c->BF_stats, E_INT, NULL, + fd->version); + + //fprintf(stderr, "=== CF ===\n"); + h->CF_codec = cram_encoder_init(cram_stats_encoding(fd, c->CF_stats), + c->CF_stats, E_INT, NULL, + fd->version); +// fprintf(stderr, "=== RN ===\n"); +// h->RN_codec = cram_encoder_init(cram_stats_encoding(fd, c->RN_stats), +// c->RN_stats, E_BYTE_ARRAY, NULL, +// fd->version); + + //fprintf(stderr, "=== AP ===\n"); + if (c->pos_sorted) { + h->AP_codec = cram_encoder_init(cram_stats_encoding(fd, c->AP_stats), + c->AP_stats, E_INT, NULL, + fd->version); + } else { + int p[2] = {0, c->max_apos}; + h->AP_codec = cram_encoder_init(E_BETA, NULL, E_INT, p, fd->version); + } + + //fprintf(stderr, "=== RG ===\n"); + h->RG_codec = cram_encoder_init(cram_stats_encoding(fd, c->RG_stats), + c->RG_stats, E_INT, NULL, + fd->version); + + //fprintf(stderr, "=== MQ ===\n"); + h->MQ_codec = cram_encoder_init(cram_stats_encoding(fd, c->MQ_stats), + c->MQ_stats, E_INT, NULL, + fd->version); + + //fprintf(stderr, "=== NS ===\n"); +#ifdef NS_external + h->NS_codec = cram_encoder_init(E_EXTERNAL, NULL, E_INT, + (void *)CRAM_EXT_NS, + fd->version); +#else + h->NS_codec = cram_encoder_init(cram_stats_encoding(fd, c->NS_stats), + c->NS_stats, E_INT, NULL, + fd->version); +#endif + + //fprintf(stderr, "=== MF ===\n"); + h->MF_codec = cram_encoder_init(cram_stats_encoding(fd, c->MF_stats), + c->MF_stats, E_INT, NULL, + fd->version); + +#ifdef TS_external + h->TS_codec = cram_encoder_init(E_EXTERNAL, NULL, E_INT, + (void *)CRAM_EXT_TS_NP, + fd->version); + h->NP_codec = cram_encoder_init(E_EXTERNAL, NULL, E_INT, + (void *)CRAM_EXT_TS_NP, + fd->version); +#else + //fprintf(stderr, "=== TS ===\n"); + h->TS_codec = cram_encoder_init(cram_stats_encoding(fd, c->TS_stats), + c->TS_stats, E_INT, NULL, + fd->version); + //fprintf(stderr, "=== NP ===\n"); + h->NP_codec = cram_encoder_init(cram_stats_encoding(fd, c->NP_stats), + c->NP_stats, E_INT, NULL, + fd->version); +#endif + + //fprintf(stderr, "=== NF ===\n"); + h->NF_codec = cram_encoder_init(cram_stats_encoding(fd, c->NF_stats), + c->NF_stats, E_INT, NULL, + fd->version); + + //fprintf(stderr, "=== RL ===\n"); + h->RL_codec = cram_encoder_init(cram_stats_encoding(fd, c->RL_stats), + c->RL_stats, E_INT, NULL, + fd->version); + + //fprintf(stderr, "=== FN ===\n"); + h->FN_codec = cram_encoder_init(cram_stats_encoding(fd, c->FN_stats), + c->FN_stats, E_INT, NULL, + fd->version); + + //fprintf(stderr, "=== FC ===\n"); + h->FC_codec = cram_encoder_init(cram_stats_encoding(fd, c->FC_stats), + c->FC_stats, E_BYTE, NULL, + fd->version); + + //fprintf(stderr, "=== FP ===\n"); + h->FP_codec = cram_encoder_init(cram_stats_encoding(fd, c->FP_stats), + c->FP_stats, E_INT, NULL, + fd->version); + + //fprintf(stderr, "=== DL ===\n"); + h->DL_codec = cram_encoder_init(cram_stats_encoding(fd, c->DL_stats), + c->DL_stats, E_INT, NULL, + fd->version); + +#ifdef BA_external + h->BA_codec = cram_encoder_init(E_EXTERNAL, NULL, E_BYTE, + (void *)CRAM_EXT_BA, + fd->version); +#else + //fprintf(stderr, "=== BA ===\n"); + h->BA_codec = cram_encoder_init(cram_stats_encoding(fd, c->BA_stats), + c->BA_stats, E_BYTE, NULL, + fd->version); +#endif + + //fprintf(stderr, "=== BS ===\n"); + h->BS_codec = cram_encoder_init(cram_stats_encoding(fd, c->BS_stats), + c->BS_stats, E_BYTE, NULL, + fd->version); + + if (fd->version == CRAM_1_VERS) { + h->TL_codec = NULL; + h->RI_codec = NULL; + h->RS_codec = NULL; + h->PD_codec = NULL; + h->HC_codec = NULL; + h->SC_codec = NULL; + + //fprintf(stderr, "=== TC ===\n"); + h->TC_codec = cram_encoder_init(cram_stats_encoding(fd, c->TC_stats), + c->TC_stats, E_BYTE, NULL, + fd->version); + + //fprintf(stderr, "=== TN ===\n"); +#ifdef TN_external + h->TN_codec = cram_encoder_init(E_EXTERNAL, NULL, E_INT, + (void *)CRAM_EXT_TN, + fd->version); +#else + h->TN_codec = cram_encoder_init(cram_stats_encoding(fd, c->TN_stats), + c->TN_stats, E_INT, NULL, + fd->version); +#endif + } else { + int i2[2] = {0, CRAM_EXT_SC}; + + h->TC_codec = NULL; + h->TN_codec = NULL; + + //fprintf(stderr, "=== TL ===\n"); + h->TL_codec = cram_encoder_init(cram_stats_encoding(fd, c->TL_stats), + c->TL_stats, E_INT, NULL, + fd->version); + + + //fprintf(stderr, "=== RI ===\n"); + h->RI_codec = cram_encoder_init(cram_stats_encoding(fd, c->RI_stats), + c->RI_stats, E_INT, NULL, + fd->version); + + //fprintf(stderr, "=== RS ===\n"); + h->RS_codec = cram_encoder_init(cram_stats_encoding(fd, c->RS_stats), + c->RS_stats, E_INT, NULL, + fd->version); + + //fprintf(stderr, "=== PD ===\n"); + h->PD_codec = cram_encoder_init(cram_stats_encoding(fd, c->PD_stats), + c->PD_stats, E_INT, NULL, + fd->version); + + //fprintf(stderr, "=== HC ===\n"); + h->HC_codec = cram_encoder_init(cram_stats_encoding(fd, c->HC_stats), + c->HC_stats, E_INT, NULL, + fd->version); + + //fprintf(stderr, "=== SC ===\n"); + h->SC_codec = cram_encoder_init(E_BYTE_ARRAY_STOP, NULL, + E_BYTE_ARRAY, (void *)i2, + fd->version); + } + + //fprintf(stderr, "=== IN ===\n"); + { + int i2[2] = {0, CRAM_EXT_IN}; + h->IN_codec = cram_encoder_init(E_BYTE_ARRAY_STOP, NULL, + E_BYTE_ARRAY, (void *)i2, + fd->version); + } + + { + //int i2[2] = {0, 1}; + //h->QS_codec = cram_encoder_init(E_BYTE_ARRAY_STOP, NULL, (void *)i2, + // fd->version); + h->QS_codec = cram_encoder_init(E_EXTERNAL, NULL, E_BYTE, + (void *)CRAM_EXT_QUAL, + fd->version); + } + { + int i2[2] = {0, CRAM_EXT_NAME}; + h->RN_codec = cram_encoder_init(E_BYTE_ARRAY_STOP, NULL, + E_BYTE_ARRAY, (void *)i2, + fd->version); + } + + + /* Encode slices */ + for (i = 0; i < c->curr_slice; i++) { + if (fd->verbose) + fprintf(stderr, "Encode slice %d\n", i); + if (cram_encode_slice(fd, c, h, c->slices[i]) != 0) + return -1; + } + + /* Create compression header */ + { + h->ref_seq_id = c->ref_seq_id; + h->ref_seq_start = c->ref_seq_start; + h->ref_seq_span = c->ref_seq_span; + h->num_records = c->num_records; + + h->mapped_qs_included = 0; // fixme + h->unmapped_qs_included = 0; // fixme + // h->... fixme + memcpy(h->substitution_matrix, CRAM_SUBST_MATRIX, 20); + + if (!(c_hdr = cram_encode_compression_header(fd, c, h))) + return -1; + } + + /* Compute landmarks */ + /* Fill out slice landmarks */ + c->num_landmarks = c->curr_slice; + c->landmark = malloc(c->num_landmarks * sizeof(*c->landmark)); + if (!c->landmark) + return -1; + + /* + * Slice offset starts after the first block, so we need to simulate + * writing it to work out the correct offset + */ + { + slice_offset = c_hdr->method == RAW + ? c_hdr->uncomp_size + : c_hdr->comp_size; + slice_offset += 2 + + itf8_size(c_hdr->content_id) + + itf8_size(c_hdr->comp_size) + + itf8_size(c_hdr->uncomp_size); + } + + c->ref_seq_id = c->slices[0]->hdr->ref_seq_id; + c->ref_seq_start = c->slices[0]->hdr->ref_seq_start; + c->ref_seq_span = c->slices[0]->hdr->ref_seq_span; + for (i = 0; i < c->curr_slice; i++) { + cram_slice *s = c->slices[i]; + + c->num_blocks += s->hdr->num_blocks + 2; + c->landmark[i] = slice_offset; + + if (s->hdr->ref_seq_start + s->hdr->ref_seq_span > + c->ref_seq_start + c->ref_seq_span) { + c->ref_seq_span = s->hdr->ref_seq_start + s->hdr->ref_seq_span + - c->ref_seq_start; + } + + slice_offset += s->hdr_block->method == RAW + ? s->hdr_block->uncomp_size + : s->hdr_block->comp_size; + + slice_offset += 2 + + itf8_size(s->hdr_block->content_id) + + itf8_size(s->hdr_block->comp_size) + + itf8_size(s->hdr_block->uncomp_size); + + for (j = 0; j < s->hdr->num_blocks; j++) { + slice_offset += 2 + + itf8_size(s->block[j]->content_id) + + itf8_size(s->block[j]->comp_size) + + itf8_size(s->block[j]->uncomp_size); + + slice_offset += s->block[j]->method == RAW + ? s->block[j]->uncomp_size + : s->block[j]->comp_size; + } + } + c->length += slice_offset; // just past the final slice + + c->comp_hdr_block = c_hdr; + + if (c->ref_seq_id >= 0) { + cram_ref_decr(fd->refs, c->ref_seq_id); + } + + /* Cache references up-front if we have unsorted access patterns */ + if (c->refs_used) { + for (i = 0; i < fd->refs->nref; i++) { + if (c->refs_used[i]) + cram_ref_decr(fd->refs, i); + } + } + + return 0; +} + + +/* + * Adds a feature code to a read within a slice. For purposes of minimising + * memory allocations and fragmentation we have one array of features for all + * reads within the slice. We return the index into this array for this new + * feature. + * + * Returns feature index on success + * -1 on failure. + */ +static int cram_add_feature(cram_container *c, cram_slice *s, + cram_record *r, cram_feature *f) { + if (s->nfeatures >= s->afeatures) { + s->afeatures = s->afeatures ? s->afeatures*2 : 1024; + s->features = realloc(s->features, s->afeatures*sizeof(*s->features)); + if (!s->features) + return -1; + } + + if (!r->nfeature++) { + r->feature = s->nfeatures; + cram_stats_add(c->FP_stats, f->X.pos); + } else { + cram_stats_add(c->FP_stats, + f->X.pos - s->features[r->feature + r->nfeature-2].X.pos); + } + cram_stats_add(c->FC_stats, f->X.code); + + s->features[s->nfeatures++] = *f; + + return 0; +} + +static int cram_add_substitution(cram_fd *fd, cram_container *c, + cram_slice *s, cram_record *r, + int pos, char base, char qual, char ref) { + cram_feature f; + + // seq=ACGTN vs ref=ACGT or seq=ACGT vs ref=ACGTN + if (fd->L2[(uc)base]<4 || (fd->L2[(uc)base]<5 && fd->L2[(uc)ref]<4)) { + f.X.pos = pos+1; + f.X.code = 'X'; + f.X.base = fd->cram_sub_matrix[ref&0x1f][base&0x1f]; + cram_stats_add(c->BS_stats, f.X.base); + } else { + f.B.pos = pos+1; + f.B.code = 'B'; + f.B.base = base; + f.B.qual = qual; + cram_stats_add(c->BA_stats, f.B.base); + cram_stats_add(c->QS_stats, f.B.qual); + BLOCK_APPEND_CHAR(s->qual_blk, qual); + } + return cram_add_feature(c, s, r, &f); +} + +static int cram_add_base(cram_fd *fd, cram_container *c, + cram_slice *s, cram_record *r, + int pos, char base, char qual) { + cram_feature f; + f.B.pos = pos+1; + f.B.code = 'B'; + f.B.base = base; + f.B.qual = qual; +#ifdef BA_external + s->BA_len++; +#else + cram_stats_add(c->BA_stats, base); +#endif + cram_stats_add(c->QS_stats, qual); + BLOCK_APPEND_CHAR(s->qual_blk, qual); + return cram_add_feature(c, s, r, &f); +} + +static int cram_add_quality(cram_fd *fd, cram_container *c, + cram_slice *s, cram_record *r, + int pos, char qual) { + cram_feature f; + f.Q.pos = pos+1; + f.Q.code = 'Q'; + f.Q.qual = qual; + cram_stats_add(c->QS_stats, qual); + BLOCK_APPEND_CHAR(s->qual_blk, qual); + return cram_add_feature(c, s, r, &f); +} + +static int cram_add_deletion(cram_container *c, cram_slice *s, cram_record *r, + int pos, int len, char *base) { + cram_feature f; + f.D.pos = pos+1; + f.D.code = 'D'; + f.D.len = len; + cram_stats_add(c->DL_stats, len); + return cram_add_feature(c, s, r, &f); +} + +static int cram_add_softclip(cram_container *c, cram_slice *s, cram_record *r, + int pos, int len, char *base, int version) { + cram_feature f; + f.S.pos = pos+1; + f.S.code = 'S'; + f.S.len = len; + if (version == CRAM_1_VERS) { + f.S.seq_idx = BLOCK_SIZE(s->base_blk); + BLOCK_APPEND(s->base_blk, base, len); + BLOCK_APPEND_CHAR(s->base_blk, '\0'); + } else { + f.S.seq_idx = BLOCK_SIZE(s->soft_blk); + if (base) { + BLOCK_APPEND(s->soft_blk, base, len); + } else { + int i; + for (i = 0; i < len; i++) + BLOCK_APPEND_CHAR(s->soft_blk, 'N'); + } + BLOCK_APPEND_CHAR(s->soft_blk, '\0'); + } + return cram_add_feature(c, s, r, &f); +} + +static int cram_add_hardclip(cram_container *c, cram_slice *s, cram_record *r, + int pos, int len, char *base) { + cram_feature f; + f.S.pos = pos+1; + f.S.code = 'H'; + f.S.len = len; + cram_stats_add(c->HC_stats, len); + return cram_add_feature(c, s, r, &f); +} + +static int cram_add_skip(cram_container *c, cram_slice *s, cram_record *r, + int pos, int len, char *base) { + cram_feature f; + f.S.pos = pos+1; + f.S.code = 'N'; + f.S.len = len; + cram_stats_add(c->RS_stats, len); + return cram_add_feature(c, s, r, &f); +} + +static int cram_add_pad(cram_container *c, cram_slice *s, cram_record *r, + int pos, int len, char *base) { + cram_feature f; + f.S.pos = pos+1; + f.S.code = 'P'; + f.S.len = len; + cram_stats_add(c->PD_stats, len); + return cram_add_feature(c, s, r, &f); +} + +static int cram_add_insertion(cram_container *c, cram_slice *s, cram_record *r, + int pos, int len, char *base) { + cram_feature f; + f.I.pos = pos+1; + if (len == 1) { + char b = base ? *base : 'N'; + f.i.code = 'i'; + f.i.base = b; +#ifdef BA_external + s->BA_len++; +#else + cram_stats_add(c->BA_stats, b); +#endif + } else { + f.I.code = 'I'; + f.I.len = len; + f.S.seq_idx = BLOCK_SIZE(s->base_blk); + if (base) { + BLOCK_APPEND(s->base_blk, base, len); + } else { + int i; + for (i = 0; i < len; i++) + BLOCK_APPEND_CHAR(s->base_blk, 'N'); + } + BLOCK_APPEND_CHAR(s->base_blk, '\0'); + } + return cram_add_feature(c, s, r, &f); +} + +/* + * Encodes auxiliary data. + * Returns the read-group parsed out of the BAM aux fields on success + * NULL on failure or no rg present (FIXME) + */ +static char *cram_encode_aux_1_0(cram_fd *fd, bam_seq_t *b, cram_container *c, + cram_slice *s, cram_record *cr) { + char *aux, *tmp, *rg = NULL, *tmp_tn; + int aux_size = bam_blk_size(b) - + ((char *)bam_aux(b) - (char *)&bam_ref(b)); + + /* Worst case is 1 nul char on every ??:Z: string, so +33% */ + BLOCK_GROW(s->aux_blk, aux_size*1.34+1); + tmp = (char *)BLOCK_END(s->aux_blk); + +#ifdef TN_external + BLOCK_GROW(s->tn_blk, aux_size); + tmp_tn = (char *)BLOCK_END(s->tn_blk); +#endif + + aux = (char *)bam_aux(b); +#ifndef TN_external + cr->TN_idx = s->nTN; +#endif + while (aux[0] != 0) { + int32_t i32; + int r; + + if (aux[0] == 'R' && aux[1] == 'G' && aux[2] == 'Z') { + rg = &aux[3]; + while (*aux++); + continue; + } + if (aux[0] == 'M' && aux[1] == 'D' && aux[2] == 'Z') { + while (*aux++); + continue; + } + if (aux[0] == 'N' && aux[1] == 'M') { + switch(aux[2]) { + case 'A': case 'C': case 'c': aux+=4; break; + case 'I': case 'i': case 'f': aux+=7; break; + default: + fprintf(stderr, "Unhandled type code for NM tag\n"); + return NULL; + } + continue; + } + + cr->ntags++; + + i32 = (aux[0]<<16) | (aux[1]<<8) | aux[2]; + kh_put(s_i2i, c->tags_used, i32, &r); + if (-1 == r) + return NULL; + +#ifndef TN_external + if (s->nTN >= s->aTN) { + s->aTN = s->aTN ? s->aTN*2 : 1024; + if (!(s->TN = realloc(s->TN, s->aTN * sizeof(*s->TN)))) + return NULL; + } + s->TN[s->nTN++] = i32; + cram_stats_add(c->TN_stats, i32); +#else + tmp_tn += itf8_put(tmp_tn, i32); +#endif + + switch(aux[2]) { + case 'A': case 'C': case 'c': + aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + *tmp++=*aux++; + break; + + case 'S': case 's': + aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + *tmp++=*aux++; *tmp++=*aux++; + break; + + case 'I': case 'i': case 'f': + aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + break; + + case 'd': + aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + break; + + case 'Z': case 'H': + aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + while ((*tmp++=*aux++)); + *tmp++ = '\t'; // stop byte + break; + + case 'B': { + int type = aux[3], blen; + uint32_t count = (uint32_t)((((unsigned char *)aux)[4]<< 0) + + (((unsigned char *)aux)[5]<< 8) + + (((unsigned char *)aux)[6]<<16) + + (((unsigned char *)aux)[7]<<24)); + // skip TN field + aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + + // We use BYTE_ARRAY_LEN with external length, so store that first + switch (type) { + case 'c': case 'C': + blen = count; + break; + case 's': case 'S': + blen = 2*count; + break; + case 'i': case 'I': case 'f': + blen = 4*count; + break; + default: + fprintf(stderr, "Unknown sub-type '%c' for aux type 'B'\n", + type); + return NULL; + + } + + tmp += itf8_put(tmp, blen+5); + + *tmp++=*aux++; // sub-type & length + *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + + // The tag data itself + memcpy(tmp, aux, blen); tmp += blen; aux += blen; + + //cram_stats_add(c->aux_B_stats, blen); + break; + } + default: + fprintf(stderr, "Unknown aux type '%c'\n", aux[2]); + return NULL; + } + } + cram_stats_add(c->TC_stats, cr->ntags); + + cr->aux = BLOCK_SIZE(s->aux_blk); + cr->aux_size = (uc *)tmp - (BLOCK_DATA(s->aux_blk) + cr->aux); + BLOCK_SIZE(s->aux_blk) = (uc *)tmp - BLOCK_DATA(s->aux_blk); + assert(s->aux_blk->byte <= s->aux_blk->alloc); + +#ifdef TN_external + cr->tn = BLOCK_SIZE(s->tn_blk); + BLOCK_SIZE(s->tn_blk) = (uc *)tmp_tn - BLOCK_DATA(s->tn_blk); + assert(s->tn_blk->byte <= s->tn_blk->alloc); +#endif + + return rg; +} + +/* + * Encodes auxiliary data. Largely duplicated from above, but done so to + * keep it simple and avoid a myriad of version ifs. + * + * Returns the read-group parsed out of the BAM aux fields on success + * NULL on failure or no rg present (FIXME) + */ +static char *cram_encode_aux(cram_fd *fd, bam_seq_t *b, cram_container *c, + cram_slice *s, cram_record *cr) { + char *aux, *orig, *tmp, *rg = NULL; +#ifdef SAMTOOLS + int aux_size = bam_get_l_aux(b); +#else + int aux_size = bam_blk_size(b) - + ((char *)bam_aux(b) - (char *)&bam_ref(b)); +#endif + cram_block *td_b = c->comp_hdr->TD_blk; + int TD_blk_size = BLOCK_SIZE(td_b), new; + char *key; + khint_t k; + + + /* Worst case is 1 nul char on every ??:Z: string, so +33% */ + BLOCK_GROW(s->aux_blk, aux_size*1.34+1); + tmp = (char *)BLOCK_END(s->aux_blk); + + + orig = aux = (char *)bam_aux(b); + + // Copy aux keys to td_b and aux values to s->aux_blk + while (aux - orig < aux_size && aux[0] != 0) { + uint32_t i32; + int r; + + if (aux[0] == 'R' && aux[1] == 'G' && aux[2] == 'Z') { + rg = &aux[3]; + while (*aux++); + continue; + } + if (aux[0] == 'M' && aux[1] == 'D' && aux[2] == 'Z') { + while (*aux++); + continue; + } + if (aux[0] == 'N' && aux[1] == 'M') { + switch(aux[2]) { + case 'A': case 'C': case 'c': aux+=4; break; + case 'S': case 's': aux+=5; break; + case 'I': case 'i': case 'f': aux+=7; break; + default: + fprintf(stderr, "Unhandled type code for NM tag\n"); + return NULL; + } + continue; + } + + BLOCK_APPEND(td_b, aux, 3); + + i32 = (aux[0]<<16) | (aux[1]<<8) | aux[2]; + kh_put(s_i2i, c->tags_used, i32, &r); + if (-1 == r) + return NULL; + + switch(aux[2]) { + case 'A': case 'C': case 'c': + aux+=3; + *tmp++=*aux++; + break; + + case 'S': case 's': + aux+=3; + *tmp++=*aux++; *tmp++=*aux++; + break; + + case 'I': case 'i': case 'f': + aux+=3; + *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + break; + + case 'd': + aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + + case 'Z': case 'H': + aux+=3; + while ((*tmp++=*aux++)); + *tmp++ = '\t'; // stop byte + break; + + case 'B': { + int type = aux[3], blen; + uint32_t count = (uint32_t)((((unsigned char *)aux)[4]<< 0) + + (((unsigned char *)aux)[5]<< 8) + + (((unsigned char *)aux)[6]<<16) + + (((unsigned char *)aux)[7]<<24)); + // skip TN field + aux+=3; + + // We use BYTE_ARRAY_LEN with external length, so store that first + switch (type) { + case 'c': case 'C': + blen = count; + break; + case 's': case 'S': + blen = 2*count; + break; + case 'i': case 'I': case 'f': + blen = 4*count; + break; + default: + fprintf(stderr, "Unknown sub-type '%c' for aux type 'B'\n", + type); + return NULL; + + } + + tmp += itf8_put(tmp, blen+5); + + *tmp++=*aux++; // sub-type & length + *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; + + // The tag data itself + memcpy(tmp, aux, blen); tmp += blen; aux += blen; + + //cram_stats_add(c->aux_B_stats, blen); + break; + } + default: + fprintf(stderr, "Unknown aux type '%c'\n", aux[2]); + return NULL; + } + } + + // FIXME: sort BLOCK_DATA(td_b) by char[3] triples + + // And and increment TD hash entry + BLOCK_APPEND_CHAR(td_b, 0); + + // Duplicate key as BLOCK_DATA() can be realloced to a new pointer. + key = string_ndup(c->comp_hdr->TD_keys, + (char *)BLOCK_DATA(td_b) + TD_blk_size, + BLOCK_SIZE(td_b) - TD_blk_size); + k = kh_put(m_s2i, c->comp_hdr->TD_hash, key, &new); + if (new < 0) { + return NULL; + } else if (new == 0) { + BLOCK_SIZE(td_b) = TD_blk_size; + } else { + kh_val(c->comp_hdr->TD_hash, k) = c->comp_hdr->nTL; + c->comp_hdr->nTL++; + } + + cr->TL = kh_val(c->comp_hdr->TD_hash, k); + cram_stats_add(c->TL_stats, cr->TL); + + cr->aux = BLOCK_SIZE(s->aux_blk); + cr->aux_size = (uc *)tmp - (BLOCK_DATA(s->aux_blk) + cr->aux); + BLOCK_SIZE(s->aux_blk) = (uc *)tmp - BLOCK_DATA(s->aux_blk); + assert(s->aux_blk->byte <= s->aux_blk->alloc); + + return rg; +} + + +/* + * Handles creation of a new container or new slice, flushing any + * existing containers when appropriate. + * + * Really this is next slice, which may or may not lead to a new container. + * + * Returns cram_container pointer on success + * NULL on failure. + */ +static cram_container *cram_next_container(cram_fd *fd, bam_seq_t *b) { + cram_container *c = fd->ctr; + cram_slice *s; + int i; + + /* First occurence */ + if (c->curr_ref == -2) + c->curr_ref = bam_ref(b); + + if (c->slice) { + s = c->slice; + if (c->multi_seq) { + s->hdr->ref_seq_id = -2; + s->hdr->ref_seq_start = 0; + s->hdr->ref_seq_span = 0; + } else { + s->hdr->ref_seq_id = c->curr_ref; + s->hdr->ref_seq_start = c->first_base; + s->hdr->ref_seq_span = c->last_base - c->first_base + 1; + } + s->hdr->num_records = c->curr_rec; + + if (c->curr_slice == 0) { + if (c->ref_seq_id != s->hdr->ref_seq_id) + c->ref_seq_id = s->hdr->ref_seq_id; + c->ref_seq_start = c->first_base; + } + + c->curr_slice++; + } + + /* Flush container */ + if (c->curr_slice == c->max_slice || + (bam_ref(b) != c->curr_ref && !c->multi_seq)) { + c->ref_seq_span = fd->last_base - c->ref_seq_start + 1; + if (fd->verbose) + fprintf(stderr, "Flush container %d/%d..%d\n", + c->ref_seq_id, c->ref_seq_start, + c->ref_seq_start + c->ref_seq_span -1); + + /* Encode slices */ + if (fd->pool) { + if (-1 == cram_flush_container_mt(fd, c)) + return NULL; + } else { + if (-1 == cram_flush_container(fd, c)) + return NULL; + + // Move to sep func, as we need cram_flush_container for + // the closing phase to flush the partial container. + for (i = 0; i < c->max_slice; i++) { + cram_free_slice(c->slices[i]); + c->slices[i] = NULL; + } + + c->slice = NULL; + c->curr_slice = 0; + + /* Easy approach for purposes of freeing stats */ + cram_free_container(c); + } + + c = fd->ctr = cram_new_container(fd->seqs_per_slice, + fd->slices_per_container); + if (!c) + return NULL; + c->record_counter = fd->record_counter; + c->curr_ref = bam_ref(b); + } + + c->last_pos = c->first_base = c->last_base = bam_pos(b)+1; + + /* New slice */ + c->slice = c->slices[c->curr_slice] = + cram_new_slice(MAPPED_SLICE, c->max_rec); + if (!c->slice) + return NULL; + + if (c->multi_seq) { + c->slice->hdr->ref_seq_id = -2; + c->slice->hdr->ref_seq_start = 0; + c->slice->last_apos = 1; + } else { + c->slice->hdr->ref_seq_id = bam_ref(b); + // wrong for unsorted data, will fix during encoding. + c->slice->hdr->ref_seq_start = bam_pos(b)+1; + c->slice->last_apos = bam_pos(b)+1; + } + + c->curr_rec = 0; + + return c; +} + +/* + * Converts a single bam record into a cram record. + * Possibly used within a thread. + * + * Returns 0 on success; + * -1 on failure + */ +static int process_one_read(cram_fd *fd, cram_container *c, + cram_slice *s, cram_record *cr, + bam_seq_t *b, int rnum) { + int i, fake_qual = 0; + char *cp, *rg; + char *ref, *seq, *qual; + + // FIXME: multi-ref containers + + ref = c->ref; + + //fprintf(stderr, "%s => %d\n", rg ? rg : "\"\"", cr->rg); + + // Fields to resolve later + //cr->mate_line; // index to another cram_record + //cr->mate_flags; // MF + //cr->ntags; // TC + cr->ntags = 0; //cram_stats_add(c->TC_stats, cr->ntags); + if (fd->version == CRAM_1_VERS) + rg = cram_encode_aux_1_0(fd, b, c, s, cr); + else + rg = cram_encode_aux(fd, b, c, s, cr); + + //cr->aux_size = b->blk_size - ((char *)bam_aux(b) - (char *)&bam_ref(b)); + //cr->aux = DSTRING_LEN(s->aux_ds); + //dstring_nappend(s->aux_ds, bam_aux(b), cr->aux_size); + + /* Read group, identified earlier */ + if (rg) { + SAM_RG *brg = sam_hdr_find_rg(fd->header, rg); + cr->rg = brg ? brg->id : -1; + } else if (fd->version == CRAM_1_VERS) { + SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); + assert(brg); + } else { + cr->rg = -1; + } + cram_stats_add(c->RG_stats, cr->rg); + + + cr->ref_id = bam_ref(b); cram_stats_add(c->RI_stats, cr->ref_id); + cr->flags = bam_flag(b); + if (bam_cigar_len(b) == 0) + cr->flags |= BAM_FUNMAP; + cram_stats_add(c->BF_stats, fd->cram_flag_swap[cr->flags & 0xfff]); + + if (!fd->no_ref) + cr->cram_flags = CRAM_FLAG_PRESERVE_QUAL_SCORES; + else + cr->cram_flags = 0; + //cram_stats_add(c->CF_stats, cr->cram_flags); + + cr->len = bam_seq_len(b); cram_stats_add(c->RL_stats, cr->len); + c->num_bases += cr->len; + cr->apos = bam_pos(b)+1; + if (c->pos_sorted) { + if (cr->apos < s->last_apos) { + c->pos_sorted = 0; + } else { + cram_stats_add(c->AP_stats, cr->apos - s->last_apos); + s->last_apos = cr->apos; + } + } else { + //cram_stats_add(c->AP_stats, cr->apos); + } + c->max_apos += (cr->apos > c->max_apos) * (cr->apos - c->max_apos); + + cr->name = BLOCK_SIZE(s->name_blk); + cr->name_len = bam_name_len(b); + cram_stats_add(c->RN_stats, cr->name_len); + + BLOCK_APPEND(s->name_blk, bam_name(b), bam_name_len(b)); + + + /* + * This seqs_ds is largely pointless and it could reuse the same memory + * over and over. + * s->base_ds is what we need for encoding. + */ + cr->seq = BLOCK_SIZE(s->seqs_blk); + cr->qual = BLOCK_SIZE(s->qual_blk); + BLOCK_GROW(s->seqs_blk, cr->len+1); + BLOCK_GROW(s->qual_blk, cr->len); + seq = cp = (char *)BLOCK_END(s->seqs_blk); + + *seq = 0; + for (i = 0; i < cr->len; i++) { + // FIXME: do 2 char at a time for efficiency +#ifdef SAMTOOLS + cp[i] = seq_nt16_str[bam_seqi(bam_seq(b), i)]; +#else + cp[i] = bam_nt16_rev_table[bam_seqi(bam_seq(b), i)]; +#endif + } + BLOCK_SIZE(s->seqs_blk) += cr->len; + + qual = cp = (char *)bam_qual(b); + + /* Copy and parse */ + if (!(cr->flags & BAM_FUNMAP)) { + int32_t *cig_to, *cig_from; + int apos = cr->apos-1, spos = 0; + + cr->cigar = s->ncigar; + cr->ncigar = bam_cigar_len(b); + while (cr->cigar + cr->ncigar >= s->cigar_alloc) { + s->cigar_alloc = s->cigar_alloc ? s->cigar_alloc*2 : 1024; + s->cigar = realloc(s->cigar, s->cigar_alloc * sizeof(*s->cigar)); + if (!s->cigar) + return -1; + } + + cig_to = (int32_t *)s->cigar; + cig_from = (int32_t *)bam_cigar(b); + + cr->feature = 0; + cr->nfeature = 0; + for (i = 0; i < cr->ncigar; i++) { + enum cigar_op cig_op = cig_from[i] & BAM_CIGAR_MASK; + int cig_len = cig_from[i] >> BAM_CIGAR_SHIFT; + cig_to[i] = cig_from[i]; + + /* Can also generate events from here for CRAM diffs */ + + switch (cig_op) { + int l; + + // Don't trust = and X ops to be correct. + case BAM_CMATCH: + case BAM_CBASE_MATCH: + case BAM_CBASE_MISMATCH: + //fprintf(stderr, "\nBAM_CMATCH\nR: %.*s\nS: %.*s\n", + // cig_len, &ref[apos], cig_len, &seq[spos]); + l = 0; + if (!fd->no_ref && cr->len) { + int end = cig_len+apos < c->ref_end + ? cig_len : c->ref_end - apos; + for (l = 0; l < end && seq[spos]; l++, apos++, spos++) { + if (ref[apos] != seq[spos]) { + //fprintf(stderr, "Subst: %d; %c vs %c\n", + // spos, ref[apos], seq[spos]); + if (cram_add_substitution(fd, c, s, cr, spos, + seq[spos], qual[spos], + ref[apos])) + return -1; + } + } + } + + if (l < cig_len && cr->len) { + /* off end of sequence or non-ref based output */ + for (; l < cig_len && seq[spos]; l++, spos++) { + if (cram_add_base(fd, c, s, cr, spos, + seq[spos], qual[spos])) + return -1; + } + apos += cig_len; + } else if (!cr->len) { + /* Seq "*" */ + apos += cig_len; + spos += cig_len; + } + break; + + case BAM_CDEL: + if (cram_add_deletion(c, s, cr, spos, cig_len, &seq[spos])) + return -1; + apos += cig_len; + break; + + case BAM_CREF_SKIP: + if (cram_add_skip(c, s, cr, spos, cig_len, &seq[spos])) + return -1; + apos += cig_len; + break; + + case BAM_CINS: + if (cram_add_insertion(c, s, cr, spos, cig_len, + cr->len ? &seq[spos] : NULL)) + return -1; + if (fd->no_ref && cr->len) { + for (l = 0; l < cig_len; l++, spos++) { + cram_add_quality(fd, c, s, cr, spos, qual[spos]); + } + } else { + spos += cig_len; + } + break; + + case BAM_CSOFT_CLIP: + if (cram_add_softclip(c, s, cr, spos, cig_len, + cr->len ? &seq[spos] : NULL, + fd->version)) + return -1; + if (fd->no_ref) { + if (cr->len) { + for (l = 0; l < cig_len; l++, spos++) { + cram_add_quality(fd, c, s, cr, spos, qual[spos]); + } + } else { + for (l = 0; l < cig_len; l++, spos++) { + cram_add_quality(fd, c, s, cr, spos, -1); + } + } + } else { + spos += cig_len; + } + break; + + case BAM_CHARD_CLIP: + if (cram_add_hardclip(c, s, cr, spos, cig_len, &seq[spos])) + return -1; + break; + + case BAM_CPAD: + if (cram_add_pad(c, s, cr, spos, cig_len, &seq[spos])) + return -1; + break; + } + } + fake_qual = spos; + cr->aend = MIN(apos, c->ref_end); + cram_stats_add(c->FN_stats, cr->nfeature); + } else { + // Unmapped + cr->cram_flags |= CRAM_FLAG_PRESERVE_QUAL_SCORES; + cr->cigar = 0; + cr->ncigar = 0; + cr->nfeature = 0; + cr->aend = cr->apos; +#ifdef BA_external + s->BA_len += cr->len; +#else + for (i = 0; i < cr->len; i++) + cram_stats_add(c->BA_stats, seq[i]); +#endif + } + + /* + * Append to the qual block now. We do this here as + * cram_add_substitution() can generate BA/QS events which need to + * be in the qual block before we append the rest of the data. + */ + if (cr->cram_flags & CRAM_FLAG_PRESERVE_QUAL_SCORES) { + /* Special case of seq "*" */ + if (cr->len == 0) { + cram_stats_add(c->RL_stats, cr->len = fake_qual); + BLOCK_GROW(s->qual_blk, cr->len); + cp = (char *)BLOCK_END(s->qual_blk); + memset(cp, 255, cr->len); + } else { + BLOCK_GROW(s->qual_blk, cr->len); + cp = (char *)BLOCK_END(s->qual_blk); + char *from = (char *)&bam_qual(b)[0]; + char *to = &cp[0]; + memcpy(to, from, cr->len); + //for (i = 0; i < cr->len; i++) cp[i] = from[i]; + } + BLOCK_SIZE(s->qual_blk) += cr->len; + } else { + if (cr->len == 0) { + cram_stats_add(c->RL_stats, cr->len = cr->aend - cr->apos + 1); + } + } + + /* Now we know apos and aend both, update mate-pair information */ + { + int new; + khint_t k; + + //fprintf(stderr, "Checking %"PRId64"/%.*s\t", rnum, + // cr->name_len, DSTRING_STR(s->name_ds)+cr->name); + if (cr->flags & BAM_FPAIRED) { + char *key = string_ndup(s->pair_keys, + (char *)BLOCK_DATA(s->name_blk)+cr->name, + cr->name_len); + if (!key) + return -1; + + k = kh_put(m_s2i, s->pair, key, &new); + if (-1 == new) + return -1; + else if (new > 0) + kh_val(s->pair, k) = rnum; + } else { + new = 1; + } + + if (new == 0) { + cram_record *p = &s->crecs[kh_val(s->pair, k)]; + + //fprintf(stderr, "paired %"PRId64"\n", kh_val(s->pair, k)); + + // copy from p to cr + cr->mate_pos = p->apos; + cram_stats_add(c->NP_stats, cr->mate_pos); + + cr->tlen = cr->aend - p->apos; + cram_stats_add(c->TS_stats, cr->tlen); + + cr->mate_flags = + ((p->flags & BAM_FMUNMAP) == BAM_FMUNMAP) * CRAM_M_UNMAP + + ((p->flags & BAM_FMREVERSE) == BAM_FMREVERSE) * CRAM_M_REVERSE; + cram_stats_add(c->MF_stats, cr->mate_flags); + + // copy from cr to p + cram_stats_del(c->NP_stats, p->mate_pos); + p->mate_pos = cr->apos; + cram_stats_add(c->NP_stats, p->mate_pos); + + cram_stats_del(c->MF_stats, p->mate_flags); + p->mate_flags = + ((cr->flags & BAM_FMUNMAP) == BAM_FMUNMAP) * CRAM_M_UNMAP + + ((cr->flags & BAM_FMREVERSE) == BAM_FMREVERSE)* CRAM_M_REVERSE; + cram_stats_add(c->MF_stats, p->mate_flags); + + cram_stats_del(c->TS_stats, p->tlen); + p->tlen = p->apos - cr->aend; + cram_stats_add(c->TS_stats, p->tlen); + + // Clear detached from cr flags + //cram_stats_del(c->CF_stats, cr->cram_flags); + cr->cram_flags &= ~CRAM_FLAG_DETACHED; + cram_stats_add(c->CF_stats, cr->cram_flags); + + // Clear detached from p flags and set downstream + cram_stats_del(c->CF_stats, p->cram_flags); + p->cram_flags &= ~CRAM_FLAG_DETACHED; + p->cram_flags |= CRAM_FLAG_MATE_DOWNSTREAM; + cram_stats_add(c->CF_stats, p->cram_flags); + + p->mate_line = rnum - (kh_val(s->pair, k) + 1); + cram_stats_add(c->NF_stats, p->mate_line); + + kh_val(s->pair, k) = rnum; + } else { + //fprintf(stderr, "unpaired\n"); + + /* Derive mate flags from this flag */ + cr->mate_flags = 0; + if (bam_flag(b) & BAM_FMUNMAP) + cr->mate_flags |= CRAM_M_UNMAP; + if (bam_flag(b) & BAM_FMREVERSE) + cr->mate_flags |= CRAM_M_REVERSE; + + cram_stats_add(c->MF_stats, cr->mate_flags); + + cr->mate_pos = MAX(bam_mate_pos(b)+1, 0); + cram_stats_add(c->NP_stats, cr->mate_pos); + + cr->tlen = bam_ins_size(b); + cram_stats_add(c->TS_stats, cr->tlen); + + cr->cram_flags |= CRAM_FLAG_DETACHED; + cram_stats_add(c->CF_stats, cr->cram_flags); + } + } + + cr->mqual = bam_map_qual(b); + cram_stats_add(c->MQ_stats, cr->mqual); + + cr->mate_ref_id = bam_mate_ref(b); + cram_stats_add(c->NS_stats, cr->mate_ref_id); + + if (!(bam_flag(b) & BAM_FUNMAP)) { + if (c->first_base > cr->apos) + c->first_base = cr->apos; + + if (c->last_base < cr->aend) + c->last_base = cr->aend; + } + + return 0; +} + +/* + * Write iterator: put BAM format sequences into a CRAM file. + * We buffer up a containers worth of data at a time. + * + * Returns 0 on success + * -1 on failure + */ +int cram_put_bam_seq(cram_fd *fd, bam_seq_t *b) { + cram_container *c; + + if (!fd->ctr) { + fd->ctr = cram_new_container(fd->seqs_per_slice, + fd->slices_per_container); + if (!fd->ctr) + return -1; + fd->ctr->record_counter = fd->record_counter; + } + c = fd->ctr; + + if (!c->slice || c->curr_rec == c->max_rec || + (bam_ref(b) != c->curr_ref && c->curr_ref >= -1)) { + int slice_rec, curr_rec, multi_seq = fd->multi_seq == 1; + int curr_ref = c->slice ? c->curr_ref : bam_ref(b); + + + /* + * Start packing slices when we routinely have under 1/4tr full. + * + * This option isn't available if we choose to embed references + * since we can only have one per slice. + */ + if (fd->multi_seq == -1 && c->curr_rec < c->max_rec/4+10 && + fd->last_slice && fd->last_slice < c->max_rec/4+10 && + !fd->embed_ref) { + if (fd->verbose && !c->multi_seq) + fprintf(stderr, "Multi-ref enabled for this container\n"); + multi_seq = 1; + } + + slice_rec = c->slice_rec; + curr_rec = c->curr_rec; + + if (fd->version == CRAM_1_VERS || + c->curr_rec == c->max_rec || fd->multi_seq != 1 || !c->slice) + if (NULL == (c = cram_next_container(fd, b))) + return -1; + + /* + * Due to our processing order, some things we've already done we + * cannot easily undo. So when we first notice we should be packing + * multiple sequences per container we emit the small partial + * container as-is and then start a fresh one in a different mode. + */ + if (multi_seq) { + fd->multi_seq = 1; + c->multi_seq = 1; + c->pos_sorted = 0; // required atm for multi_seq slices + + if (!c->refs_used) { + pthread_mutex_lock(&fd->ref_lock); + c->refs_used = calloc(fd->refs->nref, sizeof(int)); + pthread_mutex_unlock(&fd->ref_lock); + if (!c->refs_used) + return -1; + } + } + + fd->last_slice = curr_rec - slice_rec; + c->slice_rec = c->curr_rec; + + // Have we seen this reference before? + if (bam_ref(b) >= 0 && bam_ref(b) != curr_ref && !fd->embed_ref && + !fd->unsorted) { + + if (!c->refs_used) { + pthread_mutex_lock(&fd->ref_lock); + c->refs_used = calloc(fd->refs->nref, sizeof(int)); + pthread_mutex_unlock(&fd->ref_lock); + if (!c->refs_used) + return -1; + } else if (c->refs_used && c->refs_used[bam_ref(b)]) { + fprintf(stderr, "Unsorted mode enabled\n"); + pthread_mutex_lock(&fd->ref_lock); + fd->unsorted = 1; + pthread_mutex_unlock(&fd->ref_lock); + fd->multi_seq = 1; + } + } + + c->curr_ref = bam_ref(b); + if (c->refs_used && c->curr_ref >= 0) c->refs_used[c->curr_ref]++; + } + + if (!c->bams) { + /* First time through, allocate a set of bam pointers */ + pthread_mutex_lock(&fd->bam_list_lock); + if (fd->bl) { + spare_bams *spare = fd->bl; + c->bams = spare->bams; + fd->bl = spare->next; + free(spare); + } else { + c->bams = calloc(c->max_c_rec, sizeof(bam_seq_t *)); + if (!c->bams) + return -1; + } + pthread_mutex_unlock(&fd->bam_list_lock); + } + + /* Copy or alloc+copy the bam record, for later encoding */ + if (c->bams[c->curr_c_rec]) + bam_copy(&c->bams[c->curr_c_rec], b); + else + c->bams[c->curr_c_rec] = bam_dup(b); + + c->curr_rec++; + c->curr_c_rec++; + fd->record_counter++; + + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_encode.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_encode.h new file mode 100644 index 0000000000000000000000000000000000000000..9131d6ea902fcf258a0f1b88a6d2d647d544f83d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_encode.h @@ -0,0 +1,105 @@ +/* +Copyright (c) 2012-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +/*! \file + * Include cram.h instead. + * + * This is an internal part of the CRAM system and is automatically included + * when you #include cram.h. + * + * Implements the encoding portion of CRAM I/O. Also see + * cram_codecs.[ch] for the actual encoding functions themselves. + */ + +#ifndef _CRAM_WRITE_H_ +#define _CRAM_WRITE_H_ + +#ifdef __cplusplus +extern "C" { +#endif + +/* ---------------------------------------------------------------------- + * CRAM sequence iterators. + */ + +/*! Write iterator: put BAM format sequences into a CRAM file. + * + * We buffer up a containers worth of data at a time. + * + * FIXME: break this into smaller pieces. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int cram_put_bam_seq(cram_fd *fd, bam_seq_t *b); + + +/* ---------------------------------------------------------------------- + * Internal functions + */ + +/*! INTERNAL: + * Encodes a compression header block into a generic cram_block structure. + * + * @return + * Returns cram_block ptr on success; + * NULL on failure + */ +cram_block *cram_encode_compression_header(cram_fd *fd, cram_container *c, + cram_block_compression_hdr *h); + +/*! INTERNAL: + * Encodes a slice compression header. + * + * @return + * Returns cram_block on success; + * NULL on failure + */ +cram_block *cram_encode_slice_header(cram_fd *fd, cram_slice *s); + +/*! INTERNAL: + * Encodes all slices in a container into blocks. + * + * @return + * Returns 0 on success; + * -1 on failure + * + * FIXME: separate into encode_container and write_container. Ideally + * we should be able to do read_container / write_container or + * decode_container / encode_container. + */ +int cram_encode_container(cram_fd *fd, cram_container *c); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_index.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_index.c new file mode 100644 index 0000000000000000000000000000000000000000..d78b3e07fb0f1c0012929a8a226e0e14c21ff788 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_index.c @@ -0,0 +1,503 @@ +/* +Copyright (c) 2013-2014 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +/* + * The index is a gzipped tab-delimited text file with one line per slice. + * The columns are: + * 1: reference number (0 to N-1, as per BAM ref_id) + * 2: reference position of 1st read in slice (1..?) + * 3: number of reads in slice + * 4: offset of container start (relative to end of SAM header, so 1st + * container is offset 0). + * 5: slice number within container (ie which landmark). + * + * In memory, we hold this in a nested containment list. Each list element is + * a cram_index struct. Each element in turn can contain its own list of + * cram_index structs. + * + * Any start..end range which is entirely contained within another (and + * earlier as it is sorted) range will be held within it. This ensures that + * the outer list will never have containments and we can safely do a + * binary search to find the first range which overlaps any given coordinate. + */ + +#ifdef HAVE_CONFIG_H +#include "io_lib_config.h" +#endif + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "htslib/hfile.h" +#include "cram/cram.h" +#include "cram/os.h" +#include "cram/zfio.h" + +#if 0 +static void dump_index_(cram_index *e, int level) { + int i, n; + n = printf("%*s%d / %d .. %d, ", level*4, "", e->refid, e->start, e->end); + printf("%*soffset %"PRId64"\n", MAX(0,50-n), "", e->offset); + for (i = 0; i < e->nslice; i++) { + dump_index_(&e->e[i], level+1); + } +} + +static void dump_index(cram_fd *fd) { + int i; + for (i = 0; i < fd->index_sz; i++) { + dump_index_(&fd->index[i], 0); + } +} +#endif + +/* + * Loads a CRAM .crai index into memory. + * + * Returns 0 for success + * -1 for failure + */ +int cram_index_load(cram_fd *fd, const char *fn) { + char fn2[PATH_MAX]; + char buf[65536]; + ssize_t len; + kstring_t kstr = {0}; + hFILE *fp; + cram_index *idx; + cram_index **idx_stack = NULL, *ep, e; + int idx_stack_alloc = 0, idx_stack_ptr = 0; + size_t pos = 0; + + /* Check if already loaded */ + if (fd->index) + return 0; + + fd->index = calloc((fd->index_sz = 1), sizeof(*fd->index)); + if (!fd->index) + return -1; + + idx = &fd->index[0]; + idx->refid = -1; + idx->start = INT_MIN; + idx->end = INT_MAX; + + idx_stack = calloc(++idx_stack_alloc, sizeof(*idx_stack)); + idx_stack[idx_stack_ptr] = idx; + + sprintf(fn2, "%s.crai", fn); + if (!(fp = hopen(fn2, "r"))) { + perror(fn2); + free(idx_stack); + return -1; + } + + // Load the file into memory + while ((len = hread(fp, buf, 65536)) > 0) + kputsn(buf, len, &kstr); + if (len < 0 || kstr.l < 2) { + if (kstr.s) + free(kstr.s); + free(idx_stack); + return -1; + } + + if (hclose(fp)) { + if (kstr.s) + free(kstr.s); + free(idx_stack); + return -1; + } + + + // Uncompress if required + if (kstr.s[0] == 31 && (uc)kstr.s[1] == 139) { + size_t l; + char *s = zlib_mem_inflate(kstr.s, kstr.l, &l); + free(kstr.s); + if (!s) { + free(idx_stack); + return -1; + } + kstr.s = s; + kstr.l = l; + } + + + // Parse it line at a time + do { + int nchars; + char *line = &kstr.s[pos]; + + /* 1.1 layout */ + if (sscanf(line, "%d\t%d\t%d\t%"PRId64"\t%d\t%d%n", + &e.refid, + &e.start, + &e.end, + &e.offset, + &e.slice, + &e.len, + &nchars) != 6) { + free(kstr.s); + free(idx_stack); + return -1; + } + + e.end += e.start-1; + //printf("%d/%d..%d\n", e.refid, e.start, e.end); + + if (e.refid < -1) { + free(kstr.s); + free(idx_stack); + fprintf(stderr, "Malformed index file, refid %d\n", e.refid); + return -1; + } + + if (e.refid != idx->refid) { + if (fd->index_sz < e.refid+2) { + size_t index_end = fd->index_sz * sizeof(*fd->index); + fd->index_sz = e.refid+2; + fd->index = realloc(fd->index, + fd->index_sz * sizeof(*fd->index)); + memset(((char *)fd->index) + index_end, 0, + fd->index_sz * sizeof(*fd->index) - index_end); + } + idx = &fd->index[e.refid+1]; + idx->refid = e.refid; + idx->start = INT_MIN; + idx->end = INT_MAX; + idx->nslice = idx->nalloc = 0; + idx->e = NULL; + idx_stack[(idx_stack_ptr = 0)] = idx; + } + + while (!(e.start >= idx->start && e.end <= idx->end)) { + idx = idx_stack[--idx_stack_ptr]; + } + + // Now contains, so append + if (idx->nslice+1 >= idx->nalloc) { + idx->nalloc = idx->nalloc ? idx->nalloc*2 : 16; + idx->e = realloc(idx->e, idx->nalloc * sizeof(*idx->e)); + } + + e.nalloc = e.nslice = 0; e.e = NULL; + *(ep = &idx->e[idx->nslice++]) = e; + idx = ep; + + if (++idx_stack_ptr >= idx_stack_alloc) { + idx_stack_alloc *= 2; + idx_stack = realloc(idx_stack, idx_stack_alloc*sizeof(*idx_stack)); + } + idx_stack[idx_stack_ptr] = idx; + + pos += nchars; + while (pos < kstr.l && kstr.s[pos] != '\n') + pos++; + pos++; + } while (pos < kstr.l); + + free(idx_stack); + free(kstr.s); + + // dump_index(fd); + + return 0; +} + +static void cram_index_free_recurse(cram_index *e) { + if (e->e) { + int i; + for (i = 0; i < e->nslice; i++) { + cram_index_free_recurse(&e->e[i]); + } + free(e->e); + } +} + +void cram_index_free(cram_fd *fd) { + int i; + + if (!fd->index) + return; + + for (i = 0; i < fd->index_sz; i++) { + cram_index_free_recurse(&fd->index[i]); + } + free(fd->index); + + fd->index = NULL; +} + +/* + * Searches the index for the first slice overlapping a reference ID + * and position, or one immediately preceeding it if none is found in + * the index to overlap this position. (Our index may have missing + * entries, but we require at least one per reference.) + * + * If the index finds multiple slices overlapping this position we + * return the first one only. Subsequent calls should specifying + * "from" as the last slice we checked to find the next one. Otherwise + * set "from" to be NULL to find the first one. + * + * Returns the cram_index pointer on sucess + * NULL on failure + */ +cram_index *cram_index_query(cram_fd *fd, int refid, int pos, + cram_index *from) { + int i, j, k; + cram_index *e; + + if (refid+1 < 0 || refid+1 >= fd->index_sz) + return NULL; + + i = 0, j = fd->index[refid+1].nslice-1; + + if (!from) + from = &fd->index[refid+1]; + + for (k = j/2; k != i; k = (j-i)/2 + i) { + if (from->e[k].refid > refid) { + j = k; + continue; + } + + if (from->e[k].refid < refid) { + i = k; + continue; + } + + if (from->e[k].start >= pos) { + j = k; + continue; + } + + if (from->e[k].start < pos) { + i = k; + continue; + } + } + + /* The above found *a* bin overlapping, but not necessarily the first */ + while (i > 0 && from->e[i-1].end >= pos) + i--; + + /* Special case for matching a start pos */ + if (i+1 < from->nslice && + from->e[i+1].start == pos && + from->e[i+1].refid == refid) + i++; + + e = &from->e[i]; + + return e; +} + + +/* + * Skips to a container overlapping the start coordinate listed in + * cram_range. + * + * In theory we call cram_index_query multiple times, once per slice + * overlapping the range. However slices may be absent from the index + * which makes this problematic. Instead we find the left-most slice + * and then read from then on, skipping decoding of slices and/or + * whole containers when they don't overlap the specified cram_range. + * + * Returns 0 on success + * -1 on failure + */ +int cram_seek_to_refpos(cram_fd *fd, cram_range *r) { + cram_index *e; + + // Ideally use an index, so see if we have one. + if ((e = cram_index_query(fd, r->refid, r->start, NULL))) { + if (0 != cram_seek(fd, e->offset, SEEK_SET)) + if (0 != cram_seek(fd, e->offset - fd->first_container, SEEK_CUR)) + return -1; + } else { + fprintf(stderr, "Unknown reference ID. Missing from index?\n"); + return -1; + } + + if (fd->ctr) { + cram_free_container(fd->ctr); + fd->ctr = NULL; + } + + return 0; +} + + +/* + * A specialised form of cram_index_build (below) that deals with slices + * having multiple references in this (ref_id -2). In this scenario we + * decode the slice to look at the RI data series instead. + * + * Returns 0 on success + * -1 on failure + */ +static int cram_index_build_multiref(cram_fd *fd, + cram_container *c, + cram_slice *s, + zfp *fp, + off_t cpos, + int32_t landmark, + int sz) { + int i, ref = -2, ref_start = 0, ref_end; + char buf[1024]; + + if (0 != cram_decode_slice(fd, c, s, fd->header)) + return -1; + + ref_end = INT_MIN; + for (i = 0; i < s->hdr->num_records; i++) { + if (s->crecs[i].ref_id == ref) { + if (ref_end < s->crecs[i].aend) + ref_end = s->crecs[i].aend; + continue; + } + + if (ref != -2) { + sprintf(buf, "%d\t%d\t%d\t%"PRId64"\t%d\t%d\n", + ref, ref_start, ref_end - ref_start + 1, + (int64_t)cpos, landmark, sz); + zfputs(buf, fp); + } + + ref = s->crecs[i].ref_id; + ref_start = s->crecs[i].apos; + ref_end = INT_MIN; + } + + if (ref != -2) { + sprintf(buf, "%d\t%d\t%d\t%"PRId64"\t%d\t%d\n", + ref, ref_start, ref_end - ref_start + 1, + (int64_t)cpos, landmark, sz); + zfputs(buf, fp); + } + + return 0; +} + +/* + * Builds an index file. + * + * fd is a newly opened cram file that we wish to index. + * fn_base is the filename of the associated CRAM file. Internally we + * add ".crai" to this to get the index filename. + * + * Returns 0 on success + * -1 on failure + */ +int cram_index_build(cram_fd *fd, const char *fn_base) { + cram_container *c; + off_t cpos, spos, hpos; + zfp *fp; + char fn_idx[PATH_MAX]; + + if (strlen(fn_base) > PATH_MAX-6) + return -1; + + sprintf(fn_idx, "%s.crai", fn_base); + if (!(fp = zfopen(fn_idx, "wz"))) { + perror(fn_idx); + return -1; + } + + cpos = htell(fd->fp); + while ((c = cram_read_container(fd))) { + int j; + + if (fd->err) { + perror("Cram container read"); + return 1; + } + + hpos = htell(fd->fp); + + if (!(c->comp_hdr_block = cram_read_block(fd))) + return 1; + assert(c->comp_hdr_block->content_type == COMPRESSION_HEADER); + + c->comp_hdr = cram_decode_compression_header(fd, c->comp_hdr_block); + if (!c->comp_hdr) + return -1; + + // 2.0 format + for (j = 0; j < c->num_landmarks; j++) { + char buf[1024]; + cram_slice *s; + int sz; + + spos = htell(fd->fp); + assert(spos - cpos - c->offset == c->landmark[j]); + + if (!(s = cram_read_slice(fd))) { + zfclose(fp); + return -1; + } + + sz = (int)(htell(fd->fp) - spos); + + if (s->hdr->ref_seq_id == -2) { + cram_index_build_multiref(fd, c, s, fp, + cpos, c->landmark[j], sz); + } else { + sprintf(buf, "%d\t%d\t%d\t%"PRId64"\t%d\t%d\n", + s->hdr->ref_seq_id, s->hdr->ref_seq_start, + s->hdr->ref_seq_span, (int64_t)cpos, + c->landmark[j], sz); + zfputs(buf, fp); + } + + cram_free_slice(s); + } + + cpos = htell(fd->fp); + assert(cpos == hpos + c->length); + + cram_free_container(c); + } + if (fd->err) { + zfclose(fp); + return -1; + } + + + return zfclose(fp); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_index.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_index.h new file mode 100644 index 0000000000000000000000000000000000000000..5e3b8f5ae9ccedc0d74f2d19679d0d7fe2eb6ae1 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_index.h @@ -0,0 +1,98 @@ +/* +Copyright (c) 2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifndef _CRAM_INDEX_H_ +#define _CRAM_INDEX_H_ + +#ifdef __cplusplus +extern "C" { +#endif + +/* + * Loads a CRAM .crai index into memory. + * Returns 0 for success + * -1 for failure + */ +int cram_index_load(cram_fd *fd, const char *fn); + +void cram_index_free(cram_fd *fd); + +/* + * Searches the index for the first slice overlapping a reference ID + * and position. + * + * Returns the cram_index pointer on sucess + * NULL on failure + */ +cram_index *cram_index_query(cram_fd *fd, int refid, int pos, cram_index *frm); + +/* + * Skips to a container overlapping the start coordinate listed in + * cram_range. + * + * Returns 0 on success + * -1 on failure + */ +int cram_seek_to_refpos(cram_fd *fd, cram_range *r); + +void cram_index_free(cram_fd *fd); + +/* + * Skips to a container overlapping the start coordinate listed in + * cram_range. + * + * In theory we call cram_index_query multiple times, once per slice + * overlapping the range. However slices may be absent from the index + * which makes this problematic. Instead we find the left-most slice + * and then read from then on, skipping decoding of slices and/or + * whole containers when they don't overlap the specified cram_range. + * + * Returns 0 on success + * -1 on failure + */ +int cram_seek_to_refpos(cram_fd *fd, cram_range *r); + +/* + * Builds an index file. + * + * fd is a newly opened cram file that we wish to index. + * fn_base is the filename of the associated CRAM file. Internally we + * add ".crai" to this to get the index filename. + * + * Returns 0 on success + * -1 on failure + */ +int cram_index_build(cram_fd *fd, const char *fn_base); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_io.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_io.c new file mode 100644 index 0000000000000000000000000000000000000000..8abc59d173fd370637a89e7bb63b0fcad238162f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_io.c @@ -0,0 +1,3652 @@ +/* +Copyright (c) 2012-2014 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +/* + * CRAM I/O primitives. + * + * - ITF8 encoding and decoding. + * - Block based I/O + * - Zlib inflating and deflating (memory) + * - CRAM basic data structure reading and writing + * - File opening / closing + * - Reference sequence handling + */ + +/* + * TODO: BLOCK_GROW, BLOCK_RESIZE, BLOCK_APPEND and itf8_put_blk all need + * a way to return errors for when malloc fails. + */ + +#ifdef HAVE_CONFIG_H +#include "io_lib_config.h" +#endif + +#include +#include +#include +#include +#include +#include +#ifdef HAVE_LIBBZ2 +#include +#endif +#include +#include +#include +#include + +#include "cram/cram.h" +#include "cram/os.h" +#include "cram/md5.h" +#include "cram/open_trace_file.h" + +//#define REF_DEBUG + +#ifdef REF_DEBUG +#include +#define gettid() (int)syscall(SYS_gettid) + +#define RP(...) fprintf (stderr, __VA_ARGS__) +#else +#define RP(...) +#endif + +#ifdef SAMTOOLS +#include "htslib/hfile.h" +#define paranoid_hclose(fp) (hclose(fp)) +#else +#define hclose_abruptly(fp) (fclose(fp)) +#define hflush(fp) (fflush(fp)) +#define hgetc(fp) (getc(fp)) +#define hputc(c, fp) (putc((c), (fp))) +#define hread(fp, buffer, nbytes) (fread((buffer), 1, (nbytes), (fp))) +#define hseek(fp, offset, whence) (fseeko((fp), (offset), (whence))) +#define hwrite(fp, buffer, nbytes) (fwrite((buffer), 1, (nbytes), (fp))) +#define paranoid_hclose(fp) (paranoid_fclose(fp)) +#endif + +/* ---------------------------------------------------------------------- + * ITF8 encoding and decoding. + * +* Also see the itf8_get and itf8_put macros in cram_io.h + */ + +/* + * Reads an integer in ITF-8 encoding from 'cp' and stores it in + * *val. + * + * Returns the number of bytes read on success + * -1 on failure + */ +int itf8_decode(cram_fd *fd, int32_t *val_p) { + static int nbytes[16] = { + 0,0,0,0, 0,0,0,0, // 0000xxxx - 0111xxxx + 1,1,1,1, // 1000xxxx - 1011xxxx + 2,2, // 1100xxxx - 1101xxxx + 3, // 1110xxxx + 4, // 1111xxxx + }; + + static int nbits[16] = { + 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, // 0000xxxx - 0111xxxx + 0x3f, 0x3f, 0x3f, 0x3f, // 1000xxxx - 1011xxxx + 0x1f, 0x1f, // 1100xxxx - 1101xxxx + 0x0f, // 1110xxxx + 0x0f, // 1111xxxx + }; + + int32_t val = hgetc(fd->fp); + if (val == -1) + return -1; + + int i = nbytes[val>>4]; + val &= nbits[val>>4]; + + switch(i) { + case 0: + *val_p = val; + return 1; + + case 1: + val = (val<<8) | (unsigned char)hgetc(fd->fp); + *val_p = val; + return 2; + + case 2: + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + *val_p = val; + return 3; + + case 3: + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + *val_p = val; + return 4; + + case 4: // really 3.5 more, why make it different? + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<4) | (((unsigned char)hgetc(fd->fp)) & 0x0f); + *val_p = val; + } + + return 5; +} + +/* + * Encodes and writes a single integer in ITF-8 format. + * Returns 0 on success + * -1 on failure + */ +int itf8_encode(cram_fd *fd, int32_t val) { + char buf[5]; + int len = itf8_put(buf, val); + return hwrite(fd->fp, buf, len) == len ? 0 : -1; +} + +#ifndef ITF8_MACROS +/* + * As above, but decoding from memory + */ +int itf8_get(char *cp, int32_t *val_p) { + unsigned char *up = (unsigned char *)cp; + + if (up[0] < 0x80) { + *val_p = up[0]; + return 1; + } else if (up[0] < 0xc0) { + *val_p = ((up[0] <<8) | up[1]) & 0x3fff; + return 2; + } else if (up[0] < 0xe0) { + *val_p = ((up[0]<<16) | (up[1]<< 8) | up[2]) & 0x1fffff; + return 3; + } else if (up[0] < 0xf0) { + *val_p = ((up[0]<<24) | (up[1]<<16) | (up[2]<<8) | up[3]) & 0x0fffffff; + return 4; + } else { + *val_p = ((up[0] & 0x0f)<<28) | (up[1]<<20) | (up[2]<<12) | (up[3]<<4) | (up[4] & 0x0f); + return 5; + } +} + +/* + * Stores a value to memory in ITF-8 format. + * + * Returns the number of bytes required to store the number. + * This is a maximum of 5 bytes. + */ +int itf8_put(char *cp, int32_t val) { + if (!(val & ~0x00000007f)) { // 1 byte + *cp = val; + return 1; + } else if (!(val & ~0x00003fff)) { // 2 byte + *cp++ = (val >> 8 ) | 0x80; + *cp = val & 0xff; + return 2; + } else if (!(val & ~0x01fffff)) { // 3 byte + *cp++ = (val >> 16) | 0xc0; + *cp++ = (val >> 8 ) & 0xff; + *cp = val & 0xff; + return 3; + } else if (!(val & ~0x0fffffff)) { // 4 byte + *cp++ = (val >> 24) | 0xe0; + *cp++ = (val >> 16) & 0xff; + *cp++ = (val >> 8 ) & 0xff; + *cp = val & 0xff; + return 4; + } else { // 5 byte + *cp++ = 0xf0 | ((val>>28) & 0xff); + *cp++ = (val >> 20) & 0xff; + *cp++ = (val >> 12) & 0xff; + *cp++ = (val >> 4 ) & 0xff; + *cp = val & 0x0f; + return 5; + } +} +#endif + +/* 64-bit itf8 variant */ +int ltf8_put(char *cp, int64_t val) { + if (!(val & ~((1LL<<7)-1))) { + *cp = val; + return 1; + } else if (!(val & ~((1LL<<(6+8))-1))) { + *cp++ = (val >> 8 ) | 0x80; + *cp = val & 0xff; + return 2; + } else if (!(val & ~((1LL<<(5+2*8))-1))) { + *cp++ = (val >> 16) | 0xc0; + *cp++ = (val >> 8 ) & 0xff; + *cp = val & 0xff; + return 3; + } else if (!(val & ~((1LL<<(4+3*8))-1))) { + *cp++ = (val >> 24) | 0xe0; + *cp++ = (val >> 16) & 0xff; + *cp++ = (val >> 8 ) & 0xff; + *cp = val & 0xff; + return 4; + } else if (!(val & ~((1LL<<(3+4*8))-1))) { + *cp++ = (val >> 32) | 0xf0; + *cp++ = (val >> 24) & 0xff; + *cp++ = (val >> 16) & 0xff; + *cp++ = (val >> 8 ) & 0xff; + *cp = val & 0xff; + return 5; + } else if (!(val & ~((1LL<<(2+5*8))-1))) { + *cp++ = (val >> 40) | 0xf8; + *cp++ = (val >> 32) & 0xff; + *cp++ = (val >> 24) & 0xff; + *cp++ = (val >> 16) & 0xff; + *cp++ = (val >> 8 ) & 0xff; + *cp = val & 0xff; + return 6; + } else if (!(val & ~((1LL<<(1+6*8))-1))) { + *cp++ = (val >> 48) | 0xfc; + *cp++ = (val >> 40) & 0xff; + *cp++ = (val >> 32) & 0xff; + *cp++ = (val >> 24) & 0xff; + *cp++ = (val >> 16) & 0xff; + *cp++ = (val >> 8 ) & 0xff; + *cp = val & 0xff; + return 7; + } else if (!(val & ~((1LL<<(7*8))-1))) { + *cp++ = (val >> 56) | 0xfe; + *cp++ = (val >> 48) & 0xff; + *cp++ = (val >> 40) & 0xff; + *cp++ = (val >> 32) & 0xff; + *cp++ = (val >> 24) & 0xff; + *cp++ = (val >> 16) & 0xff; + *cp++ = (val >> 8 ) & 0xff; + *cp = val & 0xff; + return 8; + } else { + *cp++ = 0xff; + *cp++ = (val >> 56) & 0xff; + *cp++ = (val >> 48) & 0xff; + *cp++ = (val >> 40) & 0xff; + *cp++ = (val >> 32) & 0xff; + *cp++ = (val >> 24) & 0xff; + *cp++ = (val >> 16) & 0xff; + *cp++ = (val >> 8 ) & 0xff; + *cp = val & 0xff; + return 9; + } +} + +int ltf8_get(char *cp, int64_t *val_p) { + unsigned char *up = (unsigned char *)cp; + + if (up[0] < 0x80) { + *val_p = up[0]; + return 1; + } else if (up[0] < 0xc0) { + *val_p = (((uint64_t)up[0]<< 8) | + (uint64_t)up[1]) & (((1LL<<(6+8)))-1); + return 2; + } else if (up[0] < 0xe0) { + *val_p = (((uint64_t)up[0]<<16) | + ((uint64_t)up[1]<< 8) | + (uint64_t)up[2]) & ((1LL<<(5+2*8))-1); + return 3; + } else if (up[0] < 0xf0) { + *val_p = (((uint64_t)up[0]<<24) | + ((uint64_t)up[1]<<16) | + ((uint64_t)up[2]<< 8) | + (uint64_t)up[3]) & ((1LL<<(4+3*8))-1); + return 4; + } else if (up[0] < 0xf8) { + *val_p = (((uint64_t)up[0]<<32) | + ((uint64_t)up[1]<<24) | + ((uint64_t)up[2]<<16) | + ((uint64_t)up[3]<< 8) | + (uint64_t)up[4]) & ((1LL<<(3+4*8))-1); + return 5; + } else if (up[0] < 0xfc) { + *val_p = (((uint64_t)up[0]<<40) | + ((uint64_t)up[1]<<32) | + ((uint64_t)up[2]<<24) | + ((uint64_t)up[3]<<16) | + ((uint64_t)up[4]<< 8) | + (uint64_t)up[5]) & ((1LL<<(2+5*8))-1); + return 6; + } else if (up[0] < 0xfe) { + *val_p = (((uint64_t)up[0]<<48) | + ((uint64_t)up[1]<<40) | + ((uint64_t)up[2]<<32) | + ((uint64_t)up[3]<<24) | + ((uint64_t)up[4]<<16) | + ((uint64_t)up[5]<< 8) | + (uint64_t)up[6]) & ((1LL<<(1+6*8))-1); + return 7; + } else if (up[0] < 0xff) { + *val_p = (((uint64_t)up[1]<<48) | + ((uint64_t)up[2]<<40) | + ((uint64_t)up[3]<<32) | + ((uint64_t)up[4]<<24) | + ((uint64_t)up[5]<<16) | + ((uint64_t)up[6]<< 8) | + (uint64_t)up[7]) & ((1LL<<(7*8))-1); + return 8; + } else { + *val_p = (((uint64_t)up[1]<<56) | + ((uint64_t)up[2]<<48) | + ((uint64_t)up[3]<<40) | + ((uint64_t)up[4]<<32) | + ((uint64_t)up[5]<<24) | + ((uint64_t)up[6]<<16) | + ((uint64_t)up[7]<< 8) | + (uint64_t)up[8]); + return 9; + } +} + +int ltf8_decode(cram_fd *fd, int64_t *val_p) { + int c = hgetc(fd->fp); + int64_t val = (unsigned char)c; + if (c == -1) + return -1; + + if (val < 0x80) { + *val_p = val; + return 1; + + } else if (val < 0xc0) { + val = (val<<8) | (unsigned char)hgetc(fd->fp); + *val_p = val & (((1LL<<(6+8)))-1); + return 2; + + } else if (val < 0xe0) { + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + *val_p = val & ((1LL<<(5+2*8))-1); + return 3; + + } else if (val < 0xf0) { + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + *val_p = val & ((1LL<<(4+3*8))-1); + return 4; + + } else if (val < 0xf8) { + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + *val_p = val & ((1LL<<(3+4*8))-1); + return 5; + + } else if (val < 0xfc) { + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + *val_p = val & ((1LL<<(2+5*8))-1); + return 6; + + } else if (val < 0xfe) { + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + *val_p = val & ((1LL<<(1+6*8))-1); + return 7; + + } else if (val < 0xff) { + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + *val_p = val & ((1LL<<(7*8))-1); + return 8; + + } else { + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + val = (val<<8) | (unsigned char)hgetc(fd->fp); + *val_p = val; + } + + return 9; +} + +/* + * Pushes a value in ITF8 format onto the end of a block. + * This shouldn't be used for high-volume data as it is not the fastest + * method. + * + * Returns the number of bytes written + */ +int itf8_put_blk(cram_block *blk, int val) { + char buf[5]; + int sz; + + sz = itf8_put(buf, val); + BLOCK_APPEND(blk, buf, sz); + return sz; +} + +/* + * Decodes a 32-bit little endian value from fd and stores in val. + * + * Returns the number of bytes read on success + * -1 on failure + */ +int int32_decode(cram_fd *fd, int32_t *val) { + int32_t i; + if (4 != hread(fd->fp, &i, 4)) + return -1; + + *val = le_int4(i); + return 4; +} + +/* + * Encodes a 32-bit little endian value 'val' and writes to fd. + * + * Returns the number of bytes written on success + * -1 on failure + */ +int int32_encode(cram_fd *fd, int32_t val) { + val = le_int4(val); + if (4 != hwrite(fd->fp, &val, 4)) + return -1; + + return 4; +} + +/* As int32_decoded/encode, but from/to blocks instead of cram_fd */ +int int32_get(cram_block *b, int32_t *val) { + if (b->uncomp_size - BLOCK_SIZE(b) < 4) + return -1; + + *val = + b->data[b->byte ] | + (b->data[b->byte+1] << 8) | + (b->data[b->byte+2] << 16) | + (b->data[b->byte+3] << 24); + BLOCK_SIZE(b) += 4; + return 4; +} + +/* As int32_decoded/encode, but from/to blocks instead of cram_fd */ +int int32_put(cram_block *b, int32_t val) { + unsigned char cp[4]; + cp[0] = ( val & 0xff); + cp[1] = ((val>>8) & 0xff); + cp[2] = ((val>>16) & 0xff); + cp[3] = ((val>>24) & 0xff); + + BLOCK_APPEND(b, cp, 4); + return b->data ? 0 : -1; +} + +/* ---------------------------------------------------------------------- + * zlib compression code - from Gap5's tg_iface_g.c + * They're static here as they're only used within the cram_compress_block + * and cram_uncompress_block functions, which are the external interface. + */ +char *zlib_mem_inflate(char *cdata, size_t csize, size_t *size) { + z_stream s; + unsigned char *data = NULL; /* Uncompressed output */ + int data_alloc = 0; + int err; + + /* Starting point at uncompressed size, and scale after that */ + data = malloc(data_alloc = csize*1.2+100); + if (!data) + return NULL; + + /* Initialise zlib stream */ + s.zalloc = Z_NULL; /* use default allocation functions */ + s.zfree = Z_NULL; + s.opaque = Z_NULL; + s.next_in = (unsigned char *)cdata; + s.avail_in = csize; + s.total_in = 0; + s.next_out = data; + s.avail_out = data_alloc; + s.total_out = 0; + + //err = inflateInit(&s); + err = inflateInit2(&s, 15 + 32); + if (err != Z_OK) { + fprintf(stderr, "zlib inflateInit error: %s\n", s.msg); + free(data); + return NULL; + } + + /* Decode to 'data' array */ + for (;s.avail_in;) { + unsigned char *data_tmp; + int alloc_inc; + + s.next_out = &data[s.total_out]; + err = inflate(&s, Z_NO_FLUSH); + if (err == Z_STREAM_END) + break; + + if (err != Z_OK) { + fprintf(stderr, "zlib inflate error: %s\n", s.msg); + break; + } + + /* More to come, so realloc based on growth so far */ + alloc_inc = (double)s.avail_in/s.total_in * s.total_out + 100; + data = realloc((data_tmp = data), data_alloc += alloc_inc); + if (!data) { + free(data_tmp); + return NULL; + } + s.avail_out += alloc_inc; + } + inflateEnd(&s); + + *size = s.total_out; + return (char *)data; +} + +static char *zlib_mem_deflate(char *data, size_t size, size_t *cdata_size, + int level, int strat) { + z_stream s; + unsigned char *cdata = NULL; /* Compressed output */ + int cdata_alloc = 0; + int cdata_pos = 0; + int err; + + cdata = malloc(cdata_alloc = size*1.05+100); + if (!cdata) + return NULL; + cdata_pos = 0; + + /* Initialise zlib stream */ + s.zalloc = Z_NULL; /* use default allocation functions */ + s.zfree = Z_NULL; + s.opaque = Z_NULL; + s.next_in = (unsigned char *)data; + s.avail_in = size; + s.total_in = 0; + s.next_out = cdata; + s.avail_out = cdata_alloc; + s.total_out = 0; + s.data_type = Z_BINARY; + + err = deflateInit2(&s, level, Z_DEFLATED, 15|16, 9, strat); + if (err != Z_OK) { + fprintf(stderr, "zlib deflateInit2 error: %s\n", s.msg); + return NULL; + } + + /* Encode to 'cdata' array */ + for (;s.avail_in;) { + s.next_out = &cdata[cdata_pos]; + s.avail_out = cdata_alloc - cdata_pos; + if (cdata_alloc - cdata_pos <= 0) { + fprintf(stderr, "Deflate produced larger output than expected. Abort\n"); + return NULL; + } + err = deflate(&s, Z_NO_FLUSH); + cdata_pos = cdata_alloc - s.avail_out; + if (err != Z_OK) { + fprintf(stderr, "zlib deflate error: %s\n", s.msg); + break; + } + } + if (deflate(&s, Z_FINISH) != Z_STREAM_END) { + fprintf(stderr, "zlib deflate error: %s\n", s.msg); + } + *cdata_size = s.total_out; + + if (deflateEnd(&s) != Z_OK) { + fprintf(stderr, "zlib deflate error: %s\n", s.msg); + } + return (char *)cdata; +} + +/* ---------------------------------------------------------------------- + * CRAM blocks - the dynamically growable data block. We have code to + * create, update, (un)compress and read/write. + * + * These are derived from the deflate_interlaced.c blocks, but with the + * CRAM extension of content types and IDs. + */ + +/* + * Allocates a new cram_block structure with a specified content_type and + * id. + * + * Returns block pointer on success + * NULL on failure + */ +cram_block *cram_new_block(enum cram_content_type content_type, + int content_id) { + cram_block *b = malloc(sizeof(*b)); + if (!b) + return NULL; + b->method = b->orig_method = RAW; + b->content_type = content_type; + b->content_id = content_id; + b->comp_size = 0; + b->uncomp_size = 0; + b->data = NULL; + b->alloc = 0; + b->byte = 0; + b->bit = 7; // MSB + + return b; +} + +/* + * Reads a block from a cram file. + * Returns cram_block pointer on success. + * NULL on failure + */ +cram_block *cram_read_block(cram_fd *fd) { + cram_block *b = malloc(sizeof(*b)); + if (!b) + return NULL; + + //fprintf(stderr, "Block at %d\n", (int)ftell(fd->fp)); + + if (-1 == (b->method = hgetc(fd->fp))) { free(b); return NULL; } + if (-1 == (b->content_type= hgetc(fd->fp))) { free(b); return NULL; } + if (-1 == itf8_decode(fd, &b->content_id)) { free(b); return NULL; } + if (-1 == itf8_decode(fd, &b->comp_size)) { free(b); return NULL; } + if (-1 == itf8_decode(fd, &b->uncomp_size)) { free(b); return NULL; } + + // fprintf(stderr, " method %d, ctype %d, cid %d, csize %d, ucsize %d\n", + // b->method, b->content_type, b->content_id, b->comp_size, b->uncomp_size); + + if (b->method == RAW) { + b->alloc = b->uncomp_size; + if (!(b->data = malloc(b->uncomp_size))){ free(b); return NULL; } + if (b->uncomp_size != hread(fd->fp, b->data, b->uncomp_size)) { + free(b->data); + free(b); + return NULL; + } + } else { + b->alloc = b->comp_size; + if (!(b->data = malloc(b->comp_size))) { free(b); return NULL; } + if (b->comp_size != hread(fd->fp, b->data, b->comp_size)) { + free(b->data); + free(b); + return NULL; + } + } + + b->orig_method = b->method; + b->idx = 0; + b->byte = 0; + b->bit = 7; // MSB + + return b; +} + +/* + * Writes a CRAM block. + * Returns 0 on success + * -1 on failure + */ +int cram_write_block(cram_fd *fd, cram_block *b) { + assert(b->method != RAW || (b->comp_size == b->uncomp_size)); + + if (hputc(b->method, fd->fp) == EOF) return -1; + if (hputc(b->content_type, fd->fp) == EOF) return -1; + if (itf8_encode(fd, b->content_id) == -1) return -1; + if (itf8_encode(fd, b->comp_size) == -1) return -1; + if (itf8_encode(fd, b->uncomp_size) == -1) return -1; + + if (b->method == RAW) { + if (b->uncomp_size != hwrite(fd->fp, b->data, b->uncomp_size)) + return -1; + } else { + if (b->comp_size != hwrite(fd->fp, b->data, b->comp_size)) + return -1; + } + + return 0; +} + +/* + * Frees a CRAM block, deallocating internal data too. + */ +void cram_free_block(cram_block *b) { + if (!b) + return; + if (b->data) + free(b->data); + free(b); +} + +/* + * Uncompresses a CRAM block, if compressed. + */ +int cram_uncompress_block(cram_block *b) { + char *uncomp; + size_t uncomp_size = 0; + + if (b->uncomp_size == 0) { + // blank block + b->method = RAW; + return 0; + } + + switch (b->method) { + case RAW: + b->uncomp_size = b->comp_size; + return 0; + + case GZIP: + uncomp = zlib_mem_inflate((char *)b->data, b->comp_size, &uncomp_size); + if (!uncomp) + return -1; + if ((int)uncomp_size != b->uncomp_size) + return -1; + free(b->data); + b->data = (unsigned char *)uncomp; + b->alloc = uncomp_size; + b->method = RAW; + break; + +#ifdef HAVE_LIBBZ2 + case BZIP2: { + unsigned int usize = b->uncomp_size; + if (!(uncomp = malloc(usize))) + return -1; + if (BZ_OK != BZ2_bzBuffToBuffDecompress(uncomp, &usize, + (char *)b->data, b->comp_size, + 0, 0)) { + free(uncomp); + return -1; + } + b->data = (unsigned char *)uncomp; + b->alloc = usize; + b->method = RAW; + b->uncomp_size = usize; // Just incase it differs + break; + } +#else + case BZIP2: + fprintf(stderr, "Bzip2 compression is not compiled into this " + "version.\nPlease rebuild and try again.\n"); + return -1; +#endif + + case BM_ERROR: + default: + return -1; + } + + return 0; +} + +#ifdef HAVE_LIBBZ2 +static int cram_compress_block_bzip2(cram_fd *fd, cram_block *b, + cram_metrics *metrics, int level) { + unsigned int comp_size = b->uncomp_size*1.01 + 600; + char *comp = malloc(comp_size); + char *data = (char *)b->data; + + if (!comp) + return -1; + + if (!data) + data = ""; + + if (BZ_OK != BZ2_bzBuffToBuffCompress(comp, &comp_size, + data, b->uncomp_size, + level, 0, 30)) { + free(comp); + return -1; + } + + free(b->data); + b->data = (unsigned char *)comp; + b->method = BZIP2; + b->comp_size = comp_size; + + if (fd->verbose) + fprintf(stderr, "Compressed block ID %d from %d to %d\n", + b->content_id, b->uncomp_size, b->comp_size); + + return 0; +} +#endif + +/* + * Compresses a block using one of two different zlib strategies. If we only + * want one choice set strat2 to be -1. + * + * The logic here is that sometimes Z_RLE does a better job than Z_FILTERED + * or Z_DEFAULT_STRATEGY on quality data. If so, we'd rather use it as it is + * significantly faster. + */ +int cram_compress_block(cram_fd *fd, cram_block *b, cram_metrics *metrics, + int level, int strat, + int level2, int strat2) { + char *comp = NULL; + size_t comp_size = 0; + + if (level == 0) { + b->method = RAW; + b->comp_size = b->uncomp_size; + return 0; + } + + if (b->method != RAW) { + fprintf(stderr, "Attempt to compress an already compressed block.\n"); + return 0; + } + +#ifdef HAVE_LIBBZ2 + if (fd->use_bz2) + // metrics ignored for bzip2 + return cram_compress_block_bzip2(fd, b, metrics, level); +#endif + + pthread_mutex_lock(&fd->metrics_lock); + if (strat2 >= 0) + if (fd->verbose > 1) + fprintf(stderr, "metrics trial %d, next_trial %d, m1 %d, m2 %d\n", + metrics->trial, metrics->next_trial, + metrics->m1, metrics->m2); + + if (strat2 >= 0 && (metrics->trial > 0 || --metrics->next_trial <= 0)) { + char *c1, *c2; + size_t s1, s2; + + if (metrics->next_trial == 0) { + metrics->next_trial = 100; + metrics->trial = 3; + metrics->m1 = metrics->m2 = 0; + } + pthread_mutex_unlock(&fd->metrics_lock); + + c1 = zlib_mem_deflate((char *)b->data, b->uncomp_size, + &s1, level, strat); + c2 = zlib_mem_deflate((char *)b->data, b->uncomp_size, + &s2, level2, strat2); + if (!c1 || !c2) + return -1; + + //fprintf(stderr, "1: %6d 2: %6d %5.1f\n", s1, s2, 100.0*s1/s2); + + pthread_mutex_lock(&fd->metrics_lock); + if (s1 < 0.98 * s2) { // 2nd one should be faster alternative + if (fd->verbose > 1) + fprintf(stderr, "M1 wins %d vs %d\n", (int)s1, (int)s2); + comp = c1; comp_size = s1; + free(c2); + metrics->m1++; + } else { + if (fd->verbose > 1) + fprintf(stderr, "M2 wins %d vs %d\n", (int)s1, (int)s2); + comp = c2; comp_size = s2; + free(c1); + metrics->m2++; + } + metrics->trial--; + pthread_mutex_unlock(&fd->metrics_lock); + } else if (strat2 >= 0) { + int xlevel = metrics->m1 > metrics->m2 ? level : level2; + int xstrat = metrics->m1 > metrics->m2 ? strat : strat2; + pthread_mutex_unlock(&fd->metrics_lock); + comp = zlib_mem_deflate((char *)b->data, b->uncomp_size, &comp_size, + xlevel, xstrat); + } else { + pthread_mutex_unlock(&fd->metrics_lock); + comp = zlib_mem_deflate((char *)b->data, b->uncomp_size, &comp_size, + level, strat); + } + + if (!comp) + return -1; + + free(b->data); + b->data = (unsigned char *)comp; + b->method = GZIP; + b->comp_size = comp_size; + + if (fd->verbose) + fprintf(stderr, "Compressed block ID %d from %d to %d\n", + b->content_id, b->uncomp_size, b->comp_size); + + return 0; +} + +cram_metrics *cram_new_metrics(void) { + cram_metrics *m = malloc(sizeof(*m)); + if (!m) + return NULL; + m->m1 = m->m2 = 0; + m->trial = 2; + m->next_trial = 100; + return m; +} + +char *cram_block_method2str(enum cram_block_method m) { + switch(m) { + case RAW: return "RAW"; + case GZIP: return "GZIP"; + case BZIP2: return "BZIP2"; + case BM_ERROR: break; + } + return "?"; +} + +char *cram_content_type2str(enum cram_content_type t) { + switch (t) { + case FILE_HEADER: return "FILE_HEADER"; + case COMPRESSION_HEADER: return "COMPRESSION_HEADER"; + case MAPPED_SLICE: return "MAPPED_SLICE"; + case UNMAPPED_SLICE: return "UNMAPPED_SLICE"; + case EXTERNAL: return "EXTERNAL"; + case CORE: return "CORE"; + case CT_ERROR: break; + } + return "?"; +} + +/* + * Extra error checking on fclose to really ensure data is written. + * Care needs to be taken to handle pipes vs real files. + * + * Returns 0 on success + * -1 on failure. + */ +int paranoid_fclose(FILE *fp) { + if (-1 == fflush(fp) && errno != EBADF) { + fclose(fp); + return -1; + } + + errno = 0; + if (-1 == fsync(fileno(fp))) { + if (errno != EINVAL) { // eg pipe + fclose(fp); + return -1; + } + } + return fclose(fp); +} + +/* ---------------------------------------------------------------------- + * Reference sequence handling + * + * These revolve around the refs_t structure, which may potentially be + * shared between multiple cram_fd. + * + * We start with refs_create() to allocate an empty refs_t and then + * populate it with @SQ line data using refs_from_header(). This is done on + * cram_open(). Also at start up we can call cram_load_reference() which + * is used with "scramble -r foo.fa". This replaces the fd->refs with the + * new one specified. In either case refs2id() is then called which + * maps ref_entry names to @SQ ids (refs_t->ref_id[]). + * + * Later, possibly within a thread, we will want to know the actual ref + * seq itself, obtained by calling cram_get_ref(). This may use the + * UR: or M5: fields or the filename specified in the original + * cram_load_reference() call. + * + * Given the potential for multi-threaded reference usage, we have + * reference counting (sorry for the confusing double use of "ref") to + * track the number of callers interested in any specific reference. + */ + +void refs_free(refs_t *r) { + RP("refs_free()\n"); + + if (--r->count > 0) + return; + + if (!r) + return; + + if (r->pool) + string_pool_destroy(r->pool); + + if (r->h_meta) { + khint_t k; + + for (k = kh_begin(r->h_meta); k != kh_end(r->h_meta); k++) { + ref_entry *e; + + if (!kh_exist(r->h_meta, k)) + continue; + if (!(e = kh_val(r->h_meta, k))) + continue; + if (e->seq) + free(e->seq); + free(e); + } + + kh_destroy(refs, r->h_meta); + } + + if (r->ref_id) + free(r->ref_id); + + if (r->fp) + fclose(r->fp); + + pthread_mutex_destroy(&r->lock); + + free(r); +} + +static refs_t *refs_create(void) { + refs_t *r = calloc(1, sizeof(*r)); + + RP("refs_create()\n"); + + if (!r) + return NULL; + + if (!(r->pool = string_pool_create(8192))) + goto err; + + r->ref_id = NULL; // see refs2id() to populate. + r->count = 1; + r->last = NULL; + r->last_id = -1; + + if (!(r->h_meta = kh_init(refs))) + goto err; + + pthread_mutex_init(&r->lock, NULL); + + return r; + + err: + refs_free(r); + return NULL; +} + +/* + * Loads a FAI file for a reference.fasta. + * "is_err" indicates whether failure to load is worthy of emitting an + * error message. In some cases (eg with embedded references) we + * speculatively load, just incase, and silently ignore errors. + * + * Returns the refs_t struct on success (maybe newly allocated); + * NULL on failure + */ +static refs_t *refs_load_fai(refs_t *r_orig, char *fn, int is_err) { + struct stat sb; + FILE *fp = NULL; + char fai_fn[PATH_MAX]; + char line[8192]; + refs_t *r = r_orig; + size_t fn_l = strlen(fn); + + RP("refs_load_fai %s\n", fn); + + if (!r) + if (!(r = refs_create())) + goto err; + + /* Open reference, for later use */ + if (stat(fn, &sb) != 0) { + if (is_err) + perror(fn); + goto err; + } + + if (r->fp) + fclose(r->fp); + r->fp = NULL; + + if (!(r->fn = string_dup(r->pool, fn))) + goto err; + + if (fn_l > 4 && strcmp(&fn[fn_l-4], ".fai") == 0) + r->fn[fn_l-4] = 0; + + if (!(r->fp = fopen(r->fn, "r"))) { + if (is_err) + perror(fn); + goto err; + } + + /* Parse .fai file and load meta-data */ + sprintf(fai_fn, "%.*s.fai", PATH_MAX-5, r->fn); + + if (stat(fai_fn, &sb) != 0) { + if (is_err) + perror(fai_fn); + goto err; + } + if (!(fp = fopen(fai_fn, "r"))) { + if (is_err) + perror(fai_fn); + goto err; + } + while (fgets(line, 8192, fp) != NULL) { + ref_entry *e = malloc(sizeof(*e)); + char *cp; + int n; + khint_t k; + + if (!e) + return NULL; + + // id + for (cp = line; *cp && !isspace(*cp); cp++) + ; + *cp++ = 0; + e->name = string_dup(r->pool, line); + + // length + while (*cp && isspace(*cp)) + cp++; + e->length = strtoll(cp, &cp, 10); + + // offset + while (*cp && isspace(*cp)) + cp++; + e->offset = strtoll(cp, &cp, 10); + + // bases per line + while (*cp && isspace(*cp)) + cp++; + e->bases_per_line = strtol(cp, &cp, 10); + + // line length + while (*cp && isspace(*cp)) + cp++; + e->line_length = strtol(cp, &cp, 10); + + // filename + e->fn = r->fn; + + e->count = 0; + e->seq = NULL; + + k = kh_put(refs, r->h_meta, e->name, &n); + if (-1 == n) { + free(e); + return NULL; + } + + if (n) { + kh_val(r->h_meta, k) = e; + } else { + ref_entry *re = kh_val(r->h_meta, k); + if (re && (re->count != 0 || re->length != 0)) { + /* Keep old */ + free(e); + } else { + /* Replace old */ + if (re) + free(re); + kh_val(r->h_meta, k) = e; + } + } + } + + return r; + + err: + if (fp) + fclose(fp); + + if (!r_orig) + refs_free(r); + + return NULL; +} + +/* + * Indexes references by the order they appear in a BAM file. This may not + * necessarily be the same order they appear in the fasta reference file. + * + * Returns 0 on success + * -1 on failure + */ +int refs2id(refs_t *r, SAM_hdr *h) { + int i; + + if (r->ref_id) + free(r->ref_id); + if (r->last) + r->last = NULL; + + r->ref_id = calloc(h->nref, sizeof(*r->ref_id)); + if (!r->ref_id) + return -1; + + r->nref = h->nref; + for (i = 0; i < h->nref; i++) { + khint_t k = kh_get(refs, r->h_meta, h->ref[i].name); + if (k != kh_end(r->h_meta)) { + r->ref_id[i] = kh_val(r->h_meta, k); + } else { + fprintf(stderr, "Unable to find ref name '%s'\n", + h->ref[i].name); + } + } + + return 0; +} + +/* + * Generates refs_t entries based on @SQ lines in the header. + * Returns 0 on success + * -1 on failure + */ +static int refs_from_header(refs_t *r, cram_fd *fd, SAM_hdr *h) { + int i; + + if (!h || h->nref == 0) + return 0; + + //fprintf(stderr, "refs_from_header for %p mode %c\n", fd, fd->mode); + + /* Existing refs are fine, as long as they're compatible with the hdr. */ + i = r->nref; + if (r->nref < h->nref) + r->nref = h->nref; + + if (!(r->ref_id = realloc(r->ref_id, r->nref * sizeof(*r->ref_id)))) + return -1; + + for (; i < r->nref; i++) + r->ref_id[i] = NULL; + + /* Copy info from h->ref[i] over to r */ + for (i = 0; i < h->nref; i++) { + SAM_hdr_type *ty; + SAM_hdr_tag *tag; + khint_t k; + int n; + + if (r->ref_id[i] && 0 == strcmp(r->ref_id[i]->name, h->ref[i].name)) + continue; + + if (!(r->ref_id[i] = calloc(1, sizeof(ref_entry)))) + return -1; + + if (!h->ref[i].name) + return -1; + + r->ref_id[i]->name = string_dup(r->pool, h->ref[i].name); + r->ref_id[i]->length = 0; // marker for not yet loaded + + /* Initialise likely filename if known */ + if ((ty = sam_hdr_find(h, "SQ", "SN", h->ref[i].name))) { + if ((tag = sam_hdr_find_key(h, ty, "M5", NULL))) { + r->ref_id[i]->fn = string_dup(r->pool, tag->str+3); + //fprintf(stderr, "Tagging @SQ %s / %s\n", r->ref_id[i]->name, r->ref_id[i]->fn); + } + } + + k = kh_put(refs, r->h_meta, r->ref_id[i]->name, &n); + if (n <= 0) // already exists or error + return -1; + kh_val(r->h_meta, k) = r->ref_id[i]; + } + + return 0; +} + +/* + * Attaches a header to a cram_fd. + * + * This should be used when creating a new cram_fd for writing where + * we have an SAM_hdr already constructed (eg from a file we've read + * in). + */ +int cram_set_header(cram_fd *fd, SAM_hdr *hdr) { + fd->header = hdr; + return refs_from_header(fd->refs, fd, hdr); +} + +/* + * Converts a directory and a filename into an expanded path, replacing %s + * in directory with the filename and %[0-9]+s with portions of the filename + * Any remaining parts of filename are added to the end with /%s. + */ +void expand_cache_path(char *path, char *dir, char *fn) { + char *cp; + + while ((cp = strchr(dir, '%'))) { + strncpy(path, dir, cp-dir); + path += cp-dir; + + if (*++cp == 's') { + strcpy(path, fn); + path += strlen(fn); + fn += strlen(fn); + cp++; + } else if (*cp >= '0' && *cp <= '9') { + char *endp; + long l; + + l = strtol(cp, &endp, 10); + l = MIN(l, strlen(fn)); + if (*endp == 's') { + strncpy(path, fn, l); + path += l; + fn += l; + *path = 0; + cp = endp+1; + } else { + *path++ = '%'; + *path++ = *cp++; + } + } else { + *path++ = '%'; + *path++ = *cp++; + } + dir = cp; + } + strcpy(path, dir); + path += strlen(dir); + if (*fn && path[-1] != '/') + *path++ = '/'; + strcpy(path, fn); +} + +/* + * Make the directory containing path and any prefix directories. + */ +void mkdir_prefix(char *path, int mode) { + char *cp = strrchr(path, '/'); + if (!cp) + return; + + *cp = 0; + if (is_directory(path)) { + *cp = '/'; + return; + } + + if (mkdir(path, mode) == 0) { + chmod(path, mode); + *cp = '/'; + return; + } + + mkdir_prefix(path, mode); + mkdir(path, mode); + chmod(path, mode); + *cp = '/'; +} + +/* + * Queries the M5 string from the header and attempts to populate the + * reference from this using the REF_PATH environment. + * + * Returns 0 on sucess + * -1 on failure + */ +static int cram_populate_ref(cram_fd *fd, int id, ref_entry *r) { + char *ref_path = getenv("REF_PATH"); + SAM_hdr_type *ty; + SAM_hdr_tag *tag; + char path[PATH_MAX], path_tmp[PATH_MAX]; + char *local_cache = getenv("REF_CACHE"); + mFILE *mf; + + if (fd->verbose) + fprintf(stderr, "cram_populate_ref on fd %p, id %d\n", fd, id); + + if (!ref_path) + ref_path = "."; + + if (!r->name) + return -1; + + if (!(ty = sam_hdr_find(fd->header, "SQ", "SN", r->name))) + return -1; + + if (!(tag = sam_hdr_find_key(fd->header, ty, "M5", NULL))) + goto no_M5; + + if (fd->verbose) + fprintf(stderr, "Querying ref %s\n", tag->str+3); + + /* Use cache if available */ + if (local_cache && *local_cache) { + struct stat sb; + FILE *fp; + + expand_cache_path(path, local_cache, tag->str+3); + + if (0 == stat(path, &sb) && (fp = fopen(path, "r"))) { + r->length = sb.st_size; + r->offset = r->line_length = r->bases_per_line = 0; + + r->fn = string_dup(fd->refs->pool, path); + + if (fd->refs->fp) + fclose(fd->refs->fp); + fd->refs->fp = fp; + fd->refs->fn = r->fn; + + // Fall back to cram_get_ref() where it'll do the actual + // reading of the file. + return 0; + } + } + + /* Otherwise search */ + if ((mf = open_path_mfile(tag->str+3, ref_path, NULL))) { + size_t sz; + r->seq = mfsteal(mf, &sz); + r->length = sz; + } else { + refs_t *refs; + char *fn; + + no_M5: + /* Failed to find in search path or M5 cache, see if @SQ UR: tag? */ + if (!(tag = sam_hdr_find_key(fd->header, ty, "UR", NULL))) + return -1; + + fn = (strncmp(tag->str+3, "file:", 5) == 0) + ? tag->str+8 + : tag->str+3; + + if (fd->refs->fp) { + fclose(fd->refs->fp); + fd->refs->fp = NULL; + } + if (!(refs = refs_load_fai(fd->refs, fn, 0))) + return -1; + fd->refs = refs; + if (fd->refs->fp) { + fclose(fd->refs->fp); + fd->refs->fp = NULL; + } + + if (!fd->refs->fn) + return -1; + + if (-1 == refs2id(fd->refs, fd->header)) + return -1; + if (!fd->refs->ref_id || !fd->refs->ref_id[id]) + return -1; + + // Local copy already, so fall back to cram_get_ref(). + return 0; + } + + /* Populate the local disk cache if required */ + if (local_cache && *local_cache) { + FILE *fp; + int i; + + expand_cache_path(path, local_cache, tag->str+3); + if (fd->verbose) + fprintf(stderr, "Path='%s'\n", path); + mkdir_prefix(path, 01777); + + i = 0; + do { + sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i); + i++; + fp = fopen(path_tmp, "wx"); + } while (fp == NULL && errno == EEXIST); + if (!fp) { + perror(path_tmp); + + // Not fatal - we have the data already so keep going. + return 0; + } + + if (r->length != fwrite(r->seq, 1, r->length, fp)) { + perror(path); + } + if (-1 == paranoid_fclose(fp)) { + unlink(path_tmp); + } else { + if (0 == chmod(path_tmp, 0444)) + rename(path_tmp, path); + else + unlink(path_tmp); + } + } + + return 0; +} + +static void cram_ref_incr_locked(refs_t *r, int id) { + RP("%d INC REF %d, %d %p\n", gettid(), id, (int)(id>=0?r->ref_id[id]->count+1:-999), id>=0?r->ref_id[id]->seq:(char *)1); + + if (id < 0 || !r->ref_id[id]->seq) + return; + + if (r->last_id == id) + r->last_id = -1; + + ++r->ref_id[id]->count; +} + +void cram_ref_incr(refs_t *r, int id) { + pthread_mutex_lock(&r->lock); + cram_ref_incr_locked(r, id); + pthread_mutex_unlock(&r->lock); +} + +static void cram_ref_decr_locked(refs_t *r, int id) { + RP("%d DEC REF %d, %d %p\n", gettid(), id, (int)(id>=0?r->ref_id[id]->count-1:-999), id>=0?r->ref_id[id]->seq:(char *)1); + + if (id < 0 || !r->ref_id[id]->seq) { + assert(r->ref_id[id]->count >= 0); + return; + } + + if (--r->ref_id[id]->count <= 0) { + assert(r->ref_id[id]->count == 0); + if (r->last_id >= 0) { + if (r->ref_id[r->last_id]->count <= 0 && + r->ref_id[r->last_id]->seq) { + RP("%d FREE REF %d (%p)\n", gettid(), + r->last_id, r->ref_id[r->last_id]->seq); + free(r->ref_id[r->last_id]->seq); + r->ref_id[r->last_id]->seq = NULL; + r->ref_id[r->last_id]->length = 0; + } + r->last_id = -1; + } else { + r->last_id = id; + } + } +} + +void cram_ref_decr(refs_t *r, int id) { + pthread_mutex_lock(&r->lock); + cram_ref_decr_locked(r, id); + pthread_mutex_unlock(&r->lock); +} + +/* + * Used by cram_ref_load and cram_ref_get. The file handle will have + * already been opened, so we can catch it. The ref_entry *e informs us + * of whether this is a multi-line fasta file or a raw MD5 style file. + * Either way we create a single contiguous sequence. + * + * Returns all or part of a reference sequence on success (malloced); + * NULL on failure. + */ +static char *load_ref_portion(FILE *fp, ref_entry *e, int start, int end) { + off_t offset, len; + char *seq; + + if (end < start) + end = start; + + /* + * Compute locations in file. This is trivial for the MD5 files, but + * is still necessary for the fasta variants. + */ + offset = e->line_length + ? e->offset + (start-1)/e->bases_per_line * e->line_length + + (start-1) % e->bases_per_line + : start-1; + + len = (e->line_length + ? e->offset + (end-1)/e->bases_per_line * e->line_length + + (end-1) % e->bases_per_line + : end-1) - offset + 1; + + if (0 != fseeko(fp, offset, SEEK_SET)) { + perror("fseeko() on reference file"); + return NULL; + } + + if (len == 0 || !(seq = malloc(len))) { + return NULL; + } + + if (len != fread(seq, 1, len, fp)) { + perror("fread() on reference file"); + free(seq); + return NULL; + } + + /* Strip white-space if required. */ + if (len != end-start+1) { + int i, j; + char *cp = seq; + char *cp_to; + + for (i = j = 0; i < len; i++) { + if (cp[i] >= '!' && cp[i] <= '~') + cp[j++] = cp[i] & ~0x20; + } + cp_to = cp+j; + + if (cp_to - seq != end-start+1) { + fprintf(stderr, "Malformed reference file?\n"); + free(seq); + return NULL; + } + } else { + int i; + for (i = 0; i < len; i++) { + seq[i] = seq[i] & ~0x20; // uppercase in ASCII + } + } + + return seq; +} + +/* + * Load the entire reference 'id'. + * This also increments the reference count by 1. + * + * Returns ref_entry on success; + * NULL on failure + */ +ref_entry *cram_ref_load(refs_t *r, int id) { + ref_entry *e = r->ref_id[id]; + int start = 1, end = e->length; + char *seq; + + if (e->seq) { + return e; + } + + assert(e->count == 0); + + if (r->last) { +#ifdef REF_DEBUG + int idx = 0; + for (idx = 0; idx < r->nref; idx++) + if (r->last == r->ref_id[idx]) + break; + RP("%d cram_ref_load DECR %d\n", gettid(), idx); +#endif + assert(r->last->count > 0); + if (--r->last->count <= 0) { + RP("%d FREE REF %d (%p)\n", gettid(), id, r->ref_id[id]->seq); + if (r->last->seq) { + free(r->last->seq); + r->last->seq = NULL; + } + } + } + + /* Open file if it's not already the current open reference */ + if (strcmp(r->fn, e->fn) || r->fp == NULL) { + if (r->fp) + fclose(r->fp); + r->fn = e->fn; + if (!(r->fp = fopen(r->fn, "r"))) { + perror(r->fn); + return NULL; + } + } + + RP("%d Loading ref %d (%d..%d)\n", gettid(), id, start, end); + + if (!(seq = load_ref_portion(r->fp, e, start, end))) { + return NULL; + } + + RP("%d Loaded ref %d (%d..%d) = %p\n", gettid(), id, start, end, seq); + + RP("%d INC REF %d, %d\n", gettid(), id, (int)(e->count+1)); + e->seq = seq; + e->count++; + + /* + * Also keep track of last used ref so incr/decr loops on the same + * sequence don't cause load/free loops. + */ + RP("%d cram_ref_load INCR %d => %d\n", gettid(), id, e->count+1); + r->last = e; + e->count++; + + return e; +} + +/* + * Returns a portion of a reference sequence from start to end inclusive. + * The returned pointer is owned by either the cram_file fd or by the + * internal refs_t structure and should not be freed by the caller. + * + * The difference is whether or not this refs_t is in use by just the one + * cram_fd or by multiples, or whether we have multiple threads accessing + * references. In either case fd->shared will be true and we start using + * reference counting to track the number of users of a specific reference + * sequence. + * + * Otherwise the ref seq returned is allocated as part of cram_fd itself + * and will be freed up on the next call to cram_get_ref or cram_close. + * + * To return the entire reference sequence, specify start as 1 and end + * as 0. + * + * To cease using a reference, call cram_ref_decr(). + * + * Returns reference on success, + * NULL on failure + */ +char *cram_get_ref(cram_fd *fd, int id, int start, int end) { + ref_entry *r; + char *seq; + int ostart = start; + + if (id == -1) + return NULL; + + /* FIXME: axiomatic query of r->seq being true? + * Or shortcut for unsorted data where we load once and never free? + */ + + //fd->shared_ref = 1; // hard code for now to simplify things + + pthread_mutex_lock(&fd->ref_lock); + + RP("%d cram_get_ref on fd %p, id %d, range %d..%d\n", gettid(), fd, id, start, end); + + /* + * Unsorted data implies we want to fetch an entire reference at a time. + * We just deal with this at the moment by claiming we're sharing + * references instead, which has the same requirement. + */ + if (fd->unsorted) + fd->shared_ref = 1; + + + /* Sanity checking: does this ID exist? */ + if (id >= fd->refs->nref) { + fprintf(stderr, "No reference found for id %d\n", id); + pthread_mutex_unlock(&fd->ref_lock); + return NULL; + } + + if (!fd->refs || !fd->refs->ref_id[id]) { + fprintf(stderr, "No reference found for id %d\n", id); + pthread_mutex_unlock(&fd->ref_lock); + return NULL; + } + + if (!(r = fd->refs->ref_id[id])) { + fprintf(stderr, "No reference found for id %d\n", id); + pthread_mutex_unlock(&fd->ref_lock); + return NULL; + } + + + /* + * It has an entry, but may not have been populated yet. + * Any manually loaded .fai files have their lengths known. + * A ref entry computed from @SQ lines (M5 or UR field) will have + * r->length == 0 unless it's been loaded once and verified that we have + * an on-disk filename for it. + * + * 19 Sep 2013: Moved the lock here as the cram_populate_ref code calls + * open_path_mfile and libcurl, which isn't multi-thread safe unless I + * rewrite my code to have one curl handle per thread. + */ + pthread_mutex_lock(&fd->refs->lock); + if (r->length == 0) { + if (cram_populate_ref(fd, id, r) == -1) { + fprintf(stderr, "Failed to populate reference for id %d\n", id); + pthread_mutex_unlock(&fd->refs->lock); + pthread_mutex_unlock(&fd->ref_lock); + return NULL; + } + r = fd->refs->ref_id[id]; + } + + + /* + * We now know that we the filename containing the reference, so check + * for limits. If it's over half the reference we'll load all of it in + * memory as this will speed up subsequent calls. + */ + if (end < 1) + end = r->length; + if (end >= r->length) + end = r->length; + assert(start >= 1); + + if (end - start >= 0.5*r->length || fd->shared_ref) { + start = 1; + end = r->length; + } + + /* + * Maybe we have it cached already? If so use it. + * + * Alternatively if we don't have the sequence but we're sharing + * references and/or are asking for the entire length of it, then + * load the full reference into the refs structure and return + * a pointer to that one instead. + */ + if (fd->shared_ref || r->seq || (start == 1 && end == r->length)) { + char *cp; + + if (id >= 0) { + if (r->seq) { + cram_ref_incr_locked(fd->refs, id); + } else { + ref_entry *e; + if (!(e = cram_ref_load(fd->refs, id))) { + pthread_mutex_unlock(&fd->refs->lock); + pthread_mutex_unlock(&fd->ref_lock); + return NULL; + } + + /* unsorted data implies cache ref indefinitely, to avoid + * continually loading and unloading. + */ + if (fd->unsorted) + cram_ref_incr_locked(fd->refs, id); + } + + fd->ref = NULL; /* We never access it directly */ + fd->ref_start = 1; + fd->ref_end = r->length; + fd->ref_id = id; + + cp = fd->refs->ref_id[id]->seq + ostart-1; + } else { + fd->ref = NULL; + cp = NULL; + } + + RP("%d cram_get_ref returning for id %d, count %d\n", gettid(), id, (int)r->count); + + pthread_mutex_unlock(&fd->refs->lock); + pthread_mutex_unlock(&fd->ref_lock); + return cp; + } + + /* + * Otherwise we're not sharing, we don't have a copy of it already and + * we're only asking for a small portion of it. + * + * In this case load up just that segment ourselves, freeing any old + * small segments in the process. + */ + + /* Unmapped ref ID */ + if (id < 0) { + if (fd->ref_free) { + free(fd->ref_free); + fd->ref_free = NULL; + } + fd->ref = NULL; + fd->ref_id = id; + pthread_mutex_unlock(&fd->refs->lock); + pthread_mutex_unlock(&fd->ref_lock); + return NULL; + } + + /* Open file if it's not already the current open reference */ + if (strcmp(fd->refs->fn, r->fn) || fd->refs->fp == NULL) { + if (fd->refs->fp) + fclose(fd->refs->fp); + fd->refs->fn = r->fn; + if (!(fd->refs->fp = fopen(fd->refs->fn, "r"))) { + perror(fd->refs->fn); + pthread_mutex_unlock(&fd->refs->lock); + pthread_mutex_unlock(&fd->ref_lock); + return NULL; + } + } + + if (!(fd->ref = load_ref_portion(fd->refs->fp, r, start, end))) { + pthread_mutex_unlock(&fd->refs->lock); + pthread_mutex_unlock(&fd->ref_lock); + return NULL; + } + + if (fd->ref_free) + free(fd->ref_free); + + fd->ref_id = id; + fd->ref_start = start; + fd->ref_end = end; + fd->ref_free = fd->ref; + seq = fd->ref; + + pthread_mutex_unlock(&fd->refs->lock); + pthread_mutex_unlock(&fd->ref_lock); + + return seq + ostart - start; +} + +/* + * If fd has been opened for reading, it may be permitted to specify 'fn' + * as NULL and let the code auto-detect the reference by parsing the + * SAM header @SQ lines. + */ +int cram_load_reference(cram_fd *fd, char *fn) { + if (fn) { + fd->refs = refs_load_fai(fd->refs, fn, + !(fd->embed_ref && fd->mode == 'r')); + fn = fd->refs ? fd->refs->fn : NULL; + } + fd->ref_fn = fn; + + if ((!fd->refs || (fd->refs->nref == 0 && !fn)) && fd->header) { + if (!(fd->refs = refs_create())) + return -1; + if (-1 == refs_from_header(fd->refs, fd, fd->header)) + return -1; + } + + if (-1 == refs2id(fd->refs, fd->header)) + return -1; + + return fn ? 0 : -1; +} + +/* ---------------------------------------------------------------------- + * Containers + */ + +/* + * Creates a new container, specifying the maximum number of slices + * and records permitted. + * + * Returns cram_container ptr on success + * NULL on failure + */ +cram_container *cram_new_container(int nrec, int nslice) { + cram_container *c = calloc(1, sizeof(*c)); + if (!c) + return NULL; + + c->curr_ref = -2; + + c->max_c_rec = nrec * nslice; + c->curr_c_rec = 0; + + c->max_rec = nrec; + c->record_counter = 0; + c->num_bases = 0; + + c->max_slice = nslice; + c->curr_slice = 0; + + c->pos_sorted = 1; + c->max_apos = 0; + c->multi_seq = 0; + + c->bams = NULL; + + if (!(c->slices = (cram_slice **)calloc(nslice, sizeof(cram_slice *)))) + goto err; + c->slice = NULL; + + if (!(c->comp_hdr = cram_new_compression_header())) + goto err; + c->comp_hdr_block = NULL; + + if (!(c->BF_stats = cram_stats_create())) goto err; + if (!(c->CF_stats = cram_stats_create())) goto err; + if (!(c->RN_stats = cram_stats_create())) goto err; + if (!(c->AP_stats = cram_stats_create())) goto err; + if (!(c->RG_stats = cram_stats_create())) goto err; + if (!(c->MQ_stats = cram_stats_create())) goto err; + if (!(c->NS_stats = cram_stats_create())) goto err; + if (!(c->NP_stats = cram_stats_create())) goto err; + if (!(c->TS_stats = cram_stats_create())) goto err; + if (!(c->MF_stats = cram_stats_create())) goto err; + if (!(c->NF_stats = cram_stats_create())) goto err; + if (!(c->RL_stats = cram_stats_create())) goto err; + if (!(c->FN_stats = cram_stats_create())) goto err; + if (!(c->FC_stats = cram_stats_create())) goto err; + if (!(c->FP_stats = cram_stats_create())) goto err; + if (!(c->DL_stats = cram_stats_create())) goto err; + if (!(c->BA_stats = cram_stats_create())) goto err; + if (!(c->QS_stats = cram_stats_create())) goto err; + if (!(c->BS_stats = cram_stats_create())) goto err; + if (!(c->TC_stats = cram_stats_create())) goto err; + if (!(c->TN_stats = cram_stats_create())) goto err; + if (!(c->TL_stats = cram_stats_create())) goto err; + if (!(c->RI_stats = cram_stats_create())) goto err; + if (!(c->RS_stats = cram_stats_create())) goto err; + if (!(c->PD_stats = cram_stats_create())) goto err; + if (!(c->HC_stats = cram_stats_create())) goto err; + + //c->aux_B_stats = cram_stats_create(); + + if (!(c->tags_used = kh_init(s_i2i))) + goto err; + c->refs_used = 0; + + return c; + + err: + if (c) { + if (c->slices) + free(c->slices); + free(c); + } + return NULL; +} + +void cram_free_container(cram_container *c) { + int i; + + if (!c) + return; + + if (c->refs_used) + free(c->refs_used); + + if (c->landmark) + free(c->landmark); + + if (c->comp_hdr) + cram_free_compression_header(c->comp_hdr); + + if (c->comp_hdr_block) + cram_free_block(c->comp_hdr_block); + + if (c->slices) { + for (i = 0; i < c->max_slice; i++) + if (c->slices[i]) + cram_free_slice(c->slices[i]); + free(c->slices); + } + + if (c->TS_stats) cram_stats_free(c->TS_stats); + if (c->RG_stats) cram_stats_free(c->RG_stats); + if (c->FP_stats) cram_stats_free(c->FP_stats); + if (c->NS_stats) cram_stats_free(c->NS_stats); + if (c->RN_stats) cram_stats_free(c->RN_stats); + if (c->CF_stats) cram_stats_free(c->CF_stats); + if (c->TN_stats) cram_stats_free(c->TN_stats); + if (c->BA_stats) cram_stats_free(c->BA_stats); + if (c->TV_stats) cram_stats_free(c->TV_stats); + if (c->BS_stats) cram_stats_free(c->BS_stats); + if (c->FC_stats) cram_stats_free(c->FC_stats); + if (c->BF_stats) cram_stats_free(c->BF_stats); + if (c->AP_stats) cram_stats_free(c->AP_stats); + if (c->NF_stats) cram_stats_free(c->NF_stats); + if (c->MF_stats) cram_stats_free(c->MF_stats); + if (c->FN_stats) cram_stats_free(c->FN_stats); + if (c->RL_stats) cram_stats_free(c->RL_stats); + if (c->DL_stats) cram_stats_free(c->DL_stats); + if (c->TC_stats) cram_stats_free(c->TC_stats); + if (c->TL_stats) cram_stats_free(c->TL_stats); + if (c->MQ_stats) cram_stats_free(c->MQ_stats); + if (c->TM_stats) cram_stats_free(c->TM_stats); + if (c->QS_stats) cram_stats_free(c->QS_stats); + if (c->NP_stats) cram_stats_free(c->NP_stats); + if (c->RI_stats) cram_stats_free(c->RI_stats); + if (c->RS_stats) cram_stats_free(c->RS_stats); + if (c->PD_stats) cram_stats_free(c->PD_stats); + if (c->HC_stats) cram_stats_free(c->HC_stats); + + //if (c->aux_B_stats) cram_stats_free(c->aux_B_stats); + + if (c->tags_used) kh_destroy(s_i2i, c->tags_used); + + free(c); +} + +/* + * Reads a container header. + * + * Returns cram_container on success + * NULL on failure or no container left (fd->err == 0). + */ +cram_container *cram_read_container(cram_fd *fd) { + cram_container c2, *c; + int i, s; + size_t rd = 0; + + fd->err = 0; + + memset(&c2, 0, sizeof(c2)); + if (fd->version == CRAM_1_VERS) { + if ((s = itf8_decode(fd, &c2.length)) == -1) { + fd->eof = fd->empty_container ? 1 : 2; + return NULL; + } else { + rd+=s; + } + } else { + if ((s = int32_decode(fd, &c2.length)) == -1) { + fd->eof = fd->empty_container ? 1 : 2; + return NULL; + } else { + rd+=s; + } + } + if ((s = itf8_decode(fd, &c2.ref_seq_id)) == -1) return NULL; else rd+=s; + if ((s = itf8_decode(fd, &c2.ref_seq_start))== -1) return NULL; else rd+=s; + if ((s = itf8_decode(fd, &c2.ref_seq_span)) == -1) return NULL; else rd+=s; + if ((s = itf8_decode(fd, &c2.num_records)) == -1) return NULL; else rd+=s; + + if (fd->version == CRAM_1_VERS) { + c2.record_counter = 0; + c2.num_bases = 0; + } else { + if ((s = itf8_decode(fd, &c2.record_counter)) == -1) + return NULL; + else + rd += s; + + if ((s = ltf8_decode(fd, &c2.num_bases))== -1) + return NULL; + else + rd += s; + } + if ((s = itf8_decode(fd, &c2.num_blocks)) == -1) return NULL; else rd+=s; + if ((s = itf8_decode(fd, &c2.num_landmarks))== -1) return NULL; else rd+=s; + + if (!(c = calloc(1, sizeof(*c)))) + return NULL; + + *c = c2; + + if (!(c->landmark = malloc(c->num_landmarks * sizeof(int32_t))) && + c->num_landmarks) { + fd->err = errno; + cram_free_container(c); + return NULL; + } + for (i = 0; i < c->num_landmarks; i++) { + if ((s = itf8_decode(fd, &c->landmark[i])) == -1) { + cram_free_container(c); + return NULL; + } else { + rd += s; + } + } + c->offset = rd; + + c->slices = NULL; + c->curr_slice = 0; + c->max_slice = c->num_landmarks; + c->slice_rec = 0; + c->curr_rec = 0; + c->max_rec = 0; + + if (c->ref_seq_id == -2) { + c->multi_seq = 1; + fd->multi_seq = 1; + } + + fd->empty_container = + (c->num_records == 0 && + c->ref_seq_id == -1 && + c->ref_seq_start == 0x454f46 /* EOF */) ? 1 : 0; + + return c; +} + +/* + * Writes a container structure. + * + * Returns 0 on success + * -1 on failure + */ +int cram_write_container(cram_fd *fd, cram_container *c) { + char buf_a[1024], *buf = buf_a, *cp; + int i; + + if (50 + c->num_landmarks * 5 >= 1024) + buf = malloc(50 + c->num_landmarks * 5); + cp = buf; + + if (fd->version == CRAM_1_VERS) { + cp += itf8_put(cp, c->length); + } else { + *(int32_t *)cp = le_int4(c->length); + cp += 4; + } + if (c->multi_seq) { + cp += itf8_put(cp, -2); + cp += itf8_put(cp, 0); + cp += itf8_put(cp, 0); + } else { + cp += itf8_put(cp, c->ref_seq_id); + cp += itf8_put(cp, c->ref_seq_start); + cp += itf8_put(cp, c->ref_seq_span); + } + cp += itf8_put(cp, c->num_records); + if (fd->version != CRAM_1_VERS) { + cp += itf8_put(cp, c->record_counter); + cp += ltf8_put(cp, c->num_bases); + } + cp += itf8_put(cp, c->num_blocks); + cp += itf8_put(cp, c->num_landmarks); + for (i = 0; i < c->num_landmarks; i++) + cp += itf8_put(cp, c->landmark[i]); + if (cp-buf != hwrite(fd->fp, buf, cp-buf)) { + if (buf != buf_a) + free(buf); + return -1; + } + + if (buf != buf_a) + free(buf); + + return 0; +} + +// common component shared by cram_flush_container{,_mt} +static int cram_flush_container2(cram_fd *fd, cram_container *c) { + int i, j; + + //fprintf(stderr, "Writing container %d, sum %u\n", c->record_counter, sum); + + /* Write the container struct itself */ + if (0 != cram_write_container(fd, c)) + return -1; + + /* And the compression header */ + if (0 != cram_write_block(fd, c->comp_hdr_block)) + return -1; + + /* Followed by the slice blocks */ + for (i = 0; i < c->curr_slice; i++) { + cram_slice *s = c->slices[i]; + + if (0 != cram_write_block(fd, s->hdr_block)) + return -1; + + for (j = 0; j < s->hdr->num_blocks; j++) { + if (0 != cram_write_block(fd, s->block[j])) + return -1; + } + } + + return hflush(fd->fp) == 0 ? 0 : -1; +} + +/* + * Flushes a completely or partially full container to disk, writing + * container structure, header and blocks. This also calls the encoder + * functions. + * + * Returns 0 on success + * -1 on failure + */ +int cram_flush_container(cram_fd *fd, cram_container *c) { + /* Encode the container blocks and generate compression header */ + if (0 != cram_encode_container(fd, c)) + return -1; + + return cram_flush_container2(fd, c); +} + +typedef struct { + cram_fd *fd; + cram_container *c; +} cram_job; + +void *cram_flush_thread(void *arg) { + cram_job *j = (cram_job *)arg; + + /* Encode the container blocks and generate compression header */ + if (0 != cram_encode_container(j->fd, j->c)) { + fprintf(stderr, "cram_encode_container failed\n"); + return NULL; + } + + return arg; +} + +static int cram_flush_result(cram_fd *fd) { + int i, ret = 0; + t_pool_result *r; + + while ((r = t_pool_next_result(fd->rqueue))) { + cram_job *j = (cram_job *)r->data; + cram_container *c; + + if (!j) { + t_pool_delete_result(r, 0); + return -1; + } + + fd = j->fd; + c = j->c; + + if (0 != cram_flush_container2(fd, c)) + return -1; + + /* Free the container */ + for (i = 0; i < c->max_slice; i++) { + cram_free_slice(c->slices[i]); + c->slices[i] = NULL; + } + + c->slice = NULL; + c->curr_slice = 0; + + cram_free_container(c); + + ret |= hflush(fd->fp) == 0 ? 0 : -1; + + t_pool_delete_result(r, 1); + } + + return ret; +} + +int cram_flush_container_mt(cram_fd *fd, cram_container *c) { + cram_job *j; + + if (!fd->pool) + return cram_flush_container(fd, c); + + if (!(j = malloc(sizeof(*j)))) + return -1; + j->fd = fd; + j->c = c; + + t_pool_dispatch(fd->pool, fd->rqueue, cram_flush_thread, j); + + return cram_flush_result(fd); +} + +/* ---------------------------------------------------------------------- + * Compression headers; the first part of the container + */ + +/* + * Creates a new blank container compression header + * + * Returns header ptr on success + * NULL on failure + */ +cram_block_compression_hdr *cram_new_compression_header(void) { + cram_block_compression_hdr *hdr = calloc(1, sizeof(*hdr)); + if (!hdr) + return NULL; + + if (!(hdr->TD_blk = cram_new_block(CORE, 0))) { + free(hdr); + return NULL; + } + + if (!(hdr->TD_hash = kh_init(m_s2i))) { + cram_free_block(hdr->TD_blk); + free(hdr); + return NULL; + } + + if (!(hdr->TD_keys = string_pool_create(8192))) { + kh_destroy(m_s2i, hdr->TD_hash); + cram_free_block(hdr->TD_blk); + free(hdr); + return NULL; + } + + return hdr; +} + +void cram_free_compression_header(cram_block_compression_hdr *hdr) { + int i; + + if (hdr->landmark) + free(hdr->landmark); + + if (hdr->preservation_map) + kh_destroy(map, hdr->preservation_map); + + for (i = 0; i < CRAM_MAP_HASH; i++) { + cram_map *m, *m2; + for (m = hdr->rec_encoding_map[i]; m; m = m2) { + m2 = m->next; + if (m->codec) + m->codec->free(m->codec); + free(m); + } + } + + for (i = 0; i < CRAM_MAP_HASH; i++) { + cram_map *m, *m2; + for (m = hdr->tag_encoding_map[i]; m; m = m2) { + m2 = m->next; + if (m->codec) + m->codec->free(m->codec); + free(m); + } + } + + if (hdr->BF_codec) hdr->BF_codec->free(hdr->BF_codec); + if (hdr->CF_codec) hdr->CF_codec->free(hdr->CF_codec); + if (hdr->RL_codec) hdr->RL_codec->free(hdr->RL_codec); + if (hdr->AP_codec) hdr->AP_codec->free(hdr->AP_codec); + if (hdr->RG_codec) hdr->RG_codec->free(hdr->RG_codec); + if (hdr->MF_codec) hdr->MF_codec->free(hdr->MF_codec); + if (hdr->NS_codec) hdr->NS_codec->free(hdr->NS_codec); + if (hdr->NP_codec) hdr->NP_codec->free(hdr->NP_codec); + if (hdr->TS_codec) hdr->TS_codec->free(hdr->TS_codec); + if (hdr->NF_codec) hdr->NF_codec->free(hdr->NF_codec); + if (hdr->TC_codec) hdr->TC_codec->free(hdr->TC_codec); + if (hdr->TN_codec) hdr->TN_codec->free(hdr->TN_codec); + if (hdr->TL_codec) hdr->TL_codec->free(hdr->TL_codec); + if (hdr->FN_codec) hdr->FN_codec->free(hdr->FN_codec); + if (hdr->FC_codec) hdr->FC_codec->free(hdr->FC_codec); + if (hdr->FP_codec) hdr->FP_codec->free(hdr->FP_codec); + if (hdr->BS_codec) hdr->BS_codec->free(hdr->BS_codec); + if (hdr->IN_codec) hdr->IN_codec->free(hdr->IN_codec); + if (hdr->SC_codec) hdr->SC_codec->free(hdr->SC_codec); + if (hdr->DL_codec) hdr->DL_codec->free(hdr->DL_codec); + if (hdr->BA_codec) hdr->BA_codec->free(hdr->BA_codec); + if (hdr->MQ_codec) hdr->MQ_codec->free(hdr->MQ_codec); + if (hdr->RN_codec) hdr->RN_codec->free(hdr->RN_codec); + if (hdr->QS_codec) hdr->QS_codec->free(hdr->QS_codec); + if (hdr->Qs_codec) hdr->Qs_codec->free(hdr->Qs_codec); + if (hdr->RI_codec) hdr->RI_codec->free(hdr->RI_codec); + if (hdr->RS_codec) hdr->RS_codec->free(hdr->RS_codec); + if (hdr->PD_codec) hdr->PD_codec->free(hdr->PD_codec); + if (hdr->HC_codec) hdr->HC_codec->free(hdr->HC_codec); + + if (hdr->TL) + free(hdr->TL); + if (hdr->TD_blk) + cram_free_block(hdr->TD_blk); + if (hdr->TD_hash) + kh_destroy(m_s2i, hdr->TD_hash); + if (hdr->TD_keys) + string_pool_destroy(hdr->TD_keys); + + free(hdr); +} + + +/* ---------------------------------------------------------------------- + * Slices and slice headers + */ + +void cram_free_slice_header(cram_block_slice_hdr *hdr) { + if (!hdr) + return; + + if (hdr->block_content_ids) + free(hdr->block_content_ids); + + free(hdr); + + return; +} + +void cram_free_slice(cram_slice *s) { + if (!s) + return; + + if (s->hdr_block) + cram_free_block(s->hdr_block); + + if (s->block) { + int i; + + if (s->hdr) { + for (i = 0; i < s->hdr->num_blocks; i++) { + cram_free_block(s->block[i]); + } + } + free(s->block); + } + + if (s->block_by_id) + free(s->block_by_id); + + if (s->hdr) + cram_free_slice_header(s->hdr); + + if (s->seqs_blk) + cram_free_block(s->seqs_blk); + + if (s->qual_blk) + cram_free_block(s->qual_blk); + + if (s->name_blk) + cram_free_block(s->name_blk); + + if (s->aux_blk) + cram_free_block(s->aux_blk); + + if (s->base_blk) + cram_free_block(s->base_blk); + + if (s->soft_blk) + cram_free_block(s->soft_blk); + +#ifdef TN_external + if (s->tn_blk) + cram_free_block(s->tn_blk); +#endif + + if (s->cigar) + free(s->cigar); + + if (s->crecs) + free(s->crecs); + + if (s->features) + free(s->features); + +#ifndef TN_external + if (s->TN) + free(s->TN); +#endif + + if (s->pair_keys) + string_pool_destroy(s->pair_keys); + + if (s->pair) + kh_destroy(m_s2i, s->pair); + + free(s); +} + +/* + * Creates a new empty slice in memory, for subsequent writing to + * disk. + * + * Returns cram_slice ptr on success + * NULL on failure + */ +cram_slice *cram_new_slice(enum cram_content_type type, int nrecs) { + cram_slice *s = calloc(1, sizeof(*s)); + if (!s) + return NULL; + + if (!(s->hdr = (cram_block_slice_hdr *)calloc(1, sizeof(*s->hdr)))) + goto err; + s->hdr->content_type = type; + + s->hdr_block = NULL; + s->block = NULL; + s->block_by_id = NULL; + s->last_apos = 0; + s->id = 0; + if (!(s->crecs = malloc(nrecs * sizeof(cram_record)))) goto err; + s->cigar = NULL; + s->cigar_alloc = 0; + s->ncigar = 0; + + if (!(s->seqs_blk = cram_new_block(EXTERNAL, 0))) goto err; + if (!(s->qual_blk = cram_new_block(EXTERNAL, CRAM_EXT_QUAL))) goto err; + if (!(s->name_blk = cram_new_block(EXTERNAL, CRAM_EXT_NAME))) goto err; + if (!(s->aux_blk = cram_new_block(EXTERNAL, CRAM_EXT_TAG))) goto err; + if (!(s->base_blk = cram_new_block(EXTERNAL, CRAM_EXT_IN))) goto err; + if (!(s->soft_blk = cram_new_block(EXTERNAL, CRAM_EXT_SC))) goto err; +#ifdef TN_external + if (!(s->tn_blk = cram_new_block(EXTERNAL, CRAM_EXT_TN))) goto err; +#endif + + s->features = NULL; + s->nfeatures = s->afeatures = 0; + +#ifndef TN_external + s->TN = NULL; + s->nTN = s->aTN = 0; +#endif + + // Volatile keys as we do realloc in dstring + if (!(s->pair_keys = string_pool_create(8192))) goto err; + if (!(s->pair = kh_init(m_s2i))) goto err; + +#ifdef BA_external + s->BA_len = 0; +#endif + + return s; + + err: + if (s) + cram_free_slice(s); + + return NULL; +} + +/* + * Loads an entire slice. + * FIXME: In 1.0 the native unit of slices within CRAM is broken + * as slices contain references to objects in other slices. + * To work around this while keeping the slice oriented outer loop + * we read all slices and stitch them together into a fake large + * slice instead. + * + * Returns cram_slice ptr on success + * NULL on failure + */ +cram_slice *cram_read_slice(cram_fd *fd) { + cram_block *b = cram_read_block(fd); + cram_slice *s = calloc(1, sizeof(*s)); + int i, n, max_id, min_id; + + if (!b || !s) + goto err; + + s->hdr_block = b; + switch (b->content_type) { + case MAPPED_SLICE: + case UNMAPPED_SLICE: + if (!(s->hdr = cram_decode_slice_header(fd, b))) + goto err; + break; + + default: + fprintf(stderr, "Unexpected block of type %s\n", + cram_content_type2str(b->content_type)); + goto err; + } + + s->block = calloc(n = s->hdr->num_blocks, sizeof(*s->block)); + if (!s->block) + goto err; + + for (max_id = i = 0, min_id = INT_MAX; i < n; i++) { + if (!(s->block[i] = cram_read_block(fd))) + goto err; + + if (s->block[i]->content_type == EXTERNAL) { + if (max_id < s->block[i]->content_id) + max_id = s->block[i]->content_id; + if (min_id > s->block[i]->content_id) + min_id = s->block[i]->content_id; + } + } + if (min_id >= 0 && max_id < 1024) { + if (!(s->block_by_id = calloc(1024, sizeof(s->block[0])))) + goto err; + + for (i = 0; i < n; i++) { + if (s->block[i]->content_type != EXTERNAL) + continue; + s->block_by_id[s->block[i]->content_id] = s->block[i]; + } + } + + /* Initialise encoding/decoding tables */ + s->cigar = NULL; + s->cigar_alloc = 0; + s->ncigar = 0; + + if (!(s->seqs_blk = cram_new_block(EXTERNAL, 0))) goto err; + if (!(s->qual_blk = cram_new_block(EXTERNAL, CRAM_EXT_QUAL))) goto err; + if (!(s->name_blk = cram_new_block(EXTERNAL, CRAM_EXT_NAME))) goto err; + if (!(s->aux_blk = cram_new_block(EXTERNAL, CRAM_EXT_TAG))) goto err; + if (!(s->base_blk = cram_new_block(EXTERNAL, CRAM_EXT_IN))) goto err; + if (!(s->soft_blk = cram_new_block(EXTERNAL, CRAM_EXT_SC))) goto err; +#ifdef TN_external + if (!(s->tn_blk = cram_new_block(EXTERNAL, CRAM_EXT_TN))) goto err; +#endif + + + s->crecs = NULL; + + s->last_apos = s->hdr->ref_seq_start; + + s->id = fd->slice_num++; + + return s; + + err: + if (b) + cram_free_block(b); + if (s) { + s->hdr_block = NULL; + cram_free_slice(s); + } + return NULL; +} + + +/* ---------------------------------------------------------------------- + * CRAM file definition (header) + */ + +/* + * Reads a CRAM file definition structure. + * Returns file_def ptr on success + * NULL on failure + */ +cram_file_def *cram_read_file_def(cram_fd *fd) { + cram_file_def *def = malloc(sizeof(*def)); + if (!def) + return NULL; + + if (26 != hread(fd->fp, &def->magic[0], 26)) { + free(def); + return NULL; + } + + if (memcmp(def->magic, "CRAM", 4) != 0) { + free(def); + return NULL; + } + + if (def->major_version > 2) { + fprintf(stderr, "CRAM version number mismatch\n" + "Expected 1.x or 2.x, got %d.%d\n", + def->major_version, def->minor_version); + free(def); + return NULL; + } + + fd->first_container += 26; + fd->last_slice = 0; + + return def; +} + +/* + * Writes a cram_file_def structure to cram_fd. + * Returns 0 on success + * -1 on failure + */ +int cram_write_file_def(cram_fd *fd, cram_file_def *def) { + return (hwrite(fd->fp, &def->magic[0], 26) == 26) ? 0 : -1; +} + +void cram_free_file_def(cram_file_def *def) { + if (def) free(def); +} + +/* ---------------------------------------------------------------------- + * SAM header I/O + */ + + +/* + * Reads the SAM header from the first CRAM data block. + * Also performs minimal parsing to extract read-group + * and sample information. + + * Returns SAM hdr ptr on success + * NULL on failure + */ +SAM_hdr *cram_read_SAM_hdr(cram_fd *fd) { + int32_t header_len; + char *header; + SAM_hdr *hdr; + + /* 1.1 onwards stores the header in the first block of a container */ + if (fd->version == CRAM_1_VERS) { + /* Length */ + if (-1 == int32_decode(fd, &header_len)) + return NULL; + + /* Alloc and read */ + if (NULL == (header = malloc(header_len+1))) + return NULL; + + *header = 0; + if (header_len != hread(fd->fp, header, header_len)) + return NULL; + + fd->first_container += 4 + header_len; + } else { + cram_container *c = cram_read_container(fd); + cram_block *b; + int i, len; + + if (!c) + return NULL; + + if (c->num_blocks < 1) { + cram_free_container(c); + return NULL; + } + + if (!(b = cram_read_block(fd))) { + cram_free_container(c); + return NULL; + } + + len = b->comp_size + 2 + + itf8_size(b->content_id) + + itf8_size(b->uncomp_size) + + itf8_size(b->comp_size); + + /* Extract header from 1st block */ + if (-1 == int32_get(b, &header_len) || + b->uncomp_size - 4 < header_len) { + cram_free_container(c); + cram_free_block(b); + return NULL; + } + if (NULL == (header = malloc(header_len))) { + cram_free_container(c); + cram_free_block(b); + return NULL; + } + memcpy(header, BLOCK_END(b), header_len); + cram_free_block(b); + + /* Consume any remaining blocks */ + for (i = 1; i < c->num_blocks; i++) { + if (!(b = cram_read_block(fd))) { + cram_free_container(c); + return NULL; + } + len += b->comp_size + 2 + + itf8_size(b->content_id) + + itf8_size(b->uncomp_size) + + itf8_size(b->comp_size); + cram_free_block(b); + } + + if (c->length && c->length > len) { + // Consume padding + char *pads = malloc(c->length - len); + if (!pads) { + cram_free_container(c); + return NULL; + } + + if (c->length - len != hread(fd->fp, pads, c->length - len)) { + cram_free_container(c); + return NULL; + } + free(pads); + } + + cram_free_container(c); + } + + /* Parse */ +#ifdef SAMTOOLS + hdr = sam_hdr_parse_(header, header_len); +#else + hdr = sam_hdr_parse(header, header_len); +#endif + free(header); + + return hdr; +} + +/* + * Converts 'in' to a full pathname to store in out. + * Out must be at least PATH_MAX bytes long. + */ +static void full_path(char *out, char *in) { + if (*in == '/') { + strncpy(out, in, PATH_MAX); + out[PATH_MAX-1] = 0; + } else { + int len; + + // unable to get dir or out+in is too long + if (!getcwd(out, PATH_MAX) || + (len = strlen(out))+1+strlen(in) >= PATH_MAX) { + strncpy(out, in, PATH_MAX); + out[PATH_MAX-1] = 0; + return; + } + + sprintf(out+len, "/%.*s", PATH_MAX - len, in); + + // FIXME: cope with `pwd`/../../../foo.fa ? + } +} + +/* + * Writes a CRAM SAM header. + * Returns 0 on success + * -1 on failure + */ +//#define BLANK_BLOCK +//#define PADDED_CONTAINER +#define PADDED_BLOCK +int cram_write_SAM_hdr(cram_fd *fd, SAM_hdr *hdr) { + int header_len; + + /* 1.0 requires and UNKNOWN read-group */ + if (fd->version == CRAM_1_VERS) { + if (!sam_hdr_find_rg(hdr, "UNKNOWN")) + if (sam_hdr_add(hdr, "RG", + "ID", "UNKNOWN", "SM", "UNKNOWN", NULL)) + return -1; + } + + /* Fix M5 strings */ + if (fd->refs && !fd->no_ref) { + int i; + for (i = 0; i < hdr->nref; i++) { + SAM_hdr_type *ty; + char *ref; + + if (!(ty = sam_hdr_find(hdr, "SQ", "SN", hdr->ref[i].name))) + return -1; + + if (!sam_hdr_find_key(hdr, ty, "M5", NULL)) { + char unsigned buf[16], buf2[33]; + int j, rlen; + MD5_CTX md5; + + if (!fd->refs || + !fd->refs->ref_id || + !fd->refs->ref_id[i]) { + return -1; + } + rlen = fd->refs->ref_id[i]->length; + MD5_Init(&md5); + ref = cram_get_ref(fd, i, 1, rlen); + if (NULL == ref) return -1; + rlen = fd->refs->ref_id[i]->length; /* In case it just loaded */ + MD5_Update(&md5, ref, rlen); + MD5_Final(buf, &md5); + cram_ref_decr(fd->refs, i); + + for (j = 0; j < 16; j++) { + buf2[j*2+0] = "0123456789abcdef"[buf[j]>>4]; + buf2[j*2+1] = "0123456789abcdef"[buf[j]&15]; + } + buf2[32] = 0; + if (sam_hdr_update(hdr, ty, "M5", buf2, NULL)) + return -1; + } + + if (fd->ref_fn) { + char ref_fn[PATH_MAX]; + full_path(ref_fn, fd->ref_fn); + if (sam_hdr_update(hdr, ty, "UR", ref_fn, NULL)) + return -1; + } + } + } + + if (sam_hdr_rebuild(hdr)) + return -1; + + /* Length */ + header_len = sam_hdr_length(hdr); + if (fd->version == CRAM_1_VERS) { + if (-1 == int32_encode(fd, header_len)) + return -1; + + /* Text data */ + if (header_len != hwrite(fd->fp, sam_hdr_str(hdr), header_len)) + return -1; + } else { + /* Create a block inside a container */ + cram_block *b = cram_new_block(FILE_HEADER, 0); + cram_container *c = cram_new_container(0, 0); + int padded_length; + char *pads; + + if (!b || !c) { + if (b) cram_free_block(b); + if (c) cram_free_container(c); + return -1; + } + + int32_put(b, header_len); + BLOCK_APPEND(b, sam_hdr_str(hdr), header_len); + BLOCK_UPLEN(b); + +#ifndef BLANK_BLOCK + c->num_blocks = 1; + c->num_landmarks = 1; + if (!(c->landmark = malloc(sizeof(*c->landmark)))) { + cram_free_block(b); + cram_free_container(c); + return -1; + } + c->landmark[0] = 0; + + c->length = b->uncomp_size + 2 + + itf8_size(b->content_id) + + itf8_size(b->uncomp_size) + + itf8_size(b->comp_size); +#else + c->length = b->uncomp_size + 2 + + itf8_size(b->content_id) + + itf8_size(b->uncomp_size) + + itf8_size(b->comp_size); + + c->num_blocks = 2; + c->num_landmarks = 2; + if (!(c->landmark = malloc(2*sizeof(*c->landmark)))) + return -1; + c->landmark[0] = 0; + c->landmark[1] = c->length; + + c->length *= 2; +#endif + +#ifdef PADDED_BLOCK + padded_length = MAX(c->length*1.5, 10000) - c->length; + c->length += padded_length; + if (NULL == (pads = calloc(1, padded_length))) { + cram_free_block(b); + cram_free_container(c); + return -1; + } + BLOCK_APPEND(b, pads, padded_length); + BLOCK_UPLEN(b); + free(pads); +#endif + +#ifdef PADDED_CONTAINER + padded_length = MAX(c->length*2, 10000) - c->length; + c->length += padded_length; +#endif + + if (-1 == cram_write_container(fd, c)) { + cram_free_block(b); + cram_free_container(c); + return -1; + } + + // Keep it uncompressed + if (-1 == cram_write_block(fd, b)) { + cram_free_block(b); + cram_free_container(c); + return -1; + } + +#ifdef BLANK_BLOCK + if (-1 == cram_write_block(fd, b)) { + cram_free_block(b); + cram_free_container(c); + return -1; + } +#endif + + cram_free_block(b); + cram_free_container(c); + +#ifdef PADDED_CONTAINER + // Write out padding to allow for in-line SAM header editing + if (NULL == (pads = calloc(1, padded_length))) + return -1; + if (padded_length != hwrite(fd->fp, pads, padded_length)) + return -1; + free(pads); +#endif + } + + if (-1 == refs_from_header(fd->refs, fd, fd->header)) + return -1; + if (-1 == refs2id(fd->refs, fd->header)) + return -1; + + if (0 != hflush(fd->fp)) + return -1; + + RP("=== Finishing saving header ===\n"); + + return 0; +} + +/* ---------------------------------------------------------------------- + * The top-level cram opening, closing and option handling + */ + +/* + * Initialises the lookup tables. These could be global statics, but they're + * clumsy to setup in a multi-threaded environment unless we generate + * verbatim code and include that. + */ +static void cram_init_tables(cram_fd *fd) { + int i; + + memset(fd->L1, 4, 256); + fd->L1['A'] = 0; fd->L1['a'] = 0; + fd->L1['C'] = 1; fd->L1['c'] = 1; + fd->L1['G'] = 2; fd->L1['g'] = 2; + fd->L1['T'] = 3; fd->L1['t'] = 3; + + memset(fd->L2, 5, 256); + fd->L2['A'] = 0; fd->L2['a'] = 0; + fd->L2['C'] = 1; fd->L2['c'] = 1; + fd->L2['G'] = 2; fd->L2['g'] = 2; + fd->L2['T'] = 3; fd->L2['t'] = 3; + fd->L2['N'] = 4; fd->L2['n'] = 4; + + if (fd->version == CRAM_1_VERS) { + for (i = 0; i < 0x200; i++) { + int f = 0; + + if (i & CRAM_FPAIRED) f |= BAM_FPAIRED; + if (i & CRAM_FPROPER_PAIR) f |= BAM_FPROPER_PAIR; + if (i & CRAM_FUNMAP) f |= BAM_FUNMAP; + if (i & CRAM_FREVERSE) f |= BAM_FREVERSE; + if (i & CRAM_FREAD1) f |= BAM_FREAD1; + if (i & CRAM_FREAD2) f |= BAM_FREAD2; + if (i & CRAM_FSECONDARY) f |= BAM_FSECONDARY; + if (i & CRAM_FQCFAIL) f |= BAM_FQCFAIL; + if (i & CRAM_FDUP) f |= BAM_FDUP; + + fd->bam_flag_swap[i] = f; + } + + for (i = 0; i < 0x1000; i++) { + int g = 0; + + if (i & BAM_FPAIRED) g |= CRAM_FPAIRED; + if (i & BAM_FPROPER_PAIR) g |= CRAM_FPROPER_PAIR; + if (i & BAM_FUNMAP) g |= CRAM_FUNMAP; + if (i & BAM_FREVERSE) g |= CRAM_FREVERSE; + if (i & BAM_FREAD1) g |= CRAM_FREAD1; + if (i & BAM_FREAD2) g |= CRAM_FREAD2; + if (i & BAM_FSECONDARY) g |= CRAM_FSECONDARY; + if (i & BAM_FQCFAIL) g |= CRAM_FQCFAIL; + if (i & BAM_FDUP) g |= CRAM_FDUP; + + fd->cram_flag_swap[i] = g; + } + } else { + /* NOP */ + for (i = 0; i < 0x1000; i++) + fd->bam_flag_swap[i] = i; + for (i = 0; i < 0x1000; i++) + fd->cram_flag_swap[i] = i; + } + + memset(fd->cram_sub_matrix, 4, 32*32); + for (i = 0; i < 32; i++) { + fd->cram_sub_matrix[i]['A'&0x1f]=0; + fd->cram_sub_matrix[i]['C'&0x1f]=1; + fd->cram_sub_matrix[i]['G'&0x1f]=2; + fd->cram_sub_matrix[i]['T'&0x1f]=3; + fd->cram_sub_matrix[i]['N'&0x1f]=4; + } + for (i = 0; i < 20; i+=4) { + int j; + for (j = 0; j < 20; j++) { + fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]=3; + fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]=3; + fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]=3; + fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]=3; + } + fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][CRAM_SUBST_MATRIX[i+0]&0x1f]=0; + fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][CRAM_SUBST_MATRIX[i+1]&0x1f]=1; + fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][CRAM_SUBST_MATRIX[i+2]&0x1f]=2; + fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][CRAM_SUBST_MATRIX[i+3]&0x1f]=3; + } +} + +// Default version numbers for CRAM +static int major_version = 2; +static int minor_version = 1; + +/* + * Opens a CRAM file for read (mode "rb") or write ("wb"). + * The filename may be "-" to indicate stdin or stdout. + * + * Returns file handle on success + * NULL on failure. + */ +cram_fd *cram_open(const char *filename, const char *mode) { + cram_FILE *fp; + cram_fd *fd; + char fmode[3]= { mode[0], '\0', '\0' }; + + if (strlen(mode) > 1 && (mode[1] == 'b' || mode[1] == 'c')) { + fmode[1] = 'b'; + } + +#ifdef SAMTOOLS + fp = hopen(filename, fmode); +#else + if (strcmp(filename, "-") == 0) { + fp = (*fmode == 'r') ? stdin : stdout; + } else { + fp = fopen(filename, fmode); + } +#endif + if (!fp) + return NULL; + + fd = cram_dopen(fp, filename, mode); + if (!fd) + hclose_abruptly(fp); + + return fd; +} + +/* Opens an existing stream for reading or writing. + * + * Returns file handle on success; + * NULL on failure. + * + * cram_FILE is either htslib's hFILE or stdio's FILE, depending on how + * cram_structs.h has been configured. + */ +cram_fd *cram_dopen(cram_FILE *fp, const char *filename, const char *mode) { + int i; + char *cp; + cram_fd *fd = calloc(1, sizeof(*fd)); + if (!fd) + return NULL; + + fd->level = 5; + if (strlen(mode) > 2 && mode[2] >= '0' && mode[2] <= '9') + fd->level = mode[2] - '0'; + + fd->fp = fp; + fd->mode = *mode; + fd->first_container = 0; + + if (fd->mode == 'r') { + /* Reader */ + + if (!(fd->file_def = cram_read_file_def(fd))) + goto err; + + fd->version = fd->file_def->major_version * 100 + + fd->file_def->minor_version; + + if (!(fd->header = cram_read_SAM_hdr(fd))) + goto err; + + } else { + /* Writer */ + cram_file_def def; + + def.magic[0] = 'C'; + def.magic[1] = 'R'; + def.magic[2] = 'A'; + def.magic[3] = 'M'; + def.major_version = major_version; + def.minor_version = minor_version; + memset(def.file_id, 0, 20); + strncpy(def.file_id, filename, 20); + if (0 != cram_write_file_def(fd, &def)) + goto err; + + fd->version = def.major_version * 100 + def.minor_version; + + /* SAM header written later */ + } + + cram_init_tables(fd); + + fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename); + if (!fd->prefix) + goto err; + fd->slice_num = 0; + fd->first_base = fd->last_base = -1; + fd->record_counter = 0; + + fd->ctr = NULL; + fd->refs = refs_create(); + if (!fd->refs) + goto err; + fd->ref_id = -2; + fd->ref = NULL; + + fd->decode_md = 0; + fd->verbose = 0; + fd->seqs_per_slice = SEQS_PER_SLICE; + fd->slices_per_container = SLICE_PER_CNT; + fd->embed_ref = 0; + fd->no_ref = 0; + fd->ignore_md5 = 0; + fd->use_bz2 = 0; + fd->multi_seq = 0; + fd->unsorted = 0; + fd->shared_ref = 0; + + fd->index = NULL; + fd->own_pool = 0; + fd->pool = NULL; + fd->rqueue = NULL; + fd->job_pending = NULL; + fd->ooc = 0; + + for (i = 0; i < 7; i++) + fd->m[i] = cram_new_metrics(); + + fd->range.refid = -2; // no ref. + fd->eof = 1; // See samtools issue #150 + fd->ref_fn = NULL; + + fd->bl = NULL; + + /* Initialise dummy refs from the @SQ headers */ + if (-1 == refs_from_header(fd->refs, fd, fd->header)) + goto err; + + return fd; + + err: + if (fd) + free(fd); + + return NULL; +} + +/* + * Seek within a CRAM file. + * + * Returns 0 on success + * -1 on failure + */ +int cram_seek(cram_fd *fd, off_t offset, int whence) { + char buf[65536]; + + if (hseek(fd->fp, offset, whence) >= 0) + return 0; + + if (!(whence == SEEK_CUR && offset >= 0)) + return -1; + + /* Couldn't fseek, but we're in SEEK_CUR mode so read instead */ + while (offset > 0) { + int len = MIN(65536, offset); + if (len != hread(fd->fp, buf, len)) + return -1; + offset -= len; + } + + return 0; +} + +/* + * Flushes a CRAM file. + * Useful for when writing to stdout without wishing to close the stream. + * + * Returns 0 on success + * -1 on failure + */ +int cram_flush(cram_fd *fd) { + if (!fd) + return -1; + + if (fd->mode == 'w' && fd->ctr) { + if(fd->ctr->slice) + fd->ctr->curr_slice++; + if (-1 == cram_flush_container_mt(fd, fd->ctr)) + return -1; + } + + return 0; +} + +/* + * Closes a CRAM file. + * Returns 0 on success + * -1 on failure + */ +int cram_close(cram_fd *fd) { + spare_bams *bl, *next; + int i; + + if (!fd) + return -1; + + if (fd->mode == 'w' && fd->ctr) { + if(fd->ctr->slice) + fd->ctr->curr_slice++; + if (-1 == cram_flush_container_mt(fd, fd->ctr)) + return -1; + } + + if (fd->pool) { + t_pool_flush(fd->pool); + + if (0 != cram_flush_result(fd)) + return -1; + + pthread_mutex_destroy(&fd->metrics_lock); + pthread_mutex_destroy(&fd->ref_lock); + pthread_mutex_destroy(&fd->bam_list_lock); + + fd->ctr = NULL; // prevent double freeing + + //fprintf(stderr, "CRAM: destroy queue %p\n", fd->rqueue); + + t_results_queue_destroy(fd->rqueue); + } + + if (fd->mode == 'w') { + /* Write EOF block */ + if (30 != hwrite(fd->fp, "\x0b\x00\x00\x00\xff\xff\xff\xff" + "\xff\xe0\x45\x4f\x46\x00\x00\x00" + "\x00\x01\x00\x00\x01\x00\x06\x06" + "\x01\x00\x01\x00\x01\x00", 30)) + return -1; + +// if (1 != fwrite("\x00\x00\x00\x00\xff\xff\xff\xff" +// "\xff\xe0\x45\x4f\x46\x00\x00\x00" +// "\x00\x00\x00", 19, 1, fd->fp)) +// return -1; + } + + for (bl = fd->bl; bl; bl = next) { + int i, max_rec = fd->seqs_per_slice * fd->slices_per_container; + + next = bl->next; + for (i = 0; i < max_rec; i++) { + if (bl->bams[i]) + bam_free(bl->bams[i]); + } + free(bl->bams); + free(bl); + } + + if (paranoid_hclose(fd->fp) != 0) + return -1; + + if (fd->file_def) + cram_free_file_def(fd->file_def); + + if (fd->header) + sam_hdr_free(fd->header); + + free(fd->prefix); + + if (fd->ctr) + cram_free_container(fd->ctr); + + if (fd->refs) + refs_free(fd->refs); + if (fd->ref_free) + free(fd->ref_free); + + for (i = 0; i < 7; i++) + if (fd->m[i]) + free(fd->m[i]); + + if (fd->index) + cram_index_free(fd); + + if (fd->own_pool && fd->pool) + t_pool_destroy(fd->pool, 0); + + free(fd); + return 0; +} + +/* + * Returns 1 if we hit an EOF while reading. + */ +int cram_eof(cram_fd *fd) { + return fd->eof; +} + + +/* + * Sets options on the cram_fd. See CRAM_OPT_* definitions in cram_structs.h. + * Use this immediately after opening. + * + * Returns 0 on success + * -1 on failure + */ +int cram_set_option(cram_fd *fd, enum cram_option opt, ...) { + int r; + va_list args; + + va_start(args, opt); + r = cram_set_voption(fd, opt, args); + va_end(args); + + return r; +} + +/* + * Sets options on the cram_fd. See CRAM_OPT_* definitions in cram_structs.h. + * Use this immediately after opening. + * + * Returns 0 on success + * -1 on failure + */ +int cram_set_voption(cram_fd *fd, enum cram_option opt, va_list args) { + refs_t *refs; + + switch (opt) { + case CRAM_OPT_DECODE_MD: + fd->decode_md = va_arg(args, int); + break; + + case CRAM_OPT_PREFIX: + if (fd->prefix) + free(fd->prefix); + if (!(fd->prefix = strdup(va_arg(args, char *)))) + return -1; + break; + + case CRAM_OPT_VERBOSITY: + fd->verbose = va_arg(args, int); + break; + + case CRAM_OPT_SEQS_PER_SLICE: + fd->seqs_per_slice = va_arg(args, int); + break; + + case CRAM_OPT_SLICES_PER_CONTAINER: + fd->slices_per_container = va_arg(args, int); + break; + + case CRAM_OPT_EMBED_REF: + fd->embed_ref = va_arg(args, int); + break; + + case CRAM_OPT_NO_REF: + fd->no_ref = va_arg(args, int); + break; + + case CRAM_OPT_IGNORE_MD5: + fd->ignore_md5 = va_arg(args, int); + break; + + case CRAM_OPT_USE_BZIP2: + fd->use_bz2 = va_arg(args, int); + break; + + case CRAM_OPT_SHARED_REF: + fd->shared_ref = 1; + refs = va_arg(args, refs_t *); + if (refs != fd->refs) { + if (fd->refs) + refs_free(fd->refs); + fd->refs = refs; + fd->refs->count++; + } + break; + + case CRAM_OPT_RANGE: + fd->range = *va_arg(args, cram_range *); + return cram_seek_to_refpos(fd, &fd->range); + + case CRAM_OPT_REFERENCE: + return cram_load_reference(fd, va_arg(args, char *)); + + case CRAM_OPT_VERSION: { + int major, minor; + char *s = va_arg(args, char *); + if (2 != sscanf(s, "%d.%d", &major, &minor)) { + fprintf(stderr, "Malformed version string %s\n", s); + return -1; + } + if (!((major == 1 && minor == 0) || + (major == 2 && (minor == 0 || minor == 1)) || + (major == 3 && minor == 0))) { + fprintf(stderr, "Unknown version string; " + "use 1.0, 2.0, 2.1 or 3.0\n"); + return -1; + } + break; + } + + case CRAM_OPT_MULTI_SEQ_PER_SLICE: + fd->multi_seq = va_arg(args, int); + break; + + case CRAM_OPT_NTHREADS: { + int nthreads = va_arg(args, int); + if (nthreads > 1) { + if (!(fd->pool = t_pool_init(nthreads*2, nthreads))) + return -1; + + fd->rqueue = t_results_queue_init(); + pthread_mutex_init(&fd->metrics_lock, NULL); + pthread_mutex_init(&fd->ref_lock, NULL); + pthread_mutex_init(&fd->bam_list_lock, NULL); + fd->shared_ref = 1; + fd->own_pool = 1; + } + break; + } + + case CRAM_OPT_THREAD_POOL: + fd->pool = va_arg(args, t_pool *); + if (fd->pool) { + fd->rqueue = t_results_queue_init(); + pthread_mutex_init(&fd->metrics_lock, NULL); + pthread_mutex_init(&fd->ref_lock, NULL); + pthread_mutex_init(&fd->bam_list_lock, NULL); + } + fd->shared_ref = 1; // Needed to avoid clobbering ref between threads + fd->own_pool = 0; + + //fd->qsize = 1; + //fd->decoded = calloc(fd->qsize, sizeof(cram_container *)); + //t_pool_dispatch(fd->pool, cram_decoder_thread, fd); + break; + + default: + fprintf(stderr, "Unknown CRAM option code %d\n", opt); + return -1; + } + + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_io.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_io.h new file mode 100644 index 0000000000000000000000000000000000000000..165dc5e180b11cdad500792b25d1f5e86ab6d1cf --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_io.h @@ -0,0 +1,532 @@ +/* +Copyright (c) 2012-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +/*! \file + * Include cram.h instead. + * + * This is an internal part of the CRAM system and is automatically included + * when you #include cram.h. + * + * Implements the low level CRAM I/O primitives. + * This includes basic data types such as byte, int, ITF-8, + * maps, bitwise I/O, etc. + */ + +#ifndef _CRAM_IO_H_ +#define _CRAM_IO_H_ + +#ifdef __cplusplus +extern "C" { +#endif + +#define ITF8_MACROS + +#include +#include + +/**@{ ---------------------------------------------------------------------- + * ITF8 encoding and decoding. + * + * Also see the itf8_get and itf8_put macros. + */ + +/*! INTERNAL: Converts two characters into an integer for use in switch{} */ +#define CRAM_KEY(a,b) (((a)<<8)|((b))) + +/*! Reads an integer in ITF-8 encoding from 'fd' and stores it in + * *val. + * + * @return + * Returns the number of bytes read on success; + * -1 on failure + */ +int itf8_decode(cram_fd *fd, int32_t *val); + +#ifndef ITF8_MACROS +/*! Reads an integer in ITF-8 encoding from 'cp' and stores it in + * *val. + * + * @return + * Returns the number of bytes read on success; + * -1 on failure + */ +int itf8_get(char *cp, int32_t *val_p); + +/*! Stores a value to memory in ITF-8 format. + * + * @return + * Returns the number of bytes required to store the number. + * This is a maximum of 5 bytes. + */ +int itf8_put(char *cp, int32_t val); + +#else + +/* + * Macro implementations of the above + */ +#define itf8_get(c,v) (((uc)(c)[0]<0x80)?(*(v)=(uc)(c)[0],1):(((uc)(c)[0]<0xc0)?(*(v)=(((uc)(c)[0]<<8)|(uc)(c)[1])&0x3fff,2):(((uc)(c)[0]<0xe0)?(*(v)=(((uc)(c)[0]<<16)|((uc)(c)[1]<<8)|(uc)(c)[2])&0x1fffff,3):(((uc)(c)[0]<0xf0)?(*(v)=(((uc)(c)[0]<<24)|((uc)(c)[1]<<16)|((uc)(c)[2]<<8)|(uc)(c)[3])&0x0fffffff,4):(*(v)=(((uc)(c)[0]&0x0f)<<28)|((uc)(c)[1]<<20)|((uc)(c)[2]<<12)|((uc)(c)[3]<<4)|((uc)(c)[4]&0x0f),5))))) + +#define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) + +#define itf8_size(v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?4:5) + +#endif + +/*! Pushes a value in ITF8 format onto the end of a block. + * + * This shouldn't be used for high-volume data as it is not the fastest + * method. + * + * @return + * Returns the number of bytes written + */ +int itf8_put_blk(cram_block *blk, int val); + +/**@}*/ +/**@{ ---------------------------------------------------------------------- + * CRAM blocks - the dynamically growable data block. We have code to + * create, update, (un)compress and read/write. + * + * These are derived from the deflate_interlaced.c blocks, but with the + * CRAM extension of content types and IDs. + */ + +/*! Allocates a new cram_block structure with a specified content_type and + * id. + * + * @return + * Returns block pointer on success; + * NULL on failure + */ +cram_block *cram_new_block(enum cram_content_type content_type, + int content_id); + +/*! Reads a block from a cram file. + * + * @return + * Returns cram_block pointer on success; + * NULL on failure + */ +cram_block *cram_read_block(cram_fd *fd); + +/*! Writes a CRAM block. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int cram_write_block(cram_fd *fd, cram_block *b); + +/*! Frees a CRAM block, deallocating internal data too. + */ +void cram_free_block(cram_block *b); + +/*! Uncompress a memory block using Zlib. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +char *zlib_mem_inflate(char *cdata, size_t csize, size_t *size); + +/*! Uncompresses a CRAM block, if compressed. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int cram_uncompress_block(cram_block *b); + +/*! Compresses a block. + * + * Compresses a block using one of two different zlib strategies. If we only + * want one choice set strat2 to be -1. + * + * The logic here is that sometimes Z_RLE does a better job than Z_FILTERED + * or Z_DEFAULT_STRATEGY on quality data. If so, we'd rather use it as it is + * significantly faster. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int cram_compress_block(cram_fd *fd, cram_block *b, cram_metrics *metrics, + int level, int strat, + int level2, int strat2); + +cram_metrics *cram_new_metrics(void); +char *cram_block_method2str(enum cram_block_method m); +char *cram_content_type2str(enum cram_content_type t); + +/* --- Accessor macros for manipulating blocks on a byte by byte basis --- */ + +/* Block size and data pointer. */ +#define BLOCK_SIZE(b) ((b)->byte) +#define BLOCK_DATA(b) ((b)->data) + +/* Returns the address one past the end of the block */ +#define BLOCK_END(b) (&(b)->data[(b)->byte]) + +/* Request block to be at least 'l' bytes long */ +#define BLOCK_RESIZE(b,l) \ + do { \ + while((b)->alloc <= (l)) { \ + (b)->alloc = (b)->alloc ? (b)->alloc*1.5 : 1024; \ + (b)->data = realloc((b)->data, (b)->alloc); \ + } \ + } while(0) + +/* Ensure the block can hold at least another 'l' bytes */ +#define BLOCK_GROW(b,l) BLOCK_RESIZE((b), BLOCK_SIZE((b)) + (l)) + +/* Append string 's' of length 'l' */ +#define BLOCK_APPEND(b,s,l) \ + do { \ + BLOCK_GROW((b),(l)); \ + memcpy(BLOCK_END((b)), (s), (l)); \ + BLOCK_SIZE((b)) += (l); \ + } while (0) + +/* Append as single character 'c' */ +#define BLOCK_APPEND_CHAR(b,c) \ + do { \ + BLOCK_GROW((b),1); \ + (b)->data[(b)->byte++] = (c); \ + } while (0) + +/* Append via sprintf with 1 arg */ +#define BLOCK_APPENDF_1(b,buf,fmt, a1) \ + do { \ + int l = sprintf((buf), (fmt), (a1)); \ + BLOCK_APPEND((b), (buf), l); \ + } while (0) + +/* Append via sprintf with 2 args */ +#define BLOCK_APPENDF_2(b,buf,fmt, a1,a2) \ + do { \ + int l = sprintf((buf), (fmt), (a1), (a2)); \ + BLOCK_APPEND((b), (buf), l); \ + } while (0) + +#define BLOCK_UPLEN(b) \ + (b)->comp_size = (b)->uncomp_size = BLOCK_SIZE((b)) + +/**@}*/ +/**@{ ---------------------------------------------------------------------- + * Reference sequence handling + */ + +/*! Loads a reference set from fn and stores in the cram_fd. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int cram_load_reference(cram_fd *fd, char *fn); + +/*! Generates a lookup table in refs based on the SQ headers in SAM_hdr. + * + * Indexes references by the order they appear in a BAM file. This may not + * necessarily be the same order they appear in the fasta reference file. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int refs2id(refs_t *r, SAM_hdr *bfd); + +void refs_free(refs_t *r); + +/*! Returns a portion of a reference sequence from start to end inclusive. + * + * The returned pointer is owned by the cram_file fd and should not be freed + * by the caller. It is valid only until the next cram_get_ref is called + * with the same fd parameter (so is thread-safe if given multiple files). + * + * To return the entire reference sequence, specify start as 1 and end + * as 0. + * + * @return + * Returns reference on success; + * NULL on failure + */ +char *cram_get_ref(cram_fd *fd, int id, int start, int end); +void cram_ref_incr(refs_t *r, int id); +void cram_ref_decr(refs_t *r, int id); +/**@}*/ +/**@{ ---------------------------------------------------------------------- + * Containers + */ + +/*! Creates a new container, specifying the maximum number of slices + * and records permitted. + * + * @return + * Returns cram_container ptr on success; + * NULL on failure + */ +cram_container *cram_new_container(int nrec, int nslice); +void cram_free_container(cram_container *c); + +/*! Reads a container header. + * + * @return + * Returns cram_container on success; + * NULL on failure or no container left (fd->err == 0). + */ +cram_container *cram_read_container(cram_fd *fd); + +/*! Writes a container structure. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int cram_write_container(cram_fd *fd, cram_container *h); + +/*! Flushes a container to disk. + * + * Flushes a completely or partially full container to disk, writing + * container structure, header and blocks. This also calls the encoder + * functions. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int cram_flush_container(cram_fd *fd, cram_container *c); +int cram_flush_container_mt(cram_fd *fd, cram_container *c); + + +/**@}*/ +/**@{ ---------------------------------------------------------------------- + * Compression headers; the first part of the container + */ + +/*! Creates a new blank container compression header + * + * @return + * Returns header ptr on success; + * NULL on failure + */ +cram_block_compression_hdr *cram_new_compression_header(void); + +/*! Frees a cram_block_compression_hdr */ +void cram_free_compression_header(cram_block_compression_hdr *hdr); + + +/**@}*/ +/**@{ ---------------------------------------------------------------------- + * Slices and slice headers + */ + +/*! Frees a slice header */ +void cram_free_slice_header(cram_block_slice_hdr *hdr); + +/*! Frees a slice */ +void cram_free_slice(cram_slice *s); + +/*! Creates a new empty slice in memory, for subsequent writing to + * disk. + * + * @return + * Returns cram_slice ptr on success; + * NULL on failure + */ +cram_slice *cram_new_slice(enum cram_content_type type, int nrecs); + +/*! Loads an entire slice. + * + * FIXME: In 1.0 the native unit of slices within CRAM is broken + * as slices contain references to objects in other slices. + * To work around this while keeping the slice oriented outer loop + * we read all slices and stitch them together into a fake large + * slice instead. + * + * @return + * Returns cram_slice ptr on success; + * NULL on failure + */ +cram_slice *cram_read_slice(cram_fd *fd); + + + +/**@}*/ +/**@{ ---------------------------------------------------------------------- + * CRAM file definition (header) + */ + +/*! Reads a CRAM file definition structure. + * + * @return + * Returns file_def ptr on success; + * NULL on failure + */ +cram_file_def *cram_read_file_def(cram_fd *fd); + +/*! Writes a cram_file_def structure to cram_fd. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int cram_write_file_def(cram_fd *fd, cram_file_def *def); + +/*! Frees a cram_file_def structure. */ +void cram_free_file_def(cram_file_def *def); + + +/**@}*/ +/**@{ ---------------------------------------------------------------------- + * SAM header I/O + */ + +/*! Reads the SAM header from the first CRAM data block. + * + * Also performs minimal parsing to extract read-group + * and sample information. + * + * @return + * Returns SAM hdr ptr on success; + * NULL on failure + */ +SAM_hdr *cram_read_SAM_hdr(cram_fd *fd); + +/*! Writes a CRAM SAM header. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int cram_write_SAM_hdr(cram_fd *fd, SAM_hdr *hdr); + + +/**@}*/ +/**@{ ---------------------------------------------------------------------- + * The top-level cram opening, closing and option handling + */ + +/*! Opens a CRAM file for read (mode "rb") or write ("wb"). + * + * The filename may be "-" to indicate stdin or stdout. + * + * @return + * Returns file handle on success; + * NULL on failure. + */ +cram_fd *cram_open(const char *filename, const char *mode); + +/*! Opens an existing stream for reading or writing. + * + * @return + * Returns file handle on success; + * NULL on failure. + * + * cram_FILE is either htslib's hFILE or stdio's FILE, depending on how + * cram_structs.h has been configured. + */ +cram_fd *cram_dopen(cram_FILE *fp, const char *filename, const char *mode); + +/*! Closes a CRAM file. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int cram_close(cram_fd *fd); + +/* + * Seek within a CRAM file. + * + * Returns 0 on success + * -1 on failure + */ +int cram_seek(cram_fd *fd, off_t offset, int whence); + +/* + * Flushes a CRAM file. + * Useful for when writing to stdout without wishing to close the stream. + * + * Returns 0 on success + * -1 on failure + */ +int cram_flush(cram_fd *fd); + +/*! Checks for end of file on a cram_fd stream. + * + * @return + * Returns 0 if not at end of file + * 1 if we hit an expected EOF (end of range or EOF block) + * 2 for other EOF (end of stream without EOF block) + */ +int cram_eof(cram_fd *fd); + +/*! Sets options on the cram_fd. + * + * See CRAM_OPT_* definitions in cram_structs.h. + * Use this immediately after opening. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int cram_set_option(cram_fd *fd, enum cram_option opt, ...); + +/*! Sets options on the cram_fd. + * + * See CRAM_OPT_* definitions in cram_structs.h. + * Use this immediately after opening. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int cram_set_voption(cram_fd *fd, enum cram_option opt, va_list args); + +/*! + * Attaches a header to a cram_fd. + * + * This should be used when creating a new cram_fd for writing where + * we have an SAM_hdr already constructed (eg from a file we've read + * in). + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int cram_set_header(cram_fd *fd, SAM_hdr *hdr); + + +#ifdef __cplusplus +} +#endif + +#endif /* _CRAM_IO_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_samtools.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_samtools.c new file mode 100644 index 0000000000000000000000000000000000000000..66f2efa4bd1a521f190d5139b72f20c079bcbc97 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_samtools.c @@ -0,0 +1,144 @@ +/* +Copyright (c) 2010-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#include +#include +#include + +#include "cram/cram.h" +#include "htslib/sam.h" + +/*--------------------------------------------------------------------------- + * Samtools compatibility portion + */ +int bam_construct_seq(bam_seq_t **bp, size_t extra_len, + const char *qname, size_t qname_len, + int flag, + int rname, // Ref ID + int pos, + int end, // aligned start/end coords + int mapq, + uint32_t ncigar, const uint32_t *cigar, + int mrnm, // Mate Ref ID + int mpos, + int isize, + int len, + const char *seq, + const char *qual) { + static const char L[256] = { + 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, + 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, + 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, + 15,15,15,15,15,15,15,15,15,15,15,15,15, 0,15,15, + 15, 1,14, 2,13,15,15, 4,11,15,15,12,15, 3,15,15, + 15,15, 5, 6, 8,15, 7, 9,15,10,15,15,15,15,15,15, + 15, 1,14, 2,13,15,15, 4,11,15,15,12,15, 3,15,15, + 15,15, 5, 6, 8,15, 7, 9,15,10,15,15,15,15,15,15, + 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, + 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, + 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, + 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, + 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, + 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, + 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15, + 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15 + }; + bam1_t *b = (bam1_t *)*bp; + uint8_t *cp; + int i, bam_len; + + //b->l_aux = extra_len; // we fill this out later + + bam_len = qname_len + 1 + ncigar*4 + (len+1)/2 + len + extra_len; + if (b->m_data < bam_len) { + b->m_data = bam_len; + kroundup32(b->m_data); + b->data = (uint8_t*)realloc(b->data, b->m_data); + if (!b->data) + return -1; + } + b->l_data = bam_len; + + b->core.tid = rname; + b->core.pos = pos-1; + b->core.bin = bam_reg2bin(pos, end); + b->core.qual = mapq; + b->core.l_qname = qname_len+1; + b->core.flag = flag; + b->core.n_cigar = ncigar; + b->core.l_qseq = len; + b->core.mtid = mrnm; + b->core.mpos = mpos-1; + b->core.isize = isize; + + cp = b->data; + + strncpy((char *)cp, qname, qname_len); + cp[qname_len] = 0; + cp += qname_len+1; + memcpy(cp, cigar, ncigar*4); + cp += ncigar*4; + + for (i = 0; i+1 < len; i+=2) { + *cp++ = (L[(uc)seq[i]]<<4) + L[(uc)seq[i+1]]; + } + if (i < len) + *cp++ = L[(uc)seq[i]]<<4; + + memcpy(cp, qual, len); + + return 0; +} + +bam_hdr_t *cram_header_to_bam(SAM_hdr *h) { + int i; + bam_hdr_t *header = bam_hdr_init(); + + header->l_text = ks_len(&h->text); + header->text = malloc(header->l_text+1); + memcpy(header->text, ks_str(&h->text), header->l_text); + header->text[header->l_text] = 0; + + header->n_targets = h->nref; + header->target_name = (char **)calloc(header->n_targets, + sizeof(char *)); + header->target_len = (uint32_t *)calloc(header->n_targets, 4); + + for (i = 0; i < h->nref; i++) { + header->target_name[i] = strdup(h->ref[i].name); + header->target_len[i] = h->ref[i].len; + } + + return header; +} + +SAM_hdr *bam_header_to_cram(bam_hdr_t *h) { + return sam_hdr_parse_(h->text, h->l_text); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_samtools.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_samtools.h new file mode 100644 index 0000000000000000000000000000000000000000..f7949d0d2613285b463adb0b0e9ea9d65d30414d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_samtools.h @@ -0,0 +1,97 @@ +/* +Copyright (c) 2010-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifndef _CRAM_SAMTOOLS_H_ +#define _CRAM_SAMTOOLS_H_ + +/* Samtools compatible API */ +#define bam_blk_size(b) ((b)->l_data) +#define bam_set_blk_size(b,v) ((b)->data_len = (v)) + +#define bam_ref(b) (b)->core.tid +#define bam_pos(b) (b)->core.pos +#define bam_mate_pos(b) (b)->core.mpos +#define bam_mate_ref(b) (b)->core.mtid +#define bam_ins_size(b) (b)->core.isize +#define bam_seq_len(b) (b)->core.l_qseq +#define bam_cigar_len(b) (b)->core.n_cigar +#define bam_flag(b) (b)->core.flag +#define bam_bin(b) (b)->core.bin +#define bam_map_qual(b) (b)->core.qual +#define bam_name_len(b) (b)->core.l_qname +#define bam_name(b) bam_get_qname((b)) +#define bam_qual(b) bam_get_qual((b)) +#define bam_seq(b) bam_get_seq((b)) +#define bam_cigar(b) bam_get_cigar((b)) +#define bam_aux(b) bam_get_aux((b)) + +#define bam_dup(b) bam_copy1(bam_init1(), (b)) + +#define bam_free(b) bam_destroy1((b)) + +#define bam_reg2bin(beg,end) hts_reg2bin((beg),(end),14,5) + +#include "htslib/sam.h" + +enum cigar_op { + BAM_CMATCH_=BAM_CMATCH, + BAM_CINS_=BAM_CINS, + BAM_CDEL_=BAM_CDEL, + BAM_CREF_SKIP_=BAM_CREF_SKIP, + BAM_CSOFT_CLIP_=BAM_CSOFT_CLIP, + BAM_CHARD_CLIP_=BAM_CHARD_CLIP, + BAM_CPAD_=BAM_CPAD, + BAM_CBASE_MATCH=BAM_CEQUAL, + BAM_CBASE_MISMATCH=BAM_CDIFF +}; + +typedef bam1_t bam_seq_t; + +#include "cram/sam_header.h" + +bam_hdr_t *cram_header_to_bam(SAM_hdr *h); +SAM_hdr *bam_header_to_cram(bam_hdr_t *h); + +int bam_construct_seq(bam_seq_t **bp, size_t extra_len, + const char *qname, size_t qname_len, + int flag, + int rname, // Ref ID + int pos, + int end, // aligned start/end coords + int mapq, + uint32_t ncigar, const uint32_t *cigar, + int mrnm, // Mate Ref ID + int mpos, + int isize, + int len, + const char *seq, + const char *qual); + +#endif /* _CRAM_SAMTOOLS_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_stats.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_stats.c new file mode 100644 index 0000000000000000000000000000000000000000..18d06056211c0e8a51936f7ce977187db36dbdab --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_stats.c @@ -0,0 +1,357 @@ +/* +Copyright (c) 2012-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifdef HAVE_CONFIG_H +#include "io_lib_config.h" +#endif + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "cram/cram.h" +#include "cram/os.h" + +cram_stats *cram_stats_create(void) { + return calloc(1, sizeof(cram_stats)); +} + +void cram_stats_add(cram_stats *st, int32_t val) { + st->nsamp++; + + //assert(val >= 0); + + if (val < MAX_STAT_VAL && val >= 0) { + st->freqs[val]++; + } else { + khint_t k; + int r; + + if (!st->h) { + st->h = kh_init(m_i2i); + } + + k = kh_put(m_i2i, st->h, val, &r); + if (r == 0) + kh_val(st->h, k)++; + else if (r != -1) + kh_val(st->h, k) = 1; + else + ; // FIXME: handle error + } +} + +void cram_stats_del(cram_stats *st, int32_t val) { + st->nsamp--; + + //assert(val >= 0); + + if (val < MAX_STAT_VAL && val >= 0) { + st->freqs[val]--; + assert(st->freqs[val] >= 0); + } else if (st->h) { + khint_t k = kh_get(m_i2i, st->h, val); + + if (k != kh_end(st->h)) { + if (--kh_val(st->h, k) == 0) + kh_del(m_i2i, st->h, k); + } else { + fprintf(stderr, "Failed to remove val %d from cram_stats\n", val); + st->nsamp++; + } + } else { + fprintf(stderr, "Failed to remove val %d from cram_stats\n", val); + st->nsamp++; + } +} + +void cram_stats_dump(cram_stats *st) { + int i; + fprintf(stderr, "cram_stats:\n"); + for (i = 0; i < MAX_STAT_VAL; i++) { + if (!st->freqs[i]) + continue; + fprintf(stderr, "\t%d\t%d\n", i, st->freqs[i]); + } + if (st->h) { + khint_t k; + for (k = kh_begin(st->h); k != kh_end(st->h); k++) { + if (!kh_exist(st->h, k)) + continue; + + fprintf(stderr, "\t%d\t%d\n", kh_key(st->h, k), kh_val(st->h, k)); + } + } +} + +#if 1 +/* Returns the number of bits set in val; it the highest bit used */ +static int nbits(int v) { + static const int MultiplyDeBruijnBitPosition[32] = { + 1, 10, 2, 11, 14, 22, 3, 30, 12, 15, 17, 19, 23, 26, 4, 31, + 9, 13, 21, 29, 16, 18, 25, 8, 20, 28, 24, 7, 27, 6, 5, 32 + }; + + v |= v >> 1; // first up to set all bits 1 after the first 1 */ + v |= v >> 2; + v |= v >> 4; + v |= v >> 8; + v |= v >> 16; + + // DeBruijn magic to find top bit + return MultiplyDeBruijnBitPosition[(uint32_t)(v * 0x07C4ACDDU) >> 27]; +} +#endif + +/* + * Computes entropy from integer frequencies for various encoding methods and + * picks the best encoding. + * + * FIXME: we could reuse some of the code here for the actual encoding + * parameters too. Eg the best 'k' for SUBEXP or the code lengths for huffman. + * + * Returns the best codec to use. + */ +enum cram_encoding cram_stats_encoding(cram_fd *fd, cram_stats *st) { + enum cram_encoding best_encoding = E_NULL; + int best_size = INT_MAX, bits; + int nvals, i, ntot = 0, max_val = 0, min_val = INT_MAX, k; + int *vals = NULL, *freqs = NULL, vals_alloc = 0, *codes; + + //cram_stats_dump(st); + + /* Count number of unique symbols */ + for (nvals = i = 0; i < MAX_STAT_VAL; i++) { + if (!st->freqs[i]) + continue; + if (nvals >= vals_alloc) { + vals_alloc = vals_alloc ? vals_alloc*2 : 1024; + vals = realloc(vals, vals_alloc * sizeof(int)); + freqs = realloc(freqs, vals_alloc * sizeof(int)); + if (!vals || !freqs) { + if (vals) free(vals); + if (freqs) free(freqs); + return E_HUFFMAN; // Cannot do much else atm + } + } + vals[nvals] = i; + freqs[nvals] = st->freqs[i]; + ntot += freqs[nvals]; + if (max_val < i) max_val = i; + if (min_val > i) min_val = i; + nvals++; + } + if (st->h) { + khint_t k; + int i; + + for (k = kh_begin(st->h); k != kh_end(st->h); k++) { + if (!kh_exist(st->h, k)) + continue; + + if (nvals >= vals_alloc) { + vals_alloc = vals_alloc ? vals_alloc*2 : 1024; + vals = realloc(vals, vals_alloc * sizeof(int)); + freqs = realloc(freqs, vals_alloc * sizeof(int)); + if (!vals || !freqs) + return E_HUFFMAN; // Cannot do much else atm + } + i = kh_key(st->h, k); + vals[nvals]=i; + freqs[nvals] = kh_val(st->h, k); + ntot += freqs[nvals]; + if (max_val < i) max_val = i; + if (min_val > i) min_val = i; + nvals++; + } + } + + st->nvals = nvals; + assert(ntot == st->nsamp); + + if (nvals <= 1) { + free(vals); + free(freqs); + return E_HUFFMAN; + } + + /* + * Avoid complex stats for now, just do heuristic of HUFFMAN for small + * alphabets and BETA for anything large. + */ + free(vals); free(freqs); + return nvals < 200 ? E_HUFFMAN : E_BETA; + + /* We only support huffman now anyway... */ + //free(vals); free(freqs); return E_HUFFMAN; + + if (fd->verbose > 1) + fprintf(stderr, "Range = %d..%d, nvals=%d, ntot=%d\n", + min_val, max_val, nvals, ntot); + + /* Theoretical entropy */ + { + double dbits = 0; + for (i = 0; i < nvals; i++) { + dbits += freqs[i] * log((double)freqs[i]/ntot); + } + dbits /= -log(2); + if (fd->verbose > 1) + fprintf(stderr, "Entropy = %f\n", dbits); + } + + /* Beta */ + bits = nbits(max_val - min_val) * ntot; + if (fd->verbose > 1) + fprintf(stderr, "BETA = %d\n", bits); + if (best_size > bits) + best_size = bits, best_encoding = E_BETA; + +#if 0 + /* Unary */ + if (min_val >= 0) { + for (bits = i = 0; i < nvals; i++) + bits += freqs[i]*(vals[i]+1); + if (fd->verbose > 1) + fprintf(stderr, "UNARY = %d\n", bits); + if (best_size > bits) + best_size = bits, best_encoding = E_NULL; //E_UNARY; + } + + /* Gamma */ + for (bits = i = 0; i < nvals; i++) + bits += ((nbits(vals[i]-min_val+1)-1) + nbits(vals[i]-min_val+1)) * freqs[i]; + if (fd->verbose > 1) + fprintf(stderr, "GAMMA = %d\n", bits); + if (best_size > bits) + best_size = bits, best_encoding = E_GAMMA; + + /* Subexponential */ + for (k = 0; k < 10; k++) { + for (bits = i = 0; i < nvals; i++) { + if (vals[i]-min_val < (1<verbose > 1) + fprintf(stderr, "SUBEXP%d = %d\n", k, bits); + if (best_size > bits) + best_size = bits, best_encoding = E_SUBEXP; + } +#endif + + /* byte array len */ + + /* byte array stop */ + + /* External? Guesswork! */ + + /* Huffman */ +// qsort(freqs, nvals, sizeof(freqs[0]), sort_freqs); +// for (i = 0; i < nvals; i++) { +// fprintf(stderr, "%d = %d\n", i, freqs[i]); +// vals[i] = 0; +// } + + /* Grow freqs to 2*freqs, to store sums */ + /* Vals holds link data */ + freqs = realloc(freqs, 2*nvals*sizeof(*freqs)); + codes = calloc(2*nvals, sizeof(*codes)); + if (!freqs || !codes) + return E_HUFFMAN; // Cannot do much else atm + + /* Inefficient, use pointers to form chain so we can insert and maintain + * a sorted list? This is currently O(nvals^2) complexity. + */ + for (;;) { + int low1 = INT_MAX, low2 = INT_MAX; + int ind1 = 0, ind2 = 0; + for (i = 0; i < nvals; i++) { + if (freqs[i] < 0) + continue; + if (low1 > freqs[i]) + low2 = low1, ind2 = ind1, low1 = freqs[i], ind1 = i; + else if (low2 > freqs[i]) + low2 = freqs[i], ind2 = i; + } + if (low2 == INT_MAX) + break; + + //fprintf(stderr, "Merge ind %d (%d), %d (%d) = %d+%d, => %d=%d\n", + // ind1, vals[ind1], ind2, vals[ind2], low1, low2, + // nvals, low1+low2); + + freqs[nvals] = low1 + low2; + codes[ind1] = nvals; + codes[ind2] = nvals; + freqs[ind1] *= -1; + freqs[ind2] *= -1; + nvals++; + } + nvals = nvals/2+1; + + for (i = 0; i < nvals; i++) { + int code_len = 0; + for (k = codes[i]; k; k = codes[k]) + code_len++; + codes[i] = code_len; + freqs[i] *= -1; + //fprintf(stderr, "%d / %d => %d\n", vals[i], freqs[i], codes[i]); + } + + for (bits = i = 0; i < nvals; i++) { + bits += freqs[i] * codes[i]; + } + if (fd->verbose > 1) + fprintf(stderr, "HUFFMAN = %d\n", bits); + if (best_size >= bits) + best_size = bits, best_encoding = E_HUFFMAN; + free(codes); + + free(vals); + free(freqs); + + return best_encoding; +} + +void cram_stats_free(cram_stats *st) { + if (st->h) + kh_destroy(m_i2i, st->h); + free(st); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_stats.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_stats.h new file mode 100644 index 0000000000000000000000000000000000000000..b471e68a0caf69aa1ea56a31355bf2090d48de9b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_stats.h @@ -0,0 +1,59 @@ +/* +Copyright (c) 2012-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifndef _CRAM_STATS_H_ +#define _CRAM_STATS_H_ + +#ifdef __cplusplus +extern "C" { +#endif + +cram_stats *cram_stats_create(void); +void cram_stats_add(cram_stats *st, int32_t val); +void cram_stats_del(cram_stats *st, int32_t val); +void cram_stats_dump(cram_stats *st); +void cram_stats_free(cram_stats *st); + +/* + * Computes entropy from integer frequencies for various encoding methods and + * picks the best encoding. + * + * FIXME: we could reuse some of the code here for the actual encoding + * parameters too. Eg the best 'k' for SUBEXP or the code lengths for huffman. + * + * Returns the best codec to use. + */ +enum cram_encoding cram_stats_encoding(cram_fd *fd, cram_stats *st); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_structs.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_structs.h new file mode 100644 index 0000000000000000000000000000000000000000..6d3f1a13a22fcff8565f887d0dd0beb90256c14f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/cram_structs.h @@ -0,0 +1,752 @@ +/* +Copyright (c) 2012-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifndef _CRAM_STRUCTS_H_ +#define _CRAM_STRUCTS_H_ + +#ifdef __cplusplus +extern "C" { +#endif + +/* + * Defines in-memory structs for the basic file-format objects in the + * CRAM format. + * + * The basic file format is: + * File-def SAM-hdr Container Container ... + * + * Container: + * Service-block data-block data-block ... + * + * Multiple blocks in a container are grouped together as slices, + * also sometimes referred to as landmarks in the spec. + */ + + +#include + +#include "cram/thread_pool.h" + +#ifdef SAMTOOLS +// From within samtools/HTSlib +# include "cram/string_alloc.h" +# include "htslib/khash.h" + +// Generic hash-map integer -> integer +KHASH_MAP_INIT_INT(m_i2i, int) + +// Generic hash-set integer -> (existance) +KHASH_SET_INIT_INT(s_i2i) + +// For brevity +typedef unsigned char uc; + +/* + * A union for the preservation map. Required for khash. + */ +typedef union { + int i; + char *p; +} pmap_t; + +// Generates static functions here which isn't ideal, but we have no way +// currently to declare the kh_map_t structure here without also declaring a +// duplicate in the .c files due to the nature of the KHASH macros. +KHASH_MAP_INIT_STR(map, pmap_t) + +struct hFILE; +typedef struct hFILE cram_FILE; + +#else +// From within io_lib +# include "cram/bam.h" // For BAM header parsing +typedef FILE cram_FILE; +#endif + +#define SEQS_PER_SLICE 10000 +#define SLICE_PER_CNT 1 + +#define CRAM_SUBST_MATRIX "CGTNAGTNACTNACGNACGT" + +#define TN_external +//#define NS_external +#define TS_external +//#define BA_external + +#define MAX_STAT_VAL 1024 +//#define MAX_STAT_VAL 16 +typedef struct { + int freqs[MAX_STAT_VAL]; + khash_t(m_i2i) *h; + int nsamp; // total number of values added + int nvals; // total number of unique values added +} cram_stats; + +/* NB: matches java impl, not the spec */ +enum cram_encoding { + E_NULL = 0, + E_EXTERNAL = 1, + E_GOLOMB = 2, + E_HUFFMAN = 3, + E_BYTE_ARRAY_LEN = 4, + E_BYTE_ARRAY_STOP = 5, + E_BETA = 6, + E_SUBEXP = 7, + E_GOLOMB_RICE = 8, + E_GAMMA = 9 +}; + +enum cram_external_type { + E_INT = 1, + E_LONG = 2, + E_BYTE = 3, + E_BYTE_ARRAY = 4, + E_BYTE_ARRAY_BLOCK = 5, +}; + +/* "File Definition Structure" */ +typedef struct { + char magic[4]; + uint8_t major_version; + uint8_t minor_version; + char file_id[20]; // Filename or SHA1 checksum +} cram_file_def; + +#define CRAM_1_VERS 100 // 1.0 +#define CRAM_2_VERS 200 // 1.1, or 2.0? + +struct cram_slice; + +enum cram_block_method { + BM_ERROR = -1, + RAW = 0, + GZIP = 1, + BZIP2 = 2, +}; + +enum cram_content_type { + CT_ERROR = -1, + FILE_HEADER = 0, + COMPRESSION_HEADER = 1, + MAPPED_SLICE = 2, + UNMAPPED_SLICE = 3, // CRAM_1_VERS only + EXTERNAL = 4, + CORE = 5, +}; + +/* Compression metrics */ +typedef struct { + int m1; + int m2; + int trial; + int next_trial; +} cram_metrics; + +/* Block */ +typedef struct { + enum cram_block_method method, orig_method; + enum cram_content_type content_type; + int32_t content_id; + int32_t comp_size; + int32_t uncomp_size; + int32_t idx; /* offset into data */ + unsigned char *data; + + // For bit I/O + size_t alloc; + size_t byte; + int bit; +} cram_block; + +struct cram_codec; /* defined in cram_codecs.h */ +struct cram_map; + +#define CRAM_MAP_HASH 32 +#define CRAM_MAP(a,b) (((a)*3+(b))&(CRAM_MAP_HASH-1)) + +/* Compression header block */ +typedef struct { + int32_t ref_seq_id; + int32_t ref_seq_start; + int32_t ref_seq_span; + int32_t num_records; + int32_t num_landmarks; + int32_t *landmark; + + /* Flags from preservation map */ + int mapped_qs_included; + int unmapped_qs_included; + int unmapped_placed; + int qs_included; + int read_names_included; + int AP_delta; + // indexed by ref-base and subst. code + char substitution_matrix[5][4]; + + // TD Dictionary as a concatenated block + cram_block *TD_blk; // Tag Dictionary + int nTL; // number of TL entries in TD + unsigned char **TL; // array of size nTL, pointer into TD_blk. + khash_t(m_s2i) *TD_hash; // Keyed on TD strings, map to TL[] indices + string_alloc_t *TD_keys; // Pooled keys for TD hash. + + khash_t(map) *preservation_map; + struct cram_map *rec_encoding_map[CRAM_MAP_HASH]; + struct cram_map *tag_encoding_map[CRAM_MAP_HASH]; + + struct cram_codec *BF_codec; // bam bit flags + struct cram_codec *CF_codec; // compression flags + struct cram_codec *RL_codec; // read length + struct cram_codec *AP_codec; // alignment pos + struct cram_codec *RG_codec; // read group + struct cram_codec *MF_codec; // mate flags + struct cram_codec *NS_codec; // next frag ref ID + struct cram_codec *NP_codec; // next frag pos + struct cram_codec *TS_codec; // template size + struct cram_codec *NF_codec; // next frag distance + struct cram_codec *TC_codec; // tag count CRAM_1_VERS + struct cram_codec *TN_codec; // tag name/type CRAM_1_VERS + struct cram_codec *TL_codec; // tag line CRAM_2_VERS + struct cram_codec *FN_codec; // no. features + struct cram_codec *FC_codec; // feature code + struct cram_codec *FP_codec; // feature pos + struct cram_codec *BS_codec; // base subst feature + struct cram_codec *IN_codec; // insertion feature + struct cram_codec *SC_codec; // soft-clip feature + struct cram_codec *DL_codec; // deletion len feature + struct cram_codec *BA_codec; // base feature + struct cram_codec *RS_codec; // ref skip length feature + struct cram_codec *PD_codec; // padding length feature + struct cram_codec *HC_codec; // hard clip length feature + struct cram_codec *MQ_codec; // mapping quality + struct cram_codec *RN_codec; // read names + struct cram_codec *QS_codec; // quality value (single) + struct cram_codec *Qs_codec; // quality values (string) + struct cram_codec *RI_codec; // ref ID + struct cram_codec *TM_codec; // ? + struct cram_codec *TV_codec; // ? + + char *uncomp; // A single block of uncompressed data + size_t uncomp_size, uncomp_alloc; +} cram_block_compression_hdr; + +typedef struct cram_map { + int key; /* 0xe0 + 3 bytes */ + enum cram_encoding encoding; + int offset; /* Offset into a single block of memory */ + int size; /* Size */ + struct cram_codec *codec; + struct cram_map *next; // for noddy internal hash +} cram_map; + +/* Mapped or unmapped slice header block */ +typedef struct { + enum cram_content_type content_type; + int32_t ref_seq_id; /* if content_type == MAPPED_SLICE */ + int32_t ref_seq_start; /* if content_type == MAPPED_SLICE */ + int32_t ref_seq_span; /* if content_type == MAPPED_SLICE */ + int32_t num_records; + int32_t record_counter; + int32_t num_blocks; + int32_t num_content_ids; + int32_t *block_content_ids; + int32_t ref_base_id; /* if content_type == MAPPED_SLICE */ + unsigned char md5[16]; +} cram_block_slice_hdr; + +struct ref_entry; + +/* + * Container. + * + * Conceptually a container is split into slices, and slices into blocks. + * However on disk it's just a list of blocks and we need to query the + * block types to identify the start/end points of the slices. + * + * OR... are landmarks the start/end points of slices? + */ +typedef struct { + int32_t length; + int32_t ref_seq_id; + int32_t ref_seq_start; + int32_t ref_seq_span; + int32_t record_counter; + int64_t num_bases; + int32_t num_records; + int32_t num_blocks; + int32_t num_landmarks; + int32_t *landmark; + + /* Size of container header above */ + size_t offset; + + /* Compression header is always the first block? */ + cram_block_compression_hdr *comp_hdr; + cram_block *comp_hdr_block; + + /* For construction purposes */ + int max_slice, curr_slice; // maximum number of slices + int max_rec, curr_rec; // current and max recs per slice + int max_c_rec, curr_c_rec; // current and max recs per container + int slice_rec; // rec no. for start of this slice + int curr_ref; // current ref ID. -2 for no previous + int last_pos; // last record position + struct cram_slice **slices, *slice; + int pos_sorted; // boolean, 1=>position sorted data + int max_apos; // maximum position, used if pos_sorted==0 + int last_slice; // number of reads in last slice (0 for 1st) + int multi_seq; // true if packing multi seqs per cont/slice + int unsorted; // true is AP_delta is 0. + + /* Copied from fd before encoding, to allow multi-threading */ + int ref_start, first_base, last_base, ref_id, ref_end; + char *ref; + //struct ref_entry *ref; + + /* For multi-threading */ + bam_seq_t **bams; + + /* Statistics for encoding */ + cram_stats *TS_stats; + cram_stats *RG_stats; + cram_stats *FP_stats; + cram_stats *NS_stats; + cram_stats *RN_stats; + cram_stats *CF_stats; + cram_stats *TN_stats; + cram_stats *BA_stats; + cram_stats *TV_stats; + cram_stats *BS_stats; + cram_stats *FC_stats; + cram_stats *BF_stats; + cram_stats *AP_stats; + cram_stats *NF_stats; + cram_stats *MF_stats; + cram_stats *FN_stats; + cram_stats *RL_stats; + cram_stats *DL_stats; + cram_stats *TC_stats; + cram_stats *TL_stats; + cram_stats *MQ_stats; + cram_stats *TM_stats; + cram_stats *QS_stats; + cram_stats *NP_stats; + cram_stats *RI_stats; + cram_stats *RS_stats; + cram_stats *PD_stats; + cram_stats *HC_stats; + + khash_t(s_i2i) *tags_used; // set of tag types in use, for tag encoding map + int *refs_used; // array of frequency of ref seq IDs +} cram_container; + +/* + * A single cram record + */ +typedef struct { + struct cram_slice *s; // Filled out by cram_decode only + + int32_t ref_id; // fixed for all recs in slice? + int32_t flags; // BF + int32_t cram_flags; // CF + int32_t len; // RL + int32_t apos; // AP + int32_t rg; // RG + int32_t name; // RN; idx to s->names_blk + int32_t name_len; + int32_t mate_line; // index to another cram_record + int32_t mate_ref_id; + int32_t mate_pos; // NP + int32_t tlen; // TS + + // Auxiliary data + int32_t ntags; // TC + int32_t aux; // idx to s->aux_blk + int32_t aux_size; // total size of packed ntags in aux_blk +#ifndef TN_external + int32_t TN_idx; // TN; idx to s->TN; +#else + int32_t tn; // idx to s->tn_blk +#endif + int TL; + + int32_t seq; // idx to s->seqs_blk + int32_t qual; // idx to s->qual_blk + int32_t cigar; // idx to s->cigar + int32_t ncigar; + int32_t aend; // alignment end + int32_t mqual; // MQ + + int32_t feature; // idx to s->feature + int32_t nfeature; // number of features + int32_t mate_flags; // MF +} cram_record; + +// Accessor macros as an analogue of the bam ones +#define cram_qname(c) (&(c)->s->name_blk->data[(c)->name]) +#define cram_seq(c) (&(c)->s->seqs_blk->data[(c)->seq]) +#define cram_qual(c) (&(c)->s->qual_blk->data[(c)->qual]) +#define cram_aux(c) (&(c)->s->aux_blk->data[(c)->aux]) +#define cram_seqi(c,i) (cram_seq((c))[(i)]) +#define cram_name_len(c) ((c)->name_len) +#define cram_strand(c) (((c)->flags & BAM_FREVERSE) != 0) +#define cram_mstrand(c) (((c)->flags & BAM_FMREVERSE) != 0) +#define cram_cigar(c) (&((cr)->s->cigar)[(c)->cigar]) + +/* + * A feature is a base difference, used for the sequence reference encoding. + * (We generate these internally when writing CRAM.) + */ +typedef struct { + union { + struct { + int pos; + int code; + int base; // substitution code + } X; + struct { + int pos; + int code; + int base; // actual base & qual + int qual; + } B; + struct { + int pos; + int code; + int qual; + } Q; + struct { + int pos; + int code; + int len; + int seq_idx; // soft-clip multiple bases + } S; + struct { + int pos; + int code; + int len; + int seq_idx; // insertion multiple bases + } I; + struct { + int pos; + int code; + int base; // insertion single base + } i; + struct { + int pos; + int code; + int len; + } D; + struct { + int pos; + int code; + int len; + } N; + struct { + int pos; + int code; + int len; + } P; + struct { + int pos; + int code; + int len; + } H; + }; +} cram_feature; + +/* + * A slice is really just a set of blocks, but it + * is the logical unit for decoding a number of + * sequences. + */ +typedef struct cram_slice { + cram_block_slice_hdr *hdr; + cram_block *hdr_block; + cram_block **block; + cram_block **block_by_id; + + /* State used during encoding/decoding */ + int last_apos, max_apos; + + /* Identifier used for auto-assigning read names */ + uint64_t id; + + /* Array of decoded cram records */ + cram_record *crecs; + + /* An dynamically growing buffers for data pointed + * to by crecs[] array. + */ + uint32_t *cigar; + uint32_t cigar_alloc; + uint32_t ncigar; + cram_block *name_blk; + cram_block *seqs_blk; + cram_block *qual_blk; + cram_block *aux_blk; + cram_block *base_blk; // substitutions (soft-clips for 1.0) + cram_block *soft_blk; // soft-clips + + cram_feature *features; + int nfeatures; + int afeatures; // allocated size of features + +#ifndef TN_external + // TN field (Tag Name) + uint32_t *TN; + int nTN, aTN; // used and allocated size for TN[] +#else + cram_block *tn_blk; + int tn_id; +#endif + + string_alloc_t *pair_keys; // Pooled keys for pair hash. + khash_t(m_s2i) *pair; // for identifying read-pairs in this slice. + + char *ref; // slice of current reference + int ref_start; // start position of current reference; + int ref_end; // end position of current reference; + +#ifdef BA_external + int BA_len; + int ba_id; +#endif + int ref_id; +} cram_slice; + +/*----------------------------------------------------------------------------- + * Consider moving reference handling to cram_refs.[ch] + */ +// from fa.fai / samtools faidx files +typedef struct ref_entry { + char *name; + char *fn; + int64_t length; + int64_t offset; + int bases_per_line; + int line_length; + int64_t count; // for shared references so we know to dealloc seq + char *seq; +} ref_entry; + +KHASH_MAP_INIT_STR(refs, ref_entry*) + +// References structure. +typedef struct { + string_alloc_t *pool; // String pool for holding filenames and SN vals + + khash_t(refs) *h_meta; // ref_entry*, index by name + ref_entry **ref_id; // ref_entry*, index by ID + int nref; // number of ref_entry + + char *fn; // current file opened + FILE *fp; // and the FILE* to go with it. + + int count; // how many cram_fd sharing this refs struct + + pthread_mutex_t lock; // Mutex for multi-threaded updating + ref_entry *last; // Last queried sequence + int last_id; // Used in cram_ref_decr_locked to delay free +} refs_t; + +/*----------------------------------------------------------------------------- + * CRAM index + * + * Detect format by number of entries per line. + * 5 => 1.0 (refid, start, nseq, C offset, slice) + * 6 => 1.1 (refid, start, span, C offset, S offset, S size) + * + * Indices are stored in a nested containment list, which is trivial to set + * up as the indices are on sorted data so we're appending to the nclist + * in sorted order. Basically if a slice entirely fits within a previous + * slice then we append to that slices list. This is done recursively. + * + * Lists are sorted on two dimensions: ref id + slice coords. + */ +typedef struct cram_index { + int nslice, nalloc; // total number of slices + struct cram_index *e; // array of size nslice + + int refid; // 1.0 1.1 + int start; // 1.0 1.1 + int end; // 1.1 + int nseq; // 1.0 - undocumented + int slice; // 1.0 landmark index, 1.1 landmark value + int len; // 1.1 - size of slice in bytes + int64_t offset; // 1.0 1.1 +} cram_index; + +typedef struct { + int refid; + int start; + int end; +} cram_range; + +/*----------------------------------------------------------------------------- + */ +/* CRAM File handle */ + +typedef struct spare_bams { + bam_seq_t **bams; + struct spare_bams *next; +} spare_bams; + +typedef struct cram_fd { + cram_FILE *fp; + int mode; // 'r' or 'w' + int version; + cram_file_def *file_def; + SAM_hdr *header; + + char *prefix; + int record_counter; + int slice_num; + int err; + + // Most recent compression header decoded + //cram_block_compression_hdr *comp_hdr; + //cram_block_slice_hdr *slice_hdr; + + // Current container being processed. + cram_container *ctr; + + // positions for encoding or decoding + int first_base, last_base; + + // cached reference portion + refs_t *refs; // ref meta-data structure + char *ref, *ref_free; // current portion held in memory + int ref_id; + int ref_start; + int ref_end; + char *ref_fn; // reference fasta filename + + // compression level and metrics + int level; + cram_metrics *m[7]; + + // options + int decode_md; // Whether to export MD and NM tags + int verbose; + int seqs_per_slice; + int slices_per_container; + int embed_ref; + int no_ref; + int ignore_md5; + int use_bz2; + int shared_ref; + cram_range range; + + // lookup tables, stored here so we can be trivially multi-threaded + unsigned int bam_flag_swap[0x1000]; // cram -> bam flags + unsigned int cram_flag_swap[0x1000];// bam -> cram flags + unsigned char L1[256]; // ACGT{*} ->0123{4} + unsigned char L2[256]; // ACGTN{*}->01234{5} + char cram_sub_matrix[32][32]; // base substituion codes + + int index_sz; + cram_index *index; // array, sizeof index_sz + off_t first_container; + int eof; + int last_slice; // number of recs encoded in last slice + int multi_seq; + int unsorted; + int empty_container; // Marker for EOF block + + // thread pool + int own_pool; + t_pool *pool; + t_results_queue *rqueue; + pthread_mutex_t metrics_lock; + pthread_mutex_t ref_lock; + spare_bams *bl; + pthread_mutex_t bam_list_lock; + void *job_pending; + int ooc; // out of containers. +} cram_fd; + +enum cram_option { + CRAM_OPT_DECODE_MD, + CRAM_OPT_PREFIX, + CRAM_OPT_VERBOSITY, + CRAM_OPT_SEQS_PER_SLICE, + CRAM_OPT_SLICES_PER_CONTAINER, + CRAM_OPT_RANGE, + CRAM_OPT_VERSION, + CRAM_OPT_EMBED_REF, + CRAM_OPT_IGNORE_MD5, + CRAM_OPT_REFERENCE, + CRAM_OPT_MULTI_SEQ_PER_SLICE, + CRAM_OPT_NO_REF, + CRAM_OPT_USE_BZIP2, + CRAM_OPT_SHARED_REF, + CRAM_OPT_NTHREADS, + CRAM_OPT_THREAD_POOL, +}; + +/* BF bitfields */ +/* Corrected in 1.1. Use bam_flag_swap[bf] and BAM_* macros for 1.0 & 1.1 */ +#define CRAM_FPAIRED 256 +#define CRAM_FPROPER_PAIR 128 +#define CRAM_FUNMAP 64 +#define CRAM_FREVERSE 32 +#define CRAM_FREAD1 16 +#define CRAM_FREAD2 8 +#define CRAM_FSECONDARY 4 +#define CRAM_FQCFAIL 2 +#define CRAM_FDUP 1 + +#define CRAM_M_REVERSE 1 +#define CRAM_M_UNMAP 2 + + +/* CF bitfields */ +#define CRAM_FLAG_PRESERVE_QUAL_SCORES (1<<0) +#define CRAM_FLAG_DETACHED (1<<1) +#define CRAM_FLAG_MATE_DOWNSTREAM (1<<2) + +/* External IDs used by this implementation (only assumed during writing) */ +#define CRAM_EXT_IN 0 +#define CRAM_EXT_QUAL 1 +#define CRAM_EXT_NAME 2 +#define CRAM_EXT_TS_NP 3 +#define CRAM_EXT_TAG 4 +#define CRAM_EXT_TAG_S "\004" +#define CRAM_EXT_BA 5 +#define CRAM_EXT_TN 6 +#define CRAM_EXT_SC 7 +#define CRAM_EXT_REF 8 + +#ifdef __cplusplus +} +#endif + +#endif /* _CRAM_STRUCTS_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/files.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/files.c new file mode 100644 index 0000000000000000000000000000000000000000..48f5c32d4beb5e06fa6f83dbda8ee05b1c48a4d8 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/files.c @@ -0,0 +1,76 @@ +/* +Copyright (c) 1994, 1996-1997, 2000, 2003 MEDICAL RESEARCH COUNCIL +All rights reserved + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1 Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2 Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF +MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or +promote products derived from this software without specific prior written +permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#ifdef HAVE_CONFIG_H +#include "io_lib_config.h" +#endif + +#include "cram/misc.h" + +#include +#include +/* Alliant's Concentrix is hugely deficient */ +/* Define things we require in this program */ +/* Methinks S_IFMT and S_IFDIR aren't defined in POSIX */ +#ifndef S_ISDIR +#define S_ISDIR(m) (((m)&S_IFMT) == S_IFDIR) +#endif /*!S_ISDIR*/ +#ifndef S_ISREG +#define S_ISREG(m) (((m)&S_IFMT) == S_IFREG) +#endif /*!S_ISREG*/ + +int is_directory(char * fn) +{ + struct stat buf; + if ( stat(fn,&buf) ) return 0; + return S_ISDIR(buf.st_mode); +} + +int is_file(char * fn) +{ + struct stat buf; + if ( stat(fn,&buf) ) return 0; + return S_ISREG(buf.st_mode); +} + +int file_exists(char * fn) +{ + struct stat buf; + return ( stat(fn,&buf) == 0); +} + +int file_size(char * fn) +{ + struct stat buf; + if ( stat(fn,&buf) != 0) return 0; + return buf.st_size; +} + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/mFILE.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/mFILE.c new file mode 100644 index 0000000000000000000000000000000000000000..6407b7693813253d4f02c66416f05880f8335cba --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/mFILE.c @@ -0,0 +1,634 @@ +/* +Copyright (c) 2005-2006, 2008-2009, 2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + + +#ifdef HAVE_CONFIG_H +#include "io_lib_config.h" +#endif + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "cram/os.h" +#include "cram/mFILE.h" +#include "cram/vlen.h" + +/* + * This file contains memory-based versions of the most commonly used + * (by io_lib) stdio functions. + * + * Actual file IO takes place either on opening or closing an mFILE. + * + * Coupled to this are a bunch of rather scary macros which can be obtained + * by including stdio_hack.h. It is recommended though that you use mFILE.h + * instead and replace fopen with mfopen (etc). This is more or less + * mandatory if you wish to use both FILE and mFILE structs in a single file. + */ + +static mFILE *m_channel[3]; /* stdin, stdout and stderr fakes */ + +/* + * Reads the entirety of fp into memory. If 'fn' exists it is the filename + * associated with fp. This will be used for more optimal reading (via a + * stat to identify the size and a single read). Otherwise we use successive + * reads until EOF. + * + * Returns a malloced buffer on success of length *size + * NULL on failure + */ +static char *mfload(FILE *fp, const char *fn, size_t *size, int binary) { + struct stat sb; + char *data = NULL; + size_t allocated = 0, used = 0; + int bufsize = 8192; + +#ifdef _WIN32 + if (binary) + _setmode(_fileno(fp), _O_BINARY); + else + _setmode(_fileno(fp), _O_TEXT); +#endif + + if (fn && -1 != stat(fn, &sb)) { + data = malloc(allocated = sb.st_size); + bufsize = sb.st_size; + } else { + fn = NULL; + } + + do { + size_t len; + if (used + bufsize > allocated) { + allocated += bufsize; + data = realloc(data, allocated); + } + len = fread(data + used, 1, allocated - used, fp); + if (len > 0) + used += len; + } while (!feof(fp) && (fn == NULL || used < sb.st_size)); + + *size = used; + + return data; +} + +/* + * Creates and returns m_channel[0]. + * We initialise this on the first attempted read, which then slurps in + * all of stdin until EOF is met. + */ +mFILE *mstdin(void) { + if (m_channel[0]) + return m_channel[0]; + + m_channel[0] = mfcreate(NULL, 0); + if (NULL == m_channel[0]) return NULL; + m_channel[0]->fp = stdin; + return m_channel[0]; +} + +static void init_mstdin(void) { + static int done_stdin = 0; + if (done_stdin) + return; + + m_channel[0]->data = mfload(stdin, NULL, &m_channel[0]->size, 1); + m_channel[0]->mode = MF_READ; + done_stdin = 1; +} + +/* + * Creates and returns m_channel[1]. This is the fake for stdout. It starts as + * an empty buffer which is physically written out only when mfflush or + * mfclose are called. + */ +mFILE *mstdout(void) { + if (m_channel[1]) + return m_channel[1]; + + m_channel[1] = mfcreate(NULL, 0); + if (NULL == m_channel[1]) return NULL; + m_channel[1]->fp = stdout; + m_channel[1]->mode = MF_WRITE; + return m_channel[1]; +} + +/* + * Stderr as an mFILE. + * The code handles stderr by returning m_channel[2], but also checking + * for stderr in fprintf (the common usage of it) to auto-flush. + */ +mFILE *mstderr(void) { + if (m_channel[2]) + return m_channel[2]; + + m_channel[2] = mfcreate(NULL, 0); + if (NULL == m_channel[2]) return NULL; + m_channel[2]->fp = stderr; + m_channel[2]->mode = MF_WRITE; + return m_channel[2]; +} + + +/* + * For creating existing mFILE pointers directly from memory buffers. + */ +mFILE *mfcreate(char *data, int size) { + mFILE *mf = (mFILE *)malloc(sizeof(*mf)); + if (NULL == mf) return NULL; + mf->fp = NULL; + mf->data = data; + mf->alloced = size; + mf->size = size; + mf->eof = 0; + mf->offset = 0; + mf->flush_pos = 0; + mf->mode = MF_READ | MF_WRITE; + return mf; +} + +/* + * Recreate an existing mFILE to house new data/size. + * It also rewinds the file. + */ +void mfrecreate(mFILE *mf, char *data, int size) { + if (mf->data) + free(mf->data); + mf->data = data; + mf->size = size; + mf->alloced = size; + mf->eof = 0; + mf->offset = 0; + mf->flush_pos = 0; +} + + +/* + * Creates a new mFILE to contain the contents of the FILE pointer. + * This mFILE is purely for in-memory operations and has no links to the + * original FILE* it came from. It also doesn't close the FILE pointer. + * Consider using mfreopen() is you need different behaviour. + * + * Returns mFILE * on success + * NULL on failure. + */ +mFILE *mfcreate_from(const char *path, const char *mode_str, FILE *fp) { + mFILE *mf; + + /* Open using mfreopen() */ + if (NULL == (mf = mfreopen(path, mode_str, fp))) + return NULL; + + /* Disassociate from the input stream */ + mf->fp = NULL; + + return mf; +} + +/* + * Converts a FILE * to an mFILE *. + * Use this for wrapper functions to turn external prototypes requring + * FILE * as an argument into internal code using mFILE *. + */ +mFILE *mfreopen(const char *path, const char *mode_str, FILE *fp) { + mFILE *mf; + int r = 0, w = 0, a = 0, b = 0, x = 0, mode = 0; + + /* Parse mode: + * r = read file contents (if truncated => don't read) + * w = write on close + * a = position at end of buffer + * x = position at same location as the original fp, don't seek on flush + */ + if (strchr(mode_str, 'r')) + r = 1, mode |= MF_READ; + if (strchr(mode_str, 'w')) + w = 1, mode |= MF_WRITE | MF_TRUNC; + if (strchr(mode_str, 'a')) + w = a = 1, mode |= MF_WRITE | MF_APPEND; + if (strchr(mode_str, 'b')) + b = 1, mode |= MF_BINARY; + if (strchr(mode_str, 'x')) + x = 1; + if (strchr(mode_str, '+')) { + w = 1, mode |= MF_READ | MF_WRITE; + if (a) + r = 1; + } + + if (r) { + mf = mfcreate(NULL, 0); + if (NULL == mf) return NULL; + if (!(mode & MF_TRUNC)) { + mf->data = mfload(fp, path, &mf->size, b); + mf->alloced = mf->size; + if (!a) + fseek(fp, 0, SEEK_SET); + } + } else if (w) { + /* Write - initialise the data structures */ + mf = mfcreate(NULL, 0); + if (NULL == mf) return NULL; + } else { + fprintf(stderr, "Must specify either r, w or a for mode\n"); + return NULL; + } + mf->fp = fp; + mf->mode = mode; + + if (x) { + mf->mode |= MF_MODEX; + } + + if (a) { + mf->flush_pos = mf->size; + fseek(fp, 0, SEEK_END); + } + + return mf; +} + +/* + * Opens a file. If we have read access (r or a+) then it loads the entire + * file into memory. If We have write access then the pathname is stored. + * We do not actually write until an mfclose, which then checks this pathname. + */ +mFILE *mfopen(const char *path, const char *mode) { + FILE *fp; + + if (NULL == (fp = fopen(path, mode))) + return NULL; + return mfreopen(path, mode, fp); +} + +/* + * Closes an mFILE. If the filename is known (implying write access) then this + * also writes the data to disk. + * + * Stdout is handled by calling mfflush which writes to stdout if appropriate. + */ +int mfclose(mFILE *mf) { + if (!mf) + return -1; + + mfflush(mf); + + if (mf->fp) + fclose(mf->fp); + + mfdestroy(mf); + + return 0; +} + +/* + * Closes the file pointer contained within the mFILE without destroying + * the in-memory data. + */ +int mfdetach(mFILE *mf) { + if (!mf) + return -1; + + mfflush(mf); + + if (mf->fp) { + fclose(mf->fp); + mf->fp = NULL; + } + + return 0; +} + +/* + * Destroys an mFILE structure but does not flush or close it + */ +int mfdestroy(mFILE *mf) { + if (!mf) + return -1; + + if (mf->data) + free(mf->data); + free(mf); + + return 0; +} + +/* + * Steals that data out of an mFILE. The mFILE itself will be closed. + * It is up to the caller to free the stolen buffer. If size_out is + * not NULL, mf->size will be stored in it. + * This is more-or-less the opposite of mfcreate(). + */ + +void *mfsteal(mFILE *mf, size_t *size_out) { + void *data; + + if (!mf) return NULL; + + data = mf->data; + + if (NULL != size_out) *size_out = mf->size; + + mfdetach(mf); + mf->data = NULL; + mfdestroy(mf); + + return data; +} + +/* + * Seek/tell functions. Nothing more than updating and reporting an + * in-memory index. NB we can seek on stdin or stdout even provided we + * haven't been flushing. + */ +int mfseek(mFILE *mf, long offset, int whence) { + switch (whence) { + case SEEK_SET: + mf->offset = offset; + break; + case SEEK_CUR: + mf->offset += offset; + break; + case SEEK_END: + mf->offset = mf->size + offset; + break; + default: + errno = EINVAL; + return -1; + } + + mf->eof = 0; + return 0; +} + +long mftell(mFILE *mf) { + return mf->offset; +} + +void mrewind(mFILE *mf) { + mf->offset = 0; + mf->eof = 0; +} + +/* + * mftruncate is not directly a translation of ftruncate as the latter + * takes a file descriptor instead of a FILE *. It performs the analogous + * role though. + * + * If offset is -1 then the file is truncated to be the current file + * offset. + */ +void mftruncate(mFILE *mf, long offset) { + mf->size = offset != -1 ? offset : mf->offset; + if (mf->offset > mf->size) + mf->offset = mf->size; +} + +int mfeof(mFILE *mf) { + return mf->eof; +} + +/* + * mFILE read/write functions. Basically these turn fread/fwrite syntax + * into memcpy statements, with appropriate memory handling for writing. + */ +size_t mfread(void *ptr, size_t size, size_t nmemb, mFILE *mf) { + size_t len; + char *cptr = (char *)ptr; + + if (mf == m_channel[0]) init_mstdin(); + + if (mf->size <= mf->offset) + return 0; + + len = size * nmemb <= mf->size - mf->offset + ? size * nmemb + : mf->size - mf->offset; + if (!size) + return 0; + + memcpy(cptr, &mf->data[mf->offset], len); + mf->offset += len; + + if (len != size * nmemb) { + mf->eof = 1; + } + + return len / size; +} + +size_t mfwrite(void *ptr, size_t size, size_t nmemb, mFILE *mf) { + if (!(mf->mode & MF_WRITE)) + return 0; + + /* Append mode => forced all writes to end of file */ + if (mf->mode & MF_APPEND) + mf->offset = mf->size; + + /* Make sure we have enough room */ + while (size * nmemb + mf->offset > mf->alloced) { + size_t new_alloced = mf->alloced ? mf->alloced * 2 : 1024; + void * new_data = realloc(mf->data, new_alloced); + if (NULL == new_data) return 0; + mf->alloced = new_alloced; + mf->data = new_data; + } + + /* Record where we need to reflush from */ + if (mf->offset < mf->flush_pos) + mf->flush_pos = mf->offset; + + /* Copy the data over */ + memcpy(&mf->data[mf->offset], ptr, size * nmemb); + mf->offset += size * nmemb; + if (mf->size < mf->offset) + mf->size = mf->offset; + + return nmemb; +} + +int mfgetc(mFILE *mf) { + if (mf == m_channel[0]) init_mstdin(); + if (mf->offset < mf->size) { + return (unsigned char)mf->data[mf->offset++]; + } + + mf->eof = 1; + return -1; +} + +int mungetc(int c, mFILE *mf) { + if (mf->offset > 0) { + mf->data[--mf->offset] = c; + return c; + } + + mf->eof = 1; + return -1; +} + +char *mfgets(char *s, int size, mFILE *mf) { + int i; + + if (mf == m_channel[0]) init_mstdin(); + *s = 0; + for (i = 0; i < size-1;) { + if (mf->offset < mf->size) { + s[i] = mf->data[mf->offset++]; + if (s[i++] == '\n') + break; + } else { + mf->eof = 1; + break; + } + } + + s[i] = 0; + return i ? s : NULL; +} + +/* + * Flushes an mFILE. If this is a real open of a file in write mode then + * mFILE->fp will be set. We then write out any new data in mFILE since the + * last flush. We cannot tell what may have been modified as we don't keep + * track of that, so we typically rewrite out the entire file contents between + * the last flush_pos and the end of file. + * + * For stderr/stdout we also reset the offsets so we cannot modify things + * we've already output. + */ +int mfflush(mFILE *mf) { + if (!mf->fp) + return 0; + + /* FIXME: only do this when opened in write mode */ + if (mf == m_channel[1] || mf == m_channel[2]) { + if (mf->flush_pos < mf->size) { + size_t bytes = mf->size - mf->flush_pos; + if (fwrite(mf->data + mf->flush_pos, 1, bytes, mf->fp) < bytes) + return -1; + if (0 != fflush(mf->fp)) + return -1; + } + + /* Stdout & stderr are non-seekable streams so throw away the data */ + mf->offset = mf->size = mf->flush_pos = 0; + } + + /* only flush when opened in write mode */ + if (mf->mode & MF_WRITE) { + if (mf->flush_pos < mf->size) { + size_t bytes = mf->size - mf->flush_pos; + if (!(mf->mode & MF_MODEX)) { + fseek(mf->fp, mf->flush_pos, SEEK_SET); + } + if (fwrite(mf->data + mf->flush_pos, 1, bytes, mf->fp) < bytes) + return -1; + if (0 != fflush(mf->fp)) + return -1; + } + if (ftell(mf->fp) != -1 && + ftruncate(fileno(mf->fp), ftell(mf->fp)) == -1) + return -1; + mf->flush_pos = mf->size; + } + + return 0; +} + +/* + * A wrapper around vsprintf() to write to an mFILE. This also uses vflen() to + * estimate how many additional bytes of storage will be required for the + * vsprintf to work. + */ +int mfprintf(mFILE *mf, char *fmt, ...) { + int ret; + size_t est_length; + va_list args; + + va_start(args, fmt); + est_length = vflen(fmt, args); + va_end(args); + while (est_length + mf->offset > mf->alloced) { + size_t new_alloced = mf->alloced ? mf->alloced * 2 : 1024; + void * new_data = realloc(mf->data, new_alloced); + if (NULL == new_data) return -1; + mf->alloced = new_alloced; + mf->data = new_data; + } + + va_start(args, fmt); + ret = vsprintf(&mf->data[mf->offset], fmt, args); + va_end(args); + + if (ret > 0) { + mf->offset += ret; + if (mf->size < mf->offset) + mf->size = mf->offset; + } + + if (mf->fp == stderr) { + /* Auto-flush for stderr */ + if (0 != mfflush(mf)) return -1; + } + + return ret; +} + +/* + * Converts an mFILE from binary to ascii mode by replacing all + * cr-nl with nl. + * + * Primarily used on windows when we've uncompressed a binary file which + * happens to be a text file (eg Experiment File). Previously we would have + * seeked back to the start and used _setmode(fileno(fp), _O_TEXT). + * + * Side effect: resets offset and flush_pos back to the start. + */ +void mfascii(mFILE *mf) { + size_t p1, p2; + + for (p1 = p2 = 1; p1 < mf->size; p1++, p2++) { + if (mf->data[p1] == '\n' && mf->data[p1-1] == '\r') { + p2--; /* delete the \r */ + } + mf->data[p2] = mf->data[p1]; + } + mf->size = p2; + + mf->offset = mf->flush_pos = 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/mFILE.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/mFILE.h new file mode 100644 index 0000000000000000000000000000000000000000..5ded9a542d9064bafe4f9f00364a76a40c957db4 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/mFILE.h @@ -0,0 +1,88 @@ +/* +Copyright (c) 2005-2006, 2008-2009 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifndef _MFILE_H_ +#define _MFILE_H_ + +#include + +#ifdef __cplusplus +extern "C" { +#endif + +typedef struct { + FILE *fp; + char *data; + size_t alloced; + int eof; + int mode; /* open mode in MF_?? define bit pattern */ + size_t size; + size_t offset; + size_t flush_pos; +} mFILE; + +#define MF_READ 1 +#define MF_WRITE 2 +#define MF_APPEND 4 +#define MF_BINARY 8 +#define MF_TRUNC 16 +#define MF_MODEX 32 + +mFILE *mfreopen(const char *path, const char *mode, FILE *fp); +mFILE *mfopen(const char *path, const char *mode); +int mfdetach(mFILE *mf); +int mfclose(mFILE *mf); +int mfdestroy(mFILE *mf); +int mfseek(mFILE *mf, long offset, int whence); +long mftell(mFILE *mf); +void mrewind(mFILE *mf); +void mftruncate(mFILE *mf, long offset); +int mfeof(mFILE *mf); +size_t mfread(void *ptr, size_t size, size_t nmemb, mFILE *mf); +size_t mfwrite(void *ptr, size_t size, size_t nmemb, mFILE *mf); +int mfgetc(mFILE *mf); +int mungetc(int c, mFILE *mf); +mFILE *mfcreate(char *data, int size); +mFILE *mfcreate_from(const char *path, const char *mode_str, FILE *fp); +void mfrecreate(mFILE *mf, char *data, int size); +void *mfsteal(mFILE *mf, size_t *size_out); +char *mfgets(char *s, int size, mFILE *mf); +int mfflush(mFILE *mf); +int mfprintf(mFILE *mf, char *fmt, ...); +mFILE *mstdin(void); +mFILE *mstdout(void); +mFILE *mstderr(void); +void mfascii(mFILE *mf); + +#ifdef __cplusplus +} +#endif + +#endif /* _MFILE_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/md5.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/md5.c new file mode 100644 index 0000000000000000000000000000000000000000..68123c0fcb25fba4cc42d1b4f26e3f34ce96d5b1 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/md5.c @@ -0,0 +1,295 @@ +/* + * This is an OpenSSL-compatible implementation of the RSA Data Security, Inc. + * MD5 Message-Digest Algorithm (RFC 1321). + * + * Homepage: + * http://openwall.info/wiki/people/solar/software/public-domain-source-code/md5 + * + * Author: + * Alexander Peslyak, better known as Solar Designer + * + * This software was written by Alexander Peslyak in 2001. No copyright is + * claimed, and the software is hereby placed in the public domain. + * In case this attempt to disclaim copyright and place the software in the + * public domain is deemed null and void, then the software is + * Copyright (c) 2001 Alexander Peslyak and it is hereby released to the + * general public under the following terms: + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted. + * + * There's ABSOLUTELY NO WARRANTY, express or implied. + * + * (This is a heavily cut-down "BSD license".) + * + * This differs from Colin Plumb's older public domain implementation in that + * no exactly 32-bit integer data type is required (any 32-bit or wider + * unsigned integer data type will do), there's no compile-time endianness + * configuration, and the function prototypes match OpenSSL's. No code from + * Colin Plumb's implementation has been reused; this comment merely compares + * the properties of the two independent implementations. + * + * The primary goals of this implementation are portability and ease of use. + * It is meant to be fast, but not as fast as possible. Some known + * optimizations are not included to reduce source code size and avoid + * compile-time configuration. + */ + +#ifndef HAVE_OPENSSL + +#include + +#include "md5.h" + +/* + * The basic MD5 functions. + * + * F and G are optimized compared to their RFC 1321 definitions for + * architectures that lack an AND-NOT instruction, just like in Colin Plumb's + * implementation. + */ +#define F(x, y, z) ((z) ^ ((x) & ((y) ^ (z)))) +#define G(x, y, z) ((y) ^ ((z) & ((x) ^ (y)))) +#define H(x, y, z) ((x) ^ (y) ^ (z)) +#define I(x, y, z) ((y) ^ ((x) | ~(z))) + +/* + * The MD5 transformation for all four rounds. + */ +#define STEP(f, a, b, c, d, x, t, s) \ + (a) += f((b), (c), (d)) + (x) + (t); \ + (a) = (((a) << (s)) | (((a) & 0xffffffff) >> (32 - (s)))); \ + (a) += (b); + +/* + * SET reads 4 input bytes in little-endian byte order and stores them + * in a properly aligned word in host byte order. + * + * The check for little-endian architectures that tolerate unaligned + * memory accesses is just an optimization. Nothing will break if it + * doesn't work. + */ +#if defined(__i386__) || defined(__x86_64__) || defined(__vax__) +#define SET(n) \ + (*(MD5_u32plus *)&ptr[(n) * 4]) +#define GET(n) \ + SET(n) +#else +#define SET(n) \ + (ctx->block[(n)] = \ + (MD5_u32plus)ptr[(n) * 4] | \ + ((MD5_u32plus)ptr[(n) * 4 + 1] << 8) | \ + ((MD5_u32plus)ptr[(n) * 4 + 2] << 16) | \ + ((MD5_u32plus)ptr[(n) * 4 + 3] << 24)) +#define GET(n) \ + (ctx->block[(n)]) +#endif + +/* + * This processes one or more 64-byte data blocks, but does NOT update + * the bit counters. There are no alignment requirements. + */ +static void *body(MD5_CTX *ctx, void *data, unsigned long size) +{ + unsigned char *ptr; + MD5_u32plus a, b, c, d; + MD5_u32plus saved_a, saved_b, saved_c, saved_d; + + ptr = data; + + a = ctx->a; + b = ctx->b; + c = ctx->c; + d = ctx->d; + + do { + saved_a = a; + saved_b = b; + saved_c = c; + saved_d = d; + +/* Round 1 */ + STEP(F, a, b, c, d, SET(0), 0xd76aa478, 7) + STEP(F, d, a, b, c, SET(1), 0xe8c7b756, 12) + STEP(F, c, d, a, b, SET(2), 0x242070db, 17) + STEP(F, b, c, d, a, SET(3), 0xc1bdceee, 22) + STEP(F, a, b, c, d, SET(4), 0xf57c0faf, 7) + STEP(F, d, a, b, c, SET(5), 0x4787c62a, 12) + STEP(F, c, d, a, b, SET(6), 0xa8304613, 17) + STEP(F, b, c, d, a, SET(7), 0xfd469501, 22) + STEP(F, a, b, c, d, SET(8), 0x698098d8, 7) + STEP(F, d, a, b, c, SET(9), 0x8b44f7af, 12) + STEP(F, c, d, a, b, SET(10), 0xffff5bb1, 17) + STEP(F, b, c, d, a, SET(11), 0x895cd7be, 22) + STEP(F, a, b, c, d, SET(12), 0x6b901122, 7) + STEP(F, d, a, b, c, SET(13), 0xfd987193, 12) + STEP(F, c, d, a, b, SET(14), 0xa679438e, 17) + STEP(F, b, c, d, a, SET(15), 0x49b40821, 22) + +/* Round 2 */ + STEP(G, a, b, c, d, GET(1), 0xf61e2562, 5) + STEP(G, d, a, b, c, GET(6), 0xc040b340, 9) + STEP(G, c, d, a, b, GET(11), 0x265e5a51, 14) + STEP(G, b, c, d, a, GET(0), 0xe9b6c7aa, 20) + STEP(G, a, b, c, d, GET(5), 0xd62f105d, 5) + STEP(G, d, a, b, c, GET(10), 0x02441453, 9) + STEP(G, c, d, a, b, GET(15), 0xd8a1e681, 14) + STEP(G, b, c, d, a, GET(4), 0xe7d3fbc8, 20) + STEP(G, a, b, c, d, GET(9), 0x21e1cde6, 5) + STEP(G, d, a, b, c, GET(14), 0xc33707d6, 9) + STEP(G, c, d, a, b, GET(3), 0xf4d50d87, 14) + STEP(G, b, c, d, a, GET(8), 0x455a14ed, 20) + STEP(G, a, b, c, d, GET(13), 0xa9e3e905, 5) + STEP(G, d, a, b, c, GET(2), 0xfcefa3f8, 9) + STEP(G, c, d, a, b, GET(7), 0x676f02d9, 14) + STEP(G, b, c, d, a, GET(12), 0x8d2a4c8a, 20) + +/* Round 3 */ + STEP(H, a, b, c, d, GET(5), 0xfffa3942, 4) + STEP(H, d, a, b, c, GET(8), 0x8771f681, 11) + STEP(H, c, d, a, b, GET(11), 0x6d9d6122, 16) + STEP(H, b, c, d, a, GET(14), 0xfde5380c, 23) + STEP(H, a, b, c, d, GET(1), 0xa4beea44, 4) + STEP(H, d, a, b, c, GET(4), 0x4bdecfa9, 11) + STEP(H, c, d, a, b, GET(7), 0xf6bb4b60, 16) + STEP(H, b, c, d, a, GET(10), 0xbebfbc70, 23) + STEP(H, a, b, c, d, GET(13), 0x289b7ec6, 4) + STEP(H, d, a, b, c, GET(0), 0xeaa127fa, 11) + STEP(H, c, d, a, b, GET(3), 0xd4ef3085, 16) + STEP(H, b, c, d, a, GET(6), 0x04881d05, 23) + STEP(H, a, b, c, d, GET(9), 0xd9d4d039, 4) + STEP(H, d, a, b, c, GET(12), 0xe6db99e5, 11) + STEP(H, c, d, a, b, GET(15), 0x1fa27cf8, 16) + STEP(H, b, c, d, a, GET(2), 0xc4ac5665, 23) + +/* Round 4 */ + STEP(I, a, b, c, d, GET(0), 0xf4292244, 6) + STEP(I, d, a, b, c, GET(7), 0x432aff97, 10) + STEP(I, c, d, a, b, GET(14), 0xab9423a7, 15) + STEP(I, b, c, d, a, GET(5), 0xfc93a039, 21) + STEP(I, a, b, c, d, GET(12), 0x655b59c3, 6) + STEP(I, d, a, b, c, GET(3), 0x8f0ccc92, 10) + STEP(I, c, d, a, b, GET(10), 0xffeff47d, 15) + STEP(I, b, c, d, a, GET(1), 0x85845dd1, 21) + STEP(I, a, b, c, d, GET(8), 0x6fa87e4f, 6) + STEP(I, d, a, b, c, GET(15), 0xfe2ce6e0, 10) + STEP(I, c, d, a, b, GET(6), 0xa3014314, 15) + STEP(I, b, c, d, a, GET(13), 0x4e0811a1, 21) + STEP(I, a, b, c, d, GET(4), 0xf7537e82, 6) + STEP(I, d, a, b, c, GET(11), 0xbd3af235, 10) + STEP(I, c, d, a, b, GET(2), 0x2ad7d2bb, 15) + STEP(I, b, c, d, a, GET(9), 0xeb86d391, 21) + + a += saved_a; + b += saved_b; + c += saved_c; + d += saved_d; + + ptr += 64; + } while (size -= 64); + + ctx->a = a; + ctx->b = b; + ctx->c = c; + ctx->d = d; + + return ptr; +} + +void MD5_Init(MD5_CTX *ctx) +{ + ctx->a = 0x67452301; + ctx->b = 0xefcdab89; + ctx->c = 0x98badcfe; + ctx->d = 0x10325476; + + ctx->lo = 0; + ctx->hi = 0; +} + +void MD5_Update(MD5_CTX *ctx, void *data, unsigned long size) +{ + MD5_u32plus saved_lo; + unsigned long used, free; + + saved_lo = ctx->lo; + if ((ctx->lo = (saved_lo + size) & 0x1fffffff) < saved_lo) + ctx->hi++; + ctx->hi += size >> 29; + + used = saved_lo & 0x3f; + + if (used) { + free = 64 - used; + + if (size < free) { + memcpy(&ctx->buffer[used], data, size); + return; + } + + memcpy(&ctx->buffer[used], data, free); + data = (unsigned char *)data + free; + size -= free; + body(ctx, ctx->buffer, 64); + } + + if (size >= 64) { + data = body(ctx, data, size & ~(unsigned long)0x3f); + size &= 0x3f; + } + + memcpy(ctx->buffer, data, size); +} + +void MD5_Final(unsigned char *result, MD5_CTX *ctx) +{ + unsigned long used, free; + + used = ctx->lo & 0x3f; + + ctx->buffer[used++] = 0x80; + + free = 64 - used; + + if (free < 8) { + memset(&ctx->buffer[used], 0, free); + body(ctx, ctx->buffer, 64); + used = 0; + free = 64; + } + + memset(&ctx->buffer[used], 0, free - 8); + + ctx->lo <<= 3; + ctx->buffer[56] = ctx->lo; + ctx->buffer[57] = ctx->lo >> 8; + ctx->buffer[58] = ctx->lo >> 16; + ctx->buffer[59] = ctx->lo >> 24; + ctx->buffer[60] = ctx->hi; + ctx->buffer[61] = ctx->hi >> 8; + ctx->buffer[62] = ctx->hi >> 16; + ctx->buffer[63] = ctx->hi >> 24; + + body(ctx, ctx->buffer, 64); + + result[0] = ctx->a; + result[1] = ctx->a >> 8; + result[2] = ctx->a >> 16; + result[3] = ctx->a >> 24; + result[4] = ctx->b; + result[5] = ctx->b >> 8; + result[6] = ctx->b >> 16; + result[7] = ctx->b >> 24; + result[8] = ctx->c; + result[9] = ctx->c >> 8; + result[10] = ctx->c >> 16; + result[11] = ctx->c >> 24; + result[12] = ctx->d; + result[13] = ctx->d >> 8; + result[14] = ctx->d >> 16; + result[15] = ctx->d >> 24; + + memset(ctx, 0, sizeof(*ctx)); +} + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/md5.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/md5.h new file mode 100644 index 0000000000000000000000000000000000000000..6b065a10c831aa8c6923f088c00fd49b5bf61d6a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/md5.h @@ -0,0 +1,54 @@ +#ifdef __cplusplus +extern "C" { +#endif + +/* + * This is an OpenSSL-compatible implementation of the RSA Data Security, Inc. + * MD5 Message-Digest Algorithm (RFC 1321). + * + * Homepage: + * http://openwall.info/wiki/people/solar/software/public-domain-source-code/md5 + * + * Author: + * Alexander Peslyak, better known as Solar Designer + * + * This software was written by Alexander Peslyak in 2001. No copyright is + * claimed, and the software is hereby placed in the public domain. + * In case this attempt to disclaim copyright and place the software in the + * public domain is deemed null and void, then the software is + * Copyright (c) 2001 Alexander Peslyak and it is hereby released to the + * general public under the following terms: + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted. + * + * There's ABSOLUTELY NO WARRANTY, express or implied. + * + * See md5.c for more information. + */ + +#ifdef HAVE_OPENSSL +#include +#elif !defined(_MD5_H) +#define _MD5_H + +/* Any 32-bit or wider unsigned integer data type will do */ +typedef unsigned int MD5_u32plus; + +typedef struct { + MD5_u32plus lo, hi; + MD5_u32plus a, b, c, d; + unsigned char buffer[64]; + MD5_u32plus block[16]; +} MD5_CTX; + +extern void MD5_Init(MD5_CTX *ctx); +extern void MD5_Update(MD5_CTX *ctx, void *data, unsigned long size); +extern void MD5_Final(unsigned char *result, MD5_CTX *ctx); + +#endif + +#ifdef __cplusplus +} +#endif + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/misc.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/misc.h new file mode 100644 index 0000000000000000000000000000000000000000..681b28cff06db0392eebe9de211ddf7c2b77daa1 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/misc.h @@ -0,0 +1,110 @@ +/* +Copyright (c) 1994-1997, 2001-2002 MEDICAL RESEARCH COUNCIL +All rights reserved + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1 Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2 Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF +MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or +promote products derived from this software without specific prior written +permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/* +Copyright (c) 2003-2013 Genome Research Ltd. + +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifndef _misc_h +#define _misc_h + +#include "cram/os.h" + +#include +#include /* varargs needed for v*printf() prototypes */ +#include + +#ifdef __cplusplus +extern "C" { +#endif + +/* + * This informs gcc that crash() doesn't return, so it doesn't need to + * concern itself that code paths going via crash could mean some variables + * being undefined and then issuing uninitialised variable warnings. + * This particularly affected convert. + */ +#ifdef __GNUC__ +# define __NORETURN__ __attribute__ ((__noreturn__)) +#else +# define __NORETURN__ +#endif + +/* + * Used for printf style argument checking. We can request a function such + * as vTcl_SetResult does argument checking, avoiding bugs with using + * %d and passing in a 64-bit record. + */ +#ifdef __GNUC__ +# define __PRINTF_FORMAT__(a,b) __attribute__ ((format (printf, a, b))) +#else +# define __PRINTF_FORMAT__(a,b) +#endif + +extern int is_directory(char * fn); +extern int is_file(char * fn); +extern int file_size(char * fn); + +#define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) +#define MAX(A,B) ( ( (A) > (B) ) ? (A) : (B) ) + +#ifdef __cplusplus +} +#endif + +#endif /*_misc_h*/ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/open_trace_file.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/open_trace_file.c new file mode 100644 index 0000000000000000000000000000000000000000..d89815d57a021946411f84850efe2d86a664cf4d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/open_trace_file.c @@ -0,0 +1,386 @@ +/* +Author: James Bonfield + +Copyright (c) 2000-2001 MEDICAL RESEARCH COUNCIL +All rights reserved + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF +MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or +promote products derived from this software without specific prior written +permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +/* +Copyright (c) 2008, 2009, 2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#include +#include +#include +#include +#include +#include +#include +#include +#include "cram/os.h" +#ifndef PATH_MAX +# define PATH_MAX 1024 +#endif +#ifdef HAVE_LIBCURL +# include +#endif + +#include "cram/open_trace_file.h" +#include "cram/misc.h" + +/* + * Tokenises the search path splitting on colons (unix) or semicolons + * (windows). + * We also explicitly add a "./" to the end of the search path + * + * Returns: A new search path with items separated by nul chars. Two nul + * chars in a row represent the end of the tokenised path. + * Returns NULL for a failure. + * + * The returned data has been malloced. It is up to the caller to free this + * memory. + */ +char *tokenise_search_path(char *searchpath) { + char *newsearch; + unsigned int i, j; + size_t len; +#ifdef _WIN32 + char path_sep = ';'; +#else + char path_sep = ':'; +#endif + + if (!searchpath) + searchpath=""; + + newsearch = (char *)malloc((len = strlen(searchpath))+5); + if (!newsearch) + return NULL; + + for (i = 0, j = 0; i < len; i++) { + /* "::" => ":". Used for escaping colons in http://foo */ + if (i < len-1 && searchpath[i] == ':' && searchpath[i+1] == ':') { + newsearch[j++] = ':'; + i++; + continue; + } + + if (searchpath[i] == path_sep) { + /* Skip blank path components */ + if (j && newsearch[j-1] != 0) + newsearch[j++] = 0; + } else { + newsearch[j++] = searchpath[i]; + } + } + + if (j) + newsearch[j++] = 0; + newsearch[j++] = '.'; + newsearch[j++] = '/'; + newsearch[j++] = 0; + newsearch[j++] = 0; + + return newsearch; +} + +#ifdef HAVE_LIBCURL +mFILE *find_file_url(char *file, char *url) { + char buf[8192], *cp; + mFILE *mf = NULL, *headers = NULL; + int maxlen = 8190 - strlen(file); + static CURL *handle = NULL; + static int curl_init = 0; + char errbuf[CURL_ERROR_SIZE]; + + *errbuf = 0; + + if (!curl_init) { + if (curl_global_init(CURL_GLOBAL_ALL)) + return NULL; + + if (NULL == (handle = curl_easy_init())) + goto error; + + curl_init = 1; + } + + /* Expand %s for the trace name */ + for (cp = buf; *url && cp - buf < maxlen; url++) { + if (*url == '%' && *(url+1) == 's') { + url++; + cp += strlen(strcpy(cp, file)); + } else { + *cp++ = *url; + } + } + *cp++ = 0; + + /* Setup the curl */ + if (NULL == (mf = mfcreate(NULL, 0)) || + NULL == (headers = mfcreate(NULL, 0))) + return NULL; + + if (0 != curl_easy_setopt(handle, CURLOPT_URL, buf)) + goto error; + if (0 != curl_easy_setopt(handle, CURLOPT_CONNECTTIMEOUT, 60L)) + goto error; + if (0 != curl_easy_setopt(handle, CURLOPT_WRITEFUNCTION, + (curl_write_callback)mfwrite)) + goto error; + if (0 != curl_easy_setopt(handle, CURLOPT_WRITEDATA, mf)) + goto error; + if (0 != curl_easy_setopt(handle, CURLOPT_HEADERFUNCTION, + (curl_write_callback)mfwrite)) + goto error; + if (0 != curl_easy_setopt(handle, CURLOPT_WRITEHEADER, headers)) + goto error; + if (0 != curl_easy_setopt(handle, CURLOPT_ERRORBUFFER, errbuf)) + goto error; + + /* Fetch! */ + if (0 != curl_easy_perform(handle)) + goto error; + + /* Report errors is approproate. 404 is silent as it may have just been + * a search via RAWDATA path, everything else is worth reporting. + */ + { + float version; + int response; + char nul = 0; + mfwrite(&nul, 1, 1, headers); + if (2 == sscanf(headers->data, "HTTP/%f %d", &version, &response)) { + if (response != 200) { + if (response != 404) + fprintf(stderr, "%.*s\n", + (int)headers->size, headers->data); + goto error; + } + } + } + + if (mftell(mf) == 0) + goto error; + + mfdestroy(headers); + + mrewind(mf); + return mf; + + error: + if (mf) + mfdestroy(mf); + if (headers) + mfdestroy(headers); + if (*errbuf) + fprintf(stderr, "%s\n", errbuf); + return NULL; +} +#endif + +/* + * Searches for file in the directory 'dirname'. If it finds it, it opens + * it. This also searches for compressed versions of the file in dirname + * too. + * + * Returns mFILE pointer if found + * NULL if not + */ +static mFILE *find_file_dir(char *file, char *dirname) { + char path[PATH_MAX+1]; + size_t len = strlen(dirname); + char *cp; + + if (dirname[len-1] == '/') + len--; + + /* Special case for "./" or absolute filenames */ + if (*file == '/' || (len==1 && *dirname == '.')) { + sprintf(path, "%s", file); + } else { + /* Handle %[0-9]*s expansions, if required */ + char *path_end = path; + *path = 0; + while ((cp = strchr(dirname, '%'))) { + char *endp; + long l = strtol(cp+1, &endp, 10); + if (*endp != 's') { + strncpy(path_end, dirname, (endp+1)-dirname); + path_end += (endp+1)-dirname; + dirname = endp+1; + continue; + } + + strncpy(path_end, dirname, cp-dirname); + path_end += cp-dirname; + if (l) { + strncpy(path_end, file, l); + path_end += MIN(strlen(file), l); + file += MIN(strlen(file), l); + } else { + strcpy(path_end, file); + path_end += strlen(file); + file += strlen(file); + } + len -= (endp+1) - dirname; + dirname = endp+1; + } + strncpy(path_end, dirname, len); + path_end += MIN(strlen(dirname), len); + *path_end = 0; + if (*file) { + *path_end++ = '/'; + strcpy(path_end, file); + } + + //fprintf(stderr, "*PATH=\"%s\"\n", path); + } + + if (is_file(path)) { + return mfopen(path, "rb"); + } + + return NULL; +} + +/* + * ------------------------------------------------------------------------ + * Public functions below. + */ + +/* + * Opens a trace file named 'file'. This is initially looked for as a + * pathname relative to a file named "relative_to". This may (for + * example) be the name of an experiment file referencing the trace + * file. In this case by passing relative_to as the experiment file + * filename the trace file will be picked up in the same directory as + * the experiment file. Relative_to may be supplied as NULL. + * + * 'file' is looked for at relative_to, then the current directory, and then + * all of the locations listed in 'path' (which is a colon separated list). + * If 'path' is NULL it uses the RAWDATA environment variable instead. + * + * Returns a mFILE pointer when found. + * NULL otherwise. + */ +mFILE *open_path_mfile(char *file, char *path, char *relative_to) { + char *newsearch; + char *ele; + mFILE *fp; + + /* Use path first */ + if (!path) + path = getenv("RAWDATA"); + if (NULL == (newsearch = tokenise_search_path(path))) + return NULL; + + /* + * Step through the search path testing out each component. + * We now look through each path element treating some prefixes as + * special, otherwise we treat the element as a directory. + */ + for (ele = newsearch; *ele; ele += strlen(ele)+1) { + int i; + char *suffix[6] = {"", ".gz", ".bz2", ".sz", ".Z", ".bz2"}; + for (i = 0; i < 6; i++) { + char file2[1024]; + char *ele2; + int valid = 1; + + /* + * '|' prefixing a path component indicates that we do not + * wish to perform the compression extension searching in that + * location. + */ + if (*ele == '|') { + ele2 = ele+1; + valid = (i == 0); + } else { + ele2 = ele; + } + + sprintf(file2, "%s%s", file, suffix[i]); + +#if defined(HAVE_LIBCURL) + if (0 == strncmp(ele2, "URL=", 4)) { + if (valid && (fp = find_file_url(file2, ele2+4))) { + free(newsearch); + return fp; + } + } else +#endif + if (valid && (fp = find_file_dir(file2, ele2))) { + free(newsearch); + return fp; + } + } + } + + free(newsearch); + + /* Look in the same location as the incoming 'relative_to' filename */ + if (relative_to) { + char *cp; + char relative_path[PATH_MAX+1]; + strcpy(relative_path, relative_to); + if ((cp = strrchr(relative_path, '/'))) + *cp = 0; + if ((fp = find_file_dir(file, relative_path))) + return fp; + } + + return NULL; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/open_trace_file.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/open_trace_file.h new file mode 100644 index 0000000000000000000000000000000000000000..ee52cb05f57c2a7717c15ed21b639c90ef6983b3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/open_trace_file.h @@ -0,0 +1,115 @@ +/* +Author: James Bonfield + +Copyright (c) 2000-2001 MEDICAL RESEARCH COUNCIL +All rights reserved + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + . Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + . Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + . Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF +MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or +promote products derived from this software without specific prior written +permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +/* +Copyright (c) 2008, 2009, 2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifndef _OPEN_TRACE_FILE_H_ +#define _OPEN_TRACE_FILE_H_ + +#include "cram/mFILE.h" + +#ifdef __cplusplus +extern "C" { +#endif + +/* + * Tokenises the search path splitting on colons (unix) or semicolons + * (windows). + * We also explicitly add a "./" to the end of the search path + * + * Returns: A new search path with items separated by nul chars. Two nul + * chars in a row represent the end of the tokenised path. + * Returns NULL for a failure. + * + * The returned data has been malloced. It is up to the caller to free this + * memory. + */ +char *tokenise_search_path(char *searchpath); + +/* + * Opens a trace file named 'file'. This is initially looked for as a + * pathname relative to a file named "relative_to". This may (for + * example) be the name of an experiment file referencing the trace + * file. In this case by passing relative_to as the experiment file + * filename the trace file will be picked up in the same directory as + * the experiment file. Relative_to may be supplied as NULL. + * + * 'file' is looked for at relative_to, then the current directory, and then + * all of the locations listed in 'path' (which is a colon separated list). + * If 'path' is NULL it uses the RAWDATA environment variable instead. + * + * Returns a mFILE pointer when found. + * NULL otherwise. + */ +mFILE *open_path_mfile(char *file, char *path, char *relative_to); + +/* + * Returns a mFILE containing the entire contents of the url; + * NULL on failure. + */ +mFILE *find_file_url(char *file, char *url); + + +#ifdef __cplusplus +} +#endif + +#endif /* _OPEN_TRACE_FILE_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/os.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/os.h new file mode 100644 index 0000000000000000000000000000000000000000..b2affe0b2c29f7db626585b525ad4418ff6c59ae --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/os.h @@ -0,0 +1,306 @@ +/* +Copyright (c) 1993, 1995-2002 MEDICAL RESEARCH COUNCIL +All rights reserved + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1 Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2 Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF +MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or +promote products derived from this software without specific prior written +permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +/* +Copyright (c) 2004, 2006, 2009-2011, 2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +/* + * File: os.h + * + * Author: + * MRC Laboratory of Molecular Biology + * Hills Road + * Cambridge CB2 2QH + * United Kingdom + * + * Description: operating system specific type definitions + * + */ + +#ifndef _OS_H_ +#define _OS_H_ + +#include +#include + +#ifdef __cplusplus +extern "C" { +#endif + +/*----------------------------------------------------------------------------- + * Detection of endianness. The main part of this is done in autoconf, but + * for the case of MacOS FAT binaries we fall back on auto-sensing based on + * processor type too. + */ + +/* Set by autoconf */ +#define SP_LITTLE_ENDIAN + +/* Mac FAT binaries or unknown. Auto detect based on CPU type */ +#if !defined(SP_BIG_ENDIAN) && !defined(SP_LITTLE_ENDIAN) + +/* + * x86 equivalents + */ +#if defined(__i386__) || defined(__i386) || defined(__amd64__) || defined(__amd64) || defined(__x86_64__) || defined(__x86_64) || defined(__i686__) || defined(__i686) +# if defined(SP_BIG_ENDIAN) +# undef SP_BIG_ENDIAN +# endif +# define SP_LITTLE_ENDIAN +#endif + +/* + * DEC Alpha + */ +#if defined(__alpha__) || defined(__alpha) +# if defined(SP_LITTLE_ENDIAN) +# undef SP_LITTLE_ENDIAN +# endif +# define SP_BIG_ENDIAN +#endif + +/* + * SUN Sparc + */ +#if defined(__sparc__) || defined(__sparc) +# if defined(SP_LITTLE_ENDIAN) +# undef SP_LITTLE_ENDIAN +# endif +# define SP_BIG_ENDIAN +#endif + +/* + * PowerPC + */ +#if defined(__ppc__) || defined(__ppc) +# if defined(SP_LITTLE_ENDIAN) +# undef SP_LITTLE_ENDIAN +# endif +# define SP_BIG_ENDIAN +#endif + +/* Some catch-alls */ +#if defined(__LITTLE_ENDIAN__) || defined(__LITTLEENDIAN__) +# define SP_LITTLE_ENDIAN +#endif + +#if defined(__BIG_ENDIAN__) || defined(__BIGENDIAN__) +# define SP_BIG_ENDIAN +#endif + +#if defined(SP_BIG_ENDIAN) && defined(SP_LITTLE_ENDIAN) +# error Both BIG and LITTLE endian defined. Fix os.h and/or Makefile +#endif + +#if !defined(SP_BIG_ENDIAN) && !defined(SP_LITTLE_ENDIAN) +# error Neither BIG nor LITTLE endian defined. Fix os.h and/or Makefile +#endif + +#endif + +/*----------------------------------------------------------------------------- + * Allow for unaligned memory access. This is used in BAM code as the packed + * structure has 4-byte cigar ints after the variable length name. + * + * Consider using AX_CHECK_ALIGNED_ACCESS_REQUIRED in autoconf. + */ +#if defined(__i386__) || defined(__i386) || defined(__amd64__) || defined(__amd64) || defined(__x86_64__) || defined(__x86_64) || defined(__i686__) || defined(__i686) +# define ALLOW_UAC +#endif + +/*----------------------------------------------------------------------------- + * Byte swapping macros + */ + +/* + * Our new swap runs at the same speed on Ultrix, but substantially faster + * (300% for swap_int4, ~50% for swap_int2) on an Alpha (due to the lack of + * decent 'char' support). + * + * They also have the ability to swap in situ (src == dst). Newer code now + * relies on this so don't change back! + */ +#define iswap_int8(x) \ + (((x & 0x00000000000000ffLL) << 56) + \ + ((x & 0x000000000000ff00LL) << 40) + \ + ((x & 0x0000000000ff0000LL) << 24) + \ + ((x & 0x00000000ff000000LL) << 8) + \ + ((x & 0x000000ff00000000LL) >> 8) + \ + ((x & 0x0000ff0000000000LL) >> 24) + \ + ((x & 0x00ff000000000000LL) >> 40) + \ + ((x & 0xff00000000000000LL) >> 56)) + +#define iswap_int4(x) \ + (((x & 0x000000ff) << 24) + \ + ((x & 0x0000ff00) << 8) + \ + ((x & 0x00ff0000) >> 8) + \ + ((x & 0xff000000) >> 24)) + +#define iswap_int2(x) \ + (((x & 0x00ff) << 8) + \ + ((x & 0xff00) >> 8)) + +/* + * Linux systems may use byteswap.h to get assembly versions of byte-swap + * on intel systems. This can be as trivial as the bswap opcode, which works + * out at over 2-times faster than iswap_int4 above. + */ +#if 0 +#if defined(__linux__) +# include +# undef iswap_int8 +# undef iswap_int4 +# undef iswap_int2 +# define iswap_int8 bswap_64 +# define iswap_int4 bswap_32 +# define iswap_int2 bswap_16 +#endif +#endif + + +/* + * Macros to specify that data read in is of a particular endianness. + * The macros here swap to the appropriate order for the particular machine + * running the macro and return the new answer. These may also be used when + * writing to a file to specify that we wish to write in (eg) big endian + * format. + * + * This leads to efficient code as most of the time these macros are + * trivial. + */ +#ifdef SP_BIG_ENDIAN +#define le_int4(x) iswap_int4((x)) +#endif + +#ifdef SP_LITTLE_ENDIAN +#define le_int4(x) (x) +#endif + +/*----------------------------------------------------------------------------- + * definitions, incase they're not present + */ + +#ifndef PRId64 +#define __PRI64__ "l" +#define PRId64 __PRI64__ "d" +#define PRId32 "d" +#define PRId16 "d" +#define PRId8 "d" +#define PRIu64 __PRI64__ "u" +#define PRIu32 "u" +#define PRIu16 "u" +#define PRIu8 "u" +#endif + +/*----------------------------------------------------------------------------- + * Operating system specifics. + * These ought to be done by autoconf, but are legacy code. + */ +/* + * SunOS 4.x + * Even though we use the ANSI gcc, we make use the the standard SunOS 4.x + * libraries and include files, which are non-ansi + */ +#if defined(__sun__) && !defined(__svr4__) +#define SEEK_SET 0 +#define SEEK_CUR 1 +#define SEEK_END 2 +#endif + +/* + * Microsoft Visual C++ + * Windows + */ +#if defined(_MSC_VER) +#define popen _popen +#define pclose _pclose +#define ftruncate(fd,len) _chsize(fd,len) +#endif + + +/* + * Microsoft Windows running MinGW + */ +#if defined(__MINGW32__) +/* #define mkdir(filename,mode) mkdir((filename)) */ +#define sysconf(x) 512 +#define ftruncate(fd,len) _chsize(fd,len) +#endif + +/* Generic WIN32 API issues */ +#ifdef _WIN32 +# ifndef HAVE_FSEEKO +# if __MSVCRT_VERSION__ >= 0x800 + /* if you have MSVCR80 installed then you can use these definitions: */ +# define off_t __int64 +# define fseeko _fseeki64 +# define ftello _ftelli64 +# else + /* otherwise we're stuck with 32-bit file support */ +# define off_t long +# define fseeko fseek +# define ftello ftell +# endif +# endif /* !HAVE_FSEEKO */ +#endif /* _WIN32 */ + +#ifdef __cplusplus +} +#endif + +#endif /*_OS_H_*/ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/pooled_alloc.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/pooled_alloc.c new file mode 100644 index 0000000000000000000000000000000000000000..0d061e751188d295cdf690144f67142213b87196 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/pooled_alloc.c @@ -0,0 +1,170 @@ +/* +Copyright (c) 2009 Genome Research Ltd. +Author: Rob Davies + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifdef HAVE_CONFIG_H +#include "io_lib_config.h" +#endif + +#include +#include +#include + +#include "cram/pooled_alloc.h" + +//#define TEST_MAIN + +#define PSIZE 1024*1024 + +pool_alloc_t *pool_create(size_t dsize) { + pool_alloc_t *p; + + if (NULL == (p = (pool_alloc_t *)malloc(sizeof(*p)))) + return NULL; + + /* Minimum size is a pointer, for free list */ + dsize = (dsize + sizeof(void *) - 1) & ~(sizeof(void *)-1); + if (dsize < sizeof(void *)) + dsize = sizeof(void *); + p->dsize = dsize; + + p->npools = 0; + p->pools = NULL; + p->free = NULL; + + return p; +} + +static pool_t *new_pool(pool_alloc_t *p) { + size_t n = PSIZE / p->dsize; + pool_t *pool; + + pool = realloc(p->pools, (p->npools + 1) * sizeof(*p->pools)); + if (NULL == pool) return NULL; + p->pools = pool; + pool = &p->pools[p->npools]; + + pool->pool = malloc(n * p->dsize); + if (NULL == pool->pool) return NULL; + + pool->used = 0; + + p->npools++; + + return pool; +} + +void pool_destroy(pool_alloc_t *p) { + size_t i; + + for (i = 0; i < p->npools; i++) { + free(p->pools[i].pool); + } + free(p->pools); + free(p); +} + +void *pool_alloc(pool_alloc_t *p) { + pool_t *pool; + void *ret; + + /* Look on free list */ + if (NULL != p->free) { + ret = p->free; + p->free = *((void **)p->free); + return ret; + } + + /* Look for space in the last pool */ + if (p->npools) { + pool = &p->pools[p->npools - 1]; + if (pool->used + p->dsize < PSIZE) { + ret = ((char *) pool->pool) + pool->used; + pool->used += p->dsize; + return ret; + } + } + + /* Need a new pool */ + pool = new_pool(p); + if (NULL == pool) return NULL; + + pool->used = p->dsize; + return pool->pool; +} + +void pool_free(pool_alloc_t *p, void *ptr) { + *(void **)ptr = p->free; + p->free = ptr; +} + +#ifdef TEST_MAIN +typedef struct { + int x, y, z; +} xyz; + +#define NP 10000 +int main(void) { + int i; + xyz *item; + xyz **items; + pool_alloc_t *p = pool_create(sizeof(xyz)); + + items = (xyz **)malloc(NP * sizeof(*items)); + + for (i = 0; i < NP; i++) { + item = pool_alloc(p); + item->x = i; + item->y = i+1; + item->z = i+2; + items[i] = item; + } + + for (i = 0; i < NP; i++) { + item = items[i]; + if (i % 3) + pool_free(p, item); + } + + for (i = 0; i < NP; i++) { + item = pool_alloc(p); + item->x = 1000000+i; + item->y = 1000000+i+1; + item->z = 1000000+i+2; + } + + for (i = 0; i < NP; i++) { + item = items[i]; + printf("%d\t%d\t%d\t%d\n", i, item->x, item->y, item->z); + pool_free(p, item); + } + + return 0; +} +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/pooled_alloc.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/pooled_alloc.h new file mode 100644 index 0000000000000000000000000000000000000000..fa3c81fe09eb4b75387527d3137362483f5e0e19 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/pooled_alloc.h @@ -0,0 +1,56 @@ +/* +Copyright (c) 2009 Genome Research Ltd. +Author: Rob Davies + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifndef _POOLED_ALLOC_H_ +#define _POOLED_ALLOC_H_ + +/* + * Implements a pooled block allocator where all items are the same size, + * but we need many of them. + */ +typedef struct { + void *pool; + size_t used; +} pool_t; + +typedef struct { + size_t dsize; + size_t npools; + pool_t *pools; + void *free; +} pool_alloc_t; + +pool_alloc_t *pool_create(size_t dsize); +void pool_destroy(pool_alloc_t *p); +void *pool_alloc(pool_alloc_t *p); +void pool_free(pool_alloc_t *p, void *ptr); + + +#endif /*_POOLED_ALLOC_H_*/ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/sam_header.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/sam_header.c new file mode 100644 index 0000000000000000000000000000000000000000..2a8110cb8b31de075cfbc49641a1a8820102cab3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/sam_header.c @@ -0,0 +1,1222 @@ +/* +Copyright (c) 2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifdef HAVE_CONFIG_H +#include "io_lib_config.h" +#endif + +#include +#include + +#include "cram/sam_header.h" +#include "cram/string_alloc.h" + +#ifdef SAMTOOLS +#define sam_hdr_parse sam_hdr_parse_ +#endif + +static void sam_hdr_error(char *msg, char *line, int len, int lno) { + int j; + + for (j = 0; j < len && line[j] != '\n'; j++) + ; + fprintf(stderr, "%s at line %d: \"%.*s\"\n", msg, lno, j, line); +} + +void sam_hdr_dump(SAM_hdr *hdr) { + khint_t k; + int i; + + printf("===DUMP===\n"); + for (k = kh_begin(hdr->h); k != kh_end(hdr->h); k++) { + SAM_hdr_type *t1, *t2; + char c[2]; + + if (!kh_exist(hdr->h, k)) + continue; + + t1 = t2 = kh_val(hdr->h, k); + c[0] = kh_key(hdr->h, k)>>8; + c[1] = kh_key(hdr->h, k)&0xff; + printf("Type %.2s, count %d\n", c, t1->prev->order+1); + + do { + SAM_hdr_tag *tag; + printf(">>>%d ", t1->order); + for (tag = t1->tag; tag; tag=tag->next) { + printf("\"%.2s\":\"%.*s\"\t", + tag->str, tag->len-3, tag->str+3); + } + putchar('\n'); + t1 = t1->next; + } while (t1 != t2); + } + + /* Dump out PG chains */ + printf("\n@PG chains:\n"); + for (i = 0; i < hdr->npg_end; i++) { + int j; + printf(" %d:", i); + for (j = hdr->pg_end[i]; j != -1; j = hdr->pg[j].prev_id) { + printf("%s%d(%.*s)", + j == hdr->pg_end[i] ? " " : "->", + j, hdr->pg[j].name_len, hdr->pg[j].name); + } + printf("\n"); + } + + puts("===END DUMP==="); +} + +/* Updates the hash tables in the SAM_hdr structure. + * + * Returns 0 on success; + * -1 on failure + */ +static int sam_hdr_update_hashes(SAM_hdr *sh, + int type, + SAM_hdr_type *h_type) { + /* Add to reference hash? */ + if ((type>>8) == 'S' && (type&0xff) == 'Q') { + SAM_hdr_tag *tag; + int nref = sh->nref; + + sh->ref = realloc(sh->ref, (sh->nref+1)*sizeof(*sh->ref)); + if (!sh->ref) + return -1; + + tag = h_type->tag; + sh->ref[nref].name = NULL; + sh->ref[nref].len = 0; + sh->ref[nref].ty = h_type; + sh->ref[nref].tag = tag; + + while (tag) { + if (tag->str[0] == 'S' && tag->str[1] == 'N') { + if (!(sh->ref[nref].name = malloc(tag->len))) + return -1; + strncpy(sh->ref[nref].name, tag->str+3, tag->len-3); + sh->ref[nref].name[tag->len-3] = 0; + } else if (tag->str[0] == 'L' && tag->str[1] == 'N') { + sh->ref[nref].len = atoi(tag->str+3); + } + tag = tag->next; + } + + if (sh->ref[nref].name) { + khint_t k; + int r; + k = kh_put(m_s2i, sh->ref_hash, sh->ref[nref].name, &r); + if (-1 == r) return -1; + kh_val(sh->ref_hash, k) = nref; + } + + sh->nref++; + } + + /* Add to read-group hash? */ + if ((type>>8) == 'R' && (type&0xff) == 'G') { + SAM_hdr_tag *tag; + int nrg = sh->nrg; + + sh->rg = realloc(sh->rg, (sh->nrg+1)*sizeof(*sh->rg)); + if (!sh->rg) + return -1; + + tag = h_type->tag; + sh->rg[nrg].name = NULL; + sh->rg[nrg].name_len = 0; + sh->rg[nrg].ty = h_type; + sh->rg[nrg].tag = tag; + sh->rg[nrg].id = nrg; + + while (tag) { + if (tag->str[0] == 'I' && tag->str[1] == 'D') { + if (!(sh->rg[nrg].name = malloc(tag->len))) + return -1; + strncpy(sh->rg[nrg].name, tag->str+3, tag->len-3); + sh->rg[nrg].name[tag->len-3] = 0; + sh->rg[nrg].name_len = strlen(sh->rg[nrg].name); + } + tag = tag->next; + } + + if (sh->rg[nrg].name) { + khint_t k; + int r; + k = kh_put(m_s2i, sh->rg_hash, sh->rg[nrg].name, &r); + if (-1 == r) return -1; + kh_val(sh->rg_hash, k) = nrg; + } + + sh->nrg++; + } + + /* Add to program hash? */ + if ((type>>8) == 'P' && (type&0xff) == 'G') { + SAM_hdr_tag *tag; + int npg = sh->npg; + + sh->pg = realloc(sh->pg, (sh->npg+1)*sizeof(*sh->pg)); + if (!sh->pg) + return -1; + + tag = h_type->tag; + sh->pg[npg].name = NULL; + sh->pg[npg].name_len = 0; + sh->pg[npg].ty = h_type; + sh->pg[npg].tag = tag; + sh->pg[npg].id = npg; + sh->pg[npg].prev_id = -1; + + while (tag) { + if (tag->str[0] == 'I' && tag->str[1] == 'D') { + if (!(sh->pg[npg].name = malloc(tag->len))) + return -1; + strncpy(sh->pg[npg].name, tag->str+3, tag->len-3); + sh->pg[npg].name[tag->len-3] = 0; + sh->pg[npg].name_len = strlen(sh->pg[npg].name); + } else if (tag->str[0] == 'P' && tag->str[1] == 'P') { + // Resolve later if needed + khint_t k; + char tmp = tag->str[tag->len]; tag->str[tag->len] = 0; + k = kh_get(m_s2i, sh->pg_hash, tag->str+3); + tag->str[tag->len] = tmp; + + if (k != kh_end(sh->pg_hash)) { + int p_id = kh_val(sh->pg_hash, k); + sh->pg[npg].prev_id = sh->pg[p_id].id; + + /* Unmark previous entry as a PG termination */ + if (sh->npg_end > 0 && + sh->pg_end[sh->npg_end-1] == p_id) { + sh->npg_end--; + } else { + int i; + for (i = 0; i < sh->npg_end; i++) { + if (sh->pg_end[i] == p_id) { + memmove(&sh->pg_end[i], &sh->pg_end[i+1], + (sh->npg_end-i-1)*sizeof(*sh->pg_end)); + sh->npg_end--; + } + } + } + } else { + sh->pg[npg].prev_id = -1; + } + } + tag = tag->next; + } + + if (sh->pg[npg].name) { + khint_t k; + int r; + k = kh_put(m_s2i, sh->pg_hash, sh->pg[npg].name, &r); + if (-1 == r) return -1; + kh_val(sh->pg_hash, k) = npg; + } + + /* Add to npg_end[] array. Remove later if we find a PP line */ + if (sh->npg_end >= sh->npg_end_alloc) { + sh->npg_end_alloc = sh->npg_end_alloc + ? sh->npg_end_alloc*2 + : 4; + sh->pg_end = realloc(sh->pg_end, + sh->npg_end_alloc * sizeof(int)); + if (!sh->pg_end) + return -1; + } + sh->pg_end[sh->npg_end++] = npg; + + sh->npg++; + } + + return 0; +} + +/* + * Appends a formatted line to an existing SAM header. + * Line is a full SAM header record, eg "@SQ\tSN:foo\tLN:100", with + * optional new-line. If it contains more than 1 line then multiple lines + * will be added in order. + * + * Len is the length of the text data, or 0 if unknown (in which case + * it should be null terminated). + * + * Returns 0 on success + * -1 on failure + */ +int sam_hdr_add_lines(SAM_hdr *sh, const char *lines, int len) { + int i, lno = 1, text_offset; + char *hdr; + + if (!len) + len = strlen(lines); + + text_offset = ks_len(&sh->text); + if (EOF == kputsn(lines, len, &sh->text)) + return -1; + hdr = ks_str(&sh->text) + text_offset; + + for (i = 0; i < len; i++) { + khint32_t type; + khint_t k; + + int l_start = i, new; + SAM_hdr_type *h_type; + SAM_hdr_tag *h_tag, *last; + + if (hdr[i] != '@') { + int j; + for (j = i; j < len && hdr[j] != '\n'; j++) + ; + sam_hdr_error("Header line does not start with '@'", + &hdr[l_start], len - l_start, lno); + return -1; + } + + type = (hdr[i+1]<<8) | hdr[i+2]; + if (hdr[i+1] < 'A' || hdr[i+1] > 'z' || + hdr[i+2] < 'A' || hdr[i+2] > 'z') { + sam_hdr_error("Header line does not have a two character key", + &hdr[l_start], len - l_start, lno); + return -1; + } + + i += 3; + if (hdr[i] == '\n') + continue; + + // Add the header line type + if (!(h_type = pool_alloc(sh->type_pool))) + return -1; + if (-1 == (k = kh_put(sam_hdr, sh->h, type, &new))) + return -1; + + // Form the ring, either with self or other lines of this type + if (!new) { + SAM_hdr_type *t = kh_val(sh->h, k), *p; + p = t->prev; + + assert(p->next = t); + p->next = h_type; + h_type->prev = p; + + t->prev = h_type; + h_type->next = t; + h_type->order = p->order+1; + } else { + kh_val(sh->h, k) = h_type; + h_type->prev = h_type->next = h_type; + h_type->order = 0; + } + + // Parse the tags on this line + last = NULL; + if ((type>>8) == 'C' && (type&0xff) == 'O') { + int j; + if (hdr[i] != '\t') { + sam_hdr_error("Missing tab", + &hdr[l_start], len - l_start, lno); + return -1; + } + + for (j = ++i; j < len && hdr[j] != '\n'; j++) + ; + + if (!(h_type->tag = h_tag = pool_alloc(sh->tag_pool))) + return -1; + h_tag->str = string_ndup(sh->str_pool, &hdr[i], j-i); + h_tag->len = j-i; + h_tag->next = NULL; + if (!h_tag->str) + return -1; + + i = j; + + } else { + do { + int j; + if (hdr[i] != '\t') { + sam_hdr_error("Missing tab", + &hdr[l_start], len - l_start, lno); + return -1; + } + + for (j = ++i; j < len && hdr[j] != '\n' && hdr[j] != '\t'; j++) + ; + + if (!(h_tag = pool_alloc(sh->tag_pool))) + return -1; + h_tag->str = string_ndup(sh->str_pool, &hdr[i], j-i); + h_tag->len = j-i; + h_tag->next = NULL; + if (!h_tag->str) + return -1; + + if (h_tag->len < 3 || h_tag->str[2] != ':') { + sam_hdr_error("Malformed key:value pair", + &hdr[l_start], len - l_start, lno); + return -1; + } + + if (last) + last->next = h_tag; + else + h_type->tag = h_tag; + + last = h_tag; + i = j; + } while (i < len && hdr[i] != '\n'); + } + + /* Update RG/SQ hashes */ + if (-1 == sam_hdr_update_hashes(sh, type, h_type)) + return -1; + } + + return 0; +} + +/* + * Adds a single line to a SAM header. + * Specify type and one or more key,value pairs, ending with the NULL key. + * Eg. sam_hdr_add(h, "SQ", "ID", "foo", "LN", "100", NULL). + * + * Returns index for specific entry on success (eg 2nd SQ, 4th RG) + * -1 on failure + */ +int sam_hdr_add(SAM_hdr *sh, const char *type, ...) { + va_list args; + va_start(args, type); + return sam_hdr_vadd(sh, type, args, NULL); +} + +int sam_hdr_vadd(SAM_hdr *sh, const char *type, va_list ap, ...) { + va_list args; + SAM_hdr_type *h_type; + SAM_hdr_tag *h_tag, *last; + int new; + khint32_t type_i = (type[0]<<8) | type[1], k; + +#if defined(HAVE_VA_COPY) + va_list ap_local; +#endif + + if (EOF == kputc_('@', &sh->text)) + return -1; + if (EOF == kputsn(type, 2, &sh->text)) + return -1; + + if (!(h_type = pool_alloc(sh->type_pool))) + return -1; + if (-1 == (k = kh_put(sam_hdr, sh->h, type_i, &new))) + return -1; + kh_val(sh->h, k) = h_type; + + // Form the ring, either with self or other lines of this type + if (!new) { + SAM_hdr_type *t = kh_val(sh->h, k), *p; + p = t->prev; + + assert(p->next = t); + p->next = h_type; + h_type->prev = p; + + t->prev = h_type; + h_type->next = t; + h_type->order = p->order + 1; + } else { + h_type->prev = h_type->next = h_type; + h_type->order = 0; + } + + last = NULL; + + // Any ... varargs + va_start(args, ap); + for (;;) { + char *k, *v; + int idx; + + if (!(k = (char *)va_arg(args, char *))) + break; + v = va_arg(args, char *); + + if (EOF == kputc_('\t', &sh->text)) + return -1; + + if (!(h_tag = pool_alloc(sh->tag_pool))) + return -1; + idx = ks_len(&sh->text); + + if (EOF == kputs(k, &sh->text)) + return -1; + if (EOF == kputc_(':', &sh->text)) + return -1; + if (EOF == kputs(v, &sh->text)) + return -1; + + h_tag->len = ks_len(&sh->text) - idx; + h_tag->str = string_ndup(sh->str_pool, + ks_str(&sh->text) + idx, + h_tag->len); + h_tag->next = NULL; + if (!h_tag->str) + return -1; + + if (last) + last->next = h_tag; + else + h_type->tag = h_tag; + + last = h_tag; + } + va_end(args); + +#if defined(HAVE_VA_COPY) + va_copy(ap_local, ap); +# define ap ap_local +#endif + + // Plus the specified va_list params + for (;;) { + char *k, *v; + int idx; + + if (!(k = (char *)va_arg(ap, char *))) + break; + v = va_arg(ap, char *); + + if (EOF == kputc_('\t', &sh->text)) + return -1; + + if (!(h_tag = pool_alloc(sh->tag_pool))) + return -1; + idx = ks_len(&sh->text); + + if (EOF == kputs(k, &sh->text)) + return -1; + if (EOF == kputc_(':', &sh->text)) + return -1; + if (EOF == kputs(v, &sh->text)) + return -1; + + h_tag->len = ks_len(&sh->text) - idx; + h_tag->str = string_ndup(sh->str_pool, + ks_str(&sh->text) + idx, + h_tag->len); + h_tag->next = NULL; + if (!h_tag->str) + return -1; + + if (last) + last->next = h_tag; + else + h_type->tag = h_tag; + + last = h_tag; + } + va_end(ap); + + if (EOF == kputc('\n', &sh->text)) + return -1; + + int itype = (type[0]<<8) | type[1]; + if (-1 == sam_hdr_update_hashes(sh, itype, h_type)) + return -1; + + return h_type->order; +} + +/* + * Returns the first header item matching 'type'. If ID is non-NULL it checks + * for the tag ID: and compares against the specified ID. + * + * Returns NULL if no type/ID is found + */ +SAM_hdr_type *sam_hdr_find(SAM_hdr *hdr, char *type, + char *ID_key, char *ID_value) { + SAM_hdr_type *t1, *t2; + int itype = (type[0]<<8)|(type[1]); + khint_t k; + + /* Special case for types we have prebuilt hashes on */ + if (ID_key) { + if (type[0] == 'S' && type[1] == 'Q' && + ID_key[0] == 'S' && ID_key[1] == 'N') { + k = kh_get(m_s2i, hdr->ref_hash, ID_value); + return k != kh_end(hdr->ref_hash) + ? hdr->ref[kh_val(hdr->ref_hash, k)].ty + : NULL; + } + + if (type[0] == 'R' && type[1] == 'G' && + ID_key[0] == 'I' && ID_key[1] == 'D') { + k = kh_get(m_s2i, hdr->rg_hash, ID_value); + return k != kh_end(hdr->rg_hash) + ? hdr->rg[kh_val(hdr->rg_hash, k)].ty + : NULL; + } + + if (type[0] == 'P' && type[1] == 'G' && + ID_key[0] == 'I' && ID_key[1] == 'D') { + k = kh_get(m_s2i, hdr->pg_hash, ID_value); + return k != kh_end(hdr->pg_hash) + ? hdr->pg[kh_val(hdr->pg_hash, k)].ty + : NULL; + } + } + + k = kh_get(sam_hdr, hdr->h, itype); + if (k == kh_end(hdr->h)) + return NULL; + + if (!ID_key) + return kh_val(hdr->h, k); + + t1 = t2 = kh_val(hdr->h, k); + do { + SAM_hdr_tag *tag; + for (tag = t1->tag; tag; tag = tag->next) { + if (tag->str[0] == ID_key[0] && tag->str[1] == ID_key[1]) { + char *cp1 = tag->str+3; + char *cp2 = ID_value; + while (*cp1 && *cp1 == *cp2) + cp1++, cp2++; + if (*cp2 || *cp1) + continue; + return t1; + } + } + t1 = t1->next; + } while (t1 != t2); + + return NULL; +} + +/* + * As per SAM_hdr_type, but returns a complete line of formatted text + * for a specific head type/ID combination. If ID is NULL then it returns + * the first line of the specified type. + * + * The returned string is malloced and should be freed by the calling + * function with free(). + * + * Returns NULL if no type/ID is found. + */ +char *sam_hdr_find_line(SAM_hdr *hdr, char *type, + char *ID_key, char *ID_value) { + SAM_hdr_type *ty = sam_hdr_find(hdr, type, ID_key, ID_value); + kstring_t ks = KS_INITIALIZER; + SAM_hdr_tag *tag; + int r = 0; + + if (!ty) + return NULL; + + // Paste together the line from the hashed copy + r |= (kputc_('@', &ks) == EOF); + r |= (kputs(type, &ks) == EOF); + for (tag = ty->tag; tag; tag = tag->next) { + r |= (kputc_('\t', &ks) == EOF); + r |= (kputsn(tag->str, tag->len, &ks) == EOF); + } + + if (r) { + KS_FREE(&ks); + return NULL; + } + + return ks_str(&ks); +} + + +/* + * Looks for a specific key in a single sam header line. + * If prev is non-NULL it also fills this out with the previous tag, to + * permit use in key removal. *prev is set to NULL when the tag is the first + * key in the list. When a tag isn't found, prev (if non NULL) will be the last + * tag in the existing list. + * + * Returns the tag pointer on success + * NULL on failure + */ +SAM_hdr_tag *sam_hdr_find_key(SAM_hdr *sh, + SAM_hdr_type *type, + char *key, + SAM_hdr_tag **prev) { + SAM_hdr_tag *tag, *p = NULL; + + for (tag = type->tag; tag; p = tag, tag = tag->next) { + if (tag->str[0] == key[0] && tag->str[1] == key[1]) { + if (prev) + *prev = p; + return tag; + } + } + + if (prev) + *prev = p; + + return NULL; +} + + +/* + * Adds or updates tag key,value pairs in a header line. + * Eg for adding M5 tags to @SQ lines or updating sort order for the + * @HD line (although use the sam_hdr_sort_order() function for + * HD manipulation, which is a wrapper around this funuction). + * + * Specify multiple key,value pairs ending in NULL. + * + * Returns 0 on success + * -1 on failure + */ +int sam_hdr_update(SAM_hdr *hdr, SAM_hdr_type *type, ...) { + va_list ap; + + va_start(ap, type); + + for (;;) { + char *k, *v; + int idx; + SAM_hdr_tag *tag, *prev; + + if (!(k = (char *)va_arg(ap, char *))) + break; + v = va_arg(ap, char *); + + tag = sam_hdr_find_key(hdr, type, k, &prev); + if (!tag) { + if (!(tag = pool_alloc(hdr->tag_pool))) + return -1; + if (prev) + prev->next = tag; + else + type->tag = tag; + + tag->next = NULL; + } + + idx = ks_len(&hdr->text); + if (ksprintf(&hdr->text, "%2.2s:%s", k, v) < 0) + return -1; + tag->len = ks_len(&hdr->text) - idx; + tag->str = string_ndup(hdr->str_pool, + ks_str(&hdr->text) + idx, + tag->len); + if (!tag->str) + return -1; + } + + va_end(ap); + + return 0; +} + +#define K(a) (((a)[0]<<8)|((a)[1])) + +/* + * Reconstructs the kstring from the header hash table. + * Returns 0 on success + * -1 on failure + */ +int sam_hdr_rebuild(SAM_hdr *hdr) { + /* Order: HD then others */ + kstring_t ks = KS_INITIALIZER; + khint_t k; + + + k = kh_get(sam_hdr, hdr->h, K("HD")); + if (k != kh_end(hdr->h)) { + SAM_hdr_type *ty = kh_val(hdr->h, k); + SAM_hdr_tag *tag; + if (EOF == kputs("@HD", &ks)) + return -1; + for (tag = ty->tag; tag; tag = tag->next) { + if (EOF == kputc_('\t', &ks)) + return -1; + if (EOF == kputsn_(tag->str, tag->len, &ks)) + return -1; + } + if (EOF == kputc('\n', &ks)) + return -1; + } + + for (k = kh_begin(hdr->h); k != kh_end(hdr->h); k++) { + SAM_hdr_type *t1, *t2; + + if (!kh_exist(hdr->h, k)) + continue; + + if (kh_key(hdr->h, k) == K("HD")) + continue; + + t1 = t2 = kh_val(hdr->h, k); + do { + SAM_hdr_tag *tag; + char c[2]; + + if (EOF == kputc_('@', &ks)) + return -1; + c[0] = kh_key(hdr->h, k)>>8; + c[1] = kh_key(hdr->h, k)&0xff; + if (EOF == kputsn_(c, 2, &ks)) + return -1; + for (tag = t1->tag; tag; tag=tag->next) { + if (EOF == kputc_('\t', &ks)) + return -1; + if (EOF == kputsn_(tag->str, tag->len, &ks)) + return -1; + } + if (EOF == kputc('\n', &ks)) + return -1; + t1 = t1->next; + } while (t1 != t2); + } + + if (ks_str(&hdr->text)) + KS_FREE(&hdr->text); + + hdr->text = ks; + + return 0; +} + + +/* + * Creates an empty SAM header, ready to be populated. + * + * Returns a SAM_hdr struct on success (free with sam_hdr_free()) + * NULL on failure + */ +SAM_hdr *sam_hdr_new() { + SAM_hdr *sh = calloc(1, sizeof(*sh)); + + if (!sh) + return NULL; + + sh->h = kh_init(sam_hdr); + if (!sh->h) + goto err; + + sh->ID_cnt = 1; + sh->ref_count = 1; + + sh->nref = 0; + sh->ref = NULL; + if (!(sh->ref_hash = kh_init(m_s2i))) + goto err; + + sh->nrg = 0; + sh->rg = NULL; + if (!(sh->rg_hash = kh_init(m_s2i))) + goto err; + + sh->npg = 0; + sh->pg = NULL; + sh->npg_end = sh->npg_end_alloc = 0; + sh->pg_end = NULL; + if (!(sh->pg_hash = kh_init(m_s2i))) + goto err; + + KS_INIT(&sh->text); + + if (!(sh->tag_pool = pool_create(sizeof(SAM_hdr_tag)))) + goto err; + + if (!(sh->type_pool = pool_create(sizeof(SAM_hdr_type)))) + goto err; + + if (!(sh->str_pool = string_pool_create(8192))) + goto err; + + return sh; + + err: + if (sh->h) + kh_destroy(sam_hdr, sh->h); + + if (sh->tag_pool) + pool_destroy(sh->tag_pool); + + if (sh->type_pool) + pool_destroy(sh->type_pool); + + if (sh->str_pool) + string_pool_destroy(sh->str_pool); + + free(sh); + + return NULL; +} + + +/* + * Tokenises a SAM header into a hash table. + * Also extracts a few bits on specific data types, such as @RG lines. + * + * Returns a SAM_hdr struct on success (free with sam_hdr_free()) + * NULL on failure + */ +SAM_hdr *sam_hdr_parse(const char *hdr, int len) { + /* Make an empty SAM_hdr */ + SAM_hdr *sh; + + sh = sam_hdr_new(); + if (NULL == sh) return NULL; + + if (NULL == hdr) return sh; // empty header is permitted + + /* Parse the header, line by line */ + if (-1 == sam_hdr_add_lines(sh, hdr, len)) { + sam_hdr_free(sh); + return NULL; + } + + //sam_hdr_dump(sh); + //sam_hdr_add(sh, "RG", "ID", "foo", "SM", "bar", NULL); + //sam_hdr_rebuild(sh); + //printf(">>%s<<", ks_str(sh->text)); + + //parse_references(sh); + //parse_read_groups(sh); + + sam_hdr_link_pg(sh); + //sam_hdr_dump(sh); + + return sh; +} + +/* + * Produces a duplicate copy of hdr and returns it. + * Returns NULL on failure + */ +SAM_hdr *sam_hdr_dup(SAM_hdr *hdr) { + if (-1 == sam_hdr_rebuild(hdr)) + return NULL; + + return sam_hdr_parse(sam_hdr_str(hdr), sam_hdr_length(hdr)); +} + +/*! Increments a reference count on hdr. + * + * This permits multiple files to share the same header, all calling + * sam_hdr_free when done, without causing errors for other open files. + */ +void sam_hdr_incr_ref(SAM_hdr *hdr) { + hdr->ref_count++; +} + +/*! Increments a reference count on hdr. + * + * This permits multiple files to share the same header, all calling + * sam_hdr_free when done, without causing errors for other open files. + * + * If the reference count hits zero then the header is automatically + * freed. This makes it a synonym for sam_hdr_free(). + */ +void sam_hdr_decr_ref(SAM_hdr *hdr) { + sam_hdr_free(hdr); +} + +/*! Deallocates all storage used by a SAM_hdr struct. + * + * This also decrements the header reference count. If after decrementing + * it is still non-zero then the header is assumed to be in use by another + * caller and the free is not done. + * + * This is a synonym for sam_hdr_dec_ref(). + */ +void sam_hdr_free(SAM_hdr *hdr) { + if (!hdr) + return; + + if (--hdr->ref_count > 0) + return; + + if (ks_str(&hdr->text)) + KS_FREE(&hdr->text); + + if (hdr->h) + kh_destroy(sam_hdr, hdr->h); + + if (hdr->ref_hash) + kh_destroy(m_s2i, hdr->ref_hash); + + if (hdr->ref) { + int i; + for (i = 0; i < hdr->nref; i++) + if (hdr->ref[i].name) + free(hdr->ref[i].name); + free(hdr->ref); + } + + if (hdr->rg_hash) + kh_destroy(m_s2i, hdr->rg_hash); + + if (hdr->rg) { + int i; + for (i = 0; i < hdr->nrg; i++) + if (hdr->rg[i].name) + free(hdr->rg[i].name); + free(hdr->rg); + } + + if (hdr->pg_hash) + kh_destroy(m_s2i, hdr->pg_hash); + + if (hdr->pg) { + int i; + for (i = 0; i < hdr->npg; i++) + if (hdr->pg[i].name) + free(hdr->pg[i].name); + free(hdr->pg); + } + + if (hdr->pg_end) + free(hdr->pg_end); + + if (hdr->type_pool) + pool_destroy(hdr->type_pool); + + if (hdr->tag_pool) + pool_destroy(hdr->tag_pool); + + if (hdr->str_pool) + string_pool_destroy(hdr->str_pool); + + free(hdr); +} + +int sam_hdr_length(SAM_hdr *hdr) { + return ks_len(&hdr->text); +} + +char *sam_hdr_str(SAM_hdr *hdr) { + return ks_str(&hdr->text); +} + +/* + * Looks up a reference sequence by name and returns the numerical ID. + * Returns -1 if unknown reference. + */ +int sam_hdr_name2ref(SAM_hdr *hdr, const char *ref) { + khint_t k = kh_get(m_s2i, hdr->ref_hash, ref); + return k == kh_end(hdr->ref_hash) ? -1 : kh_val(hdr->ref_hash, k); +} + +/* + * Looks up a read-group by name and returns a pointer to the start of the + * associated tag list. + * + * Returns NULL on failure + */ +SAM_RG *sam_hdr_find_rg(SAM_hdr *hdr, const char *rg) { + khint_t k = kh_get(m_s2i, hdr->rg_hash, rg); + return k == kh_end(hdr->rg_hash) + ? NULL + : &hdr->rg[kh_val(hdr->rg_hash, k)]; +} + + +/* + * Fixes any PP links in @PG headers. + * If the entries are in order then this doesn't need doing, but incase + * our header is out of order this goes through the sh->pg[] array + * setting the prev_id field. + * + * Note we can have multiple complete chains. This code should identify the + * tails of these chains as these are the entries we have to link to in + * subsequent PP records. + * + * Returns 0 on sucess + * -1 on failure (indicating broken PG/PP records) + */ +int sam_hdr_link_pg(SAM_hdr *hdr) { + int i, j, ret = 0; + + hdr->npg_end_alloc = hdr->npg; + hdr->pg_end = realloc(hdr->pg_end, hdr->npg * sizeof(*hdr->pg_end)); + if (!hdr->pg_end) + return -1; + + for (i = 0; i < hdr->npg; i++) + hdr->pg_end[i] = i; + + for (i = 0; i < hdr->npg; i++) { + khint_t k; + SAM_hdr_tag *tag; + char tmp; + + for (tag = hdr->pg[i].tag; tag; tag = tag->next) { + if (tag->str[0] == 'P' && tag->str[1] == 'P') + break; + } + if (!tag) { + /* Chain start points */ + continue; + } + + tmp = tag->str[tag->len]; tag->str[tag->len] = 0; + k = kh_get(m_s2i, hdr->pg_hash, tag->str+3); + tag->str[tag->len] = tmp; + + if (k == kh_end(hdr->pg_hash)) { + ret = -1; + continue; + } + + hdr->pg[i].prev_id = hdr->pg[kh_val(hdr->pg_hash, k)].id; + hdr->pg_end[kh_val(hdr->pg_hash, k)] = -1; + } + + for (i = j = 0; i < hdr->npg; i++) { + if (hdr->pg_end[i] != -1) + hdr->pg_end[j++] = hdr->pg_end[i]; + } + hdr->npg_end = j; + + return ret; +} + +/* + * Returns a unique ID from a base name. + * + * The value returned is valid until the next call to + * this function. + */ +const char *sam_hdr_PG_ID(SAM_hdr *sh, const char *name) { + khint_t k = kh_get(m_s2i, sh->pg_hash, name); + if (k == kh_end(sh->pg_hash)) + return name; + + do { + sprintf(sh->ID_buf, "%.1000s.%d", name, sh->ID_cnt++); + k = kh_get(m_s2i, sh->pg_hash, sh->ID_buf); + } while (k == kh_end(sh->pg_hash)); + + return sh->ID_buf; +} + +/* + * Add an @PG line. + * + * If we wish complete control over this use sam_hdr_add() directly. This + * function uses that, but attempts to do a lot of tedious house work for + * you too. + * + * - It will generate a suitable ID if the supplied one clashes. + * - It will generate multiple @PG records if we have multiple PG chains. + * + * Call it as per sam_hdr_add() with a series of key,value pairs ending + * in NULL. + * + * Returns 0 on success + * -1 on failure + */ +int sam_hdr_add_PG(SAM_hdr *sh, const char *name, ...) { + va_list args; + va_start(args, name); + + if (sh->npg_end) { + /* Copy ends array to avoid us looping while modifying it */ + int *end = malloc(sh->npg_end * sizeof(int)); + int i, nends = sh->npg_end; + + if (!end) + return -1; + + memcpy(end, sh->pg_end, nends * sizeof(*end)); + + for (i = 0; i < nends; i++) { + if (-1 == sam_hdr_vadd(sh, "PG", args, + "ID", sam_hdr_PG_ID(sh, name), + "PN", name, + "PP", sh->pg[end[i]].name, + NULL)) { + free(end); + return -1; + } + } + + free(end); + } else { + if (-1 == sam_hdr_vadd(sh, "PG", args, + "ID", sam_hdr_PG_ID(sh, name), + "PN", name, + NULL)) + return -1; + } + + //sam_hdr_dump(sh); + + return 0; +} + +/* + * A function to help with construction of CL tags in @PG records. + * Takes an argc, argv pair and returns a single space-separated string. + * This string should be deallocated by the calling function. + * + * Returns malloced char * on success + * NULL on failure + */ +char *stringify_argv(int argc, char *argv[]) { + char *str, *cp; + size_t nbytes = 1; + int i, j; + + /* Allocate */ + for (i = 0; i < argc; i++) { + nbytes += strlen(argv[i]) + 1; + } + if (!(str = malloc(nbytes))) + return NULL; + + /* Copy */ + cp = str; + for (i = 0; i < argc; i++) { + j = 0; + while (argv[i][j]) { + if (argv[i][j] == '\t') + *cp++ = ' '; + else + *cp++ = argv[i][j]; + j++; + } + *cp++ = ' '; + } + *cp++ = 0; + + return str; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/sam_header.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/sam_header.h new file mode 100644 index 0000000000000000000000000000000000000000..b9ea2983c06138dc68f566c51613f7f32d4843ab --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/sam_header.h @@ -0,0 +1,452 @@ +/* +Copyright (c) 2013-2014 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +/*! \file + * SAM header parsing. + * + * These functions can be shared between SAM, BAM and CRAM file + * formats as all three internally use the same string encoding for + * header fields. + * + * Consider using the scram() generic API and calling + * scram_get_header() to obtain the format-specific pointer to the + * SAM_hdr struct. + */ + +/* + * TODO. + * + * - Sort order (parse to struct, enum type, updating funcs) + * - Removal of lines. + * - Updating of lines + */ + +#ifndef _SAM_HDR_H_ +#define _SAM_HDR_H_ + +#ifdef __cplusplus +extern "C" { +#endif + +#ifdef HAVE_CONFIG_H +#include "io_lib_config.h" +#endif + +#include + +#include "cram/string_alloc.h" +#include "cram/pooled_alloc.h" + +#include "htslib/khash.h" +#include "htslib/kstring.h" + +// For structure assignment. Eg kstring_t s = KS_INITIALIZER; +#define KS_INITIALIZER {0,0,0} + +// For initialisation elsewhere. Eg KS_INIT(x->str); +#define KS_INIT(ks) ((ks)->l = 0, (ks)->m = 0, (ks)->s = NULL) + +// Frees the string subfield only. Assumes 's' itself is static. +#define KS_FREE(ks) do { if ((ks)->s) free((ks)->s); } while(0) + +/* + * Proposed new SAM header parsing + +1 @SQ ID:foo LN:100 +2 @SQ ID:bar LN:200 +3 @SQ ID:ram LN:300 UR:xyz +4 @RG ID:r ... +5 @RG ID:s ... + +Hash table for 2-char @keys without dup entries. +If dup lines, we form a circular linked list. Ie hash keys = {RG, SQ}. + +HASH("SQ")--\ + | + (3) <-> 1 <-> 2 <-> 3 <-> (1) + +HASH("RG")--\ + | + (5) <-> 4 <-> 5 <-> (4) + +Items stored in the hash values also form their own linked lists: +Ie SQ->ID(foo)->LN(100) + SQ->ID(bar)->LN(200) + SQ->ID(ram)->LN(300)->UR(xyz) + RG->ID(r) + */ + +/*! A single key:value pair on a header line + * + * These form a linked list and hold strings. The strings are + * allocated from a string_alloc_t pool referenced in the master + * SAM_hdr structure. Do not attempt to free, malloc or manipulate + * these strings directly. + */ +typedef struct SAM_hdr_tag_s { + struct SAM_hdr_tag_s *next; + char *str; + int len; +} SAM_hdr_tag; + +/*! The parsed version of the SAM header string. + * + * Each header type (SQ, RG, HD, etc) points to its own SAM_hdr_type + * struct via the main hash table h in the SAM_hdr struct. + * + * These in turn consist of circular bi-directional linked lists (ie + * rings) to hold the multiple instances of the same header type + * code. For example if we have 5 \@SQ lines the primary hash table + * will key on \@SQ pointing to the first SAM_hdr_type and that in turn + * will be part of a ring of 5 elements. + * + * For each SAM_hdr_type structure we also point to a SAM_hdr_tag + * structure which holds the tokenised attributes; the tab separated + * key:value pairs per line. + */ +typedef struct SAM_hdr_item_s { + struct SAM_hdr_item_s *next; // cirular + struct SAM_hdr_item_s *prev; + SAM_hdr_tag *tag; // first tag + int order; // 0 upwards +} SAM_hdr_type; + +/*! Parsed \@SQ lines */ +typedef struct { + char *name; + uint32_t len; + SAM_hdr_type *ty; + SAM_hdr_tag *tag; +} SAM_SQ; + +/*! Parsed \@RG lines */ +typedef struct { + char *name; + SAM_hdr_type *ty; + SAM_hdr_tag *tag; + int name_len; + int id; // numerical ID +} SAM_RG; + +/*! Parsed \@PG lines */ +typedef struct { + char *name; + SAM_hdr_type *ty; + SAM_hdr_tag *tag; + int name_len; + int id; // numerical ID + int prev_id; // -1 if none +} SAM_PG; + +KHASH_MAP_INIT_INT(sam_hdr, SAM_hdr_type*) +KHASH_MAP_INIT_STR(m_s2i, int) + +/*! Primary structure for header manipulation + * + * The initial header text is held in the text kstring_t, but is also + * parsed out into SQ, RG and PG arrays. These have a hash table + * associated with each to allow lookup by ID or SN fields instead of + * their numeric array indices. Additionally PG has an array to hold + * the linked list start points (the last in a PP chain). + * + * Use the appropriate sam_hdr_* functions to edit the header, and + * call sam_hdr_rebuild() any time the textual form needs to be + * updated again. + */ +typedef struct { + kstring_t text; //!< concatenated text, indexed by SAM_hdr_tag + khash_t(sam_hdr) *h; + string_alloc_t *str_pool; //!< Pool of SAM_hdr_tag->str strings + pool_alloc_t *type_pool;//!< Pool of SAM_hdr_type structs + pool_alloc_t *tag_pool; //!< Pool of SAM_hdr_tag structs + + // @SQ lines / references + int nref; //!< Number of \@SQ lines + SAM_SQ *ref; //!< Array of parsed \@SQ lines + khash_t(m_s2i) *ref_hash; //!< Maps SQ SN field to sq[] index + + // @RG lines / read-groups + int nrg; //!< Number of \@RG lines + SAM_RG *rg; //!< Array of parsed \@RG lines + khash_t(m_s2i) *rg_hash; //!< Maps RG ID field to rg[] index + + // @PG lines / programs + int npg; //!< Number of \@PG lines + int npg_end; //!< Number of terminating \@PG lines + int npg_end_alloc; //!< Size of pg_end field + SAM_PG *pg; //!< Array of parsed \@PG lines + khash_t(m_s2i) *pg_hash; //!< Maps PG ID field to pg[] index + int *pg_end; //!< \@PG chain termination IDs + + // @cond internal + char ID_buf[1024]; // temporary buffer + int ID_cnt; + int ref_count; // number of uses of this SAM_hdr + // @endcond +} SAM_hdr; + +/*! Creates an empty SAM header, ready to be populated. + * + * @return + * Returns a SAM_hdr struct on success (free with sam_hdr_free()) + * NULL on failure + */ +SAM_hdr *sam_hdr_new(void); + +/*! Tokenises a SAM header into a hash table. + * + * Also extracts a few bits on specific data types, such as @RG lines. + * + * @return + * Returns a SAM_hdr struct on success (free with sam_hdr_free()); + * NULL on failure + */ +#ifdef SAMTOOLS +SAM_hdr *sam_hdr_parse_(const char *hdr, int len); +#else +SAM_hdr *sam_hdr_parse(const char *hdr, int len); +#endif + + +/*! Produces a duplicate copy of hdr and returns it. + * @return + * Returns NULL on failure + */ +SAM_hdr *sam_hdr_dup(SAM_hdr *hdr); + + +/*! Increments a reference count on hdr. + * + * This permits multiple files to share the same header, all calling + * sam_hdr_free when done, without causing errors for other open files. + */ +void sam_hdr_incr_ref(SAM_hdr *hdr); + + +/*! Increments a reference count on hdr. + * + * This permits multiple files to share the same header, all calling + * sam_hdr_free when done, without causing errors for other open files. + * + * If the reference count hits zero then the header is automatically + * freed. This makes it a synonym for sam_hdr_free(). + */ +void sam_hdr_decr_ref(SAM_hdr *hdr); + + +/*! Deallocates all storage used by a SAM_hdr struct. + * + * This also decrements the header reference count. If after decrementing + * it is still non-zero then the header is assumed to be in use by another + * caller and the free is not done. + * + * This is a synonym for sam_hdr_dec_ref(). + */ +void sam_hdr_free(SAM_hdr *hdr); + +/*! Returns the current length of the SAM_hdr in text form. + * + * Call sam_hdr_rebuild() first if editing has taken place. + */ +int sam_hdr_length(SAM_hdr *hdr); + +/*! Returns the string form of the SAM_hdr. + * + * Call sam_hdr_rebuild() first if editing has taken place. + */ +char *sam_hdr_str(SAM_hdr *hdr); + +/*! Appends a formatted line to an existing SAM header. + * + * Line is a full SAM header record, eg "@SQ\tSN:foo\tLN:100", with + * optional new-line. If it contains more than 1 line then multiple lines + * will be added in order. + * + * Len is the length of the text data, or 0 if unknown (in which case + * it should be null terminated). + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int sam_hdr_add_lines(SAM_hdr *sh, const char *lines, int len); + +/*! Adds a single line to a SAM header. + * + * Specify type and one or more key,value pairs, ending with the NULL key. + * Eg. sam_hdr_add(h, "SQ", "ID", "foo", "LN", "100", NULL). + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int sam_hdr_add(SAM_hdr *sh, const char *type, ...); + +/*! Adds a single line to a SAM header. + * + * This is much like sam_hdr_add() but with the additional va_list + * argument. This is followed by specifying type and one or more + * key,value pairs, ending with the NULL key. + * + * Eg. sam_hdr_vadd(h, "SQ", args, "ID", "foo", "LN", "100", NULL). + * + * The purpose of the additional va_list parameter is to permit other + * varargs functions to call this while including their own additional + * parameters; an example is in sam_hdr_add_PG(). + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int sam_hdr_vadd(SAM_hdr *sh, const char *type, va_list ap, ...); + +/*! + * @return + * Returns the first header item matching 'type'. If ID is non-NULL it checks + * for the tag ID: and compares against the specified ID. + * + * Returns NULL if no type/ID is found + */ +SAM_hdr_type *sam_hdr_find(SAM_hdr *hdr, char *type, + char *ID_key, char *ID_value); + +/*! + * + * As per SAM_hdr_type, but returns a complete line of formatted text + * for a specific head type/ID combination. If ID is NULL then it returns + * the first line of the specified type. + * + * The returned string is malloced and should be freed by the calling + * function with free(). + * + * @return + * Returns NULL if no type/ID is found. + */ +char *sam_hdr_find_line(SAM_hdr *hdr, char *type, + char *ID_key, char *ID_value); + +/*! Looks for a specific key in a single sam header line. + * + * If prev is non-NULL it also fills this out with the previous tag, to + * permit use in key removal. *prev is set to NULL when the tag is the first + * key in the list. When a tag isn't found, prev (if non NULL) will be the last + * tag in the existing list. + * + * @return + * Returns the tag pointer on success; + * NULL on failure + */ +SAM_hdr_tag *sam_hdr_find_key(SAM_hdr *sh, + SAM_hdr_type *type, + char *key, + SAM_hdr_tag **prev); + +/*! Adds or updates tag key,value pairs in a header line. + * + * Eg for adding M5 tags to @SQ lines or updating sort order for the + * @HD line (although use the sam_hdr_sort_order() function for + * HD manipulation, which is a wrapper around this funuction). + * + * Specify multiple key,value pairs ending in NULL. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int sam_hdr_update(SAM_hdr *hdr, SAM_hdr_type *type, ...); + +/*! Reconstructs the kstring from the header hash table. + * @return + * Returns 0 on success; + * -1 on failure + */ +int sam_hdr_rebuild(SAM_hdr *hdr); + +/*! Looks up a reference sequence by name and returns the numerical ID. + * @return + * Returns -1 if unknown reference. + */ +int sam_hdr_name2ref(SAM_hdr *hdr, const char *ref); + +/*! Looks up a read-group by name and returns a pointer to the start of the + * associated tag list. + * + * @return + * Returns NULL on failure + */ +SAM_RG *sam_hdr_find_rg(SAM_hdr *hdr, const char *rg); + +/*! Fixes any PP links in @PG headers. + * + * If the entries are in order then this doesn't need doing, but incase + * our header is out of order this goes through the sh->pg[] array + * setting the prev_id field. + * + * @return + * Returns 0 on sucess; + * -1 on failure (indicating broken PG/PP records) + */ +int sam_hdr_link_pg(SAM_hdr *hdr); + + +/*! Add an @PG line. + * + * If we wish complete control over this use sam_hdr_add() directly. This + * function uses that, but attempts to do a lot of tedious house work for + * you too. + * + * - It will generate a suitable ID if the supplied one clashes. + * - It will generate multiple @PG records if we have multiple PG chains. + * + * Call it as per sam_hdr_add() with a series of key,value pairs ending + * in NULL. + * + * @return + * Returns 0 on success; + * -1 on failure + */ +int sam_hdr_add_PG(SAM_hdr *sh, const char *name, ...); + +/*! + * A function to help with construction of CL tags in @PG records. + * Takes an argc, argv pair and returns a single space-separated string. + * This string should be deallocated by the calling function. + * + * @return + * Returns malloced char * on success; + * NULL on failure + */ +char *stringify_argv(int argc, char *argv[]); + +#ifdef __cplusplus +} +#endif + +#endif /* _SAM_HDR_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/string_alloc.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/string_alloc.c new file mode 100644 index 0000000000000000000000000000000000000000..d543e146874f0cb6d26b48f10602bb3643d6be36 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/string_alloc.c @@ -0,0 +1,153 @@ +/* +Copyright (c) 2010 Genome Research Ltd. +Author: Andrew Whitwham + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + + +/* + A pooled string allocator intended to cut down on the + memory overhead of many small string allocations. + + Andrew Whitwham, September 2010. +*/ + +#include +#include +#include + +#include "string_alloc.h" + +#define MIN_STR_SIZE 1024 + + +/* creates the string pool. max_length is the initial size + a single string can be. Tha max_length can grow as + needed */ + +string_alloc_t *string_pool_create(size_t max_length) { + string_alloc_t *a_str; + + if (NULL == (a_str = (string_alloc_t *)malloc(sizeof(*a_str)))) { + return NULL; + } + + if (max_length < MIN_STR_SIZE) max_length = MIN_STR_SIZE; + + a_str->nstrings = 0; + a_str->max_length = max_length; + a_str->strings = NULL; + + return a_str; +} + + +/* internal function to do the actual memory allocation */ + +static string_t *new_string_pool(string_alloc_t *a_str) { + string_t *str; + + str = realloc(a_str->strings, (a_str->nstrings + 1) * sizeof(*a_str->strings)); + + if (NULL == str) return NULL; + + a_str->strings = str; + str = &a_str->strings[a_str->nstrings]; + + str->str = malloc(a_str->max_length);; + + if (NULL == str->str) return NULL; + + str->used = 0; + a_str->nstrings++; + + return str; +} + + +/* free allocated memory */ + +void string_pool_destroy(string_alloc_t *a_str) { + size_t i; + + for (i = 0; i < a_str->nstrings; i++) { + free(a_str->strings[i].str); + } + + free(a_str->strings); + free(a_str); +} + + +/* allocate space for a string */ + +char *string_alloc(string_alloc_t *a_str, size_t length) { + string_t *str; + char *ret; + + if (length <= 0) return NULL; + + // add to last string pool if we have space + if (a_str->nstrings) { + str = &a_str->strings[a_str->nstrings - 1]; + + if (str->used + length < a_str->max_length) { + ret = str->str + str->used; + str->used += length; + return ret; + } + } + + // increase the max length if needs be + if (length > a_str->max_length) a_str->max_length = length; + + // need a new string pool + str = new_string_pool(a_str); + + if (NULL == str) return NULL; + + str->used = length; + return str->str; +} + + +/* equivalent to strdup */ + +char *string_dup(string_alloc_t *a_str, char *instr) { + return string_ndup(a_str, instr, strlen(instr)); +} + +char *string_ndup(string_alloc_t *a_str, char *instr, size_t len) { + char *str = string_alloc(a_str, len + 1); + + if (NULL == str) return NULL; + + strncpy(str, instr, len); + str[len] = 0; + + return str; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/string_alloc.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/string_alloc.h new file mode 100644 index 0000000000000000000000000000000000000000..71ae26d3fb407b1ded6a2d67172815b288ffdf97 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/string_alloc.h @@ -0,0 +1,69 @@ +/* +Copyright (c) 2010 Genome Research Ltd. +Author: Andrew Whitwham + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifndef _STRING_ALLOC_H_ +#define _STRING_ALLOC_H_ + +#ifdef __cplusplus +extern "C" { +#endif + +#include + +/* + * A pooled string allocator intended to cut down on the + * memory overhead of many small string allocations. + * + * Andrew Whitwham, September 2010. + */ + +typedef struct { + char *str; + size_t used; +} string_t; + +typedef struct { + size_t max_length; + size_t nstrings; + string_t *strings; +} string_alloc_t; + +string_alloc_t *string_pool_create(size_t max_length); +void string_pool_destroy(string_alloc_t *a_str); +char *string_alloc(string_alloc_t *a_str, size_t length); +char *string_dup(string_alloc_t *a_str, char *instr); +char *string_ndup(string_alloc_t *a_str, char *instr, size_t len); + +#endif + +#ifdef __cplusplus +} +#endif + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/thread_pool.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/thread_pool.c new file mode 100644 index 0000000000000000000000000000000000000000..90652a763ff16d47e5c0d06ed3e7acb4d3061b30 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/thread_pool.c @@ -0,0 +1,713 @@ +/* +Copyright (c) 2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#include + +#include +#include +#include +#include +#include + +#include "cram/thread_pool.h" + +//#define DEBUG +#define DEBUG_TIME + +#ifdef DEBUG +static int worker_id(t_pool *p) { + int i; + pthread_t s = pthread_self(); + for (i = 0; i < p->tsize; i++) { + if (pthread_equal(s, p->t[i])) + return i; + } + return -1; +} +#endif + +/* ---------------------------------------------------------------------------- + * A queue to hold results from the thread pool. + * + * Each thread pool may have jobs of multiple types being queued up and + * interleaved, so we allow several results queue per pool. + * + * The jobs themselves are expected to push their results onto their + * appropriate results queue. + */ + +/* + * Adds a result to the end of the result queue. + * + * Returns 0 on success; + * -1 on failure + */ +static int t_pool_add_result(t_pool_job *j, void *data) { + t_results_queue *q = j->q; + t_pool_result *r; + +#ifdef DEBUG + fprintf(stderr, "%d: Adding resulting to queue %p, serial %d\n", + worker_id(j->p), q, j->serial); +#endif + + /* No results queue is fine if we don't want any results back */ + if (!q) + return 0; + + if (!(r = malloc(sizeof(*r)))) + return -1; + + r->next = NULL; + r->data = data; + r->serial = j->serial; + + pthread_mutex_lock(&q->result_m); + if (q->result_tail) { + q->result_tail->next = r; + q->result_tail = r; + } else { + q->result_head = q->result_tail = r; + } + q->queue_len++; + q->pending--; + +#ifdef DEBUG + fprintf(stderr, "%d: Broadcasting result_avail (id %d)\n", + worker_id(j->p), r->serial); +#endif + pthread_cond_broadcast(&q->result_avail_c); +#ifdef DEBUG + fprintf(stderr, "%d: Broadcast complete\n", worker_id(j->p)); +#endif + + pthread_mutex_unlock(&q->result_m); + + return 0; +} + +/* Core of t_pool_next_result() */ +static t_pool_result *t_pool_next_result_locked(t_results_queue *q) { + t_pool_result *r, *last; + + for (last = NULL, r = q->result_head; r; last = r, r = r->next) { + if (r->serial == q->next_serial) + break; + } + + if (r) { + if (q->result_head == r) + q->result_head = r->next; + else + last->next = r->next; + + if (q->result_tail == r) + q->result_tail = last; + + if (!q->result_head) + q->result_tail = NULL; + + q->next_serial++; + q->queue_len--; + } + + return r; +} + +/* + * Pulls a result off the head of the result queue. Caller should + * free it (and any internals as appropriate) after use. This doesn't + * wait for a result to be present. + * + * Results will be returned in strict order. + * + * Returns t_pool_result pointer if a result is ready. + * NULL if not. + */ +t_pool_result *t_pool_next_result(t_results_queue *q) { + t_pool_result *r; + +#ifdef DEBUG + fprintf(stderr, "Requesting next result on queue %p\n", q); +#endif + + pthread_mutex_lock(&q->result_m); + r = t_pool_next_result_locked(q); + pthread_mutex_unlock(&q->result_m); + +#ifdef DEBUG + fprintf(stderr, "(q=%p) Found %p\n", q, r); +#endif + + return r; +} + +t_pool_result *t_pool_next_result_wait(t_results_queue *q) { + t_pool_result *r; + +#ifdef DEBUG + fprintf(stderr, "Waiting for result %d...\n", q->next_serial); +#endif + + pthread_mutex_lock(&q->result_m); + while (!(r = t_pool_next_result_locked(q))) { + /* Possible race here now avoided via _locked() call, but incase... */ + struct timeval now; + struct timespec timeout; + + gettimeofday(&now, NULL); + timeout.tv_sec = now.tv_sec + 10; + timeout.tv_nsec = now.tv_usec * 1000; + + pthread_cond_timedwait(&q->result_avail_c, &q->result_m, &timeout); + } + pthread_mutex_unlock(&q->result_m); + + return r; +} + +/* + * Returns true if there are no items on the finished results queue and + * also none still pending. + */ +int t_pool_results_queue_empty(t_results_queue *q) { + int empty; + + pthread_mutex_lock(&q->result_m); + empty = q->queue_len == 0 && q->pending == 0; + pthread_mutex_unlock(&q->result_m); + + return empty; +} + + +/* + * Returns the number of completed jobs on the results queue. + */ +int t_pool_results_queue_len(t_results_queue *q) { + int len; + + pthread_mutex_lock(&q->result_m); + len = q->queue_len; + pthread_mutex_unlock(&q->result_m); + + return len; +} + +int t_pool_results_queue_sz(t_results_queue *q) { + int len; + + pthread_mutex_lock(&q->result_m); + len = q->queue_len + q->pending; + pthread_mutex_unlock(&q->result_m); + + return len; +} + +/* + * Frees a result 'r' and if free_data is true also frees + * the internal r->data result too. + */ +void t_pool_delete_result(t_pool_result *r, int free_data) { + if (!r) + return; + + if (free_data && r->data) + free(r->data); + + free(r); +} + +/* + * Initialises a results queue. + * + * Results queue pointer on success; + * NULL on failure + */ +t_results_queue *t_results_queue_init(void) { + t_results_queue *q = malloc(sizeof(*q)); + + pthread_mutex_init(&q->result_m, NULL); + pthread_cond_init(&q->result_avail_c, NULL); + + q->result_head = NULL; + q->result_tail = NULL; + q->next_serial = 0; + q->curr_serial = 0; + q->queue_len = 0; + q->pending = 0; + + return q; +} + +/* Deallocates memory for a results queue */ +void t_results_queue_destroy(t_results_queue *q) { +#ifdef DEBUG + fprintf(stderr, "Destroying results queue %p\n", q); +#endif + + if (!q) + return; + + pthread_mutex_destroy(&q->result_m); + pthread_cond_destroy(&q->result_avail_c); + + memset(q, 0xbb, sizeof(*q)); + free(q); + +#ifdef DEBUG + fprintf(stderr, "Destroyed results queue %p\n", q); +#endif +} + +/* ---------------------------------------------------------------------------- + * The thread pool. + */ + +#define TDIFF(t2,t1) ((t2.tv_sec-t1.tv_sec)*1000000 + t2.tv_usec-t1.tv_usec) + +/* + * A worker thread. + * + * Each thread waits for the pool to be non-empty. + * As soon as this applies, one of them succeeds in getting the lock + * and then executes the job. + */ +static void *t_pool_worker(void *arg) { + t_pool *p = (t_pool *)arg; + t_pool_job *j; +#ifdef DEBUG_TIME + struct timeval t1, t2, t3; +#endif + + for (;;) { + // Pop an item off the pool queue +#ifdef DEBUG_TIME + gettimeofday(&t1, NULL); +#endif + + pthread_mutex_lock(&p->pool_m); + +#ifdef DEBUG_TIME + gettimeofday(&t2, NULL); + p->wait_time += TDIFF(t2,t1); +#endif + + p->nwaiting++; + while (!p->head && !p->shutdown) { + if (p->njobs == 0) + pthread_cond_signal(&p->empty_c); +#ifdef DEBUG_TIME + gettimeofday(&t2, NULL); +#endif + + pthread_cond_wait(&p->pending_c, &p->pool_m); + +#ifdef DEBUG_TIME + gettimeofday(&t3, NULL); + p->wait_time += TDIFF(t3,t2); +#endif + } + + p->nwaiting--; + + if (p->shutdown) { + p->total_time += TDIFF(t3,t1); +#ifdef DEBUG + fprintf(stderr, "%d: Shutting down\n", worker_id(p)); +#endif + pthread_mutex_unlock(&p->pool_m); + pthread_exit(NULL); + } + + j = p->head; + if (!(p->head = j->next)) + p->tail = NULL; + + if (p->njobs-- == p->qsize) + pthread_cond_signal(&p->full_c); + + if (p->njobs == 0) + pthread_cond_signal(&p->empty_c); + + pthread_mutex_unlock(&p->pool_m); + + // We have job 'j' - now execute it. + t_pool_add_result(j, j->func(j->arg)); +#ifdef DEBUG_TIME + pthread_mutex_lock(&p->pool_m); + gettimeofday(&t3, NULL); + p->total_time += TDIFF(t3,t1); + pthread_mutex_unlock(&p->pool_m); +#endif + memset(j, 0xbb, sizeof(*j)); + free(j); + } + + return NULL; +} + +/* + * Creates a worker pool of length qsize with tsize worker threads. + * + * Returns pool pointer on success; + * NULL on failure + */ +t_pool *t_pool_init(int qsize, int tsize) { + int i; + t_pool *p = malloc(sizeof(*p)); + p->qsize = qsize; + p->tsize = tsize; + p->njobs = 0; + p->nwaiting = 0; + p->shutdown = 0; + p->head = p->tail = NULL; +#ifdef DEBUG_TIME + p->total_time = p->wait_time = 0; +#endif + + p->t = malloc(tsize * sizeof(p->t[0])); + + pthread_mutex_init(&p->pool_m, NULL); + pthread_cond_init(&p->empty_c, NULL); + pthread_cond_init(&p->pending_c, NULL); + pthread_cond_init(&p->full_c, NULL); + + for (i = 0; i < tsize; i++) { + if (0 != pthread_create(&p->t[i], NULL, t_pool_worker, p)) + return NULL; + } + + return p; +} + +/* + * Adds an item to the work pool. + * + * FIXME: Maybe return 1,0,-1 and distinguish between job dispathed vs + * result returned. Ie rather than blocking on full queue we're permitted + * to return early on "result available" event too. + * Caller would then have a while loop around t_pool_dispatch. + * Or, return -1 and set errno to EAGAIN to indicate job not yet submitted. + * + * Returns 0 on success + * -1 on failure + */ +int t_pool_dispatch(t_pool *p, t_results_queue *q, + void *(*func)(void *arg), void *arg) { + t_pool_job *j = malloc(sizeof(*j)); + + if (!j) + return -1; + j->func = func; + j->arg = arg; + j->next = NULL; + j->p = p; + j->q = q; + if (q) { + pthread_mutex_lock(&q->result_m); + j->serial = q->curr_serial++; + q->pending++; + pthread_mutex_unlock(&q->result_m); + } else { + j->serial = 0; + } + +#ifdef DEBUG + fprintf(stderr, "Dispatching job %p for queue %p, serial %d\n", j, q, j->serial); +#endif + + pthread_mutex_lock(&p->pool_m); + + // Check if queue is full + while (p->njobs == p->qsize) + pthread_cond_wait(&p->full_c, &p->pool_m); + + p->njobs++; + + if (p->tail) { + p->tail->next = j; + p->tail = j; + } else { + p->head = p->tail = j; + } + + if (p->njobs == 1) { + // First job => tell all worker threads to start up + pthread_cond_broadcast(&p->pending_c); + } + + pthread_mutex_unlock(&p->pool_m); + +#ifdef DEBUG + fprintf(stderr, "Dispatched (serial %d)\n", j->serial); +#endif + + return 0; +} + +/* + * As above but optional non-block flag. + * + * nonblock 0 => block if input queue is full + * nonblock +1 => don't block if input queue is full, but do not add task + * nonblock -1 => add task regardless of whether queue is full (over-size) + */ +int t_pool_dispatch2(t_pool *p, t_results_queue *q, + void *(*func)(void *arg), void *arg, int nonblock) { + t_pool_job *j = malloc(sizeof(*j)); + + if (!j) + return -1; + j->func = func; + j->arg = arg; + j->next = NULL; + j->p = p; + j->q = q; + if (q) { + pthread_mutex_lock(&q->result_m); + j->serial = q->curr_serial; + pthread_mutex_unlock(&q->result_m); + } else { + j->serial = 0; + } + +#ifdef DEBUG + fprintf(stderr, "Dispatching job for queue %p, serial %d\n", q, j->serial); +#endif + + pthread_mutex_lock(&p->pool_m); + + if (p->njobs == p->qsize && nonblock == 1) { + pthread_mutex_unlock(&p->pool_m); + errno = EAGAIN; + free(j); + return -1; + } + + if (q) { + pthread_mutex_lock(&q->result_m); + q->curr_serial++; + q->pending++; + pthread_mutex_unlock(&q->result_m); + } + + // Check if queue is full + if (nonblock == 0) + while (p->njobs == p->qsize) + pthread_cond_wait(&p->full_c, &p->pool_m); + + p->njobs++; + +// if (q->curr_serial % 100 == 0) +// fprintf(stderr, "p->njobs = %d p->qsize = %d\n", p->njobs, p->qsize); + + if (p->tail) { + p->tail->next = j; + p->tail = j; + } else { + p->head = p->tail = j; + } + +#ifdef DEBUG + fprintf(stderr, "Dispatched (serial %d)\n", j->serial); +#endif + + if (p->njobs == 1) { + // First job => tell all worker threads to start up + pthread_cond_broadcast(&p->pending_c); + } + + pthread_mutex_unlock(&p->pool_m); + + return 0; +} + +/* + * Flushes the pool, but doesn't exit. This simply drains the queue and + * ensures all worker threads have finished their current task. + * + * Returns 0 on success; + * -1 on failure + */ +int t_pool_flush(t_pool *p) { +#ifdef DEBUG + fprintf(stderr, "Flushing pool %p\n", p); +#endif + + // Drains the queue + pthread_mutex_lock(&p->pool_m); + while (p->njobs || p->nwaiting != p->tsize) + pthread_cond_wait(&p->empty_c, &p->pool_m); + + pthread_mutex_unlock(&p->pool_m); + +#ifdef DEBUG + fprintf(stderr, "Flushed complete for pool %p, njobs=%d, nwaiting=%d\n", + p, p->njobs, p->nwaiting); +#endif + + return 0; +} + +/* + * Destroys a thread pool. If 'kill' is true the threads are terminated now, + * otherwise they are joined into the main thread so they will finish their + * current work load. + * + * Use t_pool_destroy(p,0) after a t_pool_flush(p) on a normal shutdown or + * t_pool_destroy(p,1) to quickly exit after a fatal error. + */ +void t_pool_destroy(t_pool *p, int kill) { + int i; + +#ifdef DEBUG + fprintf(stderr, "Destroying pool %p, kill=%d\n", p, kill); +#endif + + /* Send shutdown message to worker threads */ + if (!kill) { + pthread_mutex_lock(&p->pool_m); + p->shutdown = 1; + +#ifdef DEBUG + fprintf(stderr, "Sending shutdown request\n"); +#endif + + pthread_cond_broadcast(&p->pending_c); + pthread_mutex_unlock(&p->pool_m); + +#ifdef DEBUG + fprintf(stderr, "Shutdown complete\n"); +#endif + for (i = 0; i < p->tsize; i++) + pthread_join(p->t[i], NULL); + } else { + for (i = 0; i < p->tsize; i++) + pthread_kill(p->t[i], SIGINT); + } + + pthread_mutex_destroy(&p->pool_m); + pthread_cond_destroy(&p->empty_c); + pthread_cond_destroy(&p->pending_c); + pthread_cond_destroy(&p->full_c); + +#ifdef DEBUG_TIME + fprintf(stderr, "Total time=%f\n", p->total_time / 1000000.0); + fprintf(stderr, "Wait time=%f\n", p->wait_time / 1000000.0); + fprintf(stderr, "%d%% utilisation\n", + (int)(100 - ((100.0 * p->wait_time) / p->total_time + 0.5))); +#endif + + free(p->t); + free(p); + +#ifdef DEBUG + fprintf(stderr, "Destroyed pool %p\n", p); +#endif +} + + +/*----------------------------------------------------------------------------- + * Test app. + */ + +#ifdef TEST_MAIN + +#include +#include + +void *doit(void *arg) { + int i, k, x = 0; + int job = *(int *)arg; + int *res; + + printf("Worker: execute job %d\n", job); + + usleep(random() % 1000000); // to coerce job completion out of order + if (0) { + for (k = 0; k < 100; k++) { + for (i = 0; i < 100000; i++) { + x++; + x += x * sin(i); + x += x * cos(x); + } + } + x *= 100; + x += job; + } else { + x = job*job; + } + + printf("Worker: job %d terminating, x=%d\n", job, x); + + free(arg); + + res = malloc(sizeof(*res)); + *res = x; + + return res; +} + +#define NTHREADS 8 + +int main(int argc, char **argv) { + t_pool *p = t_pool_init(NTHREADS*2, NTHREADS); + t_results_queue *q = t_results_queue_init(); + int i; + t_pool_result *r; + + // Dispatch jobs + for (i = 0; i < 20; i++) { + int *ip = malloc(sizeof(*ip)); + *ip = i; + printf("Submitting %d\n", i); + t_pool_dispatch(p, q, doit, ip); + + // Check for results + if ((r = t_pool_next_result(q))) { + printf("RESULT: %d\n", *(int *)r->data); + t_pool_delete_result(r, 1); + } + } + + t_pool_flush(p); + + while ((r = t_pool_next_result(q))) { + printf("RESULT: %d\n", *(int *)r->data); + t_pool_delete_result(r, 1); + } + + t_pool_destroy(p, 0); + t_results_queue_destroy(q); + + return 0; +} +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/thread_pool.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/thread_pool.h new file mode 100644 index 0000000000000000000000000000000000000000..18e8b42770966c70e77a03567ca6921a8ee4f417 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/thread_pool.h @@ -0,0 +1,197 @@ +/* +Copyright (c) 2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +/* + * This file implements a thread pool for multi-threading applications. + * It consists of two distinct interfaces: thread pools an results queues. + * + * The pool of threads is given a function pointer and void* data to pass in. + * This means the pool can run jobs of multiple types, albeit first come + * first served with no job scheduling. + * + * Upon completion, the return value from the function pointer is added to + * a results queue. We may have multiple queues in use for the one pool. + * + * An example: reading from BAM and writing to CRAM with 10 threads. We'll + * have a pool of 10 threads and two results queues holding decoded BAM blocks + * and encoded CRAM blocks respectively. + */ + +#ifndef _THREAD_POOL_H_ +#define _THREAD_POOL_H_ + +#include + +struct t_pool; +struct t_results_queue; + +typedef struct t_pool_job { + void *(*func)(void *arg); + void *arg; + struct t_pool_job *next; + + struct t_pool *p; + struct t_results_queue *q; + int serial; +} t_pool_job; + +typedef struct t_res { + struct t_res *next; + int serial; // sequential number for ordering + void *data; // result itself +} t_pool_result; + +typedef struct t_pool { + int qsize; // size of queue + int njobs; // pending job count + int nwaiting; // how many workers waiting for new jobs + int shutdown; // true if pool is being destroyed + + // queue of pending jobs + t_pool_job *head, *tail; + + // threads + int tsize; // maximum number of jobs + pthread_t *t; + + // Mutexes + pthread_mutex_t pool_m; // used when updating head/tail + + pthread_cond_t empty_c; + pthread_cond_t pending_c; // not empty + pthread_cond_t full_c; + + // Debugging to check wait time + long long total_time, wait_time; +} t_pool; + +typedef struct t_results_queue { + t_pool_result *result_head; + t_pool_result *result_tail; + int next_serial; + int curr_serial; + int queue_len; // number of items in queue + int pending; // number of pending items (in progress or in pool list) + pthread_mutex_t result_m; + pthread_cond_t result_avail_c; +} t_results_queue; + + +/* + * Creates a worker pool of length qsize with tsize worker threads. + * + * Returns pool pointer on success; + * NULL on failure + */ +t_pool *t_pool_init(int qsize, int tsize); + +/* + * Adds an item to the work pool. + * + * FIXME: Maybe return 1,0,-1 and distinguish between job dispathed vs + * result returned. Ie rather than blocking on full queue we're permitted + * to return early on "result available" event too. + * Caller would then have a while loop around t_pool_dispatch. + * Or, return -1 and set errno to E_AGAIN to indicate job not yet submitted. + * + * Returns 0 on success + * -1 on failure + */ +int t_pool_dispatch(t_pool *p, t_results_queue *q, + void *(*func)(void *arg), void *arg); +int t_pool_dispatch2(t_pool *p, t_results_queue *q, + void *(*func)(void *arg), void *arg, int nonblock); + +/* + * Flushes the pool, but doesn't exit. This simply drains the queue and + * ensures all worker threads have finished their current task. + * + * Returns 0 on success; + * -1 on failure + */ +int t_pool_flush(t_pool *p); + +/* + * Destroys a thread pool. If 'kill' is true the threads are terminated now, + * otherwise they are joined into the main thread so they will finish their + * current work load. + * + * Use t_pool_destroy(p,0) after a t_pool_flush(p) on a normal shutdown or + * t_pool_destroy(p,1) to quickly exit after a fatal error. + */ +void t_pool_destroy(t_pool *p, int kill); + +/* + * Pulls a result off the head of the result queue. Caller should + * free it (and any internals as appropriate) after use. This doesn't + * wait for a result to be present. + * + * Results will be returned in strict order. + * + * Returns t_pool_result pointer if a result is ready. + * NULL if not. + */ +t_pool_result *t_pool_next_result(t_results_queue *q); +t_pool_result *t_pool_next_result_wait(t_results_queue *q); + +/* + * Frees a result 'r' and if free_data is true also frees + * the internal r->data result too. + */ +void t_pool_delete_result(t_pool_result *r, int free_data); + +/* + * Initialises a results queue. + * + * Results queue pointer on success; + * NULL on failure + */ +t_results_queue *t_results_queue_init(void); + +/* Deallocates memory for a results queue */ +void t_results_queue_destroy(t_results_queue *q); + +/* + * Returns true if there are no items on the finished results queue and + * also none still pending. + */ +int t_pool_results_queue_empty(t_results_queue *q); + +/* + * Returns the number of completed jobs on the results queue. + */ +int t_pool_results_queue_len(t_results_queue *q); + +/* + * Returns the number of completed jobs plus the number queued up to run. + */ +int t_pool_results_queue_sz(t_results_queue *q); + +#endif /* _THREAD_POOL_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/vlen.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/vlen.c new file mode 100644 index 0000000000000000000000000000000000000000..bc7e7d4b120a2bb34fe5fc0bc7fdb92724a674f3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/vlen.c @@ -0,0 +1,432 @@ +/* +Author: James Bonfield (jkb@sanger.ac.uk) + +Copyright (c) 1995-1996 MEDICAL RESEARCH COUNCIL +All rights reserved + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1 Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2 Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF +MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or +promote products derived from this software without specific prior written +permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/* +Copyright (c) 2004, 2009, 2011-2012 Genome Research Ltd. + +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifdef HAVE_CONFIG_H +#include "io_lib_config.h" +#endif + +#include +#include +#include +#include +#include + +#include "cram/vlen.h" +#include "cram/os.h" + +#ifndef MAX +#define MAX(a,b) ((a)>(b)?(a):(b)) +#endif + +#ifndef ABS +#define ABS(a) ((a)>0?(a):-(a)) +#endif + +/* #define DEBUG_printf(a,n) printf(a,n) */ +#define DEBUG_printf(a,n) + +/* + * vlen: 27/10/95 written by James Bonfield, jkb@mrc-lmb.cam.ac.uk + * + * Given sprintf style of arguments this routine returns the maximum + * size of buffer needed to allocate to use with sprintf. It errs on + * the side of caution by being simplistic in its approach: we assume + * all numbers are of maximum length. + * + * Handles the usual type conversions (%[%diuaxXcfeEgGpns]), but not + * the 'wide' character conversions (%C and %S). + * Precision is handled in the correct formats, including %*.* + * notations. + * Additionally, some of the more dubious (but probably illegal) cases + * are supported (eg "%10%" will expand to " %" on many + * systems). + * + * We also assume that the largest integer and larger pointer are 64 + * bits, which at least covers the machines we'll need it for. + */ +int flen(char *fmt, ...) +{ + va_list args; + + va_start(args, fmt); + return vflen(fmt, args); +} + +int vflen(char *fmt, va_list ap) +{ + int len = 0; + char *cp, c; + long long l; + int i; + double d; + + /* + * This code modifies 'ap', but we do not know if va_list is a structure + * or a pointer to an array so we do not know if it is a local variable + * or not. + * C99 gets around this by defining va_copy() to make copies of ap, but + * this does not exist on all systems. + * For now, I just assume that when va_list is a pointer the system also + * provides a va_copy macro to work around this problem. The only system + * I have seen needing this so far was Linux on AMD64. + */ +#if defined(HAVE_VA_COPY) + va_list ap_local; + va_copy(ap_local, ap); +# define ap ap_local +#endif + + for(cp = fmt; *cp; cp++) { + switch(*cp) { + + /* A format specifier */ + case '%': { + char *endp; + long conv_len1=0, conv_len2=0, conv_len=0; + signed int arg_size; + + /* Firstly, strip the modifier flags (+-#0 and [space]) */ + for(; (c=*++cp);) { + if ('#' == c) + len+=2; /* Worst case of "0x" */ + else if ('-' == c || '+' == c || ' ' == c) + len++; + else + break; + } + + /* Width specifier */ + l = strtol(cp, &endp, 10); + if (endp != cp) { + cp = endp; + conv_len = conv_len1 = l; + } else if (*cp == '*') { + conv_len = conv_len1 = (int)va_arg(ap, int); + cp++; + } + + /* Precision specifier */ + if ('.' == *cp) { + cp++; + conv_len2 = strtol(cp, &endp, 10); + if (endp != cp) { + cp = endp; + } else if (*cp == '*') { + conv_len2 = (int)va_arg(ap, int); + cp++; + } + conv_len = MAX(conv_len1, conv_len2); + } + + /* Short/long identifier */ + if ('h' == *cp) { + arg_size = -1; /* short */ + cp++; + } else if ('l' == *cp) { + arg_size = 1; /* long */ + cp++; + if ('l' == *cp) { + arg_size = 2; /* long long */ + cp++; + } + } else { + arg_size = 0; /* int */ + } + + /* The actual type */ + switch (*cp) { + case '%': + /* + * Not real ANSI I suspect, but we'll allow for the + * completely daft "%10%" example. + */ + len += MAX(conv_len1, 1); + break; + + case 'd': + case 'i': + case 'u': + case 'a': + case 'x': + case 'X': + /* Remember: char and short are sent as int on the stack */ + if (arg_size == -1) + l = (long)va_arg(ap, int); + else if (arg_size == 1) + l = va_arg(ap, long); + else if (arg_size == 2) + l = va_arg(ap, long long); + else + l = (long)va_arg(ap, int); + + DEBUG_printf("%d", l); + + /* + * No number can be more than 24 characters so we'll take + * the max of conv_len and 24 (23 is len(2^64) in octal). + * All that work above and we then go and estimate ;-), + * but it's needed incase someone does %500d. + */ + len += MAX(conv_len, 23); + break; + + case 'c': + i = va_arg(ap, int); + DEBUG_printf("%c", i); + /* + * Note that %10c and %.10c act differently. + * Besides, I think precision is not really allowed for %c. + */ + len += MAX(conv_len1, 1); + break; + + case 'f': + d = va_arg(ap, double); + DEBUG_printf("%f", d); + /* + * Maybe "Inf" or "NaN", but we'll not worry about that. + * Again, err on side of caution and take max of conv_len + * and max length of a double. The worst case I can + * think of is 317 characters (-1[308 zeros].000000) + * without using precision codes. That's horrid. I + * cheat and either use 317 or 15 depending on how + * large the number is as I reckon 99% of floats + * aren't that long. + */ + l = (ABS(d) > 1000000) ? 317 : 15; + l = MAX(l, conv_len1 + 2); + if (conv_len2) l += conv_len2 - 6; + len += l; + break; + + case 'e': + case 'E': + case 'g': + case 'G': + d = va_arg(ap, double); + DEBUG_printf("%g", d); + /* + * Maybe "Inf" or "NaN", but we'll not worry about that + * Again, err on side of caution and take max of conv_len + * and max length of a double (which defaults to only + * '-' + 6 + '.' + 'E[+-]xxx' == 13. + */ + len += MAX(conv_len, 13); + break; + + case 'p': + l = (long)va_arg(ap, void *); + /* + * Max pointer is 64bits == 16 chars (on alpha), + * == 20 with + "0x". + */ + DEBUG_printf("%p", (void *)l); + len += MAX(conv_len, 20); + break; + + case 'n': + /* produces no output */ + break; + + case 's': { + char *s = (char *)va_arg(ap, char *); + DEBUG_printf("%s", s); + + if (!conv_len2) { + len += MAX(conv_len, (int)strlen(s)); + } else { + len += conv_len; + } + break; + } + + default: + /* wchar_t types of 'C' and 'S' aren't supported */ + DEBUG_printf("Arg is %c\n", *cp); + } + + } + + case '\0': + break; + + default: + DEBUG_printf("%c", *cp); + len++; + } + } + + va_end(ap); + + return len+1; /* one for the null character */ +} + +#if 0 +int main() { + int l; + char buf[10000]; + + sprintf(buf, "d: %d\n", 500); + l = flen("d: %d\n", 500); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, ""); + l = flen(""); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%s\n","test"); + l = flen("%s\n", "test"); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%c\n", 'a'); + l = flen("%c\n", 'a'); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%31.30f\n", -9999.99); + l = flen("%31.30f\n", -9999.99); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%f\n", -1e308); + l = flen("%f\n", -1e308); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%.9f\n", -1e308); + l = flen("%.9f\n", -1e308); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%10.20f\n", -1.999222333); + l = flen("%10.20f\n", -1.999222333); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%#g\n", -3.14159265358e-222); + l = flen("%#g\n", -3.1415927e-222); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%e\n", -123456789123456789.1); + l = flen("%e\n", -123456789123456789.1); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%c %f %d %s %c %g %ld %s\n", 'a', 3.1, 9, "one", 'b', 4.2, 9, "two"); + l = flen("%c %f %d %s %c %g %ld %s\n", 'a', 3.1, 9, "one", 'b', 4.2, 9, "two"); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%*.*e %*c\n", 10, 5, 9.0, 20, 'x'); + l = flen("%*.*e %*c\n", 10, 5, 9.0, 20, 'x'); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%10c\n", 'z'); + l = flen("%10c\n", 'z'); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%.10c\n", 'z'); + l = flen("%.10c\n", 'z'); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%10d\n", 'z'); + l = flen("%10d\n", 'z'); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%.10d\n", 'z'); + l = flen("%.10d\n", 'z'); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%10%\n"); + l = flen("%10%\n"); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%.10%\n"); + l = flen("%.10%\n"); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%s\n", "0123456789"); + l = flen("%s\n", "0123456789"); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%5s\n", "0123456789"); + l = flen("%5s\n", "0123456789"); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%50s\n", "0123456789"); + l = flen("%50s\n", "0123456789"); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%.5s\n", "0123456789"); + l = flen("%.5s\n", "0123456789"); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%.50s\n", "0123456789"); + l = flen("%.50s\n", "0123456789"); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%5.50s\n", "0123456789"); + l = flen("%5.50s\n", "0123456789"); + printf("%d %d\n\n", strlen(buf), l); + + sprintf(buf, "%50.5s\n", "0123456789"); + l = flen("%50.5s\n", "0123456789"); + printf("%d %d\n\n", strlen(buf), l); + + return 0; +} +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/vlen.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/vlen.h new file mode 100644 index 0000000000000000000000000000000000000000..6b9b07c52158f81d14b29fd201067491b100b020 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/vlen.h @@ -0,0 +1,48 @@ +/* +Author: James Bonfield (jkb@sanger.ac.uk) + +Copyright (c) 1995-1996 MEDICAL RESEARCH COUNCIL +All rights reserved + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1 Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2 Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF +MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or +promote products derived from this software without specific prior written +permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifndef _VLEN_H_ +#define _VLEN_H_ + +#ifdef __cplusplus +extern "C" { +#endif + +extern int vflen(char *fmt, va_list ap); +extern int flen(char *fmt, ...); + +#ifdef __cplusplus +} +#endif + +#endif /* _VLEN_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/zfio.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/zfio.c new file mode 100644 index 0000000000000000000000000000000000000000..0a0ae0c96c9469a9d8973bcd12b47d0b653761ce --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/zfio.c @@ -0,0 +1,185 @@ +/* +Copyright (c) 2009-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifdef HAVE_CONFIG_H +#include "io_lib_config.h" +#endif + +#include +#include + +#include "cram/os.h" +#include "cram/zfio.h" + +/* ------------------------------------------------------------------------ */ +/* Some wrappers around FILE * vs gzFile *, allowing for either */ + +/* + * gzopen() works on both compressed and uncompressed data, but it has + * a significant performance hit even for uncompressed data (tested as + * 25s using FILE* to 46s via gzOpen and 66s via gzOpen when gzipped). + * + * Hence we use our own wrapper 'zfp' which is a FILE* when uncompressed + * and gzFile* when compressed. This also means we could hide bzopen in + * there too if desired. + */ + +off_t zftello(zfp *zf) { + return zf->fp ? ftello(zf->fp) : -1; +} + +int zfseeko(zfp *zf, off_t offset, int whence) { + return zf->fp ? fseeko(zf->fp, offset, whence) : -1; +} + + +/* + * A wrapper for either fgets or gzgets depending on what has been + * opened. + */ +char *zfgets(char *line, int size, zfp *zf) { + if (zf->fp) + return fgets(line, size, zf->fp); + else + return gzgets(zf->gz, line, size); +} + +/* + * A wrapper for either fputs or gzputs depending on what has been + * opened. + */ +int zfputs(char *line, zfp *zf) { + if (zf->fp) + return fputs(line, zf->fp); + else + return gzputs(zf->gz, line) ? 0 : EOF; +} + +/* + * Peeks at and returns the next character without consuming it from the + * input. (Ie a combination of getc and ungetc). + */ +int zfpeek(zfp *zf) { + int c; + + if (zf->fp) { + c = getc(zf->fp); + if (c != EOF) + ungetc(c, zf->fp); + } else { + c = gzgetc(zf->gz); + if (c != EOF) + gzungetc(c, zf->gz); + } + + return c; +} + +/* A replacement for either feof of gzeof */ +int zfeof(zfp *zf) { + return zf->fp ? feof(zf->fp) : gzeof(zf->gz); +} + +/* A replacement for either fopen or gzopen */ +zfp *zfopen(const char *path, const char *mode) { + char path2[1024]; + zfp *zf; + + if (!(zf = (zfp *)malloc(sizeof(*zf)))) + return NULL; + zf->fp = NULL; + zf->gz = NULL; + + /* Try normal fopen */ + if (mode[0] != 'z' && mode[1] != 'z' && + NULL != (zf->fp = fopen(path, mode))) { + unsigned char magic[2]; + if (2 != fread(magic, 1, 2, zf->fp)) { + free(zf); + return NULL; + } + if (!(magic[0] == 0x1f && + magic[1] == 0x8b)) { + fseeko(zf->fp, 0, SEEK_SET); + return zf; + } + + fclose(zf->fp); + zf->fp = NULL; + } + +#ifdef HAVE_POPEN + /* + * I've no idea why, by gzgets is VERY slow, maybe because it handles + * arbitrary seeks. + * popen to gzip -cd is 3 times faster though. + */ + if (*mode == 'w') { + } else { + if (access(path, R_OK) == 0) { + sprintf(path2, "gzip -cd < %.*s", 1000, path); + if (NULL != (zf->fp = popen(path2, "r"))) + return zf; + } + + sprintf(path2, "gzip -cd < %.*s.gz", 1000, path); + if (NULL != (zf->fp = popen(path2, "r"))) + return zf; + + printf("Failed on %s\n", path); + } else { + sprintf(path2, "gzip > %.*s", 1000, path); + if (NULL != (zf->fp = popen(path2, "w"))) + return zf; + } + + printf("Failed on %s\n", path); + } +#else + /* Gzopen instead */ + if ((zf->gz = gzopen(path, mode))) + return zf; + + sprintf(path2, "%.*s.gz", 1020, path); + if ((zf->gz = gzopen(path2, mode))) + return zf; +#endif + + perror(path); + + free(zf); + return NULL; +} + +int zfclose(zfp *zf) { + int r = (zf->fp) ? fclose(zf->fp) : gzclose(zf->gz); + free(zf); + return r; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/zfio.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/zfio.h new file mode 100644 index 0000000000000000000000000000000000000000..2d0580f4016361d3524f55b7bc8c0b47302d6806 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/cram/zfio.h @@ -0,0 +1,54 @@ +/* +Copyright (c) 2009-2013 Genome Research Ltd. +Author: James Bonfield + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger +Institute nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#ifndef _ZFIO_H_ +#define _ZFIO_H_ + +#include +#include + +/* + * Either a gzFile or a FILE. + */ +typedef struct { + FILE *fp; + gzFile gz; +} zfp; + +off_t zftello(zfp *zf); +int zfseeko(zfp *zf, off_t offset, int whence); +char *zfgets(char *line, int size, zfp *zf); +int zfputs(char *line, zfp *zf); +zfp *zfopen(const char *path, const char *mode); +int zfclose(zfp *zf); +int zfpeek(zfp *zf); +int zfeof(zfp *zf); + +#endif /* _ZFIO_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/faidx.5 b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/faidx.5 new file mode 100644 index 0000000000000000000000000000000000000000..9058e51652093fd8e47e2d9fb87c972138cc7e6c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/faidx.5 @@ -0,0 +1,124 @@ +'\" t +.TH faidx 5 "August 2013" "htslib" "Bioinformatics formats" +.SH NAME +faidx \- an index enabling random access to FASTA files +.SH SYNOPSIS +.IR file.fa .fai, +.IR file.fasta .fai +.SH DESCRIPTION +Using an \fBfai index\fP file in conjunction with a FASTA file containing +reference sequences enables efficient access to arbitrary regions within +those reference sequences. +The index file typically has the same filename as the corresponding FASTA +file, with \fB.fai\fP appended. +.P +An \fBfai index\fP file is a text file consisting of lines each with +five TAB-delimited columns: +.TS +lbl. +NAME Name of this reference sequence +LENGTH Total length of this reference sequence, in bases +OFFSET Offset within the FASTA file of this sequence's first base +LINEBASES The number of bases on each line +LINEWIDTH The number of bytes in each line, including the newline +.TE +.P +The \fBNAME\fP and \fBLENGTH\fP columns contain the same +data as would appear in the \fBSN\fP and \fBLN\fP fields of a +SAM \fB@SQ\fP header for the same reference sequence. +.P +The \fBOFFSET\fP column contains the offset within the FASTA file, in bytes +starting from zero, of the first base of this reference sequence, i.e., of +the character following the newline at the end of the "\fB>\fP" header line. +Typically the lines of a \fBfai index\fP file appear in the order in which the +reference sequences appear in the FASTA file, so \fB.fai\fP files are typically +sorted according to this column. +.P +The \fBLINEBASES\fP column contains the number of bases in each of the sequence +lines that form the body of this reference sequence, apart from the final line +which may be shorter. +The \fBLINEWIDTH\fP column contains the number of \fIbytes\fP in each of +the sequence lines (except perhaps the final line), thus differing from +\fBLINEBASES\fP in that it also counts the bytes forming the line terminator. +.SS FASTA Files +In order to be indexed with \fBsamtools faidx\fP, a FASTA file must be a text +file of the form +.LP +.RS +.RI > name +.RI [ description ...] +.br +ATGCATGCATGCATGCATGCATGCATGCAT +.br +GCATGCATGCATGCATGCATGCATGCATGC +.br +ATGCAT +.br +.RI > name +.RI [ description ...] +.br +ATGCATGCATGCAT +.br +GCATGCATGCATGC +.br +[...] +.RE +.LP +In particular, each reference sequence must be "well-formatted", i.e., all +of its sequence lines must be the same length, apart from the final sequence +line which may be shorter. +(While this sequence line length must be the same within each sequence, +it may vary between different reference sequences in the same FASTA file.) +.P +This also means that although the FASTA file may have Unix- or Windows-style +or other line termination, the newline characters present must be consistent, +at least within each reference sequence. +.P +The \fBsamtools\fP implementation uses the first word of the "\fB>\fP" header +line text (i.e., up to the first whitespace character) as the \fBNAME\fP column. +At present, there may be no whitespace between the +">" character and the \fIname\fP. +.SH EXAMPLE +For example, given this FASTA file +.LP +.RS +>one +.br +ATGCATGCATGCATGCATGCATGCATGCAT +.br +GCATGCATGCATGCATGCATGCATGCATGC +.br +ATGCAT +.br +>two another chromosome +.br +ATGCATGCATGCAT +.br +GCATGCATGCATGC +.br +.RE +.LP +formatted with Unix-style (LF) line termination, the corresponding fai index +would be +.RS +.TS +lnnnn. +one 66 5 30 31 +two 28 98 14 15 +.TE +.RE +.LP +If the FASTA file were formatted with Windows-style (CR-LF) line termination, +the fai index would be +.RS +.TS +lnnnn. +one 66 6 30 32 +two 28 103 14 16 +.TE +.RE +.SH SEE ALSO +.IR samtools (1) +.TP +http://en.wikipedia.org/wiki/FASTA_format +Further description of the FASTA format diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/faidx.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/faidx.c new file mode 100644 index 0000000000000000000000000000000000000000..05dff83120672d6bd22a50b434a6c45ad701ed91 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/faidx.c @@ -0,0 +1,421 @@ +#include "config.h" + +#include +#include +#include +#include +#include + +#include "htslib/bgzf.h" +#include "htslib/faidx.h" +#include "htslib/khash.h" +#ifdef _USE_KNETFILE +#include "htslib/knetfile.h" +#endif + +typedef struct { + int32_t line_len, line_blen; + int64_t len; + uint64_t offset; +} faidx1_t; +KHASH_MAP_INIT_STR(s, faidx1_t) + +struct __faidx_t { + BGZF *bgzf; + int n, m; + char **name; + khash_t(s) *hash; +}; + +#ifndef kroundup32 +#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) +#endif + +static inline void fai_insert_index(faidx_t *idx, const char *name, int len, int line_len, int line_blen, uint64_t offset) +{ + khint_t k; + int ret; + faidx1_t t; + if (idx->n == idx->m) { + idx->m = idx->m? idx->m<<1 : 16; + idx->name = (char**)realloc(idx->name, sizeof(char*) * idx->m); + } + idx->name[idx->n] = strdup(name); + k = kh_put(s, idx->hash, idx->name[idx->n], &ret); + t.len = len; t.line_len = line_len; t.line_blen = line_blen; t.offset = offset; + kh_value(idx->hash, k) = t; + ++idx->n; +} + +faidx_t *fai_build_core(BGZF *bgzf) +{ + char c, *name; + int l_name, m_name; + int line_len, line_blen, state; + int l1, l2; + faidx_t *idx; + uint64_t offset; + int64_t len; + + idx = (faidx_t*)calloc(1, sizeof(faidx_t)); + idx->hash = kh_init(s); + name = 0; l_name = m_name = 0; + len = line_len = line_blen = -1; state = 0; l1 = l2 = -1; offset = 0; + while ( (c=bgzf_getc(bgzf))>=0 ) { + if (c == '\n') { // an empty line + if (state == 1) { + offset = bgzf_utell(bgzf); + continue; + } else if ((state == 0 && len < 0) || state == 2) continue; + } + if (c == '>') { // fasta header + if (len >= 0) + fai_insert_index(idx, name, len, line_len, line_blen, offset); + l_name = 0; + while ( (c=bgzf_getc(bgzf))>=0 && !isspace(c)) { + if (m_name < l_name + 2) { + m_name = l_name + 2; + kroundup32(m_name); + name = (char*)realloc(name, m_name); + } + name[l_name++] = c; + } + name[l_name] = '\0'; + if ( c<0 ) { + fprintf(stderr, "[fai_build_core] the last entry has no sequence\n"); + free(name); fai_destroy(idx); + return 0; + } + if (c != '\n') while ( (c=bgzf_getc(bgzf))>=0 && c != '\n'); + state = 1; len = 0; + offset = bgzf_utell(bgzf); + } else { + if (state == 3) { + fprintf(stderr, "[fai_build_core] inlined empty line is not allowed in sequence '%s'.\n", name); + free(name); fai_destroy(idx); + return 0; + } + if (state == 2) state = 3; + l1 = l2 = 0; + do { + ++l1; + if (isgraph(c)) ++l2; + } while ( (c=bgzf_getc(bgzf))>=0 && c != '\n'); + if (state == 3 && l2) { + fprintf(stderr, "[fai_build_core] different line length in sequence '%s'.\n", name); + free(name); fai_destroy(idx); + return 0; + } + ++l1; len += l2; + if (state == 1) line_len = l1, line_blen = l2, state = 0; + else if (state == 0) { + if (l1 != line_len || l2 != line_blen) state = 2; + } + } + } + fai_insert_index(idx, name, len, line_len, line_blen, offset); + free(name); + return idx; +} + +void fai_save(const faidx_t *fai, FILE *fp) +{ + khint_t k; + int i; + for (i = 0; i < fai->n; ++i) { + faidx1_t x; + k = kh_get(s, fai->hash, fai->name[i]); + x = kh_value(fai->hash, k); +#ifdef _WIN32 + fprintf(fp, "%s\t%d\t%ld\t%d\t%d\n", fai->name[i], (int)x.len, (long)x.offset, (int)x.line_blen, (int)x.line_len); +#else + fprintf(fp, "%s\t%d\t%lld\t%d\t%d\n", fai->name[i], (int)x.len, (long long)x.offset, (int)x.line_blen, (int)x.line_len); +#endif + } +} + +faidx_t *fai_read(FILE *fp) +{ + faidx_t *fai; + char *buf, *p; + int len, line_len, line_blen; +#ifdef _WIN32 + long offset; +#else + long long offset; +#endif + fai = (faidx_t*)calloc(1, sizeof(faidx_t)); + fai->hash = kh_init(s); + buf = (char*)calloc(0x10000, 1); + while (!feof(fp) && fgets(buf, 0x10000, fp)) { + for (p = buf; *p && isgraph(*p); ++p); + *p = 0; ++p; +#ifdef _WIN32 + sscanf(p, "%d%ld%d%d", &len, &offset, &line_blen, &line_len); +#else + sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len); +#endif + fai_insert_index(fai, buf, len, line_len, line_blen, offset); + } + free(buf); + return fai; +} + +void fai_destroy(faidx_t *fai) +{ + int i; + for (i = 0; i < fai->n; ++i) free(fai->name[i]); + free(fai->name); + kh_destroy(s, fai->hash); + if (fai->bgzf) bgzf_close(fai->bgzf); + free(fai); +} + +int fai_build(const char *fn) +{ + char *str; + BGZF *bgzf; + FILE *fp; + faidx_t *fai; + str = (char*)calloc(strlen(fn) + 5, 1); + sprintf(str, "%s.fai", fn); + bgzf = bgzf_open(fn, "r"); + if ( !bgzf ) { + fprintf(stderr, "[fai_build] fail to open the FASTA file %s\n",fn); + free(str); + return -1; + } + if ( bgzf->is_compressed ) bgzf_index_build_init(bgzf); + fai = fai_build_core(bgzf); + if ( bgzf->is_compressed ) bgzf_index_dump(bgzf, fn, ".gzi"); + bgzf_close(bgzf); + fp = fopen(str, "wb"); + if ( !fp ) { + fprintf(stderr, "[fai_build] fail to write FASTA index %s\n",str); + fai_destroy(fai); free(str); + return -1; + } + fai_save(fai, fp); + fclose(fp); + free(str); + fai_destroy(fai); + return 0; +} + +#ifdef _USE_KNETFILE +FILE *download_and_open(const char *fn) +{ + const int buf_size = 1 * 1024 * 1024; + uint8_t *buf; + FILE *fp; + knetFile *fp_remote; + const char *url = fn; + const char *p; + int l = strlen(fn); + for (p = fn + l - 1; p >= fn; --p) + if (*p == '/') break; + fn = p + 1; + + // First try to open a local copy + fp = fopen(fn, "r"); + if (fp) + return fp; + + // If failed, download from remote and open + fp_remote = knet_open(url, "rb"); + if (fp_remote == 0) { + fprintf(stderr, "[download_from_remote] fail to open remote file %s\n",url); + return NULL; + } + if ((fp = fopen(fn, "wb")) == 0) { + fprintf(stderr, "[download_from_remote] fail to create file in the working directory %s\n",fn); + knet_close(fp_remote); + return NULL; + } + buf = (uint8_t*)calloc(buf_size, 1); + while ((l = knet_read(fp_remote, buf, buf_size)) != 0) + fwrite(buf, 1, l, fp); + free(buf); + fclose(fp); + knet_close(fp_remote); + + return fopen(fn, "r"); +} +#endif + +faidx_t *fai_load(const char *fn) +{ + char *str; + FILE *fp; + faidx_t *fai; + str = (char*)calloc(strlen(fn) + 5, 1); + sprintf(str, "%s.fai", fn); + +#ifdef _USE_KNETFILE + if (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn) + { + fp = download_and_open(str); + if ( !fp ) + { + fprintf(stderr, "[fai_load] failed to open remote FASTA index %s\n", str); + free(str); + return 0; + } + } + else +#endif + fp = fopen(str, "rb"); + if (fp == 0) { + fprintf(stderr, "[fai_load] build FASTA index.\n"); + fai_build(fn); + fp = fopen(str, "rb"); + if (fp == 0) { + fprintf(stderr, "[fai_load] fail to open FASTA index.\n"); + free(str); + return 0; + } + } + + fai = fai_read(fp); + fclose(fp); + + fai->bgzf = bgzf_open(fn, "rb"); + free(str); + if (fai->bgzf == 0) { + fprintf(stderr, "[fai_load] fail to open FASTA file.\n"); + return 0; + } + if ( fai->bgzf->is_compressed==1 ) + { + if ( bgzf_index_load(fai->bgzf, fn, ".gzi") < 0 ) + { + fprintf(stderr, "[fai_load] failed to load .gzi index: %s[.gzi]\n", fn); + fai_destroy(fai); + return NULL; + } + } + return fai; +} + +char *fai_fetch(const faidx_t *fai, const char *str, int *len) +{ + char *s, c; + int i, l, k, name_end; + khiter_t iter; + faidx1_t val; + khash_t(s) *h; + int beg, end; + + beg = end = -1; + h = fai->hash; + name_end = l = strlen(str); + s = (char*)malloc(l+1); + // remove space + for (i = k = 0; i < l; ++i) + if (!isspace(str[i])) s[k++] = str[i]; + s[k] = 0; l = k; + // determine the sequence name + for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end + if (i >= 0) name_end = i; + if (name_end < l) { // check if this is really the end + int n_hyphen = 0; + for (i = name_end + 1; i < l; ++i) { + if (s[i] == '-') ++n_hyphen; + else if (!isdigit(s[i]) && s[i] != ',') break; + } + if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name + s[name_end] = 0; + iter = kh_get(s, h, s); + if (iter == kh_end(h)) { // cannot find the sequence name + iter = kh_get(s, h, str); // try str as the name + if (iter == kh_end(h)) { + *len = 0; + free(s); return 0; + } else s[name_end] = ':', name_end = l; + } + } else iter = kh_get(s, h, str); + if(iter == kh_end(h)) { + fprintf(stderr, "[fai_fetch] Warning - Reference %s not found in FASTA file, returning empty sequence\n", str); + free(s); + *len = -2; + return 0; + }; + val = kh_value(h, iter); + // parse the interval + if (name_end < l) { + for (i = k = name_end + 1; i < l; ++i) + if (s[i] != ',') s[k++] = s[i]; + s[k] = 0; + beg = atoi(s + name_end + 1); + for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break; + end = i < k? atoi(s + i + 1) : val.len; + if (beg > 0) --beg; + } else beg = 0, end = val.len; + if (beg >= val.len) beg = val.len; + if (end >= val.len) end = val.len; + if (beg > end) beg = end; + free(s); + + // now retrieve the sequence + int ret = bgzf_useek(fai->bgzf, val.offset + beg / val.line_blen * val.line_len + beg % val.line_blen, SEEK_SET); + if ( ret<0 ) + { + *len = -1; + fprintf(stderr, "[fai_fetch] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)\n"); + return NULL; + } + l = 0; + s = (char*)malloc(end - beg + 2); + while ( (c=bgzf_getc(fai->bgzf))>=0 && l < end - beg ) + if (isgraph(c)) s[l++] = c; + s[l] = '\0'; + *len = l; + return s; +} + +int faidx_fetch_nseq(const faidx_t *fai) +{ + return fai->n; +} + +char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len) +{ + int l; + char c; + khiter_t iter; + faidx1_t val; + char *seq=NULL; + + // Adjust position + iter = kh_get(s, fai->hash, c_name); + if (iter == kh_end(fai->hash)) + { + *len = -2; + fprintf(stderr, "[fai_fetch_seq] The sequence \"%s\" not found\n", c_name); + return NULL; + } + val = kh_value(fai->hash, iter); + if(p_end_i < p_beg_i) p_beg_i = p_end_i; + if(p_beg_i < 0) p_beg_i = 0; + else if(val.len <= p_beg_i) p_beg_i = val.len - 1; + if(p_end_i < 0) p_end_i = 0; + else if(val.len <= p_end_i) p_end_i = val.len - 1; + + // Now retrieve the sequence + int ret = bgzf_useek(fai->bgzf, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET); + if ( ret<0 ) + { + *len = -1; + fprintf(stderr, "[fai_fetch_seq] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)\n"); + return NULL; + } + l = 0; + seq = (char*)malloc(p_end_i - p_beg_i + 2); + while ( (c=bgzf_getc(fai->bgzf))>=0 && l < p_end_i - p_beg_i + 1) + if (isgraph(c)) seq[l++] = c; + seq[l] = '\0'; + *len = l; + return seq; +} + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/hfile.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/hfile.c new file mode 100644 index 0000000000000000000000000000000000000000..0188410dd9d65d7149913c041331b878bbccd6a3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/hfile.c @@ -0,0 +1,526 @@ +/* hfile.c -- buffered low-level input/output streams. + + Copyright (C) 2013-2014 Genome Research Ltd. + + Author: John Marshall + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notices and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +DEALINGS IN THE SOFTWARE. */ + +#include +#include +#include +#include + +#include "htslib/hfile.h" +#include "hfile_internal.h" + +/* hFILE fields are used as follows: + + char *buffer; // Pointer to the start of the I/O buffer + char *begin; // First not-yet-read character / unused position + char *end; // First unfilled/unfillable position + char *limit; // Pointer to the first position past the buffer + + const hFILE_backend *backend; // Methods to refill/flush I/O buffer + + off_t offset; // Offset within the stream of buffer position 0 + int at_eof:1; // For reading, whether EOF has been seen + int has_errno; // Error number from the last failure on this stream + +For reading, begin is the first unread character in the buffer and end is the +first unfilled position: + + -----------ABCDEFGHIJKLMNO--------------- + ^buffer ^begin ^end ^limit + +For writing, begin is the first unused position and end is unused so remains +equal to buffer: + + ABCDEFGHIJKLMNOPQRSTUVWXYZ--------------- + ^buffer ^begin ^limit + ^end + +Thus if begin > end then there is a non-empty write buffer, if begin < end +then there is a non-empty read buffer, and if begin == end then both buffers +are empty. In all cases, the stream's file position indicator corresponds +to the position pointed to by begin. */ + +hFILE *hfile_init(size_t struct_size, const char *mode, size_t capacity) +{ + hFILE *fp = (hFILE *) malloc(struct_size); + if (fp == NULL) goto error; + + if (capacity == 0) capacity = 32768; + // FIXME For now, clamp input buffer sizes so mpileup doesn't eat memory + if (strchr(mode, 'r') && capacity > 32768) capacity = 32768; + + fp->buffer = (char *) malloc(capacity); + if (fp->buffer == NULL) goto error; + + fp->begin = fp->end = fp->buffer; + fp->limit = &fp->buffer[capacity]; + + fp->offset = 0; + fp->at_eof = 0; + fp->has_errno = 0; + return fp; + +error: + hfile_destroy(fp); + return NULL; +} + +void hfile_destroy(hFILE *fp) +{ + int save = errno; + if (fp) free(fp->buffer); + free(fp); + errno = save; +} + +static inline int writebuffer_is_nonempty(hFILE *fp) +{ + return fp->begin > fp->end; +} + +/* Refills the read buffer from the backend (once, so may only partially + fill the buffer), returning the number of additional characters read + (which might be 0), or negative when an error occurred. */ +static ssize_t refill_buffer(hFILE *fp) +{ + ssize_t n; + + // Move any unread characters to the start of the buffer + if (fp->begin > fp->buffer) { + fp->offset += fp->begin - fp->buffer; + memmove(fp->buffer, fp->begin, fp->end - fp->begin); + fp->end = &fp->buffer[fp->end - fp->begin]; + fp->begin = fp->buffer; + } + + // Read into the available buffer space at fp->[end,limit) + if (fp->at_eof || fp->end == fp->limit) n = 0; + else { + n = fp->backend->read(fp, fp->end, fp->limit - fp->end); + if (n < 0) { fp->has_errno = errno; return n; } + else if (n == 0) fp->at_eof = 1; + } + + fp->end += n; + return n; +} + +/* Called only from hgetc(), when our buffer is empty. */ +int hgetc2(hFILE *fp) +{ + return (refill_buffer(fp) > 0)? (unsigned char) *(fp->begin++) : EOF; +} + +ssize_t hpeek(hFILE *fp, void *buffer, size_t nbytes) +{ + size_t n = fp->end - fp->begin; + while (n < nbytes) { + ssize_t ret = refill_buffer(fp); + if (ret < 0) return ret; + else if (ret == 0) break; + else n += ret; + } + + if (n > nbytes) n = nbytes; + memcpy(buffer, fp->begin, n); + return n; +} + +/* Called only from hread(); when called, our buffer is empty and nread bytes + have already been placed in the destination buffer. */ +ssize_t hread2(hFILE *fp, void *destv, size_t nbytes, size_t nread) +{ + const size_t capacity = fp->limit - fp->buffer; + char *dest = (char *) destv; + dest += nread, nbytes -= nread; + + // Read large requests directly into the destination buffer + while (nbytes * 2 >= capacity && !fp->at_eof) { + ssize_t n = fp->backend->read(fp, dest, nbytes); + if (n < 0) { fp->has_errno = errno; return n; } + else if (n == 0) fp->at_eof = 1; + fp->offset += n; + dest += n, nbytes -= n; + nread += n; + } + + while (nbytes > 0 && !fp->at_eof) { + size_t n; + ssize_t ret = refill_buffer(fp); + if (ret < 0) return ret; + + n = fp->end - fp->begin; + if (n > nbytes) n = nbytes; + memcpy(dest, fp->begin, n); + fp->begin += n; + dest += n, nbytes -= n; + nread += n; + } + + return nread; +} + +/* Flushes the write buffer, fp->[buffer,begin), out through the backend + returning 0 on success or negative if an error occurred. */ +static ssize_t flush_buffer(hFILE *fp) +{ + const char *buffer = fp->buffer; + while (buffer < fp->begin) { + ssize_t n = fp->backend->write(fp, buffer, fp->begin - buffer); + if (n < 0) { fp->has_errno = errno; return n; } + buffer += n; + fp->offset += n; + } + + fp->begin = fp->buffer; // Leave the buffer empty + return 0; +} + +int hflush(hFILE *fp) +{ + if (flush_buffer(fp) < 0) return EOF; + if (fp->backend->flush(fp) < 0) { fp->has_errno = errno; return EOF; } + return 0; +} + +/* Called only from hputc(), when our buffer is already full. */ +int hputc2(int c, hFILE *fp) +{ + if (flush_buffer(fp) < 0) return EOF; + *(fp->begin++) = c; + return c; +} + +/* Called only from hwrite() and hputs2(); when called, our buffer is full and + ncopied bytes from the source have already been copied to our buffer. */ +ssize_t hwrite2(hFILE *fp, const void *srcv, size_t totalbytes, size_t ncopied) +{ + const char *src = (const char *) srcv; + ssize_t ret; + const size_t capacity = fp->limit - fp->buffer; + size_t remaining = totalbytes - ncopied; + src += ncopied; + + ret = flush_buffer(fp); + if (ret < 0) return ret; + + // Write large blocks out directly from the source buffer + while (remaining * 2 >= capacity) { + ssize_t n = fp->backend->write(fp, src, remaining); + if (n < 0) { fp->has_errno = errno; return n; } + fp->offset += n; + src += n, remaining -= n; + } + + // Just buffer any remaining characters + memcpy(fp->begin, src, remaining); + fp->begin += remaining; + + return totalbytes; +} + +/* Called only from hputs(), when our buffer is already full. */ +int hputs2(const char *text, size_t totalbytes, size_t ncopied, hFILE *fp) +{ + return (hwrite2(fp, text, totalbytes, ncopied) >= 0)? 0 : EOF; +} + +off_t hseek(hFILE *fp, off_t offset, int whence) +{ + off_t pos; + + if (writebuffer_is_nonempty(fp)) { + int ret = flush_buffer(fp); + if (ret < 0) return ret; + } + + pos = fp->backend->seek(fp, offset, whence); + if (pos < 0) { fp->has_errno = errno; return pos; } + + // Seeking succeeded, so discard any non-empty read buffer + fp->begin = fp->end = fp->buffer; + fp->at_eof = 0; + + fp->offset = pos; + return pos; +} + +int hclose(hFILE *fp) +{ + int err = fp->has_errno; + + if (writebuffer_is_nonempty(fp) && hflush(fp) < 0) err = fp->has_errno; + if (fp->backend->close(fp) < 0) err = errno; + hfile_destroy(fp); + + if (err) { + errno = err; + return EOF; + } + else return 0; +} + +void hclose_abruptly(hFILE *fp) +{ + int save = errno; + if (fp->backend->close(fp) < 0) { /* Ignore subsequent errors */ } + hfile_destroy(fp); + errno = save; +} + + +/*************************** + * File descriptor backend * + ***************************/ + +#include +#include +#include +#include + +#ifdef _WIN32 +#define HAVE_CLOSESOCKET +#endif + +/* For Unix, it doesn't matter whether a file descriptor is a socket. + However Windows insists on send()/recv() and its own closesocket() + being used when fd happens to be a socket. */ + +typedef struct { + hFILE base; + int fd; + int is_socket:1; +} hFILE_fd; + +static ssize_t fd_read(hFILE *fpv, void *buffer, size_t nbytes) +{ + hFILE_fd *fp = (hFILE_fd *) fpv; + ssize_t n; + do { + n = fp->is_socket? recv(fp->fd, buffer, nbytes, 0) + : read(fp->fd, buffer, nbytes); + } while (n < 0 && errno == EINTR); + return n; +} + +static ssize_t fd_write(hFILE *fpv, const void *buffer, size_t nbytes) +{ + hFILE_fd *fp = (hFILE_fd *) fpv; + ssize_t n; + do { + n = fp->is_socket? send(fp->fd, buffer, nbytes, 0) + : write(fp->fd, buffer, nbytes); + } while (n < 0 && errno == EINTR); + return n; +} + +static off_t fd_seek(hFILE *fpv, off_t offset, int whence) +{ + hFILE_fd *fp = (hFILE_fd *) fpv; + return lseek(fp->fd, offset, whence); +} + +static int fd_flush(hFILE *fpv) +{ + hFILE_fd *fp = (hFILE_fd *) fpv; + int ret; + do { +#ifdef HAVE_FDATASYNC + ret = fdatasync(fp->fd); +#else + ret = fsync(fp->fd); +#endif + // Ignore invalid-for-fsync(2) errors due to being, e.g., a pipe, + // and operation-not-supported errors (Mac OS X) + if (ret < 0 && (errno == EINVAL || errno == ENOTSUP)) ret = 0; + } while (ret < 0 && errno == EINTR); + return ret; +} + +static int fd_close(hFILE *fpv) +{ + hFILE_fd *fp = (hFILE_fd *) fpv; + int ret; + do { +#ifdef HAVE_CLOSESOCKET + ret = fp->is_socket? closesocket(fp->fd) : close(fp->fd); +#else + ret = close(fp->fd); +#endif + } while (ret < 0 && errno == EINTR); + return ret; +} + +static const struct hFILE_backend fd_backend = +{ + fd_read, fd_write, fd_seek, fd_flush, fd_close +}; + +static size_t blksize(int fd) +{ + struct stat sbuf; + if (fstat(fd, &sbuf) != 0) return 0; + return sbuf.st_blksize; +} + +static hFILE *hopen_fd(const char *filename, const char *mode) +{ + hFILE_fd *fp = NULL; + int fd = open(filename, hfile_oflags(mode), 0666); + if (fd < 0) goto error; + + fp = (hFILE_fd *) hfile_init(sizeof (hFILE_fd), mode, blksize(fd)); + if (fp == NULL) goto error; + + fp->fd = fd; + fp->is_socket = 0; + fp->base.backend = &fd_backend; + return &fp->base; + +error: + if (fd >= 0) { int save = errno; (void) close(fd); errno = save; } + hfile_destroy((hFILE *) fp); + return NULL; +} + +hFILE *hdopen(int fd, const char *mode) +{ + hFILE_fd *fp = (hFILE_fd*) hfile_init(sizeof (hFILE_fd), mode, blksize(fd)); + if (fp == NULL) return NULL; + + fp->fd = fd; + fp->is_socket = (strchr(mode, 's') != NULL); + fp->base.backend = &fd_backend; + return &fp->base; +} + +static hFILE *hopen_fd_stdinout(const char *mode) +{ + int fd = (strchr(mode, 'r') != NULL)? STDIN_FILENO : STDOUT_FILENO; + // TODO Set binary mode (for Windows) + return hdopen(fd, mode); +} + +int hfile_oflags(const char *mode) +{ + int rdwr = 0, flags = 0; + const char *s; + for (s = mode; *s; s++) + switch (*s) { + case 'r': rdwr = O_RDONLY; break; + case 'w': rdwr = O_WRONLY; flags |= O_CREAT | O_TRUNC; break; + case 'a': rdwr = O_WRONLY; flags |= O_CREAT | O_APPEND; break; + case '+': rdwr = O_RDWR; break; + default: break; + } + +#ifdef O_BINARY + flags |= O_BINARY; +#endif + + return rdwr | flags; +} + + +/********************* + * In-memory backend * + *********************/ + +typedef struct { + hFILE base; + const char *buffer; + size_t length, pos; +} hFILE_mem; + +static ssize_t mem_read(hFILE *fpv, void *buffer, size_t nbytes) +{ + hFILE_mem *fp = (hFILE_mem *) fpv; + size_t avail = fp->length - fp->pos; + if (nbytes > avail) nbytes = avail; + memcpy(buffer, fp->buffer + fp->pos, nbytes); + fp->pos += nbytes; + return nbytes; +} + +static off_t mem_seek(hFILE *fpv, off_t offset, int whence) +{ + hFILE_mem *fp = (hFILE_mem *) fpv; + size_t absoffset = (offset >= 0)? offset : -offset; + size_t origin; + + switch (whence) { + case SEEK_SET: origin = 0; break; + case SEEK_CUR: origin = fp->pos; break; + case SEEK_END: origin = fp->length; break; + default: errno = EINVAL; return -1; + } + + if ((offset < 0 && absoffset > origin) || + (offset >= 0 && absoffset > fp->length - origin)) { + errno = EINVAL; + return -1; + } + + fp->pos = origin + offset; + return fp->pos; +} + +static int mem_close(hFILE *fpv) +{ + return 0; +} + +static const struct hFILE_backend mem_backend = +{ + mem_read, NULL, mem_seek, NULL, mem_close +}; + +static hFILE *hopen_mem(const char *data, const char *mode) +{ + // TODO Implement write modes, which will require memory allocation + if (strchr(mode, 'r') == NULL) { errno = EINVAL; return NULL; } + + hFILE_mem *fp = (hFILE_mem *) hfile_init(sizeof (hFILE_mem), mode, 0); + if (fp == NULL) return NULL; + + fp->buffer = data; + fp->length = strlen(data); + fp->pos = 0; + fp->base.backend = &mem_backend; + return &fp->base; +} + + +/****************************** + * hopen() backend dispatcher * + ******************************/ + +hFILE *hopen(const char *fname, const char *mode) +{ + if (strncmp(fname, "http://", 7) == 0 || + strncmp(fname, "ftp://", 6) == 0) return hopen_net(fname, mode); + else if (strncmp(fname, "data:", 5) == 0) return hopen_mem(fname + 5, mode); + else if (strcmp(fname, "-") == 0) return hopen_fd_stdinout(mode); + else return hopen_fd(fname, mode); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/hfile_internal.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/hfile_internal.h new file mode 100644 index 0000000000000000000000000000000000000000..88b0c8eae5707b980987d46dbbfb491d259a77ba --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/hfile_internal.h @@ -0,0 +1,75 @@ +/* hfile_internal.h -- internal parts of low-level input/output streams. + + Copyright (C) 2013-2014 Genome Research Ltd. + + Author: John Marshall + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notices and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +DEALINGS IN THE SOFTWARE. */ + +#ifndef HFILE_INTERNAL_H +#define HFILE_INTERNAL_H + +#include "htslib/hfile.h" + +struct hFILE_backend { + /* As per read(2), returning the number of bytes read (possibly 0) or + negative (and setting errno) on errors. Front-end code will call this + repeatedly if necessary to attempt to get the desired byte count. */ + ssize_t (*read)(hFILE *fp, void *buffer, size_t nbytes) HTS_RESULT_USED; + + /* As per write(2), returning the number of bytes written or negative (and + setting errno) on errors. Front-end code will call this repeatedly if + necessary until the desired block is written or an error occurs. */ + ssize_t (*write)(hFILE *fp, const void *buffer, size_t nbytes) + HTS_RESULT_USED; + + /* As per lseek(2), returning the resulting offset within the stream or + negative (and setting errno) on errors. */ + off_t (*seek)(hFILE *fp, off_t offset, int whence) HTS_RESULT_USED; + + /* Performs low-level flushing, if any, e.g., fsync(2); for writing streams + only. Returns 0 for success or negative (and sets errno) on errors. */ + int (*flush)(hFILE *fp) HTS_RESULT_USED; + + /* Closes the underlying stream (for output streams, the buffer will + already have been flushed), returning 0 for success or negative (and + setting errno) on errors, as per close(2). */ + int (*close)(hFILE *fp) HTS_RESULT_USED; +}; + +/* These are called from the hopen() dispatcher, and should call hfile_init() + to malloc a struct "derived" from hFILE and initialise it appropriately, + including setting base.backend to their own backend vector. */ +hFILE *hopen_net(const char *filename, const char *mode); + +/* May be called by hopen_*() functions to decode a fopen()-style mode into + open(2)-style flags. */ +int hfile_oflags(const char *mode); + +/* Must be called by hopen_*() functions to allocate the hFILE struct and set + up its base. Capacity is a suggested buffer size (e.g., via fstat(2)) + or 0 for a default-sized buffer. */ +hFILE *hfile_init(size_t struct_size, const char *mode, size_t capacity); + +/* May be called by hopen_*() functions to undo the effects of hfile_init() + in the event opening the stream subsequently fails. (This is safe to use + even if fp is NULL. This takes care to preserve errno.) */ +void hfile_destroy(hFILE *fp); + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/hfile_net.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/hfile_net.c new file mode 100644 index 0000000000000000000000000000000000000000..53eda9442a1a8cd1b661f14b378635ddbaad465c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/hfile_net.c @@ -0,0 +1,99 @@ +/* hfile_net.c -- network backend for low-level input/output streams. + + Copyright (C) 2013-2014 Genome Research Ltd. + + Author: John Marshall + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notices and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +DEALINGS IN THE SOFTWARE. */ + +#include +#include + +#include "hfile_internal.h" + +#include "htslib/knetfile.h" + +typedef struct { + hFILE base; + knetFile *netfp; +} hFILE_net; + +static int net_inited = 0; + +#ifdef _WIN32 +static void net_exit(void) +{ + knet_win32_destroy(); +} +#endif + +static int net_init(void) +{ +#ifdef _WIN32 + if (knet_win32_init() != 0) return -1; + + // In the unlikely event atexit() fails, it's better to succeed here and + // carry on and do the I/O; then eventually when the program exits, we'll + // merely have failed to clean up properly, as if we had aborted. + (void) atexit(net_exit); +#endif + + net_inited = 1; + return 0; +} + +static ssize_t net_read(hFILE *fpv, void *buffer, size_t nbytes) +{ + hFILE_net *fp = (hFILE_net *) fpv; + return knet_read(fp->netfp, buffer, nbytes); +} + +static off_t net_seek(hFILE *fpv, off_t offset, int whence) +{ + hFILE_net *fp = (hFILE_net *) fpv; + return knet_seek(fp->netfp, offset, whence); +} + +static int net_close(hFILE *fpv) +{ + hFILE_net *fp = (hFILE_net *) fpv; + return knet_close(fp->netfp); +} + +static const struct hFILE_backend net_backend = +{ + net_read, NULL, net_seek, NULL, net_close +}; + +hFILE *hopen_net(const char *filename, const char *mode) +{ + hFILE_net *fp; + + // Do any networking initialisation if this is the first use. + if (! net_inited) { if (net_init() < 0) return NULL; } + + fp = (hFILE_net *) hfile_init(sizeof (hFILE_net), mode, 0); + if (fp == NULL) return NULL; + + fp->netfp = knet_open(filename, mode); + if (fp->netfp == NULL) { hfile_destroy((hFILE *) fp); return NULL; } + + fp->base.backend = &net_backend; + return &fp->base; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/hts.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/hts.c new file mode 100644 index 0000000000000000000000000000000000000000..0e9b2a674fa54a715f67cf0548413ad54e06fc7c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/hts.c @@ -0,0 +1,1335 @@ +#include +#include +#include +#include +#include +#include +#include +#include +#include "htslib/bgzf.h" +#include "htslib/hts.h" +#include "cram/cram.h" +#include "htslib/hfile.h" +#include "version.h" + +#include "htslib/kseq.h" +#define KS_BGZF 1 +#if KS_BGZF + // bgzf now supports gzip-compressed files + KSTREAM_INIT2(, BGZF*, bgzf_read, 65536) +#else + KSTREAM_INIT2(, gzFile, gzread, 16384) +#endif + +#include "htslib/khash.h" +KHASH_INIT2(s2i,, kh_cstr_t, int64_t, 1, kh_str_hash_func, kh_str_hash_equal) + +int hts_verbose = 3; + +const char *hts_version() +{ + return HTS_VERSION; +} + +const unsigned char seq_nt16_table[256] = { + 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, + 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, + 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, + 1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15, + 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15, + 15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15, + 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15, + 15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15, + + 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, + 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, + 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, + 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, + 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, + 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, + 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, + 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15 +}; + +const char seq_nt16_str[] = "=ACMGRSVTWYHKDBN"; + +/********************** + *** Basic file I/O *** + **********************/ + +// Decompress up to ten or so bytes by peeking at the file, which must be +// positioned at the start of a GZIP block. +static size_t decompress_peek(hFILE *fp, unsigned char *dest, size_t destsize) +{ + // Typically at most a couple of hundred bytes of input are required + // to get a few bytes of output from inflate(), so hopefully this buffer + // size suffices in general. + unsigned char buffer[512]; + z_stream zs; + ssize_t npeek = hpeek(fp, buffer, sizeof buffer); + + if (npeek < 0) return 0; + + zs.zalloc = NULL; + zs.zfree = NULL; + zs.next_in = buffer; + zs.avail_in = npeek; + zs.next_out = dest; + zs.avail_out = destsize; + if (inflateInit2(&zs, 31) != Z_OK) return 0; + + while (zs.total_out < destsize) + if (inflate(&zs, Z_SYNC_FLUSH) != Z_OK) break; + + destsize = zs.total_out; + inflateEnd(&zs); + + return destsize; +} + +// Returns whether the block contains any control characters, i.e., +// characters less than SPACE other than whitespace etc (ASCII BEL..CR). +static int is_binary(unsigned char *s, size_t n) +{ + size_t i; + for (i = 0; i < n; i++) + if (s[i] < 0x07 || (s[i] >= 0x0e && s[i] < 0x20)) return 1; + return 0; +} + +htsFile *hts_open(const char *fn, const char *mode) +{ + htsFile *fp = NULL; + hFILE *hfile = hopen(fn, mode); + if (hfile == NULL) goto error; + + fp = (htsFile*)calloc(1, sizeof(htsFile)); + if (fp == NULL) goto error; + + fp->fn = strdup(fn); + fp->is_be = ed_is_big(); + + if (strchr(mode, 'r')) { + unsigned char s[18]; + if (hpeek(hfile, s, 6) == 6 && memcmp(s, "CRAM", 4) == 0 && + s[4] >= 1 && s[4] <= 2 && s[5] <= 1) { + fp->is_cram = 1; + } + else if (hpeek(hfile, s, 18) == 18 && s[0] == 0x1f && s[1] == 0x8b && + (s[3] & 4) && memcmp(&s[12], "BC\2\0", 4) == 0) { + // The stream is BGZF-compressed. Decompress a few bytes to see + // whether it's in a binary format (e.g., BAM or BCF, starting + // with four bytes of magic including a control character) or is + // a bgzipped SAM or VCF text file. + fp->is_compressed = 1; + if (is_binary(s, decompress_peek(hfile, s, 4))) fp->is_bin = 1; + else fp->is_kstream = 1; + } + else if (hpeek(hfile, s, 2) == 2 && s[0] == 0x1f && s[1] == 0x8b) { + // Plain GZIP header... so a gzipped text file. + fp->is_compressed = 1; + fp->is_kstream = 1; + } + else if (hpeek(hfile, s, 4) == 4 && is_binary(s, 4)) { + // Binary format, but in a raw non-compressed form. + fp->is_bin = 1; + } + else { + fp->is_kstream = 1; + } + } + else if (strchr(mode, 'w') || strchr(mode, 'a')) { + fp->is_write = 1; + if (strchr(mode, 'b')) fp->is_bin = 1; + if (strchr(mode, 'c')) fp->is_cram = 1; + if (strchr(mode, 'z')) fp->is_compressed = 1; + else if (strchr(mode, 'u')) fp->is_compressed = 0; + else fp->is_compressed = 2; // not set, default behaviour + } + else goto error; + + if (fp->is_bin || (fp->is_write && fp->is_compressed==1)) { + fp->fp.bgzf = bgzf_hopen(hfile, mode); + if (fp->fp.bgzf == NULL) goto error; + } + else if (fp->is_cram) { + fp->fp.cram = cram_dopen(hfile, fn, mode); + if (fp->fp.cram == NULL) goto error; + if (!fp->is_write) + cram_set_option(fp->fp.cram, CRAM_OPT_DECODE_MD, 1); + + } + else if (fp->is_kstream) { + #if KS_BGZF + BGZF *gzfp = bgzf_hopen(hfile, mode); + #else + // TODO Implement gzip hFILE adaptor + hclose(hfile); // This won't work, especially for stdin + gzFile gzfp = strcmp(fn, "-")? gzopen(fn, "rb") : gzdopen(fileno(stdin), "rb"); + #endif + if (gzfp) fp->fp.voidp = ks_init(gzfp); + else goto error; + } + else { + fp->fp.hfile = hfile; + } + + return fp; + +error: + if (hts_verbose >= 2) + fprintf(stderr, "[E::%s] fail to open file '%s'\n", __func__, fn); + + if (hfile) + hclose_abruptly(hfile); + + if (fp) { + free(fp->fn); + free(fp->fn_aux); + free(fp); + } + return NULL; +} + +int hts_close(htsFile *fp) +{ + int ret, save; + + if (fp->is_bin || (fp->is_write && fp->is_compressed==1)) { + ret = bgzf_close(fp->fp.bgzf); + } else if (fp->is_cram) { + if (!fp->is_write) { + switch (cram_eof(fp->fp.cram)) { + case 0: + fprintf(stderr, "[E::%s] Failed to decode sequence.\n", __func__); + return -1; + case 2: + fprintf(stderr, "[W::%s] EOF marker is absent. The input is probably truncated.\n", __func__); + break; + default: /* case 1, expected EOF */ + break; + } + } + ret = cram_close(fp->fp.cram); + } else if (fp->is_kstream) { + #if KS_BGZF + BGZF *gzfp = ((kstream_t*)fp->fp.voidp)->f; + ret = bgzf_close(gzfp); + #else + gzFile gzfp = ((kstream_t*)fp->fp.voidp)->f; + ret = gzclose(gzfp); + #endif + ks_destroy((kstream_t*)fp->fp.voidp); + } else { + ret = hclose(fp->fp.hfile); + } + + save = errno; + free(fp->fn); + free(fp->fn_aux); + free(fp->line.s); + free(fp); + errno = save; + return ret; +} + +int hts_set_threads(htsFile *fp, int n) +{ + // TODO Plug in CRAM and other threading + if (fp->is_bin) { + return bgzf_mt(fp->fp.bgzf, n, 256); + } + else return 0; +} + +int hts_set_fai_filename(htsFile *fp, const char *fn_aux) +{ + free(fp->fn_aux); + if (fn_aux) { + fp->fn_aux = strdup(fn_aux); + if (fp->fn_aux == NULL) return -1; + } + else fp->fn_aux = NULL; + + return 0; +} + +// For VCF/BCF backward sweeper. Not exposing these functions because their +// future is uncertain. Things will probably have to change with hFILE... +BGZF *hts_get_bgzfp(htsFile *fp) +{ + if ( fp->is_bin ) + return fp->fp.bgzf; + else + return ((kstream_t*)fp->fp.voidp)->f; +} +int hts_useek(htsFile *fp, long uoffset, int where) +{ + if ( fp->is_bin ) + return bgzf_useek(fp->fp.bgzf, uoffset, where); + else + { + ks_rewind((kstream_t*)fp->fp.voidp); + ((kstream_t*)fp->fp.voidp)->seek_pos = uoffset; + return bgzf_useek(((kstream_t*)fp->fp.voidp)->f, uoffset, where); + } +} +long hts_utell(htsFile *fp) +{ + if ( fp->is_bin ) + return bgzf_utell(fp->fp.bgzf); + else + return ((kstream_t*)fp->fp.voidp)->seek_pos; +} + +int hts_getline(htsFile *fp, int delimiter, kstring_t *str) +{ + int ret, dret; + ret = ks_getuntil((kstream_t*)fp->fp.voidp, delimiter, str, &dret); + ++fp->lineno; + return ret; +} + +char **hts_readlist(const char *string, int is_file, int *_n) +{ + int m = 0, n = 0, dret; + char **s = 0; + if ( is_file ) + { +#if KS_BGZF + BGZF *fp = bgzf_open(string, "r"); +#else + gzFile fp = gzopen(string, "r"); +#endif + if ( !fp ) return NULL; + + kstream_t *ks; + kstring_t str; + str.s = 0; str.l = str.m = 0; + ks = ks_init(fp); + while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) + { + if (str.l == 0) continue; + n++; + hts_expand(char*,n,m,s); + s[n-1] = strdup(str.s); + } + ks_destroy(ks); +#if KS_BGZF + bgzf_close(fp); +#else + gzclose(fp); +#endif + free(str.s); + } + else + { + const char *q = string, *p = string; + while ( 1 ) + { + if (*p == ',' || *p == 0) + { + n++; + hts_expand(char*,n,m,s); + s[n-1] = (char*)calloc(p - q + 1, 1); + strncpy(s[n-1], q, p - q); + q = p + 1; + } + if ( !*p ) break; + p++; + } + } + s = (char**)realloc(s, n * sizeof(char*)); + *_n = n; + return s; +} + +char **hts_readlines(const char *fn, int *_n) +{ + int m = 0, n = 0, dret; + char **s = 0; +#if KS_BGZF + BGZF *fp = bgzf_open(fn, "r"); +#else + gzFile fp = gzopen(fn, "r"); +#endif + if ( fp ) { // read from file + kstream_t *ks; + kstring_t str; + str.s = 0; str.l = str.m = 0; + ks = ks_init(fp); + while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) { + if (str.l == 0) continue; + if (m == n) { + m = m? m<<1 : 16; + s = (char**)realloc(s, m * sizeof(char*)); + } + s[n++] = strdup(str.s); + } + ks_destroy(ks); + #if KS_BGZF + bgzf_close(fp); + #else + gzclose(fp); + #endif + s = (char**)realloc(s, n * sizeof(char*)); + free(str.s); + } else if (*fn == ':') { // read from string + const char *q, *p; + for (q = p = fn + 1;; ++p) + if (*p == ',' || *p == 0) { + if (m == n) { + m = m? m<<1 : 16; + s = (char**)realloc(s, m * sizeof(char*)); + } + s[n] = (char*)calloc(p - q + 1, 1); + strncpy(s[n++], q, p - q); + q = p + 1; + if (*p == 0) break; + } + } else return 0; + s = (char**)realloc(s, n * sizeof(char*)); + *_n = n; + return s; +} + +int hts_file_type(const char *fname) +{ + int len = strlen(fname); + if ( !strcasecmp(".vcf.gz",fname+len-7) ) return FT_VCF_GZ; + if ( !strcasecmp(".vcf",fname+len-4) ) return FT_VCF; + if ( !strcasecmp(".bcf",fname+len-4) ) return FT_BCF_GZ; + if ( !strcmp("-",fname) ) return FT_STDIN; + // ... etc + + int fd = open(fname, O_RDONLY); + if ( !fd ) return 0; + + uint8_t magic[5]; + if ( read(fd,magic,2)!=2 ) { close(fd); return 0; } + if ( !strncmp((char*)magic,"##",2) ) { close(fd); return FT_VCF; } + if ( !strncmp((char*)magic,"BCF",3) ) { close(fd); return FT_BCF; } + close(fd); + + if ( magic[0]==0x1f && magic[1]==0x8b ) // compressed + { + BGZF *fp = bgzf_open(fname, "r"); + if ( !fp ) return 0; + if ( bgzf_read(fp, magic, 3)!=3 ) { bgzf_close(fp); return 0; } + bgzf_close(fp); + if ( !strncmp((char*)magic,"##",2) ) return FT_VCF; + if ( !strncmp((char*)magic,"BCF",3) ) return FT_BCF_GZ; + } + return 0; +} + +/**************** + *** Indexing *** + ****************/ + +#define HTS_MIN_MARKER_DIST 0x10000 + +// Finds the special meta bin +// ((1<<(3 * n_lvls + 3)) - 1) / 7 + 1 +#define META_BIN(idx) ((idx)->n_bins + 1) + +#define pair64_lt(a,b) ((a).u < (b).u) + +#include "htslib/ksort.h" +KSORT_INIT(_off, hts_pair64_t, pair64_lt) + +typedef struct { + int32_t m, n; + uint64_t loff; + hts_pair64_t *list; +} bins_t; + +#include "htslib/khash.h" +KHASH_MAP_INIT_INT(bin, bins_t) +typedef khash_t(bin) bidx_t; + +typedef struct { + int32_t n, m; + uint64_t *offset; +} lidx_t; + +struct __hts_idx_t { + int fmt, min_shift, n_lvls, n_bins; + uint32_t l_meta; + int32_t n, m; + uint64_t n_no_coor; + bidx_t **bidx; + lidx_t *lidx; + uint8_t *meta; + struct { + uint32_t last_bin, save_bin; + int last_coor, last_tid, save_tid, finished; + uint64_t last_off, save_off; + uint64_t off_beg, off_end; + uint64_t n_mapped, n_unmapped; + } z; // keep internal states +}; + +static inline void insert_to_b(bidx_t *b, int bin, uint64_t beg, uint64_t end) +{ + khint_t k; + bins_t *l; + int absent; + k = kh_put(bin, b, bin, &absent); + l = &kh_value(b, k); + if (absent) { + l->m = 1; l->n = 0; + l->list = (hts_pair64_t*)calloc(l->m, 16); + } + if (l->n == l->m) { + l->m <<= 1; + l->list = (hts_pair64_t*)realloc(l->list, l->m * 16); + } + l->list[l->n].u = beg; + l->list[l->n++].v = end; +} + +static inline void insert_to_l(lidx_t *l, int64_t _beg, int64_t _end, uint64_t offset, int min_shift) +{ + int i, beg, end; + beg = _beg >> min_shift; + end = (_end - 1) >> min_shift; + if (l->m < end + 1) { + int old_m = l->m; + l->m = end + 1; + kroundup32(l->m); + l->offset = (uint64_t*)realloc(l->offset, l->m * 8); + memset(l->offset + old_m, 0xff, 8 * (l->m - old_m)); // fill l->offset with (uint64_t)-1 + } + if (beg == end) { // to save a loop in this case + if (l->offset[beg] == (uint64_t)-1) l->offset[beg] = offset; + } else { + for (i = beg; i <= end; ++i) + if (l->offset[i] == (uint64_t)-1) l->offset[i] = offset; + } + if (l->n < end + 1) l->n = end + 1; +} + +hts_idx_t *hts_idx_init(int n, int fmt, uint64_t offset0, int min_shift, int n_lvls) +{ + hts_idx_t *idx; + idx = (hts_idx_t*)calloc(1, sizeof(hts_idx_t)); + if (idx == NULL) return NULL; + idx->fmt = fmt; + idx->min_shift = min_shift; + idx->n_lvls = n_lvls; + idx->n_bins = ((1<<(3 * n_lvls + 3)) - 1) / 7; + idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; + idx->z.save_off = idx->z.last_off = idx->z.off_beg = idx->z.off_end = offset0; + idx->z.last_coor = 0xffffffffu; + if (n) { + idx->n = idx->m = n; + idx->bidx = (bidx_t**)calloc(n, sizeof(bidx_t*)); + if (idx->bidx == NULL) { free(idx); return NULL; } + idx->lidx = (lidx_t*) calloc(n, sizeof(lidx_t)); + if (idx->lidx == NULL) { free(idx->bidx); free(idx); return NULL; } + } + return idx; +} + +static void update_loff(hts_idx_t *idx, int i, int free_lidx) +{ + bidx_t *bidx = idx->bidx[i]; + lidx_t *lidx = &idx->lidx[i]; + khint_t k; + int l; + uint64_t offset0 = 0; + if (bidx) { + k = kh_get(bin, bidx, META_BIN(idx)); + if (k != kh_end(bidx)) + offset0 = kh_val(bidx, k).list[0].u; + for (l = 0; l < lidx->n && lidx->offset[l] == (uint64_t)-1; ++l) + lidx->offset[l] = offset0; + } else l = 1; + for (; l < lidx->n; ++l) // fill missing values + if (lidx->offset[l] == (uint64_t)-1) + lidx->offset[l] = lidx->offset[l-1]; + if (bidx == 0) return; + for (k = kh_begin(bidx); k != kh_end(bidx); ++k) // set loff + if (kh_exist(bidx, k)) + { + if ( kh_key(bidx, k) < idx->n_bins ) + { + int bot_bin = hts_bin_bot(kh_key(bidx, k), idx->n_lvls); + // disable linear index if bot_bin out of bounds + kh_val(bidx, k).loff = bot_bin < lidx->n ? lidx->offset[bot_bin] : 0; + } + else + kh_val(bidx, k).loff = 0; + } + if (free_lidx) { + free(lidx->offset); + lidx->m = lidx->n = 0; + lidx->offset = 0; + } +} + +static void compress_binning(hts_idx_t *idx, int i) +{ + bidx_t *bidx = idx->bidx[i]; + khint_t k; + int l, m; + if (bidx == 0) return; + // merge a bin to its parent if the bin is too small + for (l = idx->n_lvls; l > 0; --l) { + unsigned start = hts_bin_first(l); + for (k = kh_begin(bidx); k != kh_end(bidx); ++k) { + bins_t *p, *q; + if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue; + p = &kh_value(bidx, k); + if (l < idx->n_lvls && p->n > 1) ks_introsort(_off, p->n, p->list); + if ((p->list[p->n - 1].v>>16) - (p->list[0].u>>16) < HTS_MIN_MARKER_DIST) { + khint_t kp; + kp = kh_get(bin, bidx, hts_bin_parent(kh_key(bidx, k))); + if (kp == kh_end(bidx)) continue; + q = &kh_val(bidx, kp); + if (q->n + p->n > q->m) { + q->m = q->n + p->n; + kroundup32(q->m); + q->list = (hts_pair64_t*)realloc(q->list, q->m * 16); + } + memcpy(q->list + q->n, p->list, p->n * 16); + q->n += p->n; + free(p->list); + kh_del(bin, bidx, k); + } + } + } + k = kh_get(bin, bidx, 0); + if (k != kh_end(bidx)) ks_introsort(_off, kh_val(bidx, k).n, kh_val(bidx, k).list); + // merge adjacent chunks that start from the same BGZF block + for (k = kh_begin(bidx); k != kh_end(bidx); ++k) { + bins_t *p; + if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue; + p = &kh_value(bidx, k); + for (l = 1, m = 0; l < p->n; ++l) { + if (p->list[m].v>>16 >= p->list[l].u>>16) { + if (p->list[m].v < p->list[l].v) p->list[m].v = p->list[l].v; + } else p->list[++m] = p->list[l]; + } + p->n = m + 1; + } +} + +void hts_idx_finish(hts_idx_t *idx, uint64_t final_offset) +{ + int i; + if (idx == NULL || idx->z.finished) return; // do not run this function on an empty index or multiple times + if (idx->z.save_tid >= 0) { + insert_to_b(idx->bidx[idx->z.save_tid], idx->z.save_bin, idx->z.save_off, final_offset); + insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.off_beg, final_offset); + insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.n_mapped, idx->z.n_unmapped); + } + for (i = 0; i < idx->n; ++i) { + update_loff(idx, i, (idx->fmt == HTS_FMT_CSI)); + compress_binning(idx, i); + } + idx->z.finished = 1; +} + +int hts_idx_push(hts_idx_t *idx, int tid, int beg, int end, uint64_t offset, int is_mapped) +{ + int bin; + if (tid >= idx->m) { // enlarge the index + int32_t oldm = idx->m; + idx->m = idx->m? idx->m<<1 : 2; + idx->bidx = (bidx_t**)realloc(idx->bidx, idx->m * sizeof(bidx_t*)); + idx->lidx = (lidx_t*) realloc(idx->lidx, idx->m * sizeof(lidx_t)); + memset(&idx->bidx[oldm], 0, (idx->m - oldm) * sizeof(bidx_t*)); + memset(&idx->lidx[oldm], 0, (idx->m - oldm) * sizeof(lidx_t)); + } + if (idx->n < tid + 1) idx->n = tid + 1; + if (idx->z.finished) return 0; + if (idx->z.last_tid != tid || (idx->z.last_tid >= 0 && tid < 0)) { // change of chromosome + if ( tid>=0 && idx->n_no_coor ) + { + if (hts_verbose >= 1) fprintf(stderr,"[E::%s] NO_COOR reads not in a single block at the end %d %d\n", __func__, tid,idx->z.last_tid); + return -1; + } + if (tid>=0 && idx->bidx[tid] != 0) + { + if (hts_verbose >= 1) fprintf(stderr, "[E::%s] chromosome blocks not continuous\n", __func__); + return -1; + } + idx->z.last_tid = tid; + idx->z.last_bin = 0xffffffffu; + } else if (tid >= 0 && idx->z.last_coor > beg) { // test if positions are out of order + if (hts_verbose >= 1) fprintf(stderr, "[E::%s] unsorted positions\n", __func__); + return -1; + } + if ( tid>=0 ) + { + if (idx->bidx[tid] == 0) idx->bidx[tid] = kh_init(bin); + if ( is_mapped) + insert_to_l(&idx->lidx[tid], beg, end, idx->z.last_off, idx->min_shift); // last_off points to the start of the current record + } + else idx->n_no_coor++; + bin = hts_reg2bin(beg, end, idx->min_shift, idx->n_lvls); + if ((int)idx->z.last_bin != bin) { // then possibly write the binning index + if (idx->z.save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record + insert_to_b(idx->bidx[idx->z.save_tid], idx->z.save_bin, idx->z.save_off, idx->z.last_off); + if (idx->z.last_bin == 0xffffffffu && idx->z.save_bin != 0xffffffffu) { // change of chr; keep meta information + idx->z.off_end = idx->z.last_off; + insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.off_beg, idx->z.off_end); + insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.n_mapped, idx->z.n_unmapped); + idx->z.n_mapped = idx->z.n_unmapped = 0; + idx->z.off_beg = idx->z.off_end; + } + idx->z.save_off = idx->z.last_off; + idx->z.save_bin = idx->z.last_bin = bin; + idx->z.save_tid = tid; + if (tid < 0) { // come to the end of the records having coordinates + hts_idx_finish(idx, offset); + return 0; + } + } + if (is_mapped) ++idx->z.n_mapped; + else ++idx->z.n_unmapped; + idx->z.last_off = offset; + idx->z.last_coor = beg; + return 0; +} + +void hts_idx_destroy(hts_idx_t *idx) +{ + khint_t k; + int i; + if (idx == 0) return; + // For HTS_FMT_CRAI, idx actually points to a different type -- see sam.c + if (idx->fmt == HTS_FMT_CRAI) { free(idx); return; } + + for (i = 0; i < idx->m; ++i) { + bidx_t *bidx = idx->bidx[i]; + free(idx->lidx[i].offset); + if (bidx == 0) continue; + for (k = kh_begin(bidx); k != kh_end(bidx); ++k) + if (kh_exist(bidx, k)) + free(kh_value(bidx, k).list); + kh_destroy(bin, bidx); + } + free(idx->bidx); free(idx->lidx); free(idx->meta); + free(idx); +} + +static inline long idx_read(int is_bgzf, void *fp, void *buf, long l) +{ + if (is_bgzf) return bgzf_read((BGZF*)fp, buf, l); + else return (long)fread(buf, 1, l, (FILE*)fp); +} + +static inline long idx_write(int is_bgzf, void *fp, const void *buf, long l) +{ + if (is_bgzf) return bgzf_write((BGZF*)fp, buf, l); + else return (long)fwrite(buf, 1, l, (FILE*)fp); +} + +static inline void swap_bins(bins_t *p) +{ + int i; + for (i = 0; i < p->n; ++i) { + ed_swap_8p(&p->list[i].u); + ed_swap_8p(&p->list[i].v); + } +} + +static void hts_idx_save_core(const hts_idx_t *idx, void *fp, int fmt) +{ + int32_t i, size, is_be; + int is_bgzf = (fmt != HTS_FMT_BAI); + is_be = ed_is_big(); + if (is_be) { + uint32_t x = idx->n; + idx_write(is_bgzf, fp, ed_swap_4p(&x), 4); + } else idx_write(is_bgzf, fp, &idx->n, 4); + if (fmt == HTS_FMT_TBI && idx->l_meta) idx_write(is_bgzf, fp, idx->meta, idx->l_meta); + for (i = 0; i < idx->n; ++i) { + khint_t k; + bidx_t *bidx = idx->bidx[i]; + lidx_t *lidx = &idx->lidx[i]; + // write binning index + size = bidx? kh_size(bidx) : 0; + if (is_be) { // big endian + uint32_t x = size; + idx_write(is_bgzf, fp, ed_swap_4p(&x), 4); + } else idx_write(is_bgzf, fp, &size, 4); + if (bidx == 0) goto write_lidx; + for (k = kh_begin(bidx); k != kh_end(bidx); ++k) { + bins_t *p; + if (!kh_exist(bidx, k)) continue; + p = &kh_value(bidx, k); + if (is_be) { // big endian + uint32_t x; + x = kh_key(bidx, k); idx_write(is_bgzf, fp, ed_swap_4p(&x), 4); + if (fmt == HTS_FMT_CSI) { + uint64_t y = kh_val(bidx, k).loff; + idx_write(is_bgzf, fp, ed_swap_4p(&y), 8); + } + x = p->n; idx_write(is_bgzf, fp, ed_swap_4p(&x), 4); + swap_bins(p); + idx_write(is_bgzf, fp, p->list, 16 * p->n); + swap_bins(p); + } else { + idx_write(is_bgzf, fp, &kh_key(bidx, k), 4); + if (fmt == HTS_FMT_CSI) idx_write(is_bgzf, fp, &kh_val(bidx, k).loff, 8); + //int j;for(j=0;jn;++j)fprintf(stderr,"%d,%llx,%d,%llx:%llx\n",kh_key(bidx,k),kh_val(bidx, k).loff,j,p->list[j].u,p->list[j].v); + idx_write(is_bgzf, fp, &p->n, 4); + idx_write(is_bgzf, fp, p->list, p->n << 4); + } + } +write_lidx: + if (fmt != HTS_FMT_CSI) { + if (is_be) { + int32_t x = lidx->n; + idx_write(is_bgzf, fp, ed_swap_4p(&x), 4); + for (x = 0; x < lidx->n; ++x) ed_swap_8p(&lidx->offset[x]); + idx_write(is_bgzf, fp, lidx->offset, lidx->n << 3); + for (x = 0; x < lidx->n; ++x) ed_swap_8p(&lidx->offset[x]); + } else { + idx_write(is_bgzf, fp, &lidx->n, 4); + idx_write(is_bgzf, fp, lidx->offset, lidx->n << 3); + } + } + } + if (is_be) { // write the number of reads without coordinates + uint64_t x = idx->n_no_coor; + idx_write(is_bgzf, fp, &x, 8); + } else idx_write(is_bgzf, fp, &idx->n_no_coor, 8); +} + +void hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt) +{ + char *fnidx; + fnidx = (char*)calloc(1, strlen(fn) + 5); + strcpy(fnidx, fn); + if (fmt == HTS_FMT_CSI) { + BGZF *fp; + uint32_t x[3]; + int is_be, i; + is_be = ed_is_big(); + fp = bgzf_open(strcat(fnidx, ".csi"), "w"); + bgzf_write(fp, "CSI\1", 4); + x[0] = idx->min_shift; x[1] = idx->n_lvls; x[2] = idx->l_meta; + if (is_be) { + for (i = 0; i < 3; ++i) + bgzf_write(fp, ed_swap_4p(&x[i]), 4); + } else bgzf_write(fp, &x, 12); + if (idx->l_meta) bgzf_write(fp, idx->meta, idx->l_meta); + hts_idx_save_core(idx, fp, HTS_FMT_CSI); + bgzf_close(fp); + } else if (fmt == HTS_FMT_TBI) { + BGZF *fp; + fp = bgzf_open(strcat(fnidx, ".tbi"), "w"); + bgzf_write(fp, "TBI\1", 4); + hts_idx_save_core(idx, fp, HTS_FMT_TBI); + bgzf_close(fp); + } else if (fmt == HTS_FMT_BAI) { + FILE *fp; + fp = fopen(strcat(fnidx, ".bai"), "w"); + fwrite("BAI\1", 1, 4, fp); + hts_idx_save_core(idx, fp, HTS_FMT_BAI); + fclose(fp); + } else abort(); + free(fnidx); +} + +static int hts_idx_load_core(hts_idx_t *idx, void *fp, int fmt) +{ + int32_t i, n, is_be; + int is_bgzf = (fmt != HTS_FMT_BAI); + is_be = ed_is_big(); + if (idx == NULL) return -4; + for (i = 0; i < idx->n; ++i) { + bidx_t *h; + lidx_t *l = &idx->lidx[i]; + uint32_t key; + int j, absent; + bins_t *p; + h = idx->bidx[i] = kh_init(bin); + if (idx_read(is_bgzf, fp, &n, 4) != 4) return -1; + if (is_be) ed_swap_4p(&n); + for (j = 0; j < n; ++j) { + khint_t k; + if (idx_read(is_bgzf, fp, &key, 4) != 4) return -1; + if (is_be) ed_swap_4p(&key); + k = kh_put(bin, h, key, &absent); + if (absent <= 0) return -3; // Duplicate bin number + p = &kh_val(h, k); + if (fmt == HTS_FMT_CSI) { + if (idx_read(is_bgzf, fp, &p->loff, 8) != 8) return -1; + if (is_be) ed_swap_8p(&p->loff); + } else p->loff = 0; + if (idx_read(is_bgzf, fp, &p->n, 4) != 4) return -1; + if (is_be) ed_swap_4p(&p->n); + p->m = p->n; + p->list = (hts_pair64_t*)malloc(p->m * 16); + if (p->list == NULL) return -2; + if (idx_read(is_bgzf, fp, p->list, p->n<<4) != p->n<<4) return -1; + if (is_be) swap_bins(p); + } + if (fmt != HTS_FMT_CSI) { // load linear index + int j; + if (idx_read(is_bgzf, fp, &l->n, 4) != 4) return -1; + if (is_be) ed_swap_4p(&l->n); + l->m = l->n; + l->offset = (uint64_t*)malloc(l->n << 3); + if (l->offset == NULL) return -2; + if (idx_read(is_bgzf, fp, l->offset, l->n << 3) != l->n << 3) return -1; + if (is_be) for (j = 0; j < l->n; ++j) ed_swap_8p(&l->offset[j]); + for (j = 1; j < l->n; ++j) // fill missing values; may happen given older samtools and tabix + if (l->offset[j] == 0) l->offset[j] = l->offset[j-1]; + update_loff(idx, i, 1); + } + } + if (idx_read(is_bgzf, fp, &idx->n_no_coor, 8) != 8) idx->n_no_coor = 0; + if (is_be) ed_swap_8p(&idx->n_no_coor); + return 0; +} + +hts_idx_t *hts_idx_load_local(const char *fn, int fmt) +{ + uint8_t magic[4]; + int i, is_be; + hts_idx_t *idx = NULL; + is_be = ed_is_big(); + if (fmt == HTS_FMT_CSI) { + BGZF *fp; + uint32_t x[3], n; + uint8_t *meta = 0; + if ((fp = bgzf_open(fn, "r")) == 0) return NULL; + if (bgzf_read(fp, magic, 4) != 4) goto csi_fail; + if (memcmp(magic, "CSI\1", 4) != 0) goto csi_fail; + if (bgzf_read(fp, x, 12) != 12) goto csi_fail; + if (is_be) for (i = 0; i < 3; ++i) ed_swap_4p(&x[i]); + if (x[2]) { + if ((meta = (uint8_t*)malloc(x[2])) == NULL) goto csi_fail; + if (bgzf_read(fp, meta, x[2]) != x[2]) goto csi_fail; + } + if (bgzf_read(fp, &n, 4) != 4) goto csi_fail; + if (is_be) ed_swap_4p(&n); + if ((idx = hts_idx_init(n, fmt, 0, x[0], x[1])) == NULL) goto csi_fail; + idx->l_meta = x[2]; + idx->meta = meta; + meta = NULL; + if (hts_idx_load_core(idx, fp, HTS_FMT_CSI) < 0) goto csi_fail; + bgzf_close(fp); + return idx; + + csi_fail: + bgzf_close(fp); + hts_idx_destroy(idx); + free(meta); + return NULL; + + } else if (fmt == HTS_FMT_TBI) { + BGZF *fp; + uint32_t x[8]; + if ((fp = bgzf_open(fn, "r")) == 0) return NULL; + if (bgzf_read(fp, magic, 4) != 4) goto tbi_fail; + if (memcmp(magic, "TBI\1", 4) != 0) goto tbi_fail; + if (bgzf_read(fp, x, 32) != 32) goto tbi_fail; + if (is_be) for (i = 0; i < 8; ++i) ed_swap_4p(&x[i]); + if ((idx = hts_idx_init(x[0], fmt, 0, 14, 5)) == NULL) goto tbi_fail; + idx->l_meta = 28 + x[7]; + if ((idx->meta = (uint8_t*)malloc(idx->l_meta)) == NULL) goto tbi_fail; + memcpy(idx->meta, &x[1], 28); + if (bgzf_read(fp, idx->meta + 28, x[7]) != x[7]) goto tbi_fail; + if (hts_idx_load_core(idx, fp, HTS_FMT_TBI) < 0) goto tbi_fail; + bgzf_close(fp); + return idx; + + tbi_fail: + bgzf_close(fp); + hts_idx_destroy(idx); + return NULL; + + } else if (fmt == HTS_FMT_BAI) { + uint32_t n; + FILE *fp; + if ((fp = fopen(fn, "rb")) == 0) return NULL; + if (fread(magic, 1, 4, fp) != 4) goto bai_fail; + if (memcmp(magic, "BAI\1", 4) != 0) goto bai_fail; + if (fread(&n, 4, 1, fp) != 1) goto bai_fail; + if (is_be) ed_swap_4p(&n); + idx = hts_idx_init(n, fmt, 0, 14, 5); + if (hts_idx_load_core(idx, fp, HTS_FMT_BAI) < 0) goto bai_fail; + fclose(fp); + return idx; + + bai_fail: + fclose(fp); + hts_idx_destroy(idx); + return NULL; + + } else abort(); +} + +void hts_idx_set_meta(hts_idx_t *idx, int l_meta, uint8_t *meta, int is_copy) +{ + if (idx->meta) free(idx->meta); + idx->l_meta = l_meta; + if (is_copy) { + idx->meta = (uint8_t*)malloc(l_meta); + memcpy(idx->meta, meta, l_meta); + } else idx->meta = meta; +} + +uint8_t *hts_idx_get_meta(hts_idx_t *idx, int *l_meta) +{ + *l_meta = idx->l_meta; + return idx->meta; +} + +const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr) +{ + if ( !idx->n ) + { + *n = 0; + return NULL; + } + + int tid = 0, i; + const char **names = (const char**) calloc(idx->n,sizeof(const char*)); + for (i=0; in; i++) + { + bidx_t *bidx = idx->bidx[i]; + if ( !bidx ) continue; + names[tid++] = getid(hdr,i); + } + *n = tid; + return names; +} + +int hts_idx_get_stat(const hts_idx_t* idx, int tid, uint64_t* mapped, uint64_t* unmapped) +{ + if ( idx->fmt == HTS_FMT_CRAI ) { + *mapped = 0; *unmapped = 0; + return -1; + } + + bidx_t *h = idx->bidx[tid]; + khint_t k = kh_get(bin, h, META_BIN(idx)); + if (k != kh_end(h)) { + *mapped = kh_val(h, k).list[1].u; + *unmapped = kh_val(h, k).list[1].v; + return 0; + } else { + *mapped = 0; *unmapped = 0; + return -1; + } +} + +uint64_t hts_idx_get_n_no_coor(const hts_idx_t* idx) +{ + return idx->n_no_coor; +} + +/**************** + *** Iterator *** + ****************/ + +static inline int reg2bins(int64_t beg, int64_t end, hts_itr_t *itr, int min_shift, int n_lvls) +{ + int l, t, s = min_shift + (n_lvls<<1) + n_lvls; + if (beg >= end) return 0; + if (end >= 1LL<>s); e = t + (end>>s); n = e - b + 1; + if (itr->bins.n + n > itr->bins.m) { + itr->bins.m = itr->bins.n + n; + kroundup32(itr->bins.m); + itr->bins.a = (int*)realloc(itr->bins.a, sizeof(int) * itr->bins.m); + } + for (i = b; i <= e; ++i) itr->bins.a[itr->bins.n++] = i; + } + return itr->bins.n; +} + +hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec) +{ + int i, n_off, l, bin; + hts_pair64_t *off; + khint_t k; + bidx_t *bidx; + uint64_t min_off; + hts_itr_t *iter = 0; + if (tid < 0) { + int finished0 = 0; + uint64_t off0 = (uint64_t)-1; + khint_t k; + switch (tid) { + case HTS_IDX_START: + // Find the smallest offset, note that sequence ids may not be ordered sequentially + for (i=0; in; i++) + { + bidx = idx->bidx[i]; + k = kh_get(bin, bidx, META_BIN(idx)); + if (k == kh_end(bidx)) continue; + if ( off0 > kh_val(bidx, k).list[0].u ) off0 = kh_val(bidx, k).list[0].u; + } + if ( off0==(uint64_t)-1 && idx->n_no_coor ) off0 = 0; // only no-coor reads in this bam + break; + + case HTS_IDX_NOCOOR: + if ( idx->n>0 ) + { + bidx = idx->bidx[idx->n - 1]; + k = kh_get(bin, bidx, META_BIN(idx)); + if (k != kh_end(bidx)) off0 = kh_val(bidx, k).list[0].v; + } + if ( off0==(uint64_t)-1 && idx->n_no_coor ) off0 = 0; // only no-coor reads in this bam + break; + + case HTS_IDX_REST: + off0 = 0; + break; + + case HTS_IDX_NONE: + finished0 = 1; + off0 = 0; + break; + + default: + return 0; + } + if (off0 != (uint64_t)-1) { + iter = (hts_itr_t*)calloc(1, sizeof(hts_itr_t)); + iter->read_rest = 1; + iter->finished = finished0; + iter->curr_off = off0; + iter->readrec = readrec; + return iter; + } else return 0; + } + + if (beg < 0) beg = 0; + if (end < beg) return 0; + if ((bidx = idx->bidx[tid]) == 0) return 0; + + iter = (hts_itr_t*)calloc(1, sizeof(hts_itr_t)); + iter->tid = tid, iter->beg = beg, iter->end = end; iter->i = -1; + iter->readrec = readrec; + + // compute min_off + bin = hts_bin_first(idx->n_lvls) + (beg>>idx->min_shift); + do { + int first; + k = kh_get(bin, bidx, bin); + if (k != kh_end(bidx)) break; + first = (hts_bin_parent(bin)<<3) + 1; + if (bin > first) --bin; + else bin = hts_bin_parent(bin); + } while (bin); + if (bin == 0) k = kh_get(bin, bidx, bin); + min_off = k != kh_end(bidx)? kh_val(bidx, k).loff : 0; + // retrieve bins + reg2bins(beg, end, iter, idx->min_shift, idx->n_lvls); + for (i = n_off = 0; i < iter->bins.n; ++i) + if ((k = kh_get(bin, bidx, iter->bins.a[i])) != kh_end(bidx)) + n_off += kh_value(bidx, k).n; + if (n_off == 0) return iter; + off = (hts_pair64_t*)calloc(n_off, 16); + for (i = n_off = 0; i < iter->bins.n; ++i) { + if ((k = kh_get(bin, bidx, iter->bins.a[i])) != kh_end(bidx)) { + int j; + bins_t *p = &kh_value(bidx, k); + for (j = 0; j < p->n; ++j) + if (p->list[j].v > min_off) off[n_off++] = p->list[j]; + } + } + if (n_off == 0) { + free(off); return iter; + } + ks_introsort(_off, n_off, off); + // resolve completely contained adjacent blocks + for (i = 1, l = 0; i < n_off; ++i) + if (off[l].v < off[i].v) off[++l] = off[i]; + n_off = l + 1; + // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing + for (i = 1; i < n_off; ++i) + if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u; + // merge adjacent blocks + for (i = 1, l = 0; i < n_off; ++i) { + if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v; + else off[++l] = off[i]; + } + n_off = l + 1; + iter->n_off = n_off; iter->off = off; + return iter; +} + +void hts_itr_destroy(hts_itr_t *iter) +{ + if (iter) { free(iter->off); free(iter->bins.a); free(iter); } +} + +const char *hts_parse_reg(const char *s, int *beg, int *end) +{ + int i, k, l, name_end; + *beg = *end = -1; + name_end = l = strlen(s); + // determine the sequence name + for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end + if (i >= 0) name_end = i; + if (name_end < l) { // check if this is really the end + int n_hyphen = 0; + for (i = name_end + 1; i < l; ++i) { + if (s[i] == '-') ++n_hyphen; + else if (!isdigit(s[i]) && s[i] != ',') break; + } + if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name + } + // parse the interval + if (name_end < l) { + char *tmp; + tmp = (char*)alloca(l - name_end + 1); + for (i = name_end + 1, k = 0; i < l; ++i) + if (s[i] != ',') tmp[k++] = s[i]; + tmp[k] = 0; + if ((*beg = strtol(tmp, &tmp, 10) - 1) < 0) *beg = 0; + *end = *tmp? strtol(tmp + 1, &tmp, 10) : 1<<29; + if (*beg > *end) name_end = l; + } + if (name_end == l) *beg = 0, *end = 1<<29; + return s + name_end; +} + +hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec) +{ + int tid, beg, end; + char *q, *tmp; + if (strcmp(reg, ".") == 0) + return itr_query(idx, HTS_IDX_START, 0, 1<<29, readrec); + else if (strcmp(reg, "*") != 0) { + q = (char*)hts_parse_reg(reg, &beg, &end); + tmp = (char*)alloca(q - reg + 1); + strncpy(tmp, reg, q - reg); + tmp[q - reg] = 0; + if ((tid = getid(hdr, tmp)) < 0) + tid = getid(hdr, reg); + if (tid < 0) return 0; + return itr_query(idx, tid, beg, end, readrec); + } else return itr_query(idx, HTS_IDX_NOCOOR, 0, 0, readrec); +} + +int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data) +{ + int ret, tid, beg, end; + if (iter == NULL || iter->finished) return -1; + if (iter->read_rest) { + if (iter->curr_off) { // seek to the start + bgzf_seek(fp, iter->curr_off, SEEK_SET); + iter->curr_off = 0; // only seek once + } + ret = iter->readrec(fp, data, r, &tid, &beg, &end); + if (ret < 0) iter->finished = 1; + return ret; + } + if (iter->off == 0) return -1; + for (;;) { + if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk + if (iter->i == iter->n_off - 1) { ret = -1; break; } // no more chunks + if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek + bgzf_seek(fp, iter->off[iter->i+1].u, SEEK_SET); + iter->curr_off = bgzf_tell(fp); + } + ++iter->i; + } + if ((ret = iter->readrec(fp, data, r, &tid, &beg, &end)) >= 0) { + iter->curr_off = bgzf_tell(fp); + if (tid != iter->tid || beg >= iter->end) { // no need to proceed + ret = -1; break; + } else if (end > iter->beg && iter->end > beg) return ret; + } else break; // end of file or error + } + iter->finished = 1; + return ret; +} + +/********************** + *** Retrieve index *** + **********************/ + +static char *test_and_fetch(const char *fn) +{ + FILE *fp; + // FIXME Use is_remote_scheme() helper that's true for ftp/http/irods/etc + if (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn) { + const int buf_size = 1 * 1024 * 1024; + hFILE *fp_remote; + uint8_t *buf; + int l; + const char *p; + for (p = fn + strlen(fn) - 1; p >= fn; --p) + if (*p == '/') break; + ++p; // p now points to the local file name + if ((fp_remote = hopen(fn, "r")) == 0) { + if (hts_verbose >= 1) fprintf(stderr, "[E::%s] fail to open remote file '%s'\n", __func__, fn); + return 0; + } + if ((fp = fopen(p, "w")) == 0) { + if (hts_verbose >= 1) fprintf(stderr, "[E::%s] fail to create file '%s' in the working directory\n", __func__, p); + hclose_abruptly(fp_remote); + return 0; + } + if (hts_verbose >= 3) fprintf(stderr, "[M::%s] downloading file '%s' to local directory\n", __func__, fn); + buf = (uint8_t*)calloc(buf_size, 1); + while ((l = hread(fp_remote, buf, buf_size)) > 0) fwrite(buf, 1, l, fp); + free(buf); + fclose(fp); + if (hclose(fp_remote) != 0) fprintf(stderr, "[E::%s] fail to close remote file '%s'\n", __func__, fn); + return (char*)p; + } else { + if ((fp = fopen(fn, "rb")) == 0) return 0; + fclose(fp); + return (char*)fn; + } +} + +char *hts_idx_getfn(const char *fn, const char *ext) +{ + int i, l_fn, l_ext; + char *fnidx, *ret; + l_fn = strlen(fn); l_ext = strlen(ext); + fnidx = (char*)calloc(l_fn + l_ext + 1, 1); + strcpy(fnidx, fn); strcpy(fnidx + l_fn, ext); + if ((ret = test_and_fetch(fnidx)) == 0) { + for (i = l_fn - 1; i > 0; --i) + if (fnidx[i] == '.') break; + strcpy(fnidx + i, ext); + ret = test_and_fetch(fnidx); + } + if (ret == 0) { + free(fnidx); + return 0; + } + l_fn = strlen(ret); + memmove(fnidx, ret, l_fn + 1); + return fnidx; +} + +hts_idx_t *hts_idx_load(const char *fn, int fmt) +{ + char *fnidx; + hts_idx_t *idx; + fnidx = hts_idx_getfn(fn, ".csi"); + if (fnidx) fmt = HTS_FMT_CSI; + else fnidx = hts_idx_getfn(fn, fmt == HTS_FMT_BAI? ".bai" : ".tbi"); + if (fnidx == 0) return 0; + + // Check that the index file is up to date, the main file might have changed + struct stat stat_idx,stat_main; + if ( !stat(fn, &stat_main) && !stat(fnidx, &stat_idx) ) + { + if ( stat_idx.st_mtime < stat_main.st_mtime ) + fprintf(stderr, "Warning: The index file is older than the data file: %s\n", fnidx); + } + idx = hts_idx_load_local(fnidx, fmt); + free(fnidx); + return idx; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib.mk b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib.mk new file mode 100644 index 0000000000000000000000000000000000000000..28d0a8f77272b8ad1a23fa7803e03886af081f4b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib.mk @@ -0,0 +1,127 @@ +# Makefile rules useful for third-party code using htslib's public API. +# +# Copyright (C) 2013-2014 Genome Research Ltd. +# +# Author: John Marshall + +# The makefile fragment included below provides variables that can be used +# to express dependencies on headers supplied by an in-development htslib. +# If your source file foo.c #includes and , +# you can write the correct prerequisites for foo.o as: +# +# HTSDIR = +# include $(HTSDIR)/htslib.mk +# +# foo.o: foo.c $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h +# +# Variables are not provided for k*.h, as those never include other headers. + +HTSPREFIX = $(HTSDIR)/ +include $(HTSDIR)/htslib_vars.mk + +# Rules for rebuilding an in-development htslib's static and shared libraries. +# If your program foo links with libhts, adding the appropriate prerequisite +# will cause the library to be rebuilt as necessary: +# +# foo: foo.o $(HTSDIR)/libhts.a +# +# or similarly if your target requires any of the tools supplied: +# +# bar.bed.bgz.tbi: bar.bed.bgz $(HTSDIR)/tabix +# $(HTSDIR)/tabix -p bed bar.bed.bgz + +HTSLIB_PUBLIC_HEADERS = \ + $(HTSDIR)/htslib/bgzf.h \ + $(HTSDIR)/htslib/faidx.h \ + $(HTSDIR)/htslib/hfile.h \ + $(HTSDIR)/htslib/hts.h \ + $(HTSDIR)/htslib/hts_defs.h \ + $(HTSDIR)/htslib/khash.h \ + $(HTSDIR)/htslib/klist.h \ + $(HTSDIR)/htslib/knetfile.h \ + $(HTSDIR)/htslib/kseq.h \ + $(HTSDIR)/htslib/ksort.h \ + $(HTSDIR)/htslib/kstdint.h \ + $(HTSDIR)/htslib/kstring.h \ + $(HTSDIR)/htslib/sam.h \ + $(HTSDIR)/htslib/synced_bcf_reader.h \ + $(HTSDIR)/htslib/tbx.h \ + $(HTSDIR)/htslib/vcf.h \ + $(HTSDIR)/htslib/vcf_sweep.h \ + $(HTSDIR)/htslib/vcfutils.h + +HTSLIB_ALL = \ + $(HTSLIB_PUBLIC_HEADERS) \ + $(HTSDIR)/bgzf.c \ + $(HTSDIR)/faidx.c \ + $(HTSDIR)/hfile_internal.h \ + $(HTSDIR)/hfile.c \ + $(HTSDIR)/hfile_net.c \ + $(HTSDIR)/hts.c \ + $(HTSDIR)/knetfile.c \ + $(HTSDIR)/kstring.c \ + $(HTSDIR)/sam.c \ + $(HTSDIR)/synced_bcf_reader.c \ + $(HTSDIR)/tbx.c \ + $(HTSDIR)/vcf.c \ + $(HTSDIR)/vcf_sweep.c \ + $(HTSDIR)/vcfutils.c \ + $(HTSDIR)/cram/cram.h \ + $(HTSDIR)/cram/cram_codecs.c \ + $(HTSDIR)/cram/cram_codecs.h \ + $(HTSDIR)/cram/cram_decode.c \ + $(HTSDIR)/cram/cram_decode.h \ + $(HTSDIR)/cram/cram_encode.c \ + $(HTSDIR)/cram/cram_encode.h \ + $(HTSDIR)/cram/cram_index.c \ + $(HTSDIR)/cram/cram_index.h \ + $(HTSDIR)/cram/cram_io.c \ + $(HTSDIR)/cram/cram_io.h \ + $(HTSDIR)/cram/cram_samtools.c \ + $(HTSDIR)/cram/cram_samtools.h \ + $(HTSDIR)/cram/cram_stats.c \ + $(HTSDIR)/cram/cram_stats.h \ + $(HTSDIR)/cram/cram_structs.h \ + $(HTSDIR)/cram/files.c \ + $(HTSDIR)/cram/mFILE.c \ + $(HTSDIR)/cram/mFILE.h \ + $(HTSDIR)/cram/md5.c \ + $(HTSDIR)/cram/md5.h \ + $(HTSDIR)/cram/misc.h \ + $(HTSDIR)/cram/open_trace_file.c \ + $(HTSDIR)/cram/open_trace_file.h \ + $(HTSDIR)/cram/os.h \ + $(HTSDIR)/cram/pooled_alloc.c \ + $(HTSDIR)/cram/pooled_alloc.h \ + $(HTSDIR)/cram/sam_header.c \ + $(HTSDIR)/cram/sam_header.h \ + $(HTSDIR)/cram/string_alloc.c \ + $(HTSDIR)/cram/string_alloc.h \ + $(HTSDIR)/cram/thread_pool.c \ + $(HTSDIR)/cram/thread_pool.h \ + $(HTSDIR)/cram/vlen.c \ + $(HTSDIR)/cram/vlen.h \ + $(HTSDIR)/cram/zfio.c \ + $(HTSDIR)/cram/zfio.h + +$(HTSDIR)/libhts.a: $(HTSLIB_ALL) + +cd $(HTSDIR) && $(MAKE) lib-static + +$(HTSDIR)/libhts.so $(HTSDIR)/libhts.dylib: $(HTSLIB_ALL) + +cd $(HTSDIR) && $(MAKE) lib-shared + +$(HTSDIR)/bgzip: $(HTSDIR)/bgzip.c $(HTSLIB_PUBLIC_HEADERS) + +cd $(HTSDIR) && $(MAKE) bgzip + +$(HTSDIR)/tabix: $(HTSDIR)/tabix.c $(HTSLIB_PUBLIC_HEADERS) + +cd $(HTSDIR) && $(MAKE) tabix + +# Rules for phony targets. You may wish to have your corresponding phony +# targets invoke these in addition to their own recipes: +# +# clean: clean-htslib + +clean-htslib install-htslib: + +cd $(HTSDIR) && $(MAKE) $(@:-htslib=) + +.PHONY: clean-htslib install-htslib diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/bgzf.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/bgzf.h new file mode 100644 index 0000000000000000000000000000000000000000..1edce419c71efca4fcf2fc0af4c3cace3e82995d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/bgzf.h @@ -0,0 +1,313 @@ +/* The MIT License + + Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology + 2011, 2012 Attractive Chaos + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + THE SOFTWARE. +*/ + +/* The BGZF library was originally written by Bob Handsaker from the Broad + * Institute. It was later improved by the SAMtools developers. */ + +#ifndef __BGZF_H +#define __BGZF_H + +#include +#include +#include +#include + +#define BGZF_BLOCK_SIZE 0xff00 // make sure compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE +#define BGZF_MAX_BLOCK_SIZE 0x10000 + +#define BGZF_ERR_ZLIB 1 +#define BGZF_ERR_HEADER 2 +#define BGZF_ERR_IO 4 +#define BGZF_ERR_MISUSE 8 + +struct hFILE; +struct bgzf_mtaux_t; +typedef struct __bgzidx_t bgzidx_t; + +struct BGZF { + int errcode:16, is_write:2, is_be:2, compress_level:9, is_compressed:2, is_gzip:1; + int cache_size; + int block_length, block_offset; + int64_t block_address, uncompressed_address; + void *uncompressed_block, *compressed_block; + void *cache; // a pointer to a hash table + struct hFILE *fp; // actual file handle + struct bgzf_mtaux_t *mt; // only used for multi-threading + bgzidx_t *idx; // BGZF index + int idx_build_otf; // build index on the fly, set by bgzf_index_build_init() + z_stream *gz_stream;// for gzip-compressed files +}; +#ifndef HTS_BGZF_TYPEDEF +typedef struct BGZF BGZF; +#define HTS_BGZF_TYPEDEF +#endif + +#ifndef KSTRING_T +#define KSTRING_T kstring_t +typedef struct __kstring_t { + size_t l, m; + char *s; +} kstring_t; +#endif + +#ifdef __cplusplus +extern "C" { +#endif + + /****************** + * Basic routines * + ******************/ + + /** + * Open an existing file descriptor for reading or writing. + * + * @param fd file descriptor + * @param mode mode matching /[rwa][u0-9]+/: 'r' for reading, 'w' for + * writing, or 'a' for appending, while a digit specifies + * the zlib compression level. + * Note that there is a distinction between 'u' and '0': the + * first yields plain uncompressed output whereas the latter + * outputs uncompressed data wrapped in the zlib format. + * @return BGZF file handler; 0 on error + */ + BGZF* bgzf_dopen(int fd, const char *mode); + + #define bgzf_fdopen(fd, mode) bgzf_dopen((fd), (mode)) // for backward compatibility + + /** + * Open the specified file for reading or writing. + */ + BGZF* bgzf_open(const char* path, const char *mode); + + /** + * Open an existing hFILE stream for reading or writing. + */ + BGZF* bgzf_hopen(struct hFILE *fp, const char *mode); + + /** + * Close the BGZF and free all associated resources. + * + * @param fp BGZF file handler + * @return 0 on success and -1 on error + */ + int bgzf_close(BGZF *fp); + + /** + * Read up to _length_ bytes from the file storing into _data_. + * + * @param fp BGZF file handler + * @param data data array to read into + * @param length size of data to read + * @return number of bytes actually read; 0 on end-of-file and -1 on error + */ + ssize_t bgzf_read(BGZF *fp, void *data, size_t length); + + /** + * Write _length_ bytes from _data_ to the file. If no I/O errors occur, + * the complete _length_ bytes will be written (or queued for writing). + * + * @param fp BGZF file handler + * @param data data array to write + * @param length size of data to write + * @return number of bytes written (i.e., _length_); negative on error + */ + ssize_t bgzf_write(BGZF *fp, const void *data, size_t length); + + /** + * Read up to _length_ bytes directly from the underlying stream without + * decompressing. Bypasses BGZF blocking, so must be used with care in + * specialised circumstances only. + * + * @param fp BGZF file handler + * @param data data array to read into + * @param length number of raw bytes to read + * @return number of bytes actually read; 0 on end-of-file and -1 on error + */ + ssize_t bgzf_raw_read(BGZF *fp, void *data, size_t length); + + /** + * Write _length_ bytes directly to the underlying stream without + * compressing. Bypasses BGZF blocking, so must be used with care + * in specialised circumstances only. + * + * @param fp BGZF file handler + * @param data data array to write + * @param length number of raw bytes to write + * @return number of bytes actually written; -1 on error + */ + ssize_t bgzf_raw_write(BGZF *fp, const void *data, size_t length); + + /** + * Write the data in the buffer to the file. + */ + int bgzf_flush(BGZF *fp); + + /** + * Return a virtual file pointer to the current location in the file. + * No interpetation of the value should be made, other than a subsequent + * call to bgzf_seek can be used to position the file at the same point. + * Return value is non-negative on success. + */ + #define bgzf_tell(fp) (((fp)->block_address << 16) | ((fp)->block_offset & 0xFFFF)) + + /** + * Set the file to read from the location specified by _pos_. + * + * @param fp BGZF file handler + * @param pos virtual file offset returned by bgzf_tell() + * @param whence must be SEEK_SET + * @return 0 on success and -1 on error + */ + int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence); + + /** + * Check if the BGZF end-of-file (EOF) marker is present + * + * @param fp BGZF file handler opened for reading + * @return 1 if the EOF marker is present and correct; + * 2 if it can't be checked, e.g., because fp isn't seekable; + * 0 if the EOF marker is absent; + * -1 (with errno set) on error + */ + int bgzf_check_EOF(BGZF *fp); + + /** + * Check if a file is in the BGZF format + * + * @param fn file name + * @return 1 if _fn_ is BGZF; 0 if not or on I/O error + */ + int bgzf_is_bgzf(const char *fn); + + /********************* + * Advanced routines * + *********************/ + + /** + * Set the cache size. Only effective when compiled with -DBGZF_CACHE. + * + * @param fp BGZF file handler + * @param size size of cache in bytes; 0 to disable caching (default) + */ + void bgzf_set_cache_size(BGZF *fp, int size); + + /** + * Flush the file if the remaining buffer size is smaller than _size_ + * @return 0 if flushing succeeded or was not needed; negative on error + */ + int bgzf_flush_try(BGZF *fp, ssize_t size); + + /** + * Read one byte from a BGZF file. It is faster than bgzf_read() + * @param fp BGZF file handler + * @return byte read; -1 on end-of-file or error + */ + int bgzf_getc(BGZF *fp); + + /** + * Read one line from a BGZF file. It is faster than bgzf_getc() + * + * @param fp BGZF file handler + * @param delim delimitor + * @param str string to write to; must be initialized + * @return length of the string; 0 on end-of-file; negative on error + */ + int bgzf_getline(BGZF *fp, int delim, kstring_t *str); + + /** + * Read the next BGZF block. + */ + int bgzf_read_block(BGZF *fp); + + /** + * Enable multi-threading (only effective on writing and when the + * library was compiled with -DBGZF_MT) + * + * @param fp BGZF file handler; must be opened for writing + * @param n_threads #threads used for writing + * @param n_sub_blks #blocks processed by each thread; a value 64-256 is recommended + */ + int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks); + + + /******************* + * bgzidx routines * + *******************/ + + /** + * Position BGZF at the uncompressed offset + * + * @param fp BGZF file handler; must be opened for reading + * @param uoffset file offset in the uncompressed data + * @param where SEEK_SET supported atm + * + * Returns 0 on success and -1 on error. + */ + int bgzf_useek(BGZF *fp, long uoffset, int where); + + /** + * Position in uncompressed BGZF + * + * @param fp BGZF file handler; must be opened for reading + * + * Returns the current offset on success and -1 on error. + */ + long bgzf_utell(BGZF *fp); + + /** + * Tell BGZF to build index while compressing. + * + * @param fp BGZF file handler; can be opened for reading or writing. + * + * Returns 0 on success and -1 on error. + */ + int bgzf_index_build_init(BGZF *fp); + + /** + * Load BGZF index + * + * @param fp BGZF file handler + * @param bname base name + * @param suffix suffix to add to bname (can be NULL) + * + * Returns 0 on success and -1 on error. + */ + int bgzf_index_load(BGZF *fp, const char *bname, const char *suffix); + + /** + * Save BGZF index + * + * @param fp BGZF file handler + * @param bname base name + * @param suffix suffix to add to bname (can be NULL) + * + * Returns 0 on success and -1 on error. + */ + int bgzf_index_dump(BGZF *fp, const char *bname, const char *suffix); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/faidx.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/faidx.h new file mode 100644 index 0000000000000000000000000000000000000000..3153b985ffc5556d485ae73c0aac8290bd8c848b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/faidx.h @@ -0,0 +1,112 @@ +/* The MIT License + + Copyright (c) 2008 Genome Research Ltd (GRL). + + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. +*/ + +/* Contact: Heng Li , Petr Danecek */ + +#ifndef FAIDX_H +#define FAIDX_H + +/*! + @header + + Index FASTA files and extract subsequence. + + The fai file index columns are: + - chromosome name + - chromosome length: number of bases + - offset: number of bytes to skip to get to the first base + from the beginning of the file, including the length + of the sequence description string (">chr ..\n") + - line length: number of bases per line (excluding \n) + - binary line length: number of bytes, including \n + + @copyright The Wellcome Trust Sanger Institute. + */ + +struct __faidx_t; +typedef struct __faidx_t faidx_t; + +#ifdef __cplusplus +extern "C" { +#endif + + /*! + @abstract Build index for a FASTA or bgzip-compressed FASTA file. + @param fn FASTA file name + @return 0 on success; or -1 on failure + @discussion File "fn.fai" will be generated. + */ + int fai_build(const char *fn); + + /*! + @abstract Distroy a faidx_t struct. + @param fai Pointer to the struct to be destroyed + */ + void fai_destroy(faidx_t *fai); + + /*! + @abstract Load index from "fn.fai". + @param fn File name of the FASTA file + */ + faidx_t *fai_load(const char *fn); + + /*! + @abstract Fetch the sequence in a region. + @param fai Pointer to the faidx_t struct + @param reg Region in the format "chr2:20,000-30,000" + @param len Length of the region; -2 if seq not present, -1 general error + @return Pointer to the sequence; null on failure + + @discussion The returned sequence is allocated by malloc family + and should be destroyed by end users by calling free() on it. + */ + char *fai_fetch(const faidx_t *fai, const char *reg, int *len); + + /*! + @abstract Fetch the number of sequences. + @param fai Pointer to the faidx_t struct + @return The number of sequences + */ + int faidx_fetch_nseq(const faidx_t *fai); + + /*! + @abstract Fetch the sequence in a region. + @param fai Pointer to the faidx_t struct + @param c_name Region name + @param p_beg_i Beginning position number (zero-based) + @param p_end_i End position number (zero-based) + @param len Length of the region; -2 if c_name not present, -1 general error + @return Pointer to the sequence; null on failure + + @discussion The returned sequence is allocated by malloc family + and should be destroyed by end users by calling free() on it. + */ + char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/hfile.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/hfile.h new file mode 100644 index 0000000000000000000000000000000000000000..68175e7f56700a692aa3d7dc2e25fb64136fa5e2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/hfile.h @@ -0,0 +1,204 @@ +/* hfile.h -- buffered low-level input/output streams. + + Copyright (C) 2013-2014 Genome Research Ltd. + + Author: John Marshall + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notices and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +DEALINGS IN THE SOFTWARE. */ + +#ifndef HTSLIB_HFILE_H +#define HTSLIB_HFILE_H + +#include + +#include + +#include "hts_defs.h" + +#ifdef __cplusplus +extern "C" { +#endif + +/* These fields are declared here solely for the benefit of the inline functions + below. They may change in future releases. User code should not use them + directly; you should imagine that hFILE is an opaque incomplete type. */ +struct hFILE_backend; +typedef struct hFILE { + char *buffer, *begin, *end, *limit; + const struct hFILE_backend *backend; + off_t offset; + int at_eof:1; + int has_errno; +} hFILE; + +/*! + @abstract Open the named file or URL as a stream + @return An hFILE pointer, or NULL (with errno set) if an error occurred. +*/ +hFILE *hopen(const char *filename, const char *mode) HTS_RESULT_USED; + +/*! + @abstract Associate a stream with an existing open file descriptor + @return An hFILE pointer, or NULL (with errno set) if an error occurred. + @notes For socket descriptors (on Windows), mode should contain 's'. +*/ +hFILE *hdopen(int fd, const char *mode) HTS_RESULT_USED; + +/*! + @abstract Flush (for output streams) and close the stream + @return 0 if successful, or EOF (with errno set) if an error occurred. +*/ +int hclose(hFILE *fp) HTS_RESULT_USED; + +/*! + @abstract Close the stream, without flushing or propagating errors + @notes For use while cleaning up after an error only. Preserves errno. +*/ +void hclose_abruptly(hFILE *fp); + +/*! + @abstract Return the stream's error indicator + @return Non-zero (in fact, an errno value) if an error has occurred. + @notes This would be called herror() and return true/false to parallel + ferror(3), but a networking-related herror(3) function already exists. */ +static inline int herrno(hFILE *fp) +{ + return fp->has_errno; +} + +/*! + @abstract Clear the stream's error indicator +*/ +static inline void hclearerr(hFILE *fp) +{ + fp->has_errno = 0; +} + +/*! + @abstract Reposition the read/write stream offset + @return The resulting offset within the stream (as per lseek(2)), + or negative if an error occurred. +*/ +off_t hseek(hFILE *fp, off_t offset, int whence) HTS_RESULT_USED; + +/*! + @abstract Report the current stream offset + @return The offset within the stream, starting from zero. +*/ +static inline off_t htell(hFILE *fp) +{ + return fp->offset + (fp->begin - fp->buffer); +} + +/*! + @abstract Read one character from the stream + @return The character read, or EOF on end-of-file or error +*/ +static inline int hgetc(hFILE *fp) +{ + extern int hgetc2(hFILE *); + return (fp->end > fp->begin)? (unsigned char) *(fp->begin++) : hgetc2(fp); +} + +/*! + @abstract Peek at characters to be read without removing them from buffers + @param fp The file stream + @param buffer The buffer to which the peeked bytes will be written + @param nbytes The number of bytes to peek at; limited by the size of the + internal buffer, which could be as small as 4K. + @return The number of bytes peeked, which may be less than nbytes if EOF + is encountered; or negative, if there was an I/O error. + @notes The characters peeked at remain in the stream's internal buffer, + and will be returned by later hread() etc calls. +*/ +ssize_t hpeek(hFILE *fp, void *buffer, size_t nbytes) HTS_RESULT_USED; + +/*! + @abstract Read a block of characters from the file + @return The number of bytes read, or negative if an error occurred. + @notes The full nbytes requested will be returned, except as limited + by EOF or I/O errors. +*/ +static inline ssize_t HTS_RESULT_USED +hread(hFILE *fp, void *buffer, size_t nbytes) +{ + extern ssize_t hread2(hFILE *, void *, size_t, size_t); + + size_t n = fp->end - fp->begin; + if (n > nbytes) n = nbytes; + memcpy(buffer, fp->begin, n); + fp->begin += n; + return (n == nbytes)? (ssize_t) n : hread2(fp, buffer, nbytes, n); +} + +/*! + @abstract Write a character to the stream + @return The character written, or EOF if an error occurred. +*/ +static inline int hputc(int c, hFILE *fp) +{ + extern int hputc2(int, hFILE *); + if (fp->begin < fp->limit) *(fp->begin++) = c; + else c = hputc2(c, fp); + return c; +} + +/*! + @abstract Write a string to the stream + @return 0 if successful, or EOF if an error occurred. +*/ +static inline int hputs(const char *text, hFILE *fp) +{ + extern int hputs2(const char *, size_t, size_t, hFILE *); + + size_t nbytes = strlen(text), n = fp->limit - fp->begin; + if (n > nbytes) n = nbytes; + memcpy(fp->begin, text, n); + fp->begin += n; + return (n == nbytes)? 0 : hputs2(text, nbytes, n, fp); +} + +/*! + @abstract Write a block of characters to the file + @return Either nbytes, or negative if an error occurred. + @notes In the absence of I/O errors, the full nbytes will be written. +*/ +static inline ssize_t HTS_RESULT_USED +hwrite(hFILE *fp, const void *buffer, size_t nbytes) +{ + extern ssize_t hwrite2(hFILE *, const void *, size_t, size_t); + + size_t n = fp->limit - fp->begin; + if (n > nbytes) n = nbytes; + memcpy(fp->begin, buffer, n); + fp->begin += n; + return (n==nbytes)? (ssize_t) n : hwrite2(fp, buffer, nbytes, n); +} + +/*! + @abstract For writing streams, flush buffered output to the underlying stream + @return 0 if successful, or EOF if an error occurred. +*/ +int hflush(hFILE *fp) HTS_RESULT_USED; + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/hts.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/hts.h new file mode 100644 index 0000000000000000000000000000000000000000..8c9fcd8a77ba016db6f976cad50347cb11c086d8 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/hts.h @@ -0,0 +1,305 @@ +#ifndef HTS_H +#define HTS_H + +#include +#include + +#ifndef HTS_BGZF_TYPEDEF +typedef struct BGZF BGZF; +#define HTS_BGZF_TYPEDEF +#endif +struct cram_fd; +struct hFILE; + +#ifndef KSTRING_T +#define KSTRING_T kstring_t +typedef struct __kstring_t { + size_t l, m; + char *s; +} kstring_t; +#endif + +#ifndef kroundup32 +#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) +#endif + +/** + * hts_expand() - expands memory block pointed to by $ptr; + * hts_expand0() the latter sets the newly allocated part to 0. + * + * @param n requested number of elements of type type_t + * @param m size of memory allocated + */ +#define hts_expand(type_t, n, m, ptr) if ((n) > (m)) { \ + (m) = (n); kroundup32(m); \ + (ptr) = (type_t*)realloc((ptr), (m) * sizeof(type_t)); \ + } +#define hts_expand0(type_t, n, m, ptr) if ((n) > (m)) { \ + int t = (m); (m) = (n); kroundup32(m); \ + (ptr) = (type_t*)realloc((ptr), (m) * sizeof(type_t)); \ + memset(((type_t*)ptr)+t,0,sizeof(type_t)*((m)-t)); \ + } + +/************ + * File I/O * + ************/ + +typedef struct { + uint32_t is_bin:1, is_write:1, is_be:1, is_cram:1, is_compressed:2, is_kstream:1, dummy:25; + int64_t lineno; + kstring_t line; + char *fn, *fn_aux; + union { + BGZF *bgzf; + struct cram_fd *cram; + struct hFILE *hfile; + void *voidp; + } fp; +} htsFile; + +/********************** + * Exported functions * + **********************/ + +extern int hts_verbose; + +/*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */ +extern const unsigned char seq_nt16_table[256]; + +/*! @abstract Table for converting a 4-bit encoded nucleotide to a letter. */ +extern const char seq_nt16_str[]; + +#ifdef __cplusplus +extern "C" { +#endif + +/*! + @abstract Get the htslib version number + @return For released versions, a string like "N.N[.N]"; or git describe + output if using a library built within a Git repository. +*/ +const char *hts_version(void); + +/*! + @abstract Open a SAM/BAM/CRAM/VCF/BCF/etc file + @param fn The file name or "-" for stdin/stdout + @param mode Mode matching /[rwa][bcuz0-9]+/ + @discussion + With 'r' opens for reading; any further format mode letters are ignored + as the format is detected by checking the first few bytes or BGZF blocks + of the file. With 'w' or 'a' opens for writing or appending, with format + specifier letters: + b binary format (BAM, BCF, etc) rather than text (SAM, VCF, etc) + c CRAM format + u uncompressed + z compressed + [0-9] zlib compression level + Note that there is a distinction between 'u' and '0': the first yields + plain uncompressed output whereas the latter outputs uncompressed data + wrapped in the zlib format. + @example + [rw]b .. compressed BCF, BAM, FAI + [rw]u .. uncompressed BCF + [rw]z .. compressed VCF + [rw] .. uncompressed VCF +*/ +htsFile *hts_open(const char *fn, const char *mode); + +/*! + @abstract Close a file handle, flushing buffered data for output streams + @param fp The file handle to be closed + @return 0 for success, or negative if an error occurred. +*/ +int hts_close(htsFile *fp); + +int hts_getline(htsFile *fp, int delimiter, kstring_t *str); +char **hts_readlines(const char *fn, int *_n); +/*! + @abstract Parse comma-separated list or read list from a file + @param list File name or comma-separated list + @param is_file + @param _n Size of the output array (number of items read) + @return NULL on failure or pointer to newly allocated array of + strings +*/ +char **hts_readlist(const char *fn, int is_file, int *_n); + +/*! + @abstract Create extra threads to aid compress/decompression for this file + @param fp The file handle + @param n The number of worker threads to create + @return 0 for success, or negative if an error occurred. + @notes THIS THREADING API IS LIKELY TO CHANGE IN FUTURE. +*/ +int hts_set_threads(htsFile *fp, int n); + +/*! + @abstract Set .fai filename for a file opened for reading + @return 0 for success, negative on failure + @discussion + Called before *_hdr_read(), this provides the name of a .fai file + used to provide a reference list if the htsFile contains no @SQ headers. +*/ +int hts_set_fai_filename(htsFile *fp, const char *fn_aux); + +#ifdef __cplusplus +} +#endif + +/************ + * Indexing * + ************/ + +/*! +These HTS_IDX_* macros are used as special tid values for hts_itr_query()/etc, +producing iterators operating as follows: + - HTS_IDX_NOCOOR iterates over unmapped reads sorted at the end of the file + - HTS_IDX_START iterates over the entire file + - HTS_IDX_REST iterates from the current position to the end of the file + - HTS_IDX_NONE always returns "no more alignment records" +When one of these special tid values is used, beg and end are ignored. +When REST or NONE is used, idx is also ignored and may be NULL. +*/ +#define HTS_IDX_NOCOOR (-2) +#define HTS_IDX_START (-3) +#define HTS_IDX_REST (-4) +#define HTS_IDX_NONE (-5) + +#define HTS_FMT_CSI 0 +#define HTS_FMT_BAI 1 +#define HTS_FMT_TBI 2 +#define HTS_FMT_CRAI 3 + +struct __hts_idx_t; +typedef struct __hts_idx_t hts_idx_t; + +typedef struct { + uint64_t u, v; +} hts_pair64_t; + +typedef int hts_readrec_func(BGZF *fp, void *data, void *r, int *tid, int *beg, int *end); + +typedef struct { + uint32_t read_rest:1, finished:1, dummy:29; + int tid, beg, end, n_off, i; + uint64_t curr_off; + hts_pair64_t *off; + hts_readrec_func *readrec; + struct { + int n, m; + int *a; + } bins; +} hts_itr_t; + +#ifdef __cplusplus +extern "C" { +#endif + + #define hts_bin_first(l) (((1<<(((l)<<1) + (l))) - 1) / 7) + #define hts_bin_parent(l) (((l) - 1) >> 3) + + hts_idx_t *hts_idx_init(int n, int fmt, uint64_t offset0, int min_shift, int n_lvls); + void hts_idx_destroy(hts_idx_t *idx); + int hts_idx_push(hts_idx_t *idx, int tid, int beg, int end, uint64_t offset, int is_mapped); + void hts_idx_finish(hts_idx_t *idx, uint64_t final_offset); + + void hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt); + hts_idx_t *hts_idx_load(const char *fn, int fmt); + + uint8_t *hts_idx_get_meta(hts_idx_t *idx, int *l_meta); + void hts_idx_set_meta(hts_idx_t *idx, int l_meta, uint8_t *meta, int is_copy); + + int hts_idx_get_stat(const hts_idx_t* idx, int tid, uint64_t* mapped, uint64_t* unmapped); + uint64_t hts_idx_get_n_no_coor(const hts_idx_t* idx); + + const char *hts_parse_reg(const char *s, int *beg, int *end); + hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec); + void hts_itr_destroy(hts_itr_t *iter); + + typedef int (*hts_name2id_f)(void*, const char*); + typedef const char *(*hts_id2name_f)(void*, int); + typedef hts_itr_t *hts_itr_query_func(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec); + + hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec); + int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data); + const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values + + /** + * hts_file_type() - Convenience function to determine file type + * @fname: the file name + * + * Returns one of the FT_* defines. + * + * This function was added in order to avoid the need for excessive command + * line switches. + */ + #define FT_UNKN 0 + #define FT_GZ 1 + #define FT_VCF 2 + #define FT_VCF_GZ (FT_GZ|FT_VCF) + #define FT_BCF (1<<2) + #define FT_BCF_GZ (FT_GZ|FT_BCF) + #define FT_STDIN (1<<3) + int hts_file_type(const char *fname); + + +#ifdef __cplusplus +} +#endif + +static inline int hts_reg2bin(int64_t beg, int64_t end, int min_shift, int n_lvls) +{ + int l, s = min_shift, t = ((1<<((n_lvls<<1) + n_lvls)) - 1) / 7; + for (--end, l = n_lvls; l > 0; --l, s += 3, t -= 1<<((l<<1)+l)) + if (beg>>s == end>>s) return t + (beg>>s); + return 0; +} + +static inline int hts_bin_bot(int bin, int n_lvls) +{ + int l, b; + for (l = 0, b = bin; b; ++l, b = hts_bin_parent(b)); // compute the level of bin + return (bin - hts_bin_first(l)) << (n_lvls - l) * 3; +} + +/************** + * Endianness * + **************/ + +static inline int ed_is_big(void) +{ + long one= 1; + return !(*((char *)(&one))); +} +static inline uint16_t ed_swap_2(uint16_t v) +{ + return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8)); +} +static inline void *ed_swap_2p(void *x) +{ + *(uint16_t*)x = ed_swap_2(*(uint16_t*)x); + return x; +} +static inline uint32_t ed_swap_4(uint32_t v) +{ + v = ((v & 0x0000FFFFU) << 16) | (v >> 16); + return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8); +} +static inline void *ed_swap_4p(void *x) +{ + *(uint32_t*)x = ed_swap_4(*(uint32_t*)x); + return x; +} +static inline uint64_t ed_swap_8(uint64_t v) +{ + v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32); + v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16); + return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8); +} +static inline void *ed_swap_8p(void *x) +{ + *(uint64_t*)x = ed_swap_8(*(uint64_t*)x); + return x; +} + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/hts_defs.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/hts_defs.h new file mode 100644 index 0000000000000000000000000000000000000000..efc4f6cdf8af126a4c6def8333ed6e84df7cb14d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/hts_defs.h @@ -0,0 +1,47 @@ +/* hts_defs.h -- Miscellaneous definitions. + + Copyright (C) 2013-2014 Genome Research Ltd. + + Author: John Marshall + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notices and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +DEALINGS IN THE SOFTWARE. */ + +#ifndef HTSLIB_HTS_DEFS_H +#define HTSLIB_HTS_DEFS_H + +#if __clang__major__ >= 2 || __GNUC__ >= 3 +#define HTS_NORETURN __attribute__ ((__noreturn__)) +#else +#define HTS_NORETURN +#endif + +#if (defined __clang__ && __clang_major__ >= 3) || \ + (defined __GNUC__ && (__GNUC__ > 4 || (__GNUC__==4 && __GNUC_MINOR__ >= 5))) +#define HTS_RESULT_USED __attribute__ ((__warn_unused_result__)) +#else +#define HTS_RESULT_USED +#endif + +#if defined __clang__ || defined __GNUC__ +#define HTS_UNUSED __attribute__ ((__unused__)) +#else +#define HTS_UNUSED +#endif + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/kfunc.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/kfunc.h new file mode 100644 index 0000000000000000000000000000000000000000..0a6ad922f42fbbd9b1b5b0d176656ffc38124f8d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/kfunc.h @@ -0,0 +1,49 @@ +#ifndef __KFUNC_H__ +#define __KFUNC_H__ + +/* Log gamma function + * \log{\Gamma(z)} + * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245 + */ +double kf_lgamma(double z); + +/* complementary error function + * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt + * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66 + */ +double kf_erfc(double x); + +/* The following computes regularized incomplete gamma functions. + * Formulas are taken from Wiki, with additional input from Numerical + * Recipes in C (for modified Lentz's algorithm) and AS245 + * (http://lib.stat.cmu.edu/apstat/245). + * + * A good online calculator is available at: + * + * http://www.danielsoper.com/statcalc/calc23.aspx + * + * It calculates upper incomplete gamma function, which equals + * kf_gammaq(s,z)*tgamma(s). + */ + +double kf_gammap(double s, double z); +double kf_gammaq(double s, double z); + +/* Regularized incomplete beta function. The method is taken from + * Numerical Recipe in C, 2nd edition, section 6.4. The following web + * page calculates the incomplete beta function, which equals + * kf_betai(a,b,x) * gamma(a) * gamma(b) / gamma(a+b): + * + * http://www.danielsoper.com/statcalc/calc36.aspx + */ +double kf_betai(double a, double b, double x); + +/* + * n11 n12 | n1_ + * n21 n22 | n2_ + * -----------+---- + * n_1 n_2 | n + */ +double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two); + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/khash.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/khash.h new file mode 100644 index 0000000000000000000000000000000000000000..2d910dec274e191eee39ac575727ba4cc1c53292 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/khash.h @@ -0,0 +1,617 @@ +/* The MIT License + + Copyright (c) 2008, 2009, 2011 by Attractive Chaos + + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. +*/ + +/* + An example: + +#include "khash.h" +KHASH_MAP_INIT_INT(32, char) +int main() { + int ret, is_missing; + khiter_t k; + khash_t(32) *h = kh_init(32); + k = kh_put(32, h, 5, &ret); + kh_value(h, k) = 10; + k = kh_get(32, h, 10); + is_missing = (k == kh_end(h)); + k = kh_get(32, h, 5); + kh_del(32, h, k); + for (k = kh_begin(h); k != kh_end(h); ++k) + if (kh_exist(h, k)) kh_value(h, k) = 1; + kh_destroy(32, h); + return 0; +} +*/ + +/* + 2013-05-02 (0.2.8): + + * Use quadratic probing. When the capacity is power of 2, stepping function + i*(i+1)/2 guarantees to traverse each bucket. It is better than double + hashing on cache performance and is more robust than linear probing. + + In theory, double hashing should be more robust than quadratic probing. + However, my implementation is probably not for large hash tables, because + the second hash function is closely tied to the first hash function, + which reduce the effectiveness of double hashing. + + Reference: http://research.cs.vt.edu/AVresearch/hashing/quadratic.php + + 2011-12-29 (0.2.7): + + * Minor code clean up; no actual effect. + + 2011-09-16 (0.2.6): + + * The capacity is a power of 2. This seems to dramatically improve the + speed for simple keys. Thank Zilong Tan for the suggestion. Reference: + + - http://code.google.com/p/ulib/ + - http://nothings.org/computer/judy/ + + * Allow to optionally use linear probing which usually has better + performance for random input. Double hashing is still the default as it + is more robust to certain non-random input. + + * Added Wang's integer hash function (not used by default). This hash + function is more robust to certain non-random input. + + 2011-02-14 (0.2.5): + + * Allow to declare global functions. + + 2009-09-26 (0.2.4): + + * Improve portability + + 2008-09-19 (0.2.3): + + * Corrected the example + * Improved interfaces + + 2008-09-11 (0.2.2): + + * Improved speed a little in kh_put() + + 2008-09-10 (0.2.1): + + * Added kh_clear() + * Fixed a compiling error + + 2008-09-02 (0.2.0): + + * Changed to token concatenation which increases flexibility. + + 2008-08-31 (0.1.2): + + * Fixed a bug in kh_get(), which has not been tested previously. + + 2008-08-31 (0.1.1): + + * Added destructor +*/ + + +#ifndef __AC_KHASH_H +#define __AC_KHASH_H + +/*! + @header + + Generic hash table library. + */ + +#define AC_VERSION_KHASH_H "0.2.8" + +#include +#include +#include + +/* compiler specific configuration */ + +#if UINT_MAX == 0xffffffffu +typedef unsigned int khint32_t; +#elif ULONG_MAX == 0xffffffffu +typedef unsigned long khint32_t; +#endif + +#if ULONG_MAX == ULLONG_MAX +typedef unsigned long khint64_t; +#else +typedef unsigned long long khint64_t; +#endif + +#ifdef _MSC_VER +#define kh_inline __inline +#else +#define kh_inline inline +#endif + +typedef khint32_t khint_t; +typedef khint_t khiter_t; + +#define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2) +#define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1) +#define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3) +#define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1))) +#define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1))) +#define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1))) +#define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1)) + +#define __ac_fsize(m) ((m) < 16? 1 : (m)>>4) + +#ifndef kroundup32 +#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) +#endif + +#ifndef kcalloc +#define kcalloc(N,Z) calloc(N,Z) +#endif +#ifndef kmalloc +#define kmalloc(Z) malloc(Z) +#endif +#ifndef krealloc +#define krealloc(P,Z) realloc(P,Z) +#endif +#ifndef kfree +#define kfree(P) free(P) +#endif + +static const double __ac_HASH_UPPER = 0.77; + +#define __KHASH_TYPE(name, khkey_t, khval_t) \ + typedef struct { \ + khint_t n_buckets, size, n_occupied, upper_bound; \ + khint32_t *flags; \ + khkey_t *keys; \ + khval_t *vals; \ + } kh_##name##_t; + +#define __KHASH_PROTOTYPES(name, khkey_t, khval_t) \ + extern kh_##name##_t *kh_init_##name(void); \ + extern void kh_destroy_##name(kh_##name##_t *h); \ + extern void kh_clear_##name(kh_##name##_t *h); \ + extern khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key); \ + extern int kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets); \ + extern khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret); \ + extern void kh_del_##name(kh_##name##_t *h, khint_t x); + +#define __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \ + SCOPE kh_##name##_t *kh_init_##name(void) { \ + return (kh_##name##_t*)kcalloc(1, sizeof(kh_##name##_t)); \ + } \ + SCOPE void kh_destroy_##name(kh_##name##_t *h) \ + { \ + if (h) { \ + kfree((void *)h->keys); kfree(h->flags); \ + kfree((void *)h->vals); \ + kfree(h); \ + } \ + } \ + SCOPE void kh_clear_##name(kh_##name##_t *h) \ + { \ + if (h && h->flags) { \ + memset(h->flags, 0xaa, __ac_fsize(h->n_buckets) * sizeof(khint32_t)); \ + h->size = h->n_occupied = 0; \ + } \ + } \ + SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ + { \ + if (h->n_buckets) { \ + khint_t k, i, last, mask, step = 0; \ + mask = h->n_buckets - 1; \ + k = __hash_func(key); i = k & mask; \ + last = i; \ + while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \ + i = (i + (++step)) & mask; \ + if (i == last) return h->n_buckets; \ + } \ + return __ac_iseither(h->flags, i)? h->n_buckets : i; \ + } else return 0; \ + } \ + SCOPE int kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \ + { /* This function uses 0.25*n_buckets bytes of working space instead of [sizeof(key_t+val_t)+.25]*n_buckets. */ \ + khint32_t *new_flags = 0; \ + khint_t j = 1; \ + { \ + kroundup32(new_n_buckets); \ + if (new_n_buckets < 4) new_n_buckets = 4; \ + if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0; /* requested size is too small */ \ + else { /* hash table size to be changed (shrink or expand); rehash */ \ + new_flags = (khint32_t*)kmalloc(__ac_fsize(new_n_buckets) * sizeof(khint32_t)); \ + if (!new_flags) return -1; \ + memset(new_flags, 0xaa, __ac_fsize(new_n_buckets) * sizeof(khint32_t)); \ + if (h->n_buckets < new_n_buckets) { /* expand */ \ + khkey_t *new_keys = (khkey_t*)krealloc((void *)h->keys, new_n_buckets * sizeof(khkey_t)); \ + if (!new_keys) return -1; \ + h->keys = new_keys; \ + if (kh_is_map) { \ + khval_t *new_vals = (khval_t*)krealloc((void *)h->vals, new_n_buckets * sizeof(khval_t)); \ + if (!new_vals) return -1; \ + h->vals = new_vals; \ + } \ + } /* otherwise shrink */ \ + } \ + } \ + if (j) { /* rehashing is needed */ \ + for (j = 0; j != h->n_buckets; ++j) { \ + if (__ac_iseither(h->flags, j) == 0) { \ + khkey_t key = h->keys[j]; \ + khval_t val; \ + khint_t new_mask; \ + new_mask = new_n_buckets - 1; \ + if (kh_is_map) val = h->vals[j]; \ + __ac_set_isdel_true(h->flags, j); \ + while (1) { /* kick-out process; sort of like in Cuckoo hashing */ \ + khint_t k, i, step = 0; \ + k = __hash_func(key); \ + i = k & new_mask; \ + while (!__ac_isempty(new_flags, i)) i = (i + (++step)) & new_mask; \ + __ac_set_isempty_false(new_flags, i); \ + if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { /* kick out the existing element */ \ + { khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \ + if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \ + __ac_set_isdel_true(h->flags, i); /* mark it as deleted in the old hash table */ \ + } else { /* write the element and jump out of the loop */ \ + h->keys[i] = key; \ + if (kh_is_map) h->vals[i] = val; \ + break; \ + } \ + } \ + } \ + } \ + if (h->n_buckets > new_n_buckets) { /* shrink the hash table */ \ + h->keys = (khkey_t*)krealloc((void *)h->keys, new_n_buckets * sizeof(khkey_t)); \ + if (kh_is_map) h->vals = (khval_t*)krealloc((void *)h->vals, new_n_buckets * sizeof(khval_t)); \ + } \ + kfree(h->flags); /* free the working space */ \ + h->flags = new_flags; \ + h->n_buckets = new_n_buckets; \ + h->n_occupied = h->size; \ + h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \ + } \ + return 0; \ + } \ + SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ + { \ + khint_t x; \ + if (h->n_occupied >= h->upper_bound) { /* update the hash table */ \ + if (h->n_buckets > (h->size<<1)) { \ + if (kh_resize_##name(h, h->n_buckets - 1) < 0) { /* clear "deleted" elements */ \ + *ret = -1; return h->n_buckets; \ + } \ + } else if (kh_resize_##name(h, h->n_buckets + 1) < 0) { /* expand the hash table */ \ + *ret = -1; return h->n_buckets; \ + } \ + } /* TODO: to implement automatically shrinking; resize() already support shrinking */ \ + { \ + khint_t k, i, site, last, mask = h->n_buckets - 1, step = 0; \ + x = site = h->n_buckets; k = __hash_func(key); i = k & mask; \ + if (__ac_isempty(h->flags, i)) x = i; /* for speed up */ \ + else { \ + last = i; \ + while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \ + if (__ac_isdel(h->flags, i)) site = i; \ + i = (i + (++step)) & mask; \ + if (i == last) { x = site; break; } \ + } \ + if (x == h->n_buckets) { \ + if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \ + else x = i; \ + } \ + } \ + } \ + if (__ac_isempty(h->flags, x)) { /* not present at all */ \ + h->keys[x] = key; \ + __ac_set_isboth_false(h->flags, x); \ + ++h->size; ++h->n_occupied; \ + *ret = 1; \ + } else if (__ac_isdel(h->flags, x)) { /* deleted */ \ + h->keys[x] = key; \ + __ac_set_isboth_false(h->flags, x); \ + ++h->size; \ + *ret = 2; \ + } else *ret = 0; /* Don't touch h->keys[x] if present and not deleted */ \ + return x; \ + } \ + SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ + { \ + if (x != h->n_buckets && !__ac_iseither(h->flags, x)) { \ + __ac_set_isdel_true(h->flags, x); \ + --h->size; \ + } \ + } + +#define KHASH_DECLARE(name, khkey_t, khval_t) \ + __KHASH_TYPE(name, khkey_t, khval_t) \ + __KHASH_PROTOTYPES(name, khkey_t, khval_t) + +#define KHASH_INIT2(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \ + __KHASH_TYPE(name, khkey_t, khval_t) \ + __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) + +#define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \ + KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) + +/* --- BEGIN OF HASH FUNCTIONS --- */ + +/*! @function + @abstract Integer hash function + @param key The integer [khint32_t] + @return The hash value [khint_t] + */ +#define kh_int_hash_func(key) (khint32_t)(key) +/*! @function + @abstract Integer comparison function + */ +#define kh_int_hash_equal(a, b) ((a) == (b)) +/*! @function + @abstract 64-bit integer hash function + @param key The integer [khint64_t] + @return The hash value [khint_t] + */ +#define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11) +/*! @function + @abstract 64-bit integer comparison function + */ +#define kh_int64_hash_equal(a, b) ((a) == (b)) +/*! @function + @abstract const char* hash function + @param s Pointer to a null terminated string + @return The hash value + */ +static kh_inline khint_t __ac_X31_hash_string(const char *s) +{ + khint_t h = (khint_t)*s; + if (h) for (++s ; *s; ++s) h = (h << 5) - h + (khint_t)*s; + return h; +} +/*! @function + @abstract Another interface to const char* hash function + @param key Pointer to a null terminated string [const char*] + @return The hash value [khint_t] + */ +#define kh_str_hash_func(key) __ac_X31_hash_string(key) +/*! @function + @abstract Const char* comparison function + */ +#define kh_str_hash_equal(a, b) (strcmp(a, b) == 0) + +static kh_inline khint_t __ac_Wang_hash(khint_t key) +{ + key += ~(key << 15); + key ^= (key >> 10); + key += (key << 3); + key ^= (key >> 6); + key += ~(key << 11); + key ^= (key >> 16); + return key; +} +#define kh_int_hash_func2(k) __ac_Wang_hash((khint_t)key) + +/* --- END OF HASH FUNCTIONS --- */ + +/* Other convenient macros... */ + +/*! + @abstract Type of the hash table. + @param name Name of the hash table [symbol] + */ +#define khash_t(name) kh_##name##_t + +/*! @function + @abstract Initiate a hash table. + @param name Name of the hash table [symbol] + @return Pointer to the hash table [khash_t(name)*] + */ +#define kh_init(name) kh_init_##name() + +/*! @function + @abstract Destroy a hash table. + @param name Name of the hash table [symbol] + @param h Pointer to the hash table [khash_t(name)*] + */ +#define kh_destroy(name, h) kh_destroy_##name(h) + +/*! @function + @abstract Reset a hash table without deallocating memory. + @param name Name of the hash table [symbol] + @param h Pointer to the hash table [khash_t(name)*] + */ +#define kh_clear(name, h) kh_clear_##name(h) + +/*! @function + @abstract Resize a hash table. + @param name Name of the hash table [symbol] + @param h Pointer to the hash table [khash_t(name)*] + @param s New size [khint_t] + */ +#define kh_resize(name, h, s) kh_resize_##name(h, s) + +/*! @function + @abstract Insert a key to the hash table. + @param name Name of the hash table [symbol] + @param h Pointer to the hash table [khash_t(name)*] + @param k Key [type of keys] + @param r Extra return code: -1 if the operation failed; + 0 if the key is present in the hash table; + 1 if the bucket is empty (never used); 2 if the element in + the bucket has been deleted [int*] + @return Iterator to the inserted element [khint_t] + */ +#define kh_put(name, h, k, r) kh_put_##name(h, k, r) + +/*! @function + @abstract Retrieve a key from the hash table. + @param name Name of the hash table [symbol] + @param h Pointer to the hash table [khash_t(name)*] + @param k Key [type of keys] + @return Iterator to the found element, or kh_end(h) if the element is absent [khint_t] + */ +#define kh_get(name, h, k) kh_get_##name(h, k) + +/*! @function + @abstract Remove a key from the hash table. + @param name Name of the hash table [symbol] + @param h Pointer to the hash table [khash_t(name)*] + @param k Iterator to the element to be deleted [khint_t] + */ +#define kh_del(name, h, k) kh_del_##name(h, k) + +/*! @function + @abstract Test whether a bucket contains data. + @param h Pointer to the hash table [khash_t(name)*] + @param x Iterator to the bucket [khint_t] + @return 1 if containing data; 0 otherwise [int] + */ +#define kh_exist(h, x) (!__ac_iseither((h)->flags, (x))) + +/*! @function + @abstract Get key given an iterator + @param h Pointer to the hash table [khash_t(name)*] + @param x Iterator to the bucket [khint_t] + @return Key [type of keys] + */ +#define kh_key(h, x) ((h)->keys[x]) + +/*! @function + @abstract Get value given an iterator + @param h Pointer to the hash table [khash_t(name)*] + @param x Iterator to the bucket [khint_t] + @return Value [type of values] + @discussion For hash sets, calling this results in segfault. + */ +#define kh_val(h, x) ((h)->vals[x]) + +/*! @function + @abstract Alias of kh_val() + */ +#define kh_value(h, x) ((h)->vals[x]) + +/*! @function + @abstract Get the start iterator + @param h Pointer to the hash table [khash_t(name)*] + @return The start iterator [khint_t] + */ +#define kh_begin(h) (khint_t)(0) + +/*! @function + @abstract Get the end iterator + @param h Pointer to the hash table [khash_t(name)*] + @return The end iterator [khint_t] + */ +#define kh_end(h) ((h)->n_buckets) + +/*! @function + @abstract Get the number of elements in the hash table + @param h Pointer to the hash table [khash_t(name)*] + @return Number of elements in the hash table [khint_t] + */ +#define kh_size(h) ((h)->size) + +/*! @function + @abstract Get the number of buckets in the hash table + @param h Pointer to the hash table [khash_t(name)*] + @return Number of buckets in the hash table [khint_t] + */ +#define kh_n_buckets(h) ((h)->n_buckets) + +/*! @function + @abstract Iterate over the entries in the hash table + @param h Pointer to the hash table [khash_t(name)*] + @param kvar Variable to which key will be assigned + @param vvar Variable to which value will be assigned + @param code Block of code to execute + */ +#define kh_foreach(h, kvar, vvar, code) { khint_t __i; \ + for (__i = kh_begin(h); __i != kh_end(h); ++__i) { \ + if (!kh_exist(h,__i)) continue; \ + (kvar) = kh_key(h,__i); \ + (vvar) = kh_val(h,__i); \ + code; \ + } } + +/*! @function + @abstract Iterate over the values in the hash table + @param h Pointer to the hash table [khash_t(name)*] + @param vvar Variable to which value will be assigned + @param code Block of code to execute + */ +#define kh_foreach_value(h, vvar, code) { khint_t __i; \ + for (__i = kh_begin(h); __i != kh_end(h); ++__i) { \ + if (!kh_exist(h,__i)) continue; \ + (vvar) = kh_val(h,__i); \ + code; \ + } } + +/* More conenient interfaces */ + +/*! @function + @abstract Instantiate a hash set containing integer keys + @param name Name of the hash table [symbol] + */ +#define KHASH_SET_INIT_INT(name) \ + KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal) + +/*! @function + @abstract Instantiate a hash map containing integer keys + @param name Name of the hash table [symbol] + @param khval_t Type of values [type] + */ +#define KHASH_MAP_INIT_INT(name, khval_t) \ + KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) + +/*! @function + @abstract Instantiate a hash map containing 64-bit integer keys + @param name Name of the hash table [symbol] + */ +#define KHASH_SET_INIT_INT64(name) \ + KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) + +/*! @function + @abstract Instantiate a hash map containing 64-bit integer keys + @param name Name of the hash table [symbol] + @param khval_t Type of values [type] + */ +#define KHASH_MAP_INIT_INT64(name, khval_t) \ + KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) + +typedef const char *kh_cstr_t; +/*! @function + @abstract Instantiate a hash map containing const char* keys + @param name Name of the hash table [symbol] + */ +#define KHASH_SET_INIT_STR(name) \ + KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) + +/*! @function + @abstract Instantiate a hash map containing const char* keys + @param name Name of the hash table [symbol] + @param khval_t Type of values [type] + */ +#define KHASH_MAP_INIT_STR(name, khval_t) \ + KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) + +#endif /* __AC_KHASH_H */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/khash_str2int.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/khash_str2int.h new file mode 100644 index 0000000000000000000000000000000000000000..db26d72cd38ed86f876c271944257797bbe677db --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/khash_str2int.h @@ -0,0 +1,98 @@ +#ifndef __KHASH_UTILS_H__ +#define __KHASH_UTILS_H__ + +#include + +KHASH_MAP_INIT_STR(str2int, int) + +/* + * Wrappers for khash dictionaries used by mpileup. + */ + +static inline void *khash_str2int_init(void) +{ + return kh_init(str2int); +} + +/* + * Destroy the hash structure, but not the keys + */ +static inline void khash_str2int_destroy(void *_hash) +{ + khash_t(str2int) *hash = (khash_t(str2int)*)_hash; + if (hash) kh_destroy(str2int, hash); // Note that strings are not freed. +} + +/* + * Destroys both the hash structure and the keys + */ +static inline void khash_str2int_destroy_free(void *_hash) +{ + khash_t(str2int) *hash = (khash_t(str2int)*)_hash; + khint_t k; + if (hash == 0) return; + for (k = 0; k < kh_end(hash); ++k) + if (kh_exist(hash, k)) free((char*)kh_key(hash, k)); + kh_destroy(str2int, hash); +} + +/* + * Returns 1 if key exists or 0 if not + */ +static inline int khash_str2int_has_key(void *_hash, const char *str) +{ + khash_t(str2int) *hash = (khash_t(str2int)*)_hash; + khint_t k = kh_get(str2int, hash, str); + if ( k == kh_end(hash) ) return 0; + return 1; +} + +/* + * Returns 0 on success and -1 when the key is not present. On success, + * *value is set, unless NULL is passed. + */ +static inline int khash_str2int_get(void *_hash, const char *str, int *value) +{ + khash_t(str2int) *hash = (khash_t(str2int)*)_hash; + khint_t k; + if ( !hash ) return -1; + k = kh_get(str2int, hash, str); + if ( k == kh_end(hash) ) return -1; + if ( !value ) return 0; + *value = kh_val(hash, k); + return 0; +} + +/* + * Add a new string to the dictionary, auto-incrementing the value. + * On success returns the newly inserted integer id, on error -1 + * is returned. + */ +static inline int khash_str2int_inc(void *_hash, const char *str) +{ + khint_t k; + int ret; + khash_t(str2int) *hash = (khash_t(str2int)*)_hash; + if ( !hash ) return -1; + k = kh_put(str2int, hash, str, &ret); + if (ret == 0) return kh_val(hash, k); + kh_val(hash, k) = kh_size(hash) - 1; + return kh_val(hash, k); +} + +/* + * Set a new key,value pair. On success returns the bin index, on + * error -1 is returned. + */ +static inline int khash_str2int_set(void *_hash, const char *str, int value) +{ + khint_t k; + int ret; + khash_t(str2int) *hash = (khash_t(str2int)*)_hash; + if ( !hash ) return -1; + k = kh_put(str2int, hash, str, &ret); + kh_val(hash,k) = value; + return k; +} + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/klist.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/klist.h new file mode 100644 index 0000000000000000000000000000000000000000..8b33f271e14ecf8365738e773f2f7b49a25249b5 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/klist.h @@ -0,0 +1,121 @@ +/* The MIT License + + Copyright (c) 2008-2009, by Attractive Chaos + + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. +*/ + +#ifndef _AC_KLIST_H +#define _AC_KLIST_H + +#include + +#define KMEMPOOL_INIT(name, kmptype_t, kmpfree_f) \ + typedef struct { \ + size_t cnt, n, max; \ + kmptype_t **buf; \ + } kmp_##name##_t; \ + static inline kmp_##name##_t *kmp_init_##name(void) { \ + return calloc(1, sizeof(kmp_##name##_t)); \ + } \ + static inline void kmp_destroy_##name(kmp_##name##_t *mp) { \ + size_t k; \ + for (k = 0; k < mp->n; ++k) { \ + kmpfree_f(mp->buf[k]); free(mp->buf[k]); \ + } \ + free(mp->buf); free(mp); \ + } \ + static inline kmptype_t *kmp_alloc_##name(kmp_##name##_t *mp) { \ + ++mp->cnt; \ + if (mp->n == 0) return calloc(1, sizeof(kmptype_t)); \ + return mp->buf[--mp->n]; \ + } \ + static inline void kmp_free_##name(kmp_##name##_t *mp, kmptype_t *p) { \ + --mp->cnt; \ + if (mp->n == mp->max) { \ + mp->max = mp->max? mp->max<<1 : 16; \ + mp->buf = realloc(mp->buf, sizeof(kmptype_t *) * mp->max); \ + } \ + mp->buf[mp->n++] = p; \ + } + +#define kmempool_t(name) kmp_##name##_t +#define kmp_init(name) kmp_init_##name() +#define kmp_destroy(name, mp) kmp_destroy_##name(mp) +#define kmp_alloc(name, mp) kmp_alloc_##name(mp) +#define kmp_free(name, mp, p) kmp_free_##name(mp, p) + +#define KLIST_INIT(name, kltype_t, kmpfree_t) \ + struct __kl1_##name { \ + kltype_t data; \ + struct __kl1_##name *next; \ + }; \ + typedef struct __kl1_##name kl1_##name; \ + KMEMPOOL_INIT(name, kl1_##name, kmpfree_t) \ + typedef struct { \ + kl1_##name *head, *tail; \ + kmp_##name##_t *mp; \ + size_t size; \ + } kl_##name##_t; \ + static inline kl_##name##_t *kl_init_##name(void) { \ + kl_##name##_t *kl = calloc(1, sizeof(kl_##name##_t)); \ + kl->mp = kmp_init(name); \ + kl->head = kl->tail = kmp_alloc(name, kl->mp); \ + kl->head->next = 0; \ + return kl; \ + } \ + static inline void kl_destroy_##name(kl_##name##_t *kl) { \ + kl1_##name *p; \ + for (p = kl->head; p != kl->tail; p = p->next) \ + kmp_free(name, kl->mp, p); \ + kmp_free(name, kl->mp, p); \ + kmp_destroy(name, kl->mp); \ + free(kl); \ + } \ + static inline kltype_t *kl_pushp_##name(kl_##name##_t *kl) { \ + kl1_##name *q, *p = kmp_alloc(name, kl->mp); \ + q = kl->tail; p->next = 0; kl->tail->next = p; kl->tail = p; \ + ++kl->size; \ + return &q->data; \ + } \ + static inline int kl_shift_##name(kl_##name##_t *kl, kltype_t *d) { \ + kl1_##name *p; \ + if (kl->head->next == 0) return -1; \ + --kl->size; \ + p = kl->head; kl->head = kl->head->next; \ + if (d) *d = p->data; \ + kmp_free(name, kl->mp, p); \ + return 0; \ + } + +#define kliter_t(name) kl1_##name +#define klist_t(name) kl_##name##_t +#define kl_val(iter) ((iter)->data) +#define kl_next(iter) ((iter)->next) +#define kl_begin(kl) ((kl)->head) +#define kl_end(kl) ((kl)->tail) + +#define kl_init(name) kl_init_##name() +#define kl_destroy(name, kl) kl_destroy_##name(kl) +#define kl_pushp(name, kl) kl_pushp_##name(kl) +#define kl_shift(name, kl, d) kl_shift_##name(kl, d) + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/knetfile.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/knetfile.h new file mode 100644 index 0000000000000000000000000000000000000000..c9802587b364ff3c94682f680d83fcaf05b775b6 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/knetfile.h @@ -0,0 +1,75 @@ +#ifndef KNETFILE_H +#define KNETFILE_H + +#include +#include + +#ifndef _WIN32 +#define netread(fd, ptr, len) read(fd, ptr, len) +#define netwrite(fd, ptr, len) write(fd, ptr, len) +#define netclose(fd) close(fd) +#else +#include +#define netread(fd, ptr, len) recv(fd, ptr, len, 0) +#define netwrite(fd, ptr, len) send(fd, ptr, len, 0) +#define netclose(fd) closesocket(fd) +#endif + +// FIXME: currently I/O is unbuffered + +#define KNF_TYPE_LOCAL 1 +#define KNF_TYPE_FTP 2 +#define KNF_TYPE_HTTP 3 + +typedef struct knetFile_s { + int type, fd; + int64_t offset; + char *host, *port; + + // the following are for FTP only + int ctrl_fd, pasv_ip[4], pasv_port, max_response, no_reconnect, is_ready; + char *response, *retr, *size_cmd; + int64_t seek_offset; // for lazy seek + int64_t file_size; + + // the following are for HTTP only + char *path, *http_host; +} knetFile; + +#define knet_tell(fp) ((fp)->offset) +#define knet_fileno(fp) ((fp)->fd) + +#ifdef __cplusplus +extern "C" { +#endif + +#ifdef _WIN32 + int knet_win32_init(); + void knet_win32_destroy(); +#endif + + knetFile *knet_open(const char *fn, const char *mode); + + /* + This only works with local files. + */ + knetFile *knet_dopen(int fd, const char *mode); + + /* + If ->is_ready==0, this routine updates ->fd; otherwise, it simply + reads from ->fd. + */ + ssize_t knet_read(knetFile *fp, void *buf, size_t len); + + /* + This routine only sets ->offset and ->is_ready=0. It does not + communicate with the FTP server. + */ + off_t knet_seek(knetFile *fp, off_t off, int whence); + int knet_close(knetFile *fp); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/kseq.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/kseq.h new file mode 100644 index 0000000000000000000000000000000000000000..577cdc451e714b31f51f6beee5b34bb2edc97077 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/kseq.h @@ -0,0 +1,253 @@ +/* The MIT License + + Copyright (c) 2008, 2009, 2011 Attractive Chaos + + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. +*/ + +/* Last Modified: 05MAR2012 */ + +#ifndef AC_KSEQ_H +#define AC_KSEQ_H + +#include +#include +#include + +#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r +#define KS_SEP_TAB 1 // isspace() && !' ' +#define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows) +#define KS_SEP_MAX 2 + +#define __KS_TYPE(type_t) \ + typedef struct __kstream_t { \ + int begin, end; \ + int is_eof:2, bufsize:30; \ + uint64_t seek_pos; \ + type_t f; \ + unsigned char *buf; \ + } kstream_t; + +#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end) +#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0) + +#define __KS_BASIC(SCOPE, type_t, __bufsize) \ + SCOPE kstream_t *ks_init(type_t f) \ + { \ + kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \ + ks->f = f; ks->bufsize = __bufsize; \ + ks->buf = (unsigned char*)malloc(__bufsize); \ + return ks; \ + } \ + SCOPE void ks_destroy(kstream_t *ks) \ + { \ + if (!ks) return; \ + free(ks->buf); \ + free(ks); \ + } + +#define __KS_INLINED(__read) \ + static inline int ks_getc(kstream_t *ks) \ + { \ + if (ks->is_eof && ks->begin >= ks->end) return -1; \ + if (ks->begin >= ks->end) { \ + ks->begin = 0; \ + ks->end = __read(ks->f, ks->buf, ks->bufsize); \ + if (ks->end < ks->bufsize) ks->is_eof = 1; \ + if (ks->end == 0) return -1; \ + } \ + ks->seek_pos++; \ + return (int)ks->buf[ks->begin++]; \ + } \ + static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \ + { return ks_getuntil2(ks, delimiter, str, dret, 0); } + +#ifndef KSTRING_T +#define KSTRING_T kstring_t +typedef struct __kstring_t { + size_t l, m; + char *s; +} kstring_t; +#endif + +#ifndef kroundup32 +#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) +#endif + +#define __KS_GETUNTIL(SCOPE, __read) \ + SCOPE int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \ + { \ + if (dret) *dret = 0; \ + str->l = append? str->l : 0; \ + uint64_t seek_pos = str->l; \ + if (ks->begin >= ks->end && ks->is_eof) return -1; \ + for (;;) { \ + int i; \ + if (ks->begin >= ks->end) { \ + if (!ks->is_eof) { \ + ks->begin = 0; \ + ks->end = __read(ks->f, ks->buf, ks->bufsize); \ + if (ks->end < ks->bufsize) ks->is_eof = 1; \ + if (ks->end == 0) break; \ + } else break; \ + } \ + if (delimiter == KS_SEP_LINE) { \ + for (i = ks->begin; i < ks->end; ++i) \ + if (ks->buf[i] == '\n') break; \ + } else if (delimiter > KS_SEP_MAX) { \ + for (i = ks->begin; i < ks->end; ++i) \ + if (ks->buf[i] == delimiter) break; \ + } else if (delimiter == KS_SEP_SPACE) { \ + for (i = ks->begin; i < ks->end; ++i) \ + if (isspace(ks->buf[i])) break; \ + } else if (delimiter == KS_SEP_TAB) { \ + for (i = ks->begin; i < ks->end; ++i) \ + if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \ + } else i = 0; /* never come to here! */ \ + if (str->m - str->l < (size_t)(i - ks->begin + 1)) { \ + str->m = str->l + (i - ks->begin) + 1; \ + kroundup32(str->m); \ + str->s = (char*)realloc(str->s, str->m); \ + } \ + seek_pos += i - ks->begin; if ( i < ks->end ) seek_pos++; \ + memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \ + str->l = str->l + (i - ks->begin); \ + ks->begin = i + 1; \ + if (i < ks->end) { \ + if (dret) *dret = ks->buf[i]; \ + break; \ + } \ + } \ + ks->seek_pos += seek_pos; \ + if (str->s == 0) { \ + str->m = 1; \ + str->s = (char*)calloc(1, 1); \ + } else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \ + str->s[str->l] = '\0'; \ + return str->l; \ + } + +#define KSTREAM_INIT2(SCOPE, type_t, __read, __bufsize) \ + __KS_TYPE(type_t) \ + __KS_BASIC(SCOPE, type_t, __bufsize) \ + __KS_GETUNTIL(SCOPE, __read) \ + __KS_INLINED(__read) + +#define KSTREAM_INIT(type_t, __read, __bufsize) KSTREAM_INIT2(static, type_t, __read, __bufsize) + +#define KSTREAM_DECLARE(type_t, __read) \ + __KS_TYPE(type_t) \ + extern int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append); \ + extern kstream_t *ks_init(type_t f); \ + extern void ks_destroy(kstream_t *ks); \ + __KS_INLINED(__read) + +/****************** + * FASTA/Q parser * + ******************/ + +#define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0) + +#define __KSEQ_BASIC(SCOPE, type_t) \ + SCOPE kseq_t *kseq_init(type_t fd) \ + { \ + kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \ + s->f = ks_init(fd); \ + return s; \ + } \ + SCOPE void kseq_destroy(kseq_t *ks) \ + { \ + if (!ks) return; \ + free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \ + ks_destroy(ks->f); \ + free(ks); \ + } + +/* Return value: + >=0 length of the sequence (normal) + -1 end-of-file + -2 truncated quality string + */ +#define __KSEQ_READ(SCOPE) \ + SCOPE int kseq_read(kseq_t *seq) \ + { \ + int c; \ + kstream_t *ks = seq->f; \ + if (seq->last_char == 0) { /* then jump to the next header line */ \ + while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \ + if (c == -1) return -1; /* end of file */ \ + seq->last_char = c; \ + } /* else: the first header char has been read in the previous call */ \ + seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \ + if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \ + if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \ + if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \ + seq->seq.m = 256; \ + seq->seq.s = (char*)malloc(seq->seq.m); \ + } \ + while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \ + if (c == '\n') continue; /* skip empty lines */ \ + seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \ + ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \ + } \ + if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \ + if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \ + seq->seq.m = seq->seq.l + 2; \ + kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \ + seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \ + } \ + seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \ + if (c != '+') return seq->seq.l; /* FASTA */ \ + if (seq->qual.m < seq->seq.m) { /* allocate memory for qual in case insufficient */ \ + seq->qual.m = seq->seq.m; \ + seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \ + } \ + while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \ + if (c == -1) return -2; /* error: no quality string */ \ + while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \ + seq->last_char = 0; /* we have not come to the next header line */ \ + if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \ + return seq->seq.l; \ + } + +#define __KSEQ_TYPE(type_t) \ + typedef struct { \ + kstring_t name, comment, seq, qual; \ + int last_char; \ + kstream_t *f; \ + } kseq_t; + +#define KSEQ_INIT2(SCOPE, type_t, __read) \ + KSTREAM_INIT(type_t, __read, 16384) \ + __KSEQ_TYPE(type_t) \ + __KSEQ_BASIC(SCOPE, type_t) \ + __KSEQ_READ(SCOPE) + +#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) + +#define KSEQ_DECLARE(type_t) \ + __KS_TYPE(type_t) \ + __KSEQ_TYPE(type_t) \ + extern kseq_t *kseq_init(type_t fd); \ + void kseq_destroy(kseq_t *ks); \ + int kseq_read(kseq_t *seq); + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/ksort.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/ksort.h new file mode 100644 index 0000000000000000000000000000000000000000..aa0bb93e2a703068a76eac007d949908337ffb65 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/ksort.h @@ -0,0 +1,285 @@ +/* The MIT License + + Copyright (c) 2008 Genome Research Ltd (GRL). + + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. +*/ + +/* Contact: Heng Li */ + +/* + 2012-12-11 (0.1.4): + + * Defined __ks_insertsort_##name as static to compile with C99. + + 2008-11-16 (0.1.4): + + * Fixed a bug in introsort() that happens in rare cases. + + 2008-11-05 (0.1.3): + + * Fixed a bug in introsort() for complex comparisons. + + * Fixed a bug in mergesort(). The previous version is not stable. + + 2008-09-15 (0.1.2): + + * Accelerated introsort. On my Mac (not on another Linux machine), + my implementation is as fast as std::sort on random input. + + * Added combsort and in introsort, switch to combsort if the + recursion is too deep. + + 2008-09-13 (0.1.1): + + * Added k-small algorithm + + 2008-09-05 (0.1.0): + + * Initial version + +*/ + +#ifndef AC_KSORT_H +#define AC_KSORT_H + +#include +#include + +typedef struct { + void *left, *right; + int depth; +} ks_isort_stack_t; + +#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } + +#define KSORT_INIT(name, type_t, __sort_lt) \ + void ks_mergesort_##name(size_t n, type_t array[], type_t temp[]) \ + { \ + type_t *a2[2], *a, *b; \ + int curr, shift; \ + \ + a2[0] = array; \ + a2[1] = temp? temp : (type_t*)malloc(sizeof(type_t) * n); \ + for (curr = 0, shift = 0; (1ul<> 1) - 1; i != (size_t)(-1); --i) \ + ks_heapadjust_##name(i, lsize, l); \ + } \ + void ks_heapsort_##name(size_t lsize, type_t l[]) \ + { \ + size_t i; \ + for (i = lsize - 1; i > 0; --i) { \ + type_t tmp; \ + tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust_##name(0, i, l); \ + } \ + } \ + static inline void __ks_insertsort_##name(type_t *s, type_t *t) \ + { \ + type_t *i, *j, swap_tmp; \ + for (i = s + 1; i < t; ++i) \ + for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \ + swap_tmp = *j; *j = *(j-1); *(j-1) = swap_tmp; \ + } \ + } \ + void ks_combsort_##name(size_t n, type_t a[]) \ + { \ + const double shrink_factor = 1.2473309501039786540366528676643; \ + int do_swap; \ + size_t gap = n; \ + type_t tmp, *i, *j; \ + do { \ + if (gap > 2) { \ + gap = (size_t)(gap / shrink_factor); \ + if (gap == 9 || gap == 10) gap = 11; \ + } \ + do_swap = 0; \ + for (i = a; i < a + n - gap; ++i) { \ + j = i + gap; \ + if (__sort_lt(*j, *i)) { \ + tmp = *i; *i = *j; *j = tmp; \ + do_swap = 1; \ + } \ + } \ + } while (do_swap || gap > 2); \ + if (gap != 1) __ks_insertsort_##name(a, a + n); \ + } \ + void ks_introsort_##name(size_t n, type_t a[]) \ + { \ + int d; \ + ks_isort_stack_t *top, *stack; \ + type_t rp, swap_tmp; \ + type_t *s, *t, *i, *j, *k; \ + \ + if (n < 1) return; \ + else if (n == 2) { \ + if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \ + return; \ + } \ + for (d = 2; 1ul<>1) + 1; \ + if (__sort_lt(*k, *i)) { \ + if (__sort_lt(*k, *j)) k = j; \ + } else k = __sort_lt(*j, *i)? i : j; \ + rp = *k; \ + if (k != t) { swap_tmp = *k; *k = *t; *t = swap_tmp; } \ + for (;;) { \ + do ++i; while (__sort_lt(*i, rp)); \ + do --j; while (i <= j && __sort_lt(rp, *j)); \ + if (j <= i) break; \ + swap_tmp = *i; *i = *j; *j = swap_tmp; \ + } \ + swap_tmp = *i; *i = *t; *t = swap_tmp; \ + if (i-s > t-i) { \ + if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \ + s = t-i > 16? i+1 : t; \ + } else { \ + if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \ + t = i-s > 16? i-1 : s; \ + } \ + } else { \ + if (top == stack) { \ + free(stack); \ + __ks_insertsort_##name(a, a+n); \ + return; \ + } else { --top; s = (type_t*)top->left; t = (type_t*)top->right; d = top->depth; } \ + } \ + } \ + } \ + /* This function is adapted from: http://ndevilla.free.fr/median/ */ \ + /* 0 <= kk < n */ \ + type_t ks_ksmall_##name(size_t n, type_t arr[], size_t kk) \ + { \ + type_t *low, *high, *k, *ll, *hh, *mid; \ + low = arr; high = arr + n - 1; k = arr + kk; \ + for (;;) { \ + if (high <= low) return *k; \ + if (high == low + 1) { \ + if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ + return *k; \ + } \ + mid = low + (high - low) / 2; \ + if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ + if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ + if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ + KSORT_SWAP(type_t, *mid, *(low+1)); \ + ll = low + 1; hh = high; \ + for (;;) { \ + do ++ll; while (__sort_lt(*ll, *low)); \ + do --hh; while (__sort_lt(*low, *hh)); \ + if (hh < ll) break; \ + KSORT_SWAP(type_t, *ll, *hh); \ + } \ + KSORT_SWAP(type_t, *low, *hh); \ + if (hh <= k) low = ll; \ + if (hh >= k) high = hh - 1; \ + } \ + } \ + void ks_shuffle_##name(size_t n, type_t a[]) \ + { \ + int i, j; \ + for (i = n; i > 1; --i) { \ + type_t tmp; \ + j = (int)(drand48() * i); \ + tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp; \ + } \ + } + +#define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t) +#define ks_introsort(name, n, a) ks_introsort_##name(n, a) +#define ks_combsort(name, n, a) ks_combsort_##name(n, a) +#define ks_heapsort(name, n, a) ks_heapsort_##name(n, a) +#define ks_heapmake(name, n, a) ks_heapmake_##name(n, a) +#define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a) +#define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k) +#define ks_shuffle(name, n, a) ks_shuffle_##name(n, a) + +#define ks_lt_generic(a, b) ((a) < (b)) +#define ks_lt_str(a, b) (strcmp((a), (b)) < 0) + +typedef const char *ksstr_t; + +#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic) +#define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str) + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/kstdint.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/kstdint.h new file mode 100644 index 0000000000000000000000000000000000000000..e948850da47f8fd257777d2c995919dafc803a76 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/kstdint.h @@ -0,0 +1,64 @@ +#ifndef KSTDINT_H +#define KSTDINT_H + +#include + +/* Basic assumptions: 1) "char" is 8-bit; 2) there is a 8-bit, 16-bit, 32-bit + * and 64-bit integer type, respectively; 3) "short" is no less than "char", + * "int" is no less than "short", "long" is no less than "int" and "long long" + * is no less than "long"; 4) "int" is at least 16-bit, "long" at least 32-bit + * and "long long" at least 64-bit. The last two assumptions are enforced by + * the C99 spec. + * + * Following assumptions 1) and 2), we know that "signed char"=="int8_t" and + * "short"=="int16_t" for sure. Further from the assumptions, a 32-bit integer + * type must be either "int" or "long". We can test (UINT16_MAX==UINT_MAX) to + * see which is the case. Similarly, a 64-bit integer must be either "long" or + * "long long". We can test (UINT16_MAX==UINT_MAX) to get the definite answer. + */ + +/* 8-bit integers */ +typedef signed char int8_t; +typedef unsigned char uint8_t; +#define INT8_MIN (-SCHAR_MAX-1) +#define INT8_MAX SCHAR_MAX +#define UINT8_MAX UCHAR_MAX + +/* 16-bit integers */ +typedef signed short int16_t; +typedef unsigned short uint16_t; +#define INT16_MIN (-SHRT_MAX-1) +#define INT16_MAX SHRT_MAX +#define UINT16_MAX USHRT_MAX + +/* 32-bit integers */ +#if UINT16_MAX != UINT_MAX +typedef signed int int32_t; +typedef unsigned int uint32_t; +#define INT32_MIN (-INT_MAX-1) +#define INT32_MAX INT_MAX +#define UINT32_MAX UINT_MAX +#else /* then int is 16-bit and long is 32-bit, which may happen to compilers for embedded CPUs */ +typedef signed long int32_t; +typedef unsigned long uint32_t; +#define INT32_MIN (-LONG_MAX-1) +#define INT32_MAX LONG_MAX +#define UINT32_MAX ULONG_MAX +#endif /* ~UINT16_MAX!=UINT_MAX */ + +/* 64-bit integers */ +#if UINT32_MAX != ULONG_MAX +typedef signed long int64_t; +typedef unsigned long uint64_t; +#define INT64_MIN (-LONG_MAX-1) +#define INT64_MAX LONG_MAX +#define UINT64_MAX ULONG_MAX +#else +typedef signed long long int64_t; +typedef unsigned long long uint64_t; +#define INT64_MIN (-LLONG_MAX-1) +#define INT64_MAX LLONG_MAX +#define UINT64_MAX ULLONG_MAX +#endif /* ~UINT32_MAX!=ULONG_MAX */ + +#endif /* ~defined(KSTDINT_H) */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/kstring.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/kstring.h new file mode 100644 index 0000000000000000000000000000000000000000..2567efcb721f273f82f435b291abea7c7565dd1c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/kstring.h @@ -0,0 +1,270 @@ +/* The MIT License + + Copyright (c) by Attractive Chaos + + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. +*/ + +#ifndef KSTRING_H +#define KSTRING_H + +#include +#include +#include +#include +#include + +#ifndef kroundup32 +#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) +#endif + +#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ > 4) +#define KS_ATTR_PRINTF(fmt, arg) __attribute__((__format__ (__printf__, fmt, arg))) +#else +#define KS_ATTR_PRINTF(fmt, arg) +#endif + + +/* kstring_t is a simple non-opaque type whose fields are likely to be + * used directly by user code (but see also ks_str() and ks_len() below). + * A kstring_t object is initialised by either of + * kstring_t str = { 0, 0, NULL }; + * kstring_t str; ...; str.l = str.m = 0; str.s = NULL; + * and either ownership of the underlying buffer should be given away before + * the object disappears (see ks_release() below) or the kstring_t should be + * destroyed with free(str.s); */ +#ifndef KSTRING_T +#define KSTRING_T kstring_t +typedef struct __kstring_t { + size_t l, m; + char *s; +} kstring_t; +#endif + +typedef struct { + uint64_t tab[4]; + int sep, finished; + const char *p; // end of the current token +} ks_tokaux_t; + +#ifdef __cplusplus +extern "C" { +#endif + + int kvsprintf(kstring_t *s, const char *fmt, va_list ap) KS_ATTR_PRINTF(2,0); + int ksprintf(kstring_t *s, const char *fmt, ...) KS_ATTR_PRINTF(2,3); + int ksplit_core(char *s, int delimiter, int *_max, int **_offsets); + char *kstrstr(const char *str, const char *pat, int **_prep); + char *kstrnstr(const char *str, const char *pat, int n, int **_prep); + void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep); + + /* kstrtok() is similar to strtok_r() except that str is not + * modified and both str and sep can be NULL. For efficiency, it is + * actually recommended to set both to NULL in the subsequent calls + * if sep is not changed. */ + char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux); + +#ifdef __cplusplus +} +#endif + +static inline int ks_resize(kstring_t *s, size_t size) +{ + if (s->m < size) { + char *tmp; + s->m = size; + kroundup32(s->m); + if ((tmp = (char*)realloc(s->s, s->m))) + s->s = tmp; + else + return -1; + } + return 0; +} + +static inline char *ks_str(kstring_t *s) +{ + return s->s; +} + +static inline size_t ks_len(kstring_t *s) +{ + return s->l; +} + +// Give ownership of the underlying buffer away to something else (making +// that something else responsible for freeing it), leaving the kstring_t +// empty and ready to be used again, or ready to go out of scope without +// needing free(str.s) to prevent a memory leak. +static inline char *ks_release(kstring_t *s) +{ + char *ss = s->s; + s->l = s->m = 0; + s->s = NULL; + return ss; +} + +static inline int kputsn(const char *p, int l, kstring_t *s) +{ + if (s->l + l + 1 >= s->m) { + char *tmp; + s->m = s->l + l + 2; + kroundup32(s->m); + if ((tmp = (char*)realloc(s->s, s->m))) + s->s = tmp; + else + return EOF; + } + memcpy(s->s + s->l, p, l); + s->l += l; + s->s[s->l] = 0; + return l; +} + +static inline int kputs(const char *p, kstring_t *s) +{ + return kputsn(p, strlen(p), s); +} + +static inline int kputc(int c, kstring_t *s) +{ + if (s->l + 1 >= s->m) { + char *tmp; + s->m = s->l + 2; + kroundup32(s->m); + if ((tmp = (char*)realloc(s->s, s->m))) + s->s = tmp; + else + return EOF; + } + s->s[s->l++] = c; + s->s[s->l] = 0; + return c; +} + +static inline int kputc_(int c, kstring_t *s) +{ + if (s->l + 1 > s->m) { + char *tmp; + s->m = s->l + 1; + kroundup32(s->m); + if ((tmp = (char*)realloc(s->s, s->m))) + s->s = tmp; + else + return EOF; + } + s->s[s->l++] = c; + return 1; +} + +static inline int kputsn_(const void *p, int l, kstring_t *s) +{ + if (s->l + l > s->m) { + char *tmp; + s->m = s->l + l; + kroundup32(s->m); + if ((tmp = (char*)realloc(s->s, s->m))) + s->s = tmp; + else + return EOF; + } + memcpy(s->s + s->l, p, l); + s->l += l; + return l; +} + +static inline int kputw(int c, kstring_t *s) +{ + char buf[16]; + int i, l = 0; + unsigned int x = c; + if (c < 0) x = -x; + do { buf[l++] = x%10 + '0'; x /= 10; } while (x > 0); + if (c < 0) buf[l++] = '-'; + if (s->l + l + 1 >= s->m) { + char *tmp; + s->m = s->l + l + 2; + kroundup32(s->m); + if ((tmp = (char*)realloc(s->s, s->m))) + s->s = tmp; + else + return EOF; + } + for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i]; + s->s[s->l] = 0; + return 0; +} + +static inline int kputuw(unsigned c, kstring_t *s) +{ + char buf[16]; + int l, i; + unsigned x; + if (c == 0) return kputc('0', s); + for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0'; + if (s->l + l + 1 >= s->m) { + char *tmp; + s->m = s->l + l + 2; + kroundup32(s->m); + if ((tmp = (char*)realloc(s->s, s->m))) + s->s = tmp; + else + return EOF; + } + for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i]; + s->s[s->l] = 0; + return 0; +} + +static inline int kputl(long c, kstring_t *s) +{ + char buf[32]; + int i, l = 0; + unsigned long x = c; + if (c < 0) x = -x; + do { buf[l++] = x%10 + '0'; x /= 10; } while (x > 0); + if (c < 0) buf[l++] = '-'; + if (s->l + l + 1 >= s->m) { + char *tmp; + s->m = s->l + l + 2; + kroundup32(s->m); + if ((tmp = (char*)realloc(s->s, s->m))) + s->s = tmp; + else + return EOF; + } + for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i]; + s->s[s->l] = 0; + return 0; +} + +/* + * Returns 's' split by delimiter, with *n being the number of components; + * NULL on failue. + */ +static inline int *ksplit(kstring_t *s, int delimiter, int *n) +{ + int max = 0, *offsets = 0; + *n = ksplit_core(s->s, delimiter, &max, &offsets); + return offsets; +} + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/sam.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/sam.h new file mode 100644 index 0000000000000000000000000000000000000000..e046d017a366b26abfe8339deda00973f5c2a014 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/sam.h @@ -0,0 +1,401 @@ +#ifndef BAM_H +#define BAM_H + +#include +#include "hts.h" + +/********************** + *** SAM/BAM header *** + **********************/ + +/*! @typedef + @abstract Structure for the alignment header. + @field n_targets number of reference sequences + @field l_text length of the plain text in the header + @field target_len lengths of the reference sequences + @field target_name names of the reference sequences + @field text plain text + @field sdict header dictionary + */ + +typedef struct { + int32_t n_targets, ignore_sam_err; + uint32_t l_text; + uint32_t *target_len; + int8_t *cigar_tab; + char **target_name; + char *text; + void *sdict; +} bam_hdr_t; + +/**************************** + *** CIGAR related macros *** + ****************************/ + +#define BAM_CMATCH 0 +#define BAM_CINS 1 +#define BAM_CDEL 2 +#define BAM_CREF_SKIP 3 +#define BAM_CSOFT_CLIP 4 +#define BAM_CHARD_CLIP 5 +#define BAM_CPAD 6 +#define BAM_CEQUAL 7 +#define BAM_CDIFF 8 +#define BAM_CBACK 9 + +#define BAM_CIGAR_STR "MIDNSHP=XB" +#define BAM_CIGAR_SHIFT 4 +#define BAM_CIGAR_MASK 0xf +#define BAM_CIGAR_TYPE 0x3C1A7 + +#define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK) +#define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT) +#define bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)]) +#define bam_cigar_gen(l, o) ((l)<>((o)<<1)&3) // bit 1: consume query; bit 2: consume reference + +/*! @abstract the read is paired in sequencing, no matter whether it is mapped in a pair */ +#define BAM_FPAIRED 1 +/*! @abstract the read is mapped in a proper pair */ +#define BAM_FPROPER_PAIR 2 +/*! @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR */ +#define BAM_FUNMAP 4 +/*! @abstract the mate is unmapped */ +#define BAM_FMUNMAP 8 +/*! @abstract the read is mapped to the reverse strand */ +#define BAM_FREVERSE 16 +/*! @abstract the mate is mapped to the reverse strand */ +#define BAM_FMREVERSE 32 +/*! @abstract this is read1 */ +#define BAM_FREAD1 64 +/*! @abstract this is read2 */ +#define BAM_FREAD2 128 +/*! @abstract not primary alignment */ +#define BAM_FSECONDARY 256 +/*! @abstract QC failure */ +#define BAM_FQCFAIL 512 +/*! @abstract optical or PCR duplicate */ +#define BAM_FDUP 1024 +/*! @abstract supplementary alignment */ +#define BAM_FSUPPLEMENTARY 2048 + +/************************* + *** Alignment records *** + *************************/ + +/*! @typedef + @abstract Structure for core alignment information. + @field tid chromosome ID, defined by bam_hdr_t + @field pos 0-based leftmost coordinate + @field bin bin calculated by bam_reg2bin() + @field qual mapping quality + @field l_qname length of the query name + @field flag bitwise flag + @field n_cigar number of CIGAR operations + @field l_qseq length of the query sequence (read) + @field mtid chromosome ID of next read in template, defined by bam_hdr_t + @field mpos 0-based leftmost coordinate of next read in template + */ +typedef struct { + int32_t tid; + int32_t pos; + uint32_t bin:16, qual:8, l_qname:8; + uint32_t flag:16, n_cigar:16; + int32_t l_qseq; + int32_t mtid; + int32_t mpos; + int32_t isize; +} bam1_core_t; + +/*! @typedef + @abstract Structure for one alignment. + @field core core information about the alignment + @field l_data current length of bam1_t::data + @field m_data maximum length of bam1_t::data + @field data all variable-length data, concatenated; structure: qname-cigar-seq-qual-aux + + @discussion Notes: + + 1. qname is zero tailing and core.l_qname includes the tailing '\0'. + 2. l_qseq is calculated from the total length of an alignment block + on reading or from CIGAR. + 3. cigar data is encoded 4 bytes per CIGAR operation. + 4. seq is nybble-encoded according to bam_nt16_table. + */ +typedef struct { + bam1_core_t core; + int l_data, m_data; + uint8_t *data; +#ifndef BAM_NO_ID + uint64_t id; +#endif +} bam1_t; + +/*! @function + @abstract Get whether the query is on the reverse strand + @param b pointer to an alignment + @return boolean true if query is on the reverse strand + */ +#define bam_is_rev(b) (((b)->core.flag&BAM_FREVERSE) != 0) +/*! @function + @abstract Get whether the query's mate is on the reverse strand + @param b pointer to an alignment + @return boolean true if query's mate on the reverse strand + */ +#define bam_is_mrev(b) (((b)->core.flag&BAM_FMREVERSE) != 0) +/*! @function + @abstract Get the name of the query + @param b pointer to an alignment + @return pointer to the name string, null terminated + */ +#define bam_get_qname(b) ((char*)(b)->data) +/*! @function + @abstract Get the CIGAR array + @param b pointer to an alignment + @return pointer to the CIGAR array + + @discussion In the CIGAR array, each element is a 32-bit integer. The + lower 4 bits gives a CIGAR operation and the higher 28 bits keep the + length of a CIGAR. + */ +#define bam_get_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname)) +/*! @function + @abstract Get query sequence + @param b pointer to an alignment + @return pointer to sequence + + @discussion Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G, + 8 for T and 15 for N. Two bases are packed in one byte with the base + at the higher 4 bits having smaller coordinate on the read. It is + recommended to use bam_seqi() macro to get the base. + */ +#define bam_get_seq(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname) +/*! @function + @abstract Get query quality + @param b pointer to an alignment + @return pointer to quality string + */ +#define bam_get_qual(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1)) +/*! @function + @abstract Get auxiliary data + @param b pointer to an alignment + @return pointer to the concatenated auxiliary data + */ +#define bam_get_aux(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1) + (b)->core.l_qseq) +/*! @function + @abstract Get length of auxiliary data + @param b pointer to an alignment + @return length of the concatenated auxiliary data + */ +#define bam_get_l_aux(b) ((b)->l_data - ((b)->core.n_cigar<<2) - (b)->core.l_qname - (b)->core.l_qseq - (((b)->core.l_qseq + 1)>>1)) +/*! @function + @abstract Get a base on read + @param s Query sequence returned by bam1_seq() + @param i The i-th position, 0-based + @return 4-bit integer representing the base. + */ +#define bam_seqi(s, i) ((s)[(i)>>1] >> ((~(i)&1)<<2) & 0xf) + +/************************** + *** Exported functions *** + **************************/ + +#ifdef __cplusplus +extern "C" { +#endif + + /*************** + *** BAM I/O *** + ***************/ + + bam_hdr_t *bam_hdr_init(void); + bam_hdr_t *bam_hdr_read(BGZF *fp); + int bam_hdr_write(BGZF *fp, const bam_hdr_t *h); + void bam_hdr_destroy(bam_hdr_t *h); + int bam_name2id(bam_hdr_t *h, const char *ref); + bam_hdr_t* bam_hdr_dup(const bam_hdr_t *h0); + + bam1_t *bam_init1(void); + void bam_destroy1(bam1_t *b); + int bam_read1(BGZF *fp, bam1_t *b); + int bam_write1(BGZF *fp, const bam1_t *b); + bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc); + bam1_t *bam_dup1(const bam1_t *bsrc); + + int bam_cigar2qlen(int n_cigar, const uint32_t *cigar); + int bam_cigar2rlen(int n_cigar, const uint32_t *cigar); + + /*! + @abstract Calculate the rightmost base position of an alignment on the + reference genome. + + @param b pointer to an alignment + @return the coordinate of the first base after the alignment, 0-based + + @discussion For a mapped read, this is just b->core.pos + bam_cigar2rlen. + For an unmapped read (either according to its flags or if it has no cigar + string), we return b->core.pos + 1 by convention. + */ + int32_t bam_endpos(const bam1_t *b); + + int bam_str2flag(const char *str); /** returns negative value on error */ + char *bam_flag2str(int flag); /** The string must be freed by the user */ + + /************************* + *** BAM/CRAM indexing *** + *************************/ + + // These BAM iterator functions work only on BAM files. To work with either + // BAM or CRAM files use the sam_index_load() & sam_itr_*() functions. + #define bam_itr_destroy(iter) hts_itr_destroy(iter) + #define bam_itr_queryi(idx, tid, beg, end) sam_itr_queryi(idx, tid, beg, end) + #define bam_itr_querys(idx, hdr, region) sam_itr_querys(idx, hdr, region) + #define bam_itr_next(htsfp, itr, r) hts_itr_next((htsfp)->fp.bgzf, (itr), (r), 0) + + // Load .csi or .bai BAM index file. + #define bam_index_load(fn) hts_idx_load((fn), HTS_FMT_BAI) + + int bam_index_build(const char *fn, int min_shift); + + // Load BAM (.csi or .bai) or CRAM (.crai) index file. + hts_idx_t *sam_index_load(htsFile *fp, const char *fn); + + #define sam_itr_destroy(iter) hts_itr_destroy(iter) + hts_itr_t *sam_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end); + hts_itr_t *sam_itr_querys(const hts_idx_t *idx, bam_hdr_t *hdr, const char *region); + #define sam_itr_next(htsfp, itr, r) hts_itr_next((htsfp)->fp.bgzf, (itr), (r), (htsfp)) + + /*************** + *** SAM I/O *** + ***************/ + + #define sam_open(fn, mode) (hts_open((fn), (mode))) + #define sam_close(fp) hts_close(fp) + + int sam_open_mode(char *mode, const char *fn, const char *format); + + typedef htsFile samFile; + bam_hdr_t *sam_hdr_parse(int l_text, const char *text); + bam_hdr_t *sam_hdr_read(samFile *fp); + int sam_hdr_write(samFile *fp, const bam_hdr_t *h); + + int sam_parse1(kstring_t *s, bam_hdr_t *h, bam1_t *b); + int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str); + int sam_read1(samFile *fp, bam_hdr_t *h, bam1_t *b); + int sam_write1(samFile *fp, const bam_hdr_t *h, const bam1_t *b); + + /************************************* + *** Manipulating auxiliary fields *** + *************************************/ + + uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]); + int32_t bam_aux2i(const uint8_t *s); + double bam_aux2f(const uint8_t *s); + char bam_aux2A(const uint8_t *s); + char *bam_aux2Z(const uint8_t *s); + + void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data); + int bam_aux_del(bam1_t *b, uint8_t *s); + +#ifdef __cplusplus +} +#endif + +/************************** + *** Pileup and Mpileup *** + **************************/ + +#if !defined(BAM_NO_PILEUP) + +/*! @typedef + @abstract Structure for one alignment covering the pileup position. + @field b pointer to the alignment + @field qpos position of the read base at the pileup site, 0-based + @field indel indel length; 0 for no indel, positive for ins and negative for del + @field level the level of the read in the "viewer" mode + @field is_del 1 iff the base on the padded read is a deletion + @field is_head ??? + @field is_tail ??? + @field is_refskip ??? + @field aux ??? + + @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The + difference between the two functions is that the former does not + set bam_pileup1_t::level, while the later does. Level helps the + implementation of alignment viewers, but calculating this has some + overhead. + */ +typedef struct { + bam1_t *b; + int32_t qpos; + int indel, level; + uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1, aux:28; +} bam_pileup1_t; + +typedef int (*bam_plp_auto_f)(void *data, bam1_t *b); + +struct __bam_plp_t; +typedef struct __bam_plp_t *bam_plp_t; + +struct __bam_mplp_t; +typedef struct __bam_mplp_t *bam_mplp_t; + +#ifdef __cplusplus +extern "C" { +#endif + + /** + * bam_plp_init() - sets an iterator over multiple + * @func: see mplp_func in bam_plcmd.c in samtools for an example. Expected return + * status: 0 on success, -1 on end, < -1 on non-recoverable errors + * @data: user data to pass to @func + */ + bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data); + void bam_plp_destroy(bam_plp_t iter); + int bam_plp_push(bam_plp_t iter, const bam1_t *b); + const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp); + const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp); + void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt); + void bam_plp_reset(bam_plp_t iter); + + bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data); + /** + * bam_mplp_init_overlaps() - if called, mpileup will detect overlapping + * read pairs and for each base pair set the base quality of the + * lower-quality base to zero, thus effectively discarding it from + * calling. If the two bases are identical, the quality of the other base + * is increased to the sum of their qualities (capped at 200), otherwise + * it is multiplied by 0.8. + */ + void bam_mplp_init_overlaps(bam_mplp_t iter); + void bam_mplp_destroy(bam_mplp_t iter); + void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt); + int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); + +#ifdef __cplusplus +} +#endif + +#endif // ~!defined(BAM_NO_PILEUP) + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/synced_bcf_reader.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/synced_bcf_reader.h new file mode 100644 index 0000000000000000000000000000000000000000..2f79a2102ac96893102fabd15df3e84b54c5bb84 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/synced_bcf_reader.h @@ -0,0 +1,255 @@ +/* + The synced_bcf_reader allows to keep multiple VCFs open and stream them + using the next_line iterator in a seamless matter without worrying about + chromosomes and synchronizing the sites. This is used by vcfcheck to + compare multiple VCFs simultaneously and is used also for merging, + creating intersections, etc. + + The synced_bcf_reader also provides API for reading indexed BCF/VCF, + hiding differences in BCF/VCF opening, indexing and reading. + + + Example of usage: + + bcf_srs_t *sr = bcf_sr_init(); + for (i=0; ihas_line[i] +#define bcf_sr_get_line(_readers, i) ((_readers)->has_line[i] ? ((_readers)->readers[i].buffer[0]) : NULL) +#define bcf_sr_region_done(_readers,i) (!(_readers)->has_line[i] && !(_readers)->readers[i].nbuffer ? 1 : 0) + +/** + * bcf_sr_seek() - set all readers to selected position + * @seq: sequence name; NULL to seek to start + * @pos: 0-based coordinate + */ +int bcf_sr_seek(bcf_srs_t *readers, const char *seq, int pos); + +/** + * bcf_sr_set_samples() - sets active samples + * @readers: holder of the open readers + * @samples: this can be one of: file name with one sample per line; + * or column-separated list of samples; or '-' for a list of + * samples shared by all files. If first character is the + * exclamation mark, all but the listed samples are included. + * @is_file: 0: list of samples; 1: file with sample names + * + * Returns 1 if the call succeeded, or 0 on error. + */ +int bcf_sr_set_samples(bcf_srs_t *readers, const char *samples, int is_file); + +/** + * bcf_sr_set_targets(), bcf_sr_set_regions() - init targets/regions + * @readers: holder of the open readers + * @targets: list of regions, one-based and inclusive. + * @is_fname: 0: targets is a comma-separated list of regions (chr,chr:from-to) + * 1: targets is a tabix indexed file with a list of regions + * ( or ) + * + * Returns 0 if the call succeeded, or -1 on error. + * + * Both functions behave the same way, unlisted positions will be skipped by + * bcf_sr_next_line(). However, there is an important difference: regions use + * index to jump to desired positions while targets streams the whole files + * and merely skip unlisted positions. + * + * Moreover, bcf_sr_set_targets() accepts an optional parameter $alleles which + * is intepreted as a 1-based column index in the tab-delimited file where + * alleles are listed. This in principle enables to perform the COLLAPSE_* + * logic also with tab-delimited files. However, the current implementation + * considers the alleles merely as a suggestion for prioritizing one of possibly + * duplicate VCF lines. It is up to the caller to examine targets->als if + * perfect match is sought after. Note that the duplicate positions in targets + * file are currently not supported. + */ +int bcf_sr_set_targets(bcf_srs_t *readers, const char *targets, int is_file, int alleles); +int bcf_sr_set_regions(bcf_srs_t *readers, const char *regions, int is_file); + + + +/* + * bcf_sr_regions_init() + * @regions: regions can be either a comma-separated list of regions + * (chr|chr:pos|chr:from-to|chr:from-) or VCF, BED, or + * tab-delimited file (the default). Uncompressed files + * are stored in memory while bgzip-compressed and tabix-indexed + * region files are streamed. + * @is_file: 0: regions is a comma-separated list of regions + * (chr|chr:pos|chr:from-to|chr:from-) + * 1: VCF, BED or tab-delimited file + * @chr, from, to: + * Column indexes of chromosome, start position and end position + * in the tab-delimited file. The positions are 1-based and + * inclusive. + * These parameters are ignored when reading from VCF, BED or + * tabix-indexed files. When end position column is not present, + * supply 'from' in place of 'to'. When 'to' is negative, first + * abs(to) will be attempted and if that fails, 'from' will be used + * instead. + */ +bcf_sr_regions_t *bcf_sr_regions_init(const char *regions, int is_file, int chr, int from, int to); +void bcf_sr_regions_destroy(bcf_sr_regions_t *regions); + +/* + * bcf_sr_regions_seek() - seek to the chromosome block + * + * Returns 0 on success or -1 on failure. Sets reg->seq appropriately and + * reg->start,reg->end to -1. + */ +int bcf_sr_regions_seek(bcf_sr_regions_t *regions, const char *chr); + +/* + * bcf_sr_regions_next() - retrieves next region. Returns 0 on success and -1 + * when all regions have been read. The fields reg->seq, reg->start and + * reg->end are filled with the genomic coordinates on succes or with + * NULL,-1,-1 when no region is available. The coordinates are 0-based, + * inclusive. + */ +int bcf_sr_regions_next(bcf_sr_regions_t *reg); + +/* + * bcf_sr_regions_overlap() - checks if the interval overlaps any of + * the regions, the coordinates are 0-based, inclusive. The coordinate queries + * must come in ascending order. + * + * Returns 0 if the position is in regions; -1 if the position is not in the + * regions and more regions exist; -2 if not in the regions and there are no more + * regions left. + */ +int bcf_sr_regions_overlap(bcf_sr_regions_t *reg, const char *seq, int start, int end); + +/* + * bcf_sr_regions_flush() - calls repeatedly regs->missed_reg_handler() until + * all remaining records are processed. + */ +void bcf_sr_regions_flush(bcf_sr_regions_t *regs); + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/tbx.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/tbx.h new file mode 100644 index 0000000000000000000000000000000000000000..71b4ac2e0af59cc5f782ec47313cf6b963e5141d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/tbx.h @@ -0,0 +1,52 @@ +#ifndef TBX_H +#define TBX_H + +#include "hts.h" + +#define TBX_MAX_SHIFT 31 + +#define TBX_GENERIC 0 +#define TBX_SAM 1 +#define TBX_VCF 2 +#define TBX_UCSC 0x10000 + +typedef struct { + int32_t preset; + int32_t sc, bc, ec; // seq col., beg col. and end col. + int32_t meta_char, line_skip; +} tbx_conf_t; + +typedef struct { + tbx_conf_t conf; + hts_idx_t *idx; + void *dict; +} tbx_t; + +extern tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sam, tbx_conf_vcf; + +#ifdef __cplusplus +extern "C" { +#endif + + #define tbx_itr_destroy(iter) hts_itr_destroy(iter) + #define tbx_itr_queryi(tbx, tid, beg, end) hts_itr_query((tbx)->idx, (tid), (beg), (end), tbx_readrec) + #define tbx_itr_querys(tbx, s) hts_itr_querys((tbx)->idx, (s), (hts_name2id_f)(tbx_name2id), (tbx), hts_itr_query, tbx_readrec) + #define tbx_itr_next(htsfp, tbx, itr, r) hts_itr_next(hts_get_bgzfp(htsfp), (itr), (r), (tbx)) + #define tbx_bgzf_itr_next(bgzfp, tbx, itr, r) hts_itr_next((bgzfp), (itr), (r), (tbx)) + + int tbx_name2id(tbx_t *tbx, const char *ss); + + /* Internal helper function used by tbx_itr_next() */ + BGZF *hts_get_bgzfp(htsFile *fp); + int tbx_readrec(BGZF *fp, void *tbxv, void *sv, int *tid, int *beg, int *end); + + int tbx_index_build(const char *fn, int min_shift, const tbx_conf_t *conf); + tbx_t *tbx_index_load(const char *fn); + const char **tbx_seqnames(tbx_t *tbx, int *n); // free the array but not the values + void tbx_destroy(tbx_t *tbx); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/vcf.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/vcf.h new file mode 100644 index 0000000000000000000000000000000000000000..2d12f1444536c26f4341aac59e41a055dad4efd7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/vcf.h @@ -0,0 +1,828 @@ +/* + todo: + - make the function names consistent + - provide calls to abstract away structs as much as possible + */ + +#ifndef BCF_H +#define BCF_H + +#include +#include +#include +#include "hts.h" +#include "kstring.h" + + +/***************** + * Header struct * + *****************/ + +#define BCF_HL_FLT 0 // header line +#define BCF_HL_INFO 1 +#define BCF_HL_FMT 2 +#define BCF_HL_CTG 3 +#define BCF_HL_STR 4 // structured header line TAG= +#define BCF_HL_GEN 5 // generic header line + +#define BCF_HT_FLAG 0 // header type +#define BCF_HT_INT 1 +#define BCF_HT_REAL 2 +#define BCF_HT_STR 3 + +#define BCF_VL_FIXED 0 // variable length +#define BCF_VL_VAR 1 +#define BCF_VL_A 2 +#define BCF_VL_G 3 +#define BCF_VL_R 4 + +/* === Dictionary === + + The header keeps three dictonaries. The first keeps IDs in the + "FILTER/INFO/FORMAT" lines, the second keeps the sequence names and lengths + in the "contig" lines and the last keeps the sample names. bcf_hdr_t::dict[] + is the actual hash table, which is opaque to the end users. In the hash + table, the key is the ID or sample name as a C string and the value is a + bcf_idinfo_t struct. bcf_hdr_t::id[] points to key-value pairs in the hash + table in the order that they appear in the VCF header. bcf_hdr_t::n[] is the + size of the hash table or, equivalently, the length of the id[] arrays. +*/ + +#define BCF_DT_ID 0 // dictionary type +#define BCF_DT_CTG 1 +#define BCF_DT_SAMPLE 2 + +// Complete textual representation of a header line +typedef struct { + int type; // One of the BCF_HL_* type + char *key; // The part before '=', i.e. FILTER/INFO/FORMAT/contig/fileformat etc. + char *value; // Set only for generic lines, NULL for FILTER/INFO, etc. + int nkeys; // Number of structured fields + char **keys, **vals; // The key=value pairs +} bcf_hrec_t; + +typedef struct { + uint32_t info[3]; // stores Number:20, var:4, Type:4, ColType:4 for BCF_HL_FLT,INFO,FMT + bcf_hrec_t *hrec[3]; + int id; +} bcf_idinfo_t; + +typedef struct { + const char *key; + const bcf_idinfo_t *val; +} bcf_idpair_t; + +typedef struct { + int32_t n[3]; + bcf_idpair_t *id[3]; + void *dict[3]; // ID dictionary, contig dict and sample dict + char **samples; + bcf_hrec_t **hrec; + int nhrec; + int ntransl, *transl[2]; // for bcf_translate() + int nsamples_ori; // for bcf_hdr_set_samples() + uint8_t *keep_samples; + kstring_t mem; +} bcf_hdr_t; + +extern uint8_t bcf_type_shift[]; + +/************** + * VCF record * + **************/ + +#define BCF_BT_NULL 0 +#define BCF_BT_INT8 1 +#define BCF_BT_INT16 2 +#define BCF_BT_INT32 3 +#define BCF_BT_FLOAT 5 +#define BCF_BT_CHAR 7 + +#define VCF_REF 0 +#define VCF_SNP 1 +#define VCF_MNP 2 +#define VCF_INDEL 4 +#define VCF_OTHER 8 + +typedef struct { + int type, n; // variant type and the number of bases affected, negative for deletions +} variant_t; + +typedef struct { + int id; // id: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$id].key + int n, size, type; // n: number of values per-sample; size: number of bytes per-sample; type: one of BCF_BT_* types + uint8_t *p; // same as vptr and vptr_* in bcf_info_t below + uint32_t p_len; + uint32_t p_off:31, p_free:1; +} bcf_fmt_t; + +typedef struct { + int key; // key: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$key].key + int type, len; // type: one of BCF_BT_* types; len: vector length, 1 for scalars + union { + int32_t i; // integer value + float f; // float value + } v1; // only set if $len==1; for easier access + uint8_t *vptr; // pointer to data array in bcf1_t->shared.s, excluding the size+type and tag id bytes + uint32_t vptr_len; // length of the vptr block or, when set, of the vptr_mod block, excluding offset + uint32_t vptr_off:31, // vptr offset, i.e., the size of the INFO key plus size+type bytes + vptr_free:1; // indicates that vptr-vptr_off must be freed; set only when modified and the new + // data block is bigger than the original +} bcf_info_t; + + +#define BCF1_DIRTY_ID 1 +#define BCF1_DIRTY_ALS 2 +#define BCF1_DIRTY_FLT 4 +#define BCF1_DIRTY_INF 8 + +typedef struct { + int m_fmt, m_info, m_id, m_als, m_allele, m_flt; // allocated size (high-water mark); do not change + int n_flt; // Number of FILTER fields + int *flt; // FILTER keys in the dictionary + char *id, *als; // ID and REF+ALT block (\0-seperated) + char **allele; // allele[0] is the REF (allele[] pointers to the als block); all null terminated + bcf_info_t *info; // INFO + bcf_fmt_t *fmt; // FORMAT and individual sample + variant_t *var; // $var and $var_type set only when set_variant_types called + int n_var, var_type; + int shared_dirty; // if set, shared.s must be recreated on BCF output + int indiv_dirty; // if set, indiv.s must be recreated on BCF output +} bcf_dec_t; + + +#define BCF_ERR_CTG_UNDEF 1 +#define BCF_ERR_TAG_UNDEF 2 +#define BCF_ERR_NCOLS 4 + +/* + The bcf1_t structure corresponds to one VCF/BCF line. Reading from VCF file + is slower because the string is first to be parsed, packed into BCF line + (done in vcf_parse), then unpacked into internal bcf1_t structure. If it + is known in advance that some of the fields will not be required (notably + the sample columns), parsing of these can be skipped by setting max_unpack + appropriately. + Similarly, it is fast to output a BCF line because the columns (kept in + shared.s, indiv.s, etc.) are written directly by bcf_write, whereas a VCF + line must be formatted in vcf_format. + */ +typedef struct { + int32_t rid; // CHROM + int32_t pos; // POS + int32_t rlen; // length of REF + float qual; // QUAL + uint32_t n_info:16, n_allele:16; + uint32_t n_fmt:8, n_sample:24; + kstring_t shared, indiv; + bcf_dec_t d; // lazy evaluation: $d is not generated by bcf_read(), but by explicitly calling bcf_unpack() + int max_unpack; // Set to BCF_UN_STR, BCF_UN_FLT, or BCF_UN_INFO to boost performance of vcf_parse when some of the fields won't be needed + int unpacked; // remember what has been unpacked to allow calling bcf_unpack() repeatedly without redoing the work + int unpack_size[3]; // the original block size of ID, REF+ALT and FILTER + int errcode; // one of BCF_ERR_* codes +} bcf1_t; + +/******* + * API * + *******/ + +#ifdef __cplusplus +extern "C" { +#endif + + /*********************************************************************** + * BCF and VCF I/O + * + * A note about naming conventions: htslib internally represents VCF + * records as bcf1_t data structures, therefore most functions are + * prefixed with bcf_. There are a few exceptions where the functions must + * be aware of both BCF and VCF worlds, such as bcf_parse vs vcf_parse. In + * these cases, functions prefixed with bcf_ are more general and work + * with both BCF and VCF. + * + ***********************************************************************/ + + /** These macros are defined only for consistency with other parts of htslib */ + #define bcf_init1() bcf_init() + #define bcf_read1(fp,h,v) bcf_read((fp),(h),(v)) + #define vcf_read1(fp,h,v) vcf_read((fp),(h),(v)) + #define bcf_write1(fp,h,v) bcf_write((fp),(h),(v)) + #define vcf_write1(fp,h,v) vcf_write((fp),(h),(v)) + #define bcf_destroy1(v) bcf_destroy(v) + #define vcf_parse1(s,h,v) vcf_parse((s),(h),(v)) + #define bcf_clear1(v) bcf_clear(v) + #define vcf_format1(h,v,s) vcf_format((h),(v),(s)) + + /** + * bcf_hdr_init() - create an empty BCF header. + * @param mode "r" or "w" + * + * When opened for writing, the mandatory fileFormat and + * FILTER=PASS lines are added automatically. + */ + bcf_hdr_t *bcf_hdr_init(const char *mode); + + /** Destroy a BCF header struct */ + void bcf_hdr_destroy(bcf_hdr_t *h); + + /** Initialize a bcf1_t object; equivalent to calloc(1, sizeof(bcf1_t)) */ + bcf1_t *bcf_init(void); + + /** Deallocate a bcf1_t object */ + void bcf_destroy(bcf1_t *v); + + /** + * Same as bcf_destroy() but frees only the memory allocated by bcf1_t, + * not the bcf1_t object itself. + */ + void bcf_empty(bcf1_t *v); + + /** + * Make the bcf1_t object ready for next read. Intended mostly for + * internal use, the user should rarely need to call this function + * directly. + */ + void bcf_clear(bcf1_t *v); + + + /** bcf_open and vcf_open mode: please see hts_open() in hts.h */ + typedef htsFile vcfFile; + #define bcf_open(fn, mode) hts_open((fn), (mode)) + #define vcf_open(fn, mode) hts_open((fn), (mode)) + #define bcf_close(fp) hts_close(fp) + #define vcf_close(fp) hts_close(fp) + + /** Reads VCF or BCF header */ + bcf_hdr_t *bcf_hdr_read(htsFile *fp); + + /** + * bcf_hdr_set_samples() - for more efficient VCF parsing when only one/few samples are needed + * @samples: samples to include or exclude from file or as a comma-separated string. + * LIST|FILE .. select samples in list/file + * ^LIST|FILE .. exclude samples from list/file + * - .. include all samples + * NULL .. exclude all samples + * @is_file: @samples is a file (1) or a comma-separated list (1) + * + * The bottleneck of VCF reading is parsing of genotype fields. If the + * reader knows in advance that only subset of samples is needed (possibly + * no samples at all), the performance of bcf_read() can be significantly + * improved by calling bcf_hdr_set_samples after bcf_hdr_read(). + * The function bcf_read() will subset the VCF/BCF records automatically + * with the notable exception when reading records via bcf_itr_next(). + * In this case, bcf_subset_format() must be called explicitly, because + * bcf_readrec() does not see the header. + * + * Returns 0 on success, -1 on error or a positive integer if the list + * contains samples not present in the VCF header. In such a case, the + * return value is the index of the offending sample. + */ + int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file); + int bcf_subset_format(const bcf_hdr_t *hdr, bcf1_t *rec); + + + /** Writes VCF or BCF header */ + int bcf_hdr_write(htsFile *fp, const bcf_hdr_t *h); + + /** Parse VCF line contained in kstring and populate the bcf1_t struct */ + int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v); + + /** The opposite of vcf_parse. It should rarely be called directly, see vcf_write */ + int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s); + + /** + * bcf_read() - read next VCF or BCF record + * + * Returns -1 on critical errors, 0 otherwise. On errors which are not + * critical for reading, such as missing header definitions, v->errcode is + * set to one of BCF_ERR* code and must be checked before calling + * vcf_write(). + */ + int bcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v); + + /** + * bcf_unpack() - unpack/decode a BCF record (fills the bcf1_t::d field) + * + * Note that bcf_unpack() must be called even when reading VCF. It is safe + * to call the function repeatedly, it will not unpack the same field + * twice. + */ + #define BCF_UN_STR 1 // up to ALT inclusive + #define BCF_UN_FLT 2 // up to FILTER + #define BCF_UN_INFO 4 // up to INFO + #define BCF_UN_SHR (BCF_UN_STR|BCF_UN_FLT|BCF_UN_INFO) // all shared information + #define BCF_UN_FMT 8 // unpack format and each sample + #define BCF_UN_IND BCF_UN_FMT // a synonymo of BCF_UN_FMT + #define BCF_UN_ALL (BCF_UN_SHR|BCF_UN_FMT) // everything + int bcf_unpack(bcf1_t *b, int which); + + /* + * bcf_dup() - create a copy of BCF record. + * + * Note that bcf_unpack() must be called on the returned copy as if it was + * obtained from bcf_read(). Also note that bcf_dup() calls bcf_sync1(src) + * internally to reflect any changes made by bcf_update_* functions. + */ + bcf1_t *bcf_dup(bcf1_t *src); + + /** + * bcf_write() - write one VCF or BCF record. The type is determined at the open() call. + */ + int bcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v); + + /** + * The following functions work only with VCFs and should rarely be called + * directly. Usually one wants to use their bcf_* alternatives, which work + * transparently with both VCFs and BCFs. + */ + bcf_hdr_t *vcf_hdr_read(htsFile *fp); + int vcf_hdr_write(htsFile *fp, const bcf_hdr_t *h); + int vcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v); + int vcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v); + + /** Helper function for the bcf_itr_next() macro; internal use, ignore it */ + int bcf_readrec(BGZF *fp, void *null, void *v, int *tid, int *beg, int *end); + + + + /************************************************************************** + * Header querying and manipulation routines + **************************************************************************/ + + /** Create a new header using the supplied template */ + bcf_hdr_t *bcf_hdr_dup(const bcf_hdr_t *hdr); + /** Copy header lines from src to dst if not already present in dst. See also bcf_translate(). */ + void bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src); + + /** + * bcf_hdr_add_sample() - add a new sample. + * @param sample: Sample name to be added. After all samples have been added, NULL + * must be passed to update internal header structures. + */ + int bcf_hdr_add_sample(bcf_hdr_t *hdr, const char *sample); + + /** Read VCF header from a file and update the header */ + int bcf_hdr_set(bcf_hdr_t *hdr, const char *fname); + + /** Returns formatted header (newly allocated string) and its length, + * excluding the terminating \0. If is_bcf parameter is unset, IDX + * fields are discarded. + */ + char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len); + + /** Append new VCF header line, returns 0 on success */ + int bcf_hdr_append(bcf_hdr_t *h, const char *line); + int bcf_hdr_printf(bcf_hdr_t *h, const char *format, ...); + + const char *bcf_hdr_get_version(const bcf_hdr_t *hdr); + void bcf_hdr_set_version(bcf_hdr_t *hdr, const char *version); + + /** + * bcf_hdr_remove() - remove VCF header tag + * @param type: one of BCF_HL_* + * @param key: tag name + */ + void bcf_hdr_remove(bcf_hdr_t *h, int type, const char *key); + + /** + * bcf_hdr_subset() - creates a new copy of the header removing unwanted samples + * @param n: number of samples to keep + * @param samples: names of the samples to keep + * @param imap: mapping from index in @samples to the sample index in the original file + * + * Sample names not present in h0 are ignored. The number of unmatched samples can be checked + * by comparing n and bcf_hdr_nsamples(out_hdr). + * This function can be used to reorder samples. + * See also bcf_subset() which subsets individual records. + */ + bcf_hdr_t *bcf_hdr_subset(const bcf_hdr_t *h0, int n, char *const* samples, int *imap); + + /** Creates a list of sequence names. It is up to the caller to free the list (but not the sequence names) */ + const char **bcf_hdr_seqnames(const bcf_hdr_t *h, int *nseqs); + + /** Get number of samples */ + #define bcf_hdr_nsamples(hdr) (hdr)->n[BCF_DT_SAMPLE] + + + /** The following functions are for internal use and should rarely be called directly */ + bcf_hrec_t *bcf_hdr_parse_line(const bcf_hdr_t *h, const char *line, int *len); + void bcf_hrec_format(const bcf_hrec_t *hrec, kstring_t *str); + int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec); + bcf_hrec_t *bcf_hdr_get_hrec(const bcf_hdr_t *hdr, int type, const char *id); // type is one of BCF_HL_FLT,..,BCF_HL_CTG + bcf_hrec_t *bcf_hrec_dup(bcf_hrec_t *hrec); + void bcf_hrec_add_key(bcf_hrec_t *hrec, const char *str, int len); + void bcf_hrec_set_val(bcf_hrec_t *hrec, int i, const char *str, int len, int is_quoted); + int bcf_hrec_find_key(bcf_hrec_t *hrec, const char *key); + void bcf_hrec_destroy(bcf_hrec_t *hrec); + + + + /************************************************************************** + * Individual record querying and manipulation routines + **************************************************************************/ + + /** See the description of bcf_hdr_subset() */ + int bcf_subset(const bcf_hdr_t *h, bcf1_t *v, int n, int *imap); + + /** + * bcf_translate() - translate tags ids to be consistent with different header. This function + * is useful when lines from multiple VCF need to be combined. + * @dst_hdr: the destination header, to be used in bcf_write(), see also bcf_hdr_combine() + * @src_hdr: the source header, used in bcf_read() + * @src_line: line obtained by bcf_read() + */ + int bcf_translate(const bcf_hdr_t *dst_hdr, bcf_hdr_t *src_hdr, bcf1_t *src_line); + + /** + * bcf_get_variant_type[s]() - returns one of VCF_REF, VCF_SNP, etc + */ + int bcf_get_variant_types(bcf1_t *rec); + int bcf_get_variant_type(bcf1_t *rec, int ith_allele); + int bcf_is_snp(bcf1_t *v); + + /** + * bcf_update_filter() - sets the FILTER column + * @flt_ids: The filter IDs to set, numeric IDs returned by bcf_id2int(hdr, BCF_DT_ID, "PASS") + * @n: Number of filters. If n==0, all filters are removed + */ + int bcf_update_filter(const bcf_hdr_t *hdr, bcf1_t *line, int *flt_ids, int n); + /** + * bcf_add_filter() - adds to the FILTER column + * @flt_id: filter ID to add, numeric ID returned by bcf_id2int(hdr, BCF_DT_ID, "PASS") + * + * If flt_id is PASS, all existing filters are removed first. If other than PASS, existing PASS is removed. + */ + int bcf_add_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id); + /** + * bcf_remove_filter() - removes from the FILTER column + * @flt_id: filter ID to remove, numeric ID returned by bcf_id2int(hdr, BCF_DT_ID, "PASS") + * @pass: when set to 1 and no filters are present, set to PASS + */ + int bcf_remove_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id, int pass); + /** + * Returns 1 if present, 0 if absent, or -1 if filter does not exist. "PASS" and "." can be used interchangeably. + */ + int bcf_has_filter(const bcf_hdr_t *hdr, bcf1_t *line, char *filter); + /** + * bcf_update_alleles() and bcf_update_alleles_str() - update REF and ALLT column + * @alleles: Array of alleles + * @nals: Number of alleles + * @alleles_string: Comma-separated alleles, starting with the REF allele + * + * Not that in order for indexing to work correctly in presence of INFO/END tag, + * the length of reference allele (line->rlen) must be set explicitly by the caller, + * or otherwise, if rlen is zero, strlen(line->d.allele[0]) is used to set the length + * on bcf_write(). + */ + int bcf_update_alleles(const bcf_hdr_t *hdr, bcf1_t *line, const char **alleles, int nals); + int bcf_update_alleles_str(const bcf_hdr_t *hdr, bcf1_t *line, const char *alleles_string); + int bcf_update_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id); + + /* + * bcf_update_info_*() - functions for updating INFO fields + * @hdr: the BCF header + * @line: VCF line to be edited + * @key: the INFO tag to be updated + * @values: pointer to the array of values. Pass NULL to remove the tag. + * @n: number of values in the array. When set to 0, the INFO tag is removed + * + * The @string in bcf_update_info_flag() is optional, @n indicates whether + * the flag is set or removed. + * + * Returns 0 on success or negative value on error. + */ + #define bcf_update_info_int32(hdr,line,key,values,n) bcf_update_info((hdr),(line),(key),(values),(n),BCF_HT_INT) + #define bcf_update_info_float(hdr,line,key,values,n) bcf_update_info((hdr),(line),(key),(values),(n),BCF_HT_REAL) + #define bcf_update_info_flag(hdr,line,key,string,n) bcf_update_info((hdr),(line),(key),(string),(n),BCF_HT_FLAG) + #define bcf_update_info_string(hdr,line,key,string) bcf_update_info((hdr),(line),(key),(string),1,BCF_HT_STR) + int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type); + + /* + * bcf_update_format_*() - functions for updating FORMAT fields + * @values: pointer to the array of values, the same number of elements + * is expected for each sample. Missing values must be padded + * with bcf_*_missing or bcf_*_vector_end values. + * @n: number of values in the array. If n==0, existing tag is removed. + * + * The function bcf_update_format_string() is a higher-level (slower) variant of + * bcf_update_format_char(). The former accepts array of \0-terminated strings + * whereas the latter requires that the strings are collapsed into a single array + * of fixed-length strings. In case of strings with variable length, shorter strings + * can be \0-padded. Note that the collapsed strings passed to bcf_update_format_char() + * are not \0-terminated. + * + * Returns 0 on success or negative value on error. + */ + #define bcf_update_format_int32(hdr,line,key,values,n) bcf_update_format((hdr),(line),(key),(values),(n),BCF_HT_INT) + #define bcf_update_format_float(hdr,line,key,values,n) bcf_update_format((hdr),(line),(key),(values),(n),BCF_HT_REAL) + #define bcf_update_format_char(hdr,line,key,values,n) bcf_update_format((hdr),(line),(key),(values),(n),BCF_HT_STR) + #define bcf_update_genotypes(hdr,line,gts,n) bcf_update_format((hdr),(line),"GT",(gts),(n),BCF_HT_INT) // See bcf_gt_ macros below + int bcf_update_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char **values, int n); + int bcf_update_format(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type); + + // Macros for setting genotypes correctly, for use with bcf_update_genotypes only; idx corresponds + // to VCF's GT (1-based index to ALT or 0 for the reference allele) and val is the opposite, obtained + // from bcf_get_genotypes() below. + #define bcf_gt_phased(idx) ((idx+1)<<1|1) + #define bcf_gt_unphased(idx) ((idx+1)<<1) + #define bcf_gt_missing 0 + #define bcf_gt_is_phased(idx) ((idx)&1) + #define bcf_gt_allele(val) (((val)>>1)-1) + + /** Conversion between alleles indexes to Number=G genotype index (assuming diploid, all 0-based) */ + #define bcf_alleles2gt(a,b) ((a)>(b)?((a)*((a)+1)/2+(b)):((b)*((b)+1)/2+(a))) + static inline void bcf_gt2alleles(int igt, int *a, int *b) + { + int k = 0, dk = 1; + while ( k 0 ) + * for (i=0; iid[type][int_id].key) + + /** + * bcf_hdr_name2id() - Translates sequence names (chromosomes) into numeric ID + * bcf_hdr_id2name() - Translates numeric ID to sequence name + */ + static inline int bcf_hdr_name2id(const bcf_hdr_t *hdr, const char *id) { return bcf_hdr_id2int(hdr, BCF_DT_CTG, id); } + static inline const char *bcf_hdr_id2name(const bcf_hdr_t *hdr, int rid) { return hdr->id[BCF_DT_CTG][rid].key; } + static inline const char *bcf_seqname(const bcf_hdr_t *hdr, bcf1_t *rec) { return hdr->id[BCF_DT_CTG][rec->rid].key; } + + /** + * bcf_hdr_id2*() - Macros for accessing bcf_idinfo_t + * @type: one of BCF_HL_FLT, BCF_HL_INFO, BCF_HL_FMT + * @int_id: return value of bcf_id2int, must be >=0 + * + * The returned values are: + * bcf_hdr_id2length .. whether the number of values is fixed or variable, one of BCF_VL_* + * bcf_hdr_id2number .. the number of values, 0xfffff for variable length fields + * bcf_hdr_id2type .. the field type, one of BCF_HT_* + * bcf_hdr_id2coltype .. the column type, one of BCF_HL_* + * + * Notes: Prior to using the macros, the presence of the info should be + * tested with bcf_hdr_idinfo_exists(). + */ + #define bcf_hdr_id2length(hdr,type,int_id) ((hdr)->id[BCF_DT_ID][int_id].val->info[type]>>8 & 0xf) + #define bcf_hdr_id2number(hdr,type,int_id) ((hdr)->id[BCF_DT_ID][int_id].val->info[type]>>12) + #define bcf_hdr_id2type(hdr,type,int_id) ((hdr)->id[BCF_DT_ID][int_id].val->info[type]>>4 & 0xf) + #define bcf_hdr_id2coltype(hdr,type,int_id) ((hdr)->id[BCF_DT_ID][int_id].val->info[type] & 0xf) + #define bcf_hdr_idinfo_exists(hdr,type,int_id) ((int_id<0 || bcf_hdr_id2coltype(hdr,type,int_id)==0xf) ? 0 : 1) + #define bcf_hdr_id2hrec(hdr,dict_type,col_type,int_id) ((hdr)->id[(dict_type)==BCF_DT_CTG?BCF_DT_CTG:BCF_DT_ID][int_id].val->hrec[(dict_type)==BCF_DT_CTG?0:(col_type)]) + + void bcf_fmt_array(kstring_t *s, int n, int type, void *data); + uint8_t *bcf_fmt_sized_array(kstring_t *s, uint8_t *ptr); + + void bcf_enc_vchar(kstring_t *s, int l, const char *a); + void bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize); + void bcf_enc_vfloat(kstring_t *s, int n, float *a); + + + /************************************************************************** + * BCF index + * + * Note that these functions work with BCFs only. See synced_bcf_reader.h + * which provides (amongst other things) an API to work transparently with + * both indexed BCFs and VCFs. + **************************************************************************/ + + #define bcf_itr_destroy(iter) hts_itr_destroy(iter) + #define bcf_itr_queryi(idx, tid, beg, end) hts_itr_query((idx), (tid), (beg), (end), bcf_readrec) + #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec) + #define bcf_itr_next(htsfp, itr, r) hts_itr_next((htsfp)->fp.bgzf, (itr), (r), 0) + #define bcf_index_load(fn) hts_idx_load(fn, HTS_FMT_CSI) + #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr)) + + int bcf_index_build(const char *fn, int min_shift); + +#ifdef __cplusplus +} +#endif + +/******************* + * Typed value I/O * + *******************/ + +/* + Note that in contrast with BCFv2.1 specification, HTSlib implementation + allows missing values in vectors. For integer types, the values 0x80, + 0x8000, 0x80000000 are interpreted as missing values and 0x81, 0x8001, + 0x80000001 as end-of-vector indicators. Similarly for floats, the value of + 0x7F800001 is interpreted as a missing value and 0x7F800002 as an + end-of-vector indicator. + Note that the end-of-vector byte is not part of the vector. + + This trial BCF version (v2.2) is compatible with the VCF specification and + enables to handle correctly vectors with different ploidy in presence of + missing values. + */ +#define bcf_int8_vector_end (INT8_MIN+1) +#define bcf_int16_vector_end (INT16_MIN+1) +#define bcf_int32_vector_end (INT32_MIN+1) +#define bcf_str_vector_end 0 +#define bcf_int8_missing INT8_MIN +#define bcf_int16_missing INT16_MIN +#define bcf_int32_missing INT32_MIN +#define bcf_str_missing 0x07 +extern uint32_t bcf_float_vector_end; +extern uint32_t bcf_float_missing; +static inline void bcf_float_set(float *ptr, uint32_t value) +{ + union { uint32_t i; float f; } u; + u.i = value; + *ptr = u.f; +} +#define bcf_float_set_vector_end(x) bcf_float_set(&(x),bcf_float_vector_end) +#define bcf_float_set_missing(x) bcf_float_set(&(x),bcf_float_missing) +static inline int bcf_float_is_missing(float f) +{ + union { uint32_t i; float f; } u; + u.f = f; + return u.i==bcf_float_missing ? 1 : 0; +} +static inline int bcf_float_is_vector_end(float f) +{ + union { uint32_t i; float f; } u; + u.f = f; + return u.i==bcf_float_vector_end ? 1 : 0; +} + +static inline void bcf_format_gt(bcf_fmt_t *fmt, int isample, kstring_t *str) +{ + #define BRANCH(type_t, missing, vector_end) { \ + type_t *ptr = (type_t*) (fmt->p + isample*fmt->size); \ + int i; \ + for (i=0; in && ptr[i]!=vector_end; i++) \ + { \ + if ( i ) kputc("/|"[ptr[i]&1], str); \ + if ( !(ptr[i]>>1) ) kputc('.', str); \ + else kputw((ptr[i]>>1) - 1, str); \ + } \ + if (i == 0) kputc('.', str); \ + } + switch (fmt->type) { + case BCF_BT_INT8: BRANCH(int8_t, bcf_int8_missing, bcf_int8_vector_end); break; + case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_missing, bcf_int16_vector_end); break; + case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_missing, bcf_int32_vector_end); break; + default: fprintf(stderr,"FIXME: type %d in bcf_format_gt?\n", fmt->type); abort(); break; + } + #undef BRANCH +} + +static inline void bcf_enc_size(kstring_t *s, int size, int type) +{ + if (size >= 15) { + kputc(15<<4|type, s); + if (size >= 128) { + if (size >= 32768) { + int32_t x = size; + kputc(1<<4|BCF_BT_INT32, s); + kputsn((char*)&x, 4, s); + } else { + int16_t x = size; + kputc(1<<4|BCF_BT_INT16, s); + kputsn((char*)&x, 2, s); + } + } else { + kputc(1<<4|BCF_BT_INT8, s); + kputc(size, s); + } + } else kputc(size<<4|type, s); +} + +static inline int bcf_enc_inttype(long x) +{ + if (x <= INT8_MAX && x > bcf_int8_missing) return BCF_BT_INT8; + if (x <= INT16_MAX && x > bcf_int16_missing) return BCF_BT_INT16; + return BCF_BT_INT32; +} + +static inline void bcf_enc_int1(kstring_t *s, int32_t x) +{ + if (x == bcf_int32_vector_end) { + bcf_enc_size(s, 1, BCF_BT_INT8); + kputc(bcf_int8_vector_end, s); + } else if (x == bcf_int32_missing) { + bcf_enc_size(s, 1, BCF_BT_INT8); + kputc(bcf_int8_missing, s); + } else if (x <= INT8_MAX && x > bcf_int8_missing) { + bcf_enc_size(s, 1, BCF_BT_INT8); + kputc(x, s); + } else if (x <= INT16_MAX && x > bcf_int16_missing) { + int16_t z = x; + bcf_enc_size(s, 1, BCF_BT_INT16); + kputsn((char*)&z, 2, s); + } else { + int32_t z = x; + bcf_enc_size(s, 1, BCF_BT_INT32); + kputsn((char*)&z, 4, s); + } +} + +static inline int32_t bcf_dec_int1(const uint8_t *p, int type, uint8_t **q) +{ + if (type == BCF_BT_INT8) { + *q = (uint8_t*)p + 1; + return *(int8_t*)p; + } else if (type == BCF_BT_INT16) { + *q = (uint8_t*)p + 2; + return *(int16_t*)p; + } else { + *q = (uint8_t*)p + 4; + return *(int32_t*)p; + } +} + +static inline int32_t bcf_dec_typed_int1(const uint8_t *p, uint8_t **q) +{ + return bcf_dec_int1(p + 1, *p&0xf, q); +} + +static inline int32_t bcf_dec_size(const uint8_t *p, uint8_t **q, int *type) +{ + *type = *p & 0xf; + if (*p>>4 != 15) { + *q = (uint8_t*)p + 1; + return *p>>4; + } else return bcf_dec_typed_int1(p + 1, q); +} + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/vcf_sweep.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/vcf_sweep.h new file mode 100644 index 0000000000000000000000000000000000000000..9d21d8a08f201f29c6abccd0b8bc8d157de8b2dd --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/vcf_sweep.h @@ -0,0 +1,15 @@ +#ifndef __VCF_SWEEP_H__ +#define __VCF_SWEEP_H__ + +#include "hts.h" +#include "vcf.h" + +typedef struct _bcf_sweep_t bcf_sweep_t; + +bcf_sweep_t *bcf_sweep_init(const char *fname); +void bcf_sweep_destroy(bcf_sweep_t *sw); +bcf_hdr_t *bcf_sweep_hdr(bcf_sweep_t *sw); +bcf1_t *bcf_sweep_fwd(bcf_sweep_t *sw); +bcf1_t *bcf_sweep_bwd(bcf_sweep_t *sw); + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/vcfutils.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/vcfutils.h new file mode 100644 index 0000000000000000000000000000000000000000..69ed8078842232b5ffce6d33d97bacecd2fc68f2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib/vcfutils.h @@ -0,0 +1,92 @@ +/* + Time will show if this module will be merged into others + or perhaps removed completely. +*/ +#ifndef VCF_UTILS_H +#define VCF_UTILS_H + +#include "vcf.h" + + +/** + * bcf_trim_alleles() - remove ALT alleles unused in genotype fields + * @header: for access to BCF_DT_ID dictionary + * @line: VCF line obtain from vcf_parse1 + * + * Returns the number of removed alleles on success or negative + * on error: + * -1 .. some allele index is out of bounds + */ +int bcf_trim_alleles(const bcf_hdr_t *header, bcf1_t *line); + + +/** + * bcf_remove_alleles() - remove ALT alleles according to bitmask @mask + * @header: for access to BCF_DT_ID dictionary + * @line: VCF line obtained from vcf_parse1 + * @mask: alleles to remove + */ +void bcf_remove_alleles(const bcf_hdr_t *header, bcf1_t *line, int mask); + + +/** + * bcf_calc_ac() - calculate the number of REF and ALT alleles + * @header: for access to BCF_DT_ID dictionary + * @line: VCF line obtained from vcf_parse1 + * @ac: array of length line->n_allele + * @which: determine if INFO/AN,AC and indv fields be used + * + * Returns 1 if the call succeeded, or 0 if the value could not + * be determined. + * + * The value of @which determines if existing INFO/AC,AN can be + * used (BCF_UN_INFO) and and if indv fields can be splitted + * (BCF_UN_FMT). + */ +int bcf_calc_ac(const bcf_hdr_t *header, bcf1_t *line, int *ac, int which); + + +/** + * bcf_gt_type() - determines type of the genotype + * @fmt_ptr: the GT format field as set for example by set_fmt_ptr + * @isample: sample index (starting from 0) + * @ial: index of the 1st non-reference allele (starting from 1) + * @jal: index of the 2nd non-reference allele (starting from 1) + * + * Returns the type of the genotype (one of GT_HOM_RR, GT_HET_RA, + * GT_HOM_AA, GT_HET_AA, GT_HAPL_R, GT_HAPL_A or GT_UNKN). If $ial + * is not NULL and the genotype has one or more non-reference + * alleles, $ial will be set. In case of GT_HET_AA, $ial is the + * position of the allele which appeared first in ALT. If $jal is + * not null and the genotype is GT_HET_AA, $jal will be set and is + * the position of the second allele in ALT. + */ +#define GT_HOM_RR 0 // note: the actual value of GT_* matters, used in dosage r2 calculation +#define GT_HOM_AA 1 +#define GT_HET_RA 2 +#define GT_HET_AA 3 +#define GT_HAPL_R 4 +#define GT_HAPL_A 5 +#define GT_UNKN 6 +int bcf_gt_type(bcf_fmt_t *fmt_ptr, int isample, int *ial, int *jal); + +static inline int bcf_acgt2int(char c) +{ + if ( (int)c>96 ) c -= 32; + if ( c=='A' ) return 0; + if ( c=='C' ) return 1; + if ( c=='G' ) return 2; + if ( c=='T' ) return 3; + return -1; +} +#define bcf_int2acgt(i) "ACGT"[i] + +/** + * bcf_ij2G() - common task: allele indexes to Number=G index (diploid) + * @i,j: allele indexes, 0-based, i<=j + * + * Returns index to the Number=G diploid array + */ +#define bcf_ij2G(i, j) ((j)*((j)+1)/2+(i)) + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib_vars.mk b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib_vars.mk new file mode 100644 index 0000000000000000000000000000000000000000..73ac5eb530435a668bf1c8e629ea1edccee46c6d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/htslib_vars.mk @@ -0,0 +1,20 @@ +# Makefile variables useful for third-party code using htslib's public API. +# +# Copyright (C) 2013-2014 Genome Research Ltd. +# +# Author: John Marshall + +# These variables can be used to express dependencies on htslib headers. +# See htslib.mk for details. + +htslib_bgzf_h = $(HTSPREFIX)htslib/bgzf.h +htslib_faidx_h = $(HTSPREFIX)htslib/faidx.h +htslib_hfile_h = $(HTSPREFIX)htslib/hfile.h $(htslib_hts_defs_h) +htslib_hts_h = $(HTSPREFIX)htslib/hts.h +htslib_hts_defs_h = $(HTSPREFIX)htslib/hts_defs.h +htslib_sam_h = $(HTSPREFIX)htslib/sam.h $(htslib_hts_h) +htslib_synced_bcf_reader_h = $(HTSPREFIX)htslib/synced_bcf_reader.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_tbx_h) +htslib_tbx_h = $(HTSPREFIX)htslib/tbx.h $(htslib_hts_h) +htslib_vcf_h = $(HTSPREFIX)htslib/vcf.h $(htslib_hts_h) $(HTSPREFIX)htslib/kstring.h +htslib_vcf_sweep_h = $(HTSPREFIX)htslib/vcf_sweep.h $(htslib_hts_h) $(htslib_vcf_h) +htslib_vcfutils_h = $(HTSPREFIX)htslib/vcfutils.h $(htslib_vcf_h) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/kfunc.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/kfunc.c new file mode 100644 index 0000000000000000000000000000000000000000..10c09731005f1e9886e0de9fbfd2aa539900f881 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/kfunc.c @@ -0,0 +1,254 @@ +#include +#include +#include "htslib/kfunc.h" + +/* Log gamma function + * \log{\Gamma(z)} + * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245 + */ +double kf_lgamma(double z) +{ + double x = 0; + x += 0.1659470187408462e-06 / (z+7); + x += 0.9934937113930748e-05 / (z+6); + x -= 0.1385710331296526 / (z+5); + x += 12.50734324009056 / (z+4); + x -= 176.6150291498386 / (z+3); + x += 771.3234287757674 / (z+2); + x -= 1259.139216722289 / (z+1); + x += 676.5203681218835 / z; + x += 0.9999999999995183; + return log(x) - 5.58106146679532777 - z + (z-0.5) * log(z+6.5); +} + +/* complementary error function + * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt + * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66 + */ +double kf_erfc(double x) +{ + const double p0 = 220.2068679123761; + const double p1 = 221.2135961699311; + const double p2 = 112.0792914978709; + const double p3 = 33.912866078383; + const double p4 = 6.37396220353165; + const double p5 = .7003830644436881; + const double p6 = .03526249659989109; + const double q0 = 440.4137358247522; + const double q1 = 793.8265125199484; + const double q2 = 637.3336333788311; + const double q3 = 296.5642487796737; + const double q4 = 86.78073220294608; + const double q5 = 16.06417757920695; + const double q6 = 1.755667163182642; + const double q7 = .08838834764831844; + double expntl, z, p; + z = fabs(x) * M_SQRT2; + if (z > 37.) return x > 0.? 0. : 2.; + expntl = exp(z * z * - .5); + if (z < 10. / M_SQRT2) // for small z + p = expntl * ((((((p6 * z + p5) * z + p4) * z + p3) * z + p2) * z + p1) * z + p0) + / (((((((q7 * z + q6) * z + q5) * z + q4) * z + q3) * z + q2) * z + q1) * z + q0); + else p = expntl / 2.506628274631001 / (z + 1. / (z + 2. / (z + 3. / (z + 4. / (z + .65))))); + return x > 0.? 2. * p : 2. * (1. - p); +} + +/* The following computes regularized incomplete gamma functions. + * Formulas are taken from Wiki, with additional input from Numerical + * Recipes in C (for modified Lentz's algorithm) and AS245 + * (http://lib.stat.cmu.edu/apstat/245). + * + * A good online calculator is available at: + * + * http://www.danielsoper.com/statcalc/calc23.aspx + * + * It calculates upper incomplete gamma function, which equals + * kf_gammaq(s,z)*tgamma(s). + */ + +#define KF_GAMMA_EPS 1e-14 +#define KF_TINY 1e-290 + +// regularized lower incomplete gamma function, by series expansion +static double _kf_gammap(double s, double z) +{ + double sum, x; + int k; + for (k = 1, sum = x = 1.; k < 100; ++k) { + sum += (x *= z / (s + k)); + if (x / sum < KF_GAMMA_EPS) break; + } + return exp(s * log(z) - z - kf_lgamma(s + 1.) + log(sum)); +} +// regularized upper incomplete gamma function, by continued fraction +static double _kf_gammaq(double s, double z) +{ + int j; + double C, D, f; + f = 1. + z - s; C = f; D = 0.; + // Modified Lentz's algorithm for computing continued fraction + // See Numerical Recipes in C, 2nd edition, section 5.2 + for (j = 1; j < 100; ++j) { + double a = j * (s - j), b = (j<<1) + 1 + z - s, d; + D = b + a * D; + if (D < KF_TINY) D = KF_TINY; + C = b + a / C; + if (C < KF_TINY) C = KF_TINY; + D = 1. / D; + d = C * D; + f *= d; + if (fabs(d - 1.) < KF_GAMMA_EPS) break; + } + return exp(s * log(z) - z - kf_lgamma(s) - log(f)); +} + +double kf_gammap(double s, double z) +{ + return z <= 1. || z < s? _kf_gammap(s, z) : 1. - _kf_gammaq(s, z); +} + +double kf_gammaq(double s, double z) +{ + return z <= 1. || z < s? 1. - _kf_gammap(s, z) : _kf_gammaq(s, z); +} + +/* Regularized incomplete beta function. The method is taken from + * Numerical Recipe in C, 2nd edition, section 6.4. The following web + * page calculates the incomplete beta function, which equals + * kf_betai(a,b,x) * gamma(a) * gamma(b) / gamma(a+b): + * + * http://www.danielsoper.com/statcalc/calc36.aspx + */ +static double kf_betai_aux(double a, double b, double x) +{ + double C, D, f; + int j; + if (x == 0.) return 0.; + if (x == 1.) return 1.; + f = 1.; C = f; D = 0.; + // Modified Lentz's algorithm for computing continued fraction + for (j = 1; j < 200; ++j) { + double aa, d; + int m = j>>1; + aa = (j&1)? -(a + m) * (a + b + m) * x / ((a + 2*m) * (a + 2*m + 1)) + : m * (b - m) * x / ((a + 2*m - 1) * (a + 2*m)); + D = 1. + aa * D; + if (D < KF_TINY) D = KF_TINY; + C = 1. + aa / C; + if (C < KF_TINY) C = KF_TINY; + D = 1. / D; + d = C * D; + f *= d; + if (fabs(d - 1.) < KF_GAMMA_EPS) break; + } + return exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b) + a * log(x) + b * log(1.-x)) / a / f; +} +double kf_betai(double a, double b, double x) +{ + return x < (a + 1.) / (a + b + 2.)? kf_betai_aux(a, b, x) : 1. - kf_betai_aux(b, a, 1. - x); +} + +#ifdef KF_MAIN +#include +int main(int argc, char *argv[]) +{ + double x = 5.5, y = 3; + double a, b; + printf("erfc(%lg): %lg, %lg\n", x, erfc(x), kf_erfc(x)); + printf("upper-gamma(%lg,%lg): %lg\n", x, y, kf_gammaq(y, x)*tgamma(y)); + a = 2; b = 2; x = 0.5; + printf("incomplete-beta(%lg,%lg,%lg): %lg\n", a, b, x, kf_betai(a, b, x) / exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b))); + return 0; +} +#endif + + +// log\binom{n}{k} +static double lbinom(int n, int k) +{ + if (k == 0 || n == k) return 0; + return lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1); +} + +// n11 n12 | n1_ +// n21 n22 | n2_ +//-----------+---- +// n_1 n_2 | n + +// hypergeometric distribution +static double hypergeo(int n11, int n1_, int n_1, int n) +{ + return exp(lbinom(n1_, n11) + lbinom(n-n1_, n_1-n11) - lbinom(n, n_1)); +} + +typedef struct { + int n11, n1_, n_1, n; + double p; +} hgacc_t; + +// incremental version of hypergenometric distribution +static double hypergeo_acc(int n11, int n1_, int n_1, int n, hgacc_t *aux) +{ + if (n1_ || n_1 || n) { + aux->n11 = n11; aux->n1_ = n1_; aux->n_1 = n_1; aux->n = n; + } else { // then only n11 changed; the rest fixed + if (n11%11 && n11 + aux->n - aux->n1_ - aux->n_1) { + if (n11 == aux->n11 + 1) { // incremental + aux->p *= (double)(aux->n1_ - aux->n11) / n11 + * (aux->n_1 - aux->n11) / (n11 + aux->n - aux->n1_ - aux->n_1); + aux->n11 = n11; + return aux->p; + } + if (n11 == aux->n11 - 1) { // incremental + aux->p *= (double)aux->n11 / (aux->n1_ - n11) + * (aux->n11 + aux->n - aux->n1_ - aux->n_1) / (aux->n_1 - n11); + aux->n11 = n11; + return aux->p; + } + } + aux->n11 = n11; + } + aux->p = hypergeo(aux->n11, aux->n1_, aux->n_1, aux->n); + return aux->p; +} + +double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two) +{ + int i, j, max, min; + double p, q, left, right; + hgacc_t aux; + int n1_, n_1, n; + + n1_ = n11 + n12; n_1 = n11 + n21; n = n11 + n12 + n21 + n22; // calculate n1_, n_1 and n + max = (n_1 < n1_) ? n_1 : n1_; // max n11, for right tail + min = n1_ + n_1 - n; // not sure why n11-n22 is used instead of min(n_1,n1_) + if (min < 0) min = 0; // min n11, for left tail + *two = *_left = *_right = 1.; + if (min == max) return 1.; // no need to do test + q = hypergeo_acc(n11, n1_, n_1, n, &aux); // the probability of the current table + // left tail + p = hypergeo_acc(min, 0, 0, 0, &aux); + for (left = 0., i = min + 1; p < 0.99999999 * q && i<=max; ++i) // loop until underflow + left += p, p = hypergeo_acc(i, 0, 0, 0, &aux); + --i; + if (p < 1.00000001 * q) left += p; + else --i; + // right tail + p = hypergeo_acc(max, 0, 0, 0, &aux); + for (right = 0., j = max - 1; p < 0.99999999 * q && j>=0; --j) // loop until underflow + right += p, p = hypergeo_acc(j, 0, 0, 0, &aux); + ++j; + if (p < 1.00000001 * q) right += p; + else ++j; + // two-tail + *two = left + right; + if (*two > 1.) *two = 1.; + // adjust left and right + if (abs(i - n11) < abs(j - n11)) right = 1. - left + q; + else left = 1.0 - right + q; + *_left = left; *_right = right; + return q; +} + + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/knetfile.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/knetfile.c new file mode 100644 index 0000000000000000000000000000000000000000..64b3fa6f0755a36cb8a1b4939e1813c0f14fd845 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/knetfile.c @@ -0,0 +1,622 @@ +/* The MIT License + + Copyright (c) 2008 by Genome Research Ltd (GRL). + 2010 by Attractive Chaos + + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. +*/ + +/* Probably I will not do socket programming in the next few years and + therefore I decide to heavily annotate this file, for Linux and + Windows as well. -ac */ + +#include +#include +#include +#include +#include +#include +#include +#include + +#ifndef _WIN32 +#include +#include +#include +#endif + +#include "htslib/knetfile.h" + +/* In winsock.h, the type of a socket is SOCKET, which is: "typedef + * u_int SOCKET". An invalid SOCKET is: "(SOCKET)(~0)", or signed + * integer -1. In knetfile.c, I use "int" for socket type + * throughout. This should be improved to avoid confusion. + * + * In Linux/Mac, recv() and read() do almost the same thing. You can see + * in the header file that netread() is simply an alias of read(). In + * Windows, however, they are different and using recv() is mandatory. + */ + +/* This function tests if the file handler is ready for reading (or + * writing if is_read==0). */ +static int socket_wait(int fd, int is_read) +{ + fd_set fds, *fdr = 0, *fdw = 0; + struct timeval tv; + int ret; + tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out + FD_ZERO(&fds); + FD_SET(fd, &fds); + if (is_read) fdr = &fds; + else fdw = &fds; + ret = select(fd+1, fdr, fdw, 0, &tv); +#ifndef _WIN32 + if (ret == -1) perror("select"); +#else + if (ret == 0) + fprintf(stderr, "select time-out\n"); + else if (ret == SOCKET_ERROR) + fprintf(stderr, "select: %d\n", WSAGetLastError()); +#endif + return ret; +} + +#ifndef _WIN32 +/* This function does not work with Windows due to the lack of + * getaddrinfo() in winsock. It is addapted from an example in "Beej's + * Guide to Network Programming" (http://beej.us/guide/bgnet/). */ +static int socket_connect(const char *host, const char *port) +{ +#define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0) + + int on = 1, fd; + struct linger lng = { 0, 0 }; + struct addrinfo hints, *res = 0; + memset(&hints, 0, sizeof(struct addrinfo)); + hints.ai_family = AF_UNSPEC; + hints.ai_socktype = SOCK_STREAM; + /* In Unix/Mac, getaddrinfo() is the most convenient way to get + * server information. */ + if (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo"); + if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket"); + /* The following two setsockopt() are used by ftplib + * (http://nbpfaus.net/~pfau/ftplib/). I am not sure if they + * necessary. */ + if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt"); + if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt"); + if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect"); + freeaddrinfo(res); + return fd; +} +#else +/* MinGW's printf has problem with "%lld" */ +char *int64tostr(char *buf, int64_t x) +{ + int cnt; + int i = 0; + do { + buf[i++] = '0' + x % 10; + x /= 10; + } while (x); + buf[i] = 0; + for (cnt = i, i = 0; i < cnt/2; ++i) { + int c = buf[i]; buf[i] = buf[cnt-i-1]; buf[cnt-i-1] = c; + } + return buf; +} + +int64_t strtoint64(const char *buf) +{ + int64_t x; + for (x = 0; *buf != '\0'; ++buf) + x = x * 10 + ((int64_t) *buf - 48); + return x; +} +/* In windows, the first thing is to establish the TCP connection. */ +int knet_win32_init() +{ + WSADATA wsaData; + return WSAStartup(MAKEWORD(2, 2), &wsaData); +} +void knet_win32_destroy() +{ + WSACleanup(); +} +/* A slightly modfied version of the following function also works on + * Mac (and presummably Linux). However, this function is not stable on + * my Mac. It sometimes works fine but sometimes does not. Therefore for + * non-Windows OS, I do not use this one. */ +static SOCKET socket_connect(const char *host, const char *port) +{ +#define __err_connect(func) \ + do { \ + fprintf(stderr, "%s: %d\n", func, WSAGetLastError()); \ + return -1; \ + } while (0) + + int on = 1; + SOCKET fd; + struct linger lng = { 0, 0 }; + struct sockaddr_in server; + struct hostent *hp = 0; + // open socket + if ((fd = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP)) == INVALID_SOCKET) __err_connect("socket"); + if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, (char*)&on, sizeof(on)) == -1) __err_connect("setsockopt"); + if (setsockopt(fd, SOL_SOCKET, SO_LINGER, (char*)&lng, sizeof(lng)) == -1) __err_connect("setsockopt"); + // get host info + if (isalpha(host[0])) hp = gethostbyname(host); + else { + struct in_addr addr; + addr.s_addr = inet_addr(host); + hp = gethostbyaddr((char*)&addr, 4, AF_INET); + } + if (hp == 0) __err_connect("gethost"); + // connect + server.sin_addr.s_addr = *((unsigned long*)hp->h_addr); + server.sin_family= AF_INET; + server.sin_port = htons(atoi(port)); + if (connect(fd, (struct sockaddr*)&server, sizeof(server)) != 0) __err_connect("connect"); + // freehostent(hp); // strangely in MSDN, hp is NOT freed (memory leak?!) + return fd; +} +#endif + +static off_t my_netread(int fd, void *buf, off_t len) +{ + off_t rest = len, curr, l = 0; + /* recv() and read() may not read the required length of data with + * one call. They have to be called repeatedly. */ + while (rest) { + if (socket_wait(fd, 1) <= 0) break; // socket is not ready for reading + curr = netread(fd, (void*)((char*)buf + l), rest); + /* According to the glibc manual, section 13.2, a zero returned + * value indicates end-of-file (EOF), which should mean that + * read() will not return zero if EOF has not been met but data + * are not immediately available. */ + if (curr == 0) break; + l += curr; rest -= curr; + } + return l; +} + +/************************* + * FTP specific routines * + *************************/ + +static int kftp_get_response(knetFile *ftp) +{ +#ifndef _WIN32 + unsigned char c; +#else + char c; +#endif + int n = 0; + char *p; + if (socket_wait(ftp->ctrl_fd, 1) <= 0) return 0; + while (netread(ftp->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O + //fputc(c, stderr); + if (n >= ftp->max_response) { + ftp->max_response = ftp->max_response? ftp->max_response<<1 : 256; + ftp->response = (char*)realloc(ftp->response, ftp->max_response); + } + ftp->response[n++] = c; + if (c == '\n') { + if (n >= 4 && isdigit(ftp->response[0]) && isdigit(ftp->response[1]) && isdigit(ftp->response[2]) + && ftp->response[3] != '-') break; + n = 0; + continue; + } + } + if (n < 2) return -1; + ftp->response[n-2] = 0; + return strtol(ftp->response, &p, 0); +} + +static int kftp_send_cmd(knetFile *ftp, const char *cmd, int is_get) +{ + if (socket_wait(ftp->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing + int len = strlen(cmd); + if ( netwrite(ftp->ctrl_fd, cmd, len) != len ) return -1; + return is_get? kftp_get_response(ftp) : 0; +} + +static int kftp_pasv_prep(knetFile *ftp) +{ + char *p; + int v[6]; + kftp_send_cmd(ftp, "PASV\r\n", 1); + for (p = ftp->response; *p && *p != '('; ++p); + if (*p != '(') return -1; + ++p; + sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]); + memcpy(ftp->pasv_ip, v, 4 * sizeof(int)); + ftp->pasv_port = (v[4]<<8&0xff00) + v[5]; + return 0; +} + + +static int kftp_pasv_connect(knetFile *ftp) +{ + char host[80], port[10]; + if (ftp->pasv_port == 0) { + fprintf(stderr, "[kftp_pasv_connect] kftp_pasv_prep() is not called before hand.\n"); + return -1; + } + sprintf(host, "%d.%d.%d.%d", ftp->pasv_ip[0], ftp->pasv_ip[1], ftp->pasv_ip[2], ftp->pasv_ip[3]); + sprintf(port, "%d", ftp->pasv_port); + ftp->fd = socket_connect(host, port); + if (ftp->fd == -1) return -1; + return 0; +} + +int kftp_connect(knetFile *ftp) +{ + ftp->ctrl_fd = socket_connect(ftp->host, ftp->port); + if (ftp->ctrl_fd == -1) return -1; + kftp_get_response(ftp); + kftp_send_cmd(ftp, "USER anonymous\r\n", 1); + kftp_send_cmd(ftp, "PASS kftp@\r\n", 1); + kftp_send_cmd(ftp, "TYPE I\r\n", 1); + return 0; +} + +int kftp_reconnect(knetFile *ftp) +{ + if (ftp->ctrl_fd != -1) { + netclose(ftp->ctrl_fd); + ftp->ctrl_fd = -1; + } + netclose(ftp->fd); + ftp->fd = -1; + return kftp_connect(ftp); +} + +// initialize ->type, ->host, ->retr and ->size +knetFile *kftp_parse_url(const char *fn, const char *mode) +{ + knetFile *fp; + char *p; + int l; + if (strstr(fn, "ftp://") != fn) return 0; + for (p = (char*)fn + 6; *p && *p != '/'; ++p); + if (*p != '/') return 0; + l = p - fn - 6; + fp = (knetFile*)calloc(1, sizeof(knetFile)); + fp->type = KNF_TYPE_FTP; + fp->fd = -1; + /* the Linux/Mac version of socket_connect() also recognizes a port + * like "ftp", but the Windows version does not. */ + fp->port = strdup("21"); + fp->host = (char*)calloc(l + 1, 1); + if (strchr(mode, 'c')) fp->no_reconnect = 1; + strncpy(fp->host, fn + 6, l); + fp->retr = (char*)calloc(strlen(p) + 8, 1); + sprintf(fp->retr, "RETR %s\r\n", p); + fp->size_cmd = (char*)calloc(strlen(p) + 8, 1); + sprintf(fp->size_cmd, "SIZE %s\r\n", p); + fp->seek_offset = 0; + return fp; +} +// place ->fd at offset off +int kftp_connect_file(knetFile *fp) +{ + int ret; + long long file_size; + if (fp->fd != -1) { + netclose(fp->fd); + if (fp->no_reconnect) kftp_get_response(fp); + } + kftp_pasv_prep(fp); + kftp_send_cmd(fp, fp->size_cmd, 1); +#ifndef _WIN32 + if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 ) + { + fprintf(stderr,"[kftp_connect_file] %s\n", fp->response); + return -1; + } +#else + const char *p = fp->response; + while (*p != ' ') ++p; + while (*p < '0' || *p > '9') ++p; + file_size = strtoint64(p); +#endif + fp->file_size = file_size; + if (fp->offset>=0) { + char tmp[32]; +#ifndef _WIN32 + sprintf(tmp, "REST %lld\r\n", (long long)fp->offset); +#else + strcpy(tmp, "REST "); + int64tostr(tmp + 5, fp->offset); + strcat(tmp, "\r\n"); +#endif + kftp_send_cmd(fp, tmp, 1); + } + kftp_send_cmd(fp, fp->retr, 0); + kftp_pasv_connect(fp); + ret = kftp_get_response(fp); + if (ret != 150) { + fprintf(stderr, "[kftp_connect_file] %s\n", fp->response); + netclose(fp->fd); + fp->fd = -1; + return -1; + } + fp->is_ready = 1; + return 0; +} + + +/************************** + * HTTP specific routines * + **************************/ + +knetFile *khttp_parse_url(const char *fn, const char *mode) +{ + knetFile *fp; + char *p, *proxy, *q; + int l; + if (strstr(fn, "http://") != fn) return 0; + // set ->http_host + for (p = (char*)fn + 7; *p && *p != '/'; ++p); + l = p - fn - 7; + fp = (knetFile*)calloc(1, sizeof(knetFile)); + fp->http_host = (char*)calloc(l + 1, 1); + strncpy(fp->http_host, fn + 7, l); + fp->http_host[l] = 0; + for (q = fp->http_host; *q && *q != ':'; ++q); + if (*q == ':') *q++ = 0; + // get http_proxy + proxy = getenv("http_proxy"); + // set ->host, ->port and ->path + if (proxy == 0) { + fp->host = strdup(fp->http_host); // when there is no proxy, server name is identical to http_host name. + fp->port = strdup(*q? q : "80"); + fp->path = strdup(*p? p : "/"); + } else { + fp->host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy); + for (q = fp->host; *q && *q != ':'; ++q); + if (*q == ':') *q++ = 0; + fp->port = strdup(*q? q : "80"); + fp->path = strdup(fn); + } + fp->type = KNF_TYPE_HTTP; + fp->ctrl_fd = fp->fd = -1; + fp->seek_offset = 0; + return fp; +} + +int khttp_connect_file(knetFile *fp) +{ + int ret, l = 0; + char *buf, *p; + if (fp->fd != -1) netclose(fp->fd); + fp->fd = socket_connect(fp->host, fp->port); + buf = (char*)calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough. + l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", fp->path, fp->http_host); + l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset); + l += sprintf(buf + l, "\r\n"); + if ( netwrite(fp->fd, buf, l) != l ) return -1; + l = 0; + while (netread(fp->fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency + if (buf[l] == '\n' && l >= 3) + if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break; + ++l; + } + buf[l] = 0; + if (l < 14) { // prematured header + netclose(fp->fd); + fp->fd = -1; + return -1; + } + ret = strtol(buf + 8, &p, 0); // HTTP return code + if (ret == 200 && fp->offset>0) { // 200 (complete result); then skip beginning of the file + off_t rest = fp->offset; + while (rest) { + off_t l = rest < 0x10000? rest : 0x10000; + rest -= my_netread(fp->fd, buf, l); + } + } else if (ret != 206 && ret != 200) { + free(buf); + fprintf(stderr, "[khttp_connect_file] fail to open file (HTTP code: %d).\n", ret); + netclose(fp->fd); + fp->fd = -1; + return -1; + } + free(buf); + fp->is_ready = 1; + return 0; +} + +/******************** + * Generic routines * + ********************/ + +knetFile *knet_open(const char *fn, const char *mode) +{ + knetFile *fp = 0; + if (mode[0] != 'r') { + fprintf(stderr, "[kftp_open] only mode \"r\" is supported.\n"); + return 0; + } + if (strstr(fn, "ftp://") == fn) { + fp = kftp_parse_url(fn, mode); + if (fp == 0) return 0; + if (kftp_connect(fp) == -1) { + knet_close(fp); + return 0; + } + kftp_connect_file(fp); + } else if (strstr(fn, "http://") == fn) { + fp = khttp_parse_url(fn, mode); + if (fp == 0) return 0; + khttp_connect_file(fp); + } else { // local file +#ifdef _WIN32 + /* In windows, O_BINARY is necessary. In Linux/Mac, O_BINARY may + * be undefined on some systems, although it is defined on my + * Mac and the Linux I have tested on. */ + int fd = open(fn, O_RDONLY | O_BINARY); +#else + int fd = open(fn, O_RDONLY); +#endif + if (fd == -1) { + perror("open"); + return 0; + } + fp = (knetFile*)calloc(1, sizeof(knetFile)); + fp->type = KNF_TYPE_LOCAL; + fp->fd = fd; + fp->ctrl_fd = -1; + } + if (fp && fp->fd == -1) { + knet_close(fp); + return 0; + } + return fp; +} + +knetFile *knet_dopen(int fd, const char *mode) +{ + knetFile *fp = (knetFile*)calloc(1, sizeof(knetFile)); + fp->type = KNF_TYPE_LOCAL; + fp->fd = fd; + return fp; +} + +ssize_t knet_read(knetFile *fp, void *buf, size_t len) +{ + off_t l = 0; + if (fp->fd == -1) return 0; + if (fp->type == KNF_TYPE_FTP) { + if (fp->is_ready == 0) { + if (!fp->no_reconnect) kftp_reconnect(fp); + kftp_connect_file(fp); + } + } else if (fp->type == KNF_TYPE_HTTP) { + if (fp->is_ready == 0) + khttp_connect_file(fp); + } + if (fp->type == KNF_TYPE_LOCAL) { // on Windows, the following block is necessary; not on UNIX + size_t rest = len; + ssize_t curr; + while (rest) { + do { + curr = read(fp->fd, (void*)((char*)buf + l), rest); + } while (curr < 0 && EINTR == errno); + if (curr < 0) return -1; + if (curr == 0) break; + l += curr; rest -= curr; + } + } else l = my_netread(fp->fd, buf, len); + fp->offset += l; + return l; +} + +off_t knet_seek(knetFile *fp, off_t off, int whence) +{ + if (whence == SEEK_SET && off == fp->offset) return 0; + if (fp->type == KNF_TYPE_LOCAL) { + /* Be aware that lseek() returns the offset after seeking, while fseek() returns zero on success. */ + off_t offset = lseek(fp->fd, off, whence); + if (offset == -1) return -1; + fp->offset = offset; + return fp->offset; + } else if (fp->type == KNF_TYPE_FTP) { + if (whence == SEEK_CUR) fp->offset += off; + else if (whence == SEEK_SET) fp->offset = off; + else if (whence == SEEK_END) fp->offset = fp->file_size + off; + else return -1; + fp->is_ready = 0; + return fp->offset; + } else if (fp->type == KNF_TYPE_HTTP) { + if (whence == SEEK_END) { // FIXME: can we allow SEEK_END in future? + fprintf(stderr, "[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.\n"); + errno = ESPIPE; + return -1; + } + if (whence == SEEK_CUR) fp->offset += off; + else if (whence == SEEK_SET) fp->offset = off; + else return -1; + fp->is_ready = 0; + return fp->offset; + } + errno = EINVAL; + fprintf(stderr,"[knet_seek] %s\n", strerror(errno)); + return -1; +} + +int knet_close(knetFile *fp) +{ + if (fp == 0) return 0; + if (fp->ctrl_fd != -1) netclose(fp->ctrl_fd); // FTP specific + if (fp->fd != -1) { + /* On Linux/Mac, netclose() is an alias of close(), but on + * Windows, it is an alias of closesocket(). */ + if (fp->type == KNF_TYPE_LOCAL) close(fp->fd); + else netclose(fp->fd); + } + free(fp->host); free(fp->port); + free(fp->response); free(fp->retr); // FTP specific + free(fp->path); free(fp->http_host); // HTTP specific + free(fp); + return 0; +} + +#ifdef KNETFILE_MAIN +int main(void) +{ + char *buf; + knetFile *fp; + int type = 4, l; +#ifdef _WIN32 + knet_win32_init(); +#endif + buf = calloc(0x100000, 1); + if (type == 0) { + fp = knet_open("knetfile.c", "r"); + knet_seek(fp, 1000, SEEK_SET); + } else if (type == 1) { // NCBI FTP, large file + fp = knet_open("ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam", "r"); + knet_seek(fp, 2500000000ll, SEEK_SET); + l = knet_read(fp, buf, 255); + } else if (type == 2) { + fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r"); + knet_seek(fp, 1000, SEEK_SET); + } else if (type == 3) { + fp = knet_open("http://www.sanger.ac.uk/Users/lh3/index.shtml", "r"); + knet_seek(fp, 1000, SEEK_SET); + } else if (type == 4) { + fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r"); + knet_read(fp, buf, 10000); + knet_seek(fp, 20000, SEEK_SET); + knet_seek(fp, 10000, SEEK_SET); + l = knet_read(fp, buf+10000, 10000000) + 10000; + } + if (type != 4 && type != 1) { + knet_read(fp, buf, 255); + buf[255] = 0; + printf("%s\n", buf); + } else write(fileno(stdout), buf, l); + knet_close(fp); + free(buf); + return 0; +} +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/kstring.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/kstring.c new file mode 100644 index 0000000000000000000000000000000000000000..b4202f556a316b825a7902deb551fc1a4ef16461 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/kstring.c @@ -0,0 +1,229 @@ +#include +#include +#include +#include +#include +#include "htslib/kstring.h" + +int kvsprintf(kstring_t *s, const char *fmt, va_list ap) +{ + va_list args; + int l; + va_copy(args, ap); + l = vsnprintf(s->s + s->l, s->m - s->l, fmt, args); // This line does not work with glibc 2.0. See `man snprintf'. + va_end(args); + if (l + 1 > s->m - s->l) { + s->m = s->l + l + 2; + kroundup32(s->m); + s->s = (char*)realloc(s->s, s->m); + va_copy(args, ap); + l = vsnprintf(s->s + s->l, s->m - s->l, fmt, args); + va_end(args); + } + s->l += l; + return l; +} + +int ksprintf(kstring_t *s, const char *fmt, ...) +{ + va_list ap; + int l; + va_start(ap, fmt); + l = kvsprintf(s, fmt, ap); + va_end(ap); + return l; +} + +char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux) +{ + const char *p, *start; + if (sep) { // set up the table + if (str == 0 && (aux->tab[0]&1)) return 0; // no need to set up if we have finished + aux->finished = 0; + if (sep[1]) { + aux->sep = -1; + aux->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0; + for (p = sep; *p; ++p) aux->tab[*p>>6] |= 1ull<<(*p&0x3f); + } else aux->sep = sep[0]; + } + if (aux->finished) return 0; + else if (str) aux->p = str - 1, aux->finished = 0; + if (aux->sep < 0) { + for (p = start = aux->p + 1; *p; ++p) + if (aux->tab[*p>>6]>>(*p&0x3f)&1) break; + } else { + for (p = start = aux->p + 1; *p; ++p) + if (*p == aux->sep) break; + } + aux->p = p; // end of token + if (*p == 0) aux->finished = 1; // no more tokens + return (char*)start; +} + +// s MUST BE a null terminated string; l = strlen(s) +int ksplit_core(char *s, int delimiter, int *_max, int **_offsets) +{ + int i, n, max, last_char, last_start, *offsets, l; + n = 0; max = *_max; offsets = *_offsets; + l = strlen(s); + +#define __ksplit_aux do { \ + if (_offsets) { \ + s[i] = 0; \ + if (n == max) { \ + int *tmp; \ + max = max? max<<1 : 2; \ + if ((tmp = (int*)realloc(offsets, sizeof(int) * max))) { \ + offsets = tmp; \ + } else { \ + free(offsets); \ + *_offsets = NULL; \ + return 0; \ + } \ + } \ + offsets[n++] = last_start; \ + } else ++n; \ + } while (0) + + for (i = 0, last_char = last_start = 0; i <= l; ++i) { + if (delimiter == 0) { + if (isspace(s[i]) || s[i] == 0) { + if (isgraph(last_char)) __ksplit_aux; // the end of a field + } else { + if (isspace(last_char) || last_char == 0) last_start = i; + } + } else { + if (s[i] == delimiter || s[i] == 0) { + if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field + } else { + if (last_char == delimiter || last_char == 0) last_start = i; + } + } + last_char = s[i]; + } + *_max = max; *_offsets = offsets; + return n; +} + +/********************** + * Boyer-Moore search * + **********************/ + +typedef unsigned char ubyte_t; + +// reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html +static int *ksBM_prep(const ubyte_t *pat, int m) +{ + int i, *suff, *prep, *bmGs, *bmBc; + prep = (int*)calloc(m + 256, sizeof(int)); + bmGs = prep; bmBc = prep + m; + { // preBmBc() + for (i = 0; i < 256; ++i) bmBc[i] = m; + for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1; + } + suff = (int*)calloc(m, sizeof(int)); + { // suffixes() + int f = 0, g; + suff[m - 1] = m; + g = m - 1; + for (i = m - 2; i >= 0; --i) { + if (i > g && suff[i + m - 1 - f] < i - g) + suff[i] = suff[i + m - 1 - f]; + else { + if (i < g) g = i; + f = i; + while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g; + suff[i] = f - g; + } + } + } + { // preBmGs() + int j = 0; + for (i = 0; i < m; ++i) bmGs[i] = m; + for (i = m - 1; i >= 0; --i) + if (suff[i] == i + 1) + for (; j < m - 1 - i; ++j) + if (bmGs[j] == m) + bmGs[j] = m - 1 - i; + for (i = 0; i <= m - 2; ++i) + bmGs[m - 1 - suff[i]] = m - 1 - i; + } + free(suff); + return prep; +} + +void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep) +{ + int i, j, *prep = 0, *bmGs, *bmBc; + const ubyte_t *str, *pat; + str = (const ubyte_t*)_str; pat = (const ubyte_t*)_pat; + prep = (_prep == 0 || *_prep == 0)? ksBM_prep(pat, m) : *_prep; + if (_prep && *_prep == 0) *_prep = prep; + bmGs = prep; bmBc = prep + m; + j = 0; + while (j <= n - m) { + for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i); + if (i >= 0) { + int max = bmBc[str[i+j]] - m + 1 + i; + if (max < bmGs[i]) max = bmGs[i]; + j += max; + } else return (void*)(str + j); + } + if (_prep == 0) free(prep); + return 0; +} + +char *kstrstr(const char *str, const char *pat, int **_prep) +{ + return (char*)kmemmem(str, strlen(str), pat, strlen(pat), _prep); +} + +char *kstrnstr(const char *str, const char *pat, int n, int **_prep) +{ + return (char*)kmemmem(str, n, pat, strlen(pat), _prep); +} + +/*********************** + * The main() function * + ***********************/ + +#ifdef KSTRING_MAIN +#include +int main() +{ + kstring_t *s; + int *fields, n, i; + ks_tokaux_t aux; + char *p; + s = (kstring_t*)calloc(1, sizeof(kstring_t)); + // test ksprintf() + ksprintf(s, " abcdefg: %d ", 100); + printf("'%s'\n", s->s); + // test ksplit() + fields = ksplit(s, 0, &n); + for (i = 0; i < n; ++i) + printf("field[%d] = '%s'\n", i, s->s + fields[i]); + // test kstrtok() + s->l = 0; + for (p = kstrtok("ab:cde:fg/hij::k", ":/", &aux); p; p = kstrtok(0, 0, &aux)) { + kputsn(p, aux.p - p, s); + kputc('\n', s); + } + printf("%s", s->s); + // free + free(s->s); free(s); free(fields); + + { + static char *str = "abcdefgcdgcagtcakcdcd"; + static char *pat = "cd"; + char *ret, *s = str; + int *prep = 0; + while ((ret = kstrstr(s, pat, &prep)) != 0) { + printf("match: %s\n", ret); + s = ret + prep[0]; + } + free(prep); + } + return 0; +} +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/sam.5 b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/sam.5 new file mode 100644 index 0000000000000000000000000000000000000000..4c86aa8a75b108e903f00aa1732fe094ef31544c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/sam.5 @@ -0,0 +1,45 @@ +'\" t +.TH sam 5 "August 2013" "htslib" "Bioinformatics formats" +.SH NAME +sam \- Sequence Alignment/Map file format +.SH DESCRIPTION +Sequence Alignment/Map (SAM) format is TAB-delimited. Apart from the header lines, which are started +with the `@' symbol, each alignment line consists of: +.TS +nlbl. +1 QNAME Query template/pair NAME +2 FLAG bitwise FLAG +3 RNAME Reference sequence NAME +4 POS 1-based leftmost POSition/coordinate of clipped sequence +5 MAPQ MAPping Quality (Phred-scaled) +6 CIGAR extended CIGAR string +7 MRNM Mate Reference sequence NaMe (`=' if same as RNAME) +8 MPOS 1-based Mate POSistion +9 TLEN inferred Template LENgth (insert size) +10 SEQ query SEQuence on the same strand as the reference +11 QUAL query QUALity (ASCII-33 gives the Phred base quality) +12+ OPT variable OPTional fields in the format TAG:VTYPE:VALUE +.TE +.PP +Each bit in the FLAG field is defined as: +.TS +lcbl. +0x0001 p the read is paired in sequencing +0x0002 P the read is mapped in a proper pair +0x0004 u the query sequence itself is unmapped +0x0008 U the mate is unmapped +0x0010 r strand of the query (1 for reverse) +0x0020 R strand of the mate +0x0040 1 the read is the first read in a pair +0x0080 2 the read is the second read in a pair +0x0100 s the alignment is not primary +0x0200 f the read fails platform/vendor quality checks +0x0400 d the read is either a PCR or an optical duplicate +0x0800 S the alignment is supplementary +.TE +.P +where the second column gives the string representation of the FLAG field. +.SH SEE ALSO +.TP +https://github.com/samtools/hts-specs +The full SAM/BAM file format specification diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/sam.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/sam.c new file mode 100644 index 0000000000000000000000000000000000000000..bc5e3ca558e730f25a0c373217356d55bec4c739 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/sam.c @@ -0,0 +1,1797 @@ +#include +#include +#include +#include +#include +#include +#include "htslib/sam.h" +#include "htslib/bgzf.h" +#include "cram/cram.h" +#include "htslib/hfile.h" + +#include "htslib/khash.h" +KHASH_DECLARE(s2i, kh_cstr_t, int64_t) + +typedef khash_t(s2i) sdict_t; + +/********************** + *** BAM header I/O *** + **********************/ + +bam_hdr_t *bam_hdr_init() +{ + return (bam_hdr_t*)calloc(1, sizeof(bam_hdr_t)); +} + +void bam_hdr_destroy(bam_hdr_t *h) +{ + int32_t i; + if (h == NULL) return; + if (h->target_name) { + for (i = 0; i < h->n_targets; ++i) + free(h->target_name[i]); + free(h->target_name); + free(h->target_len); + } + free(h->text); free(h->cigar_tab); + if (h->sdict) kh_destroy(s2i, (sdict_t*)h->sdict); + free(h); +} + +bam_hdr_t *bam_hdr_dup(const bam_hdr_t *h0) +{ + if (h0 == NULL) return NULL; + bam_hdr_t *h; + if ((h = bam_hdr_init()) == NULL) return NULL; + // copy the simple data + h->n_targets = h0->n_targets; + h->ignore_sam_err = h0->ignore_sam_err; + h->l_text = h0->l_text; + // Then the pointery stuff + h->cigar_tab = NULL; + h->sdict = NULL; + h->text = (char*)calloc(h->l_text + 1, 1); + memcpy(h->text, h0->text, h->l_text); + h->target_len = (uint32_t*)calloc(h->n_targets, 4); + h->target_name = (char**)calloc(h->n_targets, sizeof(char*)); + int i; + for (i = 0; i < h->n_targets; ++i) { + h->target_len[i] = h0->target_len[i]; + h->target_name[i] = strdup(h0->target_name[i]); + } + return h; +} + + +static bam_hdr_t *hdr_from_dict(sdict_t *d) +{ + bam_hdr_t *h; + khint_t k; + h = bam_hdr_init(); + h->sdict = d; + h->n_targets = kh_size(d); + h->target_len = (uint32_t*)malloc(4 * h->n_targets); + h->target_name = (char**)malloc(sizeof(char*) * h->n_targets); + for (k = kh_begin(d); k != kh_end(d); ++k) { + if (!kh_exist(d, k)) continue; + h->target_name[kh_val(d, k)>>32] = (char*)kh_key(d, k); + h->target_len[kh_val(d, k)>>32] = kh_val(d, k)<<32>>32; + kh_val(d, k) >>= 32; + } + return h; +} + +bam_hdr_t *bam_hdr_read(BGZF *fp) +{ + bam_hdr_t *h; + char buf[4]; + int magic_len, has_EOF; + int32_t i = 1, name_len; + // check EOF + has_EOF = bgzf_check_EOF(fp); + if (has_EOF < 0) { + perror("[W::sam_hdr_read] bgzf_check_EOF"); + } else if (has_EOF == 0 && hts_verbose >= 2) + fprintf(stderr, "[W::%s] EOF marker is absent. The input is probably truncated.\n", __func__); + // read "BAM1" + magic_len = bgzf_read(fp, buf, 4); + if (magic_len != 4 || strncmp(buf, "BAM\1", 4)) { + if (hts_verbose >= 1) fprintf(stderr, "[E::%s] invalid BAM binary header\n", __func__); + return 0; + } + h = bam_hdr_init(); + // read plain text and the number of reference sequences + bgzf_read(fp, &h->l_text, 4); + if (fp->is_be) ed_swap_4p(&h->l_text); + h->text = (char*)malloc(h->l_text + 1); + h->text[h->l_text] = 0; // make sure it is NULL terminated + bgzf_read(fp, h->text, h->l_text); + bgzf_read(fp, &h->n_targets, 4); + if (fp->is_be) ed_swap_4p(&h->n_targets); + // read reference sequence names and lengths + h->target_name = (char**)calloc(h->n_targets, sizeof(char*)); + h->target_len = (uint32_t*)calloc(h->n_targets, 4); + for (i = 0; i != h->n_targets; ++i) { + bgzf_read(fp, &name_len, 4); + if (fp->is_be) ed_swap_4p(&name_len); + h->target_name[i] = (char*)calloc(name_len, 1); + bgzf_read(fp, h->target_name[i], name_len); + bgzf_read(fp, &h->target_len[i], 4); + if (fp->is_be) ed_swap_4p(&h->target_len[i]); + } + return h; +} + +int bam_hdr_write(BGZF *fp, const bam_hdr_t *h) +{ + char buf[4]; + int32_t i, name_len, x; + // write "BAM1" + strncpy(buf, "BAM\1", 4); + bgzf_write(fp, buf, 4); + // write plain text and the number of reference sequences + if (fp->is_be) { + x = ed_swap_4(h->l_text); + bgzf_write(fp, &x, 4); + if (h->l_text) bgzf_write(fp, h->text, h->l_text); + x = ed_swap_4(h->n_targets); + bgzf_write(fp, &x, 4); + } else { + bgzf_write(fp, &h->l_text, 4); + if (h->l_text) bgzf_write(fp, h->text, h->l_text); + bgzf_write(fp, &h->n_targets, 4); + } + // write sequence names and lengths + for (i = 0; i != h->n_targets; ++i) { + char *p = h->target_name[i]; + name_len = strlen(p) + 1; + if (fp->is_be) { + x = ed_swap_4(name_len); + bgzf_write(fp, &x, 4); + } else bgzf_write(fp, &name_len, 4); + bgzf_write(fp, p, name_len); + if (fp->is_be) { + x = ed_swap_4(h->target_len[i]); + bgzf_write(fp, &x, 4); + } else bgzf_write(fp, &h->target_len[i], 4); + } + bgzf_flush(fp); + return 0; +} + +int bam_name2id(bam_hdr_t *h, const char *ref) +{ + sdict_t *d = (sdict_t*)h->sdict; + khint_t k; + if (h->sdict == 0) { + int i, absent; + d = kh_init(s2i); + for (i = 0; i < h->n_targets; ++i) { + k = kh_put(s2i, d, h->target_name[i], &absent); + kh_val(d, k) = i; + } + h->sdict = d; + } + k = kh_get(s2i, d, ref); + return k == kh_end(d)? -1 : kh_val(d, k); +} + +/************************* + *** BAM alignment I/O *** + *************************/ + +bam1_t *bam_init1() +{ + return (bam1_t*)calloc(1, sizeof(bam1_t)); +} + +void bam_destroy1(bam1_t *b) +{ + if (b == 0) return; + free(b->data); free(b); +} + +bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc) +{ + uint8_t *data = bdst->data; + int m_data = bdst->m_data; // backup data and m_data + if (m_data < bsrc->l_data) { // double the capacity + m_data = bsrc->l_data; kroundup32(m_data); + data = (uint8_t*)realloc(data, m_data); + } + memcpy(data, bsrc->data, bsrc->l_data); // copy var-len data + *bdst = *bsrc; // copy the rest + // restore the backup + bdst->m_data = m_data; + bdst->data = data; + return bdst; +} + +bam1_t *bam_dup1(const bam1_t *bsrc) +{ + if (bsrc == NULL) return NULL; + bam1_t *bdst = bam_init1(); + if (bdst == NULL) return NULL; + return bam_copy1(bdst, bsrc); +} + +int bam_cigar2qlen(int n_cigar, const uint32_t *cigar) +{ + int k, l; + for (k = l = 0; k < n_cigar; ++k) + if (bam_cigar_type(bam_cigar_op(cigar[k]))&1) + l += bam_cigar_oplen(cigar[k]); + return l; +} + +int bam_cigar2rlen(int n_cigar, const uint32_t *cigar) +{ + int k, l; + for (k = l = 0; k < n_cigar; ++k) + if (bam_cigar_type(bam_cigar_op(cigar[k]))&2) + l += bam_cigar_oplen(cigar[k]); + return l; +} + +int32_t bam_endpos(const bam1_t *b) +{ + if (!(b->core.flag & BAM_FUNMAP) && b->core.n_cigar > 0) + return b->core.pos + bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b)); + else + return b->core.pos + 1; +} + +static inline int aux_type2size(uint8_t type) +{ + switch (type) { + case 'A': case 'c': case 'C': + return 1; + case 's': case 'S': + return 2; + case 'i': case 'I': case 'f': + return 4; + case 'd': + return 8; + case 'Z': case 'H': case 'B': + return type; + default: + return 0; + } +} + +static void swap_data(const bam1_core_t *c, int l_data, uint8_t *data, int is_host) +{ + uint8_t *s; + uint32_t *cigar = (uint32_t*)(data + c->l_qname); + uint32_t i, n; + s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2; + for (i = 0; i < c->n_cigar; ++i) ed_swap_4p(&cigar[i]); + while (s < data + l_data) { + int size; + s += 2; // skip key + size = aux_type2size(*s); ++s; // skip type + switch (size) { + case 1: ++s; break; + case 2: ed_swap_2p(s); s += 2; break; + case 4: ed_swap_4p(s); s += 4; break; + case 8: ed_swap_8p(s); s += 8; break; + case 'Z': + case 'H': + while (*s) ++s; + ++s; + break; + case 'B': + size = aux_type2size(*s); ++s; + if (is_host) memcpy(&n, s, 4), ed_swap_4p(s); + else ed_swap_4p(s), memcpy(&n, s, 4); + s += 4; + switch (size) { + case 1: s += n; break; + case 2: for (i = 0; i < n; ++i, s += 2) ed_swap_2p(s); break; + case 4: for (i = 0; i < n; ++i, s += 4) ed_swap_4p(s); break; + case 8: for (i = 0; i < n; ++i, s += 8) ed_swap_8p(s); break; + } + break; + } + } +} + +int bam_read1(BGZF *fp, bam1_t *b) +{ + bam1_core_t *c = &b->core; + int32_t block_len, ret, i; + uint32_t x[8]; + if ((ret = bgzf_read(fp, &block_len, 4)) != 4) { + if (ret == 0) return -1; // normal end-of-file + else return -2; // truncated + } + if (bgzf_read(fp, x, 32) != 32) return -3; + if (fp->is_be) { + ed_swap_4p(&block_len); + for (i = 0; i < 8; ++i) ed_swap_4p(x + i); + } + c->tid = x[0]; c->pos = x[1]; + c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff; + c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff; + c->l_qseq = x[4]; + c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7]; + b->l_data = block_len - 32; + if (b->l_data < 0 || c->l_qseq < 0) return -4; + if ((char *)bam_get_aux(b) - (char *)b->data > b->l_data) + return -4; + if (b->m_data < b->l_data) { + b->m_data = b->l_data; + kroundup32(b->m_data); + b->data = (uint8_t*)realloc(b->data, b->m_data); + if (!b->data) + return -4; + } + if (bgzf_read(fp, b->data, b->l_data) != b->l_data) return -4; + //b->l_aux = b->l_data - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2; + if (fp->is_be) swap_data(c, b->l_data, b->data, 0); + return 4 + block_len; +} + +int bam_write1(BGZF *fp, const bam1_t *b) +{ + const bam1_core_t *c = &b->core; + uint32_t x[8], block_len = b->l_data + 32, y; + int i, ok; + x[0] = c->tid; + x[1] = c->pos; + x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | c->l_qname; + x[3] = (uint32_t)c->flag<<16 | c->n_cigar; + x[4] = c->l_qseq; + x[5] = c->mtid; + x[6] = c->mpos; + x[7] = c->isize; + ok = (bgzf_flush_try(fp, 4 + block_len) >= 0); + if (fp->is_be) { + for (i = 0; i < 8; ++i) ed_swap_4p(x + i); + y = block_len; + if (ok) ok = (bgzf_write(fp, ed_swap_4p(&y), 4) >= 0); + swap_data(c, b->l_data, b->data, 1); + } else { + if (ok) ok = (bgzf_write(fp, &block_len, 4) >= 0); + } + if (ok) ok = (bgzf_write(fp, x, 32) >= 0); + if (ok) ok = (bgzf_write(fp, b->data, b->l_data) >= 0); + if (fp->is_be) swap_data(c, b->l_data, b->data, 0); + return ok? 4 + block_len : -1; +} + +/******************** + *** BAM indexing *** + ********************/ + +static hts_idx_t *bam_index(BGZF *fp, int min_shift) +{ + int n_lvls, i, fmt; + bam1_t *b; + hts_idx_t *idx; + bam_hdr_t *h; + h = bam_hdr_read(fp); + if (min_shift > 0) { + int64_t max_len = 0, s; + for (i = 0; i < h->n_targets; ++i) + if (max_len < h->target_len[i]) max_len = h->target_len[i]; + max_len += 256; + for (n_lvls = 0, s = 1< s; ++n_lvls, s <<= 3); + fmt = HTS_FMT_CSI; + } else min_shift = 14, n_lvls = 5, fmt = HTS_FMT_BAI; + idx = hts_idx_init(h->n_targets, fmt, bgzf_tell(fp), min_shift, n_lvls); + bam_hdr_destroy(h); + b = bam_init1(); + while (bam_read1(fp, b) >= 0) { + int l, ret; + l = bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b)); + if (l == 0) l = 1; // no zero-length records + ret = hts_idx_push(idx, b->core.tid, b->core.pos, b->core.pos + l, bgzf_tell(fp), !(b->core.flag&BAM_FUNMAP)); + if (ret < 0) + { + // unsorted + bam_destroy1(b); + hts_idx_destroy(idx); + return NULL; + } + } + hts_idx_finish(idx, bgzf_tell(fp)); + bam_destroy1(b); + return idx; +} + +int bam_index_build(const char *fn, int min_shift) +{ + hts_idx_t *idx; + htsFile *fp; + int ret = 0; + + if ((fp = hts_open(fn, "r")) == 0) return -1; + if (fp->is_cram) { + ret = cram_index_build(fp->fp.cram, fn); + } else { + idx = bam_index(fp->fp.bgzf, min_shift); + if ( !idx ) + { + hts_close(fp); + return -1; + } + hts_idx_save(idx, fn, min_shift > 0 + ? HTS_FMT_CSI : HTS_FMT_BAI); + hts_idx_destroy(idx); + } + hts_close(fp); + + return ret; +} + +static int bam_readrec(BGZF *fp, void *ignored, void *bv, int *tid, int *beg, int *end) +{ + bam1_t *b = bv; + int ret; + if ((ret = bam_read1(fp, b)) >= 0) { + *tid = b->core.tid; *beg = b->core.pos; + *end = b->core.pos + (b->core.n_cigar? bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b)) : 1); + } + return ret; +} + +// This is used only with read_rest=1 iterators, so need not set tid/beg/end. +static int cram_readrec(BGZF *ignored, void *fpv, void *bv, int *tid, int *beg, int *end) +{ + htsFile *fp = fpv; + bam1_t *b = bv; + return cram_get_bam_seq(fp->fp.cram, &b); +} + +// This is used only with read_rest=1 iterators, so need not set tid/beg/end. +static int sam_bam_cram_readrec(BGZF *bgzfp, void *fpv, void *bv, int *tid, int *beg, int *end) +{ + htsFile *fp = fpv; + bam1_t *b = bv; + if (fp->is_bin) return bam_read1(bgzfp, b); + else if (fp->is_cram) return cram_get_bam_seq(fp->fp.cram, &b); + else { + // TODO Need headers available to implement this for SAM files + fprintf(stderr, "[sam_bam_cram_readrec] Not implemented for SAM files -- Exiting\n"); + abort(); + } +} + +// The CRAM implementation stores the loaded index within the cram_fd rather +// than separately as is done elsewhere in htslib. So if p is a pointer to +// an hts_idx_t with p->fmt == HTS_FMT_CRAI, then it actually points to an +// hts_cram_idx_t and should be cast accordingly. +typedef struct hts_cram_idx_t { + int fmt; + cram_fd *cram; +} hts_cram_idx_t; + +hts_idx_t *sam_index_load(samFile *fp, const char *fn) +{ + if (fp->is_bin) return bam_index_load(fn); + else if (fp->is_cram) { + if (cram_index_load(fp->fp.cram, fn) < 0) return NULL; + // Cons up a fake "index" just pointing at the associated cram_fd: + hts_cram_idx_t *idx = malloc(sizeof (hts_cram_idx_t)); + if (idx == NULL) return NULL; + idx->fmt = HTS_FMT_CRAI; + idx->cram = fp->fp.cram; + return (hts_idx_t *) idx; + } + else return NULL; // TODO Would use tbx_index_load if it returned hts_idx_t +} + +static hts_itr_t *cram_itr_query(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec) +{ + const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx; + hts_itr_t *iter = (hts_itr_t *) calloc(1, sizeof(hts_itr_t)); + if (iter == NULL) return NULL; + + // Cons up a dummy iterator for which hts_itr_next() will simply invoke + // the readrec function: + iter->read_rest = 1; + iter->off = NULL; + iter->bins.a = NULL; + iter->readrec = readrec; + + if (tid >= 0) { + cram_range r = { tid, beg+1, end }; + if (cram_set_option(cidx->cram, CRAM_OPT_RANGE, &r) != 0) { free(iter); return NULL; } + iter->curr_off = 0; + // The following fields are not required by hts_itr_next(), but are + // filled in in case user code wants to look at them. + iter->tid = tid; + iter->beg = beg; + iter->end = end; + } + else switch (tid) { + case HTS_IDX_REST: + iter->curr_off = 0; + break; + case HTS_IDX_NONE: + iter->curr_off = 0; + iter->finished = 1; + break; + default: + fprintf(stderr, "[cram_itr_query] tid=%d not implemented for CRAM files -- Exiting\n", tid); + abort(); + break; + } + + return iter; +} + +hts_itr_t *sam_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end) +{ + const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx; + if (idx == NULL) + return hts_itr_query(NULL, tid, beg, end, sam_bam_cram_readrec); + else if (cidx->fmt == HTS_FMT_CRAI) + return cram_itr_query(idx, tid, beg, end, cram_readrec); + else + return hts_itr_query(idx, tid, beg, end, bam_readrec); +} + +static int cram_name2id(void *fdv, const char *ref) +{ + cram_fd *fd = (cram_fd *) fdv; + return sam_hdr_name2ref(fd->header, ref); +} + +hts_itr_t *sam_itr_querys(const hts_idx_t *idx, bam_hdr_t *hdr, const char *region) +{ + const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx; + if (cidx->fmt == HTS_FMT_CRAI) + return hts_itr_querys(idx, region, cram_name2id, cidx->cram, cram_itr_query, cram_readrec); + else + return hts_itr_querys(idx, region, (hts_name2id_f)(bam_name2id), hdr, hts_itr_query, bam_readrec); +} + +/********************** + *** SAM header I/O *** + **********************/ + +#include "htslib/kseq.h" +#include "htslib/kstring.h" + +bam_hdr_t *sam_hdr_parse(int l_text, const char *text) +{ + const char *q, *r, *p; + khash_t(s2i) *d; + d = kh_init(s2i); + for (p = text; *p; ++p) { + if (strncmp(p, "@SQ", 3) == 0) { + char *sn = 0; + int ln = -1; + for (q = p + 4;; ++q) { + if (strncmp(q, "SN:", 3) == 0) { + q += 3; + for (r = q; *r != '\t' && *r != '\n'; ++r); + sn = (char*)calloc(r - q + 1, 1); + strncpy(sn, q, r - q); + q = r; + } else if (strncmp(q, "LN:", 3) == 0) + ln = strtol(q + 3, (char**)&q, 10); + while (*q != '\t' && *q != '\n') ++q; + if (*q == '\n') break; + } + p = q; + if (sn && ln >= 0) { + khint_t k; + int absent; + k = kh_put(s2i, d, sn, &absent); + if (!absent) { + if (hts_verbose >= 2) + fprintf(stderr, "[W::%s] duplicated sequence '%s'\n", __func__, sn); + free(sn); + } else kh_val(d, k) = (int64_t)(kh_size(d) - 1)<<32 | ln; + } + } + while (*p != '\n') ++p; + } + return hdr_from_dict(d); +} + +bam_hdr_t *sam_hdr_read(htsFile *fp) +{ + if (fp->is_bin) { + return bam_hdr_read(fp->fp.bgzf); + } else if (fp->is_cram) { + return cram_header_to_bam(fp->fp.cram->header); + } else { + kstring_t str; + bam_hdr_t *h; + int has_SQ = 0; + str.l = str.m = 0; str.s = 0; + while (hts_getline(fp, KS_SEP_LINE, &fp->line) >= 0) { + if (fp->line.s[0] != '@') break; + if (fp->line.l > 3 && strncmp(fp->line.s,"@SQ",3) == 0) has_SQ = 1; + kputsn(fp->line.s, fp->line.l, &str); + kputc('\n', &str); + } + if (! has_SQ && fp->fn_aux) { + char line[2048]; + FILE *f = fopen(fp->fn_aux, "r"); + if (f == NULL) return NULL; + while (fgets(line, sizeof line, f)) { + const char *name = strtok(line, "\t"); + const char *length = strtok(NULL, "\t"); + ksprintf(&str, "@SQ\tSN:%s\tLN:%s\n", name, length); + } + fclose(f); + } + if (str.l == 0) kputsn("", 0, &str); + h = sam_hdr_parse(str.l, str.s); + h->l_text = str.l; h->text = str.s; + return h; + } +} + +int sam_hdr_write(htsFile *fp, const bam_hdr_t *h) +{ + if (fp->is_bin) { + bam_hdr_write(fp->fp.bgzf, h); + } else if (fp->is_cram) { + cram_fd *fd = fp->fp.cram; + if (cram_set_header(fd, bam_header_to_cram((bam_hdr_t *)h)) < 0) return -1; + if (fp->fn_aux) + cram_load_reference(fd, fp->fn_aux); + if (cram_write_SAM_hdr(fd, fd->header) < 0) return -1; + } else { + char *p; + hputs(h->text, fp->fp.hfile); + p = strstr(h->text, "@SQ\t"); // FIXME: we need a loop to make sure "@SQ\t" does not match something unwanted!!! + if (p == 0) { + int i; + for (i = 0; i < h->n_targets; ++i) { + fp->line.l = 0; + kputsn("@SQ\tSN:", 7, &fp->line); kputs(h->target_name[i], &fp->line); + kputsn("\tLN:", 4, &fp->line); kputw(h->target_len[i], &fp->line); kputc('\n', &fp->line); + if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; + } + } + if ( hflush(fp->fp.hfile) != 0 ) return -1; + } + return 0; +} + +/********************** + *** SAM record I/O *** + **********************/ + +int sam_parse1(kstring_t *s, bam_hdr_t *h, bam1_t *b) +{ +#define _read_token(_p) (_p); for (; *(_p) && *(_p) != '\t'; ++(_p)); if (*(_p) != '\t') goto err_ret; *(_p)++ = 0 +#define _read_token_aux(_p) (_p); for (; *(_p) && *(_p) != '\t'; ++(_p)); *(_p)++ = 0 // this is different in that it does not test *(_p)=='\t' +#define _get_mem(type_t, _x, _s, _l) ks_resize((_s), (_s)->l + (_l)); *(_x) = (type_t*)((_s)->s + (_s)->l); (_s)->l += (_l) +#define _parse_err(cond, msg) do { if ((cond) && hts_verbose >= 1) { fprintf(stderr, "[E::%s] " msg "\n", __func__); goto err_ret; } } while (0) +#define _parse_warn(cond, msg) if ((cond) && hts_verbose >= 2) fprintf(stderr, "[W::%s] " msg "\n", __func__) + + uint8_t *t; + char *p = s->s, *q; + int i; + kstring_t str; + bam1_core_t *c = &b->core; + + str.l = b->l_data = 0; + str.s = (char*)b->data; str.m = b->m_data; + memset(c, 0, 32); + if (h->cigar_tab == 0) { + h->cigar_tab = (int8_t*) malloc(128); + for (i = 0; i < 128; ++i) + h->cigar_tab[i] = -1; + for (i = 0; BAM_CIGAR_STR[i]; ++i) + h->cigar_tab[(int)BAM_CIGAR_STR[i]] = i; + } + // qname + q = _read_token(p); + kputsn_(q, p - q, &str); + c->l_qname = p - q; + // flag + c->flag = strtol(p, &p, 0); + if (*p++ != '\t') goto err_ret; // malformated flag + // chr + q = _read_token(p); + if (strcmp(q, "*")) { + _parse_err(h->n_targets == 0, "missing SAM header"); + c->tid = bam_name2id(h, q); + _parse_warn(c->tid < 0, "urecognized reference name; treated as unmapped"); + } else c->tid = -1; + // pos + c->pos = strtol(p, &p, 10) - 1; + if (*p++ != '\t') goto err_ret; + if (c->pos < 0 && c->tid >= 0) { + _parse_warn(1, "mapped query cannot have zero coordinate; treated as unmapped"); + c->tid = -1; + } + if (c->tid < 0) c->flag |= BAM_FUNMAP; + // mapq + c->qual = strtol(p, &p, 10); + if (*p++ != '\t') goto err_ret; + // cigar + if (*p != '*') { + uint32_t *cigar; + size_t n_cigar = 0; + for (q = p; *p && *p != '\t'; ++p) + if (!isdigit(*p)) ++n_cigar; + if (*p++ != '\t') goto err_ret; + _parse_err(n_cigar >= 65536, "too many CIGAR operations"); + c->n_cigar = n_cigar; + _get_mem(uint32_t, &cigar, &str, c->n_cigar<<2); + for (i = 0; i < c->n_cigar; ++i, ++q) { + int op; + cigar[i] = strtol(q, &q, 10)<= 128? -1 : h->cigar_tab[(int)*q]; + _parse_err(op < 0, "unrecognized CIGAR operator"); + cigar[i] |= op; + } + i = bam_cigar2rlen(c->n_cigar, cigar); + } else { + _parse_warn(!(c->flag&BAM_FUNMAP), "mapped query must have a CIGAR; treated as unmapped"); + c->flag |= BAM_FUNMAP; + q = _read_token(p); + i = 1; + } + c->bin = hts_reg2bin(c->pos, c->pos + i, 14, 5); + // mate chr + q = _read_token(p); + if (strcmp(q, "=") == 0) c->mtid = c->tid; + else if (strcmp(q, "*") == 0) c->mtid = -1; + else c->mtid = bam_name2id(h, q); + // mpos + c->mpos = strtol(p, &p, 10) - 1; + if (*p++ != '\t') goto err_ret; + if (c->mpos < 0 && c->mtid >= 0) { + _parse_warn(1, "mapped mate cannot have zero coordinate; treated as unmapped"); + c->mtid = -1; + } + // tlen + c->isize = strtol(p, &p, 10); + if (*p++ != '\t') goto err_ret; + // seq + q = _read_token(p); + if (strcmp(q, "*")) { + c->l_qseq = p - q - 1; + i = bam_cigar2qlen(c->n_cigar, (uint32_t*)(str.s + c->l_qname)); + _parse_err(c->n_cigar && i != c->l_qseq, "CIGAR and query sequence are of different length"); + i = (c->l_qseq + 1) >> 1; + _get_mem(uint8_t, &t, &str, i); + memset(t, 0, i); + for (i = 0; i < c->l_qseq; ++i) + t[i>>1] |= seq_nt16_table[(int)q[i]] << ((~i&1)<<2); + } else c->l_qseq = 0; + // qual + q = _read_token_aux(p); + _get_mem(uint8_t, &t, &str, c->l_qseq); + if (strcmp(q, "*")) { + _parse_err(p - q - 1 != c->l_qseq, "SEQ and QUAL are of different length"); + for (i = 0; i < c->l_qseq; ++i) t[i] = q[i] - 33; + } else memset(t, 0xff, c->l_qseq); + // aux + // Note that (like the bam1_core_t fields) this aux data in b->data is + // stored in host endianness; so there is no byte swapping needed here. + while (p < s->s + s->l) { + uint8_t type; + q = _read_token_aux(p); // FIXME: can be accelerated for long 'B' arrays + _parse_err(p - q - 1 < 6, "incomplete aux field"); + kputsn_(q, 2, &str); + q += 3; type = *q++; ++q; // q points to value + if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { + kputc_('A', &str); + kputc_(*q, &str); + } else if (type == 'i' || type == 'I') { + long x; + x = strtol(q, &q, 10); + if (x < 0) { + if (x >= INT8_MIN) { + kputc_('c', &str); kputc_(x, &str); + } else if (x >= INT16_MIN) { + int16_t y = x; + kputc_('s', &str); kputsn_((char*)&y, 2, &str); + } else { + int32_t y = x; + kputc_('i', &str); kputsn_(&y, 4, &str); + } + } else { + if (x <= UINT8_MAX) { + kputc_('C', &str); kputc_(x, &str); + } else if (x <= UINT16_MAX) { + uint16_t y = x; + kputc_('S', &str); kputsn_(&y, 2, &str); + } else { + uint32_t y = x; + kputc_('I', &str); kputsn_(&y, 4, &str); + } + } + } else if (type == 'f') { + float x; + x = strtod(q, &q); + kputc_('f', &str); kputsn_(&x, 4, &str); + } else if (type == 'd') { + double x; + x = strtod(q, &q); + kputc_('d', &str); kputsn_(&x, 8, &str); + } else if (type == 'Z' || type == 'H') { + kputc_(type, &str);kputsn_(q, p - q, &str); // note that this include the trailing NULL + } else if (type == 'B') { + int32_t n; + char *r; + _parse_err(p - q - 1 < 3, "incomplete B-typed aux field"); + type = *q++; // q points to the first ',' following the typing byte + for (r = q, n = 0; *r; ++r) + if (*r == ',') ++n; + kputc_('B', &str); kputc_(type, &str); kputsn_(&n, 4, &str); + // FIXME: to evaluate which is faster: a) aligned array and then memmove(); b) unaligned array; c) kputsn_() + if (type == 'c') while (q + 1 < p) { int8_t x = strtol(q + 1, &q, 0); kputc_(x, &str); } + else if (type == 'C') while (q + 1 < p) { uint8_t x = strtoul(q + 1, &q, 0); kputc_(x, &str); } + else if (type == 's') while (q + 1 < p) { int16_t x = strtol(q + 1, &q, 0); kputsn_(&x, 2, &str); } + else if (type == 'S') while (q + 1 < p) { uint16_t x = strtoul(q + 1, &q, 0); kputsn_(&x, 2, &str); } + else if (type == 'i') while (q + 1 < p) { int32_t x = strtol(q + 1, &q, 0); kputsn_(&x, 4, &str); } + else if (type == 'I') while (q + 1 < p) { uint32_t x = strtoul(q + 1, &q, 0); kputsn_(&x, 4, &str); } + else if (type == 'f') while (q + 1 < p) { float x = strtod(q + 1, &q); kputsn_(&x, 4, &str); } + else _parse_err(1, "unrecognized type"); + } else _parse_err(1, "unrecognized type"); + } + b->data = (uint8_t*)str.s; b->l_data = str.l; b->m_data = str.m; + return 0; + +#undef _parse_warn +#undef _parse_err +#undef _get_mem +#undef _read_token_aux +#undef _read_token +err_ret: + b->data = (uint8_t*)str.s; b->l_data = str.l; b->m_data = str.m; + return -2; +} + +int sam_read1(htsFile *fp, bam_hdr_t *h, bam1_t *b) +{ + if (fp->is_bin) { + int r = bam_read1(fp->fp.bgzf, b); + if (r >= 0) { + if (b->core.tid >= h->n_targets || b->core.tid < -1 || + b->core.mtid >= h->n_targets || b->core.mtid < -1) + return -3; + } + return r; + } else if (fp->is_cram) { + return cram_get_bam_seq(fp->fp.cram, &b); + } else { + int ret; +err_recover: + if (fp->line.l == 0) { + ret = hts_getline(fp, KS_SEP_LINE, &fp->line); + if (ret < 0) return -1; + } + ret = sam_parse1(&fp->line, h, b); + fp->line.l = 0; + if (ret < 0) { + if (hts_verbose >= 1) + fprintf(stderr, "[W::%s] parse error at line %lld\n", __func__, (long long)fp->lineno); + if (h->ignore_sam_err) goto err_recover; + } + return ret; + } +} + +int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str) +{ + int i; + uint8_t *s; + const bam1_core_t *c = &b->core; + + str->l = 0; + kputsn(bam_get_qname(b), c->l_qname-1, str); kputc('\t', str); // query name + kputw(c->flag, str); kputc('\t', str); // flag + if (c->tid >= 0) { // chr + kputs(h->target_name[c->tid] , str); + kputc('\t', str); + } else kputsn("*\t", 2, str); + kputw(c->pos + 1, str); kputc('\t', str); // pos + kputw(c->qual, str); kputc('\t', str); // qual + if (c->n_cigar) { // cigar + uint32_t *cigar = bam_get_cigar(b); + for (i = 0; i < c->n_cigar; ++i) { + kputw(bam_cigar_oplen(cigar[i]), str); + kputc(bam_cigar_opchr(cigar[i]), str); + } + } else kputc('*', str); + kputc('\t', str); + if (c->mtid < 0) kputsn("*\t", 2, str); // mate chr + else if (c->mtid == c->tid) kputsn("=\t", 2, str); + else { + kputs(h->target_name[c->mtid], str); + kputc('\t', str); + } + kputw(c->mpos + 1, str); kputc('\t', str); // mate pos + kputw(c->isize, str); kputc('\t', str); // template len + if (c->l_qseq) { // seq and qual + uint8_t *s = bam_get_seq(b); + for (i = 0; i < c->l_qseq; ++i) kputc("=ACMGRSVTWYHKDBN"[bam_seqi(s, i)], str); + kputc('\t', str); + s = bam_get_qual(b); + if (s[0] == 0xff) kputc('*', str); + else for (i = 0; i < c->l_qseq; ++i) kputc(s[i] + 33, str); + } else kputsn("*\t*", 3, str); + s = bam_get_aux(b); // aux + while (s+4 <= b->data + b->l_data) { + uint8_t type, key[2]; + key[0] = s[0]; key[1] = s[1]; + s += 2; type = *s++; + kputc('\t', str); kputsn((char*)key, 2, str); kputc(':', str); + if (type == 'A') { + kputsn("A:", 2, str); + kputc(*s, str); + ++s; + } else if (type == 'C') { + kputsn("i:", 2, str); + kputw(*s, str); + ++s; + } else if (type == 'c') { + kputsn("i:", 2, str); + kputw(*(int8_t*)s, str); + ++s; + } else if (type == 'S') { + if (s+2 <= b->data + b->l_data) { + kputsn("i:", 2, str); + kputw(*(uint16_t*)s, str); + s += 2; + } else return -1; + } else if (type == 's') { + if (s+2 <= b->data + b->l_data) { + kputsn("i:", 2, str); + kputw(*(int16_t*)s, str); + s += 2; + } else return -1; + } else if (type == 'I') { + if (s+4 <= b->data + b->l_data) { + kputsn("i:", 2, str); + kputuw(*(uint32_t*)s, str); + s += 4; + } else return -1; + } else if (type == 'i') { + if (s+4 <= b->data + b->l_data) { + kputsn("i:", 2, str); + kputw(*(int32_t*)s, str); + s += 4; + } else return -1; + } else if (type == 'f') { + if (s+4 <= b->data + b->l_data) { + ksprintf(str, "f:%g", *(float*)s); + s += 4; + } else return -1; + + } else if (type == 'd') { + if (s+8 <= b->data + b->l_data) { + ksprintf(str, "d:%g", *(double*)s); + s += 8; + } else return -1; + } else if (type == 'Z' || type == 'H') { + kputc(type, str); kputc(':', str); + while (s < b->data + b->l_data && *s) kputc(*s++, str); + if (s >= b->data + b->l_data) + return -1; + ++s; + } else if (type == 'B') { + uint8_t sub_type = *(s++); + int32_t n; + memcpy(&n, s, 4); + s += 4; // no point to the start of the array + if (s + n >= b->data + b->l_data) + return -1; + kputsn("B:", 2, str); kputc(sub_type, str); // write the typing + for (i = 0; i < n; ++i) { // FIXME: for better performance, put the loop after "if" + kputc(',', str); + if ('c' == sub_type) { kputw(*(int8_t*)s, str); ++s; } + else if ('C' == sub_type) { kputw(*(uint8_t*)s, str); ++s; } + else if ('s' == sub_type) { kputw(*(int16_t*)s, str); s += 2; } + else if ('S' == sub_type) { kputw(*(uint16_t*)s, str); s += 2; } + else if ('i' == sub_type) { kputw(*(int32_t*)s, str); s += 4; } + else if ('I' == sub_type) { kputuw(*(uint32_t*)s, str); s += 4; } + else if ('f' == sub_type) { ksprintf(str, "%g", *(float*)s); s += 4; } + } + } + } + return str->l; +} + +int sam_write1(htsFile *fp, const bam_hdr_t *h, const bam1_t *b) +{ + if (fp->is_bin) { + return bam_write1(fp->fp.bgzf, b); + } else if (fp->is_cram) { + return cram_put_bam_seq(fp->fp.cram, (bam1_t *)b); + } else { + if (sam_format1(h, b, &fp->line) < 0) return -1; + kputc('\n', &fp->line); + if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; + return fp->line.l; + } +} + +/************************ + *** Auxiliary fields *** + ************************/ + +void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data) +{ + int ori_len = b->l_data; + b->l_data += 3 + len; + if (b->m_data < b->l_data) { + b->m_data = b->l_data; + kroundup32(b->m_data); + b->data = (uint8_t*)realloc(b->data, b->m_data); + } + b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1]; + b->data[ori_len + 2] = type; + memcpy(b->data + ori_len + 3, data, len); +} + +static inline uint8_t *skip_aux(uint8_t *s) +{ + int size = aux_type2size(*s); ++s; // skip type + uint32_t n; + switch (size) { + case 'Z': + case 'H': + while (*s) ++s; + return s + 1; + case 'B': + size = aux_type2size(*s); ++s; + memcpy(&n, s, 4); s += 4; + return s + size * n; + case 0: + abort(); + break; + default: + return s + size; + } +} + +uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]) +{ + uint8_t *s; + int y = tag[0]<<8 | tag[1]; + s = bam_get_aux(b); + while (s < b->data + b->l_data) { + int x = (int)s[0]<<8 | s[1]; + s += 2; + if (x == y) return s; + s = skip_aux(s); + } + return 0; +} +// s MUST BE returned by bam_aux_get() +int bam_aux_del(bam1_t *b, uint8_t *s) +{ + uint8_t *p, *aux; + int l_aux = bam_get_l_aux(b); + aux = bam_get_aux(b); + p = s - 2; + s = skip_aux(s); + memmove(p, s, l_aux - (s - aux)); + b->l_data -= s - p; + return 0; +} + +int32_t bam_aux2i(const uint8_t *s) +{ + int type; + type = *s++; + if (type == 'c') return (int32_t)*(int8_t*)s; + else if (type == 'C') return (int32_t)*(uint8_t*)s; + else if (type == 's') return (int32_t)*(int16_t*)s; + else if (type == 'S') return (int32_t)*(uint16_t*)s; + else if (type == 'i' || type == 'I') return *(int32_t*)s; + else return 0; +} + +double bam_aux2f(const uint8_t *s) +{ + int type; + type = *s++; + if (type == 'd') return *(double*)s; + else if (type == 'f') return *(float*)s; + else return 0.0; +} + +char bam_aux2A(const uint8_t *s) +{ + int type; + type = *s++; + if (type == 'A') return *(char*)s; + else return 0; +} + +char *bam_aux2Z(const uint8_t *s) +{ + int type; + type = *s++; + if (type == 'Z' || type == 'H') return (char*)s; + else return 0; +} + +int sam_open_mode(char *mode, const char *fn, const char *format) +{ + // TODO Parse "bam5" etc for compression level + if (format == NULL) { + // Try to pick a format based on the filename extension + const char *ext = fn? strrchr(fn, '.') : NULL; + if (ext == NULL || strchr(ext, '/')) return -1; + return sam_open_mode(mode, fn, ext+1); + } + else if (strcmp(format, "bam") == 0) strcpy(mode, "b"); + else if (strcmp(format, "cram") == 0) strcpy(mode, "c"); + else if (strcmp(format, "sam") == 0) strcpy(mode, ""); + else return -1; + + return 0; +} + +#define STRNCMP(a,b,n) (strncasecmp((a),(b),(n)) || strlen(a)!=(n)) +int bam_str2flag(const char *str) +{ + char *end, *beg = (char*) str; + long int flag = strtol(str, &end, 0); + if ( end!=str ) return flag; // the conversion was successful + flag = 0; + while ( *str ) + { + end = beg; + while ( *end && *end!=',' ) end++; + if ( !STRNCMP("PAIRED",beg,end-beg) ) flag |= BAM_FPAIRED; + else if ( !STRNCMP("PROPER_PAIR",beg,end-beg) ) flag |= BAM_FPROPER_PAIR; + else if ( !STRNCMP("UNMAP",beg,end-beg) ) flag |= BAM_FUNMAP; + else if ( !STRNCMP("MUNMAP",beg,end-beg) ) flag |= BAM_FMUNMAP; + else if ( !STRNCMP("REVERSE",beg,end-beg) ) flag |= BAM_FREVERSE; + else if ( !STRNCMP("MREVERSE",beg,end-beg) ) flag |= BAM_FMREVERSE; + else if ( !STRNCMP("READ1",beg,end-beg) ) flag |= BAM_FREAD1; + else if ( !STRNCMP("READ2",beg,end-beg) ) flag |= BAM_FREAD2; + else if ( !STRNCMP("SECONDARY",beg,end-beg) ) flag |= BAM_FSECONDARY; + else if ( !STRNCMP("QCFAIL",beg,end-beg) ) flag |= BAM_FQCFAIL; + else if ( !STRNCMP("DUP",beg,end-beg) ) flag |= BAM_FDUP; + else if ( !STRNCMP("SUPPLEMENTARY",beg,end-beg) ) flag |= BAM_FSUPPLEMENTARY; + else return -1; + if ( !*end ) break; + beg = end + 1; + } + return flag; +} + +char *bam_flag2str(int flag) +{ + kstring_t str = {0,0,0}; + if ( flag&BAM_FPAIRED ) ksprintf(&str,"%s%s", str.l?",":"","PAIRED"); + if ( flag&BAM_FPROPER_PAIR ) ksprintf(&str,"%s%s", str.l?",":"","PROPER_PAIR"); + if ( flag&BAM_FUNMAP ) ksprintf(&str,"%s%s", str.l?",":"","UNMAP"); + if ( flag&BAM_FMUNMAP ) ksprintf(&str,"%s%s", str.l?",":"","MUNMAP"); + if ( flag&BAM_FREVERSE ) ksprintf(&str,"%s%s", str.l?",":"","REVERSE"); + if ( flag&BAM_FMREVERSE ) ksprintf(&str,"%s%s", str.l?",":"","MREVERSE"); + if ( flag&BAM_FREAD1 ) ksprintf(&str,"%s%s", str.l?",":"","READ1"); + if ( flag&BAM_FREAD2 ) ksprintf(&str,"%s%s", str.l?",":"","READ2"); + if ( flag&BAM_FSECONDARY ) ksprintf(&str,"%s%s", str.l?",":"","SECONDARY"); + if ( flag&BAM_FQCFAIL ) ksprintf(&str,"%s%s", str.l?",":"","QCFAIL"); + if ( flag&BAM_FDUP ) ksprintf(&str,"%s%s", str.l?",":"","DUP"); + if ( flag&BAM_FSUPPLEMENTARY ) ksprintf(&str,"%s%s", str.l?",":"","SUPPLEMENTARY"); + if ( str.l == 0 ) kputsn("", 0, &str); + return str.s; +} + + +/************************** + *** Pileup and Mpileup *** + **************************/ + +#if !defined(BAM_NO_PILEUP) + +#include + +/******************* + *** Memory pool *** + *******************/ + +typedef struct { + int k, x, y, end; +} cstate_t; + +static cstate_t g_cstate_null = { -1, 0, 0, 0 }; + +typedef struct __linkbuf_t { + bam1_t b; + int32_t beg, end; + cstate_t s; + struct __linkbuf_t *next; +} lbnode_t; + +typedef struct { + int cnt, n, max; + lbnode_t **buf; +} mempool_t; + +static mempool_t *mp_init(void) +{ + mempool_t *mp; + mp = (mempool_t*)calloc(1, sizeof(mempool_t)); + return mp; +} +static void mp_destroy(mempool_t *mp) +{ + int k; + for (k = 0; k < mp->n; ++k) { + free(mp->buf[k]->b.data); + free(mp->buf[k]); + } + free(mp->buf); + free(mp); +} +static inline lbnode_t *mp_alloc(mempool_t *mp) +{ + ++mp->cnt; + if (mp->n == 0) return (lbnode_t*)calloc(1, sizeof(lbnode_t)); + else return mp->buf[--mp->n]; +} +static inline void mp_free(mempool_t *mp, lbnode_t *p) +{ + --mp->cnt; p->next = 0; // clear lbnode_t::next here + if (mp->n == mp->max) { + mp->max = mp->max? mp->max<<1 : 256; + mp->buf = (lbnode_t**)realloc(mp->buf, sizeof(lbnode_t*) * mp->max); + } + mp->buf[mp->n++] = p; +} + +/********************** + *** CIGAR resolver *** + **********************/ + +/* s->k: the index of the CIGAR operator that has just been processed. + s->x: the reference coordinate of the start of s->k + s->y: the query coordiante of the start of s->k + */ +static inline int resolve_cigar2(bam_pileup1_t *p, int32_t pos, cstate_t *s) +{ +#define _cop(c) ((c)&BAM_CIGAR_MASK) +#define _cln(c) ((c)>>BAM_CIGAR_SHIFT) + + bam1_t *b = p->b; + bam1_core_t *c = &b->core; + uint32_t *cigar = bam_get_cigar(b); + int k; + // determine the current CIGAR operation +// fprintf(stderr, "%s\tpos=%d\tend=%d\t(%d,%d,%d)\n", bam_get_qname(b), pos, s->end, s->k, s->x, s->y); + if (s->k == -1) { // never processed + if (c->n_cigar == 1) { // just one operation, save a loop + if (_cop(cigar[0]) == BAM_CMATCH || _cop(cigar[0]) == BAM_CEQUAL || _cop(cigar[0]) == BAM_CDIFF) s->k = 0, s->x = c->pos, s->y = 0; + } else { // find the first match or deletion + for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) { + int op = _cop(cigar[k]); + int l = _cln(cigar[k]); + if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CEQUAL || op == BAM_CDIFF) break; + else if (op == BAM_CREF_SKIP) s->x += l; + else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l; + } + assert(k < c->n_cigar); + s->k = k; + } + } else { // the read has been processed before + int op, l = _cln(cigar[s->k]); + if (pos - s->x >= l) { // jump to the next operation + assert(s->k < c->n_cigar); // otherwise a bug: this function should not be called in this case + op = _cop(cigar[s->k+1]); + if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) { // jump to the next without a loop + if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l; + s->x += l; + ++s->k; + } else { // find the next M/D/N/=/X + if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l; + s->x += l; + for (k = s->k + 1; k < c->n_cigar; ++k) { + op = _cop(cigar[k]), l = _cln(cigar[k]); + if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) break; + else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l; + } + s->k = k; + } + assert(s->k < c->n_cigar); // otherwise a bug + } // else, do nothing + } + { // collect pileup information + int op, l; + op = _cop(cigar[s->k]); l = _cln(cigar[s->k]); + p->is_del = p->indel = p->is_refskip = 0; + if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation + int op2 = _cop(cigar[s->k+1]); + int l2 = _cln(cigar[s->k+1]); + if (op2 == BAM_CDEL) p->indel = -(int)l2; + else if (op2 == BAM_CINS) p->indel = l2; + else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding + int l3 = 0; + for (k = s->k + 2; k < c->n_cigar; ++k) { + op2 = _cop(cigar[k]); l2 = _cln(cigar[k]); + if (op2 == BAM_CINS) l3 += l2; + else if (op2 == BAM_CDEL || op2 == BAM_CMATCH || op2 == BAM_CREF_SKIP || op2 == BAM_CEQUAL || op2 == BAM_CDIFF) break; + } + if (l3 > 0) p->indel = l3; + } + } + if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { + p->qpos = s->y + (pos - s->x); + } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) { + p->is_del = 1; p->qpos = s->y; // FIXME: distinguish D and N!!!!! + p->is_refskip = (op == BAM_CREF_SKIP); + } // cannot be other operations; otherwise a bug + p->is_head = (pos == c->pos); p->is_tail = (pos == s->end); + } + return 1; +} + +/*********************** + *** Pileup iterator *** + ***********************/ + +// Dictionary of overlapping reads +KHASH_MAP_INIT_STR(olap_hash, lbnode_t *) +typedef khash_t(olap_hash) olap_hash_t; + +struct __bam_plp_t { + mempool_t *mp; + lbnode_t *head, *tail, *dummy; + int32_t tid, pos, max_tid, max_pos; + int is_eof, max_plp, error, maxcnt; + uint64_t id; + bam_pileup1_t *plp; + // for the "auto" interface only + bam1_t *b; + bam_plp_auto_f func; + void *data; + olap_hash_t *overlaps; +}; + +bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data) +{ + bam_plp_t iter; + iter = (bam_plp_t)calloc(1, sizeof(struct __bam_plp_t)); + iter->mp = mp_init(); + iter->head = iter->tail = mp_alloc(iter->mp); + iter->dummy = mp_alloc(iter->mp); + iter->max_tid = iter->max_pos = -1; + iter->maxcnt = 8000; + if (func) { + iter->func = func; + iter->data = data; + iter->b = bam_init1(); + } + return iter; +} + +void bam_plp_init_overlaps(bam_plp_t iter) +{ + iter->overlaps = kh_init(olap_hash); // hash for tweaking quality of bases in overlapping reads +} + +void bam_plp_destroy(bam_plp_t iter) +{ + if ( iter->overlaps ) kh_destroy(olap_hash, iter->overlaps); + mp_free(iter->mp, iter->dummy); + mp_free(iter->mp, iter->head); + if (iter->mp->cnt != 0) + fprintf(stderr, "[bam_plp_destroy] memory leak: %d. Continue anyway.\n", iter->mp->cnt); + mp_destroy(iter->mp); + if (iter->b) bam_destroy1(iter->b); + free(iter->plp); + free(iter); +} + + +//--------------------------------- +//--- Tweak overlapping reads +//--------------------------------- + +/** + * cigar_iref2iseq_set() - find the first CMATCH setting the ref and the read index + * cigar_iref2iseq_next() - get the next CMATCH base + * @cigar: pointer to current cigar block (rw) + * @cigar_max: pointer just beyond the last cigar block + * @icig: position within the current cigar block (rw) + * @iseq: position in the sequence (rw) + * @iref: position with respect to the beginning of the read (iref_pos - b->core.pos) (rw) + * + * Returns BAM_CMATCH or -1 when there is no more cigar to process or the requested position is not covered. + */ +static inline int cigar_iref2iseq_set(uint32_t **cigar, uint32_t *cigar_max, int *icig, int *iseq, int *iref) +{ + int pos = *iref; + if ( pos < 0 ) return -1; + *icig = 0; + *iseq = 0; + *iref = 0; + while ( *cigar> BAM_CIGAR_SHIFT; + + if ( cig==BAM_CSOFT_CLIP ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } + if ( cig==BAM_CHARD_CLIP ) { (*cigar)++; *icig = 0; continue; } + if ( cig==BAM_CMATCH || cig==BAM_CEQUAL || cig==BAM_CDIFF ) + { + pos -= ncig; + if ( pos < 0 ) { *icig = ncig + pos; *iseq += *icig; *iref += *icig; return BAM_CMATCH; } + (*cigar)++; *iseq += ncig; *icig = 0; *iref += ncig; + continue; + } + if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } + if ( cig==BAM_CDEL ) + { + pos -= ncig; + if ( pos<0 ) pos = 0; + (*cigar)++; *icig = 0; *iref += ncig; + continue; + } + fprintf(stderr,"todo: cigar %d\n", cig); + assert(0); + } + *iseq = -1; + return -1; +} +static inline int cigar_iref2iseq_next(uint32_t **cigar, uint32_t *cigar_max, int *icig, int *iseq, int *iref) +{ + while ( *cigar < cigar_max ) + { + int cig = (**cigar) & BAM_CIGAR_MASK; + int ncig = (**cigar) >> BAM_CIGAR_SHIFT; + + if ( cig==BAM_CMATCH || cig==BAM_CEQUAL || cig==BAM_CDIFF ) + { + if ( *icig >= ncig - 1 ) { *icig = 0; (*cigar)++; continue; } + (*iseq)++; (*icig)++; (*iref)++; + return BAM_CMATCH; + } + if ( cig==BAM_CDEL ) { (*cigar)++; (*iref) += ncig; *icig = 0; continue; } + if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } + if ( cig==BAM_CSOFT_CLIP ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } + if ( cig==BAM_CHARD_CLIP ) { (*cigar)++; *icig = 0; continue; } + fprintf(stderr,"todo: cigar %d\n", cig); + assert(0); + } + *iseq = -1; + *iref = -1; + return -1; +} + +static void tweak_overlap_quality(bam1_t *a, bam1_t *b) +{ + uint32_t *a_cigar = bam_get_cigar(a), *a_cigar_max = a_cigar + a->core.n_cigar; + uint32_t *b_cigar = bam_get_cigar(b), *b_cigar_max = b_cigar + b->core.n_cigar; + int a_icig = 0, a_iseq = 0; + int b_icig = 0, b_iseq = 0; + uint8_t *a_qual = bam_get_qual(a), *b_qual = bam_get_qual(b); + uint8_t *a_seq = bam_get_seq(a), *b_seq = bam_get_seq(b); + + int iref = b->core.pos; + int a_iref = iref - a->core.pos; + int b_iref = iref - b->core.pos; + int a_ret = cigar_iref2iseq_set(&a_cigar, a_cigar_max, &a_icig, &a_iseq, &a_iref); + if ( a_ret<0 ) return; // no overlap + int b_ret = cigar_iref2iseq_set(&b_cigar, b_cigar_max, &b_icig, &b_iseq, &b_iref); + if ( b_ret<0 ) return; // no overlap + + #if DBG + fprintf(stderr,"tweak %s n_cigar=%d %d .. %d-%d vs %d-%d\n", bam_get_qname(a), a->core.n_cigar, b->core.n_cigar, + a->core.pos+1,a->core.pos+bam_cigar2rlen(a->core.n_cigar,bam_get_cigar(a)), b->core.pos+1, b->core.pos+bam_cigar2rlen(b->core.n_cigar,bam_get_cigar(b))); + #endif + + while ( 1 ) + { + // Increment reference position + while ( a_iref>=0 && a_iref < iref - a->core.pos ) + a_ret = cigar_iref2iseq_next(&a_cigar, a_cigar_max, &a_icig, &a_iseq, &a_iref); + if ( a_ret<0 ) break; // done + if ( iref < a_iref + a->core.pos ) iref = a_iref + a->core.pos; + + while ( b_iref>=0 && b_iref < iref - b->core.pos ) + b_ret = cigar_iref2iseq_next(&b_cigar, b_cigar_max, &b_icig, &b_iseq, &b_iref); + if ( b_ret<0 ) break; // done + if ( iref < b_iref + b->core.pos ) iref = b_iref + b->core.pos; + + iref++; + if ( a_iref+a->core.pos != b_iref+b->core.pos ) continue; // only CMATCH positions, don't know what to do with indels + + if ( bam_seqi(a_seq,a_iseq) == bam_seqi(b_seq,b_iseq) ) + { + #if DBG + fprintf(stderr,"%c",seq_nt16_str[bam_seqi(a_seq,a_iseq)]); + #endif + // we are very confident about this base + int qual = a_qual[a_iseq] + b_qual[b_iseq]; + a_qual[a_iseq] = qual>200 ? 200 : qual; + b_qual[b_iseq] = 0; + } + else + { + if ( a_qual[a_iseq] >= b_qual[b_iseq] ) + { + #if DBG + fprintf(stderr,"[%c/%c]",seq_nt16_str[bam_seqi(a_seq,a_iseq)],tolower(seq_nt16_str[bam_seqi(b_seq,b_iseq)])); + #endif + a_qual[a_iseq] = 0.8 * a_qual[a_iseq]; // not so confident about a_qual anymore given the mismatch + b_qual[b_iseq] = 0; + } + else + { + #if DBG + fprintf(stderr,"[%c/%c]",tolower(seq_nt16_str[bam_seqi(a_seq,a_iseq)]),seq_nt16_str[bam_seqi(b_seq,b_iseq)]); + #endif + b_qual[b_iseq] = 0.8 * b_qual[b_iseq]; + a_qual[a_iseq] = 0; + } + } + } + #if DBG + fprintf(stderr,"\n"); + #endif +} + +// Fix overlapping reads. Simple soft-clipping did not give good results. +// Lowering qualities of unwanted bases is more selective and works better. +// +static void overlap_push(bam_plp_t iter, lbnode_t *node) +{ + if ( !iter->overlaps ) return; + + // mapped mates and paired reads only + if ( node->b.core.flag&BAM_FMUNMAP || !(node->b.core.flag&BAM_FPROPER_PAIR) ) return; + + // no overlap possible, unless some wild cigar + if ( abs(node->b.core.isize) >= 2*node->b.core.l_qseq ) return; + + khiter_t kitr = kh_get(olap_hash, iter->overlaps, bam_get_qname(&node->b)); + if ( kitr==kh_end(iter->overlaps) ) + { + int ret; + kitr = kh_put(olap_hash, iter->overlaps, bam_get_qname(&node->b), &ret); + kh_value(iter->overlaps, kitr) = node; + } + else + { + lbnode_t *a = kh_value(iter->overlaps, kitr); + tweak_overlap_quality(&a->b, &node->b); + kh_del(olap_hash, iter->overlaps, kitr); + assert(a->end-1 == a->s.end); + a->end = a->b.core.pos + bam_cigar2rlen(a->b.core.n_cigar, bam_get_cigar(&a->b)); + a->s.end = a->end - 1; + } +} + +static void overlap_remove(bam_plp_t iter, const bam1_t *b) +{ + if ( !iter->overlaps ) return; + + khiter_t kitr; + if ( b ) + { + kitr = kh_get(olap_hash, iter->overlaps, bam_get_qname(b)); + if ( kitr!=kh_end(iter->overlaps) ) + kh_del(olap_hash, iter->overlaps, kitr); + } + else + { + // remove all + for (kitr = kh_begin(iter->overlaps); kitroverlaps); kitr++) + if ( kh_exist(iter->overlaps, kitr) ) kh_del(olap_hash, iter->overlaps, kitr); + } +} + + + +// Prepares next pileup position in bam records collected by bam_plp_auto -> user func -> bam_plp_push. Returns +// pointer to the piled records if next position is ready or NULL if there is not enough records in the +// buffer yet (the current position is still the maximum position across all buffered reads). +const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp) +{ + if (iter->error) { *_n_plp = -1; return 0; } + *_n_plp = 0; + if (iter->is_eof && iter->head->next == 0) return 0; + while (iter->is_eof || iter->max_tid > iter->tid || (iter->max_tid == iter->tid && iter->max_pos > iter->pos)) { + int n_plp = 0; + lbnode_t *p, *q; + // write iter->plp at iter->pos + iter->dummy->next = iter->head; + for (p = iter->head, q = iter->dummy; p->next; q = p, p = p->next) { + if (p->b.core.tid < iter->tid || (p->b.core.tid == iter->tid && p->end <= iter->pos)) { // then remove + overlap_remove(iter, &p->b); + q->next = p->next; mp_free(iter->mp, p); p = q; + } else if (p->b.core.tid == iter->tid && p->beg <= iter->pos) { // here: p->end > pos; then add to pileup + if (n_plp == iter->max_plp) { // then double the capacity + iter->max_plp = iter->max_plp? iter->max_plp<<1 : 256; + iter->plp = (bam_pileup1_t*)realloc(iter->plp, sizeof(bam_pileup1_t) * iter->max_plp); + } + iter->plp[n_plp].b = &p->b; + if (resolve_cigar2(iter->plp + n_plp, iter->pos, &p->s)) ++n_plp; // actually always true... + } + } + iter->head = iter->dummy->next; // dummy->next may be changed + *_n_plp = n_plp; *_tid = iter->tid; *_pos = iter->pos; + // update iter->tid and iter->pos + if (iter->head->next) { + if (iter->tid > iter->head->b.core.tid) { + fprintf(stderr, "[%s] unsorted input. Pileup aborts.\n", __func__); + iter->error = 1; + *_n_plp = -1; + return 0; + } + } + if (iter->tid < iter->head->b.core.tid) { // come to a new reference sequence + iter->tid = iter->head->b.core.tid; iter->pos = iter->head->beg; // jump to the next reference + } else if (iter->pos < iter->head->beg) { // here: tid == head->b.core.tid + iter->pos = iter->head->beg; // jump to the next position + } else ++iter->pos; // scan contiguously + // return + if (n_plp) return iter->plp; + if (iter->is_eof && iter->head->next == 0) break; + } + return 0; +} + +int bam_plp_push(bam_plp_t iter, const bam1_t *b) +{ + if (iter->error) return -1; + if (b) { + if (b->core.tid < 0) { overlap_remove(iter, b); return 0; } + // Skip only unmapped reads here, any additional filtering must be done in iter->func + if (b->core.flag & BAM_FUNMAP) { overlap_remove(iter, b); return 0; } + if (iter->tid == b->core.tid && iter->pos == b->core.pos && iter->mp->cnt > iter->maxcnt) + { + overlap_remove(iter, b); + return 0; + } + bam_copy1(&iter->tail->b, b); + overlap_push(iter, iter->tail); +#ifndef BAM_NO_ID + iter->tail->b.id = iter->id++; +#endif + iter->tail->beg = b->core.pos; + iter->tail->end = b->core.pos + bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b)); + iter->tail->s = g_cstate_null; iter->tail->s.end = iter->tail->end - 1; // initialize cstate_t + if (b->core.tid < iter->max_tid) { + fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n"); + iter->error = 1; + return -1; + } + if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) { + fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n"); + iter->error = 1; + return -1; + } + iter->max_tid = b->core.tid; iter->max_pos = iter->tail->beg; + if (iter->tail->end > iter->pos || iter->tail->b.core.tid > iter->tid) { + iter->tail->next = mp_alloc(iter->mp); + iter->tail = iter->tail->next; + } + } else iter->is_eof = 1; + return 0; +} + +const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp) +{ + const bam_pileup1_t *plp; + if (iter->func == 0 || iter->error) { *_n_plp = -1; return 0; } + if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp; + else { // no pileup line can be obtained; read alignments + *_n_plp = 0; + if (iter->is_eof) return 0; + int ret; + while ( (ret=iter->func(iter->data, iter->b)) >= 0) { + if (bam_plp_push(iter, iter->b) < 0) { + *_n_plp = -1; + return 0; + } + if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp; + // otherwise no pileup line can be returned; read the next alignment. + } + if ( ret < -1 ) { iter->error = ret; *_n_plp = -1; return 0; } + bam_plp_push(iter, 0); + if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp; + return 0; + } +} + +void bam_plp_reset(bam_plp_t iter) +{ + lbnode_t *p, *q; + iter->max_tid = iter->max_pos = -1; + iter->tid = iter->pos = 0; + iter->is_eof = 0; + for (p = iter->head; p->next;) { + overlap_remove(iter, NULL); + q = p->next; + mp_free(iter->mp, p); + p = q; + } + iter->head = iter->tail; +} + +void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt) +{ + iter->maxcnt = maxcnt; +} + +/************************ + *** Mpileup iterator *** + ************************/ + +struct __bam_mplp_t { + int n; + uint64_t min, *pos; + bam_plp_t *iter; + int *n_plp; + const bam_pileup1_t **plp; +}; + +bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data) +{ + int i; + bam_mplp_t iter; + iter = (bam_mplp_t)calloc(1, sizeof(struct __bam_mplp_t)); + iter->pos = (uint64_t*)calloc(n, 8); + iter->n_plp = (int*)calloc(n, sizeof(int)); + iter->plp = (const bam_pileup1_t**)calloc(n, sizeof(bam_pileup1_t*)); + iter->iter = (bam_plp_t*)calloc(n, sizeof(bam_plp_t)); + iter->n = n; + iter->min = (uint64_t)-1; + for (i = 0; i < n; ++i) { + iter->iter[i] = bam_plp_init(func, data[i]); + iter->pos[i] = iter->min; + } + return iter; +} + +void bam_mplp_init_overlaps(bam_mplp_t iter) +{ + int i; + for (i = 0; i < iter->n; ++i) + bam_plp_init_overlaps(iter->iter[i]); +} + +void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt) +{ + int i; + for (i = 0; i < iter->n; ++i) + iter->iter[i]->maxcnt = maxcnt; +} + +void bam_mplp_destroy(bam_mplp_t iter) +{ + int i; + for (i = 0; i < iter->n; ++i) bam_plp_destroy(iter->iter[i]); + free(iter->iter); free(iter->pos); free(iter->n_plp); free(iter->plp); + free(iter); +} + +int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp) +{ + int i, ret = 0; + uint64_t new_min = (uint64_t)-1; + for (i = 0; i < iter->n; ++i) { + if (iter->pos[i] == iter->min) { + int tid, pos; + iter->plp[i] = bam_plp_auto(iter->iter[i], &tid, &pos, &iter->n_plp[i]); + if ( iter->iter[i]->error ) return -1; + iter->pos[i] = iter->plp[i] ? (uint64_t)tid<<32 | pos : 0; + } + if (iter->plp[i] && iter->pos[i] < new_min) new_min = iter->pos[i]; + } + iter->min = new_min; + if (new_min == (uint64_t)-1) return 0; + *_tid = new_min>>32; *_pos = (uint32_t)new_min; + for (i = 0; i < iter->n; ++i) { + if (iter->pos[i] == iter->min) { // FIXME: valgrind reports "uninitialised value(s) at this line" + n_plp[i] = iter->n_plp[i], plp[i] = iter->plp[i]; + ++ret; + } else n_plp[i] = 0, plp[i] = 0; + } + return ret; +} + +#endif // ~!defined(BAM_NO_PILEUP) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/synced_bcf_reader.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/synced_bcf_reader.c new file mode 100644 index 0000000000000000000000000000000000000000..238f9da08b3c59aed626e8a7979cd0875789f22c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/synced_bcf_reader.c @@ -0,0 +1,1185 @@ +#include +#include +#include +#include +#include +#include +#include +#include "htslib/synced_bcf_reader.h" +#include "htslib/kseq.h" +#include "htslib/khash_str2int.h" + +#define MAX_CSI_COOR 0x7fffffff // maximum indexable coordinate of .csi + +typedef struct +{ + uint32_t start, end; +} +region1_t; + +typedef struct _region_t +{ + region1_t *regs; + int nregs, mregs, creg; +} +region_t; + +static void _regions_add(bcf_sr_regions_t *reg, const char *chr, int start, int end); +static bcf_sr_regions_t *_regions_init_string(const char *str); +static int _regions_match_alleles(bcf_sr_regions_t *reg, int als_idx, bcf1_t *rec); + +static int *init_filters(bcf_hdr_t *hdr, const char *filters, int *nfilters) +{ + kstring_t str = {0,0,0}; + const char *tmp = filters, *prev = filters; + int nout = 0, *out = NULL; + while ( 1 ) + { + if ( *tmp==',' || !*tmp ) + { + out = (int*) realloc(out, sizeof(int)); + if ( tmp-prev==1 && *prev=='.' ) + out[nout] = -1; + else + { + str.l = 0; + kputsn(prev, tmp-prev, &str); + out[nout] = bcf_hdr_id2int(hdr, BCF_DT_ID, str.s); + } + nout++; + if ( !*tmp ) break; + prev = tmp+1; + } + tmp++; + } + if ( str.m ) free(str.s); + *nfilters = nout; + return out; +} + +int bcf_sr_set_regions(bcf_srs_t *readers, const char *regions, int is_file) +{ + assert( !readers->regions ); + if ( readers->nreaders ) + { + fprintf(stderr,"[%s:%d %s] Error: bcf_sr_set_regions() must be called before bcf_sr_add_reader()\n", __FILE__,__LINE__,__FUNCTION__); + return -1; + } + readers->regions = bcf_sr_regions_init(regions,is_file,0,1,-2); + if ( !readers->regions ) return -1; + readers->explicit_regs = 1; + readers->require_index = 1; + return 0; +} +int bcf_sr_set_targets(bcf_srs_t *readers, const char *targets, int is_file, int alleles) +{ + assert( !readers->targets ); + readers->targets = bcf_sr_regions_init(targets,is_file,0,1,-2); + if ( !readers->targets ) return -1; + readers->targets_als = alleles; + return 0; +} + +int bcf_sr_add_reader(bcf_srs_t *files, const char *fname) +{ + files->has_line = (int*) realloc(files->has_line, sizeof(int)*(files->nreaders+1)); + files->has_line[files->nreaders] = 0; + files->readers = (bcf_sr_t*) realloc(files->readers, sizeof(bcf_sr_t)*(files->nreaders+1)); + bcf_sr_t *reader = &files->readers[files->nreaders++]; + memset(reader,0,sizeof(bcf_sr_t)); + + reader->file = hts_open(fname, "r"); + if ( !reader->file ) return 0; + + reader->type = reader->file->is_bin? FT_BCF : FT_VCF; + if (reader->file->is_compressed) reader->type |= FT_GZ; + + if ( files->require_index ) + { + if ( reader->type==FT_VCF_GZ ) + { + reader->tbx_idx = tbx_index_load(fname); + if ( !reader->tbx_idx ) + { + fprintf(stderr,"[add_reader] Could not load the index of %s\n", fname); + return 0; + } + + reader->header = bcf_hdr_read(reader->file); + } + else if ( reader->type==FT_BCF_GZ ) + { + reader->header = bcf_hdr_read(reader->file); + + reader->bcf_idx = bcf_index_load(fname); + if ( !reader->bcf_idx ) + { + fprintf(stderr,"[add_reader] Could not load the index of %s\n", fname); + return 0; // not indexed..? + } + } + else + { + fprintf(stderr,"Index required, expected .vcf.gz or .bcf file: %s\n", fname); + return 0; + } + } + else + { + if ( reader->type & FT_BCF ) + { + reader->header = bcf_hdr_read(reader->file); + } + else if ( reader->type & FT_VCF ) + { + reader->header = bcf_hdr_read(reader->file); + } + else + { + fprintf(stderr,"File type not recognised: %s\n", fname); + return 0; + } + files->streaming = 1; + } + if ( files->streaming && files->nreaders>1 ) + { + fprintf(stderr,"[%s:%d %s] Error: %d readers, yet require_index not set\n", __FILE__,__LINE__,__FUNCTION__,files->nreaders); + return 0; + } + if ( files->streaming && files->regions ) + { + fprintf(stderr,"[%s:%d %s] Error: cannot tabix-jump in streaming mode\n", __FILE__,__LINE__,__FUNCTION__); + return 0; + } + if ( !reader->header ) return 0; + + reader->fname = fname; + if ( files->apply_filters ) + reader->filter_ids = init_filters(reader->header, files->apply_filters, &reader->nfilter_ids); + + // Update list of chromosomes + if ( !files->explicit_regs && !files->streaming ) + { + int n,i; + const char **names = reader->tbx_idx ? tbx_seqnames(reader->tbx_idx, &n) : bcf_hdr_seqnames(reader->header, &n); + for (i=0; iregions ) + files->regions = _regions_init_string(names[i]); + else + _regions_add(files->regions, names[i], -1, -1); + } + free(names); + } + + return 1; +} + +bcf_srs_t *bcf_sr_init(void) +{ + bcf_srs_t *files = (bcf_srs_t*) calloc(1,sizeof(bcf_srs_t)); + return files; +} + +static void bcf_sr_destroy1(bcf_sr_t *reader) +{ + if ( reader->tbx_idx ) tbx_destroy(reader->tbx_idx); + if ( reader->bcf_idx ) hts_idx_destroy(reader->bcf_idx); + bcf_hdr_destroy(reader->header); + hts_close(reader->file); + if ( reader->itr ) tbx_itr_destroy(reader->itr); + int j; + for (j=0; jmbuffer; j++) + bcf_destroy1(reader->buffer[j]); + free(reader->buffer); + free(reader->samples); + free(reader->filter_ids); +} +void bcf_sr_destroy(bcf_srs_t *files) +{ + int i; + for (i=0; inreaders; i++) + bcf_sr_destroy1(&files->readers[i]); + free(files->has_line); + free(files->readers); + for (i=0; in_smpl; i++) free(files->samples[i]); + free(files->samples); + if (files->targets) bcf_sr_regions_destroy(files->targets); + if (files->regions) bcf_sr_regions_destroy(files->regions); + if ( files->tmps.m ) free(files->tmps.s); + free(files); +} + +void bcf_sr_remove_reader(bcf_srs_t *files, int i) +{ + assert( !files->samples ); // not ready for this yet + bcf_sr_destroy1(&files->readers[i]); + if ( i+1 < files->nreaders ) + { + memmove(&files->readers[i], &files->readers[i+1], (files->nreaders-i-1)*sizeof(bcf_sr_t)); + memmove(&files->has_line[i], &files->has_line[i+1], (files->nreaders-i-1)*sizeof(int)); + } + files->nreaders--; +} + + +/* + Removes duplicate records from the buffer. The meaning of "duplicate" is + controlled by the $collapse variable, which can cause that from multiple + lines only the first is considered and the rest is ignored. + The removal is done by setting the redundant lines' positions to -1 and + moving these lines at the end of the buffer. + */ +static void collapse_buffer(bcf_srs_t *files, bcf_sr_t *reader) +{ + int irec,jrec, has_snp=0, has_indel=0, has_any=0; + for (irec=1; irec<=reader->nbuffer; irec++) + { + bcf1_t *line = reader->buffer[irec]; + if ( line->pos != reader->buffer[1]->pos ) break; + if ( files->collapse&COLLAPSE_ANY ) + { + if ( !has_any ) has_any = 1; + else line->pos = -1; + } + int line_type = bcf_get_variant_types(line); + if ( files->collapse&COLLAPSE_SNPS && line_type&(VCF_SNP|VCF_MNP) ) + { + if ( !has_snp ) has_snp = 1; + else line->pos = -1; + } + if ( files->collapse&COLLAPSE_INDELS && line_type&VCF_INDEL ) + { + if ( !has_indel ) has_indel = 1; + else line->pos = -1; + } + } + bcf1_t *tmp; + irec = jrec = 1; + while ( irec<=reader->nbuffer && jrec<=reader->nbuffer ) + { + if ( reader->buffer[irec]->pos != -1 ) { irec++; continue; } + if ( jrec<=irec ) jrec = irec+1; + while ( jrec<=reader->nbuffer && reader->buffer[jrec]->pos==-1 ) jrec++; + if ( jrec<=reader->nbuffer ) + { + tmp = reader->buffer[irec]; reader->buffer[irec] = reader->buffer[jrec]; reader->buffer[jrec] = tmp; + } + } + reader->nbuffer = irec - 1; +} + +void debug_buffer(FILE *fp, bcf_sr_t *reader) +{ + int j; + for (j=0; j<=reader->nbuffer; j++) + { + bcf1_t *line = reader->buffer[j]; + fprintf(fp,"%s%s\t%s:%d\t%s ", reader->fname,j==0?"*":"",reader->header->id[BCF_DT_CTG][line->rid].key,line->pos+1,line->n_allele?line->d.allele[0]:""); + int k; + for (k=1; kn_allele; k++) fprintf(fp," %s", line->d.allele[k]); + fprintf(fp,"\n"); + } +} + +void debug_buffers(FILE *fp, bcf_srs_t *files) +{ + int i; + for (i=0; inreaders; i++) + { + fprintf(fp, "has_line: %d\t%s\n", bcf_sr_has_line(files,i),files->readers[i].fname); + debug_buffer(fp, &files->readers[i]); + } + fprintf(fp,"\n"); +} + +static inline int has_filter(bcf_sr_t *reader, bcf1_t *line) +{ + int i, j; + if ( !line->d.n_flt ) + { + for (j=0; jnfilter_ids; j++) + if ( reader->filter_ids[j]<0 ) return 1; + return 0; + } + for (i=0; id.n_flt; i++) + { + for (j=0; jnfilter_ids; j++) + if ( line->d.flt[i]==reader->filter_ids[j] ) return 1; + } + return 0; +} + +static int _reader_seek(bcf_sr_t *reader, const char *seq, int start, int end) +{ + if ( end>=MAX_CSI_COOR ) + { + fprintf(stderr,"The coordinate is out of csi index limit: %d\n", end+1); + exit(1); + } + if ( reader->itr ) + { + hts_itr_destroy(reader->itr); + reader->itr = NULL; + } + reader->nbuffer = 0; + if ( reader->tbx_idx ) + { + int tid = tbx_name2id(reader->tbx_idx, seq); + if ( tid==-1 ) return -1; // the sequence not present in this file + reader->itr = tbx_itr_queryi(reader->tbx_idx,tid,start,end+1); + } + else + { + int tid = bcf_hdr_name2id(reader->header, seq); + if ( tid==-1 ) return -1; // the sequence not present in this file + reader->itr = bcf_itr_queryi(reader->bcf_idx,tid,start,end+1); + } + assert(reader->itr); + return 0; +} + +/* + * _readers_next_region() - jumps to next region if necessary + * Returns 0 on success or -1 when there are no more regions left + */ +static int _readers_next_region(bcf_srs_t *files) +{ + // Need to open new chromosome? Check number of lines in all readers' buffers + int i, eos = 0; + for (i=0; inreaders; i++) + if ( !files->readers[i].itr && !files->readers[i].nbuffer ) eos++; + + if ( eos!=files->nreaders ) + { + // Some of the readers still has buffered lines + return 0; + } + + // No lines in the buffer, need to open new region or quit + if ( bcf_sr_regions_next(files->regions)<0 ) return -1; + + for (i=0; inreaders; i++) + _reader_seek(&files->readers[i],files->regions->seq_names[files->regions->iseq],files->regions->start,files->regions->end); + + return 0; +} + +/* + * _reader_fill_buffer() - buffers all records with the same coordinate + */ +static void _reader_fill_buffer(bcf_srs_t *files, bcf_sr_t *reader) +{ + // Return if the buffer is full: the coordinate of the last buffered record differs + if ( reader->nbuffer && reader->buffer[reader->nbuffer]->pos != reader->buffer[1]->pos ) return; + + // No iterator (sequence not present in this file) and not streaming + if ( !reader->itr && !files->streaming ) return; + + // Fill the buffer with records starting at the same position + int i, ret = 0; + while (1) + { + if ( reader->nbuffer+1 >= reader->mbuffer ) + { + // Increase buffer size + reader->mbuffer += 8; + reader->buffer = (bcf1_t**) realloc(reader->buffer, sizeof(bcf1_t*)*reader->mbuffer); + for (i=8; i>0; i--) // initialize + { + reader->buffer[reader->mbuffer-i] = bcf_init1(); + reader->buffer[reader->mbuffer-i]->max_unpack = files->max_unpack; + reader->buffer[reader->mbuffer-i]->pos = -1; // for rare cases when VCF starts from 1 + } + } + if ( files->streaming ) + { + if ( reader->type & FT_VCF ) + { + if ( (ret=hts_getline(reader->file, KS_SEP_LINE, &files->tmps)) < 0 ) break; // no more lines + int ret = vcf_parse1(&files->tmps, reader->header, reader->buffer[reader->nbuffer+1]); + if ( ret<0 ) break; + } + else if ( reader->type & FT_BCF ) + { + if ( (ret=bcf_read1(reader->file, reader->header, reader->buffer[reader->nbuffer+1])) < 0 ) break; // no more lines + } + else + { + fprintf(stderr,"[%s:%d %s] fixme: not ready for this\n", __FILE__,__LINE__,__FUNCTION__); + exit(1); + } + } + else if ( reader->tbx_idx ) + { + if ( (ret=tbx_itr_next(reader->file, reader->tbx_idx, reader->itr, &files->tmps)) < 0 ) break; // no more lines + vcf_parse1(&files->tmps, reader->header, reader->buffer[reader->nbuffer+1]); + } + else + { + if ( (ret=bcf_itr_next(reader->file, reader->itr, reader->buffer[reader->nbuffer+1])) < 0 ) break; // no more lines + bcf_subset_format(reader->header,reader->buffer[reader->nbuffer+1]); + } + + // apply filter + if ( !reader->nfilter_ids ) + bcf_unpack(reader->buffer[reader->nbuffer+1], BCF_UN_STR); + else + { + bcf_unpack(reader->buffer[reader->nbuffer+1], BCF_UN_STR|BCF_UN_FLT); + if ( !has_filter(reader, reader->buffer[reader->nbuffer+1]) ) continue; + } + reader->nbuffer++; + + if ( reader->buffer[reader->nbuffer]->pos != reader->buffer[1]->pos ) break; // the buffer is full + } + if ( ret<0 ) + { + // done for this region + tbx_itr_destroy(reader->itr); + reader->itr = NULL; + } + if ( files->collapse && reader->nbuffer>=2 && reader->buffer[1]->pos==reader->buffer[2]->pos ) + collapse_buffer(files, reader); +} + +/* + * _readers_shift_buffer() - removes the first line and all subsequent lines with the same position + */ +static void _reader_shift_buffer(bcf_sr_t *reader) +{ + int i; + for (i=2; i<=reader->nbuffer; i++) + if ( reader->buffer[i]->pos!=reader->buffer[1]->pos ) break; + if ( i<=reader->nbuffer ) + { + // A record with a different position follows, swap it. Because of the reader's logic, + // only one such line can be present. + bcf1_t *tmp = reader->buffer[1]; reader->buffer[1] = reader->buffer[i]; reader->buffer[i] = tmp; + reader->nbuffer = 1; + } + else + reader->nbuffer = 0; // no other line +} + +/* + * _reader_match_alleles() - from multiple buffered lines selects the one which + * corresponds best to the template line. The logic is controlled by COLLAPSE_* + * Returns 0 on success or -1 when no good matching line is found. + */ +static int _reader_match_alleles(bcf_srs_t *files, bcf_sr_t *reader, bcf1_t *tmpl) +{ + int i, irec = -1; + + // if no template given, use the first available record + if ( !tmpl ) + irec = 1; + else + { + int tmpl_type = bcf_get_variant_types(tmpl); + for (i=1; i<=reader->nbuffer; i++) + { + bcf1_t *line = reader->buffer[i]; + if ( line->pos != reader->buffer[1]->pos ) break; // done with this reader + + // Easiest case: matching by position only + if ( files->collapse&COLLAPSE_ANY ) { irec=i; break; } + + int line_type = bcf_get_variant_types(line); + + // No matter what the alleles are, as long as they are both SNPs + if ( files->collapse&COLLAPSE_SNPS && tmpl_type&VCF_SNP && line_type&VCF_SNP ) { irec=i; break; } + // ... or indels + if ( files->collapse&COLLAPSE_INDELS && tmpl_type&VCF_INDEL && line_type&VCF_INDEL ) { irec=i; break; } + + // More thorough checking: REFs must match + if ( tmpl->rlen != line->rlen ) continue; // different length + if ( strcmp(tmpl->d.allele[0], line->d.allele[0]) ) continue; // the strings do not match + + int ial,jal; + if ( files->collapse==COLLAPSE_NONE ) + { + // Exact match, all alleles must be identical + if ( tmpl->n_allele!=line->n_allele ) continue; // different number of alleles, skip + + int nmatch = 1; // REF has been already checked + for (ial=1; ialn_allele; ial++) + { + for (jal=1; jaln_allele; jal++) + if ( !strcmp(tmpl->d.allele[ial], line->d.allele[jal]) ) { nmatch++; break; } + } + if ( nmatch==tmpl->n_allele ) { irec=i; break; } // found: exact match + continue; + } + + if ( line->n_allele==1 && tmpl->n_allele==1 ) { irec=i; break; } // both sites are non-variant + + // COLLAPSE_SOME: at least some ALTs must match + for (ial=1; ialn_allele; ial++) + { + for (jal=1; jaln_allele; jal++) + if ( !strcmp(tmpl->d.allele[ial], line->d.allele[jal]) ) { irec=i; break; } + if ( irec>=1 ) break; + } + if ( irec>=1 ) break; + } + if ( irec==-1 ) return -1; // no matching line was found + } + + // Set the selected line (irec) as active: set it to buffer[0], move the remaining lines forward + // and put the old bcf1_t record at the end. + bcf1_t *tmp = reader->buffer[0]; + reader->buffer[0] = reader->buffer[irec]; + for (i=irec+1; i<=reader->nbuffer; i++) reader->buffer[i-1] = reader->buffer[i]; + reader->buffer[ reader->nbuffer ] = tmp; + reader->nbuffer--; + + return 0; +} + +int _reader_next_line(bcf_srs_t *files) +{ + int i, min_pos = INT_MAX; + + // Loop until next suitable line is found or all readers have finished + while ( 1 ) + { + // Get all readers ready for the next region. + if ( files->regions && _readers_next_region(files)<0 ) break; + + // Fill buffers + const char *chr = NULL; + for (i=0; inreaders; i++) + { + _reader_fill_buffer(files, &files->readers[i]); + + // Update the minimum coordinate + if ( !files->readers[i].nbuffer ) continue; + if ( min_pos > files->readers[i].buffer[1]->pos ) + { + min_pos = files->readers[i].buffer[1]->pos; + chr = bcf_seqname(files->readers[i].header, files->readers[i].buffer[1]); + } + } + if ( min_pos==INT_MAX ) + { + if ( !files->regions ) break; + continue; + } + + // Skip this position if not present in targets + if ( files->targets ) + { + if ( bcf_sr_regions_overlap(files->targets, chr, min_pos, min_pos)<0 ) + { + // Remove all lines with this position from the buffer + for (i=0; inreaders; i++) + if ( files->readers[i].nbuffer && files->readers[i].buffer[1]->pos==min_pos ) + _reader_shift_buffer(&files->readers[i]); + min_pos = INT_MAX; + continue; + } + } + + break; // done: min_pos is set + } + + // There can be records with duplicate positions. Set the active line intelligently so that + // the alleles match. + int nret = 0; // number of readers sharing the position + bcf1_t *first = NULL; // record which will be used for allele matching + for (i=0; inreaders; i++) + { + files->has_line[i] = 0; + + // Skip readers with no records at this position + if ( !files->readers[i].nbuffer || files->readers[i].buffer[1]->pos!=min_pos ) continue; + + // Until now buffer[0] of all reader was empty and the lines started at buffer[1]. + // Now lines which are ready to be output will be moved to buffer[0]. + if ( _reader_match_alleles(files, &files->readers[i], first) < 0 ) continue; + if ( !first ) first = files->readers[i].buffer[0]; + + nret++; + files->has_line[i] = 1; + } + return nret; +} + +int bcf_sr_next_line(bcf_srs_t *files) +{ + if ( !files->targets_als ) + return _reader_next_line(files); + + while (1) + { + int i, ret = _reader_next_line(files); + if ( !ret ) return ret; + + for (i=0; inreaders; i++) + if ( files->has_line[i] ) break; + + if ( _regions_match_alleles(files->targets, files->targets_als-1, files->readers[i].buffer[0]) ) return ret; + + // Check if there are more duplicate lines in the buffers. If not, return this line as if it + // matched the targets, even if there is a type mismatch + for (i=0; inreaders; i++) + { + if ( !files->has_line[i] ) continue; + if ( files->readers[i].nbuffer==0 || files->readers[i].buffer[1]->pos!=files->readers[i].buffer[0]->pos ) continue; + break; + } + if ( i==files->nreaders ) return ret; // no more lines left, output even if target alleles are not of the same type + } +} + +static void bcf_sr_seek_start(bcf_srs_t *readers) +{ + bcf_sr_regions_t *reg = readers->regions; + int i; + for (i=0; inseqs; i++) + reg->regs[i].creg = -1; + reg->iseq = 0; +} + + +int bcf_sr_seek(bcf_srs_t *readers, const char *seq, int pos) +{ + if ( !seq && !pos ) + { + // seek to start + bcf_sr_seek_start(readers); + return 0; + } + + bcf_sr_regions_overlap(readers->regions, seq, pos, pos); + int i, nret = 0; + for (i=0; inreaders; i++) + { + nret += _reader_seek(&readers->readers[i],seq,pos,MAX_CSI_COOR-1); + } + return nret; +} + +int bcf_sr_set_samples(bcf_srs_t *files, const char *fname, int is_file) +{ + int i, j, nsmpl, free_smpl = 0; + char **smpl = NULL; + + void *exclude = (fname[0]=='^') ? khash_str2int_init() : NULL; + if ( exclude || strcmp("-",fname) ) // "-" stands for all samples + { + smpl = hts_readlist(fname, is_file, &nsmpl); + if ( !smpl ) + { + fprintf(stderr,"Could not read the file: \"%s\"\n", fname); + return 0; + } + if ( exclude ) + { + for (i=0; ireaders[0].header->samples; // intersection of all samples + nsmpl = bcf_hdr_nsamples(files->readers[0].header); + } + + files->samples = NULL; + files->n_smpl = 0; + for (i=0; inreaders; j++) + { + if ( bcf_hdr_id2int(files->readers[j].header, BCF_DT_SAMPLE, smpl[i])<0 ) break; + n_isec++; + } + if ( n_isec!=files->nreaders ) + { + fprintf(stderr,"Warning: The sample \"%s\" was not found in %s, skipping\n", smpl[i], files->readers[n_isec].fname); + continue; + } + + files->samples = (char**) realloc(files->samples, (files->n_smpl+1)*sizeof(const char*)); + files->samples[files->n_smpl++] = strdup(smpl[i]); + } + + if ( exclude ) khash_str2int_destroy(exclude); + if ( free_smpl ) + { + for (i=0; in_smpl ) + { + if ( files->nreaders>1 ) + fprintf(stderr,"No samples in common.\n"); + return 0; + } + for (i=0; inreaders; i++) + { + bcf_sr_t *reader = &files->readers[i]; + reader->samples = (int*) malloc(sizeof(int)*files->n_smpl); + reader->n_smpl = files->n_smpl; + for (j=0; jn_smpl; j++) + reader->samples[j] = bcf_hdr_id2int(reader->header, BCF_DT_SAMPLE, files->samples[j]); + } + return 1; +} + +// Add a new region into a list sorted by start,end. On input the coordinates +// are 1-based, stored 0-based, inclusive. +static void _regions_add(bcf_sr_regions_t *reg, const char *chr, int start, int end) +{ + if ( start==-1 && end==-1 ) + { + start = 0; end = MAX_CSI_COOR-1; + } + else + { + start--; end--; // store 0-based coordinates + } + + if ( !reg->seq_hash ) + reg->seq_hash = khash_str2int_init(); + + int iseq; + if ( khash_str2int_get(reg->seq_hash, chr, &iseq)<0 ) + { + // the chromosome block does not exist + iseq = reg->nseqs++; + reg->seq_names = (char**) realloc(reg->seq_names,sizeof(char*)*reg->nseqs); + reg->regs = (region_t*) realloc(reg->regs,sizeof(region_t)*reg->nseqs); + memset(®->regs[reg->nseqs-1],0,sizeof(region_t)); + reg->seq_names[iseq] = strdup(chr); + reg->regs[iseq].creg = -1; + khash_str2int_set(reg->seq_hash,reg->seq_names[iseq],iseq); + } + + region_t *creg = ®->regs[iseq]; + + // the regions may not be sorted on input: binary search + int i, min = 0, max = creg->nregs - 1; + while ( min<=max ) + { + i = (max+min)/2; + if ( start < creg->regs[i].start ) max = i - 1; + else if ( start > creg->regs[i].start ) min = i + 1; + else break; + } + if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) + { + // no such region, insert a new one just after max + hts_expand(region1_t,creg->nregs+1,creg->mregs,creg->regs); + if ( ++max < creg->nregs ) + memmove(&creg->regs[max+1],&creg->regs[max],(creg->nregs - max)*sizeof(region1_t)); + creg->regs[max].start = start; + creg->regs[max].end = end; + creg->nregs++; + } +} + +// File name or a list of genomic locations. If file name, NULL is returned. +static bcf_sr_regions_t *_regions_init_string(const char *str) +{ + bcf_sr_regions_t *reg = (bcf_sr_regions_t *) calloc(1, sizeof(bcf_sr_regions_t)); + reg->start = reg->end = -1; + reg->prev_start = reg->prev_seq = -1; + + kstring_t tmp = {0,0,0}; + const char *sp = str, *ep = str; + int from, to; + while ( 1 ) + { + while ( *ep && *ep!=',' && *ep!=':' ) ep++; + tmp.l = 0; + kputsn(sp,ep-sp,&tmp); + if ( *ep==':' ) + { + sp = ep+1; + from = strtol(sp,(char**)&ep,10); + if ( sp==ep ) + { + fprintf(stderr,"[%s:%d %s] Could not parse the region(s): %s\n", __FILE__,__LINE__,__FUNCTION__,str); + free(reg); free(tmp.s); return NULL; + } + if ( !*ep || *ep==',' ) + { + _regions_add(reg, tmp.s, from, from); + sp = ep; + continue; + } + if ( *ep!='-' ) + { + fprintf(stderr,"[%s:%d %s] Could not parse the region(s): %s\n", __FILE__,__LINE__,__FUNCTION__,str); + free(reg); free(tmp.s); return NULL; + } + ep++; + sp = ep; + to = strtol(sp,(char**)&ep,10); + if ( *ep && *ep!=',' ) + { + fprintf(stderr,"[%s:%d %s] Could not parse the region(s): %s\n", __FILE__,__LINE__,__FUNCTION__,str); + free(reg); free(tmp.s); return NULL; + } + if ( sp==ep ) to = MAX_CSI_COOR-1; + _regions_add(reg, tmp.s, from, to); + if ( !*ep ) break; + sp = ep; + } + else + { + if ( tmp.l ) _regions_add(reg, tmp.s, -1, -1); + if ( !*ep ) break; + sp = ++ep; + } + } + free(tmp.s); + return reg; +} + +// ichr,ifrom,ito are 0-based; +// returns -1 on error, 0 if the line is a comment line, 1 on success +static int _regions_parse_line(char *line, int ichr,int ifrom,int ito, char **chr,char **chr_end,int *from,int *to) +{ + *chr_end = NULL; + + if ( line[0]=='#' ) return 0; + + int k,l; // index of the start and end column of the tab-delimited file + if ( ifrom <= ito ) + k = ifrom, l = ito; + else + l = ifrom, k = ito; + + int i; + char *se = line, *ss = NULL; // start and end + char *tmp; + for (i=0; i<=k && *se; i++) + { + ss = i==0 ? se++ : ++se; + while (*se && *se!='\t') se++; + } + if ( i<=k ) return -1; + if ( k==l ) + { + *from = *to = strtol(ss, &tmp, 10); + if ( tmp==ss ) return -1; + } + else + { + if ( k==ifrom ) + *from = strtol(ss, &tmp, 10); + else + *to = strtol(ss, &tmp, 10); + if ( ss==tmp ) return -1; + + for (i=k; i0 ) ss = ++se; + while (*se && *se!='\t') se++; + } + if ( i<=ichr ) return -1; + *chr_end = se; + *chr = ss; + return 1; +} + +bcf_sr_regions_t *bcf_sr_regions_init(const char *regions, int is_file, int ichr, int ifrom, int ito) +{ + bcf_sr_regions_t *reg; + if ( !is_file ) return _regions_init_string(regions); + + reg = (bcf_sr_regions_t *) calloc(1, sizeof(bcf_sr_regions_t)); + reg->start = reg->end = -1; + reg->prev_start = reg->prev_seq = -1; + + reg->file = hts_open(regions, "rb"); + if ( !reg->file ) + { + fprintf(stderr,"[%s:%d %s] Could not open file: %s\n", __FILE__,__LINE__,__FUNCTION__,regions); + free(reg); + return NULL; + } + + reg->tbx = tbx_index_load(regions); + if ( !reg->tbx ) + { + int len = strlen(regions); + int is_bed = strcasecmp(".bed",regions+len-4) ? 0 : 1; + if ( !is_bed && !strcasecmp(".bed.gz",regions+len-7) ) is_bed = 1; + int ft_type = hts_file_type(regions); + if ( ft_type & FT_VCF ) ito = 1; + + // read the whole file, tabix index is not present + while ( hts_getline(reg->file, KS_SEP_LINE, ®->line) > 0 ) + { + char *chr, *chr_end; + int from, to, ret; + ret = _regions_parse_line(reg->line.s, ichr,ifrom,abs(ito), &chr,&chr_end,&from,&to); + if ( ret < 0 ) + { + if ( ito<0 ) + ret = _regions_parse_line(reg->line.s, ichr,ifrom,ifrom, &chr,&chr_end,&from,&to); + if ( ret<0 ) + { + fprintf(stderr,"[%s:%d] Could not parse the file %s, using the columns %d,%d[,%d]\n", __FILE__,__LINE__,regions,ichr+1,ifrom+1,ito+1); + hts_close(reg->file); reg->file = NULL; free(reg); + return NULL; + } + } + if ( !ret ) continue; + if ( is_bed ) from++; + *chr_end = 0; + _regions_add(reg, chr, from, to); + *chr_end = '\t'; + } + hts_close(reg->file); reg->file = NULL; + if ( !reg->nseqs ) { free(reg); return NULL; } + return reg; + } + + reg->seq_names = (char**) tbx_seqnames(reg->tbx, ®->nseqs); + if ( !reg->seq_hash ) + reg->seq_hash = khash_str2int_init(); + int i; + for (i=0; inseqs; i++) + { + khash_str2int_set(reg->seq_hash,reg->seq_names[i],i); + } + reg->fname = strdup(regions); + reg->is_bin = 1; + return reg; +} + +void bcf_sr_regions_destroy(bcf_sr_regions_t *reg) +{ + int i; + free(reg->fname); + if ( reg->itr ) tbx_itr_destroy(reg->itr); + if ( reg->tbx ) tbx_destroy(reg->tbx); + if ( reg->file ) hts_close(reg->file); + if ( reg->als ) free(reg->als); + if ( reg->als_str.s ) free(reg->als_str.s); + free(reg->line.s); + if ( reg->regs ) + { + // free only in-memory names, tbx names are const + for (i=0; inseqs; i++) + { + free(reg->seq_names[i]); + free(reg->regs[i].regs); + } + } + free(reg->regs); + free(reg->seq_names); + khash_str2int_destroy(reg->seq_hash); + free(reg); +} + +int bcf_sr_regions_seek(bcf_sr_regions_t *reg, const char *seq) +{ + reg->iseq = reg->start = reg->end = -1; + if ( khash_str2int_get(reg->seq_hash, seq, ®->iseq) < 0 ) return -1; // sequence seq not in regions + + // using in-memory regions + if ( reg->regs ) return 0; + + // reading regions from tabix + if ( reg->itr ) tbx_itr_destroy(reg->itr); + reg->itr = tbx_itr_querys(reg->tbx, seq); + if ( reg->itr ) return 0; + + return -1; +} + +int bcf_sr_regions_next(bcf_sr_regions_t *reg) +{ + if ( reg->iseq<0 ) return -1; + reg->start = reg->end = -1; + reg->nals = 0; + + // using in-memory regions + if ( reg->regs ) + { + while ( reg->iseq < reg->nseqs ) + { + reg->regs[reg->iseq].creg++; + if ( reg->regs[reg->iseq].creg < reg->regs[reg->iseq].nregs ) break; + reg->iseq++; + } + if ( reg->iseq >= reg->nseqs ) { reg->iseq = -1; return -1; } // no more regions left + region1_t *creg = ®->regs[reg->iseq].regs[reg->regs[reg->iseq].creg]; + reg->start = creg->start; + reg->end = creg->end; + return 0; + } + + // reading from tabix + char *chr, *chr_end; + int ichr = 0, ifrom = 1, ito = 2, is_bed = 0, from, to; + if ( reg->tbx ) + { + ichr = reg->tbx->conf.sc-1; + ifrom = reg->tbx->conf.bc-1; + ito = reg->tbx->conf.ec-1; + if ( ito<0 ) ito = ifrom; + is_bed = reg->tbx->conf.preset==TBX_UCSC ? 1 : 0; + } + + int ret = 0; + while ( !ret ) + { + if ( reg->itr ) + { + // tabix index present, reading a chromosome block + ret = tbx_itr_next(reg->file, reg->tbx, reg->itr, ®->line); + if ( ret<0 ) { reg->iseq = -1; return -1; } + } + else + { + if ( reg->is_bin ) + { + // Waited for seek which never came. Reopen in text mode and stream + // through the regions, otherwise hts_getline would fail + hts_close(reg->file); + reg->file = hts_open(reg->fname, "r"); + if ( !reg->file ) + { + fprintf(stderr,"[%s:%d %s] Could not open file: %s\n", __FILE__,__LINE__,__FUNCTION__,reg->fname); + reg->file = NULL; + bcf_sr_regions_destroy(reg); + return -1; + } + reg->is_bin = 0; + } + + // tabix index absent, reading the whole file + ret = hts_getline(reg->file, KS_SEP_LINE, ®->line); + if ( ret<0 ) { reg->iseq = -1; return -1; } + } + ret = _regions_parse_line(reg->line.s, ichr,ifrom,ito, &chr,&chr_end,&from,&to); + if ( ret<0 ) + { + fprintf(stderr,"[%s:%d] Could not parse the file %s, using the columns %d,%d,%d\n", __FILE__,__LINE__,reg->fname,ichr+1,ifrom+1,ito+1); + return -1; + } + } + if ( is_bed ) from++; + + *chr_end = 0; + if ( khash_str2int_get(reg->seq_hash, chr, ®->iseq)<0 ) + { + fprintf(stderr,"Broken tabix index? The sequence \"%s\" not in dictionary [%s]\n", chr,reg->line.s); + exit(1); + } + *chr_end = '\t'; + + reg->start = from - 1; + reg->end = to - 1; + return 0; +} + +static int _regions_match_alleles(bcf_sr_regions_t *reg, int als_idx, bcf1_t *rec) +{ + int i = 0, max_len = 0; + if ( !reg->nals ) + { + char *ss = reg->line.s; + while ( inals = 1; + while ( *se && *se!='\t' ) + { + if ( *se==',' ) reg->nals++; + se++; + } + ks_resize(®->als_str, se-ss+1+reg->nals); + reg->als_str.l = 0; + hts_expand(char*,reg->nals,reg->mals,reg->als); + reg->nals = 0; + + se = ss; + while ( *(++se) ) + { + if ( *se=='\t' ) break; + if ( *se!=',' ) continue; + reg->als[reg->nals] = ®->als_str.s[reg->als_str.l]; + kputsn(ss,se-ss,®->als_str); + if ( ®->als_str.s[reg->als_str.l] - reg->als[reg->nals] > max_len ) max_len = ®->als_str.s[reg->als_str.l] - reg->als[reg->nals]; + reg->als_str.l++; + reg->nals++; + ss = ++se; + } + reg->als[reg->nals] = ®->als_str.s[reg->als_str.l]; + kputsn(ss,se-ss,®->als_str); + if ( ®->als_str.s[reg->als_str.l] - reg->als[reg->nals] > max_len ) max_len = ®->als_str.s[reg->als_str.l] - reg->als[reg->nals]; + reg->nals++; + reg->als_type = max_len > 1 ? VCF_INDEL : VCF_SNP; // this is a simplified check, see vcf.c:bcf_set_variant_types + } + int type = bcf_get_variant_types(rec); + if ( reg->als_type & VCF_INDEL ) + return type & VCF_INDEL ? 1 : 0; + return !(type & VCF_INDEL) ? 1 : 0; +} + +int bcf_sr_regions_overlap(bcf_sr_regions_t *reg, const char *seq, int start, int end) +{ + int iseq; + if ( khash_str2int_get(reg->seq_hash, seq, &iseq)<0 ) return -1; // no such sequence + + if ( reg->prev_seq==-1 || iseq!=reg->prev_seq || reg->prev_start > start ) // new chromosome or after a seek + { + // flush regions left on previous chromosome + if ( reg->missed_reg_handler && reg->prev_seq!=-1 && reg->iseq!=-1 ) + bcf_sr_regions_flush(reg); + + bcf_sr_regions_seek(reg, seq); + reg->start = reg->end = -1; + } + if ( reg->prev_seq==iseq && reg->iseq!=iseq ) return -2; // no more regions on this chromosome + reg->prev_seq = reg->iseq; + reg->prev_start = start; + + while ( iseq==reg->iseq && reg->end < start ) + { + if ( bcf_sr_regions_next(reg) < 0 ) return -2; // no more regions left + if ( reg->iseq != iseq ) return -1; // does not overlap any regions + if ( reg->missed_reg_handler && reg->end < start ) reg->missed_reg_handler(reg, reg->missed_reg_data); + } + if ( reg->start <= end ) return 0; // region overlap + return -1; // no overlap +} + +void bcf_sr_regions_flush(bcf_sr_regions_t *reg) +{ + if ( !reg->missed_reg_handler || reg->prev_seq==-1 ) return; + while ( !bcf_sr_regions_next(reg) ) reg->missed_reg_handler(reg, reg->missed_reg_data); + return; +} + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/tabix.1 b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/tabix.1 new file mode 100644 index 0000000000000000000000000000000000000000..1bd9533d93577db59b6d97e8fcf912637c56b27d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/tabix.1 @@ -0,0 +1,132 @@ +.TH tabix 1 "11 May 2010" "tabix-0.2.0" "Bioinformatics tools" +.SH NAME +.PP +bgzip - Block compression/decompression utility +.PP +tabix - Generic indexer for TAB-delimited genome position files +.SH SYNOPSIS +.PP +.B bgzip +.RB [ \-cdhB ] +.RB [ \-b +.IR virtualOffset ] +.RB [ \-s +.IR size ] +.RI [ file ] +.PP +.B tabix +.RB [ \-0lf ] +.RB [ \-p +.R gff|bed|sam|vcf] +.RB [ \-s +.IR seqCol ] +.RB [ \-b +.IR begCol ] +.RB [ \-e +.IR endCol ] +.RB [ \-S +.IR lineSkip ] +.RB [ \-c +.IR metaChar ] +.I in.tab.bgz +.RI [ "region1 " [ "region2 " [ ... "]]]" + +.SH DESCRIPTION +.PP +Tabix indexes a TAB-delimited genome position file +.I in.tab.bgz +and creates an index file +.I in.tab.bgz.tbi +when +.I region +is absent from the command-line. The input data file must be position +sorted and compressed by +.B bgzip +which has a +.BR gzip (1) +like interface. After indexing, tabix is able to quickly retrieve data +lines overlapping +.I regions +specified in the format "chr:beginPos-endPos". Fast data retrieval also +works over network if URI is given as a file name and in this case the +index file will be downloaded if it is not present locally. + +.SH OPTIONS OF TABIX +.TP 10 +.BI "-p " STR +Input format for indexing. Valid values are: gff, bed, sam, vcf and +psltab. This option should not be applied together with any of +.BR \-s ", " \-b ", " \-e ", " \-c " and " \-0 ; +it is not used for data retrieval because this setting is stored in +the index file. [gff] +.TP +.BI "-s " INT +Column of sequence name. Option +.BR \-s ", " \-b ", " \-e ", " \-S ", " \-c " and " \-0 +are all stored in the index file and thus not used in data retrieval. [1] +.TP +.BI "-b " INT +Column of start chromosomal position. [4] +.TP +.BI "-e " INT +Column of end chromosomal position. The end column can be the same as the +start column. [5] +.TP +.BI "-S " INT +Skip first INT lines in the data file. [0] +.TP +.BI "-c " CHAR +Skip lines started with character CHAR. [#] +.TP +.B -0 +Specify that the position in the data file is 0-based (e.g. UCSC files) +rather than 1-based. +.TP +.B -h +Print the header/meta lines. +.TP +.B -B +The second argument is a BED file. When this option is in use, the input +file may not be sorted or indexed. The entire input will be read sequentially. Nonetheless, +with this option, the format of the input must be specificed correctly on the command line. +.TP +.B -f +Force to overwrite the index file if it is present. +.TP +.B -l +List the sequence names stored in the index file. +.RE + +.SH EXAMPLE +(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz; + +tabix -p gff sorted.gff.gz; + +tabix sorted.gff.gz chr1:10,000,000-20,000,000; + +.SH NOTES +It is straightforward to achieve overlap queries using the standard +B-tree index (with or without binning) implemented in all SQL databases, +or the R-tree index in PostgreSQL and Oracle. But there are still many +reasons to use tabix. Firstly, tabix directly works with a lot of widely +used TAB-delimited formats such as GFF/GTF and BED. We do not need to +design database schema or specialized binary formats. Data do not need +to be duplicated in different formats, either. Secondly, tabix works on +compressed data files while most SQL databases do not. The GenCode +annotation GTF can be compressed down to 4%. Thirdly, tabix is +fast. The same indexing algorithm is known to work efficiently for an +alignment with a few billion short reads. SQL databases probably cannot +easily handle data at this scale. Last but not the least, tabix supports +remote data retrieval. One can put the data file and the index at an FTP +or HTTP server, and other users or even web services will be able to get +a slice without downloading the entire file. + +.SH AUTHOR +.PP +Tabix was written by Heng Li. The BGZF library was originally +implemented by Bob Handsaker and modified by Heng Li for remote file +access and in-memory caching. + +.SH SEE ALSO +.PP +.BR samtools (1) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/tabix.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/tabix.c new file mode 100644 index 0000000000000000000000000000000000000000..2a30fed16b25f4b2f03fe42a846f794e3e5ef9f2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/tabix.c @@ -0,0 +1,374 @@ +#include +#include +#include +#include +#include +#include +#include +#include +#include "htslib/tbx.h" +#include "htslib/sam.h" +#include "htslib/vcf.h" +#include "htslib/kseq.h" +#include "htslib/bgzf.h" +#include "htslib/hts.h" + +typedef struct +{ + int min_shift; +} +args_t; + +static void error(const char *format, ...) +{ + va_list ap; + va_start(ap, format); + vfprintf(stderr, format, ap); + va_end(ap); + exit(EXIT_FAILURE); +} + + +#define IS_GFF (1<<0) +#define IS_BED (1<<1) +#define IS_SAM (1<<2) +#define IS_VCF (1<<3) +#define IS_BCF (1<<4) +#define IS_BAM (1<<5) +#define IS_TXT (IS_GFF|IS_BED|IS_SAM|IS_VCF) + +int file_type(const char *fname) +{ + int l = strlen(fname); + int strcasecmp(const char *s1, const char *s2); + if (l>=7 && strcasecmp(fname+l-7, ".gff.gz") == 0) return IS_GFF; + else if (l>=7 && strcasecmp(fname+l-7, ".bed.gz") == 0) return IS_BED; + else if (l>=7 && strcasecmp(fname+l-7, ".sam.gz") == 0) return IS_SAM; + else if (l>=7 && strcasecmp(fname+l-7, ".vcf.gz") == 0) return IS_VCF; + else if (l>=4 && strcasecmp(fname+l-4, ".bcf") == 0) return IS_BCF; + else if (l>=4 && strcasecmp(fname+l-4, ".bam") == 0) return IS_BAM; + return 0; +} + +#define PRINT_HEADER 1 +#define HEADER_ONLY 2 +static int query_regions(char **argv, int argc, int mode) +{ + char *fname = argv[0]; + int i, ftype = file_type(fname); + + if ( ftype & IS_TXT || !ftype ) + { + htsFile *fp = hts_open(fname,"r"); + if ( !fp ) error("Could not read %s\n", fname); + tbx_t *tbx = tbx_index_load(fname); + if ( !tbx ) error("Could not load .tbi index of %s\n", fname); + kstring_t str = {0,0,0}; + if ( mode ) + { + while ( hts_getline(fp, KS_SEP_LINE, &str) >= 0 ) + { + if ( !str.l || str.s[0]!=tbx->conf.meta_char ) break; + puts(str.s); + } + } + if ( mode!=HEADER_ONLY ) + { + for (i=1; i= 0) puts(str.s); + tbx_itr_destroy(itr); + } + } + free(str.s); + if ( hts_close(fp) ) error("hts_close returned non-zero status: %s\n", fname); + tbx_destroy(tbx); + } + else if ( ftype==IS_BCF ) // output uncompressed VCF + { + htsFile *fp = hts_open(fname,"r"); + if ( !fp ) error("Could not read %s\n", fname); + htsFile *out = hts_open("-","w"); + if ( !out ) error("Could not open stdout\n", fname); + hts_idx_t *idx = bcf_index_load(fname); + if ( !idx ) error("Could not load .csi index of %s\n", fname); + bcf_hdr_t *hdr = bcf_hdr_read(fp); + if ( !hdr ) error("Could not read the header: %s\n", fname); + if ( mode ) + { + bcf_hdr_write(out,hdr); + } + if ( mode!=HEADER_ONLY ) + { + bcf1_t *rec = bcf_init(); + for (i=1; i=0 ) bcf_write(out,hdr,rec); + tbx_itr_destroy(itr); + } + bcf_destroy(rec); + } + if ( hts_close(fp) ) error("hts_close returned non-zero status: %s\n", fname); + if ( hts_close(out) ) error("hts_close returned non-zero status for stdout\n"); + bcf_hdr_destroy(hdr); + hts_idx_destroy(idx); + } + else if ( ftype==IS_BAM ) // todo: BAM + error("Please use \"samtools view\" for querying BAM files.\n"); + return 0; +} +static int query_chroms(char *fname) +{ + const char **seq; + int i, nseq, ftype = file_type(fname); + if ( ftype & IS_TXT || !ftype ) + { + tbx_t *tbx = tbx_index_load(fname); + if ( !tbx ) error("Could not load .tbi index of %s\n", fname); + seq = tbx_seqnames(tbx, &nseq); + for (i=0; iblock_length ) return -1; + + char *buffer = fp->uncompressed_block; + int skip_until = 0; + + // Skip the header: find out the position of the data block + if ( buffer[0]==conf->meta_char ) + { + skip_until = 1; + while (1) + { + if ( buffer[skip_until]=='\n' ) + { + skip_until++; + if ( skip_until>=fp->block_length ) + { + if ( bgzf_read_block(fp) != 0 || !fp->block_length ) error("FIXME: No body in the file: %s\n", fname); + skip_until = 0; + } + // The header has finished + if ( buffer[skip_until]!=conf->meta_char ) break; + } + skip_until++; + if ( skip_until>=fp->block_length ) + { + if (bgzf_read_block(fp) != 0 || !fp->block_length) error("FIXME: No body in the file: %s\n", fname); + skip_until = 0; + } + } + } + + // Output the new header + FILE *hdr = fopen(header,"r"); + if ( !hdr ) error("%s: %s", header,strerror(errno)); + int page_size = getpagesize(); + char *buf = valloc(page_size); + BGZF *bgzf_out = bgzf_dopen(fileno(stdout), "w"); + ssize_t nread; + while ( (nread=fread(buf,1,page_size-1,hdr))>0 ) + { + if ( nreaderrcode); + } + if ( fclose(hdr) ) error("close failed: %s\n", header); + + // Output all remainig data read with the header block + if ( fp->block_length - skip_until > 0 ) + { + if (bgzf_write(bgzf_out, buffer+skip_until, fp->block_length-skip_until) < 0) error("Error: %d\n",fp->errcode); + } + if (bgzf_flush(bgzf_out) < 0) error("Error: %d\n",bgzf_out->errcode); + + while (1) + { + nread = bgzf_raw_read(fp, buf, page_size); + if ( nread<=0 ) break; + + int count = bgzf_raw_write(bgzf_out, buf, nread); + if (count != nread) error("Write failed, wrote %d instead of %d bytes.\n", count,(int)nread); + } + if (bgzf_close(bgzf_out) < 0) error("Error: %d\n",bgzf_out->errcode); + if (bgzf_close(fp) < 0) error("Error: %d\n",fp->errcode); + } + else + error("todo: reheader BCF, BAM\n"); // BCF is difficult, records contain pointers to the header. + return 0; +} + +static int usage(void) +{ + fprintf(stderr, "\n"); + fprintf(stderr, "Version: %s\n", hts_version()); + fprintf(stderr, "Usage: tabix [OPTIONS] [FILE] [REGION [...]]\n"); + fprintf(stderr, "Options:\n"); + fprintf(stderr, " -0, --zero-based coordinates are zero-based\n"); + fprintf(stderr, " -b, --begin INT column number for region start [4]\n"); + fprintf(stderr, " -c, --comment CHAR skip comment lines starting with CHAR [null]\n"); + fprintf(stderr, " -e, --end INT column number for region end (if no end, set INT to -b) [5]\n"); + fprintf(stderr, " -f, --force overwrite existing index without asking\n"); + fprintf(stderr, " -h, --print-header print also the header lines\n"); + fprintf(stderr, " -H, --only-header print only the header lines\n"); + fprintf(stderr, " -l, --list-chroms list chromosome names\n"); + fprintf(stderr, " -m, --min-shift INT set the minimal interval size to 1<= 0) + { + switch (c) + { + case 'r': reheader = optarg; break; + case 'h': mode = PRINT_HEADER; break; + case 'H': mode = HEADER_ONLY; break; + case 'l': list_chroms = 1; break; + case '0': conf.preset |= TBX_UCSC; break; + case 'b': conf.bc = atoi(optarg); break; + case 'e': conf.ec = atoi(optarg); break; + case 'c': conf.meta_char = *optarg; break; + case 'f': is_force = 1; break; + case 'm': min_shift = atoi(optarg); break; + case 'p': + if (strcmp(optarg, "gff") == 0) conf_ptr = &tbx_conf_gff; + else if (strcmp(optarg, "bed") == 0) conf_ptr = &tbx_conf_bed; + else if (strcmp(optarg, "sam") == 0) conf_ptr = &tbx_conf_sam; + else if (strcmp(optarg, "vcf") == 0) conf_ptr = &tbx_conf_vcf; + else error("The preset string not recognised: '%s'\n", optarg); + break; + case 's': conf.sc = atoi(optarg); break; + case 'S': conf.line_skip = atoi(optarg); break; + default: return usage(); + } + } + + if ( optind==argc ) return usage(); + + if ( list_chroms ) + return query_chroms(argv[optind]); + + if ( argc > optind+1 || mode==HEADER_ONLY ) + return query_regions(&argv[optind], argc-optind, mode); + + char *fname = argv[optind]; + int ftype = file_type(fname); + if ( !conf_ptr ) // no preset given + { + if ( ftype==IS_GFF ) conf_ptr = &tbx_conf_gff; + else if ( ftype==IS_BED ) conf_ptr = &tbx_conf_bed; + else if ( ftype==IS_SAM ) conf_ptr = &tbx_conf_sam; + else if ( ftype==IS_VCF ) conf_ptr = &tbx_conf_vcf; + else if ( ftype==IS_BCF ) + { + if ( min_shift <= 0 ) min_shift = 14; + } + else if ( ftype==IS_BAM ) + { + if ( min_shift <= 0 ) min_shift = 14; + } + } + if ( reheader ) + return reheader_file(fname, reheader, ftype, conf_ptr); + + if ( conf_ptr ) + conf = *conf_ptr; + + char *suffix = min_shift <= 0 ? ".tbi" : (ftype==IS_BAM ? ".bai" : ".csi"); + char *idx_fname = calloc(strlen(fname) + 5, 1); + strcat(strcpy(idx_fname, fname), suffix); + + struct stat stat_tbi, stat_file; + if ( !is_force && stat(idx_fname, &stat_tbi)==0 ) + { + // Before complaining about existing index, check if the VCF file isn't + // newer. This is a common source of errors, people tend not to notice + // that tabix failed + stat(fname, &stat_file); + if ( stat_file.st_mtime <= stat_tbi.st_mtime ) + error("[tabix] the index file exists. Please use '-f' to overwrite.\n"); + } + free(idx_fname); + + if ( min_shift > 0 ) // CSI index + { + if ( ftype==IS_BCF ) + { + if ( bcf_index_build(fname, min_shift)!=0 ) error("bcf_index_build failed: %s\n", fname); + return 0; + } + if ( ftype==IS_BAM ) + { + if ( bam_index_build(fname, min_shift)!=0 ) error("bam_index_build failed: %s\n", fname); + return 0; + } + if ( tbx_index_build(fname, min_shift, &conf)!=0 ) error("tbx_index_build failed: %s\n", fname); + return 0; + } + else + { + if ( tbx_index_build(fname, min_shift, &conf) ) error("tbx_index_build failed: %s\n", fname); + return 0; + } + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/tbx.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/tbx.c new file mode 100644 index 0000000000000000000000000000000000000000..035cb689ace0b16abc947495d3b21ed6c6c2b8f3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/tbx.c @@ -0,0 +1,290 @@ +#include +#include +#include +#include +#include +#include "htslib/tbx.h" +#include "htslib/bgzf.h" + +#include "htslib/khash.h" +KHASH_DECLARE(s2i, kh_cstr_t, int64_t) + +tbx_conf_t tbx_conf_gff = { 0, 1, 4, 5, '#', 0 }; +tbx_conf_t tbx_conf_bed = { TBX_UCSC, 1, 2, 3, '#', 0 }; +tbx_conf_t tbx_conf_psltbl = { TBX_UCSC, 15, 17, 18, '#', 0 }; +tbx_conf_t tbx_conf_sam = { TBX_SAM, 3, 4, 0, '@', 0 }; +tbx_conf_t tbx_conf_vcf = { TBX_VCF, 1, 2, 0, '#', 0 }; + +typedef struct { + int64_t beg, end; + char *ss, *se; + int tid; +} tbx_intv_t; + +static inline int get_tid(tbx_t *tbx, const char *ss, int is_add) +{ + khint_t k; + khash_t(s2i) *d; + if (tbx->dict == 0) tbx->dict = kh_init(s2i); + d = (khash_t(s2i)*)tbx->dict; + if (is_add) { + int absent; + k = kh_put(s2i, d, ss, &absent); + if (absent) { + kh_key(d, k) = strdup(ss); + kh_val(d, k) = kh_size(d) - 1; + } + } else k = kh_get(s2i, d, ss); + return k == kh_end(d)? -1 : kh_val(d, k); +} + +int tbx_name2id(tbx_t *tbx, const char *ss) +{ + return get_tid(tbx, ss, 0); +} + +int tbx_parse1(const tbx_conf_t *conf, int len, char *line, tbx_intv_t *intv) +{ + int i, b = 0, id = 1, ncols = 0; + char *s; + intv->ss = intv->se = 0; intv->beg = intv->end = -1; + for (i = 0; i <= len; ++i) { + if (line[i] == '\t' || line[i] == 0) { + ++ncols; + if (id == conf->sc) { + intv->ss = line + b; intv->se = line + i; + } else if (id == conf->bc) { + // here ->beg is 0-based. + intv->beg = intv->end = strtol(line + b, &s, 0); + if ( s==line+b ) return -1; // expected int + if (!(conf->preset&TBX_UCSC)) --intv->beg; + else ++intv->end; + if (intv->beg < 0) intv->beg = 0; + if (intv->end < 1) intv->end = 1; + } else { + if ((conf->preset&0xffff) == TBX_GENERIC) { + if (id == conf->ec) + { + intv->end = strtol(line + b, &s, 0); + if ( s==line+b ) return -1; // expected int + } + } else if ((conf->preset&0xffff) == TBX_SAM) { + if (id == 6) { // CIGAR + int l = 0, op; + char *t; + for (s = line + b; s < line + i;) { + long x = strtol(s, &t, 10); + op = toupper(*t); + if (op == 'M' || op == 'D' || op == 'N') l += x; + s = t + 1; + } + if (l == 0) l = 1; + intv->end = intv->beg + l; + } + } else if ((conf->preset&0xffff) == TBX_VCF) { + if (id == 4) { + if (b < i) intv->end = intv->beg + (i - b); + } else if (id == 8) { // look for "END=" + int c = line[i]; + line[i] = 0; + s = strstr(line + b, "END="); + if (s == line + b) s += 4; + else if (s) { + s = strstr(line + b, ";END="); + if (s) s += 5; + } + if (s) intv->end = strtol(s, &s, 0); + line[i] = c; + } + } + } + b = i + 1; + ++id; + } + } + if (intv->ss == 0 || intv->se == 0 || intv->beg < 0 || intv->end < 0) return -1; + return 0; +} + +static inline int get_intv(tbx_t *tbx, kstring_t *str, tbx_intv_t *intv, int is_add) +{ + if (tbx_parse1(&tbx->conf, str->l, str->s, intv) == 0) { + int c = *intv->se; + *intv->se = '\0'; intv->tid = get_tid(tbx, intv->ss, is_add); *intv->se = c; + return (intv->tid >= 0 && intv->beg >= 0 && intv->end >= 0)? 0 : -1; + } else { + char *type = NULL; + switch (tbx->conf.preset&0xffff) + { + case TBX_SAM: type = "TBX_SAM"; break; + case TBX_VCF: type = "TBX_VCF"; break; + case TBX_UCSC: type = "TBX_UCSC"; break; + default: type = "TBX_GENERIC"; break; + } + fprintf(stderr, "[E::%s] failed to parse %s, was wrong -p [type] used?\nThe offending line was: \"%s\"\n", __func__, type, str->s); + return -1; + } +} + +int tbx_readrec(BGZF *fp, void *tbxv, void *sv, int *tid, int *beg, int *end) +{ + tbx_t *tbx = (tbx_t *) tbxv; + kstring_t *s = (kstring_t *) sv; + int ret; + if ((ret = bgzf_getline(fp, '\n', s)) >= 0) { + tbx_intv_t intv; + get_intv(tbx, s, &intv, 0); + *tid = intv.tid; *beg = intv.beg; *end = intv.end; + } + return ret; +} + +void tbx_set_meta(tbx_t *tbx) +{ + int i, l = 0, l_nm; + uint32_t x[7]; + char **name; + uint8_t *meta; + khint_t k; + khash_t(s2i) *d = (khash_t(s2i)*)tbx->dict; + + memcpy(x, &tbx->conf, 24); + name = (char**)malloc(sizeof(char*) * kh_size(d)); + for (k = kh_begin(d), l = 0; k != kh_end(d); ++k) { + if (!kh_exist(d, k)) continue; + name[kh_val(d, k)] = (char*)kh_key(d, k); + l += strlen(kh_key(d, k)) + 1; // +1 to include '\0' + } + l_nm = x[6] = l; + meta = (uint8_t*)malloc(l_nm + 28); + if (ed_is_big()) + for (i = 0; i < 7; ++i) + x[i] = ed_swap_4(x[i]); + memcpy(meta, x, 28); + for (l = 28, i = 0; i < (int)kh_size(d); ++i) { + int x = strlen(name[i]) + 1; + memcpy(meta + l, name[i], x); + l += x; + } + free(name); + hts_idx_set_meta(tbx->idx, l, meta, 0); +} + +tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf) +{ + tbx_t *tbx; + kstring_t str; + int ret, first = 0, n_lvls, fmt; + int64_t lineno = 0; + uint64_t last_off = 0; + tbx_intv_t intv; + + str.s = 0; str.l = str.m = 0; + tbx = (tbx_t*)calloc(1, sizeof(tbx_t)); + tbx->conf = *conf; + if (min_shift > 0) n_lvls = (TBX_MAX_SHIFT - min_shift + 2) / 3, fmt = HTS_FMT_CSI; + else min_shift = 14, n_lvls = 5, fmt = HTS_FMT_TBI; + while ((ret = bgzf_getline(fp, '\n', &str)) >= 0) { + ++lineno; + if (lineno <= tbx->conf.line_skip || str.s[0] == tbx->conf.meta_char) { + last_off = bgzf_tell(fp); + continue; + } + if (first == 0) { + tbx->idx = hts_idx_init(0, fmt, last_off, min_shift, n_lvls); + first = 1; + } + get_intv(tbx, &str, &intv, 1); + ret = hts_idx_push(tbx->idx, intv.tid, intv.beg, intv.end, bgzf_tell(fp), 1); + if (ret < 0) + { + free(str.s); + tbx_destroy(tbx); + return NULL; + } + } + if ( !tbx->idx ) tbx->idx = hts_idx_init(0, fmt, last_off, min_shift, n_lvls); // empty file + if ( !tbx->dict ) tbx->dict = kh_init(s2i); + hts_idx_finish(tbx->idx, bgzf_tell(fp)); + tbx_set_meta(tbx); + free(str.s); + return tbx; +} + +void tbx_destroy(tbx_t *tbx) +{ + khash_t(s2i) *d = (khash_t(s2i)*)tbx->dict; + if (d != NULL) + { + khint_t k; + for (k = kh_begin(d); k != kh_end(d); ++k) + if (kh_exist(d, k)) free((char*)kh_key(d, k)); + } + hts_idx_destroy(tbx->idx); + kh_destroy(s2i, d); + free(tbx); +} + +int tbx_index_build(const char *fn, int min_shift, const tbx_conf_t *conf) +{ + tbx_t *tbx; + BGZF *fp; + if ( bgzf_is_bgzf(fn)!=1 ) { fprintf(stderr,"Not a BGZF file: %s\n", fn); return -1; } + if ((fp = bgzf_open(fn, "r")) == 0) return -1; + if ( !fp->is_compressed ) { bgzf_close(fp); return -1; } + tbx = tbx_index(fp, min_shift, conf); + bgzf_close(fp); + if ( !tbx ) return -1; + hts_idx_save(tbx->idx, fn, min_shift > 0? HTS_FMT_CSI : HTS_FMT_TBI); + tbx_destroy(tbx); + return 0; +} + +tbx_t *tbx_index_load(const char *fn) +{ + tbx_t *tbx; + uint8_t *meta; + char *nm, *p; + uint32_t x[7]; + int l_meta, l_nm; + tbx = (tbx_t*)calloc(1, sizeof(tbx_t)); + tbx->idx = hts_idx_load(fn, HTS_FMT_TBI); + if ( !tbx->idx ) + { + free(tbx); + return NULL; + } + meta = hts_idx_get_meta(tbx->idx, &l_meta); + memcpy(x, meta, 28); + memcpy(&tbx->conf, x, 24); + p = nm = (char*)meta + 28; + l_nm = x[6]; + for (; p - nm < l_nm; p += strlen(p) + 1) get_tid(tbx, p, 1); + return tbx; +} + +const char **tbx_seqnames(tbx_t *tbx, int *n) +{ + khash_t(s2i) *d = (khash_t(s2i)*)tbx->dict; + if (d == NULL) + { + *n = 0; + return NULL; + } + int tid, m = kh_size(d); + const char **names = (const char**) calloc(m,sizeof(const char*)); + khint_t k; + for (k=kh_begin(d); k +#include +#include +#include +#include +#include +#include +#include "htslib/kstring.h" +#include "htslib/bgzf.h" +#include "htslib/vcf.h" +#include "htslib/tbx.h" +#include "htslib/hfile.h" + +#include "htslib/khash.h" +KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t) + typedef khash_t(vdict) vdict_t; + +#include "htslib/kseq.h" +KSTREAM_DECLARE(gzFile, gzread) + + uint32_t bcf_float_missing = 0x7F800001; + uint32_t bcf_float_vector_end = 0x7F800002; + uint8_t bcf_type_shift[] = { 0, 0, 1, 2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }; +static bcf_idinfo_t bcf_idinfo_def = { .info = { 15, 15, 15 }, .hrec = { NULL, NULL, NULL}, .id = -1 }; + +/************************* + *** VCF header parser *** + *************************/ + +int bcf_hdr_sync(bcf_hdr_t *h); + +int bcf_hdr_add_sample(bcf_hdr_t *h, const char *s) +{ + if ( !s ) + { + bcf_hdr_sync(h); + return 0; + } + + const char *ss = s; + while ( !*ss && isspace(*ss) ) ss++; + if ( !*ss ) + { + fprintf(stderr,"[W::%s] Empty sample name: trailing spaces/tabs in the header line?\n", __func__); + abort(); + } + + vdict_t *d = (vdict_t*)h->dict[BCF_DT_SAMPLE]; + int ret; + char *sdup = strdup(s); + int k = kh_put(vdict, d, sdup, &ret); + if (ret) { // absent + kh_val(d, k) = bcf_idinfo_def; + kh_val(d, k).id = kh_size(d) - 1; + } else { + if (hts_verbose >= 2) + fprintf(stderr, "[W::%s] Duplicated sample name '%s'. Skipped.\n", __func__, s); + free(sdup); + return -1; + } + int n = kh_size(d); + h->samples = (char**) realloc(h->samples,sizeof(char*)*n); + h->samples[n-1] = sdup; + return 0; +} + +void bcf_hdr_parse_sample_line(bcf_hdr_t *h, const char *str) +{ + int i = 0; + const char *p, *q; + // add samples + for (p = q = str;; ++q) { + if (*q != '\t' && *q != 0 && *q != '\n') continue; + if (++i > 9) { + char *s = (char*)malloc(q - p + 1); + strncpy(s, p, q - p); + s[q - p] = 0; + bcf_hdr_add_sample(h,s); + free(s); + } + if (*q == 0 || *q == '\n') break; + p = q + 1; + } + bcf_hdr_add_sample(h,NULL); +} + +int bcf_hdr_sync(bcf_hdr_t *h) +{ + int i; + for (i = 0; i < 3; i++) + { + vdict_t *d = (vdict_t*)h->dict[i]; + khint_t k; + + // find out the largest id, there may be holes because of IDX + int max_id = -1; + for (k=kh_begin(d); k= h->n[i] ) + { + h->id[i] = (bcf_idpair_t*)realloc(h->id[i], (max_id+1)*sizeof(bcf_idpair_t)); + for (k=h->n[i]; k<=max_id; k++) + { + h->id[i][k].key = NULL; + h->id[i][k].val = NULL; + } + h->n[i] = max_id+1; + } + for (k=kh_begin(d); kid[i][kh_val(d,k).id].key = kh_key(d,k); + h->id[i][kh_val(d,k).id].val = &kh_val(d,k); + } + } + return 0; +} + +void bcf_hrec_destroy(bcf_hrec_t *hrec) +{ + free(hrec->key); + if ( hrec->value ) free(hrec->value); + int i; + for (i=0; inkeys; i++) + { + free(hrec->keys[i]); + free(hrec->vals[i]); + } + free(hrec->keys); + free(hrec->vals); + free(hrec); +} + +// Copies all fields except IDX. +bcf_hrec_t *bcf_hrec_dup(bcf_hrec_t *hrec) +{ + bcf_hrec_t *out = (bcf_hrec_t*) calloc(1,sizeof(bcf_hrec_t)); + out->type = hrec->type; + if ( hrec->key ) out->key = strdup(hrec->key); + if ( hrec->value ) out->value = strdup(hrec->value); + out->nkeys = hrec->nkeys; + out->keys = (char**) malloc(sizeof(char*)*hrec->nkeys); + out->vals = (char**) malloc(sizeof(char*)*hrec->nkeys); + int i, j = 0; + for (i=0; inkeys; i++) + { + if ( hrec->keys[i] && !strcmp("IDX",hrec->keys[i]) ) continue; + if ( hrec->keys[i] ) out->keys[j] = strdup(hrec->keys[i]); + if ( hrec->vals[i] ) out->vals[j] = strdup(hrec->vals[i]); + j++; + } + if ( i!=j ) out->nkeys--; // IDX was omitted + return out; +} + +void bcf_hrec_debug(FILE *fp, bcf_hrec_t *hrec) +{ + fprintf(fp, "key=[%s] value=[%s]", hrec->key, hrec->value?hrec->value:""); + int i; + for (i=0; inkeys; i++) + fprintf(fp, "\t[%s]=[%s]", hrec->keys[i],hrec->vals[i]); + fprintf(fp, "\n"); +} + +void bcf_header_debug(bcf_hdr_t *hdr) +{ + int i, j; + for (i=0; inhrec; i++) + { + if ( !hdr->hrec[i]->value ) + { + fprintf(stderr, "##%s=<", hdr->hrec[i]->key); + fprintf(stderr,"%s=%s", hdr->hrec[i]->keys[0], hdr->hrec[i]->vals[0]); + for (j=1; jhrec[i]->nkeys; j++) + fprintf(stderr,",%s=%s", hdr->hrec[i]->keys[j], hdr->hrec[i]->vals[j]); + fprintf(stderr,">\n"); + } + else + fprintf(stderr,"##%s=%s\n", hdr->hrec[i]->key,hdr->hrec[i]->value); + } +} + +void bcf_hrec_add_key(bcf_hrec_t *hrec, const char *str, int len) +{ + int n = ++hrec->nkeys; + hrec->keys = (char**) realloc(hrec->keys, sizeof(char*)*n); + hrec->vals = (char**) realloc(hrec->vals, sizeof(char*)*n); + assert( len ); + hrec->keys[n-1] = (char*) malloc((len+1)*sizeof(char)); + memcpy(hrec->keys[n-1],str,len); + hrec->keys[n-1][len] = 0; + hrec->vals[n-1] = NULL; +} + +void bcf_hrec_set_val(bcf_hrec_t *hrec, int i, const char *str, int len, int is_quoted) +{ + if ( !str ) { hrec->vals[i] = NULL; return; } + if ( hrec->vals[i] ) free(hrec->vals[i]); + if ( is_quoted ) + { + hrec->vals[i] = (char*) malloc((len+3)*sizeof(char)); + hrec->vals[i][0] = '"'; + memcpy(&hrec->vals[i][1],str,len); + hrec->vals[i][len+1] = '"'; + hrec->vals[i][len+2] = 0; + } + else + { + hrec->vals[i] = (char*) malloc((len+1)*sizeof(char)); + memcpy(hrec->vals[i],str,len); + hrec->vals[i][len] = 0; + } +} + +void hrec_add_idx(bcf_hrec_t *hrec, int idx) +{ + int n = ++hrec->nkeys; + hrec->keys = (char**) realloc(hrec->keys, sizeof(char*)*n); + hrec->vals = (char**) realloc(hrec->vals, sizeof(char*)*n); + hrec->keys[n-1] = strdup("IDX"); + kstring_t str = {0,0,0}; + kputw(idx, &str); + hrec->vals[n-1] = str.s; +} + +int bcf_hrec_find_key(bcf_hrec_t *hrec, const char *key) +{ + int i; + for (i=0; inkeys; i++) + if ( !strcasecmp(key,hrec->keys[i]) ) return i; + return -1; +} + +static inline int is_escaped(const char *min, const char *str) +{ + int n = 0; + while ( --str>=min && *str=='\\' ) n++; + return n%2; +} + +bcf_hrec_t *bcf_hdr_parse_line(const bcf_hdr_t *h, const char *line, int *len) +{ + const char *p = line; + if (p[0] != '#' || p[1] != '#') { *len = 0; return NULL; } + p += 2; + + const char *q = p; + while ( *q && *q!='=' ) q++; + int n = q-p; + if ( *q!='=' || !n ) { *len = q-line+1; return NULL; } // wrong format + + bcf_hrec_t *hrec = (bcf_hrec_t*) calloc(1,sizeof(bcf_hrec_t)); + hrec->key = (char*) malloc(sizeof(char)*(n+1)); + memcpy(hrec->key,p,n); + hrec->key[n] = 0; + + p = ++q; + if ( *p!='<' ) // generic field, e.g. ##samtoolsVersion=0.1.18-r579 + { + while ( *q && *q!='\n' ) q++; + hrec->value = (char*) malloc((q-p+1)*sizeof(char)); + memcpy(hrec->value, p, q-p); + hrec->value[q-p] = 0; + *len = q-line+1; + return hrec; + } + + // structured line, e.g. ##INFO= + int nopen = 1; + while ( *q && *q!='\n' && nopen ) + { + p = ++q; + while ( *q && *q!='=' ) q++; + n = q-p; + if ( *q!='=' || !n ) { *len = q-line+1; bcf_hrec_destroy(hrec); return NULL; } // wrong format + bcf_hrec_add_key(hrec, p, q-p); + p = ++q; + int quoted = *p=='"' ? 1 : 0; + if ( quoted ) p++, q++; + while (1) + { + if ( !*q ) break; + if ( quoted ) { if ( *q=='"' && !is_escaped(p,q) ) break; } + else + { + if ( *q=='<' ) nopen++; + if ( *q=='>' ) nopen--; + if ( !nopen ) break; + if ( *q==',' && nopen==1 ) break; + } + q++; + } + bcf_hrec_set_val(hrec, hrec->nkeys-1, p, q-p, quoted); + if ( quoted ) q++; + if ( *q=='>' ) { nopen--; q++; } + } + *len = q-line+1; + return hrec; +} + +// returns: 1 when hdr needs to be synced, 0 otherwise +int bcf_hdr_register_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec) +{ + // contig + int i,j,k, ret; + char *str; + if ( !strcmp(hrec->key, "contig") ) + { + hrec->type = BCF_HL_CTG; + + // Get the contig ID ($str) and length ($j) + i = bcf_hrec_find_key(hrec,"length"); + if ( i<0 ) return 0; + if ( sscanf(hrec->vals[i],"%d",&j)!=1 ) return 0; + + i = bcf_hrec_find_key(hrec,"ID"); + if ( i<0 ) return 0; + str = strdup(hrec->vals[i]); + + // Register in the dictionary + vdict_t *d = (vdict_t*)hdr->dict[BCF_DT_CTG]; + k = kh_put(vdict, d, str, &ret); + if ( !ret ) { free(str); return 0; } // already present + + int idx = bcf_hrec_find_key(hrec,"IDX"); + if ( idx!=-1 ) + { + char *tmp = hrec->vals[idx]; + idx = strtol(hrec->vals[idx], &tmp, 10); + if ( *tmp ) + { + fprintf(stderr,"[%s:%d %s] Error parsing the IDX tag, skipping.\n", __FILE__,__LINE__,__FUNCTION__); + return 0; + } + } + else + { + idx = kh_size(d) - 1; + hrec_add_idx(hrec, idx); + } + + kh_val(d, k) = bcf_idinfo_def; + kh_val(d, k).id = idx; + kh_val(d, k).info[0] = i; + kh_val(d, k).hrec[0] = hrec; + + return 1; + } + + if ( !strcmp(hrec->key, "INFO") ) hrec->type = BCF_HL_INFO; + else if ( !strcmp(hrec->key, "FILTER") ) hrec->type = BCF_HL_FLT; + else if ( !strcmp(hrec->key, "FORMAT") ) hrec->type = BCF_HL_FMT; + else if ( hrec->nkeys>0 ) { hrec->type = BCF_HL_STR; return 1; } + else return 0; + + // INFO/FILTER/FORMAT + char *id = NULL; + int type = -1, num = -1, var = -1, idx = -1; + for (i=0; inkeys; i++) + { + if ( !strcmp(hrec->keys[i], "ID") ) id = hrec->vals[i]; + else if ( !strcmp(hrec->keys[i], "IDX") ) + { + char *tmp = hrec->vals[i]; + idx = strtol(hrec->vals[i], &tmp, 10); + if ( *tmp ) + { + fprintf(stderr,"[%s:%d %s] Error parsing the IDX tag, skipping.\n", __FILE__,__LINE__,__FUNCTION__); + return 0; + } + } + else if ( !strcmp(hrec->keys[i], "Type") ) + { + if ( !strcmp(hrec->vals[i], "Integer") ) type = BCF_HT_INT; + else if ( !strcmp(hrec->vals[i], "Float") ) type = BCF_HT_REAL; + else if ( !strcmp(hrec->vals[i], "String") ) type = BCF_HT_STR; + else if ( !strcmp(hrec->vals[i], "Flag") ) type = BCF_HT_FLAG; + else + { + fprintf(stderr, "[E::%s] The type \"%s\" not supported, assuming \"String\"\n", __func__, hrec->vals[i]); + type = BCF_HT_STR; + } + } + else if ( !strcmp(hrec->keys[i], "Number") ) + { + if ( !strcmp(hrec->vals[i],"A") ) var = BCF_VL_A; + else if ( !strcmp(hrec->vals[i],"R") ) var = BCF_VL_R; + else if ( !strcmp(hrec->vals[i],"G") ) var = BCF_VL_G; + else if ( !strcmp(hrec->vals[i],".") ) var = BCF_VL_VAR; + else + { + sscanf(hrec->vals[i],"%d",&num); + var = BCF_VL_FIXED; + } + if (var != BCF_VL_FIXED) num = 0xfffff; + + } + } + uint32_t info = (uint32_t)num<<12 | var<<8 | type<<4 | hrec->type; + + if ( !id ) return 0; + str = strdup(id); + + vdict_t *d = (vdict_t*)hdr->dict[BCF_DT_ID]; + k = kh_put(vdict, d, str, &ret); + if ( !ret ) + { + // already present + free(str); + if ( kh_val(d, k).hrec[info&0xf] ) return 0; + kh_val(d, k).info[info&0xf] = info; + kh_val(d, k).hrec[info&0xf] = hrec; + return 1; + } + kh_val(d, k) = bcf_idinfo_def; + kh_val(d, k).info[info&0xf] = info; + kh_val(d, k).hrec[info&0xf] = hrec; + kh_val(d, k).id = idx==-1 ? kh_size(d) - 1 : idx; + + if ( idx==-1 ) hrec_add_idx(hrec, kh_val(d, k).id); + + return 1; +} + +int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec) +{ + hrec->type = BCF_HL_GEN; + if ( !bcf_hdr_register_hrec(hdr,hrec) ) + { + // If one of the hashed field, then it is already present + if ( hrec->type != BCF_HL_GEN ) + { + bcf_hrec_destroy(hrec); + return 0; + } + + // Is one of the generic fields and already present? + int i; + for (i=0; inhrec; i++) + { + if ( hdr->hrec[i]->type!=BCF_HL_GEN ) continue; + if ( !strcmp(hdr->hrec[i]->key,hrec->key) && !strcmp(hrec->key,"fileformat") ) break; + if ( !strcmp(hdr->hrec[i]->key,hrec->key) && !strcmp(hdr->hrec[i]->value,hrec->value) ) break; + } + if ( inhrec ) + { + bcf_hrec_destroy(hrec); + return 0; + } + } + + // New record, needs to be added + int n = ++hdr->nhrec; + hdr->hrec = (bcf_hrec_t**) realloc(hdr->hrec, n*sizeof(bcf_hrec_t*)); + hdr->hrec[n-1] = hrec; + + return hrec->type==BCF_HL_GEN ? 0 : 1; +} + +bcf_hrec_t *bcf_hdr_get_hrec(const bcf_hdr_t *hdr, int type, const char *id) +{ + int i; + if ( type==BCF_HL_GEN ) + { + for (i=0; inhrec; i++) + { + if ( hdr->hrec[i]->type!=BCF_HL_GEN ) continue; + if ( !strcmp(hdr->hrec[i]->key,id) ) return hdr->hrec[i]; + } + return NULL; + } + vdict_t *d = type==BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID]; + khint_t k = kh_get(vdict, d, id); + if ( k == kh_end(d) ) return NULL; + return kh_val(d, k).hrec[type==BCF_HL_CTG?0:type]; +} + +void bcf_hdr_check_sanity(bcf_hdr_t *hdr) +{ + static int PL_warned = 0, GL_warned = 0; + + if ( !PL_warned ) + { + int id = bcf_hdr_id2int(hdr, BCF_DT_ID, "PL"); + if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G ) + { + fprintf(stderr,"[W::%s] PL should be declared as Number=G\n", __func__); + PL_warned = 1; + } + } + if ( !GL_warned ) + { + int id = bcf_hdr_id2int(hdr, BCF_HL_FMT, "GL"); + if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G ) + { + fprintf(stderr,"[W::%s] GL should be declared as Number=G\n", __func__); + PL_warned = 1; + } + } +} + +int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt) +{ + int len, needs_sync = 0; + char *p = htxt; + + // Check sanity: "fileformat" string must come as first + bcf_hrec_t *hrec = bcf_hdr_parse_line(hdr,p,&len); + if ( !hrec->key || strcasecmp(hrec->key,"fileformat") ) + fprintf(stderr, "[W::%s] The first line should be ##fileformat; is the VCF/BCF header broken?\n", __func__); + needs_sync += bcf_hdr_add_hrec(hdr, hrec); + + // The filter PASS must appear first in the dictionary + hrec = bcf_hdr_parse_line(hdr,"##FILTER=",&len); + needs_sync += bcf_hdr_add_hrec(hdr, hrec); + + // Parse the whole header + while ( (hrec=bcf_hdr_parse_line(hdr,p,&len)) ) + { + needs_sync += bcf_hdr_add_hrec(hdr, hrec); + p += len; + } + bcf_hdr_parse_sample_line(hdr,p); + if ( needs_sync ) bcf_hdr_sync(hdr); + bcf_hdr_check_sanity(hdr); + return 0; +} + +int bcf_hdr_append(bcf_hdr_t *hdr, const char *line) +{ + int len; + bcf_hrec_t *hrec = bcf_hdr_parse_line(hdr, (char*) line, &len); + if ( !hrec ) return -1; + if ( bcf_hdr_add_hrec(hdr, hrec) ) + bcf_hdr_sync(hdr); + return 0; +} + +void bcf_hdr_remove(bcf_hdr_t *hdr, int type, const char *key) +{ + int i; + bcf_hrec_t *hrec; + while (1) + { + if ( type==BCF_HL_FLT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG ) + { + hrec = bcf_hdr_get_hrec(hdr, type, key); + if ( !hrec ) return; + + for (i=0; inhrec; i++) + if ( hdr->hrec[i]==hrec ) break; + assert( inhrec ); + + vdict_t *d = type==BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID]; + khint_t k = kh_get(vdict, d, key); + kh_val(d, k).hrec[type==BCF_HL_CTG?0:type] = NULL; + } + else + { + for (i=0; inhrec; i++) + { + if ( hdr->hrec[i]->type!=type ) continue; + if ( !strcmp(hdr->hrec[i]->key,key) ) break; + } + if ( i==hdr->nhrec ) return; + hrec = hdr->hrec[i]; + } + + hdr->nhrec--; + if ( i < hdr->nhrec ) + memmove(&hdr->hrec[i],&hdr->hrec[i+1],(hdr->nhrec-i)*sizeof(bcf_hrec_t*)); + bcf_hrec_destroy(hrec); + + bcf_hdr_sync(hdr); + } +} + +int bcf_hdr_printf(bcf_hdr_t *hdr, const char *fmt, ...) +{ + va_list ap; + va_start(ap, fmt); + int n = vsnprintf(NULL, 0, fmt, ap) + 2; + va_end(ap); + + char *line = (char*)malloc(n); + va_start(ap, fmt); + vsnprintf(line, n, fmt, ap); + va_end(ap); + + int ret = bcf_hdr_append(hdr, line); + + free(line); + return ret; +} + + +/********************** + *** BCF header I/O *** + **********************/ + +const char *bcf_hdr_get_version(const bcf_hdr_t *hdr) +{ + bcf_hrec_t *hrec = bcf_hdr_get_hrec(hdr, BCF_HL_GEN, "fileformat"); + if ( !hrec ) + { + fprintf(stderr,"No version string found, assuming VCFv4.2\n"); + return "VCFv4.2"; + } + return hrec->value; +} + +void bcf_hdr_set_version(bcf_hdr_t *hdr, const char *version) +{ + bcf_hrec_t *hrec = bcf_hdr_get_hrec(hdr, BCF_HL_GEN, "fileformat"); + if ( !hrec ) + { + int len; + kstring_t str = {0,0,0}; + ksprintf(&str,"##fileformat=%s", version); + hrec = bcf_hdr_parse_line(hdr, str.s, &len); + free(str.s); + } + else + { + free(hrec->value); + hrec->value = strdup(version); + } + bcf_hdr_sync(hdr); +} + +bcf_hdr_t *bcf_hdr_init(const char *mode) +{ + int i; + bcf_hdr_t *h; + h = (bcf_hdr_t*)calloc(1, sizeof(bcf_hdr_t)); + for (i = 0; i < 3; ++i) + h->dict[i] = kh_init(vdict); + if ( strchr(mode,'w') ) + { + bcf_hdr_append(h, "##fileformat=VCFv4.2"); + // The filter PASS must appear first in the dictionary + bcf_hdr_append(h, "##FILTER="); + } + return h; +} + +void bcf_hdr_destroy(bcf_hdr_t *h) +{ + int i; + khint_t k; + for (i = 0; i < 3; ++i) { + vdict_t *d = (vdict_t*)h->dict[i]; + if (d == 0) continue; + for (k = kh_begin(d); k != kh_end(d); ++k) + if (kh_exist(d, k)) free((char*)kh_key(d, k)); + kh_destroy(vdict, d); + free(h->id[i]); + } + for (i=0; inhrec; i++) + bcf_hrec_destroy(h->hrec[i]); + if (h->nhrec) free(h->hrec); + if (h->samples) free(h->samples); + free(h->keep_samples); + free(h->transl[0]); free(h->transl[1]); + free(h->mem.s); + free(h); +} + +bcf_hdr_t *bcf_hdr_read(htsFile *hfp) +{ + if (!hfp->is_bin) + return vcf_hdr_read(hfp); + + BGZF *fp = hfp->fp.bgzf; + uint8_t magic[5]; + bcf_hdr_t *h; + h = bcf_hdr_init("r"); + if ( bgzf_read(fp, magic, 5)<0 ) + { + fprintf(stderr,"[%s:%d %s] Failed to read the header (reading BCF in text mode?)\n", __FILE__,__LINE__,__FUNCTION__); + return NULL; + } + if (strncmp((char*)magic, "BCF\2\2", 5) != 0) + { + if (!strncmp((char*)magic, "BCF", 3)) + fprintf(stderr,"[%s:%d %s] invalid BCF2 magic string: only BCFv2.2 is supported.\n", __FILE__,__LINE__,__FUNCTION__); + else if (hts_verbose >= 2) + fprintf(stderr, "[E::%s] invalid BCF2 magic string\n", __func__); + bcf_hdr_destroy(h); + return 0; + } + int hlen; + char *htxt; + bgzf_read(fp, &hlen, 4); + htxt = (char*)malloc(hlen); + bgzf_read(fp, htxt, hlen); + bcf_hdr_parse(h, htxt); + free(htxt); + return h; +} + +int bcf_hdr_write(htsFile *hfp, const bcf_hdr_t *h) +{ + if (!hfp->is_bin) return vcf_hdr_write(hfp, h); + + int hlen; + char *htxt = bcf_hdr_fmt_text(h, 1, &hlen); + hlen++; // include the \0 byte + + BGZF *fp = hfp->fp.bgzf; + if ( bgzf_write(fp, "BCF\2\2", 5) !=5 ) return -1; + if ( bgzf_write(fp, &hlen, 4) !=4 ) return -1; + if ( bgzf_write(fp, htxt, hlen) != hlen ) return -1; + + free(htxt); + return 0; +} + +/******************** + *** BCF site I/O *** + ********************/ + +bcf1_t *bcf_init1() +{ + bcf1_t *v; + v = (bcf1_t*)calloc(1, sizeof(bcf1_t)); + return v; +} + +void bcf_clear(bcf1_t *v) +{ + int i; + for (i=0; id.m_info; i++) + { + if ( v->d.info[i].vptr_free ) + { + free(v->d.info[i].vptr - v->d.info[i].vptr_off); + v->d.info[i].vptr_free = 0; + } + } + for (i=0; id.m_fmt; i++) + { + if ( v->d.fmt[i].p_free ) + { + free(v->d.fmt[i].p - v->d.fmt[i].p_off); + v->d.fmt[i].p_free = 0; + } + } + v->rid = v->pos = v->rlen = v->unpacked = 0; + bcf_float_set_missing(v->qual); + v->n_info = v->n_allele = v->n_fmt = v->n_sample = 0; + v->shared.l = v->indiv.l = 0; + v->d.var_type = -1; + v->d.shared_dirty = 0; + v->d.indiv_dirty = 0; + v->d.n_flt = 0; + v->errcode = 0; + if (v->d.m_als) v->d.als[0] = 0; + if (v->d.m_id) v->d.id[0] = 0; +} + +void bcf_empty1(bcf1_t *v) +{ + bcf_clear1(v); + free(v->d.id); + free(v->d.als); + free(v->d.allele); free(v->d.flt); free(v->d.info); free(v->d.fmt); + if (v->d.var ) free(v->d.var); + free(v->shared.s); free(v->indiv.s); +} + +void bcf_destroy1(bcf1_t *v) +{ + bcf_empty1(v); + free(v); +} + +static inline int bcf_read1_core(BGZF *fp, bcf1_t *v) +{ + uint32_t x[8]; + int ret; + if ((ret = bgzf_read(fp, x, 32)) != 32) { + if (ret == 0) return -1; + return -2; + } + bcf_clear1(v); + x[0] -= 24; // to exclude six 32-bit integers + ks_resize(&v->shared, x[0]); + ks_resize(&v->indiv, x[1]); + memcpy(v, x + 2, 16); + v->n_allele = x[6]>>16; v->n_info = x[6]&0xffff; + v->n_fmt = x[7]>>24; v->n_sample = x[7]&0xffffff; + v->shared.l = x[0], v->indiv.l = x[1]; + + // silent fix of broken BCFs produced by earlier versions of bcf_subset, prior to and including bd6ed8b4 + if ( (!v->indiv.l || !v->n_sample) && v->n_fmt ) v->n_fmt = 0; + + bgzf_read(fp, v->shared.s, v->shared.l); + bgzf_read(fp, v->indiv.s, v->indiv.l); + return 0; +} + +#define bit_array_size(n) ((n)/8+1) +#define bit_array_set(a,i) ((a)[(i)/8] |= 1 << ((i)%8)) +#define bit_array_clear(a,i) ((a)[(i)/8] &= ~(1 << ((i)%8))) +#define bit_array_test(a,i) ((a)[(i)/8] & (1 << ((i)%8))) + +static inline uint8_t *bcf_unpack_fmt_core1(uint8_t *ptr, int n_sample, bcf_fmt_t *fmt); +int bcf_subset_format(const bcf_hdr_t *hdr, bcf1_t *rec) +{ + if ( !hdr->keep_samples ) return 0; + if ( !bcf_hdr_nsamples(hdr) ) + { + rec->indiv.l = rec->n_sample = 0; + return 0; + } + + int i, j; + uint8_t *ptr = (uint8_t*)rec->indiv.s, *dst = NULL, *src; + bcf_dec_t *dec = &rec->d; + hts_expand(bcf_fmt_t, rec->n_fmt, dec->m_fmt, dec->fmt); + for (i=0; im_fmt; ++i) dec->fmt[i].p_free = 0; + + for (i=0; in_fmt; i++) + { + ptr = bcf_unpack_fmt_core1(ptr, rec->n_sample, &dec->fmt[i]); + src = dec->fmt[i].p - dec->fmt[i].size; + if ( dst ) + { + memmove(dec->fmt[i-1].p + dec->fmt[i-1].p_len, dec->fmt[i].p - dec->fmt[i].p_off, dec->fmt[i].p_off); + dec->fmt[i].p = dec->fmt[i-1].p + dec->fmt[i-1].p_len + dec->fmt[i].p_off; + } + dst = dec->fmt[i].p; + for (j=0; jnsamples_ori; j++) + { + src += dec->fmt[i].size; + if ( !bit_array_test(hdr->keep_samples,j) ) continue; + memmove(dst, src, dec->fmt[i].size); + dst += dec->fmt[i].size; + } + rec->indiv.l -= dec->fmt[i].p_len - (dst - dec->fmt[i].p); + dec->fmt[i].p_len = dst - dec->fmt[i].p; + } + rec->unpacked |= BCF_UN_FMT; + + rec->n_sample = bcf_hdr_nsamples(hdr); + return 0; +} + +int bcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) +{ + if (!fp->is_bin) return vcf_read(fp,h,v); + int ret = bcf_read1_core(fp->fp.bgzf, v); + if ( ret!=0 || !h->keep_samples ) return ret; + return bcf_subset_format(h,v); +} + +int bcf_readrec(BGZF *fp, void *null, void *vv, int *tid, int *beg, int *end) +{ + bcf1_t *v = (bcf1_t *) vv; + int ret; + if ((ret = bcf_read1_core(fp, v)) >= 0) + *tid = v->rid, *beg = v->pos, *end = v->pos + v->rlen; + return ret; +} + +static inline void bcf1_sync_id(bcf1_t *line, kstring_t *str) +{ + // single typed string + if ( line->d.id && strcmp(line->d.id, ".") ) bcf_enc_vchar(str, strlen(line->d.id), line->d.id); + else bcf_enc_size(str, 0, BCF_BT_CHAR); +} +static inline void bcf1_sync_alleles(bcf1_t *line, kstring_t *str) +{ + // list of typed strings + int i; + for (i=0; in_allele; i++) + bcf_enc_vchar(str, strlen(line->d.allele[i]), line->d.allele[i]); + if ( !line->rlen && line->n_allele ) line->rlen = strlen(line->d.allele[0]); +} +static inline void bcf1_sync_filter(bcf1_t *line, kstring_t *str) +{ + // typed vector of integers + if ( line->d.n_flt ) bcf_enc_vint(str, line->d.n_flt, line->d.flt, -1); + else bcf_enc_vint(str, 0, 0, -1); +} + +static inline void bcf1_sync_info(bcf1_t *line, kstring_t *str) +{ + // pairs of typed vectors + int i, irm = -1; + for (i=0; in_info; i++) + { + bcf_info_t *info = &line->d.info[i]; + if ( !info->vptr ) + { + // marked for removal + if ( irm < 0 ) irm = i; + continue; + } + kputsn_(info->vptr - info->vptr_off, info->vptr_len + info->vptr_off, str); + if ( irm >=0 ) + { + bcf_info_t tmp = line->d.info[irm]; line->d.info[irm] = line->d.info[i]; line->d.info[i] = tmp; + while ( irm<=i && line->d.info[irm].vptr ) irm++; + } + } + if ( irm>=0 ) line->n_info = irm; +} + +static int bcf1_sync(bcf1_t *line) +{ + char *shared_ori = line->shared.s; + size_t prev_len; + + kstring_t tmp = {0,0,0}; + if ( !line->shared.l ) + { + // New line created via API, BCF data blocks do not exist. Get it ready for BCF output + tmp = line->shared; + bcf1_sync_id(line, &tmp); + line->unpack_size[0] = tmp.l; prev_len = tmp.l; + + bcf1_sync_alleles(line, &tmp); + line->unpack_size[1] = tmp.l - prev_len; prev_len = tmp.l; + + bcf1_sync_filter(line, &tmp); + line->unpack_size[2] = tmp.l - prev_len; + + bcf1_sync_info(line, &tmp); + line->shared = tmp; + } + else if ( line->d.shared_dirty ) + { + // The line was edited, update the BCF data block, ptr_ori points + // to the original unchanged BCF data. + uint8_t *ptr_ori = (uint8_t *) line->shared.s; + + assert( line->unpacked & BCF_UN_STR ); + + // ID: single typed string + if ( line->d.shared_dirty & BCF1_DIRTY_ID ) + bcf1_sync_id(line, &tmp); + else + kputsn_(ptr_ori, line->unpack_size[0], &tmp); + ptr_ori += line->unpack_size[0]; + line->unpack_size[0] = tmp.l; prev_len = tmp.l; + + // REF+ALT: list of typed strings + if ( line->d.shared_dirty & BCF1_DIRTY_ALS ) + bcf1_sync_alleles(line, &tmp); + else + { + kputsn_(ptr_ori, line->unpack_size[1], &tmp); + if ( !line->rlen && line->n_allele ) line->rlen = strlen(line->d.allele[0]); + } + ptr_ori += line->unpack_size[1]; + line->unpack_size[1] = tmp.l - prev_len; prev_len = tmp.l; + + if ( line->unpacked & BCF_UN_FLT ) + { + // FILTER: typed vector of integers + if ( line->d.shared_dirty & BCF1_DIRTY_FLT ) + bcf1_sync_filter(line, &tmp); + else if ( line->d.n_flt ) + kputsn_(ptr_ori, line->unpack_size[2], &tmp); + else + bcf_enc_vint(&tmp, 0, 0, -1); + ptr_ori += line->unpack_size[2]; + line->unpack_size[2] = tmp.l - prev_len; + + if ( line->unpacked & BCF_UN_INFO ) + { + // INFO: pairs of typed vectors + if ( line->d.shared_dirty & BCF1_DIRTY_INF ) + { + bcf1_sync_info(line, &tmp); + ptr_ori = (uint8_t*)line->shared.s + line->shared.l; + } + } + } + + int size = line->shared.l - (size_t)ptr_ori + (size_t)line->shared.s; + if ( size ) kputsn_(ptr_ori, size, &tmp); + + free(line->shared.s); + line->shared = tmp; + } + if ( line->shared.s != shared_ori && line->unpacked & BCF_UN_INFO ) + { + // Reallocated line->shared.s block invalidated line->d.info[].vptr pointers + size_t off_new = line->unpack_size[0] + line->unpack_size[1] + line->unpack_size[2]; + int i; + for (i=0; in_info; i++) + { + uint8_t *vptr_free = line->d.info[i].vptr_free ? line->d.info[i].vptr - line->d.info[i].vptr_off : NULL; + line->d.info[i].vptr = (uint8_t*) line->shared.s + off_new + line->d.info[i].vptr_off; + off_new += line->d.info[i].vptr_len + line->d.info[i].vptr_off; + if ( vptr_free ) + { + free(vptr_free); + line->d.info[i].vptr_free = 0; + } + } + } + + if ( line->n_sample && line->n_fmt && (!line->indiv.l || line->d.indiv_dirty) ) + { + // The genotype fields changed or are not present + tmp.l = tmp.m = 0; tmp.s = NULL; + int i, irm = -1; + for (i=0; in_fmt; i++) + { + bcf_fmt_t *fmt = &line->d.fmt[i]; + if ( !fmt->p ) + { + // marked for removal + if ( irm < 0 ) irm = i; + continue; + } + kputsn_(fmt->p - fmt->p_off, fmt->p_len + fmt->p_off, &tmp); + if ( irm >=0 ) + { + bcf_fmt_t tfmt = line->d.fmt[irm]; line->d.fmt[irm] = line->d.fmt[i]; line->d.fmt[i] = tfmt; + while ( irm<=i && line->d.fmt[irm].p ) irm++; + } + + } + if ( irm>=0 ) line->n_fmt = irm; + free(line->indiv.s); + line->indiv = tmp; + + // Reallocated line->indiv.s block invalidated line->d.fmt[].p pointers + size_t off_new = 0; + for (i=0; in_fmt; i++) + { + uint8_t *p_free = line->d.fmt[i].p_free ? line->d.fmt[i].p - line->d.fmt[i].p_off : NULL; + line->d.fmt[i].p = (uint8_t*) line->indiv.s + off_new + line->d.fmt[i].p_off; + off_new += line->d.fmt[i].p_len + line->d.fmt[i].p_off; + if ( p_free ) + { + free(p_free); + line->d.fmt[i].p_free = 0; + } + } + } + if ( !line->n_sample ) line->n_fmt = 0; + line->d.shared_dirty = line->d.indiv_dirty = 0; + return 0; +} + +bcf1_t *bcf_dup(bcf1_t *src) +{ + bcf1_sync(src); + + bcf1_t *out = bcf_init1(); + + out->rid = src->rid; + out->pos = src->pos; + out->rlen = src->rlen; + out->qual = src->qual; + out->n_info = src->n_info; out->n_allele = src->n_allele; + out->n_fmt = src->n_fmt; out->n_sample = src->n_sample; + + out->shared.m = out->shared.l = src->shared.l; + out->shared.s = (char*) malloc(out->shared.l); + memcpy(out->shared.s,src->shared.s,out->shared.l); + + out->indiv.m = out->indiv.l = src->indiv.l; + out->indiv.s = (char*) malloc(out->indiv.l); + memcpy(out->indiv.s,src->indiv.s,out->indiv.l); + + return out; +} + +int bcf_write(htsFile *hfp, const bcf_hdr_t *h, bcf1_t *v) +{ + if ( bcf_hdr_nsamples(h)!=v->n_sample ) + { + fprintf(stderr,"[%s:%d %s] Broken VCF record, the number of columns at %s:%d does not match the number of samples (%d vs %d).\n", + __FILE__,__LINE__,__FUNCTION__,bcf_seqname(h,v),v->pos+1, v->n_sample,bcf_hdr_nsamples(h)); + return -1; + } + + if ( !hfp->is_bin ) return vcf_write(hfp,h,v); + + if ( v->errcode ) + { + // vcf_parse1() encountered a new contig or tag, undeclared in the + // header. At this point, the header must have been printed, + // proceeding would lead to a broken BCF file. Errors must be checked + // and cleared by the caller before we can proceed. + fprintf(stderr,"[%s:%d %s] Unchecked error (%d), exiting.\n", __FILE__,__LINE__,__FUNCTION__,v->errcode); + exit(1); + } + bcf1_sync(v); // check if the BCF record was modified + + BGZF *fp = hfp->fp.bgzf; + uint32_t x[8]; + x[0] = v->shared.l + 24; // to include six 32-bit integers + x[1] = v->indiv.l; + memcpy(x + 2, v, 16); + x[6] = (uint32_t)v->n_allele<<16 | v->n_info; + x[7] = (uint32_t)v->n_fmt<<24 | v->n_sample; + if ( bgzf_write(fp, x, 32) != 32 ) return -1; + if ( bgzf_write(fp, v->shared.s, v->shared.l) != v->shared.l ) return -1; + if ( bgzf_write(fp, v->indiv.s, v->indiv.l) != v->indiv.l ) return -1; + return 0; +} + +/********************** + *** VCF header I/O *** + **********************/ + +bcf_hdr_t *vcf_hdr_read(htsFile *fp) +{ + kstring_t txt, *s = &fp->line; + bcf_hdr_t *h; + h = bcf_hdr_init("r"); + txt.l = txt.m = 0; txt.s = 0; + while (hts_getline(fp, KS_SEP_LINE, s) >= 0) { + if (s->l == 0) continue; + if (s->s[0] != '#') { + if (hts_verbose >= 2) + fprintf(stderr, "[E::%s] no sample line\n", __func__); + free(txt.s); + bcf_hdr_destroy(h); + return 0; + } + if (s->s[1] != '#' && fp->fn_aux) { // insert contigs here + int dret; + gzFile f; + kstream_t *ks; + kstring_t tmp; + tmp.l = tmp.m = 0; tmp.s = 0; + f = gzopen(fp->fn_aux, "r"); + ks = ks_init(f); + while (ks_getuntil(ks, 0, &tmp, &dret) >= 0) { + int c; + kputs("##contig=\n", 2, &txt); + if (dret != '\n') + while ((c = ks_getc(ks)) != '\n' && c != -1); // skip the rest of the line + } + free(tmp.s); + ks_destroy(ks); + gzclose(f); + } + kputsn(s->s, s->l, &txt); + kputc('\n', &txt); + if (s->s[1] != '#') break; + } + if ( !txt.s ) + { + fprintf(stderr,"[%s:%d %s] Could not read the header\n", __FILE__,__LINE__,__FUNCTION__); + return NULL; + } + bcf_hdr_parse(h, txt.s); + + // check tabix index, are all contigs listed in the header? add the missing ones + tbx_t *idx = tbx_index_load(fp->fn); + if ( idx ) + { + int i, n, need_sync = 0; + const char **names = tbx_seqnames(idx, &n); + for (i=0; ikey = strdup("contig"); + bcf_hrec_add_key(hrec, "ID", strlen("ID")); + bcf_hrec_set_val(hrec, hrec->nkeys-1, (char*) names[i], strlen(names[i]), 0); + bcf_hrec_add_key(hrec, "length", strlen("length")); + bcf_hrec_set_val(hrec, hrec->nkeys-1, "2147483647", strlen("2147483647"), 0); + bcf_hdr_add_hrec(h, hrec); + need_sync = 1; + } + free(names); + tbx_destroy(idx); + if ( need_sync ) + bcf_hdr_sync(h); + } + free(txt.s); + return h; +} + +int bcf_hdr_set(bcf_hdr_t *hdr, const char *fname) +{ + int i, n; + char **lines = hts_readlines(fname, &n); + if ( !lines ) return 1; + for (i=0; ivalue ) + { + int j, nout = 0; + ksprintf(str, "##%s=<", hrec->key); + for (j=0; jnkeys; j++) + { + // do not output IDX if output is VCF + if ( !is_bcf && !strcmp("IDX",hrec->keys[j]) ) continue; + if ( nout ) kputc(',',str); + ksprintf(str,"%s=%s", hrec->keys[j], hrec->vals[j]); + nout++; + } + ksprintf(str,">\n"); + } + else + ksprintf(str,"##%s=%s\n", hrec->key,hrec->value); +} + +void bcf_hrec_format(const bcf_hrec_t *hrec, kstring_t *str) +{ + _bcf_hrec_format(hrec,0,str); +} +char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) +{ + int i; + kstring_t txt = {0,0,0}; + for (i=0; inhrec; i++) + _bcf_hrec_format(hdr->hrec[i], is_bcf, &txt); + + ksprintf(&txt,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"); + if ( bcf_hdr_nsamples(hdr) ) + { + ksprintf(&txt,"\tFORMAT"); + for (i=0; isamples[i]); + } + ksprintf(&txt,"\n"); + + if ( len ) *len = txt.l; + return txt.s; +} + +const char **bcf_hdr_seqnames(const bcf_hdr_t *h, int *n) +{ + vdict_t *d = (vdict_t*)h->dict[BCF_DT_CTG]; + int tid, m = kh_size(d); + const char **names = (const char**) calloc(m,sizeof(const char*)); + khint_t k; + for (k=kh_begin(d); kis_compressed==1 ) + ret = bgzf_write(fp->fp.bgzf, htxt, hlen); + else + ret = hwrite(fp->fp.hfile, htxt, hlen); + free(htxt); + return ret<0 ? -1 : 0; +} + +/*********************** + *** Typed value I/O *** + ***********************/ + +void bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize) +{ + int32_t max = INT32_MIN + 1, min = INT32_MAX; + int i; + if (n == 0) bcf_enc_size(s, 0, BCF_BT_NULL); + else if (n == 1) bcf_enc_int1(s, a[0]); + else { + if (wsize <= 0) wsize = n; + for (i = 0; i < n; ++i) { + if (a[i] == bcf_int32_missing || a[i] == bcf_int32_vector_end ) continue; + if (max < a[i]) max = a[i]; + if (min > a[i]) min = a[i]; + } + if (max <= INT8_MAX && min > bcf_int8_vector_end) { + bcf_enc_size(s, wsize, BCF_BT_INT8); + for (i = 0; i < n; ++i) + if ( a[i]==bcf_int32_vector_end ) kputc(bcf_int8_vector_end, s); + else if ( a[i]==bcf_int32_missing ) kputc(bcf_int8_missing, s); + else kputc(a[i], s); + } else if (max <= INT16_MAX && min > bcf_int16_vector_end) { + bcf_enc_size(s, wsize, BCF_BT_INT16); + for (i = 0; i < n; ++i) + { + int16_t x; + if ( a[i]==bcf_int32_vector_end ) x = bcf_int16_vector_end; + else if ( a[i]==bcf_int32_missing ) x = bcf_int16_missing; + else x = a[i]; + kputsn((char*)&x, 2, s); + } + } else { + bcf_enc_size(s, wsize, BCF_BT_INT32); + for (i = 0; i < n; ++i) { + int32_t x = a[i]; + kputsn((char*)&x, 4, s); + } + } + } +} + +void bcf_enc_vfloat(kstring_t *s, int n, float *a) +{ + bcf_enc_size(s, n, BCF_BT_FLOAT); + kputsn((char*)a, n << 2, s); +} + +void bcf_enc_vchar(kstring_t *s, int l, const char *a) +{ + bcf_enc_size(s, l, BCF_BT_CHAR); + kputsn(a, l, s); +} + +void bcf_fmt_array(kstring_t *s, int n, int type, void *data) +{ + int j = 0; + if (n == 0) { + kputc('.', s); + return; + } + if (type == BCF_BT_CHAR) + { + char *p = (char*)data; + for (j = 0; j < n && *p; ++j, ++p) + { + if ( *p==bcf_str_missing ) kputc('.', s); + else kputc(*p, s); + } + } + else + { +#define BRANCH(type_t, is_missing, is_vector_end, kprint) { \ + type_t *p = (type_t *) data; \ + for (j=0; jl&7) { + uint64_t zero = 0; + int l = ((s->l + 7)>>3<<3) - s->l; + kputsn((char*)&zero, l, s); + } +} + +// p,q is the start and the end of the FORMAT field +int _vcf_parse_format(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, char *p, char *q) +{ + if ( !bcf_hdr_nsamples(h) ) return 0; + + char *r, *t; + int j, l, m, g; + khint_t k; + ks_tokaux_t aux1; + vdict_t *d = (vdict_t*)h->dict[BCF_DT_ID]; + kstring_t *mem = (kstring_t*)&h->mem; + mem->l = 0; + + // count the number of format fields + for (r = p, v->n_fmt = 1; *r; ++r) + if (*r == ':') ++v->n_fmt; + char *end = s->s + s->l; + if ( q>=end ) + { + fprintf(stderr,"[%s:%d %s] Error: FORMAT column with no sample columns starting at %s:%d\n", __FILE__,__LINE__,__FUNCTION__,s->s,v->pos+1); + return -1; + } + + fmt_aux_t *fmt = (fmt_aux_t*)alloca(v->n_fmt * sizeof(fmt_aux_t)); + // get format information from the dictionary + for (j = 0, t = kstrtok(p, ":", &aux1); t; t = kstrtok(0, 0, &aux1), ++j) { + *(char*)aux1.p = 0; + k = kh_get(vdict, d, t); + if (k == kh_end(d) || kh_val(d, k).info[BCF_HL_FMT] == 15) { + fprintf(stderr, "[W::%s] FORMAT '%s' is not defined in the header, assuming Type=String\n", __func__, t); + kstring_t tmp = {0,0,0}; + int l; + ksprintf(&tmp, "##FORMAT=", t); + bcf_hrec_t *hrec = bcf_hdr_parse_line(h,tmp.s,&l); + free(tmp.s); + if ( bcf_hdr_add_hrec((bcf_hdr_t*)h, hrec) ) bcf_hdr_sync((bcf_hdr_t*)h); + k = kh_get(vdict, d, t); + v->errcode = BCF_ERR_TAG_UNDEF; + } + fmt[j].max_l = fmt[j].max_m = fmt[j].max_g = 0; + fmt[j].key = kh_val(d, k).id; + fmt[j].is_gt = !strcmp(t, "GT"); + fmt[j].y = h->id[0][fmt[j].key].val->info[BCF_HL_FMT]; + } + // compute max + int n_sample_ori = -1; + r = q + 1; // r: position in the format string + m = l = g = 1, v->n_sample = 0; // m: max vector size, l: max field len, g: max number of alleles + while ( rkeep_samples ) + { + n_sample_ori++; + if ( !bit_array_test(h->keep_samples,n_sample_ori) ) + { + while ( *r!='\t' && r=end ) break; + r++; l++; + } + v->n_sample++; + if ( v->n_sample == bcf_hdr_nsamples(h) ) break; + r++; + } + + // allocate memory for arrays + for (j = 0; j < v->n_fmt; ++j) { + fmt_aux_t *f = &fmt[j]; + if ( !f->max_m ) f->max_m = 1; // omitted trailing format field + if ((f->y>>4&0xf) == BCF_HT_STR) { + f->size = f->is_gt? f->max_g << 2 : f->max_l; + } else if ((f->y>>4&0xf) == BCF_HT_REAL || (f->y>>4&0xf) == BCF_HT_INT) { + f->size = f->max_m << 2; + } else + { + fprintf(stderr, "[E::%s] the format type %d currently not supported\n", __func__, f->y>>4&0xf); + abort(); // I do not know how to do with Flag in the genotype fields + } + align_mem(mem); + f->offset = mem->l; + ks_resize(mem, mem->l + v->n_sample * f->size); + mem->l += v->n_sample * f->size; + } + for (j = 0; j < v->n_fmt; ++j) + fmt[j].buf = (uint8_t*)mem->s + fmt[j].offset; + // fill the sample fields; at beginning of the loop, t points to the first char of a format + n_sample_ori = -1; + t = q + 1; m = 0; // m: sample id + while ( tkeep_samples ) + { + n_sample_ori++; + if ( !bit_array_test(h->keep_samples,n_sample_ori) ) + { + while ( *t && ty>>4&0xf) == BCF_HT_STR) { + if (z->is_gt) { // genotypes + int32_t is_phased = 0, *x = (int32_t*)(z->buf + z->size * m); + for (l = 0;; ++t) { + if (*t == '.') ++t, x[l++] = is_phased; + else x[l++] = (strtol(t, &t, 10) + 1) << 1 | is_phased; +#if THOROUGH_SANITY_CHECKS + assert( 0 ); // success of strtol,strtod not checked +#endif + is_phased = (*t == '|'); + if (*t == ':' || *t == 0) break; + } + if ( !l ) x[l++] = 0; // An empty field, insert missing value + for (; l < z->size>>2; ++l) x[l] = bcf_int32_vector_end; + } else { + char *x = (char*)z->buf + z->size * m; + for (r = t, l = 0; *t != ':' && *t; ++t) x[l++] = *t; + for (; l < z->size; ++l) x[l] = 0; + } + } else if ((z->y>>4&0xf) == BCF_HT_INT) { + int32_t *x = (int32_t*)(z->buf + z->size * m); + for (l = 0;; ++t) { + if (*t == '.') x[l++] = bcf_int32_missing, ++t; // ++t to skip "." + else x[l++] = strtol(t, &t, 10); + if (*t == ':' || *t == 0) break; + } + if ( !l ) x[l++] = bcf_int32_missing; + for (; l < z->size>>2; ++l) x[l] = bcf_int32_vector_end; + } else if ((z->y>>4&0xf) == BCF_HT_REAL) { + float *x = (float*)(z->buf + z->size * m); + for (l = 0;; ++t) { + if (*t == '.' && !isdigit(t[1])) bcf_float_set_missing(x[l++]), ++t; // ++t to skip "." + else x[l++] = strtod(t, &t); + if (*t == ':' || *t == 0) break; + } + if ( !l ) bcf_float_set_missing(x[l++]); // An empty field, insert missing value + for (; l < z->size>>2; ++l) bcf_float_set_vector_end(x[l]); + } else abort(); + if (*t == 0) { + for (++j; j < v->n_fmt; ++j) { // fill end-of-vector values + z = &fmt[j]; + if ((z->y>>4&0xf) == BCF_HT_STR) { + if (z->is_gt) { + int32_t *x = (int32_t*)(z->buf + z->size * m); + x[0] = bcf_int32_missing; + for (l = 1; l < z->size>>2; ++l) x[l] = bcf_int32_vector_end; + } else { + char *x = (char*)z->buf + z->size * m; + if ( z->size ) x[0] = '.'; + for (l = 1; l < z->size; ++l) x[l] = 0; + } + } else if ((z->y>>4&0xf) == BCF_HT_INT) { + int32_t *x = (int32_t*)(z->buf + z->size * m); + x[0] = bcf_int32_missing; + for (l = 1; l < z->size>>2; ++l) x[l] = bcf_int32_vector_end; + } else if ((z->y>>4&0xf) == BCF_HT_REAL) { + float *x = (float*)(z->buf + z->size * m); + bcf_float_set_missing(x[0]); + for (l = 1; l < z->size>>2; ++l) bcf_float_set_vector_end(x[l]); + } + } + break; + } + else + { + if (*t == ':') ++j; + t++; + } + } + m++; t++; + } + + // write individual genotype information + kstring_t *str = &v->indiv; + int i; + if (v->n_sample > 0) { + for (i = 0; i < v->n_fmt; ++i) { + fmt_aux_t *z = &fmt[i]; + bcf_enc_int1(str, z->key); + if ((z->y>>4&0xf) == BCF_HT_STR && !z->is_gt) { + bcf_enc_size(str, z->size, BCF_BT_CHAR); + kputsn((char*)z->buf, z->size * v->n_sample, str); + } else if ((z->y>>4&0xf) == BCF_HT_INT || z->is_gt) { + bcf_enc_vint(str, (z->size>>2) * v->n_sample, (int32_t*)z->buf, z->size>>2); + } else { + bcf_enc_size(str, z->size>>2, BCF_BT_FLOAT); + kputsn((char*)z->buf, z->size * v->n_sample, str); + } + } + } + + if ( v->n_sample!=bcf_hdr_nsamples(h) ) + { + fprintf(stderr,"[%s:%d %s] Number of columns at %s:%d does not match the number of samples (%d vs %d).\n", + __FILE__,__LINE__,__FUNCTION__,bcf_seqname(h,v),v->pos+1, v->n_sample,bcf_hdr_nsamples(h)); + v->errcode |= BCF_ERR_NCOLS; + return -1; + } + + return 0; +} + +int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v) +{ + int i = 0; + char *p, *q, *r, *t; + kstring_t *str; + khint_t k; + ks_tokaux_t aux; + + bcf_clear1(v); + str = &v->shared; + memset(&aux, 0, sizeof(ks_tokaux_t)); + for (p = kstrtok(s->s, "\t", &aux), i = 0; p; p = kstrtok(0, 0, &aux), ++i) { + q = (char*)aux.p; + *q = 0; + if (i == 0) { // CHROM + vdict_t *d = (vdict_t*)h->dict[BCF_DT_CTG]; + k = kh_get(vdict, d, p); + if (k == kh_end(d)) + { + // Simple error recovery for chromosomes not defined in the header. It will not help when VCF header has + // been already printed, but will enable tools like vcfcheck to proceed. + fprintf(stderr, "[W::%s] contig '%s' is not defined in the header. (Quick workaround: index the file with tabix.)\n", __func__, p); + kstring_t tmp = {0,0,0}; + int l; + ksprintf(&tmp, "##contig=", p); + bcf_hrec_t *hrec = bcf_hdr_parse_line(h,tmp.s,&l); + free(tmp.s); + if ( bcf_hdr_add_hrec((bcf_hdr_t*)h, hrec) ) bcf_hdr_sync((bcf_hdr_t*)h); + k = kh_get(vdict, d, p); + v->errcode = BCF_ERR_CTG_UNDEF; + } + v->rid = kh_val(d, k).id; + } else if (i == 1) { // POS + v->pos = atoi(p) - 1; + } else if (i == 2) { // ID + if (strcmp(p, ".")) bcf_enc_vchar(str, q - p, p); + else bcf_enc_size(str, 0, BCF_BT_CHAR); + } else if (i == 3) { // REF + bcf_enc_vchar(str, q - p, p); + v->n_allele = 1, v->rlen = q - p; + } else if (i == 4) { // ALT + if (strcmp(p, ".")) { + for (r = t = p;; ++r) { + if (*r == ',' || *r == 0) { + bcf_enc_vchar(str, r - t, t); + t = r + 1; + ++v->n_allele; + } + if (r == q) break; + } + } + } else if (i == 5) { // QUAL + if (strcmp(p, ".")) v->qual = atof(p); + else memcpy(&v->qual, &bcf_float_missing, 4); + if ( v->max_unpack && !(v->max_unpack>>1) ) return 0; // BCF_UN_STR + } else if (i == 6) { // FILTER + if (strcmp(p, ".")) { + int32_t *a; + int n_flt = 1, i; + ks_tokaux_t aux1; + vdict_t *d = (vdict_t*)h->dict[BCF_DT_ID]; + // count the number of filters + if (*(q-1) == ';') *(q-1) = 0; + for (r = p; *r; ++r) + if (*r == ';') ++n_flt; + a = (int32_t*)alloca(n_flt * 4); + // add filters + for (t = kstrtok(p, ";", &aux1), i = 0; t; t = kstrtok(0, 0, &aux1)) { + *(char*)aux1.p = 0; + k = kh_get(vdict, d, t); + if (k == kh_end(d)) + { + // Simple error recovery for FILTERs not defined in the header. It will not help when VCF header has + // been already printed, but will enable tools like vcfcheck to proceed. + fprintf(stderr, "[W::%s] FILTER '%s' is not defined in the header\n", __func__, t); + kstring_t tmp = {0,0,0}; + int l; + ksprintf(&tmp, "##FILTER=", t); + bcf_hrec_t *hrec = bcf_hdr_parse_line(h,tmp.s,&l); + free(tmp.s); + if ( bcf_hdr_add_hrec((bcf_hdr_t*)h, hrec) ) bcf_hdr_sync((bcf_hdr_t*)h); + k = kh_get(vdict, d, t); + v->errcode = BCF_ERR_TAG_UNDEF; + } + a[i++] = kh_val(d, k).id; + } + n_flt = i; + bcf_enc_vint(str, n_flt, a, -1); + } else bcf_enc_vint(str, 0, 0, -1); + if ( v->max_unpack && !(v->max_unpack>>2) ) return 0; // BCF_UN_FLT + } else if (i == 7) { // INFO + char *key; + vdict_t *d = (vdict_t*)h->dict[BCF_DT_ID]; + v->n_info = 0; + if (strcmp(p, ".")) { + if (*(q-1) == ';') *(q-1) = 0; + for (r = key = p;; ++r) { + int c; + char *val, *end; + if (*r != ';' && *r != '=' && *r != 0) continue; + val = end = 0; + c = *r; *r = 0; + if (c == '=') { + val = r + 1; + for (end = val; *end != ';' && *end != 0; ++end); + c = *end; *end = 0; + } else end = r; + k = kh_get(vdict, d, key); + if (k == kh_end(d) || kh_val(d, k).info[BCF_HL_INFO] == 15) + { + fprintf(stderr, "[W::%s] INFO '%s' is not defined in the header, assuming Type=String\n", __func__, key); + kstring_t tmp = {0,0,0}; + int l; + ksprintf(&tmp, "##INFO=", key); + bcf_hrec_t *hrec = bcf_hdr_parse_line(h,tmp.s,&l); + free(tmp.s); + if ( bcf_hdr_add_hrec((bcf_hdr_t*)h, hrec) ) bcf_hdr_sync((bcf_hdr_t*)h); + k = kh_get(vdict, d, key); + v->errcode = BCF_ERR_TAG_UNDEF; + } + uint32_t y = kh_val(d, k).info[BCF_HL_INFO]; + ++v->n_info; + bcf_enc_int1(str, kh_val(d, k).id); + if (val == 0) { + bcf_enc_size(str, 0, BCF_BT_NULL); + } else if ((y>>4&0xf) == BCF_HT_FLAG || (y>>4&0xf) == BCF_HT_STR) { // if Flag has a value, treat it as a string + bcf_enc_vchar(str, end - val, val); + } else { // int/float value/array + int i, n_val; + char *t, *te; + for (t = val, n_val = 1; *t; ++t) // count the number of values + if (*t == ',') ++n_val; + if ((y>>4&0xf) == BCF_HT_INT) { + int32_t *z; + z = (int32_t*)alloca(n_val<<2); + for (i = 0, t = val; i < n_val; ++i, ++t) + { + z[i] = strtol(t, &te, 10); + if ( te==t ) // conversion failed + { + z[i] = bcf_int32_missing; + while ( *te && *te!=',' ) te++; + } + t = te; + } + bcf_enc_vint(str, n_val, z, -1); + if (strcmp(key, "END") == 0) v->rlen = z[0] - v->pos; + } else if ((y>>4&0xf) == BCF_HT_REAL) { + float *z; + z = (float*)alloca(n_val<<2); + for (i = 0, t = val; i < n_val; ++i, ++t) + { + z[i] = strtod(t, &te); + if ( te==t ) // conversion failed + { + bcf_float_set_missing(z[i]); + while ( *te && *te!=',' ) te++; + } + t = te; + } + bcf_enc_vfloat(str, n_val, z); + } + } + if (c == 0) break; + r = end; + key = r + 1; + } + } + if ( v->max_unpack && !(v->max_unpack>>3) ) return 0; + } else if (i == 8) // FORMAT + return _vcf_parse_format(s, h, v, p, q); + } + return 0; +} + +int vcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) +{ + int ret; + ret = hts_getline(fp, KS_SEP_LINE, &fp->line); + if (ret < 0) return -1; + return vcf_parse1(&fp->line, h, v); +} + +static inline uint8_t *bcf_unpack_fmt_core1(uint8_t *ptr, int n_sample, bcf_fmt_t *fmt) +{ + uint8_t *ptr_start = ptr; + fmt->id = bcf_dec_typed_int1(ptr, &ptr); + fmt->n = bcf_dec_size(ptr, &ptr, &fmt->type); + fmt->size = fmt->n << bcf_type_shift[fmt->type]; + fmt->p = ptr; + fmt->p_off = ptr - ptr_start; + fmt->p_free = 0; + ptr += n_sample * fmt->size; + fmt->p_len = ptr - fmt->p; + return ptr; +} + +static inline uint8_t *bcf_unpack_info_core1(uint8_t *ptr, bcf_info_t *info) +{ + uint8_t *ptr_start = ptr; + info->key = bcf_dec_typed_int1(ptr, &ptr); + info->len = bcf_dec_size(ptr, &ptr, &info->type); + info->vptr = ptr; + info->vptr_off = ptr - ptr_start; + info->vptr_free = 0; + info->v1.i = 0; + if (info->len == 1) { + if (info->type == BCF_BT_INT8 || info->type == BCF_BT_CHAR) info->v1.i = *(int8_t*)ptr; + else if (info->type == BCF_BT_INT32) info->v1.i = *(int32_t*)ptr; + else if (info->type == BCF_BT_FLOAT) info->v1.f = *(float*)ptr; + else if (info->type == BCF_BT_INT16) info->v1.i = *(int16_t*)ptr; + } + ptr += info->len << bcf_type_shift[info->type]; + info->vptr_len = ptr - info->vptr; + return ptr; +} + +int bcf_unpack(bcf1_t *b, int which) +{ + if ( !b->shared.l ) return 0; // Building a new BCF record from scratch + uint8_t *ptr = (uint8_t*)b->shared.s, *ptr_ori; + int *offset, i; + bcf_dec_t *d = &b->d; + if (which & BCF_UN_FLT) which |= BCF_UN_STR; + if (which & BCF_UN_INFO) which |= BCF_UN_SHR; + if ((which&BCF_UN_STR) && !(b->unpacked&BCF_UN_STR)) + { + kstring_t tmp; + + // ID + tmp.l = 0; tmp.s = d->id; tmp.m = d->m_id; + ptr_ori = ptr; + ptr = bcf_fmt_sized_array(&tmp, ptr); + b->unpack_size[0] = ptr - ptr_ori; + kputc('\0', &tmp); + d->id = tmp.s; d->m_id = tmp.m; + + // REF and ALT are in a single block (d->als) and d->alleles are pointers into this block + tmp.l = 0; tmp.s = d->als; tmp.m = d->m_als; + offset = (int*)alloca(b->n_allele * sizeof(int)); + ptr_ori = ptr; + for (i = 0; i < b->n_allele; ++i) { + offset[i] = tmp.l; + ptr = bcf_fmt_sized_array(&tmp, ptr); + kputc('\0', &tmp); + } + b->unpack_size[1] = ptr - ptr_ori; + d->als = tmp.s; d->m_als = tmp.m; + + hts_expand(char*, b->n_allele, d->m_allele, d->allele); // NM: hts_expand() is a macro + for (i = 0; i < b->n_allele; ++i) + d->allele[i] = d->als + offset[i]; + b->unpacked |= BCF_UN_STR; + } + if ((which&BCF_UN_FLT) && !(b->unpacked&BCF_UN_FLT)) { // FILTER + ptr = (uint8_t*)b->shared.s + b->unpack_size[0] + b->unpack_size[1]; + ptr_ori = ptr; + if (*ptr>>4) { + int type; + d->n_flt = bcf_dec_size(ptr, &ptr, &type); + hts_expand(int, d->n_flt, d->m_flt, d->flt); + for (i = 0; i < d->n_flt; ++i) + d->flt[i] = bcf_dec_int1(ptr, type, &ptr); + } else ++ptr, d->n_flt = 0; + b->unpack_size[2] = ptr - ptr_ori; + b->unpacked |= BCF_UN_FLT; + } + if ((which&BCF_UN_INFO) && !(b->unpacked&BCF_UN_INFO)) { // INFO + ptr = (uint8_t*)b->shared.s + b->unpack_size[0] + b->unpack_size[1] + b->unpack_size[2]; + hts_expand(bcf_info_t, b->n_info, d->m_info, d->info); + for (i = 0; i < d->m_info; ++i) d->info[i].vptr_free = 0; + for (i = 0; i < b->n_info; ++i) + ptr = bcf_unpack_info_core1(ptr, &d->info[i]); + b->unpacked |= BCF_UN_INFO; + } + if ((which&BCF_UN_FMT) && b->n_sample && !(b->unpacked&BCF_UN_FMT)) { // FORMAT + ptr = (uint8_t*)b->indiv.s; + hts_expand(bcf_fmt_t, b->n_fmt, d->m_fmt, d->fmt); + for (i = 0; i < d->m_fmt; ++i) d->fmt[i].p_free = 0; + for (i = 0; i < b->n_fmt; ++i) + ptr = bcf_unpack_fmt_core1(ptr, b->n_sample, &d->fmt[i]); + b->unpacked |= BCF_UN_FMT; + } + return 0; +} + +int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s) +{ + int i; + bcf_unpack((bcf1_t*)v, BCF_UN_ALL); + kputs(h->id[BCF_DT_CTG][v->rid].key, s); // CHROM + kputc('\t', s); kputw(v->pos + 1, s); // POS + kputc('\t', s); kputs(v->d.id ? v->d.id : ".", s); // ID + kputc('\t', s); // REF + if (v->n_allele > 0) kputs(v->d.allele[0], s); + else kputc('.', s); + kputc('\t', s); // ALT + if (v->n_allele > 1) { + for (i = 1; i < v->n_allele; ++i) { + if (i > 1) kputc(',', s); + kputs(v->d.allele[i], s); + } + } else kputc('.', s); + kputc('\t', s); // QUAL + if (memcmp(&v->qual, &bcf_float_missing, 4) == 0) kputc('.', s); // QUAL + else ksprintf(s, "%g", v->qual); + kputc('\t', s); // FILTER + if (v->d.n_flt) { + for (i = 0; i < v->d.n_flt; ++i) { + if (i) kputc(';', s); + kputs(h->id[BCF_DT_ID][v->d.flt[i]].key, s); + } + } else kputc('.', s); + kputc('\t', s); // INFO + if (v->n_info) { + int first = 1; + for (i = 0; i < v->n_info; ++i) { + bcf_info_t *z = &v->d.info[i]; + if ( !z->vptr ) continue; + if ( !first ) kputc(';', s); first = 0; + kputs(h->id[BCF_DT_ID][z->key].key, s); + if (z->len <= 0) continue; + kputc('=', s); + if (z->len == 1) { + if (z->type == BCF_BT_FLOAT) ksprintf(s, "%g", z->v1.f); + else if (z->type != BCF_BT_CHAR) kputw(z->v1.i, s); + else kputc(z->v1.i, s); + } else bcf_fmt_array(s, z->len, z->type, z->vptr); + } + if ( first ) kputc('.', s); + } else kputc('.', s); + // FORMAT and individual information + if (v->n_sample) + { + int i,j; + if ( v->n_fmt) + { + int gt_i = -1; + bcf_fmt_t *fmt = v->d.fmt; + int first = 1; + for (i = 0; i < (int)v->n_fmt; ++i) { + if ( !fmt[i].p ) continue; + kputc(!first ? ':' : '\t', s); first = 0; + if ( fmt[i].id<0 ) //!bcf_hdr_idinfo_exists(h,BCF_HL_FMT,fmt[i].id) ) + { + fprintf(stderr, "[E::%s] invalid BCF, the FORMAT tag id=%d not present in the header.\n", __func__, fmt[i].id); + abort(); + } + kputs(h->id[BCF_DT_ID][fmt[i].id].key, s); + if (strcmp(h->id[BCF_DT_ID][fmt[i].id].key, "GT") == 0) gt_i = i; + } + if ( first ) kputs("\t.", s); + for (j = 0; j < v->n_sample; ++j) { + kputc('\t', s); + first = 1; + for (i = 0; i < (int)v->n_fmt; ++i) { + bcf_fmt_t *f = &fmt[i]; + if ( !f->p ) continue; + if (!first) kputc(':', s); first = 0; + if (gt_i == i) + bcf_format_gt(f,j,s); + else + bcf_fmt_array(s, f->n, f->type, f->p + j * f->size); + } + if ( first ) kputc('.', s); + } + } + else + for (j=0; j<=v->n_sample; j++) + kputs("\t.", s); + } + kputc('\n', s); + return 0; +} + +int vcf_write_line(htsFile *fp, kstring_t *line) +{ + int ret; + if ( line->s[line->l-1]!='\n' ) kputc('\n',line); + if ( fp->is_compressed==1 ) + ret = bgzf_write(fp->fp.bgzf, line->s, line->l); + else + ret = hwrite(fp->fp.hfile, line->s, line->l); + return ret==line->l ? 0 : -1; +} + +int vcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) +{ + int ret; + fp->line.l = 0; + vcf_format1(h, v, &fp->line); + if ( fp->is_compressed==1 ) + ret = bgzf_write(fp->fp.bgzf, fp->line.s, fp->line.l); + else + ret = hwrite(fp->fp.hfile, fp->line.s, fp->line.l); + return ret==fp->line.l ? 0 : -1; +} + +/************************ + * Data access routines * + ************************/ + +int bcf_hdr_id2int(const bcf_hdr_t *h, int which, const char *id) +{ + khint_t k; + vdict_t *d = (vdict_t*)h->dict[which]; + k = kh_get(vdict, d, id); + return k == kh_end(d)? -1 : kh_val(d, k).id; +} + + +/******************** + *** BCF indexing *** + ********************/ + +hts_idx_t *bcf_index(htsFile *fp, int min_shift) +{ + int n_lvls, i; + bcf1_t *b; + hts_idx_t *idx; + bcf_hdr_t *h; + int64_t max_len = 0, s; + h = bcf_hdr_read(fp); + if ( !h ) return NULL; + int nids = 0; + for (i = 0; i < h->n[BCF_DT_CTG]; ++i) + { + if ( !h->id[BCF_DT_CTG][i].val ) continue; + if ( max_len < h->id[BCF_DT_CTG][i].val->info[0] ) max_len = h->id[BCF_DT_CTG][i].val->info[0]; + nids++; + } + if ( !max_len ) max_len = ((int64_t)1<<31) - 1; // In case contig line is broken. + max_len += 256; + for (n_lvls = 0, s = 1< s; ++n_lvls, s <<= 3); + idx = hts_idx_init(nids, HTS_FMT_CSI, bgzf_tell(fp->fp.bgzf), min_shift, n_lvls); + b = bcf_init1(); + while (bcf_read1(fp,h, b) >= 0) { + int ret; + ret = hts_idx_push(idx, b->rid, b->pos, b->pos + b->rlen, bgzf_tell(fp->fp.bgzf), 1); + if (ret < 0) + { + bcf_destroy1(b); + hts_idx_destroy(idx); + return NULL; + } + } + hts_idx_finish(idx, bgzf_tell(fp->fp.bgzf)); + bcf_destroy1(b); + bcf_hdr_destroy(h); + return idx; +} + +int bcf_index_build(const char *fn, int min_shift) +{ + htsFile *fp; + hts_idx_t *idx; + if ((fp = hts_open(fn, "rb")) == 0) return -1; + if ( !fp->fp.bgzf->is_compressed ) { hts_close(fp); return -1; } + idx = bcf_index(fp, min_shift); + hts_close(fp); + if ( !idx ) return -1; + hts_idx_save(idx, fn, HTS_FMT_CSI); + hts_idx_destroy(idx); + return 0; +} + +/***************** + *** Utilities *** + *****************/ + +void bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src) +{ + int i, ndst_ori = dst->nhrec, need_sync = 0; + for (i=0; inhrec; i++) + { + if ( src->hrec[i]->type==BCF_HL_GEN && src->hrec[i]->value ) + { + int j; + for (j=0; jhrec[j]->type!=BCF_HL_GEN ) continue; + if ( !strcmp(src->hrec[i]->key,dst->hrec[j]->key) && !strcmp(src->hrec[i]->value,dst->hrec[j]->value) ) break; + } + if ( j>=ndst_ori ) + need_sync += bcf_hdr_add_hrec(dst, bcf_hrec_dup(src->hrec[i])); + } + else + { + bcf_hrec_t *rec = bcf_hdr_get_hrec(dst, src->hrec[i]->type, src->hrec[i]->vals[0]); + if ( !rec ) + need_sync += bcf_hdr_add_hrec(dst, bcf_hrec_dup(src->hrec[i])); + } + } + if ( need_sync ) bcf_hdr_sync(dst); +} +int bcf_translate(const bcf_hdr_t *dst_hdr, bcf_hdr_t *src_hdr, bcf1_t *line) +{ + int i; + if ( line->errcode ) + { + fprintf(stderr,"[%s:%d %s] Unchecked error (%d), exiting.\n", __FILE__,__LINE__,__FUNCTION__,line->errcode); + exit(1); + } + if ( src_hdr->ntransl==-1 ) return 0; // no need to translate, all tags have the same id + if ( !src_hdr->ntransl ) // called for the first time, see what needs translating + { + int dict; + for (dict=0; dict<2; dict++) // BCF_DT_ID and BCF_DT_CTG + { + src_hdr->transl[dict] = (int*) malloc(src_hdr->n[dict]*sizeof(int)); + for (i=0; in[dict]; i++) + { + if ( i>=dst_hdr->n[dict] || strcmp(src_hdr->id[dict][i].key,dst_hdr->id[dict][i].key) ) + { + src_hdr->transl[dict][i] = bcf_hdr_id2int(dst_hdr,dict,src_hdr->id[dict][i].key); + src_hdr->ntransl++; + } + else + src_hdr->transl[dict][i] = -1; + } + } + if ( !src_hdr->ntransl ) + { + free(src_hdr->transl[0]); src_hdr->transl[0] = NULL; + free(src_hdr->transl[1]); src_hdr->transl[1] = NULL; + src_hdr->ntransl = -1; + } + if ( src_hdr->ntransl==-1 ) return 0; + } + bcf_unpack(line,BCF_UN_ALL); + + // CHROM + if ( src_hdr->transl[BCF_DT_CTG][line->rid] >=0 ) line->rid = src_hdr->transl[BCF_DT_CTG][line->rid]; + + // FILTER + for (i=0; id.n_flt; i++) + { + int src_id = line->d.flt[i]; + if ( src_hdr->transl[BCF_DT_ID][src_id] >=0 ) + line->d.flt[i] = src_hdr->transl[BCF_DT_ID][src_id]; + line->d.shared_dirty |= BCF1_DIRTY_FLT; + } + + // INFO + for (i=0; in_info; i++) + { + int src_id = line->d.info[i].key; + int dst_id = src_hdr->transl[BCF_DT_ID][src_id]; + if ( dst_id<0 ) continue; + int src_size = src_id>>7 ? ( src_id>>15 ? BCF_BT_INT32 : BCF_BT_INT16) : BCF_BT_INT8; + int dst_size = dst_id>>7 ? ( dst_id>>15 ? BCF_BT_INT32 : BCF_BT_INT16) : BCF_BT_INT8; + if ( src_size==dst_size ) // can overwrite + { + line->d.info[i].key = dst_id; + uint8_t *vptr = line->d.info[i].vptr - line->d.info[i].vptr_off; + if ( dst_size==BCF_BT_INT8 ) { vptr[1] = (uint8_t)dst_id; } + else if ( dst_size==BCF_BT_INT16 ) { *(uint16_t*)vptr = (uint16_t)dst_id; } + else { *(uint32_t*)vptr = (uint32_t)dst_id; } + } + else // must realloc + { + bcf_info_t *info = &line->d.info[i]; + assert( !info->vptr_free ); + kstring_t str = {0,0,0}; + bcf_enc_int1(&str, dst_id); + bcf_enc_size(&str, info->len,info->type); + info->vptr_off = str.l; + kputsn((char*)info->vptr, info->vptr_len, &str); + info->vptr = (uint8_t*)str.s + info->vptr_off; + info->vptr_free = 1; + info->key = dst_id; + line->d.shared_dirty |= BCF1_DIRTY_INF; + } + } + + // FORMAT + for (i=0; in_fmt; i++) + { + int src_id = line->d.fmt[i].id; + int dst_id = src_hdr->transl[BCF_DT_ID][src_id]; + if ( dst_id<0 ) continue; + int src_size = src_id>>7 ? ( src_id>>15 ? BCF_BT_INT32 : BCF_BT_INT16) : BCF_BT_INT8; + int dst_size = dst_id>>7 ? ( dst_id>>15 ? BCF_BT_INT32 : BCF_BT_INT16) : BCF_BT_INT8; + if ( src_size==dst_size ) // can overwrite + { + line->d.fmt[i].id = dst_id; + uint8_t *p = line->d.fmt[i].p - line->d.fmt[i].p_off; // pointer to the vector size (4bits) and BT type (4bits) + if ( dst_size==BCF_BT_INT8 ) { p[1] = dst_id; } + else if ( dst_size==BCF_BT_INT16 ) { uint8_t *x = (uint8_t*) &dst_id; p[1] = x[0]; p[2] = x[1]; } + else { uint8_t *x = (uint8_t*) &dst_id; p[1] = x[0]; p[2] = x[1]; p[3] = x[2]; p[4] = x[3]; } + } + else // must realloc + { + bcf_fmt_t *fmt = &line->d.fmt[i]; + assert( !fmt->p_free ); + kstring_t str = {0,0,0}; + bcf_enc_int1(&str, dst_id); + bcf_enc_size(&str, fmt->n, fmt->type); + fmt->p_off = str.l; + kputsn((char*)fmt->p, fmt->p_len, &str); + fmt->p = (uint8_t*)str.s + fmt->p_off; + fmt->p_free = 1; + fmt->id = dst_id; + line->d.indiv_dirty = 1; + } + } + return 0; +} + +bcf_hdr_t *bcf_hdr_dup(const bcf_hdr_t *hdr) +{ + bcf_hdr_t *hout = bcf_hdr_init("r"); + char *htxt = bcf_hdr_fmt_text(hdr, 1, NULL); + bcf_hdr_parse(hout, htxt); + free(htxt); + return hout; +} + +bcf_hdr_t *bcf_hdr_subset(const bcf_hdr_t *h0, int n, char *const* samples, int *imap) +{ + int hlen; + char *htxt = bcf_hdr_fmt_text(h0, 1, &hlen); + kstring_t str; + bcf_hdr_t *h; + str.l = str.m = 0; str.s = 0; + h = bcf_hdr_init("w"); + bcf_hdr_set_version(h,bcf_hdr_get_version(h0)); + int j; + for (j=0; j 0) { + char *p; + int i = 0, end = n? 8 : 7; + while ((p = strstr(htxt, "#CHROM\t")) != 0) + if (p > htxt && *(p-1) == '\n') break; + while ((p = strchr(p, '\t')) != 0 && i < end) ++i, ++p; + if (i != end) { + free(h); free(str.s); + return 0; // malformated header + } + kputsn(htxt, p - htxt, &str); + for (i = 0; i < n; ++i) { + imap[i] = bcf_hdr_id2int(h0, BCF_DT_SAMPLE, samples[i]); + if (imap[i] < 0) continue; + kputc('\t', &str); + kputs(samples[i], &str); + } + } else kputsn(htxt, hlen, &str); + while (str.l && (!str.s[str.l-1] || str.s[str.l-1]=='\n') ) str.l--; // kill trailing zeros and newlines + kputc('\n',&str); + bcf_hdr_parse(h, str.s); + free(str.s); + free(htxt); + return h; +} + +int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file) +{ + if ( samples && !strcmp("-",samples) ) return 0; // keep all samples + + hdr->nsamples_ori = bcf_hdr_nsamples(hdr); + if ( !samples ) { bcf_hdr_nsamples(hdr) = 0; return 0; } // exclude all samples + + int i, narr = bit_array_size(bcf_hdr_nsamples(hdr)); + hdr->keep_samples = (uint8_t*) calloc(narr,1); + if ( samples[0]=='^' ) + for (i=0; ikeep_samples,i); + + int idx, n, ret = 0; + char **smpls = hts_readlist(samples[0]=='^'?samples+1:samples, is_file, &n); + if ( !smpls ) return -1; + for (i=0; ikeep_samples, idx); + else + bit_array_set(hdr->keep_samples, idx); + } + for (i=0; insamples_ori; i++) + if ( bit_array_test(hdr->keep_samples,i) ) bcf_hdr_nsamples(hdr)++; + if ( !bcf_hdr_nsamples(hdr) ) { free(hdr->keep_samples); hdr->keep_samples=NULL; } + else + { + char **samples = (char**) malloc(sizeof(char*)*bcf_hdr_nsamples(hdr)); + idx = 0; + for (i=0; insamples_ori; i++) + if ( bit_array_test(hdr->keep_samples,i) ) samples[idx++] = strdup(hdr->samples[i]); + free(hdr->samples); + hdr->samples = samples; + + // delete original samples from the dictionary + vdict_t *d = (vdict_t*)hdr->dict[BCF_DT_SAMPLE]; + int k; + for (k = kh_begin(d); k != kh_end(d); ++k) + if (kh_exist(d, k)) free((char*)kh_key(d, k)); + kh_destroy(vdict, d); + + // add the subset back + hdr->dict[BCF_DT_SAMPLE] = d = kh_init(vdict); + for (i=0; isamples[i], &ignore); + kh_val(d, k) = bcf_idinfo_def; + kh_val(d, k).id = kh_size(d) - 1; + } + bcf_hdr_sync(hdr); + } + + return ret; +} + +int bcf_subset(const bcf_hdr_t *h, bcf1_t *v, int n, int *imap) +{ + kstring_t ind; + ind.s = 0; ind.l = ind.m = 0; + if (n) { + bcf_fmt_t *fmt; + int i, j; + fmt = (bcf_fmt_t*)alloca(v->n_fmt * sizeof(bcf_fmt_t)); + uint8_t *ptr = (uint8_t*)v->indiv.s; + for (i = 0; i < v->n_fmt; ++i) + ptr = bcf_unpack_fmt_core1(ptr, v->n_sample, &fmt[i]); + for (i = 0; i < (int)v->n_fmt; ++i) { + bcf_fmt_t *f = &fmt[i]; + bcf_enc_int1(&ind, f->id); + bcf_enc_size(&ind, f->n, f->type); + for (j = 0; j < n; ++j) + if (imap[j] >= 0) kputsn((char*)(f->p + imap[j] * f->size), f->size, &ind); + } + for (i = j = 0; j < n; ++j) if (imap[j] >= 0) ++i; + v->n_sample = i; + } else v->n_sample = 0; + if ( !v->n_sample ) v->n_fmt = 0; + free(v->indiv.s); + v->indiv = ind; + v->unpacked &= ~BCF_UN_FMT; // only BCF is ready for output, VCF will need to unpack again + return 0; +} + +int bcf_is_snp(bcf1_t *v) +{ + int i; + bcf_unpack(v, BCF_UN_STR); + for (i = 0; i < v->n_allele; ++i) + if (strlen(v->d.allele[i]) != 1) break; + return i == v->n_allele; +} + +static void bcf_set_variant_type(const char *ref, const char *alt, variant_t *var) +{ + // The most frequent case + if ( !ref[1] && !alt[1] ) + { + if ( *alt == '.' || *ref==*alt ) { var->n = 0; var->type = VCF_REF; return; } + if ( *alt == 'X' ) { var->n = 0; var->type = VCF_REF; return; } // mpileup's X allele shouldn't be treated as variant + var->n = 1; var->type = VCF_SNP; return; + } + + const char *r = ref, *a = alt; + while (*r && *a && *r==*a ) { r++; a++; } + + if ( *a && !*r ) + { + while ( *a ) a++; + var->n = (a-alt)-(r-ref); var->type = VCF_INDEL; return; + } + else if ( *r && !*a ) + { + while ( *r ) r++; + var->n = (a-alt)-(r-ref); var->type = VCF_INDEL; return; + } + else if ( !*r && !*a ) + { + var->n = 0; var->type = VCF_REF; return; + } + + const char *re = r, *ae = a; + while ( re[1] ) re++; + while ( ae[1] ) ae++; + while ( *re==*ae && re>r && ae>a ) { re--; ae--; } + if ( ae==a ) + { + if ( re==r ) { var->n = 1; var->type = VCF_SNP; return; } + var->n = -(re-r); + if ( *re==*ae ) { var->type = VCF_INDEL; return; } + var->type = VCF_OTHER; return; + } + else if ( re==r ) + { + var->n = ae-a; + if ( *re==*ae ) { var->type = VCF_INDEL; return; } + var->type = VCF_OTHER; return; + } + + var->type = ( re-r == ae-a ) ? VCF_MNP : VCF_OTHER; + var->n = ( re-r > ae-a ) ? -(re-r+1) : ae-a+1; + + // should do also complex events, SVs, etc... +} + +static void bcf_set_variant_types(bcf1_t *b) +{ + if ( !(b->unpacked & BCF_UN_STR) ) bcf_unpack(b, BCF_UN_STR); + bcf_dec_t *d = &b->d; + if ( d->n_var < b->n_allele ) + { + d->var = (variant_t *) realloc(d->var, sizeof(variant_t)*b->n_allele); + d->n_var = b->n_allele; + } + int i; + b->d.var_type = 0; + for (i=1; in_allele; i++) + { + bcf_set_variant_type(d->allele[0],d->allele[i], &d->var[i]); + b->d.var_type |= d->var[i].type; + //fprintf(stderr,"[set_variant_type] %d %s %s -> %d %d .. %d\n", b->pos+1,d->allele[0],d->allele[i],d->var[i].type,d->var[i].n, b->d.var_type); + } +} + +int bcf_get_variant_types(bcf1_t *rec) +{ + if ( rec->d.var_type==-1 ) bcf_set_variant_types(rec); + return rec->d.var_type; +} +int bcf_get_variant_type(bcf1_t *rec, int ith_allele) +{ + if ( rec->d.var_type==-1 ) bcf_set_variant_types(rec); + return rec->d.var[ith_allele].type; +} + +int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type) +{ + // Is the field already present? + int i, inf_id = bcf_hdr_id2int(hdr,BCF_DT_ID,key); + if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,inf_id) ) return -1; // No such INFO field in the header + if ( !(line->unpacked & BCF_UN_INFO) ) bcf_unpack(line, BCF_UN_INFO); + + for (i=0; in_info; i++) + if ( inf_id==line->d.info[i].key ) break; + bcf_info_t *inf = i==line->n_info ? NULL : &line->d.info[i]; + + if ( !n || (type==BCF_HT_STR && !values) ) + { + if ( inf ) + { + // Mark the tag for removal, free existing memory if necessary + if ( inf->vptr_free ) + { + free(inf->vptr - inf->vptr_off); + inf->vptr_free = 0; + } + line->d.shared_dirty |= BCF1_DIRTY_INF; + inf->vptr = NULL; + } + return 0; + } + + // Encode the values and determine the size required to accommodate the values + kstring_t str = {0,0,0}; + bcf_enc_int1(&str, inf_id); + if ( type==BCF_HT_INT ) + bcf_enc_vint(&str, n, (int32_t*)values, -1); + else if ( type==BCF_HT_REAL ) + bcf_enc_vfloat(&str, n, (float*)values); + else if ( type==BCF_HT_FLAG || type==BCF_HT_STR ) + { + if ( values==NULL ) + bcf_enc_size(&str, 0, BCF_BT_NULL); + else + bcf_enc_vchar(&str, strlen((char*)values), (char*)values); + } + else + { + fprintf(stderr, "[E::%s] the type %d not implemented yet\n", __func__, type); + abort(); + } + + // Is the INFO tag already present + if ( inf ) + { + // Is it big enough to accommodate new block? + if ( str.l <= inf->vptr_len + inf->vptr_off ) + { + if ( str.l != inf->vptr_len + inf->vptr_off ) line->d.shared_dirty |= BCF1_DIRTY_INF; + uint8_t *ptr = inf->vptr - inf->vptr_off; + memcpy(ptr, str.s, str.l); + free(str.s); + int vptr_free = inf->vptr_free; + bcf_unpack_info_core1(ptr, inf); + inf->vptr_free = vptr_free; + } + else + { + assert( !inf->vptr_free ); // fix the caller or improve here: this has been modified before + bcf_unpack_info_core1((uint8_t*)str.s, inf); + inf->vptr_free = 1; + line->d.shared_dirty |= BCF1_DIRTY_INF; + } + } + else + { + // The tag is not present, create new one + line->n_info++; + hts_expand0(bcf_info_t, line->n_info, line->d.m_info , line->d.info); + inf = &line->d.info[line->n_info-1]; + bcf_unpack_info_core1((uint8_t*)str.s, inf); + inf->vptr_free = 1; + line->d.shared_dirty |= BCF1_DIRTY_INF; + } + line->unpacked |= BCF_UN_INFO; + return 0; +} + +int bcf_update_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char **values, int n) +{ + if ( !n ) + return bcf_update_format(hdr,line,key,NULL,0,BCF_HT_STR); + + int i, max_len = 0; + for (i=0; i max_len ) max_len = len; + } + char *out = (char*) malloc(max_len*n); + if ( !out ) return -2; + for (i=0; iunpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); + + for (i=0; in_fmt; i++) + if ( line->d.fmt[i].id==fmt_id ) break; + bcf_fmt_t *fmt = i==line->n_fmt ? NULL : &line->d.fmt[i]; + + if ( !n ) + { + if ( fmt ) + { + // Mark the tag for removal, free existing memory if necessary + if ( fmt->p_free ) + { + free(fmt->p - fmt->p_off); + fmt->p_free = 0; + } + line->d.indiv_dirty = 1; + fmt->p = NULL; + } + return 0; + } + + line->n_sample = bcf_hdr_nsamples(hdr); + int nps = n / line->n_sample; // number of values per sample + assert( nps && nps*line->n_sample==n ); // must be divisible by n_sample + + // Encode the values and determine the size required to accommodate the values + kstring_t str = {0,0,0}; + bcf_enc_int1(&str, fmt_id); + if ( type==BCF_HT_INT ) + bcf_enc_vint(&str, n, (int32_t*)values, nps); + else if ( type==BCF_HT_REAL ) + { + bcf_enc_size(&str, nps, BCF_BT_FLOAT); + kputsn((char*)values, nps*line->n_sample*sizeof(float), &str); + } + else if ( type==BCF_HT_STR ) + { + bcf_enc_size(&str, nps, BCF_BT_CHAR); + kputsn((char*)values, nps*line->n_sample, &str); + } + else + { + fprintf(stderr, "[E::%s] the type %d not implemented yet\n", __func__, type); + abort(); + } + + if ( !fmt ) + { + // Not present, new format field + line->n_fmt++; + hts_expand0(bcf_fmt_t, line->n_fmt, line->d.m_fmt, line->d.fmt); + + // Special case: VCF specification requires that GT is always first + if ( line->n_fmt > 1 && key[0]=='G' && key[1]=='T' && !key[2] ) + { + for (i=line->n_fmt-1; i>0; i--) + line->d.fmt[i] = line->d.fmt[i-1]; + fmt = &line->d.fmt[0]; + } + else + fmt = &line->d.fmt[line->n_fmt-1]; + bcf_unpack_fmt_core1((uint8_t*)str.s, line->n_sample, fmt); + line->d.indiv_dirty = 1; + fmt->p_free = 1; + } + else + { + // The tag is already present, check if it is big enough to accomodate the new block + if ( str.l <= fmt->p_len + fmt->p_off ) + { + // good, the block is big enough + if ( str.l != fmt->p_len + fmt->p_off ) line->d.indiv_dirty = 1; + uint8_t *ptr = fmt->p - fmt->p_off; + memcpy(ptr, str.s, str.l); + free(str.s); + int p_free = fmt->p_free; + bcf_unpack_fmt_core1(ptr, line->n_sample, fmt); + fmt->p_free = p_free; + } + else + { + assert( !fmt->p_free ); // fix the caller or improve here: this has been modified before + bcf_unpack_fmt_core1((uint8_t*)str.s, line->n_sample, fmt); + fmt->p_free = 1; + line->d.indiv_dirty = 1; + } + } + line->unpacked |= BCF_UN_FMT; + return 0; +} + + +int bcf_update_filter(const bcf_hdr_t *hdr, bcf1_t *line, int *flt_ids, int n) +{ + if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT); + line->d.shared_dirty |= BCF1_DIRTY_FLT; + line->d.n_flt = n; + if ( !n ) return 0; + hts_expand(int, line->d.n_flt, line->d.m_flt, line->d.flt); + int i; + for (i=0; id.flt[i] = flt_ids[i]; + return 0; +} + +int bcf_add_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id) +{ + if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT); + int i; + for (i=0; id.n_flt; i++) + if ( flt_id==line->d.flt[i] ) break; + if ( id.n_flt ) return 0; // this filter is already set + line->d.shared_dirty |= BCF1_DIRTY_FLT; + if ( flt_id==0 ) // set to PASS + line->d.n_flt = 1; + else if ( line->d.n_flt==1 && line->d.flt[0]==0 ) + line->d.n_flt = 1; + else + line->d.n_flt++; + hts_expand(int, line->d.n_flt, line->d.m_flt, line->d.flt); + line->d.flt[line->d.n_flt-1] = flt_id; + return 1; +} +int bcf_remove_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id, int pass) +{ + if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT); + int i; + for (i=0; id.n_flt; i++) + if ( flt_id==line->d.flt[i] ) break; + if ( i==line->d.n_flt ) return 0; // the filter is not present + line->d.shared_dirty |= BCF1_DIRTY_FLT; + if ( i!=line->d.n_flt-1 ) memmove(line->d.flt+i,line->d.flt+i+1,line->d.n_flt-i); + line->d.n_flt--; + if ( !line->d.n_flt && pass ) bcf_add_filter(hdr,line,0); + return 0; +} + +int bcf_has_filter(const bcf_hdr_t *hdr, bcf1_t *line, char *filter) +{ + if ( filter[0]=='.' && !filter[1] ) filter = "PASS"; + int id = bcf_hdr_id2int(hdr, BCF_DT_ID, filter); + if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FLT,id) ) return -1; // not defined in the header + + if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT); + if ( id==0 && !line->d.n_flt) return 1; // PASS + + int i; + for (i=0; id.n_flt; i++) + if ( line->d.flt[i]==id ) return 1; + return 0; +} + +static inline int _bcf1_sync_alleles(const bcf_hdr_t *hdr, bcf1_t *line, int nals) +{ + line->d.shared_dirty |= BCF1_DIRTY_ALS; + + line->n_allele = nals; + hts_expand(char*, line->n_allele, line->d.m_allele, line->d.allele); + + char *als = line->d.als; + int n = 0; + while (nd.allele[n] = als; + while ( *als ) als++; + als++; + n++; + } + return 0; +} +int bcf_update_alleles(const bcf_hdr_t *hdr, bcf1_t *line, const char **alleles, int nals) +{ + kstring_t tmp = {0,0,0}; + char *free_old = NULL; + + // If the supplied alleles are not pointers to line->d.als, the existing block can be reused. + int i; + for (i=0; i=line->d.als && alleles[i]d.als+line->d.m_als ) break; + if ( i==nals ) + { + // all alleles point elsewhere, reuse the existing block + tmp.l = 0; tmp.s = line->d.als; tmp.m = line->d.m_als; + } + else + free_old = line->d.als; + + for (i=0; id.als = tmp.s; line->d.m_als = tmp.m; + free(free_old); + return _bcf1_sync_alleles(hdr,line,nals); +} + +int bcf_update_alleles_str(const bcf_hdr_t *hdr, bcf1_t *line, const char *alleles_string) +{ + kstring_t tmp; + tmp.l = 0; tmp.s = line->d.als; tmp.m = line->d.m_als; + kputs(alleles_string, &tmp); + line->d.als = tmp.s; line->d.m_als = tmp.m; + + int nals = 1; + char *t = line->d.als; + while (*t) + { + if ( *t==',' ) { *t = 0; nals++; } + t++; + } + return _bcf1_sync_alleles(hdr, line, nals); +} + +int bcf_update_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id) +{ + kstring_t tmp; + tmp.l = 0; tmp.s = line->d.id; tmp.m = line->d.m_id; + if ( id ) + kputs(id, &tmp); + else + kputs(".", &tmp); + line->d.id = tmp.s; line->d.m_id = tmp.m; + line->d.shared_dirty |= BCF1_DIRTY_ID; + return 0; +} + +bcf_fmt_t *bcf_get_fmt(const bcf_hdr_t *hdr, bcf1_t *line, const char *key) +{ + int i, id = bcf_hdr_id2int(hdr, BCF_DT_ID, key); + if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) ) return NULL; // no such FMT field in the header + if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); + for (i=0; in_fmt; i++) + { + if ( line->d.fmt[i].id==id ) return &line->d.fmt[i]; + } + return NULL; +} + +bcf_info_t *bcf_get_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key) +{ + int i, id = bcf_hdr_id2int(hdr, BCF_DT_ID, key); + if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,id) ) return NULL; // no such INFO field in the header + if ( !(line->unpacked & BCF_UN_INFO) ) bcf_unpack(line, BCF_UN_INFO); + for (i=0; in_info; i++) + { + if ( line->d.info[i].key==id ) return &line->d.info[i]; + } + return NULL; +} + +int bcf_get_info_values(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, void **dst, int *ndst, int type) +{ + int i,j, tag_id = bcf_hdr_id2int(hdr, BCF_DT_ID, tag); + if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,tag_id) ) return -1; // no such INFO field in the header + if ( bcf_hdr_id2type(hdr,BCF_HL_INFO,tag_id)!=type ) return -2; // expected different type + + if ( !(line->unpacked & BCF_UN_INFO) ) bcf_unpack(line, BCF_UN_INFO); + + for (i=0; in_info; i++) + if ( line->d.info[i].key==tag_id ) break; + if ( i==line->n_info ) return ( type==BCF_HT_FLAG ) ? 0 : -3; // the tag is not present in this record + if ( type==BCF_HT_FLAG ) return 1; + + bcf_info_t *info = &line->d.info[i]; + if ( type==BCF_HT_STR ) + { + if ( *ndst < info->len+1 ) + { + *ndst = info->len + 1; + *dst = realloc(*dst, *ndst); + } + memcpy(*dst,info->vptr,info->len); + ((uint8_t*)*dst)[info->len] = 0; + return info->len; + } + + // Make sure the buffer is big enough + int size1 = type==BCF_HT_INT ? sizeof(int32_t) : sizeof(float); + if ( *ndst < info->len ) + { + *ndst = info->len; + *dst = realloc(*dst, *ndst * size1); + } + + if ( info->len == 1 ) + { + if ( info->type==BCF_BT_FLOAT ) *((float*)*dst) = info->v1.f; + else *((int32_t*)*dst) = info->v1.i; + return 1; + } + +#define BRANCH(type_t, is_missing, is_vector_end, set_missing, out_type_t) { \ + out_type_t *tmp = (out_type_t *) *dst; \ + type_t *p = (type_t *) info->vptr; \ + for (j=0; jlen; j++) \ + { \ + if ( is_vector_end ) return j; \ + if ( is_missing ) set_missing; \ + else *tmp = p[j]; \ + tmp++; \ + } \ + return j; \ +} +switch (info->type) { + case BCF_BT_INT8: BRANCH(int8_t, p[j]==bcf_int8_missing, p[j]==bcf_int8_vector_end, *tmp=bcf_int32_missing, int32_t); break; + case BCF_BT_INT16: BRANCH(int16_t, p[j]==bcf_int16_missing, p[j]==bcf_int16_vector_end, *tmp=bcf_int32_missing, int32_t); break; + case BCF_BT_INT32: BRANCH(int32_t, p[j]==bcf_int32_missing, p[j]==bcf_int32_vector_end, *tmp=bcf_int32_missing, int32_t); break; + case BCF_BT_FLOAT: BRANCH(float, bcf_float_is_missing(p[j]), bcf_float_is_vector_end(p[j]), bcf_float_set_missing(*tmp), float); break; + default: fprintf(stderr,"TODO: %s:%d .. info->type=%d\n", __FILE__,__LINE__, info->type); exit(1); +} +#undef BRANCH +return -4; // this can never happen +} + +int bcf_get_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, char ***dst, int *ndst) +{ + int i,tag_id = bcf_hdr_id2int(hdr, BCF_DT_ID, tag); + if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,tag_id) ) return -1; // no such FORMAT field in the header + if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=BCF_HT_STR ) return -2; // expected different type + + if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); + + for (i=0; in_fmt; i++) + if ( line->d.fmt[i].id==tag_id ) break; + if ( i==line->n_fmt ) return -3; // the tag is not present in this record + bcf_fmt_t *fmt = &line->d.fmt[i]; + + int nsmpl = bcf_hdr_nsamples(hdr); + if ( !*dst ) + { + *dst = (char**) malloc(sizeof(char*)*nsmpl); + if ( !*dst ) return -4; // could not alloc + (*dst)[0] = NULL; + } + int n = (fmt->n+1)*nsmpl; + if ( *ndst < n ) + { + (*dst)[0] = realloc((*dst)[0], n); + if ( !(*dst)[0] ) return -4; // could not alloc + *ndst = n; + } + for (i=0; ip + i*fmt->n; + uint8_t *tmp = (uint8_t*)(*dst)[0] + i*(fmt->n+1); + memcpy(tmp,src,fmt->n); + tmp[fmt->n] = 0; + (*dst)[i] = (char*) tmp; + } + return n; +} + +int bcf_get_format_values(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, void **dst, int *ndst, int type) +{ + int i,j, tag_id = bcf_hdr_id2int(hdr, BCF_DT_ID, tag); + if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,tag_id) ) return -1; // no such FORMAT field in the header + if ( tag[0]=='G' && tag[1]=='T' && tag[2]==0 ) + { + // Ugly: GT field is considered to be a string by the VCF header but BCF represents it as INT. + if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=BCF_HT_STR ) return -2; + } + else if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=type ) return -2; // expected different type + + if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT); + + for (i=0; in_fmt; i++) + if ( line->d.fmt[i].id==tag_id ) break; + if ( i==line->n_fmt ) return -3; // the tag is not present in this record + bcf_fmt_t *fmt = &line->d.fmt[i]; + + if ( type==BCF_HT_STR ) + { + int n = fmt->n*bcf_hdr_nsamples(hdr); + if ( *ndst < n ) + { + *dst = realloc(*dst, n); + if ( !*dst ) return -4; // could not alloc + *ndst = n; + } + memcpy(*dst,fmt->p,n); + return n; + } + + // Make sure the buffer is big enough + int nsmpl = bcf_hdr_nsamples(hdr); + int size1 = type==BCF_HT_INT ? sizeof(int32_t) : sizeof(float); + if ( *ndst < fmt->n*nsmpl ) + { + *ndst = fmt->n*nsmpl; + *dst = realloc(*dst, *ndst*size1); + if ( !dst ) return -4; // could not alloc + } + +#define BRANCH(type_t, is_missing, is_vector_end, set_missing, set_vector_end, out_type_t) { \ + out_type_t *tmp = (out_type_t *) *dst; \ + type_t *p = (type_t*) fmt->p; \ + for (i=0; in; j++) \ + { \ + if ( is_missing ) set_missing; \ + else if ( is_vector_end ) { set_vector_end; break; } \ + else *tmp = p[j]; \ + tmp++; \ + } \ + for (; jn; j++) { set_vector_end; tmp++; } \ + p = (type_t *)((char *)p + fmt->size); \ + } \ +} +switch (fmt->type) { + case BCF_BT_INT8: BRANCH(int8_t, p[j]==bcf_int8_missing, p[j]==bcf_int8_vector_end, *tmp=bcf_int32_missing, *tmp=bcf_int32_vector_end, int32_t); break; + case BCF_BT_INT16: BRANCH(int16_t, p[j]==bcf_int16_missing, p[j]==bcf_int16_vector_end, *tmp=bcf_int32_missing, *tmp=bcf_int32_vector_end, int32_t); break; + case BCF_BT_INT32: BRANCH(int32_t, p[j]==bcf_int32_missing, p[j]==bcf_int32_vector_end, *tmp=bcf_int32_missing, *tmp=bcf_int32_vector_end, int32_t); break; + case BCF_BT_FLOAT: BRANCH(float, bcf_float_is_missing(p[j]), bcf_float_is_vector_end(p[j]), bcf_float_set_missing(*tmp), bcf_float_set_vector_end(*tmp), float); break; + default: fprintf(stderr,"TODO: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt->type); exit(1); +} +#undef BRANCH +return nsmpl*fmt->n; +} + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/vcf_sweep.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/vcf_sweep.c new file mode 100644 index 0000000000000000000000000000000000000000..2598460577c3385311512c0acc22851ea9267765 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/vcf_sweep.c @@ -0,0 +1,158 @@ +#include "htslib/vcf_sweep.h" +#include "htslib/bgzf.h" + +#define SW_FWD 0 +#define SW_BWD 1 + +struct _bcf_sweep_t +{ + htsFile *file; + bcf_hdr_t *hdr; + BGZF *fp; + + int direction; // to tell if the direction has changed + int block_size; // the size of uncompressed data to hold in memory + bcf1_t *rec; // bcf buffer + int nrec, mrec; // number of used records; total size of the buffer + int lrid, lpos, lnals, lals_len, mlals; // to check uniqueness of a record + char *lals; + + uint64_t *idx; // uncompressed offsets of VCF/BCF records + int iidx, nidx, midx; // i: current offset; n: used; m: allocated + int idx_done; // the index is built during the first pass +}; + +BGZF *hts_get_bgzfp(htsFile *fp); +int hts_useek(htsFile *file, long uoffset, int where); +long hts_utell(htsFile *file); + +static inline int sw_rec_equal(bcf_sweep_t *sw, bcf1_t *rec) +{ + if ( sw->lrid!=rec->rid ) return 0; + if ( sw->lpos!=rec->pos ) return 0; + if ( sw->lnals!=rec->n_allele ) return 0; + + char *t = rec->d.allele[sw->lnals-1]; + int len = t - rec->d.allele[0] + 1; + while ( *t ) { t++; len++; } + if ( sw->lals_len!=len ) return 0; + if ( memcmp(sw->lals,rec->d.allele[0],len) ) return 0; + return 1; +} + +static void sw_rec_save(bcf_sweep_t *sw, bcf1_t *rec) +{ + sw->lrid = rec->rid; + sw->lpos = rec->pos; + sw->lnals = rec->n_allele; + + char *t = rec->d.allele[sw->lnals-1]; + int len = t - rec->d.allele[0] + 1; + while ( *t ) { t++; len++; } + sw->lals_len = len; + hts_expand(char, len, sw->mlals, sw->lals); + memcpy(sw->lals, rec->d.allele[0], len); +} + +static void sw_fill_buffer(bcf_sweep_t *sw) +{ + if ( !sw->iidx ) return; + sw->iidx--; + + int ret = hts_useek(sw->file, sw->idx[sw->iidx], 0); + assert( ret==0 ); + + sw->nrec = 0; + bcf1_t *rec = &sw->rec[sw->nrec]; + while ( (ret=bcf_read1(sw->file, sw->hdr, rec))==0 ) + { + bcf_unpack(rec, BCF_UN_STR); + + // if not in the last block, stop at the saved record + if ( sw->iidx+1 < sw->nidx && sw_rec_equal(sw,rec) ) break; + + sw->nrec++; + hts_expand0(bcf1_t, sw->nrec+1, sw->mrec, sw->rec); + rec = &sw->rec[sw->nrec]; + } + sw_rec_save(sw, &sw->rec[0]); +} + +bcf_sweep_t *bcf_sweep_init(const char *fname) +{ + bcf_sweep_t *sw = (bcf_sweep_t*) calloc(1,sizeof(bcf_sweep_t)); + sw->file = hts_open(fname, "r"); + sw->fp = hts_get_bgzfp(sw->file); + bgzf_index_build_init(sw->fp); + sw->hdr = bcf_hdr_read(sw->file); + sw->mrec = 1; + sw->rec = (bcf1_t*) calloc(sw->mrec,(sizeof(bcf1_t))); + sw->block_size = 1024*1024*3; + sw->direction = SW_FWD; + return sw; +} + +void bcf_empty1(bcf1_t *v); +void bcf_sweep_destroy(bcf_sweep_t *sw) +{ + int i; + for (i=0; imrec; i++) bcf_empty1(&sw->rec[i]); + free(sw->idx); + free(sw->rec); + free(sw->lals); + bcf_hdr_destroy(sw->hdr); + hts_close(sw->file); + free(sw); +} + +static void sw_seek(bcf_sweep_t *sw, int direction) +{ + sw->direction = direction; + if ( direction==SW_FWD ) + hts_useek(sw->file, sw->idx[0], 0); + else + { + sw->iidx = sw->nidx; + sw->nrec = 0; + } +} + +bcf1_t *bcf_sweep_fwd(bcf_sweep_t *sw) +{ + if ( sw->direction==SW_BWD ) sw_seek(sw, SW_FWD); + + long pos = hts_utell(sw->file); + + bcf1_t *rec = &sw->rec[0]; + int ret = bcf_read1(sw->file, sw->hdr, rec); + + if ( ret!=0 ) // last record, get ready for sweeping backwards + { + sw->idx_done = 1; + sw->fp->idx_build_otf = 0; + sw_seek(sw, SW_BWD); + return NULL; + } + + if ( !sw->idx_done ) + { + if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size ) + { + sw->nidx++; + hts_expand(uint64_t, sw->nidx, sw->midx, sw->idx); + sw->idx[sw->nidx-1] = pos; + } + } + return rec; +} + +bcf1_t *bcf_sweep_bwd(bcf_sweep_t *sw) +{ + if ( sw->direction==SW_FWD ) sw_seek(sw, SW_BWD); + if ( !sw->nrec ) sw_fill_buffer(sw); + if ( !sw->nrec ) return NULL; + return &sw->rec[ --sw->nrec ]; +} + +bcf_hdr_t *bcf_sweep_hdr(bcf_sweep_t *sw) { return sw->hdr; } + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/vcfutils.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/vcfutils.c new file mode 100644 index 0000000000000000000000000000000000000000..c482405e8024a4609710112f2f267999c0d1d0ce --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/vcfutils.c @@ -0,0 +1,642 @@ +#include "htslib/vcfutils.h" + +int bcf_calc_ac(const bcf_hdr_t *header, bcf1_t *line, int *ac, int which) +{ + int i; + for (i=0; in_allele; i++) ac[i]=0; + + // Use INFO/AC,AN field only when asked + if ( which&BCF_UN_INFO ) + { + bcf_unpack(line, BCF_UN_INFO); + int an_id = bcf_hdr_id2int(header, BCF_DT_ID, "AN"); + int ac_id = bcf_hdr_id2int(header, BCF_DT_ID, "AC"); + int i, an=-1, ac_len=0, ac_type=0; + uint8_t *ac_ptr=NULL; + if ( an_id>=0 && ac_id>=0 ) + { + for (i=0; in_info; i++) + { + bcf_info_t *z = &line->d.info[i]; + if ( z->key == an_id ) an = z->v1.i; + else if ( z->key == ac_id ) { ac_ptr = z->vptr; ac_len = z->len; ac_type = z->type; } + } + } + if ( an>=0 && ac_ptr ) + { + int nac = 0; + #define BRANCH_INT(type_t) { \ + type_t *p = (type_t *) ac_ptr; \ + for (i=0; iid[BCF_DT_CTG][line->rid].key, line->pos+1); exit(1); break; + } + #undef BRANCH_INT + assert( an>=nac ); // sanity check for missing values + ac[0] = an - nac; + return 1; + } + } + + // Split genotype fields only when asked + if ( which&BCF_UN_FMT ) + { + int i, gt_id = bcf_hdr_id2int(header,BCF_DT_ID,"GT"); + if ( gt_id<0 ) return 0; + bcf_unpack(line, BCF_UN_FMT); + bcf_fmt_t *fmt_gt = NULL; + for (i=0; i<(int)line->n_fmt; i++) + if ( line->d.fmt[i].id==gt_id ) { fmt_gt = &line->d.fmt[i]; break; } + if ( !fmt_gt ) return 0; + #define BRANCH_INT(type_t,missing,vector_end) { \ + for (i=0; in_sample; i++) \ + { \ + type_t *p = (type_t*) (fmt_gt->p + i*fmt_gt->size); \ + int ial; \ + for (ial=0; ialn; ial++) \ + { \ + if ( p[ial]==vector_end ) break; /* smaller ploidy */ \ + if ( !(p[ial]>>1) || p[ial]==missing ) continue; /* missing allele */ \ + ac[(p[ial]>>1)-1]++; \ + } \ + } \ + } + switch (fmt_gt->type) { + case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break; + case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break; + case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break; + default: fprintf(stderr, "[E::%s] todo: %d at %s:%d\n", __func__, fmt_gt->type, header->id[BCF_DT_CTG][line->rid].key, line->pos+1); exit(1); break; + } + #undef BRANCH_INT + return 1; + } + return 0; +} + +int bcf_gt_type(bcf_fmt_t *fmt_ptr, int isample, int *_ial, int *_jal) +{ + int i, nals = 0, has_ref = 0, has_alt = 0, ial = 0, jal = 0; + #define BRANCH_INT(type_t,missing,vector_end) { \ + type_t *p = (type_t*) (fmt_ptr->p + isample*fmt_ptr->size); \ + for (i=0; in; i++) \ + { \ + if ( p[i] == vector_end ) break; /* smaller ploidy */ \ + if ( !p[i] || p[i] == missing ) continue; /* missing allele */ \ + int tmp = p[i]>>1; \ + if ( tmp>1 ) \ + { \ + if ( !ial ) { ial = tmp; has_alt = 1; } \ + else if ( tmp!=ial ) \ + { \ + if ( tmptype) { + case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break; + case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break; + case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break; + default: fprintf(stderr, "[E::%s] todo: fmt_type %d\n", __func__, fmt_ptr->type); exit(1); break; + } + #undef BRANCH_INT + + if ( _ial ) *_ial = ial>0 ? ial-1 : ial; + if ( _jal ) *_jal = jal>0 ? jal-1 : jal; + if ( !nals ) return GT_UNKN; + if ( nals==1 ) + return has_ref ? GT_HAPL_R : GT_HAPL_A; + if ( !has_ref ) + return has_alt==1 ? GT_HOM_AA : GT_HET_AA; + if ( !has_alt ) + return GT_HOM_RR; + return GT_HET_RA; +} + +int bcf_trim_alleles(const bcf_hdr_t *header, bcf1_t *line) +{ + int i; + bcf_fmt_t *gt = bcf_get_fmt(header, line, "GT"); + if ( !gt ) return 0; + + int *ac = (int*) calloc(line->n_allele,sizeof(int)); + + // check if all alleles are populated + #define BRANCH(type_t,missing,vector_end) { \ + for (i=0; in_sample; i++) \ + { \ + type_t *p = (type_t*) (gt->p + i*gt->size); \ + int ial; \ + for (ial=0; ialsize; ial++) \ + { \ + if ( p[ial]==vector_end ) break; /* smaller ploidy */ \ + if ( !(p[ial]>>1) || p[ial]==missing ) continue; /* missing allele */ \ + if ( (p[ial]>>1)-1 >= line->n_allele ) return -1; \ + ac[(p[ial]>>1)-1]++; \ + } \ + } \ + } + switch (gt->type) { + case BCF_BT_INT8: BRANCH(int8_t, bcf_int8_missing, bcf_int8_vector_end); break; + case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_missing, bcf_int16_vector_end); break; + case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_missing, bcf_int32_vector_end); break; + default: fprintf(stderr, "[E::%s] todo: %d at %s:%d\n", __func__, gt->type, header->id[BCF_DT_CTG][line->rid].key, line->pos+1); exit(1); break; + } + #undef BRANCH + + int rm_als = 0, nrm = 0; + for (i=1; in_allele; i++) + { + if ( !ac[i] ) { rm_als |= 1<n_allele, sizeof(int)); + + // create map of indexes from old to new ALT numbering and modify ALT + kstring_t str = {0,0,0}; + kputs(line->d.allele[0], &str); + + int nrm = 0, i,j; // i: ori alleles, j: new alleles + for (i=1, j=1; in_allele; i++) + { + if ( rm_mask & 1<d.allele[i] = NULL; + nrm++; + continue; + } + kputc(',', &str); + kputs(line->d.allele[i], &str); + map[i] = j; + j++; + } + if ( !nrm ) { free(map); free(str.s); return; } + + int nR_ori = line->n_allele; + int nR_new = line->n_allele-nrm; + assert(nR_new > 0); // should not be able to remove reference allele + int nA_ori = nR_ori-1; + int nA_new = nR_new-1; + + int nG_ori = nR_ori*(nR_ori + 1)/2; + int nG_new = nR_new*(nR_new + 1)/2; + + bcf_update_alleles_str(header, line, str.s); + + // remove from Number=G, Number=R and Number=A INFO fields. + uint8_t *dat = NULL; + int mdat = 0, ndat = 0, mdat_bytes = 0, nret; + for (i=0; in_info; i++) + { + bcf_info_t *info = &line->d.info[i]; + int vlen = bcf_hdr_id2length(header,BCF_HL_INFO,info->key); + + if ( vlen!=BCF_VL_A && vlen!=BCF_VL_G && vlen!=BCF_VL_R ) continue; // no need to change + + int type = bcf_hdr_id2type(header,BCF_HL_INFO,info->key); + if ( type==BCF_HT_FLAG ) continue; + int size = 1; + if ( type==BCF_HT_REAL || type==BCF_HT_INT ) size = 4; + + mdat = mdat_bytes / size; + nret = bcf_get_info_values(header, line, bcf_hdr_int2id(header,BCF_DT_ID,info->key), (void**)&dat, &mdat, type); + mdat_bytes = mdat * size; + if ( nret<0 ) + { + fprintf(stderr,"[%s:%d %s] Could not access INFO/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__, + bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname(header,line), line->pos+1, nret); + exit(1); + } + if ( type==BCF_HT_STR ) + { + str.l = 0; + char *ss = (char*) dat, *se = (char*) dat; + if ( vlen==BCF_VL_A || vlen==BCF_VL_R ) + { + int nexp, inc = 0; + if ( vlen==BCF_VL_A ) + { + nexp = nA_ori; + inc = 1; + } + else + nexp = nR_ori; + for (j=0; jkey), (void*)str.s, str.l, type); + if ( nret<0 ) + { + fprintf(stderr,"[%s:%d %s] Could not update INFO/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__, + bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname(header,line), line->pos+1, nret); + exit(1); + } + continue; + } + + if ( vlen==BCF_VL_A || vlen==BCF_VL_R ) + { + int inc = 0, ntop; + if ( vlen==BCF_VL_A ) + { + assert( nret==nA_ori ); + ntop = nA_ori; + ndat = nA_new; + inc = 1; + } + else + { + assert( nret==nR_ori ); + ntop = nR_ori; + ndat = nR_new; + } + int k = 0; + + #define BRANCH(type_t,is_vector_end) \ + { \ + type_t *ptr = (type_t*) dat; \ + int size = sizeof(type_t); \ + for (j=0; jkey), (void*)dat, ndat, type); + if ( nret<0 ) + { + fprintf(stderr,"[%s:%d %s] Could not update INFO/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__, + bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname(header,line), line->pos+1, nret); + exit(1); + } + } + + // Update GT fields, the allele indexes might have changed + for (i=1; in_allele; i++) if ( map[i]!=i ) break; + if ( in_allele ) + { + mdat = mdat_bytes / 4; // sizeof(int32_t) + nret = bcf_get_genotypes(header,line,(void**)&dat,&mdat); + mdat_bytes = mdat * 4; + if ( nret>0 ) + { + nret /= line->n_sample; + int32_t *ptr = (int32_t*) dat; + for (i=0; in_sample; i++) + { + for (j=0; j=0 ); + ptr[j] = (map[al]+1)<<1 | (ptr[j]&1); + } + ptr += nret; + } + bcf_update_genotypes(header, line, (void*)dat, nret*line->n_sample); + } + } + + // Remove from Number=G, Number=R and Number=A FORMAT fields. + // Assuming haploid or diploid GTs + for (i=0; in_fmt; i++) + { + bcf_fmt_t *fmt = &line->d.fmt[i]; + int vlen = bcf_hdr_id2length(header,BCF_HL_FMT,fmt->id); + + if ( vlen!=BCF_VL_A && vlen!=BCF_VL_G && vlen!=BCF_VL_R ) continue; // no need to change + + int type = bcf_hdr_id2type(header,BCF_HL_FMT,fmt->id); + if ( type==BCF_HT_FLAG ) continue; + + int size = 1; + if ( type==BCF_HT_REAL || type==BCF_HT_INT ) size = 4; + + mdat = mdat_bytes / size; + nret = bcf_get_format_values(header, line, bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), (void**)&dat, &mdat, type); + mdat_bytes = mdat * size; + if ( nret<0 ) + { + fprintf(stderr,"[%s:%d %s] Could not access FORMAT/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__, + bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname(header,line), line->pos+1, nret); + exit(1); + } + + if ( type==BCF_HT_STR ) + { + int size = nret/line->n_sample; // number of bytes per sample + str.l = 0; + if ( vlen==BCF_VL_A || vlen==BCF_VL_R ) + { + int nexp, inc = 0; + if ( vlen==BCF_VL_A ) + { + nexp = nA_ori; + inc = 1; + } + else + nexp = nR_ori; + for (j=0; jn_sample; j++) + { + char *ss = ((char*)dat) + j*size, *se = ss + size, *ptr = ss; + int k_src = 0, k_dst = 0, l = str.l; + for (k_src=0; k_src=se || !*ptr) break; + while ( ptrn_sample; j++) + { + char *ss = ((char*)dat) + j*size, *se = ss + size, *ptr = ss; + int k_src = 0, k_dst = 0, l = str.l; + int nexp = 0; // diploid or haploid? + while ( ptr=se || !*ptr ) break; + while ( ptr=se || !*ptr ) break; + } + } + else // haploid + { + for (k_src=0; k_src=se || !*ptr ) break; + while ( ptrid), (void*)str.s, str.l, type); + if ( nret<0 ) + { + fprintf(stderr,"[%s:%d %s] Could not update FORMAT/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__, + bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname(header,line), line->pos+1, nret); + exit(1); + } + continue; + } + + int nori = nret / line->n_sample; + if ( vlen==BCF_VL_A || vlen==BCF_VL_R || (vlen==BCF_VL_G && nori==nR_ori) ) // Number=A, R or haploid Number=G + { + int ntop, inc = 0; + if ( vlen==BCF_VL_A ) + { + assert( nori==nA_ori ); // todo: will fail if all values are missing + ntop = nA_ori; + ndat = nA_new*line->n_sample; + inc = 1; + } + else + { + assert( nori==nR_ori ); // todo: will fail if all values are missing + ntop = nR_ori; + ndat = nR_new*line->n_sample; + } + + #define BRANCH(type_t,is_vector_end) \ + { \ + for (j=0; jn_sample; j++) \ + { \ + type_t *ptr_src = ((type_t*)dat) + j*nori; \ + type_t *ptr_dst = ((type_t*)dat) + j*nA_new; \ + int size = sizeof(type_t); \ + int k_src, k_dst = 0; \ + for (k_src=0; k_srcn_sample; + + #define BRANCH(type_t,is_vector_end) \ + { \ + for (j=0; jn_sample; j++) \ + { \ + type_t *ptr_src = ((type_t*)dat) + j*nori; \ + type_t *ptr_dst = ((type_t*)dat) + j*nG_new; \ + int size = sizeof(type_t); \ + int ia, ib, k_dst = 0, k_src; \ + int nset = 0; /* haploid or diploid? */ \ + for (k_src=0; k_srcid), (void*)dat, ndat, type); + if ( nret<0 ) + { + fprintf(stderr,"[%s:%d %s] Could not update FORMAT/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__, + bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname(header,line), line->pos+1, nret); + exit(1); + } + } + free(dat); + free(str.s); + free(map); +} + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/version.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/version.h new file mode 100644 index 0000000000000000000000000000000000000000..7c90cef7525a4a0db8783e1b7f4b089d08862adc --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/htslib/version.h @@ -0,0 +1 @@ +#define HTS_VERSION "0.0.1" diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/README b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/README new file mode 100644 index 0000000000000000000000000000000000000000..79d6b0ce0b3ba5cf593e5a006e3802f3323c67ab --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/README @@ -0,0 +1,7 @@ +*** NOTE: this is GPL code + +Binaries built from //research/EmergingApplications/Investigations/genomics/libbwtsw + +libbwtsw-linux-amd64-release.a: gcc 4.4.7 (-O2 -g), P4 CL 35226 +bwtsw.*: VS2008 SP1 (cl.exe version 15.00.30729.01, /Zi /O2), P4 CL 35226 + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/bwtsw.idb b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/bwtsw.idb new file mode 100644 index 0000000000000000000000000000000000000000..2ab227889078e825bde5e6a766de62be2d4fa994 Binary files /dev/null and b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/bwtsw.idb differ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/bwtsw.lib b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/bwtsw.lib new file mode 100644 index 0000000000000000000000000000000000000000..c91227fe86b1dae6764332ea6743fb29e385f492 Binary files /dev/null and b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/bwtsw.lib differ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/bwtsw.pdb b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/bwtsw.pdb new file mode 100644 index 0000000000000000000000000000000000000000..5dd98527f550de030104856018a767d284223d97 Binary files /dev/null and b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/bwtsw.pdb differ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/libbwtsw-linux-amd64-release.a b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/libbwtsw-linux-amd64-release.a new file mode 100644 index 0000000000000000000000000000000000000000..ad822ae0145f8abada6030fa795cd346be812cd4 Binary files /dev/null and b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libbwtsw-bin/libbwtsw-linux-amd64-release.a differ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsort-lite/COPYING b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsort-lite/COPYING new file mode 100644 index 0000000000000000000000000000000000000000..13023f75b037835af214829c6ff45fc5a8ffe114 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsort-lite/COPYING @@ -0,0 +1,27 @@ +The libdivsufsort-lite copyright is as follows: + +Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + +Permission is hereby granted, free of charge, to any person +obtaining a copy of this software and associated documentation +files (the "Software"), to deal in the Software without +restriction, including without limitation the rights to use, +copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the +Software is furnished to do so, subject to the following +conditions: + +The above copyright notice and this permission notice shall be +included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR +OTHER DEALINGS IN THE SOFTWARE. + +See also the libdivsufsort web site: + http://libdivsufsort.googlecode.com/ for more information. diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsort-lite/README b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsort-lite/README new file mode 100644 index 0000000000000000000000000000000000000000..63c6655dea5f1e9bdfcdfb0e32262806237f36b9 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsort-lite/README @@ -0,0 +1,185 @@ +libdivsufsort - A lightweight suffix-sorting library. +----------------------------------------------------- + +Introduction: +------------- + +The libdivsufsort project provides a fast, lightweight, and robust +C API library to construct the suffix array and the Burrows-Wheeler +transformed string for any input string of a constant-size alphabet. + +The suffix-sorting algorithm runs in O(n log n) worst-case time +using only 5n+O(1) bytes of memory space, where n is the length of +the input string. + +The latest version of libdivsufsort is available at: + http://libdivsufsort.googlecode.com/ + + +License: +-------- + +libdivsufsort is released under the MIT/X11 license. See the file +COPYING for more details. + + +APIs: +----- + + * Data types + typedef int32_t saint_t; + typedef int32_t saidx_t; + typedef uint8_t sauchar_t; + + * Constructs the suffix array of a given string. + * @param T[0..n-1] The input string. + * @param SA[0..n-1] The output array or suffixes. + * @param n The length of the given string. + * @return 0 if no error occurred, -1 or -2 otherwise. + saint_t + divsufsort(const sauchar_t *T, saidx_t *SA, saidx_t n); + + * Constructs the burrows-wheeler transformed string of a given string. + * @param T[0..n-1] The input string. + * @param U[0..n-1] The output string. (can be T) + * @param A[0..n-1] The temporary array. (can be NULL) + * @param n The length of the given string. + * @return The primary index if no error occurred, -1 or -2 otherwise. + saidx_t + divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n); + + +Benchmark: +------------------ + += Specifications = +Processor: 2.66 GHz Intel Core 2 Duo E6750 +L1 Cache: (32 Kb + 32 Kb) x 2 +L2 Cache: 4 Mb +RAM: 2 Gb main memory +Operating system: Windows XP Home SP 3 (with Cygwin) +Compiler: GCC version 4.3.1 + += Programs = +Archon4r0 kvark's sorting algorithm http://forum.compression.ru/viewtopic.php?t=352 +BPR Bucket-Pointer Refinement algorithm http://bibiserv.techfak.uni-bielefeld.de/bpr/ +DC Difference-Cover algorithm (v = 32) http://www.cs.helsinki.fi/juha.karkkainen/publications/cpm03.tar.gz +DS Deep-Shallow sorting algorithm http://www.mfn.unipmn.it/~manzini/lightweight/ +divsufsort1 libdivsufsort version 1.2.3 http://libdivsufsort.googlecode.com/ +divsufsort2 libdivsufsort version 2.0.0 http://libdivsufsort.googlecode.com/ +KA Ko-Aluru algorithm http://ko.pang.cn.googlepages.com/software2 +KS Kärkkäinen-Sanders algorithm http://www.mpi-inf.mpg.de/~sanders/programs/suffix/ +MSufSort3 MSufSort version 3.1.1 beta http://www.michael-maniscalco.com/msufsort.htm +qsufsort Larsson-Sadakane algorithm http://www.larsson.dogma.net/research.html +sais Induced Sorting algorithm http://yuta.256.googlepages.com/sais + +All programs were compiled with gcc/g++ using '-O3 -fomit-frame-pointer -DNDEBUG' +optimization options. The times are the average of five runs, in seconds, and were +measured using the standard Unix/Cygwin 'time' command. (user + system) The spaces +were measured using the 'memusage' command. + += Testfiles = +Manzini's Large Corpus http://www.mfn.unipmn.it/~manzini/lightweight/corpus/ +The Gauntlet http://www.michael-maniscalco.com/testset/gauntlet/ + += Running times = + +== Manzini's Corpus == +Files Size Archon4r0 BPR DC DS divsufsort1 divsufsort2 KA KS MSufSort3 qsufsort sais +chr22.dna 34553758 6.030 6.196 22.694 7.514 5.404 5.362 16.980 50.006 7.132 10.642 10.796 +etext99 105277340 22.160 32.582 79.872 34.264 18.758 18.064 73.236 202.684 24.106 56.612 38.748 +gcc-3.0.tar 86630400 13.856 20.692 61.690 35.822 10.382 10.084 40.908 135.174 14.952 40.766 20.990 +howto 39422105 5.806 8.326 25.432 8.288 5.472 5.320 20.694 64.834 5.672 16.366 11.388 +jdk13c 69728899 18.106 22.252 61.234 32.182 9.260 9.010 34.172 101.096 11.314 39.792 16.396 +linux-2.4.5.tar 116254720 18.174 26.226 82.830 25.912 14.672 14.290 58.586 194.412 19.890 54.054 29.614 +rctail96 114711151 32.490 55.826 119.026 62.502 18.500 17.914 70.072 190.562 21.060 70.456 33.248 +rfc 116421901 20.736 35.404 91.284 29.666 16.116 15.658 64.390 196.500 17.936 61.436 32.224 +sprot34.dat 109617186 22.832 36.720 93.122 32.096 17.894 17.404 68.084 187.594 23.352 56.946 34.092 +w3c2 104201579 27.264 29.384 89.352 54.682 13.866 13.486 52.660 162.582 17.090 77.804 25.498 +totals 896819039 187.454 273.608 726.536 322.928 130.324 126.592 499.782 1485.444 162.504 484.874 252.994 + +== The Gauntlet == +Files Size Archon4r0 BPR DC DS divsufsort1 divsufsort2 KA KS MSufSort3 qsufsort sais +abac 200000 0.044 0.064 0.104 27.914 0.042 0.036 0.058 0.048 0.050 0.062 0.044 +abba 10500600 3.270 5.124 10.766 30.702 1.714 1.602 2.570 7.952 3.514 15.272 1.460 +book1x20 15375420 4.392 3.530 13.872 97.468 2.312 2.154 7.442 15.756 3.542 22.376 3.912 +fib_s14930352 14930352 12.728 10.830 18.524 179.040 3.638 3.588 3.544 10.232 6.700 18.224 2.542 +fss10 12078908 11.390 8.974 15.130 85.328 2.828 2.824 3.344 8.646 4.618 14.754 2.076 +fss9 2851443 1.002 1.210 1.644 5.256 0.410 0.416 0.618 1.290 0.554 2.836 0.336 +houston 3840000 0.344 0.708 2.226 118.960 0.118 0.128 0.520 0.744 0.242 1.230 0.238 +paper5x80 981924 0.110 0.154 0.454 0.806 0.092 0.090 0.210 0.256 0.144 0.448 0.110 +test1 2097152 0.332 2.132 1.108 8.680 0.268 0.280 0.376 1.066 1.302 2.762 0.202 +test2 2097152 0.710 0.616 1.110 8.682 0.180 0.176 0.374 1.076 3.354 2.768 0.206 +test3 2097152 0.488 213.154 1.164 1.772 0.220 0.226 0.388 1.082 0.922 3.246 0.212 +totals 67050103 34.810 246.496 66.102 564.608 11.822 11.520 19.444 48.148 24.942 83.978 11.338 + += Space (in MiBytes) = + +== Manzini's Corpus == +Files Size Archon4r0 BPR DC DS divsufsort1 divsufsort2 KA KS MSufSort3 qsufsort sais +chr22.dna 34553758 174.66 296.88 193.60 165.18 165.02 165.02 289.97 428.39 199.72 263.62 164.77 +etext99 105277340 531.13 915.48 589.85 503.23 502.25 502.25 907.34 1305.20 604.45 803.20 502.00 +gcc-3.0.tar 86630400 437.14 756.43 485.38 415.87 413.34 413.34 709.50 1074.01 497.79 660.94 413.09 +howto 39422105 199.20 367.53 220.88 188.45 188.23 188.23 331.54 488.75 227.67 300.77 187.98 +jdk13c 69728899 351.96 603.99 390.68 333.40 332.74 332.74 609.71 864.48 401.04 531.99 332.49 +linux-2.4.5.tar 116254720 586.46 1061.83 651.36 555.76 554.60 554.60 977.81 1441.30 667.39 886.95 554.35 +rctail96 114711151 578.68 987.64 642.71 548.32 547.24 547.24 1004.98 1422.16 658.43 875.18 546.99 +rfc 116421901 587.30 1005.85 652.29 556.53 555.39 555.39 956.52 1443.37 668.26 888.23 555.14 +sprot34.dat 109617186 553.01 941.95 614.17 524.03 522.95 522.95 930.06 1359.01 629.26 836.31 522.70 +w3c2 104201579 525.71 958.37 583.82 498.09 497.12 497.12 912.00 1291.87 598.82 795.00 496.87 +totals 896819039 4525.25 7895.95 5024.74 4288.86 4278.88 4278.88 7629.43 11118.54 5152.83 6842.19 4276.38 +mean - 5.29 9.23 5.88 5.01 5.00 5.00 8.92 13.00 6.02 8.00 5.00 + +== The Gauntlet == +Files Size Archon4r0 BPR DC DS divsufsort1 divsufsort2 KA KS MSufSort3 qsufsort sais +abac 200000 1.51 1.73 1.12 0.98 1.21 1.20 1.75 2.48 3.15 1.53 0.95 +abba 10500600 53.43 90.19 58.83 50.21 50.32 50.32 86.20 130.18 62.09 80.11 50.07 +book1x20 15375420 78.00 134.00 86.15 73.52 73.57 73.57 132.42 190.62 89.99 117.31 73.32 +fib_s14930352 14930352 75.75 128.15 83.65 71.71 71.44 71.44 117.16 185.10 87.43 113.91 71.19 +fss10 12078908 61.38 103.68 67.68 58.05 57.85 57.85 107.05 149.75 71.12 92.16 57.60 +fss9 2851443 14.87 24.48 15.98 13.71 13.85 13.85 25.27 35.35 18.32 21.76 13.60 +houston 3840000 19.85 36.96 21.52 18.46 18.56 18.56 28.79 47.58 23.98 29.30 18.31 +paper5x80 981924 5.45 11.40 5.50 4.72 4.93 4.93 8.59 12.17 7.63 7.49 4.68 +test1 2097152 11.07 82.00 11.75 10.10 10.25 10.25 18.34 25.99 14.01 16.00 10.00 +test2 2097152 11.07 82.00 11.75 10.10 10.25 10.25 18.34 25.99 14.01 16.00 10.00 +test3 2097152 11.07 82.00 11.75 10.05 10.25 10.25 18.34 26.00 14.63 16.00 10.12 +totals 67050103 343.45 776.59 375.68 321.61 322.48 322.47 562.25 831.21 406.36 511.57 319.84 +mean - 5.37 12.14 5.88 5.03 5.04 5.04 8.79 13.00 6.35 8.00 5.00 + + +Algorithm: +---------- + +libdivsufsort uses the following algorithms for suffix sorting. + - The improved version of Itho-Tanaka two-stage sorting algorithm. [2][6] + - A substring sorting/encoding technique. [1][3] + - Maniscalco's tandem repeat sorting algorithm. [5] + - Larsson-Sadakane sorting algorithm. [4] + + +References: +----------- + + 1. Stefan Burkhardt and Juha K"arkk"ainen. Fast lightweight suffix + array construction and checking. Proceedings of the 14th Annual + Symposium on Combinatorial Pattern Matching, LNCS 2676, + Springer, pp. 55-69, 2003. + + 2. Hideo Itoh and Hozumi Tanaka, An Efficient Method for in Memory + Construction of Suffix Arrays, Proceedings of the IEEE String + Processing and Information Retrieval Symposium, pp. 81-88, 1999. + + 3. Pang Ko and Srinivas Aluru, Space-efficient linear time + construction of suffix arrays, Proceedings of the 14th Annual + Symposium on Combinatorial Pattern Matching, pp. 200-210, 2003. + + 4. Jesper Larsson and Kunihiko Sadakane, Faster suffix sorting. + Technical report LU-CS-TR:99-214, Department of Computer + Science, Lund University, Sweden, 1999. + + 5. Michael Maniscalco, MSufSort. + http://www.michael-maniscalco.com/msufsort.htm + + 6. Yuta Mori, Short description of improved two-stage suffix sorting + algorithm, 2005. + http://homepage3.nifty.com/wpage/software/itssort.txt diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsort-lite/VERSION b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsort-lite/VERSION new file mode 100644 index 0000000000000000000000000000000000000000..227cea215648b1af34a87c9acf5b707fe02d2072 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsort-lite/VERSION @@ -0,0 +1 @@ +2.0.0 diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsort-lite/divsufsort.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsort-lite/divsufsort.c new file mode 100644 index 0000000000000000000000000000000000000000..9bbac4532fe220f4fe50a60d790afbf545ca97f7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsort-lite/divsufsort.c @@ -0,0 +1,1782 @@ +/* + * divsufsort.c for libdivsufsort-lite + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#include +#include +#include +#ifdef _OPENMP +# include +#endif +#include "divsufsort.h" + + +/*- Constants -*/ +#define INLINE __inline +#if defined(ALPHABET_SIZE) && (ALPHABET_SIZE < 1) +# undef ALPHABET_SIZE +#endif +#if !defined(ALPHABET_SIZE) +# define ALPHABET_SIZE (256) +#endif +#define BUCKET_A_SIZE (ALPHABET_SIZE) +#define BUCKET_B_SIZE (ALPHABET_SIZE * ALPHABET_SIZE) +#if defined(SS_INSERTIONSORT_THRESHOLD) +# if SS_INSERTIONSORT_THRESHOLD < 1 +# undef SS_INSERTIONSORT_THRESHOLD +# define SS_INSERTIONSORT_THRESHOLD (1) +# endif +#else +# define SS_INSERTIONSORT_THRESHOLD (8) +#endif +#if defined(SS_BLOCKSIZE) +# if SS_BLOCKSIZE < 0 +# undef SS_BLOCKSIZE +# define SS_BLOCKSIZE (0) +# elif 32768 <= SS_BLOCKSIZE +# undef SS_BLOCKSIZE +# define SS_BLOCKSIZE (32767) +# endif +#else +# define SS_BLOCKSIZE (1024) +#endif +/* minstacksize = log(SS_BLOCKSIZE) / log(3) * 2 */ +#if SS_BLOCKSIZE == 0 +# define SS_MISORT_STACKSIZE (96) +#elif SS_BLOCKSIZE <= 4096 +# define SS_MISORT_STACKSIZE (16) +#else +# define SS_MISORT_STACKSIZE (24) +#endif +#define SS_SMERGE_STACKSIZE (32) +#define TR_INSERTIONSORT_THRESHOLD (8) +#define TR_STACKSIZE (64) + + +/*- Macros -*/ +#ifndef SWAP +# define SWAP(_a, _b) do { t = (_a); (_a) = (_b); (_b) = t; } while(0) +#endif /* SWAP */ +#ifndef MIN +# define MIN(_a, _b) (((_a) < (_b)) ? (_a) : (_b)) +#endif /* MIN */ +#ifndef MAX +# define MAX(_a, _b) (((_a) > (_b)) ? (_a) : (_b)) +#endif /* MAX */ +#define STACK_PUSH(_a, _b, _c, _d)\ + do {\ + assert(ssize < STACK_SIZE);\ + stack[ssize].a = (_a), stack[ssize].b = (_b),\ + stack[ssize].c = (_c), stack[ssize++].d = (_d);\ + } while(0) +#define STACK_PUSH5(_a, _b, _c, _d, _e)\ + do {\ + assert(ssize < STACK_SIZE);\ + stack[ssize].a = (_a), stack[ssize].b = (_b),\ + stack[ssize].c = (_c), stack[ssize].d = (_d), stack[ssize++].e = (_e);\ + } while(0) +#define STACK_POP(_a, _b, _c, _d)\ + do {\ + assert(0 <= ssize);\ + if(ssize == 0) { return; }\ + (_a) = stack[--ssize].a, (_b) = stack[ssize].b,\ + (_c) = stack[ssize].c, (_d) = stack[ssize].d;\ + } while(0) +#define STACK_POP5(_a, _b, _c, _d, _e)\ + do {\ + assert(0 <= ssize);\ + if(ssize == 0) { return; }\ + (_a) = stack[--ssize].a, (_b) = stack[ssize].b,\ + (_c) = stack[ssize].c, (_d) = stack[ssize].d, (_e) = stack[ssize].e;\ + } while(0) +#define BUCKET_A(_c0) bucket_A[(_c0)] +#if ALPHABET_SIZE == 256 +#define BUCKET_B(_c0, _c1) (bucket_B[((_c1) << 8) | (_c0)]) +#define BUCKET_BSTAR(_c0, _c1) (bucket_B[((_c0) << 8) | (_c1)]) +#else +#define BUCKET_B(_c0, _c1) (bucket_B[(_c1) * ALPHABET_SIZE + (_c0)]) +#define BUCKET_BSTAR(_c0, _c1) (bucket_B[(_c0) * ALPHABET_SIZE + (_c1)]) +#endif + + +/*- Private Functions -*/ + +static const int lg_table[256]= { + -1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, + 5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5, + 6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6, + 6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7 +}; + +#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) + +static INLINE +int +ss_ilg(int n) { +#if SS_BLOCKSIZE == 0 + return (n & 0xffff0000) ? + ((n & 0xff000000) ? + 24 + lg_table[(n >> 24) & 0xff] : + 16 + lg_table[(n >> 16) & 0xff]) : + ((n & 0x0000ff00) ? + 8 + lg_table[(n >> 8) & 0xff] : + 0 + lg_table[(n >> 0) & 0xff]); +#elif SS_BLOCKSIZE < 256 + return lg_table[n]; +#else + return (n & 0xff00) ? + 8 + lg_table[(n >> 8) & 0xff] : + 0 + lg_table[(n >> 0) & 0xff]; +#endif +} + +#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */ + +#if SS_BLOCKSIZE != 0 + +static const int sqq_table[256] = { + 0, 16, 22, 27, 32, 35, 39, 42, 45, 48, 50, 53, 55, 57, 59, 61, + 64, 65, 67, 69, 71, 73, 75, 76, 78, 80, 81, 83, 84, 86, 87, 89, + 90, 91, 93, 94, 96, 97, 98, 99, 101, 102, 103, 104, 106, 107, 108, 109, +110, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, +128, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, +143, 144, 144, 145, 146, 147, 148, 149, 150, 150, 151, 152, 153, 154, 155, 155, +156, 157, 158, 159, 160, 160, 161, 162, 163, 163, 164, 165, 166, 167, 167, 168, +169, 170, 170, 171, 172, 173, 173, 174, 175, 176, 176, 177, 178, 178, 179, 180, +181, 181, 182, 183, 183, 184, 185, 185, 186, 187, 187, 188, 189, 189, 190, 191, +192, 192, 193, 193, 194, 195, 195, 196, 197, 197, 198, 199, 199, 200, 201, 201, +202, 203, 203, 204, 204, 205, 206, 206, 207, 208, 208, 209, 209, 210, 211, 211, +212, 212, 213, 214, 214, 215, 215, 216, 217, 217, 218, 218, 219, 219, 220, 221, +221, 222, 222, 223, 224, 224, 225, 225, 226, 226, 227, 227, 228, 229, 229, 230, +230, 231, 231, 232, 232, 233, 234, 234, 235, 235, 236, 236, 237, 237, 238, 238, +239, 240, 240, 241, 241, 242, 242, 243, 243, 244, 244, 245, 245, 246, 246, 247, +247, 248, 248, 249, 249, 250, 250, 251, 251, 252, 252, 253, 253, 254, 254, 255 +}; + +static INLINE +int +ss_isqrt(int x) { + int y, e; + + if(x >= (SS_BLOCKSIZE * SS_BLOCKSIZE)) { return SS_BLOCKSIZE; } + e = (x & 0xffff0000) ? + ((x & 0xff000000) ? + 24 + lg_table[(x >> 24) & 0xff] : + 16 + lg_table[(x >> 16) & 0xff]) : + ((x & 0x0000ff00) ? + 8 + lg_table[(x >> 8) & 0xff] : + 0 + lg_table[(x >> 0) & 0xff]); + + if(e >= 16) { + y = sqq_table[x >> ((e - 6) - (e & 1))] << ((e >> 1) - 7); + if(e >= 24) { y = (y + 1 + x / y) >> 1; } + y = (y + 1 + x / y) >> 1; + } else if(e >= 8) { + y = (sqq_table[x >> ((e - 6) - (e & 1))] >> (7 - (e >> 1))) + 1; + } else { + return sqq_table[x] >> 4; + } + + return (x < (y * y)) ? y - 1 : y; +} + +#endif /* SS_BLOCKSIZE != 0 */ + + +/*---------------------------------------------------------------------------*/ + +/* Compares two suffixes. */ +static INLINE +int +ss_compare(const unsigned char *T, + const int *p1, const int *p2, + int depth) { + const unsigned char *U1, *U2, *U1n, *U2n; + + for(U1 = T + depth + *p1, + U2 = T + depth + *p2, + U1n = T + *(p1 + 1) + 2, + U2n = T + *(p2 + 1) + 2; + (U1 < U1n) && (U2 < U2n) && (*U1 == *U2); + ++U1, ++U2) { + } + + return U1 < U1n ? + (U2 < U2n ? *U1 - *U2 : 1) : + (U2 < U2n ? -1 : 0); +} + + +/*---------------------------------------------------------------------------*/ + +#if (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1) + +/* Insertionsort for small size groups */ +static +void +ss_insertionsort(const unsigned char *T, const int *PA, + int *first, int *last, int depth) { + int *i, *j; + int t; + int r; + + for(i = last - 2; first <= i; --i) { + for(t = *i, j = i + 1; 0 < (r = ss_compare(T, PA + t, PA + *j, depth));) { + do { *(j - 1) = *j; } while((++j < last) && (*j < 0)); + if(last <= j) { break; } + } + if(r == 0) { *j = ~*j; } + *(j - 1) = t; + } +} + +#endif /* (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1) */ + + +/*---------------------------------------------------------------------------*/ + +#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) + +static INLINE +void +ss_fixdown(const unsigned char *Td, const int *PA, + int *SA, int i, int size) { + int j, k; + int v; + int c, d, e; + + for(v = SA[i], c = Td[PA[v]]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) { + d = Td[PA[SA[k = j++]]]; + if(d < (e = Td[PA[SA[j]]])) { k = j; d = e; } + if(d <= c) { break; } + } + SA[i] = v; +} + +/* Simple top-down heapsort. */ +static +void +ss_heapsort(const unsigned char *Td, const int *PA, int *SA, int size) { + int i, m; + int t; + + m = size; + if((size % 2) == 0) { + m--; + if(Td[PA[SA[m / 2]]] < Td[PA[SA[m]]]) { SWAP(SA[m], SA[m / 2]); } + } + + for(i = m / 2 - 1; 0 <= i; --i) { ss_fixdown(Td, PA, SA, i, m); } + if((size % 2) == 0) { SWAP(SA[0], SA[m]); ss_fixdown(Td, PA, SA, 0, m); } + for(i = m - 1; 0 < i; --i) { + t = SA[0], SA[0] = SA[i]; + ss_fixdown(Td, PA, SA, 0, i); + SA[i] = t; + } +} + + +/*---------------------------------------------------------------------------*/ + +/* Returns the median of three elements. */ +static INLINE +int * +ss_median3(const unsigned char *Td, const int *PA, + int *v1, int *v2, int *v3) { + int *t; + if(Td[PA[*v1]] > Td[PA[*v2]]) { SWAP(v1, v2); } + if(Td[PA[*v2]] > Td[PA[*v3]]) { + if(Td[PA[*v1]] > Td[PA[*v3]]) { return v1; } + else { return v3; } + } + return v2; +} + +/* Returns the median of five elements. */ +static INLINE +int * +ss_median5(const unsigned char *Td, const int *PA, + int *v1, int *v2, int *v3, int *v4, int *v5) { + int *t; + if(Td[PA[*v2]] > Td[PA[*v3]]) { SWAP(v2, v3); } + if(Td[PA[*v4]] > Td[PA[*v5]]) { SWAP(v4, v5); } + if(Td[PA[*v2]] > Td[PA[*v4]]) { SWAP(v2, v4); SWAP(v3, v5); } + if(Td[PA[*v1]] > Td[PA[*v3]]) { SWAP(v1, v3); } + if(Td[PA[*v1]] > Td[PA[*v4]]) { SWAP(v1, v4); SWAP(v3, v5); } + if(Td[PA[*v3]] > Td[PA[*v4]]) { return v4; } + return v3; +} + +/* Returns the pivot element. */ +static INLINE +int * +ss_pivot(const unsigned char *Td, const int *PA, int *first, int *last) { + int *middle; + int t; + + t = last - first; + middle = first + t / 2; + + if(t <= 512) { + if(t <= 32) { + return ss_median3(Td, PA, first, middle, last - 1); + } else { + t >>= 2; + return ss_median5(Td, PA, first, first + t, middle, last - 1 - t, last - 1); + } + } + t >>= 3; + first = ss_median3(Td, PA, first, first + t, first + (t << 1)); + middle = ss_median3(Td, PA, middle - t, middle, middle + t); + last = ss_median3(Td, PA, last - 1 - (t << 1), last - 1 - t, last - 1); + return ss_median3(Td, PA, first, middle, last); +} + + +/*---------------------------------------------------------------------------*/ + +/* Binary partition for substrings. */ +static INLINE +int * +ss_partition(const int *PA, + int *first, int *last, int depth) { + int *a, *b; + int t; + for(a = first - 1, b = last;;) { + for(; (++a < b) && ((PA[*a] + depth) >= (PA[*a + 1] + 1));) { *a = ~*a; } + for(; (a < --b) && ((PA[*b] + depth) < (PA[*b + 1] + 1));) { } + if(b <= a) { break; } + t = ~*b; + *b = *a; + *a = t; + } + if(first < a) { *first = ~*first; } + return a; +} + +/* Multikey introsort for medium size groups. */ +static +void +ss_mintrosort(const unsigned char *T, const int *PA, + int *first, int *last, + int depth) { +#define STACK_SIZE SS_MISORT_STACKSIZE + struct { int *a, *b, c; int d; } stack[STACK_SIZE]; + const unsigned char *Td; + int *a, *b, *c, *d, *e, *f; + int s, t; + int ssize; + int limit; + int v, x = 0; + + for(ssize = 0, limit = ss_ilg(last - first);;) { + + if((last - first) <= SS_INSERTIONSORT_THRESHOLD) { +#if 1 < SS_INSERTIONSORT_THRESHOLD + if(1 < (last - first)) { ss_insertionsort(T, PA, first, last, depth); } +#endif + STACK_POP(first, last, depth, limit); + continue; + } + + Td = T + depth; + if(limit-- == 0) { ss_heapsort(Td, PA, first, last - first); } + if(limit < 0) { + for(a = first + 1, v = Td[PA[*first]]; a < last; ++a) { + if((x = Td[PA[*a]]) != v) { + if(1 < (a - first)) { break; } + v = x; + first = a; + } + } + if(Td[PA[*first] - 1] < v) { + first = ss_partition(PA, first, a, depth); + } + if((a - first) <= (last - a)) { + if(1 < (a - first)) { + STACK_PUSH(a, last, depth, -1); + last = a, depth += 1, limit = ss_ilg(a - first); + } else { + first = a, limit = -1; + } + } else { + if(1 < (last - a)) { + STACK_PUSH(first, a, depth + 1, ss_ilg(a - first)); + first = a, limit = -1; + } else { + last = a, depth += 1, limit = ss_ilg(a - first); + } + } + continue; + } + + /* choose pivot */ + a = ss_pivot(Td, PA, first, last); + v = Td[PA[*a]]; + SWAP(*first, *a); + + /* partition */ + for(b = first; (++b < last) && ((x = Td[PA[*b]]) == v);) { } + if(((a = b) < last) && (x < v)) { + for(; (++b < last) && ((x = Td[PA[*b]]) <= v);) { + if(x == v) { SWAP(*b, *a); ++a; } + } + } + for(c = last; (b < --c) && ((x = Td[PA[*c]]) == v);) { } + if((b < (d = c)) && (x > v)) { + for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) { + if(x == v) { SWAP(*c, *d); --d; } + } + } + for(; b < c;) { + SWAP(*b, *c); + for(; (++b < c) && ((x = Td[PA[*b]]) <= v);) { + if(x == v) { SWAP(*b, *a); ++a; } + } + for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) { + if(x == v) { SWAP(*c, *d); --d; } + } + } + + if(a <= d) { + c = b - 1; + + if((s = a - first) > (t = b - a)) { s = t; } + for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); } + if((s = d - c) > (t = last - d - 1)) { s = t; } + for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); } + + a = first + (b - a), c = last - (d - c); + b = (v <= Td[PA[*a] - 1]) ? a : ss_partition(PA, a, c, depth); + + if((a - first) <= (last - c)) { + if((last - c) <= (c - b)) { + STACK_PUSH(b, c, depth + 1, ss_ilg(c - b)); + STACK_PUSH(c, last, depth, limit); + last = a; + } else if((a - first) <= (c - b)) { + STACK_PUSH(c, last, depth, limit); + STACK_PUSH(b, c, depth + 1, ss_ilg(c - b)); + last = a; + } else { + STACK_PUSH(c, last, depth, limit); + STACK_PUSH(first, a, depth, limit); + first = b, last = c, depth += 1, limit = ss_ilg(c - b); + } + } else { + if((a - first) <= (c - b)) { + STACK_PUSH(b, c, depth + 1, ss_ilg(c - b)); + STACK_PUSH(first, a, depth, limit); + first = c; + } else if((last - c) <= (c - b)) { + STACK_PUSH(first, a, depth, limit); + STACK_PUSH(b, c, depth + 1, ss_ilg(c - b)); + first = c; + } else { + STACK_PUSH(first, a, depth, limit); + STACK_PUSH(c, last, depth, limit); + first = b, last = c, depth += 1, limit = ss_ilg(c - b); + } + } + } else { + limit += 1; + if(Td[PA[*first] - 1] < v) { + first = ss_partition(PA, first, last, depth); + limit = ss_ilg(last - first); + } + depth += 1; + } + } +#undef STACK_SIZE +} + +#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */ + + +/*---------------------------------------------------------------------------*/ + +#if SS_BLOCKSIZE != 0 + +static INLINE +void +ss_blockswap(int *a, int *b, int n) { + int t; + for(; 0 < n; --n, ++a, ++b) { + t = *a, *a = *b, *b = t; + } +} + +static INLINE +void +ss_rotate(int *first, int *middle, int *last) { + int *a, *b, t; + int l, r; + l = middle - first, r = last - middle; + for(; (0 < l) && (0 < r);) { + if(l == r) { ss_blockswap(first, middle, l); break; } + if(l < r) { + a = last - 1, b = middle - 1; + t = *a; + do { + *a-- = *b, *b-- = *a; + if(b < first) { + *a = t; + last = a; + if((r -= l + 1) <= l) { break; } + a -= 1, b = middle - 1; + t = *a; + } + } while(1); + } else { + a = first, b = middle; + t = *a; + do { + *a++ = *b, *b++ = *a; + if(last <= b) { + *a = t; + first = a + 1; + if((l -= r + 1) <= r) { break; } + a += 1, b = middle; + t = *a; + } + } while(1); + } + } +} + + +/*---------------------------------------------------------------------------*/ + +static +void +ss_inplacemerge(const unsigned char *T, const int *PA, + int *first, int *middle, int *last, + int depth) { + const int *p; + int *a, *b; + int len, half; + int q, r; + int x; + + for(;;) { + if(*(last - 1) < 0) { x = 1; p = PA + ~*(last - 1); } + else { x = 0; p = PA + *(last - 1); } + for(a = first, len = middle - first, half = len >> 1, r = -1; + 0 < len; + len = half, half >>= 1) { + b = a + half; + q = ss_compare(T, PA + ((0 <= *b) ? *b : ~*b), p, depth); + if(q < 0) { + a = b + 1; + half -= (len & 1) ^ 1; + } else { + r = q; + } + } + if(a < middle) { + if(r == 0) { *a = ~*a; } + ss_rotate(a, middle, last); + last -= middle - a; + middle = a; + if(first == middle) { break; } + } + --last; + if(x != 0) { while(*--last < 0) { } } + if(middle == last) { break; } + } +} + + +/*---------------------------------------------------------------------------*/ + +/* Merge-forward with internal buffer. */ +static +void +ss_mergeforward(const unsigned char *T, const int *PA, + int *first, int *middle, int *last, + int *buf, int depth) { + int *a, *b, *c, *bufend; + int t; + int r; + + bufend = buf + (middle - first) - 1; + ss_blockswap(buf, first, middle - first); + + for(t = *(a = first), b = buf, c = middle;;) { + r = ss_compare(T, PA + *b, PA + *c, depth); + if(r < 0) { + do { + *a++ = *b; + if(bufend <= b) { *bufend = t; return; } + *b++ = *a; + } while(*b < 0); + } else if(r > 0) { + do { + *a++ = *c, *c++ = *a; + if(last <= c) { + while(b < bufend) { *a++ = *b, *b++ = *a; } + *a = *b, *b = t; + return; + } + } while(*c < 0); + } else { + *c = ~*c; + do { + *a++ = *b; + if(bufend <= b) { *bufend = t; return; } + *b++ = *a; + } while(*b < 0); + + do { + *a++ = *c, *c++ = *a; + if(last <= c) { + while(b < bufend) { *a++ = *b, *b++ = *a; } + *a = *b, *b = t; + return; + } + } while(*c < 0); + } + } +} + +/* Merge-backward with internal buffer. */ +static +void +ss_mergebackward(const unsigned char *T, const int *PA, + int *first, int *middle, int *last, + int *buf, int depth) { + const int *p1, *p2; + int *a, *b, *c, *bufend; + int t; + int r; + int x; + + bufend = buf + (last - middle) - 1; + ss_blockswap(buf, middle, last - middle); + + x = 0; + if(*bufend < 0) { p1 = PA + ~*bufend; x |= 1; } + else { p1 = PA + *bufend; } + if(*(middle - 1) < 0) { p2 = PA + ~*(middle - 1); x |= 2; } + else { p2 = PA + *(middle - 1); } + for(t = *(a = last - 1), b = bufend, c = middle - 1;;) { + r = ss_compare(T, p1, p2, depth); + if(0 < r) { + if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; } + *a-- = *b; + if(b <= buf) { *buf = t; break; } + *b-- = *a; + if(*b < 0) { p1 = PA + ~*b; x |= 1; } + else { p1 = PA + *b; } + } else if(r < 0) { + if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; } + *a-- = *c, *c-- = *a; + if(c < first) { + while(buf < b) { *a-- = *b, *b-- = *a; } + *a = *b, *b = t; + break; + } + if(*c < 0) { p2 = PA + ~*c; x |= 2; } + else { p2 = PA + *c; } + } else { + if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; } + *a-- = ~*b; + if(b <= buf) { *buf = t; break; } + *b-- = *a; + if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; } + *a-- = *c, *c-- = *a; + if(c < first) { + while(buf < b) { *a-- = *b, *b-- = *a; } + *a = *b, *b = t; + break; + } + if(*b < 0) { p1 = PA + ~*b; x |= 1; } + else { p1 = PA + *b; } + if(*c < 0) { p2 = PA + ~*c; x |= 2; } + else { p2 = PA + *c; } + } + } +} + +/* D&C based merge. */ +static +void +ss_swapmerge(const unsigned char *T, const int *PA, + int *first, int *middle, int *last, + int *buf, int bufsize, int depth) { +#define STACK_SIZE SS_SMERGE_STACKSIZE +#define GETIDX(a) ((0 <= (a)) ? (a) : (~(a))) +#define MERGE_CHECK(a, b, c)\ + do {\ + if(((c) & 1) ||\ + (((c) & 2) && (ss_compare(T, PA + GETIDX(*((a) - 1)), PA + *(a), depth) == 0))) {\ + *(a) = ~*(a);\ + }\ + if(((c) & 4) && ((ss_compare(T, PA + GETIDX(*((b) - 1)), PA + *(b), depth) == 0))) {\ + *(b) = ~*(b);\ + }\ + } while(0) + struct { int *a, *b, *c; int d; } stack[STACK_SIZE]; + int *l, *r, *lm, *rm; + int m, len, half; + int ssize; + int check, next; + + for(check = 0, ssize = 0;;) { + if((last - middle) <= bufsize) { + if((first < middle) && (middle < last)) { + ss_mergebackward(T, PA, first, middle, last, buf, depth); + } + MERGE_CHECK(first, last, check); + STACK_POP(first, middle, last, check); + continue; + } + + if((middle - first) <= bufsize) { + if(first < middle) { + ss_mergeforward(T, PA, first, middle, last, buf, depth); + } + MERGE_CHECK(first, last, check); + STACK_POP(first, middle, last, check); + continue; + } + + for(m = 0, len = MIN(middle - first, last - middle), half = len >> 1; + 0 < len; + len = half, half >>= 1) { + if(ss_compare(T, PA + GETIDX(*(middle + m + half)), + PA + GETIDX(*(middle - m - half - 1)), depth) < 0) { + m += half + 1; + half -= (len & 1) ^ 1; + } + } + + if(0 < m) { + lm = middle - m, rm = middle + m; + ss_blockswap(lm, middle, m); + l = r = middle, next = 0; + if(rm < last) { + if(*rm < 0) { + *rm = ~*rm; + if(first < lm) { for(; *--l < 0;) { } next |= 4; } + next |= 1; + } else if(first < lm) { + for(; *r < 0; ++r) { } + next |= 2; + } + } + + if((l - first) <= (last - r)) { + STACK_PUSH(r, rm, last, (next & 3) | (check & 4)); + middle = lm, last = l, check = (check & 3) | (next & 4); + } else { + if((next & 2) && (r == middle)) { next ^= 6; } + STACK_PUSH(first, lm, l, (check & 3) | (next & 4)); + first = r, middle = rm, check = (next & 3) | (check & 4); + } + } else { + if(ss_compare(T, PA + GETIDX(*(middle - 1)), PA + *middle, depth) == 0) { + *middle = ~*middle; + } + MERGE_CHECK(first, last, check); + STACK_POP(first, middle, last, check); + } + } +#undef STACK_SIZE +} + +#endif /* SS_BLOCKSIZE != 0 */ + + +/*---------------------------------------------------------------------------*/ + +/* Substring sort */ +static +void +sssort(const unsigned char *T, const int *PA, + int *first, int *last, + int *buf, int bufsize, + int depth, int n, int lastsuffix) { + int *a; +#if SS_BLOCKSIZE != 0 + int *b, *middle, *curbuf; + int j, k, curbufsize, limit; +#endif + int i; + + if(lastsuffix != 0) { ++first; } + +#if SS_BLOCKSIZE == 0 + ss_mintrosort(T, PA, first, last, depth); +#else + if((bufsize < SS_BLOCKSIZE) && + (bufsize < (last - first)) && + (bufsize < (limit = ss_isqrt(last - first)))) { + if(SS_BLOCKSIZE < limit) { limit = SS_BLOCKSIZE; } + buf = middle = last - limit, bufsize = limit; + } else { + middle = last, limit = 0; + } + for(a = first, i = 0; SS_BLOCKSIZE < (middle - a); a += SS_BLOCKSIZE, ++i) { +#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE + ss_mintrosort(T, PA, a, a + SS_BLOCKSIZE, depth); +#elif 1 < SS_BLOCKSIZE + ss_insertionsort(T, PA, a, a + SS_BLOCKSIZE, depth); +#endif + curbufsize = last - (a + SS_BLOCKSIZE); + curbuf = a + SS_BLOCKSIZE; + if(curbufsize <= bufsize) { curbufsize = bufsize, curbuf = buf; } + for(b = a, k = SS_BLOCKSIZE, j = i; j & 1; b -= k, k <<= 1, j >>= 1) { + ss_swapmerge(T, PA, b - k, b, b + k, curbuf, curbufsize, depth); + } + } +#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE + ss_mintrosort(T, PA, a, middle, depth); +#elif 1 < SS_BLOCKSIZE + ss_insertionsort(T, PA, a, middle, depth); +#endif + for(k = SS_BLOCKSIZE; i != 0; k <<= 1, i >>= 1) { + if(i & 1) { + ss_swapmerge(T, PA, a - k, a, middle, buf, bufsize, depth); + a -= k; + } + } + if(limit != 0) { +#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE + ss_mintrosort(T, PA, middle, last, depth); +#elif 1 < SS_BLOCKSIZE + ss_insertionsort(T, PA, middle, last, depth); +#endif + ss_inplacemerge(T, PA, first, middle, last, depth); + } +#endif + + if(lastsuffix != 0) { + /* Insert last type B* suffix. */ + int PAi[2]; PAi[0] = PA[*(first - 1)], PAi[1] = n - 2; + for(a = first, i = *(first - 1); + (a < last) && ((*a < 0) || (0 < ss_compare(T, &(PAi[0]), PA + *a, depth))); + ++a) { + *(a - 1) = *a; + } + *(a - 1) = i; + } +} + + +/*---------------------------------------------------------------------------*/ + +static INLINE +int +tr_ilg(int n) { + return (n & 0xffff0000) ? + ((n & 0xff000000) ? + 24 + lg_table[(n >> 24) & 0xff] : + 16 + lg_table[(n >> 16) & 0xff]) : + ((n & 0x0000ff00) ? + 8 + lg_table[(n >> 8) & 0xff] : + 0 + lg_table[(n >> 0) & 0xff]); +} + + +/*---------------------------------------------------------------------------*/ + +/* Simple insertionsort for small size groups. */ +static +void +tr_insertionsort(const int *ISAd, int *first, int *last) { + int *a, *b; + int t, r; + + for(a = first + 1; a < last; ++a) { + for(t = *a, b = a - 1; 0 > (r = ISAd[t] - ISAd[*b]);) { + do { *(b + 1) = *b; } while((first <= --b) && (*b < 0)); + if(b < first) { break; } + } + if(r == 0) { *b = ~*b; } + *(b + 1) = t; + } +} + + +/*---------------------------------------------------------------------------*/ + +static INLINE +void +tr_fixdown(const int *ISAd, int *SA, int i, int size) { + int j, k; + int v; + int c, d, e; + + for(v = SA[i], c = ISAd[v]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) { + d = ISAd[SA[k = j++]]; + if(d < (e = ISAd[SA[j]])) { k = j; d = e; } + if(d <= c) { break; } + } + SA[i] = v; +} + +/* Simple top-down heapsort. */ +static +void +tr_heapsort(const int *ISAd, int *SA, int size) { + int i, m; + int t; + + m = size; + if((size % 2) == 0) { + m--; + if(ISAd[SA[m / 2]] < ISAd[SA[m]]) { SWAP(SA[m], SA[m / 2]); } + } + + for(i = m / 2 - 1; 0 <= i; --i) { tr_fixdown(ISAd, SA, i, m); } + if((size % 2) == 0) { SWAP(SA[0], SA[m]); tr_fixdown(ISAd, SA, 0, m); } + for(i = m - 1; 0 < i; --i) { + t = SA[0], SA[0] = SA[i]; + tr_fixdown(ISAd, SA, 0, i); + SA[i] = t; + } +} + + +/*---------------------------------------------------------------------------*/ + +/* Returns the median of three elements. */ +static INLINE +int * +tr_median3(const int *ISAd, int *v1, int *v2, int *v3) { + int *t; + if(ISAd[*v1] > ISAd[*v2]) { SWAP(v1, v2); } + if(ISAd[*v2] > ISAd[*v3]) { + if(ISAd[*v1] > ISAd[*v3]) { return v1; } + else { return v3; } + } + return v2; +} + +/* Returns the median of five elements. */ +static INLINE +int * +tr_median5(const int *ISAd, + int *v1, int *v2, int *v3, int *v4, int *v5) { + int *t; + if(ISAd[*v2] > ISAd[*v3]) { SWAP(v2, v3); } + if(ISAd[*v4] > ISAd[*v5]) { SWAP(v4, v5); } + if(ISAd[*v2] > ISAd[*v4]) { SWAP(v2, v4); SWAP(v3, v5); } + if(ISAd[*v1] > ISAd[*v3]) { SWAP(v1, v3); } + if(ISAd[*v1] > ISAd[*v4]) { SWAP(v1, v4); SWAP(v3, v5); } + if(ISAd[*v3] > ISAd[*v4]) { return v4; } + return v3; +} + +/* Returns the pivot element. */ +static INLINE +int * +tr_pivot(const int *ISAd, int *first, int *last) { + int *middle; + int t; + + t = last - first; + middle = first + t / 2; + + if(t <= 512) { + if(t <= 32) { + return tr_median3(ISAd, first, middle, last - 1); + } else { + t >>= 2; + return tr_median5(ISAd, first, first + t, middle, last - 1 - t, last - 1); + } + } + t >>= 3; + first = tr_median3(ISAd, first, first + t, first + (t << 1)); + middle = tr_median3(ISAd, middle - t, middle, middle + t); + last = tr_median3(ISAd, last - 1 - (t << 1), last - 1 - t, last - 1); + return tr_median3(ISAd, first, middle, last); +} + + +/*---------------------------------------------------------------------------*/ + +typedef struct _trbudget_t trbudget_t; +struct _trbudget_t { + int chance; + int remain; + int incval; + int count; +}; + +static INLINE +void +trbudget_init(trbudget_t *budget, int chance, int incval) { + budget->chance = chance; + budget->remain = budget->incval = incval; +} + +static INLINE +int +trbudget_check(trbudget_t *budget, int size) { + if(size <= budget->remain) { budget->remain -= size; return 1; } + if(budget->chance == 0) { budget->count += size; return 0; } + budget->remain += budget->incval - size; + budget->chance -= 1; + return 1; +} + + +/*---------------------------------------------------------------------------*/ + +static INLINE +void +tr_partition(const int *ISAd, + int *first, int *middle, int *last, + int **pa, int **pb, int v) { + int *a, *b, *c, *d, *e, *f; + int t, s; + int x = 0; + + for(b = middle - 1; (++b < last) && ((x = ISAd[*b]) == v);) { } + if(((a = b) < last) && (x < v)) { + for(; (++b < last) && ((x = ISAd[*b]) <= v);) { + if(x == v) { SWAP(*b, *a); ++a; } + } + } + for(c = last; (b < --c) && ((x = ISAd[*c]) == v);) { } + if((b < (d = c)) && (x > v)) { + for(; (b < --c) && ((x = ISAd[*c]) >= v);) { + if(x == v) { SWAP(*c, *d); --d; } + } + } + for(; b < c;) { + SWAP(*b, *c); + for(; (++b < c) && ((x = ISAd[*b]) <= v);) { + if(x == v) { SWAP(*b, *a); ++a; } + } + for(; (b < --c) && ((x = ISAd[*c]) >= v);) { + if(x == v) { SWAP(*c, *d); --d; } + } + } + + if(a <= d) { + c = b - 1; + if((s = a - first) > (t = b - a)) { s = t; } + for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); } + if((s = d - c) > (t = last - d - 1)) { s = t; } + for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); } + first += (b - a), last -= (d - c); + } + *pa = first, *pb = last; +} + +static +void +tr_copy(int *ISA, const int *SA, + int *first, int *a, int *b, int *last, + int depth) { + /* sort suffixes of middle partition + by using sorted order of suffixes of left and right partition. */ + int *c, *d, *e; + int s, v; + + v = b - SA - 1; + for(c = first, d = a - 1; c <= d; ++c) { + if((0 <= (s = *c - depth)) && (ISA[s] == v)) { + *++d = s; + ISA[s] = d - SA; + } + } + for(c = last - 1, e = d + 1, d = b; e < d; --c) { + if((0 <= (s = *c - depth)) && (ISA[s] == v)) { + *--d = s; + ISA[s] = d - SA; + } + } +} + +static +void +tr_partialcopy(int *ISA, const int *SA, + int *first, int *a, int *b, int *last, + int depth) { + int *c, *d, *e; + int s, v; + int rank, lastrank, newrank = -1; + + v = b - SA - 1; + lastrank = -1; + for(c = first, d = a - 1; c <= d; ++c) { + if((0 <= (s = *c - depth)) && (ISA[s] == v)) { + *++d = s; + rank = ISA[s + depth]; + if(lastrank != rank) { lastrank = rank; newrank = d - SA; } + ISA[s] = newrank; + } + } + + lastrank = -1; + for(e = d; first <= e; --e) { + rank = ISA[*e]; + if(lastrank != rank) { lastrank = rank; newrank = e - SA; } + if(newrank != rank) { ISA[*e] = newrank; } + } + + lastrank = -1; + for(c = last - 1, e = d + 1, d = b; e < d; --c) { + if((0 <= (s = *c - depth)) && (ISA[s] == v)) { + *--d = s; + rank = ISA[s + depth]; + if(lastrank != rank) { lastrank = rank; newrank = d - SA; } + ISA[s] = newrank; + } + } +} + +static +void +tr_introsort(int *ISA, const int *ISAd, + int *SA, int *first, int *last, + trbudget_t *budget) { +#define STACK_SIZE TR_STACKSIZE + struct { const int *a; int *b, *c; int d, e; }stack[STACK_SIZE]; + int *a, *b, *c; + int t; + int v, x = 0; + int incr = ISAd - ISA; + int limit, next; + int ssize, trlink = -1; + + for(ssize = 0, limit = tr_ilg(last - first);;) { + + if(limit < 0) { + if(limit == -1) { + /* tandem repeat partition */ + tr_partition(ISAd - incr, first, first, last, &a, &b, last - SA - 1); + + /* update ranks */ + if(a < last) { + for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; } + } + if(b < last) { + for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; } + } + + /* push */ + if(1 < (b - a)) { + STACK_PUSH5(NULL, a, b, 0, 0); + STACK_PUSH5(ISAd - incr, first, last, -2, trlink); + trlink = ssize - 2; + } + if((a - first) <= (last - b)) { + if(1 < (a - first)) { + STACK_PUSH5(ISAd, b, last, tr_ilg(last - b), trlink); + last = a, limit = tr_ilg(a - first); + } else if(1 < (last - b)) { + first = b, limit = tr_ilg(last - b); + } else { + STACK_POP5(ISAd, first, last, limit, trlink); + } + } else { + if(1 < (last - b)) { + STACK_PUSH5(ISAd, first, a, tr_ilg(a - first), trlink); + first = b, limit = tr_ilg(last - b); + } else if(1 < (a - first)) { + last = a, limit = tr_ilg(a - first); + } else { + STACK_POP5(ISAd, first, last, limit, trlink); + } + } + } else if(limit == -2) { + /* tandem repeat copy */ + a = stack[--ssize].b, b = stack[ssize].c; + if(stack[ssize].d == 0) { + tr_copy(ISA, SA, first, a, b, last, ISAd - ISA); + } else { + if(0 <= trlink) { stack[trlink].d = -1; } + tr_partialcopy(ISA, SA, first, a, b, last, ISAd - ISA); + } + STACK_POP5(ISAd, first, last, limit, trlink); + } else { + /* sorted partition */ + if(0 <= *first) { + a = first; + do { ISA[*a] = a - SA; } while((++a < last) && (0 <= *a)); + first = a; + } + if(first < last) { + a = first; do { *a = ~*a; } while(*++a < 0); + next = (ISA[*a] != ISAd[*a]) ? tr_ilg(a - first + 1) : -1; + if(++a < last) { for(b = first, v = a - SA - 1; b < a; ++b) { ISA[*b] = v; } } + + /* push */ + if(trbudget_check(budget, a - first)) { + if((a - first) <= (last - a)) { + STACK_PUSH5(ISAd, a, last, -3, trlink); + ISAd += incr, last = a, limit = next; + } else { + if(1 < (last - a)) { + STACK_PUSH5(ISAd + incr, first, a, next, trlink); + first = a, limit = -3; + } else { + ISAd += incr, last = a, limit = next; + } + } + } else { + if(0 <= trlink) { stack[trlink].d = -1; } + if(1 < (last - a)) { + first = a, limit = -3; + } else { + STACK_POP5(ISAd, first, last, limit, trlink); + } + } + } else { + STACK_POP5(ISAd, first, last, limit, trlink); + } + } + continue; + } + + if((last - first) <= TR_INSERTIONSORT_THRESHOLD) { + tr_insertionsort(ISAd, first, last); + limit = -3; + continue; + } + + if(limit-- == 0) { + tr_heapsort(ISAd, first, last - first); + for(a = last - 1; first < a; a = b) { + for(x = ISAd[*a], b = a - 1; (first <= b) && (ISAd[*b] == x); --b) { *b = ~*b; } + } + limit = -3; + continue; + } + + /* choose pivot */ + a = tr_pivot(ISAd, first, last); + SWAP(*first, *a); + v = ISAd[*first]; + + /* partition */ + tr_partition(ISAd, first, first + 1, last, &a, &b, v); + if((last - first) != (b - a)) { + next = (ISA[*a] != v) ? tr_ilg(b - a) : -1; + + /* update ranks */ + for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; } + if(b < last) { for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; } } + + /* push */ + if((1 < (b - a)) && (trbudget_check(budget, b - a))) { + if((a - first) <= (last - b)) { + if((last - b) <= (b - a)) { + if(1 < (a - first)) { + STACK_PUSH5(ISAd + incr, a, b, next, trlink); + STACK_PUSH5(ISAd, b, last, limit, trlink); + last = a; + } else if(1 < (last - b)) { + STACK_PUSH5(ISAd + incr, a, b, next, trlink); + first = b; + } else { + ISAd += incr, first = a, last = b, limit = next; + } + } else if((a - first) <= (b - a)) { + if(1 < (a - first)) { + STACK_PUSH5(ISAd, b, last, limit, trlink); + STACK_PUSH5(ISAd + incr, a, b, next, trlink); + last = a; + } else { + STACK_PUSH5(ISAd, b, last, limit, trlink); + ISAd += incr, first = a, last = b, limit = next; + } + } else { + STACK_PUSH5(ISAd, b, last, limit, trlink); + STACK_PUSH5(ISAd, first, a, limit, trlink); + ISAd += incr, first = a, last = b, limit = next; + } + } else { + if((a - first) <= (b - a)) { + if(1 < (last - b)) { + STACK_PUSH5(ISAd + incr, a, b, next, trlink); + STACK_PUSH5(ISAd, first, a, limit, trlink); + first = b; + } else if(1 < (a - first)) { + STACK_PUSH5(ISAd + incr, a, b, next, trlink); + last = a; + } else { + ISAd += incr, first = a, last = b, limit = next; + } + } else if((last - b) <= (b - a)) { + if(1 < (last - b)) { + STACK_PUSH5(ISAd, first, a, limit, trlink); + STACK_PUSH5(ISAd + incr, a, b, next, trlink); + first = b; + } else { + STACK_PUSH5(ISAd, first, a, limit, trlink); + ISAd += incr, first = a, last = b, limit = next; + } + } else { + STACK_PUSH5(ISAd, first, a, limit, trlink); + STACK_PUSH5(ISAd, b, last, limit, trlink); + ISAd += incr, first = a, last = b, limit = next; + } + } + } else { + if((1 < (b - a)) && (0 <= trlink)) { stack[trlink].d = -1; } + if((a - first) <= (last - b)) { + if(1 < (a - first)) { + STACK_PUSH5(ISAd, b, last, limit, trlink); + last = a; + } else if(1 < (last - b)) { + first = b; + } else { + STACK_POP5(ISAd, first, last, limit, trlink); + } + } else { + if(1 < (last - b)) { + STACK_PUSH5(ISAd, first, a, limit, trlink); + first = b; + } else if(1 < (a - first)) { + last = a; + } else { + STACK_POP5(ISAd, first, last, limit, trlink); + } + } + } + } else { + if(trbudget_check(budget, last - first)) { + limit = tr_ilg(last - first), ISAd += incr; + } else { + if(0 <= trlink) { stack[trlink].d = -1; } + STACK_POP5(ISAd, first, last, limit, trlink); + } + } + } +#undef STACK_SIZE +} + + + +/*---------------------------------------------------------------------------*/ + +/* Tandem repeat sort */ +static +void +trsort(int *ISA, int *SA, int n, int depth) { + int *ISAd; + int *first, *last; + trbudget_t budget; + int t, skip, unsorted; + + trbudget_init(&budget, tr_ilg(n) * 2 / 3, n); +/* trbudget_init(&budget, tr_ilg(n) * 3 / 4, n); */ + for(ISAd = ISA + depth; -n < *SA; ISAd += ISAd - ISA) { + first = SA; + skip = 0; + unsorted = 0; + do { + if((t = *first) < 0) { first -= t; skip += t; } + else { + if(skip != 0) { *(first + skip) = skip; skip = 0; } + last = SA + ISA[t] + 1; + if(1 < (last - first)) { + budget.count = 0; + tr_introsort(ISA, ISAd, SA, first, last, &budget); + if(budget.count != 0) { unsorted += budget.count; } + else { skip = first - last; } + } else if((last - first) == 1) { + skip = -1; + } + first = last; + } + } while(first < (SA + n)); + if(skip != 0) { *(first + skip) = skip; } + if(unsorted == 0) { break; } + } +} + + +/*---------------------------------------------------------------------------*/ + +/* Sorts suffixes of type B*. */ +static +int +sort_typeBstar(const unsigned char *T, int *SA, + int *bucket_A, int *bucket_B, + int n) { + int *PAb, *ISAb, *buf; +#ifdef _OPENMP + int *curbuf; + int l; +#endif + int i, j, k, t, m, bufsize; + int c0, c1; +#ifdef _OPENMP + int d0, d1; + int tmp; +#endif + + /* Initialize bucket arrays. */ + for(i = 0; i < BUCKET_A_SIZE; ++i) { bucket_A[i] = 0; } + for(i = 0; i < BUCKET_B_SIZE; ++i) { bucket_B[i] = 0; } + + /* Count the number of occurrences of the first one or two characters of each + type A, B and B* suffix. Moreover, store the beginning position of all + type B* suffixes into the array SA. */ + for(i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) { + /* type A suffix. */ + do { ++BUCKET_A(c1 = c0); } while((0 <= --i) && ((c0 = T[i]) >= c1)); + if(0 <= i) { + /* type B* suffix. */ + ++BUCKET_BSTAR(c0, c1); + SA[--m] = i; + /* type B suffix. */ + for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { + ++BUCKET_B(c0, c1); + } + } + } + m = n - m; +/* +note: + A type B* suffix is lexicographically smaller than a type B suffix that + begins with the same first two characters. +*/ + + /* Calculate the index of start/end point of each bucket. */ + for(c0 = 0, i = 0, j = 0; c0 < ALPHABET_SIZE; ++c0) { + t = i + BUCKET_A(c0); + BUCKET_A(c0) = i + j; /* start point */ + i = t + BUCKET_B(c0, c0); + for(c1 = c0 + 1; c1 < ALPHABET_SIZE; ++c1) { + j += BUCKET_BSTAR(c0, c1); + BUCKET_BSTAR(c0, c1) = j; /* end point */ + i += BUCKET_B(c0, c1); + } + } + + if(0 < m) { + /* Sort the type B* suffixes by their first two characters. */ + PAb = SA + n - m; ISAb = SA + m; + for(i = m - 2; 0 <= i; --i) { + t = PAb[i], c0 = T[t], c1 = T[t + 1]; + SA[--BUCKET_BSTAR(c0, c1)] = i; + } + t = PAb[m - 1], c0 = T[t], c1 = T[t + 1]; + SA[--BUCKET_BSTAR(c0, c1)] = m - 1; + + /* Sort the type B* substrings using sssort. */ +#ifdef _OPENMP + tmp = omp_get_max_threads(); + buf = SA + m, bufsize = (n - (2 * m)) / tmp; + c0 = ALPHABET_SIZE - 2, c1 = ALPHABET_SIZE - 1, j = m; +#pragma omp parallel default(shared) private(curbuf, k, l, d0, d1, tmp) + { + tmp = omp_get_thread_num(); + curbuf = buf + tmp * bufsize; + k = 0; + for(;;) { + #pragma omp critical(sssort_lock) + { + if(0 < (l = j)) { + d0 = c0, d1 = c1; + do { + k = BUCKET_BSTAR(d0, d1); + if(--d1 <= d0) { + d1 = ALPHABET_SIZE - 1; + if(--d0 < 0) { break; } + } + } while(((l - k) <= 1) && (0 < (l = k))); + c0 = d0, c1 = d1, j = k; + } + } + if(l == 0) { break; } + sssort(T, PAb, SA + k, SA + l, + curbuf, bufsize, 2, n, *(SA + k) == (m - 1)); + } + } +#else + buf = SA + m, bufsize = n - (2 * m); + for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) { + for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) { + i = BUCKET_BSTAR(c0, c1); + if(1 < (j - i)) { + sssort(T, PAb, SA + i, SA + j, + buf, bufsize, 2, n, *(SA + i) == (m - 1)); + } + } + } +#endif + + /* Compute ranks of type B* substrings. */ + for(i = m - 1; 0 <= i; --i) { + if(0 <= SA[i]) { + j = i; + do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i])); + SA[i + 1] = i - j; + if(i <= 0) { break; } + } + j = i; + do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0); + ISAb[SA[i]] = j; + } + + /* Construct the inverse suffix array of type B* suffixes using trsort. */ + trsort(ISAb, SA, m, 1); + + /* Set the sorted order of tyoe B* suffixes. */ + for(i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) { + for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { } + if(0 <= i) { + t = i; + for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { } + SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t; + } + } + + /* Calculate the index of start/end point of each bucket. */ + BUCKET_B(ALPHABET_SIZE - 1, ALPHABET_SIZE - 1) = n; /* end point */ + for(c0 = ALPHABET_SIZE - 2, k = m - 1; 0 <= c0; --c0) { + i = BUCKET_A(c0 + 1) - 1; + for(c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) { + t = i - BUCKET_B(c0, c1); + BUCKET_B(c0, c1) = i; /* end point */ + + /* Move all type B* suffixes to the correct position. */ + for(i = t, j = BUCKET_BSTAR(c0, c1); + j <= k; + --i, --k) { SA[i] = SA[k]; } + } + BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */ + BUCKET_B(c0, c0) = i; /* end point */ + } + } + + return m; +} + +/* Constructs the suffix array by using the sorted order of type B* suffixes. */ +static +void +construct_SA(const unsigned char *T, int *SA, + int *bucket_A, int *bucket_B, + int n, int m) { + int *i, *j, *k; + int s; + int c0, c1, c2; + + if(0 < m) { + /* Construct the sorted order of type B suffixes by using + the sorted order of type B* suffixes. */ + for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) { + /* Scan the suffix array from right to left. */ + for(i = SA + BUCKET_BSTAR(c1, c1 + 1), + j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1; + i <= j; + --j) { + if(0 < (s = *j)) { + assert(T[s] == c1); + assert(((s + 1) < n) && (T[s] <= T[s + 1])); + assert(T[s - 1] <= T[s]); + *j = ~s; + c0 = T[--s]; + if((0 < s) && (T[s - 1] > c0)) { s = ~s; } + if(c0 != c2) { + if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; } + k = SA + BUCKET_B(c2 = c0, c1); + } + assert(k < j); + *k-- = s; + } else { + assert(((s == 0) && (T[s] == c1)) || (s < 0)); + *j = ~s; + } + } + } + } + + /* Construct the suffix array by using + the sorted order of type B suffixes. */ + k = SA + BUCKET_A(c2 = T[n - 1]); + *k++ = (T[n - 2] < c2) ? ~(n - 1) : (n - 1); + /* Scan the suffix array from left to right. */ + for(i = SA, j = SA + n; i < j; ++i) { + if(0 < (s = *i)) { + assert(T[s - 1] >= T[s]); + c0 = T[--s]; + if((s == 0) || (T[s - 1] < c0)) { s = ~s; } + if(c0 != c2) { + BUCKET_A(c2) = k - SA; + k = SA + BUCKET_A(c2 = c0); + } + assert(i < k); + *k++ = s; + } else { + assert(s < 0); + *i = ~s; + } + } +} + +/* Constructs the burrows-wheeler transformed string directly + by using the sorted order of type B* suffixes. */ +static +int +construct_BWT(const unsigned char *T, int *SA, + int *bucket_A, int *bucket_B, + int n, int m) { + int *i, *j, *k, *orig; + int s; + int c0, c1, c2; + + if(0 < m) { + /* Construct the sorted order of type B suffixes by using + the sorted order of type B* suffixes. */ + for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) { + /* Scan the suffix array from right to left. */ + for(i = SA + BUCKET_BSTAR(c1, c1 + 1), + j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1; + i <= j; + --j) { + if(0 < (s = *j)) { + assert(T[s] == c1); + assert(((s + 1) < n) && (T[s] <= T[s + 1])); + assert(T[s - 1] <= T[s]); + c0 = T[--s]; + *j = ~((int)c0); + if((0 < s) && (T[s - 1] > c0)) { s = ~s; } + if(c0 != c2) { + if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; } + k = SA + BUCKET_B(c2 = c0, c1); + } + assert(k < j); + *k-- = s; + } else if(s != 0) { + *j = ~s; +#ifndef NDEBUG + } else { + assert(T[s] == c1); +#endif + } + } + } + } + + /* Construct the BWTed string by using + the sorted order of type B suffixes. */ + k = SA + BUCKET_A(c2 = T[n - 1]); + *k++ = (T[n - 2] < c2) ? ~((int)T[n - 2]) : (n - 1); + /* Scan the suffix array from left to right. */ + for(i = SA, j = SA + n, orig = SA; i < j; ++i) { + if(0 < (s = *i)) { + assert(T[s - 1] >= T[s]); + c0 = T[--s]; + *i = c0; + if((0 < s) && (T[s - 1] < c0)) { s = ~((int)T[s - 1]); } + if(c0 != c2) { + BUCKET_A(c2) = k - SA; + k = SA + BUCKET_A(c2 = c0); + } + assert(i < k); + *k++ = s; + } else if(s != 0) { + *i = ~s; + } else { + orig = i; + } + } + + return orig - SA; +} + + +/*---------------------------------------------------------------------------*/ + +/*- Function -*/ + +int +divsufsort(const unsigned char *T, int *SA, int n) { + int *bucket_A, *bucket_B; + int m; + int err = 0; + + /* Check arguments. */ + if((T == NULL) || (SA == NULL) || (n < 0)) { return -1; } + else if(n == 0) { return 0; } + else if(n == 1) { SA[0] = 0; return 0; } + else if(n == 2) { m = (T[0] < T[1]); SA[m ^ 1] = 0, SA[m] = 1; return 0; } + + bucket_A = (int *)malloc(BUCKET_A_SIZE * sizeof(int)); + bucket_B = (int *)malloc(BUCKET_B_SIZE * sizeof(int)); + + /* Suffixsort. */ + if((bucket_A != NULL) && (bucket_B != NULL)) { + m = sort_typeBstar(T, SA, bucket_A, bucket_B, n); + construct_SA(T, SA, bucket_A, bucket_B, n, m); + } else { + err = -2; + } + + free(bucket_B); + free(bucket_A); + + return err; +} + +int +divbwt(const unsigned char *T, unsigned char *U, int *A, int n) { + int *B; + int *bucket_A, *bucket_B; + int m, pidx, i; + + /* Check arguments. */ + if((T == NULL) || (U == NULL) || (n < 0)) { return -1; } + else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; } + + if((B = A) == NULL) { B = (int *)malloc((size_t)(n + 1) * sizeof(int)); } + bucket_A = (int *)malloc(BUCKET_A_SIZE * sizeof(int)); + bucket_B = (int *)malloc(BUCKET_B_SIZE * sizeof(int)); + + /* Burrows-Wheeler Transform. */ + if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) { + m = sort_typeBstar(T, B, bucket_A, bucket_B, n); + pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m); + + /* Copy to output string. */ + U[0] = T[n - 1]; + for(i = 0; i < pidx; ++i) { U[i + 1] = (unsigned char)B[i]; } + for(i += 1; i < n; ++i) { U[i] = (unsigned char)B[i]; } + pidx += 1; + } else { + pidx = -2; + } + + free(bucket_B); + free(bucket_A); + if(A == NULL) { free(B); } + + return pidx; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsortxx/divsufsortxx.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsortxx/divsufsortxx.h new file mode 100644 index 0000000000000000000000000000000000000000..91abe52c4157788c8c7a27895d51f529ef391a0f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/libdivsufsortxx/divsufsortxx.h @@ -0,0 +1,1546 @@ +/* + * divsufsortxx.h + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +// r3 + +#ifndef _DIVSUFSORTXX_H_ +#define _DIVSUFSORTXX_H_ + +#include +#include + + +namespace divsufsortxx { + +namespace helper { + +/* Insertionsort for small size groups. */ +template +void +insertionsort(const ISAIterator_type ISAd, + SAIterator_type first, SAIterator_type last) { +typedef typename std::iterator_traits::value_type pos_type; +typedef typename std::iterator_traits::value_type value_type; + SAIterator_type a, b; + pos_type t; + value_type v, x; + + for(a = first + 1; a < last; ++a) { + for(v = ISAd[t = *a], b = a; v < (x = ISAd[*(b - 1)]);) { + do { *b = *(b - 1); } while((first < --b) && (*(b - 1) < 0)); + if(b <= first) { break; } + } + if(v == x) { *(b - 1) = ~*(b - 1); } + *b = t; + } +} + + +/*---------------------------------------------------------------------------*/ + +/* Heapsort */ + +template +void +fixdown(const StringIterator_type Td, SAIterator_type SA, pos_type i, pos_type size) { +typedef typename std::iterator_traits::value_type value_type; + pos_type j, k, t; + value_type c, d, e; + + for(t = SA[i], c = Td[t]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) { + d = Td[SA[k = j++]]; + if(d < (e = Td[SA[j]])) { k = j; d = e; } + if(d <= c) { break; } + } + SA[i] = t; +} + +/* Simple top-down heapsort. */ +template +void +heapsort(const StringIterator_type Td, SAIterator_type SA, + typename std::iterator_traits::value_type size) { +typedef typename std::iterator_traits::value_type pos_type; + pos_type i, m; + pos_type t; + + m = size; + if((size % 2) == 0) { + m--; + if(Td[SA[m / 2]] < Td[SA[m]]) { + std::iter_swap(SA + m, SA + m / 2); + } + } + + for(i = m / 2 - 1; 0 <= i; --i) { + fixdown(Td, SA, i, m); + } + + if((size % 2) == 0) { + std::iter_swap(SA, SA + m); + fixdown(Td, SA, pos_type(0), m); + } + + for(i = m - 1; 0 < i; --i) { + t = SA[0]; + SA[0] = SA[i]; + fixdown(Td, SA, pos_type(0), i); + SA[i] = t; + } +} + + +/*---------------------------------------------------------------------------*/ + +static +const int +log2table[256]= { + -1, 0, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, + 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, + 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, + 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, + 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, + 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, + 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, + 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, + 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, + 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, + 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, + 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, + 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, + 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7 +}; + +template +int +lg(numeric_type n) { + int lgsize = 0; + while(255 < n) { lgsize += 8, n >>= 8; } + return lgsize + log2table[n]; +} + +template +void +vecswap(Iterator1_type first1, Iterator1_type last1, Iterator2_type first2) { + for(; first1 != last1; ++first1, ++first2) { + std::iter_swap(first1, first2); + } +// std::swap_ranges(first1, last1, first2); +} + + +/*---------------------------------------------------------------------------*/ + +/* Returns the median of three elements. */ +template +SAIterator_type +median3(const StringIterator_type Td, + SAIterator_type v1, SAIterator_type v2, SAIterator_type v3) { + if(Td[*v1] > Td[*v2]) { std::swap(v1, v2); } + if(Td[*v2] > Td[*v3]) { + if(Td[*v1] > Td[*v3]) { return v1; } + else { return v3; } + } + return v2; +} + +/* Returns the median of five elements. */ +template +SAIterator_type +median5(const StringIterator_type Td, + SAIterator_type v1, SAIterator_type v2, SAIterator_type v3, + SAIterator_type v4, SAIterator_type v5) { + if(Td[*v2] > Td[*v3]) { std::swap(v2, v3); } + if(Td[*v4] > Td[*v5]) { std::swap(v4, v5); } + if(Td[*v2] > Td[*v4]) { std::swap(v2, v4); std::swap(v3, v5); } + if(Td[*v1] > Td[*v3]) { std::swap(v1, v3); } + if(Td[*v1] > Td[*v4]) { std::swap(v1, v4); std::swap(v3, v5); } + if(Td[*v3] > Td[*v4]) { return v4; } + return v3; +} + +/* Returns the pivot element. */ +template +SAIterator_type +pivot(const StringIterator_type Td, + SAIterator_type first, SAIterator_type last) { +typedef typename std::iterator_traits::difference_type difference_type; + difference_type t = last - first; + SAIterator_type middle = first + t / 2; + + if(t <= 512) { + if(t <= 32) { + return median3(Td, first, middle, last - 1); + } else { + t >>= 2; + return median5(Td, + first, first + t, middle, + last - 1 - t, last - 1); + } + } + t >>= 3; + return median3(Td, + median3(Td, first, first + t, first + (t << 1)), + median3(Td, middle - t, middle, middle + t), + median3(Td, last - 1 - (t << 1), last - 1 - t, last - 1)); +} + +/* Two-stage double-index controlled ternary partition */ +template +bool +partition(const StringIterator_type Td, + SAIterator_type first1, SAIterator_type first2, SAIterator_type last, + SAIterator_type &mfirst, SAIterator_type &mlast, + const typename std::iterator_traits::value_type &v) { + SAIterator_type a, b, c, d; + typename std::iterator_traits::value_type x = 0; + + for(b = first2; (b < last) && ((x = Td[*b]) == v); ++b) { } + if(((a = b) < last) && (x < v)) { + for(; (++b < last) && ((x = Td[*b]) <= v);) { + if(x == v) { std::iter_swap(b, a++); } + } + } + for(c = last; (b < --c) && ((x = Td[*c]) == v);) { } + if((b < (d = c)) && (x > v)) { + for(; (b < --c) && ((x = Td[*c]) >= v);) { + if(x == v) { std::iter_swap(c, d--); } + } + } + for(; b < c;) { + std::iter_swap(b, c); + for(; (++b < c) && ((x = Td[*b]) <= v);) { + if(x == v) { std::iter_swap(b, a++); } + } + for(; (b < --c) && ((x = Td[*c]) >= v);) { + if(x == v) { std::iter_swap(c, d--); } + } + } + + if(a <= d) { + vecswap(b - std::min(a - first1, b - a), b, first1); + vecswap(last - std::min(d + 1 - b, last - d - 1), last, b); + mfirst = first1 + (b - a), mlast = last - (d + 1 - b); + return true; + } + mfirst = first1, mlast = last; + return false; +} + + +/*---------------------------------------------------------------------------*/ + +template +struct stackinfo3 { + a_type m_a; + b_type m_b; + c_type m_c; + stackinfo3(a_type a, b_type b, c_type c) : m_a(a), m_b(b), m_c(c) { } +}; + +template +struct stackinfo4 { + a_type m_a; + b_type m_b; + c_type m_c; + d_type m_d; + stackinfo4(a_type a, b_type b, c_type c, d_type d) : m_a(a), m_b(b), m_c(c), m_d(d) { } +}; + +} /* namespace helper */ + +#define STACK_POP3(_a, _b, _c)\ + {\ + if(stack.empty()) { return; }\ + stackinfo_type tempinfo = stack.top();\ + (_a) = tempinfo.m_a, (_b) = tempinfo.m_b, (_c) = tempinfo.m_c;\ + stack.pop();\ + } +#define STACK_POP4(_a, _b, _c, _d)\ + {\ + if(stack.empty()) { return; }\ + stackinfo_type tempinfo = stack.top();\ + (_a) = tempinfo.m_a, (_b) = tempinfo.m_b, (_c) = tempinfo.m_c, (_d) = tempinfo.m_d;\ + stack.pop();\ + } +#define STACK_PUSH3(_a, _b, _c)\ + stack.push(stackinfo_type((_a), (_b), (_c))) +#define STACK_PUSH4(_a, _b, _c, _d)\ + stack.push(stackinfo_type((_a), (_b), (_c), (_d))) + + +namespace substring { + +template +int +compare(StringIterator_type T, + const SAIterator_type p1, const SAIterator_type p2, + typename std::iterator_traits::value_type depth) { + StringIterator_type U1 = T + depth + *p1, + U2 = T + depth + *p2, + U1n = T + *(p1 + 1) + 2, + U2n = T + *(p2 + 1) + 2; + for(; (U1 < U1n) && (U2 < U2n) && (*U1 == *U2); ++U1, ++U2) { } + + return U1 < U1n ? + (U2 < U2n ? (*U2 < *U1) * 2 - 1 : 1) : +// (U2 < U2n ? *U1 - *U2 : 1) : + (U2 < U2n ? -1 : 0); +} + +template +int +compare_last(StringIterator_type T, + const SAIterator_type p1, const SAIterator_type p2, + typename std::iterator_traits::value_type depth, + typename std::iterator_traits::value_type size) { + StringIterator_type U1 = T + depth + *p1, + U2 = T + depth + *p2, + U1n = T + size, + U2n = T + *(p2 + 1) + 2; + for(; (U1 < U1n) && (U2 < U2n) && (*U1 == *U2); ++U1, ++U2) { } + + return U1 < U1n ? + (U2 < U2n ? (*U2 < *U1) * 2 - 1 : 1) : +// (U2 < U2n ? *U1 - *U2 : 1) : + (U2 < U2n ? -1 : 0); +} + +template +void +insertionsort(StringIterator_type T, const SAIterator_type PA, + SAIterator_type first, SAIterator_type last, + typename std::iterator_traits::value_type depth) { + SAIterator_type a, b; + typename std::iterator_traits::value_type t; + int r; + + for(a = last - 1; first < a; --a) { + for(t = *(a - 1), b = a; 0 < (r = compare(T, PA + t, PA + *b, depth));) { + do { *(b - 1) = *b; } while((++b < last) && (*b < 0)); + if(last <= b) { break; } + } + if(r == 0) { *b = ~*b; } + *(b - 1) = t; + } +} + +template +class substring_wrapper { +private: + StringIterator_type m_Td; + const PAIterator_type m_PA; +public: + typedef typename std::iterator_traits::value_type value_type; + typedef value_type * pointer; + typedef value_type & reference; + typedef ptrdiff_t difference_type; + typedef std::random_access_iterator_tag iterator_category; + + typedef size_t size_type; + + substring_wrapper(StringIterator_type Td, const PAIterator_type PA) : m_Td(Td), m_PA(PA) { + } + + value_type + operator[](size_type i) const { + return m_Td[m_PA[i]]; + } + + substring_wrapper & + operator=(const substring_wrapper &wrapper) { + return *this; + } +}; + +template +SAIterator_type +partition(const SAIterator_type PA, + SAIterator_type first, SAIterator_type last, + typename std::iterator_traits::value_type depth) { + SAIterator_type a, b; + for(a = first, b = last - 1;; ++a, --b) { + for(; (a <= b) && ((PA[*a] + depth) >= (PA[*a + 1] + 1)); ++a) { *a = ~*a; } + for(; (a < b) && ((PA[*b] + depth) < (PA[*b + 1] + 1)); --b) { } + if(b <= a) { break; } + std::iter_swap(b, a); + *a = ~*a; + } + if(first < a) { *first = ~*first; } + return a; +} + +template +void +mintrosort(stack_type &stack, const StringIterator_type T, const SAIterator_type PA, + SAIterator_type first, SAIterator_type last, + typename std::iterator_traits::value_type depth) { +typedef typename std::iterator_traits::value_type pos_type; +typedef typename std::iterator_traits::value_type value_type; +typedef substring_wrapper wrapper_type; +typedef typename stack_type::value_type stackinfo_type; + + SAIterator_type a, b, c; + value_type v, x; + int limit; + + for(limit = helper::lg(last - first);;) { + + if((last - first) <= 8) { + if(1 < (last - first)) { insertionsort(T, PA, first, last, depth); } + STACK_POP4(first, last, depth, limit); + continue; + } + + const StringIterator_type Td = T + depth; + if(limit-- == 0) { helper::heapsort(wrapper_type(Td, PA), first, value_type( last - first )); } + if(limit < 0) { + for(a = first + 1, v = Td[PA[*first]]; a < last; ++a) { + if((x = Td[PA[*a]]) != v) { + if(1 < (a - first)) { break; } + v = x; + first = a; + } + } + if(Td[PA[*first] - 1] < v) { + first = partition(PA, first, a, depth); + } + if((a - first) <= (last - a)) { + if(1 < (a - first)) { + STACK_PUSH4(a, last, depth, -1); + last = a, depth += 1, limit = helper::lg(a - first); + } else { + first = a, limit = -1; + } + } else { + if(1 < (last - a)) { + STACK_PUSH4(first, a, depth + 1, helper::lg(a - first)); + first = a, limit = -1; + } else { + last = a, depth += 1, limit = helper::lg(a - first); + } + } + continue; + } + + /* partition */ + a = helper::pivot(wrapper_type(Td, PA), first, last); + std::iter_swap(first, a); + if(helper::partition(wrapper_type(Td, PA), first, first + 1, last, a, c, Td[PA[*first]]) != false) { + b = (Td[PA[*a]] <= Td[PA[*a] - 1]) ? a : partition(PA, a, c, depth); + + if((a - first) <= (last - c)) { + if((last - c) <= (c - b)) { + STACK_PUSH4(b, c, depth + 1, helper::lg(c - b)); + STACK_PUSH4(c, last, depth, limit); + last = a; + } else if((a - first) <= (c - b)) { + STACK_PUSH4(c, last, depth, limit); + STACK_PUSH4(b, c, depth + 1, helper::lg(c - b)); + last = a; + } else { + STACK_PUSH4(c, last, depth, limit); + STACK_PUSH4(first, a, depth, limit); + first = b, last = c, depth += 1, limit = helper::lg(c - b); + } + } else { + if((a - first) <= (c - b)) { + STACK_PUSH4(b, c, depth + 1, helper::lg(c - b)); + STACK_PUSH4(first, a, depth, limit); + first = c; + } else if((last - c) <= (c - b)) { + STACK_PUSH4(first, a, depth, limit); + STACK_PUSH4(b, c, depth + 1, helper::lg(c - b)); + first = c; + } else { + STACK_PUSH4(first, a, depth, limit); + STACK_PUSH4(c, last, depth, limit); + first = b, last = c, depth += 1, limit = helper::lg(c - b); + } + } + } else { + limit += 1; + if(Td[PA[*first] - 1] < Td[PA[*first]]) { + first = partition(PA, first, last, depth); + limit = helper::lg(last - first); + } + depth += 1; + } + } +} + +/* Merge-forward with internal buffer. */ +template +void +merge_forward(const StringIterator_type T, + const SAIterator_type PA, BufIterator_type buf, + SAIterator_type first, SAIterator_type middle, SAIterator_type last, + typename std::iterator_traits::value_type depth) { + SAIterator_type i, k; + BufIterator_type j, bufend; + typename std::iterator_traits::value_type t; + int r; + + bufend = buf + (middle - first); + helper::vecswap(first, middle, buf); + + for(t = *first, i = first, j = buf, k = middle;;) { + r = compare(T, PA + *j, PA + *k, depth); + if(r < 0) { + do { + *i++ = *j; *j++ = *i; + if(bufend <= j) { *(bufend - 1) = t; return; } + } while(*j < 0); + } else if(r > 0) { + do { + *i++ = *k; *k++ = *i; + if(last <= k) { + do { *i++ = *j; *j++ = *i; } while(j < bufend); + *(bufend - 1) = t; + return; + } + } while(*k < 0); + } else { + *k = ~*k; + do { + *i++ = *j; *j++ = *i; + if(bufend <= j) { *(bufend - 1) = t; return; } + } while(*j < 0); + + do { + *i++ = *k; *k++ = *i; + if(last <= k) { + do { *i++ = *j; *j++ = *i; } while(j < bufend); + *(bufend - 1) = t; + return; + } + } while(*k < 0); + } + } +} + +/* Merge-backward with internal buffer. */ +template +void +merge_backward(const StringIterator_type T, + const SAIterator_type PA, BufIterator_type buf, + SAIterator_type first, SAIterator_type middle, SAIterator_type last, + typename std::iterator_traits::value_type depth) { + SAIterator_type p1, p2; + SAIterator_type i, k; + BufIterator_type j, bufend; + typename std::iterator_traits::value_type t; + int r, x; + + bufend = buf + (last - middle); + helper::vecswap(middle, last, buf); + + x = 0; + if(*(bufend - 1) < 0) { x |= 1; p1 = PA + ~*(bufend - 1); } + else { p1 = PA + *(bufend - 1); } + if(*(middle - 1) < 0) { x |= 2; p2 = PA + ~*(middle - 1); } + else { p2 = PA + *(middle - 1); } + for(t = *(last - 1), i = last - 1, j = bufend - 1, k = middle - 1;;) { + + r = compare(T, p1, p2, depth); + if(r > 0) { + if(x & 1) { do { *i-- = *j; *j-- = *i; } while(*j < 0); x ^= 1; } + *i-- = *j; *j = *i; + if(j <= buf) { *buf = t; return; } + + if(*--j < 0) { x |= 1; p1 = PA + ~*j; } + else { p1 = PA + *j; } + } else if(r < 0) { + if(x & 2) { do { *i-- = *k; *k-- = *i; } while(*k < 0); x ^= 2; } + *i-- = *k; *k = *i; + if(k <= first) { + while(buf < j) { *i-- = *j; *j-- = *i; } + *i = *j, *buf = t; + return; + } + + if(*--k < 0) { x |= 2; p2 = PA + ~*k; } + else { p2 = PA + *k; } + } else { + if(x & 1) { do { *i-- = *j; *j-- = *i; } while(*j < 0); x ^= 1; } + *i-- = ~*j; *j = *i; + if(j <= buf) { *buf = t; return; } + --j; + + if(x & 2) { do { *i-- = *k; *k-- = *i; } while(*k < 0); x ^= 2; } + *i-- = *k; *k = *i; + if(k <= first) { + while(buf < j) { *i-- = *j; *j-- = *i; } + *i = *j, *buf = t; + return; + } + --k; + + if(*j < 0) { x |= 1; p1 = PA + ~*j; } + else { p1 = PA + *j; } + if(*k < 0) { x |= 2; p2 = PA + ~*k; } + else { p2 = PA + *k; } + } + } +} + +/* Faster merge (based on divide and conquer technique). */ +template +void +merge(stack_type &stack, const StringIterator_type T, const SAIterator_type PA, + SAIterator_type first, SAIterator_type middle, SAIterator_type last, + BufIterator_type buf, typename std::iterator_traits::value_type bufsize, + typename std::iterator_traits::value_type depth) { +typedef typename std::iterator_traits::difference_type difference_type; +typedef typename stack_type::value_type stackinfo_type; +#define GETIDX(a) ((0 <= (a)) ? (a) : (~(a))) +#define MERGE_CHECK(a)\ + {\ + if((0 <= *(a)) &&\ + (compare(T, PA + GETIDX(*((a) - 1)), PA + *(a), depth) == 0)) {\ + *(a) = ~*(a);\ + }\ + } + + SAIterator_type i, j; + difference_type m, len, half; + int check, next; + + for(check = 0;;) { + + if((last - middle) <= bufsize) { + if((first < middle) && (middle < last)) { + merge_backward(T, PA, buf, first, middle, last, depth); + } + if(check & 1) { MERGE_CHECK(first); } + if(check & 2) { MERGE_CHECK(last); } + STACK_POP4(first, middle, last, check); + continue; + } + + if((middle - first) <= bufsize) { + if(first < middle) { + merge_forward(T, PA, buf, first, middle, last, depth); + } + if(check & 1) { MERGE_CHECK(first); } + if(check & 2) { MERGE_CHECK(last); } + STACK_POP4(first, middle, last, check); + continue; + } + + for(m = 0, len = std::min(middle - first, last - middle), half = len >> 1; + 0 < len; + len = half, half >>= 1) { + if(compare(T, PA + GETIDX(*(middle + m + half)), + PA + GETIDX(*(middle - m - half - 1)), depth) < 0) { + m += half + 1; + half -= ((len & 1) == 0); + } + } + + if(0 < m) { + helper::vecswap(middle - m, middle, middle); + i = j = middle, next = 0; + if((middle + m) < last) { + if(*(middle + m) < 0) { + for(; *(i - 1) < 0; --i) { } + *(middle + m) = ~*(middle + m); + } + for(j = middle; *j < 0; ++j) { } + next = 1; + } + if((i - first) <= (last - j)) { + STACK_PUSH4(j, middle + m, last, (check & 2) | (next & 1)); + middle -= m, last = i, check = (check & 1); + } else { + if((i == middle) && (middle == j)) { next <<= 1; } + STACK_PUSH4(first, middle - m, i, (check & 1) | (next & 2)); + first = j, middle += m, check = (check & 2) | (next & 1); + } + } else { + if(check & 1) { MERGE_CHECK(first); } + MERGE_CHECK(middle); + if(check & 2) { MERGE_CHECK(last); } + STACK_POP4(first, middle, last, check); + } + } +#undef GETIDX +#undef MERGE_CHECK +} + +template +void +sort(const StringIterator_type T, const SAIterator_type PA, + SAIterator_type first, SAIterator_type last, + BufIterator_type buf, typename std::iterator_traits::value_type bufsize, + typename std::iterator_traits::value_type depth, + typename std::iterator_traits::value_type size, + bool lastsuffix, int blocksize = 1024) { +typedef typename std::iterator_traits::value_type pos_type; + std::stack > stack1; + std::stack > stack2; + + SAIterator_type a, b; + SAIterator_type curbuf; + pos_type i, j, k, curbufsize; + + if(lastsuffix != false) { ++first; } + for(a = first, i = 0; blocksize < (last - a); a += blocksize, ++i) { + mintrosort(stack1, T, PA, a, a + blocksize, depth); + curbuf = a + blocksize; + curbufsize = pos_type( last - (a + blocksize) ); + if(bufsize <= curbufsize) { + for(b = a, k = blocksize, j = i; j & 1; b -= k, k <<= 1, j >>= 1) { + merge(stack2, T, PA, b - k, b, b + k, curbuf, curbufsize, depth); + } + } else { + for(b = a, k = blocksize, j = i; j & 1; b -= k, k <<= 1, j >>= 1) { + merge(stack2, T, PA, b - k, b, b + k, buf, bufsize, depth); + } + } + } + mintrosort(stack1, T, PA, a, last, depth); + for(k = blocksize; i != 0; k <<= 1, i >>= 1) { + if(i & 1) { + merge(stack2, T, PA, a - k, a, last, buf, bufsize, depth); + a -= k; + } + } + + if(lastsuffix != false) { + /* Insert last type B* suffix. */ + for(a = first, i = *(first - 1); + (a < last) && ((*a < 0) || (0 < compare_last(T, PA + i, PA + *a, depth, size))); + ++a) { + *(a - 1) = *a; + } + *(a - 1) = i; + } +} + + +} /* namespace substring */ + + + +namespace doubling { + +template +void +updategroup(ISAIterator_type ISA, const SAIterator_type SA, + SAIterator_type first, SAIterator_type last) { +typedef typename std::iterator_traits::value_type value_type; +typedef typename std::iterator_traits::value_type sa_type; + SAIterator_type a, b; + value_type t; + + for(a = first; a < last; ++a) { + if(0 <= *a) { + b = a; + do { ISA[*a] = sa_type( a - SA ); } while((++a < last) && (0 <= *a)); + *b = sa_type( b - a ); + if(last <= a) { break; } + } + b = a; + do { *a = ~*a; } while(*++a < 0); + t = value_type( a - SA ); + do { ISA[*b] = t; } while(++b <= a); + } +} + +template +void +introsort(stack_type &stack, ISAIterator_type ISA, const ISAIterator_type ISAd, + const SAIterator_type SA, SAIterator_type first, SAIterator_type last) { +typedef typename std::iterator_traits::value_type value_type; +typedef typename std::iterator_traits::value_type sa_type; +typedef typename stack_type::value_type stackinfo_type; + + SAIterator_type a, b, c; + value_type v, x; + + for(int limit = helper::lg(last - first);;) { + + if((last - first) <= 8) { + if(1 < (last - first)) { + helper::insertionsort(ISAd, first, last); + updategroup(ISA, SA, first, last); + } else if((last - first) == 1) { *first = -1; } + STACK_POP3(first, last, limit); + continue; + } + + if(limit-- == 0) { + helper::heapsort(ISAd, first, value_type( last - first )); + for(a = last - 1, v = ISAd[*a]; first < a;) { + if((x = ISAd[*--a]) == v) { *a = ~*a; } + else { v = x; } + } + updategroup(ISA, SA, first, last); + STACK_POP3(first, last, limit); + continue; + } + + a = helper::pivot(ISAd, first, last); + std::iter_swap(first, a); + if(helper::partition(ISAd, first, first + 1, last, a, b, ISAd[*first]) != false) { + + /* update ranks */ + for(c = first, v = value_type( a - SA - 1 ); c < a; ++c) { ISA[*c] = v; } + if(b < last) { for(c = a, v = value_type( b - SA - 1 ); c < b; ++c) { ISA[*c] = v; } } + if((b - a) == 1) { *a = - 1; } + + if((a - first) <= (last - b)) { + if(first < a) { + STACK_PUSH3(b, last, limit); + last = a; + } else { + first = b; + } + } else { + if(b < last) { + STACK_PUSH3(first, a, limit); + first = b; + } else { + last = a; + } + } + } else { + STACK_POP3(first, last, limit); + } + } +} + +template +void +sort(ISAIterator_type ISA, SAIterator_type first, SAIterator_type last) { +typedef typename std::iterator_traits::value_type pos_type; + std::stack > stack; + SAIterator_type a, b; + pos_type t, skip, depth, size; + + for(size = pos_type( last - first ), depth = 1; -size < *first; depth *= 2) { + a = first, skip = 0; + do { + if((t = *a) < 0) { a -= t; skip += t; } + else { + if(skip != 0) { *(a + skip) = skip; skip = 0; } + b = first + ISA[t] + 1; + introsort(stack, ISA, ISA + depth, first, a, b); + a = b; + } + } while(a < last); + if(skip != 0) { *(a + skip) = skip; } + } +} + +} /* namespace doubling */ + + + +namespace tandemrepeat { + +template +void +introsort(stack_type &stack, ISAIterator_type ISA, ISAIterator_type ISAd, + const SAIterator_type SA, SAIterator_type first, SAIterator_type last, + pos_type &budget, int &chance, pos_type size) { +typedef typename std::iterator_traits::value_type value_type; +typedef typename stack_type::value_type stackinfo_type; +#define UPDATE_BUDGET(n)\ + {\ + budget -= (n);\ + if(budget <= 0) {\ + budget += size;\ + if(--chance == 0) { break; }\ + }\ + } + + SAIterator_type a, b, c, d, e; + pos_type s, t; + value_type v, x; + int limit, next; + + for(limit = helper::lg(last - first);;) { + + if(limit < 0) { + if(limit == -1) { + /* tandem repeat partition */ + helper::partition(ISAd - 1, first, first, last, a, b, value_type( last - SA - 1 )); + + /* update ranks */ + if(a < last) { + for(c = first, v = value_type( a - SA - 1 ); c < a; ++c) { ISA[*c] = v; } + } + if(b < last) { + for(c = a, v = value_type( b - SA - 1 ); c < b; ++c) { ISA[*c] = v; } + } + + /* push */ + STACK_PUSH4(ISAd, a, b, 0); + STACK_PUSH4(ISAd - 1, first, last, -2); + if((a - first) <= (last - b)) { + if(first < a) { + STACK_PUSH4(ISAd, b, last, helper::lg(last - b)); last = a; + } else { first = b; } + } else { + if(b < last) { + STACK_PUSH4(ISAd, first, a, helper::lg(a - first)); first = b; + } else { last = a; } + } + limit = helper::lg(last - first); + } else if(limit == -2) { + /* tandem repeat copy */ + stackinfo_type temp = stack.top(); stack.pop(); + a = temp.m_b, b = temp.m_c; + t = value_type( ISAd - ISA ); + v = value_type( b - SA - 1 ); + for(c = first, d = a; c < d; ++c) { + if((0 <= (s = *c - t)) && (ISA[s] == v)) { + ISA[s] = value_type( d - SA ); + *d++ = s; + } + } + for(c = last - 1, e = d, d = b; e < d; --c) { + if((0 <= (s = *c - t)) && (ISA[s] == v)) { + *--d = s; + ISA[s] = value_type( d - SA ); + } + } + STACK_POP4(ISAd, first, last, limit); + } else { + /* sorted partition */ + if(0 <= *first) { + a = first; + do { ISA[*a] = value_type( a - SA ); } while((++a < last) && (0 <= *a)); + first = a; + } + if(first < last) { + a = first; do { *a = ~*a; } while(*++a < 0); ++a; + if(a < last) { + for(c = first, v = value_type( a - SA - 1 ); c < a; ++c) { ISA[*c] = v; } + } + + /* push */ + next = (ISA[*first] == ISAd[*first]) ? -1 : helper::lg(a - first); + UPDATE_BUDGET(value_type( last - first )); + if((a - first) <= (last - a)) { + if(first < a) { + STACK_PUSH4(ISAd, a, last, -3); + ISAd += 1, last = a, limit = next; + } else { + first = a, limit = -3; + } + } else { + if(a < last) { + STACK_PUSH4(ISAd + 1, first, a, next); + first = a, limit = -3; + } else { + ISAd += 1, last = a, limit = next; + } + } + } else { + STACK_POP4(ISAd, first, last, limit); + } + } + continue; + } + + if((last - first) <= 8) { + if(1 < (last - first)) { + helper::insertionsort(ISAd, first, last); + limit = -3; + } else { + STACK_POP4(ISAd, first, last, limit); + } + continue; + } + + if(limit-- == 0) { + helper::heapsort(ISAd, first, value_type( last - first )); + for(a = last - 1, v = ISAd[*a]; first < a;) { + if((x = ISAd[*--a]) == v) { *a = ~*a; } + else { v = x; } + } + limit = -3; + continue; + } + + a = helper::pivot(ISAd, first, last); + std::iter_swap(first, a); + if(helper::partition(ISAd, first, first + 1, last, a, b, ISAd[*first]) != false) { + next = (ISA[*a] == ISAd[*a]) ? -1 : helper::lg(b - a); + + /* update ranks */ + for(c = first, v = value_type( a - SA - 1 ); c < a; ++c) { ISA[*c] = v; } + if(b < last) { for(c = a, v = value_type( b - SA - 1 ); c < b; ++c) { ISA[*c] = v; } } + + /* push */ + UPDATE_BUDGET(value_type( last - first )); + if((a - first) <= (last - b)) { + if((last - b) <= (b - a)) { + STACK_PUSH4(ISAd + 1, a, b, next); + STACK_PUSH4(ISAd, b, last, limit); + last = a; + } else if((a - first) <= (b - a)) { + STACK_PUSH4(ISAd, b, last, limit); + STACK_PUSH4(ISAd + 1, a, b, next); + last = a; + } else { + STACK_PUSH4(ISAd, b, last, limit); + STACK_PUSH4(ISAd, first, a, limit); + ISAd += 1, first = a, last = b, limit = next; + } + } else { + if((a - first) <= (b - a)) { + STACK_PUSH4(ISAd + 1, a, b, next); + STACK_PUSH4(ISAd, first, a, limit); + first = b; + } else if((last - b) <= (b - a)) { + STACK_PUSH4(ISAd, first, a, limit); + STACK_PUSH4(ISAd + 1, a, b, next); + first = b; + } else { + STACK_PUSH4(ISAd, first, a, limit); + STACK_PUSH4(ISAd, b, last, limit); + ISAd += 1, first = a, last = b, limit = next; + } + } + } else { + limit = (ISA[*first] == ISAd[*first]) ? -1 : (limit + 1), ISAd += 1; + UPDATE_BUDGET(value_type( last - first )); + } + } + + for(; stack.empty() == false; stack.pop()) { + stackinfo_type temp = stack.top(); + if(temp.m_d == -3) { + first = temp.m_b, last = temp.m_c; + for(a = first; a < last; ++a) { + if(0 <= *a) { + b = a; + do { ISA[*a] = value_type( a - SA ); } while((++a < last) && (0 <= *a)); + if(last <= a) { break; } + } + b = a; + do { *a = ~*a; } while(*++a < 0); + v = value_type( a - SA ); + do { ISA[*b] = v; } while(++b <= a); + } + } + } +#undef UPDATE_BUDGET +} + +template +bool +sort(ISAIterator_type ISA, SAIterator_type first, SAIterator_type last) { +typedef typename std::iterator_traits::value_type pos_type; + std::stack > stack; + SAIterator_type a, b; + pos_type t, skip, size, budget; + int chance; + + size = pos_type( last - first ); + if(-size < *first) { + a = first, skip = 0, budget = size; +// chance = helper::lg(size); + chance = helper::lg(size) * 2 / 3 + 1; +// chance = helper::lg(size) / 2 + 1; + do { + if((t = *a) < 0) { a -= t; skip += t; } + else { + skip = 0; + b = first + ISA[t] + 1; + introsort(stack, ISA, ISA + 1, first, a, b, budget, chance, size); + if(chance == 0) { + /* Switch to Larsson-Sadakane sorting algorithm. */ + if(first < a) { *first = -pos_type(a - first); } + return false; + } + a = b; + } + } while(a < last); + } + + return true; +} + + +} /* namespace tandemrepeat */ + + +#undef STACK_POP3 +#undef STACK_POP4 +#undef STACK_PUSH3 +#undef STACK_PUSH4 + + +static const int EXTRA_SPACE = 0; + +namespace core { +#define BUCKET_A(c0) bucket_A[(c0)] +#define BUCKET_B(c0, c1) (bucket_B[((alphabetsize_type)(c1)) * alphabetsize + (alphabetsize_type)(c0)]) +#define BUCKET_BSTAR(c0, c1) (bucket_B[((alphabetsize_type)(c0)) * alphabetsize + (alphabetsize_type)(c1)]) + +static const int MERGE_BUFSIZE = 256; + +/* Sorts suffixes of type B*. */ +template +pos_type +sort_typeBstar(const StringIterator_type T, SAIterator_type SA, + pos_type *bucket_A, pos_type *bucket_B, + pos_type n, pos_type SAsize, alphabetsize_type alphabetsize) { +typedef typename std::iterator_traits::value_type value_type; + pos_type i, j, k, t, m, bufsize; + alphabetsize_type c0, c1; + + /* Initialize bucket arrays. */ + for(i = 0; i < alphabetsize; ++i) { bucket_A[i] = 0; } + for(i = 0; i < alphabetsize * alphabetsize; ++i) { bucket_B[i] = 0; } + + /* Count the number of occurrences of the first one or two characters of each + type A, B and B* suffix. Moreover, store the beginning position of all + type B* suffixes into the array SA. */ + for(i = n - 1, m = SAsize; 0 <= i;) { + /* type A suffix. */ + do { ++BUCKET_A(T[i]); } while((0 <= --i) && (T[i] >= T[i + 1])); + if(0 <= i) { + /* type B* suffix. */ + ++BUCKET_BSTAR(T[i], T[i + 1]); + SA[--m] = i; + /* type B suffix. */ + for(--i; (0 <= i) && (T[i] <= T[i + 1]); --i) { + ++BUCKET_B(T[i], T[i + 1]); + } + } + } + m = SAsize - m; + + /* Calculate the index of start/end point of each bucket. */ + for(c0 = 0, i = -1, j = 0; c0 < alphabetsize; ++c0) { + t = i + BUCKET_A(c0); + BUCKET_A(c0) = i + j; /* start point */ + i = t + BUCKET_B(c0, c0); + for(c1 = c0 + 1; c1 < alphabetsize; ++c1) { + j += BUCKET_BSTAR(c0, c1); + BUCKET_BSTAR(c0, c1) = j; /* end point */ + i += BUCKET_B(c0, c1); + } + } + + if(0 < m) { + /* Sort the type B* suffixes by their first two characters. */ + SAIterator_type PAb = SA + SAsize - m, ISAb = SA + m; + for(i = m - 2; 0 <= i; --i) { + t = PAb[i], c0 = T[t], c1 = T[t + 1]; + SA[--BUCKET_BSTAR(c0, c1)] = i; + } + t = PAb[m - 1], c0 = T[t], c1 = T[t + 1]; + SA[--BUCKET_BSTAR(c0, c1)] = m - 1; + + /* Sort the type B* substrings using sssort. */ + bufsize = SAsize - 2 * m; + if(MERGE_BUFSIZE < bufsize) { + SAIterator_type buf = SA + m; + for(c0 = alphabetsize - 1, j = m; 0 < j; --c0) { + for(c1 = alphabetsize - 1; c0 < c1; j = i, --c1) { + i = BUCKET_BSTAR(c0, c1); + if(1 < (j - i)) { + substring::sort(T, PAb, SA + i, SA + j, buf, bufsize, 2, n, *(SA + i) == (m - 1)); + } + } + } + } else { + pos_type *lbuf = NULL; + int err = 0; + try { + lbuf = new pos_type[MERGE_BUFSIZE]; if(lbuf == NULL) { throw; } + for(c0 = alphabetsize - 1, j = m; 0 < j; --c0) { + for(c1 = alphabetsize - 1; c0 < c1; j = i, --c1) { + i = BUCKET_BSTAR(c0, c1); + if(1 < (j - i)) { + substring::sort(T, PAb, SA + i, SA + j, lbuf, MERGE_BUFSIZE, 2, n, *(SA + i) == (m - 1)); + } + } + } + } catch(...) { + err = -1; + } + delete[] lbuf; + if(err != 0) { throw; } + } + + /* Compute ranks of type B* substrings. */ + for(i = m - 1; 0 <= i; --i) { + if(0 <= SA[i]) { + j = i; + do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i])); + SA[i + 1] = i - j; + if(i <= 0) { break; } + } + j = i; + do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0); + ISAb[SA[i]] = j; + } + + /* Construct the inverse suffix array of type B* suffixes using tandemrepeat/doubling sorting algorithms. */ + if(tandemrepeat::sort(ISAb, SA, SA + m) == false) { + doubling::sort(ISAb, SA, SA + m); + } + + /* Set the sorted order of tyoe B* suffixes. */ + for(i = n - 1, j = m; 0 <= i;) { + for(--i; (0 <= i) && (T[i] >= T[i + 1]); --i) { } + if(0 <= i) { + SA[ISAb[--j]] = i; + for(--i; (0 <= i) && (T[i] <= T[i + 1]); --i) { } + } + } + + /* Calculate the index of start/end point of each bucket. */ + for(c0 = alphabetsize - 1, i = n - 1, k = m - 1; 0 <= c0; --c0) { + for(c1 = alphabetsize - 1; c0 < c1; --c1) { + t = i - BUCKET_B(c0, c1); + BUCKET_B(c0, c1) = i + 1; /* end point */ + + /* Move all type B* suffixes to the correct position. */ + for(i = t, j = BUCKET_BSTAR(c0, c1); + j <= k; + --i, --k) { SA[i] = SA[k]; } + } + t = i - BUCKET_B(c0, c0); + BUCKET_B(c0, c0) = i + 1; /* end point */ + if(c0 < (alphabetsize - 1)) { + BUCKET_BSTAR(c0, c0 + 1) = t + 1; /* start point */ + } + i = BUCKET_A(c0); + } + } + + return m; +} + +/* Constructs the suffix array by using the sorted order of type B* suffixes. */ +template +void +constructSA_from_typeBstar(const StringIterator_type T, SAIterator_type SA, + pos_type *bucket_A, pos_type *bucket_B, + pos_type n, pos_type m, alphabetsize_type alphabetsize) { +typedef typename std::iterator_traits::value_type value_type; + SAIterator_type i, j, t = SA; + pos_type s; + alphabetsize_type c0, c1, c2; + + /** An implementation version of MSufSort3's second stage. **/ + + if(0 < m) { + /* Construct the sorted order of type B suffixes by using + the sorted order of type B* suffixes. */ + for(c1 = alphabetsize - 2; 0 <= c1; --c1) { + /* Scan the suffix array from right to left. */ + for(i = SA + BUCKET_BSTAR(c1, c1 + 1), + j = SA + (BUCKET_A(c1 + 1) + 1), + c2 = -1; + i < j;) { + if(0 <= (s = *--j)) { + if((0 <= --s) && ((c0 = T[s]) <= c1)) { + *j = ~(s + 1); + if((0 < s) && (T[s - 1] > c0)) { s = ~s; } + if(c2 == c0) { *--t = s; } + else { + if(0 <= c2) { BUCKET_B(c2, c1) = t - SA; } + *(t = SA + BUCKET_B(c2 = c0, c1) - 1) = s; + } + } + } else { + *j = ~s; + } + } + } + } + + /* Construct the suffix array by using + the sorted order of type B suffixes. */ + *(t = SA + (BUCKET_A(c2 = T[n - 1]) + 1)) = n - 1; + /* Scan the suffix array from left to right. */ + for(i = SA, j = SA + n; i < j; ++i) { + if(0 <= (s = *i)) { + if((0 <= --s) && ((c0 = T[s]) >= T[s + 1])) { + if((0 < s) && (T[s - 1] < c0)) { s = ~s; } + if(c0 == c2) { *++t = s; } + else { + BUCKET_A(c2) = t - SA; + *(t = SA + (BUCKET_A(c2 = c0) + 1)) = s; + } + } + } else { + *i = ~s; + } + } +} + + +/* Constructs the burrows-wheeler transformed string directly + by using the sorted order of type B* suffixes. */ +template +SAIterator_type +constructBWT_from_typeBstar(const StringIterator_type T, SAIterator_type SA, + pos_type *bucket_A, pos_type *bucket_B, + pos_type n, pos_type m, alphabetsize_type alphabetsize) { +typedef typename std::iterator_traits::value_type value_type; + SAIterator_type i, j, t = SA, orig; + pos_type s; + alphabetsize_type c0, c1, c2; + + /** An implementation version of MSufSort3's semidirect BWT. **/ + + if(0 < m) { + /* Construct the sorted order of type B suffixes by using + the sorted order of type B* suffixes. */ + for(c1 = alphabetsize - 2; 0 <= c1; --c1) { + /* Scan the suffix array from right to left. */ + for(i = SA + BUCKET_BSTAR(c1, c1 + 1), + j = SA + (BUCKET_A(c1 + 1) + 1), + c2 = -1; + i < j;) { + if(0 <= (s = *--j)) { + if((0 <= --s) && ((c0 = T[s]) <= c1)) { + *j = ~((pos_type)c0); + if((0 < s) && (T[s - 1] > c0)) { s = ~s; } + if(c0 == c2) { *--t = s; } + else { + if(0 <= c2) { BUCKET_B(c2, c1) = pos_type( t - SA ); } + *(t = SA + BUCKET_B(c2 = c0, c1) - 1) = s; + } + } + } else { + *j = ~s; + } + } + } + } + + /* Construct the BWTed string by using + the sorted order of type B suffixes. */ + c0 = T[s = n - 1]; + if(T[s - 1] < c0) { s = ~((pos_type)T[s - 1]); } + *(t = SA + (BUCKET_A(c2 = c0) + 1)) = s; + /* Scan the suffix array from left to right. */ + for(i = SA, j = SA + n, orig = SA; i < j; ++i) { + if(0 <= (s = *i)) { + if((0 <= --s) && ((c0 = T[s]) >= T[s + 1])) { + *i = c0; + if((0 < s) && (T[s - 1] < c0)) { s = ~((pos_type)T[s - 1]); } + if(c0 == c2) { *++t = s; } + else { + BUCKET_A(c2) = pos_type( t - SA ); + *(t = SA + (BUCKET_A(c2 = c0) + 1)) = s; + } + } else if(s < 0) { orig = i; } + } else { + *i = ~s; + } + } + + return orig; +} + +#undef BUCKET_A +#undef BUCKET_B +#undef BUCKET_BSTAR +#undef TYPEB_START +#undef TYPEB_END + +} /* namespace core */ + +/*---------------------------------------------------------------------------*/ + + +/** + * Constructs the suffix array of a given string. + * + * @param T An input string iterator. + * @param T_last An input string iterator. + * @param SA An output iterator. + * @param SA_last An output iterator. + * @param alphabetsize + * @return 0 if no error occurred, -1 or -2 otherwise. + */ +template +int +constructSA(const StringIterator_type T, const StringIterator_type T_last, + SAIterator_type SA, SAIterator_type SA_last, + alphabetsize_type alphabetsize = 256) { +typedef typename std::iterator_traits::value_type pos_type; + pos_type *bucket_A = NULL, *bucket_B = NULL; + pos_type n = T_last - T, m = SA_last - SA; + int err = 0; + + /* Check arguments. */ + if((n < 0) || (m < n)) { return -1; } + else if(n == 0) { return 0; } + else if(n == 1) { *SA = 0; return 0; } + + try { + bucket_A = new pos_type[alphabetsize]; if(bucket_A == NULL) { throw; } + bucket_B = new pos_type[alphabetsize * alphabetsize]; if(bucket_B == NULL) { throw; } + m = core::sort_typeBstar(T, SA, bucket_A, bucket_B, n, m, alphabetsize); + core::constructSA_from_typeBstar(T, SA, bucket_A, bucket_B, n, m, alphabetsize); + } catch(...) { + err = -2; + } + + delete [] bucket_B; + delete [] bucket_A; + + return err; +} + +template +int +constructSA(const StringIterator_type T, SAIterator_type SA, + typename std::iterator_traits::value_type n, + alphabetsize_type alphabetsize = 256) { + return constructSA(T, T + n, SA, SA + n, alphabetsize); +} + +/** + * Constructs the burrows-wheeler transformed string of a given string. + * + * @param T An input string iterator. + * @param T_last An input string iterator. + * @param U An output string iterator. + * @param U_last An output string iterator. + * @param SA A temporary iterator. + * @param SA_last A temporary iterator. + * @param alphabetsize + * @return 0 if no error occurred, -1 or -2 otherwise. + */ +template +typename std::iterator_traits::value_type +constructBWT(const StringIterator1_type T, const StringIterator1_type T_last, + StringIterator2_type U, StringIterator2_type U_last, + SAIterator_type SA, SAIterator_type SA_last, + alphabetsize_type alphabetsize = 256) { +typedef typename std::iterator_traits::value_type value_type; +typedef typename std::iterator_traits::value_type pos_type; + SAIterator_type piter, i, k; + StringIterator2_type j; + pos_type *bucket_A = NULL, *bucket_B = NULL; + pos_type n = pos_type( T_last - T ), m = pos_type( SA_last - SA ), u = pos_type( U_last - U ), pidx = -1; + + /* Check arguments. */ + if((n < pos_type(0)) || (m < n)) { return -1; } + else if(n == 0) { return 0; } + else if(n == 1) { if(0 < u) { U[0] = T[0]; } return 1; } + + try { + bucket_A = new pos_type[alphabetsize]; if(bucket_A == NULL) { throw; } + bucket_B = new pos_type[alphabetsize * alphabetsize]; if(bucket_B == NULL) { throw; } + m = core::sort_typeBstar(T, SA, bucket_A, bucket_B, n, m, alphabetsize); + piter = core::constructBWT_from_typeBstar(T, SA, bucket_A, bucket_B, n, m, alphabetsize); + pidx = pos_type( piter - SA + 1 ); + if(0 < u) { + U[pos_type(0)] = T[n - 1]; + if(pidx <= u) { + for(i = SA, j = U + 1; i < piter; ++i, ++j) { *j = value_type(*i); } + if(n <= u) { for(i += 1; i < SA_last; ++i, ++j) { *j = value_type(*i); } } + else { for(i += 1, k = SA + u - 1; i < k; ++i, ++j) { *j = value_type(*i); } } + } else { + for(i = SA, j = U + 1, k = SA + u - 1; i < k; ++i, ++j) { *j = value_type(*i); } + } + } + } catch(...) { + pidx = -2; + } + + delete [] bucket_B; + delete [] bucket_A; + + return pidx; +} + +template +pos_type +constructBWT(const StringIterator1_type T, const StringIterator1_type T_last, + StringIterator2_type U, StringIterator2_type U_last, + alphabetsize_type alphabetsize = 256) { + pos_type *SA = NULL; + pos_type n = T_last - T, pidx = -1; + + /* Check arguments. */ + if(n < 0) { return -1; } + else if(n == 0) { return 0; } + else if(n == 1) { if(U < U_last) { U[pos_type(0)] = T[pos_type(0)]; } return 1; } + + try { + SA = new pos_type[n]; if(SA == NULL) { throw; } + pidx = constructBWT(T, T_last, U, U_last, SA, SA + n, alphabetsize); + } catch(...) { + pidx = -2; + } + delete [] SA; + + return pidx; +} + +template +pos_type +constructBWT(StringIterator_type T, StringIterator_type T_last, + alphabetsize_type alphabetsize = 256) { + return constructBWT(T, T_last, T, T_last, alphabetsize); +} + +template +typename std::iterator_traits::value_type +constructBWT(const StringIterator1_type T, StringIterator2_type U, SAIterator_type SA, + typename std::iterator_traits::value_type n, + alphabetsize_type alphabetsize = 256) { + return constructBWT(T, T + n, U, U + n, SA, SA + n, alphabetsize); +} + +template +pos_type +constructBWT(const StringIterator1_type T, StringIterator2_type U, + pos_type n, alphabetsize_type alphabetsize = 256) { + return constructBWT(T, T + n, U, U + n, alphabetsize); +} + +template +pos_type +constructBWT(StringIterator_type T, pos_type n, alphabetsize_type alphabetsize = 256) { + return constructBWT(T, T + n, alphabetsize); +} + + +} /* namespace divsufsortxx */ + +#endif /* _DIVSUFSORTXX_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..adc030f9e3937e4fedf805c2186e2812b65379db --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/CMakeLists.txt @@ -0,0 +1,20 @@ +project(lz4) +cmake_minimum_required(VERSION 2.8) + +set(INSTALL_BIN_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory for executables") +set(INSTALL_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib" CACHE PATH "Installation directory for libraries") +set(INSTALL_INC_DIR "${CMAKE_INSTALL_PREFIX}/include" CACHE PATH "Installation directory for headers") +set(INSTALL_MAN_DIR "${CMAKE_INSTALL_PREFIX}/share/man" CACHE PATH "Installation directory for manual pages") +set(INSTALL_PKGCONFIG_DIR "${CMAKE_INSTALL_PREFIX}/share/pkgconfig" CACHE PATH "Installation directory for pkgconfig (.pc) files") + +include_directories(${CMAKE_CURRENT_BINARY_DIR} ${NVBIO_SOURCE_ROOT}/include) + +set(SRCS + lz4.c + lz4frame.c + lz4hc.c + xxhash.c +) + +cuda_add_library(lz4 STATIC ${SRCS}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/LICENSE b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..b566df30352d64f904f217872fbf45bcfaac46ff --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/LICENSE @@ -0,0 +1,24 @@ +LZ4 Library +Copyright (c) 2011-2014, Yann Collet +All rights reserved. + +Redistribution and use in source and binary forms, with or without modification, +are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright notice, this + list of conditions and the following disclaimer in the documentation and/or + other materials provided with the distribution. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. \ No newline at end of file diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/Makefile b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..faffb399842e12c19a5c2cc86bb0ab2dec1ed884 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/Makefile @@ -0,0 +1,117 @@ +# ################################################################ +# LZ4 library - Makefile +# Copyright (C) Yann Collet 2011-2015 +# All rights reserved. +# +# BSD license +# Redistribution and use in source and binary forms, with or without modification, +# are permitted provided that the following conditions are met: +# +# * Redistributions of source code must retain the above copyright notice, this +# list of conditions and the following disclaimer. +# +# * Redistributions in binary form must reproduce the above copyright notice, this +# list of conditions and the following disclaimer in the documentation and/or +# other materials provided with the distribution. +# +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR +# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# +# You can contact the author at : +# - LZ4 source repository : http://code.google.com/p/lz4/ +# - LZ4 source mirror : https://github.com/Cyan4973/lz4 +# - LZ4 forum froup : https://groups.google.com/forum/#!forum/lz4c +# ################################################################ + +# Version numbers +VERSION ?= 126 +LIBVER_MAJOR=`sed -n '/define LZ4_VERSION_MAJOR/s/.*[[:blank:]]\([0-9][0-9]*\).*/\1/p' < lz4.h` +LIBVER_MINOR=`sed -n '/define LZ4_VERSION_MINOR/s/.*[[:blank:]]\([0-9][0-9]*\).*/\1/p' < lz4.h` +LIBVER_PATCH=`sed -n '/define LZ4_VERSION_RELEASE/s/.*[[:blank:]]\([0-9][0-9]*\).*/\1/p' < lz4.h` +LIBVER=$(LIBVER_MAJOR).$(LIBVER_MINOR).$(LIBVER_PATCH) + +DESTDIR?= +PREFIX ?= /usr +CFLAGS ?= -O3 +CFLAGS += -I. -std=c99 -Wall -Wextra -Wundef -Wshadow -Wcast-align -Wstrict-prototypes -pedantic + +LIBDIR?= $(PREFIX)/lib +INCLUDEDIR=$(PREFIX)/include + + +# OS X linker doesn't support -soname, and use different extension +# see : https://developer.apple.com/library/mac/documentation/DeveloperTools/Conceptual/DynamicLibraries/100-Articles/DynamicLibraryDesignGuidelines.html +ifeq ($(shell uname), Darwin) + SHARED_EXT = dylib + SHARED_EXT_MAJOR = $(LIBVER_MAJOR).$(SHARED_EXT) + SHARED_EXT_VER = $(LIBVER).$(SHARED_EXT) + SONAME_FLAGS = -install_name $(PREFIX)/lib/liblz4.$(SHARED_EXT_MAJOR) -compatibility_version $(LIBVER_MAJOR) -current_version $(LIBVER) +else + SONAME_FLAGS = -Wl,-soname=liblz4.$(SHARED_EXT).$(LIBVER_MAJOR) + SHARED_EXT = so + SHARED_EXT_MAJOR = $(SHARED_EXT).$(LIBVER_MAJOR) + SHARED_EXT_VER = $(SHARED_EXT).$(LIBVER) +endif + +default: liblz4 + +all: liblz4 + +liblz4: lz4.c lz4hc.c lz4frame.c xxhash.c + @echo compiling static library + @$(CC) $(CPPFLAGS) $(CFLAGS) -c $^ + @$(AR) rcs liblz4.a lz4.o lz4hc.o lz4frame.o xxhash.o + @echo compiling dynamic library $(LIBVER) + @$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -shared $^ -fPIC $(SONAME_FLAGS) -o $@.$(SHARED_EXT_VER) + @echo creating versioned links + @ln -sf $@.$(SHARED_EXT_VER) $@.$(SHARED_EXT_MAJOR) + @ln -sf $@.$(SHARED_EXT_VER) $@.$(SHARED_EXT) + +clean: + @rm -f core *.o *.a *.$(SHARED_EXT) *.$(SHARED_EXT).* liblz4.pc + @echo Cleaning library completed + + +#------------------------------------------------------------------------ +#make install is validated only for Linux, OSX, kFreeBSD and Hurd targets +ifneq (,$(filter $(shell uname),Linux Darwin GNU/kFreeBSD GNU)) + +liblz4.pc: liblz4.pc.in Makefile + @echo creating pkgconfig + @sed -e 's|@PREFIX@|$(PREFIX)|' \ + -e 's|@LIBDIR@|$(LIBDIR)|' \ + -e 's|@INCLUDEDIR@|$(INCLUDEDIR)|' \ + -e 's|@VERSION@|$(VERSION)|' \ + $< >$@ + +install: liblz4 liblz4.pc + @install -d -m 755 $(DESTDIR)$(LIBDIR)/pkgconfig/ $(DESTDIR)$(INCLUDEDIR)/ + @install -m 755 liblz4.$(SHARED_EXT_VER) $(DESTDIR)$(LIBDIR)/liblz4.$(SHARED_EXT_VER) + @cp -a liblz4.$(SHARED_EXT_MAJOR) $(DESTDIR)$(LIBDIR) + @cp -a liblz4.$(SHARED_EXT) $(DESTDIR)$(LIBDIR) + @cp -a liblz4.pc $(DESTDIR)$(LIBDIR)/pkgconfig/ + @install -m 644 liblz4.a $(DESTDIR)$(LIBDIR)/liblz4.a + @install -m 644 lz4.h $(DESTDIR)$(INCLUDEDIR)/lz4.h + @install -m 644 lz4hc.h $(DESTDIR)$(INCLUDEDIR)/lz4hc.h + @install -m 644 lz4frame.h $(DESTDIR)$(INCLUDEDIR)/lz4frame.h + @echo lz4 static and shared library installed + +uninstall: + @rm -f $(DESTDIR)$(LIBDIR)/liblz4.$(SHARED_EXT) + @rm -f $(DESTDIR)$(LIBDIR)/liblz4.$(SHARED_EXT_MAJOR) + @rm -f $(DESTDIR)$(LIBDIR)/pkgconfig/liblz4.pc + @[ -x $(DESTDIR)$(LIBDIR)/liblz4.$(SHARED_EXT_VER) ] && rm -f $(DESTDIR)$(LIBDIR)/liblz4.$(SHARED_EXT_VER) + @[ -f $(DESTDIR)$(LIBDIR)/liblz4.a ] && rm -f $(DESTDIR)$(LIBDIR)/liblz4.a + @[ -f $(DESTDIR)$(INCLUDEDIR)/lz4.h ] && rm -f $(DESTDIR)$(INCLUDEDIR)/lz4.h + @[ -f $(DESTDIR)$(INCLUDEDIR)/lz4hc.h ] && rm -f $(DESTDIR)$(INCLUDEDIR)/lz4hc.h + @echo lz4 libraries successfully uninstalled + +endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/liblz4.pc.in b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/liblz4.pc.in new file mode 100644 index 0000000000000000000000000000000000000000..0d05152f6b81a5b71a7c9e252fd135d88797c7f6 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/liblz4.pc.in @@ -0,0 +1,14 @@ +# LZ4 - Fast LZ compression algorithm +# Copyright (C) 2011-2014, Yann Collet. +# BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php) + +prefix=@PREFIX@ +libdir=@LIBDIR@ +includedir=@INCLUDEDIR@ + +Name: lz4 +Description: fast lossless compression algorithm library +URL: http://code.google.com/p/lz4/ +Version: @VERSION@ +Libs: -L@LIBDIR@ -llz4 +Cflags: -I@INCLUDEDIR@ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4.c new file mode 100644 index 0000000000000000000000000000000000000000..ed928ced3f154ab414f657c4dbd0193cbe7cd969 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4.c @@ -0,0 +1,1367 @@ +/* + LZ4 - Fast LZ compression algorithm + Copyright (C) 2011-2015, Yann Collet. + BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php) + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are + met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following disclaimer + in the documentation and/or other materials provided with the + distribution. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + You can contact the author at : + - LZ4 source repository : http://code.google.com/p/lz4 + - LZ4 source mirror : https://github.com/Cyan4973/lz4 + - LZ4 public forum : https://groups.google.com/forum/#!forum/lz4c +*/ + + +/************************************** + Tuning parameters +**************************************/ +/* + * HEAPMODE : + * Select how default compression functions will allocate memory for their hash table, + * in memory stack (0:default, fastest), or in memory heap (1:requires malloc()). + */ +#define HEAPMODE 0 + +/* + * CPU_HAS_EFFICIENT_UNALIGNED_MEMORY_ACCESS : + * By default, the source code expects the compiler to correctly optimize + * 4-bytes and 8-bytes read on architectures able to handle it efficiently. + * This is not always the case. In some circumstances (ARM notably), + * the compiler will issue cautious code even when target is able to correctly handle unaligned memory accesses. + * + * You can force the compiler to use unaligned memory access by uncommenting the line below. + * One of the below scenarios will happen : + * 1 - Your target CPU correctly handle unaligned access, and was not well optimized by compiler (good case). + * You will witness large performance improvements (+50% and up). + * Keep the line uncommented and send a word to upstream (https://groups.google.com/forum/#!forum/lz4c) + * The goal is to automatically detect such situations by adding your target CPU within an exception list. + * 2 - Your target CPU correctly handle unaligned access, and was already already optimized by compiler + * No change will be experienced. + * 3 - Your target CPU inefficiently handle unaligned access. + * You will experience a performance loss. Comment back the line. + * 4 - Your target CPU does not handle unaligned access. + * Program will crash. + * If uncommenting results in better performance (case 1) + * please report your configuration to upstream (https://groups.google.com/forum/#!forum/lz4c) + * An automatic detection macro will be added to match your case within future versions of the library. + */ +/* #define CPU_HAS_EFFICIENT_UNALIGNED_MEMORY_ACCESS 1 */ + + +/************************************** + CPU Feature Detection +**************************************/ +/* + * Automated efficient unaligned memory access detection + * Based on known hardware architectures + * This list will be updated thanks to feedbacks + */ +#if defined(CPU_HAS_EFFICIENT_UNALIGNED_MEMORY_ACCESS) \ + || defined(__ARM_FEATURE_UNALIGNED) \ + || defined(__i386__) || defined(__x86_64__) \ + || defined(_M_IX86) || defined(_M_X64) \ + || defined(__ARM_ARCH_7__) || defined(__ARM_ARCH_8__) \ + || (defined(_M_ARM) && (_M_ARM >= 7)) +# define LZ4_UNALIGNED_ACCESS 1 +#else +# define LZ4_UNALIGNED_ACCESS 0 +#endif + +/* + * LZ4_FORCE_SW_BITCOUNT + * Define this parameter if your target system or compiler does not support hardware bit count + */ +#if defined(_MSC_VER) && defined(_WIN32_WCE) /* Visual Studio for Windows CE does not support Hardware bit count */ +# define LZ4_FORCE_SW_BITCOUNT +#endif + + +/************************************** + Compiler Options +**************************************/ +#if defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) /* C99 */ +/* "restrict" is a known keyword */ +#else +# define restrict /* Disable restrict */ +#endif + +#ifdef _MSC_VER /* Visual Studio */ +# define FORCE_INLINE static __forceinline +# include +# pragma warning(disable : 4127) /* disable: C4127: conditional expression is constant */ +# pragma warning(disable : 4293) /* disable: C4293: too large shift (32-bits) */ +#else +# if defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) /* C99 */ +# ifdef __GNUC__ +# define FORCE_INLINE static inline __attribute__((always_inline)) +# else +# define FORCE_INLINE static inline +# endif +# else +# define FORCE_INLINE static +# endif /* __STDC_VERSION__ */ +#endif /* _MSC_VER */ + +#define GCC_VERSION (__GNUC__ * 100 + __GNUC_MINOR__) + +#if (GCC_VERSION >= 302) || (__INTEL_COMPILER >= 800) || defined(__clang__) +# define expect(expr,value) (__builtin_expect ((expr),(value)) ) +#else +# define expect(expr,value) (expr) +#endif + +#define likely(expr) expect((expr) != 0, 1) +#define unlikely(expr) expect((expr) != 0, 0) + + +/************************************** + Memory routines +**************************************/ +#include /* malloc, calloc, free */ +#define ALLOCATOR(n,s) calloc(n,s) +#define FREEMEM free +#include /* memset, memcpy */ +#define MEM_INIT memset + + +/************************************** + Includes +**************************************/ +#include "lz4.h" + + +/************************************** + Basic Types +**************************************/ +#if defined (__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) /* C99 */ +# include + typedef uint8_t BYTE; + typedef uint16_t U16; + typedef uint32_t U32; + typedef int32_t S32; + typedef uint64_t U64; +#else + typedef unsigned char BYTE; + typedef unsigned short U16; + typedef unsigned int U32; + typedef signed int S32; + typedef unsigned long long U64; +#endif + + +/************************************** + Reading and writing into memory +**************************************/ +#define STEPSIZE sizeof(size_t) + +static unsigned LZ4_64bits(void) { return sizeof(void*)==8; } + +static unsigned LZ4_isLittleEndian(void) +{ + const union { U32 i; BYTE c[4]; } one = { 1 }; /* don't use static : performance detrimental */ + return one.c[0]; +} + + +static U16 LZ4_readLE16(const void* memPtr) +{ + if ((LZ4_UNALIGNED_ACCESS) && (LZ4_isLittleEndian())) + return *(U16*)memPtr; + else + { + const BYTE* p = memPtr; + return (U16)((U16)p[0] + (p[1]<<8)); + } +} + +static void LZ4_writeLE16(void* memPtr, U16 value) +{ + if ((LZ4_UNALIGNED_ACCESS) && (LZ4_isLittleEndian())) + { + *(U16*)memPtr = value; + return; + } + else + { + BYTE* p = memPtr; + p[0] = (BYTE) value; + p[1] = (BYTE)(value>>8); + } +} + + +static U16 LZ4_read16(const void* memPtr) +{ + if (LZ4_UNALIGNED_ACCESS) + return *(U16*)memPtr; + else + { + U16 val16; + memcpy(&val16, memPtr, 2); + return val16; + } +} + +static U32 LZ4_read32(const void* memPtr) +{ + if (LZ4_UNALIGNED_ACCESS) + return *(U32*)memPtr; + else + { + U32 val32; + memcpy(&val32, memPtr, 4); + return val32; + } +} + +static U64 LZ4_read64(const void* memPtr) +{ + if (LZ4_UNALIGNED_ACCESS) + return *(U64*)memPtr; + else + { + U64 val64; + memcpy(&val64, memPtr, 8); + return val64; + } +} + +static size_t LZ4_read_ARCH(const void* p) +{ + if (LZ4_64bits()) + return (size_t)LZ4_read64(p); + else + return (size_t)LZ4_read32(p); +} + + +static void LZ4_copy4(void* dstPtr, const void* srcPtr) +{ + if (LZ4_UNALIGNED_ACCESS) + { + *(U32*)dstPtr = *(U32*)srcPtr; + return; + } + memcpy(dstPtr, srcPtr, 4); +} + +static void LZ4_copy8(void* dstPtr, const void* srcPtr) +{ +#if GCC_VERSION!=409 /* disabled on GCC 4.9, as it generates invalid opcode (crash) */ + if (LZ4_UNALIGNED_ACCESS) + { + if (LZ4_64bits()) + *(U64*)dstPtr = *(U64*)srcPtr; + else + ((U32*)dstPtr)[0] = ((U32*)srcPtr)[0], + ((U32*)dstPtr)[1] = ((U32*)srcPtr)[1]; + return; + } +#endif + memcpy(dstPtr, srcPtr, 8); +} + +/* customized version of memcpy, which may overwrite up to 7 bytes beyond dstEnd */ +static void LZ4_wildCopy(void* dstPtr, const void* srcPtr, void* dstEnd) +{ + BYTE* d = dstPtr; + const BYTE* s = srcPtr; + BYTE* e = dstEnd; + do { LZ4_copy8(d,s); d+=8; s+=8; } while (d>3); +# elif defined(__GNUC__) && (GCC_VERSION >= 304) && !defined(LZ4_FORCE_SW_BITCOUNT) + return (__builtin_ctzll((U64)val) >> 3); +# else + static const int DeBruijnBytePos[64] = { 0, 0, 0, 0, 0, 1, 1, 2, 0, 3, 1, 3, 1, 4, 2, 7, 0, 2, 3, 6, 1, 5, 3, 5, 1, 3, 4, 4, 2, 5, 6, 7, 7, 0, 1, 2, 3, 3, 4, 6, 2, 6, 5, 5, 3, 4, 5, 6, 7, 1, 2, 4, 6, 4, 4, 5, 7, 2, 6, 5, 7, 6, 7, 7 }; + return DeBruijnBytePos[((U64)((val & -(long long)val) * 0x0218A392CDABBD3FULL)) >> 58]; +# endif + } + else /* 32 bits */ + { +# if defined(_MSC_VER) && !defined(LZ4_FORCE_SW_BITCOUNT) + unsigned long r; + _BitScanForward( &r, (U32)val ); + return (int)(r>>3); +# elif defined(__GNUC__) && (GCC_VERSION >= 304) && !defined(LZ4_FORCE_SW_BITCOUNT) + return (__builtin_ctz((U32)val) >> 3); +# else + static const int DeBruijnBytePos[32] = { 0, 0, 3, 0, 3, 1, 3, 0, 3, 2, 2, 1, 3, 2, 0, 1, 3, 3, 1, 2, 2, 2, 2, 0, 3, 1, 2, 0, 1, 0, 1, 1 }; + return DeBruijnBytePos[((U32)((val & -(S32)val) * 0x077CB531U)) >> 27]; +# endif + } + } + else /* Big Endian CPU */ + { + if (LZ4_64bits()) + { +# if defined(_MSC_VER) && defined(_WIN64) && !defined(LZ4_FORCE_SW_BITCOUNT) + unsigned long r = 0; + _BitScanReverse64( &r, val ); + return (unsigned)(r>>3); +# elif defined(__GNUC__) && (GCC_VERSION >= 304) && !defined(LZ4_FORCE_SW_BITCOUNT) + return (__builtin_clzll(val) >> 3); +# else + unsigned r; + if (!(val>>32)) { r=4; } else { r=0; val>>=32; } + if (!(val>>16)) { r+=2; val>>=8; } else { val>>=24; } + r += (!val); + return r; +# endif + } + else /* 32 bits */ + { +# if defined(_MSC_VER) && !defined(LZ4_FORCE_SW_BITCOUNT) + unsigned long r = 0; + _BitScanReverse( &r, (unsigned long)val ); + return (unsigned)(r>>3); +# elif defined(__GNUC__) && (GCC_VERSION >= 304) && !defined(LZ4_FORCE_SW_BITCOUNT) + return (__builtin_clz(val) >> 3); +# else + unsigned r; + if (!(val>>16)) { r=2; val>>=8; } else { r=0; val>>=24; } + r += (!val); + return r; +# endif + } + } +} + +static unsigned LZ4_count(const BYTE* pIn, const BYTE* pMatch, const BYTE* pInLimit) +{ + const BYTE* const pStart = pIn; + + while (likely(pIn compression run slower on incompressible data */ + + +/************************************** + Local Utils +**************************************/ +int LZ4_versionNumber (void) { return LZ4_VERSION_NUMBER; } +int LZ4_compressBound(int isize) { return LZ4_COMPRESSBOUND(isize); } + + +/************************************** + Local Structures and types +**************************************/ +typedef struct { + U32 hashTable[HASH_SIZE_U32]; + U32 currentOffset; + U32 initCheck; + const BYTE* dictionary; + const BYTE* bufferStart; + U32 dictSize; +} LZ4_stream_t_internal; + +typedef enum { notLimited = 0, limitedOutput = 1 } limitedOutput_directive; +typedef enum { byPtr, byU32, byU16 } tableType_t; + +typedef enum { noDict = 0, withPrefix64k, usingExtDict } dict_directive; +typedef enum { noDictIssue = 0, dictSmall } dictIssue_directive; + +typedef enum { endOnOutputSize = 0, endOnInputSize = 1 } endCondition_directive; +typedef enum { full = 0, partial = 1 } earlyEnd_directive; + + + +/******************************** + Compression functions +********************************/ + +static U32 LZ4_hashSequence(U32 sequence, tableType_t tableType) +{ + if (tableType == byU16) + return (((sequence) * 2654435761U) >> ((MINMATCH*8)-(LZ4_HASHLOG+1))); + else + return (((sequence) * 2654435761U) >> ((MINMATCH*8)-LZ4_HASHLOG)); +} + +static U32 LZ4_hashPosition(const BYTE* p, tableType_t tableType) { return LZ4_hashSequence(LZ4_read32(p), tableType); } + +static void LZ4_putPositionOnHash(const BYTE* p, U32 h, void* tableBase, tableType_t tableType, const BYTE* srcBase) +{ + switch (tableType) + { + case byPtr: { const BYTE** hashTable = (const BYTE**)tableBase; hashTable[h] = p; return; } + case byU32: { U32* hashTable = (U32*) tableBase; hashTable[h] = (U32)(p-srcBase); return; } + case byU16: { U16* hashTable = (U16*) tableBase; hashTable[h] = (U16)(p-srcBase); return; } + } +} + +static void LZ4_putPosition(const BYTE* p, void* tableBase, tableType_t tableType, const BYTE* srcBase) +{ + U32 h = LZ4_hashPosition(p, tableType); + LZ4_putPositionOnHash(p, h, tableBase, tableType, srcBase); +} + +static const BYTE* LZ4_getPositionOnHash(U32 h, void* tableBase, tableType_t tableType, const BYTE* srcBase) +{ + if (tableType == byPtr) { const BYTE** hashTable = (const BYTE**) tableBase; return hashTable[h]; } + if (tableType == byU32) { U32* hashTable = (U32*) tableBase; return hashTable[h] + srcBase; } + { U16* hashTable = (U16*) tableBase; return hashTable[h] + srcBase; } /* default, to ensure a return */ +} + +static const BYTE* LZ4_getPosition(const BYTE* p, void* tableBase, tableType_t tableType, const BYTE* srcBase) +{ + U32 h = LZ4_hashPosition(p, tableType); + return LZ4_getPositionOnHash(h, tableBase, tableType, srcBase); +} + +static int LZ4_compress_generic( + void* ctx, + const char* source, + char* dest, + int inputSize, + int maxOutputSize, + limitedOutput_directive outputLimited, + tableType_t tableType, + dict_directive dict, + dictIssue_directive dictIssue) +{ + LZ4_stream_t_internal* const dictPtr = (LZ4_stream_t_internal*)ctx; + + const BYTE* ip = (const BYTE*) source; + const BYTE* base; + const BYTE* lowLimit; + const BYTE* const lowRefLimit = ip - dictPtr->dictSize; + const BYTE* const dictionary = dictPtr->dictionary; + const BYTE* const dictEnd = dictionary + dictPtr->dictSize; + const size_t dictDelta = dictEnd - (const BYTE*)source; + const BYTE* anchor = (const BYTE*) source; + const BYTE* const iend = ip + inputSize; + const BYTE* const mflimit = iend - MFLIMIT; + const BYTE* const matchlimit = iend - LASTLITERALS; + + BYTE* op = (BYTE*) dest; + BYTE* const olimit = op + maxOutputSize; + + U32 forwardH; + size_t refDelta=0; + + /* Init conditions */ + if ((U32)inputSize > (U32)LZ4_MAX_INPUT_SIZE) return 0; /* Unsupported input size, too large (or negative) */ + switch(dict) + { + case noDict: + default: + base = (const BYTE*)source; + lowLimit = (const BYTE*)source; + break; + case withPrefix64k: + base = (const BYTE*)source - dictPtr->currentOffset; + lowLimit = (const BYTE*)source - dictPtr->dictSize; + break; + case usingExtDict: + base = (const BYTE*)source - dictPtr->currentOffset; + lowLimit = (const BYTE*)source; + break; + } + if ((tableType == byU16) && (inputSize>=LZ4_64Klimit)) return 0; /* Size too large (not within 64K limit) */ + if (inputSize> LZ4_skipTrigger; + + if (unlikely(forwardIp > mflimit)) goto _last_literals; + + match = LZ4_getPositionOnHash(h, ctx, tableType, base); + if (dict==usingExtDict) + { + if (match<(const BYTE*)source) + { + refDelta = dictDelta; + lowLimit = dictionary; + } + else + { + refDelta = 0; + lowLimit = (const BYTE*)source; + } + } + forwardH = LZ4_hashPosition(forwardIp, tableType); + LZ4_putPositionOnHash(ip, h, ctx, tableType, base); + + } while ( ((dictIssue==dictSmall) ? (match < lowRefLimit) : 0) + || ((tableType==byU16) ? 0 : (match + MAX_DISTANCE < ip)) + || (LZ4_read32(match+refDelta) != LZ4_read32(ip)) ); + } + + /* Catch up */ + while ((ip>anchor) && (match+refDelta > lowLimit) && (unlikely(ip[-1]==match[refDelta-1]))) { ip--; match--; } + + { + /* Encode Literal length */ + unsigned litLength = (unsigned)(ip - anchor); + token = op++; + if ((outputLimited) && (unlikely(op + litLength + (2 + 1 + LASTLITERALS) + (litLength/255) > olimit))) + return 0; /* Check output limit */ + if (litLength>=RUN_MASK) + { + int len = (int)litLength-RUN_MASK; + *token=(RUN_MASK<= 255 ; len-=255) *op++ = 255; + *op++ = (BYTE)len; + } + else *token = (BYTE)(litLength< matchlimit) limit = matchlimit; + matchLength = LZ4_count(ip+MINMATCH, match+MINMATCH, limit); + ip += MINMATCH + matchLength; + if (ip==limit) + { + unsigned more = LZ4_count(ip, (const BYTE*)source, matchlimit); + matchLength += more; + ip += more; + } + } + else + { + matchLength = LZ4_count(ip+MINMATCH, match+MINMATCH, matchlimit); + ip += MINMATCH + matchLength; + } + + if ((outputLimited) && (unlikely(op + (1 + LASTLITERALS) + (matchLength>>8) > olimit))) + return 0; /* Check output limit */ + if (matchLength>=ML_MASK) + { + *token += ML_MASK; + matchLength -= ML_MASK; + for (; matchLength >= 510 ; matchLength-=510) { *op++ = 255; *op++ = 255; } + if (matchLength >= 255) { matchLength-=255; *op++ = 255; } + *op++ = (BYTE)matchLength; + } + else *token += (BYTE)(matchLength); + } + + anchor = ip; + + /* Test end of chunk */ + if (ip > mflimit) break; + + /* Fill table */ + LZ4_putPosition(ip-2, ctx, tableType, base); + + /* Test next position */ + match = LZ4_getPosition(ip, ctx, tableType, base); + if (dict==usingExtDict) + { + if (match<(const BYTE*)source) + { + refDelta = dictDelta; + lowLimit = dictionary; + } + else + { + refDelta = 0; + lowLimit = (const BYTE*)source; + } + } + LZ4_putPosition(ip, ctx, tableType, base); + if ( ((dictIssue==dictSmall) ? (match>=lowRefLimit) : 1) + && (match+MAX_DISTANCE>=ip) + && (LZ4_read32(match+refDelta)==LZ4_read32(ip)) ) + { token=op++; *token=0; goto _next_match; } + + /* Prepare next loop */ + forwardH = LZ4_hashPosition(++ip, tableType); + } + +_last_literals: + /* Encode Last Literals */ + { + int lastRun = (int)(iend - anchor); + if ((outputLimited) && (((char*)op - dest) + lastRun + 1 + ((lastRun+255-RUN_MASK)/255) > (U32)maxOutputSize)) + return 0; /* Check output limit */ + if (lastRun>=(int)RUN_MASK) { *op++=(RUN_MASK<= 255 ; lastRun-=255) *op++ = 255; *op++ = (BYTE) lastRun; } + else *op++ = (BYTE)(lastRun<= sizeof(LZ4_stream_t_internal)); /* A compilation error here means LZ4_STREAMSIZE is not large enough */ + LZ4_resetStream(lz4s); + return lz4s; +} + +int LZ4_freeStream (LZ4_stream_t* LZ4_stream) +{ + FREEMEM(LZ4_stream); + return (0); +} + + +int LZ4_loadDict (LZ4_stream_t* LZ4_dict, const char* dictionary, int dictSize) +{ + LZ4_stream_t_internal* dict = (LZ4_stream_t_internal*) LZ4_dict; + const BYTE* p = (const BYTE*)dictionary; + const BYTE* const dictEnd = p + dictSize; + const BYTE* base; + + if (dict->initCheck) LZ4_resetStream(LZ4_dict); /* Uninitialized structure detected */ + + if (dictSize < MINMATCH) + { + dict->dictionary = NULL; + dict->dictSize = 0; + return 0; + } + + if (p <= dictEnd - 64 KB) p = dictEnd - 64 KB; + base = p - dict->currentOffset; + dict->dictionary = p; + dict->dictSize = (U32)(dictEnd - p); + dict->currentOffset += dict->dictSize; + + while (p <= dictEnd-MINMATCH) + { + LZ4_putPosition(p, dict, byU32, base); + p+=3; + } + + return dict->dictSize; +} + + +static void LZ4_renormDictT(LZ4_stream_t_internal* LZ4_dict, const BYTE* src) +{ + if ((LZ4_dict->currentOffset > 0x80000000) || + ((size_t)LZ4_dict->currentOffset > (size_t)src)) /* address space overflow */ + { + /* rescale hash table */ + U32 delta = LZ4_dict->currentOffset - 64 KB; + const BYTE* dictEnd = LZ4_dict->dictionary + LZ4_dict->dictSize; + int i; + for (i=0; ihashTable[i] < delta) LZ4_dict->hashTable[i]=0; + else LZ4_dict->hashTable[i] -= delta; + } + LZ4_dict->currentOffset = 64 KB; + if (LZ4_dict->dictSize > 64 KB) LZ4_dict->dictSize = 64 KB; + LZ4_dict->dictionary = dictEnd - LZ4_dict->dictSize; + } +} + + +FORCE_INLINE int LZ4_compress_continue_generic (void* LZ4_stream, const char* source, char* dest, int inputSize, + int maxOutputSize, limitedOutput_directive limit) +{ + LZ4_stream_t_internal* streamPtr = (LZ4_stream_t_internal*)LZ4_stream; + const BYTE* const dictEnd = streamPtr->dictionary + streamPtr->dictSize; + + const BYTE* smallest = (const BYTE*) source; + if (streamPtr->initCheck) return 0; /* Uninitialized structure detected */ + if ((streamPtr->dictSize>0) && (smallest>dictEnd)) smallest = dictEnd; + LZ4_renormDictT(streamPtr, smallest); + + /* Check overlapping input/dictionary space */ + { + const BYTE* sourceEnd = (const BYTE*) source + inputSize; + if ((sourceEnd > streamPtr->dictionary) && (sourceEnd < dictEnd)) + { + streamPtr->dictSize = (U32)(dictEnd - sourceEnd); + if (streamPtr->dictSize > 64 KB) streamPtr->dictSize = 64 KB; + if (streamPtr->dictSize < 4) streamPtr->dictSize = 0; + streamPtr->dictionary = dictEnd - streamPtr->dictSize; + } + } + + /* prefix mode : source data follows dictionary */ + if (dictEnd == (const BYTE*)source) + { + int result; + if ((streamPtr->dictSize < 64 KB) && (streamPtr->dictSize < streamPtr->currentOffset)) + result = LZ4_compress_generic(LZ4_stream, source, dest, inputSize, maxOutputSize, limit, byU32, withPrefix64k, dictSmall); + else + result = LZ4_compress_generic(LZ4_stream, source, dest, inputSize, maxOutputSize, limit, byU32, withPrefix64k, noDictIssue); + streamPtr->dictSize += (U32)inputSize; + streamPtr->currentOffset += (U32)inputSize; + return result; + } + + /* external dictionary mode */ + { + int result; + if ((streamPtr->dictSize < 64 KB) && (streamPtr->dictSize < streamPtr->currentOffset)) + result = LZ4_compress_generic(LZ4_stream, source, dest, inputSize, maxOutputSize, limit, byU32, usingExtDict, dictSmall); + else + result = LZ4_compress_generic(LZ4_stream, source, dest, inputSize, maxOutputSize, limit, byU32, usingExtDict, noDictIssue); + streamPtr->dictionary = (const BYTE*)source; + streamPtr->dictSize = (U32)inputSize; + streamPtr->currentOffset += (U32)inputSize; + return result; + } +} + +int LZ4_compress_continue (LZ4_stream_t* LZ4_stream, const char* source, char* dest, int inputSize) +{ + return LZ4_compress_continue_generic(LZ4_stream, source, dest, inputSize, 0, notLimited); +} + +int LZ4_compress_limitedOutput_continue (LZ4_stream_t* LZ4_stream, const char* source, char* dest, int inputSize, int maxOutputSize) +{ + return LZ4_compress_continue_generic(LZ4_stream, source, dest, inputSize, maxOutputSize, limitedOutput); +} + + +/* Hidden debug function, to force separate dictionary mode */ +int LZ4_compress_forceExtDict (LZ4_stream_t* LZ4_dict, const char* source, char* dest, int inputSize) +{ + LZ4_stream_t_internal* streamPtr = (LZ4_stream_t_internal*)LZ4_dict; + int result; + const BYTE* const dictEnd = streamPtr->dictionary + streamPtr->dictSize; + + const BYTE* smallest = dictEnd; + if (smallest > (const BYTE*) source) smallest = (const BYTE*) source; + LZ4_renormDictT((LZ4_stream_t_internal*)LZ4_dict, smallest); + + result = LZ4_compress_generic(LZ4_dict, source, dest, inputSize, 0, notLimited, byU32, usingExtDict, noDictIssue); + + streamPtr->dictionary = (const BYTE*)source; + streamPtr->dictSize = (U32)inputSize; + streamPtr->currentOffset += (U32)inputSize; + + return result; +} + + +int LZ4_saveDict (LZ4_stream_t* LZ4_dict, char* safeBuffer, int dictSize) +{ + LZ4_stream_t_internal* dict = (LZ4_stream_t_internal*) LZ4_dict; + const BYTE* previousDictEnd = dict->dictionary + dict->dictSize; + + if ((U32)dictSize > 64 KB) dictSize = 64 KB; /* useless to define a dictionary > 64 KB */ + if ((U32)dictSize > dict->dictSize) dictSize = dict->dictSize; + + memmove(safeBuffer, previousDictEnd - dictSize, dictSize); + + dict->dictionary = (const BYTE*)safeBuffer; + dict->dictSize = (U32)dictSize; + + return dictSize; +} + + + +/**************************** + Decompression functions +****************************/ +/* + * This generic decompression function cover all use cases. + * It shall be instantiated several times, using different sets of directives + * Note that it is essential this generic function is really inlined, + * in order to remove useless branches during compilation optimization. + */ +FORCE_INLINE int LZ4_decompress_generic( + const char* const source, + char* const dest, + int inputSize, + int outputSize, /* If endOnInput==endOnInputSize, this value is the max size of Output Buffer. */ + + int endOnInput, /* endOnOutputSize, endOnInputSize */ + int partialDecoding, /* full, partial */ + int targetOutputSize, /* only used if partialDecoding==partial */ + int dict, /* noDict, withPrefix64k, usingExtDict */ + const BYTE* const lowPrefix, /* == dest if dict == noDict */ + const BYTE* const dictStart, /* only if dict==usingExtDict */ + const size_t dictSize /* note : = 0 if noDict */ + ) +{ + /* Local Variables */ + const BYTE* restrict ip = (const BYTE*) source; + const BYTE* const iend = ip + inputSize; + + BYTE* op = (BYTE*) dest; + BYTE* const oend = op + outputSize; + BYTE* cpy; + BYTE* oexit = op + targetOutputSize; + const BYTE* const lowLimit = lowPrefix - dictSize; + + const BYTE* const dictEnd = (const BYTE*)dictStart + dictSize; + const size_t dec32table[] = {4, 1, 2, 1, 4, 4, 4, 4}; + const size_t dec64table[] = {0, 0, 0, (size_t)-1, 0, 1, 2, 3}; + + const int safeDecode = (endOnInput==endOnInputSize); + const int checkOffset = ((safeDecode) && (dictSize < (int)(64 KB))); + + + /* Special cases */ + if ((partialDecoding) && (oexit> oend-MFLIMIT)) oexit = oend-MFLIMIT; /* targetOutputSize too high => decode everything */ + if ((endOnInput) && (unlikely(outputSize==0))) return ((inputSize==1) && (*ip==0)) ? 0 : -1; /* Empty output buffer */ + if ((!endOnInput) && (unlikely(outputSize==0))) return (*ip==0?1:-1); + + + /* Main Loop */ + while (1) + { + unsigned token; + size_t length; + const BYTE* match; + + /* get literal length */ + token = *ip++; + if ((length=(token>>ML_BITS)) == RUN_MASK) + { + unsigned s; + do + { + s = *ip++; + length += s; + } + while (likely((endOnInput)?ip(partialDecoding?oexit:oend-MFLIMIT)) || (ip+length>iend-(2+1+LASTLITERALS))) ) + || ((!endOnInput) && (cpy>oend-COPYLENGTH))) + { + if (partialDecoding) + { + if (cpy > oend) goto _output_error; /* Error : write attempt beyond end of output buffer */ + if ((endOnInput) && (ip+length > iend)) goto _output_error; /* Error : read attempt beyond end of input buffer */ + } + else + { + if ((!endOnInput) && (cpy != oend)) goto _output_error; /* Error : block decoding must stop exactly there */ + if ((endOnInput) && ((ip+length != iend) || (cpy > oend))) goto _output_error; /* Error : input must be consumed */ + } + memcpy(op, ip, length); + ip += length; + op += length; + break; /* Necessarily EOF, due to parsing restrictions */ + } + LZ4_wildCopy(op, ip, cpy); + ip += length; op = cpy; + + /* get offset */ + match = cpy - LZ4_readLE16(ip); ip+=2; + if ((checkOffset) && (unlikely(match < lowLimit))) goto _output_error; /* Error : offset outside destination buffer */ + + /* get matchlength */ + length = token & ML_MASK; + if (length == ML_MASK) + { + unsigned s; + do + { + if ((endOnInput) && (ip > iend-LASTLITERALS)) goto _output_error; + s = *ip++; + length += s; + } while (s==255); + if ((safeDecode) && unlikely((size_t)(op+length)<(size_t)op)) goto _output_error; /* overflow detection */ + } + length += MINMATCH; + + /* check external dictionary */ + if ((dict==usingExtDict) && (match < lowPrefix)) + { + if (unlikely(op+length > oend-LASTLITERALS)) goto _output_error; /* doesn't respect parsing restriction */ + + if (length <= (size_t)(lowPrefix-match)) + { + /* match can be copied as a single segment from external dictionary */ + match = dictEnd - (lowPrefix-match); + memcpy(op, match, length); + op += length; + } + else + { + /* match encompass external dictionary and current segment */ + size_t copySize = (size_t)(lowPrefix-match); + memcpy(op, dictEnd - copySize, copySize); + op += copySize; + copySize = length - copySize; + if (copySize > (size_t)(op-lowPrefix)) /* overlap within current segment */ + { + BYTE* const endOfMatch = op + copySize; + const BYTE* copyFrom = lowPrefix; + while (op < endOfMatch) *op++ = *copyFrom++; + } + else + { + memcpy(op, lowPrefix, copySize); + op += copySize; + } + } + continue; + } + + /* copy repeated sequence */ + cpy = op + length; + if (unlikely((op-match)<8)) + { + const size_t dec64 = dec64table[op-match]; + op[0] = match[0]; + op[1] = match[1]; + op[2] = match[2]; + op[3] = match[3]; + match += dec32table[op-match]; + LZ4_copy4(op+4, match); + op += 8; match -= dec64; + } else { LZ4_copy8(op, match); op+=8; match+=8; } + + if (unlikely(cpy>oend-12)) + { + if (cpy > oend-LASTLITERALS) goto _output_error; /* Error : last LASTLITERALS bytes must be literals */ + if (op < oend-8) + { + LZ4_wildCopy(op, match, oend-8); + match += (oend-8) - op; + op = oend-8; + } + while (opprefixSize = (size_t) dictSize; + lz4sd->prefixEnd = (BYTE*) dictionary + dictSize; + lz4sd->externalDict = NULL; + lz4sd->extDictSize = 0; + return 1; +} + +/* +*_continue() : + These decoding functions allow decompression of multiple blocks in "streaming" mode. + Previously decoded blocks must still be available at the memory position where they were decoded. + If it's not possible, save the relevant part of decoded data into a safe buffer, + and indicate where it stands using LZ4_setStreamDecode() +*/ +int LZ4_decompress_safe_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int compressedSize, int maxOutputSize) +{ + LZ4_streamDecode_t_internal* lz4sd = (LZ4_streamDecode_t_internal*) LZ4_streamDecode; + int result; + + if (lz4sd->prefixEnd == (BYTE*)dest) + { + result = LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, + endOnInputSize, full, 0, + usingExtDict, lz4sd->prefixEnd - lz4sd->prefixSize, lz4sd->externalDict, lz4sd->extDictSize); + if (result <= 0) return result; + lz4sd->prefixSize += result; + lz4sd->prefixEnd += result; + } + else + { + lz4sd->extDictSize = lz4sd->prefixSize; + lz4sd->externalDict = lz4sd->prefixEnd - lz4sd->extDictSize; + result = LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, + endOnInputSize, full, 0, + usingExtDict, (BYTE*)dest, lz4sd->externalDict, lz4sd->extDictSize); + if (result <= 0) return result; + lz4sd->prefixSize = result; + lz4sd->prefixEnd = (BYTE*)dest + result; + } + + return result; +} + +int LZ4_decompress_fast_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int originalSize) +{ + LZ4_streamDecode_t_internal* lz4sd = (LZ4_streamDecode_t_internal*) LZ4_streamDecode; + int result; + + if (lz4sd->prefixEnd == (BYTE*)dest) + { + result = LZ4_decompress_generic(source, dest, 0, originalSize, + endOnOutputSize, full, 0, + usingExtDict, lz4sd->prefixEnd - lz4sd->prefixSize, lz4sd->externalDict, lz4sd->extDictSize); + if (result <= 0) return result; + lz4sd->prefixSize += originalSize; + lz4sd->prefixEnd += originalSize; + } + else + { + lz4sd->extDictSize = lz4sd->prefixSize; + lz4sd->externalDict = (BYTE*)dest - lz4sd->extDictSize; + result = LZ4_decompress_generic(source, dest, 0, originalSize, + endOnOutputSize, full, 0, + usingExtDict, (BYTE*)dest, lz4sd->externalDict, lz4sd->extDictSize); + if (result <= 0) return result; + lz4sd->prefixSize = originalSize; + lz4sd->prefixEnd = (BYTE*)dest + originalSize; + } + + return result; +} + + +/* +Advanced decoding functions : +*_usingDict() : + These decoding functions work the same as "_continue" ones, + the dictionary must be explicitly provided within parameters +*/ + +FORCE_INLINE int LZ4_decompress_usingDict_generic(const char* source, char* dest, int compressedSize, int maxOutputSize, int safe, const char* dictStart, int dictSize) +{ + if (dictSize==0) + return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, noDict, (BYTE*)dest, NULL, 0); + if (dictStart+dictSize == dest) + { + if (dictSize >= (int)(64 KB - 1)) + return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, withPrefix64k, (BYTE*)dest-64 KB, NULL, 0); + return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, noDict, (BYTE*)dest-dictSize, NULL, 0); + } + return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, usingExtDict, (BYTE*)dest, (BYTE*)dictStart, dictSize); +} + +int LZ4_decompress_safe_usingDict(const char* source, char* dest, int compressedSize, int maxOutputSize, const char* dictStart, int dictSize) +{ + return LZ4_decompress_usingDict_generic(source, dest, compressedSize, maxOutputSize, 1, dictStart, dictSize); +} + +int LZ4_decompress_fast_usingDict(const char* source, char* dest, int originalSize, const char* dictStart, int dictSize) +{ + return LZ4_decompress_usingDict_generic(source, dest, 0, originalSize, 0, dictStart, dictSize); +} + +/* debug function */ +int LZ4_decompress_safe_forceExtDict(const char* source, char* dest, int compressedSize, int maxOutputSize, const char* dictStart, int dictSize) +{ + return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, endOnInputSize, full, 0, usingExtDict, (BYTE*)dest, (BYTE*)dictStart, dictSize); +} + + +/*************************************************** + Obsolete Functions +***************************************************/ +/* +These function names are deprecated and should no longer be used. +They are only provided here for compatibility with older user programs. +- LZ4_uncompress is totally equivalent to LZ4_decompress_fast +- LZ4_uncompress_unknownOutputSize is totally equivalent to LZ4_decompress_safe +*/ +int LZ4_uncompress (const char* source, char* dest, int outputSize) { return LZ4_decompress_fast(source, dest, outputSize); } +int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize) { return LZ4_decompress_safe(source, dest, isize, maxOutputSize); } + + +/* Obsolete Streaming functions */ + +int LZ4_sizeofStreamState() { return LZ4_STREAMSIZE; } + +static void LZ4_init(LZ4_stream_t_internal* lz4ds, const BYTE* base) +{ + MEM_INIT(lz4ds, 0, LZ4_STREAMSIZE); + lz4ds->bufferStart = base; +} + +int LZ4_resetStreamState(void* state, const char* inputBuffer) +{ + if ((((size_t)state) & 3) != 0) return 1; /* Error : pointer is not aligned on 4-bytes boundary */ + LZ4_init((LZ4_stream_t_internal*)state, (const BYTE*)inputBuffer); + return 0; +} + +void* LZ4_create (const char* inputBuffer) +{ + void* lz4ds = ALLOCATOR(8, LZ4_STREAMSIZE_U64); + LZ4_init ((LZ4_stream_t_internal*)lz4ds, (const BYTE*)inputBuffer); + return lz4ds; +} + +char* LZ4_slideInputBuffer (void* LZ4_Data) +{ + LZ4_stream_t_internal* ctx = (LZ4_stream_t_internal*)LZ4_Data; + int dictSize = LZ4_saveDict((LZ4_stream_t*)ctx, (char*)ctx->bufferStart, 64 KB); + return (char*)(ctx->bufferStart + dictSize); +} + +/* Obsolete compresson functions using User-allocated state */ + +int LZ4_sizeofState() { return LZ4_STREAMSIZE; } + +int LZ4_compress_withState (void* state, const char* source, char* dest, int inputSize) +{ + if (((size_t)(state)&3) != 0) return 0; /* Error : state is not aligned on 4-bytes boundary */ + MEM_INIT(state, 0, LZ4_STREAMSIZE); + + if (inputSize < LZ4_64Klimit) + return LZ4_compress_generic(state, source, dest, inputSize, 0, notLimited, byU16, noDict, noDictIssue); + else + return LZ4_compress_generic(state, source, dest, inputSize, 0, notLimited, LZ4_64bits() ? byU32 : byPtr, noDict, noDictIssue); +} + +int LZ4_compress_limitedOutput_withState (void* state, const char* source, char* dest, int inputSize, int maxOutputSize) +{ + if (((size_t)(state)&3) != 0) return 0; /* Error : state is not aligned on 4-bytes boundary */ + MEM_INIT(state, 0, LZ4_STREAMSIZE); + + if (inputSize < LZ4_64Klimit) + return LZ4_compress_generic(state, source, dest, inputSize, maxOutputSize, limitedOutput, byU16, noDict, noDictIssue); + else + return LZ4_compress_generic(state, source, dest, inputSize, maxOutputSize, limitedOutput, LZ4_64bits() ? byU32 : byPtr, noDict, noDictIssue); +} + +/* Obsolete streaming decompression functions */ + +int LZ4_decompress_safe_withPrefix64k(const char* source, char* dest, int compressedSize, int maxOutputSize) +{ + return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, endOnInputSize, full, 0, withPrefix64k, (BYTE*)dest - 64 KB, NULL, 64 KB); +} + +int LZ4_decompress_fast_withPrefix64k(const char* source, char* dest, int originalSize) +{ + return LZ4_decompress_generic(source, dest, 0, originalSize, endOnOutputSize, full, 0, withPrefix64k, (BYTE*)dest - 64 KB, NULL, 64 KB); +} + +#endif /* LZ4_COMMONDEFS_ONLY */ + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4.h new file mode 100644 index 0000000000000000000000000000000000000000..7778caad3aeec050dd7f1512065f28cb004c6c1c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4.h @@ -0,0 +1,315 @@ +/* + LZ4 - Fast LZ compression algorithm + Header File + Copyright (C) 2011-2014, Yann Collet. + BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php) + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are + met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following disclaimer + in the documentation and/or other materials provided with the + distribution. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + You can contact the author at : + - LZ4 source repository : http://code.google.com/p/lz4/ + - LZ4 public forum : https://groups.google.com/forum/#!forum/lz4c +*/ +#pragma once + +#if defined (__cplusplus) +extern "C" { +#endif + +/* + * lz4.h provides raw compression format functions, for optimal performance and integration into programs. + * If you need to generate data using an inter-operable format (respecting the framing specification), + * please use lz4frame.h instead. +*/ + +/************************************** + Version +**************************************/ +#define LZ4_VERSION_MAJOR 1 /* for breaking interface changes */ +#define LZ4_VERSION_MINOR 5 /* for new (non-breaking) interface capabilities */ +#define LZ4_VERSION_RELEASE 0 /* for tweaks, bug-fixes, or development */ +#define LZ4_VERSION_NUMBER (LZ4_VERSION_MAJOR *100*100 + LZ4_VERSION_MINOR *100 + LZ4_VERSION_RELEASE) +int LZ4_versionNumber (void); + +/************************************** + Tuning parameter +**************************************/ +/* + * LZ4_MEMORY_USAGE : + * Memory usage formula : N->2^N Bytes (examples : 10 -> 1KB; 12 -> 4KB ; 16 -> 64KB; 20 -> 1MB; etc.) + * Increasing memory usage improves compression ratio + * Reduced memory usage can improve speed, due to cache effect + * Default value is 14, for 16KB, which nicely fits into Intel x86 L1 cache + */ +#define LZ4_MEMORY_USAGE 14 + + +/************************************** + Simple Functions +**************************************/ + +int LZ4_compress (const char* source, char* dest, int sourceSize); +int LZ4_decompress_safe (const char* source, char* dest, int compressedSize, int maxDecompressedSize); + +/* +LZ4_compress() : + Compresses 'sourceSize' bytes from 'source' into 'dest'. + Destination buffer must be already allocated, + and must be sized to handle worst cases situations (input data not compressible) + Worst case size evaluation is provided by function LZ4_compressBound() + inputSize : Max supported value is LZ4_MAX_INPUT_SIZE + return : the number of bytes written in buffer dest + or 0 if the compression fails + +LZ4_decompress_safe() : + compressedSize : is obviously the source size + maxDecompressedSize : is the size of the destination buffer, which must be already allocated. + return : the number of bytes decompressed into the destination buffer (necessarily <= maxDecompressedSize) + If the destination buffer is not large enough, decoding will stop and output an error code (<0). + If the source stream is detected malformed, the function will stop decoding and return a negative result. + This function is protected against buffer overflow exploits, + and never writes outside of output buffer, nor reads outside of input buffer. + It is also protected against malicious data packets. +*/ + + +/************************************** + Advanced Functions +**************************************/ +#define LZ4_MAX_INPUT_SIZE 0x7E000000 /* 2 113 929 216 bytes */ +#define LZ4_COMPRESSBOUND(isize) ((unsigned int)(isize) > (unsigned int)LZ4_MAX_INPUT_SIZE ? 0 : (isize) + ((isize)/255) + 16) + +/* +LZ4_compressBound() : + Provides the maximum size that LZ4 compression may output in a "worst case" scenario (input data not compressible) + This function is primarily useful for memory allocation purposes (output buffer size). + Macro LZ4_COMPRESSBOUND() is also provided for compilation-time evaluation (stack memory allocation for example). + + isize : is the input size. Max supported value is LZ4_MAX_INPUT_SIZE + return : maximum output size in a "worst case" scenario + or 0, if input size is too large ( > LZ4_MAX_INPUT_SIZE) +*/ +int LZ4_compressBound(int isize); + + +/* +LZ4_compress_limitedOutput() : + Compress 'sourceSize' bytes from 'source' into an output buffer 'dest' of maximum size 'maxOutputSize'. + If it cannot achieve it, compression will stop, and result of the function will be zero. + This saves time and memory on detecting non-compressible (or barely compressible) data. + This function never writes outside of provided output buffer. + + sourceSize : Max supported value is LZ4_MAX_INPUT_VALUE + maxOutputSize : is the size of the destination buffer (which must be already allocated) + return : the number of bytes written in buffer 'dest' + or 0 if compression fails +*/ +int LZ4_compress_limitedOutput (const char* source, char* dest, int sourceSize, int maxOutputSize); + + +/* +LZ4_compress_withState() : + Same compression functions, but using an externally allocated memory space to store compression state. + Use LZ4_sizeofState() to know how much memory must be allocated, + and then, provide it as 'void* state' to compression functions. +*/ +int LZ4_sizeofState(void); +int LZ4_compress_withState (void* state, const char* source, char* dest, int inputSize); +int LZ4_compress_limitedOutput_withState (void* state, const char* source, char* dest, int inputSize, int maxOutputSize); + + +/* +LZ4_decompress_fast() : + originalSize : is the original and therefore uncompressed size + return : the number of bytes read from the source buffer (in other words, the compressed size) + If the source stream is detected malformed, the function will stop decoding and return a negative result. + Destination buffer must be already allocated. Its size must be a minimum of 'originalSize' bytes. + note : This function fully respect memory boundaries for properly formed compressed data. + It is a bit faster than LZ4_decompress_safe(). + However, it does not provide any protection against intentionally modified data stream (malicious input). + Use this function in trusted environment only (data to decode comes from a trusted source). +*/ +int LZ4_decompress_fast (const char* source, char* dest, int originalSize); + + +/* +LZ4_decompress_safe_partial() : + This function decompress a compressed block of size 'compressedSize' at position 'source' + into destination buffer 'dest' of size 'maxDecompressedSize'. + The function tries to stop decompressing operation as soon as 'targetOutputSize' has been reached, + reducing decompression time. + return : the number of bytes decoded in the destination buffer (necessarily <= maxDecompressedSize) + Note : this number can be < 'targetOutputSize' should the compressed block to decode be smaller. + Always control how many bytes were decoded. + If the source stream is detected malformed, the function will stop decoding and return a negative result. + This function never writes outside of output buffer, and never reads outside of input buffer. It is therefore protected against malicious data packets +*/ +int LZ4_decompress_safe_partial (const char* source, char* dest, int compressedSize, int targetOutputSize, int maxDecompressedSize); + + +/*********************************************** + Streaming Compression Functions +***********************************************/ + +#define LZ4_STREAMSIZE_U64 ((1 << (LZ4_MEMORY_USAGE-3)) + 4) +#define LZ4_STREAMSIZE (LZ4_STREAMSIZE_U64 * sizeof(long long)) +/* + * LZ4_stream_t + * information structure to track an LZ4 stream. + * important : init this structure content before first use ! + * note : only allocated directly the structure if you are statically linking LZ4 + * If you are using liblz4 as a DLL, please use below construction methods instead. + */ +typedef struct { long long table[LZ4_STREAMSIZE_U64]; } LZ4_stream_t; + +/* + * LZ4_resetStream + * Use this function to init an allocated LZ4_stream_t structure + */ +void LZ4_resetStream (LZ4_stream_t* LZ4_streamPtr); + +/* + * LZ4_createStream will allocate and initialize an LZ4_stream_t structure + * LZ4_freeStream releases its memory. + * In the context of a DLL (liblz4), please use these methods rather than the static struct. + * They are more future proof, in case of a change of LZ4_stream_t size. + */ +LZ4_stream_t* LZ4_createStream(void); +int LZ4_freeStream (LZ4_stream_t* LZ4_streamPtr); + +/* + * LZ4_loadDict + * Use this function to load a static dictionary into LZ4_stream. + * Any previous data will be forgotten, only 'dictionary' will remain in memory. + * Loading a size of 0 is allowed. + * Return : dictionary size, in bytes (necessarily <= 64 KB) + */ +int LZ4_loadDict (LZ4_stream_t* LZ4_streamPtr, const char* dictionary, int dictSize); + +/* + * LZ4_compress_continue + * Compress data block 'source', using blocks compressed before as dictionary to improve compression ratio + * Previous data blocks are assumed to still be present at their previous location. + */ +int LZ4_compress_continue (LZ4_stream_t* LZ4_streamPtr, const char* source, char* dest, int inputSize); + +/* + * LZ4_compress_limitedOutput_continue + * Same as before, but also specify a maximum target compressed size (maxOutputSize) + * If objective cannot be met, compression exits, and returns a zero. + */ +int LZ4_compress_limitedOutput_continue (LZ4_stream_t* LZ4_streamPtr, const char* source, char* dest, int inputSize, int maxOutputSize); + +/* + * LZ4_saveDict + * If previously compressed data block is not guaranteed to remain available at its memory location + * save it into a safer place (char* safeBuffer) + * Note : you don't need to call LZ4_loadDict() afterwards, + * dictionary is immediately usable, you can therefore call again LZ4_compress_continue() + * Return : dictionary size in bytes, or 0 if error + * Note : any dictSize > 64 KB will be interpreted as 64KB. + */ +int LZ4_saveDict (LZ4_stream_t* LZ4_streamPtr, char* safeBuffer, int dictSize); + + +/************************************************ + Streaming Decompression Functions +************************************************/ + +#define LZ4_STREAMDECODESIZE_U64 4 +#define LZ4_STREAMDECODESIZE (LZ4_STREAMDECODESIZE_U64 * sizeof(unsigned long long)) +typedef struct { unsigned long long table[LZ4_STREAMDECODESIZE_U64]; } LZ4_streamDecode_t; +/* + * LZ4_streamDecode_t + * information structure to track an LZ4 stream. + * init this structure content using LZ4_setStreamDecode or memset() before first use ! + * + * In the context of a DLL (liblz4) please prefer usage of construction methods below. + * They are more future proof, in case of a change of LZ4_streamDecode_t size in the future. + * LZ4_createStreamDecode will allocate and initialize an LZ4_streamDecode_t structure + * LZ4_freeStreamDecode releases its memory. + */ +LZ4_streamDecode_t* LZ4_createStreamDecode(void); +int LZ4_freeStreamDecode (LZ4_streamDecode_t* LZ4_stream); + +/* + * LZ4_setStreamDecode + * Use this function to instruct where to find the dictionary. + * Setting a size of 0 is allowed (same effect as reset). + * Return : 1 if OK, 0 if error + */ +int LZ4_setStreamDecode (LZ4_streamDecode_t* LZ4_streamDecode, const char* dictionary, int dictSize); + +/* +*_continue() : + These decoding functions allow decompression of multiple blocks in "streaming" mode. + Previously decoded blocks *must* remain available at the memory position where they were decoded (up to 64 KB) + If this condition is not possible, save the relevant part of decoded data into a safe buffer, + and indicate where is its new address using LZ4_setStreamDecode() +*/ +int LZ4_decompress_safe_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int compressedSize, int maxDecompressedSize); +int LZ4_decompress_fast_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int originalSize); + + +/* +Advanced decoding functions : +*_usingDict() : + These decoding functions work the same as + a combination of LZ4_setDictDecode() followed by LZ4_decompress_x_continue() + They are stand-alone and don't use nor update an LZ4_streamDecode_t structure. +*/ +int LZ4_decompress_safe_usingDict (const char* source, char* dest, int compressedSize, int maxDecompressedSize, const char* dictStart, int dictSize); +int LZ4_decompress_fast_usingDict (const char* source, char* dest, int originalSize, const char* dictStart, int dictSize); + + + +/************************************** + Obsolete Functions +**************************************/ +/* +Obsolete decompression functions +These function names are deprecated and should no longer be used. +They are only provided here for compatibility with older user programs. +- LZ4_uncompress is the same as LZ4_decompress_fast +- LZ4_uncompress_unknownOutputSize is the same as LZ4_decompress_safe +These function prototypes are now disabled; uncomment them if you really need them. +It is highly recommended to stop using these functions and migrate to newer ones */ +/* int LZ4_uncompress (const char* source, char* dest, int outputSize); */ +/* int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); */ + + +/* Obsolete streaming functions; use new streaming interface whenever possible */ +void* LZ4_create (const char* inputBuffer); +int LZ4_sizeofStreamState(void); +int LZ4_resetStreamState(void* state, const char* inputBuffer); +char* LZ4_slideInputBuffer (void* state); + +/* Obsolete streaming decoding functions */ +int LZ4_decompress_safe_withPrefix64k (const char* source, char* dest, int compressedSize, int maxOutputSize); +int LZ4_decompress_fast_withPrefix64k (const char* source, char* dest, int originalSize); + + +#if defined (__cplusplus) +} +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4frame.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4frame.c new file mode 100644 index 0000000000000000000000000000000000000000..5183f221e25bb26ca00259f373876dea2087dc3a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4frame.c @@ -0,0 +1,1330 @@ +/* +LZ4 auto-framing library +Copyright (C) 2011-2014, Yann Collet. +BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php) + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + +* Redistributions of source code must retain the above copyright +notice, this list of conditions and the following disclaimer. +* Redistributions in binary form must reproduce the above +copyright notice, this list of conditions and the following disclaimer +in the documentation and/or other materials provided with the +distribution. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +You can contact the author at : +- LZ4 source repository : http://code.google.com/p/lz4/ +- LZ4 public forum : https://groups.google.com/forum/#!forum/lz4c +*/ + +/* LZ4F is a stand-alone API to create LZ4-compressed Frames +* fully conformant to specification v1.4.1. +* All related operations, including memory management, are handled by the library. +* */ + + +/************************************** +Compiler Options +**************************************/ +#ifdef _MSC_VER /* Visual Studio */ +# pragma warning(disable : 4127) /* disable: C4127: conditional expression is constant */ +#endif + +#define GCC_VERSION (__GNUC__ * 100 + __GNUC_MINOR__) +#ifdef __GNUC__ +# pragma GCC diagnostic ignored "-Wmissing-braces" /* GCC bug 53119 : doesn't accept { 0 } as initializer (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=53119) */ +# pragma GCC diagnostic ignored "-Wmissing-field-initializers" /* GCC bug 53119 : doesn't accept { 0 } as initializer (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=53119) */ +#endif + + +/************************************** +Memory routines +**************************************/ +#include /* malloc, calloc, free */ +#define ALLOCATOR(s) calloc(1,s) +#define FREEMEM free +#include /* memset, memcpy, memmove */ +#define MEM_INIT memset + + +/************************************** +Includes +**************************************/ +#include "lz4frame_static.h" +#include "lz4.h" +#include "lz4hc.h" +#include "xxhash.h" + + +/************************************** +Basic Types +**************************************/ +#if defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) /* C99 */ +# include +typedef uint8_t BYTE; +typedef uint16_t U16; +typedef uint32_t U32; +typedef int32_t S32; +typedef uint64_t U64; +#else +typedef unsigned char BYTE; +typedef unsigned short U16; +typedef unsigned int U32; +typedef signed int S32; +typedef unsigned long long U64; +#endif + + +/************************************** +Constants +**************************************/ +#define KB *(1<<10) +#define MB *(1<<20) +#define GB *(1<<30) + +#define _1BIT 0x01 +#define _2BITS 0x03 +#define _3BITS 0x07 +#define _4BITS 0x0F +#define _8BITS 0xFF + +#define LZ4F_MAGICNUMBER 0x184D2204U +#define LZ4F_BLOCKUNCOMPRESSED_FLAG 0x80000000U +#define LZ4F_MAXHEADERFRAME_SIZE 7 +#define LZ4F_BLOCKSIZEID_DEFAULT max64KB + +static const U32 minHClevel = 3; + +/************************************** +Structures and local types +**************************************/ +typedef struct +{ + LZ4F_preferences_t prefs; + U32 version; + U32 cStage; + size_t maxBlockSize; + size_t maxBufferSize; + BYTE* tmpBuff; + BYTE* tmpIn; + size_t tmpInSize; + XXH32_state_t xxh; + void* lz4CtxPtr; + U32 lz4CtxLevel; /* 0: unallocated; 1: LZ4_stream_t; 3: LZ4_streamHC_t */ +} LZ4F_cctx_internal_t; + +typedef struct +{ + LZ4F_frameInfo_t frameInfo; + unsigned version; + unsigned dStage; + size_t maxBlockSize; + size_t maxBufferSize; + const BYTE* srcExpect; + BYTE* tmpIn; + size_t tmpInSize; + size_t tmpInTarget; + BYTE* tmpOutBuffer; + BYTE* dict; + size_t dictSize; + BYTE* tmpOut; + size_t tmpOutSize; + size_t tmpOutStart; + XXH32_state_t xxh; + BYTE header[8]; +} LZ4F_dctx_internal_t; + + +/************************************** +Macros +**************************************/ + + +/************************************** +Error management +**************************************/ +#define LZ4F_GENERATE_STRING(STRING) #STRING, +static const char* LZ4F_errorStrings[] = { LZ4F_LIST_ERRORS(LZ4F_GENERATE_STRING) }; + + +U32 LZ4F_isError(LZ4F_errorCode_t code) +{ + return (code > (LZ4F_errorCode_t)(-ERROR_maxCode)); +} + +const char* LZ4F_getErrorName(LZ4F_errorCode_t code) +{ + static const char* codeError = "Unspecified error code"; + if (LZ4F_isError(code)) return LZ4F_errorStrings[-(int)(code)]; + return codeError; +} + + +/************************************** +Private functions +**************************************/ +static size_t LZ4F_getBlockSize(unsigned blockSizeID) +{ + static const size_t blockSizes[4] = { 64 KB, 256 KB, 1 MB, 4 MB }; + + if (blockSizeID == 0) blockSizeID = LZ4F_BLOCKSIZEID_DEFAULT; + blockSizeID -= 4; + if (blockSizeID > 3) return (size_t)-ERROR_maxBlockSize_invalid; + return blockSizes[blockSizeID]; +} + + +/* unoptimized version; solves endianess & alignment issues */ +static void LZ4F_writeLE32 (BYTE* dstPtr, U32 value32) +{ + dstPtr[0] = (BYTE)value32; + dstPtr[1] = (BYTE)(value32 >> 8); + dstPtr[2] = (BYTE)(value32 >> 16); + dstPtr[3] = (BYTE)(value32 >> 24); +} + +static U32 LZ4F_readLE32 (const BYTE* srcPtr) +{ + U32 value32 = srcPtr[0]; + value32 += (srcPtr[1]<<8); + value32 += (srcPtr[2]<<16); + value32 += (srcPtr[3]<<24); + return value32; +} + + +static BYTE LZ4F_headerChecksum (const BYTE* header, size_t length) +{ + U32 xxh = XXH32(header, (U32)length, 0); + return (BYTE)(xxh >> 8); +} + + +/************************************** +Simple compression functions +**************************************/ +size_t LZ4F_compressFrameBound(size_t srcSize, const LZ4F_preferences_t* preferencesPtr) +{ + LZ4F_preferences_t prefs = { 0 }; + size_t headerSize; + size_t streamSize; + + if (preferencesPtr!=NULL) prefs = *preferencesPtr; + { + blockSizeID_t proposedBSID = max64KB; + size_t maxBlockSize = 64 KB; + while (prefs.frameInfo.blockSizeID > proposedBSID) + { + if (srcSize <= maxBlockSize) + { + prefs.frameInfo.blockSizeID = proposedBSID; + break; + } + proposedBSID++; + maxBlockSize <<= 2; + } + } + prefs.autoFlush = 1; + + headerSize = 7; /* basic header size (no option) including magic number */ + streamSize = LZ4F_compressBound(srcSize, &prefs); + + return headerSize + streamSize; +} + + +/* LZ4F_compressFrame() +* Compress an entire srcBuffer into a valid LZ4 frame, as defined by specification v1.4.1, in a single step. +* The most important rule is that dstBuffer MUST be large enough (dstMaxSize) to ensure compression completion even in worst case. +* You can get the minimum value of dstMaxSize by using LZ4F_compressFrameBound() +* If this condition is not respected, LZ4F_compressFrame() will fail (result is an errorCode) +* The LZ4F_preferences_t structure is optional : you can provide NULL as argument. All preferences will be set to default. +* The result of the function is the number of bytes written into dstBuffer. +* The function outputs an error code if it fails (can be tested using LZ4F_isError()) +*/ +size_t LZ4F_compressFrame(void* dstBuffer, size_t dstMaxSize, const void* srcBuffer, size_t srcSize, const LZ4F_preferences_t* preferencesPtr) +{ + LZ4F_cctx_internal_t cctxI = { 0 }; /* works because no allocation */ + LZ4F_preferences_t prefs = { 0 }; + LZ4F_compressOptions_t options = { 0 }; + LZ4F_errorCode_t errorCode; + BYTE* const dstStart = (BYTE*) dstBuffer; + BYTE* dstPtr = dstStart; + BYTE* const dstEnd = dstStart + dstMaxSize; + + + cctxI.version = LZ4F_VERSION; + cctxI.maxBufferSize = 5 MB; /* mess with real buffer size to prevent allocation; works because autoflush==1 & stableSrc==1 */ + + if (preferencesPtr!=NULL) prefs = *preferencesPtr; + { + blockSizeID_t proposedBSID = max64KB; + size_t maxBlockSize = 64 KB; + while (prefs.frameInfo.blockSizeID > proposedBSID) + { + if (srcSize <= maxBlockSize) + { + prefs.frameInfo.blockSizeID = proposedBSID; + break; + } + proposedBSID++; + maxBlockSize <<= 2; + } + } + prefs.autoFlush = 1; + if (srcSize <= LZ4F_getBlockSize(prefs.frameInfo.blockSizeID)) + prefs.frameInfo.blockMode = blockIndependent; /* no need for linked blocks */ + + options.stableSrc = 1; + + if (dstMaxSize < LZ4F_compressFrameBound(srcSize, &prefs)) + return (size_t)-ERROR_dstMaxSize_tooSmall; + + errorCode = LZ4F_compressBegin(&cctxI, dstBuffer, dstMaxSize, &prefs); /* write header */ + if (LZ4F_isError(errorCode)) return errorCode; + dstPtr += errorCode; /* header size */ + + dstMaxSize -= errorCode; + errorCode = LZ4F_compressUpdate(&cctxI, dstPtr, dstMaxSize, srcBuffer, srcSize, &options); + if (LZ4F_isError(errorCode)) return errorCode; + dstPtr += errorCode; + + errorCode = LZ4F_compressEnd(&cctxI, dstPtr, dstEnd-dstPtr, &options); /* flush last block, and generate suffix */ + if (LZ4F_isError(errorCode)) return errorCode; + dstPtr += errorCode; + + FREEMEM(cctxI.lz4CtxPtr); + + return (dstPtr - dstStart); +} + + +/*********************************** +* Advanced compression functions +* *********************************/ + +/* LZ4F_createCompressionContext() : +* The first thing to do is to create a compressionContext object, which will be used in all compression operations. +* This is achieved using LZ4F_createCompressionContext(), which takes as argument a version and an LZ4F_preferences_t structure. +* The version provided MUST be LZ4F_VERSION. It is intended to track potential version differences between different binaries. +* The function will provide a pointer to an allocated LZ4F_compressionContext_t object. +* If the result LZ4F_errorCode_t is not OK_NoError, there was an error during context creation. +* Object can release its memory using LZ4F_freeCompressionContext(); +*/ +LZ4F_errorCode_t LZ4F_createCompressionContext(LZ4F_compressionContext_t* LZ4F_compressionContextPtr, unsigned version) +{ + LZ4F_cctx_internal_t* cctxPtr; + + cctxPtr = (LZ4F_cctx_internal_t*)ALLOCATOR(sizeof(LZ4F_cctx_internal_t)); + if (cctxPtr==NULL) return (LZ4F_errorCode_t)(-ERROR_allocation_failed); + + cctxPtr->version = version; + cctxPtr->cStage = 0; /* Next stage : write header */ + + *LZ4F_compressionContextPtr = (LZ4F_compressionContext_t)cctxPtr; + + return OK_NoError; +} + + +LZ4F_errorCode_t LZ4F_freeCompressionContext(LZ4F_compressionContext_t LZ4F_compressionContext) +{ + LZ4F_cctx_internal_t* cctxPtr = (LZ4F_cctx_internal_t*)LZ4F_compressionContext; + + FREEMEM(cctxPtr->lz4CtxPtr); + FREEMEM(cctxPtr->tmpBuff); + FREEMEM(LZ4F_compressionContext); + + return OK_NoError; +} + + +/* LZ4F_compressBegin() : +* will write the frame header into dstBuffer. +* dstBuffer must be large enough to accommodate a header (dstMaxSize). Maximum header size is LZ4F_MAXHEADERFRAME_SIZE bytes. +* The result of the function is the number of bytes written into dstBuffer for the header +* or an error code (can be tested using LZ4F_isError()) +*/ +size_t LZ4F_compressBegin(LZ4F_compressionContext_t compressionContext, void* dstBuffer, size_t dstMaxSize, const LZ4F_preferences_t* preferencesPtr) +{ + LZ4F_preferences_t prefNull = { 0 }; + LZ4F_cctx_internal_t* cctxPtr = (LZ4F_cctx_internal_t*)compressionContext; + BYTE* const dstStart = (BYTE*)dstBuffer; + BYTE* dstPtr = dstStart; + BYTE* headerStart; + size_t requiredBuffSize; + + if (dstMaxSize < LZ4F_MAXHEADERFRAME_SIZE) return (size_t)-ERROR_dstMaxSize_tooSmall; + if (cctxPtr->cStage != 0) return (size_t)-ERROR_GENERIC; + if (preferencesPtr == NULL) preferencesPtr = &prefNull; + cctxPtr->prefs = *preferencesPtr; + + /* ctx Management */ + { + U32 targetCtxLevel = cctxPtr->prefs.compressionLevellz4CtxLevel < targetCtxLevel) + { + FREEMEM(cctxPtr->lz4CtxPtr); + if (cctxPtr->prefs.compressionLevellz4CtxPtr = (void*)LZ4_createStream(); + else + cctxPtr->lz4CtxPtr = (void*)LZ4_createStreamHC(); + cctxPtr->lz4CtxLevel = targetCtxLevel; + } + } + + /* Buffer Management */ + if (cctxPtr->prefs.frameInfo.blockSizeID == 0) cctxPtr->prefs.frameInfo.blockSizeID = LZ4F_BLOCKSIZEID_DEFAULT; + cctxPtr->maxBlockSize = LZ4F_getBlockSize(cctxPtr->prefs.frameInfo.blockSizeID); + + requiredBuffSize = cctxPtr->maxBlockSize + ((cctxPtr->prefs.frameInfo.blockMode == blockLinked) * 128 KB); + if (preferencesPtr->autoFlush) + requiredBuffSize = (cctxPtr->prefs.frameInfo.blockMode == blockLinked) * 64 KB; /* just needs dict */ + + if (cctxPtr->maxBufferSize < requiredBuffSize) + { + cctxPtr->maxBufferSize = requiredBuffSize; + FREEMEM(cctxPtr->tmpBuff); + cctxPtr->tmpBuff = (BYTE*)ALLOCATOR(requiredBuffSize); + if (cctxPtr->tmpBuff == NULL) return (size_t)-ERROR_allocation_failed; + } + cctxPtr->tmpIn = cctxPtr->tmpBuff; + cctxPtr->tmpInSize = 0; + XXH32_reset(&(cctxPtr->xxh), 0); + if (cctxPtr->prefs.compressionLevellz4CtxPtr)); + else + LZ4_resetStreamHC((LZ4_streamHC_t*)(cctxPtr->lz4CtxPtr), cctxPtr->prefs.compressionLevel); + + /* Magic Number */ + LZ4F_writeLE32(dstPtr, LZ4F_MAGICNUMBER); + dstPtr += 4; + headerStart = dstPtr; + + /* FLG Byte */ + *dstPtr++ = ((1 & _2BITS) << 6) /* Version('01') */ + + ((cctxPtr->prefs.frameInfo.blockMode & _1BIT ) << 5) /* Block mode */ + + (char)((cctxPtr->prefs.frameInfo.contentChecksumFlag & _1BIT ) << 2); /* Stream checksum */ + /* BD Byte */ + *dstPtr++ = (char)((cctxPtr->prefs.frameInfo.blockSizeID & _3BITS) << 4); + /* CRC Byte */ + *dstPtr++ = LZ4F_headerChecksum(headerStart, 2); + + cctxPtr->cStage = 1; /* header written, wait for data block */ + + return (dstPtr - dstStart); +} + + +/* LZ4F_compressBound() : gives the size of Dst buffer given a srcSize to handle worst case situations. +* The LZ4F_frameInfo_t structure is optional : +* you can provide NULL as argument, all preferences will then be set to default. +* */ +size_t LZ4F_compressBound(size_t srcSize, const LZ4F_preferences_t* preferencesPtr) +{ + const LZ4F_preferences_t prefsNull = { 0 }; + const LZ4F_preferences_t* prefsPtr = (preferencesPtr==NULL) ? &prefsNull : preferencesPtr; + blockSizeID_t bid = prefsPtr->frameInfo.blockSizeID; + size_t blockSize = LZ4F_getBlockSize(bid); + unsigned nbBlocks = (unsigned)(srcSize / blockSize) + 1; + size_t lastBlockSize = prefsPtr->autoFlush ? srcSize % blockSize : blockSize; + size_t blockInfo = 4; /* default, without block CRC option */ + size_t frameEnd = 4 + (prefsPtr->frameInfo.contentChecksumFlag*4); + size_t result = (blockInfo * nbBlocks) + (blockSize * (nbBlocks-1)) + lastBlockSize + frameEnd; + + return result; +} + + +typedef int (*compressFunc_t)(void* ctx, const char* src, char* dst, int srcSize, int dstSize, int level); + +static size_t LZ4F_compressBlock(void* dst, const void* src, size_t srcSize, compressFunc_t compress, void* lz4ctx, int level) +{ + /* compress one block */ + BYTE* cSizePtr = (BYTE*)dst; + U32 cSize; + cSize = (U32)compress(lz4ctx, (const char*)src, (char*)(cSizePtr+4), (int)(srcSize), (int)(srcSize-1), level); + LZ4F_writeLE32(cSizePtr, cSize); + if (cSize == 0) /* compression failed */ + { + cSize = (U32)srcSize; + LZ4F_writeLE32(cSizePtr, cSize + LZ4F_BLOCKUNCOMPRESSED_FLAG); + memcpy(cSizePtr+4, src, srcSize); + } + return cSize + 4; +} + + +static int LZ4F_localLZ4_compress_limitedOutput_withState(void* ctx, const char* src, char* dst, int srcSize, int dstSize, int level) +{ + (void) level; + return LZ4_compress_limitedOutput_withState(ctx, src, dst, srcSize, dstSize); +} + +static int LZ4F_localLZ4_compress_limitedOutput_continue(void* ctx, const char* src, char* dst, int srcSize, int dstSize, int level) +{ + (void) level; + return LZ4_compress_limitedOutput_continue((LZ4_stream_t*)ctx, src, dst, srcSize, dstSize); +} + +static int LZ4F_localLZ4_compressHC_limitedOutput_continue(void* ctx, const char* src, char* dst, int srcSize, int dstSize, int level) +{ + (void) level; + return LZ4_compressHC_limitedOutput_continue((LZ4_streamHC_t*)ctx, src, dst, srcSize, dstSize); +} + +static compressFunc_t LZ4F_selectCompression(blockMode_t blockMode, U32 level) +{ + if (level < minHClevel) + { + if (blockMode == blockIndependent) return LZ4F_localLZ4_compress_limitedOutput_withState; + return LZ4F_localLZ4_compress_limitedOutput_continue; + } + if (blockMode == blockIndependent) return LZ4_compressHC2_limitedOutput_withStateHC; + return LZ4F_localLZ4_compressHC_limitedOutput_continue; +} + +static int LZ4F_localSaveDict(LZ4F_cctx_internal_t* cctxPtr) +{ + if (cctxPtr->prefs.compressionLevel < minHClevel) + return LZ4_saveDict ((LZ4_stream_t*)(cctxPtr->lz4CtxPtr), (char*)(cctxPtr->tmpBuff), 64 KB); + return LZ4_saveDictHC ((LZ4_streamHC_t*)(cctxPtr->lz4CtxPtr), (char*)(cctxPtr->tmpBuff), 64 KB); +} + +typedef enum { notDone, fromTmpBuffer, fromSrcBuffer } LZ4F_lastBlockStatus; + +/* LZ4F_compressUpdate() +* LZ4F_compressUpdate() can be called repetitively to compress as much data as necessary. +* The most important rule is that dstBuffer MUST be large enough (dstMaxSize) to ensure compression completion even in worst case. +* If this condition is not respected, LZ4F_compress() will fail (result is an errorCode) +* You can get the minimum value of dstMaxSize by using LZ4F_compressBound() +* The LZ4F_compressOptions_t structure is optional : you can provide NULL as argument. +* The result of the function is the number of bytes written into dstBuffer : it can be zero, meaning input data was just buffered. +* The function outputs an error code if it fails (can be tested using LZ4F_isError()) +*/ +size_t LZ4F_compressUpdate(LZ4F_compressionContext_t compressionContext, void* dstBuffer, size_t dstMaxSize, const void* srcBuffer, size_t srcSize, const LZ4F_compressOptions_t* compressOptionsPtr) +{ + LZ4F_compressOptions_t cOptionsNull = { 0 }; + LZ4F_cctx_internal_t* cctxPtr = (LZ4F_cctx_internal_t*)compressionContext; + size_t blockSize = cctxPtr->maxBlockSize; + const BYTE* srcPtr = (const BYTE*)srcBuffer; + const BYTE* const srcEnd = srcPtr + srcSize; + BYTE* const dstStart = (BYTE*)dstBuffer; + BYTE* dstPtr = dstStart; + LZ4F_lastBlockStatus lastBlockCompressed = notDone; + compressFunc_t compress; + + + if (cctxPtr->cStage != 1) return (size_t)-ERROR_GENERIC; + if (dstMaxSize < LZ4F_compressBound(srcSize, &(cctxPtr->prefs))) return (size_t)-ERROR_dstMaxSize_tooSmall; + if (compressOptionsPtr == NULL) compressOptionsPtr = &cOptionsNull; + + /* select compression function */ + compress = LZ4F_selectCompression(cctxPtr->prefs.frameInfo.blockMode, cctxPtr->prefs.compressionLevel); + + /* complete tmp buffer */ + if (cctxPtr->tmpInSize > 0) /* some data already within tmp buffer */ + { + size_t sizeToCopy = blockSize - cctxPtr->tmpInSize; + if (sizeToCopy > srcSize) + { + /* add src to tmpIn buffer */ + memcpy(cctxPtr->tmpIn + cctxPtr->tmpInSize, srcBuffer, srcSize); + srcPtr = srcEnd; + cctxPtr->tmpInSize += srcSize; + /* still needs some CRC */ + } + else + { + /* complete tmpIn block and then compress it */ + lastBlockCompressed = fromTmpBuffer; + memcpy(cctxPtr->tmpIn + cctxPtr->tmpInSize, srcBuffer, sizeToCopy); + srcPtr += sizeToCopy; + + dstPtr += LZ4F_compressBlock(dstPtr, cctxPtr->tmpIn, blockSize, compress, cctxPtr->lz4CtxPtr, cctxPtr->prefs.compressionLevel); + + if (cctxPtr->prefs.frameInfo.blockMode==blockLinked) cctxPtr->tmpIn += blockSize; + cctxPtr->tmpInSize = 0; + } + } + + while ((size_t)(srcEnd - srcPtr) >= blockSize) + { + /* compress full block */ + lastBlockCompressed = fromSrcBuffer; + dstPtr += LZ4F_compressBlock(dstPtr, srcPtr, blockSize, compress, cctxPtr->lz4CtxPtr, cctxPtr->prefs.compressionLevel); + srcPtr += blockSize; + } + + if ((cctxPtr->prefs.autoFlush) && (srcPtr < srcEnd)) + { + /* compress remaining input < blockSize */ + lastBlockCompressed = fromSrcBuffer; + dstPtr += LZ4F_compressBlock(dstPtr, srcPtr, srcEnd - srcPtr, compress, cctxPtr->lz4CtxPtr, cctxPtr->prefs.compressionLevel); + srcPtr = srcEnd; + } + + /* preserve dictionary if necessary */ + if ((cctxPtr->prefs.frameInfo.blockMode==blockLinked) && (lastBlockCompressed==fromSrcBuffer)) + { + if (compressOptionsPtr->stableSrc) + { + cctxPtr->tmpIn = cctxPtr->tmpBuff; + } + else + { + int realDictSize = LZ4F_localSaveDict(cctxPtr); + if (realDictSize==0) return (size_t)-ERROR_GENERIC; + cctxPtr->tmpIn = cctxPtr->tmpBuff + realDictSize; + } + } + + /* keep tmpIn within limits */ + if ((cctxPtr->tmpIn + blockSize) > (cctxPtr->tmpBuff + cctxPtr->maxBufferSize) /* necessarily blockLinked && lastBlockCompressed==fromTmpBuffer */ + && !(cctxPtr->prefs.autoFlush)) + { + LZ4F_localSaveDict(cctxPtr); + cctxPtr->tmpIn = cctxPtr->tmpBuff + 64 KB; + } + + /* some input data left, necessarily < blockSize */ + if (srcPtr < srcEnd) + { + /* fill tmp buffer */ + size_t sizeToCopy = srcEnd - srcPtr; + memcpy(cctxPtr->tmpIn, srcPtr, sizeToCopy); + cctxPtr->tmpInSize = sizeToCopy; + } + + if (cctxPtr->prefs.frameInfo.contentChecksumFlag == contentChecksumEnabled) + XXH32_update(&(cctxPtr->xxh), srcBuffer, (unsigned)srcSize); + + return dstPtr - dstStart; +} + + +/* LZ4F_flush() +* Should you need to create compressed data immediately, without waiting for a block to be filled, +* you can call LZ4_flush(), which will immediately compress any remaining data stored within compressionContext. +* The result of the function is the number of bytes written into dstBuffer +* (it can be zero, this means there was no data left within compressionContext) +* The function outputs an error code if it fails (can be tested using LZ4F_isError()) +* The LZ4F_compressOptions_t structure is optional : you can provide NULL as argument. +*/ +size_t LZ4F_flush(LZ4F_compressionContext_t compressionContext, void* dstBuffer, size_t dstMaxSize, const LZ4F_compressOptions_t* compressOptionsPtr) +{ + LZ4F_compressOptions_t cOptionsNull = { 0 }; + LZ4F_cctx_internal_t* cctxPtr = (LZ4F_cctx_internal_t*)compressionContext; + BYTE* const dstStart = (BYTE*)dstBuffer; + BYTE* dstPtr = dstStart; + compressFunc_t compress; + + + if (cctxPtr->tmpInSize == 0) return 0; /* nothing to flush */ + if (cctxPtr->cStage != 1) return (size_t)-ERROR_GENERIC; + if (dstMaxSize < (cctxPtr->tmpInSize + 16)) return (size_t)-ERROR_dstMaxSize_tooSmall; + if (compressOptionsPtr == NULL) compressOptionsPtr = &cOptionsNull; + (void)compressOptionsPtr; /* not yet useful */ + + /* select compression function */ + compress = LZ4F_selectCompression(cctxPtr->prefs.frameInfo.blockMode, cctxPtr->prefs.compressionLevel); + + /* compress tmp buffer */ + dstPtr += LZ4F_compressBlock(dstPtr, cctxPtr->tmpIn, cctxPtr->tmpInSize, compress, cctxPtr->lz4CtxPtr, cctxPtr->prefs.compressionLevel); + if (cctxPtr->prefs.frameInfo.blockMode==blockLinked) cctxPtr->tmpIn += cctxPtr->tmpInSize; + cctxPtr->tmpInSize = 0; + + /* keep tmpIn within limits */ + if ((cctxPtr->tmpIn + cctxPtr->maxBlockSize) > (cctxPtr->tmpBuff + cctxPtr->maxBufferSize)) /* necessarily blockLinked */ + { + LZ4F_localSaveDict(cctxPtr); + cctxPtr->tmpIn = cctxPtr->tmpBuff + 64 KB; + } + + return dstPtr - dstStart; +} + + +/* LZ4F_compressEnd() +* When you want to properly finish the compressed frame, just call LZ4F_compressEnd(). +* It will flush whatever data remained within compressionContext (like LZ4_flush()) +* but also properly finalize the frame, with an endMark and a checksum. +* The result of the function is the number of bytes written into dstBuffer (necessarily >= 4 (endMark size)) +* The function outputs an error code if it fails (can be tested using LZ4F_isError()) +* The LZ4F_compressOptions_t structure is optional : you can provide NULL as argument. +* compressionContext can then be used again, starting with LZ4F_compressBegin(). The preferences will remain the same. +*/ +size_t LZ4F_compressEnd(LZ4F_compressionContext_t compressionContext, void* dstBuffer, size_t dstMaxSize, const LZ4F_compressOptions_t* compressOptionsPtr) +{ + LZ4F_cctx_internal_t* cctxPtr = (LZ4F_cctx_internal_t*)compressionContext; + BYTE* const dstStart = (BYTE*)dstBuffer; + BYTE* dstPtr = dstStart; + size_t errorCode; + + errorCode = LZ4F_flush(compressionContext, dstBuffer, dstMaxSize, compressOptionsPtr); + if (LZ4F_isError(errorCode)) return errorCode; + dstPtr += errorCode; + + LZ4F_writeLE32(dstPtr, 0); + dstPtr+=4; /* endMark */ + + if (cctxPtr->prefs.frameInfo.contentChecksumFlag == contentChecksumEnabled) + { + U32 xxh = XXH32_digest(&(cctxPtr->xxh)); + LZ4F_writeLE32(dstPtr, xxh); + dstPtr+=4; /* content Checksum */ + } + + cctxPtr->cStage = 0; /* state is now re-usable (with identical preferences) */ + + return dstPtr - dstStart; +} + + +/*********************************** +* Decompression functions +* *********************************/ + +/* Resource management */ + +/* LZ4F_createDecompressionContext() : +* The first thing to do is to create a decompressionContext object, which will be used in all decompression operations. +* This is achieved using LZ4F_createDecompressionContext(). +* The function will provide a pointer to a fully allocated and initialized LZ4F_decompressionContext object. +* If the result LZ4F_errorCode_t is not zero, there was an error during context creation. +* Object can release its memory using LZ4F_freeDecompressionContext(); +*/ +LZ4F_errorCode_t LZ4F_createDecompressionContext(LZ4F_compressionContext_t* LZ4F_decompressionContextPtr, unsigned versionNumber) +{ + LZ4F_dctx_internal_t* dctxPtr; + + dctxPtr = ALLOCATOR(sizeof(LZ4F_dctx_internal_t)); + if (dctxPtr==NULL) return (LZ4F_errorCode_t)-ERROR_GENERIC; + + dctxPtr->version = versionNumber; + *LZ4F_decompressionContextPtr = (LZ4F_compressionContext_t)dctxPtr; + return OK_NoError; +} + +LZ4F_errorCode_t LZ4F_freeDecompressionContext(LZ4F_compressionContext_t LZ4F_decompressionContext) +{ + LZ4F_dctx_internal_t* dctxPtr = (LZ4F_dctx_internal_t*)LZ4F_decompressionContext; + FREEMEM(dctxPtr->tmpIn); + FREEMEM(dctxPtr->tmpOutBuffer); + FREEMEM(dctxPtr); + return OK_NoError; +} + + +/* Decompression */ + +static size_t LZ4F_decodeHeader(LZ4F_dctx_internal_t* dctxPtr, const BYTE* srcPtr, size_t srcSize) +{ + BYTE FLG, BD, HC; + unsigned version, blockMode, blockChecksumFlag, contentSizeFlag, contentChecksumFlag, dictFlag, blockSizeID; + size_t bufferNeeded; + + /* need to decode header to get frameInfo */ + if (srcSize < 7) return (size_t)-ERROR_GENERIC; /* minimal header size */ + + /* control magic number */ + if (LZ4F_readLE32(srcPtr) != LZ4F_MAGICNUMBER) return (size_t)-ERROR_GENERIC; + srcPtr += 4; + + /* Flags */ + FLG = srcPtr[0]; + version = (FLG>>6)&_2BITS; + blockMode = (FLG>>5) & _1BIT; + blockChecksumFlag = (FLG>>4) & _1BIT; + contentSizeFlag = (FLG>>3) & _1BIT; + contentChecksumFlag = (FLG>>2) & _1BIT; + dictFlag = (FLG>>0) & _1BIT; + BD = srcPtr[1]; + blockSizeID = (BD>>4) & _3BITS; + + /* check */ + HC = LZ4F_headerChecksum(srcPtr, 2); + if (HC != srcPtr[2]) return (size_t)-ERROR_GENERIC; /* Bad header checksum error */ + + /* validate */ + if (version != 1) return (size_t)-ERROR_GENERIC; /* Version Number, only supported value */ + if (blockChecksumFlag != 0) return (size_t)-ERROR_GENERIC; /* Only supported value for the time being */ + if (contentSizeFlag != 0) return (size_t)-ERROR_GENERIC; /* Only supported value for the time being */ + if (((FLG>>1)&_1BIT) != 0) return (size_t)-ERROR_GENERIC; /* Reserved bit */ + if (dictFlag != 0) return (size_t)-ERROR_GENERIC; /* Only supported value for the time being */ + if (((BD>>7)&_1BIT) != 0) return (size_t)-ERROR_GENERIC; /* Reserved bit */ + if (blockSizeID < 4) return (size_t)-ERROR_GENERIC; /* Only supported values for the time being */ + if (((BD>>0)&_4BITS) != 0) return (size_t)-ERROR_GENERIC; /* Reserved bits */ + + /* save */ + dctxPtr->frameInfo.blockMode = blockMode; + dctxPtr->frameInfo.contentChecksumFlag = contentChecksumFlag; + dctxPtr->frameInfo.blockSizeID = blockSizeID; + dctxPtr->maxBlockSize = LZ4F_getBlockSize(blockSizeID); + + /* init */ + if (contentChecksumFlag) XXH32_reset(&(dctxPtr->xxh), 0); + + /* alloc */ + bufferNeeded = dctxPtr->maxBlockSize + ((dctxPtr->frameInfo.blockMode==blockLinked) * 128 KB); + if (bufferNeeded > dctxPtr->maxBufferSize) /* tmp buffers too small */ + { + FREEMEM(dctxPtr->tmpIn); + FREEMEM(dctxPtr->tmpOutBuffer); + dctxPtr->maxBufferSize = bufferNeeded; + dctxPtr->tmpIn = ALLOCATOR(dctxPtr->maxBlockSize); + if (dctxPtr->tmpIn == NULL) return (size_t)-ERROR_GENERIC; + dctxPtr->tmpOutBuffer= ALLOCATOR(dctxPtr->maxBufferSize); + if (dctxPtr->tmpOutBuffer== NULL) return (size_t)-ERROR_GENERIC; + } + dctxPtr->tmpInSize = 0; + dctxPtr->tmpInTarget = 0; + dctxPtr->dict = dctxPtr->tmpOutBuffer; + dctxPtr->dictSize = 0; + dctxPtr->tmpOut = dctxPtr->tmpOutBuffer; + dctxPtr->tmpOutStart = 0; + dctxPtr->tmpOutSize = 0; + + return 7; +} + + +typedef enum { dstage_getHeader=0, dstage_storeHeader, dstage_decodeHeader, + dstage_getCBlockSize, dstage_storeCBlockSize, dstage_decodeCBlockSize, + dstage_copyDirect, + dstage_getCBlock, dstage_storeCBlock, dstage_decodeCBlock, + dstage_decodeCBlock_intoDst, dstage_decodeCBlock_intoTmp, dstage_flushOut, + dstage_getSuffix, dstage_storeSuffix, dstage_checkSuffix +} dStage_t; + + +/* LZ4F_getFrameInfo() +* This function decodes frame header information, such as blockSize. +* It is optional : you could start by calling directly LZ4F_decompress() instead. +* The objective is to extract header information without starting decompression, typically for allocation purposes. +* LZ4F_getFrameInfo() can also be used *after* starting decompression, on a valid LZ4F_decompressionContext_t. +* The number of bytes read from srcBuffer will be provided within *srcSizePtr (necessarily <= original value). +* You are expected to resume decompression from where it stopped (srcBuffer + *srcSizePtr) +* The function result is an hint of the better srcSize to use for next call to LZ4F_decompress, +* or an error code which can be tested using LZ4F_isError(). +*/ +LZ4F_errorCode_t LZ4F_getFrameInfo(LZ4F_decompressionContext_t decompressionContext, LZ4F_frameInfo_t* frameInfoPtr, const void* srcBuffer, size_t* srcSizePtr) +{ + LZ4F_dctx_internal_t* dctxPtr = (LZ4F_dctx_internal_t*)decompressionContext; + + if (dctxPtr->dStage == dstage_getHeader) + { + LZ4F_errorCode_t errorCode = LZ4F_decodeHeader(dctxPtr, srcBuffer, *srcSizePtr); + if (LZ4F_isError(errorCode)) return errorCode; + *srcSizePtr = errorCode; + *frameInfoPtr = dctxPtr->frameInfo; + dctxPtr->srcExpect = NULL; + dctxPtr->dStage = dstage_getCBlockSize; + return 4; + } + + /* frameInfo already decoded */ + *srcSizePtr = 0; + *frameInfoPtr = dctxPtr->frameInfo; + return 0; +} + + +static int LZ4F_decompress_safe (const char* source, char* dest, int compressedSize, int maxDecompressedSize, const char* dictStart, int dictSize) +{ + (void)dictStart; + (void)dictSize; + return LZ4_decompress_safe (source, dest, compressedSize, maxDecompressedSize); +} + + + +static void LZ4F_updateDict(LZ4F_dctx_internal_t* dctxPtr, const BYTE* dstPtr, size_t dstSize, const BYTE* dstPtr0, unsigned withinTmp) +{ + if (dctxPtr->dictSize==0) + dctxPtr->dict = (BYTE*)dstPtr; /* priority to dictionary continuity */ + + if (dctxPtr->dict + dctxPtr->dictSize == dstPtr) /* dictionary continuity */ + { + dctxPtr->dictSize += dstSize; + return; + } + + if (dstPtr - dstPtr0 + dstSize >= 64 KB) /* dstBuffer large enough to become dictionary */ + { + dctxPtr->dict = (BYTE*)dstPtr0; + dctxPtr->dictSize = dstPtr - dstPtr0 + dstSize; + return; + } + + if ((withinTmp) && (dctxPtr->dict == dctxPtr->tmpOutBuffer)) + { + /* assumption : dctxPtr->dict + dctxPtr->dictSize == dctxPtr->tmpOut + dctxPtr->tmpOutStart */ + dctxPtr->dictSize += dstSize; + return; + } + + if (withinTmp) /* copy relevant dict portion in front of tmpOut within tmpOutBuffer */ + { +#if 0 + size_t savedDictSize = dctxPtr->tmpOut - dctxPtr->tmpOutBuffer; + memcpy(dctxPtr->tmpOutBuffer, dctxPtr->dict + dctxPtr->dictSize - dctxPtr->tmpOutStart- savedDictSize, savedDictSize); + dctxPtr->dict = dctxPtr->tmpOutBuffer; + dctxPtr->dictSize = savedDictSize + dctxPtr->tmpOutStart + dstSize; + return; + +#else + + size_t preserveSize = dctxPtr->tmpOut - dctxPtr->tmpOutBuffer; + size_t copySize = 64 KB - dctxPtr->tmpOutSize; + BYTE* oldDictEnd = dctxPtr->dict + dctxPtr->dictSize - dctxPtr->tmpOutStart; + if (dctxPtr->tmpOutSize > 64 KB) copySize = 0; + if (copySize > preserveSize) copySize = preserveSize; + + memcpy(dctxPtr->tmpOutBuffer + preserveSize - copySize, oldDictEnd - copySize, copySize); + + dctxPtr->dict = dctxPtr->tmpOutBuffer; + dctxPtr->dictSize = preserveSize + dctxPtr->tmpOutStart + dstSize; + return; +#endif + } + + if (dctxPtr->dict == dctxPtr->tmpOutBuffer) /* copy dst into tmp to complete dict */ + { + if (dctxPtr->dictSize + dstSize > dctxPtr->maxBufferSize) /* tmp buffer not large enough */ + { + size_t preserveSize = 64 KB - dstSize; /* note : dstSize < 64 KB */ + memcpy(dctxPtr->dict, dctxPtr->dict + dctxPtr->dictSize - preserveSize, preserveSize); + dctxPtr->dictSize = preserveSize; + } + memcpy(dctxPtr->dict + dctxPtr->dictSize, dstPtr, dstSize); + dctxPtr->dictSize += dstSize; + return; + } + + /* join dict & dest into tmp */ + { + size_t preserveSize = 64 KB - dstSize; /* note : dstSize < 64 KB */ + if (preserveSize > dctxPtr->dictSize) preserveSize = dctxPtr->dictSize; + memcpy(dctxPtr->tmpOutBuffer, dctxPtr->dict + dctxPtr->dictSize - preserveSize, preserveSize); + memcpy(dctxPtr->tmpOutBuffer + preserveSize, dstPtr, dstSize); + dctxPtr->dict = dctxPtr->tmpOutBuffer; + dctxPtr->dictSize = preserveSize + dstSize; + } +} + + + +/* LZ4F_decompress() +* Call this function repetitively to regenerate data compressed within srcBuffer. +* The function will attempt to decode *srcSizePtr from srcBuffer, into dstBuffer of maximum size *dstSizePtr. +* +* The number of bytes regenerated into dstBuffer will be provided within *dstSizePtr (necessarily <= original value). +* +* The number of bytes effectively read from srcBuffer will be provided within *srcSizePtr (necessarily <= original value). +* If the number of bytes read is < number of bytes provided, then the decompression operation is not complete. +* You will have to call it again, continuing from where it stopped. +* +* The function result is an hint of the better srcSize to use for next call to LZ4F_decompress. +* Basically, it's the size of the current (or remaining) compressed block + header of next block. +* Respecting the hint provides some boost to performance, since it allows less buffer shuffling. +* Note that this is just a hint, you can always provide any srcSize you want. +* When a frame is fully decoded, the function result will be 0. +* If decompression failed, function result is an error code which can be tested using LZ4F_isError(). +*/ +size_t LZ4F_decompress(LZ4F_decompressionContext_t decompressionContext, + void* dstBuffer, size_t* dstSizePtr, + const void* srcBuffer, size_t* srcSizePtr, + const LZ4F_decompressOptions_t* decompressOptionsPtr) +{ + LZ4F_dctx_internal_t* dctxPtr = (LZ4F_dctx_internal_t*)decompressionContext; + static const LZ4F_decompressOptions_t optionsNull = { 0 }; + const BYTE* const srcStart = (const BYTE*)srcBuffer; + const BYTE* const srcEnd = srcStart + *srcSizePtr; + const BYTE* srcPtr = srcStart; + BYTE* const dstStart = (BYTE*)dstBuffer; + BYTE* const dstEnd = dstStart + *dstSizePtr; + BYTE* dstPtr = dstStart; + const BYTE* selectedIn=NULL; + unsigned doAnotherStage = 1; + size_t nextSrcSizeHint = 1; + + + if (decompressOptionsPtr==NULL) decompressOptionsPtr = &optionsNull; + *srcSizePtr = 0; + *dstSizePtr = 0; + + /* expect to continue decoding src buffer where it left previously */ + if (dctxPtr->srcExpect != NULL) + { + if (srcStart != dctxPtr->srcExpect) return (size_t)-ERROR_GENERIC; + } + + /* programmed as a state machine */ + + while (doAnotherStage) + { + + switch(dctxPtr->dStage) + { + + case dstage_getHeader: + { + if (srcEnd-srcPtr >= 7) + { + selectedIn = srcPtr; + srcPtr += 7; + dctxPtr->dStage = dstage_decodeHeader; + break; + } + dctxPtr->tmpInSize = 0; + dctxPtr->dStage = dstage_storeHeader; + break; + } + + case dstage_storeHeader: + { + size_t sizeToCopy = 7 - dctxPtr->tmpInSize; + if (sizeToCopy > (size_t)(srcEnd - srcPtr)) sizeToCopy = srcEnd - srcPtr; + memcpy(dctxPtr->header + dctxPtr->tmpInSize, srcPtr, sizeToCopy); + dctxPtr->tmpInSize += sizeToCopy; + srcPtr += sizeToCopy; + if (dctxPtr->tmpInSize < 7) + { + nextSrcSizeHint = (7 - dctxPtr->tmpInSize) + 4; + doAnotherStage = 0; /* no enough src, wait to get some more */ + break; + } + selectedIn = dctxPtr->header; + dctxPtr->dStage = dstage_decodeHeader; + break; + } + + case dstage_decodeHeader: + { + LZ4F_errorCode_t errorCode = LZ4F_decodeHeader(dctxPtr, selectedIn, 7); + if (LZ4F_isError(errorCode)) return errorCode; + dctxPtr->dStage = dstage_getCBlockSize; + break; + } + + case dstage_getCBlockSize: + { + if ((srcEnd - srcPtr) >= 4) + { + selectedIn = srcPtr; + srcPtr += 4; + dctxPtr->dStage = dstage_decodeCBlockSize; + break; + } + /* not enough input to read cBlockSize field */ + dctxPtr->tmpInSize = 0; + dctxPtr->dStage = dstage_storeCBlockSize; + break; + } + + case dstage_storeCBlockSize: + { + size_t sizeToCopy = 4 - dctxPtr->tmpInSize; + if (sizeToCopy > (size_t)(srcEnd - srcPtr)) sizeToCopy = srcEnd - srcPtr; + memcpy(dctxPtr->tmpIn + dctxPtr->tmpInSize, srcPtr, sizeToCopy); + srcPtr += sizeToCopy; + dctxPtr->tmpInSize += sizeToCopy; + if (dctxPtr->tmpInSize < 4) /* not enough input to get full cBlockSize; wait for more */ + { + nextSrcSizeHint = 4 - dctxPtr->tmpInSize; + doAnotherStage=0; + break; + } + selectedIn = dctxPtr->tmpIn; + dctxPtr->dStage = dstage_decodeCBlockSize; + break; + } + + case dstage_decodeCBlockSize: + { + size_t nextCBlockSize = LZ4F_readLE32(selectedIn) & 0x7FFFFFFFU; + if (nextCBlockSize==0) /* frameEnd signal, no more CBlock */ + { + dctxPtr->dStage = dstage_getSuffix; + break; + } + if (nextCBlockSize > dctxPtr->maxBlockSize) return (size_t)-ERROR_GENERIC; /* invalid cBlockSize */ + dctxPtr->tmpInTarget = nextCBlockSize; + if (LZ4F_readLE32(selectedIn) & LZ4F_BLOCKUNCOMPRESSED_FLAG) + { + dctxPtr->dStage = dstage_copyDirect; + break; + } + dctxPtr->dStage = dstage_getCBlock; + if (dstPtr==dstEnd) + { + nextSrcSizeHint = nextCBlockSize + 4; + doAnotherStage = 0; + } + break; + } + + case dstage_copyDirect: /* uncompressed block */ + { + size_t sizeToCopy = dctxPtr->tmpInTarget; + if ((size_t)(srcEnd-srcPtr) < sizeToCopy) sizeToCopy = srcEnd - srcPtr; /* not enough input to read full block */ + if ((size_t)(dstEnd-dstPtr) < sizeToCopy) sizeToCopy = dstEnd - dstPtr; + memcpy(dstPtr, srcPtr, sizeToCopy); + if (dctxPtr->frameInfo.contentChecksumFlag) XXH32_update(&(dctxPtr->xxh), srcPtr, (U32)sizeToCopy); + + /* dictionary management */ + if (dctxPtr->frameInfo.blockMode==blockLinked) + LZ4F_updateDict(dctxPtr, dstPtr, sizeToCopy, dstStart, 0); + + srcPtr += sizeToCopy; + dstPtr += sizeToCopy; + if (sizeToCopy == dctxPtr->tmpInTarget) /* all copied */ + { + dctxPtr->dStage = dstage_getCBlockSize; + break; + } + dctxPtr->tmpInTarget -= sizeToCopy; /* still need to copy more */ + nextSrcSizeHint = dctxPtr->tmpInTarget + 4; + doAnotherStage = 0; + break; + } + + case dstage_getCBlock: /* entry from dstage_decodeCBlockSize */ + { + if ((size_t)(srcEnd-srcPtr) < dctxPtr->tmpInTarget) + { + dctxPtr->tmpInSize = 0; + dctxPtr->dStage = dstage_storeCBlock; + break; + } + selectedIn = srcPtr; + srcPtr += dctxPtr->tmpInTarget; + dctxPtr->dStage = dstage_decodeCBlock; + break; + } + + case dstage_storeCBlock: + { + size_t sizeToCopy = dctxPtr->tmpInTarget - dctxPtr->tmpInSize; + if (sizeToCopy > (size_t)(srcEnd-srcPtr)) sizeToCopy = srcEnd-srcPtr; + memcpy(dctxPtr->tmpIn + dctxPtr->tmpInSize, srcPtr, sizeToCopy); + dctxPtr->tmpInSize += sizeToCopy; + srcPtr += sizeToCopy; + if (dctxPtr->tmpInSize < dctxPtr->tmpInTarget) /* need more input */ + { + nextSrcSizeHint = (dctxPtr->tmpInTarget - dctxPtr->tmpInSize) + 4; + doAnotherStage=0; + break; + } + selectedIn = dctxPtr->tmpIn; + dctxPtr->dStage = dstage_decodeCBlock; + break; + } + + case dstage_decodeCBlock: + { + if ((size_t)(dstEnd-dstPtr) < dctxPtr->maxBlockSize) /* not enough place into dst : decode into tmpOut */ + dctxPtr->dStage = dstage_decodeCBlock_intoTmp; + else + dctxPtr->dStage = dstage_decodeCBlock_intoDst; + break; + } + + case dstage_decodeCBlock_intoDst: + { + int (*decoder)(const char*, char*, int, int, const char*, int); + int decodedSize; + + if (dctxPtr->frameInfo.blockMode == blockLinked) + decoder = LZ4_decompress_safe_usingDict; + else + decoder = LZ4F_decompress_safe; + + decodedSize = decoder((const char*)selectedIn, (char*)dstPtr, (int)dctxPtr->tmpInTarget, (int)dctxPtr->maxBlockSize, (const char*)dctxPtr->dict, (int)dctxPtr->dictSize); + if (decodedSize < 0) return (size_t)-ERROR_GENERIC; /* decompression failed */ + if (dctxPtr->frameInfo.contentChecksumFlag) XXH32_update(&(dctxPtr->xxh), dstPtr, decodedSize); + + /* dictionary management */ + if (dctxPtr->frameInfo.blockMode==blockLinked) + LZ4F_updateDict(dctxPtr, dstPtr, decodedSize, dstStart, 0); + + dstPtr += decodedSize; + dctxPtr->dStage = dstage_getCBlockSize; + break; + } + + case dstage_decodeCBlock_intoTmp: + { + /* not enough place into dst : decode into tmpOut */ + int (*decoder)(const char*, char*, int, int, const char*, int); + int decodedSize; + + if (dctxPtr->frameInfo.blockMode == blockLinked) + decoder = LZ4_decompress_safe_usingDict; + else + decoder = LZ4F_decompress_safe; + + /* ensure enough place for tmpOut */ + if (dctxPtr->frameInfo.blockMode == blockLinked) + { + if (dctxPtr->dict == dctxPtr->tmpOutBuffer) + { + if (dctxPtr->dictSize > 128 KB) + { + memcpy(dctxPtr->dict, dctxPtr->dict + dctxPtr->dictSize - 64 KB, 64 KB); + dctxPtr->dictSize = 64 KB; + } + dctxPtr->tmpOut = dctxPtr->dict + dctxPtr->dictSize; + } + else /* dict not within tmp */ + { + size_t reservedDictSpace = dctxPtr->dictSize; + if (reservedDictSpace > 64 KB) reservedDictSpace = 64 KB; + dctxPtr->tmpOut = dctxPtr->tmpOutBuffer + reservedDictSpace; + } + } + + /* Decode */ + decodedSize = decoder((const char*)selectedIn, (char*)dctxPtr->tmpOut, (int)dctxPtr->tmpInTarget, (int)dctxPtr->maxBlockSize, (const char*)dctxPtr->dict, (int)dctxPtr->dictSize); + if (decodedSize < 0) return (size_t)-ERROR_decompressionFailed; /* decompression failed */ + if (dctxPtr->frameInfo.contentChecksumFlag) XXH32_update(&(dctxPtr->xxh), dctxPtr->tmpOut, decodedSize); + dctxPtr->tmpOutSize = decodedSize; + dctxPtr->tmpOutStart = 0; + dctxPtr->dStage = dstage_flushOut; + break; + } + + case dstage_flushOut: /* flush decoded data from tmpOut to dstBuffer */ + { + size_t sizeToCopy = dctxPtr->tmpOutSize - dctxPtr->tmpOutStart; + if (sizeToCopy > (size_t)(dstEnd-dstPtr)) sizeToCopy = dstEnd-dstPtr; + memcpy(dstPtr, dctxPtr->tmpOut + dctxPtr->tmpOutStart, sizeToCopy); + + /* dictionary management */ + if (dctxPtr->frameInfo.blockMode==blockLinked) + LZ4F_updateDict(dctxPtr, dstPtr, sizeToCopy, dstStart, 1); + + dctxPtr->tmpOutStart += sizeToCopy; + dstPtr += sizeToCopy; + + /* end of flush ? */ + if (dctxPtr->tmpOutStart == dctxPtr->tmpOutSize) + { + dctxPtr->dStage = dstage_getCBlockSize; + break; + } + nextSrcSizeHint = 4; + doAnotherStage = 0; /* still some data to flush */ + break; + } + + case dstage_getSuffix: + { + size_t suffixSize = dctxPtr->frameInfo.contentChecksumFlag * 4; + if (suffixSize == 0) /* frame completed */ + { + nextSrcSizeHint = 0; + dctxPtr->dStage = dstage_getHeader; + doAnotherStage = 0; + break; + } + if ((srcEnd - srcPtr) >= 4) /* CRC present */ + { + selectedIn = srcPtr; + srcPtr += 4; + dctxPtr->dStage = dstage_checkSuffix; + break; + } + dctxPtr->tmpInSize = 0; + dctxPtr->dStage = dstage_storeSuffix; + break; + } + + case dstage_storeSuffix: + { + size_t sizeToCopy = 4 - dctxPtr->tmpInSize; + if (sizeToCopy > (size_t)(srcEnd - srcPtr)) sizeToCopy = srcEnd - srcPtr; + memcpy(dctxPtr->tmpIn + dctxPtr->tmpInSize, srcPtr, sizeToCopy); + srcPtr += sizeToCopy; + dctxPtr->tmpInSize += sizeToCopy; + if (dctxPtr->tmpInSize < 4) /* not enough input to read complete suffix */ + { + nextSrcSizeHint = 4 - dctxPtr->tmpInSize; + doAnotherStage=0; + break; + } + selectedIn = dctxPtr->tmpIn; + dctxPtr->dStage = dstage_checkSuffix; + break; + } + + case dstage_checkSuffix: + { + U32 readCRC = LZ4F_readLE32(selectedIn); + U32 resultCRC = XXH32_digest(&(dctxPtr->xxh)); + if (readCRC != resultCRC) return (size_t)-ERROR_checksum_invalid; + nextSrcSizeHint = 0; + dctxPtr->dStage = dstage_getHeader; + doAnotherStage = 0; + break; + } + } + } + + /* preserve dictionary within tmp if necessary */ + if ( (dctxPtr->frameInfo.blockMode==blockLinked) + &&(dctxPtr->dict != dctxPtr->tmpOutBuffer) + &&(!decompressOptionsPtr->stableDst) + &&((unsigned)(dctxPtr->dStage-1) < (unsigned)(dstage_getSuffix-1)) + ) + { + if (dctxPtr->dStage == dstage_flushOut) + { + size_t preserveSize = dctxPtr->tmpOut - dctxPtr->tmpOutBuffer; + size_t copySize = 64 KB - dctxPtr->tmpOutSize; + BYTE* oldDictEnd = dctxPtr->dict + dctxPtr->dictSize - dctxPtr->tmpOutStart; + if (dctxPtr->tmpOutSize > 64 KB) copySize = 0; + if (copySize > preserveSize) copySize = preserveSize; + + memcpy(dctxPtr->tmpOutBuffer + preserveSize - copySize, oldDictEnd - copySize, copySize); + + dctxPtr->dict = dctxPtr->tmpOutBuffer; + dctxPtr->dictSize = preserveSize + dctxPtr->tmpOutStart; + } + else + { + size_t newDictSize = dctxPtr->dictSize; + BYTE* oldDictEnd = dctxPtr->dict + dctxPtr->dictSize; + if ((newDictSize) > 64 KB) newDictSize = 64 KB; + + memcpy(dctxPtr->tmpOutBuffer, oldDictEnd - newDictSize, newDictSize); + + dctxPtr->dict = dctxPtr->tmpOutBuffer; + dctxPtr->dictSize = newDictSize; + dctxPtr->tmpOut = dctxPtr->tmpOutBuffer + newDictSize; + } + } + + if (srcPtrsrcExpect = srcPtr; + else + dctxPtr->srcExpect = NULL; + *srcSizePtr = (srcPtr - srcStart); + *dstSizePtr = (dstPtr - dstStart); + return nextSrcSizeHint; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4frame.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4frame.h new file mode 100644 index 0000000000000000000000000000000000000000..d73e3e28650c305363c87cf74017497de986d176 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4frame.h @@ -0,0 +1,252 @@ +/* + LZ4 auto-framing library + Header File + Copyright (C) 2011-2015, Yann Collet. + BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php) + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are + met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following disclaimer + in the documentation and/or other materials provided with the + distribution. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + You can contact the author at : + - LZ4 source repository : http://code.google.com/p/lz4/ + - LZ4 source mirror : https://github.com/Cyan4973/lz4 + - LZ4 public forum : https://groups.google.com/forum/#!forum/lz4c +*/ + +/* LZ4F is a stand-alone API to create LZ4-compressed frames + * fully conformant to specification v1.4.1. + * All related operations, including memory management, are handled by the library. + * You don't need lz4.h when using lz4frame.h. + * */ + +#pragma once + +#if defined (__cplusplus) +extern "C" { +#endif + +/************************************** + Includes +**************************************/ +#include /* size_t */ + + +/************************************** + * Error management + * ************************************/ +typedef size_t LZ4F_errorCode_t; + +unsigned LZ4F_isError(LZ4F_errorCode_t code); +const char* LZ4F_getErrorName(LZ4F_errorCode_t code); /* return error code string; useful for debugging */ + + +/************************************** + * Frame compression types + * ************************************/ +typedef enum { LZ4F_default=0, max64KB=4, max256KB=5, max1MB=6, max4MB=7 } blockSizeID_t; +typedef enum { blockLinked=0, blockIndependent} blockMode_t; +typedef enum { noContentChecksum=0, contentChecksumEnabled } contentChecksum_t; + +typedef struct { + blockSizeID_t blockSizeID; /* max64KB, max256KB, max1MB, max4MB ; 0 == default */ + blockMode_t blockMode; /* blockLinked, blockIndependent ; 0 == default */ + contentChecksum_t contentChecksumFlag; /* noContentChecksum, contentChecksumEnabled ; 0 == default */ + unsigned reserved[5]; +} LZ4F_frameInfo_t; + +typedef struct { + LZ4F_frameInfo_t frameInfo; + unsigned compressionLevel; /* 0 == default (fast mode); values above 16 count as 16 */ + unsigned autoFlush; /* 1 == always flush : reduce need for tmp buffer */ + unsigned reserved[4]; +} LZ4F_preferences_t; + + +/*********************************** + * Simple compression function + * *********************************/ +size_t LZ4F_compressFrameBound(size_t srcSize, const LZ4F_preferences_t* preferencesPtr); + +size_t LZ4F_compressFrame(void* dstBuffer, size_t dstMaxSize, const void* srcBuffer, size_t srcSize, const LZ4F_preferences_t* preferencesPtr); +/* LZ4F_compressFrame() + * Compress an entire srcBuffer into a valid LZ4 frame, as defined by specification v1.4.1. + * The most important rule is that dstBuffer MUST be large enough (dstMaxSize) to ensure compression completion even in worst case. + * You can get the minimum value of dstMaxSize by using LZ4F_compressFrameBound() + * If this condition is not respected, LZ4F_compressFrame() will fail (result is an errorCode) + * The LZ4F_preferences_t structure is optional : you can provide NULL as argument. All preferences will be set to default. + * The result of the function is the number of bytes written into dstBuffer. + * The function outputs an error code if it fails (can be tested using LZ4F_isError()) + */ + + + +/********************************** + * Advanced compression functions + * ********************************/ +typedef void* LZ4F_compressionContext_t; + +typedef struct { + unsigned stableSrc; /* 1 == src content will remain available on future calls to LZ4F_compress(); avoid saving src content within tmp buffer as future dictionary */ + unsigned reserved[3]; +} LZ4F_compressOptions_t; + +/* Resource Management */ + +#define LZ4F_VERSION 100 +LZ4F_errorCode_t LZ4F_createCompressionContext(LZ4F_compressionContext_t* LZ4F_compressionContextPtr, unsigned version); +LZ4F_errorCode_t LZ4F_freeCompressionContext(LZ4F_compressionContext_t LZ4F_compressionContext); +/* LZ4F_createCompressionContext() : + * The first thing to do is to create a compressionContext object, which will be used in all compression operations. + * This is achieved using LZ4F_createCompressionContext(), which takes as argument a version and an LZ4F_preferences_t structure. + * The version provided MUST be LZ4F_VERSION. It is intended to track potential version differences between different binaries. + * The function will provide a pointer to a fully allocated LZ4F_compressionContext_t object. + * If the result LZ4F_errorCode_t is not zero, there was an error during context creation. + * Object can release its memory using LZ4F_freeCompressionContext(); + */ + + +/* Compression */ + +size_t LZ4F_compressBegin(LZ4F_compressionContext_t compressionContext, void* dstBuffer, size_t dstMaxSize, const LZ4F_preferences_t* preferencesPtr); +/* LZ4F_compressBegin() : + * will write the frame header into dstBuffer. + * dstBuffer must be large enough to accommodate a header (dstMaxSize). Maximum header size is 19 bytes. + * The LZ4F_preferences_t structure is optional : you can provide NULL as argument, all preferences will then be set to default. + * The result of the function is the number of bytes written into dstBuffer for the header + * or an error code (can be tested using LZ4F_isError()) + */ + +size_t LZ4F_compressBound(size_t srcSize, const LZ4F_preferences_t* preferencesPtr); +/* LZ4F_compressBound() : + * Provides the minimum size of Dst buffer given srcSize to handle worst case situations. + * preferencesPtr is optional : you can provide NULL as argument, all preferences will then be set to default. + * Note that different preferences will produce in different results. + */ + +size_t LZ4F_compressUpdate(LZ4F_compressionContext_t compressionContext, void* dstBuffer, size_t dstMaxSize, const void* srcBuffer, size_t srcSize, const LZ4F_compressOptions_t* compressOptionsPtr); +/* LZ4F_compressUpdate() + * LZ4F_compressUpdate() can be called repetitively to compress as much data as necessary. + * The most important rule is that dstBuffer MUST be large enough (dstMaxSize) to ensure compression completion even in worst case. + * If this condition is not respected, LZ4F_compress() will fail (result is an errorCode) + * You can get the minimum value of dstMaxSize by using LZ4F_compressBound() + * The LZ4F_compressOptions_t structure is optional : you can provide NULL as argument. + * The result of the function is the number of bytes written into dstBuffer : it can be zero, meaning input data was just buffered. + * The function outputs an error code if it fails (can be tested using LZ4F_isError()) + */ + +size_t LZ4F_flush(LZ4F_compressionContext_t compressionContext, void* dstBuffer, size_t dstMaxSize, const LZ4F_compressOptions_t* compressOptionsPtr); +/* LZ4F_flush() + * Should you need to create compressed data immediately, without waiting for a block to be filled, + * you can call LZ4_flush(), which will immediately compress any remaining data buffered within compressionContext. + * The LZ4F_compressOptions_t structure is optional : you can provide NULL as argument. + * The result of the function is the number of bytes written into dstBuffer + * (it can be zero, this means there was no data left within compressionContext) + * The function outputs an error code if it fails (can be tested using LZ4F_isError()) + */ + +size_t LZ4F_compressEnd(LZ4F_compressionContext_t compressionContext, void* dstBuffer, size_t dstMaxSize, const LZ4F_compressOptions_t* compressOptionsPtr); +/* LZ4F_compressEnd() + * When you want to properly finish the compressed frame, just call LZ4F_compressEnd(). + * It will flush whatever data remained within compressionContext (like LZ4_flush()) + * but also properly finalize the frame, with an endMark and a checksum. + * The result of the function is the number of bytes written into dstBuffer (necessarily >= 4 (endMark size)) + * The function outputs an error code if it fails (can be tested using LZ4F_isError()) + * The LZ4F_compressOptions_t structure is optional : you can provide NULL as argument. + * compressionContext can then be used again, starting with LZ4F_compressBegin(). + */ + + +/*********************************** + * Decompression functions + * *********************************/ + +typedef void* LZ4F_decompressionContext_t; + +typedef struct { + unsigned stableDst; /* guarantee that decompressed data will still be there on next function calls (avoid storage into tmp buffers) */ + unsigned reserved[3]; +} LZ4F_decompressOptions_t; + + +/* Resource management */ + +LZ4F_errorCode_t LZ4F_createDecompressionContext(LZ4F_decompressionContext_t* ctxPtr, unsigned version); +LZ4F_errorCode_t LZ4F_freeDecompressionContext(LZ4F_decompressionContext_t ctx); +/* LZ4F_createDecompressionContext() : + * The first thing to do is to create a decompressionContext object, which will be used in all decompression operations. + * This is achieved using LZ4F_createDecompressionContext(). + * The version provided MUST be LZ4F_VERSION. It is intended to track potential version differences between different binaries. + * The function will provide a pointer to a fully allocated and initialized LZ4F_decompressionContext_t object. + * If the result LZ4F_errorCode_t is not OK_NoError, there was an error during context creation. + * Object can release its memory using LZ4F_freeDecompressionContext(); + */ + + +/* Decompression */ + +size_t LZ4F_getFrameInfo(LZ4F_decompressionContext_t ctx, + LZ4F_frameInfo_t* frameInfoPtr, + const void* srcBuffer, size_t* srcSizePtr); +/* LZ4F_getFrameInfo() + * This function decodes frame header information, such as blockSize. + * It is optional : you could start by calling directly LZ4F_decompress() instead. + * The objective is to extract header information without starting decompression, typically for allocation purposes. + * LZ4F_getFrameInfo() can also be used *after* starting decompression, on a valid LZ4F_decompressionContext_t. + * The number of bytes read from srcBuffer will be provided within *srcSizePtr (necessarily <= original value). + * You are expected to resume decompression from where it stopped (srcBuffer + *srcSizePtr) + * The function result is an hint of how many srcSize bytes LZ4F_decompress() expects for next call, + * or an error code which can be tested using LZ4F_isError(). + */ + +size_t LZ4F_decompress(LZ4F_decompressionContext_t ctx, + void* dstBuffer, size_t* dstSizePtr, + const void* srcBuffer, size_t* srcSizePtr, + const LZ4F_decompressOptions_t* optionsPtr); +/* LZ4F_decompress() + * Call this function repetitively to regenerate data compressed within srcBuffer. + * The function will attempt to decode *srcSizePtr bytes from srcBuffer, into dstBuffer of maximum size *dstSizePtr. + * + * The number of bytes regenerated into dstBuffer will be provided within *dstSizePtr (necessarily <= original value). + * + * The number of bytes read from srcBuffer will be provided within *srcSizePtr (necessarily <= original value). + * If number of bytes read is < number of bytes provided, then decompression operation is not completed. + * It typically happens when dstBuffer is not large enough to contain all decoded data. + * LZ4F_decompress() must be called again, starting from where it stopped (srcBuffer + *srcSizePtr) + * The function will check this condition, and refuse to continue if it is not respected. + * + * dstBuffer is supposed to be flushed between each call to the function, since its content will be overwritten. + * dst arguments can be changed at will with each consecutive call to the function. + * + * The function result is an hint of how many srcSize bytes LZ4F_decompress() expects for next call. + * Schematically, it's the size of the current (or remaining) compressed block + header of next block. + * Respecting the hint provides some boost to performance, since it does skip intermediate buffers. + * This is just a hint, you can always provide any srcSize you want. + * When a frame is fully decoded, the function result will be 0. (no more data expected) + * If decompression failed, function result is an error code, which can be tested using LZ4F_isError(). + */ + + + +#if defined (__cplusplus) +} +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4frame_static.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4frame_static.h new file mode 100644 index 0000000000000000000000000000000000000000..cde81862a52b6b9c6079fc24a50d568bd27d4306 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4frame_static.h @@ -0,0 +1,72 @@ +/* + LZ4 auto-framing library + Header File for static linking only + Copyright (C) 2011-2015, Yann Collet. + + BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php) + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are + met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following disclaimer + in the documentation and/or other materials provided with the + distribution. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + You can contact the author at : + - LZ4 source repository : http://code.google.com/p/lz4/ + - LZ4 source mirror : https://github.com/Cyan4973/lz4 + - LZ4 public forum : https://groups.google.com/forum/#!forum/lz4c +*/ + +#pragma once + +#if defined (__cplusplus) +extern "C" { +#endif + +/* lz4frame_static.h should be used solely in the context of static linking. + * */ + + +/************************************** + * Error management + * ************************************/ +#define LZ4F_LIST_ERRORS(ITEM) \ + ITEM(OK_NoError) ITEM(ERROR_GENERIC) \ + ITEM(ERROR_maxBlockSize_invalid) ITEM(ERROR_blockMode_invalid) ITEM(ERROR_contentChecksumFlag_invalid) \ + ITEM(ERROR_compressionLevel_invalid) \ + ITEM(ERROR_allocation_failed) \ + ITEM(ERROR_srcSize_tooLarge) ITEM(ERROR_dstMaxSize_tooSmall) \ + ITEM(ERROR_decompressionFailed) \ + ITEM(ERROR_checksum_invalid) \ + ITEM(ERROR_maxCode) + +#define LZ4F_GENERATE_ENUM(ENUM) ENUM, +typedef enum { LZ4F_LIST_ERRORS(LZ4F_GENERATE_ENUM) } LZ4F_errorCodes; /* enum is exposed, to handle specific errors; compare function result to -enum value */ + + +/************************************** + Includes +**************************************/ +#include "lz4frame.h" + + +#if defined (__cplusplus) +} +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4hc.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4hc.c new file mode 100644 index 0000000000000000000000000000000000000000..5549969c0c2f81f392094f73044f3c73d688329f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4hc.c @@ -0,0 +1,751 @@ +/* +LZ4 HC - High Compression Mode of LZ4 +Copyright (C) 2011-2014, Yann Collet. +BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php) + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + +* Redistributions of source code must retain the above copyright +notice, this list of conditions and the following disclaimer. +* Redistributions in binary form must reproduce the above +copyright notice, this list of conditions and the following disclaimer +in the documentation and/or other materials provided with the +distribution. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +You can contact the author at : +- LZ4 homepage : http://fastcompression.blogspot.com/p/lz4.html +- LZ4 source repository : http://code.google.com/p/lz4/ +*/ + + + +/************************************** + Tuning Parameter +**************************************/ +static const int LZ4HC_compressionLevel_default = 8; + + +/************************************** + Includes +**************************************/ +#include "lz4hc.h" + + +/************************************** + Local Compiler Options +**************************************/ +#if defined(__GNUC__) +# pragma GCC diagnostic ignored "-Wunused-function" +#endif + +#if defined (__clang__) +# pragma clang diagnostic ignored "-Wunused-function" +#endif + + +/************************************** + Common LZ4 definition +**************************************/ +#define LZ4_COMMONDEFS_ONLY +#include "lz4.c" + + +/************************************** + Local Constants +**************************************/ +#define DICTIONARY_LOGSIZE 16 +#define MAXD (1<> ((MINMATCH*8)-HASH_LOG)) +#define DELTANEXT(p) chainTable[(size_t)(p) & MAXD_MASK] +#define GETNEXT(p) ((p) - (size_t)DELTANEXT(p)) + +static U32 LZ4HC_hashPtr(const void* ptr) { return HASH_FUNCTION(LZ4_read32(ptr)); } + + + +/************************************** + HC Compression +**************************************/ +static void LZ4HC_init (LZ4HC_Data_Structure* hc4, const BYTE* start) +{ + MEM_INIT((void*)hc4->hashTable, 0, sizeof(hc4->hashTable)); + MEM_INIT(hc4->chainTable, 0xFF, sizeof(hc4->chainTable)); + hc4->nextToUpdate = 64 KB; + hc4->base = start - 64 KB; + hc4->inputBuffer = start; + hc4->end = start; + hc4->dictBase = start - 64 KB; + hc4->dictLimit = 64 KB; + hc4->lowLimit = 64 KB; +} + + +/* Update chains up to ip (excluded) */ +FORCE_INLINE void LZ4HC_Insert (LZ4HC_Data_Structure* hc4, const BYTE* ip) +{ + U16* chainTable = hc4->chainTable; + U32* HashTable = hc4->hashTable; + const BYTE* const base = hc4->base; + const U32 target = (U32)(ip - base); + U32 idx = hc4->nextToUpdate; + + while(idx < target) + { + U32 h = LZ4HC_hashPtr(base+idx); + size_t delta = idx - HashTable[h]; + if (delta>MAX_DISTANCE) delta = MAX_DISTANCE; + chainTable[idx & 0xFFFF] = (U16)delta; + HashTable[h] = idx; + idx++; + } + + hc4->nextToUpdate = target; +} + + +FORCE_INLINE int LZ4HC_InsertAndFindBestMatch (LZ4HC_Data_Structure* hc4, /* Index table will be updated */ + const BYTE* ip, const BYTE* const iLimit, + const BYTE** matchpos, + const int maxNbAttempts) +{ + U16* const chainTable = hc4->chainTable; + U32* const HashTable = hc4->hashTable; + const BYTE* const base = hc4->base; + const BYTE* const dictBase = hc4->dictBase; + const U32 dictLimit = hc4->dictLimit; + const U32 lowLimit = (hc4->lowLimit + 64 KB > (U32)(ip-base)) ? hc4->lowLimit : (U32)(ip - base) - (64 KB - 1); + U32 matchIndex; + const BYTE* match; + int nbAttempts=maxNbAttempts; + size_t ml=0; + + /* HC4 match finder */ + LZ4HC_Insert(hc4, ip); + matchIndex = HashTable[LZ4HC_hashPtr(ip)]; + + while ((matchIndex>=lowLimit) && (nbAttempts)) + { + nbAttempts--; + if (matchIndex >= dictLimit) + { + match = base + matchIndex; + if (*(match+ml) == *(ip+ml) + && (LZ4_read32(match) == LZ4_read32(ip))) + { + size_t mlt = LZ4_count(ip+MINMATCH, match+MINMATCH, iLimit) + MINMATCH; + if (mlt > ml) { ml = mlt; *matchpos = match; } + } + } + else + { + match = dictBase + matchIndex; + if (LZ4_read32(match) == LZ4_read32(ip)) + { + size_t mlt; + const BYTE* vLimit = ip + (dictLimit - matchIndex); + if (vLimit > iLimit) vLimit = iLimit; + mlt = LZ4_count(ip+MINMATCH, match+MINMATCH, vLimit) + MINMATCH; + if ((ip+mlt == vLimit) && (vLimit < iLimit)) + mlt += LZ4_count(ip+mlt, base+dictLimit, iLimit); + if (mlt > ml) { ml = mlt; *matchpos = base + matchIndex; } /* virtual matchpos */ + } + } + matchIndex -= chainTable[matchIndex & 0xFFFF]; + } + + return (int)ml; +} + + +FORCE_INLINE int LZ4HC_InsertAndGetWiderMatch ( + LZ4HC_Data_Structure* hc4, + const BYTE* ip, + const BYTE* iLowLimit, + const BYTE* iHighLimit, + int longest, + const BYTE** matchpos, + const BYTE** startpos, + const int maxNbAttempts) +{ + U16* const chainTable = hc4->chainTable; + U32* const HashTable = hc4->hashTable; + const BYTE* const base = hc4->base; + const U32 dictLimit = hc4->dictLimit; + const U32 lowLimit = (hc4->lowLimit + 64 KB > (U32)(ip-base)) ? hc4->lowLimit : (U32)(ip - base) - (64 KB - 1); + const BYTE* const dictBase = hc4->dictBase; + const BYTE* match; + U32 matchIndex; + int nbAttempts = maxNbAttempts; + int delta = (int)(ip-iLowLimit); + + + /* First Match */ + LZ4HC_Insert(hc4, ip); + matchIndex = HashTable[LZ4HC_hashPtr(ip)]; + + while ((matchIndex>=lowLimit) && (nbAttempts)) + { + nbAttempts--; + if (matchIndex >= dictLimit) + { + match = base + matchIndex; + if (*(iLowLimit + longest) == *(match - delta + longest)) + if (LZ4_read32(match) == LZ4_read32(ip)) + { + const BYTE* startt = ip; + const BYTE* tmpMatch = match; + const BYTE* const matchEnd = ip + MINMATCH + LZ4_count(ip+MINMATCH, match+MINMATCH, iHighLimit); + + while ((startt>iLowLimit) && (tmpMatch > iLowLimit) && (startt[-1] == tmpMatch[-1])) {startt--; tmpMatch--;} + + if ((matchEnd-startt) > longest) + { + longest = (int)(matchEnd-startt); + *matchpos = tmpMatch; + *startpos = startt; + } + } + } + else + { + match = dictBase + matchIndex; + if (LZ4_read32(match) == LZ4_read32(ip)) + { + size_t mlt; + int back=0; + const BYTE* vLimit = ip + (dictLimit - matchIndex); + if (vLimit > iHighLimit) vLimit = iHighLimit; + mlt = LZ4_count(ip+MINMATCH, match+MINMATCH, vLimit) + MINMATCH; + if ((ip+mlt == vLimit) && (vLimit < iHighLimit)) + mlt += LZ4_count(ip+mlt, base+dictLimit, iHighLimit); + while ((ip+back > iLowLimit) && (matchIndex+back > lowLimit) && (ip[back-1] == match[back-1])) back--; + mlt -= back; + if ((int)mlt > longest) { longest = (int)mlt; *matchpos = base + matchIndex + back; *startpos = ip+back; } + } + } + matchIndex -= chainTable[matchIndex & 0xFFFF]; + } + + return longest; +} + + +typedef enum { noLimit = 0, limitedOutput = 1 } limitedOutput_directive; + +#define LZ4HC_DEBUG 0 +#if LZ4HC_DEBUG +static unsigned debug = 0; +#endif + +FORCE_INLINE int LZ4HC_encodeSequence ( + const BYTE** ip, + BYTE** op, + const BYTE** anchor, + int matchLength, + const BYTE* const match, + limitedOutput_directive limitedOutputBuffer, + BYTE* oend) +{ + int length; + BYTE* token; + +#if LZ4HC_DEBUG + if (debug) printf("literal : %u -- match : %u -- offset : %u\n", (U32)(*ip - *anchor), (U32)matchLength, (U32)(*ip-match)); +#endif + + /* Encode Literal length */ + length = (int)(*ip - *anchor); + token = (*op)++; + if ((limitedOutputBuffer) && ((*op + (length>>8) + length + (2 + 1 + LASTLITERALS)) > oend)) return 1; /* Check output limit */ + if (length>=(int)RUN_MASK) { int len; *token=(RUN_MASK< 254 ; len-=255) *(*op)++ = 255; *(*op)++ = (BYTE)len; } + else *token = (BYTE)(length<>8) + (1 + LASTLITERALS) > oend)) return 1; /* Check output limit */ + if (length>=(int)ML_MASK) { *token+=ML_MASK; length-=ML_MASK; for(; length > 509 ; length-=510) { *(*op)++ = 255; *(*op)++ = 255; } if (length > 254) { length-=255; *(*op)++ = 255; } *(*op)++ = (BYTE)length; } + else *token += (BYTE)(length); + + /* Prepare next loop */ + *ip += matchLength; + *anchor = *ip; + + return 0; +} + + +static int LZ4HC_compress_generic ( + void* ctxvoid, + const char* source, + char* dest, + int inputSize, + int maxOutputSize, + int compressionLevel, + limitedOutput_directive limit + ) +{ + LZ4HC_Data_Structure* ctx = (LZ4HC_Data_Structure*) ctxvoid; + const BYTE* ip = (const BYTE*) source; + const BYTE* anchor = ip; + const BYTE* const iend = ip + inputSize; + const BYTE* const mflimit = iend - MFLIMIT; + const BYTE* const matchlimit = (iend - LASTLITERALS); + + BYTE* op = (BYTE*) dest; + BYTE* const oend = op + maxOutputSize; + + unsigned maxNbAttempts; + int ml, ml2, ml3, ml0; + const BYTE* ref=NULL; + const BYTE* start2=NULL; + const BYTE* ref2=NULL; + const BYTE* start3=NULL; + const BYTE* ref3=NULL; + const BYTE* start0; + const BYTE* ref0; + + + /* init */ + if (compressionLevel > g_maxCompressionLevel) compressionLevel = g_maxCompressionLevel; + if (compressionLevel < 1) compressionLevel = LZ4HC_compressionLevel_default; + maxNbAttempts = 1 << (compressionLevel-1); + ctx->end += inputSize; + + ip++; + + /* Main Loop */ + while (ip < mflimit) + { + ml = LZ4HC_InsertAndFindBestMatch (ctx, ip, matchlimit, (&ref), maxNbAttempts); + if (!ml) { ip++; continue; } + + /* saved, in case we would skip too much */ + start0 = ip; + ref0 = ref; + ml0 = ml; + +_Search2: + if (ip+ml < mflimit) + ml2 = LZ4HC_InsertAndGetWiderMatch(ctx, ip + ml - 2, ip + 1, matchlimit, ml, &ref2, &start2, maxNbAttempts); + else ml2 = ml; + + if (ml2 == ml) /* No better match */ + { + if (LZ4HC_encodeSequence(&ip, &op, &anchor, ml, ref, limit, oend)) return 0; + continue; + } + + if (start0 < ip) + { + if (start2 < ip + ml0) /* empirical */ + { + ip = start0; + ref = ref0; + ml = ml0; + } + } + + /* Here, start0==ip */ + if ((start2 - ip) < 3) /* First Match too small : removed */ + { + ml = ml2; + ip = start2; + ref =ref2; + goto _Search2; + } + +_Search3: + /* + * Currently we have : + * ml2 > ml1, and + * ip1+3 <= ip2 (usually < ip1+ml1) + */ + if ((start2 - ip) < OPTIMAL_ML) + { + int correction; + int new_ml = ml; + if (new_ml > OPTIMAL_ML) new_ml = OPTIMAL_ML; + if (ip+new_ml > start2 + ml2 - MINMATCH) new_ml = (int)(start2 - ip) + ml2 - MINMATCH; + correction = new_ml - (int)(start2 - ip); + if (correction > 0) + { + start2 += correction; + ref2 += correction; + ml2 -= correction; + } + } + /* Now, we have start2 = ip+new_ml, with new_ml = min(ml, OPTIMAL_ML=18) */ + + if (start2 + ml2 < mflimit) + ml3 = LZ4HC_InsertAndGetWiderMatch(ctx, start2 + ml2 - 3, start2, matchlimit, ml2, &ref3, &start3, maxNbAttempts); + else ml3 = ml2; + + if (ml3 == ml2) /* No better match : 2 sequences to encode */ + { + /* ip & ref are known; Now for ml */ + if (start2 < ip+ml) ml = (int)(start2 - ip); + /* Now, encode 2 sequences */ + if (LZ4HC_encodeSequence(&ip, &op, &anchor, ml, ref, limit, oend)) return 0; + ip = start2; + if (LZ4HC_encodeSequence(&ip, &op, &anchor, ml2, ref2, limit, oend)) return 0; + continue; + } + + if (start3 < ip+ml+3) /* Not enough space for match 2 : remove it */ + { + if (start3 >= (ip+ml)) /* can write Seq1 immediately ==> Seq2 is removed, so Seq3 becomes Seq1 */ + { + if (start2 < ip+ml) + { + int correction = (int)(ip+ml - start2); + start2 += correction; + ref2 += correction; + ml2 -= correction; + if (ml2 < MINMATCH) + { + start2 = start3; + ref2 = ref3; + ml2 = ml3; + } + } + + if (LZ4HC_encodeSequence(&ip, &op, &anchor, ml, ref, limit, oend)) return 0; + ip = start3; + ref = ref3; + ml = ml3; + + start0 = start2; + ref0 = ref2; + ml0 = ml2; + goto _Search2; + } + + start2 = start3; + ref2 = ref3; + ml2 = ml3; + goto _Search3; + } + + /* + * OK, now we have 3 ascending matches; let's write at least the first one + * ip & ref are known; Now for ml + */ + if (start2 < ip+ml) + { + if ((start2 - ip) < (int)ML_MASK) + { + int correction; + if (ml > OPTIMAL_ML) ml = OPTIMAL_ML; + if (ip + ml > start2 + ml2 - MINMATCH) ml = (int)(start2 - ip) + ml2 - MINMATCH; + correction = ml - (int)(start2 - ip); + if (correction > 0) + { + start2 += correction; + ref2 += correction; + ml2 -= correction; + } + } + else + { + ml = (int)(start2 - ip); + } + } + if (LZ4HC_encodeSequence(&ip, &op, &anchor, ml, ref, limit, oend)) return 0; + + ip = start2; + ref = ref2; + ml = ml2; + + start2 = start3; + ref2 = ref3; + ml2 = ml3; + + goto _Search3; + } + + /* Encode Last Literals */ + { + int lastRun = (int)(iend - anchor); + if ((limit) && (((char*)op - dest) + lastRun + 1 + ((lastRun+255-RUN_MASK)/255) > (U32)maxOutputSize)) return 0; /* Check output limit */ + if (lastRun>=(int)RUN_MASK) { *op++=(RUN_MASK< 254 ; lastRun-=255) *op++ = 255; *op++ = (BYTE) lastRun; } + else *op++ = (BYTE)(lastRun<base = NULL; + ((LZ4HC_Data_Structure*)LZ4_streamHCPtr)->compressionLevel = (unsigned)compressionLevel; +} + +int LZ4_loadDictHC (LZ4_streamHC_t* LZ4_streamHCPtr, const char* dictionary, int dictSize) +{ + LZ4HC_Data_Structure* ctxPtr = (LZ4HC_Data_Structure*) LZ4_streamHCPtr; + if (dictSize > 64 KB) + { + dictionary += dictSize - 64 KB; + dictSize = 64 KB; + } + LZ4HC_init (ctxPtr, (const BYTE*)dictionary); + if (dictSize >= 4) LZ4HC_Insert (ctxPtr, (const BYTE*)dictionary +(dictSize-3)); + ctxPtr->end = (const BYTE*)dictionary + dictSize; + return dictSize; +} + + +/* compression */ + +static void LZ4HC_setExternalDict(LZ4HC_Data_Structure* ctxPtr, const BYTE* newBlock) +{ + if (ctxPtr->end >= ctxPtr->base + 4) + LZ4HC_Insert (ctxPtr, ctxPtr->end-3); /* Referencing remaining dictionary content */ + /* Only one memory segment for extDict, so any previous extDict is lost at this stage */ + ctxPtr->lowLimit = ctxPtr->dictLimit; + ctxPtr->dictLimit = (U32)(ctxPtr->end - ctxPtr->base); + ctxPtr->dictBase = ctxPtr->base; + ctxPtr->base = newBlock - ctxPtr->dictLimit; + ctxPtr->end = newBlock; + ctxPtr->nextToUpdate = ctxPtr->dictLimit; /* match referencing will resume from there */ +} + +static int LZ4_compressHC_continue_generic (LZ4HC_Data_Structure* ctxPtr, + const char* source, char* dest, + int inputSize, int maxOutputSize, limitedOutput_directive limit) +{ + /* auto-init if forgotten */ + if (ctxPtr->base == NULL) + LZ4HC_init (ctxPtr, (const BYTE*) source); + + /* Check overflow */ + if ((size_t)(ctxPtr->end - ctxPtr->base) > 2 GB) + { + size_t dictSize = (size_t)(ctxPtr->end - ctxPtr->base) - ctxPtr->dictLimit; + if (dictSize > 64 KB) dictSize = 64 KB; + + LZ4_loadDictHC((LZ4_streamHC_t*)ctxPtr, (const char*)(ctxPtr->end) - dictSize, (int)dictSize); + } + + /* Check if blocks follow each other */ + if ((const BYTE*)source != ctxPtr->end) LZ4HC_setExternalDict(ctxPtr, (const BYTE*)source); + + /* Check overlapping input/dictionary space */ + { + const BYTE* sourceEnd = (const BYTE*) source + inputSize; + const BYTE* dictBegin = ctxPtr->dictBase + ctxPtr->lowLimit; + const BYTE* dictEnd = ctxPtr->dictBase + ctxPtr->dictLimit; + if ((sourceEnd > dictBegin) && ((BYTE*)source < dictEnd)) + { + if (sourceEnd > dictEnd) sourceEnd = dictEnd; + ctxPtr->lowLimit = (U32)(sourceEnd - ctxPtr->dictBase); + if (ctxPtr->dictLimit - ctxPtr->lowLimit < 4) ctxPtr->lowLimit = ctxPtr->dictLimit; + } + } + + return LZ4HC_compress_generic (ctxPtr, source, dest, inputSize, maxOutputSize, ctxPtr->compressionLevel, limit); +} + +int LZ4_compressHC_continue (LZ4_streamHC_t* LZ4_streamHCPtr, const char* source, char* dest, int inputSize) +{ + return LZ4_compressHC_continue_generic ((LZ4HC_Data_Structure*)LZ4_streamHCPtr, source, dest, inputSize, 0, noLimit); +} + +int LZ4_compressHC_limitedOutput_continue (LZ4_streamHC_t* LZ4_streamHCPtr, const char* source, char* dest, int inputSize, int maxOutputSize) +{ + return LZ4_compressHC_continue_generic ((LZ4HC_Data_Structure*)LZ4_streamHCPtr, source, dest, inputSize, maxOutputSize, limitedOutput); +} + + +/* dictionary saving */ + +int LZ4_saveDictHC (LZ4_streamHC_t* LZ4_streamHCPtr, char* safeBuffer, int dictSize) +{ + LZ4HC_Data_Structure* streamPtr = (LZ4HC_Data_Structure*)LZ4_streamHCPtr; + int prefixSize = (int)(streamPtr->end - (streamPtr->base + streamPtr->dictLimit)); + if (dictSize > 64 KB) dictSize = 64 KB; + if (dictSize < 4) dictSize = 0; + if (dictSize > prefixSize) dictSize = prefixSize; + memcpy(safeBuffer, streamPtr->end - dictSize, dictSize); + { + U32 endIndex = (U32)(streamPtr->end - streamPtr->base); + streamPtr->end = (const BYTE*)safeBuffer + dictSize; + streamPtr->base = streamPtr->end - endIndex; + streamPtr->dictLimit = endIndex - dictSize; + streamPtr->lowLimit = endIndex - dictSize; + if (streamPtr->nextToUpdate < streamPtr->dictLimit) streamPtr->nextToUpdate = streamPtr->dictLimit; + } + return dictSize; +} + + +/*********************************** + * Deprecated Functions + ***********************************/ +int LZ4_sizeofStreamStateHC(void) { return LZ4_STREAMHCSIZE; } + +int LZ4_resetStreamStateHC(void* state, const char* inputBuffer) +{ + if ((((size_t)state) & (sizeof(void*)-1)) != 0) return 1; /* Error : pointer is not aligned for pointer (32 or 64 bits) */ + LZ4HC_init((LZ4HC_Data_Structure*)state, (const BYTE*)inputBuffer); + return 0; +} + +void* LZ4_createHC (const char* inputBuffer) +{ + void* hc4 = ALLOCATOR(1, sizeof(LZ4HC_Data_Structure)); + LZ4HC_init ((LZ4HC_Data_Structure*)hc4, (const BYTE*)inputBuffer); + return hc4; +} + +int LZ4_freeHC (void* LZ4HC_Data) +{ + FREEMEM(LZ4HC_Data); + return (0); +} + +/* +int LZ4_compressHC_continue (void* LZ4HC_Data, const char* source, char* dest, int inputSize) +{ +return LZ4HC_compress_generic (LZ4HC_Data, source, dest, inputSize, 0, 0, noLimit); +} +int LZ4_compressHC_limitedOutput_continue (void* LZ4HC_Data, const char* source, char* dest, int inputSize, int maxOutputSize) +{ +return LZ4HC_compress_generic (LZ4HC_Data, source, dest, inputSize, maxOutputSize, 0, limitedOutput); +} +*/ + +int LZ4_compressHC2_continue (void* LZ4HC_Data, const char* source, char* dest, int inputSize, int compressionLevel) +{ + return LZ4HC_compress_generic (LZ4HC_Data, source, dest, inputSize, 0, compressionLevel, noLimit); +} + +int LZ4_compressHC2_limitedOutput_continue (void* LZ4HC_Data, const char* source, char* dest, int inputSize, int maxOutputSize, int compressionLevel) +{ + return LZ4HC_compress_generic (LZ4HC_Data, source, dest, inputSize, maxOutputSize, compressionLevel, limitedOutput); +} + +char* LZ4_slideInputBufferHC(void* LZ4HC_Data) +{ + LZ4HC_Data_Structure* hc4 = (LZ4HC_Data_Structure*)LZ4HC_Data; + int dictSize = LZ4_saveDictHC((LZ4_streamHC_t*)LZ4HC_Data, (char*)(hc4->inputBuffer), 64 KB); + return (char*)(hc4->inputBuffer + dictSize); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4hc.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4hc.h new file mode 100644 index 0000000000000000000000000000000000000000..ce813abaa8999c0794966447e94ec8bffa20ed4a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/lz4hc.h @@ -0,0 +1,174 @@ +/* + LZ4 HC - High Compression Mode of LZ4 + Header File + Copyright (C) 2011-2014, Yann Collet. + BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php) + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are + met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following disclaimer + in the documentation and/or other materials provided with the + distribution. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + You can contact the author at : + - LZ4 homepage : http://fastcompression.blogspot.com/p/lz4.html + - LZ4 source repository : http://code.google.com/p/lz4/ +*/ +#pragma once + + +#if defined (__cplusplus) +extern "C" { +#endif + + +int LZ4_compressHC (const char* source, char* dest, int inputSize); +/* +LZ4_compressHC : + return : the number of bytes in compressed buffer dest + or 0 if compression fails. + note : destination buffer must be already allocated. + To avoid any problem, size it to handle worst cases situations (input data not compressible) + Worst case size evaluation is provided by function LZ4_compressBound() (see "lz4.h") +*/ + +int LZ4_compressHC_limitedOutput (const char* source, char* dest, int inputSize, int maxOutputSize); +/* +LZ4_compress_limitedOutput() : + Compress 'inputSize' bytes from 'source' into an output buffer 'dest' of maximum size 'maxOutputSize'. + If it cannot achieve it, compression will stop, and result of the function will be zero. + This function never writes outside of provided output buffer. + + inputSize : Max supported value is 1 GB + maxOutputSize : is maximum allowed size into the destination buffer (which must be already allocated) + return : the number of output bytes written in buffer 'dest' + or 0 if compression fails. +*/ + + +int LZ4_compressHC2 (const char* source, char* dest, int inputSize, int compressionLevel); +int LZ4_compressHC2_limitedOutput (const char* source, char* dest, int inputSize, int maxOutputSize, int compressionLevel); +/* + Same functions as above, but with programmable 'compressionLevel'. + Recommended values are between 4 and 9, although any value between 0 and 16 will work. + 'compressionLevel'==0 means use default 'compressionLevel' value. + Values above 16 behave the same as 16. + Equivalent variants exist for all other compression functions below. +*/ + +/* Note : + Decompression functions are provided within LZ4 source code (see "lz4.h") (BSD license) +*/ + + +/************************************** + Using an external allocation +**************************************/ +int LZ4_sizeofStateHC(void); +int LZ4_compressHC_withStateHC (void* state, const char* source, char* dest, int inputSize); +int LZ4_compressHC_limitedOutput_withStateHC (void* state, const char* source, char* dest, int inputSize, int maxOutputSize); + +int LZ4_compressHC2_withStateHC (void* state, const char* source, char* dest, int inputSize, int compressionLevel); +int LZ4_compressHC2_limitedOutput_withStateHC(void* state, const char* source, char* dest, int inputSize, int maxOutputSize, int compressionLevel); + +/* +These functions are provided should you prefer to allocate memory for compression tables with your own allocation methods. +To know how much memory must be allocated for the compression tables, use : +int LZ4_sizeofStateHC(); + +Note that tables must be aligned for pointer (32 or 64 bits), otherwise compression will fail (return code 0). + +The allocated memory can be provided to the compression functions using 'void* state' parameter. +LZ4_compress_withStateHC() and LZ4_compress_limitedOutput_withStateHC() are equivalent to previously described functions. +They just use the externally allocated memory for state instead of allocating their own (on stack, or on heap). +*/ + + + +/************************************** + Experimental Streaming Functions +**************************************/ +#define LZ4_STREAMHCSIZE_U64 32774 +#define LZ4_STREAMHCSIZE (LZ4_STREAMHCSIZE_U64 * sizeof(unsigned long long)) +typedef struct { unsigned long long table[LZ4_STREAMHCSIZE_U64]; } LZ4_streamHC_t; +/* +LZ4_streamHC_t +This structure allows static allocation of LZ4 HC streaming state. +State must then be initialized using LZ4_resetStreamHC() before first use. + +Static allocation should only be used with statically linked library. +If you want to use LZ4 as a DLL, please use construction functions below, which are more future-proof. +*/ + + +LZ4_streamHC_t* LZ4_createStreamHC(void); +int LZ4_freeStreamHC (LZ4_streamHC_t* LZ4_streamHCPtr); +/* +These functions create and release memory for LZ4 HC streaming state. +Newly created states are already initialized. +Existing state space can be re-used anytime using LZ4_resetStreamHC(). +If you use LZ4 as a DLL, please use these functions instead of direct struct allocation, +to avoid size mismatch between different versions. +*/ + +void LZ4_resetStreamHC (LZ4_streamHC_t* LZ4_streamHCPtr, int compressionLevel); +int LZ4_loadDictHC (LZ4_streamHC_t* LZ4_streamHCPtr, const char* dictionary, int dictSize); + +int LZ4_compressHC_continue (LZ4_streamHC_t* LZ4_streamHCPtr, const char* source, char* dest, int inputSize); +int LZ4_compressHC_limitedOutput_continue (LZ4_streamHC_t* LZ4_streamHCPtr, const char* source, char* dest, int inputSize, int maxOutputSize); + +int LZ4_saveDictHC (LZ4_streamHC_t* LZ4_streamHCPtr, char* safeBuffer, int maxDictSize); + +/* +These functions compress data in successive blocks of any size, using previous blocks as dictionary. +One key assumption is that each previous block will remain read-accessible while compressing next block. + +Before starting compression, state must be properly initialized, using LZ4_resetStreamHC(). +A first "fictional block" can then be designated as initial dictionary, using LZ4_loadDictHC() (Optional). + +Then, use LZ4_compressHC_continue() or LZ4_compressHC_limitedOutput_continue() to compress each successive block. +They work like usual LZ4_compressHC() or LZ4_compressHC_limitedOutput(), but use previous memory blocks to improve compression. +Previous memory blocks (including initial dictionary when present) must remain accessible and unmodified during compression. + +If, for any reason, previous data block can't be preserved in memory during next compression block, +you must save it to a safer memory space, +using LZ4_saveDictHC(). +*/ + + + +/************************************** + * Deprecated Streaming Functions + * ************************************/ +/* Note : these streaming functions follows the older model, and should no longer be used */ +void* LZ4_createHC (const char* inputBuffer); +char* LZ4_slideInputBufferHC (void* LZ4HC_Data); +int LZ4_freeHC (void* LZ4HC_Data); + +int LZ4_compressHC2_continue (void* LZ4HC_Data, const char* source, char* dest, int inputSize, int compressionLevel); +int LZ4_compressHC2_limitedOutput_continue (void* LZ4HC_Data, const char* source, char* dest, int inputSize, int maxOutputSize, int compressionLevel); + +int LZ4_sizeofStreamStateHC(void); +int LZ4_resetStreamStateHC(void* state, const char* inputBuffer); + + +#if defined (__cplusplus) +} +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/xxhash.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/xxhash.c new file mode 100644 index 0000000000000000000000000000000000000000..093564cf40676b08f7d94771cf681aecda293a90 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/xxhash.c @@ -0,0 +1,935 @@ +/* +xxHash - Fast Hash algorithm +Copyright (C) 2012-2015, Yann Collet + +BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php) + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + +* Redistributions of source code must retain the above copyright +notice, this list of conditions and the following disclaimer. +* Redistributions in binary form must reproduce the above +copyright notice, this list of conditions and the following disclaimer +in the documentation and/or other materials provided with the +distribution. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +You can contact the author at : +- xxHash source repository : http://code.google.com/p/xxhash/ +- xxHash source mirror : https://github.com/Cyan4973/xxHash +- public discussion board : https://groups.google.com/forum/#!forum/lz4c +*/ + + +/************************************** +* Tuning parameters +***************************************/ +/* Unaligned memory access is automatically enabled for "common" CPU, such as x86. + * For others CPU, the compiler will be more cautious, and insert extra code to ensure aligned access is respected. + * If you know your target CPU supports unaligned memory access, you want to force this option manually to improve performance. + * You can also enable this parameter if you know your input data will always be aligned (boundaries of 4, for U32). + */ +#if defined(__ARM_FEATURE_UNALIGNED) || defined(__i386) || defined(_M_IX86) || defined(__x86_64__) || defined(_M_X64) +# define XXH_USE_UNALIGNED_ACCESS 1 +#endif + +/* XXH_ACCEPT_NULL_INPUT_POINTER : + * If the input pointer is a null pointer, xxHash default behavior is to trigger a memory access error, since it is a bad pointer. + * When this option is enabled, xxHash output for null input pointers will be the same as a null-length input. + * By default, this option is disabled. To enable it, uncomment below define : + */ +/* #define XXH_ACCEPT_NULL_INPUT_POINTER 1 */ + +/* XXH_FORCE_NATIVE_FORMAT : + * By default, xxHash library provides endian-independant Hash values, based on little-endian convention. + * Results are therefore identical for little-endian and big-endian CPU. + * This comes at a performance cost for big-endian CPU, since some swapping is required to emulate little-endian format. + * Should endian-independance be of no importance for your application, you may set the #define below to 1. + * It will improve speed for Big-endian CPU. + * This option has no impact on Little_Endian CPU. + */ +#define XXH_FORCE_NATIVE_FORMAT 0 + + +/************************************** +* Compiler Specific Options +***************************************/ +#ifdef _MSC_VER /* Visual Studio */ +# pragma warning(disable : 4127) /* disable: C4127: conditional expression is constant */ +# define FORCE_INLINE static __forceinline +#else +# if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L /* C99 */ +# ifdef __GNUC__ +# define FORCE_INLINE static inline __attribute__((always_inline)) +# else +# define FORCE_INLINE static inline +# endif +# else +# define FORCE_INLINE static +# endif /* __STDC_VERSION__ */ +#endif + + +/************************************** +* Includes & Memory related functions +***************************************/ +#include "xxhash.h" +/* Modify the local functions below should you wish to use some other memory routines */ +/* for malloc(), free() */ +#include +static void* XXH_malloc(size_t s) { return malloc(s); } +static void XXH_free (void* p) { free(p); } +/* for memcpy() */ +#include +static void* XXH_memcpy(void* dest, const void* src, size_t size) +{ + return memcpy(dest,src,size); +} + + +/************************************** +* Basic Types +***************************************/ +#if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L /* C99 */ +# include +typedef uint8_t BYTE; +typedef uint16_t U16; +typedef uint32_t U32; +typedef int32_t S32; +typedef uint64_t U64; +#else +typedef unsigned char BYTE; +typedef unsigned short U16; +typedef unsigned int U32; +typedef signed int S32; +typedef unsigned long long U64; +#endif + +#if defined(__GNUC__) && !defined(XXH_USE_UNALIGNED_ACCESS) +# define _PACKED __attribute__ ((packed)) +#else +# define _PACKED +#endif + +#if !defined(XXH_USE_UNALIGNED_ACCESS) && !defined(__GNUC__) +# ifdef __IBMC__ +# pragma pack(1) +# else +# pragma pack(push, 1) +# endif +#endif + +typedef struct _U32_S +{ + U32 v; +} _PACKED U32_S; +typedef struct _U64_S +{ + U64 v; +} _PACKED U64_S; + +#if !defined(XXH_USE_UNALIGNED_ACCESS) && !defined(__GNUC__) +# pragma pack(pop) +#endif + +#define A32(x) (((U32_S *)(x))->v) +#define A64(x) (((U64_S *)(x))->v) + + +/***************************************** +* Compiler-specific Functions and Macros +******************************************/ +#define GCC_VERSION (__GNUC__ * 100 + __GNUC_MINOR__) + +/* Note : although _rotl exists for minGW (GCC under windows), performance seems poor */ +#if defined(_MSC_VER) +# define XXH_rotl32(x,r) _rotl(x,r) +# define XXH_rotl64(x,r) _rotl64(x,r) +#else +# define XXH_rotl32(x,r) ((x << r) | (x >> (32 - r))) +# define XXH_rotl64(x,r) ((x << r) | (x >> (64 - r))) +#endif + +#if defined(_MSC_VER) /* Visual Studio */ +# define XXH_swap32 _byteswap_ulong +# define XXH_swap64 _byteswap_uint64 +#elif GCC_VERSION >= 403 +# define XXH_swap32 __builtin_bswap32 +# define XXH_swap64 __builtin_bswap64 +#else +static U32 XXH_swap32 (U32 x) +{ + return ((x << 24) & 0xff000000 ) | + ((x << 8) & 0x00ff0000 ) | + ((x >> 8) & 0x0000ff00 ) | + ((x >> 24) & 0x000000ff ); +} +static U64 XXH_swap64 (U64 x) +{ + return ((x << 56) & 0xff00000000000000ULL) | + ((x << 40) & 0x00ff000000000000ULL) | + ((x << 24) & 0x0000ff0000000000ULL) | + ((x << 8) & 0x000000ff00000000ULL) | + ((x >> 8) & 0x00000000ff000000ULL) | + ((x >> 24) & 0x0000000000ff0000ULL) | + ((x >> 40) & 0x000000000000ff00ULL) | + ((x >> 56) & 0x00000000000000ffULL); +} +#endif + + +/************************************** +* Constants +***************************************/ +#define PRIME32_1 2654435761U +#define PRIME32_2 2246822519U +#define PRIME32_3 3266489917U +#define PRIME32_4 668265263U +#define PRIME32_5 374761393U + +#define PRIME64_1 11400714785074694791ULL +#define PRIME64_2 14029467366897019727ULL +#define PRIME64_3 1609587929392839161ULL +#define PRIME64_4 9650029242287828579ULL +#define PRIME64_5 2870177450012600261ULL + + +/*************************************** +* Architecture Macros +****************************************/ +typedef enum { XXH_bigEndian=0, XXH_littleEndian=1 } XXH_endianess; +#ifndef XXH_CPU_LITTLE_ENDIAN /* XXH_CPU_LITTLE_ENDIAN can be defined externally, for example using a compiler switch */ +static const int one = 1; +# define XXH_CPU_LITTLE_ENDIAN (*(char*)(&one)) +#endif + + +/************************************** +* Macros +***************************************/ +#define XXH_STATIC_ASSERT(c) { enum { XXH_static_assert = 1/(!!(c)) }; } /* use only *after* variable declarations */ + + +/**************************** +* Memory reads +*****************************/ +typedef enum { XXH_aligned, XXH_unaligned } XXH_alignment; + +FORCE_INLINE U32 XXH_readLE32_align(const void* ptr, XXH_endianess endian, XXH_alignment align) +{ + if (align==XXH_unaligned) + return endian==XXH_littleEndian ? A32(ptr) : XXH_swap32(A32(ptr)); + else + return endian==XXH_littleEndian ? *(U32*)ptr : XXH_swap32(*(U32*)ptr); +} + +FORCE_INLINE U32 XXH_readLE32(const void* ptr, XXH_endianess endian) +{ + return XXH_readLE32_align(ptr, endian, XXH_unaligned); +} + +FORCE_INLINE U64 XXH_readLE64_align(const void* ptr, XXH_endianess endian, XXH_alignment align) +{ + if (align==XXH_unaligned) + return endian==XXH_littleEndian ? A64(ptr) : XXH_swap64(A64(ptr)); + else + return endian==XXH_littleEndian ? *(U64*)ptr : XXH_swap64(*(U64*)ptr); +} + +FORCE_INLINE U64 XXH_readLE64(const void* ptr, XXH_endianess endian) +{ + return XXH_readLE64_align(ptr, endian, XXH_unaligned); +} + + +/**************************** +* Simple Hash Functions +*****************************/ +FORCE_INLINE U32 XXH32_endian_align(const void* input, size_t len, U32 seed, XXH_endianess endian, XXH_alignment align) +{ + const BYTE* p = (const BYTE*)input; + const BYTE* bEnd = p + len; + U32 h32; +#define XXH_get32bits(p) XXH_readLE32_align(p, endian, align) + +#ifdef XXH_ACCEPT_NULL_INPUT_POINTER + if (p==NULL) + { + len=0; + bEnd=p=(const BYTE*)(size_t)16; + } +#endif + + if (len>=16) + { + const BYTE* const limit = bEnd - 16; + U32 v1 = seed + PRIME32_1 + PRIME32_2; + U32 v2 = seed + PRIME32_2; + U32 v3 = seed + 0; + U32 v4 = seed - PRIME32_1; + + do + { + v1 += XXH_get32bits(p) * PRIME32_2; + v1 = XXH_rotl32(v1, 13); + v1 *= PRIME32_1; + p+=4; + v2 += XXH_get32bits(p) * PRIME32_2; + v2 = XXH_rotl32(v2, 13); + v2 *= PRIME32_1; + p+=4; + v3 += XXH_get32bits(p) * PRIME32_2; + v3 = XXH_rotl32(v3, 13); + v3 *= PRIME32_1; + p+=4; + v4 += XXH_get32bits(p) * PRIME32_2; + v4 = XXH_rotl32(v4, 13); + v4 *= PRIME32_1; + p+=4; + } + while (p<=limit); + + h32 = XXH_rotl32(v1, 1) + XXH_rotl32(v2, 7) + XXH_rotl32(v3, 12) + XXH_rotl32(v4, 18); + } + else + { + h32 = seed + PRIME32_5; + } + + h32 += (U32) len; + + while (p+4<=bEnd) + { + h32 += XXH_get32bits(p) * PRIME32_3; + h32 = XXH_rotl32(h32, 17) * PRIME32_4 ; + p+=4; + } + + while (p> 15; + h32 *= PRIME32_2; + h32 ^= h32 >> 13; + h32 *= PRIME32_3; + h32 ^= h32 >> 16; + + return h32; +} + + +unsigned int XXH32 (const void* input, size_t len, unsigned seed) +{ +#if 0 + /* Simple version, good for code maintenance, but unfortunately slow for small inputs */ + XXH32_state_t state; + XXH32_reset(&state, seed); + XXH32_update(&state, input, len); + return XXH32_digest(&state); +#else + XXH_endianess endian_detected = (XXH_endianess)XXH_CPU_LITTLE_ENDIAN; + +# if !defined(XXH_USE_UNALIGNED_ACCESS) + if ((((size_t)input) & 3) == 0) /* Input is aligned, let's leverage the speed advantage */ + { + if ((endian_detected==XXH_littleEndian) || XXH_FORCE_NATIVE_FORMAT) + return XXH32_endian_align(input, len, seed, XXH_littleEndian, XXH_aligned); + else + return XXH32_endian_align(input, len, seed, XXH_bigEndian, XXH_aligned); + } +# endif + + if ((endian_detected==XXH_littleEndian) || XXH_FORCE_NATIVE_FORMAT) + return XXH32_endian_align(input, len, seed, XXH_littleEndian, XXH_unaligned); + else + return XXH32_endian_align(input, len, seed, XXH_bigEndian, XXH_unaligned); +#endif +} + +FORCE_INLINE U64 XXH64_endian_align(const void* input, size_t len, U64 seed, XXH_endianess endian, XXH_alignment align) +{ + const BYTE* p = (const BYTE*)input; + const BYTE* bEnd = p + len; + U64 h64; +#define XXH_get64bits(p) XXH_readLE64_align(p, endian, align) + +#ifdef XXH_ACCEPT_NULL_INPUT_POINTER + if (p==NULL) + { + len=0; + bEnd=p=(const BYTE*)(size_t)32; + } +#endif + + if (len>=32) + { + const BYTE* const limit = bEnd - 32; + U64 v1 = seed + PRIME64_1 + PRIME64_2; + U64 v2 = seed + PRIME64_2; + U64 v3 = seed + 0; + U64 v4 = seed - PRIME64_1; + + do + { + v1 += XXH_get64bits(p) * PRIME64_2; + p+=8; + v1 = XXH_rotl64(v1, 31); + v1 *= PRIME64_1; + v2 += XXH_get64bits(p) * PRIME64_2; + p+=8; + v2 = XXH_rotl64(v2, 31); + v2 *= PRIME64_1; + v3 += XXH_get64bits(p) * PRIME64_2; + p+=8; + v3 = XXH_rotl64(v3, 31); + v3 *= PRIME64_1; + v4 += XXH_get64bits(p) * PRIME64_2; + p+=8; + v4 = XXH_rotl64(v4, 31); + v4 *= PRIME64_1; + } + while (p<=limit); + + h64 = XXH_rotl64(v1, 1) + XXH_rotl64(v2, 7) + XXH_rotl64(v3, 12) + XXH_rotl64(v4, 18); + + v1 *= PRIME64_2; + v1 = XXH_rotl64(v1, 31); + v1 *= PRIME64_1; + h64 ^= v1; + h64 = h64 * PRIME64_1 + PRIME64_4; + + v2 *= PRIME64_2; + v2 = XXH_rotl64(v2, 31); + v2 *= PRIME64_1; + h64 ^= v2; + h64 = h64 * PRIME64_1 + PRIME64_4; + + v3 *= PRIME64_2; + v3 = XXH_rotl64(v3, 31); + v3 *= PRIME64_1; + h64 ^= v3; + h64 = h64 * PRIME64_1 + PRIME64_4; + + v4 *= PRIME64_2; + v4 = XXH_rotl64(v4, 31); + v4 *= PRIME64_1; + h64 ^= v4; + h64 = h64 * PRIME64_1 + PRIME64_4; + } + else + { + h64 = seed + PRIME64_5; + } + + h64 += (U64) len; + + while (p+8<=bEnd) + { + U64 k1 = XXH_get64bits(p); + k1 *= PRIME64_2; + k1 = XXH_rotl64(k1,31); + k1 *= PRIME64_1; + h64 ^= k1; + h64 = XXH_rotl64(h64,27) * PRIME64_1 + PRIME64_4; + p+=8; + } + + if (p+4<=bEnd) + { + h64 ^= (U64)(XXH_get32bits(p)) * PRIME64_1; + h64 = XXH_rotl64(h64, 23) * PRIME64_2 + PRIME64_3; + p+=4; + } + + while (p> 33; + h64 *= PRIME64_2; + h64 ^= h64 >> 29; + h64 *= PRIME64_3; + h64 ^= h64 >> 32; + + return h64; +} + + +unsigned long long XXH64 (const void* input, size_t len, unsigned long long seed) +{ +#if 0 + /* Simple version, good for code maintenance, but unfortunately slow for small inputs */ + XXH64_state_t state; + XXH64_reset(&state, seed); + XXH64_update(&state, input, len); + return XXH64_digest(&state); +#else + XXH_endianess endian_detected = (XXH_endianess)XXH_CPU_LITTLE_ENDIAN; + +# if !defined(XXH_USE_UNALIGNED_ACCESS) + if ((((size_t)input) & 7)==0) /* Input is aligned, let's leverage the speed advantage */ + { + if ((endian_detected==XXH_littleEndian) || XXH_FORCE_NATIVE_FORMAT) + return XXH64_endian_align(input, len, seed, XXH_littleEndian, XXH_aligned); + else + return XXH64_endian_align(input, len, seed, XXH_bigEndian, XXH_aligned); + } +# endif + + if ((endian_detected==XXH_littleEndian) || XXH_FORCE_NATIVE_FORMAT) + return XXH64_endian_align(input, len, seed, XXH_littleEndian, XXH_unaligned); + else + return XXH64_endian_align(input, len, seed, XXH_bigEndian, XXH_unaligned); +#endif +} + +/**************************************************** + * Advanced Hash Functions +****************************************************/ + +/*** Allocation ***/ +typedef struct +{ + U64 total_len; + U32 seed; + U32 v1; + U32 v2; + U32 v3; + U32 v4; + U32 mem32[4]; /* defined as U32 for alignment */ + U32 memsize; +} XXH_istate32_t; + +typedef struct +{ + U64 total_len; + U64 seed; + U64 v1; + U64 v2; + U64 v3; + U64 v4; + U64 mem64[4]; /* defined as U64 for alignment */ + U32 memsize; +} XXH_istate64_t; + + +XXH32_state_t* XXH32_createState(void) +{ + XXH_STATIC_ASSERT(sizeof(XXH32_state_t) >= sizeof(XXH_istate32_t)); /* A compilation error here means XXH32_state_t is not large enough */ + return (XXH32_state_t*)XXH_malloc(sizeof(XXH32_state_t)); +} +XXH_errorcode XXH32_freeState(XXH32_state_t* statePtr) +{ + XXH_free(statePtr); + return XXH_OK; +} + +XXH64_state_t* XXH64_createState(void) +{ + XXH_STATIC_ASSERT(sizeof(XXH64_state_t) >= sizeof(XXH_istate64_t)); /* A compilation error here means XXH64_state_t is not large enough */ + return (XXH64_state_t*)XXH_malloc(sizeof(XXH64_state_t)); +} +XXH_errorcode XXH64_freeState(XXH64_state_t* statePtr) +{ + XXH_free(statePtr); + return XXH_OK; +} + + +/*** Hash feed ***/ + +XXH_errorcode XXH32_reset(XXH32_state_t* state_in, U32 seed) +{ + XXH_istate32_t* state = (XXH_istate32_t*) state_in; + state->seed = seed; + state->v1 = seed + PRIME32_1 + PRIME32_2; + state->v2 = seed + PRIME32_2; + state->v3 = seed + 0; + state->v4 = seed - PRIME32_1; + state->total_len = 0; + state->memsize = 0; + return XXH_OK; +} + +XXH_errorcode XXH64_reset(XXH64_state_t* state_in, unsigned long long seed) +{ + XXH_istate64_t* state = (XXH_istate64_t*) state_in; + state->seed = seed; + state->v1 = seed + PRIME64_1 + PRIME64_2; + state->v2 = seed + PRIME64_2; + state->v3 = seed + 0; + state->v4 = seed - PRIME64_1; + state->total_len = 0; + state->memsize = 0; + return XXH_OK; +} + + +FORCE_INLINE XXH_errorcode XXH32_update_endian (XXH32_state_t* state_in, const void* input, size_t len, XXH_endianess endian) +{ + XXH_istate32_t* state = (XXH_istate32_t *) state_in; + const BYTE* p = (const BYTE*)input; + const BYTE* const bEnd = p + len; + +#ifdef XXH_ACCEPT_NULL_INPUT_POINTER + if (input==NULL) return XXH_ERROR; +#endif + + state->total_len += len; + + if (state->memsize + len < 16) /* fill in tmp buffer */ + { + XXH_memcpy((BYTE*)(state->mem32) + state->memsize, input, len); + state->memsize += (U32)len; + return XXH_OK; + } + + if (state->memsize) /* some data left from previous update */ + { + XXH_memcpy((BYTE*)(state->mem32) + state->memsize, input, 16-state->memsize); + { + const U32* p32 = state->mem32; + state->v1 += XXH_readLE32(p32, endian) * PRIME32_2; + state->v1 = XXH_rotl32(state->v1, 13); + state->v1 *= PRIME32_1; + p32++; + state->v2 += XXH_readLE32(p32, endian) * PRIME32_2; + state->v2 = XXH_rotl32(state->v2, 13); + state->v2 *= PRIME32_1; + p32++; + state->v3 += XXH_readLE32(p32, endian) * PRIME32_2; + state->v3 = XXH_rotl32(state->v3, 13); + state->v3 *= PRIME32_1; + p32++; + state->v4 += XXH_readLE32(p32, endian) * PRIME32_2; + state->v4 = XXH_rotl32(state->v4, 13); + state->v4 *= PRIME32_1; + p32++; + } + p += 16-state->memsize; + state->memsize = 0; + } + + if (p <= bEnd-16) + { + const BYTE* const limit = bEnd - 16; + U32 v1 = state->v1; + U32 v2 = state->v2; + U32 v3 = state->v3; + U32 v4 = state->v4; + + do + { + v1 += XXH_readLE32(p, endian) * PRIME32_2; + v1 = XXH_rotl32(v1, 13); + v1 *= PRIME32_1; + p+=4; + v2 += XXH_readLE32(p, endian) * PRIME32_2; + v2 = XXH_rotl32(v2, 13); + v2 *= PRIME32_1; + p+=4; + v3 += XXH_readLE32(p, endian) * PRIME32_2; + v3 = XXH_rotl32(v3, 13); + v3 *= PRIME32_1; + p+=4; + v4 += XXH_readLE32(p, endian) * PRIME32_2; + v4 = XXH_rotl32(v4, 13); + v4 *= PRIME32_1; + p+=4; + } + while (p<=limit); + + state->v1 = v1; + state->v2 = v2; + state->v3 = v3; + state->v4 = v4; + } + + if (p < bEnd) + { + XXH_memcpy(state->mem32, p, bEnd-p); + state->memsize = (int)(bEnd-p); + } + + return XXH_OK; +} + +XXH_errorcode XXH32_update (XXH32_state_t* state_in, const void* input, size_t len) +{ + XXH_endianess endian_detected = (XXH_endianess)XXH_CPU_LITTLE_ENDIAN; + + if ((endian_detected==XXH_littleEndian) || XXH_FORCE_NATIVE_FORMAT) + return XXH32_update_endian(state_in, input, len, XXH_littleEndian); + else + return XXH32_update_endian(state_in, input, len, XXH_bigEndian); +} + + + +FORCE_INLINE U32 XXH32_digest_endian (const XXH32_state_t* state_in, XXH_endianess endian) +{ + XXH_istate32_t* state = (XXH_istate32_t*) state_in; + const BYTE * p = (const BYTE*)state->mem32; + BYTE* bEnd = (BYTE*)(state->mem32) + state->memsize; + U32 h32; + + if (state->total_len >= 16) + { + h32 = XXH_rotl32(state->v1, 1) + XXH_rotl32(state->v2, 7) + XXH_rotl32(state->v3, 12) + XXH_rotl32(state->v4, 18); + } + else + { + h32 = state->seed + PRIME32_5; + } + + h32 += (U32) state->total_len; + + while (p+4<=bEnd) + { + h32 += XXH_readLE32(p, endian) * PRIME32_3; + h32 = XXH_rotl32(h32, 17) * PRIME32_4; + p+=4; + } + + while (p> 15; + h32 *= PRIME32_2; + h32 ^= h32 >> 13; + h32 *= PRIME32_3; + h32 ^= h32 >> 16; + + return h32; +} + + +U32 XXH32_digest (const XXH32_state_t* state_in) +{ + XXH_endianess endian_detected = (XXH_endianess)XXH_CPU_LITTLE_ENDIAN; + + if ((endian_detected==XXH_littleEndian) || XXH_FORCE_NATIVE_FORMAT) + return XXH32_digest_endian(state_in, XXH_littleEndian); + else + return XXH32_digest_endian(state_in, XXH_bigEndian); +} + + +FORCE_INLINE XXH_errorcode XXH64_update_endian (XXH64_state_t* state_in, const void* input, size_t len, XXH_endianess endian) +{ + XXH_istate64_t * state = (XXH_istate64_t *) state_in; + const BYTE* p = (const BYTE*)input; + const BYTE* const bEnd = p + len; + +#ifdef XXH_ACCEPT_NULL_INPUT_POINTER + if (input==NULL) return XXH_ERROR; +#endif + + state->total_len += len; + + if (state->memsize + len < 32) /* fill in tmp buffer */ + { + XXH_memcpy(((BYTE*)state->mem64) + state->memsize, input, len); + state->memsize += (U32)len; + return XXH_OK; + } + + if (state->memsize) /* some data left from previous update */ + { + XXH_memcpy(((BYTE*)state->mem64) + state->memsize, input, 32-state->memsize); + { + const U64* p64 = state->mem64; + state->v1 += XXH_readLE64(p64, endian) * PRIME64_2; + state->v1 = XXH_rotl64(state->v1, 31); + state->v1 *= PRIME64_1; + p64++; + state->v2 += XXH_readLE64(p64, endian) * PRIME64_2; + state->v2 = XXH_rotl64(state->v2, 31); + state->v2 *= PRIME64_1; + p64++; + state->v3 += XXH_readLE64(p64, endian) * PRIME64_2; + state->v3 = XXH_rotl64(state->v3, 31); + state->v3 *= PRIME64_1; + p64++; + state->v4 += XXH_readLE64(p64, endian) * PRIME64_2; + state->v4 = XXH_rotl64(state->v4, 31); + state->v4 *= PRIME64_1; + p64++; + } + p += 32-state->memsize; + state->memsize = 0; + } + + if (p+32 <= bEnd) + { + const BYTE* const limit = bEnd - 32; + U64 v1 = state->v1; + U64 v2 = state->v2; + U64 v3 = state->v3; + U64 v4 = state->v4; + + do + { + v1 += XXH_readLE64(p, endian) * PRIME64_2; + v1 = XXH_rotl64(v1, 31); + v1 *= PRIME64_1; + p+=8; + v2 += XXH_readLE64(p, endian) * PRIME64_2; + v2 = XXH_rotl64(v2, 31); + v2 *= PRIME64_1; + p+=8; + v3 += XXH_readLE64(p, endian) * PRIME64_2; + v3 = XXH_rotl64(v3, 31); + v3 *= PRIME64_1; + p+=8; + v4 += XXH_readLE64(p, endian) * PRIME64_2; + v4 = XXH_rotl64(v4, 31); + v4 *= PRIME64_1; + p+=8; + } + while (p<=limit); + + state->v1 = v1; + state->v2 = v2; + state->v3 = v3; + state->v4 = v4; + } + + if (p < bEnd) + { + XXH_memcpy(state->mem64, p, bEnd-p); + state->memsize = (int)(bEnd-p); + } + + return XXH_OK; +} + +XXH_errorcode XXH64_update (XXH64_state_t* state_in, const void* input, size_t len) +{ + XXH_endianess endian_detected = (XXH_endianess)XXH_CPU_LITTLE_ENDIAN; + + if ((endian_detected==XXH_littleEndian) || XXH_FORCE_NATIVE_FORMAT) + return XXH64_update_endian(state_in, input, len, XXH_littleEndian); + else + return XXH64_update_endian(state_in, input, len, XXH_bigEndian); +} + + + +FORCE_INLINE U64 XXH64_digest_endian (const XXH64_state_t* state_in, XXH_endianess endian) +{ + XXH_istate64_t * state = (XXH_istate64_t *) state_in; + const BYTE * p = (const BYTE*)state->mem64; + BYTE* bEnd = (BYTE*)state->mem64 + state->memsize; + U64 h64; + + if (state->total_len >= 32) + { + U64 v1 = state->v1; + U64 v2 = state->v2; + U64 v3 = state->v3; + U64 v4 = state->v4; + + h64 = XXH_rotl64(v1, 1) + XXH_rotl64(v2, 7) + XXH_rotl64(v3, 12) + XXH_rotl64(v4, 18); + + v1 *= PRIME64_2; + v1 = XXH_rotl64(v1, 31); + v1 *= PRIME64_1; + h64 ^= v1; + h64 = h64*PRIME64_1 + PRIME64_4; + + v2 *= PRIME64_2; + v2 = XXH_rotl64(v2, 31); + v2 *= PRIME64_1; + h64 ^= v2; + h64 = h64*PRIME64_1 + PRIME64_4; + + v3 *= PRIME64_2; + v3 = XXH_rotl64(v3, 31); + v3 *= PRIME64_1; + h64 ^= v3; + h64 = h64*PRIME64_1 + PRIME64_4; + + v4 *= PRIME64_2; + v4 = XXH_rotl64(v4, 31); + v4 *= PRIME64_1; + h64 ^= v4; + h64 = h64*PRIME64_1 + PRIME64_4; + } + else + { + h64 = state->seed + PRIME64_5; + } + + h64 += (U64) state->total_len; + + while (p+8<=bEnd) + { + U64 k1 = XXH_readLE64(p, endian); + k1 *= PRIME64_2; + k1 = XXH_rotl64(k1,31); + k1 *= PRIME64_1; + h64 ^= k1; + h64 = XXH_rotl64(h64,27) * PRIME64_1 + PRIME64_4; + p+=8; + } + + if (p+4<=bEnd) + { + h64 ^= (U64)(XXH_readLE32(p, endian)) * PRIME64_1; + h64 = XXH_rotl64(h64, 23) * PRIME64_2 + PRIME64_3; + p+=4; + } + + while (p> 33; + h64 *= PRIME64_2; + h64 ^= h64 >> 29; + h64 *= PRIME64_3; + h64 ^= h64 >> 32; + + return h64; +} + + +unsigned long long XXH64_digest (const XXH64_state_t* state_in) +{ + XXH_endianess endian_detected = (XXH_endianess)XXH_CPU_LITTLE_ENDIAN; + + if ((endian_detected==XXH_littleEndian) || XXH_FORCE_NATIVE_FORMAT) + return XXH64_digest_endian(state_in, XXH_littleEndian); + else + return XXH64_digest_endian(state_in, XXH_bigEndian); +} + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/xxhash.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/xxhash.h new file mode 100644 index 0000000000000000000000000000000000000000..55b45015a447e44db6840aa679b435faf90abe3f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/lz4/xxhash.h @@ -0,0 +1,156 @@ +/* + xxHash - Extremely Fast Hash algorithm + Header File + Copyright (C) 2012-2014, Yann Collet. + BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php) + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are + met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following disclaimer + in the documentation and/or other materials provided with the + distribution. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + You can contact the author at : + - xxHash source repository : http://code.google.com/p/xxhash/ +*/ + +/* Notice extracted from xxHash homepage : + +xxHash is an extremely fast Hash algorithm, running at RAM speed limits. +It also successfully passes all tests from the SMHasher suite. + +Comparison (single thread, Windows Seven 32 bits, using SMHasher on a Core 2 Duo @3GHz) + +Name Speed Q.Score Author +xxHash 5.4 GB/s 10 +CrapWow 3.2 GB/s 2 Andrew +MumurHash 3a 2.7 GB/s 10 Austin Appleby +SpookyHash 2.0 GB/s 10 Bob Jenkins +SBox 1.4 GB/s 9 Bret Mulvey +Lookup3 1.2 GB/s 9 Bob Jenkins +SuperFastHash 1.2 GB/s 1 Paul Hsieh +CityHash64 1.05 GB/s 10 Pike & Alakuijala +FNV 0.55 GB/s 5 Fowler, Noll, Vo +CRC32 0.43 GB/s 9 +MD5-32 0.33 GB/s 10 Ronald L. Rivest +SHA1-32 0.28 GB/s 10 + +Q.Score is a measure of quality of the hash function. +It depends on successfully passing SMHasher test set. +10 is a perfect score. +*/ + +#pragma once + +#if defined (__cplusplus) +extern "C" { +#endif + + +/***************************** + Includes +*****************************/ +#include /* size_t */ + + +/***************************** + Type +*****************************/ +typedef enum { XXH_OK=0, XXH_ERROR } XXH_errorcode; + + + +/***************************** + Simple Hash Functions +*****************************/ + +unsigned int XXH32 (const void* input, size_t length, unsigned seed); +unsigned long long XXH64 (const void* input, size_t length, unsigned long long seed); + +/* +XXH32() : + Calculate the 32-bits hash of sequence "length" bytes stored at memory address "input". + The memory between input & input+length must be valid (allocated and read-accessible). + "seed" can be used to alter the result predictably. + This function successfully passes all SMHasher tests. + Speed on Core 2 Duo @ 3 GHz (single thread, SMHasher benchmark) : 5.4 GB/s +XXH64() : + Calculate the 64-bits hash of sequence of length "len" stored at memory address "input". +*/ + + + +/***************************** + Advanced Hash Functions +*****************************/ +typedef struct { long long ll[ 6]; } XXH32_state_t; +typedef struct { long long ll[11]; } XXH64_state_t; + +/* +These structures allow static allocation of XXH states. +States must then be initialized using XXHnn_reset() before first use. + +If you prefer dynamic allocation, please refer to functions below. +*/ + +XXH32_state_t* XXH32_createState(void); +XXH_errorcode XXH32_freeState(XXH32_state_t* statePtr); + +XXH64_state_t* XXH64_createState(void); +XXH_errorcode XXH64_freeState(XXH64_state_t* statePtr); + +/* +These functions create and release memory for XXH state. +States must then be initialized using XXHnn_reset() before first use. +*/ + + +XXH_errorcode XXH32_reset (XXH32_state_t* statePtr, unsigned seed); +XXH_errorcode XXH32_update (XXH32_state_t* statePtr, const void* input, size_t length); +unsigned int XXH32_digest (const XXH32_state_t* statePtr); + +XXH_errorcode XXH64_reset (XXH64_state_t* statePtr, unsigned long long seed); +XXH_errorcode XXH64_update (XXH64_state_t* statePtr, const void* input, size_t length); +unsigned long long XXH64_digest (const XXH64_state_t* statePtr); + +/* +These functions calculate the xxHash of an input provided in multiple smaller packets, +as opposed to an input provided as a single block. + +XXH state space must first be allocated, using either static or dynamic method provided above. + +Start a new hash by initializing state with a seed, using XXHnn_reset(). + +Then, feed the hash state by calling XXHnn_update() as many times as necessary. +Obviously, input must be valid, meaning allocated and read accessible. +The function returns an error code, with 0 meaning OK, and any other value meaning there is an error. + +Finally, you can produce a hash anytime, by using XXHnn_digest(). +This function returns the final nn-bits hash. +You can nonetheless continue feeding the hash state with more input, +and therefore get some new hashes, by calling again XXHnn_digest(). + +When you are done, don't forget to free XXH state space, using typically XXHnn_freeState(). +*/ + + +#if defined (__cplusplus) +} +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..c82d66a492cb637182c0dac7cff4e9b8d9d5ebb0 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/CMakeLists.txt @@ -0,0 +1,23 @@ +project(moderngpu) +cmake_minimum_required(VERSION 2.8) + +find_package(CUDA) +include_directories(${CUDA_INCLUDE_DIRS}) + +set(INSTALL_BIN_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory for executables") +set(INSTALL_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib" CACHE PATH "Installation directory for libraries") +set(INSTALL_INC_DIR "${CMAKE_INSTALL_PREFIX}/include" CACHE PATH "Installation directory for headers") +set(INSTALL_MAN_DIR "${CMAKE_INSTALL_PREFIX}/share/man" CACHE PATH "Installation directory for manual pages") +set(INSTALL_PKGCONFIG_DIR "${CMAKE_INSTALL_PREFIX}/share/pkgconfig" CACHE PATH "Installation directory for pkgconfig (.pc) files") + +include_directories(${CMAKE_CURRENT_BINARY_DIR} ${NVBIO_SOURCE_ROOT}/include) + +set(SRCS + src/mgpucontext.cu + src/mgpuutil.cpp + src/mmio.cpp + src/sparsematrix.cpp +) + +cuda_add_library(moderngpu STATIC ${SRCS}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/README.md b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/README.md new file mode 100644 index 0000000000000000000000000000000000000000..84435cf935d92d277c6c5665a52e27f6fa5c036f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/README.md @@ -0,0 +1,8 @@ +moderngpu +========= + +Design patterns for GPU computing + +Modern GPU is code and commentary intended to promote new and productive ways of thinking about GPU computing. + +http://nvlabs.github.io/moderngpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctaloadbalance.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctaloadbalance.cuh new file mode 100644 index 0000000000000000000000000000000000000000..391ca367251ce7375aae7d2be7779a2206b8a16c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctaloadbalance.cuh @@ -0,0 +1,136 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../device/ctasearch.cuh" +#include "../device/loadstore.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// DeviceLoadBalancingSearch +// Upper Bound search from A (needles) into B (haystack). The A values are +// natural numbers from aBegin to aEnd. bFirst is the index of the B value at +// bBegin in shared memory. + +template +MGPU_DEVICE void DeviceSerialLoadBalanceSearch(const int* b_shared, int aBegin, + int aEnd, int bFirst, int bBegin, int bEnd, int* a_shared) { + + int bKey = b_shared[bBegin]; + + #pragma unroll + for(int i = 0; i < VT; ++i) { + bool p; + if(RangeCheck) + p = (aBegin < aEnd) && ((bBegin >= bEnd) || (aBegin < bKey)); + else + p = aBegin < bKey; + + if(p) + // Advance A (the needle). + a_shared[aBegin++] = bFirst + bBegin; + else + // Advance B (the haystack). + bKey = b_shared[++bBegin]; + } +} + +//////////////////////////////////////////////////////////////////////////////// +// CTALoadBalance +// Computes upper_bound(counting_iterator(first), b_global) - 1. + +// Unlike most other CTA* functions, CTALoadBalance loads from global memory. +// This returns the loaded B elements at the beginning or end of shared memory +// depending on the aFirst argument. + +// CTALoadBalance requires NT * VT + 2 slots of shared memory. +template +MGPU_DEVICE int4 CTALoadBalance(int destCount, InputIt b_global, + int sourceCount, int block, int tid, const int* mp_global, + int* indices_shared, bool loadPrecedingB) { + + int4 range = ComputeMergeRange(destCount, sourceCount, block, 0, NT * VT, + mp_global); + + int a0 = range.x; + int a1 = range.y; + int b0 = range.z; + int b1 = range.w; + if(!b0) loadPrecedingB = false; + + // Load one trailing term from B. If we're already at the end, fill the + // end of the buffer with destCount. + int aCount = a1 - a0; + int bCount = b1 - b0; + int extended = b1 < sourceCount; + int loadCount = bCount + extended; + int fillCount = NT * VT + 1 - loadCount - aCount; + + int* a_shared = indices_shared; + int* b_shared = indices_shared + aCount + (int)loadPrecedingB; + + // Load the B values. +// DeviceMemToMemLoop(bCount + extended + (int)loadPrecedingB, +// b_global + b0 - (int)loadPrecedingB, tid, +// b_shared - (int)loadPrecedingB); + + for(int i = tid - (int)loadPrecedingB; i < bCount + extended; i += NT) + b_shared[i] = b_global[b0 + i]; + + // Fill the end of the array with destCount. + for(int i = tid + extended; i < fillCount; i += NT) + b_shared[bCount + i] = destCount; + __syncthreads(); + + // Run a merge path to find the start of the serial merge for each thread. + int diag = VT * tid; + int mp = MergePath(mgpu::counting_iterator(a0), + aCount, b_shared, bCount, diag, mgpu::less()); + + int a0tid = a0 + mp; + int b0tid = diag - mp; + + // Subtract 1 from b0 because we want to return upper_bound - 1. + DeviceSerialLoadBalanceSearch(b_shared, a0tid, a1, b0 - 1, + b0tid, bCount, a_shared - a0); + __syncthreads(); + + b0 -= (int)loadPrecedingB; + return make_int4(a0, a1, b0, b1); +} + + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctamerge.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctamerge.cuh new file mode 100644 index 0000000000000000000000000000000000000000..538f0ece4b923c867ab6eb3bb20dd520a2d2bb68 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctamerge.cuh @@ -0,0 +1,333 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../device/ctasearch.cuh" +#include "../device/loadstore.cuh" +#include "../device/sortnetwork.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// SerialMerge + +template +MGPU_DEVICE void SerialMerge(const T* keys_shared, int aBegin, int aEnd, + int bBegin, int bEnd, T* results, int* indices, Comp comp) { + + T aKey = keys_shared[aBegin]; + T bKey = keys_shared[bBegin]; + + #pragma unroll + for(int i = 0; i < VT; ++i) { + bool p; + if(RangeCheck) + p = (bBegin >= bEnd) || ((aBegin < aEnd) && !comp(bKey, aKey)); + else + p = !comp(bKey, aKey); + + results[i] = p ? aKey : bKey; + indices[i] = p ? aBegin : bBegin - !RangeCheck; + + if(p) aKey = keys_shared[++aBegin]; + else bKey = keys_shared[++bBegin]; + } + __syncthreads(); +} + +//////////////////////////////////////////////////////////////////////////////// +// FindMergeFrame and FindMergesortInterval help mergesort (both CTA and global +// merge pass levels) locate lists within the single source array. + +// Returns (offset of a, offset of b, length of list). +MGPU_HOST_DEVICE int3 FindMergesortFrame(int coop, int block, int nv) { + // coop is the number of CTAs or threads cooperating to merge two lists into + // one. We round block down to the first CTA's ID that is working on this + // merge. + int start = ~(coop - 1) & block; + int size = nv * (coop>> 1); + return make_int3(nv * start, nv * start + size, size); +} + +// Returns (a0, a1, b0, b1) into mergesort input lists between mp0 and mp1. +MGPU_HOST_DEVICE int4 FindMergesortInterval(int3 frame, int coop, int block, + int nv, int count, int mp0, int mp1) { + + // Locate diag from the start of the A sublist. + int diag = nv * block - frame.x; + int a0 = frame.x + mp0; + int a1 = min(count, frame.x + mp1); + int b0 = min(count, frame.y + diag - mp0); + int b1 = min(count, frame.y + diag + nv - mp1); + + // The end partition of the last block for each merge operation is computed + // and stored as the begin partition for the subsequent merge. i.e. it is + // the same partition but in the wrong coordinate system, so its 0 when it + // should be listSize. Correct that by checking if this is the last block + // in this merge operation. + if(coop - 1 == ((coop - 1) & block)) { + a1 = min(count, frame.x + frame.z); + b1 = min(count, frame.y + frame.z); + } + return make_int4(a0, a1, b0, b1); +} + +//////////////////////////////////////////////////////////////////////////////// +// ComputeMergeRange + +MGPU_HOST_DEVICE int4 ComputeMergeRange(int aCount, int bCount, int block, + int coop, int NV, const int* mp_global) { + + // Load the merge paths computed by the partitioning kernel. + int mp0 = mp_global[block]; + int mp1 = mp_global[block + 1]; + int gid = NV * block; + + // Compute the ranges of the sources in global memory. + int4 range; + if(coop) { + int3 frame = FindMergesortFrame(coop, block, NV); + range = FindMergesortInterval(frame, coop, block, NV, aCount, mp0, + mp1); + } else { + range.x = mp0; // a0 + range.y = mp1; // a1 + range.z = gid - range.x; // b0 + range.w = min(aCount + bCount, gid + NV) - range.y; // b1 + } + return range; +} + +//////////////////////////////////////////////////////////////////////////////// +// CTA mergesort support + +template +MGPU_DEVICE void CTABlocksortPass(T* keys_shared, int tid, int count, + int coop, T* keys, int* indices, Comp comp) { + + int list = ~(coop - 1) & tid; + int diag = min(count, VT * ((coop - 1) & tid)); + int start = VT * list; + int a0 = min(count, start); + int b0 = min(count, start + VT * (coop / 2)); + int b1 = min(count, start + VT * coop); + + int p = MergePath(keys_shared + a0, b0 - a0, + keys_shared + b0, b1 - b0, diag, comp); + + SerialMerge(keys_shared, a0 + p, b0, b0 + diag - p, b1, keys, + indices, comp); +} + +template +MGPU_DEVICE void CTABlocksortLoop(ValType threadValues[VT], + KeyType* keys_shared, ValType* values_shared, int tid, int count, + Comp comp) { + + #pragma unroll + for(int coop = 2; coop <= NT; coop *= 2) { + int indices[VT]; + KeyType keys[VT]; + CTABlocksortPass(keys_shared, tid, count, coop, keys, + indices, comp); + + if(HasValues) { + // Exchange the values through shared memory. + DeviceThreadToShared(threadValues, tid, values_shared); + DeviceGather(NT * VT, values_shared, indices, tid, + threadValues); + } + + // Store results in shared memory in sorted order. + DeviceThreadToShared(keys, tid, keys_shared); + } +} + +//////////////////////////////////////////////////////////////////////////////// +// CTAMergesort +// Caller provides the keys in shared memory. This functions sorts the first +// count elements. + +template +MGPU_DEVICE void CTAMergesort(KeyType threadKeys[VT], ValType threadValues[VT], + KeyType* keys_shared, ValType* values_shared, int count, int tid, + Comp comp) { + + // Stable sort the keys in the thread. + if(VT * tid < count) { + if(Stable) + OddEvenTransposeSort(threadKeys, threadValues, comp); + else + OddEvenMergesort(threadKeys, threadValues, comp); + } + + // Store the locally sorted keys into shared memory. + DeviceThreadToShared(threadKeys, tid, keys_shared); + + // Recursively merge lists until the entire CTA is sorted. + CTABlocksortLoop(threadValues, keys_shared, + values_shared, tid, count, comp); +} + +template +MGPU_DEVICE void CTAMergesortKeys(KeyType threadKeys[VT], + KeyType* keys_shared, int count, int tid, Comp comp) { + + int valuesTemp[VT]; + CTAMergesort(threadKeys, valuesTemp, keys_shared, + (int*)keys_shared, count, tid, comp); +} + +template +MGPU_DEVICE void CTAMergesortPairs(KeyType threadKeys[VT], + ValType threadValues[VT], KeyType* keys_shared, ValType* values_shared, + int count, int tid, Comp comp) { + + CTAMergesort(threadKeys, threadValues, keys_shared, + values_shared, count, tid, comp); +} + +//////////////////////////////////////////////////////////////////////////////// +// DeviceMergeKeysIndices + +template +MGPU_DEVICE void DeviceMergeKeysIndices(It1 a_global, int aCount, It2 b_global, + int bCount, int4 range, int tid, T* keys_shared, T* results, int* indices, + Comp comp) { + + int a0 = range.x; + int a1 = range.y; + int b0 = range.z; + int b1 = range.w; + + if(LoadExtended) { + bool extended = (a1 < aCount) && (b1 < bCount); + aCount = a1 - a0; + bCount = b1 - b0; + int aCount2 = aCount + (int)extended; + int bCount2 = bCount + (int)extended; + + // Load one element past the end of each input to avoid having to use + // range checking in the merge loop. + DeviceLoad2ToShared(a_global + a0, aCount2, + b_global + b0, bCount2, tid, keys_shared); + + // Run a Merge Path search for each thread's starting point. + int diag = VT * tid; + int mp = MergePath(keys_shared, aCount, + keys_shared + aCount2, bCount, diag, comp); + + // Compute the ranges of the sources in shared memory. + int a0tid = mp; + int b0tid = aCount2 + diag - mp; + if(extended) { + SerialMerge(keys_shared, a0tid, 0, b0tid, 0, results, + indices, comp); + } else { + int a1tid = aCount; + int b1tid = aCount2 + bCount; + SerialMerge(keys_shared, a0tid, a1tid, b0tid, b1tid, + results, indices, comp); + } + } else { + // Use the input intervals from the ranges between the merge path + // intersections. + aCount = a1 - a0; + bCount = b1 - b0; + + // Load the data into shared memory. + DeviceLoad2ToShared(a_global + a0, aCount, b_global + b0, + bCount, tid, keys_shared); + + // Run a merge path to find the start of the serial merge for each + // thread. + int diag = VT * tid; + int mp = MergePath(keys_shared, aCount, + keys_shared + aCount, bCount, diag, comp); + + // Compute the ranges of the sources in shared memory. + int a0tid = mp; + int a1tid = aCount; + int b0tid = aCount + diag - mp; + int b1tid = aCount + bCount; + + // Serial merge into register. + SerialMerge(keys_shared, a0tid, a1tid, b0tid, b1tid, results, + indices, comp); + } +} + +//////////////////////////////////////////////////////////////////////////////// +// DeviceMerge +// Merge pairs from global memory into global memory. Useful factorization to +// enable calling from merge, mergesort, and locality sort. + +template +MGPU_DEVICE void DeviceMerge(KeysIt1 aKeys_global, ValsIt1 aVals_global, + int aCount, KeysIt2 bKeys_global, ValsIt2 bVals_global, int bCount, + int tid, int block, int4 range, KeyType* keys_shared, int* indices_shared, + KeysIt3 keys_global, ValsIt3 vals_global, Comp comp) { + + KeyType results[VT]; + int indices[VT]; + DeviceMergeKeysIndices(aKeys_global, aCount, + bKeys_global, bCount, range, tid, keys_shared, results, indices, comp); + + // Store merge results back to shared memory. + DeviceThreadToShared(results, tid, keys_shared); + + // Store merged keys to global memory. + aCount = range.y - range.x; + bCount = range.w - range.z; + DeviceSharedToGlobal(aCount + bCount, keys_shared, tid, + keys_global + NT * VT * block); + + // Copy the values. + if(HasValues) { + DeviceThreadToShared(indices, tid, indices_shared); + + DeviceTransferMergeValuesShared(aCount + bCount, + aVals_global + range.x, bVals_global + range.z, aCount, + indices_shared, tid, vals_global + NT * VT * block); + } +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctascan.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctascan.cuh new file mode 100644 index 0000000000000000000000000000000000000000..dac45822bcd63e209b9e29f0c2a88c93de8325b2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctascan.cuh @@ -0,0 +1,308 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuenums.h" +#include "../device/deviceutil.cuh" +#include "../device/intrinsics.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// CTAReduce + +template > +struct CTAReduce { + typedef typename Op::first_argument_type T; + enum { Size = NT, Capacity = NT }; + struct Storage { T shared[Capacity]; }; + + MGPU_DEVICE static T Reduce(int tid, T x, Storage& storage, Op op = Op()) { + storage.shared[tid] = x; + __syncthreads(); + + // Fold the data in half with each pass. + #pragma unroll + for(int destCount = NT / 2; destCount >= 1; destCount /= 2) { + if(tid < destCount) { + // Read from the right half and store to the left half. + x = op(x, storage.shared[destCount + tid]); + storage.shared[tid] = x; + } + __syncthreads(); + } + T total = storage.shared[0]; + __syncthreads(); + return total; + } +}; + +#if __CUDA_ARCH__ >= 300 + +template +struct CTAReduce > { + typedef mgpu::plus Op; + typedef int T; + enum { Size = NT, Capacity = WARP_SIZE }; + struct Storage { int shared[Capacity]; }; + + MGPU_DEVICE static int Reduce(int tid, int x, Storage& storage, + Op op = Op()) { + + const int NumSections = WARP_SIZE; + const int SecSize = NT / NumSections; + int lane = (SecSize - 1) & tid; + int sec = tid / SecSize; + + // In the first phase, threads cooperatively find the reduction within + // their segment. The segments are SecSize threads (NT / WARP_SIZE) + // wide. + #pragma unroll + for(int offset = 1; offset < SecSize; offset *= 2) + x = shfl_add(x, offset, SecSize); + + // The last thread in each segment stores the local reduction to shared + // memory. + if(SecSize - 1 == lane) storage.shared[sec] = x; + __syncthreads(); + + // Reduce the totals of each input segment. The spine is WARP_SIZE + // threads wide. + if(tid < NumSections) { + x = storage.shared[tid]; + #pragma unroll + for(int offset = 1; offset < NumSections; offset *= 2) + x = shfl_add(x, offset, NumSections); + storage.shared[tid] = x; + } + __syncthreads(); + + int reduction = storage.shared[NumSections - 1]; + __syncthreads(); + + return reduction; + } +}; + +template +struct CTAReduce > { + typedef mgpu::maximum Op; + enum { Size = NT, Capacity = WARP_SIZE }; + struct Storage { int shared[Capacity]; }; + + MGPU_DEVICE static int Reduce(int tid, int x, Storage& storage, + Op op = Op()) { + + const int NumSections = WARP_SIZE; + const int SecSize = NT / NumSections; + int lane = (SecSize - 1) & tid; + int sec = tid / SecSize; + + #pragma unroll + for(int offset = 1; offset < SecSize; offset *= 2) + x = shfl_max(x, offset, SecSize); + + if(SecSize - 1 == lane) storage.shared[sec] = x; + __syncthreads(); + + if(tid < NumSections) { + x = storage.shared[tid]; + #pragma unroll + for(int offset = 1; offset < NumSections; offset *= 2) + x = shfl_max(x, offset, NumSections); + storage.shared[tid] = x; + } + __syncthreads(); + + int reduction = storage.shared[NumSections - 1]; + __syncthreads(); + + return reduction; + } +}; + +#endif // __CUDA_ARCH__ >= 300 + +//////////////////////////////////////////////////////////////////////////////// +// CTAScan + +template > +struct CTAScan { + typedef typename Op::result_type T; + enum { Size = NT, Capacity = 2 * NT + 1 }; + struct Storage { T shared[Capacity]; }; + + MGPU_DEVICE static T Scan(int tid, T x, Storage& storage, T* total, + MgpuScanType type = MgpuScanTypeExc, T identity = (T)0, Op op = Op()) { + + storage.shared[tid] = x; + int first = 0; + __syncthreads(); + + #pragma unroll + for(int offset = 1; offset < NT; offset += offset) { + if(tid >= offset) + x = op(storage.shared[first + tid - offset], x); + first = NT - first; + storage.shared[first + tid] = x; + __syncthreads(); + } + *total = storage.shared[first + NT - 1]; + + if(MgpuScanTypeExc == type) + x = tid ? storage.shared[first + tid - 1] : identity; + + __syncthreads(); + return x; + } + MGPU_DEVICE static T Scan(int tid, T x, Storage& storage) { + T total; + return Scan(tid, x, storage, &total, MgpuScanTypeExc, (T)0, Op()); + } +}; + +//////////////////////////////////////////////////////////////////////////////// +// Special partial specialization for CTAScan on Kepler. +// This uses the shfl intrinsic to reduce scan latency. + +#if __CUDA_ARCH__ >= 300 + +template +struct CTAScan > { + typedef mgpu::plus Op; + enum { Size = NT, NumSegments = WARP_SIZE, SegSize = NT / NumSegments }; + enum { Capacity = NumSegments + 1 }; + struct Storage { int shared[Capacity + 1]; }; + + MGPU_DEVICE static int Scan(int tid, int x, Storage& storage, int* total, + MgpuScanType type = MgpuScanTypeExc, int identity = 0, Op op = Op()) { + + // Define WARP_SIZE segments that are NT / WARP_SIZE large. + // Each warp makes log(SegSize) shfl_add calls. + // The spine makes log(WARP_SIZE) shfl_add calls. + int lane = (SegSize - 1) & tid; + int segment = tid / SegSize; + + // Scan each segment using shfl_add. + int scan = x; + #pragma unroll + for(int offset = 1; offset < SegSize; offset *= 2) + scan = shfl_add(scan, offset, SegSize); + + // Store the reduction (last element) of each segment into storage. + if(SegSize - 1 == lane) storage.shared[segment] = scan; + __syncthreads(); + + // Warp 0 does a full shfl warp scan on the partials. The total is + // stored to shared[NumSegments]. (NumSegments = WARP_SIZE) + if(tid < NumSegments) { + int y = storage.shared[tid]; + int scan = y; + #pragma unroll + for(int offset = 1; offset < NumSegments; offset *= 2) + scan = shfl_add(scan, offset, NumSegments); + storage.shared[tid] = scan - y; + if(NumSegments - 1 == tid) storage.shared[NumSegments] = scan; + } + __syncthreads(); + + // Add the scanned partials back in and convert to exclusive scan. + scan += storage.shared[segment]; + if(MgpuScanTypeExc == type) { + scan -= x; + if(identity && !tid) scan = identity; + } + *total = storage.shared[NumSegments]; + __syncthreads(); + + return scan; + } + MGPU_DEVICE static int Scan(int tid, int x, Storage& storage) { + int total; + return Scan(tid, x, storage, &total, MgpuScanTypeExc, 0); + } +}; + +#endif // __CUDA_ARCH__ >= 300 + +//////////////////////////////////////////////////////////////////////////////// +// CTABinaryScan + +template +MGPU_DEVICE int CTABinaryScan(int tid, bool x, int* shared, int* total) { + const int NumWarps = NT / WARP_SIZE; + int warp = tid / WARP_SIZE; + int lane = (WARP_SIZE - 1); + + // Store the bit totals for each warp. + uint bits = __ballot(x); + shared[warp] = popc(bits); + __syncthreads(); + +#if __CUDA_ARCH__ >= 300 + if(tid < NumWarps) { + int x = shared[tid]; + int scan = x; + #pragma unroll + for(int offset = 1; offset < NumWarps; offset *= 2) + scan = shfl_add(scan, offset, NumWarps); + shared[tid] = scan - x; + } + __syncthreads(); + +#else + // Thread 0 scans warp totals. + if(!tid) { + int scan = 0; + #pragma unroll + for(int i = 0; i < NumWarps; ++i) { + int y = shared[i]; + shared[i] = scan; + scan += y; + } + shared[NumWarps] = scan; + } + __syncthreads(); + +#endif // __CUDA_ARCH__ >= 300 + + // Add the warp scan back into the partials. + int scan = shared[warp] + __popc(bfe(bits, 0, lane)); + *total = shared[NumWarps]; + __syncthreads(); + return scan; +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasearch.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasearch.cuh new file mode 100644 index 0000000000000000000000000000000000000000..1a060023125c5f35dc0b34257327ed0db31ea98e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasearch.cuh @@ -0,0 +1,207 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../device/deviceutil.cuh" +#include "../mgpudevice.cuh" + +namespace mgpu { + +template +MGPU_HOST_DEVICE void BinarySearchIt(It data, int& begin, int& end, T key, + int shift, Comp comp) { + + IntT scale = (1<< shift) - 1; + int mid = (int)((begin + scale * end)>> shift); + + T key2 = data[mid]; + bool pred = (MgpuBoundsUpper == Bounds) ? + !comp(key, key2) : + comp(key2, key); + if(pred) begin = mid + 1; + else end = mid; +} + +template +MGPU_HOST_DEVICE int BiasedBinarySearch(It data, int count, T key, int levels, + Comp comp) { + + int begin = 0; + int end = count; + + if(levels >= 4 && begin < end) + BinarySearchIt(data, begin, end, key, 9, comp); + if(levels >= 3 && begin < end) + BinarySearchIt(data, begin, end, key, 7, comp); + if(levels >= 2 && begin < end) + BinarySearchIt(data, begin, end, key, 5, comp); + if(levels >= 1 && begin < end) + BinarySearchIt(data, begin, end, key, 4, comp); + + while(begin < end) + BinarySearchIt(data, begin, end, key, 1, comp); + return begin; +} + +template +MGPU_HOST_DEVICE int BinarySearch(It data, int count, T key, Comp comp) { + int begin = 0; + int end = count; + while(begin < end) + BinarySearchIt(data, begin, end, key, 1, comp); + return begin; +} + +//////////////////////////////////////////////////////////////////////////////// +// MergePath search + +template +MGPU_HOST_DEVICE int MergePath(It1 a, int aCount, It2 b, int bCount, int diag, + Comp comp) { + + typedef typename std::iterator_traits::value_type T; + int begin = max(0, diag - bCount); + int end = min(diag, aCount); + + while(begin < end) { + int mid = (begin + end)>> 1; + T aKey = a[mid]; + T bKey = b[diag - 1 - mid]; + bool pred = (MgpuBoundsUpper == Bounds) ? + comp(aKey, bKey) : + !comp(bKey, aKey); + if(pred) begin = mid + 1; + else end = mid; + } + return begin; +} + + +//////////////////////////////////////////////////////////////////////////////// +// SegmentedMergePath search + +template +MGPU_HOST_DEVICE int SegmentedMergePath(InputIt keys, int aOffset, int aCount, + int bOffset, int bCount, int leftEnd, int rightStart, int diag, Comp comp) { + + // leftEnd and rightStart are defined from the origin, and diag is defined + // from aOffset. + // We only need to run a Merge Path search if the diagonal intersects the + // segment that strides the left and right halves (i.e. is between leftEnd + // and rightStart). + if(aOffset + diag <= leftEnd) return diag; + if(aOffset + diag >= rightStart) return aCount; + + bCount = min(bCount, rightStart - bOffset); + int begin = max(max(leftEnd - aOffset, 0), diag - bCount); + int end = min(diag, aCount); + + while(begin < end) { + int mid = (begin + end)>> 1; + int ai = aOffset + mid; + int bi = bOffset + diag - 1 - mid; + + bool pred = !comp(keys[bi], keys[ai]); + if(pred) begin = mid + 1; + else end = mid; + } + return begin; +} + +//////////////////////////////////////////////////////////////////////////////// +// BalancedPath search + +template +MGPU_HOST_DEVICE int2 BalancedPath(InputIt1 a, int aCount, InputIt2 b, + int bCount, int diag, int levels, Comp comp) { + + typedef typename std::iterator_traits::value_type T; + + int p = MergePath(a, aCount, b, bCount, diag, comp); + int aIndex = p; + int bIndex = diag - p; + + bool star = false; + if(bIndex < bCount) { + if(Duplicates) { + T x = b[bIndex]; + + // Search for the beginning of the duplicate run in both A and B. + // Because + int aStart = BiasedBinarySearch(a, aIndex, x, + levels, comp); + int bStart = BiasedBinarySearch(b, bIndex, x, + levels, comp); + + // The distance between the merge path and the lower_bound is the + // 'run'. We add up the a- and b- runs and evenly distribute them to + // get a stairstep path. + int aRun = aIndex - aStart; + int bRun = bIndex - bStart; + int xCount = aRun + bRun; + + // Attempt to advance b and regress a. + int bAdvance = max(xCount>> 1, bRun); + int bEnd = min(bCount, bStart + bAdvance + 1); + int bRunEnd = BinarySearch(b + bIndex, + bEnd - bIndex, x, comp) + bIndex; + bRun = bRunEnd - bStart; + + bAdvance = min(bAdvance, bRun); + int aAdvance = xCount - bAdvance; + + bool roundUp = (aAdvance == bAdvance + 1) && (bAdvance < bRun); + aIndex = aStart + aAdvance; + + if(roundUp) star = true; + } else { + if(aIndex && aCount) { + T aKey = a[aIndex - 1]; + T bKey = b[bIndex]; + + // If the last consumed element in A (aIndex - 1) is the same as + // the next element in B (bIndex), we're sitting at a starred + // partition. + if(!comp(aKey, bKey)) star = true; + } + } + } + return make_int2(aIndex, star); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasegreduce.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasegreduce.cuh new file mode 100644 index 0000000000000000000000000000000000000000..cd7cc62608b9dbe1b5bba22903ee96c218cdb019 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasegreduce.cuh @@ -0,0 +1,238 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "ctasegscan.cuh" +#include "ctasearch.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// Segmented reduce utility functions. + +// Extract the upper-bound indices from the coded ranges. Decrement to include +// the first addressed row/segment. + +struct SegReduceRange { + int begin; + int end; + int total; + bool flushLast; +}; + +MGPU_DEVICE SegReduceRange DeviceShiftRange(int limit0, int limit1) { + SegReduceRange range; + range.begin = 0x7fffffff & limit0; + range.end = 0x7fffffff & limit1; + range.total = range.end - range.begin; + range.flushLast = 0 == (0x80000000 & limit1); + range.end += !range.flushLast; + return range; +} + +// Reconstitute row/segment indices from a starting row index and packed end +// flags. Used for pre-processed versions of interval reduce and interval Spmv. +template +MGPU_DEVICE void DeviceExpandFlagsToRows(int first, int endFlags, + int rows[VT + 1]) { + + rows[0] = first; + #pragma unroll + for(int i = 0; i < VT; ++i) { + if((1<< i) & endFlags) ++first; + rows[i + 1] = first; + } +} + +//////////////////////////////////////////////////////////////////////////////// +// After loading CSR terms into shared memory, each thread binary searches +// (upper-bound) to find its starting point. Each thread then walks forward, +// emitting the csr0-relative row indices to register. + +template +MGPU_DEVICE int DeviceExpandCsrRows(int tidOffset, int* csr_shared, + int numRows, int end, int rows[VT + 1], int rowStarts[VT]) { + + // Each thread binary searches for its starting row. + int row = BinarySearch(csr_shared, numRows, tidOffset, + mgpu::less()) - 1; + + // Each thread starts at row and scans forward, emitting row IDs into + // register. Store the CTA-local row index (starts at 0) to rows and the + // start of the row (globally) to rowStarts. + int curOffset = csr_shared[row]; + int nextOffset = (row + 1 < numRows) ? csr_shared[row + 1] : end; + + rows[0] = row; + rowStarts[0] = curOffset; + int endFlags = 0; + + #pragma unroll + for(int i = 1; i <= VT; ++i) { + // Advance the row cursor when the iterator hits the next row offset. + if(tidOffset + i == nextOffset) { + // Set an end flag when the cursor advances to the next row. + endFlags |= 1<< (i - 1); + + // Advance the cursor and load the next row offset. + ++row; + curOffset = nextOffset; + nextOffset = (row + 1 < numRows) ? csr_shared[row + 1] : end; + } + rows[i] = row; + if(i < VT) rowStarts[i] = curOffset; + } + __syncthreads(); + + return endFlags; +} + +//////////////////////////////////////////////////////////////////////////////// +// DeviceSegReducePrepare +// Expand non-empty interval of CSR elements into row indices. Compute end-flags +// by comparing adjacent row IDs. + +// DeviceSegReducePrepare may be called either by a pre-processing kernel or by +// the kernel that actually evaluates the segmented reduction if no preprocesing +// is desired. +struct SegReduceTerms { + int endFlags; + int tidDelta; +}; + +template +MGPU_DEVICE SegReduceTerms DeviceSegReducePrepare(int* csr_shared, int numRows, + int tid, int gid, bool flushLast, int rows[VT + 1], int rowStarts[VT]) { + + // Pass a sentinel (end) to point to the next segment start. If we flush, + // this is the end of this tile. Otherwise it is INT_MAX + int endFlags = DeviceExpandCsrRows(gid + VT * tid, csr_shared, + numRows, flushLast ? (gid + NT * VT) : INT_MAX, rows, rowStarts); + + // Find the distance to to scan to compute carry-in for each thread. Use the + // existance of an end flag anywhere in the thread to determine if carry-out + // values from the left should propagate through to the right. + int tidDelta = DeviceFindSegScanDelta(tid, rows[0] != rows[VT], + csr_shared); + + SegReduceTerms terms = { endFlags, tidDelta }; + return terms; +} + +//////////////////////////////////////////////////////////////////////////////// +// CTASegReduce +// Core segmented reduction code. Supports fast-path and slow-path for intra-CTA +// segmented reduction. Stores partials to global memory. +// Callers feed CTASegReduce::ReduceToGlobal values in thread order. +template +struct CTASegReduce { + typedef CTASegScan SegScan; + + enum { + NV = NT * VT, + Capacity = HalfCapacity ? (NV / 2) : NV + }; + + union Storage { + typename SegScan::Storage segScanStorage; + T values[Capacity]; + }; + + template + MGPU_DEVICE static void ReduceToGlobal(const int rows[VT + 1], int total, + int tidDelta, int startRow, int block, int tid, T data[VT], + DestIt dest_global, T* carryOut_global, T identity, Op op, + Storage& storage) { + + // Run a segmented scan within the thread. + T x, localScan[VT]; + #pragma unroll + for(int i = 0; i < VT; ++i) { + x = i ? op(x, data[i]) : data[i]; + localScan[i] = x; + if(rows[i] != rows[i + 1]) x = identity; + } + + // Run a parallel segmented scan over the carry-out values to compute + // carry-in. + T carryOut; + T carryIn = SegScan::SegScanDelta(tid, tidDelta, x, + storage.segScanStorage, &carryOut, identity, op); + + // Store the carry-out for the entire CTA to global memory. + if(!tid) carryOut_global[block] = carryOut; + + dest_global += startRow; + if(HalfCapacity && total > Capacity) { + // Add carry-in to each thread-local scan value. Store directly + // to global. + #pragma unroll + for(int i = 0; i < VT; ++i) { + // Add the carry-in to the local scan. + T x2 = op(carryIn, localScan[i]); + + // Store on the end flag and clear the carry-in. + if(rows[i] != rows[i + 1]) { + carryIn = identity; + dest_global[rows[i]] = x2; + } + } + } else { + // All partials fit in shared memory. Add carry-in to each thread- + // local scan value. + #pragma unroll + for(int i = 0; i < VT; ++i) { + // Add the carry-in to the local scan. + T x2 = op(carryIn, localScan[i]); + + // Store reduction when the segment changes and clear the + // carry-in. + if(rows[i] != rows[i + 1]) { + storage.values[rows[i]] = x2; + carryIn = identity; + } + } + __syncthreads(); + + // Cooperatively store reductions to global memory. + for(int index = tid; index < total; index += NT) + dest_global[index] = storage.values[index]; + __syncthreads(); + } + } +}; + +} // namespace mgpu + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasegscan.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasegscan.cuh new file mode 100644 index 0000000000000000000000000000000000000000..7830449ac27140116d401f3c07efae2e8c4d79d5 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasegscan.cuh @@ -0,0 +1,137 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../device/ctascan.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// DeviceFindSegScanDelta +// Runs an inclusive max-index scan over binary inputs. + +template +MGPU_DEVICE int DeviceFindSegScanDelta(int tid, bool flag, int* delta_shared) { + const int NumWarps = NT / 32; + + int warp = tid / 32; + int lane = 31 & tid; + uint warpMask = 0xffffffff>> (31 - lane); // inclusive search + uint ctaMask = 0x7fffffff>> (31 - lane); // exclusive search + + uint warpBits = __ballot(flag); + delta_shared[warp] = warpBits; + __syncthreads(); + + if(tid < NumWarps) { + uint ctaBits = __ballot(0 != delta_shared[tid]); + int warpSegment = 31 - clz(ctaMask & ctaBits); + int start = (-1 != warpSegment) ? + (31 - clz(delta_shared[warpSegment]) + 32 * warpSegment) : 0; + delta_shared[NumWarps + tid] = start; + } + __syncthreads(); + + // Find the closest flag to the left of this thread within the warp. + // Include the flag for this thread. + int start = 31 - clz(warpMask & warpBits); + if(-1 != start) start += ~31 & tid; + else start = delta_shared[NumWarps + warp]; + __syncthreads(); + + return tid - start; +} + +//////////////////////////////////////////////////////////////////////////////// +// CTASegScan + +template > +struct CTASegScan { + typedef _Op Op; + typedef typename Op::result_type T; + enum { NumWarps = NT / 32, Size = NT, Capacity = 2 * NT }; + union Storage { + int delta[NumWarps]; + T values[Capacity]; + }; + + // Each thread passes the reduction of the LAST SEGMENT that it covers. + // flag is set to true if there's at least one segment flag in the thread. + // SegScan returns the reduction of values for the first segment in this + // thread over the preceding threads. + // Return the value init for the first thread. + + // When scanning single elements per thread, interpret the flag as a BEGIN + // FLAG. If tid's flag is set, its value belongs to thread tid + 1, not + // thread tid. + + // The function returns the reduction of the last segment in the CTA. + + MGPU_DEVICE static T SegScanDelta(int tid, int tidDelta, T x, + Storage& storage, T* carryOut, T identity = (T)0, Op op = Op()) { + + // Run an inclusive scan + int first = 0; + storage.values[first + tid] = x; + __syncthreads(); + + #pragma unroll + for(int offset = 1; offset < NT; offset += offset) { + if(tidDelta >= offset) + x = op(storage.values[first + tid - offset], x); + first = NT - first; + storage.values[first + tid] = x; + __syncthreads(); + } + + // Get the exclusive scan. + x = tid ? storage.values[first + tid - 1] : identity; + *carryOut = storage.values[first + NT - 1]; + __syncthreads(); + return x; + } + + MGPU_DEVICE static T SegScan(int tid, T x, bool flag, Storage& storage, + T* carryOut, T identity = (T)0, Op op = Op()) { + + // Find the left-most thread that covers the first segment of this + // thread. + int tidDelta = DeviceFindSegScanDelta(tid, flag, storage.delta); + + return SegScanDelta(tid, tidDelta, x, storage, carryOut, identity, op); + } +}; + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasegsort.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasegsort.cuh new file mode 100644 index 0000000000000000000000000000000000000000..72cfec0e529c2af69d841648d0a7cd37e51356ed --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasegsort.cuh @@ -0,0 +1,443 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../device/ctascan.cuh" +#include "../device/ctasearch.cuh" +#include "../device/loadstore.cuh" +#include "../device/sortnetwork.cuh" + +namespace mgpu { + +template +MGPU_DEVICE void SegmentedSerialMerge(const T* keys_shared, int aBegin, + int aEnd, int bBegin, int bEnd, T results[VT], int indices[VT], + int leftEnd, int rightStart, Comp comp, bool sync = true) { + + bEnd = min(rightStart, bEnd); + T aKey = keys_shared[aBegin]; + T bKey = keys_shared[bBegin]; + + #pragma unroll + for(int i = 0; i < VT; ++i) { + bool p; + + // If A has run out of inputs, emit B. + if(aBegin >= aEnd) + p = false; + else if(bBegin >= bEnd || aBegin < leftEnd) + // B has hit the end of the middle segment. + // Emit A if A has inputs remaining in the middle segment. + p = true; + else + // Emit the smaller element in the middle segment. + p = !comp(bKey, aKey); + + results[i] = p ? aKey : bKey; + indices[i] = p ? aBegin : bBegin; + if(p) aKey = keys_shared[++aBegin]; + else bKey = keys_shared[++bBegin]; + } + if(sync) { __syncthreads(); } +} + +//////////////////////////////////////////////////////////////////////////////// +// CTASegsortPass + +template +MGPU_DEVICE void CTASegsortPass(T* keys_shared, int* ranges_shared, int tid, + int pass, T results[VT], int indices[VT], int2& activeRange, Comp comp) { + + // Locate the intervals of the input lists. + int3 frame = FindMergesortFrame(2<< pass, tid, VT); + int a0 = frame.x; + int b0 = frame.y; + int listLen = frame.z; + int list = tid>> pass; + int listParity = 1 & list; + int diag = VT * tid - frame.x; + + // Fetch the active range for the list this thread's list is merging with. + int siblingRange = ranges_shared[1 ^ list]; + int siblingStart = 0x0000ffff & siblingRange; + int siblingEnd = siblingRange>> 16; + + // Create a new active range for the merge. + int leftEnd = listParity ? siblingEnd : activeRange.y; + int rightStart = listParity ? activeRange.x : siblingStart; + activeRange.x = min(activeRange.x, siblingStart); + activeRange.y = max(activeRange.y, siblingEnd); + + int p = SegmentedMergePath(keys_shared, a0, listLen, b0, listLen, leftEnd, + rightStart, diag, comp); + + int a0tid = a0 + p; + int b0tid = b0 + diag - p; + SegmentedSerialMerge(keys_shared, a0tid, b0, b0tid, b0 + listLen, + results, indices, leftEnd, rightStart, comp); + + // Store the ranges to shared memory. + if(0 == diag) + ranges_shared[list>> 1] = + (int)bfi(activeRange.y, activeRange.x, 16, 16); +} + +//////////////////////////////////////////////////////////////////////////////// +// CTASegsortLoop + +template +MGPU_DEVICE int2 CTASegsortLoop(KeyType threadKeys[VT], + ValType threadValues[VT], KeyType* keys_shared, ValType* values_shared, + int* ranges_shared, int tid, int2 activeRange, Comp comp) { + + const int NumPasses = sLogPow2::value; + #pragma unroll + for(int pass = 0; pass < NumPasses; ++pass) { + int indices[VT]; + CTASegsortPass(keys_shared, ranges_shared, tid, pass, + threadKeys, indices, activeRange, comp); + + if(HasValues) { + // Exchange values through shared memory. + DeviceThreadToShared(threadValues, tid, values_shared); + DeviceGather(NT * VT, values_shared, indices, tid, + threadValues); + } + + // Store results in shared memory in sorted order. + DeviceThreadToShared(threadKeys, tid, keys_shared); + } + return activeRange; +} + +//////////////////////////////////////////////////////////////////////////////// +// CTASegsort +// Pass keys and values in register. On return, values are returned in register +// and keys returned in shared memory. + +template +MGPU_DEVICE int2 CTASegsort(KeyType threadKeys[VT], ValType threadValues[VT], + int tid, int headFlags, KeyType* keys_shared, ValType* values_shared, + int* ranges_shared, Comp comp) { + + if(Stable) + // Odd-even transpose sort. + OddEvenTransposeSortFlags(threadKeys, threadValues, headFlags, + comp); + else + // Batcher's odd-even mergesort. + OddEvenMergesortFlags(threadKeys, threadValues, headFlags, comp); + + // Record the first and last occurrence of head flags in this segment. + int blockEnd = 31 - clz(headFlags); + if(-1 != blockEnd) blockEnd += VT * tid; + + int blockStart = ffs(headFlags); + blockStart = blockStart ? (VT * tid - 1 + blockStart) : (NT * VT); + + ranges_shared[tid] = (int)bfi(blockEnd, blockStart, 16, 16); + + // Store back to shared mem. The values are in VT-length sorted lists. + // These are merged recursively. + DeviceThreadToShared(threadKeys, tid, keys_shared); + + int2 activeRange = CTASegsortLoop(threadKeys, + threadValues, keys_shared, values_shared, ranges_shared, tid, + make_int2(blockStart, blockEnd), comp); + return activeRange; +} + + +template +MGPU_DEVICE int2 CTASegsortKeys(KeyType threadKeys[VT], int tid, int headFlags, + KeyType* keys_shared, int* ranges_shared, Comp comp) { + + int valuesTemp[VT]; + return CTASegsort(threadKeys, valuesTemp, tid, + headFlags, keys_shared, (int*)keys_shared, ranges_shared, comp); +} + +template +MGPU_DEVICE int2 CTASegsortPairs(KeyType threadKeys[VT], + ValType threadValues[VT], int tid, int headFlags, KeyType* keys_shared, + ValType* values_shared, int* ranges_shared, Comp comp) { + + return CTASegsort(threadKeys, threadValues, tid, + headFlags, keys_shared, values_shared, ranges_shared, comp); +} + +//////////////////////////////////////////////////////////////////////////////// +// DeviceSegBlocksort +// Load keys and values from global memory, sort in shared memory, and store +// back to global memory. Store the left-most and right-most encountered +// headflag locations to ranges_global to prepare for the next pass. +// This function is factored out of the blocksort kernel to allow easier +// customization of that kernel - we have two implementations currently: +// sort over indices and sort over bitfield. + +template +MGPU_DEVICE void DeviceSegBlocksort(InputIt1 keys_global, + InputIt2 values_global, int count2, KeyType* keys_shared, + ValType* values_shared, int* ranges_shared, int headFlags, int tid, + int block, OutputIt1 keysDest_global, OutputIt2 valsDest_global, + int* ranges_global, Comp comp) { + + // Load keys into register in thread order. + int gid = NT * VT * block; + KeyType threadKeys[VT]; + DeviceGlobalToShared(count2, keys_global + gid, tid, keys_shared); + DeviceSharedToThread(keys_shared, tid, threadKeys); + + // Load the values from global memory and into register in thread order. + ValType threadValues[VT]; + if(HasValues) { + DeviceGlobalToShared(count2, values_global + gid, tid, + values_shared); + DeviceSharedToThread(values_shared, tid, threadValues); + } + + // Run the CTA segmented blocksort. + int2 activeRange = CTASegsort(threadKeys, + threadValues, tid, headFlags, keys_shared, values_shared, ranges_shared, + comp); + + // Store the keys to global memory. + DeviceSharedToGlobal(count2, keys_shared, tid, + keysDest_global + gid); + + if(HasValues) { + // Store the values to global memory.xk b + DeviceThreadToShared(threadValues, tid, values_shared); + DeviceSharedToGlobal(count2, values_shared, tid, + valsDest_global + gid, false); + } + + // Store the 16-bit packed ranges. These are used by all merge kernels and + // the first level of global segmented merge path partitioning. + if(!tid) + ranges_global[block] = bfi(activeRange.y, activeRange.x, 16, 16); +} + +//////////////////////////////////////////////////////////////////////////////// +// DeviceIndicesToHeadFlags +// Load indices from an array and cooperatively turn into a head flag bitfield +// for each thread. + +template +MGPU_DEVICE int DeviceIndicesToHeadFlags(const int* indices_global, + const int* partitions_global, int tid, int block, int count2, + int* words_shared, byte* flags_shared) { + + const int FlagWordsPerThread = MGPU_DIV_UP(VT, 4); + int gid = NT * VT * block; + int p0 = partitions_global[block]; + int p1 = partitions_global[block + 1]; + + int headFlags = 0; + if(p1 > p0 || count2 < NT * VT) { + + // Clear the flag bytes, then loop through the indices and poke in flag + // values. + #pragma unroll + for(int i = 0; i < FlagWordsPerThread; ++i) + words_shared[NT * i + tid] = 0; + __syncthreads(); + + for(int index = p0 + tid; index < p1; index += NT) { + int headFlag = indices_global[index]; + flags_shared[headFlag - gid] = 1; + } + __syncthreads(); + + // Combine all the head flags for this thread. + int first = VT * tid; + int offset = first / 4; + int prev = words_shared[offset]; + int mask = 0x3210 + 0x1111 * (3 & first); + #pragma unroll + for(int i = 0; i < FlagWordsPerThread; ++i) { + // Gather the next four flags. + int next = words_shared[offset + 1 + i]; + int x = prmt(prev, next, mask); + prev = next; + + // Set the head flag bits. + if(0x00000001 & x) headFlags |= 1<< (4 * i); + if(0x00000100 & x) headFlags |= 1<< (4 * i + 1); + if(0x00010000 & x) headFlags |= 1<< (4 * i + 2); + if(0x01000000 & x) headFlags |= 1<< (4 * i + 3); + } + __syncthreads(); + + // Set head flags for out-of-range keys. + int outOfRange = min(VT, first + VT - count2); + if(outOfRange > 0) + headFlags = bfi(0xffffffff, headFlags, VT - outOfRange, outOfRange); + + // Clear head flags above VT. + headFlags &= (1<< VT) - 1; + } + return headFlags; +} + +//////////////////////////////////////////////////////////////////////////////// +// SegSortSupport + +struct SegSortSupport { + int* ranges_global; + int2* ranges2_global; + + int4* mergeList_global; + int* copyList_global; + int2* queueCounters_global; + int2* nextCounters_global; + + byte* copyStatus_global; +}; + +//////////////////////////////////////////////////////////////////////////////// +// DeviceSegSortMerge + +template +MGPU_DEVICE void DeviceSegSortMerge(const KeyType* keys_global, + const ValueType* values_global, int2 segmentRange, int tid, + int block, int4 range, int pass, KeyType* keys_shared, + int* indices_shared, KeyType* keysDest_global, ValueType* valsDest_global, + Comp comp) { + + const int NV = NT * VT; + int gid = NV * block; + + // Load the local compressed segment indices. + int a0 = range.x; + int aCount = range.y - range.x; + int b0 = range.z; + int bCount = range.w - range.z; + + DeviceLoad2ToShared(keys_global + a0, aCount, keys_global + b0, + bCount, tid, keys_shared); + + //////////////////////////////////////////////////////////////////////////// + // Run a merge path to find the starting point for each thread to merge. + // If the entire warp fits into the already-sorted segments, we can skip + // sorting it and leave its keys in shared memory. Doing this on the warp + // level rather than thread level (also legal) gives slightly better + // performance. + + int segStart = segmentRange.x; + int segEnd = segmentRange.y; + int listParity = 1 & (block>> pass); + + int warpOffset = VT * (~31 & tid); + bool sortWarp = listParity ? + // The spliced segment is to the left (segStart). + (warpOffset < segStart) : + // The spliced segment is to the right (segEnd). + (warpOffset + 32 * VT > segEnd); + + KeyType threadKeys[VT]; + int indices[VT]; + if(sortWarp) { + int diag = VT * tid; + int mp = SegmentedMergePath(keys_shared, 0, aCount, aCount, bCount, + listParity ? 0 : segEnd, listParity ? segStart : NV, diag, comp); + int a0tid = mp; + int a1tid = aCount; + int b0tid = aCount + diag - mp; + int b1tid = aCount + bCount; + + // Serial merge into register. All threads in the CTA so we hoist the + // check for list parity outside the function call to simplify the + // logic. Unlike in the blocksort, this does not cause warp divergence. + SegmentedSerialMerge(keys_shared, a0tid, a1tid, b0tid, b1tid, + threadKeys, indices, listParity ? 0 : segEnd, + listParity ? segStart : NV, comp, false); + } + __syncthreads(); + + // Store sorted data in register back to shared memory. Then copy to global. + if(sortWarp) + DeviceThreadToShared(threadKeys, tid, keys_shared, false); + __syncthreads(); + + DeviceSharedToGlobal(aCount + bCount, keys_shared, tid, + keysDest_global + gid); + + //////////////////////////////////////////////////////////////////////////// + // Use the merge indices to gather values from global memory. Store directly + // to valsDest_global. + + if(HasValues) { + // Transpose the gather indices to help coalesce loads. + if(sortWarp) + DeviceThreadToShared(indices, tid, indices_shared, false); + else { + #pragma unroll + for(int i = 0; i < VT; ++i) + indices_shared[VT * tid + i] = VT * tid + i; + } + __syncthreads(); + + DeviceTransferMergeValuesShared(aCount + bCount, + values_global + a0, values_global + b0, aCount, indices_shared, + tid, valsDest_global + NV * block); + } +} + +//////////////////////////////////////////////////////////////////////////////// +// DeviceSegSortCopy + +template +MGPU_DEVICE void DeviceSegSortCopy(const KeyType* keys_global, + const ValueType* values_global, int tid, int block, int count, + KeyType* keysDest_global, ValueType* valsDest_global) { + + int gid = NT * VT * block; + int count2 = min(NT * VT, count - gid); + + DeviceGlobalToGlobal(count2, keys_global + gid, tid, + keysDest_global + gid); + if(HasValues) + DeviceGlobalToGlobal(count2, values_global + gid, tid, + valsDest_global + gid); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasortedsearch.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasortedsearch.cuh new file mode 100644 index 0000000000000000000000000000000000000000..a345babf1de200b778804a325a5ebd561a6aa03f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/ctasortedsearch.cuh @@ -0,0 +1,208 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpudevice.cuh" +#include "../device/ctasearch.cuh" + +namespace mgpu { + + +//////////////////////////////////////////////////////////////////////////////// +// DeviceSerialSearch + +template +MGPU_DEVICE int3 DeviceSerialSearch(const T* keys_shared, int aBegin, + int aEnd, int bBegin, int bEnd, int aOffset, int bOffset, int* indices, + Comp comp) { + + const int FlagA = IndexA ? 0x80000000 : 1; + const int FlagB = IndexB ? 0x80000000 : 1; + + T aKey = keys_shared[aBegin]; + T bKey = keys_shared[bBegin]; + T aPrev, bPrev; + if(aBegin > 0) aPrev = keys_shared[aBegin - 1]; + if(bBegin > 0) bPrev = keys_shared[bBegin - 1]; + int decisions = 0; + int matchCountA = 0; + int matchCountB = 0; + + #pragma unroll + for(int i = 0; i < VT; ++i) { + bool p; + if(RangeCheck && aBegin >= aEnd) p = false; + else if(RangeCheck && bBegin >= bEnd) p = true; + else p = (MgpuBoundsUpper == Bounds) ? + comp(aKey, bKey) : + !comp(bKey, aKey); + + if(p) { + // aKey is smaller than bKey, so it is inserted before bKey. + // Save bKey's index (bBegin + first) as the result of the search + // and advance to the next needle in A. + bool match = false; + if(MatchA) { + // Test if there is an element in B that matches aKey. + if(MgpuBoundsUpper == Bounds) { + // Upper Bound: We're inserting aKey after bKey. If there + // is a match for aKey it must be bPrev. Check that bPrev + // is in range and equal to aKey. + // The predicate test result !comp(aKey, bPrev) was + // established on the previous A-advancing iteration (it + // failed the comp(aKey, bKey) test to get us to this + // point). Check the other half of the equality condition + // with a second comparison. + bool inRange = !RangeCheck || (bBegin > aEnd); + match = inRange && !comp(bPrev, aKey); + } else { + // Lower Bound: We're inserting aKey before bKey. If there + // is a match for aKey, it must be bKey. Check that bKey + // is in range and equal to aKey. + // The predicate test !comp(bKey, aKey) has established one + // half of the equality condition. We establish the other + // half with a second comparison. + bool inRange = !RangeCheck || (bBegin < bEnd); + match = inRange && !comp(aKey, bKey); + } + } + + int index = 0; + if(IndexA) index = bOffset + bBegin; + if(match) index |= FlagA; + if(IndexA || MatchA) indices[i] = index; + matchCountA += match; + + // Mark the decision bit to indicate that this iteration has + // progressed A (the needles). + decisions |= 1<< i; + aPrev = aKey; + aKey = keys_shared[++aBegin]; + } else { + // aKey is larger than bKey, so it is inserted after bKey (but we + // don't know where yet). Advance the B index to the next element in + // the haystack to continue the search for the current needle. + bool match = false; + if(MatchB) { + if(MgpuBoundsUpper == Bounds) { + // Upper Bound: aKey is not smaller than bKey. We advance to + // the next haystack element in B. If there is a match in A + // for bKey it must be aKey. By entering this branch we've + // verified that !comp(aKey, bKey). Making the reciprocal + // comparison !comp(bKey, aKey) establishes aKey == bKey. + bool inRange = !RangeCheck || + ((bBegin < bEnd) && (aBegin < aEnd)); + match = inRange && !comp(bKey, aKey); + } else { + // Lower Bound: bKey is smaller than aKey. We advance to the + // next element in B. If there is a match for bKey, it must + // be aPrev. The previous A-advancing iteration proved that + // !comp(bKey, aPrev). We test !comp(aPrev, bKey) for the + // other half of the equality condition. + bool inRange = !RangeCheck || + ((bBegin < bEnd) && (aBegin > 0)); + match = inRange && !comp(aPrev, bKey); + } + } + + int index = 0; + if(IndexB) index = aOffset + aBegin; + if(match) index |= FlagB; + if(IndexB || MatchB) indices[i] = index; + matchCountB += match; + + // Keep the decision bit cleared to indicate that this iteration + // has progressed B (the haystack). + bPrev = bKey; + bKey = keys_shared[++bBegin]; + } + } + return make_int3(decisions, matchCountA, matchCountB); +} + +//////////////////////////////////////////////////////////////////////////////// +// CTASortedSearch +// Take keys in shared memory and return indices and b-match flags in shared +// memory. +// NOTE: This function doesn't do any strided-to-thread order transposes so +// using an even number of values per thread will incur no additional bank +// conflicts. + +template +MGPU_DEVICE int2 CTASortedSearch(T* keys_shared, int aStart, int aCount, + int aEnd, int a0, int bStart, int bCount, int bEnd, int b0, bool extended, + int tid, int* indices_shared, Comp comp) { + + // Run a merge path to find the start of the serial search for each thread. + int diag = VT * tid; + int mp = MergePath(keys_shared + aStart, aCount, + keys_shared + bStart, bCount, diag, comp); + int a0tid = mp; + int b0tid = diag - mp; + + // Serial search into register. + int3 results; + int indices[VT]; + if(extended) + results = DeviceSerialSearch(keys_shared, a0tid + aStart, aEnd, b0tid + bStart, bEnd, + a0 - aStart, b0 - bStart, indices, comp); + else + results = DeviceSerialSearch(keys_shared, a0tid + aStart, aEnd, b0tid + bStart, bEnd, + a0 - aStart, b0 - bStart, indices, comp); + __syncthreads(); + + // Compact the indices into shared memory. Use the decision bits (set is A, + // cleared is B) to select the destination. + int decisions = results.x; + b0tid += aCount; + #pragma unroll + for(int i = 0; i < VT; ++i) { + if((1<< i) & decisions) { + if(IndexA || MatchA) indices_shared[a0tid++] = indices[i]; + } else { + if(IndexB || MatchB) indices_shared[b0tid++] = indices[i]; + } + } + __syncthreads(); + + // Return the match counts for A and B keys. + return make_int2(results.y, results.z); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/devicetypes.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/devicetypes.cuh new file mode 100644 index 0000000000000000000000000000000000000000..282bedd5ab237e418d390f18578ecb5510e88687 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/devicetypes.cuh @@ -0,0 +1,363 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#if __CUDA_ARCH__ == 100 + #error "COMPUTE CAPABILITY 1.0 NOT SUPPORTED BY MPGU. TRY 2.0!" +#endif + +#include +#include "../util/static.h" + +#ifdef _MSC_VER +#define INLINESYMBOL __forceinline__ +#else +#define INLINESYMBOL inline +#endif + +namespace mgpu { + +#define MGPU_HOST __host__ INLINESYMBOL +#define MGPU_DEVICE __device__ INLINESYMBOL +#define MGPU_HOST_DEVICE __host__ __device__ INLINESYMBOL + +const int WARP_SIZE = 32; +const int LOG_WARP_SIZE = 5; + +//////////////////////////////////////////////////////////////////////////////// +// Device-side comparison operators + +template +struct less : public std::binary_function { + MGPU_HOST_DEVICE bool operator()(T a, T b) { return a < b; } +}; +template +struct less_equal : public std::binary_function { + MGPU_HOST_DEVICE bool operator()(T a, T b) { return a <= b; } +}; +template +struct greater : public std::binary_function { + MGPU_HOST_DEVICE bool operator()(T a, T b) { return a > b; } +}; +template +struct greater_equal : public std::binary_function { + MGPU_HOST_DEVICE bool operator()(T a, T b) { return a >= b; } +}; +template +struct equal_to : public std::binary_function { + MGPU_HOST_DEVICE bool operator()(T a, T b) { return a == b; } +}; +template +struct not_equal_to : public std::binary_function { + MGPU_HOST_DEVICE bool operator()(T a, T b) { return a != b; } +}; + +//////////////////////////////////////////////////////////////////////////////// +// Device-side arithmetic operators + +template +struct plus : public std::binary_function { + MGPU_HOST_DEVICE T operator()(T a, T b) { return a + b; } +}; + +template +struct minus : public std::binary_function { + MGPU_HOST_DEVICE T operator()(T a, T b) { return a - b; } +}; + +template +struct multiplies : public std::binary_function { + MGPU_HOST_DEVICE T operator()(T a, T b) { return a * b; } +}; + +template +struct modulus : public std::binary_function { + MGPU_HOST_DEVICE T operator()(T a, T b) { return a % b; } +}; + +template +struct bit_or : public std::binary_function { + MGPU_HOST_DEVICE T operator()(T a, T b) { return a | b; } +}; + +template +struct bit_and : public std::binary_function { + MGPU_HOST_DEVICE T operator()(T a, T b) { return a & b; } +}; + +template +struct bit_xor : public std::binary_function { + MGPU_HOST_DEVICE T operator()(T a, T b) { return a ^ b; } +}; + +template +struct maximum : public std::binary_function { + MGPU_HOST_DEVICE T operator()(T a, T b) { return max(a, b); } +}; + +template +struct minimum : public std::binary_function { + MGPU_HOST_DEVICE T operator()(T a, T b) { return min(a, b); } +}; + +//////////////////////////////////////////////////////////////////////////////// + +template +MGPU_HOST_DEVICE void swap(T& a, T& b) { + T c = a; + a = b; + b = c; +} + +template +struct DevicePair { + T x, y; +}; + +template +MGPU_HOST_DEVICE DevicePair MakeDevicePair(T x, T y) { + DevicePair p = { x, y }; + return p; +} + +template struct numeric_limits; +template<> struct numeric_limits { + MGPU_HOST_DEVICE static int min() { return INT_MIN; } + MGPU_HOST_DEVICE static int max() { return INT_MAX; } + MGPU_HOST_DEVICE static int lowest() { return INT_MIN; } + MGPU_HOST_DEVICE static int AddIdent() { return 0; } + MGPU_HOST_DEVICE static int MulIdent() { return 1; } +}; +template<> struct numeric_limits { + MGPU_HOST_DEVICE static long long min() { return LLONG_MIN; } + MGPU_HOST_DEVICE static long long max() { return LLONG_MAX; } + MGPU_HOST_DEVICE static long long lowest() { return LLONG_MIN; } + MGPU_HOST_DEVICE static long long AddIdent() { return 0; } + MGPU_HOST_DEVICE static long long MulIdent() { return 1; } +}; +template<> struct numeric_limits { + MGPU_HOST_DEVICE static uint min() { return 0; } + MGPU_HOST_DEVICE static uint max() { return UINT_MAX; } + MGPU_HOST_DEVICE static uint lowest() { return 0; } + MGPU_HOST_DEVICE static uint AddIdent() { return 0; } + MGPU_HOST_DEVICE static uint MulIdent() { return 1; } +}; +template<> struct numeric_limits { + MGPU_HOST_DEVICE static unsigned long long min() { return 0; } + MGPU_HOST_DEVICE static unsigned long long max() { return ULLONG_MAX; } + MGPU_HOST_DEVICE static unsigned long long lowest() { return 0; } + MGPU_HOST_DEVICE static unsigned long long AddIdent() { return 0; } + MGPU_HOST_DEVICE static unsigned long long MulIdent() { return 1; } +}; +template<> struct numeric_limits { + MGPU_HOST_DEVICE static float min() { return FLT_MIN; } + MGPU_HOST_DEVICE static float max() { return FLT_MAX; } + MGPU_HOST_DEVICE static float lowest() { return -FLT_MAX; } + MGPU_HOST_DEVICE static float AddIdent() { return 0; } + MGPU_HOST_DEVICE static float MulIdent() { return 1; } +}; +template<> struct numeric_limits { + MGPU_HOST_DEVICE static double min() { return DBL_MIN; } + MGPU_HOST_DEVICE static double max() { return DBL_MAX; } + MGPU_HOST_DEVICE static double lowest() { return -DBL_MAX; } + MGPU_HOST_DEVICE static double AddIdent() { return 0; } + MGPU_HOST_DEVICE static double MulIdent() { return 1; } +}; + + +MGPU_HOST_DEVICE int2 operator+(int2 a, int2 b) { + return make_int2(a.x + b.x, a.y + b.y); +} +MGPU_HOST_DEVICE int2& operator+=(int2& a, int2 b) { + a = a + b; + return a; +} +MGPU_HOST_DEVICE int2 operator*(int2 a, int2 b) { + return make_int2(a.x * b.x, a.y * b.y); +} +MGPU_HOST_DEVICE int2& operator*=(int2& a, int2 b) { + a = a * b; + return a; +} + +template +MGPU_HOST_DEVICE T max(T a, T b) { +#if !defined(__CUDA_ARCH__) || (__CUDA_ARCH__ < 100) + return std::max(a, b); +#else + return (a < b) ? b : a; +#endif +} +template +MGPU_HOST_DEVICE T min(T a, T b) { +#if !defined(__CUDA_ARCH__) || (__CUDA_ARCH__ < 100) + return std::min(a, b); +#else + return (b < a) ? b : a; +#endif +} + +MGPU_HOST_DEVICE int2 max(int2 a, int2 b) { + return make_int2(max(a.x, b.x), max(a.y, b.y)); +} + +MGPU_HOST_DEVICE int2 min(int2 a, int2 b) { + return make_int2(min(a.x, b.x), min(a.y, b.y)); +} + +template<> struct numeric_limits { + MGPU_HOST_DEVICE static int2 min() { return make_int2(INT_MIN, INT_MIN); } + MGPU_HOST_DEVICE static int2 max() { return make_int2(INT_MAX, INT_MAX); } + MGPU_HOST_DEVICE static int2 lowest() { + return make_int2(INT_MIN, INT_MIN); + } + MGPU_HOST_DEVICE static int2 AddIdent() { return make_int2(0, 0); } + MGPU_HOST_DEVICE static int2 MulIdent() { return make_int2(1, 1); } +}; + +template +class constant_iterator : public std::iterator_traits { +public: + MGPU_HOST_DEVICE constant_iterator(T value) : _value(value) { } + + MGPU_HOST_DEVICE T operator[](ptrdiff_t i) const { + return _value; + } + MGPU_HOST_DEVICE T operator*() const { + return _value; + } + MGPU_HOST_DEVICE constant_iterator operator+(ptrdiff_t diff) const { + return constant_iterator(_value); + } + MGPU_HOST_DEVICE constant_iterator operator-(ptrdiff_t diff) const { + return constant_iterator(_value); + } + MGPU_HOST_DEVICE constant_iterator& operator+=(ptrdiff_t diff) { + return *this; + } + MGPU_HOST_DEVICE constant_iterator& operator-=(ptrdiff_t diff) { + return *this; + } +private: + T _value; +}; + +template +class counting_iterator : public std::iterator_traits { +public: + MGPU_HOST_DEVICE counting_iterator(T value) : _value(value) { } + + MGPU_HOST_DEVICE T operator[](ptrdiff_t i) { + return _value + i; + } + MGPU_HOST_DEVICE T operator*() { + return _value; + } + MGPU_HOST_DEVICE counting_iterator operator+(ptrdiff_t diff) { + return counting_iterator(_value + diff); + } + MGPU_HOST_DEVICE counting_iterator operator-(ptrdiff_t diff) { + return counting_iterator(_value - diff); + } + MGPU_HOST_DEVICE counting_iterator& operator+=(ptrdiff_t diff) { + _value += diff; + return *this; + } + MGPU_HOST_DEVICE counting_iterator& operator-=(ptrdiff_t diff) { + _value -= diff; + return *this; + } +private: + T _value; +}; + +template +class step_iterator : public std::iterator_traits { +public: + MGPU_HOST_DEVICE step_iterator(T base, T step) : + _base(base), _step(step), _offset(0) { } + + MGPU_HOST_DEVICE T operator[](ptrdiff_t i) { + return _base + (_offset + i) * _step; + } + MGPU_HOST_DEVICE T operator*() { + return _base + _offset * _step; + } + MGPU_HOST_DEVICE step_iterator operator+(ptrdiff_t diff) { + step_iterator it = *this; + it._offset += diff; + return it; + } + MGPU_HOST_DEVICE step_iterator operator-(ptrdiff_t diff) { + step_iterator it = *this; + it._offset -= diff; + return it; + } + MGPU_HOST_DEVICE step_iterator& operator+=(ptrdiff_t diff) { + _offset += diff; + return *this; + } + MGPU_HOST_DEVICE step_iterator& operator-=(ptrdiff_t diff) { + _offset -= diff; + return *this; + } +private: + ptrdiff_t _offset; + T _base, _step; +}; + +} // namespace mgpu + + +template +MGPU_HOST_DEVICE mgpu::counting_iterator operator+(ptrdiff_t diff, + mgpu::counting_iterator it) { + return it + diff; +} +template +MGPU_HOST_DEVICE mgpu::counting_iterator operator-(ptrdiff_t diff, + mgpu::counting_iterator it) { + return it + (-diff); +} +template +MGPU_HOST_DEVICE mgpu::step_iterator operator+(ptrdiff_t diff, + mgpu::step_iterator it) { + return it + diff; +} +template +MGPU_HOST_DEVICE mgpu::step_iterator operator-(ptrdiff_t diff, + mgpu::step_iterator it) { + return it + (-diff); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/deviceutil.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/deviceutil.cuh new file mode 100644 index 0000000000000000000000000000000000000000..dd0c14cf7f32d30f67e3233fc638abd3a0de1d56 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/deviceutil.cuh @@ -0,0 +1,152 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../device/intrinsics.cuh" + +namespace mgpu { + +// NVBIO_VAR_UNUSED can be prepended to a variable to turn off unused variable warnings +// this should only be used when the variable actually is used and the warning is wrong +// (e.g., variables which are used only as template parameters for kernel launches) +#if defined(__GNUC__) +#define MGPU_VAR_UNUSED __attribute__((unused)) +#else +#define MGPU_VAR_UNUSED +#endif + +// Get the difference between two pointers in bytes. +MGPU_HOST_DEVICE ptrdiff_t PtrDiff(const void* a, const void* b) { + return (const byte*)b - (const byte*)a; +} + +// Offset a pointer by i bytes. +template +MGPU_HOST_DEVICE const T* PtrOffset(const T* p, ptrdiff_t i) { + return (const T*)((const byte*)p + i); +} +template +MGPU_HOST_DEVICE T* PtrOffset(T* p, ptrdiff_t i) { + return (T*)((byte*)p + i); +} + +//////////////////////////////////////////////////////////////////////////////// +// Task range support +// Evenly distributes variable-length arrays over a fixed number of CTAs. + +MGPU_HOST int2 DivideTaskRange(int numItems, int numWorkers) { + div_t d = div(numItems, numWorkers); + return make_int2(d.quot, d.rem); +} + +MGPU_HOST_DEVICE int2 ComputeTaskRange(int block, int2 task) { + int2 range; + range.x = task.x * block; + range.x += min(block, task.y); + range.y = range.x + task.x + (block < task.y); + return range; +} + +MGPU_HOST_DEVICE int2 ComputeTaskRange(int block, int2 task, int blockSize, + int count) { + int2 range = ComputeTaskRange(block, task); + range.x *= blockSize; + range.y = min(count, range.y * blockSize); + return range; +} + +//////////////////////////////////////////////////////////////////////////////// +// DeviceExtractHeadFlags +// Input array flags is a bit array with 32 head flags per word. +// ExtractThreadHeadFlags returns numBits flags starting at bit index. + +MGPU_HOST_DEVICE uint DeviceExtractHeadFlags(const uint* flags, int index, + int numBits) { + + int index2 = index>> 5; + int shift = 31 & index; + uint headFlags = flags[index2]>> shift; + int shifted = 32 - shift; + + if(shifted < numBits) + // We also need to shift in the next set of bits. + headFlags = bfi(flags[index2 + 1], headFlags, shifted, shift); + headFlags &= (1<< numBits) - 1; + return headFlags; +} + +//////////////////////////////////////////////////////////////////////////////// +// DevicePackHeadFlags +// Pack VT bits per thread at 32 bits/thread. Will consume an integer number of +// words, because CTA size is a multiple of 32. The first NT * VT / 32 threads +// return packed words. + +template +MGPU_DEVICE uint DevicePackHeadFlags(uint threadBits, int tid, + uint* flags_shared) { + + const int WordCount = NT * VT / 32; + + // Each thread stores its thread bits to flags_shared[tid]. + flags_shared[tid] = threadBits; + __syncthreads(); + + uint packed = 0; + if(tid < WordCount) { + const int Items = MGPU_DIV_UP(32, VT); + int index = 32 * tid; + int first = index / VT; + int bit = 0; + + int rem = index - VT * first; + packed = flags_shared[first]>> rem; + bit = VT - rem; + ++first; + + #pragma unroll + for(int i = 0; i < Items; ++i) { + if(i < Items - 1 || bit < 32) { + uint x = flags_shared[first + i]; + if(bit < 32) packed |= x<< bit; + bit += VT; + } + } + } + __syncthreads(); + + return packed; +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/intrinsics.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/intrinsics.cuh new file mode 100644 index 0000000000000000000000000000000000000000..bb571e0b5d2bbbbfc11a8fd8117af571b8d1e741 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/intrinsics.cuh @@ -0,0 +1,407 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#include "../device/devicetypes.cuh" + +#pragma once + +namespace mgpu { + +MGPU_HOST_DEVICE uint2 ulonglong_as_uint2(uint64 x) { + return *reinterpret_cast(&x); +} +MGPU_HOST_DEVICE uint64 uint2_as_ulonglong(uint2 x) { + return *reinterpret_cast(&x); +} + +MGPU_HOST_DEVICE int2 longlong_as_int2(int64 x) { + return *reinterpret_cast(&x); +} +MGPU_HOST_DEVICE int64 int2_as_longlong(int2 x) { + return *reinterpret_cast(&x); +} + +MGPU_HOST_DEVICE int2 double_as_int2(double x) { + return *reinterpret_cast(&x); +} +MGPU_HOST_DEVICE double int2_as_double(int2 x) { + return *reinterpret_cast(&x); +} + +MGPU_HOST_DEVICE void SetDoubleX(double& d, int x) { + reinterpret_cast(&d)[0] = x; +} +MGPU_HOST_DEVICE int GetDoubleX(double d) { + return double_as_int2(d).x; +} +MGPU_HOST_DEVICE void SetDoubleY(double& d, int y) { + reinterpret_cast(&d)[1] = y; +} +MGPU_HOST_DEVICE int GetDoubleY(double d) { + return double_as_int2(d).y; +} + + +//////////////////////////////////////////////////////////////////////////////// +// PTX for bfe and bfi + +#if __CUDA_ARCH__ >= 200 + +MGPU_DEVICE uint bfe_ptx(uint x, uint bit, uint numBits) { + uint result; + asm("bfe.u32 %0, %1, %2, %3;" : + "=r"(result) : "r"(x), "r"(bit), "r"(numBits)); + return result; +} + + +MGPU_DEVICE uint bfi_ptx(uint x, uint y, uint bit, uint numBits) { + uint result; + asm("bfi.b32 %0, %1, %2, %3, %4;" : + "=r"(result) : "r"(x), "r"(y), "r"(bit), "r"(numBits)); + return result; +} + +MGPU_DEVICE uint prmt_ptx(uint a, uint b, uint index) { + uint ret; + asm("prmt.b32 %0, %1, %2, %3;" : "=r"(ret) : "r"(a), "r"(b), "r"(index)); + return ret; +} + +#endif // __CUDA_ARCH__ >= 200 + + +//////////////////////////////////////////////////////////////////////////////// +// shfl_up + +__device__ __forceinline__ float shfl_up(float var, + unsigned int delta, int width = 32) { + +#if __CUDA_ARCH__ >= 300 + var = __shfl_up(var, delta, width); +#endif + return var; +} + +__device__ __forceinline__ double shfl_up(double var, + unsigned int delta, int width = 32) { + +#if __CUDA_ARCH__ >= 300 + int2 p = mgpu::double_as_int2(var); + p.x = __shfl_up(p.x, delta, width); + p.y = __shfl_up(p.y, delta, width); + var = mgpu::int2_as_double(p); +#endif + + return var; +} + +//////////////////////////////////////////////////////////////////////////////// +// shfl_add + +MGPU_DEVICE int shfl_add(int x, int offset, int width = WARP_SIZE) { + int result = 0; +#if __CUDA_ARCH__ >= 300 + int mask = (WARP_SIZE - width)<< 8; + asm( + "{.reg .s32 r0;" + ".reg .pred p;" + "shfl.up.b32 r0|p, %1, %2, %3;" + "@p add.s32 r0, r0, %4;" + "mov.s32 %0, r0; }" + : "=r"(result) : "r"(x), "r"(offset), "r"(mask), "r"(x)); +#endif + return result; +} + +MGPU_DEVICE int shfl_max(int x, int offset, int width = WARP_SIZE) { + int result = 0; +#if __CUDA_ARCH__ >= 300 + int mask = (WARP_SIZE - width)<< 8; + asm( + "{.reg .s32 r0;" + ".reg .pred p;" + "shfl.up.b32 r0|p, %1, %2, %3;" + "@p max.s32 r0, r0, %4;" + "mov.s32 %0, r0; }" + : "=r"(result) : "r"(x), "r"(offset), "r"(mask), "r"(x)); +#endif + return result; +} + +//////////////////////////////////////////////////////////////////////////////// +// brev, popc, clz, bfe, bfi, prmt + +// Reverse the bits in an integer. +MGPU_HOST_DEVICE uint brev(uint x) { +#if __CUDA_ARCH__ >= 200 + uint y = __brev(x); +#else + uint y = 0; + for(int i = 0; i < 32; ++i) + y |= (1 & (x>> i))<< (31 - i); +#endif + return y; +} + +// Count number of bits in a register. +MGPU_HOST_DEVICE int popc(uint x) { +#if __CUDA_ARCH__ >= 200 + return __popc(x); +#else + int c; + for(c = 0; x; ++c) + x &= x - 1; + return c; +#endif +} + +// Count leading zeros - start from most significant bit. +MGPU_HOST_DEVICE int clz(int x) { +#if __CUDA_ARCH__ >= 200 + return __clz(x); +#else + for(int i = 31; i >= 0; --i) + if((1<< i) & x) return 31 - i; + return 32; +#endif +} + +// Find first set - start from least significant bit. LSB is 1. ffs(0) is 0. +MGPU_HOST_DEVICE int ffs(int x) { +#if __CUDA_ARCH__ >= 200 + return __ffs(x); +#else + for(int i = 0; i < 32; ++i) + if((1<< i) & x) return i + 1; + return 0; +#endif +} + +MGPU_HOST_DEVICE uint bfe(uint x, uint bit, uint numBits) { +#if __CUDA_ARCH__ >= 200 + return bfe_ptx(x, bit, numBits); +#else + return ((1<< numBits) - 1) & (x>> bit); +#endif +} + +MGPU_HOST_DEVICE uint bfi(uint x, uint y, uint bit, uint numBits) { + uint result; +#if __CUDA_ARCH__ >= 200 + result = bfi_ptx(x, y, bit, numBits); +#else + if(bit + numBits > 32) numBits = 32 - bit; + uint mask = ((1<< numBits) - 1)<< bit; + result = y & ~mask; + result |= mask & (x<< bit); +#endif + return result; +} + +MGPU_HOST_DEVICE uint prmt(uint a, uint b, uint index) { + uint result; +#if __CUDA_ARCH__ >= 200 + result = prmt_ptx(a, b, index); +#else + result = 0; + for(int i = 0; i < 4; ++i) { + uint sel = 0xf & (index>> (4 * i)); + uint x = ((7 & sel) > 3) ? b : a; + x = 0xff & (x>> (8 * (3 & sel))); + if(8 & sel) x = (128 & x) ? 0xff : 0; + result |= x<< (8 * i); + } +#endif + return result; +} + +// Find log2(x) and optionally round up to the next integer logarithm. +MGPU_HOST_DEVICE int FindLog2(int x, bool roundUp = false) { + int a = 31 - clz(x); + if(roundUp) a += !MGPU_IS_POW_2(x); + return a; +} + +//////////////////////////////////////////////////////////////////////////////// +// vset4 + +#if __CUDA_ARCH__ >= 300 + +// Performs four byte-wise comparisons and returns 1 for each byte that +// satisfies the conditional, and zero otherwise. +MGPU_DEVICE uint vset4_lt_add_ptx(uint a, uint b, uint c) { + uint result; + asm("vset4.u32.u32.lt.add %0, %1, %2, %3;" : + "=r"(result) : "r"(a), "r"(b), "r"(c)); + return result; +} +MGPU_DEVICE uint vset4_eq_ptx(uint a, uint b) { + uint result; + asm("vset4.u32.u32.eq %0, %1, %2, %3;" : + "=r"(result) : "r"(a), "r"(b), "r"(0)); + return result; +} +#endif // __CUDA_ARCH__ >= 300 + +MGPU_HOST_DEVICE uint vset4_lt_add(uint a, uint b, uint c) { + uint result; +#if __CUDA_ARCH__ >= 300 + result = vset4_lt_add_ptx(a, b, c); +#else + result = c; + if((0x000000ff & a) < (0x000000ff & b)) result += 0x00000001; + if((0x0000ff00 & a) < (0x0000ff00 & b)) result += 0x00000100; + if((0x00ff0000 & a) < (0x00ff0000 & b)) result += 0x00010000; + if((0xff000000 & a) < (0xff000000 & b)) result += 0x01000000; +#endif + return result; +} + +MGPU_HOST_DEVICE uint vset4_eq(uint a, uint b) { + uint result; +#if __CUDA_ARCH__ >= 300 + result = vset4_eq_ptx(a, b); +#else + result = 0; + if((0x000000ff & a) == (0x000000ff & b)) result = 0x00000001; + if((0x0000ff00 & a) == (0x0000ff00 & b)) result += 0x00000100; + if((0x00ff0000 & a) == (0x00ff0000 & b)) result += 0x00010000; + if((0xff000000 & a) == (0xff000000 & b)) result += 0x01000000; +#endif + return result; +} + +//////////////////////////////////////////////////////////////////////////////// +// + +MGPU_HOST_DEVICE uint umulhi(uint x, uint y) { +#if __CUDA_ARCH__ >= 100 + return __umulhi(x, y); +#else + uint64 product = (uint64)x * y; + return (uint)(product>> 32); +#endif +} + +//////////////////////////////////////////////////////////////////////////////// +// ldg() function defined for all devices and all types. Only compiles to __ldg +// intrinsic for __CUDA_ARCH__ >= 320 && __CUDA_ARCH__ < 400 for types supported +// by __ldg in sm_32_intrinsics.h + +template +struct IsLdgType { + enum { value = false }; +}; +#define DEFINE_LDG_TYPE(T) \ + template<> struct IsLdgType { enum { value = true }; }; + +template::value> +struct LdgShim { + MGPU_DEVICE static T Ldg(const T* p) { + return *p; + } +}; + +#if __CUDA_ARCH__ >= 320 && __CUDA_ARCH__ < 400 + + // List of __ldg-compatible types from sm_32_intrinsics.h. + DEFINE_LDG_TYPE(char) + DEFINE_LDG_TYPE(short) + DEFINE_LDG_TYPE(int) + DEFINE_LDG_TYPE(long long) + DEFINE_LDG_TYPE(char2) + DEFINE_LDG_TYPE(char4) + DEFINE_LDG_TYPE(short2) + DEFINE_LDG_TYPE(short4) + DEFINE_LDG_TYPE(int2) + DEFINE_LDG_TYPE(int4) + DEFINE_LDG_TYPE(longlong2) + + DEFINE_LDG_TYPE(unsigned char) + DEFINE_LDG_TYPE(unsigned short) + DEFINE_LDG_TYPE(unsigned int) + DEFINE_LDG_TYPE(unsigned long long) + DEFINE_LDG_TYPE(uchar2) + DEFINE_LDG_TYPE(uchar4) + DEFINE_LDG_TYPE(ushort2) + DEFINE_LDG_TYPE(ushort4) + DEFINE_LDG_TYPE(uint2) + DEFINE_LDG_TYPE(uint4) + DEFINE_LDG_TYPE(ulonglong2) + + DEFINE_LDG_TYPE(float) + DEFINE_LDG_TYPE(double) + DEFINE_LDG_TYPE(float2) + DEFINE_LDG_TYPE(float4) + DEFINE_LDG_TYPE(double2) + + template struct LdgShim { + MGPU_DEVICE static T Ldg(const T* p) { + return __ldg(p); + } + }; +#endif + +template +MGPU_DEVICE T ldg(const T* p) { + return LdgShim::Ldg(p); +} + +//////////////////////////////////////////////////////////////////////////////// + +// Fast division for 31-bit integers. +// Uses the method in Hacker's Delight (2nd edition) page 228. +// Evaluates for denom > 1 and x < 2^31. +struct FastDivide { + uint denom; + uint coef; + uint shift; + + MGPU_HOST_DEVICE uint Divide(uint x) { + return umulhi(x, coef)>> shift; + } + MGPU_HOST_DEVICE uint Modulus(uint x) { + return x - Divide(x) * denom; + } + + explicit FastDivide(uint denom_) { + denom = denom_; + uint p = 31 + FindLog2(denom, true); + coef = (uint)(((1ull<< p) + denom - 1) / denom); + shift = p - 32; + } +}; + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/launchbox.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/launchbox.cuh new file mode 100644 index 0000000000000000000000000000000000000000..7087b253d27384e2ee9b101349f90ac76de95358 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/launchbox.cuh @@ -0,0 +1,97 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../util/mgpucontext.h" + +namespace mgpu { + +#if __CUDA_ARCH__ >= 350 + #define MGPU_SM_TAG Sm35 +#elif __CUDA_ARCH__ >= 300 + #define MGPU_SM_TAG Sm30 +#elif __CUDA_ARCH__ >= 200 + #define MGPU_SM_TAG Sm20 +#else + #define MGPU_SM_TAG Sm20 +#endif + +#define MGPU_LAUNCH_PARAMS typename Tuning::MGPU_SM_TAG +#define MGPU_LAUNCH_BOUNDS __global__ \ + __launch_bounds__(Tuning::MGPU_SM_TAG::NT, Tuning::MGPU_SM_TAG::OCC) + +// Returns (NT, VT) from the sm version. +template +struct LaunchBoxRuntime { + static int2 GetLaunchParams(CudaContext& context) { + return GetLaunchParams(context.PTXVersion()); + } + + static int2 GetLaunchParams(int sm) { + if(sm >= 350) + return make_int2(Derived::Sm35::NT, Derived::Sm35::VT); + else if(sm >= 300) + return make_int2(Derived::Sm30::NT, Derived::Sm30::VT); + else + return make_int2(Derived::Sm20::NT, Derived::Sm20::VT); + } +}; + +// General LaunchBox for any param types. +template< + typename Sm20_, + typename Sm30_ = Sm20_, + typename Sm35_ = Sm30_> +struct LaunchBox : LaunchBoxRuntime > { + typedef Sm20_ Sm20; + typedef Sm30_ Sm30; + typedef Sm35_ Sm35; +}; + +// LaunchBox over (NT, VT, NumBlocks) +template +struct LaunchParamsVT { + enum { NT = NT_, VT = VT_, OCC = OCC_ }; +}; +template< + int NT_SM20, int VT_SM20, int OCC_SM20 = 0, + int NT_SM30 = NT_SM20, int VT_SM30 = VT_SM20, int OCC_SM30 = OCC_SM20, + int NT_SM35 = NT_SM30, int VT_SM35 = VT_SM30, int OCC_SM35 = OCC_SM30> +struct LaunchBoxVT : LaunchBox< + LaunchParamsVT, + LaunchParamsVT, + LaunchParamsVT > { }; + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/loadstore.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/loadstore.cuh new file mode 100644 index 0000000000000000000000000000000000000000..2815e7c2fa5bd5fd3152a15d4a2f7c9d0e345500 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/loadstore.cuh @@ -0,0 +1,673 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpudevice.cuh" +#include "../device/deviceutil.cuh" +#include "../device/intrinsics.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// Cooperative load functions. + +template +MGPU_DEVICE void DeviceSharedToReg(InputIt data, int tid, T* reg, + bool sync) { + + #pragma unroll + for(int i = 0; i < VT; ++i) + reg[i] = data[NT * i + tid]; + + if(sync) __syncthreads(); +} + +template +MGPU_DEVICE void DeviceGlobalToRegPred(int count, InputIt data, int tid, + T* reg, bool sync) { + + // TODO: Attempt to issue 4 loads at a time. + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + if(index < count) reg[i] = data[index]; + } + if(sync) __syncthreads(); +} + +template +MGPU_DEVICE void DeviceGlobalToReg(int count, InputIt data, int tid, + T* reg, bool sync) { + + if(count >= NT * VT) { + #pragma unroll + for(int i = 0; i < VT; ++i) + reg[i] = data[NT * i + tid]; + } else + DeviceGlobalToRegPred(count, data, tid, reg, false); + if(sync) __syncthreads(); +} +template +MGPU_DEVICE void DeviceGlobalToReg2(int count, InputIt data, int tid, + T* reg, bool sync) { + + DeviceGlobalToReg(count, data, tid, reg, false); + #pragma unroll + for(int i = VT0; i < VT1; ++i) { + int index = NT * i + tid; + if(index < count) reg[i] = data[index]; + } + if(sync) __syncthreads(); +} + +template +MGPU_DEVICE void DeviceGlobalToRegDefault(int count, InputIt data, int tid, + T* reg, T init, bool sync) { + + if(count >= NT * VT) { + #pragma unroll + for(int i = 0; i < VT; ++i) + reg[i] = data[NT * i + tid]; + } else { + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + reg[i] = init; + if(index < count) reg[i] = data[index]; + } + } + if(sync) __syncthreads(); +} +template +MGPU_DEVICE void DeviceGlobalToRegDefault2(int count, InputIt data, int tid, + T* reg, T init, bool sync) { + + DeviceGlobalToRegDefault(count, data, tid, reg, init, false); + #pragma unroll + for(int i = VT0; i < VT1; ++i) { + int index = NT * i + tid; + reg[i] = init; + if(index < count) reg[i] = data[index]; + } + if(sync) __syncthreads(); +} + +//////////////////////////////////////////////////////////////////////////////// + +template +MGPU_DEVICE void DeviceGlobalToThread(int count, InputIt data, int tid, + T* reg) { + + data += VT * tid; + if(count >= NT * VT) { + #pragma unroll + for(int i = 0; i < VT; ++i) + reg[i] = ldg(data + i); + } else { + count -= VT * tid; + #pragma unroll + for(int i = 0; i < VT; ++i) + if(i < count) reg[i] = ldg(data + i); + } +} + +template +MGPU_DEVICE void DeviceGlobalToThreadDefault(int count, InputIt data, int tid, + T* reg, T init) { + + data += VT * tid; + if(count >= NT * VT) { + #pragma unroll + for(int i = 0; i < VT; ++i) + reg[i] = ldg(data + i); + } else { + count -= VT * tid; + #pragma unroll + for(int i = 0; i < VT; ++i) + reg[i] = (i < count) ? ldg(data + i) : init; + } +} + + +//////////////////////////////////////////////////////////////////////////////// +// Cooperative store functions. + +template +MGPU_DEVICE void DeviceRegToShared(const T* reg, int tid, + OutputIt dest, bool sync) { + + typedef typename std::iterator_traits::value_type T2; + #pragma unroll + for(int i = 0; i < VT; ++i) + dest[NT * i + tid] = (T2)reg[i]; + + if(sync) __syncthreads(); +} + +template +MGPU_DEVICE void DeviceRegToGlobal(int count, const T* reg, int tid, + OutputIt dest, bool sync) { + + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + if(index < count) + dest[index] = reg[i]; + } + if(sync) __syncthreads(); +} + +//////////////////////////////////////////////////////////////////////////////// +// DeviceMemToMemLoop +// Transfer from shared memory to global, or global to shared, for transfers +// that are smaller than NT * VT in the average case. The goal is to reduce +// unnecessary comparison logic. + +template +MGPU_DEVICE void DeviceMemToMem4(int count, InputIt source, int tid, + OutputIt dest, bool sync) { + + typedef typename std::iterator_traits::value_type T; + + T x[VT]; + const int Count = (VT < 4) ? VT : 4; + if(count >= NT * VT) { + #pragma unroll + for(int i = 0; i < Count; ++i) + x[i] = source[NT * i + tid]; + #pragma unroll + for(int i = 0; i < Count; ++i) + dest[NT * i + tid] = x[i]; + } else { + #pragma unroll + for(int i = 0; i < Count; ++i) { + int index = NT * i + tid; + if(index < count) + x[i] = source[NT * i + tid]; + } + #pragma unroll + for(int i = 0; i < Count; ++i) { + int index = NT * i + tid; + if(index < count) + dest[index] = x[i]; + } + } + if(sync) __syncthreads(); +} +template +MGPU_DEVICE void DeviceMemToMemLoop(int count, InputIt source, int tid, + OutputIt dest, bool sync) { + + for(int i = 0; i < count; i += 4 * NT) + DeviceMemToMem4(count - i, source + i, tid, dest + i, + false); + if(sync) __syncthreads(); +} + + +//////////////////////////////////////////////////////////////////////////////// +// Functions to copy between shared and global memory where the average case is +// to transfer NT * VT elements. + +template +MGPU_DEVICE void DeviceSharedToGlobal(int count, const T* source, int tid, + OutputIt dest, bool sync) { + + typedef typename std::iterator_traits::value_type T2; + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + if(index < count) dest[index] = (T2)source[index]; + } + if(sync) __syncthreads(); +} + +template +MGPU_DEVICE void DeviceGlobalToShared(int count, InputIt source, int tid, + T* dest, bool sync) { + + T reg[VT]; + DeviceGlobalToReg(count, source, tid, reg, false); + DeviceRegToShared(reg, tid, dest, sync); +} + +template +MGPU_DEVICE void DeviceGlobalToShared2(int count, InputIt source, int tid, + T* dest, bool sync) { + + T reg[VT1]; + DeviceGlobalToReg2(count, source, tid, reg, false); + DeviceRegToShared(reg, tid, dest, sync); +} + + +template +MGPU_DEVICE void DeviceGlobalToSharedDefault(int count, InputIt source, int tid, + T* dest, T init, bool sync) { + + T reg[VT]; + DeviceGlobalToRegDefault(count, source, tid, reg, init, false); + DeviceRegToShared(reg, tid, dest, sync); +} + +template +MGPU_DEVICE void DeviceGlobalToSharedDefault2(int count, InputIt data, int tid, + T* dest, T init, bool sync) { + + T reg[VT1]; + DeviceGlobalToRegDefault2(count, data, tid, reg, init, false); + DeviceRegToShared(reg, tid, dest, sync); +} + + +//////////////////////////////////////////////////////////////////////////////// + +template +MGPU_DEVICE void DeviceGlobalToSharedLoop(int count, InputIt source, int tid, + T* dest, bool sync) { + + const int Granularity = MGPU_MIN(VT, 3); + DeviceGlobalToShared(count, source, tid, dest, false); + + int offset = Granularity * NT; + if(count > offset) + DeviceGlobalToShared(count - offset, + source + offset, tid, dest + offset, false); + + if(sync) __syncthreads(); + + /* + source += tid; + while(count > 0) { + T reg[Granularity]; + #pragma unroll + for(int i = 0; i < Granularity; ++i) { + int index = NT * i + tid; + if(index < count) + reg[i] = source[NT * i]; + } + DeviceRegToShared(reg, tid, dest, false); + source += Granularity * NT; + dest += Granularity * NT; + count -= Granularity * NT; + } + if(sync) __syncthreads();*/ +} + +template +MGPU_DEVICE void DeviceGlobalToGlobal(int count, InputIt source, int tid, + OutputIt dest, bool sync) { + + typedef typename std::iterator_traits::value_type T; + T values[VT]; + DeviceGlobalToReg(count, source, tid, values, false); + DeviceRegToGlobal(count, values, tid, dest, sync); +} + +//////////////////////////////////////////////////////////////////////////////// +// Transponse VT elements in NT threads (x) into thread-order registers (y) +// using only NT * VT / 2 elements of shared memory. + +template +MGPU_DEVICE void HalfSmemTranspose(const T* x, int tid, T* shared, T* y) { + + // Transpose the first half values (tid < NT / 2) + #pragma unroll + for(int i = 0; i <= VT / 2; ++i) + if(i < VT / 2 || tid < NT / 2) + shared[NT * i + tid] = x[i]; + __syncthreads(); + + if(tid < NT / 2) { + #pragma unroll + for(int i = 0; i < VT; ++i) + y[i] = shared[VT * tid + i]; + } + __syncthreads(); + + // Transpose the second half values (tid >= NT / 2) + #pragma unroll + for(int i = VT / 2; i < VT; ++i) + if(i > VT / 2 || tid >= NT / 2) + shared[NT * i - NT * VT / 2 + tid] = x[i]; + __syncthreads(); + + if(tid >= NT / 2) { + #pragma unroll + for(int i = 0; i < VT; ++i) + y[i] = shared[VT * tid + i - NT * VT / 2]; + } + __syncthreads(); +} + +//////////////////////////////////////////////////////////////////////////////// +// Gather/scatter functions + +template +MGPU_DEVICE void DeviceGather(int count, InputIt data, int indices[VT], + int tid, T* reg, bool sync) { + + if(count >= NT * VT) { + #pragma unroll + for(int i = 0; i < VT; ++i) + reg[i] = data[indices[i]]; + } else { + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + if(index < count) + reg[i] = data[indices[i]]; + } + } + if(sync) __syncthreads(); +} + +template +MGPU_DEVICE void DeviceGatherDefault(int count, InputIt data, int indices[VT], + int tid, T* reg, T identity, bool sync) { + + if(count >= NT * VT) { + #pragma unroll + for(int i = 0; i < VT; ++i) + reg[i] = data[indices[i]]; + } else { + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + reg[i] = (index < count) ? data[indices[i]] : identity; + } + } + if(sync) __syncthreads(); +} + +template +MGPU_DEVICE void DeviceScatter(int count, const T* reg, int tid, + int indices[VT], OutputIt data, bool sync) { + + if(count >= NT * VT) { + #pragma unroll + for(int i = 0; i < VT; ++i) + data[indices[i]] = reg[i]; + } else { + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + if(index < count) + data[indices[i]] = reg[i]; + } + } + if(sync) __syncthreads(); +} + +//////////////////////////////////////////////////////////////////////////////// +// Cooperative transpose functions (strided to thread order) + +template +MGPU_DEVICE void DeviceThreadToShared(const T* threadReg, int tid, T* shared, + bool sync) { + + if(1 & VT) { + // Odd grain size. Store as type T. + #pragma unroll + for(int i = 0; i < VT; ++i) + shared[VT * tid + i] = threadReg[i]; + } else { + // Even grain size. Store as DevicePair. This lets us exploit the + // 8-byte shared memory mode on Kepler. + DevicePair* dest = (DevicePair*)(shared + VT * tid); + #pragma unroll + for(int i = 0; i < VT / 2; ++i) + dest[i] = MakeDevicePair(threadReg[2 * i], threadReg[2 * i + 1]); + } + if(sync) __syncthreads(); +} + +template +MGPU_DEVICE void DeviceSharedToThread(const T* shared, int tid, T* threadReg, + bool sync) { + + if(1 & VT) { + #pragma unroll + for(int i = 0; i < VT; ++i) + threadReg[i] = shared[VT * tid + i]; + } else { + const DevicePair* source = (const DevicePair*)(shared + VT * tid); + #pragma unroll + for(int i = 0; i < VT / 2; ++i) { + DevicePair p = source[i]; + threadReg[2 * i] = p.x; + threadReg[2 * i + 1] = p.y; + } + } + if(sync) __syncthreads(); +} + +//////////////////////////////////////////////////////////////////////////////// +// DeviceLoad2 - load from pointers of the same type. Optimize for a single LD +// statement. + +template +MGPU_DEVICE void DeviceLoad2ToReg(const T* a_global, int aCount, + const T* b_global, int bCount, int tid, T* reg, bool sync) { + + int b0 = b_global - a_global - aCount; + int total = aCount + bCount; + if(total >= NT * VT0) { + #pragma unroll + for(int i = 0; i < VT0; ++i) { + int index = NT * i + tid; + reg[i] = a_global[index + ((index >= aCount) ? b0 : 0)]; + } + } else { + #pragma unroll + for(int i = 0; i < VT0; ++i) { + int index = NT * i + tid; + if(index < total) + reg[i] = a_global[index + ((index >= aCount) ? b0 : 0)]; + } + } + #pragma unroll + for(int i = VT0; i < VT1; ++i) { + int index = NT * i + tid; + if(index < total) + reg[i] = a_global[index + ((index >= aCount) ? b0 : 0)]; + } +} + +template +MGPU_DEVICE void DeviceLoad2ToShared(const T* a_global, int aCount, + const T* b_global, int bCount, int tid, T* shared, bool sync) { + + T reg[VT1]; + DeviceLoad2ToReg(a_global, aCount, b_global, bCount, tid, + reg, false); + DeviceRegToShared(reg, tid, shared, sync); +} + +//////////////////////////////////////////////////////////////////////////////// +// DeviceLoad2 - load from pointers of different types. Uses two LD statements. + +template +MGPU_DEVICE void DeviceLoad2ToReg(InputIt1 a_global, int aCount, + InputIt2 b_global, int bCount, int tid, T* reg, bool sync) { + + b_global -= aCount; + int total = aCount + bCount; + if(total >= NT * VT0) { + #pragma unroll + for(int i = 0; i < VT0; ++i) { + int index = NT * i + tid; + if(index < aCount) reg[i] = a_global[index]; + else reg[i] = b_global[index]; + } + } else { + #pragma unroll + for(int i = 0; i < VT0; ++i) { + int index = NT * i + tid; + if(index < aCount) reg[i] = a_global[index]; + else if(index < total) reg[i] = b_global[index]; + } + } + #pragma unroll + for(int i = VT0; i < VT1; ++i) { + int index = NT * i + tid; + if(index < aCount) reg[i] = a_global[index]; + else if(index < total) reg[i] = b_global[index]; + } +} + +template +MGPU_DEVICE void DeviceLoad2ToShared(InputIt1 a_global, int aCount, + InputIt2 b_global, int bCount, int tid, T* shared, bool sync) { + + T reg[VT1]; + DeviceLoad2ToReg(a_global, aCount, b_global, bCount, tid, + reg, false); + DeviceRegToShared(reg, tid, shared, sync); +} + + +//////////////////////////////////////////////////////////////////////////////// +// DeviceGatherGlobalToGlobal + +template +MGPU_DEVICE void DeviceGatherGlobalToGlobal(int count, InputIt data_global, + const int* indices_shared, int tid, OutputIt dest_global, bool sync) { + + typedef typename std::iterator_traits::value_type ValType; + ValType values[VT]; + + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + if(index < count) { + int gather = indices_shared[index]; + values[i] = data_global[gather]; + } + } + if(sync) __syncthreads(); + DeviceRegToGlobal(count, values, tid, dest_global, false); +} + +//////////////////////////////////////////////////////////////////////////////// +// DeviceTransferMergeValues +// Gather in a merge-like value from two input arrays and store to a single +// output. Like DeviceGatherGlobalToGlobal, but for two arrays at once. + +template +MGPU_DEVICE void DeviceTransferMergeValuesReg(int count, InputIt1 a_global, + InputIt2 b_global, int bStart, const int* indices, int tid, + T* reg, bool sync) { + + b_global -= bStart; + if(count >= NT * VT) { + #pragma unroll + for(int i = 0; i < VT; ++i) { + reg[i] = (indices[i] < bStart) ? a_global[indices[i]] : + b_global[indices[i]]; + } + } else { + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + if(index < count) + reg[i] = (indices[i] < bStart) ? a_global[indices[i]] : + b_global[indices[i]]; + } + } + if(sync) __syncthreads(); +} + +template +MGPU_DEVICE void DeviceTransferMergeValuesShared(int count, InputIt1 a_global, + InputIt2 b_global, int bStart, const int* indices_shared, int tid, + OutputIt dest_global, bool sync) { + + int indices[VT]; + DeviceSharedToReg(indices_shared, tid, indices); + + typedef typename std::iterator_traits::value_type ValType; + ValType reg[VT]; + DeviceTransferMergeValuesReg(count, a_global, b_global, bStart, + indices, tid, reg, sync); + DeviceRegToGlobal(count, reg, tid, dest_global, sync); +} + +template +MGPU_DEVICE void DeviceTransferMergeValuesReg(int count, const T* a_global, + const T* b_global, int bStart, const int* indices, int tid, T* reg, + bool sync) { + + int bOffset = (int)(b_global - a_global - bStart); + + if(count >= NT * VT) { + #pragma unroll + for(int i = 0; i < VT; ++i) { + int gather = indices[i]; + if(gather >= bStart) gather += bOffset; + reg[i] = a_global[gather]; + } + } else { + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + int gather = indices[i]; + if(gather >= bStart) gather += bOffset; + if(index < count) + reg[i] = a_global[gather]; + } + } + if(sync) __syncthreads(); +} + +template +MGPU_DEVICE void DeviceTransferMergeValuesShared(int count, const T* a_global, + const T* b_global, int bStart, const int* indices_shared, int tid, + OutputIt dest_global, bool sync) { + + int indices[VT]; + DeviceSharedToReg(indices_shared, tid, indices); + + T reg[VT]; + DeviceTransferMergeValuesReg(count, a_global, b_global, bStart, + indices, tid, reg, sync); + DeviceRegToGlobal(count, reg, tid, dest_global, sync); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/serialsets.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/serialsets.cuh new file mode 100644 index 0000000000000000000000000000000000000000..15b9b0534941bbcea43ac6e02549833648895eaf --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/serialsets.cuh @@ -0,0 +1,235 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../device/deviceutil.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// SerialSetIntersection +// Emit A if A and B are in range and equal. + +template +MGPU_DEVICE int SerialSetIntersection(const T* data, int aBegin, int aEnd, + int bBegin, int bEnd, int end, T* results, int* indices, Comp comp) { + + const int MinIterations = VT / 2; + int commit = 0; + + #pragma unroll + for(int i = 0; i < VT; ++i) { + bool test = RangeCheck ? + ((aBegin + bBegin < end) && (aBegin < aEnd) && (bBegin < bEnd)) : + (i < MinIterations || (aBegin + bBegin < end)); + + if(test) { + T aKey = data[aBegin]; + T bKey = data[bBegin]; + + bool pA = comp(aKey, bKey); + bool pB = comp(bKey, aKey); + + // The outputs must come from A by definition of set interection. + results[i] = aKey; + indices[i] = aBegin; + + if(!pB) ++aBegin; + if(!pA) ++bBegin; + if(pA == pB) commit |= 1<< i; + } + } + return commit; +} + +//////////////////////////////////////////////////////////////////////////////// +// SerialSetUnion +// Emit A if A <= B. Emit B if B < A. + +template +MGPU_DEVICE int SerialSetUnion(const T* data, int aBegin, int aEnd, + int bBegin, int bEnd, int end, T* results, int* indices, Comp comp) { + + const int MinIterations = VT / 2; + int commit = 0; + + #pragma unroll + for(int i = 0; i < VT; ++i) { + bool test = RangeCheck ? + (aBegin + bBegin < end) : + (i < MinIterations || (aBegin + bBegin < end)); + + if(test) { + T aKey = data[aBegin]; + T bKey = data[bBegin]; + + bool pA = false, pB = false; + if(RangeCheck && aBegin >= aEnd) + pB = true; + else if(RangeCheck && bBegin >= bEnd) + pA = true; + else { + // Both are in range. + pA = comp(aKey, bKey); + pB = comp(bKey, aKey); + } + + // Output A in case of a tie, so check if b < a. + results[i] = pB ? bKey : aKey; + indices[i] = pB ? bBegin : aBegin; + if(!pB) ++aBegin; + if(!pA) ++bBegin; + commit |= 1<< i; + } + } + return commit; +} + +//////////////////////////////////////////////////////////////////////////////// +// SerialSetDifference +// Emit A if A < B. + +template +MGPU_DEVICE int SerialSetDifference(const T* data, int aBegin, int aEnd, + int bBegin, int bEnd, int end, T* results, int* indices, Comp comp) { + + const int MinIterations = VT / 2; + int commit = 0; + + #pragma unroll + for(int i = 0; i < VT; ++i) { + bool test = RangeCheck ? + (aBegin + bBegin < end) : + (i < MinIterations || (aBegin + bBegin < end)); + if(test) { + T aKey = data[aBegin]; + T bKey = data[bBegin]; + + bool pA = false, pB = false; + if(RangeCheck && aBegin >= aEnd) + pB = true; + else if(RangeCheck && bBegin >= bEnd) + pA = true; + else { + pA = comp(aKey, bKey); + pB = comp(bKey, aKey); + } + + // The outputs must come from A by definition of set difference. + results[i] = aKey; + indices[i] = aBegin; + if(!pB) ++aBegin; + if(!pA) ++bBegin; + if(pA) commit |= 1<< i; + } + } + return commit; +} + +//////////////////////////////////////////////////////////////////////////////// +// SerialSetSymDiff +// Emit A if A < B and emit B if B < A. + +template +MGPU_DEVICE int SerialSetSymDiff(const T* data, int aBegin, int aEnd, + int bBegin, int bEnd, int end, T* results, int* indices, Comp comp) { + + const int MinIterations = VT / 2; + int commit = 0; + + #pragma unroll + for(int i = 0; i < VT; ++i) { + bool test = RangeCheck ? + (aBegin + bBegin < end) : + (i < MinIterations || (aBegin + bBegin < end)); + if(test) { + T aKey = data[aBegin]; + T bKey = data[bBegin]; + + bool pA = false, pB = false; + if(RangeCheck && (bBegin >= bEnd)) + pA = true; + else if(RangeCheck && (aBegin >= aEnd)) + pB = true; + else { + pA = comp(aKey, bKey); + pB = comp(bKey, aKey); + } + + results[i] = pA ? aKey : bKey; + indices[i] = pA ? aBegin : bBegin; + if(!pA) ++bBegin; + if(!pB) ++aBegin; + if(pA != pB) commit |= 1<< i; + } + } + return commit; +} + +//////////////////////////////////////////////////////////////////////////////// +// SerialSetOp +// Uses the MgpuSetOp enum to statically select one of the four serial ops +// above. + +template +MGPU_DEVICE int SerialSetOp(const T* data, int aBegin, int aEnd, + int bBegin, int bEnd, int star, T* results, int* indices, Comp comp) { + + int end = aBegin + bBegin + VT - star; + if(RangeCheck) end = min(end, aEnd + bEnd); + int commit; + switch(Op) { + case MgpuSetOpIntersection: + commit = SerialSetIntersection(data, aBegin, + aEnd, bBegin, bEnd, end, results, indices, comp); + break; + case MgpuSetOpUnion: + commit = SerialSetUnion(data, aBegin, aEnd, + bBegin, bEnd, end, results, indices, comp); + break; + case MgpuSetOpDiff: + commit = SerialSetDifference(data, aBegin, aEnd, + bBegin, bEnd, end, results, indices, comp); + break; + case MgpuSetOpSymDiff: + commit = SerialSetSymDiff(data, aBegin, aEnd, + bBegin, bEnd, end, results, indices, comp); + break; + } + __syncthreads(); + return commit; +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/sortnetwork.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/sortnetwork.cuh new file mode 100644 index 0000000000000000000000000000000000000000..a605e2496e43b54c280575255a1454e3d8ea8925 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/device/sortnetwork.cuh @@ -0,0 +1,168 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../device/deviceutil.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// Odd-even transposition sorting network. Sorts keys and values in-place in +// register. +// http://en.wikipedia.org/wiki/Odd%E2%80%93even_sort + +// CUDA Compiler does not currently unroll these loops correctly. Write using +// template loop unrolling. +/* +template +MGPU_DEVICE void OddEvenTransposeSort(T* keys, V* values, Comp comp) { + #pragma unroll + for(int level = 0; level < VT; ++level) { + + #pragma unroll + for(int i = 1 & level; i < VT - 1; i += 2) { + if(comp(keys[i + 1], keys[i])) { + mgpu::swap(keys[i], keys[i + 1]); + mgpu::swap(values[i], values[i + 1]); + } + } + } +}*/ + +template +struct OddEvenTransposeSortT { + // Sort segments marked by head flags. If the head flag between i and i + 1 + // is set (so that (2<< i) & flags is true), the values belong to different + // segments and are not swapped. + template + static MGPU_DEVICE void Sort(K* keys, V* values, int flags, Comp comp) { + #pragma unroll + for(int i = 1 & I; i < VT - 1; i += 2) + if((0 == ((2<< i) & flags)) && comp(keys[i + 1], keys[i])) { + mgpu::swap(keys[i], keys[i + 1]); + mgpu::swap(values[i], values[i + 1]); + } + OddEvenTransposeSortT::Sort(keys, values, flags, comp); + } +}; +template struct OddEvenTransposeSortT { + template + static MGPU_DEVICE void Sort(K* keys, V* values, int flags, Comp comp) { } +}; + +template +MGPU_DEVICE void OddEvenTransposeSort(K* keys, V* values, Comp comp) { + OddEvenTransposeSortT<0, VT>::Sort(keys, values, 0, comp); +} +template +MGPU_DEVICE void OddEvenTransposeSortFlags(K* keys, V* values, int flags, + Comp comp) { + OddEvenTransposeSortT<0, VT>::Sort(keys, values, flags, comp); +} + +//////////////////////////////////////////////////////////////////////////////// +// Batcher Odd-Even Mergesort network +// Unstable but executes much faster than the transposition sort. +// http://en.wikipedia.org/wiki/Batcher_odd%E2%80%93even_mergesort + +template +struct OddEvenMergesortT { + template + MGPU_DEVICE static void CompareAndSwap(K* keys, V* values, int flags, + int a, int b, Comp comp) { + if(b < Count) { + // Mask the bits between a and b. Any head flags in this interval + // means the keys are in different segments and must not be swapped. + const int Mask = ((2<< b) - 1) ^ ((2<< a) - 1); + if(!(Mask & flags) && comp(keys[b], keys[a])) { + mgpu::swap(keys[b], keys[a]); + mgpu::swap(values[b], values[a]); + } + } + } + + template + struct OddEvenMerge { + template + MGPU_DEVICE static void Merge(K* keys, V* values, int flags, + Comp comp) { + // Compare and swap + const int M = 2 * R; + OddEvenMerge::Merge(keys, values, flags, comp); + OddEvenMerge::Merge(keys, values, flags, comp); + + #pragma unroll + for(int i = Low2 + R; i + R < Low2 + Width; i += M) + CompareAndSwap(keys, values, flags, i, i + R, comp); + } + }; + template + struct OddEvenMerge { + template + MGPU_DEVICE static void Merge(K* keys, V* values, int flags, + Comp comp) { + CompareAndSwap(keys, values, flags, Low2, Low2 + R, comp); + } + }; + + template + MGPU_DEVICE static void Sort(K* keys, V* values, int flags, + Comp comp) { + + const int M = Width / 2; + OddEvenMergesortT::Sort(keys, values, flags, comp); + OddEvenMergesortT::Sort(keys, values, flags, comp); + OddEvenMerge<1, Low>::Merge(keys, values, flags, comp); + } +}; +template struct OddEvenMergesortT<1, Low, Count> { + template + MGPU_DEVICE static void Sort(K* keys, V* values, int flags, + Comp comp) { } +}; + +template +MGPU_DEVICE void OddEvenMergesort(K* keys, V* values, Comp comp) { + const int Width = 1<< sLogPow2::value; + OddEvenMergesortT::Sort(keys, values, 0, comp); +} +template +MGPU_DEVICE void OddEvenMergesortFlags(K* keys, V* values, int flags, + Comp comp) { + const int Width = 1<< sLogPow2::value; + OddEvenMergesortT::Sort(keys, values, flags, comp); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/bulkinsert.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/bulkinsert.cuh new file mode 100644 index 0000000000000000000000000000000000000000..964733e6a068720bc206d5db6fcd6e058f8d5dc4 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/bulkinsert.cuh @@ -0,0 +1,173 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuhost.cuh" +#include "../kernels/search.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// KernelBulkInsert + +template +struct CTABulkInsert { + enum { NV = NT * VT }; + union Storage { + int indices[NV]; + typename CTAScan::Storage scanStorage; + }; + + // Returns gather indices in strided order. + template + MGPU_DEVICE static void BuildGatherIndices(int4 range, + IndicesIt indices_global, int tid, Storage& storage) { + + int a0 = range.x; + int b0 = range.z; + int aCount = range.y - range.x; + + // Load the indices. + int indices[VT]; + DeviceGlobalToReg(aCount, indices_global + a0, tid, indices); + + // Initialize the indices to 0. + #pragma unroll + for(int i = 0; i < VT; ++i) + storage.indices[NT * i + tid] = 0; + __syncthreads(); + + // Set the counters for all the loaded indices. This has the effect of + // pushing the scanned values to the right, causing the B data to be + // inserted to the right of each insertion point. + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + if(index < aCount) storage.indices[index + indices[i] - b0] = 1; + } + __syncthreads(); + + // Run a raking scan over the indices. + int x = 0; + #pragma unroll + for(int i = 0; i < VT; ++i) + x += indices[i] = storage.indices[VT * tid + i]; + __syncthreads(); + + // Run a CTA scan over the thread totals. + int scan = CTAScan::Scan(tid, x, storage.scanStorage); + + // Complete the scan to compute merge-style gather indices. Indices + // between in the interval (0, aCount) are from array A (the new + // values). Indices in (aCount, aCount + bCount) are from array B (the + // sources). This style of indexing lets us use + // DeviceTransferMergeValues to do global memory transfers. + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = VT * tid + i; + int gather = indices[i] ? scan++ : aCount + index - scan; + storage.indices[index] = gather; + } + __syncthreads(); + } +}; + +// Insert the values from a_global into the positions marked by indices_global. +template +MGPU_LAUNCH_BOUNDS void KernelBulkInsert(InputIt1 a_global, + IndicesIt indices_global, int aCount, InputIt2 b_global, int bCount, + const int* mp_global, OutputIt dest_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + typedef typename std::iterator_traits::value_type T; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + + union Shared { + typename CTABulkInsert::Storage storage; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + + int4 range = ComputeMergeRange(aCount, bCount, block, 0, NV, mp_global); + + CTABulkInsert::BuildGatherIndices(range, indices_global, tid, + shared.storage); + + int a0 = range.x; // A is array of values to insert. + int b0 = range.z; // B is source array. + aCount = range.y - range.x; + bCount = range.w - range.z; + + DeviceTransferMergeValuesShared(aCount + bCount, a_global + a0, + b_global + b0, aCount, shared.storage.indices, tid, + dest_global + a0 + b0, false); +} + + +//////////////////////////////////////////////////////////////////////////////// +// BulkInsert +// Insert elements from A into elements from B before indices. + +template +MGPU_HOST void BulkInsert(InputIt1 a_global, IndicesIt indices_global, + int aCount, InputIt2 b_global, int bCount, OutputIt dest_global, + CudaContext& context) { + + typedef LaunchBoxVT< + 128, 7, 0, + 128, 7, 0, + 128, 7, 0 + > Tuning; + int2 launch = Tuning::GetLaunchParams(context); + const int NV = launch.x * launch.y; + + MGPU_MEM(int) partitionsDevice = MergePathPartitions( + indices_global, aCount, mgpu::counting_iterator(0), bCount, NV, 0, + mgpu::less(), context); + + int numBlocks = MGPU_DIV_UP(aCount + bCount, NV); + KernelBulkInsert<<>>( + a_global, indices_global, aCount, b_global, bCount, + partitionsDevice->get(), dest_global); + MGPU_SYNC_CHECK("KernelBulkInsert"); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/bulkremove.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/bulkremove.cuh new file mode 100644 index 0000000000000000000000000000000000000000..91ffd8c7f85c768972e54d2a264645bd0d76c861 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/bulkremove.cuh @@ -0,0 +1,150 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuhost.cuh" +#include "../kernels/search.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// KernelBulkRemove +// Copy the values that are not matched by an index. This is like the +// anti-gather. + +template +MGPU_LAUNCH_BOUNDS void KernelBulkRemove(InputIt source_global, int sourceCount, + IndicesIt indices_global, int indicesCount, const int* p_global, + OutputIt dest_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + typedef typename std::iterator_traits::value_type T; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + + typedef CTAScan S; + union Shared { + int indices[NV]; + typename S::Storage scan; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = block * NV; + sourceCount = min(NV, sourceCount - gid); + + // Search for begin and end iterators of interval to load. + int p0 = p_global[block]; + int p1 = p_global[block + 1]; + + // Set the flags to 1. The default is to copy a value. + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + shared.indices[index] = index < sourceCount; + } + __syncthreads(); + + // Load the indices into register. + int begin = p0; + int indexCount = p1 - begin; + int indices[VT]; + DeviceGlobalToReg(indexCount, indices_global + begin, tid, indices); + + // Set the counter to 0 for each index we've loaded. + #pragma unroll + for(int i = 0; i < VT; ++i) + if(NT * i + tid < indexCount) + shared.indices[indices[i] - gid] = 0; + __syncthreads(); + + // Run a raking scan over the flags. We count the set flags - this is the + // number of elements to load in per thread. + int x = 0; + #pragma unroll + for(int i = 0; i < VT; ++i) + x += indices[i] = shared.indices[VT * tid + i]; + __syncthreads(); + + // Run a CTA scan and scatter the gather indices to shared memory. + int scan = S::Scan(tid, x, shared.scan); + #pragma unroll + for(int i = 0; i < VT; ++i) + if(indices[i]) shared.indices[scan++] = VT * tid + i; + __syncthreads(); + + // Load the gather indices into register. + DeviceSharedToReg(shared.indices, tid, indices); + + // Gather the data into register. The number of values to copy is + // sourceCount - indexCount. + source_global += gid; + int count = sourceCount - indexCount; + T values[VT]; + DeviceGather(count, source_global, indices, tid, values, false); + + // Store all the valid registers to dest_global. + DeviceRegToGlobal(count, values, tid, dest_global + gid - begin); +} + +//////////////////////////////////////////////////////////////////////////////// +// BulkRemove + +template +MGPU_HOST void BulkRemove(InputIt source_global, int sourceCount, + IndicesIt indices_global, int indicesCount, OutputIt dest_global, + CudaContext& context) { + + const int NT = 128; + const int VT = 11; + typedef LaunchBoxVT Tuning; + int2 launch = Tuning::GetLaunchParams(context); + const int NV = launch.x * launch.y; + + MGPU_MEM(int) partitionsDevice = BinarySearchPartitions( + sourceCount, indices_global, indicesCount, NV, mgpu::less(), + context); + + int numBlocks = MGPU_DIV_UP(sourceCount, NV); + KernelBulkRemove<<>>( + source_global, sourceCount, indices_global, indicesCount, + partitionsDevice->get(), dest_global); + MGPU_SYNC_CHECK("KernelBulkRemove"); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/csrtools.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/csrtools.cuh new file mode 100644 index 0000000000000000000000000000000000000000..2a0bc43acf5af99c867fdfdd85b42f2d776c1974 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/csrtools.cuh @@ -0,0 +1,442 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../device/ctasegreduce.cuh" +#include "../kernels/scan.cuh" +#include "../kernels/bulkinsert.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// KernelPartitionCsrPlus +// Standard upper-bound partitioning. + +template +__global__ void KernelPartitionCsrSegReduce(int nz, int nv, CsrIt csr_global, + int numRows, const int* numRows2, int numPartitions, int* limits_global) { + + if(numRows2) numRows = *numRows2; + + int gid = NT * blockIdx.x + threadIdx.x; + if(gid < numPartitions) { + int key = min(nv * gid, nz); + + int ub; + if(key == nz) ub = numRows; + else { + // Upper-bound search for this partition. + ub = BinarySearch(csr_global, numRows, key, + mgpu::less()) - 1; + + // Check if limit points to matching value. + if(key != csr_global[ub]) ub |= 0x80000000; + } + limits_global[gid] = ub; + } +} + +template +MGPU_HOST MGPU_MEM(int) PartitionCsrSegReduce(int count, int nv, + CsrIt csr_global, int numRows, const int* numRows2, int numPartitions, + CudaContext& context) { + + // Allocate one int per partition. + MGPU_MEM(int) limitsDevice = context.Malloc(numPartitions); + + int numBlocks2 = MGPU_DIV_UP(numPartitions, 64); + KernelPartitionCsrSegReduce<64><<>>( + count, nv, csr_global, numRows, numRows2, numPartitions, + limitsDevice->get()); + MGPU_SYNC_CHECK("KernelPartitionCsrSegReduce"); + + return limitsDevice; +} + +//////////////////////////////////////////////////////////////////////////////// +// KernelBuildCsrPlus + +template +MGPU_LAUNCH_BOUNDS void KernelBuildCsrPlus(int count, CsrIt csr_global, + const int* limits_global, int* threadCodes_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + + union Shared { + int csr[NV + 1]; + typename CTAScan::Storage scanStorage; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + int count2 = min(NV, count - gid); + + int limit0 = limits_global[block]; + int limit1 = limits_global[block + 1]; + + // Transform the row limits into ranges. + SegReduceRange range = DeviceShiftRange(limit0, limit1); + int numRows = range.end - range.begin; + + // Load the Csr interval. + DeviceGlobalToSharedLoop(numRows, csr_global + range.begin, tid, + shared.csr); + + // Flatten Csr->COO and return the segmented scan terms. + int rows[VT + 1], rowStarts[VT]; + SegReduceTerms terms = DeviceSegReducePrepare(shared.csr, + numRows, tid, gid, range.flushLast, rows, rowStarts); + + // Combine terms into bit field. + // threadCodes: + // 12:0 - end flags for up to 13 values per thread. + // 19:13 - tid delta for up to 128 threads. + // 30:20 - scan offset for streaming partials. + int threadCodes = terms.endFlags | (terms.tidDelta<< 13) | (rows[0]<< 20); + threadCodes_global[NT * block + tid] = threadCodes; +} + +template +MGPU_HOST MGPU_MEM(int) BuildCsrPlus(int count, CsrIt csr_global, + const int* limits_global, int numBlocks, CudaContext& context) { + + int2 launch = Tuning::GetLaunchParams(context); + + // Allocate one int per thread. + MGPU_MEM(int) threadCodesDevice = context.Malloc(launch.x * numBlocks); + + KernelBuildCsrPlus + <<>>(count, csr_global, + limits_global, threadCodesDevice->get()); + MGPU_SYNC_CHECK("KernelBuildCsrPlus"); + + return threadCodesDevice; +} + +//////////////////////////////////////////////////////////////////////////////// +// CsrStripEmpties +// Removes empty rows from a Csr array. The returned array has numRows2 +// non-empty rows in the front followed by (numRows - numRows2) BulkInsert +// offsets in the back. + +template +MGPU_LAUNCH_BOUNDS void KernelCsrStripEmptiesUpsweep(int nz, CsrIt csr_global, + int numRows, int* counts_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + + union Shared { + int indices[NT * (VT + 1)]; + typename CTAReduce::Storage reduceStorage; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + int numRows2 = min(NV + 1, numRows - gid); + + // Load one index per element plus one halo element. + DeviceGlobalToSharedDefault2(numRows2, csr_global + gid, + tid, shared.indices, nz); + + // Count the number of valid rows. + int validRowCount = 0; + int row = shared.indices[VT * tid]; + #pragma unroll + for(int i = 0; i < VT; ++i) { + int next = shared.indices[VT * tid + 1 + i]; + validRowCount += row != next; + row = next; + } + __syncthreads(); + + validRowCount = CTAReduce::Reduce(tid, validRowCount, + shared.reduceStorage); + if(!tid) + counts_global[block] = validRowCount; +} + +template +MGPU_LAUNCH_BOUNDS void KernelCsrStripEmptiesDownsweep(int nz, CsrIt csr_global, + SourcesIt sources_global, int numRows, const int* scan_global, + int* csr2_global, int* sources2_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + + union Shared { + int indices[NT * (VT + 1)]; + typename CTAScan::Storage scanStorage; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + int numRows2 = min(NV + 1, numRows - gid); + + // The total number of valid rows is at the end of the scan array. + int invalidStart = scan_global[gridDim.x]; + + // scan_global is the offset at which to store the first valid row offset. + int scanOffset = scan_global[block]; + + // Load one index per element plus one halo element. + DeviceGlobalToSharedDefault2(numRows2, csr_global + gid, + tid, shared.indices, nz); + + // Count the number of skipped (empty) rows. + int validRowCount = 0; + int rows[VT + 1]; + rows[0] = shared.indices[VT * tid]; + #pragma unroll + for(int i = 0; i < VT; ++i) { + rows[i + 1] = shared.indices[VT * tid + i + 1]; + validRowCount += rows[i] != rows[i + 1]; + } + __syncthreads(); + + // Scan the number valid rows. + int totalValid; + int scan = CTAScan::Scan(tid, validRowCount, shared.scanStorage, + &totalValid); + int validScan = scan; + int invalidScan = totalValid + VT * tid - validScan; + + // Stream the valid row offsets to the front and the invalid row indices + // to the back. + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = VT * tid + i; + bool invalid = index >= numRows2 || rows[i] == rows[i + 1]; + int dest = invalid ? invalidScan++ : validScan++; + shared.indices[dest] = invalid ? (gid + index) : rows[i]; + } + __syncthreads(); + + // Cooperatively store valid row offsets and invalid row insertion points + // to global memory. + for(int i = tid; i < totalValid; i += NT) + csr2_global[scanOffset + i] = shared.indices[i]; + + numRows2 = min(NV, numRows2); + int invalidRank = gid - scanOffset; + int totalInvalid = numRows2 - totalValid; + for(int i = tid; i < totalInvalid; i += NT) { + // Subtract the rank of the invalid row from its index. This serves as + // a BulkInsert-style insertion point. + int invalidRank2 = invalidRank + i; + csr2_global[invalidStart + invalidRank2] = + shared.indices[totalValid + i] - invalidRank2; + } + __syncthreads(); + + // Store the total number of valid rows to the end of the Csr2 array. + if(!block && !tid) + csr2_global[numRows] = invalidStart; + + if(Indirect) { + // Load the indirect source offsets in thread order. + int sources[VT]; + DeviceGlobalToShared(numRows2, sources_global + gid, tid, + shared.indices); + DeviceSharedToThread(shared.indices, tid, sources); + + // Compact the valid source offsets to smem. + #pragma unroll + for(int i = 0; i < VT; ++i) + if(rows[i] != rows[i + 1]) + shared.indices[scan++] = sources[i]; + __syncthreads(); + + // Cooperatively store compacted source offsets. + for(int i = tid; i < totalValid; i += NT) + sources2_global[scanOffset + i] = shared.indices[i]; + } +} + +template +MGPU_HOST void CsrStripEmpties(int nz, CsrIt csr_global, + SourcesIt sources_global, int numRows, int* csr2_global, + int* sources2_global, int* numRows2, CudaContext& context) { + + typedef LaunchBoxVT< + 128, 3, 0, + 128, 3, 0, + 128, 3, 0 + > Tuning; + int2 launch = Tuning::GetLaunchParams(context); + int NV = launch.x * launch.y; + + int numBlocks = MGPU_DIV_UP(numRows, NV); + MGPU_MEM(int) countsDevice = context.Malloc(numBlocks + 1); + + // Count the non-empty row counts for each CTA. + KernelCsrStripEmptiesUpsweep + <<>>( + nz, csr_global, numRows, countsDevice->get()); + MGPU_SYNC_CHECK("KernelCsrStripEmpties"); + + // Scan the non-empty row counts. + Scan(countsDevice->get(), numBlocks, 0, mgpu::plus(), + countsDevice->get() + numBlocks, numRows2, countsDevice->get(), + context); + + // Compact the non-empty rows to the front. Append the indices of all + // empty rows to the end of the array. + KernelCsrStripEmptiesDownsweep + <<>>( + nz, csr_global, sources_global, numRows, countsDevice->get(), + csr2_global, sources2_global); + MGPU_SYNC_CHECK("KernelCsrStringEmptiesDownsweep"); +} + +//////////////////////////////////////////////////////////////////////////////// +// CsrBulkInsert +// A specialized version of BulkInsert which reads the insertion count from +// global memory rather than as a kernel argument--this lets us avoid a costly +// device->host copy after running CsrStripEmpties. + +template +__global__ void KernelCsrBulkInsertPartition(const int* csr2_global, + int numRows, int* mp_global, int numSearches, int nv) { + + int partition = NT * blockIdx.x + threadIdx.x; + int numRows2 = csr2_global[numRows]; + int aCount = numRows - numRows2; + int bCount = numRows2; + + const int* indices_global = csr2_global + numRows2; + + if(partition < numSearches) { + int diag = nv * partition; + int mp = MergePath(indices_global, aCount, + mgpu::counting_iterator(0), bCount, min(diag, numRows), + mgpu::less()); + mp_global[partition] = mp; + } +} + +template +MGPU_LAUNCH_BOUNDS void KernelCsrBulkInsertSpecial(const int* csr2_global, + const T* data_global, int numRows, const int* mp_global, T identity, + OutputIt dest_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + + union Shared { + typename CTABulkInsert::Storage storage; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + int count2 = min(NV, numRows - gid); + + int numRows2 = csr2_global[numRows]; + int4 range = ComputeMergeRange(numRows, 0, block, 0, NV, mp_global); + + int aCount = numRows - numRows2; + + const int* indices_global = csr2_global + numRows2; + CTABulkInsert::BuildGatherIndices(range, indices_global, tid, + shared.storage); + + int indices[VT]; + DeviceSharedToReg(shared.storage.indices, tid, indices); + + int b0 = range.z; // B is source array offset. + aCount = range.y - range.x; + + data_global += b0 - aCount; + T values[VT]; + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = indices[i]; + if(index < aCount) values[i] = identity; + else if(index < count2) values[i] = data_global[index]; + } + + DeviceRegToGlobal(count2, values, tid, dest_global + gid); +} + +template +MGPU_HOST void CsrBulkInsert(const int* csr2_global, int numRows, + const T* data_global, T identity, DestIt dest_global, + CudaContext& context) { + + typedef LaunchBoxVT< + 128, 3, 0, + 128, 3, 0, + 128, 3, 0 + > Tuning; + int2 launch = Tuning::GetLaunchParams(context); + int NV = launch.x * launch.y; + + int numBlocks = MGPU_DIV_UP(numRows, NV); + int numPartitions = numBlocks + 1; + int numPartitionBlocks = MGPU_DIV_UP(numPartitions, 64); + + // Run a Merge Path partitioning to divide the data over equal intervals. + MGPU_MEM(int) partitionsDevice = context.Malloc(numPartitions); + KernelCsrBulkInsertPartition<64> + <<>>(csr2_global, + numRows, partitionsDevice->get(), numPartitions, NV); + MGPU_SYNC_CHECK("KernelCsrBulkInsertPartition"); + + // Launch the special Csr BulkInsert kernel to plug the empty rows with + // the identity element. + KernelCsrBulkInsertSpecial + <<>>(csr2_global, + data_global, numRows, partitionsDevice->get(), identity, dest_global); + MGPU_SYNC_CHECK("KernelCsrBulkInsertSpecial"); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/cubradixsort.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/cubradixsort.cuh new file mode 100644 index 0000000000000000000000000000000000000000..c083568091748eec1692b985a83e5a0173454fc1 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/cubradixsort.cuh @@ -0,0 +1,46 @@ +#include "device/deviceutil.cuh" +#include "cub/cub.cuh" + +namespace mgpu { + +template +bool CubRadixSort(Key* keys_global, Key* keys2_global, int count, int beginBit, + int endBit, CudaContext& context) { + + cub::DoubleBuffer keys(keys_global, keys2_global); + + size_t tempBytes = 0; + cub::DeviceRadixSort::SortKeys(0, tempBytes, keys, count, beginBit, endBit, + context.Stream()); + + MGPU_MEM(byte) tempDevice = context.Malloc(tempBytes); + + cub::DeviceRadixSort::SortKeys(tempDevice->get(), tempBytes, keys, count, + beginBit, endBit, context.Stream()); + MGPU_SYNC_CHECK("cub::DeviceRadixSort::SortKeys"); + + return 1 == keys.selector; +} + +template +bool CubRadixSort(Key* keys_global, Key* keys2_global, Value* values_global, + Value* values2_global, int count, int beginBit, int endBit, + CudaContext& context) { + + cub::DoubleBuffer keys(keys_global, keys2_global); + cub::DoubleBuffer values(values_global, values2_global); + + size_t tempBytes = 0; + cub::DeviceRadixSort::SortPairs(0, tempBytes, keys, values, count, + beginBit, endBit, context.Stream()); + + MGPU_MEM(byte) tempDevice = context.Malloc(tempBytes); + + cub::DeviceRadixSort::SortPairs(tempDevice->get(), tempBytes, keys, values, + count, beginBit, endBit, context.Stream()); + MGPU_SYNC_CHECK("cub::DeviceRadixSort::SortPairs"); + + return 1 == keys.selector; +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/intervalmove.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/intervalmove.cuh new file mode 100644 index 0000000000000000000000000000000000000000..c9811a9047d0ad4d470a5b7eb68ca33861fef03d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/intervalmove.cuh @@ -0,0 +1,299 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuhost.cuh" +#include "../device/launchbox.cuh" +#include "../device/loadstore.cuh" +#include "../device/ctaloadbalance.cuh" +#include "../kernels/search.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// KernelIntervalExpand + +template +MGPU_LAUNCH_BOUNDS void KernelIntervalExpand(int destCount, + IndicesIt indices_global, ValuesIt values_global, int sourceCount, + const int* mp_global, OutputIt output_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + typedef typename std::iterator_traits::value_type T; + + union Shared { + int indices[NT * (VT + 1)]; + T values[NT * VT]; + }; + __shared__ Shared shared; + int tid = threadIdx.x; + int block = blockIdx.x; + + // Compute the input and output intervals this CTA processes. + int4 range = CTALoadBalance(destCount, indices_global, sourceCount, + block, tid, mp_global, shared.indices, true); + + // The interval indices are in the left part of shared memory (moveCount). + // The scan of interval counts are in the right part (intervalCount). + destCount = range.y - range.x; + sourceCount = range.w - range.z; + + // Copy the source indices into register. + int sources[VT]; + DeviceSharedToReg(shared.indices, tid, sources); + + // Load the source fill values into shared memory. Each value is fetched + // only once to reduce latency and L2 traffic. + DeviceMemToMemLoop(sourceCount, values_global + range.z, tid, + shared.values); + + // Gather the values from shared memory into register. This uses a shared + // memory broadcast - one instance of a value serves all the threads that + // comprise its fill operation. + T values[VT]; + DeviceGather(destCount, shared.values - range.z, sources, tid, + values, false); + + // Store the values to global memory. + DeviceRegToGlobal(destCount, values, tid, output_global + range.x); +} + +//////////////////////////////////////////////////////////////////////////////// +// IntervalExpand + +template +MGPU_HOST void IntervalExpand(int moveCount, IndicesIt indices_global, + ValuesIt values_global, int intervalCount, OutputIt output_global, + CudaContext& context) { + + const int NT = 128; + const int VT = 7; + typedef LaunchBoxVT Tuning; + int2 launch = Tuning::GetLaunchParams(context); + + int NV = launch.x * launch.y; + int numBlocks = MGPU_DIV_UP(moveCount + intervalCount, NV); + + // Partition the input and output sequences so that the load-balancing + // search results in a CTA fit in shared memory. + MGPU_MEM(int) partitionsDevice = MergePathPartitions( + mgpu::counting_iterator(0), moveCount, indices_global, + intervalCount, NV, 0, mgpu::less(), context); + + KernelIntervalExpand<<>>( + moveCount, indices_global, values_global, intervalCount, + partitionsDevice->get(), output_global); + MGPU_SYNC_CHECK("KernelIntervalExpand"); +} + +//////////////////////////////////////////////////////////////////////////////// +// KernelIntervalMove + +template +MGPU_LAUNCH_BOUNDS void KernelIntervalMove(int moveCount, + GatherIt gather_global, ScatterIt scatter_global, IndicesIt indices_global, + int intervalCount, InputIt input_global, const int* mp_global, + OutputIt output_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + + __shared__ int indices_shared[NT * (VT + 1)]; + int tid = threadIdx.x; + int block = blockIdx.x; + + // Load balance the move IDs (counting_iterator) over the scan of the + // interval sizes. + int4 range = CTALoadBalance(moveCount, indices_global, + intervalCount, block, tid, mp_global, indices_shared, true); + + // The interval indices are in the left part of shared memory (moveCount). + // The scan of interval counts are in the right part (intervalCount). + moveCount = range.y - range.x; + intervalCount = range.w - range.z; + int* move_shared = indices_shared; + int* intervals_shared = indices_shared + moveCount; + int* intervals_shared2 = intervals_shared - range.z; + + // Read out the interval indices and scan offsets. + int interval[VT], rank[VT]; + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + int gid = range.x + index; + interval[i] = range.z; + if(index < moveCount) { + interval[i] = move_shared[index]; + rank[i] = gid - intervals_shared2[interval[i]]; + } + } + __syncthreads(); + + // Load and distribute the gather and scatter indices. + int gather[VT], scatter[VT]; + if(Gather) { + // Load the gather pointers into intervals_shared. + DeviceMemToMemLoop(intervalCount, gather_global + range.z, tid, + intervals_shared); + + // Make a second pass through shared memory. Grab the start indices of + // the interval for each item and add the scan into it for the gather + // index. + #pragma unroll + for(int i = 0; i < VT; ++i) + gather[i] = intervals_shared2[interval[i]] + rank[i]; + __syncthreads(); + } + if(Scatter) { + // Load the scatter pointers into intervals_shared. + DeviceMemToMemLoop(intervalCount, scatter_global + range.z, tid, + intervals_shared); + + // Make a second pass through shared memory. Grab the start indices of + // the interval for each item and add the scan into it for the scatter + // index. + #pragma unroll + for(int i = 0; i < VT; ++i) + scatter[i] = intervals_shared2[interval[i]] + rank[i]; + __syncthreads(); + } + + // Gather the data into register. + typedef typename std::iterator_traits::value_type T; + T data[VT]; + if(Gather) + DeviceGather(moveCount, input_global, gather, tid, data, false); + else + DeviceGlobalToReg(moveCount, input_global + range.x, tid, data); + + // Scatter the data into global. + if(Scatter) + DeviceScatter(moveCount, data, tid, scatter, output_global, + false); + else + DeviceRegToGlobal(moveCount, data, tid, + output_global + range.x); +} + +//////////////////////////////////////////////////////////////////////////////// +// IntervalGather + +template +MGPU_HOST void IntervalGather(int moveCount, GatherIt gather_global, + IndicesIt indices_global, int intervalCount, InputIt input_global, + OutputIt output_global, CudaContext& context) { + + const int NT = 128; + const int VT = 7; + typedef LaunchBoxVT Tuning; + int2 launch = Tuning::GetLaunchParams(context); + + int NV = launch.x * launch.y; + int numBlocks = MGPU_DIV_UP(moveCount + intervalCount, NV); + + MGPU_MEM(int) partitionsDevice = MergePathPartitions( + mgpu::counting_iterator(0), moveCount, indices_global, + intervalCount, NV, 0, mgpu::less(), context); + + KernelIntervalMove + <<>>(moveCount, gather_global, + (const int*)0, indices_global, intervalCount, input_global, + partitionsDevice->get(), output_global); + MGPU_SYNC_CHECK("KernelIntervalMove"); +} + +//////////////////////////////////////////////////////////////////////////////// +// IntervalScatter + +template +MGPU_HOST void IntervalScatter(int moveCount, ScatterIt scatter_global, + IndicesIt indices_global, int intervalCount, InputIt input_global, + OutputIt output_global, CudaContext& context) { + + const int NT = 128; + const int VT = 7; + typedef LaunchBoxVT Tuning; + int2 launch = Tuning::GetLaunchParams(context); + + int NV = launch.x * launch.y; + int numBlocks = MGPU_DIV_UP(moveCount + intervalCount, NV); + + MGPU_MEM(int) partitionsDevice = MergePathPartitions( + mgpu::counting_iterator(0), moveCount, indices_global, + intervalCount, NV, 0, mgpu::less(), context); + + KernelIntervalMove + <<>>(moveCount, (const int*)0, + scatter_global, indices_global, intervalCount, input_global, + partitionsDevice->get(), output_global); + MGPU_SYNC_CHECK("KernelIntervalMove"); +} + +//////////////////////////////////////////////////////////////////////////////// +// IntervalMove + +template +MGPU_HOST void IntervalMove(int moveCount, GatherIt gather_global, + ScatterIt scatter_global, IndicesIt indices_global, int intervalCount, + InputIt input_global, OutputIt output_global, CudaContext& context) { + + const int NT = 128; + const int VT = 7; + typedef LaunchBoxVT Tuning; + int2 launch = Tuning::GetLaunchParams(context); + + int NV = launch.x * launch.y; + int numBlocks = MGPU_DIV_UP(moveCount + intervalCount, NV); + + MGPU_MEM(int) partitionsDevice = MergePathPartitions( + mgpu::counting_iterator(0), moveCount, indices_global, + intervalCount, NV, 0, mgpu::less(), context); + + KernelIntervalMove + <<>>(moveCount, gather_global, + scatter_global, indices_global, intervalCount, input_global, + partitionsDevice->get(), output_global); + MGPU_SYNC_CHECK("KernelIntervalMove"); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/join.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/join.cuh new file mode 100644 index 0000000000000000000000000000000000000000..3e35436f53638e75e38f4a247720a6f6d22cbb69 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/join.cuh @@ -0,0 +1,303 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#include "../mgpuhost.cuh" +#include "../device/ctaloadbalance.cuh" +#include "sortedsearch.cuh" +#include "scan.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// KernelLeftJoin + +template +MGPU_LAUNCH_BOUNDS void KernelLeftJoin(int total, const int* aLowerBound_global, + const int* aCountsScan_global, int aCount, const int* mp_global, + int* aIndices_global, int* bIndices_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + + __shared__ int indices_shared[NT * (VT + 1)]; + int tid = threadIdx.x; + int block = blockIdx.x; + + int4 range = CTALoadBalance(total, aCountsScan_global, aCount, + block, tid, mp_global, indices_shared, true); + int outputCount = range.y - range.x; + int inputCount = range.w - range.z; + int* output_shared = indices_shared; + int* input_shared = indices_shared + outputCount; + + int aIndex[VT], rank[VT]; + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + if(index < outputCount) { + int gid = range.x + index; + aIndex[i] = output_shared[index]; + rank[i] = gid - input_shared[aIndex[i] - range.z]; + aIndices_global[gid] = aIndex[i]; + } + } + __syncthreads(); + + // Load the lower bound of A into B for each element of A. + DeviceMemToMemLoop(inputCount, aLowerBound_global + range.z, tid, + input_shared); + + // Store the lower bound of A into B back for every output. + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + if(index < outputCount) { + int gid = range.x + index; + int lb = input_shared[aIndex[i] - range.z]; + int bIndex; + if(LeftJoin) + bIndex = (0x80000000 & lb) ? + ((0x7fffffff & lb) + rank[i]) : + -1; + else + bIndex = lb + rank[i]; + bIndices_global[gid] = bIndex; + } + } +} + +struct LeftJoinEqualityOp { + MGPU_HOST_DEVICE int operator()(int lb, int ub) const { + lb &= 0x7fffffff; + return max(1, ub - lb); + } +}; + +//////////////////////////////////////////////////////////////////////////////// +// Right-join compaction kernels. + +template +__global__ void KernelRightJoinUpsweep(const uint64* matches_global, int count, + int* totals_global) { + + typedef CTAReduce R; + __shared__ typename R::Storage reduce; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = 8 * NT * block; + int count2 = min(8 * NT, count - gid); + + int x = 0; + if(gid + 8 * tid < count) { + uint64 packed = matches_global[NT * block + tid]; + count2 -= 8 * tid; + if(count2 < 8) { + // Clear the bits above count2 + uint64 mask = (1ll<< (8 * count2)) - 1; + packed = (packed & mask) | (0x0101010101010101ll & ~mask); + } + uint2 pair = ulonglong_as_uint2(packed); + x = 8 - popc(pair.x) - popc(pair.y); + } + + int total = R::Reduce(tid, x, reduce); + if(!tid) totals_global[block] = total; +} + +template +__global__ void KernelRightJoinDownsweep(const uint64* matches_global, + int count, const int* scan_global, int* rightJoin_global) { + + typedef CTAScan S; + union Shared { + int indices[8 * NT]; + typename S::Storage scan; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = 8 * NT * block; + int count2 = min(8 * NT, count - gid); + + int start = scan_global[block]; + + uint64 packed; + int x = 0; + if(gid + 8 * tid < count) { + packed = matches_global[NT * block + tid]; + count2 -= 8 * tid; + if(count2 < 8) { + // Clear the bits above count2 + uint64 mask = (1ll<< (8 * count2)) - 1; + packed = (packed & mask) | (0x0101010101010101ll & ~mask); + } + uint2 pair = ulonglong_as_uint2(packed); + x = 8 - popc(pair.x) - popc(pair.y); + + packed ^= 0x0101010101010101ll; + } + + int total; + int scan = S::Scan(tid, x, shared.scan, &total); + + if(x) { + #pragma unroll + for(int i = 0; i < 8; ++i) + if((1ll<< (8 * i)) & packed) + shared.indices[scan++] = gid + 8 * tid + i; + } + __syncthreads(); + + DeviceMemToMemLoop(total, shared.indices, tid, + rightJoin_global + start, false); +} + +//////////////////////////////////////////////////////////////////////////////// +// RelationalJoin + +template +MGPU_HOST int RelationalJoin(InputIt1 a_global, int aCount, InputIt2 b_global, + int bCount, MGPU_MEM(int)* ppAJoinIndices, MGPU_MEM(int)* ppBJoinIndices, + Comp comp, CudaContext& context) { + + typedef typename std::iterator_traits::value_type T; + const bool SupportLeft = MgpuJoinKindLeft == Kind || + MgpuJoinKindOuter == Kind; + const bool SupportRight = MgpuJoinKindRight == Kind || + MgpuJoinKindOuter == Kind; + + const MgpuSearchType LeftType = SupportLeft ? + MgpuSearchTypeIndexMatch : MgpuSearchTypeIndex; + + MGPU_MEM(int) aLowerBound = context.Malloc(aCount); + MGPU_MEM(byte) bMatches; + + // Find the lower bound of A into B. If we are right joining also return the + // set of matches of B into A. + int rightJoinTotal = 0; + if(SupportRight) { + // Support a right or outer join. Count the number of B elements that + // have matches in A. These matched values are included in the inner + // join part. The other values (bCount - bMatchCount) are copied to the + // end for the right join part. + bMatches = context.Malloc(bCount); + int bMatchCount; + SortedSearch(a_global, + aCount, b_global, bCount, aLowerBound->get(), bMatches->get(), comp, + context, 0, &bMatchCount); + rightJoinTotal = bCount - bMatchCount; + } else + SortedSearch(a_global, + aCount, b_global, bCount, aLowerBound->get(), (int*)0, comp, + context, 0, 0); + + // Use the lower bounds to compute the counts for each element. + MGPU_MEM(int) aCounts = context.Malloc(aCount); + if(SupportLeft) + SortedEqualityCount(a_global, aCount, b_global, bCount, + aLowerBound->get(), aCounts->get(), comp, LeftJoinEqualityOp(), + context); + else + SortedEqualityCount(a_global, aCount, b_global, bCount, + aLowerBound->get(), aCounts->get(), comp, SortedEqualityOp(), + context); + + // Scan the product counts. This is part of the load-balancing search. + int leftJoinTotal; + ScanExc(aCounts->get(), aCount, &leftJoinTotal, context); + + // Allocate space for the join indices from the sum of left and right join + // sizes. + int joinTotal = leftJoinTotal + rightJoinTotal; + MGPU_MEM(int) aIndicesDevice = context.Malloc(joinTotal); + MGPU_MEM(int) bIndicesDevice = context.Malloc(joinTotal); + + // Launch the inner/left join kernel. Run an upper-bounds partitioning + // to load-balance the data. + typedef LaunchBoxVT<128, 7> Tuning; + int2 launch = Tuning::GetLaunchParams(context); + int NV = launch.x * launch.y; + + MGPU_MEM(int) partitionsDevice = MergePathPartitions( + mgpu::counting_iterator(0), leftJoinTotal, aCounts->get(), + aCount, NV, 0, mgpu::less(), context); + + int numBlocks = MGPU_DIV_UP(leftJoinTotal + aCount, NV); + KernelLeftJoin + <<>>(leftJoinTotal, + aLowerBound->get(), aCounts->get(), aCount, partitionsDevice->get(), + aIndicesDevice->get(), bIndicesDevice->get()); + MGPU_SYNC_CHECK("KernelLeftJoin"); + + // Launch the right join kernel. Compact the non-matches from B into A. + if(SupportRight) { + const int NT = 128; + int numBlocks = MGPU_DIV_UP(bCount, 8 * NT); + + MGPU_MEM(int) totals = context.Malloc(numBlocks); + KernelRightJoinUpsweep<<>>( + (const uint64*)bMatches->get(), bCount, totals->get()); + MGPU_SYNC_CHECK("KernelRightJoinUpsweep"); + + ScanExc(totals->get(), numBlocks, context); + + KernelRightJoinDownsweep<<>>( + (const uint64*)bMatches->get(), bCount, totals->get(), + bIndicesDevice->get() + leftJoinTotal); + MGPU_SYNC_CHECK("KernelRightJoinDownsweep"); + + cudaMemset(aIndicesDevice->get() + leftJoinTotal, -1, + sizeof(int) * rightJoinTotal); + } + + *ppAJoinIndices = aIndicesDevice; + *ppBJoinIndices = bIndicesDevice; + return joinTotal; +} + +template +MGPU_HOST int RelationalJoin(InputIt1 a_global, int aCount, InputIt2 b_global, + int bCount, MGPU_MEM(int)* ppAJoinIndices, MGPU_MEM(int)* ppBJoinIndices, + CudaContext& context) { + + typedef typename std::iterator_traits::value_type T; + return RelationalJoin(a_global, aCount, b_global, bCount, + ppAJoinIndices, ppBJoinIndices, mgpu::less(), context); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/loadbalance.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/loadbalance.cuh new file mode 100644 index 0000000000000000000000000000000000000000..6626ba282065ce0bd26406f043268722747539f0 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/loadbalance.cuh @@ -0,0 +1,88 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuhost.cuh" +#include "../device/ctaloadbalance.cuh" +#include "../kernels/search.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// KernelLoadBalance + +template +MGPU_LAUNCH_BOUNDS void KernelLoadBalance(int aCount, InputIt b_global, + int bCount, const int* mp_global, int* indices_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + __shared__ int indices_shared[NT * (VT + 1)]; + + int tid = threadIdx.x; + int block = blockIdx.x; + int4 range = CTALoadBalance(aCount, b_global, bCount, block, tid, + mp_global, indices_shared, false); + aCount = range.y - range.x; + + DeviceSharedToGlobal(aCount, indices_shared, tid, + indices_global + range.x, false); +} + +//////////////////////////////////////////////////////////////////////////////// +// LoadBalanceSearch + +template +MGPU_HOST void LoadBalanceSearch(int aCount, InputIt b_global, int bCount, + int* indices_global, CudaContext& context) { + + const int NT = 128; + const int VT = 7; + typedef LaunchBoxVT Tuning; + int2 launch = Tuning::GetLaunchParams(context); + const int NV = launch.x * launch.y; + + MGPU_MEM(int) partitionsDevice = MergePathPartitions( + mgpu::counting_iterator(0), aCount, b_global, bCount, NV, 0, + mgpu::less(), context); + + int numBlocks = MGPU_DIV_UP(aCount + bCount, NV); + KernelLoadBalance<<>>( + aCount, b_global, bCount, partitionsDevice->get(), indices_global); + MGPU_SYNC_CHECK("KernelLoadBalance"); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/localitysort.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/localitysort.cuh new file mode 100644 index 0000000000000000000000000000000000000000..d5fda4859b95fb8433a8447b1cd0ced3dab7541f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/localitysort.cuh @@ -0,0 +1,125 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuhost.cuh" +#include "../kernels/mergesort.cuh" +#include "../kernels/segmentedsort.cuh" + +namespace mgpu { + +template +MGPU_HOST void LocalitySortKeys(T* data_global, int count, CudaContext& context, + Comp comp, bool verbose) { + + const int NT = 128; + const int VT = 11; + typedef LaunchBoxVT Tuning; + int2 launch = Tuning::GetLaunchParams(context); + const int NV = launch.x * launch.y; + + int numBlocks = MGPU_DIV_UP(count, NV); + int numPasses = FindLog2(numBlocks, true); + + SegSortSupport support; + MGPU_MEM(byte) mem = AllocSegSortBuffers(count, NV, support, false, + context); + + MGPU_MEM(T) destDevice = context.Malloc(count); + T* source = data_global; + T* dest = destDevice->get(); + + KernelBlocksort + <<>>(source, (const int*)0, + count, (1 & numPasses) ? dest : source, (int*)0, comp); + MGPU_SYNC_CHECK("KernelBlocksort"); + + if(1 & numPasses) std::swap(source, dest); + + SegSortPasses(support, source, (int*)0, count, + numBlocks, numPasses, dest, (int*)0, comp, context, verbose); +} +template +MGPU_HOST void LocalitySortKeys(T* data_global, int count, CudaContext& context, + bool verbose) { + LocalitySortKeys(data_global, count, context, mgpu::less(), verbose); +} + +template +MGPU_HOST void LocalitySortPairs(KeyType* keys_global, ValType* values_global, + int count, CudaContext& context, Comp comp, bool verbose) { + + const int NT = 128; + const int VT = 7; + typedef LaunchBoxVT Tuning; + int2 launch = Tuning::GetLaunchParams(context); + const int NV = launch.x * launch.y; + + int numBlocks = MGPU_DIV_UP(count, NV); + int numPasses = FindLog2(numBlocks, true); + + SegSortSupport support; + MGPU_MEM(byte) mem = AllocSegSortBuffers(count, NV, support, false, + context); + + MGPU_MEM(KeyType) keysDestDevice = context.Malloc(count); + MGPU_MEM(ValType) valsDestDevice = context.Malloc(count); + + KeyType* keysSource = keys_global; + KeyType* keysDest = keysDestDevice->get(); + ValType* valsSource = values_global; + ValType* valsDest = valsDestDevice->get(); + + KernelBlocksort<<>>( + keysSource, valsSource, count, (1 & numPasses) ? keysDest : keysSource, + (1 & numPasses) ? valsDest : valsSource, comp); + MGPU_SYNC_CHECK("KernelBlocksort"); + + if(1 & numPasses) { + std::swap(keysSource, keysDest); + std::swap(valsSource, valsDest); + } + + SegSortPasses(support, keysSource, valsSource, count, + numBlocks, numPasses, keysDest, valsDest, comp, context, verbose); +} +template +MGPU_HOST void LocalitySortPairs(KeyType* keys_global, ValType* values_global, + int count, CudaContext& context, bool verbose) { + LocalitySortPairs(keys_global, values_global, count, context, + mgpu::less(), verbose); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/merge.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/merge.cuh new file mode 100644 index 0000000000000000000000000000000000000000..2259be7da77a447b6f17b48e4377b9453d135018 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/merge.cuh @@ -0,0 +1,152 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuhost.cuh" +#include "../device/ctamerge.cuh" +#include "../kernels/search.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// KernelMerge + +template +MGPU_LAUNCH_BOUNDS void KernelMerge(KeysIt1 aKeys_global, ValsIt1 aVals_global, + int aCount, KeysIt2 bKeys_global, ValsIt2 bVals_global, int bCount, + const int* mp_global, int coop, KeysIt3 keys_global, ValsIt3 vals_global, + Comp comp) { + + typedef MGPU_LAUNCH_PARAMS Params; + typedef typename std::iterator_traits::value_type KeyType; + typedef typename std::iterator_traits::value_type ValType; + + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + union Shared { + KeyType keys[NT * (VT + 1)]; + int indices[NV]; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + + int4 range = ComputeMergeRange(aCount, bCount, block, coop, NT * VT, + mp_global); + + DeviceMerge(aKeys_global, aVals_global, + aCount, bKeys_global, bVals_global, bCount, tid, block, range, + shared.keys, shared.indices, keys_global, vals_global, comp); +} + +//////////////////////////////////////////////////////////////////////////////// +// MergeKeys + +template +MGPU_HOST void MergeKeys(KeysIt1 aKeys_global, int aCount, KeysIt2 bKeys_global, + int bCount, KeysIt3 keys_global, Comp comp, CudaContext& context) { + + typedef typename std::iterator_traits::value_type T; + typedef LaunchBoxVT< + 128, 23, 0, + 128, 11, 0, + 128, (sizeof(T) > 4) ? 7 : 11, 0 + > Tuning; + int2 launch = Tuning::GetLaunchParams(context); + + const int NV = launch.x * launch.y; + MGPU_MEM(int) partitionsDevice = MergePathPartitions( + aKeys_global, aCount, bKeys_global, bCount, NV, 0, comp, context); + + int numBlocks = MGPU_DIV_UP(aCount + bCount, NV); + KernelMerge + <<>>(aKeys_global, + (const int*)0, aCount, bKeys_global, (const int*)0, bCount, + partitionsDevice->get(), 0, keys_global, (int*)0, comp); + MGPU_SYNC_CHECK("KernelMerge"); +} +template +MGPU_HOST void MergeKeys(KeysIt1 aKeys_global, int aCount, KeysIt2 bKeys_global, + int bCount, KeysIt3 keys_global, CudaContext& context) { + + typedef mgpu::less::value_type> Comp; + return MergeKeys(aKeys_global, aCount, bKeys_global, bCount, keys_global, + Comp(), context); +} + +//////////////////////////////////////////////////////////////////////////////// +// MergePairs + +template +MGPU_HOST void MergePairs(KeysIt1 aKeys_global, ValsIt1 aVals_global, + int aCount, KeysIt2 bKeys_global, ValsIt2 bVals_global, int bCount, + KeysIt3 keys_global, ValsIt3 vals_global, Comp comp, CudaContext& context) { + + typedef typename std::iterator_traits::value_type T; + typedef LaunchBoxVT< + 128, 11, 0, + 128, 11, 0, + 128, (sizeof(T) > 4) ? 7 : 11, 0 + > Tuning; + int2 launch = Tuning::GetLaunchParams(context); + + const int NV = launch.x * launch.y; + MGPU_MEM(int) partitionsDevice = MergePathPartitions( + aKeys_global, aCount, bKeys_global, bCount, NV, 0, comp, context); + + int numBlocks = MGPU_DIV_UP(aCount + bCount, NV); + KernelMerge + <<>>(aKeys_global, + aVals_global, aCount, bKeys_global, bVals_global, bCount, + partitionsDevice->get(), 0, keys_global, vals_global, comp); + MGPU_SYNC_CHECK("KernelMerge"); +} +template +MGPU_HOST void MergePairs(KeysIt1 aKeys_global, ValsIt1 aVals_global, + int aCount, KeysIt2 bKeys_global, ValsIt2 bVals_global, int bCount, + KeysIt3 keys_global, ValsIt3 vals_global, CudaContext& context) { + + typedef mgpu::less::value_type> Comp; + return MergePairs(aKeys_global, aVals_global, aCount, bKeys_global, + bVals_global, bCount, keys_global, vals_global, Comp(), context); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/mergesort.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/mergesort.cuh new file mode 100644 index 0000000000000000000000000000000000000000..4b527c50a1c3e77876488d834258bf093aeec5f2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/mergesort.cuh @@ -0,0 +1,268 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuhost.cuh" +#include "../kernels/merge.cuh" + +namespace mgpu { + +template +MGPU_LAUNCH_BOUNDS void KernelBlocksort(KeyIt1 keysSource_global, + ValIt1 valsSource_global, int count, KeyIt2 keysDest_global, + ValIt2 valsDest_global, Comp comp) { + + typedef MGPU_LAUNCH_PARAMS Params; + typedef typename std::iterator_traits::value_type KeyType; + typedef typename std::iterator_traits::value_type ValType; + + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + union Shared { + KeyType keys[NT * (VT + 1)]; + ValType values[NV]; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + int count2 = min(NV, count - gid); + + // Load the values into thread order. + ValType threadValues[VT]; + if(HasValues) { + DeviceGlobalToShared(count2, valsSource_global + gid, tid, + shared.values); + DeviceSharedToThread(shared.values, tid, threadValues); + } + + // Load keys into shared memory and transpose into register in thread order. + KeyType threadKeys[VT]; + DeviceGlobalToShared(count2, keysSource_global + gid, tid, + shared.keys); + DeviceSharedToThread(shared.keys, tid, threadKeys); + + // If we're in the last tile, set the uninitialized keys for the thread with + // a partial number of keys. + int first = VT * tid; + if(first + VT > count2 && first < count2) { + KeyType maxKey = threadKeys[0]; + #pragma unroll + for(int i = 1; i < VT; ++i) + if(first + i < count2) + maxKey = comp(maxKey, threadKeys[i]) ? threadKeys[i] : maxKey; + + // Fill in the uninitialized elements with max key. + #pragma unroll + for(int i = 0; i < VT; ++i) + if(first + i >= count2) threadKeys[i] = maxKey; + } + + CTAMergesort(threadKeys, threadValues, shared.keys, + shared.values, count2, tid, comp); + + // Store the sorted keys to global. + DeviceSharedToGlobal(count2, shared.keys, tid, + keysDest_global + gid); + + if(HasValues) { + DeviceThreadToShared(threadValues, tid, shared.values); + DeviceSharedToGlobal(count2, shared.values, tid, + valsDest_global + gid); + } +} + +//////////////////////////////////////////////////////////////////////////////// +// MergesortKeys + +template +MGPU_HOST void MergesortKeys(T* data_global, int count, Comp comp, + CudaContext& context) { + + typedef LaunchBoxVT< + 256, 11, 0, + 256, (sizeof(T) > 4) ? 7 : 11, 0, + 256, (sizeof(T) > 4) ? 7 : 11, 0 + > Tuning; + int2 launch = Tuning::GetLaunchParams(context); + + const int NV = launch.x * launch.y; + int numBlocks = MGPU_DIV_UP(count, NV); + int numPasses = FindLog2(numBlocks, true); + + MGPU_MEM(T) destDevice = context.Malloc(count); + T* source = data_global; + T* dest = destDevice->get(); + + KernelBlocksort + <<>>(source, (const int*)0, + count, (1 & numPasses) ? dest : source, (int*)0, comp); + MGPU_SYNC_CHECK("KernelBlocksort"); + + if(1 & numPasses) std::swap(source, dest); + + for(int pass = 0; pass < numPasses; ++pass) { + int coop = 2<< pass; + MGPU_MEM(int) partitionsDevice = MergePathPartitions( + source, count, source, 0, NV, coop, comp, context); + + KernelMerge + <<>>(source, + (const int*)0, count, source, (const int*)0, 0, + partitionsDevice->get(), coop, dest, (int*)0, comp); + MGPU_SYNC_CHECK("KernelMerge"); + + std::swap(dest, source); + } +} +template +MGPU_HOST void MergesortKeys(T* data_global, int count, CudaContext& context) { + MergesortKeys(data_global, count, mgpu::less(), context); +} + +//////////////////////////////////////////////////////////////////////////////// +// MergesortPairs + +template +MGPU_HOST void MergesortPairs(KeyType* keys_global, ValType* values_global, + int count, Comp comp, CudaContext& context) { + + typedef LaunchBoxVT< + 256, 11, 0, + 256, (sizeof(KeyType) > 4) ? 7 : 11, 0, + 256, (sizeof(KeyType) > 4) ? 7 : 11, 0 + > Tuning; + int2 launch = Tuning::GetLaunchParams(context); + + const int NV = launch.x * launch.y; + int numBlocks = MGPU_DIV_UP(count, NV); + int numPasses = FindLog2(numBlocks, true); + + MGPU_MEM(KeyType) keysDestDevice = context.Malloc(count); + MGPU_MEM(ValType) valsDestDevice = context.Malloc(count); + KeyType* keysSource = keys_global; + KeyType* keysDest = keysDestDevice->get(); + ValType* valsSource = values_global; + ValType* valsDest = valsDestDevice->get(); + + KernelBlocksort<<>>( + keysSource, valsSource, count, (1 & numPasses) ? keysDest : keysSource, + (1 & numPasses) ? valsDest : valsSource, comp); + MGPU_SYNC_CHECK("KernelBlocksort"); + + if(1 & numPasses) { + std::swap(keysSource, keysDest); + std::swap(valsSource, valsDest); + } + + for(int pass = 0; pass < numPasses; ++pass) { + int coop = 2<< pass; + MGPU_MEM(int) partitionsDevice = MergePathPartitions( + keysSource, count, keysSource, 0, NV, coop, comp, context); + + KernelMerge + <<>>(keysSource, + valsSource, count, keysSource, valsSource, 0, + partitionsDevice->get(), coop, keysDest, valsDest, comp); + MGPU_SYNC_CHECK("KernelMerge"); + + std::swap(keysDest, keysSource); + std::swap(valsDest, valsSource); + } +} +template +MGPU_HOST void MergesortPairs(KeyType* keys_global, ValType* values_global, + int count, CudaContext& context) { + MergesortPairs(keys_global, values_global, count, mgpu::less(), + context); +} + +template +MGPU_HOST void MergesortIndices(KeyType* keys_global, int* values_global, + int count, Comp comp, CudaContext& context) { + + const int NT = 256; + const int VT = 11; + typedef LaunchBoxVT Tuning; + int2 launch = Tuning::GetLaunchParams(context); + + const int NV = launch.x * launch.y; + int numBlocks = MGPU_DIV_UP(count, NV); + int numPasses = FindLog2(numBlocks, true); + + MGPU_MEM(KeyType) keysDestDevice = context.Malloc(count); + MGPU_MEM(int) valsDestDevice = context.Malloc(count); + KeyType* keysSource = keys_global; + KeyType* keysDest = keysDestDevice->get(); + int* valsSource = values_global; + int* valsDest = valsDestDevice->get(); + + KernelBlocksort<<>>( + keysSource, mgpu::counting_iterator(0), count, + (1 & numPasses) ? keysDest : keysSource, + (1 & numPasses) ? valsDest : valsSource, comp); + MGPU_SYNC_CHECK("KernelBlocksort"); + + if(1 & numPasses) { + std::swap(keysSource, keysDest); + std::swap(valsSource, valsDest); + } + + for(int pass = 0; pass < numPasses; ++pass) { + int coop = 2<< pass; + MGPU_MEM(int) partitionsDevice = MergePathPartitions( + keysSource, count, keysSource, 0, NV, coop, comp, context); + + KernelMerge + <<>>(keysSource, + valsSource, count, keysSource, valsSource, 0, + partitionsDevice->get(), coop, keysDest, valsDest, comp); + MGPU_SYNC_CHECK("KernelMerge"); + + std::swap(keysDest, keysSource); + std::swap(valsDest, valsSource); + } +} +template +MGPU_HOST void MergesortIndices(KeyType* keys_global, int* values_global, + int count, CudaContext& context) { + MergesortIndices(keys_global, values_global, count, mgpu::less(), + context); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/reduce.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/reduce.cuh new file mode 100644 index 0000000000000000000000000000000000000000..29defc0b2331990a5572b4b1bfb4ba585ffb9e3f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/reduce.cuh @@ -0,0 +1,144 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuhost.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// KernelReduce + +template +MGPU_LAUNCH_BOUNDS void KernelReduce(InputIt data_global, int count, + T identity, Op op, T* reduction_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + typedef CTAReduce R; + + union Shared { + typename R::Storage reduceStorage; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + int count2 = min(NV, count - gid); + + // Load a full tile into register in strided order. Set out-of-range values + // with identity. + T data[VT]; + DeviceGlobalToRegDefault(count2, data_global + gid, tid, data, + identity); + + // Sum elements within each thread. + T x; + #pragma unroll + for(int i = 0; i < VT; ++i) + x = i ? op(x, data[i]) : data[i]; + + // Sum thread-totals over the CTA. + x = R::Reduce(tid, x, shared.reduceStorage, op); + + // Store the tile's reduction to global memory. + if(!tid) + reduction_global[block] = x; +} + +//////////////////////////////////////////////////////////////////////////////// +// Reduce + +template +MGPU_HOST void Reduce(InputIt data_global, int count, T identity, Op op, + T* reduce_global, T* reduce_host, CudaContext& context) { + + MGPU_MEM(T) totalDevice; + if(!reduce_global) { + totalDevice = context.Malloc(1); + reduce_global = totalDevice->get(); + } + + if(count <= 256) { + typedef LaunchBoxVT<256, 1> Tuning; + KernelReduce<<<1, 256, 0, context.Stream()>>>( + data_global, count, identity, op, reduce_global); + MGPU_SYNC_CHECK("KernelReduce"); + + } else if(count <= 768) { + typedef LaunchBoxVT<256, 3> Tuning; + KernelReduce<<<1, 256, 0, context.Stream()>>>( + data_global, count, identity, op, reduce_global); + MGPU_SYNC_CHECK("KernelReduce"); + + } else if(count <= 512 * ((sizeof(T) > 4) ? 4 : 8)) { + typedef LaunchBoxVT<512, (sizeof(T) > 4) ? 4 : 8> Tuning; + KernelReduce<<<1, 512, 0, context.Stream()>>>( + data_global, count, identity, op, reduce_global); + MGPU_SYNC_CHECK("KernelReduce"); + + } else { + // Launch a grid and reduce tiles to temporary storage. + typedef LaunchBoxVT<256, (sizeof(T) > 4) ? 8 : 16> Tuning; + int2 launch = Tuning::GetLaunchParams(context); + int NV = launch.x * launch.y; + int numBlocks = MGPU_DIV_UP(count, NV); + + MGPU_MEM(T) reduceDevice = context.Malloc(numBlocks); + KernelReduce<<>>( + data_global, count, identity, op, reduceDevice->get()); + MGPU_SYNC_CHECK("KernelReduce"); + + Reduce(reduceDevice->get(), numBlocks, identity, op, reduce_global, + (T*)0, context); + } + + if(reduce_host) + copyDtoH(reduce_host, reduce_global, 1); +} + +template +MGPU_HOST typename std::iterator_traits::value_type +Reduce(InputIt data_global, int count, CudaContext& context) { + typedef typename std::iterator_traits::value_type T; + T result; + Reduce(data_global, count, (T)0, mgpu::plus(), (T*)0, &result, context); + return result; +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/reducebykey.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/reducebykey.cuh new file mode 100644 index 0000000000000000000000000000000000000000..c70484b8805a39e561fbf815635d53ebaadb3942 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/reducebykey.cuh @@ -0,0 +1,289 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#include "../kernels/segreducecsr.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// KernelReduceByKeyPreprocess +// Stream through keys and find discontinuities. Compress these into a bitfield +// for each thread in the reduction CTA. Emit a count of discontinuities. +// These are scanned to provide limits. +template +MGPU_LAUNCH_BOUNDS void KernelReduceByKeyPreprocess(KeysIt keys_global, + int count, int* threadCodes_global, int* counts_global, Comp comp) { + + typedef typename std::iterator_traits::value_type T; + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + + const int VT = Params::VT; + const int NV = NT * VT; + + union Shared { + T keys[NT * (VT + 1)]; + int indices[NT]; + typename CTAScan::Storage scanStorage; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + int count2 = min(NV + 1, count - gid); + + // Load the keys for this tile with one following element. This allows us + // to determine end flags for all segments. + DeviceGlobalToShared2(count2, keys_global + gid, tid, + shared.keys); + + // Compare adjacent keys in each thread and mark discontinuities in + // endFlags bits. + int endFlags = 0; + if(count2 > NV) { + T key = shared.keys[VT * tid]; + #pragma unroll + for(int i = 0; i < VT; ++i) { + T next = shared.keys[VT * tid + 1 + i]; + if(!comp(key, next)) endFlags |= 1<< i; + key = next; + } + } else { + T key = shared.keys[VT * tid]; + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = VT * tid + 1 + i; + T next = shared.keys[index]; + if(index == count2 || (index < count2 && !comp(key, next))) + endFlags |= 1<< i; + key = next; + } + } + __syncthreads(); + + // Count the number of encountered end flags. + int total; + int scan = CTAScan::Scan(tid, popc(endFlags), shared.scanStorage, + &total); + + if(!tid) + counts_global[block] = total; + + if(total) { + // Find the segmented scan start for this thread. + int tidDelta = DeviceFindSegScanDelta(tid, 0 != endFlags, + shared.indices); + + // threadCodes: + // 12:0 - end flags for up to 13 values per thread. + // 19:13 - tid delta for up to 128 threads. + // 30:20 - scan offset for streaming partials. + int threadCodes = endFlags | (tidDelta<< 13) | (scan<< 20); + threadCodes_global[NT * block + tid] = threadCodes; + } +} + +//////////////////////////////////////////////////////////////////////////////// +// KernelReduceByKeyEmit + +template +MGPU_LAUNCH_BOUNDS void KernelReduceByKeyEmit(KeysIt keys_global, + int count, const int* threadCodes_global, const int* limits_global, + KeyType* keysDest_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + + union Shared { + int indices[NV]; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + + int limit0 = limits_global[block]; + int limit1 = limits_global[block + 1]; + int threadCodes = threadCodes_global[NT * block + tid]; + + int total = limit1 - limit0; + if(total) { + // Reconstruct row IDs from thread codes and the starting row offset. + int rows[VT + 1]; + DeviceExpandFlagsToRows(threadCodes>> 20, threadCodes, rows); + + // Compact the location of the last element in each segment. + int index = gid + VT * tid; + #pragma unroll + for(int i = 0; i < VT; ++i) + if(rows[i] != rows[i + 1]) + shared.indices[rows[i]] = index + i; + __syncthreads(); + + // Copy a key from the start of each segment. + for(int i = tid; i < total; i += NT) { + int pos = shared.indices[i] + 1; + int seg = limit0 + i + 1; + if(pos >= count) { + pos = 0; + seg = 0; + } + keysDest_global[seg] = keys_global[pos]; + } + } +} + +//////////////////////////////////////////////////////////////////////////////// +// ReduceByKeyPreprocess + +template +MGPU_HOST void ReduceByKeyPreprocess(int count, KeysIt keys_global, + KeyType* keysDest_global, Comp comp, int* count_host, int* count_global, + std::auto_ptr* ppData, CudaContext& context) { + + typedef typename SegReducePreprocessTuning::Tuning Tuning; + int2 launch = Tuning::GetLaunchParams(context); + int NV = launch.x * launch.y; + + const bool AsyncTransfer = true; + + std::auto_ptr + data(new ReduceByKeyPreprocessData); + + int numBlocks = MGPU_DIV_UP(count, NV); + data->count = count; + data->numBlocks = numBlocks; + data->limitsDevice = context.Malloc(numBlocks + 1); + data->threadCodesDevice = context.Malloc(numBlocks * launch.x); + + // Fill out thread codes for each thread in the processing CTAs. + KernelReduceByKeyPreprocess + <<>>(keys_global, count, + data->threadCodesDevice->get(), data->limitsDevice->get(), comp); + MGPU_SYNC_CHECK("KernelReduceByKeyPreprocess"); + + // Scan the output counts. + Scan(data->limitsDevice->get(), numBlocks, 0, + mgpu::plus(), data->limitsDevice->get() + numBlocks, (int*)0, + data->limitsDevice->get(), context); + + // Queue up a transfer of the row total. + if(count_global) + copyDtoD(count_global, data->limitsDevice->get() + numBlocks, 1, + context.Stream()); + if(count_host) { + if(AsyncTransfer) { + cudaError_t error = cudaMemcpyAsync(context.PageLocked(), + data->limitsDevice->get() + numBlocks, sizeof(int), + cudaMemcpyDeviceToHost, context.Stream()); + error = cudaEventRecord(context.Event(), context.Stream()); + } else + copyDtoH(count_host, data->limitsDevice->get() + numBlocks, 1); + } + + // Output one key per segment. + if(keysDest_global) { + KernelReduceByKeyEmit + <<>>(keys_global, + count, data->threadCodesDevice->get(), data->limitsDevice->get(), + keysDest_global); + MGPU_SYNC_CHECK("KernelReduceByKeyEmit"); + } + + // Retrieve the number of rows. + if(AsyncTransfer && count_host) { + cudaError_t error = cudaEventSynchronize(context.Event()); + *count_host = *context.PageLocked(); + } + data->numSegments = count_host ? *count_host : -1; + + *ppData = data; +} + +//////////////////////////////////////////////////////////////////////////////// +// ReduceByKey host function. + +template +MGPU_HOST void ReduceByKey(KeysIt keys_global, InputIt data_global, int count, + ValType identity, Op op, Comp comp, KeyType* keysDest_global, + DestIt dest_global, int* count_host, int* count_global, + CudaContext& context) { + + std::auto_ptr data; + MGPU_MEM(int) countsDevice = context.Malloc(1); + if(count_host && !count_global) count_global = countsDevice->get(); + + // Preprocess the keys and emit the first key in each segment. + ReduceByKeyPreprocess(count, keys_global, keysDest_global, comp, + (int*)0, count_global, &data, context); + + const bool AsyncTransfer = true; + if(count_host) { + if(AsyncTransfer) { + cudaError_t error = cudaMemcpyAsync(context.PageLocked(), + count_global, sizeof(int), cudaMemcpyDeviceToHost, + context.Stream()); + error = cudaEventRecord(context.Event(), context.Stream()); + } else + copyDtoH(count_host, count_global, 1); + } + + // Evaluate the segmented reduction. + SegReduceApply(*data, data_global, identity, op, dest_global, context); + + // Retrieve the number of segments. + if(AsyncTransfer && count_host) { + cudaError_t error = cudaEventSynchronize(context.Event()); + *count_host = *context.PageLocked(); + } +} + +//////////////////////////////////////////////////////////////////////////////// +// ReduceByKeyApply + +template +MGPU_HOST void ReduceByKeyApply(const ReduceByKeyPreprocessData& preprocess, + InputIt data_global, T identity, Op op, DestIt dest_global, + CudaContext& context) { + + return SegReduceApply(preprocess, data_global, identity, op, dest_global, + context); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/scan.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/scan.cuh new file mode 100644 index 0000000000000000000000000000000000000000..728dacdc5c9bda8d1f0ecf16e0f8c6b9ef812f15 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/scan.cuh @@ -0,0 +1,234 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpudevice.cuh" +#include "../kernels/reduce.cuh" + +namespace mgpu { + + +//////////////////////////////////////////////////////////////////////////////// + +template +struct CTATileScan { + enum { NV = NT * VT }; + typedef CTAScan S; + + union Storage { + T data[NV]; + typename S::Storage scanStorage; + }; + + template + MGPU_DEVICE static T DeviceScanTile(DataIt data_global, int count, int tid, + T identity, Op op, T start, DestIt dest_global, Storage& storage) { + + T data[VT]; + if(VT > 1) { + DeviceGlobalToSharedDefault(count, data_global, tid, + storage.data, identity); + DeviceSharedToThread(storage.data, tid, data); + } else + DeviceGlobalToRegDefault(count, data_global, tid, data, + identity); + + // Reduce within each thread for thread totals. + T x; + #pragma unroll + for(int i = 0; i < VT; ++i) + x = i ? op(x, data[i]) : data[i]; + + // Reduce thread totals across the tile. + T total; + x = S::Scan(tid, x, storage.scanStorage, &total, MgpuScanTypeExc, + identity, op); + + // Add the scan as carry-in and scan into shared memory. + T localScan[VT]; + x = op(x, start); + + #pragma unroll + for(int i = 0; i < VT; ++i) { + if(MgpuScanTypeExc == Type) + localScan[i] = x; + x = op(x, data[i]); + if(MgpuScanTypeInc == Type) + localScan[i] = x; + } + + if(VT > 1) { + // Transpose into shared memory and store to dest_global. + DeviceThreadToShared(localScan, tid, storage.data); + DeviceSharedToGlobal(count, storage.data, tid, dest_global); + } else + DeviceRegToGlobal(count, localScan, tid, dest_global); + + // Return the reduction of all elements in this tile. + return total; + } +}; + +// KernelScanParallel. +// Scan all inputs in a single CTA. +template +MGPU_LAUNCH_BOUNDS void KernelScanParallel(DataIt data_global, int count, + T identity, Op op, T* total_global, OutputIt dest_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + + typedef CTATileScan TileScan; + union Shared { + typename TileScan::Storage tileScanStorage; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + + // Scan from data_global into dest_global. + T total = TileScan::DeviceScanTile(data_global, count, tid, identity, + op, identity, dest_global, shared.tileScanStorage); + + if(!tid && total_global) + *total_global = total; +} + +template +MGPU_LAUNCH_BOUNDS void KernelScanDownsweep(DataIt data_global, int count, + const T* reduction_global, T identity, Op op, OutputIt dest_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + + typedef CTATileScan TileScan; + __shared__ typename TileScan::Storage tileScanStorage; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + int count2 = min(NV, count - gid); + + // Load the reduction of the previous tiles. + T start = reduction_global[block]; + + // Scan from data_global into dest_global. + TileScan::DeviceScanTile(data_global + gid, count2, tid, + identity, op, start, dest_global + gid, tileScanStorage); +} + +//////////////////////////////////////////////////////////////////////////////// + +template +MGPU_HOST void Scan(DataIt data_global, int count, T identity, Op op, + T* reduce_global, T* reduce_host, DestIt dest_global, + CudaContext& context) { + + MGPU_MEM(T) totalDevice; + if(reduce_host && !reduce_global) { + totalDevice = context.Malloc(1); + reduce_global = totalDevice->get(); + } + + if(count <= 256) { + typedef LaunchBoxVT<256, 1> Tuning; + KernelScanParallel<<<1, 256, 0, context.Stream()>>>( + data_global, count, identity, op, reduce_global, dest_global); + MGPU_SYNC_CHECK("KernelScanParallel"); + + } else if(count <= 768) { + typedef LaunchBoxVT<256, 3> Tuning; + KernelScanParallel<<<1, 256, 0, context.Stream()>>>( + data_global, count, identity, op, reduce_global, dest_global); + MGPU_SYNC_CHECK("KernelScanParallel"); + + } else if (count <= 512 * 5) { + typedef LaunchBoxVT<512, 5> Tuning; + KernelScanParallel<<<1, 512, 0, context.Stream()>>>( + data_global, count, identity, op, reduce_global, dest_global); + MGPU_SYNC_CHECK("KernelScanParallel"); + + } else { + typedef LaunchBoxVT< + 128, (sizeof(T) > 4) ? 7 : 15, 0, + 128, 7, 0, + 128, 7, 0 + > Tuning; + int2 launch = Tuning::GetLaunchParams(context); + int NV = launch.x * launch.y; + int numBlocks = MGPU_DIV_UP(count, NV); + MGPU_MEM(T) reduceDevice = context.Malloc(numBlocks + 1); + + // Reduce tiles into reduceDevice. + KernelReduce<<>>( + data_global, count, identity, op, reduceDevice->get()); + MGPU_SYNC_CHECK("KernelReduce"); + + // Recurse to scan the reductions. + Scan(reduceDevice->get(), numBlocks, identity, op, + reduce_global, (T*)0, reduceDevice->get(), context); + + // Add scanned reductions back into output and scan. + KernelScanDownsweep + <<>>(data_global, count, + reduceDevice->get(), identity, op, dest_global); + MGPU_SYNC_CHECK("KernelScanDownsweep"); + } + if(reduce_host) + copyDtoH(reduce_host, reduce_global, 1); +} + +template +MGPU_HOST void ScanExc(InputIt data_global, int count, T* total, + CudaContext& context) { + + Scan(data_global, count, (T)0, mgpu::plus(), (T*)0, + total, data_global,context); +} + +template +MGPU_HOST void ScanExc(InputIt data_global, int count, CudaContext& context) { + typedef typename std::iterator_traits::value_type T; + Scan(data_global, count, (T)0, mgpu::plus(), (T*)0, + (T*)0, data_global, context); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/search.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/search.cuh new file mode 100644 index 0000000000000000000000000000000000000000..b8838105058ad60f711dc66392a08c29e1a5a429 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/search.cuh @@ -0,0 +1,160 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuhost.cuh" +#include "../device/ctamerge.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// BinarySearchPartitions + +template +__global__ void KernelBinarySearch(int count, It data_global, int numItems, + int nv, int* partitions_global, int numSearches, Comp comp) { + + int gid = NT * blockIdx.x + threadIdx.x; + if(gid < numSearches) { + int p = BinarySearch(data_global, numItems, + min(nv * gid, count), comp); + partitions_global[gid] = p; + } +} + +template +MGPU_MEM(int) BinarySearchPartitions(int count, It1 data_global, int numItems, + int nv, Comp comp, CudaContext& context) { + + const int NT = 64; + int numBlocks = MGPU_DIV_UP(count, nv); + int numPartitionBlocks = MGPU_DIV_UP(numBlocks + 1, NT); + MGPU_MEM(int) partitionsDevice = context.Malloc(numBlocks + 1); + + KernelBinarySearch + <<>>(count, data_global, + numItems, nv, partitionsDevice->get(), numBlocks + 1, comp); + MGPU_SYNC_CHECK("KernelBinarySearch"); + + return partitionsDevice; +} + +//////////////////////////////////////////////////////////////////////////////// +// MergePathPartitions + +template +__global__ void KernelMergePartition(It1 a_global, int aCount, It2 b_global, + int bCount, int nv, int coop, int* mp_global, int numSearches, Comp comp) { + + int partition = NT * blockIdx.x + threadIdx.x; + if(partition < numSearches) { + int a0 = 0, b0 = 0; + int gid = nv * partition; + if(coop) { + int3 frame = FindMergesortFrame(coop, partition, nv); + a0 = frame.x; + b0 = min(aCount, frame.y); + bCount = min(aCount, frame.y + frame.z) - b0; + aCount = min(aCount, frame.x + frame.z) - a0; + + // Put the cross-diagonal into the coordinate system of the input + // lists. + gid -= a0; + } + int mp = MergePath(a_global + a0, aCount, b_global + b0, bCount, + min(gid, aCount + bCount), comp); + mp_global[partition] = mp; + } +} + +template +MGPU_MEM(int) MergePathPartitions(It1 a_global, int aCount, It2 b_global, + int bCount, int nv, int coop, Comp comp, CudaContext& context) { + + const int NT = 64; + int numPartitions = MGPU_DIV_UP(aCount + bCount, nv); + int numPartitionBlocks = MGPU_DIV_UP(numPartitions + 1, NT); + MGPU_MEM(int) partitionsDevice = context.Malloc(numPartitions + 1); + + KernelMergePartition + <<>>(a_global, aCount, + b_global, bCount, nv, coop, partitionsDevice->get(), numPartitions + 1, + comp); + MGPU_SYNC_CHECK("KernelMergePartition"); + + return partitionsDevice; +} + +//////////////////////////////////////////////////////////////////////////////// +// FindSetPartitions + +template +__global__ void KernelSetPartition(InputIt1 a_global, int aCount, + InputIt2 b_global, int bCount, int nv, int* bp_global, int numSearches, + Comp comp) { + + int gid = NT * blockIdx.x + threadIdx.x; + if(gid < numSearches) { + int diag = min(aCount + bCount, gid * nv); + + // Search with level 4 bias. This helps the binary search converge + // quickly for small runs of duplicates (the common case). + int2 bp = BalancedPath(a_global, aCount, b_global, + bCount, diag, 4, comp); + + if(bp.y) bp.x |= 0x80000000; + bp_global[gid] = bp.x; + } +} + +template +MGPU_MEM(int) FindSetPartitions(It1 a_global, int aCount, It2 b_global, + int bCount, int nv, Comp comp, CudaContext& context) { + + const int NT = 64; + int numPartitions = MGPU_DIV_UP(aCount + bCount, nv); + int numPartitionBlocks = MGPU_DIV_UP(numPartitions + 1, NT); + MGPU_MEM(int) partitionsDevice = context.Malloc(numPartitions + 1); + + KernelSetPartition + <<>>(a_global, aCount, + b_global, bCount, nv, partitionsDevice->get(), numPartitions + 1, comp); + MGPU_SYNC_CHECK("KernelSetPartition"); + + return partitionsDevice; +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/segmentedsort.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/segmentedsort.cuh new file mode 100644 index 0000000000000000000000000000000000000000..3fdaa69b6374f570bf70ca7d47cd13983b1671b3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/segmentedsort.cuh @@ -0,0 +1,771 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuhost.cuh" +#include "../device/ctamerge.cuh" +#include "../device/ctasegsort.cuh" +#include "../kernels/search.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// KernelSegBlocksortIndices + +template +MGPU_LAUNCH_BOUNDS void KernelSegBlocksortIndices(InputIt1 keys_global, + InputIt2 values_global, int count, const int* indices_global, + const int* partitions_global, OutputIt1 keysDest_global, + OutputIt2 valsDest_global, int* ranges_global, Comp comp) { + + typedef typename std::iterator_traits::value_type KeyType; + typedef typename std::iterator_traits::value_type ValType; + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + + const int FlagWordsPerThread = MGPU_DIV_UP(VT, 4); + struct Shared { + union { + byte flags[NV]; + int words[NT * FlagWordsPerThread]; + KeyType keys[NV]; + ValType values[NV]; + }; + int ranges[NT]; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + int count2 = min(NV, count - gid); + + int headFlags = DeviceIndicesToHeadFlags(indices_global, + partitions_global, tid, block, count2, shared.words, shared.flags); + + DeviceSegBlocksort(keys_global, values_global, + count2, shared.keys, shared.values, shared.ranges, headFlags, tid, + block, keysDest_global, valsDest_global, ranges_global, comp); +} + +//////////////////////////////////////////////////////////////////////////////// +// KernelSegBlocksortFlags + +template +MGPU_LAUNCH_BOUNDS void KernelSegBlocksortFlags(InputIt1 keys_global, + InputIt2 values_global, int count, const uint* flags_global, + OutputIt1 keysDest_global, OutputIt2 valsDest_global, int* ranges_global, + Comp comp) { + + typedef typename std::iterator_traits::value_type KeyType; + typedef typename std::iterator_traits::value_type ValType; + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + struct Shared { + union { + KeyType keys[NV + VT]; + ValType values[NV]; + }; + union { + int ranges[NT]; + uint flags[NT]; + }; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + int count2 = min(NV, count - gid); + + // Load the head flags and keys. + int flagsToLoad = min(32, count2 - 32 * tid); + uint flags = 0xffffffff; + if(flagsToLoad > 0) { + flags = flags_global[(NV / 32) * block + tid]; + if(flagsToLoad < 32) + flags |= 0xffffffff<< (31 & count2); + } + shared.flags[tid] = flags; + __syncthreads(); + + // Each thread extracts its own head flags from the array in shared memory. + flags = DeviceExtractHeadFlags(shared.flags, VT * tid, VT); + + DeviceSegBlocksort(keys_global, values_global, + count2, shared.keys, shared.values, shared.ranges, flags, tid, block, + keysDest_global, valsDest_global, ranges_global, comp); +} + +//////////////////////////////////////////////////////////////////////////////// +// KernelSegSortMerge + +template +MGPU_LAUNCH_BOUNDS void KernelSegSortMerge(const KeyType* keys_global, + const ValueType* values_global, SegSortSupport support, int count, + int pass, KeyType* keysDest_global, ValueType* valsDest_global, Comp comp) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + union Shared { + KeyType keys[NT * (VT + 1)]; + int indices[NV]; + int4 range; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + + // Check for merge work. + while(true) { + if(!tid) { + int4 range = make_int4(-1, 0, 0, 0); + int next = atomicAdd(&support.queueCounters_global->x, -1) - 1; + if(next >= 0) range = support.mergeList_global[next]; + shared.range = range; + } + __syncthreads(); + + int4 range = shared.range; + __syncthreads(); + + if(range.x < 0) break; + + int block = range.w; + int gid = NV * block; + int count2 = min(NV, count - gid); + range.w = count2 - (range.y - range.x) + range.z; + + if(Segments) { + int compressedRange = support.ranges_global[block]; + int segStart = 0x0000ffff & compressedRange; + int segEnd = compressedRange>> 16; + + DeviceSegSortMerge(keys_global, values_global, + make_int2(segStart, segEnd), tid, block, range, pass, + shared.keys, shared.indices, keysDest_global, valsDest_global, + comp); + } else + // Unsegmented merge (from device/ctamerge.cuh) + DeviceMerge(keys_global, values_global, + 0, keys_global, values_global, 0, tid, block, range, + shared.keys, shared.indices, keysDest_global, valsDest_global, + comp); + } + + // Check for copy work. + while(true) { + if(!tid) { + int list = -1; + int next = atomicAdd(&support.queueCounters_global->y, -1) - 1; + if(next >= 0) list = support.copyList_global[next]; + shared.range.x = list; + } + __syncthreads(); + + int listBlock = shared.range.x; + __syncthreads(); + + if(listBlock < 0) break; + + DeviceSegSortCopy(keys_global, values_global, + tid, listBlock, count, keysDest_global, valsDest_global); + } +} + +//////////////////////////////////////////////////////////////////////////////// +// DeviceSegSortCreateJob +// Job-queueing code that is called by both seg sort partition kernels. + +template +MGPU_DEVICE void DeviceSegSortCreateJob(SegSortSupport support, + int count, bool active, int3 frame, int tid, int pass, int nv, int block, + int p0, int p1, int* shared) { + + typedef CTAScan S; + typename S::Storage* scan = (typename S::Storage*)shared; + + // Compute the gid'th work time. + bool mergeOp = false; + bool copyOp = false; + int gid = nv * block; + int count2 = min(nv, count - gid); + + int4 mergeRange; + if(active) { + mergeRange = FindMergesortInterval(frame, 2<< pass, block, nv, count, + p0, p1); + + // Merge if the source interval does not exactly cover the destination + // interval. Otherwise copy or skip. + int2 interval = (gid < frame.y) ? + make_int2(mergeRange.x, mergeRange.y) : // A coverage + make_int2(mergeRange.z, mergeRange.w); // B coverage. + + mergeOp = (gid != interval.x) || (interval.y - interval.x != count2); + copyOp = !mergeOp && (!pass || !support.copyStatus_global[block]); + + // if(mergeOp) + // printf("%4d: %8d (%8d, %8d, %8d) (%8d, %8d: %4d) (%8d, %8d: %4d)\n", block, + // gid, frame.x, frame.y, frame.y + frame.z, mergeRange.x, mergeRange.y, mergeRange.y - mergeRange.x, + // mergeRange.z, mergeRange.w, mergeRange.w - mergeRange.z); + + // Use the 4th component to store the tile index. The actual b1 + // term is inferred from the tile size and array length. + mergeRange.w = block; + } + + int mergeTotal, copyTotal; + int mergeScan = S::Scan(tid, mergeOp, *scan, &mergeTotal); + int copyScan = S::Scan(tid, copyOp, *scan, ©Total); + if(!tid) { + shared[0] = atomicAdd(&support.queueCounters_global->x, mergeTotal); + shared[1] = atomicAdd(&support.queueCounters_global->y, copyTotal); + } + __syncthreads(); + + if(mergeOp) { + support.copyStatus_global[block] = 0; + support.mergeList_global[shared[0] + mergeScan] = mergeRange; + } + if(copyOp) { + support.copyStatus_global[block] = 1; + support.copyList_global[shared[1] + copyScan] = block; + } +} + + +//////////////////////////////////////////////////////////////////////////////// +// KernelSegSortPartitionBase +// KernelSegSortPartitionDerived + +template +__global__ void KernelSegSortPartitionBase(const KeyType* keys_global, + SegSortSupport support, int count, int nv, int numPartitions, Comp comp) { + + union Shared { + int partitions[NT]; + typename CTAScan::Storage scan; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int partition = tid + (NT - 1) * blockIdx.x; + + // Compute one extra partition per CTA. If the CTA size is 128 threads, we + // compute 128 partitions and 127 blocks. The next CTA then starts at + // partition 127 rather than 128. This relieves us from having to launch + // a second kernel to build the work queues. + int p0; + int3 frame; + if(partition < numPartitions) { + frame = FindMergesortFrame(2, partition, nv); + int listLen = frame.z; + int a0 = frame.x; + int b0 = min(frame.y, count); + int diag = nv * partition - a0; + int aCount = min(listLen, count - a0); + int bCount = min(listLen, count - b0); + + if(Segments) { + // Segmented merge path calculation. Use the ranges as constraints. + int leftRange = support.ranges_global[~1 & partition]; + int rightRange = support.ranges_global[ + min(numPartitions - 2, 1 | partition)]; + + // Unpack the left and right ranges. Transform them into the global + // coordinate system by adding a0 or b0. + int leftStart = 0x0000ffff & leftRange; + int leftEnd = leftRange>> 16; + if(nv == leftStart) leftStart = count; + else leftStart += a0; + if(-1 != leftEnd) leftEnd += a0; + + int rightStart = 0x0000ffff & rightRange; + int rightEnd = rightRange>> 16; + if(nv == rightStart) rightStart = count; + else rightStart += b0; + if(-1 != rightEnd) rightEnd += b0; + + if(0 == diag) + support.ranges2_global[partition>> 1] = make_int2( + min(leftStart, rightStart), + max(leftEnd, rightEnd)); + + p0 = SegmentedMergePath(keys_global, a0, aCount, b0, bCount, + leftEnd, rightStart, diag, comp); + + } else + // Unsegmented merge path search. + p0 = MergePath(keys_global + a0, aCount, + keys_global + b0, bCount, diag, comp); + + shared.partitions[tid] = p0; + } + __syncthreads(); + + bool active = (tid < NT - 1) && (partition < numPartitions - 1); + int p1 = active ? shared.partitions[tid + 1] : 0; + __syncthreads(); + + DeviceSegSortCreateJob(support, count, active, frame, tid, 0, nv, + partition, p0, p1, shared.partitions); +} + +template +__global__ void KernelSegSortPartitionDerived(const KeyType* keys_global, + SegSortSupport support, int count, int numSources, int pass, int nv, + int numPartitions, Comp comp) { + + union Shared { + int partitions[NT]; + typename CTAScan::Storage scan; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int partition = tid + (NT - 1) * blockIdx.x; + + int3 frame; + int p0; + if(partition < numPartitions) { + frame = FindMergesortFrame(2<< pass, partition, nv); + int listLen = frame.z; + int a0 = frame.x; + int b0 = min(frame.y, count); + int aCount = min(listLen, count - a0); + int bCount = min(listLen, count - b0); + int diag = min(nv * partition - a0, aCount + bCount); + + if(Segments) { + int rangeIndex = partition>> pass; + int2 leftRange = support.ranges2_global[~1 & rangeIndex]; + int2 rightRange = support.ranges2_global[ + min(numSources - 1, 1 | rangeIndex)]; + + int leftEnd = leftRange.y; + int rightStart = max(b0, rightRange.x); + p0 = SegmentedMergePath(keys_global, a0, aCount, b0, bCount, + leftEnd, rightStart, diag, comp); + + if(0 == diag) + support.ranges2_global[numSources + (rangeIndex>> 1)] = + make_int2( + min(leftRange.x, rightRange.x), + max(leftRange.y, rightRange.y)); + + } else + // Unsegmented merge path search. + p0 = MergePath(keys_global + a0, aCount, + keys_global + b0, bCount, diag, comp); + + shared.partitions[tid] = p0; + } + __syncthreads(); + + bool active = (tid < NT - 1) && (partition < numPartitions - 1); + int p1 = active ? shared.partitions[tid + 1] : 0; + __syncthreads(); + + DeviceSegSortCreateJob(support, count, active, frame, tid, pass, nv, + partition, p0, p1, shared.partitions); + + // Clear the counters for the next pass. + if(!partition) *support.nextCounters_global = make_int2(0, 0); +} + +//////////////////////////////////////////////////////////////////////////////// +// AllocSegSortBuffers + +MGPU_HOST MGPU_MEM(byte) AllocSegSortBuffers(int count, int nv, + SegSortSupport& support, bool segments, CudaContext& context) { + + int numBlocks = MGPU_DIV_UP(count, nv); + int numPasses = FindLog2(numBlocks, true); + int numRanges = 1; + int numBlocks2 = MGPU_DIV_UP(numBlocks, 2); + for(int pass = 1; pass < numPasses; ++pass) { + numRanges += numBlocks2; + numBlocks2 = MGPU_DIV_UP(numBlocks2, 2); + } + + int rangesSize = MGPU_ROUND_UP_POW2(sizeof(int) * numBlocks, 128); + int ranges2Size = MGPU_ROUND_UP_POW2(sizeof(int2) * numRanges, 128); + int mergeListSize = MGPU_ROUND_UP_POW2(sizeof(int4) * numBlocks, 128); + int copyListSize = MGPU_ROUND_UP_POW2(sizeof(int) * numBlocks, 128); + int countersSize = MGPU_ROUND_UP_POW2(sizeof(int4), 128); + int copyStatusSize = MGPU_ROUND_UP_POW2(sizeof(byte) * numBlocks, 128); + + if(!segments) rangesSize = ranges2Size = 0; + + int total = rangesSize + ranges2Size + mergeListSize + copyListSize + + countersSize + copyStatusSize; + MGPU_MEM(byte) mem = context.Malloc(total); + + if(segments) { + support.ranges_global = PtrOffset((int*)mem->get(), 0); + support.ranges2_global = PtrOffset((int2*)support.ranges_global, + rangesSize); + support.mergeList_global = PtrOffset((int4*)support.ranges2_global, + ranges2Size); + } else { + support.ranges_global = 0; + support.ranges2_global = 0; + support.mergeList_global = (int4*)mem->get(); + } + + support.copyList_global = PtrOffset((int*)support.mergeList_global, + mergeListSize); + support.queueCounters_global = PtrOffset((int2*)support.copyList_global, + copyListSize); + support.nextCounters_global = PtrOffset(support.queueCounters_global, + sizeof(int2)); + support.copyStatus_global = PtrOffset((byte*)support.queueCounters_global, + countersSize); + + // Fill the counters with 0s on the first run. + cudaMemsetAsync(support.queueCounters_global, 0, sizeof(int4), + context.Stream()); + + return mem; +} + +class SegSortPassInfo { +public: + SegSortPassInfo(int numBlocks_) : + numBlocks(numBlocks_), totalMerge(0), totalCopy(0) { } + + void Pass(SegSortSupport& support, int pass) { + int2 counters; + cudaMemcpy(&counters, support.queueCounters_global, sizeof(int2), + cudaMemcpyDeviceToHost); + + printf("pass %2d: %7d (%6.2lf%%) %7d (%6.2lf%%)\n", pass, + counters.x, 100.0 * counters.x / numBlocks, + counters.y, 100.0 * counters.y / numBlocks); + + totalMerge += counters.x; + totalCopy += counters.y; + } + void Final(int numPasses) { + if(numPasses) { + printf("average: %7d (%6.2lf%%) %7d (%6.2lf%%)\n", + totalMerge / numPasses, + 100.0 * totalMerge / (numPasses * numBlocks), + totalCopy / numPasses, + 100.0 * totalCopy / (numPasses * numBlocks)); + printf("total : %7d (%6.2lf%%) %7d (%6.2lf%%)\n", + totalMerge, 100.0 * totalMerge / numBlocks, + totalCopy, 100.0 * totalCopy / numBlocks); + } + } + + int numBlocks, totalMerge, totalCopy; +}; + +//////////////////////////////////////////////////////////////////////////////// +// SegSortPasses +// Multi-pass segmented mergesort process. Factored out to allow simpler +// specialization over head flags delivery in blocksort. + +template +MGPU_HOST void SegSortPasses(SegSortSupport& support, +KeyType* keysSource_global, ValType* valsSource_global, + int count, int numBlocks, int numPasses, KeyType* keysDest_global, + ValType* valsDest_global, Comp comp, CudaContext& context, bool verbose) { + + int2 launch = Tuning::GetLaunchParams(context); + int NV = launch.x * launch.y; + + const int NT2 = 64; + int numPartitions = numBlocks + 1; + int numPartBlocks = MGPU_DIV_UP(numPartitions, NT2 - 1); + int numCTAs = min(numBlocks, 16 * 6); + int numBlocks2 = MGPU_DIV_UP(numBlocks, 2); + + SegSortPassInfo info(numBlocks); + for(int pass = 0; pass < numPasses; ++pass) { + if(0 == pass) { + KernelSegSortPartitionBase + <<>>(keysSource_global, + support, count, NV, numPartitions, comp); + MGPU_SYNC_CHECK("KernelSegSortPartitionBase"); + } else { + KernelSegSortPartitionDerived + <<>>(keysSource_global, + support, count, numBlocks2, pass, NV, numPartitions, comp); + MGPU_SYNC_CHECK("KernelSegSortPartitionDerived"); + + support.ranges2_global += numBlocks2; + numBlocks2 = MGPU_DIV_UP(numBlocks2, 2); + } + if(verbose) info.Pass(support, pass); + + KernelSegSortMerge + <<>>(keysSource_global, + valsSource_global, support, count, pass, keysDest_global, + valsDest_global, comp); + MGPU_SYNC_CHECK("KernelSegSortMerge"); + + std::swap(keysDest_global, keysSource_global); + std::swap(valsDest_global, valsSource_global); + std::swap(support.queueCounters_global, support.nextCounters_global); + } + if(verbose) info.Final(numPasses); +} + +//////////////////////////////////////////////////////////////////////////////// +// Segmented sort from head flags in a bit field. + +template +MGPU_HOST void SegSortKeysFromFlags(T* data_global, int count, + const uint* flags_global, CudaContext& context, Comp comp, + bool verbose) { + + MGPU_VAR_UNUSED const bool Stable = true; + + typedef LaunchBoxVT< + 128, 11, 0, + 128, 11, 0, + 128, (sizeof(T) > 4) ? 7 : 11, 0 + > Tuning; + int2 launch = Tuning::GetLaunchParams(context); + const int NV = launch.x * launch.y; + + int numBlocks = MGPU_DIV_UP(count, NV); + int numPasses = FindLog2(numBlocks, true); + + SegSortSupport support; + MGPU_MEM(byte) mem = AllocSegSortBuffers(count, NV, support, true, context); + + MGPU_MEM(T) destDevice = context.Malloc(count); + T* source = data_global; + T* dest = destDevice->get(); + + KernelSegBlocksortFlags + <<>>(source, (const int*)0, + count, flags_global, (1 & numPasses) ? dest : source, (int*)0, + support.ranges_global, comp); + MGPU_SYNC_CHECK("KernelSegBlocksortFlags"); + + if(1 & numPasses) std::swap(source, dest); + + SegSortPasses(support, source, (int*)0, count, + numBlocks, numPasses, dest, (int*)0, comp, context, verbose); +} + +template +MGPU_HOST void SegSortKeysFromFlags(T* data_global, int count, + const uint* flags_global, CudaContext& context, bool verbose) { + + SegSortKeysFromFlags(data_global, count, flags_global, context, + mgpu::less(), verbose); +} + +template +MGPU_HOST void SegSortPairsFromFlags(KeyType* keys_global, + ValType* values_global, int count, const uint* flags_global, + CudaContext& context, Comp comp, bool verbose) { + + MGPU_VAR_UNUSED const bool Stable = true; + + typedef LaunchBoxVT< + 128, 11, 0, + 128, 7, 0, + 128, 7, 0 + > Tuning; + int2 launch = Tuning::GetLaunchParams(context); + const int NV = launch.x * launch.y; + + int numBlocks = MGPU_DIV_UP(count, NV); + int numPasses = FindLog2(numBlocks, true); + + SegSortSupport support; + MGPU_MEM(byte) mem = AllocSegSortBuffers(count, NV, support, true, context); + + MGPU_MEM(KeyType) keysDestDevice = context.Malloc(count); + MGPU_MEM(ValType) valsDestDevice = context.Malloc(count); + + KeyType* keysSource = keys_global; + KeyType* keysDest = keysDestDevice->get(); + ValType* valsSource = values_global; + ValType* valsDest = valsDestDevice->get(); + + KernelSegBlocksortFlags + <<>>(keysSource, valsSource, + count, flags_global, (1 & numPasses) ? keysDest : keysSource, + (1 & numPasses) ? valsDest : valsSource, support.ranges_global, + comp); + MGPU_SYNC_CHECK("KernelSegBlocksortFlags"); + + std::vector rangesHost(numBlocks); + copyDtoH(&rangesHost[0], support.ranges_global, numBlocks); + + if(1 & numPasses) { + std::swap(keysSource, keysDest); + std::swap(valsSource, valsDest); + } + + SegSortPasses(support, keysSource, valsSource, count, + numBlocks, numPasses, keysDest, valsDest, comp, context, verbose); +} +template +MGPU_HOST void SegSortPairsFromFlags(KeyType* keys_global, + ValType* values_global, int count, const uint* flags_global, + CudaContext& context, bool verbose) { + + SegSortPairsFromFlags(keys_global, values_global, count, flags_global, + context, mgpu::less(), verbose); +} + +//////////////////////////////////////////////////////////////////////////////// +// Segmented sort from head flags passed as indices + +template +MGPU_HOST void SegSortKeysFromIndices(T* data_global, int count, + const int* indices_global, int indicesCount, CudaContext& context, + Comp comp, bool verbose) { + + MGPU_VAR_UNUSED const bool Stable = true; + + typedef LaunchBoxVT< + 128, 11, 0, + 128, 11, 0, + 128, (sizeof(T) > 4) ? 7 : 11, 0 + > Tuning; + int2 launch = Tuning::GetLaunchParams(context); + const int NV = launch.x * launch.y; + + int numBlocks = MGPU_DIV_UP(count, NV); + int numPasses = FindLog2(numBlocks, true); + + SegSortSupport support; + MGPU_MEM(byte) mem = AllocSegSortBuffers(count, NV, support, true, context); + + MGPU_MEM(T) destDevice = context.Malloc(count); + T* source = data_global; + T* dest = destDevice->get(); + + MGPU_MEM(int) partitionsDevice = BinarySearchPartitions( + count, indices_global, indicesCount, NV, mgpu::less(), context); + + KernelSegBlocksortIndices + <<>>(source, (const int*)0, + count, indices_global, partitionsDevice->get(), + (1 & numPasses) ? dest : source, (int*)0, support.ranges_global, comp); + MGPU_SYNC_CHECK("KernelSegBlocksortIndices"); + + if(1 & numPasses) std::swap(source, dest); + + SegSortPasses(support, source, (int*)0, count, + numBlocks, numPasses, dest, (int*)0, comp, context, verbose); +} + +template +MGPU_HOST void SegSortKeysFromIndices(T* data_global, int count, + const int* indices_global, int indicesCount, CudaContext& context, + bool verbose) { + + SegSortKeysFromIndices(data_global, count, indices_global, indicesCount, + context, mgpu::less(), verbose); +} + +template +MGPU_HOST void SegSortPairsFromIndices(KeyType* keys_global, + ValType* values_global, int count, const int* indices_global, + int indicesCount, CudaContext& context, Comp comp, bool verbose) { + + MGPU_VAR_UNUSED const bool Stable = true; + + typedef LaunchBoxVT< + 128, 11, 0, + 128, 7, 0, + 128, 7, 0 + > Tuning; + int2 launch = Tuning::GetLaunchParams(context); + const int NV = launch.x * launch.y; + + int numBlocks = MGPU_DIV_UP(count, NV); + int numPasses = FindLog2(numBlocks, true); + + SegSortSupport support; + MGPU_MEM(byte) mem = AllocSegSortBuffers(count, NV, support, true, context); + + MGPU_MEM(KeyType) keysDestDevice = context.Malloc(count); + MGPU_MEM(ValType) valsDestDevice = context.Malloc(count); + + KeyType* keysSource = keys_global; + KeyType* keysDest = keysDestDevice->get(); + ValType* valsSource = values_global; + ValType* valsDest = valsDestDevice->get(); + + MGPU_MEM(int) partitionsDevice = BinarySearchPartitions( + count, indices_global, indicesCount, NV, mgpu::less(), context); + + KernelSegBlocksortIndices + <<>>(keysSource, valsSource, + count, indices_global, partitionsDevice->get(), + (1 & numPasses) ? keysDest : keysSource, + (1 & numPasses) ? valsDest : valsSource, support.ranges_global, comp); + MGPU_SYNC_CHECK("KernelSegBlocksortIndices"); + + if(1 & numPasses) { + std::swap(keysSource, keysDest); + std::swap(valsSource, valsDest); + } + + SegSortPasses(support, keysSource, valsSource, count, + numBlocks, numPasses, keysDest, valsDest, comp, context, verbose); +} +template +MGPU_HOST void SegSortPairsFromIndices(KeyType* keys_global, + ValType* values_global, int count, const int* indices_global, + int indicesCount, CudaContext& context, bool verbose) { + + SegSortPairsFromIndices(keys_global, values_global, count, indices_global, + indicesCount, context, mgpu::less(), verbose); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/segreduce.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/segreduce.cuh new file mode 100644 index 0000000000000000000000000000000000000000..9da045fae82c6d5df9adf8ff85d71253aec13952 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/segreduce.cuh @@ -0,0 +1,240 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../kernels/csrtools.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// SegReducePreprocess + +struct SegReducePreprocessData { + int count, numSegments, numSegments2; + int numBlocks; + MGPU_MEM(int) limitsDevice; + MGPU_MEM(int) threadCodesDevice; + + // If csr2Device is set, use BulkInsert to finalize results into + // dest_global. + MGPU_MEM(int) csr2Device; +}; + +// Generic function for prep +template +MGPU_HOST void SegReducePreprocess(int count, CsrIt csr_global, int numSegments, + bool supportEmpty, std::auto_ptr* ppData, + CudaContext& context) { + + std::auto_ptr data(new SegReducePreprocessData); + + int2 launch = Tuning::GetLaunchParams(context); + int NV = launch.x * launch.y; + + int numBlocks = MGPU_DIV_UP(count, NV); + data->count = count; + data->numSegments = data->numSegments2 = numSegments; + data->numBlocks = numBlocks; + + // Filter out empty rows and build a replacement structure. + if(supportEmpty) { + MGPU_MEM(int) csr2Device = context.Malloc(numSegments + 1); + CsrStripEmpties(count, csr_global, (const int*)0, numSegments, + csr2Device->get(), (int*)0, (int*)&data->numSegments2, context); + if(data->numSegments2 < numSegments) { + csr_global = csr2Device->get(); + numSegments = data->numSegments2; + data->csr2Device = csr2Device; + } + } + + data->limitsDevice = PartitionCsrSegReduce(count, NV, csr_global, + numSegments, (const int*)0, numBlocks + 1, context); + data->threadCodesDevice = BuildCsrPlus(count, csr_global, + data->limitsDevice->get(), numBlocks, context); + + *ppData = data; +} + +//////////////////////////////////////////////////////////////////////////////// +// SegReduceSpine +// Compute the carry-in in-place. Return the carry-out for the entire tile. +// A final spine-reducer scans the tile carry-outs and adds into individual +// results. + +template +__global__ void KernelSegReduceSpine1(const int* limits_global, int count, + DestIt dest_global, const T* carryIn_global, T identity, Op op, + T* carryOut_global) { + + typedef CTASegScan SegScan; + union Shared { + typename SegScan::Storage segScanStorage; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NT * block + tid; + + // Load the current carry-in and the current and next row indices. + int row = (gid < count) ? + (0x7fffffff & limits_global[gid]) : + INT_MAX; + int row2 = (gid + 1 < count) ? + (0x7fffffff & limits_global[gid + 1]) : + INT_MAX; + + T carryIn2 = (gid < count) ? carryIn_global[gid] : identity; + T dest = (gid < count) ? dest_global[row] : identity; + + // Run a segmented scan of the carry-in values. + bool endFlag = row != row2; + + T carryOut; + T x = SegScan::SegScan(tid, carryIn2, endFlag, shared.segScanStorage, + &carryOut, identity, op); + + // Store the reduction at the end of a segment to dest_global. + if(endFlag) + dest_global[row] = op(x, dest); + + // Store the CTA carry-out. + if(!tid) carryOut_global[block] = carryOut; +} + +template +__global__ void KernelSegReduceSpine2(const int* limits_global, int numBlocks, + int count, int nv, DestIt dest_global, const T* carryIn_global, T identity, + Op op) { + + typedef CTASegScan SegScan; + struct Shared { + typename SegScan::Storage segScanStorage; + int carryInRow; + T carryIn; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + + for(int i = 0; i < numBlocks; i += NT) { + int gid = (i + tid) * nv; + + // Load the current carry-in and the current and next row indices. + int row = (gid < count) ? + (0x7fffffff & limits_global[gid]) : INT_MAX; + int row2 = (gid + nv < count) ? + (0x7fffffff & limits_global[gid + nv]) : INT_MAX; + T carryIn2 = (i + tid < numBlocks) ? carryIn_global[i + tid] : identity; + T dest = (gid < count) ? dest_global[row] : identity; + + // Run a segmented scan of the carry-in values. + bool endFlag = row != row2; + + T carryOut; + T x = SegScan::SegScan(tid, carryIn2, endFlag, shared.segScanStorage, + &carryOut, identity, op); + + // Add the carry-in to the reductions when we get to the end of a segment. + if(endFlag) { + // Add the carry-in from the last loop iteration to the carry-in + // from this loop iteration. + if(i && row == shared.carryInRow) + x = op(shared.carryIn, x); + dest_global[row] = op(x, dest); + } + + // Set the carry-in for the next loop iteration. + if(i + NT < numBlocks) { + __syncthreads(); + if(i > 0) { + // Add in the previous carry-in. + if(NT - 1 == tid) { + shared.carryIn = (shared.carryInRow == row2) ? + op(shared.carryIn, carryOut) : carryOut; + shared.carryInRow = row2; + } + } else { + if(NT - 1 == tid) { + shared.carryIn = carryOut; + shared.carryInRow = row2; + } + } + __syncthreads(); + } + } +} + +template +MGPU_HOST void SegReduceSpine(const int* limits_global, int count, + DestIt dest_global, const T* carryIn_global, T identity, Op op, + CudaContext& context) { + + const int NT = 128; + int numBlocks = MGPU_DIV_UP(count, NT); + + // Fix-up the segment outputs between the original tiles. + MGPU_MEM(T) carryOutDevice = context.Malloc(numBlocks); + KernelSegReduceSpine1<<>>( + limits_global, count, dest_global, carryIn_global, identity, op, + carryOutDevice->get()); + MGPU_SYNC_CHECK("KernelSegReduceSpine1"); + + // Loop over the segments that span the tiles of + // KernelSegReduceSpine1 and fix those. + if(numBlocks > 1) { + KernelSegReduceSpine2<<<1, NT, 0, context.Stream()>>>( + limits_global, numBlocks, count, NT, dest_global, + carryOutDevice->get(), identity, op); + MGPU_SYNC_CHECK("KernelSegReduceSpine2"); + } +} + +//////////////////////////////////////////////////////////////////////////////// +// Common LaunchBox structure for segmented reductions. + +template +struct SegReduceTuning { + enum { + NT = NT_, + VT = VT_, + OCC = OCC_, + HalfCapacity = HalfCapacity_, + LdgTranspose = LdgTranspose_ + }; +}; + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/segreducecsr.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/segreducecsr.cuh new file mode 100644 index 0000000000000000000000000000000000000000..42aa67a3779b69e51faf0aa1b2f81a1b5949ddb6 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/segreducecsr.cuh @@ -0,0 +1,512 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuhost.cuh" +#include "../kernels/segreduce.cuh" +#include "../kernels/bulkinsert.cuh" + +namespace mgpu { + +// SegReduceCSR - Normal +template +struct SegReduceNormalTuning { + typedef LaunchBox< + SegReduceTuning<128, 11, 0, false, false>, + SegReduceTuning<128, 7, 0, true, false>, + SegReduceTuning<128, (size > sizeof(int)) ? 11 : 7, 0, true, true> + > Tuning; +}; + +// SegReduceCSR - Preprocess +template +struct SegReducePreprocessTuning { + typedef LaunchBox< + SegReduceTuning<128, 11, 0, false, false>, + SegReduceTuning<128, 11, 0, true, false>, + SegReduceTuning<128, 11, 0, true, (size > 4) ? false : true> + > Tuning; +}; + +// SegReduceCSR - Indirect +template +struct SegReduceIndirectTuning { + typedef LaunchBox< + SegReduceTuning<128, 11, 0, false, false>, + SegReduceTuning<128, 7, 0, true, false>, + SegReduceTuning<128, 7, 0, true, true> + > Tuning; +}; + +//////////////////////////////////////////////////////////////////////////////// +// CTAIntervalSegReduceGather +// Storage and logic for segmented reduce and interval reduce. +// Pass the Reduce function data in thread order. + +template +struct CTASegReduceLoad { + enum { + NV = NT * VT, + Capacity = HalfCapacity ? (NV / 2) : NV + }; + + union Storage { + int sources[NV]; + T data[Capacity]; + }; + + // Load elements from multiple segments and store in thread order. + template + MGPU_DEVICE static void LoadDirect(int count2, int tid, int gid, + InputIt data_global, T identity, T data[VT], Storage& storage) { + + if(LdgTranspose) { + // Load data in thread order from data_global + gid. + DeviceGlobalToThreadDefault(count2, data_global + gid, + tid, data, identity); + } else { + // Load data in strided order from data_global + gid. + T stridedData[VT]; + DeviceGlobalToRegDefault(count2, data_global + gid, tid, + stridedData, identity); + + if(HalfCapacity) + HalfSmemTranspose(stridedData, tid, storage.data, data); + else { + DeviceRegToShared(stridedData, tid, storage.data); + DeviceSharedToThread(storage.data, tid, data); + } + } + } + + // Load elements from multiple segments and store in thread order. + template + MGPU_DEVICE static void LoadIndirect(int count2, int tid, int gid, + int numSegments, int startSeg, const int segs[VT + 1], + const int segStarts[VT], InputIt data_global, SourcesIt sources_global, + T identity, T data[VT], Storage& storage) { + + T stridedData[VT]; + + // Load source offsets from sources_global into smem. + DeviceGlobalToSharedLoop(numSegments, sources_global + startSeg, + tid, storage.sources); + + // Compute the offset of each element within its segment. + int indices[VT]; + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = VT * tid + i; + int segOffset = gid + index - segStarts[i]; + int source = storage.sources[segs[i]]; + indices[i] = (index < count2) ? (source + segOffset) : 0; + } + __syncthreads(); + + if(LdgTranspose) { + // Directly load in thread order. + #pragma unroll + for(int i = 0; i < VT; ++i) + data[i] = ldg(data_global + indices[i]); + } else { + // Transpose indices through shared memory. + DeviceThreadToShared(indices, tid, storage.sources); + DeviceSharedToReg(storage.sources, tid, indices); + + // Cooperatively load all data elements. + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + stridedData[i] = (index < count2) ? + data_global[indices[i]] : + identity; + } + if(HalfCapacity) + HalfSmemTranspose(stridedData, tid, storage.data, data); + else { + DeviceRegToShared(stridedData, tid, storage.data); + DeviceSharedToThread(storage.data, tid, data); + } + } + } + + // Load elements from a single segment and store in thread order. + template + MGPU_DEVICE static void LoadIndirectFast(int tid, int gid, + int startSeg, CsrIt csr_global, InputIt data_global, + SourcesIt sources_global, T data[VT], Storage& storage) { + + int source = sources_global[startSeg]; + int csr = csr_global[startSeg]; + + int offset = source + gid - csr; + + // Round down to a multiple of NT. This guarantees all loads are + // cache-line aligned. + int mod = offset % NT; + int start = offset - mod; + + data_global += start; + data[0] = data_global[(tid < mod) ? (NV + tid) : tid]; + #pragma unroll + for(int i = 1; i < VT; ++i) + data[i] = data_global[NT * i + tid]; + } +}; + + +//////////////////////////////////////////////////////////////////////////////// +// KernelSegReduceCsr + +template +MGPU_LAUNCH_BOUNDS void KernelSegReduceCsr(CsrIt csr_global, + SourcesIt sources_global, int count, const int* limits_global, + InputIt data_global, T identity, Op op, DestIt dest_global, + T* carryOut_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + const bool HalfCapacity = (sizeof(T) > sizeof(int)) && Params::HalfCapacity; + const bool LdgTranspose = Params::LdgTranspose; + + typedef CTAReduce FastReduce; + typedef CTASegReduce SegReduce; + typedef CTASegReduceLoad + SegReduceLoad; + + union Shared { + int csr[NV + 1]; + typename FastReduce::Storage reduceStorage; + typename SegReduce::Storage segReduceStorage; + typename SegReduceLoad::Storage loadStorage; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + int count2 = min(NV, count - gid); + + int limit0 = limits_global[block]; + int limit1 = limits_global[block + 1]; + + SegReduceRange range; + SegReduceTerms terms; + int segs[VT + 1], segStarts[VT]; + T data[VT]; + if(Indirect) { + // Indirect load. We need to load the CSR terms before loading any data. + range = DeviceShiftRange(limit0, limit1); + int numSegments = range.end - range.begin; + + if(range.total) { + + // Load the CSR interval. + DeviceGlobalToSharedLoop(numSegments, + csr_global + range.begin, tid, shared.csr); + + // Compute the segmented scan terms. + terms = DeviceSegReducePrepare(shared.csr, numSegments, + tid, gid, range.flushLast, segs, segStarts); + + // Load tile of data in thread order from segment IDs. + SegReduceLoad::LoadIndirect(count2, tid, gid, numSegments, + range.begin, segs, segStarts, data_global, sources_global, + identity, data, shared.loadStorage); + } else { + SegReduceLoad::LoadIndirectFast(tid, gid, range.begin, csr_global, + data_global, sources_global, data, shared.loadStorage); + } + + } else { + // Direct load. It is more efficient to load the full tile before + // dealing with data dependencies. + SegReduceLoad::LoadDirect(count2, tid, gid, data_global, identity, + data, shared.loadStorage); + + range = DeviceShiftRange(limit0, limit1); + int numSegments = range.end - range.begin; + + if(range.total) { + // Load the CSR interval. + DeviceGlobalToSharedLoop(numSegments, + csr_global + range.begin, tid, shared.csr); + + // Compute the segmented scan terms. + terms = DeviceSegReducePrepare(shared.csr, numSegments, + tid, gid, range.flushLast, segs, segStarts); + } + } + + if(range.total) { + // Reduce tile data and store to dest_global. Write tile's carry-out + // term to carryOut_global. + SegReduce::ReduceToGlobal(segs, range.total, terms.tidDelta, + range.begin, block, tid, data, dest_global, carryOut_global, + identity, op, shared.segReduceStorage); + } else { + T x; + #pragma unroll + for(int i = 0; i < VT; ++i) + x = i ? op(x, data[i]) : data[i]; + x = FastReduce::Reduce(tid, x, shared.reduceStorage, op); + if(!tid) + carryOut_global[block] = x; + } +} + +//////////////////////////////////////////////////////////////////////////////// +// SegReduceHost +// Generic host implementation for seg-reduce and interval-reduce. + +template +MGPU_HOST void SegReduceInner(InputIt data_global, CsrIt csr_global, + SourcesIt sources_global, int count, int numSegments, + const int* numSegments2_global, DestIt dest_global, T identity, Op op, + CudaContext& context) { + + int2 launch = Tuning::GetLaunchParams(context); + int NV = launch.x * launch.y; + + int numBlocks = MGPU_DIV_UP(count, NV); + + // Use upper-bound binary search to partition the CSR structure into tiles. + MGPU_MEM(int) limitsDevice = PartitionCsrSegReduce(count, NV, csr_global, + numSegments, numSegments2_global, numBlocks + 1, context); + + // Segmented reduction without source intervals. + MGPU_MEM(T) carryOutDevice = context.Malloc(numBlocks); + KernelSegReduceCsr + <<>>(csr_global, + sources_global, count, limitsDevice->get(), data_global, identity, op, + dest_global, carryOutDevice->get()); + MGPU_SYNC_CHECK("KernelSegReduceCsr"); + + // Add carry-in values. + SegReduceSpine(limitsDevice->get(), numBlocks, dest_global, + carryOutDevice->get(), identity, op, context); +} + +template +MGPU_HOST void SegReduceHost(InputIt data_global, CsrIt csr_global, + SourcesIt sources_global, int count, int numSegments, bool supportEmpty, + DestIt dest_global, T identity, Op op, CudaContext& context) { + + if(supportEmpty) { + // Allocate space for Csr2 and Sources2. + MGPU_MEM(int) csr2Device = context.Malloc(numSegments + 1); + MGPU_MEM(int) sources2Device; + if(Indirect) sources2Device = context.Malloc(numSegments); + + // Strip the empties from Csr and store in Csr2. + CsrStripEmpties(count, csr_global, sources_global, numSegments, + csr2Device->get(), Indirect ? sources2Device->get() : (int*)0, + (int*)0, context); + + // Run the segmented reduction in the Csr2 coordinate space. + MGPU_MEM(T) destDevice = context.Malloc(numSegments); + SegReduceInner(data_global, csr2Device->get(), + Indirect ? sources2Device->get() : (const int*)0, count, -1, + csr2Device->get() + numSegments, destDevice->get(), identity, op, + context); + + // Transform into the Csr space with BulkInsert. + CsrBulkInsert(csr2Device->get(), numSegments, destDevice->get(), identity, + dest_global, context); + + } else { + // Evaluate the reduction directly into dest_global. + SegReduceInner(data_global, csr_global, + sources_global, count, numSegments, (const int*)0, dest_global, + identity, op, context); + } +} + +template +MGPU_HOST void SegReduceCsr(InputIt data_global, CsrIt csr_global, int count, + int numSegments, bool supportEmpty, OutputIt dest_global, T identity, Op op, + CudaContext& context) { + + typedef typename SegReduceNormalTuning::Tuning Tuning; + + SegReduceHost(data_global, csr_global, (const int*)0, + count, numSegments, supportEmpty, dest_global, identity, op, context); +} + +template +MGPU_HOST void IndirectReduceCsr(InputIt data_global, CsrIt csr_global, + SourcesIt sources_global, int count, int numSegments, bool supportEmpty, + OutputIt dest_global, T identity, Op op, CudaContext& context) { + + typedef typename SegReduceIndirectTuning::Tuning Tuning; + + SegReduceHost(data_global, csr_global, sources_global, count, + numSegments, supportEmpty, dest_global, identity, op, context); +} + +//////////////////////////////////////////////////////////////////////////////// +// seg-reduce-csr preprocessed format. + +template +MGPU_HOST void SegReduceCsrPreprocess(int count, CsrIt csr_global, int numSegments, + bool supportEmpty, std::auto_ptr* ppData, + CudaContext& context) { + + typedef typename SegReducePreprocessTuning::Tuning Tuning; + SegReducePreprocess(count, csr_global, numSegments, supportEmpty, + ppData, context); +} + +template +MGPU_LAUNCH_BOUNDS void KernelSegReduceApply(const int* threadCodes_global, + int count, const int* limits_global, InputIt data_global, T identity, + Op op, DestIt dest_global, T* carryOut_global) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + const bool HalfCapacity = (sizeof(T) > sizeof(int)) && Params::HalfCapacity; + const bool LdgTranspose = Params::LdgTranspose; + + typedef CTAReduce FastReduce; + typedef CTASegReduce SegReduce; + typedef CTASegReduceLoad + SegReduceLoad; + + union Shared { + int csr[NV]; + typename FastReduce::Storage reduceStorage; + typename SegReduce::Storage segReduceStorage; + typename SegReduceLoad::Storage loadStorage; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + int count2 = min(NV, count - gid); + + int limit0 = limits_global[block]; + int limit1 = limits_global[block + 1]; + int threadCodes = threadCodes_global[NT * block + tid]; + + // Load the data and transpose into thread order. + T data[VT]; + SegReduceLoad::LoadDirect(count2, tid, gid, data_global, identity, data, + shared.loadStorage); + + // Compute the range. + SegReduceRange range = DeviceShiftRange(limit0, limit1); + + if(range.total) { + // Expand the segment indices. + int segs[VT + 1]; + DeviceExpandFlagsToRows(threadCodes>> 20, threadCodes, segs); + + // Reduce tile data and store to dest_global. Write tile's carry-out + // term to carryOut_global. + int tidDelta = 0x7f & (threadCodes>> 13); + SegReduce::ReduceToGlobal(segs, range.total, tidDelta, range.begin, + block, tid, data, dest_global, carryOut_global, identity, op, + shared.segReduceStorage); + } else { + // If there are no end flags in this CTA, use a fast reduction. + T x; + #pragma unroll + for(int i = 0; i < VT; ++i) + x = i ? op(x, data[i]) : data[i]; + x = FastReduce::Reduce(tid, x, shared.reduceStorage, op); + if(!tid) + carryOut_global[block] = x; + } +} + +template +MGPU_HOST void SegReduceApply(const SegReducePreprocessData& preprocess, + InputIt data_global, T identity, Op op, DestIt dest_global, + CudaContext& context) { + + typedef typename SegReducePreprocessTuning::Tuning Tuning; + int2 launch = Tuning::GetLaunchParams(context); + + if(preprocess.csr2Device.get()) { + // Support empties. + MGPU_MEM(T) tempOutDevice = context.Malloc(preprocess.numSegments2); + MGPU_MEM(T) carryOutDevice = context.Malloc(preprocess.numBlocks); + KernelSegReduceApply + <<>>( + preprocess.threadCodesDevice->get(), preprocess.count, + preprocess.limitsDevice->get(), data_global, identity, op, + tempOutDevice->get(), carryOutDevice->get()); + MGPU_SYNC_CHECK("KernelSegReduceApply"); + + // Add the carry-in values. + SegReduceSpine(preprocess.limitsDevice->get(), preprocess.numBlocks, + tempOutDevice->get(), carryOutDevice->get(), identity, op, context); + + // Insert identity into the empty segments and stream into dest_global. + BulkInsert(mgpu::constant_iterator(identity), + preprocess.csr2Device->get() + preprocess.numSegments2, + preprocess.numSegments - preprocess.numSegments2, + tempOutDevice->get(), preprocess.numSegments2, dest_global, + context); + } else { + // No empties. + MGPU_MEM(T) carryOutDevice = context.Malloc(preprocess.numBlocks); + KernelSegReduceApply + <<>>( + preprocess.threadCodesDevice->get(), preprocess.count, + preprocess.limitsDevice->get(), data_global, identity, op, + dest_global, carryOutDevice->get()); + MGPU_SYNC_CHECK("KernelSegReduceApply"); + + // Add the carry-in values. + SegReduceSpine(preprocess.limitsDevice->get(), preprocess.numBlocks, + dest_global, carryOutDevice->get(), identity, op, context); + } +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/sets.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/sets.cuh new file mode 100644 index 0000000000000000000000000000000000000000..6292b5a5608c77da5d621705d9dfb748c63a81ba --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/sets.cuh @@ -0,0 +1,377 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuhost.cuh" +#include "../device/serialsets.cuh" +#include "../kernels/scan.cuh" +#include "../kernels/search.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// DeviceComputeSetAvailability +// Load set keys from global memory and run the local Balanced Path and serial +// set ops. Return the results and indices in register. + +template +MGPU_DEVICE int DeviceComputeSetAvailability(InputIt1 a_global, int aCount, + InputIt2 b_global, int bCount, const int* bp_global, Comp comp, + int tid, int block, T* results, int* indices, int4& range, + bool& extended, T* keys_shared) { + + const int NV = NT * VT; + int gid = NV * block; + int bp0 = bp_global[block]; + int bp1 = bp_global[block + 1]; + + // Compute the intervals into the two source arrays. + int a0 = 0x7fffffff & bp0; + int a1 = 0x7fffffff & bp1; + int b0 = gid - a0; + int b1 = min(aCount + bCount, gid + NV) - a1; + + // If the most sig bit flag is set, we're dealing with a 'starred' diagonal + // that shifts the point of intersection up. + int bit0 = (0x80000000 & bp0) ? 1 : 0; + int bit1 = (0x80000000 & bp1) ? 1 : 0; + b0 += bit0; + b1 += bit1; + + // Attempt to load an 'extended' frame by grabbing an extra value from each + // array. + int aCount2 = a1 - a0; + int bCount2 = b1 - b0; + extended = (a1 < aCount) && (b1 < bCount); + int bStart = aCount2 + (int)extended; + + DeviceLoad2ToShared(a_global + a0, aCount2 + (int)extended, + b_global + b0, bCount2 + (int)extended, tid, keys_shared); + int count = aCount2 + bCount2; + + // Run a Balanced Path search for each thread's starting point. + int diag = min(VT * tid - bit0, count); + int2 bp = BalancedPath(keys_shared, aCount2, + keys_shared + bStart, bCount2, diag, 2, comp); + + int a0tid = bp.x; + int b0tid = VT * tid + bp.y - bp.x - bit0; + + int commit; + if(extended) + commit = SerialSetOp(keys_shared, a0tid, aCount2, + bStart + b0tid, bStart + bCount2, bp.y, results, indices, comp); + else + commit = SerialSetOp(keys_shared, a0tid, aCount2, + bStart + b0tid, bStart + bCount2, bp.y, results, indices, comp); + + range = make_int4(a0, a1, b0, b1); + return commit; +} + +//////////////////////////////////////////////////////////////////////////////// +// KernelSetOp + +template +MGPU_LAUNCH_BOUNDS void KernelSetOp(KeysIt1 aKeys_global, ValsIt1 aVals_global, + int aCount, KeysIt2 bKeys_global, ValsIt2 bVals_global, int bCount, + int* counts_global, const int* bp_global, KeysIt3 keys_global, + ValsIt3 values_global, Comp comp) { + + typedef typename std::iterator_traits::value_type KeyType; + typedef typename std::iterator_traits::value_type ValType; + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + + typedef CTAReduce R; + typedef CTAScan S; + + union Shared { + KeyType keys[NT * (VT + 1)]; + int indices[NV]; + typename R::Storage reduceStorage; + typename S::Storage scanStorage; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + + // Run the set operation. Return a bitfield for the selected keys. + KeyType results[VT]; + int indices[VT]; + int4 range; + bool extended; + int commit = DeviceComputeSetAvailability( + aKeys_global, aCount, bKeys_global, bCount, bp_global, comp, tid, block, + results, indices, range, extended, shared.keys); + aCount = range.y - range.x; + bCount = range.w - range.z; + + // scan or reduce over the number of emitted keys per thread. + int outputCount = popc(commit); + int outputTotal; + if(0 == Stage) { + // Stage 0 - count the outputs. + outputTotal = R::Reduce(tid, outputCount, shared.reduceStorage); + } else { + int globalStart = (1 == Stage) ? counts_global[block] : (NV * block); + + // Stage 1 or 2 - stream the keys. + int scan = S::Scan(tid, outputCount, shared.scanStorage, &outputTotal); + + // Write the commit results to shared memory. + int start = scan; + #pragma unroll + for(int i = 0; i < VT; ++i) + if((1<< i) & commit) + shared.keys[start++] = results[i]; + __syncthreads(); + + // Store keys to global memory. + DeviceSharedToGlobal(outputTotal, shared.keys, tid, + keys_global + globalStart); + + if(HasValues) { + // indices[] has gather indices in thread order. Compact and store + // these to shared memory for a transpose to strided order. + start = scan; + #pragma unroll + for(int i = 0; i < VT; ++i) + if((1<< i) & commit) + shared.indices[start++] = indices[i]; + __syncthreads(); + + aVals_global += range.x; + bVals_global += range.z; + values_global += globalStart; + if(MgpuSetOpIntersection == Op || MgpuSetOpDiff == Op) + DeviceGatherGlobalToGlobal(outputTotal, aVals_global, + shared.indices, tid, values_global, false); + else + DeviceTransferMergeValuesShared(outputTotal, + aVals_global, bVals_global, aCount + (int)extended, + shared.indices, tid, values_global, false); + } + } + + if(1 != Stage && !tid) + counts_global[block] = outputTotal; +} + +//////////////////////////////////////////////////////////////////////////////// +// KernelSetCompact + +template +__global__ void KernelSetCompact(const T* source_global, const int* scan_global, + int numSegments, int blockSize, OutputIt dest_global) { + + const int NumWarps = NT / WARP_SIZE; + int tid = threadIdx.x; + int warp = tid / WARP_SIZE; + int lane = (WARP_SIZE - 1) & tid; + int block = blockIdx.x; + + int gid = block * NumWarps + warp; + if(gid >= numSegments) return; + + int start = scan_global[gid]; + int end = scan_global[gid + 1]; + + source_global += blockSize * gid; + dest_global += start; + + // Round the count up by 4 * WARP_SIZE and unroll to get four outstanding + // loads. This makes the outer loop non-divergent. + int count = end - start; + for(int i = 0; i < count; i += 4 * WARP_SIZE) { + int count2 = min(4 * WARP_SIZE, count - i); + T values[4]; + DeviceGlobalToReg(count2, source_global + i, lane, + values); + DeviceRegToGlobal(count2, values, lane, + dest_global + i); + } +} + +//////////////////////////////////////////////////////////////////////////////// +// SetOpKeys + +template +MGPU_HOST int SetOpKeys(It1 a_global, int aCount, It2 b_global, int bCount, + MGPU_MEM(T)* ppKeys_global, Comp comp, CudaContext& context, bool compact) { + + typedef LaunchBoxVT< + 128, 23, 0, + 128, 11, 0, + 128, 11, 0 + > Tuning; + int2 launch = Tuning::GetLaunchParams(context); + const int NV = launch.x * launch.y; + int numBlocks = MGPU_DIV_UP(aCount + bCount, NV); + + // BalancedPath search to establish partitions. + MGPU_MEM(int) partitionsDevice = FindSetPartitions(a_global, + aCount, b_global, bCount, NV, comp, context); + + MGPU_MEM(int) countsDevice = context.Malloc(numBlocks + 1); + MGPU_MEM(T) keysDevice; + int total; + if(compact) { + // Allocate enough temporary space for all outputs. + MGPU_MEM(T) keysTempDevice = context.Malloc(NV * numBlocks); + + KernelSetOp + <<>>(a_global, + (const int*)0, aCount, b_global, (const int*)0, bCount, + countsDevice->get(), partitionsDevice->get(), keysTempDevice->get(), + (int*)0, comp); + MGPU_SYNC_CHECK("KernelSetOp"); + + // Scan block counts. + Scan(countsDevice->get(), numBlocks, 0, + mgpu::plus(), countsDevice->get() + numBlocks, &total, + countsDevice->get(), context); + + // Compact keys into destination. + keysDevice = context.Malloc(total); + + const int NT2 = 256; + int numCompactBlocks = MGPU_DIV_UP(numBlocks, NT2 / WARP_SIZE); + KernelSetCompact<256><<>>( + keysTempDevice->get(), countsDevice->get(), numBlocks, NV, + keysDevice->get()); + MGPU_SYNC_CHECK("KernelSetCompact"); + + } else { + KernelSetOp + <<>>(a_global, + (const int*)0, aCount, b_global, (const int*)0, bCount, + countsDevice->get(), partitionsDevice->get(), (T*)0, (int*)0, comp); + MGPU_SYNC_CHECK("KernelSetOp"); + + // Scan block counts. + ScanExc(countsDevice->get(), numBlocks, &total, context); + + // Allocate storage for the keys. Run the set operations again, but + // this time stream the outputs. + keysDevice = context.Malloc(total); + KernelSetOp + <<>>(a_global, (int*)0, + aCount, b_global, (int*)0, bCount, countsDevice->get(), + partitionsDevice->get(), keysDevice->get(), (int*)0, comp); + MGPU_SYNC_CHECK("KernelSetOp"); + } + *ppKeys_global = keysDevice; + return total; +} +template +MGPU_HOST int SetOpKeys(It1 a_global, int aCount, It2 b_global, int bCount, + MGPU_MEM(T)* ppKeys_global, CudaContext& context, bool compact) { + + typedef mgpu::less::value_type> Comp; + return SetOpKeys(a_global, aCount, b_global, bCount, + ppKeys_global, Comp(), context, compact); +} + +//////////////////////////////////////////////////////////////////////////////// +// SetOpPairs + +template +MGPU_HOST int SetOpPairs(KeysIt1 aKeys_global, ValsIt1 aVals_global, int aCount, + KeysIt2 bKeys_global, ValsIt2 bVals_global, int bCount, + MGPU_MEM(KeyType)* ppKeys_global, MGPU_MEM(ValType)* ppVals_global, + Comp comp, CudaContext& context) { + + const int NT = 128; + const int VT = 7; + typedef LaunchBoxVT Tuning; + int2 launch = Tuning::GetLaunchParams(context); + const int NV = launch.x * launch.y; + int numBlocks = MGPU_DIV_UP(aCount + bCount, NV); + + // BalancedPath search to establish partitions. + MGPU_MEM(int) partitionsDevice = FindSetPartitions(aKeys_global, + aCount, bKeys_global, bCount, NV, comp, context); + + // Run the kernel once to count outputs per block. + MGPU_MEM(int) countsDevice = context.Malloc(numBlocks + 1); + KernelSetOp + <<>>(aKeys_global, + (const int*)0, aCount, bKeys_global, (const int*)0, bCount, + countsDevice->get(), partitionsDevice->get(), (KeyType*)0, (int*)0, + comp); + MGPU_SYNC_CHECK("KernelSetOp"); + + // Scan outputs and allocate output arrays. + int total; + ScanExc(countsDevice->get(), numBlocks, &total, context); + MGPU_MEM(KeyType) keysDevice = context.Malloc(total); + MGPU_MEM(ValType) valsDevice = context.Malloc(total); + + // Recompute and stream the outputs. + KernelSetOp + <<>>(aKeys_global, + aVals_global, aCount, bKeys_global, bVals_global, bCount, + countsDevice->get(), partitionsDevice->get(), keysDevice->get(), + valsDevice->get(), comp); + MGPU_SYNC_CHECK("KernelSetOp"); + + *ppKeys_global = keysDevice; + *ppVals_global = valsDevice; + return total; +} +template +MGPU_HOST int SetOpPairs(KeysIt1 aKeys_global, ValsIt1 aVals_global, int aCount, + KeysIt2 bKeys_global, ValsIt2 bVals_global, int bCount, + MGPU_MEM(KeyType)* ppKeys_global, MGPU_MEM(ValType)* ppVals_global, + CudaContext& context) { + + typedef mgpu::less::value_type> Comp; + return SetOpPairs(aKeys_global, aVals_global, aCount, + bKeys_global, bVals_global, bCount, ppKeys_global, ppVals_global, + Comp(), context); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/sortedsearch.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/sortedsearch.cuh new file mode 100644 index 0000000000000000000000000000000000000000..b4e18948511dd09e8c56fa30366ca5baa5669e77 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/sortedsearch.cuh @@ -0,0 +1,342 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuhost.cuh" +#include "../device/ctasortedsearch.cuh" +#include "../kernels/search.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// DeviceLoadSortedSearch +// Loads data from global memory and performs a sorted search. Leaves the +// indices in shared memory. + +template +MGPU_DEVICE int2 DeviceLoadSortedSearch(int4 range, InputIt1 a_global, + int aCount, InputIt2 b_global, int bCount, int tid, int block, + T* keys_shared, int* indices_shared, Comp comp) { + + int a0 = range.x; + int a1 = range.y; + int b0 = range.z; + int b1 = range.w; + int aCount2 = a1 - a0; + int bCount2 = b1 - b0; + + // For matching: + // If UpperBound + // MatchA requires preceding B + // MatchB requires trailing A + // If LowerBound + // MatchA requires trailing B + // MatchB requires preceding A + int leftA = MatchB && (MgpuBoundsLower == Bounds) && (a0 > 0); + int leftB = MatchA && (MgpuBoundsUpper == Bounds) && (b0 > 0); + int rightA = a1 < aCount; + int rightB = b1 < bCount; + + int aStart = leftA; + int aEnd = aStart + aCount2 + rightA; + int bStart = aEnd + leftB; + int bEnd = bStart + bCount2 + rightB; + + // Cooperatively load all the data including halos. + DeviceLoad2ToShared(a_global + a0 - leftA, aEnd, + b_global + b0 - leftB, bEnd - aEnd, tid, keys_shared); + + // Run the serial searches and compact the indices into shared memory. + bool extended = rightA && rightB && (!MatchA || leftB) && + (!MatchB || leftA); + int2 matchCount = CTASortedSearch(keys_shared, aStart, aCount2, aEnd, a0, bStart, bCount2, bEnd, + b0, extended, tid, indices_shared, comp); + + return matchCount; +} + +//////////////////////////////////////////////////////////////////////////////// +// KernelSortedSearch + +// If Indices is true, return the array of lower_bound or upper_bound of needles +// A and haystack B. + +// If MatchA is true, set the most significant bit (0x80000000) of each index + +// If there is at least one element in the sequence B that matches the element +// in A. + +// If MatchB is 1, return a true or false flag if there is at least one element +// in A that matches the element in B. + +// If MatchB is 2, return the upper_bound of B into A. Set the most significant +// bit of each match index if there is at least one element in A that matches +// the element in B. This element will immediately precede the returned index. + +template +MGPU_LAUNCH_BOUNDS void KernelSortedSearch(InputIt1 a_global, int aCount, + InputIt2 b_global, int bCount, const int* mp_global, + OutputIt1 aIndices_global, OutputIt2 bIndices_global, int* aMatchCount, + int* bMatchCount, Comp comp) { + + typedef typename std::iterator_traits::value_type T; + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + + typedef CTAReduce R; + union Shared { + T keys[NT * (VT + 1)]; + int indices[NV]; + typename R::Storage reduce; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int4 range = ComputeMergeRange(aCount, bCount, block, 0, NV, mp_global); + + int2 matchCount = DeviceLoadSortedSearch(range, a_global, aCount, b_global, bCount, tid, block, + shared.keys, shared.indices, comp); + aCount = range.y - range.x; + bCount = range.w - range.z; + + // Store A indices to global memory. + if(IndexA || MatchA) + DeviceMemToMemLoop(aCount, shared.indices, tid, + aIndices_global + range.x); + + // Store B match flags to global memory. + if(IndexB || MatchB) + DeviceMemToMemLoop(bCount, shared.indices + aCount, tid, + bIndices_global + range.z); + + // Set the atomic counters for A matches and B matches. + if((MatchA || MatchB) && (aMatchCount || bMatchCount)) { + int x = bfi(matchCount.y, matchCount.x, 16, 16); + int total = R::Reduce(tid, x, shared.reduce); + if(!tid && aMatchCount) atomicAdd(aMatchCount, 0xffff & total); + if(!tid && bMatchCount) atomicAdd(bMatchCount, total>> 16); + } +} + +//////////////////////////////////////////////////////////////////////////////// +// SortedSearch + +template +MGPU_HOST void SortedSearch(InputIt1 a_global, int aCount, InputIt2 b_global, + int bCount, OutputIt1 aIndices_global, OutputIt2 bIndices_global, + Comp comp, CudaContext& context, int* aMatchCount, int* bMatchCount) { + + MGPU_VAR_UNUSED const bool IndexA = MgpuSearchTypeIndex == TypeA || + MgpuSearchTypeIndexMatch == TypeA; + MGPU_VAR_UNUSED const bool MatchA = MgpuSearchTypeMatch == TypeA || + MgpuSearchTypeIndexMatch == TypeA; + MGPU_VAR_UNUSED const bool IndexB = MgpuSearchTypeIndex == TypeB || + MgpuSearchTypeIndexMatch == TypeB; + MGPU_VAR_UNUSED const bool MatchB = MgpuSearchTypeMatch == TypeB || + MgpuSearchTypeIndexMatch == TypeB; + + typedef typename std::iterator_traits::value_type T; + typedef LaunchBoxVT< + 128, 11, 0, + 128, 7, 0, + 128, 7, 0 + > Tuning; + int2 launch = Tuning::GetLaunchParams(context); + const int NV = launch.x * launch.y; + + int numBlocks = MGPU_DIV_UP(aCount + bCount, NV); + + // Run a global merge path for each CTA to find partitions. + MGPU_MEM(int) partitionsDevice = MergePathPartitions(a_global, + aCount, b_global, bCount, NV, 0, comp, context); + + // Allocate counters if we want match totals returned. + MGPU_MEM(int) counters; + int* aMatchDevice = 0, *bMatchDevice = 0; + if(aMatchCount || bMatchCount) { + counters = context.Malloc(2); + cudaMemsetAsync(counters->get(), 0, 2 * sizeof(int), context.Stream()); + aMatchDevice = counters->get(); + bMatchDevice = aMatchDevice + 1; + } + + // Launch the kernel. + KernelSortedSearch + <<>>(a_global, aCount, + b_global, bCount, partitionsDevice->get(), aIndices_global, + bIndices_global, aMatchDevice, bMatchDevice, comp); + MGPU_SYNC_CHECK("KernelSortedSearch"); + + // Copy counters back to host memory. + if((MatchA && aMatchCount) || (MatchB && bMatchCount)) { + int2 host; + cudaMemcpy(&host, counters->get(), sizeof(int2), + cudaMemcpyDeviceToHost); + if(aMatchCount) *aMatchCount = host.x; + if(bMatchCount) *bMatchCount = host.y; + } +} +template +MGPU_HOST void SortedSearch(InputIt1 a_global, int aCount, InputIt2 b_global, + int bCount, OutputIt1 aIndices_global, OutputIt2 bIndices_global, + CudaContext& context, int* aMatchCount, int* bMatchCount) { + + typedef mgpu::less::value_type> C; + SortedSearch(a_global, aCount, b_global, bCount, + aIndices_global, bIndices_global, C(), context, aMatchCount, + bMatchCount); +} + +template +MGPU_HOST void SortedSearch(InputIt1 a_global, int aCount, InputIt2 b_global, + int bCount, OutputIt aIndices_global, Comp comp, CudaContext& context) { + + SortedSearch(a_global, + aCount, b_global, bCount, aIndices_global, (int*)0, comp, context); +} +template +MGPU_HOST void SortedSearch(InputIt1 a_global, int aCount, InputIt2 b_global, + int bCount, OutputIt aIndices_global, CudaContext& context) { + + typedef mgpu::less::value_type> C; + SortedSearch(a_global, aCount, b_global, bCount, aIndices_global, + C(), context); +} + +//////////////////////////////////////////////////////////////////////////////// +// SortedEqualityCount +// Provide arrays A, B, and lower_bound(A, B). This function returns the number +// of elements in B that match each element in A. This is a building block for +// relational joins. + +struct SortedEqualityOp { + MGPU_HOST_DEVICE int operator()(int lb, int ub) const { + return ub - lb; + } +}; + +template +MGPU_LAUNCH_BOUNDS void KernelSortedEqualityCount(InputIt1 a_global, int aCount, + InputIt2 b_global, int bCount, const int* mp_global, InputIt3 lb_global, + OutputIt counts_global, Comp comp, Op op) { + + typedef typename std::iterator_traits::value_type T; + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + + union Shared { + T keys[NT * (VT + 1)]; + int indices[NV]; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int4 range = ComputeMergeRange(aCount, bCount, block, 0, NV, mp_global); + + // Compute the upper bound. + int2 matchCount = DeviceLoadSortedSearch(range, a_global, aCount, b_global, bCount, tid, + block, shared.keys, shared.indices, comp); + int aCount2 = range.y - range.x; + + // Load the lower bounds computed by the previous launch. + int lb[VT]; + DeviceGlobalToReg(aCount2, lb_global + range.x, tid, lb); + + // Subtract the lower bound from the upper bound and store the count. + counts_global += range.x; + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = NT * i + tid; + if(index < aCount2) { + int count = op(lb[i], shared.indices[index]); + counts_global[index] = count; + } + } +} + +template +MGPU_HOST void SortedEqualityCount(InputIt1 a_global, int aCount, + InputIt2 b_global, int bCount, InputIt3 lb_global, OutputIt counts_global, + Comp comp, Op op, CudaContext& context) { + + const int NT = 128; + const int VT = 11; + typedef LaunchBoxVT Tuning; + int2 launch = Tuning::GetLaunchParams(context); + const int NV = launch.x * launch.y; + + MGPU_MEM(int) partitionsDevice = MergePathPartitions( + a_global, aCount, b_global, bCount, NV, 0, comp, context); + + int numBlocks = MGPU_DIV_UP(aCount + bCount, NV); + KernelSortedEqualityCount + <<>>(a_global, aCount, + b_global, bCount, partitionsDevice->get(), lb_global, counts_global, + comp, op); + MGPU_SYNC_CHECK("KernelSortedEqualityCount"); +} +template +MGPU_HOST void SortedEqualityCount(InputIt1 a_global, int aCount, + InputIt2 b_global, int bCount, InputIt3 lb_global, OutputIt counts_global, + Op op, CudaContext& context) { + + typedef mgpu::less::value_type> C; + SortedEqualicyCount(a_global, aCount, b_global, bCount, lb_global, + counts_global, C(), op, context); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/spmvcsr.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/spmvcsr.cuh new file mode 100644 index 0000000000000000000000000000000000000000..1a369577dc7c8f12aaf0637e09cb365385d2b6a4 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/kernels/spmvcsr.cuh @@ -0,0 +1,564 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "../mgpuhost.cuh" +#include "../kernels/segreduce.cuh" +#include "../kernels/bulkinsert.cuh" + +namespace mgpu { + +template +struct SpmvTuningNormal { + enum { Indirect = false }; + typedef LaunchBox< + SegReduceTuning<128, 11, 0, false, false>, + SegReduceTuning<128, 11, 0, true, false>, + SegReduceTuning<128, 7, 0, true, false> + > Tuning; +}; + +template +struct SpmvTuningIndirect { + enum { Indirect = true }; + typedef LaunchBox< + SegReduceTuning<128, 11, 0, false, false>, + SegReduceTuning<128, 11, 0, true, false>, + SegReduceTuning<128, 7, 0, true, false> + > Tuning; +}; + +template +struct SpmvTuningPreprocess { + enum { Indirect = false }; + typedef LaunchBox< + SegReduceTuning<128, 11, 0, false, false>, + SegReduceTuning<128, 11, 0, true, false>, + SegReduceTuning<128, (Size > 4) ? 11 : 7, 0, true, false> + > Tuning; +}; + + +//////////////////////////////////////////////////////////////////////////////// +// CTASpmvLoad +// Loads matrix values and column indices and gathers vector values. Finds +// products and transposes terms into register output in thread order. + +template +struct CTASpmvLoad { + enum { + NV = NT * VT, + Capacity = HalfCapacity ? (NV / 2) : NV + }; + typedef CTASegReduce SegReduce; + + union Storage { + int sources[NV]; + T data[Capacity]; + typename SegReduce::Storage segReduceStorage; + }; + + template + MGPU_DEVICE static void LoadDirect(int count2, int tid, int gid, + MatrixIt matrix_global, ColumnsIt cols_global, VecIt vec_global, + T identity, MulOp mulOp, T data[VT], Storage& storage) { + + // Load columns directly from cols_global. + int columns[VT]; + DeviceGlobalToRegDefault(count2, cols_global + gid, tid, + columns, 0); + + // Load data into stridedData. + T matrixData[VT]; + if(LoadLeft) + DeviceGlobalToRegDefault(count2, matrix_global + gid, + tid, matrixData, identity); + + // Use ldg to load vector data in strided order. + T vecData[VT]; + #pragma unroll + for(int i = 0; i < VT; ++i) + vecData[i] = ldg(vec_global + columns[i]); + + // Clear out the out-of-range inputs. + if(count2 < NV) { + #pragma unroll + for(int i = 0; i < VT; ++i) + if(NT * i + tid >= count2) + vecData[i] = identity; + } + + // Multiply matrix and vector values together. + T stridedData[VT]; + #pragma unroll + for(int i = 0; i < VT; ++i) + stridedData[i] = LoadLeft ? + mulOp(matrixData[i], vecData[i]) : vecData[i]; + + // Transpose from strided to thread order. + if(HalfCapacity) + HalfSmemTranspose(stridedData, tid, storage.data, data); + else { + DeviceRegToShared(stridedData, tid, storage.data); + DeviceSharedToThread(storage.data, tid, data); + } + } + + template + MGPU_DEVICE static void LoadIndirect(int count2, int tid, int gid, + int numRows, int startRow, const int rows[VT], const int rowStarts[VT], + SourcesIt sources_global, MatrixIt matrix_global, + ColumnsIt cols_global, VecIt vec_global, T identity, MulOp mulOp, + T data[VT], Storage& storage) { + + // Load source offsets from sources_global into smem. + DeviceGlobalToSharedLoop(numRows, sources_global + startRow, + tid, storage.sources); + + // Compute the offset of each element within its row. + int indices[VT]; + #pragma unroll + for(int i = 0; i < VT; ++i) { + int index = VT * tid + i; + int rowOffset = gid + index - rowStarts[i]; + int source = storage.sources[rows[i]]; + indices[i] = source + rowOffset; + } + __syncthreads(); + + // Transpose indices through shared memory into strided order. + DeviceThreadToShared(indices, tid, storage.sources); + DeviceSharedToReg(storage.sources, tid, indices); + + // Gather columns from cols_global. + int columns[VT]; + DeviceGatherDefault(count2, cols_global, indices, tid, + columns, 0); + + // Gather data into stridedData. + T matrixData[VT]; + if(LoadLeft) + DeviceGatherDefault(count2, matrix_global, indices, + tid, matrixData, identity); + + // Use ldg to load vector data in strided order. + T vecData[VT]; + #pragma unroll + for(int i = 0; i < VT; ++i) + vecData[i] = ldg(vec_global + columns[i]); + + // Multiply matrix and vector values together. + T stridedData[VT]; + #pragma unroll + for(int i = 0; i < VT; ++i) + stridedData[i] = LoadLeft ? + mulOp(matrixData[i], vecData[i]) : vecData[i]; + + // Transpose from strided to thread order. + if(HalfCapacity) + HalfSmemTranspose(stridedData, tid, storage.data, data); + else { + DeviceRegToShared(stridedData, tid, storage.data); + DeviceSharedToThread(storage.data, tid, data); + } + } +}; + +//////////////////////////////////////////////////////////////////////////////// +// KernelSpmvCsr + +template +MGPU_LAUNCH_BOUNDS void KernelSpmvCsr(MatrixIt matrix_global, + ColsIt cols_global, int nz, CsrIt csr_global, SourcesIt sources_global, + VecIt vec_global, const int* limits_global, DestIt dest_global, + T* carryOut_global, T identity, MulOp mulOp, AddOp addOp) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + const bool HalfCapacity = (sizeof(T) > sizeof(int)) && Params::HalfCapacity; + + typedef CTAReduce FastReduce; + typedef CTASegReduce SegReduce; + typedef CTASpmvLoad SpmvLoad; + + union Shared { + int csr[NV + 1]; + typename SegReduce::Storage segReduceStorage; + typename SpmvLoad::Storage spmvLoadStorage; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + int count2 = min(NV, nz - gid); + + // Retrieve the left and right row limits. + int limit0 = limits_global[block]; + int limit1 = limits_global[block + 1]; + + SegReduceRange range; + SegReduceTerms terms; + int rows[VT + 1], rowStarts[VT]; + T data[VT]; + + if(Indirect) { + // Transform the row limits into ranges. + range = DeviceShiftRange(limit0, limit1); + int numRows = range.end - range.begin; + + // Load the CSR interval. + DeviceGlobalToSharedLoop(numRows, csr_global + range.begin, tid, + shared.csr); + + // Flatten CSR->COO and return the segmented scan terms. + terms = DeviceSegReducePrepare(shared.csr, numRows, tid, gid, + range.flushLast, rows, rowStarts); + + // Load tile of data in thread order from row IDs. + SpmvLoad::LoadIndirect(count2, tid, gid, numRows, range.begin, rows, + rowStarts, sources_global, matrix_global, cols_global, vec_global, + identity, mulOp, data, shared.spmvLoadStorage); + } else { + // This is a direct load so we don't have a data-dependency on the + // limits. + SpmvLoad::LoadDirect(count2, tid, gid, matrix_global, cols_global, + vec_global, identity, mulOp, data, shared.spmvLoadStorage); + + // Transform the row limits into ranges. + range = DeviceShiftRange(limit0, limit1); + int numRows = range.end - range.begin; + + // Load the CSR interval. + DeviceGlobalToSharedLoop(numRows, csr_global + range.begin, tid, + shared.csr); + + // Flatten CSR->COO and return the segmented scan terms. + terms = DeviceSegReducePrepare(shared.csr, numRows, tid, gid, + range.flushLast, rows, rowStarts); + } + + // Reduce tile data and store to dest_global. Write tile's carry-out + // term to carryOut_global. + SegReduce::ReduceToGlobal(rows, range.total, terms.tidDelta, + range.begin, block, tid, data, dest_global, carryOut_global, + identity, addOp, shared.segReduceStorage); +} + +//////////////////////////////////////////////////////////////////////////////// +// SpmvCsrHost + +template +MGPU_HOST void SpmvCsrInner(MatrixIt matrix_global, ColsIt cols_global, int nz, + CsrIt csr_global, SourcesIt sources_global, int numRows, + const int* numRows2_global, VecIt vec_global, DestIt dest_global, + T identity, MulOp mulOp, AddOp addOp, CudaContext& context) { + + int2 launch = Tuning::GetLaunchParams(context); + int NV = launch.x * launch.y; + + int numBlocks = MGPU_DIV_UP(nz, NV); + + // Use upper-bound binary search to partition the CSR structure into tiles. + MGPU_MEM(int) limitsDevice = PartitionCsrSegReduce(nz, NV, csr_global, + numRows, numRows2_global, numBlocks + 1, context); + + // Evaluate the Spmv product. + MGPU_MEM(T) carryOutDevice = context.Malloc(numBlocks); + KernelSpmvCsr + <<>>(matrix_global, + cols_global, nz, csr_global, sources_global, vec_global, + limitsDevice->get(), dest_global, carryOutDevice->get(), identity, + mulOp, addOp); + MGPU_SYNC_CHECK("KernelSpmvCsr"); + + // Add the carry-in values. + SegReduceSpine(limitsDevice->get(), numBlocks, dest_global, + carryOutDevice->get(), identity, addOp, context); +} + + +template +MGPU_HOST void SpmvCsrHost(MatrixIt matrix_global, ColsIt cols_global, int nz, + CsrIt csr_global, SourcesIt sources_global, int numRows, VecIt vec_global, + bool supportEmpty, DestIt dest_global, T identity, MulOp mulOp, AddOp addOp, + CudaContext& context) { + + if(supportEmpty) { + // Allocate space for CSR2 and Sources2. + MGPU_MEM(int) csr2Device = context.Malloc(numRows + 1); + MGPU_MEM(int) sources2Device; + if(Indirect) sources2Device = context.Malloc(numRows); + + // Strip the empties from CSR and store in CSR2. + CsrStripEmpties(nz, csr_global, sources_global, numRows, + csr2Device->get(), Indirect ? sources2Device->get() : (int*)0, + (int*)0, context); + + // Run the Spmv in the CSR2 coordinate space. + MGPU_MEM(T) destDevice = context.Malloc(numRows); + SpmvCsrInner(matrix_global, cols_global, nz, + csr2Device->get(), Indirect ? sources2Device->get() : (const int*)0, + -1, csr2Device->get() + numRows, vec_global, + destDevice->get(), identity, mulOp, addOp, context); + + // Transform into the CSR space with BulkInsert. + CsrBulkInsert(csr2Device->get(), numRows, destDevice->get(), identity, + dest_global, context); + + } else { + SpmvCsrInner(matrix_global, cols_global, nz, + csr_global, sources_global, numRows, (const int*)0, vec_global, + dest_global, identity, mulOp, addOp, context); + } +} + +//////////////////////////////////////////////////////////////////////////////// +// Spmv host functions + +template +struct spmv_pass_through : public std::binary_function { + MGPU_HOST_DEVICE T operator()(T a, T b) { return a; } +}; + +template +MGPU_HOST void SpmvCsrUnary( ColsIt cols_global, int nz, CsrIt csr_global, + int numRows, VecIt vec_global, bool supportEmpty, DestIt dest_global, + T identity, AddOp addOp, CudaContext& context) { + + typedef typename SpmvTuningNormal::Tuning Tuning; + SpmvCsrHost((const T*)0, cols_global, nz, csr_global, + (const int*)0, numRows, vec_global, supportEmpty, dest_global, + identity, spmv_pass_through(), addOp, context); +} + +template +MGPU_HOST void SpmvCsrBinary(MatrixIt matrix_global, ColsIt cols_global, int nz, + CsrIt csr_global, int numRows, VecIt vec_global, bool supportEmpty, + DestIt dest_global, T identity, MulOp mulOp, AddOp addOp, + CudaContext& context) { + + typedef typename SpmvTuningNormal::Tuning Tuning; + SpmvCsrHost(matrix_global, cols_global, nz, csr_global, + (const int*)0, numRows, vec_global, supportEmpty, dest_global, + identity, mulOp, addOp, context); +} + +template +MGPU_HOST void SpmvCsrIndirectUnary(ColsIt cols_global, int nz, + CsrIt csr_global, SourcesIt sources_global, int numRows, VecIt vec_global, + bool supportEmpty, DestIt dest_global, T identity, AddOp addOp, + CudaContext& context) { + + typedef typename SpmvTuningIndirect::Tuning Tuning; + SpmvCsrHost((const T*)0, cols_global, nz, csr_global, + sources_global, numRows, vec_global, supportEmpty, dest_global, + identity, spmv_pass_through(), addOp, context); +} + +template +MGPU_HOST void SpmvCsrIndirectBinary(MatrixIt matrix_global, ColsIt cols_global, + int nz, CsrIt csr_global, SourcesIt sources_global, int numRows, + VecIt vec_global, bool supportEmpty, DestIt dest_global, T identity, + MulOp mulOp, AddOp addOp, CudaContext& context) { + + typedef typename SpmvTuningIndirect::Tuning Tuning; + SpmvCsrHost(matrix_global, cols_global, nz, csr_global, + sources_global, numRows, vec_global, supportEmpty, dest_global, + identity, mulOp, addOp, context); +} + +//////////////////////////////////////////////////////////////////////////////// +// Spmv preprocessing + +template +MGPU_HOST void SpmvPreprocessUnary(int nz, CsrIt csr_global, int numRows, + bool supportEmpty, std::auto_ptr* ppData, + CudaContext& context) { + + typedef typename SpmvTuningPreprocess::Tuning Tuning; + SegReducePreprocess(nz, csr_global, numRows, supportEmpty, ppData, + context); +} + +template +MGPU_HOST void SpmvPreprocessBinary(int nz, CsrIt csr_global, int numRows, + bool supportEmpty, std::auto_ptr* ppData, + CudaContext& context) { + + typedef typename SpmvTuningPreprocess::Tuning Tuning; + SegReducePreprocess(nz, csr_global, numRows, supportEmpty, ppData, + context); +} + +//////////////////////////////////////////////////////////////////////////////// +// KernelSpmvApply + +template +MGPU_LAUNCH_BOUNDS void KernelSpmvApply(const int* threadCodes_global, + MatrixIt matrix_global, ColsIt cols_global, int nz, VecIt vec_global, + const int* limits_global, DestIt dest_global, T* carryOut_global, + T identity, MulOp mulOp, AddOp addOp) { + + typedef MGPU_LAUNCH_PARAMS Params; + const int NT = Params::NT; + const int VT = Params::VT; + const int NV = NT * VT; + const bool HalfCapacity = (sizeof(T) > sizeof(int)) && Params::HalfCapacity; + + typedef CTASegReduce SegReduce; + typedef CTASpmvLoad SpmvLoad; + + union Shared { + typename SegReduce::Storage segReduceStorage; + typename SpmvLoad::Storage spmvLoadStorage; + }; + __shared__ Shared shared; + + int tid = threadIdx.x; + int block = blockIdx.x; + int gid = NV * block; + int count2 = min(NV, nz - gid); + + // Retrieve the left and right row limits and thread codes.. + int limit0 = limits_global[block]; + int limit1 = limits_global[block + 1]; + int threadCodes = threadCodes_global[NT * block + tid]; + + // Load the tile's data before dereferencing limit0/limit1. + T data[VT]; + SpmvLoad::LoadDirect(count2, tid, gid, matrix_global, cols_global, + vec_global, identity, mulOp, data, shared.spmvLoadStorage); + + // Transform the row limits into ranges. + SegReduceRange range = DeviceShiftRange(limit0, limit1); + + // Expand the row indices. + int rows[VT + 1]; + DeviceExpandFlagsToRows(threadCodes>> 20, threadCodes, rows); + + // Reduce tile data and store to dest_global. Write tile's carry-out + // term to carryOut_global. + int tidDelta = 0x7f & (threadCodes>> 13); + SegReduce::ReduceToGlobal(rows, range.total, tidDelta, range.begin, + block, tid, data, dest_global, carryOut_global, identity, addOp, + shared.segReduceStorage); +} + +template +MGPU_HOST void SpmvApplyHost(const SpmvPreprocessData& preprocess, + MatrixIt matrix_global, ColsIt cols_global, VecIt vec_global, + DestIt dest_global, T identity, MulOp mulOp, AddOp addOp, + CudaContext& context) { + + typedef typename SpmvTuningPreprocess::Tuning Tuning; + int2 launch = Tuning::GetLaunchParams(context); + + if(preprocess.csr2Device.get()) { + // Support empties. + MGPU_MEM(T) destDevice = context.Malloc(preprocess.numSegments2); + MGPU_MEM(T) carryOutDevice = context.Malloc(preprocess.numBlocks); + KernelSpmvApply + <<>>( + preprocess.threadCodesDevice->get(), matrix_global, cols_global, + preprocess.count, vec_global, preprocess.limitsDevice->get(), + destDevice->get(), carryOutDevice->get(), identity, mulOp, + addOp); + + // Add the carry-in values. + SegReduceSpine(preprocess.limitsDevice->get(), preprocess.numBlocks, + destDevice->get(), carryOutDevice->get(), identity, addOp, + context); + + // Transform into the CSR space with BulkInsert. + CsrBulkInsert(preprocess.csr2Device->get(), preprocess.numSegments, + destDevice->get(), identity, dest_global, context); + + } else { + // No empties. + + // Evaluate the Spmv product. + MGPU_MEM(T) carryOutDevice = context.Malloc(preprocess.numBlocks); + KernelSpmvApply + <<>>( + preprocess.threadCodesDevice->get(), matrix_global, cols_global, + preprocess.count, vec_global, preprocess.limitsDevice->get(), + dest_global, carryOutDevice->get(), identity, mulOp, addOp); + MGPU_SYNC_CHECK("KernelSpmvApply"); + + // Add the carry-in values. + SegReduceSpine(preprocess.limitsDevice->get(), preprocess.numBlocks, + dest_global, carryOutDevice->get(), identity, addOp, context); + } +} + +template +MGPU_HOST void SpmvUnaryApply(const SpmvPreprocessData& preprocess, + ColsIt cols_global, VecIt vec_global, DestIt dest_global, T identity, + AddOp addOp, CudaContext& context) { + + SpmvApplyHost(preprocess, (const T*)0, cols_global, vec_global, + dest_global, identity, spmv_pass_through(), addOp, context); +} + +template +MGPU_HOST void SpmvBinaryApply(const SpmvPreprocessData& preprocess, + MatrixIt matrix_global, ColsIt cols_global, VecIt vec_global, + DestIt dest_global, T identity, MulOp mulOp, AddOp addOp, + CudaContext& context) { + + SpmvApplyHost(preprocess, matrix_global, cols_global, vec_global, + dest_global, identity, mulOp, addOp, context); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/mgpudevice.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/mgpudevice.cuh new file mode 100644 index 0000000000000000000000000000000000000000..18e00740735853fc34ee3edde8efbdda38276514 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/mgpudevice.cuh @@ -0,0 +1,290 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "mgpuenums.h" +#include "device/deviceutil.cuh" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// device/loadstore.cuh + +// For 0 <= i < VT: +// index = NT * i + tid; +// reg[i] = data[index]; +// Synchronize after load. +template +MGPU_DEVICE void DeviceSharedToReg(InputIt data, int tid, T* reg, + bool sync = true); + +// For 0 <= i < VT: +// index = NT * i + tid; +// if(index < count) reg[i] = data[index]; +// No synchronize after load. +template +MGPU_DEVICE void DeviceGlobalToReg(int count, InputIt data, int tid, + T* reg, bool sync = false); + +template +MGPU_DEVICE void DeviceGlobalToRegDefault(int count, InputIt data, int tid, + T* reg, T init, bool sync = false); + +// For 0 <= i < VT: +// index = NT * i + tid; +// if(index < count) reg[i] = data[index]; +// No synchronize after load. +template +MGPU_DEVICE void DeviceGlobalToReg(int count, InputIt data, int tid, + T* reg, bool sync = false); + +// For 0 <= i < VT: +// index = NT * i + tid; +// if(index < count) reg[i] = data[index]; +// No synchronize after load. +template +MGPU_DEVICE void DeviceGlobalToRegDefault2(int count, InputIt data, int tid, + T* reg, T init, bool sync = false); + +// For 0 <= i < VT: +// index = NT * i + tid; +// if(index < count) reg[i] = data[index]; +// No synchronize after load. +// No optimized code path for count < NV (smaller generated code). +template +MGPU_DEVICE void DeviceGlobalToRegLoop(int count, InputIt data, int tid, + T* reg, bool sync = false); + + +// For 0 <= i < VT: +// index = VT * tid + i. +// if(index < count) reg[i] = data[index]; +// No synchronize after load. +template +MGPU_DEVICE void DeviceGlobalToThread(int count, InputIt data, int tid, + T* reg); + +template +MGPU_DEVICE void DeviceGlobalToThreadDefault(int count, InputIt data, int tid, + T* reg, T init); + +// For 0 <= i < VT: +// index = NT * i + tid; +// if(index < count) data[index] = reg[i]; +// Synchronize after load. +template +MGPU_DEVICE void DeviceRegToShared(const T* reg, int tid, OutputIt dest, + bool sync = true); + +// For 0 <= i < VT: +// index = NT * i + tid; +// if(index < count) data[index] = reg[i]; +// No synchronize after load. +template +MGPU_DEVICE void DeviceRegToGlobal(int count, const T* reg, int tid, + OutputIt dest, bool sync = false); + +// For 0 <= index < count: +// dest[index] = source[index]; +// This function is intended to replace DeviceGlobalToShared in cases where +// count is much less than NT * VT. +template +MGPU_DEVICE void DeviceMemToMemLoop(int count, InputIt source, int tid, + OutputIt dest, bool sync = true); + +// For 0 <= index < count: +// dest[index] = source[index]; +// Synchronize after store. +template +MGPU_DEVICE void DeviceSharedToGlobal(int count, const T* source, int tid, + OutputIt dest, bool sync = true); + +// For 0 <= index < count: +// dest[index] = source[index]; +// Synchronize after store. +template +MGPU_DEVICE void DeviceGlobalToShared(int count, InputIt source, int tid, + T* dest, bool sync = true); + +template +MGPU_DEVICE void DeviceGlobalToShared2(int count, InputIt source, int tid, + T* dest, bool sync = true); + +// For 0 <= index < count: +// dest[index] = source[index]; +// Synchronize after store. +// No optimized code path for count < NV (smaller generated code). +template +MGPU_DEVICE void DeviceGlobalToSharedLoop(int count, InputIt source, int tid, + T* dest, bool sync = true); + +template +MGPU_DEVICE void DeviceGlobalToSharedDefault(int count, InputIt source, int tid, + T* dest, T init, bool sync = true); + +template +MGPU_DEVICE void DeviceGlobalToSharedDefault2(int count, InputIt source, + int tid, T* dest, T init, bool sync = true); + +// For 0 <= index < count: +// dest[index] = source[index]; +// No synchronize. +template +MGPU_DEVICE void DeviceGlobalToGlobal(int count, InputIt source, int tid, + OutputIt dest, bool sync = false); + +// Transponse VT elements in NT threads (x) into thread-order registers (y) +// using only NT * VT / 2 elements of shared memory. +template +MGPU_DEVICE void HalfSmemTranspose(const T* x, int tid, T* shared, T* y); + +// For 0 <= i < VT: +// index = NT * i + tid; +// if(index < count) +// gather = indices[index]; +// reg[i] = data[gather]; +// Synchronize after load. +template +MGPU_DEVICE void DeviceGather(int count, InputIt data, int indices[VT], + int tid, T* reg, bool sync = true); + +template +MGPU_DEVICE void DeviceGatherDefault(int count, InputIt data, int indices[VT], + int tid, T* reg, T identity, bool sync = true); + +// For 0 <= i < VT: +// index = NT * i + tid; +// if(index < count) +// scatter = indices[index]; +// data[scatter] = reg[i]; +// Synchronize after store. +template +MGPU_DEVICE void DeviceScatter(int count, const T* reg, int tid, + int indices[VT], OutputIt data, bool sync = true); + +// For 0 <= i < VT: +// shared[VT * tid + i] = threadReg[i]; +// Synchronize after store. +// Note this function moves data in THREAD ORDER. +// (DeviceRegToShared moves data in STRIDED ORDER). +template +MGPU_DEVICE void DeviceThreadToShared(const T* threadReg, int tid, T* shared, + bool sync = true); + +// For 0 <= i < VT: +// threadReg[i] = shared[VT * tid + i]; +// Synchronize after load. +// Note this function moves data in THREAD ORDER. +// (DeviceSharedToReg moves data in STRIDED ORDER). +template +MGPU_DEVICE void DeviceSharedToThread(const T* shared, int tid, T* threadReg, + bool sync = true); + +// For 0 <= index < aCount: +// shared[index] = a_global[index]; +// For 0 <= index < bCount: +// shared[aCount + index] = b_global[index]; +// VT0 is the lower-bound for predication-free execution: +// If count >= NT * VT0, a predication-free branch is taken. +// VT1 is the upper-bound for loads: +// NT * VT1 must >= aCount + bCount. + +template +MGPU_DEVICE void DeviceLoad2ToReg(const T* a_global, int aCount, + const T* b_global, int bCount, int tid, T* reg, bool sync = false); + +template +MGPU_DEVICE void DeviceLoad2ToShared(const T* a_global, int aCount, + const T* b_global, int bCount, int tid, T* shared, bool sync = true); + +template +MGPU_DEVICE void DeviceLoad2ToReg(InputIt1 a_global, int aCount, + InputIt2 b_global, int bCount, int tid, T* reg, bool sync = false); + +template +MGPU_DEVICE void DeviceLoad2ToShared(InputIt1 a_global, int aCount, + InputIt2 b_global, int bCount, int tid, T* shared, bool sync = true); + +// For 0 <= i < VT +// index = NT * i + tid; +// if(index < count) +// gather = indices_shared[index]; +// dest_global[index] = data_global[gather]; +// Synchronize after load. +template +MGPU_DEVICE void DeviceGatherGlobalToGlobal(int count, InputIt data_global, + const int* indices_shared, int tid, OutputIt dest_global, + bool sync = true); + +// For 0 <= i < VT +// index = NT * i + tid +// if(index < count) +// gather = indices[index]; +// if(gather < aCount) data = a_global[gather]; +// else data = b_global[gather - aCount]; +// dest_global[index] = data; +// Synchronize after load. +template +MGPU_DEVICE void DeviceTransferMergeValuesReg(int count, InputIt1 a_global, + InputIt2 b_global, int bStart, const int* indices, int tid, + T* reg, bool sync = false); + +template +MGPU_DEVICE void DeviceTransferMergeValuesShared(int count, InputIt1 a_global, + InputIt2 b_global, int bStart, const int* indices_shared, int tid, + OutputIt dest_global, bool sync = true); + +template +MGPU_DEVICE void DeviceTransferMergeValuesReg(int count, const T* a_global, + const T* b_global, int bStart, const int* indices, int tid, + T* reg, bool sync = false); + +template +MGPU_DEVICE void DeviceTransferMergeValuesShared(int count, const T* a_global, + const T* b_global, int bStart, const int* indices_shared, int tid, + OutputIt dest_global, bool sync = true); + + + +} // namespace mgpu + + +#include "device/launchbox.cuh" +#include "device/loadstore.cuh" +#include "device/ctasegscan.cuh" diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/mgpuenums.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/mgpuenums.h new file mode 100644 index 0000000000000000000000000000000000000000..be2b8314a8ad23db79a0e8bc4cd60a6b4b6357b4 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/mgpuenums.h @@ -0,0 +1,70 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +namespace mgpu { + +enum MgpuBounds { + MgpuBoundsLower, + MgpuBoundsUpper +}; + +enum MgpuScanType { + MgpuScanTypeExc, + MgpuScanTypeInc +}; + +enum MgpuSearchType { + MgpuSearchTypeNone, + MgpuSearchTypeIndex, + MgpuSearchTypeMatch, + MgpuSearchTypeIndexMatch +}; + +enum MgpuJoinKind { + MgpuJoinKindInner, + MgpuJoinKindLeft, + MgpuJoinKindRight, + MgpuJoinKindOuter +}; + +enum MgpuSetOp { + MgpuSetOpIntersection, + MgpuSetOpUnion, + MgpuSetOpDiff, + MgpuSetOpSymDiff +}; + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/mgpuhost.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/mgpuhost.cuh new file mode 100644 index 0000000000000000000000000000000000000000..933113e4ca6b6c41cb20c584fc48c5c92d27c58d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/mgpuhost.cuh @@ -0,0 +1,815 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "mgpudevice.cuh" +#include "util/mgpucontext.h" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// kernels/reduce.cuh + +// Reduce input and return variable in device memory or host memory, or both. +// Provide a non-null pointer to retrieve data. +template +MGPU_HOST void Reduce(InputIt data_global, int count, T identity, Op op, + T* reduce_global, T* reduce_host, CudaContext& context); + +// T = std::iterator_traits::value_type. +// Reduce with identity = 0 and op = mgpu::plus. +// Returns the value in host memory. +template +MGPU_HOST typename std::iterator_traits::value_type +Reduce(InputIt data_global, int count, CudaContext& context); + + +//////////////////////////////////////////////////////////////////////////////// +// kernels/scan.cuh + +// Scan inputs in device memory. +// MgpuScanType may be: +// MgpuScanTypeExc (exclusive) or +// MgpuScanTypeInc (inclusive). +// Return the total in device memory, host memory, or both. +template +MGPU_HOST void Scan(DataIt data_global, int count, T identity, Op op, + T* reduce_global, T* reduce_host, DestIt dest_global, + CudaContext& context); + +// Exclusive scan with identity = 0 and op = mgpu::plus. +// Returns the total in host memory. +template +MGPU_HOST void ScanExc(InputIt data_global, int count, TotalType* total, + CudaContext& context); + +// Like above, but don't return the total. +template +MGPU_HOST void ScanExc(InputIt data_global, int count, CudaContext& context); + +//////////////////////////////////////////////////////////////////////////////// +// kernels/bulkremove.cuh + +// Compact the elements in source_global by removing elements identified by +// indices_global. indices_global must be unique, sorted, and range between 0 +// and sourceCount - 1. The number of outputs is sourceCount - indicesCount. + +// IndicesIt should resolve to an integer type. iterators like step_iterator +// are supported. + +// If sourceCount = 10, indicesCount = 6, and indices = (1, 3, 4, 5, 7, 8), then +// dest = A0 A2 A6 A9. (All indices between 0 and sourceCount - 1 except those +// in indices_global). +template +MGPU_HOST void BulkRemove(InputIt source_global, int sourceCount, + IndicesIt indices_global, int indicesCount, OutputIt dest_global, + CudaContext& context); + + +//////////////////////////////////////////////////////////////////////////////// +// kernels/bulkinsert.cuh + +// Combine aCount elements in a_global with bCount elements in b_global. +// Each element a_global[i] is inserted before position indices_global[i] and +// stored to dest_global. The insertion indices are relative to the B array, +// not the output. Indices must be sorted but not necessarily unique. + +// If aCount = 5, bCount = 3, and indices = (1, 1, 2, 3, 3), the output is: +// B0 A0 A1 B1 A2 B2 A3 A4. +template +MGPU_HOST void BulkInsert(InputIt1 a_global, IndicesIt indices_global, + int aCount, InputIt2 b_global, int bCount, OutputIt dest_global, + CudaContext& context); + + +//////////////////////////////////////////////////////////////////////////////// +// kernels/merge.cuh + +// MergeKeys merges two arrays of sorted inputs with C++-comparison semantics. +// aCount items from aKeys_global and bCount items from bKeys_global are merged +// into aCount + bCount items in keys_global. +// Comp is a comparator type supporting strict weak ordering. +// If !comp(b, a), then a is placed before b in the output. +template +MGPU_HOST void MergeKeys(KeysIt1 aKeys_global, int aCount, KeysIt2 bKeys_global, + int bCount, KeysIt3 keys_global, Comp comp, CudaContext& context); + +// MergeKeys specialized with Comp = mgpu::less. +template +MGPU_HOST void MergeKeys(KeysIt1 aKeys_global, int aCount, KeysIt2 bKeys_global, + int bCount, KeysIt3 keys_global, CudaContext& context); + +// MergePairs merges two arrays of sorted inputs by key and copies values. +// If !comp(bKey, aKey), then aKey is placed before bKey in the output, and +// the corresponding aData is placed before bData. This corresponds to *_by_key +// functions in Thrust. +template +MGPU_HOST void MergePairs(KeysIt1 aKeys_global, ValsIt1 aVals_global, + int aCount, KeysIt2 bKeys_global, ValsIt2 bVals_global, int bCount, + KeysIt3 keys_global, ValsIt3 vals_global, Comp comp, CudaContext& context); + +// MergePairs specialized with Comp = mgpu::less. +template +MGPU_HOST void MergePairs(KeysIt1 aKeys_global, ValsIt1 aVals_global, + int aCount, KeysIt2 bKeys_global, ValsIt2 bVals_global, int bCount, + KeysIt3 keys_global, ValsIt3 vals_global, CudaContext& context); + + +//////////////////////////////////////////////////////////////////////////////// +// kernels/mergesort.cuh + +// MergesortKeys sorts data_global using comparator Comp. +// If !comp(b, a), then a comes before b in the output. The data is sorted +// in-place. +template +MGPU_HOST void MergesortKeys(T* data_global, int count, Comp comp, + CudaContext& context); + +// MergesortKeys specialized with Comp = mgpu::less. +template +MGPU_HOST void MergesortKeys(T* data_global, int count, CudaContext& context); + +// MergesortPairs sorts data by key, copying data. This corresponds to +// sort_by_key in Thrust. +template +MGPU_HOST void MergesortPairs(KeyType* keys_global, ValType* values_global, + int count, Comp comp, CudaContext& context); + +// MergesortPairs specialized with Comp = mgpu::less. +template +MGPU_HOST void MergesortPairs(KeyType* keys_global, ValType* values_global, + int count, CudaContext& context); + +// MergesortIndices is like MergesortPairs where values_global is treated as +// if initialized with integers (0 ... count - 1). +template +MGPU_HOST void MergesortIndices(KeyType* keys_global, int* values_global, + int count, Comp comp, CudaContext& context); + +// MergesortIndices specialized with Comp = mgpu::less. +template +MGPU_HOST void MergesortIndices(KeyType* keys_global, int* values_global, + int count, CudaContext& context); + + +//////////////////////////////////////////////////////////////////////////////// +// kernels/segmentedsort.cuh + +// Mergesort count items in-place in data_global. Keys are compared with Comp +// (as they are in MergesortKeys), however keys remain inside the segments +// defined by flags_global. + +// flags_global is a bitfield cast to uint*. Each bit in flags_global is a +// segment head flag. Only keys between segment head flags (inclusive on the +// left and exclusive on the right) may be exchanged. The first element is +// assumed to start a segment, regardless of the value of bit 0. + +// Passing verbose=true causes the function to print mergepass statistics to the +// console. This may be helpful for developers to understand the performance +// characteristics of the function and how effectively it early-exits merge +// operations. +template +MGPU_HOST void SegSortKeysFromFlags(T* data_global, int count, + const uint* flags_global, CudaContext& context, Comp comp, + bool verbose = false); + +// SegSortKeysFromFlags specialized with Comp = mgpu::less. +template +MGPU_HOST void SegSortKeysFromFlags(T* data_global, int count, + const uint* flags_global, CudaContext& context, bool verbose = false); + +// Segmented sort using head flags and supporting value exchange. +template +MGPU_HOST void SegSortPairsFromFlags(KeyType* keys_global, + ValType* values_global, int count, const uint* flags_global, + CudaContext& context, Comp comp, bool verbose = false); + +// SegSortPairsFromFlags specialized with Comp = mgpu::less. +template +MGPU_HOST void SegSortPairsFromFlags(KeyType* keys_global, + ValType* values_global, int count, const uint* flags_global, + CudaContext& context, bool verbose = false); + +// Segmented sort using segment indices rather than head flags. indices_global +// is a sorted and unique list of indicesCount segment start locations. These +// indices correspond to the set bits in the flags_global field. A segment +// head index for position 0 may be omitted. +template +MGPU_HOST void SegSortKeysFromIndices(T* data_global, int count, + const int* indices_global, int indicesCount, CudaContext& context, + Comp comp, bool verbose = false); + +// SegSortKeysFromIndices specialized with Comp = mgpu::less. +template +MGPU_HOST void SegSortKeysFromIndices(T* data_global, int count, + const int* indices_global, int indicesCount, CudaContext& context, + bool verbose = false); + +// Segmented sort using segment indices and supporting value exchange. +template +MGPU_HOST void SegSortPairsFromIndices(KeyType* keys_global, + ValType* values_global, int count, const int* indices_global, + int indicesCount, CudaContext& context, Comp comp, bool verbose = false); + +// SegSortPairsFromIndices specialized with Comp = mgpu::less. +template +MGPU_HOST void SegSortPairsFromIndices(KeyType* keys_global, + ValType* values_global, int count, const int* indices_global, + int indicesCount, CudaContext& context, bool verbose = false); + + +//////////////////////////////////////////////////////////////////////////////// +// kernels/localitysort.cuh + +// LocalitySortKeys is a version of MergesortKeys optimized for non-uniformly +// random input arrays. If the keys begin close to their sorted destinations, +// this function may exploit the structure to early-exit merge passes. + +// Passing verbose=true causes the function to print mergepass statistics to the +// console. This may be helpful for developers to understand the performance +// characteristics of the function and how effectively it early-exits merge +// operations. +template +MGPU_HOST void LocalitySortKeys(T* data_global, int count, CudaContext& context, + Comp comp, bool verbose = false); + +// LocalitySortKeys specialized with Comp = mgpu::less. +template +MGPU_HOST void LocalitySortKeys(T* data_global, int count, CudaContext& context, + bool verbose = false); + +// Locality sort supporting value exchange. +template +MGPU_HOST void LocalitySortPairs(KeyType* keys_global, ValType* values_global, + int count, CudaContext& context, Comp comp, bool verbose = false); + +// LocalitySortPairs specialized with Comp = mpgu::less. +template +MGPU_HOST void LocalitySortPairs(KeyType* keys_global, ValType* values_global, + int count, CudaContext& context, bool verbose = false); + + +//////////////////////////////////////////////////////////////////////////////// +// kernels/sortedsearch.cuh + +// Vectorized sorted search. This is the most general form of the function. +// Executes two simultaneous linear searches on two sorted inputs. + +// Bounds: +// MgpuBoundsLower - +// lower-bound search of A into B. +// upper-bound search of B into A. +// MgpuBoundsUpper - +// upper-bound search of A into B. +// lower-bound search of B into A. +// Type[A|B]: +// MgpuSearchTypeNone - no output for this input. +// MgpuSearchTypeIndex - return search indices as integers. +// MgpuSearchTypeMatch - return 0 (no match) or 1 (match). +// For TypeA, returns 1 if there is at least 1 matching element in B +// for element in A. +// For TypeB, returns 1 if there is at least 1 matching element in A +// for element in B. +// MgpuSearchTypeIndexMatch - return search indices as integers. Most +// significant bit is match bit. +// aMatchCount, bMatchCount - If Type is Match or IndexMatch, return the total +// number of elements in A or B with matches in B or A, if the pointer is +// not null. This generates a synchronous cudaMemcpyDeviceToHost call that +// callers using streams should be aware of. +template +MGPU_HOST void SortedSearch(InputIt1 a_global, int aCount, InputIt2 b_global, + int bCount, OutputIt1 aIndices_global, OutputIt2 bIndices_global, + Comp comp, CudaContext& context, int* aMatchCount = 0, + int* bMatchCount = 0); + +// SortedSearch specialized with Comp = mgpu::less. +template +MGPU_HOST void SortedSearch(InputIt1 a_global, int aCount, InputIt2 b_global, + int bCount, OutputIt1 aIndices_global, OutputIt2 bIndices_global, + CudaContext& context, int* aMatchCount = 0, int* bMatchCount = 0); + +// SortedSearch specialized with +// TypeA = MgpuSearchTypeIndex +// TypeB = MgpuSearchTypeNone +// aMatchCount = bMatchCount = 0. +template +MGPU_HOST void SortedSearch(InputIt1 a_global, int aCount, InputIt2 b_global, + int bCount, OutputIt aIndices_global, Comp comp, CudaContext& context); + +// SortedSearch specialized with Comp = mgpu::less. +template +MGPU_HOST void SortedSearch(InputIt1 a_global, int aCount, InputIt2 b_global, + int bCount, OutputIt aIndices_global, CudaContext& context); + +// SortedEqualityCount returns the difference between upper-bound (computed by +// this function) and lower-bound (passed as an argument). That is, it computes +// the number of occurences of a key in B that match each key in A. + +// The provided operator must have a method: +// int operator()(int lb, int ub) const; +// It returns the count given the lower- and upper-bound indices. +// +// An object SortedEqualityOp is provided: +// struct SortedEqualityOp { +// MGPU_HOST_DEVICE int operator()(int lb, int ub) const { +// return ub - lb; +// } +// }; +template +MGPU_HOST void SortedEqualityCount(InputIt1 a_global, int aCount, + InputIt2 b_global, int bCount, InputIt3 lb_global, OutputIt counts_global, + Comp comp, Op op, CudaContext& context); + +// Specialization of SortedEqualityCount with Comp = mgpu::less. +template +MGPU_HOST void SortedEqualityCount(InputIt1 a_global, int aCount, + InputIt2 b_global, int bCount, InputIt3 lb_global, OutputIt counts_global, + Op op, CudaContext& context); + +//////////////////////////////////////////////////////////////////////////////// +// kernels/loadbalance.cuh + +// LoadBalanceSearch is a special vectorized sorted search. Consider bCount +// objects that generate a variable number of work items, with aCount work +// items in total. The caller computes an exclusive scan of the work-item counts +// into b_global. + +// indices_global has aCount outputs. indices_global[i] is the index of the +// object that generated the i'th work item. +// Eg: +// work-item counts: 2, 5, 3, 0, 1. +// scan counts: 0, 2, 7, 10, 10. aCount = 11. +// +// LoadBalanceSearch computes the upper-bound of counting_iterator(0) with +// the scan of the work-item counts and subtracts 1: +// LBS: 0, 0, 1, 1, 1, 1, 1, 2, 2, 2, 4. + +// This is equivalent to expanding the index of each object by the object's +// work-item count. + + +template +MGPU_HOST void LoadBalanceSearch(int aCount, InputIt b_global, int bCount, + int* indices_global, CudaContext& context); + +//////////////////////////////////////////////////////////////////////////////// +// kernels/intervalmove.cuh + +// IntervalExpand duplicates intervalCount items in values_global. +// indices_global is an intervalCount-sized array filled with the scan of item +// expand counts. moveCount is the total number of outputs (sum of expand +// counts). + +// Eg: +// values = 0, 1, 2, 3, 4, 5, 6, 7, 8 +// counts = 1, 2, 1, 0, 4, 2, 3, 0, 2 +// indices = 0, 1, 3, 4, 4, 8, 10, 13, 13 (moveCount = 15). +// Expand values[i] by counts[i]: +// output = 0, 1, 1, 2, 4, 4, 4, 4, 5, 5, 6, 6, 6, 8, 8 +template +MGPU_HOST void IntervalExpand(int moveCount, IndicesIt indices_global, + ValuesIt values_global, int intervalCount, OutputIt output_global, + CudaContext& context); + +// IntervalMove is a load-balanced and vectorized device memcpy. +// It copies intervalCount variable-length intervals from user-defined sources +// to user-defined destinations. If destination intervals overlap, results are +// undefined. + +// Eg: +// Interval counts: +// 0: 3 9 1 9 8 5 10 2 5 2 +// 10: 8 6 5 2 4 0 8 2 5 6 +// Scan of interval counts (indices_global): +// 0: 0 3 12 13 22 30 35 45 47 52 +// 10: 54 62 68 73 75 79 79 87 89 94 (moveCount = 100). +// Interval gather (gather_global): +// 0: 75 86 17 2 67 24 37 11 95 35 +// 10: 52 18 47 0 13 75 78 60 62 29 +// Interval scatter (scatter_global): +// 0: 10 80 99 27 41 71 15 0 36 13 +// 10: 89 49 66 97 76 76 2 25 61 55 + +// This vectorizes into 20 independent memcpy operations which are load-balanced +// across CTAs: +// move 0: (75, 78)->(10, 13) move 10: (52, 60)->(10, 18) +// move 1: (86, 95)->(80, 89) move 11: (18, 24)->(49, 55) +// move 2: (17, 18)->(99,100) move 12: (47, 52)->(66, 71) +// move 3: ( 2, 11)->(27, 36) move 13: ( 0, 2)->(97, 99) +// move 4: (67, 75)->(41, 49) move 14: (13, 17)->(76, 80) +// move 5: (24, 29)->(71, 76) move 15: (75, 75)->(76, 76) +// move 6: (37, 47)->(15, 25) move 16: (78, 86)->( 2, 10) +// move 7: (11, 13)->( 0, 3) move 17: (60, 62)->(25, 27) +// move 8: (95,100)->(36, 41) move 18: (62, 67)->(61, 66) +// move 9: (35, 37)->(13, 15) move 19: (29, 35)->(55, 61) +template +MGPU_HOST void IntervalMove(int moveCount, GatherIt gather_global, + ScatterIt scatter_global, IndicesIt indices_global, int intervalCount, + InputIt input_global, OutputIt output_global, CudaContext& context); + +// IntervalGather is a specialization of IntervalMove that stores output data +// sequentially into output_global. For the example above, IntervalGather treats +// scatter_global the same as indices_global. +template +MGPU_HOST void IntervalGather(int moveCount, GatherIt gather_global, + IndicesIt indices_global, int intervalCount, InputIt input_global, + OutputIt output_global, CudaContext& context); + +// IntervalScatter is a specialization of IntervalMove that loads input data +// sequentially from input_global. For the example above, IntervalScatter treats +// gather_global the same as indices_global. +template +MGPU_HOST void IntervalScatter(int moveCount, ScatterIt scatter_global, + IndicesIt indices_global, int intervalCount, InputIt input_global, + OutputIt output_global, CudaContext& context); + + +//////////////////////////////////////////////////////////////////////////////// +// kernels/join.cuh + +// RelationalJoin is a sort-merge join that returns indices into one of the four +// relational joins: +// MgpuJoinKindInner +// MgpuJoinKindLeft +// MgpuJoinKindRight +// MgpuJoinKindOuter. + +// A = 100, 101, 103, 103 +// B = 100, 100, 102, 103 +// Outer join: +// ai, bi a[ai], b[bi] +// 0: (0, 0) - (100, 100) // cross-product expansion for key 100 +// 1: (0, 1) - (100, 100) +// 2: (1, -) - (101, ---) // left-join for key 101 +// 3: (-, 2) - (---, 102) // right-join for key 102 +// 4: (3, 3) - (103, 103) // cross-product expansion for key 103 + +// MgpuJoinKindLeft drops the right-join on line 3. +// MgpuJoinKindRight drops the left-join on line 2. +// MgpuJoinKindInner drops both the left- and right-joins. + +// The caller passes MGPU_MEM(int) pointers to hold indices. Memory is allocated +// by the join function using the allocator associated with the context. It +// returns the number of outputs. + +// RelationalJoin performs one cudaMemcpyDeviceToHost to retrieve the size of +// the output array. This is a synchronous operation and may prevent queueing +// for callers using streams. +template +MGPU_HOST int RelationalJoin(InputIt1 a_global, int aCount, InputIt2 b_global, + int bCount, MGPU_MEM(int)* ppAJoinIndices, MGPU_MEM(int)* ppBJoinIndices, + Comp comp, CudaContext& context); + +// Specialization of RelationJoil with Comp = mgpu::less. +template +MGPU_HOST int RelationalJoin(InputIt1 a_global, int aCount, InputIt2 b_global, + int bCount, MGPU_MEM(int)* ppAJoinIndices, MGPU_MEM(int)* ppBJoinIndices, + CudaContext& context); + + +//////////////////////////////////////////////////////////////////////////////// +// kernels/sets.cuh + +// SetOpKeys implements multiset operations with C++ set_* semantics. +// MgpuSetOp may be: +// MgpuSetOpIntersection - like std::set_intersection +// MgpuSetOpUnion - like std::set_union +// MgpuSetOpDiff - like std::set_difference +// MgpuSetOpSymDiff - like std::set_symmetric_difference + +// Setting Duplicates to false increases performance for inputs with no +// duplicate keys in either array. + +// The caller passes MGPU_MEM(T) pointers to hold outputs. Memory is allocated +// by the multiset function using the allocator associated with the context. It +// returns the number of outputs. + +// SetOpKeys performs one cudaMemcpyDeviceToHost to retrieve the size of +// the output array. This is a synchronous operation and may prevent queueing +// for callers using streams. + +// If compact = true, SetOpKeys pre-allocates an output buffer is large as the +// sum of the input arrays. Partials results are computed into this temporary +// array before being moved into the final array. It consumes more space but +// results in higher performance. +template +MGPU_HOST int SetOpKeys(It1 a_global, int aCount, It2 b_global, int bCount, + MGPU_MEM(T)* ppKeys_global, Comp comp, CudaContext& context, + bool compact = true); + +// Specialization of SetOpKeys with Comp = mgpu::less. +template +MGPU_HOST int SetOpKeys(It1 a_global, int aCount, It2 b_global, int bCount, + MGPU_MEM(T)* ppKeys_global, CudaContext& context, bool compact = true); + +// SetOpPairs runs multiset operations by key and supports value exchange. +template +MGPU_HOST int SetOpPairs(KeysIt1 aKeys_global, ValsIt1 aVals_global, int aCount, + KeysIt2 bKeys_global, ValsIt2 bVals_global, int bCount, + MGPU_MEM(KeyType)* ppKeys_global, MGPU_MEM(ValType)* ppVals_global, + Comp comp, CudaContext& context); + +// Specialization of SetOpPairs with Comp = mgpu::less. +template +MGPU_HOST int SetOpPairs(KeysIt1 aKeys_global, ValsIt1 aVals_global, int aCount, + KeysIt2 bKeys_global, ValsIt2 bVals_global, int bCount, + MGPU_MEM(KeyType)* ppKeys_global, MGPU_MEM(ValType)* ppVals_global, + CudaContext& context); + +//////////////////////////////////////////////////////////////////////////////// +// kernels/segreducecsr.cuh + +// SegReducePreprocessData is defined in segreduce.cuh. It includes: +// - limits for CSR->tiles +// - packed thread codes for each thread in the reduction +// - (optional) CSR2 array of filtered segment offsets +struct SegReducePreprocessData; + +// SegReduceCsr runs a segmented reduction given an input and a sorted list of +// segment start offsets. This implementation requires operators support +// commutative (a + b = b + a) and associative (a + (b + c) = (a + b) + c) +// evaluation. + +// In the segmented reduction, reduce-by-key, and Spmv documentation, "segment" +// and "row" are used interchangably. A +// + +// InputIt data_global - Data value input. +// int count - Size of input array data_global. +// CsrIt csr_global - List of integers for start of each segment. +// The first entry must be 0 (indicating that the +// first segment starts at offset 0). +// Equivalent to exc-scan of segment sizes. +// If supportEmpty is false: must be ascending. +// If supportEmpty is true: must be non-descending. +// int numSegments - Size of segment list csr_global. Must be >= 1. +// bool supportEmpty - Basic seg-reduce code does not support empty +// segments. +// Set supportEmpty = true to add pre- and post- +// processing to support empty segments. +// OutputIt dest_global - Output array for segmented reduction. Allocate +// numSegments elements. Should be same data type as +// InputIt and identity. +// T identity - Identity for reduction operation. Eg, use 0 for +// addition or 1 for multiplication. +// Op op - Reduction operator. Model on std::plus<>. MGPU +// provides operators mgpu::plus<>, minus<>, +// multiplies<>, modulus<>, bit_or<> bit_and<>, +// bit_xor<>, maximum<>, and minimum<>. +// CudaContext& context - MGPU context support object. All kernels are +// launched on the associated stream. +template +MGPU_HOST void SegReduceCsr(InputIt data_global, int count, CsrIt csr_global, + int numSegments, bool supportEmpty, OutputIt dest_global, T identity, Op op, + CudaContext& context); + +// IndirectReduceCsr is like SegReduceCsr but with one level of source +// indirection. The start of each segment/row i in data_global starts at +// sources_global[i]. +// SourcesIt sources_global - List of integers for source data of each segment. +// Must be numSegments in size. +template +MGPU_HOST void IndirectReduceCsr(InputIt data_global, int count, + CsrIt csr_global, SourcesIt sources_global, int numSegments, + bool supportEmpty, OutputIt dest_global, T identity, Op op, + CudaContext& context); + +// SegReduceCsrPreprocess accelerates multiple seg-reduce calls on different +// data with the same segment geometry. Partitioning and CSR->CSR2 transform is +// off-loaded to a preprocessing pass. The actual reduction is evaluated by +// SegReduceApply. +template +MGPU_HOST void SegReduceCsrPreprocess(int count, CsrIt csr_global, + int numSegments, bool supportEmpty, + std::auto_ptr* ppData, CudaContext& context); + +template +MGPU_HOST void SegReduceApply(const SegReducePreprocessData& preprocess, + InputIt data_global, T identity, Op op, DestIt dest_global, + CudaContext& context); + +//////////////////////////////////////////////////////////////////////////////// +// kernels/reducebykey.csr + +typedef SegReducePreprocessData ReduceByKeyPreprocessData; + +// ReduceByKey runs a segmented reduction given a data input and a matching set +// of keys. This implementation requires operators support commutative +// (a + b = b + a) and associative (a + (b + c) = (a + b) + c) evaluation. +// It roughly matches the behavior of thrust::reduce_by_key. + +// KeysIt keys_global - Key identifier for the segment. +// InputIt data_global - Data value input. +// int count - Size of input arrays keys_global and +// data_global. +// ValType identity - Identity for reduction operation. Eg, use 0 for +// addition or 1 for multiplication. +// Op op - Reduction operator. Model on std::plus<>. MGPU +// provides operators mgpu::plus<>, minus<>, +// multiplies<>, modulus<>, bit_or<> bit_and<>, +// bit_xor<>, maximum<>, and minimum<>. +// Comp comp - Operator for comparing adjacent adjacent keys. +// Must return true if two adjacent keys are in the +// same segment. Use mgpu::equal_to() by +// default. +// KeyType* keysDest_global - If this pointer is not null, return the first +// key from each segment. Must be sized to at least +// the number of segments. +// DestIt dest_global - Holds the reduced data. Must be sized to at least +// the number of segments. +// int* count_host - The number of segments, returned in host memory. +// May be null. +// int* count_global - The number of segments, returned in device memory. +// This avoids a D->H synchronization. May be null. +// CudaContext& context - MGPU context support object. +template +MGPU_HOST void ReduceByKey(KeysIt keys_global, InputIt data_global, int count, + ValType identity, Op op, Comp comp, KeyType* keysDest_global, + DestIt dest_global, int* count_host, int* count_global, + CudaContext& context); + +// ReduceByKeyPreprocess accelerates multiple reduce-by-key calls on different +// data with the same segment geometry. The actual reduction is evaluated by +// ReduceByKeyApply. +// Note that the caller must explicitly specify the ValType argument. Kernel +// tunings are based on the value type, not the key type. +template +MGPU_HOST void ReduceByKeyPreprocess(int count, KeysIt keys_global, + KeyType* keysDest_global, Comp comp, int* count_host, int* count_global, + std::auto_ptr* ppData, CudaContext& context); + +template +MGPU_HOST void ReduceByKeyApply(const ReduceByKeyPreprocessData& preprocess, + InputIt data_global, T identity, Op op, DestIt dest_global, + CudaContext& context); + +//////////////////////////////////////////////////////////////////////////////// +// kernels/spmvcsr.cuh + +typedef SegReducePreprocessData SpmvPreprocessData; + +// SpmvCsr[Unary|Binary] evaluates the product of a sparse matrix (CSR format) +// with a dense vector. +// SpmvCsrIndirect[Unary|Binary] uses indirection to lookup the start of each +// matrix_global and cols_global on a per-row basis. + +// Unary methods reduce on the right-hand side vector values. +// Binary methods reduce the product of the left-hand side matrix value with the +// right-hand side vector values. + +// MatrixIt matrix_global - Left-hand side data for binary Spmv. There are nz +// non-zero matrix elements. These are loaded and +// combined with the vector values with mulOp. +// ColsIt cols_global - Row identifiers for the right-hand side of the +// matrix/value products. If element i is the k'th +// non-zero in row j, the product is formed as +// matrix_global[i] * vec_global[cols_global[i]] +// for direct indexing, or, +// m = source_global[j] + k +// matrix_global[m] * vec_global[cols_global[m]]. +// int nz - Number of non-zeros in LHS matrix. Size of +// matrix_global and cols_global. +// CsrIt csr_global - List of integers for start of each row. +// The first entry must be 0 (indicating that the +// first row starts at offset 0). +// Equivalent to exc-scan of row sizes. +// If supportEmpty is false: must be ascending. +// If supportEmpty is true: must be non-descending. +// SourcesIt sources_global - An indirection array to source each row's data. +// The size of each row i is +// size_i = csr_global[i + 1] - csr_global[i]. +// The starting offset for both the data and column +// identifiers is +// offset_i = sources_global[i]. +// The direct Spmv methods (i.e. those not taking +// a sources_global parameter) can be thought of as +// indirect methods with sources_global = csr_global. +// int numRows - Size of segment list csr_global. Must be >= 1. +// VecIt vec_global - Input array. Size is the width of the matrix. +// For unary Spmv, these values are reduced. +// For binary Spmv, the products of the matrix and +// vector values are reduced. +// bool supportEmpty - Basic seg-reduce code does not support empty rows. +// Set supportEmpty = true to add pre- and post- +// processing to support empty rows. +// DestIt dest_global - Output array. Must be numRows in size. +// T identity - Identity for reduction operation. Eg, use 0 for +// addition or 1 for multiplication. +// MulOp mulOp - Reduction operator for combining matrix value with +// vector value. Only defined for binary Spmv. +// Use mgpu::multiplies() for default behavior. +// AddOp addOp - Reduction operator for reducing vector values +// (unary Spmv) or matrix-vector products (binary +// Spmv). Use mgpu::plus() for default behavior. +// CudaContext& context - MGPU context support object. All kernels are +// launched on the associated stream. +template +MGPU_HOST void SpmvCsrUnary(ColsIt cols_global, int nz, CsrIt csr_global, + int numRows, VecIt vec_global, bool supportEmpty, DestIt dest_global, + T identity, AddOp addOp, CudaContext& context); + +template +MGPU_HOST void SpmvCsrBinary(MatrixIt matrix_global, ColsIt cols_global, + int nz, CsrIt csr_global, int numRows, VecIt vec_global, + bool supportEmpty, DestIt dest_global, T identity, MulOp mulOp, AddOp addOp, + CudaContext& context); + +template +MGPU_HOST void SpmvCsrIndirectUnary(ColsIt cols_global, int nz, + CsrIt csr_global, SourcesIt sources_global, int numRows, VecIt vec_global, + bool supportEmpty, DestIt dest_global, T identity, AddOp addOp, + CudaContext& context); + +template +MGPU_HOST void SpmvCsrIndirectBinary(MatrixIt matrix_global, ColsIt cols_global, + int nz, CsrIt csr_global, SourcesIt sources_global, int numRows, + VecIt vec_global, bool supportEmpty, DestIt dest_global, T identity, + MulOp mulOp, AddOp addOp, CudaContext& context); + +// SpmvPreprocess[Unary|Binary] accelerates multiple Spmv calls on different +// matrix/vector pairs with the same matrix geometry. The actual reduction is +// evaluated Spmv[Unary|Binary]Apply. +template +MGPU_HOST void SpmvPreprocessUnary(int nz, CsrIt csr_global, int numRows, + bool supportEmpty, std::auto_ptr* ppData, + CudaContext& context); + +template +MGPU_HOST void SpmvPreprocessBinary(int nz, CsrIt csr_global, int numRows, + bool supportEmpty, std::auto_ptr* ppData, + CudaContext& context); + +template +MGPU_HOST void SpmvUnaryApply(const SpmvPreprocessData& preprocess, + ColsIt cols_global, VecIt vec_global, DestIt dest_global, T identity, + AddOp addOp, CudaContext& context); + +template +MGPU_HOST void SpmvBinaryApply(const SpmvPreprocessData& preprocess, + MatrixIt matrix_global, ColsIt cols_global, VecIt vec_global, + DestIt dest_global, T identity, MulOp mulOp, AddOp addOp, + CudaContext& context); + +} // namespace mgpu + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/mmio.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/mmio.h new file mode 100644 index 0000000000000000000000000000000000000000..7cfd0a1b7ae7572e85b8c10bcb2fd0b3333ad0b6 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/mmio.h @@ -0,0 +1,133 @@ +/* +* Matrix Market I/O library for ANSI C +* +* See http://math.nist.gov/MatrixMarket for details. +* +* +*/ + +#ifndef MM_IO_H +#define MM_IO_H + +#define MM_MAX_LINE_LENGTH 1025 +#define MatrixMarketBanner "%%MatrixMarket" +#define MM_MAX_TOKEN_LENGTH 64 + +typedef char MM_typecode[4]; + +char *mm_typecode_to_str(MM_typecode matcode); + +int mm_read_banner(FILE *f, MM_typecode *matcode); +int mm_read_mtx_crd_size(FILE *f, int *M, int *N, int *nz); +int mm_read_mtx_array_size(FILE *f, int *M, int *N); + +int mm_write_banner(FILE *f, MM_typecode matcode); +int mm_write_mtx_crd_size(FILE *f, int M, int N, int nz); +int mm_write_mtx_array_size(FILE *f, int M, int N); + + +/********************* MM_typecode query fucntions ***************************/ + +#define mm_is_matrix(typecode) ((typecode)[0]=='M') + +#define mm_is_sparse(typecode) ((typecode)[1]=='C') +#define mm_is_coordinate(typecode)((typecode)[1]=='C') +#define mm_is_dense(typecode) ((typecode)[1]=='A') +#define mm_is_array(typecode) ((typecode)[1]=='A') + +#define mm_is_complex(typecode) ((typecode)[2]=='C') +#define mm_is_real(typecode) ((typecode)[2]=='R') +#define mm_is_pattern(typecode) ((typecode)[2]=='P') +#define mm_is_integer(typecode) ((typecode)[2]=='I') + +#define mm_is_symmetric(typecode)((typecode)[3]=='S') +#define mm_is_general(typecode) ((typecode)[3]=='G') +#define mm_is_skew(typecode) ((typecode)[3]=='K') +#define mm_is_hermitian(typecode)((typecode)[3]=='H') + +int mm_is_valid(MM_typecode matcode); /* too complex for a macro */ + + +/********************* MM_typecode modify fucntions ***************************/ + +#define mm_set_matrix(typecode) ((*typecode)[0]='M') +#define mm_set_coordinate(typecode) ((*typecode)[1]='C') +#define mm_set_array(typecode) ((*typecode)[1]='A') +#define mm_set_dense(typecode) mm_set_array(typecode) +#define mm_set_sparse(typecode) mm_set_coordinate(typecode) + +#define mm_set_complex(typecode)((*typecode)[2]='C') +#define mm_set_real(typecode) ((*typecode)[2]='R') +#define mm_set_pattern(typecode)((*typecode)[2]='P') +#define mm_set_integer(typecode)((*typecode)[2]='I') + + +#define mm_set_symmetric(typecode)((*typecode)[3]='S') +#define mm_set_general(typecode)((*typecode)[3]='G') +#define mm_set_skew(typecode) ((*typecode)[3]='K') +#define mm_set_hermitian(typecode)((*typecode)[3]='H') + +#define mm_clear_typecode(typecode) ((*typecode)[0]=(*typecode)[1]= \ + (*typecode)[2]=' ',(*typecode)[3]='G') + +#define mm_initialize_typecode(typecode) mm_clear_typecode(typecode) + + +/********************* Matrix Market error codes ***************************/ + + +#define MM_COULD_NOT_READ_FILE 11 +#define MM_PREMATURE_EOF 12 +#define MM_NOT_MTX 13 +#define MM_NO_HEADER 14 +#define MM_UNSUPPORTED_TYPE 15 +#define MM_LINE_TOO_LONG 16 +#define MM_COULD_NOT_WRITE_FILE 17 + + +/******************** Matrix Market internal definitions ******************** + + MM_matrix_typecode: 4-character sequence + + ojbect sparse/ data storage + dense type scheme + + string position: [0] [1] [2] [3] + + Matrix typecode: M(atrix) C(oord) R(eal) G(eneral) + A(array) C(omplex) H(ermitian) + P(attern) S(ymmetric) + I(nteger) K(kew) + + ***********************************************************************/ + +#define MM_MTX_STR "matrix" +#define MM_ARRAY_STR "array" +#define MM_DENSE_STR "array" +#define MM_COORDINATE_STR "coordinate" +#define MM_SPARSE_STR "coordinate" +#define MM_COMPLEX_STR "complex" +#define MM_REAL_STR "real" +#define MM_INT_STR "integer" +#define MM_GENERAL_STR "general" +#define MM_SYMM_STR "symmetric" +#define MM_HERM_STR "hermitian" +#define MM_SKEW_STR "skew-symmetric" +#define MM_PATTERN_STR "pattern" + + +/* high level routines */ + +int mm_write_mtx_crd(char fname[], int M, int N, int nz, int I[], int J[], + double val[], MM_typecode matcode); +int mm_read_mtx_crd_data(FILE *f, int M, int N, int nz, int I[], int J[], + double val[], MM_typecode matcode); +int mm_read_mtx_crd_entry(FILE *f, int *I, int *J, double *real, double *img, + MM_typecode matcode); + +int mm_read_unsymmetric_sparse(const char *fname, int *M_, int *N_, int *nz_, + double **val_, int **I_, int **J_); + + + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/moderngpu.cuh b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/moderngpu.cuh new file mode 100644 index 0000000000000000000000000000000000000000..1f1cdbf3bdfea07440b780cf1debf96fb14be46e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/moderngpu.cuh @@ -0,0 +1,52 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "kernels/reduce.cuh" +#include "kernels/scan.cuh" +#include "kernels/bulkremove.cuh" +#include "kernels/bulkinsert.cuh" +#include "kernels/merge.cuh" +#include "kernels/mergesort.cuh" +#include "kernels/segmentedsort.cuh" +#include "kernels/localitysort.cuh" +#include "kernels/sortedsearch.cuh" +#include "kernels/loadbalance.cuh" +#include "kernels/intervalmove.cuh" +#include "kernels/join.cuh" +#include "kernels/sets.cuh" +#include "kernels/segreducecsr.cuh" +#include "kernels/reducebykey.cuh" +#include "kernels/spmvcsr.cuh" diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/sparsematrix.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/sparsematrix.h new file mode 100644 index 0000000000000000000000000000000000000000..2a21994a34ff79a6c8381370258f03011f8ff6dd --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/sparsematrix.h @@ -0,0 +1,124 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "util/static.h" + +namespace mgpu { + +struct SparseMatrix { + int height, width, nz; + std::vector csr; // height + std::vector cols; // nz + std::vector matrix; // nz +}; + +bool ReadSparseMatrix(FILE* f, std::auto_ptr* ppMatrix, + std::string& err); + +bool ReadSparseMatrix(const char* filename, + std::auto_ptr* ppMatrix, std::string& err); + +bool LoadBinaryMatrix(const char* filename, + std::auto_ptr* ppMatrix); + +bool StoreBinaryMatrix(const char* filename, const SparseMatrix& matrix); + +bool LoadCachedMatrix(const char* filename, + std::auto_ptr* ppMatrix, std::string& err); + +// Multiply the matrix by a vector of 1s. +template +void SpmvTest(const SparseMatrix& m, T* results) { + memset(results, 0, sizeof(T) * m.height); + for(int row = 0; row < m.height; ++row) { + T product = 0; + int begin = m.csr[row]; + int end = (row + 1 < m.height) ? m.csr[row + 1] : m.nz; + for(int i = begin; i < end; ++i) + product += (T)m.matrix[i]; + + results[row] = product; + } +} + +template +void CompareVecs(const T* test, const T* ref, int count) { + for(int i = 0; i < count; ++i) { + double x = ref[i]; + double y = test[i]; + double diff = fabs(x - y); + + if(diff > 1.0e-5) { + if(y > 0) { + if(1.01 * x < y || 0.99 * x > y) { + printf("BAD OUTPUT AT COMPONENT %d: %8.5e vs %8.5e\n", i, + x, y); + // exit(0); + return; + } + } else { + if(1.01 * x > y || 0.99 * x < y) { + printf("BAD OUTPUT AT COMPONENT %d: %8.5e vs %8.5e\n", i, + x, y); + // exit(0); + return; + } + } + } + } +} + +struct MatrixStats { + int height, width, nz; + + // Row density moments: + double mean; + double stddev; + double skewness; +}; + +MatrixStats ComputeMatrixStats(const SparseMatrix& m); + +int64 MulSparseMatrices(const SparseMatrix& A, const SparseMatrix& B, + std::auto_ptr* ppC); + + +int64 ComputeProductCount(const SparseMatrix& A, const SparseMatrix& B); + +void ComputeColRanges(const SparseMatrix& A, const SparseMatrix& B, + int* colMin, int* colMax); + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/format.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/format.h new file mode 100644 index 0000000000000000000000000000000000000000..19912f5fff482441a6bca481e057ae945f481f87 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/format.h @@ -0,0 +1,148 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "static.h" +#include +#include +#include +#include + +namespace mgpu { + +// Like sprintf but dynamically allocates sufficient output to hold the entire +// text. +std::string stringprintf(const char* format, ...); + +// Returns xxx.xx(K|M|B) +std::string FormatInteger(int64 x); + +const char* TypeIdString(const std::type_info& ti); + +template +const char* TypeIdName() { + return TypeIdString(typeid(T)); +} + +struct FormatOpPrintf { + const char* format; + FormatOpPrintf(const char* f) : format(f) { } + + template + std::string operator()(int index, T x) const { + return stringprintf(format, x); + } +}; + +struct FormatOpMaskBit { + const char* format; + FormatOpMaskBit(const char* f) : format(f) { } + + std::string operator()(int index, int x) const { + return stringprintf(format, (0x80000000 & x) ? '*' : ' ', + 0x7fffffff & x); + } +}; + +struct FormatOpMarkArray { + const char* format; + const int* marks; + int numMarks; + + FormatOpMarkArray(const char* f, const int* m, int n) : + format(f), marks(m), numMarks(n) { } + + std::string operator()(int index, int x) const { + // Search for index in the array of marks. + bool mark = std::binary_search(marks, marks + numMarks, index); + return stringprintf(format, mark ? '*' : ' ', x); + } +}; + +template +std::string FormatArrayOp(const T* data, size_t count, Op op, int numCols) { + std::string s; + size_t numRows = MGPU_DIV_UP(count, numCols); + for(size_t row(0); row < numRows; ++row) { + size_t left = row * numCols; + s.append(stringprintf("%5d: ", left)); + + for(size_t col(left); col < std::min(left + numCols, count); ++col) { + s.append(op(col, data[col])); + s.push_back(' '); + } + s.push_back('\n'); + } + return s; +} + +template +std::string FormatArray(const T* data, size_t count, const char* format, + int numCols) { + return FormatArrayOp(data, count, FormatOpPrintf(format), numCols); +} + +template +std::string FormatArray(const std::vector& data, const char* format, + int numCols) { + return FormatArray(&data[0], (int)data.size(), format, numCols); +} +template +std::string FormatArrayOp(const std::vector& data, Op op, int numCols) { + return FormatArrayOp(&data[0], (int)data.size(), op, numCols); +} + +template +void PrintArray(const T* data, size_t count, const char* format, int numCols) { + std::string s = FormatArray(data, count, format, numCols); + printf("%s", s.c_str()); +} + +template +void PrintArray(const std::vector& data, const char* format, int numCols) { + std::string s = FormatArray(data, format, numCols); + printf("%s", s.c_str()); +} + +template +void PrintArrayOp(const std::vector& data, Op op, int numCols) { + std::string s = FormatArrayOp(data, op, numCols); + printf("%s", s.c_str()); +} + + + + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/mgpualloc.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/mgpualloc.h new file mode 100644 index 0000000000000000000000000000000000000000..60e1bbedf1d1d16ff69fc3cec77df80d61c277ae --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/mgpualloc.h @@ -0,0 +1,98 @@ + +#pragma once + +#include "util/util.h" +#include + +namespace mgpu { + +class CudaDevice; + +class CudaContext; +typedef intrusive_ptr ContextPtr; + +//////////////////////////////////////////////////////////////////////////////// +// Customizable allocator. + +// CudaAlloc is the interface class all allocator accesses. Users may derive +// this, implement custom allocators, and set it to the device with +// CudaDevice::SetAllocator. + +class CudaAlloc : public CudaBase { +public: + virtual cudaError_t Malloc(size_t size, void** p) = 0; + virtual bool Free(void* p) = 0; + virtual void Clear() = 0; + + virtual ~CudaAlloc() { } + + CudaDevice& Device() { return _device; } + +protected: + CudaAlloc(CudaDevice& device) : _device(device) { } + CudaDevice& _device; +}; + +// A concrete class allocator that simply calls cudaMalloc and cudaFree. +class CudaAllocSimple : public CudaAlloc { +public: + CudaAllocSimple(CudaDevice& device) : CudaAlloc(device) { } + + virtual cudaError_t Malloc(size_t size, void** p); + virtual bool Free(void* p); + virtual void Clear() { } + virtual ~CudaAllocSimple() { } +}; + +// A concrete class allocator that uses exponentially-spaced buckets and an LRU +// to reuse allocations. This is the default allocator. It is shared between +// all contexts on the device. +class CudaAllocBuckets : public CudaAlloc { +public: + CudaAllocBuckets(CudaDevice& device); + virtual ~CudaAllocBuckets(); + + virtual cudaError_t Malloc(size_t size, void** p); + virtual bool Free(void* p); + virtual void Clear(); + + size_t Allocated() const { return _allocated; } + size_t Committed() const { return _committed; } + size_t Capacity() const { return _capacity; } + + bool SanityCheck() const; + + void SetCapacity(size_t capacity, size_t maxObjectSize) { + _capacity = capacity; + _maxObjectSize = maxObjectSize; + Clear(); + } + +private: + static const int NumBuckets = 84; + static const size_t BucketSizes[NumBuckets]; + + struct MemNode; + typedef std::list MemList; + typedef std::map AddressMap; + typedef std::multimap PriorityMap; + + struct MemNode { + AddressMap::iterator address; + PriorityMap::iterator priority; + int bucket; + }; + + void Compact(size_t extra); + void FreeNode(MemList::iterator memIt); + int LocateBucket(size_t size) const; + + AddressMap _addressMap; + PriorityMap _priorityMap; + MemList _memLists[NumBuckets + 1]; + + size_t _maxObjectSize, _capacity, _allocated, _committed; + int _counter; +}; + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/mgpucontext.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/mgpucontext.h new file mode 100644 index 0000000000000000000000000000000000000000..22d983541aa3428df0eccf075dc4bba109e84d1d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/mgpucontext.h @@ -0,0 +1,513 @@ +#pragma once + +#include "util/util.h" +#include "util/format.h" +#include "mgpualloc.h" +#include + +namespace mgpu { + + +#ifdef _DEBUG +#define MGPU_SYNC_CHECK(s) { \ + cudaError_t error = cudaDeviceSynchronize(); \ + if(cudaSuccess != error) { \ + printf("CUDA ERROR %d %s\n%s:%d.\n%s\n", \ + error, cudaGetErrorString(error), __FILE__, __LINE__, s); \ + exit(0); \ + } \ +} +#else +#define MGPU_SYNC_CHECK(s) +#endif + +template +void copyDtoH(T* dest, const T* source, int count) { + cudaMemcpy(dest, source, sizeof(T) * count, cudaMemcpyDeviceToHost); +} +template +void copyDtoD(T* dest, const T* source, int count, cudaStream_t stream = 0) { + cudaMemcpyAsync(dest, source, sizeof(T) * count, cudaMemcpyDeviceToDevice, + stream); +} +template +void copyDtoH(std::vector& dest, const T* source, int count) { + dest.resize(count); + if(count) + copyDtoH(&dest[0], source, count); +} + +template +void copyHtoD(T* dest, const T* source, int count) { + cudaMemcpy(dest, source, sizeof(T) * count, cudaMemcpyHostToDevice); +} +template +void copyHtoD(T* dest, const std::vector& source) { + if(source.size()) + copyHtoD(dest, &source[0], source.size()); +} + + +//////////////////////////////////////////////////////////////////////////////// + +class CudaContext; +typedef intrusive_ptr ContextPtr; +typedef intrusive_ptr AllocPtr; + +class CudaException : public std::exception { +public: + cudaError_t error; + + CudaException() throw() { } + CudaException(cudaError_t e) throw() : error(e) { } + CudaException(const CudaException& e) throw() : error(e.error) { } + + virtual const char* what() const throw() { + return "CUDA runtime error"; + } +}; + + +//////////////////////////////////////////////////////////////////////////////// +// CudaEvent and CudaTimer. +// Exception-safe wrappers around cudaEvent_t. + +class CudaEvent : public noncopyable { +public: + CudaEvent() { + cudaEventCreate(&_event); + } + explicit CudaEvent(int flags) { + cudaEventCreateWithFlags(&_event, flags); + } + ~CudaEvent() { + cudaEventDestroy(_event); + } + operator cudaEvent_t() { return _event; } + void Swap(CudaEvent& rhs) { + std::swap(_event, rhs._event); + } +private: + cudaEvent_t _event; +}; + +class CudaTimer : noncopyable { + CudaEvent start, end; +public: + void Start(); + double Split(); + double Throughput(int count, int numIterations); +}; + + +//////////////////////////////////////////////////////////////////////////////// + +struct DeviceGroup; + +class CudaDevice : public noncopyable { + friend struct DeviceGroup; +public: + static int DeviceCount(); + static CudaDevice& ByOrdinal(int ordinal); + static CudaDevice& Selected(); + + // Device properties. + const cudaDeviceProp& Prop() const { return _prop; } + int Ordinal() const { return _ordinal; } + int NumSMs() const { return _prop.multiProcessorCount; } + int ArchVersion() const { return 100 * _prop.major + 10 * _prop.minor; } + + // LaunchBox properties. + int PTXVersion() const { return _ptxVersion; } + + std::string DeviceString() const; + + // Set this device as the active device on the thread. + void SetActive(); + +private: + CudaDevice() { } // hide the destructor. + int _ordinal; + int _ptxVersion; + cudaDeviceProp _prop; +}; + +//////////////////////////////////////////////////////////////////////////////// +// CudaDeviceMem +// Exception-safe CUDA device memory container. Use the MGPU_MEM(T) macro for +// the type of the reference-counting container. +// CudaDeviceMem AddRefs the allocator that returned the memory, releasing the +// pointer when the object is destroyed. + +template +class CudaDeviceMem : public CudaBase { + friend class CudaMemSupport; +public: + ~CudaDeviceMem(); + + const T* get() const { return _p; } + T* get() { return _p; } + + operator const T*() const { return get(); } + operator T*() { return get(); } + + // Size is in units of T, not bytes. + size_t Size() const { return _size; } + + // Copy from this to the argument array. + cudaError_t ToDevice(T* data, size_t count) const; + cudaError_t ToDevice(size_t srcOffest, size_t bytes, void* data) const; + cudaError_t ToHost(T* data, size_t count) const; + cudaError_t ToHost(std::vector& data) const; + cudaError_t ToHost(std::vector& data, size_t count) const; + cudaError_t ToHost(size_t srcOffset, size_t bytes, void* data) const; + + // Copy from the argument array to this. + cudaError_t FromDevice(const T* data, size_t count); + cudaError_t FromDevice(size_t dstOffset, size_t bytes, const void* data); + cudaError_t FromHost(const std::vector& data); + cudaError_t FromHost(const std::vector& data, size_t count); + cudaError_t FromHost(const T* data, size_t count); + cudaError_t FromHost(size_t destOffset, size_t bytes, const void* data); + +private: + friend class CudaContext; + CudaDeviceMem(CudaAlloc* alloc) : _p(0), _size(0), _alloc(alloc) { } + + AllocPtr _alloc; + T* _p; + size_t _size; +}; + +typedef intrusive_ptr AllocPtr; +#define MGPU_MEM(type) mgpu::intrusive_ptr< mgpu::CudaDeviceMem< type > > + +//////////////////////////////////////////////////////////////////////////////// +// CudaMemSupport +// Convenience functions for allocating device memory and copying to it from +// the host. These functions are factored into their own class for clarity. +// The class is derived by CudaContext. + +class CudaMemSupport : public CudaBase { + friend class CudaDevice; + friend class CudaContext; +public: + CudaDevice& Device() { return _alloc->Device(); } + + // Swap out the associated allocator. + void SetAllocator(CudaAlloc* alloc) { + assert(alloc->Device().Ordinal() == _alloc->Device().Ordinal()); + _alloc.reset(alloc); + } + + // Access the associated allocator. + CudaAlloc* GetAllocator() { return _alloc.get(); } + + // Support for creating arrays. + template + MGPU_MEM(T) Malloc(size_t count); + + template + MGPU_MEM(T) Malloc(const T* data, size_t count); + + template + MGPU_MEM(T) Malloc(const std::vector& data); + + template + MGPU_MEM(T) Fill(size_t count, T fill); + + template + MGPU_MEM(T) FillAscending(size_t count, T first, T step); + + template + MGPU_MEM(T) GenRandom(size_t count, T min, T max); + + template + MGPU_MEM(T) SortRandom(size_t count, T min, T max); + + template + MGPU_MEM(T) GenFunc(size_t count, Func f); + +protected: + CudaMemSupport() { } + AllocPtr _alloc; +}; + +//////////////////////////////////////////////////////////////////////////////// + +class CudaContext; +typedef mgpu::intrusive_ptr ContextPtr; + +// Create a context on the default stream (0). +ContextPtr CreateCudaDevice(int ordinal); +ContextPtr CreateCudaDevice(int argc, char** argv, bool printInfo = false); + +// Create a context on a new stream. +ContextPtr CreateCudaDeviceStream(int ordinal); +ContextPtr CreateCudaDeviceStream(int argc, char** argv, + bool printInfo = false); + +// Create a context and attach to an existing stream. +ContextPtr CreateCudaDeviceAttachStream(cudaStream_t stream); +ContextPtr CreateCudaDeviceAttachStream(int ordinal, cudaStream_t stream); + +struct ContextGroup; + +class CudaContext : public CudaMemSupport { + friend struct ContextGroup; + + friend ContextPtr CreateCudaDevice(int ordinal); + friend ContextPtr CreateCudaDeviceStream(int ordinal); + friend ContextPtr CreateCudaDeviceAttachStream(int ordinal, + cudaStream_t stream); +public: + static CudaContext& StandardContext(int ordinal = -1); + + // 4KB of page-locked memory per context. + int* PageLocked() { return _pageLocked; } + cudaStream_t AuxStream() const { return _auxStream; } + + int NumSMs() { return Device().NumSMs(); } + int ArchVersion() { return Device().ArchVersion(); } + int PTXVersion() { return Device().PTXVersion(); } + std::string DeviceString() { return Device().DeviceString(); } + + cudaStream_t Stream() const { return _stream; } + + // Set this device as the active device on the thread. + void SetActive() { Device().SetActive(); } + + // Access the included event. + CudaEvent& Event() { return _event; } + + // Use the included timer. + CudaTimer& Timer() { return _timer; } + void Start() { _timer.Start(); } + double Split() { return _timer.Split(); } + double Throughput(int count, int numIterations) { + return _timer.Throughput(count, numIterations); + } + + virtual long AddRef() { + return _noRefCount ? 1 : CudaMemSupport::AddRef(); + } + virtual void Release() { + if(!_noRefCount) CudaMemSupport::Release(); + } +private: + CudaContext(CudaDevice& device, bool newStream, bool standard); + ~CudaContext(); + + AllocPtr CreateDefaultAlloc(CudaDevice& device); + + bool _ownStream; + cudaStream_t _stream; + cudaStream_t _auxStream; + CudaEvent _event; + CudaTimer _timer; + bool _noRefCount; + int* _pageLocked; +}; + +//////////////////////////////////////////////////////////////////////////////// +// CudaDeviceMem method implementations + +template +cudaError_t CudaDeviceMem::ToDevice(T* data, size_t count) const { + return ToDevice(0, sizeof(T) * count, data); +} +template +cudaError_t CudaDeviceMem::ToDevice(size_t srcOffset, size_t bytes, + void* data) const { + cudaError_t error = cudaMemcpy(data, (char*)_p + srcOffset, bytes, + cudaMemcpyDeviceToDevice); + if(cudaSuccess != error) { + printf("CudaDeviceMem::ToDevice copy error %d\n", error); + exit(0); + } + return error; +} + +template +cudaError_t CudaDeviceMem::ToHost(T* data, size_t count) const { + return ToHost(0, sizeof(T) * count, data); +} +template +cudaError_t CudaDeviceMem::ToHost(std::vector& data, size_t count) const { + data.resize(count); + cudaError_t error = cudaSuccess; + if(_size) error = ToHost(&data[0], count); + return error; +} +template +cudaError_t CudaDeviceMem::ToHost(std::vector& data) const { + return ToHost(data, _size); +} +template +cudaError_t CudaDeviceMem::ToHost(size_t srcOffset, size_t bytes, + void* data) const { + + cudaError_t error = cudaMemcpy(data, (char*)_p + srcOffset, bytes, + cudaMemcpyDeviceToHost); + if(cudaSuccess != error) { + printf("CudaDeviceMem::ToHost copy error %d\n", error); + exit(0); + } + return error; +} + +template +cudaError_t CudaDeviceMem::FromDevice(const T* data, size_t count) { + return FromDevice(0, sizeof(T) * count, data); +} +template +cudaError_t CudaDeviceMem::FromDevice(size_t dstOffset, size_t bytes, + const void* data) { + if(dstOffset + bytes > sizeof(T) * _size) + return cudaErrorInvalidValue; + cudaMemcpy(_p + dstOffset, data, bytes, cudaMemcpyDeviceToDevice); + return cudaSuccess; +} +template +cudaError_t CudaDeviceMem::FromHost(const std::vector& data, + size_t count) { + cudaError_t error = cudaSuccess; + if(data.size()) error = FromHost(&data[0], count); + return error; +} +template +cudaError_t CudaDeviceMem::FromHost(const std::vector& data) { + return FromHost(data, data.size()); +} +template +cudaError_t CudaDeviceMem::FromHost(const T* data, size_t count) { + return FromHost(0, sizeof(T) * count, data); +} +template +cudaError_t CudaDeviceMem::FromHost(size_t dstOffset, size_t bytes, + const void* data) { + if(dstOffset + bytes > sizeof(T) * _size) + return cudaErrorInvalidValue; + cudaMemcpy(_p + dstOffset, data, bytes, cudaMemcpyHostToDevice); + return cudaSuccess; +} +template +CudaDeviceMem::~CudaDeviceMem() { + _alloc->Free(_p); +} + +//////////////////////////////////////////////////////////////////////////////// +// CudaMemSupport method implementations + +template +MGPU_MEM(T) CudaMemSupport::Malloc(size_t count) { + MGPU_MEM(T) mem(new CudaDeviceMem(_alloc.get())); + mem->_size = count; + cudaError_t error = _alloc->Malloc(sizeof(T) * count, (void**)&mem->_p); + if(cudaSuccess != error) { + printf("cudaMalloc error %d\n", error); + exit(0); + throw CudaException(cudaErrorMemoryAllocation); + } +#ifdef DEBUG + // Initialize the memory to -1 in debug mode. +// cudaMemset(mem->get(), -1, count); +#endif + + return mem; +} + +template +MGPU_MEM(T) CudaMemSupport::Malloc(const T* data, size_t count) { + MGPU_MEM(T) mem = Malloc(count); + mem->FromHost(data, count); + return mem; +} + +template +MGPU_MEM(T) CudaMemSupport::Malloc(const std::vector& data) { + MGPU_MEM(T) mem = Malloc(data.size()); + if(data.size()) mem->FromHost(&data[0], data.size()); + return mem; +} + +template +MGPU_MEM(T) CudaMemSupport::Fill(size_t count, T fill) { + std::vector data(count, fill); + return Malloc(data); +} + +template +MGPU_MEM(T) CudaMemSupport::FillAscending(size_t count, T first, T step) { + std::vector data(count); + for(size_t i = 0; i < count; ++i) + data[i] = first + i * step; + return Malloc(data); +} + +template +MGPU_MEM(T) CudaMemSupport::GenRandom(size_t count, T min, T max) { + std::vector data(count); + for(size_t i = 0; i < count; ++i) + data[i] = Rand(min, max); + return Malloc(data); +} + +template +MGPU_MEM(T) CudaMemSupport::SortRandom(size_t count, T min, T max) { + std::vector data(count); + for(size_t i = 0; i < count; ++i) + data[i] = Rand(min, max); + std::sort(data.begin(), data.end()); + return Malloc(data); +} + +template +MGPU_MEM(T) CudaMemSupport::GenFunc(size_t count, Func f) { + std::vector data(count); + for(size_t i = 0; i < count; ++i) + data[i] = f(i); + + MGPU_MEM(T) mem = Malloc(count); + mem->FromHost(data, count); + return mem; +} + +//////////////////////////////////////////////////////////////////////////////// +// Format methods that operate directly on device mem. + +template +std::string FormatArrayOp(const CudaDeviceMem& mem, int count, Op op, + int numCols) { + std::vector host; + mem.ToHost(host, count); + return FormatArrayOp(host, op, numCols); +} + +template +std::string FormatArrayOp(const CudaDeviceMem& mem, Op op, int numCols) { + return FormatArrayOp(mem, mem.Size(), op, numCols); +} + +template +void PrintArray(const CudaDeviceMem& mem, int count, const char* format, + int numCols) { + std::string s = FormatArrayOp(mem, count, FormatOpPrintf(format), numCols); + printf("%s", s.c_str()); +} + +template +void PrintArray(const CudaDeviceMem& mem, const char* format, int numCols) { + PrintArray(mem, mem.Size(), format, numCols); +} +template +void PrintArrayOp(const CudaDeviceMem& mem, Op op, int numCols) { + std::string s = FormatArrayOp(mem, op, numCols); + printf("%s", s.c_str()); +} + + +//////////////////////////////////////////////////////////////////////////////// + + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/static.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/static.h new file mode 100644 index 0000000000000000000000000000000000000000..c7209077506a51b2c0797bbc123d969deb447d92 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/static.h @@ -0,0 +1,183 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#ifndef MGPU_MIN +#define MGPU_MIN(x, y) (((x) <= (y)) ? (x) : (y)) +#define MGPU_MAX(x, y) (((x) >= (y)) ? (x) : (y)) +#define MGPU_MAX0(x) (((x) >= 0) ? (x) : 0) +#define MGPU_ABS(x) (((x) >= 0) ? (x) : (-x)) + +#define MGPU_DIV_UP(x, y) (((x) + (y) - 1) / (y)) +#define MGPU_DIV_ROUND(x, y) (((x) + (y) / 2) / (y)) +#define MGPU_ROUND_UP(x, y) ((y) * MGPU_DIV_UP(x, y)) +#define MGPU_SHIFT_DIV_UP(x, y) (((x) + ((1<< (y)) - 1))>> y) +#define MGPU_ROUND_UP_POW2(x, y) (((x) + (y) - 1) & ~((y) - 1)) +#define MGPU_ROUND_DOWN_POW2(x, y) ((x) & ~((y) - 1)) +#define MGPU_IS_POW_2(x) (0 == ((x) & ((x) - 1))) + +#endif // MGPU_MIN + +namespace mgpu { + + +typedef unsigned char byte; + +typedef unsigned int uint; +typedef signed short int16; + +typedef unsigned short ushort; +typedef unsigned short uint16; + +typedef long long int64; +typedef unsigned long long uint64; + +// IsPow2::value is true if X is a power of 2. +template struct sIsPow2 { + enum { value = 0 == (X & (X - 1)) }; +}; + +// Finds the base-2 logarithm of X. value is -1 if X is not a power of 2. +template struct sLogPow2 { + enum { extra = sIsPow2::value ? 0 : (roundUp ? 1 : 0) }; + enum { inner = sLogPow2::inner + 1 }; + enum { value = inner + extra }; +}; +template struct sLogPow2<0, roundUp> { + enum { inner = 0 }; + enum { value = 0 }; +}; +template struct sLogPow2<1, roundUp> { + enum { inner = 0 }; + enum { value = 0 }; +}; + +template +struct sDivUp { + enum { value = (X + Y - 1) / Y }; +}; + +template struct sDiv2RoundUp { + enum { value = sDiv2RoundUp::value, levels - 1>::value }; +}; +template struct sDiv2RoundUp { + enum { value = count }; +}; + +template +struct sDivSafe { + enum { value = X / Y }; +}; +template +struct sDivSafe { + enum { value = 0 }; +}; + +template +struct sRoundUp { + enum { rem = X % Y }; + enum { value = X + (rem ? (Y - rem) : 0) }; +}; + +template +struct sRoundDown { + enum { rem = X % Y }; + enum { value = X - rem }; +}; + +// IntegerDiv is a template for avoiding divisions by zero in template +// evaluation. Templates always evaluate both b and c in an expression like +// a ? b : c, and will error if either rhs contains an illegal expression, +// even if the ternary is explictly designed to guard against that. +template +struct sIntegerDiv { + enum { value = X / (Y ? Y : (X + 1)) }; +}; + +template +struct sMax { + enum { value = (X >= Y) ? X : Y }; +}; +template +struct sMin { + enum { value = (X <= Y) ? X : Y }; +}; + +template +struct sAbs { + enum { value = (X >= 0) ? X : -X }; +}; + + +// Finds the number of powers of 2 in the prime factorization of X. +template struct sNumFactorsOf2 { + enum { shifted = X >> 1 }; + enum { value = 1 + sNumFactorsOf2::value }; +}; +template struct sNumFactorsOf2 { + enum { value = 0 }; +}; + +// Returns the divisor for a conflict-free transpose. +template struct sBankConflictDivisor { + enum { value = + (1 & X) ? 0 : + (sIsPow2::value ? NumBanks : + (1<< sNumFactorsOf2::value)) }; + enum { log_value = sLogPow2::value }; +}; + +template struct sConflictFreeStorage { + enum { count = NT * X }; + enum { divisor = sBankConflictDivisor::value }; + enum { padding = sDivSafe::value }; + enum { value = count + padding }; +}; + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/util.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/util.h new file mode 100644 index 0000000000000000000000000000000000000000..a6bec330fee5dc45b55b4b1de37e570738647e42 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/include/util/util.h @@ -0,0 +1,124 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#pragma once + +#include "static.h" + +namespace mgpu { + +extern int Rand(int min, int max); +extern int64 Rand(int64 min, int64 max); +extern uint Rand(uint min, uint max); +extern uint64 Rand(uint64 min, uint64 max); +extern float Rand(float min, float max); +extern double Rand(double min, double max); + + +//////////////////////////////////////////////////////////////////////////////// +// intrusive_ptr + +// boost::noncopyable, moved here so we don't have dependency on boost +class noncopyable { +protected: + noncopyable() {} + ~noncopyable() {} +private: + noncopyable(const noncopyable&) { } + const noncopyable& operator=(const noncopyable&) { return *this; } +}; + +class CudaBase : public noncopyable { +public: + CudaBase() : _ref(0) { } + virtual ~CudaBase() { } + virtual long AddRef() { + // return BOOST_INTERLOCKED_INCREMENT(&_ref); + return ++_ref; + } + virtual void Release() { + // if(!BOOST_INTERLOCKED_DECREMENT(&_ref)) delete this; + if(!--_ref) delete this; + } +private: + long _ref; +}; + +inline long intrusive_ptr_add_ref(CudaBase* base) { + return base->AddRef(); +} + +inline void intrusive_ptr_release(CudaBase* base) { + base->Release(); +} + +template +class intrusive_ptr { +public: + intrusive_ptr() : _p(0) { } + explicit intrusive_ptr(T* p) : _p(p) { + if(p) intrusive_ptr_add_ref(p); + } + intrusive_ptr(const intrusive_ptr& rhs) : _p(rhs._p) { + if(_p) intrusive_ptr_add_ref(_p); + } + ~intrusive_ptr() { + if(_p) intrusive_ptr_release(_p); + } + intrusive_ptr& operator=(const intrusive_ptr& rhs) { + intrusive_ptr(rhs.get()).swap(*this); + return *this; + } + + void reset(T* p = 0) { + intrusive_ptr(p).swap(*this); + } + T* release() { + T* p = _p; + _p = 0; + return p; + } + + T* get() const { return _p; } + operator T*() const { return _p; } + T* operator->() const { return _p; } + + void swap(intrusive_ptr& rhs) { + std::swap(_p, rhs._p); + } +private: + T* _p; +}; + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/src/mgpucontext.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/src/mgpucontext.cu new file mode 100644 index 0000000000000000000000000000000000000000..5cec2a102d6617a8dd0da0ca97838463b7bdf043 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/src/mgpucontext.cu @@ -0,0 +1,553 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#include "util/mgpucontext.h" + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// CudaTimer + +void CudaTimer::Start() { + cudaEventRecord(start); + cudaDeviceSynchronize(); +} +double CudaTimer::Split() { + cudaEventRecord(end); + cudaDeviceSynchronize(); + float t; + cudaEventElapsedTime(&t, start, end); + start.Swap(end); + return (t / 1000.0); +} +double CudaTimer::Throughput(int count, int numIterations) { + double elapsed = Split(); + return (double)numIterations * count / elapsed; +} + +//////////////////////////////////////////////////////////////////////////////// +// CudaDevice + +__global__ void KernelVersionShim() { } + +struct DeviceGroup { + int numCudaDevices; + CudaDevice** cudaDevices; + + DeviceGroup() { + numCudaDevices = -1; + cudaDevices = 0; + } + + int GetDeviceCount() { + if(-1 == numCudaDevices) { + cudaError_t error = cudaGetDeviceCount(&numCudaDevices); + if(cudaSuccess != error || numCudaDevices <= 0) { + fprintf(stderr, "ERROR ENUMERATING CUDA DEVICES.\nExiting.\n"); + exit(0); + } + cudaDevices = new CudaDevice*[numCudaDevices]; + memset(cudaDevices, 0, sizeof(CudaDevice*) * numCudaDevices); + } + return numCudaDevices; + } + + CudaDevice* GetByOrdinal(int ordinal) { + if(ordinal >= GetDeviceCount()) return 0; + + if(!cudaDevices[ordinal]) { + // Retrieve the device properties. + CudaDevice* device = cudaDevices[ordinal] = new CudaDevice; + device->_ordinal = ordinal; + cudaError_t error = cudaGetDeviceProperties(&device->_prop, + ordinal); + if(cudaSuccess != error) { + fprintf(stderr, "FAILURE TO CREATE CUDA DEVICE %d\n", ordinal); + exit(0); + } + + // Get the compiler version for this device. + cudaSetDevice(ordinal); + cudaFuncAttributes attr; + error = cudaFuncGetAttributes(&attr, KernelVersionShim); + if(cudaSuccess == error) + device->_ptxVersion = 10 * attr.ptxVersion; + else { + printf("NOT COMPILED WITH COMPATIBLE PTX VERSION FOR DEVICE" + " %d\n", ordinal); + // The module wasn't compiled with support for this device. + device->_ptxVersion = 0; + } + } + return cudaDevices[ordinal]; + } + + ~DeviceGroup() { + if(cudaDevices) { + for(int i = 0; i < numCudaDevices; ++i) + delete cudaDevices[i]; + delete [] cudaDevices; + } + cudaDeviceReset(); + } +}; + +std::auto_ptr deviceGroup; + + +int CudaDevice::DeviceCount() { + if(!deviceGroup.get()) + deviceGroup.reset(new DeviceGroup); + return deviceGroup->GetDeviceCount(); +} + +CudaDevice& CudaDevice::ByOrdinal(int ordinal) { + if(ordinal < 0 || ordinal >= DeviceCount()) { + fprintf(stderr, "CODE REQUESTED INVALID CUDA DEVICE %d\n", ordinal); + exit(0); + } + return *deviceGroup->GetByOrdinal(ordinal); +} + +CudaDevice& CudaDevice::Selected() { + int ordinal; + cudaError_t error = cudaGetDevice(&ordinal); + if(cudaSuccess != error) { + fprintf(stderr, "ERROR RETRIEVING CUDA DEVICE ORDINAL\n"); + exit(0); + } + return ByOrdinal(ordinal); +} + +void CudaDevice::SetActive() { + cudaError_t error = cudaSetDevice(_ordinal); + if(cudaSuccess != error) { + fprintf(stderr, "ERROR SETTING CUDA DEVICE TO ORDINAL %d\n", _ordinal); + exit(0); + } +} + +std::string CudaDevice::DeviceString() const { + size_t freeMem, totalMem; + cudaError_t error = cudaMemGetInfo(&freeMem, &totalMem); + if(cudaSuccess != error) { + fprintf(stderr, "ERROR RETRIEVING MEM INFO FOR CUDA DEVICE %d\n", + _ordinal); + exit(0); + } + + double memBandwidth = (_prop.memoryClockRate * 1000.0) * + (_prop.memoryBusWidth / 8 * 2) / 1.0e9; + + std::string s = stringprintf( + "%s : %8.3lf Mhz (Ordinal %d)\n" + "%d SMs enabled. Compute Capability sm_%d%d\n" + "FreeMem: %6dMB TotalMem: %6dMB %2d-bit pointers.\n" + "Mem Clock: %8.3lf Mhz x %d bits (%5.1lf GB/s)\n" + "ECC %s\n\n", + _prop.name, _prop.clockRate / 1000.0, _ordinal, + _prop.multiProcessorCount, _prop.major, _prop.minor, + (int)(freeMem / (1<< 20)), (int)(totalMem / (1<< 20)), 8 * sizeof(int*), + _prop.memoryClockRate / 1000.0, _prop.memoryBusWidth, memBandwidth, + _prop.ECCEnabled ? "Enabled" : "Disabled"); + return s; +} + +//////////////////////////////////////////////////////////////////////////////// +// CudaContext + +struct ContextGroup { + CudaContext** standardContexts; + int numDevices; + + ContextGroup() { + numDevices = CudaDevice::DeviceCount(); + standardContexts = new CudaContext*[numDevices]; + memset(standardContexts, 0, sizeof(CudaContext*) * numDevices); + } + + CudaContext* GetByOrdinal(int ordinal) { + if(!standardContexts[ordinal]) { + CudaDevice& device = CudaDevice::ByOrdinal(ordinal); + standardContexts[ordinal] = new CudaContext(device, false, true); + } + return standardContexts[ordinal]; + } + + ~ContextGroup() { + if(standardContexts) { + for(int i = 0; i < numDevices; ++i) + delete standardContexts[i]; + delete [] standardContexts; + } + } +}; +std::auto_ptr contextGroup; + +CudaContext::CudaContext(CudaDevice& device, bool newStream, bool standard) : + _event(cudaEventDisableTiming /*| cudaEventBlockingSync */), + _stream(0), _noRefCount(standard), _pageLocked(0) { + + // Create an allocator. + if(standard) + _alloc.reset(new CudaAllocSimple(device)); + else + _alloc = CreateDefaultAlloc(device); + + if(newStream) cudaStreamCreate(&_stream); + _ownStream = newStream; + + // Allocate 4KB of page-locked memory. + cudaError_t error = cudaMallocHost((void**)&_pageLocked, 4096); + if(cudaSuccess != error) { + fprintf(stderr, "ERROR ALLOCATING PAGE-LOCKED MEMORY FOR CUDA DEVICE %d\n", + device.Ordinal()); + exit(0); + } + +// Allocate an auxiliary stream. + error = cudaStreamCreate(&_auxStream); +} + +CudaContext::~CudaContext() { + if(_pageLocked) + cudaFreeHost(_pageLocked); + if(_ownStream && _stream) + cudaStreamDestroy(_stream); + if(_auxStream) + cudaStreamDestroy(_auxStream); +} + +AllocPtr CudaContext::CreateDefaultAlloc(CudaDevice& device) { + intrusive_ptr alloc(new CudaAllocBuckets(device)); + size_t freeMem, totalMem; + + cudaError_t error = cudaMemGetInfo(&freeMem, &totalMem); + if(cudaSuccess != error) { + fprintf(stderr, "ERROR RETRIEVING MEM INFO FOR CUDA DEVICE %d\n", + device.Ordinal()); + exit(0); + } + + // Maintain a buffer of 128MB with max objects of 64MB. + alloc->SetCapacity(128<< 20, 64<< 20); + + return AllocPtr(alloc.get()); +} + +CudaContext& CudaContext::StandardContext(int ordinal) { + bool setActive = -1 != ordinal; + if(-1 == ordinal) { + cudaError_t error = cudaGetDevice(&ordinal); + if(cudaSuccess != error) { + fprintf(stderr, "ERROR RETRIEVING CUDA DEVICE ORDINAL\n"); + exit(0); + } + } + int numDevices = CudaDevice::DeviceCount(); + + if(ordinal < 0 || ordinal >= numDevices) { + fprintf(stderr, "CODE REQUESTED INVALID CUDA DEVICE %d\n", ordinal); + exit(0); + } + + if(!contextGroup.get()) + contextGroup.reset(new ContextGroup); + + CudaContext& context = //*contextGroup->standardContexts[ordinal]; + *contextGroup->GetByOrdinal(ordinal); + if(!context.PTXVersion()) { + fprintf(stderr, "This CUDA executable was not compiled with support" + " for device %d (sm_%2d)\n", ordinal, context.ArchVersion() / 10); + exit(0); + } + + if(setActive) context.SetActive(); + return context; +} + +ContextPtr CreateCudaDevice(int ordinal) { + CudaDevice& device = CudaDevice::ByOrdinal(ordinal); + ContextPtr context(new CudaContext(device, false, false)); + return context; +} +ContextPtr CreateCudaDevice(int argc, char** argv, bool printInfo) { + int ordinal = 0; + if(argc >= 2 && !sscanf(argv[1], "%d", &ordinal)) { + fprintf(stderr, "INVALID COMMAND LINE ARGUMENT - NOT A CUDA ORDINAL\n"); + exit(0); + } + ContextPtr context = CreateCudaDevice(ordinal); + if(!context->PTXVersion()) { + fprintf(stderr, "This CUDA executable was not compiled with support" + " for device %d (sm_%2d)\n", ordinal, context->ArchVersion() / 10); + exit(0); + } + + context->SetActive(); + if(printInfo) + printf("%s\n", context->Device().DeviceString().c_str()); + return context; +} + +ContextPtr CreateCudaDeviceStream(int ordinal) { + ContextPtr context(new CudaContext( + CudaDevice::ByOrdinal(ordinal), true, false)); + return context; +} + +ContextPtr CreateCudaDeviceStream(int argc, char** argv, bool printInfo) { + int ordinal = 0; + if(argc >= 2 && !sscanf(argv[1], "%d", &ordinal)) { + fprintf(stderr, "INVALID COMMAND LINE ARGUMENT - NOT A CUDA ORDINAL\n"); + exit(0); + } + ContextPtr context = CreateCudaDeviceStream(ordinal); + if(!context->PTXVersion()) { + fprintf(stderr, "This CUDA executable was not compiled with support" + " for device %d (sm_%2d)\n", ordinal, context->ArchVersion() / 10); + exit(0); + } + + context->SetActive(); + if(printInfo) + printf("%s\n", context->Device().DeviceString().c_str()); + return context; +} + +ContextPtr CreateCudaDeviceAttachStream(int ordinal, cudaStream_t stream) { + ContextPtr context(new CudaContext( + CudaDevice::ByOrdinal(ordinal), false, false)); + context->_stream = stream; + return context; +} + +ContextPtr CreateCudaDeviceAttachStream(cudaStream_t stream) { + int ordinal; + cudaGetDevice(&ordinal); + return CreateCudaDeviceAttachStream(ordinal, stream); +} + +//////////////////////////////////////////////////////////////////////////////// +// CudaAllocSimple + +cudaError_t CudaAllocSimple::Malloc(size_t size, void** p) { + cudaError_t error = cudaSuccess; + *p = 0; + if(size) error = cudaMalloc(p, size); + + if(cudaSuccess != error) { + printf("CUDA MALLOC ERROR %d\n", error); + exit(0); + } + + return error; +} + +bool CudaAllocSimple::Free(void* p) { + cudaError_t error = cudaSuccess; + if(p) error = cudaFree(p); + return cudaSuccess == error; +} + +//////////////////////////////////////////////////////////////////////////////// +// CudaAllocBuckets + +CudaAllocBuckets::CudaAllocBuckets(CudaDevice& device) : CudaAlloc(device) { + _maxObjectSize = _capacity = _allocated = _committed = 0; + _counter = 0; +} + +CudaAllocBuckets::~CudaAllocBuckets() { + SetCapacity(0, 0); + assert(!_allocated); +} + +bool CudaAllocBuckets::SanityCheck() const { + // Iterate through all allocated objects and verify sizes. + size_t allocatedCount = 0, committedCount = 0; + for(AddressMap::const_iterator i = _addressMap.begin(); + i != _addressMap.end(); ++i) { + + int bucket = i->second->bucket; + size_t size = (bucket < NumBuckets) ? BucketSizes[bucket] : 0; + allocatedCount += size; + + if(i->second->priority == _priorityMap.end()) + committedCount += size; + } + + return allocatedCount == _allocated && committedCount == _committed; +} + +cudaError_t CudaAllocBuckets::Malloc(size_t size, void** p) { + + // Locate the bucket index and adjust the size of the allocation to the + // bucket size. + size_t allocSize = size; + size_t commitSize = 0; + int bucket = LocateBucket(size); + if(bucket < NumBuckets) + allocSize = commitSize = BucketSizes[bucket]; + + // Peel off an already-allocated node and reuse it. + MemList& list = _memLists[bucket]; + if(list.size() && list.front().priority != _priorityMap.end()) { + MemList::iterator memIt = list.begin(); + + _priorityMap.erase(memIt->priority); + memIt->priority = _priorityMap.end(); + + list.splice(list.end(), list, memIt); + _committed += commitSize; + + *p = memIt->address->first; + return cudaSuccess; + } + + // Shrink if this allocation would put us over the limit. + Compact(commitSize); + + cudaError_t error = cudaSuccess; + *p = 0; + if(size) error = cudaMalloc(p, allocSize); + while((cudaErrorMemoryAllocation == error) && (_committed < _allocated)) { + SetCapacity(_capacity - _capacity / 10, _maxObjectSize); + error = cudaMalloc(&p, size); + } + if(cudaSuccess != error) return error; + + MemList::iterator memIt = + _memLists[bucket].insert(_memLists[bucket].end(), MemNode()); + memIt->bucket = bucket; + memIt->address = _addressMap.insert(std::make_pair(*p, memIt)).first; + memIt->priority = _priorityMap.end(); + _allocated += commitSize; + _committed += commitSize; + + assert(SanityCheck()); + + return cudaSuccess; +} + +bool CudaAllocBuckets::Free(void* p) { + AddressMap::iterator it = _addressMap.find(p); + if(it == _addressMap.end()) { + // If the pointer was not found in the address map, cudaFree it anyways + // but return false. + if(p) cudaFree(p); + return false; + } + + // Because we're freeing a page, it had better not be in the priority queue. + MemList::iterator memIt = it->second; + assert(memIt->priority == _priorityMap.end()); + + // Always free allocations larger than the largest bucket + it->second->priority = _priorityMap.insert( + std::make_pair(_counter++ - memIt->bucket, memIt)); + + // Freed nodes are moved to the front, committed nodes are moved to the + // end. + int bucket = memIt->bucket; + size_t commitSize = (bucket < NumBuckets) ? BucketSizes[bucket] : 0; + + MemList& list = _memLists[bucket]; + list.splice(list.begin(), list, memIt); + _committed -= commitSize; + + // Delete data that's not cached. + if(NumBuckets == bucket) + FreeNode(memIt); + + Compact(0); + return true; +} + +void CudaAllocBuckets::Clear() { + Compact(_allocated); +} + +void CudaAllocBuckets::FreeNode(CudaAllocBuckets::MemList::iterator memIt) { + if(memIt->address->first) cudaFree(memIt->address->first); + + int bucket = memIt->bucket; + size_t commitSize = (bucket < NumBuckets) ? BucketSizes[bucket] : 0; + _addressMap.erase(memIt->address); + if(memIt->priority != _priorityMap.end()) + _priorityMap.erase(memIt->priority); + else + _committed -= commitSize; + _allocated -= commitSize; + + _memLists[bucket].erase(memIt); + + assert(SanityCheck()); +} + +void CudaAllocBuckets::Compact(size_t extra) { + while(_allocated + extra > _capacity && _allocated > _committed) { + // Walk the priority queue from beginning to end removing nodes. + MemList::iterator memIt = _priorityMap.begin()->second; + FreeNode(memIt); + } +} + +// Exponentially spaced buckets. +const size_t CudaAllocBuckets::BucketSizes[CudaAllocBuckets::NumBuckets] = { + 256, 512, 1024, 2048, 4096, 8192, + 12288, 16384, 24576, 32768, 49152, 65536, + 98304, 131072, 174848, 218624, 262144, 349696, + 436992, 524288, 655360, 786432, 917504, 1048576, + 1310720, 1572864, 1835008, 2097152, 2516736, 2936064, + 3355648, 3774976, 4194304, 4893440, 5592576, 6291456, + 6990592, 7689728, 8388608, 9786880, 11184896, 12582912, + 13981184, 15379200, 16777216, 18874368, 20971520, 23068672, + 25165824, 27262976, 29360128, 31457280, 33554432, 36910080, + 40265472, 43620864, 46976256, 50331648, 53687296, 57042688, + 60398080, 63753472, 67108864, 72701440, 78293760, 83886080, + 89478656, 95070976, 100663296, 106255872, 111848192, 117440512, + 123033088, 128625408, 134217728, 143804928, 153391872, 162978816, + 172565760, 182152704, 191739648, 201326592, 210913792, 220500736 +}; + +int CudaAllocBuckets::LocateBucket(size_t size) const { + if(size > _maxObjectSize || size > BucketSizes[NumBuckets - 1]) + return NumBuckets; + + return (int)(std::lower_bound(BucketSizes, BucketSizes + NumBuckets, size) - + BucketSizes); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/src/mgpuutil.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/src/mgpuutil.cpp new file mode 100644 index 0000000000000000000000000000000000000000..db34beabe39ea8d952296d551e449ec532ee4c38 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/src/mgpuutil.cpp @@ -0,0 +1,170 @@ +/****************************************************************************** + * Copyright (c) 2013, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + ******************************************************************************/ + +/****************************************************************************** + * + * Code and text by Sean Baxter, NVIDIA Research + * See http://nvlabs.github.io/moderngpu for repository and documentation. + * + ******************************************************************************/ + +#include "util/format.h" +#include +#include +#include + +#define MGPU_RAND_NS std::tr1 + +#ifdef _MSC_VER +#include +#else +#include +#endif + +namespace mgpu { + +//////////////////////////////////////////////////////////////////////////////// +// String formatting utilities. + +std::string stringprintf(const char* format, ...) { + va_list args; + va_start(args, format); + int len = vsnprintf(0, 0, format, args); + va_end(args); + + // allocate space. + std::string text; + text.resize(len); + + va_start(args, format); + vsnprintf(&text[0], len + 1, format, args); + va_end(args); + + return text; +} + +std::string FormatInteger(int64 x) { + std::string s; + if(x < 1000) + s = stringprintf("%6d", (int)x); + else if(x < 1000000) { + if(0 == (x % 1000)) + s = stringprintf("%5dK", (int)(x / 1000)); + else + s = stringprintf("%5.1lfK", x / 1.0e3); + } else if(x < 1000000000ll) { + if(0 == (x % 1000000ll)) + s = stringprintf("%5dM", (int)(x / 1000000)); + else + s = stringprintf("%5.1lfM", x / 1.0e6); + } else { + if(0 == (x % 1000000000ll)) + s = stringprintf("%5dB", (int)(x / 1000000000ll)); + else + s = stringprintf("%5.1lfB", x / 1.0e9); + } + return s; +} + +class TypeIdMap { + typedef std::map Map; + Map _map; + + void Insert(const std::type_info& ti, const char* name) { + _map[ti.name()] = name; + } +public: + TypeIdMap() { + Insert(typeid(char), "char"); + Insert(typeid(byte), "byte"); + Insert(typeid(short), "short"); + Insert(typeid(ushort), "ushort"); + Insert(typeid(int), "int"); + Insert(typeid(int64), "int64"); + Insert(typeid(uint), "uint"); + Insert(typeid(uint64), "uint64"); + Insert(typeid(float), "float"); + Insert(typeid(double), "double"); + Insert(typeid(int2), "int2"); + Insert(typeid(int3), "int3"); + Insert(typeid(int4), "int4"); + Insert(typeid(uint2), "uint2"); + Insert(typeid(uint3), "uint3"); + Insert(typeid(uint4), "uint4"); + Insert(typeid(float2), "float2"); + Insert(typeid(float3), "float3"); + Insert(typeid(float4), "float4"); + Insert(typeid(double2), "double2"); + Insert(typeid(double3), "double3"); + Insert(typeid(double4), "double4"); + Insert(typeid(char*), "char*"); + } + const char* name(const std::type_info& ti) { + const char* n = ti.name(); + Map::iterator it = _map.find(n); + if(it != _map.end()) + n = it->second; + return n; + } +}; + +const char* TypeIdString(const std::type_info& ti) { + static TypeIdMap typeIdMap; + return typeIdMap.name(ti); +} + +//////////////////////////////////////////////////////////////////////////////// +// Random number generators. + +MGPU_RAND_NS::mt19937 mt19937; + +int Rand(int min, int max) { + MGPU_RAND_NS::uniform_int r(min, max); + return r(mt19937); +} +int64 Rand(int64 min, int64 max) { + MGPU_RAND_NS::uniform_int r(min, max); + return r(mt19937); +} +uint Rand(uint min, uint max) { + MGPU_RAND_NS::uniform_int r(min, max); + return r(mt19937); +} +uint64 Rand(uint64 min, uint64 max) { + MGPU_RAND_NS::uniform_int r(min, max); + return r(mt19937); +} +float Rand(float min, float max) { + MGPU_RAND_NS::uniform_real r(min, max); + return r(mt19937); +} +double Rand(double min, double max) { + MGPU_RAND_NS::uniform_real r(min, max); + return r(mt19937); +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/src/mmio.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/src/mmio.cpp new file mode 100644 index 0000000000000000000000000000000000000000..931f43621cd190acadc35f844ff30536e42f0995 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/moderngpu/src/mmio.cpp @@ -0,0 +1,511 @@ +/* +* Matrix Market I/O library for ANSI C +* +* See http://math.nist.gov/MatrixMarket for details. +* +* +*/ + + +#include +#include +#include +#include + +#include "mmio.h" + +int mm_read_unsymmetric_sparse(const char *fname, int *M_, int *N_, int *nz_, + double **val_, int **I_, int **J_) +{ + FILE *f; + MM_typecode matcode; + int M, N, nz; + int i; + double *val; + int *I, *J; + + if ((f = fopen(fname, "r")) == NULL) + return -1; + + + if (mm_read_banner(f, &matcode) != 0) + { + printf("mm_read_unsymetric: Could not process Matrix Market banner "); + printf(" in file [%s]\n", fname); + return -1; + } + + + + if ( !(mm_is_real(matcode) && mm_is_matrix(matcode) && + mm_is_sparse(matcode))) + { + fprintf(stderr, "Sorry, this application does not support "); + fprintf(stderr, "Market Market type: [%s]\n", + mm_typecode_to_str(matcode)); + return -1; + } + + /* find out size of sparse matrix: M, N, nz .... */ + + if (mm_read_mtx_crd_size(f, &M, &N, &nz) !=0) + { + fprintf(stderr, "read_unsymmetric_sparse(): could not parse matrix size.\n"); + return -1; + } + + *M_ = M; + *N_ = N; + *nz_ = nz; + + /* reseve memory for matrices */ + + I = (int *) malloc(nz * sizeof(int)); + J = (int *) malloc(nz * sizeof(int)); + val = (double *) malloc(nz * sizeof(double)); + + *val_ = val; + *I_ = I; + *J_ = J; + + /* NOTE: when reading in doubles, ANSI C requires the use of the "l" */ + /* specifier as in "%lg", "%lf", "%le", otherwise errors will occur */ + /* (ANSI C X3.159-1989, Sec. 4.9.6.2, p. 136 lines 13-15) */ + + for (i=0; i +#include +#include +#include "sparsematrix.h" +#include "mmio.h" + +namespace mgpu { + +struct MatrixElement { + int row, col; + double value; + bool operator<(const MatrixElement& b) const { + if(row < b.row) return true; + if(b.row < row) return false; + return col < b.col; + } +}; + +bool ReadSparseMatrix(FILE* f, std::auto_ptr* ppMatrix, + std::string& err) { + + MM_typecode matcode; + int code = mm_read_banner(f, &matcode); + if(code) { + err = "Not a sparse matrix.\n"; + return false; + } + + bool isPattern = mm_is_pattern(matcode); + bool isReal = mm_is_real(matcode); + + if(!(isPattern || isReal) || !mm_is_matrix(matcode) || + !mm_is_coordinate(matcode) || !mm_is_sparse(matcode)) { + err = "Not a real matrix.\n"; + return false; + } + + int nz; + int height, width; + code = mm_read_mtx_crd_size(f, &height, &width, &nz); + std::vector elements; + elements.reserve(nz); + + for(int i = 0; i < nz; ++i) { + MatrixElement e; + int x, y; + + if(isReal) { + int count = fscanf(f, "%d %d %lf", &y, &x, &e.value); + if(3 != count) { + std::ostringstream oss; + oss<< "Error parsing line "<< (i + 1); + err = oss.str(); + return false; + } + } else if(isPattern) { + int count = fscanf(f, "%d %df", &y, &x); + if(2 != count) { + std::ostringstream oss; + oss<< "Error parsing line "<< (i + 1); + err = oss.str(); + return false; + } + e.value = 1; + } + e.row = y - 1; + e.col = x - 1; + elements.push_back(e); + + if((mm_is_symmetric(matcode) || mm_is_skew(matcode)) && (x != y)) { + std::swap(e.row, e.col); + if(mm_is_skew(matcode)) e.value = -e.value; + elements.push_back(e); + } + } + + std::sort(elements.begin(), elements.end()); + + std::auto_ptr m(new SparseMatrix); + + nz = (int)elements.size(); + m->height = height; + m->width = width; + m->nz = nz; + m->csr.resize(height + 1); + m->cols.resize(nz); + m->matrix.resize(nz); + for(int i = 0; i < nz; ++i) { + MatrixElement e = elements[i]; + ++m->csr[e.row]; + m->cols[i] = e.col; + m->matrix[i] = e.value; + } + + // scan the counts into CSR. + int scan = 0; + for(int i = 0; i < height; ++i) { + int count = m->csr[i]; + m->csr[i] = scan; + scan += count; + } + m->csr[height] = scan; + + *ppMatrix = m; + + return true; +} + +bool ReadSparseMatrix(const char* filename, + std::auto_ptr* ppMatrix, std::string& err) { + + FILE* f = fopen(filename, "r"); + if(!f) { + err = "Could not open file."; + return false; + } + + bool success = ReadSparseMatrix(f, ppMatrix, err); + + fclose(f); + return success; +} + +bool LoadBinaryMatrix(const char* filename, + std::auto_ptr* ppMatrix) { + + FILE* f = fopen(filename, "rb"); + if(!f) return false; + + std::auto_ptr m(new SparseMatrix); + fread(&m->height, 4, 1, f); + fread(&m->width, 4, 1, f); + fread(&m->nz, 4, 1, f); + + m->csr.resize(m->height + 1); + m->cols.resize(m->nz); + m->matrix.resize(m->nz); + + fread(&m->csr[0], 4, m->height + 1, f); + fread(&m->cols[0], 4, m->nz, f); + fread(&m->matrix[0], 8, m->nz, f); + + fclose(f); + + *ppMatrix = m; + return true; +} + +bool StoreBinaryMatrix(const char* filename, const SparseMatrix& m) { + + FILE* f = fopen(filename, "wb"); + if(!f) return false; + + fwrite(&m.height, 4, 1, f); + fwrite(&m.width, 4, 1, f); + fwrite(&m.nz, 4, 1, f); + + fwrite(&m.csr[0], 4, m.height + 1, f); + fwrite(&m.cols[0], 4, m.nz, f); + fwrite(&m.matrix[0], 8, m.nz, f); + + fclose(f); + return true; +} + +bool LoadCachedMatrix(const char* filename, + std::auto_ptr* ppMatrix, std::string& err) { + + // Attempt to load the binary matrix. If that fails, load the Matrix Market + // ASCII matrix and store as binary. + std::auto_ptr m; + char s[260]; + sprintf(s, "%s.bin", filename); + bool success = LoadBinaryMatrix(s, &m); + if(!success) { + success = ReadSparseMatrix(filename, &m, err); + if(!success) return false; + + printf("Creating temp file %s...\n", s); + StoreBinaryMatrix(s, *m); + } + *ppMatrix = m; + return true; +} + +//////////////////////////////////////////////////////////////////////////////// + +MatrixStats ComputeMatrixStats(const SparseMatrix& m) { + MatrixStats stats; + stats.height = m.height; + stats.width = m.width; + stats.nz = m.nz; + stats.mean = (double)m.nz / m.height; + + // Compute the second moment. + double variance = 0; + for(int i = 0; i < m.height; ++i) { + int count = m.csr[i + 1] - m.csr[i]; + double x = count - stats.mean; + variance += x * x; + } + stats.stddev = sqrt(variance / m.height); + + // Compute the third moment. + double skewness = 0; + for(int i = 0; i < m.height; ++i) { + int count = m.csr[i + 1] - m.csr[i]; + double x = count - stats.mean; + skewness += x * x * x; + } + stats.skewness = skewness / m.height / pow(stats.stddev, 3.0); + + return stats; +} + +//////////////////////////////////////////////////////////////////////////////// +// MulSparseMatrices + +int64 MulSparseMatrices(const SparseMatrix& A, const SparseMatrix& B, + std::auto_ptr* ppC) { + + std::auto_ptr C(new SparseMatrix); + C->height = A.height; + C->width = B.width; + C->nz = 0; + + int64 numProducts = 0; + for(int row = 0; row < A.height; ++row) { + std::map rowMap; + int aCsr0 = A.csr[row]; + int aCsr1 = (row + 1 < A.height) ? A.csr[row + 1] : A.nz; + + for(int i = aCsr0; i < aCsr1; ++i) { + int aCol = A.cols[i]; + double x = A.matrix[i]; + + int bCsr0 = B.csr[aCol]; + int bCsr1 = (aCol + 1 < B.height) ? B.csr[aCol + 1] : B.nz; + + numProducts += bCsr1 - bCsr0; + + for(int j = bCsr0; j < bCsr1; ++j) + rowMap[B.cols[j]] += x * B.matrix[j]; + } + + // Read out the row data. + std::map::const_iterator i = rowMap.begin(); + C->csr.push_back(C->nz); + while(i != rowMap.end()) { + C->cols.push_back(i->first); + C->matrix.push_back(i->second); + ++i; + } + C->nz += (int)rowMap.size(); + } + + *ppC = C; + return numProducts; +} + + +int64 ComputeProductCount(const SparseMatrix& A, const SparseMatrix& B) { + int64 numProducts = 0; + for(int ai = 0; ai < A.nz; ++ai) { + int aCol = A.cols[ai]; + int bCsr0 = B.csr[aCol]; + int bCsr1 = (aCol + 1 < B.width) ? B.csr[aCol + 1] : B.nz; + numProducts += bCsr1 - bCsr0; + } + return numProducts; +} + +void ComputeColRanges(const SparseMatrix& A, const SparseMatrix& B, + int* colMin, int* colMax) { + + // Loop over all NZ elements in A and do two lookups into B. + for(int row = 0; row < A.height; ++row) { + int cMin = B.width; + int cMax = 0; + + int csr0 = A.csr[row]; + int csr1 = A.csr[row + 1]; + for(int i = csr0; i < csr1; ++i) { + int aCol = A.cols[i]; + cMin = std::min(cMin, B.cols[B.csr[aCol]]); + cMax = std::max(cMax, B.cols[B.csr[aCol + 1] - 1]); + } + colMin[row] = cMin; + colMax[row] = cMax; + } +} + +} // namespace mgpu diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/README.md b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/README.md new file mode 100644 index 0000000000000000000000000000000000000000..5bbed931c35f23ae99b4fe2e82409d6f977e45ba --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/README.md @@ -0,0 +1,12 @@ +Priority-Deque + +============== + + + +This project is my implementation of a double-ended priority queue (a priority deque) as a C++ class template. + +Goals: +Interface similar to STL's priority_queue. +Performance competitive with STL's priority_queue. +Provide the strongest exception-safety guarantee possible without compromising performance. \ No newline at end of file diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/interval_heap.hpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/interval_heap.hpp new file mode 100644 index 0000000000000000000000000000000000000000..32f8c181ca6c555bf1f58db0433a6c1f52c64772 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/interval_heap.hpp @@ -0,0 +1,579 @@ +/*----------------------------------------------------------------------------*\ +| Copyright (C) 2013 Nathaniel McClatchey | +| Released under the Boost Software License Version 1.0, which may be found | +| at http://www.boost.org/LICENSE_1_0.txt | +\*----------------------------------------------------------------------------*/ + +/*! @file interval_heap.hpp +// interval_heap.hpp provides functions for creating interval heaps by +// rearranging a range of elements. A valid interval heap has the following +// properties: +// Given elements A and B, A is less than B iff compare(A,B), where compare +// is a binary functor describing a strict weak ordering. +// Left and right bounds are those with even and odd indices, respectively. +// A right bound is never less than its corresponding left bound. +// A left bound is never less than the left bound of its parent. +// A right bound is never less than the right bounds of its children. +// @remark Exception-safety: All functions in interval_heap.hpp provide at +// least the basic exception-safety guarantee. That is, no element will be lost +// in the event of an exception. Elements may, however, no longer form an +// interval heap. +// @remark Exception-safety: Pre-C++11: If the comparison and swap don't throw, +// neither do any of the interval-heap functions. +// @remark Exception-safety: C++11: If the comparison, move-assign, and +// move-construct, do not throw, neither do any of the interval-heap functions. +*/ + +#ifndef BOOST_HEAP_INTERVAL_HEAP_HPP_ +#define BOOST_HEAP_INTERVAL_HEAP_HPP_ + +#ifndef __cplusplus +#error interval_heap.hpp requires a C++ compiler. +#endif + +// Grab std::swap and std::move, while avoiding as much baggage as possible. +#if (__cplusplus >= 201103L) +#include +#else +#include +#endif +// Grab iterator data, for better use of templates. +#include + +namespace boost { +namespace heap { +//------------------------------User-Accessible--------------------------------- +//! @brief Moves elements in [first,last) to form an interval heap. +template +void make_interval_heap (Iterator first, Iterator last, Compare compare); + +//! @brief Expands the interval heap to include the element at last-1. +template ::value_type> > +void push_interval_heap (Iterator first, Iterator last, Compare compare); + +//!@{ +//! @brief Moves a minimal element to the back of the range for popping. +template +void pop_interval_heap_min (Iterator first, Iterator last, Compare compare); +//! @brief Moves a maximal element to the back of the range for popping. +template +void pop_interval_heap_max (Iterator first, Iterator last, Compare compare); + +//! @brief Moves an element to the back of the range for popping. +template +void pop_interval_heap (Iterator first, Iterator last, + typename std::iterator_traits::difference_type index, + Compare compare); +//!@} +//! @brief Restores the interval-heap property if one element violates it. +template +void update_interval_heap (Iterator first, Iterator last, + typename std::iterator_traits::difference_type index, + Compare compare); + +//! @brief Sorts an interval heap in ascending order. +template +void sort_interval_heap (Iterator first, Iterator last, Compare compare); +//! @brief Finds the largest subrange that qualifies as an interval heap. +template +Iterator is_interval_heap_until (Iterator first, Iterator last,Compare compare); +//! @brief Checks whether the range is an interval heap. +template +bool is_interval_heap (Iterator first, Iterator last, Compare compare); + + +//-------------------------------Book-Keeping----------------------------------- +namespace interval_heap_internal { +//! @brief Restores the interval-heap property if one leaf element violates it. +template +void sift_leaf (Iterator first, Iterator last, + typename std::iterator_traits::difference_type index, + Compare compare); +//! @brief Moves an element up the interval heap. +template +void sift_up (Iterator first, Offset index, Compare compare,Offset limit_child); +//! @brief Moves an element between min/max bounds, and up the interval heap. +template +void sift_leaf_max (Iterator first, Iterator last, Offset index, + Compare compare, Offset limit_child); +//! @brief Moves an element between min/max bounds, and up the interval heap. +template +void sift_leaf_min (Iterator first, Iterator last, Offset index, + Compare compare, Offset limit_child); +//! @brief Restores the interval-heap property if one element violates it. +template +void sift_down (Iterator first, Iterator last, Offset index, Compare compare, + Offset limit_child); +} // Namespace interval_heap_internal + +/*! @details This function restores the interval-heap property violated by the +// specified element. +// @param first,last A range of random-access iterators. +// @param index The offset, from @a first, of the offending element. +// @param compare A comparison object. +// @pre @a index is in the range [ 0, @a last - @a first). +// @pre [ @a first, @a last) is a valid interval heap, if the element at +// @a first + @a index is ignored. +// @post [ @a first, @a last) is a valid interval heap. +// @invariant No element is added to or removed from the range. +// @remark Complexity: O(log n) +// @remark Exception safety: Basic if move/copy/swap provide the basic +// guarantee. Strong if they do not throw exceptions. +*/ +template +void update_interval_heap (Iterator first, Iterator last, + typename std::iterator_traits::difference_type index, + Compare compare) +{ + using namespace std; + using interval_heap_internal::sift_down; + typedef typename iterator_traits::difference_type Offset; + if (index & 1) + sift_down(first, last, index, compare,2); + else + sift_down(first, last, index, compare, 2); +} + +/*! @details This function expands an interval heap from [ @a first, @a last - +// 1) to [ @a first, @a last), maintaining the interval-heap property. This is +// typically used to add a new element to the interval heap. +// @param first,last A range of random-access iterators. +// @param compare A comparison object. +// @pre [ @a first, @a last - 1) is a valid interval heap. +// @post [ @a first, @a last) is a valid interval heap. +// @invariant No element is added to or removed from the range. +// @remark Complexity: O(log n) +// @remark Exception safety: As strong as sift_interval_heap. +*/ +template +void push_interval_heap (Iterator first, Iterator last, Compare compare) { + using interval_heap_internal::sift_leaf; + sift_leaf(first, last, (last - first) - 1, compare); +} + +/*! @details This function moves a specified element to the end of the range of +// iterators. This is typically done so that the element can be efficiently +// removed (by @a pop_back, for example). +// @param first,last A range of random-access iterators. +// @param index The offset, from @a first, of the element to be removed. +// @param compare A comparison object. +// @pre [ @a first, @a last) is a valid interval heap. +// @pre @a index is in the range [ 0, @a last - @a first) +// @post [ @a first, @a last - 1) is a valid interval heap. +// @post The element originally at @a first + @a index has been moved to +// @a last - 1. +// @invariant No element is added to or removed from the range. +// @remark Complexity: O(log n) +// @remark Exception safety: As strong as sift_interval_heap. +*/ +template +void pop_interval_heap (Iterator first, Iterator last, + typename std::iterator_traits::difference_type index, + Compare compare) +{ + using namespace std; + --last; + swap(*(first + index), *last); + try { + update_interval_heap(first, last, index, compare); + } catch (...) { +// Roll back for strong guarantee. + swap(*last, *(first + index)); + throw; + } +} + +/*! @details This function moves a minimal element to the end of the range of +// iterators. This is typically done so that the element can be efficiently +// removed (by @a pop_back, for example), but can also be used to sort the +// range in descending order. +// @param first,last A range of random-access iterators. +// @param compare A comparison object. +// @pre [ @a first, @a last) is a valid interval heap. +// @post A minimal element from the range has been moved to @a last - 1. +// @post [ @a first, @a last - 1) is a valid interval heap. +// @invariant No element is added to or removed from the range. +// @remark Complexity: O(log n) +// @remark Exception safety: As strong as sift_interval_heap. +*/ +template +void pop_interval_heap_min (Iterator first, Iterator last, Compare compare) { + using namespace std; + using interval_heap_internal::sift_down; + typedef typename iterator_traits::difference_type Offset; + --last; + swap(*first, *last); + try { + sift_down(first, last, 0, compare, 2); + } catch (...) { +// Roll back for strong guarantee. + swap(*last, *first); + throw; + } +} + +/*! @details This function moves a maximal element to the end of the range of +// iterators. This is typically done so that the element can be efficiently +// removed (by @a pop_back, for example), but can also be used to sort the +// range in ascending order. +// @param first,last A range of random-access iterators. +// @param compare A comparison object. +// @pre [ @a first, @a last) is a valid interval heap. +// @post A maximal element from the range has been moved to @a last - 1. +// @post [ @a first, @a last - 1) is a valid interval heap. +// @invariant No element is added to or removed from the range. +// @remark Complexity: O(log n) +// @remark Exception safety: As strong as sift_interval_heap. +*/ +template +void pop_interval_heap_max (Iterator first, Iterator last, Compare compare) { + using namespace std; + using interval_heap_internal::sift_down; + typedef typename iterator_traits::difference_type Offset; +// Nothing to be done. + if (last - first <= 2) + return; + --last; + swap(*(first + 1), *last); + try { + sift_down(first, last, 1, compare, 2); + } catch (...) { +// Roll back for strong guarantee. + swap(*last, *(first + 1)); + throw; + } +} + +/*! @details This function takes an interval heap and sorts its elements in +// ascending order. +// @param first,last A range of random-access iterators. +// @param compare A comparison object. +// @pre [ @a first, @a last) is a valid interval heap. +// @post [ @a first, @a last) is sorted in ascending order. +// @invariant No element is added to or removed from the range. +// @remark Complexity: O(n log n) +// @remark Exception safety: Basic +*/ +template +void sort_interval_heap (Iterator first, Iterator last, Compare compare) { + Iterator cursor = last; + while (cursor != first) { +// If this throws, anything I do to try to fix it is also likely to throw. + pop_interval_heap_max(first, cursor, compare); + --cursor; + } +} + +//! @brief Finds the largest subrange that forms a valid interval heap. +//! @remark Exception safety: Non-throwing +template +Iterator is_interval_heap_until (Iterator first, Iterator last, Compare compare) +{ + using namespace std; + typedef typename iterator_traits::difference_type Offset; + + Offset index = static_cast(0); + + try { + Offset index_end = last - first; + while (index < index_end) { + Iterator cursor = first + index; +// Check whether it is a valid interval. + if ((index & 1) && compare(*cursor, *(cursor - 1))) + return cursor; + if (index >= 2) { +// If there exists a parent interval, check for containment. + Iterator parent = first + ((index / 2 - 1) | 1); + if (index & 1) { + if (compare(*parent, *cursor)) + return cursor; + } else { + if (compare(*parent, *cursor)) + return cursor; + if (compare(*cursor, *(parent - 1))) + return cursor; + } + } + ++index; + } + } catch (...) { + return first + index; + } + return last; +} + +//! @brief Checks whether the range is a valid interval heap. +//! @remark Exception safety: Non-throwing +template +bool is_interval_heap (Iterator first, Iterator last, Compare compare) { + try { + return (is_interval_heap_until(first, last, compare) + == last); + } catch (...) { + return false; + } +} + +/*! @details This function moves elements in a range to from an interval-heap. +// @param first,last A range of random-access iterators. +// @param compare A comparison object. +// @post [ @a first, @a last) is a valid interval heap. +// @invariant No element is added to or removed from the range. +// @remark Complexity: O(n) +//! @remark Exception safety: Basic +*/ +template +void make_interval_heap (Iterator first, Iterator last, Compare compare) { + using namespace std; + using interval_heap_internal::sift_down; + typedef typename iterator_traits::difference_type Offset; + + Offset index_end = last - first; +// Double-heap property holds vacuously. + if (index_end <= 1) + return; +// Prevents overflow when number of elements approaches maximum possible index. + const Offset end_parent = index_end / 2 - 1; +// If the final interval is a singleton, it's already OK. Skip it. + Offset index = index_end ^ (index_end & 1); + do { + index -= 2; + const Offset stop = (index <= end_parent) ? (index * 2 + 2) : index_end; +// If compare throws, heap property cannot be verified or enforced. +// If swap throws, heap property is violated and cannot be enforced. + if (compare(*(first + index + 1), *(first + index))) + swap(*(first + index + 1), *(first + index)); + + sift_down(first, last, index + 1, + compare, stop); + sift_down(first, last, index, + compare, stop); + + } while (index >= 2); +} + +namespace interval_heap_internal { +//! @remark Exception safety: Strong if move/swap doesn't throw. +template +void sift_up (Iterator first, Offset origin, Compare compare, Offset limit_child) +{ +// Use the most specialized available functions. + using namespace std; + typedef typename iterator_traits::value_type Value; +// Keeping the information about the origin permits strong exception guarantee. + Offset index = origin; +#if (__cplusplus >= 201103L) // C++11 + Value swap_space = std::move_if_noexcept(*(first + index)); +#endif + try { + while (index >= limit_child) { + const Offset parent = ((index / 2 - 1) | 1) ^ (left_bound ? 1 : 0); +#if (__cplusplus >= 201103L) // C++11 + if (compare((left_bound ? swap_space : *(first + parent)), + (left_bound ? *(first + parent) : swap_space))) { + *(first + index) = std::move_if_noexcept(*(first + parent)); +#else + if (compare(*(first + (left_bound ? index : parent)), + *(first + (left_bound ? parent : index)))) { + swap(*(first + index), *(first + parent)); +#endif + index = parent; + } else + break; + } + } catch (...) { +// Note: This rolls back comparison exceptions. Move exceptions can't be fixed. +#if (__cplusplus < 201103L) // Not C++11 +// I need the extra space because elements are being moved in the direction of +// travel. + Value swap_space; + swap(*(first + index), swap_space); +#endif + swap(*(first + origin), swap_space); + while (origin > index) { + origin = ((origin / 2 - 1) | 1) ^ (left_bound ? 1 : 0); + swap(*(first + origin), swap_space); + } + throw; + } +#if (__cplusplus >= 201103L) // C++11 + *(first + index) = std::move_if_noexcept(swap_space); +#endif +} + +//! @remark Exception safety: As strong as sift_up. +template +void sift_leaf_max (Iterator first, Iterator last, Offset index, + Compare compare, Offset limit_child) +{ +// Use the most specialized swap function. + using namespace std; + const Offset index_end = last - first; + +// Index of corresponding element + const Offset co_index = (index * 2 < index_end) ? (index * 2) : (index ^ 1); + if (compare(*(first + index), *(first + co_index))) { + swap(*(first + index), *(first + co_index)); + try { + sift_up(first, co_index, compare, + limit_child); + } catch (...) { // Rollback for strong guarantee. + swap(*(first + index), *(first + co_index)); + throw; + } + } else + sift_up(first, index, compare, + limit_child); +} + +//! @remark Exception safety: As strong as sift_up. +template +void sift_leaf_min (Iterator first, Iterator last, Offset index, + Compare compare, Offset limit_child) +{ +// Use the most specialized swap function. + using namespace std; + const Offset index_end = last - first; + +// Index of corresponding element (initial assumption) + Offset co_index = index | 1; +// Co-index is past the end of the heap. Move to its parent, if possible. + if (co_index >= index_end) { +// Only one element. + if (co_index == 1) + return; + co_index = (co_index / 2 - 1) | 1; + } + if (compare(*(first + co_index), *(first + index))) { + swap(*(first + index), *(first + co_index)); + try { + sift_up(first, co_index, compare, + limit_child); + } catch (...) { // Rollback for strong guarantee. + swap(*(first + index), *(first + co_index)); + throw; + } + } else + sift_up(first, index, compare, limit_child); +} + +//! @remark Exception safety: As strong as sift_up. +template +void sift_down (Iterator first, Iterator last, Offset origin, Compare compare, + Offset limit_child) +{ +// Use the most specialized available functions. + using namespace std; + typedef typename iterator_traits::value_type Value; +// By keeping track of where I started, I can roll back all changes. + Offset index = origin; +#if (__cplusplus >= 201103L) // C++11 + Value limbo = std::move_if_noexcept(*(first + index)); +#endif + + const Offset index_end = last - first; +// One past the last element with two children. + const Offset end_parent = index_end / 2 - + ((left_bound && ((index_end & 3) == 0)) ? 2 : 1); + try { // This try-catch block rolls back after exceptions. + while (index < end_parent) { + Offset child = index * 2 + (left_bound ? 2 : 1); +// If compare throws, heap property cannot be verified or enforced. + try { // This try-catch block ensures no element is left in limbo. + if (compare(*(first + child + (left_bound ? 2 : 0)), + *(first + child + (left_bound ? 0 : 2)))) + child += 2; + } catch (...) { +#if (__cplusplus >= 201103L) // C++11 +// Pull the moving element out of limbo, to avoid leaks. + *(first + index) = std::move_if_noexcept(limbo); +#endif + throw; + } +#if (__cplusplus >= 201103L) // C++11 + *(first + index) = std::move_if_noexcept(*(first + child)); +#else + swap(*(first + index), *(first + child)); +#endif + index = child; + } +// Special case when index has exactly one child. + if (index <= end_parent + (left_bound ? 0 : 1)) { + Offset child = index * 2 + (left_bound ? 2 : 1); + if (child < index_end) { +// Need to treat singletons (child + 1) as both upper and lower bounds. + if (!left_bound && (child + 1 < index_end)) { +// Calculating this outside the if-statement simplifies exception-handling. + bool swap_required; + try { + swap_required = compare(*(first + child), *(first + child + 1)); + } catch (...) { +// Pull the moving element out of limbo. +#if (__cplusplus >= 201103L) + *(first + index) = std::move_if_noexcept(limbo); +#endif + throw; + } + if (swap_required) { + ++child; +#if (__cplusplus >= 201103L) // C++11 + *(first + index) = std::move_if_noexcept(*(first + child)); + *(first + child) = std::move_if_noexcept(limbo); +#else + swap(*(first + index), *(first + child)); +#endif +// Important for the rollback. + index = child; + sift_leaf_min(first, last, index, + compare, limit_child); + return; + } + } +#if (__cplusplus >= 201103L) // C++11 + *(first + index) = std::move_if_noexcept(*(first + child)); +#else + swap(*(first + index), *(first + child)); +#endif + index = child; + } + } +// Pull the moving element out of limbo. +#if (__cplusplus >= 201103L) // C++11 + *(first + index) = std::move_if_noexcept(limbo); +#endif + if (left_bound) + sift_leaf_min(first, last, index, compare, + limit_child); + else + sift_leaf_max(first, last, index, compare, + limit_child); + } catch (...) { +// Rolls back comparison exceptions. Move exceptions can't be reliably fixed. + while (index > origin) { + const Offset parent = ((index / 2 - 1) | 1) ^ (left_bound ? 1 : 0); + swap(*(first + parent), *(first + index)); + index = parent; + } + throw; + } +} + +//! @remark Exception safety: As strong as sift_up. +template +void sift_leaf (Iterator first, Iterator last, + typename std::iterator_traits::difference_type index, + Compare compare) +{ + using namespace std; + typedef typename iterator_traits::difference_type Offset; + if (index & 1) + sift_leaf_max(first, last, index, compare, 2); + else + sift_leaf_min(first, last, index, compare, 2); +} +} // Namespace interval_heap_internal +} // Namespace heap +} // Namespace boost + +#endif // BOOST_HEAP_INTERVAL_HEAP_HPP_ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/main.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/main.cpp new file mode 100644 index 0000000000000000000000000000000000000000..48be9182bde4a4808c25bf0a5f16dc9189ef1469 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/main.cpp @@ -0,0 +1,207 @@ +//#define NDEBUG 1 + +#ifndef __cplusplus +#error A C++ compiler is required. +#endif + +#include +#include +#include +#include +#include +#include + +#include "priority_deque.hpp" +#include "priority_deque_verify.hpp" + +int main(); + +//! @todo More tests! + +#define BENCHMARK +#define VERIFY_HEAP + +template +void benchmark_priority_queue (unsigned benchmark_elements) { + pq_t pq; + clock_t bench_begin, bench_mid, bench_end; + std::cout << "Benchmark results: "; +// First, fill the queue with most of the elements, to get a better idea of the average case. + for (unsigned n = benchmark_elements / 2; n--;) + pq.push(rand()); +// Test how long it takes to fill the rest of the way. + bench_begin = clock(); + for (unsigned n = benchmark_elements / 2; n--;) + pq.push(rand()); + bench_mid = clock(); + std::cout << "Push: " << (bench_mid - bench_begin) << " (" << static_cast(bench_mid - bench_begin) / CLOCKS_PER_SEC << "s)"; + +// Test time required to remove the same number of elements. + bench_mid = clock(); + for (unsigned n = benchmark_elements / 2; n--;) + pq.pop(); + bench_end = clock(); + std::cout << ", Pop: " << (bench_end - bench_mid) << " (" << static_cast(bench_end - bench_mid) / CLOCKS_PER_SEC << "s)\n"; +} + +int main() { + std::cout << "__cplusplus = " << __cplusplus << "\n"; +#ifndef NDEBUG + std::cout << "Debug mode (asserts active).\n"; +#endif + srand(clock()); + + using boost::container::priority_deque; + using boost::heap::is_interval_heap; + using std::priority_queue; + +// Begin tests +{ + priority_deque test_deque; +// Sufficient sample size for observing all potential interesting behaviors. + for (int i = 0; i < 256; ++i) { + try { + test_deque.push(i); + if (std::find(test_deque.begin(), test_deque.end(), i) == test_deque.end()) { + std::cerr << "Element lost .\n"; + break; + } + if (!is_interval_heap(test_deque.begin(), test_deque.end(), std::less())) { + std::cerr << "Heap corrupted .\n"; + break; + } + if (test_deque.maximum() != i) + std::cerr << "Incorrect maximum. i = " << i << "\n"; + } catch (...) { + std::cerr << "Exception thrown .\n"; + break; + } + } + std::vector test_vector; + for (int i = 0; i < 256; ++i) { + test_vector.push_back(i); + std::random_shuffle(test_vector.begin(), test_vector.end()); + try { + test_deque.clear(); + test_deque.merge(test_vector); + if (test_deque.size() != test_vector.size()) + std::cerr << "Merge changed number of elements.\n"; + for (int j = 0; j <= i; ++j) { + if (std::find(test_deque.begin(), test_deque.end(), j) == test_deque.end()) { + std::cerr << "Element removed .\n"; + break; + } + } + if (!is_interval_heap(test_deque.begin(), test_deque.end(), std::less())) { + std::cerr << "Heap corrupted .\n"; + break; + } + } catch (...) { + std::cerr << "Exception thrown .\n"; + break; + } + } +} +// Benchmark performance relative to std::priority_queue. +#ifdef BENCHMARK +{ + typedef intmax_t benchmark_type; + const unsigned benchmark_elements = 20000000; + std::cout << "PD: "; + benchmark_priority_queue >(benchmark_elements); + std::cout << "PQ: "; + benchmark_priority_queue >(benchmark_elements); +} +#endif + +#ifdef VERIFY_HEAP + std::cout << "\n\nTesting heap integrity after:\n"; + const int element_total = 3001;//8192 * 2000; + priority_deque pd; + + std::cout << "'push' (" << element_total << "x)\n"; + for (int n = 1; n <= element_total; ++n) { + pd.push(rand()); + if (is_valid_until(pd) != pd.end()) { + std::cout << "Failed push (error in replace_leaf)\n"; + break; + } + } + + srand(25346); + std::vector v; + for (int n = 1; n <= 5; ++n) + v.push_back(rand()); + for (int n = 1; n <= 1; ++n) { + std::cout << "'merge' (" << v.size() << " elements)\n"; + + /*for (auto it = v.begin(); it != v.end(); ++it) + std::cout << *it << ", "; + std::cout << "\n";*/ + boost::heap::make_interval_heap(v.begin(), v.end(), std::less()); + if (!boost::heap::is_interval_heap(v.begin(), v.end(), std::less())) { + std::cout << "Failed\n"; + for (auto it = v.begin(); it != v.end(); ++it) + std::cout << *it << ", "; + std::cout << "\n"; + } + std::random_shuffle(v.begin(), v.end()); + v.push_back(rand()); + } + /*for (int n = 1; n < 64; ++n) { + std::cout << "'merge' (" << v.size() << " elements)\n"; + pd.clear(); + pd.merge(v.begin(), v.end()); + if (is_valid_until(pd) != pd.end()) + std::cout << "Failed merge (error in make_valid)\n"; + v.push_back(rand()); + }*/ + + std::cout << "'set' (" << element_total << "x)\n"; + for (int t = 0; t < element_total; ++t) { + pd.update(pd.begin() + rand() % pd.size(), rand()); + if (is_valid_until(pd) != pd.end()) { + std::cout << "Failed random-access set (error in replace)\n"; + break; + } + } + + std::cout << "'pop_minimum' (" << pd.size() << "x)\n"; + while (!pd.empty()) { + pd.pop_minimum(); + if (is_valid_until(pd) != pd.end()) { + std::cout << "Failed pop_minimum (error in replace)\n"; + break; + } + } + pd.clear(); + + std::cout << "'push', 'pop_maximum', 'pop_minimum', 'erase', 'set' (indefinitely)\n"; + boost::container::priority_deque test_pd; + for (int n = 0; n < 13; ++n) { + test_pd.push(rand()); + if (is_valid_until(pd) != pd.end()) + std::cout << "Failed push (error in replace_leaf)\n"; + } + int last_rand = -1; + while (true) { + if (test_pd.size() < 3000) { + last_rand = -1; + test_pd.push(rand()); + } else { + last_rand = rand() % 8; + switch (last_rand) { + case 0: test_pd.pop_maximum(); break; + case 1: test_pd.pop_minimum(); break; + case 2: test_pd.erase(test_pd.begin() + rand() % test_pd.size()); break; + default: test_pd.update(test_pd.begin() + rand() % test_pd.size(), rand()); + } + } + if (is_valid_until(pd) != pd.end()) { + std::cout << "An error has occurred! (code " << last_rand << ").\n"; + break; + } + } +#endif + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/priority_deque.hpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/priority_deque.hpp new file mode 100644 index 0000000000000000000000000000000000000000..9676aa8b2e511265ce17d0545b2132f43d2a2721 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/priority_deque.hpp @@ -0,0 +1,525 @@ +/*----------------------------------------------------------------------------*\ +| Copyright (C) 2012-2013 Nathaniel McClatchey | +| Released under the Boost Software License Version 1.0, which may be found | +| at http://www.boost.org/LICENSE_1_0.txt | +\*----------------------------------------------------------------------------*/ + +/*! @file priority_deque.hpp +// priority_deque.hpp provides the class priority_deque as a thin wrapper +// around the functions provided by interval_heap.hpp. +// @remark Exception-safety: If the means of movement -- move, copy, or swap, +// depending on exception specifications -- do not throw, the guarantee is as +// strong as that of the action on the underlying container. (Unless otherwise +// specified) +// @note Providing a stronger guarantee is impractical. +*/ + +#ifndef BOOST_CONTAINER_PRIORITY_DEQUE_HPP_ +#define BOOST_CONTAINER_PRIORITY_DEQUE_HPP_ + +#ifndef __cplusplus +#error priority_deque.hpp requires a C++ compiler. +#endif + +// Default comparison (std::less) +#include +// Default container (std::vector) +#include +// Grab std::move, if available. +#if (__cplusplus >= 201103L) +#include +#endif +// Interval-heap management. +#include "interval_heap.hpp" + +// Choose the best available version of the assert macro. +#ifdef BOOST_ASSERT_MSG +#define BOOST_CONTAINER_PRIORITY_DEQUE_ASSERT(x,m) BOOST_ASSERT_MSG(x,m) +#elif defined assert +#define BOOST_CONTAINER_PRIORITY_DEQUE_ASSERT(x,m) assert(x) +#else +#define BOOST_CONTAINER_PRIORITY_DEQUE_ASSERT(x,m) +#endif + +namespace boost { +namespace container { +//! @brief Efficient double-ended priority queue. +template , + typename Compare =::std::less > +class priority_deque; + +//! @brief Swaps the elements of two priority deques. +template +void swap (priority_deque& deque1, + priority_deque& deque2); + +//----------------------------Priority Deque Class-----------------------------| +/*! @brief Efficient double-ended priority queue. + * @author Nathaniel McClatchey + * @copyright Boost Software License Version 1.0 + * @param Type Type of elements in the priority deque. + * @param Sequence Underlying sequence container. Must provide random-access + * iterators, %front(), %push_back(Type const &), and %pop_back(). + * Defaults to std::vector. + * @param Compare Comparison class. %Compare(A, B) should return true if %A + * should be placed earlier than %B in a strict weak ordering. + * Defaults to std::less, which encapsulates operator<. + * @details Priority deques are adaptors, designed to provide efficient + * insertion and access to both ends of a weakly-ordered list of elements. + * As a container adaptor, priority_deque is implemented on top of another + * container type. By default, this is std::vector, but a different container + * may be specified explicitly. + * Although the priority deque does permit iteration through its elements, + * there is no ordering guaranteed, as different implementations may benefit + * from different structures, and all iterators should be discarded after using + * any function not labeled const. + * @note %priority_deque does not provide a stable ordering. If both A +class priority_deque { +//----------------------------------Public-------------------------------------| + public: +//---------------------------------Typedefs------------------------------------| +//! @details Underlying container type. + typedef Sequence container_type; + typedef typename container_type::value_type value_type; + typedef Compare value_compare; +//! @details STL Container specifies that this is an unsigned integral type. + typedef typename container_type::size_type size_type; +//! @details May be used to examine, but not modify, an element in the deque. + typedef typename container_type::const_reference const_reference; + typedef typename container_type::reference reference; + typedef typename container_type::pointer pointer; + typedef pointer const_pointer; +//! @details May be used to examine, but not modify, elements in the deque. + typedef typename container_type::const_iterator const_iterator; + typedef const_iterator iterator; +//! @details STL Container specifies that this is a signed integral type. + typedef typename container_type::difference_type difference_type; +//-------------------------------Constructors----------------------------------| +//! @brief Constructs a new priority deque. +#if (__cplusplus >= 201103L) + explicit priority_deque (const Compare& =Compare(), + Sequence&& =Sequence()); +//! @overload + priority_deque (const Compare&, const Sequence&); +#else + explicit priority_deque (const Compare& =Compare(), + const Sequence& =Sequence()); +#endif +//! @brief Constructs a new priority deque from a sequence of elements. +#if (__cplusplus >= 201103L) + template + priority_deque (InputIterator first, InputIterator last, + const Compare& =Compare(), + Sequence&& =Sequence()); +//! @overload + template + priority_deque (InputIterator first, InputIterator last, + const Compare&, const Sequence&); +#else + template + priority_deque (InputIterator first, InputIterator last, + const Compare& =Compare(), + const Sequence& =Sequence()); +#endif +//-----------------------------Restricted Access-------------------------------| +//! @brief Copies an element into the priority deque. + void push (const value_type&); +#if (__cplusplus >= 201103L) +//!@overload + void push (value_type&&); +//! @brief Emplaces an element into the priority deque. + template + void emplace (Args&&...); +#endif + +//!@{ +//! @brief Accesses a maximal element in the deque. + const_reference maximum (void) const; +//! @brief Accesses a minimal element in the deque. + const_reference minimum (void) const; +//! @details Identical to std::priority_queue top(). @see @a maximum + inline const_reference top (void) const { return maximum(); }; +//!@} +//!@{ +//! @brief Removes a maximal element from the deque. + void pop_maximum (void); +//! @brief Removes a minimal element from the deque. + void pop_minimum (void); +//! @details Identical to std::priority_queue pop(). @see @a pop_maximum + inline void pop (void) { pop_maximum(); }; +//!@} + +//--------------------------------Deque Size-----------------------------------| +//!@{ +//! @brief Returns true if the priority deque is empty, false if it is not. + inline bool empty (void) const {return sequence_.empty();}; +//! @brief Returns the number of elements in the priority deque. + inline size_type size (void) const {return sequence_.size(); }; +//! @brief Returns the maximum number of elements that can be contained. + inline size_type max_size (void) const { + return sequence_.max_size(); + }; +//!@} + +//--------------------------Whole-Deque Operations-----------------------------| +//! @brief Removes all elements from the priority deque. + inline void clear (void) { sequence_.clear(); }; +//! @brief Moves the elements from this deque into another, and vice-versa. + void swap (priority_deque&); +//!@{ +//! @brief Merges a sequence of elements into the priority deque. + template + void merge (InputIterator first, InputIterator last); +//! @brief Merges a container's elements into the priority deque. + template + inline void merge (const SourceContainer& source) { + merge(source.begin(), source.end()); + } +//!@} + +//-------------------------------Random Access---------------------------------| +//!@{ +//! @brief Returns a const iterator at the beginning of the sequence. + inline const_iterator begin (void) const {return sequence_.begin();}; +//! @brief Returns a const iterator past the end of the sequence. + inline const_iterator end (void) const { return sequence_.end(); }; +//! @brief Modifies a specified element of the deque. + void update (const_iterator, const value_type&); +#if (__cplusplus >= 201103L) +//!@overload + void update (const_iterator, value_type&&); +#endif +//! @brief Removes a specified element from the deque. + void erase (const_iterator); +//!@} + +//---------------------------Boost.Heap Concepts-------------------------------| +// size() has constant complexity + static const bool constant_time_size = true; +// priority deque does not have ordered iterators + static const bool has_ordered_iterators = false; +// priority deque is efficiently mergable + static const bool is_mergable = true; +// priority deque does not have a stable heap order + static const bool is_stable = false; +// priority deque does not have a reserve() member + static const bool has_reserve = false; + +//--------------------------------Protected------------------------------------| + protected: + inline container_type& sequence (void) { return sequence_; }; + inline const container_type& sequence (void) const { return sequence_; }; + inline value_compare& compare (void) { return compare_; }; + inline const value_compare& compare (void) const { return compare_; }; +//---------------------------------Private-------------------------------------| + private: + Sequence sequence_; + Compare compare_; +}; + +//-------------------------------Constructors----------------------------------| +//----------------------------Default Constructor------------------------------| +/** @param comp Comparison class. +// @param seq Container class. +// @post Deque contains copies of all elements from @a sequence. +// +// @remark Complexity: O(n) +*/ +template +priority_deque::priority_deque (const C& comp, const S& seq) + : sequence_(seq), compare_(comp) +{ + heap::make_interval_heap(sequence_.begin(), sequence_.end(), compare_); +} +#if (__cplusplus >= 201103L) +template +priority_deque::priority_deque (const C& comp, S&& seq) + : sequence_(std::move(seq)), compare_(comp) +{ + heap::make_interval_heap(sequence_.begin(), sequence_.end(), compare_); +} +#endif + +//---------------------------Create from Iterators-----------------------------| +/** @param first,last Range of elements. +// @param comp Instance of comparison class. +// @param seq Instance of container class. +// @post Deque contains copies of all elements in @a sequence (if specified) +// and in the range [ @a first, @a last). +// +// @remark Complexity: O(n) +*/ +template +template +priority_deque::priority_deque (InputIterator first,InputIterator last, + const C& comp, const S& seq) +: sequence_(seq), compare_(comp) +{ + try { + sequence_.insert(sequence_.end(), first, last); + heap::make_interval_heap(sequence_.begin(), sequence_.end(), compare_); + } catch (...) { + heap::make_interval_heap(sequence_.begin(), sequence_.end(), compare_); + throw; + } +} +#if (__cplusplus >= 201103L) +template +template +priority_deque::priority_deque (InputIterator first,InputIterator last, + const C& comp, S&& seq) +: sequence_(std::move(seq)), compare_(comp) +{ + try { + sequence_.insert(sequence_.end(), first, last); + heap::make_interval_heap(sequence_.begin(), sequence_.end(), compare_); + } catch (...) { + heap::make_interval_heap(sequence_.begin(), sequence_.end(), compare_); + throw; + } +} +#endif + +//-----------------------------Restricted Access-------------------------------| +//------------------------------Insert / Emplace-------------------------------| +/** @param value Element to add the the priority deque. +// @post Priority deque contains @a value or a copy of @a value. +// @post All iterators and references are invalidated. +// +// @remark Complexity: O(log n) +*/ +template +void priority_deque::push (const value_type& value) { + try { + sequence_.push_back(value); + } catch (...) { + heap::push_interval_heap(sequence_.begin(), sequence_.end(), compare_); + throw; + } + heap::push_interval_heap(sequence_.begin(), sequence_.end(), compare_); +} +#if (__cplusplus >= 201103L) +template +void priority_deque::push (value_type&& value) { + try { + sequence_.push_back(std::move(value)); + } catch (...) { + heap::push_interval_heap(sequence_.begin(), sequence_.end(), compare_); + throw; + } + heap::push_interval_heap(sequence_.begin(), sequence_.end(), compare_); +} + +template +template +void priority_deque::emplace (Args&&... args) { + try { + sequence_.emplace_back(std::forward(args)...); + } catch (...) { + heap::push_interval_heap(sequence_.begin(), sequence_.end(), compare_); + throw; + } + heap::push_interval_heap(sequence_.begin(), sequence_.end(), compare_); +} +#endif + +//---------------------------Observe Maximum/Minimum---------------------------| +/** @return Const reference to a maximal element in the priority deque. +// @pre Priority deque contains one or more elements. +// @see minimum, pop_maximum +// +// @remark Complexity: O(1) +*/ +template +inline typename priority_deque::const_reference + priority_deque::maximum (void) const +{ + BOOST_CONTAINER_PRIORITY_DEQUE_ASSERT(!empty(), + "Empty priority deque has no maximal element. Reference undefined."); + const_iterator it = sequence_.begin() + 1; + return (it == sequence_.end()) ? sequence_.front() : *it; +} +/** @return Const reference to a minimal element in the priority deque. +// @pre Priority deque contains one or more elements. +// @see maximum, pop_minimum +// +// @remark Complexity: O(1) +*/ +template +typename priority_deque::const_reference + priority_deque::minimum (void) const +{ + BOOST_CONTAINER_PRIORITY_DEQUE_ASSERT(!empty(), + "Empty priority deque has no minimal element. Reference undefined."); + return sequence_.front(); +} +//---------------------------Remove Maximum/Minimum----------------------------| +/** @pre Priority deque contains one or more elements. +// @post A maximal element has been removed from the priority deque. +// @post All iterators and references are invalidated. +// @see maximum, pop, pop_minimum +// +// @remark Complexity: O(log n) +*/ +template +void priority_deque::pop_minimum (void) { + BOOST_CONTAINER_PRIORITY_DEQUE_ASSERT(!empty(), + "Empty priority deque has no maximal element. Removal impossible."); + heap::pop_interval_heap_min(sequence_.begin(), sequence_.end(), compare_); + try { + sequence_.pop_back(); + } catch (...) { +// If pop_back has a strong guarantee, this will restore the heap. + heap::push_interval_heap(sequence_.begin(), sequence_.end(), compare_); + throw; + } +} +/** @pre Priority deque contains one or more elements. +// @post A minimal element has been removed from the priority deque. +// @post All iterators and references are invalidated. +// @see minimum, pop_maximum +// +// @remark Complexity: O(log n) +*/ +template +void priority_deque::pop_maximum (void) { + BOOST_CONTAINER_PRIORITY_DEQUE_ASSERT(!empty(), + "Empty priority deque has no minimal element. Removal undefined."); + heap::pop_interval_heap_max(sequence_.begin(), sequence_.end(), compare_); + try { + sequence_.pop_back(); + } catch (...) { +// If pop_back has a strong guarantee, this will restore the heap. + heap::push_interval_heap(sequence_.begin(), sequence_.end(), compare_); + throw; + } +} + +//--------------------------Whole-Deque Operations-----------------------------| +//-----------------------------------Merge-------------------------------------| +/** @param first,last Input iterators bounding the range [ @a first, @a last) +// @post Priority deque contains its original elements, and copies of those in +// the range. +// @post All iterators and references are invalidated. +// +// @remark Complexity: O(n) +// @remark Exception safety: Basic. +*/ +template +template +void priority_deque::merge (InputIterator first, InputIterator last) { + try { + sequence_.insert(sequence_.end(), first, last); + heap::make_interval_heap(sequence_.begin(), sequence_.end(), compare_); + } catch (...) { // Try to fix the problem. + heap::make_interval_heap(sequence_.begin(), sequence_.end(), compare_); + throw; + } +} + +//----------------------------Swap Specialization------------------------------| +/** @param other Priority deque with which to swap. +// @post Deque contains the elements from @a source, and @a source contains the +// elements from this deque. +// @post All iterators and references are invalidated. +// @note Sequence containers are required to have swap functions. +// @remark Complexity: O(1) +*/ +template +inline void priority_deque::swap (priority_deque& other) { + sequence_.swap(other.sequence_); +} + +/** @relates priority_deque +// @param deque1,deque2 Priority deques. +// @post @a deque1 contains the elements originally in @a deque2, and @a deque2 +// contains the elements originally in @a deque1 +// @post All iterators and references are invalidated. +// +// @remark Complexity: O(1) +*/ +template +inline void swap (priority_deque& deque1, + priority_deque& deque2) +{ + deque1.swap(deque2); +} + +//---------------------------Random-Access Mutators----------------------------| +/** @param random_it A valid iterator in the range [begin, end). +// @param value The new value. +// @pre Priority deque contains one or more elements. +// @post The element at @a random_it is set to @a value. +// @post All iterators and references are invalidated. +// @see erase +// +// Elements within the deque may be unordered. +// @remark Complexity: O(log n) +// @remark Exception safety: Basic. Exceptions won't lose elements, but may +// corrupt the heap. +*/ +template +void priority_deque::update (const_iterator random_it, + const value_type& value) +{ + const difference_type index = random_it - begin(); + BOOST_CONTAINER_PRIORITY_DEQUE_ASSERT((0 <= index) && + (index < end() - begin()), "Iterator out of bounds; can't set element."); +// Providing the strong guarantee would require saving a copy. + *(sequence_.begin() + index) = value; + heap::update_interval_heap(sequence_.begin(),sequence_.end(),index,compare_); +} +#if (__cplusplus >= 201103L) +template +void priority_deque::update (const_iterator random_it, + value_type&& value) +{ + const difference_type index = random_it - begin(); + BOOST_CONTAINER_PRIORITY_DEQUE_ASSERT((0 <= index) && + (index < end() - begin()), "Iterator out of bounds; can't set element."); +// Providing the strong guarantee would require saving a copy. + *(sequence_.begin() + index) = std::move(value); + heap::update_interval_heap(sequence_.begin(),sequence_.end(),index,compare_); +} +#endif + +/** @param random_it An iterator in the range [begin, end) +// @pre Priority deque contains one or more elements. +// @post The deque no longer contains the element previously at @a random_it. +// @post All iterators and references are invalidated. +// @see set +// @remark Complexity: O(log n) +*/ +template +void priority_deque::erase (const_iterator random_it) { + const difference_type index = random_it - begin(); + BOOST_CONTAINER_PRIORITY_DEQUE_ASSERT((0 <= index) && + (index < end() - begin()), "Iterator out of bounds; can't erase element."); + heap::pop_interval_heap(sequence_.begin(), sequence_.end(),index,compare_); + try { + sequence_.pop_back(); + } catch (...) { +// If pop_back has the strong guarantee, this will re-make the interval heap. + heap::push_interval_heap(sequence_.begin(), sequence_.end(), compare_); + throw; + } +} + +} // Namespace boost::container +} // Namespace boost + +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/priority_deque_verify.hpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/priority_deque_verify.hpp new file mode 100644 index 0000000000000000000000000000000000000000..7add86f45f7b08241ca509d2c9d74e2c6cf51a72 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/priority-deque/priority_deque_verify.hpp @@ -0,0 +1,20 @@ +#ifndef PRIORITY_DEQUE_VERIFY_HPP_ +#define PRIORITY_DEQUE_VERIFY_HPP_ + +#include "priority_deque.hpp" +#include "interval_heap.hpp" + +// Thouroughly checks a priority deque for heap corruption and returns the +// first instance of corruption (or the end iterator if there is none). +// Note: Assumes comparison object is default-constructed. +template +typename boost::container::priority_deque::const_iterator + is_valid_until (const boost::container::priority_deque& pd) +{ + C compare; + return boost::heap::is_interval_heap_until(pd.begin(), pd.end(), compare); +} + + + +#endif // PRIORITY_DEQUE_VERIFY_HPP_ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/adler32.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/adler32.c new file mode 100644 index 0000000000000000000000000000000000000000..a868f073d8a0e35dcb3ec812b41b1d3f0acdd84d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/adler32.c @@ -0,0 +1,179 @@ +/* adler32.c -- compute the Adler-32 checksum of a data stream + * Copyright (C) 1995-2011 Mark Adler + * For conditions of distribution and use, see copyright notice in zlib.h + */ + +/* @(#) $Id$ */ + +#include "zutil.h" + +#define local static + +local uLong adler32_combine_ OF((uLong adler1, uLong adler2, z_off64_t len2)); + +#define BASE 65521 /* largest prime smaller than 65536 */ +#define NMAX 5552 +/* NMAX is the largest n such that 255n(n+1)/2 + (n+1)(BASE-1) <= 2^32-1 */ + +#define DO1(buf,i) {adler += (buf)[i]; sum2 += adler;} +#define DO2(buf,i) DO1(buf,i); DO1(buf,i+1); +#define DO4(buf,i) DO2(buf,i); DO2(buf,i+2); +#define DO8(buf,i) DO4(buf,i); DO4(buf,i+4); +#define DO16(buf) DO8(buf,0); DO8(buf,8); + +/* use NO_DIVIDE if your processor does not do division in hardware -- + try it both ways to see which is faster */ +#ifdef NO_DIVIDE +/* note that this assumes BASE is 65521, where 65536 % 65521 == 15 + (thank you to John Reiser for pointing this out) */ +# define CHOP(a) \ + do { \ + unsigned long tmp = a >> 16; \ + a &= 0xffffUL; \ + a += (tmp << 4) - tmp; \ + } while (0) +# define MOD28(a) \ + do { \ + CHOP(a); \ + if (a >= BASE) a -= BASE; \ + } while (0) +# define MOD(a) \ + do { \ + CHOP(a); \ + MOD28(a); \ + } while (0) +# define MOD63(a) \ + do { /* this assumes a is not negative */ \ + z_off64_t tmp = a >> 32; \ + a &= 0xffffffffL; \ + a += (tmp << 8) - (tmp << 5) + tmp; \ + tmp = a >> 16; \ + a &= 0xffffL; \ + a += (tmp << 4) - tmp; \ + tmp = a >> 16; \ + a &= 0xffffL; \ + a += (tmp << 4) - tmp; \ + if (a >= BASE) a -= BASE; \ + } while (0) +#else +# define MOD(a) a %= BASE +# define MOD28(a) a %= BASE +# define MOD63(a) a %= BASE +#endif + +/* ========================================================================= */ +uLong ZEXPORT adler32(adler, buf, len) + uLong adler; + const Bytef *buf; + uInt len; +{ + unsigned long sum2; + unsigned n; + + /* split Adler-32 into component sums */ + sum2 = (adler >> 16) & 0xffff; + adler &= 0xffff; + + /* in case user likes doing a byte at a time, keep it fast */ + if (len == 1) { + adler += buf[0]; + if (adler >= BASE) + adler -= BASE; + sum2 += adler; + if (sum2 >= BASE) + sum2 -= BASE; + return adler | (sum2 << 16); + } + + /* initial Adler-32 value (deferred check for len == 1 speed) */ + if (buf == Z_NULL) + return 1L; + + /* in case short lengths are provided, keep it somewhat fast */ + if (len < 16) { + while (len--) { + adler += *buf++; + sum2 += adler; + } + if (adler >= BASE) + adler -= BASE; + MOD28(sum2); /* only added so many BASE's */ + return adler | (sum2 << 16); + } + + /* do length NMAX blocks -- requires just one modulo operation */ + while (len >= NMAX) { + len -= NMAX; + n = NMAX / 16; /* NMAX is divisible by 16 */ + do { + DO16(buf); /* 16 sums unrolled */ + buf += 16; + } while (--n); + MOD(adler); + MOD(sum2); + } + + /* do remaining bytes (less than NMAX, still just one modulo) */ + if (len) { /* avoid modulos if none remaining */ + while (len >= 16) { + len -= 16; + DO16(buf); + buf += 16; + } + while (len--) { + adler += *buf++; + sum2 += adler; + } + MOD(adler); + MOD(sum2); + } + + /* return recombined sums */ + return adler | (sum2 << 16); +} + +/* ========================================================================= */ +local uLong adler32_combine_(adler1, adler2, len2) + uLong adler1; + uLong adler2; + z_off64_t len2; +{ + unsigned long sum1; + unsigned long sum2; + unsigned rem; + + /* for negative len, return invalid adler32 as a clue for debugging */ + if (len2 < 0) + return 0xffffffffUL; + + /* the derivation of this formula is left as an exercise for the reader */ + MOD63(len2); /* assumes len2 >= 0 */ + rem = (unsigned)len2; + sum1 = adler1 & 0xffff; + sum2 = rem * sum1; + MOD(sum2); + sum1 += (adler2 & 0xffff) + BASE - 1; + sum2 += ((adler1 >> 16) & 0xffff) + ((adler2 >> 16) & 0xffff) + BASE - rem; + if (sum1 >= BASE) sum1 -= BASE; + if (sum1 >= BASE) sum1 -= BASE; + if (sum2 >= (BASE << 1)) sum2 -= (BASE << 1); + if (sum2 >= BASE) sum2 -= BASE; + return sum1 | (sum2 << 16); +} + +/* ========================================================================= */ +uLong ZEXPORT adler32_combine(adler1, adler2, len2) + uLong adler1; + uLong adler2; + z_off_t len2; +{ + return adler32_combine_(adler1, adler2, len2); +} + +uLong ZEXPORT adler32_combine64(adler1, adler2, len2) + uLong adler1; + uLong adler2; + z_off64_t len2; +{ + return adler32_combine_(adler1, adler2, len2); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/crc32.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/crc32.h new file mode 100644 index 0000000000000000000000000000000000000000..9e0c7781025148380d130d6f7b6e590117ad3a8c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/crc32.h @@ -0,0 +1,441 @@ +/* crc32.h -- tables for rapid CRC calculation + * Generated automatically by crc32.c + */ + +local const z_crc_t FAR crc_table[TBLS][256] = +{ + { + 0x00000000UL, 0x77073096UL, 0xee0e612cUL, 0x990951baUL, 0x076dc419UL, + 0x706af48fUL, 0xe963a535UL, 0x9e6495a3UL, 0x0edb8832UL, 0x79dcb8a4UL, + 0xe0d5e91eUL, 0x97d2d988UL, 0x09b64c2bUL, 0x7eb17cbdUL, 0xe7b82d07UL, + 0x90bf1d91UL, 0x1db71064UL, 0x6ab020f2UL, 0xf3b97148UL, 0x84be41deUL, + 0x1adad47dUL, 0x6ddde4ebUL, 0xf4d4b551UL, 0x83d385c7UL, 0x136c9856UL, + 0x646ba8c0UL, 0xfd62f97aUL, 0x8a65c9ecUL, 0x14015c4fUL, 0x63066cd9UL, + 0xfa0f3d63UL, 0x8d080df5UL, 0x3b6e20c8UL, 0x4c69105eUL, 0xd56041e4UL, + 0xa2677172UL, 0x3c03e4d1UL, 0x4b04d447UL, 0xd20d85fdUL, 0xa50ab56bUL, + 0x35b5a8faUL, 0x42b2986cUL, 0xdbbbc9d6UL, 0xacbcf940UL, 0x32d86ce3UL, + 0x45df5c75UL, 0xdcd60dcfUL, 0xabd13d59UL, 0x26d930acUL, 0x51de003aUL, + 0xc8d75180UL, 0xbfd06116UL, 0x21b4f4b5UL, 0x56b3c423UL, 0xcfba9599UL, + 0xb8bda50fUL, 0x2802b89eUL, 0x5f058808UL, 0xc60cd9b2UL, 0xb10be924UL, + 0x2f6f7c87UL, 0x58684c11UL, 0xc1611dabUL, 0xb6662d3dUL, 0x76dc4190UL, + 0x01db7106UL, 0x98d220bcUL, 0xefd5102aUL, 0x71b18589UL, 0x06b6b51fUL, + 0x9fbfe4a5UL, 0xe8b8d433UL, 0x7807c9a2UL, 0x0f00f934UL, 0x9609a88eUL, + 0xe10e9818UL, 0x7f6a0dbbUL, 0x086d3d2dUL, 0x91646c97UL, 0xe6635c01UL, + 0x6b6b51f4UL, 0x1c6c6162UL, 0x856530d8UL, 0xf262004eUL, 0x6c0695edUL, + 0x1b01a57bUL, 0x8208f4c1UL, 0xf50fc457UL, 0x65b0d9c6UL, 0x12b7e950UL, + 0x8bbeb8eaUL, 0xfcb9887cUL, 0x62dd1ddfUL, 0x15da2d49UL, 0x8cd37cf3UL, + 0xfbd44c65UL, 0x4db26158UL, 0x3ab551ceUL, 0xa3bc0074UL, 0xd4bb30e2UL, + 0x4adfa541UL, 0x3dd895d7UL, 0xa4d1c46dUL, 0xd3d6f4fbUL, 0x4369e96aUL, + 0x346ed9fcUL, 0xad678846UL, 0xda60b8d0UL, 0x44042d73UL, 0x33031de5UL, + 0xaa0a4c5fUL, 0xdd0d7cc9UL, 0x5005713cUL, 0x270241aaUL, 0xbe0b1010UL, + 0xc90c2086UL, 0x5768b525UL, 0x206f85b3UL, 0xb966d409UL, 0xce61e49fUL, + 0x5edef90eUL, 0x29d9c998UL, 0xb0d09822UL, 0xc7d7a8b4UL, 0x59b33d17UL, + 0x2eb40d81UL, 0xb7bd5c3bUL, 0xc0ba6cadUL, 0xedb88320UL, 0x9abfb3b6UL, + 0x03b6e20cUL, 0x74b1d29aUL, 0xead54739UL, 0x9dd277afUL, 0x04db2615UL, + 0x73dc1683UL, 0xe3630b12UL, 0x94643b84UL, 0x0d6d6a3eUL, 0x7a6a5aa8UL, + 0xe40ecf0bUL, 0x9309ff9dUL, 0x0a00ae27UL, 0x7d079eb1UL, 0xf00f9344UL, + 0x8708a3d2UL, 0x1e01f268UL, 0x6906c2feUL, 0xf762575dUL, 0x806567cbUL, + 0x196c3671UL, 0x6e6b06e7UL, 0xfed41b76UL, 0x89d32be0UL, 0x10da7a5aUL, + 0x67dd4accUL, 0xf9b9df6fUL, 0x8ebeeff9UL, 0x17b7be43UL, 0x60b08ed5UL, + 0xd6d6a3e8UL, 0xa1d1937eUL, 0x38d8c2c4UL, 0x4fdff252UL, 0xd1bb67f1UL, + 0xa6bc5767UL, 0x3fb506ddUL, 0x48b2364bUL, 0xd80d2bdaUL, 0xaf0a1b4cUL, + 0x36034af6UL, 0x41047a60UL, 0xdf60efc3UL, 0xa867df55UL, 0x316e8eefUL, + 0x4669be79UL, 0xcb61b38cUL, 0xbc66831aUL, 0x256fd2a0UL, 0x5268e236UL, + 0xcc0c7795UL, 0xbb0b4703UL, 0x220216b9UL, 0x5505262fUL, 0xc5ba3bbeUL, + 0xb2bd0b28UL, 0x2bb45a92UL, 0x5cb36a04UL, 0xc2d7ffa7UL, 0xb5d0cf31UL, + 0x2cd99e8bUL, 0x5bdeae1dUL, 0x9b64c2b0UL, 0xec63f226UL, 0x756aa39cUL, + 0x026d930aUL, 0x9c0906a9UL, 0xeb0e363fUL, 0x72076785UL, 0x05005713UL, + 0x95bf4a82UL, 0xe2b87a14UL, 0x7bb12baeUL, 0x0cb61b38UL, 0x92d28e9bUL, + 0xe5d5be0dUL, 0x7cdcefb7UL, 0x0bdbdf21UL, 0x86d3d2d4UL, 0xf1d4e242UL, + 0x68ddb3f8UL, 0x1fda836eUL, 0x81be16cdUL, 0xf6b9265bUL, 0x6fb077e1UL, + 0x18b74777UL, 0x88085ae6UL, 0xff0f6a70UL, 0x66063bcaUL, 0x11010b5cUL, + 0x8f659effUL, 0xf862ae69UL, 0x616bffd3UL, 0x166ccf45UL, 0xa00ae278UL, + 0xd70dd2eeUL, 0x4e048354UL, 0x3903b3c2UL, 0xa7672661UL, 0xd06016f7UL, + 0x4969474dUL, 0x3e6e77dbUL, 0xaed16a4aUL, 0xd9d65adcUL, 0x40df0b66UL, + 0x37d83bf0UL, 0xa9bcae53UL, 0xdebb9ec5UL, 0x47b2cf7fUL, 0x30b5ffe9UL, + 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0xb523c688UL, 0x88649a83UL, 0xbf0e5882UL, 0xe6b01e80UL, 0xd1dadc81UL, + 0x54cc9384UL, 0x63a65185UL, 0x3a181787UL, 0x0d72d586UL, 0xa0d0e2a9UL, + 0x97ba20a8UL, 0xce0466aaUL, 0xf96ea4abUL, 0x7c78ebaeUL, 0x4b1229afUL, + 0x12ac6fadUL, 0x25c6adacUL, 0x1881f1a7UL, 0x2feb33a6UL, 0x765575a4UL, + 0x413fb7a5UL, 0xc429f8a0UL, 0xf3433aa1UL, 0xaafd7ca3UL, 0x9d97bea2UL, + 0xd073c4b5UL, 0xe71906b4UL, 0xbea740b6UL, 0x89cd82b7UL, 0x0cdbcdb2UL, + 0x3bb10fb3UL, 0x620f49b1UL, 0x55658bb0UL, 0x6822d7bbUL, 0x5f4815baUL, + 0x06f653b8UL, 0x319c91b9UL, 0xb48adebcUL, 0x83e01cbdUL, 0xda5e5abfUL, + 0xed3498beUL + }, + { + 0x00000000UL, 0x6567bcb8UL, 0x8bc809aaUL, 0xeeafb512UL, 0x5797628fUL, + 0x32f0de37UL, 0xdc5f6b25UL, 0xb938d79dUL, 0xef28b4c5UL, 0x8a4f087dUL, + 0x64e0bd6fUL, 0x018701d7UL, 0xb8bfd64aUL, 0xddd86af2UL, 0x3377dfe0UL, + 0x56106358UL, 0x9f571950UL, 0xfa30a5e8UL, 0x149f10faUL, 0x71f8ac42UL, + 0xc8c07bdfUL, 0xada7c767UL, 0x43087275UL, 0x266fcecdUL, 0x707fad95UL, + 0x1518112dUL, 0xfbb7a43fUL, 0x9ed01887UL, 0x27e8cf1aUL, 0x428f73a2UL, + 0xac20c6b0UL, 0xc9477a08UL, 0x3eaf32a0UL, 0x5bc88e18UL, 0xb5673b0aUL, + 0xd00087b2UL, 0x6938502fUL, 0x0c5fec97UL, 0xe2f05985UL, 0x8797e53dUL, + 0xd1878665UL, 0xb4e03addUL, 0x5a4f8fcfUL, 0x3f283377UL, 0x8610e4eaUL, + 0xe3775852UL, 0x0dd8ed40UL, 0x68bf51f8UL, 0xa1f82bf0UL, 0xc49f9748UL, + 0x2a30225aUL, 0x4f579ee2UL, 0xf66f497fUL, 0x9308f5c7UL, 0x7da740d5UL, + 0x18c0fc6dUL, 0x4ed09f35UL, 0x2bb7238dUL, 0xc518969fUL, 0xa07f2a27UL, + 0x1947fdbaUL, 0x7c204102UL, 0x928ff410UL, 0xf7e848a8UL, 0x3d58149bUL, + 0x583fa823UL, 0xb6901d31UL, 0xd3f7a189UL, 0x6acf7614UL, 0x0fa8caacUL, + 0xe1077fbeUL, 0x8460c306UL, 0xd270a05eUL, 0xb7171ce6UL, 0x59b8a9f4UL, + 0x3cdf154cUL, 0x85e7c2d1UL, 0xe0807e69UL, 0x0e2fcb7bUL, 0x6b4877c3UL, + 0xa20f0dcbUL, 0xc768b173UL, 0x29c70461UL, 0x4ca0b8d9UL, 0xf5986f44UL, + 0x90ffd3fcUL, 0x7e5066eeUL, 0x1b37da56UL, 0x4d27b90eUL, 0x284005b6UL, + 0xc6efb0a4UL, 0xa3880c1cUL, 0x1ab0db81UL, 0x7fd76739UL, 0x9178d22bUL, + 0xf41f6e93UL, 0x03f7263bUL, 0x66909a83UL, 0x883f2f91UL, 0xed589329UL, + 0x546044b4UL, 0x3107f80cUL, 0xdfa84d1eUL, 0xbacff1a6UL, 0xecdf92feUL, + 0x89b82e46UL, 0x67179b54UL, 0x027027ecUL, 0xbb48f071UL, 0xde2f4cc9UL, + 0x3080f9dbUL, 0x55e74563UL, 0x9ca03f6bUL, 0xf9c783d3UL, 0x176836c1UL, + 0x720f8a79UL, 0xcb375de4UL, 0xae50e15cUL, 0x40ff544eUL, 0x2598e8f6UL, + 0x73888baeUL, 0x16ef3716UL, 0xf8408204UL, 0x9d273ebcUL, 0x241fe921UL, + 0x41785599UL, 0xafd7e08bUL, 0xcab05c33UL, 0x3bb659edUL, 0x5ed1e555UL, + 0xb07e5047UL, 0xd519ecffUL, 0x6c213b62UL, 0x094687daUL, 0xe7e932c8UL, + 0x828e8e70UL, 0xd49eed28UL, 0xb1f95190UL, 0x5f56e482UL, 0x3a31583aUL, + 0x83098fa7UL, 0xe66e331fUL, 0x08c1860dUL, 0x6da63ab5UL, 0xa4e140bdUL, + 0xc186fc05UL, 0x2f294917UL, 0x4a4ef5afUL, 0xf3762232UL, 0x96119e8aUL, + 0x78be2b98UL, 0x1dd99720UL, 0x4bc9f478UL, 0x2eae48c0UL, 0xc001fdd2UL, + 0xa566416aUL, 0x1c5e96f7UL, 0x79392a4fUL, 0x97969f5dUL, 0xf2f123e5UL, + 0x05196b4dUL, 0x607ed7f5UL, 0x8ed162e7UL, 0xebb6de5fUL, 0x528e09c2UL, + 0x37e9b57aUL, 0xd9460068UL, 0xbc21bcd0UL, 0xea31df88UL, 0x8f566330UL, + 0x61f9d622UL, 0x049e6a9aUL, 0xbda6bd07UL, 0xd8c101bfUL, 0x366eb4adUL, + 0x53090815UL, 0x9a4e721dUL, 0xff29cea5UL, 0x11867bb7UL, 0x74e1c70fUL, + 0xcdd91092UL, 0xa8beac2aUL, 0x46111938UL, 0x2376a580UL, 0x7566c6d8UL, + 0x10017a60UL, 0xfeaecf72UL, 0x9bc973caUL, 0x22f1a457UL, 0x479618efUL, + 0xa939adfdUL, 0xcc5e1145UL, 0x06ee4d76UL, 0x6389f1ceUL, 0x8d2644dcUL, + 0xe841f864UL, 0x51792ff9UL, 0x341e9341UL, 0xdab12653UL, 0xbfd69aebUL, + 0xe9c6f9b3UL, 0x8ca1450bUL, 0x620ef019UL, 0x07694ca1UL, 0xbe519b3cUL, + 0xdb362784UL, 0x35999296UL, 0x50fe2e2eUL, 0x99b95426UL, 0xfcdee89eUL, + 0x12715d8cUL, 0x7716e134UL, 0xce2e36a9UL, 0xab498a11UL, 0x45e63f03UL, + 0x208183bbUL, 0x7691e0e3UL, 0x13f65c5bUL, 0xfd59e949UL, 0x983e55f1UL, + 0x2106826cUL, 0x44613ed4UL, 0xaace8bc6UL, 0xcfa9377eUL, 0x38417fd6UL, + 0x5d26c36eUL, 0xb389767cUL, 0xd6eecac4UL, 0x6fd61d59UL, 0x0ab1a1e1UL, + 0xe41e14f3UL, 0x8179a84bUL, 0xd769cb13UL, 0xb20e77abUL, 0x5ca1c2b9UL, + 0x39c67e01UL, 0x80fea99cUL, 0xe5991524UL, 0x0b36a036UL, 0x6e511c8eUL, + 0xa7166686UL, 0xc271da3eUL, 0x2cde6f2cUL, 0x49b9d394UL, 0xf0810409UL, + 0x95e6b8b1UL, 0x7b490da3UL, 0x1e2eb11bUL, 0x483ed243UL, 0x2d596efbUL, + 0xc3f6dbe9UL, 0xa6916751UL, 0x1fa9b0ccUL, 0x7ace0c74UL, 0x9461b966UL, + 0xf10605deUL +#endif + } +}; diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/inflate.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/inflate.h new file mode 100644 index 0000000000000000000000000000000000000000..95f4986d400223bad542e5b34a7e6284a039425e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/inflate.h @@ -0,0 +1,122 @@ +/* inflate.h -- internal inflate state definition + * Copyright (C) 1995-2009 Mark Adler + * For conditions of distribution and use, see copyright notice in zlib.h + */ + +/* WARNING: this file should *not* be used by applications. It is + part of the implementation of the compression library and is + subject to change. Applications should only use zlib.h. + */ + +/* define NO_GZIP when compiling if you want to disable gzip header and + trailer decoding by inflate(). NO_GZIP would be used to avoid linking in + the crc code when it is not needed. For shared libraries, gzip decoding + should be left enabled. */ +#ifndef NO_GZIP +# define GUNZIP +#endif + +/* Possible inflate modes between inflate() calls */ +typedef enum { + HEAD, /* i: waiting for magic header */ + FLAGS, /* i: waiting for method and flags (gzip) */ + TIME, /* i: waiting for modification time (gzip) */ + OS, /* i: waiting for extra flags and operating system (gzip) */ + EXLEN, /* i: waiting for extra length (gzip) */ + EXTRA, /* i: waiting for extra bytes (gzip) */ + NAME, /* i: waiting for end of file name (gzip) */ + COMMENT, /* i: waiting for end of comment (gzip) */ + HCRC, /* i: waiting for header crc (gzip) */ + DICTID, /* i: waiting for dictionary check value */ + DICT, /* waiting for inflateSetDictionary() call */ + TYPE, /* i: waiting for type bits, including last-flag bit */ + TYPEDO, /* i: same, but skip check to exit inflate on new block */ + STORED, /* i: waiting for stored size (length and complement) */ + COPY_, /* i/o: same as COPY below, but only first time in */ + COPY, /* i/o: waiting for input or output to copy stored block */ + TABLE, /* i: waiting for dynamic block table lengths */ + LENLENS, /* i: waiting for code length code lengths */ + CODELENS, /* i: waiting for length/lit and distance code lengths */ + LEN_, /* i: same as LEN below, but only first time in */ + LEN, /* i: waiting for length/lit/eob code */ + LENEXT, /* i: waiting for length extra bits */ + DIST, /* i: waiting for distance code */ + DISTEXT, /* i: waiting for distance extra bits */ + MATCH, /* o: waiting for output space to copy string */ + LIT, /* o: waiting for output space to write literal */ + CHECK, /* i: waiting for 32-bit check value */ + LENGTH, /* i: waiting for 32-bit length (gzip) */ + DONE, /* finished check, done -- remain here until reset */ + BAD, /* got a data error -- remain here until reset */ + MEM, /* got an inflate() memory error -- remain here until reset */ + SYNC /* looking for synchronization bytes to restart inflate() */ +} inflate_mode; + +/* + State transitions between above modes - + + (most modes can go to BAD or MEM on error -- not shown for clarity) + + Process header: + HEAD -> (gzip) or (zlib) or (raw) + (gzip) -> FLAGS -> TIME -> OS -> EXLEN -> EXTRA -> NAME -> COMMENT -> + HCRC -> TYPE + (zlib) -> DICTID or TYPE + DICTID -> DICT -> TYPE + (raw) -> TYPEDO + Read deflate blocks: + TYPE -> TYPEDO -> STORED or TABLE or LEN_ or CHECK + STORED -> COPY_ -> COPY -> TYPE + TABLE -> LENLENS -> CODELENS -> LEN_ + LEN_ -> LEN + Read deflate codes in fixed or dynamic block: + LEN -> LENEXT or LIT or TYPE + LENEXT -> DIST -> DISTEXT -> MATCH -> LEN + LIT -> LEN + Process trailer: + CHECK -> LENGTH -> DONE + */ + +/* state maintained between inflate() calls. Approximately 10K bytes. */ +struct inflate_state { + inflate_mode mode; /* current inflate mode */ + int last; /* true if processing last block */ + int wrap; /* bit 0 true for zlib, bit 1 true for gzip */ + int havedict; /* true if dictionary provided */ + int flags; /* gzip header method and flags (0 if zlib) */ + unsigned dmax; /* zlib header max distance (INFLATE_STRICT) */ + unsigned long check; /* protected copy of check value */ + unsigned long total; /* protected copy of output count */ + gz_headerp head; /* where to save gzip header information */ + /* sliding window */ + unsigned wbits; /* log base 2 of requested window size */ + unsigned wsize; /* window size or zero if not using window */ + unsigned whave; /* valid bytes in the window */ + unsigned wnext; /* window write index */ + unsigned char FAR *window; /* allocated sliding window, if needed */ + /* bit accumulator */ + unsigned long hold; /* input bit accumulator */ + unsigned bits; /* number of bits in "in" */ + /* for string and stored block copying */ + unsigned length; /* literal or length of data to copy */ + unsigned offset; /* distance back to copy string from */ + /* for table and code decoding */ + unsigned extra; /* extra bits needed */ + /* fixed and dynamic code tables */ + code const FAR *lencode; /* starting table for length/literal codes */ + code const FAR *distcode; /* starting table for distance codes */ + unsigned lenbits; /* index bits for lencode */ + unsigned distbits; /* index bits for distcode */ + /* dynamic table building */ + unsigned ncode; /* number of code length code lengths */ + unsigned nlen; /* number of length code lengths */ + unsigned ndist; /* number of distance code lengths */ + unsigned have; /* number of code lengths in lens[] */ + code FAR *next; /* next available space in codes[] */ + unsigned short lens[320]; /* temporary storage for code lengths */ + unsigned short work[288]; /* work area for code table building */ + code codes[ENOUGH]; /* space for code tables */ + int sane; /* if false, allow invalid distance too far */ + int back; /* bits back of last unprocessed length/lit */ + unsigned was; /* initial length of match */ +}; diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/uncompr.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/uncompr.c new file mode 100644 index 0000000000000000000000000000000000000000..ad98be3a5d88afd479d3442cd234747ca259c60d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/uncompr.c @@ -0,0 +1,59 @@ +/* uncompr.c -- decompress a memory buffer + * Copyright (C) 1995-2003, 2010 Jean-loup Gailly. + * For conditions of distribution and use, see copyright notice in zlib.h + */ + +/* @(#) $Id$ */ + +#define ZLIB_INTERNAL +#include "zlib.h" + +/* =========================================================================== + Decompresses the source buffer into the destination buffer. sourceLen is + the byte length of the source buffer. Upon entry, destLen is the total + size of the destination buffer, which must be large enough to hold the + entire uncompressed data. (The size of the uncompressed data must have + been saved previously by the compressor and transmitted to the decompressor + by some mechanism outside the scope of this compression library.) + Upon exit, destLen is the actual size of the compressed buffer. + + uncompress returns Z_OK if success, Z_MEM_ERROR if there was not + enough memory, Z_BUF_ERROR if there was not enough room in the output + buffer, or Z_DATA_ERROR if the input data was corrupted. +*/ +int ZEXPORT uncompress (dest, destLen, source, sourceLen) + Bytef *dest; + uLongf *destLen; + const Bytef *source; + uLong sourceLen; +{ + z_stream stream; + int err; + + stream.next_in = (Bytef*)source; + stream.avail_in = (uInt)sourceLen; + /* Check for source > 64K on 16-bit machine: */ + if ((uLong)stream.avail_in != sourceLen) return Z_BUF_ERROR; + + stream.next_out = dest; + stream.avail_out = (uInt)*destLen; + if ((uLong)stream.avail_out != *destLen) return Z_BUF_ERROR; + + stream.zalloc = (alloc_func)0; + stream.zfree = (free_func)0; + + err = inflateInit(&stream); + if (err != Z_OK) return err; + + err = inflate(&stream, Z_FINISH); + if (err != Z_STREAM_END) { + inflateEnd(&stream); + if (err == Z_NEED_DICT || (err == Z_BUF_ERROR && stream.avail_in == 0)) + return Z_DATA_ERROR; + return err; + } + *destLen = stream.total_out; + + err = inflateEnd(&stream); + return err; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/zlib.3.pdf b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/zlib.3.pdf new file mode 100644 index 0000000000000000000000000000000000000000..485306cda8d604d1c96f67ce73885263d053d921 Binary files /dev/null and b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/zlib.3.pdf differ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/zlib.pc.in b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/zlib.pc.in new file mode 100644 index 0000000000000000000000000000000000000000..7e5acf9c77e7749e710a8960de27d8eff7d94786 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/zlib.pc.in @@ -0,0 +1,13 @@ +prefix=@prefix@ +exec_prefix=@exec_prefix@ +libdir=@libdir@ +sharedlibdir=@sharedlibdir@ +includedir=@includedir@ + +Name: zlib +Description: zlib compression library +Version: @VERSION@ + +Requires: +Libs: -L${libdir} -L${sharedlibdir} -lz +Cflags: -I${includedir} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/zlib2ansi b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/zlib2ansi new file mode 100644 index 0000000000000000000000000000000000000000..15e3e165f37decb7c403a892438650de80f3b928 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/zlib2ansi @@ -0,0 +1,152 @@ +#!/usr/bin/perl + +# Transform K&R C function definitions into ANSI equivalent. +# +# Author: Paul Marquess +# Version: 1.0 +# Date: 3 October 2006 + +# TODO +# +# Asumes no function pointer parameters. unless they are typedefed. +# Assumes no literal strings that look like function definitions +# Assumes functions start at the beginning of a line + +use strict; +use warnings; + +local $/; +$_ = <>; + +my $sp = qr{ \s* (?: /\* .*? \*/ )? \s* }x; # assume no nested comments + +my $d1 = qr{ $sp (?: [\w\*\s]+ $sp)* $sp \w+ $sp [\[\]\s]* $sp }x ; +my $decl = qr{ $sp (?: \w+ $sp )+ $d1 }xo ; +my $dList = qr{ $sp $decl (?: $sp , $d1 )* $sp ; $sp }xo ; + + +while (s/^ + ( # Start $1 + ( # Start $2 + .*? # Minimal eat content + ( ^ \w [\w\s\*]+ ) # $3 -- function name + \s* # optional whitespace + ) # $2 - Matched up to before parameter list + + \( \s* # Literal "(" + optional whitespace + ( [^\)]+ ) # $4 - one or more anythings except ")" + \s* \) # optional whitespace surrounding a Literal ")" + + ( (?: $dList )+ ) # $5 + + $sp ^ { # literal "{" at start of line + ) # Remember to $1 + //xsom + ) +{ + my $all = $1 ; + my $prefix = $2; + my $param_list = $4 ; + my $params = $5; + + StripComments($params); + StripComments($param_list); + $param_list =~ s/^\s+//; + $param_list =~ s/\s+$//; + + my $i = 0 ; + my %pList = map { $_ => $i++ } + split /\s*,\s*/, $param_list; + my $pMatch = '(\b' . join('|', keys %pList) . '\b)\W*$' ; + + my @params = split /\s*;\s*/, $params; + my @outParams = (); + foreach my $p (@params) + { + if ($p =~ /,/) + { + my @bits = split /\s*,\s*/, $p; + my $first = shift @bits; + $first =~ s/^\s*//; + push @outParams, $first; + $first =~ /^(\w+\s*)/; + my $type = $1 ; + push @outParams, map { $type . $_ } @bits; + } + else + { + $p =~ s/^\s+//; + push @outParams, $p; + } + } + + + my %tmp = map { /$pMatch/; $_ => $pList{$1} } + @outParams ; + + @outParams = map { " $_" } + sort { $tmp{$a} <=> $tmp{$b} } + @outParams ; + + print $prefix ; + print "(\n" . join(",\n", @outParams) . ")\n"; + print "{" ; + +} + +# Output any trailing code. +print ; +exit 0; + + +sub StripComments +{ + + no warnings; + + # Strip C & C++ coments + # From the perlfaq + $_[0] =~ + + s{ + /\* ## Start of /* ... */ comment + [^*]*\*+ ## Non-* followed by 1-or-more *'s + ( + [^/*][^*]*\*+ + )* ## 0-or-more things which don't start with / + ## but do end with '*' + / ## End of /* ... */ comment + + | ## OR C++ Comment + // ## Start of C++ comment // + [^\n]* ## followed by 0-or-more non end of line characters + + | ## OR various things which aren't comments: + + ( + " ## Start of " ... " string + ( + \\. ## Escaped char + | ## OR + [^"\\] ## Non "\ + )* + " ## End of " ... " string + + | ## OR + + ' ## Start of ' ... ' string + ( + \\. ## Escaped char + | ## OR + [^'\\] ## Non '\ + )* + ' ## End of ' ... ' string + + | ## OR + + . ## Anything other char + [^/"'\\]* ## Chars which doesn't start a comment, string or escape + ) + }{$2}gxs; + +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/zutil.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/zutil.h new file mode 100644 index 0000000000000000000000000000000000000000..4e3dcc6ae9f7ac4987e4ccdfe234a68c87c15780 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/contrib/zlib-1.2.7/zutil.h @@ -0,0 +1,252 @@ +/* zutil.h -- internal interface and configuration of the compression library + * Copyright (C) 1995-2012 Jean-loup Gailly. + * For conditions of distribution and use, see copyright notice in zlib.h + */ + +/* WARNING: this file should *not* be used by applications. It is + part of the implementation of the compression library and is + subject to change. Applications should only use zlib.h. + */ + +/* @(#) $Id$ */ + +#ifndef ZUTIL_H +#define ZUTIL_H + +#ifdef HAVE_HIDDEN +# define ZLIB_INTERNAL __attribute__((visibility ("hidden"))) +#else +# define ZLIB_INTERNAL +#endif + +#include "zlib.h" + +#if defined(STDC) && !defined(Z_SOLO) +# if !(defined(_WIN32_WCE) && defined(_MSC_VER)) +# include +# endif +# include +# include +#endif + +#ifdef Z_SOLO + typedef long ptrdiff_t; /* guess -- will be caught if guess is wrong */ +#endif + +#ifndef local +# define local static +#endif +/* compile with -Dlocal if your debugger can't find static symbols */ + +typedef unsigned char uch; +typedef uch FAR uchf; +typedef unsigned short ush; +typedef ush FAR ushf; +typedef unsigned long ulg; + +extern const char * const z_errmsg[10]; /* indexed by 2-zlib_error */ +/* (size given to avoid silly warnings with Visual C++) */ + +#define ERR_MSG(err) z_errmsg[Z_NEED_DICT-(err)] + +#define ERR_RETURN(strm,err) \ + return (strm->msg = (char*)ERR_MSG(err), (err)) +/* To be used only when the state is known to be valid */ + + /* common constants */ + +#ifndef DEF_WBITS +# define DEF_WBITS MAX_WBITS +#endif +/* default windowBits for decompression. MAX_WBITS is for compression only */ + +#if MAX_MEM_LEVEL >= 8 +# define DEF_MEM_LEVEL 8 +#else +# define DEF_MEM_LEVEL MAX_MEM_LEVEL +#endif +/* default memLevel */ + +#define STORED_BLOCK 0 +#define STATIC_TREES 1 +#define DYN_TREES 2 +/* The three kinds of block type */ + +#define MIN_MATCH 3 +#define MAX_MATCH 258 +/* The minimum and maximum match lengths */ + +#define PRESET_DICT 0x20 /* preset dictionary flag in zlib header */ + + /* target dependencies */ + +#if defined(MSDOS) || (defined(WINDOWS) && !defined(WIN32)) +# define OS_CODE 0x00 +# ifndef Z_SOLO +# if defined(__TURBOC__) || defined(__BORLANDC__) +# if (__STDC__ == 1) && (defined(__LARGE__) || defined(__COMPACT__)) + /* Allow compilation with ANSI keywords only enabled */ + void _Cdecl farfree( void *block ); + void *_Cdecl farmalloc( unsigned long nbytes ); +# else +# include +# endif +# else /* MSC or DJGPP */ +# include +# endif +# endif +#endif + +#ifdef AMIGA +# define OS_CODE 0x01 +#endif + +#if defined(VAXC) || defined(VMS) +# define OS_CODE 0x02 +# define F_OPEN(name, mode) \ + fopen((name), (mode), "mbc=60", "ctx=stm", "rfm=fix", "mrs=512") +#endif + +#if defined(ATARI) || defined(atarist) +# define OS_CODE 0x05 +#endif + +#ifdef OS2 +# define OS_CODE 0x06 +# if defined(M_I86) && !defined(Z_SOLO) +# include +# endif +#endif + +#if defined(MACOS) || defined(TARGET_OS_MAC) +# define OS_CODE 0x07 +# ifndef Z_SOLO +# if defined(__MWERKS__) && __dest_os != __be_os && __dest_os != __win32_os +# include /* for fdopen */ +# else +# ifndef fdopen +# define fdopen(fd,mode) NULL /* No fdopen() */ +# endif +# endif +# endif +#endif + +#ifdef TOPS20 +# define OS_CODE 0x0a +#endif + +#ifdef WIN32 +# ifndef __CYGWIN__ /* Cygwin is Unix, not Win32 */ +# define OS_CODE 0x0b +# endif +#endif + +#ifdef __50SERIES /* Prime/PRIMOS */ +# define OS_CODE 0x0f +#endif + +#if defined(_BEOS_) || defined(RISCOS) +# define fdopen(fd,mode) NULL /* No fdopen() */ +#endif + +#if (defined(_MSC_VER) && (_MSC_VER > 600)) && !defined __INTERIX +# if defined(_WIN32_WCE) +# define fdopen(fd,mode) NULL /* No fdopen() */ +# ifndef _PTRDIFF_T_DEFINED + typedef int ptrdiff_t; +# define _PTRDIFF_T_DEFINED +# endif +# else +# define fdopen(fd,type) _fdopen(fd,type) +# endif +#endif + +#if defined(__BORLANDC__) && !defined(MSDOS) + #pragma warn -8004 + #pragma warn -8008 + #pragma warn -8066 +#endif + +/* provide prototypes for these when building zlib without LFS */ +#if !defined(_WIN32) && (!defined(_LARGEFILE64_SOURCE) || _LFS64_LARGEFILE-0 == 0) + ZEXTERN uLong ZEXPORT adler32_combine64 OF((uLong, uLong, z_off_t)); + ZEXTERN uLong ZEXPORT crc32_combine64 OF((uLong, uLong, z_off_t)); +#endif + + /* common defaults */ + +#ifndef OS_CODE +# define OS_CODE 0x03 /* assume Unix */ +#endif + +#ifndef F_OPEN +# define F_OPEN(name, mode) fopen((name), (mode)) +#endif + + /* functions */ + +#if defined(pyr) || defined(Z_SOLO) +# define NO_MEMCPY +#endif +#if defined(SMALL_MEDIUM) && !defined(_MSC_VER) && !defined(__SC__) + /* Use our own functions for small and medium model with MSC <= 5.0. + * You may have to use the same strategy for Borland C (untested). + * The __SC__ check is for Symantec. + */ +# define NO_MEMCPY +#endif +#if defined(STDC) && !defined(HAVE_MEMCPY) && !defined(NO_MEMCPY) +# define HAVE_MEMCPY +#endif +#ifdef HAVE_MEMCPY +# ifdef SMALL_MEDIUM /* MSDOS small or medium model */ +# define zmemcpy _fmemcpy +# define zmemcmp _fmemcmp +# define zmemzero(dest, len) _fmemset(dest, 0, len) +# else +# define zmemcpy memcpy +# define zmemcmp memcmp +# define zmemzero(dest, len) memset(dest, 0, len) +# endif +#else + void ZLIB_INTERNAL zmemcpy OF((Bytef* dest, const Bytef* source, uInt len)); + int ZLIB_INTERNAL zmemcmp OF((const Bytef* s1, const Bytef* s2, uInt len)); + void ZLIB_INTERNAL zmemzero OF((Bytef* dest, uInt len)); +#endif + +/* Diagnostic functions */ +#ifdef DEBUG +# include + extern int ZLIB_INTERNAL z_verbose; + extern void ZLIB_INTERNAL z_error OF((char *m)); +# define Assert(cond,msg) {if(!(cond)) z_error(msg);} +# define Trace(x) {if (z_verbose>=0) fprintf x ;} +# define Tracev(x) {if (z_verbose>0) fprintf x ;} +# define Tracevv(x) {if (z_verbose>1) fprintf x ;} +# define Tracec(c,x) {if (z_verbose>0 && (c)) fprintf x ;} +# define Tracecv(c,x) {if (z_verbose>1 && (c)) fprintf x ;} +#else +# define Assert(cond,msg) +# define Trace(x) +# define Tracev(x) +# define Tracevv(x) +# define Tracec(c,x) +# define Tracecv(c,x) +#endif + +#ifndef Z_SOLO + voidpf ZLIB_INTERNAL zcalloc OF((voidpf opaque, unsigned items, + unsigned size)); + void ZLIB_INTERNAL zcfree OF((voidpf opaque, voidpf ptr)); +#endif + +#define ZALLOC(strm, items, size) \ + (*((strm)->zalloc))((strm)->opaque, (items), (size)) +#define ZFREE(strm, addr) (*((strm)->zfree))((strm)->opaque, (voidpf)(addr)) +#define TRY_FREE(s, p) {if (p) ZFREE(s, p);} + +/* Reverse the bytes in a 32-bit value */ +#define ZSWAP32(q) ((((q) >> 24) & 0xff) + (((q) >> 8) & 0xff00) + \ + (((q) & 0xff00) << 8) + (((q) & 0xff) << 24)) + +#endif /* ZUTIL_H */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/doxy/Doxyfile.bk b/methods/ring/utils/fast_gicp/thirdparty/nvbio/doxy/Doxyfile.bk new file mode 100644 index 0000000000000000000000000000000000000000..063f8a0b0a6b6434a1f1a47cbd822880ea257720 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/doxy/Doxyfile.bk @@ -0,0 +1,1803 @@ +# Doxyfile 1.7.5.1 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or sequence of words) that should +# identify the project. Note that if you do not use Doxywizard you need +# to put quotes around the project name if it contains spaces. + +PROJECT_NAME = NVBIO + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + +PROJECT_NUMBER = + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer +# a quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = + +# With the PROJECT_LOGO tag one can specify an logo or icon that is +# included in the documentation. The maximum height of the logo should not +# exceed 55 pixels and the maximum width should not exceed 200 pixels. +# Doxygen will copy the logo to the output directory. + +PROJECT_LOGO = + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + +OUTPUT_DIRECTORY = + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + +CREATE_SUBDIRS = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, +# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English +# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, +# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak, +# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + +ABBREVIATE_BRIEF = "The $name class" \ + "The $name widget" \ + "The $name file" \ + is \ + provides \ + specifies \ + contains \ + represents \ + a \ + an \ + the + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + +FULL_PATH_NAMES = YES + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful if your file system +# doesn't support long names like on DOS, Mac, or CD-ROM. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + +TAB_SIZE = 8 + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for +# Java. For instance, namespaces will be presented as packages, qualified +# scopes will look different, etc. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources only. Doxygen will then generate output that is more tailored for +# Fortran. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for +# VHDL. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given extension. +# Doxygen has a built-in mapping, but you can override or extend it using this +# tag. The format is ext=language, where ext is a file extension, and language +# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C, +# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make +# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C +# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions +# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). This also makes the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. +# Doxygen will parse them like normal C++ but will assume all classes use public +# instead of private inheritance when no explicit protection keyword is present. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate getter +# and setter methods for a property. Setting this option to YES (the default) +# will make doxygen replace the get and set methods by a property in the +# documentation. This will only work if the methods are indeed getting or +# setting a simple type. If this is not the case, or you want to show the +# methods anyway, you should set this option to NO. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and +# unions are shown inside the group in which they are included (e.g. using +# @ingroup) instead of on a separate page (for HTML and Man pages) or +# section (for LaTeX and RTF). + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and +# unions with only public data fields will be shown inline in the documentation +# of the scope in which they are defined (i.e. file, namespace, or group +# documentation), provided this scope is documented. If set to NO (the default), +# structs, classes, and unions are shown on a separate page (for HTML and Man +# pages) or section (for LaTeX and RTF). + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = NO + +# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to +# determine which symbols to keep in memory and which to flush to disk. +# When the cache is full, less often used symbols will be written to disk. +# For small to medium size projects (<1000 input files) the default value is +# probably good enough. For larger projects a too small cache size can cause +# doxygen to be busy swapping symbols to and from disk most of the time +# causing a significant performance penalty. +# If the system has enough physical memory increasing the cache will improve the +# performance by keeping more symbols in memory. Note that the value works on +# a logarithmic scale so increasing the size by one will roughly double the +# memory usage. The cache size is given by this formula: +# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, +# corresponding to a cache size of 2^16 = 65536 symbols + +SYMBOL_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + +EXTRACT_PRIVATE = NO + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + +EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespaces are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + +CASE_SENSE_NAMES = NO + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + +HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + +SHOW_INCLUDE_FILES = YES + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen +# will list include files with double quotes in the documentation +# rather than with sharp brackets. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen +# will sort the (brief and detailed) documentation of class members so that +# constructors and destructors are listed first. If set to NO (the default) +# the constructors will appear in the respective orders defined by +# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. +# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO +# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to +# do proper type resolution of all parameters of a function it will reject a +# match between the prototype and the implementation of a member function even +# if there is only one candidate or it is obvious which candidate to choose +# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen +# will still accept a match between prototype and implementation in such cases. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or macro consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and macros in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + +SHOW_USED_FILES = YES + +# If the sources in your project are distributed over multiple directories +# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy +# in the documentation. The default is NO. + +SHOW_DIRECTORIES = NO + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. The create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. +# You can optionally specify a file name after the option, if omitted +# DoxygenLayout.xml will be used as the name of the layout file. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files +# containing the references data. This must be a list of .bib files. The +# .bib extension is automatically appended if omitted. Using this command +# requires the bibtex tool to be installed. See also +# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style +# of the bibliography can be controlled using LATEX_BIB_STYLE. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + +WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + +WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + +WARN_IF_DOC_ERROR = YES + +# The WARN_NO_PARAMDOC option can be enabled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = C:/p4research/research/EmergingApplications/Investigations/genomics/nvbio/src/nvbio + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh +# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py +# *.f90 *.f *.for *.vhd *.vhdl + +FILE_PATTERNS = *.c \ + *.cc \ + *.cxx \ + *.cpp \ + *.c++ \ + *.d \ + *.java \ + *.ii \ + *.ixx \ + *.ipp \ + *.i++ \ + *.inl \ + *.h \ + *.hh \ + *.hxx \ + *.hpp \ + *.h++ \ + *.idl \ + *.odl \ + *.cs \ + *.php \ + *.php3 \ + *.inc \ + *.m \ + *.mm \ + *.dox \ + *.py \ + *.f90 \ + *.f \ + *.for \ + *.vhd \ + *.vhdl + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# Note that relative paths are relative to directory from which doxygen is run. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + +EXAMPLE_PATTERNS = * + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. If FILTER_PATTERNS is specified, this tag will be +# ignored. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty or if +# non of the patterns match the file name, INPUT_FILTER is applied. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) +# and it is also possible to disable source filtering for a specific pattern +# using *.ext= (so without naming a filter). This option only has effect when +# FILTER_SOURCE_FILES is enabled. + +FILTER_SOURCE_PATTERNS = + +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + +SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES +# then for each documented function all documented +# functions referencing it will be listed. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. Otherwise they will link to the documentation. + +REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + +ALPHABETICAL_INDEX = YES + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. Note that when using a custom header you are responsible +# for the proper inclusion of any scripts and style sheets that doxygen +# needs, which is dependent on the configuration options used. +# It is adviced to generate a default header using "doxygen -w html +# header.html footer.html stylesheet.css YourConfigFile" and then modify +# that header. Note that the header is subject to change so you typically +# have to redo this when upgrading to a newer version of doxygen or when +# changing the value of configuration settings such as GENERATE_TREEVIEW! + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify an additional +# user-defined cascading style sheet that is included after the standard +# style sheets created by doxygen. Using this option one can overrule +# certain style aspects. This is preferred over using HTML_STYLESHEET +# since it does not replace the standard style sheet and is therefor more +# robust against future updates. Doxygen will copy the style sheet file to +# the output directory. + +HTML_EXTRA_STYLESHEET = extra_stylesheet.css + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that +# the files will be copied as-is; there are no commands or markers available. + +HTML_EXTRA_FILES = images/nvidia.png +HTML_EXTRA_FILES += images/nvidia_cubes.png +HTML_EXTRA_FILES += images/cuda.png +HTML_EXTRA_FILES += images/cuda_small.png +HTML_EXTRA_FILES += images/tree.png + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. +# Doxygen will adjust the colors in the stylesheet and background images +# according to this color. Hue is specified as an angle on a colorwheel, +# see http://en.wikipedia.org/wiki/Hue for more information. +# For instance the value 0 represents red, 60 is yellow, 120 is green, +# 180 is cyan, 240 is blue, 300 purple, and 360 is red again. +# The allowed range is 0 to 359. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of +# the colors in the HTML output. For a value of 0 the output will use +# grayscales only. A value of 255 will produce the most vivid colors. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to +# the luminance component of the colors in the HTML output. Values below +# 100 gradually make the output lighter, whereas values above 100 make +# the output darker. The value divided by 100 is the actual gamma applied, +# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2, +# and 100 does not change the gamma. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting +# this to NO can help when comparing the output of multiple runs. + +HTML_TIMESTAMP = YES + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + +HTML_ALIGN_MEMBERS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = NO + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) +# of the generated HTML documentation. + +GENERATE_HTMLHELP = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + +GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated +# that can be used as input for Qt's qhelpgenerator to generate a +# Qt Compressed Help (.qch) of the generated HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to +# add. For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see +# +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's +# filter section matches. +# +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files +# will be generated, which together with the HTML files, form an Eclipse help +# plugin. To install this plugin and make it available under the help contents +# menu in Eclipse, the contents of the directory containing the HTML and XML +# files needs to be copied into the plugins directory of eclipse. The name of +# the directory within the plugins directory should be the same as +# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before +# the help appears. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have +# this name. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + +DISABLE_INDEX = NO + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values +# (range [0,1..20]) that doxygen will group on one line in the generated HTML +# documentation. Note that a value of 0 will completely suppress the enum +# values from appearing in the overview section. + +ENUM_VALUES_PER_LINE = 4 + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value is set to YES, a side panel will be generated +# containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). +# Windows users are probably better off using the HTML help feature. + +GENERATE_TREEVIEW = NO + +# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, +# and Class Hierarchy pages using a tree view instead of an ordered list. + +USE_INLINE_TREES = NO + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + +TREEVIEW_WIDTH = 250 + +# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open +# links to external symbols imported via tag files in a separate window. + +EXT_LINKS_IN_WINDOW = NO + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are +# not supported properly for IE 6.0, but are supported on all modern browsers. +# Note that when changing this option you need to delete any form_*.png files +# in the HTML output before the changes have effect. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax +# (see http://www.mathjax.org) which uses client side Javascript for the +# rendering instead of using prerendered bitmaps. Use this if you do not +# have LaTeX installed or if you want to formulas look prettier in the HTML +# output. When enabled you also need to install MathJax separately and +# configure the path to it using the MATHJAX_RELPATH option. + +USE_MATHJAX = NO + +# When MathJax is enabled you need to specify the location relative to the +# HTML output directory using the MATHJAX_RELPATH option. The destination +# directory should contain the MathJax.js script. For instance, if the mathjax +# directory is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the +# mathjax.org site, so you can quickly see the result without installing +# MathJax, but it is strongly recommended to install a local copy of MathJax +# before deployment. + +MATHJAX_RELPATH = http://www.mathjax.org/mathjax + +# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension +# names that should be enabled during MathJax rendering. + +MATHJAX_EXTENSIONS = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box +# for the HTML output. The underlying search engine uses javascript +# and DHTML and should work on any modern browser. Note that when using +# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets +# (GENERATE_DOCSET) there is already a search function so this one should +# typically be disabled. For large projects the javascript based search engine +# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution. + +SEARCHENGINE = YES + +# When the SERVER_BASED_SEARCH tag is enabled the search engine will be +# implemented using a PHP enabled web server instead of at the web client +# using Javascript. Doxygen will generate the search PHP script and index +# file to put on the web server. The advantage of the server +# based approach is that it scales better to large projects and allows +# full text search. The disadvantages are that it is more difficult to setup +# and does not have live searching capabilities. + +SERVER_BASED_SEARCH = NO + +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + +GENERATE_LATEX = YES + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. +# Note that when enabling USE_PDFLATEX this option is only used for +# generating bitmaps for formulas in the HTML output, but not in the +# Makefile that is written to the output directory. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, letter, legal and +# executive. If left blank a4wide will be used. + +PAPER_TYPE = a4 + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for +# the generated latex document. The footer should contain everything after +# the last chapter. If it is left blank doxygen will generate a +# standard footer. Notice: only use this tag if you know what you are doing! + +LATEX_FOOTER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + +LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + +LATEX_HIDE_INDICES = NO + +# If LATEX_SOURCE_CODE is set to YES then doxygen will include +# source code with syntax highlighting in the LaTeX output. +# Note that which sources are shown also depends on other settings +# such as SOURCE_BROWSER. + +LATEX_SOURCE_CODE = NO + +# The LATEX_BIB_STYLE tag can be used to specify the style to use for the +# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See +# http://en.wikipedia.org/wiki/BibTeX for more info. + +LATEX_BIB_STYLE = plain + +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + +MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + +XML_OUTPUT = xml + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. This is useful +# if you want to understand what is going on. On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + +MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_DEFINED tags. + +EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# pointed to by INCLUDE_PATH will be searched when a #include is found. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition that +# overrules the definition found in the source code. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all references to function-like macros +# that are alone on a line, have an all uppercase name, and do not end with a +# semicolon, because these will confuse the parser if not removed. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES option can be used to specify one or more tagfiles. +# Optionally an initial location of the external documentation +# can be added for each tagfile. The format of a tag file without +# this location is as follows: +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths or +# URLs. If a location is present for each tag, the installdox tool +# does not have to be run to correct the links. +# Note that each tag file must have a unique name +# (where the name does NOT include the path) +# If a tag file is not located in the directory in which doxygen +# is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + +EXTERNAL_GROUPS = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + +PERL_PATH = /usr/bin/perl + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option also works with HAVE_DOT disabled, but it is recommended to +# install and use dot, since it yields more powerful graphs. + +CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see +# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + +HAVE_DOT = NO + +# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is +# allowed to run in parallel. When set to 0 (the default) doxygen will +# base this on the number of processors available in the system. You can set it +# explicitly to a value larger than 0 to get control over the balance +# between CPU load and processing speed. + +DOT_NUM_THREADS = 0 + +# By default doxygen will use the Helvetica font for all dot files that +# doxygen generates. When you want a differently looking font you can specify +# the font name using DOT_FONTNAME. You need to make sure dot is able to find +# the font, which can be done by putting it in a standard location or by setting +# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the +# directory containing the font. + +DOT_FONTNAME = Helvetica + +# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. +# The default size is 10pt. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the Helvetica font. +# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to +# set the path where dot can find it. + +DOT_FONTPATH = + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. Setting this tag to YES will force the +# the CLASS_DIAGRAMS tag to NO. + +CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect implementation dependencies (inheritance, containment, and +# class references variables) of the class with other documented classes. + +COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for groups, showing the direct groups dependencies + +GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. + +UML_LOOK = NO + +# If set to YES, the inheritance and collaboration graphs will show the +# relations between templates and their instances. + +TEMPLATE_RELATIONS = NO + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT +# tags are set to YES then doxygen will generate a graph for each documented +# file showing the direct and indirect include dependencies of the file with +# other documented files. + +INCLUDE_GRAPH = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and +# HAVE_DOT tags are set to YES then doxygen will generate a graph for each +# documented header file showing the documented files that directly or +# indirectly include this file. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH and HAVE_DOT options are set to YES then +# doxygen will generate a call dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable call graphs +# for selected functions only using the \callgraph command. + +CALL_GRAPH = NO + +# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then +# doxygen will generate a caller dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable caller +# graphs for selected functions only using the \callergraph command. + +CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will generate a graphical hierarchy of all classes instead of a textual one. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES +# then doxygen will show the dependencies a directory has on other directories +# in a graphical way. The dependency relations are determined by the #include +# relations between the files in the directories. + +DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. Possible values are svg, png, jpg, or gif. +# If left blank png will be used. If you choose svg you need to set +# HTML_FILE_EXTENSION to xhtml in order to make the SVG files +# visible in IE 9+ (other browsers do not have this requirement). + +DOT_IMAGE_FORMAT = png + +# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to +# enable generation of interactive SVG images that allow zooming and panning. +# Note that this requires a modern browser other than Internet Explorer. +# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you +# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files +# visible. Older versions of IE do not have SVG support. + +INTERACTIVE_SVG = NO + +# The tag DOT_PATH can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the +# \dotfile command). + +DOTFILE_DIRS = + +# The MSCFILE_DIRS tag can be used to specify one or more directories that +# contain msc files that are included in the documentation (see the +# \mscfile command). + +MSCFILE_DIRS = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of +# nodes that will be shown in the graph. If the number of nodes in a graph +# becomes larger than this value, doxygen will truncate the graph, which is +# visualized by representing a node as a red box. Note that doxygen if the +# number of direct children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not +# seem to support this out of the box. Warning: Depending on the platform used, +# enabling this option may lead to badly anti-aliased labels on the edges of +# a graph (i.e. they become hard to read). + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) +# support this, this feature is disabled by default. + +DOT_MULTI_TARGETS = NO + +# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will +# generate a legend page explaining the meaning of the various boxes and +# arrows in the dot generated graphs. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will +# remove the intermediate dot files that are used to generate +# the various graphs. + +DOT_CLEANUP = YES diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/doxy/Doxyfile.in b/methods/ring/utils/fast_gicp/thirdparty/nvbio/doxy/Doxyfile.in new file mode 100644 index 0000000000000000000000000000000000000000..ad81de304fed68503e5f5c3cc84ba8877e0850a5 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/doxy/Doxyfile.in @@ -0,0 +1,1818 @@ +# Doxyfile 1.7.5.1 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or sequence of words) that should +# identify the project. Note that if you do not use Doxywizard you need +# to put quotes around the project name if it contains spaces. + +PROJECT_NAME = NVBIO + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + +PROJECT_NUMBER = + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer +# a quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = + +# With the PROJECT_LOGO tag one can specify an logo or icon that is +# included in the documentation. The maximum height of the logo should not +# exceed 55 pixels and the maximum width should not exceed 200 pixels. +# Doxygen will copy the logo to the output directory. + +PROJECT_LOGO = + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + +OUTPUT_DIRECTORY = + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + +CREATE_SUBDIRS = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, +# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English +# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, +# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak, +# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + +ABBREVIATE_BRIEF = "The $name class" \ + "The $name widget" \ + "The $name file" \ + is \ + provides \ + specifies \ + contains \ + represents \ + a \ + an \ + the + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + +FULL_PATH_NAMES = YES + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful if your file system +# doesn't support long names like on DOS, Mac, or CD-ROM. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + +TAB_SIZE = 8 + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for +# Java. For instance, namespaces will be presented as packages, qualified +# scopes will look different, etc. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources only. Doxygen will then generate output that is more tailored for +# Fortran. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for +# VHDL. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given extension. +# Doxygen has a built-in mapping, but you can override or extend it using this +# tag. The format is ext=language, where ext is a file extension, and language +# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C, +# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make +# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C +# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions +# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). This also makes the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. +# Doxygen will parse them like normal C++ but will assume all classes use public +# instead of private inheritance when no explicit protection keyword is present. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate getter +# and setter methods for a property. Setting this option to YES (the default) +# will make doxygen replace the get and set methods by a property in the +# documentation. This will only work if the methods are indeed getting or +# setting a simple type. If this is not the case, or you want to show the +# methods anyway, you should set this option to NO. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and +# unions are shown inside the group in which they are included (e.g. using +# @ingroup) instead of on a separate page (for HTML and Man pages) or +# section (for LaTeX and RTF). + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and +# unions with only public data fields will be shown inline in the documentation +# of the scope in which they are defined (i.e. file, namespace, or group +# documentation), provided this scope is documented. If set to NO (the default), +# structs, classes, and unions are shown on a separate page (for HTML and Man +# pages) or section (for LaTeX and RTF). + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = NO + +# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to +# determine which symbols to keep in memory and which to flush to disk. +# When the cache is full, less often used symbols will be written to disk. +# For small to medium size projects (<1000 input files) the default value is +# probably good enough. For larger projects a too small cache size can cause +# doxygen to be busy swapping symbols to and from disk most of the time +# causing a significant performance penalty. +# If the system has enough physical memory increasing the cache will improve the +# performance by keeping more symbols in memory. Note that the value works on +# a logarithmic scale so increasing the size by one will roughly double the +# memory usage. The cache size is given by this formula: +# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, +# corresponding to a cache size of 2^16 = 65536 symbols + +SYMBOL_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + +EXTRACT_PRIVATE = NO + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + +EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespaces are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + +CASE_SENSE_NAMES = NO + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + +HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + +SHOW_INCLUDE_FILES = YES + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen +# will list include files with double quotes in the documentation +# rather than with sharp brackets. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen +# will sort the (brief and detailed) documentation of class members so that +# constructors and destructors are listed first. If set to NO (the default) +# the constructors will appear in the respective orders defined by +# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. +# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO +# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to +# do proper type resolution of all parameters of a function it will reject a +# match between the prototype and the implementation of a member function even +# if there is only one candidate or it is obvious which candidate to choose +# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen +# will still accept a match between prototype and implementation in such cases. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or macro consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and macros in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + +SHOW_USED_FILES = YES + +# If the sources in your project are distributed over multiple directories +# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy +# in the documentation. The default is NO. + +SHOW_DIRECTORIES = NO + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. The create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. +# You can optionally specify a file name after the option, if omitted +# DoxygenLayout.xml will be used as the name of the layout file. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files +# containing the references data. This must be a list of .bib files. The +# .bib extension is automatically appended if omitted. Using this command +# requires the bibtex tool to be installed. See also +# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style +# of the bibliography can be controlled using LATEX_BIB_STYLE. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + +WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + +WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + +WARN_IF_DOC_ERROR = YES + +# The WARN_NO_PARAMDOC option can be enabled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = @CMAKE_CURRENT_SOURCE_DIR@ + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh +# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py +# *.f90 *.f *.for *.vhd *.vhdl + +FILE_PATTERNS = *.c \ + *.cc \ + *.cxx \ + *.cpp \ + *.c++ \ + *.d \ + *.java \ + *.ii \ + *.ixx \ + *.ipp \ + *.i++ \ + *.inl \ + *.h \ + *.hh \ + *.hxx \ + *.hpp \ + *.h++ \ + *.idl \ + *.odl \ + *.cs \ + *.php \ + *.php3 \ + *.inc \ + *.m \ + *.mm \ + *.dox \ + *.py \ + *.f90 \ + *.f \ + *.for \ + *.vhd \ + *.vhdl + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# Note that relative paths are relative to directory from which doxygen is run. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + +EXAMPLE_PATTERNS = * + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. If FILTER_PATTERNS is specified, this tag will be +# ignored. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty or if +# non of the patterns match the file name, INPUT_FILTER is applied. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) +# and it is also possible to disable source filtering for a specific pattern +# using *.ext= (so without naming a filter). This option only has effect when +# FILTER_SOURCE_FILES is enabled. + +FILTER_SOURCE_PATTERNS = + +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + +SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES +# then for each documented function all documented +# functions referencing it will be listed. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. Otherwise they will link to the documentation. + +REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + +ALPHABETICAL_INDEX = YES + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. Note that when using a custom header you are responsible +# for the proper inclusion of any scripts and style sheets that doxygen +# needs, which is dependent on the configuration options used. +# It is adviced to generate a default header using "doxygen -w html +# header.html footer.html stylesheet.css YourConfigFile" and then modify +# that header. Note that the header is subject to change so you typically +# have to redo this when upgrading to a newer version of doxygen or when +# changing the value of configuration settings such as GENERATE_TREEVIEW! + +HTML_HEADER = header.html + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify an additional +# user-defined cascading style sheet that is included after the standard +# style sheets created by doxygen. Using this option one can overrule +# certain style aspects. This is preferred over using HTML_STYLESHEET +# since it does not replace the standard style sheet and is therefor more +# robust against future updates. Doxygen will copy the style sheet file to +# the output directory. + +HTML_EXTRA_STYLESHEET = extra_stylesheet.css + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that +# the files will be copied as-is; there are no commands or markers available. + +HTML_EXTRA_FILES = images/nvidia.png +HTML_EXTRA_FILES += images/nvidia_cubes.png +HTML_EXTRA_FILES += images/cuda.png +HTML_EXTRA_FILES += images/cuda_small.png +HTML_EXTRA_FILES += images/tree.png +HTML_EXTRA_FILES += images/browse-icon.png +HTML_EXTRA_FILES += images/groups-icon.png +HTML_EXTRA_FILES += images/download-icon.png +HTML_EXTRA_FILES += images/benchmark-fm-index.png +HTML_EXTRA_FILES += images/benchmark-fm-index-speedup.png +HTML_EXTRA_FILES += images/benchmark-sw.png +HTML_EXTRA_FILES += images/benchmark-bwt.png +HTML_EXTRA_FILES += images/benchmark-nvbowtie-speedup.png +HTML_EXTRA_FILES += images/benchmark-qgram-counting.png +HTML_EXTRA_FILES += images/benchmark-qgram-indexing.png +HTML_EXTRA_FILES += images/nvBowtie-ROC-se-100.png +HTML_EXTRA_FILES += images/nvBowtie-ROC-pe-100.png +HTML_EXTRA_FILES += images/nvBowtie-ROC-pe-100-large-indels.png +HTML_EXTRA_FILES += images/nvBowtie-ROC-pe-250.png +HTML_EXTRA_FILES += images/nvBowtie-ROC-pe-100-zoom.png + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. +# Doxygen will adjust the colors in the stylesheet and background images +# according to this color. Hue is specified as an angle on a colorwheel, +# see http://en.wikipedia.org/wiki/Hue for more information. +# For instance the value 0 represents red, 60 is yellow, 120 is green, +# 180 is cyan, 240 is blue, 300 purple, and 360 is red again. +# The allowed range is 0 to 359. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of +# the colors in the HTML output. For a value of 0 the output will use +# grayscales only. A value of 255 will produce the most vivid colors. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to +# the luminance component of the colors in the HTML output. Values below +# 100 gradually make the output lighter, whereas values above 100 make +# the output darker. The value divided by 100 is the actual gamma applied, +# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2, +# and 100 does not change the gamma. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting +# this to NO can help when comparing the output of multiple runs. + +HTML_TIMESTAMP = YES + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + +HTML_ALIGN_MEMBERS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = NO + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) +# of the generated HTML documentation. + +GENERATE_HTMLHELP = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + +GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated +# that can be used as input for Qt's qhelpgenerator to generate a +# Qt Compressed Help (.qch) of the generated HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to +# add. For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see +# +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's +# filter section matches. +# +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files +# will be generated, which together with the HTML files, form an Eclipse help +# plugin. To install this plugin and make it available under the help contents +# menu in Eclipse, the contents of the directory containing the HTML and XML +# files needs to be copied into the plugins directory of eclipse. The name of +# the directory within the plugins directory should be the same as +# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before +# the help appears. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have +# this name. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + +DISABLE_INDEX = NO + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values +# (range [0,1..20]) that doxygen will group on one line in the generated HTML +# documentation. Note that a value of 0 will completely suppress the enum +# values from appearing in the overview section. + +ENUM_VALUES_PER_LINE = 4 + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value is set to YES, a side panel will be generated +# containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). +# Windows users are probably better off using the HTML help feature. + +GENERATE_TREEVIEW = NO + +# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, +# and Class Hierarchy pages using a tree view instead of an ordered list. + +USE_INLINE_TREES = NO + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + +TREEVIEW_WIDTH = 250 + +# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open +# links to external symbols imported via tag files in a separate window. + +EXT_LINKS_IN_WINDOW = NO + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are +# not supported properly for IE 6.0, but are supported on all modern browsers. +# Note that when changing this option you need to delete any form_*.png files +# in the HTML output before the changes have effect. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax +# (see http://www.mathjax.org) which uses client side Javascript for the +# rendering instead of using prerendered bitmaps. Use this if you do not +# have LaTeX installed or if you want to formulas look prettier in the HTML +# output. When enabled you also need to install MathJax separately and +# configure the path to it using the MATHJAX_RELPATH option. + +USE_MATHJAX = NO + +# When MathJax is enabled you need to specify the location relative to the +# HTML output directory using the MATHJAX_RELPATH option. The destination +# directory should contain the MathJax.js script. For instance, if the mathjax +# directory is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the +# mathjax.org site, so you can quickly see the result without installing +# MathJax, but it is strongly recommended to install a local copy of MathJax +# before deployment. + +MATHJAX_RELPATH = http://www.mathjax.org/mathjax + +# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension +# names that should be enabled during MathJax rendering. + +MATHJAX_EXTENSIONS = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box +# for the HTML output. The underlying search engine uses javascript +# and DHTML and should work on any modern browser. Note that when using +# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets +# (GENERATE_DOCSET) there is already a search function so this one should +# typically be disabled. For large projects the javascript based search engine +# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution. + +SEARCHENGINE = YES + +# When the SERVER_BASED_SEARCH tag is enabled the search engine will be +# implemented using a PHP enabled web server instead of at the web client +# using Javascript. Doxygen will generate the search PHP script and index +# file to put on the web server. The advantage of the server +# based approach is that it scales better to large projects and allows +# full text search. The disadvantages are that it is more difficult to setup +# and does not have live searching capabilities. + +SERVER_BASED_SEARCH = NO + +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + +GENERATE_LATEX = YES + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. +# Note that when enabling USE_PDFLATEX this option is only used for +# generating bitmaps for formulas in the HTML output, but not in the +# Makefile that is written to the output directory. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, letter, legal and +# executive. If left blank a4wide will be used. + +PAPER_TYPE = a4 + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for +# the generated latex document. The footer should contain everything after +# the last chapter. If it is left blank doxygen will generate a +# standard footer. Notice: only use this tag if you know what you are doing! + +LATEX_FOOTER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + +LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + +LATEX_HIDE_INDICES = NO + +# If LATEX_SOURCE_CODE is set to YES then doxygen will include +# source code with syntax highlighting in the LaTeX output. +# Note that which sources are shown also depends on other settings +# such as SOURCE_BROWSER. + +LATEX_SOURCE_CODE = NO + +# The LATEX_BIB_STYLE tag can be used to specify the style to use for the +# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See +# http://en.wikipedia.org/wiki/BibTeX for more info. + +LATEX_BIB_STYLE = plain + +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + +MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + +XML_OUTPUT = xml + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. This is useful +# if you want to understand what is going on. On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + +MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_DEFINED tags. + +EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# pointed to by INCLUDE_PATH will be searched when a #include is found. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition that +# overrules the definition found in the source code. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all references to function-like macros +# that are alone on a line, have an all uppercase name, and do not end with a +# semicolon, because these will confuse the parser if not removed. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES option can be used to specify one or more tagfiles. +# Optionally an initial location of the external documentation +# can be added for each tagfile. The format of a tag file without +# this location is as follows: +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths or +# URLs. If a location is present for each tag, the installdox tool +# does not have to be run to correct the links. +# Note that each tag file must have a unique name +# (where the name does NOT include the path) +# If a tag file is not located in the directory in which doxygen +# is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + +EXTERNAL_GROUPS = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + +PERL_PATH = /usr/bin/perl + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option also works with HAVE_DOT disabled, but it is recommended to +# install and use dot, since it yields more powerful graphs. + +CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see +# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + +HAVE_DOT = NO + +# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is +# allowed to run in parallel. When set to 0 (the default) doxygen will +# base this on the number of processors available in the system. You can set it +# explicitly to a value larger than 0 to get control over the balance +# between CPU load and processing speed. + +DOT_NUM_THREADS = 0 + +# By default doxygen will use the Helvetica font for all dot files that +# doxygen generates. When you want a differently looking font you can specify +# the font name using DOT_FONTNAME. You need to make sure dot is able to find +# the font, which can be done by putting it in a standard location or by setting +# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the +# directory containing the font. + +DOT_FONTNAME = Helvetica + +# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. +# The default size is 10pt. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the Helvetica font. +# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to +# set the path where dot can find it. + +DOT_FONTPATH = + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. Setting this tag to YES will force the +# the CLASS_DIAGRAMS tag to NO. + +CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect implementation dependencies (inheritance, containment, and +# class references variables) of the class with other documented classes. + +COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for groups, showing the direct groups dependencies + +GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. + +UML_LOOK = NO + +# If set to YES, the inheritance and collaboration graphs will show the +# relations between templates and their instances. + +TEMPLATE_RELATIONS = NO + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT +# tags are set to YES then doxygen will generate a graph for each documented +# file showing the direct and indirect include dependencies of the file with +# other documented files. + +INCLUDE_GRAPH = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and +# HAVE_DOT tags are set to YES then doxygen will generate a graph for each +# documented header file showing the documented files that directly or +# indirectly include this file. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH and HAVE_DOT options are set to YES then +# doxygen will generate a call dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable call graphs +# for selected functions only using the \callgraph command. + +CALL_GRAPH = NO + +# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then +# doxygen will generate a caller dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable caller +# graphs for selected functions only using the \callergraph command. + +CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will generate a graphical hierarchy of all classes instead of a textual one. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES +# then doxygen will show the dependencies a directory has on other directories +# in a graphical way. The dependency relations are determined by the #include +# relations between the files in the directories. + +DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. Possible values are svg, png, jpg, or gif. +# If left blank png will be used. If you choose svg you need to set +# HTML_FILE_EXTENSION to xhtml in order to make the SVG files +# visible in IE 9+ (other browsers do not have this requirement). + +DOT_IMAGE_FORMAT = png + +# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to +# enable generation of interactive SVG images that allow zooming and panning. +# Note that this requires a modern browser other than Internet Explorer. +# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you +# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files +# visible. Older versions of IE do not have SVG support. + +INTERACTIVE_SVG = NO + +# The tag DOT_PATH can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the +# \dotfile command). + +DOTFILE_DIRS = + +# The MSCFILE_DIRS tag can be used to specify one or more directories that +# contain msc files that are included in the documentation (see the +# \mscfile command). + +MSCFILE_DIRS = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of +# nodes that will be shown in the graph. If the number of nodes in a graph +# becomes larger than this value, doxygen will truncate the graph, which is +# visualized by representing a node as a red box. Note that doxygen if the +# number of direct children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not +# seem to support this out of the box. Warning: Depending on the platform used, +# enabling this option may lead to badly anti-aliased labels on the edges of +# a graph (i.e. they become hard to read). + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). 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+ + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/fmmap/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/fmmap/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..80f79961478ba7b56dcd19539c9e15ebfd58d396 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/fmmap/CMakeLists.txt @@ -0,0 +1,8 @@ +nvbio_module(fmmap) + +addsources( +fmmap.cu +) + +cuda_add_executable(fmmap ${fmmap_srcs}) +target_link_libraries(fmmap nvbio zlibstatic lz4 crcstatic ${SYSTEM_LINK_LIBRARIES}) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/fmmap/fmmap.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/fmmap/fmmap.cu new file mode 100644 index 0000000000000000000000000000000000000000..b840ca81edf026afba087249d34d09f99789ead8 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/fmmap/fmmap.cu @@ -0,0 +1,541 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// fmmap.cu +// + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "util.h" + +using namespace nvbio; + +// alignment params +// +struct Params +{ + uint32 seed_len; + uint32 seed_intv; + uint32 merge_intv; +}; + +// query stats +// +struct Stats +{ + Stats() : + time(0), + extract_time(0), + rank_time(0), + locate_time(0), + align_time(0), + reads(0), + aligned(0), + queries(0), + occurrences(0) {} + + float time; + float extract_time; + float rank_time; + float locate_time; + float align_time; + uint64 reads; + uint64 aligned; + uint64 queries; + uint64 occurrences; +}; + +// the pipeline state +// +struct Pipeline +{ + typedef io::FMIndexDataDevice::fm_index_type fm_index_type; + typedef FMIndexFilterDevice fm_filter_type; + + Params params; // program options + SharedPointer ref_data; // reference data + SharedPointer fm_data; // fm-index data + fm_filter_type fm_filter; // fm-index filter +}; + +// transform an (index-pos,seed-id) hit into a diagonal (text-pos = index-pos - seed-pos, read-id) +struct hit_to_diagonal +{ + typedef uint2 argument_type; + typedef uint2 result_type; + + // constructor + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + hit_to_diagonal(const string_set_infix_coord_type* _seed_coords) : seed_coords(_seed_coords) {} + + // functor operator + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint2 operator() (const uint2 hit) const + { + const uint32 index_pos = hit.x; + const uint32 seed_id = hit.y; + + const string_set_infix_coord_type seed = seed_coords[ seed_id ]; + + const uint32 read_pos = infix_begin( seed ); + const uint32 read_id = string_id( seed ); + + return make_uint2( index_pos - read_pos, read_id ); + } + + const string_set_infix_coord_type* seed_coords; +}; + +// extract a set of uniformly spaced seeds from a string-set and return it as an InfixSet +// +template +InfixSet +extract_seeds( + const string_set_type string_set, // the input string-set + const uint32 seed_len, // the seeds length + const uint32 seed_interval, // the spacing between seeds + nvbio::vector& seed_coords) // the output vector of seed coordinates +{ + // enumerate all seeds + const uint32 n_seeds = enumerate_string_set_seeds( + string_set, + uniform_seeds_functor<>( seed_len, seed_interval ), + seed_coords ); + + // and build the output infix-set + return InfixSet( + n_seeds, + string_set, + nvbio::plain_view( seed_coords ) ); +} + +// a functor to extract the read infixes from the hit diagonals +// +struct read_infixes +{ + // constructor + NVBIO_HOST_DEVICE + read_infixes(const io::ConstSequenceDataView reads) : + m_reads( reads ) {} + + // functor operator + NVBIO_HOST_DEVICE + string_infix_coord_type operator() (const uint2 diagonal) const + { + const io::SequenceDataAccess reads( m_reads ); + + const uint32 read_id = diagonal.y; + + // fetch the read range + return reads.get_range( read_id ); + } + + const io::ConstSequenceDataView m_reads; +}; + +// a functor to extract the genome infixes from the hit diagonals +// +template +struct genome_infixes +{ + typedef const io::SequenceDataAccess read_access_type; + + // constructor + NVBIO_HOST_DEVICE + genome_infixes(const uint32 genome_len, const io::ConstSequenceDataView reads) : + m_genome_len( genome_len ), + m_reads( reads ) {} + + // functor operator + NVBIO_HOST_DEVICE + string_infix_coord_type operator() (const uint2 diagonal) const + { + const io::SequenceDataAccess reads( m_reads ); + + const uint32 read_id = diagonal.y; + const uint32 text_pos = diagonal.x; + + // fetch the read range + const uint2 read_range = reads.get_range( read_id ); + const uint32 read_len = read_range.y - read_range.x; + + // compute the segment of text to align to + const uint32 genome_begin = text_pos > BAND_LEN/2 ? text_pos - BAND_LEN/2 : 0u; + const uint32 genome_end = nvbio::min( genome_begin + read_len + BAND_LEN, m_genome_len ); + + return make_uint2( genome_begin, genome_end ); + } + + const uint32 m_genome_len; + const io::ConstSequenceDataView m_reads; +}; + +// a functor to extract the score from a sink +// +struct sink_score +{ + typedef aln::BestSink argument_type; + typedef int16 result_type; + + // functor operator + NVBIO_HOST_DEVICE + int16 operator() (const aln::BestSink& sink) const { return sink.score; } +}; + +// perform q-gram index mapping +// +void map( + Pipeline& pipeline, + const io::SequenceDataDevice& reads, + nvbio::vector& best_scores, + Stats& stats) +{ + typedef io::SequenceDataAccess genome_access_type; + typedef genome_access_type::sequence_stream_type genome_string; + typedef io::SequenceDataAccess read_access_type; + typedef read_access_type::sequence_string_set_type read_string_set_type; + typedef read_access_type::sequence_stream_type read_stream; + typedef string_set_infix_coord_type infix_coord_type; + typedef nvbio::vector infix_vector_type; + typedef InfixSet seed_string_set_type; + + // fetch the program options + const Params& params = pipeline.params; + + // fetch the genome string + const genome_access_type genome_access( *pipeline.ref_data ); + const uint32 genome_len = genome_access.bps(); + const genome_string genome( genome_access.sequence_stream() ); + + // fetch an fm-index view + const Pipeline::fm_index_type fm_index = pipeline.fm_data->index(); + + // fetch the fm-index filter + Pipeline::fm_filter_type& fm_filter = pipeline.fm_filter; + + // prepare some vectors to store the query qgrams + infix_vector_type seed_coords; + + Timer timer; + timer.start(); + + const read_access_type reads_access( reads ); + const read_string_set_type read_string_set = reads_access.sequence_string_set(); + const seed_string_set_type seed_string_set = extract_seeds( + read_string_set, + params.seed_len, + params.seed_intv, + seed_coords ); + + cudaDeviceSynchronize(); + timer.stop(); + const float extract_time = timer.seconds(); + + stats.queries += seed_string_set.size(); + stats.extract_time += extract_time; + + // + // search the sorted seeds with the FM-index filter + // + + const uint32 batch_size = 16*1024*1024; + + typedef uint2 hit_type; // each hit will be an (index-pos,seed-id) coordinate pair + + // prepare storage for the output hits + nvbio::vector hits( batch_size ); + nvbio::vector out_reads( batch_size ); + nvbio::vector out_scores( batch_size ); + nvbio::vector temp_storage; + + timer.start(); + + // first step: rank the query seeds + const uint64 n_hits = fm_filter.rank( fm_index, seed_string_set ); + + cudaDeviceSynchronize(); + timer.stop(); + stats.rank_time += timer.seconds(); + stats.occurrences += n_hits; + + nvbio::vector > sinks( batch_size ); + nvbio::vector genome_infix_coords( batch_size ); + nvbio::vector read_infix_coords( batch_size ); + + static const uint32 BAND_LEN = 31; + + // loop through large batches of hits and locate & merge them + for (uint64 hits_begin = 0; hits_begin < n_hits; hits_begin += batch_size) + { + const uint64 hits_end = nvbio::min( hits_begin + batch_size, n_hits ); + + timer.start(); + + fm_filter.locate( + hits_begin, + hits_end, + hits.begin() ); + + cudaDeviceSynchronize(); + timer.stop(); + stats.locate_time += timer.seconds(); + + // transform the (index-pos,seed-id) hit coordinates into diagonals, (text-pos = index-pos - seed-pos, read-id) + thrust::transform( + hits.begin(), + hits.begin() + hits_end - hits_begin, + hits.begin(), + hit_to_diagonal( nvbio::plain_view( seed_coords ) ) ); + + timer.start(); + + // build the set of read infixes + thrust::transform( + hits.begin(), + hits.begin() + hits_end - hits_begin, + read_infix_coords.begin(), + read_infixes( nvbio::plain_view( reads ) ) ); + + // build the set of genome infixes + thrust::transform( + hits.begin(), + hits.begin() + hits_end - hits_begin, + genome_infix_coords.begin(), + genome_infixes( genome_len, nvbio::plain_view( reads ) ) ); + + typedef nvbio::vector::const_iterator infix_iterator; + + const SparseStringSet read_infix_set( + hits_end - hits_begin, + reads_access.sequence_stream(), + read_infix_coords.begin() ); + + const SparseStringSet genome_infix_set( + hits_end - hits_begin, + genome, + genome_infix_coords.begin() ); + + typedef aln::MyersTag<5u> myers_dna5_tag; + //const aln::SimpleGotohScheme gotoh( 2, -2, -5, -3 ); + aln::batch_banded_alignment_score( + aln::make_edit_distance_aligner(), + //aln::make_gotoh_aligner( gotoh ), + read_infix_set, + genome_infix_set, + sinks.begin(), + aln::DeviceThreadScheduler(), + reads.max_sequence_len(), + reads.max_sequence_len() + BAND_LEN ); + + cudaDeviceSynchronize(); + timer.stop(); + stats.align_time += timer.seconds(); + + // compute the best score for each read in this batch; + // note that we divide the string-id by 2 to merge results coming from the forward + // and reverse-complemented strands + cuda::reduce_by_key( + hits_end - hits_begin, + thrust::make_transform_iterator( + hits.begin(), + make_composition_functor( divide_by_two(), component_functor( 1u ) ) ), // take the second component divided by 2 + thrust::make_transform_iterator( sinks.begin(), sink_score() ), + out_reads.begin(), + out_scores.begin(), + thrust::maximum(), + temp_storage ); + + // and keep track of the global best + update_scores( + hits_end - hits_begin, + nvbio::plain_view( out_reads ), + nvbio::plain_view( out_scores ), + nvbio::plain_view( best_scores ) ); + + log_verbose(stderr, "\r processed %6.2f %% reads", 100.0f * float( hits_end ) / float( n_hits )); + } + log_verbose_cont(stderr, "\n"); +} + +// main test entry point +// +int main(int argc, char* argv[]) +{ + // + // perform some basic option parsing + // + + const uint32 batch_reads = 1*1024*1024; + const uint32 batch_bps = 100*1024*1024; + + const char* reads = argv[argc-1]; + const char* index = argv[argc-2]; + + Params params; + params.seed_len = 22; + params.seed_intv = 10; + params.merge_intv = 16; + uint32 max_reads = uint32(-1); + int16 score_threshold = -20; + + for (int i = 0; i < argc; ++i) + { + if (strcmp( argv[i], "-s" ) == 0) + { + params.seed_len = uint32( atoi( argv[++i] ) ); + params.seed_intv = uint32( atoi( argv[++i] ) ); + } + if (strcmp( argv[i], "-m" ) == 0) + params.merge_intv = uint32( atoi( argv[++i] ) ); + else if (strcmp( argv[i], "-max-reads" ) == 0) + max_reads = uint32( atoi( argv[++i] ) ); + else if (strcmp( argv[i], "-t" ) == 0) + score_threshold = int16( atoi( argv[++i] ) ); + } + + io::SequenceDataHost h_ref; + if (!io::load_sequence_file( DNA, &h_ref, index )) + { + log_error(stderr, " failed loading reference \"%s\"\n", index); + return 1u; + } + + io::FMIndexDataHost h_fmi; + if (!h_fmi.load( index, io::FMIndexData::FORWARD | io::FMIndexData::SA )) + { + log_error(stderr, " failed loading index \"%s\"\n", index); + return 1u; + } + + Pipeline pipeline; + + // store the program options + pipeline.params = params; + + // build its device version + pipeline.ref_data = new io::SequenceDataDevice( h_ref ); + + // build its device version + pipeline.fm_data = new io::FMIndexDataDevice( h_fmi, io::FMIndexData::FORWARD | + io::FMIndexData::SA ); + + // open a read file + log_info(stderr, " opening reads file... started\n"); + + SharedPointer read_data_file( + io::open_sequence_file( + reads, + io::Phred33, + 2*max_reads, + uint32(-1), + io::SequenceEncoding( io::FORWARD | io::REVERSE_COMPLEMENT ) ) ); + + // check whether the file opened correctly + if (read_data_file == NULL || read_data_file->is_ok() == false) + { + log_error(stderr, " failed opening file \"%s\"\n", reads); + return 1u; + } + log_info(stderr, " opening reads file... done\n"); + + // keep stats + Stats stats; + + io::SequenceDataHost h_read_data; + + while (1) + { + // load a batch of reads + if (io::next( DNA_N, &h_read_data, read_data_file.get(), batch_reads, batch_bps ) == 0) + break; + + log_info(stderr, " loading reads... started\n"); + + // copy it to the device + const io::SequenceDataDevice d_read_data = h_read_data; + + const uint32 n_reads = d_read_data.size() / 2; + + log_info(stderr, " loading reads... done\n"); + log_info(stderr, " %u reads\n", n_reads); + + const int16 worst_score = Field_traits::min(); + nvbio::vector best_scores( n_reads, worst_score ); + nvbio::vector temp_storage; + + Timer timer; + timer.start(); + + map( + pipeline, + d_read_data, + best_scores, + stats ); + + timer.stop(); + const float time = timer.seconds(); + + // accumulate the number of aligned reads + stats.reads += n_reads; + stats.time += time; + + // count how many reads have a score >= score_threshold + const uint32 n_aligned = cuda::reduce( + n_reads, + thrust::make_transform_iterator( best_scores.begin(), above_threshold( score_threshold ) ), + thrust::plus(), + temp_storage ); + + stats.aligned += n_aligned; + + log_info(stderr, " aligned %6.2f %% reads (%6.2f K reads/s)\n", 100.0f * float( stats.aligned ) / float( stats.reads ), (1.0e-3f * float( stats.reads )) / stats.time); + log_verbose(stderr, " breakdown:\n"); + log_verbose(stderr, " extract throughput : %.2f B seeds/s\n", (1.0e-9f * float( stats.queries )) / stats.extract_time); + log_verbose(stderr, " rank throughput : %6.2f K reads/s\n", (1.0e-3f * float( stats.reads )) / stats.rank_time); + log_verbose(stderr, " : %6.2f B seeds/s\n", (1.0e-9f * float( stats.queries )) / stats.rank_time); + log_verbose(stderr, " locate throughput : %6.2f K reads/s\n", (1.0e-3f * float( stats.reads )) / stats.locate_time); + log_verbose(stderr, " align throughput : %6.2f K reads/s\n", (1.0e-3f * float( stats.reads )) / stats.align_time); + log_verbose(stderr, " : %6.2f M hits/s\n", (1.0e-6f * float( stats.occurrences )) / stats.align_time); + log_verbose(stderr, " occurrences : %.3f B\n", 1.0e-9f * float( stats.occurrences ) ); + } + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/fmmap/util.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/fmmap/util.h new file mode 100644 index 0000000000000000000000000000000000000000..61f0ad602e6a202bc31e2ff4e854d6baf1a98e42 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/fmmap/util.h @@ -0,0 +1,92 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include + +using namespace nvbio; + +// divide by two +// +struct divide_by_two +{ + typedef uint32 argument_type; + typedef uint32 result_type; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + result_type operator() (const argument_type op) const { return op / 2u; } +}; + +// return 1 or 0 depending on whether a number is >= than a given threshold +struct above_threshold +{ + typedef int16 argument_type; + typedef uint32 result_type; + + // constructor + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + above_threshold(const int16 _t) : t(_t) {} + + // functor operator + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const int16 s) { return s >= t ? 1u : 0u; } + + const int16 t; +}; + +// update the best scores vector +// +__global__ +void update_scores_kernel( + const uint32 n, + const uint32* reads, + const int16* scores, + int16* best) +{ + const uint32 i = threadIdx.x + blockIdx.x * blockDim.x; + if (i >= n) return; + + const uint32 read_id = reads[i]; + const int16 score = scores[i]; + + best[ read_id ] = nvbio::max( best[ read_id ], score ); +} + +// update the best scores vector +// +void update_scores( + const uint32 n, + const uint32* reads, + const int16* scores, + int16* best) +{ + const uint32 block_dim = 128; + const uint32 n_blocks = util::divide_ri( n, block_dim ); + + update_scores_kernel<<>>( n, reads, scores, best ); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/hello_world/hello_world.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/hello_world/hello_world.cu new file mode 100644 index 0000000000000000000000000000000000000000..ac7130f9e3aa46655bcf8854d221719e38be2e9f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/hello_world/hello_world.cu @@ -0,0 +1,65 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// hello_world.cu +// + +#include +#include +#include +#include +#include +#include + + +using namespace nvbio; + + +// main test entry point +// +int main(int argc, char* argv[]) +{ + // our hello world ASCII string + const char dna_string[] = "ACGTTGCA"; + const uint32 len = (uint32)strlen( dna_string ); + + // our DNA alphabet size + const uint32 ALPHABET_SIZE = 2u; + + // instantiate a packed host vector + nvbio::PackedVector h_dna( len ); + + // pack our ASCII string + string_to_dna( + dna_string, // begin iterator of our ASCII string + h_dna.begin() ); // begin iterator of our output string + + // copy the packed vector to the device + nvbio::PackedVector d_dna( h_dna ); + + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/hello_world2/hello_world2.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/hello_world2/hello_world2.cu new file mode 100644 index 0000000000000000000000000000000000000000..34fdea015f7ff8f0e9a4d114ae556311bb9027c6 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/hello_world2/hello_world2.cu @@ -0,0 +1,105 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// hello_world2.cu +// + +#include +#include +#include +#include +#include +#include + + +using namespace nvbio; + +template +struct print_strings +{ + typedef typename string_set_type::string_type string_type; + + NVBIO_HOST_DEVICE + void operator() (const string_type& string) const + { + char seed[4]; + dna_to_string( + string, + length( string ), + seed ); + + printf("%s\n", seed); + } +}; + +// main test entry point +// +int main(int argc, char* argv[]) +{ + // our hello world ASCII string + const char dna_string[] = "ACGTTGCA"; + const uint32 len = (uint32)strlen( dna_string ); + + // our DNA alphabet size + const uint32 ALPHABET_SIZE = AlphabetTraits::SYMBOL_SIZE; + + // instantiate a packed host vector + nvbio::PackedVector h_dna( len ); + + // pack our ASCII string + nvbio::assign( len, nvbio::from_string( dna_string ), h_dna.begin() ); + + // instantiate a packed host vector + nvbio::PackedVector d_dna( h_dna ); + + // prepare a vector to store the coordinates of the resulting infixes + nvbio::vector d_seed_coords; + + const uint32 n_seeds = enumerate_string_seeds( + len, // the input string length + uniform_seeds_functor<>( 3u, 1u ), // a seeding functor, specifying to extract all 3-mers offset by 1 base each + d_seed_coords ); // the output infix coordinates + + // define an infix-set to represent the resulting infixes + typedef nvbio::PackedVector::iterator packed_iterator_type; + typedef nvbio::vector::const_iterator infix_iterator_type; + typedef InfixSet infix_set_type; + + const infix_set_type seeds( + n_seeds, // the number of infixes in the set + d_dna.begin(), // the underlying string + d_seed_coords.begin() ); // the iterator to the infix coordinates + + thrust::for_each( + seeds.begin(), + seeds.end(), + print_strings() ); + + cudaDeviceSynchronize(); + + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/mem/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/mem/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..38521359b845e1ef084e0b04358ac8f9b5baddef --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/mem/CMakeLists.txt @@ -0,0 +1,8 @@ +nvbio_module(mem) + +addsources( +mem.cu +) + +cuda_add_executable(mem ${mem_srcs}) +target_link_libraries(mem nvbio zlibstatic lz4 crcstatic ${SYSTEM_LINK_LIBRARIES}) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/mem/mem.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/mem/mem.cu new file mode 100644 index 0000000000000000000000000000000000000000..c247cc60cdc44cbc259b8674c6810c86b3b5d56c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/mem/mem.cu @@ -0,0 +1,224 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// mem.cu +// + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +// main test entry point +// +int main(int argc, char* argv[]) +{ + // + // perform some basic option parsing + // + + const uint32 batch_reads = 512*1024; + const uint32 batch_bps = 50*1024*1024; + + const char* reads = argv[argc-1]; + const char* index = argv[argc-2]; + + uint32 max_reads = uint32(-1); + uint32 min_intv = 1u; + uint32 max_intv = 10000u; + uint32 min_span = 19u; + + for (int i = 0; i < argc; ++i) + { + if (strcmp( argv[i], "-max-reads" ) == 0) + max_reads = uint32( atoi( argv[++i] ) ); + else if (strcmp( argv[i], "-min-intv" ) == 0) + min_intv = atoi( argv[++i] ); + else if (strcmp( argv[i], "-max-intv" ) == 0) + max_intv = atoi( argv[++i] ); + else if (strcmp( argv[i], "-min-span" ) == 0) + min_span = atoi( argv[++i] ); + } + + const uint32 fm_flags = io::FMIndexData::FORWARD | + io::FMIndexData::REVERSE | + io::FMIndexData::SA; + + SharedPointer h_ref; + + h_ref = io::map_sequence_file( index ); + if (h_ref == NULL) + h_ref = io::load_sequence_file( DNA, index ); + + if (h_ref == NULL) + { + log_error(stderr, " failed loading reference \"%s\"\n", index); + return 1u; + } + + io::FMIndexData *h_fmi = NULL; + io::FMIndexDataMMAP mmap_loader; + io::FMIndexDataHost file_loader; + + if (mmap_loader.load( index )) + h_fmi = &mmap_loader; + else + { + if (!file_loader.load( index, fm_flags )) + { + log_error(stderr, " failed loading index \"%s\"\n", index); + return 1u; + } + + h_fmi = &file_loader; + } + + // build its device version + const io::SequenceDataDevice d_ref( *h_ref ); + const io::FMIndexDataDevice d_fmi( *h_fmi, fm_flags ); + + typedef io::SequenceDataAccess genome_access_type; + typedef genome_access_type::sequence_stream_type genome_type; + + // fetch the genome string + const genome_access_type d_genome_access( d_ref ); + const genome_type d_genome( d_genome_access.sequence_stream() ); + + // open a read file + log_info(stderr, " opening reads file... started\n"); + + SharedPointer read_data_file( + io::open_sequence_file( + reads, + io::Phred33, + 2*max_reads, + uint32(-1), + io::SequenceEncoding( io::FORWARD | io::REVERSE_COMPLEMENT ) ) ); + + // check whether the file opened correctly + if (read_data_file == NULL || read_data_file->is_ok() == false) + { + log_error(stderr, " failed opening file \"%s\"\n", reads); + return 1u; + } + log_info(stderr, " opening reads file... done\n"); + + typedef io::FMIndexDataDevice::fm_index_type fm_index_type; + typedef MEMFilterDevice mem_filter_type; + + // fetch the FM-index + const fm_index_type f_index = d_fmi.index(); + const fm_index_type r_index = d_fmi.rindex(); + + // create a MEM filter + mem_filter_type mem_filter; + + const uint32 mems_batch = 16*1024*1024; + nvbio::vector mems( mems_batch ); + + io::SequenceDataHost h_read_data; + + // load a batch of reads + while (io::next( DNA_N, &h_read_data, read_data_file.get(), batch_reads, batch_bps )) + { + log_info(stderr, " loading reads... started\n"); + + // copy it to the device + const io::SequenceDataDevice d_read_data( h_read_data ); + const io::SequenceDataAccess d_read_access( d_read_data ); + + const uint32 n_reads = d_read_data.size() / 2; + + log_info(stderr, " loading reads... done\n"); + log_info(stderr, " %u reads\n", n_reads); + + log_info(stderr, " ranking MEMs... started\n"); + + Timer timer; + timer.start(); + + mem_filter.rank( + f_index, + r_index, + d_read_access.sequence_string_set(), + min_intv, + max_intv, + min_span ); + + cudaDeviceSynchronize(); + timer.stop(); + + const uint64 n_mems = mem_filter.n_mems(); + + log_info(stderr, " ranking MEMs... done\n"); + log_info(stderr, " %.1f avg ranges\n", float( mem_filter.n_ranges() ) / float( n_reads ) ); + log_info(stderr, " %.1f avg MEMs\n", float( n_mems ) / float( n_reads ) ); + log_info(stderr, " %.1f K reads/s\n", 1.0e-3f * float(n_reads) / timer.seconds()); + + log_info(stderr, " locating MEMs... started\n"); + + float locate_time = 0.0f; + + // loop through large batches of hits and locate & merge them + for (uint64 mems_begin = 0; mems_begin < n_mems; mems_begin += mems_batch) + { + const uint64 mems_end = nvbio::min( mems_begin + mems_batch, n_mems ); + + timer.start(); + + mem_filter.locate( + mems_begin, + mems_end, + mems.begin() ); + + cudaDeviceSynchronize(); + timer.stop(); + locate_time += timer.seconds(); + + log_verbose(stderr, "\r %5.2f%% (%4.1f M MEMs/s)", + 100.0f * float( mems_end ) / float( n_mems ), + 1.0e-6f * float( mems_end ) / locate_time ); + } + log_verbose_cont(stderr, "\n" ); + + log_info(stderr, " locating MEMs... done\n"); + } + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/proteinsw/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/proteinsw/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f6f47be7268983b7f1eaa19ef167cf74d508f11 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/proteinsw/CMakeLists.txt @@ -0,0 +1,8 @@ +nvbio_module(proteinsw) + +addsources( +proteinsw.cu +) + +cuda_add_executable(proteinsw ${proteinsw_srcs}) +target_link_libraries(proteinsw nvbio zlibstatic lz4 crcstatic ${SYSTEM_LINK_LIBRARIES}) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/proteinsw/proteinsw.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/proteinsw/proteinsw.cu new file mode 100644 index 0000000000000000000000000000000000000000..0bcad79bb7e2280c5c673fe64ca4f03bd95e9300 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/proteinsw/proteinsw.cu @@ -0,0 +1,233 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// proteinsw.cu +// + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +int8 s_blosum62[] = +{ + 4, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -2, -4, -1, -1, -1, 1, 0, 0, -3, -2, -2, -1, 0, + 0, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -4, -3, -3, -3, -1, -1, -1, -2, -2, -3, -3, -2, +-2, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -4, -1, 0, -2, 0, -1, -3, -4, -3, 4, 1, -1, +-1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -4, -1, 2, 0, 0, -1, -2, -3, -2, 1, 4, -1, +-2, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -4, -3, -3, -2, -2, -1, 1, 3, -3, -3, -1, + 0, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, 0, -4, -2, -2, -2, 0, -2, -3, -2, -3, -1, -2, -1, +-2, -3, -1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -4, -2, 0, 0, -1, -2, -3, -2, 2, 0, 0, -1, +-1, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -4, -3, -3, -3, -2, -1, 3, -3, -1, -3, -3, -1, +-1, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -4, -1, 1, 2, 0, -1, -2, -3, -2, 0, 1, -1, +-1, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -4, -3, -2, -2, -2, -1, 1, -2, -1, -4, -3, -1, +-1, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -4, -2, 0, -1, -1, -1, 1, -1, -1, -3, -1, -1, +-2, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, -4, -2, 0, 0, 1, 0, -3, -4, -2, 3, 0, -1, +-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, +-1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, -4, 7, -1, -2, -1, -1, -2, -4, -3, -2, -1, -2, +-1, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -4, -1, 5, 1, 0, -1, -2, -2, -1, 0, 3, -1, +-1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -4, -2, 1, 5, -1, -1, -3, -3, -2, -1, 0, -1, + 1, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -4, -1, 0, -1, 4, 1, -2, -3, -2, 0, 0, 0, + 0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -4, -1, -1, -1, 1, 5, 0, -2, -2, -1, -1, 0, + 0, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -4, -2, -2, -3, -2, 0, 4, -3, -1, -3, -2, -1, +-3, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -4, -2, -3, -3, -2, -3, 11, 2, -4, -3, -2, +-2, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -4, -3, -1, -2, -2, -2, -1, 2, 7, -3, -2, -1, +-2, -3, 4, 1, -3, -1, 0, -3, 0, -4, -3, 3, -4, -2, 0, -1, 0, -1, -3, -4, -3, 4, 1, -1, +-1, -3, 1, 4, -3, -2, 0, -3, 1, -3, -1, 0, -4, -1, 3, 0, 0, -1, -2, -3, -2, 1, 4, -1, + 0, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -4, -2, -1, -1, 0, 0, -1, -2, -1, -1, -1, -1, +}; + +// A scoring scheme class that will be used in conjunction with the \ref GotohAligner; +// +template +struct BlosumScheme +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE BlosumScheme(const matrix_iterator m, const int32 gap_open, const int32 gap_ext) : + m_matrix(m), m_gap_open(gap_open), m_gap_ext(gap_ext) {} + + // return the maximum match bonus at the given quality score + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 match(const uint8 q = 0) const { return 11; }; + + // return the substitution score at the given (reference,query) position (r_i,q_j), + // with values (r,q) and quality score qq + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 substitution( + const uint32 r_i, const uint32 q_j, + const uint8 r, const uint8 q, + const uint8 qq = 0) const { return int8( m_matrix[ r + q*24 ] ); }; + + // return gap open and extension penalties for the pattern (query) and the text (reference) + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 pattern_gap_open() const { return m_gap_open; }; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 pattern_gap_extension() const { return m_gap_ext; }; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 text_gap_open() const { return m_gap_open; }; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 text_gap_extension() const { return m_gap_ext; }; + + const matrix_iterator m_matrix; + const int32 m_gap_open; + const int32 m_gap_ext; +}; + +// main test entry point +// +int main(int argc, char* argv[]) +{ + log_info(stderr, "protein SW... started\n"); + const uint32 n_tests = 10; + const uint32 n_strings = 50000; + const uint32 P = 128; + const uint32 T = 1024; + + // alloc a device vector for holding the Blosum-62 scoring matrix + nvbio::vector d_blosum62( 24*24 ); + + // copy the matrix to the device + thrust::copy( s_blosum62, s_blosum62 + 24*24, d_blosum62.begin() ); + + // alloc the storage for the host strings + nvbio::vector h_pattern_strings( P * n_strings ); + nvbio::vector h_text_strings( T * n_strings ); + + // fill the strings with random characters + LCG_random rand; + for (uint32 i = 0; i < P * n_strings; ++i) + h_pattern_strings[i] = nvbio::min( uint8( rand.next() * 24.0f ), (uint8)23u ); + for (uint32 i = 0; i < T * n_strings; ++i) + h_text_strings[i] = nvbio::min( uint8( rand.next() * 24.0f ), (uint8)23u ); + + // copy to the device + nvbio::vector d_pattern_strings( h_pattern_strings ); + nvbio::vector d_text_strings( h_text_strings ); + nvbio::vector d_pattern_offsets( n_strings + 1 ); + nvbio::vector d_text_offsets( n_strings + 1 ); + + // build the string offsets + thrust::sequence( d_pattern_offsets.begin(), d_pattern_offsets.end(), 0u, P ); + thrust::sequence( d_text_offsets.begin(), d_text_offsets.end(), 0u, T ); + + // prepare a vector of alignment sinks + nvbio::vector< device_tag, aln::BestSink< uint32 > > sinks( n_strings ); + + { + const aln::SimpleGotohScheme scoring( 1, -1, -5, -3 ); + + Timer timer; + timer.start(); + + for (uint32 i = 0; i < n_tests; ++i) + { + // and execute the batch alignment, on a GPU device + aln::batch_alignment_score( + aln::make_gotoh_aligner( scoring ), + make_concatenated_string_set( n_strings, (const uint8*)raw_pointer( d_pattern_strings ), (const uint32*)raw_pointer( d_pattern_offsets ) ), + make_concatenated_string_set( n_strings, (const uint8*)raw_pointer( d_text_strings ), (const uint32*)raw_pointer( d_text_offsets ) ), + sinks.begin(), + aln::DeviceThreadScheduler(), + P, T ); + } + cudaDeviceSynchronize(); + + timer.stop(); + log_info(stderr, " GCUPS (Constant/P): %.1f\n", (1.0e-9f * float(P*T) * float(n_strings) * float(n_tests))/timer.seconds()); + } + { + const aln::SimpleGotohScheme scoring( 1, -1, -5, -3 ); + + Timer timer; + timer.start(); + + for (uint32 i = 0; i < n_tests; ++i) + { + // and execute the batch alignment, on a GPU device + aln::batch_alignment_score( + aln::make_gotoh_aligner( scoring ), + make_concatenated_string_set( n_strings, (const uint8*)raw_pointer( d_pattern_strings ), (const uint32*)raw_pointer( d_pattern_offsets ) ), + make_concatenated_string_set( n_strings, (const uint8*)raw_pointer( d_text_strings ), (const uint32*)raw_pointer( d_text_offsets ) ), + sinks.begin(), + aln::DeviceThreadScheduler(), + P, T ); + } + cudaDeviceSynchronize(); + + timer.stop(); + log_info(stderr, " GCUPS (Constant/T): %.1f\n", (1.0e-9f * float(P*T) * float(n_strings) * float(n_tests))/timer.seconds()); + } + { + const BlosumScheme< cuda::ldg_pointer > scoring( cuda::make_ldg_pointer( raw_pointer( d_blosum62 ) ), -5, -3 ); + + Timer timer; + timer.start(); + + for (uint32 i = 0; i < n_tests; ++i) + { + // and execute the batch alignment, on a GPU device + aln::batch_alignment_score( + aln::make_gotoh_aligner( scoring ), + make_concatenated_string_set( n_strings, (const uint8*)raw_pointer( d_pattern_strings ), (const uint32*)raw_pointer( d_pattern_offsets ) ), + make_concatenated_string_set( n_strings, (const uint8*)raw_pointer( d_text_strings ), (const uint32*)raw_pointer( d_text_offsets ) ), + sinks.begin(), + aln::DeviceThreadBlockScheduler<128,1>(), + P, T ); + } + cudaDeviceSynchronize(); + + timer.stop(); + log_info(stderr, " GCUPS (Blosum62/P): %.1f\n", (1.0e-9f * float(P*T) * float(n_strings) * float(n_tests))/timer.seconds()); + } + { + const BlosumScheme< cuda::ldg_pointer > scoring( cuda::make_ldg_pointer( raw_pointer( d_blosum62 ) ), -5, -3 ); + + Timer timer; + timer.start(); + + for (uint32 i = 0; i < n_tests; ++i) + { + // and execute the batch alignment, on a GPU device + aln::batch_alignment_score( + aln::make_gotoh_aligner( scoring ), + make_concatenated_string_set( n_strings, (const uint8*)raw_pointer( d_pattern_strings ), (const uint32*)raw_pointer( d_pattern_offsets ) ), + make_concatenated_string_set( n_strings, (const uint8*)raw_pointer( d_text_strings ), (const uint32*)raw_pointer( d_text_offsets ) ), + sinks.begin(), + aln::DeviceThreadBlockScheduler<128,1>(), + P, T ); + } + cudaDeviceSynchronize(); + + timer.stop(); + log_info(stderr, " GCUPS (Blosum62/T): %.1f\n", (1.0e-9f * float(P*T) * float(n_strings) * float(n_tests))/timer.seconds()); + } + + log_info(stderr, "protein SW... done\n"); + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/proteinsw/proteinsw_qp.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/proteinsw/proteinsw_qp.cu new file mode 100644 index 0000000000000000000000000000000000000000..cf168eb0af6fbbb68e64ef4cc2666c7879a1ef97 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/proteinsw/proteinsw_qp.cu @@ -0,0 +1,227 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// seeding.cu +// + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +int8 s_blosum62[] = +{ + 4, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -2, -4, -1, -1, -1, 1, 0, 0, -3, -2, -2, -1, 0, + 0, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -4, -3, -3, -3, -1, -1, -1, -2, -2, -3, -3, -2, +-2, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -4, -1, 0, -2, 0, -1, -3, -4, -3, 4, 1, -1, +-1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -4, -1, 2, 0, 0, -1, -2, -3, -2, 1, 4, -1, +-2, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -4, -3, -3, -2, -2, -1, 1, 3, -3, -3, -1, + 0, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, 0, -4, -2, -2, -2, 0, -2, -3, -2, -3, -1, -2, -1, +-2, -3, -1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -4, -2, 0, 0, -1, -2, -3, -2, 2, 0, 0, -1, +-1, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -4, -3, -3, -3, -2, -1, 3, -3, -1, -3, -3, -1, +-1, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -4, -1, 1, 2, 0, -1, -2, -3, -2, 0, 1, -1, +-1, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -4, -3, -2, -2, -2, -1, 1, -2, -1, -4, -3, -1, +-1, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -4, -2, 0, -1, -1, -1, 1, -1, -1, -3, -1, -1, +-2, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, -4, -2, 0, 0, 1, 0, -3, -4, -2, 3, 0, -1, +-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, +-1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, -4, 7, -1, -2, -1, -1, -2, -4, -3, -2, -1, -2, +-1, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -4, -1, 5, 1, 0, -1, -2, -2, -1, 0, 3, -1, +-1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -4, -2, 1, 5, -1, -1, -3, -3, -2, -1, 0, -1, + 1, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -4, -1, 0, -1, 4, 1, -2, -3, -2, 0, 0, 0, + 0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -4, -1, -1, -1, 1, 5, 0, -2, -2, -1, -1, 0, + 0, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -4, -2, -2, -3, -2, 0, 4, -3, -1, -3, -2, -1, +-3, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -4, -2, -3, -3, -2, -3, 11, 2, -4, -3, -2, +-2, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -4, -3, -1, -2, -2, -2, -1, 2, 7, -3, -2, -1, +-2, -3, 4, 1, -3, -1, 0, -3, 0, -4, -3, 3, -4, -2, 0, -1, 0, -1, -3, -4, -3, 4, 1, -1, +-1, -3, 1, 4, -3, -2, 0, -3, 1, -3, -1, 0, -4, -1, 3, 0, 0, -1, -2, -3, -2, 1, 4, -1, + 0, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -4, -2, -1, -1, 0, 0, -1, -2, -1, -1, -1, -1, +}; + +template +struct BlosumScheme +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE BlosumScheme(const matrix_iterator m, const int32 gap_open, const int32 gap_ext) : + m_matrix(m), m_gap_open(gap_open), m_gap_ext(gap_ext) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 match(const uint8 q = 0) const { return 11; }; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 substitution(const uint32 r_i, const uint32 q_j, const uint8 r, const uint8 q, const uint8 qq = 0) const { return int8( m_matrix[ r + q*24 ] ); }; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 pattern_gap_open() const { return m_gap_open; }; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 pattern_gap_extension() const { return m_gap_ext; }; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 text_gap_open() const { return m_gap_open; }; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 text_gap_extension() const { return m_gap_ext; }; + + const matrix_iterator m_matrix; + const int32 m_gap_open; + const int32 m_gap_ext; +}; + +template +struct QueryProfile +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE QueryProfile(const matrix_iterator m, const int32 gap_open, const int32 gap_ext) : + m_matrix(m), m_gap_open(gap_open), m_gap_ext(gap_ext) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 match(const uint8 q = 0) const { return 11; }; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 substitution(const uint32 r_i, const uint32 q_j, const uint8 r, const uint8 q, const uint8 qq = 0) const { return int8( m_matrix[ r + q_j*24 ] ); }; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 pattern_gap_open() const { return m_gap_open; }; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 pattern_gap_extension() const { return m_gap_ext; }; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 text_gap_open() const { return m_gap_open; }; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 text_gap_extension() const { return m_gap_ext; }; + + const matrix_iterator m_matrix; + const int32 m_gap_open; + const int32 m_gap_ext; +}; + +// main test entry point +// +int main(int argc, char* argv[]) +{ + log_info(stderr, "protein SW... started\n"); + const uint32 n_tests = 10; + const uint32 n_strings = 50000; + const uint32 P = 100; + const uint32 T = 1000; + + // alloc a device vector for holding the BLOSUM62 scoring matrix + nvbio::vector d_blosum62( 24*24 ); + + // copy the matrix to the device + thrust::copy( s_blosum62, s_blosum62 + 24*24, d_blosum62.begin() ); + + // alloc the storage for the host strings + nvbio::vector h_pattern_strings( P * n_strings ); + nvbio::vector h_pattern_profiles( P * n_strings * 24 ); + nvbio::vector h_text_strings( T * n_strings ); + + // fill the strings with random characters + LCG_random rand; + for (uint32 i = 0; i < n_strings; ++i) + { + for (uint32 j = 0; j < P; ++j) + { + h_pattern_strings[i*P + j] = nvbio::min( uint8( rand.next() * 24.0f ), (uint8)23u ); + + const uint8 q = h_pattern_strings[i*P + j]; + for (uint32 r = 0; r < 24; ++r) + h_pattern_profiles[i*P + j*24 + r] = s_blosum62[ r + q*24 ]; + } + } + for (uint32 i = 0; i < T * n_strings; ++i) + h_text_strings[i] = nvbio::min( uint8( rand.next() * 24.0f ), (uint8)23u ); + + // copy to the device + nvbio::vector d_pattern_strings( h_pattern_strings ); + nvbio::vector d_pattern_profiles( h_pattern_profiles ); + nvbio::vector d_text_strings( h_text_strings ); + nvbio::vector d_pattern_offsets( n_strings + 1 ); + nvbio::vector d_text_offsets( n_strings + 1 ); + + // build the string offsets + thrust::sequence( d_pattern_offsets.begin(), d_pattern_offsets.end(), 0u, P ); + thrust::sequence( d_text_offsets.begin(), d_text_offsets.end(), 0u, T ); + + // prepare a vector of alignment sinks + nvbio::vector< device_tag, aln::BestSink< uint32 > > sinks( n_strings ); + + { + const aln::SimpleGotohScheme scoring( 1, -1, -5, -3 ); + + Timer timer; + timer.start(); + + for (uint32 i = 0; i < n_tests; ++i) + { + // and execute the batch alignment, on a GPU device + aln::batch_alignment_score( + aln::make_gotoh_aligner( scoring ), + make_concatenated_string_set( n_strings, (const uint8*)raw_pointer( d_pattern_strings ), (const uint32*)raw_pointer( d_pattern_offsets ) ), + make_concatenated_string_set( n_strings, (const uint8*)raw_pointer( d_text_strings ), (const uint32*)raw_pointer( d_text_offsets ) ), + sinks.begin(), + aln::DeviceThreadScheduler() ); + } + cudaDeviceSynchronize(); + + timer.stop(); + log_info(stderr, " GCUPS (Constant): %.1f\n", (1.0e-9f * float(P*T) * float(n_strings) * float(n_tests))/timer.seconds()); + } + { + const BlosumScheme< cuda::ldg_pointer > scoring( cuda::make_ldg_pointer( raw_pointer( d_blosum62 ) ), -5, -3 ); + + Timer timer; + timer.start(); + + for (uint32 i = 0; i < n_tests; ++i) + { + // and execute the batch alignment, on a GPU device + aln::batch_alignment_score( + aln::make_gotoh_aligner( scoring ), + make_concatenated_string_set( n_strings, (const uint8*)raw_pointer( d_pattern_strings ), (const uint32*)raw_pointer( d_pattern_offsets ) ), + make_concatenated_string_set( n_strings, (const uint8*)raw_pointer( d_text_strings ), (const uint32*)raw_pointer( d_text_offsets ) ), + sinks.begin(), + aln::DeviceThreadBlockScheduler<128,1>() ); + } + cudaDeviceSynchronize(); + + timer.stop(); + log_info(stderr, " GCUPS (Blosum62): %.1f\n", (1.0e-9f * float(P*T) * float(n_strings) * float(n_tests))/timer.seconds()); + } + { + //const QueryProfile< cuda::ldg_pointer > scoring( cuda::make_ldg_pointer( raw_pointer( d_pattern_profiles ) ), -5, -3 ); + const QueryProfile scoring( raw_pointer( d_pattern_profiles ), -5, -3 ); + + Timer timer; + timer.start(); + + for (uint32 i = 0; i < n_tests; ++i) + { + // and execute the batch alignment, on a GPU device + aln::batch_alignment_score( + aln::make_gotoh_aligner( scoring ), + make_concatenated_string_set( n_strings, thrust::make_constant_iterator(0), (const uint32*)raw_pointer( d_pattern_offsets ) ), + make_concatenated_string_set( n_strings, (const uint8*)raw_pointer( d_text_strings ), (const uint32*)raw_pointer( d_text_offsets ) ), + sinks.begin(), + aln::DeviceThreadBlockScheduler<128,1>() ); + } + cudaDeviceSynchronize(); + + timer.stop(); + log_info(stderr, " GCUPS (Blosum62): %.1f\n", (1.0e-9f * float(P*T) * float(n_strings) * float(n_tests))/timer.seconds()); + } + + log_info(stderr, "protein SW... done\n"); + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/qmap/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/qmap/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..6a6fa991d5e927b1572f23fd7b63a05db7c4beca --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/qmap/CMakeLists.txt @@ -0,0 +1,8 @@ +nvbio_module(qmap) + +addsources( +qmap.cu +) + +cuda_add_executable(qmap ${qmap_srcs}) +target_link_libraries(qmap nvbio zlibstatic lz4 crcstatic ${SYSTEM_LINK_LIBRARIES}) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/qmap/alignment.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/qmap/alignment.h new file mode 100644 index 0000000000000000000000000000000000000000..30b870608eccee6e089d093667224eff568048d0 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/qmap/alignment.h @@ -0,0 +1,111 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// alignment.h +// + +#pragma once + +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +// a functor to extract the read infixes from the hit diagonals +// +struct read_infixes +{ + // constructor + NVBIO_HOST_DEVICE + read_infixes(const io::ConstSequenceDataView reads) : + m_reads( reads ) {} + + // functor operator + NVBIO_HOST_DEVICE + string_infix_coord_type operator() (const uint2 diagonal) const + { + const io::SequenceDataAccess reads( m_reads ); + + const uint32 read_id = diagonal.y; + + // fetch the read range + return reads.get_range( read_id ); + } + + const io::ConstSequenceDataView m_reads; +}; + +// a functor to extract the genome infixes from the hit diagonals +// +template +struct genome_infixes +{ + // constructor + NVBIO_HOST_DEVICE + genome_infixes(const uint32 genome_len, const io::ConstSequenceDataView reads) : + m_genome_len( genome_len ), + m_reads( reads ) {} + + // functor operator + NVBIO_HOST_DEVICE + string_infix_coord_type operator() (const uint2 diagonal) const + { + const io::SequenceDataAccess reads( m_reads ); + + const uint32 read_id = diagonal.y; + const uint32 text_pos = diagonal.x; + + // fetch the read range + const uint2 read_range = reads.get_range( read_id ); + const uint32 read_len = read_range.y - read_range.x; + + // compute the segment of text to align to + const uint32 genome_begin = text_pos > BAND_LEN/2 ? text_pos - BAND_LEN/2 : 0u; + const uint32 genome_end = nvbio::min( genome_begin + read_len + BAND_LEN, m_genome_len ); + + return make_uint2( genome_begin, genome_end ); + } + + const uint32 m_genome_len; + const io::ConstSequenceDataView m_reads; +}; + +// a functor to extract the score from a sink +// +struct sink_score +{ + typedef aln::BestSink argument_type; + typedef int16 result_type; + + // functor operator + NVBIO_HOST_DEVICE + int16 operator() (const aln::BestSink& sink) const { return sink.score; } +}; diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/qmap/qmap.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/qmap/qmap.cu new file mode 100644 index 0000000000000000000000000000000000000000..889a98d69e3c61f3c80c4ea3960a973d8e4b42d7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/qmap/qmap.cu @@ -0,0 +1,515 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// qmap.cu +// + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "alignment.h" +#include "util.h" + +using namespace nvbio; + +// query stats +// +struct Stats +{ + Stats() : + time(0), + build_time(0), + extract_time(0), + rank_time(0), + locate_time(0), + align_time(0), + reads(0), + aligned(0), + queries(0), + matches(0), + occurrences(0), + merged(0) {} + + float time; + float build_time; + float extract_time; + float rank_time; + float locate_time; + float align_time; + uint64 reads; + uint64 aligned; + uint64 queries; + uint64 matches; + uint64 occurrences; + uint64 merged; +}; + +// build a set of q-grams from a given string, together with their sorted counterpart +// +template +void build_qgrams( + const uint32 Q, + const uint32 genome_len, + const uint32 genome_offset, + const genome_string genome, + const uint32 n_queries, + qgram_vector_type& qgrams, + qgram_vector_type& sorted_qgrams, + index_vector_type& sorted_indices) +{ + // build the q-grams + qgrams.resize( n_queries ); + generate_qgrams( Q, 2u, genome_len, genome, n_queries, thrust::make_counting_iterator(genome_offset), qgrams.begin() ); + + // sort the q-grams + sorted_qgrams = qgrams; + sorted_indices.resize( n_queries ); + thrust::copy( + thrust::make_counting_iterator(genome_offset), + thrust::make_counting_iterator(genome_offset) + n_queries, + sorted_indices.begin() ); + + thrust::sort_by_key( sorted_qgrams.begin(), sorted_qgrams.end(), sorted_indices.begin() ); +} + +// build a q-gram set-index from a string-set +// +template +void qgram_set_index_build( + const uint32 Q, + const uint32 seed_interval, + const string_set_type string_set, + QGramSetIndexDevice& qgram_index) +{ + log_verbose(stderr, " building q-gram set-index... started\n"); + + Timer timer; + timer.start(); + + // build the q-gram set index + qgram_index.build( + Q, // q-gram size + 2u, // implicitly convert N to A + string_set, + uniform_seeds_functor<>( Q, seed_interval ), + 12u ); + + cudaDeviceSynchronize(); + timer.stop(); + const float time = timer.seconds(); + + log_verbose(stderr, " building q-gram set-index... done\n"); + log_verbose(stderr, " indexed q-grams : %6.2f M q-grams\n", 1.0e-6f * float( qgram_index.n_qgrams )); + log_verbose(stderr, " unique q-grams : %6.2f M q-grams\n", 1.0e-6f * float( qgram_index.n_unique_qgrams )); + log_verbose(stderr, " throughput : %5.1f M q-grams/s\n", 1.0e-6f * float( qgram_index.n_qgrams ) / time); + log_verbose(stderr, " memory usage : %5.1f MB\n", float( qgram_index.used_device_memory() ) / float(1024*1024) ); +} + +// perform q-gram index mapping +// +template +void map( + qgram_index_type& qgram_index, + qgram_filter_type& qgram_filter, + const uint32 merge_intv, + const io::SequenceDataDevice& reads, + const uint32 n_queries, + const uint32 genome_len, + const uint32 genome_offset, + const genome_string genome, + nvbio::vector& best_scores, + Stats& stats) +{ + typedef typename qgram_index_type::system_tag system_tag; + + // prepare some vectors to store the query qgrams + nvbio::vector qgrams( n_queries ); + nvbio::vector sorted_qgrams( n_queries ); + nvbio::vector sorted_indices( n_queries ); + + const uint32 Q = qgram_index.Q; + + Timer timer; + timer.start(); + + build_qgrams( + Q, + genome_len, + genome_offset, + genome, + n_queries, + qgrams, + sorted_qgrams, + sorted_indices ); + + cudaDeviceSynchronize(); + timer.stop(); + const float extract_time = timer.seconds(); + + stats.queries += n_queries; + stats.extract_time += extract_time; + + // + // search the sorted query q-grams with a q-gram filter + // + + const uint32 batch_size = 32*1024*1024; + + typedef typename qgram_filter_type::hit_type hit_type; + typedef typename qgram_filter_type::diagonal_type diagonal_type; + + // prepare storage for the output hits + nvbio::vector hits( batch_size ); + nvbio::vector merged_hits( batch_size ); + nvbio::vector merged_counts( batch_size ); + nvbio::vector scores( batch_size ); + nvbio::vector out_reads( batch_size ); + nvbio::vector out_scores( batch_size ); + nvbio::vector temp_storage; + + timer.start(); + + // first step: rank the query q-grams + const uint64 n_hits = qgram_filter.rank( + qgram_index, + n_queries, + nvbio::raw_pointer( sorted_qgrams ), + nvbio::raw_pointer( sorted_indices ) ); + + cudaDeviceSynchronize(); + timer.stop(); + stats.rank_time += timer.seconds(); + stats.occurrences += n_hits; + + nvbio::vector > sinks( batch_size ); + nvbio::vector genome_infix_coords( batch_size ); + nvbio::vector read_infix_coords( batch_size ); + + const static uint32 BAND_LEN = 31; + + // loop through large batches of hits and locate & merge them + for (uint64 hits_begin = 0; hits_begin < n_hits; hits_begin += batch_size) + { + typedef io::SequenceDataAccess read_access_type; + typedef read_access_type::sequence_string_set_type read_string_set_type; + typedef read_access_type::sequence_stream_type read_stream; + + // build an access pointer to the sequence data + const read_access_type reads_access( reads ); + + const uint64 hits_end = nvbio::min( hits_begin + batch_size, n_hits ); + + timer.start(); + + qgram_filter.locate( + hits_begin, + hits_end, + hits.begin() ); + + const uint32 n_merged = qgram_filter.merge( + merge_intv, + hits_end - hits_begin, + hits.begin(), + merged_hits.begin(), + merged_counts.begin() ); + + cudaDeviceSynchronize(); + timer.stop(); + stats.locate_time += timer.seconds(); + stats.merged += n_merged; + + timer.start(); + + // build the set of read infixes + thrust::transform( + merged_hits.begin(), + merged_hits.begin() + hits_end - hits_begin, + read_infix_coords.begin(), + read_infixes( nvbio::plain_view( reads ) ) ); + + // build the set of genome infixes + thrust::transform( + merged_hits.begin(), + merged_hits.begin() + hits_end - hits_begin, + genome_infix_coords.begin(), + genome_infixes( genome_len, nvbio::plain_view( reads ) ) ); + + typedef nvbio::vector::const_iterator infix_iterator; + + // build a view of the reads + const SparseStringSet read_infix_set( + hits_end - hits_begin, + reads_access.sequence_stream(), + read_infix_coords.begin() ); + + const SparseStringSet genome_infix_set( + hits_end - hits_begin, + genome, + genome_infix_coords.begin() ); + + typedef aln::MyersTag<5u> myers_dna5_tag; + aln::batch_banded_alignment_score( + aln::make_edit_distance_aligner(), + read_infix_set, + genome_infix_set, + sinks.begin(), + aln::DeviceThreadScheduler(), + reads.max_sequence_len(), + reads.max_sequence_len() + BAND_LEN ); + + cudaDeviceSynchronize(); + timer.stop(); + stats.align_time += timer.seconds(); + + // compute the best score for each read in this batch; + // note that we divide the string-id by 2 to merge results coming from the forward + // and reverse-complemented strands + cuda::reduce_by_key( + n_merged, + thrust::make_transform_iterator( + merged_hits.begin(), + make_composition_functor( divide_by_two(), component_functor( 1u ) ) ), // take the second component divided by 2 + thrust::make_transform_iterator( sinks.begin(), sink_score() ), + out_reads.begin(), + out_scores.begin(), + thrust::maximum(), + temp_storage ); + + // and keep track of the global best + update_scores( + n_merged, + nvbio::plain_view( out_reads ), + nvbio::plain_view( out_scores ), + nvbio::plain_view( best_scores ) ); + } +} + +// main test entry point +// +int main(int argc, char* argv[]) +{ + // + // perform some basic option parsing + // + + const uint32 batch_reads = 1*1024*1024; + const uint32 batch_bps = 100*1024*1024; + const uint32 queries_batch = 16*1024*1024; + + const char* reads = argv[argc-1]; + const char* index = argv[argc-2]; + + uint32 Q = 20; + uint32 Q_intv = 10; + uint32 merge_intv = 16; + uint32 max_reads = uint32(-1); + int16 score_threshold = -20; + + for (int i = 0; i < argc; ++i) + { + if (strcmp( argv[i], "-q" ) == 0) + { + Q = uint32( atoi( argv[++i] ) ); + Q_intv = uint32( atoi( argv[++i] ) ); + } + if (strcmp( argv[i], "-m" ) == 0) + merge_intv = uint32( atoi( argv[++i] ) ); + else if (strcmp( argv[i], "-max-reads" ) == 0) + max_reads = uint32( atoi( argv[++i] ) ); + else if (strcmp( argv[i], "-t" ) == 0) + score_threshold = int16( atoi( argv[++i] ) ); + } + + log_info(stderr, "qmap... started\n"); + + // load a genome archive... + log_visible(stderr, " loading reference index ... started\n"); + log_info(stderr, " file: \"%s\"\n", index); + + io::SequenceDataHost h_genome_data; + if (io::load_sequence_file( DNA, &h_genome_data, index ) == false) + { + log_error(stderr, " failed loading index \"%s\"\n", index); + return 1u; + } + + log_visible(stderr, " loading reference index ... done\n"); + log_verbose(stderr, " sequences : %u\n", h_genome_data.size() ); + log_verbose(stderr, " bps : %u\n", h_genome_data.bps() ); + log_verbose(stderr, " avg bps : %u (min: %u, max: %u)\n", + h_genome_data.avg_sequence_len(), + h_genome_data.min_sequence_len(), + h_genome_data.max_sequence_len() ); + + // build its device version + const io::SequenceDataDevice d_genome_data( h_genome_data ); + const io::SequenceDataAccess d_genome_access( d_genome_data ); + + typedef io::SequenceDataAccess::sequence_stream_type genome_type; + + // fetch the genome string + const uint32 genome_len = d_genome_data.bps(); + const genome_type d_genome( d_genome_access.sequence_stream() ); + + // open a read file + log_info(stderr, " opening reads file... started\n"); + + SharedPointer read_data_file( + io::open_sequence_file( + reads, + io::Phred33, + 2*max_reads, + uint32(-1), + io::SequenceEncoding( io::FORWARD | io::REVERSE_COMPLEMENT ) ) ); + + // check whether the file opened correctly + if (read_data_file == NULL || read_data_file->is_ok() == false) + { + log_error(stderr, " failed opening file \"%s\"\n", reads); + return 1u; + } + log_info(stderr, " opening reads file... done\n"); + + // keep stats + Stats stats; + + io::SequenceDataHost h_read_data; + + while (1) + { + // load a batch of reads + if (io::next( DNA_N, &h_read_data, read_data_file.get(), batch_reads, batch_bps ) == 0) + break; + + log_info(stderr, " loading reads... started\n"); + + // copy it to the device + const io::SequenceDataDevice d_read_data( h_read_data ); + const io::SequenceDataAccess d_read_access( d_read_data ); + + const uint32 n_reads = d_read_data.size() / 2; + + log_info(stderr, " loading reads... done\n"); + log_info(stderr, " %u reads\n", n_reads); + + // prepare some typedefs for the involved string-sets and infixes + typedef io::SequenceDataAccess read_access_type; // the read view type + typedef read_access_type::sequence_string_set_type string_set_type; // the read string-set + typedef string_set_infix_coord_type infix_coord_type; // the infix coordinate type, for string-sets + typedef nvbio::vector infix_vector_type; // the device vector type for infix coordinates + typedef InfixSet seed_set_type; // the infix-set type for representing seeds + + // fetch the actual read string-set + const string_set_type d_read_string_set = d_read_access.sequence_string_set(); + + // build the q-gram index + QGramSetIndexDevice qgram_index; + + qgram_set_index_build( + Q, + Q_intv, + d_read_string_set, + qgram_index ); + + typedef QGramFilterDevice qgram_filter_type; + qgram_filter_type qgram_filter; + + float time = 0.0f; + + const int16 worst_score = Field_traits::min(); + nvbio::vector best_scores( n_reads, worst_score ); + nvbio::vector temp_storage; + + // stream through the genome + for (uint32 genome_begin = 0; genome_begin < genome_len; genome_begin += queries_batch) + { + const uint32 genome_end = nvbio::min( genome_begin + queries_batch, genome_len ); + + Timer timer; + timer.start(); + + map( + qgram_index, + qgram_filter, + merge_intv, + d_read_data, + genome_end - genome_begin, + genome_len, + genome_begin, + d_genome, + best_scores, + stats ); + + cudaDeviceSynchronize(); + timer.stop(); + time += timer.seconds(); + + const float genome_ratio = float( genome_end ) / float( genome_len ); + + log_verbose(stderr, "\r aligned %5.2f%% of genome (%6.2f K reads/s)", 100.0f * genome_ratio, (1.0e-3f * n_reads) * genome_ratio / time ); + } + log_verbose_cont(stderr, "\n"); + + // accumulate the number of aligned reads + stats.reads += n_reads; + stats.time += time; + + // count how many reads have a score >= score_threshold + const uint32 n_aligned = cuda::reduce( + n_reads, + thrust::make_transform_iterator( best_scores.begin(), above_threshold( score_threshold ) ), + thrust::plus(), + temp_storage ); + + stats.aligned += n_aligned; + + log_info(stderr, " aligned %6.2f %% reads (%6.2f K reads/s)\n", 100.0f * float( stats.aligned ) / float( stats.reads ), (1.0e-3f * float( stats.reads )) / stats.time); + log_verbose(stderr, " breakdown:\n"); + log_verbose(stderr, " extract throughput : %.2f B q-grams/s\n", (1.0e-9f * float( stats.queries )) / stats.extract_time); + log_verbose(stderr, " rank throughput : %6.2f K reads/s\n", (1.0e-3f * float( stats.reads )) / stats.rank_time); + log_verbose(stderr, " : %6.2f B seeds/s\n", (1.0e-9f * float( stats.queries )) / stats.rank_time); + log_verbose(stderr, " locate throughput : %6.2f K reads/s\n", (1.0e-3f * float( stats.reads )) / stats.locate_time); + log_verbose(stderr, " align throughput : %6.2f K reads/s\n", (1.0e-3f * float( stats.reads )) / stats.align_time); + log_verbose(stderr, " : %6.2f M hits/s\n", (1.0e-6f * float( stats.merged )) / stats.align_time); + log_verbose(stderr, " occurrences : %.3f B\n", 1.0e-9f * float( stats.occurrences ) ); + log_verbose(stderr, " merged occurrences : %.3f B (%.1f %%)\n", 1.0e-9f * float( stats.merged ), 100.0f * float(stats.merged)/float(stats.occurrences)); + } + + log_info(stderr, "qmap... done\n"); + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/qmap/util.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/qmap/util.h new file mode 100644 index 0000000000000000000000000000000000000000..61f0ad602e6a202bc31e2ff4e854d6baf1a98e42 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/qmap/util.h @@ -0,0 +1,92 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include + +using namespace nvbio; + +// divide by two +// +struct divide_by_two +{ + typedef uint32 argument_type; + typedef uint32 result_type; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + result_type operator() (const argument_type op) const { return op / 2u; } +}; + +// return 1 or 0 depending on whether a number is >= than a given threshold +struct above_threshold +{ + typedef int16 argument_type; + typedef uint32 result_type; + + // constructor + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + above_threshold(const int16 _t) : t(_t) {} + + // functor operator + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const int16 s) { return s >= t ? 1u : 0u; } + + const int16 t; +}; + +// update the best scores vector +// +__global__ +void update_scores_kernel( + const uint32 n, + const uint32* reads, + const int16* scores, + int16* best) +{ + const uint32 i = threadIdx.x + blockIdx.x * blockDim.x; + if (i >= n) return; + + const uint32 read_id = reads[i]; + const int16 score = scores[i]; + + best[ read_id ] = nvbio::max( best[ read_id ], score ); +} + +// update the best scores vector +// +void update_scores( + const uint32 n, + const uint32* reads, + const int16* scores, + int16* best) +{ + const uint32 block_dim = 128; + const uint32 n_blocks = util::divide_ri( n, block_dim ); + + update_scores_kernel<<>>( n, reads, scores, best ); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/seeding/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/seeding/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..5124d212ffa9a3053cf1c3908d0d90bdddc7898d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/seeding/CMakeLists.txt @@ -0,0 +1,8 @@ +nvbio_module(seeding) + +addsources( +seeding.cu +) + +cuda_add_executable(seeding ${seeding_srcs}) +target_link_libraries(seeding nvbio zlibstatic lz4 crcstatic ${SYSTEM_LINK_LIBRARIES}) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/seeding/seeding.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/seeding/seeding.cu new file mode 100644 index 0000000000000000000000000000000000000000..402b9a20055cfb718c5fdec51088885df45ef458 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/seeding/seeding.cu @@ -0,0 +1,147 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// seeding.cu +// + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +// extract a set of uniformly spaced seeds from a string-set and return it as an InfixSet +// +template +InfixSet +extract_seeds( + const string_set_type string_set, // the input string-set + const uint32 seed_len, // the seeds length + const uint32 seed_interval, // the spacing between seeds + nvbio::vector& seed_coords) // the output vector of seed coordinates +{ + // enumerate all seeds + const uint32 n_seeds = enumerate_string_set_seeds( + string_set, + uniform_seeds_functor<>( seed_len, seed_interval ), + seed_coords ); + + // and build the output infix-set + return InfixSet( + n_seeds, + string_set, + nvbio::plain_view( seed_coords ) ); +} + +// main test entry point +// +int main(int argc, char* argv[]) +{ + // + // perform some basic option parsing + // + + uint32 n_bps = 10000000; + const char* reads = "./data/SRR493095_1.fastq.gz"; + + for (int i = 0; i < argc; ++i) + { + if (strcmp( argv[i], "-bps" ) == 0) + n_bps = uint32( atoi( argv[++i] ) )*1000u; + else if (strcmp( argv[i], "-reads" ) == 0) + reads = argv[++i]; + } + + // start our program + log_info(stderr, "seeding... started\n"); + + // open a read file + log_info(stderr, " loading reads... started\n"); + + SharedPointer read_data_file( + io::open_sequence_file( + reads, + io::Phred33, + uint32(-1), + uint32(-1) ) ); + + // check whether the file opened correctly + if (read_data_file == NULL || read_data_file->is_ok() == false) + { + log_error(stderr, " failed opening file \"%s\"\n", reads); + return 1u; + } + + const uint32 batch_size = uint32(-1); + const uint32 batch_bps = n_bps; + + // load a batch of reads + io::SequenceDataHost h_read_data; + + io::next( DNA_N, &h_read_data, read_data_file.get(), batch_size, batch_bps ); + + // copy it to the device + const io::SequenceDataDevice d_read_data( h_read_data ); + + log_info(stderr, " loading reads... done\n"); + log_info(stderr, " %u reads\n", d_read_data.size()); + + // prepare some typedefs for the involved string-sets and infixes + typedef io::SequenceDataAccess read_access_type; + typedef read_access_type::sequence_string_set_type string_set_type; // the read string-set + typedef string_set_infix_coord_type infix_coord_type; // the infix coordinate type, for string-sets + typedef nvbio::vector infix_vector_type; // the device vector type for infix coordinates + typedef InfixSet seed_set_type; // the infix-set type for representing seeds + + // build a read accessor + const read_access_type d_read_access( d_read_data ); + + // fetch the actual read string-set + const string_set_type d_read_string_set = d_read_access.sequence_string_set(); + + // prepare enough storage for the seed coordinates + infix_vector_type d_seed_coords; + + // extract the seeds and get the corresponding string-set representation + const seed_set_type d_seed_set = extract_seeds( + d_read_string_set, + 20u, + 10u, + d_seed_coords ); + + // output some stats + log_info(stderr, "seeding... done\n"); + log_info(stderr, " %u seeds\n", d_seed_set.size()); + + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/waveletfm/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/waveletfm/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..f5f2959488e3f8f09ad4e85fb67aec1c92877f26 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/waveletfm/CMakeLists.txt @@ -0,0 +1,8 @@ +nvbio_module(waveletfm) + +addsources( +waveletfm.cu +) + +cuda_add_executable(waveletfm ${waveletfm_srcs}) +target_link_libraries(waveletfm nvbio moderngpu zlibstatic lz4 crcstatic ${SYSTEM_LINK_LIBRARIES}) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/waveletfm/waveletfm.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/waveletfm/waveletfm.cu new file mode 100644 index 0000000000000000000000000000000000000000..c38b0feeeb16ffad6f1f1eabf3d128d6a4786091 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/examples/waveletfm/waveletfm.cu @@ -0,0 +1,137 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// waveletfm.cu +// +// Protein Search using a Wavelet Tree and an FM-index +// + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +// main test entry point +// +int main(int argc, char* argv[]) +{ + log_info(stderr, "waveletfm... started\n"); + + const char* proteins = "ACDEFGHIKLMNOPQRSTVWYBZX"; + const uint32 text_len = 24; + const uint32 alphabet_bits = AlphabetTraits::SYMBOL_SIZE; + const uint32 alphabet_size = 1u << alphabet_bits; + + // print the text + log_info(stderr, " text: %s\n", proteins); + + // allocate a host packed vector + PackedVector h_text( text_len ); + + // pack the string + from_string( proteins, proteins + text_len, h_text.begin() ); + + // copy it to the device + PackedVector d_text( h_text ); + + // allocate a vector for the BWT + PackedVector d_bwt( text_len + 1 ); + + BWTParams bwt_params; + + // build the BWT + const uint32 primary = cuda::bwt( text_len, d_text.begin(), d_bwt.begin(), &bwt_params ); + + // print the BWT + { + char proteins_bwt[ 25 ]; + + to_string( d_bwt.begin(), d_bwt.begin() + text_len, proteins_bwt ); + + log_info(stderr, " bwt: %s (primary %u)\n", proteins_bwt, primary); + } + + // define our wavelet tree storage type and its plain view + typedef WaveletTreeStorage wavelet_tree_type; + typedef WaveletTreeStorage::const_plain_view_type wavelet_tree_view_type; + + // build a wavelet tree + wavelet_tree_type wavelet_bwt; + + // setup the wavelet tree + setup( text_len, d_bwt.begin(), wavelet_bwt ); + + typedef nvbio::vector::const_iterator l2_iterator; + typedef fm_index fm_index_type; + + // take the const view of the wavelet tree + const wavelet_tree_view_type wavelet_bwt_view = plain_view( (const wavelet_tree_type&)wavelet_bwt ); + + // build the L2 vector + nvbio::vector L2(alphabet_size+1); + + // note we perform this on the host, even though the wavelet tree is on the device - + // gonna be slow, but it's not much stuff, and this is just an example anyway... + // and we just want to show that NVBIO is designed to make everything work! + L2[0] = 0; + for (uint32 i = 1; i <= alphabet_size; ++i) + L2[i] = L2[i-1] + rank( wavelet_bwt_view, text_len, i-1u ); + + // build the FM-index + const fm_index_type fmi( + text_len, + primary, + L2.begin(), + wavelet_bwt_view, + null_type() ); + + // do some string matching using our newly built FM-index - once again + // we are doing it on the host, though all data is on the device: the entire + // loop would be better moved to the device in a real app. + log_info(stderr, " string matching:\n"); + for (uint32 i = 0; i < text_len; ++i) + { + // match the i-th suffix of the text + const uint32 pattern_len = text_len - i; + + // compute the SA range containing the occurrences of the pattern we are after + const uint2 range = match( fmi, d_text.begin() + i, pattern_len ); + + // print the number of occurrences of our pattern, equal to the SA range size + log_info(stderr, " rank(%s): %u\n", proteins + i, 1u + range.y - range.x); + } + + log_info(stderr, "waveletfm... done\n"); + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBWT/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBWT/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..f3142c05f437196b083668eddecba39e17462482 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBWT/CMakeLists.txt @@ -0,0 +1,10 @@ +nvbio_module(nvBWT) + +addsources( +nvBWT.cu +filelist.cpp +) + +cuda_add_executable(nvBWT ${nvBWT_srcs}) +target_link_libraries(nvBWT nvbio zlibstatic crcstatic moderngpu ${SYSTEM_LINK_LIBRARIES}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBWT/filelist.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBWT/filelist.cpp new file mode 100644 index 0000000000000000000000000000000000000000..db3d4201b37da1ef126492ec214738c30dcdd2c3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBWT/filelist.cpp @@ -0,0 +1,116 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include +#ifdef _WIN32 +#include +#else +#include +#endif +#include +#include +#include + +/* Appends sorted list of files matching pattern to out_list. + * Should work on linux or windows */ +void list_files(const char* pattern, std::vector& out_list) +{ +#ifdef _WIN32 + const char dirsep = '\\'; +#else + const char dirsep = '/'; +#endif + + std::string base_input_name(pattern); + size_t last_slash = base_input_name.rfind(dirsep); + std::string base_path = base_input_name.substr( 0, last_slash+1 ); + log_info(stderr, "directory : \"%s\"\n", base_path.c_str()); + + typedef std::pair sortkey; + std::vector files; + sortkey temp; + +#ifdef _WIN32 + + _finddata_t file_info; + intptr_t find_handle = _findfirst( base_input_name.c_str(), &file_info ); + if (find_handle == -1) + { + log_error(stderr, "unable to locate \"%s\"", base_input_name.c_str()); + exit(1); + } + + do { + temp.second = base_path + std::string( file_info.name ); + files.push_back(temp); + } while (_findnext( find_handle, &file_info) != -1); + +#else + + glob_t info; + int stat = glob( base_input_name.c_str(), 0, 0, &info ); + if( stat != 0 ) + { + fprintf(stderr, "unable to locate \"%s\"", base_input_name.c_str()); + exit(1); + } + for(nvbio::uint32 i=0; i::iterator iter; + for(iter=files.begin(); iter!=files.end(); ++iter) { + size_t end, begin; + std::string numstring; + end = iter->second.find_last_of("."); + end = iter->second.find_last_of("0123456789", end); + if( end == std::string::npos ) { + // no numbers in file + iter->first = -1; // sort will be random but before numbers + } else { + begin = 1 + iter->second.find_last_not_of("0123456789", end); + numstring = iter->second.substr(begin, end-begin+1); + iter->first = atoi( numstring.c_str() ); + } + } + std::sort(files.begin(), files.end()); + + for(iter=files.begin(); iter!=files.end(); ++iter) { + out_list.push_back(iter->second); + } +} + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBWT/filelist.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBWT/filelist.h new file mode 100644 index 0000000000000000000000000000000000000000..72b9b7a31c552f7e31bd9975f1156c831eca8277 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBWT/filelist.h @@ -0,0 +1,32 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + + +/* Returns sorted list of files matching pattern + * Should work on linux or windows */ +void list_files(const char* pattern, std::vector& out_list); + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBWT/nvBWT.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBWT/nvBWT.cu new file mode 100644 index 0000000000000000000000000000000000000000..ec90b691aabba28550749b79598a54503a954b1e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBWT/nvBWT.cu @@ -0,0 +1,813 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// nvBWT.cu +// + +#define NVBIO_CUDA_DEBUG + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include "filelist.h" + +// PAC File Type +enum PacType { BPAC = 0, WPAC = 1 }; + +using namespace nvbio; + +unsigned char nst_nt4_table[256] = { + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5 /*'-'*/, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 +}; + + +#define RAND 0 +#define RAND48 1 + +#if (GENERATOR == RAND) || ((GENERATOR == RAND48) && defined(WIN32)) + +// generate random base pairs using rand() +inline void srand_bp(const unsigned int s) { srand(s); } +inline float frand() { return float(rand()) / float(RAND_MAX); } +inline uint8 rand_bp() { return uint8( frand() * 4 ) & 3; } + +#elif (GENERATOR == RAND48) + +// generate random base pairs using rand48() +inline void srand_bp(const unsigned int s) { srand48(s); } +inline uint8 rand_bp() { return uint8( drand48() * 4 ) & 3; } + +#endif + +struct Counter +{ + Counter() : m_size(0), m_reads(0) {} + + void begin_read() { m_reads++; } + void end_read() {} + + void id(const uint8 c) {} + void read(const uint8 c) { m_size++; } + + uint64 m_size; + uint32 m_reads; +}; + +template +struct Writer +{ + Writer(stream_type stream, const uint32 reads, const uint64 max_size) : + m_max_size(max_size), m_size(0), m_stream( stream ) + { + m_bntseq.seed = 11; + m_bntseq.anns_data.resize( reads ); + m_bntseq.anns_info.resize( reads ); + + srand_bp( m_bntseq.seed ); + + for (uint32 i = 0; i < 4; ++i) + m_freq[i] = 0; + } + + void begin_read() + { + BNTAnnData& ann_data = m_bntseq.anns_data[ m_bntseq.n_seqs ]; + ann_data.len = 0; + ann_data.gi = 0; + ann_data.offset = m_size; + ann_data.n_ambs = 0; + + BNTAnnInfo& ann_info = m_bntseq.anns_info[ m_bntseq.n_seqs ]; + ann_info.anno = "null"; + + m_lasts = 0; + } + void end_read() + { + m_bntseq.n_seqs++; + } + + void id(const uint8 c) + { + m_bntseq.anns_info[ m_bntseq.n_seqs ].name.push_back(char(c)); + } + void read(const uint8 s) + { + if (m_size < m_max_size) + { + const uint8 c = nst_nt4_table[s]; + + const uint8 sc = c < 4 ? c : rand_bp(); + + m_stream[ m_size ] = sc; + + // keep track of the symbol frequencies + ++m_freq[sc]; + + if (c >= 4) // we have an N + { + if (m_lasts == s) // contiguous N + { + // increment length of the last hole + ++m_bntseq.ambs.back().len; + } + else + { + // beginning of a new hole + BNTAmb amb; + amb.len = 1; + amb.offset = m_size; + amb.amb = s; + + m_bntseq.ambs.push_back( amb ); + + ++m_bntseq.anns_data[ m_bntseq.n_seqs ].n_ambs; + ++m_bntseq.n_holes; + } + } + // save last symbol + m_lasts = s; + + // update sequence length + BNTAnnData& ann_data = m_bntseq.anns_data[ m_bntseq.n_seqs ]; + ann_data.len++; + } + + m_bntseq.l_pac++; + + m_size++; + } + + uint64 m_max_size; + uint64 m_size; + stream_type m_stream; + + BNTSeq m_bntseq; + uint8 m_lasts; + + uint32 m_freq[4]; +}; + +template +bool save_stream(FILE* output_file, const uint64 seq_words, const StreamType* stream) +{ + for (uint64 words = 0; words < seq_words; words += 1024) + { + const uint32 n_words = (uint32)nvbio::min( uint64(1024u), uint64(seq_words - words) ); + if (fwrite( stream + words, sizeof(StreamType), n_words, output_file ) != n_words) + return false; + } + return true; +} + +// +// .wpac file +// +void save_wpac(const uint32 seq_length, const uint32* string_storage, const char* pac_name) +{ + log_info(stderr, "\nwriting \"%s\"... started\n", pac_name); + + const uint32 seq_words = util::divide_ri( seq_length, 16 ); + + FILE* output_file = fopen( pac_name, "wb" ); + if (output_file == NULL) + { + log_error(stderr, " could not open output file \"%s\"!\n", pac_name ); + exit(1); + } + + // write the sequence length as a uint64 + const uint64 len = seq_length; + fwrite( &len, sizeof(len), 1u, output_file ); + + // save the uint32 stream + if (save_stream( output_file, seq_words, string_storage ) == false) + { + log_error(stderr, " writing failed!\n"); + exit(1); + } + + fclose( output_file ); + log_info(stderr, "writing \"%s\"... done\n", pac_name); +} + +// +// .pac file +// +void save_bpac(const uint32 seq_length, const uint32* string_storage, const char* pac_name) +{ + typedef PackedStream stream_type; + typedef PackedStream< uint8*, uint8,2,true,int64> pac_stream_type; + + log_info(stderr, "\nwriting \"%s\"... started\n", pac_name); + + const uint32 bps_per_byte = 4u; + const uint64 seq_bytes = (seq_length + bps_per_byte - 1u) / bps_per_byte; + + FILE* output_file = fopen( pac_name, "wb" ); + if (output_file == NULL) + { + log_error(stderr, " could not open output file \"%s\"!\n", pac_name ); + exit(1); + } + + // copy the uint32 packed stream into a uint8 pac stream + thrust::host_vector pac_storage( seq_bytes ); + pac_stream_type pac_string( nvbio::plain_view( pac_storage ) ); + stream_type string( string_storage ); + + for (uint32 i = 0; i < seq_length; ++i) + pac_string[i] = string[i]; + + // save the uint8 stream + if (save_stream( output_file, seq_bytes, nvbio::raw_pointer( pac_storage ) ) == false) + { + log_error(stderr, " writing failed!\n"); + exit(1); + } + // the following code makes the pac file size always (l_pac/4+1+1) + if (seq_length % 4 == 0) + { + const uint8 ct = 0; + fwrite( &ct, 1, 1, output_file ); + } + { + const uint8 ct = seq_length % 4; + fwrite( &ct, 1, 1, output_file ); + } + + fclose( output_file ); + log_info(stderr, "writing \"%s\"... done\n", pac_name); +} + +// +// .pac | .wpac file +// +void save_pac(const uint32 seq_length, const uint32* string_storage, const char* pac_name, const PacType pac_type) +{ + if (pac_type == BPAC) + save_bpac( seq_length, string_storage, pac_name ); + else + save_wpac( seq_length, string_storage, pac_name ); +} + +// +// .bwt file +// +void save_bwt(const uint32 seq_length, const uint32 seq_words, const uint32 primary, const uint32* cumFreq, const uint32* h_bwt_storage, const char* bwt_name) +{ + log_info(stderr, "\nwriting \"%s\"... started\n", bwt_name); + FILE* output_file = fopen( bwt_name, "wb" ); + if (output_file == NULL) + { + log_error(stderr, " could not open output file \"%s\"!\n", bwt_name ); + exit(1); + } + fwrite( &primary, sizeof(uint32), 1, output_file ); + fwrite( cumFreq, sizeof(uint32), 4, output_file ); + if (save_stream( output_file, seq_words, h_bwt_storage ) == false) + { + log_error(stderr, " writing failed!\n"); + exit(1); + } + fclose( output_file ); + log_info(stderr, "writing \"%s\"... done\n", bwt_name); +} + +// +// .sa file +// +void save_ssa(const uint32 seq_length, const uint32 sa_intv, const uint32 ssa_len, const uint32 primary, const uint32* cumFreq, const uint32* h_ssa, const char* sa_name) +{ + log_info(stderr, "\nwriting \"%s\"... started\n", sa_name); + FILE* output_file = fopen( sa_name, "wb" ); + if (output_file == NULL) + { + log_error(stderr, " could not open output file \"%s\"!\n", sa_name ); + exit(1); + } + + fwrite( &primary, sizeof(uint32), 1u, output_file ); + fwrite( &cumFreq, sizeof(uint32), 4u, output_file ); + fwrite( &sa_intv, sizeof(uint32), 1u, output_file ); + fwrite( &seq_length, sizeof(uint32), 1u, output_file ); + fwrite( &h_ssa[1], sizeof(uint32), ssa_len-1, output_file ); + fclose( output_file ); + log_info(stderr, "writing \"%s\"... done\n", sa_name); +} + +int build( + const char* input_name, + const char* output_name, + const char* pac_name, + const char* rpac_name, + const char* bwt_name, + const char* rbwt_name, + const char* sa_name, + const char* rsa_name, + const uint64 max_length, + const PacType pac_type, + const bool compute_crc) +{ + std::vector sortednames; + list_files(input_name, sortednames); + + uint32 n_inputs = (uint32)sortednames.size(); + log_info(stderr, "\ncounting bps... started\n"); + // count entire sequence length + Counter counter; + + for (uint32 i = 0; i < n_inputs; ++i) + { + log_info(stderr, " counting \"%s\"\n", sortednames[i].c_str()); + + FASTA_inc_reader fasta( sortednames[i].c_str() ); + if (fasta.valid() == false) + { + log_error(stderr, " unable to open file\n"); + exit(1); + } + + while (fasta.read( 1024, counter ) == 1024); + } + log_info(stderr, "counting bps... done\n"); + + const uint64 seq_length = nvbio::min( (uint64)counter.m_size, (uint64)max_length ); + const uint32 bps_per_word = sizeof(uint32)*4u; + const uint64 seq_words = (seq_length + bps_per_word - 1u) / bps_per_word; + + log_info(stderr, "\nstats:\n"); + log_info(stderr, " reads : %u\n", counter.m_reads ); + log_info(stderr, " sequence length : %llu bps (%.1f MB)\n", + seq_length, + float(seq_words*sizeof(uint32))/float(1024*1024)); + log_info(stderr, " buffer size : %.1f MB\n", + 2*seq_words*sizeof(uint32)/1.0e6f ); + + const uint32 sa_intv = nvbio::io::FMIndexData::SA_INT; + const uint32 ssa_len = (seq_length + sa_intv) / sa_intv; + + // allocate the actual storage + thrust::host_vector h_string_storage( seq_words+1 ); + thrust::host_vector h_bwt_storage( seq_words+1 ); + thrust::host_vector h_ssa( ssa_len ); + + typedef PackedStream const_stream_type; + typedef PackedStream< uint32*,uint8,io::FMIndexData::BWT_BITS,io::FMIndexData::BWT_BIG_ENDIAN> stream_type; + + stream_type h_string( nvbio::plain_view( h_string_storage ) ); + + uint32 cumFreq[4] = { 0, 0, 0, 0 }; + + log_info(stderr, "\nbuffering bps... started\n"); + // read all files + { + Writer writer( h_string, counter.m_reads, seq_length ); + + for (uint32 i = 0; i < n_inputs; ++i) + { + log_info(stderr, " buffering \"%s\"\n", sortednames[i].c_str()); + + FASTA_inc_reader fasta( sortednames[i].c_str() ); + if (fasta.valid() == false) + { + log_error(stderr, " unable to open file!\n"); + exit(1); + } + + while (fasta.read( 1024, writer ) == 1024); + } + + save_bns( writer.m_bntseq, output_name ); + + // compute the cumulative symbol frequencies + cumFreq[0] = writer.m_freq[0]; + cumFreq[1] = writer.m_freq[1] + cumFreq[0]; + cumFreq[2] = writer.m_freq[2] + cumFreq[1]; + cumFreq[3] = writer.m_freq[3] + cumFreq[2]; + + if (cumFreq[3] != seq_length) + { + log_error(stderr, " mismatching symbol frequencies!\n"); + log_error(stderr, " (%u, %u, %u, %u)\n", cumFreq[0], cumFreq[1], cumFreq[2], cumFreq[3]); + exit(1); + } + } + log_info(stderr, "buffering bps... done\n"); + + if (compute_crc) + { + const uint32 crc = crcCalc( h_string, uint32(seq_length) ); + log_info(stderr, " crc: %u\n", crc); + } + + try + { + BWTParams params; + uint32 primary; + + thrust::device_vector d_string_storage( h_string_storage ); + thrust::device_vector d_bwt_storage( seq_words+1 ); + + const_stream_type d_string( nvbio::plain_view( d_string_storage ) ); + stream_type d_bwt( nvbio::plain_view( d_bwt_storage ) ); + + Timer timer; + + log_info(stderr, "\nbuilding forward BWT... started\n"); + timer.start(); + { + StringBWTSSAHandler output( + seq_length, // string length + d_string, // string + sa_intv, // SSA sampling interval + d_bwt, // output bwt iterator + nvbio::plain_view( h_ssa ) ); // output ssa iterator + + cuda::blockwise_suffix_sort( + seq_length, + d_string, + output, + ¶ms ); + + // remove the dollar symbol + output.remove_dollar(); + + primary = output.primary(); + } + timer.stop(); + log_info(stderr, "building forward BWT... done: %um:%us\n", uint32(timer.seconds()/60), uint32(timer.seconds())%60); + log_info(stderr, " primary: %u\n", primary); + + // save everything to disk + { + // copy to the host + thrust::copy( d_bwt_storage.begin(), + d_bwt_storage.begin() + seq_words, + h_bwt_storage.begin() ); + + if (compute_crc) + { + const_stream_type h_bwt( nvbio::plain_view( h_bwt_storage ) ); + const uint32 crc = crcCalc( h_bwt, uint32(seq_length) ); + log_info(stderr, " crc: %u\n", crc); + } + + save_pac( seq_length, nvbio::plain_view( h_string_storage ), pac_name, pac_type ); + save_bwt( seq_length, seq_words, primary, cumFreq, nvbio::plain_view( h_bwt_storage ), bwt_name ); + save_ssa( seq_length, sa_intv, ssa_len, primary, cumFreq, nvbio::plain_view( h_ssa ), sa_name ); + } + + // reverse the string in h_string_storage + { + // reuse the bwt storage to build the reverse + uint32* h_rbase_stream = nvbio::plain_view( h_bwt_storage ); + stream_type h_rstring( h_rbase_stream ); + + // reverse the string + for (uint32 i = 0; i < seq_length; ++i) + h_rstring[i] = h_string[ seq_length - i - 1u ]; + + // and now swap the vectors + h_bwt_storage.swap( h_string_storage ); + h_string = stream_type( nvbio::plain_view( h_string_storage ) ); + + // and copy back the new string to the device + d_string_storage = h_string_storage; + } + + log_info(stderr, "\nbuilding reverse BWT... started\n"); + timer.start(); + { + StringBWTSSAHandler output( + seq_length, // string length + d_string, // string + sa_intv, // SSA sampling interval + d_bwt, // output bwt iterator + nvbio::plain_view( h_ssa ) ); // output ssa iterator + + cuda::blockwise_suffix_sort( + seq_length, + d_string, + output, + ¶ms ); + + // remove the dollar symbol + output.remove_dollar(); + + primary = output.primary(); + } + timer.stop(); + log_info(stderr, "building reverse BWT... done: %um:%us\n", uint32(timer.seconds()/60), uint32(timer.seconds())%60); + log_info(stderr, " primary: %u\n", primary); + + // save everything to disk + { + // copy to the host + thrust::copy( d_bwt_storage.begin(), + d_bwt_storage.begin() + seq_words, + h_bwt_storage.begin() ); + + if (compute_crc) + { + const_stream_type h_bwt( nvbio::plain_view( h_bwt_storage ) ); + const uint32 crc = crcCalc( h_bwt, uint32(seq_length) ); + log_info(stderr, " crc: %u\n", crc); + } + + save_pac( seq_length, nvbio::plain_view( h_string_storage ), rpac_name, pac_type ); + save_bwt( seq_length, seq_words, primary, cumFreq, nvbio::plain_view( h_bwt_storage ), rbwt_name ); + save_ssa( seq_length, sa_intv, ssa_len, primary, cumFreq, nvbio::plain_view( h_ssa ), rsa_name ); + } + } + catch (nvbio::cuda_error e) + { + log_error(stderr, "caught a nvbio::cuda_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::bad_alloc e) + { + log_error(stderr, "caught a nvbio::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::logic_error e) + { + log_error(stderr, "caught a nvbio::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::runtime_error e) + { + log_error(stderr, "caught a nvbio::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::bad_alloc e) + { + log_error(stderr, "caught a std::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::logic_error e) + { + log_error(stderr, "caught a std::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::runtime_error e) + { + log_error(stderr, "caught a std::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (...) + { + log_error(stderr,"unknown exception caught!\n"); + exit(1); + } + return 0; +} + +int main(int argc, char* argv[]) +{ + crcInit(); + + if (argc < 2) + { + log_info(stderr, "please specify input and output file names, e.g:\n"); + log_info(stderr, " nvBWT [options] myinput.*.fa output-prefix\n"); + log_info(stderr, " options:\n"); + log_info(stderr, " -v | --verbosity select verbosity\n"); + log_info(stderr, " -m | --max-length clamp input to max_length\n"); + log_info(stderr, " -b | --byte-packing output byte packed .pac\n"); + log_info(stderr, " -w | --word-packing output word packed .wpac\n"); + log_info(stderr, " -c | --crc compute crcs\n"); + log_info(stderr, " -d | --device cuda device\n"); + exit(0); + } + + const char* file_names[2] = { NULL, NULL }; + uint64 max_length = uint64(-1); + PacType pac_type = BPAC; + bool crc = false; + int cuda_device = -1; + + uint32 n_files = 0; + for (int32 i = 1; i < argc; ++i) + { + const char* arg = argv[i]; + + if ((strcmp( arg, "-m" ) == 0) || + (strcmp( arg, "--max-length" ) == 0)) + { + max_length = atoi( argv[++i] ); + } + else if ((strcmp( argv[i], "-v" ) == 0) || + (strcmp( argv[i], "-verbosity" ) == 0) || + (strcmp( argv[i], "--verbosity" ) == 0)) + { + set_verbosity( Verbosity( atoi( argv[++i] ) ) ); + } + else if ((strcmp( arg, "-b" ) == 0) || + (strcmp( arg, "--byte-packing" ) == 0)) + { + pac_type = BPAC; + } + else if ((strcmp( arg, "-w" ) == 0) || + (strcmp( arg, "--word-packing" ) == 0)) + { + pac_type = WPAC; + } + else if ((strcmp( arg, "-c" ) == 0) || + (strcmp( arg, "--crc" ) == 0)) + { + crc = true; + } + else if ((strcmp( arg, "-d" ) == 0) || + (strcmp( arg, "--device" ) == 0)) + { + cuda_device = atoi( argv[++i] ); + } + else + file_names[ n_files++ ] = argv[i]; + } + + const char* input_name = file_names[0]; + const char* output_name = file_names[1]; + std::string pac_string = std::string( output_name ) + (pac_type == BPAC ? ".pac" : ".wpac"); + const char* pac_name = pac_string.c_str(); + std::string rpac_string = std::string( output_name ) + (pac_type == BPAC ? ".rpac" : ".rwpac"); + const char* rpac_name = rpac_string.c_str(); + std::string bwt_string = std::string( output_name ) + ".bwt"; + const char* bwt_name = bwt_string.c_str(); + std::string rbwt_string = std::string( output_name ) + ".rbwt"; + const char* rbwt_name = rbwt_string.c_str(); + std::string sa_string = std::string( output_name ) + ".sa"; + const char* sa_name = sa_string.c_str(); + std::string rsa_string = std::string( output_name ) + ".rsa"; + const char* rsa_name = rsa_string.c_str(); + + log_info(stderr, "max length : %lld\n", max_length); + log_info(stderr, "input : \"%s\"\n", input_name); + log_info(stderr, "output : \"%s\"\n", output_name); + + try + { + int device_count; + cudaGetDeviceCount(&device_count); + cuda::check_error("cuda-check"); + + log_verbose(stderr, " cuda devices : %d\n", device_count); + + // inspect and select cuda devices + if (device_count) + { + if (cuda_device == -1) + { + int best_device = 0; + cudaDeviceProp best_device_prop; + cudaGetDeviceProperties( &best_device_prop, best_device ); + + for (int device = 0; device < device_count; ++device) + { + cudaDeviceProp device_prop; + cudaGetDeviceProperties( &device_prop, device ); + log_verbose(stderr, " device %d has compute capability %d.%d\n", device, device_prop.major, device_prop.minor); + log_verbose(stderr, " SM count : %u\n", device_prop.multiProcessorCount); + log_verbose(stderr, " SM clock rate : %u Mhz\n", device_prop.clockRate / 1000); + log_verbose(stderr, " memory clock rate : %.1f Ghz\n", float(device_prop.memoryClockRate) * 1.0e-6f); + + if (device_prop.major >= best_device_prop.major && + device_prop.minor >= best_device_prop.minor) + { + best_device_prop = device_prop; + best_device = device; + } + } + cuda_device = best_device; + } + log_verbose(stderr, " chosen device %d\n", cuda_device); + { + cudaDeviceProp device_prop; + cudaGetDeviceProperties( &device_prop, cuda_device ); + log_verbose(stderr, " device name : %s\n", device_prop.name); + log_verbose(stderr, " compute capability : %d.%d\n", device_prop.major, device_prop.minor); + } + cudaSetDevice( cuda_device ); + } + + size_t free, total; + cudaMemGetInfo(&free, &total); + NVBIO_CUDA_DEBUG_STATEMENT( log_info(stderr,"device mem : total: %.1f GB, free: %.1f GB\n", float(total)/float(1024*1024*1024), float(free)/float(1024*1024*1024)) ); + + cuda::check_error("cuda-memory-check"); + + return build( input_name, output_name, pac_name, rpac_name, bwt_name, rbwt_name, sa_name, rsa_name, max_length, pac_type, crc ); + } + catch (nvbio::cuda_error e) + { + log_error(stderr, "caught a nvbio::cuda_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (nvbio::bad_alloc e) + { + log_error(stderr, "caught a nvbio::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (nvbio::logic_error e) + { + log_error(stderr, "caught a nvbio::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (nvbio::runtime_error e) + { + log_error(stderr, "caught a nvbio::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (thrust::system::system_error e) + { + log_error(stderr, "caught a thrust::system_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (std::bad_alloc e) + { + log_error(stderr, "caught a std::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (std::logic_error e) + { + log_error(stderr, "caught a std::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (std::runtime_error e) + { + log_error(stderr, "caught a std::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (...) + { + log_error(stderr, "caught an unknown exception!\n"); + return 1; + } +} + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..0e888e1a705fb2d9001996154bf290c88f83d00e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/CMakeLists.txt @@ -0,0 +1,12 @@ +nvbio_module(nvBowtie) + +addsources( +nvBowtie.cpp +) + +nvbio_add_module_directory(bowtie2) +nvbio_add_module_directory(bowtie2/cuda) + +cuda_add_executable(nvBowtie ${nvBowtie_srcs}) +target_link_libraries(nvBowtie nvbio zlibstatic lz4 crcstatic ${SYSTEM_LINK_LIBRARIES}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..76313fc05ab6ad319fe5ff7bd5c0df6836d69c60 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/CMakeLists.txt @@ -0,0 +1,4 @@ +addsources( +quality_coeffs.cpp +quality_coeffs.h +) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..170ff34af9eaf75f49fa0880a0d21d8d5a3e69c2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/CMakeLists.txt @@ -0,0 +1,76 @@ +addsources( +aligner_all_ed.cu +aligner_all_sw.cu +aligner_all.h +aligner_best_approx_ed.cu +aligner_best_approx.h +aligner_best_approx_paired_ed.cu +aligner_best_approx_paired.h +aligner_best_approx_paired_sw.cu +aligner_best_approx_sw.cu +aligner_best_exact.h +aligner.h +aligner_init.cu +aligner_inst.h +aligner_sort.cu +compute_thread.cu +compute_thread.h +checksums.cu +checksums.h +defs.h +fmindex_def.h +input_thread.cpp +input_thread.h +locate.h +locate_inl.h +mapping.cu +mapping.h +mapping_impl.h +mapping_inl.h +mapq.cpp +mapq.h +params.h +params.cpp +persist.cu +persist.h +pipeline_states.h +reduce.cu +reduce.h +reduce_impl.h +reduce_inl.h +score_all.cu +score_all_impl.h +score_all_inl.h +score_best.cu +score_best_impl.h +score_best_inl.h +score_gapped.cu +score_ungapped.cu +score_paired.cu +score_paired_impl.h +score_paired_inl.h +score_opposite_impl.h +score_opposite_inl.h +score.h +scoring.h +scoring_inl.h +scoring_queues.h +scoring_queues_inl.h +scoring_queues_test.cu +seed_hit.h +select.cu +select.h +select_impl.h +select_inl.h +seed_hit_deque_array.cu +seed_hit_deque_array.h +seed_hit_deque_array_inl.h +seed_hit_deque_array_test.cu +stats.cpp +stats.h +traceback.cu +traceback.h +traceback_impl.h +traceback_inl.h +utils.h +) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner.h new file mode 100644 index 0000000000000000000000000000000000000000..c8538000c2e64fa1c4429a42216d13aeabda9b01 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner.h @@ -0,0 +1,388 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + + + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +struct Aligner +{ + static const uint32 MAX_READ_LEN = MAXIMUM_READ_LENGTH; + + typedef FMIndexDef::type fmi_type; + typedef FMIndexDef::type rfmi_type; + + typedef ReadsDef::read_storage_type read_storage_type; + typedef ReadsDef::read_base_type read_base_type; + typedef ReadsDef::read_qual_type read_qual_type; + typedef ReadsDef::read_view_type read_view_type; + typedef ReadsDef::type read_batch_type; + + typedef io::LdgSequenceDataView genome_view_type; + typedef io::SequenceDataAccess genome_access_type; + typedef genome_access_type::sequence_stream_type genome_iterator; + + + uint32 ID; + uint32 BATCH_SIZE; + + thrust::device_vector dp_buffer_dvec; + uint8* dp_buffer_dptr; + + SeedHitDequeArray hit_deques; + + nvbio::cuda::PingPongQueues seed_queues; + ScoringQueues scoring_queues; + + thrust::device_vector idx_queue_dvec; + uint32* idx_queue_dptr; + thrust::device_vector sorting_queue_dvec; + + thrust::device_vector reseed_dvec; + uint8* reseed_dptr; + thrust::device_vector trys_dvec; + uint32* trys_dptr; + thrust::device_vector rseeds_dvec; + uint32* rseeds_dptr; + thrust::device_vector flags_dvec; + uint8* flags_dptr; + nvbio::vector temp_dvec; + + thrust::device_vector best_data_dvec; + thrust::device_vector best_data_dvec_o; + io::Alignment* best_data_dptr; + io::Alignment* best_data_dptr_o; + thrust::device_vector mapq_dvec; + uint8* mapq_dptr; + + // --- paired-end vectors --------------------------------- // + thrust::device_vector opposite_queue_dvec; + uint32* opposite_queue_dptr; + + // --- all-mapping vectors -------------------------------- // + thrust::device_vector buffer_alignments_dvec; + io::Alignment* buffer_alignments_dptr; + thrust::device_vector buffer_read_info_dvec; + uint32* buffer_read_info_dptr; + thrust::device_vector output_alignments_dvec; + io::Alignment* output_alignments_dptr; + thrust::device_vector output_read_info_dvec; + uint32* output_read_info_dptr; + + thrust::device_vector hits_count_scan_dvec; + uint32* hits_count_scan_dptr; + thrust::device_vector hits_range_scan_dvec; + uint64* hits_range_scan_dptr; + // -------------------------------------------------------- // + + nvbio::DeviceVectorArray mds; + nvbio::DeviceVectorArray cigar; + thrust::device_vector cigar_coords_dvec; + uint2* cigar_coords_dptr; + + thrust::device_vector hits_stats_dvec; + thrust::host_vector hits_stats_hvec; + uint64* hits_stats_dptr; + + uint32 batch_number; + + nvbio::cuda::SortEnactor sort_enactor; + // --------------------------------------------------------------------------------------------- // + + // file object that we're writing into + io::OutputFile *output_file; + + static uint32 band_length(const uint32 max_dist) + { + //return max_dist*2+1; + // compute band length + uint32 band_len = 4; + while (band_len-1 < max_dist*2+1) + band_len *= 2; + band_len -= 1; + return band_len; + } + + Aligner() : output_file(NULL) {} + + bool init(const uint32 id, const uint32 batch_size, const Params& params, const EndType type); + + void keep_stats(const uint32 count, Stats& stats); + + template + void best_approx( + const Params& params, + const fmi_type fmi, + const rfmi_type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + const io::SequenceDataDevice& read_data, + io::HostOutputBatchSE& cpu_batch, + Stats& stats); + + template < + typename scoring_tag, + typename scoring_scheme_type> + void best_approx_score( + const Params& params, + const fmi_type fmi, + const rfmi_type rfmi, + const scoring_scheme_type& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + const io::SequenceDataDevice& read_data, + const uint32 seeding_pass, + const uint32 seed_queue_size, + const uint32* seed_queue, + Stats& stats); + + template + void best_approx( + const Params& params, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + const io::SequenceDataDevice& read_data1, + const io::SequenceDataDevice& read_data2, + io::HostOutputBatchPE& cpu_batch, + Stats& stats); + + template < + typename scoring_tag, + typename scoring_scheme_type> + void best_approx_score( + const Params& params, + const fmi_type fmi, + const rfmi_type rfmi, + const scoring_scheme_type& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + const uint32 anchor, + const io::SequenceDataDevice& read_data1, + const io::SequenceDataDevice& read_data2, + const uint32 seeding_pass, + const uint32 seed_queue_size, + const uint32* seed_queue, + Stats& stats); + + template + void all( + const Params& params, + const fmi_type fmi, + const rfmi_type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + const io::SequenceDataDevice& read_data, + io::HostOutputBatchSE& cpu_batch, + Stats& stats); + + template + void score_all( + const Params& params, + const fmi_type fmi, + const rfmi_type rfmi, + const UberScoringScheme& input_scoring_scheme, + const scoring_scheme_type& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + const io::SequenceDataDevice& read_data, + io::HostOutputBatchSE& cpu_batch, + const uint32 seed_queue_size, + const uint32* seed_queue, + Stats& stats, + uint64& total_alignments); + + #if defined(__CUDACC__) + // return a pointer to an "index" into the given sorted keys + // + template + std::pair sort_64_bits( + const uint32 count, + const iterator_type keys) + { + thrust::copy( + keys, + keys + count, + thrust::device_ptr( (uint64*)raw_pointer( sorting_queue_dvec ) ) ); + + return sort_64_bits( count ); + } + #endif + + // return a pointer to an "index" into the given sorted keys + // + std::pair sort_64_bits( + const uint32 count); + + // return a pointer to an "index" into the given keys sorted by their hi bits + // + uint32* sort_hi_bits( + const uint32 count, + const uint32* keys); + + // sort a set of keys in place + // + void sort_inplace( + const uint32 count, + uint32* keys); + + bool init_alloc(const uint32 BATCH_SIZE, const Params& params, const EndType type, bool do_alloc, std::pair* mem_stats = NULL); +}; + +// Compute the total number of matches found +void hits_stats( + const uint32 batch_size, + const SeedHit* hit_data, + const uint32* hit_counts, + uint64* hit_stats); + +void ring_buffer_to_plain_array( + const uint32* buffer, + const uint32 buffer_size, + const uint32 begin, + const uint32 end, + uint32* output); + +#if defined(__CUDACC__) + +// initialize a set of alignments +// +template +__global__ +void init_alignments_kernel( + const ReadBatch read_batch, + const ScoreFunction worst_score_fun, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 mate) +{ + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= read_batch.size()) return; + + // compute the read length + const uint2 read_range = read_batch.get_range( thread_id ); + const uint32 read_len = read_range.y - read_range.x; + + const int32 worst_score = worst_score_fun( read_len ); + + io::Alignment a1 = io::Alignment( uint32(-1), io::Alignment::max_ed(), worst_score, mate ); + io::Alignment a2 = io::Alignment( uint32(-1), io::Alignment::max_ed(), worst_score, mate ); + best_data[ thread_id ] = a1; + best_data[ thread_id + best_stride ] = a2; +} + +// initialize a set of alignments +// +template +void init_alignments( + const ReadBatch read_batch, + const ScoreFunction worst_score_fun, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 mate = 0) +{ + const int blocks = (read_batch.size() + BLOCKDIM-1) / BLOCKDIM; + + init_alignments_kernel<<>>( + read_batch, + worst_score_fun, + best_data, + best_stride, + mate ); +} + +#endif // defined(__CUDACC__) + +// mark unaligned reads that need reseeding +// +void mark_unaligned( + const uint32 n_active_reads, + const uint32* active_reads, + const io::Alignment* best_data, + uint8* reseed); + +// mark unique unaligned read pairs as discordant +// +void mark_discordant( + const uint32 n_reads, + io::Alignment* anchor_data, + io::Alignment* opposite_data, + const uint32 stride); + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_all.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_all.h new file mode 100644 index 0000000000000000000000000000000000000000..8ed85800712f406656d5dfd7cbe971c798074bd1 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_all.h @@ -0,0 +1,694 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +template +void Aligner::all( + const Params& params, + const fmi_type fmi, + const rfmi_type rfmi, + const UberScoringScheme& input_scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + const io::SequenceDataDevice& read_data, + io::HostOutputBatchSE& cpu_batch, + Stats& stats) +{ + // prepare the scoring system + typedef typename ScoringSchemeSelector::type scoring_scheme_type; + typedef typename scoring_scheme_type::threshold_score_type threshold_score_type; + + scoring_scheme_type scoring_scheme = ScoringSchemeSelector::scheme( input_scoring_scheme ); + + // cast the reads to use proper iterators + const read_batch_type reads( plain_view( read_data ) ); + + Timer timer; + Timer global_timer; + + const uint32 count = read_data.size(); + //const uint32 band_len = band_length( params.max_dist ); + + seed_queues.in_size = count; + + thrust::copy( // this is only done to pass a list of tasks to the + thrust::make_counting_iterator(0u), // score_all method + thrust::make_counting_iterator(0u) + count, + seed_queues.in_queue.begin() ); + + // clear mapq's + thrust::fill( mapq_dvec.begin(), mapq_dvec.end(), uint8(255) ); + + // + // Unlike Bowtie2, in the context of all-mapping we perform a single seed & extension pass. + // However, during seed mapping, if we find too many hits for a given seeding pattern, + // we try another one with shifted seeds. + // + + uint64 n_alignments = 0; + + uint32 max_seeds = 0u; + for (uint32 s = read_data.min_sequence_len(); s <= read_data.max_sequence_len(); ++s) + max_seeds = nvbio::max( max_seeds, uint32( s / params.seed_freq(s) ) ); + +#if 0 + for (uint32 seed = 0; seed < max_seeds; ++seed) + { + // initialize the seed hit counts + hit_deques.clear_deques(); + + log_debug(stderr, " map seed %u\n", seed); + + // + // perform mapping + // + SeedHitDequeArrayDeviceView hits = hit_deques.device_view(); + + if (params.allow_sub == 0) + { + timer.start(); + + map_exact( + reads, fmi, rfmi, + hits, + make_uint2( seed, seed+1 ), + params, + params.fw, + params.rc ); + + optional_device_synchronize(); + nvbio::cuda::check_error("mapping kernel"); + + timer.stop(); + stats.map.add( count, timer.seconds() ); + } + else + { + timer.start(); + + map_approx( + reads, fmi, rfmi, + hits, + make_uint2( seed, seed+1 ), + params, + params.fw, + params.rc ); + + optional_device_synchronize(); + nvbio::cuda::check_error("mapping kernel"); + + timer.stop(); + stats.map.add( count, timer.seconds() ); + } + + // take some stats on the hits we got + if (params.keep_stats) + keep_stats( reads.size(), stats ); + + log_debug(stderr, " score\n"); + score_all( + params, + fmi, + rfmi, + input_scoring_scheme, + scoring_scheme, + reference_data, + driver_data, + read_data, + count, + seed_queues.raw_input_queue(), + stats, + n_alignments ); + } +#else + // initialize the seed hit counts + hit_deques.clear_deques(); + + // + // perform mapping + // + log_debug(stderr, " map (%u seeds)\n", max_seeds); + { + SeedHitDequeArrayDeviceView hits = hit_deques.device_view(); + + if (params.allow_sub == 0) + { + timer.start(); + + map_exact( + reads, fmi, rfmi, + hits, + make_uint2( 0u, max_seeds ), + params, + params.fw, + params.rc ); + + optional_device_synchronize(); + nvbio::cuda::check_error("mapping kernel"); + + timer.stop(); + stats.map.add( count, timer.seconds() ); + } + else + { + timer.start(); + + map_approx( + reads, fmi, rfmi, + hits, + make_uint2( 0u, max_seeds ), + params, + params.fw, + params.rc ); + + optional_device_synchronize(); + nvbio::cuda::check_error("mapping kernel"); + + timer.stop(); + stats.map.add( count, timer.seconds() ); + } + + // take some stats on the hits we got + if (params.keep_stats) + keep_stats( reads.size(), stats ); + } + + log_debug(stderr, " score\n"); + score_all( + params, + fmi, + rfmi, + input_scoring_scheme, + scoring_scheme, + reference_data, + driver_data, + read_data, + cpu_batch, + count, + seed_queues.raw_input_queue(), + stats, + n_alignments ); +#endif +} + +// a simple functor to merge the read-id, RC flag and location into a single 64-bit sorting key +// +struct SortingKeys +{ + typedef uint32 argument_type; + typedef uint64 result_type; + + SortingKeys(const HitQueuesDeviceView _hits) : hits( _hits ) {} + + NVBIO_HOST_DEVICE + uint64 operator() (const uint32 i) const + { + const uint64 loc = hits.loc[i]; + const uint64 read_id = hits.read_id[i]; + const uint64 rc = hits.seed[i].rc; + + return loc + (read_id << 33) + (rc << 32); + } + + const HitQueuesDeviceView hits; +}; + +// a pseudo-iterator to evaluate the predicate (it[i] <= it[i-1]) for arbitrary iterators +// +template +struct difference_transform +{ + typedef uint32 argument_type; + typedef bool result_type; + + // constructor + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + difference_transform(const Iterator _it) : it( _it ) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool operator() (const uint32 i) const { return it[i] != it[i-1]; } + + Iterator it; +}; + +template +void Aligner::score_all( + const Params& params, + const fmi_type fmi, + const rfmi_type rfmi, + const UberScoringScheme& input_scoring_scheme, + const scoring_scheme_type& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + const io::SequenceDataDevice& read_data, + io::HostOutputBatchSE& cpu_batch, + const uint32 seed_queue_size, + const uint32* seed_queue, + Stats& stats, + uint64& total_alignments) +{ + // prepare the scoring system + //typedef typename scoring_scheme_type::threshold_score_type threshold_score_type; + + //threshold_score_type threshold_score = scoring_scheme.threshold_score(); + const int32 score_limit = scoring_scheme_type::worst_score; + + Timer timer; + Timer global_timer; + + const uint32 count = read_data.size(); + const uint32 band_len = band_length( params.max_dist ); + + // cast the reads to use proper iterators + const read_batch_type reads( plain_view( read_data ) ); + + // cast the genome to use proper iterators + const io::LdgSequenceDataView genome_view( plain_view( reference_data ) ); + const genome_access_type genome_access( genome_view ); + const uint32 genome_len = genome_access.bps(); + const genome_iterator genome = genome_access.sequence_stream(); + + // + // At this point we have a queue full of reads, each with an associated set of + // seed hits encoded as a (sorted) list of SA ranges. + // For each read we need to: + // 1. select some seed hit to process (i.e. a row in one of the SA ranges) + // 2. locate it, i.e. converting from SA to linear coordinates + // 3. score it + // 4. if the score is acceptable, backtrack the extension + // The whole process is carried out as a pipeline composed by 4 different stages + // communicating through work queues. + // At the end of each pipeline iteration, the reads which are still alive, in the + // sense they contain more seed hits to process, are pushed to an output queue. + // The output queue is then reused in the next round as the input queue, and + // viceversa. + // + // NOTE: in all-mapping mode, we ultimately need to explore exahustively the set of seed + // hits for each read, and report all the alignments found. + // If we process the seed hits from all reads simultaneously, reporting all their + // alignments sorted by read would require an external sorting pass, as the amount of + // storage could be fairly dramatic. + // However, we can also simply process all the seed hits from the first read first, + // followed by all the ones from the second read, and so on. + // This has also the advantage of sharing the same read data across many seed extensions, + // lowering the overall memory traffic. + // In order to distribute work evenly we can: + // run a scan on the number of SA ranges from each read (A) + // run a scan on all the SA range sizes (B) + // assign a thread per hit, and find the corresponding SA range by a binary search in (B), + // followed by another binary search in (A) to find the corresponding read. + // + + // run a scan on the number of SA ranges from each read + thrust::inclusive_scan( hit_deques.counts().begin(), hit_deques.counts().begin() + count, hits_count_scan_dvec.begin() ); + + const uint32 n_reads = reads.size(); + + // gather all the range sizes, sorted by read, in a compacted array + const uint32 n_hit_ranges = hits_count_scan_dvec[ count-1 ]; + if (n_hit_ranges == 0) + return; + + log_verbose(stderr, " ranges : %u\n", n_hit_ranges); + + SeedHitDequeArrayDeviceView hits = hit_deques.device_view(); + + gather_ranges( + n_hit_ranges, + n_reads, + hits, + hits_count_scan_dptr, + hits_range_scan_dptr ); + + optional_device_synchronize(); + nvbio::cuda::check_error("gather ranges kernel"); + + // run a scan on all the SA range sizes + thrust::inclusive_scan( hits_range_scan_dvec.begin(), hits_range_scan_dvec.begin() + n_hit_ranges, hits_range_scan_dvec.begin() ); + + const uint64 n_hits = hits_range_scan_dvec[ n_hit_ranges-1 ]; + log_verbose(stderr, " hits : %llu\n", n_hits); + + #if defined(NVBIO_CUDA_DEBUG) + { + uint64 total_hits = 0; + thrust::host_vector h_counts = hit_deques.counts(); + thrust::host_vector h_hits = hit_deques.hits(); + thrust::host_vector h_index = hit_deques.index(); + for (uint32 i = 0; i < n_reads; ++i) + { + uint32 cnt = h_counts[i]; + uint32 index = h_index[i]; + for (uint32 j = 0; j < cnt; ++j) + { + const SeedHit hit = h_hits[ index + j ]; + total_hits += hit.get_range().y - hit.get_range().x; + } + } + if (n_hits != total_hits) + { + log_error(stderr, " expected %llu hits, computed %llu\n", total_hits, n_hits); + throw nvbio::runtime_error("invalid number of hits"); + } + } + #endif + + // + // Loop through batches of BATCH_SIZE seed hits. The seed hits are extracted + // from the compressed variable-sized list of SA ranges, located and scored. + // If the extension is successful, they are queued to a ring-buffer for + // back-tracking. The ring-buffer is twice as large as the batch size, so as + // to allow temporary overflows. + // + + uint32 buffer_offset = 0; + uint32 buffer_count = 0; + + typedef AllMappingPipelineState pipeline_type; + + pipeline_type pipeline( + 0u, + reads, + reads, + genome_len, + genome, + fmi, + rfmi, + scoring_scheme, + score_limit, + *this ); + + // setup the hits queue according to whether we select multiple hits per read or not + scoring_queues.hits_index.setup( 1u, BATCH_SIZE ); + + HitQueues& hit_queues = scoring_queues.hits; + +// uint32* score_idx_dptr = nvbio::device_view( hit_queues.ssa ); + + for (uint64 hit_offset = 0; hit_offset < n_hits; hit_offset += BATCH_SIZE) + { + const uint32 hit_count = std::min( uint32(n_hits - hit_offset), BATCH_SIZE ); + + timer.start(); + + SeedHitDequeArrayDeviceView hits = hit_deques.device_view(); + + log_debug(stderr, " select\n"); + select_all( + hit_offset, + hit_count, + n_reads, + n_hit_ranges, + n_hits, + hits, + hits_count_scan_dptr, + hits_range_scan_dptr, + nvbio::device_view( hit_queues ) ); + + optional_device_synchronize(); + nvbio::cuda::check_error("selecting kernel"); + + timer.stop(); + stats.select.add( hit_count, timer.seconds() ); + + // update pipeline + pipeline.n_hits_per_read = 1u; + pipeline.hits_queue_size = hit_count; + pipeline.scoring_queues = scoring_queues.device_view(); + + log_debug(stderr, " locate\n"); + timer.start(); + + pipeline.idx_queue = sort_hi_bits( + hit_count, + nvbio::device_view( hit_queues.loc ) ); + + timer.stop(); + stats.sort.add( hit_count, timer.seconds() ); + + // and locate their position in linear coordinates + locate_init( + reads, fmi, rfmi, + hit_count, + pipeline.idx_queue, + nvbio::device_view( hit_queues ), + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("locate-init kernel"); + + locate_lookup( + reads, fmi, rfmi, + hit_count, + pipeline.idx_queue, + nvbio::device_view( hit_queues ), + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("locate-lookup kernel"); + + timer.stop(); + stats.locate.add( hit_count, timer.seconds() ); + + timer.start(); + + // sort the selected hits by their linear genome coordinate + const SortingKeys make_keys( nvbio::device_view( hit_queues ) ); + + std::pair sorting_idx = sort_64_bits( + hit_count, + thrust::make_transform_iterator( thrust::make_counting_iterator(0), make_keys ) ); + + if (1) + { + log_debug(stderr, " dedup"); + nvbio::transform( + hit_count-1u, + thrust::make_counting_iterator(0) + 1u, + flags_dvec.begin() + 1u, + difference_transform( sorting_idx.second ) ); + + optional_device_synchronize(); + nvbio::cuda::check_error("dedup kernel"); + + flags_dvec[0] = 1u; + + // mark straddling seeds + mark_straddling( + hit_count, + pipeline.idx_queue, + genome_view.size(), + genome_view.sequence_index(), + pipeline.scoring_queues.hits, + flags_dptr, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("mark-straddling kernel"); + + pipeline.idx_queue = (sorting_idx.first == idx_queue_dptr) ? + idx_queue_dptr + BATCH_SIZE : + idx_queue_dptr; + + // reset the hits queue size + pipeline.hits_queue_size = nvbio::copy_flagged( + hit_count, + sorting_idx.first, + flags_dptr, + pipeline.idx_queue, + temp_dvec ); + + optional_device_synchronize(); + nvbio::cuda::check_error("copy-flagged kernel"); + + log_debug_cont(stderr, " (%u/%u - %.2f)\n", pipeline.hits_queue_size, hit_count, float(pipeline.hits_queue_size)/float(hit_count)); + } + else + pipeline.idx_queue = sorting_idx.first; + + timer.stop(); + stats.sort.add( hit_count, timer.seconds() ); + + // + // assign a score to all selected hits + // + timer.start(); + + log_debug(stderr, " score\n"); + const uint32 n_alignments = nvbio::bowtie2::cuda::score_all( + band_len, + pipeline, + params, + buffer_offset + buffer_count, + BATCH_SIZE*2 ); + + optional_device_synchronize(); + nvbio::cuda::check_error("score kernel"); + + timer.stop(); + stats.score.add( hit_count, timer.seconds() ); + + total_alignments += n_alignments; + log_verbose(stderr, "\r alignments : %u (%.1fM) %.1f%% ", n_alignments, float(total_alignments)*1.0e-6f, 100.0f * float(hit_offset + hit_count)/float(n_hits)); + log_debug_cont(stderr,"\n"); + + buffer_count += n_alignments; + + // + // perform backtracking and compute CIGARs for the found alignments + // + while (buffer_count) + { + // if it's not the very last pass, break out of the loop as + // soon as we have less than BATCH_SIZE elements to process + if (hit_offset + hit_count < n_hits) + { + if (buffer_count < BATCH_SIZE) + break; + } + + timer.start(); + + const uint32 n_backtracks = std::min( + buffer_count, + BATCH_SIZE ); + + { + // copy the read infos to the plain output buffer + { + ring_buffer_to_plain_array( + buffer_read_info_dptr, + BATCH_SIZE*2, + buffer_offset, + buffer_offset + buffer_count, + output_read_info_dptr ); + + optional_device_synchronize(); + nvbio::cuda::check_error("ring-buffer copy kernel"); + } + + // sort the alignments by read-id & RC flag to gain coherence + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + n_backtracks, + idx_queue_dvec.begin() ); + + thrust::sort_by_key( + output_read_info_dvec.begin(), + output_read_info_dvec.begin() + n_backtracks, + idx_queue_dvec.begin() ); + } + + // initialize cigars & MDS pools + cigar.clear(); + mds.clear(); + + log_debug(stderr, " traceback (%u alignments)\n", n_backtracks); + banded_traceback_all( + n_backtracks, + idx_queue_dptr, // input indices + buffer_offset, // alignment ring-buffer offset + BATCH_SIZE*2, // alignment ring-buffer size + output_alignments_dptr, // output alignments + band_len, // band length + pipeline, // pipeline state + params ); // global params + + optional_device_synchronize(); + nvbio::cuda::check_error("backtracking kernel"); + + if (cigar.has_overflown()) + throw nvbio::runtime_error("CIGAR vector overflow\n"); + + log_debug(stderr, " finish\n"); + finish_alignment_all( + n_backtracks, + idx_queue_dptr, // input indices + buffer_offset, // alignment ring-buffer offset + BATCH_SIZE*2, // alignment ring-buffer size + output_alignments_dptr, // output alignments + band_len, // band length + pipeline, // pipeline state + input_scoring_scheme.sw, // always use Smith-Waterman to compute the final scores + params ); // global params + + optional_device_synchronize(); + nvbio::cuda::check_error("alignment kernel"); + + if (mds.has_overflown()) + throw nvbio::runtime_error("MDS vector overflow\n"); + + timer.stop(); + stats.backtrack.add( n_backtracks, timer.seconds() ); + + // wrap the results in a DeviceOutputBatchSE and process it + log_debug(stderr, " output\n"); + { + io::DeviceOutputBatchSE gpu_batch( + n_backtracks, + output_alignments_dvec, + io::DeviceCigarArray(cigar, cigar_coords_dvec), + mds, + mapq_dvec, + &output_read_info_dvec ); + + cpu_batch.readback( gpu_batch ); + + output_file->process( cpu_batch ); + } + + buffer_count -= n_backtracks; + buffer_offset = (buffer_offset + n_backtracks) % (BATCH_SIZE*2); + } + } + log_verbose_nl(stderr); + + log_debug(stderr, " alignments: %llu\n", total_alignments); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_all_ed.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_all_ed.cu new file mode 100644 index 0000000000000000000000000000000000000000..554fcf3de15e23e8840de919c7123a596d544d9b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_all_ed.cu @@ -0,0 +1,61 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +void all_ed( + Aligner& aligner, + const Params& params, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + io::SequenceDataDevice& read_data, + io::HostOutputBatchSE& cpu_batch, + Stats& stats) +{ + aligner.all( + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + read_data, + cpu_batch, + stats ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_all_sw.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_all_sw.cu new file mode 100644 index 0000000000000000000000000000000000000000..2228bf23f37c475b7cedfc0beb3b7f30c02ca656 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_all_sw.cu @@ -0,0 +1,61 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +void all_sw( + Aligner& aligner, + const Params& params, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + io::SequenceDataDevice& read_data, + io::HostOutputBatchSE& cpu_batch, + Stats& stats) +{ + aligner.all( + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + read_data, + cpu_batch, + stats ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx.h new file mode 100644 index 0000000000000000000000000000000000000000..25409e08403ac2cb946aca169057f367fbcaecff --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx.h @@ -0,0 +1,840 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +template +struct MapqFunctorSE +{ + typedef uint32 argument_type; + typedef uint8 result_type; + + MapqFunctorSE( + MapqCalculator _mapq_eval, + const io::Alignment* _best_data, + const uint32 _best_stride, + const ReadData _read_data) : + mapq_eval( _mapq_eval ), + best_data( _best_data ), + best_stride( _best_stride ), + read_data( _read_data ) {} + + NVBIO_HOST_DEVICE + uint8 operator() (const uint32 read_id) const + { + const io::BestAlignments best( best_data[ read_id ], best_data[ read_id + best_stride ] ); + + const uint32 read_offset = read_data.sequence_index()[ read_id ]; + const uint32 read_len = read_data.sequence_index()[ read_id + 1 ] - read_offset; + + return uint8( mapq_eval( + io::BestPairedAlignments( best, io::BestAlignments() ), + read_len, + read_len ) ); + } + + const MapqCalculator mapq_eval; + const io::Alignment* best_data; + const uint32 best_stride; + const ReadData read_data; +}; + +template +void Aligner::best_approx( + const Params& params, + const fmi_type fmi, + const rfmi_type rfmi, + const UberScoringScheme& input_scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + const io::SequenceDataDevice& read_data, + io::HostOutputBatchSE& cpu_batch, + Stats& stats) +{ + // cast the genome to use proper iterators + const genome_view_type genome_view( plain_view( reference_data ) ); + const genome_access_type genome_access( genome_view ); + const uint32 genome_len = genome_access.bps(); + const genome_iterator genome = genome_access.sequence_stream(); + + // prepare the scoring system + typedef typename ScoringSchemeSelector::type scoring_scheme_type; + typedef typename scoring_scheme_type::threshold_score_type threshold_score_type; + + scoring_scheme_type scoring_scheme = ScoringSchemeSelector::scheme( input_scoring_scheme ); + + threshold_score_type threshold_score = scoring_scheme.threshold_score(); + //const int32 score_limit = scoring_scheme_type::worst_score; + + // start timing + Timer timer; + Timer global_timer; + nvbio::cuda::Timer device_timer; + + const uint32 count = read_data.size(); + const uint32 band_len = band_length( params.max_dist ); + + // create a device-side read batch + const read_view_type reads_view = plain_view( read_data ); + const read_batch_type reads( reads_view ); + + // initialize best-alignments + init_alignments( reads, threshold_score, best_data_dptr, BATCH_SIZE ); + + seed_queues.resize( count ); + + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + count, + seed_queues.in_queue.begin() ); + + // + // Similarly to Bowtie2, we perform a number of seed & extension passes. + // Whether a read is re-seeded is determined at run time based on seed hit and + // alignment statistics. + // Hence, the number of reads actively processed in each pass can vary substantially. + // In order to keep the cores and all its lanes busy, we use a pair of input & output + // queues to compact the set of active reads in each round, swapping them at each + // iteration. + // + + // filter away reads that map exactly + if (0) + { + // initialize output seeding queue size + seed_queues.clear_output(); + + // + // perform whole read mapping + // + { + timer.start(); + device_timer.start(); + + // initialize the seed hit counts + hit_deques.clear_deques(); + + SeedHitDequeArrayDeviceView hits = hit_deques.device_view(); + + log_debug(stderr, "[%u] map\n", ID); + map_whole_read( + reads, fmi, rfmi, + seed_queues.device_view(), + reseed_dptr, + hits, + params, + params.fw, + params.rc ); + + optional_device_synchronize(); + nvbio::cuda::check_error("mapping kernel"); + + device_timer.stop(); + timer.stop(); + stats.map.add( seed_queues.in_size, timer.seconds(), device_timer.seconds() ); + } + + best_approx_score( + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + read_data, + uint32(-1), + seed_queues.in_size, + seed_queues.raw_input_queue(), + stats ); + + log_verbose( stderr, "[%u] %.1f %% reads map exactly\n", ID, 100.0f * float(count - seed_queues.output_size())/float(count) ); + + // copy the reads that need reseeding + seed_queues.out_size[0] = nvbio::copy_flagged( + seed_queues.in_size, + (uint32*)seed_queues.raw_input_queue(), + reseed_dptr, + (uint32*)seed_queues.raw_output_queue(), + temp_dvec ); + + // swap input & output queues + seed_queues.swap(); + } + + for (uint32 seeding_pass = 0; seeding_pass < params.max_reseed+1; ++seeding_pass) + { + // check whether the input queue is empty + if (seed_queues.in_size == 0) + break; + + // initialize output seeding queue size + seed_queues.clear_output(); + + // + // perform mapping + // + { + timer.start(); + device_timer.start(); + + hit_deques.clear_deques(); + + SeedHitDequeArrayDeviceView hits = hit_deques.device_view(); + + log_debug(stderr, "[%u] map\n", ID); + map( + reads, fmi, rfmi, + seeding_pass, seed_queues.device_view(), + reseed_dptr, + hits, + params, + params.fw, + params.rc ); + + optional_device_synchronize(); + nvbio::cuda::check_error("mapping kernel"); + + device_timer.stop(); + timer.stop(); + stats.map.add( seed_queues.in_size, timer.seconds(), device_timer.seconds() ); + + // check if we need to persist this seeding pass + if (params.persist_batch == -1 || batch_number == (uint32) params.persist_batch && + params.persist_seeding == -1 || seeding_pass == (uint32) params.persist_seeding) + persist_hits( params.persist_file, "hits", 0u, count, hit_deques ); + } + + // take some stats on the hits we got + if (seeding_pass == 0 && params.keep_stats) + keep_stats( reads.size(), stats ); + + best_approx_score( + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + read_data, + seeding_pass, + seed_queues.in_size, + seed_queues.raw_input_queue(), + stats ); + + // mark unaligned reads + mark_unaligned( + seed_queues.in_size, + seed_queues.raw_input_queue(), + best_data_dptr, + reseed_dptr ); + + // copy the reads that need reseeding + seed_queues.out_size[0] = nvbio::copy_flagged( + seed_queues.in_size, + (uint32*)seed_queues.raw_input_queue(), + reseed_dptr, + (uint32*)seed_queues.raw_output_queue(), + temp_dvec ); + + // swap input & output queues + seed_queues.swap(); + } + + // + // At this point, for each read we have the scores and rough alignment positions of the + // best two alignments: to compute the final results we need to backtrack the DP extension, + // and compute accessory CIGARS and MD strings. + // + + // compute mapq + { + log_debug(stderr, "[%u] compute mapq\n", ID); + typedef BowtieMapq2< SmithWatermanScoringScheme<> > mapq_evaluator_type; + + mapq_evaluator_type mapq_eval( input_scoring_scheme.sw ); + + MapqFunctorSE mapq_functor( mapq_eval, best_data_dptr, BATCH_SIZE, reads_view ); + + nvbio::transform( + count, + thrust::make_counting_iterator(0), + mapq_dvec.begin(), + mapq_functor ); + } + + TracebackPipelineState traceback_state( + reads, + reads, + genome_len, + genome, + scoring_scheme, + *this ); + + // + // perform backtracking and compute cigars for the best alignments + // + { + // initialize cigars & MDS pools + cigar.clear(); + mds.clear(); + + timer.start(); + device_timer.start(); + + log_debug(stderr, "[%u] backtrack\n", ID); + banded_traceback_best( + 0u, + count, + NULL, + best_data_dptr, + BATCH_SIZE, + band_len, + traceback_state, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("backtracking kernel"); + if (cigar.has_overflown()) + throw nvbio::runtime_error("CIGAR vector overflow\n"); + + device_timer.stop(); + timer.stop(); + stats.backtrack.add( count, timer.seconds(), device_timer.seconds() ); + + timer.start(); + device_timer.start(); + + log_debug(stderr, "[%u] alignment\n", ID); + finish_alignment_best( + 0u, + count, + NULL, + best_data_dptr, + BATCH_SIZE, + band_len, + traceback_state, + input_scoring_scheme.sw, // always use Smith-Waterman for the final scoring of the found alignments + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("alignment kernel"); + if (mds.has_overflown()) + throw nvbio::runtime_error("MDS vector overflow\n"); + + device_timer.stop(); + timer.stop(); + stats.finalize.add( count, timer.seconds(), device_timer.seconds() ); + } + + // wrap the results in a DeviceOutputBatchSE and process + if (output_file) + { + timer.start(); + + io::DeviceOutputBatchSE gpu_batch( + count, + best_data_dvec, + io::DeviceCigarArray(cigar, cigar_coords_dvec), + mds, + mapq_dvec); + + cpu_batch.readback( gpu_batch ); + + timer.stop(); + stats.alignments_DtoH.add( count, timer.seconds() ); + + timer.start(); + + log_debug(stderr, "[%u] output\n", ID); + output_file->process( cpu_batch ); + + timer.stop(); + stats.io.add( count, timer.seconds() ); + } + + // TODO: decide whether to output second best alignments + #if 0 + { + // clear mapq's + thrust::fill( mapq_dvec.begin(), mapq_dvec.begin() + count, uint8(255) ); + + // overlap the second-best indices with the loc queue + thrust::device_vector& second_idx_dvec = scoring_queues.hits.loc; + + // compact the indices of the second-best alignments + const uint32 n_second = uint32( thrust::copy_if( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + count, + best_data_dvec.begin(), + second_idx_dvec.begin(), + io::has_second() ) - second_idx_dvec.begin() ); // FIXME: this has to be fixed since best_data_dvec is now + // a strided vector of io::Alignment's rather than a vector of + // io::BestAlignment's + + // + // perform backtracking and compute cigars for the second-best alignments + // + if (n_second) + { + // initialize cigars & MDS pools + cigar.clear(); + mds.clear(); + + timer.start(); + device_timer.start(); + + uint32* second_idx = thrust::raw_pointer_cast( &second_idx_dvec[0] ); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug(stderr, "[%u] second-best backtrack (%u)\n", ID, n_second) ); + banded_traceback_best( + 1u, + n_second, + second_idx, + best_data_dptr, + BATCH_SIZE, + band_len, + traceback_state, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("second-best backtracking kernel"); + if (cigar.has_overflown()) + throw nvbio::runtime_error("CIGAR vector overflow\n"); + + device_timer.stop(); + timer.stop(); + stats.backtrack.add( n_second, timer.seconds(), device_timer.seconds() ); + + timer.start(); + device_timer.start(); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug(stderr, "[%u] second-best alignment (%u)\n", ID, n_second) ); + finish_alignment_best( + 1u, + n_second, + second_idx, + best_data_dptr, + BATCH_SIZE, + band_len, + traceback_state, + input_scoring_scheme.sw, // always use Smith-Waterman for the final scoring of the found alignments + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("second-best alignment kernel"); + if (mds.has_overflown()) + throw nvbio::runtime_error("MDS vector overflow\n"); + + device_timer.stop(); + timer.stop(); + stats.finalize.add( n_second, timer.seconds(), device_timer.seconds() ); + } + + // wrap the results in a DeviceOutputBatchSE and process them + if (output_file) + { + timer.start(); + + io::DeviceOutputBatchSE gpu_batch( + count, + best_data_dvec, + io::DeviceCigarArray(cigar, cigar_coords_dvec), + mds, + mapq_dvec); + + cpu_batch.readback( gpu_batch ); + + timer.stop(); + stats.alignments_DtoH.add( count, timer.seconds() ); + + timer.start(); + + output_file->process( cpu_batch ); + + timer.stop(); + stats.io.add( count, timer.seconds() ); + } + } + #endif + + // keep alignment stats + { + log_debug(stderr, "[%u] track stats\n", ID); + thrust::host_vector h_best_data( BATCH_SIZE*2 ); + thrust::host_vector h_mapq( BATCH_SIZE ); + + thrust::copy( best_data_dvec.begin(), best_data_dvec.begin() + count, h_best_data.begin() ); + thrust::copy( best_data_dvec.begin() + BATCH_SIZE, best_data_dvec.begin() + count + BATCH_SIZE, h_best_data.begin() + BATCH_SIZE ); + thrust::copy( mapq_dvec.begin(), mapq_dvec.begin() + count, h_mapq.begin() ); + + for (uint32 i = 0; i < count; ++i) + { + const io::BestAlignments best( h_best_data[i], h_best_data[i + BATCH_SIZE] ); + const uint8 mapq = h_mapq[i]; + + stats.track_alignment_statistics( &stats.mate1, best, mapq ); + } + } +} + +template < + typename scoring_tag, + typename scoring_scheme_type> +void Aligner::best_approx_score( + const Params& params, + const fmi_type fmi, + const rfmi_type rfmi, + const scoring_scheme_type& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + const io::SequenceDataDevice& read_data, + const uint32 seeding_pass, + const uint32 seed_queue_size, + const uint32* seed_queue, + Stats& stats) +{ + // prepare the scoring system + typedef typename scoring_scheme_type::threshold_score_type threshold_score_type; + + //threshold_score_type threshold_score = scoring_scheme.threshold_score(); + const int32 score_limit = scoring_scheme_type::worst_score; + + Timer timer; + Timer global_timer; + nvbio::cuda::Timer device_timer; + +// const uint32 count = read_data.size(); + const uint32 band_len = band_length( params.max_dist ); + + // cast the reads to use proper iterators + const read_view_type reads_view = plain_view( read_data ); + const read_batch_type reads( reads_view ); + + // cast the genome to use proper iterators + const genome_view_type genome_view( plain_view( reference_data ) ); + const genome_access_type genome_access( genome_view ); + const uint32 genome_len = genome_access.bps(); + const genome_iterator genome = genome_access.sequence_stream(); + + NVBIO_VAR_UNUSED thrust::device_vector::iterator hit_read_id_iterator = scoring_queues.hits.read_id.begin(); + NVBIO_VAR_UNUSED thrust::device_vector::iterator loc_queue_iterator = scoring_queues.hits.loc.begin(); + NVBIO_VAR_UNUSED thrust::device_vector::iterator score_queue_iterator = scoring_queues.hits.score.begin(); + + // + // At this point we have a queue full of reads, each with an associated set of + // seed hits encoded as a (sorted) list of SA ranges. + // For each read we need to: + // 1. select some seed hit to process (i.e. a row in one of the SA ranges) + // 2. locate it, i.e. converting from SA to linear coordinates + // 3. and score it + // until some search criteria are satisfied. + // The output queue is then reused in the next round as the input queue, and + // viceversa. + // + + ScoringQueues::active_reads_storage_type& active_read_queues = scoring_queues.active_reads; + + active_read_queues.resize( seed_queue_size ); + + thrust::transform( + thrust::device_ptr( seed_queue ), + thrust::device_ptr( seed_queue ) + seed_queue_size, + active_read_queues.in_queue.begin(), + pack_read( params.top_seed ) ); + + // keep track of the number of extensions performed for each of the active reads + uint32 n_ext = 0; + + typedef BestApproxScoringPipelineState pipeline_type; + + pipeline_type pipeline( + 0u, + reads, + reads, + genome_len, + genome, + fmi, + rfmi, + scoring_scheme, + score_limit, + *this ); + + // initialize the hit selection & scoring pipeline + select_init( + pipeline, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("select-init kernel"); + + // prepeare the selection context + SelectBestApproxContext select_context( trys_dptr ); + + for (uint32 extension_pass = 0; active_read_queues.in_size && n_ext < params.max_ext; ++extension_pass) + { + log_debug(stderr, "[%u] pass:\n[%u] batch: %u\n[%u] seeding pass: %d\n[%u] extension pass: %u\n", ID, ID, batch_number, ID, seeding_pass, ID, extension_pass); + + // check if we need to persist this seeding pass + if (params.persist_batch == -1 || batch_number == (uint32) params.persist_batch && + params.persist_seeding == -1 || seeding_pass == (uint32) params.persist_seeding && + params.persist_extension == -1 || extension_pass == (uint32) params.persist_extension) + persist_hits( params.persist_file, "hits", 0u, reads.size(), hit_deques ); + + // initialize all the scoring output queues + scoring_queues.clear_output(); + + // sort the active read infos + #if 0 + { + timer.start(); + device_timer.start(); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug(stderr, "[%u] read sort\n", ID) ); + sort_inplace( active_read_queues.in_size, active_read_queues.raw_input_queue() ); + + device_timer.stop(); + timer.stop(); + stats.sort.add( active_read_queues.in_size, timer.seconds(), device_timer.seconds() ); + } + #endif + + timer.start(); + device_timer.start(); + + // keep track of how many hits per read we are generating + pipeline.n_hits_per_read = 1; + + if ((active_read_queues.in_size <= BATCH_SIZE/2) && + (params.no_multi_hits == false)) + { + // + // The queue of actively processed reads is very small: at this point + // it's better to select multiple hits to process in each round. + // This adds some book-keeping overheads, but allows to make larger + // kernel launches. + // + + // the maximum number of extensions we can perform in one iteration + // is at most 4096, as we use 12 bits to encode the extension index + const uint32 max_ext = std::min( 4096u, params.max_ext - n_ext ); + + // try to generate BATCH_SIZE items to process + pipeline.n_hits_per_read = std::min( + BATCH_SIZE / active_read_queues.in_size, + max_ext ); + } + // else + // + // The queue of actively processed reads is sufficiently large to allow + // selecting & scoring one seed hit at a time and still have large kernel + // launches. This is algorithmically the most efficient choice (because + // it enables frequent early outs), so let's choose it. + // + + // setup the hits queue according to whether we select multiple hits per read or not + scoring_queues.hits_index.setup( pipeline.n_hits_per_read, active_read_queues.in_size ); + + // update pipeline + pipeline.scoring_queues = scoring_queues.device_view(); + + log_debug(stderr, "[%u] select (%u active reads)\n", ID, active_read_queues.in_size); + select( + select_context, + pipeline, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("select kernel"); + + // this sync point seems very much needed: if we don't place it, we won't see + // the right number of hits later on... + cudaDeviceSynchronize(); + + device_timer.stop(); + timer.stop(); + stats.select.add( active_read_queues.in_size * pipeline.n_hits_per_read, timer.seconds(), device_timer.seconds() ); + + // swap input & output queues + active_read_queues.swap(); + + // update pipeline view + pipeline.scoring_queues = scoring_queues.device_view(); + + // fetch the new queue size + if (active_read_queues.in_size == 0) + break; + + // fetch the output queue size + pipeline.hits_queue_size = pipeline.n_hits_per_read > 1 ? scoring_queues.hits_count() : active_read_queues.in_size; + if (pipeline.hits_queue_size == 0) + continue; + + // use the parent queue only if we chose the multiple-hits per read pipeline + // check if we need to persist this seeding pass + if (params.persist_batch == -1 || batch_number == (uint32) params.persist_batch && + params.persist_seeding == -1 || seeding_pass == (uint32) params.persist_seeding && + params.persist_extension == -1 || extension_pass == (uint32) params.persist_extension) + persist_selection( params.persist_file, "selection", + 0u, + active_read_queues.in_size, + active_read_queues.raw_input_queue(), + pipeline.n_hits_per_read, + pipeline.hits_queue_size, + scoring_queues.hits_index, + scoring_queues.hits ); + + log_debug(stderr, "[%u] selected %u hits\n", ID, pipeline.hits_queue_size); + NVBIO_CUDA_DEBUG_STATEMENT( log_debug( stderr, "[%u] crc: %llu\n", ID, device_checksum( hit_read_id_iterator, hit_read_id_iterator + pipeline.hits_queue_size ) ) ); + NVBIO_CUDA_DEBUG_STATEMENT( log_debug( stderr, "[%u] crc: %llu\n", ID, device_checksum( loc_queue_iterator, loc_queue_iterator + pipeline.hits_queue_size ) ) ); + + timer.start(); + device_timer.start(); + + // sort the selected hits by their SA coordinate + log_debug(stderr, "[%u] locate sort\n", ID); + pipeline.idx_queue = sort_hi_bits( pipeline.hits_queue_size, pipeline.scoring_queues.hits.loc ); + + device_timer.stop(); + timer.stop(); + stats.sort.add( pipeline.hits_queue_size, timer.seconds(), device_timer.seconds() ); + + timer.start(); + device_timer.start(); + + // NOTE: only 75-80% of these locations are unique. + // It might pay off to do a compaction beforehand. + + // and locate their position in linear coordinates + log_debug(stderr, "[%u] locate init\n", ID); + locate_init( pipeline, params ); + + optional_device_synchronize(); + + log_debug(stderr, "[%u] locate lookup\n", ID); + locate_lookup( pipeline, params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("locating kernel"); + + device_timer.stop(); + timer.stop(); + stats.locate.add( pipeline.hits_queue_size, timer.seconds(), device_timer.seconds() ); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug( stderr, "[%u] crc: %llu\n", ID, device_checksum( loc_queue_iterator, loc_queue_iterator + pipeline.hits_queue_size ) ) ); + + // + // Start the real scoring work... + // + + timer.start(); + device_timer.start(); + + // sort the selected hits by their linear genome coordinate + // TODO: sub-sort by read position/RC flag so as to (1) get better coherence, + // (2) allow removing duplicate extensions + log_debug(stderr, "[%u] score sort\n", ID); + pipeline.idx_queue = sort_hi_bits( pipeline.hits_queue_size, pipeline.scoring_queues.hits.loc ); + + device_timer.stop(); + timer.stop(); + stats.sort.add( pipeline.hits_queue_size, timer.seconds(), device_timer.seconds() ); + + // + // assign a score to all selected hits (currently in the output queue) + // + float score_time = 0.0f; + float dev_score_time = 0.0f; + timer.start(); + device_timer.start(); + + score_best( + band_len, + pipeline, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("score kernel"); + + device_timer.stop(); + timer.stop(); + score_time += timer.seconds(); + dev_score_time += device_timer.seconds(); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug( stderr, "[%u] crc: %llu\n", ID, device_checksum( score_queue_iterator, score_queue_iterator + pipeline.hits_queue_size ) ) ); + + // check if we need to persist this seeding pass + if (params.persist_batch == -1 || batch_number == (uint32) params.persist_batch && + params.persist_seeding == -1 || seeding_pass == (uint32) params.persist_seeding && + params.persist_extension == -1 || extension_pass == (uint32) params.persist_extension) + persist_scores( params.persist_file, "scores", 0u, reads.size(), pipeline.n_hits_per_read, pipeline.hits_queue_size, scoring_queues ); + + timer.start(); + device_timer.start(); + + const ReduceBestApproxContext reduce_context( pipeline.trys, n_ext ); + + // reduce the multiple scores to find the best two alignments + // (one thread per active read). + log_debug(stderr, "[%u] score reduce\n", ID); + score_reduce( + reduce_context, + pipeline, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("score-reduce kernel"); + + // keep track of the number of extensions performed for each of the active reads + n_ext += pipeline.n_hits_per_read; + + device_timer.stop(); + timer.stop(); + stats.score.add( pipeline.hits_queue_size, score_time + timer.seconds(), dev_score_time + device_timer.seconds() ); + } +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_ed.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_ed.cu new file mode 100644 index 0000000000000000000000000000000000000000..89358c64175e122fb11b2d5326e4e7824bed5962 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_ed.cu @@ -0,0 +1,61 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +void best_approx_ed( + Aligner& aligner, + const Params& params, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + io::SequenceDataDevice& read_data, + io::HostOutputBatchSE& cpu_batch, + Stats& stats) +{ + aligner.best_approx( + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + read_data, + cpu_batch, + stats ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_paired.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_paired.h new file mode 100644 index 0000000000000000000000000000000000000000..072b6d498d683bda60c0f5f4457a77d7d6d1b60f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_paired.h @@ -0,0 +1,1192 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +template +struct MapqFunctorPE +{ + MapqFunctorPE( + const uint32 _mate, + MapqCalculator _mapq_eval, + const io::Alignment* _best_data, + const io::Alignment* _best_data_o, + const uint32 _best_stride, + const ReadData _read_data1, + const ReadData _read_data2) : + mapq_eval( _mapq_eval ), + best_data( _best_data ), + best_data_o( _best_data_o ), + best_stride( _best_stride ), + read_data1( _read_data1 ), + read_data2( _read_data2 ), + mate( _mate ) {} + + NVBIO_HOST_DEVICE + uint8 operator() (const uint32 read_id) + { + io::BestAlignments best( best_data[ read_id ], best_data[ read_id + best_stride ] ); + io::BestAlignments best_o( best_data_o[ read_id ], best_data_o[ read_id + best_stride ] ); + io::BestPairedAlignments best_paired( + (mate == 0) ? best : best_o, + (mate == 0) ? best_o : best ); + + const uint32 read_offset1 = read_data1.sequence_index()[ read_id ]; + const uint32 read_len1 = read_data1.sequence_index()[ read_id + 1 ] - read_offset1; + + const uint32 read_offset2 = read_data2.sequence_index()[ read_id ]; + const uint32 read_len2 = read_data2.sequence_index()[ read_id + 1 ] - read_offset2; + + return uint8( mapq_eval( + best_paired, + best_paired.anchor_mate<0>() ? read_len2 : read_len1, + best_paired.anchor_mate<0>() ? read_len1 : read_len2 ) ); + } + + const MapqCalculator mapq_eval; + const io::Alignment* best_data; + const io::Alignment* best_data_o; + const uint32 best_stride; + const ReadData read_data1; + const ReadData read_data2; + const uint32 mate; +}; + +template < + typename scoring_tag> +void Aligner::best_approx( + const Params& params, + const fmi_type fmi, + const rfmi_type rfmi, + const UberScoringScheme& input_scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + const io::SequenceDataDevice& read_data1, + const io::SequenceDataDevice& read_data2, + io::HostOutputBatchPE& cpu_batch, + Stats& stats) +{ + // prepare the scoring system + typedef typename ScoringSchemeSelector::type scoring_scheme_type; + typedef typename scoring_scheme_type::threshold_score_type threshold_score_type; + + scoring_scheme_type scoring_scheme = ScoringSchemeSelector::scheme( input_scoring_scheme ); + + threshold_score_type threshold_score = scoring_scheme.threshold_score(); + //const int32 score_limit = scoring_scheme_type::worst_score; + + // start timing + nvbio::Timer timer; + nvbio::cuda::Timer device_timer; + + const uint32 count = read_data1.size(); + const uint32 band_len = band_length( params.max_dist ); + + // cast the genome to use proper iterators + const io::LdgSequenceDataView genome_view( plain_view( reference_data ) ); + const genome_access_type genome_access( genome_view ); + const uint32 genome_len = genome_access.bps(); + const genome_iterator genome = genome_access.sequence_stream(); + + // cast the reads to use proper iterators + const read_view_type reads_view1 = plain_view( read_data1 ); + const read_view_type reads_view2 = plain_view( read_data2 ); + const read_batch_type reads1( reads_view1 ); + const read_batch_type reads2( reads_view2 ); + + // initialize best-alignments + init_alignments( reads1, threshold_score, best_data_dptr, BATCH_SIZE, 0u ); + init_alignments( reads2, threshold_score, best_data_dptr_o, BATCH_SIZE, 1u ); + + for (uint32 anchor = 0; anchor < 2; ++anchor) + { + log_debug(stderr, "[%u] anchor mate: %u\n", ID, anchor); + + // start with a full seed queue + seed_queues.in_size = count; + + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + count, + seed_queues.in_queue.begin() ); + + // + // Similarly to Bowtie2, we perform a number of seed & extension passes. + // Whether a read is re-seeded is determined at run time based on seed hit and + // alignment statistics. + // Hence, the number of reads actively processed in each pass can vary substantially. + // In order to keep the cores and all its lanes busy, we use a pair of input & output + // queues to compact the set of active reads in each round, swapping them at each + // iteration. + // + + const bool fw_strand = + (anchor == 0) ? (params.pe_policy == io::PE_POLICY_FF || // anchor = 0 + params.pe_policy == io::PE_POLICY_FR) : + (params.pe_policy == io::PE_POLICY_FF || // anchor = 1 + params.pe_policy == io::PE_POLICY_RF); + const bool fw = fw_strand ? params.fw : params.rc; + const bool rc = fw_strand ? params.rc : params.fw; + + for (uint32 seeding_pass = 0; seeding_pass < params.max_reseed+1; ++seeding_pass) + { + // check whether the input queue is empty + if (seed_queues.in_size == 0) + break; + + const uint32 n_active_reads = seed_queues.in_size; + + // initialize output seeding queue size + seed_queues.clear_output(); + + // check if we need to persist this seeding pass + if (batch_number == (uint32) params.persist_batch && + seeding_pass == (uint32) params.persist_seeding) + persist_reads( params.persist_file, "reads", anchor, n_active_reads, seed_queues.in_queue.begin() ); + + // + // perform mapping + // + { + log_debug(stderr, "[%u] mapping (%u active reads)\n", ID, n_active_reads); + timer.start(); + device_timer.start(); + + // initialize the seed hit counts + hit_deques.clear_deques(); + + SeedHitDequeArrayDeviceView hits = hit_deques.device_view(); + + map( + anchor ? reads2 : reads1, fmi, rfmi, + seeding_pass, seed_queues.device_view(), + reseed_dptr, + hits, + params, + fw, + rc ); + + optional_device_synchronize(); + nvbio::cuda::check_error("mapping kernel"); + + device_timer.stop(); + timer.stop(); + stats.map.add( n_active_reads, timer.seconds(), device_timer.seconds() ); +/* + #if defined(NVBIO_CUDA_DEBUG) + { + uint64 crc, sum; + hits_checksum( n_active_reads, hit_deques, crc, sum ); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug( stderr, "[%u] crc cnts: %llu\n", ID, device_checksum( hit_deques.counts().begin(), hit_deques.counts().begin() + count ) ) ); + NVBIO_CUDA_DEBUG_STATEMENT( log_debug( stderr, "[%u] crc hits: %llu\n", ID, crc ) ); + NVBIO_CUDA_DEBUG_STATEMENT( log_debug( stderr, "[%u] sum hits: %llu\n", ID, sum ) ); + } + #endif +*/ + // check if we need to persist this seeding pass + if (batch_number == (uint32) params.persist_batch && + seeding_pass == (uint32) params.persist_seeding) + persist_hits( params.persist_file, "hits", anchor, count, hit_deques ); + } + + // take some stats on the hits we got + if (seeding_pass == 0 && anchor == 0 && params.keep_stats) + keep_stats( reads1.size(), stats ); + + best_approx_score( + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + anchor, + anchor ? read_data2 : read_data1, + anchor ? read_data1 : read_data2, + seeding_pass, + seed_queues.in_size, + seed_queues.raw_input_queue(), + stats ); + + // copy the reads that need reseeding + seed_queues.out_size[0] = nvbio::copy_flagged( + seed_queues.in_size, + (uint32*)seed_queues.raw_input_queue(), + reseed_dptr, + (uint32*)seed_queues.raw_output_queue(), + temp_dvec ); + + // swap input & output queues + seed_queues.swap(); + } + } + + // + // At this point, for each read we have the scores and rough alignment positions of the + // best two alignments: to compute the final results we need to backtrack the DP extension, + // and compute accessory CIGARs and MD strings. + // + + thrust::device_vector::iterator best_anchor_iterator = best_data_dvec.begin(); + thrust::device_vector::iterator best_opposite_iterator = best_data_dvec_o.begin(); + + io::Alignment* best_anchor_ptr = thrust::raw_pointer_cast( best_anchor_iterator.base() ); + io::Alignment* best_opposite_ptr = thrust::raw_pointer_cast( best_opposite_iterator.base() ); + + // reclassify here "discordant" alignments as "paired" (if discordant alignments are allowed) + if (params.pe_discordant) + { + mark_discordant( + count, + best_anchor_ptr, + best_opposite_ptr, + BATCH_SIZE ); + } + + // compute mapq for the first mate + { + log_debug(stderr, "[%u] compute mapq\n", ID); + typedef BowtieMapq2< SmithWatermanScoringScheme<> > mapq_evaluator_type; + + mapq_evaluator_type mapq_eval( input_scoring_scheme.sw ); + + MapqFunctorPE mapq_functor( 0u, mapq_eval, best_anchor_ptr, best_opposite_ptr, BATCH_SIZE, reads_view1, reads_view2 ); + + nvbio::transform( + count, + thrust::make_counting_iterator(0), + mapq_dvec.begin(), + mapq_functor ); + } + + TracebackPipelineState traceback_state( + reads1, + reads2, + genome_len, + genome, + scoring_scheme, + *this ); + + // + // perform backtracking and compute cigars for the best alignments + // + { + // initialize cigars & MDS + cigar.clear(); + mds.clear(); + + timer.start(); + device_timer.start(); + + log_debug(stderr, "[%u] backtracking\n", ID); + banded_traceback_best( + 0u, + count, + NULL, + best_anchor_ptr, + BATCH_SIZE, + band_len, + traceback_state, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("backtracking kernel"); + if (cigar.has_overflown()) + throw nvbio::runtime_error("CIGAR vector overflow\n"); + + device_timer.stop(); + timer.stop(); + stats.backtrack.add( count, timer.seconds(), device_timer.seconds() ); + + timer.start(); + device_timer.start(); + + log_debug(stderr, "[%u] alignment\n", ID); + finish_alignment_best( + 0u, + count, + NULL, + best_anchor_ptr, + BATCH_SIZE, + band_len, + traceback_state, + input_scoring_scheme.sw, // always use Smith-Waterman for the final scoring of the found alignments + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("alignment kernel"); + if (mds.has_overflown()) + throw nvbio::runtime_error("MDS vector overflow\n"); + + device_timer.stop(); + timer.stop(); + stats.finalize.add( count, timer.seconds(), device_timer.seconds() ); + } + + // wrap the results in a DeviceOutputBatchSE and process it + { + timer.start(); + + io::DeviceOutputBatchSE gpu_batch( + count, + best_data_dvec, + io::DeviceCigarArray(cigar, cigar_coords_dvec), + mds, + mapq_dvec); + + cpu_batch.readback( gpu_batch, io::MATE_1 ); + + timer.stop(); + stats.alignments_DtoH.add( count, timer.seconds() ); + } + + // compute mapq for the second mate + { + log_debug(stderr, "[%u] compute mapq\n", ID); + typedef BowtieMapq2< SmithWatermanScoringScheme<> > mapq_evaluator_type; + + mapq_evaluator_type mapq_eval( input_scoring_scheme.sw ); + + MapqFunctorPE mapq_functor( 1u, mapq_eval, best_anchor_ptr, best_opposite_ptr, BATCH_SIZE, reads_view1, reads_view2 ); + + nvbio::transform( + count, + thrust::make_counting_iterator(0), + mapq_dvec.begin(), + mapq_functor ); + } + + // + // perform backtracking and compute cigars for the opposite mates of the best paired alignments + // + { + // initialize cigars & MDS + cigar.clear(); + mds.clear(); + + // + // these alignments are of two kinds: concordant, or discordant: this requires some attention, + // as true opposite paired alignments require full DP backtracking, while unpaired or discordant + // alignments require the banded version. + // + timer.start(); + device_timer.start(); + + // overlap the paired indices with the loc queue + thrust::device_vector::iterator paired_idx_begin = scoring_queues.hits.loc.begin(); + + // compact the indices of the best concordant alignments + const uint32 n_paired = uint32( thrust::copy_if( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + count, + best_opposite_iterator, + paired_idx_begin, + io::is_concordant() ) - paired_idx_begin ); + + if (n_paired) + { + log_debug(stderr, "[%u] paired opposite: %u\n", ID, n_paired); + const uint32* paired_idx = thrust::raw_pointer_cast( paired_idx_begin.base() ); + + log_debug(stderr, "[%u] paired opposite backtracking\n", ID); + opposite_traceback_best( + 0u, + n_paired, + paired_idx, + best_opposite_ptr, + BATCH_SIZE, + traceback_state, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("paired opposite backtracking kernel"); + if (cigar.has_overflown()) + throw nvbio::runtime_error("CIGAR vector overflow\n"); + } + + // overlap the unpaired indices with the loc queue + thrust::device_vector::iterator unpaired_idx_begin = scoring_queues.hits.loc.begin(); + + // compact the indices of the best unpaired or discordant alignments + const uint32 n_unpaired = uint32( thrust::copy_if( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + count, + best_opposite_iterator, + unpaired_idx_begin, + io::is_not_concordant() ) - unpaired_idx_begin ); + + if (n_unpaired) + { + log_debug(stderr, "[%u] unpaired opposite: %u\n", ID, n_unpaired); + const uint32* unpaired_idx = thrust::raw_pointer_cast( unpaired_idx_begin.base() ); + + log_debug(stderr, "[%u] unpaired opposite backtracking\n", ID); + banded_traceback_best( + 0u, + n_unpaired, + unpaired_idx, + best_opposite_ptr, + BATCH_SIZE, + band_len, + traceback_state, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("unpaired opposite backtracking kernel"); + if (cigar.has_overflown()) + throw nvbio::runtime_error("CIGAR vector overflow\n"); + } + + device_timer.stop(); + timer.stop(); + stats.backtrack_opposite.add( n_paired + n_unpaired, timer.seconds(), device_timer.seconds() ); + + timer.start(); + device_timer.start(); + + thrust::device_vector::iterator aligned_idx_begin = scoring_queues.hits.loc.begin(); + + // compact the indices of the best opposite alignments (concordant or not) + const uint32 n_aligned = uint32( thrust::copy_if( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + count, + best_opposite_iterator, + aligned_idx_begin, + io::is_aligned() ) - aligned_idx_begin ); + + if (n_aligned) + { + log_debug(stderr, "[%u] opposite alignment: %u\n", ID, n_aligned); + const uint32* aligned_idx = thrust::raw_pointer_cast( aligned_idx_begin.base() ); + + finish_opposite_alignment_best( + 0u, + n_aligned, + aligned_idx, + best_opposite_ptr, + BATCH_SIZE, + band_len, + traceback_state, + input_scoring_scheme.sw, // always use Smith-Waterman for the final scoring of the found alignments + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("opposite alignment kernel"); + if (mds.has_overflown()) + throw nvbio::runtime_error("MDS vector overflow\n"); + } + + device_timer.stop(); + timer.stop(); + stats.finalize.add( count, timer.seconds(), device_timer.seconds() ); + + // wrap the results in a DeviceOutputBatchSE and process it + if (output_file) + { + timer.start(); + + io::DeviceOutputBatchSE gpu_batch( + count, + best_data_dvec_o, + io::DeviceCigarArray(cigar, cigar_coords_dvec), + mds, + mapq_dvec); + + cpu_batch.readback( gpu_batch, io::MATE_2 ); + + timer.stop(); + stats.alignments_DtoH.add( count, timer.seconds() ); + + timer.start(); + + output_file->process( cpu_batch ); + + timer.stop(); + stats.io.add( count, timer.seconds() ); + } + } + + // TODO: decide whether to output second best alignments + #if 0 + { + // clear mapq's + thrust::fill( mapq_dvec.begin(), mapq_dvec.begin() + count, uint8(255) ); + + // overlap the second-best indices with the loc queue + thrust::device_vector::iterator second_idx_begin = scoring_queues.hits.loc.begin(); + + // compact the indices of the second-best alignments + const uint32 n_second = uint32( thrust::copy_if( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + count, + best_anchor_iterator, + second_idx_begin, + io::has_second() ) - second_idx_begin ); + + // + // perform backtracking and compute cigars for the second-best alignments + // + if (n_second) + { + // initialize cigars & MDS + cigar.clear(); + mds.clear(); + + timer.start(); + device_timer.start(); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug(stderr, "[%u] second-best: %u\n", ID, n_second) ); + const uint32* second_idx = thrust::raw_pointer_cast( second_idx_begin.base() ); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug(stderr, "[%u] second-best backtracking\n", ID) ); + banded_traceback_best( + 1u, + n_second, + second_idx, + best_anchor_ptr, + BATCH_SIZE, + band_len, + traceback_state, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("second-best backtracking kernel"); + if (cigar.has_overflown()) + throw nvbio::runtime_error("CIGAR vector overflow\n"); + + device_timer.stop(); + timer.stop(); + stats.backtrack.add( n_second, timer.seconds(), device_timer.seconds() ); + + timer.start(); + device_timer.start(); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug(stderr, "[%u] second-best alignment\n", ID) ); + finish_alignment_best( + 1u, + n_second, + second_idx, + best_anchor_ptr, + BATCH_SIZE, + band_len, + traceback_state, + input_scoring_scheme.sw, // always use Smith-Waterman for the final scoring of the found alignments + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("second-best alignment kernel"); + if (mds.has_overflown()) + throw nvbio::runtime_error("MDS vector overflow\n"); + + device_timer.stop(); + timer.stop(); + stats.finalize.add( n_second, timer.seconds(), device_timer.seconds() ); + } + + // wrap the results in a DeviceOutputBatchSE and process it + { + timer.start(); + + io::DeviceOutputBatchSE gpu_batch( + count, + best_data_dvec, + io::DeviceCigarArray(cigar, cigar_coords_dvec), + mds, + mapq_dvec); + + cpu_batch.readback( gpu_batch, io::MATE_1 ); + + timer.stop(); + stats.alignments_DtoH.add( count, timer.seconds() ); + } + + // + // perform backtracking and compute cigars for the opposite mates of the second-best paired alignments + // + { + // initialize cigars & MDS pools + cigar.clear(); + mds.clear(); + + timer.start(); + device_timer.start(); + + // + // these alignments are of two kinds: paired, or unpaired: this requires some attention, + // as true opposite paired alignments require full DP backtracking, while unpaired + // alignments require the banded version. + // + + // compact the indices of the second-best paired alignments + const uint32 n_second_paired = uint32( thrust::copy_if( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + count, + best_opposite_iterator, + second_idx_begin, + io::has_second_paired() ) - second_idx_begin ); + + const uint32* second_idx = thrust::raw_pointer_cast( second_idx_begin.base() ); + + if (n_second_paired) + { + NVBIO_CUDA_DEBUG_STATEMENT( log_debug(stderr, "[%u] second-best paired: %u\n", ID, n_second_paired) ); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug(stderr, "[%u] second-best paired opposite backtracking\n", ID) ); + opposite_traceback_best( + 1u, + n_second_paired, + second_idx, + best_opposite_ptr, + BATCH_SIZE, + traceback_state, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("second-best paired opposite backtracking kernel"); + if (cigar.has_overflown()) + throw nvbio::runtime_error("CIGAR vector overflow\n"); + } + + // compact the indices of the second-best unpaired alignments + const uint32 n_second_unpaired = uint32( thrust::copy_if( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + count, + best_opposite_iterator, + second_idx_begin, + io::has_second_unpaired() ) - second_idx_begin ); + + if (n_second_unpaired) + { + NVBIO_CUDA_DEBUG_STATEMENT( log_debug(stderr, "[%u] second-best unpaired: %u\n", ID, n_second_unpaired) ); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug(stderr, "[%u] second-best unpaired opposite backtracking\n", ID) ); + banded_traceback_best( + 1u, + n_second_unpaired, + second_idx, + best_opposite_ptr, + BATCH_SIZE, + band_len, + traceback_state, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("second-best unpaired opposite backtracking kernel"); + if (cigar.has_overflown()) + throw nvbio::runtime_error("CIGAR vector overflow\n"); + } + + device_timer.stop(); + timer.stop(); + stats.backtrack_opposite.add( n_second_paired + n_second_unpaired, timer.seconds(), device_timer.seconds() ); + + timer.start(); + device_timer.start(); + + // compact the indices of the second-best alignments + const uint32 n_second = uint32( thrust::copy_if( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + count, + best_opposite_iterator, + second_idx_begin, + io::has_second() ) - second_idx_begin ); + + if (n_second) + { + // compute alignment only on the opposite mates with a second-best + NVBIO_CUDA_DEBUG_STATEMENT( log_debug(stderr, "[%u] second-best opposite alignment\n", ID) ); + finish_opposite_alignment_best( + 1u, + n_second, + second_idx, + best_opposite_ptr, + BATCH_SIZE, + band_len, + traceback_state, + input_scoring_scheme.sw, // always use Smith-Waterman for the final scoring of the found alignments + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("second-best opposite alignment kernel"); + if (mds.has_overflown()) + throw nvbio::runtime_error("MDS vector overflow\n"); + } + + device_timer.stop(); + timer.stop(); + stats.finalize.add( n_second, timer.seconds(), device_timer.seconds() ); + + // wrap the results in a DeviceOutputBatchSE and process it + if (output_file) + { + timer.start(); + + io::DeviceOutputBatchSE gpu_batch( + count, + best_data_dvec_o, + io::DeviceCigarArray(cigar, cigar_coords_dvec), + mds, + mapq_dvec); + + cpu_batch.readback( gpu_batch, io::MATE_2 ); + + timer.stop(); + stats.alignments_DtoH.add( count, timer.seconds() ); + + timer.start(); + + output_file->process( cpu_batch ); + + timer.stop(); + stats.io.add( count, timer.seconds() ); + } + } + } + #endif + + // keep alignment stats + { + log_debug(stderr, "[%u] track stats\n", ID); + thrust::host_vector h_best_data( BATCH_SIZE*2 ); + thrust::host_vector h_best_data_o( BATCH_SIZE*2 ); + thrust::host_vector h_mapq( BATCH_SIZE ); + + thrust::copy( best_data_dvec.begin(), best_data_dvec.begin() + count, h_best_data.begin() ); + thrust::copy( best_data_dvec.begin() + BATCH_SIZE, best_data_dvec.begin() + count + BATCH_SIZE, h_best_data.begin() + BATCH_SIZE ); + thrust::copy( best_data_dvec_o.begin(), best_data_dvec_o.begin() + count, h_best_data_o.begin() ); + thrust::copy( best_data_dvec_o.begin() + BATCH_SIZE, best_data_dvec_o.begin() + count + BATCH_SIZE, h_best_data_o.begin() + BATCH_SIZE ); + thrust::copy( mapq_dvec.begin(), mapq_dvec.begin() + count, h_mapq.begin() ); + + for (uint32 i = 0; i < count; ++i) + { + const io::BestAlignments best( h_best_data[i], h_best_data[i + BATCH_SIZE] ); + const io::BestAlignments best_o( h_best_data_o[i], h_best_data_o[i + BATCH_SIZE] ); + const uint8 mapq = h_mapq[i]; + + stats.track_alignment_statistics( best, best_o, mapq ); + } + } + + // increase the batch number + ++batch_number; +} + +template < + typename scoring_tag, + typename scoring_scheme_type> +void Aligner::best_approx_score( + const Params& params, + const fmi_type fmi, + const rfmi_type rfmi, + const scoring_scheme_type& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + const uint32 anchor, + const io::SequenceDataDevice& read_data1, + const io::SequenceDataDevice& read_data2, + const uint32 seeding_pass, + const uint32 seed_queue_size, + const uint32* seed_queue, + Stats& stats) +{ + log_debug(stderr, "[%u] score\n", ID); + // prepare the scoring system + typedef typename scoring_scheme_type::threshold_score_type threshold_score_type; + + //threshold_score_type threshold_score = scoring_scheme.threshold_score(); + const int32 score_limit = scoring_scheme_type::worst_score; + + // start processing + Timer timer; + Timer global_timer; + nvbio::cuda::Timer device_timer; + + global_timer.start(); + + const uint32 band_len = band_length( params.max_dist ); + + const read_view_type reads_view1 = plain_view( read_data1 ); + const read_view_type reads_view2 = plain_view( read_data2 ); + const read_batch_type reads1( reads_view1 ); + const read_batch_type reads2( reads_view2 ); + + const io::LdgSequenceDataView genome_view( plain_view( reference_data ) ); + const genome_access_type genome_access( genome_view ); + const uint32 genome_len = genome_access.bps(); + const genome_iterator genome = genome_access.sequence_stream(); + + NVBIO_VAR_UNUSED thrust::device_vector::iterator loc_queue_iterator = scoring_queues.hits.loc.begin(); + thrust::device_vector::iterator score_queue_iterator = scoring_queues.hits.score.begin(); + thrust::device_vector::iterator opposite_score_queue_iterator = scoring_queues.hits.opposite_score.begin(); + thrust::device_vector::iterator opposite_queue_iterator = opposite_queue_dvec.begin(); + + // + // At this point we have a queue full of reads, each with an associated set of + // seed hits encoded as a (sorted) list of SA ranges. + // For each read we need to: + // 1. select some seed hit to process (i.e. a row in one of the SA ranges) + // 2. locate it, i.e. converting from SA to linear coordinates + // 3. and score it + // until some search criteria are satisfied. + // The output queue is then reused in the next round as the input queue, and + // viceversa. + // + ScoringQueues::active_reads_storage_type& active_read_queues = scoring_queues.active_reads; + + active_read_queues.resize( seed_queue_size ); + + thrust::transform( + thrust::device_ptr( seed_queue ), + thrust::device_ptr( seed_queue ) + seed_queue_size, + active_read_queues.in_queue.begin(), + pack_read( params.top_seed ) ); + + // keep track of the number of extensions performed for each of the active reads + uint32 n_ext = 0; + + typedef BestApproxScoringPipelineState pipeline_type; + + pipeline_type pipeline( + anchor, + reads1, + reads2, + genome_len, + genome, + fmi, + rfmi, + scoring_scheme, + score_limit, + *this ); + + // initialize the hit selection & scoring pipeline + select_init( + pipeline, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("select-init kernel"); + + // prepeare the selection context + SelectBestApproxContext select_context( trys_dptr ); + + for (uint32 extension_pass = 0; active_read_queues.in_size && n_ext < params.max_ext; ++extension_pass) + { + log_debug(stderr, "[%u] pass:\n[%u] batch:[%u] %u\n[%u] seeding pass: %u\n[%u] extension pass: %u\n", ID, ID, batch_number, ID, seeding_pass, ID, extension_pass); + + // initialize all the scoring output queues + scoring_queues.clear_output(); + + // sort the active read infos + #if 0 + { + timer.start(); + device_timer.start(); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug(stderr, "[%u] read sort\n", ID) ); + sort_inplace( active_read_queues.in_size, active_read_queues.raw_input_queue() ); + + device_timer.stop(); + timer.stop(); + stats.sort.add( active_read_queues.in_size, timer.seconds(), device_timer.seconds() ); + } + #endif + + timer.start(); + device_timer.start(); + + // keep track of how many hits per read we are generating + pipeline.n_hits_per_read = 1; + + if ((active_read_queues.in_size <= BATCH_SIZE/2) && + (params.no_multi_hits == false)) + { + // + // The queue of actively processed reads is very small: at this point + // it's better to select multiple hits to process in each round. + // This adds some book keeping overheads, but allows to make larger + // kernel launches. + // + + // the maximum number of extensions we can perform in one iteration + // is at most 4096, as we use 12 bits to encode the extension index + const uint32 max_ext = std::min( 4096u, params.max_ext - n_ext ); + + // try to generate BATCH_SIZE items to process + pipeline.n_hits_per_read = std::min( + BATCH_SIZE / active_read_queues.in_size, + max_ext ); + } + // else + // + // The queue of actively processed reads is sufficiently large to allow + // selecting & scoring one seed hit at a time and still have large kernel + // launches. This is algorithmically the most efficient choice (because + // it enables frequent early outs), so let's choose it. + // + + // setup the hits queue according to whether we select multiple hits per read or not + scoring_queues.hits_index.setup( pipeline.n_hits_per_read, active_read_queues.in_size ); + + // update pipeline + pipeline.scoring_queues = scoring_queues.device_view(); + + log_debug(stderr, "[%u] select\n", ID); + select( + select_context, + pipeline, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("select kernel"); + + // this sync point seems very much needed: if we don't place it, we won't see + // the right number of hits later on... + cudaDeviceSynchronize(); + + device_timer.stop(); + timer.stop(); + stats.select.add( active_read_queues.in_size * pipeline.n_hits_per_read, timer.seconds(), device_timer.seconds() ); + + // swap input & output queues + active_read_queues.swap(); + + // update pipeline view + pipeline.scoring_queues = scoring_queues.device_view(); + + // fetch the new queue size + if (active_read_queues.in_size == 0) + break; + + // fetch the output queue size + pipeline.hits_queue_size = pipeline.n_hits_per_read > 1 ? scoring_queues.hits_count() : active_read_queues.in_size; + if (pipeline.hits_queue_size == 0) + continue; + + // use the parent queue only if we chose the multiple-hits per read pipeline + // check if we need to persist this seeding pass + if (batch_number == (uint32) params.persist_batch && + seeding_pass == (uint32) params.persist_seeding && + extension_pass == (uint32) params.persist_extension) + persist_selection( params.persist_file, "selection", + anchor, + active_read_queues.in_size, + active_read_queues.raw_input_queue(), + pipeline.n_hits_per_read, + pipeline.hits_queue_size, + scoring_queues.hits_index, + scoring_queues.hits ); + + log_debug(stderr, "[%u] selected %u hits\n", ID, pipeline.hits_queue_size); + + timer.start(); + device_timer.start(); + + // sort the selected hits by their SA coordinate + log_debug(stderr, "[%u] locate sort\n", ID); + pipeline.idx_queue = sort_hi_bits( pipeline.hits_queue_size, pipeline.scoring_queues.hits.loc ); + + device_timer.stop(); + timer.stop(); + stats.sort.add( pipeline.hits_queue_size, timer.seconds(), device_timer.seconds() ); + + timer.start(); + device_timer.start(); + + // NOTE: only 75-80% of these locations are unique. + // It might pay off to do a compaction beforehand. + + // and locate their position in linear coordinates + log_debug(stderr, "[%u] locate init\n", ID); + locate_init( pipeline, params ); + + optional_device_synchronize(); + + log_debug(stderr, "[%u] locate lookup\n", ID); + locate_lookup( pipeline, params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("locating kernel"); + + device_timer.stop(); + timer.stop(); + stats.locate.add( pipeline.hits_queue_size, timer.seconds(), device_timer.seconds() ); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug( stderr, "[%u] crc: %llu\n", ID, device_checksum( loc_queue_iterator, loc_queue_iterator + pipeline.hits_queue_size ) ) ); + + // + // Start the real scoring work... + // + + timer.start(); + device_timer.start(); + + // sort the selected hits by their linear genome coordinate + // TODO: sub-sort by read position/RC flag so as to (1) get better coherence, + // (2) allow removing duplicate extensions + log_debug(stderr, "[%u] score sort\n", ID); + pipeline.idx_queue = sort_hi_bits( pipeline.hits_queue_size, pipeline.scoring_queues.hits.loc ); + + device_timer.stop(); + timer.stop(); + stats.sort.add( pipeline.hits_queue_size, timer.seconds(), device_timer.seconds() ); + + // + // assign a score to all selected hits (currently in the output queue) + // + float score_time = 0.0f; + float dev_score_time = 0.0f; + timer.start(); + device_timer.start(); + + anchor_score_best( + band_len, + pipeline, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("score kernel"); + + device_timer.stop(); + timer.stop(); + score_time += timer.seconds(); + dev_score_time += device_timer.seconds(); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug( stderr, "[%u] crc: %llu\n", ID, device_checksum( score_queue_iterator, score_queue_iterator + pipeline.hits_queue_size ) ) ); + + // + // compact the list of candidate hits (with a valid anchor mate score) and perform DP alignment + // on the opposite mates + // + + timer.start(); + device_timer.start(); + + // NOTE: + // Here we want the output opposite_queue to contain the list of indices *into* idx_queue, so as to keep the + // original sorting order by genome coordintes used for scoring the anchor. + // Down the pipeline the scoring kernel will address the problems by idx_queue[ opposite_score_queue[ thread_id ] ]. + log_debug(stderr, "[%u] compact opposite\n", ID); + const int32 worst_score = scoring_scheme_type::worst_score; + + pipeline.opposite_queue_size = uint32( thrust::copy_if( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + pipeline.hits_queue_size, + thrust::make_permutation_iterator( score_queue_iterator, thrust::device_ptr( pipeline.idx_queue ) ), // gather from the indexed score queue + opposite_queue_iterator, + bind_second_functor< not_equal_functor >( worst_score ) ) - opposite_queue_iterator ); + + // make sure the reducer sees correct scores + thrust::fill( + opposite_score_queue_iterator, + opposite_score_queue_iterator + pipeline.hits_queue_size, + worst_score ); + + if (pipeline.opposite_queue_size) + { + // perform DP alignment on the opposite mates + log_debug(stderr, "[%u] score opposite (%u)\n", ID, pipeline.opposite_queue_size ); + opposite_score_best( + pipeline, + params ); + + NVBIO_CUDA_DEBUG_STATEMENT( log_debug( stderr, "[%u] crc: %llu\n", device_checksum( opposite_score_queue_iterator, opposite_score_queue_iterator + pipeline.hits_queue_size ) ) ); + + // check if we need to persist this seeding pass + if (batch_number == (uint32) params.persist_batch && + seeding_pass == (uint32) params.persist_seeding && + extension_pass == (uint32) params.persist_extension) + persist_scores( params.persist_file, "opposite-score", + anchor, + active_read_queues.in_size, + pipeline.n_hits_per_read, + pipeline.hits_queue_size, + scoring_queues ); + } + + optional_device_synchronize(); + nvbio::cuda::check_error("opposite-score kernel"); + + device_timer.stop(); + timer.stop(); + stats.opposite_score.add( pipeline.opposite_queue_size, timer.seconds(), device_timer.seconds() ); + //stats.opposite_score.user[0] += score_mate_work_queue_stats.utilization(nvbio::cuda::STREAM_EVENT); + //stats.opposite_score.user[1] += score_mate_work_queue_stats.utilization(nvbio::cuda::RUN_EVENT); + //stats.opposite_score.user[2] += score_mate_work_queue_stats.avg_iterations(); + //stats.opposite_score.user[3] = nvbio::max( stats.opposite_score.user[3], score_mate_work_queue_stats.max_iterations() - score_mate_work_queue_stats.avg_iterations() ); + + timer.start(); + device_timer.start(); + + const ReduceBestApproxContext reduce_context( pipeline.trys, n_ext ); + + // reduce the multiple scores to find the best two alignments + // (one thread per active read). + log_debug(stderr, "[%u] score reduce\n", ID); + score_reduce_paired( + reduce_context, + pipeline, + params ); + + optional_device_synchronize(); + nvbio::cuda::check_error("score-reduce kernel"); + + // keep track of the number of extensions performed for each of the active reads + n_ext += pipeline.n_hits_per_read; + + device_timer.stop(); + timer.stop(); + stats.score.add( pipeline.hits_queue_size, score_time + timer.seconds(), dev_score_time + device_timer.seconds() ); + } + + optional_device_synchronize(); + global_timer.stop(); + stats.scoring_pipe.add( seed_queue_size, global_timer.seconds(), global_timer.seconds() ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_paired_ed.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_paired_ed.cu new file mode 100644 index 0000000000000000000000000000000000000000..b3ddd8ef703933c73d7e5cf81e233c1d17c3b8b5 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_paired_ed.cu @@ -0,0 +1,63 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +void best_approx_ed( + Aligner& aligner, + const Params& params, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + io::SequenceDataDevice& read_data1, + io::SequenceDataDevice& read_data2, + io::HostOutputBatchPE& cpu_batch, + Stats& stats) +{ + aligner.best_approx( + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + read_data1, + read_data2, + cpu_batch, + stats ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_paired_sw.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_paired_sw.cu new file mode 100644 index 0000000000000000000000000000000000000000..6bb133b1039f84437af3481d18b4e9628d3648f1 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_paired_sw.cu @@ -0,0 +1,63 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +void best_approx_sw( + Aligner& aligner, + const Params& params, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + io::SequenceDataDevice& read_data1, + io::SequenceDataDevice& read_data2, + io::HostOutputBatchPE& cpu_batch, + Stats& stats) +{ + aligner.best_approx( + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + read_data1, + read_data2, + cpu_batch, + stats ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_sw.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_sw.cu new file mode 100644 index 0000000000000000000000000000000000000000..9fe25dbd59c505627f569db49e1852bceaf93a7e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_approx_sw.cu @@ -0,0 +1,61 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +void best_approx_sw( + Aligner& aligner, + const Params& params, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + io::SequenceDataDevice& read_data, + io::HostOutputBatchSE& cpu_batch, + Stats& stats) +{ + aligner.best_approx( + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + read_data, + cpu_batch, + stats ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_exact.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_exact.h new file mode 100644 index 0000000000000000000000000000000000000000..50973689c3addc40e667d8412bd8b5b1eee40e75 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_best_exact.h @@ -0,0 +1,691 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +template < + typename FMI, + typename rFMI, + typename scoring_scheme_type> +void Aligner::best_exact( + const Params& params, + const FMI fmi, + const rFMI rfmi, + const scoring_scheme_type& scoring_scheme, + const io::FMIndexDataCUDA& driver_data, + io::ReadDataCUDA& read_data, + const uint32 output_set, + Stats& stats) +{ + typedef uint32 read_storage_type; + typedef uint4 read_storage_type4; + typedef READ_TEX_SELECTOR( const uint32*, nvbio::cuda::ldg_pointer ) read_base_type; + typedef READ_TEX_SELECTOR( const uint4*, nvbio::cuda::ldg_pointer ) read_base_type4; + + typedef read_storage_type read_storage_type_A; + typedef read_base_type read_base_type_A; + + #if USE_UINT4_PACKING + typedef read_storage_type4 read_storage_type_B; + typedef read_base_type4 read_base_type_B; + #else + typedef read_storage_type read_storage_type_B; + typedef read_base_type read_base_type_B; + #endif + + Timer timer; + Timer global_timer; + + const uint32 count = read_data.size(); + const uint32 band_len = band_length( params.max_dist ); + + //// make sure the current output set is not currently being flushed + //ScopedLock lock( &output_thread.m_lock[ output_set ] ); + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + count, + seed_queue_dvec.begin() ); + + seed_queue_size_dvec[0] = count; + + // + // Similarly to Bowtie2, we perform a number of seed & extension passes, except + // that here we extract just one seed per pass. + // Since reads may have different length, and the search might for some might terminate + // earlier than for others, the number of reads actively processed in each pass can vary + // substantially. + // In order to keep the cores and all its lanes busy, we use a pair of input & output + // queues to compact the set of active reads in each round, swapping them at each + // iteration. + // + + // initialize seeding queues + HostQueues seed_queues; + seed_queues.in_size = count; + seed_queues.in_queue = seed_queue_dptr; + seed_queues.out_size = NULL; // for mapping, we initially setup a NULL output queue + seed_queues.out_queue = NULL; // for mapping, we initially setup a NULL output queue + + // initialize the seed hit counts + thrust::fill( cnts_dvec.begin(), cnts_dvec.end(), uint32(0) ); + + Batch reads_A( + 0, count, + read_base_type_A( (const read_storage_type_A*)read_data.read_stream() ), + read_data.read_index(), + read_data.qual_stream()); + + // + // perform mapping + // + { + timer.start(); + + #if 0 + bowtie2_map_exact( + reads_A, fmi, rfmi, + 0u, seed_queues.device(), + hits_dptr, cnts_dptr, + params ); + #else + bowtie2_map_exact( + reads_A, fmi, rfmi, + hits_dptr, cnts_dptr, + params ); + #endif + cudaThreadSynchronize(); + nvbio::cuda::check_error("mapping kernel"); + + timer.stop(); + stats.map.add( seed_queues.in_size, timer.seconds() ); + } + + // take some stats on the hits we got + if (params.keep_stats) + keep_stats( reads_A.size(), stats ); + + // setup output queue + seed_queues.out_size = seed_queue_size_dptr; + seed_queues.out_queue = seed_queue_dptr + BATCH_SIZE; + + const uint32 max_seeds = read_data.m_max_read_len / params.seed_len; + + thrust::device_vector hits_level_dvec( BATCH_SIZE ); + thrust::device_vector cnts_level_dvec( BATCH_SIZE ); + + for (uint32 seed_idx = 0; seed_queues.in_size && seed_idx < max_seeds; ++seed_idx) + { + { + const uint32 blocks = (read_data.size() + BLOCKDIM-1) / BLOCKDIM; + + thrust::fill( hits_stats_dvec.begin(), hits_stats_dvec.end(), 0u ); + bowtie2_hits_stats( read_data.size(), hits_dptr, cnts_dptr, hits_stats_dptr ); + + cudaThreadSynchronize(); + nvbio::cuda::check_error("hit stats kernel"); + + cudaThreadSynchronize(); + nvbio::cuda::check_error("hit stats kernel"); + + hits_stats_hvec = hits_stats_dvec; + + const uint64 n_hits = hits_stats_hvec[ HIT_STATS_TOTAL ]; + fprintf(stderr, "\nseed idx: %u (%u active reads - %.2f M global hits)\n", seed_idx, seed_queues.in_size, float(n_hits) * 1.0e-6f); + } + + extract_top_range( + reads_A, hits_dptr, cnts_dptr, + thrust::raw_pointer_cast( &hits_level_dvec.front() ), + thrust::raw_pointer_cast( &cnts_level_dvec.front() ) ); + + cudaThreadSynchronize(); + nvbio::cuda::check_error("extract-top-range kernel"); + + best_exact_score( + params, + fmi, + rfmi, + scoring_scheme, + driver_data, + read_data, + seed_idx, + seed_queues, + thrust::raw_pointer_cast( &hits_level_dvec.front() ), + thrust::raw_pointer_cast( &cnts_level_dvec.front() ), + stats ); + + // initialize output seeding queue size + seed_queues.clear_output(); + + bowtie2_prune_search( + seed_idx, + seed_queues.device(), + best_data_dptr ); + + cudaThreadSynchronize(); + nvbio::cuda::check_error("pruning kernel"); + + // swap input & output queues + seed_queues.swap(); + } + + // + // At this point, for each read we have the scores and rough alignment positions of the + // best two alignments: to compute the final results we need to backtrack the DP extension, + // and compute accessory CIGARS and MD strings. + // + + Batch reads_B( + 0, count, + read_base_type_B( (const read_storage_type_B*)read_data.read_stream() ), + read_data.read_index(), + read_data.qual_stream()); + + // + // perform backtracking and compute cigars for the best alignments + // + timer.start(); + { + BacktrackBestContext<0,edit_distance_scoring> context( + best_data_dptr, + NULL ); + + bowtie2_backtrack( + read_data.max_read_len(), + band_len, + count, + reads_B, + scoring_scheme, + driver_data.genome_length(), + driver_data.genome_stream(), + cigar_dptr, + cigar_coords_dptr, + mds_dptr, + count, + context, + params ); + + cudaThreadSynchronize(); + nvbio::cuda::check_error("backtracking kernel"); + } + timer.stop(); + stats.backtrack.add( count, timer.seconds() ); + + // copy best cigars back to the host + cigar_coords_hvec1[output_set] = cigar_coords_dvec; + nvbio::cuda::copy( cigar_dvec, cigar_hvec1[output_set] ); + nvbio::cuda::copy( mds_dvec, mds_hvec1[output_set] ); + + // overlap the second-best indices with the loc queue + thrust::device_vector& second_idx_dvec = loc_queue_dvec; + + // compact the indices of the second-best alignments + const uint32 n_second = uint32( thrust::copy_if( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + count, + best_data_dvec.begin(), + second_idx_dvec.begin(), + has_second() ) - second_idx_dvec.begin() ); + + // + // perform backtracking and compute cigars for the second-best alignments + // + if (n_second) + { + timer.start(); + + uint32* second_idx = thrust::raw_pointer_cast( &second_idx_dvec[0] ); + + BacktrackBestContext<1,edit_distance_scoring> context( + best_data_dptr, + second_idx ); + + bowtie2_backtrack( + read_data.max_read_len(), + band_len, + n_second, + reads_B, + scoring_scheme, + driver_data.genome_length(), + driver_data.genome_stream(), + cigar_dptr, + cigar_coords_dptr, + mds_dptr, + count, + context, + params ); + + cudaThreadSynchronize(); + nvbio::cuda::check_error("second-best backtracking kernel"); + + timer.stop(); + stats.backtrack.add( n_second, timer.seconds() ); + } + + // copy second-best cigars back to the host + cigar_coords_hvec2[output_set] = cigar_coords_dvec; + nvbio::cuda::copy( cigar_dvec, cigar_hvec2[output_set] ); + nvbio::cuda::copy( mds_dvec, mds_hvec2[output_set] ); + + // copy results back to the host + thrust::copy( best_data_dvec.begin(), best_data_dvec.begin() + count, best_data_hvec[output_set].begin() ); +} + +template < + typename FMI, + typename rFMI, + typename scoring_scheme_type> +void Aligner::best_exact_score( + const Params& params, + const FMI fmi, + const rFMI rfmi, + const scoring_scheme_type& scoring_scheme, + const io::FMIndexDataCUDA& driver_data, + io::ReadDataCUDA& read_data, + const uint32 seed_idx, + HostQueues& seed_queues, + SeedHit* hits_level_dptr, + uint32* cnts_level_dptr, + Stats& stats) +{ + #if USE_UINT4_PACKING + typedef uint32 read_storage_type; + #else + typedef uint4 read_storage_type; + #endif + typedef READ_TEX_SELECTOR( const read_storage_type*, nvbio::cuda::ldg_pointer ) read_base_type; + + uint32 hits_to_process; + { + thrust::fill( hits_stats_dvec.begin(), hits_stats_dvec.end(), 0u ); + bowtie2_hits_stats( read_data.size(), hits_dptr, cnts_dptr, hits_stats_dptr ); + + cudaThreadSynchronize(); + nvbio::cuda::check_error("hit stats kernel"); + + hits_stats_hvec = hits_stats_dvec; + + hits_to_process = hits_stats_hvec[ HIT_STATS_TOTAL ]; + } + + Timer timer; + Timer global_timer; + + const uint32 count = read_data.size(); + const uint32 band_len = band_length( seed_idx ); + + Batch reads( + 0, count, + read_base_type( (const read_storage_type*)read_data.read_stream() ), + read_data.read_index(), + read_data.qual_stream()); + + // + // At this point we have a queue full of reads, each with an associated set of + // seed hits encoded as a (sorted) list of SA ranges. + // For each read we need to: + // 1. select some seed hit to process (i.e. a row in one of the SA ranges) + // 2. locate it, i.e. converting from SA to linear coordinates + // 3. and score it + // until some search criteria are satisfied. + // The output queue is then reused in the next round as the input queue, and + // viceversa. + // + HostQueues hit_queues; + hit_queues.in_size = seed_queues.in_size; + hit_queues.in_queue = hits_queue_dptr; + hit_queues.out_size = hits_queue_size_dptr; + hit_queues.out_queue = hits_queue_dptr + BATCH_SIZE; + + cudaMemcpy( hit_queues.in_queue, seed_queues.in_queue, sizeof(uint32) * hit_queues.in_size, cudaMemcpyDeviceToDevice ); + + bool first_run = true; + + SelectBestExactContext select_context( + best_data_dptr, + params.max_dist, + seed_idx, + seed_idx == 0 ? true : false ); // init + + // use the score queue to store temporary packed seed data + uint32* seed_data_dptr = (uint32*)score_queue_dptr; + + uint32 processed_hits = 0; + + while (hit_queues.in_size) + { + // sort the input queue + thrust::sort( + hits_queue_dvec.begin() + (hit_queues.in_queue - hits_queue_dptr), + hits_queue_dvec.begin() + (hit_queues.in_queue - hits_queue_dptr) + hit_queues.in_size ); + + fprintf(stderr,"\rcount: %u (%.2f / %.2f M hits processed) ", hit_queues.in_size, float(processed_hits) * 1.0e-6f, float(hits_to_process) * 1.0e-6f); + hit_queues.clear_output(); + + /*if (hit_queues.in_size < read_data.size() / 500) + { + // we can safely ignore this small set of active reads, as we'll drop only + // a given amount of sensitivity + return; + } + else*/ if (hit_queues.in_size > 128u*1024u) + { + // + // The queue of actively processed reads is sufficiently large to allow + // selecting & scoring one seed hit at a time and still have large kernel + // launches. This is algorithmically the most efficient choice (because + // it enables frequent early outs), so let's choose it. + // + timer.start(); + + // + // select and locate the next round of hits for the reads in the input queue + // + bowtie2_select( + first_run, + reads, fmi, rfmi, hits_level_dptr, cnts_level_dptr, + select_context, + hit_queues.in_size, + hit_queues.in_queue, + hit_queues.out_size, + hit_queues.out_queue, + loc_queue_dptr, + seed_data_dptr, + params ); + + first_run = false; + + cudaThreadSynchronize(); + nvbio::cuda::check_error("selecting kernel"); + + timer.stop(); + stats.select.add( hit_queues.in_size, timer.seconds() ); + + // fetch the new queue size + hit_queues.swap(); + if (hit_queues.in_size == 0) + break; + + processed_hits += hit_queues.in_size; + + timer.start(); + + // sort the selected hits by their SA coordinate + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + hit_queues.in_size, + idx_queue_dvec.begin() ); + + thrust::sort_by_key( + loc_queue_dvec.begin(), + loc_queue_dvec.begin() + hit_queues.in_size, + idx_queue_dvec.begin() ); + + timer.stop(); + stats.sort.add( hit_queues.in_size, timer.seconds() ); + + // NOTE: only 75-80% of these locations are unique. + // It might pay off to do a compaction beforehand. + + // and locate their position in linear coordinates + bowtie2_locate( + reads, fmi, rfmi, + hit_queues.in_size, + loc_queue_dptr, + idx_queue_dptr, + seed_data_dptr, + params ); + + cudaThreadSynchronize(); + nvbio::cuda::check_error("locating kernel"); + + timer.stop(); + stats.locate.add( hit_queues.in_size, timer.seconds() ); + + timer.start(); + + // sort the selected hits by their linear genome coordinate + // TODO: sub-sort by read position/RC flag so as to (1) get better coherence, + // (2) allow removing duplicate extensions + thrust::sort_by_key( + loc_queue_dvec.begin(), + loc_queue_dvec.begin() + hit_queues.in_size, + idx_queue_dvec.begin() ); + + timer.stop(); + stats.sort.add( hit_queues.in_size, timer.seconds() ); + + // + // assign a score to all selected hits (currently in the output queue) + // + if (hit_queues.in_size) + { + timer.start(); + + ScoreBestContext context( + NULL, + hit_queues.in_queue, + score_queue_dptr, + best_data_dptr, + seed_idx ); + + // compute the score for each selected hit (one thread per hit). + bowtie2_score( + band_len, + reads, + context, + hit_queues.in_size, + idx_queue_dptr, + loc_queue_dptr, + driver_data.genome_length(), + driver_data.genome_stream(), + params ); + + cudaThreadSynchronize(); + nvbio::cuda::check_error("score kernel"); + + const ReduceBestExactContext reduce_context; + + bowtie2_score_reduce( + reads, reduce_context, hits_level_dptr, cnts_level_dptr, + best_data_dptr, + hit_queues.in_size, + hit_queues.in_queue, + loc_queue_dptr, + score_queue_dptr, + params ); + + cudaThreadSynchronize(); + nvbio::cuda::check_error("score-reduce kernel"); + + timer.stop(); + stats.score.add( hit_queues.in_size, timer.seconds() ); + } + } + else + { + // + // The queue of actively processed reads is very small: at this point + // it's better to select multiple hits to process in each round. + // This adds some book keeping overheads, but allows to make larger + // kernel launches. + // + timer.start(); + + score_output_count_dvec[0] = 0; + + // the maximum number of extensions we can perform in one iteration + // is at most 4096, as we use 12 bits to encode the extension index + const uint32 max_ext = 4096; + + // try to generate 256K items to process + const uint32 n_multi = + std::min( + (256u*1024u) / hit_queues.in_size, + max_ext ); + + const uint32 score_output_queue_stride = hit_queues.in_size; + + bowtie2_select_multi( + first_run, + reads, fmi, rfmi, hits_level_dptr, cnts_level_dptr, + select_context, + hit_queues.in_size, + hit_queues.in_queue, + hit_queues.out_size, + hit_queues.out_queue, + score_output_count_dptr, + loc_queue_dptr, + seed_data_dptr, + score_parent_queue_dptr, + score_output_queue_dptr, + score_output_queue_stride, + n_multi, + params ); + + first_run = false; + + cudaThreadSynchronize(); + nvbio::cuda::check_error("select-multi kernel"); + + timer.stop(); + stats.select.add( hit_queues.in_size * n_multi, timer.seconds() ); + + // swap the input & output queues + hit_queues.swap(); + + // fetch the output queue size + const uint32 score_queue_size = score_output_count_dvec[0]; + if (score_queue_size == 0) + break; + + processed_hits += score_queue_size; + + timer.start(); + + // sort the selected hits by their SA coordinate + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + score_queue_size, + idx_queue_dvec.begin() ); + + thrust::sort_by_key( + loc_queue_dvec.begin(), + loc_queue_dvec.begin() + score_queue_size, + idx_queue_dvec.begin() ); + + timer.stop(); + stats.sort.add( score_queue_size, timer.seconds() ); + + // and locate their position in linear coordinates + bowtie2_locate( + reads, fmi, rfmi, + score_queue_size, + loc_queue_dptr, + idx_queue_dptr, + seed_data_dptr, + params ); + + cudaThreadSynchronize(); + nvbio::cuda::check_error("locating kernel"); + + timer.stop(); + stats.locate.add( score_queue_size, timer.seconds() ); + + timer.start(); + + // sort the selected hits by their linear genome coordinate + // TODO: sub-sort by read_id/RC flag so as to (1) get better coherence, + // (2) allow removing duplicate extensions + thrust::sort_by_key( + loc_queue_dvec.begin(), + loc_queue_dvec.begin() + score_queue_size, + idx_queue_dvec.begin() ); + + timer.stop(); + stats.sort.add( hit_queues.in_size, timer.seconds() ); + + // + // assign a score to all selected hits (currently in the output queue) + // + if (score_queue_size) + { + timer.start(); + + ScoreBestContext context( + score_parent_queue_dptr, + hit_queues.in_queue, + score_queue_dptr, + best_data_dptr, + seed_idx ); + + // compute the score for each selected hit (one thread per hit). + bowtie2_score( + band_len, + reads, + context, + score_queue_size, + idx_queue_dptr, + loc_queue_dptr, + driver_data.genome_length(), + driver_data.genome_stream(), + params ); + + cudaThreadSynchronize(); + nvbio::cuda::check_error("score-multi kernel"); + + const ReduceBestExactContext reduce_context; + + // reduce the multiple scores to find the best two alignments + // (one thread per active read). + bowtie2_score_multi_reduce( + reads, reduce_context, hits_level_dptr, cnts_level_dptr, + best_data_dptr, + hit_queues.in_size, + hit_queues.in_queue, + score_output_queue_stride, + score_output_queue_dptr, + score_parent_queue_dptr, + score_queue_dptr, + loc_queue_dptr, + params ); + + cudaThreadSynchronize(); + nvbio::cuda::check_error("score-multi-reduce kernel"); + + timer.stop(); + stats.score.add( score_queue_size, timer.seconds() ); + } + } + } +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_init.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_init.cu new file mode 100644 index 0000000000000000000000000000000000000000..ff768bdb184ee26170c394962810de668adee73a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_init.cu @@ -0,0 +1,503 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +template +T* resize(bool do_alloc, thrust::device_vector& vec, const uint32 size, uint64& bytes) +{ + bytes += size * sizeof(T); + if (do_alloc) + { + vec.resize( size ); + return thrust::raw_pointer_cast(&vec.front()); + } + return NULL; +} + +template +T* resize(bool do_alloc, thrust::host_vector& vec, const uint32 size, uint64& bytes) +{ + bytes += size * sizeof(T); + if (do_alloc) + { + vec.resize( size ); + return thrust::raw_pointer_cast(&vec.front()); + } + return NULL; +} + +template +T* resize(bool do_alloc, std::vector& vec, const uint32 size, uint64& bytes) +{ + bytes += size * sizeof(T); + if (do_alloc) + { + vec.resize( size ); + return &vec[0]; + } + return NULL; +} + +bool Aligner::init_alloc(const uint32 BATCH_SIZE, const Params& params, const EndType type, bool do_alloc, std::pair* mem_stats) +{ + size_t free, total; + cudaMemGetInfo(&free, &total); + + //const uint32 band_len = (type == kPairedEnds) ? MAXIMUM_BAND_LENGTH : band_length( params.max_dist ); + + uint64 d_allocated_bytes = 0; + uint64 h_allocated_bytes = 0; + + // alloc the seeding queues + d_allocated_bytes += seed_queues.resize_arena( BATCH_SIZE, do_alloc ); + + // alloc the hit deques + d_allocated_bytes += hit_deques.resize( BATCH_SIZE, params.max_hits, do_alloc ); + if (params.randomized) + rseeds_dptr = resize( do_alloc, rseeds_dvec, BATCH_SIZE, d_allocated_bytes ); + + // alloc the scoring queues + d_allocated_bytes += scoring_queues.resize( BATCH_SIZE, BATCH_SIZE, do_alloc ); // TODO: pass read-end 'type' field + + idx_queue_dptr = resize( do_alloc, idx_queue_dvec, BATCH_SIZE*2, d_allocated_bytes ); // 2x for ping-pong buffers + if (params.mode != AllMapping) + resize( do_alloc, sorting_queue_dvec, BATCH_SIZE*2, d_allocated_bytes ); // 2x for ping-pong buffers + else + resize( do_alloc, sorting_queue_dvec, BATCH_SIZE*2*4, d_allocated_bytes ); // 4x for 64-bit sorting + + nvbio::cuda::check_error("allocating queues"); + + mapq_dptr = resize( do_alloc, mapq_dvec, BATCH_SIZE, d_allocated_bytes ); + + if (params.mode != AllMapping) + { + reseed_dptr = resize( do_alloc, reseed_dvec, BATCH_SIZE, d_allocated_bytes ); + trys_dptr = resize( do_alloc, trys_dvec, BATCH_SIZE, d_allocated_bytes ); + best_data_dptr = resize( do_alloc, best_data_dvec, BATCH_SIZE*2, d_allocated_bytes ); + + if (type == kPairedEnds) + best_data_dptr_o = resize( do_alloc, best_data_dvec_o, BATCH_SIZE*2, d_allocated_bytes ); + } + else + { + // in all-mapping mode we store the temporary output in a double-buffered ring-buffer + buffer_alignments_dptr = resize( do_alloc, buffer_alignments_dvec, BATCH_SIZE*2, d_allocated_bytes ); + buffer_read_info_dptr = resize( do_alloc, buffer_read_info_dvec, BATCH_SIZE*2, d_allocated_bytes ); + + output_alignments_dptr = resize( do_alloc, output_alignments_dvec, BATCH_SIZE, d_allocated_bytes ); + output_read_info_dptr = resize( do_alloc, output_read_info_dvec, BATCH_SIZE, d_allocated_bytes ); + + flags_dptr = resize( do_alloc, flags_dvec, BATCH_SIZE, d_allocated_bytes ); + } + nvbio::cuda::check_error("allocating output buffers"); + + hits_stats_dptr = resize( do_alloc, hits_stats_dvec, 128, d_allocated_bytes ); + resize( do_alloc, hits_stats_hvec, 128, d_allocated_bytes ); + + if (params.mode == AllMapping) + { + hits_count_scan_dptr = resize( do_alloc, hits_count_scan_dvec, BATCH_SIZE+1, d_allocated_bytes ); + hits_range_scan_dptr = resize( do_alloc, hits_range_scan_dvec, params.max_hits * BATCH_SIZE+1, d_allocated_bytes ); + } + + //const uint32 n_cigar_entries = BATCH_SIZE*(MAXIMUM_BAND_LEN_MULT*band_len+1); + //const uint32 n_mds_entries = BATCH_SIZE*MAX_READ_LEN; + const uint32 n_cigar_entries = (128 * BATCH_SIZE)/sizeof(io::Cigar); // 256MB + const uint32 n_mds_entries = (256 * BATCH_SIZE)/sizeof(uint8); // 256MB + if (do_alloc) + { + log_verbose(stderr, "[%u] allocating %u MB of string storage\n[%u] CIGARs : %u MB\n[%u] MDs : %u MB\n", + ID, uint32(n_cigar_entries * sizeof(io::Cigar) + n_mds_entries)/(1024*1024), + ID, uint32(n_cigar_entries * sizeof(io::Cigar))/(1024*1024), + ID, n_mds_entries/(1024*1024) ); + } + + // allocate CIGARs & MDs + d_allocated_bytes += cigar.resize( BATCH_SIZE, n_cigar_entries, do_alloc ); + d_allocated_bytes += mds.resize( BATCH_SIZE, n_mds_entries, do_alloc ); + + // allocate CIGAR coords + cigar_coords_dptr = resize( do_alloc, cigar_coords_dvec, BATCH_SIZE, d_allocated_bytes ); + nvbio::cuda::check_error("allocating CIGARs"); + + if (type == kPairedEnds) + { + // allocate the device queue + opposite_queue_dptr = resize( do_alloc, opposite_queue_dvec, BATCH_SIZE, d_allocated_bytes ); + } + + // allocate DP storage + uint32 dp_storage = 0; + + { + // + // allocate two thirds of available device memory for scoring / traceback + // + + const uint32 bytes_per_read = uint32( float( params.avg_read_length ) * 1.5f ); + + const uint64 read_mem = bytes_per_read * BATCH_SIZE * (type == kPairedEnds ? 2u : 1u); + // assume 250B per read + + const uint64 guard_band = 512*1024*1024 + // we want to leave 512MB free, + read_mem; // needed for kernels using lmem + + const uint64 min_dp_storage = 64*1024*1024; // minimum amount of DP storage + + if (do_alloc) + cudaMemGetInfo(&free, &total); + else if (free >= d_allocated_bytes + guard_band + min_dp_storage) + free -= d_allocated_bytes; + else + return false; + + const uint32 free_words = uint32( free / 4u ); + const uint32 min_free_words = uint32( guard_band / 4u ); + + uint32 target_words = (free_words * 2u) / 3u; + target_words = nvbio::min( target_words, free_words - min_free_words ); + + const uint32 buffer_words = target_words; + if (do_alloc) + log_verbose(stderr, "[%u] allocating %u MB of DP storage\n", ID, (buffer_words*4)/(1024*1024) ); + + dp_storage = buffer_words * sizeof(uint32); + } + + // allocate a large temporary buffer to for scoring and traceback + dp_buffer_dptr = resize( do_alloc, dp_buffer_dvec, dp_storage, d_allocated_bytes ); + + nvbio::cuda::check_error("allocating alignment buffers"); + + if (mem_stats) + { + mem_stats->first = h_allocated_bytes; + mem_stats->second = d_allocated_bytes; + } + return true; +} + +bool Aligner::init(const uint32 id, const uint32 batch_size, const Params& params, const EndType type) +{ + ID = id; + BATCH_SIZE = batch_size; + + // initialize the batch number + batch_number = 0; + + try { + std::pair mem_stats; + + init_alloc( batch_size, params, type, false, &mem_stats ); + + log_stats(stderr, "[%u] allocating alignment buffers... started\n[%u] estimated: HOST %lu MB, DEVICE %lu MB)\n", + ID, + ID, + mem_stats.first / (1024*1024), + mem_stats.second / (1024*1024) ); + + init_alloc( batch_size, params, type, true, &mem_stats ); + + log_stats(stderr, "[%u] allocating alignment buffers... done\n[%u] allocated: HOST %lu MB, DEVICE %lu MB)\n", + ID, + ID, + mem_stats.first / (1024*1024), + mem_stats.second / (1024*1024) ); + } + catch (...) { + log_error(stderr, "[%u] allocating alignment buffers failed!\n", ID); + return false; + } + return true; +} + +// Compute the total number of matches found +__global__ +void hits_stats_kernel( + const uint32 batch_size, + const SeedHit* hit_data, + const uint32* hit_counts, + uint64* hit_stats) +{ + const uint32 read_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (read_id >= batch_size) return; + + const uint32 hit_ranges = hit_counts[ read_id ]; + + strided_iterator hits( hit_data+read_id, batch_size ); + + typedef vector_view< strided_iterator > Storage; + typedef priority_deque< SeedHit, Storage, hit_compare > HitQueue; + Storage qStore( hit_ranges, hits ); + HitQueue hitheap( qStore, HitQueue::CONSTRUCTED ); + + __shared__ uint32 shared_max_range; + __shared__ uint32 shared_max_hits; + __shared__ uint32 shared_top_max_hits; + + shared_max_range = 0; + shared_max_hits = 0; + shared_top_max_hits = 0; + + __syncthreads(); + + uint32 hits_cnt = 0; + uint32 max_range = 0; + for (uint32 i = 0; i < hit_ranges; ++i) + { + hits_cnt += hits[i].get_range_size(); + max_range = nvbio::max( max_range, hits[i].get_range_size() ); + } + + const SeedHit top = hit_ranges ? hitheap.top() : SeedHit(); + const uint32 top_cnt = hit_ranges ? top.get_range().y - top.get_range().x : 0u; + + // update the number of ranges and number of total hits + atomicAdd( hit_stats + HIT_STATS_RANGES, uint64(hit_ranges) ); + atomicAdd( hit_stats + HIT_STATS_TOTAL, uint64(hits_cnt) ); + atomicAdd( hit_stats + HIT_STATS_TOP, uint64(top_cnt) ); + + // bin the number of hits, and update the bin counter + const uint32 log_hits = hits_cnt == 0 ? 0u : nvbio::log2( hits_cnt )+1u; + atomicAdd( hit_stats + HIT_STATS_BINS + log_hits, uint64(1u) ); + + // bin the number of top hits, and update the bin counter + const uint32 log_top_hits = top_cnt == 0 ? 0u : nvbio::log2( top_cnt )+1u; + atomicAdd( hit_stats + HIT_STATS_TOP_BINS + log_top_hits, uint64(1u) ); + + // update the maximum + if (shared_max_range < max_range) + atomicMax( &shared_max_range, max_range ); + + // update the maximum + if (shared_max_hits < hits_cnt) + atomicMax( &shared_max_hits, hits_cnt ); + + // update the maximum + if (shared_top_max_hits < top_cnt) + atomicMax( &shared_top_max_hits, top_cnt ); + + __syncthreads(); + + // update the maximum + if (threadIdx.x == 0) + { + if (hit_stats[ HIT_STATS_MAX_RANGE ] < shared_max_range) + atomicMax( (uint32*)(hit_stats + HIT_STATS_MAX_RANGE), shared_max_range ); + if (hit_stats[ HIT_STATS_MAX ] < shared_max_hits) + atomicMax( (uint32*)(hit_stats + HIT_STATS_MAX), shared_max_hits ); + if (hit_stats[ HIT_STATS_TOP_MAX ] < shared_top_max_hits) + atomicMax( (uint32*)(hit_stats + HIT_STATS_TOP_MAX), shared_top_max_hits ); + } +} + +void Aligner::keep_stats(const uint32 count, Stats& stats) +{ + thrust::fill( hits_stats_dvec.begin(), hits_stats_dvec.end(), 0u ); + hits_stats( + count, + nvbio::device_view( hit_deques.hits() ), + nvbio::device_view( hit_deques.counts() ), + hits_stats_dptr ); + + cudaThreadSynchronize(); + nvbio::cuda::check_error("hit stats kernel"); + + nvbio::cuda::thrust_copy_vector(hits_stats_hvec, hits_stats_dvec); + + // poll until previous stats have been consumed + //while (output_thread.stats.stats_ready) {} + + stats.hits_ranges += hits_stats_hvec[ HIT_STATS_RANGES ]; + stats.hits_total += hits_stats_hvec[ HIT_STATS_TOTAL ]; + stats.hits_max = std::max( stats.hits_max, uint32( hits_stats_hvec[ HIT_STATS_MAX ] ) ); + stats.hits_max_range = std::max( stats.hits_max_range, uint32( hits_stats_hvec[ HIT_STATS_MAX_RANGE ] ) ); + stats.hits_top_total += hits_stats_hvec[ HIT_STATS_TOP ]; + stats.hits_top_max = std::max( stats.hits_top_max, uint32( hits_stats_hvec[ HIT_STATS_TOP_MAX ] ) ); + for (uint32 i = 0; i < 28; ++i) + { + stats.hits_bins[i] += hits_stats_hvec[ HIT_STATS_BINS + i ]; + stats.hits_top_bins[i] += hits_stats_hvec[ HIT_STATS_TOP_BINS + i ]; + } + stats.hits_stats++; + + // mark stats as ready to be consumed + //output_thread.stats.stats_ready = true; +} + +// Compute the total number of matches found +void hits_stats( + const uint32 batch_size, + const SeedHit* hit_data, + const uint32* hit_counts, + uint64* hit_stats) +{ + const uint32 blocks = (batch_size + BLOCKDIM-1) / BLOCKDIM; + + hits_stats_kernel<<>>( batch_size, hit_data, hit_counts, hit_stats ); +} + +// copy the contents of a section of a ring buffer into a plain array +struct ring_buffer_to_plain_array_functor +{ + // constructor + ring_buffer_to_plain_array_functor( + const uint32* _buffer, + const uint32 _buffer_size, + const uint32 _begin, + const uint32 _end, + uint32* _output) + : buffer( _buffer ), + buffer_size( _buffer_size ), + begin( _begin ), + end( _end ), + output( _output ) {} + + // functor operator + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 i) const + { + if (begin + i < end) + output[i] = buffer[ (begin + i) % buffer_size ]; + } + + const uint32* buffer; + const uint32 buffer_size; + const uint32 begin; + const uint32 end; + uint32* output; +}; + +void ring_buffer_to_plain_array( + const uint32* buffer, + const uint32 buffer_size, + const uint32 begin, + const uint32 end, + uint32* output) +{ + nvbio::for_each( + end - begin, + thrust::make_counting_iterator(0), + ring_buffer_to_plain_array_functor( + buffer, + buffer_size, + begin, + end, + output ) ); +} + +// initialize a set of alignments +// +__global__ +void mark_unaligned_kernel( + const uint32 n_active_reads, + const uint32* active_reads, + const io::Alignment* best_data, + uint8* reseed) +{ + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= n_active_reads) return; + + // fetch the read + const uint32 read_id = active_reads[ thread_id ]; + + // mark if unaligned + if (!best_data[ read_id ].is_aligned()) + reseed[ thread_id ] = 1u; +} + +// mark unaligned reads that need reseeding +// +void mark_unaligned( + const uint32 n_active_reads, + const uint32* active_reads, + const io::Alignment* best_data, + uint8* reseed) +{ + const int blocks = (n_active_reads + BLOCKDIM-1) / BLOCKDIM; + + mark_unaligned_kernel<<>>( + n_active_reads, + active_reads, + best_data, + reseed ); +} + +// initialize a set of alignments +// +__global__ +void mark_discordant_kernel( + const uint32 n_reads, + io::Alignment* anchor_data, + io::Alignment* opposite_data, + const uint32 stride) +{ + const uint32 read_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (read_id >= n_reads) return; + + // A pair of alignments is considered "discordant" if they are unique and + // they are not concordant. + if (anchor_data[ read_id ].is_concordant() == false && // anchor is : unpaired + anchor_data[ read_id ].is_aligned() == true && // aligned + anchor_data[ read_id + stride ].is_aligned() == false && // unique + opposite_data[ read_id ].is_aligned() == true && // opposite is : aligned + opposite_data[ read_id + stride ].is_aligned() == false) // unique + { + // mark as paired and discordant + anchor_data[ read_id ].m_paired = 1u; + anchor_data[ read_id ].m_discordant = 1u; + opposite_data[ read_id ].m_paired = 1u; + opposite_data[ read_id ].m_discordant = 1u; + } +} + +// mark unique unaligned read pairs as discordant +// +void mark_discordant( + const uint32 n_reads, + io::Alignment* anchor_data, + io::Alignment* opposite_data, + const uint32 stride) +{ + const int blocks = (n_reads + BLOCKDIM-1) / BLOCKDIM; + + mark_discordant_kernel<<>>( + n_reads, + anchor_data, + opposite_data, + stride ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_inst.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_inst.h new file mode 100644 index 0000000000000000000000000000000000000000..56c140524915fed3104bbf9a2300bf625eed88d1 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_inst.h @@ -0,0 +1,112 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +void all_ed( + Aligner& aligner, + const Params& params, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + io::SequenceDataDevice& read_data, + io::HostOutputBatchSE& cpu_batch, + Stats& stats); + +void all_sw( + Aligner& aligner, + const Params& params, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + io::SequenceDataDevice& read_data, + io::HostOutputBatchSE& cpu_batch, + Stats& stats); + +void best_approx_ed( + Aligner& aligner, + const Params& params, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + io::SequenceDataDevice& read_data, + io::HostOutputBatchSE& cpu_batch, + Stats& stats); + +void best_approx_sw( + Aligner& aligner, + const Params& params, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + io::SequenceDataDevice& read_data, + io::HostOutputBatchSE& cpu_batch, + Stats& stats); + +void best_approx_ed( + Aligner& aligner, + const Params& params, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + io::SequenceDataDevice& read_data1, + io::SequenceDataDevice& read_data2, + io::HostOutputBatchPE& cpu_batch, + Stats& stats); + +void best_approx_sw( + Aligner& aligner, + const Params& params, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const UberScoringScheme& scoring_scheme, + const io::SequenceDataDevice& reference_data, + const io::FMIndexDataDevice& driver_data, + io::SequenceDataDevice& read_data1, + io::SequenceDataDevice& read_data2, + io::HostOutputBatchPE& cpu_batch, + Stats& stats); + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_sort.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_sort.cu new file mode 100644 index 0000000000000000000000000000000000000000..6999a29340fa6accf8616d65f5e8ff6f0ab6ab39 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/aligner_sort.cu @@ -0,0 +1,109 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// return a pointer to an "index" into the given keys sorted by their hi bits +// +uint32* Aligner::sort_hi_bits( + const uint32 count, + const uint32* keys) +{ + thrust::transform( + thrust::device_ptr( keys ), + thrust::device_ptr( keys ) + count, + sorting_queue_dvec.begin(), + hi_bits_functor() ); + + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + count, + idx_queue_dvec.begin() ); + + // Create ping-pong storage wrapper + nvbio::cuda::SortBuffers double_buffer; + double_buffer.keys[0] = thrust::raw_pointer_cast( &sorting_queue_dvec.front() ); + double_buffer.keys[1] = thrust::raw_pointer_cast( &sorting_queue_dvec.front() + BATCH_SIZE ); + double_buffer.values[0] = idx_queue_dptr; + double_buffer.values[1] = idx_queue_dptr + BATCH_SIZE; + + sort_enactor.sort( count, double_buffer ); + + return double_buffer.values[double_buffer.selector]; +} + +// return a pointer to an "index" into the given sorted keys +// +std::pair Aligner::sort_64_bits( + const uint32 count) +{ + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + count, + idx_queue_dvec.begin() ); + + // Create ping-pong storage wrapper + nvbio::cuda::SortBuffers double_buffer; + double_buffer.keys[0] = reinterpret_cast( raw_pointer( sorting_queue_dvec ) ); + double_buffer.keys[1] = reinterpret_cast( raw_pointer( sorting_queue_dvec ) ) + BATCH_SIZE; + double_buffer.values[0] = idx_queue_dptr; + double_buffer.values[1] = idx_queue_dptr + BATCH_SIZE; + + sort_enactor.sort( count, double_buffer ); + + return std::make_pair( + double_buffer.values[double_buffer.selector], + double_buffer.keys[double_buffer.selector] ); +} + +// sort a set of keys in place +// +void Aligner::sort_inplace( + const uint32 count, + uint32* keys) +{ + // create the ping-pong storage wrapper + nvbio::cuda::SortBuffers double_buffer; + double_buffer.keys[0] = keys; + double_buffer.keys[1] = (uint32*)thrust::raw_pointer_cast( &sorting_queue_dvec.front() ); + + // enact the sort + sort_enactor.sort( count, double_buffer ); + + // copy the sorted data back in place if it ended up in the temporary buffer + if (double_buffer.selector) + cudaMemcpy( keys, double_buffer.keys[1], count * sizeof(uint32), cudaMemcpyDeviceToDevice ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio \ No newline at end of file diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/alignment_utils.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/alignment_utils.h new file mode 100644 index 0000000000000000000000000000000000000000..c47cc946d4898da922d7ec775c1ad0401ef5de2f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/alignment_utils.h @@ -0,0 +1,355 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +namespace detail { + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Alignment +///@{ + +///@addtogroup AlignmentDetail +///@{ + +/// +/// Frame the opposite mate alignment's direction & orientation +/// +/// \param policy input paired end policy +/// \param anchor 0 iff anchor is mate 1, 1 otherwise +/// \param anchor_fw true iff anchor aligned forward +/// \param left true iff opposite mate must be to the left of the anchor +/// \param fw true iff opposite mate must align forward +/// +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +void frame_opposite_mate( + const int policy, + const uint32 anchor, + const bool anchor_fw, + bool& left, + bool& fw) +{ + const bool anchor_1 = (anchor == 0); + + switch(policy) + { + case io::PE_POLICY_FF: + { + left = (anchor_1 != anchor_fw); + fw = anchor_fw; + break; + } + case io::PE_POLICY_RR: + { + left = (anchor_1 == anchor_fw); + fw = anchor_fw; + break; + } + case io::PE_POLICY_FR: + { + left = !anchor_fw; + fw = !anchor_fw; + break; + } + case io::PE_POLICY_RF: + { + left = anchor_fw; + fw = !anchor_fw; + break; + } + } +} + +/// +/// compute the target minimum score for a valid extension of a paired-end alignment +/// +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +int32 compute_target_score(const io::BestPairedAlignments& best, const int32 a_worst_score, const int32 o_worst_score) +{ + if (best.has_second_paired() == false) + return a_worst_score + o_worst_score; + + // reproduce Bowtie2's score bounding behavior (under its default setting 'tighten = 3') + const int32 delta = best.best_score() - best.second_score(); + return best.second_score() + (delta * 3)/4; +} + +enum AlignmentStreamType +{ + SCORE_STREAM = 0, + OPPOSITE_SCORE_STREAM = 1, + TRACEBACK_STREAM = 2, +}; + +/// +/// A backtracking context, forming a CIGAR on the go. +/// As the length is unknown till the very end, the CIGAR is stored backwards. +/// +template +struct Backtracker +{ + // constructor + NVBIO_FORCEINLINE NVBIO_DEVICE + Backtracker(vector vec, const uint32 _capacity) : out(vec), size(0), prev(255), capacity(_capacity) {} + + // encode a soft clipping operation + NVBIO_FORCEINLINE NVBIO_DEVICE + void clip(const uint32 l) + { + if (l) + { + NVBIO_CUDA_DEBUG_ASSERT( size < capacity, "Backtracker: exceeded maximum CIGAR size!\n" ); + out[size++] = io::Cigar( io::Cigar::SOFT_CLIPPING, l ); + } + } + + // encode a new operation + NVBIO_FORCEINLINE NVBIO_DEVICE + void push(uint8 type) + { + NVBIO_CUDA_DEBUG_ASSERT( type == aln::SUBSTITUTION || + type == aln::DELETION || + type == aln::INSERTION, + "Backtracker: unknown op type %u\n", uint32(type) ); + + // perform run-length encoding of the symbol sequence + if (prev == type) + out[size-1u].m_len++; + else + { + NVBIO_CUDA_DEBUG_ASSERT( size < capacity, "Backtracker: exceeded maximum CIGAR size!\n" ); + // encode a new symbol + out[size++] = io::Cigar( type, 1u ); + prev = type; + } + } + + vector out; + uint32 size; + uint8 prev; + uint32 capacity; +}; + +/// a container for the strings to be aligned +/// +template +struct AlignmentStrings +{ + typedef typename PipelineType::genome_iterator genome_iterator; + typedef typename PipelineType::read_batch_type read_batch_type; + typedef typename PipelineType::scheme_type scheme_type; + typedef AlignerType aligner_type; + + static const uint32 CACHE_SIZE = 64; + typedef nvbio::lmem_cache_tag lmem_cache_type; + + typedef ReadLoader pattern_loader_type; + typedef typename pattern_loader_type::string_type pattern_string; + typedef typename pattern_string::qual_string_type qual_string; + + typedef PackedStringLoader< + typename genome_iterator::storage_iterator, + genome_iterator::SYMBOL_SIZE, + genome_iterator::BIG_ENDIAN, + lmem_cache_type> text_loader_type; + typedef typename text_loader_type::iterator text_iterator; + typedef vector_view text_string; + + + template + NVBIO_HOST_DEVICE + void load(const PipelineType& pipeline, const context_type* context) + { + // select the read batch based on context->mate + read_batch_type reads = context->mate ? + pipeline.reads_o : + pipeline.reads; + + const DirType read_dir = context->read_rc ? FORWARD : REVERSE; + const ReadType read_type = context->read_rc ? COMPLEMENT : STANDARD; + + pattern = pattern_loader.load( + reads, + context->read_range, + read_dir, // the reads are loaded in REVERSE fashion, so we invert this flag here + read_type ); + + quals = pattern.qualities(); + text = text_string( + context->genome_end - context->genome_begin, + text_loader.load( pipeline.genome + context->genome_begin, context->genome_end - context->genome_begin ) ); + } + + pattern_loader_type pattern_loader; + text_loader_type text_loader; + pattern_string pattern; + qual_string quals; + text_string text; +}; + +/// Base class for the alignment contexts +/// +template +struct AlignmentStreamContext {}; + +/// Base class for the scoring alignment contexts +/// +template <> +struct AlignmentStreamContext +{ + aln::BestSink sink; ///< output alignment sink +}; + +/// Base class for the scoring alignment contexts +/// +template <> +struct AlignmentStreamContext +{ + #if DP_REPORT_MULTIPLE + aln::BestColumnSink sink; ///< output alignment sink + #else + aln::BestSink sink; ///< output alignment sink + #endif +}; + +/// Base class for the traceback alignment contexts +/// +template <> +struct AlignmentStreamContext +{ + io::Cigar cigar[1024]; ///< output CIGAR storage + Backtracker backtracer; ///< output alignment backtracer + aln::Alignment alignment; ///< output alignment + + /// constructor + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + AlignmentStreamContext() : backtracer( cigar, 1024u ) {} +}; + +/// +/// A base stream class to be used in conjunction with the aln::BatchedAlignmentScore class. +/// This class implements the load_strings() method, which performs read and genome loading, and +/// defers the implementation of init_context() to its inheritors, BestScoreStream, +/// BestAnchorScoreStream, and BestOppositeScoreStream. +/// +template +struct AlignmentStreamBase +{ + typedef AlignmentStrings strings_type; + typedef typename PipelineType::scheme_type scheme_type; + typedef AlignerType aligner_type; + + /// an alignment context + /// + struct context_type : AlignmentStreamContext + { + uint32 idx; + uint32 mate; + uint2 read_range; + uint32 read_id; + uint32 read_rc; + uint32 genome_begin; + uint32 genome_end; + int32 min_score; + }; + + /// constructor + /// + AlignmentStreamBase( + const PipelineType _pipeline, + const aligner_type _aligner, + const ParamsPOD _params) : + m_pipeline( _pipeline ), m_aligner( _aligner ), m_params( _params ) {} + + /// get the aligner + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + const aligner_type& aligner() const { return m_aligner; }; + + /// return the pattern length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 pattern_length(const uint32 i, const context_type* context) const + { + return context->read_range.y - context->read_range.x; + } + + /// return the text length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 text_length(const uint32 i, const context_type* context) const + { + return context->genome_end - context->genome_begin; + } + + /// initialize the strings corresponding to the i-th context + /// + /// \param i problem index + /// \param window_begin pattern window to load + /// \param window_end pattern window to load + /// \param context initialized context + /// \param strings output strings + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void load_strings( + const uint32 i, + const uint32 window_begin, + const uint32 window_end, + const context_type* context, + strings_type* strings) const + { + // load the strings + strings->load( m_pipeline, context ); + } + + PipelineType m_pipeline; ///< the pipeline object + aligner_type m_aligner; ///< the aligner + ParamsPOD m_params; ///< global parameters +}; + +///@} // group AlignmentDetail +///@} // group Alignment +///@} // group nvBowtie + +} // namespace detail + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/checksums.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/checksums.cu new file mode 100644 index 0000000000000000000000000000000000000000..2050cea46bd5f43af2a23cc44c76a1cdccb56852 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/checksums.cu @@ -0,0 +1,80 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// compute a checksum for the returned SA ranges +// +void hits_checksum( + const uint32 n_reads, + SeedHitDequeArray& hit_deques, + uint64& crc, + uint64& sum) +{ + thrust::device_vector hits_count_scan_dvec( n_reads ); + + // run a scan on the number of SA ranges from each read + thrust::inclusive_scan( hit_deques.counts().begin(), hit_deques.counts().begin() + n_reads, hits_count_scan_dvec.begin() ); + + // compute how many ranges we have + const uint32 n_hit_ranges = hits_count_scan_dvec[ n_reads-1 ]; + + // gather all the range sizes, sorted by read, in a compacted array + thrust::device_vector hits_range_scan_dvec( n_hit_ranges ); + + SeedHitDequeArrayDeviceView hits = hit_deques.device_view(); + + gather_ranges( + n_hit_ranges, + n_reads, + hits, + thrust::raw_pointer_cast( &hits_count_scan_dvec.front() ), + thrust::raw_pointer_cast( &hits_range_scan_dvec.front() ) ); + + // compute the crc + crc = device_checksum( + hits_range_scan_dvec.begin(), + hits_range_scan_dvec.begin() + n_hit_ranges ); + + // scan the ranges + thrust::inclusive_scan( hits_range_scan_dvec.begin(), hits_range_scan_dvec.begin() + n_hit_ranges, hits_range_scan_dvec.begin() ); + + // fetch the total + sum = hits_range_scan_dvec[ n_hit_ranges - 1 ]; +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/checksums.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/checksums.h new file mode 100644 index 0000000000000000000000000000000000000000..e4b1d366e994a459eb7a091524a81e0853560378 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/checksums.h @@ -0,0 +1,82 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +struct SeedHit; + +// compute a checksum of a device sequence +// +template +uint64 device_checksum( + Iterator begin, + Iterator end) +{ + typedef typename thrust::iterator_traits::value_type value_type; + + const uint32 n = uint32( end - begin ); + + // copy values to a temporary vector + thrust::device_vector debug_copy_dvec( n ); + thrust::copy( + begin, + end, + debug_copy_dvec.begin() ); + + // sort temporary vector + thrust::sort( debug_copy_dvec.begin(), debug_copy_dvec.end() ); + + // copy to the host + thrust::host_vector debug_copy_hvec( debug_copy_dvec ); + + // compute a crc + const char* ptr = (const char*)thrust::raw_pointer_cast( &debug_copy_hvec.front() ); + return crcCalc( ptr, sizeof(value_type)*n ); +} + +// compute a checksum for the returned SA ranges +// +void hits_checksum( + const uint32 n_reads, + SeedHitDequeArray& hit_deques, + uint64& crc, + uint64& sum); + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/compute_thread.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/compute_thread.cu new file mode 100644 index 0000000000000000000000000000000000000000..b757b1e2aa3ae1365d602cf89dab7e23269e948a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/compute_thread.cu @@ -0,0 +1,738 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +//#define NVBIO_ENABLE_PROFILING + +#define MOD_NAMESPACE +#define MOD_NAMESPACE_BEGIN namespace bowtie2 { namespace driver { +#define MOD_NAMESPACE_END }} +#define MOD_NAMESPACE_NAME bowtie2::driver + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +ComputeThreadSE::ComputeThreadSE( + const uint32 _thread_id, + const uint32 _device_id, + const io::SequenceData& _reference_data, + const io::FMIndexData& _driver_data, + const std::map& _options, + const Params& _params, + Stats& _stats) : + thread_id( _thread_id ), + device_id( _device_id ), + reference_data_host( _reference_data ), + driver_data_host( _driver_data ), + options( _options ), + input_thread( NULL ), + output_file( NULL ), + params( _params ), + stats( _stats ) +{ + log_visible(stderr, "[%u] nvBowtie cuda driver created on device %u\n", thread_id, device_id); + + // initialize the selected device + cudaSetDevice( device_id ); + cudaSetDeviceFlags( cudaDeviceMapHost | cudaDeviceLmemResizeToMax ); + + aligner = SharedPointer( new Aligner() ); + + Timer timer; + timer.start(); + + const bool need_reverse = + (params.allow_sub == 0 && USE_REVERSE_INDEX) || + (params.allow_sub == 1 && params.subseed_len == 0 && params.mode == BestMappingApprox); + + reference_data_device.reset( new io::SequenceDataDevice( reference_data_host ) ); + + driver_data_device.reset( new io::FMIndexDataDevice( driver_data_host, + io::FMIndexDataDevice::FORWARD | + (need_reverse ? io::FMIndexDataDevice::REVERSE : 0u) | + io::FMIndexDataDevice::SA ) ); + + timer.stop(); + + log_stats(stderr, "[%u] allocated device driver data (%.2f GB - %.1fs)\n", thread_id, float(driver_data_device->allocated()) / 1.0e9f, timer.seconds() ); +} + +// gauge the favourite batch size +// +uint32 ComputeThreadSE::gauge_batch_size() +{ + // switch to the selected device + cudaSetDevice( device_id ); + + uint32 BATCH_SIZE; + + for (BATCH_SIZE = params.max_batch_size*1024; BATCH_SIZE >= 16*1024; BATCH_SIZE /= 2) + { + std::pair mem_stats; + + // gauge how much memory we'd need + if (aligner->init_alloc( BATCH_SIZE, params, kSingleEnd, false, &mem_stats ) == true) + { + log_stats(stderr, "[%u] estimated allocation sizes: HOST %lu MB, DEVICE %lu MB)\n", + thread_id, + mem_stats.first / (1024*1024), + mem_stats.second / (1024*1024) ); + break; + } + } + + return BATCH_SIZE; +} + +void ComputeThreadSE::do_run() +{ + log_visible(stderr, "[%u] nvBowtie cuda driver... started\n", thread_id); + + // switch to the selected device + cudaSetDevice( device_id ); + + // build an empty report + FILE* html_output = (params.report != std::string("")) ? fopen( params.report.c_str(), "w" ) : NULL; + if (html_output) + { + // encapsulate the document + { + html::html_object html( html_output ); + { + const char* meta_list = ""; + + { html::header_object hd( html_output, "Bowtie2 Report", html::style(), meta_list ); } + { html::body_object body( html_output ); } + } + } + fclose( html_output ); + } + + Timer timer; + + io::SequenceDataDevice& reference_data = *reference_data_device.get(); + io::FMIndexDataDevice& driver_data = *driver_data_device.get(); + + log_stats(stderr, "[%u] allocated device driver data (%.2f GB - %.1fs)\n", thread_id, float(driver_data.allocated()) / 1.0e9f, timer.seconds() ); + + typedef FMIndexDef::type fm_index_type; + + fm_index_type fmi = driver_data.index(); + fm_index_type rfmi = driver_data.rindex(); + + size_t free, total; + cudaMemGetInfo(&free, &total); + log_stats(stderr, "[%u] device has %ld of %ld MB free\n", thread_id, free/1024/1024, total/1024/1024); + + const uint32 BATCH_SIZE = input_thread->batch_size(); + + log_stats(stderr, "[%u] processing reads in batches of %uK\n", thread_id, BATCH_SIZE/1024); + + // setup the output file + aligner->output_file = output_file; + + // initialize the aligner + if (aligner->init( thread_id, BATCH_SIZE, params, kSingleEnd ) == false) + return; + + nvbio::cuda::check_error("cuda initializations"); + + cudaMemGetInfo(&free, &total); + log_stats(stderr, "[%u] ready to start processing: device has %ld MB free\n", thread_id, free/1024/1024); + + Timer global_timer; + global_timer.start(); + + UberScoringScheme& scoring_scheme = params.scoring_scheme; + + uint32 n_reads = 0; + + io::SequenceDataHost local_read_data_host; + io::HostOutputBatchSE local_output_batch_host; + + // loop through the batches of reads + while (1) + { + uint32 read_begin; + + Timer io_timer; + io_timer.start(); + + io::SequenceDataHost* read_data_host = input_thread->next( &read_begin ); + + io_timer.stop(); + stats.read_io.add( read_data_host ? read_data_host->size() : 0u, io_timer.seconds() ); + + if (read_data_host == NULL) + { + log_verbose(stderr, "[%u] end of input reached\n", thread_id); + break; + } + + if (read_data_host->max_sequence_len() > Aligner::MAX_READ_LEN) + { + log_error(stderr, "[%u] unsupported read length %u (maximum is %u)\n", thread_id, + read_data_host->max_sequence_len(), + Aligner::MAX_READ_LEN ); + break; + } + + // make a local copy of the host batch + local_read_data_host = *read_data_host; + + // mark this set as ready to be reused + input_thread->release( read_data_host ); + + Timer timer; + timer.start(); + + //aligner.output_file->start_batch( &local_read_data_host ); + local_output_batch_host.read_data = &local_read_data_host; + + io::SequenceDataDevice read_data( local_read_data_host ); + cudaThreadSynchronize(); + + timer.stop(); + stats.read_HtoD.add( read_data.size(), timer.seconds() ); + + const uint32 count = read_data.size(); + log_info(stderr, "[%u] aligning reads [%u, %u]\n", thread_id, read_begin, read_begin + count - 1u); + log_verbose(stderr, "[%u] %u reads\n", thread_id, count); + log_verbose(stderr, "[%u] %.3f M bps (%.1f MB)\n", thread_id, float(read_data.bps())/1.0e6f, float(read_data.words()*sizeof(uint32)+read_data.bps()*sizeof(char))/float(1024*1024)); + log_verbose(stderr, "[%u] %.1f bps/read (min: %u, max: %u)\n", thread_id, float(read_data.bps())/float(read_data.size()), read_data.min_sequence_len(), read_data.max_sequence_len()); + + if (params.mode == AllMapping) + { + if (params.scoring_mode == EditDistanceMode) + { + all_ed( + *aligner, + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + read_data, + local_output_batch_host, + stats ); + } + else + { + all_sw( + *aligner, + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + read_data, + local_output_batch_host, + stats ); + } + } + else + { + if (params.scoring_mode == EditDistanceMode) + { + best_approx_ed( + *aligner, + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + read_data, + local_output_batch_host, + stats ); + } + else + { + best_approx_sw( + *aligner, + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + read_data, + local_output_batch_host, + stats ); + } + } + + global_timer.stop(); + stats.global_time += global_timer.seconds(); + global_timer.start(); + + //aligner->output_file->end_batch(); + + // increase the total reads counter + n_reads += count; + + log_verbose(stderr, "[%u] %.1f K reads/s\n", thread_id, 1.0e-3f * float(n_reads) / stats.global_time); + } + + global_timer.stop(); + stats.global_time += global_timer.seconds(); + stats.n_reads = n_reads; + + if (params.report.length()) + nvbio::bowtie2::cuda::generate_device_report( thread_id, stats, stats.mate1, params.report.c_str() ); + + log_visible(stderr, "[%u] nvBowtie cuda driver... done\n", thread_id); + + log_stats(stderr, "[%u] total : %.2f sec (avg: %.1fK reads/s).\n", thread_id, stats.global_time, 1.0e-3f * float(n_reads)/stats.global_time); + log_stats(stderr, "[%u] mapping : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s, %.2f device sec).\n", thread_id, stats.map.time, 1.0e-6f * stats.map.avg_speed(), 1.0e-6f * stats.map.max_speed, stats.map.device_time); + log_stats(stderr, "[%u] selecting : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s, %.2f device sec).\n", thread_id, stats.select.time, 1.0e-6f * stats.select.avg_speed(), 1.0e-6f * stats.select.max_speed, stats.select.device_time); + log_stats(stderr, "[%u] sorting : %.2f sec (avg: %.3fM seeds/s, max: %.3fM seeds/s, %.2f device sec).\n", thread_id, stats.sort.time, 1.0e-6f * stats.sort.avg_speed(), 1.0e-6f * stats.sort.max_speed, stats.sort.device_time); + log_stats(stderr, "[%u] scoring : %.2f sec (avg: %.3fM seeds/s, max: %.3fM seeds/s, %.2f device sec).\n", thread_id, stats.score.time, 1.0e-6f * stats.score.avg_speed(), 1.0e-6f * stats.score.max_speed, stats.score.device_time); + log_stats(stderr, "[%u] locating : %.2f sec (avg: %.3fM seeds/s, max: %.3fM seeds/s, %.2f device sec).\n", thread_id, stats.locate.time, 1.0e-6f * stats.locate.avg_speed(), 1.0e-6f * stats.locate.max_speed, stats.locate.device_time); + log_stats(stderr, "[%u] backtracking : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s, %.2f device sec).\n", thread_id, stats.backtrack.time, 1.0e-6f * stats.backtrack.avg_speed(), 1.0e-6f * stats.backtrack.max_speed, stats.backtrack.device_time); + log_stats(stderr, "[%u] finalizing : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s, %.2f device sec).\n", thread_id, stats.finalize.time, 1.0e-6f * stats.finalize.avg_speed(), 1.0e-6f * stats.finalize.max_speed, stats.finalize.device_time); + log_stats(stderr, "[%u] results DtoH : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s).\n", thread_id, stats.alignments_DtoH.time, 1.0e-6f * stats.alignments_DtoH.avg_speed(), 1.0e-6f * stats.alignments_DtoH.max_speed); + log_stats(stderr, "[%u] results I/O : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s).\n", thread_id, stats.io.time, 1.0e-6f * stats.io.avg_speed(), 1.0e-6f * stats.io.max_speed); + log_stats(stderr, "[%u] reads HtoD : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s).\n", thread_id, stats.read_HtoD.time, 1.0e-6f * stats.read_HtoD.avg_speed(), 1.0e-6f * stats.read_HtoD.max_speed); + log_stats(stderr, "[%u] reads I/O : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s).\n", thread_id, stats.read_io.time, 1.0e-6f * stats.read_io.avg_speed(), 1.0e-6f * stats.read_io.max_speed); +} + + +void ComputeThreadSE::run() +{ + try { + do_run(); + } + catch (nvbio::cuda_error e) + { + log_error(stderr, "caught a nvbio::cuda_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::bad_alloc e) + { + log_error(stderr, "caught a nvbio::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::logic_error e) + { + log_error(stderr, "caught a nvbio::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::runtime_error e) + { + log_error(stderr, "caught a nvbio::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::bad_alloc e) + { + log_error(stderr, "caught a std::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::logic_error e) + { + log_error(stderr, "caught a std::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::runtime_error e) + { + log_error(stderr, "caught a std::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (...) + { + log_error(stderr, "caught an unknown exception!\n"); + } +} + +ComputeThreadPE::ComputeThreadPE( + const uint32 _thread_id, + const uint32 _device_id, + const io::SequenceData& _reference_data, + const io::FMIndexData& _driver_data, + const std::map& _options, + const Params& _params, + Stats& _stats) : + thread_id( _thread_id ), + device_id( _device_id ), + reference_data_host( _reference_data ), + driver_data_host( _driver_data ), + options( _options ), + input_thread( NULL ), + output_file( NULL ), + params( _params ), + stats( _stats ) +{ + log_visible(stderr, "[%u] nvBowtie cuda driver created on device %u\n", thread_id, device_id); + + // initialize the selected device + cudaSetDevice( device_id ); + cudaSetDeviceFlags( cudaDeviceMapHost | cudaDeviceLmemResizeToMax ); + + aligner = SharedPointer( new Aligner() ); + + Timer timer; + timer.start(); + + const bool need_reverse = + (params.allow_sub == 0 && USE_REVERSE_INDEX) || + (params.allow_sub == 1 && params.subseed_len == 0 && params.mode == BestMappingApprox); + + reference_data_device.reset( new io::SequenceDataDevice( reference_data_host ) ); + + driver_data_device.reset( new io::FMIndexDataDevice( driver_data_host, + io::FMIndexDataDevice::FORWARD | + (need_reverse ? io::FMIndexDataDevice::REVERSE : 0u) | + io::FMIndexDataDevice::SA ) ); + + timer.stop(); + + log_stats(stderr, "[%u] allocated device driver data (%.2f GB - %.1fs)\n", thread_id, float(driver_data_device->allocated()) / 1.0e9f, timer.seconds() ); +} + +// gauge the favourite batch size +// +uint32 ComputeThreadPE::gauge_batch_size() +{ + // switch to the selected device + cudaSetDevice( device_id ); + + uint32 BATCH_SIZE; + + for (BATCH_SIZE = params.max_batch_size*1024; BATCH_SIZE >= 16*1024; BATCH_SIZE /= 2) + { + std::pair mem_stats; + + // gauge how much memory we'd need + if (aligner->init_alloc( BATCH_SIZE, params, kPairedEnds, false, &mem_stats ) == true) + { + log_stats(stderr, "[%u] estimated allocation sizes: HOST %lu MB, DEVICE %lu MB)\n", + thread_id, + mem_stats.first / (1024*1024), + mem_stats.second / (1024*1024) ); + break; + } + } + + return BATCH_SIZE; +} + +void ComputeThreadPE::do_run() +{ + log_visible(stderr, "[%u] nvBowtie cuda driver... started\n", thread_id); + + // switch to the selected device + cudaSetDevice( device_id ); + + // build an empty report + FILE* html_output = (params.report != std::string("")) ? fopen( params.report.c_str(), "w" ) : NULL; + if (html_output) + { + // encapsulate the document + { + html::html_object html( html_output ); + { + const char* meta_list = ""; + + { html::header_object hd( html_output, "Bowtie2 Report", html::style(), meta_list ); } + { html::body_object body( html_output ); } + } + } + fclose( html_output ); + } + + Timer timer; + + io::SequenceDataDevice& reference_data = *reference_data_device.get(); + io::FMIndexDataDevice& driver_data = *driver_data_device.get(); + + typedef FMIndexDef::type fm_index_type; + + fm_index_type fmi = driver_data.index(); + fm_index_type rfmi = driver_data.rindex(); + + size_t free, total; + cudaMemGetInfo(&free, &total); + log_stats(stderr, "[%u] device has %ld of %ld MB free\n", thread_id, free/1024/1024, total/1024/1024); + + const uint32 BATCH_SIZE = input_thread->batch_size(); + + log_stats(stderr, "[%u] processing reads in batches of %uK\n", thread_id, BATCH_SIZE/1024); + + // setup the output file + aligner->output_file = output_file; + + // initialize the aligner + if (aligner->init( thread_id, BATCH_SIZE, params, kPairedEnds ) == false) + return; + + nvbio::cuda::check_error("cuda initializations"); + + cudaMemGetInfo(&free, &total); + log_stats(stderr, "[%u] ready to start processing: device has %ld MB free\n", thread_id, free/1024/1024); + + size_t stack_size_limit; + cudaDeviceGetLimit( &stack_size_limit, cudaLimitStackSize ); + log_debug(stderr, "[%u] max cuda stack size: %u\n", thread_id, stack_size_limit); + + Timer global_timer; + global_timer.start(); + + UberScoringScheme& scoring_scheme = params.scoring_scheme; + + uint32 n_reads = 0; + + io::SequenceDataHost local_read_data_host1; + io::SequenceDataHost local_read_data_host2; + io::HostOutputBatchPE local_output_batch_host; + + // loop through the batches of reads + while (1) + { + uint32 read_begin; + + Timer io_timer; + io_timer.start(); + + std::pair read_data_host_pair = input_thread->next( &read_begin ); + + io::SequenceDataHost* read_data_host1 = read_data_host_pair.first; + io::SequenceDataHost* read_data_host2 = read_data_host_pair.second; + + io_timer.stop(); + stats.read_io.add( read_data_host1 ? read_data_host1->size() : 0u, io_timer.seconds() ); + + if (read_data_host1 == NULL || + read_data_host2 == NULL) + { + log_verbose(stderr, "[%u] end of input reached\n", thread_id); + break; + } + + if ((read_data_host1->max_sequence_len() > Aligner::MAX_READ_LEN) || + (read_data_host2->max_sequence_len() > Aligner::MAX_READ_LEN)) + { + log_error(stderr, "[%u] unsupported read length %u (maximum is %u)\n", + thread_id, + nvbio::max(read_data_host1->max_sequence_len(), read_data_host2->max_sequence_len()), + Aligner::MAX_READ_LEN ); + break; + } + + // make a local copy of the host batch + local_read_data_host1 = *read_data_host1; + local_read_data_host2 = *read_data_host2; + + // mark this set as ready to be reused + input_thread->release( read_data_host_pair ); + + Timer timer; + timer.start(); + + //aligner.output_file->start_batch( &local_read_data_host1, &local_read_data_host2 ); + local_output_batch_host.read_data[0] = &local_read_data_host1; + local_output_batch_host.read_data[1] = &local_read_data_host2; + + io::SequenceDataDevice read_data1( local_read_data_host1/*, io::ReadDataDevice::READS | io::ReadDataDevice::QUALS*/ ); + io::SequenceDataDevice read_data2( local_read_data_host2/*, io::ReadDataDevice::READS | io::ReadDataDevice::QUALS*/ ); + + timer.stop(); + stats.read_HtoD.add( read_data1.size(), timer.seconds() ); + + const uint32 count = read_data1.size(); + log_info(stderr, "[%u] aligning reads [%u, %u]\n", thread_id, read_begin, read_begin + count - 1u); + log_verbose(stderr, "[%u] %u reads\n", thread_id, count); + log_verbose(stderr, "[%u] %.3f M bps (%.1f MB)\n", thread_id, + float(read_data1.bps() + read_data2.bps())/1.0e6f, + float(read_data1.words()*sizeof(uint32)+read_data1.bps()*sizeof(char))/float(1024*1024)+ + float(read_data2.words()*sizeof(uint32)+read_data2.bps()*sizeof(char))/float(1024*1024)); + log_verbose(stderr, "[%u] %.1f bps/read (min: %u, max: %u)\n", thread_id, + float(read_data1.bps()+read_data2.bps())/float(read_data1.size()+read_data2.size()), + nvbio::min( read_data1.min_sequence_len(), read_data2.min_sequence_len() ), + nvbio::max( read_data1.max_sequence_len(), read_data2.max_sequence_len() )); + + if (params.mode == AllMapping) + { + log_error(stderr, "[%u] paired-end all-mapping is not yet supported!\n", thread_id); + exit(1); + } + else + { + if (params.scoring_mode == EditDistanceMode) + { + best_approx_ed( + *aligner, + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + read_data1, + read_data2, + local_output_batch_host, + stats ); + } + else + { + best_approx_sw( + *aligner, + params, + fmi, + rfmi, + scoring_scheme, + reference_data, + driver_data, + read_data1, + read_data2, + local_output_batch_host, + stats ); + } + } + + global_timer.stop(); + stats.global_time += global_timer.seconds(); + global_timer.start(); + + //aligner.output_file->end_batch(); + + // increase the total reads counter + n_reads += count; + + log_verbose(stderr, "[%u] %.1f K reads/s\n", thread_id, 1.0e-3f * float(n_reads) / stats.global_time); + } + + global_timer.stop(); + stats.global_time += global_timer.seconds(); + + if (params.report.length()) + nvbio::bowtie2::cuda::generate_device_report( thread_id, stats, stats.concordant, params.report.c_str() ); + + log_visible(stderr, "[%u] nvBowtie cuda driver... done\n", thread_id); + + log_stats(stderr, "[%u] total : %.2f sec (avg: %.1fK reads/s).\n", thread_id, stats.global_time, 1.0e-3f * float(n_reads)/stats.global_time); + log_stats(stderr, "[%u] mapping : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s, %.2f device sec).\n", thread_id, stats.map.time, 1.0e-6f * stats.map.avg_speed(), 1.0e-6f * stats.map.max_speed, stats.map.device_time); + log_stats(stderr, "[%u] scoring : %.2f sec (avg: %.1fM reads/s, max: %.3fM reads/s, %.2f device sec).).\n", thread_id, stats.scoring_pipe.time, 1.0e-6f * stats.scoring_pipe.avg_speed(), 1.0e-6f * stats.scoring_pipe.max_speed, stats.scoring_pipe.device_time); + log_stats(stderr, "[%u] selecting : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s, %.2f device sec).\n", thread_id, stats.select.time, 1.0e-6f * stats.select.avg_speed(), 1.0e-6f * stats.select.max_speed, stats.select.device_time); + log_stats(stderr, "[%u] sorting : %.2f sec (avg: %.3fM seeds/s, max: %.3fM seeds/s, %.2f device sec).\n", thread_id, stats.sort.time, 1.0e-6f * stats.sort.avg_speed(), 1.0e-6f * stats.sort.max_speed, stats.sort.device_time); + log_stats(stderr, "[%u] scoring(a) : %.2f sec (avg: %.3fM seeds/s, max: %.3fM seeds/s, %.2f device sec).\n", thread_id, stats.score.time, 1.0e-6f * stats.score.avg_speed(), 1.0e-6f * stats.score.max_speed, stats.score.device_time); + log_stats(stderr, "[%u] scoring(o) : %.2f sec (avg: %.3fM seeds/s, max: %.3fM seeds/s, %.2f device sec).\n", thread_id, stats.opposite_score.time, 1.0e-6f * stats.opposite_score.avg_speed(), 1.0e-6f * stats.opposite_score.max_speed, stats.opposite_score.device_time); + log_stats(stderr, "[%u] locating : %.2f sec (avg: %.3fM seeds/s, max: %.3fM seeds/s, %.2f device sec).\n", thread_id, stats.locate.time, 1.0e-6f * stats.locate.avg_speed(), 1.0e-6f * stats.locate.max_speed, stats.locate.device_time); + log_stats(stderr, "[%u] backtracing(a) : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s, %.2f device sec).\n", thread_id, stats.backtrack.time, 1.0e-6f * stats.backtrack.avg_speed(), 1.0e-6f * stats.backtrack.max_speed, stats.backtrack.device_time); + log_stats(stderr, "[%u] backtracing(o) : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s, %.2f device sec).\n", thread_id, stats.backtrack_opposite.time, 1.0e-6f * stats.backtrack_opposite.avg_speed(), 1.0e-6f * stats.backtrack_opposite.max_speed, stats.backtrack_opposite.device_time); + log_stats(stderr, "[%u] finalizing : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s, %.2f device sec).\n", thread_id, stats.finalize.time, 1.0e-6f * stats.finalize.avg_speed(), 1.0e-6f * stats.finalize.max_speed, stats.finalize.device_time); + log_stats(stderr, "[%u] results DtoH : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s).\n", thread_id, stats.alignments_DtoH.time, 1.0e-6f * stats.alignments_DtoH.avg_speed(), 1.0e-6f * stats.alignments_DtoH.max_speed); + log_stats(stderr, "[%u] results I/O : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s).\n", thread_id, stats.io.time, 1.0e-6f * stats.io.avg_speed(), 1.0e-6f * stats.io.max_speed); + log_stats(stderr, "[%u] reads HtoD : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s).\n", thread_id, stats.read_HtoD.time, 1.0e-6f * stats.read_HtoD.avg_speed(), 1.0e-6f * stats.read_HtoD.max_speed); + log_stats(stderr, "[%u] reads I/O : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s).\n", thread_id, stats.read_io.time, 1.0e-6f * stats.read_io.avg_speed(), 1.0e-6f * stats.read_io.max_speed); +} + +void ComputeThreadPE::run() +{ + try { + do_run(); + } + catch (nvbio::cuda_error e) + { + log_error(stderr, "caught a nvbio::cuda_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::bad_alloc e) + { + log_error(stderr, "caught a nvbio::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::logic_error e) + { + log_error(stderr, "caught a nvbio::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::runtime_error e) + { + log_error(stderr, "caught a nvbio::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::bad_alloc e) + { + log_error(stderr, "caught a std::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::logic_error e) + { + log_error(stderr, "caught a std::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::runtime_error e) + { + log_error(stderr, "caught a std::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (...) + { + log_error(stderr, "caught an unknown exception!\n"); + } +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/compute_thread.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/compute_thread.h new file mode 100644 index 0000000000000000000000000000000000000000..c348f278949e72b8c322a1ecc922fbc977740bf7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/compute_thread.h @@ -0,0 +1,136 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include +#include +#include + +namespace nvbio { namespace io { struct OutputFile; } } + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +struct InputThreadSE; +struct InputThreadPE; +struct Aligner; +struct Stats; + +struct ComputeThreadSE : public Thread +{ + /// constructor + /// + ComputeThreadSE( + const uint32 _thread_id, + const uint32 _device_id, + const io::SequenceData& _reference_data, + const io::FMIndexData& _driver_data, + const std::map& _options, + const Params& _params, + Stats& _stats); + + /// gauge the favourite batch size + /// + uint32 gauge_batch_size(); + + /// setup the input thread + /// + void set_input(InputThreadSE* _input_thread) { input_thread = _input_thread; } + + /// setup the input thread + /// + void set_output(io::OutputFile* _output_file) { output_file = _output_file; } + + void run(); + + void do_run(); + + const uint32 thread_id; + const uint32 device_id; + const io::SequenceData& reference_data_host; + const io::FMIndexData& driver_data_host; + const std::map& options; + InputThreadSE* input_thread; + io::OutputFile* output_file; + Params params; + Stats& stats; + SharedPointer aligner; + SharedPointer reference_data_device; + SharedPointer driver_data_device; +}; + +struct ComputeThreadPE : public Thread +{ + /// constructor + /// + ComputeThreadPE( + const uint32 _thread_id, + const uint32 _device_id, + const io::SequenceData& _reference_data, + const io::FMIndexData& _driver_data, + const std::map& _options, + const Params& _params, + Stats& _stats); + + /// gauge the favourite batch size + /// + uint32 gauge_batch_size(); + + /// setup the input thread + /// + void set_input(InputThreadPE* _input_thread) { input_thread = _input_thread; } + + /// setup the input thread + /// + void set_output(io::OutputFile* _output_file) { output_file = _output_file; } + + void run(); + + void do_run(); + + const uint32 thread_id; + const uint32 device_id; + const io::SequenceData& reference_data_host; + const io::FMIndexData& driver_data_host; + const std::map& options; + InputThreadPE* input_thread; + io::OutputFile* output_file; + Params params; + Stats& stats; + SharedPointer aligner; + SharedPointer reference_data_device; + SharedPointer driver_data_device; +}; + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/defs.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/defs.h new file mode 100644 index 0000000000000000000000000000000000000000..43c0d9f5cdeb231c80a0873b60b22d48dd7de95b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/defs.h @@ -0,0 +1,212 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/// +///\file defs.h +/// + +/// \defgroup nvBowtie nvBowtie +/// see \ref nvBowtieArch + +#pragma once + +//#define NVBIO_CUDA_DEBUG +//#define NVBIO_CUDA_NON_BLOCKING_ASSERTS +//#define NVBIO_CUDA_ASSERTS + +#define USE_TEX 1 +#define USE_TEX_READS 1 +#define USE_UINT4_PACKING 0 + +#if USE_TEX +#define TEX_STATEMENT(x) x +#define TEX_SELECTOR( vec, tex ) tex +#else +#define TEX_STATEMENT(x) +#define TEX_SELECTOR( vec, tex ) vec +#endif + +#if USE_TEX_READS +#define READ_TEX_STATEMENT(x) x +#define READ_TEX_SELECTOR( vec, tex ) tex +#else +#define READ_TEX_STATEMENT(x) +#define READ_TEX_SELECTOR( vec, tex ) vec +#endif + +#define USE_WARP_SYNCHRONOUS_QUEUES 1 +#define USE_REVERSE_INDEX 0 + +#define DO_OPTIONAL_SYNCHRONIZE 1 +#define DO_DEVICE_TIMING 0 + +#define DP_REPORT_MULTIPLE 0 + +#include +#include +#include // FIXME: for PE_POLICY! +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Defs +///@{ + +enum EndType { kSingleEnd = 0u, kPairedEnds = 1u }; + +// We assume reads contain, on average, this many bps +enum { AVG_READ_LENGTH = 175 }; +// The device will launch blocks of size BLOCKDIM. +enum { BLOCKDIM = 96 }; +// The device will launch blocks of size BLOCKDIM. +enum { SCORE_MATE_BLOCKDIM = 128 }; +// Edit distance kernel band size. +// for N errors we need band length 2*N+1 +enum { MAX_BAND_LEN = 63 }; +// We allow for at most this read length +enum { MAXIMUM_READ_LENGTH = 512 }; +// We allow for at most this insert length +enum { MAXIMUM_INSERT_LENGTH = 1024 }; +// We allow for at most this band length +enum { MAXIMUM_BAND_LENGTH = 31 }; +// We allow at most MAXIMUM_BAND_LENGTH*MAXIMUM_BAND_LEN_MULT errors +enum { MAXIMUM_BAND_LEN_MULT = 4 }; + +enum { BANDED_DP_CHECKPOINTS = 16 }; +enum { FULL_DP_CHECKPOINTS = 64 }; + +// Maximum number of words allocated for local memory strings +enum { LMEM_CACHE_WORDS = 64 }; + +struct edit_distance_scoring_tag {}; +struct smith_waterman_scoring_tag {}; + +/// +/// A helper class to track debugging info +/// +struct DebugState +{ + uint32 read_id; + bool select; + bool locate; + bool score; + bool score_bad; + bool score_info; + bool reduce; + bool traceback; + bool asserts; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool show_select (const uint32 id) const { return select && id == read_id; } + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool show_locate (const uint32 id) const { return locate && id == read_id; } + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool show_score (const uint32 id, const bool good) const { return score && id == read_id && (score_bad || good); } + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool show_score_info (const uint32 id) const { return score_info && id == read_id; } + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool show_reduce (const uint32 id) const { return reduce && id == read_id; } + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool show_traceback (const uint32 id) const { return traceback && id == read_id; } +}; + +enum { + HIT_STATS_RANGES = 0, + HIT_STATS_MAX_RANGE = 1, + HIT_STATS_TOTAL = 2, + HIT_STATS_MAX = 3, + HIT_STATS_TOP = 4, + HIT_STATS_TOP_MAX = 5, + HIT_STATS_BINS = 6, + HIT_STATS_TOP_BINS = 6 + 32, +}; + +///@} // group Defs + +/// +/// A simple POD struct to represent a read id and its top flag status in a packed uint32 +/// +struct packed_read +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + packed_read() {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + packed_read(const uint32 _read_id, const uint32 _top_flag = 1u) : + read_id( _read_id ), top_flag(_top_flag) {} + + uint32 read_id:31, top_flag:1; +}; + +/// +/// A simple POD struct to represent a seed's information in a packed uint32: +/// - position in read +/// - FM-index direction +/// - reverse-complement flag +/// - top flag +/// +struct packed_seed +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + packed_seed() {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + packed_seed(const uint32 _pos_in_read, const uint32 _index_dir, const uint32 _rc, const uint32 _top_flag) : + pos_in_read(_pos_in_read), index_dir(_index_dir), rc(_rc), top_flag(_top_flag) {} + + uint32 pos_in_read:12, index_dir:1, rc:1, top_flag:1; +}; + +/// pack-read functor, converting an integer read id into a packed_read +/// +struct pack_read +{ + typedef uint32 argument_type; + typedef packed_read result_type; + + /// default constructor + /// + pack_read() : top_flag(0u) {} + + /// constructor + /// + /// \param _top_flag top flag + /// + pack_read(const uint32 _top_flag) : top_flag(_top_flag) {} + + /// functor operator + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + packed_read operator() (const uint32 i) const { return packed_read(i, top_flag); } + + uint32 top_flag; +}; + +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/fmindex_def.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/fmindex_def.h new file mode 100644 index 0000000000000000000000000000000000000000..7363181dabd65d7e2ada98216f2159479bc027ea --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/fmindex_def.h @@ -0,0 +1,49 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +struct FMIndexDef +{ + typedef io::FMIndexDataDevice::count_table_type count_table_type; + typedef io::FMIndexDataDevice::occ_type occ_type; + typedef io::FMIndexDataDevice::bwt_type bwt_type; + typedef io::FMIndexDataDevice::ssa_type ssa_type; + typedef io::FMIndexDataDevice::rank_dict_type rank_dict_type; + typedef io::FMIndexDataDevice::fm_index_type type; +}; + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/func.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/func.h new file mode 100644 index 0000000000000000000000000000000000000000..0905b8688caac04e28040d20529efe0cb612b8b9 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/func.h @@ -0,0 +1,76 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +///@addtogroup nvBowtie +///@{ + +struct SimpleFunc +{ + enum Type { LinearFunc = 0, LogFunc = 1, SqrtFunc = 2 }; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + SimpleFunc(const Type _type = LinearFunc, const float _k = 0.0f, const float _m = 1.0f) : type(_type), k(_k), m(_m) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + int32 operator() (const int32 x) const + { + return int32( k + m * (type == LogFunc ? logf(float(x)) : + type == SqrtFunc ? sqrtf(float(x)) : + float(x)) ); + } + + const char* type_string() const + { + return type == LogFunc ? "log" : + type == SqrtFunc ? "sqrt" : + "linear"; + } + const char* type_symbol() const + { + return type == LogFunc ? "G" : + type == SqrtFunc ? "S" : + "L"; + } + + Type type; + float k; + float m; +}; + +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/input_thread.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/input_thread.cpp new file mode 100644 index 0000000000000000000000000000000000000000..d705bc0c66150a6c20f8d4baf6ea3b156d156a6c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/input_thread.cpp @@ -0,0 +1,339 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +void InputThreadSE::run() +{ + log_verbose( stderr, "starting background input thread\n" ); + + try + { + // fill up the free pool + { + ScopedLock lock( &m_free_pool_lock ); + for (uint32 i = 0; i < BUFFERS; ++i) + m_free_pool.push( &m_read_data_storage[i] ); + } + + while (1u) + { + io::SequenceDataHost* read_data = NULL; + + // loop until the free pool gets filled + while (read_data == NULL) + { + ScopedLock lock( &m_free_pool_lock ); + + if (m_free_pool.empty() == false) + { + read_data = m_free_pool.top(); + m_free_pool.pop(); + } + + yield(); + } + + log_debug( stderr, " reading input batch %u\n", m_set ); + + Timer timer; + timer.start(); + + const int ret = io::next( DNA_N, read_data, m_read_data_stream, m_batch_size, m_batch_size*m_read_length ); + + timer.stop(); + + if (ret) + { + ScopedLock lock( &m_ready_pool_lock ); + m_ready_pool.push_front( read_data ); + m_ready_poolN.push_front( m_reads ); + + m_reads += read_data->size(); + + m_stats.read_io.add( read_data->size(), timer.seconds() ); + } + else + { + // stop the thread + m_done = true; + host_release_fence(); + break; + } + + // switch to the next set + ++m_set; + } + } + catch (nvbio::bad_alloc e) + { + log_error(stderr, "caught a nvbio::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::logic_error e) + { + log_error(stderr, "caught a nvbio::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::runtime_error e) + { + log_error(stderr, "caught a nvbio::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::bad_alloc e) + { + log_error(stderr, "caught a std::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::logic_error e) + { + log_error(stderr, "caught a std::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::runtime_error e) + { + log_error(stderr, "caught a std::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (...) + { + log_error(stderr, "caught an unknown exception!\n"); + exit(1); + } +} + +// get a batch +// +io::SequenceDataHost* InputThreadSE::next(uint32* offset) +{ + // loop until the ready pool gets filled + while (1) + { + ScopedLock lock( &m_ready_pool_lock ); + + if (m_ready_pool.empty() == false) + { + // pop from the ready pool + io::SequenceDataHost* read_data = m_ready_pool.back(); + m_ready_pool.pop_back(); + if (offset) *offset = m_ready_poolN.back(); + m_ready_poolN.pop_back(); + return read_data; + } + else if (m_done) + { + if (offset) *offset = m_reads; + return NULL; + } + + yield(); + } +} + +// release a batch +// +void InputThreadSE::release(io::SequenceDataHost* read_data) +{ + // push back to the free pool + ScopedLock lock( &m_free_pool_lock ); + m_free_pool.push( read_data ); +} + +void InputThreadPE::run() +{ + log_verbose( stderr, "starting background paired-end input thread\n" ); + + try + { + // fill up the free pool + { + ScopedLock lock( &m_free_pool_lock ); + for (uint32 i = 0; i < BUFFERS; ++i) + { + m_free_pool1.push( &m_read_data_storage1[i] ); + m_free_pool2.push( &m_read_data_storage2[i] ); + } + } + + while (1u) + { + io::SequenceDataHost* read_data1 = NULL; + io::SequenceDataHost* read_data2 = NULL; + + // loop until the free pool gets filled + while (read_data1 == NULL || read_data2 == NULL) + { + ScopedLock lock( &m_free_pool_lock ); + + if (m_free_pool1.empty() == false && + m_free_pool2.empty() == false) + { + read_data1 = m_free_pool1.top(); m_free_pool1.pop(); + read_data2 = m_free_pool2.top(); m_free_pool2.pop(); + } + + yield(); + } + + log_debug( stderr, " reading input batch %u\n", m_set ); + + Timer timer; + timer.start(); + + const int ret1 = io::next( DNA_N, read_data1, m_read_data_stream1, m_batch_size, m_batch_size*m_read_length ); + const int ret2 = io::next( DNA_N, read_data2, m_read_data_stream2, read_data1->size() ); + + timer.stop(); + + if (ret1 && ret2) + { + ScopedLock lock( &m_ready_pool_lock ); + m_ready_pool1.push_front( read_data1 ); + m_ready_pool2.push_front( read_data2 ); + m_ready_poolN.push_front( m_reads ); + + m_reads += read_data1->size(); + + m_stats.read_io.add( read_data1->size(), timer.seconds() ); + } + else + { + // stop the thread + m_done = true; + host_release_fence(); + break; + } + + // switch to the next set + ++m_set; + } + } + catch (nvbio::bad_alloc e) + { + log_error(stderr, "caught a nvbio::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::logic_error e) + { + log_error(stderr, "caught a nvbio::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::runtime_error e) + { + log_error(stderr, "caught a nvbio::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::bad_alloc e) + { + log_error(stderr, "caught a std::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::logic_error e) + { + log_error(stderr, "caught a std::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::runtime_error e) + { + log_error(stderr, "caught a std::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (...) + { + log_error(stderr, "caught an unknown exception!\n"); + exit(1); + } +} + +// get a batch +// +std::pair InputThreadPE::next(uint32* offset) +{ + // loop until the ready pool gets filled + while (1) + { + ScopedLock lock( &m_ready_pool_lock ); + + if (m_ready_pool1.empty() == false && + m_ready_pool2.empty() == false) + { + // pop from the ready pool + std::pair read_data; + read_data.first = m_ready_pool1.back(); m_ready_pool1.pop_back(); + read_data.second = m_ready_pool2.back(); m_ready_pool2.pop_back(); + if (offset) *offset = m_ready_poolN.back(); + m_ready_poolN.pop_back(); + return read_data; + } + else if (m_done) + { + if (offset) *offset = m_reads; + return std::pair( NULL, NULL ); + } + + yield(); + + } +} + +// release a batch +// +void InputThreadPE::release(std::pair read_data) +{ + // push back to the free pool + ScopedLock lock( &m_free_pool_lock ); + m_free_pool1.push( read_data.first ); + m_free_pool2.push( read_data.second ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/input_thread.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/input_thread.h new file mode 100644 index 0000000000000000000000000000000000000000..4e5d7c8a020c261869f610cc4ded8390c18ce3fc --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/input_thread.h @@ -0,0 +1,144 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// +// A class implementing a background input thread, providing +// a set of input read-streams which are read in parallel to the +// operations performed by the main thread. +// + +struct InputThreadSE : public Thread +{ + static const uint32 BUFFERS = 4; + + InputThreadSE(io::SequenceDataStream* read_data_stream, Stats& _stats, const uint32 batch_size, const uint32 read_length) : + m_read_data_stream( read_data_stream ), m_stats( _stats ), m_batch_size( batch_size ), m_read_length( read_length ), m_set(0), m_reads(0), m_done(false) + {} + + void run(); + + // get a batch + // + io::SequenceDataHost* next(uint32* offset = NULL); + + // release a batch + // + void release(io::SequenceDataHost* read_data); + + // return the batch size + // + uint32 batch_size() const { return m_batch_size; } + +private: + io::SequenceDataStream* m_read_data_stream; + Stats& m_stats; + uint32 m_batch_size; + uint32 m_read_length; + uint32 m_set; + uint32 m_reads; + + io::SequenceDataHost m_read_data_storage[BUFFERS]; + + Mutex m_free_pool_lock; + std::stack m_free_pool; + + Mutex m_ready_pool_lock; + std::deque m_ready_pool; + std::deque m_ready_poolN; + + volatile bool m_done; +}; + +// +// A class implementing a background input thread, providing +// a set of input read-streams which are read in parallel to the +// operations performed by the main thread. +// + +struct InputThreadPE : public Thread +{ + static const uint32 BUFFERS = 4; + + InputThreadPE(io::SequenceDataStream* read_data_stream1, io::SequenceDataStream* read_data_stream2, Stats& _stats, const uint32 batch_size, const uint32 read_length) : + m_read_data_stream1( read_data_stream1 ), m_read_data_stream2( read_data_stream2 ), m_stats( _stats ), m_batch_size( batch_size ), m_read_length( read_length ), m_set(0), m_reads(0), m_done(false) + {} + + void run(); + + // get a batch + // + std::pair next(uint32* offset = NULL); + + // release a batch + // + void release(std::pair read_data); + + // return the batch size + // + uint32 batch_size() const { return m_batch_size; } + +private: + io::SequenceDataStream* m_read_data_stream1; + io::SequenceDataStream* m_read_data_stream2; + Stats& m_stats; + uint32 m_batch_size; + uint32 m_read_length; + uint32 m_set; + uint32 m_reads; + + io::SequenceDataHost m_read_data_storage1[BUFFERS]; + io::SequenceDataHost m_read_data_storage2[BUFFERS]; + + Mutex m_free_pool_lock; + std::stack m_free_pool1; + std::stack m_free_pool2; + + Mutex m_ready_pool_lock; + std::deque m_ready_pool1; + std::deque m_ready_pool2; + std::deque m_ready_poolN; + + volatile bool m_done; +}; + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/locate.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/locate.h new file mode 100644 index 0000000000000000000000000000000000000000..17a31f618bb19e3d97a1c3c74945242d488266e6 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/locate.h @@ -0,0 +1,155 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/// +///\file locate.h +/// + +#pragma once + +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +template struct BaseScoringPipelineState; +template struct BestApproxScoringPipelineState; + +///@addtogroup nvBowtie +///@{ + +/// \defgroup Locate +/// +/// The functions in this module implement a pipeline stage in which all the previously selected hits (\ref Select) +/// locations are converted from Suffix Array coordinates to linear genome coordinates. +/// In terms of inputs and outputs, this stage takes the HitQueues::seed and HitQueues::loc fields, and rewrite +/// the HitQueues::loc field with the linear value. +/// +/// \b inputs: +/// - HitQueues::seed +/// - HitQueues::loc +/// +/// \b outputs: +/// - HitQueues::loc +/// + +///@addtogroup Locate +///@{ + +/// +/// Locate the SA row of the the hits in the HitQueues. +/// Since the input might have been sorted to gather locality, the entries +/// in the HitQueues are now specified by an index (idx_queue). +/// This function reads HitQueues::seed and HitQueues::loc fields and rewrites +/// the HitQueues::loc field. +/// +template +void locate( + const BatchType read_batch, const FMType fmi, const rFMType rfmi, + const uint32 in_count, + const uint32* idx_queue, + HitQueuesDeviceView hits, + const ParamsPOD params); + +/// +/// Locate the SA row of the the hits in the HitQueues. +/// Since the input might have been sorted to gather locality, the entries +/// in the HitQueues are now specified by an index (idx_queue). +/// This function reads HitQueues::seed and HitQueues::loc fields and writes +/// the HitQueues::loc and HitQueues::ssa fields with temporary values that +/// can be later consumed by locate_lookup. +/// +template +void locate_init( + const BatchType read_batch, const FMType fmi, const rFMType rfmi, + const uint32 in_count, + const uint32* idx_queue, + HitQueuesDeviceView hits, + const ParamsPOD params); + +/// +/// Locate the SA row of the the hits in the HitQueues. +/// Since the input might have been sorted to gather locality, the entries +/// in the HitQueues are now specified by an index (idx_queue). +/// This function reads HitQueues::seed, HitQueues::loc and HitQueues::ssa fields +/// (which must have been previously produced by a call to locate_init) and rewrites +/// the HitQueues::loc field with the final linear coordinate value. +/// +template +void locate_lookup( + const BatchType read_batch, const FMType fmi, const rFMType rfmi, + const uint32 in_count, + const uint32* idx_queue, + HitQueuesDeviceView hits, + const ParamsPOD params); + +/// +/// Locate the SA row of the the hits in the HitQueues. +/// This function reads HitQueues::seed and HitQueues::loc fields and writes +/// the HitQueues::loc and HitQueues::ssa fields with temporary values that +/// can be later consumed by locate_lookup. +/// +template +void locate_init( + const BaseScoringPipelineState& pipeline, + const ParamsPOD params); + +/// +/// Locate the SA row of the the hits in the HitQueues. +/// This function reads HitQueues::seed, HitQueues::loc and HitQueues::ssa fields +/// (which must have been previously produced by a call to locate_init) and rewrites +/// the HitQueues::loc field with the final linear coordinate value. +/// +template +void locate_lookup( + const BaseScoringPipelineState& pipeline, + const ParamsPOD params); + +/// +/// mark seeds straddling the reference boundaries. +/// +template +void mark_straddling( + const uint32 in_count, + const uint32* idx_queue, + const uint32 reference_count, + const index_iterator reference_index, + HitQueuesDeviceView hits, + flags_iterator flags, + const ParamsPOD params); + +///@} // group Locate +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio + +#include diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/locate_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/locate_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..a0b2e3948cab3e6685356fdd93c261539747a234 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/locate_inl.h @@ -0,0 +1,391 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +namespace detail { + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Locate +///@{ + +///@addtogroup LocateDetail +///@{ + +/// +/// transform an SA index to linear coordinates using either the forward or reverse FM-index +/// +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +uint32 locate(const FMType& fmi, const rFMType& rfmi, const uint32 dir, const uint32 r) +{ + if (same_type::pred) + { + const FMType fmi_ref = dir == FORWARD ? fmi : rfmi; + const uint32 g_pos = locate( fmi_ref, r ); + NVBIO_CUDA_ASSERT( g_pos < fmi_ref.length() ); + return (dir == REVERSE) ? + rfmi.length()-1 - g_pos : g_pos; + } + else + { + if (dir == FORWARD) + return locate(fmi, r); + else + return rfmi.length()-1 - locate(rfmi, r); + } +} +/// +/// first pass of a two pass method to transform an SA index to linear coordinates using either the forward or reverse FM-index +/// +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +uint2 locate_init(const FMType& fmi, const rFMType& rfmi, const uint32 dir, const uint32 r) +{ + if (same_type::pred) + { + const FMType fmi_ref = dir == FORWARD ? fmi : rfmi; + return locate_ssa_iterator( fmi_ref, r ); + } + else + { + if (dir == FORWARD) + return locate_ssa_iterator( fmi, r ); + else + return locate_ssa_iterator( rfmi, r ); + } +} + +/// +/// second pass of a two pass method to transform an SA index to linear coordinates using either the forward or reverse FM-index +/// +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +uint32 locate_lookup(const FMType& fmi, const rFMType& rfmi, const uint32 dir, const uint2 it) +{ + if (same_type::pred) + { + const FMType fmi_ref = dir == FORWARD ? fmi : rfmi; + const uint32 g_pos = lookup_ssa_iterator( fmi_ref, it ); + return (dir == REVERSE) ? + rfmi.length()-1 - g_pos : g_pos; + } + else + { + if (dir == FORWARD) + return lookup_ssa_iterator( fmi, it ); + else + return rfmi.length()-1 - lookup_ssa_iterator( rfmi, it ); + } +} + +/// +/// Locate the next SA row in the queue. +/// Since the input loc_queue might have been sorted to gather locality, the +/// corresponding entry in seed_queue is now specified by an index (idx_queue). +/// +template __global__ +void locate_kernel( + const BatchType read_batch, const FMType fmi, const rFMType rfmi, + const uint32 in_count, + const uint32* idx_queue, + HitQueuesDeviceView hits, + const ParamsPOD params) +{ + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= in_count) return; + + const uint32 sa_idx = idx_queue[ thread_id ]; // fetch the sorting queue index + + HitReference hit( hits, sa_idx ); + const uint32 sa_pos = hit.loc; // fetch the SA coordinate + const packed_seed info = hit.seed; // fetch the attached info + const uint32 index_dir = info.index_dir; // decode the index direction + const uint32 pos_in_read = info.pos_in_read; // decode the seed's position in the read + + // locate the SA row and calculate the global position + const uint32 g_pos = locate( fmi, rfmi, index_dir, sa_pos ) - pos_in_read; + + // overwrite the locate queue with the final position + hit.loc = g_pos; +} + +/// +/// Locate the next SA row in the queue. +/// Since the input loc_queue might have been sorted to gather locality, the +/// corresponding entry in seed_queue is now specified by an index (idx_queue). +/// +template __global__ +void locate_init_kernel( + const BatchType read_batch, const FMType fmi, const rFMType rfmi, + const uint32 in_count, + const uint32* idx_queue, + HitQueuesDeviceView hits, + const ParamsPOD params) +{ + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= in_count) return; + + const uint32 sa_idx = idx_queue[ thread_id ]; // fetch the sorting queue index + + HitReference hit( hits, sa_idx ); + const uint32 sa_pos = hit.loc; // fetch the SA coordinate + const packed_seed info = hit.seed; // fetch the attached info + const uint32 index_dir = info.index_dir; // decode the index direction + + // locate the SA row and calculate the global position + const uint2 ssa = locate_init( fmi, rfmi, index_dir, sa_pos ); + + // overwrite the locate queue with the final position + hit.loc = ssa.x; + hit.ssa = ssa.y; +} +/// +/// Locate the next SA row in the queue. +/// Since the input loc_queue might have been sorted to gather locality, the +/// corresponding entry in seed_queue is now specified by an index (idx_queue). +/// +template __global__ +void locate_lookup_kernel( + const BatchType read_batch, const FMType fmi, const rFMType rfmi, + const uint32 in_count, + const uint32* idx_queue, + HitQueuesDeviceView hits, + const ParamsPOD params) +{ + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= in_count) return; + + const uint32 sa_idx = idx_queue[ thread_id ]; // fetch the sorting queue index + + HitReference hit( hits, sa_idx ); + const uint32 sa_pos = hit.loc; // fetch the SA coordinate + const uint32 sa_off = hit.ssa; // fetch the SSA offset + const packed_seed info = hit.seed; // fetch the attached info + const uint32 index_dir = info.index_dir; // decode the index direction + const uint32 pos_in_read = info.pos_in_read; // decode the seed's position in the read + + // locate the SA row and calculate the global position + const uint32 g_pos = locate_lookup( fmi, rfmi, index_dir, make_uint2( sa_pos, sa_off ) ) - pos_in_read; + + // overwrite the locate queue with the final position + hit.loc = g_pos; +} + +/// +/// mark seeds straddling the reference boundaries. +/// +template __global__ +void mark_straddling_kernel( + const uint32 in_count, + const uint32* idx_queue, + const uint32 reference_count, + const index_iterator reference_index, + HitQueuesDeviceView hits, + flags_iterator flags, + const ParamsPOD params) +{ + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= in_count) return; + + const uint32 sa_idx = idx_queue[ thread_id ]; // fetch the sorting queue index + + HitReference hit( hits, sa_idx ); + const uint32 g_pos = hit.loc; // fetch the global reference coordinate + + // find the sequence + const uint32 seq_begin = upper_bound_index( + g_pos, + reference_index, + reference_count+1u ) - 1u; + + // find the sequence + const uint32 seq_end = upper_bound_index( + g_pos + params.seed_len, + reference_index, + reference_count+1u ) - 1u; + + if (seq_begin != seq_end) + flags[ thread_id ] = 0; +} + +///@} // group LocateDetail +///@} // group Locate +///@} // group nvBowtie + +} // namespace detail + +// +// Locate the next SA row in the queue. +// Since the input loc_queue might have been sorted to gather locality, the +// corresponding entry in seed_queue is now specified by an index (idx_queue). +// +template +void locate( + const BatchType read_batch, const FMType fmi, const rFMType rfmi, + const uint32 in_count, + const uint32* idx_queue, + HitQueuesDeviceView hits, + const ParamsPOD params) +{ + const int blocks = (in_count + BLOCKDIM-1) / BLOCKDIM; + + detail::locate_kernel<<>>( + read_batch, fmi, rfmi, + in_count, + idx_queue, + hits, + params ); +} + +// +// Locate the next SA row in the queue. +// Since the input loc_queue might have been sorted to gather locality, the +// corresponding entry in seed_queue is now specified by an index (idx_queue). +// +template +void locate_init( + const BatchType read_batch, const FMType fmi, const rFMType rfmi, + const uint32 in_count, + const uint32* idx_queue, + HitQueuesDeviceView hits, + const ParamsPOD params) +{ + const int blocks = (in_count + BLOCKDIM-1) / BLOCKDIM; + + detail::locate_init_kernel<<>>( + read_batch, fmi, rfmi, + in_count, + idx_queue, + hits, + params ); +} + +// +// Locate the next SA row in the queue. +// Since the input loc_queue might have been sorted to gather locality, the +// corresponding entry in seed_queue is now specified by an index (idx_queue). +// +template +void locate_init( + const BaseScoringPipelineState& pipeline, + const ParamsPOD params) +{ + locate_init( + pipeline.reads, + pipeline.fmi, + pipeline.rfmi, + pipeline.hits_queue_size, + pipeline.idx_queue, + pipeline.scoring_queues.hits, + params ); +} + +// +// Locate the next SA row in the queue. +// Since the input loc_queue might have been sorted to gather locality, the +// corresponding entry in seed_queue is now specified by an index (idx_queue). +// +template +void locate_lookup( + const BatchType read_batch, const FMType fmi, const rFMType rfmi, + const uint32 in_count, + const uint32* idx_queue, + HitQueuesDeviceView hits, + const ParamsPOD params) +{ + const int blocks = (in_count + BLOCKDIM-1) / BLOCKDIM; + + detail::locate_lookup_kernel<<>>( + read_batch, fmi, rfmi, + in_count, + idx_queue, + hits, + params ); +} + +// +// Locate the next SA row in the queue. +// Since the input loc_queue might have been sorted to gather locality, the +// corresponding entry in seed_queue is now specified by an index (idx_queue). +// +template +void locate_lookup( + const BaseScoringPipelineState& pipeline, + const ParamsPOD params) +{ + const int blocks = (pipeline.hits_queue_size + BLOCKDIM-1) / BLOCKDIM; + + detail::locate_lookup_kernel<<>>( + pipeline.reads, + pipeline.fmi, + pipeline.rfmi, + pipeline.hits_queue_size, + pipeline.idx_queue, + pipeline.scoring_queues.hits, + params ); +} + +// +// mark seeds straddling the reference boundaries. +// +template +void mark_straddling( + const uint32 in_count, + const uint32* idx_queue, + const uint32 reference_count, + const index_iterator reference_index, + HitQueuesDeviceView hits, + flags_iterator flags, + const ParamsPOD params) +{ + const int blocks = (in_count + BLOCKDIM-1) / BLOCKDIM; + + detail::mark_straddling_kernel<<>>( + in_count, + idx_queue, + reference_count, + reference_index, + hits, + flags, + params ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapping.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapping.cu new file mode 100644 index 0000000000000000000000000000000000000000..49c06d2ddcdcd236a7e205b60d12b666a3061697 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapping.cu @@ -0,0 +1,191 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// +// For all i in [0, #seed hit ranges[, output the seed hit range size in +// out_ranges[i]. +// +__global__ +void gather_ranges_kernel( + const uint32 count, + const uint32 n_reads, + const SeedHitDequeArrayDeviceView hits, + const uint32* hit_counts_scan, + uint64* out_ranges) +{ + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= count) return; + + // do a binary search, looking for thread_id in hit_counts_scan, + // to find the corresponding read id. + const uint32 read_id = upper_bound_index( thread_id, hit_counts_scan, n_reads ); + + // at this point we can figure out which seed hit / SA range this thread is + // responsible of + const uint32 count_offset = read_id ? hit_counts_scan[read_id-1] : 0u; + + const uint32 range_id = thread_id - count_offset; + + const SeedHit* hits_data = hits.get_data( read_id ); + + const uint2 range = hits_data[ range_id ].get_range(); + + // and we can compute the corresponding range size + out_ranges[ thread_id ] = range.y - range.x; +} + +// +// dispatch the call to gather_ranges_kernel +// +void gather_ranges( + const uint32 count, + const uint32 n_reads, + const SeedHitDequeArrayDeviceView hits, + const uint32* hit_counts_scan, + uint64* out_ranges) +{ + const int blocks = (count + BLOCKDIM-1) / BLOCKDIM; + + gather_ranges_kernel<<>>( count, n_reads, hits, hit_counts_scan, out_ranges ); +} + + +// +// perform exact read mapping +// +void map_whole_read( + const ReadsDef::type& read_batch, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + map_whole_read_t( read_batch, fmi, rfmi, queues, reseed, hits, params, fw, rc ); +} + +// +// perform one run of exact seed mapping for all the reads in the input queue, +// writing reads that need another run in the output queue +// +void map_exact( + const ReadsDef::type& read_batch, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + map_exact_t( read_batch, fmi, rfmi, retry, queues, reseed, hits, params, fw, rc ); +} + +// +// perform multiple runs of exact seed mapping in one go and keep the best +// +void map_exact( + const ReadsDef::type& read_batch, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + SeedHitDequeArrayDeviceView hits, + const uint2 seed_range, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + map_exact_t( read_batch, fmi, rfmi, hits, seed_range, params, fw, rc ); +} + +// +// perform one run of approximate seed mapping for all the reads in the input queue, +// writing reads that need another run in the output queue +// +void map_approx( + const ReadsDef::type& read_batch, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + map_approx_t( read_batch, fmi, rfmi, retry, queues, reseed, hits, params, fw, rc ); +} + +// +// perform multiple runs of approximate seed mapping in one go and keep the best +// +void map_approx( + const ReadsDef::type& read_batch, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + SeedHitDequeArrayDeviceView hits, + const uint2 seed_range, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + map_approx_t( read_batch, fmi, rfmi, hits, seed_range, params, fw, rc ); +} + +// +// perform one run of seed mapping +// +void map( + const ReadsDef::type& read_batch, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + map_t( read_batch, fmi, rfmi, retry, queues, reseed, hits, params, fw, rc ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapping.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapping.h new file mode 100644 index 0000000000000000000000000000000000000000..6e413cdb732bf7d4a9f0e929643c017ef5495c17 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapping.h @@ -0,0 +1,180 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/// +///\file mapping.h +/// + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +///@addtogroup nvBowtie +///@{ + +/// \defgroup Mapping +/// +/// The functions in this module implement the very first pipeline stage: seed mapping. +/// In this stage each read is broken up into many short, possibly overlapping seeds +/// which get mapped against the reference genome using an FM-index. +/// The output is a vector of variable-lenth "priority deques", one for each read, +/// containing the set of Suffix Array ranges (\ref SeedHits) where the seeds align, +/// prioritized by the inverse of the range size (see \ref SeedHitDequeArray). +/// +/// The module implements many mapping algorithms: +/// +/// - exact: allowing exact matches only +/// - approx-hybrid: allowing 0 mismatches in a subseed of the seed, and up to 1 mismatch in the rest +/// - approx-case-pruning: allowing 1 mismatch across the entire seed, using 2 FM-indices to perform +/// the search with case pruning (i.e. searching an alignment with 0 mismatches in the first half of +/// the seed in the forward FM-index, and an alignment with 0 mismatches in the second half in the +/// reverse FM-index). +/// + +///@addtogroup Mapping +///@{ + +/// +/// For all the seed hit ranges, output the range size in out_ranges. +/// +void gather_ranges( + const uint32 count, + const uint32 n_reads, + SeedHitDequeArrayDeviceView hits, + const uint32* hit_counts_scan, + uint64* out_ranges); + +/// +/// perform exact read mapping +/// +void map_whole_read( + const ReadsDef::type& read_batch, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc); + +/// +/// perform one run of exact seed mapping for all the reads in the input queue, +/// writing reads that need another run in the output queue +/// +void map_exact( + const ReadsDef::type& read_batch, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc); + +/// +/// perform multiple runs of exact seed mapping in one go and keep the best +/// +void map_exact( + const ReadsDef::type& read_batch, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + SeedHitDequeArrayDeviceView hits, + const uint2 seed_range, + const ParamsPOD params, + const bool fw, + const bool rc); + +/// +/// perform one run of approximate seed mapping for all the reads in the input queue, +/// writing reads that need another run in the output queue +/// +void map_approx( + const ReadsDef::type& read_batch, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc); + +/// +/// perform multiple runs of approximate seed mapping in one go and keep the best +/// +void map_approx( + const ReadsDef::type& read_batch, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + SeedHitDequeArrayDeviceView hits, + const uint2 seed_range, + const ParamsPOD params, + const bool fw, + const bool rc); + +/// +/// perform one run of seed mapping +/// +void map( + const ReadsDef::type& read_batch, + const FMIndexDef::type fmi, + const FMIndexDef::type rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc); + +///@} // group Mapping +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapping_impl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapping_impl.h new file mode 100644 index 0000000000000000000000000000000000000000..52ce656c33b200d71b242f592e142434ae905ebc --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapping_impl.h @@ -0,0 +1,181 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/// +///\file mapping.h +/// + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +///@addtogroup nvBowtie +///@{ + +/// \defgroup Mapping +/// +/// The functions in this module implement the very first pipeline stage: seed mapping. +/// In this stage each read is broken up into many short, possibly overlapping seeds +/// which get mapped against the reference genome using an FM-index. +/// The output is a vector of variable-lenth "priority deques", one for each read, +/// containing the set of Suffix Array ranges (\ref SeedHits) where the seeds align, +/// prioritized by the inverse of the range size (see \ref SeedHitDequeArray). +/// +/// The module implements many mapping algorithms: +/// +/// - exact: allowing exact matches only +/// - approx-hybrid: allowing 0 mismatches in a subseed of the seed, and up to 1 mismatch in the rest +/// - approx-case-pruning: allowing 1 mismatch across the entire seed, using 2 FM-indices to perform +/// the search with case pruning (i.e. searching an alignment with 0 mismatches in the first half of +/// the seed in the forward FM-index, and an alignment with 0 mismatches in the second half in the +/// reverse FM-index). +/// + +///@addtogroup Mapping +///@{ + +/// +/// perform exact read mapping +/// +template +void map_whole_read_t( + const BatchType& read_batch, const FMType fmi, const rFMType rfmi, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc); + +/// +/// perform one run of exact seed mapping for all the reads in the input queue, +/// writing reads that need another run in the output queue +/// +template +void map_exact_t( + const BatchType& read_batch, const FMType fmi, const rFMType rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc); + +/// +/// perform multiple runs of exact seed mapping in one go and keep the best +/// +template +void map_exact_t( + const BatchType& read_batch, const FMType fmi, const rFMType rfmi, + SeedHitDequeArrayDeviceView hits, + const uint2 seed_range, + const ParamsPOD params, + const bool fw, + const bool rc); + +/// +/// perform one run of approximate seed mapping using case pruning for all the reads in +/// the input queue, writing reads that need another run in the output queue +/// +template +void map_case_pruning_t( + const BatchType& read_batch, const FMType fmi, const rFMType rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc); + +/// +/// perform one run of approximate seed mapping for all the reads in the input queue, +/// writing reads that need another run in the output queue +/// +template +void map_approx_t( + const BatchType& read_batch, const FMType fmi, const rFMType rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc); + +/// +/// perform multiple runs of approximate seed mapping in one go and keep the best +/// +template +void map_approx_t( + const BatchType& read_batch, const FMType fmi, const rFMType rfmi, + SeedHitDequeArrayDeviceView hits, + const uint2 seed_range, + const ParamsPOD params, + const bool fw, + const bool rc); + +/// +/// perform one run of seed mapping +/// +template +void map_t( + const BatchType& read_batch, const FMType fmi, const rFMType rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc); + +///@} // group Mapping +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio + +#include diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapping_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapping_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..d3afea144887b5e1633984040c83ad8b62417999 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapping_inl.h @@ -0,0 +1,848 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +namespace detail { + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Mapping +///@{ + +///@addtogroup MappingDetail +///@{ + +// Checks if the seed's Ns are compatible with the search, i.e. +// if there are 0 Ns in the exactly-matched region, and at most 1 N +// in the inexact matching region. +template +NVBIO_DEVICE NVBIO_FORCEINLINE +bool check_N(const ReadStream& seed, const uint32 exact_len, const uint32 seed_len) +{ + for (uint32 i = 0; i < exact_len; ++i) + if (seed[i] >= 4) + return false; + + uint32 N_count = 0; + for (uint32 i = exact_len; i < seed_len; ++i) + { + if (seed[i] >= 4 && ++N_count > 1) + return false; + } + return true; +} + +// This function is a lot like match_reverse, +// except that it accepts lower and upper bounds on the sequence stream +template< typename FMType, typename StreamType > NVBIO_DEVICE NVBIO_FORCEINLINE +uint2 match_range(uint2 range, const FMType index, StreamType query, + uint32 begin, uint32 end) +{ + for (uint32 i = begin; i < end && range.x <= range.y; ++i) + { + const uint8 c = query[i]; + if (c > 3) return make_uint2(1, 0); + + const uint2 bwt_cnts = rank(index, make_uint2(range.x-1, range.y), c); + range.x = index.L2(c) + bwt_cnts.x + 1; + range.y = index.L2(c) + bwt_cnts.y; + } + return range; +} + +// Store an array of hits into a SeedHitDequeArray +// +NVBIO_DEVICE NVBIO_FORCEINLINE +void store_deque( + SeedHitDequeArrayDeviceView hit_deques, + const uint32 read_id, + const uint32 n_hits, + const SeedHit* hitstorage) +{ + SeedHit* hit_data = hit_deques.alloc_deque( read_id, n_hits ); + if (hit_data != NULL) + { + hit_deques.resize_deque( read_id, n_hits ); + for (uint32 i = 0; i < n_hits; ++i) + hit_data[i] = hitstorage[i]; + } +} + +enum { CHECK_EXACT=1u, IGNORE_EXACT=0u }; +enum MappingAlgorithm +{ + EXACT_MAPPING = 0u, + APPROX_MAPPING = 1u, + CASE_PRUNING_MAPPING = 2u, +}; + +/// This is the guts of our mapper. We look for hits that match exactly +/// in the range [0, len1) and have one mismatch in [len1, len2). If +/// find_exact is set, we also check for a perfect match. +template< bool find_exact, + typename Stream, + typename FMType, + typename HitType> NVBIO_DEVICE NVBIO_FORCEINLINE +void map(const Stream query, + /*const*/ uint32 len1, + const uint32 len2, + const FMType index, + const SeedHit::Flags hit_flags, + HitType& hitheap, uint32 max_hits, + uint32& range_sum, + uint32& range_count) +{ + // TODO: + // if we know there is one (and only one) N in the second part of the seed, + // we could avoid doing the mismatch search at all other positions. + // However, due to the control divergence it would generate, it might be + // better to filter these seeds away and leave them for a second kernel + // call. + // + + // if there is an N, we can do exact matching till the N + uint32 N_pos = 0; + uint32 N_cnt = 0; + for (uint32 i = 0; i < len2; ++i) + { + const uint8 c = query[i]; + if (c > 3) + { + // if the N is in our exact-matching region, or it is the second one, we cannot align this + if (i < len1 || N_cnt) return; + + N_pos = i; + N_cnt++; + } + } + // do exact-matching till the N, if there is one + len1 = N_cnt ? N_pos : len1; + + // Exact Match first half of read + uint2 base_range = make_uint2(0, index.length()); + base_range = match_range(base_range, index, query, 0, len1); + + // Allow an error in the next batch + for(uint32 i = len1; i < len2 && base_range.x <= base_range.y; ++i) + { + const uint8 c = query[i]; + + // Get ranges for all chars at pos i + uint4 occ_lo, occ_hi; + rank4(index, make_uint2(base_range.x-1, base_range.y), &occ_lo, &occ_hi); + + // Try each character + for (uint8 sub = 0; sub < 4; ++sub) + { + if (sub != c && comp(occ_hi, sub) > comp(occ_lo, sub)) + { + // Manually insert sub + uint2 range = make_uint2(index.L2(sub) + comp(occ_lo, sub) + 1, + index.L2(sub) + comp(occ_hi, sub) ); + + // Extend match to end of read + range = match_range(range, index, query, i+1, len2); + + // Store Result + if (range.x <= range.y) { + if (hitheap.size() == max_hits) + hitheap.pop_bottom(); + hitheap.push(SeedHit(hit_flags, inclusive_to_exclusive(range))); + + range_sum += range.y - range.x + 1u; + range_count++; + } + } + } + + // Extend base_range + if (c < 4) { + base_range.x = index.L2(c) + comp(occ_lo, c) + 1; + base_range.y = index.L2(c) + comp(occ_hi, c); + } else { base_range = make_uint2(1, 0); break; } + } + + if (find_exact && base_range.x <= base_range.y) + { + if (hitheap.size() == max_hits) + hitheap.pop_bottom(); + hitheap.push(SeedHit(hit_flags, inclusive_to_exclusive(base_range))); + + range_sum += base_range.y - base_range.x + 1u; + range_count++; + } +} + +/// abstract seed-mapper interface +template +struct seed_mapper {}; + +/// +/// perform exact seed-mapping +/// +template <> +struct seed_mapper +{ + template + NVBIO_FORCEINLINE NVBIO_DEVICE + static void enact( + const FMType fmi, const rFMType rfmi, + const SeedIterator seed, + const uint2 read_range, + const uint32 pos, + const uint32 seed_len, + HitType& hitheap, + uint32& range_sum, + uint32& range_count, + const ParamsPOD& params, + const bool fw, + const bool rc) + { + const OffsetXform forward_offset(0); + const ReverseXform reverse_offset(seed_len); + + typedef index_transform_iterator< SeedIterator, OffsetXform > fSeedReader; + typedef index_transform_iterator< SeedIterator, ReverseXform > rSeedReader; + + SeedHit::Flags flags; + uint2 range; + + // forward scan, forward index=0 + const fSeedReader f_reader(seed, forward_offset); + if (util::count_occurrences( f_reader, seed_len, 4u, 1u )) + return; + + if (fw) + { + range = make_uint2(0, fmi.length()); + range = match_range(range, fmi, f_reader, 0, seed_len); + if (range.x <= range.y) + { + flags = SeedHit::build_flags(STANDARD, FORWARD, read_range.y-pos-seed_len); + if (hitheap.size() == params.max_hits) + hitheap.pop_bottom(); + hitheap.push(SeedHit(flags, inclusive_to_exclusive(range))); + + range_sum += range.y - range.x + 1u; + range_count++; + } + } + + if (rc) + { + #if USE_REVERSE_INDEX + // Complement seed=1, forward scan, reverse index=1 + const transform_iterator > cf_reader(f_reader, complement_functor<4>()); + + range = make_uint2(0, rfmi.length()); + range = match_range(range, rfmi, cf_reader, 0, seed_len); + if (range.x <= range.y) + { + flags = SeedHit::build_flags(COMPLEMENT, REVERSE, pos-read_range.x+seed_len-1); + if (hitheap.size() == params.max_hits) + hitheap.pop_bottom(); + hitheap.push(SeedHit(flags, inclusive_to_exclusive(range))); + } + #else + // Complement seed=1, reverse scan, forward index=0 + const rSeedReader r_reader(seed, reverse_offset); + const transform_iterator > cr_reader(r_reader, complement_functor<4>()); + + range = make_uint2(0, fmi.length()); + range = match_range(range, fmi, cr_reader, 0, seed_len); + if (range.x <= range.y) + { + flags = SeedHit::build_flags(COMPLEMENT, FORWARD, pos-read_range.x); + if (hitheap.size() == params.max_hits) + hitheap.pop_bottom(); + hitheap.push(SeedHit(flags, inclusive_to_exclusive(range))); + + range_sum += range.y - range.x + 1u; + range_count++; + } + #endif + } + } +}; + +/// +/// perform approximate seed-mapping allowing 0 mismatches in the subseed and 1 mismatch in +/// the remainder of the seed +/// +template <> +struct seed_mapper +{ + template + NVBIO_FORCEINLINE NVBIO_DEVICE + static void enact( + const FMType fmi, const rFMType rfmi, + const SeedIterator seed, + const uint2 read_range, + const uint32 pos, + const uint32 seed_len, + HitType& hitheap, + uint32& range_sum, + uint32& range_count, + const ParamsPOD& params, + const bool fw, + const bool rc) + { + const OffsetXform forward_offset(0); + const ReverseXform reverse_offset(seed_len); + + typedef index_transform_iterator< SeedIterator, OffsetXform > fSeedReader; + typedef index_transform_iterator< SeedIterator, ReverseXform > rSeedReader; + + SeedHit::Flags flags; + + // Standard seed=0, forward scan, forward index=0 + const fSeedReader f_reader(seed, forward_offset); + if (util::count_occurrences( f_reader, seed_len, 4u, 2u )) + return; + + if (fw) + { + flags = SeedHit::build_flags(STANDARD, FORWARD, read_range.y-pos-seed_len); + map (f_reader, params.subseed_len, seed_len, fmi, flags, hitheap, params.max_hits, range_sum, range_count); + } + + // Complement seed=1, reverse scan, forward index=0 + if (rc) + { + const rSeedReader r_reader(seed, reverse_offset); + const transform_iterator > cr_reader(r_reader, complement_functor<4>()); + flags = SeedHit::build_flags(COMPLEMENT, FORWARD, pos-read_range.x); + map(cr_reader, params.subseed_len, seed_len, fmi, flags, hitheap, params.max_hits, range_sum, range_count); + } + } +}; + +/// +/// perform approximate seed-mapping allowing 1 mismatch using case-pruning, i.e: +/// * split the seed in two, +/// * perform exact mapping of the first half and allow 1 mismatch in the second half +/// * perform exact mapping of the second half and allow 1 mismatch in the first half +/// +template <> +struct seed_mapper +{ + template + NVBIO_FORCEINLINE NVBIO_DEVICE + static void enact( + const FMType fmi, const rFMType rfmi, + const SeedIterator seed, + const uint2 read_range, + const uint32 pos, + const uint32 seed_len, + HitType& hitheap, + uint32& range_sum, + uint32& range_count, + const ParamsPOD& params, + const bool fw, + const bool rc) + { + const OffsetXform forward_offset(0); + const ReverseXform reverse_offset(seed_len); + + typedef index_transform_iterator< SeedIterator, OffsetXform > fSeedReader; + typedef index_transform_iterator< SeedIterator, ReverseXform > rSeedReader; + + SeedHit::Flags flags; + + // Standard seed=0, forward scan, forward index=0 + const fSeedReader f_reader(seed, forward_offset); + if (fw) + { + flags = SeedHit::build_flags(STANDARD, FORWARD, read_range.y-pos-seed_len); + map (f_reader, (seed_len )/2, seed_len, fmi, flags, hitheap, params.max_hits, range_sum, range_count); + } + // Standard seed=0, reverse scan, reverse index=1 + const rSeedReader r_reader(seed, reverse_offset); + if (fw) + { + flags = SeedHit::build_flags(STANDARD, REVERSE, read_range.y-pos-1); + map(r_reader, (seed_len+1)/2, seed_len, rfmi, flags, hitheap, params.max_hits, range_sum, range_count); + } + + // Complement seed=1, forward scan, reverse index=1 + if (rc) + { + const transform_iterator > cf_reader(f_reader, complement_functor<4>()); + flags = SeedHit::build_flags(COMPLEMENT, REVERSE, pos-read_range.x+seed_len-1); + map (cf_reader, (seed_len )/2, seed_len, rfmi, flags, hitheap, params.max_hits, range_sum, range_count); + } + + // Complement seed=1, reverse scan, forward index=0 + if (rc) + { + const transform_iterator > cr_reader(r_reader, complement_functor<4>()); + flags = SeedHit::build_flags(COMPLEMENT, FORWARD, pos-read_range.x); + map(cr_reader, (seed_len+1)/2, seed_len, fmi, flags, hitheap, params.max_hits, range_sum, range_count); + } + } +}; + +/// +/// Exact whole read filtering kernel. Maps the entire read exactly +/// +template __global__ +void map_whole_read_kernel( + const BatchType read_batch, const FMType fmi, const rFMType rfmi, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + typedef PackedStringLoader< + typename BatchType::sequence_storage_iterator, + BatchType::SEQUENCE_BITS, + BatchType::SEQUENCE_BIG_ENDIAN, + uncached_tag > packed_loader_type; + typedef typename packed_loader_type::iterator seed_iterator; + + // instantiate a packed loader to cache the seed in local memory + packed_loader_type packer_loader; + + // instantiate storage for a local memory hits queue + SeedHit local_hits[512]; + + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + const uint32 grid_size = BLOCKDIM * gridDim.x; + + for (uint32 id = thread_id; id < queues.in_size; id += grid_size) + { + const uint32 read_id = queues.in_queue[ id ]; + NVBIO_CUDA_ASSERT( read_id < read_batch.size() ); + const uint2 read_range = read_batch.get_range( read_id ); + + // filter away short strings + if (read_range.y - read_range.x < params.min_read_len) + { + hits.resize_deque( read_id, 0 ); + return; + } + + typedef SeedHitDequeArrayDeviceView::hit_vector_type hit_storage_type; + typedef SeedHitDequeArrayDeviceView::hit_deque_type hit_deque_type; + hit_deque_type hitheap( hit_storage_type( 0, local_hits ), true ); + + uint32 range_sum = 0; + uint32 range_count = 0; + + // load the whole read + const seed_iterator read = packer_loader.load( read_batch.sequence_stream() + read_range.x, read_range.y - read_range.x ); + + // map the read + seed_mapper::enact( + fmi, rfmi, + read, + read_range, + read_range.x, + read_range.y - read_range.x, + hitheap, + range_sum, + range_count, + params, + fw, + rc ); + + // save the hits + store_deque( hits, read_id, hitheap.size(), local_hits ); + + // enqueue for re-seeding if there are no hits + if (reseed) + reseed[ id ] = (range_count == 0); + } +} + +/// +/// Seed filtering kernel. Maps the set of seeds for each read in the input +/// queue, filling the corresponding hit priority-deque, and fills the output queue with +/// the list of reads that need reseeding. +/// +template __global__ +void map_queues_kernel( + const BatchType read_batch, const FMType fmi, const rFMType rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + typedef PackedStringLoader< + typename BatchType::sequence_storage_iterator, + BatchType::SEQUENCE_BITS, + BatchType::SEQUENCE_BIG_ENDIAN, + uncached_tag > packed_loader_type; + //lmem_cache_tag<128> > packed_loader_type; // TODO: this produces a crashing kernel, for no good reason + typedef typename packed_loader_type::iterator seed_iterator; + + // instantiate a packed loader to cache the seed in local memory + packed_loader_type packer_loader; + + // instantiate storage for a local memory hits queue + SeedHit local_hits[512]; + + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + const uint32 grid_size = BLOCKDIM * gridDim.x; + + for (uint32 id = thread_id; id < queues.in_size; id += grid_size) + { + const uint32 read_id = queues.in_queue[ id ]; + NVBIO_CUDA_ASSERT( read_id < read_batch.size() ); + const uint2 read_range = read_batch.get_range( read_id ); + const uint32 read_len = read_range.y - read_range.x; + + // filter away short strings + if (read_len < params.min_read_len) + { + hits.resize_deque( read_id, 0 ); + continue; + } + + const uint32 seed_len = nvbio::min( params.seed_len, read_len ); + const uint32 seed_freq = (uint32)params.seed_freq( read_len ); + const uint32 retry_stride = seed_freq/(params.max_reseed+1); + + typedef SeedHitDequeArrayDeviceView::hit_vector_type hit_storage_type; + typedef SeedHitDequeArrayDeviceView::hit_deque_type hit_deque_type; + hit_deque_type hitheap( hit_storage_type( 0, local_hits ), true ); + + uint32 range_sum = 0; + uint32 range_count = 0; + + // loop over seeds + for (uint32 pos = read_range.x + retry * retry_stride; pos + seed_len <= read_range.y; pos += seed_freq) + { + const seed_iterator seed = packer_loader.load( read_batch.sequence_stream() + pos, seed_len ); + + seed_mapper::enact( + fmi, rfmi, + seed, + read_range, + pos, + seed_len, + hitheap, + range_sum, + range_count, + params, + fw, + rc ); + } + + // save the hits + store_deque( hits, read_id, hitheap.size(), local_hits ); + + // enqueue for re-seeding if there are too many hits + if (reseed) + reseed[ id ] = (range_count == 0 || range_sum >= params.rep_seeds * range_count); + + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.read_id == read_id, "map: ranges[%u], rows[%u]\n", read_id, range_count, range_sum ); + } +} + +/// +/// Seed filtering kernel. Maps the set of seeds for each read in the input +/// queue, filling the corresponding hit priority-deque. +/// Internally performs re-seeding to find a good seeding scheme. +/// +template __global__ +void map_kernel( + const BatchType read_batch, const FMType fmi, const rFMType rfmi, + SeedHitDequeArrayDeviceView hits, + const uint2 seed_range, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + typedef PackedStringLoader< + typename BatchType::sequence_storage_iterator, + BatchType::SEQUENCE_BITS, + BatchType::SEQUENCE_BIG_ENDIAN, + uncached_tag > packed_loader_type; + //lmem_cache_tag<128> > packed_loader_type; // TODO: this produces a crashing kernel, for no good reason + typedef typename packed_loader_type::iterator seed_iterator; + + // instantiate a packed loader to cache the seed in local memory + packed_loader_type packer_loader; + + // instantiate storage for a local memory hits queue + SeedHit local_hits[512]; + + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + const uint32 grid_size = BLOCKDIM * gridDim.x; + + for (uint32 read_id = thread_id; read_id < read_batch.size(); read_id += grid_size) + { + const uint2 read_range = read_batch.get_range( read_id ); + const uint32 read_len = read_range.y - read_range.x; + + // filter away short strings + if (read_len < params.min_read_len) + { + hits.resize_deque( read_id, 0 ); + return; + } + + const uint32 seed_len = nvbio::min( params.seed_len, read_len ); + const uint32 seed_freq = (uint32)params.seed_freq( read_len ); + const uint32 retry_stride = seed_freq/(params.max_reseed+1); + + typedef SeedHitDequeArrayDeviceView::hit_vector_type hit_storage_type; + typedef SeedHitDequeArrayDeviceView::hit_deque_type hit_deque_type; + hit_deque_type hitheap( hit_storage_type( 0, local_hits ), true ); + + bool active = true; + + //for (uint32 retry = 0; retry <= params.max_reseed; ++retry) // TODO: this makes the kernel crash even when + // max_reseed is 0, for apparently no good reason... + for (uint32 retry = 0; retry <= 0; ++retry) + { + if (active) + { + // restore the result heap + hitheap.clear(); + + uint32 range_sum = 0; + uint32 range_count = 0; + + for (uint32 i = seed_range.x; i < seed_range.y; ++i) + { + const uint32 pos = read_range.x + retry * retry_stride + i * seed_freq; + if (pos + seed_len <= read_range.y) + { + const seed_iterator seed = packer_loader.load( read_batch.sequence_stream() + pos, seed_len ); + + seed_mapper::enact( + fmi, rfmi, + seed, + read_range, + pos, + seed_len, + hitheap, + range_sum, + range_count, + params, + fw, + rc ); + } + } + + // check whether we could stop here or if we need re-seeding + if (retry == params.max_reseed || range_count == 0 && range_sum < params.rep_seeds * range_count) + active = false; + } + } + + // save the hits + store_deque( hits, read_id, hitheap.size(), local_hits ); + } +} + +///@} // group MappingDetail +///@} // group Mapping +///@} // group nvBowtie + +} // namespace detail + +// +// call the map-sub kernel +// +template +void map_case_pruning_t( + const BatchType& read_batch, const FMType fmi, const rFMType rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + const int blocks = nvbio::cuda::max_active_blocks( detail::map_queues_kernel, BLOCKDIM, 0 ); + detail::map_queues_kernel <<>>( + read_batch, fmi, rfmi, retry, queues, reseed, hits, params, fw, rc ); +} + +// +// call the map-hybrid kernel +// +template +void map_approx_t( + const BatchType& read_batch, const FMType fmi, const rFMType rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + const int blocks = nvbio::cuda::max_active_blocks( detail::map_queues_kernel, BLOCKDIM, 0 ); + detail::map_queues_kernel <<>>( + read_batch, fmi, rfmi, retry, queues, reseed, hits, params, fw, rc ); +} + +// +// call the map-hybrid kernel +// +template +void map_approx_t( + const BatchType& read_batch, const FMType fmi, const rFMType rfmi, + SeedHitDequeArrayDeviceView hits, + const uint2 seed_range, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + const int blocks = nvbio::cuda::max_active_blocks( detail::map_kernel, BLOCKDIM, 0 ); + detail::map_kernel <<>>( + read_batch, fmi, rfmi, hits, seed_range, params, fw, rc ); +} + +// +// call the map-exact kernel +// +template +void map_whole_read_t( + const BatchType& read_batch, const FMType fmi, const rFMType rfmi, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + const uint32 blocks = nvbio::cuda::max_active_blocks( detail::map_whole_read_kernel, BLOCKDIM, 0 ); + detail::map_whole_read_kernel<<>> ( + read_batch, fmi, rfmi, queues, reseed, hits, params, fw, rc ); +} + +// +// call the map-exact kernel +// +template +void map_exact_t( + const BatchType& read_batch, const FMType fmi, const rFMType rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + const uint32 blocks = nvbio::cuda::max_active_blocks( detail::map_queues_kernel, BLOCKDIM, 0 ); + detail::map_queues_kernel <<>>( + read_batch, fmi, rfmi, retry, queues, reseed, hits, params, fw, rc ); +} + +// +// call the map-exact kernel +// +template +void map_exact_t( + const BatchType& read_batch, const FMType fmi, const rFMType rfmi, + SeedHitDequeArrayDeviceView hits, + const uint2 seed_range, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + const uint32 blocks = nvbio::cuda::max_active_blocks( detail::map_kernel, BLOCKDIM, 0 ); + detail::map_kernel <<>>( + read_batch, fmi, rfmi, hits, seed_range, params, fw, rc ); +} + +// +// call the appropriate mapping kernel +// +template +void map_t( + const BatchType& read_batch, const FMType fmi, const rFMType rfmi, + const uint32 retry, + const nvbio::cuda::PingPongQueuesView queues, + uint8* reseed, + SeedHitDequeArrayDeviceView hits, + const ParamsPOD params, + const bool fw, + const bool rc) +{ + // check whether we allow substitutions + if (params.allow_sub) + { + // check whether we have to perform exact matching on a subseed + if (params.subseed_len == 0) + { + // call the hybrid fuzzy mapping kernel + map_case_pruning_t( + read_batch, fmi, rfmi, retry, queues, reseed, hits, params, fw, rc ); + } + else + { + // call the hybrid exact-fuzzy mapping kernel + map_approx_t( + read_batch, fmi, rfmi, retry, queues, reseed, hits, params, fw, rc ); + } + } + else + { + // call the hybrid exact mapping kernel + map_exact_t( + read_batch, fmi, rfmi, retry, queues, reseed, hits, params, fw, rc ); + } +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapq.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapq.cpp new file mode 100644 index 0000000000000000000000000000000000000000..e11a79b981306da7f0d451fa88691cf2a69bdcae --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapq.cpp @@ -0,0 +1,36 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapq.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapq.h new file mode 100644 index 0000000000000000000000000000000000000000..1cf58bc312bf06c0262bae5e0b85965201284a2a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/mapq.h @@ -0,0 +1,335 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +/// Bowtie2 Mapping Quality Calculator, V3 +/// +template +struct BowtieMapq3 +{ + typedef ScoringSchemeType scoring_scheme_type; + + /// constructor + /// + BowtieMapq3(const ScoringSchemeType sc) : m_sc(sc) {} + + /// compute mapping quality + /// + NVBIO_HOST_DEVICE + uint32 operator() ( + const io::BestPairedAlignments& best_alignments, + const uint32 read_len, + const uint32 o_read_len) const + { + // no second best alignment, perfect score + const int unpaired_one_perfect = 44; + + // no second best alignment + const int unpaired_one[11] = + { + 43, 42, 41, 36, 32, 27, 20, 11, 4, 1, 0 + }; + + // two alignment scores, the best of which has perfect score + const int unpaired_two_perfect[11] = + { + 2, 16, 23, 30, 31, 32, 34, 36, 38, 40, 42 + }; + + // two alignment scores, the best of which has a non perfect score + const int unpaired_two[11][11] = + { + { 2, 2, 2, 1, 1, 0, 0, 0, 0, 0, 0 }, + { 20, 14, 7, 3, 2, 1, 0, 0, 0, 0, 0 }, + { 20, 16, 10, 6, 3, 1, 0, 0, 0, 0, 0 }, + { 20, 17, 13, 9, 3, 1, 1, 0, 0, 0, 0 }, + { 21, 19, 15, 9, 5, 2, 2, 0, 0, 0, 0 }, + { 22, 21, 16, 11, 10, 5, 0, 0, 0, 0, 0 }, + { 23, 22, 19, 16, 11, 0, 0, 0, 0, 0, 0 }, + { 24, 25, 21, 30, 0, 0, 0, 0, 0, 0, 0 }, + { 30, 26, 29, 0, 0, 0, 0, 0, 0, 0, 0 }, + { 30, 27, 0, 0, 0, 0, 0, 0, 0, 0, 0 }, + { 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }, + }; + + // paired alignment, one perfect score + const int paired_one_perfect = 44; + + // + // TODO: if paired, return paired_one_perfect + // + if (best_alignments.is_paired()) + return paired_one_perfect; + + const float max_score = (float)m_sc.perfect_score( read_len ); + const float min_score = (float)m_sc.min_score( read_len ); + const float norm_factor = 10.0f / (max_score - min_score); + + // check whether the best score is beyond the minimum threshold + if (best_alignments.best_score() < min_score) + return 0; + + const int best = std::max( (int)max_score - best_alignments.best_score(), 0 ); // negated best score + const int best_bin = (int)(float(best) * norm_factor + 0.5f); + + const bool has_second = best_alignments.has_second(); + +// if (info) +// { +// info->best = best; +// info->second_best = has_second ? best_alignments.second_score() : 255; +// } + + // check whether there are two alignment scores or just one + if (has_second) + { + const int diff = best_alignments.best_score() - best_alignments.second_score(); + const int diff_bin = (int)(float(diff) * norm_factor + 0.5f); + + if (best == max_score) + return unpaired_two_perfect[best_bin]; + else + return unpaired_two[diff_bin][best_bin]; + } + else + { + if (best == max_score) + return unpaired_one_perfect; + else + return unpaired_one[best_bin]; + } + } + +private: + ScoringSchemeType m_sc; +}; + +/// Bowtie2 Mapping Quality Calculator, V2 +/// +template +struct BowtieMapq2 +{ + typedef ScoringSchemeType scoring_scheme_type; + + /// constructor + /// + BowtieMapq2(const ScoringSchemeType sc) : m_sc(sc) {} + + /// compute mapping quality + /// + NVBIO_HOST_DEVICE + uint32 operator() ( + const io::BestPairedAlignments& best_alignments, + const uint32 read_len, + const uint32 o_read_len) const + { + bool has_second = best_alignments.has_second(); + + const float max_score = (float)m_sc.perfect_score( read_len ) + + (best_alignments.is_paired() ? m_sc.perfect_score( o_read_len ) : 0); + const float min_score = (float)m_sc.min_score( read_len ) + + (best_alignments.is_paired() ? m_sc.min_score( o_read_len ) : 0); + + const float diff = (max_score - min_score); // range of scores + + const float best = (float)best_alignments.best_score(); + float second_best = min_score-1; + + if (best < min_score) + return 0; + + // best score but normalized so that 0 = worst valid score + const float best_over = best - min_score; + +// if (info) +// { +// info->best = (int32)best; +// info->second_best = (int32)second_best; +// } + + if (m_sc.m_monotone) + { + // global alignment + if (!has_second) + { + if (best_over >= diff * 0.8f) return 42; + else if (best_over >= diff * 0.7f) return 40; + else if (best_over >= diff * 0.6f) return 24; + else if (best_over >= diff * 0.5f) return 23; + else if (best_over >= diff * 0.4f) return 8; + else if (best_over >= diff * 0.3f) return 3; + else return 0; + } + else + { + second_best = (float)best_alignments.second_score(); +// if (info) +// info->second_best = (int32)second_best; + + const float best_diff = fabsf(fabsf( best ) - fabsf( second_best )); + + if (best_diff >= diff * 0.9f) + return (best_over == diff) ? 39 : 33; + else if (best_diff >= diff * 0.8f) + return (best_over == diff) ? 38 : 27; + else if (best_diff >= diff * 0.7f) + return (best_over == diff) ? 37 : 26; + else if (best_diff >= diff * 0.6f) + return (best_over == diff) ? 36 : 22; + else if (best_diff >= diff * 0.5f) + { + // top third is still pretty good + if (best_over == diff) return 35; + else if (best_over >= diff * 0.84f) return 25; + else if (best_over >= diff * 0.68f) return 16; + else return 5; + } + else if (best_diff >= diff * 0.4f) + { + // top third is still pretty good + if (best_over == diff) return 34; + else if (best_over >= diff * 0.84f) return 21; + else if (best_over >= diff * 0.68f) return 14; + else return 4; + } + else if (best_diff >= diff * 0.3f) + { + // top third is still pretty good + if (best_over == diff) return 32; + else if (best_over >= diff * 0.88f) return 18; + else if (best_over >= diff * 0.67f) return 15; + else return 3; + } + else if (best_diff >= diff * 0.2f) + { + // top third is still pretty good + if (best_over == diff) return 31; + else if (best_over >= diff * 0.88f) return 17; + else if (best_over >= diff * 0.67f) return 11; + else return 0; + } + else if (best_diff >= diff * 0.1f) + { + // top third is still pretty good + if (best_over == diff) return 30; + else if (best_over >= diff * 0.88f) return 12; + else if (best_over >= diff * 0.67f) return 7; + else return 0; + } + else if (best_diff > 0) + { + // top third is still pretty good + return (best_over >= diff * 0.67f) ? 6 : 2; + } + else + { + // top third is still pretty good + return (best_over >= diff * 0.67f) ? 1 : 0; + } + } + } + else + { + // local alignment + if (!has_second) + { + if (best_over >= diff * 0.8f) return 44; + else if (best_over >= diff * 0.7f) return 42; + else if (best_over >= diff * 0.6f) return 41; + else if (best_over >= diff * 0.5f) return 36; + else if (best_over >= diff * 0.4f) return 28; + else if (best_over >= diff * 0.3f) return 24; + else return 22; + } + else + { + second_best = (float)best_alignments.second_score(); +// if (info) +// info->second_best = (int32)second_best; + + const float best_diff = fabsf(fabsf( best ) - fabsf( second_best )); + + if (best_diff >= diff * 0.9f) return 40; + else if (best_diff >= diff * 0.8f) return 39; + else if (best_diff >= diff * 0.7f) return 38; + else if (best_diff >= diff * 0.6f) return 37; + else if (best_diff >= diff * 0.5f) + { + if (best_over == diff) return 35; + else if (best_over >= diff * 0.50f) return 25; + else return 20; + } + else if (best_diff >= diff * 0.4f) + { + if (best_over == diff) return 34; + else if (best_over >= diff * 0.50f) return 21; + else return 19; + } + else if (best_diff >= diff * 0.3f) + { + if (best_over == diff) return 33; + else if (best_over >= diff * 0.5f) return 18; + else return 16; + } + else if (best_diff >= diff * 0.2f) + { + if (best_over == diff) return 32; + else if (best_over >= diff * 0.5f) return 17; + else return 12; + } + else if (best_diff >= diff * 0.1f) + { + if (best_over == diff) return 31; + else if (best_over >= diff * 0.5f) return 14; + else return 9; + } + else if (best_diff > 0) + return (best_over >= diff * 0.5f) ? 11 : 2; + else + return (best_over >= diff * 0.5f) ? 1 : 0; + } + } + } + +private: + ScoringSchemeType m_sc; +}; + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/params.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/params.cpp new file mode 100644 index 0000000000000000000000000000000000000000..3c718cf7348da6d318ad9c9689867baa2a06ca6f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/params.cpp @@ -0,0 +1,363 @@ +#include +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +std::map load_options(const char* name) +{ + std::map options; + + FILE* file = fopen( name, "r" ); + if (file == NULL) + { + log_warning( stderr, "failed opening \"%s\"\n", name ); + return options; + } + + char key[1024]; + char value[1024]; + + while (fscanf( file, "%s %s", key, value ) == 2) + options[ key ] = std::string( value ); + + fclose( file ); + + return options; +} + +// bogus implementation of a function to check if a string is a number +bool is_number(const char* str, uint32 len = uint32(-1)) +{ + if (str[0] == '-') + ++str; + + for (uint32 l = 0; *str != '\0' && l < len; ++l) + { + const char c = *str; ++str; + if (c == '.') continue; + if (c >= '0' && c <= '9') continue; + return false; + } + return true; +} + +// bogus implementation of a function to check if an option is a function +SimpleFunc parse_function(const char* str, const SimpleFunc def) +{ + if (str[1] != ',') + return def; + + if (!(str[0] == 'C' || + str[0] == 'L' || + str[0] == 'G' || + str[0] == 'S')) + return def; + + SimpleFunc ret; + ret.type = (str[0] == 'C') ? SimpleFunc::LinearFunc : + (str[0] == 'L') ? SimpleFunc::LinearFunc : + (str[0] == 'G') ? SimpleFunc::LogFunc : + SimpleFunc::SqrtFunc; + + std::string nums = std::string( str + 2 ); + const size_t c = nums.find(','); + if (c == std::string::npos) + return def; + + if (is_number( nums.c_str(), (uint32)c ) == false) return def; + if (is_number( nums.c_str() + c + 1 ) == false) return def; + + const std::string num1 = nums.substr( 0, c ); + const std::string num2 = std::string( nums.c_str() + c + 1 ); + + ret.k = (float)atof( num1.c_str() ); + ret.m = (float)atof( nums.c_str() + c + 1 ); + + // take care of transforming constant functions in linear ones + if (str[0] == 'C') + { + //ret.k += ret.m; + ret.m = 0.0f; + } + return ret; +} + +template +SimpleFunc func_option(const options_type& options, const char* name, const SimpleFunc func) +{ + return (options.find( std::string(name) ) != options.end()) ? + parse_function( options.find(std::string(name))->second.c_str(), func ) : + func; +} + +template +SimpleFunc func_option(const options_type& options, const char* name1, const char* name2, const SimpleFunc func) +{ + return + (options.find( std::string(name1) ) != options.end()) ? + parse_function( options.find(std::string(name1))->second.c_str(), func ) : + (options.find( std::string(name2) ) != options.end()) ? + parse_function( options.find(std::string(name2))->second.c_str(), func ) : + func; +} + +void parse_options(Params& params, const std::map& options, bool init) +{ + const bool old_local = params.alignment_type == LocalAlignment; + const uint32 old_scoring_mode = params.scoring_mode; + + params.mode = mapping_mode( string_option(options, "mode", init ? "best" : mapping_mode( params.mode )).c_str() ); // mapping mode + params.scoring_mode = scoring_mode( string_option(options, "scoring", init ? "sw" : scoring_mode( params.scoring_mode )).c_str() ); // scoring mode + params.alignment_type = uint_option(options, "local", init ? 0u : params.alignment_type == LocalAlignment ) ? LocalAlignment : EndToEndAlignment; // local alignment + params.keep_stats = bool_option(options, "stats", init ? 1u : params.keep_stats); // keep stats + params.max_hits = uint_option(options, "max-hits", init ? 100u : params.max_hits); // too big = memory exhaustion + params.max_dist = uint_option(options, "max-dist", init ? 15u : params.max_dist); // must be <= MAX_BAND_LEN/2 + params.max_effort_init = uint_option(options, "max-effort-init", init ? 15u : params.max_effort_init); // initial scoring effort limit + params.max_effort = uint_option(options, "max-effort", "D", init ? 15u : params.max_effort); // scoring effort limit + params.min_ext = uint_option(options, "min-ext", init ? 30u : params.min_ext); // min # of extensions + params.max_ext = uint_option(options, "max-ext", init ? 400u : params.max_ext); // max # of extensions + params.max_reseed = uint_option(options, "max-reseed", "R", init ? 2u : params.max_reseed); // max # of reseeding rounds + params.rep_seeds = uint_option(options, "rep-seeds", init ? 300u : params.rep_seeds); // reseeding threshold + params.allow_sub = uint_option(options, "N", init ? 0u : params.allow_sub); // allow substitution in seed + params.mapq_filter = uint_option(options, "mapQ-filter", "Q", init ? 0u : params.mapq_filter); // filter anything below this + params.report = string_option(options, "report", init ? "" : params.report.c_str()); // generate a report file + params.scoring_file = string_option(options, "scoring-scheme", init ? "" : params.scoring_file.c_str()); + params.randomized = bool_option(options, "rand", init ? 1u : params.randomized); // use randomized selection + params.randomized =!bool_option(options, "no-rand", !params.randomized); // don't use randomized selection + params.top_seed = uint_option(options, "top", init ? 0u : params.top_seed); // explore top seed entirely + params.min_read_len = uint_option(options, "min-read-len", init ? 12u : params.min_read_len); // minimum read length + params.ungapped_mates = bool_option(options, "ungapped-mates", "ug", init ? 0u : params.ungapped_mates); // ungapped mate alignment + params.fw = !bool_option(options, "nofw", init ? false : !params.fw); // fw alignment + params.rc = !bool_option(options, "norc", init ? false : !params.rc); // rc alignment + + // force the all-mapping mode with the '--all|-a' option + if (uint_option(options, "all", "a", params.mode == AllMapping)) + params.mode = AllMapping; + + // force Edit-Distance scoring with the '--ed' option + if (uint_option(options, "ed", params.scoring_mode == EditDistanceMode)) + params.scoring_mode = EditDistanceMode; + + // force Smith-Waterman scoring with the '--sw' option + if (uint_option(options, "sw", params.scoring_mode == SmithWatermanMode)) + params.scoring_mode = SmithWatermanMode; + + const bool local = params.alignment_type == LocalAlignment; + + // set the default seeding values, or reset them if the alignment type has been changed + if (init || (local != old_local)) + { + params.seed_len = local ? 20 : 22u; + params.seed_freq = SimpleFunc( SimpleFunc::SqrtFunc, 1.0f, (local ? 0.75f : 1.15f) ); + } + + params.seed_len = uint_option(options, "seed-len", "L", params.seed_len); // no greater than 32 + params.seed_freq = func_option( options, "seed-freq", "i", params.seed_freq ); // seed interval + params.subseed_len = uint_option(options, "subseed-len", init ? 0u : params.subseed_len); // no greater than 32 + + params.pe_overlap = bool_option(options, "overlap", init ? true : params.pe_overlap); // paired-end overlap + params.pe_overlap = !bool_option(options, "no-overlap", !params.pe_overlap); // paired-end overlap + params.pe_dovetail = bool_option(options, "dovetail", init ? false : params.pe_dovetail); // paired-end dovetail + params.pe_unpaired = !bool_option(options, "no-mixed", init ? false :!params.pe_unpaired); // paired-end no-mixed + params.pe_discordant = !bool_option(options, "no-discordant", init ? false :!params.pe_discordant); // paired-end no-discordant + params.pe_discordant = bool_option(options, "discordant", params.pe_discordant); // paired-end discordant + params.min_frag_len = uint_option(options, "minins", "I", init ? 0u : params.min_frag_len); // paired-end minimum fragment length + params.max_frag_len = uint_option(options, "maxins", "X", init ? 500u : params.max_frag_len); // paired-end maximum fragment length + + // the maximum batch of reads processed in parallel + params.max_batch_size = uint_option(options, "batch-size", init ? 1024u : params.max_batch_size ); // maximum batch size + params.avg_read_length = uint_option(options, "read-length", init ? AVG_READ_LENGTH : params.avg_read_length ); // average read length + + // internal controls + params.scoring_window = uint_option(options, "scoring-window", init ? 32u : params.scoring_window); // scoring window size + params.debug.read_id = (uint32)int_option(options, "debug-read", init ? -1 : (int32)params.debug.read_id); // debug read id + params.debug.select = bool_option(options, "debug-select", init ? false: params.debug.select); // debug select kernel + params.debug.locate = bool_option(options, "debug-locate", init ? false: params.debug.locate); // debug locate kernel + params.debug.score = bool_option(options, "debug-score", init ? true : params.debug.score); // debug score kernel + params.debug.score_bad = bool_option(options, "debug-score-bad", init ? false: params.debug.score_bad); // debug score bad + params.debug.score_info = bool_option(options, "debug-score-info", init ? false: params.debug.score_info); // debug score info + params.debug.reduce = bool_option(options, "debug-reduce", init ? true : params.debug.reduce); // debug reduce kernel + params.debug.traceback = bool_option(options, "debug-traceback", init ? true : params.debug.traceback); // debug traceback kernel + params.debug.asserts = bool_option(options, "debug-asserts", init ? true : params.debug.asserts); // debug asserts + + params.persist_batch = int_option(options, "persist-batch", init ? -1 : params.persist_batch); // persist pass + params.persist_seeding = int_option(options, "persist-seeding", init ? -1 : params.persist_seeding); // persist pass + params.persist_extension = int_option(options, "persist-extension", init ? -1 : params.persist_extension); // persist pass + params.persist_file = string_option(options, "persist-file", init ? "" : params.persist_file.c_str() ); // persist file + + params.no_multi_hits = int_option(options, "no-multi-hits", init ? 0 : params.no_multi_hits ); // disable multi-hit selection + + params.max_effort_init = nvbio::max( params.max_effort_init, params.max_effort ); + params.max_ext = nvbio::max( params.max_ext, params.max_effort ); + + UberScoringScheme& sc = params.scoring_scheme; + + // set the default ED values, or reset them if the scoring mode has been changed + if (init || (params.scoring_mode != old_scoring_mode)) + sc.ed.m_score_min = SimpleFunc( SimpleFunc::LinearFunc, -(float)params.max_dist, 0.0f ); + + // set the default SW values, or reset them if the alignment type has been changed + if (init || (local != old_local)) + { + sc.sw = local ? + SmithWatermanScoringScheme<>::local() : + SmithWatermanScoringScheme<>(); + } + + // load scoring scheme from file + if (params.scoring_file != "") + sc.sw = load_scoring_scheme( params.scoring_file.c_str(), AlignmentType( params.alignment_type ) ); + + // score-min + sc.ed.m_score_min = func_option( options, "score-min", sc.ed.m_score_min ); + sc.sw.m_score_min = func_option( options, "score-min", sc.sw.m_score_min ); + + // match bonus + sc.sw.m_match.m_val = int_option( options, "ma", sc.sw.m_match.m_val ); + + // mismatch penalties + const int2 mp = int2_option( options, "mp", make_int2( sc.sw.m_mmp.m_max_val, sc.sw.m_mmp.m_min_val ) ); + sc.sw.m_mmp.m_max_val = mp.x; + sc.sw.m_mmp.m_min_val = mp.y; + + // np + sc.sw.m_np.m_val = int_option( options, "np", sc.sw.m_np.m_val ); + + // read gaps + const int2 rdg = int2_option( options, "rdg", make_int2( sc.sw.m_read_gap_const, sc.sw.m_read_gap_coeff ) ); + sc.sw.m_read_gap_const = rdg.x; + sc.sw.m_read_gap_coeff = rdg.y; + + // reference gaps + const int2 rfg = int2_option( options, "rfg", make_int2( sc.sw.m_ref_gap_const, sc.sw.m_ref_gap_coeff ) ); + sc.sw.m_ref_gap_const = rfg.x; + sc.sw.m_ref_gap_coeff = rfg.y; + + // presets + if (params.alignment_type == EndToEndAlignment) + { + if (uint_option(options, "very-fast", 0u)) + { + params.max_effort = 5u; + params.max_reseed = 1u; + params.seed_len = 22u; + params.seed_freq = SimpleFunc( SimpleFunc::SqrtFunc, 0.0f, 2.5f ); + } + if (uint_option(options, "fast", 0u)) + { + params.max_effort = 10u; + params.max_reseed = 2u; + params.seed_len = 22u; + params.seed_freq = SimpleFunc( SimpleFunc::SqrtFunc, 0.0f, 2.5f ); + } + if (uint_option(options, "sensitive", 0u)) + { + params.max_effort = 15u; + params.max_reseed = 2u; + params.seed_len = 22u; + params.seed_freq = SimpleFunc( SimpleFunc::SqrtFunc, 1.0f, 1.15f ); + } + if (uint_option(options, "very-sensitive", 0u)) + { + params.max_effort = 20u; + params.max_reseed = 3u; + params.seed_len = 20u; + params.seed_freq = SimpleFunc( SimpleFunc::SqrtFunc, 1.0f, 0.5f ); + } + + if (uint_option(options, "very-fast-local", 0u)) + { + if (uint_option(options, "end-to-end", 0u ) == 0) + { + params.alignment_type = LocalAlignment; + params.max_effort = 5u; + params.max_reseed = 1u; + params.seed_len = 25u; + params.seed_freq = SimpleFunc( SimpleFunc::SqrtFunc, 1.0f, 2.0f ); + } + else + log_warning(stderr, "--very-fast-local is incompatible with --end-to-end\n"); + } + if (uint_option(options, "fast-local", 0u)) + { + if (uint_option(options, "end-to-end", 0u ) == 0) + { + params.alignment_type = LocalAlignment; + params.max_effort = 10u; + params.max_reseed = 2u; + params.seed_len = 22u; + params.seed_freq = SimpleFunc( SimpleFunc::SqrtFunc, 1.0f, 1.75f ); + } + else + log_warning(stderr, "--fast-local is incompatible with --end-to-end\n"); + } + if (uint_option(options, "sensitive-local", 0u)) + { + if (uint_option(options, "end-to-end", 0u ) == 0) + { + params.alignment_type = LocalAlignment; + params.max_effort = 15u; + params.max_reseed = 2u; + params.seed_len = 20u; + params.seed_freq = SimpleFunc( SimpleFunc::SqrtFunc, 1.0f, 0.75f ); + } + else + log_warning(stderr, "--sensitive-local is incompatible with --end-to-end\n"); + } + if (uint_option(options, "very-sensitive-local", 0u)) + { + if (uint_option(options, "end-to-end", 0u ) == 0) + { + params.alignment_type = LocalAlignment; + params.max_effort = 20u; + params.max_reseed = 3u; + params.seed_len = 20u; + params.seed_freq = SimpleFunc( SimpleFunc::SqrtFunc, 1.0f, 0.5f ); + } + else + log_warning(stderr, "--very-sensitive-local is incompatible with --end-to-end\n"); + } + } + else + { + if (uint_option(options, "very-fast", "very-fast-local", 0u)) + { + params.max_effort = 5u; + params.max_reseed = 1u; + params.seed_len = 25u; + params.seed_freq = SimpleFunc( SimpleFunc::SqrtFunc, 1.0f, 2.0f ); + } + if (uint_option(options, "fast", "fast-local", 0u)) + { + params.max_effort = 10u; + params.max_reseed = 2u; + params.seed_len = 22u; + params.seed_freq = SimpleFunc( SimpleFunc::SqrtFunc, 1.0f, 1.75f ); + } + if (uint_option(options, "sensitive", "sensitive-local", 0u)) + { + params.max_effort = 15u; + params.max_reseed = 2u; + params.seed_len = 20u; + params.seed_freq = SimpleFunc( SimpleFunc::SqrtFunc, 1.0f, 0.75f ); + } + if (uint_option(options, "very-sensitive", "very-sensitive-local", 0u)) + { + params.max_effort = 20u; + params.max_reseed = 3u; + params.seed_len = 20u; + params.seed_freq = SimpleFunc( SimpleFunc::SqrtFunc, 1.0f, 0.5f ); + } + } +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/params.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/params.h new file mode 100644 index 0000000000000000000000000000000000000000..4f162c2b17551fb18ed4a9ca2af4c3169915da1c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/params.h @@ -0,0 +1,170 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +///@addtogroup nvBowtie +///@{ + +enum MappingMode { + BestMappingApprox = 0, + BestMappingExact = 1, + AllMapping = 2 +}; + +enum ScoringMode { + EditDistanceMode = 0, + SmithWatermanMode = 1, +}; + +static const char* s_mapping_mode[] = { + "best", + "best-exact", + "all" +}; +inline const char* mapping_mode(const uint32 mode) +{ + return s_mapping_mode[ mode ]; +} + +inline uint32 mapping_mode(const char* str) +{ + if (strcmp( str, "best" ) == 0) + return BestMappingApprox; + else if (strcmp( str, "best-exact" ) == 0) + return BestMappingExact; + else + return AllMapping; +} + +static const char* s_scoring_mode[] = { + "ed", + "sw" +}; +inline const char* scoring_mode(const uint32 mode) +{ + return s_scoring_mode[ mode ]; +} + +inline uint32 scoring_mode(const char* str) +{ + if (strcmp( str, "ed" ) == 0) + return EditDistanceMode; + else if (strcmp( str, "sw" ) == 0) + return SmithWatermanMode; + else + return EditDistanceMode; +} + +/// +/// A POD structure holding all of nvBowtie's parameters +/// +struct ParamsPOD +{ + bool keep_stats; + bool randomized; + bool fw; + bool rc; + uint32 mode; + uint32 scoring_mode; + uint32 alignment_type; + uint32 top_seed; + uint32 seed_len; + SimpleFunc seed_freq; + uint32 max_hits; + uint32 max_dist; + uint32 max_effort_init; + uint32 max_effort; + uint32 min_ext; + uint32 max_ext; + uint32 max_reseed; + uint32 rep_seeds; + uint32 allow_sub; + uint32 subseed_len; + uint32 mapq_filter; + uint32 min_read_len; + uint32 max_batch_size; + uint32 avg_read_length; + bool ungapped_mates; + + // paired-end options + uint32 pe_policy; + bool pe_overlap; + bool pe_dovetail; + bool pe_unpaired; + bool pe_discordant; + uint32 min_frag_len; + uint32 max_frag_len; + + // Scoring scheme + UberScoringScheme scoring_scheme; + + // Internal fields + uint32 scoring_window; + DebugState debug; +}; + +/// +/// A non-POD structure holding all of nvBowtie's parameters plus a few extra string options +/// +struct Params : public ParamsPOD +{ + std::string report; + std::string scoring_file; + + int32 persist_batch; + int32 persist_seeding; + int32 persist_extension; + std::string persist_file; + + int32 no_multi_hits; +}; + +/// +/// load options from a file +/// +std::map load_options(const char* name); + +/// +/// parse options +/// +void parse_options(Params& params, const std::map& options, bool init); + +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/persist.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/persist.cu new file mode 100644 index 0000000000000000000000000000000000000000..6359dc05f722cfe04b0006d6c177f66104f59b8e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/persist.cu @@ -0,0 +1,388 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +namespace { + +std::string mate_file_name(const std::string& file_name, const uint32 anchor) +{ + const size_t dot = file_name.find('.'); + if (dot == std::string::npos) + return file_name + (anchor ? ".2" : ".1"); + else + { + std::string output = file_name; + output.insert( dot, (anchor ? ".2" : ".1") ); + return output; + } +} + +} // anonymous namespace + +// clear the persisting files +// +void persist_clear(const std::string& file_name) +{ + // clear mate 0 + { + const std::string mate_file = mate_file_name( file_name, 0u ); + FILE* file = fopen( mate_file.c_str(), "w" ); fclose( file ); + } + // clear mate 1 + { + const std::string mate_file = mate_file_name( file_name, 0u ); + FILE* file = fopen( mate_file.c_str(), "w" ); fclose( file ); + } +} + +// compute a set of hits +// +void persist_hits( + const std::string& file_name, + const char* name, + const uint32 anchor, + const uint32 count, + const SeedHitDequeArray& hit_deques) +{ + // check whether we need to persist anything + if (file_name == "") + return; + + const std::string mate_file = mate_file_name( file_name, anchor ); + + FILE* file = fopen( mate_file.c_str(), "a+" ); + + SeedHitDequeArrayHostStorage hit_deques_h = static_cast( hit_deques ); + + fprintf( file, "\n---------------------------------------------------------------------------------\n" ); + fprintf( file, "%s\n", name ); + fprintf( file, "---------------------------------------------------------------------------------\n" ); + for (uint32 i = 0; i < count; ++i) + fprintf( file, "cnt[%u] = %u\n", i, uint32(hit_deques_h.m_counts[i]) ); + fprintf( file, "\n" ); + + for (uint32 i = 0; i < count; ++i) + { + const uint32 n_ranges = hit_deques_h.m_counts[i]; + const SeedHit* hits = &hit_deques_h.m_hits[0] + hit_deques_h.m_index[i]; + + fprintf( file, "hits[%u] = [%u]{\n", i, n_ranges ); + for (uint32 j = 0; j < n_ranges; ++j) + { + const SeedHit hit = hits[j]; + fprintf( file, " range[%u] = { (%u, %u - %u), dir[%u], pos[%u], rc[%u] }\n", + j, hit.get_range().x, hit.get_range().y, hit.get_range().y - hit.get_range().x, + hit.get_indexdir(), + hit.get_posinread(), + hit.get_readtype() ); + } + fprintf( file, "}\n" ); + } + fprintf( file, "\n" ); + + fclose( file ); +} + +// persist a set of reads +// +void persist_reads( + const std::string& file_name, + const char* name, + const uint32 anchor, + const uint32 count, + const thrust::device_vector::iterator iterator) +{ + // check whether we need to persist anything + if (file_name == "") + return; + + const std::string mate_file = mate_file_name( file_name, anchor ); + + FILE* file = fopen( mate_file.c_str(), "a+" ); + + thrust::host_vector hvec( count ); + thrust::copy( + iterator, + iterator + count, + hvec.begin() ); + + fprintf( file, "\n---------------------------------------------------------------------------------\n" ); + fprintf( file, "%s\n", name ); + fprintf( file, "---------------------------------------------------------------------------------\n" ); + for (uint32 i = 0; i < count; ++i) + fprintf( file, "read[%u] = %u\n", i, hvec[i] ); + fprintf( file, "\n" ); + + fclose( file ); +} + +// persist a set of selected hits +// +void persist_selection( + const std::string& file_name, + const char* name, + const uint32 anchor, + const uint32 read_count, + const packed_read* read_infos_dptr, + const uint32 n_multi, + const uint32 hits_queue_size, + const ReadHitsIndex& hits_index, + const HitQueues& hits_queue) +{ + // check whether we need to persist anything + if (file_name == "") + return; + + const std::string mate_file = mate_file_name( file_name, anchor ); + + FILE* file = fopen( mate_file.c_str(), "a+" ); + + fprintf( file, "\n---------------------------------------------------------------------------------\n" ); + fprintf( file, "%s\n", name ); + fprintf( file, "---------------------------------------------------------------------------------\n" ); + + thrust::host_vector loc_vec( hits_queue.loc ); + thrust::host_vector seed_vec( hits_queue.seed ); + + if (n_multi > 1) + { + const uint32 link_stride = hits_index.m_stride; + thrust::host_vector link_hvec( hits_index.m_links ); + thrust::host_vector read_infos_hvec( read_count ); + thrust::host_vector idx_hvec( read_count ); + + uint32* link_hptr = thrust::raw_pointer_cast( &link_hvec.front() ); + uint32* read_infos_hptr = (uint32*)thrust::raw_pointer_cast( &read_infos_hvec.front() ); + + cudaDeviceSynchronize(); + cudaMemcpy( read_infos_hptr, read_infos_dptr, read_count * sizeof(uint32), cudaMemcpyDeviceToHost ); + cudaDeviceSynchronize(); + + // sort the reads so as to show everything in the same order all the times + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + read_count, + idx_hvec.begin() ); + + thrust::sort_by_key( + read_infos_hvec.begin(), + read_infos_hvec.end(), + idx_hvec.begin() ); + + fprintf( file, "selection = [reads: %u - batch-size: %u - link-stride: %u]\n", read_count, n_multi, link_stride ); + for (uint32 i = 0; i < read_count; ++i) + { + const packed_read *read_info = (packed_read *)&read_infos_hvec[i]; + + const uint32 idx = idx_hvec[i]; + const uint32 n = link_hvec[idx]; + + fprintf( file, "read[%06u:%06u:%u] = [%02u]{", i, read_info->read_id, read_info->top_flag, n ); + if (n) + { + strided_iterator link_vec( link_hptr + idx + link_stride, link_stride ); + + for (uint32 j = 0; j < n; ++j) + { + const packed_seed seed = seed_vec[ link_vec[j] ]; + const uint32 loc = loc_vec[ link_vec[j] ]; + fprintf( file, " seed[pos:%u,dir:%u,rc:%u,top:%u,loc:%u]\n", (uint32)seed.pos_in_read, (uint32)seed.index_dir, (uint32)seed.rc, (uint32)seed.top_flag, loc ); + } + } + fprintf( file, "}\n" ); + } + } + else + { + thrust::host_vector read_infos_hvec( read_count ); + thrust::host_vector idx_hvec( read_count ); + + uint32* read_infos_hptr = (uint32*)thrust::raw_pointer_cast( &read_infos_hvec.front() ); + + cudaDeviceSynchronize(); + cudaMemcpy( read_infos_hptr, read_infos_dptr, read_count * sizeof(uint32), cudaMemcpyDeviceToHost ); + cudaDeviceSynchronize(); + + // sort the reads so as to show everything in the same order all the times + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + read_count, + idx_hvec.begin() ); + + thrust::sort_by_key( + read_infos_hvec.begin(), + read_infos_hvec.end(), + idx_hvec.begin() ); + + fprintf( file, "selection = [reads: %u - batch-size: 1]\n", read_count ); + for (uint32 i = 0; i < read_count; ++i) + { + const packed_read *read_info = (packed_read *)&read_infos_hvec[i]; + + const uint32 idx = idx_hvec[i]; + fprintf( file, "read[%06u:%06u:%u] = [%02u]{", i, read_info->read_id, read_info->top_flag, 1u ); + + const packed_seed seed = seed_vec[ idx ]; + const uint32 loc = loc_vec[ idx ]; + fprintf( file, " seed[pos:%u,dir:%u,rc:%u,top:%u,loc:%u]\n", (uint32)seed.pos_in_read, (uint32)seed.index_dir, (uint32)seed.rc, (uint32)seed.top_flag, loc ); + + fprintf( file, "}\n" ); + } + } + fclose( file ); +} + +// persist a set of scores +// +void persist_scores( + const std::string& file_name, + const char* name, + const uint32 anchor, + const uint32 read_count, + const uint32 n_multi, + const uint32 hits_queue_size, + const ScoringQueues& scoring_queues) +{ + // check whether we need to persist anything + if (file_name == "") + return; + + const std::string mate_file = mate_file_name( file_name, anchor ); + + FILE* file = fopen( mate_file.c_str(), "a+" ); + + fprintf( file, "\n---------------------------------------------------------------------------------\n" ); + fprintf( file, "%s\n", name ); + fprintf( file, "---------------------------------------------------------------------------------\n" ); + + thrust::host_vector read_infos_hvec( scoring_queues.active_reads.in_queue ); + thrust::host_vector score_hvec( scoring_queues.hits.score ); + + uint32* read_infos_hptr = (uint32*)thrust::raw_pointer_cast( &read_infos_hvec.front() ); + int32* score_hptr = thrust::raw_pointer_cast( &score_hvec.front() ); + + if (n_multi > 1) + { + const uint32 link_stride = scoring_queues.hits_index.m_stride; + thrust::host_vector link_hvec( scoring_queues.hits_index.m_links ); + thrust::host_vector idx_hvec( read_count ); + + uint32* link_hptr = thrust::raw_pointer_cast( &link_hvec.front() ); + + // sort the reads so as to show everything in the same order all the times + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + read_count, + idx_hvec.begin() ); + + thrust::sort_by_key( + read_infos_hptr, + read_infos_hptr + read_count, + idx_hvec.begin() ); + + fprintf( file, "scores = [reads: %u - batch-size: %u - link-stride: %u]\n", read_count, n_multi, link_stride ); + for (uint32 i = 0; i < read_count; ++i) + { + const packed_read *read_info = (packed_read *)&read_infos_hvec[i]; + + const uint32 idx = idx_hvec[i]; + const uint32 n = link_hvec[idx]; + if (n) + { + strided_iterator link_vec( link_hptr + idx + link_stride, link_stride ); + + fprintf( file, "read[%06u:%06u:%u] = {\n", i, read_info->read_id, read_info->top_flag ); + for (uint32 j = 0; j < n; ++j) + { + const uint32 link = link_vec[j]; + fprintf( file, " score[%04u] = %d\n", j, score_hvec[link] ); + } + fprintf( file, "}\n" ); + } + } + fprintf( file, "\n" ); + + // sort + thrust::sort( + score_hvec.begin(), + score_hvec.end() ); + + // write sorted score list + fprintf( file, "\n" ); + for (uint32 i = 0; i < hits_queue_size; ++i) + fprintf( file, "score[%u] = %d\n", i, score_hvec[i] ); + fprintf( file, "\n" ); + + int64 sum = 0; + for (uint32 i = 0; i < hits_queue_size; ++i) + sum += score_hvec[i]; + fprintf( file, "sum = %lld\n", sum ); + + // compute a crc + const char* ptr = (const char*)score_hptr; + const uint64 crc = crcCalc( ptr, sizeof(int32)*hits_queue_size ); + fprintf( file, "crc = %llu\n", crc ); + } + else + { + thrust::host_vector idx_hvec( read_count ); + + // sort the reads so as to show everything in the same order all the times + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + read_count, + idx_hvec.begin() ); + + thrust::sort_by_key( + read_infos_hptr, + read_infos_hptr + read_count, + idx_hvec.begin() ); + + for (uint32 i = 0; i < read_count; ++i) + { + const packed_read *read_info = (packed_read *)&read_infos_hvec[i]; + + const uint32 idx = idx_hvec[i]; + const uint32 score = score_hvec[idx]; + fprintf( file, "read[%06u:%06u:%u] : score[%d]\n", i, read_info->read_id, read_info->top_flag, score ); + } + fprintf( file, "\n" ); + } + fclose( file ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/persist.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/persist.h new file mode 100644 index 0000000000000000000000000000000000000000..7c9a52d351efa152e2f3ed825d4802d041f5db85 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/persist.h @@ -0,0 +1,93 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +struct SeedHit; +struct HitQueue; +struct SeedHitDequeArray; + +// clear the persisting files +// +void persist_clear(const std::string& file_name); + +// persist a set of hits +// +void persist_hits( + const std::string& file_name, + const char* name, + const uint32 anchor, + const uint32 count, + const SeedHitDequeArray& hit_deques); + +// persist a set of reads +// +void persist_reads( + const std::string& file_name, + const char* name, + const uint32 anchor, + const uint32 count, + const thrust::device_vector::iterator iterator); + +// persist a set of selected hits +// +void persist_selection( + const std::string& file_name, + const char* name, + const uint32 anchor, + const uint32 read_count, + const packed_read* read_infos_dptr, + const uint32 n_multi, + const uint32 hits_queue_size, + const ReadHitsIndex& hits_index, + const HitQueues& hits_queue); + +// persist a set of scores +// +void persist_scores( + const std::string& file_name, + const char* name, + const uint32 anchor, + const uint32 read_count, + const uint32 n_multi, + const uint32 hits_queue_size, + const ScoringQueues& scoring_queues); + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/pipeline_states.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/pipeline_states.h new file mode 100644 index 0000000000000000000000000000000000000000..4dbc377c53837c44b3b224333c2602aeb551d8e3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/pipeline_states.h @@ -0,0 +1,301 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +///@addtogroup nvBowtie +///@{ + +///@defgroup PipelineStates Pipeline States +/// +/// This module defines a set of classes that represent the state of the various pipelines on the device. +/// All their members are device-views - objects and arrays that can and should be dereferenced from +/// device kernels only. +/// +/// There are a few different classes, corresponding to different scoring and traceback pipelines: +/// +/// - BaseScoringPipelineState: the basic scoring pipeline class every scoring pipeline inherits from +/// - BestApproxScoringPipelineState: the best-approximate scoring pipeline +/// - TracebackPipelineState: the traceback pipeline +/// + +///@addtogroup PipelineStates +///@{ + +/// +/// Base pipeline state object that other scoring pipeline classes will inherit from (see \ref PipelineStates). +/// +template +struct BaseScoringPipelineState +{ + typedef Aligner::fmi_type fmi_type; + typedef Aligner::rfmi_type rfmi_type; + typedef Aligner::read_batch_type read_batch_type; + typedef Aligner::genome_iterator genome_iterator; + typedef ScoringScheme scheme_type; + + BaseScoringPipelineState( + const uint32 _anchor, + const read_batch_type _reads, + const read_batch_type _reads_o, + const uint32 _genome_len, + const genome_iterator _genome, + const fmi_type _fmi, + const rfmi_type _rfmi, + const ScoringScheme _scoring_scheme, + const int32 _score_limit, + Aligner& _aligner) : + anchor ( _anchor ), + reads ( _reads ), + reads_o ( _reads_o ), + genome_length ( _genome_len ), + genome ( _genome ), + fmi ( _fmi ), + rfmi ( _rfmi ), + hits ( _aligner.hit_deques.device_view() ), + scoring_queues ( _aligner.scoring_queues.device_view() ), + opposite_queue ( _aligner.opposite_queue_dptr ), + dp_buffer ( _aligner.dp_buffer_dptr ), + dp_buffer_size ( _aligner.dp_buffer_dvec.size() ), + scoring_scheme ( _scoring_scheme ), + score_limit ( _score_limit ) + {} + + /// return the set of reads corresponding to a given mate + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + const read_batch_type& get_reads(const uint32 mate) const { return mate ? reads_o : reads; } + + const uint32 anchor; + const read_batch_type reads; + const read_batch_type reads_o; + + const uint32 genome_length; + const genome_iterator genome; + + const fmi_type fmi; + const rfmi_type rfmi; + + SeedHitDequeArrayDeviceView hits; + + ScoringQueuesDeviceView scoring_queues; + + uint32 n_hits_per_read; + uint32 hits_queue_size; + uint32* idx_queue; + uint32 opposite_queue_size; + uint32* opposite_queue; + + uint8* dp_buffer; + uint64 dp_buffer_size; + + const ScoringScheme scoring_scheme; + const int32 score_limit; +}; + +/// +/// This object encapsulates the pipeline state for scoring best-approximate alignments (see \ref PipelineStates). +/// +template +struct BestApproxScoringPipelineState : public BaseScoringPipelineState +{ + typedef BaseScoringPipelineState base_type; + typedef Aligner::fmi_type fmi_type; + typedef Aligner::rfmi_type rfmi_type; + typedef Aligner::read_batch_type read_batch_type; + typedef Aligner::genome_iterator genome_iterator; + typedef ScoringScheme scheme_type; + + BestApproxScoringPipelineState( + const uint32 _anchor, + const read_batch_type _reads, + const read_batch_type _reads_o, + const uint32 _genome_len, + const genome_iterator _genome, + const fmi_type _fmi, + const rfmi_type _rfmi, + const ScoringScheme _scoring_scheme, + const int32 _score_limit, + Aligner& _aligner) : + base_type( + _anchor, + _reads, + _reads_o, + _genome_len, + _genome, + _fmi, + _rfmi, + _scoring_scheme, + _score_limit, + _aligner ), + trys ( _aligner.trys_dptr ), + rseeds ( _aligner.rseeds_dptr ), + best_alignments ( _aligner.best_data_dptr ), + best_alignments_o ( _aligner.best_data_dptr_o ), + best_stride ( _aligner.BATCH_SIZE ) + {} + + uint32* trys; + uint32* rseeds; + + io::Alignment* best_alignments; + io::Alignment* best_alignments_o; + uint32 best_stride; +}; + +/// +/// This object encapsulates the pipeline state for scoring best-approximate alignments (see \ref PipelineStates). +/// +template +struct AllMappingPipelineState : public BaseScoringPipelineState +{ + typedef BaseScoringPipelineState base_type; + typedef Aligner::fmi_type fmi_type; + typedef Aligner::rfmi_type rfmi_type; + typedef Aligner::read_batch_type read_batch_type; + typedef Aligner::genome_iterator genome_iterator; + typedef ScoringScheme scheme_type; + + AllMappingPipelineState( + const uint32 _anchor, + const read_batch_type _reads, + const read_batch_type _reads_o, + const uint32 _genome_len, + const genome_iterator _genome, + const fmi_type _fmi, + const rfmi_type _rfmi, + const ScoringScheme _scoring_scheme, + const int32 _score_limit, + Aligner& _aligner) : + base_type( + _anchor, + _reads, + _reads_o, + _genome_len, + _genome, + _fmi, + _rfmi, + _scoring_scheme, + _score_limit, + _aligner ), + output_read_info ( _aligner.output_read_info_dptr ), + buffer_read_info ( _aligner.buffer_read_info_dptr ), + buffer_alignments ( _aligner.buffer_alignments_dptr ), + cigar ( nvbio::device_view( _aligner.cigar ) ), + cigar_coords ( nvbio::device_view( _aligner.cigar_coords_dvec ) ), + mds ( nvbio::device_view( _aligner.mds ) ), + dp_buffer ( nvbio::device_view( _aligner.dp_buffer_dvec ) ), + dp_buffer_size ( _aligner.dp_buffer_dvec.size() ) + {} + + uint32* output_read_info; + uint32* buffer_read_info; + io::Alignment* buffer_alignments; + + nvbio::VectorArrayView cigar; ///< cigar arena + uint2* cigar_coords; ///< cigar coords + nvbio::VectorArrayView mds; ///< mds arena + + uint8* dp_buffer; ///< DP buffer + uint64 dp_buffer_size; ///< DP buffer size +}; + +/// +/// This object encapsulates the state of the pipeline during traceback. +/// As such, it includes references to the following objects: +/// +/// * the reads for both mates +/// * the genome iterator +/// * the CIGAR and MD string arenas +/// * the temporary DP buffer +/// +template +struct TracebackPipelineState +{ + typedef Aligner::read_batch_type read_batch_type; + typedef Aligner::genome_iterator genome_iterator; + typedef ScoringScheme scheme_type; + + /// constructor + /// + /// \param _reads1 the reads corresponding to mate #1 + /// \param _reads2 the reads corresponding to mate #2 + /// \param _genome_len the length of the genome + /// \param _genome the genome iterator + /// \param _aligner the aligner object + TracebackPipelineState( + const read_batch_type _reads1, + const read_batch_type _reads2, + const uint32 _genome_len, + const genome_iterator _genome, + const ScoringScheme _scoring_scheme, + Aligner& _aligner) : + reads ( _reads1 ), + reads_o ( _reads2 ), + genome_length ( _genome_len ), + genome ( _genome ), + scoring_scheme ( _scoring_scheme ), + cigar ( nvbio::device_view( _aligner.cigar ) ), + cigar_coords ( nvbio::device_view( _aligner.cigar_coords_dvec ) ), + mds ( nvbio::device_view( _aligner.mds ) ), + dp_buffer ( nvbio::device_view( _aligner.dp_buffer_dvec ) ), + dp_buffer_size ( _aligner.dp_buffer_dvec.size() ) + {} + + /// return the set of reads corresponding to a given mate + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + const read_batch_type& get_reads(const uint32 mate) const { return mate ? reads_o : reads; } + + const read_batch_type reads; ///< first mates + const read_batch_type reads_o; ///< second mates + + const uint32 genome_length; ///< genome length + const genome_iterator genome; ///< genome iterator + + const ScoringScheme scoring_scheme; ///< scoring scheme + + nvbio::VectorArrayView cigar; ///< cigar arena + uint2* cigar_coords; ///< cigar coords + nvbio::VectorArrayView mds; ///< mds arena + + uint8* dp_buffer; ///< DP buffer + uint64 dp_buffer_size; ///< DP buffer size +}; + +///@} // group PipelineStates +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reads_def.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reads_def.h new file mode 100644 index 0000000000000000000000000000000000000000..b5fb1a0274c56f303b1f7f99da87f4d75e6216cd --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reads_def.h @@ -0,0 +1,49 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +struct ReadsDef +{ + typedef typename binary_switch::type read_storage_type; + typedef typename binary_switch,USE_TEX_READS>::type read_base_type; + typedef typename binary_switch, USE_TEX_READS>::type read_qual_type; + typedef io::SequenceDataViewCore read_view_type; + typedef io::SequenceDataAccess type; +}; + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reduce.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reduce.cu new file mode 100644 index 0000000000000000000000000000000000000000..3627870a465db0f925d2c41ec0254f5efb4df366 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reduce.cu @@ -0,0 +1,87 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/// +///\file reduce.cu +/// + +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +/// +/// Reduce the scores associated to each read in the scoring queue to find the best 2 alignments. +/// +void score_reduce( + const ReduceBestApproxContext context, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params) +{ + score_reduce_t( context, pipeline, params ); +} + +/// +/// Reduce the scores associated to each read in the scoring queue to find the best 2 alignments. +/// +void score_reduce( + const ReduceBestApproxContext context, + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params) +{ + score_reduce_t( context, pipeline, params ); +} + +/// +/// Reduce the scores associated to each paired-end read in the scoring queue to find the best 2 alignments. +/// +void score_reduce_paired( + const ReduceBestApproxContext context, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params) +{ + score_reduce_paired_t( context, pipeline, params ); +} + +/// +/// Reduce the scores associated to each paired-end read in the scoring queue to find the best 2 alignments. +/// +void score_reduce_paired( + const ReduceBestApproxContext context, + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params) +{ + score_reduce_paired_t( context, pipeline, params ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reduce.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reduce.h new file mode 100644 index 0000000000000000000000000000000000000000..64f18797cf79fbe2a12985b9bb816bbe4f6e0118 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reduce.h @@ -0,0 +1,172 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/// +///\file reduce.h +/// + +#pragma once + +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +struct ParamsPOD; + +template struct BaseScoringPipelineState; +template struct BestApproxScoringPipelineState; + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Reduce +///@{ + +/// +/// A context class for the score_reduce_kernel to be used in best-approx pipeline. +/// +/// \details +/// Implements the basic extension bail-out mechanisms of Bowtie2, namely stopping +/// when a given number of extensions of a read failed in a row. +/// This is done keeping a vector of per-read extension 'trys' counters, which +/// start from the maximum allowed number, and get decremented towards zero upon +/// each failure, or reset upon successful extensions. +/// +struct ReduceBestApproxContext +{ + /// constructor + /// + /// \param trys trys vector + /// \param n_ext total number of extensions (i.e. extension loops) already performed + /// + ReduceBestApproxContext(uint32* trys, const uint32 n_ext) : m_trys( trys ), m_ext( n_ext ) {} + + /// this method is called from score_reduce_kernel to report updates to the best score. + /// + NVBIO_FORCEINLINE NVBIO_DEVICE + void best_score(const uint32 read_id, const ParamsPOD& params) const + { + // reset the try counter + m_trys[ read_id ] = params.max_effort; + } + /// this method is called from score_reduce_kernel to report updates to the second best score. + /// + NVBIO_FORCEINLINE NVBIO_DEVICE + void second_score(const uint32 read_id, const ParamsPOD& params) const + { + // reset the try counter + m_trys[ read_id ] = params.max_effort; + } + /// this method is called from score_reduce_kernel to report extension failures. + /// + NVBIO_FORCEINLINE NVBIO_DEVICE + bool failure(const uint32 idx, const uint32 read_id, const uint32 top_flag, const ParamsPOD& params) const + { + if (m_trys[ read_id ] > 0) + { + if (((m_ext+idx >= params.min_ext) && (top_flag == 0) && (--m_trys[ read_id ] == 0)) || // bowtie2 does 1 more alignment than effort limit, we don't + (m_ext+idx >= params.max_ext)) + return true; + } + return false; + } + +private: + uint32* m_trys; + uint32 m_ext; +}; + +/// +/// A context class for the score_reduce_kernel to be used in best-exact pipeline. +/// +/// \details +/// A trivial implementation, that never bails out. +/// +struct ReduceBestExactContext +{ + ReduceBestExactContext() {} + + /// this method is called from score_reduce_kernel to report updates to the best score. + /// + NVBIO_FORCEINLINE NVBIO_DEVICE + void best_score(const uint32 read_id, const ParamsPOD& params) const {} + + /// this method is called from score_reduce_kernel to report updates to the second best score. + /// + NVBIO_FORCEINLINE NVBIO_DEVICE + void second_score(const uint32 read_id, const ParamsPOD& params) const {} + + /// this method is called from score_reduce_kernel to report extension failures. + /// + NVBIO_FORCEINLINE NVBIO_DEVICE + bool failure(const uint32 idx, const uint32 read_id, const uint32 top_flag, const ParamsPOD& params) const { return false; } +}; + +/// +/// Reduce the scores associated to each read in the scoring queue to find the best 2 alignments. +/// +void score_reduce( + const ReduceBestApproxContext context, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params); + +/// +/// Reduce the scores associated to each read in the scoring queue to find the best 2 alignments. +/// +void score_reduce( + const ReduceBestApproxContext context, + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params); + +/// +/// Reduce the scores associated to each paired-end read in the scoring queue to find the best 2 alignments. +/// +void score_reduce_paired( + const ReduceBestApproxContext context, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params); + +/// +/// Reduce the scores associated to each paired-end read in the scoring queue to find the best 2 alignments. +/// +void score_reduce_paired( + const ReduceBestApproxContext context, + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params); + +///@} // group Reduce +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio + +#include diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reduce_impl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reduce_impl.h new file mode 100644 index 0000000000000000000000000000000000000000..2db8f354ec91059f1805469344cfcd47719b310c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reduce_impl.h @@ -0,0 +1,79 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/// +///\file reduce.h +/// + +#pragma once + +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +template struct BaseScoringPipelineState; +template struct BestApproxScoringPipelineState; + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Reduce +///@{ + +/// +/// Reduce the scores associated to each read in the scoring queue to find the best 2 alignments. +/// +template +void score_reduce_t( + const ReduceContext context, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params); + +/// +/// Reduce the scores associated to each paired-end read in the scoring queue to find the best 2 alignments. +/// +template +void score_reduce_paired_t( + const ReduceContext context, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params); + +///@} // group Reduce +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio + +#include diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reduce_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reduce_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..91f4696d33657abb669b0fad3a3be5bf3993e0ed --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/reduce_inl.h @@ -0,0 +1,541 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/// +///\file reduce_inl.h +/// + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +namespace detail { + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Reduce +///@{ + +///@addtogroup ReduceDetail +///@{ + +/// +/// +/// Reduce the list of scores associated to each read in the input queue to find +/// the best 2 alignments. +/// +/// \details +/// this kernel takes a batch of extension results (one per active read, indexed by a sorting id) +/// and 'reduces' them with best 2 results found so far. +/// The kernel is parameterized by a templated context which can take further actions upon +/// updates to the best or second best scores, as well as bailing-out on failures. +/// +/// \param context the template context +/// \param pipeline the pipeline state +/// \param params algorithm parameters +/// +template __global__ +void score_reduce_kernel( + const ReduceContext context, + PipelineType pipeline, + const ParamsPOD params) +{ + typedef ScoringQueuesDeviceView scoring_queues_type; + typedef ReadHitsReference read_hits_type; + typedef typename read_hits_type::reference hit_type; + + scoring_queues_type& scoring_queues = pipeline.scoring_queues; + + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= scoring_queues.active_read_count()) return; + + // fetch the active read corresponding to this thread + read_hits_type read_hits( scoring_queues, thread_id ); + + const uint32 read_id = read_hits.read_info().read_id; + + // fetch the best alignments + io::BestAlignments best( + pipeline.best_alignments[ read_id ], + pipeline.best_alignments[ read_id + pipeline.best_stride ] ); + + // setup the read stream + const uint2 read_range = pipeline.reads.get_range(read_id); + const uint32 read_len = read_range.y - read_range.x; + + const uint32 count = read_hits.size(); + + for (uint32 i = 0; i < count; ++i) + { + hit_type hit = read_hits[i]; + NVBIO_CUDA_DEBUG_ASSERT( hit.read_id == read_id, "reduce hit[%u][%u]: expected id %u, got: %u (slot: %u)\n", thread_id, i, read_id, hit.read_id, scoring_queues.hits_index( thread_id, i )); + + const packed_seed seed_info = hit.seed; + const uint32 read_rc = seed_info.rc; + const uint32 top_flag = seed_info.top_flag; + + const int32 score = hit.score; + const uint32 g_pos = hit.loc; + + // skip locations that we have already visited without paying the extension attempt + if ((read_rc == best.m_a1.m_rc && g_pos == best.m_a1.m_align) || + (read_rc == best.m_a2.m_rc && g_pos == best.m_a2.m_align)) + continue; + + if (score > best.m_a1.score()) + { + context.best_score( read_id, params ); + + // set the first best score + best.m_a2 = best.m_a1; + best.m_a1 = io::Alignment( g_pos, 0u, score, read_rc ); + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_reduce( read_id ), "update best: (parent[%u:%u])\n score[%d], rc[%u], pos[%u]\n", thread_id, i, score, read_rc, g_pos ); + } + else if ((score > best.m_a2.score()) && io::distinct_alignments( best.m_a1.m_align, best.m_a1.m_rc, g_pos, read_rc, read_len/2 )) + { + context.second_score( read_id, params ); + + // set the second best score + best.m_a2 = io::Alignment( g_pos, 0u, score, read_rc ); + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_reduce( read_id ), "update second: (parent[%u:%u])\n score[%d], rc[%u], pos[%u]\n", thread_id, i, score, read_rc, g_pos ); + } + else if (context.failure( i, read_id, top_flag, params )) + { + // stop traversal + pipeline.hits.erase( read_id ); + + // NOTE: we keep using the score entries rather than breaking here, + // as we've already gone through the effort of computing them, and + // this reduction is only a minor amount of work. + } + } + + // report best alignments + pipeline.best_alignments[ read_id ] = best.m_a1; + pipeline.best_alignments[ read_id + pipeline.best_stride ] = best.m_a2; +} + +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +void update_best( + const uint32 read_id, + io::BestPairedAlignments& best_pairs, + const io::PairedAlignments& pair, + ReduceContext& context, + const ParamsPOD params) +{ + context.best_score( read_id, params ); + + // the old best becomes second-best, and the second-best gets updated + best_pairs.m_a2 = best_pairs.m_a1; + best_pairs.m_o2 = best_pairs.m_o1; + best_pairs.m_a1 = pair.m_a; + best_pairs.m_o1 = pair.m_o; + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_reduce( read_id ), "update best (anchor[%u]):\n 1. score[%d], rc[%u], pos[%u]\n 2. score[%d], rc[%u], pos[%u,%u]\n", pair.m_a.mate(), pair.m_a.score(), pair.m_a.is_rc(), pair.m_a.alignment(), pair.m_o.score(), pair.m_o.is_rc(), pair.m_o.alignment(), pair.m_o.alignment() + pair.m_o.sink() ); +} + +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +void replace_best( + const uint32 read_id, + io::BestPairedAlignments& best_pairs, + const io::PairedAlignments& pair, + ReduceContext& context, + const ParamsPOD params) +{ + context.best_score( read_id, params ); + + best_pairs.m_a1 = pair.m_a; + best_pairs.m_o1 = pair.m_o; + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_reduce( read_id ), "update best (anchor[%u]):\n 1. score[%d], rc[%u], pos[%u]\n 2. score[%d], rc[%u], pos[%u,%u]\n", pair.m_a.mate(), pair.m_a.score(), pair.m_a.is_rc(), pair.m_a.alignment(), pair.m_o.score(), pair.m_o.is_rc(), pair.m_o.alignment, pair.m_o.alignment() + pair.m_o.sink() ); +} + +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +void update_second( + const uint32 read_id, + io::BestPairedAlignments& best_pairs, + const io::PairedAlignments& pair, + ReduceContext& context, + const ParamsPOD params) +{ + context.second_score( read_id, params ); + + best_pairs.m_a2 = pair.m_a; + best_pairs.m_o2 = pair.m_o; + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_reduce( read_id ), "update second (anchor[%u]):\n 1. score[%d], rc[%u], pos[%u]\n 2. score[%d], rc[%u], pos[%u,%u]\n", pair.m_a.mate(), pair.m_a.score(), pair.m_a.is_rc(), pair.m_a.alignment(), pair.m_o.score(), pair.m_o.is_rc(), pair.m_o.alignment, pair.m_o.alignment() + pair.m_o.sink() ); +} + +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +bool try_update( + const uint32 read_id, + io::BestPairedAlignments& best_pairs, + const io::PairedAlignments& pair, + const uint32 min_distance, + ReduceContext& context, + const ParamsPOD params) +{ + const int32 score = pair.score(); + + // sometimes, we might find an alignment which is better than what previously found, despite not being distinct from it... + if (distinct_alignments( best_pairs.pair<0>(), pair, min_distance ) == false) + { + // this alignment is a candidate for replacing the best one + // + + if (score > best_pairs.best_score()) + replace_best( read_id, best_pairs, pair, context, params ); + + // skip locations that we have already visited, without paying the extension attempt + return true; + } + else if (distinct_alignments( best_pairs.pair<1>(), pair, min_distance ) == false) + { + // this alignment is a candidate for replacing the second-best one + // + + if (score > best_pairs.best_score()) // is it better than the best? + update_best( read_id, best_pairs, pair, context, params ); + else if (score > best_pairs.second_score()) // is it better than the second-best? + update_second( read_id, best_pairs, pair, context, params ); + + // skip locations that we have already visited, without paying the extension attempt + return true; + } + // check if the best alignment was unpaired or had a worse score + else if (best_pairs.is_paired() == false || score > best_pairs.best_score()) + { + update_best( read_id, best_pairs, pair, context, params ); + return true; + } // check if the second-best alignment was unpaired or had a worse score + else if (best_pairs.has_second_paired() == false || score > best_pairs.second_score()) + { + update_second( read_id, best_pairs, pair, context, params ); + return true; + } + return false; +} + +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +void update_best( + const uint32 read_id, + io::Alignment& a1, + io::Alignment& a2, + const io::Alignment& a, + ReduceContext& context, + const ParamsPOD params) +{ + context.best_score( read_id, params ); // pretend we did find something useful, even though for unpaired alignments + + a2 = a1; + a1 = a; + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_reduce( read_id ), "update best unpaired[%u]:\n 1. score[%d], rc[%u], pos[%u]\n", a.mate(), a.score(), a.is_rc(), a.alignment() ); +} + +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +void replace_best( + const uint32 read_id, + io::Alignment& a1, + io::Alignment& a2, + const io::Alignment& a, + ReduceContext& context, + const ParamsPOD params) +{ + context.best_score( read_id, params ); // pretend we did find something useful, even though for unpaired alignments + + a1 = a; + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_reduce( read_id ), "update best unpaired[%u]:\n 1. score[%d], rc[%u], pos[%u]\n", a.mate(), a.score(), a.is_rc(), a.alignment() ); +} + +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +void update_second( + const uint32 read_id, + io::Alignment& a1, + io::Alignment& a2, + const io::Alignment& a, + ReduceContext& context, + const ParamsPOD params) +{ + context.second_score( read_id, params ); // pretend we did find something useful, even though for unpaired alignments + + a2 = a; + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_reduce( read_id ), "update second unpaired[%u]:\n score[%d], rc[%u], pos[%u]\n", a.mate(), i, a.score(), a.is_rc(), a.alignment() ); +} + +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +bool try_update( + const uint32 read_id, + io::Alignment& a1, + io::Alignment& a2, + const io::Alignment& a, + const uint32 min_distance, + ReduceContext& context, + const ParamsPOD params) +{ + // sometimes, we might find an alignment which is better than what previously found, despite not being distinct from it... + if (distinct_alignments( a1, a, min_distance ) == false) + { + // this alignment is a candidate for replacing the best one + // + + if (a.score() > a1.score()) + replace_best( read_id, a1, a2, a, context, params ); + + // skip locations that we have already visited, without paying the extension attempt + return true; + } + else if (distinct_alignments( a2, a, min_distance ) == false) + { + // this alignment is a candidate for replacing the second-best one + // + + if (a.score() > a1.score()) // is it better than the best? + update_best( read_id, a1, a2, a, context, params ); + else if (a.score() > a2.score()) // is it better than the second-best? + update_second( read_id, a1, a2, a, context, params ); + + // skip locations that we have already visited, without paying the extension attempt + return true; + } + else if (a.score() > a1.score()) + { + update_best( read_id, a1, a2, a, context, params ); + return true; + } + else if (a.score() > a2.score()) + { + update_second( read_id, a1, a2, a, context, params ); + return true; + } + return false; +} + +/// +/// Reduce the list of scores associated to each read in the input queue to find +/// the best 2 alignments. +/// +/// \details +/// this kernel takes a batch of extension results (one per active read, indexed by a sorting id) +/// and 'reduces' them with best 2 results found so far. +/// The kernel is parameterized by a templated context which can take further actions upon +/// updates to the best or second best scores, as well as bailing-out on failures. +/// +/// \param context the template context +/// \param pipeline the pipeline state +/// \param params algorithm parameters +/// +template __global__ +void score_reduce_paired_kernel( + const ReduceContext context, + PipelineType pipeline, + const ParamsPOD params) +{ + typedef ScoringQueuesDeviceView scoring_queues_type; + typedef ReadHitsReference read_hits_type; + typedef typename read_hits_type::reference hit_type; + + scoring_queues_type& scoring_queues = pipeline.scoring_queues; + + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= scoring_queues.active_read_count()) return; + + const uint32 anchor = pipeline.anchor; + + // fetch the active read corresponding to this thread + read_hits_type read_hits( scoring_queues, thread_id ); + + const uint32 read_id = read_hits.read_info().read_id; + + // fetch current best alignments + io::BestPairedAlignments best_pairs = io::BestPairedAlignments( + io::BestAlignments( pipeline.best_alignments[ read_id ], + pipeline.best_alignments[ read_id + pipeline.best_stride ] ), + io::BestAlignments( pipeline.best_alignments_o[ read_id ], + pipeline.best_alignments_o[ read_id + pipeline.best_stride ] ) ); + + // setup the read stream + const uint2 read_range = pipeline.reads.get_range(read_id); + const uint32 read_len = read_range.y - read_range.x; + + const uint32 count = read_hits.size(); + + // sort the entries in the score queue so that we process them in the order they were selected + for (uint32 i = 0; i < count; ++i) + { + hit_type hit = read_hits[i]; + NVBIO_CUDA_DEBUG_ASSERT( hit.read_id == read_id, "reduce hit[%u][%u]: expected id %u, got: %u (slot: %u)\n", thread_id, i, read_id, hit.read_id, read_hits.slot(i) ); + + const packed_seed seed_info = hit.seed; + const uint32 read_rc = seed_info.rc; + const uint32 top_flag = seed_info.top_flag; + + const uint2 g_pos = make_uint2( hit.loc, hit.sink ); + const int32 score_a = hit.score; + const int32 score_o = hit.opposite_score; + const int32 score_o2 = hit.opposite_score2; + //const int32 score = score_a + score_o; + //const int32 score2 = score_a + score_o2; + + // compute opposite mate placement & orientation + bool o_left; + bool o_fw; + + detail::frame_opposite_mate( + params.pe_policy, + anchor, + !read_rc, + o_left, + o_fw ); + + const uint2 o_g_pos = make_uint2( hit.opposite_loc, hit.opposite_sink ); + const uint2 o_g_pos2 = make_uint2( hit.opposite_loc, hit.opposite_sink2 ); + const uint32 o_read_rc = !o_fw; + + const io::PairedAlignments pair( + io::Alignment( g_pos.x, g_pos.y - g_pos.x, score_a, read_rc, anchor, score_o > pipeline.score_limit ), + io::Alignment( o_g_pos.x, o_g_pos.y - o_g_pos.x, score_o, o_read_rc, !anchor, score_o > pipeline.score_limit ) ); + + const io::PairedAlignments pair2( + io::Alignment( g_pos.x, g_pos.y - g_pos.x, score_a, read_rc, anchor, score_o2 > pipeline.score_limit ), + io::Alignment( o_g_pos2.x, o_g_pos2.y - o_g_pos2.x, score_o2, o_read_rc, !anchor, score_o2 > pipeline.score_limit ) ); + + bool updated = false; + + const uint32 min_distance = read_len/4; + + if (pair.is_paired()) + { + if (try_update( read_id, best_pairs, pair, min_distance, context, params )) + updated = true; + + // and now rinse & repeat with the second hit + if (pair2.is_paired()) + { + if (try_update( read_id, best_pairs, pair2, min_distance, context, params )) + updated = true; + } + } + else if ((params.pe_unpaired == true) && (best_pairs.is_paired() == false)) + { + // + // We didn't find a paired alignment yet - hence we proceed keeping track of the best unpaired alignments + // for the first and second mate separately. + // We store best two alignments for the first mate in best_pairs.m_a*, and the ones of the second mate in best_pairs.m_o*. + // + + const io::Alignment& a = pair.m_a; + io::Alignment& a1 = anchor ? best_pairs.m_o1 : best_pairs.m_a1; + io::Alignment& a2 = anchor ? best_pairs.m_o2 : best_pairs.m_a2; + + // + // update the first mate alignments + // + + if (try_update( read_id, a1, a2, a, min_distance, context, params )) + updated = true; + } + + if ((updated == false) && context.failure( i, read_id, top_flag, params )) + { + // stop traversal + pipeline.hits.erase( read_id ); + //NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_reduce( read_id ), "discard: (parent[%u:%u])\n score[%d + %d], rc[%u], pos[%u]\n", anchor, thread_id, i, score_a, score_o, read_rc, g_pos ); + } + } + + // report best alignments + pipeline.best_alignments[ read_id ] = best_pairs.m_a1; + pipeline.best_alignments[ read_id + pipeline.best_stride ] = best_pairs.m_a2; + pipeline.best_alignments_o[ read_id ] = best_pairs.m_o1; + pipeline.best_alignments_o[ read_id + pipeline.best_stride ] = best_pairs.m_o2; +} + +///@} // group ReduceDetail +///@} // group Reduce +///@} // group nvBowtie + +} // namespace detail + +// +// Reduce the scores associated to each read in the input queue to find +// the best 2 alignments. +// +template +void score_reduce_t( + const ReduceContext context, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params) +{ + typedef BestApproxScoringPipelineState pipeline_type; + + const int blocks = (pipeline.scoring_queues.active_reads.in_size + BLOCKDIM-1) / BLOCKDIM; + + detail::score_reduce_kernel <<>>( + context, + pipeline, + params ); +} + +// +// call the scoring kernel +// +template +void score_reduce_paired_t( + const ReduceContext context, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params) +{ + typedef BestApproxScoringPipelineState pipeline_type; + + const int blocks = (pipeline.scoring_queues.active_reads.in_size + BLOCKDIM-1) / BLOCKDIM; + + detail::score_reduce_paired_kernel <<>>( + context, + pipeline, + params ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score.cu new file mode 100644 index 0000000000000000000000000000000000000000..1d50832807bb2a8c196680f435ecd1cb4b6d5d6d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score.cu @@ -0,0 +1,212 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// +// execute a batch of single-ended banded-alignment score calculations, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// +// \b outputs: +// - HitQueues::score +// - HitQueues::sink +// +void score_best( + const uint32 band_len, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params) +{ + score_best_t( band_len, pipeline, params ); +} + +// +// execute a batch of single-ended banded-alignment score calculations, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// +// \b outputs: +// - HitQueues::score +// - HitQueues::sink +// +void score_best( + const uint32 band_len, + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params) +{ + score_best_t( band_len, pipeline, params ); +} + +// +// execute a batch of single-ended banded-alignment score calculations, all-mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// +// \b outputs: +// - HitQueues::score +// - HitQueues::sink +// +// \param band_len alignment band length +// \param pipeline all mapping pipeline +// \param params alignment params +// \param buffer_offset ring buffer offset +// \param buffer_size ring buffer size +// \return number of valid alignments +uint32 score_all( + const uint32 band_len, + const AllMappingPipelineState& pipeline, + const ParamsPOD& params, + const uint32 buffer_offset, + const uint32 buffer_size) +{ + return score_all_t( band_len, pipeline, params, buffer_offset, buffer_size ); +} + +// +// execute a batch of single-ended banded-alignment score calculations, all-mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// +// \b outputs: +// - HitQueues::score +// - HitQueues::sink +// +// \param band_len alignment band length +// \param pipeline all mapping pipeline +// \param params alignment params +// \param buffer_offset ring buffer offset +// \param buffer_size ring buffer size +// \return number of valid alignments +uint32 score_all( + const uint32 band_len, + const AllMappingPipelineState >& pipeline, + const ParamsPOD& params, + const uint32 buffer_offset, + const uint32 buffer_size) +{ + return score_all_t( band_len, pipeline, params, buffer_offset, buffer_size ); +} + +// +// execute a batch of banded-alignment score calculations for the anchor mates, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// +// \b outputs: +// - HitQueues::score +// - HitQueues::sink +// +void anchor_score_best( + const uint32 band_len, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params) +{ + anchor_score_best_t( band_len, pipeline, params ); +} + +// +// execute a batch of banded-alignment score calculations for the anchor mates, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// +// \b outputs: +// - HitQueues::score +// - HitQueues::sink +// +void anchor_score_best( + const uint32 band_len, + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params) +{ + anchor_score_best_t( band_len, pipeline, params ); +} + +// +// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// - HitQueues::score +// - HitQueues::sink +// +// \b outputs: +// - HitQueues::opposite_score +// - HitQueues::opposite_loc +// - HitQueues::opposite_sink +// +void opposite_score_best( + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params) +{ + opposite_score_best_t( pipeline, params ); +} + +// +// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// - HitQueues::score +// - HitQueues::sink +// +// \b outputs: +// - HitQueues::opposite_score +// - HitQueues::opposite_loc +// - HitQueues::opposite_sink +// +void opposite_score_best( + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params) +{ + opposite_score_best_t( pipeline, params ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score.h new file mode 100644 index 0000000000000000000000000000000000000000..ba410ecfb674426979d3eb29aaaa4fe6b684ceb3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score.h @@ -0,0 +1,221 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +struct ParamsPOD; + +template struct BaseScoringPipelineState; +template struct BestApproxScoringPipelineState; +template struct AllMappingPipelineState; + +///@addtogroup nvBowtie +///@{ + +/// \defgroup Scoring +/// +/// The functions in this module implement a pipeline stage in which all the seed hits currently +/// in the \ref ScoringQueues get "extended" and scored using DP alignment against the reference genome. +/// +/// \b inputs: +/// - HitQueues::seed +/// - HitQueues::loc +/// +/// \b outputs: +/// - HitQueues::score +/// - HitQueues::sink +/// - HitQueues::opposite_score +/// - HitQueues::opposite_loc +/// - HitQueues::opposite_sink +/// + +///@addtogroup Scoring +///@{ + +/// +/// execute a batch of single-ended banded-alignment score calculations, best mapping +/// +/// \b inputs: +/// - HitQueues::seed +/// - HitQueues::loc +/// +/// \b outputs: +/// - HitQueues::score +/// - HitQueues::sink +/// +void score_best( + const uint32 band_len, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params); + +/// +/// execute a batch of single-ended banded-alignment score calculations, best mapping +/// +/// \b inputs: +/// - HitQueues::seed +/// - HitQueues::loc +/// +/// \b outputs: +/// - HitQueues::score +/// - HitQueues::sink +/// +void score_best( + const uint32 band_len, + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params); + +/// +/// execute a batch of single-ended banded-alignment score calculations, all-mapping +/// +/// \b inputs: +/// - HitQueues::seed +/// - HitQueues::loc +/// +/// \b outputs: +/// - HitQueues::score +/// - HitQueues::sink +/// +/// \param band_len alignment band length +/// \param pipeline all mapping pipeline +/// \param params alignment params +/// \param buffer_offset ring buffer offset +/// \param buffer_size ring buffer size +/// \return number of valid alignments +uint32 score_all( + const uint32 band_len, + const AllMappingPipelineState& pipeline, + const ParamsPOD& params, + const uint32 buffer_offset, + const uint32 buffer_size); + +/// +/// execute a batch of single-ended banded-alignment score calculations, all-mapping +/// +/// \b inputs: +/// - HitQueues::seed +/// - HitQueues::loc +/// +/// \b outputs: +/// - HitQueues::score +/// - HitQueues::sink +/// +/// \param band_len alignment band length +/// \param pipeline all mapping pipeline +/// \param params alignment params +/// \param buffer_offset ring buffer offset +/// \param buffer_size ring buffer size +/// \return number of valid alignments +uint32 score_all( + const uint32 band_len, + const AllMappingPipelineState >& pipeline, + const ParamsPOD& params, + const uint32 buffer_offset, + const uint32 buffer_size); + +/// +/// execute a batch of banded-alignment score calculations for the anchor mates, best mapping +/// +/// \b inputs: +/// - HitQueues::seed +/// - HitQueues::loc +/// +/// \b outputs: +/// - HitQueues::score +/// - HitQueues::sink +/// +void anchor_score_best( + const uint32 band_len, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params); + +/// +/// execute a batch of banded-alignment score calculations for the anchor mates, best mapping +/// +/// \b inputs: +/// - HitQueues::seed +/// - HitQueues::loc +/// +/// \b outputs: +/// - HitQueues::score +/// - HitQueues::sink +/// +void anchor_score_best( + const uint32 band_len, + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params); + +/// +/// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping +/// +/// \b inputs: +/// - HitQueues::seed +/// - HitQueues::loc +/// - HitQueues::score +/// - HitQueues::sink +/// +/// \b outputs: +/// - HitQueues::opposite_score +/// - HitQueues::opposite_loc +/// - HitQueues::opposite_sink +/// +void opposite_score_best( + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params); + +/// +/// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping +/// +/// \b inputs: +/// - HitQueues::seed +/// - HitQueues::loc +/// - HitQueues::score +/// - HitQueues::sink +/// +/// \b outputs: +/// - HitQueues::opposite_score +/// - HitQueues::opposite_loc +/// - HitQueues::opposite_sink +/// +void opposite_score_best( + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params); + +///@} // group Scoring +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_all.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_all.cu new file mode 100644 index 0000000000000000000000000000000000000000..8de6d162bb5aeaa6e0af6000a17120ad2eb558c9 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_all.cu @@ -0,0 +1,94 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// +// execute a batch of single-ended banded-alignment score calculations, all-mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// +// \b outputs: +// - HitQueues::score +// - HitQueues::sink +// +// \param band_len alignment band length +// \param pipeline all mapping pipeline +// \param params alignment params +// \param buffer_offset ring buffer offset +// \param buffer_size ring buffer size +// \return number of valid alignments +uint32 score_all( + const uint32 band_len, + const AllMappingPipelineState& pipeline, + const ParamsPOD& params, + const uint32 buffer_offset, + const uint32 buffer_size) +{ + return score_all_t( band_len, pipeline, params, buffer_offset, buffer_size ); +} + +// +// execute a batch of single-ended banded-alignment score calculations, all-mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// +// \b outputs: +// - HitQueues::score +// - HitQueues::sink +// +// \param band_len alignment band length +// \param pipeline all mapping pipeline +// \param params alignment params +// \param buffer_offset ring buffer offset +// \param buffer_size ring buffer size +// \return number of valid alignments +uint32 score_all( + const uint32 band_len, + const AllMappingPipelineState >& pipeline, + const ParamsPOD& params, + const uint32 buffer_offset, + const uint32 buffer_size) +{ + return score_all_t( band_len, pipeline, params, buffer_offset, buffer_size ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_all_impl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_all_impl.h new file mode 100644 index 0000000000000000000000000000000000000000..49863ae9b518d96f7acf3fb76bdb460289c2a69f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_all_impl.h @@ -0,0 +1,79 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +template struct BaseScoringPipelineState; +template struct BestApproxScoringPipelineState; + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Scoring +///@{ + +/// +/// execute a batch of single-ended banded-alignment score calculations, all-mapping +/// +/// \b inputs: +/// - HitQueues::seed +/// - HitQueues::loc +/// +/// \b outputs: +/// - HitQueues::score +/// - HitQueues::sink +/// +/// \param band_len alignment band length +/// \param pipeline all mapping pipeline +/// \param params alignment params +/// \param buffer_offset ring buffer offset +/// \param buffer_size ring buffer size +/// \return number of valid alignments +template +uint32 score_all_t( + const uint32 band_len, + const AllMappingPipelineState& pipeline, + const ParamsPOD params, + const uint32 buffer_offset, + const uint32 buffer_size); + +///@} // group Scoring +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio + +#include diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_all_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_all_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..b998fa16ceb5c9be5108f8812b2febdd6932b1c7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_all_inl.h @@ -0,0 +1,277 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +namespace detail { + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Scoring +///@{ + +///@addtogroup ScoringDetail +///@{ + +/// +/// A scoring stream, fetching the input hits to score from the hit queue +/// indexed by the input sorting order, and assigning them their score and sink +/// attributes. +/// +template +struct AllScoreStream : public AlignmentStreamBase +{ + typedef AlignmentStreamBase base_type; + typedef typename base_type::context_type context_type; + typedef typename base_type::scheme_type scheme_type; + + /// constructor + /// + /// \param _band_len effective band length; + /// NOTE: this value must match the template BAND_LEN parameter + /// used for instantiating aln::BatchedBandedAlignmentScore. + /// + /// \param _pipeline the pipeline object + /// + /// \param _aligner the aligner object + /// + AllScoreStream( + const uint32 _band_len, + const PipelineType _pipeline, + const AlignerType _aligner, + const ParamsPOD _params, + const uint32 _buffer_offset, + const uint32 _buffer_size, + uint32* _counter) : + base_type( _pipeline, _aligner, _params ), m_band_len( _band_len ), + m_buffer_offset( _buffer_offset ), + m_buffer_size( _buffer_size ), + m_counter( _counter ) {} + + /// return the maximum pattern length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 max_pattern_length() const { return base_type::m_pipeline.reads.max_sequence_len(); } + + /// return the maximum text length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 max_text_length() const { return base_type::m_pipeline.reads.max_sequence_len() + m_band_len; } + + /// return the stream size + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 size() const { return base_type::m_pipeline.hits_queue_size; } + + /// initialize the i-th context + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool init_context( + const uint32 i, + context_type* context) const + { + context->idx = base_type::m_pipeline.idx_queue[i]; + + // initialize the sink + context->sink = aln::BestSink(); + + // fetch the hit to process + HitReference hit = base_type::m_pipeline.scoring_queues.hits[ context->idx ]; + + // setup the read info + context->mate = 0; + context->read_rc = hit.seed.rc; + context->read_id = hit.read_id; + context->read_range = base_type::m_pipeline.reads.get_range( context->read_id ); + + // setup the genome range + const uint32 g_pos = hit.loc; + + const uint32 read_len = context->read_range.y - context->read_range.x; + context->genome_begin = g_pos > m_band_len/2 ? g_pos - m_band_len/2 : 0u; + context->genome_end = nvbio::min( context->genome_begin + m_band_len + read_len, base_type::m_pipeline.genome_length ); + + // setup the minimum score + context->min_score = base_type::m_pipeline.scoring_scheme.min_score( read_len ); + return true; + } + + /// handle the output + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void output( + const uint32 i, + const context_type* context) const + { + const aln::BestSink sink = context->sink; + + // append all valid alignments to a list + if (sink.score >= context->min_score) + { + HitReference hit = base_type::m_pipeline.scoring_queues.hits[ context->idx ]; + + #if defined(NVBIO_DEVICE_COMPILATION) + const uint32 slot = atomicAdd( m_counter, 1u ); + #else + const uint32 slot = (*m_counter)++; + #endif + base_type::m_pipeline.buffer_read_info[ (m_buffer_offset + slot) % m_buffer_size ] = hit.read_id; //(hit.read_id << 1) | hit.seed.rc; + base_type::m_pipeline.buffer_alignments[ (m_buffer_offset + slot) % m_buffer_size ] = io::Alignment( hit.loc, 0u, sink.score, hit.seed.rc ); + // TODO: rewrite hit.loc + // hit.loc = context->genome_begin; + NVBIO_CUDA_DEBUG_PRINT_IF( base_type::m_params.debug.show_score( context->read_id, (sink.score >= context->min_score) ), "score: %d (rc[%u], pos[%u], [qid %u])]\n", sink.score, context->read_rc, context->genome_begin, i ); + } + } + + const uint32 m_band_len; + const uint32 m_buffer_offset; + const uint32 m_buffer_size; + uint32* m_counter; +}; + +/// +/// dispatch the execution of a batch of single-ended banded-alignment score calculations +/// +template +void banded_score_all( + const uint32 band_len, + const pipeline_type& pipeline, + const aligner_type aligner, + const ParamsPOD params, + const uint32 buffer_offset, + const uint32 buffer_size, + uint32* counter) +{ + const uint32 static_band_len = + (band_len < 4) ? 3u : + (band_len < 8) ? 7u : + (band_len < 16) ? 15u : + 31u; + + typedef AllScoreStream stream_type; + + stream_type stream( + static_band_len, + pipeline, + aligner, + params, + buffer_offset, + buffer_size, + counter ); + + //typedef aln::DeviceThreadScheduler scheduler_type; + typedef aln::DeviceStagedThreadScheduler scheduler_type; + + if (band_len < 4) + { + aln::BatchedBandedAlignmentScore<3u,stream_type,scheduler_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else if (band_len < 8) + { + aln::BatchedBandedAlignmentScore<7u,stream_type,scheduler_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else if (band_len < 16) + { + aln::BatchedBandedAlignmentScore<15u,stream_type,scheduler_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else + { + aln::BatchedBandedAlignmentScore<31u,stream_type,scheduler_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } +} + +///@} // group ScoringDetail +///@} // group Scoring +///@} // group nvBowtie + +} // namespace detail + +// +// execute a batch of single-ended banded-alignment score calculations, best mapping +// +// \param band_len alignment band length +// \param pipeline all mapping pipeline +// \param params alignment params +// \param buffer_offset ring buffer offset +// \param buffer_size ring buffer size +// \return number of valid alignments +template +uint32 score_all_t( + const uint32 band_len, + const AllMappingPipelineState& pipeline, + const ParamsPOD params, + const uint32 ring_offset, + const uint32 ring_size) +{ + thrust::device_vector counter(1,0); + + if (params.alignment_type == LocalAlignment) + { + detail::banded_score_all( + band_len, + pipeline, + pipeline.scoring_scheme.local_aligner(), + params, + ring_offset, + ring_size, + nvbio::device_view(counter) ); + } + else + { + detail::banded_score_all( + band_len, + pipeline, + pipeline.scoring_scheme.end_to_end_aligner(), + params, + ring_offset, + ring_size, + nvbio::device_view(counter) ); + } + //cudaDeviceSynchronize(); + //nvbio::cuda::check_error("score kernel"); + return counter[0]; +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_best.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_best.cu new file mode 100644 index 0000000000000000000000000000000000000000..6da0adbe7bc1f86cb05230bad2611b1e55b3c202 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_best.cu @@ -0,0 +1,78 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// +// execute a batch of single-ended banded-alignment score calculations, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// +// \b outputs: +// - HitQueues::score +// - HitQueues::sink +// +void score_best( + const uint32 band_len, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params) +{ + score_best_t( band_len, pipeline, params ); +} + +// +// execute a batch of single-ended banded-alignment score calculations, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// +// \b outputs: +// - HitQueues::score +// - HitQueues::sink +// +void score_best( + const uint32 band_len, + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params) +{ + score_best_t( band_len, pipeline, params ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_best_impl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_best_impl.h new file mode 100644 index 0000000000000000000000000000000000000000..ee593347c2727948468d6f4912e3fdb7ce77b4ee --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_best_impl.h @@ -0,0 +1,71 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +template struct BaseScoringPipelineState; +template struct BestApproxScoringPipelineState; + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Scoring +///@{ + +/// +/// execute a batch of single-ended banded-alignment score calculations, best mapping +/// +/// \b inputs: +/// - HitQueues::seed +/// - HitQueues::loc +/// +/// \b outputs: +/// - HitQueues::score +/// - HitQueues::sink +/// +template +void score_best_t( + const uint32 band_len, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params); + +///@} // group Scoring +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio + +#include diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_best_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_best_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..78b829092c623c1cf6d36ba7711e5cabb3375479 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_best_inl.h @@ -0,0 +1,238 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +namespace detail { + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Scoring +///@{ + +///@addtogroup ScoringDetail +///@{ + +/// +/// A scoring stream, fetching the input hits to score from the hit queue +/// indexed by the input sorting order, and assigning them their score and sink +/// attributes. +/// +template +struct BestScoreStream : public AlignmentStreamBase +{ + typedef AlignmentStreamBase base_type; + typedef typename base_type::context_type context_type; + typedef typename base_type::scheme_type scheme_type; + + /// constructor + /// + /// \param _band_len effective band length; + /// NOTE: this value must match the template BAND_LEN parameter + /// used for instantiating aln::BatchedBandedAlignmentScore. + /// + /// \param _pipeline the pipeline object + /// + /// \param _aligner the aligner object + /// + BestScoreStream( + const uint32 _band_len, + const PipelineType _pipeline, + const AlignerType _aligner, + const ParamsPOD _params) : + base_type( _pipeline, _aligner, _params ), m_band_len( _band_len ) {} + + /// return the maximum pattern length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 max_pattern_length() const { return base_type::m_pipeline.reads.max_read_len(); } + + /// return the maximum text length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 max_text_length() const { return base_type::m_pipeline.reads.max_read_len() + m_band_len; } + + /// return the stream size + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 size() const { return base_type::m_pipeline.hits_queue_size; } + + /// initialize the i-th context + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool init_context( + const uint32 i, + context_type* context) const + { + context->idx = base_type::m_pipeline.idx_queue[i]; + + // fetch the hit to process + HitReference hit = base_type::m_pipeline.scoring_queues.hits[ context->idx ]; + + // setup the read info + context->mate = 0u; + context->read_rc = hit.seed.rc; + context->read_id = hit.read_id; + context->read_range = base_type::m_pipeline.reads.get_range( context->read_id ); + + // setup the genome range + const uint32 g_pos = hit.loc; + + const uint32 read_len = context->read_range.y - context->read_range.x; + context->genome_begin = g_pos > m_band_len/2 ? g_pos - m_band_len/2 : 0u; + context->genome_end = nvbio::min( context->genome_begin + m_band_len + read_len, base_type::m_pipeline.genome_length ); + + // initialize the sink + context->sink = aln::BestSink(); + + // setup the minimum score + const io::Alignment second_best = base_type::m_pipeline.best_alignments[ context->read_id + base_type::m_pipeline.best_stride ]; + context->min_score = nvbio::max( second_best.score(), base_type::m_pipeline.score_limit ); + + NVBIO_CUDA_DEBUG_PRINT_IF( base_type::m_params.debug.show_score_info( context->read_id ), "score-min: %d (rc[%u], pos[%u], [qid %u])]\n", context->min_score, context->read_rc, context->genome_begin, i ); + return true; + } + + /// handle the output + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void output( + const uint32 i, + const context_type* context) const + { + // write the final hit.score and hit.sink attributes + HitReference hit = base_type::m_pipeline.scoring_queues.hits[ context->idx ]; + + const aln::BestSink sink = context->sink; + hit.score = nvbio::max( sink.score, scheme_type::worst_score ); + hit.sink = context->genome_begin + sink.sink.x; + + // TODO: rewrite hit.loc + // hit.loc = context->genome_begin; + NVBIO_CUDA_DEBUG_PRINT_IF( base_type::m_params.debug.show_score( context->read_id, (sink.score >= context->min_score) ), "score: %d (rc[%u], pos[%u], [qid %u])]\n", sink.score, context->read_rc, context->genome_begin, i ); + } + + const uint32 m_band_len; +}; + +/// +/// dispatch the execution of a batch of single-ended banded-alignment score calculations +/// +template +void banded_score_best( + const uint32 band_len, + const pipeline_type& pipeline, + const aligner_type aligner, + const ParamsPOD params) +{ + const uint32 static_band_len = + (band_len < 4) ? 3u : + (band_len < 8) ? 7u : + (band_len < 16) ? 15u : + 31u; + + typedef BestScoreStream stream_type; + + stream_type stream( + static_band_len, + pipeline, + aligner, + params ); + + typedef aln::DeviceThreadScheduler scheduler_type; + //typedef aln::DeviceStagedThreadScheduler scheduler_type; + + if (band_len < 4) + { + aln::BatchedBandedAlignmentScore<3u,stream_type,scheduler_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else if (band_len < 8) + { + aln::BatchedBandedAlignmentScore<7u,stream_type,scheduler_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else if (band_len < 16) + { + aln::BatchedBandedAlignmentScore<15u,stream_type,scheduler_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else + { + aln::BatchedBandedAlignmentScore<31u,stream_type,scheduler_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } +} + +///@} // group ScoringDetail +///@} // group Scoring +///@} // group nvBowtie + +} // namespace detail + +// +// execute a batch of single-ended banded-alignment score calculations, best mapping +// +template +void score_best_t( + const uint32 band_len, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params) +{ + if (params.alignment_type == LocalAlignment) + { + detail::banded_score_best( + band_len, + pipeline, + pipeline.scoring_scheme.local_aligner(), + params ); + } + else + { + detail::banded_score_best( + band_len, + pipeline, + pipeline.scoring_scheme.end_to_end_aligner(), + params ); + } +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_gapped.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_gapped.cu new file mode 100644 index 0000000000000000000000000000000000000000..a07e3f594e06acdd5c936f6731924826e6bf8d20 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_gapped.cu @@ -0,0 +1,106 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// +// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping +// +template +void gapped_opposite_score_best_t( + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params) +{ + if (params.alignment_type == LocalAlignment) + { + detail::opposite_score_best( + pipeline, + pipeline.scoring_scheme.local_aligner(), + params ); + } + else + { + detail::opposite_score_best( + pipeline, + pipeline.scoring_scheme.end_to_end_aligner(), + params ); + } +} + +// +// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// - HitQueues::score +// - HitQueues::sink +// +// \b outputs: +// - HitQueues::opposite_score +// - HitQueues::opposite_loc +// - HitQueues::opposite_sink +// +void gapped_opposite_score_best( + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params) +{ + gapped_opposite_score_best_t( pipeline, params ); +} + +// +// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// - HitQueues::score +// - HitQueues::sink +// +// \b outputs: +// - HitQueues::opposite_score +// - HitQueues::opposite_loc +// - HitQueues::opposite_sink +// +void gapped_opposite_score_best( + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params) +{ + gapped_opposite_score_best_t( pipeline, params ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_opposite_impl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_opposite_impl.h new file mode 100644 index 0000000000000000000000000000000000000000..67aa93e1849068bf88c0a838f066bc57386a3952 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_opposite_impl.h @@ -0,0 +1,73 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +template struct BaseScoringPipelineState; +template struct BestApproxScoringPipelineState; + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Scoring +///@{ + +/// +/// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping +/// +/// \b inputs: +/// - HitQueues::seed +/// - HitQueues::loc +/// - HitQueues::score +/// - HitQueues::sink +/// +/// \b outputs: +/// - HitQueues::opposite_score +/// - HitQueues::opposite_loc +/// - HitQueues::opposite_sink +/// +template +void opposite_score_best_t( + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params); + +///@} // group Scoring +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio + +#include diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_opposite_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_opposite_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..82fed39ed33f4ed6bb092c075a18733f62902470 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_opposite_inl.h @@ -0,0 +1,280 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +namespace detail { + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Scoring +///@{ + +///@addtogroup ScoringDetail +///@{ + +/// +/// A scoring stream, fetching the input hits to score from the hit queue +/// indexed by the input sorting order, and assigning them their score and sink +/// attributes. +/// +template +struct BestOppositeScoreStream : public AlignmentStreamBase +{ + typedef AlignmentStreamBase base_type; + typedef typename base_type::context_type context_type; + typedef typename base_type::scheme_type scheme_type; + + /// constructor + /// + /// \param _band_len effective band length; + /// NOTE: this value must match the template BAND_LEN parameter + /// used for instantiating aln::BatchedBandedAlignmentScore. + /// + /// \param _pipeline the pipeline object + /// + /// \param _aligner the aligner object + /// + BestOppositeScoreStream( + const PipelineType _pipeline, + const AlignerType _aligner, + const ParamsPOD _params) : + base_type( _pipeline, _aligner, _params ) {} + + /// return the maximum pattern length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 max_pattern_length() const { return base_type::m_pipeline.reads_o.max_sequence_len(); } + + /// return the maximum text length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 max_text_length() const { return base_type::m_params.max_frag_len; } + + /// return the stream size + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 size() const { return base_type::m_pipeline.opposite_queue_size; } + + /// initialize the i-th context + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool init_context( + const uint32 i, + context_type* context) const + { + context->idx = base_type::m_pipeline.idx_queue[ base_type::m_pipeline.opposite_queue[i] ]; + + // initialize score and sink + context->sink.invalidate(); + + // fetch the hit to process + HitReference hit = base_type::m_pipeline.scoring_queues.hits[ context->idx ]; + + const uint32 read_rc = hit.seed.rc; + const uint32 read_id = hit.read_id; + + const uint32 g_pos = hit.loc; + + const uint2 a_read_range = base_type::m_pipeline.reads.get_range( read_id ); + const uint32 a_len = a_read_range.y - a_read_range.x; + const int32 a_optimal_score = base_type::m_pipeline.scoring_scheme.perfect_score( a_len ); + const int32 a_worst_score = base_type::m_pipeline.scoring_scheme.min_score( a_len ); + + const uint2 o_read_range = base_type::m_pipeline.reads_o.get_range( read_id ); + const uint32 o_len = o_read_range.y - o_read_range.x; + const int32 o_optimal_score = base_type::m_pipeline.scoring_scheme.perfect_score( o_len ); + const int32 o_worst_score = base_type::m_pipeline.scoring_scheme.min_score( o_len ); + + // compute the pair score threshold + const int32 anchor_score = hit.score; + + const io::BestPairedAlignments best = io::BestPairedAlignments( + io::BestAlignments( base_type::m_pipeline.best_alignments[ read_id ], base_type::m_pipeline.best_alignments[ read_id + base_type::m_pipeline.best_stride ] ), + io::BestAlignments( base_type::m_pipeline.best_alignments_o[ read_id ], base_type::m_pipeline.best_alignments_o[ read_id + base_type::m_pipeline.best_stride ] ) ); + + const int32 target_pair_score = nvbio::min( + compute_target_score( best, a_worst_score, o_worst_score ) + 1, + a_optimal_score + o_optimal_score ); + + int32 target_mate_score = target_pair_score - anchor_score; + + #if 1 + // + // bound the score of this mate by the worst score allowed for its own read length. + // NOTE: disabling this is equivalent to allowing a worst score proportional to the total + // length of the read pair. + // + + target_mate_score = nvbio::max( target_mate_score, o_worst_score ); + #endif + + // assign the final score threshold + context->min_score = nvbio::max( target_mate_score, base_type::m_pipeline.score_limit ); + + #if DP_REPORT_MULTIPLE + context->sink.set_min_score( context->min_score ); + #endif + + // check if it's even possible to reach the score threshold + if (context->min_score > o_optimal_score) + { + NVBIO_CUDA_DEBUG_PRINT_IF( base_type::m_params.debug.show_score( context->read_id, false ), "score opposite: min-score too high: %d > %d (mate[%u], rc[%u], [qid %u])\n", context->min_score, o_optimal_score, base_type::m_pipeline.anchor ? 0u : 1u, context->read_rc, i ); + return false; + } + + // frame the alignment + bool o_left; + bool o_fw; + + frame_opposite_mate( + base_type::m_params.pe_policy, + base_type::m_pipeline.anchor, + !read_rc, + o_left, + o_fw ); + + // setup the read info + context->mate = 1u; + context->read_rc = !o_fw; + context->read_id = read_id; + context->read_range = o_read_range; + + // FIXME: re-implement the logic of Bowtie2's otherMate() function! + const int32 max_ref_gaps = aln::max_text_gaps( base_type::aligner(), context->min_score, o_len ); + const uint32 o_gapped_len = o_len + max_ref_gaps; + + if (o_left) + { + const uint32 max_end = g_pos + a_len + o_gapped_len > base_type::m_params.min_frag_len ? g_pos + a_len + o_gapped_len - base_type::m_params.min_frag_len : 0u; + context->genome_begin = g_pos + a_len > base_type::m_params.max_frag_len ? (g_pos + a_len) - base_type::m_params.max_frag_len : 0u; + context->genome_end = base_type::m_params.pe_overlap ? g_pos + a_len : g_pos; + context->genome_end = nvbio::min( context->genome_end, max_end ); + } + else + { + const uint32 min_begin = g_pos + base_type::m_params.min_frag_len > o_gapped_len ? g_pos + base_type::m_params.min_frag_len - o_gapped_len : 0u; + context->genome_end = g_pos + base_type::m_params.max_frag_len; + context->genome_begin = base_type::m_params.pe_overlap ? g_pos : g_pos + a_len; + context->genome_begin = nvbio::max( context->genome_begin, min_begin ); + } + context->genome_end = nvbio::min( context->genome_end, base_type::m_pipeline.genome_length ); + + // don't align if completely outside genome + if (context->genome_begin >= base_type::m_pipeline.genome_length) + return false; + + // bound against genome end + context->genome_end = nvbio::min( context->genome_end, base_type::m_pipeline.genome_length ); + + // skip locations that we have already visited + const uint32 mate = base_type::m_pipeline.anchor ? 0u : 1u; + const bool skip = (mate == best.m_a1.m_mate && (context->read_rc == best.m_a1.m_rc && g_pos == best.m_a1.m_align)) || + (mate == best.m_o1.m_mate && (context->read_rc == best.m_o1.m_rc && g_pos == best.m_o1.m_align)) || + (mate == best.m_a2.m_mate && (context->read_rc == best.m_a2.m_rc && g_pos == best.m_a2.m_align)) || + (mate == best.m_o2.m_mate && (context->read_rc == best.m_o2.m_rc && g_pos == best.m_o2.m_align)) || + (context->genome_begin == context->genome_end); + + return !skip; + } + + /// handle the output + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void output( + const uint32 i, + const context_type* context) const + { + // write the final hit.score and hit.sink attributes + HitReference hit = base_type::m_pipeline.scoring_queues.hits[ context->idx ]; + + #if DP_REPORT_MULTIPLE + const aln::BestColumnSink& sink = context->sink; + uint32 best_idx1, best_idx2; + + sink.best2( best_idx1, best_idx2, (context->read_range.y - context->read_range.x) / 2u ); + + const uint32 genome_sink = sink.sinks[best_idx1].x != uint32(-1) ? sink.sinks[best_idx1].x : 0u; + const uint32 genome_sink2 = sink.sinks[best_idx2].x != uint32(-1) ? sink.sinks[best_idx2].x : 0u; + + hit.opposite_score = (sink.scores[best_idx1] >= context->min_score) ? sink.scores[best_idx1] : scheme_type::worst_score; + hit.opposite_score2 = (sink.scores[best_idx2] >= context->min_score) ? sink.scores[best_idx2] : scheme_type::worst_score; + #else + const aln::BestSink sink = context->sink; + const uint32 genome_sink = sink.sink.x != uint32(-1) ? sink.sink.x : 0u; + const uint32 genome_sink2 = 0u; + + hit.opposite_score = (sink.score >= context->min_score) ? sink.score : scheme_type::worst_score; + hit.opposite_score2 = scheme_type::worst_score; + #endif + + hit.opposite_loc = context->genome_begin; + hit.opposite_sink = context->genome_begin + genome_sink; + hit.opposite_sink2 = context->genome_begin + genome_sink2; + NVBIO_CUDA_DEBUG_PRINT_IF( base_type::m_params.debug.show_score( context->read_id, (sink.score >= context->min_score) ), "score opposite: %d (min[%d], mate[%u], rc[%u], pos[%u:%u], [qid %u])\n", sink.score, context->min_score, base_type::m_pipeline.anchor ? 0u : 1u, context->read_rc, context->genome_begin, context->genome_end, i ); + } +}; + +/// +/// dispatch the execution of a batch of alignment score calculations for the opposite mates +/// +template +void opposite_score_best( + const pipeline_type& pipeline, + const aligner_type aligner, + const ParamsPOD params) +{ + typedef BestOppositeScoreStream stream_type; + + stream_type stream( + pipeline, + aligner, + params ); + + aln::BatchedAlignmentScore > batch; + //aln::BatchedAlignmentScore batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); +} + +///@} // group ScoringDetail +///@} // group Scoring +///@} // group nvBowtie + +} // namespace detail + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_paired.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_paired.cu new file mode 100644 index 0000000000000000000000000000000000000000..ebc026cbced2d710ed68c3851576e70e24c464b0 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_paired.cu @@ -0,0 +1,142 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// +// execute a batch of banded-alignment score calculations for the anchor mates, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// +// \b outputs: +// - HitQueues::score +// - HitQueues::sink +// +void anchor_score_best( + const uint32 band_len, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params) +{ + anchor_score_best_t( band_len, pipeline, params ); +} + +// +// execute a batch of banded-alignment score calculations for the anchor mates, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// +// \b outputs: +// - HitQueues::score +// - HitQueues::sink +// +void anchor_score_best( + const uint32 band_len, + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params) +{ + anchor_score_best_t( band_len, pipeline, params ); +} + +void ungapped_opposite_score_best( + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params); + +void ungapped_opposite_score_best( + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params); + +void gapped_opposite_score_best( + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params); + +void gapped_opposite_score_best( + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params); + +// +// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// - HitQueues::score +// - HitQueues::sink +// +// \b outputs: +// - HitQueues::opposite_score +// - HitQueues::opposite_loc +// - HitQueues::opposite_sink +// +void opposite_score_best( + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params) +{ + if (params.ungapped_mates) + ungapped_opposite_score_best( pipeline, params ); + else + gapped_opposite_score_best( pipeline, params ); +} + +// +// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// - HitQueues::score +// - HitQueues::sink +// +// \b outputs: +// - HitQueues::opposite_score +// - HitQueues::opposite_loc +// - HitQueues::opposite_sink +// +void opposite_score_best( + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params) +{ + if (params.ungapped_mates) + ungapped_opposite_score_best( pipeline, params ); + else + gapped_opposite_score_best( pipeline, params ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_paired_impl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_paired_impl.h new file mode 100644 index 0000000000000000000000000000000000000000..0e139ee414568f2e1ef9006e280fa4342fbfce8f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_paired_impl.h @@ -0,0 +1,71 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +template struct BaseScoringPipelineState; +template struct BestApproxScoringPipelineState; + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Scoring +///@{ + +/// +/// execute a batch of banded-alignment score calculations for the anchor mates, best mapping +/// +/// \b inputs: +/// - HitQueues::seed +/// - HitQueues::loc +/// +/// \b outputs: +/// - HitQueues::score +/// - HitQueues::sink +/// +template +void anchor_score_best_t( + const uint32 band_len, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params); + +///@} // group Scoring +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio + +#include diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_paired_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_paired_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..9474bd5e9cfce6065dd89bd2e72b206c0743af9d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_paired_inl.h @@ -0,0 +1,276 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +namespace detail { + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Scoring +///@{ + +///@addtogroup ScoringDetail +///@{ + +/// +/// A scoring stream, fetching the input hits to score from the hit queue +/// indexed by the input sorting order, and assigning them their score and sink +/// attributes. +/// +template +struct BestAnchorScoreStream : public AlignmentStreamBase +{ + typedef AlignmentStreamBase base_type; + typedef typename base_type::context_type context_type; + typedef typename base_type::scheme_type scheme_type; + + /// constructor + /// + /// \param _band_len effective band length; + /// NOTE: this value must match the template BAND_LEN parameter + /// used for instantiating aln::BatchedBandedAlignmentScore. + /// + /// \param _pipeline the pipeline object + /// + /// \param _aligner the aligner object + /// + BestAnchorScoreStream( + const uint32 _band_len, + const PipelineType _pipeline, + const AlignerType _aligner, + const ParamsPOD _params) : + base_type( _pipeline, _aligner, _params ), m_band_len( _band_len ) {} + + /// return the maximum pattern length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 max_pattern_length() const { return base_type::m_pipeline.reads.max_read_len(); } + + /// return the maximum text length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 max_text_length() const { return base_type::m_pipeline.reads.max_read_len() + m_band_len; } + + /// return the stream size + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 size() const { return base_type::m_pipeline.hits_queue_size; } + + /// initialize the i-th context + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool init_context( + const uint32 i, + context_type* context) const + { + context->idx = base_type::m_pipeline.idx_queue[i]; + + // initialize the sink + context->sink = aln::BestSink(); + + // fetch the hit to process + HitReference hit = base_type::m_pipeline.scoring_queues.hits[ context->idx ]; + + const uint32 read_rc = hit.seed.rc; + const uint32 read_id = hit.read_id; + + const io::BestPairedAlignments best = io::BestPairedAlignments( + io::BestAlignments( base_type::m_pipeline.best_alignments[ read_id ], base_type::m_pipeline.best_alignments[ read_id + base_type::m_pipeline.best_stride ] ), + io::BestAlignments( base_type::m_pipeline.best_alignments_o[ read_id ], base_type::m_pipeline.best_alignments_o[ read_id + base_type::m_pipeline.best_stride ] ) ); + + // compute the optimal score of the opposite mate + const uint2 o_read_range = base_type::m_pipeline.reads_o.get_range( read_id ); + const uint32 o_read_len = o_read_range.y - o_read_range.x; + const int32 o_optimal_score = base_type::m_pipeline.scoring_scheme.perfect_score( o_read_len ); + const int32 o_worst_score = base_type::m_pipeline.scoring_scheme.min_score( o_read_len ); + + const uint2 a_read_range = base_type::m_pipeline.reads.get_range( read_id ); + const uint32 a_read_len = a_read_range.y - a_read_range.x; + const int32 a_optimal_score = base_type::m_pipeline.scoring_scheme.perfect_score( a_read_len ); + const int32 a_worst_score = base_type::m_pipeline.scoring_scheme.min_score( a_read_len ); + + const int32 target_pair_score = nvbio::min( + compute_target_score( best, a_worst_score, o_worst_score ) + 1, + a_optimal_score + o_optimal_score ); + + int32 target_mate_score = target_pair_score - o_optimal_score; + + #if 1 + // + // bound the score of this mate by the worst score allowed for its own read length. + // NOTE: disabling this is equivalent to allowing a worst score proportional to the total + // length of the read pair. + // + + target_mate_score = nvbio::max( target_mate_score, a_worst_score ); + #endif + + // setup the read info + context->mate = 0; + context->read_rc = read_rc; + context->read_id = read_id; + context->read_range = a_read_range; + + // setup the genome range + const uint32 g_pos = hit.loc; + + context->genome_begin = g_pos > m_band_len/2 ? g_pos - m_band_len/2 : 0u; + context->genome_end = nvbio::min( context->genome_begin + m_band_len + a_read_len, base_type::m_pipeline.genome_length ); + + // skip locations that we have already visited + const uint32 mate = base_type::m_pipeline.anchor; + const bool skip = (mate == best.m_a1.m_mate && (read_rc == best.m_a1.m_rc && g_pos == best.m_a1.m_align)) || + (mate == best.m_o1.m_mate && (read_rc == best.m_o1.m_rc && g_pos == best.m_o1.m_align)) || + (mate == best.m_a2.m_mate && (read_rc == best.m_a2.m_rc && g_pos == best.m_a2.m_align)) || + (mate == best.m_o2.m_mate && (read_rc == best.m_o2.m_rc && g_pos == best.m_o2.m_align)) || + (context->min_score > a_optimal_score); + + // setup the minimum score + context->min_score = skip ? Field_traits::max() : nvbio::max( target_mate_score, base_type::m_pipeline.score_limit ); + + return !skip; + } + + /// handle the output + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void output( + const uint32 i, + const context_type* context) const + { + // write the final hit.score and hit.sink attributes + HitReference hit = base_type::m_pipeline.scoring_queues.hits[ context->idx ]; + + const aln::BestSink sink = context->sink; + hit.score = (sink.score >= context->min_score) ? sink.score : scheme_type::worst_score; + hit.sink = context->genome_begin + sink.sink.x; + // TODO: rewrite hit.loc + // hit.loc = context->genome_begin; + NVBIO_CUDA_DEBUG_PRINT_IF( base_type::m_params.debug.show_score( context->read_id, (sink.score >= context->min_score) ), "score anchor: %d (min[%d], mate[%u], rc[%u], pos[%u], [qid %u])\n", sink.score, context->min_score, base_type::m_pipeline.anchor, context->read_rc, context->genome_begin, i ); + } + + const uint32 m_band_len; +}; + +/// +/// dispatch the execution of a batch of banded-alignment score calculations for the anchor mates +/// +template +void banded_anchor_score_best( + const uint32 band_len, + const pipeline_type& pipeline, + const aligner_type aligner, + const ParamsPOD params) +{ + const uint32 static_band_len = + (band_len < 4) ? 3u : + (band_len < 8) ? 7u : + (band_len < 16) ? 15u : + 31u; + + typedef BestAnchorScoreStream stream_type; + + stream_type stream( + static_band_len, + pipeline, + aligner, + params ); + + typedef aln::DeviceThreadScheduler scheduler_type; + //typedef aln::DeviceStagedThreadScheduler scheduler_type; + + if (band_len < 4) + { + aln::BatchedBandedAlignmentScore<3u,stream_type,scheduler_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else if (band_len < 8) + { + aln::BatchedBandedAlignmentScore<7u,stream_type,scheduler_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else if (band_len < 16) + { + aln::BatchedBandedAlignmentScore<15u,stream_type,scheduler_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else + { + aln::BatchedBandedAlignmentScore<31u,stream_type,scheduler_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } +} + +///@} // group ScoringDetail +///@} // group Scoring +///@} // group nvBowtie + +} // namespace detail + +// +// execute a batch of banded-alignment score calculations for the anchor mates, best mapping +// +template +void anchor_score_best_t( + const uint32 band_len, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params) +{ + if (params.alignment_type == LocalAlignment) + { + detail::banded_anchor_score_best( + band_len, + pipeline, + pipeline.scoring_scheme.local_aligner(), + params ); + } + else + { + detail::banded_anchor_score_best( + band_len, + pipeline, + pipeline.scoring_scheme.end_to_end_aligner(), + params ); + } +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_ungapped.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_ungapped.cu new file mode 100644 index 0000000000000000000000000000000000000000..4b0fd6ef75c8422b5c3efe2ce008ec4dfd8e1d8b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/score_ungapped.cu @@ -0,0 +1,106 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// +// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping +// +template +void ungapped_opposite_score_best_t( + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params) +{ + if (params.alignment_type == LocalAlignment) + { + detail::opposite_score_best( + pipeline, + pipeline.scoring_scheme.ungapped_local_aligner(), + params ); + } + else + { + detail::opposite_score_best( + pipeline, + pipeline.scoring_scheme.ungapped_end_to_end_aligner(), + params ); + } +} + +// +// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// - HitQueues::score +// - HitQueues::sink +// +// \b outputs: +// - HitQueues::opposite_score +// - HitQueues::opposite_loc +// - HitQueues::opposite_sink +// +void ungapped_opposite_score_best( + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD& params) +{ + ungapped_opposite_score_best_t( pipeline, params ); +} + +// +// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping +// +// \b inputs: +// - HitQueues::seed +// - HitQueues::loc +// - HitQueues::score +// - HitQueues::sink +// +// \b outputs: +// - HitQueues::opposite_score +// - HitQueues::opposite_loc +// - HitQueues::opposite_sink +// +void ungapped_opposite_score_best( + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD& params) +{ + ungapped_opposite_score_best_t( pipeline, params ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring.h new file mode 100644 index 0000000000000000000000000000000000000000..0fa9ee064efbf4102a174ba38298ec5c9a8a1a4f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring.h @@ -0,0 +1,442 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/// +///\file scoring.h +/// + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Alignment +///@{ + +enum AlignmentType { + EndToEndAlignment = 0, + LocalAlignment = 1, +}; + +enum CostType { + ROUNDED_QUAL_COST = 1, + QUAL_COST = 2, + CONSTANT_COST = 3 +}; + +/// +/// Rounded quality cost function +/// +template +struct RoundedQualCost +{ + static const CostType COST_TYPE = ROUNDED_QUAL_COST; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + RoundedQualCost() {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + RoundedQualCost(const T min_val, const T max_val) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + T operator() (const int i) const { return T( phred_to_maq(i) ); } +}; + +/// +/// Simple quality cost function +/// +template +struct QualCost +{ + static const CostType COST_TYPE = QUAL_COST; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + QualCost() : m_min_val(0), m_max_val(0) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + QualCost(const T min_val, const T max_val) : m_min_val( min_val ), m_max_val( max_val ) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + T operator() (const int i) const + { + const float frac = (float)(nvbio::min(i, 40) / 40.0f); + return m_min_val + T( frac * (m_max_val - m_min_val) ); + } + + T m_min_val; + T m_max_val; +}; + +/// +/// Constant cost function +/// +template +struct ConstantCost +{ + static const CostType COST_TYPE = CONSTANT_COST; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + ConstantCost() : m_val(0) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + ConstantCost(const T min_val, const T max_val) : m_val( max_val ) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + T operator() (const int i) const { return T( m_val ); } + + T m_val; +}; + +/// +/// This class implements an edit-distance based scoring scheme for short read alignment. +/// While the original bowtie2 code base always performs alignment using Gotoh's algorithm +/// (i.e. Smith-Waterman with affine gap penalties), nvBowtie also supports edit-distance, +/// which is sometimes better suited for very short reads (e.g. ~100bps). +/// +struct EditDistanceScoringScheme +{ + typedef EditDistanceScoringScheme scheme_type; + typedef SimpleFunc threshold_score_type; + typedef aln::EditDistanceTag aligner_tag; + + typedef aln::EditDistanceAligner local_aligner_type; + typedef aln::EditDistanceAligner end_to_end_aligner_type; + + typedef aln::EditDistanceAligner ungapped_local_aligner_type; + typedef aln::EditDistanceAligner ungapped_end_to_end_aligner_type; + + static const int32 inf_score = 0; + static const int32 worst_score = -(1 << 8); + + /// return the local aligner + /// + local_aligner_type local_aligner() const { return local_aligner_type(); } + + /// return the end_to_end aligner + /// + end_to_end_aligner_type end_to_end_aligner() const { return end_to_end_aligner_type(); } + + /// return the local aligner + /// + ungapped_local_aligner_type ungapped_local_aligner() const { return ungapped_local_aligner_type(); } + + /// return the end_to_end aligner + /// + ungapped_end_to_end_aligner_type ungapped_end_to_end_aligner() const { return ungapped_end_to_end_aligner_type(); } + + // ---------- constructors -------------------------------------------------------------------- // + + /// default constructor + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + EditDistanceScoringScheme() : m_score_min( SimpleFunc::LinearFunc, -5.0f, 0.0f ) {} + + // ---------- begin: limits ------------------------------------------------------------------- // + + /// best achievable score for a read of given length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + int32 perfect_score(const uint32 read_len) const { return 0; } + + /// min score + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + int32 min_score(const uint32 len) const { return m_score_min( len ); } + + /// min score function + /// + SimpleFunc threshold_score() const + { + return m_score_min; + } + + // ---------- end: limits ---------------------------------------------------------------------- // + +public: + SimpleFunc m_score_min; // minimum read score function +}; + +/// +/// This class implements a scoring scheme for short read alignment, +/// taking into account matches, mismatches, insertions, deletions, +/// ambiguous bases and base qualities. +/// In practice, it reproduces exactly bowtie2's original scoring +/// scheme employing a Gotoh aligner. +/// +template < + typename MMCost = QualCost, + typename NCost = ConstantCost > +struct SmithWatermanScoringScheme +{ + typedef SmithWatermanScoringScheme scheme_type; + typedef aln::GotohTag aligner_tag; + + typedef aln::GotohAligner local_aligner_type; + typedef aln::GotohAligner end_to_end_aligner_type; + + typedef aln::HammingDistanceAligner ungapped_local_aligner_type; + typedef aln::HammingDistanceAligner ungapped_end_to_end_aligner_type; + + typedef ConstantCost MatchCost; + typedef MMCost MismatchCost; + + typedef MatchCost match_cost_function; + typedef MismatchCost mismatch_cost_function; + typedef NCost N_cost_function; + + typedef SimpleFunc threshold_score_type; + + static const int32 inf_score = -(1 << 16); + static const int32 worst_score = inf_score; + + /// return the local aligner + /// + local_aligner_type local_aligner() const { return local_aligner_type(*this); } + + /// return the end_to_end aligner + /// + end_to_end_aligner_type end_to_end_aligner() const { return end_to_end_aligner_type(*this); } + + /// return the local aligner + /// + ungapped_local_aligner_type ungapped_local_aligner() const { return ungapped_local_aligner_type(*this); } + + /// return the end_to_end aligner + /// + ungapped_end_to_end_aligner_type ungapped_end_to_end_aligner() const { return ungapped_end_to_end_aligner_type(*this); } + + // ---------- constructors -------------------------------------------------------------------- // + + /// return a preconfigured scoring scheme + /// + static SmithWatermanScoringScheme base1(); + + /// return preconfigured scoring scheme for local mapping + /// + static SmithWatermanScoringScheme local(); + + /// default constructor + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + SmithWatermanScoringScheme(); + + /// constructor + /// + /// \param options key/value string options + SmithWatermanScoringScheme( + const std::map& options, + const AlignmentType type = LocalAlignment); + + // ---------- begin: limits ------------------------------------------------------------------- // + + /// min score + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + int32 min_score(const uint32 len) const { return m_score_min( len ); } + + /// min score function + /// + SimpleFunc threshold_score() const { return m_score_min; } + + /// best achievable score for a read of given length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + int32 perfect_score(const uint32 read_len) const { return int32(read_len) * match( 0 ); } + + // ---------- end: limits ---------------------------------------------------------------------- // + + // -------- begin: aln::GotohAligner interface ----------------------------------------------------------------- // + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 match(const uint8 q = 0) const { return m_match(q); } + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 mismatch(const uint8 q = 0) const { return -m_mmp(q); } + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 mismatch(const uint8 r, const uint8 q, const uint8 qq = 0) const { return -m_mmp(qq); } + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 substitution(const uint32 r_i, const uint32 q_j, const uint8 r, const uint8 q, const uint8 qq = 0) const { return r == q ? m_match(qq) : -m_mmp(qq); } + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 pattern_gap_open() const { return -m_read_gap_const - m_read_gap_coeff; } + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 pattern_gap_extension() const { return -m_read_gap_coeff; } + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 text_gap_open() const { return -m_ref_gap_const - m_ref_gap_coeff; } + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 text_gap_extension() const { return -m_ref_gap_coeff; } + // -------- end: aln::GotohAligner interface ------------------------------------------------------------------- // + + // -------- begin: helper methods to perform final scoring --------------------------------------------------- // + // NOTE: technically we could use the same interface used by the SW module, but wheareas that is geared + // towards dynamic programming, this one is simpler to use when just linearly scanning through a given + // alignment + + /// score of a given alignment + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + int score(const uint8 read, const uint8 ref_mask, int q) const + { + return (read > 3 || ref_mask > 15) ? // is there an N? + -m_np(q) : // N score + ((ref_mask & (1u << read)) != 0) ? // is there a match ? + m_match(q) : // match score + -m_mmp(q); // mismatch score + } + + /// marginal penalty for an N with given quality + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + int n(int q) const { return m_np( q < 255 ? q : 255 ); } + + /// cumulative penalty of a gap of length 'i' in the read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + int cumulative_insertion(const uint32 i) const + { + return m_read_gap_const + m_read_gap_coeff * i; + } + + /// cumulative penalty of a gap of length 'i' in the reference + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + int cumulative_deletion(const uint32 i) const + { + return m_ref_gap_const + m_ref_gap_coeff * i; + } + // -------- end: helper methods to perform final scoring --------------------------------------------------- // + +public: + SimpleFunc m_score_min; // minimum read score function + float m_n_ceil_const; // constant for the function governing the ceiling on the number of N's, depending on the read-length + float m_n_ceil_coeff; // coefficient for the function governing the ceiling on the number of N's, depending on the read-length + int m_read_gap_const; // reap gap open penalty + int m_read_gap_coeff; // reap gap extension penalty + int m_ref_gap_const; // reference gap open penalty + int m_ref_gap_coeff; // reference gap extension penalty + int m_gap_free; // length of the gap-free area at the beginning of each read + MatchCost m_match; // match bonus function (function of the quality score) + MMCost m_mmp; // mismatch penalty function (function of the quality score) + NCost m_np; // N-penalty function (function of the quality score) + bool m_monotone; // is this scoring scheme monotone? (i.e. match bonus == 0) + bool m_local; // are we doing local alignment? + +private: + static SimpleFunc::Type func_type(const std::string& type); + static SimpleFunc min_score_function(const std::map& options); + static MatchCost match_cost(const std::map& options); + static MMCost mm_cost(const std::map& options); + static NCost n_cost(const std::map& options); +}; + +/// a helper struct to make an aligner given the AlignmentType (LocalAlignment|EndToEndAlignment) and the scheme (EditDistanceScoringScheme|SmithWatermanScoringScheme) +/// +template struct make_aligner_dispatch {}; + +/// a helper struct to make an aligner given the AlignmentType (LocalAlignment|EndToEndAlignment) and the scheme (EditDistanceScoringScheme|SmithWatermanScoringScheme) +/// +template struct make_aligner_dispatch { typedef typename scheme_type::local_aligner_type type; static type make(const scheme_type& scheme) { return scheme.local_aligner(); } }; + +/// a helper struct to make an aligner given the AlignmentType (LocalAlignment|EndToEndAlignment) and the scheme (EditDistanceScoringScheme|SmithWatermanScoringScheme) +/// +template struct make_aligner_dispatch { typedef typename scheme_type::local_aligner_type type; static type make(const scheme_type& scheme) { return scheme.end_to_end_aligner(); } }; + +/// a helper function to make an aligner given the AlignmentType (LocalAlignment|EndToEndAlignment) and the scheme (EditDistanceScoringScheme|SmithWatermanScoringScheme) +/// +template +typename make_aligner_dispatch::type +make_aligner(const scheme_type& scheme) { return make_aligner_dispatch::make(); } + +/// load a Smith-Waterman scoring scheme from disk +/// +SmithWatermanScoringScheme<> load_scoring_scheme(const char* name, const AlignmentType type); + +/// +/// An uber class containing both an EditDistanceScoringScheme and a SmithWatermanScoringScheme, +/// needed to do option parsing, *before* it is known which of the two we are going to use +/// +struct UberScoringScheme +{ + EditDistanceScoringScheme ed; + SmithWatermanScoringScheme<> sw; +}; + +/// +/// select which scoring system (edit distance/smith waterman) to use based on the scoring tag +/// +template +struct ScoringSchemeSelector +{}; + +/// edit_distance_scoring_tag specialization of ScoringSchemeSelector +/// +template <> +struct ScoringSchemeSelector +{ + typedef EditDistanceScoringScheme type; + + static EditDistanceScoringScheme scheme(const UberScoringScheme& _scheme) { return _scheme.ed; } +}; + +/// smith_waterman_scoring_tag specialization of ScoringSchemeSelector +/// +template <> +struct ScoringSchemeSelector +{ + typedef SmithWatermanScoringScheme<> type; + + static SmithWatermanScoringScheme<> scheme(const UberScoringScheme& _scheme) { return _scheme.sw; } +}; + +/// +/// return the scoring scheme tag, given the scoring scheme +/// +template +struct ScoringSchemeTag {}; + +/// EditDistanceScoringScheme specialization of ScoringSchemeTag +/// +template <> +struct ScoringSchemeTag< EditDistanceScoringScheme > { typedef edit_distance_scoring_tag type; }; + +/// SmithWatermanScoringScheme specialization of ScoringSchemeTag +/// +template < + typename MMCost, + typename NCost > +struct ScoringSchemeTag< SmithWatermanScoringScheme > { typedef smith_waterman_scoring_tag type; }; + +///@} // group Alignment +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio + +#include diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..2f77735aa925942091213ed8dba8eba557a47288 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring_inl.h @@ -0,0 +1,201 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +inline +SmithWatermanScoringScheme<> load_scoring_scheme(const char* name, const AlignmentType type) +{ + FILE* file = fopen( name, "r" ); + if (file == NULL) + return SmithWatermanScoringScheme<>(); + + std::map options; + char key[1024]; + char value[1024]; + + while (fscanf( file, "%s %s", key, value ) == 2) + options[ key ] = std::string( value ); + + fclose( file ); + + return SmithWatermanScoringScheme<>( options, type ); +} + +template < + typename MMCost, + typename NCost> +SmithWatermanScoringScheme SmithWatermanScoringScheme::base1() +{ + std::map options; + options["match"] = std::string("1"); + options["mm-penalty-min"] = std::string("3"); + options["mm-penalty-max"] = std::string("3"); + options["N-penalty-min"] = std::string("3"); + options["N-penalty-max"] = std::string("3"); + options["score-min-const"] = std::string("37.0f"); + options["score-min-coeff"] = std::string("0.3f"); + options["N-ceil-const"] = std::string("2.0f"); + options["N-ceil-coeff"] = std::string("0.1f"); + options["read-gap-const"] = std::string("11"); + options["read-gap-coeff"] = std::string("4"); + options["ref-gap-const"] = std::string("11"); + options["ref-gap-coeff"] = std::string("4"); + options["gap-free"] = std::string("5"); + return SmithWatermanScoringScheme( options ); +} + +template < + typename MMCost, + typename NCost> +SmithWatermanScoringScheme SmithWatermanScoringScheme::local() +{ + std::map options; + options["match"] = std::string("2"); + options["mm-penalty-min"] = std::string("2"); + options["mm-penalty-max"] = std::string("6"); + options["N-penalty-min"] = std::string("1"); + options["N-penalty-max"] = std::string("1"); + options["score-min-const"] = std::string("0.0f"); + options["score-min-coeff"] = std::string("10.0f"); + options["score-min-type"] = std::string("log"); + options["N-ceil-const"] = std::string("0.0f"); + options["N-ceil-coeff"] = std::string("0.15f"); + options["read-gap-const"] = std::string("5"); + options["read-gap-coeff"] = std::string("3"); + options["ref-gap-const"] = std::string("5"); + options["ref-gap-coeff"] = std::string("3"); + options["gap-free"] = std::string("5"); + return SmithWatermanScoringScheme( options, LocalAlignment ); +} + +// default constructor +// +template < + typename MMCost, + typename NCost> +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +SmithWatermanScoringScheme::SmithWatermanScoringScheme() : + m_score_min( SimpleFunc::LinearFunc, -0.6f, -0.6f ), + m_n_ceil_const( 0.0f ), + m_n_ceil_coeff( 0.15f ), + m_read_gap_const( 5 ), + m_read_gap_coeff( 3 ), + m_ref_gap_const( 5 ), + m_ref_gap_coeff( 3 ), + m_gap_free( 5 ), + m_match( 0, 0 ), + m_mmp( 2, 6 ), + m_np( 1, 1 ), + m_monotone( true ), + m_local( false ) +{} + +// constructor +// +// \param options key/value string options +template < + typename MMCost, + typename NCost> +SmithWatermanScoringScheme::SmithWatermanScoringScheme( + const std::map& options, + const AlignmentType type) : + m_score_min( min_score_function(options) ), + m_n_ceil_const( float_option( options, "N-ceil-const", 0.0f ) ), + m_n_ceil_coeff( float_option( options, "N-ceil-coeff", 0.15f ) ), + m_read_gap_const( int_option( options, "read-gap-const", 5 ) ), + m_read_gap_coeff( int_option( options, "read-gap-coeff", 3 ) ), + m_ref_gap_const( int_option( options, "ref-gap-const", 5 ) ), + m_ref_gap_coeff( int_option( options, "ref-gap-coeff", 3 ) ), + m_gap_free( int_option( options, "gap-free", 5 ) ), + m_match( match_cost(options) ), + m_mmp( mm_cost(options) ), + m_np( n_cost(options) ), + m_monotone( m_match(0) == 0 ), + m_local( type == LocalAlignment ? true : false ) +{} + + +template < + typename MMCost, + typename NCost> +SimpleFunc::Type SmithWatermanScoringScheme::func_type(const std::string& type) +{ + if (strcmp( type.c_str(), "log" ) == 0) + return SimpleFunc::LogFunc; + else if (strcmp( type.c_str(), "sqrt" ) == 0) + return SimpleFunc::SqrtFunc; + + return SimpleFunc::LinearFunc; +} + +template < + typename MMCost, + typename NCost> +SimpleFunc SmithWatermanScoringScheme::min_score_function(const std::map& options) +{ + return SimpleFunc( + func_type( string_option( options, "score-min-type", "linear" ) ), + float_option( options, "score-min-const", -0.6f ), // 37.0f + float_option( options, "score-min-coeff", -0.6f ) ); // 0.3f +} +template < + typename MMCost, + typename NCost> +typename SmithWatermanScoringScheme::MatchCost SmithWatermanScoringScheme::match_cost(const std::map& options) +{ + const int match_cost = int_option( options, "match", 0 ); + return MatchCost( match_cost, match_cost ); +} +template < + typename MMCost, + typename NCost> +MMCost SmithWatermanScoringScheme::mm_cost(const std::map& options) +{ + const int mmp_min = int_option( options, "mm-penalty-min", 2 ); + const int mmp_max = int_option( options, "mm-penalty-max", 6 ); + return MMCost( mmp_min, mmp_max ); +} +template < + typename MMCost, + typename NCost> +NCost SmithWatermanScoringScheme::n_cost(const std::map& options) +{ + const int np_min = int_option( options, "N-penalty-min", 1 ); + const int np_max = int_option( options, "N-penalty-max", 1 ); + return NCost( np_min, np_max ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring_queues.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring_queues.h new file mode 100644 index 0000000000000000000000000000000000000000..be805e6a2f5492cb34432a22910cd59827503779 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring_queues.h @@ -0,0 +1,581 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/// +///\file scoring_queues.h +/// + +#pragma once + +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +///@addtogroup nvBowtie +///@{ + +/// \defgroup ScoringQueuesModule Scoring Queues +/// +/// This module contains a set of classes used to represent the scoring queues employed throughout +/// all of nvBowtie in best mapping mode. +/// Conceptually, the queues (ScoringQueues) represent a set of "active" reads, and a nested sequence of variable length +/// seed hit lists bound to the active reads. +/// +/// The hits (HitQueues) in turn are represented by a set of attributes that are computed during different pipeline +/// stages: the hit location, its RC flags, its alignment score, its alignment sink, and so on. +/// +/// In order to achieve maximum access performance, all of these attributes are stored in SOA layout: +/// the classes in this module serve the purpose of providing a structured AOS-like view over the raw data. +/// + +///@addtogroup ScoringQueuesModule +///@{ + +// forward declaration +template struct HitReference; +template struct ReadHitReference; +template struct ReadHitBinder; + +struct HitQueuesDeviceView; +struct ScoringQueuesDeviceView; +struct ReadHitsIndexDeviceView; + +/// +/// This data structure represents a collection of hit arrays bound to a set of reads. +/// For each read it stores an array of hits of arbitrary length. +/// +/// Internally, the links from a read to its hits are stored inside a contiguous memory arena +/// using the following strided layout: +/// +/// \verbatim +/// ****************************************************** +/// * read0 * read1 * ... * readN * +/// ****************************************************** +/// count | count | ... | count +/// -----------|---------|---------------------|---------- +/// hit0 | hit0 | ... | hit0 +/// -----------|---------|---------------------|---------- +/// hit1 | hit1 | ... | hit1 +/// -----------|---------|---------------------|---------- +/// ... | ... | ... | ... +/// -----------|---------|---------------------|---------- +/// hitM | hitM | ... | hitM +/// ------------------------------------------------------ +/// \endverbatim +/// +/// In practice, if the arena has size max_size, and the stride is N, one can represent +/// up to M = max_size / N hits per read. +/// +struct ReadHitsIndex +{ + typedef thrust::device_vector links_storage_type; + typedef ReadHitsIndexDeviceView device_view_type; + + enum Mode { + SingleHitPerRead = 0u, + MultipleHitsPerRead = 1u, + }; + + /// alloc enough storage for max_size hits + /// + uint64 resize(const uint32 max_size, const bool do_alloc); + + /// setup the number of input reads + /// + void setup(const uint32 n_hits_per_read, const uint32 in_reads); + + /// return the queue mode + /// + Mode mode() const { return m_mode; } + + /// return a view of the data structure + /// + ReadHitsIndexDeviceView device_view(); + +public: + links_storage_type m_links; ///< links arena + uint32 m_stride; ///< access stride + Mode m_mode; ///< single/multiple hits mode +}; + +/// +/// This data structure represents a collection of hit arrays bound to a set of reads. +/// For each read it stores an array of hits of arbitrary length. +/// +struct ReadHitsIndexDeviceView +{ + typedef typename device_view_subtype::type links_storage_type; + + /// + /// An auxiliary class to represent the hit array bound to a given read + /// + struct HitArray + { + /// constructor + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + HitArray(ReadHitsIndexDeviceView& index, const uint32 read_index) : m_index(index), m_read_index(read_index) {} + + /// set the number of hits + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void resize(const uint32 size) const { m_index.set_hit_count( m_read_index, size ); } + + /// return the number of hits + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 size() const { return m_index.hit_count( m_read_index ); } + + /// return the i-th hit link + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32& operator[] (const uint32 slot) { return m_index( m_read_index, slot ); } + + /// return the i-th hit link + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator[] (const uint32 slot) const { return m_index( m_read_index, slot ); } + + private: + ReadHitsIndexDeviceView& m_index; + uint32 m_read_index; + }; + + // define the reference type + typedef HitArray reference; + + + /// constructor + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + ReadHitsIndexDeviceView( + links_storage_type links = links_storage_type(), + const uint32 stride = 0u) : m_links( links ), m_stride( stride ) {} + + /// return the number of hits bound to a read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 hit_count(const uint32 read_index) const { return m_links[ read_index ]; } + + /// setup the number of hits + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void set_hit_count(const uint32 read_index, const uint32 count) { m_links[ read_index ] = count; } + + /// return the i-th hit link bound to a given read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32& operator() (const uint32 read_index, const uint32 slot) { return m_links[ read_index + (1u + slot) * m_stride ]; } + + /// return the i-th hit link bound to a given read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const uint32 read_index, const uint32 slot) const { return m_links[ read_index + (1u + slot) * m_stride ]; } + + /// return the hit array bound to a given read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + HitArray operator[] (const uint32 read_index) { return HitArray( *this, read_index ); } + +public: + links_storage_type m_links; + uint32 m_stride; + + friend struct HitArray; +}; + +/// +/// The collection of queues defining the set of hits - each queue holds one element/attribute per hit +/// +struct HitQueues +{ + typedef thrust::device_vector index_storage_type; + typedef thrust::device_vector seed_storage_type; + typedef thrust::device_vector ssa_storage_type; + typedef thrust::device_vector loc_storage_type; + typedef thrust::device_vector score_storage_type; + typedef thrust::device_vector sink_storage_type; + + typedef HitQueuesDeviceView device_view_type; ///< view subtype + typedef HitReference reference; ///< reference subtype + + /// resize all queues + /// + uint64 resize(const uint32 size, const bool do_alloc); + + /// return a view of the data structure + /// + HitQueuesDeviceView device_view(); + + index_storage_type read_id; ///< hit -> read mapping + seed_storage_type seed; ///< hit info + ssa_storage_type ssa; ///< hit ssa info + loc_storage_type loc; ///< hit locations + score_storage_type score; ///< hit scores + sink_storage_type sink; ///< hit sinks + loc_storage_type opposite_loc; ///< hit locations, opposite mate + score_storage_type opposite_score; ///< hit scores, opposite mate + sink_storage_type opposite_sink; ///< hit sinks, opposite mate + score_storage_type opposite_score2; ///< hit scores, opposite mate + sink_storage_type opposite_sink2; ///< hit sinks, opposite mate +}; +/// +/// A view of the HitQueues class +/// +struct HitQueuesDeviceView +{ + typedef typename device_view_subtype::type index_storage_type; + typedef typename device_view_subtype::type seed_storage_type; + typedef typename device_view_subtype::type ssa_storage_type; + typedef typename device_view_subtype::type loc_storage_type; + typedef typename device_view_subtype::type score_storage_type; + typedef typename device_view_subtype::type sink_storage_type; + + typedef HitQueuesDeviceView device_view_type; ///< view subtype + typedef HitReference reference; ///< reference subtype + + /// constructor + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + HitQueuesDeviceView( + index_storage_type _read_id = index_storage_type(), // hit -> read mapping + seed_storage_type _seed = seed_storage_type(), // hit info + ssa_storage_type _ssa = ssa_storage_type(), // hit ssa info + loc_storage_type _loc = loc_storage_type(), // hit locations + score_storage_type _score = score_storage_type(), // hit scores + sink_storage_type _sink = sink_storage_type(), // hit sinks + loc_storage_type _opposite_loc = loc_storage_type(), // hit locations, opposite mate + score_storage_type _opposite_score = score_storage_type(), // hit scores, opposite mate + sink_storage_type _opposite_sink = sink_storage_type(), // hit sinks, opposite mate + score_storage_type _opposite_score2 = score_storage_type(), // hit scores, opposite mate + sink_storage_type _opposite_sink2 = sink_storage_type()); // hit sinks, opposite mate + + /// return a reference to a given hit + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + HitReference operator[] (const uint32 i); + + /// return a reference to a given hit + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + HitReference operator[] (const uint32 i) const; + + index_storage_type read_id; ///< hit -> read mapping + seed_storage_type seed; ///< hit info + ssa_storage_type ssa; ///< hit ssa info + loc_storage_type loc; ///< hit locations + score_storage_type score; ///< hit scores + sink_storage_type sink; ///< hit sinks + loc_storage_type opposite_loc; ///< hit locations, opposite mate + score_storage_type opposite_score; ///< hit scores, opposite mate + sink_storage_type opposite_sink; ///< hit sinks, opposite mate + score_storage_type opposite_score2; ///< hit scores, opposite mate + sink_storage_type opposite_sink2; ///< hit sinks, opposite mate +}; + +/// +/// The collection of queues needed by the scoring pipeline. +/// Particularly: +/// +/// - a ping-pong set of input/output active-read queues, +/// storing information about the read-id and some flags representing +/// their pipeline state. +/// +/// - a set of hits, and a read->hits index +/// these can essentially be seen as forming a nested sequence of hits, +/// with a variable length set of hits bound to each read. +/// +/// The scoring pipeline is essentially a two-stage self-feeding loop: +/// +/// In the first stage, a certain amount of hits are selected for scoring +/// for each input active-read. +/// Reads for which no hits are selected become inactive, and reads which +/// stay active are output to the output queue together with their hits. +/// +/// In the second stage, the queues are swapped, the output queue becomes +/// the input, and the hits bound ot each active read gets scored. +/// +/// This class provides two accessors to represent: +/// +/// - "references" to the reads in the input queue (ReadHitsReference), and +/// +/// - "binders" to reads in the output queue (ReadHitsBinder), +/// useful for binding output reads in the first stage. +/// +struct ScoringQueues +{ + typedef nvbio::cuda::PingPongQueues active_reads_storage_type; + typedef HitQueues hits_storage_type; + typedef ReadHitsIndex read_hits_index_type; + typedef thrust::device_vector pool_type; + + typedef ScoringQueuesDeviceView device_view_type; + + /// constructor + /// + ScoringQueues() : hits_pool(1) {} + + /// resize + /// + uint64 resize(const uint32 n_reads, const uint32 n_hits, const bool do_alloc); + + /// clear output queues + /// + void clear_output() { hits_pool[0] = 0u; active_reads.clear_output(); } + + /// return the number of allocated hits + /// + uint32 hits_count() { return hits_pool[0]; } + + /// return a view of the data structure + /// + ScoringQueuesDeviceView device_view(); + + active_reads_storage_type active_reads; ///< set of active reads + hits_storage_type hits; ///< nested sequence + read_hits_index_type hits_index; ///< read -> hits mapping + pool_type hits_pool; ///< pool counter +}; +/// +/// A view of the ScoringQueues class +/// +struct ScoringQueuesDeviceView +{ + typedef typename device_view_subtype::type active_reads_storage_type; + typedef typename device_view_subtype::type hits_storage_type; + typedef typename device_view_subtype::type read_hits_index_type; + typedef typename device_view_subtype::type pool_type; + + /// constructor + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + ScoringQueuesDeviceView() {} + + /// constructor + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + ScoringQueuesDeviceView( + active_reads_storage_type _active_reads, // set of active reads + hits_storage_type _hits, // nested sequence of read hits + read_hits_index_type _hits_index, // read -> hits mapping + pool_type _hits_pool); // pool counter + + /// return the number of active reads in the input queue + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 active_read_count() const { return active_reads.in_size; } + + /// return the read info for a given entry of the input queue + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + packed_read active_read(const uint32 read_index) const { return active_reads.in_queue[read_index]; } + + active_reads_storage_type active_reads; ///< set of active reads + hits_storage_type hits; ///< nested sequence of read hits + read_hits_index_type hits_index; ///< read -> hits mapping + pool_type hits_pool; ///< pool counter +}; + +/// +/// A reference to a hit +/// +/// \tparam HitQueuesType can be either HitQueues or HitQueuesView. +/// +template +struct HitReference +{ + typedef typename reference_subtype::type index_type; + typedef typename reference_subtype::type seed_type; + typedef typename reference_subtype::type ssa_type; + typedef typename reference_subtype::type loc_type; + typedef typename reference_subtype::type score_type; + typedef typename reference_subtype::type sink_type; + + /// constructor + /// + /// \param hits hits container + /// \param hit_index index of this hit + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + HitReference(HitQueuesType& hits, const uint32 hit_index); + + index_type read_id; ///< parent read index + seed_type seed; ///< seed reference + ssa_type ssa; ///< ssa reference + loc_type loc; ///< loc reference + score_type score; ///< score reference + sink_type sink; ///< sink reference + loc_type opposite_loc; ///< opposite mate's loc reference + score_type opposite_score; ///< opposite mate's score reference + sink_type opposite_sink; ///< opposite mate's sink reference + score_type opposite_score2; ///< opposite mate's score reference + sink_type opposite_sink2; ///< opposite mate's sink reference +}; + +/// +/// A reference to the collection of hits bound to a given read (in the input queue) +/// +template +struct ReadHitsReference +{ + typedef typename ScoringQueuesType::read_hits_index_type read_hits_index_type; + typedef typename ScoringQueuesType::hits_storage_type hits_storage_type; + typedef HitReference reference; + + /// constructor + /// + /// \param queues scoring queues + /// \param read_index index of this read + /// \param selector input/output queue selector + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + ReadHitsReference(ScoringQueuesType& queues, const uint32 read_index = uint32(-1)); + + /// bind this object to a given index + /// + /// \param read_index output index of this read + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void bind(const uint32 read_index); + + /// size of the hits vector + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 size() const; + + /// return the i-th element + /// NOTE: this method is only valid after the i-th hit has been bound. + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + HitReference operator[] (const uint32 i) const; + + /// access the packed_read info in the selected queue + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + packed_read read_info() const; + + /// return the slot where the i-th element is stored + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 slot(const uint32 i) const; + +private: + ScoringQueuesType& m_queues; ///< view of the hits container + uint32 m_read_index; ///< read index +}; + + +/// +/// A class used to bind a read and its hits to the output queue +/// +template +struct ReadHitsBinder +{ + typedef typename ScoringQueuesType::read_hits_index_type read_hits_index_type; + typedef typename ScoringQueuesType::hits_storage_type hits_storage_type; + typedef HitReference reference; + + /// constructor + /// + /// \param queues scoring queues + /// \param read_index index of this read + /// \param selector input/output queue selector + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + ReadHitsBinder(ScoringQueuesType& queues, const uint32 read_index = uint32(-1)); + + /// bind this object to a given index + /// + /// \param read_index output index of this read + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void bind(const uint32 read_index); + + /// resize the hits vector + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void resize(const uint32 size); + + /// size of the hits vector + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 size() const; + + /// return the i-th element + /// NOTE: this method is only valid after the i-th hit has been bound. + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + HitReference operator[] (const uint32 i) const; + + /// access the packed_read info in the selected queue + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + packed_read read_info() const; + + /// set the read info + /// + /// \param read_index output index of this read + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void set_read_info(const packed_read info); + + /// bind the i-th hit to a given location + /// + /// \param i index of the hit to bind relative to this read + /// \param slot address of the bound hit in the HitQueues + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void bind_hit(const uint32 i, const uint32 slot); + +private: + ScoringQueuesType& m_queues; ///< view of the hits container + uint32 m_read_index; ///< read index +}; + +///@} // group ScoringQueuesModule +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 + +// return a view of the queues +// +inline +bowtie2::cuda::ScoringQueuesDeviceView device_view(bowtie2::cuda::ScoringQueues& queues) { return queues.device_view(); } + +// return a view of the queues +// +inline +bowtie2::cuda::HitQueuesDeviceView device_view(bowtie2::cuda::HitQueues& queues) { return queues.device_view(); } + +// return a view of the index +// +inline +bowtie2::cuda::ReadHitsIndexDeviceView device_view(bowtie2::cuda::ReadHitsIndex& index) { return index.device_view(); } + +} // namespace nvbio + +#include diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring_queues_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring_queues_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..6ea83de702c910c208a226f041e15cf9fb0479dd --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring_queues_inl.h @@ -0,0 +1,369 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// alloc enough storage for max_size hits +// +inline +uint64 ReadHitsIndex::resize(const uint32 max_size, const bool do_alloc) +{ + const uint32 n = 2u*max_size; + if (do_alloc) m_links.resize( n ); + return n * sizeof(uint32); +} + +// setup the number of input reads +// +inline +void ReadHitsIndex::setup(const uint32 n_hits_per_read, const uint32 in_reads) +{ + m_mode = n_hits_per_read > 1 ? + MultipleHitsPerRead : + SingleHitPerRead; + + m_stride = in_reads; + + if (n_hits_per_read == 1) + { + // fill the links structure + thrust::fill( + m_links.begin(), + m_links.begin() + in_reads, + uint32(1u) ); + + // fill the links structure + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(in_reads), + m_links.begin() + in_reads ); + } +} + +// return a view of the data structure +// +inline +ReadHitsIndexDeviceView ReadHitsIndex::device_view() +{ + return ReadHitsIndexDeviceView( + nvbio::device_view( m_links ), + m_stride ); +} + +// setup all queues +// +inline +uint64 HitQueues::resize(const uint32 size, const bool do_alloc) +{ + uint64 bytes = 0; + if (do_alloc) read_id.resize( size ); bytes += size * sizeof(uint32); + if (do_alloc) seed.resize( size ); bytes += size * sizeof(packed_seed); + if (do_alloc) ssa.resize( size ); bytes += size * sizeof(uint32); + if (do_alloc) loc.resize( size ); bytes += size * sizeof(uint32); + if (do_alloc) score.resize( size ); bytes += size * sizeof(int32); + if (do_alloc) sink.resize( size ); bytes += size * sizeof(uint32); + if (do_alloc) opposite_loc.resize( size ); bytes += size * sizeof(uint32); + if (do_alloc) opposite_score.resize( size ); bytes += size * sizeof(int32); + if (do_alloc) opposite_sink.resize( size ); bytes += size * sizeof(uint32); + if (do_alloc) opposite_score2.resize( size ); bytes += size * sizeof(int32); + if (do_alloc) opposite_sink2.resize( size ); bytes += size * sizeof(uint32); + return bytes; +} + +// return a view of the data structure +// +inline +HitQueuesDeviceView HitQueues::device_view() +{ + return HitQueuesDeviceView( + nvbio::device_view( read_id ), + nvbio::device_view( seed ), + nvbio::device_view( ssa ), + nvbio::device_view( loc ), + nvbio::device_view( score ), + nvbio::device_view( sink ), + nvbio::device_view( opposite_loc ), + nvbio::device_view( opposite_score ), + nvbio::device_view( opposite_sink ), + nvbio::device_view( opposite_score2 ), + nvbio::device_view( opposite_sink2 ) ); +} + +// constructor +// +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +HitQueuesDeviceView::HitQueuesDeviceView( + index_storage_type _read_id, // hit -> read mapping + seed_storage_type _seed, // hit info + ssa_storage_type _ssa, // hit ssa info + loc_storage_type _loc, // hit locations + score_storage_type _score, // hit scores + sink_storage_type _sink, // hit sinks + loc_storage_type _opposite_loc, // hit locations, opposite mate + score_storage_type _opposite_score, // hit scores, opposite mate + sink_storage_type _opposite_sink, // hit sinks, opposite mate + score_storage_type _opposite_score2, // hit scores, opposite mate + sink_storage_type _opposite_sink2) : // hit sinks, opposite mate + read_id( _read_id ), + seed( _seed ), + ssa( _ssa ), + loc( _loc ), + score( _score ), + sink( _sink ), + opposite_loc( _opposite_loc ), + opposite_score( _opposite_score ), + opposite_sink( _opposite_sink ), + opposite_score2( _opposite_score2 ), + opposite_sink2( _opposite_sink2 ) +{} + +// resize +// +inline +uint64 ScoringQueues::resize(const uint32 n_reads, const uint32 n_hits, const bool do_alloc) +{ + uint64 bytes = 0; + bytes += active_reads.resize_arena( n_reads, do_alloc ); + bytes += hits.resize( n_hits, do_alloc ); + bytes += hits_index.resize( n_hits, do_alloc ); + return bytes; +} + +// return a reference to a given hit +// +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +HitReference HitQueuesDeviceView::operator[] (const uint32 i) +{ + return HitReference( *this, i ); +} + +// return a reference to a given hit +// +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +HitReference HitQueuesDeviceView::operator[] (const uint32 i) const +{ + return HitReference( *const_cast( this ), i ); +} + +// constructor +// +// \param hits hits container +// \param hit_index index of this hit +#pragma hd_warning_disable +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +HitReference::HitReference(HitQueuesType& hits, const uint32 hit_index) : + read_id ( hits.read_id[ hit_index ] ), + seed ( hits.seed[ hit_index ] ), + ssa ( hits.ssa[ hit_index ] ), + loc ( hits.loc[ hit_index ] ), + score ( hits.score[ hit_index ] ), + sink ( hits.sink[ hit_index ] ), + opposite_loc ( hits.opposite_loc[ hit_index ] ), + opposite_score ( hits.opposite_score[ hit_index ] ), + opposite_sink ( hits.opposite_sink[ hit_index ] ), + opposite_score2 ( hits.opposite_score2[ hit_index ] ), + opposite_sink2 ( hits.opposite_sink2[ hit_index ] ) +{} + +// return a view of the data structure +// +inline +ScoringQueuesDeviceView ScoringQueues::device_view() +{ + return ScoringQueuesDeviceView( + nvbio::device_view( active_reads ), + nvbio::device_view( hits ), + nvbio::device_view( hits_index ), + nvbio::device_view( hits_pool ) ); +} + +// constructor +// +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +ScoringQueuesDeviceView::ScoringQueuesDeviceView( + active_reads_storage_type _active_reads, // set of active reads + hits_storage_type _hits, // nested sequence of read hits + read_hits_index_type _hits_index, // read -> hits mapping + pool_type _hits_pool) : // pool counter + active_reads ( _active_reads ), + hits ( _hits ), + hits_index ( _hits_index ), + hits_pool ( _hits_pool ) +{} + +// constructor +// +// \param index read -> hits index +// \param hits hits container +// \param read_index index of this read +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +ReadHitsReference::ReadHitsReference(ScoringQueuesType& queues, const uint32 read_index) : + m_queues( queues ), + m_read_index( read_index ) +{} + +// size of the hits vector +// +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +uint32 ReadHitsReference::size() const +{ + return m_queues.hits_index.hit_count( m_read_index ); +} + +// return the i-th element +// +#pragma hd_warning_disable +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +typename ReadHitsReference::reference +ReadHitsReference::operator[] (const uint32 i) const +{ + const uint32 hit_index = m_queues.hits_index( m_read_index, i ); + return m_queues.hits[ hit_index ]; +} + +// return the slot where the i-th element is stored +// +#pragma hd_warning_disable +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +uint32 +ReadHitsReference::slot(const uint32 i) const +{ + return m_queues.hits_index( m_read_index, i ); +} + +// bind this read to its new output location +// +// \param read_index output index of this read +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +void ReadHitsReference::bind(const uint32 read_index) +{ + m_read_index = read_index; +} + +// access the packed_read info in the selected queue +// +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +packed_read ReadHitsReference::read_info() const +{ + return m_queues.active_reads.in_queue[ m_read_index ]; +} + + +// constructor +// +// \param index read -> hits index +// \param hits hits container +// \param read_index index of this read +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +ReadHitsBinder::ReadHitsBinder(ScoringQueuesType& queues, const uint32 read_index) : + m_queues( queues ), + m_read_index( read_index ) +{} + +// bind this read to its new output location +// +// \param read_index output index of this read +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +void ReadHitsBinder::bind(const uint32 read_index) +{ + m_read_index = read_index; +} + +// resize the hits vector +// +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +void ReadHitsBinder::resize(const uint32 size) +{ + m_queues.hits_index.set_hit_count( m_read_index, size ); +} + +// size of the hits vector +// +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +uint32 ReadHitsBinder::size() const +{ + return m_queues.hits_index.hit_count( m_read_index ); +} + +// return the i-th element +// +#pragma hd_warning_disable +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +typename ReadHitsBinder::reference +ReadHitsBinder::operator[] (const uint32 i) const +{ + const uint32 hit_index = m_queues.hits_index( m_read_index, i ); + return m_queues.hits[ hit_index ]; +} + +// access the packed_read info in the selected queue +// +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +packed_read ReadHitsBinder::read_info() const +{ + return m_queues.active_reads.out_queue[ m_read_index ]; +} + +// set the packed_read info +// +// \param read_index output index of this read +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +void ReadHitsBinder::set_read_info(const packed_read info) +{ + m_queues.active_reads.out_queue[ m_read_index ] = info; +} + +// bind the i-th hit to a given location +// +// \param i index of the hit to bind relative to this read +// \param slot address of the bound hit in the HitQueues +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +void ReadHitsBinder::bind_hit(const uint32 i, const uint32 slot) +{ + m_queues.hits_index( m_read_index, i ) = slot; +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring_queues_test.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring_queues_test.cu new file mode 100644 index 0000000000000000000000000000000000000000..c009d21aaf74ab67bee57a3d01b49c2e5b80c9b0 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/scoring_queues_test.cu @@ -0,0 +1,381 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +//#define NVBIO_CUDA_DEBUG +//#define NVBIO_CUDA_ASSERTS + +#include +#include +#include +#include +#include +#include +#include + + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +namespace { // anonymous namespace + +// +// Setup the contents of a ReadHitsIndex object through a ReadHitsIndexDeviceView. +// Implicitly also testing ReadHitsIndexDeviceView::reference. +// +__global__ +void setup_read_hits_index_kernel(ReadHitsIndexDeviceView read_hits_index, const uint32 n_reads, uint32* error) +{ + const uint32 read_index = threadIdx.x; + if (read_index >= n_reads) + return; + + // fetch the hits bound to this read + ReadHitsIndexDeviceView::reference hit_indices( read_hits_index, read_index ); + + // bound 2 hits to this read + hit_indices.resize( 2u ); + hit_indices[0] = read_index * 2u + 0u; + hit_indices[1] = read_index * 2u + 1u; +} + +// +// Check the contents of a ReadHitsIndex object through a ReadHitsIndexDeviceView. +// Implicitly also testing ReadHitsIndexDeviceView::reference. +// +__global__ +void check_read_hits_index_kernel(ReadHitsIndexDeviceView read_hits_index, const uint32 n_reads, uint32* error) +{ + const uint32 read_index = threadIdx.x; + if (read_index >= n_reads) + return; + + // fetch the hits bound to this read + ReadHitsIndexDeviceView::reference hit_indices( read_hits_index, read_index ); + + // make sure the number of hits bound to this read match our expectations + if (hit_indices.size() != 2u) + { + *error = 1; + return; + } + + // make sure their values match our expectations + if ((hit_indices[0] != read_index * 2u + 0u) || + (hit_indices[1] != read_index * 2u + 1u)) + { + *error = 2; + return; + } + + // make sure direct indexing work + if ((hit_indices[0] != read_hits_index( read_index, 0u )) || + (hit_indices[1] != read_hits_index( read_index, 1u ))) + { + *error = 3; + return; + } +} + +#pragma hd_warning_disable +template +NVBIO_HOST_DEVICE +void set_hit(HitReference hit, const uint32 read_id) +{ + hit.read_id = read_id; + hit.ssa = 0; + hit.loc = 1; + hit.score = 2; + hit.sink = 3; + hit.opposite_loc = 4; + hit.opposite_score = 5; + hit.opposite_sink = 6; +} +#pragma hd_warning_disable +template +NVBIO_HOST_DEVICE +bool check_hit(HitReference hit, const uint32 read_id) +{ + return (hit.read_id != read_id || + hit.ssa != 0 || + hit.loc != 1 || + hit.score != 2 || + hit.sink != 3 || + hit.opposite_loc != 4 || + hit.opposite_score != 5 || + hit.opposite_sink != 6); +} + +// +// Setup the contents of a HitQueues object through a HitQueuesDeviceView. +// Implicitly also testing HitReference. +// +__global__ +void setup_hit_queues_kernel(HitQueuesDeviceView hit_queues, const uint32 n_hits, uint32* error) +{ + const uint32 hit_index = threadIdx.x; + if (hit_index >= n_hits) + return; + + // take a reference to this hit + HitReference hit = hit_queues[ hit_index ]; + + // set it up + set_hit( hit, hit_index ); // assign a unique index as the read_id, for testing purposes +} +// +// Check the contents of a HitQueues object through a HitQueuesDeviceView. +// Implicitly also testing HitReference. +// +__global__ +void check_hit_queues_kernel(HitQueuesDeviceView hit_queues, const uint32 n_hits, uint32* error) +{ + const uint32 hit_index = threadIdx.x; + if (hit_index >= n_hits) + return; + + // take a reference to this hit + HitReference hit = hit_queues[ hit_index ]; + + // check that its values match our expectations + if (check_hit( hit, hit_index )) + *error = 1; +} + +// +// Test the ReadHitsReference object. +// At this point the read_hits_index and the hit_queues have been already setup, and we just need to make sure +// we can dereference them correctly through ReadHitsReference proxies. +// +__global__ +void test_read_hits_ref_kernel(ScoringQueuesDeviceView queues, const uint32 n_reads, uint32* error) +{ + const uint32 read_index = threadIdx.x; + if (read_index >= n_reads) + return; + + typedef ReadHitsReference read_hits_reference; + typedef typename read_hits_reference::reference hit_reference; + + // create a reference to the sequence of hits bound to this read + read_hits_reference read_hits( queues, read_index ); + + //read_hits.set_read_info( packed_read( read_index ) ); + + // check that we have 2 hits for each read + if (read_hits.size() != 2u) + { + *error = 1; + return; + } + + // make sure the hits bound to this read match our expectations + { + // examine the first hit + hit_reference hit = read_hits[0]; + + if (check_hit( hit, read_index*2u + 0u )) + { + *error = 2; + return; + } + } + { + // examine the second hit + hit_reference hit = read_hits[1]; + + if (check_hit( hit, read_index*2u + 1u )) + { + *error = 3; + return; + } + } +} + +// +// Test emission of new hits using a ReadHitsBinder +// +__global__ +void test_read_binder_kernel(ScoringQueuesDeviceView queues, const uint32 n_reads, uint32* error) +{ + const uint32 read_index = threadIdx.x; + if (read_index >= n_reads) + return; + + typedef ReadHitsReference read_hits_reference; + typedef ReadHitsBinder read_hits_binder; + typedef typename read_hits_reference::reference hit_reference; + + // create a hit binder for this read + packed_read src_read_info = queues.active_read( read_index ); + read_hits_binder dst_read_hits( queues ); + + // drop all odd reads + if ((read_index & 1) == 1) + return; + + // get a new slot for the read + const uint32 dst_slot = atomicAdd( queues.active_reads.out_size, 1u ); + + // bind the read to its new location in the output queue + dst_read_hits.bind( dst_slot ); + + // copy from parent + dst_read_hits.set_read_info( src_read_info ); + + // set the number of hits + dst_read_hits.resize( 1u ); + + // get a new slot for a hit + const uint32 hit_slot = atomicAdd( queues.hits_pool, 1u ); + + // bind the hit + dst_read_hits.bind_hit( 0u, hit_slot ); + + // and set it + set_hit( dst_read_hits[0], read_index ); +} + +} // anonymous namespace + +void test_scoring_queues() +{ + const uint32 n_hits = 100; + const uint32 n_reads = 50; + const uint32 n_hits_per_read = 2; + + ScoringQueues queues; + + queues.resize( n_reads, n_hits, true ); + + // test ReadHitsIndex interfaces + ReadHitsIndex& read_hits_index = queues.hits_index; + { + log_info( stderr, "test ReadHitsIndex... started\n" ); + + read_hits_index.setup( n_hits_per_read, n_reads ); + + thrust::device_vector error(1,0); + + setup_read_hits_index_kernel<<<1,128>>>( read_hits_index.device_view(), n_reads, device_view( error ) ); + check_read_hits_index_kernel<<<1,128>>>( read_hits_index.device_view(), n_reads, device_view( error ) ); + cudaThreadSynchronize(); + + const uint32 error_code = error[0]; + if (error_code) + { + log_error( stderr, "test ReadHitsIndex... failed! (error code %u)\n", error_code ); + exit(1); + } + + log_info( stderr, "test ReadHitsIndex... done\n" ); + } + + // test HitQueues interfaces + HitQueues& hit_queues = queues.hits; + { + log_info( stderr, "test HitQueues... started\n" ); + + // check host-side access + for (uint32 i = 0; i < 10; ++i) + { + HitReference hit( hit_queues, i ); + + set_hit( hit, i ); + } + for (uint32 i = 0; i < 10; ++i) + { + HitReference hit( hit_queues, i ); + + if (check_hit( hit, i )) + { + log_error( stderr, "test HitQueues... failed! (host-side referencing)\n" ); + exit(1); + } + } + + thrust::device_vector error(1,0); + + setup_hit_queues_kernel<<<1,128>>>( hit_queues.device_view(), n_hits, device_view( error ) ); + check_hit_queues_kernel<<<1,128>>>( hit_queues.device_view(), n_hits, device_view( error ) ); + cudaThreadSynchronize(); + + const uint32 error_code = error[0]; + if (error_code) + { + log_error( stderr, "test HitQueues... failed! (error code %u)\n", error_code ); + exit(1); + } + + log_info( stderr, "test HitQueues... done\n" ); + } + + // test ReadHitsReference object + { + log_info( stderr, "test ReadHitsReference... started\n" ); + + thrust::device_vector error(1,0); + + test_read_hits_ref_kernel<<<1,128>>>( queues.device_view(), n_reads, device_view( error ) ); + cudaThreadSynchronize(); + + const uint32 error_code = error[0]; + if (error_code) + { + log_error( stderr, "test ReadHitsReference... failed! (error code %u)\n", error_code ); + exit(1); + } + + log_info( stderr, "test ReadHitsReference... done\n" ); + } + + // test ReadHitsBinder object + { + log_info( stderr, "test ReadHitsBinder... started\n" ); + + thrust::device_vector error(1,0); + + // clear output queues + queues.clear_output(); + + test_read_binder_kernel<<<1,128>>>( queues.device_view(), n_reads, device_view( error ) ); + cudaThreadSynchronize(); + + const uint32 error_code = error[0]; + if (error_code) + { + log_error( stderr, "test ReadHitsBinder... failed! (error code %u)\n", error_code ); + exit(1); + } + + log_info( stderr, "test ReadHitsBinder... done\n" ); + } +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit.h new file mode 100644 index 0000000000000000000000000000000000000000..27d0e60ba01e5c7e187130277b1cc36ba259d5ab --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit.h @@ -0,0 +1,251 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/// +///\file seed_hit.h +/// + +#pragma once + +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +///@addtogroup nvBowtie +///@{ + +///@addtogroup SeedHits +///@{ + +/// +/// Represents a seed match in the FM-index as an SA range, tracking the direction of the read +/// and that of the FM-index. +/// +struct SeedHit +{ + struct Flags { uint32 m_pos:10, m_rc:1, m_indexdir:1; }; + + /// build the compressed seed flags for a hit + /// + NVBIO_HOST_DEVICE NVBIO_FORCEINLINE + static Flags build_flags( + const ReadType readtype, + const DirType indexdir, + const uint32 pos) + { + Flags flags; + flags.m_pos = pos; + flags.m_rc = readtype; + flags.m_indexdir = indexdir; + return flags; + } + + /// constructor + /// + NVBIO_HOST_DEVICE NVBIO_FORCEINLINE + SeedHit() {} + + /// constructor + /// + /// \param readtype select between forward and reverse-complemented read + /// \param indexdir direction in the FM-index + /// \param pos seed position within the read + /// \param range SA range + NVBIO_HOST_DEVICE NVBIO_FORCEINLINE + SeedHit(const ReadType readtype, + const DirType indexdir, + const uint32 pos, + const uint2& range) + : m_range_begin( range.x ), + m_range_delta( range.y - range.x ), + m_pos( pos ), + m_rc( readtype ), + m_indexdir( indexdir ) + { + NVBIO_CUDA_ASSERT( range.x <= range.y ); + NVBIO_CUDA_ASSERT( range.y - range.x < (1u << 20) ); + } + + /// constructor + /// + /// \param flags compressed seed flags + /// \param range SA range + NVBIO_HOST_DEVICE NVBIO_FORCEINLINE + SeedHit(const Flags flags, + const uint2& range) + : m_range_begin( range.x ), + m_range_delta( range.y - range.x ), + m_pos( flags.m_pos ), + m_rc( flags.m_rc ), + m_indexdir( flags.m_indexdir ) + { + NVBIO_CUDA_ASSERT( range.x <= range.y ); + NVBIO_CUDA_ASSERT( range.y - range.x < (1u << 20) ); + } + + /// set the SA range + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void set_range(const uint2 range) + { + NVBIO_CUDA_ASSERT( range.x <= range.y ); + NVBIO_CUDA_ASSERT( range.y - range.x < (1u << 20) ); + m_range_begin = range.x; + m_range_delta = range.y - range.x; + } + + /// get the SA range + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint2 get_range() const + { return make_uint2( m_range_begin, m_range_begin + m_range_delta ); } + + /// is empty + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool empty() const + { return m_range_delta == 0; } + + /// get the size of the SA range + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 get_range_size() const + { return m_range_delta; } + + /// return the front of the SA range + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 front() const { return m_range_begin; } + + /// return the back of the SA range + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 back() const { return m_range_begin + m_range_delta - 1u; } + + /// pop the front of the SA range + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 pop_front() + { + const uint32 r = m_range_begin++; + --m_range_delta; + return r; + } + + /// pop n-elements from the front of the SA range + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 pop_front(const uint32 n) + { + const uint32 r = m_range_begin; + m_range_begin += n; + m_range_delta -= n; + return r; + } + + /// pop the back of the SA range + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 pop_back() + { + --m_range_delta; + return m_range_begin + m_range_delta; + } + + /// pop n-elements from the back of the SA range + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 pop_back(const uint32 n) + { + m_range_delta -= n; + return m_range_begin + m_range_delta; + } + + /// set the seed position in the read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void set_posinread(const uint32 p) + { m_pos = p; } + + /// set the read flags + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void set_readtype(const ReadType d) + { m_rc = d; } + + /// set the FM-index orientation + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void set_indexdir(const DirType d) + { m_indexdir = d; } + + /// get the seed position in the read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 get_posinread() const + { return m_pos; } + + /// get the read flags + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + ReadType get_readtype() const + { return ReadType( m_rc ); } + + /// get the FM-index orientation + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + DirType get_indexdir() const + { return DirType( m_indexdir ); } + +private: + uint32 m_range_begin; + uint32 m_range_delta:20, m_pos:10, m_rc:1, m_indexdir:1; +}; + +struct hit_compare +{ + NVBIO_HOST_DEVICE NVBIO_FORCEINLINE + bool operator() (const SeedHit& f, const SeedHit& s) + { + const uint32 size_f = f.get_range_size(); + const uint32 size_s = s.get_range_size(); + return (size_f > size_s); + } +}; + +///@} // group SeedHits +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit_deque_array.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit_deque_array.cu new file mode 100644 index 0000000000000000000000000000000000000000..06c650e2e266b4f433b007b5a531699819c33ad0 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit_deque_array.cu @@ -0,0 +1,71 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// resize the arena +// +// \return # of allocated bytes +uint64 SeedHitDequeArray::resize(const uint32 n_reads, const uint32 max_hits, const bool do_alloc) +{ + uint64 bytes = 0u; + uint32 max_nodes = SumTree::node_count( max_hits ); + if (do_alloc) m_counts.resize( n_reads ); bytes += n_reads * sizeof(uint32); + if (do_alloc) m_index.resize( n_reads ); bytes += n_reads * sizeof(uint32); + if (do_alloc) m_hits.resize( n_reads * max_hits ); bytes += n_reads * max_hits * sizeof(SeedHit); + if (do_alloc) m_probs.resize( n_reads * max_nodes ); bytes += n_reads * max_nodes * sizeof(float); + if (do_alloc) m_probs_index.resize( n_reads ); bytes += n_reads * sizeof(uint32); + if (do_alloc) m_pool.resize( 1, 0u ); bytes += sizeof(uint32); + if (do_alloc) m_probs_pool.resize( 1, 0u ); bytes += sizeof(uint32); + + if (do_alloc) thrust::fill( m_counts.begin(), m_counts.end(), uint32(0) ); + if (do_alloc) thrust::fill( m_index.begin(), m_index.end(), uint32(0) ); + if (do_alloc) thrust::fill( m_probs_index.begin(), m_probs_index.end(), uint32(0) ); + return bytes; +} + +/// clear all deques +/// +void SeedHitDequeArray::clear_deques() +{ + // reset deque size counters + thrust::fill( m_counts.begin(), m_counts.end(), uint32(0) ); + thrust::fill( m_index.begin(), m_index.end(), uint32(0) ); + thrust::fill( m_probs_index.begin(), m_probs_index.end(), uint32(0) ); + + m_pool[0] = 0; // reset the arena + m_probs_pool[0] = 0; // reset the arena +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit_deque_array.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit_deque_array.h new file mode 100644 index 0000000000000000000000000000000000000000..208f2f2cb721e64e9f233cceea4e3c0883ee5aab --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit_deque_array.h @@ -0,0 +1,354 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/// +///\file seed_hit_deque_array.h +/// + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +///@addtogroup nvBowtie +///@{ + +///@addtogroup SeedHits +///@{ + +struct SeedHitDequeArrayDeviceView; + +template struct SeedHitDequeReference; + +/// +/// The SeedHitDequeArray device storage class +/// +struct SeedHitDequeArrayDeviceStorage +{ + typedef thrust::device_vector hits_storage_type; + typedef thrust::device_vector index_storage_type; + typedef thrust::device_vector prob_storage_type; + + hits_storage_type m_hits; ///< global arena of seed hit SA ranges + index_storage_type m_counts; ///< per-read seed hit counters + prob_storage_type m_probs; ///< global arena of SA probabilities + index_storage_type m_index; ///< per-read index marking the beginning of the read's hits vector in the global arena + index_storage_type m_probs_index; ///< per-read index marking the beginning of the read's hits vector in the global arena + index_storage_type m_pool; ///< pool counter for the global arena + index_storage_type m_probs_pool; ///< pool counter for the global arena +}; + +/// +/// The SeedHitDequeArray host storage class +/// +struct SeedHitDequeArrayHostStorage +{ + typedef thrust::host_vector hits_storage_type; + typedef thrust::host_vector index_storage_type; + typedef thrust::host_vector prob_storage_type; + + /// copy constructor + /// + SeedHitDequeArrayHostStorage(const SeedHitDequeArrayDeviceStorage& other) { (*this)= other; } + + /// copy from a device object + /// + SeedHitDequeArrayHostStorage& operator=(const SeedHitDequeArrayDeviceStorage& other) + { + nvbio::cuda::thrust_copy_vector( m_hits, other.m_hits ); + nvbio::cuda::thrust_copy_vector( m_counts, other.m_counts ); + nvbio::cuda::thrust_copy_vector( m_probs, other.m_probs ); + nvbio::cuda::thrust_copy_vector( m_index, other.m_index ); + nvbio::cuda::thrust_copy_vector( m_probs_index, other.m_probs_index ); + nvbio::cuda::thrust_copy_vector( m_pool, other.m_pool ); + nvbio::cuda::thrust_copy_vector( m_probs_pool, other.m_probs_pool ); + return *this; + } + + hits_storage_type m_hits; ///< global arena of seed hit SA ranges + index_storage_type m_counts; ///< per-read seed hit counters + prob_storage_type m_probs; ///< global arena of SA probabilities + index_storage_type m_index; ///< per-read index marking the beginning of the read's hits vector in the global arena + index_storage_type m_probs_index; ///< per-read index marking the beginning of the read's hits vector in the global arena + index_storage_type m_pool; ///< pool counter for the global arena + index_storage_type m_probs_pool; ///< pool counter for the global arena +}; + +/// +/// An array containing a priority deque of SeedHit's per read +/// +struct SeedHitDequeArray : public SeedHitDequeArrayDeviceStorage +{ + typedef SeedHitDequeArrayDeviceStorage::hits_storage_type hits_storage_type; + typedef SeedHitDequeArrayDeviceStorage::index_storage_type index_storage_type; + typedef SeedHitDequeArrayDeviceStorage::prob_storage_type prob_storage_type; + + typedef SeedHitDequeArrayDeviceView device_view_type; + + /// resize the arena + /// + /// \return # of allocated bytes + uint64 resize(const uint32 n_reads, const uint32 max_hits, const bool do_alloc = true); + + /// clear all deques + /// + void clear_deques(); + + /// return the device view + /// + SeedHitDequeArrayDeviceView device_view(); + + /// return the hits vector + /// + hits_storage_type& hits() { return m_hits; } + + /// return the counts vector + /// + index_storage_type& counts() { return m_counts; } + + /// return the index vector + /// + index_storage_type& index() { return m_index; } + + /// return the probs vector + /// + prob_storage_type& probs() { return m_probs; } +}; + +/// +/// An array containing a priority deque of SeedHit's per read +/// +struct SeedHitDequeArrayDeviceView +{ + typedef typename device_view_subtype< thrust::device_vector >::type hits_storage_type; + typedef typename device_view_subtype< thrust::device_vector >::type index_storage_type; + typedef typename device_view_subtype< thrust::device_vector >::type prob_storage_type; + + typedef vector_view hit_vector_type; + typedef priority_deque hit_deque_type; + + typedef SeedHitDequeReference reference; + + /// constructor + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + SeedHitDequeArrayDeviceView( + index_storage_type counts = index_storage_type(), + index_storage_type index = index_storage_type(), + hits_storage_type hits = hits_storage_type(), + index_storage_type probs_index = index_storage_type(), + prob_storage_type probs = prob_storage_type(), + index_storage_type pool = index_storage_type(), + index_storage_type probs_pool = index_storage_type()); + + /// return a reference to the given deque + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + reference operator[] (const uint32 read_id); + + /// allocate some storage for the deque bound to a given read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + SeedHit* alloc_deque(const uint32 read_id, const uint32 size); + + /// resize the deque bound to a given read + /// NOTE: this method doesn't alloc or release any memory! alloc_deque() must have been previously called. + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void resize_deque(const uint32 read_id, const uint32 size) { m_counts[read_id] = size; } + + /// get the size of the hit vector bound to a given read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 get_size(const uint32 read_id) const { return m_counts[read_id]; } + + /// get the storage for the hit vector bound to a given read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + SeedHit* get_data(const uint32 read_id) const { return m_hits.base() + m_index[read_id]; } + + /// get the storage for the hit vector bound to a given read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + float* get_probs(const uint32 read_id) const { return m_probs.base() + m_probs_index[read_id]; } + + /// erase the set of hits bound to a read. + /// NOTE: this method doesn't release the previously allocated memory! + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void erase(const uint32 read_id) { m_counts[read_id] = 0; } + + /// return the deque bound to a given read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + hit_deque_type get_deque(const uint32 read_id, bool build_heap = false) const; + +//private: + hits_storage_type m_hits; ///< global arena of seed hit SA ranges + index_storage_type m_counts; ///< per-read seed hit counters + prob_storage_type m_probs; ///< global arena of SA probabilities + index_storage_type m_index; ///< per-read index marking the beginning of the read's hits vector in the global arena + index_storage_type m_probs_index; ///< per-read index marking the beginning of the read's hits vector in the global arena + index_storage_type m_pool; ///< pool counter for the global arena + index_storage_type m_probs_pool; ///< pool counter for the global arena +}; + +/// +/// Implements a reference to a hit deque bound to a read. +/// Provides methods for atomically allocating the deque's storage, as well as +/// a deque and plain array interface. +/// +template +struct SeedHitDequeReference +{ + typedef vector_view hit_vector_type; + typedef priority_deque hit_deque_type; + + /// constructor + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + SeedHitDequeReference(SeedHitDequeArrayType& deques, const uint32 read_id) : + m_deques( deques ), + m_read_id( read_id ), + m_deque( deques.get_deque( read_id ) ) {} + + /// destructor + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + ~SeedHitDequeReference() + { + // update the size of the deque if dirty + m_deques.resize_deque( m_read_id, m_deque.size() ); + } + + /// allocate some storage for the deque bound to a given read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + SeedHit* alloc(const uint32 size) + { + SeedHit* storage = m_deques.alloc_deque( m_read_id, size ); + m_deque = m_deques.get_deque( m_read_id ); // re-assign the deque + return storage; + } + + /// allocate some storage for the deque bound to a given read + /// NOTE: this method doesn't expand or release the previously allocated memory! + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void resize(const uint32 size) + { + m_deques.resize_deque( m_read_id, size ); + m_deque = m_deques.get_deque( m_read_id ); // re-assign the deque + } + + /// get the size of the hit vector bound to a given read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 size() const { return m_deque.size(); } + + /// get the storage for the hit vector bound to a given read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + SeedHit* get_data() const { return m_deques.get_data( m_read_id ); } + + /// get the storage for the hit vector bound to a given read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + float* get_probs() const { return m_deques.get_probs( m_read_id ); } + + /// erase the set of hits bound to a read. + /// NOTE: this method doesn't release the previously allocated memory! + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void erase() { m_deques.erase( m_read_id ); m_deque = get_deque( m_read_id ); } + + /// return the deque bound to a given read + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + hit_deque_type get_deque(bool build_heap = false) const { return m_deques.get_deque( m_read_id, build_heap ); } + + /// push a seed-hit + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void push(const SeedHit hit) { m_deque.push( hit ); } + + /// pop from the front + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void pop_top() { m_deque.pop_top(); } + + /// pop from the front + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void pop_bottom() { m_deque.pop_bottom(); } + + /// pop from the top + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void pop() { m_deque.pop(); } + + /// top + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + const SeedHit& top() const { return m_deque.top(); } + + /// bottom + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + const SeedHit& bottom() const { return m_deque.bottom(); } + + /// return the i-th seed-hit (unsorted) + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + SeedHit& operator[] (const uint32 i) { return get_data()[i]; } + +private: + SeedHitDequeArrayType& m_deques; ///< reference to deque array + uint32 m_read_id; ///< read id + hit_deque_type m_deque; ///< local deque object for this read +}; + +///@} // group SeedHits +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio + +#include diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit_deque_array_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit_deque_array_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..71e3a9ec62ab6196f5802d06bd2b97b3facde8b7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit_deque_array_inl.h @@ -0,0 +1,113 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// return the device view +// +inline +SeedHitDequeArrayDeviceView SeedHitDequeArray::device_view() +{ + return SeedHitDequeArrayDeviceView( + nvbio::device_view( m_counts ), + nvbio::device_view( m_index ), + nvbio::device_view( m_hits ), + nvbio::device_view( m_probs_index ), + nvbio::device_view( m_probs ), + nvbio::device_view( m_pool ), + nvbio::device_view( m_probs_pool ) ); +} + +// constructor +// +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +SeedHitDequeArrayDeviceView::SeedHitDequeArrayDeviceView( + index_storage_type counts, + index_storage_type index, + hits_storage_type hits, + index_storage_type probs_index, + prob_storage_type probs, + index_storage_type pool, + index_storage_type probs_pool) : + m_counts( counts ), + m_hits( hits ), + m_probs( probs ), + m_index( index ), + m_probs_index( probs_index ), + m_pool( pool ), + m_probs_pool( probs_pool ) +{} + +// return a reference to the given deque +// +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +SeedHitDequeArrayDeviceView::reference SeedHitDequeArrayDeviceView::operator[] (const uint32 read_id) +{ + return reference( *this, read_id ); +} + +// allocate some storage for the deque bound to a given read +// +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +SeedHit* SeedHitDequeArrayDeviceView::alloc_deque(const uint32 read_id, const uint32 size) +{ +#if defined(__CUDA_ARCH__) && __CUDA_ARCH__ > 0 + m_counts[read_id] = 0u; + const uint32 index = size ? atomicAdd( m_pool, size ) : 0u; + const uint32 probs_index = size ? atomicAdd( m_probs_pool, SumTree::node_count( size ) ) : 0u; + if (index < m_hits.size()) + { + m_index[read_id] = index; + m_probs_index[read_id] = probs_index; + return m_hits + m_index[read_id]; + } + else + { + // allocation failed + m_index[read_id] = 0; + m_probs_index[read_id] = 0; + return NULL; + } +#else + return NULL; +#endif +} + +// return the deque bound to a given read +// +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +typename SeedHitDequeArrayDeviceView::hit_deque_type SeedHitDequeArrayDeviceView::get_deque(const uint32 read_id, bool build_heap) const +{ + hit_vector_type hit_vector( m_counts[read_id], get_data( read_id ) ); + return hit_deque_type( hit_vector, build_heap ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit_deque_array_test.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit_deque_array_test.cu new file mode 100644 index 0000000000000000000000000000000000000000..583583c3a8e5cf2fec3a3230a1fd06187cc8e900 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/seed_hit_deque_array_test.cu @@ -0,0 +1,121 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +//#define NVBIO_CUDA_DEBUG +//#define NVBIO_CUDA_ASSERTS + +#include +#include +#include +#include +#include +#include +#include + + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +namespace { // anonymous namespace + +__global__ +void setup_deques_kernel(SeedHitDequeArrayDeviceView seed_hit_deques, const uint32 n_reads, uint32* error) +{ + if (threadIdx.x >= n_reads) + return; + + typedef SeedHitDequeArrayDeviceView::reference hit_deque_reference; + typedef SeedHitDequeArrayDeviceView::hit_deque_type hit_deque_type; + + // fetch the deque bound to this read + hit_deque_reference hit_deque = seed_hit_deques[ threadIdx.x ]; + + // alloc storage for 2 entries in this read's deque + hit_deque.alloc( 2u ); + + // push first hit + hit_deque.push( SeedHit( STANDARD, FORWARD, threadIdx.x * 2u + 1u, make_uint2( 0, 100 ) ) ); + + // push second hit + hit_deque.push( SeedHit( STANDARD, FORWARD, threadIdx.x * 2u + 0u, make_uint2( 0, 10 ) ) ); +} + +__global__ +void check_deques_kernel(SeedHitDequeArrayDeviceView seed_hit_deques, const uint32 n_reads, uint32* error) +{ + if (threadIdx.x >= n_reads) + return; + + typedef SeedHitDequeArrayDeviceView::reference hit_deque_reference; + typedef SeedHitDequeArrayDeviceView::hit_deque_type hit_deque_type; + + // fetch the deque bound to this read + hit_deque_reference hit_deque = seed_hit_deques[ threadIdx.x ]; + + SeedHit hit; + + // pop first hit + hit = hit_deque.top(); hit_deque.pop(); + if (hit.get_posinread() != threadIdx.x * 2u + 0u) + *error = 1; + + // pop second hit + hit = hit_deque.top(); hit_deque.pop(); + if (hit.get_posinread() != threadIdx.x * 2u + 1u) + *error = 2; +} + +} // anonymous namespace + +void test_seed_hit_deques() +{ + log_info(stderr, "test seed_hit_deques... started\n"); + SeedHitDequeArray seed_hit_deques; + + const uint32 n_hits = 100; + const uint32 n_reads = 50; + + const uint64 bytes = seed_hit_deques.resize( n_reads, n_hits ); + log_info(stderr, " allocated %llu bytes\n", bytes); + + thrust::device_vector error(1,0); + + setup_deques_kernel<<<1,128>>>( seed_hit_deques.device_view(), n_reads, device_view( error ) ); + check_deques_kernel<<<1,128>>>( seed_hit_deques.device_view(), n_reads, device_view( error ) ); + cudaThreadSynchronize(); + + const uint32 error_code = error[0]; + if (error_code) + log_error( stderr, "test_read_hits_index failed! (error code: %u)\n", error_code ); + + log_info(stderr, "test seed_hit_deques... done\n"); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/select.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/select.cu new file mode 100644 index 0000000000000000000000000000000000000000..81d116d1e54ae72f6902dc752b4f526a140eaa89 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/select.cu @@ -0,0 +1,289 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +__global__ +void select_init_kernel( + const uint32 count, + const char* read_names, + const uint32* read_names_idx, + SeedHitDequeArrayDeviceView hits, + uint32* trys, + uint32* rseeds, + const ParamsPOD params) +{ + // + // NOTE: here we are initializing constants for ALL the reads in a batch, + // including inactive ones. This works because we always access these fields + // by read id throughout the entire pipeline. + // + + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= count) return; + + // initialize the number of trys + if (trys) + trys[ thread_id ] = params.max_effort_init; + + // initialize the probability trees + if (params.randomized) + { + // initialize the generator + //rseeds[ thread_id ] = 0u; + { + // compute a hash of the read name + const uint32 off = read_names_idx[ thread_id ]; + const uint32 len = read_names_idx[ thread_id + 1u ] - off; + + const char* read_name = read_names + off; + + // djb2 hashing function + uint32 hash = 5381; + for (uint32 i = 0; i < len && read_name[i]; ++i) + hash = ((hash << 5) + hash) ^ read_name[i]; + + rseeds[ thread_id ] = hash; + } + + typedef SumTree ProbTree; + + // check whether we have a non-zero number of hits, otherwise we can go home + const uint32 n_hits = hits.get_size( thread_id ); + if (n_hits == 0u) + return; + + // build the probability tree + float* hit_probs = hits.get_probs( thread_id ); + const SeedHit* hit_data = hits.get_data( thread_id ); + + for (uint32 i = 0; i < n_hits; ++i) + { + const SeedHit hit = hit_data[i]; + const uint2 range = hit.get_range(); + hit_probs[i] = 1.0f / (float(range.y - range.x) * + float(range.y - range.x)); + } + if (params.top_seed) + hit_probs[0] = 0.0f; // assign zero probability to the top hit, as we will deterministically visit it + + // setup the tree + ProbTree prob_tree( nvbio::max( n_hits, 1u ), hit_probs ); + prob_tree.setup(); + } +} + +// +// Initialize the hit-selection pipeline +// +void select_init( + const uint32 count, + const char* read_names, + const uint32* read_names_idx, + SeedHitDequeArrayDeviceView hits, + uint32* trys, + uint32* rseeds, + const ParamsPOD params) +{ + const int blocks = (count + BLOCKDIM-1) / BLOCKDIM; + + select_init_kernel<<>>( + count, + read_names, + read_names_idx, + hits, + trys, + rseeds, + params ); +} + +// +// Initialize the hit-selection pipeline +// +void select_init(BestApproxScoringPipelineState& pipeline, const ParamsPOD& params) +{ + select_init_t( pipeline, params ); +} + +// +// Initialize the hit-selection pipeline +// +void select_init(BestApproxScoringPipelineState >& pipeline, const ParamsPOD& params) +{ + select_init_t( pipeline, params ); +} + +// +// Prepare for a round of seed extension by selecting the next SA row from each +// of the seed-hit deque arrays (SeedHitDequeArray) bound to the active-reads in +// the scoring queues (ScoringQueues::active_reads). +// +void select( + const SelectBestApproxContext context, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params) +{ + select_t( context, pipeline, params ); +} + +// +// Prepare for a round of seed extension by selecting the next SA row from each +// of the seed-hit deque arrays (SeedHitDequeArray) bound to the active-reads in +// the scoring queues (ScoringQueues::active_reads). +// +void select( + const SelectBestApproxContext context, + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD params) +{ + select_t( context, pipeline, params ); +} + +/// +/// select next hit extensions for all-mapping +/// +__global__ +void select_all_kernel( + const uint64 begin, + const uint32 count, + const uint32 n_reads, + const uint32 n_hit_ranges, + const uint64 n_hits, + SeedHitDequeArrayDeviceView hits, + const uint32* hit_count_scan, + const uint64* hit_range_scan, + HitQueuesDeviceView hit_queues) +{ + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= count) return; + + // each thread is responsible to process a hit, starting from 'begin' + const uint64 global_hit_id = begin + thread_id; + + // do a binary search, looking for thread_id in hit_range_scan, + // to find the corresponding seed hit. + const uint32 global_range_id = uint32( upper_bound( global_hit_id, hit_range_scan, n_hit_ranges ) - hit_range_scan ); + + // at this point we can figure out which read this range belongs to + const uint32 read_id = uint32( upper_bound( global_range_id, hit_count_scan, n_reads ) - hit_count_scan ); + + // now we have everything we need to access the proper hit_data + const SeedHit* hit_data = hits.get_data( read_id ); + + // compute the local range index within this read + const uint32 count_offset = read_id ? hit_count_scan[ read_id-1 ] : 0u; + const uint32 range_id = global_range_id - count_offset; + + const SeedHit* hit = &hit_data[ range_id ]; + + // compute the local hit index within this range + const uint64 range_offset = global_range_id ? hit_range_scan[ global_range_id-1 ] : 0u; + const uint32 hit_id = uint32( global_hit_id - range_offset ); + + const uint32 r_type = hit->get_readtype() ? 1u : 0u; + + HitReference out_hit( hit_queues, thread_id ); + out_hit.loc = hit->front() + hit_id; + out_hit.seed = packed_seed( hit->get_posinread(), hit->get_indexdir(), r_type, 0u ); + out_hit.read_id = read_id; +} + +/// +/// select next hit extensions from the top seed ranges +/// +__global__ +void select_n_from_top_range_kernel( + const uint32 begin, + const uint32 count, + const uint32 n_reads, + SeedHitDequeArrayDeviceView hits, + const uint32* hit_range_scan, + uint32* loc_queue, + packed_seed* seed_queue, + packed_read* read_info) +{ + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= count) return; + + // each thread is responsible to process a hit, starting from 'begin' + const uint64 global_hit_id = begin + thread_id; + + // do a binary search, looking for thread_id in hit_range_scan, + // to find the corresponding read id. + const uint32 read_id = uint32( upper_bound( global_hit_id, hit_range_scan, n_reads ) - hit_range_scan ); + + // now we have everything we need to access the proper hit_data + const SeedHit* hit_data = hits.get_data( read_id ); + + // fetch the top range + const SeedHit* hit = &hit_data[0]; + + // compute the local hit index within this range + const uint64 range_offset = global_hit_id ? hit_range_scan[ read_id-1 ] : 0u; + const uint32 hit_id = uint32( global_hit_id - range_offset ); + + const uint32 r_type = hit->get_readtype() ? 1u : 0u; + + loc_queue[ thread_id ] = hit->front() + hit_id; + seed_queue[ thread_id ] = packed_seed( hit->get_posinread(), hit->get_indexdir(), r_type, 0u ); + read_info[ thread_id ] = packed_read( read_id ); +} + +void select_all( + const uint64 begin, + const uint32 count, + const uint32 n_reads, + const uint32 n_hit_ranges, + const uint64 n_hits, + const SeedHitDequeArrayDeviceView hits, + const uint32* hit_count_scan, + const uint64* hit_range_scan, + HitQueuesDeviceView hit_queues) +{ + const int blocks = (count + BLOCKDIM-1) / BLOCKDIM; + + select_all_kernel<<>>( + begin, + count, + n_reads, + n_hit_ranges, + n_hits, + hits, + hit_count_scan, + hit_range_scan, + hit_queues ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/select.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/select.h new file mode 100644 index 0000000000000000000000000000000000000000..642674a6d594c917fc1d15b6fe684a2e1ba79d74 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/select.h @@ -0,0 +1,174 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/// +///\file select.h +/// + +#pragma once + +#include +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +template struct BaseScoringPipelineState; +template struct BestApproxScoringPipelineState; + +///@addtogroup nvBowtie +///@{ + +/// \defgroup Select +/// +/// The functions in this module implement a pipeline stage in which, for all the active reads in the +/// \ref ScoringQueues, a group of seed hits is selected for a new round of \ref Scoring. +/// In terms of inputs and outputs, this stage takes the set of input ScoringQueues::active_reads, and +/// fills the ScoringQueues::hits with a new set of hits, writing the HitQueues::read_id, HitQueues::seed, +/// and HitQueues::loc fields. The hits' location specified by the HitQueues::loc field is expressed in +/// Suffix Array coordinates. +/// Finally, this stage is also responsible for producing a new set of ScoringQueues::active_reads. +/// +/// \b inputs: +/// - SeedHitDequeArray +/// - ScoringQueues::active_reads +/// +/// \b outputs: +/// - SeedHitDequeArray +/// - ScoringQueues::active_reads +/// - HitQueues::read_id +/// - HitQueues::seed +/// - HitQueues::loc +/// + +///@addtogroup Select +///@{ + +/// +/// Initialize the hit-selection pipeline +/// +void select_init( + const uint32 count, + const char* read_names, + const uint32* read_names_idx, + const SeedHitDequeArrayDeviceView hits, + uint32* trys, + uint32* rseeds, + const ParamsPOD params); + +/// +/// Initialize the hit-selection pipeline +/// +void select_init(BestApproxScoringPipelineState& pipeline, const ParamsPOD& params); + +/// +/// Initialize the hit-selection pipeline +/// +void select_init(BestApproxScoringPipelineState >& pipeline, const ParamsPOD& params); + +/// +/// a context class for the select_kernel +/// +struct SelectBestApproxContext +{ + // constructor + // + // \param trys the per-read vector of extension trys + // + SelectBestApproxContext(uint32* trys) : m_trys( trys ) {} + + // stopping function + // + // \return true iff we can stop the hit selection process + // + NVBIO_FORCEINLINE NVBIO_DEVICE + bool stop(const uint32 read_id) const { return m_trys[ read_id ] == 0; } + +private: + uint32* m_trys; +}; + +/// +/// select next hit extensions from the top seed ranges +/// +__global__ +void select_n_from_top_range_kernel( + const uint32 begin, + const uint32 count, + const uint32 n_reads, + const SeedHit* hit_data, + const uint32* hit_range_scan, + uint32* loc_queue, + uint32* seed_queue, + uint32* read_info); + +/// +/// Prepare for a round of seed extension by selecting the next SA row from each +/// of the seed-hit deque arrays (SeedHitDequeArray) bound to the active-reads in +/// the scoring queues (ScoringQueues::active_reads). +/// +void select( + const SelectBestApproxContext context, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params); + +/// +/// Prepare for a round of seed extension by selecting the next SA row from each +/// of the seed-hit deque arrays (SeedHitDequeArray) bound to the active-reads in +/// the scoring queues (ScoringQueues::active_reads). +/// +void select( + const SelectBestApproxContext context, + const BestApproxScoringPipelineState >& pipeline, + const ParamsPOD params); + +/// +/// Select next hit extensions for all-mapping +/// +void select_all( + const uint64 begin, + const uint32 count, + const uint32 n_reads, + const uint32 n_hit_ranges, + const uint64 n_hits, + const SeedHitDequeArrayDeviceView hits, + const uint32* hit_count_scan, + const uint64* hit_range_scan, + HitQueuesDeviceView scoring_queues); + +///@} // group Select +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/select_impl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/select_impl.h new file mode 100644 index 0000000000000000000000000000000000000000..f76ee6d473147dbfe0e77e3896a2f8d40f6f07f2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/select_impl.h @@ -0,0 +1,148 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +/// +///\file select.h +/// + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +template struct BaseScoringPipelineState; +template struct BestApproxScoringPipelineState; + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Select +///@{ + +/// +/// Initialize the hit-selection pipeline +/// +template +void select_init_t(BestApproxScoringPipelineState& pipeline, const ParamsPOD& params); + +/// +/// Prepare for a round of seed extension by selecting the next SA row from each +/// of the seed-hit deque arrays (SeedHitDequeArray) bound to the active-reads in +/// the scoring queues (ScoringQueues::active_reads). +/// +template +void select( + const BatchType read_batch, + SeedHitDequeArrayDeviceView hits, + const ContextType context, + ScoringQueuesDeviceView scoring_queues, + const ParamsPOD params); + +/// +/// Prepare for a round of seed extension by selecting the next SA row from each +/// of the seed-hit deque arrays (SeedHitDequeArray) bound to the active-reads in +/// the scoring queues (ScoringQueues::active_reads). +/// +template +void rand_select( + const BatchType read_batch, + SeedHitDequeArrayDeviceView hits, + uint32* rseeds, + const ContextType context, + ScoringQueuesDeviceView scoring_queues, + const ParamsPOD params); + +/// +/// Prepare for a round of seed extension by selecting a set of up +/// to 'n_multi' SA rows from each of the seed-hit deque arrays (SeedHitDequeArray) +/// bound to the active-reads in the scoring queues (ScoringQueues::active_reads). +/// +/// For each read in the input queue, this kernel generates: +/// 1. one or zero output reads, in the main output read queue, +/// 2. zero to 'n_multi' SA rows. These are made of three entries, +/// one in 'loc_queue', identifying the corresponding SA index, +/// one in 'seed_queue', storing information about the seed hit, +/// and one in 'parent_queue', storing the index of the "parent" +/// read in the output queue (i.e. the slot where the read is +/// is being stored) +/// +template +void select_multi( + const BatchType read_batch, + SeedHitDequeArrayDeviceView hits, + const ContextType context, + ScoringQueuesDeviceView scoring_queues, + const uint32 n_multi, + const ParamsPOD params); + +/// +/// Prepare for a round of seed extension by selecting the next SA row from each +/// of the seed-hit deque arrays (SeedHitDequeArray) bound to the active-reads in +/// the scoring queues (ScoringQueues::active_reads). +/// +template +void select( + const BatchType read_batch, + SeedHitDequeArrayDeviceView hits, + uint32* rseeds, + const ContextType context, + ScoringQueuesDeviceView scoring_queues, + const uint32 n_multi, + const ParamsPOD params); + +/// +/// Prepare for a round of seed extension by selecting the next SA row from each +/// of the seed-hit deque arrays (SeedHitDequeArray) bound to the active-reads in +/// the scoring queues (ScoringQueues::active_reads). +/// +template +void select_t( + const ContextType context, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params); + +///@} // group Select +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio + +#include diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/select_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/select_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..4c68e779aa109404c355a686c9e4351234b0a85e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/select_inl.h @@ -0,0 +1,810 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// +// Initialize the hit-selection pipeline +// +template +void select_init_t(BestApproxScoringPipelineState& pipeline, const ParamsPOD& params) +{ + select_init( + pipeline.reads.size(), + pipeline.reads.name_stream(), + pipeline.reads.name_index(), + pipeline.hits, + pipeline.trys, + pipeline.rseeds, + params ); +} + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Select +///@{ + +///@addtogroup SelectDetail +///@{ + +/// +/// Prepare for a round of seed extension by selecting the next SA row +/// +template __global__ +void select_kernel( + const BatchType read_batch, + SeedHitDequeArrayDeviceView hits, + const ContextType context, + ScoringQueuesDeviceView scoring_queues, + const ParamsPOD params) +{ + __shared__ volatile uint32 sm_broadcast[BLOCKDIM >> 5]; + volatile uint32& warp_broadcast = sm_broadcast[ warp_id() ]; + + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= scoring_queues.active_read_count()) return; + + // Fetch the next item from the work queue + const packed_read read_info = scoring_queues.active_read( thread_id ); + const uint32 read_id = read_info.read_id; + uint32 top_flag = read_info.top_flag; + + NVBIO_CUDA_ASSERT( read_id < read_batch.size() ); + + // check whether we finished our loop + if (context.stop( read_id )) + return; + + typedef SeedHitDequeArrayDeviceView::reference hit_deque_reference; + + // check whether there's any hits left + hit_deque_reference hit_deque = hits[ read_id ]; + if (hit_deque.size() == 0) + return; + + // get a reference to the top element in the hit queue + SeedHit* hit = const_cast( &hit_deque.top() ); + + // check whether this hit's range became empty + if (hit->empty()) + { + // pop the top of the hit queue + hit_deque.pop_top(); + + // update the hit reference + if (hit_deque.size() == 0) + return; + + hit = const_cast( &hit_deque.top() ); + + // no longer on the top seed, unmask the top flag + top_flag = 0u; + } + + // fetch next SA row from the selected hit + const uint32 sa_pos = hit->pop_front(); + const uint32 r_type = hit->get_readtype() ? 1u : 0u; + + const uint32 slot = alloc( scoring_queues.active_reads.out_size, &warp_broadcast ); + NVBIO_CUDA_ASSERT( slot < scoring_queues.active_reads.in_size ); + + // write the output active read + scoring_queues.active_reads.out_queue[slot] = packed_read( read_id, top_flag ); + + // write the output hit + HitReference out_hit( scoring_queues.hits, slot ); + out_hit.read_id = read_id; + out_hit.loc = sa_pos; + out_hit.seed = packed_seed( hit->get_posinread(), hit->get_indexdir(), r_type, top_flag ); + + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_select( read_id ), "select() : selected SA[%u:%u:%u] in slot [%u])\n", sa_pos, hit->get_indexdir(), hit->get_posinread(), slot); +} + +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +uint32 randomized_select(ProbTree& prob_tree, SeedHit* hits_data, uint32* rseeds, const uint32 read_id) +{ + for (uint32 i = 0; i < 10; ++i) + { + #if 1 + // pick a new random value + const uint32 ri = 1664525u * rseeds[ read_id ] + 1013904223u; + + // store the new state + rseeds[ read_id ] = ri; + + // convert to a float + const float rf = float(ri) / float(0xFFFFFFFFu); + #else + // advance the QMC sampler + const float rf = radical_inverse( rseeds[ read_id ]++ ); + #endif + + // select the next hit + const uint32 hit_id = sample( prob_tree, rf ); + //NVBIO_CUDA_ASSERT( hit_id < hits.get_size( read_id ) ); + + SeedHit* hit = &hits_data[ hit_id ]; + + // this should never happen if we had infinite precision, but in practice because of rounding errors prob_tree.sum() might + // be non-zero even though its leaf values are: let's just check for this and call it a day. + if (hit->empty() == false) + return hit_id; + } + return 0; +} + +/// +/// Prepare for a round of seed extension by selecting the next SA row +/// +template __global__ +void rand_select_kernel( + const BatchType read_batch, + SeedHitDequeArrayDeviceView hits, + uint32* rseeds, + const ContextType context, + ScoringQueuesDeviceView scoring_queues, + const ParamsPOD params) +{ + typedef SumTree< float* > ProbTree; + + __shared__ volatile uint32 sm_broadcast[BLOCKDIM >> 5]; + volatile uint32& warp_broadcast = sm_broadcast[ warp_id() ]; + + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= scoring_queues.active_read_count()) return; + + // Fetch the next item from the work queue + const packed_read read_info = scoring_queues.active_read( thread_id ); + const uint32 read_id = read_info.read_id; + uint32 top_flag = read_info.top_flag; + + NVBIO_CUDA_ASSERT( read_id < read_batch.size() ); + + // check whether we finished our loop + if (context.stop( read_id )) + return; + + typedef SeedHitDequeArrayDeviceView::reference hit_deque_reference; + + // check whether there's any hits left + hit_deque_reference hit_deque = hits[ read_id ]; + if (hit_deque.size() == 0) + return; + + ProbTree prob_tree( hit_deque.size(), hit_deque.get_probs() ); + SeedHit* hits_data( hit_deque.get_data() ); + + // check if the tree still contains some unexplored entries + if (prob_tree.sum() <= 0.0f) + { + // stop traversal + hits.erase( read_id ); + return; + } + + // check if the top hit became empty + if (top_flag && hits_data[0].empty()) + top_flag = 0; + + const uint32 hit_id = top_flag ? 0 : randomized_select( prob_tree, hits_data, rseeds, read_id ); + + // fetch the selected hit + SeedHit* hit = &hits_data[ hit_id ]; + + // this should never happen if we had infinite precision, but in practice because of rounding errors prob_tree.sum() might + // be non-zero even though its leaf values are: let's just check for this and call it a day. + if (hit->empty()) + { + // stop traversal + hits.erase( read_id ); + return; + } + + // fetch next SA row from the selected hit + const uint32 sa_pos = hit->pop_front(); + const uint32 r_type = hit->get_readtype() ? 1u : 0u; + + // if the range for the selected seed hit became empty, zero out its probability + if (hit->empty()) + prob_tree.set( hit_id, 0.0f ); + + const uint32 slot = alloc( scoring_queues.active_reads.out_size, &warp_broadcast ); + NVBIO_CUDA_ASSERT( slot < scoring_queues.active_reads.in_size ); + + // write the output active read + scoring_queues.active_reads.out_queue[slot] = packed_read( read_id, top_flag ); + + /* + typedef ReadHitsBinder read_hits_binder; + typedef typename read_hits_binder::reference hit_reference; + + // create a hit binder for this read + read_hits_binder dst_read_hits( scoring_queues, slot ); + + // copy from parent + dst_read_hits.set_read_info( packed_read( read_id, top_flag ) ); + + // bind the hit + dst_read_hits.bind_hit( 0u, slot ); // write the output hit + */ + + HitReference out_hit( scoring_queues.hits, slot ); + out_hit.read_id = read_id; + out_hit.loc = sa_pos; + out_hit.seed = packed_seed( hit->get_posinread(), hit->get_indexdir(), r_type, top_flag ); + + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_select( read_id ), "select() : selected hit[%u], SA[%u:%u:%u] in slot [%u])\n", hit_id, sa_pos, hit->get_indexdir(), hit->get_posinread(), slot); +} + +/// +/// Prepare for a round of seed extension by selecting a set of up +/// to 'n_multi' next SA rows. +/// For each read in the input queue, this kernel generates: +/// 1. one or zero output reads, in the main output read queue, +/// 2. zero to 'n_multi' SA rows. These are made of three entries, +/// one in 'loc_queue', identifying the corresponding SA index, +/// one in 'seed_queue', storing information about the seed hit, +/// and one in 'parent_queue', storing the index of the "parent" +/// read in the output queue (i.e. the slot where the read is +/// is being stored) +/// +template __global__ +void select_multi_kernel( + const BatchType read_batch, + SeedHitDequeArrayDeviceView hits, + const ContextType context, + ScoringQueuesDeviceView scoring_queues, + const uint32 n_multi, + const ParamsPOD params) +{ + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= scoring_queues.active_read_count()) return; + + const packed_read read_info = scoring_queues.active_read( thread_id ); + const uint32 read_id = read_info.read_id; + uint32 top_flag = read_info.top_flag; + + NVBIO_CUDA_ASSERT( read_id < read_batch.size() ); + + // check whether we finished our loop + if (context.stop( read_id )) + return; + + typedef SeedHitDequeArrayDeviceView::reference hit_deque_reference; + + // check whether there's any hits left + hit_deque_reference hit_deque = hits[ read_id ]; + if (hit_deque.size() == 0) + return; + + typedef ReadHitsBinder read_hits_binder; + typedef typename read_hits_binder::reference hit_reference; + + // create a hit binder for this read + read_hits_binder dst_read_hits( scoring_queues ); + + uint32 output_lane = uint32(-1); + uint32 n_selected_hits = 0u; + +#if 0 + for (uint32 i = 0; i < n_multi; ++i) + { + // get a reference to the top element in the hit queue + SeedHit* hit = const_cast( &hit_deque.top() ); + + // check whether this hit's range became empty + if (hit->empty()) + { + // pop the top of the hit queue + hit_deque.pop_top(); + + // update the hit reference + if (hit_deque.size() == 0) + break; + else + { + hit = const_cast( &hit_deque.top() ); + + // no longer on the top seed, unmask the top flag + top_flag = 0u; + } + } + + if (output_lane == uint32(-1)) + { + // grab a slot in the output read queue - we'll call this the 'output_lane' + output_lane = atomicAdd( scoring_queues.active_reads.out_size, 1u ); + NVBIO_CUDA_ASSERT( output_lane < scoring_queues.active_reads.in_size ); + + // bind the read to its new location in the output queue + dst_read_hits.bind( output_lane ); + } + + // fetch next SA row from the selected hit + const uint32 sa_pos = hit->pop_front(); + const uint32 r_type = hit->get_readtype() ? 1u : 0u; + + // grab an output slot for writing our hit + const uint32 slot = atomicAdd( scoring_queues.hits_pool, 1u ); + + // bind the hit + dst_read_hits.bind_hit( n_selected_hits, slot ); + + hit_reference out_hit = dst_read_hits[ n_selected_hits ]; + out_hit.read_id = read_id; + out_hit.loc = sa_pos; + out_hit.seed = packed_seed( hit->get_posinread(), hit->get_indexdir(), r_type, top_flag ); + + ++n_selected_hits; + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_select( read_id ), "select() : selected SA[%u:%u:%u] in slot [%u], output-lane[%u:%u])\n", sa_pos, hit->get_indexdir(), hit->get_posinread(), slot, output_lane, i); + } +#else + // NOTE: the following loop relies on fragile, unsupported + // warp-synchronous logic. + // To make the work queue allocations work correctly, we need + // to make sure that all threads within each warp keep executing + // the loop until the very last thread is done. + // As the compiler takes true branches first, we achieve this + // by keeping an active flag and looping until it's true. + __shared__ volatile uint32 sm_broadcast1[BLOCKDIM >> 5]; + __shared__ volatile uint32 sm_broadcast2[BLOCKDIM >> 5]; + volatile uint32& warp_broadcast1 = sm_broadcast1[ warp_id() ]; + volatile uint32& warp_broadcast2 = sm_broadcast2[ warp_id() ]; + + bool active = true; + + for (uint32 i = 0; i < n_multi && __any(active); ++i) + { + SeedHit* hit = NULL; + + // check whether this thread is actually active, or idling around + if (active) + { + // get a reference to the top element in the hit queue + hit = const_cast( &hit_deque.top() ); + + // check whether this hit's range became empty + if (hit->empty()) + { + // pop the top of the hit queue + hit_deque.pop_top(); + + // update the hit reference + if (hit_deque.size() == 0) + { + active = false; + // NOTE: it would be tempting to just break here, but + // this would break the warp-synchronous allocation + // below. + } + else + { + hit = const_cast( &hit_deque.top() ); + + // no longer on the top seed, unmask the top flag + top_flag = 0u; + } + } + } + + // is this thread still active? + if (active) + { + if (output_lane == uint32(-1)) + { + // grab a slot in the output read queue - we'll call this the 'output_lane' + output_lane = alloc( scoring_queues.active_reads.out_size, &warp_broadcast1 ); + + // bind the read to its new location in the output queue + dst_read_hits.bind( output_lane ); + + NVBIO_CUDA_ASSERT( output_lane < scoring_queues.active_reads.in_size ); + } + + // fetch next SA row from the selected hit + const uint32 sa_pos = hit->pop_front(); + const uint32 r_type = hit->get_readtype() ? 1u : 0u; + + // grab an output slot for writing our hit + const uint32 slot = alloc( scoring_queues.hits_pool, &warp_broadcast2 ); + + // bind the hit + dst_read_hits.bind_hit( n_selected_hits, slot ); + + hit_reference out_hit = dst_read_hits[ n_selected_hits ]; + out_hit.read_id = read_id; + out_hit.loc = sa_pos; + out_hit.seed = packed_seed( hit->get_posinread(), hit->get_indexdir(), r_type, top_flag ); + + ++n_selected_hits; + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_select( read_id ), "select() : selected SA[%u:%u:%u] in slot [%u], output-lane[%u:%u])\n", sa_pos, hit->get_indexdir(), hit->get_posinread(), slot, output_lane, i); + } + } +#endif + + // write the output read info. + // NOTE: this must be done at the very end, because only now we know the final state of the top_flag. + if (output_lane != uint32(-1)) + { + // setup the output-lane's read-info + dst_read_hits.set_read_info( packed_read( read_id, top_flag ) ); + + // set the number of hits + dst_read_hits.resize( n_selected_hits ); + } +} + +/// +/// Prepare for a round of seed extension by selecting a set of up +/// to 'n_multi' next SA rows. +/// For each read in the input queue, this kernel generates: +/// 1. one or zero output reads, in the main output read queue, +/// 2. zero to 'n_multi' SA rows. These are made of three entries, +/// one in 'loc_queue', identifying the corresponding SA index, +/// one in 'seed_queue', storing information about the seed hit, +/// and one in 'parent_queue', storing the index of the "parent" +/// read in the output queue (i.e. the slot where the read is +/// is being stored) +/// +template __global__ +void rand_select_multi_kernel( + const BatchType read_batch, + SeedHitDequeArrayDeviceView hits, + uint32* rseeds, + const ContextType context, + ScoringQueuesDeviceView scoring_queues, + const uint32 n_multi, + const ParamsPOD params) +{ + typedef SumTree< float* > ProbTree; + + const uint32 thread_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (thread_id >= scoring_queues.active_read_count()) return; + + const packed_read read_info = scoring_queues.active_read( thread_id ); + const uint32 read_id = read_info.read_id; + uint32 top_flag = read_info.top_flag; + + NVBIO_CUDA_ASSERT( read_id < read_batch.size() ); + + // check whether we finished our loop + if (context.stop( read_id )) + return; + + typedef SeedHitDequeArrayDeviceView::reference hit_deque_reference; + + // check whether there's any hits left + hit_deque_reference hit_deque = hits[ read_id ]; + if (hit_deque.size() == 0) + return; + + ProbTree prob_tree( hit_deque.size(), hit_deque.get_probs() ); + SeedHit* hits_data( hit_deque.get_data() ); + + typedef ReadHitsBinder read_hits_binder; + typedef typename read_hits_binder::reference hit_reference; + + // create a hit binder for this read + read_hits_binder dst_read_hits( scoring_queues ); + + uint32 output_lane = uint32(-1); + uint32 n_selected_hits = 0u; + + for (uint32 i = 0; i < n_multi; ++i) + { + // check if the tree still contains some unexplored entries + if (prob_tree.sum() <= 0.0f) + { + // stop traversal + hits.erase( read_id ); + break; + } + + // check if the top hit became empty + if (top_flag && hits_data[0].empty()) + top_flag = 0; + + const uint32 hit_id = top_flag ? 0 : randomized_select( prob_tree, hits_data, rseeds, read_id ); + + // fetch the selected hit + SeedHit* hit = &hits_data[ hit_id ]; + + // this should never happen if we had infinite precision, but in practice because of rounding errors prob_tree.sum() might + // be non-zero even though its leaf values are: let's just check for this and call it a day. + if (hit->empty()) + { + // stop traversal + hits.erase( read_id ); + continue; + } + + // fetch next SA row from the selected hit + const uint32 sa_pos = hit->pop_front(); + const uint32 r_type = hit->get_readtype() ? 1u : 0u; + + // if the range for the selected seed hit became empty, zero out its probability + if (hit->empty()) + prob_tree.set( hit_id, 0.0f ); + + if (output_lane == uint32(-1)) + { + // grab a slot in the output read queue - we'll call this the 'output_lane' + output_lane = atomicAdd( scoring_queues.active_reads.out_size, 1u ); + NVBIO_CUDA_ASSERT( output_lane < scoring_queues.active_reads.in_size ); + + // bind the read to its new location in the output queue + dst_read_hits.bind( output_lane ); + } + + // grab an output slot for writing our hit + const uint32 slot = atomicAdd( scoring_queues.hits_pool, 1u ); + NVBIO_CUDA_ASSERT( slot < scoring_queues.hits.read_id.size() ); + + // bind the hit + dst_read_hits.bind_hit( n_selected_hits, slot ); + + hit_reference out_hit = dst_read_hits[ n_selected_hits ]; + out_hit.read_id = read_id; + out_hit.loc = sa_pos; + out_hit.seed = packed_seed( hit->get_posinread(), hit->get_indexdir(), r_type, top_flag ); + + ++n_selected_hits; + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_select( read_id ), "select() : selected SA[%u:%u:%u] in slot [%u], output-lane[%u:%u])\n", sa_pos, hit->get_indexdir(), hit->get_posinread(), slot, output_lane, i); + } + + // write the output read info. + // NOTE: this must be done at the very end, because only now we know the final state of the top_flag. + if (output_lane != uint32(-1)) + { + // setup the output-lane's read-info + dst_read_hits.set_read_info( packed_read( read_id, top_flag ) ); + + // set the number of hits + dst_read_hits.resize( n_selected_hits ); + } +} + +///@} // group SelectDetail +///@} // group Select +///@} // group nvBowtie + +// +// Prepare for a round of seed extension by selecting the next SA row +// +template +void select( + const BatchType read_batch, + SeedHitDequeArrayDeviceView hits, + const ContextType context, + ScoringQueuesDeviceView scoring_queues, + const ParamsPOD params) +{ + const int blocks = (scoring_queues.active_reads.in_size + BLOCKDIM-1) / BLOCKDIM; + + select_kernel<<>>( + read_batch, + hits, + context, + scoring_queues, + params ); +} + +// +// Prepare for a round of seed extension by selecting the next SA row +// +template +void rand_select( + const BatchType read_batch, + SeedHitDequeArrayDeviceView hits, + uint32* rseeds, + const ContextType context, + ScoringQueuesDeviceView scoring_queues, + const ParamsPOD params) +{ + const int blocks = (scoring_queues.active_reads.in_size + BLOCKDIM-1) / BLOCKDIM; + + rand_select_kernel<<>>( + read_batch, + hits, + rseeds, + context, + scoring_queues, + params ); +} + +// +// Prepare for a round of seed extension by selecting a set of up +// to 'n_multi' next SA rows. +// For each read in the input queue, this kernel generates: +// 1. one or zero output reads, in the main output read queue, +// 2. zero to 'n_multi' SA rows. These are made of three entries, +// one in 'loc_queue', identifying the corresponding SA index, +// one in 'seed_queue', storing information about the seed hit, +// and one in 'parent_queue', storing the index of the "parent" +// read in the output queue (i.e. the slot where the read is +// is being stored) +// +template +void select_multi( + const BatchType read_batch, + SeedHitDequeArrayDeviceView hits, + const ContextType context, + ScoringQueuesDeviceView scoring_queues, + const uint32 n_multi, + const ParamsPOD params) +{ + const int blocks = (scoring_queues.active_reads.in_size + BLOCKDIM-1) / BLOCKDIM; + + select_multi_kernel<<>>( + read_batch, + hits, + context, + scoring_queues, + n_multi, + params ); +} + +// +// Prepare for a round of seed extension by selecting a set of up +// to 'n_multi' next SA rows. +// For each read in the input queue, this kernel generates: +// 1. one or zero output reads, in the main output read queue, +// 2. zero to 'n_multi' SA rows. These are made of three entries, +// one in 'loc_queue', identifying the corresponding SA index, +// one in 'seed_queue', storing information about the seed hit, +// and one in 'parent_queue', storing the index of the "parent" +// read in the output queue (i.e. the slot where the read is +// is being stored) +// +template +void rand_select_multi( + const BatchType read_batch, + SeedHitDequeArrayDeviceView hits, + uint32* rseeds, + const ContextType context, + ScoringQueuesDeviceView scoring_queues, + const uint32 n_multi, + const ParamsPOD params) +{ + const int blocks = (scoring_queues.active_reads.in_size + BLOCKDIM-1) / BLOCKDIM; + + rand_select_multi_kernel<<>>( + read_batch, + hits, rseeds, + context, + scoring_queues, + n_multi, + params ); +} + +// +// Prepare for a round of seed extension by selecting the next SA rows for each read +// +template +void select( + const BatchType read_batch, + SeedHitDequeArrayDeviceView hits, + uint32* rseeds, + const ContextType context, + ScoringQueuesDeviceView scoring_queues, + const uint32 n_multi, + const ParamsPOD params) +{ + // + // Dispatch the call to the proper version based on whether we are performing + // single-hit or batched-hit selection, and whether we use randomization or not. + // + if (params.randomized) + { + if (n_multi > 1) + { + // batched-hit selection + rand_select_multi( + read_batch, + hits, rseeds, + context, + scoring_queues, + n_multi, + params ); + } + else + { + // randomized single-hit selection + rand_select( + read_batch, + hits, rseeds, + context, + scoring_queues, + params ); + } + } + else + { + if (n_multi > 1) + { + // batched-hit selection + select_multi( + read_batch, + hits, + context, + scoring_queues, + n_multi, + params ); + } + else + { + // non-randomized single-hit selection + select( + read_batch, + hits, + context, + scoring_queues, + params ); + } + } +} + +// +// Prepare for a round of seed extension by selecting the next SA rows for each read +// +template +void select_t( + const ContextType context, + const BestApproxScoringPipelineState& pipeline, + const ParamsPOD params) +{ + select( + pipeline.reads, + pipeline.hits, + pipeline.rseeds, + context, + pipeline.scoring_queues, + pipeline.n_hits_per_read, + params ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/stats.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/stats.cpp new file mode 100644 index 0000000000000000000000000000000000000000..1f5229d9ad1ba1db042deb2872ee0a5e469a681f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/stats.cpp @@ -0,0 +1,1319 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include +#include + +#ifndef WIN32 +#include +#endif + + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +void generate_kernel_table(const uint32 id, const char* report, const KernelStats& stats); + +Stats::Stats(const Params _params) : + n_reads(0), + params( _params ) +{ + global_time = 0.0f; + + hits_total = 0u; + hits_ranges = 0u; + hits_max = 0u; + hits_max_range = 0u; + hits_top_total = 0u; + hits_top_max = 0u; + hits_stats = 0u; + + for (uint32 i = 0; i < 28; ++i) + hits_bins[i] = hits_top_bins[i] = 0; + + map.name = "map"; map.units = "reads"; + select.name = "select"; select.units = "seeds"; + sort.name = "sort"; sort.units = "seeds"; + locate.name = "locate"; locate.units = "seeds"; + score.name = "score"; score.units = "seeds"; + opposite_score.name = "score-opposite"; opposite_score.units = "seeds"; + backtrack.name = "backtrack"; backtrack.units = "reads"; + backtrack_opposite.name = "backtrack-opposite"; backtrack_opposite.units = "reads"; + finalize.name = "finalize"; finalize.units = "reads"; + alignments_DtoH.name = "alignments-DtoH"; alignments_DtoH.units = "reads"; + read_HtoD.name = "reads-HtoD"; read_HtoD.units = "reads"; + read_io.name = "reads-IO"; read_io.units = "reads"; + io.name = "IO"; io.units = "reads"; + + opposite_score.user_names[0] = "queue::get utilization"; opposite_score.user_avg[0] = true; + opposite_score.user_names[1] = "queue::run utilization"; opposite_score.user_avg[1] = true; + opposite_score.user_names[2] = "queue::run T_avg"; opposite_score.user_avg[2] = true; + opposite_score.user_names[3] = "queue::run T_sigma"; opposite_score.user_avg[3] = false; +} + +void Stats::track_alignment_statistics( + const io::BestAlignments& alignment1, + const io::BestAlignments& alignment2, + const uint8 mapq) +{ + n_reads++; + + const uint32 log_mapq = mapq ? nvbio::log2(mapq) + 1u : 0u; + + if (alignment1.best().is_concordant()) + { + // keep track of mapping quality histogram + concordant.mapq_bins[mapq]++; + concordant.mapq_log_bins[log_mapq]++; + + // count this read as mapped + concordant.n_mapped++; + + if (!alignment1.second_best().is_paired()) + { + // we only have one score; count as a unique alignment + concordant.n_unique++; + } + else + { + // we have two best scores, which implies two (or more) alignment positions + // count as multiple alignment + concordant.n_multiple++; + } + + // compute final alignment score + const int32 first = alignment1.best().score() + alignment2.best().score(); + const int32 second = alignment1.second_best().is_paired() ? + alignment1.second_best().score() + alignment2.second_best().score() : + Field_traits::min(); + + // if the two best scores are equal, count as ambiguous + if (first == second) + concordant.n_ambiguous++; + else { + // else, the first score must be higher... + NVBIO_CUDA_ASSERT(first > second); + /// ... which counts as a nonambiguous alignment + concordant.n_unambiguous++; + } + + // compute edit distance scores + const uint32 first_ed = alignment1.best().ed() + alignment2.best().ed(); + const uint32 second_ed = alignment1.second_best().is_paired() ? + alignment1.second_best().ed() + alignment2.second_best().ed() : 255u; + + // update best edit-distance histograms + if (first_ed < concordant.mapped_ed_histogram.size()) + { + concordant.mapped_ed_histogram[first_ed]++; + if (alignment1.best().is_rc()) + concordant.mapped_ed_histogram_fwd[first_ed]++; + else + concordant.mapped_ed_histogram_rev[first_ed]++; + + const uint32 log_first_ed = first_ed ? nvbio::log2(first_ed) + 1 : 0; + concordant.mapped_log_ed_histogram[log_first_ed]++; + } + + // track edit-distance correlation + if (first_ed + 1 < 64) + { + if (second_ed + 1 < 64) + concordant.mapped_ed_correlation[first_ed + 1][second_ed + 1]++; + else + concordant.mapped_ed_correlation[first_ed + 1][0]++; + } + } + else if (alignment1.best().is_discordant()) + { + // keep track of mapping quality histogram + discordant.mapq_bins[mapq]++; + discordant.mapq_log_bins[log_mapq]++; + + // count this read as mapped + discordant.n_mapped++; + + if (!alignment1.second_best().is_paired()) + { + // we only have one score; count as a unique alignment + discordant.n_unique++; + } + else + { + // we have two best scores, which implies two (or more) alignment positions + // count as multiple alignment + discordant.n_multiple++; + } + + // compute final alignment score + const int32 first = alignment1.best().score() + alignment2.best().score(); + const int32 second = alignment1.second_best().is_paired() ? + alignment1.second_best().score() + alignment2.second_best().score() : + Field_traits::min(); + + // if the two best scores are equal, count as ambiguous + if (first == second) + discordant.n_ambiguous++; + else { + // else, the first score must be higher... + NVBIO_CUDA_ASSERT(first > second); + /// ... which counts as a nonambiguous alignment + discordant.n_unambiguous++; + } + + // compute edit distance scores + const uint32 first_ed = alignment1.best().ed() + alignment2.best().ed(); + const uint32 second_ed = alignment1.second_best().is_paired() ? + alignment1.second_best().ed() + alignment2.second_best().ed() : 255u; + + // update best edit-distance histograms + if (first_ed < discordant.mapped_ed_histogram.size()) + { + discordant.mapped_ed_histogram[first_ed]++; + if (alignment1.best().is_rc()) + discordant.mapped_ed_histogram_fwd[first_ed]++; + else + discordant.mapped_ed_histogram_rev[first_ed]++; + + const uint32 log_first_ed = first_ed ? nvbio::log2(first_ed) + 1 : 0; + discordant.mapped_log_ed_histogram[log_first_ed]++; + } + + // track edit-distance correlation + if (first_ed + 1 < 64) + { + if (second_ed + 1 < 64) + discordant.mapped_ed_correlation[first_ed + 1][second_ed + 1]++; + else + discordant.mapped_ed_correlation[first_ed + 1][0]++; + } + } + else + { + // + // track discordand alignments separately for each mate + // + + const io::BestAlignments& aln1 = alignment1.best().mate() == 0 ? alignment1 : alignment2; + const io::BestAlignments& aln2 = alignment1.best().mate() == 0 ? alignment2 : alignment1; + + track_alignment_statistics( &mate1, aln1, mapq ); + track_alignment_statistics( &mate2, aln2, mapq ); + } +} + +void Stats::track_alignment_statistics( + AlignmentStats* mate, + const io::BestAlignments& alignment, + const uint8 mapq) +{ + // check if the mate is aligned + if (!alignment.best().is_aligned()) + { + mate->mapped_ed_correlation[0][0]++; + return; + } + + // count this read as mapped + mate->n_mapped++; + + const uint32 log_mapq = mapq ? nvbio::log2(mapq) + 1u : 0u; + + // keep track of mapping quality histogram + mate->mapq_bins[mapq]++; + mate->mapq_log_bins[log_mapq]++; + + if (!alignment.second_best().is_aligned()) + { + // we only have one score; count as a unique alignment + mate->n_unique++; + } + else + { + // we have two best scores, which implies two (or more) alignment positions + // count as multiple alignment + mate->n_multiple++; + } + + // compute final alignment score + const int32 first = alignment.best().score(); + const int32 second = alignment.second_best().score(); + + // if the two best scores are equal, count as ambiguous + if (first == second) + mate->n_ambiguous++; + else { + // else, the first score must be higher... + NVBIO_CUDA_ASSERT(first > second); + /// ... which counts as a nonambiguous alignment + mate->n_unambiguous++; + } + + // compute edit distance scores + const uint32 first_ed = alignment.best().ed(); + const uint32 second_ed = alignment.second_best().ed(); + + // update best edit-distance histograms + if (first_ed < mate->mapped_ed_histogram.size()) + { + mate->mapped_ed_histogram[first_ed]++; + if (alignment.best().is_rc()) + mate->mapped_ed_histogram_fwd[first_ed]++; + else + mate->mapped_ed_histogram_rev[first_ed]++; + + const uint32 log_first_ed = first_ed ? nvbio::log2(first_ed) + 1 : 0; + mate->mapped_log_ed_histogram[log_first_ed]++; + } + + // track edit-distance correlation + if (first_ed + 1 < 64) + { + if (second_ed + 1 < 64) + mate->mapped_ed_correlation[first_ed + 1][second_ed + 1]++; + else + mate->mapped_ed_correlation[first_ed + 1][0]++; + } +} + +namespace { // anonymous + +std::string generate_file_name(const char* report, const uint32 id, const char* name) +{ + std::string file_name = report; + char id_name[2048]; sprintf( id_name, "%u.%s", id, name ); + { + const size_t offset = file_name.find(".html"); + file_name.replace( offset+1, file_name.length() - offset - 1, id_name ); + file_name.append( ".html" ); + } + return file_name; +} + +std::string device_file_name(const char* report, const uint32 i) +{ + std::string file_name = report; + char name[32]; sprintf( name, "%u", i ); + { + const size_t offset = file_name.find(".html"); + file_name.replace( offset+1, file_name.length() - offset - 1, name ); + file_name.append( ".html" ); + } + return file_name; +} + +// return the local file name from a path +// +const char* local_file(const std::string& file_name) +{ + #if WIN32 + const size_t pos = file_name.find_last_of("/\\"); + #else + const size_t pos = file_name.rfind('/'); + #endif + + if (pos == std::string::npos) + return file_name.c_str(); + else + return file_name.c_str() + pos + 1u; +} + +void add_param(FILE* html_output, const char* name, const uint32 val, bool alt) +{ + html::tr_object tr( html_output, "class", alt ? "alt" : "none", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, name ); + html::td_object( html_output, html::FORMATTED, NULL, "%u", val ); +} +void add_param(FILE* html_output, const char* name, const float val, bool alt) +{ + html::tr_object tr( html_output, "class", alt ? "alt" : "none", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, name ); + html::td_object( html_output, html::FORMATTED, NULL, "%f", val ); +} +void add_param(FILE* html_output, const char* name, const char* val, bool alt) +{ + html::tr_object tr( html_output, "class", alt ? "alt" : "none", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, name ); + html::td_object( html_output, html::FORMATTED, NULL, "%s", val ); +} + +void stats_string(char* buffer, const uint32 px, const char* units, const float v, const float p, const float range) +{ + sprintf(buffer,"%.1f %s \'", px, v, units, 2.0f + range * p); +} + +} // anonymous namespace + +void generate_report_header(const uint32 n_reads, const Params& params, AlignmentStats& aln_stats, const uint32 n_devices, const Stats* device_stats, const char* report) +{ + if (report == NULL) + return; + + FILE* html_output = fopen( report, "w" ); + if (html_output == NULL) + { + log_warning( stderr, "unable to write HTML report \"%s\"\n", report ); + return; + } + + { + const uint32 n_mapped = aln_stats.n_mapped; + + html::html_object html( html_output ); + { + const char* meta_list = ""; + + html::header_object hd( html_output, "Bowtie2 Report", html::style(), meta_list ); + { + html::body_object body( html_output ); + + // + // params + // + { + html::table_object table( html_output, "params", "params", "parameters" ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "parameter name" ); + html::th_object( html_output, html::FORMATTED, NULL, "value" ); + } + add_param( html_output, "randomized", params.randomized ? "yes" : "no", true ); + add_param( html_output, "N", params.allow_sub, false ); + add_param( html_output, "seed-len", params.seed_len, true ); + add_param( html_output, "subseed-len", params.subseed_len, false ); + add_param( html_output, "seed-freq", params.seed_freq.type_symbol(), true ); + add_param( html_output, "seed-freq", params.seed_freq.k, true ); + add_param( html_output, "seed-freq", params.seed_freq.m, true ); + add_param( html_output, "max-reseed", params.max_reseed, false ); + add_param( html_output, "rep-seeds", params.rep_seeds, true ); + add_param( html_output, "max-hits", params.max_hits, false ); + add_param( html_output, "max-dist", params.max_dist, true ); + add_param( html_output, "max-effort", params.max_effort, false ); + add_param( html_output, "min-ext", params.min_ext, true ); + add_param( html_output, "max-ext", params.max_ext, false ); + add_param( html_output, "mapQ-filter", params.mapq_filter, true ); + add_param( html_output, "scoring", params.scoring_file.c_str(), false ); + add_param( html_output, "report", params.report.c_str(), true ); + } + + // + // per-device stats + // + { + char span_string[1024]; + + html::table_object table( html_output, "device-stats", "stats", "device stats" ); + + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + html::th_object( html_output, html::FORMATTED, NULL, "time" ); + html::th_object( html_output, html::FORMATTED, NULL, "avg speed" ); + html::th_object( html_output, html::FORMATTED, NULL, "reads" ); + } + float global_time = 0.0f; + for (uint32 i = 0; i < n_devices; ++i) + global_time += device_stats[i].global_time; + + for (uint32 i = 0; i < n_devices; ++i) + { + char link_name[1024]; + char device_name[64]; + sprintf( device_name, "device %u", i ); + sprintf( link_name, "%s", local_file( device_file_name( report, i ) ), device_name ); + const char* cls = "none"; + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, link_name ); + stats_string( span_string, 40, "s", device_stats[i].global_time, device_stats[i].global_time / global_time, 75.0f ); + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, span_string ); + html::td_object( html_output, html::FORMATTED, NULL, "%.2f K reads/s", 1.0e-3f * float(device_stats[i].n_reads) / device_stats[i].global_time ); + html::td_object( html_output, html::FORMATTED, NULL, "%.2f M", float(device_stats[i].n_reads) * 1.0e-6f ); + } + } + + // + // mapping stats + // + { + html::table_object table( html_output, "mapping-stats", "stats", "mapping stats" ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + html::th_object( html_output, html::FORMATTED, NULL, "mapped" ); + html::th_object( html_output, html::FORMATTED, NULL, "ambiguous" ); + html::th_object( html_output, html::FORMATTED, NULL, "multiple" ); + } + { + html::tr_object tr( html_output, "class", "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "reads" ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f %%", 100.0f * float(n_mapped)/float(n_reads) ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f %%", 100.0f * float(aln_stats.n_ambiguous)/float(n_reads) ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f %%", 100.0f * float(aln_stats.n_multiple)/float(n_reads) ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "edit distance" ); + html::th_object( html_output, html::FORMATTED, NULL, "total" ); + html::th_object( html_output, html::FORMATTED, NULL, "forward" ); + html::th_object( html_output, html::FORMATTED, NULL, "reverse" ); + } + uint32 best_bin[2] = {0}; + uint32 best_bin_val[2] = {0}; + for (uint32 i = 0; i < aln_stats.mapped_ed_histogram.size(); ++i) + { + const uint32 v = aln_stats.mapped_ed_histogram[i]; + + if (best_bin_val[0] < v) + { + best_bin_val[1] = best_bin_val[0]; + best_bin[1] = best_bin[0]; + best_bin_val[0] = v; + best_bin[0] = i; + } + else if (best_bin_val[1] < v) + { + best_bin_val[1] = v; + best_bin[1] = i; + } + } + for (uint32 i = 0; i < aln_stats.mapped_ed_histogram.size(); ++i) + { + const uint32 v = aln_stats.mapped_ed_histogram[i]; + const uint32 vf = aln_stats.mapped_ed_histogram_fwd[i]; + const uint32 vr = aln_stats.mapped_ed_histogram_rev[i]; + + if (float(v)/float(n_reads) < 1.0e-3f) + continue; + + html::tr_object tr( html_output, "class", i % 2 ? "none" : "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "%u", i ); + const char* cls = i == best_bin[0] ? "yellow" : i == best_bin[1] ? "orange" : "none"; + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, "%.1f %%", 100.0f * float(v)/float(n_reads) ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f %%", 100.0f * float(vf)/float(n_reads) ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f %%", 100.0f * float(vr)/float(n_reads) ); + } + } + + // + // mapping quality stats + // + { + html::table_object table( html_output, "mapping-quality-stats", "stats", "mapping quality stats" ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "mapQ" ); + html::th_object( html_output, html::FORMATTED, NULL, "percentage" ); + } + + // rebin to a logarithmic scale + uint64 bins[7] = {0}; + for (uint32 i = 0; i < 64; ++i) + { + const uint32 log_mapq = i ? nvbio::log2(i) + 1 : 0; + bins[log_mapq] += aln_stats.mapq_bins[i]; + } + + // compute best bins + uint32 best_bin[2] = {0}; + uint64 best_bin_val[2] = {0}; + for (uint32 i = 0; i < 7; ++i) + { + if (best_bin_val[0] < bins[i]) + { + best_bin_val[1] = best_bin_val[0]; + best_bin[1] = best_bin[0]; + best_bin_val[0] = bins[i]; + best_bin[0] = i; + } + else if (best_bin_val[1] < bins[i]) + { + best_bin_val[1] = bins[i]; + best_bin[1] = i; + } + } + + // output html table + for (uint32 i = 0; i < 7; ++i) + { + const uint32 bin_size = 1u << (i-1); + + char buffer[1024]; + if (i <= 1) + sprintf( buffer, "%u", i ); + else if (bin_size < 1024) + sprintf( buffer, "%u - %u", bin_size, bin_size*2-1 ); + + html::tr_object tr( html_output, "class", i % 2 ? "none" : "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, buffer ); + const char* cls = i == best_bin[0] ? "yellow" : i == best_bin[1] ? "orange" : "none"; + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, "%.1f %%", 100.0f * float(bins[i])/float(n_reads) ); + } + } + // + // best2-mapping stats + // + { + // compute best 2 entries among double alignments + uint2 best_bin2[2] = { make_uint2(0,0) }; + uint32 best_bin2_val[2] = { 0 }; + + for (uint32 i = 1; i <= 16; ++i) + { + for (uint32 j = 1; j <= 16; ++j) + { + if (best_bin2_val[0] < aln_stats.mapped_ed_correlation[i][j]) + { + best_bin2_val[1] = best_bin2_val[0]; + best_bin2[1] = best_bin2[0]; + best_bin2_val[0] = aln_stats.mapped_ed_correlation[i][j]; + best_bin2[0] = make_uint2(i,j); + } + else if (best_bin2_val[1] < aln_stats.mapped_ed_correlation[i][j]) + { + best_bin2_val[1] = aln_stats.mapped_ed_correlation[i][j]; + best_bin2[1] = make_uint2(i,j); + } + } + } + + // compute best 2 entries among single alignments + uint2 best_bin1[2] = { make_uint2(0,0) }; + uint32 best_bin1_val[2] = { 0 }; + + for (uint32 i = 0; i <= 16; ++i) + { + if (best_bin1_val[0] < aln_stats.mapped_ed_correlation[i][0]) + { + best_bin1_val[1] = best_bin1_val[0]; + best_bin1[1] = best_bin1[0]; + best_bin1_val[0] = aln_stats.mapped_ed_correlation[i][0]; + best_bin1[0] = make_uint2(i,0); + } + else if (best_bin1_val[1] < aln_stats.mapped_ed_correlation[i][0]) + { + best_bin1_val[1] = aln_stats.mapped_ed_correlation[i][0]; + best_bin1[1] = make_uint2(i,0); + } + } + + html::table_object table( html_output, "best2-mapping-stats", "stats", "best2 mapping stats" ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + for (uint32 i = 0; i <= 16; ++i) + html::th_object( html_output, html::FORMATTED, NULL, (i == 0 ? "-" : "%u"), i-1 ); + } + for (uint32 i = 0; i <= 16; ++i) + { + html::tr_object tr( html_output, "class", i % 2 ? "none" : "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, (i == 0 ? "-" : "%u"), i-1 ); + + for (uint32 j = 0; j <= 16; ++j) + { + const uint32 v = aln_stats.mapped_ed_correlation[i][j]; + + if (100.0f * float(v)/float(n_reads) >= 0.1f) + { + const char* cls = ((i == best_bin1[0].x && j == best_bin1[0].y) || + (i == best_bin2[0].x && j == best_bin2[0].y)) ? "yellow" : + ((i == best_bin1[1].x && j == best_bin1[1].y) || + (i == best_bin2[1].x && j == best_bin2[1].y)) ? "orange" : + (i == j) ? "pink" : + (i+1 == j) ? "azure" : "none"; + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, "%.1f %%", 100.0f * float(v)/float(n_reads) ); + } + else if (100.0f * float(v)/float(n_reads) >= 0.01f) + html::td_object( html_output, html::FORMATTED, "class", "small", NULL, "%.2f %%", 100.0f * float(v)/float(n_reads) ); + else + { + const char* cls = (i > params.max_dist+1 || j > params.max_dist+1) ? "gray" : "none"; + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, "-" ); + } + } + } + } + } + } + } + + fclose( html_output ); +} + +void generate_device_report(const uint32 id, Stats& stats, AlignmentStats& aln_stats, const char* report) +{ + if (report == NULL) + return; + + std::vector kernel_stats; + kernel_stats.push_back( &stats.map ); + kernel_stats.push_back( &stats.select ); + kernel_stats.push_back( &stats.sort ); + kernel_stats.push_back( &stats.locate ); + kernel_stats.push_back( &stats.score ); + kernel_stats.push_back( &stats.opposite_score ); + kernel_stats.push_back( &stats.backtrack ); + kernel_stats.push_back( &stats.backtrack_opposite ); + kernel_stats.push_back( &stats.finalize ); + kernel_stats.push_back( &stats.alignments_DtoH ); + kernel_stats.push_back( &stats.read_HtoD ); + kernel_stats.push_back( &stats.read_io ); + + //if (stats.params.keep_stats) + { + for (uint32 i = 0; i < kernel_stats.size(); ++i) + generate_kernel_table( id, report, *kernel_stats[i] ); + } + + const std::string device_report = device_file_name( report, id ); + + FILE* html_output = fopen( device_report.c_str(), "w" ); + if (html_output == NULL) + { + log_warning( stderr, "unable to write HTML report \"%s\"\n", device_report.c_str() ); + return; + } + + { + const uint32 n_reads = stats.n_reads; + const uint32 n_mapped = aln_stats.n_mapped; + + html::html_object html( html_output ); + { + const char* meta_list = ""; + + html::header_object hd( html_output, "Bowtie2 Report", html::style(), meta_list ); + { + html::body_object body( html_output ); + + // + // speed stats + // + { + char span_string[1024]; + + html::table_object table( html_output, "speed-stats", "stats", "speed stats" ); + float worst_time[2] = {0}; + uint32 worst[2] = {0}; + + for (uint32 i = 0; i < kernel_stats.size(); ++i) + { + const float time = kernel_stats[i]->time; + + if (worst_time[0] < time) + { + worst_time[1] = worst_time[0]; + worst[1] = worst[0]; + worst_time[0] = time; + worst[0] = i; + } + else if (worst_time[1] < time) + { + worst_time[1] = time; + worst[1] = i; + } + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + html::th_object( html_output, html::FORMATTED, NULL, "time" ); + html::th_object( html_output, html::FORMATTED, NULL, "avg speed" ); + html::th_object( html_output, html::FORMATTED, NULL, "max speed" ); + } + { + html::tr_object tr( html_output, "class", "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "total" ); + html::td_object( html_output, html::FORMATTED, "class", "red", NULL, "%.1f s", stats.global_time ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f K reads/s", 1.0e-3f * float(n_reads)/stats.global_time ); + html::td_object( html_output, "-", NULL ); + } + for (uint32 i = 0; i < kernel_stats.size(); ++i) + { + const KernelStats& kstats = *kernel_stats[i]; + const char* name = kstats.name.c_str(); + const char* units = kstats.units.c_str(); + const std::string file_name = generate_file_name( report, id, name ); + + char link_name[1024]; + sprintf( link_name, "%s", local_file( file_name ), name ); + const char* cls = worst[0] == i ? "yellow" : worst[1] == i ? "orange" : "none"; + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, link_name ); + stats_string( span_string, 40, "s", kstats.time, kstats.time / stats.global_time, 75.0f ); + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, span_string ); + html::td_object( html_output, html::FORMATTED, NULL, "%.2f M %s/s", 1.0e-6f * float(kstats.calls)/kstats.time, units ); + html::td_object( html_output, html::FORMATTED, NULL, "%.2f M %s/s", 1.0e-6f * kstats.max_speed, units ); + } + } + // + // mapping stats + // + { + html::table_object table( html_output, "mapping-stats", "stats", "mapping stats" ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + html::th_object( html_output, html::FORMATTED, NULL, "mapped" ); + html::th_object( html_output, html::FORMATTED, NULL, "ambiguous" ); + html::th_object( html_output, html::FORMATTED, NULL, "multiple" ); + } + { + html::tr_object tr( html_output, "class", "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "reads" ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f %%", 100.0f * float(n_mapped)/float(n_reads) ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f %%", 100.0f * float(aln_stats.n_ambiguous)/float(n_reads) ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f %%", 100.0f * float(aln_stats.n_multiple)/float(n_reads) ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "edit distance" ); + html::th_object( html_output, html::FORMATTED, NULL, "total" ); + html::th_object( html_output, html::FORMATTED, NULL, "forward" ); + html::th_object( html_output, html::FORMATTED, NULL, "reverse" ); + } + uint32 best_bin[2] = {0}; + uint32 best_bin_val[2] = {0}; + for (uint32 i = 0; i < aln_stats.mapped_ed_histogram.size(); ++i) + { + const uint32 v = aln_stats.mapped_ed_histogram[i]; + + if (best_bin_val[0] < v) + { + best_bin_val[1] = best_bin_val[0]; + best_bin[1] = best_bin[0]; + best_bin_val[0] = v; + best_bin[0] = i; + } + else if (best_bin_val[1] < v) + { + best_bin_val[1] = v; + best_bin[1] = i; + } + } + for (uint32 i = 0; i < aln_stats.mapped_ed_histogram.size(); ++i) + { + const uint32 v = aln_stats.mapped_ed_histogram[i]; + const uint32 vf = aln_stats.mapped_ed_histogram_fwd[i]; + const uint32 vr = aln_stats.mapped_ed_histogram_rev[i]; + + if (float(v)/float(n_reads) < 1.0e-3f) + continue; + + html::tr_object tr( html_output, "class", i % 2 ? "none" : "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "%u", i ); + const char* cls = i == best_bin[0] ? "yellow" : i == best_bin[1] ? "orange" : "none"; + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, "%.1f %%", 100.0f * float(v)/float(n_reads) ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f %%", 100.0f * float(vf)/float(n_reads) ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f %%", 100.0f * float(vr)/float(n_reads) ); + } + } + // + // mapping quality stats + // + { + html::table_object table( html_output, "mapping-quality-stats", "stats", "mapping quality stats" ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "mapQ" ); + html::th_object( html_output, html::FORMATTED, NULL, "percentage" ); + } + + // rebin to a logarithmic scale + uint64 bins[7] = {0}; + for (uint32 i = 0; i < 64; ++i) + { + const uint32 log_mapq = i ? nvbio::log2(i) + 1 : 0; + bins[log_mapq] += aln_stats.mapq_bins[i]; + } + + // compute best bins + uint32 best_bin[2] = {0}; + uint64 best_bin_val[2] = {0}; + for (uint32 i = 0; i < 7; ++i) + { + if (best_bin_val[0] < bins[i]) + { + best_bin_val[1] = best_bin_val[0]; + best_bin[1] = best_bin[0]; + best_bin_val[0] = bins[i]; + best_bin[0] = i; + } + else if (best_bin_val[1] < bins[i]) + { + best_bin_val[1] = bins[i]; + best_bin[1] = i; + } + } + + // output html table + for (uint32 i = 0; i < 7; ++i) + { + const uint32 bin_size = 1u << (i-1); + + char buffer[1024]; + if (i <= 1) + sprintf( buffer, "%u", i ); + else if (bin_size < 1024) + sprintf( buffer, "%u - %u", bin_size, bin_size*2-1 ); + + html::tr_object tr( html_output, "class", i % 2 ? "none" : "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, buffer ); + const char* cls = i == best_bin[0] ? "yellow" : i == best_bin[1] ? "orange" : "none"; + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, "%.1f %%", 100.0f * float(bins[i])/float(n_reads) ); + } + } + // + // best2-mapping stats + // + { + // compute best 2 entries among double alignments + uint2 best_bin2[2] = { make_uint2(0,0) }; + uint32 best_bin2_val[2] = { 0 }; + + for (uint32 i = 1; i <= 16; ++i) + { + for (uint32 j = 1; j <= 16; ++j) + { + if (best_bin2_val[0] < aln_stats.mapped_ed_correlation[i][j]) + { + best_bin2_val[1] = best_bin2_val[0]; + best_bin2[1] = best_bin2[0]; + best_bin2_val[0] = aln_stats.mapped_ed_correlation[i][j]; + best_bin2[0] = make_uint2(i,j); + } + else if (best_bin2_val[1] < aln_stats.mapped_ed_correlation[i][j]) + { + best_bin2_val[1] = aln_stats.mapped_ed_correlation[i][j]; + best_bin2[1] = make_uint2(i,j); + } + } + } + + // compute best 2 entries among single alignments + uint2 best_bin1[2] = { make_uint2(0,0) }; + uint32 best_bin1_val[2] = { 0 }; + + for (uint32 i = 0; i <= 16; ++i) + { + if (best_bin1_val[0] < aln_stats.mapped_ed_correlation[i][0]) + { + best_bin1_val[1] = best_bin1_val[0]; + best_bin1[1] = best_bin1[0]; + best_bin1_val[0] = aln_stats.mapped_ed_correlation[i][0]; + best_bin1[0] = make_uint2(i,0); + } + else if (best_bin1_val[1] < aln_stats.mapped_ed_correlation[i][0]) + { + best_bin1_val[1] = aln_stats.mapped_ed_correlation[i][0]; + best_bin1[1] = make_uint2(i,0); + } + } + + html::table_object table( html_output, "best2-mapping-stats", "stats", "best2 mapping stats" ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + for (uint32 i = 0; i <= 16; ++i) + html::th_object( html_output, html::FORMATTED, NULL, (i == 0 ? "-" : "%u"), i-1 ); + } + for (uint32 i = 0; i <= 16; ++i) + { + html::tr_object tr( html_output, "class", i % 2 ? "none" : "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, (i == 0 ? "-" : "%u"), i-1 ); + + for (uint32 j = 0; j <= 16; ++j) + { + const uint32 v = aln_stats.mapped_ed_correlation[i][j]; + + if (100.0f * float(v)/float(n_reads) >= 0.1f) + { + const char* cls = ((i == best_bin1[0].x && j == best_bin1[0].y) || + (i == best_bin2[0].x && j == best_bin2[0].y)) ? "yellow" : + ((i == best_bin1[1].x && j == best_bin1[1].y) || + (i == best_bin2[1].x && j == best_bin2[1].y)) ? "orange" : + (i == j) ? "pink" : + (i+1 == j) ? "azure" : "none"; + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, "%.1f %%", 100.0f * float(v)/float(n_reads) ); + } + else if (100.0f * float(v)/float(n_reads) >= 0.01f) + html::td_object( html_output, html::FORMATTED, "class", "small", NULL, "%.2f %%", 100.0f * float(v)/float(n_reads) ); + else + { + const char* cls = (i > stats.params.max_dist+1 || j > stats.params.max_dist+1) ? "gray" : "none"; + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, "-" ); + } + } + } + } + // + // seeding stats + // + if (stats.params.keep_stats) + { + // copy stats locally + uint64 hits_total = stats.hits_total; + uint64 hits_ranges = stats.hits_ranges; + uint32 hits_max = stats.hits_max; + uint32 hits_max_range = stats.hits_max_range; + uint64 hits_top_total = stats.hits_top_total; + uint32 hits_top_max = stats.hits_top_max; + uint64 hits_bins[28]; + uint64 hits_bins_sum = 0; + uint64 hits_top_bins[28]; + uint64 hits_top_bins_sum = 0; + for (uint32 i = 0; i < 28; ++i) + { + hits_bins_sum += hits_bins[i] = stats.hits_bins[i]; + hits_top_bins_sum += hits_top_bins[i] = stats.hits_top_bins[i]; + } + + html::table_object table( html_output, "seeding-stats", "stats", "seeding stats" ); + char buffer[1024]; + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + html::th_object( html_output, html::FORMATTED, NULL, "seed hits" ); + html::th_object( html_output, html::FORMATTED, NULL, "top-seed hits" ); + html::th_object( html_output, html::FORMATTED, NULL, "seed ranges" ); + html::th_object( html_output, html::FORMATTED, NULL, "range size" ); + } + { + html::tr_object tr( html_output, "class", "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "avg" ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f", float(hits_total)/float(n_reads) ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f", float(hits_top_total)/float(n_reads) ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f", float(hits_ranges)/float(n_reads) ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f", float(hits_total)/float(hits_ranges) ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "max" ); + html::td_object( html_output, html::FORMATTED, NULL, "%u", hits_max ); + html::td_object( html_output, html::FORMATTED, NULL, "%u", hits_top_max ); + html::td_object( html_output, html::FORMATTED, NULL, "" ); + html::td_object( html_output, html::FORMATTED, NULL, "%u", hits_max_range ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "# hits" ); + html::th_object( html_output, html::FORMATTED, NULL, "%% of seeds" ); + html::th_object( html_output, html::FORMATTED, NULL, "%% of top-seeds" ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + } + uint32 max_bin = 0; + uint32 best_bin[2] = {0}; + uint64 best_bin_val[2] = {0}; + uint32 best_top_bin[2] = {0}; + uint64 best_top_bin_val[2] = {0}; + for (uint32 i = 0; i < 28; ++i) + { + max_bin = float(hits_bins[i]) / float(hits_bins_sum) > 0.001f ? i : max_bin; + max_bin = float(hits_top_bins[i]) / float(hits_top_bins_sum) > 0.001f ? i : max_bin; + + if (best_bin_val[0] < hits_bins[i]) + { + best_bin_val[1] = best_bin_val[0]; + best_bin[1] = best_bin[0]; + best_bin_val[0] = hits_bins[i]; + best_bin[0] = i; + } + else if (best_bin_val[1] < hits_bins[i]) + { + best_bin_val[1] = hits_bins[i]; + best_bin[1] = i; + } + + if (best_top_bin_val[0] < hits_top_bins[i]) + { + best_top_bin_val[1] = best_top_bin_val[0]; + best_top_bin[1] = best_top_bin[0]; + best_top_bin_val[0] = hits_top_bins[i]; + best_top_bin[0] = i; + } + else if (best_top_bin_val[1] < hits_top_bins[i]) + { + best_top_bin_val[1] = hits_top_bins[i]; + best_top_bin[1] = i; + } + } + for (uint32 i = 0; i < max_bin; ++i) + { + const uint32 bin_size = 1u << (i-1); + + html::tr_object tr( html_output, "class", i % 2 ? "none" : "alt", NULL ); + if (i <= 1) + sprintf( buffer, "%u", i ); + else if (bin_size < 512) + sprintf( buffer, "%u - %u", bin_size, bin_size*2-1 ); + else if (bin_size == 512) + sprintf( buffer, "0.5K - 1K" ); + else + sprintf( buffer, "%uK - %uK", bin_size/1024, bin_size*2/1024 ); + + const char* cls = i == best_bin[0] ? "yellow" : i == best_bin[1] ? "orange" : "none"; + const char* cls_top = i == best_top_bin[0] ? "yellow" : i == best_top_bin[1] ? "orange" : "none"; + + html::th_object( html_output, html::FORMATTED, NULL, buffer ); + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, "%4.1f %%", 100.0f * float(hits_bins[i]) / float(hits_bins_sum) ); + html::td_object( html_output, html::FORMATTED, "class", cls_top, NULL, "%4.1f %%", 100.0f * float(hits_top_bins[i]) / float(hits_top_bins_sum) ); + html::td_object( html_output, html::FORMATTED, NULL, "" ); + html::td_object( html_output, html::FORMATTED, NULL, "" ); + } + } + } + } + } + fclose( html_output ); +} + +template +void find_gt2(const uint32 n, const T* table, uint32 best_bin[2]) +{ + best_bin[0] = best_bin[1] = 0; + T best_bin_val[2] = {0}; + for (uint32 i = 0; i < n; ++i) + { + if (best_bin_val[0] < table[i]) + { + best_bin_val[1] = best_bin_val[0]; + best_bin[1] = best_bin[0]; + best_bin_val[0] = table[i]; + best_bin[0] = i; + } + else if (best_bin_val[1] < table[i]) + { + best_bin_val[1] = table[i]; + best_bin[1] = i; + } + } +} + +void generate_kernel_table(const uint32 id, const char* report, const KernelStats& stats) +{ + const char* name = stats.name.c_str(); + const char* units = stats.units.c_str(); + const std::string file_name = generate_file_name( report, id, name ); + + const std::deque< std::pair >& table = stats.info; + + FILE* html_output = fopen( file_name.c_str(), "w" ); + if (html_output == NULL) + { + log_warning( stderr, "unable to write HTML report \"%s\"\n", file_name.c_str() ); + return; + } + + { + html::html_object html( html_output ); + { + const char* meta_list = ""; + + html::header_object hd( html_output, "Bowtie2 Report", html::style(), meta_list ); + { + html::body_object body( html_output ); + + // + // kernel summary stats + // + { + uint32 bin_calls[32] = {0}; + float bin_sum_time[32] = {0.0f}; + float bin_avg_time[32] = {0.0f}; + float bin_speed[32] = {0.0f}; + + float total_time = stats.time; + float avg_speed = total_time ? float(double(stats.calls) / double(stats.time)) : 0.0f; + float max_speed = 0.0f; + + for (uint32 bin = 0; bin < 32; ++bin) + { + bin_calls[bin] = stats.bin_calls[bin]; + bin_sum_time[bin] = stats.bin_time[bin]; + bin_avg_time[bin] = stats.bin_calls[bin] ? stats.bin_time[bin] / stats.bin_calls[bin] : 0.0f; + bin_speed[bin] = stats.bin_time[bin] ? float(double(stats.bin_items[bin]) / double(stats.bin_time[bin])) : 0.0f; + //bin_speed[bin] = stats.bin_calls[bin] ? stats.bin_speed[bin] / stats.bin_calls[bin] : 0.0f; + + max_speed = std::max( max_speed, bin_speed[bin] ); + } + + char buffer1[1024]; + char buffer2[1024]; + sprintf( buffer1, "%s-summary-stats", name ); + sprintf( buffer2, "%s summary stats", name ); + html::table_object tab( html_output, buffer1, "stats", buffer2 ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "items" ); + html::td_object( html_output, html::FORMATTED, NULL, "%.2f M", float(stats.calls) * 1.0e-6f ); + } + // write "user" stats + for (uint32 i = 0; i < 32; ++i) + { + if (stats.user_names[i] == NULL) + break; + + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, stats.user_names[i] ); + html::td_object( html_output, html::FORMATTED, NULL, "%.3f %s", + stats.user_avg[i] ? stats.user[i]/float(stats.num) : + stats.user[i], + stats.user_units[i] ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "batch size (%s)", units ); + html::th_object( html_output, html::FORMATTED, NULL, "calls" ); + html::th_object( html_output, html::FORMATTED, NULL, "avg time" ); + html::th_object( html_output, html::FORMATTED, NULL, "sum time" ); + html::th_object( html_output, html::FORMATTED, NULL, "cumul. time" ); + html::th_object( html_output, html::FORMATTED, NULL, "speed" ); + } + + uint32 best_avg_bin[2]; + uint32 best_sum_bin[2]; + find_gt2( 32, bin_avg_time, best_avg_bin ); + find_gt2( 32, bin_sum_time, best_sum_bin ); + + float cum_time = 0.0f; + + float max_avg_time = 0.0f; + float max_sum_time = 0.0f; + for (uint32 i = 0; i < 32; ++i) + { + max_avg_time = nvbio::max( bin_avg_time[i], max_avg_time ); + max_sum_time = nvbio::max( bin_sum_time[i], max_sum_time ); + } + + char span_string[1024]; + for (uint32 i = 0; i < 32; ++i) + { + if (bin_calls[i] == 0) + continue; + + const float speed = bin_speed[i]; + + cum_time += bin_sum_time[i]; + + const uint32 bin_size = 1u << i; + html::tr_object tr( html_output, "class", i % 2 ? "none" : "alt", NULL ); + if (bin_size == 1) + html::th_object( html_output, html::FORMATTED, NULL, "1" ); + else if (bin_size < 512) + html::th_object( html_output, html::FORMATTED, NULL, "%u - %u", bin_size, bin_size*2-1 ); + else if (bin_size == 512) + html::th_object( html_output, html::FORMATTED, NULL, "512 - 1K" ); + else if (bin_size < 512*1024) + html::th_object( html_output, html::FORMATTED, NULL, "%uK- %uK", bin_size/1024, (bin_size*2)/1024 ); + else if (bin_size == 512*1024) + html::th_object( html_output, html::FORMATTED, NULL, "512K - 1M" ); + + const char* avg_cls = i == best_avg_bin[0] ? "yellow" : i == best_avg_bin[1] ? "orange" : "none"; + const char* sum_cls = i == best_sum_bin[0] ? "yellow" : i == best_sum_bin[1] ? "orange" : "none"; + const char* spd_cls = speed == max_speed ? "yellow" : speed < avg_speed * 0.1f ? "red" : speed < max_speed * 0.1f ? "pink" : "none"; + + html::td_object( html_output, html::FORMATTED, NULL, "%u", bin_calls[i] ); + stats_string( span_string, 60, "ms", 1000.0f * bin_avg_time[i], bin_avg_time[i] / max_avg_time, 50.0f ); + html::td_object( html_output, html::FORMATTED, "class", avg_cls, NULL, span_string ); + stats_string( span_string, 60, "ms", 1000.0f * bin_sum_time[i], bin_sum_time[i] / max_sum_time, 50.0f ); + html::td_object( html_output, html::FORMATTED, "class", sum_cls, NULL, span_string ); + html::td_object( html_output, html::FORMATTED, NULL, "%.1f %%", 100.0f * cum_time / total_time ); + html::td_object( html_output, html::FORMATTED, "class", spd_cls, NULL, "%.1f %c %s/s", speed * (speed >= 1.0e6f ? 1.0e-6f : 1.0e-3f), speed >= 1.0e6f ? 'M' : 'K', units ); + } + } + // + // kernel table stats + // + { + char buffer1[1024]; + char buffer2[1024]; + sprintf( buffer1, "%s-stats", name ); + sprintf( buffer2, "%s stats", name ); + html::table_object tab( html_output, buffer1, "stats", buffer2 ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "launch" ); + html::th_object( html_output, html::FORMATTED, NULL, "batch size (%s)", units ); + html::th_object( html_output, html::FORMATTED, NULL, "time" ); + html::th_object( html_output, html::FORMATTED, NULL, "speed" ); + } + uint32 best_bin[2] = {0}; + float best_bin_val[2] = {0}; + for (uint32 i = 0; i < table.size(); ++i) + { + if (best_bin_val[0] < table[i].second) + { + best_bin_val[1] = best_bin_val[0]; + best_bin[1] = best_bin[0]; + best_bin_val[0] = table[i].second; + best_bin[0] = i; + } + else if (best_bin_val[1] < table[i].second) + { + best_bin_val[1] = table[i].second; + best_bin[1] = i; + } + } + + float max_time = 0.0f; + float max_speed = 0.0f; + for (uint32 i = 0; i < table.size(); ++i) + { + const float speed = float(table[i].first) / table[i].second; + max_time = nvbio::max( float(table[i].second), max_time ); + max_speed = nvbio::max( speed, max_speed ); + } + + char span_string[1024]; + char units_string[1024]; + for (uint32 i = 0; i < table.size(); ++i) + { + const float speed = float(table[i].first) / table[i].second; + html::tr_object tr( html_output, "class", i % 2 ? "none" : "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "%u", i ); + const char* cls = i == best_bin[0] ? "yellow" : i == best_bin[1] ? "orange" : "none"; + html::td_object( html_output, html::FORMATTED, NULL, "%.1f %c", float(table[i].first) * (table[i].first > 1000000 ? 1.0e-6f : 1.0e-3f), table[i].first > 1000000 ? 'M' : 'K' ); + stats_string( span_string, 50, "ms", 1000.0f * float(table[i].second), float(table[i].second) / max_time, 50.0f ); + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, span_string ); + sprintf(units_string, "%c %s/s", speed > 1000000 ? 'M' : 'K', units ); + stats_string( span_string, 100, units_string, speed * (speed >= 1.0e6f ? 1.0e-6f : 1.0e-3f), speed / max_speed, 50.0f ); + html::td_object( html_output, html::FORMATTED, NULL, span_string ); + } + } + } + } + } + fclose( html_output ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/stats.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/stats.h new file mode 100644 index 0000000000000000000000000000000000000000..95d6464c55387a167dc665fdd046d73d67569202 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/stats.h @@ -0,0 +1,185 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include +#include + +namespace nvbio { namespace io { struct BestAlignments; } } + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +typedef nvbio::TimeSeries KernelStats; + + +struct AlignmentStats +{ + AlignmentStats() + : n_mapped(0), + n_ambiguous(0), + n_unambiguous(0), + n_unique(0), + n_multiple(0), + mapped_ed_histogram(4096, 0), + mapped_ed_histogram_fwd(4096, 0), + mapped_ed_histogram_rev(4096, 0), + mapped_log_ed_histogram(12, 0) + { + for(uint32 c = 0; c < 64; c++) + mapq_bins[c] = 0; + + for(uint32 c = 0; c < 8; c++) + mapq_log_bins[c] = 0; + + for(uint32 c = 0; c < 64; c++) + for(uint32 d = 0; d < 64; d++) + mapped_ed_correlation[c][d] = 0; + } + + // mapping quality stats + uint64 mapq_bins[64]; + uint64 mapq_log_bins[8]; + + // mapping stats + uint32 n_mapped; // number of mapped reads + + uint32 n_ambiguous; // number of reads mapped to more than one place with the same score + uint32 n_unambiguous; // number of reads with a single best score (even if mapped to multiple locations) + + uint32 n_unique; // number of reads mapped to a single location + uint32 n_multiple; // number of reads mapped to more than one location + + // edit distance scoring histograms + std::vector mapped_ed_histogram; // aggregate histogram of edit-distance scores per read + std::vector mapped_ed_histogram_fwd; // histogram of edit-distance scores for reads mapped to the forward sequence + std::vector mapped_ed_histogram_rev; // histogram of edit-distance scores for reads mapped to the reverse-complemented sequence + std::vector mapped_log_ed_histogram; // aggregate histogram of log edit-distance scores per read + std::vector mapped_log_mapq_histogram; // aggregate histogram of log mapq scores per read + + // edit distance correlation (xxxnsubtil: what exactly does this measure?) + uint32 mapped_ed_correlation[64][64]; + + // merge stats + void merge(const AlignmentStats& stats) + { + n_mapped += stats.n_mapped; + n_ambiguous += stats.n_ambiguous; + n_unambiguous += stats.n_unambiguous; + n_unique += stats.n_unique; + n_multiple += stats.n_multiple; + + for (uint32 i = 0; i < mapped_ed_histogram.size(); ++i) + { + mapped_ed_histogram[i] += stats.mapped_ed_histogram[i]; + mapped_ed_histogram_fwd[i] += stats.mapped_ed_histogram_fwd[i]; + mapped_ed_histogram_rev[i] += stats.mapped_ed_histogram_rev[i]; + } + for (uint32 i = 0; i < 12; ++i) + mapped_log_ed_histogram[i] += stats.mapped_log_ed_histogram[i]; + + for(uint32 c = 0; c < 64; c++) + mapq_bins[c] += stats.mapq_bins[c]; + + for(uint32 c = 0; c < 8; c++) + mapq_log_bins[c] += stats.mapq_log_bins[c]; + + for(uint32 c = 0; c < 64; c++) + for(uint32 d = 0; d < 64; d++) + mapped_ed_correlation[c][d] += stats.mapped_ed_correlation[c][d]; + } +}; + +// +// Global statistics +// +struct Stats +{ + // constructor + Stats(const Params _params = Params()); + + // timing stats + float global_time; + KernelStats map; + KernelStats select; + KernelStats sort; + KernelStats locate; + KernelStats score; + KernelStats opposite_score; + KernelStats backtrack; + KernelStats backtrack_opposite; + KernelStats finalize; + KernelStats alignments_DtoH; + KernelStats read_HtoD; + KernelStats read_io; + KernelStats io; + KernelStats scoring_pipe; + + // detailed mapping stats + AlignmentStats concordant; + AlignmentStats discordant; + AlignmentStats mate1; + AlignmentStats mate2; + + // mapping stats + uint32 n_reads; + + // extensive (seeding) stats + uint64 hits_total; + uint64 hits_ranges; + uint32 hits_max; + uint32 hits_max_range; + uint64 hits_top_total; + uint32 hits_top_max; + uint64 hits_bins[28]; + uint64 hits_top_bins[28]; + uint32 hits_stats; + + Params params; + + void track_alignment_statistics( + const io::BestAlignments& alignment1, + const io::BestAlignments& alignment2, + const uint8 mapq); + + void track_alignment_statistics( + AlignmentStats* mate, + const io::BestAlignments& alignment, + const uint8 mapq); +}; + +void generate_report_header(const uint32 n_reads, const Params& params, AlignmentStats& aln_stats, const uint32 n_devices, const Stats* device_stats, const char* report); +void generate_device_report(const uint32 id, Stats& stats, AlignmentStats& aln_stats, const char* report); + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/string_utils.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/string_utils.h new file mode 100644 index 0000000000000000000000000000000000000000..e66bb740424156dbf3862618deeb7811e115860b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/string_utils.h @@ -0,0 +1,77 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// helper class to convert {uint32,uint4} to uint32 streams +template +struct StreamAdapterBase {}; + +// helper class to convert uint32 to uint32 streams +template +struct StreamAdapterBase +{ + typedef const_cached_iterator type; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + static type adapt(const Iterator it) { return type( it ); } +}; + +// helper class to convert uint4 to uint32 streams +template +struct StreamAdapterBase +{ + typedef const_cached_iterator BaseCachedIterator; + typedef const_cached_iterator< uint4_as_uint32_iterator > type; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + static type adapt(const Iterator it) { return type( uint4_as_uint32_iterator( BaseCachedIterator(it) ) ); } +}; + +// helper class to convert {uint32,uint4} to uint32 streams +template +struct StreamAdapter +{ + typedef typename std::iterator_traits::value_type value_type; + typedef StreamAdapterBase adapter_type; + typedef typename adapter_type::type type; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + static type adapt(const Iterator it) { return adapter_type::adapt( it ); } +}; + +} // namespace cuda +} // namespace bowtie2 + +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/traceback.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/traceback.cu new file mode 100644 index 0000000000000000000000000000000000000000..2276a344d28318823e7c9e43647bf6c868ba6931 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/traceback.cu @@ -0,0 +1,261 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +// +// execute a batch of banded-alignment traceback calculations +// +void banded_traceback_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const TracebackPipelineState& pipeline, + const ParamsPOD& params) +{ + if (aln_idx) + banded_traceback_best_t<1>( count, idx, best_data, best_stride, band_len, pipeline, params ); + else + banded_traceback_best_t<0>( count, idx, best_data, best_stride, band_len, pipeline, params ); +} + +// +// execute a batch of banded-alignment traceback calculations +// +void banded_traceback_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const TracebackPipelineState >& pipeline, + const ParamsPOD& params) +{ + if (aln_idx) + banded_traceback_best_t<1>( count, idx, best_data, best_stride, band_len, pipeline, params ); + else + banded_traceback_best_t<0>( count, idx, best_data, best_stride, band_len, pipeline, params ); +} + +// +// execute a batch of opposite alignment traceback calculations +// +void opposite_traceback_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const TracebackPipelineState& pipeline, + const ParamsPOD& params) +{ + if (aln_idx) + opposite_traceback_best_t<1>( count, idx, best_data, best_stride, pipeline, params ); + else + opposite_traceback_best_t<0>( count, idx, best_data, best_stride, pipeline, params ); +} + +// +// execute a batch of opposite alignment traceback calculations +// +void opposite_traceback_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const TracebackPipelineState >& pipeline, + const ParamsPOD& params) +{ + if (aln_idx) + opposite_traceback_best_t<1>( count, idx, best_data, best_stride, pipeline, params ); + else + opposite_traceback_best_t<0>( count, idx, best_data, best_stride, pipeline, params ); +} + + +// +// execute a batch of banded-alignment traceback calculations +// +void banded_traceback_all( + const uint32 count, + const uint32* idx, + const uint32 buffer_offset, + const uint32 buffer_size, + io::Alignment* alignments, + const uint32 band_len, + const AllMappingPipelineState& pipeline, + const ParamsPOD& params) +{ + banded_traceback_all_t( count, idx, buffer_offset, buffer_size, alignments, band_len, pipeline, params ); +} + +// +// execute a batch of banded-alignment traceback calculations +// +void banded_traceback_all( + const uint32 count, + const uint32* idx, + const uint32 buffer_offset, + const uint32 buffer_size, + io::Alignment* alignments, + const uint32 band_len, + const AllMappingPipelineState >& pipeline, + const ParamsPOD& params) +{ + banded_traceback_all_t( count, idx, buffer_offset, buffer_size, alignments, band_len, pipeline, params ); +} + +// +// finish a batch of alignment calculations +// +void finish_alignment_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const TracebackPipelineState& pipeline, + const SmithWatermanScoringScheme<> scoring_scheme, + const ParamsPOD& params) +{ + if (aln_idx) + finish_alignment_best_t<1>( count, idx, best_data, best_stride, band_len, pipeline, scoring_scheme, params ); + else + finish_alignment_best_t<0>( count, idx, best_data, best_stride, band_len, pipeline, scoring_scheme, params ); +} + +// +// finish a batch of alignment calculations +// +void finish_alignment_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const TracebackPipelineState >& pipeline, + const SmithWatermanScoringScheme<> scoring_scheme, + const ParamsPOD& params) +{ + if (aln_idx) + finish_alignment_best_t<1>( count, idx, best_data, best_stride, band_len, pipeline, scoring_scheme, params ); + else + finish_alignment_best_t<0>( count, idx, best_data, best_stride, band_len, pipeline, scoring_scheme, params ); +} + +// +// finish a batch of opposite alignment calculations +// +void finish_opposite_alignment_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const TracebackPipelineState& pipeline, + const SmithWatermanScoringScheme<> scoring_scheme, + const ParamsPOD& params) +{ + if (aln_idx) + finish_opposite_alignment_best_t<1>( count, idx, best_data, best_stride, band_len, pipeline, scoring_scheme, params ); + else + finish_opposite_alignment_best_t<0>( count, idx, best_data, best_stride, band_len, pipeline, scoring_scheme, params ); +} + +// +// finish a batch of opposite alignment calculations +// +void finish_opposite_alignment_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const TracebackPipelineState >& pipeline, + const SmithWatermanScoringScheme<> scoring_scheme, + const ParamsPOD& params) +{ + if (aln_idx) + finish_opposite_alignment_best_t<1>( count, idx, best_data, best_stride, band_len, pipeline, scoring_scheme, params ); + else + finish_opposite_alignment_best_t<0>( count, idx, best_data, best_stride, band_len, pipeline, scoring_scheme, params ); +} + +// +// finish a batch of alignment calculations, all-mapping +// +void finish_alignment_all( + const uint32 count, + const uint32* idx, + const uint32 buffer_offset, + const uint32 buffer_size, + io::Alignment* alignments, + const uint32 band_len, + const AllMappingPipelineState& pipeline, + const SmithWatermanScoringScheme<> scoring_scheme, + const ParamsPOD& params) +{ + finish_alignment_all_t( count, idx, buffer_offset, buffer_size, alignments, band_len, pipeline, scoring_scheme, params ); +} + +// +// finish a batch of alignment calculations, all-mapping +// +void finish_alignment_all( + const uint32 count, + const uint32* idx, + const uint32 buffer_offset, + const uint32 buffer_size, + io::Alignment* alignments, + const uint32 band_len, + const AllMappingPipelineState >& pipeline, + const SmithWatermanScoringScheme<> scoring_scheme, + const ParamsPOD& params) +{ + finish_alignment_all_t( count, idx, buffer_offset, buffer_size, alignments, band_len, pipeline, scoring_scheme, params ); +} + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio + +#include diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/traceback.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/traceback.h new file mode 100644 index 0000000000000000000000000000000000000000..ade1383b56066d9d95a4c8b5a1595e108f3569c7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/traceback.h @@ -0,0 +1,220 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include + +namespace nvbio { +namespace io { + struct Alignment; + struct BestAlignments; +} // namespace io +} // namespace nvbio + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +struct ParamsPOD; + +template struct TracebackPipelineState; +template struct AllMappingPipelineState; + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Traceback +///@{ + +/// +/// execute a batch of banded-alignment traceback calculations +/// +void banded_traceback_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const TracebackPipelineState& pipeline, + const ParamsPOD& params); + +/// +/// execute a batch of banded-alignment traceback calculations +/// +void banded_traceback_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const TracebackPipelineState >& pipeline, + const ParamsPOD& params); + +/// +/// execute a batch of opposite alignment traceback calculations +/// +void opposite_traceback_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const TracebackPipelineState& pipeline, + const ParamsPOD& params); + +/// +/// execute a batch of opposite alignment traceback calculations +/// +void opposite_traceback_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const TracebackPipelineState >& pipeline, + const ParamsPOD& params); + +/// +/// execute a batch of banded-alignment traceback calculations +/// +void banded_traceback_all( + const uint32 count, + const uint32* idx, + const uint32 buffer_offset, + const uint32 buffer_size, + io::Alignment* alignments, + const uint32 band_len, + const AllMappingPipelineState& pipeline, + const ParamsPOD& params); + +/// +/// execute a batch of banded-alignment traceback calculations +/// +void banded_traceback_all( + const uint32 count, + const uint32* idx, + const uint32 buffer_offset, + const uint32 buffer_size, + io::Alignment* alignments, + const uint32 band_len, + const AllMappingPipelineState >& pipeline, + const ParamsPOD& params); + +/// +/// finish a batch of alignment calculations +/// +void finish_alignment_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const TracebackPipelineState& pipeline, + const SmithWatermanScoringScheme<> scoring_scheme, + const ParamsPOD& params); + +/// +/// finish a batch of alignment calculations +/// +void finish_alignment_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const TracebackPipelineState >& pipeline, + const SmithWatermanScoringScheme<> scoring_scheme, + const ParamsPOD& params); + +/// +/// finish a batch of opposite alignment calculations +/// +void finish_opposite_alignment_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const TracebackPipelineState& pipeline, + const SmithWatermanScoringScheme<> scoring_scheme, + const ParamsPOD& params); + +/// +/// finish a batch of opposite alignment calculations +/// +void finish_opposite_alignment_best( + const uint32 aln_idx, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const TracebackPipelineState >& pipeline, + const SmithWatermanScoringScheme<> scoring_scheme, + const ParamsPOD& params); + +/// +/// finish a batch of alignment calculations, all-mapping +/// +void finish_alignment_all( + const uint32 count, + const uint32* idx, + const uint32 buffer_offset, + const uint32 buffer_size, + io::Alignment* alignments, + const uint32 band_len, + const AllMappingPipelineState& pipeline, + const SmithWatermanScoringScheme<> scoring_scheme, + const ParamsPOD& params); + +/// +/// finish a batch of alignment calculations, all-mapping +/// +void finish_alignment_all( + const uint32 count, + const uint32* idx, + const uint32 buffer_offset, + const uint32 buffer_size, + io::Alignment* alignments, + const uint32 band_len, + const AllMappingPipelineState >& pipeline, + const SmithWatermanScoringScheme<> scoring_scheme, + const ParamsPOD& params); + +///@} // group Traceback +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/traceback_impl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/traceback_impl.h new file mode 100644 index 0000000000000000000000000000000000000000..5894a565cea14cc4f2c4bd25ed7bdfb0a53dc27e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/traceback_impl.h @@ -0,0 +1,165 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include // for dna_to_char + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Traceback +///@{ + +template +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +uint32 read_cigar_length( + const vector_type cigar, + const uint32 cigar_len) +{ + uint32 r = 0; + for (uint32 i = 0; i < cigar_len; ++i) + { + const uint32 l = cigar[ cigar_len - i - 1u ].m_len; + const uint32 op = cigar[ cigar_len - i - 1u ].m_type; + if (op != io::Cigar::DELETION) r += l; + } + return r; +} + +enum MateType +{ + AnchorMate = 0, + OppositeMate = 1, +}; + +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +const char* mate_string(const MateType mate) { return mate == OppositeMate ? "opposite" : "anchor"; } + +/// +/// execute a batch of banded-alignment traceback calculations +/// +template +void banded_traceback_best_t( + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const pipeline_type& pipeline, + const ParamsPOD params); + +/// +/// execute a batch of opposite alignment traceback calculations +/// +template +void opposite_traceback_best_t( + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const pipeline_type& pipeline, + const ParamsPOD params); + +/// +/// execute a batch of banded-alignment traceback calculations +/// +template +void banded_traceback_all_t( + const uint32 count, + const uint32* idx, + const uint32 buffer_offset, + const uint32 buffer_size, + io::Alignment* alignments, + const uint32 band_len, + const pipeline_type& pipeline, + const ParamsPOD params); + +/// +/// finish a batch of alignment calculations +/// +template +void finish_alignment_best_t( + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const pipeline_type& pipeline, + const scoring_scheme_type scoring_scheme, + const ParamsPOD params); + +/// +/// finish a batch of opposite alignment calculations +/// +template +void finish_opposite_alignment_best_t( + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const pipeline_type& pipeline, + const scoring_scheme_type scoring_scheme, + const ParamsPOD params); + +/// +/// finish a batch of alignment calculations, all-mapping +/// +template +void finish_alignment_all_t( + const uint32 count, + const uint32* idx, + const uint32 buffer_offset, + const uint32 buffer_size, + io::Alignment* alignments, + const uint32 band_len, + const pipeline_type& pipeline, + const scoring_scheme_type scoring_scheme, + const ParamsPOD params); + +///@} // group Traceback +///@} // group nvBowtie + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio + +#include diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/traceback_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/traceback_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..aedd487d19b92af4461b29d773b0342449b078b4 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/traceback_inl.h @@ -0,0 +1,1032 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +namespace detail { + +///@addtogroup nvBowtie +///@{ + +///@addtogroup Traceback +///@{ + +///@addtogroup TracebackDetail +///@{ + +/// +/// A scoring stream, fetching the input hits to score from the hit queue +/// indexed by the input sorting order, and assigning them their score and sink +/// attributes. +/// +template +struct BestTracebackStream : public AlignmentStreamBase +{ + typedef AlignmentStreamBase base_type; + typedef typename base_type::context_type context_type; + typedef typename base_type::scheme_type scheme_type; + + /// constructor + /// + /// \param _band_len effective band length; + /// NOTE: this value must match the template BAND_LEN parameter + /// used for instantiating aln::BatchedBandedAlignmentScore. + /// + /// \param _pipeline the pipeline object + /// + /// \param _aligner the aligner object + /// + BestTracebackStream( + const MateType _mate_type, + const uint32 _count, + const uint32* _idx, + io::Alignment* _best_data, + const uint32 _best_stride, + const uint32 _band_len, + const PipelineType _pipeline, + const AlignerType _aligner, + const ParamsPOD _params) : + base_type( _pipeline, _aligner, _params ), m_mate_type( _mate_type ), m_count(_count), m_idx(_idx), m_best_data(_best_data), m_best_stride( _best_stride ), m_band_len( _band_len ) {} + + /// return the maximum pattern length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 max_pattern_length() const { return MAXIMUM_READ_LENGTH; } + + /// return the maximum text length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 max_text_length() const { return MAXIMUM_INSERT_LENGTH; } + + /// return the mate type + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + MateType mate_type() const { return m_mate_type; } + + /// return the stream size + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 size() const { return m_count; } + + /// initialize the i-th context + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool init_context( + const uint32 i, + context_type* context) const + { + context->idx = m_idx ? m_idx[ i ] : i; + + const io::Alignment& alignment = m_best_data[ context->idx + ALN_IDX * m_best_stride ]; + if (alignment.is_aligned() == false) + return false; + + context->min_score = alignment.score(); + + // setup the read info + context->mate = alignment.mate(); + context->read_rc = alignment.is_rc(); + context->read_id = context->idx; + context->read_range = base_type::m_pipeline.get_reads( context->mate ).get_range( context->read_id ); + + const uint32 read_len = context->read_range.y - context->read_range.x; + + // setup the genome range + const bool paired_opposite_alignment = (m_mate_type == OppositeMate && alignment.is_concordant()); + const uint32 g_pos = paired_opposite_alignment ? + alignment.alignment() : + alignment.alignment() > m_band_len/2 ? alignment.alignment() - m_band_len/2 : 0u; + const uint32 g_len = paired_opposite_alignment ? + alignment.sink() : + m_band_len + read_len; + + context->genome_begin = g_pos; + context->genome_end = nvbio::min( context->genome_begin + g_len, base_type::m_pipeline.genome_length ); + return true; + } + + /// handle the output + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void output( + const uint32 i, + const context_type* context) + { + const uint32 cigar_len = context->backtracer.size; + if (cigar_len == 0) + return; + + // alloc the output cigar + io::Cigar* cigar = base_type::m_pipeline.cigar.alloc( context->read_id, cigar_len ); + NVBIO_CUDA_ASSERT_IF( base_type::m_params.debug.asserts, cigar != NULL, "%s backtrack(): unable to allocate CIGAR!\n read[%u], mate[%u], cigar: %u!\n", mate_string( m_mate_type ), context->read_id, context->mate, cigar_len ); + if (cigar) + { + // copy the local cigar to the output one + for (uint32 i = 0; i < cigar_len; ++i) + cigar[i] = context->cigar[i]; + } + + // write the cigar coords + base_type::m_pipeline.cigar_coords[ context->read_id ] = make_uint2( context->alignment.source.x + (context->alignment.source.y << 16), context->backtracer.size ); + NVBIO_CUDA_DEBUG_PRINT_IF( base_type::m_params.debug.show_traceback( context->read_id ), "BestTracebackStream<%u>:\n mate[%u], cigar-coords[%u:%u,%u]\n", ALN_IDX, context->mate, context->alignment.source.x, context->alignment.source.y, context->backtracer.size ); + + NVBIO_CUDA_DEBUG_CHECK_IF( base_type::m_params.debug.show_traceback( context->read_id ), context->alignment.sink.x != uint32(-1) && context->alignment.sink.y != uint32(-1), "\nerror:\n %s backtrack(): failed to re-align!\n read[%u], rc[%u], mate[%u] (expected score: %d)\n", mate_string( m_mate_type ), context->read_id, context->read_rc, context->mate, context->min_score ); + NVBIO_CUDA_DEBUG_CHECK_IF( base_type::m_params.debug.show_traceback( context->read_id ), context->alignment.score == context->min_score, "\nerror:\n %s backtrack(): score %d different from previously calculated value %d!\n read[%u], rc[%u], mate[%u]\n", mate_string( m_mate_type ), context->alignment.score, context->min_score, context->read_id, context->read_rc, context->mate ); + NVBIO_CUDA_ASSERT_IF( base_type::m_params.debug.asserts, context->alignment.sink.x != uint32(-1) && context->alignment.sink.y != uint32(-1), "%s backtrack(): failed to re-align!\n read[%u], rc[%u], mate[%u] (expected score: %d)\n", mate_string( m_mate_type ), context->read_id, context->read_rc, context->mate, context->min_score ); + NVBIO_CUDA_ASSERT_IF( base_type::m_params.debug.asserts, context->alignment.score == context->min_score, "%s backtrack(): score %d different from previously calculated value %d!\n read[%u], rc[%u], mate[%u]\n", mate_string( m_mate_type ), context->alignment.score, context->min_score, context->read_id, context->read_rc, context->mate ); + + NVBIO_CUDA_ASSERT_IF( base_type::m_params.debug.asserts, + read_cigar_length( cigar, context->backtracer.size ) == context->read_range.y - context->read_range.x, + "%s backtrack(): CIGAR length != read length\n read[%u]\n cigar len: %u\n read len: %u\n source: (%u, %u)\n sink: (%u, %u)\n", mate_string( m_mate_type ), + context->read_id, read_cigar_length( cigar, context->backtracer.size ), context->read_range.y - context->read_range.x, context->alignment.source.x, context->alignment.source.y, context->alignment.sink.x, context->alignment.sink.y ); + } + + /// handle the output + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void finish( + const uint32 i, + const context_type* context, + const uint32 ed, + const int32 score) + { + // rewrite the alignment + io::Alignment& aln = m_best_data[ context->read_id + ALN_IDX * m_best_stride ]; + aln.m_align = context->genome_begin; + aln.m_ed = ed; + aln.m_score_sgn = score < 0 ? 1 : 0; + aln.m_score = score < 0 ? -score : score; + + NVBIO_CUDA_DEBUG_PRINT_IF( base_type::m_params.debug.show_traceback( context->read_id ), "BestTracebackStream<%u>:\n mate[%u], ed[%u], score[%d], pos[%u], rc[%u]\n", ALN_IDX, aln.mate(), aln.ed(), aln.score(), aln.alignment(), uint32( aln.is_rc() )); + } + + const MateType m_mate_type; + const uint32 m_count; + const uint32* m_idx; + io::Alignment* m_best_data; + const uint32 m_best_stride; + const uint32 m_band_len; +}; + +/// +/// dispatch the execution of a batch of single-ended banded-alignment traceback calculations +/// +template +void banded_traceback_best( + const MateType mate_type, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const pipeline_type& pipeline, + const aligner_type aligner, + const ParamsPOD params) +{ + const uint32 static_band_len = + (band_len < 4) ? 3u : + (band_len < 8) ? 7u : + (band_len < 16) ? 15u : + 31u; + + typedef BestTracebackStream stream_type; + + stream_type stream( + mate_type, + count, + idx, + best_data, + best_stride, + static_band_len, + pipeline, + aligner, + params ); + + NVBIO_VAR_UNUSED const uint32 CHECKPOINTS = BANDED_DP_CHECKPOINTS; + + if (band_len < 4) + { + aln::BatchedBandedAlignmentTraceback<3u,CHECKPOINTS,stream_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else if (band_len < 8) + { + aln::BatchedBandedAlignmentTraceback<7u,CHECKPOINTS,stream_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else if (band_len < 16) + { + aln::BatchedBandedAlignmentTraceback<15u,CHECKPOINTS,stream_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else + { + aln::BatchedBandedAlignmentTraceback<31u,CHECKPOINTS,stream_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } +} + +/// +/// dispatch the execution of a batch of full DP alignment traceback calculations +/// +template +void traceback_best( + const MateType mate_type, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const pipeline_type& pipeline, + const aligner_type aligner, + const ParamsPOD params) +{ + typedef BestTracebackStream stream_type; + + stream_type stream( + mate_type, + count, + idx, + best_data, + best_stride, + 0u, // band-len + pipeline, + aligner, + params ); + + typedef aln::DeviceThreadBlockScheduler<128,9> scheduler_type; + + aln::BatchedAlignmentTraceback batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); +} + +/// +/// A scoring stream, fetching the input hits to score from the hit queue +/// indexed by the input sorting order, and assigning them their score and sink +/// attributes. +/// +template +struct AllTracebackStream : public AlignmentStreamBase +{ + typedef AlignmentStreamBase base_type; + typedef typename base_type::context_type context_type; + typedef typename base_type::scheme_type scheme_type; + + /// constructor + /// + /// \param _band_len effective band length; + /// NOTE: this value must match the template BAND_LEN parameter + /// used for instantiating aln::BatchedBandedAlignmentScore. + /// + /// \param _pipeline the pipeline object + /// + /// \param _aligner the aligner object + /// + AllTracebackStream( + const uint32 _count, + const uint32* _idx, + const uint32 _buffer_offset, + const uint32 _buffer_size, + io::Alignment* _alignments, + const uint32 _band_len, + const PipelineType _pipeline, + const AlignerType _aligner, + const ParamsPOD _params) : + base_type( _pipeline, _aligner, _params ), + m_mate_type( AnchorMate ), + m_count(_count), + m_idx(_idx), + m_buffer_offset(_buffer_offset), + m_buffer_size(_buffer_size), + m_alignments(_alignments), + m_band_len( _band_len ) {} + + /// return the maximum pattern length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 max_pattern_length() const { return MAXIMUM_READ_LENGTH; } + + /// return the maximum text length + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 max_text_length() const { return MAXIMUM_INSERT_LENGTH; } + + /// return the mate type + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + MateType mate_type() const { return m_mate_type; } + + /// return the stream size + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 size() const { return m_count; } + + /// initialize the i-th context + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool init_context( + const uint32 i, + context_type* context) const + { + context->idx = i; + + const uint32 buffer_idx = (m_idx[ i ] + m_buffer_offset) % m_buffer_size; + const io::Alignment& alignment = base_type::m_pipeline.buffer_alignments[ buffer_idx ]; + + // setup the read info + context->mate = alignment.mate(); + context->read_rc = alignment.is_rc(); + context->read_id = base_type::m_pipeline.output_read_info[ i ]; + context->read_range = base_type::m_pipeline.get_reads( context->mate ).get_range( context->read_id ); + + const uint32 read_len = context->read_range.y - context->read_range.x; + + // setup the genome range + const uint32 g_pos = alignment.alignment() > m_band_len/2 ? alignment.alignment() - m_band_len/2 : 0u; + const uint32 g_len = m_band_len + read_len; + + context->genome_begin = g_pos; + context->genome_end = nvbio::min( context->genome_begin + g_len, base_type::m_pipeline.genome_length ); + return true; + } + + /// handle the output + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void output( + const uint32 i, + const context_type* context) + { + const uint32 cigar_len = context->backtracer.size; + if (cigar_len == 0) + return; + + // alloc the output cigar + io::Cigar* cigar = base_type::m_pipeline.cigar.alloc( context->idx, cigar_len ); + NVBIO_CUDA_ASSERT_IF( base_type::m_params.debug.asserts, cigar != NULL, "%s backtrack(): unable to allocate CIGAR!\n aln[%u], read[%u], mate[%u], cigar: %u!\n", mate_string( m_mate_type ), context->idx, context->read_id, context->mate, cigar_len ); + if (cigar) + { + // copy the local cigar to the output one + for (uint32 i = 0; i < cigar_len; ++i) + cigar[i] = context->cigar[i]; + } + + // write the cigar coords + base_type::m_pipeline.cigar_coords[ context->idx ] = make_uint2( context->alignment.source.x + (context->alignment.source.y << 16), context->backtracer.size ); + NVBIO_CUDA_DEBUG_PRINT_IF( base_type::m_params.debug.show_traceback( context->read_id ), "AllTracebackStream:\n mate[%u], cigar-coords[%u:%u,%u]\n", context->mate, context->alignment.source.x, context->alignment.source.y, context->backtracer.size ); + + NVBIO_CUDA_DEBUG_CHECK_IF( base_type::m_params.debug.show_traceback( context->read_id ), context->alignment.sink.x != uint32(-1) && context->alignment.sink.y != uint32(-1), "\nerror:\n backtrack(): failed to re-align!\n read[%u], rc[%u], mate[%u] (expected score: %d)\n", context->read_id, context->read_rc, context->mate, context->min_score ); + NVBIO_CUDA_DEBUG_CHECK_IF( base_type::m_params.debug.show_traceback( context->read_id ), context->alignment.score == context->min_score, "\nerror:\n backtrack(): score %d different from previously calculated value %d!\n read[%u], rc[%u], mate[%u]\n", context->alignment.score, context->min_score, context->read_id, context->read_rc, context->mate ); + NVBIO_CUDA_ASSERT_IF( base_type::m_params.debug.asserts, context->alignment.sink.x != uint32(-1) && context->alignment.sink.y != uint32(-1), "backtrack(): failed to re-align!\n read[%u], rc[%u], mate[%u] (expected score: %d)\n", context->read_id, context->read_rc, context->mate, context->min_score ); + NVBIO_CUDA_ASSERT_IF( base_type::m_params.debug.asserts, context->alignment.score == context->min_score, "backtrack(): score %d different from previously calculated value %d!\n read[%u], rc[%u], mate[%u]\n", context->alignment.score, context->min_score, context->read_id, context->read_rc, context->mate ); + + NVBIO_CUDA_ASSERT_IF( base_type::m_params.debug.asserts, + read_cigar_length( cigar, context->backtracer.size ) == context->read_range.y - context->read_range.x, + "backtrack(): CIGAR length != read length\n read[%u]\n cigar len: %u\n read len: %u\n source: (%u, %u)\n sink: (%u, %u)\n", + context->read_id, read_cigar_length( cigar, context->backtracer.size ), context->read_range.y - context->read_range.x, context->alignment.source.x, context->alignment.source.y, context->alignment.sink.x, context->alignment.sink.y ); + } + + /// handle the output + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void finish( + const uint32 i, + const context_type* context, + const uint32 ed, + const int32 score) + { + const uint32 buffer_idx = (m_idx[ i ] + m_buffer_offset) % m_buffer_size; + const io::Alignment& in_alignment = base_type::m_pipeline.buffer_alignments[ buffer_idx ]; + io::Alignment& out_alignment = m_alignments[ context->idx ]; + + // rewrite the alignment + out_alignment = io::Alignment( + context->genome_begin, + ed, + score, + in_alignment.is_rc(), + in_alignment.is_paired(), + in_alignment.is_discordant() ); + + NVBIO_CUDA_DEBUG_PRINT_IF( base_type::m_params.debug.show_traceback( context->read_id ), "finish-alignment:\n mate[%u], ed[%u], score[%d], pos[%u], rc[%u]\n", context->mate, out_alignment.ed(), out_alignment.score(), out_alignment.alignment(), uint32( out_alignment.is_rc() )); + } + + const MateType m_mate_type; + const uint32 m_count; + const uint32* m_idx; + const uint32 m_buffer_offset; + const uint32 m_buffer_size; + io::Alignment* m_alignments; + const uint32 m_band_len; +}; + +/// +/// dispatch the execution of a batch of single-ended banded-alignment traceback calculations +/// +template +void banded_traceback_all( + const uint32 count, + const uint32* idx, + const uint32 buffer_offset, + const uint32 buffer_size, + io::Alignment* alignments, + const uint32 band_len, + const pipeline_type& pipeline, + const aligner_type aligner, + const ParamsPOD params) +{ + const uint32 static_band_len = + (band_len < 4) ? 3u : + (band_len < 8) ? 7u : + (band_len < 16) ? 15u : + 31u; + + typedef AllTracebackStream stream_type; + + stream_type stream( + count, + idx, + buffer_offset, + buffer_size, + alignments, + static_band_len, + pipeline, + aligner, + params ); + + NVBIO_VAR_UNUSED const uint32 CHECKPOINTS = BANDED_DP_CHECKPOINTS; + + if (band_len < 4) + { + aln::BatchedBandedAlignmentTraceback<3u,CHECKPOINTS,stream_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else if (band_len < 8) + { + aln::BatchedBandedAlignmentTraceback<7u,CHECKPOINTS,stream_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else if (band_len < 16) + { + aln::BatchedBandedAlignmentTraceback<15u,CHECKPOINTS,stream_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } + else + { + aln::BatchedBandedAlignmentTraceback<31u,CHECKPOINTS,stream_type> batch; + + batch.enact( stream, pipeline.dp_buffer_size, pipeline.dp_buffer ); + } +} + + +/// +/// finish computing the final alignments, i.e. computing the MD strings and the final scores (given the CIGARs) +/// +template __global__ +void finish_alignment_kernel( + stream_type stream, + pipeline_type pipeline, + const scheme_type scoring_scheme, + const ParamsPOD params) +{ + const uint32 work_id = threadIdx.x + BLOCKDIM*blockIdx.x; + if (work_id >= stream.size()) return; + + typedef typename stream_type::aligner_type aligner_type; + typedef typename stream_type::context_type context_type; + typedef typename stream_type::strings_type strings_type; + + // load the alignment context + context_type context; + if (stream.init_context( work_id, &context ) == false) + return; + + // compute the end of the current DP matrix window + const uint32 read_len = stream.pattern_length( work_id, &context ); + + // load the strings to be aligned + strings_type strings; + stream.load_strings( work_id, 0, read_len, &context, &strings ); + + const uint2 cigar_coord = pipeline.cigar_coords[ context.idx ]; + const uint32 cigar_offset = cigar_coord.x & 0xFFFF; + const uint32 cigar_length = cigar_coord.y; + + // + // compute actual score: this is needed because we might be using plain edit distance in + // the first stage rather than doing full SW. We also take the chance to compute the MD + // string here. + // + const io::Cigar* cigar_vector = pipeline.cigar[ context.idx ]; + + // bail-out if no CIGAR's available! + if (cigar_vector == NULL) + return; + + const uint32 SUB_MASK = 1u << io::Cigar::SUBSTITUTION; + const uint32 DEL_MASK = 1u << io::Cigar::DELETION; + const uint32 INS_MASK = 1u << io::Cigar::INSERTION; + const uint32 CLP_MASK = 1u << io::Cigar::SOFT_CLIPPING; + + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_traceback( context.read_id ), "\nfinish_alignment(%s):\n cigar slot: %u\n", stream.mate_type() == OppositeMate ? "opposite" : "anchor", pipeline.cigar.slot( context.read_id ) ); + + // alloc some local memory for the MDS + const uint32 MDS_LMEM = 2048; + uint8 mds_local[MDS_LMEM]; + + // leave a blank space in the MDS vector to store its length later on + uint32 mds_len = 2; + uint8 mds_op = io::MDS_INVALID; + + uint32 ed = 0; + int32 score = 0; + + const uint32 g_len = strings.text.length(); + + for (uint32 i = 0, j = 0/*read_pos*/, k = cigar_offset; i < cigar_length; ++i) + { + const uint32 l = cigar_vector[ cigar_length - i - 1u ].m_len; + const uint32 t = cigar_vector[ cigar_length - i - 1u ].m_type; + + NVBIO_CUDA_ASSERT_IF( params.debug.asserts, (t == io::Cigar::SUBSTITUTION) || (t == io::Cigar::DELETION) || (t == io::Cigar::INSERTION) || (t == io::Cigar::SOFT_CLIPPING), "finish_alignment(%s): unknown op!\n read[%u], mate[%u], op[%u]: %u\n", stream.mate_type() == OppositeMate ? "opposite" : "anchor", context.read_id, context.mate, i, t ); + + const uint8 t_mask = 1u << t; + + // handle deletions & insertions + if (t_mask & (INS_MASK | DEL_MASK | CLP_MASK)) + //if (t_mask & DEL_MASK) // track deletions only + { + NVBIO_CUDA_ASSERT_IF( params.debug.asserts, mds_len+2 < MDS_LMEM, "finish_alignment(%s): exceeded MDS length!\n read[%u], mate[%u], mds: %u!\n", stream.mate_type() == OppositeMate ? "opposite" : "anchor", context.read_id, context.mate, mds_len+2 ); + mds_op = t_mask & DEL_MASK ? io::MDS_DELETION : io::MDS_INSERTION; + mds_local[ mds_len++ ] = mds_op; + mds_local[ mds_len++ ] = l; + + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_traceback( context.read_id ), "\n%c[%03u] ", t_mask & DEL_MASK ? 'D' : 'I', l); + NVBIO_CUDA_ASSERT_IF( params.debug.asserts, l, "finish_alignment(%s): zero-length MDS[%u:%u] (%c)\n", context.read_id, mds_len-1, t_mask & DEL_MASK ? 'D' : 'I', l); + } + + for (uint32 n = 0; n < l; ++n) + { + // advance j and k + j += (t_mask & (SUB_MASK | INS_MASK | CLP_MASK)) ? 1u : 0u; + k += (t_mask & (SUB_MASK | DEL_MASK)) ? 1u : 0u; + NVBIO_CUDA_ASSERT_IF( params.debug.asserts, (j <= read_len) && (k <= g_len), "finish_alignment(%s): coordinates out-of-bounds!\n read[%u], mate[%u], (%u,%u) > (%u,%u) @ %u\n", stream.mate_type() == OppositeMate ? "opposite" : "anchor", context.read_id, context.mate, j, k, read_len, g_len, context.genome_begin ); + NVBIO_CUDA_ASSERT_IF( params.debug.asserts, (t_mask & (SUB_MASK | INS_MASK | CLP_MASK)) ? (j > 0) : true, "finish_alignment(%s): accessed read at -1!\n read[%u], mate[%u]\n", stream.mate_type() == OppositeMate ? "opposite" : "anchor", context.read_id, context.mate ); + NVBIO_CUDA_ASSERT_IF( params.debug.asserts, (t_mask & (SUB_MASK | DEL_MASK)) ? (k > 0) : true, "finish_alignment(%s): accessed genome at -1!\n read[%u], mate[%u]\n", stream.mate_type() == OppositeMate ? "opposite" : "anchor", context.read_id, context.mate ); + + const uint8 readc = j > 0 ? strings.pattern[j-1] : 255u; + const uint8 refc = k > 0 ? strings.text[k-1] : 255u; + + if (t_mask == SUB_MASK) + { + if (readc == refc) + { + NVBIO_CUDA_ASSERT_IF( params.debug.asserts, mds_len < MDS_LMEM, "finish_alignment(%s): exceeded MDS length!\n read[%u], mds: %u!\n", stream.mate_type() == OppositeMate ? "opposite" : "anchor", context.read_id, mds_len+2 ); + + // handle the most common case first: a character match + if (mds_op == io::MDS_MATCH && (mds_local[ mds_len-1 ] < 255)) + { + // prolong the sequence of previous matches + mds_local[ mds_len-1 ]++; + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_traceback( context.read_id ), "%c", dna_to_char(readc) ); + } + else + { + // start a new sequence of matches + NVBIO_CUDA_ASSERT_IF( params.debug.asserts, mds_len+2 < MDS_LMEM, "finish_alignment(%s): exceeded MDS length!\n read[%u], mds: %u!\n", stream.mate_type() == OppositeMate ? "opposite" : "anchor", context.read_id, mds_len+2 ); + mds_local[ mds_len++ ] = mds_op = io::MDS_MATCH; + mds_local[ mds_len++ ] = 1; + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_traceback( context.read_id ), "\nM[%03u] %c", l, dna_to_char(readc) ); + } + } + else + { + // handle mismatches + NVBIO_CUDA_ASSERT_IF( params.debug.asserts, mds_len+2 < MDS_LMEM, "finish_alignment(%s): exceeded MDS length!\n read[%u], mds: %u!\n", stream.mate_type() == OppositeMate ? "opposite" : "anchor", context.read_id, mds_len+2 ); + mds_local[ mds_len++ ] = mds_op = io::MDS_MISMATCH; + mds_local[ mds_len++ ] = readc; + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_traceback( context.read_id ), "\nS[%03u] %c", l, dna_to_char(readc) ); + ++ed; + } + } + else //if (t_mask & DEL_MASK) // track deletions only + { + // handle all the rare cases together: deletions/insertions + NVBIO_CUDA_ASSERT_IF( params.debug.asserts, mds_len+1 < MDS_LMEM, "finish_alignment(%s): exceeded MDS length!\n read[%u], mds: %u!\n", stream.mate_type() == OppositeMate ? "opposite" : "anchor", context.read_id, mds_len+1 ); + mds_local[ mds_len++ ] = t_mask & DEL_MASK ? refc : readc; + + if (t_mask != CLP_MASK) // don't count soft-clipping in the edit-distance calculation + ++ed; + + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_traceback( context.read_id ), "%c", dna_to_char( (t_mask & DEL_MASK) ? refc : readc ) ); + } + + if (t_mask == SUB_MASK) + { + // score the substitution + const uint8 q = strings.quals[j-1]; + const int32 delta = scoring_scheme.score( readc, 1u << refc, q ); + score += delta; + NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_traceback( context.read_id ) && delta, " S(%d,%d)", delta, q ); + } + } + + if (t_mask == INS_MASK) { score -= scoring_scheme.cumulative_deletion( l ); NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_traceback( context.read_id ), " D(%d)", scoring_scheme.cumulative_deletion( l ) ); } + else if (t_mask == DEL_MASK) { score -= scoring_scheme.cumulative_insertion( l ); NVBIO_CUDA_DEBUG_PRINT_IF( params.debug.show_traceback( context.read_id ), " I(%d)", scoring_scheme.cumulative_insertion( l ) ); } + } + + #if 0 + #if defined(NVBIO_CUDA_DEBUG) + if (params.debug.show_traceback( context.read_id )) + { + char read_str[512]; + char gen_str[512]; + char cigar_str[512]; + char mm_string[512]; + + dna_to_string( strings.pattern, read_len, read_str ); + dna_to_string( strings.text, g_len, gen_str ); + + for (uint32 i = 0; i < read_len; ++i) + mm_string[i] = '0' - int32( scoring_scheme.mismatch( strings.quals[i] ) ); + mm_string[read_len] = '\0'; + + uint32 j = 0; + for (uint32 i = 0; i < cigar_coord.y; ++i) + { + const uint32 l = cigar_vector[ cigar_coord.y - i - 1u ].m_len; + const uint32 t = cigar_vector[ cigar_coord.y - i - 1u ].m_type; + for (uint32 n = 0; n < l; ++n) + cigar_str[j++] = "MID"[t]; + } + cigar_str[j] = '\0'; + NVBIO_CUDA_DEBUG_PRINT("\nfinish_alignment:\n score: %d, %d, ed: %u, (genome offset: %u)\n read : %s\n genome: %s\n quals : %s\n cigar : %s\n mds len: %u\n", alignment.score(), score, ed, cigar_offset, read_str, gen_str, mm_string, cigar_str, mds_len); + } + #endif + #endif + + // store the MDS length in the first two bytes + NVBIO_CUDA_ASSERT_IF( params.debug.asserts, mds_len < 65536, "finish_alignment(%s): exceeded representable MDS length!\n aln[%u], read[%u], mate[%u], mds: %u!\n", stream.mate_type() == OppositeMate ? "opposite" : "anchor", context.idx, context.read_id, context.mate, mds_len ); + mds_local[0] = uint8( mds_len & 0xFF ); + mds_local[1] = uint8( mds_len >> 8 ); + + // alloc the output mds + uint8* mds_vector = pipeline.mds.alloc( context.idx, mds_len ); + NVBIO_CUDA_ASSERT_IF( params.debug.asserts, mds_vector != NULL, "finish_alignment(%s): unable to allocate MDS!\n aln[%u], read[%u], mate[%u], mds: %u!\n", stream.mate_type() == OppositeMate ? "opposite" : "anchor", context.idx, context.read_id, context.mate, mds_len ); + if (mds_vector) + { + // copy the local mds to the output one + for (uint32 i = 0; i < mds_len; ++i) + mds_vector[i] = mds_local[i]; + } + + // output the finished alignment + stream.finish( work_id, &context, ed, score ); +} + +/// +/// finish computing the final alignments, i.e. computing the MD strings and the final scores (given the CIGARs) +/// +template +void finish_alignment_best( + const MateType mate_type, + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const pipeline_type& pipeline, + const scheme_type scoring_scheme, + const ParamsPOD params) +{ + const uint32 static_band_len = + (band_len < 4) ? 3u : + (band_len < 8) ? 7u : + (band_len < 16) ? 15u : + 31u; + + typedef typename pipeline_type::scheme_type::local_aligner_type aligner_type; + + typedef BestTracebackStream stream_type; + + stream_type stream( + mate_type, + count, + idx, + best_data, + best_stride, + static_band_len, + pipeline, + pipeline.scoring_scheme.local_aligner(), + params ); + + const uint32 n_blocks = (count + BLOCKDIM-1) / BLOCKDIM; + + finish_alignment_kernel<<>>( + stream, + pipeline, + scoring_scheme, + params ); + + // check for overflows + //if (mds.allocated_size() >= mds.arena_size()) + // log_error( stderr, "finish_alignment(): exceeded MDS pool size\n" ); +} + +/// +/// finish computing the final alignments, i.e. computing the MD strings and the final scores (given the CIGARs) +/// +template +void finish_alignment_all( + const uint32 count, + const uint32* idx, + const uint32 buffer_offset, + const uint32 buffer_size, + io::Alignment* alignments, + const uint32 band_len, + const pipeline_type& pipeline, + const scheme_type scoring_scheme, + const ParamsPOD params) +{ + const uint32 static_band_len = + (band_len < 4) ? 3u : + (band_len < 8) ? 7u : + (band_len < 16) ? 15u : + 31u; + + typedef typename pipeline_type::scheme_type::local_aligner_type aligner_type; + + typedef AllTracebackStream stream_type; + + stream_type stream( + count, + idx, + buffer_offset, + buffer_size, + alignments, + static_band_len, + pipeline, + pipeline.scoring_scheme.local_aligner(), + params ); + + const uint32 n_blocks = (count + BLOCKDIM-1) / BLOCKDIM; + + finish_alignment_kernel<<>>( + stream, + pipeline, + scoring_scheme, + params ); + + // check for overflows + //if (mds.allocated_size() >= mds.arena_size()) + // log_error( stderr, "finish_alignment(): exceeded MDS pool size\n" ); +} + +///@} // group TracebackDetail +///@} // group Traceback +///@} // group nvBowtie + +} // namespace detail + +// +// execute a batch of banded-alignment traceback calculations +// +template +void banded_traceback_best_t( + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const pipeline_type& pipeline, + const ParamsPOD params) +{ + if (params.alignment_type == LocalAlignment) + { + detail::banded_traceback_best( + AnchorMate, + count, + idx, + best_data, + best_stride, + band_len, + pipeline, + pipeline.scoring_scheme.local_aligner(), + params ); + } + else + { + detail::banded_traceback_best( + AnchorMate, + count, + idx, + best_data, + best_stride, + band_len, + pipeline, + pipeline.scoring_scheme.end_to_end_aligner(), + params ); + } +} + +// +// execute a batch of opposite alignment traceback calculations +// +template +void opposite_traceback_best_t( + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const pipeline_type& pipeline, + const ParamsPOD params) +{ + if (params.alignment_type == LocalAlignment) + { + detail::traceback_best( + OppositeMate, + count, + idx, + best_data, + best_stride, + pipeline, + pipeline.scoring_scheme.local_aligner(), + params ); + } + else + { + detail::traceback_best( + OppositeMate, + count, + idx, + best_data, + best_stride, + pipeline, + pipeline.scoring_scheme.end_to_end_aligner(), + params ); + } +} + +// +// execute a batch of banded-alignment traceback calculations +// +template +void banded_traceback_all_t( + const uint32 count, + const uint32* idx, + const uint32 buffer_offset, + const uint32 buffer_size, + io::Alignment* alignments, + const uint32 band_len, + const pipeline_type& pipeline, + const ParamsPOD params) +{ + if (params.alignment_type == LocalAlignment) + { + detail::banded_traceback_all( + count, + idx, + buffer_offset, + buffer_size, + alignments, + band_len, + pipeline, + pipeline.scoring_scheme.local_aligner(), + params ); + } + else + { + detail::banded_traceback_all( + count, + idx, + buffer_offset, + buffer_size, + alignments, + band_len, + pipeline, + pipeline.scoring_scheme.end_to_end_aligner(), + params ); + } +} + +// +// finish a batch of alignment calculations +// +template +void finish_alignment_best_t( + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const pipeline_type& pipeline, + const scoring_scheme_type scoring_scheme, + const ParamsPOD params) +{ + detail::finish_alignment_best( + AnchorMate, + count, + idx, + best_data, + best_stride, + band_len, + pipeline, + scoring_scheme, + params ); +} + +// +// finish a batch of opposite alignment calculations +// +template +void finish_opposite_alignment_best_t( + const uint32 count, + const uint32* idx, + io::Alignment* best_data, + const uint32 best_stride, + const uint32 band_len, + const pipeline_type& pipeline, + const scoring_scheme_type scoring_scheme, + const ParamsPOD params) +{ + detail::finish_alignment_best( + OppositeMate, + count, + idx, + best_data, + best_stride, + band_len, + pipeline, + scoring_scheme, + params ); +} + +// +// finish a batch of alignment calculations +// +template +void finish_alignment_all_t( + const uint32 count, + const uint32* idx, + const uint32 buffer_offset, + const uint32 buffer_size, + io::Alignment* alignments, + const uint32 band_len, + const pipeline_type& pipeline, + const scoring_scheme_type scoring_scheme, + const ParamsPOD params) +{ + detail::finish_alignment_all( + count, + idx, + buffer_offset, + buffer_size, + alignments, + band_len, + pipeline, + scoring_scheme, + params ); +} + + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/utils.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/utils.h new file mode 100644 index 0000000000000000000000000000000000000000..c0ebef9f6c41834806a478a349f5bcee9d14188b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/cuda/utils.h @@ -0,0 +1,77 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + +inline void optional_device_synchronize() +{ +#if DO_OPTIONAL_SYNCHRONIZE + cudaDeviceSynchronize(); +#endif +} + +#if DO_DEVICE_TIMING +typedef nvbio::cuda::Timer DeviceTimer; +#else +typedef nvbio::FakeTimer DeviceTimer; +#endif + +// convert a range from a [begin,last] representation to a [begin,end) one +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +uint2 inclusive_to_exclusive(const uint2 range) { return make_uint2( range.x, range.y + 1u ); } + +#ifdef __CUDACC__ + +// alloc some slots from a counter using a warp-synchronous reduction +NVBIO_FORCEINLINE NVBIO_DEVICE uint32 alloc(uint32* counter, volatile uint32 *warp_broadcast) +{ +#if USE_WARP_SYNCHRONOUS_QUEUES + const uint32 mask = __ballot( true ); + const uint32 pop_scan = __popc( mask << (32u - warp_tid()) ); + const uint32 pop_count = __popc( mask ); + if (pop_scan == 0) + *warp_broadcast = atomicAdd( counter, pop_count ); + + return *warp_broadcast + pop_scan; +#else + return atomicAdd( counter, 1u ); +#endif +} + +#endif // __CUDACC__ + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/quality_coeffs.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/quality_coeffs.cpp new file mode 100644 index 0000000000000000000000000000000000000000..36f03d2db4d84606b34c61402026e82df8f5b7ce --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/quality_coeffs.cpp @@ -0,0 +1,98 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include + +namespace nvbio { +namespace bowtie2 { + +/// map Phred quality scores into their maq equivalents +/// +unsigned char s_phred_to_maq[] = { + 0, 0, 0, 0, 0, + 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, + 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, + 30 +}; + +/// map Solexa quality values to Phred scale +/// +unsigned char s_solexa_to_phred[] = { + 0, 1, 1, 1, 1, 1, 1, 2, 2, 3, + 3, 4, 4, 5, 5, 6, 7, 8, 9, 10, + 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, + 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, + 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, + 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, + 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, + 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, + 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, + 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, + 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, + 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, + 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, + 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, + 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, + 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, + 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, + 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, + 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, + 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, + 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, + 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, + 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, + 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, + 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, + 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, + 250, 251, 252, 253, 254, 255 +}; + +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/quality_coeffs.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/quality_coeffs.h new file mode 100644 index 0000000000000000000000000000000000000000..0614f45b13b40baf5bdc84e23e27f20543ad284f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/bowtie2/quality_coeffs.h @@ -0,0 +1,57 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include + +namespace nvbio { +namespace bowtie2 { + +/// map Phred quality scores into their maq equivalents +/// +extern unsigned char s_phred_to_maq[]; + +/// map Solexa quality values to Phred scale +/// +extern unsigned char s_solexa_to_phred[]; + +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +char phred_to_maq(int q) +{ + return + q < 5 ? + 0 : + (q < 15) ? + 10 : + (q < 25) ? + 20 : + 30; +} + +} // namespace bowtie2 +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/nvBowtie.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/nvBowtie.cpp new file mode 100644 index 0000000000000000000000000000000000000000..2665426fa3b61eab96d562c9b11f13088db567b3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvBowtie/nvBowtie.cpp @@ -0,0 +1,949 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// nvBowtie.cpp : Defines the entry point for the console application. +// + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +void crcInit(); + +namespace nvbio { +namespace bowtie2 { +namespace cuda { + + void test_seed_hit_deques(); + void test_scoring_queues(); + +} // namespace cuda +} // namespace bowtie2 +} // namespace nvbio + +using namespace nvbio; + +// bogus implementation of a function to check if a string is a number +bool is_number(const char* str, uint32 len = uint32(-1)) +{ + if (str[0] == '-') + ++str; + + for (uint32 l = 0; *str != '\0' && l < len; ++l) + { + const char c = *str; ++str; + if (c == '.') continue; + if (c >= '0' && c <= '9') continue; + return false; + } + return true; +} + +void log_ed(nvbio::bowtie2::cuda::AlignmentStats& stats) +{ + if (stats.n_mapped == 0) + return; + + const std::vector& mapped = stats.mapped_log_ed_histogram; + log_stats(stderr, " ed :"); + for (uint32 i = 0; i < mapped.size(); ++i) + { + if (float(mapped[i])/float(stats.n_mapped) > 1.0e-3f) + log_stats_cont(stderr, " %5u ", i ? 1u << (i-1) : 0u ); + } + log_stats_cont(stderr,"\n"); + log_stats(stderr, " :"); + for (uint32 i = 0; i < mapped.size(); ++i) + { + if (float(mapped[i])/float(stats.n_mapped) > 1.0e-3f) + log_stats_cont(stderr, " %6.2f%%", 100.0f * float(mapped[i])/float(stats.n_mapped) ); + } + log_stats_cont(stderr,"\n"); +} +void log_mapq(nvbio::bowtie2::cuda::AlignmentStats& stats) +{ + if (stats.n_mapped == 0) + return; + + log_stats(stderr, " mapq :"); + for (uint32 i = 0; i < 8; ++i) + log_stats_cont(stderr, " %5u ", i ? 1u << (i-1) : 0u ); + log_stats_cont(stderr,"\n"); + log_stats(stderr, " :"); + for (uint32 i = 0; i < 8; ++i) + log_stats_cont(stderr, " %6.2f%%", 100.0f * float(stats.mapq_log_bins[i])/float(stats.n_mapped) ); + log_stats_cont(stderr,"\n"); +} + +int main(int argc, char* argv[]) +{ + //cudaSetDeviceFlags( cudaDeviceMapHost | cudaDeviceLmemResizeToMax ); + + crcInit(); + + if (argc == 1 || + (argc == 2 && strcmp( argv[1], "--help" ) == 0) || + (argc == 2 && strcmp( argv[1], "-h" ) == 0)) + { + log_info(stderr,"nvBowtie [options]\n"); + log_info(stderr,"options:\n"); + log_info(stderr," General:\n"); + log_info(stderr," -U file-name unpaired reads\n"); + log_info(stderr," -1 file-name first mate reads\n"); + log_info(stderr," -2 file-name second mate reads\n"); + log_info(stderr," -S file-name output file (.sam|.bam)\n"); + log_info(stderr," -x file-name reference index\n"); + log_info(stderr," --verbosity int [5] verbosity level\n"); + log_info(stderr," --upto | -u int [-1] maximum number of reads to process\n"); + log_info(stderr," --trim3 | -3 int [0] trim the first N bases of 3'\n"); + log_info(stderr," --trim5 | -5 int [0] trim the first N bases of 5'\n"); + log_info(stderr," --nofw do not align the forward strand\n"); + log_info(stderr," --norc do not align the reverse-complemented strand\n"); + log_info(stderr," --device int [0] select the given cuda device(s) (e.g. --device 0 --device 1 ...)\n"); + log_info(stderr," --file-ref load reference from file\n"); + log_info(stderr," --server-ref load reference from server\n"); + log_info(stderr," --phred33 qualities are ASCII characters equal to Phred quality + 33\n"); + log_info(stderr," --phred64 qualities are ASCII characters equal to Phred quality + 64\n"); + log_info(stderr," --solexa-quals qualities are in the Solexa format\n"); + log_info(stderr," --rg-id string add the RG-ID field of the SAM output header\n"); + log_info(stderr," --rg string,val add an RG-TAG field of the SAM output header\n"); + log_info(stderr," Paired-End:\n"); + log_info(stderr," --ff paired mates are forward-forward\n"); + log_info(stderr," --fr paired mates are forward-reverse\n"); + log_info(stderr," --rf paired mates are reverse-forward\n"); + log_info(stderr," --rr paired mates are reverse-reverse\n"); + log_info(stderr," --minins int [0] minimum insert length\n"); + log_info(stderr," --minins int [500] maximum insert length\n"); + log_info(stderr," --overlap allow overlapping mates\n"); + log_info(stderr," --dovetail allow dovetailing mates\n"); + log_info(stderr," --no-mixed only report paired alignments\n"); + log_info(stderr," --ungapped-mates | -ug perform ungapped mate alignment\n"); + log_info(stderr," Seeding:\n"); + log_info(stderr," --seed-len | -L int [22] seed lengths\n"); + log_info(stderr," --seed-freq | -i {G|L|S},x,y seed interval, as x + y*func(read-len) (G=log,L=linear,S=sqrt)\n"); + log_info(stderr," --max-hits int [100] maximum amount of seed hits\n"); + log_info(stderr," --max-reseed | -R int [2] number of reseeding rounds\n"); + log_info(stderr," Extension:\n"); + log_info(stderr," --all | -a perform all-mapping (i.e. find and report all alignments)\n"); + log_info(stderr," --local perform local alignment\n"); + log_info(stderr," --rand randomized seed selection\n"); + log_info(stderr," --no-rand do not randomize seed hit selection\n"); + log_info(stderr," --max-dist int [15] maximum edit distance\n"); + log_info(stderr," --max-effort-init int [15] initial maximum number of consecutive extension failures\n"); + log_info(stderr," --max-effort | -D int [15] maximum number of consecutive extension failures\n"); + log_info(stderr," --min-ext int [30] minimum number of extensions per read\n"); + log_info(stderr," --max-ext int [400] maximum number of extensions per read\n"); + log_info(stderr," --fast apply the fast presets\n"); + log_info(stderr," --very-fast apply the very-fast presets\n"); + log_info(stderr," --sensitive apply the sensitive presets\n"); + log_info(stderr," --very-sensitive apply the very-sensitive presets\n"); + log_info(stderr," --fast-local apply the fast presets\n"); + log_info(stderr," --very-fast-local apply the very-fast presets\n"); + log_info(stderr," --sensitive-local apply the sensitive presets\n"); + log_info(stderr," --very-sensitive-local apply the very-sensitive presets\n"); + log_info(stderr," Scoring:\n"); + log_info(stderr," --scoring {sw|ed} Smith-Waterman / Edit-Distance scoring\n"); + log_info(stderr," --score-min {G|L|S},x,y minimum score function, as x + y*func(read-len)\n"); + log_info(stderr," --ma int match bonus\n"); + log_info(stderr," --mp int,int mismatch min/max penalties\n"); + log_info(stderr," --np int N penalty\n"); + log_info(stderr," --rdg int,int read open/extension gap penalties\n"); + log_info(stderr," --rfg int,int reference open/extension gap penalties\n"); + log_info(stderr," Reporting:\n"); + log_info(stderr," --mapQ-filter | -Q int [0] minimum mapQ threshold\n"); + exit(0); + } + else if (argc == 2 && strcmp( argv[1], "-test" ) == 0) + { + log_visible(stderr, "nvBowtie tests... started\n"); + nvbio::bowtie2::cuda::test_seed_hit_deques(); + nvbio::bowtie2::cuda::test_scoring_queues(); + log_visible(stderr, "nvBowtie tests... done\n"); + exit(0); + } + else if (argc == 2 && strcmp( argv[1], "--version" ) == 0) + { + fprintf(stderr, "nvBowtie version %s\n", NVBIO_VERSION_STRING); + exit(0); + } + + // setup the number of OMP threads + omp_set_num_threads( omp_get_num_procs() ); + + uint32 max_reads = uint32(-1); + uint32 max_read_len = uint32(-1); + uint32 trim3 = 0; + uint32 trim5 = 0; + //bool debug = false; + bool from_file = false; + bool paired_end = false; + io::PairedEndPolicy pe_policy = io::PE_POLICY_FR; + io::QualityEncoding qencoding = io::Phred33; + std::vector cuda_devices; + + std::map string_options; + + std::string argstr; + for (int32 i = 1; i < argc; ++i) + { + argstr += " "; + argstr += argv[i]; + } + + std::string rg_id; + std::string rg_string; + + bool legacy_cmdline = true; + + const char* read_name1 = ""; + const char* read_name2 = ""; + const char* reference_name = ""; + const char* output_name = ""; + + for (int32 i = 1; i < argc; ++i) + { + if (strcmp( argv[i], "--pe" ) == 0 || + strcmp( argv[i], "-paired-ends" ) == 0 || + strcmp( argv[i], "--paired-ends" ) == 0) + paired_end = true; + else if (strcmp( argv[i], "--ff" ) == 0) + pe_policy = io::PE_POLICY_FF; + else if (strcmp( argv[i], "--fr" ) == 0) + pe_policy = io::PE_POLICY_FR; + else if (strcmp( argv[i], "--rf" ) == 0) + pe_policy = io::PE_POLICY_RF; + else if (strcmp( argv[i], "--rr" ) == 0) + pe_policy = io::PE_POLICY_RR; + else if (strcmp( argv[i], "-max-reads" ) == 0 || + strcmp( argv[i], "--max-reads" ) == 0 || + strcmp( argv[i], "-u" ) == 0 || + strcmp( argv[i], "--upto" ) == 0) + max_reads = (uint32)atoi( argv[++i] ); + else if (strcmp( argv[i], "-max-read-len" ) == 0 || + strcmp( argv[i], "--max-read-len" ) == 0) + max_read_len = (uint32)atoi( argv[++i] ); + else if (strcmp( argv[i], "-3") == 0 || + strcmp( argv[i], "--trim3") == 0) + trim3 = (uint32)atoi( argv[++i] ); + else if (strcmp( argv[i], "-5") == 0 || + strcmp( argv[i], "--trim5") == 0) + trim5 = (uint32)atoi( argv[++i] ); + else if (strcmp( argv[i], "-file-ref" ) == 0 || + strcmp( argv[i], "--file-ref" ) == 0) + from_file = true; + else if (strcmp( argv[i], "-server-ref" ) == 0 || + strcmp( argv[i], "--server-ref" ) == 0) + from_file = false; + else if (strcmp( argv[i], "-input" ) == 0 || + strcmp( argv[i], "--input" ) == 0) + { + if (strcmp( argv[i+1], "file" ) == 0) + from_file = true; + else if (strcmp( argv[i+1], "server" ) == 0) + from_file = false; + else + log_warning(stderr, "unknown \"%s\" input, skipping\n", argv[i+1]); + + ++i; + } + else if (strcmp( argv[i], "-phred33" ) == 0 || + strcmp( argv[i], "--phred33" ) == 0) + qencoding = io::Phred33; + else if (strcmp( argv[i], "-phred64" ) == 0 || + strcmp( argv[i], "--phred64" ) == 0) + qencoding = io::Phred64; + else if (strcmp( argv[i], "-solexa-quals" ) == 0 || + strcmp( argv[i], "--solexa-quals" ) == 0) + qencoding = io::Solexa; + else if (strcmp( argv[i], "-device" ) == 0 || + strcmp( argv[i], "--device" ) == 0) + cuda_devices.push_back( atoi( argv[++i] ) ); + else if (strcmp( argv[i], "-verbosity" ) == 0 || + strcmp( argv[i], "--verbosity" ) == 0) + set_verbosity( Verbosity( atoi( argv[++i] ) ) ); + else if (strcmp( argv[i], "-rg-id" ) == 0 || + strcmp( argv[i], "--rg-id" ) == 0) + rg_id = argv[++i]; + else if (strcmp( argv[i], "-rg" ) == 0 || + strcmp( argv[i], "--rg" ) == 0) + { + rg_string += "\t"; + rg_string += argv[++i]; + } + else if (strcmp( argv[i], "-1") == 0) + { + legacy_cmdline = false; + paired_end = true; + read_name1 = argv[++i]; + } + else if (strcmp( argv[i], "-2") == 0) + { + legacy_cmdline = false; + paired_end = true; + read_name2 = argv[++i]; + } + else if (strcmp( argv[i], "-U") == 0) + { + legacy_cmdline = false; + paired_end = false; + read_name1 = argv[++i]; + } + else if (strcmp( argv[i], "-S") == 0) + { + legacy_cmdline = false; + output_name = argv[++i]; + } + else if (strcmp( argv[i], "-x") == 0) + { + legacy_cmdline = false; + reference_name = argv[++i]; + } + else if (argv[i][0] == '-') + { + // add unknown option to the string options + const std::string key = std::string( argv[i][1] == '-' ? argv[i] + 2 : argv[i] + 1 ); + const char* next = argv[i+1]; + + if (is_number(next) || next[0] != '-') + { + const std::string val = std::string( next ); ++i; + string_options.insert( std::make_pair( key, val ) ); + } + else + string_options.insert( std::make_pair( key, "1" ) ); + } + } + + if (strlen( read_name1 ) == 0 && + strlen( read_name2 ) == 0) + { + log_error(stderr, "must specify at least one read input with -U/-1/-2\n"); + return 1; + } + + log_info(stderr, "nvBowtie... started\n"); + log_debug(stderr, " %-16s : %d\n", "max-reads", max_reads); + log_debug(stderr, " %-16s : %d\n", "max-length", max_read_len); + log_debug(stderr, " %-16s : %s\n", "quals", qencoding == io::Phred33 ? "phred33" : + qencoding == io::Phred64 ? "phred64" : + "solexa"); + if (paired_end) + { + log_debug(stderr, " %-16s : %s\n", "pe-policy", + pe_policy == io::PE_POLICY_FF ? "ff" : + pe_policy == io::PE_POLICY_FR ? "fr" : + pe_policy == io::PE_POLICY_RF ? "rf" : + "rr" ); + } + if (string_options.empty() == false) + { + for (std::map::const_iterator it = string_options.begin(); it != string_options.end(); ++it) + log_debug(stderr, " %-16s : %s\n", it->first.c_str(), it->second.c_str()); + } + log_debug(stderr, "\n"); + + try + { + int device_count; + cudaGetDeviceCount(&device_count); + cuda::check_error("cuda-check"); + + log_verbose(stderr, " cuda devices : %d\n", device_count); + + // inspect and select cuda devices + if (device_count > 0) + { + if (cuda_devices.empty()) + { + int best_device = 0; + cudaDeviceProp best_device_prop; + cudaGetDeviceProperties( &best_device_prop, best_device ); + + for (int device = 0; device < device_count; ++device) + { + cudaDeviceProp device_prop; + cudaGetDeviceProperties( &device_prop, device ); + log_verbose(stderr, " device %d has compute capability %d.%d\n", device, device_prop.major, device_prop.minor); + log_verbose(stderr, " SM count : %u\n", device_prop.multiProcessorCount); + log_verbose(stderr, " SM clock rate : %u Mhz\n", device_prop.clockRate / 1000); + log_verbose(stderr, " memory clock rate : %.1f Ghz\n", float(device_prop.memoryClockRate) * 1.0e-6f); + + if (device_prop.major >= best_device_prop.major && + device_prop.minor >= best_device_prop.minor) + { + best_device_prop = device_prop; + best_device = device; + } + } + cuda_devices.push_back( best_device ); + } + + for (size_t i = 0; i < cuda_devices.size(); ++i) + { + cudaDeviceProp device_prop; + cudaGetDeviceProperties( &device_prop, cuda_devices[i] ); + log_verbose(stderr, " chosen device %d\n", cuda_devices[i]); + log_verbose(stderr, " device name : %s\n", device_prop.name); + log_verbose(stderr, " compute capability : %d.%d\n", device_prop.major, device_prop.minor); + } + } + else + { + log_error(stderr, "no available CUDA devices\n"); + exit(1); + } + + if (legacy_cmdline) + { + const uint32 arg_offset = paired_end ? argc-4 : argc-3; + reference_name = argv[arg_offset]; + if (paired_end) + { + read_name1 = argv[arg_offset+1]; + read_name2 = argv[arg_offset+2]; + } + else + read_name1 = argv[arg_offset+1]; + + output_name = argv[argc-1]; + } + + // + // Parse program options + // + + // WARNING: we don't do any error checking on passed parameters! + bowtie2::cuda::Params params; + params.pe_policy = pe_policy; + { + bool init = true; + std::string config = string_option( string_options, "config", "" ); + if (config != "") { bowtie2::cuda::parse_options( params, bowtie2::cuda::load_options( config.c_str() ), init ); init = false; } + bowtie2::cuda::parse_options( params, string_options, init ); + + } + if (params.alignment_type == bowtie2::cuda::LocalAlignment && + params.scoring_mode == bowtie2::cuda::EditDistanceMode) + { + log_warning(stderr, "edit-distance scoring is incompatible with local alignment, switching to Smith-Waterman\n"); + params.scoring_mode = bowtie2::cuda::SmithWatermanMode; + } + + // + // Load the reference + // + + SharedPointer reference_data; + SharedPointer driver_data; + if (from_file) + { + log_visible(stderr, "loading reference index... started\n"); + log_info(stderr, " file: \"%s\"\n", reference_name); + + // load the reference data + reference_data = io::load_sequence_file( DNA, reference_name ); + if (reference_data == NULL) + { + log_error(stderr, "unable to load reference index \"%s\"\n", reference_name); + return 1; + } + + log_visible(stderr, "loading reference index... done\n"); + + nvbio::io::FMIndexDataHost* loader = new nvbio::io::FMIndexDataHost; + if (!loader->load( reference_name )) + { + log_error(stderr, "unable to load reference index \"%s\"\n", reference_name); + return 1; + } + + driver_data = loader; + } + else + { + log_visible(stderr, "mapping reference index... started\n"); + log_info(stderr, " file: \"%s\"\n", reference_name); + + // map the reference data + reference_data = io::map_sequence_file( reference_name ); + if (reference_data == NULL) + { + log_visible(stderr, "mapping reference index... failed\n"); + log_visible(stderr, "loading reference index... started\n"); + log_info(stderr, " file: \"%s\"\n", reference_name); + + // load the reference data + reference_data = io::load_sequence_file( DNA, reference_name ); + if (reference_data == NULL) + { + log_error(stderr, "unable to load reference index \"%s\"\n", reference_name); + return 1; + } + + log_visible(stderr, "loading reference index... done\n"); + + nvbio::io::FMIndexDataHost* loader = new nvbio::io::FMIndexDataHost; + if (!loader->load( reference_name )) + { + log_error(stderr, "unable to load reference index \"%s\"\n", reference_name); + return 1; + } + + driver_data = loader; + } + else + { + log_visible(stderr, "mapping reference index... done\n"); + + nvbio::io::FMIndexDataMMAP* loader = new nvbio::io::FMIndexDataMMAP; + if (!loader->load( reference_name )) + { + log_error(stderr, "unable to load reference index \"%s\"\n", reference_name); + return 1; + } + + driver_data = loader; + } + } + + // + // Setup the output file + // + + SharedPointer output_file( io::OutputFile::open( + output_name, + paired_end ? io::PAIRED_END : io::SINGLE_END, + io::BNT(*reference_data) ) ); + + output_file->set_rg( rg_id.c_str(), rg_string.c_str() ); + output_file->set_program( + "nvBowtie", + "nvBowtie", + NVBIO_VERSION_STRING, + argstr.c_str() ); + + output_file->configure_mapq_evaluator(params.mapq_filter); + output_file->header(); + + if (paired_end) + { + // + // Open the input read files + // + + log_visible(stderr, "opening read file [1] \"%s\"\n", read_name1); + SharedPointer read_data_file1( + nvbio::io::open_sequence_file( + strcmp( read_name1, "-" ) == 0 ? "" : read_name1, + qencoding, + max_reads, + max_read_len, + io::REVERSE, + trim3, + trim5 ) + ); + + if (read_data_file1 == NULL || read_data_file1->is_ok() == false) + { + log_error(stderr, "unable to open read file \"%s\"\n", read_name1); + return 1; + } + + log_visible(stderr, "opening read file [2] \"%s\"\n", read_name2); + SharedPointer read_data_file2( + nvbio::io::open_sequence_file( + strcmp( read_name2, "-" ) == 0 ? "" : read_name2, + qencoding, + max_reads, + max_read_len, + io::REVERSE, + trim3, + trim5 ) + ); + + if (read_data_file2 == NULL || read_data_file2->is_ok() == false) + { + log_error(stderr, "unable to open read file \"%s\"\n", read_name2); + return 1; + } + + + // print the command line options + { + const bowtie2::cuda::SimpleFunc& score_min = bowtie2::cuda::EditDistanceMode ? + params.scoring_scheme.ed.m_score_min : + params.scoring_scheme.sw.m_score_min; + + log_verbose(stderr, " mode = %s\n", bowtie2::cuda::mapping_mode( params.mode )); + log_verbose(stderr, " scoring = %s\n", bowtie2::cuda::scoring_mode( params.scoring_mode )); + log_verbose(stderr, " score-min = %s:%.2f:%.2f\n", score_min.type_string(), score_min.k, score_min.m); + log_verbose(stderr, " alignment type = %s\n", params.alignment_type == bowtie2::cuda::LocalAlignment ? "local" : "end-to-end"); + log_verbose(stderr, " pe-policy = %s\n", + pe_policy == io::PE_POLICY_FF ? "ff" : + pe_policy == io::PE_POLICY_FR ? "fr" : + pe_policy == io::PE_POLICY_RF ? "rf" : + "rr" ); + log_verbose(stderr, " seed length = %u\n", params.seed_len); + log_verbose(stderr, " seed interval = (%s, %.3f, %.3f)\n", params.seed_freq.type_symbol(), params.seed_freq.k, params.seed_freq.m); + log_verbose(stderr, " seed rounds = %u\n", params.max_reseed); + log_verbose(stderr, " max hits = %u\n", params.max_hits); + log_verbose(stderr, " max edit dist = %u\n", params.max_dist); + log_verbose(stderr, " max effort = %u\n", params.max_effort); + log_verbose(stderr, " substitutions = %u\n", params.allow_sub); + log_verbose(stderr, " mapq filter = %u\n", params.mapq_filter); + log_verbose(stderr, " randomized = %s\n", params.randomized ? "yes" : "no"); + if (params.allow_sub) + log_verbose(stderr, " subseed length = %u\n", params.subseed_len); + } + + // + // Setup the compute threads + // + + uint32 batch_size = uint32(-1); + + std::vector< bowtie2::cuda::Stats > device_stats( cuda_devices.size() ); + std::vector< SharedPointer > compute_threads( cuda_devices.size() ); + + for (uint32 i = 0; i < cuda_devices.size(); ++i) + { + device_stats[i] = bowtie2::cuda::Stats( params ); + + compute_threads[i] = SharedPointer( + new bowtie2::cuda::ComputeThreadPE( + i, + cuda_devices[i], + *reference_data, + *driver_data, + string_options, + params, + device_stats[i] ) ); + + batch_size = nvbio::min( batch_size, compute_threads[i]->gauge_batch_size() ); + } + + // + // Setup the input thread + // + + Timer timer; + timer.start(); + + bowtie2::cuda::Stats input_stats( params ); + + bowtie2::cuda::InputThreadPE input_thread( read_data_file1.get(), read_data_file2.get(), input_stats, batch_size, params.avg_read_length ); + input_thread.create(); + + for (uint32 i = 0; i < cuda_devices.size(); ++i) + { + compute_threads[i]->set_input( &input_thread ); + compute_threads[i]->set_output( output_file.get() ); + compute_threads[i]->create(); + } + + uint32 n_reads = 0; + bowtie2::cuda::AlignmentStats concordant; + bowtie2::cuda::AlignmentStats discordant; + bowtie2::cuda::AlignmentStats mate1; + bowtie2::cuda::AlignmentStats mate2; + + for (uint32 i = 0; i < cuda_devices.size(); ++i) + { + compute_threads[i]->join(); + + n_reads += device_stats[i].n_reads; + concordant.merge( device_stats[i].concordant ); + discordant.merge( device_stats[i].discordant ); + mate1.merge( device_stats[i].mate1 ); + mate2.merge( device_stats[i].mate2 ); + } + + input_thread.join(); + + timer.stop(); + + log_verbose( stderr, " compute threads joined\n" ); + + // close the output file + output_file->close(); + + // + // Print statistics + // + + // transfer I/O statistics + io::IOStats iostats = output_file->get_aggregate_statistics(); + const bowtie2::cuda::KernelStats& io = iostats.output_process_timings; + + log_stats(stderr, " total : %.2f sec (avg: %.3fK reads/s).\n", timer.seconds(), 1.0e-3f * float(n_reads) / timer.seconds()); + log_stats(stderr, " reads I/O : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s).\n", input_stats.read_io.time, 1.0e-6f * input_stats.read_io.avg_speed(), 1.0e-6f * input_stats.read_io.max_speed); + log_stats(stderr, " results I/O : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s).\n", io.time, 1.0e-6f * io.avg_speed(), 1.0e-6f * io.max_speed); + + uint32& n_mapped = concordant.n_mapped; + uint32& n_unique = concordant.n_unique; + uint32& n_ambiguous = concordant.n_ambiguous; + uint32& n_nonambiguous = concordant.n_unambiguous; + uint32& n_multiple = concordant.n_multiple; + { + log_stats(stderr, " concordant reads : %.2f %% - of these:\n", 100.0f * float(n_mapped)/float(n_reads) ); + log_stats(stderr, " aligned uniquely : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(n_unique)/float(n_mapped), 100.0f * float(n_mapped - n_multiple)/float(n_reads) ); + log_stats(stderr, " aligned unambiguously : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(n_nonambiguous)/float(n_mapped), 100.0f * float(n_nonambiguous)/float(n_reads) ); + log_stats(stderr, " aligned ambiguously : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(n_ambiguous)/float(n_mapped), 100.0f * float(n_ambiguous)/float(n_reads) ); + log_stats(stderr, " aligned multiply : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(n_multiple)/float(n_mapped), 100.0f * float(n_multiple)/float(n_reads) ); + log_ed( concordant ); + log_mapq( concordant ); + + log_stats(stderr, " discordant reads : %.2f %%\n", 100.0f * float(discordant.n_mapped)/float(n_reads) ); + log_ed( discordant ); + log_mapq( discordant ); + + log_stats(stderr, " mate1 : %.2f %% - of these:\n", 100.0f * float(mate1.n_mapped)/float(n_reads) ); + if (mate1.n_mapped) + { + log_stats(stderr, " aligned uniquely : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(mate1.n_unique)/float(mate1.n_mapped), 100.0f * float(mate1.n_mapped - mate1.n_multiple)/float(n_reads) ); + log_stats(stderr, " aligned unambiguously : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(mate1.n_unambiguous)/float(mate1.n_mapped), 100.0f * float(mate1.n_unambiguous)/float(n_reads) ); + log_stats(stderr, " aligned ambiguously : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(mate1.n_ambiguous)/float(mate1.n_mapped), 100.0f * float(mate1.n_ambiguous)/float(n_reads) ); + log_stats(stderr, " aligned multiply : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(mate1.n_multiple)/float(mate1.n_mapped), 100.0f * float(mate1.n_multiple)/float(n_reads) ); + } + + log_stats(stderr, " mate2 : %.2f %% - of these:\n", 100.0f * float(mate2.n_mapped)/float(n_reads) ); + if (mate2.n_mapped) + { + log_stats(stderr, " aligned uniquely : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(mate2.n_unique)/float(mate2.n_mapped), 100.0f * float(mate2.n_mapped - mate2.n_multiple)/float(n_reads) ); + log_stats(stderr, " aligned unambiguously : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(mate2.n_unambiguous)/float(mate2.n_mapped), 100.0f * float(mate2.n_unambiguous)/float(n_reads) ); + log_stats(stderr, " aligned ambiguously : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(mate2.n_ambiguous)/float(mate2.n_mapped), 100.0f * float(mate2.n_ambiguous)/float(n_reads) ); + log_stats(stderr, " aligned multiply : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(mate2.n_multiple)/float(mate2.n_mapped), 100.0f * float(mate2.n_multiple)/float(n_reads) ); + } + } + + // generate an html report + if (params.report.length()) + bowtie2::cuda::generate_report_header( n_reads, params, concordant, (uint32)cuda_devices.size(), &device_stats[0], params.report.c_str() ); + } + else + { + // + // Open the input read file + // + + log_visible(stderr, "opening read file \"%s\"\n", read_name1); + SharedPointer read_data_file( + io::open_sequence_file( + strcmp( read_name1, "-" ) == 0 ? "" : read_name1, + qencoding, + max_reads, + max_read_len, + io::REVERSE, + trim3, + trim5 ) + ); + + if (read_data_file == NULL || read_data_file->is_ok() == false) + { + log_error(stderr, "unable to open read file \"%s\"\n", read_name1); + return 1; + } + + // print the command line options + { + const bowtie2::cuda::SimpleFunc& score_min = params.scoring_mode == bowtie2::cuda::EditDistanceMode ? + params.scoring_scheme.ed.m_score_min : + params.scoring_scheme.sw.m_score_min; + + log_verbose(stderr, " mode = %s\n", bowtie2::cuda::mapping_mode( params.mode )); + log_verbose(stderr, " scoring = %s\n", bowtie2::cuda::scoring_mode( params.scoring_mode )); + log_verbose(stderr, " score-min = %s:%.2f:%.2f\n", score_min.type_string(), score_min.k, score_min.m); + log_verbose(stderr, " alignment type = %s\n", params.alignment_type == bowtie2::cuda::LocalAlignment ? "local" : "end-to-end"); + log_verbose(stderr, " seed length = %u\n", params.seed_len); + log_verbose(stderr, " seed interval = (%s, %.3f, %.3f)\n", params.seed_freq.type_symbol(), params.seed_freq.k, params.seed_freq.m); + log_verbose(stderr, " seed rounds = %u\n", params.max_reseed); + log_verbose(stderr, " max hits = %u\n", params.max_hits); + log_verbose(stderr, " max edit dist = %u\n", params.max_dist); + log_verbose(stderr, " max effort = %u\n", params.max_effort); + log_verbose(stderr, " substitutions = %u\n", params.allow_sub); + log_verbose(stderr, " mapq filter = %u\n", params.mapq_filter); + log_verbose(stderr, " randomized = %s\n", params.randomized ? "yes" : "no"); + if (params.allow_sub) + log_verbose(stderr, " subseed length = %u\n", params.subseed_len); + } + + // + // Setup the compute threads + // + + uint32 batch_size = uint32(-1); + + std::vector< bowtie2::cuda::Stats > device_stats( cuda_devices.size() ); + std::vector< SharedPointer > compute_threads( cuda_devices.size() ); + + for (uint32 i = 0; i < cuda_devices.size(); ++i) + { + device_stats[i] = bowtie2::cuda::Stats( params ); + + compute_threads[i] = SharedPointer( + new bowtie2::cuda::ComputeThreadSE( + i, + cuda_devices[i], + *reference_data, + *driver_data, + string_options, + params, + device_stats[i] ) ); + + batch_size = nvbio::min( batch_size, compute_threads[i]->gauge_batch_size() ); + } + + // + // Setup the input thread + // + + Timer timer; + timer.start(); + + bowtie2::cuda::Stats input_stats( params ); + + bowtie2::cuda::InputThreadSE input_thread( read_data_file.get(), input_stats, batch_size, params.avg_read_length ); + input_thread.create(); + + for (uint32 i = 0; i < cuda_devices.size(); ++i) + { + compute_threads[i]->set_input( &input_thread ); + compute_threads[i]->set_output( output_file.get() ); + compute_threads[i]->create(); + } + + uint32 n_reads = 0; + bowtie2::cuda::AlignmentStats mate1; + + for (uint32 i = 0; i < cuda_devices.size(); ++i) + { + compute_threads[i]->join(); + + n_reads += device_stats[i].n_reads; + mate1.merge( device_stats[i].mate1 ); + } + + input_thread.join(); + + timer.stop(); + + log_verbose( stderr, " compute threads joined\n" ); + + // close the output file + output_file->close(); + + // + // Print statistics + // + + // transfer I/O statistics + io::IOStats iostats = output_file->get_aggregate_statistics(); + const bowtie2::cuda::KernelStats& io = iostats.output_process_timings; + + log_stats(stderr, " total : %.2f sec (avg: %.3fK reads/s).\n", timer.seconds(), 1.0e-3f * float(n_reads) / timer.seconds()); + log_stats(stderr, " reads I/O : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s).\n", input_stats.read_io.time, 1.0e-6f * input_stats.read_io.avg_speed(), 1.0e-6f * input_stats.read_io.max_speed); + log_stats(stderr, " results I/O : %.2f sec (avg: %.3fM reads/s, max: %.3fM reads/s).\n", io.time, 1.0e-6f * io.avg_speed(), 1.0e-6f * io.max_speed); + + uint32& n_mapped = mate1.n_mapped; + uint32& n_unique = mate1.n_unique; + uint32& n_ambiguous = mate1.n_ambiguous; + uint32& n_nonambiguous = mate1.n_unambiguous; + uint32& n_multiple = mate1.n_multiple; + { + log_stats(stderr, " mapped reads : %.2f %% - of these:\n", 100.0f * float(n_mapped)/float(n_reads) ); + log_stats(stderr, " aligned uniquely : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(n_unique)/float(n_mapped), 100.0f * float(n_mapped - n_multiple)/float(n_reads) ); + log_stats(stderr, " aligned unambiguously : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(n_nonambiguous)/float(n_mapped), 100.0f * float(n_nonambiguous)/float(n_reads) ); + log_stats(stderr, " aligned ambiguously : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(n_ambiguous)/float(n_mapped), 100.0f * float(n_ambiguous)/float(n_reads) ); + log_stats(stderr, " aligned multiply : %4.1f%% (%4.1f%% of total)\n", 100.0f * float(n_multiple)/float(n_mapped), 100.0f * float(n_multiple)/float(n_reads) ); + log_ed( mate1 ); + log_mapq( mate1 ); + } + + // generate an html report + if (params.report.length()) + bowtie2::cuda::generate_report_header( n_reads, params, mate1, (uint32)cuda_devices.size(), &device_stats[0], params.report.c_str() ); + } + + log_info( stderr, "nvBowtie... done\n" ); + } + catch (nvbio::cuda_error e) + { + log_error(stderr, "caught a nvbio::cuda_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::bad_alloc e) + { + log_error(stderr, "caught a nvbio::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::logic_error e) + { + log_error(stderr, "caught a nvbio::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::runtime_error e) + { + log_error(stderr, "caught a nvbio::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::bad_alloc e) + { + log_error(stderr, "caught a std::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::logic_error e) + { + log_error(stderr, "caught a std::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::runtime_error e) + { + log_error(stderr, "caught a std::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (...) + { + log_error(stderr, "caught an unknown exception!\n"); + } + + return 0; +} + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvExtractReads/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvExtractReads/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..7571b8dd69adf9db49a86f504cf8141a9d81ab8b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvExtractReads/CMakeLists.txt @@ -0,0 +1,9 @@ +nvbio_module(nvExtractReads) + +addsources( +nvExtractReads.cu +) + +cuda_add_executable(nvExtractReads ${nvExtractReads_srcs}) +target_link_libraries(nvExtractReads nvbio zlibstatic lz4 crcstatic ${SYSTEM_LINK_LIBRARIES}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvExtractReads/nvExtractReads.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvExtractReads/nvExtractReads.cu new file mode 100644 index 0000000000000000000000000000000000000000..15b5ddb2b670ffc561d890d6bd27f34eb24b4c27 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvExtractReads/nvExtractReads.cu @@ -0,0 +1,349 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// nvExtractReads.cu +// + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +bool to_ascii(const char* reads_name, void* output_file, void* output_index, const io::QualityEncoding qencoding, const io::SequenceEncoding flags) +{ + log_visible(stderr, "opening read file \"%s\"\n", reads_name); + SharedPointer read_data_file( + nvbio::io::open_sequence_file(reads_name, + qencoding, + uint32(-1), + uint32(-1), + flags ) + ); + + if (read_data_file == NULL || read_data_file->is_ok() == false) + { + log_error(stderr, " failed opening file \"%s\"\n", reads_name); + return false; + } + + const uint32 batch_size = 512*1024; + + std::vector char_read( 1024*1024 ); + std::vector index( 512*1024 + 1u ); + + uint64 offset = 0u; + + uint32 n_reads = 0; + + io::SequenceDataHost h_read_data; + + // loop through all read batches + while (1) + { + // load a new batch of reads + if (io::next( DNA_N, &h_read_data, read_data_file.get(), batch_size ) == 0) + break; + + const io::SequenceDataAccess h_read_access( h_read_data ); + + // loop through all reads + for (uint32 i = 0; i < h_read_data.size(); ++i) + { + const io::SequenceDataAccess::sequence_string read = h_read_access.get_read(i); + + dna_to_string( read, read.length(), &char_read[0] ); + + char_read[ read.length() ] = '\n'; + + const uint32 n_written = (uint32)gzwrite( output_file, &char_read[0], sizeof(char) * (read.length()+1) ); + if (n_written < read.length()+1) + { + log_error( stderr, "unable to write to output\n"); + return false; + } + } + + if (output_index) + { + // collect the sequence offsets + for (uint32 i = 0; i < h_read_data.size(); ++i) + index[i] = offset + h_read_data.sequence_index()[i+1]; + + // write the sequence offsets + gzwrite( output_file, &index[0], sizeof(uint64) * h_read_data.size() ); + } + + // update the global sequence offset + offset += h_read_data.bps(); + + // update the global number of output reads + n_reads += h_read_data.size(); + + const uint64 n_bytes = gzoffset( output_file ); + log_verbose(stderr,"\r %u reads (%.2fGB - %.2fB/read - %.2fB/bp) ", n_reads, float( n_bytes ) / float(1024*1024*1024), float(n_bytes)/float(n_reads), float(n_bytes)/float(offset)); + } + log_verbose_cont(stderr,"\n"); + return true; +} + +template +bool to_packed(const char* reads_name, void* output_file, void* output_index, const io::QualityEncoding qencoding, const io::SequenceEncoding flags) +{ + log_visible(stderr, "opening read file \"%s\"\n", reads_name); + SharedPointer read_data_file( + nvbio::io::open_sequence_file(reads_name, + qencoding, + uint32(-1), + uint32(-1), + flags ) + ); + + if (read_data_file == NULL || read_data_file->is_ok() == false) + { + log_error(stderr, " failed opening file \"%s\"\n", reads_name); + return false; + } + + static const uint32 SYMBOLS_PER_WORD = 32u / SYMBOL_SIZE; + + const uint32 batch_size = 512*1024; + + uint32 n_reads = 0; + + io::SequenceDataHost h_read_data; + + typedef PackedStream packed_stream_type; + + std::vector words( 1024*1024 ); + std::vector index( 512*1024 + 1u ); + + uint32 rem = 0u; + uint64 offset = 0u; + + // loop through all read batches + while (1) + { + // load a new batch of reads + if (io::next( DNA_N, &h_read_data, read_data_file.get(), batch_size ) == 0) + break; + + // reserve enough storage + words.resize( h_read_data.words() + 1u ); + + packed_stream_type packed_reads( &words[0] ); + + const io::SequenceDataAccess h_read_access( h_read_data ); + + nvbio::assign( h_read_access.bps(), h_read_access.sequence_stream(), packed_reads + rem ); + + // write all whole words + const uint32 n_bps = h_read_access.bps() + rem; + const uint32 whole_words = n_bps / SYMBOLS_PER_WORD; + + gzwrite( output_file, &words[0], sizeof(uint32) * whole_words ); + + // save the last non-whole word + words[0] = words[ whole_words ]; + + // save the number of unwritten symbols left + rem = n_bps & (SYMBOLS_PER_WORD-1); + + if (output_index) + { + // collect the sequence offsets + for (uint32 i = 0; i < h_read_data.size(); ++i) + index[i] = offset + h_read_data.sequence_index()[i+1]; + + // write the sequence offsets + gzwrite( output_file, &index[0], sizeof(uint64) * h_read_data.size() ); + } + + // update the global sequence offset + offset += h_read_data.bps(); + + // update the global number of output reads + n_reads += h_read_data.size(); + + const uint64 n_bytes = gzoffset( output_file ); + log_verbose(stderr,"\r %u reads (%.2fGB - %.2fB/read - %.2fB/bp) ", n_reads, float( n_bytes ) / float(1024*1024*1024), float(n_bytes)/float(n_reads), float(n_bytes)/float(offset)); + } + log_verbose_cont(stderr,"\n"); + return true; +} + +enum Format +{ + ASCII_FORMAT = 0u, + PACKED2_FORMAT = 1u, + PACKED4_FORMAT = 2u, +}; + +int main(int argc, char* argv[]) +{ + if (argc < 2) + { + log_info(stderr, "nvExtractReads [options] input output\n"); + log_info(stderr, " extract a set of reads to a plain ASCII_FORMAT or packed file with one read per line (.txt)\n\n"); + log_info(stderr, "options:\n"); + log_info(stderr, " --verbosity\n"); + log_info(stderr, " -F | --skip-forward skip forward strand\n"); + log_info(stderr, " -R | --skip-reverse skip forward strand\n"); + log_info(stderr, " -a | --ascii ASCII_FORMAT output\n"); + log_info(stderr, " -p2 | --packed-2 2-bits packed output\n"); + log_info(stderr, " -p4 | --packed-4 4-bits packed output\n"); + log_info(stderr, " -i | --idx string save an index file\n"); + exit(0); + } + + const char* reads_name = argv[argc-2]; + const char* out_name = argv[argc-1]; + const char* idx_name = NULL; + bool forward = true; + bool reverse = true; + Format format = ASCII_FORMAT; + io::QualityEncoding qencoding = io::Phred33; + + for (int i = 0; i < argc - 2; ++i) + { + if (strcmp( argv[i], "-verbosity" ) == 0 || + strcmp( argv[i], "--verbosity" ) == 0) + { + set_verbosity( Verbosity( atoi( argv[++i] ) ) ); + } + else if (strcmp( argv[i], "-F" ) == 0 || + strcmp( argv[i], "--skip-forward" ) == 0) // skip forward strand + { + forward = false; + } + else if (strcmp( argv[i], "-R" ) == 0 || + strcmp( argv[i], "--skip-reverse" ) == 0) // skip reverse strand + { + reverse = false; + } + else if (strcmp( argv[i], "-a" ) == 0 || + strcmp( argv[i], "--ascii" ) == 0) // ascii format + { + format = ASCII_FORMAT; + } + else if (strcmp( argv[i], "-p2" ) == 0 || + strcmp( argv[i], "--packed-2" ) == 0) // 2-bits packed + { + format = PACKED2_FORMAT; + } + else if (strcmp( argv[i], "-p4" ) == 0 || + strcmp( argv[i], "--packed-4" ) == 0) // 4-bits packed + { + format = PACKED4_FORMAT; + } + else if (strcmp( argv[i], "-i" ) == 0 || + strcmp( argv[i], "--idx" ) == 0) // index file + { + idx_name = argv[++i]; + } + } + + std::string out_string = out_name; + // parse out file extension; look for .fastq.gz, .fastq suffixes + uint32 len = uint32( strlen(out_name) ); + bool is_gzipped = false; + + // do we have a .gz suffix? + if (len >= strlen(".gz")) + { + if (strcmp(&out_name[len - strlen(".gz")], ".gz") == 0) + { + is_gzipped = true; + len = uint32(len - strlen(".gz")); + } + } + + void* output_file = NULL; + void* output_index = NULL; + + if (format == ASCII_FORMAT) + { + // open a plain ASCII_FORMAT file + output_file = gzopen( out_name, is_gzipped ? "w1R" : "w" ); + } + else + { + // open a binary file + output_file = gzopen( out_name, is_gzipped ? "wb1R" : "wbT" ); + } + + if (output_file == NULL) + { + log_error(stderr, " failed opening file \"%s\"\n", out_name); + return 1; + } + + if (idx_name) + { + output_index = fopen( idx_name, "wb" ); + if (output_index == NULL) + { + log_error(stderr, " failed opening file \"%s\"\n", idx_name); + return 1; + } + } + + log_visible(stderr,"nvExtractReads... started\n"); + + uint32 encoding_flags = 0u; + if (forward) encoding_flags |= io::FORWARD; + if (reverse) encoding_flags |= io::REVERSE_COMPLEMENT; + + bool success; + + switch (format) + { + case ASCII_FORMAT: + success = to_ascii( reads_name, output_file, output_index, qencoding, io::SequenceEncoding(encoding_flags) ); + break; + case PACKED2_FORMAT: + success = to_packed<2u>( reads_name, output_file, output_index, qencoding, io::SequenceEncoding(encoding_flags) ); + break; + case PACKED4_FORMAT: + success = to_packed<4u>( reads_name, output_file, output_index, qencoding, io::SequenceEncoding(encoding_flags) ); + break; + } + + if (output_file) gzclose( output_file ); + if (output_index) gzclose( output_index ); + + log_visible(stderr,"nvExtractReads... done\n"); + return success ? 0u : 1u; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvFM-server/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvFM-server/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..79289e47793b1df193f21177edbdd3c53f0066da --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvFM-server/CMakeLists.txt @@ -0,0 +1,9 @@ +nvbio_module("nvFM-server") + +addsources( +nvFM-server.cpp +) + +cuda_add_executable(nvFM-server ${nvFM-server_srcs}) +target_link_libraries(nvFM-server nvbio crcstatic ${SYSTEM_LINK_LIBRARIES}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvFM-server/nvFM-server.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvFM-server/nvFM-server.cpp new file mode 100644 index 0000000000000000000000000000000000000000..20f36977bc1e719a13023e06d221faa3360e036c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvFM-server/nvFM-server.cpp @@ -0,0 +1,61 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// nvFM-server.cpp : Defines the entry point for the console application. +// + +#include +#include +#include +#include +#include + +using namespace nvbio; + +int main(int argc, char* argv[]) +{ + if (argc == 1) + { + fprintf(stderr, "nvFM-server genome-prefix mapped-name\n"); + exit(1); + } + + fprintf(stderr, "nvFM-server started\n"); + + const char* file_name = argv[1]; + const char* mapped_name = argc == 3 ? argv[2] : argv[1]; + + io::SequenceDataMMAPServer reference_driver; + reference_driver.load( DNA, file_name, mapped_name ); + + io::FMIndexDataMMAPServer fmindex_driver; + fmindex_driver.load( file_name, mapped_name ); + + getc(stdin); + return 0; +} + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..f76033a294d483b827b008b8b8c5ca3f7fd6e038 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/CMakeLists.txt @@ -0,0 +1,17 @@ +nvbio_module(nvLighter) + +addsources( +error_correct.cu +error_correct.h +input_thread.cu +input_thread.h +output_thread.h +output_thread.cu +nvLighter.cu +sample_kmers.cu +sample_kmers.h +) + +cuda_add_executable(nvLighter ${nvLighter_srcs}) +target_link_libraries(nvLighter nvbio moderngpu zlibstatic lz4 crcstatic ${SYSTEM_LINK_LIBRARIES}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/bloom_filters.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/bloom_filters.h new file mode 100644 index 0000000000000000000000000000000000000000..6236b6abb80ebcb5897be0f9d2b406eca26a039a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/bloom_filters.h @@ -0,0 +1,120 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// bloom_filters.h +// + +#pragma once + +#include "utils.h" +#include +#include +#include +#include +#include +#include + +///@defgroup nvLighterModule nvLighter +/// This module contains all of \subpage nvlighter_page "nvLighter"'s class hierarchy. +/// nvLighter is composed of the following important pieces: +///\par +/// - the BloomFilters class, containing all the per-device data needed during nvLighter's execution, +/// i.e. the sampled and trusted kmers Bloom filters and the error correction statistics +/// - the InputStage, i.e. an object encapsulating an nvbio::Pipeline stage loading read batches +/// - the OutputStage, i.e. an object encapsulating an nvbio::Pipeline stage writing read batches +/// - the SampleKmersStage, i.e. an object encapsulating an nvbio::Pipeline stage performing kmer sampling +/// - the TrustedKmersStage, i.e. an object encapsulating an nvbio::Pipeline stage performing trusted kmer marking +/// - the ErrorCorrectStage, i.e. an object encapsulating an nvbio::Pipeline stage performing the actual error correction +/// + +///@addtogroup nvLighterModule +///@{ + +/// The kmer Bloom filter types +/// +enum KmersType { SAMPLED_KMERS = 0, TRUSTED_KMERS = 1 }; + +/// Bloom filters container - this class contains all the per-device data +/// needed during nvLighter's execution +/// +template +struct BloomFilters +{ + /// setup the internal storage + /// + bool setup(const int _device, const uint64 sampled_words, const uint64 trusted_words); + + const nvbio::vector& get_kmers(const KmersType type) const; + nvbio::vector& get_kmers(const KmersType type); + + void get_kmers(const KmersType type, nvbio::vector& bf); + void set_kmers(const KmersType type, const nvbio::vector& bf); + void set_threshold(const nvbio::vector& _threshold); + + void set_device() const; + void device_memory(size_t* free_device, size_t* total_device) const; + +public: + int device; + nvbio::vector sampled_kmers_storage; + nvbio::vector trusted_kmers_storage; + nvbio::vector threshold; + nvbio::vector stats; +}; + +/// merge several Bloom filters +/// +inline +void merge( + BloomFilters* h_bloom_filters, + const uint32 device_count, + BloomFilters* d_bloom_filters, + const KmersType type); + +/// merge several stats +/// +inline +void merged_stats( + const BloomFilters* h_bloom_filters, + const uint32 device_count, + const BloomFilters* d_bloom_filters, + nvbio::vector& stats); + +/// compute Bloom filter usage statistics +/// +template +void compute_bloom_filter_stats( + const BloomFilters& bloom_filters, + const KmersType type, + const uint32 K, + float& occupancy, + float& approx_size, + float& fp); + +///@} // group nvLighterModule + +#include "bloom_filters_inl.h" diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/bloom_filters_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/bloom_filters_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..639cb6ef853aa556a489a7cd035662268779f0d3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/bloom_filters_inl.h @@ -0,0 +1,280 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// bloom_filters_inl.h +// + +#pragma once + +// setup the internal storage +// +template +bool BloomFilters::setup(const int _device, const uint64 sampled_words, const uint64 trusted_words) +{ + device = _device; + + log_info(stderr, " setup device %d\n", device); + set_device(); + + // gather device memory stats + size_t free_device, total_device; + device_memory( &free_device, &total_device ); + log_stats(stderr, " device has %ld of %ld MB free\n", free_device/1024/1024, total_device/1024/1024); + + const uint32 bytes_per_word = 4u; + const uint64 needed_bytes = (sampled_words + trusted_words)*bytes_per_word + 256*1024*1024; + + if (needed_bytes > free_device) + { + log_warning(stderr, " insufficient memory: %.2f GB required\n", float( needed_bytes ) / float(1024*1024*1024)); + return false; + } + + log_info(stderr, " allocating sampled kmer filter (%.2f GB)\n", float( sampled_words*bytes_per_word ) / float(1024*1024*1024)); + sampled_kmers_storage.resize( sampled_words, 0u ); + + log_info(stderr, " allocating trusted kmer filter (%.2f GB)\n", float( trusted_words*bytes_per_word ) / float(1024*1024*1024)); + trusted_kmers_storage.resize( trusted_words, 0u ); + + stats.resize( 10 ); + return true; +} + +template +const nvbio::vector& BloomFilters::get_kmers(const KmersType type) const +{ + return (type == SAMPLED_KMERS) ? sampled_kmers_storage : + trusted_kmers_storage; +} +template +nvbio::vector& BloomFilters::get_kmers(const KmersType type) +{ + return (type == SAMPLED_KMERS) ? sampled_kmers_storage : + trusted_kmers_storage; +} +template +void BloomFilters::get_kmers(const KmersType type, nvbio::vector& bf) +{ + set_device(); + + if (type == SAMPLED_KMERS) bf = sampled_kmers_storage; + else bf = trusted_kmers_storage; +} +template +void BloomFilters::set_kmers(const KmersType type, const nvbio::vector& bf) +{ + set_device(); + + if (type == SAMPLED_KMERS) sampled_kmers_storage = bf; + else trusted_kmers_storage = bf; +} +template +void BloomFilters::set_threshold(const nvbio::vector& _threshold) +{ + set_device(); + + threshold = _threshold; +} + +template +void BloomFilters::set_device() const +{ + if (nvbio::equal()) + cudaSetDevice( device ); +} +template +void BloomFilters::device_memory(size_t* free_device, size_t* total_device) const +{ + if (nvbio::equal()) + cudaMemGetInfo( free_device, total_device ); + else + *free_device = *total_device = 1024llu * 1024llu * 1024llu * 1024llu; // TODO! +} + +// merge several Bloom filters +// +inline +void merge( + BloomFilters* h_bloom_filters, + const uint32 device_count, + BloomFilters* d_bloom_filters, + const KmersType type) +{ + // merge the Bloom filters on the host + if (h_bloom_filters && device_count) + { + log_info(stderr," merge filters\n"); + + // get the host Bloom filter + nvbio::vector& bf = h_bloom_filters->get_kmers( type ); + nvbio::vector bf2; + + // merge with all the device ones + for (uint32 d = 0; d < device_count; ++d) + { + d_bloom_filters[d].get_kmers( type, bf2 ); + + #pragma omp parallel for + for (int64 i = 0; i < (int64)bf.size(); ++i) + bf[i] |= bf2[i]; + } + + // broadcast the merged Bloom filter to all devices + for (uint32 d = 0; d < device_count; ++d) + d_bloom_filters[d].set_kmers( type, bf ); + } + else if (device_count > 1) + { + log_info(stderr," merge filters\n"); + nvbio::vector bf; + nvbio::vector bf2; + + // get the first device Bloom filter + d_bloom_filters[0].get_kmers( type, bf ); + + // merge with all the rest + for (uint32 d = 1; d < device_count; ++d) + { + d_bloom_filters[d].get_kmers( type, bf2 ); + + #pragma omp parallel for + for (int64 i = 0; i < (int64)bf.size(); ++i) + bf[i] |= bf2[i]; + } + + // broadcast the merged Bloom filter to all devices + for (uint32 d = 0; d < device_count; ++d) + d_bloom_filters[d].set_kmers( type, bf ); + } +} + + +// merge several stats +// +inline +void merged_stats( + const BloomFilters* h_bloom_filters, + const uint32 device_count, + const BloomFilters* d_bloom_filters, + nvbio::vector& stats) +{ + // merge the stats on the host + nvbio::vector stats2; + + // copy the first + if (h_bloom_filters) + stats = h_bloom_filters->stats; + else + stats.resize( 10, uint64(0) ); + + // and merge with all the rest + for (uint32 d = 0; d < device_count; ++d) + { + d_bloom_filters[d].set_device(); + + stats2 = d_bloom_filters[d].stats; + + for (size_t i = 0; i < stats.size(); ++i) + stats[i] += stats2[i]; + } +} + +// helper functor to compute a blocked Bloom filter's occupancy +// +struct block_occupancy_functor +{ + typedef uint4 argument_type; + typedef double result_type; + + block_occupancy_functor(const uint32 k) : K(float(k)) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + double operator() (const uint4 block) const + { + const uint32 used = + nvbio::popc( block.x ) + + nvbio::popc( block.y ) + + nvbio::popc( block.z ) + + nvbio::popc( block.w ); + return powf( float(used)/128.0f, K ); + } + + const float K; +}; + +// compute Bloom filter usage statistics +// +template +void compute_bloom_filter_stats( + const BloomFilters& bloom_filters, + const KmersType type, + const uint32 K, + float& occupancy, + float& approx_size, + float& fp) +{ + typedef typename nvbio::if_equal, const uint32*>::type uint_pointer_type; + typedef typename nvbio::if_equal, const uint4*>::type uint4_pointer_type; + + bloom_filters.set_device(); + + const nvbio::vector& bf = bloom_filters.get_kmers( type ); + + const uint32 n_words = uint32( bf.size() ); + const uint32* words = raw_pointer( bf ); + + // compute the number of bits set + nvbio::vector temp_storage; + + const uint64 bits_per_word = 32; + + const uint64 bits_set = nvbio::reduce( + n_words, + thrust::make_transform_iterator( + thrust::make_transform_iterator( + uint_pointer_type( words ), nvbio::popc_functor() ), + nvbio::cast_functor() ), + thrust::plus(), + temp_storage ); + + occupancy = float( double( bits_set ) / double( n_words * bits_per_word ) ); + approx_size = float( -(double( n_words * bits_per_word ) * std::log( 1.0 - occupancy )) / double(K) ); + + #if 0 + // compute the actual false positive rate + fp = std::pow( occupancy, K ); + #else + // compute the actual false positive rate - using the block-occupancy + fp = float( nvbio::reduce( + n_words / 4, + thrust::make_transform_iterator( + uint4_pointer_type( (const uint4*)words ), + block_occupancy_functor( K ) ), + thrust::plus(), + temp_storage ) / double(n_words / 4) ); + #endif +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/error_correct.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/error_correct.cu new file mode 100644 index 0000000000000000000000000000000000000000..e537afc9a82f2292bae1d10c1a1d594f4a86cc66 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/error_correct.cu @@ -0,0 +1,939 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// sample_kmers.h +// + +#include "error_correct.h" +#include "utils.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +/// +/// A functor to sample kmers and insert them in a Bloom filter +/// +template +struct ErrorCorrectFunctor +{ + /// constructor + /// + ///\param _k kmer length + ///\param _alpha the sampling frequency + ///\param _string_set the input string set to sample + ///\param _filter the kmer Bloom filter + /// + NVBIO_HOST_DEVICE + ErrorCorrectFunctor( + const uint32 _k, + string_set_type _string_set, + qual_set_type _qual_set, + const trusted_filter_type _trusted_filter, + uint64* _stats, + const float _max_correction, + const uint8 _bad_quality, + const uint8 _new_quality) : + K(int(_k)), kmask( (uint64(1u) << (K*2))-1u ), + string_set( _string_set ), + qual_set( _qual_set ), + trusted_kmers(_trusted_filter), + stats(_stats), + max_correction(_max_correction), + bad_quality(_bad_quality), + new_quality(_new_quality) {} + + /// is trusted + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool is_trusted(const KmerCode& kmer) const + { + return kmer.is_valid() && trusted_kmers[ kmer.code ]; + } + + /// build the stored kmers list + /// + template + NVBIO_HOST_DEVICE + void mark_solid_kmers(const int read_len, const string_type& read, bool* solid) const + { + KmerCode kmer( K ); + for (int i = 0; i < K-1; ++i) + kmer.push_back( read[i] ); + + for (int i = K-1; i < read_len; ++i) + { + kmer.push_back( read[i] ); + + solid[ i - K + 1 ] = is_trusted( kmer ); + } + } + + /// find the longest stored kmer + /// + NVBIO_HOST_DEVICE + int2 find_longest_solid_kmer(const int kmer_count, const bool* solid) const + { + int longest_count = 0, stored_count = 0; + int begin = -1; + for (int i = 0; i < kmer_count; ++i) + { + if (solid[i]) + ++stored_count; + else + { + if (longest_count < stored_count) + { + longest_count = stored_count; + begin = i - stored_count; + } + stored_count = 0; + } + } + if (longest_count < stored_count) + { + longest_count = stored_count; + begin = kmer_count - stored_count; + } + + if (longest_count == 0) + return make_int2( 0, 0 ); // unreliable read! + + if (longest_count >= kmer_count) + return make_int2( begin, kmer_count ); + + return make_int2( begin, begin + longest_count ); + } + + /// find the next non-solid position, left to right (i.e. in [from,to), from <= to) + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + int find_right_nonsolid(const int from, const int to, const bool* solid) const + { + for (int k = from; k < to; ++k) + if (!solid[k]) + return k; + + return to; + } + + /// find the next non-solid position, right to left (i.e. in [to,from], from >= to) + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + int find_left_nonsolid(const int from, const int to, const bool* solid) const + { + for (int k = from; k >= to; --k) + if (!solid[k]) + return k; + + return to - 1; + } + + /// find the best right change + /// + template + NVBIO_HOST_DEVICE + KmerCode best_right_change(const int read_len, const string_type& read, const int from, const int to, const KmerCode& fixed_kmer, int& best_to, int& best_change, int& best_count) const + { + KmerCode best_kmer; + + best_to = -1; + best_change = -1; + best_count = 0; + + for (int j = 0; j < 4; ++j) + { + KmerCode kmer = fixed_kmer; + kmer.push_back( j ); + if (!is_trusted( kmer )) + continue; + + if (best_to == -1) + best_to = from-1; + + // check how many kmers this change can fix + int k; + + for (k = from; k <= to; ++k) + { + kmer.push_back( read[k] ); + if (!is_trusted( kmer )) + break; + } + + // Try to extend 1 position + if (k > to && to == read_len - 1) + { + for (int m = 0; m < K - 1 - (to - from + 1); ++m) + { + for (int l = 0; l < 4; ++l) + { + KmerCode tmp_kmer( kmer ); + tmp_kmer.push_back( l ); + + if (is_trusted( tmp_kmer )) + { + kmer.push_back( l ); + ++k; + break; + } + } + } + } + + if (k > best_to) + { + best_count = 1; + best_to = k; + best_change = j; + best_kmer = kmer; + } + else if (k == best_to) + { + ++best_count; + if (k == from && j == 0) + { + best_count = 1; + best_change = j; + best_kmer = kmer; + } + else if (k == from && best_change == 0) // [jp]: not sure this is correct - it seems it's setting best_count to 1 + best_count = 1; // whenever the previous change was an 'A', but not if it was any other letter + } + } + return best_kmer; + } + + template + NVBIO_HOST_DEVICE + bool check_right(KmerCode tmp_kmer, const string_type& read, const int pos, const int len) const + { + for (int t = 0; t < len; ++t) + { + tmp_kmer.push_back( read[pos + t] ); + if (!is_trusted( tmp_kmer )) + return false; + } + return true; + } + + template + NVBIO_HOST_DEVICE + bool adjust_right(const int read_len, const string_type& read, KmerCode kmer, const int pos) const + { + // check whether it is possible to extend by K/2 + 1 bases + if (pos + K/2 + 1 >= read_len) + return false; + + for (int c = 0; c < 4; ++c) + { + if (c == read[pos - 1]) + continue; + + KmerCode tmp_kmer = kmer; + tmp_kmer.shift_right( 1 ); + tmp_kmer.push_back( c ); + + if (is_trusted( tmp_kmer )) + { + // test whether this branch makes sense + if (check_right( tmp_kmer, read, pos, K/2 + 1 )) + return true; + } + } + return false; + } + + template + NVBIO_HOST_DEVICE + void fix_right( + const int read_len, const string_type& read, const int2 longest_range, + int* fix, + const bool* solid, + int& trimStart, + int& badSuffix, + bool& ambiguous) const + { + const int longest_count = longest_range.y - longest_range.x; + + const int kmer_count = read_len - K + 1; + + // from now on, i is the "current" index in the read we are fixing + int i = longest_range.y; + + // scan right + KmerCode kmer( K ); + if (longest_range.y >= kmer_count) + { + // the kmers are all correct, force skip the correction. + i = read_len + 1; + } + else + { + // build the first kmer to fix + if (longest_count < K) + { + for (i = longest_range.y; i < longest_range.y - 1 + K; ++i) + kmer.push_back( read[i] ); + } + else + { + // adjust the anchor if necessary + for (int j = K / 2 - 1; j >= 0; --j) + { + for (i = longest_range.y - j - 1; i < longest_range.y - j + K - 1; ++i) + kmer.push_back( read[i] ); + + if (adjust_right( read_len, read, kmer, i )) + { + // adjust the anchor + --i; + kmer.shift_right( 1 ); + break; + } + } + } + } + + for (; i < read_len;) + { + const int from = i + 1; + const int to = (i + K - 1 < read_len) ? i + K - 1 : read_len - 1; + + int best_to; + int best_change; + int best_count; + + // find the best right change + const KmerCode tmp_kmer = best_right_change( read_len, read, from, to, kmer, best_to, best_change, best_count ); + + if (best_to == -1 || (best_count > 1 && (best_to <= to || to - i + 1 < K))) + { + trimStart = i; + break; + } + + if (best_count <= 1) + { + // unambiguous fix + fix[i] = best_change; + } + else + { + // ambiguous fix + fix[i] = -2; + ambiguous = true; + } + + if (best_to >= read_len) + break; + + if (best_to <= to) + { + // there are multiple errors in the region + kmer = tmp_kmer; + kmer.shift_right( 1 ); + i = best_to; + } + else + { + // search for next error. + const int k = find_right_nonsolid( to - K + 2, kmer_count, solid ); + // [jp] shouldn't it be k = from? [to - K + 2 = (i + K - 1) - K + 2 = from + K - 2 - K + 2 = from] + + if (k >= kmer_count) + break; + + kmer.restart(); + for (i = k; i < k + K - 1; ++i) + { + if (fix[i] < 0) kmer.push_back( read[i] ); + else kmer.push_back( fix[i] ); + } + } + } + } + + /// find the best left change + /// + template + NVBIO_HOST_DEVICE + KmerCode best_left_change(const int read_len, const string_type& read, const int from, const int to, const KmerCode& fixed_kmer, int& best_to, int& best_change, int& best_count) const + { + KmerCode best_kmer; + + best_to = read_len + 1; + best_change = -1; + best_count = 0; + + for (int j = 0; j < 4; ++j) + { + KmerCode kmer = fixed_kmer; + kmer.push_front( j ); + + if (!is_trusted( kmer )) + continue; + + if (best_to == read_len + 1) + best_to = from + 1; + + int k; + + // check how many kmers this change can fix + for (k = from; k >= to; --k) + { + kmer.push_front( read[k] ); + if (!is_trusted( kmer )) + break; + } + + // try extension + if (k < to && to == 0) + { + for (int m = 0; m < K - 1 - (from - to + 1); ++m) + { + for (int l = 0; l < 4; ++l) + { + KmerCode tmp_kmer( kmer ); + tmp_kmer.push_front( l ); + if (is_trusted( tmp_kmer )) + { + kmer.push_front( l ); + --k; + break; + } + } + } + } + + if (k < best_to) + { + best_count = 1; + best_to = k; + best_change = j; + best_kmer = kmer; + } + else if (k == best_to) + { + ++best_count; + if (k == from && j == read[from+1]) + { + best_count = 1; + best_change = j; + best_kmer = kmer; + } + else if (k == from && best_change == read[from+1]) + best_count = 1; + } + } + return best_kmer; + } + + template + NVBIO_HOST_DEVICE + bool check_left(KmerCode tmp_kmer, const string_type& read, const int pos, const int len) const + { + for (int t = 0; t < len; ++t) + { + tmp_kmer.push_front( read[pos - t] ); + if (!is_trusted( tmp_kmer )) + return false; + } + return true; + } + + template + NVBIO_HOST_DEVICE + bool adjust_left(const int read_len, const string_type& read, KmerCode kmer, const int pos) const + { + // check whether it is possible to extend by K/2 + 1 bases + if (pos - 1 - K/2 < 0) + return false; + + for (int c = 0; c < 4; ++c) + { + if (c == read[pos]) + continue; + + KmerCode tmp_kmer = kmer; + tmp_kmer.push_back( 0 ); // append an 'A' + tmp_kmer.push_front( c ); + if (is_trusted( tmp_kmer )) + { + // test whether this branch makes sense + if (check_left( tmp_kmer, read, pos - 1, K/2 + 1 )) + return true; + } + } + return false; + } + + template + NVBIO_HOST_DEVICE + void fix_left( + const int read_len, const string_type& read, const int2 longest_range, + int* fix, + const bool* solid, + int& trimStart, + int& badPrefix, + bool& ambiguous) const + { + const int longest_count = longest_range.y - longest_range.x; + + KmerCode kmer( K ); + + // from now on, i is the "current" index in the read we are fixing + int i; + + if (longest_range.x) + { + // force skip + i = -1; + } + else + { + // set the starting point + i = longest_range.x - 1; + + if (longest_count < K) + { + kmer.restart(); + for (i = longest_range.x; i < longest_range.x + K - 1; ++i) + kmer.push_back( read[i] ); + + kmer.push_back( 0 ); + } + else + { + // adjust the left side of the anchor + for (int j = K / 2 - 1; j >= 0; --j) + { + const int pos = longest_range.x + j; + + kmer.restart(); + for (i = pos; i < pos + K; ++i) + kmer.push_back( read[i] ); + + if (adjust_left( read_len, read, kmer, pos )) + { + // adjust the anchor + i = pos; + kmer.push_back( 0 ); // append an 'A' + break; + } + } + } + } + + for (; i >= 0;) + { + KmerCode fixed_kmer( kmer ); + + const int from = i - 1; + const int to = nvbio::max( i - K + 1, 0 ); + + int best_to; + int best_change; + int best_count; + + // find the best left change + const KmerCode tmp_kmer = best_left_change( read_len, read, from, to, kmer, best_to, best_change, best_count ); + + if (best_to == read_len + 1 || (best_count > 1 && (best_to >= to || i - to + 1 < K))) + { + badPrefix = i + 1; + break; + } + + if (best_count <= 1) + fix[i] = best_change; + else + { + fix[i] = -2; + ambiguous = true; + } + + if (best_to < 0) + break; + + if (best_to >= to) + { + kmer = tmp_kmer; + kmer.push_front( 0 ); // prepend an 'A' + i = best_to; + } + else + { + // search for next error + const int k = find_left_nonsolid( to - 1, 0, solid ); + + if (k < 0) + break; + + kmer.restart(); + for (i = k + 1; i < k + K; ++i) + { + if (fix[i] < 0) kmer.push_back( read[i] ); + else kmer.push_back( fix[i] ); + } + i = k; + kmer.push_back( 0 ); // append an 'A' + } + } + } + + template + NVBIO_HOST_DEVICE + int correct(read_type read, qual_type qual, int& badPrefix, int& badSuffix) const + { + badPrefix = 0; + badSuffix = 0; + + const int read_len = (int)length( read ); + if (read_len < K) + return 0; + + int fix[MAX_READ_LENGTH]; + bool solid[MAX_READ_LENGTH]; + + int trimStart = -1; + bool ambiguous = false; + + // + // build the solid array + // + + mark_solid_kmers( read_len, read, solid ); + + const int kmer_count = read_len - K + 1; + + // + // mark trusted kmers + // + + trimStart = read_len; + for (int i = 0; i < read_len; ++i) + fix[i] = -1; + + // find the longest trusted kmer + const int2 longest_range = find_longest_solid_kmer( kmer_count, solid ); + const int longest_count = longest_range.y - longest_range.x; + + if (longest_count == 0) + return -1; // unreliable read! + + // check whether all kmers are reliable + if (longest_count >= kmer_count) + return 0; + + // fix the right end of the read + fix_right( read_len, read, longest_range, fix, solid, trimStart, badSuffix, ambiguous ); + + // fix the left end of the read + fix_left( read_len, read, longest_range, fix, solid, trimStart, badPrefix, ambiguous ); + + float correct_count = 0; + + const uint8 N = 4; + + for (int i = 0; i < read_len; ++i) + { + if (i >= K && (fix[i - K] >= 0 && read[i - K] < N)) + { + correct_count -= (qual[i - K] <= bad_quality) ? 0.5f : 1.0f; + } + if (fix[i] >= 0 && read[i] < N) + { + correct_count += (qual[i] <= bad_quality) ? 0.5f : 1.0f; + } + if (correct_count > max_correction) + return -1; // unreliable correction + } + + int corrections = 0; + + for (int i = badPrefix; i < trimStart; ++i) + { + if (fix[i] < 0) + continue; + + if (read[i] != fix[i]) + { + // fix the base + read[i] = fix[i]; + + // fix the quality score + if (new_quality != uint8('\0')) + qual[i] = new_quality; + + ++corrections; + } + } + + badSuffix = read_len - trimStart; + + if (corrections == 0 && badPrefix == 0 && badSuffix == 0 && ambiguous) + return -1; + + return corrections; + } + + /// functor operator + /// + ///\param s input string index + /// + NVBIO_HOST_DEVICE + void operator() (const uint32 s) const + { + typedef typename string_set_type::string_type read_type; + typedef typename qual_set_type::string_type qual_type; + + // fetch the i-th string + read_type read = string_set[s]; + qual_type qual = qual_set[s]; + + int badPrefix, badSuffix; + + int corrections = correct( read, qual, badPrefix, badSuffix ); + + if (corrections == 0) + atomic_add( stats + ERROR_FREE, 1u ); + else if (corrections > 0) + atomic_add( stats + CORRECTIONS, corrections ); + else + atomic_add( stats + UNFIXABLE, 1u ); + + if (badSuffix > 0) + { + atomic_add( stats + TRIMMED_READS, 1u ); + atomic_add( stats + TRIMMED_BASES, badSuffix ); + } + } + + const int K; + const uint64 kmask; + mutable string_set_type string_set; + mutable qual_set_type qual_set; + const trusted_filter_type trusted_kmers; + uint64* stats; + const float max_correction; + const uint8 bad_quality; + const uint8 new_quality; +}; + +// process the next batch +// +bool ErrorCorrectStage::process(PipelineContext& context) +{ + typedef nvbio::io::SequenceDataEdit::sequence_string_set_type string_set_type; + typedef nvbio::io::SequenceDataEdit::qual_string_set_type qual_set_type; + + // declare the Bloom filter types + typedef nvbio::blocked_bloom_filter > trusted_filter_type; + + // declare the error corrector functor + typedef ErrorCorrectFunctor functor_type; + + log_debug(stderr, " error correction... started\n" ); + + // fetch the input + io::SequenceDataHost* h_read_data = context.input( 0 ); + + float time = 0.0f; + + // introduce a timing scope + try + { + const nvbio::ScopedTimer timer( &time ); + + if (device >= 0) + { + // set the device + cudaSetDevice( device ); + + // copy it to the device + nvbio::io::SequenceDataDevice d_read_data( *h_read_data ); + + nvbio::io::SequenceDataView d_read_view( d_read_data ); + + // build an editable view + nvbio::io::SequenceDataEdit d_read_edit( d_read_view ); + + // build the Bloom filter + trusted_filter_type trusted_filter( TRUSTED_KMERS_FILTER_K, trusted_filter_size, (const uint4*)trusted_filter_storage ); + + // build the kmer sampling functor + const functor_type error_corrector( + k, + d_read_edit.sequence_string_set(), + d_read_edit.qual_string_set(), + trusted_filter, + stats_vec, + max_correction, + uint8(bad_quality), + uint8(new_quality) ); + + // and apply the functor to all reads in the batch + device_for_each( + d_read_view.size(), + error_corrector ); + + cudaDeviceSynchronize(); + nvbio::cuda::check_error("error-correct"); + + // fetch the output + nvbio::io::SequenceDataHost* output = context.output(); + + // copy the modified device data to the output + *output = d_read_data; + } + else + { + omp_set_num_threads( -device ); + + // fetch the output + nvbio::io::SequenceDataHost* output = context.output(); + + // copy from the input + *output = *h_read_data; + + nvbio::io::SequenceDataView h_read_view( *output ); + + // build an editable view + nvbio::io::SequenceDataEdit h_read_edit( h_read_view ); + + // build the Bloom filter + trusted_filter_type trusted_filter( TRUSTED_KMERS_FILTER_K, trusted_filter_size, (const uint4*)trusted_filter_storage ); + + // build the kmer sampling functor + const functor_type error_corrector( + k, + h_read_edit.sequence_string_set(), + h_read_edit.qual_string_set(), + trusted_filter, + stats_vec, + max_correction, + uint8(bad_quality), + uint8(new_quality) ); + + // and apply the functor to all reads in the batch + host_for_each( + h_read_view.size(), + error_corrector ); + } + } + catch (nvbio::cuda_error e) + { + log_error(stderr, "[ErrorCorrectStage] caught a nvbio::cuda_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::bad_alloc e) + { + log_error(stderr, "[ErrorCorrectStage] caught a nvbio::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::logic_error e) + { + log_error(stderr, "[ErrorCorrectStage] caught a nvbio::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::runtime_error e) + { + log_error(stderr, "[ErrorCorrectStage] caught a nvbio::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (thrust::system::system_error e) + { + log_error(stderr, "[ErrorCorrectStage] caught a thrust::system_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::bad_alloc e) + { + log_error(stderr, "[ErrorCorrectStage] caught a std::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::logic_error e) + { + log_error(stderr, "[ErrorCorrectStage] caught a std::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::runtime_error e) + { + log_error(stderr, "[ErrorCorrectStage] caught a std::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (...) + { + log_error(stderr, "[ErrorCorrectStage] caught an unknown exception!\n"); + exit(1); + } + + // update the time stats + stats->m_mutex.lock(); + stats->m_time += time; + + log_info(stderr, "\r processed reads [%llu, %llu] (%.1fM / %.2fG bps, %.1fK reads/s, %.1fM bps/s - %s<%d>) ", + stats->m_reads, + stats->m_reads + h_read_data->size(), + 1.0e-6f * (h_read_data->bps()), + 1.0e-9f * (stats->m_bps + h_read_data->bps()), + stats->m_time ? (1.0e-3f * (stats->m_reads + h_read_data->size())) / stats->m_time : 0.0f, + stats->m_time ? (1.0e-6f * (stats->m_bps + h_read_data->bps() )) / stats->m_time : 0.0f, + device >= 0 ? "gpu" : "cpu", + device >= 0 ? device : -device ); + + log_debug_cont(stderr, "\n"); + log_debug(stderr, " error correction... done\n" ); + log_debug(stderr, " peak memory : %.1f GB\n", float( peak_resident_memory() ) / float(1024*1024*1024)); + + stats->m_reads += h_read_data->size(); + stats->m_bps += h_read_data->bps(); + stats->m_mutex.unlock(); + + return true; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/error_correct.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/error_correct.h new file mode 100644 index 0000000000000000000000000000000000000000..eb7c32053e3a83c9fbb216f7951602048763d81c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/error_correct.h @@ -0,0 +1,104 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// error_correct.h +// + +#pragma once + +#include "utils.h" +#include +#include +#include +#include +#include +#include +#include +#include + +///@addtogroup nvLighterModule +///@{ + +/// +/// A small class implementing an nvbio::Pipeline stage performing the actual error correction work +/// +struct ErrorCorrectStage +{ + typedef nvbio::io::SequenceDataHost argument_type; + typedef nvbio::io::SequenceDataHost return_type; + + /// empty constructor + /// + ErrorCorrectStage() {} + + /// constructor + /// + ///\param _k kmer length + ///\param _alpha the sampling frequency + ///\param _filter_size the kmer Bloom filter's size, in bits + ///\param _filter_storage the kmer Bloom filter's storage + /// + ErrorCorrectStage( + const int _device, + const uint32 _k, + const uint64 _trusted_filter_size, + const uint32* _trusted_filter_storage, + uint64* _stats_vec, + const float _max_correction, + const char _bad_quality, + const char _new_quality, + SequenceStats* _stats) : + device( _device ), + k( _k ), + trusted_filter_size( _trusted_filter_size ), + trusted_filter_storage( _trusted_filter_storage ), + stats_vec(_stats_vec), + max_correction( _max_correction ), + bad_quality( _bad_quality ), + new_quality( _new_quality ), + stats( _stats ) + {} + + /// process the next batch + /// + bool process(nvbio::PipelineContext& context); + + int device; + uint32 k; + uint64 trusted_filter_size; + const uint32* trusted_filter_storage; + uint64* stats_vec; + float max_correction; + char bad_quality; + char new_quality; + SequenceStats* stats; + + nvbio::for_each_enactor host_for_each; + nvbio::for_each_enactor device_for_each; +}; + +///@} // group nvLighterModule diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/input_thread.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/input_thread.cu new file mode 100644 index 0000000000000000000000000000000000000000..704c9b9401b26fe15942679a9c82e8d3753b82f0 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/input_thread.cu @@ -0,0 +1,79 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// input_thread.cu +// + +#include "input_thread.h" +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +// fill the next batch +// +bool InputStage::process(nvbio::PipelineContext& context) +{ + m_data->m_mutex.lock(); + + nvbio::Timer timer; + timer.start(); + + // fetch the output + nvbio::io::SequenceDataHost* h_read_data = context.output(); + + const int ret = nvbio::io::next( DNA_N, h_read_data, m_data->m_file, m_data->m_max_strings, m_data->m_max_bps ); + + timer.stop(); + m_data->m_time += timer.seconds(); + m_data->m_reads += h_read_data->size(); + m_data->m_bps += h_read_data->bps(); + + if (h_read_data->max_sequence_len() > MAX_READ_LENGTH) + { + log_error(stderr, " maximum read length exceeded: %u > %u\n", h_read_data->max_sequence_len(), MAX_READ_LENGTH); + return false; + } + + log_verbose(stderr, "\r loaded reads [%llu, %llu] (%.1fM / %.2fG bps, %.1fK reads/s, %.1fM bps/s) ", + m_data->m_reads, + m_data->m_reads + h_read_data->size(), + 1.0e-6f * (h_read_data->bps()), + 1.0e-9f * (m_data->m_bps + h_read_data->bps()), + m_data->m_time ? (1.0e-3f * (m_data->m_reads + h_read_data->size())) / m_data->m_time : 0.0f, + m_data->m_time ? (1.0e-6f * (m_data->m_bps + h_read_data->bps() )) / m_data->m_time : 0.0f ); + log_debug_cont(stderr, "\n"); + + m_data->m_mutex.unlock(); + + return ret; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/input_thread.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/input_thread.h new file mode 100644 index 0000000000000000000000000000000000000000..2067f358065d7fa0ada86734af21b9a0dc194adb --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/input_thread.h @@ -0,0 +1,105 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// input_thread.h +// + +#pragma once + +#include "utils.h" +#include +#include +#include +#include +#include +#include +#include + +///@addtogroup nvLighterModule +///@{ + +/// A small class encapsulating the core data needed by all input threads, +/// i.e. the actual input file, a lock, and the relative statistics +/// +struct InputStageData +{ + /// constructor + /// + ///\param file input sequence file + ///\param max_strings maximum number of strings per batch + ///\param max_bps maximum number of base pairs per batch + /// + InputStageData(nvbio::io::SequenceDataStream* file, const uint32 max_strings, const uint32 max_bps) : + m_file ( file ), + m_max_strings ( max_strings ), + m_max_bps ( max_bps ), + m_reads ( 0 ), + m_bps ( 0 ), + m_time ( 0.0f ) + {} + + nvbio::Mutex m_mutex; + nvbio::io::SequenceDataStream* m_file; + uint32 m_max_strings; + uint32 m_max_bps; + uint64 m_reads; + uint64 m_bps; + float m_time; +}; + +/// +/// A small class implementing an nvbio::Pipeline stage reading sequence batches from a file +/// +struct InputStage +{ + typedef void argument_type; + typedef nvbio::io::SequenceDataHost return_type; + + /// constructor + /// + ///\param file input sequence file + ///\param max_strings maximum number of strings per batch + ///\param max_bps maximum number of base pairs per batch + /// + InputStage() : m_data(NULL) {} + + /// constructor + /// + ///\param file input sequence file + ///\param max_strings maximum number of strings per batch + ///\param max_bps maximum number of base pairs per batch + /// + InputStage(InputStageData* data) : m_data(data) {} + + /// fill the next batch + /// + bool process(nvbio::PipelineContext& context); + + InputStageData* m_data; +}; + +///@} // group nvLighterModule diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/nvLighter.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/nvLighter.cu new file mode 100644 index 0000000000000000000000000000000000000000..591f1f1c8bce4a2e337b4f85c73a7a7072f9641d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/nvLighter.cu @@ -0,0 +1,828 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// nvLighter.cu +// + +//#define NVBIO_CUDA_DEBUG + +#include +#include +#include + +#include "bloom_filters.h" +#include "input_thread.h" +#include "output_thread.h" +#include "sample_kmers.h" +#include "error_correct.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + + +void cumulative_binomial_distribution(double F[], uint32 l, double p) +{ + // p is the probability of getting 1 + double coef = 1 ; + double exp = pow( 1 - p, l ); + + F[0] = pow( 1 - p, l ); + for (uint32 i = 1 ; i <= l ; ++i) + { + coef = coef / i * (l - i + 1); + exp = exp / (1 - p) * p; + F[i] = F[i-1] + coef * exp; + } +} + +char get_bad_quality(nvbio::io::SequenceDataStream* reads_file) +{ + int i; + int histogram1[300], histogram2[300]; + + // fetch some reads + io::SequenceDataHost reads; + + memset( histogram1, 0, sizeof( histogram1 )) ; + memset( histogram2, 0, sizeof( histogram2 ) ) ; + + int n_reads = 0; + + for (int batch = 0 ; batch < 100; ++batch) + { + const int ret = nvbio::io::next( ASCII, &reads, reads_file, 10000, 10000000 ); + if (ret == 0) + break; + + const nvbio::io::SequenceDataAccess reads_view( reads ); + + typedef nvbio::io::SequenceDataAccess::qual_string qual_string; + + for (uint32 i = 0; i < reads.size(); ++i) + { + const qual_string quals = reads_view.get_quals(i); + + ++histogram2[ (int)quals[ quals.length() - 1 ] ]; + ++histogram1[ (int)quals[0] ]; + } + + n_reads += reads.size(); + } + + // rewind the file + if (reads_file->rewind() == false) + { + log_error(stderr, " failed rewinding reads file\n"); + return 1; + } + + int cnt = 0; + for (i = 0 ; i < 300; ++i) + { + cnt += histogram1[i]; + if (cnt > n_reads * 0.05f) + break; + } + const int t1 = i - 1; + cnt = 0; + for (i = 0; i < 300 ; ++i) + { + cnt += histogram2[i]; + if (cnt > n_reads * 0.05f) + break; + } + const int t2 = i; + return (char)nvbio::min( t1, t2 ); +} + +float infer_alpha(nvbio::io::SequenceDataStream* reads_file, const uint64 genome_size) +{ + log_info(stderr, " inferring alpha... started\n" ); + + nvbio::io::SequenceDataHost reads; + + uint64 n_reads = 0; + uint64 n_bps = 0; + float time = 0.0f; + + while (1) + { + Timer timer; + timer.start(); + + const int ret = nvbio::io::next( ASCII, &reads, reads_file, 512*1024, 128*1024*1024 ); + if (ret == 0) + break; + + timer.stop(); + time += timer.seconds(); + + log_verbose(stderr, "\r input: %llu reads, %.2f%c bps (%.1f Mbps/s) ", + n_reads, n_bps >= 1.0e9f ? 'B' : 'M', + float(n_bps)*(n_bps >= 1.0e-9f ? 1.0e-9f : 1.0e-6f), + 1.0e-6f * float(n_bps)/time ); + + n_reads += reads.size(); + n_bps += reads.bps(); + } + log_verbose_cont(stderr, "\n"); + + const float coverage = float( double( n_bps ) / double( genome_size ) ); + const float alpha = 7.0f / coverage; + + log_info(stderr, " inferring alpha... done\n" ); + log_stats(stderr, " input: %llu reads, %.2f%c bps, %.3fx coverage\n", + n_reads, n_bps >= 1.0e9f ? 'B' : 'M', + float(n_bps)*(n_bps >= 1.0e-9f ? 1.0e-9f : 1.0e-6f), + coverage ); + + log_visible(stderr, " inferred alpha: %f\n", alpha ); + + // rewind the file + if (reads_file->rewind() == false) + { + log_error(stderr, " failed rewinding reads file\n"); + return 1; + } + + return alpha; +} + +int main(int argc, char* argv[]) +{ + if ((argc < 3) || (strcmp( argv[1], "--help" ) == 0)) + { + log_visible(stderr, "nvLighter - Copyright 2015, NVIDIA Corporation\n"); + log_info(stderr, "usage:\n"); + log_info(stderr, " nvLighter [options] input_file output_file\n"); + log_info(stderr, " options:\n"); + log_info(stderr, " -v int (0-6) [5] # verbosity level\n"); + log_info(stderr, " -zlib string [1R] # e.g. \"1\", ..., \"9\", \"1R\"\n"); + log_info(stderr, " -t int [auto] # number of CPU threads\n"); + log_info(stderr, " -d int [0] # add the specified GPU device\n"); + log_info(stderr, " -k k-mer genome-size alpha # error correction parameters\n"); + log_info(stderr, " -K k-mer genome-size # error correction parameters\n"); + log_info(stderr, " -maxcor int [4] # maximum correction factor\n"); + log_info(stderr, " -newQual int [disabled] # new quality score value\n"); + log_info(stderr, " -no-cpu # disable CPU usage\n"); + log_info(stderr, " -no-gpu # disable GPU usage\n"); + return 0; + } + + const char* reads_name = argv[argc-2]; + const char* output_name = argv[argc-1]; + const char* comp_level = "1R"; + io::QualityEncoding qencoding = io::Phred; + int threads = 0; + uint32 k = 11u; + uint64 genome_size = 0; + float alpha = 0.0; + float max_correction = 4.0f; + char new_quality = 0; + float bf_factor = 1.0f; // original: 1.5 + bool cpu = true; + bool gpu = true; + + std::vector devices(0); + + for (int i = 0; i < argc - 2; ++i) + { + if ((strcmp( argv[i], "-v" ) == 0) || + (strcmp( argv[i], "-verbosity" ) == 0) || + (strcmp( argv[i], "--verbosity" ) == 0)) + { + set_verbosity( Verbosity( atoi( argv[++i] ) ) ); + } + else if ((strcmp( argv[i], "-c" ) == 0) || + (strcmp( argv[i], "--compression" ) == 0) || + (strcmp( argv[i], "-zlib" ) == 0)) // setup compression level + { + comp_level = argv[++i]; + } + else if ((strcmp( argv[i], "-t" ) == 0) || + (strcmp( argv[i], "-threads" ) == 0) || + (strcmp( argv[i], "--threads" ) == 0)) // setup number of threads + { + threads = atoi( argv[++i] ); + } + else if ((strcmp( argv[i], "-d" ) == 0) || + (strcmp( argv[i], "-device" ) == 0) || + (strcmp( argv[i], "--device" ) == 0)) // add a device + { + devices.push_back( atoi( argv[++i] ) ); + } + else if ((strcmp( argv[i], "-no-cpu" ) == 0) || // remove CPU + (strcmp( argv[i], "--no-cpu" ) == 0)) + cpu = false; + else if ((strcmp( argv[i], "-no-gpu" ) == 0) || // remove GPU + (strcmp( argv[i], "--no-gpu" ) == 0)) + gpu = false; + else if (strcmp( argv[i], "-k" ) == 0) // setup kmer length, genome size and sampling frequency + { + k = atoi( argv[++i] ); + genome_size = atol( argv[++i] ); + alpha = atof( argv[++i] ); + } + else if (strcmp( argv[i], "-K" ) == 0) // setup kmer length, genome size and sampling frequency + { + k = atoi( argv[++i] ); + genome_size = atol( argv[++i] ); + alpha = 0.0f; + } + else if (strcmp( argv[i], "-maxcor" ) == 0) // setup max correction factor + max_correction = (float)atoi( argv[++i] ); + else if (strcmp( argv[i], "-newQual" ) == 0) // setup new quality + new_quality = argv[++i][0]; + else if (strcmp( argv[i], "-bf" ) == 0) // Bloom filter expansion factor + bf_factor = atof( argv[++i] ); + } + + // if no devices were specified, and the gpu is enabled, pick GPU 0 + if (gpu && (devices.size() == 0)) + devices.push_back(0); + + uint32 device_count = uint32( devices.size() ); + + // check whether the genome size has been specified + if (genome_size == 0u) + { + log_error(stderr, "must specify the k-mer and genome size with the option: -k k genome-size alpha\n" ); + return 1; + } + + try + { + log_visible(stderr,"nvLighter... started\n"); + + // compute the optimal Bloom filter size scaling factors + const float sampled_kmers_bf_factor = optimal_bloom_filter_bits_per_key( 0.01f ); + const float trusted_kmers_bf_factor = optimal_bloom_filter_bits_per_key( 0.0005f ); + + log_verbose(stderr, " optimal m(0.01f) = %.2f\n", sampled_kmers_bf_factor ); + log_verbose(stderr, " optimal k(0.01f) = %u\n", optimal_bloom_filter_hashes( sampled_kmers_bf_factor ) ); + + log_verbose(stderr, " optimal m(0.0005f) = %.2f\n", trusted_kmers_bf_factor ); + log_verbose(stderr, " optimal k(0.0005f) = %u\n", optimal_bloom_filter_hashes( trusted_kmers_bf_factor ) ); + + // compute the Bloom filter sizes, in words + const uint64 sampled_kmers_bf_words = align<8u>( uint64( float(genome_size) * bf_factor * (sampled_kmers_bf_factor / 32.0f) ) ); + const uint64 trusted_kmers_bf_words = align<8u>( uint64( float(genome_size) * bf_factor * (trusted_kmers_bf_factor / 32.0f) ) ); + + const uint32 bits_per_word = 32u; + + // now set the number of CPU threads + threads = threads > 0 ? threads : omp_get_num_procs(); + + //omp_set_num_threads( threads ); + omp_set_num_threads( omp_get_num_procs() ); // use all threads for the merging steps... + omp_set_nested(1); + + // setup the device Bloom filters + BloomFilters h_bloom_filters; + BloomFilters* h_bloom_filters_ptr = &h_bloom_filters; + BloomFilters d_bloom_filters[16]; + + for (int i = device_count-1; i >= 0; --i) + { + if (d_bloom_filters[i].setup( devices[i], sampled_kmers_bf_words, trusted_kmers_bf_words ) == false) + devices.erase( devices.begin() + i ); + } + device_count = uint32( devices.size() ); + + if (gpu && (device_count == 0)) + { + log_warning(stderr, " no available GPU devices\n"); + + // revert to using the CPU even if -no-cpu was specified + if (cpu == false) + { + cpu = true; + log_warning(stderr, " switching the CPU on\n"); + } + } + + if (cpu && h_bloom_filters.setup( -1, sampled_kmers_bf_words, trusted_kmers_bf_words ) == false) + cpu = false; + + if (cpu == false) + { + h_bloom_filters_ptr = NULL; + + if (device_count == 0) + { + log_error(stderr, " no available CPU or GPU devices\n"); + return 1; + } + } + + // + // open the output file + // + + log_info(stderr, " opening output file \"%s\"... started\n", output_name); + + SharedPointer output_file( + nvbio::io::open_output_sequence_file( + output_name, + comp_level ) ); + + if (output_file == NULL || output_file->is_ok() == false) + { + log_error(stderr, " failed opening output \"%s\"\n", output_name); + return 1; + } + log_info(stderr, " opening output file \"%s\"... done\n", output_name); + + // + // open the reads file + // + + uint32 max_block_strings = 512*1024; + uint32 max_block_bps = 64*1024*1024; + + log_info(stderr, " opening read file \"%s\"... started\n", reads_name); + + SharedPointer read_data_file( + nvbio::io::open_sequence_file( + reads_name, + qencoding, + uint32(-1), + uint32(-1), + io::FORWARD ) + ); + + if (read_data_file == NULL || read_data_file->is_ok() == false) + { + log_error(stderr, " failed opening file \"%s\"\n", reads_name); + return 1; + } + log_info(stderr, " opening read file \"%s\"... done\n", reads_name); + + // infer alpha if necessary + if (alpha <= 0.0f) + { + alpha = infer_alpha( read_data_file.get(), genome_size ); + + if (alpha >= 1.0f) + { + log_error(stderr, " alpha cannot be greater than 1, coverage likely too low\n"); + exit(1); + } + } + + const char bad_quality = get_bad_quality( read_data_file.get() ); + log_info(stderr, " bad quality threshold: '%c'\n", bad_quality); + + log_info(stderr," sample kmers... started\n"); + { + // + // The following code implements a parallel nvbio::Pipeline to sample kmers from the input + // reads. The pipeline is composed several subpipelines, one per active device, each made + // of two stages (which will be run in separate threads): an InputStage, and a + // SampleKmersStage doing the actual sampling work. + // + + log_debug(stderr, " assemble pipeline\n"); + + // build the input stage + InputStageData input_stage_data( read_data_file.get(), max_block_strings, max_block_bps ); + InputStage input_stage[16]; + + // build the sink + SampleKmersStage sample_stage[16]; + SequenceStats sample_stats; + + // setup the pipeline stages + if (cpu) + { + // host stages + input_stage[device_count] = InputStage( &input_stage_data ); + sample_stage[device_count] = SampleKmersStage( + -threads, + k, + alpha, + sampled_kmers_bf_words * bits_per_word, + raw_pointer( h_bloom_filters.sampled_kmers_storage ), + &sample_stats ); + } + for (uint32 i = 0; i < device_count; ++i) + { + // device stages + input_stage[i] = InputStage( &input_stage_data ); + sample_stage[i] = SampleKmersStage( + devices[i], + k, + alpha, + sampled_kmers_bf_words * bits_per_word, + raw_pointer( d_bloom_filters[i].sampled_kmers_storage ), + &sample_stats ); + } + + // build the pipeline + nvbio::Pipeline pipeline; + for (uint32 i = 0; i < device_count + (cpu ? 1 : 0); ++i) + { + const uint32 in0 = pipeline.append_stage( &input_stage[i], 4u ); + const uint32 out = pipeline.append_sink( &sample_stage[i] ); + pipeline.add_dependency( in0, out ); + } + log_debug(stderr, " start pipeline\n"); + + Timer timer; + timer.start(); + + // and run it! + pipeline.run(); + + log_info_cont(stderr, "\n"); + merge( h_bloom_filters_ptr, device_count, d_bloom_filters, SAMPLED_KMERS ); + + timer.stop(); + const float time = timer.seconds(); + + log_verbose(stderr," total time : %.1fs\n", time); + log_verbose(stderr," peak memory : %.1f GB\n", float( peak_resident_memory() ) / float(1024*1024*1024)); + } + log_info(stderr," sample kmers... done\n"); + + log_info(stderr," mark trusted kmers... started\n"); + { + // + // The following code implements a parallel nvbio::Pipeline to mark trusted kmers in the input + // reads. The pipeline is composed several subpipelines, one per active device, each made + // of two stages (which will be run in separate threads): an InputStage, and a + // TrustedKmersStage doing the actual marking work. + // + + // gather Bloom filter statistics + nvbio::vector threshold( 100, 0u ); + { + double untrustF[100][100]; + + // compute the number of bits set + float occupancy; + float approx_size; + float FP; + + if (device_count) + { + compute_bloom_filter_stats( + d_bloom_filters[0], + SAMPLED_KMERS, + SAMPLED_KMERS_FILTER_K, + occupancy, + approx_size, + FP ); + } + else + { + compute_bloom_filter_stats( + h_bloom_filters, + SAMPLED_KMERS, + SAMPLED_KMERS_FILTER_K, + occupancy, + approx_size, + FP ); + } + + log_stats(stderr, " sampled kmers:\n" ); + log_stats(stderr, " occupancy : %f\n", occupancy ); + log_stats(stderr, " #kmers (approx) : %.1f\n", approx_size ); + log_stats(stderr, " FP rate : %f\n", FP ); + + // compute the i-th untrustF table + for (uint32 i = 1; i <= k; ++i) + { + int d = (int)(0.1 / alpha * 2); + if (d < 2) + d = 2; + + const double p = 1.0 - pow( (1.0 - alpha), d ); + + cumulative_binomial_distribution( untrustF[i], i, p + FP - p * FP ); + } + + // compute the threshold table + for (uint32 i = 1; i <= k; ++i) + { + for (uint32 j = 0; j <= i; ++j) + { + if (untrustF[i][j] >= 1 - 0.5 * 1e-2) + { + threshold[i] = j; + break; + } + } + } + log_verbose(stderr, " thresholds = {"); + for (uint32 i = 1; i <= k; ++i) + log_verbose_cont(stderr, " %u,", threshold[i]); + log_verbose_cont(stderr, " }\n"); + } + h_bloom_filters.set_threshold( threshold ); + for (uint32 i = 0; i < device_count; ++i) + d_bloom_filters[i].set_threshold( threshold ); + + log_debug(stderr, " rewind reads\n"); + if (read_data_file->rewind() == false) + { + log_error(stderr, " failed rewinding file \"%s\"\n", reads_name); + return 1; + } + log_debug(stderr, " assemble pipeline\n"); + + // build the input stages + InputStageData input_stage_data( read_data_file.get(), max_block_strings, max_block_bps ); + InputStage input_stage[16]; + + // build the trusted-kmer marking stages + SequenceStats marking_stats; + TrustedKmersStage marking_stage[16]; + + // setup the pipeline stages + if (cpu) + { + // host stages + input_stage[device_count] = InputStage( &input_stage_data ); + marking_stage[device_count] = TrustedKmersStage( + -threads, + k, + sampled_kmers_bf_words * bits_per_word, raw_pointer( h_bloom_filters.sampled_kmers_storage ), + trusted_kmers_bf_words * bits_per_word, raw_pointer( h_bloom_filters.trusted_kmers_storage ), + raw_pointer( h_bloom_filters.threshold ), + &marking_stats ); + } + for (uint32 i = 0; i < device_count; ++i) + { + // device stages + input_stage[i] = InputStage( &input_stage_data ); + marking_stage[i] = TrustedKmersStage( + devices[i], + k, + sampled_kmers_bf_words * bits_per_word, raw_pointer( d_bloom_filters[i].sampled_kmers_storage ), + trusted_kmers_bf_words * bits_per_word, raw_pointer( d_bloom_filters[i].trusted_kmers_storage ), + raw_pointer( d_bloom_filters[i].threshold ), + &marking_stats ); + } + + // build the pipeline + nvbio::Pipeline pipeline; + for (uint32 i = 0; i < device_count + (cpu ? 1 : 0); ++i) + { + const uint32 in0 = pipeline.append_stage( &input_stage[i], 4u ); + const uint32 out = pipeline.append_sink( &marking_stage[i] ); + pipeline.add_dependency( in0, out ); + } + log_debug(stderr, " start pipeline\n"); + + Timer timer; + timer.start(); + + // and run it! + pipeline.run(); + + log_info_cont(stderr, "\n"); + merge( h_bloom_filters_ptr, device_count, d_bloom_filters, TRUSTED_KMERS ); + + timer.stop(); + const float time = timer.seconds(); + + log_verbose(stderr," total time : %.1fs\n", time); + log_verbose(stderr," peak memory : %.1f GB\n", float( peak_resident_memory() ) / float(1024*1024*1024)); + } + log_info(stderr," mark trusted kmers... done\n"); + + log_info(stderr," error correction... started\n"); + { + // + // The following code implements a parallel nvbio::Pipeline to error-correct the input + // reads. The pipeline is composed several subpipelines, one per active device, each made + // of three stages (which will be run in separate threads): an InputStage, an + // ErrorCorrectStage doing the actual error correction work, and a final OutputStage. + // + + // gather Bloom filter statistics + { + // compute the number of bits set + float occupancy; + float approx_size; + float FP; + + if (device_count) + { + compute_bloom_filter_stats( + d_bloom_filters[0], + TRUSTED_KMERS, + TRUSTED_KMERS_FILTER_K, + occupancy, + approx_size, + FP ); + } + else + { + compute_bloom_filter_stats( + h_bloom_filters, + TRUSTED_KMERS, + TRUSTED_KMERS_FILTER_K, + occupancy, + approx_size, + FP ); + } + + log_stats(stderr, " trusted kmers:\n" ); + log_stats(stderr, " occupancy : %f\n", occupancy ); + log_stats(stderr, " #kmers (approx) : %.1f\n", approx_size ); + log_stats(stderr, " FP rate : %f\n", FP ); + } + + log_debug(stderr, " rewind reads\n"); + if (read_data_file->rewind() == false) + { + log_error(stderr, " failed rewinding file \"%s\"\n", reads_name); + return 1; + } + log_debug(stderr, " assemble pipeline\n"); + + // build the input stages + InputStageData input_stage_data( read_data_file.get(), max_block_strings, max_block_bps ); + InputStage input_stage[16]; + + // build the error correction stages + SequenceStats ec_stats; + ErrorCorrectStage ec_stage[16]; + + // build the output stages + OutputStageData output_stage_data( output_file.get() ); + OutputStage output_stage[16]; + + // setup the pipeline stages + if (cpu) + { + // build the input stage + input_stage[device_count] = InputStage( &input_stage_data ); + + // build the sink + ec_stage[device_count] = ErrorCorrectStage( + -threads, + k, + trusted_kmers_bf_words * bits_per_word, raw_pointer( h_bloom_filters.trusted_kmers_storage ), + raw_pointer( h_bloom_filters.stats ), + max_correction, + bad_quality, + new_quality, + &ec_stats ); + + // build the input stage + output_stage[device_count] = OutputStage( &output_stage_data ); + } + for (uint32 i = 0; i < device_count; ++i) + { + // build the input stage + input_stage[i] = InputStage( &input_stage_data ); + + // build the sink + ec_stage[i] = ErrorCorrectStage( + devices[i], + k, + trusted_kmers_bf_words * bits_per_word, raw_pointer( d_bloom_filters[i].trusted_kmers_storage ), + raw_pointer( d_bloom_filters[i].stats ), + max_correction, + bad_quality, + new_quality, + &ec_stats ); + + // build the input stage + output_stage[i] = OutputStage( &output_stage_data ); + } + log_debug(stderr, " start pipeline\n"); + + // build the pipeline + nvbio::Pipeline pipeline; + for (uint32 i = 0; i < device_count + (cpu ? 1 : 0); ++i) + { + const uint32 in = pipeline.append_stage( &input_stage[i], 4u ); + const uint32 ec = pipeline.append_stage( &ec_stage[i] ); + const uint32 out = pipeline.append_sink( &output_stage[i] ); + pipeline.add_dependency( in, ec ); + pipeline.add_dependency( ec, out ); + } + + Timer timer; + timer.start(); + + // and run it! + pipeline.run(); + + timer.stop(); + const float time = timer.seconds(); + + log_info_cont(stderr, "\n"); + + nvbio::vector stats; + merged_stats( h_bloom_filters_ptr, device_count, d_bloom_filters, stats ); + + log_info(stderr," stats :\n"); + log_info(stderr," error free reads : %llu\n", uint64( stats[ERROR_FREE] )); + log_info(stderr," unfixable reads : %llu\n", uint64( stats[UNFIXABLE] )); + log_info(stderr," corrected bases : %llu\n", uint64( stats[CORRECTIONS] )); + + log_verbose(stderr," total time : %.1fs\n", time); + log_verbose(stderr," peak memory : %.1f GB\n", float( peak_resident_memory() ) / float(1024*1024*1024)); + } + log_info(stderr," error correction... done\n"); + + log_visible(stderr,"nvLighter... done\n"); + } + catch (nvbio::cuda_error e) + { + log_error(stderr, "caught a nvbio::cuda_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (nvbio::bad_alloc e) + { + log_error(stderr, "caught a nvbio::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (nvbio::logic_error e) + { + log_error(stderr, "caught a nvbio::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (nvbio::runtime_error e) + { + log_error(stderr, "caught a nvbio::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (thrust::system::system_error e) + { + log_error(stderr, "caught a thrust::system_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (std::bad_alloc e) + { + log_error(stderr, "caught a std::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (std::logic_error e) + { + log_error(stderr, "caught a std::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (std::runtime_error e) + { + log_error(stderr, "caught a std::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (...) + { + log_error(stderr, "caught an unknown exception!\n"); + return 1; + } + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/output_thread.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/output_thread.cu new file mode 100644 index 0000000000000000000000000000000000000000..9d95de5eef826fce9d3205830984e423bb902f58 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/output_thread.cu @@ -0,0 +1,139 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// output_thread.cu +// + +#include "output_thread.h" +#include "utils.h" +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +// fill the next batch +// +bool OutputStage::process(PipelineContext& context) +{ + try + { + // fetch the h_read_data + io::SequenceDataHost* h_read_data = context.input( 0 ); + + log_debug(stderr, " writing... started (%u, %u)\n", h_read_data->size(), h_read_data->bps() ); + + Timer timer; + timer.start(); + + data->m_mutex.lock(); + data->m_file->next( *h_read_data ); + + if (data->m_file->is_ok() == false) + { + log_error(stderr, "[OutputStage] failed writing output\n"); + exit(1); + } + + timer.stop(); + data->m_time += timer.seconds(); + + log_verbose(stderr, "\r written reads [%u, %u] (%.1fM / %.2fG bps, %.1fK reads/s, %.1fM bps/s) ", + data->m_reads, + data->m_reads + h_read_data->size(), + 1.0e-6f * (h_read_data->bps()), + 1.0e-9f * (data->m_bps + h_read_data->bps()), + data->m_time ? (1.0e-3f * (data->m_reads + h_read_data->size())) / data->m_time : 0.0f, + data->m_time ? (1.0e-6f * (data->m_bps + h_read_data->bps() )) / data->m_time : 0.0f ); + log_debug_cont(stderr, "\n"); + + data->m_reads += h_read_data->size(); + data->m_bps += h_read_data->bps(); + data->m_mutex.unlock(); + + log_debug(stderr, " writing... done (%.1f Mbps/s)\n", data->m_time ? (1.0e-6f * float(data->m_bps)) / data->m_time : 0.0f); + } + catch (nvbio::cuda_error e) + { + log_error(stderr, "[OutputStage] caught a nvbio::cuda_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::bad_alloc e) + { + log_error(stderr, "[OutputStage] caught a nvbio::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::logic_error e) + { + log_error(stderr, "[OutputStage] caught a nvbio::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::runtime_error e) + { + log_error(stderr, "[OutputStage] caught a nvbio::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (thrust::system::system_error e) + { + log_error(stderr, "[OutputStage] caught a thrust::system_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::bad_alloc e) + { + log_error(stderr, "[OutputStage] caught a std::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::logic_error e) + { + log_error(stderr, "[OutputStage] caught a std::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::runtime_error e) + { + log_error(stderr, "[OutputStage] caught a std::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (...) + { + log_error(stderr, "[OutputStage] caught an unknown exception!\n"); + exit(1); + } + return true; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/output_thread.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/output_thread.h new file mode 100644 index 0000000000000000000000000000000000000000..b6841ea46b89e997417be04863c7a72cb9107e02 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/output_thread.h @@ -0,0 +1,81 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// output_thread.h +// + +#pragma once + +#include "utils.h" +#include +#include +#include + +///@addtogroup nvLighterModule +///@{ + +/// A small class encapsulating the core data needed by all output threads, +/// i.e. the output file and its relevant statistics +/// +struct OutputStageData : public SequenceStats +{ + /// constructor + /// + ///\param file input sequence file + ///\param max_strings maximum number of strings per batch + ///\param max_bps maximum number of base pairs per batch + /// + OutputStageData(nvbio::io::SequenceDataOutputStream* file) : m_file( file ) {} + + nvbio::io::SequenceDataOutputStream* m_file; +}; + +/// +/// A small class implementing an nvbio::Pipeline stage reading sequence batches from a file +/// +struct OutputStage +{ + typedef nvbio::io::SequenceDataHost argument_type; + + /// empty constructor + /// + OutputStage() : data(NULL) {} + + /// constructor + /// + ///\param file input sequence file + /// + OutputStage(OutputStageData* _data) : data(_data) {} + + /// fill the next batch + /// + bool process(nvbio::PipelineContext& context); + + OutputStageData* data; +}; + +///@} // group nvLighterModule diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/sample_kmers.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/sample_kmers.cu new file mode 100644 index 0000000000000000000000000000000000000000..c6e379fc03361835bfbb4964f210f5066bd438f5 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/sample_kmers.cu @@ -0,0 +1,636 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// sample_kmers.h +// + +#include "sample_kmers.h" +#include "utils.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +/// +/// A functor to sample kmers and insert them in a Bloom filter +/// +template +struct SampleKmersFunctor +{ + /// constructor + /// + ///\param _k kmer length + ///\param _alpha the sampling frequency + ///\param _string_set the input string set to sample + ///\param _filter the kmer Bloom filter + /// + NVBIO_HOST_DEVICE + SampleKmersFunctor( + const uint32 _k, + const float _alpha, + const string_set_type _string_set, + filter_type _filter) : + k(_k), kmask( (uint64(1u) << (k*2))-1u ), alpha( _alpha ), string_set( _string_set ), filter(_filter) {} + + /// functor operator + /// + ///\param i input string index + /// + NVBIO_HOST_DEVICE + void operator() (const uint32 i) const + { + typedef typename string_set_type::string_type string_type; + typedef typename string_traits::forward_iterator forward_iterator; + + // fetch the i-th string + const string_type string = string_set[i]; + + const uint32 len = length( string ); + if (len < k) + return; + + // build a forward string iterator + forward_iterator it( string.begin() ); + + // start with an empty kmer + uint64 kmer = 0u; + uint32 kmer_len = 0u; + + // initialie a random number generator + LCG_random random( hash(i) ); + + for (uint32 j = 0; j < len; ++j) + { + // fetch the next character + const uint8 c = *it; ++it; + + if (c < 4) // make sure this is not an N + { + kmer |= c; // insert the new character at the end of the kmer (in a big-endian encoding) + if (kmer_len < k) + kmer_len++; + + if (kmer_len >= k) // check whether we have an actual 'k'-mer + { + if (float( random.next() ) / float(LCG_random::MAX) < alpha) + { + // insert the kmer + filter.insert( kmer ); + } + } + + // shift the kmer to the right, dropping the last symbol + kmer <<= 2; + kmer &= kmask; + } + else + { + // an N, skip all k-mers containing it + it += k-1; + j += k-1; + + // and reset the kmer + kmer = 0u; + kmer_len = 0u; + } + } + } + + const uint32 k; + const uint64 kmask; + const float alpha; + string_set_type string_set; + mutable filter_type filter; +}; + + +// process the next batch +// +bool SampleKmersStage::process(PipelineContext& context) +{ + typedef nvbio::io::SequenceDataAccess::sequence_string_set_type string_set_type; + + // declare the Bloom filter type + typedef nvbio::blocked_bloom_filter filter_type; + + typedef SampleKmersFunctor functor_type; + + // fetch the input + nvbio::io::SequenceDataHost* h_read_data = context.input( 0 ); + + float time = 0.0f; + + // introduce a timing scope + try + { + const nvbio::ScopedTimer timer( &time ); + + if (device >= 0) + { + // + // Device (GPU) path + // + + // set the device + cudaSetDevice( device ); + + // copy it to the device + nvbio::io::SequenceDataDevice d_read_data( *h_read_data ); + + // build a view + const nvbio::io::SequenceDataAccess d_read_view( d_read_data ); + + // build the Bloom filter + filter_type filter( SAMPLED_KMERS_FILTER_K, filter_size, (uint64_2*)filter_storage ); + //filter_type filter( filter_size, filter_storage ); + + // build the kmer sampling functor + const functor_type kmer_filter( + k, + alpha, + d_read_view.sequence_string_set(), + filter ); + + device_for_each( d_read_view.size(), kmer_filter ); + + cudaDeviceSynchronize(); + cuda::check_error("sample-kmers"); + } + else + { + // + // Host (CPU) path + // + + omp_set_num_threads( -device ); + + // build a view + const io::SequenceDataAccess h_read_view( *h_read_data ); + + // build the Bloom filter + filter_type filter( SAMPLED_KMERS_FILTER_K, filter_size, (uint64_2*)filter_storage ); + + // build the kmer sampling functor + const functor_type kmer_filter( + k, + alpha, + h_read_view.sequence_string_set(), + filter ); + + host_for_each( + h_read_view.size(), + kmer_filter ); + } + } + catch (nvbio::cuda_error e) + { + log_error(stderr, "[SampleKmersStage] caught a nvbio::cuda_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::bad_alloc e) + { + log_error(stderr, "[SampleKmersStage] caught a nvbio::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::logic_error e) + { + log_error(stderr, "[SampleKmersStage] caught a nvbio::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::runtime_error e) + { + log_error(stderr, "[SampleKmersStage] caught a nvbio::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (thrust::system::system_error e) + { + log_error(stderr, "[SampleKmersStage] caught a thrust::system_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::bad_alloc e) + { + log_error(stderr, "[SampleKmersStage] caught a std::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::logic_error e) + { + log_error(stderr, "[SampleKmersStage] caught a std::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::runtime_error e) + { + log_error(stderr, "[SampleKmersStage] caught a std::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (...) + { + log_error(stderr, "[SampleKmersStage] caught an unknown exception!\n"); + exit(1); + } + + // update the time stats + stats->m_mutex.lock(); + stats->m_time += time; + + log_info(stderr, "\r processed reads [%llu, %llu] (%.1fM / %.2fG bps, %.1fK reads/s, %.1fM bps/s - %s<%d>) ", + stats->m_reads, + stats->m_reads + h_read_data->size(), + 1.0e-6f * (h_read_data->bps()), + 1.0e-9f * (stats->m_bps + h_read_data->bps()), + stats->m_time ? (1.0e-3f * (stats->m_reads + h_read_data->size())) / stats->m_time : 0.0f, + stats->m_time ? (1.0e-6f * (stats->m_bps + h_read_data->bps() )) / stats->m_time : 0.0f, + device >= 0 ? "gpu" : "cpu", + device >= 0 ? device : -device ); + + log_debug_cont(stderr, "\n"); + log_debug(stderr," peak memory : %.1f GB\n", float( peak_resident_memory() ) / float(1024*1024*1024)); + + stats->m_reads += h_read_data->size(); + stats->m_bps += h_read_data->bps(); + stats->m_mutex.unlock(); + return true; +} + + +/// +/// A functor to sample kmers and insert them in a Bloom filter +/// +template +struct TrustedKmersFunctor +{ + /// constructor + /// + ///\param _k kmer length + ///\param _alpha the sampling frequency + ///\param _string_set the input string set to sample + ///\param _filter the kmer Bloom filter + /// + NVBIO_HOST_DEVICE + TrustedKmersFunctor( + const uint32 _k, + const string_set_type _string_set, + const sampled_filter_type _sampled_filter, + trusted_filter_type _trusted_filter, + const threshold_type _threshold) : + k(_k), kmask( (uint64(1u) << (k*2))-1u ), + string_set( _string_set ), + sampled_filter(_sampled_filter), + trusted_filter(_trusted_filter), + threshold(_threshold) {} + + /// functor operator + /// + ///\param i input string index + /// + NVBIO_HOST_DEVICE + void operator() (const uint32 i) const + { + typedef typename string_set_type::string_type string_type; + typedef nvbio::StringPrefetcher< string_type, nvbio::lmem_cache_tag > string_prefetcher_type; + typedef typename string_prefetcher_type::string_type local_string_type; + typedef typename nvbio::string_traits::forward_iterator forward_iterator; + + //bool occur[MAX_READ_LENGTH]; + uint32 occur_storage[MAX_READ_LENGTH/32]; + + nvbio::PackedStream occur( occur_storage ); + + // instantiate a prefetcher + string_prefetcher_type string_prefetcher; + + // fetch the i-th string + //const string_type string = string_set[i]; + const local_string_type string = string_prefetcher.load( string_set[i] ); + + const uint32 len = length( string ); + if (len < k) + return; + + // build a forward string iterator + forward_iterator it( string.begin() ); + + // start with an empty kmer + uint64 kmer = 0u; + uint32 kmer_len = 0u; + + const int32 occur_cnt = len - k + 1; + + // initialize all to false + for (uint32 j = 0; j < (occur_cnt+31)/32; ++j) + occur_storage[j] = 0u; + + // mark occurring kmers + for (uint32 j = 0; j < len; ++j) + { + // fetch the next character + const uint8 c = *it; ++it; + + if (c < 4) // make sure this is not an N + { + kmer |= c; // insert the new character at the end of the kmer (in a big-endian encoding) + if (kmer_len < k) + kmer_len++; + + if (kmer_len >= k) // check whether we have an actual 'k'-mer + { + if (sampled_filter[ kmer ]) + occur[j - k + 1] = true; + } + + // shift the kmer to the right, dropping the last symbol + kmer <<= 2; + kmer &= kmask; + } + else + { + // an N, skip all kmers containing it + it += k-1; + j += k-1; + + // and reset the kmer + kmer = 0u; + kmer_len = 0u; + } + } + + // mark trusted kmers + int32 zero_cnt = 0; + int32 one_cnt = 0; + + // reset the forward iterator + it = forward_iterator( string.begin() ); + + // start with an empty kmer + kmer = 0u; + kmer_len = 0u; + + // keep a k-bits mask of trusted positions + const uint64 trusted_mask = (uint64(1u) << k) - 1u; + uint64 trusted = 0u; + + for (uint32 j = 0; j < len; ++j) + { + if (j >= k) + { + if (occur[j - k]) --one_cnt; + else --zero_cnt; + } + + if (j < occur_cnt) + { + if (occur[j]) ++one_cnt; + else ++zero_cnt; + } + + const int32 sum = one_cnt + zero_cnt; + + //if (qual[j] <= bad_quality) + //{ + // trusted[j] = false; + // continue ; + //} + + trusted |= (one_cnt > threshold[sum]) ? 1u : 0u; + + // fetch the next character + const uint8 c = *it; ++it; + + if (c < 4) // if an N, skip it (the kmers containing it will be marked as untrusted and skipped as well) + { + kmer |= c; // insert the new character at the end of the kmer (in a big-endian encoding) + + if (popc( trusted ) == k) // check whether we have an actual 'k'-mer - i.e. k trusted positions in a row + trusted_filter.insert( kmer ); + } + + // shift the kmer to the right, dropping the last symbol + kmer <<= 2; + kmer &= kmask; + + // shift the trusted bits by one to the right, dropping the last symbol + trusted <<= 1; + trusted &= trusted_mask; + } + } + + const uint32 k; + const uint64 kmask; + string_set_type string_set; + const sampled_filter_type sampled_filter; + mutable trusted_filter_type trusted_filter; + const threshold_type threshold; +}; + +// process the next batch +// +bool TrustedKmersStage::process(PipelineContext& context) +{ + typedef nvbio::io::SequenceDataAccess::sequence_string_set_type string_set_type; + + // fetch the input + nvbio::io::SequenceDataHost* h_read_data = context.input( 0 ); + + float time = 0.0f; + + // introduce a timing scope + try + { + const nvbio::ScopedTimer timer( &time ); + + if (device >= 0) + { + // + // Device (GPU) path + // + + // declare the Bloom filter types + typedef nvbio::blocked_bloom_filter > sampled_filter_type; + typedef nvbio::blocked_bloom_filter trusted_filter_type; + + typedef TrustedKmersFunctor > functor_type; + + // set the device + cudaSetDevice( device ); + + // copy it to the device + io::SequenceDataDevice d_read_data( *h_read_data ); + + // build a view + const io::SequenceDataAccess d_read_view( d_read_data ); + + // build the Bloom filter + sampled_filter_type sampled_filter( SAMPLED_KMERS_FILTER_K, sampled_filter_size, (const uint4*)sampled_filter_storage ); + trusted_filter_type trusted_filter( TRUSTED_KMERS_FILTER_K, trusted_filter_size, (uint64_2*)trusted_filter_storage ); + + // build the kmer sampling functor + const functor_type kmer_filter( + k, + d_read_view.sequence_string_set(), + sampled_filter, + trusted_filter, + cuda::make_ldg_pointer(threshold) ); + + // and apply the functor to all reads in the batch + device_for_each( + d_read_view.size(), + kmer_filter ); + + cudaDeviceSynchronize(); + cuda::check_error("mark-trusted-kmers"); + } + else + { + // + // Host (CPU) path + // + + omp_set_num_threads( -device ); + + // declare the Bloom filter types + typedef nvbio::blocked_bloom_filter sampled_filter_type; + typedef nvbio::blocked_bloom_filter trusted_filter_type; + + typedef TrustedKmersFunctor functor_type; + + // build a view + const nvbio::io::SequenceDataAccess h_read_view( *h_read_data ); + + // build the Bloom filter + sampled_filter_type sampled_filter( SAMPLED_KMERS_FILTER_K, sampled_filter_size, (const uint64_2*)sampled_filter_storage ); + trusted_filter_type trusted_filter( TRUSTED_KMERS_FILTER_K, trusted_filter_size, (uint64_2*)trusted_filter_storage ); + + // build the kmer sampling functor + const TrustedKmersFunctor kmer_filter( + k, + h_read_view.sequence_string_set(), + sampled_filter, + trusted_filter, + threshold ); + + // and apply the functor to all reads in the batch + host_for_each( + h_read_view.size(), + kmer_filter ); + } + } + catch (nvbio::cuda_error e) + { + log_error(stderr, "[TrustedKmersStage] caught a nvbio::cuda_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::bad_alloc e) + { + log_error(stderr, "[TrustedKmersStage] caught a nvbio::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::logic_error e) + { + log_error(stderr, "[TrustedKmersStage] caught a nvbio::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (nvbio::runtime_error e) + { + log_error(stderr, "[TrustedKmersStage] caught a nvbio::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (thrust::system::system_error e) + { + log_error(stderr, "[TrustedKmersStage] caught a thrust::system_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::bad_alloc e) + { + log_error(stderr, "[TrustedKmersStage] caught a std::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::logic_error e) + { + log_error(stderr, "[TrustedKmersStage] caught a std::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (std::runtime_error e) + { + log_error(stderr, "[TrustedKmersStage] caught a std::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + exit(1); + } + catch (...) + { + log_error(stderr, "[TrustedKmersStage] caught an unknown exception!\n"); + exit(1); + } + + // update the time stats + stats->m_mutex.lock(); + stats->m_time += time; + + log_info(stderr, "\r processed reads [%llu, %llu] (%.1fM / %.2fG bps, %.1fK reads/s, %.1fM bps/s - %s<%d>) ", + stats->m_reads, + stats->m_reads + h_read_data->size(), + 1.0e-6f * (h_read_data->bps()), + 1.0e-9f * (stats->m_bps + h_read_data->bps()), + stats->m_time ? (1.0e-3f * (stats->m_reads + h_read_data->size())) / stats->m_time : 0.0f, + stats->m_time ? (1.0e-6f * (stats->m_bps + h_read_data->bps() )) / stats->m_time : 0.0f, + device >= 0 ? "gpu" : "cpu", + device >= 0 ? device : -device ); + + log_debug_cont(stderr, "\n"); + log_debug(stderr," peak memory : %.1f GB\n", float( peak_resident_memory() ) / float(1024*1024*1024)); + + stats->m_reads += h_read_data->size(); + stats->m_bps += h_read_data->bps(); + stats->m_mutex.unlock(); + return true; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/sample_kmers.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/sample_kmers.h new file mode 100644 index 0000000000000000000000000000000000000000..30c479133cbb593968b6bdd05cf6f992b89a45e4 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/sample_kmers.h @@ -0,0 +1,149 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// sample_kmers.h +// + +#pragma once + +#include "utils.h" +#include +#include +#include +#include +#include +#include +#include +#include + +///@addtogroup nvLighterModule +///@{ + +/// +/// A small class implementing an nvbio::Pipeline sink stage building the sampled kmers filter +/// +struct SampleKmersStage +{ + typedef nvbio::io::SequenceDataHost argument_type; + + /// empty constructor + /// + SampleKmersStage() {} + + /// constructor + /// + ///\param _k kmer length + ///\param _alpha the sampling frequency + ///\param _filter_size the kmer Bloom filter's size, in bits + ///\param _filter_storage the kmer Bloom filter's storage + /// + SampleKmersStage( + const int _device, + const uint32 _k, + const float _alpha, + const uint64 _filter_size, + uint32* _filter_storage, + SequenceStats* _stats) : + device( _device ), + k( _k ), + alpha( _alpha ), + filter_size( _filter_size ), + filter_storage( _filter_storage ), + stats( _stats ) + {} + + /// process the next batch + /// + bool process(nvbio::PipelineContext& context); + + int device; + uint32 k; + float alpha; + uint64 filter_size; + uint32* filter_storage; + SequenceStats* stats; + + nvbio::for_each_enactor host_for_each; + nvbio::for_each_enactor device_for_each; +}; + + +/// +/// A small class implementing an nvbio::Pipeline sink stage building the trusted kmers filter +/// +struct TrustedKmersStage +{ + typedef nvbio::io::SequenceDataHost argument_type; + + /// default constructor + /// + TrustedKmersStage() {} + + /// constructor + /// + ///\param _k kmer length + ///\param _alpha the sampling frequency + ///\param _filter_size the kmer Bloom filter's size, in bits + ///\param _filter_storage the kmer Bloom filter's storage + /// + TrustedKmersStage( + const int _device, + const uint32 _k, + const uint64 _sampled_filter_size, + const uint32* _sampled_filter_storage, + const uint64 _trusted_filter_size, + uint32* _trusted_filter_storage, + const uint32* _threshold, + SequenceStats* _stats) : + device( _device ), + k( _k ), + sampled_filter_size( _sampled_filter_size ), + sampled_filter_storage( _sampled_filter_storage ), + trusted_filter_size( _trusted_filter_size ), + trusted_filter_storage( _trusted_filter_storage ), + threshold(_threshold), + stats( _stats ) + {} + + /// process the next batch + /// + bool process(nvbio::PipelineContext& context); + + int device; + uint32 k; + uint64 sampled_filter_size; + const uint32* sampled_filter_storage; + uint64 trusted_filter_size; + uint32* trusted_filter_storage; + const uint32* threshold; + SequenceStats* stats; + + nvbio::for_each_enactor host_for_each; + nvbio::for_each_enactor device_for_each; +}; + +///@} // group nvLighterModule diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/utils.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/utils.h new file mode 100644 index 0000000000000000000000000000000000000000..7441c09f5f1e07bd2c6983bf05defb02be0b754a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvLighter/utils.h @@ -0,0 +1,148 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// utils.h +// + +#pragma once + +#include +#include +#include + +enum { + ERROR_FREE = 0, + CORRECTIONS = 1, + UNFIXABLE = 2, + TRIMMED_READS = 3, + TRIMMED_BASES = 4 +}; + +typedef nvbio::uint8 uint8; +typedef nvbio::int16 int16; +typedef nvbio::uint16 uint16; +typedef nvbio::int32 int32; +typedef nvbio::uint32 uint32; +typedef nvbio::int64 int64; +typedef nvbio::uint64 uint64; +typedef nvbio::uint64_2 uint64_2; +typedef nvbio::uint64_4 uint64_4; + +//static const uint32 SAMPLED_KMERS_FILTER_K = 9; // optimal number of hashes for a Bloom filter with false probability rate of 0.01 +//static const uint32 TRUSTED_KMERS_FILTER_K = 11; // optimal number of hashes for a Bloom filter with false probability rate of 0.0005 +//static const uint32 SAMPLED_KMERS_FILTER_K = 7; // optimal number of hashes for a Bloom filter with false probability rate of 0.01 +//static const uint32 TRUSTED_KMERS_FILTER_K = 11; // optimal number of hashes for a Bloom filter with false probability rate of 0.0005 +static const uint32 SAMPLED_KMERS_FILTER_K = 5; // this parameter should theoretically achieve a worse false probability rate than 0.01, yet in practice it does better +static const uint32 TRUSTED_KMERS_FILTER_K = 8; // this parameter should theoretically achieve a worse false probability rate than 0.0005, yet in practice it does better + +struct hash_functor1 +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint64 operator() (const uint64 kmer) const { return nvbio::hash( kmer ); } +}; +struct hash_functor2 +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint64 operator() (const uint64 kmer) const { return nvbio::hash2( kmer ); } +}; + +enum { MAX_READ_LENGTH = 2048 }; + +struct KmerCode +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + KmerCode() : mask(0), code(0), len(0), invalid(-1) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + KmerCode(const int l) : mask(0), code(0), len(l), invalid(-1) + { + for (int i = 0 ; i < len; ++i) + { + mask = mask << 2u; + mask = mask | 3u; + } + } + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + KmerCode(const KmerCode& k) : mask(k.mask), code(k.code), len(k.len), invalid(k.invalid) + {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void restart() { code = 0ull ; invalid = -1 ; } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void push_back(const uint8 c) + { + if (invalid != -1) + invalid++; + + code = ((code << 2ull) & mask) | uint64(c & 3); + if (c >= 4) + invalid = 0; + + if (invalid >= len) + invalid = -1; + } + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void push_front(const uint8 c) + { + shift_right( 1 ); + + if (c >= 4) + invalid = len - 1; + + code = (code | ((uint64(c & 3)) << (2ull * (len - 1)))) & mask; + } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void shift_right(int k) + { + if (invalid != -1) + invalid -= k; + + code = (code >> (2ull * k)) & (mask >> (2ull * k)); + if (invalid < 0) + invalid = -1; + } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool is_valid() const { return invalid == -1; } + + uint64 mask; + uint64 code; + int len; + int invalid; +}; + +struct SequenceStats +{ + SequenceStats() : m_reads(0), m_bps(0), m_time(0) {} + + nvbio::Mutex m_mutex; + uint64 m_reads; + uint64 m_bps; + float m_time; +}; diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..341205796fb5ddf794c3bb80f8a3caf3159d337b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/CMakeLists.txt @@ -0,0 +1,19 @@ +nvbio_module("nvMicroAssembly") + +addsources( +haplotype_caller.cu +haplotype_caller.h +assembly.h +assembly_graph_inl.h +assembly_graph.h +kmers_inl.h +kmers.h +regions.h +bam_io.h +bam_io.cu +) + +include_directories(${PROJECT_SOURCE_DIR}/contrib/htslib ${PROJECT_SOURCE_DIR}/contrib/zlib) + +cuda_add_executable(nvMicroAssembly ${nvMicroAssembly_srcs}) +target_link_libraries(nvMicroAssembly htslib nvbio zlibstatic lz4 crcstatic ${SYSTEM_LINK_LIBRARIES}) diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/assembly.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/assembly.h new file mode 100644 index 0000000000000000000000000000000000000000..2cc26a05e1bef7714d180ae6a6deacf49a88094c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/assembly.h @@ -0,0 +1,65 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include + +#include "haplotype_caller.h" +#include "assembly_types.h" + +using namespace nvbio; + +void local_assembly(assembly_pipeline* pipeline) +{ + // [read correction] + + // create assembly graphs for given kmer size(s) + debruijn_graph assembly_graph; + assembly_graph.construct_graph( + pipeline->d_seq_set, + pipeline->d_active_region_ids, + pipeline->kmer_size, + false); + + printf("Constructed assembly graph for kmer size %u with %u nodes and %u edges \n", + pipeline->kmer_size, assembly_graph.n_nodes, assembly_graph.n_edges); + + //assembly_graph.print_dot_graph(pipeline->d_seq_set); + + // check complexity + + // assembly_graph.topological_sort(); + + // check for cycles + // post-process: pruning, dangling chain recovery... + + // find best paths + //assembly_graph.find_k_best_paths(pipeline->k_best_haplotypes); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/assembly_graph.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/assembly_graph.h new file mode 100644 index 0000000000000000000000000000000000000000..f44cbbef438948dbb6b87a117fe4326bde81be26 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/assembly_graph.h @@ -0,0 +1,135 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once +#include "assembly_types.h" + +using namespace nvbio; + +#define ASSEMBLY_MIN_BASE_QUALITY 6 + +struct debruijn_graph +{ + uint32 kmer_size; // kmer_size used to build the graph + uint32 n_nodes; + uint32 n_edges; + uint32 n_subgraphs; + + // global CSR representation + D_VectorSetKmerCoord nodes; + D_VectorU32 node_adjancency_map; + D_VectorU32 node_adj_offests; + D_VectorU32 node_out_degrees; + D_VectorU32 node_in_degrees; + D_VectorU32 edge_counts; // edge multiplicities + D_VectorU32 edge_weights; // transitions probabilities + D_VectorU8 edge_ref_flags; // flags each edge if the reference haplotype contains it + + D_VectorU32 node_in_adjancency_map; + D_VectorU32 node_in_adj_offests; + + // local active region subgraphs + D_VectorU32 subgraph_source_ids; + D_VectorU32 subgraph_sink_ids; + D_VectorU32 subgraph_n_nodes; + + // topological sort + D_VectorU32 topo_sorted_uids; // topologically sorted nodes + D_VectorU32 topo_sorted_offsets; + + // properties + D_VectorU8 low_complexity; + D_VectorU8 cycle_presence; // each sub-graph is marked 1 if it contains a cycle + + + // kernel view + struct view + { + D_VectorU32::plain_view_type node_adjancency_map; + D_VectorU32::plain_view_type node_adj_offests; + D_VectorU32::plain_view_type node_out_degrees; + D_VectorU32::plain_view_type node_in_degrees; + D_VectorU32::plain_view_type edge_counts; + D_VectorU32::plain_view_type edge_weights; + + D_VectorU32::plain_view_type subgraph_source_ids; + D_VectorU32::plain_view_type subgraph_sink_ids; + D_VectorU32::plain_view_type subgraph_n_nodes; + + D_VectorU32::plain_view_type topo_sorted_uids; + D_VectorU32::plain_view_type topo_sorted_offsets; + + D_VectorU8::plain_view_type cycle_presence; + + D_VectorU32::plain_view_type node_in_adjancency_map; + D_VectorU32::plain_view_type node_in_adj_offests; + }; + + operator view() { + view v = { + plain_view(node_adjancency_map), + plain_view(node_adj_offests), + plain_view(node_out_degrees), + plain_view(node_in_degrees), + plain_view(edge_counts), + plain_view(edge_weights), + plain_view(subgraph_source_ids), + plain_view(subgraph_sink_ids), + plain_view(subgraph_n_nodes), + plain_view(topo_sorted_uids), + plain_view(topo_sorted_offsets), + plain_view(cycle_presence), + plain_view(node_in_adjancency_map), + plain_view(node_in_adj_offests) + }; + return v; + } + + + // construction + bool construct_graph(const D_SequenceSet& sequence_set, const D_VectorU32& d_active_region_ids, + const uint32 kmer_size, const bool allow_low_complexity); + void compute_edge_weights(); + void compute_in_degrees(); + void compute_in_adjacencies(); + void compute_subgraph_n_nodes(); + void compute_complexity(); + + // validation + bool is_low_complexity(const uint32 subgraph_id) { return low_complexity[subgraph_id];} + bool has_cycles(const uint32 subgraph_id) { return cycle_presence[subgraph_id];} + + // search + void topological_sort(); + void find_k_best_paths(const uint32 k); + + // debugging + void print_dot_graph(const D_SequenceSet& sequence_set); +}; + +#include "assembly_graph_inl.h" + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/assembly_graph_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/assembly_graph_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..c87ab8629ae41964f5f85aec8a67d97dbab27738 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/assembly_graph_inl.h @@ -0,0 +1,668 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include "kmers.h" + +#define TOPO_SORT_LOCAL_NODE_SET_SIZE 200 +#define MAX_IN_DEGREE 20 + +struct graph_functor +{ + debruijn_graph::view graph; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + graph_functor(debruijn_graph::view _graph) : graph(_graph) { } +}; + +struct topological_sort_functor : public graph_functor +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + topological_sort_functor(debruijn_graph::view _graph) : graph_functor(_graph) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 graph_id) + { + const uint32 source = graph.subgraph_source_ids[graph_id]; + const uint32 n_nodes = graph.subgraph_n_nodes[graph_id]; + uint32 L_offset = graph.topo_sorted_offsets[graph_id]; // ordered UID output offset + uint32 n_sorted = 0; // number of nodes sorted so far + + uint32 S[TOPO_SORT_LOCAL_NODE_SET_SIZE]; // set of nodes with in-degree 0 + S[0] = source; + uint32 s_first = 0; + uint32 s_last = 1; + + while(s_last - s_first != 0) { + const uint32 n = S[s_first]; + // remove from S + s_first++; + + // add to ordered list + graph.topo_sorted_uids[L_offset + n_sorted] = n; + n_sorted++; + + // traverse the out neighbors + uint32 out_degree = graph.node_out_degrees[n]; + uint32 nbr_offset = graph.node_adj_offests[n]; + for(uint32 i = 0; i < out_degree; i++) { + uint32 m = graph.node_adjancency_map[nbr_offset + i]; + graph.node_in_degrees[m]--; + if(graph.node_in_degrees[m] == 0) { + // add to S + if(s_first > 0) { + s_first--; + S[s_first] = m; + } else { + if(s_last >= TOPO_SORT_LOCAL_NODE_SET_SIZE) { + printf("ERROR: Topological sort exceeded max locally allocated set size!\n"); + graph.cycle_presence[graph_id] = true; //TODO: handle this case + } + S[s_last] = m; + s_last++; + } + } + } + } + + if(n_sorted != n_nodes) { + printf("Found cycle! %u %u \n", n_sorted, n_nodes); + graph.cycle_presence[graph_id] = true; // found a cycle! + } + graph.cycle_presence[graph_id] = false; + } +}; + +struct find_k_best_paths_functor : public graph_functor +{ + const uint32 k; + uint32* topk_scores; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + find_k_best_paths_functor(debruijn_graph::view _graph, const uint32 _k, uint32* _topk_scores) : + graph_functor(_graph), k(_k), topk_scores(_topk_scores) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 graph_id) + { + const uint32 n_nodes = graph.subgraph_n_nodes[graph_id]; + const uint32 order_offset = graph.topo_sorted_offsets[graph_id]; + + for(uint32 i = 0; i < n_nodes; i++) { // for each node in topological order + const uint32 n = graph.topo_sorted_uids[order_offset + i]; + const uint32 in_degree = graph.node_in_degrees[n]; + const uint32 in_nbr_offset = graph.node_in_adj_offests[n]; + + // compute the top k paths to n + uint8 nbr_top_offsets[MAX_IN_DEGREE]; // keep track of how many paths consumed per in-neighbor + for(uint32 j = 0; j < k; j++) { + uint32 max_score = 0; + bool set_score = false; + for(uint32 v = 0; v < in_degree; v++) { + const uint32 m = graph.node_in_adjancency_map[in_nbr_offset + v]; + uint32 j_score_offset = nbr_top_offsets[v]*n_nodes + m; + if(topk_scores[j_score_offset] == 0) continue; + set_score = true; + + // find edge weight (TODO: pre-compute this) + uint32 edge_weight = 0; + for(uint32 l = 0; l < graph.node_out_degrees[m]; l++) { + if(graph.node_adjancency_map[graph.node_adj_offests[m + l]] == m) { + edge_weight = graph.edge_weights[graph.node_adj_offests[m + l]]; + break; + } + } + + uint32 new_score = topk_scores[j_score_offset] + edge_weight; + if(new_score > max_score) { + max_score = new_score; + nbr_top_offsets[v]++; + } + } + if(set_score) { + topk_scores[j*n_nodes + n] = max_score; + // TODO: keep pointers + } else { + break; // consumed all the paths to this node + } + } + } + } +}; + +struct edge_weights_functor : public graph_functor +{ + NVBIO_HOST_DEVICE + edge_weights_functor(debruijn_graph::view _graph) : graph_functor(_graph) { } + + NVBIO_DEVICE + void operator() (const uint32 node_uid) + { + const uint32 nbr_offset = graph.node_adjancency_map[node_uid]; + const uint32 out_degree = graph.node_in_degrees[node_uid]; + + uint32 total_support = 0; // TODO: compute as a reduction + for(uint32 i = 0; i < out_degree; i++) { + total_support += graph.edge_counts[nbr_offset + i]; + } + + for(uint32 i = 0; i < out_degree; i++) { + + graph.edge_weights[nbr_offset + i] = log10((float)graph.edge_counts[nbr_offset + i]) - log10((float)total_support); + } + + } +}; + +struct flip_edges : public graph_functor +{ + NVBIO_HOST_DEVICE + flip_edges(debruijn_graph::view _graph) : graph_functor(_graph) { } + + NVBIO_DEVICE // TODO: add atomicCAS to atomics.h for both host and device + void operator() (const uint32 node_uid) + { + const uint32 nbr_offset = graph.node_adjancency_map[node_uid]; + const uint32 n_nbrs = graph.node_in_degrees[node_uid]; + + for(uint32 i = 0; i < n_nbrs; i++) { + const uint32 nbr_uid = graph.node_adjancency_map[nbr_offset + i]; + const uint32 offset = graph.node_in_adj_offests[nbr_uid]; + // atomically get an index + uint32 idx = 0; + uint32 val = atomicCAS(&graph.node_in_adjancency_map[idx], (uint32) -1, node_uid); + while(val != (uint32) -1) { + idx++; + val = atomicCAS(&graph.node_in_adjancency_map[idx], (uint32) -1, node_uid); + } + } + + } +}; + +// converts a coordinate to the corresponding sequence -- used for debugging +template +struct coord_to_seq +{ + typedef typename string_set_type::string_type sequence; + const string_set_type string_set; + const uint32 kmer_size; + const SequenceSetKmerCoord* nodes; + uint8* sequences; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + coord_to_seq(const uint32 _kmer_size, const string_set_type _string_set, const SequenceSetKmerCoord* _nodes, uint8* _sequences) : + kmer_size(_kmer_size), string_set(_string_set), nodes(_nodes), + sequences(_sequences) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint64 node_idx) const + { + const SequenceSetKmerCoord node_coord = nodes[node_idx]; + const sequence seq = string_set[node_coord.x]; + const uint32 seq_pos = node_coord.y; + const uint64 offset = kmer_size * node_idx; + + for (uint32 i = 0; i < kmer_size; i++) { + uint8 c = dna_to_char(seq[seq_pos + i]); + sequences[offset + i] = c; + } + } +}; + + + +template +struct extract_active_region_source_sink +{ + const string_set_type string_set; + const SequenceSetKmerCoord* coords; + const uint32* seq_active_region_ids; + const uint32* global_to_UID_map; + const uint32* global_to_sorted_map; + uint32* source_ids; + uint32* sink_ids; + uint32 kmer_size; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + extract_active_region_source_sink(const string_set_type _string_set, const uint32 _kmer_size, + const SequenceSetKmerCoord* _coords, + const uint32* _seq_active_region_ids, const uint32* _global_to_UID_map, const uint32* _global_to_sorted_map, + uint32* _source_ids, uint32* _sink_ids): + string_set(_string_set), kmer_size(_kmer_size), + coords(_coords), seq_active_region_ids(_seq_active_region_ids), + global_to_UID_map(_global_to_UID_map), global_to_sorted_map(_global_to_sorted_map), + source_ids(_source_ids), sink_ids(_sink_ids) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 global_coord_idx) const + { + const SequenceSetKmerCoord source_coord = coords[global_to_sorted_map[global_coord_idx]]; + + // determine if the coord is the source coord of a reference sequence (first seq in each region) + if(global_coord_idx != 0 && coords[global_to_sorted_map[global_coord_idx - 1]].w == source_coord.w) return; + // set the source + source_ids[source_coord.w] = global_to_UID_map[source_coord.z]; + + // find and set the sink + const uint32 seq_len = string_set[source_coord.x].length(); + const uint32 n_kmers = seq_len - kmer_size + 1; + const SequenceSetKmerCoord sink_coord = coords[global_to_sorted_map[global_coord_idx + n_kmers - 1]]; // last coord of the ref + sink_ids[sink_coord.w] = global_to_UID_map[sink_coord.z]; + } +}; + +// construct a debruijn assembly graph with the given kmer length +bool debruijn_graph::construct_graph(const D_SequenceSet& d_sequence_set, const D_VectorU32& d_active_region_ids, + const uint32 _kmer_size, bool allow_low_complexity) +{ + kmer_size = _kmer_size; + D_KmerSet graph_kmer_set(d_sequence_set, d_active_region_ids); + + // --- NODE extraction --- + graph_kmer_set.kmer_size = kmer_size; + graph_kmer_set.gen_kmer_coords(); + graph_kmer_set.init_alloc_temp_space(); + graph_kmer_set.gen_kmer_64b_keys(); + graph_kmer_set.sort_kmers_by_64b_keys(); + graph_kmer_set.partition_kmers_by_uniqueness(); + graph_kmer_set.gen_global_to_sorted_id_map(); + graph_kmer_set.mark_unique_kmers(); + graph_kmer_set.extract_super_kmers(); // handle kmers that are repeats + segmented_sort_super_kmers_lexicographic( + graph_kmer_set.string_set, + graph_kmer_set.n_super_coords, + graph_kmer_set.super_coords, + graph_kmer_set.super_prefix_uids, + graph_kmer_set.super_suffix_uids); + + // extract repeat kmer nodes (as well as U-R, R-R, and R-U repeat edges) + D_VectorU32 repeat_edges_from_uids; + D_VectorU32 repeat_edges_to_uids; + D_VectorU32 repeat_edge_counts; + graph_kmer_set.collapse_and_extract_non_overlaps(nodes, repeat_edges_from_uids, repeat_edges_to_uids, repeat_edge_counts); + + // extract unique kmer nodes + thrust::copy_n( + thrust::make_permutation_iterator( + thrust::make_permutation_iterator( // unique coordinates + graph_kmer_set.coords.begin(), + graph_kmer_set.kmers_64b_unique_idxs.begin()), + thrust::make_permutation_iterator( + graph_kmer_set.global_to_UID_map.begin(), // global id -> UID + thrust::make_transform_iterator( // coord -> global ids + thrust::make_permutation_iterator( // unique coordinates + graph_kmer_set.coords.begin(), + graph_kmer_set.kmers_64b_unique_idxs.begin()), + get_global_id()))), + graph_kmer_set.n_unique, + nodes.begin()); + + // extract the source and sink subgraph nodes (for each active region) + /*n_subgraphs = d_active_region_ids[d_active_region_ids.size()-1] + 1; + subgraph_source_ids.resize(n_subgraphs); + subgraph_sink_ids.resize(n_subgraphs); + thrust::for_each( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + graph_kmer_set.n_kmers, + extract_active_region_source_sink(d_sequence_set, kmer_size, + plain_view(graph_kmer_set.coords), plain_view(d_active_region_ids), + plain_view(graph_kmer_set.global_to_UID_map), plain_view(graph_kmer_set.global_to_sorted_id_map), + plain_view(subgraph_source_ids), plain_view(subgraph_sink_ids)));*/ + + printf("Number of kmers %u \n", graph_kmer_set.n_kmers); + printf("Number distinct kmers %u \n", graph_kmer_set.n_distinct); + printf("Number unique kmers %u \n", graph_kmer_set.n_unique); + + // --- ADJACENCY MAP construction --- + uint32 n_unique_nodes = graph_kmer_set.n_unique; + n_nodes = graph_kmer_set.n_unique + graph_kmer_set.n_repeat; + node_adj_offests.resize(n_nodes + 1); + node_out_degrees.resize(n_nodes); // number of outgoing edges per nodes + + // generate edge (k+1)mers + graph_kmer_set.kmer_size = kmer_size + 1; + graph_kmer_set.gen_kmer_coords(); + graph_kmer_set.filter_coords_by_prefix_uniqueness(graph_kmer_set.global_unique_flag_map); // keep only the edges starting with a unique kmer + graph_kmer_set.gen_kmer_64b_keys(); + graph_kmer_set.segmented_sort_kmers_by_64b_keys(); // to guarantee same prefix edges are consecutive by region + graph_kmer_set.count_kmers(); // U-U and U-R edge counts + + // get the prefix node UID of each U-U and U-R edge + D_VectorU32 unique_prefix_node_uids(graph_kmer_set.n_unique); + thrust::transform( + thrust::make_transform_iterator( + graph_kmer_set.kmers_64b_unique_idxs.begin(), + get_prefix_global_id_by_idx(plain_view(graph_kmer_set.coords))), + thrust::make_transform_iterator( + graph_kmer_set.kmers_64b_unique_idxs.begin() + graph_kmer_set.n_unique, + get_prefix_global_id_by_idx(plain_view(graph_kmer_set.coords))), + unique_prefix_node_uids.begin(), + global_to_uid(plain_view(graph_kmer_set.global_to_UID_map))); + + D_VectorU32 unique_suffix_node_uids(graph_kmer_set.n_unique); // TODO: fuse with above + thrust::transform( + thrust::make_transform_iterator( + graph_kmer_set.kmers_64b_unique_idxs.begin(), + get_suffix_global_id_by_idx(plain_view(graph_kmer_set.coords))), + thrust::make_transform_iterator( + graph_kmer_set.kmers_64b_unique_idxs.begin() + graph_kmer_set.n_unique, + get_suffix_global_id_by_idx(plain_view(graph_kmer_set.coords))), + unique_suffix_node_uids.begin(), + global_to_uid(plain_view(graph_kmer_set.global_to_UID_map))); + + // count the number of outgoing edges per unique kmer (i.e. of type U-U and U-R) + // reduce by UID (edges starting with the same unique kmer will be consecutive) + D_VectorU32 unique_prefix_uids_idx(n_unique_nodes); + D_VectorU32 unique_prefix_counts(n_unique_nodes); + uint32 n_unique_prefix_uids = thrust::reduce_by_key( + thrust::make_counting_iterator(0), + thrust::make_counting_iterator(0) + graph_kmer_set.n_unique, + thrust::constant_iterator(1), + unique_prefix_uids_idx.begin(), + unique_prefix_counts.begin(), + kmer_uid_eq(plain_view(unique_prefix_node_uids))).first - unique_prefix_uids_idx.begin(); + + // scatter counts based on UIDs + thrust::scatter( + unique_prefix_counts.begin(), + unique_prefix_counts.begin() + n_unique_prefix_uids, + thrust::make_permutation_iterator( + unique_prefix_node_uids.begin(), + unique_prefix_uids_idx.begin()), + node_out_degrees.begin()); + + // count the number of outgoing edges per repeat kmer (i.e. of type U-R, R-R and R-U) + thrust::sort_by_key( + repeat_edges_from_uids.begin(), + repeat_edges_from_uids.end(), + thrust::make_zip_iterator(thrust::make_tuple(repeat_edges_to_uids.begin(), repeat_edge_counts.begin()))); + + D_VectorU32 repeat_prefix_uids_idx(repeat_edges_from_uids.size()); + D_VectorU32 repeat_prefix_counts(repeat_edges_from_uids.size()); + uint32 n_repeat_prefix_uids = thrust::reduce_by_key( + thrust::make_counting_iterator(0), + thrust::make_counting_iterator(0) + repeat_edges_from_uids.size(), + thrust::constant_iterator(1), + repeat_prefix_uids_idx.begin(), + repeat_prefix_counts.begin(), + kmer_uid_eq (plain_view(repeat_edges_from_uids))).first - repeat_prefix_uids_idx.begin(); + + // we need to discard the beginning of this vector corresponding to U-R edges + // by counting the number of unique prefixes + thrust::device_vector temp_storage; + uint32 n_unique_prefixes = cuda::reduce( + n_repeat_prefix_uids, + thrust::make_transform_iterator( + thrust::make_permutation_iterator( + repeat_edges_from_uids.begin(), + repeat_prefix_uids_idx.begin()), + is_unique_uid(n_unique_nodes)), + thrust::plus(), + temp_storage); + + // scatter counts based on UIDs + thrust::scatter( + repeat_prefix_counts.begin() + n_unique_prefixes, + repeat_prefix_counts.begin() + n_repeat_prefix_uids, + thrust::make_permutation_iterator( + repeat_edges_from_uids.begin(), + repeat_prefix_uids_idx.begin() + n_unique_prefixes), + node_out_degrees.begin()); + + // prefix sum to get the offsets + cuda::inclusive_scan( + n_nodes, + node_out_degrees.begin(), + node_adj_offests.begin() + 1, + thrust::plus(), + temp_storage); + + // fill out the adjacency map: U-R, R-R, R-U edges + n_edges = node_adj_offests[n_nodes]; + node_adjancency_map.resize(n_edges); + edge_counts.resize(n_edges); + thrust::for_each( + repeat_prefix_uids_idx.begin(), + repeat_prefix_uids_idx.begin() + n_repeat_prefix_uids, + extract_repeat_adjacencies( + plain_view(node_adj_offests), + plain_view(repeat_edges_from_uids), + plain_view(repeat_edges_to_uids), + plain_view(repeat_edge_counts), + plain_view(node_adjancency_map), + plain_view(edge_counts))); + + // fill out U-U edges + thrust::for_each( + unique_prefix_uids_idx.begin(), + unique_prefix_uids_idx.begin() + n_unique_prefix_uids, + extract_unique_adjacencies( + plain_view(node_adj_offests), + plain_view(unique_prefix_node_uids), + plain_view(unique_suffix_node_uids), + plain_view(graph_kmer_set.kmers_counts), + plain_view(node_adjancency_map), + plain_view(edge_counts))); + +// // TODO: prune low weight chains +// // TODO: merge chains + + return true; +} + +// --- note: the functionality below has not yet been fully tested + +void debruijn_graph::compute_edge_weights() +{ + edge_weights.resize(n_edges); + thrust::for_each( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + n_nodes, + edge_weights_functor(*this)); +} + +// compute the in-degree of each node in the graph +// the number of times a node UID occurs in the adjacency map +// is the node's in-degree +void debruijn_graph::compute_in_degrees() +{ + // sort the adjacency map + D_VectorU32 adj_map(node_adjancency_map); + thrust::sort(adj_map.begin(), adj_map.end()); + + D_VectorU32 distinct_node_UIDs(n_nodes); + D_VectorU32 counts(n_nodes); + uint32 n_distinct = thrust::reduce_by_key( + adj_map.begin(), + adj_map.end(), + thrust::make_constant_iterator(1), + distinct_node_UIDs.begin(), + counts.begin()).first - distinct_node_UIDs.begin(); + + node_in_degrees.resize(n_nodes); + thrust::scatter( + counts.begin(), + counts.begin() + n_distinct, + distinct_node_UIDs.begin(), + node_in_degrees.begin()); + + // prefix sum to get the offsets + thrust::device_vector temp_storage; + node_in_adj_offests.resize(n_nodes + 1); + cuda::inclusive_scan( + n_nodes, + node_in_degrees.begin(), + node_in_adj_offests.begin() + 1, + thrust::plus(), + temp_storage); +} + +void debruijn_graph::compute_in_adjacencies() +{ + // sort the adjacency map + node_in_adjancency_map.resize(n_edges); + thrust::fill(node_in_adjancency_map.begin(), node_in_adjancency_map.end(), (uint32) -1); + + thrust::for_each( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + n_nodes, + flip_edges(*this)); +} + +void debruijn_graph::compute_subgraph_n_nodes() +{ + // sort the adjacency map + D_VectorU32 active_region_ids(n_nodes); + thrust::transform( + nodes.begin(), + nodes.begin() + n_nodes, + active_region_ids.begin(), + get_kmer_reg_id()); + + thrust::sort(active_region_ids.begin(), active_region_ids.end()); + + D_VectorU32 active_regions(n_subgraphs); + D_VectorU32 counts(n_subgraphs); + uint32 n_distinct = thrust::reduce_by_key( + active_region_ids.begin(), + active_region_ids.end(), + thrust::make_constant_iterator(1), + active_regions.begin(), + counts.begin()).first - active_regions.begin(); + + subgraph_n_nodes.resize(n_subgraphs); + thrust::scatter( + counts.begin(), + counts.begin() + n_distinct, + active_regions.begin(), + subgraph_n_nodes.begin()); + + // prefix sum to get the offsets + thrust::device_vector temp_storage; + topo_sorted_offsets.resize(n_subgraphs + 1); + cuda::inclusive_scan( + n_subgraphs, + subgraph_n_nodes.begin(), + topo_sorted_offsets.begin() + 1, + thrust::plus(), + temp_storage); +} + +void debruijn_graph::compute_complexity() +{ + //returns true if n_repeats * 4 > n_unique +} + +// performs a topological sort of the nodes in each subgraph +// for each subgraph: all nodes are on a path from source to sink +void debruijn_graph::topological_sort() +{ + compute_in_degrees(); + compute_subgraph_n_nodes(); + + topo_sorted_uids.resize(n_nodes); + cycle_presence.resize(n_subgraphs); + thrust::for_each( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + n_subgraphs, + topological_sort_functor(*this)); +} + +void debruijn_graph::find_k_best_paths(const uint32 k) +{ + compute_in_degrees(); + compute_in_adjacencies(); + + // allocate top k space for each node + D_VectorU32 topk_scores(k*n_nodes); + thrust::for_each( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + n_subgraphs, + find_k_best_paths_functor(*this, k, plain_view(topk_scores))); +} + +// writes a DOT graph representation +void debruijn_graph::print_dot_graph(const D_SequenceSet& string_set) +{ + D_VectorU8 d_labels(kmer_size*n_nodes); + thrust::for_each( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + n_nodes, + coord_to_seq(kmer_size, string_set, plain_view(nodes), plain_view(d_labels))); + H_VectorU8 labels = d_labels; + + std::ofstream dot_file; + dot_file.open("cuda_test_graph.txt"); + for(uint64 i = 0; i < n_nodes; i++) { + uint32 n_out_edges = node_adj_offests[i+1] - node_adj_offests[i]; + uint64 offset = node_adj_offests[i]; + + uint64 label_offset = i*kmer_size; + std::string node_seq(labels.begin() + label_offset, labels.begin() + label_offset + kmer_size); + + for(uint32 j = 0; j < n_out_edges; j++) { + uint64 nbr_uid = node_adjancency_map[offset + j]; + //uint32 count = edge_counts[offset + j]; + + label_offset = nbr_uid*kmer_size; + std::string nbr_seq(labels.begin() + label_offset, labels.begin() + label_offset + kmer_size); + + dot_file << node_seq << "_" << i << "\t" << nbr_seq << "_" << nbr_uid << "\n"; + } + } + dot_file.close(); + + dot_file.open("cuda_test_graph.dot"); + + dot_file << "digraph assemblyGraphs { \n"; + for(uint64 i = 0; i < n_nodes; i++) { + uint32 n_out_edges = node_adj_offests[i+1] - node_adj_offests[i]; + uint64 offset = node_adj_offests[i]; + + uint64 label_offset = i*kmer_size; + std::string node_seq(labels.begin() + label_offset, labels.begin() + label_offset + kmer_size); + + for(uint32 j = 0; j < n_out_edges; j++) { + uint64 nbr_uid = node_adjancency_map[offset + j]; + uint32 count = edge_counts[offset + j]; + + label_offset = nbr_uid*kmer_size; + std::string nbr_seq(labels.begin() + label_offset, labels.begin() + label_offset + kmer_size); + + dot_file << node_seq << "_" << i << " -> " << nbr_seq << "_" << nbr_uid << " [label=\"" << count<< "\"];\n"; + } + } + + for(uint64 i = 0; i < n_nodes; i++) { + uint64 offset = i*kmer_size; + std::string node_seq(labels.begin() + offset, labels.begin() + offset + kmer_size); + dot_file << node_seq << "_" << i << " [label=\"" << node_seq << "\",shape=box];\n"; + } + dot_file << "}"; + dot_file.close(); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/assembly_types.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/assembly_types.h new file mode 100644 index 0000000000000000000000000000000000000000..ecc45224fe4e6ece68a4b0cda0cad7ee0f77b9b4 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/assembly_types.h @@ -0,0 +1,116 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +#define DNA_SYMBOL_BITS 2U +#define DNA_SYMBOL_MASK ((1u << DNA_SYMBOL_BITS) - 1u) + +typedef nvbio::vector D_VectorU8; +typedef nvbio::vector H_VectorU8; +typedef nvbio::vector D_VectorU16; +typedef nvbio::vector H_VectorU16; +typedef nvbio::vector D_VectorU32; +typedef nvbio::vector H_VectorU32; +typedef nvbio::vector D_VectorU64; +typedef nvbio::vector H_VectorU64; +typedef nvbio::vector D_VectorI32; +typedef nvbio::vector H_VectorI32; +typedef nvbio::vector D_VectorU64_2; +typedef nvbio::vector H_VectorU64_2; + +typedef nvbio::PackedVector H_VectorDNA; +typedef nvbio::PackedVector D_VectorDNA; +typedef H_VectorDNA::stream_type H_StreamDNA; +typedef H_VectorDNA::const_stream_type H_ConstStreamDNA; +typedef D_VectorDNA::stream_type D_StreamDNA; +typedef D_VectorDNA::const_stream_type D_ConstStreamDNA; + +typedef ConcatenatedStringSet H_SequenceSet; +typedef ConcatenatedStringSet D_SequenceSet; +typedef string_set_infix_coord_type SequenceSetKmerCoord; +typedef nvbio::vector H_VectorSetKmerCoord; +typedef nvbio::vector D_VectorSetKmerCoord; + +typedef nvbio::vector::iterator H_KmerIterator; +typedef nvbio::vector::iterator D_KmerIterator; + +typedef nvbio::io::SequenceDataAccess::sequence_string_set_type RefSequenceSet; + +typedef const ulong2* ranges_iterator; +typedef nvbio::SparseStringSet H_RefRangesSet; +typedef nvbio::SparseStringSet D_RefRangesSet; + + +/* BAM IO */ +typedef nvbio::PackedVector H_VectorDNA16; +typedef nvbio::PackedVector D_VectorDNA16; +struct cigar_op +{ + uint32 len:24, op:4; + + enum + { + OP_M = 0, + OP_I = 1, + OP_D = 2, + OP_N = 3, + OP_S = 4, + OP_H = 5, + OP_P = 6, + OP_MATCH = 7, + OP_X = 8, + }; + + NVBIO_HOST_DEVICE char ascii_op(void) const + { + return op == 0 ? 'M' : + op == 1 ? 'I' : + op == 2 ? 'D' : + op == 3 ? 'N' : + op == 4 ? 'S' : + op == 5 ? 'H' : + op == 6 ? 'P' : + op == 7 ? '=' : + 'X'; + } +}; + +typedef nvbio::vector D_VectorCigarOp; +typedef nvbio::vector H_VectorCigarOp; + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/bam_io.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/bam_io.cu new file mode 100644 index 0000000000000000000000000000000000000000..ce0e8798e40019f91f66e72e27bc59aa278958e1 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/bam_io.cu @@ -0,0 +1,284 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include "assembly_types.h" +#include "bam_io.h" + + +using namespace nvbio; + +/** ---- Read Functionality ---- **/ + +HTSBAMReader::HTSBAMReader(const char *fname) +{ + fp = sam_open(fname, "r"); + if (fp == NULL) { + throw nvbio::runtime_error("Could not open %s", fname); + } + header = sam_hdr_read(fp); + fp_offset = bgzf_tell(fp->fp.bgzf); + if (header == NULL) { + throw nvbio::runtime_error("Error parsing BAM file header"); + } +} + +HTSBAMReader::~HTSBAMReader() +{ + bam_hdr_destroy(header); + sam_close(fp); +} + +void HTSBAMReader::parse_aln_rec(BAM_alignment_batch_SoA& batch, bam1_t* b, H_VectorU32& cigar_temp) { + + if(batch.field_mask & BAM_POSITIONS) { + batch.positions.push_back(b->core.pos); + } + if(batch.field_mask & BAM_REFIDS) { + batch.refIDs.push_back(b->core.tid); + } + if(batch.field_mask & BAM_MAPQ) { + batch.bin.push_back(b->core.bin); + } + if(batch.field_mask & BAM_MAPQ) { + batch.mapq.push_back(b->core.qual); + } + if(batch.field_mask & BAM_FLAGS) { + batch.flags.push_back(b->core.flag); + } + if(batch.field_mask == BAM_ALL) { + batch.next_refIDs.push_back(b->core.mtid); + batch.next_positions.push_back(b->core.mpos); + } + + // data portion + uint32 offset = 0; + const uint64 read_name_off = batch.names.size(); + const uint32 read_name_len = b->core.l_qname; + if(batch.field_mask & BAM_NAMES) { + batch.names.resize(read_name_off + read_name_len + 1); + memcpy(&batch.names[read_name_off], b->data, read_name_len); + batch.names[read_name_off + read_name_len] = '\0'; + } + offset += read_name_len; + + BAM_CRQ_index crq_index(batch.cigars.size(), b->core.n_cigar, batch.reads.size(), b->core.l_qseq, batch.qualities.size(), b->core.l_qseq); + if(batch.field_mask & (BAM_CIGARS | BAM_QUALITIES | BAM_READS)) { + batch.crq_index.push_back(crq_index); + } + + const uint32 cigar_len = b->core.n_cigar; + if(batch.field_mask & BAM_CIGARS) { + cigar_temp.resize(cigar_len); + if (cigar_len) { + memcpy(&cigar_temp[0], b->data + offset, sizeof(uint32) * cigar_len); + for(uint32 c = 0; c < cigar_len; c++) { + cigar_op op; + op.op = cigar_temp[c] & 0xf; + op.len = cigar_temp[c] >> 4; + batch.cigars.push_back(op); + } + } + } + if (cigar_len) { + offset += sizeof(uint32)*cigar_len; + } + + if(batch.field_mask & BAM_READS) { + // figure out the length of the sequence data, rounded up to reach a dword boundary + const uint32 padded_read_len_bp = ((b->core.l_qseq + 7) / 8) * 8; + //const uint64 required_words = util::divide_ri(b->core.l_qseq, 8); + // make sure we have enough memory, then read in the sequence + batch.reads.resize(crq_index.read_start + padded_read_len_bp); + uint64 *storage = (uint64 *)batch.reads.addrof(crq_index.read_start); + memcpy(storage, b->data + offset, b->core.l_qseq / 2); + } + offset += b->core.l_qseq / 2; + + if(batch.field_mask & BAM_QUALITIES) { + batch.qualities.resize(crq_index.qual_start + b->core.l_qseq); + memcpy(&batch.qualities[crq_index.qual_start], b->data + offset, b->core.l_qseq); + } + offset += b->core.l_qseq; + + const uint32 aux_len = b->l_data - offset; + BAM_NAUX_index idx(batch.aux_data.size(), aux_len, read_name_off); + if(batch.field_mask & (BAM_AUX | BAM_NAMES)) { + batch.aln_index.push_back(idx); + } + if(batch.field_mask & BAM_AUX) { + const uint64 aux_start = batch.aux_data.size(); + batch.aux_data.resize(aux_start + aux_len); + memcpy(&batch.aux_data[aux_start], b->data + offset, aux_len); + } + offset += aux_len; +} + +// returns false if no records were read +bool HTSBAMReader::read_aln_batch(BAM_alignment_batch_SoA& batch, const uint64 batch_size) +{ + batch.reset(); + H_VectorU32 cigar_temp(64); + bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t)); + for(uint64 aln_id = 0; aln_id < batch_size; aln_id++) { + if (sam_read1(fp, header, b) < 0) break; + parse_aln_rec(batch, b, cigar_temp); + batch.num_alns++; + if(batch.num_alns % 10000000 == 0) { + printf("Loaded %llu records. \n", batch.num_alns); + } + } + + if (batch.num_alns == 0) { + return false; + } + return true; +} + +// loads reads overlapping the specified interval [s, e] (including the end points) +// the interval is 0-based (note: the record position is 0-based) +// this is a temporary hack -- should use bam index file instead +// returns false if no records were read +bool HTSBAMReader::read_aln_batch_intv(BAM_alignment_batch_SoA& batch, const uint32 contig, const uint64 start, const uint64 end) +{ + long new_offset = -1; + + H_VectorU32 cigar_temp(64); + bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t)); + while(1) { + if (sam_read1(fp, header, b) < 0) break; + if(b->core.tid > contig || (b->core.tid == contig && b->core.pos > end)) break; // reads one more record, should jump back + if(b->core.flag & BAM_FUNMAP) continue; + if(b->core.tid == contig && (bam_endpos(b) >= start)) { + if(new_offset == -1) { + new_offset = bgzf_tell(fp->fp.bgzf); + } + //printf("Read: %u %u %u\n", b->core.tid+1, b->core.pos+1, b->core.l_qseq); + parse_aln_rec(batch, b, cigar_temp); + batch.num_alns++; + } + } + + if(new_offset != -1) { + fp_offset = new_offset; + } + + bgzf_seek(fp->fp.bgzf, fp_offset, SEEK_SET); + + if (batch.num_alns == 0) { + return false; + } + return true; +} + +bool HTSBAMReader::read_aln_batch(std::vector& batch, const uint64 batch_size) { + bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t)); + uint64 aln_id = 0; + for(aln_id = 0; aln_id < batch_size; aln_id++) { + if (sam_read1(fp, header, b) < 0) break; + batch.push_back(b); + } + if (aln_id == 0) { + return false; + } + return true; +} + + +/** ---- Write Functionality ---- **/ + +HTSBAMWriter::HTSBAMWriter(const char *fname) +{ + fp = sam_open(fname, "wb"); + if (fp == NULL) { + throw nvbio::runtime_error("Could not open %s for writing", fname); + } +} + +HTSBAMWriter::~HTSBAMWriter() +{ + if (fp) { + sam_close(fp); + fp = NULL; + } +} + +void HTSBAMWriter::write_hdr(bam_hdr_t* header) +{ + sam_hdr_write(fp, header); +} + +// assumes the batch contains all the fields +void HTSBAMWriter::write_aln_batch(BAM_alignment_batch_SoA& batch, H_VectorU64 shuffle_idx, bam_hdr_t* header) +{ + bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t)); + b->data = (uint8_t*)malloc(ALNREC_SIZE_ALLOC); + b->m_data = ALNREC_SIZE_ALLOC; + for(uint64 idx = 0; idx < batch.num_alns; idx++) { + uint64 i = shuffle_idx[idx]; + BAM_CRQ_index crq = batch.crq_index[i]; + BAM_NAUX_index naux = batch.aln_index[i]; + bam1_core_t *c = &b->core; + c->tid = batch.refIDs[i]; + c->pos = batch.positions[i]; + c->bin = batch.bin[i]; + c->qual = batch.mapq[i]; + if(i < batch.num_alns-1) { + c->l_qname = batch.aln_index[i+1].name_start-naux.name_start-1; // remove the trailing \0 + } else { + c->l_qname = batch.names.size()-naux.name_start-1; + } + c->flag = batch.flags[i]; + c->n_cigar = crq.cigar_len; + c->l_qseq = crq.read_len; + c->mtid = batch.next_refIDs[i]; + c->mpos = batch.next_positions[i]; + c->isize = 0; //TODO + + b->l_data = c->l_qname*sizeof(uint8) + crq.cigar_len*sizeof(cigar_op) + crq.qual_len*sizeof(uint8) + + (crq.read_len/2)*sizeof(uint8) + naux.aux_data_len*sizeof(uint8); + if(b->l_data > b->m_data) { + b->data = (uint8_t*)realloc(b->data, b->l_data); + b->m_data = b->l_data; + } + //qname-cigar-seq-qual-aux + memcpy(b->data, &batch.names[naux.name_start], c->l_qname); + memcpy(b->data, &batch.cigars[crq.cigar_start], crq.cigar_len); + memcpy(b->data, (uint64 *)batch.reads.addrof(crq.read_start), crq.read_len/2); + memcpy(b->data, &batch.qualities[crq.qual_start], crq.qual_len); + memcpy(b->data, &batch.aux_data[naux.aux_data_start], naux.aux_data_len); + + sam_write1(fp, header, b); + } + free(b->data); + free(b); +} + +void HTSBAMWriter::write_aln_batch(std::vector& batch, H_VectorU64 shuffle_idx, bam_hdr_t* header) { + for(uint64 i = 0; i < batch.size(); i++) { + sam_write1(fp, header, batch[i]); + } +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/bam_io.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/bam_io.h new file mode 100644 index 0000000000000000000000000000000000000000..f50e07869ced9ce5fad77f9f40013381e0119519 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/bam_io.h @@ -0,0 +1,377 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include + +#include "assembly_types.h" + +using namespace nvbio; + +/**------------- BAM Format -------------**/ + +// BAM header +struct BAM_header +{ + uint8 magic[4]; // BAM magic string + int32 l_text; // length of the header text + std::string text; // the header text itself + int32 n_ref; // number of reference sequences + std::vector sq_names; // reference sequence names + H_VectorU32 sq_lengths; // reference sequence lengths +}; + +// BAM alignment record header +struct BAM_alignment_header +{ + int32 block_size; // length of the remainder of the alignment record + int32 refID; // reference sequence ID, -1 <= refID < n_ref (-1 for a read without a mapping position) + int32 pos; // 0-based leftmost coordinate + uint32 bin_mq_nl; // bin << 16 | MAPQ << 8 | l_read_name + uint32 flag_nc; // FLAG << 16 | n_cigar_op + int32 l_seq; // length of the sequence + int32 next_refID; // refID of the next segment (-1 <= next_refID < n_ref) + int32 next_pos; // 0-based leftmost pos of the next segment + int32 tlen; // template length + + uint32 bin(void) const { return bin_mq_nl >> 16; } + uint32 mapq(void) const { return (bin_mq_nl & 0xff00) >> 8; } + uint32 l_read_name(void) const { return bin_mq_nl & 0xff; } + uint32 flags(void) const { return flag_nc >> 16; } + uint32 num_cigar_ops(void) const { return flag_nc & 0xffff; } +}; + +// BAM alignment record +// consists of the alignment header followed by a variable-length +// data block; the auxiliary data is of block_size - ftell() bytes +struct BAM_alignment_record +{ + BAM_alignment_header header; // alignment info + H_VectorU8 data; // qname + cigar + seq + qual + aux +}; + +// contiguous batch of raw alignment records +struct BAM_alignment_batch_raw +{ + H_VectorU8 recs; // raw byte array of alignment records + H_VectorU64 offsets; // offsets into alignment records (num_recs + 1) +}; + +typedef enum +{ + BAM_NAMES = 1, + BAM_CIGARS = 2, + BAM_READS = 4, + BAM_QUALITIES = 8, + BAM_FLAGS = 16, + BAM_POSITIONS = 32, + BAM_REFIDS = 64, + BAM_MAPQ = 128, + BAM_AUX = 256, + BAM_BIN = 512, + BAM_ALL = 0xFFFF +} BAM_field_masks; + +typedef enum +{ + BAM_FLAGS_PAIRED = 1, + BAM_FLAGS_PROPER_PAIR = 2, + BAM_FLAGS_UNMAPPED = 4, + BAM_FLAGS_MATE_UNMAPPED = 8, + BAM_FLAGS_REVERSE = 16, + BAM_FLAGS_MATE_REVERSE = 32, + BAM_FLAGS_READ_1 = 64, + BAM_FLAGS_READ_2 = 128, + BAM_FLAGS_SECONDARY = 256, + BAM_FLAGS_QC_FAILED = 512, + BAM_FLAGS_DUPLICATE = 1024 +} BAM_alignment_flags; + + +// ----- SoA Functionality ------ + +// CRQ: cigars, reads, qualities +struct BAM_CRQ_index +{ + uint64 cigar_start, cigar_len; + uint64 read_start, read_len; + uint64 qual_start, qual_len; + + BAM_CRQ_index(): cigar_start(0), cigar_len(0), read_start(0), read_len(0), qual_start(0), qual_len(0) { } + BAM_CRQ_index(uint64 cigar_start, uint64 cigar_len, uint64 read_start, uint64 read_len, uint64 qual_start, uint64 qual_len) + : cigar_start(cigar_start), cigar_len(cigar_len), read_start(read_start), read_len(read_len), + qual_start(qual_start), qual_len(qual_len) { } +}; + +struct BAM_NAUX_index +{ + uint64 aux_data_start; + uint32 aux_data_len; + uint64 name_start; + + BAM_NAUX_index() : aux_data_start(0), aux_data_len(0), name_start(0) { } + BAM_NAUX_index(uint64 aux_data_start, uint32 aux_data_len, uint64 name_start) + : aux_data_start(aux_data_start), aux_data_len(aux_data_len), name_start(name_start) { } +}; + +#define H_BATCH_SIZE_ALLOC 10000000U +#define ALNREC_SIZE_ALLOC 512 + +typedef nvbio::vector D_VectorCRQIndex; +typedef nvbio::vector H_VectorCRQIndex; + +// batch of alignment records as SoA +// host-only now +struct BAM_alignment_batch_SoA +{ + BAM_alignment_batch_SoA(): field_mask(BAM_ALL), num_alns(0) { reserve(); } + BAM_alignment_batch_SoA(uint32 fields): field_mask(fields), num_alns(0) { reserve(); } + + uint32 field_mask; // record fields stored + uint64 num_alns; + H_VectorCigarOp cigars; + H_VectorDNA16 reads; + H_VectorU16 bin; + H_VectorU8 qualities; + H_VectorU16 flags; + H_VectorU32 positions; + H_VectorU32 refIDs; + H_VectorU8 mapq; + H_VectorU8 aux_data; + H_VectorU8 names; + H_VectorU32 next_positions; + H_VectorU32 next_refIDs; + nvbio::vector crq_index; // CRQ: cigars, reads, qualities + nvbio::vector aln_index; // names, aux + + void reserve() + { + if(field_mask & BAM_POSITIONS) positions.reserve(H_BATCH_SIZE_ALLOC); + if(field_mask & BAM_REFIDS) refIDs.reserve(H_BATCH_SIZE_ALLOC); + if(field_mask & BAM_BIN) bin.reserve(H_BATCH_SIZE_ALLOC); + if(field_mask & BAM_MAPQ) mapq.reserve(H_BATCH_SIZE_ALLOC); + if(field_mask & BAM_FLAGS) flags.reserve(H_BATCH_SIZE_ALLOC); + if(field_mask & (BAM_CIGARS | BAM_QUALITIES | BAM_READS)) crq_index.reserve(H_BATCH_SIZE_ALLOC); + if(field_mask & BAM_CIGARS) cigars.reserve(H_BATCH_SIZE_ALLOC * 32); + if(field_mask & BAM_READS) reads.reserve(H_BATCH_SIZE_ALLOC * 125); + if(field_mask & BAM_QUALITIES) qualities.reserve(H_BATCH_SIZE_ALLOC * 125); + if(field_mask & (BAM_AUX | BAM_NAMES)) aln_index.reserve(H_BATCH_SIZE_ALLOC); + if(field_mask & BAM_AUX) aux_data.reserve(H_BATCH_SIZE_ALLOC * 64); + if(field_mask & BAM_NAMES) names.reserve(H_BATCH_SIZE_ALLOC * 256); + if(field_mask == BAM_ALL) { + next_positions.reserve(H_BATCH_SIZE_ALLOC); + next_refIDs.reserve(H_BATCH_SIZE_ALLOC); + } + } + + void allocate(const BAM_alignment_batch_SoA& size_batch) + { + if(field_mask & BAM_POSITIONS) positions.resize(size_batch.positions.size()); + if(field_mask & BAM_REFIDS) refIDs.resize(size_batch.refIDs.size()); + if(field_mask & BAM_BIN) bin.resize(size_batch.bin.size()); + if(field_mask & BAM_MAPQ) mapq.resize(size_batch.mapq.size()); + if(field_mask & BAM_FLAGS) flags.resize(size_batch.flags.size()); + if(field_mask & (BAM_CIGARS | BAM_QUALITIES | BAM_READS)) crq_index.resize(size_batch.crq_index.size()); + if(field_mask & BAM_CIGARS) cigars.resize(size_batch.cigars.size()); + if(field_mask & BAM_READS) reads.resize(size_batch.reads.size()); + if(field_mask & BAM_QUALITIES) qualities.resize(size_batch.qualities.size()); + if(field_mask & (BAM_AUX | BAM_NAMES)) aln_index.resize(size_batch.aln_index.size()); + if(field_mask & BAM_AUX) aux_data.resize(size_batch.aux_data.size()); + if(field_mask & BAM_NAMES) names.resize(size_batch.names.size()); + if(field_mask == BAM_ALL) { + next_positions.resize(size_batch.next_positions.size()); + next_refIDs.resize(size_batch.next_refIDs.size()); + } + } + + void reset() + { + num_alns = 0; + positions.clear(); + refIDs.clear(); + bin.clear(); + mapq.clear(); + flags.clear(); + crq_index.clear(); + cigars.clear(); + reads.clear(); + qualities.clear(); + aln_index.clear(); + aux_data.clear(); + names.clear(); + next_positions.clear(); + next_refIDs.clear(); + } + + void free() + { + // force the memory to be freed by swapping + positions = H_VectorU32(); + refIDs = H_VectorU32(); + bin = H_VectorU16(); + mapq = H_VectorU8(); + flags = H_VectorU16(); + cigars = H_VectorCigarOp(); + reads = H_VectorDNA16(); + qualities = H_VectorU8(); + aux_data = H_VectorU8(); + names = H_VectorU8(); + crq_index = nvbio::vector(); + aln_index = nvbio::vector(); + next_positions = H_VectorU32(); + next_refIDs = H_VectorU32(); + } + + void shuffle(BAM_alignment_batch_SoA& batch_out, H_VectorU64 shuffle_idx) { + batch_out.allocate(*this); + + if(field_mask & BAM_POSITIONS) { + thrust::gather(shuffle_idx.begin(), shuffle_idx.end(), positions.begin(), batch_out.positions.begin()); + } + if(field_mask & BAM_REFIDS) { + thrust::gather(shuffle_idx.begin(), shuffle_idx.end(), refIDs.begin(), batch_out.refIDs.begin()); + } + if(field_mask & BAM_BIN) { + thrust::gather(shuffle_idx.begin(), shuffle_idx.end(), bin.begin(), batch_out.bin.begin()); + } + if(field_mask & BAM_MAPQ) { + thrust::gather(shuffle_idx.begin(), shuffle_idx.end(), mapq.begin(), batch_out.mapq.begin()); + } + if(field_mask & BAM_FLAGS) { + thrust::gather(shuffle_idx.begin(), shuffle_idx.end(), flags.begin(), batch_out.flags.begin()); + } + if(field_mask & BAM_QUALITIES) { + uint64 cigar_offset = 0; + for(uint64 i = 0; i < num_alns; i++) { + uint64 idx = shuffle_idx[i]; + thrust::copy_n(cigars.begin() + crq_index[idx].cigar_start, crq_index[idx].cigar_len, + batch_out.cigars.begin() + cigar_offset); + batch_out.crq_index[i].cigar_start = cigar_offset; + batch_out.crq_index[i].cigar_len = crq_index[idx].cigar_len; + cigar_offset += crq_index[idx].cigar_len; + } + } + if(field_mask & BAM_READS) { + uint64 read_offset = 0; + for(uint64 i = 0; i < num_alns; i++) { + uint64 idx = shuffle_idx[i]; + uint64* data_in = (uint64 *)reads.addrof(crq_index[idx].read_start); + uint64* data_out = (uint64 *)batch_out.reads.addrof(read_offset); + memcpy(data_out, data_in, crq_index[idx].read_len/2); + batch_out.crq_index[i].read_start = read_offset; + batch_out.crq_index[i].read_len = crq_index[idx].read_len; + const uint32 padded_read_len_bp = ((crq_index[idx].read_len + 7) / 8) * 8; + read_offset += padded_read_len_bp; + } + } + if(field_mask & BAM_QUALITIES) { + uint64 qual_offset = 0; + for(uint64 i = 0; i < num_alns; i++) { + uint64 idx = shuffle_idx[i]; + thrust::copy_n(qualities.begin() + crq_index[idx].qual_start, crq_index[idx].qual_len, + batch_out.qualities.begin() + qual_offset); + batch_out.crq_index[i].qual_start = qual_offset; + batch_out.crq_index[i].qual_len = crq_index[idx].qual_len; + qual_offset += crq_index[idx].qual_len; + } + } + if(field_mask & BAM_AUX) { + uint64 aux_offset = 0; + for(uint64 i = 0; i < num_alns; i++) { + uint64 idx = shuffle_idx[i]; + thrust::copy_n(aux_data.begin() + aln_index[idx].aux_data_start, aln_index[idx].aux_data_len, batch_out.aux_data.begin() + aux_offset); + batch_out.aln_index[i].aux_data_start = aux_offset; + batch_out.aln_index[i].aux_data_len = aln_index[idx].aux_data_len; + aux_offset += aln_index[idx].aux_data_len; + } + } + if(field_mask & BAM_NAMES){ + uint64 names_offset = 0; + for(uint64 i = 0; i < num_alns; i++) { + uint64 idx = shuffle_idx[i]; + uint32 len; + if(idx < num_alns-1) { + len = aln_index[idx+1].name_start-aln_index[idx].name_start; + } else { + len = names.size()-aln_index[idx].name_start; + } + thrust::copy_n(names.begin() + aln_index[idx].name_start, len, batch_out.names.begin() + names_offset); + batch_out.aln_index[i].name_start = names_offset; + names_offset += len; + } + } + if(field_mask == BAM_ALL) { + thrust::gather(shuffle_idx.begin(), shuffle_idx.end(), next_positions.begin(), batch_out.next_positions.begin()); + thrust::gather(shuffle_idx.begin(), shuffle_idx.end(), next_refIDs.begin(), batch_out.next_refIDs.begin()); + } + } +}; + + +/**------------------- BAM Reader -------------**/ + +// htslib-based BAM file reader +struct HTSBAMReader +{ +public: + bam_hdr_t* header; + +private: + samFile* fp; + long fp_offset; + +public: + HTSBAMReader(const char *fname); + ~HTSBAMReader(); + + bool read_aln_batch(std::vector& batch, const uint64 batch_size = 1000000); + bool read_aln_batch(BAM_alignment_batch_SoA& batch, const uint64 batch_size = 1000000); + bool read_aln_batch_intv(BAM_alignment_batch_SoA& batch, const uint32 contig = 1u, const uint64 start = 0u, const uint64 end = 1000000); +private: + bool read_hdr(void); + void parse_aln_rec(BAM_alignment_batch_SoA& batch, bam1_t* b, H_VectorU32& cigar_temp); +}; + +/**------------------- BAM Writer -------------**/ + +// htslib-based BAM file writer +struct HTSBAMWriter +{ +private: + samFile* fp; + +public: + HTSBAMWriter(const char *fname); + ~HTSBAMWriter(); + + void write_hdr(bam_hdr_t* header); + void write_aln_batch(std::vector& batch, H_VectorU64 shuffle_idx, bam_hdr_t* header); + void write_aln_batch(BAM_alignment_batch_SoA& batch, H_VectorU64 shuffle_idx, bam_hdr_t* header); +}; diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/haplotype_caller.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/haplotype_caller.cu new file mode 100644 index 0000000000000000000000000000000000000000..1745eb51ee35775ed57db8004a584c7c42408883 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/haplotype_caller.cu @@ -0,0 +1,106 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include + +#include "assembly_types.h" +#include "haplotype_caller.h" +#include "bam_io.h" +#include "assembly.h" + +// loads reads overlapping multiple active regions from a BAM file +// BAM index files should be used instead for better performance +// note: start_pos is 0-based +void load_active_regions_temp(const char* bam_fname, + const uint32 n_active_regions, + const uint32 active_region_size, + uint32 start_pos, + H_VectorActiveRegions& active_regions, + BAM_alignment_batch_SoA& h_batch) +{ + HTSBAMReader bam_reader(bam_fname); + for(uint32 i = 0; i < n_active_regions; i++) { + active_region r; + r.genome_loc.contig = 0u; + r.genome_loc.start = start_pos; + r.genome_loc.stop = start_pos + active_region_size - 1; + r.read_batch_offset = h_batch.num_alns; + if(!bam_reader.read_aln_batch_intv(h_batch, r.genome_loc.contig, r.genome_loc.start, r.genome_loc.stop)) { + printf("No reads were loaded for region %u starting at %u. \n", i, start_pos); + } + r.n_reads = h_batch.num_alns - r.read_batch_offset; + active_regions.push_back(r); + start_pos += active_region_size; + } +} + +// main local de-novo assemply engine +void haplotype_caller_pipeline(const char* ref_fname, const char* bam_fname, + const uint32 n_regions, const uint32 start_pos /*0-based*/) +{ + cuda::Timer timer; + assembly_pipeline pipeline; + + // 1. load the genome reference + io::SequenceDataHost h_ref; + if (!io::load_sequence_file(DNA_N, &h_ref, ref_fname)) { + printf("Failed to load the FASTA reference file \"%s\"\n", ref_fname); + exit(1); + } + + // 2. load BAM alignments (BAM must be sorted) + BAM_alignment_batch_SoA h_read_batch(BAM_READS); + H_VectorActiveRegions h_active_regions; + load_active_regions_temp(bam_fname, n_regions, pipeline.active_region_size, start_pos, h_active_regions, h_read_batch); + + // 3. prepare the active region reference haplotypes and the read sequences for assembly + pipeline.prep_assembly_sequences(h_ref, h_read_batch, h_active_regions); + + // 4. de-novo local assembly + timer.start(); + local_assembly(&pipeline); + timer.stop(); + printf("Total assembly time : %.8fs\n", timer.seconds()); + +} + +int main(int argc, char **argv) +{ + if(argc < 3) { + printf("Usage: ./assembly [options] \n"); + exit(1); + } + + try { + haplotype_caller_pipeline(argv[1], argv[2], atoi(argv[3]), atoi(argv[4])-1 /*1-based */); + } + catch (nvbio::runtime_error& e) { + printf("%s\n", e.what()); + exit(1); + } + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/haplotype_caller.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/haplotype_caller.h new file mode 100644 index 0000000000000000000000000000000000000000..8844834c1adeec962c954760229f3ddcc6cf0cea --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/haplotype_caller.h @@ -0,0 +1,138 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + + +#pragma once + +#include "assembly_types.h" +#include "bam_io.h" +#include "kmers.h" +#include "regions.h" +#include "assembly_graph.h" + +using namespace nvbio; + +/** HaplotypeCaller Pipeline Structures **/ + +struct assembly_pipeline +{ + // ---- Parameters ---- + + const static uint32 kmer_size = 10; + const static uint32 k_best_haplotypes = 12; + const static uint32 active_region_size = 100; + const static bool increaze_kmer_size_for_cycles = false; + const static uint32 max_reads_in_region_per_sample = 1000; + const static uint32 min_reads_per_alignment_start = 5; + const static uint32 max_ref_size = 1000; + const static uint32 ref_padding = 100; + + // ---- Data ---- + + // reference genome + io::SequenceDataDevice d_ref; + RefSequenceSet d_ref_seqs; + + // active regions + D_VectorU32 d_active_region_ids; + D_VectorU32 d_active_region_offsets; + + // read sequences + D_SequenceSet d_seq_set; + D_VectorDNA d_set_seqs_data; + D_VectorU64 d_set_offsets; + + // read correction + + // assembly results + + + // load the reference genome on the device + void load_ref(io::SequenceDataHost& h_ref) { + d_ref = h_ref; + const io::SequenceDataAccess d_ref_access(d_ref); + d_ref_seqs = d_ref_access.sequence_string_set(); + } + + void prep_assembly_sequences(const io::SequenceDataHost& h_ref, + const BAM_alignment_batch_SoA& read_batch, + const H_VectorActiveRegions active_regions) + { + // prepare the ref haplotypes and the reads overlapping the regions + const io::SequenceDataAccess h_ref_access(h_ref); + const io::SequenceDataAccess::sequence_string_set_type h_ref_seqs = h_ref_access.sequence_string_set(); + uint64 n_seqs = read_batch.num_alns + active_regions.size(); // includes the ref sequences + H_VectorDNA h_seqs; + H_VectorU64 h_offsets(n_seqs+1); + H_VectorU32 h_active_region_ids(n_seqs); + H_VectorU32 h_active_region_offsets(active_regions.size()); + uint64 offset = 0u; + + // load each active region + uint64 n_seqs_loaded = 0; + for(uint32 r = 0; r < active_regions.size(); r++) { + h_active_region_offsets[r] = n_seqs_loaded; + // reference haplotype + active_region region = active_regions[r]; + const io::SequenceDataAccess::sequence_string_set_type::string_type seq = h_ref_seqs[region.genome_loc.contig]; + for(uint32 i = region.genome_loc.start; i <= region.genome_loc.stop; i++) { + h_seqs.push_back(char_to_dna(nvbio::to_char(seq[i]))); + } + h_active_region_ids[n_seqs_loaded] = r; + h_offsets[n_seqs_loaded] = offset; + offset += region.genome_loc.stop - region.genome_loc.start + 1; + n_seqs_loaded++; + + // reads overlapping the region + for(uint64 i = region.read_batch_offset; i < region.read_batch_offset + region.n_reads; i++) { + for(uint32 j = 0; j < read_batch.crq_index[i].read_len; j += 2) { + uint8 c1 = read_batch.reads[read_batch.crq_index[i].read_start + j]; + uint8 c2 = read_batch.reads[read_batch.crq_index[i].read_start + j + 1]; + h_seqs.push_back(char_to_dna(iupac16_to_char(c2))); + h_seqs.push_back(char_to_dna(iupac16_to_char(c1))); + } + h_offsets[n_seqs_loaded] = offset; + h_active_region_ids[n_seqs_loaded] = r; + offset += read_batch.crq_index[i].read_len; + n_seqs_loaded++; + } + } + h_offsets[n_seqs_loaded] = offset; + + cuda::Timer timer; + timer.start(); + d_active_region_ids = h_active_region_ids; + //d_active_region_offsets = h_active_region_offsets; + d_set_seqs_data = h_seqs; + D_StreamDNA stream((uint32*) plain_view(d_set_seqs_data.m_storage)); + d_set_offsets = h_offsets; + d_seq_set = D_SequenceSet(n_seqs_loaded, stream, nvbio::plain_view(d_set_offsets)); + timer.stop(); + printf("Total input data transfer time : %.8fs\n", timer.seconds()); + printf("Loaded %llu sequences \n", n_seqs_loaded); + } +}; diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/kmers.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/kmers.h new file mode 100644 index 0000000000000000000000000000000000000000..dd3ba17e767e2411f13284ef709c53210ecc1b51 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/kmers.h @@ -0,0 +1,131 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include "assembly_types.h" + +using namespace nvbio; + +#define MAX_TEMP_SPACE_BATCHES 5 + +// set of kmers from a set of sequences +template +struct D_KmerSet +{ + const string_set_type string_set; // string set from which the kmers are extracted + D_VectorU32 active_region_ids; // active region id of each sequence in the set + uint32 kmer_size; // kmer size used to extract the kmers + + D_VectorSetKmerCoord coords; // coordinates in the sequence set + D_VectorU64 kmers_64b; // kmer keys: 64-bit compacted kmer sequence + D_VectorU64 kmers_64b_distinct; // distinct kmer keys + + D_VectorU32 kmers_64b_unique_idxs; // indices to unique kmers in the sorted coordinate vector + D_VectorU32 kmers_64b_repeat_idxs; // indices to unique kmers in the sorted coordinate vector + D_VectorU32 global_to_sorted_id_map;// map[i] = sorted array index of coord with global id i + D_VectorU32 global_to_UID_map; // map from global id to the kmer UID + D_VectorU8 global_unique_flag_map; // map[i] = 1 if kmer with global id i is unique; 0, otherwise + + D_VectorU32 kmers_counts; // number of occurrences of each kmer in the set + + uint32 n_kmers; // total number of kmers in the set + uint32 n_distinct; // number of distinct kmer keys in the set + uint32 n_unique; // number of distinct unique kmers (unique := kmer does not occur more than once in a sequence) + uint32 n_repeat; // number of non-unique kmers that are extracted as graph nodes + + + // super kmers (to handle non-unique kmers) + D_VectorSetKmerCoord super_coords; + D_VectorU32 super_prefix_uids; + D_VectorU32 super_suffix_uids; + uint32 n_super_coords; + + // scratch space + D_VectorU32 scratch_u32; + uint32 n_alloc; + uint32 selector; + + D_KmerSet(): kmer_size(0), n_kmers(0), n_distinct(0), n_unique(0), n_repeat(0), n_super_coords(0), + n_alloc(0), selector(0) {} + D_KmerSet(const string_set_type _string_set, const uint32 _kmer_size): + string_set(_string_set), kmer_size(_kmer_size), + n_kmers(0), n_distinct(0), n_unique(0), n_repeat(0), n_super_coords(0), + n_alloc(0), selector(0) { } + D_KmerSet(const string_set_type _string_set, const D_VectorU32& _active_region_ids): + string_set(_string_set), active_region_ids(_active_region_ids), + kmer_size(0), n_kmers(0), n_distinct(0), n_unique(0), n_repeat(0), n_super_coords(0), + n_alloc(0), selector(0) { } + + void gen_kmer_coords(); + void gen_kmer_64b_keys(); + void sort_kmers_by_64b_keys(); + void segmented_sort_kmers_by_64b_keys(); + template + void sort_kmers_by_64b_keys_meta(const meta_iterator_type meta_data); + void sort_kmers_by_64b_keys_seqid(); + template + void sort_kmers_by_64b_keys_seqid_meta(const meta_iterator_type meta_data); + void count_kmers_rle(); + void count_kmers(); + void count_distinct_by_prefix(D_VectorU32& prefix_unique_id_map); + void partition_kmers_by_uniqueness(); + void gen_prefix_map(); + void gen_global_unique_map(); + void gen_global_UID_map(); + void gen_global_to_sorted_id_map(); + void mark_unique_kmers(); + void filter_coords_by_prefix_uniqueness(const D_VectorU8& unique_map); + void extract_super_kmers(); + void collapse_and_extract_non_overlaps(D_VectorSetKmerCoord& kmers_out, D_VectorU32& prefix_ids_out, + D_VectorU32& suffix_ids_out, D_VectorU32& counts_out); + void count_distinct_by_prefix(); + + + void init_alloc_temp_space() + { + n_alloc = MAX_TEMP_SPACE_BATCHES; + scratch_u32.resize(n_alloc*n_kmers); + } + + D_VectorU32::iterator get_scratch_space(uint32 size) + { + if((size > n_kmers) || ((selector + 1) > MAX_TEMP_SPACE_BATCHES)) { + printf("Requested more memory than batch size \n"); + exit(-1); + } + selector++; + return scratch_u32.begin() + (selector-1)*n_kmers; + } + + void reset_scratch_space() + { + selector = 0; + } +}; + +#include "kmers_inl.h" diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/kmers_inl.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/kmers_inl.h new file mode 100644 index 0000000000000000000000000000000000000000..6e5ce71a0ef3d386eea1d30c64521fb92c06dfb0 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/kmers_inl.h @@ -0,0 +1,1630 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include +#include +#include + +#include "assembly_types.h" + +/* K-mer Extraction/Counting/Uniqueness Functionality */ + +// extract the string set sequence id from the kmer coordinates +struct get_kmer_seq_id : public thrust::unary_function +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const SequenceSetKmerCoord kmer_coord) const + { + return kmer_coord.x; + } +}; + +struct get_kmer_reg_id +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const SequenceSetKmerCoord kmer_coord) const + { + return kmer_coord.w; + } +}; + +// extract the kmer size from the kmer coordinates +struct get_kmer_size : public thrust::unary_function +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const SequenceSetKmerCoord kmer_coord) const + { + return kmer_coord.z - kmer_coord.y; + } +}; + +struct get_global_id : public thrust::unary_function +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const SequenceSetKmerCoord coord) const + { + return coord.z; + } +}; + +// store the global kmer id in its coordinate +struct set_global_id +{ + SequenceSetKmerCoord* coords; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + set_global_id(SequenceSetKmerCoord* coords) : coords(coords) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 idx) const + { + coords[idx].z = idx; + } +}; + +// store the global kmer id and the active region id in its coordinate +struct set_global_id_region_id +{ + SequenceSetKmerCoord* coords; + const uint32* active_region_ids; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + set_global_id_region_id(SequenceSetKmerCoord* coords, const uint32* _active_region_ids) : + coords(coords), active_region_ids(_active_region_ids) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 idx) const + { + SequenceSetKmerCoord& coord = coords[idx]; + coord.z = idx; // since the kmer size is fixed, can reuse this field + coord.w = active_region_ids[coord.x]; + } +}; + +// maps from the coordinate of a kmer +// to the global id of its prefix +struct get_prefix_global_id : public thrust::unary_function +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const SequenceSetKmerCoord coord) const + { + return coord.z + coord.x; + } +}; + +// maps from the id of a kmer +// to the global id of its prefix +struct get_prefix_global_id_by_idx : public thrust::unary_function +{ + const SequenceSetKmerCoord* coords; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + get_prefix_global_id_by_idx(const SequenceSetKmerCoord* _coords): + coords(_coords) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const uint32 idx) const + { + const SequenceSetKmerCoord coord = coords[idx]; + return coord.z + coord.x; + } +}; + +// maps from the id of a kmer +// to the global id of its suffix +struct get_suffix_global_id_by_idx : public thrust::unary_function +{ + const SequenceSetKmerCoord* coords; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + get_suffix_global_id_by_idx(const SequenceSetKmerCoord* _coords): + coords(_coords) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const uint32 idx) const + { + const SequenceSetKmerCoord coord = coords[idx]; + return coord.z + coord.x + 1; + } +}; + +// creates a map from the id of a kmer +// to the global id of its prefix +struct compute_prefix_global_id +{ + const SequenceSetKmerCoord* coords; + uint32* prefix_ids; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + compute_prefix_global_id(const SequenceSetKmerCoord* _coords, uint32* _prefix_ids): + coords(_coords), prefix_ids(_prefix_ids) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 id) const + { + const SequenceSetKmerCoord coord = coords[id]; + prefix_ids[id] = coord.z + coord.x; + } +}; + +// creates a map from the id of a kmer +// to the global id of its suffix +struct compute_suffix_global_id +{ + const SequenceSetKmerCoord* coords; + uint32* suffix_ids; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + compute_suffix_global_id(const SequenceSetKmerCoord* _coords, uint32* _suffix_ids): + coords(_coords), suffix_ids(_suffix_ids) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 id) const + { + const SequenceSetKmerCoord coord = coords[id]; + suffix_ids[id] = coord.z + coord.x + 1; + } +}; + +// maps kmer global id to its UID +struct global_to_uid : public thrust::unary_function +{ + const uint32* uid_map; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + global_to_uid(const uint32* _uid_map) : uid_map(_uid_map) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const uint32 global_id) const + { + return uid_map[global_id]; + } +}; + +// creates a map from the global id to the id in the sorted array +struct global_to_sorted_id +{ + uint32* global_to_sorted_id_map; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + global_to_sorted_id(uint32* _map) : global_to_sorted_id_map(_map) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const thrust::tuple idx_coord) const + { + const uint32 idx = thrust::get<0>(idx_coord); + const SequenceSetKmerCoord coord = thrust::get<1>(idx_coord); + global_to_sorted_id_map[coord.z] = idx; // TODO: not coalesced + } +}; + +// compute the kmer keys: 64-bit compacted kmer sequence +template +struct kmers_to_64b_functor +{ + typedef typename string_set_type::string_type sequence; + const string_set_type string_set; + const uint32 kmer_size; + const uint32 dna_symbol_size; + const uint32 symbol_mask; + + NVBIO_HOST_DEVICE + kmers_to_64b_functor(const uint32 _kmer_size, const uint32 _dna_symbol_size, const string_set_type _string_set) : + kmer_size(_kmer_size), dna_symbol_size(_dna_symbol_size), symbol_mask((1u << dna_symbol_size) - 1u), + string_set(_string_set) {} + + NVBIO_HOST_DEVICE + uint64 operator() (const SequenceSetKmerCoord kmer_coord) const + { + const sequence seq = string_set[kmer_coord.x]; + const uint32 seq_pos = kmer_coord.y; + const uint32 seq_len = seq.length(); + + uint64 kmer_key = 0u; + for (uint32 i = 0; i < kmer_size; i++) { + kmer_key |= uint64(seq_pos + i < seq_len ? (seq[seq_pos + i] & symbol_mask) : 0u) << ((kmer_size-1-i)*dna_symbol_size); //(i*dna_symbol_size); + } + return kmer_key; + } +}; + +// equality based on kmer key and sequence id coordinate +struct kmer_key_sid_eq +{ + const uint64* keys; + const SequenceSetKmerCoord* coords; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + kmer_key_sid_eq(const uint64* _keys, const SequenceSetKmerCoord* _coords): + keys(_keys), coords(_coords) { } + + NVBIO_HOST_DEVICE bool operator()(const uint32 i, const uint32 j) + { + return keys[i] == keys[j] && coords[i].x == coords[j].x; + } +}; + +// equality based on kmer key and region id coordinate +struct kmer_key_rid_eq +{ + const uint64* keys; + const SequenceSetKmerCoord* coords; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + kmer_key_rid_eq(const uint64* _keys, const SequenceSetKmerCoord* _coords): + keys(_keys), coords(_coords) { } + + NVBIO_HOST_DEVICE bool operator()(const uint32 i, const uint32 j) + { + return keys[i] == keys[j] && coords[i].w == coords[j].w; + } +}; + +// equality based on sequence id and position +struct kmer_pos_sid_eq +{ + const SequenceSetKmerCoord* coords; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + kmer_pos_sid_eq(const SequenceSetKmerCoord* _coords): coords(_coords) { } + + NVBIO_HOST_DEVICE bool operator()(const uint32 i, const uint32 j) + { + const SequenceSetKmerCoord ci = coords[i]; + const SequenceSetKmerCoord cj = coords[j]; + return ci.y == cj.y && ci.x == cj.x; + } +}; + +// equality based on kmer key only +struct kmer_uid_eq +{ + const uint32* keys; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + kmer_uid_eq(const uint32* _keys) : keys(_keys) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool operator()(const uint32 i, const uint32 j) + { + return keys[i] == keys[j]; + } +}; + +// extract i-th word from the kmer in a string set +template +struct kmer_word_extractor_functor +{ + typedef typename string_set_type::string_type sequence; + const string_set_type string_set; + const uint32 dna_symbol_size; + const uint32 symbol_offset; + const uint32 symbols_per_word; + const SequenceSetKmerCoord* coords; + const uint32 i; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + kmer_word_extractor_functor(const string_set_type _string_set, const uint32 _dna_symbol_size, + const SequenceSetKmerCoord* _coords, const uint32 _i) : + dna_symbol_size(_dna_symbol_size), + symbol_offset(uint32(8u*sizeof(uint32)) - dna_symbol_size), + symbols_per_word(uint32(8u * sizeof(uint32))/dna_symbol_size), + coords(_coords), string_set(_string_set), i(_i) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const uint32 kmer_idx) const + { + SequenceSetKmerCoord kmer_coord = coords[kmer_idx]; + const uint32 kmer_pos = kmer_coord.y; + const uint32 kmer_size = kmer_coord.z - kmer_coord.y; // TODO: z-field is currently used for the global id, use kmer_size if fixed + const sequence seq = string_set[kmer_coord.x]; + const uint32 seq_len = seq.length(); + + uint32 word = 0u; + for (uint32 j = 0; j < kmer_size; j++) { + const uint32 jj = kmer_pos + i*symbols_per_word + j; + const uint32 c = jj < seq_len ? char_to_iupac16(dna_to_char(seq[jj])) : 0u; + word |= (c << (symbol_offset - j*dna_symbol_size)); + } + return word; + } +}; + +// add tuples of kmer and sequence counts +struct kmer_count_tuple_sum +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + thrust::tuple operator() (const thrust::tuple& x, const thrust::tuple& y) const + { + return thrust::tuple(thrust::get<0>(x) + thrust::get<0>(y), thrust::get<1>(x) + thrust::get<1>(y)); + } +}; + +// check if a kmer occurs more than once in at least one sequence +// given a tuple of the number of sequences that contain it and +// the number of times it occurs in all the sequences +struct is_unique_kmer +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool operator() (const thrust::tuple& nSeq_nOcc) const + { + return thrust::get<0>(nSeq_nOcc) >= thrust::get<1>(nSeq_nOcc); + } +}; + +// given the last id of a kmer in the group of consecutive equal kmers +// mark all identical consecutive kmers as unique in the map +struct mark_kmer_uniqueness +{ + uint8* is_unique_map; + const uint64* sorted_kmer_keys; + const SequenceSetKmerCoord* sorted_coords; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + mark_kmer_uniqueness(uint8* _is_unique_map, const uint64* _sorted_kmer_keys, const SequenceSetKmerCoord* _sorted_coords) : + is_unique_map(_is_unique_map), sorted_kmer_keys(_sorted_kmer_keys), sorted_coords(_sorted_coords) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 kmer_id) const + { + const uint64 kmer_key = sorted_kmer_keys[kmer_id]; + const uint32 rid = sorted_coords[kmer_id].w; + + int32 idx = kmer_id; + while(idx >= 0) { + if(sorted_coords[idx].w != rid || sorted_kmer_keys[idx] != kmer_key) break; + is_unique_map[idx] = 1; //TODO: thrust documentation states first, but last in experiments + idx--; + } + } +}; + +struct store_kmer_unique_ids +{ + uint32* unique_id_map; + const uint64* sorted_kmer_keys; + const SequenceSetKmerCoord* sorted_coords; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + store_kmer_unique_ids(uint32* _unique_id_map, const uint64* _sorted_kmer_keys, const SequenceSetKmerCoord* _sorted_coords) : + unique_id_map(_unique_id_map), sorted_kmer_keys(_sorted_kmer_keys), sorted_coords(_sorted_coords) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const thrust::tuple& uid_kid) const + { + const uint32 uid = thrust::get<0>(uid_kid); + const uint32 kid = thrust::get<1>(uid_kid); + const uint64 kmer_key = sorted_kmer_keys[kid]; + const uint32 rid = sorted_coords[kid].w; + + int32 idx = kid; + while(idx >= 0) { + if(sorted_coords[idx].w != rid || sorted_kmer_keys[idx] != kmer_key) break; + unique_id_map[idx] = uid; + idx--; //TODO: thrust documentation states first, but last in experiments + } + } +}; + +//struct populate_unique_kmer_data +//{ +// const uint64* sorted_kmer_keys; +// const SequenceSetKmerCoord* sorted_coords; +// const uint32* unique_kmer_idxs; +// +// // fill in unique kmer annotations +// uint8* unique_flag_map; +// uint32* unique_UID_map; +// +// NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +// populate_unique_kmer_data(const uint64* _sorted_kmer_keys, const SequenceSetKmerCoord* _coords, +// const uint32* _unique_kmer_idxs, uint8* _unique_flag_map, uint32* _unique_UID_map) : +// sorted_kmer_keys(_sorted_kmer_keys), sorted_coords(_coords), unique_kmer_idxs(_unique_kmer_idxs), +// unique_flag_map(_unique_flag_map), unique_UID_map (_unique_UID_map) { } +// +// NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +// void operator() (const uint32 uid) const +// { +// const uint32 unique_kmer_idx = unique_kmer_idxs[uid]; +// const uint64 key = sorted_kmer_keys[unique_kmer_idx]; // find the group of coordinates with this key and region +// const uint32 region = sorted_coords[unique_kmer_idx].w; +// uint32 global_kmer_id = sorted_coords[unique_kmer_idx].z; +// unique_flag_map[global_kmer_id] = 1; +// unique_UID_map[global_kmer_id] = uid; +// +// int32 idx = unique_kmer_idx - 1; +// while(idx >= 0) { +// if(sorted_kmer_keys[idx] != key || sorted_coords[idx].w != region) break; +// global_kmer_id = sorted_coords[idx].z; +// unique_flag_map[global_kmer_id] = 1; //TODO: thrust documentation states first, but last in experiments +// unique_UID_map[global_kmer_id] = uid; +// idx--; +// } +// } +//}; + +struct populate_unique_kmer_data +{ + const uint32* kmer_counts; + const SequenceSetKmerCoord* sorted_coords; + const uint32* unique_kmer_idxs; + + // fill in unique kmer annotations + uint8* unique_flag_map; + uint32* unique_UID_map; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + populate_unique_kmer_data(const uint32* _kmer_counts, const SequenceSetKmerCoord* _coords, + const uint32* _unique_kmer_idxs, uint8* _unique_flag_map, uint32* _unique_UID_map) : + kmer_counts(_kmer_counts), sorted_coords(_coords), unique_kmer_idxs(_unique_kmer_idxs), + unique_flag_map(_unique_flag_map), unique_UID_map (_unique_UID_map) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 uid) const + { + const uint32 unique_kmer_idx = unique_kmer_idxs[uid]; + const uint32 count = kmer_counts[uid]; + uint32 global_kmer_id = sorted_coords[unique_kmer_idx].z; + unique_flag_map[global_kmer_id] = 1; + unique_UID_map[global_kmer_id] = uid; + + for(uint32 i = 1; i < count; i++) { + global_kmer_id = sorted_coords[unique_kmer_idx - i].z; //TODO: thrust bug: pointer to last instead of first + unique_flag_map[global_kmer_id] = 1; // TODO: not coalesced + unique_UID_map[global_kmer_id] = uid; + } + } +}; + +// marks kmers that have a prefix satisfying the following: +// the prefix is unique and has a matching kmer +// (i.e. it is not the last (k-1)mer in the sequence) +struct mark_unique_prefix_kmer +{ + uint8* unique_prefix_map; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + mark_unique_prefix_kmer(uint8* _unique_prefix_map) : unique_prefix_map(_unique_prefix_map) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const thrust::tuple& uflag_prefix) const + { + const uint8 is_unique_prefix = thrust::get<0>(uflag_prefix); + const uint32 kmer_id = thrust::get<1>(uflag_prefix); + + if((is_unique_prefix == 1) && (kmer_id != (uint32) -1)) { + unique_prefix_map[kmer_id] = 1; // TODO: writes not coalesced + } + } +}; + +// ---------- Super-kmers: chains of consecutive kmers + +// given a non-unique kmer N, finds the closest unique predecessor and successor kmers in the sequence, P and S +// returns the new coordinate for the chain starting with the P and ending with S [P...N...S] +// returns a dummy coordinate (N.x, -1, -1, 0) if no such previous unique kmer exists +// TODO: could use shared memory here +template +struct extract_super_kmers_functor +{ + typedef typename string_set_type::string_type sequence; + const string_set_type string_set; + const uint32* repeat_global_ids; // global ids of the repeat kmers + const uint8* global_unique_flag_map; // unsorted + const uint32* global_UID_map; + const uint32* global_sorted_idx_map; + const SequenceSetKmerCoord* coords; // sorted + const uint32 kmer_size; + + // structures to populate + SequenceSetKmerCoord* super_coords; + uint32* prefix_uids; + uint32* suffix_uids; + + NVBIO_HOST_DEVICE + extract_super_kmers_functor(const uint32* _repeat_global_ids, + const uint8* _is_unique_map, const uint32* _global_UID_map, const uint32* _sorted_idx_map, + const SequenceSetKmerCoord* _coords, const string_set_type _string_set, const uint32 _kmer_size, + SequenceSetKmerCoord* _super_coords, uint32* _prefix_uids, uint32* _suffix_uids): + repeat_global_ids(_repeat_global_ids), global_unique_flag_map(_is_unique_map), global_UID_map(_global_UID_map), + global_sorted_idx_map(_sorted_idx_map), + coords(_coords), string_set(_string_set), kmer_size(_kmer_size), + super_coords(_super_coords), prefix_uids(_prefix_uids), suffix_uids(_suffix_uids){ } + + NVBIO_HOST_DEVICE + void operator()(const uint32 idx) const { + const uint32 global_id = repeat_global_ids[idx]; + const SequenceSetKmerCoord coord = coords[global_sorted_idx_map[global_id]]; + const sequence seq = string_set[coord.x]; + const uint32 seq_len = seq.length(); + SequenceSetKmerCoord super_coord = make_uint4(coord.x, (uint32)-1, (uint32)-1, coord.w); + uint32 prefix_id = (uint32) -1; + uint32 suffix_id = (uint32) -1; + + // find the unique predecessor + uint32 i = 1u; + while(i <= coord.y) { // search only this sequence + if(global_unique_flag_map[global_id-i] == 1) { + super_coord.y = coord.y - i; + super_coord.z = coord.y + kmer_size; + prefix_id = global_UID_map[global_id-i]; + break; + } + i++; + } + + if(super_coord.y != (uint32) -1) { // otherwise this chain will be ignored + // find the unique successor + i = 1u; + while(i < seq_len - coord.y - kmer_size + 1) { // search only until the end of the sequence + if(global_unique_flag_map[global_id+i] == 1) { + super_coord.z = coord.y + i + kmer_size; + suffix_id = global_UID_map[global_id+i]; + break; + } + i++; + } + } + + super_coords[idx] = super_coord; + prefix_uids[idx] = prefix_id; + suffix_uids[idx] = suffix_id; + } +}; + +template +struct print_super_kmer_functor +{ + typedef typename string_set_type::string_type sequence; + const string_set_type string_set; + const SequenceSetKmerCoord* coords; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + print_super_kmer_functor(const string_set_type _string_set, const SequenceSetKmerCoord* _coords) : + coords(_coords), string_set(_string_set) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 kmer_idx) const + { + SequenceSetKmerCoord kmer_coord = coords[kmer_idx]; + const uint32 kmer_pos = kmer_coord.y; + const uint32 kmer_size = kmer_coord.z - kmer_coord.y; + const sequence seq = string_set[kmer_coord.x]; + const uint32 seq_len = seq.length(); + + uint8 kmer_seq[14]; + for (uint32 k = 0; k < kmer_size; k++) { + uint8 c = iupac16_to_char(char_to_iupac16(dna_to_char(seq[kmer_pos + k]))); + kmer_seq[k] = c; + } + kmer_seq[kmer_size] = '\0'; + + printf("id: %llu, reg %u, seq %s \n", kmer_idx, kmer_coord.w, kmer_seq); + } +}; + +// returns true if the super kmer does not represent a valid chain of kmers +// based on the value of its unique predecessor id +struct is_invalid_super_kmer +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool operator()(const uint32 chain_prefix_id) + { + return chain_prefix_id == (uint32) -1; + } +}; + +struct is_unique_suffix_id : public thrust::unary_function +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool operator()(const uint32 suffix_id) + { + return suffix_id != (uint32) -1; + } +}; + +struct is_unique_uid : public thrust::unary_function +{ + const uint32 max_unique_uid; + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + is_unique_uid(const uint32 _max_unique_uid) : max_unique_uid(_max_unique_uid) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint8 operator()(const uint32 uid) + { + return uid < max_unique_uid; + } +}; + +struct is_repeat_kmer +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool operator()(const uint8 flag) + { + return (flag != 1); + } +}; + +// collapse kmers that start at the same position and belong to the same sequence +// by just returning the one with max length +struct collapse_same_start_kmers +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + thrust::tuple operator() ( + const thrust::tuple& x, + const thrust::tuple& y) const + { + const SequenceSetKmerCoord i = thrust::get<0>(x); + const SequenceSetKmerCoord j = thrust::get<0>(y); + + if(i.z > j.z) { + return x; + } + return y; + } +}; + +// computes the max prefix overlap with the closest lexicographically smaller super-kmer +// assumes that the function is not called for idx == 0 +// returns the number of kmers by which the chains overlap +// no overlap if the previous kmer is from a different region +template +struct find_max_kmer_overlaps +{ + typedef typename string_set_type::string_type sequence; + const string_set_type string_set; + const SequenceSetKmerCoord* coords; // sorted in lexicographic order + const uint32 kmer_size; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + find_max_kmer_overlaps(const string_set_type _string_set, const SequenceSetKmerCoord* _coords, + const uint32 _kmer_size): string_set(_string_set), coords(_coords), kmer_size(_kmer_size) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const uint32 idx) const + { + const SequenceSetKmerCoord coord_curr = coords[idx]; + const SequenceSetKmerCoord coord_prev = coords[idx-1]; + + if(coord_curr.w != coord_prev.w) return 0; + + const sequence seq_curr = string_set[coord_curr.x]; + const sequence seq_prev = string_set[coord_prev.x]; + const uint32 max_overlap = + (coord_curr.z - coord_curr.y) > (coord_prev.z - coord_prev.y) ? + (coord_prev.z - coord_prev.y) : (coord_curr.z - coord_curr.y); + + uint32 overlap = 0u; + for (uint32 j = 0; j < max_overlap; j++) + { + if(seq_curr[coord_curr.y + j] == seq_prev[coord_prev.y +j]) { + overlap++; + } else { + break; + } + } + uint32 n_ovp = (overlap >= kmer_size) ? overlap - kmer_size + 1 : 0; + return n_ovp; + } +}; + +// returns the number of kmers that did not overlap with the lexicographic +// super-kmer predecessor and are not unique +// i.e. total number of kmers in the chain - number of overlapping kmers +// does not count the unique first and last kmers +struct num_non_overlapped_repeats : public thrust::unary_function +{ + const SequenceSetKmerCoord* coords; + const uint32* suffix_kmer_ids; + const uint32* overlaps; + const uint32 kmer_size; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + num_non_overlapped_repeats(const SequenceSetKmerCoord* _coords, + const uint32* _suffix_kmer_ids, + const uint32* _overlaps, + const uint32 _kmer_size): + coords(_coords), suffix_kmer_ids(_suffix_kmer_ids), overlaps(_overlaps), kmer_size(_kmer_size) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const uint32 idx) const + { + const SequenceSetKmerCoord coord = coords[idx]; + uint32 len = coord.z - coord.y; + const uint32 n_kmers = (len >= kmer_size) ? len - kmer_size + 1 : 0; + + uint32 n_unique = 0; + if(overlaps[idx] == 0) { + n_unique++; // skip the header unique kmer if this is the first chain starting with this kmer + // otherwise, it will be included in the overlap + } + if(overlaps[idx] != n_kmers && suffix_kmer_ids[idx] != (uint32) -1) { // if not all the kmers overlapped + n_unique++; // skip the last unique kmer + } + return n_kmers - overlaps[idx] - n_unique; + } +}; + +struct num_adj_repeats : public thrust::unary_function +{ + const SequenceSetKmerCoord* coords; + const uint32* suffix_kmer_ids; + const uint32* overlaps; + const uint32 kmer_size; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + num_adj_repeats(const SequenceSetKmerCoord* _coords, + const uint32* _suffix_kmer_ids, + const uint32* _overlaps, + const uint32 _kmer_size): + coords(_coords), suffix_kmer_ids(_suffix_kmer_ids), overlaps(_overlaps), kmer_size(_kmer_size) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const uint32 idx) const + { + const SequenceSetKmerCoord coord = coords[idx]; + uint32 len = coord.z - coord.y; + const uint32 n_kmers = (len >= kmer_size) ? len - kmer_size + 1 : 0; // TODO: remove len check + + uint32 n_repeat_kmers_to_extract = n_kmers - overlaps[idx]; + if(overlaps[idx] == 0) { + n_repeat_kmers_to_extract--; // skip the first unique kmer + } + if(overlaps[idx] != n_kmers && suffix_kmer_ids[idx] != (uint32) -1) { // if not all the kmers overlapped + n_repeat_kmers_to_extract--; // skip the last unique kmer + } + + // number of kmers to extract will be the same as number of edges, plus RU edge if exists + uint32 n_adj = n_repeat_kmers_to_extract; + if(overlaps[idx] != n_kmers && suffix_kmer_ids[idx] != (uint32) -1) { // if not all the kmers overlapped + n_adj++; // add the last R-U edge + } + + return n_adj; + } +}; + +template +struct extract_non_overlapped_repeats +{ + typedef typename string_set_type::string_type sequence; + const string_set_type string_set; + const SequenceSetKmerCoord* super_coords; + const uint32* super_prefix_global_ids; + const uint32* super_suffix_global_ids; + const uint32* chain_offsets; + const uint32* adj_extraction_offsets; + const uint32* chain_overlaps; + const uint32 kmer_size; + const uint32 uid_offset; + const uniform_seeds_functor<> seeder; + + SequenceSetKmerCoord* kmers_out; + uint32* prefix_uids; + uint32* suffix_uids; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + extract_non_overlapped_repeats(const string_set_type _string_set, + const SequenceSetKmerCoord* _chain_coords, + const uint32* _chain_pref_gids, const uint32* _chain_suffix_gids, + const uint32* _chain_offsets, + const uint32* _adj_extraction_offsets, + const uint32* _chain_overlaps, + const uint32 _kmer_size, const uint32 _uid_offset, + SequenceSetKmerCoord* _kmers_out, uint32* _prefix_uids, uint32* _suffix_uids): + string_set(_string_set), + super_coords(_chain_coords), + super_prefix_global_ids(_chain_pref_gids), + super_suffix_global_ids(_chain_suffix_gids), + chain_offsets(_chain_offsets), + adj_extraction_offsets(_adj_extraction_offsets), + chain_overlaps(_chain_overlaps), + kmer_size(_kmer_size), uid_offset(_uid_offset), + kmers_out(_kmers_out), + prefix_uids(_prefix_uids), suffix_uids(_suffix_uids), + seeder(_kmer_size, 1u) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 idx) const + { + const SequenceSetKmerCoord chain_coord = super_coords[idx]; + const sequence seq = string_set[chain_coord.x]; + const uint32 seq_len = seq.length(); + const uint32 offset = chain_offsets[idx] + uid_offset; + const uint32 adj_offset = adj_extraction_offsets[idx]; + + const uint8 unique_suffix = (super_suffix_global_ids[idx] != (uint32) -1); + const uint32 n_kmers_to_extract = chain_offsets[idx+1] - chain_offsets[idx]; + + uint32 len = chain_coord.z - chain_coord.y; + const uint32 n_kmers = (len >= kmer_size) ? len - kmer_size + 1 : 0; // TODO: remove len check + + // if everything overlapped or nothing to extract and no possible R-U edge + if(chain_overlaps[idx] == n_kmers || (n_kmers_to_extract + unique_suffix == 0)) return; + + const uint32 kmer_id = (chain_coord.z - unique_suffix) - n_kmers_to_extract - kmer_size + 1; + for (uint32 j = 0; j < n_kmers_to_extract; j++) { + const uint2 kmer = seeder.seed(seq_len, kmer_id + j); + kmers_out[offset + j] = make_uint4(chain_coord.x, kmer.x, kmer.y, chain_coord.w); + + suffix_uids[adj_offset + j] = offset + j; + if(j < n_kmers_to_extract - 1) { + prefix_uids[adj_offset + j + 1] = offset + j; + } else { + if(unique_suffix == 1) { + prefix_uids[adj_offset + j + 1] = offset + j; // the last kmer is a prefix only to the RU (k+1)mer + } + } + } + if(unique_suffix == 1) { + suffix_uids[adj_offset + n_kmers_to_extract] = super_suffix_global_ids[idx]; + } + + // find the first prefix + if(chain_overlaps[idx] == 0 || chain_overlaps[idx] == 1) { + // overlap is just the unique header kmer or none + // use the unique id of the kmer + prefix_uids[adj_offset] = super_prefix_global_ids[idx]; + } else { + uint32 pred_chain_idx = idx - 1; + while(1) { + if(chain_overlaps[pred_chain_idx] >= chain_overlaps[idx]) { // not stored by the previous chain // >=2 + pred_chain_idx--; + } else { + // ignores the unique predecessor that overlapped and was not extracted + prefix_uids[adj_offset] = uid_offset + chain_offsets[pred_chain_idx] + (chain_overlaps[idx] - chain_overlaps[pred_chain_idx]) - 2; // last overlapped kmer + break; + } + } + } + } +}; + +struct count_overlapped_adjacencies +{ + const uint32* adj_extraction_offsets; + const uint32* overlaps; + uint32* counts; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + count_overlapped_adjacencies(const uint32* _adj_extraction_offsets, const uint32* _overlaps, uint32* _counts): + adj_extraction_offsets(_adj_extraction_offsets), + overlaps(_overlaps), + counts(_counts) { } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 idx) const + { + int32 n_to_update = overlaps[idx] - 1; + if(n_to_update <= 0) return; + + uint32 pred_chain_idx = idx - 1; + while(n_to_update > 0) { + const int32 pred_overlap = overlaps[pred_chain_idx] - 1; + if(pred_overlap >= n_to_update) { // everything is shared with the pred + pred_chain_idx--; + } else { + // update the counts in this pred chain + const uint32 n_update_pred = n_to_update - (pred_overlap > 0 ? pred_overlap : 0); + const uint32 pred_offset = adj_extraction_offsets[pred_chain_idx]; + for(uint32 i = 0; i < n_update_pred; i++) { + nvbio::atomic_add(&counts[pred_offset + i], 1); + } + n_to_update -= n_update_pred; + } + } + } +}; + +struct extract_repeat_adjacencies +{ + const uint32* node_offsets; + const uint32* prefix_uids; + const uint32* suffix_uids; + const uint32* edge_counts; + uint32* node_adj_map; + uint32* edge_counts_shuffled; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + extract_repeat_adjacencies(const uint32* _node_offsets, const uint32* _prefix_uids, + const uint32* _suffix_uids, const uint32* _edge_counts, + uint32* _node_adj_map, uint32* _edge_counts_shuffled): + node_offsets(_node_offsets), + prefix_uids(_prefix_uids), + suffix_uids(_suffix_uids), + edge_counts(_edge_counts), + node_adj_map(_node_adj_map), + edge_counts_shuffled(_edge_counts_shuffled){ } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 prefix_idx) const + { + const uint32 from_uid = prefix_uids[prefix_idx]; + const uint32 offset = node_offsets[from_uid]; + const uint32 num_edges = node_offsets[from_uid+1] - node_offsets[from_uid]; + + uint32 i = 0; + while(i < num_edges) { // at most this many prefixes to handle + if(prefix_idx < i) break; + const uint32 uid = prefix_uids[prefix_idx - i]; + if(uid != from_uid) break; // handled all the prefixes with the given UID + node_adj_map[offset + i] = suffix_uids[prefix_idx - i]; + edge_counts_shuffled[offset + i] = edge_counts[prefix_idx - i]; + i++; + } + } +}; + +struct extract_unique_adjacencies +{ + const uint32* node_offsets; + const uint32* prefix_uids; + const uint32* suffix_uids; + const uint32* edge_counts; + uint32* node_adj_map; + uint32* edge_counts_shuffled; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + extract_unique_adjacencies(const uint32* _node_offsets, const uint32* _prefix_uids, + const uint32* _suffix_uids, const uint32* _edge_counts, + uint32* _node_adj_map, uint32* _edge_counts_shuffled): + node_offsets(_node_offsets), + prefix_uids(_prefix_uids), + suffix_uids(_suffix_uids), + edge_counts(_edge_counts), + node_adj_map(_node_adj_map), + edge_counts_shuffled(_edge_counts_shuffled){ } + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint32 prefix_idx) const + { + const uint32 from_uid = prefix_uids[prefix_idx]; + const uint32 offset_last = node_offsets[from_uid+1] - 1; + const uint32 num_edges = node_offsets[from_uid+1] - node_offsets[from_uid]; + + uint32 i = 0; + uint32 n_unique = 0; + while(i < num_edges) { // at most this many prefixes to handle + if(prefix_idx < i) break; + const uint32 uid = prefix_uids[prefix_idx - i]; + if(uid != from_uid) break; // handled all the prefixes with the given UID + if(suffix_uids[prefix_idx - i] == (uint32) -1) { // repeat (TODO: fill with -1) + i++; + continue; + } + node_adj_map[offset_last - n_unique] = suffix_uids[prefix_idx - i]; // fill out from the end + edge_counts_shuffled[offset_last - n_unique] = edge_counts[prefix_idx - i]; + i++; + n_unique++; + } + } +}; + +// converts a coordinate to the corresponding sequence -- used for debugging +template +struct super_coord_to_seq +{ + typedef typename string_set_type::string_type sequence; + const string_set_type string_set; + const SequenceSetKmerCoord* super_coords; + const uint32* offsets; + uint8* sequences; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + super_coord_to_seq(const string_set_type _string_set, + const SequenceSetKmerCoord* _super_coords, const uint32* _offsets, + uint8* _sequences) : + string_set(_string_set), super_coords(_super_coords), offsets(_offsets), + sequences(_sequences) {} + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void operator() (const uint64 idx) const + { + const SequenceSetKmerCoord coord = super_coords[idx]; + const sequence seq = string_set[coord.x]; + const uint32 seq_pos = coord.y; + const uint32 offset = offsets[idx]; + + for (uint32 i = 0; i < coord.z - coord.y; i++) { + uint8 c = dna_to_char(seq[seq_pos + i]); + sequences[offset + i] = c; + } + } +}; + +// generate the coordinates of each kmer in the given set +template +void D_KmerSet::gen_kmer_coords() +{ + n_kmers = enumerate_string_set_seeds( + string_set, + uniform_seeds_functor<>(kmer_size, 1u), + coords); + + // record the index into the kmer array in the coordinates vector + thrust::for_each( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + n_kmers, + set_global_id_region_id(plain_view(coords), plain_view(active_region_ids))); +} + +// generate the 64-bit compacted kmer sequence keys +// assumes the coordinates have already been generated +template +void D_KmerSet::gen_kmer_64b_keys() +{ + kmers_64b.resize(n_kmers); + thrust::transform( + coords.begin(), + coords.begin() + n_kmers, + kmers_64b.begin(), + kmers_to_64b_functor(kmer_size, 2, string_set)); +} + +// sort the kmers based on the 64-bit kmer sequence key only +// assumes the keys have already been generated +template +void D_KmerSet::sort_kmers_by_64b_keys() +{ + // identical keys from the same sequence will be consecutive + // identical keys from the same region will also be consecutive + thrust::stable_sort_by_key( + kmers_64b.begin(), + kmers_64b.begin() + n_kmers, + coords.begin()); +} + +// stable sort the kmers based on the 64-bit kmer sequence key +// assumes the kmers are sorted by seq id only already +// assumes the keys have already been generated +template +template +void D_KmerSet::sort_kmers_by_64b_keys_meta(const meta_iterator_type meta_data) +{ + thrust::stable_sort_by_key( + kmers_64b.begin(), + kmers_64b.begin() + n_kmers, + thrust::make_zip_iterator(thrust::make_tuple(coords.begin(), meta_data))); +} + +// sort the kmers based on the 64-bit kmer sequence key by region +// assumes the keys have already been generated +template +void D_KmerSet::segmented_sort_kmers_by_64b_keys() +{ + // identical keys from the same sequence will be consecutive + // identical keys from the same region will also be consecutive + thrust::stable_sort_by_key( + kmers_64b.begin(), + kmers_64b.begin() + n_kmers, + coords.begin()); + + D_VectorU32::iterator region_ids = get_scratch_space(n_kmers); + thrust::transform( + coords.begin(), + coords.begin() + n_kmers, + region_ids, + get_kmer_reg_id()); + + thrust::stable_sort_by_key( + region_ids, + region_ids + n_kmers, + thrust::make_zip_iterator(thrust::make_tuple(coords.begin(), kmers_64b.begin()))); + + reset_scratch_space(); +} + +// sort kmers by key and set sequence id +// doing 2-pass sort to use the much faster thrust radix-sort +// instead of merge-sort on custom keys +template +void D_KmerSet::sort_kmers_by_64b_keys_seqid() +{ + thrust::stable_sort_by_key( + kmers_64b.begin(), + kmers_64b.begin() + n_kmers, + coords.begin()); + D_VectorU32 seq_ids(n_kmers); + thrust::transform( + coords.begin(), + coords.begin() + n_kmers, + seq_ids.begin(), + get_kmer_seq_id()); + thrust::stable_sort_by_key( + seq_ids.begin(), + seq_ids.begin() + n_kmers, + thrust::make_zip_iterator(thrust::make_tuple(kmers_64b.begin(), coords.begin()))); +} + +// sort kmers by key and set sequence id +// sort the additional meta-data along with the kmers +// doing 2-pass sort to use the much faster thrust radix-sort +// instead of merge-sort on custom keys +template +template +void D_KmerSet::sort_kmers_by_64b_keys_seqid_meta(const meta_iterator_type meta_data) +{ + thrust::stable_sort_by_key( + kmers_64b.begin(), + kmers_64b.begin() + n_kmers, + thrust::make_zip_iterator(thrust::make_tuple(coords.begin(), meta_data))); + D_VectorU32 seq_ids(n_kmers); + thrust::transform( + coords.begin(), + coords.begin() + n_kmers, + seq_ids.begin(), + get_kmer_seq_id()); + thrust::stable_sort_by_key( + seq_ids.begin(), + seq_ids.begin() + n_kmers, + thrust::make_zip_iterator(thrust::make_tuple(kmers_64b.begin(), coords.begin(), meta_data))); +} + +// sort kmers in lexicographic order - sorts the indices and returns the iterator +// kmer length can vary +// if kmer_size is set, all kmers are assumed to have this size +template +D_VectorU32::iterator sort_kmers_lexicographic(const string_set_type string_set, + D_VectorSetKmerCoord& coords, + const uint32 n_kmers, const uint32 fixed_kmer_size, + D_VectorU32& indices) +{ + const uint32 WORD_BITS = uint32(8u * sizeof(uint32)); + const uint32 SYMBOL_SIZE = 4u; + const uint32 SYMBOLS_PER_WORD = WORD_BITS/SYMBOL_SIZE; + + // maximum size of a kmer in the set + uint32 max_length = fixed_kmer_size; + if(fixed_kmer_size == 0u) { + max_length = thrust::reduce( + thrust::make_transform_iterator(coords.begin(), get_kmer_size()), + thrust::make_transform_iterator(coords.begin() + n_kmers, get_kmer_size()), + 0u, + thrust::maximum()); + } + + // maximum number of words needed to represent a kmer + const uint32 max_words = (max_length + SYMBOLS_PER_WORD-1)/SYMBOLS_PER_WORD; + + // ----- LSD radix-sort (word by word) ----- + //uint32 n_kmers = coords.size(); + D_VectorU32 radices(2*n_kmers); // kmer words (sort keys) + indices.resize(2*n_kmers); // kmer ids (values to be sorted) + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(n_kmers), + indices.begin()); + + // ping-pong buffers + cuda::SortBuffers sort_buffers; + cuda::SortEnactor sort_enactor; + sort_buffers.selector = 0; + sort_buffers.keys[0] = nvbio::device_view(radices); + sort_buffers.keys[1] = nvbio::device_view(radices) + n_kmers; + sort_buffers.values[0] = nvbio::device_view(indices); + sort_buffers.values[1] = nvbio::device_view(indices) + n_kmers; + + // sort in LSD order + for (int32 word_idx = max_words-1; word_idx >= 0; --word_idx) { + // extract the given radix word from each kmer + thrust::transform( + indices.begin() + sort_buffers.selector * n_kmers, + indices.begin() + sort_buffers.selector * n_kmers + n_kmers, + radices.begin() + sort_buffers.selector * n_kmers, + kmer_word_extractor_functor( + string_set, + SYMBOL_SIZE, + plain_view(coords), + word_idx)); + // sort the words + sort_enactor.sort(n_kmers, sort_buffers); + } + + return indices.begin() + sort_buffers.selector * n_kmers; +} + +template +void segmented_sort_super_kmers_lexicographic(const string_set_type string_set, uint32 n_coords, + D_VectorSetKmerCoord& super_coords, D_VectorU32& super_prefix_ids, D_VectorU32& super_suffix_ids) +{ + D_VectorU32 ids(n_coords); + D_VectorSetKmerCoord temp(super_coords); + D_VectorU32 temp_pref(super_prefix_ids); + D_VectorU32 temp_suf(super_suffix_ids); + + // first pass: sort by coord key + D_VectorU32::iterator sorted_ids = sort_kmers_lexicographic(string_set, super_coords, n_coords, 0u, ids); + thrust::gather( + sorted_ids, + sorted_ids + n_coords, + temp.begin(), + super_coords.begin()); + thrust::gather( + sorted_ids, + sorted_ids + n_coords, + thrust::make_zip_iterator(thrust::make_tuple(temp_pref.begin(), temp_suf.begin())), + thrust::make_zip_iterator(thrust::make_tuple(super_prefix_ids.begin(), super_suffix_ids.begin()))); + + // second pass: stable sort by region id => as a result coord keys will be sorted by region + //D_VectorU32 reg_ids(n_coords); + thrust::transform( + super_coords.begin(), + super_coords.begin() + n_coords, + ids.begin(), + get_kmer_reg_id()); + + thrust::stable_sort_by_key( + ids.begin(), + ids.begin() + n_coords, + thrust::make_zip_iterator(thrust::make_tuple(super_coords.begin(), super_prefix_ids.begin(), super_suffix_ids.begin()))); +} + +// count the kmer occurrences across all the sequences in the set +// assumes that the keys have been sorted +template +void D_KmerSet::count_kmers_rle() +{ + // count the number of distinct keys and extract them + kmers_64b_distinct.resize(n_kmers); + kmers_counts.resize(n_kmers); + D_VectorU8 d_temp_storage; + n_distinct = cuda::runlength_encode( + n_kmers, + kmers_64b.begin(), + kmers_64b_distinct.begin(), + kmers_counts.begin(), + d_temp_storage); +} + +// count the kmer occurrences across all the sequences in the set +// assumes that the keys have been sorted +template +void D_KmerSet::count_kmers() +{ + // count the number of distinct keys and extract them + kmers_64b_unique_idxs.resize(n_kmers); + kmers_counts.resize(n_kmers); + n_unique = thrust::reduce_by_key( + thrust::counting_iterator(0), + thrust::counting_iterator(0) + n_kmers, + thrust::constant_iterator(1), + kmers_64b_unique_idxs.begin(), + kmers_counts.begin(), + kmer_key_rid_eq(plain_view(kmers_64b), plain_view(coords))).first - kmers_64b_unique_idxs.begin(); +} + +// partition kmers by index into the sorted kmer key set +// based on whether they are unique or not +// a kmer is not unique if it occurs more than once in at least one sequence +template +void D_KmerSet::partition_kmers_by_uniqueness() +{ + // count the number of distinct kmers per sequence + D_VectorU32::iterator distinct_idxs_per_seq = get_scratch_space(n_kmers); + D_VectorU32::iterator count_per_seq = get_scratch_space(n_kmers); + thrust::counting_iterator ids(0); + uint64 n_distinct_per_seq = thrust::reduce_by_key( + ids, + ids + n_kmers, + thrust::constant_iterator(1), + distinct_idxs_per_seq, + count_per_seq, + kmer_key_sid_eq(plain_view(kmers_64b), plain_view(coords))).first - distinct_idxs_per_seq; + + D_VectorU32::iterator distinct_idxs = get_scratch_space(n_distinct_per_seq); + D_VectorU32::iterator seq_count = get_scratch_space(n_distinct_per_seq); // number of sequences containing the same kmer + D_VectorU32::iterator kmer_counts = get_scratch_space(n_distinct_per_seq); // number of kmer occurrences across all sequences + n_distinct = thrust::reduce_by_key( + distinct_idxs_per_seq, + distinct_idxs_per_seq + n_distinct_per_seq, + thrust::make_zip_iterator(thrust::make_tuple(thrust::constant_iterator(1), count_per_seq)), + distinct_idxs, + thrust::make_zip_iterator(thrust::make_tuple(seq_count, kmer_counts)), + kmer_key_rid_eq(plain_view(kmers_64b), plain_view(coords)), + kmer_count_tuple_sum()).first - distinct_idxs; + + // partition the distinct indices into unique and non-unique kmers + kmers_64b_unique_idxs.resize(n_distinct); + kmers_counts.resize(n_distinct); + n_unique = thrust::copy_if( + thrust::make_zip_iterator(thrust::make_tuple(distinct_idxs, kmer_counts)), + thrust::make_zip_iterator(thrust::make_tuple(distinct_idxs + n_distinct, kmer_counts + n_distinct)), + thrust::make_zip_iterator(thrust::make_tuple(seq_count, kmer_counts)), + thrust::make_zip_iterator(thrust::make_tuple(kmers_64b_unique_idxs.begin(), kmers_counts.begin())), + is_unique_kmer()) - thrust::make_zip_iterator(thrust::make_tuple(kmers_64b_unique_idxs.begin(), kmers_counts.begin())); + + reset_scratch_space(); +} + +template +void D_KmerSet::gen_global_unique_map() +{ + D_VectorU8 unique_map_sorted(n_kmers); + thrust::for_each( + kmers_64b_unique_idxs.begin(), + kmers_64b_unique_idxs.begin() + n_unique, + mark_kmer_uniqueness(plain_view(unique_map_sorted), plain_view(kmers_64b), plain_view(coords))); + + global_unique_flag_map.resize(n_kmers); + thrust::gather( + global_to_sorted_id_map.begin(), + global_to_sorted_id_map.begin() + n_kmers, + unique_map_sorted.begin(), + global_unique_flag_map.begin()); +} + +template +void D_KmerSet::gen_global_UID_map() +{ + D_VectorU32 id_map_sorted(n_kmers); + thrust::fill(id_map_sorted.begin(), id_map_sorted.begin() + n_kmers, (uint32) -1); + thrust::for_each( + thrust::make_zip_iterator(thrust::make_tuple(thrust::make_counting_iterator(0u), kmers_64b_unique_idxs.begin())), + thrust::make_zip_iterator(thrust::make_tuple(thrust::make_counting_iterator(0u) + n_unique, kmers_64b_unique_idxs.begin() + n_unique)), + store_kmer_unique_ids(plain_view(id_map_sorted), plain_view(kmers_64b), plain_view(coords))); + + global_to_UID_map.resize(n_kmers); + thrust::gather( + global_to_sorted_id_map.begin(), + global_to_sorted_id_map.begin() + n_kmers, + id_map_sorted.begin(), + global_to_UID_map.begin()); +} + +template +void D_KmerSet::gen_global_to_sorted_id_map() +{ + global_to_sorted_id_map.resize(n_kmers); + thrust::for_each( + thrust::make_zip_iterator(thrust::make_tuple(thrust::make_counting_iterator(0u), coords.begin())), + thrust::make_zip_iterator(thrust::make_tuple(thrust::make_counting_iterator(0u) + n_kmers, coords.begin() + n_kmers)), + global_to_sorted_id(plain_view(global_to_sorted_id_map))); +} + +template +void D_KmerSet::mark_unique_kmers() +{ + global_unique_flag_map.resize(n_kmers); + global_to_UID_map.resize(n_kmers); + thrust::fill(global_to_UID_map.begin(), global_to_UID_map.begin() + n_kmers, (uint32) -1); + thrust::for_each( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + n_unique, + populate_unique_kmer_data(plain_view(kmers_counts), plain_view(coords), plain_view(kmers_64b_unique_idxs), + plain_view(global_unique_flag_map), plain_view(global_to_UID_map))); +} + + +struct test_funct : public thrust::unary_function +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator()(const uint32 uid) + { + return uid; + } +}; + +// only keep the coordinates that have a unique prefix +template +void D_KmerSet::filter_coords_by_prefix_uniqueness(const D_VectorU8& unique_map) +{ + D_VectorSetKmerCoord unique_pref_coords(n_kmers); + uint32 n_unique_coords = thrust::copy_if( // remove_if + coords.begin(), + coords.begin() + n_kmers, + thrust::make_permutation_iterator( + unique_map.begin(), + thrust::make_transform_iterator(coords.begin(), get_prefix_global_id())), + unique_pref_coords.begin(), + thrust::identity()) - unique_pref_coords.begin(); + + thrust::copy(unique_pref_coords.begin(), unique_pref_coords.begin() + n_unique_coords, coords.begin()); + n_kmers = n_unique_coords; +} + +// for every kmer that is not unique N +// find its closest unique predecessor P and successor S kmer in the same sequence +// and output a kmer chain (P ->... N ... -> S) +// as a new 'super' kmer coordinate +template +void D_KmerSet::extract_super_kmers() +{ + // collect the ids of the repeat kmers + kmers_64b_repeat_idxs.resize(n_kmers); + uint32 n_chains = thrust::copy_if( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + n_kmers, + global_unique_flag_map.begin(), + kmers_64b_repeat_idxs.begin(), + thrust::logical_not()) - kmers_64b_repeat_idxs.begin(); + + D_VectorSetKmerCoord super_kmers(n_chains); + D_VectorU32 prefix_uids(n_chains); + D_VectorU32 suffix_uids(n_chains); + thrust::for_each( + thrust::make_counting_iterator(0), + thrust::make_counting_iterator(0) + n_chains, + extract_super_kmers_functor( + plain_view(kmers_64b_repeat_idxs), + plain_view(global_unique_flag_map), + plain_view(global_to_UID_map), + plain_view(global_to_sorted_id_map), + plain_view(coords), + string_set, + kmer_size, + plain_view(super_kmers), + plain_view(prefix_uids), + plain_view(suffix_uids))); + + // collapse chains that belong to the same sequence and same unique kmer predecessor + // (these will be consecutive by construction) + // keep the max chain length coord per same kmer and seq id + // -- will keep one copy of the chains that is terminated with a unique kmer + // and the longest chain amongst the ones that are not + super_coords.resize(n_chains); + super_prefix_uids.resize(n_chains); + super_suffix_uids.resize(n_chains); + uint32 n_collapsed_chains = thrust::reduce_by_key( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + n_chains, + thrust::make_zip_iterator(thrust::make_tuple(super_kmers.begin(), prefix_uids.begin(), suffix_uids.begin())), + thrust::make_discard_iterator(), + thrust::make_zip_iterator(thrust::make_tuple(super_coords.begin(), super_prefix_uids.begin(), super_suffix_uids.begin())), + kmer_pos_sid_eq(plain_view(super_kmers)), + collapse_same_start_kmers()).second - thrust::make_zip_iterator(thrust::make_tuple(super_coords.begin(), super_prefix_uids.begin(), super_suffix_uids.begin())); + + // eliminate non-unique kmers that are not preceded by a unique kmer + D_VectorSetKmerCoord t1(n_chains); + D_VectorU32 t2(n_chains); + D_VectorU32 t3(n_chains); + n_super_coords = thrust::remove_copy_if( + thrust::make_zip_iterator(thrust::make_tuple( + super_coords.begin(), + super_prefix_uids.begin(), + super_suffix_uids.begin())), + thrust::make_zip_iterator(thrust::make_tuple( + super_coords.begin() + n_collapsed_chains, + super_prefix_uids.begin() + n_collapsed_chains, + super_suffix_uids.begin() + n_collapsed_chains)), + super_prefix_uids.begin(), + thrust::make_zip_iterator(thrust::make_tuple( + t1.begin(), + t2.begin(), + t3.begin())), + is_invalid_super_kmer()) - thrust::make_zip_iterator(thrust::make_tuple( + t1.begin(), + t2.begin(), + t3.begin())); + + + thrust::copy(t1.begin(), t1.begin() + n_chains, super_coords.begin()); + thrust::copy(t2.begin(), t2.begin() + n_chains, super_prefix_uids.begin()); + thrust::copy(t3.begin(), t3.begin() + n_chains, super_suffix_uids.begin()); + + //super_coords.erase(super_coords.begin() + n_super_coords, super_coords.end()); + //super_prefix_uids.erase(super_prefix_uids.begin() + n_super_coords, super_prefix_uids.end()); + //super_suffix_uids.erase(super_suffix_uids.begin() + n_super_coords, super_suffix_uids.end()); + +// printf("Collapsed Filtered Super Kmer Coords: \n"); +// for(uint64 i = 0; i < n_collapsed_chains_filtered; i++) { +// SequenceSetKmerCoord c = (SequenceSetKmerCoord) super_coords[i]; +// printf("coord [%u %u %u %u] pref %llu suf %llu\n", c.x, c.y, c.z, c.w, (uint64) super_prefix_global_ids[i], +// (uint64) super_suffix_global_ids[i]); +// } + + reset_scratch_space(); +} + +// collapses lexicographically sorted chains of kmers by computing their prefix overlaps +// and extracting kmers not included in the overlapping region +// along with kmer adjacencies and adjacency count information +template +void D_KmerSet::collapse_and_extract_non_overlaps(D_VectorSetKmerCoord& kmers_out, + D_VectorU32& prefix_ids_out, D_VectorU32& suffix_ids_out, D_VectorU32& adj_counts) +{ + uint32 n_super_kmers = n_super_coords; + + // find overlap with the previous chain (in sorted order) + // overlap is measured in # of shared prefix kmers + D_VectorU32 max_predecessor_overlaps(n_super_kmers); + thrust::transform( + thrust::make_counting_iterator(1u), // skip the first chain + thrust::make_counting_iterator(0u) + n_super_kmers, + max_predecessor_overlaps.begin() + 1, + find_max_kmer_overlaps(string_set, plain_view(super_coords), kmer_size)); + + // find the number of kmer nodes that need to be created + // the first kmer in a chain is a unique kmer and should be ignored + // the last kmer in the chain might be unique, in which case it is also ignored + thrust::device_vector temp_storage; + D_VectorU32 chain_extraction_offsets(n_super_kmers + 1); + cuda::inclusive_scan( + n_super_kmers, + thrust::make_transform_iterator( + thrust::make_counting_iterator(0u), + num_non_overlapped_repeats( + plain_view(super_coords), + plain_view(super_suffix_uids), + plain_view(max_predecessor_overlaps), kmer_size)), + chain_extraction_offsets.begin() + 1, + thrust::plus(), + temp_storage); + + D_VectorU32 adj_extraction_offsets(n_super_kmers + 1); + cuda::inclusive_scan( + n_super_kmers, + thrust::make_transform_iterator( + thrust::make_counting_iterator(0u), + num_adj_repeats( + plain_view(super_coords), + plain_view(super_suffix_uids), + plain_view(max_predecessor_overlaps), kmer_size)), + adj_extraction_offsets.begin() + 1, + thrust::plus(), + temp_storage); + + // extract non-unique kmers and the (k+1)mer prefix and suffix kmer ids from the collapsed chains + n_repeat = chain_extraction_offsets[n_super_kmers]; + uint32 n_prefsuf_to_extract = adj_extraction_offsets[n_super_kmers]; + + //printf("n_super_coords %u \n", n_super_coords); + //printf("n_repeat %u \n", n_repeat); + //printf("Num X-R-X edges %u \n", n_prefsuf_to_extract); + + // allocate the necessary storage and populate + kmers_out.resize(n_unique + n_repeat); + prefix_ids_out.resize(n_prefsuf_to_extract); + suffix_ids_out.resize(n_prefsuf_to_extract); + thrust::for_each( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + n_super_kmers, + extract_non_overlapped_repeats( + string_set, + plain_view(super_coords), + plain_view(super_prefix_uids), + plain_view(super_suffix_uids), + plain_view(chain_extraction_offsets), + plain_view(adj_extraction_offsets), + plain_view(max_predecessor_overlaps), + kmer_size, n_unique, + plain_view(kmers_out), + plain_view(prefix_ids_out), + plain_view(suffix_ids_out))); + + + // count the number of repeated kmer adjacencies + adj_counts.resize(n_prefsuf_to_extract); + thrust::fill(adj_counts.begin(), adj_counts.begin() + n_prefsuf_to_extract, 1); + thrust::for_each( + thrust::make_counting_iterator(1u), + thrust::make_counting_iterator(0u) + n_super_kmers, + count_overlapped_adjacencies( + plain_view(adj_extraction_offsets), + plain_view(max_predecessor_overlaps), + plain_view(adj_counts))); + +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/regions.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/regions.h new file mode 100644 index 0000000000000000000000000000000000000000..1f35ca6a030c6555d48dce8dce20a70c7d4d8a00 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvMicroAssembly/regions.h @@ -0,0 +1,50 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +using namespace nvbio; + +// location on the genome +// 0-based +struct genome_loc +{ + uint32 contig; + uint64 start; + uint64 stop; +}; + +// window of interest in the genome likely to contain variants +struct active_region +{ + genome_loc genome_loc; // location in the genome + uint32 span; // span: region + reads (some can overlap) + uint32 n_reads; // number of reads overlapping the region + uint64 read_batch_offset; +}; + +typedef nvbio::vector H_VectorActiveRegions; diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSSA/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSSA/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..2780c7b8ed90e52ce7582a0f31475eac55c29575 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSSA/CMakeLists.txt @@ -0,0 +1,9 @@ +nvbio_module(nvSSA) + +addsources( +nvSSA.cpp +) + +cuda_add_executable(nvSSA ${nvSSA_srcs}) +target_link_libraries(nvSSA nvbio crcstatic ${SYSTEM_LINK_LIBRARIES}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSSA/nvSSA.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSSA/nvSSA.cpp new file mode 100644 index 0000000000000000000000000000000000000000..6cfd834047c6fd203b1af340cc3aa55a61c9e47f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSSA/nvSSA.cpp @@ -0,0 +1,122 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// cuFMIndex.cpp : Defines the entry point for the console application. +// + +#include +#include +#include +#include +#include +#include + +void crcInit(); + +using namespace nvbio; + +int main(int argc, char* argv[]) +{ + cudaSetDeviceFlags( cudaDeviceMapHost ); + + crcInit(); + + if (argc == 1) + { + log_info(stderr,"nvSSA [-gpu] input-prefix [output-prefix]\n"); + exit(0); + } + + int base_arg = 0; + const char* input; + const char* output; + if (strcmp( argv[1], "-gpu" ) == 0) + base_arg = 2; + else + base_arg = 1; + + input = argv[base_arg]; + if (argc == base_arg+2) + output = argv[base_arg+1]; + else + output = argv[base_arg]; + + // + // Save sampled suffix array in a format compatible with BWA's + // + nvbio::io::FMIndexDataHost driver_data; + if (!driver_data.load( input )) + return 1; + + nvbio::io::FMIndexData::ssa_storage_type ssa, rssa; + + if (strcmp( argv[1], "-gpu" ) == 0) + { + nvbio::io::FMIndexDataDevice driver_data_cuda( + driver_data, + nvbio::io::FMIndexDataDevice::FORWARD | nvbio::io::FMIndexDataDevice::REVERSE ); + + nvbio::io::FMIndexDataDevice::ssa_storage_type ssa_cuda, rssa_cuda; + + init_ssa( driver_data_cuda, ssa_cuda, rssa_cuda ); + + ssa = ssa_cuda; + rssa = rssa_cuda; + } + else + init_ssa( driver_data, ssa, rssa ); + + const uint32 sa_intv = nvbio::io::FMIndexData::SA_INT; + const uint32 ssa_len = (driver_data.m_seq_length + sa_intv) / sa_intv; + + log_info(stderr, "saving SSA... started\n"); + { + std::string file_name = std::string( output ) + std::string(".sa"); + FILE* file = fopen( file_name.c_str(), "wb" ); + + fwrite( &driver_data.m_primary, sizeof(uint32), 1u, file ); + fwrite( &driver_data.m_L2+1, sizeof(uint32), 4u, file ); + fwrite( &sa_intv, sizeof(uint32), 1u, file ); + fwrite( &driver_data.m_seq_length, sizeof(uint32), 1u, file ); + fwrite( &ssa.m_ssa[1], sizeof(uint32), ssa_len-1, file ); + fclose( file ); + } + { + std::string file_name = std::string( output ) + std::string(".rsa"); + FILE* file = fopen( file_name.c_str(), "wb" ); + + fwrite( &driver_data.m_rprimary, sizeof(uint32), 1u, file ); + fwrite( &driver_data.m_L2+1, sizeof(uint32), 4u, file ); + fwrite( &sa_intv, sizeof(uint32), 1u, file ); + fwrite( &driver_data.m_seq_length, sizeof(uint32), 1u, file ); + fwrite( &rssa.m_ssa[1], sizeof(uint32), ssa_len-1, file ); + fclose( file ); + } + log_info(stderr, "saving SSA... done\n"); + return 0; +} + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSetBWT/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSetBWT/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..e0cadbe9d430904556d37841ef306cc68faed290 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSetBWT/CMakeLists.txt @@ -0,0 +1,10 @@ +nvbio_module(nvSetBWT) + +addsources( +input_thread.h +nvSetBWT.cu +) + +cuda_add_executable(nvSetBWT ${nvSetBWT_srcs}) +target_link_libraries(nvSetBWT nvbio moderngpu zlibstatic lz4 crcstatic ${SYSTEM_LINK_LIBRARIES}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSetBWT/input_thread.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSetBWT/input_thread.h new file mode 100644 index 0000000000000000000000000000000000000000..03bf4ba11c0e1f998d9be9f3ea84e4a2249238b0 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSetBWT/input_thread.h @@ -0,0 +1,86 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// input_thread.h +// + +#pragma once + +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +/// +/// A small class implementing a Pipeline stage reading sequence batches from a file +/// +struct InputStage +{ + typedef void argument_type; + typedef io::SequenceDataHost return_type; + + /// constructor + /// + ///\param file input sequence file + ///\param max_strings maximum number of strings per batch + ///\param max_bps maximum number of base pairs per batch + /// + InputStage(io::SequenceDataStream* file, const uint32 max_strings, const uint32 max_bps) : + m_file ( file ), + m_max_strings ( max_strings ), + m_max_bps ( max_bps ) + {} + + /// fill the next batch + /// + bool process(PipelineContext& context) + { + Timer timer; + timer.start(); + + // fetch the output + io::SequenceDataHost* output = context.output(); + + log_debug(stderr, " loading.. started (%u, %u)\n", m_max_strings, m_max_bps); + const int ret = io::next( DNA, output, m_file, m_max_strings, m_max_bps ); + log_debug(stderr, " loading.. done\n"); + + timer.stop(); + m_time += timer.seconds(); + return ret; + } + + io::SequenceDataStream* m_file; + uint32 m_max_strings; + uint32 m_max_bps; + float m_time; +}; diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSetBWT/nvSetBWT.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSetBWT/nvSetBWT.cu new file mode 100644 index 0000000000000000000000000000000000000000..a1c66fae581b86e298a329d1ef4c77a47338d11d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvSetBWT/nvSetBWT.cu @@ -0,0 +1,435 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// nvSetBWT.cu +// + +//#define NVBIO_CUDA_DEBUG + +#include +#include + +#include "input_thread.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +static const uint32 SYMBOL_SIZE = io::SequenceDataAccess::SEQUENCE_BITS; +static const bool BIG_ENDIAN = io::SequenceDataAccess::SEQUENCE_BIG_ENDIAN; + +typedef io::SequenceDataAccess::sequence_storage_iterator storage_iterator; +typedef io::SequenceDataAccess::index_iterator offsets_iterator; + +typedef BWTEContext BWTE_context_type; + +/// +/// A small class implementing a Pipeline stage reading sequence batches from a file +/// +struct SortStage +{ + typedef io::SequenceDataHost argument_type; + typedef BWTEBlock return_type; + + /// constructor + /// + ///\param file input sequence file + ///\param max_strings maximum number of strings per batch + ///\param max_bps maximum number of base pairs per batch + /// + SortStage(BWTE_context_type& context) : m_context( context ) {} + + /// fill the next batch + /// + bool process(PipelineContext& context) + { + // fetch the input + io::SequenceDataHost* h_read_data = context.input(0); + + // fetch the output + BWTEBlock* block = context.output(); + + // build a view + const io::SequenceDataAccess h_read_view( *h_read_data ); + + m_context.sort_block( + 0u, + h_read_data->size(), + h_read_view.sequence_string_set(), + *block ); + + return true; + } + + BWTE_context_type& m_context; +}; + +/// +/// A small class implementing a Pipeline stage reading sequence batches from a file +/// +struct SinkStage +{ + typedef io::SequenceDataHost argument_type; + + /// constructor + /// + ///\param file input sequence file + ///\param max_strings maximum number of strings per batch + ///\param max_bps maximum number of base pairs per batch + /// + SinkStage( + BWTE_context_type& context, + PagedText& bwt, + SparseSymbolSet& dollars) : + m_context( context ), + m_bwt( bwt ), + m_dollars( dollars ), + n_reads( 0 ), + m_time( 0.0f ) + {} + + /// fill the next batch + /// + bool process(PipelineContext& context) + { + const ScopedTimer timer( &m_time ); + + // fetch the input + io::SequenceDataHost* h_read_data = context.input( 0 ); + + // build a view + const io::SequenceDataAccess h_read_view( *h_read_data ); + + log_info(stderr, " block [%u, %u] (%u / %.2fG bps, %.1f M suffixes/s)\n", + n_reads, n_reads + h_read_data->size(), h_read_data->bps(), + 1.0e-9f * m_bwt.size(), + m_time ? (1.0e-6f * m_bwt.size()) / m_time : 0.0f ); + log_debug(stderr," peak memory : %.1f GB\n", float( peak_resident_memory() ) / float(1024*1024*1024)); + + /* + m_context.append_block( + 0u, + h_read_data->size(), + h_read_view.sequence_string_set(), + m_bwt, + m_dollars, + true ); + */ + + // fetch the second input + BWTEBlock* block = context.input( 1 ); + + m_context.merge_block( + 0u, + h_read_data->size(), + h_read_view.sequence_string_set(), + *block, + m_bwt, + m_dollars, + true ); + + n_reads += h_read_data->size(); + return true; + } + + BWTE_context_type& m_context; + PagedText& m_bwt; + SparseSymbolSet& m_dollars; + uint32 n_reads; + float m_time; +}; + +int main(int argc, char* argv[]) +{ + if (argc < 2) + { + log_visible(stderr, "nvSetBWT - Copyright 2013-2014, NVIDIA Corporation\n"); + log_info(stderr, "usage:\n"); + log_info(stderr, " nvSetBWT [options] input_file output_file\n"); + log_info(stderr, " options:\n"); + log_info(stderr, " -v | --verbosity int (0-6) [5]\n"); + log_info(stderr, " -c | --compression string [1R] (e.g. \"1\", ..., \"9\", \"1R\")\n"); + log_info(stderr, " -t | --threads int [auto]\n"); + log_info(stderr, " -b | --bucketing int [16] (# of bits used for bucketing)\n"); + log_info(stderr, " -F | --skip-forward\n"); + log_info(stderr, " -R | --skip-reverse\n"); + log_info(stderr, " output formats:\n"); + log_info(stderr, " .txt ASCII\n"); + log_info(stderr, " .txt.gz ASCII, gzip compressed\n"); + log_info(stderr, " .txt.bgz ASCII, block-gzip compressed\n"); + log_info(stderr, " .bwt 2-bit packed binary\n"); + log_info(stderr, " .bwt.gz 2-bit packed binary, gzip compressed\n"); + log_info(stderr, " .bwt.bgz 2-bit packed binary, block-gzip compressed\n"); + log_info(stderr, " .bwt4 4-bit packed binary\n"); + log_info(stderr, " .bwt4.gz 4-bit packed binary, gzip compressed\n"); + log_info(stderr, " .bwt4.bgz 4-bit packed binary, block-gzip compressed\n"); + return 0; + } + + const char* reads_name = argv[argc-2]; + const char* output_name = argv[argc-1]; + bool forward = true; + bool reverse = true; + const char* comp_level = "1R"; + io::QualityEncoding qencoding = io::Phred33; + int threads = 0; + + for (int i = 0; i < argc - 2; ++i) + { + if ((strcmp( argv[i], "-v" ) == 0) || + (strcmp( argv[i], "-verbosity" ) == 0) || + (strcmp( argv[i], "--verbosity" ) == 0)) + { + set_verbosity( Verbosity( atoi( argv[++i] ) ) ); + } + else if ((strcmp( argv[i], "-F" ) == 0) || + (strcmp( argv[i], "--skip-forward" ) == 0)) // skip forward strand + { + forward = false; + } + else if ((strcmp( argv[i], "-R" ) == 0) || + (strcmp( argv[i], "--skip-reverse" ) == 0)) // skip reverse strand + { + reverse = false; + } + else if ((strcmp( argv[i], "-c" ) == 0) || + (strcmp( argv[i], "--compression" ) == 0)) // setup compression level + { + comp_level = argv[++i]; + } + else if ((strcmp( argv[i], "-t" ) == 0) || + (strcmp( argv[i], "--threads" ) == 0)) // setup number of threads + { + threads = atoi( argv[++i] ); + } + } + + try + { + log_visible(stderr,"nvSetBWT... started\n"); + + // build an output file + SharedPointer output_handler = SharedPointer( open_bwt_file( output_name, comp_level ) ); + if (output_handler == NULL) + { + log_error(stderr, " failed to create an output handler\n"); + return 1; + } + + // gather device memory stats + size_t free_device, total_device; + cudaMemGetInfo(&free_device, &total_device); + cuda::check_error("cuda-check"); + + log_stats(stderr, " device has %ld of %ld MB free\n", free_device/1024/1024, total_device/1024/1024); + + #ifdef _OPENMP + // now set the number of CPU threads + omp_set_num_threads( threads > 0 ? threads : omp_get_num_procs() ); + omp_set_nested(1); + #pragma omp parallel + { + log_verbose(stderr, " running on multiple threads (%d)\n", omp_get_thread_num()); + } + #endif + + uint32 encoding_flags = 0u; + if (forward) encoding_flags |= io::FORWARD; + if (reverse) encoding_flags |= io::REVERSE_COMPLEMENT; + + + log_visible(stderr, "opening read file \"%s\"\n", reads_name); + SharedPointer read_data_file( + nvbio::io::open_sequence_file( + reads_name, + qencoding, + uint32(-1), + uint32(-1), + io::SequenceEncoding( encoding_flags ) ) + ); + + if (read_data_file == NULL || read_data_file->is_ok() == false) + { + log_error(stderr, " failed opening file \"%s\"\n", reads_name); + return false; + } + + // output vectors + PagedText bwt; + SparseSymbolSet dollars; + + // get the current device + int current_device; + cudaGetDevice( ¤t_device ); + + // build a BWTEContext + BWTE_context_type bwte_context( current_device ); + + // find out how big a block can we alloc + uint32 max_block_suffixes = 256*1024*1024; + uint32 max_block_strings = 16*1024*1024; + + while (bwte_context.needed_device_memory( max_block_strings, max_block_suffixes ) + 256u*1024u*1024u >= free_device) + max_block_suffixes /= 2; + + log_verbose(stderr, " block size: %u\n", max_block_suffixes); + + // reserve enough space for the block processing + bwte_context.reserve( max_block_strings, max_block_suffixes ); + + cudaMemGetInfo(&free_device, &total_device); + log_stats(stderr, " device has %ld of %ld MB free\n", free_device/1024/1024, total_device/1024/1024); + + // build the input stage + InputStage input_stage( read_data_file.get(), max_block_strings, max_block_suffixes - max_block_strings ); + + // build the sort stage + SortStage sort_stage( bwte_context ); + + // build the sink + SinkStage sink_stage( bwte_context, bwt, dollars ); + + // build the pipeline + Pipeline pipeline; + const uint32 in0 = pipeline.append_stage( &input_stage, 4u ); + const uint32 in1 = pipeline.append_stage( &sort_stage, 4u ); + const uint32 out = pipeline.append_sink( &sink_stage ); + pipeline.add_dependency( in0, out ); + pipeline.add_dependency( in0, in1 ); + pipeline.add_dependency( in1, out ); + + Timer timer; + timer.start(); + + // and run it! + pipeline.run(); + + log_info(stderr," writing output... started\n"); + + // write out the results + for (uint32 i = 0; i < bwt.page_count(); ++i) + { + // find the dollars corresponding to this page + const uint64 page_begin = bwt.get_page_offset(i); + const uint64 page_end = bwt.get_page_offset(i+1); + + const uint64 dollars_begin = nvbio::lower_bound_index( + page_begin, + dollars.pos(), + dollars.size() ); + + const uint64 dollars_end = nvbio::lower_bound_index( + page_end, + dollars.pos(), + dollars.size() ); + + //log_debug(stderr," page[%u] : %llu symbols (%llu,%llu), %llu dollars (%llu,%llu)\n", i, page_end - page_begin, page_begin, page_end, dollars_end - dollars_begin, dollars_begin, dollars_end); + + // and output the page + output_handler->process( + bwt.get_page_size(i), + SYMBOL_SIZE, + (const uint32*)bwt.get_page(i), + dollars_end - dollars_begin, + dollars.pos() + dollars_begin, + dollars.ids() + dollars_begin ); + } + + log_info(stderr," writing output... done\n"); + + timer.stop(); + const float time = timer.seconds(); + + log_verbose(stderr," total time : %.1fs\n", time); + log_verbose(stderr," peak memory : %.1f GB\n", float( peak_resident_memory() ) / float(1024*1024*1024)); + log_visible(stderr,"nvSetBWT... done\n"); + } + catch (nvbio::cuda_error e) + { + log_error(stderr, "caught a nvbio::cuda_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (nvbio::bad_alloc e) + { + log_error(stderr, "caught a nvbio::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (nvbio::logic_error e) + { + log_error(stderr, "caught a nvbio::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (nvbio::runtime_error e) + { + log_error(stderr, "caught a nvbio::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (std::bad_alloc e) + { + log_error(stderr, "caught a std::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (std::logic_error e) + { + log_error(stderr, "caught a std::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (std::runtime_error e) + { + log_error(stderr, "caught a std::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + return 1; + } + catch (...) + { + log_error(stderr, "caught an unknown exception!\n"); + return 1; + } + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..a7e279cd0c1448a31bb7387418322f9a89852c47 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/CMakeLists.txt @@ -0,0 +1,21 @@ +nvbio_module(nvbio-aln-diff) + +addsources( +alignment_bam.cpp +alignment.cpp +alignment_dbg.cpp +alignment.h +filter.h +html.h +se_analyzer.h +se_analyzer.cpp +pe_analyzer.h +pe_analyzer.cpp +stats.h +utils.h +nvbio-aln-diff.cpp +) + +cuda_add_executable(nvbio-aln-diff ${nvbio-aln-diff_srcs}) +target_link_libraries(nvbio-aln-diff bamtools nvbio zlibstatic crcstatic ${SYSTEM_LINK_LIBRARIES}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/alignment.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/alignment.cpp new file mode 100644 index 0000000000000000000000000000000000000000..8c49bac83dc72198847d8651e3d57183e30d47ed --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/alignment.cpp @@ -0,0 +1,49 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include + +namespace nvbio { +namespace alndiff { + +AlignmentStream* open_dbg_file(const char* file_name); +AlignmentStream* open_bam_file(const char* file_name); + +AlignmentStream* open_alignment_file(const char* file_name) +{ + if (strcmp( file_name + strlen(file_name) - 4u, ".dbg" ) == 0) + return open_dbg_file( file_name ); + if (strcmp( file_name + strlen(file_name) - 4u, ".bam" ) == 0) + return open_bam_file( file_name ); + + return NULL; +} + +} // alndiff namespace +} // nvbio namespace diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/alignment.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/alignment.h new file mode 100644 index 0000000000000000000000000000000000000000..a02fbf068a5d2fab0affbcd55b4a4e9ab028fc3f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/alignment.h @@ -0,0 +1,162 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include + +namespace nvbio { +namespace alndiff { + +struct Alignment +{ + enum { PAIRED = 1, + PROPER_PAIR = 2, + UNMAPPED = 4, + MATE_UNMAPPED = 8, + REVERSE = 16, + MATE_REVERSE = 32, + READ_1 = 64, + READ_2 = 128, + SECONDARY = 256, + QC_FAILED = 512, + DUPLICATE = 1024 + }; + + Alignment() : + read_id( uint32(-1) ), + read_len( 0 ), + mate( 0 ), + pos( 0 ), + ref_id( uint32(-1) ), + flag( UNMAPPED ), + score( -65536 ), + mapQ( 0 ), + ed( 255 ), + subs( 0 ), + ins( 0 ), + dels( 0 ), + n_mm( 0 ), + n_gapo( 0 ), + n_gape( 0 ), + has_second( 0 ), + sec_score( -65536 ) {} + + bool is_mapped() const { return (pos != 0) && ((flag & UNMAPPED) == 0); } + bool is_rc() const { return (flag & REVERSE) != 0; } + bool is_unique() const { return is_mapped() && (has_second == false); } + bool is_ambiguous() const { return is_mapped() && has_second && (sec_score == score); } + + uint16 mapped_read_bases() const { return subs + ins; } + uint16 mapped_ref_bases() const { return subs + dels; } + uint16 trimmed() const { return read_len - subs - ins; } + + uint32 read_id; + uint32 read_len; + uint32 mate; + uint32 pos; + uint32 ref_id; + uint32 flag; + int32 score; + uint8 mapQ; + uint8 ed; + uint16 subs; + uint16 ins; + uint16 dels; + uint8 n_mm; + uint8 n_gapo; + uint8 n_gape; + uint8 has_second; + int32 sec_score; +}; + +inline +bool distant(const Alignment& a1, const Alignment& a2) +{ + return (int64(a1.pos) < int64(a2.pos) - a1.read_len) || + (int64(a1.pos) > int64(a2.pos) + a1.read_len); +} + +struct AlignmentPair +{ + AlignmentPair() {} + AlignmentPair(const Alignment m1, const Alignment m2) : mate1(m1), mate2(m2) {} + + uint32 read_id() const { return mate1.read_id; } + uint32 read_len() const { return mate1.read_len + mate2.read_len; } + int32 score() const { return mate1.score + mate2.score; } + uint8 mapQ() const { return mate1.mapQ; } + uint8 ed() const { return mate1.ed + mate2.ed; } + uint16 subs() const { return mate1.subs + mate2.subs; } + uint16 ins() const { return mate1.ins + mate2.ins; } + uint16 dels() const { return mate1.dels + mate2.dels; } + uint8 n_mm() const { return mate1.n_mm + mate2.n_mm; } + uint8 n_gapo() const { return mate1.n_gapo + mate2.n_gapo; } + uint8 n_gape() const { return mate1.n_gape + mate2.n_gape; } + bool has_second() const { return mate1.has_second && mate2.has_second; } + int32 sec_score() const { return mate1.sec_score + mate2.sec_score; } + + bool is_mapped() const { return mate1.is_mapped() && mate2.is_mapped(); } + bool is_mapped_paired() const { return mate1.is_mapped() && mate2.is_mapped() && (mate1.flag & Alignment::PROPER_PAIR) && (mate2.flag & Alignment::PROPER_PAIR); } + bool is_mapped_unpaired() const { return mate1.is_mapped() && mate2.is_mapped() && (((mate1.flag & Alignment::PROPER_PAIR) == 0) || ((mate2.flag & Alignment::PROPER_PAIR) == 0)); } + bool is_unique_paired() const { return is_mapped_paired() && mate1.is_unique() && mate2.is_unique(); } + bool is_ambiguous_paired()const { return is_mapped_paired() && has_second() && (score() == sec_score()); } + + uint16 mapped_read_bases() const { return subs() + ins(); } + uint16 mapped_ref_bases() const { return subs() + dels(); } + uint16 trimmed() const { return read_len() - subs() - ins(); } + + const Alignment& operator[] (const uint32 i) const { return *(&mate1 + i); } + + Alignment mate1; + Alignment mate2; +}; + +struct AlignmentStream +{ + /// virtual destructor + /// + virtual ~AlignmentStream() {} + + /// return if the stream is ok + /// + virtual bool is_ok() { return false; } + + /// get the next batch + /// + virtual uint32 next_batch( + const uint32 count, + Alignment* batch) { return 0; } +}; + +/// open an alignment file +/// +AlignmentStream* open_alignment_file(const char* file_name); + +} // alndiff namespace +} // nvbio namespace diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/alignment_bam.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/alignment_bam.cpp new file mode 100644 index 0000000000000000000000000000000000000000..4a306da71a46d1bc619776b72910bb88e2738beb --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/alignment_bam.cpp @@ -0,0 +1,155 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include + +namespace nvbio { +namespace alndiff { + +struct BAMAlignmentStream : public AlignmentStream +{ + BAMAlignmentStream(const char* file_name) + { + log_verbose(stderr, "opening BAM file \"%s\"... started\n", file_name); + m_bam_reader.Open( file_name ); + m_offset = 0; + log_verbose(stderr, "opening BAM file \"%s\"... done\n", file_name); + } + + // return if the stream is ok + // + bool is_ok() { return true; } // TODO: add a mechanism to bamtools to know whether the file opened correctly + + // get the next batch + // + uint32 next_batch( + const uint32 count, + Alignment* batch) + { + uint32 n_read = 0; + + while (n_read < count) + { + Alignment* aln = batch + n_read; + + // clean the alignment + *aln = Alignment(); + + BamTools::BamAlignment bam_aln; + + if (m_bam_reader.GetNextAlignment( bam_aln ) == false) + break; + + aln->read_id = uint32( crcCalc( bam_aln.Name.c_str(), uint32(bam_aln.Name.length()) ) ); + aln->read_len = bam_aln.Length; + aln->mate = bam_aln.IsFirstMate() ? 0u : 1u; + aln->flag = bam_aln.AlignmentFlag; + aln->pos = bam_aln.Position; + if (aln->is_mapped()) + { + aln->ref_id = bam_aln.RefID; + aln->mapQ = uint8( bam_aln.MapQuality ); + bam_aln.GetEditDistance( aln->ed ); + + analyze_cigar( bam_aln.CigarData, aln ); + + bam_aln.GetTag( "AS", aln->score ); + aln->has_second = bam_aln.GetTag( "XS", aln->sec_score ); + bam_aln.GetTag( "XM", aln->n_mm ); + bam_aln.GetTag( "XO", aln->n_gapo ); + bam_aln.GetTag( "XG", aln->n_gape ); + + const char* md = bam_aln.GetTag( "MD" ); + if (md) + analyze_md( md, aln ); + } + + ++n_read; + } + m_offset += n_read; + return n_read; + } + + void analyze_cigar(const std::vector& cigar, Alignment* aln) + { + aln->subs = aln->ins = aln->dels = 0; + + for (uint32 i = 0; i < cigar.size(); ++i) + { + const BamTools::CigarOp op = cigar[i]; + + if (op.Type == 'X') + ++aln->n_mm; + + if (op.Type == 'M' || op.Type == 'X' || op.Type == '=') + aln->subs += op.Length; + else if (op.Type == 'I') + aln->ins += op.Length; + else if (op.Type == 'D') + aln->dels += op.Length; + } + } + void analyze_md(const char* md, Alignment* aln) + { + aln->n_mm = 0; + + for (; *md != '\0'; ++md) + { + const char c = *md; + + if (c >= '0' && + c <= '9') + continue; + + if (c >= 'A' && + c <= 'Z') + ++aln->n_mm; + + if (c == '^') + { + // a deletion, skip it + for (++md; *md != '\0' && (*md <= '0' || *md >= '9'); ++md) {} + } + } + } + + BamTools::BamReader m_bam_reader; + uint32 m_offset; +}; + +AlignmentStream* open_bam_file(const char* file_name) +{ + return new BAMAlignmentStream( file_name ); +} + +} // alndiff namespace +} // nvbio namespace + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/alignment_dbg.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/alignment_dbg.cpp new file mode 100644 index 0000000000000000000000000000000000000000..d0cdfd20e9e4f721c89ed99b3fb41c502085f167 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/alignment_dbg.cpp @@ -0,0 +1,132 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include + +namespace nvbio { +namespace alndiff { + +struct DebugAlignmentStream : public AlignmentStream +{ + struct Info + { + uint32 flag; + uint32 ref_id; + // 8-bytes + uint8 mate; + uint8 mapQ; + uint8 ed; + uint8 pad; + // 12-bytes + uint16 subs:16; + uint8 ins; + uint8 dels; + // 16-bytes + uint8 mms; + uint8 gapo; + uint8 gape; + uint8 has_second; + // 20-bytes + int32 score; + int32 sec_score; + // 24-bytes + }; + + DebugAlignmentStream(const char* file_name) + { + m_file = gzopen( file_name, "rb" ); + } + + // return if the stream is ok + // + bool is_ok() { return m_file != NULL; } + + // get the next batch + // + uint32 next_batch( + const uint32 count, + Alignment* batch) + { + uint32 n_read = 0; + + Info info; + + while (n_read < count) + { + Alignment* aln = batch + n_read; + + // clean the alignment + *aln = Alignment(); + + // read id + if (gzread( m_file, &aln->read_id, sizeof(uint32) ) == 0) + break; + + // read length + gzread( m_file, &aln->read_len, sizeof(uint32) ); + + // alignment position + gzread( m_file, &aln->pos, sizeof(uint32) ); + + if (aln->pos != uint32(0)) + { + gzread( m_file, &info, sizeof(Info) ); + + aln->flag = info.flag; + aln->ref_id = info.ref_id; + aln->mate = info.mate; + aln->score = info.score; + aln->mapQ = info.mapQ; + aln->ed = info.ed; + aln->subs = info.subs; + aln->ins = info.ins; + aln->dels = info.dels; + aln->n_mm = info.mms; + aln->n_gapo = info.gapo; + aln->n_gape = info.gape; + aln->has_second = info.has_second; + aln->sec_score = info.sec_score; + } + + ++n_read; + } + return n_read; + } + + gzFile m_file; +}; + +AlignmentStream* open_dbg_file(const char* file_name) +{ + return new DebugAlignmentStream( file_name ); +} + +} // alndiff namespace +} // nvbio namespace + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/filter.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/filter.h new file mode 100644 index 0000000000000000000000000000000000000000..1c946cdfec4721bd72aecca7445a56b1577c03c7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/filter.h @@ -0,0 +1,111 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include + +namespace nvbio { +namespace alndiff { + +struct Filter +{ + enum Flags { DISTANT = 1u, DISCORDANT = 2u, DIFFERENT_REF = 4u, ALL = 0xFFFFFFFFu }; + enum Statistics { ED = 1u, MAPQ = 2u, MMS = 4u, INS = 8u, DELS = 16u, SCORE = 32u }; + + // empty constructor + // + Filter() : m_file(NULL), m_filtered(0) {} + + // constructor + // + // \param file_name output file name + // \param flags read flags (DISTANT | DISCORDANT | DIFFERENT_REF | ALL) accepted by the filter + // \param stats statistics accepted by the filter + // \param delta filtering threshold + // + Filter(const char* file_name, const uint32 flags, const uint32 stats, const int32 delta) : + m_file( NULL ), + m_flags( flags ), + m_stats( stats ), + m_delta( delta ), + m_filtered(0) + { + if (file_name) + { + log_verbose(stderr, "opening filter file \"%s\"... done\n", file_name); + m_file = fopen( file_name, "wb" ); + if (m_file == NULL) + log_warning( stderr, "unable to open filter file \"%s\"\n", file_name ); + } + } + // destructor + // + ~Filter() + { + if (m_file) + { + fclose( m_file ); + log_verbose(stderr, "closing filter file... done\n"); + } + } + + // push a statistic into the filter + // + void operator() (const int32 delta, const uint32 flags, const Statistics stat, const uint32 read_id) + { + if (m_file == NULL) + return; + + if ((m_flags & flags) && + (m_stats & stat) && + (m_delta > 0 ? delta >= m_delta : delta <= m_delta)) + { + fwrite( &read_id, sizeof(uint32), 1u, m_file ); + + ++m_filtered; + } + } + + // get filtered count + // + uint32 filtered() const { return m_filtered; } + + // flush the file + // + void flush() { if (m_file) fflush( m_file ); } + + FILE* m_file; + uint32 m_flags; + uint32 m_stats; + int32 m_delta; + uint32 m_filtered; +}; + +} // namespace alndiff +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/html.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/html.h new file mode 100644 index 0000000000000000000000000000000000000000..ad6111cfea7ad505998e8a21b67fb0321bf57c47 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/html.h @@ -0,0 +1,746 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include +#include + +namespace nvbio { +namespace alndiff { + +inline +std::string generate_file_name(const char* report, const char* name) +{ + std::string file_name = report; + { + const size_t offset = file_name.find(".html"); + file_name.replace( offset+1, file_name.length() - offset - 1, name ); + file_name.append( ".html" ); + } + return file_name; +} +inline +void add_param(FILE* html_output, const char* name, const uint32 val, bool alt) +{ + html::tr_object tr( html_output, "class", alt ? "alt" : "none", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, name ); + html::td_object( html_output, html::FORMATTED, NULL, "%u", val ); +} +inline +void add_param(FILE* html_output, const char* name, const float val, bool alt) +{ + html::tr_object tr( html_output, "class", alt ? "alt" : "none", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, name ); + html::td_object( html_output, html::FORMATTED, NULL, "%f", val ); +} +inline +void add_param(FILE* html_output, const char* name, const char* val, bool alt) +{ + html::tr_object tr( html_output, "class", alt ? "alt" : "none", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, name ); + html::td_object( html_output, html::FORMATTED, NULL, "%s", val ); +} + +// find greatest two values in a table +// +template +void find_gt2(const int32 first_row, const int32 last_row, const T& table, int32 best_bin[2]) +{ + best_bin[0] = 0; + best_bin[1] = 1; + uint32 best_bin_val[2] = {0}; + for (int32 i = first_row; i <= last_row; ++i) + { + if (best_bin_val[0] < table[i]) + { + best_bin_val[1] = best_bin_val[0]; + best_bin[1] = best_bin[0]; + best_bin_val[0] = table[i]; + best_bin[0] = i; + } + else if (best_bin_val[1] < table[i]) + { + best_bin_val[1] = table[i]; + best_bin[1] = i; + } + } +} + +// compute first row with a non-zero display value +// +template +int32 first_display_row(const Histogram& table, const uint32 total, const int32 last_row = 0) +{ + const int32 X = XX; + + int32 first_row = last_row; + for (int32 i = last_row; i > -X; --i) + { + if (100.0f * float(table[i])/float(total) > 0.01f) + first_row = i; + } + return first_row; +} + +// compute last row with a non-zero display value +// +template +int32 last_display_row(const Histogram& table, const uint32 total, const int32 first_row = 0) +{ + const int32 X = XX; + + int32 last_row = first_row; + for (int32 i = first_row; i < X; ++i) + { + if (100.0f * float(table[i])/float(total) > 0.01f) + last_row = i; + } + return last_row; +} + +// compute first and last rows with a non-zero display value +// +template +int2 display_range(const Histogram& table, const uint32 total) +{ + return make_int2( + first_display_row( table, total ), + last_display_row( table, total ) ); +} + +inline +void stats_string(char* buffer, const float v, const float range) +{ + sprintf(buffer,"%5.2f %%%% \'", v, 2.0f + range * v/100.0f); +} + +template +void generate_diff_table( + FILE* html_output, + const char* stat_by, + const char* name, + const Bins bin_type, + const Histogram& stats_l, + const Histogram& stats_r, + const uint32 total, + const uint32 n_mapped_both) +{ + const int32 X = XX; + + // + // kernel summary stats + // + { + char buffer1[1024]; + char buffer2[1024]; + sprintf( buffer1, "%s-summary-stats", name ); + sprintf( buffer2, "%s [%s] summary stats", name, stat_by ); + html::table_object tab( html_output, buffer1, "stats", buffer2 ); + { + html::tr_object tr(html_output, NULL); + html::th_object(html_output, html::FORMATTED, NULL, "file names"); + html::td_object(html_output, html::FORMATTED, "colspan", "2", "align", "center", NULL, "[L]"/*, aln_file_name1*/); + html::td_object(html_output, html::FORMATTED, "colspan", "2", "align", "center", NULL, "[R]"/*, aln_file_name2*/); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + html::th_object( html_output, html::FORMATTED, NULL, "better/equal" ); + html::th_object( html_output, html::FORMATTED, NULL, "equal" ); + html::th_object( html_output, html::FORMATTED, NULL, "better" ); + html::th_object( html_output, html::FORMATTED, NULL, "worse" ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "items" ); + html::td_object( html_output, html::FORMATTED, NULL, "%.2f M", float(stats_l.count) * 1.0e-6f ); + html::td_object( html_output, html::FORMATTED, NULL, "%.2f M", float(stats_l[0]) * 1.0e-6f ); + html::td_object( html_output, html::FORMATTED, "class", "yellow", NULL, "%.2f M", float(stats_l.all_but(0)) * 1.0e-6f ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%.2f M", float(stats_r.all_but(0)) * 1.0e-6f ); + } + { + html::tr_object tr( html_output, "class", "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "%% of total" ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %%", 100.0f * float(stats_l.count)/float(total) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %%", 100.0f * float(stats_l[0])/float(total) ); + html::td_object( html_output, html::FORMATTED, "class", "yellow", NULL, "%5.2f %%", 100.0f * float(stats_l.all_but(0))/float(total) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %%", 100.0f * float(stats_r.all_but(0))/float(total) ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "%% of %s", stat_by ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %%", 100.0f * float(stats_l.count)/float(n_mapped_both) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %%", 100.0f * float(stats_l[0])/float(n_mapped_both) ); + html::td_object( html_output, html::FORMATTED, "class", "yellow", NULL, "%5.2f %%", 100.0f * float(stats_l.all_but(0))/float(n_mapped_both) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %%", 100.0f * float(stats_r.all_but(0))/float(n_mapped_both) ); + } + } + + // + // table stats + // + { + char buffer1[1024]; + char buffer2[1024]; + sprintf( buffer1, "%s-stats", name ); + sprintf( buffer2, "%s [%s] stats", name, stat_by ); + html::table_object tab( html_output, buffer1, "stats", buffer2 ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "bin" ); + html::th_object( html_output, html::FORMATTED, NULL, "%% of total" ); + html::th_object( html_output, html::FORMATTED, NULL, "%% of %s", stat_by ); + html::th_object( html_output, html::FORMATTED, NULL, "%% of diff" ); + html::th_object( html_output, html::FORMATTED, NULL, "cumulative (+)" ); + html::th_object( html_output, html::FORMATTED, NULL, "cumulative (-)" ); + } + + const Histogram& table = stats_l; + const Histogram& table_neg = stats_r; + + int32 best_bin[2] = {0}; + find_gt2( 0, X-1, table, best_bin ); + + const int32 last_row = last_display_row( stats_l, n_mapped_both ); + const int32 last_row_neg = last_display_row( stats_r, n_mapped_both ); + + // compute cumulative values, from best to worst + float cum_pos[X]; + float cum_neg[X]; + cum_pos[X-1] = 100.0f * float(table[X-1])/float(n_mapped_both); + for (int32 i = X-2; i >= 0; --i) + cum_pos[i] = 100.0f * float(table[i])/float(n_mapped_both) + cum_pos[i+1]; + cum_neg[0] = cum_pos[0]; + for (int32 i = 1; i < X; ++i) + cum_neg[i] = 100.0f * float(table_neg[i])/float(n_mapped_both) + cum_neg[i-1]; + + const float max_perc = 48.0f; + + char span_string[1024]; + for (int32 i = last_row_neg; i > 0; --i) + { + html::tr_object tr( html_output, "class", i % 2 ? "none" : "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "%d", -int32(bin_type == LOG ? log_bin_range(i) : i) ); + stats_string( span_string, 100.0f * float(table_neg[i]) / float(total), max_perc ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, span_string ); + stats_string( span_string, 100.0f * float(table_neg[i]) / float(n_mapped_both), max_perc ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, span_string ); + stats_string( span_string, stats_r.count ? 100.0f * float(table_neg[i]) / float(stats_r.count) : 0.0f, max_perc ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, span_string ); + stats_string( span_string, cum_neg[i], max_perc ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, span_string ); + stats_string( span_string, 100.0f - cum_neg[i] + 100.0f * float(table_neg[i])/float(n_mapped_both), max_perc ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, span_string ); + } + for (int32 i = 0; i <= last_row; ++i) + { + html::tr_object tr( html_output, "class", i % 2 ? "none" : "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "%d", (bin_type == LOG ? log_bin_range(i) : i) ); + const char* cls = i == best_bin[0] ? "yellow" : i == best_bin[1] ? "orange" : "none"; + stats_string( span_string, 100.0f * float(table_neg[i]) / float(total), max_perc ); + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, span_string ); + stats_string( span_string, 100.0f * float(table[i]) / float(n_mapped_both), max_perc ); + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, span_string ); + stats_string( span_string, stats_l.count ? 100.0f * float(table[i]) / float(stats_l.count) : 0.0f, max_perc ); + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, span_string ); + stats_string( span_string, cum_pos[i], max_perc ); + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, span_string ); + stats_string( span_string, 100.0f - cum_pos[i] + 100.0f * float(table[i])/float(n_mapped_both), max_perc ); + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, span_string ); + } + } +} + +template +void generate_table( + FILE* html_output, + const char* stat_by, + const char* name, + const Bins bin_type, + const Histogram& stats, + const uint32 total) +{ + // + // table stats + // + + const int32 X = XX; + + const Histogram& table = stats; + + // find range, negative values + const int2 row_range = display_range( stats, total ); + + // compute best 2 entries + int32 best_bin[2] = { 0, 1 }; + + find_gt2( row_range.x, row_range.y, stats, best_bin ); + + // write HTML table + { + char buffer1[1024]; + char buffer2[1024]; + sprintf( buffer1, "%s-stats", name ); + sprintf( buffer2, "%s [%s] stats", name, stat_by ); + html::table_object tab( html_output, buffer1, "stats", buffer2 ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "bin" ); + html::th_object( html_output, html::FORMATTED, NULL, "%%" ); + } + + char span_string[1024]; + const float max_perc = 70.0f; + for (int32 i = row_range.x; i <= row_range.y; ++i) + { + html::tr_object tr( html_output, "class", i % 2 ? "none" : "alt", NULL ); + + const int32 c = bin_type == LOG ? log_bin_range(i >= 0 ? i : -i) : i >= 0 ? i : -i; + + const char* cls = (i == best_bin[0]) ? "yellow" : + (i == best_bin[1]) ? "orange" : + "none"; + + html::th_object( html_output, html::FORMATTED, NULL, "%d", i >= 0 ? c : -c ); + stats_string( span_string, total ? 100.0f * float(table[i]) / float(total) : 0.0f, max_perc ); + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, span_string ); + } + } +} + +template +void generate_table( + FILE* html_output, + const char* stat_by, + const char* name, + const Bins bin_type, + const Histogram& stats_l, + const Histogram& stats_r, + const uint32 l_count, + const uint32 r_count) +{ + // + // table stats + // + + const int2 row_range_l = display_range( stats_l, l_count ); + const int2 row_range_r = display_range( stats_r, r_count ); + const int2 row_range = make_int2( nvbio::min( row_range_l.x, row_range_r.x ), + nvbio::max( row_range_l.y, row_range_r.y ) ); + + // compute best 2 entries + int32 best_bin[2] = { 0, 1 }; + int32 worst_bin[2] = { 0, 1 }; + + find_gt2( row_range.x, row_range.y, stats_l, best_bin ); + find_gt2( row_range.x, row_range.y, stats_r, worst_bin ); + + // write table + { + char buffer1[1024]; + char buffer2[1024]; + sprintf( buffer1, "%s-stats", name ); + sprintf( buffer2, "%s [%s] stats", name, stat_by ); + html::table_object tab( html_output, buffer1, "stats", buffer2 ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "bin" ); + html::th_object( html_output, html::FORMATTED, NULL, "[L]" ); + html::th_object( html_output, html::FORMATTED, NULL, "[R]" ); + } + + char span_string[1024]; + const float max_perc = 70.0f; + for (int32 i = row_range.x; i <= row_range.y; ++i) + { + html::tr_object tr( html_output, "class", i % 2 ? "none" : "alt", NULL ); + + const int32 c = bin_type == LOG ? log_bin_range(i >= 0 ? i : -i) : i >= 0 ? i : -i; + + const char* cls_l = (i == best_bin[0]) ? "yellow" : + (i == best_bin[1]) ? "orange" : + "none"; + const char* cls_r = (i == worst_bin[0]) ? "red" : + (i == worst_bin[1]) ? "orange" : + "pink"; + + html::th_object( html_output, html::FORMATTED, NULL, "%d", i >= 0 ? c : -c ); + stats_string( span_string, l_count ? 100.0f * float(stats_l[i]) / float(l_count) : 0.0f, max_perc ); + html::td_object( html_output, html::FORMATTED, "class", cls_l, NULL, span_string ); + stats_string( span_string, r_count ? 100.0f * float(stats_r[i]) / float(r_count) : 0.0f, max_perc ); + html::td_object( html_output, html::FORMATTED, "class", cls_r, NULL, span_string ); + } + } +} + +template +void generate_table2d( + FILE* html_output, + const char* stat_by, + const char* name, + const Histogram2d& stats_l, + const Histogram2d& stats_r, + const char* bin_name, + const std::vector& X_bins, + const std::vector& Y_bins, + const uint32 total, + const uint32 n_mapped_both, + const bool diff_table) +{ + const int32 X = int32(XX); + const int32 Y = int32(YY); + + // + // table stats + // + { + char buffer1[1024]; + char buffer2[1024]; + sprintf( buffer1, "%s-stats-%s", name, bin_name ); + sprintf( buffer2, "%s [%s] stats by %s", name, stat_by, bin_name ); + + // determine the first and last columns + int32 first_col = 0; + int32 last_col = 0; + if (diff_table) + { + first_col = 0; + last_col = Y-1; + } + else + { + for (int32 i = -X+1; i < X; ++i) + { + for (int32 j = 0; j > -Y; --j) + { + if (stats_l(i,j) > 0 || + stats_r(i,j) > 0) + first_col = j; + } + for (int32 j = 0; j < Y; ++j) + { + if (stats_l(i,j) > 0 || + stats_r(i,j) > 0) + last_col = j; + } + } + } + + // determine the first and last row + int32 first_row = 0; + for (int32 i = 0; i > -X; --i) + { + for (int32 j = last_col; j >= first_col; --j) + { + if (stats_l(i,j) > 0 || + stats_r(i,j) > 0) + first_row = i; + } + } + int32 last_row = 0; + for (int32 i = 0; i < X; ++i) + { + for (int32 j = last_col; j >= first_col; --j) + { + if (stats_l(i,j) > 0 || + stats_r(i,j) > 0) + last_row = i; + } + } + + // compute best 2 entries + int2 best_bin[2] = { make_int2(0,0) }; + uint32 best_bin_val[2] = { 0 }; + + for (int32 i = first_row; i <= last_row; ++i) + { + for (int32 j = first_col; j <= last_col; ++j) + { + if (best_bin_val[0] < stats_l(i,j)) + { + best_bin_val[1] = best_bin_val[0]; + best_bin[1] = best_bin[0]; + best_bin_val[0] = stats_l(i,j); + best_bin[0] = make_int2(i,j); + } + else if (best_bin_val[1] < stats_l(i,j)) + { + best_bin_val[1] = stats_l(i,j); + best_bin[1] = make_int2(i,j); + } + } + } + + // compute worst 2 entries + int2 worst_bin[2] = { make_int2(0,0) }; + uint32 worst_bin_val[2] = { 0 }; + + for (int32 i = first_row; i <= last_row; ++i) + { + for (int32 j = (diff_table ? 1 : first_col); j <= last_col; ++j) + { + if (worst_bin_val[0] < stats_r(i,j)) + { + worst_bin_val[1] = worst_bin_val[0]; + worst_bin[1] = worst_bin[0]; + worst_bin_val[0] = stats_r(i,j); + worst_bin[0] = make_int2(i,j); + } + else if (worst_bin_val[1] < stats_l(i,j)) + { + worst_bin_val[1] = stats_r(i,j); + worst_bin[1] = make_int2(i,j); + } + } + } + + html::table_object table( html_output, buffer1, "stats", buffer2 ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + for (int32 j = last_col; j >= (diff_table ? 1 : first_col); --j) + html::th_object( html_output, html::FORMATTED, NULL, "%s%s", j >= 0 ? "" : "-", Y_bins[j >= 0 ? j : -j].c_str() ); + + for (int32 j = first_col; j <= last_col; ++j) + html::th_object( html_output, html::FORMATTED, NULL, "%s%s", j >= 0 ? "" : "-", Y_bins[j >= 0 ? j : -j].c_str() ); + + html::th_object( html_output, html::FORMATTED, NULL, "%s", name ); + } + + for (int32 i = first_row; i <= last_row; ++i) + { + html::tr_object tr( html_output, "class", i % 2 ? "none" : "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "%s%s", i >= 0 ? "" : "-", X_bins[i >= 0 ? i : -i].c_str() ); + + for (int32 j = last_col; j >= (diff_table ? 1 : first_col); --j) + { + const float sval = 100.0f * float(stats_r(i,j))/float(n_mapped_both); + if (sval >= 0.1f) + { + const char* cls = (i == worst_bin[0].x && j == worst_bin[0].y) ? "red" : + (i == worst_bin[1].x && j == worst_bin[1].y) ? "orange" : + "pink"; + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, "%.1f %%", sval ); + } + else if (sval >= 0.01f) + html::td_object( html_output, html::FORMATTED, "class", "smallpink", NULL, "%.2f %%", sval ); + else + { + const char* cls = sval == 0.0f ? "gray" : "pink"; + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, "-" ); + } + } + for (int32 j = first_col; j <= last_col; ++j) + { + const float sval = 100.0f * float(stats_l(i,j))/float(n_mapped_both); + if (sval >= 0.1f) + { + const char* cls = (i == best_bin[0].x && j == best_bin[0].y) ? "yellow" : + (i == best_bin[1].x && j == best_bin[1].y) ? "orange" : + "none"; + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, "%.1f %%", sval ); + } + else if (sval >= 0.01f) + html::td_object( html_output, html::FORMATTED, "class", "small", NULL, "%.2f %%", sval ); + else + { + const char* cls = sval == 0.0f ? "gray" : "none"; + html::td_object( html_output, html::FORMATTED, "class", cls, NULL, "-" ); + } + } + html::td_object( html_output, html::FORMATTED, "class", "gray", NULL, "" ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "%s", bin_name ); + for (int32 i = last_col; i >= (diff_table ? 1 : first_col); --i) + html::td_object( html_output, html::FORMATTED, "class", "gray", NULL, "" ); + for (int32 i = first_col; i <= last_col; ++i) + html::td_object( html_output, html::FORMATTED, "class", "gray", NULL, "" ); + html::td_object( html_output, html::FORMATTED, "class", "gray", NULL, "" ); + } + } +} + +inline +void generate_table(const char* file_name, + const char* stat_by, + const char* name, + const char* diff_name, + const Bins bin_type, + const StatsPartition& stats_l, + const StatsPartition& stats_r, + const uint32 total, + const uint32 n_mapped_both, + const bool absolute_values = true) +{ + FILE* html_output = fopen( file_name, "w" ); + if (html_output == NULL) + { + log_warning( stderr, "unable to write HTML report \"%s\"\n", file_name ); + return; + } + + std::vector read_bins; + read_bins.push_back( "0" ); + for (uint32 x = 0; x < 12; ++x) + { + char buffer[16]; + sprintf(buffer, "%d", read_length_bin_range(x)); + read_bins.push_back( buffer ); + } + + std::vector log_bins; + for (uint32 y = 0; y < 32; ++y) + { + if (y == 0) + log_bins.push_back( "0" ); + else if (y == 1) + log_bins.push_back( "1" ); + else if (y == 2) + log_bins.push_back( "2" ); + else + { + char buffer[16]; + sprintf(buffer, "2^%u", y-1); + log_bins.push_back( buffer ); + } + } + + { + html::html_object html( html_output ); + { + const char* meta_list = ""; + + html::header_object hd( html_output, "nv-aln-diff report", html::style(), meta_list ); + { + html::body_object body( html_output ); + + generate_diff_table( html_output, + stat_by, + diff_name, + bin_type, + stats_l.diff_hist, + stats_r.diff_hist, + total, + n_mapped_both ); + + generate_table2d( html_output, + stat_by, + diff_name, + stats_l.diff_hist_by_length, + stats_r.diff_hist_by_length, + "read length", + read_bins, + log_bins, + total, + n_mapped_both, + true ); + + generate_table2d( html_output, + stat_by, + diff_name, + stats_l.diff_hist_by_value_pos, + stats_r.diff_hist_by_value_pos, + "best value", + log_bins, + log_bins, + total, + n_mapped_both, + true ); + + generate_table2d( html_output, + stat_by, + diff_name, + stats_l.diff_hist_by_mapQ1, + stats_r.diff_hist_by_mapQ1, + "mapQ [L]", + log_bins, + log_bins, + total, + n_mapped_both, + true ); + + generate_table2d( html_output, + stat_by, + diff_name, + stats_l.diff_hist_by_mapQ2, + stats_r.diff_hist_by_mapQ2, + "mapQ [R]", + log_bins, + log_bins, + total, + n_mapped_both, + true ); + + if (absolute_values) + { + generate_table( html_output, + stat_by, + name, + bin_type, + stats_l.hist, + stats_r.hist, + stats_l.hist.count, + stats_r.hist.count ); + + generate_table2d( html_output, + stat_by, + name, + stats_l.hist_by_length, + stats_r.hist_by_length, + "read length", + read_bins, + log_bins, + total, + n_mapped_both, + false ); + + generate_table2d( html_output, + stat_by, + name, + stats_l.hist_by_mapQ, + stats_r.hist_by_mapQ, + "mapQ", + log_bins, + log_bins, + total, + n_mapped_both, + false ); + } + } + } + } + fclose( html_output ); +} + +} // namespace alndiff +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/nvbio-aln-diff.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/nvbio-aln-diff.cpp new file mode 100644 index 0000000000000000000000000000000000000000..bf8f1e979bd5b7ae3fb9845c37452f2f2e0311c2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/nvbio-aln-diff.cpp @@ -0,0 +1,477 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +void crcInit(); + +using namespace nvbio; +using namespace alndiff; + + +int main(int argc, char* argv[]) +{ + crcInit(); + + int cuda_device = -1; + int device_count; + cudaGetDeviceCount(&device_count); + log_verbose(stderr, " cuda devices : %d\n", device_count); + + const char* report_name = NULL; + + const char* filter_name = NULL; + uint32 filter_flags = Filter::ALL; + uint32 filter_stats = Filter::ALL; + int32 filter_delta = 5; + bool paired = false; + bool id_check = true; + + int arg = 1; + while (arg < argc) + { + if (strcmp( argv[arg], "-device" ) == 0) + { + cuda_device = atoi(argv[++arg]); + ++arg; + } + else if (strcmp( argv[arg], "-paired" ) == 0) + { + paired = true; + ++arg; + } + else if (strcmp( argv[arg], "-report" ) == 0) + { + report_name = argv[++arg]; + ++arg; + } + else if (strcmp( argv[arg], "-no-ids" ) == 0) + { + id_check = false; + ++arg; + } + else if (strcmp( argv[arg], "-filter" ) == 0) + { + filter_name = argv[++arg]; + + const std::string flags_string( argv[++arg] ); + const std::string stats_string( argv[++arg] ); + filter_delta = atoi(argv[++arg]); + ++arg; + + char temp[256]; + + // parse the filter flags + const char* begin = flags_string.c_str(); + const char* end = begin; + filter_flags = 0u; + + while (1) + { + while (*end != '|' && *end != '\0') + { + temp[end - begin] = *end; + end++; + } + + temp[end - begin] = '\0'; + + if (strcmp( temp, "distant" ) == 0) + filter_flags |= Filter::DISTANT; + else if (strcmp( temp, "discordant" ) == 0) + filter_flags |= Filter::DISCORDANT; + else if (strcmp( temp, "diff-ref" ) == 0) + filter_flags |= Filter::DIFFERENT_REF; + + if (*end == '\0') + break; + + ++end; begin = end; + } + + // parse the filter stats + begin = stats_string.c_str(); + end = begin; + filter_stats = 0u; + + while (1) + { + while (*end != '|' && *end != '\0') + { + temp[end - begin] = *end; + end++; + } + + temp[end - begin] = '\0'; + + if (strcmp( temp, "ed" ) == 0) + filter_stats |= Filter::ED; + else if (strcmp( temp, "mapQ" ) == 0) + filter_stats |= Filter::MAPQ; + else if (strcmp( temp, "mms" ) == 0) + filter_stats |= Filter::MMS; + else if (strcmp( temp, "ins" ) == 0) + filter_stats |= Filter::INS; + else if (strcmp( temp, "dels" ) == 0) + filter_stats |= Filter::DELS; + + if (*end == '\0') + break; + + ++end; begin = end; + } + } + else + break; + } + + // inspect and select cuda devices + if (device_count) + { + if (cuda_device == -1) + { + int best_device = 0; + cudaDeviceProp best_device_prop; + cudaGetDeviceProperties( &best_device_prop, best_device ); + + for (int device = 0; device < device_count; ++device) + { + cudaDeviceProp device_prop; + cudaGetDeviceProperties( &device_prop, device ); + log_verbose(stderr, " device %d has compute capability %d.%d\n", device, device_prop.major, device_prop.minor); + log_verbose(stderr, " SM count : %u\n", device_prop.multiProcessorCount); + log_verbose(stderr, " SM clock rate : %u Mhz\n", device_prop.clockRate / 1000); + log_verbose(stderr, " memory clock rate : %.1f Ghz\n", float(device_prop.memoryClockRate) * 1.0e-6f); + + if (device_prop.major >= best_device_prop.major && + device_prop.minor >= best_device_prop.minor) + { + best_device_prop = device_prop; + best_device = device; + } + } + cuda_device = best_device; + } + log_verbose(stderr, " chosen device %d\n", cuda_device); + { + cudaDeviceProp device_prop; + cudaGetDeviceProperties( &device_prop, cuda_device ); + log_verbose(stderr, " device name : %s\n", device_prop.name); + log_verbose(stderr, " compute capability : %d.%d\n", device_prop.major, device_prop.minor); + } + cudaSetDevice( cuda_device ); + } + + if (argc < arg + 2) + { + log_info(stderr, "nvbio-aln-diff [OPTIONS] \n"); + log_info(stderr, "OPTIONS:\n"); + log_info(stderr, " -paired # paired-end input\n" ); + log_info(stderr, " -no-ids # do not perform id checks\n" ); + log_info(stderr, " -report # HTML report\n" ); + log_info(stderr, " -filter \n" ); + log_info(stderr, " \n" ); + log_info(stderr, " \n" ); + log_info(stderr, " int:delta\n" ); + return 0; + } + + if (filter_name) + { + std::string filter_flags_string; + if (filter_flags & Filter::DISTANT) + filter_flags_string += std::string(filter_flags_string.length() ? "|" : "") + "distant"; + if (filter_flags & Filter::DISCORDANT) + filter_flags_string += std::string(filter_flags_string.length() ? "|" : "") + "discordant"; + if (filter_flags & Filter::DIFFERENT_REF) + filter_flags_string += std::string(filter_flags_string.length() ? "|" : "") + "diff-ref"; + + std::string filter_stats_string; + if (filter_stats & Filter::ED) + filter_stats_string += std::string(filter_stats_string.length() ? "|" : "") + "ed"; + if (filter_stats & Filter::MAPQ) + filter_stats_string += std::string(filter_stats_string.length() ? "|" : "") + "mapQ"; + if (filter_stats & Filter::MMS) + filter_stats_string += std::string(filter_stats_string.length() ? "|" : "") + "mms"; + if (filter_stats & Filter::INS) + filter_stats_string += std::string(filter_stats_string.length() ? "|" : "") + "ins"; + if (filter_stats & Filter::DELS) + filter_stats_string += std::string(filter_stats_string.length() ? "|" : "") + "dels"; + + log_info(stderr, "filter file : %s\n", filter_name); + log_info(stderr, " flags : %s\n", filter_flags_string.c_str()); + log_info(stderr, " stats : %s\n", filter_stats_string.c_str()); + log_info(stderr, " delta : %d\n", filter_delta); + } + + if (argc == arg + 2) + { + const char *aln_file_nameL = argv[arg]; + const char *aln_file_nameR = argv[arg+1]; + + if (paired) + { + const char *aln_file_nameL = argv[arg]; + const char *aln_file_nameR = argv[arg+1]; + + SharedPointer aln_streamL = SharedPointer( open_alignment_file( aln_file_nameL ) ); + SharedPointer aln_streamR = SharedPointer( open_alignment_file( aln_file_nameR ) ); + + if (aln_streamL == NULL || aln_streamL->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameL); exit(1); } + if (aln_streamR == NULL || aln_streamR->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameR); exit(1); } + + const uint32 BATCH_SIZE = 500000; + std::vector batchL( BATCH_SIZE ); + std::vector batchR( BATCH_SIZE ); + + Filter filter( filter_name, filter_flags, filter_stats, filter_delta ); + SharedPointer analyzer = SharedPointer( new PEAnalyzer( filter, id_check ) ); + + uint32 n_batch = 0; + while (1) + { + const uint32 batch_sizeL = aln_streamL->next_batch( BATCH_SIZE, &batchL[0] ); + const uint32 batch_sizeR = aln_streamR->next_batch( BATCH_SIZE, &batchR[0] ); + + const uint32 min_batch_size = nvbio::min( batch_sizeL, batch_sizeR ); + const uint32 max_batch_size = nvbio::max( batch_sizeL, batch_sizeR ); + + if (min_batch_size != max_batch_size) + log_warning(stderr, "alignment files have different size\n"); + + log_info(stderr, "analizing batch[%u]: %u alignments (%.1f M)\n", n_batch, min_batch_size, float(n_batch * BATCH_SIZE + min_batch_size)*1.0e-6f); + + for (uint32 i = 0; i < min_batch_size; i += 2) + { + const Alignment* alnL1 = &batchL[i]; + const Alignment* alnL2 = &batchL[i+1]; + const Alignment* alnR1 = &batchR[i]; + const Alignment* alnR2 = &batchR[i+1]; + + if (alnL1->is_mapped() && alnL1->mate == alnL2->mate) + { + log_error(stderr, "alignments %u and %u in \"%s\" refer to the same mate, must come from different reads\n", i, i+1, aln_file_nameL); + return 1; + } + if (alnR1->is_mapped() && alnR1->mate == alnR2->mate) + { + log_error(stderr, "alignments %u and %u in \"%s\" refer to the same mate, must come from different reads\n", i, i+1, aln_file_nameR); + return 1; + } + + if (alnL1->mate) std::swap( alnL1, alnL2 ); + if (alnR1->mate) std::swap( alnR1, alnR2 ); + + analyzer->push( + AlignmentPair( *alnL1, *alnL2 ), + AlignmentPair( *alnR1, *alnR2 )); + } + + if (report_name) + analyzer->generate_report( aln_file_nameL, aln_file_nameR, report_name ); + + analyzer->flush(); + + log_verbose(stderr, " mismatched : %5.2f%%\n", 100.0f * analyzer->mismatched()); + log_verbose(stderr, " mapped [L] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L()); + log_verbose(stderr, " mapped [R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_R()); + log_verbose(stderr, " mapped [L&R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L_and_R()); + log_verbose(stderr, " mapped/unmapped [L] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L_not_R()); + log_verbose(stderr, " mapped/unmapped [R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_R_not_L()); + log_verbose(stderr, " paired [L] : %5.2f%%\n", 100.0f * analyzer->paired.avg_L()); + log_verbose(stderr, " paired [R] : %5.2f%%\n", 100.0f * analyzer->paired.avg_R()); + log_verbose(stderr, " paired [L&R] : %5.2f%%\n", 100.0f * analyzer->paired.avg_L_and_R()); + log_verbose(stderr, " paired/unpaired [L] : %5.2f%%\n", 100.0f * analyzer->paired.avg_L_not_R()); + log_verbose(stderr, " paired/unpaired [R] : %5.2f%%\n", 100.0f * analyzer->paired.avg_R_not_L()); + log_verbose(stderr, " different ref : %5.2f%%\n", 100.0f * analyzer->different_ref()); + log_verbose(stderr, " distant : %5.2f%%\n", 100.0f * analyzer->distant()); + log_verbose(stderr, " discordant : %5.2f%%\n", 100.0f * analyzer->discordant()); + log_verbose(stderr, " filtered : %u\n", analyzer->filtered()); + + if (min_batch_size < BATCH_SIZE) + break; + + ++n_batch; + } + } + else + { + SharedPointer aln_streamL = SharedPointer( open_alignment_file( aln_file_nameL ) ); + SharedPointer aln_streamR = SharedPointer( open_alignment_file( aln_file_nameR ) ); + + if (aln_streamL == NULL || aln_streamL->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameL); exit(1); } + if (aln_streamR == NULL || aln_streamR->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameR); exit(1); } + + const uint32 BATCH_SIZE = 500000; + std::vector batchL( BATCH_SIZE ); + std::vector batchR( BATCH_SIZE ); + + Filter filter( filter_name, filter_flags, filter_stats, filter_delta ); + SharedPointer analyzer = SharedPointer( new SEAnalyzer( filter ) ); + + uint32 n_batch = 0; + while (1) + { + const uint32 batch_sizeL = aln_streamL->next_batch( BATCH_SIZE, &batchL[0] ); + const uint32 batch_sizeR = aln_streamR->next_batch( BATCH_SIZE, &batchR[0] ); + + if (batch_sizeL != batch_sizeR) + log_warning(stderr, "alignment files have different size\n"); + + const uint32 min_batch_size = nvbio::min( batch_sizeL, batch_sizeR ); + + log_info(stderr, "analizing batch[%u]: %u alignments (%.1f M)\n", n_batch, min_batch_size, float(n_batch * BATCH_SIZE + min_batch_size)*1.0e-6f); + + for (uint32 i = 0; i < min_batch_size; ++i) + analyzer->push( batchL[i], batchR[i] ); + + if (report_name) + analyzer->generate_report( aln_file_nameL, aln_file_nameR, report_name ); + + analyzer->flush(); + + log_verbose(stderr, " mismatched : %5.2f%%\n", 100.0f * analyzer->mismatched()); + log_verbose(stderr, " mapped [L] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L()); + log_verbose(stderr, " mapped [R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_R()); + log_verbose(stderr, " mapped [L&R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L_and_R()); + log_verbose(stderr, " mapped/unmapped [L] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L_not_R()); + log_verbose(stderr, " mapped/unmapped [R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_R_not_L()); + log_verbose(stderr, " different ref : %5.2f%%\n", 100.0f * analyzer->different_ref()); + log_verbose(stderr, " distant : %5.2f%%\n", 100.0f * analyzer->distant()); + log_verbose(stderr, " discordant : %5.2f%%\n", 100.0f * analyzer->discordant()); + log_verbose(stderr, " filtered : %u\n", analyzer->filtered()); + + if (min_batch_size < BATCH_SIZE) + break; + + ++n_batch; + } + } + } + else if (argc == arg + 4) + { + const char *aln_file_nameL1 = argv[arg]; + const char *aln_file_nameL2 = argv[arg+1]; + const char *aln_file_nameR1 = argv[arg+2]; + const char *aln_file_nameR2 = argv[arg+3]; + + const char* aln_file_nameL = aln_file_nameL1; + const char* aln_file_nameR = aln_file_nameR1; + + SharedPointer aln_streamL1 = SharedPointer( open_alignment_file( aln_file_nameL1 ) ); + SharedPointer aln_streamL2 = SharedPointer( open_alignment_file( aln_file_nameL2 ) ); + SharedPointer aln_streamR1 = SharedPointer( open_alignment_file( aln_file_nameR1 ) ); + SharedPointer aln_streamR2 = SharedPointer( open_alignment_file( aln_file_nameR2 ) ); + + if (aln_streamL1 == NULL || aln_streamL1->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameL1); exit(1); } + if (aln_streamL2 == NULL || aln_streamL2->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameL2); exit(1); } + + if (aln_streamR2 == NULL || aln_streamR1->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameR1); exit(1); } + if (aln_streamR2 == NULL || aln_streamR2->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameR2); exit(1); } + + const uint32 BATCH_SIZE = 500000; + std::vector batchL1( BATCH_SIZE ); + std::vector batchL2( BATCH_SIZE ); + std::vector batchR1( BATCH_SIZE ); + std::vector batchR2( BATCH_SIZE ); + + Filter filter( filter_name, filter_flags, filter_stats, filter_delta ); + SharedPointer analyzer = SharedPointer( new PEAnalyzer( filter, id_check ) ); + + uint32 n_batch = 0; + while (1) + { + const uint32 batch_sizeL1 = aln_streamL1->next_batch( BATCH_SIZE, &batchL1[0] ); + const uint32 batch_sizeL2 = aln_streamL2->next_batch( BATCH_SIZE, &batchL2[0] ); + const uint32 batch_sizeR1 = aln_streamR1->next_batch( BATCH_SIZE, &batchR1[0] ); + const uint32 batch_sizeR2 = aln_streamR2->next_batch( BATCH_SIZE, &batchR2[0] ); + + const uint32 min_batch_size = nvbio::min( + nvbio::min( batch_sizeL1, batch_sizeL2 ), + nvbio::min( batch_sizeR1, batch_sizeR2 ) ); + + const uint32 max_batch_size = nvbio::min( + nvbio::max( batch_sizeL1, batch_sizeL2 ), + nvbio::max( batch_sizeR1, batch_sizeR2 ) ); + + if (min_batch_size != max_batch_size) + log_warning(stderr, "alignment files have different size\n"); + + log_info(stderr, "analizing batch[%u]: %u alignments (%.1f M)\n", n_batch, min_batch_size, float(n_batch * BATCH_SIZE + min_batch_size)*1.0e-6f); + + for (uint32 i = 0; i < min_batch_size; ++i) + analyzer->push( + AlignmentPair( batchL1[i], batchL2[i] ), + AlignmentPair( batchR1[i], batchR2[i] )); + + if (report_name) + analyzer->generate_report( aln_file_nameL, aln_file_nameR, report_name ); + + analyzer->flush(); + + log_verbose(stderr, " mismatched : %5.2f%%\n", 100.0f * analyzer->mismatched()); + log_verbose(stderr, " mapped [L] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L()); + log_verbose(stderr, " mapped [R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_R()); + log_verbose(stderr, " mapped [L&R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L_and_R()); + log_verbose(stderr, " mapped/unmapped [L] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L_not_R()); + log_verbose(stderr, " mapped/unmapped [R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_R_not_L()); + log_verbose(stderr, " paired [L] : %5.2f%%\n", 100.0f * analyzer->paired.avg_L()); + log_verbose(stderr, " paired [R] : %5.2f%%\n", 100.0f * analyzer->paired.avg_R()); + log_verbose(stderr, " paired [L&R] : %5.2f%%\n", 100.0f * analyzer->paired.avg_L_and_R()); + log_verbose(stderr, " paired/unpaired [L] : %5.2f%%\n", 100.0f * analyzer->paired.avg_L_not_R()); + log_verbose(stderr, " paired/unpaired [R] : %5.2f%%\n", 100.0f * analyzer->paired.avg_R_not_L()); + log_verbose(stderr, " different ref : %5.2f%%\n", 100.0f * analyzer->different_ref()); + log_verbose(stderr, " distant : %5.2f%%\n", 100.0f * analyzer->distant()); + log_verbose(stderr, " discordant : %5.2f%%\n", 100.0f * analyzer->discordant()); + log_verbose(stderr, " filtered : %u\n", analyzer->filtered()); + + if (min_batch_size < BATCH_SIZE) + break; + + ++n_batch; + } + } + + cudaDeviceReset(); + return 0; +} + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/pe_analyzer.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/pe_analyzer.cpp new file mode 100644 index 0000000000000000000000000000000000000000..abd3059a9d270e799e1427ff561af1cc10f6fffb --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/pe_analyzer.cpp @@ -0,0 +1,684 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include + +namespace nvbio { +namespace alndiff { + +PEAnalyzer::PEAnalyzer(Filter& filter, const bool id_check) : + m_filter( filter ), + m_id_check( id_check ) +{ + n = 0; + n_mismatched = 0; +} + +void PEAnalyzer::push( + const AlignmentPair& alnL, + const AlignmentPair& alnR) +{ + if ((m_id_check && alnL[0].read_id != alnR[0].read_id) || + (m_id_check && alnL[1].read_id != alnR[1].read_id) || + alnL[0].read_len != alnR[0].read_len || + alnL[1].read_len != alnR[1].read_len) + { + n_mismatched++; + return; + } + + mapped.push( alnL.is_mapped(), alnR.is_mapped() ); + paired.push( alnL.is_mapped_paired(), alnR.is_mapped_paired() ); + unique.push( alnL.is_unique_paired(), alnR.is_unique_paired() ); + ambiguous.push( alnL.is_ambiguous_paired(), alnR.is_ambiguous_paired() ); + + if ((alnL.is_mapped_paired() == true) && (alnR.is_mapped_paired() == false)) paired_L_not_R_by_mapQ.push( log_bin( alnL.mapQ() ) ); + if ((alnR.is_mapped_paired() == true) && (alnL.is_mapped_paired() == false)) paired_R_not_L_by_mapQ.push( log_bin( alnR.mapQ() ) ); + if ((alnL.is_unique_paired() == true) && (alnR.is_unique_paired() == false)) unique_L_not_R_by_mapQ.push( log_bin( alnL.mapQ() ) ); + if ((alnR.is_unique_paired() == true) && (alnL.is_unique_paired() == false)) unique_R_not_L_by_mapQ.push( log_bin( alnR.mapQ() ) ); + if ((alnL.is_ambiguous_paired() == true) && (alnR.is_ambiguous_paired() == false)) ambiguous_L_not_R_by_mapQ.push( log_bin( alnL.mapQ() ) ); + if ((alnR.is_ambiguous_paired() == true) && (alnL.is_ambiguous_paired() == false)) ambiguous_R_not_L_by_mapQ.push( log_bin( alnR.mapQ() ) ); + + // edit-distance correlation stats + //if (alnL.is_mapped_paired()) sec_ed_by_ed_l.push( alnL.ed()+1, alnL.has_second() ? alnL.sec_ed()+1 : 0u ); + //else sec_ed_by_ed_l.push( 0u, 0u ); + + // edit-distance correlation stats + //if (alnR.is_mapped_paired()) sec_ed_by_ed_r.push( alnR.ed()+1, alnR.has_second() ? alnR.sec_ed()+1 : 0u ); + //else sec_ed_by_ed_r.push( 0u, 0u ); + + if (alnL.is_mapped_paired() && alnR.is_mapped_paired()) + { + const uint32 mapQ_bin = log_bin( alnR.mapQ() ); + + uint32 read_flags = 0u; + + if ((alnL[0].ref_id != alnR[0].ref_id) && + (alnL[1].ref_id != alnR[1].ref_id)) + { + n_different_ref12.push( mapQ_bin ); + n_different_ref.push( mapQ_bin ); + n_distant12.push( mapQ_bin ); + n_distant.push( mapQ_bin ); + + if ((alnL.is_unique_paired() == true) && + (alnR.is_unique_paired() == true)) + { + n_different_ref_unique.push( mapQ_bin ); + n_distant_unique.push( mapQ_bin ); + } + if ((alnL.is_ambiguous_paired() == false) && + (alnR.is_ambiguous_paired() == false)) + { + n_different_ref_not_ambiguous.push( mapQ_bin ); + n_distant_not_ambiguous.push( mapQ_bin ); + } + + read_flags |= Filter::DISTANT; + read_flags |= Filter::DIFFERENT_REF; + } + else if (alnL[0].ref_id != alnR[0].ref_id) + { + n_different_ref1.push( mapQ_bin ); + n_different_ref.push( mapQ_bin ); + n_distant1.push( mapQ_bin ); + n_distant.push( mapQ_bin ); + + if ((alnL.is_unique_paired() == true) && + (alnR.is_unique_paired() == true)) + { + n_different_ref_unique.push( mapQ_bin ); + n_distant_unique.push( mapQ_bin ); + } + if ((alnL.is_ambiguous_paired() == false) && + (alnR.is_ambiguous_paired() == false)) + { + n_different_ref_not_ambiguous.push( mapQ_bin ); + n_distant_not_ambiguous.push( mapQ_bin ); + } + + read_flags |= Filter::DISTANT; + read_flags |= Filter::DIFFERENT_REF; + } + else if (alnL[1].ref_id != alnR[1].ref_id) + { + n_different_ref2.push( mapQ_bin ); + n_different_ref.push( mapQ_bin ); + n_distant2.push( mapQ_bin ); + n_distant.push( mapQ_bin ); + + if ((alnL.is_unique_paired() == true) && + (alnR.is_unique_paired() == true)) + { + n_different_ref_unique.push( mapQ_bin ); + n_distant_unique.push( mapQ_bin ); + } + if ((alnL.is_ambiguous_paired() == false) && + (alnR.is_ambiguous_paired() == false)) + { + n_different_ref_not_ambiguous.push( mapQ_bin ); + n_distant_not_ambiguous.push( mapQ_bin ); + } + + read_flags |= Filter::DISTANT; + read_flags |= Filter::DIFFERENT_REF; + } + else if (alndiff::distant( alnL[0], alnR[0] ) && alndiff::distant( alnL[1], alnR[1] )) + { + n_distant12.push( mapQ_bin ); + n_distant.push( mapQ_bin ); + + if ((alnL.is_unique_paired() == true) && + (alnR.is_unique_paired() == true)) + n_distant_unique.push( mapQ_bin ); + if ((alnL.is_ambiguous_paired() == false) && + (alnR.is_ambiguous_paired() == false)) + n_distant_not_ambiguous.push( mapQ_bin ); + + read_flags |= Filter::DISTANT; + } + else if (alndiff::distant( alnL[0], alnR[0] )) + { + n_distant1.push( mapQ_bin ); + n_distant.push( mapQ_bin ); + + if ((alnL.is_unique_paired() == true) && + (alnR.is_unique_paired() == true)) + n_distant_unique.push( mapQ_bin ); + if ((alnL.is_ambiguous_paired() == false) && + (alnR.is_ambiguous_paired() == false)) + n_distant_not_ambiguous.push( mapQ_bin ); + + read_flags |= Filter::DISTANT; + } + else if (alndiff::distant( alnL[1], alnR[1] )) + { + n_distant2.push( mapQ_bin ); + n_distant.push( mapQ_bin ); + + if ((alnL.is_unique_paired() == true) && + (alnR.is_unique_paired() == true)) + n_distant_unique.push( mapQ_bin ); + if ((alnL.is_ambiguous_paired() == false) && + (alnR.is_ambiguous_paired() == false)) + n_distant_not_ambiguous.push( mapQ_bin ); + + read_flags |= Filter::DISTANT; + } + + if ((alnL[0].is_rc() != alnR[0].is_rc()) && + (alnL[1].is_rc() != alnR[1].is_rc())) + { + n_discordant12.push( mapQ_bin ); + n_discordant.push( mapQ_bin ); + + if ((alnL.is_unique_paired() == true) && + (alnR.is_unique_paired() == true)) + n_discordant_unique.push( mapQ_bin ); + if ((alnL.is_ambiguous_paired() == false) && + (alnR.is_ambiguous_paired() == false)) + n_discordant_not_ambiguous.push( mapQ_bin ); + + read_flags |= Filter::DISCORDANT; + } + if (alnL[0].is_rc() != alnR[0].is_rc()) + { + n_discordant1.push( mapQ_bin ); + n_discordant.push( mapQ_bin ); + + if ((alnL.is_unique_paired() == true) && + (alnR.is_unique_paired() == true)) + n_discordant_unique.push( mapQ_bin ); + if ((alnL.is_ambiguous_paired() == false) && + (alnR.is_ambiguous_paired() == false)) + n_discordant_not_ambiguous.push( mapQ_bin ); + + read_flags |= Filter::DISCORDANT; + } + else if (alnL[1].is_rc() != alnR[1].is_rc()) + { + n_discordant2.push( mapQ_bin ); + n_discordant.push( mapQ_bin ); + + if ((alnL.is_unique_paired() == true) && + (alnR.is_unique_paired() == true)) + n_discordant_unique.push( mapQ_bin ); + if ((alnL.is_ambiguous_paired() == false) && + (alnR.is_ambiguous_paired() == false)) + n_discordant_not_ambiguous.push( mapQ_bin ); + + read_flags |= Filter::DISCORDANT; + } + + const uint32 length_bin = read_length_bin( alnL.read_len() ); + + // generic stats + { + // score + m_filter( al_stats.higher_score.push( alnL.score(), alnR.score(), length_bin, alnL.mapQ(), alnR.mapQ() ), read_flags, Filter::SCORE, alnL.read_id() ); + + // ed + m_filter( al_stats.lower_ed.push( alnL.ed(), alnR.ed(), length_bin, alnL.mapQ(), alnR.mapQ() ), read_flags, Filter::ED, alnL.read_id() ); + + // mapQ + m_filter( al_stats.higher_mapQ.push( alnL.mapQ(), alnR.mapQ(), length_bin, alnL.mapQ(), alnR.mapQ() ), read_flags, Filter::MAPQ, alnL.read_id() ); + + // longer mapping + al_stats.longer_mapping.push( alnL.mapped_read_bases(), alnR.mapped_read_bases(), length_bin, alnL.mapQ(), alnR.mapQ() ); + + al_stats.lower_subs.push( alnL.subs(), alnR.subs(), length_bin, alnL.mapQ(), alnR.mapQ() ); + m_filter( al_stats.lower_mms.push( alnL.n_mm(), alnR.n_mm(), length_bin, alnL.mapQ(), alnR.mapQ() ), read_flags, Filter::MMS, alnL.read_id() ); + m_filter( al_stats.lower_ins.push( alnL.ins(), alnR.ins(), length_bin, alnL.mapQ(), alnR.mapQ() ), read_flags, Filter::INS, alnL.read_id() ); + m_filter( al_stats.lower_dels.push( alnL.dels(), alnR.dels(), length_bin, alnL.mapQ(), alnR.mapQ() ), read_flags, Filter::DELS, alnL.read_id() ); + + al_stats.higher_pos.push( alnL[0].pos, alnR[0].pos, length_bin, alnL.mapQ(), alnR.mapQ() ); + // TODO: this is a 2d quantity + + //if (alnL.has_second()) + sec_score_by_score_l.push( log_bin( alnL.score() ), log_bin( alnL.score() - alnL.sec_score() ) ); + + //if (alnR.has_second()) + sec_score_by_score_r.push( log_bin( alnR.score() ), log_bin( alnR.score() - alnR.sec_score() ) ); + } + if (read_flags & Filter::DISTANT) + { + // ed + distant_stats.lower_ed.push( alnL.ed(), alnR.ed(), length_bin, alnL.mapQ(), alnR.mapQ() ); + + // mapQ + distant_stats.higher_mapQ.push( alnL.mapQ(), alnR.mapQ(), length_bin, alnL.mapQ(), alnR.mapQ() ); + + // longer mapping + distant_stats.longer_mapping.push( alnL.mapped_read_bases(), alnR.mapped_read_bases(), length_bin, alnL.mapQ(), alnR.mapQ() ); + + distant_stats.lower_subs.push( alnL.subs(), alnR.subs(), length_bin, alnL.mapQ(), alnR.mapQ() ); + distant_stats.lower_mms.push( alnL.n_mm(), alnR.n_mm(), length_bin, alnL.mapQ(), alnR.mapQ() ); + distant_stats.lower_ins.push( alnL.ins(), alnR.ins(), length_bin, alnL.mapQ(), alnR.mapQ() ); + distant_stats.lower_dels.push( alnL.dels(), alnR.dels(), length_bin, alnL.mapQ(), alnR.mapQ() ); + + distant_stats.higher_pos.push( alnL[0].pos, alnR[0].pos, length_bin, alnL.mapQ(), alnR.mapQ() ); + // TODO: this is a 2d quantity + } + if (read_flags & Filter::DISCORDANT) + { + // ed + discordant_stats.lower_ed.push( alnL.ed(), alnR.ed(), length_bin, alnL.mapQ(), alnR.mapQ() ); + + // mapQ + discordant_stats.higher_mapQ.push( alnL.mapQ(), alnR.mapQ(), length_bin, alnL.mapQ(), alnR.mapQ() ); + + // longer mapping + discordant_stats.longer_mapping.push( alnL.mapped_read_bases(), alnR.mapped_read_bases(), length_bin, alnL.mapQ(), alnR.mapQ() ); + + discordant_stats.lower_subs.push( alnL.subs(), alnR.subs(), length_bin, alnL.mapQ(), alnR.mapQ() ); + discordant_stats.lower_mms.push( alnL.n_mm(), alnR.n_mm(), length_bin, alnL.mapQ(), alnR.mapQ() ); + discordant_stats.lower_ins.push( alnL.ins(), alnR.ins(), length_bin, alnL.mapQ(), alnR.mapQ() ); + discordant_stats.lower_dels.push( alnL.dels(), alnR.dels(), length_bin, alnL.mapQ(), alnR.mapQ() ); + + discordant_stats.higher_pos.push( alnL[0].pos, alnR[0].pos, length_bin, alnL.mapQ(), alnR.mapQ() ); + // TODO: this is a 2d quantity + } + } + + ++n; +} + +namespace { + +void generate_summary_header(FILE* html_output) +{ + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + html::th_object( html_output, html::FORMATTED, NULL, "better" ); + html::th_object( html_output, html::FORMATTED, "class", "red", NULL, "worse" ); +} +template +void generate_summary_cell(FILE* html_output, const std::string file_name, const char* type, const StatsType& stats, const uint32 n, const char* cls) +{ + char link_name[1024]; + sprintf( link_name, "%s", local_file( file_name ), type ); + html::tr_object tr( html_output, "class", cls, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, link_name ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %%", 100.0f * float(stats.l.diff_hist.all_but(0))/float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %%", 100.0f * float(stats.r.diff_hist.all_but(0))/float(n) ); +} + +} // anonymous namespace + +void PEAnalyzer::generate_report(const char* aln_file_nameL, const char* aln_file_nameR, const char* report) +{ + if (report == NULL) + return; + + const std::string mapped_bps_name = generate_file_name( report, "mapped-bps" ); + const std::string score_name = generate_file_name( report, "score" ); + const std::string ed_name = generate_file_name( report, "ed" ); + const std::string mapQ_name = generate_file_name( report, "mapQ" ); + const std::string mms_name = generate_file_name( report, "mms" ); + const std::string ins_name = generate_file_name( report, "ins" ); + const std::string dels_name = generate_file_name( report, "dels" ); + const std::string pos_name = generate_file_name( report, "pos" ); + + const std::string distant_mapped_bps_name = generate_file_name( report, "distant_stats.mapped-bps" ); + const std::string distant_ed_name = generate_file_name( report, "distant_stats.ed" ); + const std::string distant_mapQ_name = generate_file_name( report, "distant_stats.mapQ" ); + const std::string distant_mms_name = generate_file_name( report, "distant_stats.mms" ); + const std::string distant_ins_name = generate_file_name( report, "distant_stats.ins" ); + const std::string distant_dels_name = generate_file_name( report, "distant_stats.dels" ); + const std::string distant_pos_name = generate_file_name( report, "distant_stats.pos" ); + + const std::string discordant_mapped_bps_name = generate_file_name( report, "discordant_stats.mapped-bps" ); + const std::string discordant_ed_name = generate_file_name( report, "discordant_stats.ed" ); + const std::string discordant_mapQ_name = generate_file_name( report, "discordant_stats.mapQ" ); + const std::string discordant_mms_name = generate_file_name( report, "discordant_stats.mms" ); + const std::string discordant_ins_name = generate_file_name( report, "discordant_stats.ins" ); + const std::string discordant_dels_name = generate_file_name( report, "discordant_stats.dels" ); + const std::string discordant_pos_name = generate_file_name( report, "discordant_stats.pos" ); + + generate_table( mapped_bps_name.c_str(), "paired L & R", "mapped bps", "mapped bps diff", al_stats.longer_mapping.bin_type(), al_stats.longer_mapping.l, al_stats.longer_mapping.r, n, paired.L_and_R ); + generate_table( score_name.c_str(), "paired L & R", "score", "score diff", al_stats.higher_score.bin_type(), al_stats.higher_score.l, al_stats.higher_score.r, n, paired.L_and_R ); + generate_table( ed_name.c_str(), "paired L & R", "edit distance", "edit distance diff", al_stats.lower_ed.bin_type(), al_stats.lower_ed.l, al_stats.lower_ed.r, n, paired.L_and_R ); + generate_table( mapQ_name.c_str(), "paired L & R", "mapQ", "mapQ diff", al_stats.higher_mapQ.bin_type(), al_stats.higher_mapQ.l, al_stats.higher_mapQ.r, n, paired.L_and_R ); + generate_table( mms_name.c_str(), "paired L & R", "mms", "mms diff", al_stats.lower_mms.bin_type(), al_stats.lower_mms.l, al_stats.lower_mms.r, n, paired.L_and_R ); + generate_table( ins_name.c_str(), "paired L & R", "ins", "ins diff", al_stats.lower_ins.bin_type(), al_stats.lower_ins.l, al_stats.lower_ins.r, n, paired.L_and_R ); + generate_table( dels_name.c_str(), "paired L & R", "dels", "dels diff", al_stats.lower_dels.bin_type(), al_stats.lower_dels.l, al_stats.lower_dels.r, n, paired.L_and_R ); + generate_table( pos_name.c_str(), "paired L & R", "position", "distance", al_stats.higher_pos.bin_type(), al_stats.higher_pos.l, al_stats.higher_pos.r, n, paired.L_and_R, false ); + + generate_table( distant_mapped_bps_name.c_str(), "distant", "mapped bps", "mapped bps diff", distant_stats.longer_mapping.bin_type(), distant_stats.longer_mapping.l, distant_stats.longer_mapping.r, n, n_distant.count ); + generate_table( distant_ed_name.c_str(), "distant", "edit distance", "edit distance diff", distant_stats.lower_ed.bin_type(), distant_stats.lower_ed.l, distant_stats.lower_ed.r, n, n_distant.count ); + generate_table( distant_mapQ_name.c_str(), "distant", "mapQ", "mapQ diff", distant_stats.higher_mapQ.bin_type(), distant_stats.higher_mapQ.l, distant_stats.higher_mapQ.r, n, n_distant.count ); + generate_table( distant_mms_name.c_str(), "distant", "mms", "mms diff", distant_stats.lower_mms.bin_type(), distant_stats.lower_mms.l, distant_stats.lower_mms.r, n, n_distant.count ); + generate_table( distant_ins_name.c_str(), "distant", "ins", "ins diff", distant_stats.lower_ins.bin_type(), distant_stats.lower_ins.l, distant_stats.lower_ins.r, n, n_distant.count ); + generate_table( distant_dels_name.c_str(), "distant", "dels", "dels diff", distant_stats.lower_dels.bin_type(), distant_stats.lower_dels.l, distant_stats.lower_dels.r, n, n_distant.count ); + generate_table( distant_pos_name.c_str(), "distant", "position", "distance", distant_stats.higher_pos.bin_type(), distant_stats.higher_pos.l, distant_stats.higher_pos.r, n, n_distant.count, false ); + + generate_table( discordant_mapped_bps_name.c_str(), "discordant", "mapped bps", "mapped bps diff", discordant_stats.longer_mapping.bin_type(), discordant_stats.longer_mapping.l, discordant_stats.longer_mapping.r, n, n_discordant.count ); + generate_table( discordant_ed_name.c_str(), "discordant", "edit distance","edit distance diff", discordant_stats.lower_ed.bin_type(), discordant_stats.lower_ed.l, discordant_stats.lower_ed.r, n, n_discordant.count ); + generate_table( discordant_mapQ_name.c_str(), "discordant", "mapQ", "mapQ diff", discordant_stats.higher_mapQ.bin_type(), discordant_stats.higher_mapQ.l, discordant_stats.higher_mapQ.r, n, n_discordant.count ); + generate_table( discordant_mms_name.c_str(), "discordant", "mms", "mms diff", discordant_stats.lower_mms.bin_type(), discordant_stats.lower_mms.l, discordant_stats.lower_mms.r, n, n_discordant.count ); + generate_table( discordant_ins_name.c_str(), "discordant", "ins", "ins diff", discordant_stats.lower_ins.bin_type(), discordant_stats.lower_ins.l, discordant_stats.lower_ins.r, n, n_discordant.count ); + generate_table( discordant_dels_name.c_str(), "discordant", "dels", "dels diff", discordant_stats.lower_dels.bin_type(), discordant_stats.lower_dels.l, discordant_stats.lower_dels.r, n, n_discordant.count ); + generate_table( discordant_pos_name.c_str(), "discordant", "position", "distance", discordant_stats.higher_pos.bin_type(), discordant_stats.higher_pos.l, discordant_stats.higher_pos.r, n, n_discordant.count, false ); + + FILE* html_output = fopen( report, "w" ); + if (html_output == NULL) + { + log_warning( stderr, "unable to write HTML report \"%s\"\n", report ); + return; + } + + std::vector log_bins; + for (uint32 y = 0; y < 11; ++y) + { + if (y == 0) + log_bins.push_back( "0" ); + else if (y == 1) + log_bins.push_back( "1" ); + else if (y == 2) + log_bins.push_back( "2" ); + else + { + char buffer[16]; + sprintf(buffer, "2^%u", y-1); + log_bins.push_back( buffer ); + } + } + log_bins.push_back( "inf" ); + + std::vector ed_bins; + ed_bins.push_back("-"); + for (uint32 y = 0; y < 16; ++y) + { + char buffer[16]; + sprintf(buffer, "%u", y); + ed_bins.push_back( buffer ); + } + + const Histogram<8> cum_different_ref = reverse_cumulative( n_different_ref ); + const Histogram<8> cum_different_ref12 = reverse_cumulative( n_different_ref12 ); + const Histogram<8> cum_different_ref1 = reverse_cumulative( n_different_ref1 ); + const Histogram<8> cum_different_ref2 = reverse_cumulative( n_different_ref2 ); + const Histogram<8> cum_different_ref_unique = reverse_cumulative( n_different_ref_unique ); + const Histogram<8> cum_different_ref_not_ambiguous = reverse_cumulative( n_different_ref_not_ambiguous ); + + const Histogram<8> cum_distant = reverse_cumulative( n_distant ); + const Histogram<8> cum_distant12 = reverse_cumulative( n_distant12 ); + const Histogram<8> cum_distant1 = reverse_cumulative( n_distant1 ); + const Histogram<8> cum_distant2 = reverse_cumulative( n_distant2 ); + const Histogram<8> cum_distant_unique = reverse_cumulative( n_distant_unique ); + const Histogram<8> cum_distant_not_ambiguous = reverse_cumulative( n_distant_not_ambiguous ); + + const Histogram<8> cum_discordant = reverse_cumulative( n_discordant ); + const Histogram<8> cum_discordant12 = reverse_cumulative( n_discordant12 ); + const Histogram<8> cum_discordant1 = reverse_cumulative( n_discordant1 ); + const Histogram<8> cum_discordant2 = reverse_cumulative( n_discordant2 ); + const Histogram<8> cum_discordant_unique = reverse_cumulative( n_discordant_unique ); + const Histogram<8> cum_discordant_not_ambiguous = reverse_cumulative( n_discordant_not_ambiguous ); + + const uint32 HI_MAPQ_BIN = 6; // >= 32 + { + html::html_object html( html_output ); + { + const char* meta_list = ""; + + html::header_object hd( html_output, "nv-aln-diff report", html::style(), meta_list ); + { + html::body_object body( html_output ); + + // + // alignment stats + // + { + html::table_object table( html_output, "alignment-stats", "stats", "alignment stats" ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + html::th_object( html_output, html::FORMATTED, NULL, "L = %s", aln_file_nameL ); + html::th_object( html_output, html::FORMATTED, NULL, "R = %s", aln_file_nameR ); + html::th_object( html_output, html::FORMATTED, NULL, "L & R" ); + html::th_object( html_output, html::FORMATTED, NULL, "L \\ R" ); + html::th_object( html_output, html::FORMATTED, NULL, "R \\ L" ); + } + { + html::tr_object tr( html_output, "class", "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "mapped"); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %%", 100.0f * float(mapped.L) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %%", 100.0f * float(mapped.R) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "green", NULL, "%5.2f %%", 100.0f * float(mapped.L_and_R) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %%", 100.0f * float(mapped.L_not_R) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %%", 100.0f * float(mapped.R_not_L) / float(n) ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "paired"); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %%", 100.0f * float(paired.L) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %%", 100.0f * float(paired.R) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "green", NULL, "%5.2f %%", 100.0f * float(paired.L_and_R) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(paired.L_not_R) / float(n), 100.0f * float(paired_L_not_R_by_mapQ[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %% (%.3f %%)", 100.0f * float(paired.R_not_L) / float(n), 100.0f * float(paired_R_not_L_by_mapQ[HI_MAPQ_BIN]) / float(n) ); + } + { + html::tr_object tr( html_output, "class", "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "unique"); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %%", 100.0f * float(unique.L) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %%", 100.0f * float(unique.R) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "green", NULL, "%5.2f %%", 100.0f * float(unique.L_and_R) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(unique.L_not_R) / float(n), 100.0f * float(unique_L_not_R_by_mapQ[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %% (%.3f %%)", 100.0f * float(unique.R_not_L) / float(n), 100.0f * float(unique_R_not_L_by_mapQ[HI_MAPQ_BIN]) / float(n) ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "ambiguous"); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %%", 100.0f * float(ambiguous.L) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %%", 100.0f * float(ambiguous.R) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "green", NULL, "%5.2f %%", 100.0f * float(ambiguous.L_and_R) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(ambiguous.L_not_R) / float(n), 100.0f * float(ambiguous_L_not_R_by_mapQ[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %% (%.3f %%)", 100.0f * float(ambiguous.R_not_L) / float(n), 100.0f * float(ambiguous_R_not_L_by_mapQ[HI_MAPQ_BIN]) / float(n) ); + } + } + // + // discordance stats + // + { + html::table_object table( html_output, "discordance-stats", "stats", "discordance stats" ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + html::th_object( html_output, html::FORMATTED, NULL, "items" ); + html::th_object( html_output, html::FORMATTED, NULL, "%% of total" ); + html::th_object( html_output, html::FORMATTED, NULL, "mate 1" ); + html::th_object( html_output, html::FORMATTED, NULL, "mate 2" ); + html::th_object( html_output, html::FORMATTED, NULL, "mate 1 & 2" ); + html::th_object( html_output, html::FORMATTED, NULL, "unique" ); + html::th_object( html_output, html::FORMATTED, NULL, "not-ambiguous" ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "different reference" ); + html::td_object( html_output, html::FORMATTED, NULL, "%.2f M (%.2f M)", float(cum_different_ref[0]) * 1.0e-6f, float(cum_different_ref[HI_MAPQ_BIN]) * 1.0e-6f ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_different_ref[0]) / float(n), 100.0f * float(cum_different_ref[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_different_ref1[0]) / float(n), 100.0f * float(cum_different_ref1[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_different_ref2[0]) / float(n), 100.0f * float(cum_different_ref2[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_different_ref12[0]) / float(n), 100.0f * float(cum_different_ref12[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_different_ref_unique[0]) / float(n), 100.0f * float(cum_different_ref_unique[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_different_ref_not_ambiguous[0]) / float(n), 100.0f * float(cum_different_ref_not_ambiguous[HI_MAPQ_BIN]) / float(n) ); + } + { + html::tr_object tr( html_output, "class", "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "distant" ); + html::td_object( html_output, html::FORMATTED, NULL, "%.2f M (%.2f M)", float(cum_distant[0]) * 1.0e-6f, float(cum_distant[HI_MAPQ_BIN]) * 1.0e-6f ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_distant[0]) / float(n), 100.0f * float(cum_distant[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_distant1[0]) / float(n), 100.0f * float(cum_distant1[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_distant2[0]) / float(n), 100.0f * float(cum_distant2[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_distant12[0]) / float(n), 100.0f * float(cum_distant12[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_distant_unique[0]) / float(n), 100.0f * float(cum_distant_unique[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_distant_not_ambiguous[0]) / float(n), 100.0f * float(cum_distant_not_ambiguous[HI_MAPQ_BIN]) / float(n) ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "discordant" ); + html::td_object( html_output, html::FORMATTED, NULL, "%.2f M (%.2f M)", float(cum_discordant[0]) * 1.0e-6f, float(cum_discordant[HI_MAPQ_BIN]) * 1.0e-6f ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_discordant[0]) / float(n), 100.0f * float(cum_discordant[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_discordant1[0]) / float(n), 100.0f * float(cum_discordant1[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_discordant2[0]) / float(n), 100.0f * float(cum_discordant2[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_discordant12[0]) / float(n), 100.0f * float(cum_discordant12[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_discordant_unique[0]) / float(n), 100.0f * float(cum_discordant_unique[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_discordant_not_ambiguous[0]) / float(n), 100.0f * float(cum_discordant_not_ambiguous[HI_MAPQ_BIN]) / float(n) ); + } + } + // + // summary stats + // + { + html::table_object table( html_output, "summary-stats", "stats", "summary stats" ); + // ------------------------------------------- generic -------------------------------------------------- // + generate_summary_header( html_output ); + generate_summary_cell( html_output, mapped_bps_name, "mapped bases", al_stats.longer_mapping, n, "none" ); + generate_summary_cell( html_output, score_name, "score", al_stats.higher_score, n, "alt" ); + generate_summary_cell( html_output, ed_name, "edit distance",al_stats.lower_ed, n, "none" ); + generate_summary_cell( html_output, mapQ_name, "mapQ", al_stats.higher_mapQ, n, "alt" ); + generate_summary_cell( html_output, mms_name, "mismatches", al_stats.lower_mms, n, "none" ); + generate_summary_cell( html_output, ins_name, "insertions", al_stats.lower_ins, n, "alt" ); + generate_summary_cell( html_output, dels_name, "deletions", al_stats.lower_dels, n, "none" ); + generate_summary_cell( html_output, pos_name, "distance", al_stats.higher_pos, n, "alt" ); + // ------------------------------------------- distant -------------------------------------------------- // + generate_summary_header( html_output ); + generate_summary_cell( html_output, distant_mapped_bps_name, "mapped bases [distant]", distant_stats.longer_mapping, n, "none" ); + generate_summary_cell( html_output, distant_ed_name, "edit distance [distant]",distant_stats.lower_ed, n, "alt" ); + generate_summary_cell( html_output, distant_mapQ_name, "mapQ [distant]", distant_stats.higher_mapQ, n, "none" ); + generate_summary_cell( html_output, distant_mms_name, "mismatches [distant]", distant_stats.lower_mms, n, "alt" ); + generate_summary_cell( html_output, distant_ins_name, "insertions [distant]", distant_stats.lower_ins, n, "none" ); + generate_summary_cell( html_output, distant_dels_name, "deletions [distant]", distant_stats.lower_dels, n, "alt" ); + generate_summary_cell( html_output, distant_pos_name, "distance [distant]", distant_stats.higher_pos, n, "none" ); + // ------------------------------------------- discordant ---------------------------------------------- // + generate_summary_header( html_output ); + generate_summary_cell( html_output, discordant_mapped_bps_name, "mapped bases [discordant]", discordant_stats.longer_mapping, n, "alt" ); + generate_summary_cell( html_output, discordant_ed_name, "edit distance [discordant]",discordant_stats.lower_ed, n, "none" ); + generate_summary_cell( html_output, discordant_mapQ_name, "mapQ [discordant]", discordant_stats.higher_mapQ, n, "alt" ); + generate_summary_cell( html_output, discordant_mms_name, "mismatches [discordant]", discordant_stats.lower_mms, n, "none" ); + generate_summary_cell( html_output, discordant_ins_name, "insertions [discordant]", discordant_stats.lower_ins, n, "alt" ); + generate_summary_cell( html_output, discordant_dels_name, "deletions [discordant]", discordant_stats.lower_dels, n, "none" ); + generate_summary_cell( html_output, discordant_pos_name, "distance [discordant]", discordant_stats.higher_pos, n, "alt" ); + } + + // paired L not R + generate_table( + html_output, + "by mapQ", + "paired (L \\ R) vs (R \\ L)", + LOG, + paired_L_not_R_by_mapQ, + paired_R_not_L_by_mapQ, + n, + n ); + + // unique L not R + generate_table( + html_output, + "by mapQ", + "unique (L \\ R) vs (R \\ L)", + LOG, + unique_L_not_R_by_mapQ, + unique_R_not_L_by_mapQ, + n, + n ); + + // unique L not R + generate_table( + html_output, + "by mapQ", + "ambiguous (L \\ R) vs (R \\ L)", + LOG, + ambiguous_L_not_R_by_mapQ, + ambiguous_R_not_L_by_mapQ, + n, + n ); + + // different reference by mapQ + generate_table( + html_output, + "paired L & R", + "different reference by mapQ", + LOG, + n_different_ref, + paired.L_and_R ); + + // different reference by mapQ + generate_table( + html_output, + "paired L & R", + "distant by mapQ", + LOG, + n_distant, + paired.L_and_R ); + + // discordant reference by mapQ + generate_table( + html_output, + "paired L & R", + "discordant by mapQ", + LOG, + n_discordant, + paired.L_and_R ); + + // second score by score + generate_table2d( + html_output, + "paired L & R", + "second score", + sec_score_by_score_l, + sec_score_by_score_r, + "score", + log_bins, + log_bins, + n, + paired.L_and_R, + false ); + + // second score by score + /*generate_table2d( + html_output, + "paired L & R", + "second ed", + sec_ed_by_ed_l, + sec_ed_by_ed_r, + "ed", + ed_bins, + ed_bins, + n, + n, + false );*/ + } + } + } + fclose( html_output ); +} + +} // namespace alndiff +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/pe_analyzer.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/pe_analyzer.h new file mode 100644 index 0000000000000000000000000000000000000000..12d3056c626b2a2db3e08b08aae671bbdbf4bf5b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/pe_analyzer.h @@ -0,0 +1,110 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include + +namespace nvbio { +namespace alndiff { + +struct PEAnalyzer +{ + PEAnalyzer(Filter& filter, const bool id_check); + + void push( + const AlignmentPair& alnL, + const AlignmentPair& alnR); + + void generate_report(const char* aln_file_nameL, const char* aln_file_nameR, const char* report); + + // flush any open files + // + void flush() { m_filter.flush(); } + + float mismatched() const { return float(n_mismatched)/float(n + n_mismatched); } + + float different_ref() const { return float(n_different_ref.count)/float(n); } + float distant() const { return float(n_distant.count)/float(n); } + float discordant() const { return float(n_discordant.count)/float(n); } + uint32 filtered() const { return m_filter.filtered(); } + + Filter& m_filter; + bool m_id_check; + + BooleanStats mapped; + BooleanStats paired; + BooleanStats unique; + BooleanStats ambiguous; + BooleanStats not_ambiguous; + + Histogram<8> paired_L_not_R_by_mapQ; + Histogram<8> paired_R_not_L_by_mapQ; + Histogram<8> unique_L_not_R_by_mapQ; + Histogram<8> unique_R_not_L_by_mapQ; + Histogram<8> ambiguous_L_not_R_by_mapQ; + Histogram<8> ambiguous_R_not_L_by_mapQ; + + uint32 n; + uint32 n_mismatched; + + Histogram<8> n_different_ref12; + Histogram<8> n_different_ref1; + Histogram<8> n_different_ref2; + Histogram<8> n_different_ref; + Histogram<8> n_different_ref_unique; + Histogram<8> n_different_ref_not_ambiguous; + + Histogram<8> n_distant12; + Histogram<8> n_distant1; + Histogram<8> n_distant2; + Histogram<8> n_distant; + Histogram<8> n_distant_unique; + Histogram<8> n_distant_not_ambiguous; + + Histogram<8> n_discordant12; + Histogram<8> n_discordant1; + Histogram<8> n_discordant2; + Histogram<8> n_discordant; + Histogram<8> n_discordant_unique; + Histogram<8> n_discordant_not_ambiguous; + + AlignmentStats al_stats; + AlignmentStats distant_stats; + AlignmentStats discordant_stats; + + Histogram2d<12,12> sec_score_by_score_l; + Histogram2d<12,12> sec_score_by_score_r; + + Histogram2d<16,16> sec_ed_by_ed_l; + Histogram2d<16,16> sec_ed_by_ed_r; +}; + +} // namespace alndiff +} // namespace nvbio \ No newline at end of file diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/se_analyzer.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/se_analyzer.cpp new file mode 100644 index 0000000000000000000000000000000000000000..9c1e78e34666b51c0879c0d4edb56d6a73becbcc --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/se_analyzer.cpp @@ -0,0 +1,415 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include + +namespace nvbio { +namespace alndiff { + +SEAnalyzer::SEAnalyzer(Filter& filter) : + m_filter( filter ) +{ + n = 0; + n_mismatched = 0; +} + +void SEAnalyzer::push( + const Alignment& alnL, + const Alignment& alnR) +{ + if (alnL.read_id != alnR.read_id || + alnL.read_len != alnR.read_len) + { + n_mismatched++; + return; + } + + mapped.push( alnL.is_mapped(), alnR.is_mapped() ); + unique.push( alnL.is_unique(), alnR.is_unique() ); + ambiguous.push( alnL.is_ambiguous(), alnR.is_ambiguous() ); + + if ((alnL.is_mapped() == true) && (alnR.is_mapped() == false)) mapped_L_not_R_by_mapQ.push( log_bin( alnL.mapQ ) ); + if ((alnR.is_mapped() == true) && (alnL.is_mapped() == false)) mapped_R_not_L_by_mapQ.push( log_bin( alnR.mapQ ) ); + if ((alnL.is_unique() == true) && (alnR.is_unique() == false)) unique_L_not_R_by_mapQ.push( log_bin( alnL.mapQ ) ); + if ((alnR.is_unique() == true) && (alnL.is_unique() == false)) unique_R_not_L_by_mapQ.push( log_bin( alnR.mapQ ) ); + if ((alnL.is_ambiguous() == true) && (alnR.is_ambiguous() == false)) ambiguous_L_not_R_by_mapQ.push( log_bin( alnL.mapQ ) ); + if ((alnR.is_ambiguous() == true) && (alnL.is_ambiguous() == false)) ambiguous_R_not_L_by_mapQ.push( log_bin( alnR.mapQ ) ); + + if (alnL.is_mapped() && alnR.is_mapped()) + { + const uint32 mapQ_bin = log_bin( alnR.mapQ ); + + uint32 read_flags = 0u; + + if (alnL.ref_id != alnR.ref_id) + { + n_different_ref.push( mapQ_bin ); + n_distant.push( mapQ_bin ); + read_flags |= Filter::DISTANT; + read_flags |= Filter::DIFFERENT_REF; + } + else if (alndiff::distant( alnL, alnR )) + { + n_distant.push( mapQ_bin ); + read_flags |= Filter::DISTANT; + } + + if (alnL.is_rc() != alnR.is_rc()) + { + n_discordant.push( mapQ_bin ); + read_flags |= Filter::DISCORDANT; + } + + const uint32 length_bin = read_length_bin( alnL.read_len ); + + // generic stats + { + // ed + m_filter( al_stats.lower_ed.push( alnL.ed, alnR.ed, length_bin, alnL.mapQ, alnR.mapQ ), read_flags, Filter::ED, alnL.read_id ); + + // mapQ + m_filter( al_stats.higher_mapQ.push( alnL.mapQ, alnR.mapQ, length_bin, alnL.mapQ, alnR.mapQ ), read_flags, Filter::MAPQ, alnL.read_id ); + + // longer mapping + al_stats.longer_mapping.push( alnL.mapped_read_bases(), alnR.mapped_read_bases(), length_bin, alnL.mapQ, alnR.mapQ ); + + al_stats.lower_subs.push( alnL.subs, alnR.subs, length_bin, alnL.mapQ, alnR.mapQ ); + m_filter( al_stats.lower_mms.push( alnL.n_mm, alnR.n_mm, length_bin, alnL.mapQ, alnR.mapQ ), read_flags, Filter::MMS, alnL.read_id ); + m_filter( al_stats.lower_ins.push( alnL.ins, alnR.ins, length_bin, alnL.mapQ, alnR.mapQ ), read_flags, Filter::INS, alnL.read_id ); + m_filter( al_stats.lower_dels.push( alnL.dels, alnR.dels, length_bin, alnL.mapQ, alnR.mapQ ), read_flags, Filter::DELS, alnL.read_id ); + + al_stats.higher_pos.push( alnL.pos, alnR.pos, length_bin, alnL.mapQ, alnR.mapQ ); + } + if (read_flags & Filter::DISTANT) + { + // ed + distant_stats.lower_ed.push( alnL.ed, alnR.ed, length_bin, alnL.mapQ, alnR.mapQ ); + + // mapQ + distant_stats.higher_mapQ.push( alnL.mapQ, alnR.mapQ, length_bin, alnL.mapQ, alnR.mapQ ); + + // longer mapping + distant_stats.longer_mapping.push( alnL.mapped_read_bases(), alnR.mapped_read_bases(), length_bin, alnL.mapQ, alnR.mapQ ); + + distant_stats.lower_subs.push( alnL.subs, alnR.subs, length_bin, alnL.mapQ, alnR.mapQ ); + distant_stats.lower_mms.push( alnL.n_mm, alnR.n_mm, length_bin, alnL.mapQ, alnR.mapQ ); + distant_stats.lower_ins.push( alnL.ins, alnR.ins, length_bin, alnL.mapQ, alnR.mapQ ); + distant_stats.lower_dels.push( alnL.dels, alnR.dels, length_bin, alnL.mapQ, alnR.mapQ ); + distant_stats.higher_pos.push( alnL.pos, alnR.pos, length_bin, alnL.mapQ, alnR.mapQ ); + } + if (read_flags & Filter::DISCORDANT) + { + // ed + discordant_stats.lower_ed.push( alnL.ed, alnR.ed, length_bin, alnL.mapQ, alnR.mapQ ); + + // mapQ + discordant_stats.higher_mapQ.push( alnL.mapQ, alnR.mapQ, length_bin, alnL.mapQ, alnR.mapQ ); + + // longer mapping + discordant_stats.longer_mapping.push( alnL.mapped_read_bases(), alnR.mapped_read_bases(), length_bin, alnL.mapQ, alnR.mapQ ); + + discordant_stats.lower_subs.push( alnL.subs, alnR.subs, length_bin, alnL.mapQ, alnR.mapQ ); + discordant_stats.lower_mms.push( alnL.n_mm, alnR.n_mm, length_bin, alnL.mapQ, alnR.mapQ ); + discordant_stats.lower_ins.push( alnL.ins, alnR.ins, length_bin, alnL.mapQ, alnR.mapQ ); + discordant_stats.lower_dels.push( alnL.dels, alnR.dels, length_bin, alnL.mapQ, alnR.mapQ ); + discordant_stats.higher_pos.push( alnL.pos, alnR.pos, length_bin, alnL.mapQ, alnR.mapQ ); + } + } + + ++n; +} + +namespace { + +void generate_summary_header(FILE* html_output) +{ + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + html::th_object( html_output, html::FORMATTED, NULL, "better" ); + html::th_object( html_output, html::FORMATTED, "class", "red", NULL, "worse" ); +} +template +void generate_summary_cell(FILE* html_output, const std::string file_name, const char* type, const StatsType& stats, const uint32 n) +{ + char link_name[1024]; + sprintf( link_name, "%s", local_file( file_name ), type ); + html::tr_object tr( html_output, "class", "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, link_name ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %%", 100.0f * float(stats.l.diff_hist.all_but(0))/float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %%", 100.0f * float(stats.r.diff_hist.all_but(0))/float(n) ); +} + +} // anonymous namespace + +void SEAnalyzer::generate_report(const char* aln_file_name1, const char* aln_file_name2, const char* report) +{ + if (report == NULL) + return; + + const std::string mapped_bps_name = generate_file_name( report, "mapped-bps" ); + const std::string ed_name = generate_file_name( report, "ed" ); + const std::string mapQ_name = generate_file_name( report, "mapQ" ); + const std::string mms_name = generate_file_name( report, "mms" ); + const std::string ins_name = generate_file_name( report, "ins" ); + const std::string dels_name = generate_file_name( report, "dels" ); + const std::string pos_name = generate_file_name( report, "pos" ); + + const std::string distant_mapped_bps_name = generate_file_name( report, "distant_stats.mapped-bps" ); + const std::string distant_ed_name = generate_file_name( report, "distant_stats.ed" ); + const std::string distant_mapQ_name = generate_file_name( report, "distant_stats.mapQ" ); + const std::string distant_mms_name = generate_file_name( report, "distant_stats.mms" ); + const std::string distant_ins_name = generate_file_name( report, "distant_stats.ins" ); + const std::string distant_dels_name = generate_file_name( report, "distant_stats.dels" ); + const std::string distant_pos_name = generate_file_name( report, "distant_stats.pos" ); + + const std::string discordant_mapped_bps_name = generate_file_name( report, "discordant_stats.mapped-bps" ); + const std::string discordant_ed_name = generate_file_name( report, "discordant_stats.ed" ); + const std::string discordant_mapQ_name = generate_file_name( report, "discordant_stats.mapQ" ); + const std::string discordant_mms_name = generate_file_name( report, "discordant_stats.mms" ); + const std::string discordant_ins_name = generate_file_name( report, "discordant_stats.ins" ); + const std::string discordant_dels_name = generate_file_name( report, "discordant_stats.dels" ); + const std::string discordant_pos_name = generate_file_name( report, "discordant_stats.pos" ); + + generate_table( mapped_bps_name.c_str(), "mapped L & R", "mapped bps", "mapped bps diff", al_stats.longer_mapping.bin_type(), al_stats.longer_mapping.l, al_stats.longer_mapping.r, n, mapped.L_and_R ); + generate_table( ed_name.c_str(), "mapped L & R", "edit distance", "edit distance diff", al_stats.lower_ed.bin_type(), al_stats.lower_ed.l, al_stats.lower_ed.r, n, mapped.L_and_R ); + generate_table( mapQ_name.c_str(), "mapped L & R", "mapQ", "mapQ diff", al_stats.higher_mapQ.bin_type(), al_stats.higher_mapQ.l, al_stats.higher_mapQ.r, n, mapped.L_and_R ); + generate_table( mms_name.c_str(), "mapped L & R", "mms", "mms diff", al_stats.lower_mms.bin_type(), al_stats.lower_mms.l, al_stats.lower_mms.r, n, mapped.L_and_R ); + generate_table( ins_name.c_str(), "mapped L & R", "ins", "ins diff", al_stats.lower_ins.bin_type(), al_stats.lower_ins.l, al_stats.lower_ins.r, n, mapped.L_and_R ); + generate_table( dels_name.c_str(), "mapped L & R", "dels", "dels diff", al_stats.lower_dels.bin_type(), al_stats.lower_dels.l, al_stats.lower_dels.r, n, mapped.L_and_R ); + generate_table( pos_name.c_str(), "mapped L & R", "position", "distance", al_stats.higher_pos.bin_type(), al_stats.higher_pos.l, al_stats.higher_pos.r, n, mapped.L_and_R, false ); + + generate_table( distant_mapped_bps_name.c_str(), "distant", "mapped bps", "mapped bps diff", distant_stats.longer_mapping.bin_type(), distant_stats.longer_mapping.l, distant_stats.longer_mapping.r, n, n_distant.count ); + generate_table( distant_ed_name.c_str(), "distant", "edit distance", "edit distance diff", distant_stats.lower_ed.bin_type(), distant_stats.lower_ed.l, distant_stats.lower_ed.r, n, n_distant.count ); + generate_table( distant_mapQ_name.c_str(), "distant", "mapQ", "mapQ diff", distant_stats.higher_mapQ.bin_type(), distant_stats.higher_mapQ.l, distant_stats.higher_mapQ.r, n, n_distant.count ); + generate_table( distant_mms_name.c_str(), "distant", "mms", "mms diff", distant_stats.lower_mms.bin_type(), distant_stats.lower_mms.l, distant_stats.lower_mms.r, n, n_distant.count ); + generate_table( distant_ins_name.c_str(), "distant", "ins", "ins diff", distant_stats.lower_ins.bin_type(), distant_stats.lower_ins.l, distant_stats.lower_ins.r, n, n_distant.count ); + generate_table( distant_dels_name.c_str(), "distant", "dels", "dels diff", distant_stats.lower_dels.bin_type(), distant_stats.lower_dels.l, distant_stats.lower_dels.r, n, n_distant.count ); + generate_table( distant_pos_name.c_str(), "distant", "position", "distance", distant_stats.higher_pos.bin_type(), distant_stats.higher_pos.l, distant_stats.higher_pos.r, n, n_distant.count, false ); + + generate_table( discordant_mapped_bps_name.c_str(), "discordant", "mapped bps", "mapped bps diff", discordant_stats.longer_mapping.bin_type(), discordant_stats.longer_mapping.l, discordant_stats.longer_mapping.r, n, n_discordant.count ); + generate_table( discordant_ed_name.c_str(), "discordant", "edit distance", "edit distance diff", discordant_stats.lower_ed.bin_type(), discordant_stats.lower_ed.l, discordant_stats.lower_ed.r, n, n_discordant.count ); + generate_table( discordant_mapQ_name.c_str(), "discordant", "mapQ", "mapQ diff", discordant_stats.higher_mapQ.bin_type(), discordant_stats.higher_mapQ.l, discordant_stats.higher_mapQ.r, n, n_discordant.count ); + generate_table( discordant_mms_name.c_str(), "discordant", "mms", "mms diff", discordant_stats.lower_mms.bin_type(), discordant_stats.lower_mms.l, discordant_stats.lower_mms.r, n, n_discordant.count ); + generate_table( discordant_ins_name.c_str(), "discordant", "ins", "ins diff", discordant_stats.lower_ins.bin_type(), discordant_stats.lower_ins.l, discordant_stats.lower_ins.r, n, n_discordant.count ); + generate_table( discordant_dels_name.c_str(), "discordant", "dels", "dels diff", discordant_stats.lower_dels.bin_type(), discordant_stats.lower_dels.l, discordant_stats.lower_dels.r, n, n_discordant.count ); + generate_table( discordant_pos_name.c_str(), "discordant", "position", "distance", discordant_stats.higher_pos.bin_type(), discordant_stats.higher_pos.l, discordant_stats.higher_pos.r, n, n_discordant.count, false ); + + FILE* html_output = fopen( report, "w" ); + if (html_output == NULL) + { + log_warning( stderr, "unable to write HTML report \"%s\"\n", report ); + return; + } + + const Histogram<8> cum_different_ref = reverse_cumulative( n_different_ref ); + const Histogram<8> cum_distant = reverse_cumulative( n_distant ); + const Histogram<8> cum_discordant = reverse_cumulative( n_discordant ); + + const uint32 HI_MAPQ_BIN = 6; // >= 32 + { + html::html_object html( html_output ); + { + const char* meta_list = ""; + + html::header_object hd( html_output, "nv-aln-diff report", html::style(), meta_list ); + { + html::body_object body( html_output ); + + // + // alignment stats + // + { + html::table_object table( html_output, "alignment-stats", "stats", "alignment stats" ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + html::th_object( html_output, html::FORMATTED, NULL, "L = %s", aln_file_name1 ); + html::th_object( html_output, html::FORMATTED, NULL, "R = %s", aln_file_name2 ); + html::th_object( html_output, html::FORMATTED, NULL, "L & R" ); + html::th_object( html_output, html::FORMATTED, NULL, "L \\ R" ); + html::th_object( html_output, html::FORMATTED, NULL, "R \\ L" ); + } + { + html::tr_object tr( html_output, "class", "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "mapped"); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %%", 100.0f * float(mapped.L) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %%", 100.0f * float(mapped.R) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "green", NULL, "%5.2f %%", 100.0f * float(mapped.L_and_R) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(mapped.L_not_R) / float(n), 100.0f * float(mapped_L_not_R_by_mapQ[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %% (%.3f %%)", 100.0f * float(mapped.R_not_L) / float(n), 100.0f * float(mapped_R_not_L_by_mapQ[HI_MAPQ_BIN]) / float(n) ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "unique"); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %%", 100.0f * float(unique.L) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %%", 100.0f * float(unique.R) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "green", NULL, "%5.2f %%", 100.0f * float(unique.L_and_R) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(unique.L_not_R) / float(n), 100.0f * float(unique_L_not_R_by_mapQ[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %% (%.3f %%)", 100.0f * float(unique.R_not_L) / float(n), 100.0f * float(unique_R_not_L_by_mapQ[HI_MAPQ_BIN]) / float(n) ); + } + { + html::tr_object tr( html_output, "class", "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "ambiguous"); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %%", 100.0f * float(ambiguous.L) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %%", 100.0f * float(ambiguous.R) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "green", NULL, "%5.2f %%", 100.0f * float(ambiguous.L_and_R) / float(n) ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(ambiguous.L_not_R) / float(n), 100.0f * float(ambiguous_L_not_R_by_mapQ[HI_MAPQ_BIN]) / float(n) ); + html::td_object( html_output, html::FORMATTED, "class", "pink", NULL, "%5.2f %% (%.3f %%)", 100.0f * float(ambiguous.R_not_L) / float(n), 100.0f * float(ambiguous_R_not_L_by_mapQ[HI_MAPQ_BIN]) / float(n) ); + } + } + // + // discordance stats + // + { + html::table_object table( html_output, "discordance-stats", "stats", "discordance stats" ); + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "" ); + html::th_object( html_output, html::FORMATTED, NULL, "items" ); + html::th_object( html_output, html::FORMATTED, NULL, "%% of total" ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "different reference" ); + html::td_object( html_output, html::FORMATTED, NULL, "%.2f M (%.2f M)", float(cum_different_ref[0]) * 1.0e-6f, float(cum_different_ref[HI_MAPQ_BIN]) * 1.0e-6f ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_different_ref[0]) / float(n), 100.0f * float(cum_different_ref[HI_MAPQ_BIN]) / float(n) ); + } + { + html::tr_object tr( html_output, "class", "alt", NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "distant" ); + html::td_object( html_output, html::FORMATTED, NULL, "%.2f M (%.2f M)", float(cum_distant[0]) * 1.0e-6f, float(cum_distant[HI_MAPQ_BIN]) * 1.0e-6f ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_distant[0]) / float(n), 100.0f * float(cum_distant[HI_MAPQ_BIN]) / float(n) ); + } + { + html::tr_object tr( html_output, NULL ); + html::th_object( html_output, html::FORMATTED, NULL, "discordant" ); + html::td_object( html_output, html::FORMATTED, NULL, "%.2f M (%.2f M)", float(cum_discordant[0]) * 1.0e-6f, float(cum_discordant[HI_MAPQ_BIN]) * 1.0e-6f ); + html::td_object( html_output, html::FORMATTED, NULL, "%5.2f %% (%.3f %%)", 100.0f * float(cum_discordant[0]) / float(n), 100.0f * float(cum_discordant[HI_MAPQ_BIN]) / float(n) ); + } + } + // + // summary stats + // + { + html::table_object table( html_output, "summary-stats", "stats", "summary stats" ); + generate_summary_header( html_output ); + generate_summary_cell( html_output, mapped_bps_name, "mapped bases", al_stats.longer_mapping, n ); + generate_summary_cell( html_output, ed_name, "edit distance",al_stats.lower_ed, n ); + generate_summary_cell( html_output, mapQ_name, "mapQ", al_stats.higher_mapQ, n ); + generate_summary_cell( html_output, mms_name, "mismatches", al_stats.lower_mms, n ); + generate_summary_cell( html_output, ins_name, "insertions", al_stats.lower_ins, n ); + generate_summary_cell( html_output, dels_name, "deletions", al_stats.lower_dels, n ); + generate_summary_cell( html_output, pos_name, "distance", al_stats.higher_pos, n ); + // ------------------------------------------- distant -------------------------------------------------- // + generate_summary_header( html_output ); + generate_summary_cell( html_output, distant_mapped_bps_name, "mapped bases [distant]", distant_stats.longer_mapping, n ); + generate_summary_cell( html_output, distant_ed_name, "edit distance [distant]",distant_stats.lower_ed, n ); + generate_summary_cell( html_output, distant_mapQ_name, "mapQ [distant]", distant_stats.higher_mapQ, n ); + generate_summary_cell( html_output, distant_mms_name, "mismatches [distant]", distant_stats.lower_mms, n ); + generate_summary_cell( html_output, distant_ins_name, "insertions [distant]", distant_stats.lower_ins, n ); + generate_summary_cell( html_output, distant_dels_name, "deletions [distant]", distant_stats.lower_dels, n ); + generate_summary_cell( html_output, distant_pos_name, "distance [distant]", distant_stats.higher_pos, n ); + // ------------------------------------------- discordant ---------------------------------------------- // + generate_summary_header( html_output ); + generate_summary_cell( html_output, discordant_mapped_bps_name, "mapped bases [discordant]", discordant_stats.longer_mapping, n ); + generate_summary_cell( html_output, discordant_ed_name, "edit distance [discordant]",discordant_stats.lower_ed, n ); + generate_summary_cell( html_output, discordant_mapQ_name, "mapQ [discordant]", discordant_stats.higher_mapQ, n ); + generate_summary_cell( html_output, discordant_mms_name, "mismatches [discordant]", discordant_stats.lower_mms, n ); + generate_summary_cell( html_output, discordant_ins_name, "insertions [discordant]", discordant_stats.lower_ins, n ); + generate_summary_cell( html_output, discordant_dels_name, "deletions [discordant]", discordant_stats.lower_dels, n ); + generate_summary_cell( html_output, discordant_pos_name, "distance [discordant]", discordant_stats.higher_pos, n ); + } + + // mapped L not R + generate_table( + html_output, + "by mapQ", + "mapped (L \\ R) vs (R \\ L)", + LOG, + mapped_L_not_R_by_mapQ, + mapped_R_not_L_by_mapQ, + n, + n ); + + // unique L not R + generate_table( + html_output, + "by mapQ", + "unique (L \\ R) vs (R \\ L)", + LOG, + unique_L_not_R_by_mapQ, + unique_R_not_L_by_mapQ, + n, + n ); + + // unique L not R + generate_table( + html_output, + "by mapQ", + "ambiguous (L \\ R) vs (R \\ L)", + LOG, + ambiguous_L_not_R_by_mapQ, + ambiguous_R_not_L_by_mapQ, + n, + n ); + + // different reference by mapQ + generate_table( + html_output, + "mapped L & R", + "different reference by mapQ", + LOG, + n_different_ref, + mapped.L_and_R ); + + // different reference by mapQ + generate_table( + html_output, + "mapped L & R", + "distant by mapQ", + LOG, + n_distant, + mapped.L_and_R ); + + // discordant reference by mapQ + generate_table( + html_output, + "mapped L & R", + "discordant by mapQ", + LOG, + n_discordant, + mapped.L_and_R ); + } + } + } + fclose( html_output ); +} + +} // namespace alndiff +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/se_analyzer.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/se_analyzer.h new file mode 100644 index 0000000000000000000000000000000000000000..3ea7b038ae84d436ea27fc31eb8b1ce0fe572427 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/se_analyzer.h @@ -0,0 +1,84 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include + +namespace nvbio { +namespace alndiff { + +struct SEAnalyzer +{ + SEAnalyzer(Filter& filter); + + void push( + const Alignment& aln1, + const Alignment& aln2); + + void generate_report(const char* aln_file_name1, const char* aln_file_name2, const char* report); + + // flush any open files + // + void flush() { m_filter.flush(); } + + float mismatched() const { return float(n_mismatched)/float(n + n_mismatched); } + float different_ref() const { return float(n_different_ref.count)/float(n); } + float distant() const { return float(n_distant.count)/float(n); } + float discordant() const { return float(n_discordant.count)/float(n); } + uint32 filtered() const { return m_filter.filtered(); } + + Filter& m_filter; + + BooleanStats mapped; + BooleanStats unique; + BooleanStats ambiguous; + BooleanStats not_ambiguous; + + Histogram<8> mapped_L_not_R_by_mapQ; + Histogram<8> mapped_R_not_L_by_mapQ; + Histogram<8> unique_L_not_R_by_mapQ; + Histogram<8> unique_R_not_L_by_mapQ; + Histogram<8> ambiguous_L_not_R_by_mapQ; + Histogram<8> ambiguous_R_not_L_by_mapQ; + + uint32 n; + uint32 n_mismatched; + + Histogram<8> n_different_ref; + Histogram<8> n_distant; + Histogram<8> n_discordant; + + AlignmentStats al_stats; + AlignmentStats distant_stats; + AlignmentStats discordant_stats; +}; + +} // namespace alndiff +} // namespace nvbio \ No newline at end of file diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/stats.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/stats.h new file mode 100644 index 0000000000000000000000000000000000000000..13b9f82e018038afb7794387568d171c4036be3f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/stats.h @@ -0,0 +1,150 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include + +namespace nvbio { +namespace alndiff { + +enum Type { LOWER = 0, HIGHER = 1 }; +enum Bins { LINEAR = 0, LOG = 1 }; + +struct StatsPartition +{ + Histogram<256> hist; + Histogram2d<12,10> hist_by_length; + Histogram2d<12,10> hist_by_mapQ; + Histogram<256> diff_hist; + Histogram2d<12,10> diff_hist_by_length; + Histogram2d<32,10> diff_hist_by_value_neg; + Histogram2d<32,10> diff_hist_by_value_pos; + Histogram2d<7,12> diff_hist_by_mapQ1; + Histogram2d<7,12> diff_hist_by_mapQ2; +}; + +template +struct Stats +{ + static const Type TYPE = TYPE_T; + static const Bins BINS = BINS_T; + + typedef StatsPartition Partition; + + Bins bin_type() const { return BINS; } + + int32 push(const int32 val1, const int32 val2, const uint32 length_bin, const uint32 mapQ1, const uint32 mapQ2) + { + l.hist.push( (BINS == LOG) ? log_bin(val1) : val1 ); + l.hist_by_length.push( length_bin, log_bin( val1 ) ); + l.hist_by_mapQ.push( log_bin( mapQ1 ), log_bin( val1 ) ); + + r.hist.push( (BINS == LOG) ? log_bin(val2) : val2 ); + r.hist_by_length.push( length_bin, log_bin( val2 ) ); + r.hist_by_mapQ.push( log_bin( mapQ2 ), log_bin( val2) ); + + if (TYPE == LOWER) + { + const int32 diff = int32(val2) - int32(val1); + if (diff >= 0) + { + const int32 log_diff = log_bin( diff ); + l.diff_hist.push( (BINS == LOG) ? log_diff : diff ); + l.diff_hist_by_length.push( length_bin, log_diff ); + l.diff_hist_by_mapQ1.push( log_bin(mapQ1), log_diff ); + l.diff_hist_by_mapQ2.push( log_bin(mapQ2), log_diff ); + if (val1 < 0) + l.diff_hist_by_value_neg.push( log_bin(-val1), log_diff ); + else + l.diff_hist_by_value_pos.push( log_bin(val1), log_diff ); + } + if (diff <= 0) + { + const int32 log_diff = log_bin( -diff ); + r.diff_hist.push( (BINS == LOG) ? log_diff : -diff ); + r.diff_hist_by_length.push( length_bin, log_diff ); + r.diff_hist_by_mapQ1.push( log_bin(mapQ1), log_diff ); + r.diff_hist_by_mapQ2.push( log_bin(mapQ2), log_diff ); + if (val2 < 0) + r.diff_hist_by_value_neg.push( log_bin(-val2), log_diff ); + else + r.diff_hist_by_value_pos.push( log_bin(val2), log_diff ); + } + return diff; + } + else + { + const int32 diff = int32(val1) - int32(val2); + if (diff >= 0) + { + const int32 log_diff = log_bin( diff ); + l.diff_hist.push( (BINS == LOG) ? log_diff : diff ); + l.diff_hist_by_length.push( length_bin, log_diff ); + l.diff_hist_by_mapQ1.push( log_bin(mapQ1), log_diff ); + l.diff_hist_by_mapQ2.push( log_bin(mapQ2), log_diff ); + if (val2 < 0) + l.diff_hist_by_value_neg.push( log_bin(-val2), log_diff ); + else + l.diff_hist_by_value_pos.push( log_bin(val2), log_diff ); + } + if (diff <= 0) + { + const int32 log_diff = log_bin( -diff ); + r.diff_hist.push( (BINS == LOG) ? log_diff : -diff ); + r.diff_hist_by_length.push( length_bin, log_diff ); + r.diff_hist_by_mapQ1.push( log_bin(mapQ1), log_diff ); + r.diff_hist_by_mapQ2.push( log_bin(mapQ2), log_diff ); + if (val1 < 0) + r.diff_hist_by_value_neg.push( log_bin(-val1), log_diff ); + else + r.diff_hist_by_value_pos.push( log_bin(val1), log_diff ); + } + return diff; + } + } + + Partition l; + Partition r; +}; + +struct AlignmentStats +{ + Stats higher_score; + Stats lower_ed; + Stats higher_mapQ; + Stats longer_mapping; + Stats higher_pos; + Stats lower_subs; + Stats lower_ins; + Stats lower_dels; + Stats lower_mms; +}; + +} // namespace alndiff +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/utils.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/utils.h new file mode 100644 index 0000000000000000000000000000000000000000..38047095c08b256543d4c79cf887c80b08f5cdd8 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvbio-aln-diff/utils.h @@ -0,0 +1,226 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include + +namespace nvbio { +namespace alndiff { + +struct BooleanStats +{ + BooleanStats() : L(0), R(0), L_not_R(0), R_not_L(0), L_and_R(0), n(0) {} + + void push(const bool l, const bool r) + { + L += (l == true) ? 1u : 0u; + R += (r == true) ? 1u : 0u; + L_not_R += (l == true) && (r == false) ? 1u : 0u; + R_not_L += (r == true) && (l == false) ? 1u : 0u; + L_and_R += (l == true) && (r == true) ? 1u : 0u; + ++n; + } + + float avg_L() const { return n ? float(L) / float(n) : 0.0f; } + float avg_R() const { return n ? float(R) / float(n) : 0.0f; } + float avg_L_not_R() const { return n ? float(L_not_R) / float(n) : 0.0f; } + float avg_R_not_L() const { return n ? float(R_not_L) / float(n) : 0.0f; } + float avg_L_and_R() const { return n ? float(L_and_R) / float(n) : 0.0f; } + + uint32 L; + uint32 R; + uint32 L_not_R; + uint32 R_not_L; + uint32 L_and_R; + uint32 n; +}; + +template +struct Histogram +{ + Histogram() : count(0) + { + for (uint32 i = 0; i < 2*X; ++i) + bins[i] = 0; + } + + uint32 all_but(const uint32 i) const { return count - bins[i+X]; } + + uint32 operator[] (const int32 i) const { return bins[i + X]; } + + void push(const int32 i) + { + const int32 bin = nvbio::min(nvbio::max(int32(i + X),0),int32(2*X-1)); + ++bins[bin]; + ++count; + } + + uint32 count; + uint32 bins[2*X]; +}; + +// accumulate histogram values bottom-up +template +Histogram cumulative(const Histogram& I) +{ + Histogram H; + H.count = I.count; + H.bins[0] = I.bins[0]; + for (int32 i = 1; i < 2*X; ++i) + H.bins[i] = I.bins[i] + H.bins[i-1]; + return H; +} +// accumulate histogram values top-down +template +Histogram reverse_cumulative(const Histogram& I) +{ + Histogram H; + H.count = I.count; + H.bins[2*X-1] = I.bins[2*X-1]; + for (int32 i = 2*X-2; i >= 0; --i) + H.bins[i] = I.bins[i] + H.bins[i+1]; + return H; +} + +template +struct Histogram2d +{ + Histogram2d() : count(0) + { + for (uint32 i = 0; i < 2*X; ++i) + for (uint32 j = 0; j < 2*Y; ++j) + bins[i][j] = 0; + } + + void push(const int32 x, const int32 y) + { + const int32 bin_x = nvbio::min(nvbio::max(int32(x + X),0),int32(2*X-1)); + const int32 bin_y = nvbio::min(nvbio::max(int32(y + Y),0),int32(2*Y-1)); + ++bins[bin_x][bin_y]; + ++count; + } + uint32 operator() (const int32 i, const int32 j) const { return bins[i + X][j + Y]; } + + uint32 count; + uint32 bins[2*X][2*Y]; +}; + +inline +uint32 read_length_bin_range(const uint32 bin) +{ + switch (bin) + { + case 0: + return 16; + case 1: + return 36; + case 2: + return 100; + case 3: + return 150; + case 4: + return 200; + case 5: + return 250; + case 6: + return 300; + case 7: + return 350; + case 8: + return 400; + case 9: + return 450; + case 10: + return 500; + default: + return 1000; + } +} + +inline +uint32 read_length_bin(const uint32 read_len) +{ + if (read_len <= 16) + return 0; + else if (read_len <= 36) + return 1; + else if (read_len <= 100) + return 2; + else if (read_len <= 150) + return 3; + else if (read_len <= 200) + return 4; + else if (read_len <= 250) + return 5; + else if (read_len <= 300) + return 6; + else if (read_len <= 350) + return 7; + else if (read_len <= 400) + return 8; + else if (read_len <= 450) + return 9; + else if (read_len <= 500) + return 10; + else + return 11; +} +inline int32 log_bin(const int32 x) +{ + return x == 0 ? 0u : + x < 0 ? -int32(1u + nvbio::log2(-x)) : + int32(1u + nvbio::log2(x)); +} +inline int32 log_bin_range(const int32 bin) +{ + return bin == 0 ? 0 : + bin < 0 ? -int32(1u << (-bin+1)) : + int32(1u << (bin-1)); +} + +// return the local file name from a path +// +inline const char* local_file(const std::string& file_name) +{ + #if WIN32 + const size_t pos = file_name.find_last_of("/\\"); + #else + const size_t pos = file_name.rfind('/'); + #endif + + if (pos == std::string::npos) + return file_name.c_str(); + else + return file_name.c_str() + pos + 1u; +} + +} // namespace alndiff +} // namespace nvbio diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..30ea43417a2d8b394bd87cf66b9cd3a34a7d924b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/CMakeLists.txt @@ -0,0 +1,22 @@ +nvbio_module(nvmem) + +addsources( +nvmem.cu +pipeline.h +options.h +options.cpp +mem-search.h +mem-search.cu +build-chains.h +build-chains.cu +filter-chains.h +filter-chains.cu +align.h +align.cu +util.h +util.cu +) + +cuda_add_executable(nvmem ${nvmem_srcs}) +target_link_libraries(nvmem nvbio zlibstatic crcstatic lz4 ${SYSTEM_LINK_LIBRARIES}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/align.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/align.cu new file mode 100644 index 0000000000000000000000000000000000000000..0aeedfee3f7e7c3e6fe066678fcd32dd337c5bdd --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/align.cu @@ -0,0 +1,384 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include "align.h" +#include "mem-search.h" +#include "options.h" +#include "pipeline.h" +#include "util.h" + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +// initialize the alignment pipeline +// +void align_init(struct pipeline_state *pipeline, const io::SequenceDataDevice *batch) +{ + struct chains_state *chn = &pipeline->chn; + struct alignment_state *aln = &pipeline->aln; + + const uint32 n_reads = pipeline->chunk.read_end - pipeline->chunk.read_begin; + const uint32 n_chains = chn->n_chains; + + // initially, target the device + pipeline->system = DEVICE; + + // reserve enough storage + if (aln->stencil.size() < n_reads) + { + aln->begin_chains.clear(); aln->begin_chains.resize( n_reads ); + aln->end_chains.clear(); aln->end_chains.resize( n_reads ); + aln->stencil.clear(); aln->stencil.resize( n_reads ); + aln->temp_queue.clear(); aln->temp_queue.resize( n_reads ); + aln->query_spans.clear(); aln->query_spans.resize( n_reads ); + aln->ref_spans.clear(); aln->ref_spans.resize( n_reads ); + aln->sinks.clear(); aln->sinks.resize( n_reads ); + } + + // find the first chain for each read + thrust::lower_bound( + chn->chain_reads.begin(), + chn->chain_reads.begin() + n_chains, + thrust::make_counting_iterator( pipeline->chunk.read_begin ), + thrust::make_counting_iterator( pipeline->chunk.read_end ), + aln->begin_chains.begin() ); + + // find the ending chain for each read + thrust::upper_bound( + chn->chain_reads.begin(), + chn->chain_reads.begin() + n_chains, + thrust::make_counting_iterator( pipeline->chunk.read_begin ), + thrust::make_counting_iterator( pipeline->chunk.read_end ), + aln->end_chains.begin() ); + + aln->n_active = n_reads; +} + +#define MEM_SHORT_EXT 50 +#define MEM_SHORT_LEN 200 + +// a functor to compute the size of a span +// +struct span_size +{ + typedef uint2 argument_type; + typedef uint32 result_type; + + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 operator() (const uint2 span) const { return span.y - span.x; } +}; + +// a functor to extract the reference span from a chain +// +struct span_functor +{ + typedef io::SequenceDataAccess reads_access_type; + typedef io::SequenceDataAccess reference_access_type; + + NVBIO_HOST_DEVICE + span_functor( + const runtime_options _options, + const reads_access_type _reads, + const reference_access_type _reference, + const chains_view _chains, + const uint32* _active_chains, + uint2* _query_spans, + uint2* _ref_spans, + uint8* _flags) : + options ( _options ), + reads ( _reads ), + reference ( _reference ), + chains ( _chains ), + active_chains ( _active_chains ), + query_spans ( _query_spans ), + ref_spans ( _ref_spans ), + flags ( _flags ) {} + + // the functor operator + NVBIO_HOST_DEVICE + void operator() (const uint32 idx) const + { + const uint32 chain_idx = active_chains[idx]; + const chain_reference chain = chains[chain_idx]; + + const uint32 len = chain.size(); + + uint2 qspan = make_uint2( uint32(-1), 0u ); + uint2 rspan = make_uint2( uint32(-1), 0u ); + + // loop through all seeds in this chain + for (uint32 i = 0; i < len; ++i) + { + // fetch the i-th seed + const chains_view::mem_type seed = chain[i]; + + qspan.x = nvbio::min( qspan.x, seed.span().x ); + qspan.y = nvbio::max( qspan.y, seed.span().y ); + + rspan.x = nvbio::min( rspan.x, seed.index_pos() ); + rspan.y = nvbio::max( rspan.y, seed.index_pos() + seed.span().y - seed.span().x ); + } + + const uint32 read_id = chain.read(); + const uint2 read_range = reads.get_range( read_id ); + const uint32 read_len = read_range.y - read_range.x; + + qspan.x = qspan.x > MEM_SHORT_EXT ? qspan.x - MEM_SHORT_EXT : 0u; + qspan.y = qspan.y + MEM_SHORT_EXT < read_len ? qspan.y + MEM_SHORT_EXT : read_len; + + rspan.x = rspan.x > MEM_SHORT_EXT ? rspan.x - MEM_SHORT_EXT : 0u; + rspan.y = rspan.y + MEM_SHORT_EXT < reference.bps() ? rspan.y + MEM_SHORT_EXT : reference.bps(); + + const uint32 qdelta = qspan.y - qspan.x; + const uint32 rdelta = rspan.y - rspan.x; + + if ((qspan.x <= 10 || qspan.y >= read_len - 10) || // because ksw_align() does not support end-to-end alignment + (rdelta > qdelta + MEM_SHORT_EXT || qdelta > rdelta + MEM_SHORT_EXT) || + (qdelta >= options.w * 4 || rdelta >= options.w * 4)) + { + flags[idx] = 0; // because ksw_align() does not support end-to-end alignment + return; + } + + // save the resulting spans + query_spans[idx] = make_uint2( qspan.x + read_range.x, qspan.y + read_range.x ); + ref_spans[idx] = rspan; + + // flag to perform short alignment + flags[idx] = 1; + } + + const runtime_options options; + const reads_access_type reads; + const reference_access_type reference; + const chains_view chains; + const uint32* active_chains; + uint2* query_spans; + uint2* ref_spans; + uint8* flags; +}; + + +// perform banded alignment +// +template +uint32 align_short( + chains_state *chn, + alignment_state *aln, + const io::SequenceData *reference, + const io::SequenceData *reads) +{ + typedef io::SequenceDataAccess read_access_type; + typedef io::SequenceDataAccess reference_access_type; + + // prepare POD access pointers to the reads and reference + const read_access_type reads_access( *reads ); + const reference_access_type reference_access( *reference ); + + // + // During alignment, we essentially keep a queue of "active" reads, corresponding + // to those reads for which there's more chains to process; at every step, we select + // one new chain from each read as an alignment candidate, removing it from the set. + // This is done keeping a set of (begin,end) pointers per read and advancing the + // begin field - when a range becomes empty, it's removed + // + uint32 n_active = aln->n_active; + + // build a stencil of the active reads, stencil[i] = (begin_chains[i] != end_chains[i]) + transform( + n_active, + aln->begin_chains.begin(), + aln->end_chains.begin(), + aln->stencil.begin(), + nvbio::not_equal_functor() ); + + nvbio::vector temp_storage; + + // filter away reads that are done processing because there's no more chains + copy_flagged( + n_active, + aln->begin_chains.begin(), + aln->stencil.begin(), + aln->temp_queue.begin(), + temp_storage ); + + aln->begin_chains.swap( aln->temp_queue ); + + n_active = copy_flagged( + n_active, + aln->end_chains.begin(), + aln->stencil.begin(), + aln->temp_queue.begin(), + temp_storage ); + + aln->end_chains.swap( aln->temp_queue ); + + // reset the number of active reads + aln->n_active = n_active; + + // check whether there's no more work to do + if (n_active == 0) + return 0u; + + // now build a view of the chains + const chains_view chains( *chn ); + + typedef typename alignment_state::sink_type sink_type; + + const nvbio::vector& cur_chains = aln->begin_chains; + nvbio::vector& query_spans = aln->query_spans; + nvbio::vector& ref_spans = aln->ref_spans; + nvbio::vector& stencil = aln->stencil; + nvbio::vector& list = aln->temp_queue; + nvbio::vector& sinks = aln->sinks; + + // compute the chain query-spans + for_each( + n_active, + thrust::make_counting_iterator(0u), + span_functor( + command_line_options, + reads_access, + reference_access, + chains, + raw_pointer( cur_chains ), + raw_pointer( query_spans ), + raw_pointer( ref_spans ), + raw_pointer( stencil ) ) ); + + // copy the list of indices to the short alignment problems + const uint32 n_alns = copy_flagged( + n_active, + thrust::make_counting_iterator(0u), + stencil.begin(), + list.begin(), + temp_storage ); + + if (n_alns) + { + // + // perform a Gotoh batched alignment between two string-sets: + // the string-sets here are sparse subsets of the symbol streams holding + // the reads and the reference data + // + + typedef read_access_type::sequence_stream_type read_stream_type; + typedef reference_access_type::sequence_stream_type reference_stream_type; + typedef thrust::permutation_iterator infix_iterator; + + const infix_iterator reads_infixes = thrust::make_permutation_iterator( raw_pointer( query_spans ), raw_pointer( list ) ); + const infix_iterator reference_infixes = thrust::make_permutation_iterator( raw_pointer( ref_spans ), raw_pointer( list ) ); + + // build the sparse subset of the reads sequence + const SparseStringSet read_infix_set( + n_alns, + reads_access.sequence_stream(), + reads_infixes ); + + // build the sparse subset of the reference sequence + const SparseStringSet reference_infix_set( + n_alns, + reference_access.sequence_stream(), + reference_infixes ); + + // compute the largest reference span + const uint32 max_rspan = nvbio::reduce( + n_alns, + thrust::make_transform_iterator( reference_infixes, span_size() ), + thrust::maximum(), + temp_storage ); + + const aln::SimpleGotohScheme gotoh( 2, -2, -5, -3 ); // TODO: assign the correct scores here + + // invoke the parallel alignment + aln::batch_alignment_score( + aln::make_gotoh_aligner( gotoh ), + read_infix_set, + reference_infix_set, + sinks.begin(), + aln::DeviceThreadScheduler(), + reads_access.max_sequence_len(), + max_rspan ); + + // TODO: + // - check which alignments were successful + // - perform a reverse alignment to find the source cell of each alignment + } + // add one to the processed chains + nvbio::transform( + n_active, + aln->begin_chains.begin(), + thrust::make_constant_iterator( 1u ), + aln->begin_chains.begin(), + nvbio::add_functor() ); + + return n_active; +} + +// perform banded alignment +// +uint32 align( + struct pipeline_state *pipeline, + const nvbio::io::SequenceDataHost *reads_host, + const nvbio::io::SequenceDataDevice *reads_device) +{ + if (pipeline->system == DEVICE && // if currently on the device, + pipeline->aln.n_active < 16*1024) // but too little parallelism... + { + // copy the state of the pipeline to the host + pipeline->system = HOST; + pipeline->h_chn = pipeline->chn; + pipeline->h_aln = pipeline->aln; + } + + if (pipeline->system == HOST) + { + return align_short( + &pipeline->h_chn, + &pipeline->h_aln, + (const io::SequenceData*)pipeline->mem.reference_data_host, + (const io::SequenceData*)reads_host ); + } + else + { + return align_short( + &pipeline->chn, + &pipeline->aln, + (const io::SequenceData*)pipeline->mem.reference_data_device, + (const io::SequenceData*)reads_device ); + } +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/align.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/align.h new file mode 100644 index 0000000000000000000000000000000000000000..34834474da8e5c0915c3aa19f5dc3256efc73e0c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/align.h @@ -0,0 +1,43 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include + +/// initialize the alignment pipeline +/// +void align_init(struct pipeline_state *pipeline, const nvbio::io::SequenceDataDevice *batch); + +/// perform banded alignment +/// +/// \return the number of remaining active reads to align +/// +nvbio::uint32 align( + struct pipeline_state *pipeline, + const nvbio::io::SequenceDataHost *reads_host, + const nvbio::io::SequenceDataDevice *reads_device); diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/build-chains.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/build-chains.cu new file mode 100644 index 0000000000000000000000000000000000000000..73f3d7c99fbb8b83f5c31c3ff8d542902d9bbbdf --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/build-chains.cu @@ -0,0 +1,295 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include "build-chains.h" +#include "mem-search.h" +#include "options.h" +#include "pipeline.h" +#include "util.h" + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +// a functor to extract the read id from a mem +struct mem_read_id_functor +{ + typedef mem_state::mem_type argument_type; + typedef uint32 result_type; + + NVBIO_HOST_DEVICE + uint32 operator() (const argument_type mem) const { return mem.string_id(); } +}; + +// a class to keep track of a chain +struct chain +{ + // construct an empty chain + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + chain() : id(uint32(-1)) {} + + // construct a new chain from a single seed + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + chain(const uint32 _id, const mem_state::mem_type seed) : + id( _id ), + ref( seed.index_pos() ), + span_beg( seed.span().x ), + last_ref( seed.index_pos() ), + last_span( seed.span() ) + {} + + // test whether we can merge the given mem into this chain + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool merge(const mem_state::mem_type seed, const uint32 w, const uint32 max_chain_gap) + { + const uint32 seed_len = seed.span().y - seed.span().x; + const uint32 last_len = last_span.y - last_span.x; + const uint32 rbeg = ref; + const uint32 rend = last_ref + last_len; + + // check whether seed is contained in the chain + if (seed.span().x >= span_beg && seed.span().y <= last_span.y && seed.index_pos() >= rbeg && seed.index_pos() + seed_len <= rend) + return true; // contained seed; do nothing + + const int32 x = seed.span().x - last_span.x; // always non-negative + const int32 y = seed.index_pos() - last_ref; + if ((y >= 0) && (x - y <= w) && (x - last_len < max_chain_gap) && (y - last_len < max_chain_gap)) + { + // grow the chain + last_span = seed.span(); + last_ref = seed.index_pos(); + return true; + } + return false; + } + + uint32 id; // chain id + uint32 ref; // reference coordinate of the first seed in the chain + uint32 span_beg; // read span begin + uint32 last_ref; // the reference coordinate of the last seed in the chain + uint2 last_span; // the read span of the last seed in the chain +}; + +struct chain_compare +{ + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool operator() (const chain& chain1, const chain& chain2) const + { + // compare by the reference coordinate of the first seed of each chain + return chain1.ref < chain2.ref; + } +}; + +// assign a chain id to all MEMs for the current pipeline::chunk of reads +__global__ +void build_chains_kernel( + const read_chunk chunk, // the current sub-batch + const uint32 pass_number, // the pass number - we process up to N seeds per pass + const uint32 n_active, // the number of active reads in this pass + const uint32* active_reads, // the set of active reads + uint8* active_flags, // the output set of active read flags + const uint32 w, // w parameter + const uint32 max_chain_gap, // max chain gap parameter + const uint32 n_mems, // the total number of MEMs for this chunk of reads + const mem_state::mem_type* mems, // the MEMs for this chunk of reads + const uint32* mems_index, // a sorting index into the MEMs specifying the processing order + uint64* mems_chains) // the output chain IDs corresponding to the sorted MEMs +{ + const uint32 thread_id = threadIdx.x + blockIdx.x * blockDim.x; + if (thread_id >= n_active) + return; + + const uint32 read_id = active_reads[ thread_id ]; + + // find the first seed belonging to this read + const uint32 mem_begin = uint32( nvbio::lower_bound( + read_id, + nvbio::make_transform_iterator( mems, mem_read_id_functor() ), + n_mems ) - nvbio::make_transform_iterator( mems, mem_read_id_functor() ) ); + + // find the first seed belonging to the next read + const uint32 mem_end = uint32( nvbio::lower_bound( + read_id+1u, + nvbio::make_transform_iterator( mems, mem_read_id_functor() ), + n_mems ) - nvbio::make_transform_iterator( mems, mem_read_id_functor() ) ); + + // the maximum amount of chains we can output in one pass + const uint32 MAX_CHAINS = 128; + + // keep a priority queue of the chains organized by the reference coordinate of their leftmost seed + typedef nvbio::vector_view chain_vector_type; + typedef nvbio::priority_queue chain_queue_type; + + chain chain_queue_storage[MAX_CHAINS+1]; + chain_queue_type chain_queue( chain_vector_type( 0u, chain_queue_storage ) ); + + // keep a counter tracking the number of chains that get created + // + // NOTE: here we conservatively assume that in the previous passes we have + // created the maximum number of chains, so as to avoid assigning an already + // taken ID to a new chain (which would result in merging potentially unrelated + // chains) + uint64 n_chains = pass_number * MAX_CHAINS; + + // compute the first and ending MEM to process in this pass + const uint32 mem_batch_begin = mem_begin + pass_number * MAX_CHAINS; + const uint32 mem_batch_end = nvbio::min( mem_batch_begin + MAX_CHAINS, mem_end ); + + // process the seeds in order + for (uint32 i = mem_batch_begin; i < mem_batch_end; ++i) + { + const uint32 seed_idx = mems_index[i]; + const mem_state::mem_type seed = mems[ seed_idx ]; + + // the chain id for this seed, to be determined + uint32 chain_id; + + // insert seed + if (chain_queue.empty()) + { + // get a new chain id + chain_id = n_chains++; + + // build a new chain + chain_queue.push( chain( chain_id, seed ) ); + } + else + { + // find the closest chain... + chain_queue_type::iterator chain_it = chain_queue.upper_bound( chain( 0u, seed ) ); + + // and test whether we can merge this seed into it + if (chain_it != chain_queue.end() && + chain_it->merge( seed, w, max_chain_gap ) == false) + { + // get a new chain id + chain_id = n_chains++; + + // build a new chain + chain_queue.push( chain( chain_id, seed ) ); + } + else + { + // merge with the existing chain + chain_id = chain_it->id; + } + } + + // write out the chain id (OR'd with the read id) + mems_chains[i] = chain_id | (uint64( read_id ) << 32); + } + + // write out whether we need more passes + active_flags[ thread_id ] = (mem_batch_begin < mem_end) ? 1u : 0u; +} + +// build chains for the current pipeline::chunk of reads +void build_chains(pipeline_state *pipeline, const io::SequenceDataDevice *reads) +{ + const ScopedTimer timer( &pipeline->stats.chain_time ); // keep track of the time spent here + + struct chains_state *chn = &pipeline->chn; + + const uint32 n_reads = pipeline->chunk.read_end - pipeline->chunk.read_begin; + const uint32 n_mems = pipeline->chunk.mem_end - pipeline->chunk.mem_begin; + + // skip pathological cases + if (n_mems == 0u) + return; + + // + // Here we are going to run multiple passes of the same kernel, as we cannot fit + // all chains in local memory at once... + // + + // prepare some ping-pong queues for tracking active reads that need more passes + nvbio::vector active_reads( n_reads ); + nvbio::vector active_flags( n_reads ); + nvbio::vector out_reads( n_reads ); + nvbio::vector temp_storage; + + // initialize the active reads queue + thrust::copy( + thrust::make_counting_iterator(0u) + pipeline->chunk.read_begin, + thrust::make_counting_iterator(0u) + pipeline->chunk.read_end, + active_reads.begin() ); + + uint32 n_active = n_reads; + + for (uint32 pass_number = 0u; n_active; ++pass_number) + { + const uint32 block_dim = 128; + const uint32 n_blocks = util::divide_ri( n_active, block_dim ); + + // assign a chain id to each mem + build_chains_kernel<<>>( + pipeline->chunk, + pass_number, + n_active, + nvbio::plain_view( active_reads ), + nvbio::plain_view( active_flags ), + command_line_options.w, + command_line_options.max_chain_gap, + n_mems, + nvbio::plain_view( chn->mems ), + nvbio::plain_view( chn->mems_index ), + nvbio::plain_view( chn->mems_chain ) ); + + optional_device_synchronize(); + cuda::check_error("build-chains kernel"); + + // shrink the set of active reads + n_active = copy_flagged( + n_active, // the number of input elements + active_reads.begin(), // the input sequence of elements to copy + active_flags.begin(), // the input sequence of copy flags + out_reads.begin(), // the output sequence of copied elements + temp_storage ); // some temporary storage + + active_reads.swap( out_reads ); + } + + // sort mems by chain id + // NOTE: it's important here to use a stable-sort, so as to guarantee preserving + // the ordering by left-coordinate of the MEMs + thrust::sort_by_key( // TODO: this is slow, switch to nvbio::cuda::SortEnactor + chn->mems_chain.begin(), + chn->mems_chain.begin() + n_mems, + chn->mems_index.begin() ); + + optional_device_synchronize(); + nvbio::cuda::check_error("build-chains kernel"); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/build-chains.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/build-chains.h new file mode 100644 index 0000000000000000000000000000000000000000..037bb0230feb2c27d1a3b17f1b26dd4bd3001c5a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/build-chains.h @@ -0,0 +1,38 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include + +/// build chains for the current pipeline::chunk of reads +/// +void build_chains(struct pipeline_state *pipeline, const nvbio::io::SequenceDataDevice *reads); + +/// filter chains for the current pipeline::chunk of reads +/// +void filter_chains(struct pipeline_state *pipeline, const nvbio::io::SequenceDataDevice *reads); diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/filter-chains.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/filter-chains.cu new file mode 100644 index 0000000000000000000000000000000000000000..7ea51d6cae65810ae8a9c8355ed01026a11ed54d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/filter-chains.cu @@ -0,0 +1,334 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include "filter-chains.h" +#include "mem-search.h" +#include "options.h" +#include "pipeline.h" +#include "util.h" + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +// compute the coverage for each chain in a set +__global__ +void chain_coverage_kernel( + const uint32 n_chains, // the number of chains + const uint32* chain_reads, // the chain reads + const uint32* chain_offsets, // the chain offsets + const uint32* chain_lengths, // the chain lengths + const mem_state::mem_type* mems, // the MEMs for this chunk of reads + const uint32* mems_index, // a sorting index into the MEMs specifying their processing order + uint2* chain_ranges, // the output chain ranges + uint64* chain_weights) // the output chain weights +{ + const uint32 chain_id = threadIdx.x + blockIdx.x * blockDim.x; + if (chain_id >= n_chains) + return; + + const uint32 read = chain_reads[ chain_id ]; + const uint32 begin = chain_offsets[ chain_id ]; + const uint32 end = chain_lengths[ chain_id ] + begin; + + uint2 range = make_uint2( uint32(-1), 0u ); + uint32 weight = 0; + + // NOTE: we assume here the MEMs of a chain appear sorted by their left coordinate + for (uint32 i = begin; i < end; ++i) + { + const mem_state::mem_type seed = mems[ mems_index[i] ]; + + const uint2 span = seed.span(); + + if (span.x >= range.y) + weight += span.y - span.x; + else if (span.y > range.y) + weight += span.y - range.y; + + range.x = nvbio::min( range.x, seed.span().x ); + range.y = nvbio::max( range.y, seed.span().y ); + } + + // write out the outputs + chain_ranges[ chain_id ] = range; + chain_weights[ chain_id ] = uint64( weight ) | (uint64( read ) << 32); +} + +// filter the chains belonging to each read +__global__ +void chain_filter_kernel( + const read_chunk chunk, // the current sub-batch + const uint32 n_chains, // the number of chains + const uint32* chain_reads, // the chain reads + const uint32* chain_index, // the chain order + const uint2* chain_ranges, // the chain ranges + const uint64* chain_weights, // the chain weights + const float mask_level, // input option + const float chain_drop_ratio, // input option + const uint32 min_seed_len, // input option + uint8* chain_flags) // the output flags +{ + const uint32 read_id = threadIdx.x + blockIdx.x * blockDim.x + chunk.read_begin; + if (read_id >= chunk.read_end) + return; + + const uint32 begin = uint32( nvbio::lower_bound( read_id, chain_reads, n_chains ) - chain_reads ); + const uint32 end = uint32( nvbio::upper_bound( read_id, chain_reads, n_chains ) - chain_reads ); + + // skip pathological cases + if (begin == end) + return; + + // keep the first chain + chain_flags[ chain_index[begin] ] = 1u; // mark to keep + + // and loop through all the rest to decide which ones to keep + uint32 n = 1; + + for (uint32 i = begin + 1; i < end; ++i) + { + const uint2 i_span = chain_ranges[ chain_index[i] ]; + const uint32 i_w = chain_weights[ i ] & 0xFFFFFFFFu; // already sorted as chain_index + + uint32 j; + for (j = begin; j < begin + n; ++j) + { + const uint2 j_span = chain_ranges[ chain_index[j] ]; + const uint32 j_w = chain_weights[ j ] & 0xFFFFFFFFu; // already sorted as chain_index + + const uint32 max_begin = nvbio::max( i_span.x, j_span.x ); + const uint32 min_end = nvbio::min( i_span.y, j_span.y ); + + if (min_end > max_begin) // have overlap + { + const uint32 min_l = nvbio::min( i_span.y - i_span.x, j_span.y - j_span.x ); + if (min_end - max_begin >= min_l * mask_level) // significant overlap + { + chain_flags[ chain_index[i] ] = 1u; // mark to keep + + if (i_w < j_w * chain_drop_ratio && + j_w - i_w >= min_seed_len * 2) + break; + } + } + } + if (j == n) // no significant overlap with better chains, keep it. + { + chain_flags[ chain_index[i] ] = 1u; // mark to keep + + ++n; + } + } +} + +// filter chains for the current pipeline::chunk of reads +void filter_chains(pipeline_state *pipeline, const io::SequenceDataDevice *reads) +{ + const ScopedTimer timer( &pipeline->stats.chain_time ); // keep track of the time spent here + + struct chains_state *chn = &pipeline->chn; + + const uint32 n_reads = pipeline->chunk.read_end - pipeline->chunk.read_begin; + const uint32 n_mems = pipeline->chunk.mem_end - pipeline->chunk.mem_begin; + + // skip pathological cases + if (n_mems == 0u) + return; + + // extract the list of unique chain ids together with their counts, i.e. the chain lengths + nvbio::vector unique_chains( n_mems ); + nvbio::vector unique_counts( n_mems ); + nvbio::vector temp_storage; + + const uint32 n_chains = runlength_encode( + n_mems, + chn->mems_chain.begin(), // the input chain ids, one per seed + unique_chains.begin(), // the output "unique" chain ids + unique_counts.begin(), // the output repetition counts, i.e. the chain lengths + temp_storage ); // some temp storage + + // resize the chain vectors if needed + uint32 reserved_space = uint32( chn->chain_lengths.size() ); + if (n_chains > reserved_space) + { + chn->chain_lengths.clear(); chn->chain_lengths.resize( n_chains ); + chn->chain_offsets.clear(); chn->chain_offsets.resize( n_chains ); + chn->chain_reads.clear(); chn->chain_reads.resize( n_chains ); + + reserved_space = n_chains; + } + + // copy their lengths + thrust::copy( + unique_counts.begin(), + unique_counts.begin() + n_chains, + chn->chain_lengths.begin() ); + + // find the offset to the beginning of each chain + thrust::lower_bound( + chn->mems_chain.begin(), // the beginning of the sorted list of keys to search in + chn->mems_chain.begin() + n_mems, // the end of the sorted list of keys to search in + unique_chains.begin(), // the beginning of the sequence of values to search + unique_chains.begin() + n_chains, // the end of the sequence of values to search + chn->chain_offsets.begin() ); // the output sequence + + // extract the read-id frome the chain ids + thrust::transform( + unique_chains.begin(), // the beginning of the input sequence to transform + unique_chains.begin() + n_chains, // the end of the input sequence to transform + chn->chain_reads.begin(), // the beginning othe output sequence + nvbio::hi_bits_functor() ); // the functor to apply, in this case a 32-bit left shift + + // debug check: make sure the chain offsets are sorted + if (is_sorted( n_chains, chn->chain_offsets.begin() ) == false) + { + log_error(stderr, "filter_chains: chain offsets are not sorted!\n"); + exit(0); + } + + // debug check: make sure the chains are sorted by read + if (is_sorted( n_chains, chn->chain_reads.begin() ) == false) + { + log_error(stderr, "filter_chains: chains are not sorted by read!\n"); + exit(0); + } + + nvbio::vector chain_ranges( n_chains ); + nvbio::vector chain_weights( n_chains ); + nvbio::vector chain_index( reserved_space ); // potentially a little bigger because we'll reuse + // it for the final filtering... + + optional_device_synchronize(); + cuda::check_error("chain-coverage-init"); + + // compute chain coverages + { + const uint32 block_dim = 128; + const uint32 n_blocks = util::divide_ri( n_chains, block_dim ); + + chain_coverage_kernel<<>>( + n_chains, + nvbio::plain_view( chn->chain_reads ), + nvbio::plain_view( chn->chain_offsets ), + nvbio::plain_view( chn->chain_lengths ), + nvbio::plain_view( chn->mems ), + nvbio::plain_view( chn->mems_index ), + nvbio::plain_view( chain_ranges ), + nvbio::plain_view( chain_weights ) ); + + optional_device_synchronize(); + cuda::check_error("chain-coverage kernel"); + } + + // sort the chains by weight + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + n_chains, + chain_index.begin() ); + + thrust::sort_by_key( // TODO: this is slow, switch to nvbio::cuda::SortEnactor + chain_weights.begin(), + chain_weights.begin() + n_chains, + chain_index.begin() ); + + nvbio::vector chain_flags( n_chains ); + thrust::fill( chain_flags.begin(), chain_flags.begin() + n_chains, 0u ); + + // filter chains: set the flags for the chains to be kept + { + const uint32 block_dim = 128; + const uint32 n_blocks = util::divide_ri( n_reads, block_dim ); + + chain_filter_kernel<<>>( + pipeline->chunk, + n_chains, + nvbio::plain_view( chn->chain_reads ), + nvbio::plain_view( chain_index ), + nvbio::plain_view( chain_ranges ), + nvbio::plain_view( chain_weights ), + command_line_options.mask_level, + command_line_options.chain_drop_ratio, + command_line_options.min_seed_len, + nvbio::plain_view( chain_flags ) ); + + optional_device_synchronize(); + cuda::check_error("chain-filter kernel"); + } + + // filter chain_reads + const uint32 n_filtered_chains = copy_flagged( + n_chains, // the number of input elements + chn->chain_reads.begin(), // the input sequence of flagged elements to copy + chain_flags.begin(), // the input sequence of flags + chain_index.begin(), // the output sequence of copied elements + temp_storage ); // some temporary storage + + chn->chain_reads.swap( chain_index ); + + // debug check: make sure the chains are sorted by read + if (is_sorted( n_filtered_chains, chn->chain_reads.begin() ) == false) + { + log_error(stderr, "filter_chains: filtered chains are not sorted by read!\n"); + exit(0); + } + + // filter chain_offsets + cuda::copy_flagged( + n_chains, // the number of input elements + chn->chain_offsets.begin(), // the input sequence of flagged elements to copy + chain_flags.begin(), // the input sequence of flags + chain_index.begin(), // the output sequence of copied elements + temp_storage ); // some temporary storage + + chn->chain_offsets.swap( chain_index ); + + // filter chain_lengths + cuda::copy_flagged( + n_chains, // the number of input elements + chn->chain_lengths.begin(), // the input sequence of flagged elements to copy + chain_flags.begin(), // the input sequence of flags + chain_index.begin(), // the output sequence of copied elements + temp_storage ); // some temporary storage + + chn->chain_lengths.swap( chain_index ); + + // assign the output number of chains + chn->n_chains = n_filtered_chains; + + // keep stats + pipeline->stats.n_chains += n_filtered_chains; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/filter-chains.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/filter-chains.h new file mode 100644 index 0000000000000000000000000000000000000000..6b93d4c5a26a544281aac34293351740e9282739 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/filter-chains.h @@ -0,0 +1,34 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include + +/// filter chains for the current pipeline::chunk of reads +/// +void filter_chains(struct pipeline_state *pipeline, const nvbio::io::SequenceDataDevice *reads); diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/mem-search.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/mem-search.cu new file mode 100644 index 0000000000000000000000000000000000000000..a9a9df126edd2b2418d7cfb253df3e255498a47c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/mem-search.cu @@ -0,0 +1,264 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include "mem-search.h" +#include "options.h" +#include "pipeline.h" +#include "util.h" + +#include +#include +#include +#include +#include +#include +#include + +using namespace nvbio; + +static io::SequenceData *load_genome(const char *name) +{ + if (command_line_options.genome_use_mmap) + { + // try loading via mmap first + io::SequenceDataMMAP *mmap_loader = io::map_sequence_file( name ); + if (mmap_loader) + return mmap_loader; + } + + // fall back to file name + io::SequenceDataHost *file_loader = io::load_sequence_file( DNA, name ); + if (file_loader == NULL) + { + log_error(stderr, "could not load genome %s\n"); + exit(1); + } + return file_loader; +} + +static io::FMIndexData *load_index(const char *name, uint32 flags) +{ + if (command_line_options.genome_use_mmap) + { + // try loading via mmap first + io::FMIndexDataMMAP *mmap_loader = new io::FMIndexDataMMAP(); + if (mmap_loader->load(name)) + return mmap_loader; + + delete mmap_loader; + } + + // fall back to file name + io::FMIndexDataHost *file_loader = new io::FMIndexDataHost(); + if (!file_loader->load(name, flags)) + { + log_error(stderr, "could not load index %s\n"); + exit(1); + } + return file_loader; +} + +void mem_init(struct pipeline_state *pipeline) +{ + // load the genome on the host + pipeline->mem.reference_data_host = load_genome(command_line_options.genome_file_name); + // copy genome data to device + pipeline->mem.reference_data_device = new io::SequenceDataDevice(*pipeline->mem.reference_data_host); + + // this specifies which portions of the FM index data to load + const uint32 fm_flags = io::FMIndexData::FORWARD | + io::FMIndexData::REVERSE | + io::FMIndexData::SA; + + // load the genome on the host + pipeline->mem.fmindex_data_host = load_index(command_line_options.genome_file_name, fm_flags); + // copy genome data to device + pipeline->mem.fmindex_data_device = new io::FMIndexDataDevice(*pipeline->mem.fmindex_data_host, fm_flags); + + pipeline->mem.f_index = pipeline->mem.fmindex_data_device->index(); + pipeline->mem.r_index = pipeline->mem.fmindex_data_device->rindex(); +} + +// search MEMs for all reads in batch +void mem_search(struct pipeline_state *pipeline, const io::SequenceDataDevice *reads) +{ + ScopedTimer timer( &pipeline->stats.search_time ); // keep track of the time spent here + + struct mem_state *mem = &pipeline->mem; + + const uint32 n_reads = reads->size(); + + // reset the filter + mem->mem_filter = mem_state::mem_filter_type(); + + const io::SequenceDataAccess read_access( *reads ); + + // search for MEMs + mem->mem_filter.rank( + mem->f_index, + mem->r_index, + read_access.sequence_string_set(), + command_line_options.min_intv, + command_line_options.max_intv, + command_line_options.min_seed_len, + command_line_options.split_len, + command_line_options.split_width); + + log_verbose(stderr, "%.1f average ranges\n", float(mem->mem_filter.n_ranges()) / float(n_reads)); + log_verbose(stderr, "%.1f average MEMs\n", float(mem->mem_filter.n_mems()) / float(n_reads)); + + optional_device_synchronize(); + nvbio::cuda::check_error("mem-search kernel"); +} + +// given the first read in a chunk, determine a suitably sized chunk of reads +// (for which we can locate all MEMs in one go), updating pipeline::chunk +void fit_read_chunk( + struct pipeline_state *pipeline, + const io::SequenceDataDevice *reads, + const uint32 read_begin) // first read in the chunk +{ + const ScopedTimer timer( &pipeline->stats.search_time ); // keep track of the time spent here + + struct mem_state *mem = &pipeline->mem; + + const uint32 max_hits = command_line_options.mems_batch; + + // + // use a binary search to locate the ending read forming a chunk with up to max_hits + // + + pipeline->chunk.read_begin = read_begin; + + // skip pathological cases + if (mem->mem_filter.n_ranges() == 0) + { + pipeline->chunk.read_end = reads->size(); + pipeline->chunk.mem_begin = 0u; + pipeline->chunk.mem_end = 0u; + return; + } + + // determine the index of the first hit in the chunk + pipeline->chunk.mem_begin = mem->mem_filter.first_hit( read_begin ); + + // perform a binary search to find the end of our batch + pipeline->chunk.read_end = nvbio::string_batch_bound( mem->mem_filter, pipeline->chunk.mem_begin + max_hits ); + + // determine the index of the ending hit in the chunk + pipeline->chunk.mem_end = mem->mem_filter.first_hit( pipeline->chunk.read_end ); + + // check whether we couldn't produce a non-empty batch + if (pipeline->chunk.mem_begin == pipeline->chunk.mem_end && + pipeline->chunk.mem_end < mem->mem_filter.n_mems()) + { + const uint32 mem_count = mem->mem_filter.first_hit( read_begin+1 ) - pipeline->chunk.mem_begin; + log_error(stderr,"read %u/%u has too many MEMs (%u), exceeding maximum batch size\n", read_begin, reads->size(), mem_count ); + exit(1); + } +} + +// a functor to extract the reference location from a mem +struct mem_loc_functor +{ + typedef mem_state::mem_type argument_type; + typedef uint64 result_type; + + NVBIO_HOST_DEVICE + uint64 operator() (const argument_type mem) const + { + return uint64( mem.index_pos() ) | (uint64( mem.string_id() ) << 32); + } +}; + +// a functor to extract the reference left coordinate from a mem +struct mem_left_coord_functor +{ + typedef mem_state::mem_type argument_type; + typedef uint64 result_type; + + NVBIO_HOST_DEVICE + uint64 operator() (const argument_type mem) const + { + return uint64( mem.span().x ) | (uint64( mem.string_id() ) << 32); + } +}; + +// locate all mems in the range defined by pipeline::chunk +void mem_locate(struct pipeline_state *pipeline, const io::SequenceDataDevice *reads) +{ + const ScopedTimer timer( &pipeline->stats.locate_time ); // keep track of the time spent here + + struct mem_state *mem = &pipeline->mem; + struct chains_state *chn = &pipeline->chn; + + if (chn->mems.size() < command_line_options.mems_batch) + { + chn->mems.resize( command_line_options.mems_batch ); + chn->mems_index.resize( command_line_options.mems_batch ); + chn->mems_chain.resize( command_line_options.mems_batch ); + } + + const uint32 n_mems = pipeline->chunk.mem_end - pipeline->chunk.mem_begin; + + // skip pathological cases + if (n_mems == 0u) + return; + + chn->n_mems = n_mems; + + mem->mem_filter.locate( + pipeline->chunk.mem_begin, + pipeline->chunk.mem_end, + chn->mems.begin() ); + + // sort the mems by reference location + nvbio::vector loc( n_mems ); + + thrust::transform( + chn->mems.begin(), + chn->mems.begin() + n_mems, + loc.begin(), + mem_left_coord_functor() ); + //mem_loc_functor() ); + + thrust::copy( + thrust::make_counting_iterator(0u), + thrust::make_counting_iterator(0u) + n_mems, + chn->mems_index.begin() ); + + // TODO: this is slow, switch to nvbio::cuda::SortEnactor + thrust::sort_by_key( + loc.begin(), + loc.begin() + n_mems, + chn->mems_index.begin() ); + + optional_device_synchronize(); + nvbio::cuda::check_error("mem-locate kernel"); + + pipeline->stats.n_mems += n_mems; // keep track of the number of mems produced +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/mem-search.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/mem-search.h new file mode 100644 index 0000000000000000000000000000000000000000..0648c1f722e6c6a915d378d0c283835bf5987aeb --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/mem-search.h @@ -0,0 +1,50 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include + +/// initialize the MEM-search pipeline +/// +void mem_init(struct pipeline_state *pipeline); + +/// search MEMs for the given batch of reads +/// +void mem_search(struct pipeline_state *pipeline, const nvbio::io::SequenceDataDevice *reads); + +/// given the first read in a chunk, determine a suitably sized chunk of reads +/// (for which we can locate all MEMs in one go), updating pipeline::chunk +/// +void fit_read_chunk( + struct pipeline_state *pipeline, + const nvbio::io::SequenceDataDevice *batch, + const nvbio::uint32 read_begin); // first read in the chunk + +/// locate all mems in the range defined by pipeline::chunk +/// +void mem_locate(struct pipeline_state *pipeline, const nvbio::io::SequenceDataDevice *reads); diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/nvmem.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/nvmem.cu new file mode 100644 index 0000000000000000000000000000000000000000..8557b044be8f9255dbb217159f9c6cadeb7fc551 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/nvmem.cu @@ -0,0 +1,216 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include +#include +#include +#include // cuda::check_error +#include +#include +#include +#ifdef _OPENMP +#include +#endif + +#include "options.h" +#include "util.h" +#include "pipeline.h" +#include "mem-search.h" +#include "build-chains.h" +#include "filter-chains.h" +#include "align.h" + +using namespace nvbio; + +int run(int argc, char **argv) +{ + parse_command_line(argc, argv); + gpu_init(); + + #ifdef _OPENMP + // now set the number of CPU threads + omp_set_num_threads( omp_get_num_procs() ); + #pragma omp parallel + { + log_verbose(stderr, " running on multiple threads (%d)\n", omp_get_thread_num()); + } + #endif + + pipeline_state pipeline; + + // start the pipeline on the device + pipeline.system = DEVICE; + + // load the fmindex and prepare the SMEM search + mem_init(&pipeline); + + // open the input read file + SharedPointer input = SharedPointer( + io::open_sequence_file( + command_line_options.input_file_name, + io::Phred33, + uint32(-1), + uint32(-1), + io::SequenceEncoding(io::FORWARD | io::REVERSE_COMPLEMENT) ) ); + + if (input == NULL || input->is_ok() == false) + { + log_error(stderr, "failed to open read file %s\n", command_line_options.input_file_name); + exit(1); + } + + // open the output file + pipeline.output = io::OutputFile::open(command_line_options.output_file_name, + io::SINGLE_END, + io::BNT(*pipeline.mem.reference_data_host)); + + if (!pipeline.output) + { + log_error(stderr, "failed to open output file %s\n", command_line_options.output_file_name); + exit(1); + } + + Timer global_timer; + Timer timer; + + io::SequenceDataHost host_reads; + + // go! + for(;;) + { + global_timer.start(); + timer.start(); + + // read the next batch + if (io::next( DNA_N, &host_reads, input.get(), command_line_options.batch_size, uint32(-1) ) == 0) + break; // EOF + + log_info(stderr, "processing reads [%llu,%llu)\n", pipeline.stats.n_reads, pipeline.stats.n_reads + host_reads.size()/2); + + // copy batch to the device + const io::SequenceDataDevice device_reads( host_reads ); + + timer.stop(); + pipeline.stats.io_time += timer.seconds(); + + // search for MEMs + mem_search(&pipeline, &device_reads); + + // now start a loop where we break the read batch into smaller chunks for + // which we can locate all MEMs and build all chains + for (uint32 read_begin = 0; read_begin < host_reads.size(); read_begin = pipeline.chunk.read_end) + { + // determine the next chunk of reads to process + fit_read_chunk(&pipeline, &device_reads, read_begin); + + log_verbose(stderr, "processing chunk\n"); + log_verbose(stderr, " reads : [%u,%u)\n", pipeline.chunk.read_begin, pipeline.chunk.read_end); + log_verbose(stderr, " mems : [%u,%u)\n", pipeline.chunk.mem_begin, pipeline.chunk.mem_end); + + // locate all MEMs in the current chunk + mem_locate(&pipeline, &device_reads); + + // build the chains + build_chains(&pipeline, &device_reads); + + // filter the chains + filter_chains(&pipeline, &device_reads); + + log_verbose(stderr, " chains: %u\n", pipeline.chn.n_chains); + + // initialize the alignment sub-pipeline + align_init(&pipeline, &device_reads); + + // and loop until there's work to do + while (align(&pipeline, &host_reads, &device_reads)) + { + log_verbose(stderr, "\r active: %u", pipeline.aln.n_active); + } + log_verbose_cont(stderr, "\n"); + } + global_timer.stop(); + pipeline.stats.n_reads += host_reads.size()/2; + pipeline.stats.time += global_timer.seconds(); + + log_stats(stderr, " time: %5.1fs (%.1f K reads/s)\n", pipeline.stats.time, 1.0e-3f * float(pipeline.stats.n_reads)/pipeline.stats.time); + log_stats(stderr, " io : %6.2f %%\n", 100.0f * pipeline.stats.io_time/pipeline.stats.time); + log_stats(stderr, " search : %6.2f %%\n", 100.0f * pipeline.stats.search_time/pipeline.stats.time); + log_stats(stderr, " locate : %6.2f %%\n", 100.0f * pipeline.stats.locate_time/pipeline.stats.time); + log_stats(stderr, " chain : %6.2f %%\n", 100.0f * pipeline.stats.chain_time/pipeline.stats.time); + } + + pipeline.output->close(); + return 0; +} + +int main(int argc, char **argv) +{ + try + { + return run( argc, argv ); + } + catch (nvbio::cuda_error e) + { + log_error(stderr, "caught a nvbio::cuda_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::bad_alloc e) + { + log_error(stderr, "caught a nvbio::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::logic_error e) + { + log_error(stderr, "caught a nvbio::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (nvbio::runtime_error e) + { + log_error(stderr, "caught a nvbio::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::bad_alloc e) + { + log_error(stderr, "caught a std::bad_alloc exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::logic_error e) + { + log_error(stderr, "caught a std::logic_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (std::runtime_error e) + { + log_error(stderr, "caught a std::runtime_error exception:\n"); + log_error(stderr, " %s\n", e.what()); + } + catch (...) + { + log_error(stderr, "caught an unknown exception!\n"); + } + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/options.cpp b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/options.cpp new file mode 100644 index 0000000000000000000000000000000000000000..2667e0ce2e209f03b7b36055b498b3838a941467 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/options.cpp @@ -0,0 +1,109 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include "options.h" +#include +#include +#include + +struct runtime_options command_line_options; + +static void usage(void) +{ + fprintf(stderr, "usage: nvmem [-f|--file-ref] \n"); + fprintf(stderr, "\n"); + fprintf(stderr, " -f, --file-ref Read the genome from file directly (do not use mmap)\n"); + fprintf(stderr, "\n"); + exit(1); +} + +#if defined(WIN32) + +void parse_command_line(int argc, char **argv) +{ + for (int i = 0; i < argc-3; ++i) + { + if (strcmp( argv[i], "-f" ) == 0 || + strcmp( argv[i], "--file-ref" ) == 0) + command_line_options.genome_use_mmap = false; + } + + if (argc < 3) + { + // missing required arguments or too many arguments + usage(); + } + + command_line_options.genome_file_name = argv[argc-3]; + command_line_options.input_file_name = argv[argc-2]; + command_line_options.output_file_name = argv[argc-1]; +} + +#else + +#include +#include + +#include + +void parse_command_line(int argc, char **argv) +{ + static const char *options_short = "f:o"; + static struct option options_long[] = { + { "file-ref", no_argument, NULL, 'f' }, + { NULL, 0, NULL, 0 }, + }; + + int ch; + while((ch = getopt_long(argc, argv, options_short, options_long, NULL)) != -1) + { + switch(ch) + { + case 'f': + // -f, --file-ref + command_line_options.genome_use_mmap = false; + break; + + case '?': + case ':': + default: + usage(); + } + } + + if (optind != argc - 3) + { + // missing required arguments or too many arguments + usage(); + } + + command_line_options.genome_file_name = argv[optind]; + command_line_options.input_file_name = argv[optind + 1]; + command_line_options.output_file_name = argv[optind + 2]; +} + +#endif \ No newline at end of file diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/options.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/options.h new file mode 100644 index 0000000000000000000000000000000000000000..f3102f74d7f2b589fe817ddb255fb20be81c9361 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/options.h @@ -0,0 +1,85 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include + +using namespace nvbio; + +struct runtime_options +{ + // genome file name or shared memory handle name + const char *genome_file_name; + // input reads file name + const char *input_file_name; + // output alignment file name + const char *output_file_name; + + // whether to allow using mmap() to load the genome + bool genome_use_mmap; + // input read batch size + uint64 batch_size; + + // MEM search options + uint32 min_intv; // min and max interval sizes for MEM search + uint32 max_intv; + uint32 min_seed_len; // minimum read span, MEMs that span less than this many bps will be dropped + uint32 mems_batch; // number of MEMs to locate at once + uint32 w; + uint32 max_chain_gap; + uint32 split_len; + uint32 split_width; + float mask_level; + float chain_drop_ratio; + + NVBIO_HOST_DEVICE + runtime_options() + { + genome_file_name = NULL; + input_file_name = NULL; + output_file_name = NULL; + + // default options + genome_use_mmap = true; + batch_size = 256 * 1024; + min_intv = 1; + max_intv = 10000; + min_seed_len = 19; + mems_batch = 16 * 1024 * 1024; + split_len = 28; + split_width = 10; + mask_level = 0.5f; + chain_drop_ratio = 0.5f; + w = 100; + max_chain_gap = 10000; + }; +}; + +extern struct runtime_options command_line_options; + +void parse_command_line(int argc, char **argv); diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/pipeline.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/pipeline.h new file mode 100644 index 0000000000000000000000000000000000000000..fe6503377c7b6f3f7c6c2a7eb72eeace0d8e1ff0 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/pipeline.h @@ -0,0 +1,299 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#include +#include +#include +#include +#include + +#include "mem-search.h" + +using namespace nvbio; + +/// pipeline stats +/// +struct pipeline_stats +{ + pipeline_stats() : + time ( 0.0f ), + io_time ( 0.0f ), + search_time ( 0.0f ), + locate_time ( 0.0f ), + chain_time ( 0.0f ), + n_reads ( 0 ), + n_mems ( 0 ), + n_chains ( 0 ) + {} + + float time; + float io_time; + float search_time; + float locate_time; + float chain_time; + + uint64 n_reads; + uint64 n_mems; + uint64 n_chains; +}; + +/// the MEM-searching pipeline state +/// +struct mem_state +{ + typedef nvbio::io::SequenceDataAccess::sequence_stream_type genome_type; + typedef nvbio::io::FMIndexDataDevice::fm_index_type fm_index_type; + typedef nvbio::MEMFilterDevice mem_filter_type; + typedef mem_filter_type::mem_type mem_type; + + nvbio::io::SequenceData *reference_data_host; + nvbio::io::SequenceDataDevice *reference_data_device; + nvbio::io::FMIndexData *fmindex_data_host; + nvbio::io::FMIndexDataDevice *fmindex_data_device; + + fm_index_type f_index; ///< the forward FM-index object + fm_index_type r_index; ///< the reverse FM-index object + + mem_filter_type mem_filter; ///< our MEM filter object, used to rank and locate MEMs and keep track of statistics +}; + +/// the state of the MEM chains relative to a set of reads +/// +template +struct chains_state +{ + typedef mem_state::mem_type mem_type; + typedef nvbio::vector mem_vector_type; + + template + chains_state& operator=(const chains_state& other); + + mem_vector_type mems; ///< the result vector for mem_search + uint32 n_mems; ///< the number of mems + + nvbio::vector mems_index; ///< a sorting index into the mems (initially by reference location, then by chain id) + nvbio::vector mems_chain; ///< the chain IDs of each mem + + // the list of chains + nvbio::vector chain_offsets; ///< the first seed of each chain + nvbio::vector chain_lengths; ///< the number of seeds in each chain + nvbio::vector chain_reads; ///< the read (strand) id of each chain + uint32 n_chains; ///< the number of chains +}; + +/// a small object acting as a "reference" for a chain +/// +struct chain_reference; + +/// a POD structure to view chains as if they were stored in AOS format; +/// unlike chains_state, this class can be passed as a kernel parameter and its members +/// can be accessed from the device. +/// +struct chains_view +{ + typedef mem_state::mem_type mem_type; + typedef const uint32* index_vector_type; + typedef const mem_type* mem_vector_type; + + /// constructor + /// + template + chains_view(const chains_state& state) : + mems( plain_view( state.mems ) ), + mems_index( plain_view( state.mems_index ) ), + chain_offsets( plain_view( state.chain_offsets ) ), + chain_lengths( plain_view( state.chain_lengths ) ), + chain_reads( plain_view( state.chain_reads ) ), + n_chains( state.n_chains ) + {} + + /// return a "reference" to the i-th chain + /// + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + chain_reference operator[] (const uint32 i) const; + + mem_vector_type mems; ///< the result vector for mem_search + index_vector_type mems_index; ///< a sorting index into the mems (initially by reference location, then by chain id) + + index_vector_type chain_offsets; ///< the first seed of each chain + index_vector_type chain_lengths; ///< the number of seeds in each chain + index_vector_type chain_reads; ///< the read (strand) id of each chain + uint32 n_chains; ///< the number of chains +}; + +/// a small object acting as a "reference" for a chain, allowing to view it as if was a single object +/// +struct chain_reference +{ + typedef mem_state::mem_type mem_type; + + /// constructor + /// + NVBIO_HOST_DEVICE + chain_reference(const chains_view& _chains, const uint32 _i) : chains(_chains), idx(_i) {} + + /// return the read this chain belongs to + /// + NVBIO_HOST_DEVICE + uint32 read() const { return chains.chain_reads[ idx ]; } + + /// return the number of seeds in this chain + /// + NVBIO_HOST_DEVICE + uint32 size() const { return chains.chain_lengths[ idx ]; } + + /// return the i-th seed in this chain + /// + NVBIO_HOST_DEVICE + mem_type operator[] (const uint32 i) const + { + // grab the offset to the first seed of this chain + const uint32 offset = chains.chain_offsets[ idx ]; + + // return the requested seed, remembering they are sorted by chain through an index + return chains.mems[ chains.mems_index[ offset + i ] ]; + } + + const chains_view& chains; + const uint32 idx; +}; + +// return a "reference" to the i-th chain +// +NVBIO_FORCEINLINE NVBIO_HOST_DEVICE +chain_reference chains_view::operator[] (const uint32 i) const +{ + return chain_reference( *this, i ); +} + +/// a contiguous subset of reads from a batch associated with all their MEMs +/// +struct read_chunk +{ + read_chunk() : + read_begin(0), + read_end(0), + mem_begin(0), + mem_end(0) {} + + uint32 read_begin; ///< ID of the first read in this chunk + uint32 read_end; ///< ID of the ending read in this chunk + + uint32 mem_begin; ///< index of the first hit for the first read + uint32 mem_end; ///< index of the last hit for the last read +}; + +/// the alignment sub-pipeline state +/// +/// during alignment, we essentially keep a queue of "active" reads, corresponding +/// to those reads for which there's more chains to process; at every step, we select +/// one new chain from each read as an alignment candidate, removing it from the set. +/// This is done keeping a set of (begin,end) pointers per read and advancing the +/// begin field - when a range becomes empty, it's removed +/// +template +struct alignment_state +{ + typedef aln::Best2Sink sink_type; + + template + alignment_state& operator=(const alignment_state& other); + + uint32 n_active; ///< the number of active reads in the alignment queue + nvbio::vector begin_chains; ///< the first chain for each read in the processing queue + nvbio::vector end_chains; ///< the ending chain for each read in the processing queue + nvbio::vector query_spans; ///< the query chain spans + nvbio::vector ref_spans; ///< the reference chain spans + nvbio::vector temp_queue; ///< a temporary queue + nvbio::vector stencil; ///< a temporary stencil vector + nvbio::vector sinks; ///< a temporary stencil vector +}; + +/// a flag to identify the system in use +/// +enum SystemFlag { DEVICE = 0, HOST = 1 }; + +/// the state of the pipeline +/// +struct pipeline_state +{ + SystemFlag system; ///< specify whether we are using the device or the host + nvbio::io::OutputFile* output; ///< the alignment output + mem_state mem; ///< the mem state + chains_state chn; ///< the device chains state + alignment_state aln; ///< the device alignment state + chains_state h_chn; ///< the host chains state + alignment_state h_aln; ///< the host alignment state + read_chunk chunk; ///< the current read chunk + pipeline_stats stats; ///< the pipeline stats +}; + + +template +template +chains_state& chains_state::operator=(const chains_state& other) +{ + n_mems = other.n_mems; + n_chains = other.n_chains; + + mems.resize( n_mems ); + mems_index.resize( n_mems ); + + chain_offsets.resize( n_chains ); + chain_lengths.resize( n_chains ); + chain_reads.resize( n_chains ); + + thrust::copy( other.mems.begin(), other.mems.begin() + n_mems, mems.begin() ); + thrust::copy( other.mems_index.begin(), other.mems_index.begin() + n_mems, mems_index.begin() ); + + thrust::copy( other.chain_offsets.begin(), other.chain_offsets.begin() + n_chains, chain_offsets.begin() ); + thrust::copy( other.chain_lengths.begin(), other.chain_lengths.begin() + n_chains, chain_lengths.begin() ); + thrust::copy( other.chain_reads.begin(), other.chain_reads.begin() + n_chains, chain_reads.begin() ); + return *this; +} + +template +template +alignment_state& alignment_state::operator=(const alignment_state& other) +{ + n_active = other.n_active; + + begin_chains.resize( n_active ); + end_chains.resize( n_active ); + query_spans.resize( n_active ); + ref_spans.resize( n_active ); + temp_queue.resize( n_active ); + stencil.resize( n_active ); + + thrust::copy( other.begin_chains.begin(), other.begin_chains.begin() + n_active, begin_chains.begin() ); + thrust::copy( other.end_chains.begin(), other.end_chains.begin() + n_active, end_chains.begin() ); + thrust::copy( other.query_spans.begin(), other.query_spans.begin() + n_active, query_spans.begin() ); + thrust::copy( other.ref_spans.begin(), other.ref_spans.begin() + n_active, ref_spans.begin() ); + return *this; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/util.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/util.cu new file mode 100644 index 0000000000000000000000000000000000000000..6ac447d41d3344ce66c6f481d7e5512bd3386388 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/util.cu @@ -0,0 +1,75 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#include + +#include "util.h" + +// pick the best GPU to run on +void gpu_init(void) +{ + int device_count = 0; + cudaError_t err; + + cudaSetDeviceFlags(cudaDeviceMapHost | cudaDeviceLmemResizeToMax); + + err = cudaGetDeviceCount(&device_count); + if (err != cudaSuccess) + { + fprintf(stderr, "gpu_init: error enumerating GPUs (%d)\n", err); + exit(1); + } + + if (device_count == 0) + { + fprintf(stderr, "gpu_init: no devices found\n"); + exit(1); + } + + // pick the best device to run on + cudaDeviceProp best_dev_prop; + int best_dev = 0; + int dev; + + cudaGetDeviceProperties(&best_dev_prop, 0); + + for(dev = 0; dev < device_count; dev++) + { + cudaDeviceProp prop; + cudaGetDeviceProperties(&prop, dev); + + if (prop.major >= best_dev_prop.major && + prop.minor >= best_dev_prop.minor) + { + best_dev_prop = prop; + best_dev = dev; + } + } + + cudaSetDevice(best_dev); + fprintf(stderr, "Running on %s (%d MB)\n", best_dev_prop.name, best_dev_prop.totalGlobalMem / 1024 / 1024); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/util.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/util.h new file mode 100644 index 0000000000000000000000000000000000000000..b92e238df2aa983175b689b84dd14d7e0c1ab41b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/nvmem/util.h @@ -0,0 +1,40 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +#pragma once + +#define DO_OPTIONAL_SYNCHRONIZE 1 + +void gpu_init(void); + + +inline void optional_device_synchronize() +{ +#if DO_OPTIONAL_SYNCHRONIZE + cudaDeviceSynchronize(); +#endif +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..06789332b103345c40aebd4028ea72cce6311afa --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/CMakeLists.txt @@ -0,0 +1,12 @@ +# note: this assumes htslib is installed system-wide, need to fix +nvbio_module(bamsort) + +addsources( +bam_io.cu +bam_io.h +bam_sort.cu +) + +cuda_add_executable(bamsort ${bamsort_srcs}) +target_link_libraries(bamsort htslib nvbio moderngpu zlibstatic crcstatic ${SYSTEM_LINK_LIBRARIES}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bam_io.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bam_io.cu new file mode 100644 index 0000000000000000000000000000000000000000..6f376db655012d98cbc674068ac6b57edefba115 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bam_io.cu @@ -0,0 +1,718 @@ +/* + * Copyright (c) 2012-14, NVIDIA CORPORATION. All rights reserved. + * + * NVIDIA CORPORATION and its licensors retain all intellectual property + * and proprietary rights in and to this software, related documentation + * and any modifications thereto. Any use, reproduction, disclosure or + * distribution of this software and related documentation without an express + * license agreement from NVIDIA CORPORATION is strictly prohibited. + * + * + * + * + * + * + * + * + */ + +#include +#include + +#include +#include + +#include "bam_io.h" + + +using namespace nvbio; + +/** ---- Read Functionality ---- **/ + +BAMReader::BAMReader(const char *fname) : eof(false) +{ + fp = gzopen(fname, "rb"); + if (fp == NULL) { + throw nvbio::runtime_error("Could not open %s", fname); + } + if (!read_hdr()) { + throw nvbio::runtime_error("Error parsing BAM file header"); + } +} + +BAMReader::~BAMReader() +{ + gzclose(fp); +} + +#define GZREAD(field) \ + if (read_data(&(field), sizeof(field), __LINE__) == false) { \ + eof = true; \ + return false; \ + } + +// parse the BAM header +bool BAMReader::read_hdr(void) +{ + GZREAD(header.magic); + if (header.magic[0] != 'B' || header.magic[1] != 'A' || + header.magic[2] != 'M' || header.magic[3] != '\1') { + throw nvbio::runtime_error("error parsing BAM file (invalid magic)"); + } + GZREAD(header.l_text); + header.text.resize(header.l_text); + read_data(&header.text[0], header.l_text, __LINE__); + + // read reference sequence data + GZREAD(header.n_ref); + for(int c = 0; c < header.n_ref; c++) { + std::string name; + int32 l_name, l_ref; + GZREAD(l_name); + name.resize(l_name); + read_data(&name[0], l_name, __LINE__); + GZREAD(l_ref); + header.sq_names.push_back(name); + header.sq_lengths.push_back(l_ref); + } + data_start = gztell(fp); + return true; +} + +// load a batch of alignment records (AoS) +bool BAMReader::read_aln_batch(std::vector& batch, const uint64 batch_size) +{ + uint64 aln_id; + for(aln_id = 0; aln_id < batch_size; aln_id++) { + if (eof) { break;} + + BAM_alignment_record record; + GZREAD(record.header.block_size); + z_off_t read_block_start = gztell(fp); + GZREAD(record.header.refID); + GZREAD(record.header.pos); + GZREAD(record.header.bin_mq_nl); + GZREAD(record.header.flag_nc); + GZREAD(record.header.l_seq); + GZREAD(record.header.next_refID); + GZREAD(record.header.next_pos); + GZREAD(record.header.tlen); + + // read the data section + const uint32 data_len = record.header.block_size - (gztell(fp) - read_block_start); + record.data.resize(data_len); + read_data(&record.data[0], data_len, __LINE__); + + // store the record + batch.push_back(record); + } + if (aln_id == 0) { + return false; + } + return true; +} + +// load a contiguous batch of raw byte alignment records (AoS) +bool BAMReader::read_aln_batch_raw(BAM_alignment_batch_raw& raw_batch, const uint64 batch_size) +{ + uint64 byte_offset = 0; + uint64 aln_id; + raw_batch.recs.resize(H_BATCH_SIZE_ALLOC*sizeof(BAM_alignment_record)); // size doesn't include the record data portion + for(aln_id = 0; aln_id < batch_size; aln_id++) { + if (eof) { break;} + // read the size of the record + uint32 record_size; + if(!read_data(&record_size, sizeof(uint32), __LINE__)) { + eof = true; + break; + } + // allocate space + raw_batch.recs.resize(byte_offset + record_size + sizeof(uint32)); + raw_batch.offsets.push_back(byte_offset); + // store the size + memcpy(&raw_batch.recs[byte_offset], &record_size, sizeof(uint32)); + byte_offset += sizeof(uint32); + // read the data + read_data(&raw_batch.recs[byte_offset], record_size, __LINE__); + byte_offset += record_size; + } + if (byte_offset == 0) { + return false; + } + raw_batch.offsets.push_back(byte_offset); + return true; +} + +// load a batch of alignment records (SoA) +// load only the fields specified by the batch field_mask +bool BAMReader::read_aln_batch(BAM_alignment_batch_SoA& batch, const uint64 batch_size) +{ + batch.reset(); + H_VectorU32 cigar_temp(64); + BAM_alignment_header align; + for(uint64 aln_id = 0; aln_id < batch_size; aln_id++) { + if (eof) { break; } + + GZREAD(align.block_size); + z_off_t read_block_start = gztell(fp); + GZREAD(align.refID); + GZREAD(align.pos); + GZREAD(align.bin_mq_nl); + GZREAD(align.flag_nc); + GZREAD(align.l_seq); + GZREAD(align.next_refID); + GZREAD(align.next_pos); + GZREAD(align.tlen); + + if(batch.field_mask & BAM_POSITIONS) { + batch.positions.push_back(align.pos); + } + + if(batch.field_mask & BAM_REFIDS) { + if (align.refID < 0 || align.refID >= header.n_ref) { + batch.refIDs.push_back(uint32(-1)); + } else { + batch.refIDs.push_back(align.refID); + } + } + + if(batch.field_mask & BAM_MAPQ) { + batch.mapq.push_back(align.mapq()); + } + + if(batch.field_mask & BAM_FLAGS) { + batch.flags.push_back(align.flags()); + } + + const uint64 read_name_off = batch.names.size(); + const uint32 read_name_len = align.l_read_name(); + if(batch.field_mask & BAM_NAMES) { + batch.names.resize(read_name_off + read_name_len + 1); + read_data(&batch.names[read_name_off], read_name_len, __LINE__); + batch.names[read_name_off + read_name_len] = '\0'; + } else { + gzseek(fp, read_name_len, SEEK_CUR); + } + + BAM_CRQ_index crq_index(batch.cigars.size(), align.num_cigar_ops(), batch.reads.size(), align.l_seq, batch.qualities.size(), align.l_seq); + if(batch.field_mask & (BAM_CIGARS | BAM_QUALITIES | BAM_READS)) { + batch.crq_index.push_back(crq_index); + } + + const uint32 cigar_len = (align.flag_nc & 0xffff); + if(batch.field_mask & BAM_CIGARS) { + cigar_temp.resize(cigar_len); + if (cigar_len) { + read_data(&cigar_temp[0], sizeof(uint32) * cigar_len, __LINE__); + for(uint32 c = 0; c < cigar_len; c++) { + cigar_op op; + op.op = cigar_temp[c] & 0xf; + op.len = cigar_temp[c] >> 4; + batch.cigars.push_back(op); + } + } + } else { + if (cigar_len) { + gzseek(fp, sizeof(uint32) * cigar_len, SEEK_CUR); + } + } + + if(batch.field_mask & BAM_READS) { + // figure out the length of the sequence data, rounded up to reach a dword boundary + const uint32 padded_read_len_bp = ((align.l_seq + 7) / 8) * 8; + // make sure we have enough memory, then read in the sequence + batch.reads.resize(crq_index.read_start + padded_read_len_bp); + uint64 *storage = (uint64 *)batch.reads.addrof(crq_index.read_start); + read_data(storage, align.l_seq / 2, __LINE__); + } else { + gzseek(fp, align.l_seq / 2, SEEK_CUR); + } + + if(batch.field_mask & BAM_QUALITIES) { + batch.qualities.resize(crq_index.read_start + align.l_seq); + read_data(&batch.qualities[crq_index.read_start], align.l_seq, __LINE__); + } else { + gzseek(fp, align.l_seq, SEEK_CUR); + } + + const uint32 aux_len = align.block_size - (gztell(fp) - read_block_start); + // align index + if(batch.field_mask & (BAM_AUX | BAM_NAMES)) { + BAM_NAUX_index idx(batch.aux_data.size(), aux_len, read_name_off); + batch.aln_index.push_back(idx); + } + if(batch.field_mask & BAM_AUX) { + const uint64 aux_start = batch.aux_data.size(); + batch.aux_data.resize(aux_start + aux_len); + read_data(&batch.aux_data[aux_start], aux_len, __LINE__); + } else { + gzseek(fp, aux_len, SEEK_CUR); + } + + batch.num_alns++; + } + + if (batch.num_alns == 0) { + return false; + } + return true; +} + +bool BAMReader::toSoA(const BAM_alignment_batch_raw& batch, BAM_alignment_batch_SoA& soa_batch) +{ + soa_batch.reset(); + BAM_alignment_header align; + H_VectorU32 cigar_temp(64); + int offset; + for(uint64 idx = 0; idx < batch.offsets.size()-1; idx++) { + uint32 len = batch.offsets[idx + 1] - batch.offsets[idx]; + const uint8* data = &batch.recs.data()[batch.offsets[idx]]; + + offset = sizeof(uint32); + memcpy(&align.refID, data + offset, sizeof(uint32)); + offset += sizeof(uint32); + memcpy(&align.pos, data + offset, sizeof(uint32)); + offset += sizeof(uint32); + memcpy(&align.bin_mq_nl, data + offset, sizeof(uint32)); + offset += sizeof(uint32); + memcpy(&align.flag_nc, data + offset, sizeof(uint32)); + offset += sizeof(uint32); + memcpy(&align.l_seq, data + offset, sizeof(uint32)); + offset += sizeof(uint32); + // skip remainder + offset += 3*sizeof(int32); + + if(soa_batch.field_mask & BAM_REFIDS) { + if (align.refID < 0 || align.refID >= header.n_ref) { + soa_batch.refIDs.push_back(uint32(-1)); + } else { + soa_batch.refIDs.push_back(align.refID); + } + } + + if(soa_batch.field_mask & BAM_POSITIONS) { + soa_batch.positions.push_back(align.pos); + } + + if(soa_batch.field_mask & BAM_MAPQ) { + soa_batch.mapq.push_back(align.mapq()); + } + + if(soa_batch.field_mask & BAM_FLAGS) { + soa_batch.flags.push_back(align.flags()); + } + + const uint32 read_name_off = soa_batch.names.size(); + const uint32 read_name_len = align.l_read_name(); + if(soa_batch.field_mask & BAM_NAMES) { + soa_batch.names.resize(read_name_off + read_name_len + 1); + memcpy(&soa_batch.names[read_name_off], data + offset, read_name_len); + soa_batch.names[read_name_off + read_name_len] = '\0'; + } + offset += read_name_len; + + BAM_CRQ_index crq_index(soa_batch.cigars.size(), align.num_cigar_ops(), + soa_batch.reads.size(), align.l_seq, soa_batch.qualities.size(), align.l_seq); + if(soa_batch.field_mask & (BAM_CIGARS | BAM_QUALITIES | BAM_READS)) { + soa_batch.crq_index.push_back(crq_index); + } + + const uint32 cigar_len = (align.flag_nc & 0xffff); + if(soa_batch.field_mask & BAM_CIGARS) { + cigar_temp.resize(cigar_len); + if (cigar_len) { + memcpy(&cigar_temp[0], data + offset, sizeof(uint32) * cigar_len); + for(uint32 c = 0; c < cigar_len; c++) { + cigar_op op; + op.op = cigar_temp[c] & 0xf; + op.len = cigar_temp[c] >> 4; + soa_batch.cigars.push_back(op); + } + } + } + if (cigar_len) { + offset += sizeof(uint32)*cigar_len; + } + + if(soa_batch.field_mask & BAM_READS) { + // figure out the length of the sequence data, rounded up to reach a dword boundary + const uint32 padded_read_len_bp = ((align.l_seq + 7) / 8) * 8; + // make sure we have enough memory, then read in the sequence + soa_batch.reads.resize(crq_index.read_start + padded_read_len_bp); + uint64 *storage = (uint64 *)soa_batch.reads.addrof(crq_index.read_start); + memcpy(storage, data + offset, align.l_seq / 2); + } + offset += align.l_seq / 2; + + if(soa_batch.field_mask & BAM_QUALITIES) { + soa_batch.qualities.resize(crq_index.read_start + align.l_seq); + memcpy(&soa_batch.qualities[crq_index.read_start], data + offset, align.l_seq); + } + offset += align.l_seq; + + const uint32 aux_len = len - offset; + // align index + if(soa_batch.field_mask & (BAM_AUX | BAM_NAMES)) { + BAM_NAUX_index idx(soa_batch.aux_data.size(), aux_len, read_name_off); + soa_batch.aln_index.push_back(idx); + } + if(soa_batch.field_mask & BAM_AUX) { + const uint64 aux_start = soa_batch.aux_data.size(); + soa_batch.aux_data.resize(aux_start + aux_len); + memcpy(&soa_batch.aux_data[aux_start], data + offset, aux_len); + } + offset += aux_len; + + soa_batch.num_alns++; + } + + if (soa_batch.num_alns == 0) { + return false; + } + return true; +} + +bool BAMReader::read_data(void *output, unsigned int len, int line) +{ + if(len == 0) { + return true; + } + if (eof) { + return false; + } + int ret = gzread(fp, output, len); + if (ret > 0) { + return true; + } else { // check for EOF separately; zlib will not always return Z_STREAM_END at EOF below + if (gzeof(fp)) { + eof = true; + } else { // ask zlib what happened and inform the user + int err; + const char *msg = gzerror(fp, &err); + assert(err != Z_STREAM_END); // we're making the assumption that we never see Z_STREAM_END here + if (err == 0) { + ret = gzread(fp, output, len); + if (ret > 0) { + return true; + } else { + throw nvbio::runtime_error("Error processing BAM file (line %d): zlib error %d (%s) ret = %d", line, err, msg, ret); + } + } + } + return false; + } +} + +HTSBAMReader::HTSBAMReader(const char *fname) +{ + fp = sam_open(fname, "r"); + if (fp == NULL) { + throw nvbio::runtime_error("Could not open %s", fname); + } + header = sam_hdr_read(fp); + if (header == NULL) { + throw nvbio::runtime_error("Error parsing BAM file header"); + } +} + +HTSBAMReader::~HTSBAMReader() +{ + bam_hdr_destroy(header); + sam_close(fp); +} + +// returns false if no records were read +bool HTSBAMReader::read_aln_batch(BAM_alignment_batch_SoA& batch, const uint64 batch_size) +{ + batch.reset(); + H_VectorU32 cigar_temp(64); + bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t)); + for(uint64 aln_id = 0; aln_id < batch_size; aln_id++) { + if (sam_read1(fp, header, b) < 0) break; + + if(batch.field_mask & BAM_POSITIONS) { + batch.positions.push_back(b->core.pos); + } + if(batch.field_mask & BAM_REFIDS) { + batch.refIDs.push_back(b->core.tid); + } + if(batch.field_mask & BAM_MAPQ) { + batch.bin.push_back(b->core.bin); + } + if(batch.field_mask & BAM_MAPQ) { + batch.mapq.push_back(b->core.qual); + } + if(batch.field_mask & BAM_FLAGS) { + batch.flags.push_back(b->core.flag); + } + if(batch.field_mask == BAM_ALL) { + batch.next_refIDs.push_back(b->core.mtid); + batch.next_positions.push_back(b->core.mpos); + } + + // data portion + uint32 offset = 0; + const uint64 read_name_off = batch.names.size(); + const uint32 read_name_len = b->core.l_qname; + if(batch.field_mask & BAM_NAMES) { + batch.names.resize(read_name_off + read_name_len + 1); + memcpy(&batch.names[read_name_off], b->data, read_name_len); + batch.names[read_name_off + read_name_len] = '\0'; + } + offset += read_name_len; + + BAM_CRQ_index crq_index(batch.cigars.size(), b->core.n_cigar, batch.reads.size(), b->core.l_qseq, batch.qualities.size(), b->core.l_qseq); + if(batch.field_mask & (BAM_CIGARS | BAM_QUALITIES | BAM_READS)) { + batch.crq_index.push_back(crq_index); + } + + const uint32 cigar_len = b->core.n_cigar; + if(batch.field_mask & BAM_CIGARS) { + cigar_temp.resize(cigar_len); + if (cigar_len) { + memcpy(&cigar_temp[0], b->data + offset, sizeof(uint32) * cigar_len); + for(uint32 c = 0; c < cigar_len; c++) { + cigar_op op; + op.op = cigar_temp[c] & 0xf; + op.len = cigar_temp[c] >> 4; + batch.cigars.push_back(op); + } + } + } + if (cigar_len) { + offset += sizeof(uint32)*cigar_len; + } + + if(batch.field_mask & BAM_READS) { + // figure out the length of the sequence data, rounded up to reach a dword boundary + const uint32 padded_read_len_bp = ((b->core.l_qseq + 7) / 8) * 8; + // make sure we have enough memory, then read in the sequence + batch.reads.resize(crq_index.read_start + padded_read_len_bp); + uint64 *storage = (uint64 *)batch.reads.addrof(crq_index.read_start); + memcpy(storage, b->data + offset, b->core.l_qseq / 2); + } + offset += b->core.l_qseq / 2; + + if(batch.field_mask & BAM_QUALITIES) { + batch.qualities.resize(crq_index.qual_start + b->core.l_qseq); + memcpy(&batch.qualities[crq_index.qual_start], b->data + offset, b->core.l_qseq); + } + offset += b->core.l_qseq; + + const uint32 aux_len = b->l_data - offset; + BAM_NAUX_index idx(batch.aux_data.size(), aux_len, read_name_off); + if(batch.field_mask & (BAM_AUX | BAM_NAMES)) { + batch.aln_index.push_back(idx); + } + if(batch.field_mask & BAM_AUX) { + const uint64 aux_start = batch.aux_data.size(); + batch.aux_data.resize(aux_start + aux_len); + memcpy(&batch.aux_data[aux_start], b->data + offset, aux_len); + } + offset += aux_len; + + batch.num_alns++; + + if(batch.num_alns % 10000000 == 0) { + printf("Loaded %llu records. \n", batch.num_alns); + } + } + + if (batch.num_alns == 0) { + return false; + } + return true; +} + +bool HTSBAMReader::read_aln_batch(std::vector& batch, const uint64 batch_size) { + bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t)); + uint64 aln_id = 0; + for(aln_id = 0; aln_id < batch_size; aln_id++) { + if (sam_read1(fp, header, b) < 0) break; + batch.push_back(b); + } + if (aln_id == 0) { + return false; + } + return true; +} + + +/** ---- Write Functionality ---- **/ + +BAMWriter::BAMWriter(const char *fname) +{ + fp = fopen(fname, "wt"); + if (fp == NULL) { + throw nvbio::runtime_error("Could not open %s for writing", fname); + } + + // set a 256kb output buffer on fp and make sure it's not line buffered + // this makes sure small fwrites do not land on disk straight away + // (256kb was chosen based on the default stripe size for Linux mdraid RAID-5 volumes) + setvbuf(fp, NULL, _IOFBF, 256 * 1024); +} + +BAMWriter::~BAMWriter() +{ + if (fp) { + fclose(fp); + fp = NULL; + } +} + +void BAMWriter::write_header(BAM_header& header) { + data_buffer.append_data(&header.magic[0], 4); + data_buffer.append_int32(header.l_text); + // header text might be larger than the buffer size + // cannot append the entire string + if(header.l_text <= data_buffer.get_remaining_size()) { + data_buffer.append_string(header.text.c_str()); + } else { + const char* header_text = header.text.c_str(); + for(int i = 0; i < header.l_text; i++) { + if (data_buffer.is_full()) { + write_block(data_buffer); + } + data_buffer.append_int8(header_text[i]); + } + } + if (data_buffer.is_full()) { + write_block(data_buffer); + } + + data_buffer.append_int32(header.n_ref); + for(int i = 0; i < header.n_ref; i++) { + data_buffer.append_int32((int32) header.sq_names[i].length()); + + if(header.sq_names[i].length() <= data_buffer.get_remaining_size()) { + data_buffer.append_string(header.sq_names[i].c_str()); + } else { + const char* seq_text = header.sq_names[i].c_str(); + for(uint32 j = 0; j < header.sq_names[i].length(); j++) { + if (data_buffer.is_full()) { + write_block(data_buffer); + } + data_buffer.append_int8(seq_text[j]); + } + } + if (data_buffer.is_full()) { + write_block(data_buffer); + } + data_buffer.append_int8(0); + data_buffer.append_int32(header.sq_lengths[i]); + } + + if (data_buffer.get_pos()) { + write_block(data_buffer); + } +} + +// write out raw byte record data in the order specified by shuffle_idx +void BAMWriter::write_aln_batch_raw(BAM_alignment_batch_raw& batch, H_VectorU64 shuffle_idx) +{ + for(uint64 i = 0; i < shuffle_idx.size(); i++) { + uint64 idx = shuffle_idx[i]; + uint32 len = batch.offsets[idx + 1] - batch.offsets[idx]; + // records can be of varying size, must ensure sufficient buffer space + if(len <= data_buffer.get_remaining_size()) { + data_buffer.append_data(&batch.recs[batch.offsets[idx]], len); + } else { + for(uint32 j = 0; j < len; j++) { + if (data_buffer.is_full()) { + write_block(data_buffer); + } + data_buffer.append_int8(batch.recs[batch.offsets[idx + j]]); + } + } + if (data_buffer.is_full()) { + write_block(data_buffer); + } + } + if (data_buffer.get_pos()) { + write_block(data_buffer); + } +} + +void BAMWriter::write_block(io::DataBuffer& block) +{ + io::DataBuffer compressed; + bgzf.start_block(compressed); + bgzf.compress(compressed, block); + bgzf.end_block(compressed); + fwrite(compressed.get_base_ptr(), compressed.pos, 1, fp); + block.rewind(); +} + +HTSBAMWriter::HTSBAMWriter(const char *fname) +{ + fp = sam_open(fname, "wb"); + if (fp == NULL) { + throw nvbio::runtime_error("Could not open %s for writing", fname); + } +} + +HTSBAMWriter::~HTSBAMWriter() +{ + if (fp) { + sam_close(fp); + fp = NULL; + } +} + +void HTSBAMWriter::write_hdr(bam_hdr_t* header) +{ + sam_hdr_write(fp, header); +} + +// assumes the batch contains all the fields +void HTSBAMWriter::write_aln_batch(BAM_alignment_batch_SoA& batch, H_VectorU64 shuffle_idx, bam_hdr_t* header) +{ + bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t)); + b->data = (uint8_t*)malloc(ALNREC_SIZE_ALLOC); + b->m_data = ALNREC_SIZE_ALLOC; + for(uint64 idx = 0; idx < batch.num_alns; idx++) { + uint64 i = shuffle_idx[idx]; + BAM_CRQ_index crq = batch.crq_index[i]; + BAM_NAUX_index naux = batch.aln_index[i]; + bam1_core_t *c = &b->core; + c->tid = batch.refIDs[i]; + c->pos = batch.positions[i]; + c->bin = batch.bin[i]; + c->qual = batch.mapq[i]; + if(i < batch.num_alns-1) { + c->l_qname = batch.aln_index[i+1].name_start-naux.name_start-1; // remove the trailing \0 + } else { + c->l_qname = batch.names.size()-naux.name_start-1; + } + c->flag = batch.flags[i]; + c->n_cigar = crq.cigar_len; + c->l_qseq = crq.read_len; + c->mtid = batch.next_refIDs[i]; + c->mpos = batch.next_positions[i]; + c->isize = 0; //TODO + + b->l_data = c->l_qname*sizeof(uint8) + crq.cigar_len*sizeof(cigar_op) + crq.qual_len*sizeof(uint8) + + (crq.read_len/2)*sizeof(uint8) + naux.aux_data_len*sizeof(uint8); + if(b->l_data > b->m_data) { + b->data = (uint8_t*)realloc(b->data, b->l_data); + b->m_data = b->l_data; + } + //qname-cigar-seq-qual-aux + memcpy(b->data, &batch.names[naux.name_start], c->l_qname); + memcpy(b->data, &batch.cigars[crq.cigar_start], crq.cigar_len); + memcpy(b->data, (uint64 *)batch.reads.addrof(crq.read_start), crq.read_len/2); + memcpy(b->data, &batch.qualities[crq.qual_start], crq.qual_len); + memcpy(b->data, &batch.aux_data[naux.aux_data_start], naux.aux_data_len); + + sam_write1(fp, header, b); + } + free(b->data); + free(b); +} + +void HTSBAMWriter::write_aln_batch(std::vector& batch, H_VectorU64 shuffle_idx, bam_hdr_t* header) { + for(uint64 i = 0; i < batch.size(); i++) { + sam_write1(fp, header, batch[i]); + } +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bam_io.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bam_io.h new file mode 100644 index 0000000000000000000000000000000000000000..dd8a3b124e83802e7c45aa49acc2143397eadc0d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bam_io.h @@ -0,0 +1,423 @@ +/* + * Copyright (c) 2012-14, NVIDIA CORPORATION. All rights reserved. + * + * NVIDIA CORPORATION and its licensors retain all intellectual property + * and proprietary rights in and to this software, related documentation + * and any modifications thereto. Any use, reproduction, disclosure or + * distribution of this software and related documentation without an express + * license agreement from NVIDIA CORPORATION is strictly prohibited. + * + * + * + * + * + * + * + * + */ + +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "bamsort_types.h" + +#include +#include +#include +#include +#include + +using namespace nvbio; + +/**------------- BAM Format -------------**/ + +// BAM header +struct BAM_header +{ + uint8 magic[4]; // BAM magic string + int32 l_text; // length of the header text + std::string text; // the header text itself + int32 n_ref; // number of reference sequences + std::vector sq_names; // reference sequence names + H_VectorU32 sq_lengths; // reference sequence lengths +}; + +// BAM alignment record header +struct BAM_alignment_header +{ + int32 block_size; // length of the remainder of the alignment record + int32 refID; // reference sequence ID, -1 <= refID < n_ref (-1 for a read without a mapping position) + int32 pos; // 0-based leftmost coordinate + uint32 bin_mq_nl; // bin << 16 | MAPQ << 8 | l_read_name + uint32 flag_nc; // FLAG << 16 | n_cigar_op + int32 l_seq; // length of the sequence + int32 next_refID; // refID of the next segment (-1 <= next_refID < n_ref) + int32 next_pos; // 0-based leftmost pos of the next segment + int32 tlen; // template length + + uint32 bin(void) const { return bin_mq_nl >> 16; } + uint32 mapq(void) const { return (bin_mq_nl & 0xff00) >> 8; } + uint32 l_read_name(void) const { return bin_mq_nl & 0xff; } + uint32 flags(void) const { return flag_nc >> 16; } + uint32 num_cigar_ops(void) const { return flag_nc & 0xffff; } +}; + +// BAM alignment record +// consists of the alignment header followed by a variable-length +// data block; the auxiliary data is of block_size - ftell() bytes +struct BAM_alignment_record +{ + BAM_alignment_header header; // alignment info + H_VectorU8 data; // qname + cigar + seq + qual + aux +}; + +// contiguous batch of raw alignment records +struct BAM_alignment_batch_raw +{ + H_VectorU8 recs; // raw byte array of alignment records + H_VectorU64 offsets; // offsets into alignment records (num_recs + 1) +}; + +typedef enum +{ + BAM_NAMES = 1, + BAM_CIGARS = 2, + BAM_READS = 4, + BAM_QUALITIES = 8, + BAM_FLAGS = 16, + BAM_POSITIONS = 32, + BAM_REFIDS = 64, + BAM_MAPQ = 128, + BAM_AUX = 256, + BAM_BIN = 512, + BAM_ALL = 0xFFFF +} BAM_field_masks; + +typedef enum +{ + BAM_FLAGS_PAIRED = 1, + BAM_FLAGS_PROPER_PAIR = 2, + BAM_FLAGS_UNMAPPED = 4, + BAM_FLAGS_MATE_UNMAPPED = 8, + BAM_FLAGS_REVERSE = 16, + BAM_FLAGS_MATE_REVERSE = 32, + BAM_FLAGS_READ_1 = 64, + BAM_FLAGS_READ_2 = 128, + BAM_FLAGS_SECONDARY = 256, + BAM_FLAGS_QC_FAILED = 512, + BAM_FLAGS_DUPLICATE = 1024 +} BAM_alignment_flags; + + +// ----- SoA Functionality ------ + +// CRQ: cigars, reads, qualities +struct BAM_CRQ_index +{ + uint64 cigar_start, cigar_len; + uint64 read_start, read_len; + uint64 qual_start, qual_len; + + BAM_CRQ_index(): cigar_start(0), cigar_len(0), read_start(0), read_len(0), qual_start(0), qual_len(0) { } + BAM_CRQ_index(uint64 cigar_start, uint64 cigar_len, uint64 read_start, uint64 read_len, uint64 qual_start, uint64 qual_len) + : cigar_start(cigar_start), cigar_len(cigar_len), read_start(read_start), read_len(read_len), + qual_start(qual_start), qual_len(qual_len) { } +}; + +struct BAM_NAUX_index +{ + uint64 aux_data_start; + uint32 aux_data_len; + uint64 name_start; + + BAM_NAUX_index() : aux_data_start(0), aux_data_len(0), name_start(0) { } + BAM_NAUX_index(uint64 aux_data_start, uint32 aux_data_len, uint64 name_start) + : aux_data_start(aux_data_start), aux_data_len(aux_data_len), name_start(name_start) { } +}; + +#define H_BATCH_SIZE_ALLOC 10000000U +#define ALNREC_SIZE_ALLOC 512 + +// batch of alignment records as SoA +// host-only now +struct BAM_alignment_batch_SoA +{ + BAM_alignment_batch_SoA(): field_mask(BAM_ALL), num_alns(0) { reserve(); } + BAM_alignment_batch_SoA(uint32 fields): field_mask(fields), num_alns(0) { reserve(); } + + uint32 field_mask; // record fields stored + uint64 num_alns; + H_VectorCigarOp cigars; + H_VectorDNA16 reads; + H_VectorU16 bin; + H_VectorU8 qualities; + H_VectorU16 flags; + H_VectorU32 positions; + H_VectorU32 refIDs; + H_VectorU8 mapq; + H_VectorU8 aux_data; + H_VectorU8 names; + H_VectorU32 next_positions; + H_VectorU32 next_refIDs; + nvbio::vector crq_index; // CRQ: cigars, reads, qualities + nvbio::vector aln_index; // names, aux + + void reserve() + { + if(field_mask & BAM_POSITIONS) positions.reserve(H_BATCH_SIZE_ALLOC); + if(field_mask & BAM_REFIDS) refIDs.reserve(H_BATCH_SIZE_ALLOC); + if(field_mask & BAM_BIN) bin.reserve(H_BATCH_SIZE_ALLOC); + if(field_mask & BAM_MAPQ) mapq.reserve(H_BATCH_SIZE_ALLOC); + if(field_mask & BAM_FLAGS) flags.reserve(H_BATCH_SIZE_ALLOC); + if(field_mask & (BAM_CIGARS | BAM_QUALITIES | BAM_READS)) crq_index.reserve(H_BATCH_SIZE_ALLOC); + if(field_mask & BAM_CIGARS) cigars.reserve(H_BATCH_SIZE_ALLOC * 32); + if(field_mask & BAM_READS) reads.reserve(H_BATCH_SIZE_ALLOC * 125); + if(field_mask & BAM_QUALITIES) qualities.reserve(H_BATCH_SIZE_ALLOC * 125); + if(field_mask & (BAM_AUX | BAM_NAMES)) aln_index.reserve(H_BATCH_SIZE_ALLOC); + if(field_mask & BAM_AUX) aux_data.reserve(H_BATCH_SIZE_ALLOC * 64); + if(field_mask & BAM_NAMES) names.reserve(H_BATCH_SIZE_ALLOC * 256); + if(field_mask == BAM_ALL) { + next_positions.reserve(H_BATCH_SIZE_ALLOC); + next_refIDs.reserve(H_BATCH_SIZE_ALLOC); + } + } + + void allocate(const BAM_alignment_batch_SoA& size_batch) + { + if(field_mask & BAM_POSITIONS) positions.resize(size_batch.positions.size()); + if(field_mask & BAM_REFIDS) refIDs.resize(size_batch.refIDs.size()); + if(field_mask & BAM_BIN) bin.resize(size_batch.bin.size()); + if(field_mask & BAM_MAPQ) mapq.resize(size_batch.mapq.size()); + if(field_mask & BAM_FLAGS) flags.resize(size_batch.flags.size()); + if(field_mask & (BAM_CIGARS | BAM_QUALITIES | BAM_READS)) crq_index.resize(size_batch.crq_index.size()); + if(field_mask & BAM_CIGARS) cigars.resize(size_batch.cigars.size()); + if(field_mask & BAM_READS) reads.resize(size_batch.reads.size()); + if(field_mask & BAM_QUALITIES) qualities.resize(size_batch.qualities.size()); + if(field_mask & (BAM_AUX | BAM_NAMES)) aln_index.resize(size_batch.aln_index.size()); + if(field_mask & BAM_AUX) aux_data.resize(size_batch.aux_data.size()); + if(field_mask & BAM_NAMES) names.resize(size_batch.names.size()); + if(field_mask == BAM_ALL) { + next_positions.resize(size_batch.next_positions.size()); + next_refIDs.resize(size_batch.next_refIDs.size()); + } + } + + void reset() + { + num_alns = 0; + positions.clear(); + refIDs.clear(); + bin.clear(); + mapq.clear(); + flags.clear(); + crq_index.clear(); + cigars.clear(); + reads.clear(); + qualities.clear(); + aln_index.clear(); + aux_data.clear(); + names.clear(); + next_positions.clear(); + next_refIDs.clear(); + } + + void free() + { + // force the memory to be freed by swapping + positions = H_VectorU32(); + refIDs = H_VectorU32(); + bin = H_VectorU16(); + mapq = H_VectorU8(); + flags = H_VectorU16(); + cigars = H_VectorCigarOp(); + reads = H_VectorDNA16(); + qualities = H_VectorU8(); + aux_data = H_VectorU8(); + names = H_VectorU8(); + crq_index = nvbio::vector(); + aln_index = nvbio::vector(); + next_positions = H_VectorU32(); + next_refIDs = H_VectorU32(); + } + + void shuffle(BAM_alignment_batch_SoA& batch_out, H_VectorU64 shuffle_idx) { + batch_out.allocate(*this); + + if(field_mask & BAM_POSITIONS) { + thrust::gather(shuffle_idx.begin(), shuffle_idx.end(), positions.begin(), batch_out.positions.begin()); + } + if(field_mask & BAM_REFIDS) { + thrust::gather(shuffle_idx.begin(), shuffle_idx.end(), refIDs.begin(), batch_out.refIDs.begin()); + } + if(field_mask & BAM_BIN) { + thrust::gather(shuffle_idx.begin(), shuffle_idx.end(), bin.begin(), batch_out.bin.begin()); + } + if(field_mask & BAM_MAPQ) { + thrust::gather(shuffle_idx.begin(), shuffle_idx.end(), mapq.begin(), batch_out.mapq.begin()); + } + if(field_mask & BAM_FLAGS) { + thrust::gather(shuffle_idx.begin(), shuffle_idx.end(), flags.begin(), batch_out.flags.begin()); + } + if(field_mask & BAM_QUALITIES) { + uint64 cigar_offset = 0; + for(uint64 i = 0; i < num_alns; i++) { + uint64 idx = shuffle_idx[i]; + thrust::copy_n(cigars.begin() + crq_index[idx].cigar_start, crq_index[idx].cigar_len, + batch_out.cigars.begin() + cigar_offset); + batch_out.crq_index[i].cigar_start = cigar_offset; + batch_out.crq_index[i].cigar_len = crq_index[idx].cigar_len; + cigar_offset += crq_index[idx].cigar_len; + } + } + if(field_mask & BAM_READS) { + uint64 read_offset = 0; + for(uint64 i = 0; i < num_alns; i++) { + uint64 idx = shuffle_idx[i]; + uint64* data_in = (uint64 *)reads.addrof(crq_index[idx].read_start); + uint64* data_out = (uint64 *)batch_out.reads.addrof(read_offset); + memcpy(data_out, data_in, crq_index[idx].read_len/2); + batch_out.crq_index[i].read_start = read_offset; + batch_out.crq_index[i].read_len = crq_index[idx].read_len; + const uint32 padded_read_len_bp = ((crq_index[idx].read_len + 7) / 8) * 8; + read_offset += padded_read_len_bp; + } + } + if(field_mask & BAM_QUALITIES) { + uint64 qual_offset = 0; + for(uint64 i = 0; i < num_alns; i++) { + uint64 idx = shuffle_idx[i]; + thrust::copy_n(qualities.begin() + crq_index[idx].qual_start, crq_index[idx].qual_len, + batch_out.qualities.begin() + qual_offset); + batch_out.crq_index[i].qual_start = qual_offset; + batch_out.crq_index[i].qual_len = crq_index[idx].qual_len; + qual_offset += crq_index[idx].qual_len; + } + } + if(field_mask & BAM_AUX) { + uint64 aux_offset = 0; + for(uint64 i = 0; i < num_alns; i++) { + uint64 idx = shuffle_idx[i]; + thrust::copy_n(aux_data.begin() + aln_index[idx].aux_data_start, aln_index[idx].aux_data_len, batch_out.aux_data.begin() + aux_offset); + batch_out.aln_index[i].aux_data_start = aux_offset; + batch_out.aln_index[i].aux_data_len = aln_index[idx].aux_data_len; + aux_offset += aln_index[idx].aux_data_len; + } + } + if(field_mask & BAM_NAMES){ + uint64 names_offset = 0; + for(uint64 i = 0; i < num_alns; i++) { + uint64 idx = shuffle_idx[i]; + uint32 len; + if(idx < num_alns-1) { + len = aln_index[idx+1].name_start-aln_index[idx].name_start; + } else { + len = names.size()-aln_index[idx].name_start; + } + thrust::copy_n(names.begin() + aln_index[idx].name_start, len, batch_out.names.begin() + names_offset); + batch_out.aln_index[i].name_start = names_offset; + names_offset += len; + } + } + if(field_mask == BAM_ALL) { + thrust::gather(shuffle_idx.begin(), shuffle_idx.end(), next_positions.begin(), batch_out.next_positions.begin()); + thrust::gather(shuffle_idx.begin(), shuffle_idx.end(), next_refIDs.begin(), batch_out.next_refIDs.begin()); + } + } +}; + + +/**------------------- BAM Reader -------------**/ + +struct BAMReader +{ +public: + BAM_header header; + +private: + gzFile fp; + z_off_t data_start; + bool eof; + +public: + BAMReader(const char *fname); + ~BAMReader(); + + bool read_aln(const BAM_alignment_record& record); + bool read_aln_batch(std::vector& batch, const uint64 batch_size = 1000000); + bool read_aln_batch(BAM_alignment_batch_SoA& batch, const uint64 batch_size = 1000000); + bool read_aln_batch_raw(BAM_alignment_batch_raw& batch, const uint64 batch_size = 1000000); + void toSoA(const std::vector& batch, BAM_alignment_batch_SoA& soa_batch); + bool toSoA(const BAM_alignment_batch_raw& batch, BAM_alignment_batch_SoA& soa_batch); +private: + bool read_hdr(void); + bool read_data(void *output, unsigned int len, int line); + char* parse_header_tag(uint32 *len, const char *tag, char *start_ptr, char *end_ptr); +}; + +// htslib-based BAM file reader +struct HTSBAMReader +{ +public: + bam_hdr_t* header; + +private: + samFile* fp; + +public: + HTSBAMReader(const char *fname); + ~HTSBAMReader(); + + bool read_aln_batch(std::vector& batch, const uint64 batch_size = 1000000); + bool read_aln_batch(BAM_alignment_batch_SoA& batch, const uint64 batch_size = 1000000); +private: + bool read_hdr(void); +}; + +/**------------------- BAM Writer -------------**/ + +struct BAMWriter +{ +private: + FILE *fp; + io::DataBuffer data_buffer; + io::BGZFCompressor bgzf; + +public: + BAMWriter(const char *fname); + ~BAMWriter(); + + void write_header(BAM_header& header); + void write_aln_batch(std::vector& batch); + void write_aln_batch_raw(BAM_alignment_batch_raw& batch, H_VectorU64 shuffle_idx); + void write_aln(std::vector& batch, uint64 id); + +private: + void write_block(io::DataBuffer& block); +}; + + +// htslib-based BAM file writer +struct HTSBAMWriter +{ +private: + samFile* fp; + +public: + HTSBAMWriter(const char *fname); + ~HTSBAMWriter(); + + void write_hdr(bam_hdr_t* header); + void write_aln_batch(std::vector& batch, H_VectorU64 shuffle_idx, bam_hdr_t* header); + void write_aln_batch(BAM_alignment_batch_SoA& batch, H_VectorU64 shuffle_idx, bam_hdr_t* header); +}; diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bam_sort.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bam_sort.cu new file mode 100644 index 0000000000000000000000000000000000000000..deb6cf0d7c6bea36928a0a2804e12a4e614c648e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bam_sort.cu @@ -0,0 +1,722 @@ +/* + * Copyright (c) 2012-14, NVIDIA CORPORATION. All rights reserved. + * + * NVIDIA CORPORATION and its licensors retain all intellectual property + * and proprietary rights in and to this software, related documentation + * and any modifications thereto. Any use, reproduction, disclosure or + * distribution of this software and related documentation without an express + * license agreement from NVIDIA CORPORATION is strictly prohibited. + * + * + * + * + * + * + * + * + */ + +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include + +#include +#include + +#include "bam_io.h" +#include "bam_sort.h" + +//#ifdef _OPENMP +#include +//#endif + +using namespace nvbio; + +int test_sorted(const H_KVP_batch& result); + +/** --------- Sorting Modules -------- **/ + +// generate sort keys +void sortkey_gen(bamsort_context* context) +{ + thrust::for_each(context->active_read_ids.begin(), + context->active_read_ids.end(), + generate_sort_keys(*context)); +} + +// local sort of key-val pairs on the device +void sort(bamsort_context* context) +{ + thrust::sort_by_key(context->sort_keys.begin(), context->sort_keys.end(), context->active_read_ids.begin()); +} + +// used by out-of-core merge for searching a sorted array +// to find the position until which all the elements are less than the pivot +// TODO: ensure thrust uses binary search +uint32 find_split_idx(bamsort_context* context, const uint64 len, const uint64 pivot) +{ + return thrust::distance(context->patch_searched.begin(), + thrust::partition_point(context->patch_searched.begin(), context->patch_searched.begin() + len, is_less(pivot))); +} + +// out-of-core merge of two sorted batches +// for single GPU: sequentially merge the pivot elements on the CPU to determine the partitions +// since only one partition at a time can be merged on the device -- this is to avoid +// extracting and sorting the pivot elements separately; +// TODO: optimize if pivots have the same value +void merge_batches_1GPU(bamsort_context* context, const H_KVP_batch* b1, const H_KVP_batch* b2, H_KVP_batch* out, + float& merge_time, float& data_time, float& search_time) +{ + cuda::Timer timer; + + // partition info + uint64 b1_npivots = b1->keys.size() / PIVOT_SAMPLING_INTERVAL; + uint64 b2_npivots = b2->keys.size() / PIVOT_SAMPLING_INTERVAL; + uint64 b1_pivot = 1, b2_pivot = 1; + uint64 p1L = 0, p1H = 0; // batch partition limits [L, H) + uint64 p2L = 0, p2H = 0; + uint64 p1_size = 0, p2_size = 0; + uint64 out_idx = 0; + + // mgpu context + int current_device; + cudaGetDevice(¤t_device); + mgpu::ContextPtr mgpu_ctxt = mgpu::CreateCudaDevice(current_device); + + while(1) { + // check if we're in the last partition + if(b1_pivot > b1_npivots || b2_pivot > b2_npivots) { + break; // still need to merge the batch remainders + } + // find the next partition + p1L = p1H; + p2L = p2H; + + timer.start(); + if(b1->keys[b1_pivot*PIVOT_SAMPLING_INTERVAL-1] <= b2->keys[b2_pivot*PIVOT_SAMPLING_INTERVAL-1]) { + p1H = b1_pivot*PIVOT_SAMPLING_INTERVAL; + // only need to search this patch since the pivots are sorted + NVBIO_CUDA_ASSERT(context->patch_searched.size() <= PIVOT_SAMPLING_INTERVAL); + thrust::copy(b2->keys.begin() + p2L, b2->keys.begin() + b2_pivot*PIVOT_SAMPLING_INTERVAL, context->patch_searched.begin()); + p2H = p2L + find_split_idx(context, b2_pivot*PIVOT_SAMPLING_INTERVAL - p2L, b1->keys[b1_pivot*PIVOT_SAMPLING_INTERVAL-1]); + b1_pivot++; // advance the pivot pointer + } else { + p2H = b2_pivot*PIVOT_SAMPLING_INTERVAL; + NVBIO_CUDA_ASSERT(context->patch_searched.size() <= PIVOT_SAMPLING_INTERVAL); + thrust::copy(b1->keys.begin() + p1L, b1->keys.begin() + b1_pivot*PIVOT_SAMPLING_INTERVAL, context->patch_searched.begin()); + p1H = p1L + find_split_idx(context, b1_pivot*PIVOT_SAMPLING_INTERVAL - p1L, b2->keys[b2_pivot*PIVOT_SAMPLING_INTERVAL-1]); + b2_pivot++; + } + timer.stop(); + search_time += timer.seconds(); + p1_size = p1H - p1L; + p2_size = p2H - p2L; + //printf("Partition sizes: %llu %llu \n", p1_size, p2_size); + + // if one of the batch partitions is empty, we are done + if(p1_size == 0) { + thrust::copy(b2->keys.begin() + p2L, b2->keys.begin() + p2H, out->keys.begin()+out_idx); + thrust::copy(b2->ids.begin() + p2L, b2->ids.begin() + p2H, out->ids.begin()+out_idx); + out_idx += p2_size; + continue; + } else if(p2_size == 0) { + thrust::copy(b1->keys.begin() + p1L, b1->keys.begin() + p1H, out->keys.begin()+out_idx); + thrust::copy(b1->ids.begin() + p1L, b1->ids.begin() + p1H, out->ids.begin()+out_idx); + out_idx += p1_size; + continue; + } // TODO: if the sizes are less than a given threshold, merge on the CPU + + // transfer the partitions to the device + NVBIO_CUDA_ASSERT(context->p1.keys.size() <= 2*PIVOT_SAMPLING_INTERVAL); + NVBIO_CUDA_ASSERT(context->p2.keys.size() <= 2*PIVOT_SAMPLING_INTERVAL); + NVBIO_CUDA_ASSERT(context->r.keys.size() <= 2*PIVOT_SAMPLING_INTERVAL); + + timer.start(); + thrust::copy(b1->keys.begin() + p1L, b1->keys.begin() + p1H, context->p1.keys.begin()); + thrust::copy(b2->keys.begin() + p2L, b2->keys.begin() + p2H, context->p2.keys.begin()); + thrust::copy(b1->ids.begin() + p1L, b1->ids.begin() + p1H, context->p1.ids.begin()); + thrust::copy(b2->ids.begin() + p2L, b2->ids.begin() + p2H, context->p2.ids.begin()); + timer.stop(); + data_time += timer.seconds(); + + // merge + timer.start(); + mgpu::MergePairs(context->p1.keys.begin(), context->p1.ids.begin(), p1_size, + context->p2.keys.begin(), context->p2.ids.begin(), p2_size, + context->r.keys.begin(), context->r.ids.begin(), *mgpu_ctxt); + timer.stop(); + merge_time += timer.seconds(); + + // transfer the results to the host + timer.start(); + thrust::copy(context->r.keys.begin(), context->r.keys.begin() + p1_size + p2_size, out->keys.begin()+out_idx); + thrust::copy(context->r.ids.begin(), context->r.ids.begin() + p1_size + p2_size, out->ids.begin()+out_idx); + timer.stop(); + data_time += timer.seconds(); + + out_idx += p1_size + p2_size; + } + + // merge the final pieces + p1_size = b1->keys.size() - p1H; + p2_size = b2->keys.size() - p2H; + //printf("Final partition sizes: %llu %llu \n", p1_size, p2_size); + + // if one of the batch remainders is empty, we are done + if(p1_size == 0) { + thrust::copy(b2->keys.begin() + p2H, b2->keys.end(), out->keys.begin()+out_idx); + thrust::copy(b2->ids.begin() + p2H, b2->ids.end(), out->ids.begin()+out_idx); + return; + } else if(p2_size == 0) { + thrust::copy(b1->keys.begin() + p1H, b1->keys.end(), out->keys.begin()+out_idx); + thrust::copy(b1->ids.begin() + p1H, b1->ids.end(), out->ids.begin()+out_idx); + return; + } + NVBIO_CUDA_ASSERT(context->p1.keys.size() <= 2*PIVOT_SAMPLING_INTERVAL); + NVBIO_CUDA_ASSERT(context->p2.keys.size() <= 2*PIVOT_SAMPLING_INTERVAL); + NVBIO_CUDA_ASSERT(context->r.keys.size() <= 2*PIVOT_SAMPLING_INTERVAL); + + timer.start(); + thrust::copy(b1->keys.begin() + p1H, b1->keys.end(), context->p1.keys.begin()); + thrust::copy(b2->keys.begin() + p2H, b2->keys.end(), context->p2.keys.begin()); + thrust::copy(b1->ids.begin() + p1H, b1->ids.end(), context->p1.ids.begin()); + thrust::copy(b2->ids.begin() + p2H, b2->ids.end(), context->p2.ids.begin()); + timer.stop(); + data_time += timer.seconds(); + + timer.start(); + mgpu::MergePairs(context->p1.keys.begin(), context->p1.ids.begin(), p1_size, + context->p2.keys.begin(), context->p2.ids.begin(), p2_size, + context->r.keys.begin(), context->r.ids.begin(), *mgpu_ctxt); + timer.stop(); + merge_time += timer.seconds(); + + timer.start(); + thrust::copy(context->r.keys.begin(), context->r.keys.begin() + p1_size + p2_size, out->keys.begin()+out_idx); + thrust::copy(context->r.ids.begin(), context->r.ids.begin() + p1_size + p2_size, out->ids.begin()+out_idx); + timer.stop(); + data_time += timer.seconds(); +} + +// out-of-core merge of two sorted batches +// two GPUs +void merge_batches_2GPU(H_KVP_batch* b1, H_KVP_batch* b2, H_KVP_batch* out) +{ + // partition info + uint64 b1_npivots = (b1->keys.size()-1) / PIVOT_SAMPLING_INTERVAL; + uint64 b2_npivots = (b2->keys.size()-1) / PIVOT_SAMPLING_INTERVAL; + + // 1. sort the pivots + H_VectorU64 pivots(b1_npivots + b2_npivots); + for(uint64 i = 0; i < b1_npivots; i++) { + pivots[i] = b1->keys[(i+1)*PIVOT_SAMPLING_INTERVAL-1]; + } + for(uint64 i = 0; i < b2_npivots; i++) { + pivots[b1_npivots + i] = b2->keys[(i+1)*PIVOT_SAMPLING_INTERVAL-1]; + } + thrust::sort(pivots.begin(), pivots.end()); + + printf("Merge: found and sorted pivots. Num pivots %llu \n", (uint64) pivots.size()); + + std::vector batches(2); + std::vector pivot_idx(2); + batches[0] = b1; + batches[1] = b2; + + // 2. search each batch for the partition delimiters + omp_set_num_threads(2); + #pragma omp parallel + { + int tid = omp_get_thread_num(); + cudaSetDevice(tid); + + H_KVP_batch* b = batches[tid]; + D_VectorU64 d_bkeys(D_BATCH_SIZE); + pivot_idx[tid].resize(pivots.size()); + + uint64 num_processed = 0; + uint64 pid = 0; + + while(num_processed < b->keys.size() && pid < pivots.size()) { + uint64 batch_size = D_BATCH_SIZE; + if(b->keys.size() - num_processed < D_BATCH_SIZE) { + batch_size = b->keys.size() - num_processed; + } + thrust::copy(b->keys.begin() + num_processed, b->keys.begin() + num_processed + batch_size, d_bkeys.begin()); + + // find as many pivots as possible in the loaded partition + while(1) { + if(pid >= pivots.size() || pivots[pid] > b->keys[num_processed + batch_size - 1]) { + break; // load the next batch + } + // pivot is in the loaded section + uint64 offset = thrust::distance(d_bkeys.begin(), + thrust::partition_point(d_bkeys.begin(), d_bkeys.begin() + batch_size, is_less(pivots[pid]))); + + pivot_idx[tid][pid] = num_processed + offset; + pid++; + } + num_processed += batch_size; + } + + if(pid < pivots.size()) { + // if pid == 0, all elements in this batch are smaller than the elements in the second batch + for(uint64 i = pid; i < pivots.size(); i++) { + pivot_idx[tid][i] = b->keys.size(); + } + } + + printf("Thread %d processed %llu elements \n", tid, num_processed); + } + + // 3. find partition offsets into output + // TODO: optimize out empty partitions (when pivots are equal) + uint64 num_partitions = pivots.size() + 1; + H_VectorU64 p_offsets(num_partitions); + p_offsets[0] = 0; + for(uint64 i = 1; i < num_partitions; i++) { + p_offsets[i] = pivot_idx[0][i-1] + pivot_idx[1][i-1]; + } + printf("Total number of partitions: %llu \n", num_partitions); + + std::vector mgpu_ctxt(2); + mgpu_ctxt[0] = mgpu::CreateCudaDevice(0); + mgpu_ctxt[1] = mgpu::CreateCudaDevice(1); + + // 4. merge the partitions + omp_set_num_threads(2); + #pragma omp parallel + { + int tid = omp_get_thread_num(); + cudaSetDevice(tid); + + bamsort_context context; + context.allocate_partition(); + uint64 p1L, p1H; // batch partition limits [L, H) + uint64 p2L, p2H; + uint64 p1_size, p2_size; + uint64 part_id = tid; + + while(part_id < num_partitions) { + uint64 out_idx = p_offsets[part_id]; + + if(part_id == 0) { + p1L = 0; + p2L = 0; + } else { + p1L = pivot_idx[0][part_id-1]; + p2L = pivot_idx[1][part_id-1]; + } + + if(part_id == num_partitions - 1) { + p1H = b1->keys.size(); + p2H = b2->keys.size(); + } else { + p1H = pivot_idx[0][part_id]; + p2H = pivot_idx[1][part_id]; + } + + p1_size = p1H - p1L; + p2_size = p2H - p2L; + printf("Thread %d. Partition sizes: %llu %llu\n", tid, p1_size, p2_size); + + // if one of the batch partitions is empty, we are done + if(p1_size == 0) { + thrust::copy(b2->keys.begin() + p2L, b2->keys.begin() + p2H, out->keys.begin()+out_idx); + thrust::copy(b2->ids.begin() + p2L, b2->ids.begin() + p2H, out->ids.begin()+out_idx); + part_id += 2; + continue; + } else if(p2_size == 0) { + thrust::copy(b1->keys.begin() + p1L, b1->keys.begin() + p1H, out->keys.begin()+out_idx); + thrust::copy(b1->ids.begin() + p1L, b1->ids.begin() + p1H, out->ids.begin()+out_idx); + part_id += 2; + continue; + } + + // transfer the partitions to the device + thrust::copy(b1->keys.begin() + p1L, b1->keys.begin() + p1H, context.p1.keys.begin()); + thrust::copy(b2->keys.begin() + p2L, b2->keys.begin() + p2H, context.p2.keys.begin()); + thrust::copy(b1->ids.begin() + p1L, b1->ids.begin() + p1H, context.p1.ids.begin()); + thrust::copy(b2->ids.begin() + p2L, b2->ids.begin() + p2H, context.p2.ids.begin()); + + // merge + mgpu::MergePairs(context.p1.keys.begin(), context.p1.ids.begin(), p1_size, + context.p2.keys.begin(), context.p2.ids.begin(), p2_size, + context.r.keys.begin(), context.r.ids.begin(), *mgpu_ctxt[tid]); + + // transfer the results to the host + thrust::copy(context.r.keys.begin(), context.r.keys.begin() + p1_size + p2_size, out->keys.begin()+out_idx); + thrust::copy(context.r.ids.begin(), context.r.ids.begin() + p1_size + p2_size, out->ids.begin()+out_idx); + + part_id += 2; + } + } +} + +/** ------ Sorting Pipelines ---------- **/ + +// full load -> sort -> store (no IO-compute overlapping) +// single GPU +void bamsort_pipeline_basic(const char* in_fname, const char* out_fname) +{ + cuda::Timer timer, timer_alloc, timer_all; + float sort_time = 0, keygen_time = 0, data_time = 0, merge_time = 0, merge_data_time = 0, merge_search_time = 0; + //timer_all.start(); + + // 1. load BAM + timer.start(); + HTSBAMReader bam_reader(in_fname); + BAM_alignment_batch_SoA h_batch(BAM_POSITIONS | BAM_REFIDS | BAM_FLAGS); + bam_reader.read_aln_batch(h_batch, H_BATCH_SIZE); + timer.stop(); + printf("BAM load time: %.4fs\n", timer.seconds()); + printf("Total number of alignments: %llu \n", h_batch.num_alns); + + timer_all.start(); + // 2. split and sort + int num_batches = 0; + uint64 num_aln_loaded = 0; + std::list sorted_kvp_batches; // container for the sorted batches + bamsort_context device_context; // device data for sorting + + while(num_aln_loaded < h_batch.num_alns) { + // transfer the next batch to the device + timer.start(); + device_context.load_batch(h_batch, num_aln_loaded, D_BATCH_SIZE); + timer.stop(); + data_time += timer.seconds(); + + // generate the sort keys + timer.start(); + sortkey_gen(&device_context); + timer.stop(); + keygen_time += timer.seconds(); + + // sort + timer.start(); + sort(&device_context); + timer.stop(); + sort_time += timer.seconds(); + + // save sorted batches on the host + timer.start(); + H_KVP_batch* sorted_batch = new H_KVP_batch(); + sorted_batch->keys.resize(device_context.sort_keys.size()); + sorted_batch->ids.resize(device_context.sort_keys.size()); + thrust::copy(device_context.sort_keys.begin(), device_context.sort_keys.end(), sorted_batch->keys.begin()); + thrust::copy(device_context.active_read_ids.begin(), device_context.active_read_ids.end(), sorted_batch->ids.begin()); + sorted_kvp_batches.push_back(sorted_batch); + timer.stop(); + data_time += timer.seconds(); + + num_batches += 1; + num_aln_loaded += sorted_batch->ids.size(); + printf("Processed %d batches and %llu reads \n", num_batches, num_aln_loaded); + } + printf("Local keygen-only time : %.4fs\n", keygen_time); + printf("Local batch sorting-only time : %.4fs\n", sort_time); + printf("Local device data allocation and transfer time : %.4fs\n", data_time); + + // free device data + device_context.free_local_sort_batch(); + + // 3. merge + H_KVP_batch* final_result = sorted_kvp_batches.front(); + if(sorted_kvp_batches.size() != 1) { + device_context.allocate_partition(); + } + timer.start(); + float alloc_time = 0; + while(sorted_kvp_batches.size() > 1) { + timer_alloc.start(); + H_KVP_batch* out = new H_KVP_batch(); + H_KVP_batch* b1 = sorted_kvp_batches.front(); + sorted_kvp_batches.pop_front(); + H_KVP_batch* b2 = sorted_kvp_batches.front(); + sorted_kvp_batches.pop_front(); + + // allocate space for the merged batches + out->keys.resize(b1->keys.size() + b2->keys.size()); + out->ids.resize(out->keys.size()); + timer_alloc.stop(); + alloc_time += timer_alloc.seconds(); + + // merge + merge_batches_1GPU(&device_context, b1, b2, out, merge_time, merge_data_time, merge_search_time); + sorted_kvp_batches.push_back(out); + + // free batch memory + b1->free(); + b2->free(); + free(b1); + free(b2); + + if(sorted_kvp_batches.size() == 1) { // merged down to one sequence + final_result = out; + break; + } + } + timer.stop(); + printf("Device merge-only time : %.4fs\n", merge_time); + printf("Device merge data time : %.4fs\n", merge_data_time); + printf("Device merge search time : %.4fs\n", merge_search_time); + printf("Merge out alloc time : %.4fs\n", alloc_time); + printf("Total merge time : %.4fs\n", timer.seconds()); + + timer_all.stop(); + + test_sorted(*final_result); + + timer.start(); + //BAM_alignment_batch_SoA out_batch(h_batch.field_mask); + //h_batch.shuffle(out_batch, final_result->ids); + timer.stop(); + printf("Shuffle time : %.4fs\n", timer.seconds()); + + // 4. write BAM output + timer.start(); + HTSBAMWriter bam_writer(out_fname); + //bam_writer.write_hdr(bam_reader.header); + //bam_writer.write_aln_batch(h_batch, final_result->ids, bam_reader.header); + timer.stop(); + printf("BAM write time : %.4fs\n", timer.seconds()); + + //timer_all.stop(); + printf("Total BAMSORT time : %.4fs\n", timer_all.seconds()); +} + +// full load -> sort -> store (no overlapping) +// multi-GPU +void bamsort_pipeline_multigpu(const char* in_fname, const char* out_fname) +{ + cuda::Timer timer, timer_all; + + // 1. load BAM + timer.start(); + HTSBAMReader bam_reader(in_fname); + BAM_alignment_batch_SoA h_batch(BAM_POSITIONS | BAM_REFIDS | BAM_FLAGS); + bam_reader.read_aln_batch(h_batch, H_BATCH_SIZE); + timer.stop(); + printf("BAM load time: %.4fs\n", timer.seconds()); + printf("Total number of alignments: %llu \n", h_batch.num_alns); + + int num_dev = 0; + cudaGetDeviceCount(&num_dev); + printf("Total number of CPUs: %d\n", omp_get_num_procs()); + printf("Total number of GPUs: %d\n", num_dev); + for (int i = 0; i < num_dev; i++) { + cudaDeviceProp dprop; + cudaGetDeviceProperties(&dprop, i); + printf(" %d: %s\n", i, dprop.name); + } + + // 2. split and sort + //TODO: figure out # devices that is appropriate to use based on load size (when num_dev > 2) + if(h_batch.num_alns <= D_MIN_BATCH_SIZE) { + printf("Running on a single device (load size is <= minimum single device size) \n"); + num_dev = 1; + } + + uint64 thread_batch_size = h_batch.num_alns/num_dev; + std::vector thread_sorted_batches(num_dev); + timer_all.start(); + omp_set_num_threads(num_dev); + #pragma omp parallel + { + int tid = omp_get_thread_num(); + cudaSetDevice(tid); + int devId; + cudaGetDevice(&devId); + printf("Thread %d device %d\n", tid, devId); + + cuda::Timer ttimer; + uint64 toffset = tid * thread_batch_size; + uint64 tsize = thread_batch_size; + if(tid == num_dev-1) { + tsize = h_batch.num_alns - toffset; // remainder + } + printf("Thread %d offset %llu size %llu\n", tid, toffset, tsize); + + std::list sorted_kvp_batches; // host container for the sorted batches + bamsort_context device_context; + uint64 num_aln_loaded = 0; + ttimer.start(); + while(num_aln_loaded < tsize) { + // transfer the next batch to the device + uint64 batch_size = D_BATCH_SIZE; + if(tsize - num_aln_loaded < D_BATCH_SIZE) { + batch_size = tsize - num_aln_loaded; + } + device_context.load_batch(h_batch, toffset + num_aln_loaded, batch_size); + sortkey_gen(&device_context); + sort(&device_context); + + // save sorted batches on the host + H_KVP_batch* sorted_batch = new H_KVP_batch(); + sorted_batch->keys.resize(device_context.sort_keys.size()); + sorted_batch->ids.resize(device_context.sort_keys.size()); + thrust::copy(device_context.sort_keys.begin(), device_context.sort_keys.end(), sorted_batch->keys.begin()); + thrust::copy(device_context.active_read_ids.begin(), device_context.active_read_ids.end(), sorted_batch->ids.begin()); + sorted_kvp_batches.push_back(sorted_batch); + num_aln_loaded += sorted_batch->ids.size(); + printf("Thread %d processed %llu records \n", tid, (uint64) sorted_batch->ids.size()); + } + ttimer.stop(); + printf("Thread %d done with local sorting. Time %.4fs \n", tid, ttimer.seconds()); + device_context.free_local_sort_batch(); + + // merge down to a single batch on each device + if(sorted_kvp_batches.size() == 1) { + thread_sorted_batches[tid] = sorted_kvp_batches.front(); + } else { + device_context.allocate_partition(); + } + ttimer.start(); + while(sorted_kvp_batches.size() > 1) { + H_KVP_batch* out = new H_KVP_batch(); + H_KVP_batch* b1 = sorted_kvp_batches.front(); + sorted_kvp_batches.pop_front(); + H_KVP_batch* b2 = sorted_kvp_batches.front(); + sorted_kvp_batches.pop_front(); + // allocate space for the merged batches + out->keys.resize(b1->keys.size() + b2->keys.size()); + out->ids.resize(out->keys.size()); + float t1, t2, t3; + merge_batches_1GPU(&device_context, b1, b2, out, t1, t2, t3); + sorted_kvp_batches.push_back(out); + b1->free(); + b2->free(); + free(b1); + free(b2); + if(sorted_kvp_batches.size() == 1) { // merged down to one sequence + thread_sorted_batches[tid] = out; + break; + } + } + ttimer.stop(); + printf("Thread %d done with merging. Time %.4fs \n", tid, ttimer.seconds()); + } + H_KVP_batch* final_result = new H_KVP_batch(); + if(num_dev == 2) { //TODO: generalize to any number of devices + final_result->keys.resize(thread_sorted_batches[0]->keys.size() + thread_sorted_batches[1]->keys.size()); + final_result->ids.resize(final_result->keys.size()); + merge_batches_2GPU(thread_sorted_batches[0], thread_sorted_batches[1], final_result); + } + timer_all.stop(); + printf("Total sort time : %.4fs\n", timer_all.seconds()); + + test_sorted(*final_result); + + // 4. write BAM output + timer.start(); + HTSBAMWriter bam_writer(out_fname); + //bam_writer.write_header(bam_reader.header); + //bam_writer.write_aln_batch(h_batch, final_result.ids, bam_reader.header); + timer.stop(); + printf("BAM write time : %.4fs\n", timer.seconds()); +} + +// permute the sorted BAM file +void generate_unsorted_bam(const char* in_fname, const char* out_fname) { + try { + // load + BAMReader bam_reader(in_fname); + BAM_header hdr = bam_reader.header; + BAM_alignment_batch_raw sorted_batch; + bam_reader.read_aln_batch_raw(sorted_batch, H_BATCH_SIZE); + uint64 num_loaded = sorted_batch.offsets.size()-1; + printf("Total number of loaded alignments: %llu \n", num_loaded); + + // generate permutation + std::vector perm(num_loaded); + for (uint64 i=0; i \n"); + exit(1); + } + + try { + //generate_unsorted_bam(argv[1], argv[2]); + //duplicate_unsorted_bam(argv[1], argv[2], 1000); + bamsort_pipeline_basic(argv[1], argv[2]); + //bamsort_pipeline_multigpu(argv[1], argv[2]); + } catch (nvbio::runtime_error& e) { + printf("%s\n", e.what()); + exit(1); + } + return 0; +} + +int test_sorted(const H_KVP_batch& result) +{ + // check that all the keys are in ascending order + uint64 k = 0; + for(uint64 i = 0; i < result.keys.size(); i++) { + if(k > result.keys[i]) { + printf("Failed test; out of order: %llu %llu %llu %llu %llu \n", (uint64) k, (uint64) result.keys[i], (uint64) result.keys[i-1], i, i-1); + return 0; + } + k = result.keys[i]; + } + + printf("Passed test! \n"); + return 1; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bam_sort.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bam_sort.h new file mode 100644 index 0000000000000000000000000000000000000000..b85f09b61add24441498fd963d028b2619b653fd --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bam_sort.h @@ -0,0 +1,234 @@ +/* + * Copyright (c) 2012-14, NVIDIA CORPORATION. All rights reserved. + * + * NVIDIA CORPORATION and its licensors retain all intellectual property + * and proprietary rights in and to this software, related documentation + * and any modifications thereto. Any use, reproduction, disclosure or + * distribution of this software and related documentation without an express + * license agreement from NVIDIA CORPORATION is strictly prohibited. + * + * + * + * + * + * + * + * + */ + +#pragma once + +#include "bamsort_types.h" +#include "bam_io.h" + +using namespace nvbio; + +/** Sorting Utilities **/ + +#define PIVOT_SAMPLING_INTERVAL 50000000 +#define D_BATCH_SIZE 100000000 +#define D_MIN_BATCH_SIZE 10000000 +#define H_BATCH_SIZE 100000000 + +// pair of key-value(id) vectors +struct H_KVP_batch +{ + H_VectorU64 keys; + H_VectorU64 ids; + + void free() + { + keys = H_VectorU64(); + ids = H_VectorU64(); + } +}; + +struct D_KVP_batch +{ + D_VectorU64 keys; + D_VectorU64 ids; + + struct view + { + D_VectorU64::const_plain_view_type keys; + D_VectorU64::const_plain_view_type ids; + }; + + operator view() const { + view v = { + plain_view(keys), + plain_view(ids), + }; + return v; + } + + void free() + { + keys = D_VectorU64(); + ids = D_VectorU64(); + } +}; + +/** BAM Sort Pipeline Context (sort data on the device) **/ + +struct bamsort_context +{ + // alignment data + D_VectorU32 pos; + D_VectorU32 seq_ids; + D_VectorU16 flags; + + // local sorting + D_VectorU64 active_read_ids; + uint64 read_offset; // global read id offset + D_VectorU64 sort_keys; // sort keys + + // out-of-core merge + D_VectorU64 patch_searched; + D_KVP_batch p1, p2, r; // partitions and result + + struct view + { + // TODO: const + D_VectorU32::plain_view_type pos; + D_VectorU32::plain_view_type seq_ids; + D_VectorU16::plain_view_type flags; + D_VectorU64::plain_view_type active_read_ids; + D_VectorU64::plain_view_type sort_keys; + uint64 read_offset; + D_KVP_batch::view p1; + D_KVP_batch::view p2; + D_KVP_batch::view r; + }; + + operator view() { + view v = { + plain_view(pos), + plain_view(seq_ids), + plain_view(flags), + plain_view(active_read_ids), + plain_view(sort_keys), + read_offset, + p1, + p2, + r + }; + return v; + } + + // allocate and load the data onto the device + // loads the entire host batch + void load_batch(const BAM_alignment_batch_SoA& batch, const uint64 start_read_id) + { + // initialize the read ids + read_offset = start_read_id; + active_read_ids.resize(batch.num_alns); + thrust::sequence(active_read_ids.begin(), + active_read_ids.begin() + batch.num_alns, + read_offset); + + // load the data for position sorting + pos.resize(batch.num_alns); + seq_ids.resize(batch.num_alns); + flags.resize(batch.num_alns); + thrust::copy(batch.positions.begin(), batch.positions.end(), pos.begin()); + thrust::copy(batch.refIDs.begin(), batch.refIDs.end(), seq_ids.begin()); + thrust::copy(batch.flags.begin(), batch.flags.end(), flags.begin()); + + // allocate space for the keys + sort_keys.resize(batch.num_alns); + } + + // allocate and load the data onto the device + // loads a batch_size interval of the host batch only starting with read_offset + void load_batch(const BAM_alignment_batch_SoA& batch, const uint64 start_read_id, const uint64 batch_size) + { + read_offset = start_read_id; + uint64 n = read_offset; + if((batch.num_alns - read_offset) >= batch_size) { + n = batch_size; + } else { + n = batch.num_alns - read_offset; + } + + // initialize the read ids + active_read_ids.resize(n); + thrust::sequence(active_read_ids.begin(), active_read_ids.begin() + n, read_offset); + + // allocate space + pos.resize(n); + seq_ids.resize(n); + flags.resize(n); + sort_keys.resize(n); + + // load the data for sorting + thrust::copy(batch.positions.begin() + read_offset, + batch.positions.begin() + read_offset + n, pos.begin()); + thrust::copy(batch.refIDs.begin() + read_offset, + batch.refIDs.begin() + read_offset + n, seq_ids.begin()); + thrust::copy(batch.flags.begin() + read_offset, + batch.flags.begin() + read_offset, flags.begin()); + } + + // free the data used for local sorting + void free_local_sort_batch() + { + active_read_ids = D_VectorU64(); + pos = D_VectorU32(); + seq_ids = D_VectorU32(); + flags = D_VectorU16(); + sort_keys = D_VectorU64(); + } + + // allocate memory for the merge partitions + // allocate instead of reserve to prevent dynamic allocations + void allocate_partition() + { + p1.keys.resize(2*PIVOT_SAMPLING_INTERVAL); + p1.ids.resize(2*PIVOT_SAMPLING_INTERVAL); + p2.keys.resize(2*PIVOT_SAMPLING_INTERVAL); + p2.ids.resize(2*PIVOT_SAMPLING_INTERVAL); + r.keys.resize(2*PIVOT_SAMPLING_INTERVAL); + r.ids.resize(2*PIVOT_SAMPLING_INTERVAL); + patch_searched.resize(PIVOT_SAMPLING_INTERVAL); + } +}; + +/** Sorting Pipeline Functors **/ + +// encapsulates common state for thrust functors +struct bamsort_lambda +{ + bamsort_context::view ctx; + bamsort_lambda(bamsort_context::view ctx) : ctx(ctx) { } +}; + +// generates the sorting keys from the alignment position +// unmapped reads (pos = -1) will have the largest key +// and automatically be placed at the end of the file +// (might want to handle them separately instead) +struct generate_sort_keys : public bamsort_lambda +{ + generate_sort_keys(bamsort_context::view ctx) + : bamsort_lambda(ctx) { } + + NVBIO_HOST_DEVICE void operator() (const uint64 idx) { + uint64 read_index = idx - ctx.read_offset; + uint64& key = ctx.sort_keys[read_index]; + key = (uint64) ctx.seq_ids[read_index] << 32; + key |= (ctx.pos[read_index] + 1) << 1; + key |= ((ctx.flags[read_index] & BAM_FLAGS_REVERSE) != 0); + } +}; + +// compares the elements to a pivot value +// return true if the element is smaller than the pivot +struct is_less +{ + uint64 pivot; + is_less (uint64 p) : pivot(p) {} + + NVBIO_HOST_DEVICE bool operator() (const uint64& x) const { + return x <= pivot; + } +}; diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bamsort_types.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bamsort_types.h new file mode 100644 index 0000000000000000000000000000000000000000..10785fe8d97a4ce76a5aa35997f39da39e14e1bd --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/bamsort/bamsort_types.h @@ -0,0 +1,101 @@ +/* + * Copyright (c) 2012-14, NVIDIA CORPORATION. All rights reserved. + * + * NVIDIA CORPORATION and its licensors retain all intellectual property + * and proprietary rights in and to this software, related documentation + * and any modifications thereto. Any use, reproduction, disclosure or + * distribution of this software and related documentation without an express + * license agreement from NVIDIA CORPORATION is strictly prohibited. + * + * + * + * + * + * + * + * + */ + +#pragma once + +#include +#include +#include + +using namespace nvbio; + + +typedef nvbio::vector D_VectorU8; +typedef nvbio::vector H_VectorU8; +typedef nvbio::vector D_VectorU16; +typedef nvbio::vector H_VectorU16; +typedef nvbio::vector D_VectorU32; +typedef nvbio::vector H_VectorU32; +typedef nvbio::vector D_VectorU64; +typedef nvbio::vector H_VectorU64; + +typedef nvbio::vector D_VectorI32; +typedef nvbio::vector H_VectorI32; + +typedef nvbio::PackedVector H_VectorDNA16; +typedef nvbio::PackedVector D_VectorDNA16; +typedef H_VectorDNA16::stream_type H_StreamDNA16; +typedef D_VectorDNA16::stream_type D_StreamDNA16; + +typedef nvbio::PackedVector H_PackedVector_1b; +typedef nvbio::PackedVector D_PackedVector_1b; + +typedef nvbio::PackedVector H_PackedVector_2b; +typedef nvbio::PackedVector D_PackedVector_2b; + +// this is evil: endianess between reference data and sequence data doesn't seem to match... +typedef nvbio::PackedVector::stream_type H_PackedReference; +typedef nvbio::PackedVector::stream_type D_PackedReference; + +typedef nvbio::vector D_VectorU32_2; +typedef nvbio::vector H_VectorU32_2; +typedef nvbio::vector D_VectorU16_2; +typedef nvbio::vector H_VectorU16_2; + +// we only use 1 bit per entry on the active location list +// however, because we write to this using multiple threads that are scanning reads concurrently, +// we need to make sure we don't access the same dword from different threads +// sizing this to 4 bits per symbol ensures that, because input reads are padded to a dword boundary +typedef D_VectorDNA16 D_ActiveLocationList; +typedef H_VectorDNA16 H_ActiveLocationList; +typedef D_ActiveLocationList::plain_view_type D_ActiveLocationStream; +typedef H_ActiveLocationList::plain_view_type H_ActiveLocationStream; + +struct cigar_op +{ + uint32 len:24, op:4; + + enum + { + OP_M = 0, + OP_I = 1, + OP_D = 2, + OP_N = 3, + OP_S = 4, + OP_H = 5, + OP_P = 6, + OP_MATCH = 7, + OP_X = 8, + }; + + NVBIO_HOST_DEVICE char ascii_op(void) const + { + return op == 0 ? 'M' : + op == 1 ? 'I' : + op == 2 ? 'D' : + op == 3 ? 'N' : + op == 4 ? 'S' : + op == 5 ? 'H' : + op == 6 ? 'P' : + op == 7 ? '=' : + 'X'; + } +}; + +typedef nvbio::vector D_VectorCigarOp; +typedef nvbio::vector H_VectorCigarOp; diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/README.md b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/README.md new file mode 100644 index 0000000000000000000000000000000000000000..418742c51ecf7f762988647f0f8a5bddbb5b5fd2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/README.md @@ -0,0 +1,214 @@ +PSA: Pairwise sequence alignment benchmarking +============================================= + +This is a project to benchmark Smith & Waterman implementations designed for GPU processors. +The project includes samples for input data, dataset generators, basic sequence conversion primitives and Smith & Waterman implementations. Most of them review the literature approaches or extend the NVBIO implementations. + +###SW-G Prototypes + +In order to give a general overview, the following implementations are included and benchmarked in the project: + + 1. Register tilling using 32bit integer instructions (GPU baseline). + 2. Using video instructions (processing 4 elements per register). + 3. Combining video instructions and integer instructions (processing 4 cells per register). + 4. Using integer instructions (processing​ 4 cells per register). It uses a custom set of primitives to simulate MAX video instructions using integer instructions. + + * Also includes: several warp-wide GPU implementations based on CPU SIMD approaches (farrar [1] and wozniak [2]), baseline CPU implementations and experimental codes to tune the cell resolution of the DP matrix or the DP tilling process strategy. + * Benchmarks adapted to simulate the SW-G behaviour inside a read mapper. + + +``` +[1] Striped Smith–Waterman speeds database searches six times over other SIMD implementations. +[2] Using video-oriented instructions to speed up sequence comparison. +``` + + +###Performance Results + +Smith & Waterman - Gotoh (Using 2bits per base) performance in GCUPS for Maxwell and Kepler platforms: + + ​​​​ Performance (GCUPS) | GTX TITAN BLACK (kepler)| GTX TITAN X (maxwell) | + -------------------------------------|---------------------------|-----------------------| + 1) Register tilling (32b) | 100.31 | 129.03 | + 2) Video instructions (8b) | 111.77 | 17.85 | + 3) Mixing video & integer inst. (8b) | 157.73 | 46.38 | + 4) Integer instructions (8b) | 49.98 | 66.95 | + + +The benchmarks can also run the SW-G implementations reading the candidates from a reference instead of reading them from a packed list of candidates. The objective is to simulate a real read alignment scenario from a mapper, analyzing the performance penalty of the random-gather accesses to de reference. + + ​​​​ Performance (GCUPS) | GTX TITAN BLACK (kepler)| GTX TITAN X (maxwell) | + ---------------------------|---------------------------|-----------------------| + 1) Regiser tilling (32b) | 75.86 | 128.06 | + + +###Detailed executables + +#####Tools +* `gregions`: Input-data generator for the benchmarks. +* `checksum`: Analyzes the divergence results and depicts the overflow result scores. + +#####Benchmarks +* `benchmark_swg_2b_integer_gpu`: Baseline GPU implementation, using tilling strategies and different resolution cell scores. +* `benchmark_swg_2b_video_gpu`: GPU packs 4 cells per register and uses video instructions to process the DP cells of 8 bits. +* `benchmark_swg_2b_mixed_gpu`: GPU packs 4 cells per register and uses a mixing with video instructions and integer instructions to process the DP cells of 8 bits. +* `benchmark_swg_2b_mixedsim_gpu`: GPU packs 4 cells per register just using integer/logical instructions to process the DP cells of 8 bits. + +* `benchmark_swg_ref_2b_integer_gpu`: Same baseline GPU version but reading the candidates from the reference to simulate the performance in a short mapper. + +#####Miscellaneous benchmarks +* `benchmark_swg_cpu`: Baseline CPU to validate the functionality. +* `benchmark_swg_farrar_gpu`: Farrar striped implementation using warp-wide strategy GPU (needs kepler shuffle instructions). +* `benchmark_swg_wozniak_gpu`: Wozniak anti-diagonal implementation using warp-wide strategy GPU (needs kepler shuffle instructions). + + +###Input/Output data + +This section explains the necessary data to run the SW-G benchmarks. The project includes some small samples of input data to run the code with different genomes files and sets of candidate-query. It is described how to create the datasets at the end of this document. + +####Input Data + +To perform the DP alignment benchmark, an input data is necessary with the pair of query-candidate. There are two input formats: (1) using an explicit storage of the candidates that pack (in raw or ASCII mode) all the query-candidate pair or (2) using an implicit storage saving the candidate position in the reference. + +The files with the next filename syntax extensions: + +1. ````*.regions````: uses an explicit storage of candidates. +2. ````*.ref.regions````: uses an implicit storage of candidates. + +Example: +```1K-100nt.prof.1000.100.21.regions``` stores 1000 queries of 100nt size x 21 candidates per query = 21K alignments + +* These input-files are generated from *.profile files with the executable ```gregions```. + +####Output data + +The results are represented by a list of positions in the DP (sink) and the score of the best alignment. Each line of the output file represents one alignment. +Sample for the first output lines: + +~~~~~~ +==> data/1K-100nt.prof.1000.100.21.regions.sw-gotoh.32b.cpu <== +21235 +0 2 119 +1 34 117 +2 16 116 +3 25 114 +4 31 79 +5 35 109 +6 32 49 +7 39 40 +8 44 118 +~~~~~~ + +* Each line contains: alignment id, best score, column sink position. + +#####Checking the outputs + +The ```checksum ``` program compares the output of 2 result files of alignments and returns the differences between them and the overflows produced by the reduced resolutions of the DP cells (8 bits, 16 bits and 32 bits) + +~~~~ +$bin/checksum data/1K-100nt.prof.1000.100.21.regions.nvbio-1th.32b.tc.gpu data/1K-100nt.prof.1000.100.21.ref.regions.gotoh.video.ref.8b.gpu +[INFO] Loading results: data/1K-100nt.prof.1000.100.21.regions.nvbio-1th.32b.tc.gpu ... +[INFO] Loading results: data/1K-100nt.prof.1000.100.21.ref.regions.gotoh.video.ref.8b.gpu ... +[INFO] Checking results ... +Number of candidates benchmarked: [ 21231 ] +Total 'False positives' REPORTED: 0 (0.00 %) + => Groups REPORTED: 0 (0.00 %) +[INFO] Comparing results ... + => Total with maxScoring: 0 (0.00 %) + => Total under maxScoring: 0 (0.00 %) +TOTAL DIFFERENT RESULTS: 0 (0.00 %) +[INFO] Intersecting results ... +Intersection results: + => Total detected alignments: 0 (0.00 %) + => Total undetected alignments: 0 (0.00 %) + => Total overhead alignments: 0 (0.00 %) +~~~~ + +###Compiling process + +Use ```make``` to compile each of the binaries itemized above, the executable will be generated in the bin folder. + +#####Examples + +Compile the input dataset generator: + +~~~~~ +make gregions +~~~~~ + +To compile the benchmarks it is necessary to indicate the size of the query and candidate in compiler time as parameters of the make command: + +~~~~~ +make benchmark_swg_cpu squery=100 scandidate=120 +~~~~~ + + +###Executing process + +There are 2 types of benchmarks, (A) using just the +(B) using + +#####Examples + +A. Using the explicit packed query-candidate input: + +~~~~~~ +bin/benchmark_swg_cpu data/1K-100nt.prof.1000.100.21.regions +~~~~~~ + +B. Using the implicit query-reference position input, that requires the original reference: + +~~~~~~ +bin/bench_swg_ref_2b_integer_gpu_100 data/1K-100nt.prof.1000.100.21.ref.regions data/profiles/hsapiens_v37.fa +~~~~~~ + +* In the benchmarking process it is recommendable: + 1. The use of nvprof to measure the kernel timings, with the goal of reducing the host synchronization overheads. + 2. Use input data larger than 120K alignments for a full GPU utilization. + +#####Output example + +~~~~~~ +$bin/benchmark_swg_cpu data/1K-100nt.prof.1000.100.21.regions +SMITH & WATERMAN GOTOH +CPU VERSION WHOLE MATRIX +CONFIG - MATCH: 2, MISMATCH: -5, OPEN_INDEL: -2, EXTEND_INDEL: -1 +Build: Aug 5 2015 - 16:19:15 +FORMAT: 9 +FORMAT: 9 +TIME: 1.327312 GCUPS: 0.191982 +AVERAGE_QUERY_SIZE: 100, AVERAGE_CANDIDATES_PER_QUERY: 21, NUM_CANDIDATES: 21235 +~~~~~~ + +The results file have the file name: ```*.gpu```, an example of this file is: _1K-100nt.prof.1000.100.21.ref.regions.gotoh.video.ref.8b.gpu_ + +###How to generate different input datasets + +The program ```gregions``` generates the input data from the ```*.prof``` files. +The *.profile files can be generated by the ```GEM short read mapper``` from any input data, using the profile options. + +Several samples of *.profile files are included in the data folder of this project. Any of them can be used directly or replicated several times to increase artificially the size of the input data. + +Syntax: + +~~~~~~~ +bin/gregions format_output ratio_size_candidates alignment_profile fasta_reference_genome +~~~~~~~ + +#####Examples + +```gregions``` can be used to generate two types of input data: + +A. To generate the explicit packed query-candidate input format: + +~~~~~~ +bin/gregions 0 1.2 data/1K-100nt.prof data/profiles/hsapiens_v37.fa +~~~~~~ + +B. To generate the implicit query-reference position input format, that later requires the original reference for the benchmark: + +~~~~~~ +bin/gregions 1 1.2 data/1K-100nt.prof data/profiles/hsapiens_v37.fa +~~~~~~ + +* This parameters will generate an implicit input-data with the positions of the candidates in the reference. Each of the queries have a size of 100nt and the candidates have a size of 120nt. \ No newline at end of file diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-1000nt.prof b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-1000nt.prof new file mode 100644 index 0000000000000000000000000000000000000000..bd9c67236cc45c2fa96a1c89e40ba7de37ed281c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-1000nt.prof @@ -0,0 +1,1000 @@ 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+ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:104594340:-1 HG:+:419766556:-1 HG:+:429108678:-1 HG:+:470722334:-1 HG:+:495809128:-1 HG:+:721672757:-1 HG:+:776050427:-1 HG:+:848796703:-1 HG:+:1187043397:-1 HG:+:1505621232:-1 HG:+:1699649451:-1 HG:+:1740558425:-1 HG:+:1832176959:-1 HG:+:1840119571:-1 HG:+:1911032313:-1 HG:+:1977148406:-1 HG:+:2013820083:-1 HG:+:2052856491:-1 HG:+:2228635167:-1 HG:+:2261546322:-1 HG:+:2813669883:-1 HG:+:3005813017:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:580095430:-1 HG:+:777207533:-1 HG:+:1477985103:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:5637110:-1 HG:+:74377066:-1 HG:+:174704874:-1 HG:+:404395235:-1 HG:+:430972103:-1 HG:+:512145423:-1 HG:+:738132094:-1 HG:+:1050716287:-1 HG:+:1155716258:-1 HG:+:1166535610:-1 HG:+:1210922222:-1 HG:+:1357199790:-1 HG:+:1751373500:-1 HG:+:1917095167:-1 HG:+:2139372910:-1 HG:+:2613195982:-1 HG:+:2801362017:-1 HG:+:2958304919:-1 HG:+:2967008199:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:66523269:-1 HG:+:74065692:-1 HG:+:77157489:-1 HG:+:231564518:-1 HG:+:240106337:-1 HG:+:263381895:-1 HG:+:456569537:-1 HG:+:573237617:-1 HG:+:576713540:-1 HG:+:579648332:-1 HG:+:1002049439:-1 HG:+:1043686904:-1 HG:+:1189608703:-1 HG:+:1203175239:-1 HG:+:1611086821:-1 HG:+:1854703508:-1 HG:+:1908993716:-1 HG:+:1996376332:-1 HG:+:2141831881:-1 HG:+:2145646021:-1 HG:+:2260412194:-1 HG:+:2377284824:-1 HG:+:2737340049:-1 HG:+:2894112743:-1 HG:+:2962930949:-1 HG:+:2974960381:-1 HG:+:2980329080:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:539358059:-1 HG:+:1079671350:-1 HG:+:1434500943:-1 HG:+:2585898986:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:1724126046:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:106914496:-1 HG:+:603829910:-1 HG:+:621532651:-1 HG:+:769489164:-1 HG:+:863176059:-1 HG:+:923965743:-1 HG:+:1159545809:-1 HG:+:1251244139:-1 HG:+:1305356817:-1 HG:+:1347228440:-1 HG:+:1468960144:-1 HG:+:1497746208:-1 HG:+:1687835645:-1 HG:+:1851821305:-1 HG:+:2918394374:-1 HG:+:3022160947:-1 HG:+:3022635102:-1 HG:+:3031214151:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:54223976:-1 HG:+:107351203:-1 HG:+:299006984:-1 HG:+:476132986:-1 HG:+:587324265:-1 HG:+:788124398:-1 HG:+:908827168:-1 HG:+:1141442662:-1 HG:+:1524513950:-1 HG:+:1524558113:-1 HG:+:1621951656:-1 HG:+:1764485450:-1 HG:+:1913923092:-1 HG:+:2969321021:-1 HG:+:3024847481:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:7850339:-1 HG:+:51220431:-1 HG:+:78250762:-1 HG:+:103248485:-1 HG:+:189945691:-1 HG:+:231888067:-1 HG:+:272193792:-1 HG:+:283167772:-1 HG:+:299209042:-1 HG:+:302740468:-1 HG:+:377697917:-1 HG:+:443385924:-1 HG:+:595161148:-1 HG:+:621532645:-1 HG:+:632873764:-1 HG:+:682508132:-1 HG:+:705559322:-1 HG:+:709470379:-1 HG:+:709924000:-1 HG:+:774768099:-1 HG:+:880706780:-1 HG:+:949132466:-1 HG:+:994667176:-1 HG:+:1119931774:-1 HG:+:1180833775:-1 HG:+:1195477043:-1 HG:+:1205324876:-1 HG:+:1223265806:-1 HG:+:1339637786:-1 HG:+:1359571915:-1 HG:+:1362956879:-1 HG:+:1386913179:-1 HG:+:1534282253:-1 HG:+:1563449858:-1 HG:+:1765872880:-1 HG:+:1767185491:-1 HG:+:1788920913:-1 HG:+:1789241278:-1 HG:+:1866201627:-1 HG:+:1921128617:-1 HG:+:1984913144:-1 HG:+:2171934883:-1 HG:+:2189249026:-1 HG:+:2247658288:-1 HG:+:2307007580:-1 HG:+:2334906426:-1 HG:+:2474500883:-1 HG:+:2545517206:-1 HG:+:2550916634:-1 HG:+:2584175867:-1 HG:+:2621355064:-1 HG:+:2669369652:-1 HG:+:2806469290:-1 HG:+:2812223370:-1 HG:+:2907194511:-1 HG:+:2912850725:-1 HG:+:2945880542:-1 HG:+:2952114280:-1 HG:+:2962141009:-1 HG:+:2967293845:-1 HG:+:2973293827:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:87946794:-1 HG:+:454923033:-1 HG:+:1685759304:-1 HG:+:2630954564:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:788534177:-1 HG:+:828080131:-1 HG:+:2034129890:-1 HG:+:2772419658:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:431320930:-1 HG:+:566253947:-1 HG:+:710449568:-1 HG:+:908917041:-1 HG:+:933452920:-1 HG:+:1079293534:-1 HG:+:1116282869:-1 HG:+:1195564205:-1 HG:+:1384885412:-1 HG:+:1445438980:-1 HG:+:1622497825:-1 HG:+:1901662591:-1 HG:+:1915706125:-1 HG:+:2117110691:-1 HG:+:2171894239:-1 HG:+:2280638381:-1 HG:+:2421230167:-1 HG:+:2463066795:-1 HG:+:2966394799:-1 HG:+:2985039699:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:764879638:-1 HG:+:1401792512:-1 HG:+:1533277953:-1 HG:+:1979987338:-1 HG:+:2259268022:-1 HG:+:2618216250:-1 HG:+:2777998337:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:262828282:-1 HG:+:668265802:-1 HG:+:847809305:-1 HG:+:900256294:-1 HG:+:996568803:-1 HG:+:1071802637:-1 HG:+:1180008095:-1 HG:+:1180012889:-1 HG:+:1193424409:-1 HG:+:1352590242:-1 HG:+:1684331963:-1 HG:+:2153330346:-1 HG:+:2975624943:-1 HG:+:2975734697:-1 HG:+:3006157813:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:321198762:-1 HG:+:524924112:-1 HG:+:886079921:-1 HG:+:1030224826:-1 HG:+:1685991530:-1 HG:+:1962958759:-1 HG:+:2165156069:-1 HG:+:2441541731:-1 HG:+:2819381424:-1 HG:+:2827308557:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:63239056:-1 HG:+:99161080:-1 HG:+:236842991:-1 HG:+:384211459:-1 HG:+:403694576:-1 HG:+:451258944:-1 HG:+:513706929:-1 HG:+:827152003:-1 HG:+:920976860:-1 HG:+:942128161:-1 HG:+:994071519:-1 HG:+:1033690155:-1 HG:+:1131841591:-1 HG:+:1161221622:-1 HG:+:1332552201:-1 HG:+:1414326604:-1 HG:+:1549305343:-1 HG:+:1801324725:-1 HG:+:1830938565:-1 HG:+:1878303421:-1 HG:+:2011988197:-1 HG:+:2334878392:-1 HG:+:2407722191:-1 HG:+:2415592825:-1 HG:+:2531357037:-1 HG:+:2565997699:-1 HG:+:2616302904:-1 HG:+:2717328855:-1 HG:+:2773771849:-1 HG:+:2855864641:-1 HG:+:3026334978:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:349893546:-1 HG:+:819181502:-1 HG:+:905891165:-1 HG:+:922198320:-1 HG:+:936113136:-1 HG:+:1132755093:-1 HG:+:1516579616:-1 HG:+:1622024405:-1 HG:+:1931651478:-1 HG:+:2141974825:-1 HG:+:2547597055:-1 HG:+:2575426618:-1 HG:+:2964619538:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:48874364:-1 HG:+:51220435:-1 HG:+:68136958:-1 HG:+:70252230:-1 HG:+:107197720:-1 HG:+:118996827:-1 HG:+:191663082:-1 HG:+:231821139:-1 HG:+:268600136:-1 HG:+:271455248:-1 HG:+:291551504:-1 HG:+:408133952:-1 HG:+:410913004:-1 HG:+:418521297:-1 HG:+:450131931:-1 HG:+:479300802:-1 HG:+:551329597:-1 HG:+:575779268:-1 HG:+:632395588:-1 HG:+:657796147:-1 HG:+:658780689:-1 HG:+:682508142:-1 HG:+:705609037:-1 HG:+:712521334:-1 HG:+:717773735:-1 HG:+:758689013:-1 HG:+:762961254:-1 HG:+:811510594:-1 HG:+:828080132:-1 HG:+:878380647:-1 HG:+:892469795:-1 HG:+:943754483:-1 HG:+:972269384:-1 HG:+:983554815:-1 HG:+:991937716:-1 HG:+:1005901458:-1 HG:+:1010282624:-1 HG:+:1026998812:-1 HG:+:1027562508:-1 HG:+:1145956291:-1 HG:+:1187724603:-1 HG:+:1209310630:-1 HG:+:1218330409:-1 HG:+:1246864100:-1 HG:+:1276060045:-1 HG:+:1352291085:-1 HG:+:1362956889:-1 HG:+:1486050385:-1 HG:+:1489321467:-1 HG:+:1688106490:-1 HG:+:1738865962:-1 HG:+:1747298248:-1 HG:+:1853352455:-1 HG:+:1939440369:-1 HG:+:2028567496:-1 HG:+:2033304664:-1 HG:+:2038337156:-1 HG:+:2078382806:-1 HG:+:2083141838:-1 HG:+:2132923769:-1 HG:+:2153564425:-1 HG:+:2167914827:-1 HG:+:2179486722:-1 HG:+:2226144448:-1 HG:+:2237629821:-1 HG:+:2241364026:-1 HG:+:2267024051:-1 HG:+:2269880006:-1 HG:+:2354333218:-1 HG:+:2403528644:-1 HG:+:2413225765:-1 HG:+:2473769773:-1 HG:+:2508885300:-1 HG:+:2550573880:-1 HG:+:2572655757:-1 HG:+:2613673050:-1 HG:+:2700664664:-1 HG:+:2823898939:-1 HG:+:2956849396:-1 HG:+:2967939316:-1 HG:+:2998471438:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:149101861:-1 HG:+:153334002:-1 HG:+:689594750:-1 HG:+:689594813:-1 HG:+:876196081:-1 HG:+:883127003:-1 HG:+:936456545:-1 HG:+:1035435686:-1 HG:+:1309276105:-1 HG:+:1398320889:-1 HG:+:1423972181:-1 HG:+:1730424421:-1 HG:+:1949964056:-1 HG:+:2190701553:-1 HG:+:2460421668:-1 HG:+:2604660173:-1 HG:+:2690257170:-1 HG:+:2701144152:-1 HG:+:2707832410:-1 HG:+:2824938196:-1 HG:+:2878241804:-1 HG:+:2905544461:-1 HG:+:3061356180:-1 HG:+:3062989929:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:294467940:-1 HG:+:612322978:-1 HG:+:2159216020:-1 HG:+:2291606812:-1 HG:+:2461495864:-1 HG:+:2929613823:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:70252226:-1 HG:+:163151876:-1 HG:+:668714817:-1 HG:+:713019348:-1 HG:+:1097663067:-1 HG:+:1163106704:-1 HG:+:1247693636:-1 HG:+:1475214581:-1 HG:+:1717629807:-1 HG:+:1971297277:-1 HG:+:2249318867:-1 HG:+:2359960340:-1 HG:+:2489347362:-1 HG:+:2893008979:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:288833565:-1 HG:+:695651367:-1 HG:+:986952603:-1 HG:+:1630503936:-1 HG:+:1677208835:-1 HG:+:1681127319:-1 HG:+:1726780348:-1 HG:+:1731462070:-1 HG:+:1731683800:-1 HG:+:1812829559:-1 HG:+:1827969129:-1 HG:+:1862749028:-1 HG:+:1951354237:-1 HG:+:2139924574:-1 HG:+:2161513661:-1 HG:+:2464730141:-1 HG:+:2473769782:-1 HG:+:2914172433:-1 HG:+:2979823448:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:748984294:-1 HG:+:997840340:-1 HG:+:1230258803:-1 HG:+:1873878567:-1 HG:+:2276982474:-1 HG:+:2691268461:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:423391264:-1 HG:+:457005589:-1 HG:+:554750712:-1 HG:+:764812262:-1 HG:+:949324250:-1 HG:+:1014662542:-1 HG:+:1014662593:-1 HG:+:1187923602:-1 HG:+:1378479857:-1 HG:+:1426726504:-1 HG:+:1627828152:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:41903840:-1 HG:+:118079208:-1 HG:+:575779270:-1 HG:+:651529970:-1 HG:+:805182021:-1 HG:+:969414926:-1 HG:+:988392951:-1 HG:+:1055939916:-1 HG:+:1152522014:-1 HG:+:1339301492:-1 HG:+:1346205662:-1 HG:+:1482302904:-1 HG:+:1512495568:-1 HG:+:1639013847:-1 HG:+:1845645678:-1 HG:+:1846122105:-1 HG:+:1922426966:-1 HG:+:2022598970:-1 HG:+:2135118881:-1 HG:+:2179946564:-1 HG:+:2192432728:-1 HG:+:2809439233:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:25589875:-1 HG:+:25660201:-1 HG:+:30615374:-1 HG:+:224906379:-1 HG:+:376873824:-1 HG:+:399679001:-1 HG:+:429108668:-1 HG:+:1066760117:-1 HG:+:1492126947:-1 HG:+:1997193891:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:405656143:-1 HG:+:733983780:-1 HG:+:848796689:-1 HG:+:1282774622:-1 HG:+:1497477021:-1 HG:+:1739908612:-1 HG:+:1763161543:-1 HG:+:2013651954:-1 HG:+:2107711728:-1 HG:+:2148222020:-1 HG:+:2243524101:-1 HG:+:2497360592:-1 HG:+:2694444520:-1 HG:+:2804748207:-1 HG:+:2936917325:-1 HG:+:2983105513:-1 HG:+:3015468197:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:65075657:-1 HG:+:238221080:-1 HG:+:260832442:-1 HG:+:589554729:-1 HG:+:610587382:-1 HG:+:872145713:-1 HG:+:900441125:-1 HG:+:1264529930:-1 HG:+:1418811555:-1 HG:+:1502146210:-1 HG:+:1510842714:-1 HG:+:1532797837:-1 HG:+:1585852920:-1 HG:+:2256022451:-1 HG:+:2545517212:-1 HG:+:2596412243:-1 HG:+:2651068006:-1 HG:+:2726712173:-1 HG:+:2917552810:-1 HG:+:2919855036:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:581278819:-1 HG:+:589387262:-1 HG:+:835263593:-1 HG:+:835384388:-1 HG:+:924018766:-1 HG:+:1170310093:-1 HG:+:1358526585:-1 HG:+:1478378490:-1 HG:+:1739343978:-1 HG:+:1875591360:-1 HG:+:2056842263:-1 HG:+:2519151943:-1 HG:+:2519277993:-1 HG:+:2902042205:-1 HG:+:2963069405:-1 HG:+:3023618163:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTGACTTCTGTACACCTTGCAGGCTCAACACATTATGGAACTGCCAAGGCTTGGACTTGCACCCTCTGAAGCTACAGCCCAAGCTGTACTTTGCCCCTTTTTAACCATGGGCTTGAGTGCTGGGACATGGCAACCAAGTCCTTAGGTTGGCACCACCAGCAGGGAGCGCCCTGGGCCAGACCCAGGTAACCAATTTTCCTCCT HG:+:192169729:-1 HG:+:390045991:-1 HG:+:512109707:-1 HG:+:682508148:-1 HG:+:724183390:-1 HG:+:733983798:-1 HG:+:753925882:-1 HG:+:881281017:-1 HG:+:1384885420:-1 HG:+:1607839395:-1 HG:+:1608178419:-1 HG:+:1657346175:-1 HG:+:1667273084:-1 HG:+:1930376217:-1 HG:+:2189186151:-1 HG:+:2275104243:-1 HG:+:2280735870:-1 HG:+:2927063287:-1 HG:+:2958826953:-1 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:168443264:-1 HG:+:265782991:-1 HG:+:300419521:-1 HG:+:376396488:-1 HG:+:511175328:-1 HG:+:573481083:-1 HG:+:591316727:-1 HG:+:702988401:-1 HG:+:763380897:-1 HG:+:767753354:-1 HG:+:806701896:-1 HG:+:881694971:-1 HG:+:895141040:-1 HG:+:911296319:57 HG:+:993016787:-1 HG:+:1150011333:-1 HG:+:1226567226:-1 HG:+:1248472878:-1 HG:+:1323750310:-1 HG:+:1377364401:-1 HG:+:1430748003:-1 HG:+:1484326399:-1 HG:+:1565549452:-1 HG:+:1570961283:-1 HG:+:1630026215:-1 HG:+:1635260155:-1 HG:+:1712616863:-1 HG:+:1735386146:-1 HG:+:1916936443:-1 HG:+:1946284723:-1 HG:+:2034615040:-1 HG:+:2045325390:-1 HG:+:2047395446:-1 HG:+:2117758394:-1 HG:+:2140518454:-1 HG:+:2240764661:-1 HG:+:2530928198:-1 HG:+:2657701110:-1 HG:+:2757262668:-1 HG:+:2802599753:-1 HG:+:2814736979:-1 HG:+:2863295964:-1 HG:+:2906185641:-1 HG:+:2925715173:-1 HG:+:2960510690:-1 HG:+:2965945330:-1 HG:+:2974329632:-1 HG:+:3008461144:-1 HG:+:3028368972:-1 HG:+:3042383835:-1 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:14442573:-1 HG:+:283934369:-1 HG:+:420659737:-1 HG:+:429141392:-1 HG:+:442016423:-1 HG:+:580467781:-1 HG:+:911296333:57 HG:+:962813108:-1 HG:+:1044413214:-1 HG:+:1406127101:-1 HG:+:1451571020:-1 HG:+:1530378931:-1 HG:+:1581172147:-1 HG:+:1735386156:-1 HG:+:1837257411:-1 HG:+:1972394137:-1 HG:+:1990865602:-1 HG:+:2279284225:-1 HG:+:2293380852:-1 HG:+:2358471879:-1 HG:+:2796293706:-1 HG:+:2975699725:-1 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:272127606:-1 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:444033795:-1 HG:+:911296331:57 HG:+:1285283727:-1 HG:+:2119288370:-1 HG:+:2550805332:-1 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:266006216:-1 HG:+:710302279:-1 HG:+:1387855324:-1 HG:+:1400763553:-1 HG:+:1621729542:-1 HG:+:1825118268:-1 HG:+:1893350322:-1 HG:+:2168683029:-1 HG:+:2176845175:-1 HG:+:2569786382:-1 HG:+:2608981833:-1 HG:+:2813350098:-1 HG:+:2907534491:-1 HG:+:2944180496:-1 HG:+:2961933720:-1 HG:+:3011649290:-1 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:77624521:-1 HG:+:115306336:-1 HG:+:232627561:-1 HG:+:299537187:-1 HG:+:307782580:-1 HG:+:521610964:-1 HG:+:593722195:-1 HG:+:779513314:-1 HG:+:794679936:-1 HG:+:818945590:-1 HG:+:850346557:-1 HG:+:975964126:-1 HG:+:1085637513:-1 HG:+:1222811808:-1 HG:+:1283628223:-1 HG:+:1551634263:-1 HG:+:1564661225:-1 HG:+:1644945658:-1 HG:+:1850726654:-1 HG:+:1943075502:-1 HG:+:1952471787:-1 HG:+:1984084339:-1 HG:+:2143481871:-1 HG:+:2344139448:-1 HG:+:2463036489:-1 HG:+:2553622088:-1 HG:+:2648394948:-1 HG:+:2702498658:-1 HG:+:2737618702:-1 HG:+:2962519942:-1 HG:+:2972888380:-1 HG:+:2979286771:-1 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:2272283151:-1 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:2979001246:-1 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:911296317:57 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:911296329:57 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:911296322:57 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:1352507591:-1 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:911296337:57 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:181497990:-1 HG:+:823231915:-1 HG:+:1904326457:-1 HG:+:2796197450:-1 HG:+:2810886216:-1 HG:+:2864566894:-1 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:969638955:-1 HG:+:1622564898:-1 HG:+:1966012305:-1 HG:+:2643124391:-1 +AGGAGGAAAATTGGTTACCTGGGTCTGGCCCAGGGCGCTCCCTGCTGGTGGTGCCAACCTAAGGACTTGGTTGCCATGTCCCAGCACTCAAGCCCATGGTTAAAAAGGGGCAAAGTACAGCTTGGGCTGTAGCTTCAGAGGGTGCAAGTCCAAGCCTTGGCAGTTCCATAATGTGTTGAGCCTGCAAGGTGTACAGAAGTCAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT HG:+:102334094:-1 HG:+:846964095:-1 HG:+:911296334:57 HG:+:1011709018:-1 HG:+:1129532041:-1 HG:+:1319218873:-1 HG:+:1855645239:-1 HG:+:2953533320:-1 HG:+:3036097155:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:9000755:-1 HG:+:15909030:-1 HG:+:28521487:-1 HG:+:36531698:-1 HG:+:39372749:-1 HG:+:97616768:-1 HG:+:112218515:-1 HG:+:167456151:-1 HG:+:201842110:-1 HG:+:244661737:-1 HG:+:269244985:-1 HG:+:275641395:-1 HG:+:275764956:-1 HG:+:287806728:-1 HG:+:323896466:-1 HG:+:432793308:-1 HG:+:455938721:-1 HG:+:473456572:-1 HG:+:481143606:-1 HG:+:540684573:-1 HG:+:541254443:-1 HG:+:662331182:-1 HG:+:687509491:-1 HG:+:729505465:-1 HG:+:828770264:-1 HG:+:875895921:-1 HG:+:918669867:-1 HG:+:960598645:-1 HG:+:1020547422:-1 HG:+:1024215583:-1 HG:+:1030461004:-1 HG:+:1088056272:-1 HG:+:1150938261:-1 HG:+:1238834065:-1 HG:+:1240136247:-1 HG:+:1335053780:-1 HG:+:1420564436:-1 HG:+:1433248830:-1 HG:+:1631074140:-1 HG:+:1633915177:-1 HG:+:1669460473:-1 HG:+:1670620438:-1 HG:+:1829870692:-1 HG:+:1893737089:-1 HG:+:1993334911:-1 HG:+:2004566317:-1 HG:+:2129716749:-1 HG:+:2183986960:-1 HG:+:2227637983:-1 HG:+:2497664425:-1 HG:+:2544414979:-1 HG:+:2554561917:-1 HG:+:2554935783:-1 HG:+:2574031257:-1 HG:+:2697973089:-1 HG:+:2698102886:-1 HG:+:2748578608:-1 HG:+:2764020000:-1 HG:+:2778218153:-1 HG:+:2816368369:-1 HG:+:2867585992:-1 HG:+:2883467346:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:617788858:-1 HG:+:620988430:-1 HG:+:692136166:-1 HG:+:938022712:-1 HG:+:1205070720:-1 HG:+:1396288541:-1 HG:+:1642082894:-1 HG:+:1717357557:-1 HG:+:1871838229:-1 HG:+:2352736153:-1 HG:+:2417135691:-1 HG:+:2436627677:-1 HG:+:2463467632:-1 HG:+:2859499594:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:18877738:-1 HG:+:188102244:-1 HG:+:267000733:-1 HG:+:540458674:-1 HG:+:558525117:-1 HG:+:600780344:-1 HG:+:607844140:-1 HG:+:661385104:-1 HG:+:980272506:-1 HG:+:1136720845:-1 HG:+:1269682255:-1 HG:+:1289132924:-1 HG:+:1519718601:-1 HG:+:1546526591:-1 HG:+:1546526726:-1 HG:+:1735570541:-1 HG:+:2008627986:-1 HG:+:2060679495:-1 HG:+:2069992362:-1 HG:+:2080291734:-1 HG:+:2235469310:-1 HG:+:2265668820:-1 HG:+:2270010317:-1 HG:+:2408677192:-1 HG:+:2468184477:-1 HG:+:2578390177:-1 HG:+:2651754690:-1 HG:+:2661593404:-1 HG:+:2689797998:-1 HG:+:2695686082:-1 HG:+:2719007592:-1 HG:+:2729663340:-1 HG:+:2827914119:-1 HG:+:2860893894:-1 HG:+:2929665951:-1 HG:+:3003980289:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:545225369:-1 HG:+:911208821:44 HG:+:1689200503:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:911208825:44 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:763635106:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:1220549645:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:1118331275:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:956285619:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:911208822:44 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:1791627460:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:911208824:44 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:1487300054:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:911208827:44 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:1303727793:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:911208823:44 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAAATTTACACGGTTTATCAGGTATAAAACAAAAGTTATTCTGCTATCCTTACTTGCTTTCTCTGGTCTGTCAGTGTTCTGTCTCCACTCTAAATAATCTAATCTTCATGATTTCAGTTTAGTCATAGACTGATATAGTTAAAAAAATAATATTCCTCTGCATGATCAAAGCCATTTAAAGAAGACCAGGAATCATTAATTGT HG:+:911208840:44 +ACAATTAATGATTCCTGGTCTTCTTTAAATGGCTTTGATCATGCAGAGGAATATTATTTTTTTAACTATATCAGTCTATGACTAAACTGAAATCATGAAGATTAGATTATTTAGAGTGGAGACAGAACACTGACAGACCAGAGAAAGCAAGTAAGGATAGCAGAATAACTTTTGTTTTATACCTGATAAACCGTGTAAATTTAAAGCAGAAATGACTGAACAATAATTAAACAGTATGAAGCAGATTTATTTTGAACTACTTGACAAGCTTAGATCTAAGTTAGGCTTTTTGAGAATGAAATGCACTGACATATACATCATTATGAAAAGAGTATAGTCTACTTTAAACCTCAATTACCAGAAAACTAAAATAACTTGAGATAAAATTTCACTCTTTCAGGACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG HG:+:2698915664:-1 +ACAATTAATGATTCCTGGTCTTCTTTAAATGGCTTTGATCATGCAGAGGAATATTATTTTTTTAACTATATCAGTCTATGACTAAACTGAAATCATGAAGATTAGATTATTTAGAGTGGAGACAGAACACTGACAGACCAGAGAAAGCAAGTAAGGATAGCAGAATAACTTTTGTTTTATACCTGATAAACCGTGTAAATTTAAAGCAGAAATGACTGAACAATAATTAAACAGTATGAAGCAGATTTATTTTGAACTACTTGACAAGCTTAGATCTAAGTTAGGCTTTTTGAGAATGAAATGCACTGACATATACATCATTATGAAAAGAGTATAGTCTACTTTAAACCTCAATTACCAGAAAACTAAAATAACTTGAGATAAAATTTCACTCTTTCAGGACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG HG:+:2823758793:-1 +ACAATTAATGATTCCTGGTCTTCTTTAAATGGCTTTGATCATGCAGAGGAATATTATTTTTTTAACTATATCAGTCTATGACTAAACTGAAATCATGAAGATTAGATTATTTAGAGTGGAGACAGAACACTGACAGACCAGAGAAAGCAAGTAAGGATAGCAGAATAACTTTTGTTTTATACCTGATAAACCGTGTAAATTTAAAGCAGAAATGACTGAACAATAATTAAACAGTATGAAGCAGATTTATTTTGAACTACTTGACAAGCTTAGATCTAAGTTAGGCTTTTTGAGAATGAAATGCACTGACATATACATCATTATGAAAAGAGTATAGTCTACTTTAAACCTCAATTACCAGAAAACTAAAATAACTTGAGATAAAATTTCACTCTTTCAGGACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG HG:+:2012637464:-1 HG:+:2039268212:-1 +ACAATTAATGATTCCTGGTCTTCTTTAAATGGCTTTGATCATGCAGAGGAATATTATTTTTTTAACTATATCAGTCTATGACTAAACTGAAATCATGAAGATTAGATTATTTAGAGTGGAGACAGAACACTGACAGACCAGAGAAAGCAAGTAAGGATAGCAGAATAACTTTTGTTTTATACCTGATAAACCGTGTAAATTTAAAGCAGAAATGACTGAACAATAATTAAACAGTATGAAGCAGATTTATTTTGAACTACTTGACAAGCTTAGATCTAAGTTAGGCTTTTTGAGAATGAAATGCACTGACATATACATCATTATGAAAAGAGTATAGTCTACTTTAAACCTCAATTACCAGAAAACTAAAATAACTTGAGATAAAATTTCACTCTTTCAGGACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG HG:+:1756014572:-1 HG:+:1959968298:-1 +ACAATTAATGATTCCTGGTCTTCTTTAAATGGCTTTGATCATGCAGAGGAATATTATTTTTTTAACTATATCAGTCTATGACTAAACTGAAATCATGAAGATTAGATTATTTAGAGTGGAGACAGAACACTGACAGACCAGAGAAAGCAAGTAAGGATAGCAGAATAACTTTTGTTTTATACCTGATAAACCGTGTAAATTTAAAGCAGAAATGACTGAACAATAATTAAACAGTATGAAGCAGATTTATTTTGAACTACTTGACAAGCTTAGATCTAAGTTAGGCTTTTTGAGAATGAAATGCACTGACATATACATCATTATGAAAAGAGTATAGTCTACTTTAAACCTCAATTACCAGAAAACTAAAATAACTTGAGATAAAATTTCACTCTTTCAGGACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG HG:+:204330755:-1 HG:+:542082862:-1 HG:+:875148590:-1 HG:+:1627785066:-1 HG:+:1871995342:-1 HG:+:2718526446:-1 HG:+:2760931202:-1 +ACAATTAATGATTCCTGGTCTTCTTTAAATGGCTTTGATCATGCAGAGGAATATTATTTTTTTAACTATATCAGTCTATGACTAAACTGAAATCATGAAGATTAGATTATTTAGAGTGGAGACAGAACACTGACAGACCAGAGAAAGCAAGTAAGGATAGCAGAATAACTTTTGTTTTATACCTGATAAACCGTGTAAATTTAAAGCAGAAATGACTGAACAATAATTAAACAGTATGAAGCAGATTTATTTTGAACTACTTGACAAGCTTAGATCTAAGTTAGGCTTTTTGAGAATGAAATGCACTGACATATACATCATTATGAAAAGAGTATAGTCTACTTTAAACCTCAATTACCAGAAAACTAAAATAACTTGAGATAAAATTTCACTCTTTCAGGACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG HG:+:33131040:-1 HG:+:275806393:-1 HG:+:288697430:-1 HG:+:428395443:-1 HG:+:678003246:-1 HG:+:893140695:-1 HG:+:1162534885:-1 HG:+:1432875884:-1 HG:+:1492659136:-1 HG:+:1539932333:-1 HG:+:1898627081:-1 HG:+:1957911437:-1 HG:+:2170145447:-1 HG:+:2268054770:-1 HG:+:2302439577:-1 HG:+:2517913048:-1 HG:+:2567546585:-1 HG:+:2717219340:-1 HG:+:2855197464:-1 HG:+:2889497792:-1 +ACAATTAATGATTCCTGGTCTTCTTTAAATGGCTTTGATCATGCAGAGGAATATTATTTTTTTAACTATATCAGTCTATGACTAAACTGAAATCATGAAGATTAGATTATTTAGAGTGGAGACAGAACACTGACAGACCAGAGAAAGCAAGTAAGGATAGCAGAATAACTTTTGTTTTATACCTGATAAACCGTGTAAATTTAAAGCAGAAATGACTGAACAATAATTAAACAGTATGAAGCAGATTTATTTTGAACTACTTGACAAGCTTAGATCTAAGTTAGGCTTTTTGAGAATGAAATGCACTGACATATACATCATTATGAAAAGAGTATAGTCTACTTTAAACCTCAATTACCAGAAAACTAAAATAACTTGAGATAAAATTTCACTCTTTCAGGACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG HG:+:161200371:-1 HG:+:515713585:-1 HG:+:731186509:-1 HG:+:1150705681:-1 HG:+:1362428181:-1 HG:+:1545125252:-1 HG:+:1882548209:-1 HG:+:2336408736:-1 HG:+:2338096564:-1 HG:+:2426639478:-1 HG:+:2505362943:-1 HG:+:2578048008:-1 HG:+:2764650184:-1 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAGGAGGCCTTAAACGGGAAGACCAAGTGTGCACAGATTTAAAAAATAAGTTAAAATAAATAATTAAAATCTTTAAAGAAGGCATCAAGATAAATTTAACTATATAGCTTCTATTTCCAGTAATCTCTTAGATATCCGCTGTACTCATCTTTCCTTGTTTTTTTGTGCTTACCTAATCTGGATACTTCGCCACGATTAGAATT HG:+:857242985:48 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAGGAGGCCTTAAACGGGAAGACCAAGTGTGCACAGATTTAAAAAATAAGTTAAAATAAATAATTAAAATCTTTAAAGAAGGCATCAAGATAAATTTAACTATATAGCTTCTATTTCCAGTAATCTCTTAGATATCCGCTGTACTCATCTTTCCTTGTTTTTTTGTGCTTACCTAATCTGGATACTTCGCCACGATTAGAATT HG:+:857242984:48 HG:+:2619475265:-1 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAGGAGGCCTTAAACGGGAAGACCAAGTGTGCACAGATTTAAAAAATAAGTTAAAATAAATAATTAAAATCTTTAAAGAAGGCATCAAGATAAATTTAACTATATAGCTTCTATTTCCAGTAATCTCTTAGATATCCGCTGTACTCATCTTTCCTTGTTTTTTTGTGCTTACCTAATCTGGATACTTCGCCACGATTAGAATT HG:+:857242974:48 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAGGAGGCCTTAAACGGGAAGACCAAGTGTGCACAGATTTAAAAAATAAGTTAAAATAAATAATTAAAATCTTTAAAGAAGGCATCAAGATAAATTTAACTATATAGCTTCTATTTCCAGTAATCTCTTAGATATCCGCTGTACTCATCTTTCCTTGTTTTTTTGTGCTTACCTAATCTGGATACTTCGCCACGATTAGAATT HG:+:32311051:-1 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAGGAGGCCTTAAACGGGAAGACCAAGTGTGCACAGATTTAAAAAATAAGTTAAAATAAATAATTAAAATCTTTAAAGAAGGCATCAAGATAAATTTAACTATATAGCTTCTATTTCCAGTAATCTCTTAGATATCCGCTGTACTCATCTTTCCTTGTTTTTTTGTGCTTACCTAATCTGGATACTTCGCCACGATTAGAATT HG:+:857242989:48 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAGGAGGCCTTAAACGGGAAGACCAAGTGTGCACAGATTTAAAAAATAAGTTAAAATAAATAATTAAAATCTTTAAAGAAGGCATCAAGATAAATTTAACTATATAGCTTCTATTTCCAGTAATCTCTTAGATATCCGCTGTACTCATCTTTCCTTGTTTTTTTGTGCTTACCTAATCTGGATACTTCGCCACGATTAGAATT HG:+:857242969:48 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAGGAGGCCTTAAACGGGAAGACCAAGTGTGCACAGATTTAAAAAATAAGTTAAAATAAATAATTAAAATCTTTAAAGAAGGCATCAAGATAAATTTAACTATATAGCTTCTATTTCCAGTAATCTCTTAGATATCCGCTGTACTCATCTTTCCTTGTTTTTTTGTGCTTACCTAATCTGGATACTTCGCCACGATTAGAATT HG:+:857242968:48 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAGGAGGCCTTAAACGGGAAGACCAAGTGTGCACAGATTTAAAAAATAAGTTAAAATAAATAATTAAAATCTTTAAAGAAGGCATCAAGATAAATTTAACTATATAGCTTCTATTTCCAGTAATCTCTTAGATATCCGCTGTACTCATCTTTCCTTGTTTTTTTGTGCTTACCTAATCTGGATACTTCGCCACGATTAGAATT HG:+:587769706:-1 HG:+:857242980:48 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAGGAGGCCTTAAACGGGAAGACCAAGTGTGCACAGATTTAAAAAATAAGTTAAAATAAATAATTAAAATCTTTAAAGAAGGCATCAAGATAAATTTAACTATATAGCTTCTATTTCCAGTAATCTCTTAGATATCCGCTGTACTCATCTTTCCTTGTTTTTTTGTGCTTACCTAATCTGGATACTTCGCCACGATTAGAATT HG:+:857242987:48 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAGGAGGCCTTAAACGGGAAGACCAAGTGTGCACAGATTTAAAAAATAAGTTAAAATAAATAATTAAAATCTTTAAAGAAGGCATCAAGATAAATTTAACTATATAGCTTCTATTTCCAGTAATCTCTTAGATATCCGCTGTACTCATCTTTCCTTGTTTTTTTGTGCTTACCTAATCTGGATACTTCGCCACGATTAGAATT HG:+:857242977:48 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAGGAGGCCTTAAACGGGAAGACCAAGTGTGCACAGATTTAAAAAATAAGTTAAAATAAATAATTAAAATCTTTAAAGAAGGCATCAAGATAAATTTAACTATATAGCTTCTATTTCCAGTAATCTCTTAGATATCCGCTGTACTCATCTTTCCTTGTTTTTTTGTGCTTACCTAATCTGGATACTTCGCCACGATTAGAATT HG:+:2005749911:-1 +AATTCTAATCGTGGCGAAGTATCCAGATTAGGTAAGCACAAAAAAACAAGGAAAGATGAGTACAGCGGATATCTAAGAGATTACTGGAAATAGAAGCTATATAGTTAAATTTATCTTGATGCCTTCTTTAAAGATTTTAATTATTTATTTTAACTTATTTTTTAAATCTGTGCACACTTGGTCTTCCCGTTTAAGGCCTCCTTGTGGTCTCCTCGGGAGCCCAGGTAGTCCTGACACACTTGGGTACAACCAACATGGTGATATGGTTTGGCTCTGTGTCACCCATAGAAATCTTCATTTTGAATTGTAATCCCCAATGTTGGAGGTAAGGGCCTGGTAGGAGATGATCATCATGGGGGAGGGATTTCCCCCTTGCTGTTCTCAAGATAGTGAGTGAGTTCTCATGAGATCTGGTTGGTTTAAAAGTGTGTGGCGACCTCCCCTTCACTCTCTTCCTCCTGTTCCAGTCATGTAAGACGTGCCTGACTTCCCCTTCGGCCTGCCGCCATGAATTGAAGGTTTCCTGGAGGCCGTCCCTACCCCATGCTTCCTGTACAGCTGCGGGACTGTGAGCCAATTAAATCTCTTTTCTTTATAAATTATTCAATCTAGGTAGCTCTTCATAGCAGTGTGAGAATGGACTAAGACAACTGGCCTTCGCCTTTAAGTTCCTAAATTCATGTGGGTGTACCTGCTCCTGGATCTACACCTTTTTGGTCTGGGCGTCTGAACCCTTCTCAGTAGGTGGGCCCTAGGCTTTGATCCAGGCCACAGGGAGAAATCCTAGCATTCATTTTTCCCTTCCACTGCTTTCCAACTACTGCTAGTCTAAGGAGAGGTAGATACTATGAACTTGGGAGTTGAATAAGGTGGACACTTTGGGCTTAAAGTTTTCTAGAAAATTAGGCAATCATTAAGTTGTAATATTCATATTGTCCATAAGCATCAAACAACTCTGCTGCGTAACAAAAAGAATAATCTTTTTTCTTGAAGTCTAGTA HG:+:1224162064:-1 +AATTCTAATCGTGGCGAAGTATCCAGATTAGGTAAGCACAAAAAAACAAGGAAAGATGAGTACAGCGGATATCTAAGAGATTACTGGAAATAGAAGCTATATAGTTAAATTTATCTTGATGCCTTCTTTAAAGATTTTAATTATTTATTTTAACTTATTTTTTAAATCTGTGCACACTTGGTCTTCCCGTTTAAGGCCTCCTTGTGGTCTCCTCGGGAGCCCAGGTAGTCCTGACACACTTGGGTACAACCAACATGGTGATATGGTTTGGCTCTGTGTCACCCATAGAAATCTTCATTTTGAATTGTAATCCCCAATGTTGGAGGTAAGGGCCTGGTAGGAGATGATCATCATGGGGGAGGGATTTCCCCCTTGCTGTTCTCAAGATAGTGAGTGAGTTCTCATGAGATCTGGTTGGTTTAAAAGTGTGTGGCGACCTCCCCTTCACTCTCTTCCTCCTGTTCCAGTCATGTAAGACGTGCCTGACTTCCCCTTCGGCCTGCCGCCATGAATTGAAGGTTTCCTGGAGGCCGTCCCTACCCCATGCTTCCTGTACAGCTGCGGGACTGTGAGCCAATTAAATCTCTTTTCTTTATAAATTATTCAATCTAGGTAGCTCTTCATAGCAGTGTGAGAATGGACTAAGACAACTGGCCTTCGCCTTTAAGTTCCTAAATTCATGTGGGTGTACCTGCTCCTGGATCTACACCTTTTTGGTCTGGGCGTCTGAACCCTTCTCAGTAGGTGGGCCCTAGGCTTTGATCCAGGCCACAGGGAGAAATCCTAGCATTCATTTTTCCCTTCCACTGCTTTCCAACTACTGCTAGTCTAAGGAGAGGTAGATACTATGAACTTGGGAGTTGAATAAGGTGGACACTTTGGGCTTAAAGTTTTCTAGAAAATTAGGCAATCATTAAGTTGTAATATTCATATTGTCCATAAGCATCAAACAACTCTGCTGCGTAACAAAAAGAATAATCTTTTTTCTTGAAGTCTAGTA HG:+:1377654276:-1 +AATTCTAATCGTGGCGAAGTATCCAGATTAGGTAAGCACAAAAAAACAAGGAAAGATGAGTACAGCGGATATCTAAGAGATTACTGGAAATAGAAGCTATATAGTTAAATTTATCTTGATGCCTTCTTTAAAGATTTTAATTATTTATTTTAACTTATTTTTTAAATCTGTGCACACTTGGTCTTCCCGTTTAAGGCCTCCTTGTGGTCTCCTCGGGAGCCCAGGTAGTCCTGACACACTTGGGTACAACCAACATGGTGATATGGTTTGGCTCTGTGTCACCCATAGAAATCTTCATTTTGAATTGTAATCCCCAATGTTGGAGGTAAGGGCCTGGTAGGAGATGATCATCATGGGGGAGGGATTTCCCCCTTGCTGTTCTCAAGATAGTGAGTGAGTTCTCATGAGATCTGGTTGGTTTAAAAGTGTGTGGCGACCTCCCCTTCACTCTCTTCCTCCTGTTCCAGTCATGTAAGACGTGCCTGACTTCCCCTTCGGCCTGCCGCCATGAATTGAAGGTTTCCTGGAGGCCGTCCCTACCCCATGCTTCCTGTACAGCTGCGGGACTGTGAGCCAATTAAATCTCTTTTCTTTATAAATTATTCAATCTAGGTAGCTCTTCATAGCAGTGTGAGAATGGACTAAGACAACTGGCCTTCGCCTTTAAGTTCCTAAATTCATGTGGGTGTACCTGCTCCTGGATCTACACCTTTTTGGTCTGGGCGTCTGAACCCTTCTCAGTAGGTGGGCCCTAGGCTTTGATCCAGGCCACAGGGAGAAATCCTAGCATTCATTTTTCCCTTCCACTGCTTTCCAACTACTGCTAGTCTAAGGAGAGGTAGATACTATGAACTTGGGAGTTGAATAAGGTGGACACTTTGGGCTTAAAGTTTTCTAGAAAATTAGGCAATCATTAAGTTGTAATATTCATATTGTCCATAAGCATCAAACAACTCTGCTGCGTAACAAAAAGAATAATCTTTTTTCTTGAAGTCTAGTA HG:+:281233308:-1 HG:+:1290201469:-1 +AATTCTAATCGTGGCGAAGTATCCAGATTAGGTAAGCACAAAAAAACAAGGAAAGATGAGTACAGCGGATATCTAAGAGATTACTGGAAATAGAAGCTATATAGTTAAATTTATCTTGATGCCTTCTTTAAAGATTTTAATTATTTATTTTAACTTATTTTTTAAATCTGTGCACACTTGGTCTTCCCGTTTAAGGCCTCCTTGTGGTCTCCTCGGGAGCCCAGGTAGTCCTGACACACTTGGGTACAACCAACATGGTGATATGGTTTGGCTCTGTGTCACCCATAGAAATCTTCATTTTGAATTGTAATCCCCAATGTTGGAGGTAAGGGCCTGGTAGGAGATGATCATCATGGGGGAGGGATTTCCCCCTTGCTGTTCTCAAGATAGTGAGTGAGTTCTCATGAGATCTGGTTGGTTTAAAAGTGTGTGGCGACCTCCCCTTCACTCTCTTCCTCCTGTTCCAGTCATGTAAGACGTGCCTGACTTCCCCTTCGGCCTGCCGCCATGAATTGAAGGTTTCCTGGAGGCCGTCCCTACCCCATGCTTCCTGTACAGCTGCGGGACTGTGAGCCAATTAAATCTCTTTTCTTTATAAATTATTCAATCTAGGTAGCTCTTCATAGCAGTGTGAGAATGGACTAAGACAACTGGCCTTCGCCTTTAAGTTCCTAAATTCATGTGGGTGTACCTGCTCCTGGATCTACACCTTTTTGGTCTGGGCGTCTGAACCCTTCTCAGTAGGTGGGCCCTAGGCTTTGATCCAGGCCACAGGGAGAAATCCTAGCATTCATTTTTCCCTTCCACTGCTTTCCAACTACTGCTAGTCTAAGGAGAGGTAGATACTATGAACTTGGGAGTTGAATAAGGTGGACACTTTGGGCTTAAAGTTTTCTAGAAAATTAGGCAATCATTAAGTTGTAATATTCATATTGTCCATAAGCATCAAACAACTCTGCTGCGTAACAAAAAGAATAATCTTTTTTCTTGAAGTCTAGTA HG:+:1058207944:-1 +AATTCTAATCGTGGCGAAGTATCCAGATTAGGTAAGCACAAAAAAACAAGGAAAGATGAGTACAGCGGATATCTAAGAGATTACTGGAAATAGAAGCTATATAGTTAAATTTATCTTGATGCCTTCTTTAAAGATTTTAATTATTTATTTTAACTTATTTTTTAAATCTGTGCACACTTGGTCTTCCCGTTTAAGGCCTCCTTGTGGTCTCCTCGGGAGCCCAGGTAGTCCTGACACACTTGGGTACAACCAACATGGTGATATGGTTTGGCTCTGTGTCACCCATAGAAATCTTCATTTTGAATTGTAATCCCCAATGTTGGAGGTAAGGGCCTGGTAGGAGATGATCATCATGGGGGAGGGATTTCCCCCTTGCTGTTCTCAAGATAGTGAGTGAGTTCTCATGAGATCTGGTTGGTTTAAAAGTGTGTGGCGACCTCCCCTTCACTCTCTTCCTCCTGTTCCAGTCATGTAAGACGTGCCTGACTTCCCCTTCGGCCTGCCGCCATGAATTGAAGGTTTCCTGGAGGCCGTCCCTACCCCATGCTTCCTGTACAGCTGCGGGACTGTGAGCCAATTAAATCTCTTTTCTTTATAAATTATTCAATCTAGGTAGCTCTTCATAGCAGTGTGAGAATGGACTAAGACAACTGGCCTTCGCCTTTAAGTTCCTAAATTCATGTGGGTGTACCTGCTCCTGGATCTACACCTTTTTGGTCTGGGCGTCTGAACCCTTCTCAGTAGGTGGGCCCTAGGCTTTGATCCAGGCCACAGGGAGAAATCCTAGCATTCATTTTTCCCTTCCACTGCTTTCCAACTACTGCTAGTCTAAGGAGAGGTAGATACTATGAACTTGGGAGTTGAATAAGGTGGACACTTTGGGCTTAAAGTTTTCTAGAAAATTAGGCAATCATTAAGTTGTAATATTCATATTGTCCATAAGCATCAAACAACTCTGCTGCGTAACAAAAAGAATAATCTTTTTTCTTGAAGTCTAGTA HG:+:621486707:-1 +AATTCTAATCGTGGCGAAGTATCCAGATTAGGTAAGCACAAAAAAACAAGGAAAGATGAGTACAGCGGATATCTAAGAGATTACTGGAAATAGAAGCTATATAGTTAAATTTATCTTGATGCCTTCTTTAAAGATTTTAATTATTTATTTTAACTTATTTTTTAAATCTGTGCACACTTGGTCTTCCCGTTTAAGGCCTCCTTGTGGTCTCCTCGGGAGCCCAGGTAGTCCTGACACACTTGGGTACAACCAACATGGTGATATGGTTTGGCTCTGTGTCACCCATAGAAATCTTCATTTTGAATTGTAATCCCCAATGTTGGAGGTAAGGGCCTGGTAGGAGATGATCATCATGGGGGAGGGATTTCCCCCTTGCTGTTCTCAAGATAGTGAGTGAGTTCTCATGAGATCTGGTTGGTTTAAAAGTGTGTGGCGACCTCCCCTTCACTCTCTTCCTCCTGTTCCAGTCATGTAAGACGTGCCTGACTTCCCCTTCGGCCTGCCGCCATGAATTGAAGGTTTCCTGGAGGCCGTCCCTACCCCATGCTTCCTGTACAGCTGCGGGACTGTGAGCCAATTAAATCTCTTTTCTTTATAAATTATTCAATCTAGGTAGCTCTTCATAGCAGTGTGAGAATGGACTAAGACAACTGGCCTTCGCCTTTAAGTTCCTAAATTCATGTGGGTGTACCTGCTCCTGGATCTACACCTTTTTGGTCTGGGCGTCTGAACCCTTCTCAGTAGGTGGGCCCTAGGCTTTGATCCAGGCCACAGGGAGAAATCCTAGCATTCATTTTTCCCTTCCACTGCTTTCCAACTACTGCTAGTCTAAGGAGAGGTAGATACTATGAACTTGGGAGTTGAATAAGGTGGACACTTTGGGCTTAAAGTTTTCTAGAAAATTAGGCAATCATTAAGTTGTAATATTCATATTGTCCATAAGCATCAAACAACTCTGCTGCGTAACAAAAAGAATAATCTTTTTTCTTGAAGTCTAGTA HG:+:801109950:-1 HG:+:1098972737:-1 HG:+:2267756201:-1 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTCTATATAGCTAGAGACGTAGTGATATCTAACGTTTTTCTGATTGCAACCCCCAGGGTCTGCCTTGACAGTCAATGGACTGAGTACTAGAGTCAAGTACATTTACTTGGGAGAATTCGTTTTTCTCGATGTTATCAGTCTTTTAAAAGGGTATTGAGCAGAAAAAGAGTATTAGATTTAACTAATTTTAAACTGCATTTTGA HG:+:156606700:-1 HG:+:237092324:-1 HG:+:960281414:-1 HG:+:1459391003:45 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTCTATATAGCTAGAGACGTAGTGATATCTAACGTTTTTCTGATTGCAACCCCCAGGGTCTGCCTTGACAGTCAATGGACTGAGTACTAGAGTCAAGTACATTTACTTGGGAGAATTCGTTTTTCTCGATGTTATCAGTCTTTTAAAAGGGTATTGAGCAGAAAAAGAGTATTAGATTTAACTAATTTTAAACTGCATTTTGA HG:+:1459390991:45 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTCTATATAGCTAGAGACGTAGTGATATCTAACGTTTTTCTGATTGCAACCCCCAGGGTCTGCCTTGACAGTCAATGGACTGAGTACTAGAGTCAAGTACATTTACTTGGGAGAATTCGTTTTTCTCGATGTTATCAGTCTTTTAAAAGGGTATTGAGCAGAAAAAGAGTATTAGATTTAACTAATTTTAAACTGCATTTTGA HG:+:1459391002:45 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTCTATATAGCTAGAGACGTAGTGATATCTAACGTTTTTCTGATTGCAACCCCCAGGGTCTGCCTTGACAGTCAATGGACTGAGTACTAGAGTCAAGTACATTTACTTGGGAGAATTCGTTTTTCTCGATGTTATCAGTCTTTTAAAAGGGTATTGAGCAGAAAAAGAGTATTAGATTTAACTAATTTTAAACTGCATTTTGA HG:+:1459391006:45 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTCTATATAGCTAGAGACGTAGTGATATCTAACGTTTTTCTGATTGCAACCCCCAGGGTCTGCCTTGACAGTCAATGGACTGAGTACTAGAGTCAAGTACATTTACTTGGGAGAATTCGTTTTTCTCGATGTTATCAGTCTTTTAAAAGGGTATTGAGCAGAAAAAGAGTATTAGATTTAACTAATTTTAAACTGCATTTTGA HG:+:1459390990:45 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTCTATATAGCTAGAGACGTAGTGATATCTAACGTTTTTCTGATTGCAACCCCCAGGGTCTGCCTTGACAGTCAATGGACTGAGTACTAGAGTCAAGTACATTTACTTGGGAGAATTCGTTTTTCTCGATGTTATCAGTCTTTTAAAAGGGTATTGAGCAGAAAAAGAGTATTAGATTTAACTAATTTTAAACTGCATTTTGA HG:+:1459390992:45 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTCTATATAGCTAGAGACGTAGTGATATCTAACGTTTTTCTGATTGCAACCCCCAGGGTCTGCCTTGACAGTCAATGGACTGAGTACTAGAGTCAAGTACATTTACTTGGGAGAATTCGTTTTTCTCGATGTTATCAGTCTTTTAAAAGGGTATTGAGCAGAAAAAGAGTATTAGATTTAACTAATTTTAAACTGCATTTTGA HG:+:1459390995:45 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTCTATATAGCTAGAGACGTAGTGATATCTAACGTTTTTCTGATTGCAACCCCCAGGGTCTGCCTTGACAGTCAATGGACTGAGTACTAGAGTCAAGTACATTTACTTGGGAGAATTCGTTTTTCTCGATGTTATCAGTCTTTTAAAAGGGTATTGAGCAGAAAAAGAGTATTAGATTTAACTAATTTTAAACTGCATTTTGA HG:+:1459390996:45 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTCTATATAGCTAGAGACGTAGTGATATCTAACGTTTTTCTGATTGCAACCCCCAGGGTCTGCCTTGACAGTCAATGGACTGAGTACTAGAGTCAAGTACATTTACTTGGGAGAATTCGTTTTTCTCGATGTTATCAGTCTTTTAAAAGGGTATTGAGCAGAAAAAGAGTATTAGATTTAACTAATTTTAAACTGCATTTTGA HG:+:913682198:-1 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTCTATATAGCTAGAGACGTAGTGATATCTAACGTTTTTCTGATTGCAACCCCCAGGGTCTGCCTTGACAGTCAATGGACTGAGTACTAGAGTCAAGTACATTTACTTGGGAGAATTCGTTTTTCTCGATGTTATCAGTCTTTTAAAAGGGTATTGAGCAGAAAAAGAGTATTAGATTTAACTAATTTTAAACTGCATTTTGA HG:+:285064063:-1 HG:+:1459391004:45 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTCTATATAGCTAGAGACGTAGTGATATCTAACGTTTTTCTGATTGCAACCCCCAGGGTCTGCCTTGACAGTCAATGGACTGAGTACTAGAGTCAAGTACATTTACTTGGGAGAATTCGTTTTTCTCGATGTTATCAGTCTTTTAAAAGGGTATTGAGCAGAAAAAGAGTATTAGATTTAACTAATTTTAAACTGCATTTTGA HG:+:1934961736:-1 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTCTATATAGCTAGAGACGTAGTGATATCTAACGTTTTTCTGATTGCAACCCCCAGGGTCTGCCTTGACAGTCAATGGACTGAGTACTAGAGTCAAGTACATTTACTTGGGAGAATTCGTTTTTCTCGATGTTATCAGTCTTTTAAAAGGGTATTGAGCAGAAAAAGAGTATTAGATTTAACTAATTTTAAACTGCATTTTGA HG:+:1459390993:45 +TCAAAATGCAGTTTAAAATTAGTTAAATCTAATACTCTTTTTCTGCTCAATACCCTTTTAAAAGACTGATAACATCGAGAAAAACGAATTCTCCCAAGTAAATGTACTTGACTCTAGTACTCAGTCCATTGACTGTCAAGGCAGACCCTGGGGGTTGCAATCAGAAAAACGTTAGATATCACTACGTCTCTAGCTATATAGAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC HG:+:2645246355:-1 +TCAAAATGCAGTTTAAAATTAGTTAAATCTAATACTCTTTTTCTGCTCAATACCCTTTTAAAAGACTGATAACATCGAGAAAAACGAATTCTCCCAAGTAAATGTACTTGACTCTAGTACTCAGTCCATTGACTGTCAAGGCAGACCCTGGGGGTTGCAATCAGAAAAACGTTAGATATCACTACGTCTCTAGCTATATAGAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC HG:+:10314713:-1 +TCAAAATGCAGTTTAAAATTAGTTAAATCTAATACTCTTTTTCTGCTCAATACCCTTTTAAAAGACTGATAACATCGAGAAAAACGAATTCTCCCAAGTAAATGTACTTGACTCTAGTACTCAGTCCATTGACTGTCAAGGCAGACCCTGGGGGTTGCAATCAGAAAAACGTTAGATATCACTACGTCTCTAGCTATATAGAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC HG:+:2167921956:-1 +TCAAAATGCAGTTTAAAATTAGTTAAATCTAATACTCTTTTTCTGCTCAATACCCTTTTAAAAGACTGATAACATCGAGAAAAACGAATTCTCCCAAGTAAATGTACTTGACTCTAGTACTCAGTCCATTGACTGTCAAGGCAGACCCTGGGGGTTGCAATCAGAAAAACGTTAGATATCACTACGTCTCTAGCTATATAGAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC HG:+:2717239492:-1 +TCAAAATGCAGTTTAAAATTAGTTAAATCTAATACTCTTTTTCTGCTCAATACCCTTTTAAAAGACTGATAACATCGAGAAAAACGAATTCTCCCAAGTAAATGTACTTGACTCTAGTACTCAGTCCATTGACTGTCAAGGCAGACCCTGGGGGTTGCAATCAGAAAAACGTTAGATATCACTACGTCTCTAGCTATATAGAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC HG:+:540240583:-1 HG:+:860688245:-1 HG:+:926165064:-1 HG:+:1444413446:-1 HG:+:1448260086:-1 HG:+:1471628862:-1 HG:+:1567199725:-1 HG:+:1750023297:-1 HG:+:1794729940:-1 HG:+:2110098179:-1 HG:+:2345518098:-1 HG:+:2349312318:-1 HG:+:2351944376:-1 HG:+:2544595889:-1 HG:+:2544813824:-1 HG:+:2608125480:-1 +TCAAAATGCAGTTTAAAATTAGTTAAATCTAATACTCTTTTTCTGCTCAATACCCTTTTAAAAGACTGATAACATCGAGAAAAACGAATTCTCCCAAGTAAATGTACTTGACTCTAGTACTCAGTCCATTGACTGTCAAGGCAGACCCTGGGGGTTGCAATCAGAAAAACGTTAGATATCACTACGTCTCTAGCTATATAGAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC HG:+:183213969:-1 HG:+:1184650485:-1 HG:+:2269285332:-1 +TCAAAATGCAGTTTAAAATTAGTTAAATCTAATACTCTTTTTCTGCTCAATACCCTTTTAAAAGACTGATAACATCGAGAAAAACGAATTCTCCCAAGTAAATGTACTTGACTCTAGTACTCAGTCCATTGACTGTCAAGGCAGACCCTGGGGGTTGCAATCAGAAAAACGTTAGATATCACTACGTCTCTAGCTATATAGAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC HG:+:231017630:-1 HG:+:778375632:-1 HG:+:943486678:-1 HG:+:1234275425:-1 HG:+:1554527711:-1 HG:+:1610337203:-1 HG:+:1753269999:-1 HG:+:1819711177:-1 HG:+:2119224408:-1 HG:+:2162387155:-1 HG:+:2425722506:-1 HG:+:2458338751:-1 HG:+:2568250999:-1 HG:+:2672461915:-1 HG:+:2720482997:-1 HG:+:2824411045:-1 +TCAAAATGCAGTTTAAAATTAGTTAAATCTAATACTCTTTTTCTGCTCAATACCCTTTTAAAAGACTGATAACATCGAGAAAAACGAATTCTCCCAAGTAAATGTACTTGACTCTAGTACTCAGTCCATTGACTGTCAAGGCAGACCCTGGGGGTTGCAATCAGAAAAACGTTAGATATCACTACGTCTCTAGCTATATAGAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC HG:+:118409577:-1 HG:+:661703591:-1 HG:+:1077695541:-1 HG:+:1426054489:-1 HG:+:1677160529:-1 HG:+:1745328414:-1 HG:+:1889354619:-1 HG:+:1966327037:-1 HG:+:2049834396:-1 HG:+:2067313431:-1 HG:+:2372626639:-1 HG:+:2535941399:-1 HG:+:2655382262:-1 HG:+:2732381817:-1 HG:+:2753982499:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:9549773:-1 HG:+:9564159:-1 HG:+:12322776:-1 HG:+:38467921:-1 HG:+:112189176:-1 HG:+:169945881:-1 HG:+:179835555:-1 HG:+:181873637:-1 HG:+:208959446:-1 HG:+:212507649:-1 HG:+:224442586:-1 HG:+:314427377:-1 HG:+:370010332:-1 HG:+:378595148:-1 HG:+:381583900:-1 HG:+:389809601:-1 HG:+:397846541:-1 HG:+:410565111:-1 HG:+:445881528:-1 HG:+:462972140:-1 HG:+:483083434:-1 HG:+:620350665:-1 HG:+:659029167:-1 HG:+:679497580:-1 HG:+:845075288:-1 HG:+:860829494:-1 HG:+:895182703:-1 HG:+:910794802:-1 HG:+:913492133:-1 HG:+:913537351:-1 HG:+:915930122:-1 HG:+:938056555:-1 HG:+:946210072:-1 HG:+:949130653:-1 HG:+:997907453:-1 HG:+:1061064075:-1 HG:+:1106141198:-1 HG:+:1207302614:-1 HG:+:1218934491:-1 HG:+:1238018851:-1 HG:+:1255120706:-1 HG:+:1301361800:-1 HG:+:1303640732:-1 HG:+:1330969047:-1 HG:+:1334402647:-1 HG:+:1336587411:-1 HG:+:1336604248:-1 HG:+:1432552381:-1 HG:+:1491562893:-1 HG:+:1514579814:-1 HG:+:1520469988:-1 HG:+:1521334525:-1 HG:+:1541985207:-1 HG:+:1567720400:-1 HG:+:1570551895:-1 HG:+:1572479235:-1 HG:+:1579467388:-1 HG:+:1583050337:-1 HG:+:1604791944:-1 HG:+:1613561117:-1 HG:+:1640012573:-1 HG:+:1653778185:-1 HG:+:1656167164:-1 HG:+:1656688725:-1 HG:+:1673272187:-1 HG:+:1696802436:-1 HG:+:1702311164:-1 HG:+:1749207266:-1 HG:+:1754479377:-1 HG:+:1755872783:-1 HG:+:1782341021:-1 HG:+:1783676824:-1 HG:+:1785813193:-1 HG:+:1819935549:-1 HG:+:1834121138:-1 HG:+:1922151707:-1 HG:+:1924277462:-1 HG:+:1927047178:-1 HG:+:1932995050:-1 HG:+:2017481991:-1 HG:+:2061606716:-1 HG:+:2062343444:-1 HG:+:2071701323:-1 HG:+:2076883572:-1 HG:+:2080316244:-1 HG:+:2219474871:-1 HG:+:2359244009:-1 HG:+:2402091634:-1 HG:+:2414299150:-1 HG:+:2429385831:-1 HG:+:2431219581:-1 HG:+:2432055670:-1 HG:+:2439198712:-1 HG:+:2465399552:-1 HG:+:2484614282:-1 HG:+:2485650704:-1 HG:+:2486453654:-1 HG:+:2512783587:-1 HG:+:2521022448:-1 HG:+:2538492577:-1 HG:+:2548304046:-1 HG:+:2559896625:-1 HG:+:2571242315:-1 HG:+:2571845954:-1 HG:+:2574950439:-1 HG:+:2590186698:-1 HG:+:2591268966:-1 HG:+:2627861295:-1 HG:+:2635027614:-1 HG:+:2649237519:-1 HG:+:2650591222:-1 HG:+:2651886539:-1 HG:+:2661610747:-1 HG:+:2662875839:-1 HG:+:2666132482:-1 HG:+:2696741317:-1 HG:+:2699633850:-1 HG:+:2710983244:-1 HG:+:2712593530:-1 HG:+:2740092206:-1 HG:+:2750076798:-1 HG:+:2770188027:-1 HG:+:2872775251:-1 HG:+:2875369139:-1 HG:+:2877796497:-1 HG:+:2886456502:-1 HG:+:3034334337:-1 HG:+:3051627882:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:32762047:-1 HG:+:36651567:-1 HG:+:258103169:-1 HG:+:434726621:-1 HG:+:519271259:-1 HG:+:819326995:-1 HG:+:1020240453:-1 HG:+:1052776054:-1 HG:+:1166927527:-1 HG:+:1202186595:-1 HG:+:1267620142:-1 HG:+:1481438516:-1 HG:+:1488273161:-1 HG:+:1566305275:-1 HG:+:2004733708:-1 HG:+:2155976197:-1 HG:+:2366685804:-1 HG:+:2403048320:-1 HG:+:2540770411:-1 HG:+:2669709171:-1 HG:+:2694198461:-1 HG:+:2708838918:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:1117409723:-1 HG:+:1143779707:-1 HG:+:2152778999:-1 HG:+:2803499830:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:483364017:-1 HG:+:560012826:-1 HG:+:730369831:-1 HG:+:1009759256:-1 HG:+:1197728005:-1 HG:+:1280795587:-1 HG:+:2985157998:-1 HG:+:3013735926:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:286714502:-1 HG:+:289159148:-1 HG:+:408589504:-1 HG:+:460930218:-1 HG:+:519656866:-1 HG:+:576828464:-1 HG:+:602423645:-1 HG:+:623744566:-1 HG:+:647696176:-1 HG:+:653732351:-1 HG:+:695104309:-1 HG:+:704244007:-1 HG:+:708752402:-1 HG:+:883081573:-1 HG:+:917392440:-1 HG:+:960562964:-1 HG:+:1002658422:-1 HG:+:1027502136:-1 HG:+:1043021358:-1 HG:+:1045972825:-1 HG:+:1301971504:-1 HG:+:1349392674:-1 HG:+:1486666184:-1 HG:+:1610611239:-1 HG:+:1718800355:-1 HG:+:1736089412:-1 HG:+:1745710939:-1 HG:+:1767250325:-1 HG:+:1814150319:-1 HG:+:1862531105:-1 HG:+:1992084453:-1 HG:+:2044207620:-1 HG:+:2080275488:-1 HG:+:2080523455:-1 HG:+:2133454787:-1 HG:+:2168213323:-1 HG:+:2177911612:-1 HG:+:2183252209:-1 HG:+:2264925883:-1 HG:+:2347097769:-1 HG:+:2349869298:-1 HG:+:2464210725:-1 HG:+:2473602242:-1 HG:+:2516623121:-1 HG:+:2613524178:-1 HG:+:2631878116:-1 HG:+:2638433123:-1 HG:+:2673214546:-1 HG:+:2760781807:-1 HG:+:2929653130:-1 HG:+:2966415671:-1 HG:+:2984631812:-1 HG:+:3017741457:-1 HG:+:3023691280:-1 HG:+:3061140100:-1 HG:+:3064614522:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:174852665:-1 HG:+:240638153:-1 HG:+:690267170:-1 HG:+:818722389:-1 HG:+:821317022:-1 HG:+:827617749:-1 HG:+:860399847:-1 HG:+:885120291:-1 HG:+:944215228:-1 HG:+:1121167333:-1 HG:+:1124628166:-1 HG:+:1156453464:-1 HG:+:1210096761:-1 HG:+:1302990478:-1 HG:+:1319893384:-1 HG:+:1370717006:-1 HG:+:1465824721:-1 HG:+:1913775441:-1 HG:+:2002813334:-1 HG:+:2056456682:-1 HG:+:2299075194:-1 HG:+:2302584304:-1 HG:+:2508519410:-1 HG:+:2563198689:-1 HG:+:2617909524:-1 HG:+:2962387649:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:320148665:-1 HG:+:447322785:-1 HG:+:1816790081:-1 HG:+:1823905442:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:2886661769:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:17740218:-1 HG:+:97579451:-1 HG:+:1862445029:-1 HG:+:2869508294:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:363745480:-1 HG:+:493317089:-1 HG:+:504872612:-1 HG:+:725044955:-1 HG:+:920783660:-1 HG:+:1136275598:-1 HG:+:1630140311:-1 HG:+:2464559308:-1 HG:+:2577913734:-1 HG:+:2740918057:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:188003406:-1 HG:+:2030837207:-1 HG:+:2144698684:-1 HG:+:2170131817:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:313449033:-1 HG:+:458700508:-1 HG:+:532664144:-1 HG:+:908049309:-1 HG:+:990153704:-1 HG:+:2243967356:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:239413945:-1 HG:+:844740189:-1 HG:+:1355730621:-1 HG:+:2129536139:-1 HG:+:2224779533:-1 HG:+:2761590597:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:5002506:-1 HG:+:37670442:-1 HG:+:81679756:-1 HG:+:84452152:-1 HG:+:268238685:-1 HG:+:281455134:-1 HG:+:309560711:-1 HG:+:327797874:-1 HG:+:375764961:-1 HG:+:403502749:-1 HG:+:407988518:-1 HG:+:428917367:-1 HG:+:457553315:-1 HG:+:467238175:-1 HG:+:469767424:-1 HG:+:501819602:-1 HG:+:501819631:-1 HG:+:532266249:-1 HG:+:548461576:-1 HG:+:576595630:-1 HG:+:636529128:-1 HG:+:664987204:-1 HG:+:716117822:-1 HG:+:773709699:-1 HG:+:843862707:-1 HG:+:861229289:-1 HG:+:996791318:-1 HG:+:1037296749:-1 HG:+:1077108148:-1 HG:+:1101621996:-1 HG:+:1111606241:-1 HG:+:1141106765:-1 HG:+:1148205191:-1 HG:+:1160675509:-1 HG:+:1172369981:-1 HG:+:1190930998:-1 HG:+:1406252978:-1 HG:+:1447170184:-1 HG:+:1466282971:-1 HG:+:1501861138:-1 HG:+:1503619398:-1 HG:+:1727141967:-1 HG:+:1729331702:-1 HG:+:1735753218:-1 HG:+:1770943186:-1 HG:+:1834975934:-1 HG:+:2027267233:-1 HG:+:2079024616:-1 HG:+:2080751583:-1 HG:+:2142373523:-1 HG:+:2227948592:-1 HG:+:2244118038:-1 HG:+:2256709331:-1 HG:+:2271795501:-1 HG:+:2274563688:-1 HG:+:2381034318:-1 HG:+:2393615813:-1 HG:+:2395520091:-1 HG:+:2466163690:-1 HG:+:2492862427:-1 HG:+:2513452771:-1 HG:+:2553299557:-1 HG:+:2639396731:-1 HG:+:2691789232:-1 HG:+:2896880039:-1 HG:+:2920598854:-1 HG:+:3034353930:-1 HG:+:3061815419:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:239518690:-1 HG:+:358690697:-1 HG:+:612805565:-1 HG:+:1005677388:-1 HG:+:1063645906:-1 HG:+:1256744536:-1 HG:+:1392200078:-1 HG:+:1672883540:-1 HG:+:1689088017:-1 HG:+:2405675059:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:353147707:-1 HG:+:888550075:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:30503173:-1 HG:+:53692772:-1 HG:+:80384448:-1 HG:+:298970796:-1 HG:+:312984541:-1 HG:+:328813443:-1 HG:+:414823232:-1 HG:+:446792354:-1 HG:+:498376592:-1 HG:+:708862380:-1 HG:+:727379247:-1 HG:+:855366971:-1 HG:+:887023804:-1 HG:+:922320351:-1 HG:+:939194228:-1 HG:+:973694475:-1 HG:+:1012287216:-1 HG:+:1227109154:-1 HG:+:1398124015:-1 HG:+:1470044203:-1 HG:+:1682104740:-1 HG:+:1748926926:-1 HG:+:1776363630:-1 HG:+:1815296989:-1 HG:+:2042795603:-1 HG:+:2156220074:-1 HG:+:2159403974:-1 HG:+:2349687695:-1 HG:+:2403421901:-1 HG:+:2405283127:-1 HG:+:2460942615:-1 HG:+:2463341297:-1 HG:+:2608170394:-1 HG:+:2638613260:-1 HG:+:2963674443:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:5087267:-1 HG:+:49180124:-1 HG:+:74311721:-1 HG:+:180316741:-1 HG:+:185430620:-1 HG:+:192811359:-1 HG:+:202055728:-1 HG:+:216085907:-1 HG:+:222783431:-1 HG:+:298284453:-1 HG:+:352969893:-1 HG:+:354699227:-1 HG:+:369803609:-1 HG:+:435866097:-1 HG:+:446968583:-1 HG:+:452683734:-1 HG:+:504604154:-1 HG:+:590738760:-1 HG:+:597366564:-1 HG:+:624556946:-1 HG:+:647120104:-1 HG:+:650123350:-1 HG:+:655877961:-1 HG:+:752269857:-1 HG:+:827667703:-1 HG:+:869196146:-1 HG:+:945183426:-1 HG:+:956599972:-1 HG:+:980760524:-1 HG:+:1034570947:-1 HG:+:1082087290:-1 HG:+:1083231265:-1 HG:+:1085757205:-1 HG:+:1154648751:-1 HG:+:1166984434:-1 HG:+:1195951648:-1 HG:+:1226876500:-1 HG:+:1252166420:-1 HG:+:1290996868:-1 HG:+:1297288834:-1 HG:+:1297571239:-1 HG:+:1315295182:-1 HG:+:1321416445:-1 HG:+:1359358654:-1 HG:+:1408184309:-1 HG:+:1410611782:-1 HG:+:1426337557:-1 HG:+:1431452683:-1 HG:+:1446827440:-1 HG:+:1474635988:-1 HG:+:1506061790:-1 HG:+:1515285854:-1 HG:+:1557282999:-1 HG:+:1628276143:-1 HG:+:1654687126:-1 HG:+:1714253905:-1 HG:+:1733289637:-1 HG:+:1751294880:-1 HG:+:1861424056:-1 HG:+:1889302357:-1 HG:+:1891995394:-1 HG:+:1900657538:-1 HG:+:1994173905:-1 HG:+:2036208317:-1 HG:+:2051407808:-1 HG:+:2074995384:-1 HG:+:2111212093:-1 HG:+:2128513298:-1 HG:+:2222023353:-1 HG:+:2338054764:-1 HG:+:2347507287:-1 HG:+:2354988208:-1 HG:+:2435943784:-1 HG:+:2537885995:-1 HG:+:2544494459:-1 HG:+:2563967305:-1 HG:+:2634976926:-1 HG:+:2762969407:-1 HG:+:2769750188:-1 HG:+:2799592544:-1 HG:+:2885646677:-1 HG:+:2885868338:-1 HG:+:2996634673:-1 HG:+:3001977752:-1 HG:+:3021851870:-1 HG:+:3054092702:-1 HG:+:3060096236:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:389571852:-1 HG:+:558414297:-1 HG:+:573498573:-1 HG:+:607247641:-1 HG:+:1010697604:-1 HG:+:1011593765:-1 HG:+:1067122889:-1 HG:+:1068673773:-1 HG:+:1116095968:-1 HG:+:1349902884:-1 HG:+:1386505527:-1 HG:+:2401060978:-1 HG:+:2616127355:-1 HG:+:2626212917:-1 HG:+:2735820764:-1 HG:+:2820365463:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:8330028:-1 HG:+:79179523:-1 HG:+:179951294:-1 HG:+:542196961:-1 HG:+:717780290:-1 HG:+:1358530363:-1 HG:+:1635830623:-1 HG:+:2353560876:-1 HG:+:2360572577:-1 HG:+:2971015933:-1 HG:+:3040481489:-1 HG:+:3044656462:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:393032047:-1 HG:+:459741789:-1 HG:+:629535787:-1 HG:+:904945679:-1 HG:+:1039806502:-1 HG:+:1336584968:-1 HG:+:1873886011:-1 HG:+:1909026685:-1 HG:+:2053899555:-1 HG:+:2619794785:-1 HG:+:2964049654:-1 HG:+:3022290567:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:119279348:-1 HG:+:270213363:-1 HG:+:369359433:-1 HG:+:418288068:-1 HG:+:564591997:-1 HG:+:607461300:-1 HG:+:723801257:-1 HG:+:806858727:-1 HG:+:1065985266:-1 HG:+:1295967640:-1 HG:+:1311430464:-1 HG:+:1366981370:-1 HG:+:1541327132:-1 HG:+:1739237271:-1 HG:+:1786612501:-1 HG:+:2398970690:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:15117203:-1 HG:+:174355660:-1 HG:+:369577330:-1 HG:+:622186626:-1 HG:+:688691620:-1 HG:+:773709137:-1 HG:+:898688162:-1 HG:+:1222993849:-1 HG:+:1396799840:-1 HG:+:1537236717:-1 HG:+:1539951608:-1 HG:+:1834607883:-1 HG:+:2274355573:-1 HG:+:2676839530:-1 HG:+:2693988173:-1 HG:+:2704961766:-1 HG:+:2931552989:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTTTTTTTTTTTTTTTGAGCAAAACTAAGTGGGTTCTGGGAATACAGCCATATCCTATAATCTCCTGAAATTAGTAAACTACAAGATTAATTTCAAGATATATCTCCCTACACAGGAAAATCTTAGGTGTTACTAAACCAAATACCTCTTCATTTTATTGATATACGTTTCTTTTTGGCGGTGGGGAGGACGGAGTCTTGCTC HG:+:286095525:-1 HG:+:441536431:-1 HG:+:488672110:-1 HG:+:1069742476:-1 HG:+:1760079453:-1 HG:+:1816507155:-1 HG:+:1898241195:-1 HG:+:2068114837:-1 HG:+:2115138478:-1 HG:+:2130431754:-1 HG:+:2371273320:-1 HG:+:2764387269:-1 HG:+:2768374596:-1 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:35639199:-1 HG:+:143900172:-1 HG:+:149453579:-1 HG:+:461860365:-1 HG:+:617875565:-1 HG:+:898585287:-1 HG:+:1103596721:-1 HG:+:1105765040:-1 HG:+:1202867802:-1 HG:+:1667136887:-1 HG:+:1678990014:-1 HG:+:1757327678:-1 HG:+:1982896131:-1 HG:+:2153246021:-1 HG:+:2373082992:-1 HG:+:2424304400:-1 HG:+:2459993788:-1 HG:+:2493923324:-1 HG:+:2578880439:-1 HG:+:2674988965:-1 HG:+:2709911464:-1 HG:+:2754281944:-1 HG:+:2819323411:-1 HG:+:3012630957:-1 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:2694373061:49 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:2694373039:49 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:2694373060:49 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:2694373040:49 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:2694373049:49 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:2694373058:49 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:2042491063:-1 HG:+:2694373059:49 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:2694373042:49 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:87511100:-1 HG:+:2694373044:49 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:2694373048:49 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:2694373050:49 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:2007981629:-1 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:2694373057:49 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:322603001:-1 HG:+:1179140808:-1 +GAGCAAGACTCCGTCCTCCCCACCGCCAAAAAGAAACGTATATCAATAAAATGAAGAGGTATTTGGTTTAGTAACACCTAAGATTTTCCTGTGTAGGGAGATATATCTTGAAATTAATCTTGTAGTTTACTAATTTCAGGAGATTATAGGATATGGCTGTATTCCCAGAACCCACTTAGTTTTGCTCAAAAAAAAAAAAAAAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA HG:+:2591273022:-1 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACACTAAGGATTTGCATCTGGATTAAAAGGAATTACTCTGAGAATAATTTAATTCCAATAGTTGGAGGAAATTGTCTCCTGTGATCAGTACAATTTGCCACAGTTTTAAACATGTGGGTGACAATGACTGACTTTCATATTTCTGTCCTCGGCAGACGTGACTGTACACAACTGAGTCGCAGCCACTCTCAGAGGGGATTGCA HG:+:2277191461:-1 HG:+:2821050360:55 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACACTAAGGATTTGCATCTGGATTAAAAGGAATTACTCTGAGAATAATTTAATTCCAATAGTTGGAGGAAATTGTCTCCTGTGATCAGTACAATTTGCCACAGTTTTAAACATGTGGGTGACAATGACTGACTTTCATATTTCTGTCCTCGGCAGACGTGACTGTACACAACTGAGTCGCAGCCACTCTCAGAGGGGATTGCA HG:+:2821050364:55 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACACTAAGGATTTGCATCTGGATTAAAAGGAATTACTCTGAGAATAATTTAATTCCAATAGTTGGAGGAAATTGTCTCCTGTGATCAGTACAATTTGCCACAGTTTTAAACATGTGGGTGACAATGACTGACTTTCATATTTCTGTCCTCGGCAGACGTGACTGTACACAACTGAGTCGCAGCCACTCTCAGAGGGGATTGCA HG:+:2821050349:55 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACACTAAGGATTTGCATCTGGATTAAAAGGAATTACTCTGAGAATAATTTAATTCCAATAGTTGGAGGAAATTGTCTCCTGTGATCAGTACAATTTGCCACAGTTTTAAACATGTGGGTGACAATGACTGACTTTCATATTTCTGTCCTCGGCAGACGTGACTGTACACAACTGAGTCGCAGCCACTCTCAGAGGGGATTGCA HG:+:2821050351:55 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACACTAAGGATTTGCATCTGGATTAAAAGGAATTACTCTGAGAATAATTTAATTCCAATAGTTGGAGGAAATTGTCTCCTGTGATCAGTACAATTTGCCACAGTTTTAAACATGTGGGTGACAATGACTGACTTTCATATTTCTGTCCTCGGCAGACGTGACTGTACACAACTGAGTCGCAGCCACTCTCAGAGGGGATTGCA HG:+:215046134:-1 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACACTAAGGATTTGCATCTGGATTAAAAGGAATTACTCTGAGAATAATTTAATTCCAATAGTTGGAGGAAATTGTCTCCTGTGATCAGTACAATTTGCCACAGTTTTAAACATGTGGGTGACAATGACTGACTTTCATATTTCTGTCCTCGGCAGACGTGACTGTACACAACTGAGTCGCAGCCACTCTCAGAGGGGATTGCA HG:+:2821050352:55 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACACTAAGGATTTGCATCTGGATTAAAAGGAATTACTCTGAGAATAATTTAATTCCAATAGTTGGAGGAAATTGTCTCCTGTGATCAGTACAATTTGCCACAGTTTTAAACATGTGGGTGACAATGACTGACTTTCATATTTCTGTCCTCGGCAGACGTGACTGTACACAACTGAGTCGCAGCCACTCTCAGAGGGGATTGCA HG:+:2821050353:55 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACACTAAGGATTTGCATCTGGATTAAAAGGAATTACTCTGAGAATAATTTAATTCCAATAGTTGGAGGAAATTGTCTCCTGTGATCAGTACAATTTGCCACAGTTTTAAACATGTGGGTGACAATGACTGACTTTCATATTTCTGTCCTCGGCAGACGTGACTGTACACAACTGAGTCGCAGCCACTCTCAGAGGGGATTGCA HG:+:719484937:-1 HG:+:2821050348:55 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACACTAAGGATTTGCATCTGGATTAAAAGGAATTACTCTGAGAATAATTTAATTCCAATAGTTGGAGGAAATTGTCTCCTGTGATCAGTACAATTTGCCACAGTTTTAAACATGTGGGTGACAATGACTGACTTTCATATTTCTGTCCTCGGCAGACGTGACTGTACACAACTGAGTCGCAGCCACTCTCAGAGGGGATTGCA HG:+:2736082823:-1 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACACTAAGGATTTGCATCTGGATTAAAAGGAATTACTCTGAGAATAATTTAATTCCAATAGTTGGAGGAAATTGTCTCCTGTGATCAGTACAATTTGCCACAGTTTTAAACATGTGGGTGACAATGACTGACTTTCATATTTCTGTCCTCGGCAGACGTGACTGTACACAACTGAGTCGCAGCCACTCTCAGAGGGGATTGCA HG:+:2821050357:55 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACACTAAGGATTTGCATCTGGATTAAAAGGAATTACTCTGAGAATAATTTAATTCCAATAGTTGGAGGAAATTGTCTCCTGTGATCAGTACAATTTGCCACAGTTTTAAACATGTGGGTGACAATGACTGACTTTCATATTTCTGTCCTCGGCAGACGTGACTGTACACAACTGAGTCGCAGCCACTCTCAGAGGGGATTGCA HG:+:2821050358:55 +TGCAATCCCCTCTGAGAGTGGCTGCGACTCAGTTGTGTACAGTCACGTCTGCCGAGGACAGAAATATGAAAGTCAGTCATTGTCACCCACATGTTTAAAACTGTGGCAAATTGTACTGATCACAGGAGACAATTTCCTCCAACTATTGGAATTAAATTATTCTCAGAGTAATTCCTTTTAATCCAGATGCAAATCCTTAGTGTCTATAGATATTAAATAAGAACCTGCAGGGCTCCTCGACTTAAGTTTCCTACTGTTATCACTCTCATATTCTCAGTAGATAAGAGCCAAAATGTCACTGGGTGCCGAGTAAATATGGGAAGCTCAGATACATTGCTTTTATCAATGTTTGGCGGGCTTATTCGGTTTAAGCCTGGAACCAAATAATAACACATTTAAGGAGGACCTGACTGTCCTTAAATGAAATATTAATACTGAAGAGGAAAAAGTATCAGGCCATGCTTCTACCCGAGTGGGACAGAGGTAAGAAATCTAGAATGCAGCTTTTGGGTAGCCCAACAACTTGAAATTTCTTAACAGGACAAAGAAAGCCCAGCCAACATGAATGAGTTTATTTCCCTTTATTGAGATAAGAAAAGCCACTAACCCTCGAGCCTGAGGATATTTTTTACCTGTTTCTTCTTCCATTAAAGTTAGGGGTTACTCTTACAAGTCCAGTGATTTTAGACACATGGAACCGATCAACTTTGAATCCTGGGAATCCTTTCCTTTAAGAGTGGTGTATTACCTGTCTTTATATTGAACTCTTAGGGACCTTCTGCCTTGCCAGTTATCTCTCCCTTGTCTCTGAAGACCTAGACCTTTCTTTTTCCTTCCTTCCTATTTTACTTCCTGTGAACTGTGTCTTGACTGTATCGTATTAGCTTCTTGTTTCTCAACGTTTTTATCCTCACTACGTGGAGATAAATGTATGTCACTGAAGTTCTTAAATAAGTGGAGTCATAAGAAAAACATGGACTAACTAATCTGAACTACGATA HG:+:2063024798:-1 +TGCAATCCCCTCTGAGAGTGGCTGCGACTCAGTTGTGTACAGTCACGTCTGCCGAGGACAGAAATATGAAAGTCAGTCATTGTCACCCACATGTTTAAAACTGTGGCAAATTGTACTGATCACAGGAGACAATTTCCTCCAACTATTGGAATTAAATTATTCTCAGAGTAATTCCTTTTAATCCAGATGCAAATCCTTAGTGTCTATAGATATTAAATAAGAACCTGCAGGGCTCCTCGACTTAAGTTTCCTACTGTTATCACTCTCATATTCTCAGTAGATAAGAGCCAAAATGTCACTGGGTGCCGAGTAAATATGGGAAGCTCAGATACATTGCTTTTATCAATGTTTGGCGGGCTTATTCGGTTTAAGCCTGGAACCAAATAATAACACATTTAAGGAGGACCTGACTGTCCTTAAATGAAATATTAATACTGAAGAGGAAAAAGTATCAGGCCATGCTTCTACCCGAGTGGGACAGAGGTAAGAAATCTAGAATGCAGCTTTTGGGTAGCCCAACAACTTGAAATTTCTTAACAGGACAAAGAAAGCCCAGCCAACATGAATGAGTTTATTTCCCTTTATTGAGATAAGAAAAGCCACTAACCCTCGAGCCTGAGGATATTTTTTACCTGTTTCTTCTTCCATTAAAGTTAGGGGTTACTCTTACAAGTCCAGTGATTTTAGACACATGGAACCGATCAACTTTGAATCCTGGGAATCCTTTCCTTTAAGAGTGGTGTATTACCTGTCTTTATATTGAACTCTTAGGGACCTTCTGCCTTGCCAGTTATCTCTCCCTTGTCTCTGAAGACCTAGACCTTTCTTTTTCCTTCCTTCCTATTTTACTTCCTGTGAACTGTGTCTTGACTGTATCGTATTAGCTTCTTGTTTCTCAACGTTTTTATCCTCACTACGTGGAGATAAATGTATGTCACTGAAGTTCTTAAATAAGTGGAGTCATAAGAAAAACATGGACTAACTAATCTGAACTACGATA HG:+:654379983:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:1474079774:-1 HG:+:1520577061:-1 HG:+:1665632735:-1 HG:+:1744579459:-1 HG:+:2010812089:-1 HG:+:2245363734:-1 HG:+:2606469627:-1 HG:+:2609464700:-1 HG:+:2627262006:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:89442601:-1 HG:+:337083178:-1 HG:+:485694484:-1 HG:+:513678576:-1 HG:+:605396316:-1 HG:+:950301900:-1 HG:+:1115889987:-1 HG:+:1282884872:-1 HG:+:1312320027:-1 HG:+:1390794058:-1 HG:+:1481780172:-1 HG:+:2812951637:-1 HG:+:2872178418:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:57609724:-1 HG:+:103691895:-1 HG:+:217016332:-1 HG:+:266901274:-1 HG:+:325954649:-1 HG:+:604571738:-1 HG:+:679561954:-1 HG:+:751613838:-1 HG:+:762007631:-1 HG:+:1072083099:-1 HG:+:1142625236:-1 HG:+:1187924027:-1 HG:+:1286165952:-1 HG:+:1359253057:-1 HG:+:1440253866:-1 HG:+:1543191926:-1 HG:+:2155204745:-1 HG:+:2196750638:-1 HG:+:2237637579:-1 HG:+:2242795751:-1 HG:+:2471669736:-1 HG:+:2585363922:-1 HG:+:3035076457:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:54110538:-1 HG:+:238427679:-1 HG:+:373835082:-1 HG:+:498495076:-1 HG:+:518201874:-1 HG:+:663928798:-1 HG:+:1428956153:-1 HG:+:1529153839:-1 HG:+:1624416616:-1 HG:+:1857374356:-1 HG:+:2352512333:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:96887680:-1 HG:+:1737995986:-1 HG:+:2251989960:-1 HG:+:3018320041:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:425496382:-1 HG:+:683982776:-1 HG:+:685714935:-1 HG:+:826195167:-1 HG:+:839030549:-1 HG:+:2798519476:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:1398192677:-1 HG:+:1956323525:-1 HG:+:2136679100:-1 HG:+:2391219126:-1 HG:+:2983485230:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:115012298:-1 HG:+:471640942:-1 HG:+:670830117:-1 HG:+:705449910:-1 HG:+:940362528:-1 HG:+:1325089827:-1 HG:+:1461881081:-1 HG:+:1625226058:-1 HG:+:1684770412:-1 HG:+:2032731616:-1 HG:+:2930924002:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:102745970:-1 HG:+:394710216:-1 HG:+:938966756:-1 HG:+:1710286557:-1 HG:+:1897303436:-1 HG:+:2253631031:-1 HG:+:2376424619:-1 HG:+:2903960207:-1 HG:+:2918063122:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:606324572:-1 HG:+:1352565360:-1 HG:+:1449471741:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:77709493:-1 HG:+:211842071:-1 HG:+:1035018793:-1 HG:+:1059473493:-1 HG:+:1117593070:-1 HG:+:1175490777:-1 HG:+:1476404089:-1 HG:+:1783544933:-1 HG:+:1788232148:-1 HG:+:1828283065:-1 HG:+:2796732928:-1 HG:+:2856236975:-1 HG:+:3099140760:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:36720444:-1 HG:+:439164056:-1 HG:+:495918002:-1 HG:+:2888222592:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:550420246:-1 HG:+:1154217802:-1 HG:+:1711087904:-1 HG:+:1983566629:-1 HG:+:2396752726:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:7429847:-1 HG:+:52740593:-1 HG:+:174899009:-1 HG:+:195203264:-1 HG:+:374335678:-1 HG:+:380096377:-1 HG:+:380484943:-1 HG:+:405697853:-1 HG:+:414700776:-1 HG:+:527891023:-1 HG:+:595374708:-1 HG:+:739321890:-1 HG:+:758961176:-1 HG:+:781835400:-1 HG:+:849723716:-1 HG:+:871150414:-1 HG:+:888344975:-1 HG:+:1185085516:-1 HG:+:1220648828:-1 HG:+:1483894148:-1 HG:+:1789946552:-1 HG:+:1845052887:-1 HG:+:2052824367:-1 HG:+:2078300188:-1 HG:+:2168556097:-1 HG:+:2193228797:-1 HG:+:2226916659:-1 HG:+:2231125347:-1 HG:+:2236846324:-1 HG:+:2556340180:-1 HG:+:2587663706:-1 HG:+:2620352165:-1 HG:+:2627974991:-1 HG:+:2799551420:-1 HG:+:2972097681:-1 HG:+:3041202716:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:548949644:-1 HG:+:593553788:-1 HG:+:2436605594:-1 HG:+:2931855438:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:235795804:-1 HG:+:455960494:-1 HG:+:611476163:-1 HG:+:657828549:-1 HG:+:1082171066:-1 HG:+:2193355083:-1 HG:+:2426745232:-1 HG:+:2700090459:-1 HG:+:2722682960:-1 HG:+:2923219493:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:146951946:-1 HG:+:199098188:-1 HG:+:627792558:-1 HG:+:654049189:-1 HG:+:655181683:-1 HG:+:750847731:-1 HG:+:853067542:-1 HG:+:1053122359:-1 HG:+:1265599051:-1 HG:+:1684475235:-1 HG:+:1717879840:-1 HG:+:1982545876:-1 HG:+:2006439582:-1 HG:+:2154588537:-1 HG:+:2999103900:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:88824092:-1 HG:+:90892624:-1 HG:+:174312289:-1 HG:+:227043746:-1 HG:+:294900534:-1 HG:+:449496717:-1 HG:+:529374663:-1 HG:+:551720094:-1 HG:+:683065125:-1 HG:+:811032883:-1 HG:+:1265285461:-1 HG:+:1341458128:-1 HG:+:1461377891:-1 HG:+:2248679219:-1 HG:+:2289476910:-1 HG:+:2335437392:-1 HG:+:2351558542:-1 HG:+:2376837397:-1 HG:+:2431358287:-1 HG:+:2439443702:-1 HG:+:2550877493:-1 HG:+:2577706136:-1 HG:+:2920535807:-1 HG:+:2947990822:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:1024000682:-1 HG:+:1166069204:-1 HG:+:1523972011:-1 HG:+:2252912057:-1 HG:+:2603173817:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:96101056:-1 HG:+:2601319910:-1 HG:+:2689702474:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:2440607:-1 HG:+:26617114:-1 HG:+:276316544:-1 HG:+:370392547:-1 HG:+:917108775:-1 HG:+:990121697:-1 HG:+:1015036516:-1 HG:+:1061382460:-1 HG:+:1072960131:-1 HG:+:1087714969:-1 HG:+:1096535828:-1 HG:+:1446515863:-1 HG:+:1516627362:-1 HG:+:1677763958:-1 HG:+:1686060058:-1 HG:+:1860870621:-1 HG:+:1962571755:-1 HG:+:2046584027:-1 HG:+:2238810822:-1 HG:+:2495057906:-1 HG:+:2565144500:-1 HG:+:2576751972:-1 HG:+:2672199101:-1 HG:+:2677178366:-1 HG:+:2854897119:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:675070714:-1 HG:+:1457727860:-1 HG:+:2361464387:-1 HG:+:2954606212:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:221497259:-1 HG:+:579772357:-1 HG:+:623978547:-1 HG:+:738331873:-1 HG:+:1156390186:-1 HG:+:1979879348:-1 HG:+:2172251435:-1 HG:+:2246267014:-1 HG:+:2250548242:-1 HG:+:2691091368:-1 HG:+:2935560181:-1 HG:+:3035861763:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACGTGTATGTGTACCATAGGAGATCGCACTCGAAATGTTCACGGCAACATTTATTTGCAAACTTTAAGTATTAGAACCATCCATACGTTCAATCAACAGTAGAACGGTATAAGTAAATAACAAGGTATTCACACAATAAAATACCGTCACAACAAGTGAAAATGAATGAAGTGCAACCACATGCAACAATATGAACAAATTTC HG:+:65048448:-1 HG:+:189661330:-1 HG:+:279048988:-1 HG:+:402028497:-1 HG:+:416415121:-1 HG:+:493196975:-1 HG:+:672369060:-1 HG:+:774681719:-1 HG:+:848439462:-1 HG:+:1517602925:-1 HG:+:1790625462:-1 HG:+:1823897463:-1 HG:+:1831093849:-1 HG:+:1886253358:-1 HG:+:2170730474:-1 HG:+:2290449871:-1 HG:+:2359024281:-1 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:517101960:43 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:517101967:43 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:3025149531:-1 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:517101975:43 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:517101983:43 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:517101971:43 HG:+:1698149699:-1 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:517101974:43 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:517101976:43 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:517101985:43 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:517101961:43 HG:+:1914055843:-1 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:517101964:43 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:517101966:43 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:638073916:-1 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:517101977:43 +GAAATTTGTTCATATTGTTGCATGTGGTTGCACTTCATTCATTTTCACTTGTTGTGACGGTATTTTATTGTGTGAATACCTTGTTATTTACTTATACCGTTCTACTGTTGATTGAACGTATGGATGGTTCTAATACTTAAAGTTTGCAAATAAATGTTGCCGTGAACATTTCGAGTGCGATCTCCTATGGTACACATACACGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC HG:+:517101981:43 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:30845341:-1 HG:+:3033653779:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653784:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653789:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653801:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653800:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653782:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:1350428109:-1 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653787:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:1561148529:-1 HG:+:3033653794:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:2527601927:-1 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653799:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:1676182135:-1 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653802:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653806:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653780:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653783:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653786:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:159175274:-1 HG:+:3033653788:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653791:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653795:50 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:546247952:-1 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTGAAGAGAGAGACATGGGGAGGTCCCCCACCTGAGGAAGGTGGAGGGCTCCAAGGGCTGGGGGGAGGGTGCGGAAGCCCTAGGCAAGGCCTGACAGCAGGACGACCCCTCCAAGATCAAAGTCCCTCCCAGGCCTCTGGTGGCCACTGCACAAGGTGCCTGACCTCTGGTTGGAGGTAGCAGGTGAGTGGCAGGTGCCTGGA HG:+:3033653805:50 +TCCAGGCACCTGCCACTCACCTGCTACCTCCAACCAGAGGTCAGGCACCTTGTGCAGTGGCCACCAGAGGCCTGGGAGGGACTTTGATCTTGGAGGGGTCGTCCTGCTGTCAGGCCTTGCCTAGGGCTTCCGCACCCTCCCCCCAGCCCTTGGAGCCCTCCACCTTCCTCAGGTGGGGGACCTCCCCATGTCTCTCTCTTCAGGTGTGTAAAGCCGAGGACACCCTGGGGAGTTGGGAAGGTGGAGGGTCCCCCTTGCTGCCAGGTCCCCAGGCCCCTCCAACCTGCATGAGCTGCAGAAATCCTTCCAAGTGCACCAGTTCCCCAGCTCTAGTGTATTTGCCTGCCAGTTCCTTGTCTGCCTCCCCTGAGCTGCTCTGCCAGGTTCAGCAGCATCATGGACAATGCCCATGGGCTCTGTGGCTGGGGCCCCCTGGAGCTGGGGCTGGCCCTAGTCCTGATAGAGTCCTCCCACACCCGTGGACGGATCTGACTCCAATCATCTCCACCACTTCCATCTGGGGGTGCAGGAGGTGAGGGGAGGCCCAGGCCTTAGGCTACATTCTGTCCACCTTGTCCCATCCCCCAACGGACATGGCCCTTGGGGTGGGAGAGCTGATTCCTCTCATGAATTCCAAAAGACATCGTTCATCCAGGGCCCCAGTGTCTGGTGGGGTCCAGGGAGATCTGCCCCACCTTACCTAGGGGGCTCCATGTCTGGGTTGCAGCCCCTCCCAGGCTGTGGGGTCAGGGTCTGGCAAGCACAGGGAGCCCAGGGGAGGAGGGAGGGGCCTCTTCCCGGTTGGGGGCAGGTGTGGTTAGGGCCTTCTCTGTCTGGGCCCCTGTGGCGATCAAGCAGGTGGGTGTTCAAAGGTGAAGGAGACTTCTGTGGGGGGAAACGGGAGACACCTGTAGACACCAATGACAAAACAGCTCAATAAGGGGTGGTGGTGCCAGAAGCCCTTTGGTACTGTAGAGGCCCAGAGGAAACACTCAGGACT HG:+:2827182746:-1 +TCCAGGCACCTGCCACTCACCTGCTACCTCCAACCAGAGGTCAGGCACCTTGTGCAGTGGCCACCAGAGGCCTGGGAGGGACTTTGATCTTGGAGGGGTCGTCCTGCTGTCAGGCCTTGCCTAGGGCTTCCGCACCCTCCCCCCAGCCCTTGGAGCCCTCCACCTTCCTCAGGTGGGGGACCTCCCCATGTCTCTCTCTTCAGGTGTGTAAAGCCGAGGACACCCTGGGGAGTTGGGAAGGTGGAGGGTCCCCCTTGCTGCCAGGTCCCCAGGCCCCTCCAACCTGCATGAGCTGCAGAAATCCTTCCAAGTGCACCAGTTCCCCAGCTCTAGTGTATTTGCCTGCCAGTTCCTTGTCTGCCTCCCCTGAGCTGCTCTGCCAGGTTCAGCAGCATCATGGACAATGCCCATGGGCTCTGTGGCTGGGGCCCCCTGGAGCTGGGGCTGGCCCTAGTCCTGATAGAGTCCTCCCACACCCGTGGACGGATCTGACTCCAATCATCTCCACCACTTCCATCTGGGGGTGCAGGAGGTGAGGGGAGGCCCAGGCCTTAGGCTACATTCTGTCCACCTTGTCCCATCCCCCAACGGACATGGCCCTTGGGGTGGGAGAGCTGATTCCTCTCATGAATTCCAAAAGACATCGTTCATCCAGGGCCCCAGTGTCTGGTGGGGTCCAGGGAGATCTGCCCCACCTTACCTAGGGGGCTCCATGTCTGGGTTGCAGCCCCTCCCAGGCTGTGGGGTCAGGGTCTGGCAAGCACAGGGAGCCCAGGGGAGGAGGGAGGGGCCTCTTCCCGGTTGGGGGCAGGTGTGGTTAGGGCCTTCTCTGTCTGGGCCCCTGTGGCGATCAAGCAGGTGGGTGTTCAAAGGTGAAGGAGACTTCTGTGGGGGGAAACGGGAGACACCTGTAGACACCAATGACAAAACAGCTCAATAAGGGGTGGTGGTGCCAGAAGCCCTTTGGTACTGTAGAGGCCCAGAGGAAACACTCAGGACT HG:+:1676651699:-1 HG:+:3034241094:-1 +TCCAGGCACCTGCCACTCACCTGCTACCTCCAACCAGAGGTCAGGCACCTTGTGCAGTGGCCACCAGAGGCCTGGGAGGGACTTTGATCTTGGAGGGGTCGTCCTGCTGTCAGGCCTTGCCTAGGGCTTCCGCACCCTCCCCCCAGCCCTTGGAGCCCTCCACCTTCCTCAGGTGGGGGACCTCCCCATGTCTCTCTCTTCAGGTGTGTAAAGCCGAGGACACCCTGGGGAGTTGGGAAGGTGGAGGGTCCCCCTTGCTGCCAGGTCCCCAGGCCCCTCCAACCTGCATGAGCTGCAGAAATCCTTCCAAGTGCACCAGTTCCCCAGCTCTAGTGTATTTGCCTGCCAGTTCCTTGTCTGCCTCCCCTGAGCTGCTCTGCCAGGTTCAGCAGCATCATGGACAATGCCCATGGGCTCTGTGGCTGGGGCCCCCTGGAGCTGGGGCTGGCCCTAGTCCTGATAGAGTCCTCCCACACCCGTGGACGGATCTGACTCCAATCATCTCCACCACTTCCATCTGGGGGTGCAGGAGGTGAGGGGAGGCCCAGGCCTTAGGCTACATTCTGTCCACCTTGTCCCATCCCCCAACGGACATGGCCCTTGGGGTGGGAGAGCTGATTCCTCTCATGAATTCCAAAAGACATCGTTCATCCAGGGCCCCAGTGTCTGGTGGGGTCCAGGGAGATCTGCCCCACCTTACCTAGGGGGCTCCATGTCTGGGTTGCAGCCCCTCCCAGGCTGTGGGGTCAGGGTCTGGCAAGCACAGGGAGCCCAGGGGAGGAGGGAGGGGCCTCTTCCCGGTTGGGGGCAGGTGTGGTTAGGGCCTTCTCTGTCTGGGCCCCTGTGGCGATCAAGCAGGTGGGTGTTCAAAGGTGAAGGAGACTTCTGTGGGGGGAAACGGGAGACACCTGTAGACACCAATGACAAAACAGCTCAATAAGGGGTGGTGGTGCCAGAAGCCCTTTGGTACTGTAGAGGCCCAGAGGAAACACTCAGGACT HG:+:1094204293:-1 +TCCAGGCACCTGCCACTCACCTGCTACCTCCAACCAGAGGTCAGGCACCTTGTGCAGTGGCCACCAGAGGCCTGGGAGGGACTTTGATCTTGGAGGGGTCGTCCTGCTGTCAGGCCTTGCCTAGGGCTTCCGCACCCTCCCCCCAGCCCTTGGAGCCCTCCACCTTCCTCAGGTGGGGGACCTCCCCATGTCTCTCTCTTCAGGTGTGTAAAGCCGAGGACACCCTGGGGAGTTGGGAAGGTGGAGGGTCCCCCTTGCTGCCAGGTCCCCAGGCCCCTCCAACCTGCATGAGCTGCAGAAATCCTTCCAAGTGCACCAGTTCCCCAGCTCTAGTGTATTTGCCTGCCAGTTCCTTGTCTGCCTCCCCTGAGCTGCTCTGCCAGGTTCAGCAGCATCATGGACAATGCCCATGGGCTCTGTGGCTGGGGCCCCCTGGAGCTGGGGCTGGCCCTAGTCCTGATAGAGTCCTCCCACACCCGTGGACGGATCTGACTCCAATCATCTCCACCACTTCCATCTGGGGGTGCAGGAGGTGAGGGGAGGCCCAGGCCTTAGGCTACATTCTGTCCACCTTGTCCCATCCCCCAACGGACATGGCCCTTGGGGTGGGAGAGCTGATTCCTCTCATGAATTCCAAAAGACATCGTTCATCCAGGGCCCCAGTGTCTGGTGGGGTCCAGGGAGATCTGCCCCACCTTACCTAGGGGGCTCCATGTCTGGGTTGCAGCCCCTCCCAGGCTGTGGGGTCAGGGTCTGGCAAGCACAGGGAGCCCAGGGGAGGAGGGAGGGGCCTCTTCCCGGTTGGGGGCAGGTGTGGTTAGGGCCTTCTCTGTCTGGGCCCCTGTGGCGATCAAGCAGGTGGGTGTTCAAAGGTGAAGGAGACTTCTGTGGGGGGAAACGGGAGACACCTGTAGACACCAATGACAAAACAGCTCAATAAGGGGTGGTGGTGCCAGAAGCCCTTTGGTACTGTAGAGGCCCAGAGGAAACACTCAGGACT HG:+:1890648723:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:1298607823:-1 HG:+:1439875810:-1 HG:+:1440002561:-1 HG:+:1440016283:-1 HG:+:1440105446:-1 HG:+:1440174114:-1 HG:+:1440188814:-1 HG:+:1440214746:-1 HG:+:1722888500:-1 HG:+:1865979417:-1 HG:+:1865981650:-1 HG:+:2442355663:-1 HG:+:2939473241:-1 HG:+:2942952211:-1 HG:+:2942956221:-1 HG:+:2942959180:-1 HG:+:2942976858:-1 HG:+:2942978226:-1 HG:+:2942979422:-1 HG:+:2942979766:-1 HG:+:2943011797:-1 HG:+:2943013170:-1 HG:+:2943022473:-1 HG:+:2943044885:-1 HG:+:3056086606:-1 HG:+:3056113027:-1 HG:+:3056118320:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:2939181663:-1 HG:+:2939253217:-1 HG:+:2939257023:-1 HG:+:2939269103:-1 HG:+:2939272941:-1 HG:+:2939273978:-1 HG:+:2939287769:-1 HG:+:2939290021:-1 HG:+:2939304638:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:582825946:-1 HG:+:927870018:-1 HG:+:927880310:-1 HG:+:927908139:-1 HG:+:927909122:-1 HG:+:927912250:-1 HG:+:927921334:-1 HG:+:927921845:-1 HG:+:927945020:-1 HG:+:1291702586:-1 HG:+:1295688393:-1 HG:+:1295771879:-1 HG:+:1606139988:-1 HG:+:1606141355:-1 HG:+:1606142205:-1 HG:+:1866425340:-1 HG:+:1866639318:-1 HG:+:1866646833:-1 HG:+:1989178596:-1 HG:+:1989216527:-1 HG:+:1989223900:-1 HG:+:1989239387:-1 HG:+:2327298534:-1 HG:+:2327301531:-1 HG:+:2687409969:-1 HG:+:2795954076:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:1682325890:-1 HG:+:2229825781:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:506342507:-1 HG:+:573445726:-1 HG:+:573453915:-1 HG:+:1295521202:-1 HG:+:1436528118:-1 HG:+:1722874752:-1 HG:+:1866484657:-1 HG:+:1867271902:-1 HG:+:1870676486:-1 HG:+:1985553041:-1 HG:+:2327303588:-1 HG:+:2444820353:-1 HG:+:2444829521:-1 HG:+:2444985387:-1 HG:+:2521956820:-1 HG:+:2521959725:-1 HG:+:2683883305:-1 HG:+:2683900624:-1 HG:+:2687615677:-1 HG:+:2943019915:-1 HG:+:2943069799:-1 HG:+:3046366574:-1 HG:+:3056087298:-1 HG:+:3056089992:-1 HG:+:3056092589:-1 HG:+:3056111459:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:228128466:-1 HG:+:481477525:-1 HG:+:981371911:-1 HG:+:2877219865:-1 HG:+:2939199334:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:1309973488:-1 HG:+:1804131875:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:51672441:-1 HG:+:214411714:-1 HG:+:536065246:-1 HG:+:1069948660:-1 HG:+:1469238524:-1 HG:+:1780289248:-1 HG:+:2582199642:-1 HG:+:2769095203:-1 HG:+:2855501558:-1 HG:+:2968209030:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:978793302:-1 HG:+:1337025783:-1 HG:+:1393301396:-1 HG:+:3026496727:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:1838469422:-1 HG:+:2291760414:-1 HG:+:2683865449:-1 HG:+:2683901866:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:87119690:-1 HG:+:345905043:-1 HG:+:347453758:-1 HG:+:743357181:-1 HG:+:786269017:-1 HG:+:1247386240:-1 HG:+:2964756504:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:602547348:-1 HG:+:1322682214:-1 HG:+:1518068950:-1 HG:+:1794150887:-1 HG:+:2729414265:-1 HG:+:2943046177:-1 HG:+:3015980214:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:74901950:-1 HG:+:486349894:-1 HG:+:927900345:-1 HG:+:927945367:-1 HG:+:1200215727:-1 HG:+:1295691740:-1 HG:+:1295708029:-1 HG:+:1295713121:-1 HG:+:1295729594:-1 HG:+:1440076043:-1 HG:+:1866372780:-1 HG:+:1867203661:-1 HG:+:1870627970:-1 HG:+:1870790233:-1 HG:+:1870814682:-1 HG:+:1985492928:-1 HG:+:1985644944:-1 HG:+:1985646311:-1 HG:+:1985650110:-1 HG:+:1989238017:-1 HG:+:1989247030:-1 HG:+:2036710999:-1 HG:+:2221729683:-1 HG:+:2272371596:-1 HG:+:2442354643:-1 HG:+:2584277419:-1 HG:+:2654937977:-1 HG:+:2683849625:-1 HG:+:2683901875:-1 HG:+:2821530126:-1 HG:+:2942946731:-1 HG:+:2942953080:-1 HG:+:3056111287:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:505533013:-1 HG:+:643450403:-1 HG:+:893257168:-1 HG:+:1169727588:-1 HG:+:1449978729:-1 HG:+:1837284578:-1 HG:+:2514340665:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:165261770:-1 HG:+:823214948:-1 HG:+:1010307868:-1 HG:+:1028736976:-1 HG:+:1171593047:-1 HG:+:1440163576:-1 HG:+:1553236798:-1 HG:+:1948562138:-1 HG:+:2039126063:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:1497656367:-1 HG:+:2939165245:-1 HG:+:2939177021:-1 HG:+:2939186510:-1 HG:+:2939187116:-1 HG:+:2939191603:-1 HG:+:2939251437:-1 HG:+:2939260991:-1 HG:+:2939261994:-1 HG:+:2939268713:-1 HG:+:2939284837:-1 HG:+:2939300980:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:898701768:-1 HG:+:1228299408:-1 HG:+:1257822592:-1 HG:+:2303495388:-1 HG:+:2385757458:-1 HG:+:2570301140:-1 HG:+:2798451740:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:152700340:-1 HG:+:1445428870:-1 HG:+:2939138347:-1 HG:+:2939247082:-1 HG:+:2939295947:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:501311169:-1 HG:+:782706798:-1 HG:+:1253469803:-1 HG:+:1669700786:-1 HG:+:1997910004:-1 HG:+:2053539583:-1 HG:+:2265586451:-1 HG:+:2416947569:-1 HG:+:2828052294:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:18225126:-1 HG:+:274866005:-1 HG:+:433112816:-1 HG:+:434359218:-1 HG:+:477897431:-1 HG:+:491615443:-1 HG:+:512342128:-1 HG:+:764892034:-1 HG:+:777560565:-1 HG:+:818485029:-1 HG:+:826142213:-1 HG:+:866516413:-1 HG:+:890016093:-1 HG:+:901313240:-1 HG:+:910516054:-1 HG:+:927001071:-1 HG:+:993015058:-1 HG:+:999838893:-1 HG:+:1193407805:-1 HG:+:1254195784:-1 HG:+:1261681869:-1 HG:+:1287959008:-1 HG:+:1462925204:-1 HG:+:1535456343:-1 HG:+:1552790138:-1 HG:+:1705495189:-1 HG:+:1717991338:-1 HG:+:1808088707:-1 HG:+:1913217225:-1 HG:+:2157969680:-1 HG:+:2658014263:-1 HG:+:2760022628:-1 HG:+:2802398572:-1 HG:+:2818094700:-1 HG:+:2916647441:-1 HG:+:2965516958:-1 HG:+:2970799235:-1 HG:+:2970938895:-1 HG:+:3040260655:-1 HG:+:3040403442:-1 HG:+:3049821581:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:58375887:-1 HG:+:430419151:-1 HG:+:465963106:-1 HG:+:618927903:-1 HG:+:891533220:-1 HG:+:912148862:-1 HG:+:1189354979:-1 HG:+:1196103522:-1 HG:+:1321968377:-1 HG:+:1419417967:-1 HG:+:1436526032:-1 HG:+:1569325568:-1 HG:+:1633303388:-1 HG:+:1858331641:-1 HG:+:2382339576:-1 HG:+:2473867948:-1 HG:+:3007647755:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:76854661:-1 HG:+:96051188:-1 HG:+:315733626:-1 HG:+:418654859:-1 HG:+:462419843:-1 HG:+:473492365:-1 HG:+:702043958:-1 HG:+:1020209266:-1 HG:+:1020265797:-1 HG:+:1047151219:-1 HG:+:1080556436:-1 HG:+:1095997722:-1 HG:+:1134324808:-1 HG:+:1166573686:-1 HG:+:1450373643:-1 HG:+:1688326344:-1 HG:+:1770663460:-1 HG:+:2061659166:-1 HG:+:2134173272:-1 HG:+:2146506658:-1 HG:+:2667325836:-1 HG:+:2683865450:-1 HG:+:2683901867:-1 HG:+:2732601169:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:42989349:-1 HG:+:61742568:-1 HG:+:196967362:-1 HG:+:421814278:-1 HG:+:440540348:-1 HG:+:569170914:-1 HG:+:591532304:-1 HG:+:966900087:-1 HG:+:1178891739:-1 HG:+:1486974641:-1 HG:+:1488150538:-1 HG:+:1694185470:-1 HG:+:1865616416:-1 HG:+:1924327976:-1 HG:+:2157272644:-1 HG:+:2157274277:-1 HG:+:2191416003:-1 HG:+:2246852071:-1 HG:+:2259396288:-1 HG:+:2516499599:-1 HG:+:2771919559:-1 HG:+:2902020336:-1 HG:+:2931228192:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:1436531032:-1 HG:+:1440025408:-1 HG:+:1440032044:-1 HG:+:1440068163:-1 HG:+:1440174458:-1 HG:+:1440184106:-1 HG:+:1440211656:-1 HG:+:1722883621:-1 HG:+:1722894309:-1 HG:+:1948567281:-1 HG:+:1989244978:-1 HG:+:2683888157:-1 HG:+:2942957984:-1 HG:+:2942982035:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAGTTTTTATCTTTGAATATGCCCATTTTTACAGTGTGCTACAATGGGCTTGGCAAATGTTCCTTCACAGATTCAGCAAAAGAATGTTTTGCAACTTAGCAGATTCAAAAAGAAGTTTTAAGCCTTTGAGCTGATTCCACACTTAACAAGCAGTTTCACAGATAGCTTCTTGATAGTTTTTATGGGGGGATATCCTGTTTTCA HG:+:1440171054:-1 HG:+:1865979939:-1 HG:+:1988847086:-1 HG:+:2521950835:-1 HG:+:2748086960:-1 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:228728358:-1 HG:+:228737561:-1 HG:+:228740114:-1 HG:+:2444735131:-1 HG:+:2444739233:-1 HG:+:2687568598:45 HG:+:2687701129:-1 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:2687568600:45 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:2687568601:45 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:2687568590:45 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:2687568608:45 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:2687568587:45 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:2687568592:45 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:2687568603:45 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:1708418436:-1 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:2687483496:-1 HG:+:2687568610:45 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:2687568588:45 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:228717812:-1 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:2687568589:45 HG:+:2687687462:-1 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:2687568591:45 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:2687568593:45 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:2687568596:45 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:23198378:-1 +TGAAAACAGGATATCCCCCCATAAAAACTATCAAGAAGCTATCTGTGAAACTGCTTGTTAAGTGTGGAATCAGCTCAAAGGCTTAAAACTTCTTTTTGAATCTGCTAAGTTGCAAAACATTCTTTTGCTGAATCTGTGAAGGAACATTTGCCAAGCCCATTGTAGCACACTGTAAAAATGGGCATATTCAAAGATAAAAACTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC HG:+:11894916:-1 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTACAATAAATTGATGGGTAAATTAAATTATTAACAAATTATGAATAAACTTTTTAGAATGGATATGTTCTATAGCTTGATTGTGCTGATAGTAAAGAGATACCGGTATTTATCAAACTCACTTAATTGGACACTTAAAATGAATGTATCTTATCAGATGGTAAATTACACCTTAAGTAAAGTTGATTTTAAAAAACTATTATTGCATATACATTAGAAGCATTAGATAAGAACACTTTACATACAGTACCTACAAAATTCCTACAAGTTTTCAACAGTGATACTGCTTCGTTATCTTTGTCACACAATGGCATATATCGCAATAATATTCTCCAAAACAATGTGCTTACATTCTTCACAAGTCTGTTTGGGCCTAAAAAAGAAACCATAATTAAAAACTGCA HG:+:379226184:-1 HG:+:462630725:-1 HG:+:766905404:49 HG:+:1096768863:-1 HG:+:1434875693:-1 HG:+:1912692644:-1 HG:+:3062441880:-1 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTACAATAAATTGATGGGTAAATTAAATTATTAACAAATTATGAATAAACTTTTTAGAATGGATATGTTCTATAGCTTGATTGTGCTGATAGTAAAGAGATACCGGTATTTATCAAACTCACTTAATTGGACACTTAAAATGAATGTATCTTATCAGATGGTAAATTACACCTTAAGTAAAGTTGATTTTAAAAAACTATTATTGCATATACATTAGAAGCATTAGATAAGAACACTTTACATACAGTACCTACAAAATTCCTACAAGTTTTCAACAGTGATACTGCTTCGTTATCTTTGTCACACAATGGCATATATCGCAATAATATTCTCCAAAACAATGTGCTTACATTCTTCACAAGTCTGTTTGGGCCTAAAAAAGAAACCATAATTAAAAACTGCA HG:+:766905409:49 HG:+:1952785137:-1 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTACAATAAATTGATGGGTAAATTAAATTATTAACAAATTATGAATAAACTTTTTAGAATGGATATGTTCTATAGCTTGATTGTGCTGATAGTAAAGAGATACCGGTATTTATCAAACTCACTTAATTGGACACTTAAAATGAATGTATCTTATCAGATGGTAAATTACACCTTAAGTAAAGTTGATTTTAAAAAACTATTATTGCATATACATTAGAAGCATTAGATAAGAACACTTTACATACAGTACCTACAAAATTCCTACAAGTTTTCAACAGTGATACTGCTTCGTTATCTTTGTCACACAATGGCATATATCGCAATAATATTCTCCAAAACAATGTGCTTACATTCTTCACAAGTCTGTTTGGGCCTAAAAAAGAAACCATAATTAAAAACTGCA HG:+:766905407:49 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTACAATAAATTGATGGGTAAATTAAATTATTAACAAATTATGAATAAACTTTTTAGAATGGATATGTTCTATAGCTTGATTGTGCTGATAGTAAAGAGATACCGGTATTTATCAAACTCACTTAATTGGACACTTAAAATGAATGTATCTTATCAGATGGTAAATTACACCTTAAGTAAAGTTGATTTTAAAAAACTATTATTGCATATACATTAGAAGCATTAGATAAGAACACTTTACATACAGTACCTACAAAATTCCTACAAGTTTTCAACAGTGATACTGCTTCGTTATCTTTGTCACACAATGGCATATATCGCAATAATATTCTCCAAAACAATGTGCTTACATTCTTCACAAGTCTGTTTGGGCCTAAAAAAGAAACCATAATTAAAAACTGCA HG:+:766905401:49 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTACAATAAATTGATGGGTAAATTAAATTATTAACAAATTATGAATAAACTTTTTAGAATGGATATGTTCTATAGCTTGATTGTGCTGATAGTAAAGAGATACCGGTATTTATCAAACTCACTTAATTGGACACTTAAAATGAATGTATCTTATCAGATGGTAAATTACACCTTAAGTAAAGTTGATTTTAAAAAACTATTATTGCATATACATTAGAAGCATTAGATAAGAACACTTTACATACAGTACCTACAAAATTCCTACAAGTTTTCAACAGTGATACTGCTTCGTTATCTTTGTCACACAATGGCATATATCGCAATAATATTCTCCAAAACAATGTGCTTACATTCTTCACAAGTCTGTTTGGGCCTAAAAAAGAAACCATAATTAAAAACTGCA HG:+:766905408:49 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTACAATAAATTGATGGGTAAATTAAATTATTAACAAATTATGAATAAACTTTTTAGAATGGATATGTTCTATAGCTTGATTGTGCTGATAGTAAAGAGATACCGGTATTTATCAAACTCACTTAATTGGACACTTAAAATGAATGTATCTTATCAGATGGTAAATTACACCTTAAGTAAAGTTGATTTTAAAAAACTATTATTGCATATACATTAGAAGCATTAGATAAGAACACTTTACATACAGTACCTACAAAATTCCTACAAGTTTTCAACAGTGATACTGCTTCGTTATCTTTGTCACACAATGGCATATATCGCAATAATATTCTCCAAAACAATGTGCTTACATTCTTCACAAGTCTGTTTGGGCCTAAAAAAGAAACCATAATTAAAAACTGCA HG:+:766905403:49 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTACAATAAATTGATGGGTAAATTAAATTATTAACAAATTATGAATAAACTTTTTAGAATGGATATGTTCTATAGCTTGATTGTGCTGATAGTAAAGAGATACCGGTATTTATCAAACTCACTTAATTGGACACTTAAAATGAATGTATCTTATCAGATGGTAAATTACACCTTAAGTAAAGTTGATTTTAAAAAACTATTATTGCATATACATTAGAAGCATTAGATAAGAACACTTTACATACAGTACCTACAAAATTCCTACAAGTTTTCAACAGTGATACTGCTTCGTTATCTTTGTCACACAATGGCATATATCGCAATAATATTCTCCAAAACAATGTGCTTACATTCTTCACAAGTCTGTTTGGGCCTAAAAAAGAAACCATAATTAAAAACTGCA HG:+:1481694229:-1 HG:+:2824456196:-1 +TGCAGTTTTTAATTATGGTTTCTTTTTTAGGCCCAAACAGACTTGTGAAGAATGTAAGCACATTGTTTTGGAGAATATTATTGCGATATATGCCATTGTGTGACAAAGATAACGAAGCAGTATCACTGTTGAAAACTTGTAGGAATTTTGTAGGTACTGTATGTAAAGTGTTCTTATCTAATGCTTCTAATGTATATGCAATAATAGTTTTTTAAAATCAACTTTACTTAAGGTGTAATTTACCATCTGATAAGATACATTCATTTTAAGTGTCCAATTAAGTGAGTTTGATAAATACCGGTATCTCTTTACTATCAGCACAATCAAGCTATAGAACATATCCATTCTAAAAAGTTTATTCATAATTTGTTAATAATTTAATTTACCCATCAATTTATTGTAATAACTATTTAGAATTTTACCTTTGGATTATAAAATATGTTTTATATAAAGTGTTTTATGGGCAACTTGAGGTAGAGAATTGGGATAAATTTTTCTTTGTAAAAATTAGTATTTAAAAATTATCTAAGAAATACAGGTGATTTTATAAAAATTGGAAAAAACAGAAAGTAGAATAATAAAAATAAAATAACCAGAGCCCTAACCACAGACAAGCTACTGTTTGACATGTCGGTGTATAAGGAATATTTTCTTTCTTAAAAATCTCGAGTTATTTTAGATGTATATTAAAGACATGTATGTAAAGTGTGTCTAAAGTACAGTAACAGTGAATAAGCCACGAGTTTAGGAAGGAATGTTACAATACTTGTCAAAGCCAAGTGTTCCGTGTTCAGTCCTTTCTTCTTGTCCTGCTTGGAGGTAATCACTGTCTTGAATATTTTAATCACTTTCTTGCTTTTTTTTGTTTTTTTGTTTTTTTAAAATATAGTTTGTTTTTAAGGAAGGATAACCAACCTACCAAAAGATACAGAAATTATAAGCAAATGATTTTATGATTTAACAAATGACAATGCCTTTGTAAACCACTACCCCAGATCAA HG:+:561958622:-1 HG:+:1864499571:-1 +TGCAGTTTTTAATTATGGTTTCTTTTTTAGGCCCAAACAGACTTGTGAAGAATGTAAGCACATTGTTTTGGAGAATATTATTGCGATATATGCCATTGTGTGACAAAGATAACGAAGCAGTATCACTGTTGAAAACTTGTAGGAATTTTGTAGGTACTGTATGTAAAGTGTTCTTATCTAATGCTTCTAATGTATATGCAATAATAGTTTTTTAAAATCAACTTTACTTAAGGTGTAATTTACCATCTGATAAGATACATTCATTTTAAGTGTCCAATTAAGTGAGTTTGATAAATACCGGTATCTCTTTACTATCAGCACAATCAAGCTATAGAACATATCCATTCTAAAAAGTTTATTCATAATTTGTTAATAATTTAATTTACCCATCAATTTATTGTAATAACTATTTAGAATTTTACCTTTGGATTATAAAATATGTTTTATATAAAGTGTTTTATGGGCAACTTGAGGTAGAGAATTGGGATAAATTTTTCTTTGTAAAAATTAGTATTTAAAAATTATCTAAGAAATACAGGTGATTTTATAAAAATTGGAAAAAACAGAAAGTAGAATAATAAAAATAAAATAACCAGAGCCCTAACCACAGACAAGCTACTGTTTGACATGTCGGTGTATAAGGAATATTTTCTTTCTTAAAAATCTCGAGTTATTTTAGATGTATATTAAAGACATGTATGTAAAGTGTGTCTAAAGTACAGTAACAGTGAATAAGCCACGAGTTTAGGAAGGAATGTTACAATACTTGTCAAAGCCAAGTGTTCCGTGTTCAGTCCTTTCTTCTTGTCCTGCTTGGAGGTAATCACTGTCTTGAATATTTTAATCACTTTCTTGCTTTTTTTTGTTTTTTTGTTTTTTTAAAATATAGTTTGTTTTTAAGGAAGGATAACCAACCTACCAAAAGATACAGAAATTATAAGCAAATGATTTTATGATTTAACAAATGACAATGCCTTTGTAAACCACTACCCCAGATCAA HG:+:2124269881:-1 +TGCAGTTTTTAATTATGGTTTCTTTTTTAGGCCCAAACAGACTTGTGAAGAATGTAAGCACATTGTTTTGGAGAATATTATTGCGATATATGCCATTGTGTGACAAAGATAACGAAGCAGTATCACTGTTGAAAACTTGTAGGAATTTTGTAGGTACTGTATGTAAAGTGTTCTTATCTAATGCTTCTAATGTATATGCAATAATAGTTTTTTAAAATCAACTTTACTTAAGGTGTAATTTACCATCTGATAAGATACATTCATTTTAAGTGTCCAATTAAGTGAGTTTGATAAATACCGGTATCTCTTTACTATCAGCACAATCAAGCTATAGAACATATCCATTCTAAAAAGTTTATTCATAATTTGTTAATAATTTAATTTACCCATCAATTTATTGTAATAACTATTTAGAATTTTACCTTTGGATTATAAAATATGTTTTATATAAAGTGTTTTATGGGCAACTTGAGGTAGAGAATTGGGATAAATTTTTCTTTGTAAAAATTAGTATTTAAAAATTATCTAAGAAATACAGGTGATTTTATAAAAATTGGAAAAAACAGAAAGTAGAATAATAAAAATAAAATAACCAGAGCCCTAACCACAGACAAGCTACTGTTTGACATGTCGGTGTATAAGGAATATTTTCTTTCTTAAAAATCTCGAGTTATTTTAGATGTATATTAAAGACATGTATGTAAAGTGTGTCTAAAGTACAGTAACAGTGAATAAGCCACGAGTTTAGGAAGGAATGTTACAATACTTGTCAAAGCCAAGTGTTCCGTGTTCAGTCCTTTCTTCTTGTCCTGCTTGGAGGTAATCACTGTCTTGAATATTTTAATCACTTTCTTGCTTTTTTTTGTTTTTTTGTTTTTTTAAAATATAGTTTGTTTTTAAGGAAGGATAACCAACCTACCAAAAGATACAGAAATTATAAGCAAATGATTTTATGATTTAACAAATGACAATGCCTTTGTAAACCACTACCCCAGATCAA HG:+:1805463043:-1 +TGCAGTTTTTAATTATGGTTTCTTTTTTAGGCCCAAACAGACTTGTGAAGAATGTAAGCACATTGTTTTGGAGAATATTATTGCGATATATGCCATTGTGTGACAAAGATAACGAAGCAGTATCACTGTTGAAAACTTGTAGGAATTTTGTAGGTACTGTATGTAAAGTGTTCTTATCTAATGCTTCTAATGTATATGCAATAATAGTTTTTTAAAATCAACTTTACTTAAGGTGTAATTTACCATCTGATAAGATACATTCATTTTAAGTGTCCAATTAAGTGAGTTTGATAAATACCGGTATCTCTTTACTATCAGCACAATCAAGCTATAGAACATATCCATTCTAAAAAGTTTATTCATAATTTGTTAATAATTTAATTTACCCATCAATTTATTGTAATAACTATTTAGAATTTTACCTTTGGATTATAAAATATGTTTTATATAAAGTGTTTTATGGGCAACTTGAGGTAGAGAATTGGGATAAATTTTTCTTTGTAAAAATTAGTATTTAAAAATTATCTAAGAAATACAGGTGATTTTATAAAAATTGGAAAAAACAGAAAGTAGAATAATAAAAATAAAATAACCAGAGCCCTAACCACAGACAAGCTACTGTTTGACATGTCGGTGTATAAGGAATATTTTCTTTCTTAAAAATCTCGAGTTATTTTAGATGTATATTAAAGACATGTATGTAAAGTGTGTCTAAAGTACAGTAACAGTGAATAAGCCACGAGTTTAGGAAGGAATGTTACAATACTTGTCAAAGCCAAGTGTTCCGTGTTCAGTCCTTTCTTCTTGTCCTGCTTGGAGGTAATCACTGTCTTGAATATTTTAATCACTTTCTTGCTTTTTTTTGTTTTTTTGTTTTTTTAAAATATAGTTTGTTTTTAAGGAAGGATAACCAACCTACCAAAAGATACAGAAATTATAAGCAAATGATTTTATGATTTAACAAATGACAATGCCTTTGTAAACCACTACCCCAGATCAA HG:+:2773917690:-1 HG:+:2906443856:-1 +TGCAGTTTTTAATTATGGTTTCTTTTTTAGGCCCAAACAGACTTGTGAAGAATGTAAGCACATTGTTTTGGAGAATATTATTGCGATATATGCCATTGTGTGACAAAGATAACGAAGCAGTATCACTGTTGAAAACTTGTAGGAATTTTGTAGGTACTGTATGTAAAGTGTTCTTATCTAATGCTTCTAATGTATATGCAATAATAGTTTTTTAAAATCAACTTTACTTAAGGTGTAATTTACCATCTGATAAGATACATTCATTTTAAGTGTCCAATTAAGTGAGTTTGATAAATACCGGTATCTCTTTACTATCAGCACAATCAAGCTATAGAACATATCCATTCTAAAAAGTTTATTCATAATTTGTTAATAATTTAATTTACCCATCAATTTATTGTAATAACTATTTAGAATTTTACCTTTGGATTATAAAATATGTTTTATATAAAGTGTTTTATGGGCAACTTGAGGTAGAGAATTGGGATAAATTTTTCTTTGTAAAAATTAGTATTTAAAAATTATCTAAGAAATACAGGTGATTTTATAAAAATTGGAAAAAACAGAAAGTAGAATAATAAAAATAAAATAACCAGAGCCCTAACCACAGACAAGCTACTGTTTGACATGTCGGTGTATAAGGAATATTTTCTTTCTTAAAAATCTCGAGTTATTTTAGATGTATATTAAAGACATGTATGTAAAGTGTGTCTAAAGTACAGTAACAGTGAATAAGCCACGAGTTTAGGAAGGAATGTTACAATACTTGTCAAAGCCAAGTGTTCCGTGTTCAGTCCTTTCTTCTTGTCCTGCTTGGAGGTAATCACTGTCTTGAATATTTTAATCACTTTCTTGCTTTTTTTTGTTTTTTTGTTTTTTTAAAATATAGTTTGTTTTTAAGGAAGGATAACCAACCTACCAAAAGATACAGAAATTATAAGCAAATGATTTTATGATTTAACAAATGACAATGCCTTTGTAAACCACTACCCCAGATCAA HG:+:680734413:-1 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGGCGTGAGTCCACCACGCCTGGGCTACATTTCGAATTTTCAACGATGGGGAGACCAGATTGGTTGAAGAAGAGACAATAAAAAATGTGGGCAGGTTGGGTGCAGTAGCTCACGCCTGTAATCCAGCACTTTGGGAGGTTGACTCGGGCAGATCAACTGAGGTTGGGAGTTGAGACCAGCCTGACCAACGTGGGGGAAACCCC HG:+:548925523:-1 HG:+:850533655:-1 HG:+:1340242438:-1 HG:+:1393453665:-1 HG:+:2668073383:46 HG:+:2673264507:-1 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGGCGTGAGTCCACCACGCCTGGGCTACATTTCGAATTTTCAACGATGGGGAGACCAGATTGGTTGAAGAAGAGACAATAAAAAATGTGGGCAGGTTGGGTGCAGTAGCTCACGCCTGTAATCCAGCACTTTGGGAGGTTGACTCGGGCAGATCAACTGAGGTTGGGAGTTGAGACCAGCCTGACCAACGTGGGGGAAACCCC HG:+:1344178871:-1 HG:+:2668073386:46 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGGCGTGAGTCCACCACGCCTGGGCTACATTTCGAATTTTCAACGATGGGGAGACCAGATTGGTTGAAGAAGAGACAATAAAAAATGTGGGCAGGTTGGGTGCAGTAGCTCACGCCTGTAATCCAGCACTTTGGGAGGTTGACTCGGGCAGATCAACTGAGGTTGGGAGTTGAGACCAGCCTGACCAACGTGGGGGAAACCCC HG:+:1497619676:-1 HG:+:2676923724:-1 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGGCGTGAGTCCACCACGCCTGGGCTACATTTCGAATTTTCAACGATGGGGAGACCAGATTGGTTGAAGAAGAGACAATAAAAAATGTGGGCAGGTTGGGTGCAGTAGCTCACGCCTGTAATCCAGCACTTTGGGAGGTTGACTCGGGCAGATCAACTGAGGTTGGGAGTTGAGACCAGCCTGACCAACGTGGGGGAAACCCC HG:+:569447259:-1 HG:+:873833098:-1 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGGCGTGAGTCCACCACGCCTGGGCTACATTTCGAATTTTCAACGATGGGGAGACCAGATTGGTTGAAGAAGAGACAATAAAAAATGTGGGCAGGTTGGGTGCAGTAGCTCACGCCTGTAATCCAGCACTTTGGGAGGTTGACTCGGGCAGATCAACTGAGGTTGGGAGTTGAGACCAGCCTGACCAACGTGGGGGAAACCCC HG:+:2668073378:46 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGGCGTGAGTCCACCACGCCTGGGCTACATTTCGAATTTTCAACGATGGGGAGACCAGATTGGTTGAAGAAGAGACAATAAAAAATGTGGGCAGGTTGGGTGCAGTAGCTCACGCCTGTAATCCAGCACTTTGGGAGGTTGACTCGGGCAGATCAACTGAGGTTGGGAGTTGAGACCAGCCTGACCAACGTGGGGGAAACCCC HG:+:2668073377:46 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGGCGTGAGTCCACCACGCCTGGGCTACATTTCGAATTTTCAACGATGGGGAGACCAGATTGGTTGAAGAAGAGACAATAAAAAATGTGGGCAGGTTGGGTGCAGTAGCTCACGCCTGTAATCCAGCACTTTGGGAGGTTGACTCGGGCAGATCAACTGAGGTTGGGAGTTGAGACCAGCCTGACCAACGTGGGGGAAACCCC HG:+:605374493:-1 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGGCGTGAGTCCACCACGCCTGGGCTACATTTCGAATTTTCAACGATGGGGAGACCAGATTGGTTGAAGAAGAGACAATAAAAAATGTGGGCAGGTTGGGTGCAGTAGCTCACGCCTGTAATCCAGCACTTTGGGAGGTTGACTCGGGCAGATCAACTGAGGTTGGGAGTTGAGACCAGCCTGACCAACGTGGGGGAAACCCC HG:+:2668073397:46 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGGCGTGAGTCCACCACGCCTGGGCTACATTTCGAATTTTCAACGATGGGGAGACCAGATTGGTTGAAGAAGAGACAATAAAAAATGTGGGCAGGTTGGGTGCAGTAGCTCACGCCTGTAATCCAGCACTTTGGGAGGTTGACTCGGGCAGATCAACTGAGGTTGGGAGTTGAGACCAGCCTGACCAACGTGGGGGAAACCCC HG:+:2668073390:46 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGGCGTGAGTCCACCACGCCTGGGCTACATTTCGAATTTTCAACGATGGGGAGACCAGATTGGTTGAAGAAGAGACAATAAAAAATGTGGGCAGGTTGGGTGCAGTAGCTCACGCCTGTAATCCAGCACTTTGGGAGGTTGACTCGGGCAGATCAACTGAGGTTGGGAGTTGAGACCAGCCTGACCAACGTGGGGGAAACCCC HG:+:2668073392:46 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGGCGTGAGTCCACCACGCCTGGGCTACATTTCGAATTTTCAACGATGGGGAGACCAGATTGGTTGAAGAAGAGACAATAAAAAATGTGGGCAGGTTGGGTGCAGTAGCTCACGCCTGTAATCCAGCACTTTGGGAGGTTGACTCGGGCAGATCAACTGAGGTTGGGAGTTGAGACCAGCCTGACCAACGTGGGGGAAACCCC HG:+:2295113715:-1 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGGCGTGAGTCCACCACGCCTGGGCTACATTTCGAATTTTCAACGATGGGGAGACCAGATTGGTTGAAGAAGAGACAATAAAAAATGTGGGCAGGTTGGGTGCAGTAGCTCACGCCTGTAATCCAGCACTTTGGGAGGTTGACTCGGGCAGATCAACTGAGGTTGGGAGTTGAGACCAGCCTGACCAACGTGGGGGAAACCCC HG:+:2668073391:46 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGGCGTGAGTCCACCACGCCTGGGCTACATTTCGAATTTTCAACGATGGGGAGACCAGATTGGTTGAAGAAGAGACAATAAAAAATGTGGGCAGGTTGGGTGCAGTAGCTCACGCCTGTAATCCAGCACTTTGGGAGGTTGACTCGGGCAGATCAACTGAGGTTGGGAGTTGAGACCAGCCTGACCAACGTGGGGGAAACCCC HG:+:2668073394:46 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGGCGTGAGTCCACCACGCCTGGGCTACATTTCGAATTTTCAACGATGGGGAGACCAGATTGGTTGAAGAAGAGACAATAAAAAATGTGGGCAGGTTGGGTGCAGTAGCTCACGCCTGTAATCCAGCACTTTGGGAGGTTGACTCGGGCAGATCAACTGAGGTTGGGAGTTGAGACCAGCCTGACCAACGTGGGGGAAACCCC HG:+:738344728:-1 +GGGGTTTCCCCCACGTTGGTCAGGCTGGTCTCAACTCCCAACCTCAGTTGATCTGCCCGAGTCAACCTCCCAAAGTGCTGGATTACAGGCGTGAGCTACTGCACCCAACCTGCCCACATTTTTTATTGTCTCTTCTTCAACCAATCTGGTCTCCCCATCGTTGAAAATTCGAAATGTAGCCCAGGCGTGGTGGACTCACGCCTGTACTCCCAGGCACTTTGGGAGGCTGAGGTGGGTGGATCACTTGAACTTAGAGGGTCAGGAGTTACAGACCAGCCTGGCCAACATGGTGAAATCCCTGTCCTCTGGCCGGACACAGTGGCTCATGCCTGTTATCCAGCCACAGTGGGAGCTGAGGTGGGCGGATCACCTGTAGGTTGGAGGTTCGAGATGAGCGTGTCCAACGTGGTGAAATCCTGTCTCTACTAAAAACACAAAAATCAGCCTGGCTTGGTGGCAGGGCGCCTGTATTTCCACGTTACTTGGGAGGCTGAGGCAGAGAATCCTTGAACCCGGGAGGCGGGAGGTTGCAGTGAGCCGAAATCATACCACTGCACTCCAGCCTGGGTGACAAGAGCGAGACTCTGTCTCAAAAACAACAACAAAAAAAAAAACAGGAAACACGGGCTCCCCTGACCCCACTTCTCCCCCACAGCCTCTCTCCCTCTTCCCCTTCGTCAGCCAGATCCTCATTCCTGTCTATTACTCCTAGCCTCCCAACTCCTGCTTCTGACCCTGGGGCCCCTCTTAGTCTCCAGTGAGCTCAGACGCTCTTCAGGGTTGAGTCGATGGCTCCTAACCCACCCTCGTCCCATCTGGGCCTCCCCCTGCCTGGTCCGGTTTTGCCTCTGACTTCCCCTGGCAGTTCCTTACTCAGCCAGTCTGTGGTGGGTGTCAACTTCAACCCTCCATGCCACGTGCTCCCCCAGGATTTCTGTCATCTCCTGACGCACCCCAGGGGACTCTCAGTGCATCCCAGTCAGCACCTCCTTCTTTTTTT HG:+:2647527260:-1 +GGGGTTTCCCCCACGTTGGTCAGGCTGGTCTCAACTCCCAACCTCAGTTGATCTGCCCGAGTCAACCTCCCAAAGTGCTGGATTACAGGCGTGAGCTACTGCACCCAACCTGCCCACATTTTTTATTGTCTCTTCTTCAACCAATCTGGTCTCCCCATCGTTGAAAATTCGAAATGTAGCCCAGGCGTGGTGGACTCACGCCTGTACTCCCAGGCACTTTGGGAGGCTGAGGTGGGTGGATCACTTGAACTTAGAGGGTCAGGAGTTACAGACCAGCCTGGCCAACATGGTGAAATCCCTGTCCTCTGGCCGGACACAGTGGCTCATGCCTGTTATCCAGCCACAGTGGGAGCTGAGGTGGGCGGATCACCTGTAGGTTGGAGGTTCGAGATGAGCGTGTCCAACGTGGTGAAATCCTGTCTCTACTAAAAACACAAAAATCAGCCTGGCTTGGTGGCAGGGCGCCTGTATTTCCACGTTACTTGGGAGGCTGAGGCAGAGAATCCTTGAACCCGGGAGGCGGGAGGTTGCAGTGAGCCGAAATCATACCACTGCACTCCAGCCTGGGTGACAAGAGCGAGACTCTGTCTCAAAAACAACAACAAAAAAAAAAACAGGAAACACGGGCTCCCCTGACCCCACTTCTCCCCCACAGCCTCTCTCCCTCTTCCCCTTCGTCAGCCAGATCCTCATTCCTGTCTATTACTCCTAGCCTCCCAACTCCTGCTTCTGACCCTGGGGCCCCTCTTAGTCTCCAGTGAGCTCAGACGCTCTTCAGGGTTGAGTCGATGGCTCCTAACCCACCCTCGTCCCATCTGGGCCTCCCCCTGCCTGGTCCGGTTTTGCCTCTGACTTCCCCTGGCAGTTCCTTACTCAGCCAGTCTGTGGTGGGTGTCAACTTCAACCCTCCATGCCACGTGCTCCCCCAGGATTTCTGTCATCTCCTGACGCACCCCAGGGGACTCTCAGTGCATCCCAGTCAGCACCTCCTTCTTTTTTT HG:+:2872582064:-1 +GGGGTTTCCCCCACGTTGGTCAGGCTGGTCTCAACTCCCAACCTCAGTTGATCTGCCCGAGTCAACCTCCCAAAGTGCTGGATTACAGGCGTGAGCTACTGCACCCAACCTGCCCACATTTTTTATTGTCTCTTCTTCAACCAATCTGGTCTCCCCATCGTTGAAAATTCGAAATGTAGCCCAGGCGTGGTGGACTCACGCCTGTACTCCCAGGCACTTTGGGAGGCTGAGGTGGGTGGATCACTTGAACTTAGAGGGTCAGGAGTTACAGACCAGCCTGGCCAACATGGTGAAATCCCTGTCCTCTGGCCGGACACAGTGGCTCATGCCTGTTATCCAGCCACAGTGGGAGCTGAGGTGGGCGGATCACCTGTAGGTTGGAGGTTCGAGATGAGCGTGTCCAACGTGGTGAAATCCTGTCTCTACTAAAAACACAAAAATCAGCCTGGCTTGGTGGCAGGGCGCCTGTATTTCCACGTTACTTGGGAGGCTGAGGCAGAGAATCCTTGAACCCGGGAGGCGGGAGGTTGCAGTGAGCCGAAATCATACCACTGCACTCCAGCCTGGGTGACAAGAGCGAGACTCTGTCTCAAAAACAACAACAAAAAAAAAAACAGGAAACACGGGCTCCCCTGACCCCACTTCTCCCCCACAGCCTCTCTCCCTCTTCCCCTTCGTCAGCCAGATCCTCATTCCTGTCTATTACTCCTAGCCTCCCAACTCCTGCTTCTGACCCTGGGGCCCCTCTTAGTCTCCAGTGAGCTCAGACGCTCTTCAGGGTTGAGTCGATGGCTCCTAACCCACCCTCGTCCCATCTGGGCCTCCCCCTGCCTGGTCCGGTTTTGCCTCTGACTTCCCCTGGCAGTTCCTTACTCAGCCAGTCTGTGGTGGGTGTCAACTTCAACCCTCCATGCCACGTGCTCCCCCAGGATTTCTGTCATCTCCTGACGCACCCCAGGGGACTCTCAGTGCATCCCAGTCAGCACCTCCTTCTTTTTTT HG:+:1495349682:-1 HG:+:2499489535:-1 +GGGGTTTCCCCCACGTTGGTCAGGCTGGTCTCAACTCCCAACCTCAGTTGATCTGCCCGAGTCAACCTCCCAAAGTGCTGGATTACAGGCGTGAGCTACTGCACCCAACCTGCCCACATTTTTTATTGTCTCTTCTTCAACCAATCTGGTCTCCCCATCGTTGAAAATTCGAAATGTAGCCCAGGCGTGGTGGACTCACGCCTGTACTCCCAGGCACTTTGGGAGGCTGAGGTGGGTGGATCACTTGAACTTAGAGGGTCAGGAGTTACAGACCAGCCTGGCCAACATGGTGAAATCCCTGTCCTCTGGCCGGACACAGTGGCTCATGCCTGTTATCCAGCCACAGTGGGAGCTGAGGTGGGCGGATCACCTGTAGGTTGGAGGTTCGAGATGAGCGTGTCCAACGTGGTGAAATCCTGTCTCTACTAAAAACACAAAAATCAGCCTGGCTTGGTGGCAGGGCGCCTGTATTTCCACGTTACTTGGGAGGCTGAGGCAGAGAATCCTTGAACCCGGGAGGCGGGAGGTTGCAGTGAGCCGAAATCATACCACTGCACTCCAGCCTGGGTGACAAGAGCGAGACTCTGTCTCAAAAACAACAACAAAAAAAAAAACAGGAAACACGGGCTCCCCTGACCCCACTTCTCCCCCACAGCCTCTCTCCCTCTTCCCCTTCGTCAGCCAGATCCTCATTCCTGTCTATTACTCCTAGCCTCCCAACTCCTGCTTCTGACCCTGGGGCCCCTCTTAGTCTCCAGTGAGCTCAGACGCTCTTCAGGGTTGAGTCGATGGCTCCTAACCCACCCTCGTCCCATCTGGGCCTCCCCCTGCCTGGTCCGGTTTTGCCTCTGACTTCCCCTGGCAGTTCCTTACTCAGCCAGTCTGTGGTGGGTGTCAACTTCAACCCTCCATGCCACGTGCTCCCCCAGGATTTCTGTCATCTCCTGACGCACCCCAGGGGACTCTCAGTGCATCCCAGTCAGCACCTCCTTCTTTTTTT HG:+:155423769:-1 HG:+:888141697:-1 HG:+:1010599451:-1 HG:+:1182031556:-1 HG:+:1270701534:-1 HG:+:1547867601:-1 HG:+:1677653540:-1 HG:+:1726103572:-1 HG:+:1849098238:-1 HG:+:1893744678:-1 HG:+:1895631988:-1 HG:+:2359746664:-1 HG:+:2508400189:-1 HG:+:2537283915:-1 HG:+:2662128654:-1 HG:+:2663725287:-1 HG:+:2668667671:-1 HG:+:2872515881:-1 HG:+:2921887768:-1 HG:+:3034425680:-1 +GGGGTTTCCCCCACGTTGGTCAGGCTGGTCTCAACTCCCAACCTCAGTTGATCTGCCCGAGTCAACCTCCCAAAGTGCTGGATTACAGGCGTGAGCTACTGCACCCAACCTGCCCACATTTTTTATTGTCTCTTCTTCAACCAATCTGGTCTCCCCATCGTTGAAAATTCGAAATGTAGCCCAGGCGTGGTGGACTCACGCCTGTACTCCCAGGCACTTTGGGAGGCTGAGGTGGGTGGATCACTTGAACTTAGAGGGTCAGGAGTTACAGACCAGCCTGGCCAACATGGTGAAATCCCTGTCCTCTGGCCGGACACAGTGGCTCATGCCTGTTATCCAGCCACAGTGGGAGCTGAGGTGGGCGGATCACCTGTAGGTTGGAGGTTCGAGATGAGCGTGTCCAACGTGGTGAAATCCTGTCTCTACTAAAAACACAAAAATCAGCCTGGCTTGGTGGCAGGGCGCCTGTATTTCCACGTTACTTGGGAGGCTGAGGCAGAGAATCCTTGAACCCGGGAGGCGGGAGGTTGCAGTGAGCCGAAATCATACCACTGCACTCCAGCCTGGGTGACAAGAGCGAGACTCTGTCTCAAAAACAACAACAAAAAAAAAAACAGGAAACACGGGCTCCCCTGACCCCACTTCTCCCCCACAGCCTCTCTCCCTCTTCCCCTTCGTCAGCCAGATCCTCATTCCTGTCTATTACTCCTAGCCTCCCAACTCCTGCTTCTGACCCTGGGGCCCCTCTTAGTCTCCAGTGAGCTCAGACGCTCTTCAGGGTTGAGTCGATGGCTCCTAACCCACCCTCGTCCCATCTGGGCCTCCCCCTGCCTGGTCCGGTTTTGCCTCTGACTTCCCCTGGCAGTTCCTTACTCAGCCAGTCTGTGGTGGGTGTCAACTTCAACCCTCCATGCCACGTGCTCCCCCAGGATTTCTGTCATCTCCTGACGCACCCCAGGGGACTCTCAGTGCATCCCAGTCAGCACCTCCTTCTTTTTTT HG:+:113380944:-1 HG:+:541363733:-1 HG:+:1378323051:-1 HG:+:1616453941:-1 HG:+:1701584961:-1 HG:+:2301811769:-1 HG:+:2372728612:-1 HG:+:2419507875:-1 HG:+:2476180885:-1 HG:+:2554799666:-1 HG:+:2904800878:-1 +GGGGTTTCCCCCACGTTGGTCAGGCTGGTCTCAACTCCCAACCTCAGTTGATCTGCCCGAGTCAACCTCCCAAAGTGCTGGATTACAGGCGTGAGCTACTGCACCCAACCTGCCCACATTTTTTATTGTCTCTTCTTCAACCAATCTGGTCTCCCCATCGTTGAAAATTCGAAATGTAGCCCAGGCGTGGTGGACTCACGCCTGTACTCCCAGGCACTTTGGGAGGCTGAGGTGGGTGGATCACTTGAACTTAGAGGGTCAGGAGTTACAGACCAGCCTGGCCAACATGGTGAAATCCCTGTCCTCTGGCCGGACACAGTGGCTCATGCCTGTTATCCAGCCACAGTGGGAGCTGAGGTGGGCGGATCACCTGTAGGTTGGAGGTTCGAGATGAGCGTGTCCAACGTGGTGAAATCCTGTCTCTACTAAAAACACAAAAATCAGCCTGGCTTGGTGGCAGGGCGCCTGTATTTCCACGTTACTTGGGAGGCTGAGGCAGAGAATCCTTGAACCCGGGAGGCGGGAGGTTGCAGTGAGCCGAAATCATACCACTGCACTCCAGCCTGGGTGACAAGAGCGAGACTCTGTCTCAAAAACAACAACAAAAAAAAAAACAGGAAACACGGGCTCCCCTGACCCCACTTCTCCCCCACAGCCTCTCTCCCTCTTCCCCTTCGTCAGCCAGATCCTCATTCCTGTCTATTACTCCTAGCCTCCCAACTCCTGCTTCTGACCCTGGGGCCCCTCTTAGTCTCCAGTGAGCTCAGACGCTCTTCAGGGTTGAGTCGATGGCTCCTAACCCACCCTCGTCCCATCTGGGCCTCCCCCTGCCTGGTCCGGTTTTGCCTCTGACTTCCCCTGGCAGTTCCTTACTCAGCCAGTCTGTGGTGGGTGTCAACTTCAACCCTCCATGCCACGTGCTCCCCCAGGATTTCTGTCATCTCCTGACGCACCCCAGGGGACTCTCAGTGCATCCCAGTCAGCACCTCCTTCTTTTTTT HG:+:301762870:-1 HG:+:1087263990:-1 HG:+:1215273041:-1 HG:+:1372883445:-1 HG:+:2466394851:-1 +GGGGTTTCCCCCACGTTGGTCAGGCTGGTCTCAACTCCCAACCTCAGTTGATCTGCCCGAGTCAACCTCCCAAAGTGCTGGATTACAGGCGTGAGCTACTGCACCCAACCTGCCCACATTTTTTATTGTCTCTTCTTCAACCAATCTGGTCTCCCCATCGTTGAAAATTCGAAATGTAGCCCAGGCGTGGTGGACTCACGCCTGTACTCCCAGGCACTTTGGGAGGCTGAGGTGGGTGGATCACTTGAACTTAGAGGGTCAGGAGTTACAGACCAGCCTGGCCAACATGGTGAAATCCCTGTCCTCTGGCCGGACACAGTGGCTCATGCCTGTTATCCAGCCACAGTGGGAGCTGAGGTGGGCGGATCACCTGTAGGTTGGAGGTTCGAGATGAGCGTGTCCAACGTGGTGAAATCCTGTCTCTACTAAAAACACAAAAATCAGCCTGGCTTGGTGGCAGGGCGCCTGTATTTCCACGTTACTTGGGAGGCTGAGGCAGAGAATCCTTGAACCCGGGAGGCGGGAGGTTGCAGTGAGCCGAAATCATACCACTGCACTCCAGCCTGGGTGACAAGAGCGAGACTCTGTCTCAAAAACAACAACAAAAAAAAAAACAGGAAACACGGGCTCCCCTGACCCCACTTCTCCCCCACAGCCTCTCTCCCTCTTCCCCTTCGTCAGCCAGATCCTCATTCCTGTCTATTACTCCTAGCCTCCCAACTCCTGCTTCTGACCCTGGGGCCCCTCTTAGTCTCCAGTGAGCTCAGACGCTCTTCAGGGTTGAGTCGATGGCTCCTAACCCACCCTCGTCCCATCTGGGCCTCCCCCTGCCTGGTCCGGTTTTGCCTCTGACTTCCCCTGGCAGTTCCTTACTCAGCCAGTCTGTGGTGGGTGTCAACTTCAACCCTCCATGCCACGTGCTCCCCCAGGATTTCTGTCATCTCCTGACGCACCCCAGGGGACTCTCAGTGCATCCCAGTCAGCACCTCCTTCTTTTTTT HG:+:334699742:-1 HG:+:335486755:-1 HG:+:478311823:-1 HG:+:549183264:-1 HG:+:730792554:-1 HG:+:810494325:-1 HG:+:913795410:-1 HG:+:1034529916:-1 HG:+:1083856994:-1 HG:+:1196868599:-1 HG:+:1519063544:-1 HG:+:1779429482:-1 HG:+:1927628649:-1 HG:+:1934533943:-1 HG:+:1992738006:-1 HG:+:2389192444:-1 HG:+:2743220793:-1 HG:+:2760648973:-1 HG:+:2872785993:-1 HG:+:3030703645:-1 +GGGGTTTCCCCCACGTTGGTCAGGCTGGTCTCAACTCCCAACCTCAGTTGATCTGCCCGAGTCAACCTCCCAAAGTGCTGGATTACAGGCGTGAGCTACTGCACCCAACCTGCCCACATTTTTTATTGTCTCTTCTTCAACCAATCTGGTCTCCCCATCGTTGAAAATTCGAAATGTAGCCCAGGCGTGGTGGACTCACGCCTGTACTCCCAGGCACTTTGGGAGGCTGAGGTGGGTGGATCACTTGAACTTAGAGGGTCAGGAGTTACAGACCAGCCTGGCCAACATGGTGAAATCCCTGTCCTCTGGCCGGACACAGTGGCTCATGCCTGTTATCCAGCCACAGTGGGAGCTGAGGTGGGCGGATCACCTGTAGGTTGGAGGTTCGAGATGAGCGTGTCCAACGTGGTGAAATCCTGTCTCTACTAAAAACACAAAAATCAGCCTGGCTTGGTGGCAGGGCGCCTGTATTTCCACGTTACTTGGGAGGCTGAGGCAGAGAATCCTTGAACCCGGGAGGCGGGAGGTTGCAGTGAGCCGAAATCATACCACTGCACTCCAGCCTGGGTGACAAGAGCGAGACTCTGTCTCAAAAACAACAACAAAAAAAAAAACAGGAAACACGGGCTCCCCTGACCCCACTTCTCCCCCACAGCCTCTCTCCCTCTTCCCCTTCGTCAGCCAGATCCTCATTCCTGTCTATTACTCCTAGCCTCCCAACTCCTGCTTCTGACCCTGGGGCCCCTCTTAGTCTCCAGTGAGCTCAGACGCTCTTCAGGGTTGAGTCGATGGCTCCTAACCCACCCTCGTCCCATCTGGGCCTCCCCCTGCCTGGTCCGGTTTTGCCTCTGACTTCCCCTGGCAGTTCCTTACTCAGCCAGTCTGTGGTGGGTGTCAACTTCAACCCTCCATGCCACGTGCTCCCCCAGGATTTCTGTCATCTCCTGACGCACCCCAGGGGACTCTCAGTGCATCCCAGTCAGCACCTCCTTCTTTTTTT HG:+:317666951:-1 HG:+:318474962:-1 HG:+:644974210:-1 HG:+:868850014:-1 HG:+:957684343:-1 HG:+:1228713239:-1 HG:+:1302555439:-1 HG:+:1552020889:-1 HG:+:1723789211:-1 HG:+:1778901151:-1 HG:+:1857066018:-1 HG:+:1886875944:-1 HG:+:2001473842:-1 HG:+:2032508415:-1 HG:+:2045429198:-1 HG:+:2296709258:-1 HG:+:2300584960:-1 HG:+:2387485988:-1 HG:+:2899520075:-1 HG:+:2977785421:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:86540500:144 HG:+:107095668:-1 HG:+:185203618:198 HG:+:320356573:178 HG:+:327640690:188 HG:+:333244716:197 HG:+:431849938:149 HG:+:460563621:146 HG:+:573430814:-1 HG:+:581249005:187 HG:+:603550987:182 HG:+:638647788:150 HG:+:736882013:160 HG:+:773670484:144 HG:+:778978296:-1 HG:+:799068538:144 HG:+:838070969:154 HG:+:875998314:158 HG:+:896985853:163 HG:+:919318441:178 HG:+:979185072:139 HG:+:1075928733:-1 HG:+:1145405841:157 HG:+:1172982127:149 HG:+:1316630887:148 HG:+:1319856446:158 HG:+:1380709328:144 HG:+:1466116027:-1 HG:+:1505011744:156 HG:+:1560503463:-1 HG:+:1642102047:136 HG:+:1709996903:-1 HG:+:1749035202:154 HG:+:1754531118:-1 HG:+:1824448704:134 HG:+:1828298300:157 HG:+:1829502122:160 HG:+:1901546623:176 HG:+:2037667443:152 HG:+:2237909912:153 HG:+:2260063572:168 HG:+:2346363446:142 HG:+:2352264247:138 HG:+:2435387508:157 HG:+:2581082663:171 HG:+:2823732637:152 HG:+:2847150821:-1 HG:+:2919984578:-1 HG:+:2928605058:-1 HG:+:2935739540:174 HG:+:2952060115:-1 HG:+:2964687280:176 HG:+:3013036004:143 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:166072370:153 HG:+:197260978:159 HG:+:221383405:186 HG:+:317069581:171 HG:+:429083861:176 HG:+:564165020:-1 HG:+:588546848:185 HG:+:834068356:164 HG:+:857215385:160 HG:+:960836404:160 HG:+:1149006240:-1 HG:+:1215475022:167 HG:+:1336804938:178 HG:+:1510137365:159 HG:+:1513331870:140 HG:+:1646638817:143 HG:+:1699634244:146 HG:+:1729930733:149 HG:+:1732960471:-1 HG:+:2038482539:165 HG:+:2038705019:145 HG:+:2111295495:152 HG:+:2115008943:148 HG:+:2444718144:192 HG:+:2475779340:162 HG:+:2852273858:143 HG:+:2974437199:155 HG:+:3009458129:160 HG:+:3052700799:155 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:55899274:169 HG:+:423678183:146 HG:+:533865042:158 HG:+:603228428:161 HG:+:743492994:161 HG:+:751422365:187 HG:+:997131155:170 HG:+:1011354161:162 HG:+:1258323932:150 HG:+:1500371818:162 HG:+:1543629235:168 HG:+:1548402271:-1 HG:+:1941598634:144 HG:+:2234234058:163 HG:+:2539548471:164 HG:+:2978681869:187 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HG:+:1455934625:168 HG:+:1478113064:-1 HG:+:1495521129:-1 HG:+:1506522772:199 HG:+:1541021623:165 HG:+:1552822763:150 HG:+:1619401293:161 HG:+:1760802212:143 HG:+:1763683943:185 HG:+:1791529298:178 HG:+:1839416394:147 HG:+:1878960496:158 HG:+:1919755240:-1 HG:+:1941598645:144 HG:+:1972072950:160 HG:+:1989691890:164 HG:+:2017787035:159 HG:+:2117032028:193 HG:+:2133759754:146 HG:+:2153960439:178 HG:+:2160451531:190 HG:+:2225837351:187 HG:+:2232681013:147 HG:+:2234799819:137 HG:+:2249648881:152 HG:+:2254204004:145 HG:+:2257510615:148 HG:+:2288775325:148 HG:+:2334065147:200 HG:+:2394251325:-1 HG:+:2567011835:148 HG:+:2601708351:148 HG:+:2632700547:174 HG:+:2649044828:141 HG:+:2649958194:165 HG:+:2694641448:-1 HG:+:2701608212:188 HG:+:2733230448:-1 HG:+:2735487493:180 HG:+:2743722807:146 HG:+:2803209178:-1 HG:+:2805467554:169 HG:+:2823732642:152 HG:+:2894235968:-1 HG:+:2913363758:-1 HG:+:2918640672:-1 HG:+:2926982767:148 HG:+:2932140689:183 HG:+:2947054835:-1 HG:+:2948244795:-1 HG:+:2970713642:161 HG:+:2976505733:152 HG:+:3017551672:151 HG:+:3022841254:-1 HG:+:3027937135:144 HG:+:3040174211:161 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:50032559:-1 HG:+:152559986:-1 HG:+:364923943:-1 HG:+:417741251:153 HG:+:598820409:-1 HG:+:733213828:-1 HG:+:926605132:-1 HG:+:1055961002:-1 HG:+:1472986452:-1 HG:+:1624153399:-1 HG:+:1822092621:-1 HG:+:2243596336:-1 HG:+:2254781080:-1 HG:+:2282869298:-1 HG:+:2648096237:-1 HG:+:2748441177:-1 HG:+:2915264096:-1 HG:+:2950071270:197 HG:+:2975115216:-1 HG:+:3020982453:-1 HG:+:3022457230:-1 HG:+:3042202421:-1 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HG:+:347213768:-1 HG:+:663088665:-1 HG:+:912405143:154 HG:+:1318717082:-1 HG:+:1504295062:-1 HG:+:2167236597:-1 HG:+:2858164210:152 HG:+:2956332600:-1 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HG:+:105238663:161 HG:+:117763146:141 HG:+:121318983:152 HG:+:366241904:-1 HG:+:432804801:146 HG:+:521112991:150 HG:+:557976363:-1 HG:+:581192643:-1 HG:+:655467250:164 HG:+:868916647:-1 HG:+:959607384:145 HG:+:1004802179:-1 HG:+:1167374178:-1 HG:+:1257709831:-1 HG:+:1323722031:-1 HG:+:1481195942:156 HG:+:1763845298:144 HG:+:1855096828:-1 HG:+:1948100733:150 HG:+:1948259627:156 HG:+:1989402445:154 HG:+:2472293019:-1 HG:+:2897375971:148 HG:+:2955767628:199 HG:+:2986076975:163 HG:+:2990905748:164 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:69884085:-1 HG:+:99194741:188 HG:+:147329899:166 HG:+:159297556:-1 HG:+:181913034:-1 HG:+:182891778:-1 HG:+:191442441:157 HG:+:225280126:-1 HG:+:228062442:142 HG:+:294904650:-1 HG:+:294906332:175 HG:+:358007449:-1 HG:+:373818932:-1 HG:+:378835820:151 HG:+:388897067:165 HG:+:392168320:-1 HG:+:409466016:153 HG:+:409932016:139 HG:+:436911250:160 HG:+:436930095:175 HG:+:450319168:190 HG:+:459606566:149 HG:+:470942809:-1 HG:+:522216620:169 HG:+:527772343:-1 HG:+:576716349:-1 HG:+:636707553:-1 HG:+:655134579:178 HG:+:671052711:-1 HG:+:715609023:-1 HG:+:771512069:-1 HG:+:794789667:166 HG:+:796103374:174 HG:+:796424163:174 HG:+:807959554:-1 HG:+:878713861:-1 HG:+:886339515:176 HG:+:899449815:-1 HG:+:900136019:-1 HG:+:900744225:-1 HG:+:908702826:-1 HG:+:915488774:155 HG:+:967135690:-1 HG:+:970084266:-1 HG:+:983486145:-1 HG:+:993504286:145 HG:+:993623682:-1 HG:+:1009230193:151 HG:+:1038674085:-1 HG:+:1042090534:-1 HG:+:1061982941:149 HG:+:1120091484:165 HG:+:1152551841:-1 HG:+:1157475001:-1 HG:+:1157926811:-1 HG:+:1179715325:-1 HG:+:1184074763:-1 HG:+:1189902025:-1 HG:+:1190651906:159 HG:+:1193432471:-1 HG:+:1196796709:156 HG:+:1204806157:180 HG:+:1209502783:-1 HG:+:1258323940:150 HG:+:1358628066:-1 HG:+:1375632731:-1 HG:+:1379659791:-1 HG:+:1444468549:-1 HG:+:1458361172:-1 HG:+:1465895033:159 HG:+:1483235522:-1 HG:+:1497762444:169 HG:+:1500810579:189 HG:+:1507910442:-1 HG:+:1508226638:-1 HG:+:1550928839:-1 HG:+:1566808114:181 HG:+:1568742320:-1 HG:+:1615560584:154 HG:+:1660780527:172 HG:+:1726988607:-1 HG:+:1729175534:-1 HG:+:1729696047:-1 HG:+:1736730310:-1 HG:+:1736835035:-1 HG:+:1736860260:-1 HG:+:1741792830:151 HG:+:1745085438:153 HG:+:1846228226:-1 HG:+:1856289465:-1 HG:+:1913951817:-1 HG:+:1941485670:157 HG:+:1965367224:-1 HG:+:1967472181:-1 HG:+:1984234330:149 HG:+:2132907252:145 HG:+:2169097483:-1 HG:+:2225502829:-1 HG:+:2242141659:198 HG:+:2260063574:168 HG:+:2263166198:-1 HG:+:2281290079:143 HG:+:2344929796:-1 HG:+:2362121138:155 HG:+:2363136881:-1 HG:+:2391920426:135 HG:+:2444718163:192 HG:+:2538899621:-1 HG:+:2552151445:-1 HG:+:2586036931:-1 HG:+:2586692205:-1 HG:+:2586714199:-1 HG:+:2613295880:-1 HG:+:2623148903:-1 HG:+:2639876274:-1 HG:+:2799198680:172 HG:+:2800265459:-1 HG:+:2902265727:-1 HG:+:2924106544:-1 HG:+:2938305370:-1 HG:+:2943734410:164 HG:+:2944341717:171 HG:+:2948355430:149 HG:+:2955379455:147 HG:+:2958632844:156 HG:+:2968069616:156 HG:+:2970859677:191 HG:+:2988782986:-1 HG:+:3019114560:151 HG:+:3019356406:-1 HG:+:3040321045:195 HG:+:3052876017:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:258847853:-1 HG:+:288741587:-1 HG:+:511023163:-1 HG:+:2144955162:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:79398038:184 HG:+:105238672:161 HG:+:174115320:145 HG:+:176327932:154 HG:+:255438619:-1 HG:+:403354629:-1 HG:+:425621741:151 HG:+:557558465:182 HG:+:749713113:180 HG:+:764163278:186 HG:+:789224877:155 HG:+:835068897:148 HG:+:870426423:161 HG:+:897500001:147 HG:+:971895148:140 HG:+:1038041055:148 HG:+:1120047991:148 HG:+:1428684189:166 HG:+:1558161384:143 HG:+:1724962433:162 HG:+:1761722284:147 HG:+:1914777974:155 HG:+:2044100235:156 HG:+:2126179086:148 HG:+:2144635052:174 HG:+:2168514515:-1 HG:+:2231071715:145 HG:+:2241397802:-1 HG:+:2249200781:160 HG:+:2612835836:168 HG:+:2649751524:142 HG:+:2741291507:153 HG:+:2863768047:159 HG:+:2907388310:147 HG:+:2926110167:-1 HG:+:2944341716:171 HG:+:2957206795:162 HG:+:2976296276:-1 HG:+:2987245771:153 HG:+:2994663481:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:461006530:-1 HG:+:957080579:-1 HG:+:963489758:-1 HG:+:1534223739:-1 HG:+:2084545696:-1 HG:+:3026747726:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:92721235:142 HG:+:96265658:199 HG:+:99508131:-1 HG:+:169008181:-1 HG:+:170020907:175 HG:+:171689221:-1 HG:+:179402761:-1 HG:+:189389487:-1 HG:+:245790708:-1 HG:+:264833173:149 HG:+:265351140:156 HG:+:287955793:-1 HG:+:308908683:-1 HG:+:332251152:-1 HG:+:419230971:-1 HG:+:433938691:-1 HG:+:494423311:172 HG:+:565763043:-1 HG:+:581475296:-1 HG:+:596646240:-1 HG:+:599642131:150 HG:+:601966523:156 HG:+:604998757:-1 HG:+:619936172:-1 HG:+:657141738:-1 HG:+:674502252:-1 HG:+:720898674:-1 HG:+:738535178:160 HG:+:750922953:178 HG:+:765467652:143 HG:+:780031091:159 HG:+:794364997:-1 HG:+:817289009:-1 HG:+:902444336:-1 HG:+:935259334:-1 HG:+:958367223:153 HG:+:979633949:175 HG:+:1018512244:-1 HG:+:1020562321:-1 HG:+:1073888890:-1 HG:+:1074382310:139 HG:+:1082160054:-1 HG:+:1092759886:148 HG:+:1095729234:-1 HG:+:1195501185:-1 HG:+:1200457324:-1 HG:+:1330869283:181 HG:+:1368466597:176 HG:+:1390220731:-1 HG:+:1469307468:152 HG:+:1472174763:-1 HG:+:1475137921:160 HG:+:1482707756:171 HG:+:1504628235:-1 HG:+:1530591674:-1 HG:+:1615729666:-1 HG:+:1621508764:-1 HG:+:1635655477:-1 HG:+:1703544437:-1 HG:+:1708564295:143 HG:+:1729918559:-1 HG:+:1765224999:163 HG:+:1773779987:174 HG:+:1780835607:172 HG:+:1832659957:145 HG:+:1845217304:-1 HG:+:1889120858:172 HG:+:1912689731:151 HG:+:1915979973:-1 HG:+:1924990347:-1 HG:+:1941485669:157 HG:+:1966536209:-1 HG:+:1997949133:-1 HG:+:2015138737:-1 HG:+:2028064990:-1 HG:+:2033048820:-1 HG:+:2051034097:166 HG:+:2084667188:-1 HG:+:2139562242:153 HG:+:2142562434:-1 HG:+:2142817142:-1 HG:+:2162707943:-1 HG:+:2234548264:141 HG:+:2249583494:183 HG:+:2258931527:156 HG:+:2354547402:-1 HG:+:2377948752:173 HG:+:2469132427:-1 HG:+:2516127200:-1 HG:+:2539727694:-1 HG:+:2549826828:156 HG:+:2585594690:-1 HG:+:2604120953:-1 HG:+:2946745589:149 HG:+:2967419600:161 HG:+:2967544800:157 HG:+:3011631682:138 HG:+:3017551649:151 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:88517074:-1 HG:+:796195269:-1 HG:+:814627743:-1 HG:+:839498379:-1 HG:+:844027247:-1 HG:+:912267559:-1 HG:+:1242575380:188 HG:+:1561832741:-1 HG:+:1874209811:159 HG:+:2008085515:-1 HG:+:2197827761:153 HG:+:2231902839:159 HG:+:2304459726:-1 HG:+:2984276757:-1 HG:+:2996780970:161 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:1143143204:-1 HG:+:2129502130:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:47475010:153 HG:+:88750863:-1 HG:+:101288432:-1 HG:+:101288542:-1 HG:+:120119739:176 HG:+:158837422:151 HG:+:169469848:152 HG:+:308740129:141 HG:+:358299352:171 HG:+:398715961:159 HG:+:400075770:155 HG:+:425305004:147 HG:+:446207429:142 HG:+:476225514:141 HG:+:480643690:142 HG:+:480737859:155 HG:+:506398994:-1 HG:+:582498029:161 HG:+:588698768:165 HG:+:612152957:176 HG:+:687261177:153 HG:+:699557604:164 HG:+:718884241:154 HG:+:745801605:154 HG:+:746148602:147 HG:+:746638652:154 HG:+:757213208:-1 HG:+:757716367:-1 HG:+:766732081:152 HG:+:787060208:149 HG:+:800390481:149 HG:+:826226155:153 HG:+:849087987:157 HG:+:870280445:165 HG:+:908828089:-1 HG:+:909305111:166 HG:+:914548489:-1 HG:+:915018417:179 HG:+:937099125:-1 HG:+:944551382:-1 HG:+:972687444:149 HG:+:973196614:149 HG:+:991899293:149 HG:+:1007051283:164 HG:+:1038716087:-1 HG:+:1042648176:148 HG:+:1064609386:149 HG:+:1073843986:143 HG:+:1148234648:162 HG:+:1148456593:173 HG:+:1173770371:149 HG:+:1229140188:-1 HG:+:1257544411:159 HG:+:1287945748:164 HG:+:1313204326:170 HG:+:1315938102:191 HG:+:1384035444:149 HG:+:1424162272:-1 HG:+:1449282436:153 HG:+:1450140259:159 HG:+:1463531979:145 HG:+:1463554126:152 HG:+:1473714123:146 HG:+:1510221165:148 HG:+:1527674214:138 HG:+:1545538907:162 HG:+:1552822758:150 HG:+:1555151066:165 HG:+:1660540612:-1 HG:+:1726137312:164 HG:+:1758744344:150 HG:+:1761706155:148 HG:+:1761722281:147 HG:+:1790668414:167 HG:+:1797266868:145 HG:+:1824376000:-1 HG:+:1825863170:-1 HG:+:1828298322:157 HG:+:1843957893:142 HG:+:1871255444:180 HG:+:1901017137:-1 HG:+:1904724636:-1 HG:+:1910014334:166 HG:+:1917634027:144 HG:+:1940137719:-1 HG:+:1980162430:147 HG:+:1989518328:167 HG:+:2048984046:172 HG:+:2063976193:148 HG:+:2125756603:153 HG:+:2133544221:144 HG:+:2179948120:159 HG:+:2222167449:163 HG:+:2248505076:190 HG:+:2249762402:156 HG:+:2253521628:-1 HG:+:2266297853:-1 HG:+:2303298990:-1 HG:+:2362330100:154 HG:+:2441169233:151 HG:+:2444998095:168 HG:+:2612835852:168 HG:+:2679783387:194 HG:+:2680454564:163 HG:+:2688115609:155 HG:+:2723832090:-1 HG:+:2728715943:146 HG:+:2846978496:145 HG:+:2853040830:166 HG:+:2897375975:148 HG:+:2897414391:156 HG:+:2897551669:158 HG:+:2953220556:-1 HG:+:2954141181:150 HG:+:2956671346:148 HG:+:2961356220:160 HG:+:2967144012:181 HG:+:2967400713:153 HG:+:2978212257:158 HG:+:2981762010:150 HG:+:2981831401:153 HG:+:2991349644:-1 HG:+:3017240782:152 HG:+:3045775742:-1 HG:+:3058246458:162 HG:+:3059398017:180 HG:+:3096680390:164 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:95951557:175 HG:+:301371998:152 HG:+:333877246:164 HG:+:400900485:173 HG:+:423678192:146 HG:+:756880142:184 HG:+:795240013:-1 HG:+:824902041:173 HG:+:851398178:-1 HG:+:873698283:-1 HG:+:926306305:-1 HG:+:971720371:145 HG:+:979707659:173 HG:+:991562492:164 HG:+:1006126009:182 HG:+:1147488111:141 HG:+:1491341017:176 HG:+:1564926510:168 HG:+:1718770333:167 HG:+:1820491372:-1 HG:+:1908156472:-1 HG:+:2006022558:-1 HG:+:2020287269:-1 HG:+:2035327611:-1 HG:+:2117032026:193 HG:+:2137326280:145 HG:+:2156471696:164 HG:+:2172415324:-1 HG:+:2649958192:165 HG:+:2730284892:-1 HG:+:2799753855:164 HG:+:2858634165:-1 HG:+:2909509511:130 HG:+:2944532642:-1 HG:+:2949501110:-1 HG:+:2961198408:165 HG:+:3053282255:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:54942150:-1 HG:+:89540449:163 HG:+:146484973:163 HG:+:250084079:-1 HG:+:388940449:183 HG:+:475243282:153 HG:+:643699389:162 HG:+:777560223:173 HG:+:911484768:185 HG:+:1010172389:158 HG:+:1180511588:155 HG:+:1184126950:188 HG:+:1270400552:-1 HG:+:1444468552:-1 HG:+:1540556000:161 HG:+:1629833951:-1 HG:+:2037386853:-1 HG:+:2616890159:157 HG:+:2989378866:-1 HG:+:3029225399:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:53684645:-1 HG:+:356563275:-1 HG:+:535088438:-1 HG:+:641556683:-1 HG:+:644019720:-1 HG:+:1136768358:-1 HG:+:1256206123:-1 HG:+:1559583374:-1 HG:+:1794680374:-1 HG:+:1850229233:-1 HG:+:1970522454:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:773271832:-1 HG:+:2013097325:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:259786602:-1 HG:+:1625938992:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:183568922:-1 HG:+:1936701701:-1 HG:+:2573502653:-1 HG:+:2753601008:-1 HG:+:2915856917:-1 HG:+:3045984517:200 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:338352129:-1 HG:+:926441747:-1 HG:+:963967569:-1 HG:+:1627623567:-1 HG:+:1758322520:-1 HG:+:2109247756:-1 HG:+:2359028905:-1 HG:+:2593494095:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:2663221450:-1 HG:+:2902407523:-1 HG:+:2933335237:-1 HG:+:2933373314:-1 HG:+:2933629626:-1 HG:+:2933868716:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:292067824:-1 HG:+:296196955:-1 HG:+:386035004:-1 HG:+:1017868999:-1 HG:+:1276284397:-1 HG:+:1347863261:-1 HG:+:1584724356:-1 HG:+:1585110602:-1 HG:+:1585739846:-1 HG:+:1726230278:-1 HG:+:1810791129:-1 HG:+:1848167921:-1 HG:+:2019291309:-1 HG:+:2231325697:-1 HG:+:2341153464:198 HG:+:2442693106:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:92127265:-1 HG:+:233927265:-1 HG:+:246908640:-1 HG:+:687179447:-1 HG:+:737404140:-1 HG:+:1227295689:-1 HG:+:1769172512:-1 HG:+:2000419704:-1 HG:+:2028578064:-1 HG:+:2051940484:-1 HG:+:2161812311:-1 HG:+:2270561406:-1 HG:+:2351579587:-1 HG:+:2385177331:-1 HG:+:2973464465:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:76220666:-1 HG:+:111335366:-1 HG:+:198706657:-1 HG:+:200019725:-1 HG:+:243640755:-1 HG:+:264574685:-1 HG:+:308684987:-1 HG:+:324979325:-1 HG:+:432057655:-1 HG:+:504815139:-1 HG:+:597652623:-1 HG:+:616257349:-1 HG:+:665857837:-1 HG:+:750857389:-1 HG:+:843180059:-1 HG:+:896163742:-1 HG:+:998214400:-1 HG:+:1006992585:-1 HG:+:1011026317:-1 HG:+:1118017479:-1 HG:+:1140534164:-1 HG:+:1189016625:-1 HG:+:1216646073:-1 HG:+:1220625009:-1 HG:+:1377212321:-1 HG:+:1445014685:-1 HG:+:1568483320:-1 HG:+:1663272585:-1 HG:+:1912354148:-1 HG:+:1991599060:-1 HG:+:2016172368:-1 HG:+:2035970696:-1 HG:+:2057524282:-1 HG:+:2129839585:-1 HG:+:2153238796:170 HG:+:2260014724:-1 HG:+:2495536877:-1 HG:+:2495904145:-1 HG:+:2526097355:-1 HG:+:2569123605:-1 HG:+:2574630098:-1 HG:+:2603599693:-1 HG:+:2850762537:-1 HG:+:2875493782:-1 HG:+:2892717075:-1 HG:+:2964300058:164 HG:+:3055829341:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:247890643:150 HG:+:248694016:157 HG:+:470578152:-1 HG:+:568373323:-1 HG:+:650469691:-1 HG:+:719369747:-1 HG:+:744944466:-1 HG:+:818591041:-1 HG:+:919071509:-1 HG:+:944507217:155 HG:+:969838237:-1 HG:+:971720361:145 HG:+:1199026846:-1 HG:+:1244072115:163 HG:+:1248541339:-1 HG:+:1274085678:-1 HG:+:1303216366:-1 HG:+:1489881237:151 HG:+:1563186600:-1 HG:+:1680883388:-1 HG:+:2023670724:-1 HG:+:2167564547:-1 HG:+:2328123014:161 HG:+:2330790419:160 HG:+:2520162397:-1 HG:+:2607695727:-1 HG:+:2641553617:-1 HG:+:2689070724:155 HG:+:2956369150:-1 HG:+:2961356210:160 HG:+:3055631381:151 HG:+:3058270097:188 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:100737197:-1 HG:+:208878947:148 HG:+:397476657:-1 HG:+:430946295:-1 HG:+:462700520:-1 HG:+:519483881:162 HG:+:524504851:140 HG:+:605643545:155 HG:+:819256022:144 HG:+:925089526:162 HG:+:1749835446:147 HG:+:1761960657:-1 HG:+:1850013083:-1 HG:+:1919878489:-1 HG:+:1937771911:-1 HG:+:2370436373:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:165660225:-1 HG:+:561312231:150 HG:+:1571291137:155 HG:+:1749884144:-1 HG:+:1894101095:139 HG:+:2034992646:165 HG:+:2735075904:-1 HG:+:2772833642:-1 HG:+:2957235230:159 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:176694915:-1 HG:+:493830231:-1 HG:+:699843371:-1 HG:+:935843410:147 HG:+:946263641:-1 HG:+:1178607032:150 HG:+:1399996394:-1 HG:+:1509035243:-1 HG:+:2225999588:-1 HG:+:2360239163:-1 HG:+:2444495000:-1 HG:+:2490808580:-1 HG:+:2907542064:-1 HG:+:3002414223:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:55578479:-1 HG:+:709537573:-1 HG:+:746530999:151 HG:+:958884097:-1 HG:+:1139461395:-1 HG:+:1219367688:-1 HG:+:1245949023:151 HG:+:1462991028:140 HG:+:1706284522:165 HG:+:1877835063:161 HG:+:1913216880:-1 HG:+:2582838929:-1 HG:+:2946974645:161 HG:+:2982241375:150 HG:+:3058361401:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:733387:-1 HG:+:80334987:145 HG:+:184828475:-1 HG:+:224210612:-1 HG:+:714001392:-1 HG:+:780295110:-1 HG:+:1158464177:166 HG:+:1179976605:184 HG:+:1839146968:152 HG:+:1923233807:-1 HG:+:3013053293:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:89622816:165 HG:+:195639743:151 HG:+:518958432:164 HG:+:743492990:161 HG:+:964678920:170 HG:+:1346897660:163 HG:+:1571671219:151 HG:+:2014945323:153 HG:+:2241899406:180 HG:+:2576078200:149 HG:+:2964687286:176 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:308953149:-1 HG:+:528618204:-1 HG:+:914751965:154 HG:+:1244325265:167 HG:+:1990110644:148 HG:+:2123610354:-1 HG:+:2357315499:-1 HG:+:2360464918:-1 HG:+:2616769570:148 HG:+:2742311260:143 HG:+:2943617671:-1 HG:+:2976299216:159 HG:+:3051604711:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:965749212:-1 HG:+:1007255803:164 HG:+:1251052453:-1 HG:+:1450260869:194 HG:+:1564926513:168 HG:+:1615560594:154 HG:+:1638311831:-1 HG:+:1834875524:162 HG:+:1852476496:139 HG:+:2067377144:-1 HG:+:2363685404:-1 HG:+:2558619115:-1 HG:+:2885993772:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGACGCAGAAAAGGCCGTTTGATAAATTCAACACATCTTCATGCTAAAAACACTCAATAAACTAGGTATCGATGGGATGTATCTCAAAATAATTAAGAGCTATTTTTATCAAACCCACAGCCAAGTATCATACTGAATGGGCATTAATCTGGAAGAATTCCTTTGAAACTGGCCATAAGACAAAAGATGCCCTCTGTCACCAC HG:+:769884165:153 HG:+:817288700:-1 HG:+:1479885162:161 HG:+:1501932243:142 HG:+:1565440049:140 +GTGGTGACAGAGGGCATCTTTTGTCTTATGGCCAGTTTCAAAGGAATTCTTCCAGATTAATGCCCATTCAGTATGATACTTGGCTGTGGGTTTGATAAAAATAGCTCTTAATTATTTTGAGATACATCCCATCGATACCTAGTTTATTGAGTGTTTTTAGCATGAAGATGTGTTGAATTTATCAAACGGCCTTTTCTGCGTCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT HG:+:185165935:169 HG:+:433291551:164 HG:+:448901009:-1 HG:+:496379128:151 HG:+:504355291:150 HG:+:511530488:156 HG:+:613131953:164 HG:+:629561604:152 HG:+:638457517:147 HG:+:709813173:167 HG:+:810776069:144 HG:+:856660728:147 HG:+:922190025:148 HG:+:1028660806:164 HG:+:1107274327:139 HG:+:1171678090:154 HG:+:1242763386:174 HG:+:1378569111:130 HG:+:1381198554:146 HG:+:1489737644:154 HG:+:1523524393:-1 HG:+:1871010669:179 HG:+:1915934464:162 HG:+:2278940976:159 HG:+:2589232097:164 HG:+:2658207533:164 HG:+:2694499253:145 HG:+:2701585214:45 HG:+:2965692477:146 HG:+:2969038200:139 HG:+:2989481678:175 +GTGGTGACAGAGGGCATCTTTTGTCTTATGGCCAGTTTCAAAGGAATTCTTCCAGATTAATGCCCATTCAGTATGATACTTGGCTGTGGGTTTGATAAAAATAGCTCTTAATTATTTTGAGATACATCCCATCGATACCTAGTTTATTGAGTGTTTTTAGCATGAAGATGTGTTGAATTTATCAAACGGCCTTTTCTGCGTCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT HG:+:2701585209:45 +GTGGTGACAGAGGGCATCTTTTGTCTTATGGCCAGTTTCAAAGGAATTCTTCCAGATTAATGCCCATTCAGTATGATACTTGGCTGTGGGTTTGATAAAAATAGCTCTTAATTATTTTGAGATACATCCCATCGATACCTAGTTTATTGAGTGTTTTTAGCATGAAGATGTGTTGAATTTATCAAACGGCCTTTTCTGCGTCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT HG:+:2701585211:45 +GTGGTGACAGAGGGCATCTTTTGTCTTATGGCCAGTTTCAAAGGAATTCTTCCAGATTAATGCCCATTCAGTATGATACTTGGCTGTGGGTTTGATAAAAATAGCTCTTAATTATTTTGAGATACATCCCATCGATACCTAGTTTATTGAGTGTTTTTAGCATGAAGATGTGTTGAATTTATCAAACGGCCTTTTCTGCGTCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT HG:+:1874548486:162 HG:+:2925315692:-1 +GTGGTGACAGAGGGCATCTTTTGTCTTATGGCCAGTTTCAAAGGAATTCTTCCAGATTAATGCCCATTCAGTATGATACTTGGCTGTGGGTTTGATAAAAATAGCTCTTAATTATTTTGAGATACATCCCATCGATACCTAGTTTATTGAGTGTTTTTAGCATGAAGATGTGTTGAATTTATCAAACGGCCTTTTCTGCGTCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT HG:+:1002882715:-1 HG:+:2701585217:45 +GTGGTGACAGAGGGCATCTTTTGTCTTATGGCCAGTTTCAAAGGAATTCTTCCAGATTAATGCCCATTCAGTATGATACTTGGCTGTGGGTTTGATAAAAATAGCTCTTAATTATTTTGAGATACATCCCATCGATACCTAGTTTATTGAGTGTTTTTAGCATGAAGATGTGTTGAATTTATCAAACGGCCTTTTCTGCGTCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT HG:+:2701585219:45 +GTGGTGACAGAGGGCATCTTTTGTCTTATGGCCAGTTTCAAAGGAATTCTTCCAGATTAATGCCCATTCAGTATGATACTTGGCTGTGGGTTTGATAAAAATAGCTCTTAATTATTTTGAGATACATCCCATCGATACCTAGTTTATTGAGTGTTTTTAGCATGAAGATGTGTTGAATTTATCAAACGGCCTTTTCTGCGTCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT HG:+:97590748:-1 +GTGGTGACAGAGGGCATCTTTTGTCTTATGGCCAGTTTCAAAGGAATTCTTCCAGATTAATGCCCATTCAGTATGATACTTGGCTGTGGGTTTGATAAAAATAGCTCTTAATTATTTTGAGATACATCCCATCGATACCTAGTTTATTGAGTGTTTTTAGCATGAAGATGTGTTGAATTTATCAAACGGCCTTTTCTGCGTCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT HG:+:2375187511:-1 +GTGGTGACAGAGGGCATCTTTTGTCTTATGGCCAGTTTCAAAGGAATTCTTCCAGATTAATGCCCATTCAGTATGATACTTGGCTGTGGGTTTGATAAAAATAGCTCTTAATTATTTTGAGATACATCCCATCGATACCTAGTTTATTGAGTGTTTTTAGCATGAAGATGTGTTGAATTTATCAAACGGCCTTTTCTGCGTCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT HG:+:183716294:-1 HG:+:230658843:174 HG:+:302067182:153 HG:+:473404778:157 HG:+:629484908:170 HG:+:767680040:-1 HG:+:925830288:166 HG:+:1253720114:152 HG:+:1363976433:135 HG:+:1542718407:151 HG:+:1552026359:129 HG:+:1933179411:148 HG:+:1946750710:-1 HG:+:2166969339:167 HG:+:2701585208:45 HG:+:2946840238:178 +GTGGTGACAGAGGGCATCTTTTGTCTTATGGCCAGTTTCAAAGGAATTCTTCCAGATTAATGCCCATTCAGTATGATACTTGGCTGTGGGTTTGATAAAAATAGCTCTTAATTATTTTGAGATACATCCCATCGATACCTAGTTTATTGAGTGTTTTTAGCATGAAGATGTGTTGAATTTATCAAACGGCCTTTTCTGCGTCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT HG:+:1030413:-1 HG:+:433733157:164 HG:+:948551127:-1 HG:+:1482175920:-1 HG:+:2130958627:153 HG:+:3051681064:-1 +GTGGTGACAGAGGGCATCTTTTGTCTTATGGCCAGTTTCAAAGGAATTCTTCCAGATTAATGCCCATTCAGTATGATACTTGGCTGTGGGTTTGATAAAAATAGCTCTTAATTATTTTGAGATACATCCCATCGATACCTAGTTTATTGAGTGTTTTTAGCATGAAGATGTGTTGAATTTATCAAACGGCCTTTTCTGCGTCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT HG:+:118409686:-1 HG:+:367150275:-1 HG:+:449412448:-1 HG:+:590471663:-1 HG:+:753428276:162 HG:+:756992253:-1 HG:+:809062061:165 HG:+:1200750295:152 HG:+:1287008878:156 HG:+:1450977665:169 HG:+:1482102003:-1 HG:+:1765915792:150 HG:+:1848592949:151 HG:+:1879021604:154 HG:+:2389248375:148 HG:+:2550467236:-1 HG:+:2701585207:45 HG:+:2764280032:-1 HG:+:3030381138:-1 +GTGGTGACAGAGGGCATCTTTTGTCTTATGGCCAGTTTCAAAGGAATTCTTCCAGATTAATGCCCATTCAGTATGATACTTGGCTGTGGGTTTGATAAAAATAGCTCTTAATTATTTTGAGATACATCCCATCGATACCTAGTTTATTGAGTGTTTTTAGCATGAAGATGTGTTGAATTTATCAAACGGCCTTTTCTGCGTCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT HG:+:793134311:159 HG:+:797860968:161 HG:+:898261251:153 HG:+:924951524:157 HG:+:975096689:159 HG:+:1033028783:174 HG:+:1139622939:150 HG:+:1282702062:143 HG:+:1418480235:174 HG:+:1557683985:140 HG:+:2006850152:159 HG:+:2461101764:150 +GTGGTGACAGAGGGCATCTTTTGTCTTATGGCCAGTTTCAAAGGAATTCTTCCAGATTAATGCCCATTCAGTATGATACTTGGCTGTGGGTTTGATAAAAATAGCTCTTAATTATTTTGAGATACATCCCATCGATACCTAGTTTATTGAGTGTTTTTAGCATGAAGATGTGTTGAATTTATCAAACGGCCTTTTCTGCGTCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT HG:+:300838287:149 HG:+:468804746:-1 HG:+:744436142:199 HG:+:1164039835:161 HG:+:1383944683:159 HG:+:1408684270:157 HG:+:1457214831:143 HG:+:1544076598:155 HG:+:1791671329:146 HG:+:1818423294:151 HG:+:2251102144:-1 HG:+:2811590749:-1 HG:+:2924331255:-1 HG:+:2985952274:-1 HG:+:3058848131:172 +GTGGTGACAGAGGGCATCTTTTGTCTTATGGCCAGTTTCAAAGGAATTCTTCCAGATTAATGCCCATTCAGTATGATACTTGGCTGTGGGTTTGATAAAAATAGCTCTTAATTATTTTGAGATACATCCCATCGATACCTAGTTTATTGAGTGTTTTTAGCATGAAGATGTGTTGAATTTATCAAACGGCCTTTTCTGCGTCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT HG:+:96058894:-1 HG:+:157609075:-1 HG:+:575202397:195 HG:+:1190532364:142 HG:+:1252693649:-1 HG:+:1469262464:-1 HG:+:1485180978:-1 HG:+:1624162634:150 HG:+:1993283211:156 HG:+:2006724422:-1 HG:+:2134292905:-1 HG:+:2594841214:-1 HG:+:2701585210:45 HG:+:3062561484:188 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:52436614:-1 HG:+:59112958:-1 HG:+:153684637:-1 HG:+:200502998:-1 HG:+:215753366:-1 HG:+:269518898:-1 HG:+:452672424:-1 HG:+:476046750:-1 HG:+:519897728:-1 HG:+:590989647:-1 HG:+:601538525:-1 HG:+:610252766:-1 HG:+:615035584:-1 HG:+:644981013:-1 HG:+:645175774:-1 HG:+:648027765:-1 HG:+:730965571:-1 HG:+:802510812:-1 HG:+:805557411:-1 HG:+:1015279372:-1 HG:+:1018302031:-1 HG:+:1020194968:-1 HG:+:1049594051:-1 HG:+:1079885418:-1 HG:+:1255573282:-1 HG:+:1369334578:-1 HG:+:1417536255:-1 HG:+:1435056693:-1 HG:+:1484393632:-1 HG:+:1612145283:-1 HG:+:1629245051:-1 HG:+:1646050257:-1 HG:+:1654614828:-1 HG:+:1674435190:-1 HG:+:1700889394:-1 HG:+:1741584864:-1 HG:+:1862435681:-1 HG:+:1891700236:-1 HG:+:1901067823:-1 HG:+:1902125676:-1 HG:+:1935071790:-1 HG:+:1951920818:-1 HG:+:2110942688:-1 HG:+:2127186235:-1 HG:+:2160735029:-1 HG:+:2183627113:-1 HG:+:2184896176:-1 HG:+:2249235510:-1 HG:+:2270003097:-1 HG:+:2293068798:-1 HG:+:2414455997:-1 HG:+:2431330364:-1 HG:+:2439423480:-1 HG:+:2439627958:-1 HG:+:2476482858:-1 HG:+:2479239342:-1 HG:+:2500085579:-1 HG:+:2540396080:-1 HG:+:2557542960:-1 HG:+:2560704062:-1 HG:+:2599974214:-1 HG:+:2627012832:-1 HG:+:2629585461:-1 HG:+:2680624797:-1 HG:+:2696538165:-1 HG:+:2717244454:-1 HG:+:2815481312:-1 HG:+:2861822388:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:338193201:-1 HG:+:371186769:-1 HG:+:447115145:-1 HG:+:531831655:-1 HG:+:540239414:-1 HG:+:1020101278:-1 HG:+:1791086938:-1 HG:+:1907930573:-1 HG:+:2025295961:-1 HG:+:2047846618:-1 HG:+:2281846664:-1 HG:+:2515760166:-1 HG:+:2528186798:-1 HG:+:2667773452:-1 HG:+:2875412937:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:457913980:-1 HG:+:1239252986:-1 HG:+:2519957445:-1 HG:+:2910681960:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:1819034:-1 HG:+:38145123:-1 HG:+:78360618:-1 HG:+:84492979:-1 HG:+:112955427:-1 HG:+:156230436:-1 HG:+:158086188:-1 HG:+:217896687:-1 HG:+:274261722:-1 HG:+:482877913:-1 HG:+:483234572:-1 HG:+:682290029:-1 HG:+:773202723:-1 HG:+:824646772:-1 HG:+:840576974:-1 HG:+:891814241:-1 HG:+:957644233:-1 HG:+:1055738909:-1 HG:+:1069729106:-1 HG:+:1225507034:-1 HG:+:1260607096:-1 HG:+:1299282111:-1 HG:+:1301688362:-1 HG:+:1325305106:-1 HG:+:1372483360:-1 HG:+:1380910140:-1 HG:+:1390767619:-1 HG:+:1454687792:-1 HG:+:1491879310:-1 HG:+:1558620230:-1 HG:+:1646623890:-1 HG:+:1651974275:-1 HG:+:1692271644:-1 HG:+:1692337446:-1 HG:+:1754497708:-1 HG:+:1761698304:-1 HG:+:1875769382:-1 HG:+:1878088684:-1 HG:+:2064949669:-1 HG:+:2067701121:-1 HG:+:2130414543:-1 HG:+:2133866110:-1 HG:+:2230948753:-1 HG:+:2231822350:-1 HG:+:2348361772:-1 HG:+:2359862041:-1 HG:+:2363028921:-1 HG:+:2387704406:-1 HG:+:2432211807:-1 HG:+:2458238980:-1 HG:+:2536056690:-1 HG:+:2558764147:-1 HG:+:2675699965:-1 HG:+:2676233039:-1 HG:+:2700504477:-1 HG:+:2766468224:-1 HG:+:2780192149:-1 HG:+:2812472524:-1 HG:+:2851961531:-1 HG:+:2863817286:-1 HG:+:2886307056:-1 HG:+:2995162594:-1 HG:+:3035718270:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:212176444:-1 HG:+:329004136:-1 HG:+:497323069:-1 HG:+:518582516:-1 HG:+:1136617070:-1 HG:+:1363118459:-1 HG:+:1629801282:-1 HG:+:1959003463:-1 HG:+:2529133108:-1 HG:+:2577128898:-1 HG:+:2665564049:-1 HG:+:2876105224:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:11170300:-1 HG:+:40339922:-1 HG:+:40709946:-1 HG:+:44643759:-1 HG:+:47666891:-1 HG:+:206849315:-1 HG:+:213024761:-1 HG:+:232057795:-1 HG:+:234248371:-1 HG:+:334881254:-1 HG:+:477885300:-1 HG:+:565058283:-1 HG:+:605790067:-1 HG:+:625039183:-1 HG:+:745069509:-1 HG:+:774647934:-1 HG:+:830520305:-1 HG:+:866942288:-1 HG:+:893086623:-1 HG:+:896412885:-1 HG:+:918872472:-1 HG:+:934912834:-1 HG:+:1263710823:-1 HG:+:1270061098:-1 HG:+:1281843643:-1 HG:+:1380594509:-1 HG:+:1390383722:-1 HG:+:1423566922:-1 HG:+:1448162621:-1 HG:+:1491952586:-1 HG:+:1507607453:-1 HG:+:1612869149:-1 HG:+:1667171629:-1 HG:+:1750604394:-1 HG:+:1774707485:-1 HG:+:1862265223:-1 HG:+:1862583775:-1 HG:+:1892313007:-1 HG:+:2028156257:-1 HG:+:2036810125:-1 HG:+:2121235738:-1 HG:+:2130844385:-1 HG:+:2253360925:-1 HG:+:2277418728:-1 HG:+:2358232111:-1 HG:+:2372189695:-1 HG:+:2408776638:-1 HG:+:2439845154:-1 HG:+:2439877119:-1 HG:+:2525815116:-1 HG:+:2545507891:-1 HG:+:2546692382:-1 HG:+:2565465539:-1 HG:+:2569041065:-1 HG:+:2576759783:-1 HG:+:2582181278:-1 HG:+:2586746085:-1 HG:+:2625078691:-1 HG:+:2650696534:-1 HG:+:2683497715:-1 HG:+:2689734951:-1 HG:+:2752850088:-1 HG:+:2866562909:-1 HG:+:2869666638:-1 HG:+:2922554094:-1 HG:+:2972413174:-1 HG:+:3013099404:-1 HG:+:3014674196:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:451700816:-1 HG:+:492308062:-1 HG:+:1091739127:-1 HG:+:1134126130:-1 HG:+:1227566741:-1 HG:+:1470570835:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:646706869:-1 HG:+:1904600804:-1 HG:+:1970805672:-1 HG:+:2072351351:-1 HG:+:2390604860:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:216762933:-1 HG:+:321919613:-1 HG:+:683786803:-1 HG:+:831020678:-1 HG:+:1637750749:-1 HG:+:1704282499:-1 HG:+:1774621811:-1 HG:+:2343439229:-1 HG:+:2918067832:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:1149242327:-1 HG:+:1239831326:-1 HG:+:1656368716:-1 HG:+:1898249183:-1 HG:+:2936789113:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:261632488:-1 HG:+:705308195:-1 HG:+:912260020:-1 HG:+:1006357578:-1 HG:+:1406005351:-1 HG:+:1728880158:-1 HG:+:2251545860:-1 HG:+:2256330724:-1 HG:+:2565773892:-1 HG:+:2608810435:-1 HG:+:2651613725:-1 HG:+:2709221312:-1 HG:+:2926578713:-1 HG:+:3003032492:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:22632290:-1 HG:+:189623324:-1 HG:+:348909674:-1 HG:+:393564485:-1 HG:+:629891246:-1 HG:+:643965432:-1 HG:+:1423659863:-1 HG:+:1444688276:-1 HG:+:1457360674:-1 HG:+:1628554377:-1 HG:+:1662591456:-1 HG:+:2149405975:-1 HG:+:2190534891:-1 HG:+:2192598841:-1 HG:+:2621858518:-1 HG:+:2887323555:-1 HG:+:3034050059:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:387280471:-1 HG:+:468602230:-1 HG:+:478836280:-1 HG:+:1102095972:-1 HG:+:1251546273:-1 HG:+:1365941602:-1 HG:+:1946396397:-1 HG:+:2757340098:-1 HG:+:2961965820:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:649574216:-1 HG:+:796770546:-1 HG:+:918769459:-1 HG:+:1306544523:-1 HG:+:1968645966:-1 HG:+:1998980107:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:807285311:-1 HG:+:1028140123:-1 HG:+:1074667830:-1 HG:+:1151866548:-1 HG:+:1165356789:-1 HG:+:1222046655:-1 HG:+:1231081822:-1 HG:+:2121303473:-1 HG:+:2872085470:-1 HG:+:2887142974:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:79534756:-1 HG:+:91055471:-1 HG:+:172986513:-1 HG:+:189312433:-1 HG:+:332120243:-1 HG:+:528919264:-1 HG:+:608315786:-1 HG:+:748406163:-1 HG:+:910890356:-1 HG:+:1211788492:-1 HG:+:1452055130:-1 HG:+:1515224483:-1 HG:+:1517195205:-1 HG:+:1542551895:-1 HG:+:1687066649:-1 HG:+:1937156293:-1 HG:+:1945679373:-1 HG:+:2405000318:-1 HG:+:2931323899:-1 HG:+:2971438052:-1 HG:+:3040785449:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:267634204:-1 HG:+:763877719:-1 HG:+:802444529:-1 HG:+:956419901:-1 HG:+:1079303834:-1 HG:+:1095515923:-1 HG:+:1102480724:-1 HG:+:1476442840:-1 HG:+:1513146354:-1 HG:+:1664391149:-1 HG:+:1877504095:-1 HG:+:2034556355:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:1300633701:-1 HG:+:1647538601:-1 HG:+:1835295594:-1 HG:+:2052880874:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:803422213:-1 HG:+:2709016598:-1 HG:+:2929085371:-1 HG:+:2929194854:-1 HG:+:2929245246:-1 HG:+:2933671401:-1 HG:+:2933713112:-1 HG:+:2933765350:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:38291721:-1 HG:+:236986667:-1 HG:+:1211006578:-1 HG:+:1291071887:-1 HG:+:2380999830:-1 HG:+:2539465292:-1 HG:+:2993462635:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:1255477025:-1 HG:+:1914605602:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:464346423:-1 HG:+:722699104:-1 HG:+:782655277:-1 HG:+:1021076458:-1 HG:+:1133213917:-1 HG:+:1168086491:-1 HG:+:2156578661:-1 HG:+:2170411862:-1 HG:+:2884202620:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:937486127:-1 HG:+:1254011334:-1 HG:+:2064312617:-1 HG:+:2285318693:-1 HG:+:3017295366:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:94960477:-1 HG:+:189308468:-1 HG:+:269138645:-1 HG:+:659635103:-1 HG:+:885675349:-1 HG:+:921053756:-1 HG:+:984164967:-1 HG:+:1327041021:-1 HG:+:1364793331:-1 HG:+:1408593791:-1 HG:+:1706784953:-1 HG:+:2666006717:-1 HG:+:3024644257:-1 HG:+:3028468217:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:346238843:-1 HG:+:1013302271:-1 HG:+:1180702378:-1 HG:+:1262014121:-1 HG:+:1617343169:-1 HG:+:1881259936:-1 HG:+:2847527550:-1 HG:+:3021503979:-1 HG:+:3057430867:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGGGAGGCTGAGGCAGGTGGATCACCTGGAGGTCTAGGAGTTTGGAGACCAGCTTGGCCAACATGGTGACCATTCTCTACTAAAAATACAAAATCACCCTGGTGTGGTGCATGCGTCTGTAATCCCAGCGTACTCGGAGGCTGAGGCAGGAGAATCGGCTTGACCCAGGAGGCGAGGTTGGCAGTGAGCTGAGATTGCGACCA HG:+:305682680:-1 HG:+:312379852:-1 HG:+:668726844:-1 HG:+:685818102:-1 HG:+:713532476:-1 HG:+:963811152:-1 HG:+:1048765132:-1 HG:+:1215679387:-1 HG:+:1332817641:-1 HG:+:1455958809:-1 HG:+:1557587689:-1 HG:+:1626680420:-1 HG:+:1698915611:-1 HG:+:1810484517:-1 HG:+:1963436026:-1 HG:+:2025933732:-1 HG:+:2029496452:-1 HG:+:2619280807:-1 HG:+:2736659127:-1 HG:+:2890156426:-1 HG:+:2965593699:-1 +TGGTCGCAATCTCAGCTCACTGCCAACCTCGCCTCCTGGGTCAAGCCGATTCTCCTGCCTCAGCCTCCGAGTACGCTGGGATTACAGACGCATGCACCACACCAGGGTGATTTTGTATTTTTAGTAGAGAATGGTCACCATGTTGGCCAAGCTGGTCTCCAAACTCCTAGACCTCCAGGTGATCCACCTGCCTCAGCCTCCCAAAGGTTCTGGGATTACAGGCGTGACCCACCGTGCCTAAGTCGATTTTCATTTTCTTCTTTTGTGCTTTCTATAATTTTTCCAAGTTTCCAAAATGGACATTTTAAAAATGTATTATTTTATAATAAAAAGGGGTGGTAGTTAGGTAACATGGAATACACACTAAAAATCAGAACGTGTGGAAACAGCTCTCAACAGTCACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT HG:+:35712331:-1 HG:+:40725590:-1 HG:+:112920468:-1 HG:+:156665849:-1 HG:+:158002719:-1 HG:+:191919722:-1 HG:+:238793317:-1 HG:+:258840762:-1 HG:+:310279052:-1 HG:+:358991108:-1 HG:+:382970642:-1 HG:+:384130153:-1 HG:+:385828929:-1 HG:+:468720089:-1 HG:+:486041597:-1 HG:+:508086969:53 HG:+:512561647:-1 HG:+:561622470:-1 HG:+:565199582:-1 HG:+:586481556:-1 HG:+:591036498:-1 HG:+:630928616:-1 HG:+:645265945:-1 HG:+:648786551:-1 HG:+:715081816:-1 HG:+:717513701:-1 HG:+:773685921:-1 HG:+:777402027:-1 HG:+:831975043:-1 HG:+:872393453:-1 HG:+:918900091:-1 HG:+:980497364:-1 HG:+:1002983946:-1 HG:+:1004536100:-1 HG:+:1038194648:-1 HG:+:1050207521:-1 HG:+:1068503116:-1 HG:+:1073231021:-1 HG:+:1092202674:-1 HG:+:1107153604:-1 HG:+:1267082990:-1 HG:+:1300140611:-1 HG:+:1309199898:-1 HG:+:1340461948:-1 HG:+:1421629773:-1 HG:+:1435552398:-1 HG:+:1449928077:-1 HG:+:1467121117:-1 HG:+:1488627367:-1 HG:+:1491865877:-1 HG:+:1504341760:-1 HG:+:1513896183:-1 HG:+:1539946918:-1 HG:+:1539980749:-1 HG:+:1574644856:-1 HG:+:1586168150:-1 HG:+:1605228788:-1 HG:+:1619366387:-1 HG:+:1635441094:-1 HG:+:1665885114:-1 HG:+:1667800929:-1 HG:+:1694541168:-1 HG:+:1784657078:-1 HG:+:1806443941:-1 HG:+:1816876973:-1 HG:+:1863887197:-1 HG:+:1877629669:-1 HG:+:1893357473:-1 HG:+:1973159524:-1 HG:+:2051824407:-1 HG:+:2105092884:-1 HG:+:2110693471:-1 HG:+:2161249581:-1 HG:+:2170042403:-1 HG:+:2222268870:-1 HG:+:2235817307:-1 HG:+:2276889982:-1 HG:+:2349261355:-1 HG:+:2363840797:-1 HG:+:2397858423:-1 HG:+:2398064376:-1 HG:+:2430952081:-1 HG:+:2457013681:-1 HG:+:2477718557:-1 HG:+:2484892196:-1 HG:+:2497361133:-1 HG:+:2511727323:-1 HG:+:2519628576:-1 HG:+:2527528556:-1 HG:+:2529248495:-1 HG:+:2537239768:-1 HG:+:2549205290:-1 HG:+:2563944064:-1 HG:+:2573869825:-1 HG:+:2574762132:-1 HG:+:2578681289:-1 HG:+:2593066145:-1 HG:+:2593101071:-1 HG:+:2595916340:-1 HG:+:2641760748:-1 HG:+:2661510480:-1 HG:+:2664294626:-1 HG:+:2664419783:-1 HG:+:2664846347:-1 HG:+:2673174669:-1 HG:+:2675734806:-1 HG:+:2676965954:-1 HG:+:2679285015:-1 HG:+:2699260413:-1 HG:+:2708488983:-1 HG:+:2743977412:-1 HG:+:2753850109:-1 HG:+:2754105116:-1 HG:+:2763564567:-1 HG:+:2854630258:-1 HG:+:2855192980:-1 HG:+:2876358842:-1 HG:+:2888006440:-1 HG:+:2925276720:-1 HG:+:2935771379:-1 HG:+:3014999576:-1 HG:+:3017279282:-1 HG:+:3044362153:-1 +TGGTCGCAATCTCAGCTCACTGCCAACCTCGCCTCCTGGGTCAAGCCGATTCTCCTGCCTCAGCCTCCGAGTACGCTGGGATTACAGACGCATGCACCACACCAGGGTGATTTTGTATTTTTAGTAGAGAATGGTCACCATGTTGGCCAAGCTGGTCTCCAAACTCCTAGACCTCCAGGTGATCCACCTGCCTCAGCCTCCCAAAGGTTCTGGGATTACAGGCGTGACCCACCGTGCCTAAGTCGATTTTCATTTTCTTCTTTTGTGCTTTCTATAATTTTTCCAAGTTTCCAAAATGGACATTTTAAAAATGTATTATTTTATAATAAAAAGGGGTGGTAGTTAGGTAACATGGAATACACACTAAAAATCAGAACGTGTGGAAACAGCTCTCAACAGTCACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT HG:+:508086964:53 +TGGTCGCAATCTCAGCTCACTGCCAACCTCGCCTCCTGGGTCAAGCCGATTCTCCTGCCTCAGCCTCCGAGTACGCTGGGATTACAGACGCATGCACCACACCAGGGTGATTTTGTATTTTTAGTAGAGAATGGTCACCATGTTGGCCAAGCTGGTCTCCAAACTCCTAGACCTCCAGGTGATCCACCTGCCTCAGCCTCCCAAAGGTTCTGGGATTACAGGCGTGACCCACCGTGCCTAAGTCGATTTTCATTTTCTTCTTTTGTGCTTTCTATAATTTTTCCAAGTTTCCAAAATGGACATTTTAAAAATGTATTATTTTATAATAAAAAGGGGTGGTAGTTAGGTAACATGGAATACACACTAAAAATCAGAACGTGTGGAAACAGCTCTCAACAGTCACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT HG:+:508086966:53 +TGGTCGCAATCTCAGCTCACTGCCAACCTCGCCTCCTGGGTCAAGCCGATTCTCCTGCCTCAGCCTCCGAGTACGCTGGGATTACAGACGCATGCACCACACCAGGGTGATTTTGTATTTTTAGTAGAGAATGGTCACCATGTTGGCCAAGCTGGTCTCCAAACTCCTAGACCTCCAGGTGATCCACCTGCCTCAGCCTCCCAAAGGTTCTGGGATTACAGGCGTGACCCACCGTGCCTAAGTCGATTTTCATTTTCTTCTTTTGTGCTTTCTATAATTTTTCCAAGTTTCCAAAATGGACATTTTAAAAATGTATTATTTTATAATAAAAAGGGGTGGTAGTTAGGTAACATGGAATACACACTAAAAATCAGAACGTGTGGAAACAGCTCTCAACAGTCACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT HG:+:2360011198:-1 +TGGTCGCAATCTCAGCTCACTGCCAACCTCGCCTCCTGGGTCAAGCCGATTCTCCTGCCTCAGCCTCCGAGTACGCTGGGATTACAGACGCATGCACCACACCAGGGTGATTTTGTATTTTTAGTAGAGAATGGTCACCATGTTGGCCAAGCTGGTCTCCAAACTCCTAGACCTCCAGGTGATCCACCTGCCTCAGCCTCCCAAAGGTTCTGGGATTACAGGCGTGACCCACCGTGCCTAAGTCGATTTTCATTTTCTTCTTTTGTGCTTTCTATAATTTTTCCAAGTTTCCAAAATGGACATTTTAAAAATGTATTATTTTATAATAAAAAGGGGTGGTAGTTAGGTAACATGGAATACACACTAAAAATCAGAACGTGTGGAAACAGCTCTCAACAGTCACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT HG:+:508086963:53 +TGGTCGCAATCTCAGCTCACTGCCAACCTCGCCTCCTGGGTCAAGCCGATTCTCCTGCCTCAGCCTCCGAGTACGCTGGGATTACAGACGCATGCACCACACCAGGGTGATTTTGTATTTTTAGTAGAGAATGGTCACCATGTTGGCCAAGCTGGTCTCCAAACTCCTAGACCTCCAGGTGATCCACCTGCCTCAGCCTCCCAAAGGTTCTGGGATTACAGGCGTGACCCACCGTGCCTAAGTCGATTTTCATTTTCTTCTTTTGTGCTTTCTATAATTTTTCCAAGTTTCCAAAATGGACATTTTAAAAATGTATTATTTTATAATAAAAAGGGGTGGTAGTTAGGTAACATGGAATACACACTAAAAATCAGAACGTGTGGAAACAGCTCTCAACAGTCACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT HG:+:508086970:53 +TGGTCGCAATCTCAGCTCACTGCCAACCTCGCCTCCTGGGTCAAGCCGATTCTCCTGCCTCAGCCTCCGAGTACGCTGGGATTACAGACGCATGCACCACACCAGGGTGATTTTGTATTTTTAGTAGAGAATGGTCACCATGTTGGCCAAGCTGGTCTCCAAACTCCTAGACCTCCAGGTGATCCACCTGCCTCAGCCTCCCAAAGGTTCTGGGATTACAGGCGTGACCCACCGTGCCTAAGTCGATTTTCATTTTCTTCTTTTGTGCTTTCTATAATTTTTCCAAGTTTCCAAAATGGACATTTTAAAAATGTATTATTTTATAATAAAAAGGGGTGGTAGTTAGGTAACATGGAATACACACTAAAAATCAGAACGTGTGGAAACAGCTCTCAACAGTCACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT HG:+:508086968:53 HG:+:2987752433:-1 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACTGTCACAAGGTCCCACAATAGGCTGCTGCAAGCTTGAGGAGCGAGGGAGAGTCAGTCCAAGTCCCAAAACGGAAGAACTTGGAGTCTAATGTTCAAGAGCAGGAAGCATCCAGCCTGGAGAAAGTATGCAGGCTCGGAGGCTAGGCCAGGTCTGGCCTTTTTCACATTTTCTGCCTGCTTTATATTCACTGGCAGCTTGAT HG:+:1208197338:-1 HG:+:2173403053:-1 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACTGTCACAAGGTCCCACAATAGGCTGCTGCAAGCTTGAGGAGCGAGGGAGAGTCAGTCCAAGTCCCAAAACGGAAGAACTTGGAGTCTAATGTTCAAGAGCAGGAAGCATCCAGCCTGGAGAAAGTATGCAGGCTCGGAGGCTAGGCCAGGTCTGGCCTTTTTCACATTTTCTGCCTGCTTTATATTCACTGGCAGCTTGAT HG:+:78866888:-1 HG:+:78866932:-1 HG:+:143682989:-1 HG:+:147870498:-1 HG:+:149601537:-1 HG:+:329313910:-1 HG:+:418866339:-1 HG:+:836308117:-1 HG:+:918897447:-1 HG:+:1006641579:-1 HG:+:1338130057:-1 HG:+:1556278330:-1 HG:+:1611544159:-1 HG:+:1614499059:-1 HG:+:1965359278:-1 HG:+:2408048790:-1 HG:+:2543843476:-1 HG:+:2656550248:-1 HG:+:2878074767:-1 HG:+:2946732038:-1 HG:+:3013652900:-1 HG:+:3025538731:-1 HG:+:3031707904:-1 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACTGTCACAAGGTCCCACAATAGGCTGCTGCAAGCTTGAGGAGCGAGGGAGAGTCAGTCCAAGTCCCAAAACGGAAGAACTTGGAGTCTAATGTTCAAGAGCAGGAAGCATCCAGCCTGGAGAAAGTATGCAGGCTCGGAGGCTAGGCCAGGTCTGGCCTTTTTCACATTTTCTGCCTGCTTTATATTCACTGGCAGCTTGAT HG:+:2817198702:55 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACTGTCACAAGGTCCCACAATAGGCTGCTGCAAGCTTGAGGAGCGAGGGAGAGTCAGTCCAAGTCCCAAAACGGAAGAACTTGGAGTCTAATGTTCAAGAGCAGGAAGCATCCAGCCTGGAGAAAGTATGCAGGCTCGGAGGCTAGGCCAGGTCTGGCCTTTTTCACATTTTCTGCCTGCTTTATATTCACTGGCAGCTTGAT HG:+:2817198692:55 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACTGTCACAAGGTCCCACAATAGGCTGCTGCAAGCTTGAGGAGCGAGGGAGAGTCAGTCCAAGTCCCAAAACGGAAGAACTTGGAGTCTAATGTTCAAGAGCAGGAAGCATCCAGCCTGGAGAAAGTATGCAGGCTCGGAGGCTAGGCCAGGTCTGGCCTTTTTCACATTTTCTGCCTGCTTTATATTCACTGGCAGCTTGAT HG:+:2817198694:55 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACTGTCACAAGGTCCCACAATAGGCTGCTGCAAGCTTGAGGAGCGAGGGAGAGTCAGTCCAAGTCCCAAAACGGAAGAACTTGGAGTCTAATGTTCAAGAGCAGGAAGCATCCAGCCTGGAGAAAGTATGCAGGCTCGGAGGCTAGGCCAGGTCTGGCCTTTTTCACATTTTCTGCCTGCTTTATATTCACTGGCAGCTTGAT HG:+:2817198700:55 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACTGTCACAAGGTCCCACAATAGGCTGCTGCAAGCTTGAGGAGCGAGGGAGAGTCAGTCCAAGTCCCAAAACGGAAGAACTTGGAGTCTAATGTTCAAGAGCAGGAAGCATCCAGCCTGGAGAAAGTATGCAGGCTCGGAGGCTAGGCCAGGTCTGGCCTTTTTCACATTTTCTGCCTGCTTTATATTCACTGGCAGCTTGAT HG:+:2817198701:55 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACTGTCACAAGGTCCCACAATAGGCTGCTGCAAGCTTGAGGAGCGAGGGAGAGTCAGTCCAAGTCCCAAAACGGAAGAACTTGGAGTCTAATGTTCAAGAGCAGGAAGCATCCAGCCTGGAGAAAGTATGCAGGCTCGGAGGCTAGGCCAGGTCTGGCCTTTTTCACATTTTCTGCCTGCTTTATATTCACTGGCAGCTTGAT HG:+:2817198685:55 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACTGTCACAAGGTCCCACAATAGGCTGCTGCAAGCTTGAGGAGCGAGGGAGAGTCAGTCCAAGTCCCAAAACGGAAGAACTTGGAGTCTAATGTTCAAGAGCAGGAAGCATCCAGCCTGGAGAAAGTATGCAGGCTCGGAGGCTAGGCCAGGTCTGGCCTTTTTCACATTTTCTGCCTGCTTTATATTCACTGGCAGCTTGAT HG:+:2817198686:55 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACTGTCACAAGGTCCCACAATAGGCTGCTGCAAGCTTGAGGAGCGAGGGAGAGTCAGTCCAAGTCCCAAAACGGAAGAACTTGGAGTCTAATGTTCAAGAGCAGGAAGCATCCAGCCTGGAGAAAGTATGCAGGCTCGGAGGCTAGGCCAGGTCTGGCCTTTTTCACATTTTCTGCCTGCTTTATATTCACTGGCAGCTTGAT HG:+:2817198696:55 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACTGTCACAAGGTCCCACAATAGGCTGCTGCAAGCTTGAGGAGCGAGGGAGAGTCAGTCCAAGTCCCAAAACGGAAGAACTTGGAGTCTAATGTTCAAGAGCAGGAAGCATCCAGCCTGGAGAAAGTATGCAGGCTCGGAGGCTAGGCCAGGTCTGGCCTTTTTCACATTTTCTGCCTGCTTTATATTCACTGGCAGCTTGAT HG:+:3014694390:-1 +ATCAAGCTGCCAGTGAATATAAAGCAGGCAGAAAATGTGAAAAAGGCCAGACCTGGCCTAGCCTCCGAGCCTGCATACTTTCTCCAGGCTGGATGCTTCCTGCTCTTGAACATTAGACTCCAAGTTCTTCCGTTTTGGGACTTGGACTGACTCTCCCTCGCTCCTCAAGCTTGCAGCAGCCTATTGTGGGACCTTGTGACAGTGTAAGTTAATACTTAATAAACTCCAGATAGATAGTATAGATAGATAGATAGATAGATAATAGATAGATAGATATCGCCTATTAGTTCTGTCCCCTCTGAGAACCTGACCTAATACAGTTTAGGAAACCAAGTATGAACCTTCCAACCATGTGGCTGTCTGCTTGGGGACACTCAGTACCAACTTCAGGCTTAACGTTGGAGTGGAACCACAGATGCCCTTGAAACAGATTAGCTGGGACCACAAAGGCTGGAAGGCCAGCAAGCAGGAGGCCAAGACTCCTTGAGGCCAAGCTGGGATAAAATGCACCCTTATTCCCACCACAGCTGCTCCTAGCTTCGGATTTGGCATGGTGTGCTGGAGCAGACACCCTTCGCCATCCTCTCCTGTTGCTCAGCTATGTTTGAGTTTGGAGAGCGACAATGGGTGCTTGCTGCTCTCCTCGACCAAAACTACAGCTACAAGCTCAGGGAGATGAAATTTCCCTCAGGCAGCTTCCGTCTGTCTCTTAGGGAGTCATCCTTACTGGAGGAGCCTCGGGGTTCTCAGAGGGCACCTTGTCCGGGCCTTGTCCCTTCATAGCAGGACCTGGATCAGGTAGCTCGCAGAGGTTGGAGCAACCATGACTGTGCTACCTTGGTTGCTTCTCCAGGCCCAGTCCATACTGGGGTTGATTTGAAAGAATATTTACACTAAAAGGGCTTAAGCAGAGGGAAGATTTCACTGCCTCTTATCTTCTCATAGTTTAGAAAAACAACCAACATTTCACTGAACGCGTGACCCTGTGGTGCCTGTGTTT HG:+:811613102:-1 +ATCAAGCTGCCAGTGAATATAAAGCAGGCAGAAAATGTGAAAAAGGCCAGACCTGGCCTAGCCTCCGAGCCTGCATACTTTCTCCAGGCTGGATGCTTCCTGCTCTTGAACATTAGACTCCAAGTTCTTCCGTTTTGGGACTTGGACTGACTCTCCCTCGCTCCTCAAGCTTGCAGCAGCCTATTGTGGGACCTTGTGACAGTGTAAGTTAATACTTAATAAACTCCAGATAGATAGTATAGATAGATAGATAGATAGATAATAGATAGATAGATATCGCCTATTAGTTCTGTCCCCTCTGAGAACCTGACCTAATACAGTTTAGGAAACCAAGTATGAACCTTCCAACCATGTGGCTGTCTGCTTGGGGACACTCAGTACCAACTTCAGGCTTAACGTTGGAGTGGAACCACAGATGCCCTTGAAACAGATTAGCTGGGACCACAAAGGCTGGAAGGCCAGCAAGCAGGAGGCCAAGACTCCTTGAGGCCAAGCTGGGATAAAATGCACCCTTATTCCCACCACAGCTGCTCCTAGCTTCGGATTTGGCATGGTGTGCTGGAGCAGACACCCTTCGCCATCCTCTCCTGTTGCTCAGCTATGTTTGAGTTTGGAGAGCGACAATGGGTGCTTGCTGCTCTCCTCGACCAAAACTACAGCTACAAGCTCAGGGAGATGAAATTTCCCTCAGGCAGCTTCCGTCTGTCTCTTAGGGAGTCATCCTTACTGGAGGAGCCTCGGGGTTCTCAGAGGGCACCTTGTCCGGGCCTTGTCCCTTCATAGCAGGACCTGGATCAGGTAGCTCGCAGAGGTTGGAGCAACCATGACTGTGCTACCTTGGTTGCTTCTCCAGGCCCAGTCCATACTGGGGTTGATTTGAAAGAATATTTACACTAAAAGGGCTTAAGCAGAGGGAAGATTTCACTGCCTCTTATCTTCTCATAGTTTAGAAAAACAACCAACATTTCACTGAACGCGTGACCCTGTGGTGCCTGTGTTT HG:+:2476907800:-1 +ATCAAGCTGCCAGTGAATATAAAGCAGGCAGAAAATGTGAAAAAGGCCAGACCTGGCCTAGCCTCCGAGCCTGCATACTTTCTCCAGGCTGGATGCTTCCTGCTCTTGAACATTAGACTCCAAGTTCTTCCGTTTTGGGACTTGGACTGACTCTCCCTCGCTCCTCAAGCTTGCAGCAGCCTATTGTGGGACCTTGTGACAGTGTAAGTTAATACTTAATAAACTCCAGATAGATAGTATAGATAGATAGATAGATAGATAATAGATAGATAGATATCGCCTATTAGTTCTGTCCCCTCTGAGAACCTGACCTAATACAGTTTAGGAAACCAAGTATGAACCTTCCAACCATGTGGCTGTCTGCTTGGGGACACTCAGTACCAACTTCAGGCTTAACGTTGGAGTGGAACCACAGATGCCCTTGAAACAGATTAGCTGGGACCACAAAGGCTGGAAGGCCAGCAAGCAGGAGGCCAAGACTCCTTGAGGCCAAGCTGGGATAAAATGCACCCTTATTCCCACCACAGCTGCTCCTAGCTTCGGATTTGGCATGGTGTGCTGGAGCAGACACCCTTCGCCATCCTCTCCTGTTGCTCAGCTATGTTTGAGTTTGGAGAGCGACAATGGGTGCTTGCTGCTCTCCTCGACCAAAACTACAGCTACAAGCTCAGGGAGATGAAATTTCCCTCAGGCAGCTTCCGTCTGTCTCTTAGGGAGTCATCCTTACTGGAGGAGCCTCGGGGTTCTCAGAGGGCACCTTGTCCGGGCCTTGTCCCTTCATAGCAGGACCTGGATCAGGTAGCTCGCAGAGGTTGGAGCAACCATGACTGTGCTACCTTGGTTGCTTCTCCAGGCCCAGTCCATACTGGGGTTGATTTGAAAGAATATTTACACTAAAAGGGCTTAAGCAGAGGGAAGATTTCACTGCCTCTTATCTTCTCATAGTTTAGAAAAACAACCAACATTTCACTGAACGCGTGACCCTGTGGTGCCTGTGTTT HG:+:1019559696:-1 +ATCAAGCTGCCAGTGAATATAAAGCAGGCAGAAAATGTGAAAAAGGCCAGACCTGGCCTAGCCTCCGAGCCTGCATACTTTCTCCAGGCTGGATGCTTCCTGCTCTTGAACATTAGACTCCAAGTTCTTCCGTTTTGGGACTTGGACTGACTCTCCCTCGCTCCTCAAGCTTGCAGCAGCCTATTGTGGGACCTTGTGACAGTGTAAGTTAATACTTAATAAACTCCAGATAGATAGTATAGATAGATAGATAGATAGATAATAGATAGATAGATATCGCCTATTAGTTCTGTCCCCTCTGAGAACCTGACCTAATACAGTTTAGGAAACCAAGTATGAACCTTCCAACCATGTGGCTGTCTGCTTGGGGACACTCAGTACCAACTTCAGGCTTAACGTTGGAGTGGAACCACAGATGCCCTTGAAACAGATTAGCTGGGACCACAAAGGCTGGAAGGCCAGCAAGCAGGAGGCCAAGACTCCTTGAGGCCAAGCTGGGATAAAATGCACCCTTATTCCCACCACAGCTGCTCCTAGCTTCGGATTTGGCATGGTGTGCTGGAGCAGACACCCTTCGCCATCCTCTCCTGTTGCTCAGCTATGTTTGAGTTTGGAGAGCGACAATGGGTGCTTGCTGCTCTCCTCGACCAAAACTACAGCTACAAGCTCAGGGAGATGAAATTTCCCTCAGGCAGCTTCCGTCTGTCTCTTAGGGAGTCATCCTTACTGGAGGAGCCTCGGGGTTCTCAGAGGGCACCTTGTCCGGGCCTTGTCCCTTCATAGCAGGACCTGGATCAGGTAGCTCGCAGAGGTTGGAGCAACCATGACTGTGCTACCTTGGTTGCTTCTCCAGGCCCAGTCCATACTGGGGTTGATTTGAAAGAATATTTACACTAAAAGGGCTTAAGCAGAGGGAAGATTTCACTGCCTCTTATCTTCTCATAGTTTAGAAAAACAACCAACATTTCACTGAACGCGTGACCCTGTGGTGCCTGTGTTT HG:+:1812965350:-1 +ATCAAGCTGCCAGTGAATATAAAGCAGGCAGAAAATGTGAAAAAGGCCAGACCTGGCCTAGCCTCCGAGCCTGCATACTTTCTCCAGGCTGGATGCTTCCTGCTCTTGAACATTAGACTCCAAGTTCTTCCGTTTTGGGACTTGGACTGACTCTCCCTCGCTCCTCAAGCTTGCAGCAGCCTATTGTGGGACCTTGTGACAGTGTAAGTTAATACTTAATAAACTCCAGATAGATAGTATAGATAGATAGATAGATAGATAATAGATAGATAGATATCGCCTATTAGTTCTGTCCCCTCTGAGAACCTGACCTAATACAGTTTAGGAAACCAAGTATGAACCTTCCAACCATGTGGCTGTCTGCTTGGGGACACTCAGTACCAACTTCAGGCTTAACGTTGGAGTGGAACCACAGATGCCCTTGAAACAGATTAGCTGGGACCACAAAGGCTGGAAGGCCAGCAAGCAGGAGGCCAAGACTCCTTGAGGCCAAGCTGGGATAAAATGCACCCTTATTCCCACCACAGCTGCTCCTAGCTTCGGATTTGGCATGGTGTGCTGGAGCAGACACCCTTCGCCATCCTCTCCTGTTGCTCAGCTATGTTTGAGTTTGGAGAGCGACAATGGGTGCTTGCTGCTCTCCTCGACCAAAACTACAGCTACAAGCTCAGGGAGATGAAATTTCCCTCAGGCAGCTTCCGTCTGTCTCTTAGGGAGTCATCCTTACTGGAGGAGCCTCGGGGTTCTCAGAGGGCACCTTGTCCGGGCCTTGTCCCTTCATAGCAGGACCTGGATCAGGTAGCTCGCAGAGGTTGGAGCAACCATGACTGTGCTACCTTGGTTGCTTCTCCAGGCCCAGTCCATACTGGGGTTGATTTGAAAGAATATTTACACTAAAAGGGCTTAAGCAGAGGGAAGATTTCACTGCCTCTTATCTTCTCATAGTTTAGAAAAACAACCAACATTTCACTGAACGCGTGACCCTGTGGTGCCTGTGTTT HG:+:256330926:-1 HG:+:591708578:-1 HG:+:824312981:-1 HG:+:2402503119:-1 HG:+:2427460811:-1 HG:+:2494632286:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:15097353:-1 HG:+:36281431:-1 HG:+:52147461:-1 HG:+:113338838:-1 HG:+:146889179:-1 HG:+:150072871:-1 HG:+:161022889:-1 HG:+:168569102:-1 HG:+:209269744:-1 HG:+:226176029:-1 HG:+:234777066:-1 HG:+:239696659:-1 HG:+:240183926:-1 HG:+:311321486:-1 HG:+:322195639:-1 HG:+:382908185:-1 HG:+:386977686:-1 HG:+:423486813:-1 HG:+:527873732:-1 HG:+:536885411:-1 HG:+:538119930:-1 HG:+:540435867:-1 HG:+:541452419:-1 HG:+:558934196:-1 HG:+:600475506:-1 HG:+:611853563:-1 HG:+:615629250:-1 HG:+:630956524:-1 HG:+:664141223:-1 HG:+:671468227:-1 HG:+:674010234:-1 HG:+:676698272:-1 HG:+:686169811:-1 HG:+:692140310:-1 HG:+:737926468:-1 HG:+:758350334:-1 HG:+:773478051:-1 HG:+:773742021:-1 HG:+:774880917:-1 HG:+:781573195:-1 HG:+:792177285:-1 HG:+:795747967:-1 HG:+:882991576:-1 HG:+:916079940:-1 HG:+:976627404:-1 HG:+:1018668853:-1 HG:+:1019223114:-1 HG:+:1022065185:-1 HG:+:1057365270:-1 HG:+:1072894850:-1 HG:+:1084154518:-1 HG:+:1206572821:-1 HG:+:1224574744:-1 HG:+:1235529635:-1 HG:+:1235809273:-1 HG:+:1238912121:-1 HG:+:1260777829:-1 HG:+:1261434474:-1 HG:+:1263202311:-1 HG:+:1273339378:-1 HG:+:1288972250:-1 HG:+:1290329678:-1 HG:+:1299283442:-1 HG:+:1305486348:-1 HG:+:1309032720:-1 HG:+:1321213980:-1 HG:+:1335046375:-1 HG:+:1362786482:-1 HG:+:1365113081:-1 HG:+:1376999683:-1 HG:+:1381833365:-1 HG:+:1383229523:-1 HG:+:1415016505:-1 HG:+:1422897602:-1 HG:+:1467470382:-1 HG:+:1502300097:-1 HG:+:1508860261:-1 HG:+:1530468141:-1 HG:+:1565285070:-1 HG:+:1580448544:-1 HG:+:1582751809:-1 HG:+:1604630972:-1 HG:+:1613063527:-1 HG:+:1634862653:-1 HG:+:1656586910:-1 HG:+:1665810995:-1 HG:+:1671914249:-1 HG:+:1675337606:-1 HG:+:1702119166:-1 HG:+:1712283759:-1 HG:+:1726464707:-1 HG:+:1779243121:-1 HG:+:1783489372:-1 HG:+:1801815186:-1 HG:+:1805734062:-1 HG:+:1862461634:-1 HG:+:1875702334:-1 HG:+:1893235884:-1 HG:+:1923622272:-1 HG:+:1967122025:-1 HG:+:1972414017:-1 HG:+:1973899664:-1 HG:+:1985076549:-1 HG:+:2028713154:-1 HG:+:2036331992:-1 HG:+:2041908908:-1 HG:+:2044607320:-1 HG:+:2054898700:-1 HG:+:2068382956:-1 HG:+:2071764917:-1 HG:+:2073889513:-1 HG:+:2074606202:-1 HG:+:2079056598:-1 HG:+:2105117418:-1 HG:+:2112699582:-1 HG:+:2114010516:-1 HG:+:2117147943:-1 HG:+:2127557502:-1 HG:+:2130833792:-1 HG:+:2168943499:-1 HG:+:2265398051:-1 HG:+:2268091871:-1 HG:+:2270119550:-1 HG:+:2272050217:-1 HG:+:2272268218:-1 HG:+:2274077928:-1 HG:+:2277847492:-1 HG:+:2281227660:-1 HG:+:2298839700:-1 HG:+:2327978150:-1 HG:+:2330645569:-1 HG:+:2335834062:-1 HG:+:2336854298:-1 HG:+:2347997053:-1 HG:+:2361312241:-1 HG:+:2372302944:-1 HG:+:2375506924:-1 HG:+:2378365036:-1 HG:+:2380569249:-1 HG:+:2381544827:-1 HG:+:2381763699:-1 HG:+:2383702939:-1 HG:+:2409972449:-1 HG:+:2420537088:-1 HG:+:2427780308:-1 HG:+:2431628823:-1 HG:+:2432263798:-1 HG:+:2440371847:-1 HG:+:2443617949:-1 HG:+:2462877218:-1 HG:+:2468438345:-1 HG:+:2480365729:-1 HG:+:2482415898:-1 HG:+:2484903629:-1 HG:+:2518153235:-1 HG:+:2526005354:-1 HG:+:2535940749:-1 HG:+:2536700941:-1 HG:+:2556851322:-1 HG:+:2557465730:-1 HG:+:2560405873:-1 HG:+:2574158126:-1 HG:+:2584803208:-1 HG:+:2590691363:-1 HG:+:2610916041:-1 HG:+:2625829160:-1 HG:+:2639177558:-1 HG:+:2672374047:-1 HG:+:2673903526:-1 HG:+:2680551616:-1 HG:+:2680606289:-1 HG:+:2695996905:-1 HG:+:2700102330:-1 HG:+:2710463030:-1 HG:+:2710619158:-1 HG:+:2712895544:-1 HG:+:2715232968:-1 HG:+:2728441798:-1 HG:+:2735862799:-1 HG:+:2750882803:-1 HG:+:2767607345:-1 HG:+:2796970814:-1 HG:+:2799059789:-1 HG:+:2799901818:-1 HG:+:2852385038:83 HG:+:2858343248:-1 HG:+:2860990475:-1 HG:+:2867915167:-1 HG:+:2872669679:-1 HG:+:2883157563:-1 HG:+:2893856509:-1 HG:+:2900723492:-1 HG:+:2933784846:-1 HG:+:2958071037:-1 HG:+:2967363114:-1 HG:+:3020268827:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:21000359:-1 HG:+:32072607:-1 HG:+:34130965:-1 HG:+:55854940:-1 HG:+:116531091:-1 HG:+:155831346:-1 HG:+:200690102:-1 HG:+:209340672:-1 HG:+:291986031:-1 HG:+:293541534:-1 HG:+:319247353:-1 HG:+:352431664:-1 HG:+:423961563:-1 HG:+:426417724:-1 HG:+:477873979:-1 HG:+:512599233:-1 HG:+:624702129:-1 HG:+:717314065:-1 HG:+:731451691:-1 HG:+:765048828:-1 HG:+:802196104:-1 HG:+:876079315:-1 HG:+:922470970:-1 HG:+:932233397:-1 HG:+:989311144:-1 HG:+:1000803148:-1 HG:+:1012152821:-1 HG:+:1029111824:-1 HG:+:1061940526:-1 HG:+:1105590905:-1 HG:+:1166744027:-1 HG:+:1222824249:-1 HG:+:1391528499:-1 HG:+:1395835364:-1 HG:+:1540725623:-1 HG:+:1565037701:-1 HG:+:1574561928:-1 HG:+:1581517720:-1 HG:+:1608531334:-1 HG:+:1623989233:-1 HG:+:1673746088:-1 HG:+:1842372138:-1 HG:+:1889210382:-1 HG:+:2049451920:-1 HG:+:2071295586:-1 HG:+:2121285275:-1 HG:+:2137618263:-1 HG:+:2277903892:-1 HG:+:2368949128:-1 HG:+:2399910254:-1 HG:+:2431612884:-1 HG:+:2432429002:-1 HG:+:2436418194:-1 HG:+:2493350456:-1 HG:+:2504398639:-1 HG:+:2505319760:-1 HG:+:2520792244:-1 HG:+:2537750529:-1 HG:+:2550775141:-1 HG:+:2560197588:-1 HG:+:2643410948:-1 HG:+:2695441830:-1 HG:+:2712790745:-1 HG:+:2750058461:-1 HG:+:2760289246:-1 HG:+:2768961851:-1 HG:+:2816972552:-1 HG:+:2823542279:-1 HG:+:2905568563:-1 HG:+:2920704546:-1 HG:+:3055019173:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:9439288:-1 HG:+:10241255:-1 HG:+:117527362:-1 HG:+:305192502:-1 HG:+:320327446:-1 HG:+:321789537:-1 HG:+:380268394:-1 HG:+:387670287:-1 HG:+:452409342:-1 HG:+:632312483:-1 HG:+:688221085:-1 HG:+:691219191:-1 HG:+:778583251:-1 HG:+:833802101:-1 HG:+:875752178:-1 HG:+:1236557124:-1 HG:+:1715594645:-1 HG:+:1762392451:-1 HG:+:1881440234:-1 HG:+:1993142678:-1 HG:+:2032486986:-1 HG:+:2263353891:-1 HG:+:2289740348:-1 HG:+:2412602353:-1 HG:+:2657707810:-1 HG:+:2689724240:-1 HG:+:2936859892:-1 HG:+:2948593164:-1 HG:+:3055015844:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:288905865:-1 HG:+:409364824:-1 HG:+:451119393:-1 HG:+:1723683926:93 HG:+:2061193889:-1 HG:+:2327643206:-1 HG:+:2328649803:-1 HG:+:2921700404:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:18279603:-1 HG:+:67888031:-1 HG:+:78436727:-1 HG:+:115152356:-1 HG:+:156289231:-1 HG:+:231563193:-1 HG:+:276746846:-1 HG:+:466265262:-1 HG:+:508045158:-1 HG:+:524580887:-1 HG:+:874014972:-1 HG:+:879958911:-1 HG:+:934082073:-1 HG:+:979959322:-1 HG:+:1051330486:-1 HG:+:1083441069:-1 HG:+:1173629332:-1 HG:+:1211195117:-1 HG:+:1213157611:-1 HG:+:1333258821:-1 HG:+:1415095760:-1 HG:+:1672687031:-1 HG:+:1673288963:-1 HG:+:1703825206:-1 HG:+:1725500452:-1 HG:+:1740244113:-1 HG:+:1780533188:-1 HG:+:2084635836:-1 HG:+:2135288460:-1 HG:+:2274274894:-1 HG:+:2438845387:-1 HG:+:2516430749:-1 HG:+:2516481008:-1 HG:+:2566429192:-1 HG:+:2576012377:-1 HG:+:2594025775:-1 HG:+:2661278899:-1 HG:+:2662993078:-1 HG:+:2673447708:-1 HG:+:2698526914:-1 HG:+:2706838900:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:483386157:-1 HG:+:592791383:-1 HG:+:617895007:-1 HG:+:687195095:-1 HG:+:1236657904:-1 HG:+:1755251730:-1 HG:+:2251751162:-1 HG:+:2263664109:-1 HG:+:2818027649:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:12015470:-1 HG:+:28583808:-1 HG:+:101163149:-1 HG:+:157007840:-1 HG:+:198122768:-1 HG:+:236818667:-1 HG:+:259079850:-1 HG:+:300141565:-1 HG:+:819787120:-1 HG:+:898408448:-1 HG:+:920045855:-1 HG:+:933816073:-1 HG:+:953590240:-1 HG:+:993859484:-1 HG:+:1019009510:-1 HG:+:1041902979:-1 HG:+:1204525755:-1 HG:+:1225525324:-1 HG:+:1303607615:-1 HG:+:1488418594:-1 HG:+:1496109144:-1 HG:+:1522113294:-1 HG:+:1623564716:-1 HG:+:1939128398:-1 HG:+:1949923378:-1 HG:+:2035902928:-1 HG:+:2037498828:-1 HG:+:2079953124:-1 HG:+:2081488066:-1 HG:+:2228212822:-1 HG:+:2231720703:-1 HG:+:2235942297:-1 HG:+:2347691926:-1 HG:+:2382521810:-1 HG:+:2425821237:-1 HG:+:2438939417:-1 HG:+:2466642233:-1 HG:+:2477505853:-1 HG:+:2479203450:-1 HG:+:2505273805:-1 HG:+:2548033768:-1 HG:+:2556913851:-1 HG:+:2594959414:-1 HG:+:2694147412:-1 HG:+:2754249938:-1 HG:+:2777332643:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:31667745:-1 HG:+:179162319:-1 HG:+:219764976:-1 HG:+:361638239:-1 HG:+:371563658:-1 HG:+:676704670:-1 HG:+:1058215159:-1 HG:+:1087258691:-1 HG:+:1090951394:-1 HG:+:1226825975:-1 HG:+:1327200026:-1 HG:+:1487601589:-1 HG:+:1692682927:-1 HG:+:1935051800:-1 HG:+:2001083577:-1 HG:+:2013936154:-1 HG:+:2107324268:-1 HG:+:2158535967:-1 HG:+:2277965727:-1 HG:+:2458544926:-1 HG:+:2547225540:-1 HG:+:2564643659:-1 HG:+:2625130810:-1 HG:+:2707166734:-1 HG:+:2861313777:-1 HG:+:2873023793:-1 HG:+:3017038320:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:1723683923:93 HG:+:1960928865:-1 HG:+:2327643482:-1 HG:+:2328650087:-1 HG:+:2852385042:83 HG:+:2931822910:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:147728014:-1 HG:+:293559317:-1 HG:+:301801365:-1 HG:+:534483914:-1 HG:+:791508064:-1 HG:+:1053518143:-1 HG:+:1201543496:-1 HG:+:1273890007:-1 HG:+:1426717490:-1 HG:+:1568762011:-1 HG:+:1878538365:-1 HG:+:2018409309:-1 HG:+:2046900672:-1 HG:+:2301834569:-1 HG:+:2404021501:-1 HG:+:2899328259:-1 HG:+:2929429035:-1 HG:+:2969336974:-1 HG:+:3009315332:-1 HG:+:3101734639:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:235297276:-1 HG:+:1723683931:93 HG:+:2327643210:-1 HG:+:2328649807:-1 HG:+:2852385046:83 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:2512819:-1 HG:+:872485809:-1 HG:+:1276905122:-1 HG:+:2706961685:-1 HG:+:2947800230:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:42083991:-1 HG:+:56162683:-1 HG:+:423889990:-1 HG:+:802215261:-1 HG:+:1723683924:93 HG:+:2173335095:-1 HG:+:2327643483:-1 HG:+:2328650088:-1 HG:+:2360287663:-1 HG:+:2575555748:-1 HG:+:2585310065:-1 HG:+:2814340502:-1 HG:+:3028723162:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:1101367968:-1 HG:+:1530227631:-1 HG:+:1910445458:-1 HG:+:2178519075:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:58760798:-1 HG:+:692170342:-1 HG:+:748922878:-1 HG:+:778702774:-1 HG:+:961217047:-1 HG:+:1072446125:-1 HG:+:1095820086:-1 HG:+:1095839511:-1 HG:+:1398911305:-1 HG:+:1650613388:-1 HG:+:2062913061:-1 HG:+:2077433137:-1 HG:+:2104472808:-1 HG:+:2182826376:-1 HG:+:2463378077:-1 HG:+:2488573328:-1 HG:+:2631809796:-1 HG:+:2669341307:-1 HG:+:2670939479:-1 HG:+:2933381954:-1 HG:+:2933879994:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:307172892:-1 HG:+:455968957:-1 HG:+:473110206:-1 HG:+:913957760:-1 HG:+:957538983:-1 HG:+:1030963787:-1 HG:+:1067258907:-1 HG:+:1172585280:-1 HG:+:1184520748:-1 HG:+:1327145223:-1 HG:+:1398698828:-1 HG:+:1401491046:-1 HG:+:1445889248:-1 HG:+:1475880541:-1 HG:+:1539451133:-1 HG:+:1635299863:-1 HG:+:1672566075:-1 HG:+:1688272744:-1 HG:+:1795891339:-1 HG:+:1884495074:-1 HG:+:2239807982:-1 HG:+:2240787188:-1 HG:+:2499326613:-1 HG:+:2590806462:-1 HG:+:2754695596:-1 HG:+:2829408308:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:333658116:-1 HG:+:1459080074:-1 HG:+:2950217908:-1 HG:+:3056325721:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:2235825085:-1 HG:+:2396403139:-1 HG:+:2531777247:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:203679010:-1 HG:+:360059654:-1 HG:+:363950648:-1 HG:+:367966571:-1 HG:+:386210044:-1 HG:+:431055397:-1 HG:+:461395240:-1 HG:+:461987270:-1 HG:+:1017407625:-1 HG:+:1091387061:-1 HG:+:1094243473:-1 HG:+:1119748260:-1 HG:+:1402938854:-1 HG:+:1513667905:-1 HG:+:1723683925:93 HG:+:1887032300:-1 HG:+:1908236482:-1 HG:+:1934416033:-1 HG:+:1941830414:-1 HG:+:1944854094:-1 HG:+:1994264100:-1 HG:+:2033386405:-1 HG:+:2067971281:-1 HG:+:2220756004:-1 HG:+:2552734800:-1 HG:+:2693229690:-1 HG:+:2827707843:-1 HG:+:2888650469:-1 HG:+:3000533027:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:163631198:-1 HG:+:961545006:-1 HG:+:1624536694:-1 HG:+:2303876605:-1 HG:+:2505292962:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:32723108:-1 HG:+:149392178:-1 HG:+:385026301:-1 HG:+:482659680:-1 HG:+:680222021:-1 HG:+:799122510:-1 HG:+:1194227664:-1 HG:+:1528058975:-1 HG:+:1556533601:-1 HG:+:1686802809:-1 HG:+:1736632757:-1 HG:+:1896302824:-1 HG:+:2002000057:-1 HG:+:2185266723:-1 HG:+:2186701098:-1 HG:+:2467108110:-1 HG:+:2574198767:-1 HG:+:2581650283:-1 HG:+:2621251606:-1 HG:+:2680845253:-1 HG:+:2701401516:-1 HG:+:2716133905:-1 HG:+:2755760672:-1 HG:+:2764192943:-1 HG:+:3025160162:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:9950897:-1 HG:+:32979048:-1 HG:+:162553368:-1 HG:+:183100460:-1 HG:+:207140716:-1 HG:+:222006538:-1 HG:+:256031277:-1 HG:+:258554960:-1 HG:+:264725873:-1 HG:+:275618818:-1 HG:+:300957675:-1 HG:+:337346951:-1 HG:+:351234403:-1 HG:+:356304891:-1 HG:+:411332918:-1 HG:+:439812959:-1 HG:+:540540454:-1 HG:+:551640198:-1 HG:+:553294742:-1 HG:+:619824779:-1 HG:+:657829862:-1 HG:+:659765119:-1 HG:+:663280039:-1 HG:+:677212581:-1 HG:+:688249117:-1 HG:+:731045856:-1 HG:+:736661462:-1 HG:+:779300844:-1 HG:+:834667589:-1 HG:+:844815729:-1 HG:+:850982120:-1 HG:+:854046876:-1 HG:+:925057684:-1 HG:+:933291771:-1 HG:+:957016965:-1 HG:+:981272378:-1 HG:+:991306183:-1 HG:+:995931808:-1 HG:+:1000319338:-1 HG:+:1018963952:-1 HG:+:1041185500:-1 HG:+:1043627088:-1 HG:+:1047840894:-1 HG:+:1084646583:-1 HG:+:1099616872:-1 HG:+:1241766088:-1 HG:+:1264125696:-1 HG:+:1287529758:-1 HG:+:1302069036:-1 HG:+:1321253912:-1 HG:+:1340225187:-1 HG:+:1420422383:-1 HG:+:1444319070:-1 HG:+:1451333768:-1 HG:+:1471456849:-1 HG:+:1528566936:-1 HG:+:1537506627:-1 HG:+:1543522167:-1 HG:+:1548814722:-1 HG:+:1611877642:-1 HG:+:1615034111:-1 HG:+:1669227910:-1 HG:+:1692460995:-1 HG:+:1723683922:93 HG:+:1732994052:-1 HG:+:1746739705:-1 HG:+:1898585840:-1 HG:+:1941336392:-1 HG:+:2038465551:-1 HG:+:2044782307:-1 HG:+:2175946344:-1 HG:+:2229613989:-1 HG:+:2241495207:-1 HG:+:2327643478:-1 HG:+:2328650083:-1 HG:+:2338702129:-1 HG:+:2348865864:-1 HG:+:2353154717:-1 HG:+:2353154749:-1 HG:+:2360876312:-1 HG:+:2367984407:-1 HG:+:2382319348:-1 HG:+:2416364558:-1 HG:+:2477583412:-1 HG:+:2576136304:-1 HG:+:2584950052:-1 HG:+:2625040739:-1 HG:+:2627979464:-1 HG:+:2633694184:-1 HG:+:2712647078:-1 HG:+:2721181151:-1 HG:+:2727212976:-1 HG:+:2733192246:-1 HG:+:2852385039:83 HG:+:2853793552:-1 HG:+:2870593980:-1 HG:+:2925615586:-1 HG:+:2928652505:-1 HG:+:2932338239:-1 HG:+:2954466678:-1 HG:+:3018635015:-1 HG:+:3055032506:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:75258248:-1 HG:+:286479570:-1 HG:+:405813382:-1 HG:+:525711047:-1 HG:+:575486739:-1 HG:+:910709688:-1 HG:+:913697383:-1 HG:+:943003739:-1 HG:+:1084046530:-1 HG:+:1141035925:-1 HG:+:1473479550:-1 HG:+:1558673275:-1 HG:+:1694743789:-1 HG:+:1715906656:-1 HG:+:1920468215:-1 HG:+:1928596586:-1 HG:+:1980220703:-1 HG:+:2004313256:-1 HG:+:2012338345:-1 HG:+:2036204408:-1 HG:+:2040991430:-1 HG:+:2254978036:-1 HG:+:2257819325:-1 HG:+:2805712232:-1 HG:+:2807302183:-1 HG:+:2870881260:-1 HG:+:2909127022:-1 HG:+:2928556140:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:76891358:-1 HG:+:442855034:-1 HG:+:870164406:-1 HG:+:908363698:-1 HG:+:1245837281:-1 HG:+:1267456806:-1 HG:+:1764131992:-1 HG:+:2380571391:-1 HG:+:2646995550:-1 HG:+:2809628064:-1 HG:+:2972906558:-1 HG:+:3041909162:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:253071043:-1 HG:+:1319737567:-1 HG:+:1553966685:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:939601384:-1 HG:+:1695006403:-1 HG:+:1703293244:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:281451302:-1 HG:+:475708895:-1 HG:+:631060144:-1 HG:+:708230006:-1 HG:+:767019918:-1 HG:+:836281571:-1 HG:+:1044714989:-1 HG:+:1088917429:-1 HG:+:1666467141:-1 HG:+:1788973405:-1 HG:+:1796451090:-1 HG:+:1858856244:-1 HG:+:1999872089:-1 HG:+:1999903433:-1 HG:+:2126456656:-1 HG:+:2149622901:-1 HG:+:2356729772:-1 HG:+:2388709371:-1 HG:+:2497326878:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:320649535:-1 HG:+:1738557536:-1 HG:+:1752074409:-1 HG:+:2290160271:-1 HG:+:2859582156:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:1723683932:93 HG:+:2327643211:-1 HG:+:2328649808:-1 HG:+:2852385047:83 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:919101031:-1 HG:+:1174567939:-1 HG:+:1348239561:-1 HG:+:1416996180:-1 HG:+:1671548815:-1 HG:+:2070060410:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:444098970:-1 HG:+:934867706:-1 HG:+:1178208107:-1 HG:+:1921362989:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:306679368:-1 HG:+:1400909056:-1 HG:+:1702085763:-1 HG:+:2983862689:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:9421620:-1 HG:+:554362894:-1 HG:+:1021712241:-1 HG:+:1142346719:-1 HG:+:1205609643:-1 HG:+:1723683933:93 HG:+:1797542041:-1 HG:+:1802849347:-1 HG:+:1802849357:-1 HG:+:2178661746:-1 HG:+:2327643212:-1 HG:+:2328649809:-1 HG:+:2345540555:-1 HG:+:2676429460:-1 HG:+:2852385048:83 HG:+:2857602513:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:507377461:-1 HG:+:831353518:-1 HG:+:954782874:-1 HG:+:1655533542:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:2047369764:-1 HG:+:2276953540:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:1728869286:-1 HG:+:2993580796:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:12719611:-1 HG:+:481083551:-1 HG:+:1422109123:-1 HG:+:1520459866:-1 HG:+:1533844780:-1 HG:+:1618153200:-1 HG:+:1723683934:93 HG:+:1778917186:-1 HG:+:2125434437:-1 HG:+:2327643214:-1 HG:+:2328649811:-1 HG:+:2739493011:-1 HG:+:2975674571:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCATTATCGTATACTGGAAAAATTGAGATTGGGATTTTGACATGAAGTGCGGAAATGTGGATTGGGTCCATTTAGTTTACCTAAACAGATGATGAATACTAACTGTTCTACGAAGCATTCCCTAGTGTAAGTTTTGGCCTGTGTGTGTAGTGACGGGACAGTGAGAATGAGGTCTTGGAACGTGGAGCGCATTGTGGGCCTGTT HG:+:643455361:-1 HG:+:2272833012:-1 HG:+:2327643216:-1 HG:+:2328649813:-1 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:5368416:-1 HG:+:16739695:-1 HG:+:24275610:-1 HG:+:25933825:-1 HG:+:33176000:-1 HG:+:44823567:-1 HG:+:47144870:-1 HG:+:52089176:-1 HG:+:92452064:-1 HG:+:95290474:-1 HG:+:150589861:-1 HG:+:172420600:-1 HG:+:173713889:-1 HG:+:178769649:-1 HG:+:184647692:-1 HG:+:202118547:-1 HG:+:212324370:-1 HG:+:214789978:-1 HG:+:231049728:-1 HG:+:236293868:-1 HG:+:241236788:-1 HG:+:245069080:-1 HG:+:274624333:-1 HG:+:276639405:-1 HG:+:277023494:-1 HG:+:346464211:-1 HG:+:371768654:-1 HG:+:371857667:-1 HG:+:401554766:-1 HG:+:407513910:-1 HG:+:418956074:-1 HG:+:425174875:-1 HG:+:440406917:-1 HG:+:451715683:-1 HG:+:457338843:-1 HG:+:457754422:-1 HG:+:459773439:-1 HG:+:466182488:-1 HG:+:468541186:-1 HG:+:469546549:-1 HG:+:477829744:-1 HG:+:479619144:-1 HG:+:491946145:-1 HG:+:519272011:-1 HG:+:529703440:-1 HG:+:531999622:-1 HG:+:533834377:-1 HG:+:538145993:-1 HG:+:547592979:-1 HG:+:561773251:-1 HG:+:565370137:-1 HG:+:606142748:-1 HG:+:612856225:-1 HG:+:622250762:-1 HG:+:626954058:-1 HG:+:631792006:-1 HG:+:639014260:-1 HG:+:678930274:-1 HG:+:712866661:-1 HG:+:716011616:-1 HG:+:733648381:-1 HG:+:738544607:-1 HG:+:759024765:-1 HG:+:776840532:-1 HG:+:780397301:-1 HG:+:783617091:-1 HG:+:790317755:-1 HG:+:801114489:-1 HG:+:814896176:-1 HG:+:819306557:-1 HG:+:821082767:-1 HG:+:856102601:-1 HG:+:856302578:-1 HG:+:869021433:-1 HG:+:869254305:-1 HG:+:877955539:-1 HG:+:890053860:-1 HG:+:913977319:-1 HG:+:946637884:-1 HG:+:959882675:-1 HG:+:961166322:-1 HG:+:1006177386:-1 HG:+:1026307988:-1 HG:+:1028639540:-1 HG:+:1035110207:-1 HG:+:1042241427:-1 HG:+:1044872007:-1 HG:+:1047231002:-1 HG:+:1058375717:-1 HG:+:1075636074:-1 HG:+:1077544649:-1 HG:+:1083262278:-1 HG:+:1093427392:-1 HG:+:1096758924:-1 HG:+:1097308266:-1 HG:+:1100236815:-1 HG:+:1100999644:-1 HG:+:1102270911:-1 HG:+:1104564209:-1 HG:+:1119483638:-1 HG:+:1139787801:-1 HG:+:1143610859:-1 HG:+:1145608891:-1 HG:+:1146130750:-1 HG:+:1167767182:-1 HG:+:1169011847:-1 HG:+:1179814970:-1 HG:+:1223485556:-1 HG:+:1223780913:-1 HG:+:1238385223:-1 HG:+:1238777219:-1 HG:+:1258376829:-1 HG:+:1278052191:-1 HG:+:1278712543:-1 HG:+:1281830795:-1 HG:+:1289510362:-1 HG:+:1297021069:-1 HG:+:1305528216:-1 HG:+:1332124835:-1 HG:+:1335824050:-1 HG:+:1335923145:-1 HG:+:1344956860:-1 HG:+:1350350506:-1 HG:+:1361957777:-1 HG:+:1364174361:-1 HG:+:1373607919:-1 HG:+:1374083598:-1 HG:+:1377074487:-1 HG:+:1377164795:-1 HG:+:1385367967:-1 HG:+:1394893761:-1 HG:+:1419375736:-1 HG:+:1431674080:-1 HG:+:1442398625:-1 HG:+:1447662525:-1 HG:+:1449751236:-1 HG:+:1457798231:-1 HG:+:1480390407:-1 HG:+:1492921070:-1 HG:+:1494244245:-1 HG:+:1511808701:-1 HG:+:1515422842:-1 HG:+:1515641539:-1 HG:+:1517029506:-1 HG:+:1518072077:-1 HG:+:1518679400:-1 HG:+:1558557548:-1 HG:+:1577069039:-1 HG:+:1578552524:-1 HG:+:1579081827:-1 HG:+:1579897275:-1 HG:+:1580281234:-1 HG:+:1580302679:-1 HG:+:1580697608:-1 HG:+:1582654591:-1 HG:+:1583811361:-1 HG:+:1605299286:-1 HG:+:1606494571:88 HG:+:1630675867:-1 HG:+:1639809757:-1 HG:+:1651952709:-1 HG:+:1652112553:-1 HG:+:1655138483:-1 HG:+:1667374635:-1 HG:+:1670561244:-1 HG:+:1673425473:-1 HG:+:1680212304:-1 HG:+:1713628520:-1 HG:+:1716379026:-1 HG:+:1718414553:-1 HG:+:1718485232:-1 HG:+:1727381391:-1 HG:+:1745377973:-1 HG:+:1752579560:-1 HG:+:1756458324:-1 HG:+:1766425307:-1 HG:+:1774894925:-1 HG:+:1783761771:-1 HG:+:1784595660:-1 HG:+:1787167956:-1 HG:+:1803803473:-1 HG:+:1812484563:-1 HG:+:1819733409:-1 HG:+:1883450743:-1 HG:+:1903955173:-1 HG:+:1911592569:-1 HG:+:1928137884:-1 HG:+:1934255700:-1 HG:+:1953002471:-1 HG:+:1959731593:-1 HG:+:1960095805:-1 HG:+:1963148486:-1 HG:+:2014264014:-1 HG:+:2016094105:-1 HG:+:2020000851:-1 HG:+:2021966676:-1 HG:+:2048597272:-1 HG:+:2050081226:-1 HG:+:2055275228:-1 HG:+:2061515414:-1 HG:+:2064812895:-1 HG:+:2108392868:-1 HG:+:2110847292:-1 HG:+:2119429433:-1 HG:+:2119594968:-1 HG:+:2133359491:-1 HG:+:2138424706:-1 HG:+:2151784581:-1 HG:+:2158149616:-1 HG:+:2222654989:-1 HG:+:2235506996:-1 HG:+:2255377832:-1 HG:+:2303602316:-1 HG:+:2304317450:-1 HG:+:2336137910:-1 HG:+:2337837486:-1 HG:+:2348100332:-1 HG:+:2350074713:-1 HG:+:2350729899:-1 HG:+:2359032000:-1 HG:+:2363628366:-1 HG:+:2374901588:-1 HG:+:2375442341:-1 HG:+:2378202101:-1 HG:+:2380099196:-1 HG:+:2386590331:-1 HG:+:2410687057:-1 HG:+:2412085554:-1 HG:+:2418737951:-1 HG:+:2418784728:-1 HG:+:2434289446:-1 HG:+:2439554662:-1 HG:+:2440680511:-1 HG:+:2442690198:-1 HG:+:2443321574:42 HG:+:2487578828:-1 HG:+:2490899447:-1 HG:+:2495172920:-1 HG:+:2496516009:-1 HG:+:2498685649:-1 HG:+:2501612546:-1 HG:+:2504356829:-1 HG:+:2507903784:-1 HG:+:2509416205:-1 HG:+:2513595380:-1 HG:+:2526026544:-1 HG:+:2528525456:-1 HG:+:2533565925:-1 HG:+:2533683778:-1 HG:+:2541659042:-1 HG:+:2552350112:-1 HG:+:2562920965:-1 HG:+:2563911817:-1 HG:+:2574144530:-1 HG:+:2574486472:-1 HG:+:2575295992:-1 HG:+:2575435251:-1 HG:+:2591505713:-1 HG:+:2613866332:-1 HG:+:2628598321:-1 HG:+:2649388242:-1 HG:+:2664095358:-1 HG:+:2667438643:-1 HG:+:2667704842:-1 HG:+:2674340447:-1 HG:+:2676427164:-1 HG:+:2677014136:-1 HG:+:2677073249:-1 HG:+:2677854850:-1 HG:+:2680788366:-1 HG:+:2693105801:-1 HG:+:2698867723:-1 HG:+:2698911553:-1 HG:+:2700103612:-1 HG:+:2704708006:-1 HG:+:2707392275:-1 HG:+:2709911533:-1 HG:+:2713277124:-1 HG:+:2713758730:-1 HG:+:2727558233:-1 HG:+:2735100314:-1 HG:+:2750941106:-1 HG:+:2752570501:-1 HG:+:2752730181:-1 HG:+:2753152695:-1 HG:+:2776091937:-1 HG:+:2777364706:-1 HG:+:2812107254:-1 HG:+:2849250083:-1 HG:+:2872517113:-1 HG:+:2873480950:-1 HG:+:2873578216:-1 HG:+:2897842582:-1 HG:+:2899523949:-1 HG:+:2904209198:-1 HG:+:2933796891:-1 HG:+:2951395688:-1 HG:+:2981563229:-1 HG:+:2984481989:-1 HG:+:2987165445:-1 HG:+:3014926054:-1 HG:+:3016223143:-1 HG:+:3028479036:-1 HG:+:3038995087:-1 HG:+:3052316525:-1 HG:+:3097069340:-1 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:1606494563:88 HG:+:2443321566:42 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:2443321576:42 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:1325962782:-1 HG:+:1372845127:-1 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:2443321561:42 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:2443321565:42 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:1606494562:88 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:2443321570:42 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:1606494564:88 HG:+:2443321577:42 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:1273770284:-1 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:1606494561:88 HG:+:2443321564:42 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:1606494565:88 HG:+:2443321568:42 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:641047699:-1 HG:+:2443321573:42 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:995071036:-1 +AACAGGCCCACAATGCGCTCCACGTTCCAAGACCTCATTCTCACTGTCCCGTCACTACACACACAGGCCAAAACTTACACTAGGGAATGCTTCGTAGAACAGTTAGTATTCATCATCTGTTTAGGTAAACTAAATGGACCCAATCCACATTTCCGCACTTCATGTCAAAATCCCAATCTCAATTTTTCCAGTATACGATAATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA HG:+:1750270594:-1 HG:+:2370610561:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:444289365:-1 HG:+:1224312554:-1 HG:+:1465144718:-1 HG:+:1628902010:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:82389694:-1 HG:+:185424732:-1 HG:+:243302126:-1 HG:+:294664406:-1 HG:+:437262385:-1 HG:+:787547202:-1 HG:+:870557025:-1 HG:+:884407269:-1 HG:+:885993474:-1 HG:+:993167155:-1 HG:+:1133730731:-1 HG:+:1477642792:-1 HG:+:1523906615:-1 HG:+:1584814099:-1 HG:+:1585200289:-1 HG:+:1585827004:-1 HG:+:1756683104:-1 HG:+:1785298069:-1 HG:+:1909757746:-1 HG:+:2157549377:-1 HG:+:2251674864:-1 HG:+:2510241067:-1 HG:+:2611631692:-1 HG:+:2920428421:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:337031707:-1 HG:+:1409507846:-1 HG:+:1487498981:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:828761747:-1 HG:+:871857403:-1 HG:+:1244245449:-1 HG:+:1442177833:-1 HG:+:2227889411:-1 HG:+:2376242635:-1 HG:+:2471862799:-1 HG:+:2529371583:-1 HG:+:2756621625:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:494675604:-1 HG:+:526822392:-1 HG:+:621308820:-1 HG:+:714549826:-1 HG:+:885014337:-1 HG:+:1158741857:-1 HG:+:1707785544:-1 HG:+:1861063416:-1 HG:+:1940928284:-1 HG:+:2692872947:-1 HG:+:2798983806:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:104687730:-1 HG:+:431663134:-1 HG:+:720590326:-1 HG:+:939264129:-1 HG:+:1022978543:-1 HG:+:1144606886:-1 HG:+:1416658809:-1 HG:+:1450441045:-1 HG:+:1550322393:-1 HG:+:2012985469:-1 HG:+:2345597894:-1 HG:+:2655008737:-1 HG:+:2750987189:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:465892379:-1 HG:+:716159324:-1 HG:+:1243954038:-1 HG:+:1718414857:-1 HG:+:2060043097:-1 HG:+:2180140243:-1 HG:+:2367503621:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:885886360:-1 HG:+:1083532794:-1 HG:+:1746800051:-1 HG:+:2054568425:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:175939725:-1 HG:+:903922608:-1 HG:+:1287338270:-1 HG:+:1314382840:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:114927466:-1 HG:+:181987909:-1 HG:+:187167989:-1 HG:+:419026757:-1 HG:+:1171200612:-1 HG:+:1330383094:-1 HG:+:2178888041:-1 HG:+:2402688034:-1 HG:+:2649254838:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:214251692:-1 HG:+:2683425708:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:235319955:-1 HG:+:2002843748:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:899780076:-1 HG:+:1356290916:-1 HG:+:2056107936:-1 HG:+:2338973251:-1 HG:+:2984194213:-1 HG:+:3060164680:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:341159840:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:244176656:-1 HG:+:701316648:-1 HG:+:2423758904:-1 HG:+:2609455709:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:258909033:-1 HG:+:405782276:-1 HG:+:473243234:-1 HG:+:859513766:-1 HG:+:976938955:-1 HG:+:1047774031:-1 HG:+:1167865937:-1 HG:+:1189236961:-1 HG:+:1205383658:-1 HG:+:1353197155:-1 HG:+:1399294149:-1 HG:+:1525459454:-1 HG:+:1743093560:-1 HG:+:1971052303:-1 HG:+:1992681443:-1 HG:+:2023777156:-1 HG:+:2041536968:-1 HG:+:2048729019:-1 HG:+:2054801028:-1 HG:+:2077012937:-1 HG:+:2581898099:-1 HG:+:2613292622:-1 HG:+:2621934549:-1 HG:+:2655765432:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:476788477:-1 HG:+:618448230:-1 HG:+:2345951523:-1 HG:+:2424224451:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:164160512:-1 HG:+:264618417:-1 HG:+:364430213:-1 HG:+:378506151:-1 HG:+:423188423:-1 HG:+:484562495:-1 HG:+:855624415:-1 HG:+:1095832923:-1 HG:+:1199405098:-1 HG:+:1377203399:-1 HG:+:1653327190:-1 HG:+:1747654786:-1 HG:+:1844592134:-1 HG:+:2069524903:-1 HG:+:2229847145:-1 HG:+:2648784224:-1 HG:+:2691677135:-1 HG:+:2753984526:-1 HG:+:2860594225:-1 HG:+:2887209255:-1 HG:+:2931325540:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:752579232:-1 HG:+:1384041547:-1 HG:+:1472382481:-1 HG:+:2639195232:-1 HG:+:2730967253:-1 HG:+:2873377739:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:47211908:-1 HG:+:498939702:-1 HG:+:530053388:-1 HG:+:639063799:-1 HG:+:787435765:-1 HG:+:808492469:-1 HG:+:879597765:-1 HG:+:946582224:-1 HG:+:969603913:-1 HG:+:1382000163:-1 HG:+:2015742190:-1 HG:+:2071436807:-1 HG:+:2105355358:-1 HG:+:2148158627:-1 HG:+:2297649030:-1 HG:+:2379540629:-1 HG:+:2801919900:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:37396242:-1 HG:+:110690623:-1 HG:+:156772101:-1 HG:+:779902381:-1 HG:+:831118558:-1 HG:+:843446901:-1 HG:+:1066452602:-1 HG:+:1279700705:-1 HG:+:1324267386:-1 HG:+:1469103338:-1 HG:+:1573556664:-1 HG:+:1763666863:-1 HG:+:1785626404:-1 HG:+:1872388997:-1 HG:+:2266282679:-1 HG:+:2467845525:-1 HG:+:2642450868:-1 HG:+:2654105872:-1 HG:+:2705023808:-1 HG:+:2722260590:-1 HG:+:2820886758:-1 HG:+:2864931333:-1 HG:+:2873536381:-1 HG:+:2992558685:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATCGTATTTATGAAAAAAATGATTTACAGGTGAAGTTCTTCTGGGGGCAGAAGAAAAGCTTTATCTAAAACTCCCTAAGAAGAAAGATAAGTCATTTTTCTCCTCTTAAATGGATCTTCAGCTAGGAACAAGGTATAAGCTTACTGGTATTAAGGTAAGTGCCCATTCGAGCAGTTCTGTCTGCTCTGATTGGTCAGTGATGC HG:+:8686685:-1 HG:+:31936506:-1 HG:+:67871331:-1 HG:+:75921849:-1 HG:+:104355169:-1 HG:+:169512818:-1 HG:+:186060713:-1 HG:+:217733636:-1 HG:+:477372169:-1 HG:+:493282367:-1 HG:+:515122665:-1 HG:+:517305593:-1 HG:+:557840147:-1 HG:+:803225750:-1 HG:+:819967025:-1 HG:+:873215070:-1 HG:+:877873614:-1 HG:+:899482322:-1 HG:+:926761815:-1 HG:+:999416017:-1 HG:+:1131249171:-1 HG:+:1167593410:-1 HG:+:1208320400:-1 HG:+:1249500562:-1 HG:+:1278251721:-1 HG:+:1342800087:-1 HG:+:1350673719:-1 HG:+:1378039468:-1 HG:+:1422038366:-1 HG:+:1441376160:-1 HG:+:1443964413:-1 HG:+:1492946729:-1 HG:+:1513442083:-1 HG:+:1706288459:-1 HG:+:1823184982:-1 HG:+:1900020070:-1 HG:+:1990195451:-1 HG:+:2059986320:-1 HG:+:2078679418:-1 HG:+:2132892527:-1 HG:+:2157812315:-1 HG:+:2187936102:-1 HG:+:2283481290:-1 HG:+:2375177180:-1 HG:+:2617358397:-1 HG:+:2753140169:-1 HG:+:2764744812:-1 HG:+:2806108235:-1 HG:+:2853790741:-1 HG:+:2910343717:-1 HG:+:2933050200:-1 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:2026629730:54 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:2026629727:54 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:2026627881:-1 HG:+:2026629728:54 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:2026629720:54 HG:+:2275971421:-1 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:2026629717:54 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:2026629733:54 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:2026629718:54 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:2026629719:54 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:2026629721:54 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:2026629724:54 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:577336059:-1 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:2026629732:54 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:2026629723:54 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:2010493331:-1 +GCATCACTGACCAATCAGAGCAGACAGAACTGCTCGAATGGGCACTTACCTTAATACCAGTAAGCTTATACCTTGTTCCTAGCTGAAGATCCATTTAAGAGGAGAAAAATGACTTATCTTTCTTCTTAGGGAGTTTTAGATAAAGCTTTTCTTCTGCCCCCAGAAGAACTTCACCTGTAAATCATTTTTTTCATAAATACGATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC HG:+:2026629725:54 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:533567697:-1 HG:+:658619617:-1 HG:+:1837007220:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:73846451:-1 HG:+:78850782:-1 HG:+:306185778:-1 HG:+:324283820:-1 HG:+:798668114:-1 HG:+:1006455408:-1 HG:+:1069068015:-1 HG:+:1072721032:-1 HG:+:1361868734:-1 HG:+:1473488755:-1 HG:+:1762445102:-1 HG:+:2472886735:-1 HG:+:2560766937:-1 HG:+:2648650655:-1 HG:+:2797188730:-1 HG:+:2798383067:-1 HG:+:2924598683:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:69568327:-1 HG:+:211308788:-1 HG:+:603505298:-1 HG:+:727148792:-1 HG:+:1057900815:-1 HG:+:1388800392:-1 HG:+:1889634873:-1 HG:+:2507290999:-1 HG:+:2723515419:-1 HG:+:2871398256:-1 HG:+:3034084269:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:1153865138:-1 HG:+:2389868603:-1 HG:+:2390165924:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:529155923:-1 HG:+:733376798:-1 HG:+:1108242526:-1 HG:+:1694511768:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:166250400:-1 HG:+:413548425:-1 HG:+:414393746:-1 HG:+:504939270:-1 HG:+:704238577:-1 HG:+:979935222:-1 HG:+:1051809711:-1 HG:+:1319640013:-1 HG:+:1378625273:-1 HG:+:1913437038:-1 HG:+:2120180105:-1 HG:+:2228056526:-1 HG:+:2392792766:-1 HG:+:2641518166:-1 HG:+:2725211338:-1 HG:+:2753563556:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:68161960:-1 HG:+:165288140:-1 HG:+:207163427:-1 HG:+:234396531:-1 HG:+:325986628:-1 HG:+:517918187:-1 HG:+:548526557:-1 HG:+:659809208:-1 HG:+:1424567206:-1 HG:+:1646960503:-1 HG:+:1907167679:-1 HG:+:2920911409:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:157759430:-1 HG:+:256013832:-1 HG:+:258449998:-1 HG:+:338527024:-1 HG:+:356949041:-1 HG:+:414847962:-1 HG:+:570068629:-1 HG:+:602753391:-1 HG:+:623189240:-1 HG:+:651554704:-1 HG:+:656793001:-1 HG:+:831836697:-1 HG:+:847726654:-1 HG:+:938560086:-1 HG:+:949969499:-1 HG:+:1074749738:-1 HG:+:1155289725:-1 HG:+:1159215294:-1 HG:+:1204435913:-1 HG:+:1409826005:-1 HG:+:1483003335:-1 HG:+:1624587712:-1 HG:+:1643995372:-1 HG:+:1646694166:-1 HG:+:1746877337:-1 HG:+:1910778749:-1 HG:+:1914364922:-1 HG:+:2125642485:-1 HG:+:2139029397:-1 HG:+:2145717315:-1 HG:+:2168864400:-1 HG:+:2190617625:-1 HG:+:2632878479:-1 HG:+:2639948923:-1 HG:+:2765978964:-1 HG:+:2935038929:-1 HG:+:3010302388:-1 HG:+:3055334962:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:394536161:-1 HG:+:566861061:-1 HG:+:773613767:-1 HG:+:1144339230:-1 HG:+:1885699105:-1 HG:+:2165011336:-1 HG:+:2269935787:-1 HG:+:2342255181:-1 HG:+:2434770436:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:686279217:-1 HG:+:2304829923:-1 HG:+:2409183250:-1 HG:+:2530248031:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:322359141:-1 HG:+:1738647169:-1 HG:+:1833596915:-1 HG:+:1964619994:-1 HG:+:2380141958:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:304108484:-1 HG:+:671332612:-1 HG:+:2161168674:-1 HG:+:2639959412:-1 HG:+:2653711145:-1 HG:+:2656639241:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:1135681330:-1 HG:+:1330394071:-1 HG:+:2293161789:-1 HG:+:2729960776:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:162576309:-1 HG:+:513124132:-1 HG:+:1495569548:-1 HG:+:2281986946:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:813990026:-1 HG:+:899658092:-1 HG:+:1431574566:-1 HG:+:2027917043:-1 HG:+:2042368954:-1 HG:+:2262125927:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:172219339:-1 HG:+:483677969:-1 HG:+:562688240:-1 HG:+:1384579436:-1 HG:+:1809504454:-1 HG:+:1925467702:-1 HG:+:2581183932:-1 HG:+:2859456573:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:265394976:-1 HG:+:482445815:-1 HG:+:482557195:-1 HG:+:1235549861:-1 HG:+:1327246963:-1 HG:+:1661225642:-1 HG:+:1671016375:-1 HG:+:1879829187:-1 HG:+:1885365084:-1 HG:+:1933329711:-1 HG:+:2497571225:-1 HG:+:2633362245:-1 HG:+:2669670279:-1 HG:+:2737537112:-1 HG:+:2756245772:-1 HG:+:2779462963:-1 HG:+:2874146356:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:935830198:-1 HG:+:1668838731:-1 HG:+:1828319734:-1 HG:+:2467663218:-1 HG:+:2595250183:-1 HG:+:2906224890:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:587941068:-1 HG:+:778176566:-1 HG:+:983579977:-1 HG:+:1046342757:-1 HG:+:1500553680:-1 HG:+:2162282665:-1 HG:+:2179268729:-1 HG:+:2241646264:-1 HG:+:2264656744:-1 HG:+:2424163354:-1 HG:+:2472449692:-1 HG:+:2476847277:-1 HG:+:2528779536:-1 HG:+:2716180521:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:74091188:-1 HG:+:454032214:-1 HG:+:1267635969:-1 HG:+:2417724387:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:187047333:-1 HG:+:371798833:-1 HG:+:397009417:-1 HG:+:431173719:-1 HG:+:760992351:-1 HG:+:824524281:-1 HG:+:987061999:-1 HG:+:1093217444:-1 HG:+:1129175260:-1 HG:+:1144790710:-1 HG:+:1366202916:-1 HG:+:1367848335:-1 HG:+:1441766780:-1 HG:+:1483289682:-1 HG:+:1512995851:-1 HG:+:1950275660:-1 HG:+:2176754211:-1 HG:+:2536004603:-1 HG:+:2951406277:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:79004010:-1 HG:+:119261779:-1 HG:+:120504928:-1 HG:+:171061143:-1 HG:+:251863333:-1 HG:+:286519489:-1 HG:+:307116394:-1 HG:+:416680701:-1 HG:+:427851220:-1 HG:+:510979053:-1 HG:+:529084044:-1 HG:+:568592553:-1 HG:+:703093380:-1 HG:+:753264808:-1 HG:+:763836363:-1 HG:+:807031659:-1 HG:+:817096800:-1 HG:+:855799184:-1 HG:+:957713054:-1 HG:+:986597374:-1 HG:+:1036648539:-1 HG:+:1059504565:-1 HG:+:1116159592:-1 HG:+:1192184775:-1 HG:+:1299632330:-1 HG:+:1309457691:-1 HG:+:1340013779:-1 HG:+:1374291043:-1 HG:+:1502345371:-1 HG:+:1661849020:-1 HG:+:1732389106:-1 HG:+:1770682952:-1 HG:+:1845689735:-1 HG:+:1944896448:-1 HG:+:1978826340:-1 HG:+:2059536386:-1 HG:+:2262721674:-1 HG:+:2271300942:-1 HG:+:2390984610:-1 HG:+:2462559983:-1 HG:+:2613497000:-1 HG:+:2650150173:-1 HG:+:2701494432:-1 HG:+:2761564257:-1 HG:+:2944298408:-1 HG:+:2967151297:-1 HG:+:3051610512:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTGTGGAAGAAGGAAAGGAAAAGACTGGTGGCCAGGGAAGACGGCTTGCAGGCTACGTCGAAGTGAAATAGTCAAGAAATAATTCAGTTAAGATCAATCAAACACTCCCAGTATCTATTGGGAATGTCAGGCGTTGTGCCAAGGTAACTGGGGTACACAAGATTGACTTAGTGCGTCCCTAGAAGAGGGAAGACCCGAGTAAG HG:+:767459718:-1 +CTTACTCGGGTCTTCCCTCTTCTAGGGACGCACTAAGTCAATCTTGTGTACCCCAGTTACCTTGGCACAACGCCTGACATTCCCAATAGATACTGGGAGTGTTTGATTGATCTTAACTGAATTATTTCTTGACTATTTCACTTCGACGTAGCCTGCAAGCCGTCTTCCCTGGCCACCAGTCTTTTCCTTTCCTTCTTCCACACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA HG:+:353688803:-1 HG:+:1100362169:-1 HG:+:1201272320:48 HG:+:1395162387:-1 HG:+:1478067913:-1 HG:+:1542216792:-1 HG:+:2944626384:-1 +CTTACTCGGGTCTTCCCTCTTCTAGGGACGCACTAAGTCAATCTTGTGTACCCCAGTTACCTTGGCACAACGCCTGACATTCCCAATAGATACTGGGAGTGTTTGATTGATCTTAACTGAATTATTTCTTGACTATTTCACTTCGACGTAGCCTGCAAGCCGTCTTCCCTGGCCACCAGTCTTTTCCTTTCCTTCTTCCACACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA HG:+:1201272328:48 +CTTACTCGGGTCTTCCCTCTTCTAGGGACGCACTAAGTCAATCTTGTGTACCCCAGTTACCTTGGCACAACGCCTGACATTCCCAATAGATACTGGGAGTGTTTGATTGATCTTAACTGAATTATTTCTTGACTATTTCACTTCGACGTAGCCTGCAAGCCGTCTTCCCTGGCCACCAGTCTTTTCCTTTCCTTCTTCCACACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA HG:+:1201272337:48 +CTTACTCGGGTCTTCCCTCTTCTAGGGACGCACTAAGTCAATCTTGTGTACCCCAGTTACCTTGGCACAACGCCTGACATTCCCAATAGATACTGGGAGTGTTTGATTGATCTTAACTGAATTATTTCTTGACTATTTCACTTCGACGTAGCCTGCAAGCCGTCTTCCCTGGCCACCAGTCTTTTCCTTTCCTTCTTCCACACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA HG:+:378054541:-1 HG:+:1201272319:48 +CTTACTCGGGTCTTCCCTCTTCTAGGGACGCACTAAGTCAATCTTGTGTACCCCAGTTACCTTGGCACAACGCCTGACATTCCCAATAGATACTGGGAGTGTTTGATTGATCTTAACTGAATTATTTCTTGACTATTTCACTTCGACGTAGCCTGCAAGCCGTCTTCCCTGGCCACCAGTCTTTTCCTTTCCTTCTTCCACACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA HG:+:1201272321:48 +CTTACTCGGGTCTTCCCTCTTCTAGGGACGCACTAAGTCAATCTTGTGTACCCCAGTTACCTTGGCACAACGCCTGACATTCCCAATAGATACTGGGAGTGTTTGATTGATCTTAACTGAATTATTTCTTGACTATTTCACTTCGACGTAGCCTGCAAGCCGTCTTCCCTGGCCACCAGTCTTTTCCTTTCCTTCTTCCACACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA HG:+:1201272323:48 +CTTACTCGGGTCTTCCCTCTTCTAGGGACGCACTAAGTCAATCTTGTGTACCCCAGTTACCTTGGCACAACGCCTGACATTCCCAATAGATACTGGGAGTGTTTGATTGATCTTAACTGAATTATTTCTTGACTATTTCACTTCGACGTAGCCTGCAAGCCGTCTTCCCTGGCCACCAGTCTTTTCCTTTCCTTCTTCCACACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA HG:+:1201272324:48 +CTTACTCGGGTCTTCCCTCTTCTAGGGACGCACTAAGTCAATCTTGTGTACCCCAGTTACCTTGGCACAACGCCTGACATTCCCAATAGATACTGGGAGTGTTTGATTGATCTTAACTGAATTATTTCTTGACTATTTCACTTCGACGTAGCCTGCAAGCCGTCTTCCCTGGCCACCAGTCTTTTCCTTTCCTTCTTCCACACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA HG:+:1201272325:48 +CTTACTCGGGTCTTCCCTCTTCTAGGGACGCACTAAGTCAATCTTGTGTACCCCAGTTACCTTGGCACAACGCCTGACATTCCCAATAGATACTGGGAGTGTTTGATTGATCTTAACTGAATTATTTCTTGACTATTTCACTTCGACGTAGCCTGCAAGCCGTCTTCCCTGGCCACCAGTCTTTTCCTTTCCTTCTTCCACACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA HG:+:1201272327:48 +CTTACTCGGGTCTTCCCTCTTCTAGGGACGCACTAAGTCAATCTTGTGTACCCCAGTTACCTTGGCACAACGCCTGACATTCCCAATAGATACTGGGAGTGTTTGATTGATCTTAACTGAATTATTTCTTGACTATTTCACTTCGACGTAGCCTGCAAGCCGTCTTCCCTGGCCACCAGTCTTTTCCTTTCCTTCTTCCACACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA HG:+:1201272332:48 +CTTACTCGGGTCTTCCCTCTTCTAGGGACGCACTAAGTCAATCTTGTGTACCCCAGTTACCTTGGCACAACGCCTGACATTCCCAATAGATACTGGGAGTGTTTGATTGATCTTAACTGAATTATTTCTTGACTATTTCACTTCGACGTAGCCTGCAAGCCGTCTTCCCTGGCCACCAGTCTTTTCCTTTCCTTCTTCCACACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA HG:+:1201272340:48 +CTTACTCGGGTCTTCCCTCTTCTAGGGACGCACTAAGTCAATCTTGTGTACCCCAGTTACCTTGGCACAACGCCTGACATTCCCAATAGATACTGGGAGTGTTTGATTGATCTTAACTGAATTATTTCTTGACTATTTCACTTCGACGTAGCCTGCAAGCCGTCTTCCCTGGCCACCAGTCTTTTCCTTTCCTTCTTCCACACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA HG:+:1229611516:-1 +CTTACTCGGGTCTTCCCTCTTCTAGGGACGCACTAAGTCAATCTTGTGTACCCCAGTTACCTTGGCACAACGCCTGACATTCCCAATAGATACTGGGAGTGTTTGATTGATCTTAACTGAATTATTTCTTGACTATTTCACTTCGACGTAGCCTGCAAGCCGTCTTCCCTGGCCACCAGTCTTTTCCTTTCCTTCTTCCACACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA HG:+:1201272326:48 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:419189585:-1 HG:+:1377399122:-1 HG:+:2771433399:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:1203391901:-1 HG:+:1355619461:-1 HG:+:1772893479:-1 HG:+:2006015258:-1 HG:+:2337071371:-1 HG:+:2810066851:-1 HG:+:2920296182:-1 HG:+:3021463615:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:119232497:-1 HG:+:361958294:-1 HG:+:865353687:-1 HG:+:970909364:-1 HG:+:1169386029:-1 HG:+:2167442293:-1 HG:+:2914391503:-1 HG:+:3020744686:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:1001233050:-1 HG:+:1204701915:-1 HG:+:2026119208:-1 HG:+:2122385264:-1 HG:+:2402194225:-1 HG:+:2666626037:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:405444309:-1 HG:+:425728054:-1 HG:+:926706691:-1 HG:+:931678140:-1 HG:+:1697706299:-1 HG:+:1984635200:-1 HG:+:2397739521:-1 HG:+:2465913246:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:834957463:-1 HG:+:2083989510:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:625548960:-1 HG:+:1659559026:-1 HG:+:2061789278:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:836838072:-1 HG:+:2610619160:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:410853932:-1 HG:+:589636769:-1 HG:+:920610195:-1 HG:+:1022049274:-1 HG:+:1027211369:-1 HG:+:1391491150:-1 HG:+:1495650260:-1 HG:+:1514741656:-1 HG:+:2195501395:-1 HG:+:2468072668:-1 HG:+:2935762584:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:302982671:-1 HG:+:1243892072:-1 HG:+:1410387591:-1 HG:+:1544360632:-1 HG:+:1613227560:-1 HG:+:1850354424:-1 HG:+:2556260300:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:17904116:-1 HG:+:67931357:-1 HG:+:220600954:-1 HG:+:231071347:-1 HG:+:323833285:-1 HG:+:413294090:-1 HG:+:420922520:-1 HG:+:467821582:-1 HG:+:554236815:-1 HG:+:682602289:-1 HG:+:1118583266:-1 HG:+:1208943450:-1 HG:+:1352095337:-1 HG:+:1360204009:-1 HG:+:1521260245:-1 HG:+:1534553113:-1 HG:+:2066785137:-1 HG:+:2081097298:-1 HG:+:2161758488:-1 HG:+:2180630467:-1 HG:+:2333341903:-1 HG:+:2351509472:-1 HG:+:2415289316:-1 HG:+:2573511423:-1 HG:+:2700481418:-1 HG:+:2967314178:-1 HG:+:3027811972:-1 HG:+:3064930486:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:417625485:-1 HG:+:631981732:-1 HG:+:667977768:-1 HG:+:2960922252:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:152848297:-1 HG:+:301915930:-1 HG:+:307709291:-1 HG:+:324044565:-1 HG:+:374091021:-1 HG:+:487980742:-1 HG:+:1062728328:-1 HG:+:1286269255:-1 HG:+:1740050034:-1 HG:+:2037512513:-1 HG:+:2043424375:-1 HG:+:2532811820:-1 HG:+:2538489468:-1 HG:+:2813297226:-1 HG:+:2879435198:-1 HG:+:3097269302:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:20343589:-1 HG:+:78549785:-1 HG:+:119523019:-1 HG:+:185063948:-1 HG:+:368496793:-1 HG:+:387871590:-1 HG:+:411693700:-1 HG:+:411847868:-1 HG:+:423056422:-1 HG:+:515802798:-1 HG:+:602764738:-1 HG:+:613153188:-1 HG:+:628123166:-1 HG:+:658607672:-1 HG:+:681579761:-1 HG:+:690036534:-1 HG:+:703536202:-1 HG:+:737183118:-1 HG:+:757841637:-1 HG:+:789402791:-1 HG:+:853821753:-1 HG:+:878498516:-1 HG:+:910856377:-1 HG:+:921350338:-1 HG:+:1187070988:-1 HG:+:1246277303:-1 HG:+:1247475733:-1 HG:+:1279004254:-1 HG:+:1420445568:-1 HG:+:1535773715:-1 HG:+:1948991155:-1 HG:+:2037583521:-1 HG:+:2177419296:-1 HG:+:2360930629:-1 HG:+:2770271980:-1 HG:+:2956350831:-1 HG:+:2969245768:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:534090:-1 HG:+:438625926:-1 HG:+:573396382:-1 HG:+:1392829158:-1 HG:+:1848521816:-1 HG:+:2156918812:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:255072942:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:72280181:-1 HG:+:1361248799:-1 HG:+:1363723953:-1 HG:+:2015309560:-1 HG:+:2066361657:-1 HG:+:2279360982:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:1163859844:-1 HG:+:1290579101:-1 HG:+:1795430421:-1 HG:+:1865948961:-1 HG:+:1932111479:-1 HG:+:1949948517:-1 HG:+:2030973036:-1 HG:+:2189856177:-1 HG:+:2228762029:-1 HG:+:2385796120:-1 HG:+:2584122436:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:1147471769:-1 HG:+:1248379560:-1 HG:+:1667779870:-1 HG:+:2818867810:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:215984427:-1 HG:+:1278082676:-1 HG:+:2299255321:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:213296296:-1 HG:+:488386891:-1 HG:+:582139427:-1 HG:+:634517095:-1 HG:+:1830935266:-1 HG:+:2380313154:-1 HG:+:2585978334:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:60208738:-1 HG:+:66469256:-1 HG:+:438971508:-1 HG:+:460634576:-1 HG:+:568650163:-1 HG:+:599870024:-1 HG:+:748281355:-1 HG:+:824095674:-1 HG:+:841554331:-1 HG:+:880151931:-1 HG:+:944468115:-1 HG:+:949391519:-1 HG:+:990662339:-1 HG:+:1207811027:-1 HG:+:1322885226:-1 HG:+:1331081398:-1 HG:+:1413065484:-1 HG:+:1458286165:-1 HG:+:1522147720:-1 HG:+:1539678216:-1 HG:+:1550307189:-1 HG:+:1580492783:-1 HG:+:1582796151:-1 HG:+:1604675029:-1 HG:+:1910251326:-1 HG:+:2161347220:-1 HG:+:2174542173:-1 HG:+:2242867610:-1 HG:+:2298676885:-1 HG:+:2342547714:-1 HG:+:2362680310:-1 HG:+:2490881656:-1 HG:+:2593023031:-1 HG:+:2721971038:-1 HG:+:2875276717:-1 HG:+:3001694985:-1 HG:+:3008863082:-1 HG:+:3035756746:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:69163419:-1 HG:+:77908535:-1 HG:+:78748254:-1 HG:+:92542412:-1 HG:+:108861105:-1 HG:+:152871100:-1 HG:+:154315156:-1 HG:+:186696050:-1 HG:+:198960567:-1 HG:+:255472886:-1 HG:+:270699758:-1 HG:+:319852353:-1 HG:+:320603591:-1 HG:+:322786882:-1 HG:+:325817170:-1 HG:+:341041452:-1 HG:+:351985801:-1 HG:+:394467500:-1 HG:+:399716786:-1 HG:+:404344903:-1 HG:+:408374643:-1 HG:+:416435600:-1 HG:+:438095940:-1 HG:+:456608379:-1 HG:+:506587840:-1 HG:+:511210801:-1 HG:+:523079283:-1 HG:+:534922675:-1 HG:+:546958779:-1 HG:+:580948374:-1 HG:+:581822760:-1 HG:+:591127414:-1 HG:+:623482868:-1 HG:+:688156454:-1 HG:+:714121616:-1 HG:+:736270558:-1 HG:+:736402087:-1 HG:+:754623851:-1 HG:+:769690871:-1 HG:+:791825472:-1 HG:+:800635413:-1 HG:+:813863965:-1 HG:+:818573119:-1 HG:+:835868759:-1 HG:+:838824300:-1 HG:+:868091091:-1 HG:+:893143327:-1 HG:+:894387586:-1 HG:+:901617190:-1 HG:+:901724164:-1 HG:+:924227904:-1 HG:+:931248099:-1 HG:+:933251599:-1 HG:+:937985851:-1 HG:+:995736514:-1 HG:+:1004253407:-1 HG:+:1019797075:-1 HG:+:1034736920:-1 HG:+:1036425937:-1 HG:+:1050714060:-1 HG:+:1067987959:-1 HG:+:1070330240:-1 HG:+:1082393528:-1 HG:+:1086922346:-1 HG:+:1092755880:-1 HG:+:1098978258:-1 HG:+:1112119974:-1 HG:+:1136931927:-1 HG:+:1153507355:-1 HG:+:1188945642:-1 HG:+:1205934885:-1 HG:+:1209714450:-1 HG:+:1237432367:-1 HG:+:1261021122:-1 HG:+:1266924741:-1 HG:+:1301635077:-1 HG:+:1317986076:-1 HG:+:1322285851:-1 HG:+:1325585965:-1 HG:+:1335331005:-1 HG:+:1338925350:-1 HG:+:1381610626:-1 HG:+:1387122417:-1 HG:+:1420465761:-1 HG:+:1421129106:-1 HG:+:1425228260:-1 HG:+:1440954877:-1 HG:+:1450716778:-1 HG:+:1468816132:-1 HG:+:1478133067:-1 HG:+:1505215526:-1 HG:+:1522926899:-1 HG:+:1534998489:-1 HG:+:1553942970:-1 HG:+:1617672921:-1 HG:+:1622640911:-1 HG:+:1625650751:-1 HG:+:1646760698:-1 HG:+:1654677899:-1 HG:+:1672468712:-1 HG:+:1681555082:-1 HG:+:1691386092:-1 HG:+:1749432910:-1 HG:+:1751565669:-1 HG:+:1755660747:-1 HG:+:1763399086:-1 HG:+:1772823714:-1 HG:+:1788002476:-1 HG:+:1916417284:-1 HG:+:1930517137:-1 HG:+:1969774260:-1 HG:+:2006015252:-1 HG:+:2021514408:-1 HG:+:2022312217:-1 HG:+:2022674358:-1 HG:+:2028223879:-1 HG:+:2051215958:-1 HG:+:2056847774:-1 HG:+:2082134115:-1 HG:+:2120414172:-1 HG:+:2142430481:-1 HG:+:2153054018:-1 HG:+:2228290483:-1 HG:+:2260571441:-1 HG:+:2298121382:-1 HG:+:2328049578:-1 HG:+:2330716982:-1 HG:+:2330881775:-1 HG:+:2335905691:-1 HG:+:2341220712:-1 HG:+:2348310667:-1 HG:+:2351574912:-1 HG:+:2418267047:-1 HG:+:2422921214:-1 HG:+:2461460288:-1 HG:+:2468627905:-1 HG:+:2472887079:-1 HG:+:2514508001:-1 HG:+:2514727264:-1 HG:+:2551775396:-1 HG:+:2583305477:-1 HG:+:2605221659:-1 HG:+:2605267686:-1 HG:+:2606455784:-1 HG:+:2610066516:-1 HG:+:2712112990:-1 HG:+:2723825670:-1 HG:+:2738066767:-1 HG:+:2742078276:-1 HG:+:2762347221:-1 HG:+:2762599335:-1 HG:+:2769333790:-1 HG:+:2803354288:-1 HG:+:2858752077:-1 HG:+:2864725709:-1 HG:+:2890168457:-1 HG:+:2902106653:-1 HG:+:2905520245:-1 HG:+:2932932585:-1 HG:+:2965781074:-1 HG:+:2995440545:-1 HG:+:3005219091:-1 HG:+:3011151913:-1 HG:+:3014094172:-1 HG:+:3014389514:-1 HG:+:3014647340:-1 HG:+:3014951726:-1 HG:+:3022565558:-1 HG:+:3054818228:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:696423251:-1 HG:+:788701176:-1 HG:+:1165360707:-1 HG:+:1238631399:-1 HG:+:1329708469:-1 HG:+:1398186710:-1 HG:+:1480013117:-1 HG:+:1943789762:-1 HG:+:2069605721:-1 HG:+:2151233864:-1 HG:+:2401072310:-1 HG:+:2600306802:-1 HG:+:2623084859:-1 HG:+:2697734736:-1 HG:+:2986455504:-1 HG:+:3045315043:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:18220730:-1 HG:+:70070623:-1 HG:+:79383642:-1 HG:+:183157008:-1 HG:+:204207177:-1 HG:+:389799685:-1 HG:+:521289930:-1 HG:+:526378622:-1 HG:+:1050930894:-1 HG:+:1101467196:-1 HG:+:1338435898:-1 HG:+:1356285748:-1 HG:+:1454986413:-1 HG:+:1462700414:-1 HG:+:1704620821:-1 HG:+:1747023008:-1 HG:+:1758359111:-1 HG:+:1809829779:-1 HG:+:1907241105:-1 HG:+:1923191131:-1 HG:+:2126962362:-1 HG:+:2192332823:-1 HG:+:2258093987:-1 HG:+:2293689504:-1 HG:+:2471613845:-1 HG:+:2557136474:-1 HG:+:2678674393:-1 HG:+:2879440966:-1 HG:+:2895963784:-1 HG:+:2907879035:-1 HG:+:2962024517:-1 HG:+:3022670484:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTGATGTAGGTATACATTTGTGAAACTATTACCCCAACCAAGCTACTGACTATTATCCATCAGCTCACACATCTTTTAAGTGAAATACTTGAATATTTACTCTCTTAGCAAATTTCAAGTATACACTACGTTATTATTAATTATAGGTGCCATATGTTAAATTAGATCTCTAGAACTTATTCATGCTATAACTGAAAGTTTGT HG:+:479258107:-1 HG:+:529104280:-1 HG:+:572213566:-1 HG:+:576937811:-1 HG:+:696156084:-1 HG:+:891204038:-1 HG:+:950119753:-1 HG:+:1167370004:-1 HG:+:1337881356:-1 HG:+:1485544377:-1 HG:+:1629682290:-1 HG:+:1846032540:-1 HG:+:1882139450:-1 HG:+:2133357653:-1 HG:+:2163017950:-1 HG:+:2234118944:-1 HG:+:2271199752:-1 HG:+:2384398223:-1 HG:+:2726873372:-1 HG:+:3006237622:-1 +ACAAACTTTCAGTTATAGCATGAATAAGTTCTAGAGATCTAATTTAACATATGGCACCTATAATTAATAATAACGTAGTGTATACTTGAAATTTGCTAAGAGAGTAAATATTCAAGTATTTCACTTAAAAGATGTGTGAGCTGATGGATAATAGTCAGTAGCTTGGTTGGGGTAATAGTTTCACAAATGTATACCTACATCAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT HG:+:1255375717:50 +ACAAACTTTCAGTTATAGCATGAATAAGTTCTAGAGATCTAATTTAACATATGGCACCTATAATTAATAATAACGTAGTGTATACTTGAAATTTGCTAAGAGAGTAAATATTCAAGTATTTCACTTAAAAGATGTGTGAGCTGATGGATAATAGTCAGTAGCTTGGTTGGGGTAATAGTTTCACAAATGTATACCTACATCAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT HG:+:1255375715:50 +ACAAACTTTCAGTTATAGCATGAATAAGTTCTAGAGATCTAATTTAACATATGGCACCTATAATTAATAATAACGTAGTGTATACTTGAAATTTGCTAAGAGAGTAAATATTCAAGTATTTCACTTAAAAGATGTGTGAGCTGATGGATAATAGTCAGTAGCTTGGTTGGGGTAATAGTTTCACAAATGTATACCTACATCAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT HG:+:796683745:-1 +ACAAACTTTCAGTTATAGCATGAATAAGTTCTAGAGATCTAATTTAACATATGGCACCTATAATTAATAATAACGTAGTGTATACTTGAAATTTGCTAAGAGAGTAAATATTCAAGTATTTCACTTAAAAGATGTGTGAGCTGATGGATAATAGTCAGTAGCTTGGTTGGGGTAATAGTTTCACAAATGTATACCTACATCAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT HG:+:1322726882:-1 +ACAAACTTTCAGTTATAGCATGAATAAGTTCTAGAGATCTAATTTAACATATGGCACCTATAATTAATAATAACGTAGTGTATACTTGAAATTTGCTAAGAGAGTAAATATTCAAGTATTTCACTTAAAAGATGTGTGAGCTGATGGATAATAGTCAGTAGCTTGGTTGGGGTAATAGTTTCACAAATGTATACCTACATCAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT HG:+:1255375699:50 +ACAAACTTTCAGTTATAGCATGAATAAGTTCTAGAGATCTAATTTAACATATGGCACCTATAATTAATAATAACGTAGTGTATACTTGAAATTTGCTAAGAGAGTAAATATTCAAGTATTTCACTTAAAAGATGTGTGAGCTGATGGATAATAGTCAGTAGCTTGGTTGGGGTAATAGTTTCACAAATGTATACCTACATCAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT HG:+:1255375700:50 +ACAAACTTTCAGTTATAGCATGAATAAGTTCTAGAGATCTAATTTAACATATGGCACCTATAATTAATAATAACGTAGTGTATACTTGAAATTTGCTAAGAGAGTAAATATTCAAGTATTTCACTTAAAAGATGTGTGAGCTGATGGATAATAGTCAGTAGCTTGGTTGGGGTAATAGTTTCACAAATGTATACCTACATCAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT HG:+:1255375701:50 +ACAAACTTTCAGTTATAGCATGAATAAGTTCTAGAGATCTAATTTAACATATGGCACCTATAATTAATAATAACGTAGTGTATACTTGAAATTTGCTAAGAGAGTAAATATTCAAGTATTTCACTTAAAAGATGTGTGAGCTGATGGATAATAGTCAGTAGCTTGGTTGGGGTAATAGTTTCACAAATGTATACCTACATCAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT HG:+:1255375708:50 +ACAAACTTTCAGTTATAGCATGAATAAGTTCTAGAGATCTAATTTAACATATGGCACCTATAATTAATAATAACGTAGTGTATACTTGAAATTTGCTAAGAGAGTAAATATTCAAGTATTTCACTTAAAAGATGTGTGAGCTGATGGATAATAGTCAGTAGCTTGGTTGGGGTAATAGTTTCACAAATGTATACCTACATCAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT HG:+:1255375703:50 +ACAAACTTTCAGTTATAGCATGAATAAGTTCTAGAGATCTAATTTAACATATGGCACCTATAATTAATAATAACGTAGTGTATACTTGAAATTTGCTAAGAGAGTAAATATTCAAGTATTTCACTTAAAAGATGTGTGAGCTGATGGATAATAGTCAGTAGCTTGGTTGGGGTAATAGTTTCACAAATGTATACCTACATCAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT HG:+:1255375704:50 +ACAAACTTTCAGTTATAGCATGAATAAGTTCTAGAGATCTAATTTAACATATGGCACCTATAATTAATAATAACGTAGTGTATACTTGAAATTTGCTAAGAGAGTAAATATTCAAGTATTTCACTTAAAAGATGTGTGAGCTGATGGATAATAGTCAGTAGCTTGGTTGGGGTAATAGTTTCACAAATGTATACCTACATCAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT HG:+:1255375697:50 +ACAAACTTTCAGTTATAGCATGAATAAGTTCTAGAGATCTAATTTAACATATGGCACCTATAATTAATAATAACGTAGTGTATACTTGAAATTTGCTAAGAGAGTAAATATTCAAGTATTTCACTTAAAAGATGTGTGAGCTGATGGATAATAGTCAGTAGCTTGGTTGGGGTAATAGTTTCACAAATGTATACCTACATCAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT HG:+:53363789:-1 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCACATTTTTTGTTAGATTTACTCCTTAGTATTTCAATGTTTTGGGTTGCTATTTTATCAACTAATTAATTAATTATTTAGAGATAGGGTTCTTGCTCTGTTGCCTGGGCTGAGTGCAGTGGTACAATCATAGCTCACTGCACCCTTGAATCCCTGGGCTCAGGCAATCCTCTTGTTTCAGCCTCTTGAGTAGGTAGACTATA HG:+:2535766564:32 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCACATTTTTTGTTAGATTTACTCCTTAGTATTTCAATGTTTTGGGTTGCTATTTTATCAACTAATTAATTAATTATTTAGAGATAGGGTTCTTGCTCTGTTGCCTGGGCTGAGTGCAGTGGTACAATCATAGCTCACTGCACCCTTGAATCCCTGGGCTCAGGCAATCCTCTTGTTTCAGCCTCTTGAGTAGGTAGACTATA HG:+:776292744:-1 HG:+:2535766548:32 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCACATTTTTTGTTAGATTTACTCCTTAGTATTTCAATGTTTTGGGTTGCTATTTTATCAACTAATTAATTAATTATTTAGAGATAGGGTTCTTGCTCTGTTGCCTGGGCTGAGTGCAGTGGTACAATCATAGCTCACTGCACCCTTGAATCCCTGGGCTCAGGCAATCCTCTTGTTTCAGCCTCTTGAGTAGGTAGACTATA HG:+:2535766561:32 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCACATTTTTTGTTAGATTTACTCCTTAGTATTTCAATGTTTTGGGTTGCTATTTTATCAACTAATTAATTAATTATTTAGAGATAGGGTTCTTGCTCTGTTGCCTGGGCTGAGTGCAGTGGTACAATCATAGCTCACTGCACCCTTGAATCCCTGGGCTCAGGCAATCCTCTTGTTTCAGCCTCTTGAGTAGGTAGACTATA HG:+:2535766549:32 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCACATTTTTTGTTAGATTTACTCCTTAGTATTTCAATGTTTTGGGTTGCTATTTTATCAACTAATTAATTAATTATTTAGAGATAGGGTTCTTGCTCTGTTGCCTGGGCTGAGTGCAGTGGTACAATCATAGCTCACTGCACCCTTGAATCCCTGGGCTCAGGCAATCCTCTTGTTTCAGCCTCTTGAGTAGGTAGACTATA HG:+:1426756511:-1 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCACATTTTTTGTTAGATTTACTCCTTAGTATTTCAATGTTTTGGGTTGCTATTTTATCAACTAATTAATTAATTATTTAGAGATAGGGTTCTTGCTCTGTTGCCTGGGCTGAGTGCAGTGGTACAATCATAGCTCACTGCACCCTTGAATCCCTGGGCTCAGGCAATCCTCTTGTTTCAGCCTCTTGAGTAGGTAGACTATA HG:+:2330222884:-1 HG:+:2535766550:32 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCACATTTTTTGTTAGATTTACTCCTTAGTATTTCAATGTTTTGGGTTGCTATTTTATCAACTAATTAATTAATTATTTAGAGATAGGGTTCTTGCTCTGTTGCCTGGGCTGAGTGCAGTGGTACAATCATAGCTCACTGCACCCTTGAATCCCTGGGCTCAGGCAATCCTCTTGTTTCAGCCTCTTGAGTAGGTAGACTATA HG:+:238219673:-1 HG:+:322158156:-1 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCACATTTTTTGTTAGATTTACTCCTTAGTATTTCAATGTTTTGGGTTGCTATTTTATCAACTAATTAATTAATTATTTAGAGATAGGGTTCTTGCTCTGTTGCCTGGGCTGAGTGCAGTGGTACAATCATAGCTCACTGCACCCTTGAATCCCTGGGCTCAGGCAATCCTCTTGTTTCAGCCTCTTGAGTAGGTAGACTATA HG:+:669246924:-1 HG:+:2535766551:32 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCACATTTTTTGTTAGATTTACTCCTTAGTATTTCAATGTTTTGGGTTGCTATTTTATCAACTAATTAATTAATTATTTAGAGATAGGGTTCTTGCTCTGTTGCCTGGGCTGAGTGCAGTGGTACAATCATAGCTCACTGCACCCTTGAATCCCTGGGCTCAGGCAATCCTCTTGTTTCAGCCTCTTGAGTAGGTAGACTATA HG:+:2535766557:32 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCACATTTTTTGTTAGATTTACTCCTTAGTATTTCAATGTTTTGGGTTGCTATTTTATCAACTAATTAATTAATTATTTAGAGATAGGGTTCTTGCTCTGTTGCCTGGGCTGAGTGCAGTGGTACAATCATAGCTCACTGCACCCTTGAATCCCTGGGCTCAGGCAATCCTCTTGTTTCAGCCTCTTGAGTAGGTAGACTATA HG:+:278944126:-1 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCACATTTTTTGTTAGATTTACTCCTTAGTATTTCAATGTTTTGGGTTGCTATTTTATCAACTAATTAATTAATTATTTAGAGATAGGGTTCTTGCTCTGTTGCCTGGGCTGAGTGCAGTGGTACAATCATAGCTCACTGCACCCTTGAATCCCTGGGCTCAGGCAATCCTCTTGTTTCAGCCTCTTGAGTAGGTAGACTATA HG:+:2535766563:32 +TATAGTCTACCTACTCAAGAGGCTGAAACAAGAGGATTGCCTGAGCCCAGGGATTCAAGGGTGCAGTGAGCTATGATTGTACCACTGCACTCAGCCCAGGCAACAGAGCAAGAACCCTATCTCTAAATAATTAATTAATTAGTTGATAAAATAGCAACCCAAAACATTGAAATACTAAGGAGTAAATCTAACAAAAAATGTGCAAGCCTCTTTTGAGGAAAAGTTATAATCAAGAATATTATAATAGTAAAAGAAGATTAATAAATTATCAAGGTCTTAAAATTGGAAGTGTACACTATTAGTGCCGATTCTTCCTAAATTCATCTGTAGATTGACATTTCAATAAAAATTCTGGTTAGTAGTATTTTGTAATGCTAATTAATAAAATTTCCATAAAAGACAAGTCTCACAAATAACCAAAGATACTTCCAAAGAAATACAAGGTGAAAAGATTTGCCTAATCAGATATCAAGATTTAATATAAAGCCATATTAAATTAAAGAAATTGTGAGATAGGTGTAGAGATAGATTTATAGATCAAGTGGAACTTAATGACCCAGAAACAGATCCAGCCATATATGAAAACTTATTTTATGAATAGAGGAGGCATTGTAGATCATGGGGAAAGGATAGATTTTTTTTTTTTTCAATAAATGATACCAGCACAATCGGTTATTCATTTAAAAAAAAAAAAGAGGAAAGAAAGAAATGGATTCCCTTATCTTATGCCTATACACAAAAATCAATTCCCGATAAAGACTTAAATATGTACTAAAGAGGTGAAGCTGTTAAATGGTTAAGGAGAATATCGTTATAACCTCAGGATAGGAAGATTTTTGTTGTATAAGACACAGCAAGTAACAAACTACAAAAGAAAAGATTGATTACTTAAACTCCACTCAAGAACTCTGTTCATCAAATACGTCATAAGGGAGTCTGAAAAGCCTGTAAATCCTAGCACTTTCGGAGGCCAAGGCCGGCAGATTGCTTGAGCCCAGGA HG:+:630756000:-1 +TATAGTCTACCTACTCAAGAGGCTGAAACAAGAGGATTGCCTGAGCCCAGGGATTCAAGGGTGCAGTGAGCTATGATTGTACCACTGCACTCAGCCCAGGCAACAGAGCAAGAACCCTATCTCTAAATAATTAATTAATTAGTTGATAAAATAGCAACCCAAAACATTGAAATACTAAGGAGTAAATCTAACAAAAAATGTGCAAGCCTCTTTTGAGGAAAAGTTATAATCAAGAATATTATAATAGTAAAAGAAGATTAATAAATTATCAAGGTCTTAAAATTGGAAGTGTACACTATTAGTGCCGATTCTTCCTAAATTCATCTGTAGATTGACATTTCAATAAAAATTCTGGTTAGTAGTATTTTGTAATGCTAATTAATAAAATTTCCATAAAAGACAAGTCTCACAAATAACCAAAGATACTTCCAAAGAAATACAAGGTGAAAAGATTTGCCTAATCAGATATCAAGATTTAATATAAAGCCATATTAAATTAAAGAAATTGTGAGATAGGTGTAGAGATAGATTTATAGATCAAGTGGAACTTAATGACCCAGAAACAGATCCAGCCATATATGAAAACTTATTTTATGAATAGAGGAGGCATTGTAGATCATGGGGAAAGGATAGATTTTTTTTTTTTTCAATAAATGATACCAGCACAATCGGTTATTCATTTAAAAAAAAAAAAGAGGAAAGAAAGAAATGGATTCCCTTATCTTATGCCTATACACAAAAATCAATTCCCGATAAAGACTTAAATATGTACTAAAGAGGTGAAGCTGTTAAATGGTTAAGGAGAATATCGTTATAACCTCAGGATAGGAAGATTTTTGTTGTATAAGACACAGCAAGTAACAAACTACAAAAGAAAAGATTGATTACTTAAACTCCACTCAAGAACTCTGTTCATCAAATACGTCATAAGGGAGTCTGAAAAGCCTGTAAATCCTAGCACTTTCGGAGGCCAAGGCCGGCAGATTGCTTGAGCCCAGGA HG:+:40054781:-1 +TATAGTCTACCTACTCAAGAGGCTGAAACAAGAGGATTGCCTGAGCCCAGGGATTCAAGGGTGCAGTGAGCTATGATTGTACCACTGCACTCAGCCCAGGCAACAGAGCAAGAACCCTATCTCTAAATAATTAATTAATTAGTTGATAAAATAGCAACCCAAAACATTGAAATACTAAGGAGTAAATCTAACAAAAAATGTGCAAGCCTCTTTTGAGGAAAAGTTATAATCAAGAATATTATAATAGTAAAAGAAGATTAATAAATTATCAAGGTCTTAAAATTGGAAGTGTACACTATTAGTGCCGATTCTTCCTAAATTCATCTGTAGATTGACATTTCAATAAAAATTCTGGTTAGTAGTATTTTGTAATGCTAATTAATAAAATTTCCATAAAAGACAAGTCTCACAAATAACCAAAGATACTTCCAAAGAAATACAAGGTGAAAAGATTTGCCTAATCAGATATCAAGATTTAATATAAAGCCATATTAAATTAAAGAAATTGTGAGATAGGTGTAGAGATAGATTTATAGATCAAGTGGAACTTAATGACCCAGAAACAGATCCAGCCATATATGAAAACTTATTTTATGAATAGAGGAGGCATTGTAGATCATGGGGAAAGGATAGATTTTTTTTTTTTTCAATAAATGATACCAGCACAATCGGTTATTCATTTAAAAAAAAAAAAGAGGAAAGAAAGAAATGGATTCCCTTATCTTATGCCTATACACAAAAATCAATTCCCGATAAAGACTTAAATATGTACTAAAGAGGTGAAGCTGTTAAATGGTTAAGGAGAATATCGTTATAACCTCAGGATAGGAAGATTTTTGTTGTATAAGACACAGCAAGTAACAAACTACAAAAGAAAAGATTGATTACTTAAACTCCACTCAAGAACTCTGTTCATCAAATACGTCATAAGGGAGTCTGAAAAGCCTGTAAATCCTAGCACTTTCGGAGGCCAAGGCCGGCAGATTGCTTGAGCCCAGGA HG:+:2286536065:-1 +TATAGTCTACCTACTCAAGAGGCTGAAACAAGAGGATTGCCTGAGCCCAGGGATTCAAGGGTGCAGTGAGCTATGATTGTACCACTGCACTCAGCCCAGGCAACAGAGCAAGAACCCTATCTCTAAATAATTAATTAATTAGTTGATAAAATAGCAACCCAAAACATTGAAATACTAAGGAGTAAATCTAACAAAAAATGTGCAAGCCTCTTTTGAGGAAAAGTTATAATCAAGAATATTATAATAGTAAAAGAAGATTAATAAATTATCAAGGTCTTAAAATTGGAAGTGTACACTATTAGTGCCGATTCTTCCTAAATTCATCTGTAGATTGACATTTCAATAAAAATTCTGGTTAGTAGTATTTTGTAATGCTAATTAATAAAATTTCCATAAAAGACAAGTCTCACAAATAACCAAAGATACTTCCAAAGAAATACAAGGTGAAAAGATTTGCCTAATCAGATATCAAGATTTAATATAAAGCCATATTAAATTAAAGAAATTGTGAGATAGGTGTAGAGATAGATTTATAGATCAAGTGGAACTTAATGACCCAGAAACAGATCCAGCCATATATGAAAACTTATTTTATGAATAGAGGAGGCATTGTAGATCATGGGGAAAGGATAGATTTTTTTTTTTTTCAATAAATGATACCAGCACAATCGGTTATTCATTTAAAAAAAAAAAAGAGGAAAGAAAGAAATGGATTCCCTTATCTTATGCCTATACACAAAAATCAATTCCCGATAAAGACTTAAATATGTACTAAAGAGGTGAAGCTGTTAAATGGTTAAGGAGAATATCGTTATAACCTCAGGATAGGAAGATTTTTGTTGTATAAGACACAGCAAGTAACAAACTACAAAAGAAAAGATTGATTACTTAAACTCCACTCAAGAACTCTGTTCATCAAATACGTCATAAGGGAGTCTGAAAAGCCTGTAAATCCTAGCACTTTCGGAGGCCAAGGCCGGCAGATTGCTTGAGCCCAGGA HG:+:630583840:-1 HG:+:694573450:-1 HG:+:864608278:-1 HG:+:1959449295:-1 HG:+:2387331854:-1 HG:+:2663649529:-1 HG:+:3005407183:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:23849723:-1 HG:+:44249337:-1 HG:+:65145329:-1 HG:+:67963593:-1 HG:+:92387786:-1 HG:+:198090459:-1 HG:+:323896086:-1 HG:+:537228157:-1 HG:+:543666790:-1 HG:+:649533675:-1 HG:+:664862885:-1 HG:+:672741907:-1 HG:+:676834681:-1 HG:+:688058880:-1 HG:+:1041192635:-1 HG:+:1047769177:-1 HG:+:1058110595:-1 HG:+:1063122411:-1 HG:+:1152313524:-1 HG:+:1222889656:-1 HG:+:1235247757:-1 HG:+:1258874842:-1 HG:+:1275373423:-1 HG:+:1304063042:-1 HG:+:1337113010:-1 HG:+:1376350665:-1 HG:+:1411404532:-1 HG:+:1411409810:-1 HG:+:1421314244:-1 HG:+:1448562272:-1 HG:+:1479344450:-1 HG:+:1520257273:-1 HG:+:1626023253:-1 HG:+:1741420552:-1 HG:+:1757269598:-1 HG:+:1757318652:-1 HG:+:1795863332:-1 HG:+:1891462051:-1 HG:+:1908715051:-1 HG:+:2069348786:-1 HG:+:2245211377:-1 HG:+:2295730080:-1 HG:+:2386168589:64 HG:+:2394130884:-1 HG:+:2428756202:-1 HG:+:2467982871:-1 HG:+:2557733305:-1 HG:+:2567389517:-1 HG:+:2666725855:-1 HG:+:2672050961:-1 HG:+:2676252241:-1 HG:+:2678507474:-1 HG:+:2679169448:-1 HG:+:2706741244:-1 HG:+:2751796809:-1 HG:+:2819335332:-1 HG:+:2822577896:-1 HG:+:2900210606:-1 HG:+:2929617446:-1 HG:+:2947545139:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:27340785:-1 HG:+:53632749:-1 HG:+:162446261:-1 HG:+:309924539:-1 HG:+:346209952:-1 HG:+:659525873:-1 HG:+:861727877:-1 HG:+:873413098:-1 HG:+:1022547855:-1 HG:+:1171588185:-1 HG:+:1258126928:-1 HG:+:1300123203:-1 HG:+:1335189234:-1 HG:+:1467554249:-1 HG:+:1499240860:-1 HG:+:1574399919:-1 HG:+:1657162591:-1 HG:+:1710416484:-1 HG:+:1787780550:-1 HG:+:1801853091:-1 HG:+:1893683080:-1 HG:+:1965425682:-1 HG:+:2027455639:-1 HG:+:2072463650:-1 HG:+:2338686777:-1 HG:+:2341475264:-1 HG:+:2359941309:-1 HG:+:2386058225:-1 HG:+:2413797533:-1 HG:+:2503049543:-1 HG:+:2543083587:-1 HG:+:2547226433:-1 HG:+:2560173209:-1 HG:+:2575257118:-1 HG:+:2600555847:-1 HG:+:2680052078:-1 HG:+:2715290894:-1 HG:+:2879770740:-1 HG:+:2928297229:-1 HG:+:3039582683:-1 HG:+:3060959086:-1 HG:+:3061367166:-1 HG:+:3063000915:-1 HG:+:3064433081:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:278277990:-1 HG:+:1299068301:-1 HG:+:1309247373:-1 HG:+:1452424086:-1 HG:+:1554769487:-1 HG:+:1674687742:-1 HG:+:1863564719:-1 HG:+:2124253734:-1 HG:+:2414652039:-1 HG:+:2499548749:-1 HG:+:2600297757:-1 HG:+:3016969755:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:9865069:-1 HG:+:29041260:-1 HG:+:40483686:-1 HG:+:237178215:-1 HG:+:346533485:-1 HG:+:452349311:-1 HG:+:676515416:-1 HG:+:748262899:-1 HG:+:815845698:-1 HG:+:842160784:-1 HG:+:939001735:-1 HG:+:953258382:-1 HG:+:954601236:-1 HG:+:1086354994:-1 HG:+:1104546873:-1 HG:+:1362982113:-1 HG:+:1430947496:-1 HG:+:1710886235:-1 HG:+:1724322673:-1 HG:+:1873469390:-1 HG:+:1951460562:-1 HG:+:2049825474:-1 HG:+:2227782739:-1 HG:+:2456415804:-1 HG:+:2468628651:-1 HG:+:2476497482:-1 HG:+:2639399187:-1 HG:+:2664645884:-1 HG:+:2666484423:-1 HG:+:2666502884:-1 HG:+:2900415442:-1 HG:+:2905955571:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:377344484:-1 HG:+:924751727:-1 HG:+:1133744862:-1 HG:+:1508519268:-1 HG:+:1523946810:-1 HG:+:1534241280:-1 HG:+:1545355978:-1 HG:+:1572300372:-1 HG:+:1576994593:-1 HG:+:2268896321:-1 HG:+:2421805544:-1 HG:+:2441479753:-1 HG:+:2537793570:-1 HG:+:2557203735:-1 HG:+:2558050570:-1 HG:+:2605123116:-1 HG:+:2664938222:-1 HG:+:2670885438:-1 HG:+:2693080669:-1 HG:+:2700371500:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:48065525:-1 HG:+:80470478:-1 HG:+:473379653:-1 HG:+:649092592:-1 HG:+:832338181:-1 HG:+:953998559:-1 HG:+:1910686462:-1 HG:+:2516326644:-1 HG:+:2714466179:-1 HG:+:2815603465:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:1049449624:-1 HG:+:1839671501:-1 HG:+:2001466685:-1 HG:+:2386168576:64 HG:+:2955337713:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:222864140:-1 HG:+:321800940:-1 HG:+:846746272:-1 HG:+:1183398190:-1 HG:+:1246072310:-1 HG:+:1395076924:-1 HG:+:1556946706:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:2386168575:64 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:2386168598:64 HG:+:2521396363:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:2386168599:64 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:1245000686:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:2386168591:64 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:2391928018:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAATGTACATTAAAATTATGTGAATTATAATCCTGTAAAGCTATTTTAATGGAAAATTTTCCATCAGGTATGAGGAGACAGAATAAAATCTGGCAAAATCACAGCCTTATCCCAAAAGGGACATTGATGTATATAATTTTTAAAACTTTTTTTCATATGTTAATGATTTAATTTCAATAAGACTTCCTTCCTTATTTTATTGTT HG:+:384632249:-1 HG:+:542508216:-1 HG:+:954005568:-1 HG:+:1080410334:-1 HG:+:1254832606:-1 HG:+:1278739403:-1 HG:+:1575096931:-1 HG:+:1740427331:-1 HG:+:1757471807:-1 HG:+:2075571384:-1 HG:+:2076791929:-1 HG:+:2536187011:-1 HG:+:2541639844:-1 HG:+:2766385114:-1 +AACAATAAAATAAGGAAGGAAGTCTTATTGAAATTAAATCATTAACATATGAAAAAAAGTTTTAAAAATTATATACATCAATGTCCCTTTTGGGATAAGGCTGTGATTTTGCCAGATTTTATTCTGTCTCCTCATACCTGATGGAAAATTTTCCATTAAAATAGCTTTACAGGATTATAATTCACATAATTTTAATGTACATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA HG:+:184459948:-1 +AACAATAAAATAAGGAAGGAAGTCTTATTGAAATTAAATCATTAACATATGAAAAAAAGTTTTAAAAATTATATACATCAATGTCCCTTTTGGGATAAGGCTGTGATTTTGCCAGATTTTATTCTGTCTCCTCATACCTGATGGAAAATTTTCCATTAAAATAGCTTTACAGGATTATAATTCACATAATTTTAATGTACATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA HG:+:78163218:-1 HG:+:302025091:-1 HG:+:430219075:-1 HG:+:538149511:-1 HG:+:541961242:-1 HG:+:829560199:-1 HG:+:856310686:-1 HG:+:1057182221:-1 HG:+:1496776730:-1 HG:+:1532706926:-1 HG:+:1755535195:-1 HG:+:1796997359:-1 HG:+:2002790039:-1 HG:+:2695584172:-1 HG:+:2701332750:-1 HG:+:2872088964:-1 HG:+:3049871775:-1 +AACAATAAAATAAGGAAGGAAGTCTTATTGAAATTAAATCATTAACATATGAAAAAAAGTTTTAAAAATTATATACATCAATGTCCCTTTTGGGATAAGGCTGTGATTTTGCCAGATTTTATTCTGTCTCCTCATACCTGATGGAAAATTTTCCATTAAAATAGCTTTACAGGATTATAATTCACATAATTTTAATGTACATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA HG:+:8094544:-1 HG:+:212335905:-1 HG:+:328400357:-1 HG:+:422498784:-1 HG:+:699904812:-1 HG:+:976522683:-1 HG:+:996656382:-1 HG:+:1305485213:-1 HG:+:1361669025:-1 HG:+:1448845299:-1 HG:+:1490655288:-1 HG:+:1745479448:-1 HG:+:2112613605:-1 HG:+:2235309048:-1 HG:+:2363476025:-1 HG:+:2504114276:-1 HG:+:2508105234:-1 HG:+:2508849569:-1 HG:+:2666473600:-1 HG:+:2678373067:-1 +AACAATAAAATAAGGAAGGAAGTCTTATTGAAATTAAATCATTAACATATGAAAAAAAGTTTTAAAAATTATATACATCAATGTCCCTTTTGGGATAAGGCTGTGATTTTGCCAGATTTTATTCTGTCTCCTCATACCTGATGGAAAATTTTCCATTAAAATAGCTTTACAGGATTATAATTCACATAATTTTAATGTACATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA HG:+:262103902:-1 HG:+:333794984:-1 HG:+:1019622567:-1 HG:+:1101762664:-1 HG:+:1425024659:-1 HG:+:1430910925:-1 HG:+:1825510765:-1 HG:+:2477884831:-1 HG:+:2589213703:-1 HG:+:2671456086:-1 HG:+:2701978397:-1 HG:+:2760656318:-1 HG:+:2859979305:-1 HG:+:2982216081:-1 HG:+:3051297441:-1 +AACAATAAAATAAGGAAGGAAGTCTTATTGAAATTAAATCATTAACATATGAAAAAAAGTTTTAAAAATTATATACATCAATGTCCCTTTTGGGATAAGGCTGTGATTTTGCCAGATTTTATTCTGTCTCCTCATACCTGATGGAAAATTTTCCATTAAAATAGCTTTACAGGATTATAATTCACATAATTTTAATGTACATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA HG:+:260939307:-1 HG:+:1113116565:-1 HG:+:1139769155:-1 HG:+:2237733358:-1 HG:+:2643713920:-1 +AACAATAAAATAAGGAAGGAAGTCTTATTGAAATTAAATCATTAACATATGAAAAAAAGTTTTAAAAATTATATACATCAATGTCCCTTTTGGGATAAGGCTGTGATTTTGCCAGATTTTATTCTGTCTCCTCATACCTGATGGAAAATTTTCCATTAAAATAGCTTTACAGGATTATAATTCACATAATTTTAATGTACATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA HG:+:51735043:-1 HG:+:80853149:-1 HG:+:99066291:-1 HG:+:100694840:-1 HG:+:115058472:-1 HG:+:164597145:-1 HG:+:171718616:-1 HG:+:249383587:-1 HG:+:307070044:-1 HG:+:308836882:-1 HG:+:417003476:-1 HG:+:446778840:-1 HG:+:472699430:-1 HG:+:612848875:-1 HG:+:630324133:-1 HG:+:668291282:-1 HG:+:709385442:-1 HG:+:719526490:-1 HG:+:720891932:-1 HG:+:760991481:-1 HG:+:860599833:-1 HG:+:913898286:-1 HG:+:926690368:-1 HG:+:1017993620:-1 HG:+:1074537694:-1 HG:+:1091970436:-1 HG:+:1163806507:-1 HG:+:1164228008:-1 HG:+:1165521874:-1 HG:+:1284782860:-1 HG:+:1304900977:-1 HG:+:1330008156:-1 HG:+:1361846369:-1 HG:+:1370316502:-1 HG:+:1415859128:-1 HG:+:1546957629:-1 HG:+:1570214460:-1 HG:+:1576276682:-1 HG:+:1703480593:-1 HG:+:1703908869:-1 HG:+:1765024606:-1 HG:+:1765220481:-1 HG:+:1778261823:-1 HG:+:1905400446:-1 HG:+:1906928404:-1 HG:+:1925982076:-1 HG:+:1965143612:-1 HG:+:2001401401:-1 HG:+:2119026433:-1 HG:+:2405606871:-1 HG:+:2516263079:-1 HG:+:2560744610:-1 HG:+:2592131418:-1 HG:+:2622663029:-1 HG:+:2697131313:-1 HG:+:2743311759:-1 HG:+:2816139652:-1 HG:+:2893188197:-1 HG:+:3011529055:-1 HG:+:3015755094:-1 +AACAATAAAATAAGGAAGGAAGTCTTATTGAAATTAAATCATTAACATATGAAAAAAAGTTTTAAAAATTATATACATCAATGTCCCTTTTGGGATAAGGCTGTGATTTTGCCAGATTTTATTCTGTCTCCTCATACCTGATGGAAAATTTTCCATTAAAATAGCTTTACAGGATTATAATTCACATAATTTTAATGTACATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA HG:+:2931470080:-1 +AACAATAAAATAAGGAAGGAAGTCTTATTGAAATTAAATCATTAACATATGAAAAAAAGTTTTAAAAATTATATACATCAATGTCCCTTTTGGGATAAGGCTGTGATTTTGCCAGATTTTATTCTGTCTCCTCATACCTGATGGAAAATTTTCCATTAAAATAGCTTTACAGGATTATAATTCACATAATTTTAATGTACATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA HG:+:923955334:-1 HG:+:2387622409:-1 +AACAATAAAATAAGGAAGGAAGTCTTATTGAAATTAAATCATTAACATATGAAAAAAAGTTTTAAAAATTATATACATCAATGTCCCTTTTGGGATAAGGCTGTGATTTTGCCAGATTTTATTCTGTCTCCTCATACCTGATGGAAAATTTTCCATTAAAATAGCTTTACAGGATTATAATTCACATAATTTTAATGTACATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA HG:+:378264198:-1 HG:+:2486116815:-1 +AACAATAAAATAAGGAAGGAAGTCTTATTGAAATTAAATCATTAACATATGAAAAAAAGTTTTAAAAATTATATACATCAATGTCCCTTTTGGGATAAGGCTGTGATTTTGCCAGATTTTATTCTGTCTCCTCATACCTGATGGAAAATTTTCCATTAAAATAGCTTTACAGGATTATAATTCACATAATTTTAATGTACATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA HG:+:211682555:-1 HG:+:943992544:-1 HG:+:950212618:-1 HG:+:1237790182:-1 HG:+:1241638937:-1 HG:+:1255872637:-1 HG:+:1527375315:-1 HG:+:1540876698:-1 HG:+:2007493129:-1 HG:+:2059965689:-1 HG:+:2305459666:-1 HG:+:2588503259:-1 +AACAATAAAATAAGGAAGGAAGTCTTATTGAAATTAAATCATTAACATATGAAAAAAAGTTTTAAAAATTATATACATCAATGTCCCTTTTGGGATAAGGCTGTGATTTTGCCAGATTTTATTCTGTCTCCTCATACCTGATGGAAAATTTTCCATTAAAATAGCTTTACAGGATTATAATTCACATAATTTTAATGTACATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA HG:+:6241597:-1 HG:+:8067858:-1 HG:+:1007525353:-1 HG:+:2250412043:-1 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTTGAACTCCACGTGGGGAGTGCAAGGAAATAACTTTTATAAGGTGTTCATAGAAACAGGAAAAAATATTTGATTTGGTTAAAGTGGAAAGTCCTTAGAGTTTAGTGGCAGTTTTTAATTGGTTGAAGTCTCTACTTAGCAGTTAGTTCATGGTTTTTGGATGGGTTCCACTTAGTTTTGTTGTTTTTGTTTTGTTTTTCGCT HG:+:80940622:-1 HG:+:212174204:-1 HG:+:244493417:-1 HG:+:312196836:-1 HG:+:401562105:-1 HG:+:428584982:-1 HG:+:449520739:-1 HG:+:474554712:-1 HG:+:476974048:-1 HG:+:565064761:-1 HG:+:569050642:-1 HG:+:572845842:-1 HG:+:715060217:-1 HG:+:853755029:-1 HG:+:1159698583:-1 HG:+:1288683646:-1 HG:+:1911566431:-1 HG:+:1959990296:-1 HG:+:2003577070:-1 HG:+:2013346012:-1 HG:+:2021617592:-1 HG:+:2271290720:-1 HG:+:2377004354:-1 HG:+:2392888795:-1 HG:+:2470469247:-1 HG:+:2471101671:42 HG:+:2561351520:-1 HG:+:2628555839:-1 HG:+:2862912659:-1 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTTGAACTCCACGTGGGGAGTGCAAGGAAATAACTTTTATAAGGTGTTCATAGAAACAGGAAAAAATATTTGATTTGGTTAAAGTGGAAAGTCCTTAGAGTTTAGTGGCAGTTTTTAATTGGTTGAAGTCTCTACTTAGCAGTTAGTTCATGGTTTTTGGATGGGTTCCACTTAGTTTTGTTGTTTTTGTTTTGTTTTTCGCT HG:+:2471101670:42 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTTGAACTCCACGTGGGGAGTGCAAGGAAATAACTTTTATAAGGTGTTCATAGAAACAGGAAAAAATATTTGATTTGGTTAAAGTGGAAAGTCCTTAGAGTTTAGTGGCAGTTTTTAATTGGTTGAAGTCTCTACTTAGCAGTTAGTTCATGGTTTTTGGATGGGTTCCACTTAGTTTTGTTGTTTTTGTTTTGTTTTTCGCT HG:+:2001141067:-1 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTTGAACTCCACGTGGGGAGTGCAAGGAAATAACTTTTATAAGGTGTTCATAGAAACAGGAAAAAATATTTGATTTGGTTAAAGTGGAAAGTCCTTAGAGTTTAGTGGCAGTTTTTAATTGGTTGAAGTCTCTACTTAGCAGTTAGTTCATGGTTTTTGGATGGGTTCCACTTAGTTTTGTTGTTTTTGTTTTGTTTTTCGCT HG:+:2471101666:42 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTTGAACTCCACGTGGGGAGTGCAAGGAAATAACTTTTATAAGGTGTTCATAGAAACAGGAAAAAATATTTGATTTGGTTAAAGTGGAAAGTCCTTAGAGTTTAGTGGCAGTTTTTAATTGGTTGAAGTCTCTACTTAGCAGTTAGTTCATGGTTTTTGGATGGGTTCCACTTAGTTTTGTTGTTTTTGTTTTGTTTTTCGCT HG:+:2471101667:42 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTTGAACTCCACGTGGGGAGTGCAAGGAAATAACTTTTATAAGGTGTTCATAGAAACAGGAAAAAATATTTGATTTGGTTAAAGTGGAAAGTCCTTAGAGTTTAGTGGCAGTTTTTAATTGGTTGAAGTCTCTACTTAGCAGTTAGTTCATGGTTTTTGGATGGGTTCCACTTAGTTTTGTTGTTTTTGTTTTGTTTTTCGCT HG:+:600038086:-1 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTTGAACTCCACGTGGGGAGTGCAAGGAAATAACTTTTATAAGGTGTTCATAGAAACAGGAAAAAATATTTGATTTGGTTAAAGTGGAAAGTCCTTAGAGTTTAGTGGCAGTTTTTAATTGGTTGAAGTCTCTACTTAGCAGTTAGTTCATGGTTTTTGGATGGGTTCCACTTAGTTTTGTTGTTTTTGTTTTGTTTTTCGCT HG:+:2471101665:42 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTTGAACTCCACGTGGGGAGTGCAAGGAAATAACTTTTATAAGGTGTTCATAGAAACAGGAAAAAATATTTGATTTGGTTAAAGTGGAAAGTCCTTAGAGTTTAGTGGCAGTTTTTAATTGGTTGAAGTCTCTACTTAGCAGTTAGTTCATGGTTTTTGGATGGGTTCCACTTAGTTTTGTTGTTTTTGTTTTGTTTTTCGCT HG:+:2471101669:42 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTTGAACTCCACGTGGGGAGTGCAAGGAAATAACTTTTATAAGGTGTTCATAGAAACAGGAAAAAATATTTGATTTGGTTAAAGTGGAAAGTCCTTAGAGTTTAGTGGCAGTTTTTAATTGGTTGAAGTCTCTACTTAGCAGTTAGTTCATGGTTTTTGGATGGGTTCCACTTAGTTTTGTTGTTTTTGTTTTGTTTTTCGCT HG:+:2471101675:42 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTTGAACTCCACGTGGGGAGTGCAAGGAAATAACTTTTATAAGGTGTTCATAGAAACAGGAAAAAATATTTGATTTGGTTAAAGTGGAAAGTCCTTAGAGTTTAGTGGCAGTTTTTAATTGGTTGAAGTCTCTACTTAGCAGTTAGTTCATGGTTTTTGGATGGGTTCCACTTAGTTTTGTTGTTTTTGTTTTGTTTTTCGCT HG:+:377204359:-1 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTTGAACTCCACGTGGGGAGTGCAAGGAAATAACTTTTATAAGGTGTTCATAGAAACAGGAAAAAATATTTGATTTGGTTAAAGTGGAAAGTCCTTAGAGTTTAGTGGCAGTTTTTAATTGGTTGAAGTCTCTACTTAGCAGTTAGTTCATGGTTTTTGGATGGGTTCCACTTAGTTTTGTTGTTTTTGTTTTGTTTTTCGCT HG:+:2471101672:42 +AGCGAAAAACAAAACAAAAACAACAAAACTAAGTGGAACCCATCCAAAAACCATGAACTAACTGCTAAGTAGAGACTTCAACCAATTAAAAACTGCCACTAAACTCTAAGGACTTTCCACTTTAACCAAATCAAATATTTTTTCCTGTTTCTATGAACACCTTATAAAAGTTATTTCCTTGCACTCCCCACGTGGAGTTCAACACCCAACCGCTTGCAGTCTGGTGCTGCCGGATTCATAGATTGCTGAGTGCTCAAGTACACTTCTTAAGATATGCCTAAGTTCATTTTAATACTGGTTAAATGTAAAATTTTAGCTATAAAATGATAGAGCTTTTAAAAATATAGGATACCACATATTACTATACACAGTCATTCCTCAACATCATGGGAACTTGGTTCCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG HG:+:1328108201:-1 HG:+:2404753254:-1 +AGCGAAAAACAAAACAAAAACAACAAAACTAAGTGGAACCCATCCAAAAACCATGAACTAACTGCTAAGTAGAGACTTCAACCAATTAAAAACTGCCACTAAACTCTAAGGACTTTCCACTTTAACCAAATCAAATATTTTTTCCTGTTTCTATGAACACCTTATAAAAGTTATTTCCTTGCACTCCCCACGTGGAGTTCAACACCCAACCGCTTGCAGTCTGGTGCTGCCGGATTCATAGATTGCTGAGTGCTCAAGTACACTTCTTAAGATATGCCTAAGTTCATTTTAATACTGGTTAAATGTAAAATTTTAGCTATAAAATGATAGAGCTTTTAAAAATATAGGATACCACATATTACTATACACAGTCATTCCTCAACATCATGGGAACTTGGTTCCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG HG:+:984700247:-1 HG:+:1323135209:-1 +AGCGAAAAACAAAACAAAAACAACAAAACTAAGTGGAACCCATCCAAAAACCATGAACTAACTGCTAAGTAGAGACTTCAACCAATTAAAAACTGCCACTAAACTCTAAGGACTTTCCACTTTAACCAAATCAAATATTTTTTCCTGTTTCTATGAACACCTTATAAAAGTTATTTCCTTGCACTCCCCACGTGGAGTTCAACACCCAACCGCTTGCAGTCTGGTGCTGCCGGATTCATAGATTGCTGAGTGCTCAAGTACACTTCTTAAGATATGCCTAAGTTCATTTTAATACTGGTTAAATGTAAAATTTTAGCTATAAAATGATAGAGCTTTTAAAAATATAGGATACCACATATTACTATACACAGTCATTCCTCAACATCATGGGAACTTGGTTCCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG HG:+:1831911309:-1 HG:+:2254634463:-1 +AGCGAAAAACAAAACAAAAACAACAAAACTAAGTGGAACCCATCCAAAAACCATGAACTAACTGCTAAGTAGAGACTTCAACCAATTAAAAACTGCCACTAAACTCTAAGGACTTTCCACTTTAACCAAATCAAATATTTTTTCCTGTTTCTATGAACACCTTATAAAAGTTATTTCCTTGCACTCCCCACGTGGAGTTCAACACCCAACCGCTTGCAGTCTGGTGCTGCCGGATTCATAGATTGCTGAGTGCTCAAGTACACTTCTTAAGATATGCCTAAGTTCATTTTAATACTGGTTAAATGTAAAATTTTAGCTATAAAATGATAGAGCTTTTAAAAATATAGGATACCACATATTACTATACACAGTCATTCCTCAACATCATGGGAACTTGGTTCCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG HG:+:62601426:-1 HG:+:69595436:-1 HG:+:95198692:-1 HG:+:202207560:-1 HG:+:486751565:-1 HG:+:543159419:-1 HG:+:620662971:-1 HG:+:687280606:-1 HG:+:694084468:-1 HG:+:724844930:-1 HG:+:1032618147:-1 HG:+:1355343754:-1 HG:+:1389367302:-1 HG:+:1541260924:-1 HG:+:1638079030:-1 HG:+:1677824885:-1 HG:+:1820802724:-1 HG:+:2107223506:-1 HG:+:2637546211:-1 HG:+:2662688091:-1 +AGCGAAAAACAAAACAAAAACAACAAAACTAAGTGGAACCCATCCAAAAACCATGAACTAACTGCTAAGTAGAGACTTCAACCAATTAAAAACTGCCACTAAACTCTAAGGACTTTCCACTTTAACCAAATCAAATATTTTTTCCTGTTTCTATGAACACCTTATAAAAGTTATTTCCTTGCACTCCCCACGTGGAGTTCAACACCCAACCGCTTGCAGTCTGGTGCTGCCGGATTCATAGATTGCTGAGTGCTCAAGTACACTTCTTAAGATATGCCTAAGTTCATTTTAATACTGGTTAAATGTAAAATTTTAGCTATAAAATGATAGAGCTTTTAAAAATATAGGATACCACATATTACTATACACAGTCATTCCTCAACATCATGGGAACTTGGTTCCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG HG:+:84368568:-1 HG:+:100987012:-1 HG:+:428820895:-1 HG:+:918775437:-1 HG:+:1073991268:-1 HG:+:1077230000:-1 HG:+:1106523090:-1 HG:+:1453278752:-1 HG:+:1467373106:-1 HG:+:1474525717:-1 HG:+:1655455766:-1 HG:+:1735821176:-1 HG:+:1743339193:-1 HG:+:1763377457:-1 HG:+:2527351699:-1 HG:+:2711917236:-1 HG:+:2727539147:-1 +AGCGAAAAACAAAACAAAAACAACAAAACTAAGTGGAACCCATCCAAAAACCATGAACTAACTGCTAAGTAGAGACTTCAACCAATTAAAAACTGCCACTAAACTCTAAGGACTTTCCACTTTAACCAAATCAAATATTTTTTCCTGTTTCTATGAACACCTTATAAAAGTTATTTCCTTGCACTCCCCACGTGGAGTTCAACACCCAACCGCTTGCAGTCTGGTGCTGCCGGATTCATAGATTGCTGAGTGCTCAAGTACACTTCTTAAGATATGCCTAAGTTCATTTTAATACTGGTTAAATGTAAAATTTTAGCTATAAAATGATAGAGCTTTTAAAAATATAGGATACCACATATTACTATACACAGTCATTCCTCAACATCATGGGAACTTGGTTCCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG HG:+:57744255:-1 HG:+:214076770:-1 HG:+:287064539:-1 HG:+:965136217:-1 HG:+:1127410318:-1 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCACTGCTTCTCTCACTTCGTTCTCTGTCACCTTTGTTCATGGGCTTGTTGTTTCATTGGCTATTGGATGGCTCTTCTAACTCCAGCATTATGTTATGGTTCCAGTCAGGAATAAGAGGGAAACTGATTACTTCCATGAGGAAGGCTTCCGTCAGCAACATCGTACTCATAACTGGATTGGCCTAAAAGAGTGACTGACCTACA HG:+:69591332:-1 HG:+:210221136:-1 HG:+:384672860:-1 HG:+:395126060:-1 HG:+:400235266:-1 HG:+:551677411:-1 HG:+:683959088:36 HG:+:693457399:-1 HG:+:698828270:-1 HG:+:710431684:-1 HG:+:759041312:-1 HG:+:890097947:-1 HG:+:980824605:-1 HG:+:1071933647:-1 HG:+:1131289270:-1 HG:+:1291430779:-1 HG:+:1313331523:-1 HG:+:1355158178:-1 HG:+:1370709563:-1 HG:+:1456703866:-1 HG:+:1546405226:-1 HG:+:1802757977:-1 HG:+:1921063492:-1 HG:+:1932366921:-1 HG:+:1988792712:-1 HG:+:2066622905:-1 HG:+:2170254109:-1 HG:+:2172010664:-1 HG:+:2191084771:-1 HG:+:2302144430:-1 HG:+:2371393159:-1 HG:+:2541742712:-1 HG:+:2651990268:-1 HG:+:2658078257:-1 HG:+:2731556360:-1 HG:+:2748031431:-1 HG:+:2800380416:-1 HG:+:2814421240:-1 HG:+:2903221995:-1 HG:+:2975559204:-1 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCACTGCTTCTCTCACTTCGTTCTCTGTCACCTTTGTTCATGGGCTTGTTGTTTCATTGGCTATTGGATGGCTCTTCTAACTCCAGCATTATGTTATGGTTCCAGTCAGGAATAAGAGGGAAACTGATTACTTCCATGAGGAAGGCTTCCGTCAGCAACATCGTACTCATAACTGGATTGGCCTAAAAGAGTGACTGACCTACA HG:+:683959087:36 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCACTGCTTCTCTCACTTCGTTCTCTGTCACCTTTGTTCATGGGCTTGTTGTTTCATTGGCTATTGGATGGCTCTTCTAACTCCAGCATTATGTTATGGTTCCAGTCAGGAATAAGAGGGAAACTGATTACTTCCATGAGGAAGGCTTCCGTCAGCAACATCGTACTCATAACTGGATTGGCCTAAAAGAGTGACTGACCTACA HG:+:683959091:36 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCACTGCTTCTCTCACTTCGTTCTCTGTCACCTTTGTTCATGGGCTTGTTGTTTCATTGGCTATTGGATGGCTCTTCTAACTCCAGCATTATGTTATGGTTCCAGTCAGGAATAAGAGGGAAACTGATTACTTCCATGAGGAAGGCTTCCGTCAGCAACATCGTACTCATAACTGGATTGGCCTAAAAGAGTGACTGACCTACA HG:+:683959085:36 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCACTGCTTCTCTCACTTCGTTCTCTGTCACCTTTGTTCATGGGCTTGTTGTTTCATTGGCTATTGGATGGCTCTTCTAACTCCAGCATTATGTTATGGTTCCAGTCAGGAATAAGAGGGAAACTGATTACTTCCATGAGGAAGGCTTCCGTCAGCAACATCGTACTCATAACTGGATTGGCCTAAAAGAGTGACTGACCTACA HG:+:683959084:36 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCACTGCTTCTCTCACTTCGTTCTCTGTCACCTTTGTTCATGGGCTTGTTGTTTCATTGGCTATTGGATGGCTCTTCTAACTCCAGCATTATGTTATGGTTCCAGTCAGGAATAAGAGGGAAACTGATTACTTCCATGAGGAAGGCTTCCGTCAGCAACATCGTACTCATAACTGGATTGGCCTAAAAGAGTGACTGACCTACA HG:+:2551976633:-1 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCACTGCTTCTCTCACTTCGTTCTCTGTCACCTTTGTTCATGGGCTTGTTGTTTCATTGGCTATTGGATGGCTCTTCTAACTCCAGCATTATGTTATGGTTCCAGTCAGGAATAAGAGGGAAACTGATTACTTCCATGAGGAAGGCTTCCGTCAGCAACATCGTACTCATAACTGGATTGGCCTAAAAGAGTGACTGACCTACA HG:+:683959076:36 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCACTGCTTCTCTCACTTCGTTCTCTGTCACCTTTGTTCATGGGCTTGTTGTTTCATTGGCTATTGGATGGCTCTTCTAACTCCAGCATTATGTTATGGTTCCAGTCAGGAATAAGAGGGAAACTGATTACTTCCATGAGGAAGGCTTCCGTCAGCAACATCGTACTCATAACTGGATTGGCCTAAAAGAGTGACTGACCTACA HG:+:683959079:36 HG:+:1681780906:-1 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCACTGCTTCTCTCACTTCGTTCTCTGTCACCTTTGTTCATGGGCTTGTTGTTTCATTGGCTATTGGATGGCTCTTCTAACTCCAGCATTATGTTATGGTTCCAGTCAGGAATAAGAGGGAAACTGATTACTTCCATGAGGAAGGCTTCCGTCAGCAACATCGTACTCATAACTGGATTGGCCTAAAAGAGTGACTGACCTACA HG:+:683959083:36 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCACTGCTTCTCTCACTTCGTTCTCTGTCACCTTTGTTCATGGGCTTGTTGTTTCATTGGCTATTGGATGGCTCTTCTAACTCCAGCATTATGTTATGGTTCCAGTCAGGAATAAGAGGGAAACTGATTACTTCCATGAGGAAGGCTTCCGTCAGCAACATCGTACTCATAACTGGATTGGCCTAAAAGAGTGACTGACCTACA HG:+:683959090:36 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCACTGCTTCTCTCACTTCGTTCTCTGTCACCTTTGTTCATGGGCTTGTTGTTTCATTGGCTATTGGATGGCTCTTCTAACTCCAGCATTATGTTATGGTTCCAGTCAGGAATAAGAGGGAAACTGATTACTTCCATGAGGAAGGCTTCCGTCAGCAACATCGTACTCATAACTGGATTGGCCTAAAAGAGTGACTGACCTACA HG:+:107426205:-1 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCACTGCTTCTCTCACTTCGTTCTCTGTCACCTTTGTTCATGGGCTTGTTGTTTCATTGGCTATTGGATGGCTCTTCTAACTCCAGCATTATGTTATGGTTCCAGTCAGGAATAAGAGGGAAACTGATTACTTCCATGAGGAAGGCTTCCGTCAGCAACATCGTACTCATAACTGGATTGGCCTAAAAGAGTGACTGACCTACA HG:+:210160114:-1 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCACTGCTTCTCTCACTTCGTTCTCTGTCACCTTTGTTCATGGGCTTGTTGTTTCATTGGCTATTGGATGGCTCTTCTAACTCCAGCATTATGTTATGGTTCCAGTCAGGAATAAGAGGGAAACTGATTACTTCCATGAGGAAGGCTTCCGTCAGCAACATCGTACTCATAACTGGATTGGCCTAAAAGAGTGACTGACCTACA HG:+:2358149402:-1 +TGTAGGTCAGTCACTCTTTTAGGCCAATCCAGTTATGAGTACGATGTTGCTGACGGAAGCCTTCCTCATGGAAGTAATCAGTTTCCCTCTTATTCCTGACTGGAACCATAACATAATGCTGGAGTTAGAAGAGCCATCCAATAGCCAATGAAACAACAAGCCCATGAACAAAGGTGACAGAGAACGAAGTGAGAGAAGCAGTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG HG:+:2112077346:-1 +TGTAGGTCAGTCACTCTTTTAGGCCAATCCAGTTATGAGTACGATGTTGCTGACGGAAGCCTTCCTCATGGAAGTAATCAGTTTCCCTCTTATTCCTGACTGGAACCATAACATAATGCTGGAGTTAGAAGAGCCATCCAATAGCCAATGAAACAACAAGCCCATGAACAAAGGTGACAGAGAACGAAGTGAGAGAAGCAGTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG HG:+:822795845:-1 HG:+:1921656213:-1 +TGTAGGTCAGTCACTCTTTTAGGCCAATCCAGTTATGAGTACGATGTTGCTGACGGAAGCCTTCCTCATGGAAGTAATCAGTTTCCCTCTTATTCCTGACTGGAACCATAACATAATGCTGGAGTTAGAAGAGCCATCCAATAGCCAATGAAACAACAAGCCCATGAACAAAGGTGACAGAGAACGAAGTGAGAGAAGCAGTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG HG:+:2119428778:-1 +TGTAGGTCAGTCACTCTTTTAGGCCAATCCAGTTATGAGTACGATGTTGCTGACGGAAGCCTTCCTCATGGAAGTAATCAGTTTCCCTCTTATTCCTGACTGGAACCATAACATAATGCTGGAGTTAGAAGAGCCATCCAATAGCCAATGAAACAACAAGCCCATGAACAAAGGTGACAGAGAACGAAGTGAGAGAAGCAGTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG HG:+:748860827:-1 HG:+:792865943:-1 +TGTAGGTCAGTCACTCTTTTAGGCCAATCCAGTTATGAGTACGATGTTGCTGACGGAAGCCTTCCTCATGGAAGTAATCAGTTTCCCTCTTATTCCTGACTGGAACCATAACATAATGCTGGAGTTAGAAGAGCCATCCAATAGCCAATGAAACAACAAGCCCATGAACAAAGGTGACAGAGAACGAAGTGAGAGAAGCAGTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG HG:+:2569785002:-1 +TGTAGGTCAGTCACTCTTTTAGGCCAATCCAGTTATGAGTACGATGTTGCTGACGGAAGCCTTCCTCATGGAAGTAATCAGTTTCCCTCTTATTCCTGACTGGAACCATAACATAATGCTGGAGTTAGAAGAGCCATCCAATAGCCAATGAAACAACAAGCCCATGAACAAAGGTGACAGAGAACGAAGTGAGAGAAGCAGTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG HG:+:75745730:-1 HG:+:2140363888:-1 +TGTAGGTCAGTCACTCTTTTAGGCCAATCCAGTTATGAGTACGATGTTGCTGACGGAAGCCTTCCTCATGGAAGTAATCAGTTTCCCTCTTATTCCTGACTGGAACCATAACATAATGCTGGAGTTAGAAGAGCCATCCAATAGCCAATGAAACAACAAGCCCATGAACAAAGGTGACAGAGAACGAAGTGAGAGAAGCAGTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG HG:+:2623667451:-1 +TGTAGGTCAGTCACTCTTTTAGGCCAATCCAGTTATGAGTACGATGTTGCTGACGGAAGCCTTCCTCATGGAAGTAATCAGTTTCCCTCTTATTCCTGACTGGAACCATAACATAATGCTGGAGTTAGAAGAGCCATCCAATAGCCAATGAAACAACAAGCCCATGAACAAAGGTGACAGAGAACGAAGTGAGAGAAGCAGTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG HG:+:2081459901:-1 +TGTAGGTCAGTCACTCTTTTAGGCCAATCCAGTTATGAGTACGATGTTGCTGACGGAAGCCTTCCTCATGGAAGTAATCAGTTTCCCTCTTATTCCTGACTGGAACCATAACATAATGCTGGAGTTAGAAGAGCCATCCAATAGCCAATGAAACAACAAGCCCATGAACAAAGGTGACAGAGAACGAAGTGAGAGAAGCAGTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG HG:+:190169199:-1 HG:+:785369705:-1 HG:+:965016860:-1 HG:+:1012554906:-1 HG:+:1248257150:-1 HG:+:1578503094:-1 HG:+:1579032348:-1 HG:+:1579847979:-1 HG:+:1580648059:-1 HG:+:1821753925:-1 HG:+:1871023047:-1 HG:+:2024740632:-1 HG:+:2643314088:-1 +TGTAGGTCAGTCACTCTTTTAGGCCAATCCAGTTATGAGTACGATGTTGCTGACGGAAGCCTTCCTCATGGAAGTAATCAGTTTCCCTCTTATTCCTGACTGGAACCATAACATAATGCTGGAGTTAGAAGAGCCATCCAATAGCCAATGAAACAACAAGCCCATGAACAAAGGTGACAGAGAACGAAGTGAGAGAAGCAGTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG HG:+:5214183:-1 HG:+:262486406:-1 HG:+:298576358:-1 HG:+:355874999:-1 HG:+:470584864:-1 HG:+:779119422:-1 HG:+:817168476:-1 HG:+:1142338043:-1 HG:+:1267654920:-1 HG:+:1757443818:-1 HG:+:2422299677:-1 HG:+:2695136956:-1 +TGTAGGTCAGTCACTCTTTTAGGCCAATCCAGTTATGAGTACGATGTTGCTGACGGAAGCCTTCCTCATGGAAGTAATCAGTTTCCCTCTTATTCCTGACTGGAACCATAACATAATGCTGGAGTTAGAAGAGCCATCCAATAGCCAATGAAACAACAAGCCCATGAACAAAGGTGACAGAGAACGAAGTGAGAGAAGCAGTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG HG:+:720002168:-1 HG:+:888124285:-1 HG:+:933016236:-1 HG:+:1787535105:-1 HG:+:1827042485:-1 HG:+:1970876556:-1 HG:+:1982750245:-1 HG:+:2644382570:-1 HG:+:2915733785:-1 +TGTAGGTCAGTCACTCTTTTAGGCCAATCCAGTTATGAGTACGATGTTGCTGACGGAAGCCTTCCTCATGGAAGTAATCAGTTTCCCTCTTATTCCTGACTGGAACCATAACATAATGCTGGAGTTAGAAGAGCCATCCAATAGCCAATGAAACAACAAGCCCATGAACAAAGGTGACAGAGAACGAAGTGAGAGAAGCAGTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG HG:+:630772543:-1 HG:+:823482976:-1 HG:+:1520136629:-1 HG:+:2394418635:-1 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA 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HG:+:79634187:83 HG:+:101625879:154 HG:+:121146762:82 HG:+:222469213:-1 HG:+:398716626:108 HG:+:425717191:-1 HG:+:745219153:76 HG:+:763992871:138 HG:+:796196637:-1 HG:+:822536601:-1 HG:+:840865138:109 HG:+:910470911:105 HG:+:934419752:98 HG:+:980003616:138 HG:+:985359761:-1 HG:+:1044026802:172 HG:+:1063372849:-1 HG:+:1145900601:145 HG:+:1180111332:68 HG:+:1248347742:67 HG:+:1249640337:52 HG:+:1265627319:154 HG:+:1318539651:72 HG:+:1459144809:94 HG:+:1507998470:104 HG:+:1511445127:-1 HG:+:1523135167:72 HG:+:1617519206:94 HG:+:1644240033:86 HG:+:1706668895:92 HG:+:1853422402:-1 HG:+:1992349798:-1 HG:+:2019594958:-1 HG:+:2190351765:-1 HG:+:2443641705:-1 HG:+:2811592567:-1 HG:+:2942773308:79 HG:+:2945135269:103 HG:+:2951037053:114 HG:+:2954149396:-1 HG:+:2976889496:98 HG:+:2989472089:143 HG:+:3006629984:88 HG:+:3057379800:-1 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:1249640359:52 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:166470484:108 HG:+:422767267:103 HG:+:496748387:71 HG:+:498900641:-1 HG:+:630137558:87 HG:+:637232919:-1 HG:+:1454899223:105 HG:+:1616832633:116 HG:+:1765572543:105 HG:+:1777287383:92 HG:+:2363135364:115 HG:+:2748216204:100 HG:+:2997670800:180 HG:+:3051516910:78 HG:+:3060494501:117 HG:+:3062103791:116 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:758055655:147 HG:+:1892526636:-1 HG:+:2961376277:183 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:501211215:71 HG:+:1151966096:166 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:372981363:-1 HG:+:749300158:131 HG:+:790156487:74 HG:+:1543694372:91 HG:+:1578042327:-1 HG:+:1584402914:-1 HG:+:1737205605:-1 HG:+:1888610299:94 HG:+:2228479531:-1 HG:+:3015957980:91 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:383558405:76 HG:+:383624960:76 HG:+:509071784:-1 HG:+:705651535:82 HG:+:803291861:70 HG:+:1166624908:-1 HG:+:1436609320:90 HG:+:1439673027:90 HG:+:1522525773:73 HG:+:1563950111:173 HG:+:1824072080:72 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:60079773:101 HG:+:69911580:102 HG:+:158277227:136 HG:+:312086578:106 HG:+:318076321:104 HG:+:416796519:106 HG:+:417262330:112 HG:+:514938500:-1 HG:+:574900053:82 HG:+:582596957:-1 HG:+:586803072:128 HG:+:627994407:75 HG:+:628396718:87 HG:+:629585020:92 HG:+:654623023:200 HG:+:723477741:125 HG:+:751498920:137 HG:+:800391157:139 HG:+:956057144:108 HG:+:983169413:77 HG:+:1102249727:123 HG:+:1118145878:97 HG:+:1256228411:70 HG:+:1256624434:87 HG:+:1442907759:-1 HG:+:1457132605:-1 HG:+:1466002649:111 HG:+:1485599284:116 HG:+:1529687260:66 HG:+:1529842171:-1 HG:+:1571261787:127 HG:+:1648530558:102 HG:+:1776823525:103 HG:+:1836505803:104 HG:+:1855813929:86 HG:+:1867070189:-1 HG:+:1932919496:117 HG:+:1993374770:95 HG:+:2028965746:77 HG:+:2140261764:149 HG:+:2226703443:67 HG:+:2237596790:128 HG:+:2237702291:94 HG:+:2239957351:-1 HG:+:2240064855:80 HG:+:2266606955:104 HG:+:2362330778:107 HG:+:2456439799:105 HG:+:2957525317:111 HG:+:2964988953:94 HG:+:2971056852:101 HG:+:3040522540:106 HG:+:3046274720:-1 HG:+:3063823155:88 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:833463514:118 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:1266408238:91 HG:+:1507419625:74 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:655248285:165 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:2284045299:75 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:169875730:-1 HG:+:249059427:80 HG:+:358203242:83 HG:+:924364986:75 HG:+:1001797412:80 HG:+:1295020287:-1 HG:+:1353370392:-1 HG:+:1507076327:-1 HG:+:1531052068:100 HG:+:2552412715:92 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:63889469:-1 HG:+:438981209:169 HG:+:559754415:-1 HG:+:596100911:116 HG:+:1081501399:-1 HG:+:1248174972:-1 HG:+:1298547446:-1 HG:+:1465748832:-1 HG:+:1726986965:-1 HG:+:1729173892:-1 HG:+:1729694405:-1 HG:+:2133760421:152 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:459012862:69 HG:+:465371904:89 HG:+:498428960:98 HG:+:1069213956:95 HG:+:1150114641:79 HG:+:1163348005:71 HG:+:1295020306:-1 HG:+:1999786039:-1 HG:+:2052697824:79 HG:+:2559362916:70 HG:+:2604667095:87 HG:+:2950855290:68 HG:+:2956621825:157 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAAGTGCCATCCCCCATCAAGCTACCAATGCCTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATAATGGAACCAAAAAGAGCCCTCATCGCCAAAGTCAATCCTAAGCCAAAAGAACAAAGACTTGGAAGGCATCACACTACCTGACTTCAAACTATACTACAAGTCTACAGTAACCAAACAGCACGGTACTGGTA HG:+:444588403:86 HG:+:650068075:83 HG:+:971134324:71 HG:+:1120536051:96 HG:+:1681674959:80 HG:+:1736489528:94 HG:+:1821847066:-1 HG:+:2408402564:94 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:14709978:78 HG:+:43581349:67 HG:+:96518301:79 HG:+:152404856:73 HG:+:180653291:84 HG:+:223956056:-1 HG:+:237183934:68 HG:+:270357021:90 HG:+:301329669:74 HG:+:333848180:72 HG:+:376187405:67 HG:+:410959021:68 HG:+:423643808:70 HG:+:425598484:70 HG:+:445184036:73 HG:+:535977460:118 HG:+:574833435:72 HG:+:591228669:84 HG:+:603081444:72 HG:+:651329481:-1 HG:+:752706538:77 HG:+:766669382:69 HG:+:789987181:75 HG:+:801800599:71 HG:+:834982985:91 HG:+:861750681:73 HG:+:923115899:75 HG:+:938275192:79 HG:+:1003341101:66 HG:+:1003473178:77 HG:+:1008710667:76 HG:+:1009257395:76 HG:+:1047194554:134 HG:+:1055531094:-1 HG:+:1117771364:69 HG:+:1140294841:-1 HG:+:1164143254:84 HG:+:1243505366:-1 HG:+:1243864075:166 HG:+:1270996066:65 HG:+:1283360479:78 HG:+:1288224619:88 HG:+:1326873248:72 HG:+:1337856321:74 HG:+:1472880855:-1 HG:+:1477539434:108 HG:+:1478680438:162 HG:+:1522700593:75 HG:+:1540729898:78 HG:+:1558697080:69 HG:+:1645983706:-1 HG:+:1647499329:73 HG:+:1699751827:67 HG:+:1699947492:94 HG:+:1703066375:78 HG:+:1776950957:-1 HG:+:1791929596:85 HG:+:1830740744:-1 HG:+:1841426722:84 HG:+:1848871836:73 HG:+:1858359869:83 HG:+:1864778304:70 HG:+:1924957281:67 HG:+:1953155044:71 HG:+:2006470956:73 HG:+:2009418641:72 HG:+:2023459749:85 HG:+:2134494123:73 HG:+:2144368230:77 HG:+:2219006651:77 HG:+:2234700062:74 HG:+:2243374056:73 HG:+:2288847175:75 HG:+:2358610706:75 HG:+:2381087669:74 HG:+:2391615420:-1 HG:+:2409741481:73 HG:+:2441730393:93 HG:+:2470557515:97 HG:+:2528939459:62 HG:+:2564765731:64 HG:+:2567168299:76 HG:+:2914492783:171 HG:+:2957192700:137 HG:+:2963349069:69 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:60931383:187 HG:+:187726818:105 HG:+:331035245:-1 HG:+:435958240:77 HG:+:784333303:92 HG:+:1073527703:79 HG:+:1322956459:143 HG:+:1444194061:79 HG:+:1848592276:105 HG:+:2742451954:85 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:944600677:81 HG:+:2114335511:93 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:51489913:-1 HG:+:52637842:80 HG:+:64391849:72 HG:+:71279889:79 HG:+:73279728:81 HG:+:89179634:119 HG:+:103394817:76 HG:+:112698588:76 HG:+:145912842:-1 HG:+:147454548:-1 HG:+:159729163:88 HG:+:172951585:71 HG:+:180653293:84 HG:+:185222084:75 HG:+:185857610:74 HG:+:195895292:68 HG:+:248678576:81 HG:+:261913661:71 HG:+:265663218:71 HG:+:269281960:162 HG:+:271377980:71 HG:+:279146834:76 HG:+:280910314:76 HG:+:298486956:71 HG:+:301329671:74 HG:+:302466593:-1 HG:+:306139230:72 HG:+:319908153:-1 HG:+:321494866:72 HG:+:322958994:78 HG:+:326254675:69 HG:+:327123598:-1 HG:+:328584611:67 HG:+:328761175:66 HG:+:348133299:77 HG:+:365543479:-1 HG:+:373713751:-1 HG:+:374602504:71 HG:+:383474371:72 HG:+:385489976:72 HG:+:398332196:85 HG:+:403506228:72 HG:+:431883150:103 HG:+:432676573:84 HG:+:432862248:72 HG:+:447751253:71 HG:+:447804050:68 HG:+:498977759:70 HG:+:510492347:90 HG:+:528729034:-1 HG:+:535977462:118 HG:+:546406939:68 HG:+:562945327:78 HG:+:576730557:-1 HG:+:578518191:-1 HG:+:581049818:133 HG:+:590074752:69 HG:+:591458605:77 HG:+:591903157:75 HG:+:593611957:-1 HG:+:599893418:187 HG:+:604829159:73 HG:+:622408174:81 HG:+:624965718:-1 HG:+:627195219:67 HG:+:627422218:65 HG:+:656669674:104 HG:+:656953740:-1 HG:+:670182629:174 HG:+:683211112:64 HG:+:701250613:69 HG:+:701490513:129 HG:+:735449297:64 HG:+:743274836:83 HG:+:752170586:83 HG:+:752706540:77 HG:+:757332611:72 HG:+:759306726:76 HG:+:759849118:73 HG:+:761757217:89 HG:+:762482257:95 HG:+:766669384:69 HG:+:773482118:-1 HG:+:777465138:72 HG:+:787803941:71 HG:+:789412761:83 HG:+:802082205:70 HG:+:802265548:73 HG:+:804883891:70 HG:+:811645485:75 HG:+:818457330:73 HG:+:818620258:191 HG:+:818925134:196 HG:+:837947679:75 HG:+:851104285:71 HG:+:854601683:77 HG:+:866600674:127 HG:+:874173802:69 HG:+:919797470:76 HG:+:927460813:79 HG:+:934203393:-1 HG:+:938299977:77 HG:+:938789058:81 HG:+:964381491:75 HG:+:964717300:75 HG:+:964825747:84 HG:+:982488307:126 HG:+:987586351:80 HG:+:987677436:75 HG:+:987734553:88 HG:+:997214866:77 HG:+:1007853850:68 HG:+:1007867376:72 HG:+:1008710669:76 HG:+:1009257397:76 HG:+:1009568377:75 HG:+:1043085803:76 HG:+:1062148094:-1 HG:+:1068429516:70 HG:+:1068580866:150 HG:+:1120127372:80 HG:+:1120314364:88 HG:+:1132692562:75 HG:+:1139152580:85 HG:+:1147050592:73 HG:+:1161510323:107 HG:+:1165525319:-1 HG:+:1165715277:-1 HG:+:1170719051:67 HG:+:1177778928:87 HG:+:1191769910:74 HG:+:1192031439:69 HG:+:1195884986:71 HG:+:1196006340:74 HG:+:1222421198:115 HG:+:1251833123:71 HG:+:1261199993:79 HG:+:1266395460:97 HG:+:1267963414:73 HG:+:1295032102:87 HG:+:1296652857:81 HG:+:1297272556:82 HG:+:1305417044:132 HG:+:1317276831:77 HG:+:1323184410:97 HG:+:1346725749:70 HG:+:1348323346:74 HG:+:1351849720:-1 HG:+:1353621550:69 HG:+:1375338081:81 HG:+:1379487702:73 HG:+:1393520208:73 HG:+:1395060596:81 HG:+:1406912679:-1 HG:+:1407055657:88 HG:+:1408210372:72 HG:+:1429062495:84 HG:+:1454824789:63 HG:+:1454977435:73 HG:+:1457193725:70 HG:+:1468303326:74 HG:+:1477539436:108 HG:+:1485000935:68 HG:+:1497412086:69 HG:+:1497592356:72 HG:+:1497866656:76 HG:+:1507851306:69 HG:+:1508389437:66 HG:+:1508440378:68 HG:+:1524872086:76 HG:+:1540729900:78 HG:+:1545338090:77 HG:+:1551464027:-1 HG:+:1558893765:-1 HG:+:1559747722:-1 HG:+:1561861467:74 HG:+:1569588392:170 HG:+:1569601359:90 HG:+:1608236407:76 HG:+:1620873648:73 HG:+:1621270347:74 HG:+:1624527640:72 HG:+:1624545167:72 HG:+:1627823667:104 HG:+:1644141072:77 HG:+:1653240893:165 HG:+:1658432162:98 HG:+:1658989167:68 HG:+:1685310966:129 HG:+:1735837902:103 HG:+:1738576151:88 HG:+:1738660176:-1 HG:+:1772247145:99 HG:+:1772287522:77 HG:+:1802368124:66 HG:+:1823588438:72 HG:+:1829724435:78 HG:+:1832445154:-1 HG:+:1833269928:108 HG:+:1837599653:77 HG:+:1848871838:73 HG:+:1850617575:72 HG:+:1853171315:82 HG:+:1866681580:79 HG:+:1867473534:90 HG:+:1902783140:69 HG:+:1903238103:82 HG:+:1905731928:74 HG:+:1960589725:74 HG:+:1967445656:87 HG:+:1977284083:102 HG:+:1984210274:92 HG:+:1992946793:74 HG:+:1992975682:76 HG:+:1993042673:108 HG:+:1995489732:190 HG:+:2006470958:73 HG:+:2019153163:77 HG:+:2031384030:80 HG:+:2031432393:94 HG:+:2127726544:-1 HG:+:2133071025:77 HG:+:2153021850:69 HG:+:2177893425:-1 HG:+:2193340490:68 HG:+:2225610781:72 HG:+:2227035824:67 HG:+:2227079871:69 HG:+:2228719066:81 HG:+:2236549213:68 HG:+:2240328062:94 HG:+:2241355464:76 HG:+:2272380328:73 HG:+:2286509155:70 HG:+:2286647091:78 HG:+:2339490717:-1 HG:+:2358610708:75 HG:+:2360959649:-1 HG:+:2369580607:87 HG:+:2391615422:-1 HG:+:2442605318:86 HG:+:2443833585:131 HG:+:2469411478:70 HG:+:2475089094:69 HG:+:2485674136:74 HG:+:2485938917:103 HG:+:2486803650:-1 HG:+:2503223696:76 HG:+:2567168301:76 HG:+:2567909577:-1 HG:+:2606685936:83 HG:+:2608970056:72 HG:+:2613660340:-1 HG:+:2615183338:72 HG:+:2626242841:71 HG:+:2628665684:71 HG:+:2634922888:72 HG:+:2635277123:127 HG:+:2641084176:76 HG:+:2656496178:70 HG:+:2671561093:87 HG:+:2730914689:79 HG:+:2730998244:70 HG:+:2759818052:66 HG:+:2770646571:72 HG:+:2797618301:139 HG:+:2816897905:67 HG:+:2852361063:70 HG:+:2882857119:67 HG:+:2892572733:-1 HG:+:2892624761:-1 HG:+:2895156520:71 HG:+:2910001512:-1 HG:+:2910006852:92 HG:+:2912563907:188 HG:+:2913296534:71 HG:+:2917222870:77 HG:+:2932036620:190 HG:+:2956888129:116 HG:+:2966845400:92 HG:+:2970929771:-1 HG:+:2971621009:87 HG:+:2971646471:78 HG:+:2971963304:90 HG:+:2975093289:-1 HG:+:2975642322:79 HG:+:2977867622:77 HG:+:2982336751:79 HG:+:2986197341:-1 HG:+:2994662620:-1 HG:+:3006095806:180 HG:+:3006272565:76 HG:+:3019183603:-1 HG:+:3023028994:77 HG:+:3023274866:-1 HG:+:3028239443:67 HG:+:3035563346:70 HG:+:3044307374:83 HG:+:3051402829:95 HG:+:3059472817:93 HG:+:3096937521:-1 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:933170403:69 HG:+:990694913:82 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:416609879:72 HG:+:435958241:77 HG:+:982072018:67 HG:+:1036382635:85 HG:+:1140335313:81 HG:+:1259397100:196 HG:+:1295313360:-1 HG:+:1692147742:65 HG:+:1848871831:73 HG:+:2146141476:79 HG:+:2158794581:88 HG:+:2227035817:67 HG:+:2419596534:79 HG:+:2522223684:160 HG:+:2702718722:86 HG:+:2858512711:86 HG:+:2937642405:80 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:867336118:151 HG:+:1355577159:66 HG:+:2967842169:75 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:78944260:-1 HG:+:96900177:134 HG:+:188722532:76 HG:+:316096879:92 HG:+:375035985:145 HG:+:513673217:169 HG:+:562951911:119 HG:+:590971544:99 HG:+:603081439:72 HG:+:628102259:159 HG:+:757105445:105 HG:+:792800408:77 HG:+:873022075:102 HG:+:959358898:119 HG:+:967649513:108 HG:+:1113140862:104 HG:+:1135068787:139 HG:+:1141243929:101 HG:+:1160895104:103 HG:+:1178339323:161 HG:+:1318274932:118 HG:+:1469063388:-1 HG:+:1475852457:150 HG:+:1481347324:101 HG:+:1563799602:111 HG:+:1717701985:88 HG:+:1749643254:124 HG:+:1797886985:131 HG:+:1836619881:87 HG:+:1870629399:-1 HG:+:2048960477:76 HG:+:2077720779:125 HG:+:2233257708:102 HG:+:2240226572:131 HG:+:2394035924:124 HG:+:2649889710:75 HG:+:2687631833:111 HG:+:2735342944:130 HG:+:2951001719:71 HG:+:3005777393:70 HG:+:3045044578:123 HG:+:3062745575:88 HG:+:3097016319:79 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:163610894:74 HG:+:270683217:78 HG:+:425805737:-1 HG:+:574833417:72 HG:+:861750663:73 HG:+:1033661375:79 HG:+:1205286416:63 HG:+:1520122327:70 HG:+:1977284063:102 HG:+:2991094419:78 HG:+:3004965886:-1 HG:+:3057840165:87 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:75364537:96 HG:+:499380078:85 HG:+:546406935:68 HG:+:673754350:136 HG:+:1426352590:100 HG:+:1510154371:-1 HG:+:1864630439:84 HG:+:2009326499:151 HG:+:2302147904:103 HG:+:2329598519:87 HG:+:2606037649:121 HG:+:2846207394:112 HG:+:3021377412:159 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:743557981:80 HG:+:832990685:-1 HG:+:973012209:-1 HG:+:1010857680:78 HG:+:1291658657:84 HG:+:1477148343:163 HG:+:1547359869:101 HG:+:1559121743:161 HG:+:1686704480:112 HG:+:1866611223:110 HG:+:2249548022:109 HG:+:2942824207:-1 HG:+:3018433023:-1 HG:+:3057680858:109 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:923882202:95 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:47589787:-1 HG:+:62040222:116 HG:+:103394815:76 HG:+:146663257:86 HG:+:186694151:152 HG:+:302325784:187 HG:+:356542180:-1 HG:+:390313013:102 HG:+:407382125:134 HG:+:503977176:119 HG:+:506449878:90 HG:+:507884164:95 HG:+:508399908:93 HG:+:717704092:90 HG:+:751056874:108 HG:+:763130967:131 HG:+:768732807:112 HG:+:807099813:150 HG:+:825831890:128 HG:+:846166478:114 HG:+:850922766:108 HG:+:854192096:171 HG:+:863194000:130 HG:+:879251511:92 HG:+:910005966:-1 HG:+:931537948:-1 HG:+:947233632:-1 HG:+:957183134:157 HG:+:994892808:87 HG:+:995120567:93 HG:+:996362769:-1 HG:+:1028384853:-1 HG:+:1050677047:160 HG:+:1118990518:83 HG:+:1133748330:153 HG:+:1137282523:113 HG:+:1142615734:111 HG:+:1147836317:-1 HG:+:1227932844:-1 HG:+:1247282873:-1 HG:+:1429320773:147 HG:+:1444187643:-1 HG:+:1453659781:101 HG:+:1458634408:-1 HG:+:1459142121:-1 HG:+:1497560018:98 HG:+:1561651003:147 HG:+:1564200845:106 HG:+:1564219027:157 HG:+:1606807528:104 HG:+:1646360001:169 HG:+:1648009468:188 HG:+:1864729055:159 HG:+:1956173835:-1 HG:+:1960676752:-1 HG:+:1997655161:110 HG:+:2080863589:-1 HG:+:2156468723:-1 HG:+:2161417812:-1 HG:+:2163854811:84 HG:+:2189936228:-1 HG:+:2287148718:113 HG:+:2350616762:-1 HG:+:2395086881:144 HG:+:2653831572:134 HG:+:2735669905:92 HG:+:2737490970:158 HG:+:2828646244:-1 HG:+:2939514185:-1 HG:+:2958578906:130 HG:+:2961989047:150 HG:+:3050994523:152 HG:+:3051900313:172 HG:+:3056106248:188 HG:+:3057778632:-1 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:167933702:-1 HG:+:214925062:-1 HG:+:808700175:-1 HG:+:1111555148:-1 HG:+:1864354878:103 HG:+:2039059808:-1 HG:+:2120271237:-1 HG:+:2559248545:-1 HG:+:2956087557:104 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:1627823640:104 HG:+:2623198429:148 HG:+:2923301386:195 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:1493381379:118 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:1022118782:91 HG:+:2136990013:90 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:1322142115:90 HG:+:1611189566:89 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:1557188144:-1 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:743614179:89 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:499256966:86 HG:+:1139365601:101 HG:+:1267963396:73 HG:+:2567781094:85 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:51371710:121 HG:+:719326703:107 HG:+:757738450:132 HG:+:1051985270:95 HG:+:1168826397:-1 HG:+:2956738393:119 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:462886571:-1 HG:+:824636747:-1 HG:+:999955486:93 HG:+:1266380494:93 HG:+:1390109031:-1 HG:+:1699572448:-1 HG:+:1725275457:132 HG:+:2056836663:-1 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:464388803:126 HG:+:512758494:153 HG:+:2068976577:126 HG:+:2149552650:134 +TACCAGTACCGTGCTGTTTGGTTACTGTAGACTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTTCCAAGTCTTTGTTCTTTTGGCTTAGGATTGACTTTGGCGATGAGGGCTCTTTTTGGTTCCATTATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGATGGGGGATGGCACTTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC HG:+:520856798:101 HG:+:646131206:-1 HG:+:934583700:104 HG:+:1507715391:83 HG:+:1647466586:110 HG:+:2056187622:179 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCTTGTTCTGGTAGTCACAGGACAATTGGGAGTCATTTAGTGGCATTTAAGGGGTGGGGGACCAGACAGGCTGGACAACCTGCAGTACATGGGATGGTCTAGCACAAGCCACAAATATTCTATGTCCCCCACGGACTTCCAGTCTCCCCTGGAAGGGCTGAAAAGCCTACGCCATTTACCTGTACAACAACAAGGGGTTTCCT HG:+:306597275:-1 HG:+:730076087:-1 HG:+:841481282:-1 HG:+:955377401:-1 HG:+:1196702583:-1 HG:+:1227099672:-1 HG:+:1486257509:-1 HG:+:2642309683:45 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCTTGTTCTGGTAGTCACAGGACAATTGGGAGTCATTTAGTGGCATTTAAGGGGTGGGGGACCAGACAGGCTGGACAACCTGCAGTACATGGGATGGTCTAGCACAAGCCACAAATATTCTATGTCCCCCACGGACTTCCAGTCTCCCCTGGAAGGGCTGAAAAGCCTACGCCATTTACCTGTACAACAACAAGGGGTTTCCT HG:+:2642309682:45 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCTTGTTCTGGTAGTCACAGGACAATTGGGAGTCATTTAGTGGCATTTAAGGGGTGGGGGACCAGACAGGCTGGACAACCTGCAGTACATGGGATGGTCTAGCACAAGCCACAAATATTCTATGTCCCCCACGGACTTCCAGTCTCCCCTGGAAGGGCTGAAAAGCCTACGCCATTTACCTGTACAACAACAAGGGGTTTCCT HG:+:2642309679:45 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCTTGTTCTGGTAGTCACAGGACAATTGGGAGTCATTTAGTGGCATTTAAGGGGTGGGGGACCAGACAGGCTGGACAACCTGCAGTACATGGGATGGTCTAGCACAAGCCACAAATATTCTATGTCCCCCACGGACTTCCAGTCTCCCCTGGAAGGGCTGAAAAGCCTACGCCATTTACCTGTACAACAACAAGGGGTTTCCT HG:+:2066676622:-1 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCTTGTTCTGGTAGTCACAGGACAATTGGGAGTCATTTAGTGGCATTTAAGGGGTGGGGGACCAGACAGGCTGGACAACCTGCAGTACATGGGATGGTCTAGCACAAGCCACAAATATTCTATGTCCCCCACGGACTTCCAGTCTCCCCTGGAAGGGCTGAAAAGCCTACGCCATTTACCTGTACAACAACAAGGGGTTTCCT HG:+:2642309691:45 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCTTGTTCTGGTAGTCACAGGACAATTGGGAGTCATTTAGTGGCATTTAAGGGGTGGGGGACCAGACAGGCTGGACAACCTGCAGTACATGGGATGGTCTAGCACAAGCCACAAATATTCTATGTCCCCCACGGACTTCCAGTCTCCCCTGGAAGGGCTGAAAAGCCTACGCCATTTACCTGTACAACAACAAGGGGTTTCCT HG:+:2642309692:45 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCTTGTTCTGGTAGTCACAGGACAATTGGGAGTCATTTAGTGGCATTTAAGGGGTGGGGGACCAGACAGGCTGGACAACCTGCAGTACATGGGATGGTCTAGCACAAGCCACAAATATTCTATGTCCCCCACGGACTTCCAGTCTCCCCTGGAAGGGCTGAAAAGCCTACGCCATTTACCTGTACAACAACAAGGGGTTTCCT HG:+:2642309696:45 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCTTGTTCTGGTAGTCACAGGACAATTGGGAGTCATTTAGTGGCATTTAAGGGGTGGGGGACCAGACAGGCTGGACAACCTGCAGTACATGGGATGGTCTAGCACAAGCCACAAATATTCTATGTCCCCCACGGACTTCCAGTCTCCCCTGGAAGGGCTGAAAAGCCTACGCCATTTACCTGTACAACAACAAGGGGTTTCCT HG:+:2642309697:45 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCTTGTTCTGGTAGTCACAGGACAATTGGGAGTCATTTAGTGGCATTTAAGGGGTGGGGGACCAGACAGGCTGGACAACCTGCAGTACATGGGATGGTCTAGCACAAGCCACAAATATTCTATGTCCCCCACGGACTTCCAGTCTCCCCTGGAAGGGCTGAAAAGCCTACGCCATTTACCTGTACAACAACAAGGGGTTTCCT HG:+:2642309685:45 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCTTGTTCTGGTAGTCACAGGACAATTGGGAGTCATTTAGTGGCATTTAAGGGGTGGGGGACCAGACAGGCTGGACAACCTGCAGTACATGGGATGGTCTAGCACAAGCCACAAATATTCTATGTCCCCCACGGACTTCCAGTCTCCCCTGGAAGGGCTGAAAAGCCTACGCCATTTACCTGTACAACAACAAGGGGTTTCCT HG:+:2642309690:45 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCTTGTTCTGGTAGTCACAGGACAATTGGGAGTCATTTAGTGGCATTTAAGGGGTGGGGGACCAGACAGGCTGGACAACCTGCAGTACATGGGATGGTCTAGCACAAGCCACAAATATTCTATGTCCCCCACGGACTTCCAGTCTCCCCTGGAAGGGCTGAAAAGCCTACGCCATTTACCTGTACAACAACAAGGGGTTTCCT HG:+:912070928:-1 +AGGAAACCCCTTGTTGTTGTACAGGTAAATGGCGTAGGCTTTTCAGCCCTTCCAGGGGAGACTGGAAGTCCGTGGGGGACATAGAATATTTGTGGCTTGTGCTAGACCATCCCATGTACTGCAGGTTGTCCAGCCTGTCTGGTCCCCCACCCCTTAAATGCCACTAAATGACTCCCAATTGTCCTGTGACTACCAGAACAAGCCCCATGGATTTTCCAGATGCTTTTTCAAGCATTTTGGGTTTTGTTTGCATGTAATAGAAGCCAGCAGACAGTTTGGATCAGGGAAGTGAAGTGACCCAACCTAGGTTTTAAAGAGATCTGCCTATTCATAAAAATAATGAAGGGGAGGCTGTAGGTTTCTGTGTTCACTTACGCAAGACTCGGCCCCCAAGAGTGAGCTGCAGAGGGTACCAGGCTGACCTCCTGTCTGTCTCAAAGCTTAAGACTCACCCAGAAGTCTGTCTTTCTACCCAGAAGCACCTAGACCCATCCTATCAGAGGCCTCCCTCTAATGAGGAGTAGGGTGGGGGCAACCCCATGGTGTCCTTTGTGCCTAAACCTTTACAATAACAGGTTGTTGGCTGTCACCTGAAGCAGGTTTTCAACCATCACTCCCTTCCCACCATACACACACTCCCAGCTCATTTTGAGTTCCTTTTCTGCAATAAATAACAGATTCTTGCAAAGTGGTTAGAAGAAATTAGTAAGTTAAGCCTCACACTAGGGTTATTTTGCCAGGAGACCTTCCTTTCCTAGGTTAACCCCCTCCACCCACGTGGGCACCCAGTGGGATCTGCTGCAGTCTGCGCCAGGGTTTGCTTGGCCTGCAAGGGTGGCCATGGCAGATGCCCTTTCCTTGTAACTGGAATCCCCCATAGCCTGGCCTTCCAGTACAGTAGAGAGAATAATTGGATAAACCCTAAACTGGAAATTACAAACAATAACCTACTCTGTTAGTTTACATATGAAACTACTTAAGCAAGTCCTTTTTATTTTAT HG:+:2571312433:-1 +AGGAAACCCCTTGTTGTTGTACAGGTAAATGGCGTAGGCTTTTCAGCCCTTCCAGGGGAGACTGGAAGTCCGTGGGGGACATAGAATATTTGTGGCTTGTGCTAGACCATCCCATGTACTGCAGGTTGTCCAGCCTGTCTGGTCCCCCACCCCTTAAATGCCACTAAATGACTCCCAATTGTCCTGTGACTACCAGAACAAGCCCCATGGATTTTCCAGATGCTTTTTCAAGCATTTTGGGTTTTGTTTGCATGTAATAGAAGCCAGCAGACAGTTTGGATCAGGGAAGTGAAGTGACCCAACCTAGGTTTTAAAGAGATCTGCCTATTCATAAAAATAATGAAGGGGAGGCTGTAGGTTTCTGTGTTCACTTACGCAAGACTCGGCCCCCAAGAGTGAGCTGCAGAGGGTACCAGGCTGACCTCCTGTCTGTCTCAAAGCTTAAGACTCACCCAGAAGTCTGTCTTTCTACCCAGAAGCACCTAGACCCATCCTATCAGAGGCCTCCCTCTAATGAGGAGTAGGGTGGGGGCAACCCCATGGTGTCCTTTGTGCCTAAACCTTTACAATAACAGGTTGTTGGCTGTCACCTGAAGCAGGTTTTCAACCATCACTCCCTTCCCACCATACACACACTCCCAGCTCATTTTGAGTTCCTTTTCTGCAATAAATAACAGATTCTTGCAAAGTGGTTAGAAGAAATTAGTAAGTTAAGCCTCACACTAGGGTTATTTTGCCAGGAGACCTTCCTTTCCTAGGTTAACCCCCTCCACCCACGTGGGCACCCAGTGGGATCTGCTGCAGTCTGCGCCAGGGTTTGCTTGGCCTGCAAGGGTGGCCATGGCAGATGCCCTTTCCTTGTAACTGGAATCCCCCATAGCCTGGCCTTCCAGTACAGTAGAGAGAATAATTGGATAAACCCTAAACTGGAAATTACAAACAATAACCTACTCTGTTAGTTTACATATGAAACTACTTAAGCAAGTCCTTTTTATTTTAT HG:+:2270541240:-1 +AGGAAACCCCTTGTTGTTGTACAGGTAAATGGCGTAGGCTTTTCAGCCCTTCCAGGGGAGACTGGAAGTCCGTGGGGGACATAGAATATTTGTGGCTTGTGCTAGACCATCCCATGTACTGCAGGTTGTCCAGCCTGTCTGGTCCCCCACCCCTTAAATGCCACTAAATGACTCCCAATTGTCCTGTGACTACCAGAACAAGCCCCATGGATTTTCCAGATGCTTTTTCAAGCATTTTGGGTTTTGTTTGCATGTAATAGAAGCCAGCAGACAGTTTGGATCAGGGAAGTGAAGTGACCCAACCTAGGTTTTAAAGAGATCTGCCTATTCATAAAAATAATGAAGGGGAGGCTGTAGGTTTCTGTGTTCACTTACGCAAGACTCGGCCCCCAAGAGTGAGCTGCAGAGGGTACCAGGCTGACCTCCTGTCTGTCTCAAAGCTTAAGACTCACCCAGAAGTCTGTCTTTCTACCCAGAAGCACCTAGACCCATCCTATCAGAGGCCTCCCTCTAATGAGGAGTAGGGTGGGGGCAACCCCATGGTGTCCTTTGTGCCTAAACCTTTACAATAACAGGTTGTTGGCTGTCACCTGAAGCAGGTTTTCAACCATCACTCCCTTCCCACCATACACACACTCCCAGCTCATTTTGAGTTCCTTTTCTGCAATAAATAACAGATTCTTGCAAAGTGGTTAGAAGAAATTAGTAAGTTAAGCCTCACACTAGGGTTATTTTGCCAGGAGACCTTCCTTTCCTAGGTTAACCCCCTCCACCCACGTGGGCACCCAGTGGGATCTGCTGCAGTCTGCGCCAGGGTTTGCTTGGCCTGCAAGGGTGGCCATGGCAGATGCCCTTTCCTTGTAACTGGAATCCCCCATAGCCTGGCCTTCCAGTACAGTAGAGAGAATAATTGGATAAACCCTAAACTGGAAATTACAAACAATAACCTACTCTGTTAGTTTACATATGAAACTACTTAAGCAAGTCCTTTTTATTTTAT HG:+:1753724808:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:22535214:-1 HG:+:40839369:-1 HG:+:111054887:-1 HG:+:168409159:-1 HG:+:183946024:-1 HG:+:242176189:-1 HG:+:374741528:-1 HG:+:419798695:-1 HG:+:441646537:-1 HG:+:482304962:-1 HG:+:499146791:-1 HG:+:532946484:-1 HG:+:582485337:-1 HG:+:641052177:-1 HG:+:693659106:-1 HG:+:704934179:-1 HG:+:715487973:-1 HG:+:871189881:-1 HG:+:896935419:-1 HG:+:933173922:-1 HG:+:935698590:-1 HG:+:946320350:-1 HG:+:1012189846:-1 HG:+:1065194841:-1 HG:+:1073862310:-1 HG:+:1085506107:-1 HG:+:1118398511:-1 HG:+:1130131105:-1 HG:+:1142606280:-1 HG:+:1168836493:-1 HG:+:1179406360:-1 HG:+:1244550402:-1 HG:+:1255399253:-1 HG:+:1290782223:-1 HG:+:1297319970:-1 HG:+:1348990156:-1 HG:+:1371370236:-1 HG:+:1379939012:-1 HG:+:1468427838:-1 HG:+:1472702769:-1 HG:+:1474288967:-1 HG:+:1503552477:-1 HG:+:1585284470:-1 HG:+:1610534738:-1 HG:+:1622582123:-1 HG:+:1624860490:-1 HG:+:1654077077:-1 HG:+:1667278644:-1 HG:+:1668416266:-1 HG:+:1737913207:-1 HG:+:1740864290:-1 HG:+:1760820038:-1 HG:+:1772136315:-1 HG:+:1802312432:-1 HG:+:1832934053:-1 HG:+:1843784688:-1 HG:+:1873436324:-1 HG:+:1879475469:-1 HG:+:1966024229:-1 HG:+:1980141837:-1 HG:+:2061431340:-1 HG:+:2076849411:-1 HG:+:2132097254:-1 HG:+:2142450760:-1 HG:+:2149097548:-1 HG:+:2155020797:-1 HG:+:2180076746:-1 HG:+:2220157898:-1 HG:+:2232155433:-1 HG:+:2265861557:-1 HG:+:2436048596:-1 HG:+:2462145679:-1 HG:+:2552810813:-1 HG:+:2668523211:-1 HG:+:2706276630:-1 HG:+:2706632178:-1 HG:+:2748100754:-1 HG:+:2755919208:-1 HG:+:2806056044:-1 HG:+:2813047866:-1 HG:+:2813695369:-1 HG:+:2921352471:-1 HG:+:2935138239:-1 HG:+:2976162805:-1 HG:+:3028795457:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:39309035:-1 HG:+:117780169:-1 HG:+:389861090:-1 HG:+:1444646569:-1 HG:+:2332785070:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:142837214:-1 HG:+:143388933:-1 HG:+:258856890:-1 HG:+:1251545696:-1 HG:+:2023306929:-1 HG:+:2461131541:-1 HG:+:2536431606:167 HG:+:3006223031:-1 HG:+:3097577794:-1 HG:+:3098517008:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:2115397317:-1 HG:+:2536431607:167 HG:+:2817761478:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:391881589:-1 HG:+:2473698809:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:2536431610:167 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:1235986732:-1 HG:+:1736964299:-1 HG:+:1941729086:-1 HG:+:1946420337:-1 HG:+:2013964114:-1 HG:+:2879589940:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:724627418:-1 HG:+:727275457:-1 HG:+:971452336:-1 HG:+:1958377549:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:99278630:-1 HG:+:106407123:-1 HG:+:208129751:-1 HG:+:235999214:-1 HG:+:245199808:-1 HG:+:377056165:-1 HG:+:435354492:-1 HG:+:448819716:-1 HG:+:482314569:-1 HG:+:547936098:-1 HG:+:895723174:-1 HG:+:908778819:-1 HG:+:1138001299:-1 HG:+:1296601325:-1 HG:+:1352130736:-1 HG:+:1426907267:-1 HG:+:1500904292:-1 HG:+:1750235511:-1 HG:+:1793705492:-1 HG:+:1811708546:-1 HG:+:1850614834:-1 HG:+:1979013770:-1 HG:+:2011512641:-1 HG:+:2057200686:-1 HG:+:2103997934:-1 HG:+:2115752175:-1 HG:+:2239025219:-1 HG:+:2352670538:-1 HG:+:2600405236:-1 HG:+:2715770783:-1 HG:+:2796725743:-1 HG:+:2810872932:-1 HG:+:3099133575:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:48861229:-1 HG:+:110826415:-1 HG:+:166993961:-1 HG:+:219959995:-1 HG:+:474238792:-1 HG:+:579188156:-1 HG:+:588000451:-1 HG:+:691652433:-1 HG:+:737755174:-1 HG:+:779575592:-1 HG:+:902254023:-1 HG:+:918166279:-1 HG:+:953237310:-1 HG:+:1050372918:-1 HG:+:1112928016:-1 HG:+:1280723366:-1 HG:+:1394469039:-1 HG:+:1543414246:-1 HG:+:1694859039:-1 HG:+:1737891298:-1 HG:+:1761931580:-1 HG:+:1765514948:-1 HG:+:1769453758:-1 HG:+:1845200083:-1 HG:+:1847560502:-1 HG:+:2188760938:-1 HG:+:2229111456:-1 HG:+:2279555367:-1 HG:+:2284088478:-1 HG:+:2354935909:-1 HG:+:2516717534:-1 HG:+:2522290351:-1 HG:+:2536431608:167 HG:+:2552999360:-1 HG:+:2611390015:-1 HG:+:2876292724:-1 HG:+:2897928478:-1 HG:+:2974639060:-1 HG:+:3004286512:-1 HG:+:3027576167:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:356697640:-1 HG:+:2536431292:-1 HG:+:2676119567:-1 HG:+:3036240091:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:178211776:-1 HG:+:806661342:-1 HG:+:1651696673:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:171492572:-1 HG:+:199101454:-1 HG:+:403305653:-1 HG:+:749910027:-1 HG:+:1079022900:-1 HG:+:1131444191:-1 HG:+:1276776420:-1 HG:+:1353652451:-1 HG:+:1714694672:-1 HG:+:1736828605:-1 HG:+:1795633270:-1 HG:+:2037295724:-1 HG:+:2519726596:-1 HG:+:2966119291:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:710193025:-1 HG:+:2170560427:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:72982868:-1 HG:+:1095456815:-1 HG:+:1155699097:-1 HG:+:2262395231:-1 HG:+:2554354762:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:842245039:-1 HG:+:981680295:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:67386059:-1 HG:+:170141185:-1 HG:+:179106593:-1 HG:+:328884122:-1 HG:+:356906204:-1 HG:+:389507023:-1 HG:+:437932662:-1 HG:+:439768866:-1 HG:+:475937342:-1 HG:+:577488953:-1 HG:+:694327394:-1 HG:+:880643063:-1 HG:+:894989303:-1 HG:+:902892449:-1 HG:+:908702195:-1 HG:+:1005093943:-1 HG:+:1041935325:-1 HG:+:1132910661:-1 HG:+:1245197377:-1 HG:+:1304134174:-1 HG:+:1497422388:-1 HG:+:1763672338:-1 HG:+:1800325617:-1 HG:+:2276490240:-1 HG:+:2647162012:-1 HG:+:2798405250:-1 HG:+:2922529666:-1 HG:+:2938320521:-1 HG:+:2966930337:-1 HG:+:2968694073:-1 HG:+:2991509787:-1 HG:+:3000865955:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:1651318812:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:164415656:-1 HG:+:317294218:-1 HG:+:536232510:-1 HG:+:568264135:-1 HG:+:1008843503:-1 HG:+:1185218094:-1 HG:+:1207440180:-1 HG:+:1374821731:-1 HG:+:1523564808:-1 HG:+:1576383525:-1 HG:+:2264289061:-1 HG:+:2478545152:-1 HG:+:2505484244:-1 HG:+:2559419129:-1 HG:+:2596521891:-1 HG:+:2700047748:-1 HG:+:2820868594:-1 HG:+:3014069780:-1 HG:+:3025651414:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:171308039:-1 HG:+:399698036:-1 HG:+:472510310:-1 HG:+:474330980:-1 HG:+:595123309:-1 HG:+:660286762:-1 HG:+:1126231783:-1 HG:+:1150097499:-1 HG:+:2257449824:-1 HG:+:2379466280:-1 HG:+:2396857611:-1 HG:+:2519625053:-1 HG:+:2758323140:-1 HG:+:2884167761:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:1768859335:-1 HG:+:1965055207:-1 HG:+:2408073107:-1 HG:+:2426482332:-1 HG:+:2536431611:167 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:681309418:-1 HG:+:1736178559:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:303088582:-1 HG:+:2536431609:167 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:1550883462:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAAATCAGCACTTGCAATGTAAAGGAGGCTATCCAATGGCAAGATGAGAAATCACAAAAGAATTAGAGGTAATAGCATCCCAGAACTGACATAAGGATGTGAATAGTTACCCATACCCAAAAGTCCAAAAGGAAATGATGTGATTATAATTTATATCACATTGTAGATATGACATAGGAGTACTAAGAAAGTCTTCAGAAAGG HG:+:107542388:-1 HG:+:348033794:-1 HG:+:664894259:-1 HG:+:1012806035:-1 HG:+:1089970662:-1 HG:+:1144802123:-1 HG:+:1166847076:-1 HG:+:1225310123:-1 HG:+:1336092210:-1 HG:+:1654569443:-1 HG:+:1713777079:-1 HG:+:1858661341:-1 HG:+:2281350965:-1 HG:+:2378747068:-1 HG:+:2461541329:-1 HG:+:2646437080:-1 HG:+:2755958593:-1 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:80578619:-1 HG:+:99326642:-1 HG:+:186676006:-1 HG:+:321257369:-1 HG:+:581492344:-1 HG:+:647693724:-1 HG:+:797307481:-1 HG:+:799550275:-1 HG:+:854398602:-1 HG:+:904636448:-1 HG:+:1034737003:-1 HG:+:1260038174:-1 HG:+:1269285435:-1 HG:+:1296629243:-1 HG:+:1432653926:-1 HG:+:1452617444:-1 HG:+:1572553731:-1 HG:+:1584024879:-1 HG:+:1585537843:-1 HG:+:1655247983:-1 HG:+:2005321741:-1 HG:+:2014623166:-1 HG:+:2043057408:-1 HG:+:2146355460:-1 HG:+:2337151086:-1 HG:+:2498918319:-1 HG:+:2751240547:-1 HG:+:2780935126:-1 HG:+:2805740860:-1 HG:+:2829513529:-1 HG:+:2859749157:-1 HG:+:2881933871:-1 HG:+:2883569379:-1 HG:+:2949305483:-1 HG:+:2987695992:-1 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:1702232936:49 HG:+:2534951732:169 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:1702232942:49 HG:+:2534951738:169 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:1408310822:-1 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:1004063200:-1 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:1702232933:49 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:2534952047:-1 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:2534951735:169 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:1702232935:49 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:1702232940:49 HG:+:2534951736:169 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:1702232943:49 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:2761292691:-1 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:1702232937:49 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:1702232941:49 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:1702232929:49 +CCTTTCTGAAGACTTTCTTAGTACTCCTATGTCATATCTACAATGTGATATAAATTATAATCACATCATTTCCTTTTGGACTTTTGGGTATGGGTAACTATTCACATCCTTATGTCAGTTCTGGGATGCTATTACCTCTAATTCTTTTGTGATTTCTCATCTTGCCATTGGATAGCCTCCTTTACATTGCAAGTGCTGATTTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG HG:+:1702232934:49 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:204039035:-1 HG:+:630769193:-1 HG:+:871305599:-1 HG:+:992367817:-1 HG:+:1097311139:-1 HG:+:1423066015:-1 HG:+:1551427737:-1 HG:+:1696765571:-1 HG:+:2046353217:-1 HG:+:2075282183:-1 HG:+:2138805221:-1 HG:+:2384891626:-1 HG:+:2905491918:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:499098019:-1 HG:+:775000465:-1 HG:+:1338743517:-1 HG:+:2764746408:-1 HG:+:2914205901:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:20934102:-1 HG:+:46445943:-1 HG:+:120619642:-1 HG:+:148887626:-1 HG:+:353549702:-1 HG:+:525216629:-1 HG:+:540327211:-1 HG:+:849703278:-1 HG:+:900275017:-1 HG:+:1043800456:-1 HG:+:1087314226:-1 HG:+:1400974591:-1 HG:+:1881043125:-1 HG:+:2033628993:-1 HG:+:2734802246:-1 HG:+:3100277310:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:18507862:-1 HG:+:64998627:-1 HG:+:95250221:-1 HG:+:95488724:-1 HG:+:101352446:-1 HG:+:455565010:-1 HG:+:458545084:-1 HG:+:501847242:-1 HG:+:506567478:-1 HG:+:511919851:-1 HG:+:535303364:-1 HG:+:766221848:-1 HG:+:956209588:-1 HG:+:960120337:-1 HG:+:978587824:-1 HG:+:1093148405:-1 HG:+:1211179712:-1 HG:+:1255499945:-1 HG:+:1307407434:-1 HG:+:1331123459:-1 HG:+:1367476627:-1 HG:+:1444610612:-1 HG:+:1449329480:-1 HG:+:1500234276:-1 HG:+:1582838937:-1 HG:+:1640098652:-1 HG:+:1660589807:-1 HG:+:1723676081:-1 HG:+:1754936179:-1 HG:+:1927867914:-1 HG:+:2054769483:-1 HG:+:2079742300:-1 HG:+:2137740926:-1 HG:+:2236079752:-1 HG:+:2270026540:-1 HG:+:2272700526:-1 HG:+:2361835472:-1 HG:+:2364923433:-1 HG:+:2392417775:-1 HG:+:2464842287:-1 HG:+:2516673194:-1 HG:+:2565640500:-1 HG:+:2572941744:-1 HG:+:2625793710:-1 HG:+:2659083181:-1 HG:+:2660137253:-1 HG:+:2666224096:-1 HG:+:2710293271:-1 HG:+:2713460966:-1 HG:+:2854408314:-1 HG:+:2865374979:-1 HG:+:2867852834:-1 HG:+:2951888339:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:537043381:-1 HG:+:2416678684:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:174068418:-1 HG:+:2028516546:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:386595956:-1 HG:+:465583785:-1 HG:+:528017660:-1 HG:+:956982143:-1 HG:+:1120438391:-1 HG:+:1121042388:-1 HG:+:1333447384:-1 HG:+:1504280669:-1 HG:+:1763987021:-1 HG:+:2018028930:-1 HG:+:2247198426:-1 HG:+:2255763810:-1 HG:+:2376824543:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:709581206:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:906728619:-1 HG:+:1171366248:-1 HG:+:2512681557:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:2247418792:-1 HG:+:2727483462:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:940009841:-1 HG:+:1287493391:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:772490497:-1 HG:+:967637235:-1 HG:+:1784751249:-1 HG:+:2585467037:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:69333323:-1 HG:+:81785949:-1 HG:+:102060587:-1 HG:+:176139277:-1 HG:+:213841349:-1 HG:+:213949431:-1 HG:+:214944204:-1 HG:+:269274736:-1 HG:+:478243766:-1 HG:+:510498595:-1 HG:+:664958213:-1 HG:+:866682372:-1 HG:+:868809232:-1 HG:+:1015853462:-1 HG:+:1042594124:-1 HG:+:1082963354:-1 HG:+:1208295209:-1 HG:+:1233753322:-1 HG:+:1305257154:-1 HG:+:1401765226:-1 HG:+:1725699710:-1 HG:+:1746285730:-1 HG:+:1771738534:-1 HG:+:1825044043:-1 HG:+:1831066189:-1 HG:+:1994340192:-1 HG:+:1996691492:-1 HG:+:2181774728:-1 HG:+:2252487298:-1 HG:+:2270612564:-1 HG:+:2296893790:-1 HG:+:2346503235:-1 HG:+:2617213300:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:16134173:-1 HG:+:44217360:-1 HG:+:206673267:-1 HG:+:326962672:-1 HG:+:335009735:-1 HG:+:335114627:-1 HG:+:347052695:-1 HG:+:508084486:-1 HG:+:612352175:-1 HG:+:618044089:-1 HG:+:637688164:-1 HG:+:676900482:-1 HG:+:793585567:-1 HG:+:801097471:-1 HG:+:882176432:-1 HG:+:1008724810:-1 HG:+:1309063251:-1 HG:+:1309623066:-1 HG:+:1371362123:-1 HG:+:1374899200:-1 HG:+:1385469537:-1 HG:+:1471769453:-1 HG:+:1494282345:-1 HG:+:1768420860:-1 HG:+:1782532682:-1 HG:+:1799829664:-1 HG:+:1878853505:-1 HG:+:1959925754:-1 HG:+:1962686367:-1 HG:+:1970207320:-1 HG:+:1999953024:-1 HG:+:2133173942:-1 HG:+:2293424590:-1 HG:+:2430646090:-1 HG:+:2476264476:-1 HG:+:2484968395:-1 HG:+:2555270500:-1 HG:+:2573369161:-1 HG:+:2670481057:-1 HG:+:2674088757:-1 HG:+:2697306411:-1 HG:+:2764322223:-1 HG:+:2855478893:-1 HG:+:2872600411:-1 HG:+:2872791497:-1 HG:+:2878913907:-1 HG:+:2886002017:-1 HG:+:2981290811:-1 HG:+:3018303362:-1 HG:+:3020791842:-1 HG:+:3064880540:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:650838298:-1 HG:+:1670514842:-1 HG:+:1969820405:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:53140445:-1 HG:+:55169671:-1 HG:+:120385278:-1 HG:+:143459399:-1 HG:+:175901359:-1 HG:+:206850292:-1 HG:+:217529501:-1 HG:+:275188926:-1 HG:+:311384645:-1 HG:+:314632073:-1 HG:+:401669348:-1 HG:+:402403627:-1 HG:+:427643403:-1 HG:+:449609593:-1 HG:+:468451339:-1 HG:+:478665424:-1 HG:+:502330454:-1 HG:+:558819370:-1 HG:+:575177382:-1 HG:+:580493149:-1 HG:+:596308815:-1 HG:+:601487551:-1 HG:+:617595071:-1 HG:+:637944872:-1 HG:+:642936815:-1 HG:+:677711334:-1 HG:+:695408371:-1 HG:+:768486569:-1 HG:+:786523504:-1 HG:+:876006528:-1 HG:+:943277524:-1 HG:+:1001975814:-1 HG:+:1015855956:-1 HG:+:1018064578:-1 HG:+:1058460955:-1 HG:+:1076497714:-1 HG:+:1077534835:-1 HG:+:1095057795:-1 HG:+:1119886574:-1 HG:+:1139889252:-1 HG:+:1198187323:-1 HG:+:1207018360:-1 HG:+:1217613521:-1 HG:+:1235730077:-1 HG:+:1240000033:-1 HG:+:1266581746:-1 HG:+:1266752649:-1 HG:+:1285182887:-1 HG:+:1289613020:-1 HG:+:1334981733:-1 HG:+:1335374364:-1 HG:+:1362846294:-1 HG:+:1390784573:-1 HG:+:1401583514:-1 HG:+:1406848661:-1 HG:+:1446641868:-1 HG:+:1502033311:-1 HG:+:1534355604:-1 HG:+:1559064317:-1 HG:+:1577819928:-1 HG:+:1674059478:-1 HG:+:1688516544:-1 HG:+:1692196004:-1 HG:+:1693994277:-1 HG:+:1706986451:-1 HG:+:1755519951:-1 HG:+:1757405613:-1 HG:+:1757431031:-1 HG:+:1824887208:-1 HG:+:1838092874:-1 HG:+:1848434602:-1 HG:+:1848844552:-1 HG:+:1848981779:-1 HG:+:1886032769:-1 HG:+:1920481610:-1 HG:+:1970494446:-1 HG:+:2022974119:-1 HG:+:2061766672:-1 HG:+:2133744162:-1 HG:+:2134862400:-1 HG:+:2136728029:-1 HG:+:2146934188:-1 HG:+:2156357857:-1 HG:+:2291425010:-1 HG:+:2351073739:-1 HG:+:2353119270:-1 HG:+:2359603406:-1 HG:+:2426620062:-1 HG:+:2467669774:-1 HG:+:2472737720:-1 HG:+:2480218485:-1 HG:+:2481167579:-1 HG:+:2500902704:-1 HG:+:2517325671:-1 HG:+:2556898481:-1 HG:+:2576475823:-1 HG:+:2619690049:-1 HG:+:2622173600:-1 HG:+:2667184572:-1 HG:+:2667896094:-1 HG:+:2681624758:-1 HG:+:2709409256:-1 HG:+:2713428121:-1 HG:+:2713743906:-1 HG:+:2791559140:-1 HG:+:2804352859:-1 HG:+:2813232656:-1 HG:+:2815442491:-1 HG:+:2821701262:-1 HG:+:2825984559:-1 HG:+:2882245532:-1 HG:+:2905154035:-1 HG:+:2913284234:-1 HG:+:2951652424:-1 HG:+:2964307682:-1 HG:+:3049666314:-1 HG:+:3095926494:-1 HG:+:3096056591:-1 HG:+:3097955771:-1 HG:+:3100961379:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:1614394827:-1 HG:+:1960458292:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:208429182:-1 HG:+:1386657423:-1 HG:+:1416519264:-1 HG:+:2985719787:-1 HG:+:3056966622:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:362690334:-1 HG:+:636654471:-1 HG:+:877289726:-1 HG:+:974248064:-1 HG:+:1300434994:-1 HG:+:1624628511:-1 HG:+:1804359977:-1 HG:+:2037436778:-1 HG:+:2061769554:-1 HG:+:2667272788:-1 HG:+:2682248363:-1 HG:+:2967756665:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:57830632:-1 HG:+:796010464:-1 HG:+:796526440:-1 HG:+:1427899623:-1 HG:+:1559813868:-1 HG:+:2004424132:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:68762325:-1 HG:+:286747088:-1 HG:+:319507774:-1 HG:+:435993373:-1 HG:+:444456506:-1 HG:+:466184221:-1 HG:+:582468526:-1 HG:+:606641592:-1 HG:+:614109932:-1 HG:+:654077503:-1 HG:+:705244184:-1 HG:+:768868154:-1 HG:+:844993737:-1 HG:+:866943473:-1 HG:+:901591548:-1 HG:+:1095606997:-1 HG:+:1096887122:-1 HG:+:1249381011:-1 HG:+:1349242717:-1 HG:+:1466914312:-1 HG:+:1470283285:-1 HG:+:1492792054:-1 HG:+:1493385686:-1 HG:+:1542606789:-1 HG:+:1694107142:-1 HG:+:1819119719:-1 HG:+:1841321928:-1 HG:+:2147649442:-1 HG:+:2192237088:-1 HG:+:2340269562:-1 HG:+:2349497383:-1 HG:+:2468161389:-1 HG:+:2777904383:-1 HG:+:2947463786:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:77548608:-1 HG:+:100466268:-1 HG:+:1063677198:-1 HG:+:1343315711:-1 HG:+:1410829419:-1 HG:+:1994149676:-1 HG:+:2547293600:-1 HG:+:2729822342:-1 HG:+:3052460324:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:24553793:-1 HG:+:25142901:-1 HG:+:69669965:-1 HG:+:150172383:-1 HG:+:159225806:-1 HG:+:168175434:-1 HG:+:212015450:-1 HG:+:217012765:-1 HG:+:382493938:-1 HG:+:383671957:-1 HG:+:435581413:-1 HG:+:445666748:-1 HG:+:470014848:-1 HG:+:540222820:-1 HG:+:618893794:-1 HG:+:646694142:-1 HG:+:684282191:-1 HG:+:732651351:-1 HG:+:823100679:-1 HG:+:859465537:-1 HG:+:918386996:-1 HG:+:972858726:-1 HG:+:978555707:-1 HG:+:1087614886:-1 HG:+:1106170391:-1 HG:+:1117558318:-1 HG:+:1126352522:-1 HG:+:1176013030:-1 HG:+:1276695411:-1 HG:+:1360166347:-1 HG:+:1368370363:-1 HG:+:1381009315:-1 HG:+:1443781682:-1 HG:+:1492940331:-1 HG:+:1585608558:-1 HG:+:1607005576:-1 HG:+:1615854320:-1 HG:+:1619167918:-1 HG:+:1819610335:-1 HG:+:1835420064:-1 HG:+:1855683858:-1 HG:+:1904874394:-1 HG:+:1915785315:-1 HG:+:1992017090:-1 HG:+:2002861570:-1 HG:+:2013720939:-1 HG:+:2043490687:-1 HG:+:2131340022:-1 HG:+:2150180498:-1 HG:+:2175570392:-1 HG:+:2241541395:-1 HG:+:2405014609:-1 HG:+:2482363013:-1 HG:+:2495980548:-1 HG:+:2609165478:-1 HG:+:2634011836:-1 HG:+:2724897332:-1 HG:+:2791966108:-1 HG:+:2900648291:-1 HG:+:2916499837:-1 HG:+:2983136711:-1 HG:+:3100821367:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:378515695:-1 HG:+:1331348995:-1 HG:+:2121853927:-1 HG:+:2490298606:-1 HG:+:2540145035:-1 HG:+:2601078112:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:75432289:-1 HG:+:80168559:-1 HG:+:289113932:-1 HG:+:543081093:-1 HG:+:653033716:-1 HG:+:728177313:-1 HG:+:897834947:-1 HG:+:1119076051:-1 HG:+:1134327381:-1 HG:+:1835243478:-1 HG:+:1999226114:-1 HG:+:2021575741:-1 HG:+:2183452042:-1 HG:+:2235319084:-1 HG:+:2398549367:-1 HG:+:2547367410:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:322166653:-1 HG:+:427026239:-1 HG:+:661745069:-1 HG:+:837059655:-1 HG:+:1065330372:-1 HG:+:1575867434:-1 HG:+:1733511358:-1 HG:+:1911233857:-1 HG:+:1996987151:-1 HG:+:2721262677:-1 HG:+:2821020908:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:348908964:-1 HG:+:537389211:-1 HG:+:955107589:-1 HG:+:1196825700:-1 HG:+:1663342022:-1 HG:+:1718689720:-1 HG:+:2198332113:-1 HG:+:2536524516:-1 HG:+:2647310009:-1 HG:+:2979091035:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:4896766:-1 HG:+:9683763:-1 HG:+:12656136:-1 HG:+:12723424:-1 HG:+:13142208:-1 HG:+:13365941:-1 HG:+:13425065:-1 HG:+:13645862:-1 HG:+:15495653:-1 HG:+:23534674:-1 HG:+:35424622:-1 HG:+:36663421:-1 HG:+:62167087:-1 HG:+:155391230:-1 HG:+:236555742:-1 HG:+:238564762:-1 HG:+:265126054:-1 HG:+:296570310:-1 HG:+:305131518:-1 HG:+:310452564:-1 HG:+:323734372:-1 HG:+:356624629:-1 HG:+:369420144:-1 HG:+:371303848:-1 HG:+:382106522:-1 HG:+:412045254:-1 HG:+:422045959:-1 HG:+:461038733:-1 HG:+:504258140:-1 HG:+:532055793:-1 HG:+:540325534:-1 HG:+:561301979:-1 HG:+:664914559:-1 HG:+:688603365:-1 HG:+:690109722:-1 HG:+:793221490:-1 HG:+:810519810:-1 HG:+:881021345:-1 HG:+:893257662:-1 HG:+:950481014:-1 HG:+:990149577:-1 HG:+:1001108863:-1 HG:+:1007995598:-1 HG:+:1008889366:-1 HG:+:1035351241:-1 HG:+:1051352569:-1 HG:+:1057675615:-1 HG:+:1092101829:-1 HG:+:1094265928:-1 HG:+:1099657626:-1 HG:+:1099913397:-1 HG:+:1133861748:-1 HG:+:1138840218:-1 HG:+:1167966449:-1 HG:+:1178270097:-1 HG:+:1204366036:-1 HG:+:1213293248:-1 HG:+:1219249064:-1 HG:+:1229157287:-1 HG:+:1239721478:-1 HG:+:1250729512:-1 HG:+:1309242117:-1 HG:+:1344695484:-1 HG:+:1371147253:-1 HG:+:1415260644:-1 HG:+:1441688775:-1 HG:+:1445723515:-1 HG:+:1458174093:-1 HG:+:1470354843:-1 HG:+:1514776189:-1 HG:+:1528320177:-1 HG:+:1531374306:-1 HG:+:1538560972:-1 HG:+:1563989664:-1 HG:+:1572263576:-1 HG:+:1671251285:-1 HG:+:1687564267:-1 HG:+:1693772495:-1 HG:+:1702504512:-1 HG:+:1819635658:-1 HG:+:1863069062:-1 HG:+:1864923540:-1 HG:+:1880008463:-1 HG:+:1892752450:-1 HG:+:1905560978:-1 HG:+:1935920366:-1 HG:+:1936415525:-1 HG:+:1958691597:-1 HG:+:1973663833:-1 HG:+:2049921796:-1 HG:+:2068251634:-1 HG:+:2107232855:-1 HG:+:2120746444:-1 HG:+:2131815991:-1 HG:+:2143813821:-1 HG:+:2254864593:-1 HG:+:2305251365:-1 HG:+:2346422991:-1 HG:+:2348794499:-1 HG:+:2392785263:-1 HG:+:2399915514:-1 HG:+:2411194923:-1 HG:+:2440682180:-1 HG:+:2467142478:-1 HG:+:2477822772:-1 HG:+:2479305608:-1 HG:+:2495266618:-1 HG:+:2518207881:-1 HG:+:2521482192:-1 HG:+:2530642058:-1 HG:+:2541281630:-1 HG:+:2541876355:-1 HG:+:2569573318:-1 HG:+:2591964679:-1 HG:+:2596633279:-1 HG:+:2620789423:-1 HG:+:2649800681:-1 HG:+:2664273305:-1 HG:+:2664757905:-1 HG:+:2666886381:-1 HG:+:2676899044:-1 HG:+:2696081115:-1 HG:+:2700448808:-1 HG:+:2719018542:-1 HG:+:2728820551:-1 HG:+:2741856935:-1 HG:+:2748833227:-1 HG:+:2763401100:-1 HG:+:2816308920:-1 HG:+:2871179922:-1 HG:+:2882462659:-1 HG:+:2890456091:-1 HG:+:2975103550:-1 HG:+:3000279696:-1 HG:+:3011967961:-1 HG:+:3016217507:-1 HG:+:3035149002:-1 HG:+:3035646108:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:87752786:-1 HG:+:179287597:-1 HG:+:315150860:-1 HG:+:425165537:-1 HG:+:622823711:-1 HG:+:653335552:-1 HG:+:829727110:-1 HG:+:1054689626:-1 HG:+:1408864717:-1 HG:+:1631861330:-1 HG:+:2080822393:-1 HG:+:2234882314:-1 HG:+:2235219046:-1 HG:+:2287656247:-1 HG:+:2327749764:-1 HG:+:2634294056:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:34119244:-1 HG:+:51516101:-1 HG:+:171172535:-1 HG:+:230251692:-1 HG:+:424483399:-1 HG:+:427894871:-1 HG:+:712708592:-1 HG:+:808329632:-1 HG:+:1360900933:-1 HG:+:2128278299:-1 HG:+:2583375648:-1 HG:+:2804385678:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:6689820:-1 HG:+:275315817:-1 HG:+:501556665:-1 HG:+:578203200:-1 HG:+:1558386257:-1 HG:+:1659082573:-1 HG:+:2507765763:-1 HG:+:2995680730:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:154624923:-1 HG:+:1301845910:-1 HG:+:1467695519:-1 HG:+:1694885589:-1 HG:+:1883006993:-1 HG:+:2243166647:-1 HG:+:2630305707:-1 HG:+:2775298976:-1 HG:+:2819985490:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:21625381:-1 HG:+:102408726:-1 HG:+:432583864:-1 HG:+:440079186:-1 HG:+:796293240:-1 HG:+:852424246:-1 HG:+:1223183387:-1 HG:+:2604274864:-1 HG:+:2707691626:-1 HG:+:2752781056:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGACGGGGTTTTCACCATGTTTGTCCAGGCTTCGGTCTCGAACGTCCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAGTGCCTGGGAGTACAGGCATGAGTCCACCATGCCTGCCAACTTTCTGTAGCTTCTACATCAGGCACTTACCTACTTTGGCTTCCACCTTTTATGTTATGGAGATGGCTTCTTCCCTTAA HG:+:225312348:-1 HG:+:363456103:-1 HG:+:449938584:-1 HG:+:561316510:-1 HG:+:643317743:-1 HG:+:784574446:-1 HG:+:1147843537:-1 HG:+:1368800597:-1 HG:+:1480044105:-1 HG:+:1581826270:-1 HG:+:1610026320:-1 HG:+:1742144949:-1 HG:+:1779061449:-1 HG:+:1909268215:-1 HG:+:2182769348:-1 HG:+:2224368013:-1 HG:+:2224403135:-1 HG:+:2224451091:-1 HG:+:2268352410:-1 HG:+:2559990512:-1 +TTAAGGGAAGAAGCCATCTCCATAACATAAAAGGTGGAAGCCAAAGTAGGTAAGTGCCTGATGTAGAAGCTACAGAAAGTTGGCAGGCATGGTGGACTCATGCCTGTACTCCCAGGCACTTTGGGAGGCCAAAGCAGGTGGATCACCTGAGGTCAGGGACGTTCGAGACCGAAGCCTGGACAAACATGGTGAAAACCCCGTCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC HG:+:96591034:48 HG:+:288205865:-1 HG:+:303208582:-1 HG:+:424581923:-1 HG:+:508493386:-1 HG:+:612238470:-1 HG:+:1055726754:-1 HG:+:1094645142:-1 HG:+:1118795534:-1 HG:+:1330850948:-1 HG:+:1424049549:-1 HG:+:1710978374:-1 HG:+:1763155766:-1 HG:+:1784998013:-1 HG:+:1863333886:-1 HG:+:1880813182:-1 HG:+:1894617868:-1 HG:+:2130423402:-1 HG:+:2224615986:-1 HG:+:2247728431:-1 HG:+:2302694406:-1 HG:+:2500446764:-1 HG:+:2815266529:-1 +TTAAGGGAAGAAGCCATCTCCATAACATAAAAGGTGGAAGCCAAAGTAGGTAAGTGCCTGATGTAGAAGCTACAGAAAGTTGGCAGGCATGGTGGACTCATGCCTGTACTCCCAGGCACTTTGGGAGGCCAAAGCAGGTGGATCACCTGAGGTCAGGGACGTTCGAGACCGAAGCCTGGACAAACATGGTGAAAACCCCGTCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC HG:+:96591021:48 +TTAAGGGAAGAAGCCATCTCCATAACATAAAAGGTGGAAGCCAAAGTAGGTAAGTGCCTGATGTAGAAGCTACAGAAAGTTGGCAGGCATGGTGGACTCATGCCTGTACTCCCAGGCACTTTGGGAGGCCAAAGCAGGTGGATCACCTGAGGTCAGGGACGTTCGAGACCGAAGCCTGGACAAACATGGTGAAAACCCCGTCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC HG:+:96591025:48 +TTAAGGGAAGAAGCCATCTCCATAACATAAAAGGTGGAAGCCAAAGTAGGTAAGTGCCTGATGTAGAAGCTACAGAAAGTTGGCAGGCATGGTGGACTCATGCCTGTACTCCCAGGCACTTTGGGAGGCCAAAGCAGGTGGATCACCTGAGGTCAGGGACGTTCGAGACCGAAGCCTGGACAAACATGGTGAAAACCCCGTCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC HG:+:96591030:48 HG:+:1359878951:-1 +TTAAGGGAAGAAGCCATCTCCATAACATAAAAGGTGGAAGCCAAAGTAGGTAAGTGCCTGATGTAGAAGCTACAGAAAGTTGGCAGGCATGGTGGACTCATGCCTGTACTCCCAGGCACTTTGGGAGGCCAAAGCAGGTGGATCACCTGAGGTCAGGGACGTTCGAGACCGAAGCCTGGACAAACATGGTGAAAACCCCGTCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC HG:+:96591026:48 +TTAAGGGAAGAAGCCATCTCCATAACATAAAAGGTGGAAGCCAAAGTAGGTAAGTGCCTGATGTAGAAGCTACAGAAAGTTGGCAGGCATGGTGGACTCATGCCTGTACTCCCAGGCACTTTGGGAGGCCAAAGCAGGTGGATCACCTGAGGTCAGGGACGTTCGAGACCGAAGCCTGGACAAACATGGTGAAAACCCCGTCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC HG:+:96591031:48 HG:+:481203953:-1 +TTAAGGGAAGAAGCCATCTCCATAACATAAAAGGTGGAAGCCAAAGTAGGTAAGTGCCTGATGTAGAAGCTACAGAAAGTTGGCAGGCATGGTGGACTCATGCCTGTACTCCCAGGCACTTTGGGAGGCCAAAGCAGGTGGATCACCTGAGGTCAGGGACGTTCGAGACCGAAGCCTGGACAAACATGGTGAAAACCCCGTCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC HG:+:1495610252:-1 +TTAAGGGAAGAAGCCATCTCCATAACATAAAAGGTGGAAGCCAAAGTAGGTAAGTGCCTGATGTAGAAGCTACAGAAAGTTGGCAGGCATGGTGGACTCATGCCTGTACTCCCAGGCACTTTGGGAGGCCAAAGCAGGTGGATCACCTGAGGTCAGGGACGTTCGAGACCGAAGCCTGGACAAACATGGTGAAAACCCCGTCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC HG:+:96591033:48 +TTAAGGGAAGAAGCCATCTCCATAACATAAAAGGTGGAAGCCAAAGTAGGTAAGTGCCTGATGTAGAAGCTACAGAAAGTTGGCAGGCATGGTGGACTCATGCCTGTACTCCCAGGCACTTTGGGAGGCCAAAGCAGGTGGATCACCTGAGGTCAGGGACGTTCGAGACCGAAGCCTGGACAAACATGGTGAAAACCCCGTCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC HG:+:51555369:-1 +TTAAGGGAAGAAGCCATCTCCATAACATAAAAGGTGGAAGCCAAAGTAGGTAAGTGCCTGATGTAGAAGCTACAGAAAGTTGGCAGGCATGGTGGACTCATGCCTGTACTCCCAGGCACTTTGGGAGGCCAAAGCAGGTGGATCACCTGAGGTCAGGGACGTTCGAGACCGAAGCCTGGACAAACATGGTGAAAACCCCGTCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC HG:+:14243442:-1 HG:+:283656356:-1 HG:+:294259403:-1 HG:+:406065827:-1 HG:+:746812414:-1 HG:+:939122290:-1 HG:+:1608411122:-1 HG:+:1609638721:-1 HG:+:1855864656:-1 HG:+:2223167199:-1 HG:+:2365301918:-1 HG:+:2463862860:-1 HG:+:2869911698:-1 HG:+:2911569391:-1 HG:+:2989198232:-1 HG:+:2991355014:-1 HG:+:3098393459:-1 +TTAAGGGAAGAAGCCATCTCCATAACATAAAAGGTGGAAGCCAAAGTAGGTAAGTGCCTGATGTAGAAGCTACAGAAAGTTGGCAGGCATGGTGGACTCATGCCTGTACTCCCAGGCACTTTGGGAGGCCAAAGCAGGTGGATCACCTGAGGTCAGGGACGTTCGAGACCGAAGCCTGGACAAACATGGTGAAAACCCCGTCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC HG:+:114683587:-1 HG:+:157702551:-1 HG:+:408484974:-1 HG:+:496741516:-1 HG:+:926654465:-1 HG:+:998439622:-1 HG:+:1017215957:-1 HG:+:1027479066:-1 HG:+:1079182755:-1 HG:+:1146914786:-1 HG:+:1263954254:-1 HG:+:1417376703:-1 HG:+:1925879600:-1 HG:+:1934063461:-1 HG:+:2141259371:-1 HG:+:2170534817:-1 HG:+:2682440556:-1 HG:+:2903625275:-1 HG:+:3031590643:-1 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600587:54 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600562:54 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:770458788:-1 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600564:54 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600567:54 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600572:54 HG:+:425504282:-1 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600582:54 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600584:54 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600585:54 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600560:54 HG:+:590948394:-1 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600561:54 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600573:54 HG:+:1246408742:-1 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600576:54 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600578:54 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600579:54 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAATGACACTAATGTTAATCTAAATTGAATCTGGGAAATGTGGCAATAAAAGTTAATAATTTACAGTAGAAATTGTTCTTCAGTAAAATTCTAAGTGAATGCCCACTAACTGAATTTCAGGAATTTTGCTCAAAAGGCTTATAGGGTATGTGGCAATCCAATGGCTTACTTTCAAATATGGTTTTTACACTACCAAAACTAATT HG:+:63600575:54 +AATTAGTTTTGGTAGTGTAAAAACCATATTTGAAAGTAAGCCATTGGATTGCCACATACCCTATAAGCCTTTTGAGCAAAATTCCTGAAATTCAGTTAGTGGGCATTCACTTAGAATTTTACTGAAGAACAATTTCTACTGTAAATTATTAACTTTTATTGCCACATTTCCCAGATTCAATTTAGATTAACATTAGTGTCATTTCTCAAACAGAAATAATCATCCTAATTATCTTTGAACGAAGAGCTTGCACTGTTATGTACCTTTCAAGGCTTTTAATTTTATCTTATTTATTTGGCAGGTACTGTGTATGTGGTCGCTGGGGCTGAGAGAAGCTGGAAAGGATGACACTTGATGGGAATTGATAAGTTGAAAATCATTCAATAATTGAGGTTTATGGCATTTGGTTTTCTCTGCCGAGGGGCATACTCAGAGAGCTGATGAAATGTGCGGGGCTAAACGAGGCTGAATCCCTAAATGGCTTCTGAATACAACATTTATTTACTGGCCAGTAAAGTTTAGCAAACCAGTCCAGGTGCTGTTGACAGTAGGCACAAACCGAGTGACAACAGACAAGCTTTGACTGTGTTGGGCTAAGGTAGGCTTTGGGAACCTTACTGCTTACTGCCTCCCCACAGTATGTGGCAAAGTCTAAAGGAGCAGCCAATGGCCACACCAAACCCCCGTTGCTATGGTAGCAGCTACTTCAAACATAGTTTCATTGAATAGGAGCTCATTTGACCCTTGGACCAGAACCAAGGCTCTAAATTGGCAGGACAGAGAATCGGAGTAATTTGTATCATTTCAATTAGTTACTCGCTCGCAATAACAGGGAGGTCATGACTTTCTGCCATGATTACTGCCCTATGGCAACCAAGCTTGAATGTACCATCAGTTTCCAAATACTTTCACTTAATAAATGTAGGTCATAACAAGGCTTCGATTGTTGGGGGGTGCACTAACAAAGGTGAATATCCGACTCTGCAACTGAACGAGCGGA HG:+:1479202102:-1 +AATTAGTTTTGGTAGTGTAAAAACCATATTTGAAAGTAAGCCATTGGATTGCCACATACCCTATAAGCCTTTTGAGCAAAATTCCTGAAATTCAGTTAGTGGGCATTCACTTAGAATTTTACTGAAGAACAATTTCTACTGTAAATTATTAACTTTTATTGCCACATTTCCCAGATTCAATTTAGATTAACATTAGTGTCATTTCTCAAACAGAAATAATCATCCTAATTATCTTTGAACGAAGAGCTTGCACTGTTATGTACCTTTCAAGGCTTTTAATTTTATCTTATTTATTTGGCAGGTACTGTGTATGTGGTCGCTGGGGCTGAGAGAAGCTGGAAAGGATGACACTTGATGGGAATTGATAAGTTGAAAATCATTCAATAATTGAGGTTTATGGCATTTGGTTTTCTCTGCCGAGGGGCATACTCAGAGAGCTGATGAAATGTGCGGGGCTAAACGAGGCTGAATCCCTAAATGGCTTCTGAATACAACATTTATTTACTGGCCAGTAAAGTTTAGCAAACCAGTCCAGGTGCTGTTGACAGTAGGCACAAACCGAGTGACAACAGACAAGCTTTGACTGTGTTGGGCTAAGGTAGGCTTTGGGAACCTTACTGCTTACTGCCTCCCCACAGTATGTGGCAAAGTCTAAAGGAGCAGCCAATGGCCACACCAAACCCCCGTTGCTATGGTAGCAGCTACTTCAAACATAGTTTCATTGAATAGGAGCTCATTTGACCCTTGGACCAGAACCAAGGCTCTAAATTGGCAGGACAGAGAATCGGAGTAATTTGTATCATTTCAATTAGTTACTCGCTCGCAATAACAGGGAGGTCATGACTTTCTGCCATGATTACTGCCCTATGGCAACCAAGCTTGAATGTACCATCAGTTTCCAAATACTTTCACTTAATAAATGTAGGTCATAACAAGGCTTCGATTGTTGGGGGGTGCACTAACAAAGGTGAATATCCGACTCTGCAACTGAACGAGCGGA HG:+:80171730:-1 HG:+:212346033:-1 HG:+:258064628:-1 HG:+:339392533:-1 HG:+:451538505:-1 HG:+:628756693:-1 HG:+:751821701:-1 HG:+:763784814:-1 HG:+:968378745:-1 HG:+:1010187844:-1 HG:+:1109497927:-1 HG:+:1366988518:-1 HG:+:1461587149:-1 HG:+:1573059889:-1 HG:+:1682337421:-1 HG:+:1872390466:-1 HG:+:2163872984:-1 HG:+:2242739812:-1 HG:+:2459329841:-1 HG:+:2913281036:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:30772558:-1 HG:+:43951751:-1 HG:+:108243865:-1 HG:+:239695736:-1 HG:+:440130724:-1 HG:+:457004671:-1 HG:+:485304221:-1 HG:+:485476109:-1 HG:+:546977875:-1 HG:+:793808166:-1 HG:+:898749683:-1 HG:+:1016043189:-1 HG:+:1024550281:-1 HG:+:1028844471:-1 HG:+:1219475215:-1 HG:+:1231563336:-1 HG:+:1422624737:-1 HG:+:1523409908:-1 HG:+:1813323290:-1 HG:+:2172061603:-1 HG:+:2299322932:-1 HG:+:2791106960:-1 HG:+:2799868813:-1 HG:+:2889964830:-1 HG:+:2892252137:-1 HG:+:2932123066:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:1657542829:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:93225470:-1 HG:+:1172779562:-1 HG:+:1616873119:-1 HG:+:2052726320:-1 HG:+:2270365026:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:1300707410:-1 HG:+:1540602668:-1 HG:+:2650996886:-1 HG:+:2818273668:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:1214498646:-1 HG:+:1219753226:-1 HG:+:1635297009:-1 HG:+:1734053726:-1 HG:+:2812142280:-1 HG:+:2938271456:-1 HG:+:2947277777:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:331586517:-1 HG:+:432822919:-1 HG:+:729026497:-1 HG:+:1003561812:-1 HG:+:1143546076:-1 HG:+:1331975237:-1 HG:+:1360510706:-1 HG:+:1385157511:-1 HG:+:2013651045:-1 HG:+:2252666438:-1 HG:+:2801014041:-1 HG:+:2887271668:-1 HG:+:3006761155:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:428369392:-1 HG:+:1315618869:-1 HG:+:1789165081:-1 HG:+:1817835422:-1 HG:+:1817835469:-1 HG:+:1927874194:-1 HG:+:2283700191:-1 HG:+:2371589772:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:981083613:-1 HG:+:2036564516:-1 HG:+:2159775732:-1 HG:+:2188570297:-1 HG:+:2648177071:-1 HG:+:2896448402:-1 HG:+:2905426081:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:29750786:-1 HG:+:1361391485:-1 HG:+:2536764041:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:705334475:-1 HG:+:1759562980:-1 HG:+:1865164766:-1 HG:+:2231267498:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:3028516723:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:4928150:-1 HG:+:116058350:-1 HG:+:302380230:-1 HG:+:427664610:-1 HG:+:444882636:-1 HG:+:539767684:-1 HG:+:633671017:-1 HG:+:809690132:-1 HG:+:875033582:-1 HG:+:1112790955:-1 HG:+:1170464164:-1 HG:+:1186983467:-1 HG:+:1273549689:-1 HG:+:1470192057:-1 HG:+:1565199236:-1 HG:+:1571705492:-1 HG:+:1736285612:-1 HG:+:1780478615:-1 HG:+:1831460756:-1 HG:+:2149526041:-1 HG:+:2291318413:-1 HG:+:2395546339:-1 HG:+:2590783465:-1 HG:+:2610303637:-1 HG:+:2874953581:-1 HG:+:2900952041:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:494102182:-1 HG:+:645101967:-1 HG:+:753138683:-1 HG:+:806881559:-1 HG:+:1020004897:-1 HG:+:1151983777:-1 HG:+:1628515201:-1 HG:+:1746189412:-1 HG:+:1877483301:-1 HG:+:2045254142:-1 HG:+:2281989400:-1 HG:+:2901542174:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:165981459:-1 HG:+:603568454:-1 HG:+:896314884:-1 HG:+:965268586:-1 HG:+:1036090655:-1 HG:+:1499446885:-1 HG:+:1910715924:-1 HG:+:1949999645:-1 HG:+:2268447117:-1 HG:+:2801463094:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:73920675:-1 HG:+:444035835:-1 HG:+:486560594:-1 HG:+:728766623:-1 HG:+:793915992:-1 HG:+:794589465:-1 HG:+:1189520292:-1 HG:+:1502573642:-1 HG:+:2077285535:-1 HG:+:2147988455:-1 HG:+:2462865369:-1 HG:+:2583167577:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:241632532:-1 HG:+:315523312:-1 HG:+:646423848:-1 HG:+:653328415:-1 HG:+:2225517794:-1 HG:+:2381870972:-1 HG:+:2468622699:-1 HG:+:2550571997:-1 HG:+:2730858874:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:466678828:-1 HG:+:650653680:-1 HG:+:834067108:-1 HG:+:1642027376:-1 HG:+:1773807963:-1 HG:+:2283958427:-1 HG:+:2297637215:-1 HG:+:2418288168:-1 HG:+:2489378979:-1 HG:+:2632679432:-1 HG:+:2734195359:-1 HG:+:2863404462:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:116741761:-1 HG:+:120779546:-1 HG:+:154165995:-1 HG:+:170792567:-1 HG:+:206079052:-1 HG:+:213562812:-1 HG:+:680841722:-1 HG:+:703742096:-1 HG:+:1014259552:-1 HG:+:1146430324:-1 HG:+:1420940132:-1 HG:+:1710581229:-1 HG:+:2250491999:-1 HG:+:2473937373:-1 HG:+:2821183256:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:7341434:-1 HG:+:29582258:-1 HG:+:82310839:-1 HG:+:107134312:-1 HG:+:222088113:-1 HG:+:287422924:-1 HG:+:678385194:-1 HG:+:796668809:-1 HG:+:1262874050:-1 HG:+:1897280862:-1 HG:+:2256326307:-1 HG:+:2502140594:-1 HG:+:2734465996:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:823053133:-1 HG:+:845610016:-1 HG:+:1006189183:-1 HG:+:1285535953:-1 HG:+:1340959983:-1 HG:+:1441936447:-1 HG:+:2275994862:-1 HG:+:2437765761:-1 HG:+:2903465059:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:337524961:-1 HG:+:2628963955:-1 HG:+:2734722970:-1 HG:+:3028494175:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:245611731:-1 HG:+:468583836:-1 HG:+:576170974:-1 HG:+:1150889584:-1 HG:+:1168151160:-1 HG:+:1241757808:-1 HG:+:1473655925:-1 HG:+:1927439398:-1 HG:+:2024959817:-1 HG:+:2027264723:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:48816849:-1 HG:+:49732509:-1 HG:+:79111291:-1 HG:+:164518602:-1 HG:+:204613926:-1 HG:+:260954672:-1 HG:+:455470211:-1 HG:+:528600407:-1 HG:+:538750551:-1 HG:+:570480000:-1 HG:+:576668729:-1 HG:+:646455117:-1 HG:+:672401694:-1 HG:+:750164788:-1 HG:+:759044046:-1 HG:+:760092596:-1 HG:+:787344214:-1 HG:+:790921306:-1 HG:+:791642888:-1 HG:+:823549567:-1 HG:+:831076463:-1 HG:+:834898718:-1 HG:+:865253633:-1 HG:+:869435694:-1 HG:+:872929978:-1 HG:+:915977515:-1 HG:+:953667330:-1 HG:+:955151513:-1 HG:+:962863832:-1 HG:+:986262341:-1 HG:+:1015244869:-1 HG:+:1015248102:-1 HG:+:1025659118:-1 HG:+:1081897267:-1 HG:+:1098823266:-1 HG:+:1116592408:-1 HG:+:1129458804:-1 HG:+:1180007012:-1 HG:+:1236897379:-1 HG:+:1267978853:-1 HG:+:1329529783:-1 HG:+:1377779799:-1 HG:+:1397808210:-1 HG:+:1427677763:-1 HG:+:1444995691:-1 HG:+:1463582289:-1 HG:+:1514543060:-1 HG:+:1518088292:-1 HG:+:1529699268:-1 HG:+:1677106094:-1 HG:+:1683125489:-1 HG:+:1693114508:-1 HG:+:1765873976:-1 HG:+:1888673041:-1 HG:+:1923249103:-1 HG:+:1990119684:-1 HG:+:2038306962:-1 HG:+:2038629202:-1 HG:+:2071257943:-1 HG:+:2075331754:-1 HG:+:2079792100:-1 HG:+:2136261372:-1 HG:+:2173289381:-1 HG:+:2182288395:-1 HG:+:2192017224:-1 HG:+:2196160460:-1 HG:+:2199238519:-1 HG:+:2240810672:-1 HG:+:2342017012:-1 HG:+:2545472545:-1 HG:+:2720344836:-1 HG:+:2829645131:-1 HG:+:2916520489:-1 HG:+:2931969920:-1 HG:+:2959401457:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:80978053:-1 HG:+:115058610:-1 HG:+:155842746:-1 HG:+:298479339:-1 HG:+:315574190:-1 HG:+:354441702:-1 HG:+:631695270:-1 HG:+:703994959:-1 HG:+:734017276:-1 HG:+:810908929:-1 HG:+:829076823:-1 HG:+:917223319:-1 HG:+:1004741929:-1 HG:+:1044577914:-1 HG:+:1219793588:-1 HG:+:1240330897:-1 HG:+:1274523402:-1 HG:+:1329612276:-1 HG:+:1564299980:-1 HG:+:1794524059:-1 HG:+:1996377695:-1 HG:+:2156464325:-1 HG:+:2227661305:-1 HG:+:2237430328:-1 HG:+:2238000253:-1 HG:+:2367940587:-1 HG:+:2475144587:-1 HG:+:2603024582:-1 HG:+:2627241433:-1 HG:+:2633952696:-1 HG:+:2857650568:-1 HG:+:2957092788:-1 HG:+:3006796602:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:41297928:-1 HG:+:167638722:-1 HG:+:568410213:-1 HG:+:634986906:-1 HG:+:664199513:-1 HG:+:962762314:-1 HG:+:1303747393:-1 HG:+:1448034798:-1 HG:+:1858388386:-1 HG:+:1942715473:-1 HG:+:2232816867:-1 HG:+:2811611200:-1 HG:+:2874845638:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:374710138:-1 HG:+:538424815:-1 HG:+:939326829:-1 HG:+:1110244994:-1 HG:+:1550248684:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAGGGAAAAAGCCCCTTGTAAAAACCATCAGATTCTCGTGGAAACCACTATCACAGAACAGTATGGGGGTAAACCAACCCATGATTCAGTGTACCTCCACGGGTCACTCCCAGGACAAGATGAGATTTGGGTGGGGACACAGCCAAACCATATCAGGCAGTGACTGAAGCAGGCACTGGATAGGATTTTGTAGAATTTACCTG HG:+:33704236:-1 HG:+:58604155:-1 HG:+:237252377:-1 HG:+:292923929:-1 HG:+:352782357:-1 HG:+:580828327:-1 HG:+:655831648:-1 HG:+:845556353:-1 HG:+:1100845232:-1 HG:+:1210478914:-1 HG:+:1746516269:-1 HG:+:2049191771:-1 HG:+:2225938482:-1 HG:+:2464327069:-1 HG:+:2765244720:-1 HG:+:2911584082:-1 HG:+:2961999513:-1 +CAGGTAAATTCTACAAAATCCTATCCAGTGCCTGCTTCAGTCACTGCCTGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGTCCTGGGAGTGACCCGTGGAGGTACACTGAATCATGGGTTGGTTTACCCCCATACTGTTCTGTGATAGTGGTTTCCACGAGAATCTGATGGTTTTTACAAGGGGCTTTTTCCCTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA HG:+:697119847:55 +CAGGTAAATTCTACAAAATCCTATCCAGTGCCTGCTTCAGTCACTGCCTGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGTCCTGGGAGTGACCCGTGGAGGTACACTGAATCATGGGTTGGTTTACCCCCATACTGTTCTGTGATAGTGGTTTCCACGAGAATCTGATGGTTTTTACAAGGGGCTTTTTCCCTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA HG:+:2436361738:-1 +CAGGTAAATTCTACAAAATCCTATCCAGTGCCTGCTTCAGTCACTGCCTGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGTCCTGGGAGTGACCCGTGGAGGTACACTGAATCATGGGTTGGTTTACCCCCATACTGTTCTGTGATAGTGGTTTCCACGAGAATCTGATGGTTTTTACAAGGGGCTTTTTCCCTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA HG:+:697119820:55 +CAGGTAAATTCTACAAAATCCTATCCAGTGCCTGCTTCAGTCACTGCCTGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGTCCTGGGAGTGACCCGTGGAGGTACACTGAATCATGGGTTGGTTTACCCCCATACTGTTCTGTGATAGTGGTTTCCACGAGAATCTGATGGTTTTTACAAGGGGCTTTTTCCCTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA HG:+:697119824:55 +CAGGTAAATTCTACAAAATCCTATCCAGTGCCTGCTTCAGTCACTGCCTGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGTCCTGGGAGTGACCCGTGGAGGTACACTGAATCATGGGTTGGTTTACCCCCATACTGTTCTGTGATAGTGGTTTCCACGAGAATCTGATGGTTTTTACAAGGGGCTTTTTCCCTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA HG:+:697119832:55 +CAGGTAAATTCTACAAAATCCTATCCAGTGCCTGCTTCAGTCACTGCCTGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGTCCTGGGAGTGACCCGTGGAGGTACACTGAATCATGGGTTGGTTTACCCCCATACTGTTCTGTGATAGTGGTTTCCACGAGAATCTGATGGTTTTTACAAGGGGCTTTTTCCCTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA HG:+:697119834:55 +CAGGTAAATTCTACAAAATCCTATCCAGTGCCTGCTTCAGTCACTGCCTGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGTCCTGGGAGTGACCCGTGGAGGTACACTGAATCATGGGTTGGTTTACCCCCATACTGTTCTGTGATAGTGGTTTCCACGAGAATCTGATGGTTTTTACAAGGGGCTTTTTCCCTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA HG:+:1471676700:-1 +CAGGTAAATTCTACAAAATCCTATCCAGTGCCTGCTTCAGTCACTGCCTGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGTCCTGGGAGTGACCCGTGGAGGTACACTGAATCATGGGTTGGTTTACCCCCATACTGTTCTGTGATAGTGGTTTCCACGAGAATCTGATGGTTTTTACAAGGGGCTTTTTCCCTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA HG:+:697119838:55 +CAGGTAAATTCTACAAAATCCTATCCAGTGCCTGCTTCAGTCACTGCCTGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGTCCTGGGAGTGACCCGTGGAGGTACACTGAATCATGGGTTGGTTTACCCCCATACTGTTCTGTGATAGTGGTTTCCACGAGAATCTGATGGTTTTTACAAGGGGCTTTTTCCCTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA HG:+:697119839:55 +CAGGTAAATTCTACAAAATCCTATCCAGTGCCTGCTTCAGTCACTGCCTGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGTCCTGGGAGTGACCCGTGGAGGTACACTGAATCATGGGTTGGTTTACCCCCATACTGTTCTGTGATAGTGGTTTCCACGAGAATCTGATGGTTTTTACAAGGGGCTTTTTCCCTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA HG:+:697119823:55 +CAGGTAAATTCTACAAAATCCTATCCAGTGCCTGCTTCAGTCACTGCCTGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGTCCTGGGAGTGACCCGTGGAGGTACACTGAATCATGGGTTGGTTTACCCCCATACTGTTCTGTGATAGTGGTTTCCACGAGAATCTGATGGTTTTTACAAGGGGCTTTTTCCCTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA HG:+:697119841:55 +CAGGTAAATTCTACAAAATCCTATCCAGTGCCTGCTTCAGTCACTGCCTGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGTCCTGGGAGTGACCCGTGGAGGTACACTGAATCATGGGTTGGTTTACCCCCATACTGTTCTGTGATAGTGGTTTCCACGAGAATCTGATGGTTTTTACAAGGGGCTTTTTCCCTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA HG:+:1695576672:-1 +CAGGTAAATTCTACAAAATCCTATCCAGTGCCTGCTTCAGTCACTGCCTGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGTCCTGGGAGTGACCCGTGGAGGTACACTGAATCATGGGTTGGTTTACCCCCATACTGTTCTGTGATAGTGGTTTCCACGAGAATCTGATGGTTTTTACAAGGGGCTTTTTCCCTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA HG:+:415137391:-1 HG:+:571834251:-1 HG:+:697119845:55 HG:+:1764393768:-1 HG:+:1889782118:-1 HG:+:1901139841:-1 HG:+:2176843672:-1 HG:+:2242496761:-1 HG:+:3006519242:-1 +CAGGTAAATTCTACAAAATCCTATCCAGTGCCTGCTTCAGTCACTGCCTGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGTCCTGGGAGTGACCCGTGGAGGTACACTGAATCATGGGTTGGTTTACCCCCATACTGTTCTGTGATAGTGGTTTCCACGAGAATCTGATGGTTTTTACAAGGGGCTTTTTCCCTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA HG:+:263228203:-1 HG:+:423501909:-1 HG:+:835039751:-1 HG:+:878678827:-1 HG:+:2083216421:-1 HG:+:2427595402:-1 HG:+:2607865773:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:1519576:-1 HG:+:23078924:-1 HG:+:28777565:-1 HG:+:33698652:-1 HG:+:34615330:-1 HG:+:92482560:-1 HG:+:93444439:-1 HG:+:98913732:-1 HG:+:110540747:-1 HG:+:149807782:-1 HG:+:174855591:-1 HG:+:181179531:-1 HG:+:249190291:-1 HG:+:276811938:-1 HG:+:288815307:-1 HG:+:292089210:-1 HG:+:294506237:-1 HG:+:308422407:-1 HG:+:324059325:-1 HG:+:377337201:-1 HG:+:406718772:-1 HG:+:450410360:-1 HG:+:464270465:-1 HG:+:510675101:-1 HG:+:569105846:-1 HG:+:569105901:-1 HG:+:569105956:-1 HG:+:577703809:-1 HG:+:601396831:-1 HG:+:613937228:-1 HG:+:618058579:-1 HG:+:672176982:-1 HG:+:676240308:-1 HG:+:676507756:-1 HG:+:704047507:-1 HG:+:793253659:-1 HG:+:866919915:-1 HG:+:919346292:-1 HG:+:952541708:-1 HG:+:993332069:-1 HG:+:1019669784:-1 HG:+:1037413605:-1 HG:+:1045850231:-1 HG:+:1050808289:-1 HG:+:1054052674:-1 HG:+:1058643396:-1 HG:+:1105971002:-1 HG:+:1199835556:-1 HG:+:1217868081:-1 HG:+:1277700636:-1 HG:+:1300461092:-1 HG:+:1308784450:-1 HG:+:1323954697:-1 HG:+:1334362129:-1 HG:+:1335854811:-1 HG:+:1335953895:-1 HG:+:1336815454:-1 HG:+:1339536944:-1 HG:+:1383436709:-1 HG:+:1416051510:-1 HG:+:1435526057:-1 HG:+:1460125042:-1 HG:+:1470887787:-1 HG:+:1526641916:-1 HG:+:1543962180:-1 HG:+:1637564497:-1 HG:+:1668037530:-1 HG:+:1691236394:-1 HG:+:1695609221:-1 HG:+:1702488010:-1 HG:+:1767740365:-1 HG:+:1862686975:-1 HG:+:1888352703:-1 HG:+:1893500495:-1 HG:+:1958958318:-1 HG:+:1978577119:-1 HG:+:1990286249:-1 HG:+:2021742527:-1 HG:+:2034475348:-1 HG:+:2060059392:-1 HG:+:2072291931:-1 HG:+:2105157034:-1 HG:+:2134024003:-1 HG:+:2193990216:-1 HG:+:2245348744:-1 HG:+:2263780411:-1 HG:+:2268378660:-1 HG:+:2277093524:-1 HG:+:2298493520:-1 HG:+:2392746006:-1 HG:+:2406368775:-1 HG:+:2424902134:-1 HG:+:2432688952:-1 HG:+:2433604052:-1 HG:+:2459873796:-1 HG:+:2502677955:-1 HG:+:2504530758:-1 HG:+:2517337087:-1 HG:+:2520080845:-1 HG:+:2530750053:-1 HG:+:2556728175:-1 HG:+:2562025778:-1 HG:+:2564716437:-1 HG:+:2594653092:-1 HG:+:2602806944:-1 HG:+:2641070194:-1 HG:+:2649573414:-1 HG:+:2661998311:-1 HG:+:2670890954:-1 HG:+:2674771778:-1 HG:+:2681266536:-1 HG:+:2699144597:-1 HG:+:2709186898:-1 HG:+:2748829622:-1 HG:+:2764780802:-1 HG:+:2797514844:-1 HG:+:2847691589:-1 HG:+:2890484978:-1 HG:+:2891037854:-1 HG:+:2904457742:-1 HG:+:2921380718:-1 HG:+:2928639428:-1 HG:+:2949364600:-1 HG:+:2951677408:-1 HG:+:3000665900:-1 HG:+:3016704118:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:773798406:-1 HG:+:1299496535:-1 HG:+:2074099295:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:13402265:-1 HG:+:13623062:-1 HG:+:300295688:-1 HG:+:315988466:-1 HG:+:402792854:-1 HG:+:600876633:-1 HG:+:606472248:-1 HG:+:727207190:-1 HG:+:842438278:-1 HG:+:916342695:-1 HG:+:1270404071:-1 HG:+:1334610776:-1 HG:+:1653821591:-1 HG:+:1664928559:-1 HG:+:1702888975:-1 HG:+:1754184585:-1 HG:+:1894078686:-1 HG:+:2005164674:-1 HG:+:2068701579:-1 HG:+:2148599966:-1 HG:+:2220825075:-1 HG:+:2275702558:-1 HG:+:2527918573:-1 HG:+:2575006697:-1 HG:+:2869412225:-1 HG:+:2876985219:-1 HG:+:2902720045:-1 HG:+:2928631888:-1 HG:+:2952223564:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:89503271:-1 HG:+:325684374:-1 HG:+:366456852:-1 HG:+:755831231:-1 HG:+:814682350:-1 HG:+:856410059:-1 HG:+:960194875:-1 HG:+:1153670379:-1 HG:+:1200980742:-1 HG:+:1343630204:-1 HG:+:1483493445:-1 HG:+:1796380819:-1 HG:+:1878414231:-1 HG:+:1928830214:-1 HG:+:1960866752:-1 HG:+:2140657497:-1 HG:+:2260641945:-1 HG:+:2266161412:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:2198080824:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:634362225:-1 HG:+:634548978:-1 HG:+:1012116561:-1 HG:+:2479971618:-1 HG:+:2819826354:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:2022577579:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:6973810:-1 HG:+:11720354:-1 HG:+:150143090:-1 HG:+:224547283:-1 HG:+:335457258:-1 HG:+:367070534:-1 HG:+:385743661:-1 HG:+:403293348:-1 HG:+:715644302:-1 HG:+:937957421:-1 HG:+:953510859:-1 HG:+:1382436663:-1 HG:+:1415495813:-1 HG:+:1494855413:-1 HG:+:1775877306:-1 HG:+:1787354606:-1 HG:+:1899791122:-1 HG:+:2220913033:-1 HG:+:2756144619:-1 HG:+:2767748521:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:4290611:-1 HG:+:9547337:-1 HG:+:19627830:-1 HG:+:22765007:-1 HG:+:24492683:-1 HG:+:30587689:-1 HG:+:38485420:-1 HG:+:85305252:-1 HG:+:155992784:-1 HG:+:167924646:-1 HG:+:179225028:-1 HG:+:226695702:-1 HG:+:228039090:-1 HG:+:281268162:-1 HG:+:295222015:-1 HG:+:305147589:-1 HG:+:314219217:-1 HG:+:315244020:-1 HG:+:334603722:-1 HG:+:356008181:-1 HG:+:383991190:-1 HG:+:388634378:-1 HG:+:405134569:-1 HG:+:415706067:-1 HG:+:466770037:-1 HG:+:482242928:-1 HG:+:483553156:-1 HG:+:491592350:-1 HG:+:501917560:-1 HG:+:531651362:-1 HG:+:545786620:-1 HG:+:555181652:-1 HG:+:565587704:-1 HG:+:590885122:-1 HG:+:623392712:-1 HG:+:671839861:-1 HG:+:675315145:-1 HG:+:682039151:-1 HG:+:717226486:-1 HG:+:751732128:-1 HG:+:754701652:-1 HG:+:786141844:-1 HG:+:786471979:-1 HG:+:800699598:-1 HG:+:822174457:-1 HG:+:839755060:-1 HG:+:861501981:-1 HG:+:877073368:-1 HG:+:914570951:-1 HG:+:918851550:-1 HG:+:933094697:-1 HG:+:943490139:-1 HG:+:976264643:-1 HG:+:1015784612:-1 HG:+:1016495050:-1 HG:+:1019030388:-1 HG:+:1019697222:-1 HG:+:1027221966:-1 HG:+:1031021194:-1 HG:+:1053900864:-1 HG:+:1056128498:-1 HG:+:1070029628:-1 HG:+:1079871782:-1 HG:+:1143643316:-1 HG:+:1180449251:-1 HG:+:1181228333:-1 HG:+:1220809741:-1 HG:+:1240740746:-1 HG:+:1266100639:-1 HG:+:1301881766:-1 HG:+:1302883966:-1 HG:+:1306531488:-1 HG:+:1338453621:-1 HG:+:1341490140:-1 HG:+:1349585180:-1 HG:+:1362532537:-1 HG:+:1364186467:-1 HG:+:1383799505:-1 HG:+:1391418475:-1 HG:+:1392088473:-1 HG:+:1394770791:-1 HG:+:1401635973:-1 HG:+:1426509482:-1 HG:+:1459591772:-1 HG:+:1460524924:-1 HG:+:1491441443:-1 HG:+:1499266611:-1 HG:+:1542769987:-1 HG:+:1616848661:-1 HG:+:1619334563:-1 HG:+:1638152868:-1 HG:+:1638937930:-1 HG:+:1647235399:-1 HG:+:1670544694:-1 HG:+:1673785597:-1 HG:+:1680876285:-1 HG:+:1692137604:-1 HG:+:1712029874:-1 HG:+:1725740302:-1 HG:+:1756028693:-1 HG:+:1848013073:-1 HG:+:1862697668:-1 HG:+:1863279212:-1 HG:+:1863573388:-1 HG:+:1873432495:-1 HG:+:1878421547:-1 HG:+:1880632950:-1 HG:+:1881149322:-1 HG:+:1881610996:-1 HG:+:1884934828:-1 HG:+:1894327549:-1 HG:+:1923742559:-1 HG:+:1934592514:-1 HG:+:1982458647:-1 HG:+:2017671073:-1 HG:+:2020140345:-1 HG:+:2021759651:-1 HG:+:2025162297:-1 HG:+:2051997378:-1 HG:+:2061247067:-1 HG:+:2065997843:-1 HG:+:2066069170:-1 HG:+:2066154109:-1 HG:+:2075951287:-1 HG:+:2076291173:-1 HG:+:2115270491:-1 HG:+:2117986089:-1 HG:+:2130436190:-1 HG:+:2145828655:-1 HG:+:2192579173:-1 HG:+:2195334888:-1 HG:+:2235410429:-1 HG:+:2278419486:-1 HG:+:2328409603:-1 HG:+:2329420764:-1 HG:+:2330914159:-1 HG:+:2340466421:-1 HG:+:2352162193:-1 HG:+:2364945647:-1 HG:+:2406351542:-1 HG:+:2438043427:-1 HG:+:2476973772:-1 HG:+:2479994552:-1 HG:+:2485062447:-1 HG:+:2488576880:-1 HG:+:2502171959:-1 HG:+:2511191397:-1 HG:+:2525971440:-1 HG:+:2549511423:-1 HG:+:2558674053:-1 HG:+:2565991754:-1 HG:+:2566371815:-1 HG:+:2585098128:-1 HG:+:2587784633:-1 HG:+:2591595655:-1 HG:+:2592442509:-1 HG:+:2646938338:-1 HG:+:2652134439:-1 HG:+:2663990940:-1 HG:+:2665215228:-1 HG:+:2670282010:-1 HG:+:2671032472:-1 HG:+:2671255258:-1 HG:+:2675729366:-1 HG:+:2676549296:-1 HG:+:2693263709:-1 HG:+:2696148079:-1 HG:+:2697946694:-1 HG:+:2700646985:-1 HG:+:2702247546:-1 HG:+:2703779748:-1 HG:+:2730890885:-1 HG:+:2738373130:-1 HG:+:2767966321:-1 HG:+:2804019143:-1 HG:+:2816972980:-1 HG:+:2851005932:-1 HG:+:2872848926:-1 HG:+:2884674564:-1 HG:+:2897033941:-1 HG:+:2994860631:-1 HG:+:3000142780:-1 HG:+:3004414257:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:55557780:-1 HG:+:335032922:-1 HG:+:631193622:-1 HG:+:830590710:-1 HG:+:1345465080:-1 HG:+:1489557310:-1 HG:+:1489837643:-1 HG:+:1770726143:-1 HG:+:1911407688:-1 HG:+:1945203380:-1 HG:+:2235774843:-1 HG:+:2759596993:-1 HG:+:2965516165:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:520756465:-1 HG:+:663144661:-1 HG:+:667840980:-1 HG:+:688931127:-1 HG:+:836883801:-1 HG:+:1904821835:-1 HG:+:1910975281:-1 HG:+:1970537904:-1 HG:+:2552284411:-1 HG:+:2644457915:-1 HG:+:2725060570:-1 HG:+:3030820383:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:143908052:-1 HG:+:305685085:-1 HG:+:305685230:-1 HG:+:330472296:-1 HG:+:848987393:-1 HG:+:940478918:-1 HG:+:1132440397:-1 HG:+:1309642179:-1 HG:+:1767886120:-1 HG:+:1809848165:-1 HG:+:1828866483:-1 HG:+:2046531188:-1 HG:+:2155464895:-1 HG:+:2241347763:-1 HG:+:2301998937:-1 HG:+:2354315045:-1 HG:+:2360773096:-1 HG:+:2401425143:-1 HG:+:2401426594:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:283006870:-1 HG:+:569467960:-1 HG:+:595425968:-1 HG:+:646878157:-1 HG:+:657670409:-1 HG:+:784620898:-1 HG:+:807919255:-1 HG:+:857058668:-1 HG:+:894222091:-1 HG:+:1087595660:-1 HG:+:1171318025:-1 HG:+:1252298262:-1 HG:+:1323668470:-1 HG:+:1345736664:-1 HG:+:1492774162:-1 HG:+:1664869755:-1 HG:+:1886120098:-1 HG:+:2116801590:-1 HG:+:2225357340:-1 HG:+:2254403231:-1 HG:+:2527873260:-1 HG:+:2722088373:-1 HG:+:2955979788:-1 HG:+:3007013303:-1 HG:+:3022982591:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:76559866:-1 HG:+:154494935:-1 HG:+:165309784:-1 HG:+:212091212:-1 HG:+:351811163:-1 HG:+:486577725:-1 HG:+:540486376:-1 HG:+:719463564:-1 HG:+:733783596:-1 HG:+:752875002:-1 HG:+:863276320:-1 HG:+:919916683:-1 HG:+:1396783769:-1 HG:+:1784628582:-1 HG:+:1844390130:-1 HG:+:1968560349:-1 HG:+:2040015975:-1 HG:+:2055550062:-1 HG:+:2070574130:-1 HG:+:2280349699:-1 HG:+:2532971059:-1 HG:+:2577806857:-1 HG:+:2810285261:-1 HG:+:2874334915:-1 HG:+:2967567326:-1 HG:+:2969076160:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:1015152993:-1 HG:+:1027799606:-1 HG:+:1564613587:-1 HG:+:1853476857:-1 HG:+:1879266241:-1 HG:+:2634535878:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:215418689:-1 HG:+:532115677:-1 HG:+:924637220:-1 HG:+:960992919:-1 HG:+:1421669278:-1 HG:+:2641993486:-1 HG:+:2764744520:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:288107626:-1 HG:+:370320131:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:651824210:-1 HG:+:654730065:-1 HG:+:674818720:-1 HG:+:720514798:-1 HG:+:972001173:-1 HG:+:977054474:-1 HG:+:1176603375:-1 HG:+:1407969268:-1 HG:+:1904212052:-1 HG:+:2052048662:-1 HG:+:2183694536:-1 HG:+:2504394893:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:389582541:-1 HG:+:427920173:-1 HG:+:428765684:-1 HG:+:457671001:-1 HG:+:619078263:-1 HG:+:764523950:-1 HG:+:1088537369:-1 HG:+:1095471220:-1 HG:+:1265580328:-1 HG:+:1342280464:-1 HG:+:1374409960:-1 HG:+:1398782289:-1 HG:+:1433212788:-1 HG:+:1673972441:-1 HG:+:2993721480:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:269354710:-1 HG:+:526486177:-1 HG:+:567590243:-1 HG:+:624561408:-1 HG:+:707236307:-1 HG:+:709203846:-1 HG:+:992122204:-1 HG:+:1163085223:-1 HG:+:1216417276:-1 HG:+:1326923469:-1 HG:+:1331087238:-1 HG:+:1571335740:-1 HG:+:1623731067:-1 HG:+:1806396158:-1 HG:+:1809730933:-1 HG:+:1847897445:-1 HG:+:1919501995:-1 HG:+:2298855315:-1 HG:+:2353450433:-1 HG:+:2473308139:-1 HG:+:2667676408:-1 HG:+:2978315042:-1 HG:+:2997103755:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:225898106:-1 HG:+:514950033:-1 HG:+:544378571:-1 HG:+:579526054:-1 HG:+:1096925638:-1 HG:+:1557908249:-1 HG:+:1943255778:-1 HG:+:2011358779:-1 HG:+:2133782913:-1 HG:+:2879458657:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:9392875:-1 HG:+:17559617:-1 HG:+:59181419:-1 HG:+:166222497:-1 HG:+:341167299:-1 HG:+:485560505:-1 HG:+:570870756:-1 HG:+:757321196:-1 HG:+:955150614:-1 HG:+:999268708:-1 HG:+:1272491947:-1 HG:+:1497708086:-1 HG:+:1635043406:-1 HG:+:1640547378:-1 HG:+:1693236077:-1 HG:+:1811725155:-1 HG:+:1818808997:-1 HG:+:1826640991:-1 HG:+:1839927744:-1 HG:+:2141954352:-1 HG:+:2466938751:-1 HG:+:2499909503:-1 HG:+:2515591473:-1 HG:+:2680953892:-1 HG:+:2681839510:-1 HG:+:2681839551:-1 HG:+:2682627386:-1 HG:+:2683311285:-1 HG:+:2821607769:-1 HG:+:2896506032:-1 HG:+:3032909120:-1 HG:+:3032928347:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:69356949:-1 HG:+:461940085:-1 HG:+:917032290:-1 HG:+:1050606887:-1 HG:+:1428154940:-1 HG:+:1693177295:-1 HG:+:2069754957:-1 HG:+:2153177854:-1 HG:+:2182214495:-1 HG:+:2625238875:-1 HG:+:2825475777:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:90606653:-1 HG:+:104590414:-1 HG:+:493332620:-1 HG:+:719485802:-1 HG:+:762575264:-1 HG:+:805074543:-1 HG:+:974502214:-1 HG:+:977239970:-1 HG:+:991195465:-1 HG:+:1007222960:-1 HG:+:1038234588:-1 HG:+:1104514922:-1 HG:+:1170105266:-1 HG:+:1183005224:-1 HG:+:1211123878:-1 HG:+:1212633395:-1 HG:+:1250612347:-1 HG:+:1283398673:-1 HG:+:1407723004:-1 HG:+:1473043729:-1 HG:+:1531749752:-1 HG:+:1565509896:-1 HG:+:1623329276:-1 HG:+:1659505112:-1 HG:+:1689666822:-1 HG:+:1918631125:-1 HG:+:1978455440:-1 HG:+:2030250839:-1 HG:+:2350747755:-1 HG:+:2609972280:-1 HG:+:2622195521:-1 HG:+:2883076197:-1 HG:+:2908681541:-1 HG:+:2929239031:-1 HG:+:2933759128:-1 HG:+:2933842230:-1 HG:+:2979619132:-1 HG:+:3053496909:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:23492631:-1 HG:+:221344363:-1 HG:+:234372392:-1 HG:+:261228229:-1 HG:+:501068733:-1 HG:+:696848035:-1 HG:+:697962746:-1 HG:+:924275654:-1 HG:+:1298682765:-1 HG:+:1378937781:-1 HG:+:1399472665:-1 HG:+:1422285904:-1 HG:+:1509934512:-1 HG:+:1814480766:-1 HG:+:2029919562:-1 HG:+:2370628078:-1 HG:+:2485765101:-1 HG:+:2508631500:-1 HG:+:2561649933:-1 HG:+:3046177094:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:506081148:-1 HG:+:1523414656:-1 HG:+:1751506135:-1 HG:+:1825960824:-1 HG:+:2360390042:-1 HG:+:2848697364:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:300060446:-1 HG:+:738505151:-1 HG:+:1176733961:-1 HG:+:1362004753:-1 HG:+:1432701094:-1 HG:+:1671371702:-1 HG:+:1684269464:-1 HG:+:1881603394:-1 HG:+:2421769798:-1 HG:+:2546328366:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:450484150:-1 HG:+:814804099:-1 HG:+:1308653616:-1 HG:+:2484197006:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGAGAAAATGTTTTCTCTCTTGATTTAAAATTTCTACTTTTATCCATCTTGTAAAAACCAATTTTGTCTCAGCAGTTAAATTTGATAGCATTAATTATGGATGGTCTAGACGTTGAGATTTGTCTTGAATATCAAACTGCTTCATTTCTAGAACTTCTGATAAACATACAGATGATAGCTTTCACAGTACTGGCCTAGGAAACTGCAGACCTCGGCAAACAAGGTGACAGGGTAGAAAAAGCATGGGAACAGGTGTGTGAGAGCTGTGCTAAGGATTAACTTCACTGGTCATGTGTCTTTTATTTTTAAGTTCCAGCAATCCAATTAGATACAAACAACTCCATCCTTCCTTTAGTTACTTGGAACCTGGGATGATCCTGTTAATTACTCCATGCCTCAGGTT HG:+:85699835:-1 HG:+:151081482:-1 HG:+:762272242:-1 HG:+:1160305274:-1 HG:+:3013248258:-1 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:32239681:-1 HG:+:37585831:-1 HG:+:44274339:-1 HG:+:50472410:-1 HG:+:65305486:-1 HG:+:81356106:-1 HG:+:106032823:-1 HG:+:149827765:-1 HG:+:153564998:-1 HG:+:154254391:-1 HG:+:162511544:-1 HG:+:202333541:-1 HG:+:220106776:-1 HG:+:225843673:-1 HG:+:240220221:-1 HG:+:296519233:-1 HG:+:345143770:-1 HG:+:401215505:-1 HG:+:409168342:-1 HG:+:409841085:-1 HG:+:449543321:-1 HG:+:457666358:-1 HG:+:476871924:-1 HG:+:487660084:-1 HG:+:493286297:-1 HG:+:525167781:-1 HG:+:527365989:-1 HG:+:530117140:-1 HG:+:534496420:-1 HG:+:564952453:-1 HG:+:647744014:-1 HG:+:692480245:-1 HG:+:714307507:-1 HG:+:774417500:-1 HG:+:790225371:-1 HG:+:850874871:-1 HG:+:924739086:-1 HG:+:955387521:-1 HG:+:956515339:-1 HG:+:979767219:-1 HG:+:1015250524:-1 HG:+:1026881401:-1 HG:+:1171206721:-1 HG:+:1174089260:-1 HG:+:1176680355:-1 HG:+:1182720615:-1 HG:+:1226307730:-1 HG:+:1249027549:-1 HG:+:1254461979:-1 HG:+:1277183556:-1 HG:+:1277733401:-1 HG:+:1305993777:-1 HG:+:1309822334:-1 HG:+:1310341398:-1 HG:+:1332503160:-1 HG:+:1335098573:-1 HG:+:1335648011:-1 HG:+:1337862796:-1 HG:+:1380442034:-1 HG:+:1387370783:-1 HG:+:1417710893:-1 HG:+:1435032512:-1 HG:+:1491296752:-1 HG:+:1500253507:-1 HG:+:1543739264:-1 HG:+:1561293173:-1 HG:+:1654529867:-1 HG:+:1690466480:-1 HG:+:1693709443:-1 HG:+:1704878075:-1 HG:+:1724341723:-1 HG:+:1750641574:-1 HG:+:1766996236:-1 HG:+:1820077691:-1 HG:+:1873256657:-1 HG:+:1882774164:-1 HG:+:1940503695:-1 HG:+:2005206452:-1 HG:+:2065719517:-1 HG:+:2112164996:-1 HG:+:2117082877:-1 HG:+:2134939796:-1 HG:+:2157824492:-1 HG:+:2158381001:-1 HG:+:2162010897:-1 HG:+:2183839379:-1 HG:+:2186013796:51 HG:+:2221020960:-1 HG:+:2289252187:-1 HG:+:2425749633:-1 HG:+:2458172733:-1 HG:+:2476708975:-1 HG:+:2479899159:-1 HG:+:2494020520:-1 HG:+:2555100264:-1 HG:+:2561438536:-1 HG:+:2666253645:-1 HG:+:2670994192:-1 HG:+:2674656312:-1 HG:+:2681369323:-1 HG:+:2698361295:-1 HG:+:2702213921:-1 HG:+:2709301054:-1 HG:+:2715484056:-1 HG:+:2731838214:-1 HG:+:2751856566:-1 HG:+:2767854260:-1 HG:+:2816877926:-1 HG:+:2828413106:-1 HG:+:2881107522:-1 HG:+:2881186257:-1 HG:+:2908118376:-1 HG:+:2914662207:-1 HG:+:2934212158:-1 HG:+:2986818658:-1 HG:+:3055679918:-1 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:2186013800:51 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:1415160006:-1 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:545453505:-1 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:2186013805:51 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:2186013792:51 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:2186013793:51 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:2186013797:51 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:2186013798:51 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:2186013803:51 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:2186013802:51 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:2186013804:51 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:1259804192:-1 HG:+:2186013795:51 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:526105436:-1 HG:+:593730456:-1 HG:+:1882564800:-1 HG:+:2195383228:-1 HG:+:2289298510:-1 +AACCTGAGGCATGGAGTAATTAACAGGATCATCCCAGGTTCCAAGTAACTAAAGGAAGGATGGAGTTGTTTGTATCTAATTGGATTGCTGGAACTTAAAAATAAAAGACACATGACCAGTGAAGTTAATCCTTAGCACAGCTCTCACACACCTGTTCCCATGCTTTTTCTACCCTGTCACCTTGTTTGCCGAGGTCTGCAGTTTCCTAGGCCAGTACTGTGAAAGCTATCATCTGTATGTTTATCAGAAGTTCTAGAAATGAAGCAGTTTGATATTCAAGACAAATCTCAACGTCTAGACCATCCATAATTAATGCTATCAAATTTAACTGCTGAGACAAAATTGGTTTTTACAAGATGGATAAAAGTAGAAATTTTAAATCAAGAGAGAAAACATTTTCTCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA HG:+:1306123942:-1 HG:+:1306490354:-1 HG:+:1307954216:-1 HG:+:2479984771:-1 HG:+:2501823727:-1 HG:+:2847535920:-1 HG:+:2904028067:-1 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTATATAGGTGATTAATTCTTAAGTACCCTACAGTAGGGCTAGGACAAAAGATTCCATGGCTAACTGGCAGAGGTAGATAAAAAACACTTGTGTTACTCAAAAAACCAAGTAAATACCTAATCAAAATTCTAGCACACCAGCTAATTAGTGATCATTATATTTTTGAGTTTTAGCACCTTTTTATTACCCTCTCATTAATCCAGGGCAATTTTATCAACTAGTACCCTGGCGAAAGGCAAATAATGGAAAAGTAAAAATTAGGAAATGGGAGGTTCCAGATAGTTTTAGACAGACCATAGTAGTAAAAGGACAAAACTATCTAAAGGTTTGTGTAATGATAGTAAAGAAAATCTAAAAAAGAATTTTTTTTTTTAATTTTATAGAGAACAGGGTCTCAACAGGG HG:+:64280688:-1 HG:+:90448072:-1 HG:+:165138355:-1 HG:+:578035173:-1 HG:+:826316146:-1 HG:+:1039059658:-1 HG:+:1576998328:-1 HG:+:1863245380:-1 HG:+:1918203751:-1 HG:+:1970623925:-1 HG:+:2265009718:-1 HG:+:2352883860:-1 HG:+:2379096982:-1 HG:+:2496552861:-1 HG:+:2635819689:-1 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTATATAGGTGATTAATTCTTAAGTACCCTACAGTAGGGCTAGGACAAAAGATTCCATGGCTAACTGGCAGAGGTAGATAAAAAACACTTGTGTTACTCAAAAAACCAAGTAAATACCTAATCAAAATTCTAGCACACCAGCTAATTAGTGATCATTATATTTTTGAGTTTTAGCACCTTTTTATTACCCTCTCATTAATCCAGGGCAATTTTATCAACTAGTACCCTGGCGAAAGGCAAATAATGGAAAAGTAAAAATTAGGAAATGGGAGGTTCCAGATAGTTTTAGACAGACCATAGTAGTAAAAGGACAAAACTATCTAAAGGTTTGTGTAATGATAGTAAAGAAAATCTAAAAAAGAATTTTTTTTTTTAATTTTATAGAGAACAGGGTCTCAACAGGG HG:+:486254143:-1 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTATATAGGTGATTAATTCTTAAGTACCCTACAGTAGGGCTAGGACAAAAGATTCCATGGCTAACTGGCAGAGGTAGATAAAAAACACTTGTGTTACTCAAAAAACCAAGTAAATACCTAATCAAAATTCTAGCACACCAGCTAATTAGTGATCATTATATTTTTGAGTTTTAGCACCTTTTTATTACCCTCTCATTAATCCAGGGCAATTTTATCAACTAGTACCCTGGCGAAAGGCAAATAATGGAAAAGTAAAAATTAGGAAATGGGAGGTTCCAGATAGTTTTAGACAGACCATAGTAGTAAAAGGACAAAACTATCTAAAGGTTTGTGTAATGATAGTAAAGAAAATCTAAAAAAGAATTTTTTTTTTTAATTTTATAGAGAACAGGGTCTCAACAGGG HG:+:283979620:-1 HG:+:719850551:-1 HG:+:860393391:46 HG:+:1172578969:-1 HG:+:1677457195:-1 HG:+:1771118756:-1 HG:+:1916112520:-1 HG:+:2803373111:-1 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTATATAGGTGATTAATTCTTAAGTACCCTACAGTAGGGCTAGGACAAAAGATTCCATGGCTAACTGGCAGAGGTAGATAAAAAACACTTGTGTTACTCAAAAAACCAAGTAAATACCTAATCAAAATTCTAGCACACCAGCTAATTAGTGATCATTATATTTTTGAGTTTTAGCACCTTTTTATTACCCTCTCATTAATCCAGGGCAATTTTATCAACTAGTACCCTGGCGAAAGGCAAATAATGGAAAAGTAAAAATTAGGAAATGGGAGGTTCCAGATAGTTTTAGACAGACCATAGTAGTAAAAGGACAAAACTATCTAAAGGTTTGTGTAATGATAGTAAAGAAAATCTAAAAAAGAATTTTTTTTTTTAATTTTATAGAGAACAGGGTCTCAACAGGG HG:+:860393397:46 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTATATAGGTGATTAATTCTTAAGTACCCTACAGTAGGGCTAGGACAAAAGATTCCATGGCTAACTGGCAGAGGTAGATAAAAAACACTTGTGTTACTCAAAAAACCAAGTAAATACCTAATCAAAATTCTAGCACACCAGCTAATTAGTGATCATTATATTTTTGAGTTTTAGCACCTTTTTATTACCCTCTCATTAATCCAGGGCAATTTTATCAACTAGTACCCTGGCGAAAGGCAAATAATGGAAAAGTAAAAATTAGGAAATGGGAGGTTCCAGATAGTTTTAGACAGACCATAGTAGTAAAAGGACAAAACTATCTAAAGGTTTGTGTAATGATAGTAAAGAAAATCTAAAAAAGAATTTTTTTTTTTAATTTTATAGAGAACAGGGTCTCAACAGGG HG:+:860393400:46 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTATATAGGTGATTAATTCTTAAGTACCCTACAGTAGGGCTAGGACAAAAGATTCCATGGCTAACTGGCAGAGGTAGATAAAAAACACTTGTGTTACTCAAAAAACCAAGTAAATACCTAATCAAAATTCTAGCACACCAGCTAATTAGTGATCATTATATTTTTGAGTTTTAGCACCTTTTTATTACCCTCTCATTAATCCAGGGCAATTTTATCAACTAGTACCCTGGCGAAAGGCAAATAATGGAAAAGTAAAAATTAGGAAATGGGAGGTTCCAGATAGTTTTAGACAGACCATAGTAGTAAAAGGACAAAACTATCTAAAGGTTTGTGTAATGATAGTAAAGAAAATCTAAAAAAGAATTTTTTTTTTTAATTTTATAGAGAACAGGGTCTCAACAGGG HG:+:860393392:46 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTATATAGGTGATTAATTCTTAAGTACCCTACAGTAGGGCTAGGACAAAAGATTCCATGGCTAACTGGCAGAGGTAGATAAAAAACACTTGTGTTACTCAAAAAACCAAGTAAATACCTAATCAAAATTCTAGCACACCAGCTAATTAGTGATCATTATATTTTTGAGTTTTAGCACCTTTTTATTACCCTCTCATTAATCCAGGGCAATTTTATCAACTAGTACCCTGGCGAAAGGCAAATAATGGAAAAGTAAAAATTAGGAAATGGGAGGTTCCAGATAGTTTTAGACAGACCATAGTAGTAAAAGGACAAAACTATCTAAAGGTTTGTGTAATGATAGTAAAGAAAATCTAAAAAAGAATTTTTTTTTTTAATTTTATAGAGAACAGGGTCTCAACAGGG HG:+:860393393:46 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTATATAGGTGATTAATTCTTAAGTACCCTACAGTAGGGCTAGGACAAAAGATTCCATGGCTAACTGGCAGAGGTAGATAAAAAACACTTGTGTTACTCAAAAAACCAAGTAAATACCTAATCAAAATTCTAGCACACCAGCTAATTAGTGATCATTATATTTTTGAGTTTTAGCACCTTTTTATTACCCTCTCATTAATCCAGGGCAATTTTATCAACTAGTACCCTGGCGAAAGGCAAATAATGGAAAAGTAAAAATTAGGAAATGGGAGGTTCCAGATAGTTTTAGACAGACCATAGTAGTAAAAGGACAAAACTATCTAAAGGTTTGTGTAATGATAGTAAAGAAAATCTAAAAAAGAATTTTTTTTTTTAATTTTATAGAGAACAGGGTCTCAACAGGG HG:+:860393398:46 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTATATAGGTGATTAATTCTTAAGTACCCTACAGTAGGGCTAGGACAAAAGATTCCATGGCTAACTGGCAGAGGTAGATAAAAAACACTTGTGTTACTCAAAAAACCAAGTAAATACCTAATCAAAATTCTAGCACACCAGCTAATTAGTGATCATTATATTTTTGAGTTTTAGCACCTTTTTATTACCCTCTCATTAATCCAGGGCAATTTTATCAACTAGTACCCTGGCGAAAGGCAAATAATGGAAAAGTAAAAATTAGGAAATGGGAGGTTCCAGATAGTTTTAGACAGACCATAGTAGTAAAAGGACAAAACTATCTAAAGGTTTGTGTAATGATAGTAAAGAAAATCTAAAAAAGAATTTTTTTTTTTAATTTTATAGAGAACAGGGTCTCAACAGGG HG:+:111215090:-1 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTATATAGGTGATTAATTCTTAAGTACCCTACAGTAGGGCTAGGACAAAAGATTCCATGGCTAACTGGCAGAGGTAGATAAAAAACACTTGTGTTACTCAAAAAACCAAGTAAATACCTAATCAAAATTCTAGCACACCAGCTAATTAGTGATCATTATATTTTTGAGTTTTAGCACCTTTTTATTACCCTCTCATTAATCCAGGGCAATTTTATCAACTAGTACCCTGGCGAAAGGCAAATAATGGAAAAGTAAAAATTAGGAAATGGGAGGTTCCAGATAGTTTTAGACAGACCATAGTAGTAAAAGGACAAAACTATCTAAAGGTTTGTGTAATGATAGTAAAGAAAATCTAAAAAAGAATTTTTTTTTTTAATTTTATAGAGAACAGGGTCTCAACAGGG HG:+:860393408:46 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTATATAGGTGATTAATTCTTAAGTACCCTACAGTAGGGCTAGGACAAAAGATTCCATGGCTAACTGGCAGAGGTAGATAAAAAACACTTGTGTTACTCAAAAAACCAAGTAAATACCTAATCAAAATTCTAGCACACCAGCTAATTAGTGATCATTATATTTTTGAGTTTTAGCACCTTTTTATTACCCTCTCATTAATCCAGGGCAATTTTATCAACTAGTACCCTGGCGAAAGGCAAATAATGGAAAAGTAAAAATTAGGAAATGGGAGGTTCCAGATAGTTTTAGACAGACCATAGTAGTAAAAGGACAAAACTATCTAAAGGTTTGTGTAATGATAGTAAAGAAAATCTAAAAAAGAATTTTTTTTTTTAATTTTATAGAGAACAGGGTCTCAACAGGG HG:+:860393411:46 HG:+:2712068700:-1 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTATATAGGTGATTAATTCTTAAGTACCCTACAGTAGGGCTAGGACAAAAGATTCCATGGCTAACTGGCAGAGGTAGATAAAAAACACTTGTGTTACTCAAAAAACCAAGTAAATACCTAATCAAAATTCTAGCACACCAGCTAATTAGTGATCATTATATTTTTGAGTTTTAGCACCTTTTTATTACCCTCTCATTAATCCAGGGCAATTTTATCAACTAGTACCCTGGCGAAAGGCAAATAATGGAAAAGTAAAAATTAGGAAATGGGAGGTTCCAGATAGTTTTAGACAGACCATAGTAGTAAAAGGACAAAACTATCTAAAGGTTTGTGTAATGATAGTAAAGAAAATCTAAAAAAGAATTTTTTTTTTTAATTTTATAGAGAACAGGGTCTCAACAGGG HG:+:252318579:-1 HG:+:860393418:46 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTATATAGGTGATTAATTCTTAAGTACCCTACAGTAGGGCTAGGACAAAAGATTCCATGGCTAACTGGCAGAGGTAGATAAAAAACACTTGTGTTACTCAAAAAACCAAGTAAATACCTAATCAAAATTCTAGCACACCAGCTAATTAGTGATCATTATATTTTTGAGTTTTAGCACCTTTTTATTACCCTCTCATTAATCCAGGGCAATTTTATCAACTAGTACCCTGGCGAAAGGCAAATAATGGAAAAGTAAAAATTAGGAAATGGGAGGTTCCAGATAGTTTTAGACAGACCATAGTAGTAAAAGGACAAAACTATCTAAAGGTTTGTGTAATGATAGTAAAGAAAATCTAAAAAAGAATTTTTTTTTTTAATTTTATAGAGAACAGGGTCTCAACAGGG HG:+:860393417:46 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTATATAGGTGATTAATTCTTAAGTACCCTACAGTAGGGCTAGGACAAAAGATTCCATGGCTAACTGGCAGAGGTAGATAAAAAACACTTGTGTTACTCAAAAAACCAAGTAAATACCTAATCAAAATTCTAGCACACCAGCTAATTAGTGATCATTATATTTTTGAGTTTTAGCACCTTTTTATTACCCTCTCATTAATCCAGGGCAATTTTATCAACTAGTACCCTGGCGAAAGGCAAATAATGGAAAAGTAAAAATTAGGAAATGGGAGGTTCCAGATAGTTTTAGACAGACCATAGTAGTAAAAGGACAAAACTATCTAAAGGTTTGTGTAATGATAGTAAAGAAAATCTAAAAAAGAATTTTTTTTTTTAATTTTATAGAGAACAGGGTCTCAACAGGG HG:+:237779105:-1 +CCCTGTTGAGACCCTGTTCTCTATAAAATTAAAAAAAAAAATTCTTTTTTAGATTTTCTTTACTATCATTACACAAACCTTTAGATAGTTTTGTCCTTTTACTACTATGGTCTGTCTAAAACTATCTGGAACCTCCCATTTCCTAATTTTTACTTTTCCATTATTTGCCTTTCGCCAGGGTACTAGTTGATAAAATTGCCCTGGATTAATGAGAGGGTAATAAAAAGGTGCTAAAACTCAAAAATATAATGATCACTAATTAGCTGGTGTGCTAGAATTTTGATTAGGTATTTACTTGGTTTTTTGAGTAACACAAGTGTTTTTTATCTACCTCTGCCAGTTAGCCATGGAATCTTTTGTCCTAGCCCTACTGTAGGGTACTTAAGAATTAATCACCTATATAAAGAAAAGGCAGTTTATTTTGGTTTGCTGGTCCTTTGTAAGAAAGAGAGGGGCTGAAGTACGACCTTTGCTACCTTTCCTTTCCGGTCACTAATGGCTCCAGCTTGGACCCTTTACAGTTGGTGTTTTCTTTGGCACTGAAGTTGAGCCAGCAGGTATCAGGGATTTATCAAAATATCCTAGTTAACCTTTTGGTCTATAGTGTGTCTTTATTTCAATTCTTTTCTTTTCTTTTATTTTTTTTCTCATAGCAACTAGCCTACATTTCCAGACCATTCTAAAATCTATGAATATTTGAATAAGTGACTGGTGGTTCAGATACATCTATTTGCTGGGGAGTAGGGAGAGAAAGAAAAAGAAAAAAACAATCCAGGAAGCAGCATTGTTGTTATCTTAGCACTGTTTTCTCTTTGTGTATAGCTTTATGCAAGCTGATTGGATTTTTTAGCGTTAGCCTTAGATGAACTATCTGGTGGAATAAAATTATTTTGTGGTTTGGAACTACATGTATTTGCTTCCTTCTCTTTCAGGATTGGAATACTGTGGGTAATGAAGGGTTAATTTAGTTCATGATAATAACAAAAGCTGAATGGTTTCG HG:+:447462736:-1 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:566211721:43 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:566211709:43 HG:+:1494364542:-1 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:566211707:43 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:240595383:-1 HG:+:566211713:43 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:566211714:43 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:1565711620:-1 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:2765870875:-1 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:566211705:43 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:1288458231:-1 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:566211716:43 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:714285022:-1 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:566211720:43 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:2722747741:-1 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:566211710:43 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:566211711:43 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:935226769:-1 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:348103387:-1 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTACTATCAACTGGCTCTCGGAATTGATGCAATTGCCTCCTAATGGTCGTACCTGCTTCTATTACTTTCCTGCTACAGCCCTGTCCTCTACACAGCAGCCAGAGTGATCCTTTAAAAATGTACGTCAAAAGAGGTCACTCTCTGCCAGACCCTGCAATGGCTCTCATTTACACTAAGGAGTCTAAGTGTGTAGAAGGCCAGGAAGACCCAACCACGTCGGCTCCACTTCCCACTTCCCCACCACTCATCTCCCCAACCGTGATGTCTTTCAACTCTCACCTTTGTTCGGCACCAGACCCAGCTACACTGACCTCTGTGCTGTTGCTGGAATATTCTAGGTTCTACTGAGGGCTGCAGAGCCTTTGCCTTTGGCTGGTCCCTCTGCCTGGAATGCCCTTCCTCAG HG:+:2775976883:-1 +CTGAGGAAGGGCATTCCAGGCAGAGGGACCAGCCAAAGGCAAAGGCTCTGCAGCCCTCAGTAGAACCTAGAATATTCCAGCAACAGCACAGAGGTCAGTGTAGCTGGGTCTGGTGCCGAACAAAGGTGAGAGTTGAAAGACATCACGGTTGGGGAGATGAGTGGTGGGGAAGTGGGAAGTGGAGCCGACGTGGTTGGGTCTTCCTGGCCTTCTACACACTTAGACTCCTTAGTGTAAATGAGAGCCATTGCAGGGTCTGGCAGAGAGTGACCTCTTTTGACGTACATTTTTAAAGGATCACTCTGGCTGCTGTGTAGAGGACAGGGCTGTAGCAGGAAAGTAATAGAAGCAGGTACGACCATTAGGAGGCAATTGCATCAATTCCGAGAGCCAGTTGATAGTAGCTGGGACCTGAGTAATAGCTGTTGGAAGCGGGTTTGAGCCAGATTCTGAATAAAGTGAAGGGTAGAGCCCACAGGAGTTTCCACTTCCTATGGCTCCTACCTTCCAACCTCCACTAGCTCATGTGCTTTAAGAAATGGCAGGATTTTACAAGAAGAGAAAGAAAAAAAACATTCCAAACTAAATGAAAGTAGAAAAGCAAAGCAGAAGAAAAGAAAACACAATTAATTAACAGGCCATTGTAAATAGAAAATTTGACTAGAGTGGAGAACTAATATAGGGAAGCCATGGAAGGTCAGTTTAGAGTCAGATATTATAATTAGATGTCTTCAGTGTGGGTTAAGTAACTTCTGACATCATCCTGTCCTCAGTGAGAAATATTGTCAATGTTTTGGGGAAAAAATAACAAGACGAGAATGTTAAGGCTTAGGGAAATGATTTAGACTCTGGGAAGCATTTTGAGGGTGAGTTTCTTGGTGGCAGCGAGATTTCTCACAGAACTTCTAACAAAACAAGTGCTTTAACCAAAGCGAGGGCAGTTTGTAGGGAGTAAGAGAACAAGGTTTTTAGCATCAGACAAACATGGGTGGGATGCTGA HG:+:283973967:-1 +CTGAGGAAGGGCATTCCAGGCAGAGGGACCAGCCAAAGGCAAAGGCTCTGCAGCCCTCAGTAGAACCTAGAATATTCCAGCAACAGCACAGAGGTCAGTGTAGCTGGGTCTGGTGCCGAACAAAGGTGAGAGTTGAAAGACATCACGGTTGGGGAGATGAGTGGTGGGGAAGTGGGAAGTGGAGCCGACGTGGTTGGGTCTTCCTGGCCTTCTACACACTTAGACTCCTTAGTGTAAATGAGAGCCATTGCAGGGTCTGGCAGAGAGTGACCTCTTTTGACGTACATTTTTAAAGGATCACTCTGGCTGCTGTGTAGAGGACAGGGCTGTAGCAGGAAAGTAATAGAAGCAGGTACGACCATTAGGAGGCAATTGCATCAATTCCGAGAGCCAGTTGATAGTAGCTGGGACCTGAGTAATAGCTGTTGGAAGCGGGTTTGAGCCAGATTCTGAATAAAGTGAAGGGTAGAGCCCACAGGAGTTTCCACTTCCTATGGCTCCTACCTTCCAACCTCCACTAGCTCATGTGCTTTAAGAAATGGCAGGATTTTACAAGAAGAGAAAGAAAAAAAACATTCCAAACTAAATGAAAGTAGAAAAGCAAAGCAGAAGAAAAGAAAACACAATTAATTAACAGGCCATTGTAAATAGAAAATTTGACTAGAGTGGAGAACTAATATAGGGAAGCCATGGAAGGTCAGTTTAGAGTCAGATATTATAATTAGATGTCTTCAGTGTGGGTTAAGTAACTTCTGACATCATCCTGTCCTCAGTGAGAAATATTGTCAATGTTTTGGGGAAAAAATAACAAGACGAGAATGTTAAGGCTTAGGGAAATGATTTAGACTCTGGGAAGCATTTTGAGGGTGAGTTTCTTGGTGGCAGCGAGATTTCTCACAGAACTTCTAACAAAACAAGTGCTTTAACCAAAGCGAGGGCAGTTTGTAGGGAGTAAGAGAACAAGGTTTTTAGCATCAGACAAACATGGGTGGGATGCTGA HG:+:1816864478:-1 +CTGAGGAAGGGCATTCCAGGCAGAGGGACCAGCCAAAGGCAAAGGCTCTGCAGCCCTCAGTAGAACCTAGAATATTCCAGCAACAGCACAGAGGTCAGTGTAGCTGGGTCTGGTGCCGAACAAAGGTGAGAGTTGAAAGACATCACGGTTGGGGAGATGAGTGGTGGGGAAGTGGGAAGTGGAGCCGACGTGGTTGGGTCTTCCTGGCCTTCTACACACTTAGACTCCTTAGTGTAAATGAGAGCCATTGCAGGGTCTGGCAGAGAGTGACCTCTTTTGACGTACATTTTTAAAGGATCACTCTGGCTGCTGTGTAGAGGACAGGGCTGTAGCAGGAAAGTAATAGAAGCAGGTACGACCATTAGGAGGCAATTGCATCAATTCCGAGAGCCAGTTGATAGTAGCTGGGACCTGAGTAATAGCTGTTGGAAGCGGGTTTGAGCCAGATTCTGAATAAAGTGAAGGGTAGAGCCCACAGGAGTTTCCACTTCCTATGGCTCCTACCTTCCAACCTCCACTAGCTCATGTGCTTTAAGAAATGGCAGGATTTTACAAGAAGAGAAAGAAAAAAAACATTCCAAACTAAATGAAAGTAGAAAAGCAAAGCAGAAGAAAAGAAAACACAATTAATTAACAGGCCATTGTAAATAGAAAATTTGACTAGAGTGGAGAACTAATATAGGGAAGCCATGGAAGGTCAGTTTAGAGTCAGATATTATAATTAGATGTCTTCAGTGTGGGTTAAGTAACTTCTGACATCATCCTGTCCTCAGTGAGAAATATTGTCAATGTTTTGGGGAAAAAATAACAAGACGAGAATGTTAAGGCTTAGGGAAATGATTTAGACTCTGGGAAGCATTTTGAGGGTGAGTTTCTTGGTGGCAGCGAGATTTCTCACAGAACTTCTAACAAAACAAGTGCTTTAACCAAAGCGAGGGCAGTTTGTAGGGAGTAAGAGAACAAGGTTTTTAGCATCAGACAAACATGGGTGGGATGCTGA HG:+:2306805746:-1 +CTGAGGAAGGGCATTCCAGGCAGAGGGACCAGCCAAAGGCAAAGGCTCTGCAGCCCTCAGTAGAACCTAGAATATTCCAGCAACAGCACAGAGGTCAGTGTAGCTGGGTCTGGTGCCGAACAAAGGTGAGAGTTGAAAGACATCACGGTTGGGGAGATGAGTGGTGGGGAAGTGGGAAGTGGAGCCGACGTGGTTGGGTCTTCCTGGCCTTCTACACACTTAGACTCCTTAGTGTAAATGAGAGCCATTGCAGGGTCTGGCAGAGAGTGACCTCTTTTGACGTACATTTTTAAAGGATCACTCTGGCTGCTGTGTAGAGGACAGGGCTGTAGCAGGAAAGTAATAGAAGCAGGTACGACCATTAGGAGGCAATTGCATCAATTCCGAGAGCCAGTTGATAGTAGCTGGGACCTGAGTAATAGCTGTTGGAAGCGGGTTTGAGCCAGATTCTGAATAAAGTGAAGGGTAGAGCCCACAGGAGTTTCCACTTCCTATGGCTCCTACCTTCCAACCTCCACTAGCTCATGTGCTTTAAGAAATGGCAGGATTTTACAAGAAGAGAAAGAAAAAAAACATTCCAAACTAAATGAAAGTAGAAAAGCAAAGCAGAAGAAAAGAAAACACAATTAATTAACAGGCCATTGTAAATAGAAAATTTGACTAGAGTGGAGAACTAATATAGGGAAGCCATGGAAGGTCAGTTTAGAGTCAGATATTATAATTAGATGTCTTCAGTGTGGGTTAAGTAACTTCTGACATCATCCTGTCCTCAGTGAGAAATATTGTCAATGTTTTGGGGAAAAAATAACAAGACGAGAATGTTAAGGCTTAGGGAAATGATTTAGACTCTGGGAAGCATTTTGAGGGTGAGTTTCTTGGTGGCAGCGAGATTTCTCACAGAACTTCTAACAAAACAAGTGCTTTAACCAAAGCGAGGGCAGTTTGTAGGGAGTAAGAGAACAAGGTTTTTAGCATCAGACAAACATGGGTGGGATGCTGA HG:+:1390653571:-1 +CTGAGGAAGGGCATTCCAGGCAGAGGGACCAGCCAAAGGCAAAGGCTCTGCAGCCCTCAGTAGAACCTAGAATATTCCAGCAACAGCACAGAGGTCAGTGTAGCTGGGTCTGGTGCCGAACAAAGGTGAGAGTTGAAAGACATCACGGTTGGGGAGATGAGTGGTGGGGAAGTGGGAAGTGGAGCCGACGTGGTTGGGTCTTCCTGGCCTTCTACACACTTAGACTCCTTAGTGTAAATGAGAGCCATTGCAGGGTCTGGCAGAGAGTGACCTCTTTTGACGTACATTTTTAAAGGATCACTCTGGCTGCTGTGTAGAGGACAGGGCTGTAGCAGGAAAGTAATAGAAGCAGGTACGACCATTAGGAGGCAATTGCATCAATTCCGAGAGCCAGTTGATAGTAGCTGGGACCTGAGTAATAGCTGTTGGAAGCGGGTTTGAGCCAGATTCTGAATAAAGTGAAGGGTAGAGCCCACAGGAGTTTCCACTTCCTATGGCTCCTACCTTCCAACCTCCACTAGCTCATGTGCTTTAAGAAATGGCAGGATTTTACAAGAAGAGAAAGAAAAAAAACATTCCAAACTAAATGAAAGTAGAAAAGCAAAGCAGAAGAAAAGAAAACACAATTAATTAACAGGCCATTGTAAATAGAAAATTTGACTAGAGTGGAGAACTAATATAGGGAAGCCATGGAAGGTCAGTTTAGAGTCAGATATTATAATTAGATGTCTTCAGTGTGGGTTAAGTAACTTCTGACATCATCCTGTCCTCAGTGAGAAATATTGTCAATGTTTTGGGGAAAAAATAACAAGACGAGAATGTTAAGGCTTAGGGAAATGATTTAGACTCTGGGAAGCATTTTGAGGGTGAGTTTCTTGGTGGCAGCGAGATTTCTCACAGAACTTCTAACAAAACAAGTGCTTTAACCAAAGCGAGGGCAGTTTGTAGGGAGTAAGAGAACAAGGTTTTTAGCATCAGACAAACATGGGTGGGATGCTGA HG:+:298697123:-1 HG:+:417616517:-1 HG:+:545702014:-1 HG:+:941850241:-1 HG:+:1005564860:-1 HG:+:1059147675:-1 HG:+:1286460361:-1 HG:+:1365864929:-1 HG:+:1368678197:-1 HG:+:1368916038:-1 HG:+:1442858509:-1 HG:+:1661188436:-1 HG:+:1835336523:-1 HG:+:2144603713:-1 HG:+:2364546702:-1 HG:+:2632745861:-1 HG:+:2863040045:-1 HG:+:2965393053:-1 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCAAAGGAACTTATAGCCATTTACTCAGGCAAACTTTAACATGAAGGAAAGGGGGAGTACACTGTTGGATATGGGGCACCAGTTAATGCTAACTCAGGCACCTAAAACACTATTATGGTCCCTCCTGTTAAGCGAGATATATTATGTGTCAAGTAAGCAATAGGGTTTTCGTAGCTCATGTCTACCTCACAGACAGCCTAGGATTCAATTCTTGTGATCATTTCCTCACTTTTCAATAAATAGTTGTAATGGATATACTAAGCATTGGTAGGAGTCCTCACTCTAGATGCTTTGATAAAATAAAATAAGAGTTATTATAGTAAGGTACAGCAAGTGGTAAGCCTCTGAGACTACCTTTCTACTCCACCAACATAATTAATCAAAAACAACATTGCAATTCAGA HG:+:673211684:-1 HG:+:731863871:-1 HG:+:1326239347:-1 HG:+:2601126641:-1 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCAAAGGAACTTATAGCCATTTACTCAGGCAAACTTTAACATGAAGGAAAGGGGGAGTACACTGTTGGATATGGGGCACCAGTTAATGCTAACTCAGGCACCTAAAACACTATTATGGTCCCTCCTGTTAAGCGAGATATATTATGTGTCAAGTAAGCAATAGGGTTTTCGTAGCTCATGTCTACCTCACAGACAGCCTAGGATTCAATTCTTGTGATCATTTCCTCACTTTTCAATAAATAGTTGTAATGGATATACTAAGCATTGGTAGGAGTCCTCACTCTAGATGCTTTGATAAAATAAAATAAGAGTTATTATAGTAAGGTACAGCAAGTGGTAAGCCTCTGAGACTACCTTTCTACTCCACCAACATAATTAATCAAAAACAACATTGCAATTCAGA HG:+:333857226:-1 HG:+:573370442:-1 HG:+:577213086:-1 HG:+:1113085633:-1 HG:+:1322495086:-1 HG:+:1872016213:-1 HG:+:2435056308:-1 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCAAAGGAACTTATAGCCATTTACTCAGGCAAACTTTAACATGAAGGAAAGGGGGAGTACACTGTTGGATATGGGGCACCAGTTAATGCTAACTCAGGCACCTAAAACACTATTATGGTCCCTCCTGTTAAGCGAGATATATTATGTGTCAAGTAAGCAATAGGGTTTTCGTAGCTCATGTCTACCTCACAGACAGCCTAGGATTCAATTCTTGTGATCATTTCCTCACTTTTCAATAAATAGTTGTAATGGATATACTAAGCATTGGTAGGAGTCCTCACTCTAGATGCTTTGATAAAATAAAATAAGAGTTATTATAGTAAGGTACAGCAAGTGGTAAGCCTCTGAGACTACCTTTCTACTCCACCAACATAATTAATCAAAAACAACATTGCAATTCAGA HG:+:286393729:-1 HG:+:640830310:50 HG:+:1014231156:-1 HG:+:2814732436:-1 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCAAAGGAACTTATAGCCATTTACTCAGGCAAACTTTAACATGAAGGAAAGGGGGAGTACACTGTTGGATATGGGGCACCAGTTAATGCTAACTCAGGCACCTAAAACACTATTATGGTCCCTCCTGTTAAGCGAGATATATTATGTGTCAAGTAAGCAATAGGGTTTTCGTAGCTCATGTCTACCTCACAGACAGCCTAGGATTCAATTCTTGTGATCATTTCCTCACTTTTCAATAAATAGTTGTAATGGATATACTAAGCATTGGTAGGAGTCCTCACTCTAGATGCTTTGATAAAATAAAATAAGAGTTATTATAGTAAGGTACAGCAAGTGGTAAGCCTCTGAGACTACCTTTCTACTCCACCAACATAATTAATCAAAAACAACATTGCAATTCAGA HG:+:640830307:50 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCAAAGGAACTTATAGCCATTTACTCAGGCAAACTTTAACATGAAGGAAAGGGGGAGTACACTGTTGGATATGGGGCACCAGTTAATGCTAACTCAGGCACCTAAAACACTATTATGGTCCCTCCTGTTAAGCGAGATATATTATGTGTCAAGTAAGCAATAGGGTTTTCGTAGCTCATGTCTACCTCACAGACAGCCTAGGATTCAATTCTTGTGATCATTTCCTCACTTTTCAATAAATAGTTGTAATGGATATACTAAGCATTGGTAGGAGTCCTCACTCTAGATGCTTTGATAAAATAAAATAAGAGTTATTATAGTAAGGTACAGCAAGTGGTAAGCCTCTGAGACTACCTTTCTACTCCACCAACATAATTAATCAAAAACAACATTGCAATTCAGA HG:+:640830312:50 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCAAAGGAACTTATAGCCATTTACTCAGGCAAACTTTAACATGAAGGAAAGGGGGAGTACACTGTTGGATATGGGGCACCAGTTAATGCTAACTCAGGCACCTAAAACACTATTATGGTCCCTCCTGTTAAGCGAGATATATTATGTGTCAAGTAAGCAATAGGGTTTTCGTAGCTCATGTCTACCTCACAGACAGCCTAGGATTCAATTCTTGTGATCATTTCCTCACTTTTCAATAAATAGTTGTAATGGATATACTAAGCATTGGTAGGAGTCCTCACTCTAGATGCTTTGATAAAATAAAATAAGAGTTATTATAGTAAGGTACAGCAAGTGGTAAGCCTCTGAGACTACCTTTCTACTCCACCAACATAATTAATCAAAAACAACATTGCAATTCAGA HG:+:640830297:50 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCAAAGGAACTTATAGCCATTTACTCAGGCAAACTTTAACATGAAGGAAAGGGGGAGTACACTGTTGGATATGGGGCACCAGTTAATGCTAACTCAGGCACCTAAAACACTATTATGGTCCCTCCTGTTAAGCGAGATATATTATGTGTCAAGTAAGCAATAGGGTTTTCGTAGCTCATGTCTACCTCACAGACAGCCTAGGATTCAATTCTTGTGATCATTTCCTCACTTTTCAATAAATAGTTGTAATGGATATACTAAGCATTGGTAGGAGTCCTCACTCTAGATGCTTTGATAAAATAAAATAAGAGTTATTATAGTAAGGTACAGCAAGTGGTAAGCCTCTGAGACTACCTTTCTACTCCACCAACATAATTAATCAAAAACAACATTGCAATTCAGA HG:+:640830308:50 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCAAAGGAACTTATAGCCATTTACTCAGGCAAACTTTAACATGAAGGAAAGGGGGAGTACACTGTTGGATATGGGGCACCAGTTAATGCTAACTCAGGCACCTAAAACACTATTATGGTCCCTCCTGTTAAGCGAGATATATTATGTGTCAAGTAAGCAATAGGGTTTTCGTAGCTCATGTCTACCTCACAGACAGCCTAGGATTCAATTCTTGTGATCATTTCCTCACTTTTCAATAAATAGTTGTAATGGATATACTAAGCATTGGTAGGAGTCCTCACTCTAGATGCTTTGATAAAATAAAATAAGAGTTATTATAGTAAGGTACAGCAAGTGGTAAGCCTCTGAGACTACCTTTCTACTCCACCAACATAATTAATCAAAAACAACATTGCAATTCAGA HG:+:640830311:50 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCAAAGGAACTTATAGCCATTTACTCAGGCAAACTTTAACATGAAGGAAAGGGGGAGTACACTGTTGGATATGGGGCACCAGTTAATGCTAACTCAGGCACCTAAAACACTATTATGGTCCCTCCTGTTAAGCGAGATATATTATGTGTCAAGTAAGCAATAGGGTTTTCGTAGCTCATGTCTACCTCACAGACAGCCTAGGATTCAATTCTTGTGATCATTTCCTCACTTTTCAATAAATAGTTGTAATGGATATACTAAGCATTGGTAGGAGTCCTCACTCTAGATGCTTTGATAAAATAAAATAAGAGTTATTATAGTAAGGTACAGCAAGTGGTAAGCCTCTGAGACTACCTTTCTACTCCACCAACATAATTAATCAAAAACAACATTGCAATTCAGA HG:+:640830298:50 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCAAAGGAACTTATAGCCATTTACTCAGGCAAACTTTAACATGAAGGAAAGGGGGAGTACACTGTTGGATATGGGGCACCAGTTAATGCTAACTCAGGCACCTAAAACACTATTATGGTCCCTCCTGTTAAGCGAGATATATTATGTGTCAAGTAAGCAATAGGGTTTTCGTAGCTCATGTCTACCTCACAGACAGCCTAGGATTCAATTCTTGTGATCATTTCCTCACTTTTCAATAAATAGTTGTAATGGATATACTAAGCATTGGTAGGAGTCCTCACTCTAGATGCTTTGATAAAATAAAATAAGAGTTATTATAGTAAGGTACAGCAAGTGGTAAGCCTCTGAGACTACCTTTCTACTCCACCAACATAATTAATCAAAAACAACATTGCAATTCAGA HG:+:640830301:50 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCAAAGGAACTTATAGCCATTTACTCAGGCAAACTTTAACATGAAGGAAAGGGGGAGTACACTGTTGGATATGGGGCACCAGTTAATGCTAACTCAGGCACCTAAAACACTATTATGGTCCCTCCTGTTAAGCGAGATATATTATGTGTCAAGTAAGCAATAGGGTTTTCGTAGCTCATGTCTACCTCACAGACAGCCTAGGATTCAATTCTTGTGATCATTTCCTCACTTTTCAATAAATAGTTGTAATGGATATACTAAGCATTGGTAGGAGTCCTCACTCTAGATGCTTTGATAAAATAAAATAAGAGTTATTATAGTAAGGTACAGCAAGTGGTAAGCCTCTGAGACTACCTTTCTACTCCACCAACATAATTAATCAAAAACAACATTGCAATTCAGA HG:+:640830304:50 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCAAAGGAACTTATAGCCATTTACTCAGGCAAACTTTAACATGAAGGAAAGGGGGAGTACACTGTTGGATATGGGGCACCAGTTAATGCTAACTCAGGCACCTAAAACACTATTATGGTCCCTCCTGTTAAGCGAGATATATTATGTGTCAAGTAAGCAATAGGGTTTTCGTAGCTCATGTCTACCTCACAGACAGCCTAGGATTCAATTCTTGTGATCATTTCCTCACTTTTCAATAAATAGTTGTAATGGATATACTAAGCATTGGTAGGAGTCCTCACTCTAGATGCTTTGATAAAATAAAATAAGAGTTATTATAGTAAGGTACAGCAAGTGGTAAGCCTCTGAGACTACCTTTCTACTCCACCAACATAATTAATCAAAAACAACATTGCAATTCAGA HG:+:2040526408:-1 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCAAAGGAACTTATAGCCATTTACTCAGGCAAACTTTAACATGAAGGAAAGGGGGAGTACACTGTTGGATATGGGGCACCAGTTAATGCTAACTCAGGCACCTAAAACACTATTATGGTCCCTCCTGTTAAGCGAGATATATTATGTGTCAAGTAAGCAATAGGGTTTTCGTAGCTCATGTCTACCTCACAGACAGCCTAGGATTCAATTCTTGTGATCATTTCCTCACTTTTCAATAAATAGTTGTAATGGATATACTAAGCATTGGTAGGAGTCCTCACTCTAGATGCTTTGATAAAATAAAATAAGAGTTATTATAGTAAGGTACAGCAAGTGGTAAGCCTCTGAGACTACCTTTCTACTCCACCAACATAATTAATCAAAAACAACATTGCAATTCAGA HG:+:640830317:50 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:2569151975:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:333178322:-1 HG:+:638138391:-1 HG:+:1052241904:-1 HG:+:1510229401:-1 HG:+:2697548384:-1 HG:+:2806125954:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:415612125:-1 HG:+:767771655:-1 HG:+:787403622:-1 HG:+:903798809:-1 HG:+:1554696116:-1 HG:+:2909934082:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:119146800:-1 HG:+:184669190:-1 HG:+:195650692:-1 HG:+:315861718:-1 HG:+:348837493:-1 HG:+:395209047:-1 HG:+:501903324:-1 HG:+:687785769:-1 HG:+:823002641:-1 HG:+:942854368:-1 HG:+:961635595:-1 HG:+:971433741:-1 HG:+:992545119:-1 HG:+:1083733596:-1 HG:+:1120290505:-1 HG:+:1120897649:-1 HG:+:1140394151:-1 HG:+:1186189503:-1 HG:+:1248728435:-1 HG:+:1314892197:-1 HG:+:1575024670:-1 HG:+:1709784375:-1 HG:+:1709894844:-1 HG:+:1825686228:-1 HG:+:1851809130:-1 HG:+:1958752953:-1 HG:+:2039231163:-1 HG:+:2108805202:-1 HG:+:2130500316:-1 HG:+:2141894424:-1 HG:+:2157723559:-1 HG:+:2179113256:-1 HG:+:2192060155:-1 HG:+:2402215474:-1 HG:+:2465300492:-1 HG:+:2480671841:-1 HG:+:2611299347:-1 HG:+:2644092777:-1 HG:+:2647174766:-1 HG:+:2653639784:-1 HG:+:2980089263:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:73148789:-1 HG:+:195137537:-1 HG:+:303642941:-1 HG:+:623102612:-1 HG:+:838300169:-1 HG:+:868382471:-1 HG:+:1177424595:-1 HG:+:1617650367:-1 HG:+:2176006806:-1 HG:+:2682309404:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:417404211:-1 HG:+:502359673:-1 HG:+:714260483:-1 HG:+:855780507:-1 HG:+:2186313956:-1 HG:+:2569620681:-1 HG:+:2824316365:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:1663236753:-1 HG:+:1925779704:-1 HG:+:2775267476:-1 HG:+:2957487949:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:1397139937:-1 HG:+:1654828776:-1 HG:+:1926696561:-1 HG:+:2399766533:-1 HG:+:2505405753:-1 HG:+:3019544980:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:936070786:-1 HG:+:2077653551:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:302139283:-1 HG:+:824090818:-1 HG:+:2118707341:-1 HG:+:2260699857:-1 HG:+:2723694655:-1 HG:+:3032038684:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:175932492:-1 HG:+:436167777:-1 HG:+:821163863:-1 HG:+:1797257181:-1 HG:+:2675817775:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:65958565:-1 HG:+:294320391:-1 HG:+:557857516:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:607238527:-1 HG:+:1215309204:-1 HG:+:1316431668:-1 HG:+:1459856809:-1 HG:+:1777507271:-1 HG:+:2608872768:-1 HG:+:2608873670:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:1046768855:-1 HG:+:1966415912:-1 HG:+:1995519217:-1 HG:+:2966502258:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:283100179:-1 HG:+:396157392:-1 HG:+:760175952:-1 HG:+:845926102:-1 HG:+:918719144:-1 HG:+:976497790:-1 HG:+:1000724013:-1 HG:+:1340686911:-1 HG:+:1448394139:-1 HG:+:1451168868:-1 HG:+:1841705858:-1 HG:+:2116846106:-1 HG:+:2559536618:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:115176539:-1 HG:+:301181539:-1 HG:+:693565107:-1 HG:+:1064778089:-1 HG:+:1197334757:-1 HG:+:1201269774:-1 HG:+:1283534171:-1 HG:+:1327182714:-1 HG:+:1475600910:-1 HG:+:1613837375:-1 HG:+:1668854214:-1 HG:+:2993356918:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:1033718270:-1 HG:+:1255224068:-1 HG:+:1317021743:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:257914833:-1 HG:+:379065588:-1 HG:+:807613911:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:409577125:-1 HG:+:527879602:-1 HG:+:690790997:-1 HG:+:1207822480:-1 HG:+:1530401207:-1 HG:+:1562745458:-1 HG:+:1762452314:-1 HG:+:2178637223:-1 HG:+:2362145934:-1 HG:+:2393962396:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:685818748:-1 HG:+:1687086982:-1 HG:+:2756323430:-1 HG:+:2948655637:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:152414981:-1 HG:+:593164507:-1 HG:+:1003338059:-1 HG:+:1791400561:-1 HG:+:2530359606:-1 HG:+:2925401222:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:51010220:-1 HG:+:281199137:-1 HG:+:339414436:-1 HG:+:416731103:-1 HG:+:424501305:-1 HG:+:588919793:-1 HG:+:750484133:-1 HG:+:753129927:-1 HG:+:816891341:-1 HG:+:1108704893:-1 HG:+:1258903685:-1 HG:+:1284449542:-1 HG:+:1323099041:-1 HG:+:1405575695:-1 HG:+:1414115687:-1 HG:+:1470285070:-1 HG:+:1492532961:-1 HG:+:1633327783:-1 HG:+:1665319516:-1 HG:+:1697722952:-1 HG:+:2157696224:-1 HG:+:2266995048:-1 HG:+:2299279961:-1 HG:+:2340625356:-1 HG:+:2402891169:-1 HG:+:2503426817:-1 HG:+:2632645457:-1 HG:+:2643633611:-1 HG:+:2986817226:-1 HG:+:2997067440:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:11355153:-1 HG:+:395881805:-1 HG:+:934381235:-1 HG:+:946288184:-1 HG:+:1047666677:-1 HG:+:1048149594:-1 HG:+:1736900007:-1 HG:+:2518354561:-1 HG:+:2629527214:-1 HG:+:2810356702:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTTATAGTTTCACATTAATTTTAGTTCAGTTACATTATGTTTTACTTTCAGTTTAAAAATTTACTATTGGTTAAAACATTACCCCAAAACAGAAGTTGTGTCTGCAATTATACAATATTGTAGTGGATTTTTCAAAAAATATCTTACGATTGTTAAAAGAATAATTGGGGTACAAAATAGGAAGTAATCAACTGGGATATAAATAAAATGTAAAGAAGTTACAGTACTGCAGCACAAGGGAAGCAACATTAGTTTGGTGATACCTTTGCAGCACGTATGTTAACTTAGGCCAGAGAGACTTAGGCGTGAATATTACACACTCCAGAGGAATGACCAGGACTTGTATAGTCCCATTTTCATGCTGCTGATAAAGACATATGCAAGACTGGGCAATTTACCAATA HG:+:490758681:-1 HG:+:599288966:-1 HG:+:605638133:-1 HG:+:654912370:-1 HG:+:759598076:-1 HG:+:796662219:-1 HG:+:999788384:-1 HG:+:1034373278:-1 HG:+:1043978188:-1 HG:+:1523082014:-1 HG:+:1551694379:-1 HG:+:1697921991:-1 HG:+:1904692345:-1 HG:+:2045350263:-1 HG:+:2548472713:-1 HG:+:2821815025:-1 HG:+:2880412632:-1 HG:+:2893706628:-1 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:674744114:-1 HG:+:1810943532:-1 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:1318671997:55 HG:+:2968451238:-1 HG:+:2979948005:-1 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:1318671993:55 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:1318671981:55 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:1318671982:55 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:1318671983:55 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:1318671986:55 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:1318671987:55 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:1318671984:55 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:1318671985:55 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:880648908:-1 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:1801919231:-1 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:1318671991:55 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:1318671994:55 +TATTGGTAAATTGCCCAGTCTTGCATATGTCTTTATCAGCAGCATGAAAATGGGACTATACAAGTCCTGGTCATTCCTCTGGAGTGTGTAATATTCACGCCTAAGTCTCTCTGGCCTAAGTTAACATACGTGCTGCAAAGGTATCACCAAACTAATGTTGCTTCCCTTGTGCTGCAGTACTGTAACTTCTTTACATTTTATTTATATCCCAGTTGATTACTTCCTATTTTGTACCCCAATTATTCTTTTAACAATCGTAAGATATTTTTTGAAAAATCCACTACAATATTGTATAATTGCAGACACAACTTCTGTTTTGGGGTAATGTTTTAACCAATAGTAAATTTTTAAACTGAAAGTAAAACATAATGTAACTGAACTAAAATTAATGTGAAACTATAAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA HG:+:1318672000:55 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGAAGTTTTAAAAAATGGTTTAACCATACGTAAAGGAGGAAAAGGAAACAAAAACTAAAAAAGGGAGAAAAACAAACAGAAACAAAATAAAACCAAAAAAGGAGAAACAACAGAAACAACAAAATAAAACCCTGTCAAATTTTGAGCTTAATGTACCAATAGAGTACATTTAAACTGTAAAGGGTCTAAATAGAATAGGTTAAAGACAGGAGATTGGCAGTGTGGATTAAAAATATCGACCCAATTATGTTGCTCTCTGTAACAAACAAACAAAAGCCCATAGGAAGATTGAAAGTAAAAAGTGTGATAAAAGATATATTATGACAAACATTTATTTAAAAAGAAAGCACATGTGGCTATATTATATAAACCATACAATAGACCCCAGAGCAAGGAAAAATTA HG:+:478299687:57 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGAAGTTTTAAAAAATGGTTTAACCATACGTAAAGGAGGAAAAGGAAACAAAAACTAAAAAAGGGAGAAAAACAAACAGAAACAAAATAAAACCAAAAAAGGAGAAACAACAGAAACAACAAAATAAAACCCTGTCAAATTTTGAGCTTAATGTACCAATAGAGTACATTTAAACTGTAAAGGGTCTAAATAGAATAGGTTAAAGACAGGAGATTGGCAGTGTGGATTAAAAATATCGACCCAATTATGTTGCTCTCTGTAACAAACAAACAAAAGCCCATAGGAAGATTGAAAGTAAAAAGTGTGATAAAAGATATATTATGACAAACATTTATTTAAAAAGAAAGCACATGTGGCTATATTATATAAACCATACAATAGACCCCAGAGCAAGGAAAAATTA HG:+:73713570:-1 HG:+:436925677:-1 HG:+:478299697:57 HG:+:483946814:-1 HG:+:710991582:-1 HG:+:710991616:-1 HG:+:778196130:-1 HG:+:1380064734:-1 HG:+:1412255567:-1 HG:+:2247740508:-1 HG:+:2260098123:-1 HG:+:2501356466:-1 HG:+:2601341724:-1 HG:+:2975540010:-1 HG:+:2988058727:-1 HG:+:2989228710:-1 HG:+:3003228142:-1 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGAAGTTTTAAAAAATGGTTTAACCATACGTAAAGGAGGAAAAGGAAACAAAAACTAAAAAAGGGAGAAAAACAAACAGAAACAAAATAAAACCAAAAAAGGAGAAACAACAGAAACAACAAAATAAAACCCTGTCAAATTTTGAGCTTAATGTACCAATAGAGTACATTTAAACTGTAAAGGGTCTAAATAGAATAGGTTAAAGACAGGAGATTGGCAGTGTGGATTAAAAATATCGACCCAATTATGTTGCTCTCTGTAACAAACAAACAAAAGCCCATAGGAAGATTGAAAGTAAAAAGTGTGATAAAAGATATATTATGACAAACATTTATTTAAAAAGAAAGCACATGTGGCTATATTATATAAACCATACAATAGACCCCAGAGCAAGGAAAAATTA HG:+:478299682:57 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGAAGTTTTAAAAAATGGTTTAACCATACGTAAAGGAGGAAAAGGAAACAAAAACTAAAAAAGGGAGAAAAACAAACAGAAACAAAATAAAACCAAAAAAGGAGAAACAACAGAAACAACAAAATAAAACCCTGTCAAATTTTGAGCTTAATGTACCAATAGAGTACATTTAAACTGTAAAGGGTCTAAATAGAATAGGTTAAAGACAGGAGATTGGCAGTGTGGATTAAAAATATCGACCCAATTATGTTGCTCTCTGTAACAAACAAACAAAAGCCCATAGGAAGATTGAAAGTAAAAAGTGTGATAAAAGATATATTATGACAAACATTTATTTAAAAAGAAAGCACATGTGGCTATATTATATAAACCATACAATAGACCCCAGAGCAAGGAAAAATTA HG:+:620369649:-1 HG:+:925199116:-1 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGAAGTTTTAAAAAATGGTTTAACCATACGTAAAGGAGGAAAAGGAAACAAAAACTAAAAAAGGGAGAAAAACAAACAGAAACAAAATAAAACCAAAAAAGGAGAAACAACAGAAACAACAAAATAAAACCCTGTCAAATTTTGAGCTTAATGTACCAATAGAGTACATTTAAACTGTAAAGGGTCTAAATAGAATAGGTTAAAGACAGGAGATTGGCAGTGTGGATTAAAAATATCGACCCAATTATGTTGCTCTCTGTAACAAACAAACAAAAGCCCATAGGAAGATTGAAAGTAAAAAGTGTGATAAAAGATATATTATGACAAACATTTATTTAAAAAGAAAGCACATGTGGCTATATTATATAAACCATACAATAGACCCCAGAGCAAGGAAAAATTA HG:+:478299689:57 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGAAGTTTTAAAAAATGGTTTAACCATACGTAAAGGAGGAAAAGGAAACAAAAACTAAAAAAGGGAGAAAAACAAACAGAAACAAAATAAAACCAAAAAAGGAGAAACAACAGAAACAACAAAATAAAACCCTGTCAAATTTTGAGCTTAATGTACCAATAGAGTACATTTAAACTGTAAAGGGTCTAAATAGAATAGGTTAAAGACAGGAGATTGGCAGTGTGGATTAAAAATATCGACCCAATTATGTTGCTCTCTGTAACAAACAAACAAAAGCCCATAGGAAGATTGAAAGTAAAAAGTGTGATAAAAGATATATTATGACAAACATTTATTTAAAAAGAAAGCACATGTGGCTATATTATATAAACCATACAATAGACCCCAGAGCAAGGAAAAATTA HG:+:1864937414:-1 diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-100nt.prof b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-100nt.prof new file mode 100644 index 0000000000000000000000000000000000000000..fe27fd30b23bc6f9b9c5182c8beee7e26d173063 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-100nt.prof @@ -0,0 +1,1000 @@ +NCAAAAAATAGATGAGGAGGGAATACTTTCAAACTCATTCTATGTGGCCAGCATTACACTGATACCAAAACCAGACAAAGTCACATCAGAAAAAGACTAT chr1:+:520962678:13 chr1:+:579189473:17 chr1:+:983608085:11 chr1:+:984468852:14 chr1:+:1155857153:16 chr1:+:1453619708:19 chr1:+:1475274180:19 chr1:+:1822204695:16 chr1:+:2369888652:19 chr1:+:2396498556:-1 chr1:+:2918216833:18 chr1:+:2970805204:18 chr1:+:3040266577:17 +NCAAAAAATAGATGAGGAGGGAATACTTTCAAACTCATTCTATGTGGCCAGCATTACACTGATACCAAAACCAGACAAAGTCACATCAGAAAAAGACTAT chr1:+:14744058:-1 chr1:+:28018565:-1 chr1:+:236208503:-1 chr1:+:350705102:-1 chr1:+:478975175:-1 chr1:+:580301754:-1 chr1:+:707381470:-1 chr1:+:716498103:-1 chr1:+:757040352:-1 chr1:+:881021518:-1 chr1:+:932850417:-1 chr1:+:935272051:-1 chr1:+:989476397:-1 chr1:+:1326225405:-1 chr1:+:1422447657:-1 chr1:+:1458762517:-1 chr1:+:1674328130:-1 chr1:+:1805929785:-1 chr1:+:1877903572:-1 chr1:+:1894124675:-1 chr1:+:2011336245:-1 chr1:+:2044914465:-1 chr1:+:2053623439:-1 chr1:+:2105018645:-1 chr1:+:2193002057:-1 chr1:+:2280933640:-1 chr1:+:2652877477:-1 chr1:+:2655554071:-1 chr1:+:2896447991:-1 chr1:+:2965734771:-1 chr1:+:3011893290:-1 +NCAAAAAATAGATGAGGAGGGAATACTTTCAAACTCATTCTATGTGGCCAGCATTACACTGATACCAAAACCAGACAAAGTCACATCAGAAAAAGACTAT chr1:+:379238326:-1 chr1:+:564103418:-1 chr1:+:707593082:-1 chr1:+:772155209:-1 chr1:+:1100891190:-1 chr1:+:1183575920:-1 chr1:+:1543032880:-1 chr1:+:1613270350:-1 chr1:+:1619556082:-1 chr1:+:1621989787:-1 chr1:+:2164144705:-1 chr1:+:2369333128:-1 chr1:+:2464657225:-1 chr1:+:2808902608:-1 chr1:+:2959151241:-1 chr1:+:3014527324:-1 +NCAAAAAATAGATGAGGAGGGAATACTTTCAAACTCATTCTATGTGGCCAGCATTACACTGATACCAAAACCAGACAAAGTCACATCAGAAAAAGACTAT chr1:+:93779982:-1 chr1:+:105149034:-1 chr1:+:248882566:-1 chr1:+:794565636:-1 chr1:+:923125394:-1 chr1:+:999776191:-1 chr1:+:1010380184:-1 chr1:+:1019263924:-1 chr1:+:1131805703:-1 chr1:+:2169110725:-1 chr1:+:2371842381:-1 chr1:+:2649152832:-1 chr1:+:2910700589:-1 chr1:+:2948289946:-1 +NCAAAAAATAGATGAGGAGGGAATACTTTCAAACTCATTCTATGTGGCCAGCATTACACTGATACCAAAACCAGACAAAGTCACATCAGAAAAAGACTAT chr1:+:154084197:-1 chr1:+:416898147:-1 chr1:+:482528237:-1 chr1:+:576717011:-1 chr1:+:786745048:-1 chr1:+:798502357:-1 chr1:+:806313290:-1 chr1:+:981139456:-1 chr1:+:1109878223:-1 chr1:+:1144291156:-1 chr1:+:1232546593:-1 chr1:+:1330993055:-1 chr1:+:1495622014:-1 chr1:+:1544385008:-1 chr1:+:1830440686:-1 chr1:+:1848795838:-1 chr1:+:2733872360:20 chr1:+:2959718999:-1 chr1:+:2993356254:-1 +ATAGTCTTTTTCTGATGTGACTTTGTCTGGTTTTGGTATCAGTGTAATGCTGGCCACATAGAATGAGTTTGAAAGTATTCCCTCCTCATCTATTTTTTGN chr1:+:2008252857:1 +GTTCCAGATCTTAGAAGAAAGGCTTTCAGTTTTTCCCCATTCAGTATGATACTAGCTGTTGGCCTGTTGTATATGGCTTTTATTATCTTGAGATTAGTGT chr1:+:63851539:12 chr1:+:403046114:16 chr1:+:520439118:11 chr1:+:533539444:13 chr1:+:588849966:12 chr1:+:727979019:13 chr1:+:934319127:11 chr1:+:1148426880:12 chr1:+:1771909591:9 chr1:+:1855467755:15 chr1:+:1915180743:13 chr1:+:1924916725:13 chr1:+:2008252476:0 chr1:+:2121741269:12 chr1:+:2260798537:20 chr1:+:2953070573:13 chr1:+:2982531372:10 chr1:+:2997521835:10 chr1:+:3001239890:10 chr1:+:3009341821:11 chr1:+:3022685893:12 +ATTCAACTAACAGAGATGAACCTTTCTTTTTACAGAGCAGTTTTGAAACACTCTTTTTGTGGAATCTGAAAGTGGATATTTGGATAGCTTTGAGGATTTN chr1:+:341527246:13 chr1:+:341533565:16 chr1:+:341556242:12 chr1:+:341557939:9 chr1:+:341559641:9 chr1:+:341560317:8 chr1:+:341560997:10 chr1:+:341563542:11 chr1:+:341564222:10 chr1:+:341566767:11 chr1:+:341567785:10 chr1:+:341569825:10 chr1:+:341570505:9 chr1:+:341572207:9 chr1:+:341572545:14 chr1:+:341574243:10 chr1:+:341574923:9 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chr1:+:1916302057:-1 chr1:+:2150644307:-1 chr1:+:2263122026:-1 chr1:+:2293675710:-1 chr1:+:2401691574:-1 chr1:+:2416857224:-1 chr1:+:2543141695:-1 chr1:+:2667511764:-1 chr1:+:2726490678:-1 chr1:+:2726692168:-1 chr1:+:2730349779:-1 chr1:+:2748400135:-1 chr1:+:2748402510:-1 chr1:+:2757360534:-1 chr1:+:2757837770:-1 chr1:+:2781459795:-1 chr1:+:2792375377:-1 chr1:+:2792390815:-1 chr1:+:2792398839:-1 chr1:+:2792410370:-1 chr1:+:2809822570:-1 chr1:+:2825701049:-1 chr1:+:2878027716:-1 chr1:+:2881661570:-1 chr1:+:2918332691:-1 chr1:+:2919846237:-1 chr1:+:2992640533:-1 chr1:+:3049966295:-1 chr1:+:3049996613:-1 chr1:+:3050014555:-1 chr1:+:3050020186:-1 chr1:+:3050025793:-1 chr1:+:3050031390:-1 chr1:+:3050037002:-1 chr1:+:3050042608:-1 chr1:+:3050048215:-1 chr1:+:3050128485:-1 chr1:+:3050132065:-1 chr1:+:3050163983:-1 chr1:+:3065118742:-1 +TAATGAACTCGAATGTAATTGACTGGAATGGAATGTACATGAATGGAATGTAATCGAATGCAAAGTAATCCAATGGAATAGAATCTAATGCAATAAAATC chr1:+:724307:-1 chr1:+:224199612:-1 chr1:+:740132241:-1 chr1:+:1042165470:-1 chr1:+:1719147397:-1 chr1:+:1719154253:-1 chr1:+:1719162619:-1 chr1:+:1719162888:-1 chr1:+:1719165118:-1 chr1:+:1719166046:-1 chr1:+:1719171455:-1 chr1:+:1719178199:-1 chr1:+:1719182817:-1 chr1:+:1719244574:-1 chr1:+:1719244629:-1 chr1:+:1719492804:-1 chr1:+:1719505175:-1 chr1:+:1719523527:-1 chr1:+:2470962087:-1 chr1:+:2748388097:-1 chr1:+:2748392561:-1 chr1:+:2792414480:-1 chr1:+:2792429741:-1 chr1:+:2792429771:-1 chr1:+:2792435281:-1 chr1:+:2792451048:-1 chr1:+:2792451468:-1 chr1:+:2792457010:-1 chr1:+:3050134866:-1 chr1:+:3050154793:-1 chr1:+:3101239721:-1 chr1:+:3101246560:-1 chr1:+:3101246585:-1 +TAATGAACTCGAATGTAATTGACTGGAATGGAATGTACATGAATGGAATGTAATCGAATGCAAAGTAATCCAATGGAATAGAATCTAATGCAATAAAATC chr1:+:106966592:-1 chr1:+:170087988:-1 chr1:+:210171862:-1 chr1:+:263392455:-1 chr1:+:353969177:-1 chr1:+:461672177:-1 chr1:+:480492121:-1 chr1:+:514263285:-1 chr1:+:608504274:-1 chr1:+:636110064:-1 chr1:+:638085015:-1 chr1:+:702477309:-1 chr1:+:747176427:-1 chr1:+:761620842:-1 chr1:+:762147855:-1 chr1:+:1011355957:-1 chr1:+:1034111350:-1 chr1:+:1140632357:-1 chr1:+:1141022247:-1 chr1:+:1159252205:-1 chr1:+:1215434199:-1 chr1:+:1272335977:-1 chr1:+:1295407074:-1 chr1:+:1295415032:-1 chr1:+:1295447829:-1 chr1:+:1323313380:-1 chr1:+:1412434751:-1 chr1:+:1430980988:-1 chr1:+:1445522195:-1 chr1:+:1451416346:-1 chr1:+:1499791558:-1 chr1:+:1554131418:-1 chr1:+:1694707356:-1 chr1:+:1719493771:-1 chr1:+:1728838902:-1 chr1:+:1744609937:-1 chr1:+:1901119923:-1 chr1:+:1998056613:-1 chr1:+:2031468006:-1 chr1:+:2049871672:-1 chr1:+:2121727100:-1 chr1:+:2146463110:-1 chr1:+:2172100525:-1 chr1:+:2283837871:-1 chr1:+:2389028919:-1 chr1:+:2443701916:-1 chr1:+:2443702807:-1 chr1:+:2443702833:-1 chr1:+:2465415439:-1 chr1:+:2587442322:-1 chr1:+:2792760171:-1 chr1:+:2807696491:-1 chr1:+:2816714626:-1 chr1:+:2847238454:-1 chr1:+:3010745897:-1 chr1:+:3050131378:-1 chr1:+:3050152539:-1 chr1:+:3050152783:-1 chr1:+:3065104969:-1 chr1:+:3100119706:-1 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chr1:+:48132236:-1 chr1:+:518157257:-1 chr1:+:523270852:-1 chr1:+:825052248:-1 chr1:+:1153956071:-1 chr1:+:1176970958:-1 chr1:+:1243377928:-1 chr1:+:1656027518:-1 chr1:+:1684675591:-1 chr1:+:1798679762:-1 chr1:+:1991451706:-1 chr1:+:2179575401:-1 chr1:+:2255961463:-1 chr1:+:2364405796:-1 chr1:+:2648084389:-1 +NGTGTTGATCAGACTAAGAAACAATATGTCAATTTCAGTTAAAAACGAAGAAATGTGTCCAATAAAGTATATACAGAGCTACACAGTGTAATTCAACTCA chr1:+:185960837:-1 chr1:+:194935937:-1 chr1:+:638638707:-1 chr1:+:857673812:-1 chr1:+:878470195:-1 chr1:+:886733497:-1 chr1:+:1007876041:-1 chr1:+:1312563801:-1 chr1:+:1325115449:-1 chr1:+:1471943020:-1 chr1:+:1684853372:-1 chr1:+:1864359386:-1 chr1:+:2934336140:-1 chr1:+:2991674919:-1 +TGAGTTGAATTACACTGTGTAGCTCTGTATATACTTTATTGGACACATTTCTTCGTTTTTAACTGAAATTGACATATTGTTTCTTAGTCTGATCAACACN chr1:+:1838373464:1 +ATGGCATTGTTTATTAAGTTGCATGCCCCTGATGAACAGCTTCTTCATGTGCCAAGTGGCCACTTATATATCCTTTTCTGTCACATATCTGTTTAGTACC chr1:+:1838373108:0 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chr1:+:2256256047:-1 chr1:+:2266213811:-1 chr1:+:2402477390:-1 chr1:+:2404129441:-1 chr1:+:2434842898:-1 chr1:+:2553927329:-1 chr1:+:2568742458:-1 chr1:+:2687772289:-1 chr1:+:2914773702:-1 chr1:+:3004710303:-1 +TACAGAAGTGGCCAATGGCAGCAGAATCCTTCTCTGAATGGACGGCTGAATACAGCACAGGCAACCAGGAAGCAATGTCTATTCCTAATTTCCAAATGTC chr1:+:176425748:-1 chr1:+:429651925:-1 chr1:+:514622741:-1 chr1:+:680106414:-1 chr1:+:723854716:-1 chr1:+:999005600:-1 chr1:+:1012087143:-1 chr1:+:1178806545:-1 chr1:+:1271443172:-1 chr1:+:1472111343:-1 chr1:+:1539557629:-1 chr1:+:1546355665:-1 chr1:+:1625100652:-1 chr1:+:1757177780:-1 chr1:+:1765998373:-1 chr1:+:2127298794:-1 chr1:+:2132827223:-1 chr1:+:2178849745:-1 chr1:+:2187452265:-1 chr1:+:2243485671:-1 chr1:+:2297455112:-1 chr1:+:2538636951:-1 chr1:+:2585287693:-1 chr1:+:2822942502:-1 +GACATTTGGAAATTAGGAATAGACATTGCTTCCTGGTTGCCTGTGCTGTATTCAGCCGTCCATTCAGAGAAGGATTCTGCTGCCATTGGCCACTTCTGTA chr1:+:1524695062:0 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chr1:+:2122614607:-1 chr1:+:2266424395:-1 chr1:+:2688119660:-1 +AGAGAAGGAACCTCATACAGGCTGTTTTTGCTTAGCTCAAGCATTTATGAAAACAATGGCAATTCAAGCAAAAAGATCAAAAACTAATTGCCTGGTGGTT chr1:+:46266727:-1 chr1:+:485386158:-1 chr1:+:530806171:-1 chr1:+:886360990:-1 chr1:+:984331557:-1 chr1:+:1064113786:-1 chr1:+:1717007040:-1 chr1:+:1876020138:-1 chr1:+:1876368622:-1 chr1:+:2115073936:-1 chr1:+:2148615087:-1 chr1:+:2412735137:-1 chr1:+:2564530371:-1 +AACCACCAGGCAATTAGTTTTTGATCTTTTTGCTTGAATTGCCATTGTTTTCATAAATGCTTGAGCTAAGCAAAAACAGCCTGTATGAGGTTCCTTCTCT chr1:+:1246667215:0 +GTCCTCCCCCTACCTTCCCAAATTTGATCCTGTCAGTCCTCTGCTTAAAACCATTCATATCATCACATCTACACTTAGGACAAAGCACAAAGTCTCTGCA chr1:+:85355629:-1 chr1:+:1116191605:-1 chr1:+:1266013145:-1 +GTCCTCCCCCTACCTTCCCAAATTTGATCCTGTCAGTCCTCTGCTTAAAACCATTCATATCATCACATCTACACTTAGGACAAAGCACAAAGTCTCTGCA chr1:+:33590871:-1 chr1:+:162301715:-1 chr1:+:164031582:-1 chr1:+:200345698:-1 chr1:+:209809083:-1 chr1:+:217168665:-1 chr1:+:260641587:-1 chr1:+:283865852:-1 chr1:+:288912990:-1 chr1:+:484143951:-1 chr1:+:497065133:-1 chr1:+:650391413:-1 chr1:+:667335064:-1 chr1:+:679787058:-1 chr1:+:773541281:-1 chr1:+:795616863:-1 chr1:+:811296033:-1 chr1:+:819011628:-1 chr1:+:949481366:-1 chr1:+:985004992:-1 chr1:+:1015725604:-1 chr1:+:1128575643:-1 chr1:+:1572455902:-1 chr1:+:1613044661:-1 chr1:+:1664020750:-1 chr1:+:1743143217:-1 chr1:+:1859431287:-1 chr1:+:1907420076:-1 chr1:+:1911494445:-1 chr1:+:1914955417:-1 chr1:+:1940476970:-1 chr1:+:2236885575:-1 chr1:+:2271096681:-1 chr1:+:2391045901:-1 chr1:+:2484603246:-1 chr1:+:2532108081:-1 chr1:+:2583802703:-1 chr1:+:2813164374:-1 chr1:+:2952462861:-1 chr1:+:3031236362:-1 chr1:+:3034005631:-1 +GTCCTCCCCCTACCTTCCCAAATTTGATCCTGTCAGTCCTCTGCTTAAAACCATTCATATCATCACATCTACACTTAGGACAAAGCACAAAGTCTCTGCA chr1:+:70289454:-1 chr1:+:88547846:-1 chr1:+:89612749:-1 chr1:+:251380115:-1 chr1:+:262403842:-1 chr1:+:357340374:-1 chr1:+:361566550:-1 chr1:+:391021780:-1 chr1:+:555261301:-1 chr1:+:878694790:-1 chr1:+:1136343918:-1 chr1:+:1178354984:-1 chr1:+:1241520987:-1 chr1:+:1270664759:-1 chr1:+:1431406197:-1 chr1:+:1558182731:-1 chr1:+:2247778689:-1 chr1:+:2356084820:-1 chr1:+:2470058519:-1 chr1:+:2555773502:-1 chr1:+:2768287596:-1 +TGCAGAGACTTTGTGCTTTGTCCTAAGTGTAGATGTGATGATATGAATGGTTTTAAGCAGAGGACTGACAGGATCAAATTTGGGAAGGTAGGGGGAGGAC chr1:+:466394708:0 +CCCTGTGGAGCTTATAGTCTAGGGAACTTAGACAACAATATAATTATTCGAACCTGCAATTTATCAAGGGTAAATCAGGGAGGAACATGGCACAGTGAGA chr1:+:466394351:0 +ATCTGAGACAAGGCAAGTCCCTTCCACTTATGAGCCTGTAAAATCAAAAGCAAGCTGGTTACTTCCTAGATACAATGGGGGTACAGGTATTGGGTAAATA chr1:+:68861128:-1 chr1:+:104958762:8 chr1:+:117700385:7 chr1:+:208689609:6 chr1:+:238708810:5 chr1:+:262363655:9 chr1:+:324383585:5 chr1:+:355038721:4 chr1:+:381944198:4 chr1:+:408134325:0 chr1:+:432490604:6 chr1:+:453619045:6 chr1:+:471172092:10 chr1:+:507234610:8 chr1:+:592163920:4 chr1:+:595023377:7 chr1:+:625267371:4 chr1:+:632944124:11 chr1:+:672174825:7 chr1:+:675335926:11 chr1:+:763550587:6 chr1:+:764677226:5 chr1:+:801611270:5 chr1:+:828080503:7 chr1:+:840030435:6 chr1:+:848932221:7 chr1:+:858893780:5 chr1:+:886376826:10 chr1:+:908706119:3 chr1:+:933005155:9 chr1:+:975334246:8 chr1:+:983555185:5 chr1:+:986993866:6 chr1:+:999445448:8 chr1:+:1012007706:8 chr1:+:1036077787:11 chr1:+:1149969974:6 chr1:+:1198624860:6 chr1:+:1232550865:8 chr1:+:1268579234:5 chr1:+:1318934520:6 chr1:+:1450658769:7 chr1:+:1458674965:7 chr1:+:1462434971:8 chr1:+:1467932784:4 chr1:+:1490601588:7 chr1:+:1556353007:5 chr1:+:1622305525:8 chr1:+:1632741824:4 chr1:+:1635893398:5 chr1:+:1705426447:6 chr1:+:1805188246:4 chr1:+:1805469366:5 chr1:+:1835540854:5 chr1:+:1837732709:10 chr1:+:1896191829:8 chr1:+:1924937780:6 chr1:+:1929657667:8 chr1:+:1971962626:9 chr1:+:2113418166:4 chr1:+:2225142439:8 chr1:+:2230451614:15 chr1:+:2241205831:5 chr1:+:2253766558:9 chr1:+:2423169977:6 chr1:+:2587501505:8 chr1:+:2699030165:5 chr1:+:2728677581:8 chr1:+:2730149871:4 chr1:+:2731790522:5 chr1:+:2797831356:5 chr1:+:2800969135:6 chr1:+:2804748577:5 chr1:+:2888841351:8 chr1:+:2978884729:4 +TGTGGGGTCAGATCCCCCACACAGAGCCCCTACTGGGGTACCGTCTAGTGGAGCTATGAAAAGAGGGCCACCATCCTCCAGACTCCAGAATGGTAGATCC chr1:+:60202911:16 chr1:+:106474770:15 chr1:+:629041822:9 chr1:+:690827273:-1 chr1:+:1206779480:13 chr1:+:1503819104:17 chr1:+:1550215690:12 chr1:+:1747412296:14 chr1:+:1858142876:-1 chr1:+:2070619725:14 chr1:+:2607421307:18 chr1:+:2654957037:13 +TGTGGGGTCAGATCCCCCACACAGAGCCCCTACTGGGGTACCGTCTAGTGGAGCTATGAAAAGAGGGCCACCATCCTCCAGACTCCAGAATGGTAGATCC chr1:+:269233597:13 chr1:+:408087630:13 chr1:+:465970156:19 chr1:+:683147907:14 chr1:+:730881279:10 chr1:+:751954099:17 chr1:+:772691734:13 chr1:+:779420624:15 chr1:+:1070888730:19 chr1:+:1125866312:13 chr1:+:1155799456:12 chr1:+:1251340524:13 chr1:+:1317918763:14 chr1:+:1430748064:17 chr1:+:1484149068:13 chr1:+:1855851722:14 chr1:+:2014484878:14 chr1:+:2186496853:18 chr1:+:2829611307:14 chr1:+:3027157245:14 +TGTGGGGTCAGATCCCCCACACAGAGCCCCTACTGGGGTACCGTCTAGTGGAGCTATGAAAAGAGGGCCACCATCCTCCAGACTCCAGAATGGTAGATCC chr1:+:373140652:-1 chr1:+:922509578:12 chr1:+:2148441272:14 chr1:+:2772397756:16 chr1:+:2800987727:-1 chr1:+:3020724092:16 +TGTGGGGTCAGATCCCCCACACAGAGCCCCTACTGGGGTACCGTCTAGTGGAGCTATGAAAAGAGGGCCACCATCCTCCAGACTCCAGAATGGTAGATCC chr1:+:29327091:-1 chr1:+:335986786:-1 chr1:+:338625540:16 chr1:+:366172898:12 chr1:+:459002181:13 chr1:+:544272047:15 chr1:+:717891524:10 chr1:+:1820712139:13 chr1:+:2036512498:12 +TGTGGGGTCAGATCCCCCACACAGAGCCCCTACTGGGGTACCGTCTAGTGGAGCTATGAAAAGAGGGCCACCATCCTCCAGACTCCAGAATGGTAGATCC chr1:+:170176884:13 chr1:+:348188366:14 chr1:+:645014796:11 chr1:+:1856609243:11 chr1:+:1981331171:15 chr1:+:2050523504:13 chr1:+:2345225035:18 chr1:+:2345604948:10 +GGATCTACCATTCTGGAGTCTGGAGGATGGTGGCCCTCTTTTCATAGCTCCACTAGACGGTACCCCAGTAGGGGCTCTGTGTGGGGGATCTGACCCCACA chr1:+:60178030:14 chr1:+:88491301:12 chr1:+:231821891:12 chr1:+:408134703:0 chr1:+:769489912:10 chr1:+:898500254:15 chr1:+:1045180381:13 chr1:+:1198625238:12 chr1:+:1342147416:-1 chr1:+:2581496830:-1 chr1:+:2733571420:13 chr1:+:2801664083:16 +CACTGGTCAAGATGTACTGAGTACCCACTACATGTGAAGCACTTTAATAGGTACTATGAGAAAATAGATGAACAAACACTGGGGAAAAAAGGCCATTCAT chr1:+:2981026014:0 +TCCAGCAACTTCTTTGCACTCCCTTTGCACATATCCAGTGTTTCTAGCCTTTCTGTTTTTGCTTATGCTCTTCTTCTGCCTGGAATGCCTTTCCACCTTT chr1:+:23432469:-1 chr1:+:510644706:-1 chr1:+:513605029:-1 chr1:+:726588910:-1 chr1:+:750314783:-1 chr1:+:1391021456:-1 chr1:+:1497331693:-1 chr1:+:1686345082:-1 chr1:+:1709182401:-1 chr1:+:2189220308:-1 chr1:+:2934063675:-1 +TCCAGCAACTTCTTTGCACTCCCTTTGCACATATCCAGTGTTTCTAGCCTTTCTGTTTTTGCTTATGCTCTTCTTCTGCCTGGAATGCCTTTCCACCTTT chr1:+:70361293:-1 chr1:+:159472666:-1 chr1:+:166845740:-1 chr1:+:477897600:-1 chr1:+:498548977:-1 chr1:+:619944230:-1 chr1:+:627598522:-1 chr1:+:692336833:-1 chr1:+:710283403:-1 chr1:+:764036983:-1 chr1:+:787034086:-1 chr1:+:888288828:-1 chr1:+:920179781:-1 chr1:+:955579766:-1 chr1:+:1017187136:-1 chr1:+:1077366636:-1 chr1:+:1117442535:-1 chr1:+:1187479163:-1 chr1:+:1190589371:-1 chr1:+:1211863212:-1 chr1:+:1262242341:-1 chr1:+:1278476601:-1 chr1:+:1286870867:-1 chr1:+:1320904249:-1 chr1:+:1370782758:-1 chr1:+:1378508367:-1 chr1:+:1379953235:-1 chr1:+:1440521199:-1 chr1:+:1440525274:-1 chr1:+:1495787484:-1 chr1:+:1525971991:-1 chr1:+:1529864425:-1 chr1:+:1537163611:-1 chr1:+:1555437812:-1 chr1:+:1688984804:-1 chr1:+:1698223837:-1 chr1:+:1698470827:-1 chr1:+:1787201266:-1 chr1:+:1823677620:-1 chr1:+:1878273073:-1 chr1:+:1906166568:-1 chr1:+:1999078518:-1 chr1:+:2059332356:-1 chr1:+:2068530791:-1 chr1:+:2107451453:-1 chr1:+:2145043806:-1 chr1:+:2165912377:-1 chr1:+:2276053997:-1 chr1:+:2382590329:-1 chr1:+:2505610526:-1 chr1:+:2555573715:-1 chr1:+:2616335752:-1 chr1:+:2680595445:-1 chr1:+:2683086242:-1 chr1:+:2724040420:-1 chr1:+:2805033727:-1 chr1:+:2818346375:-1 chr1:+:2825571725:-1 chr1:+:2847824708:-1 chr1:+:2887582186:-1 chr1:+:3008666207:-1 chr1:+:3044202905:-1 chr1:+:3044485658:-1 chr1:+:3044494430:-1 chr1:+:3059544102:-1 chr1:+:3061456804:-1 chr1:+:3061486237:-1 chr1:+:3061521533:-1 chr1:+:3063090546:-1 chr1:+:3063119981:-1 chr1:+:3063155277:-1 +TCCAGCAACTTCTTTGCACTCCCTTTGCACATATCCAGTGTTTCTAGCCTTTCTGTTTTTGCTTATGCTCTTCTTCTGCCTGGAATGCCTTTCCACCTTT chr1:+:326807289:-1 chr1:+:328862406:-1 chr1:+:499200496:-1 chr1:+:1051554198:-1 chr1:+:1655418373:-1 chr1:+:1787914834:-1 chr1:+:2104319865:-1 chr1:+:2180363359:-1 chr1:+:3028376216:-1 +TCCAGCAACTTCTTTGCACTCCCTTTGCACATATCCAGTGTTTCTAGCCTTTCTGTTTTTGCTTATGCTCTTCTTCTGCCTGGAATGCCTTTCCACCTTT chr1:+:721315489:-1 chr1:+:1332112725:-1 chr1:+:1332112797:-1 chr1:+:1704792859:-1 chr1:+:2999694173:-1 +AAAGGTGGAAAGGCATTCCAGGCAGAAGAAGAGCATAAGCAAAAACAGAAAGGCTAGAAACACTGGATATGTGCAAAGGGAGTGCAAAGAAGTTGCTGGA chr1:+:1666752809:-1 chr1:+:2981026391:0 +AGGCCTCCCATGCCCAGGCCCCAGTGTTCAGTGACTCCTGCCTGCACTCCCACAGGGTCCCGGAAGTTCCCCCACTCAGCGGCATCTCTGCATGTGTCGG chr1:+:1813578147:0 +CTTGGAGACAAGACCTCACTGCTGAGTGCTGGTCCCCTCGCCAGGTACTCATTTGCTGGAATGTCCCCCACACAGGTGCAAAGAGCACAGTGACCAGGAG chr1:+:675578591:-1 chr1:+:2723727685:-1 +CTTGGAGACAAGACCTCACTGCTGAGTGCTGGTCCCCTCGCCAGGTACTCATTTGCTGGAATGTCCCCCACACAGGTGCAAAGAGCACAGTGACCAGGAG chr1:+:409219389:-1 chr1:+:1456478456:-1 +CTTGGAGACAAGACCTCACTGCTGAGTGCTGGTCCCCTCGCCAGGTACTCATTTGCTGGAATGTCCCCCACACAGGTGCAAAGAGCACAGTGACCAGGAG chr1:+:11852753:-1 chr1:+:13874819:-1 chr1:+:205521505:-1 chr1:+:397361187:-1 chr1:+:715223016:-1 chr1:+:784403862:-1 chr1:+:837115807:-1 chr1:+:1133386821:-1 chr1:+:1137910261:-1 chr1:+:1251799428:-1 chr1:+:1263568264:-1 chr1:+:1464881579:-1 chr1:+:1578421266:-1 chr1:+:1578950516:-1 chr1:+:1579764522:-1 chr1:+:1638071285:-1 chr1:+:1689456930:-1 chr1:+:1872309424:-1 chr1:+:3028992044:-1 +CTCCTGGTCACTGTGCTCTTTGCACCTGTGTGGGGGACATTCCAGCAAATGAGTACCTGGCGAGGGGACCAGCACTCAGCAGTGAGGTCTTGTCTCCAAG chr1:+:1813578499:0 +CCTAGGTGGAGCTAATTATAGTAAAGCTTTTTATTAAGTTTTTTTGTTTTTCAAAAATTTTGGAATCCGGCACTCTAGTTGGGCTATTTTTATAATAATA chr1:+:1213512337:0 +TTTGTATTTTTAGTAGCGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTTAGGTGATCTGCCCGCCTCGGCCTCCCAAAGTGCTG chr1:+:2870186096:6 +TTTGTATTTTTAGTAGCGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTTAGGTGATCTGCCCGCCTCGGCCTCCCAAAGTGCTG chr1:+:271746647:10 chr1:+:465802049:8 chr1:+:950070278:3 chr1:+:952514113:9 chr1:+:1239475551:2 chr1:+:1299691807:12 chr1:+:1349626072:3 chr1:+:1383271340:7 chr1:+:1463713873:6 chr1:+:1630275539:9 chr1:+:1702407823:6 chr1:+:2071423501:5 chr1:+:2235462914:4 chr1:+:2460024865:3 chr1:+:2769049297:4 chr1:+:2847433268:9 chr1:+:2915545551:6 +CAGCACTTTGGGAGGCCGAGGCGGGCAGATCACCTAAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCTGTCGCTACTAAAAATACAAA chr1:+:38425359:19 chr1:+:402168876:9 chr1:+:774131729:14 chr1:+:936943516:17 chr1:+:1213512702:0 chr1:+:1276952965:7 chr1:+:1795865154:15 chr1:+:1800876113:15 chr1:+:1902818021:7 chr1:+:1938829404:11 chr1:+:2071532553:9 chr1:+:2303750998:13 chr1:+:2469168397:10 chr1:+:2711492987:8 chr1:+:2755081970:13 chr1:+:2981655639:7 chr1:+:2992404902:10 +TGGATGGTAGGATAATGGGTGACTGTTATGTTCTGTCATCTTCTCTATATTTTCCAAATTTTCTACAATGAACCCAACTTTCATTTTTGTGATGCTGAAA chr1:+:118676996:-1 chr1:+:242021334:-1 chr1:+:840937308:-1 chr1:+:845935392:-1 chr1:+:1675806823:-1 chr1:+:1889669099:-1 chr1:+:1963747389:-1 chr1:+:1982225104:-1 chr1:+:2198926226:-1 +TGGATGGTAGGATAATGGGTGACTGTTATGTTCTGTCATCTTCTCTATATTTTCCAAATTTTCTACAATGAACCCAACTTTCATTTTTGTGATGCTGAAA chr1:+:68609564:-1 chr1:+:356933032:-1 chr1:+:431959777:-1 chr1:+:686601495:-1 chr1:+:961829082:-1 chr1:+:970342134:-1 chr1:+:1106151094:-1 chr1:+:1217034503:-1 chr1:+:1354910561:-1 chr1:+:1477235002:-1 chr1:+:1544472757:-1 chr1:+:1753817407:-1 chr1:+:1938848427:-1 chr1:+:2012026563:-1 chr1:+:2115023216:-1 chr1:+:2559279888:-1 chr1:+:2735403548:-1 chr1:+:2909934659:-1 chr1:+:2958872387:-1 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chr1:+:2429318121:-1 chr1:+:2431794319:-1 chr1:+:2464080302:-1 chr1:+:2474165042:-1 chr1:+:2538981384:-1 chr1:+:2706711731:-1 chr1:+:2732542192:-1 chr1:+:2856676767:-1 chr1:+:2894115229:-1 chr1:+:2901511729:-1 chr1:+:3014438741:-1 +CACCTGGTCTCTAGTGATCCTTCTGCCTAGGCCTCTCAAAGTGCTAGGATTACAGGTCTGAGCCACTGTGCCCAGCCCCTCCCCTCTTGAATGCTAGGAT chr1:+:178623069:-1 chr1:+:265494309:-1 chr1:+:295236033:-1 chr1:+:662892337:-1 chr1:+:1008566158:-1 chr1:+:1017587575:-1 chr1:+:1019737480:-1 chr1:+:1312967439:-1 chr1:+:1766493945:-1 chr1:+:1882804155:-1 chr1:+:1913042653:-1 chr1:+:2267451564:-1 chr1:+:2761237784:-1 chr1:+:2957600185:-1 +CACCTGGTCTCTAGTGATCCTTCTGCCTAGGCCTCTCAAAGTGCTAGGATTACAGGTCTGAGCCACTGTGCCCAGCCCCTCCCCTCTTGAATGCTAGGAT chr1:+:42349840:-1 chr1:+:118790857:-1 chr1:+:258725002:-1 chr1:+:267259552:-1 chr1:+:360895861:-1 chr1:+:398778433:-1 chr1:+:403727461:-1 chr1:+:427371113:-1 chr1:+:542219560:-1 chr1:+:601592968:-1 chr1:+:745706129:-1 chr1:+:748093507:-1 chr1:+:955953800:-1 chr1:+:1015242805:-1 chr1:+:1065620295:-1 chr1:+:1083078191:-1 chr1:+:1160311135:-1 chr1:+:1273366976:-1 chr1:+:1337050092:-1 chr1:+:1418733486:-1 chr1:+:1475603240:-1 chr1:+:1750542365:-1 chr1:+:1758409316:-1 chr1:+:1796331066:-1 chr1:+:1952415081:-1 chr1:+:2128176430:-1 chr1:+:2264302602:-1 chr1:+:2273127796:-1 chr1:+:2290032729:-1 chr1:+:2291924477:-1 chr1:+:2335750516:-1 chr1:+:2372134254:-1 chr1:+:2418254272:-1 chr1:+:2425659790:-1 chr1:+:2491013498:-1 chr1:+:2534103990:-1 chr1:+:2536188517:-1 chr1:+:2549793710:-1 chr1:+:2573777014:-1 chr1:+:2667688440:-1 chr1:+:2676472675:-1 chr1:+:2714012241:-1 chr1:+:2791744064:-1 chr1:+:3059923130:-1 +CACCTGGTCTCTAGTGATCCTTCTGCCTAGGCCTCTCAAAGTGCTAGGATTACAGGTCTGAGCCACTGTGCCCAGCCCCTCCCCTCTTGAATGCTAGGAT chr1:+:32678119:-1 chr1:+:258631199:-1 chr1:+:381046628:-1 chr1:+:542656987:-1 chr1:+:1308364120:-1 chr1:+:1308578385:-1 chr1:+:1308606407:-1 chr1:+:1308634428:-1 chr1:+:1333579820:-1 chr1:+:1391466980:-1 chr1:+:1951542175:-1 chr1:+:2197853672:-1 chr1:+:2299725652:-1 chr1:+:2467618902:20 chr1:+:2497534224:-1 chr1:+:2713793024:-1 +ATCCTAGCATTCAAGAGGGGAGGGGCTGGGCACAGTGGCTCAGACCTGTAATCCTAGCACTTTGAGAGGCCTAGGCAGAAGGATCACTAGAGACCAGGTG chr1:+:1856766955:0 +TCATCTATGCACTTATGAATTAAAGGTCTTATTTTTTGATGCTTGCTCACCTGTCTAGGCAGTTGTGACCTGAAATTTGATAACTTCTGTACTAGTTAAT chr1:+:1856766553:0 +GAGCAAATCCTCCAGGAAATACGGGACTATGTGAAAAGACCAAATCTACATCTGTTTGGTGTATCTGAAAATGATGGGGAGAATGGAACCAAGTTGGAAC chr1:+:303066093:9 chr1:+:490735847:10 chr1:+:582458284:8 chr1:+:589811577:8 chr1:+:649893790:8 chr1:+:687259698:7 chr1:+:1495519638:13 chr1:+:2011256277:10 chr1:+:2327803306:7 chr1:+:2331246248:9 chr1:+:2463249225:9 chr1:+:2689069264:10 chr1:+:2993964448:7 +GAGCAAATCCTCCAGGAAATACGGGACTATGTGAAAAGACCAAATCTACATCTGTTTGGTGTATCTGAAAATGATGGGGAGAATGGAACCAAGTTGGAAC chr1:+:34559308:9 chr1:+:34717654:8 chr1:+:66119106:12 chr1:+:106490081:9 chr1:+:217612008:13 chr1:+:379578482:10 chr1:+:409464553:16 chr1:+:459605087:14 chr1:+:462992483:11 chr1:+:556170293:9 chr1:+:557490834:11 chr1:+:580682537:13 chr1:+:624776412:15 chr1:+:627774499:9 chr1:+:705194228:13 chr1:+:709535641:15 chr1:+:749107658:12 chr1:+:763335640:14 chr1:+:763933296:10 chr1:+:780265170:12 chr1:+:991993565:9 chr1:+:1127565185:15 chr1:+:1129884121:8 chr1:+:1142830775:9 chr1:+:1189590797:10 chr1:+:1336803510:15 chr1:+:1364658693:12 chr1:+:1409324623:7 chr1:+:1491339546:11 chr1:+:1531925409:9 chr1:+:1664682442:8 chr1:+:1708250833:10 chr1:+:1790638729:12 chr1:+:1876227161:12 chr1:+:1907217774:11 chr1:+:2256265959:7 chr1:+:2443269789:16 chr1:+:2721056212:9 chr1:+:2743815869:13 chr1:+:2938331924:14 chr1:+:2946600526:11 chr1:+:2956068752:13 chr1:+:2966292001:13 chr1:+:3026235113:17 +GAGCAAATCCTCCAGGAAATACGGGACTATGTGAAAAGACCAAATCTACATCTGTTTGGTGTATCTGAAAATGATGGGGAGAATGGAACCAAGTTGGAAC chr1:+:629582754:10 chr1:+:1735245596:15 +GAGCAAATCCTCCAGGAAATACGGGACTATGTGAAAAGACCAAATCTACATCTGTTTGGTGTATCTGAAAATGATGGGGAGAATGGAACCAAGTTGGAAC chr1:+:116725089:-1 chr1:+:192255906:-1 chr1:+:351735342:-1 chr1:+:1044102093:-1 chr1:+:1137170627:14 chr1:+:1193210631:9 chr1:+:1204430515:8 chr1:+:1268512010:14 chr1:+:1512964849:-1 chr1:+:1718429144:9 chr1:+:1737505630:-1 chr1:+:1844572143:15 chr1:+:1932217601:-1 chr1:+:2259328086:-1 chr1:+:2356647914:15 chr1:+:2472972278:9 chr1:+:3009967442:-1 +GTTCCAACTTGGTTCCATTCTCCCCATCATTTTCAGATACACCAAACAGATGTAGATTTGGTCTTTTCACATAGTCCCGTATTTCCTGGAGGATTTGCTC chr1:+:166397269:17 chr1:+:186230305:8 chr1:+:551795097:8 chr1:+:644539658:13 chr1:+:679075860:11 chr1:+:743327573:9 chr1:+:934775793:13 chr1:+:947143997:8 chr1:+:982677235:13 chr1:+:1181684817:15 chr1:+:1244062960:14 chr1:+:1547243743:10 chr1:+:2024810792:11 chr1:+:2104558582:12 chr1:+:2256421489:8 chr1:+:2819286365:12 chr1:+:2936910057:11 chr1:+:2977871035:8 +GTTCCAACTTGGTTCCATTCTCCCCATCATTTTCAGATACACCAAACAGATGTAGATTTGGTCTTTTCACATAGTCCCGTATTTCCTGGAGGATTTGCTC chr1:+:78859101:-1 chr1:+:115331513:15 chr1:+:185225488:7 chr1:+:402561658:-1 chr1:+:784987205:7 chr1:+:1272815572:-1 chr1:+:1478176644:6 chr1:+:1687544497:-1 chr1:+:1787456083:6 chr1:+:1861499770:-1 chr1:+:1978152828:-1 chr1:+:2105382573:-1 chr1:+:2950035623:-1 chr1:+:3097019736:7 +GTTCCAACTTGGTTCCATTCTCCCCATCATTTTCAGATACACCAAACAGATGTAGATTTGGTCTTTTCACATAGTCCCGTATTTCCTGGAGGATTTGCTC chr1:+:87094598:10 chr1:+:152408266:8 chr1:+:238204990:12 chr1:+:241063161:12 chr1:+:300841026:10 chr1:+:305619466:12 chr1:+:345173016:11 chr1:+:364025747:11 chr1:+:389697391:-1 chr1:+:412334512:-1 chr1:+:416814437:13 chr1:+:495162843:10 chr1:+:519753892:11 chr1:+:528291793:-1 chr1:+:563295125:11 chr1:+:600530291:-1 chr1:+:613146961:12 chr1:+:731749437:11 chr1:+:769510985:13 chr1:+:781551024:11 chr1:+:855117175:7 chr1:+:891386231:-1 chr1:+:998078762:9 chr1:+:1012099894:11 chr1:+:1117717444:10 chr1:+:1120495212:10 chr1:+:1146008852:11 chr1:+:1171842730:13 chr1:+:1180666391:15 chr1:+:1260703661:10 chr1:+:1267103648:8 chr1:+:1267222963:8 chr1:+:1412137349:-1 chr1:+:1499601579:9 chr1:+:1700958059:10 chr1:+:1705913961:9 chr1:+:1713303298:13 chr1:+:1734078938:13 chr1:+:1777196114:12 chr1:+:1822882431:13 chr1:+:1834056783:11 chr1:+:1866065403:10 chr1:+:1875024108:9 chr1:+:1994032598:12 chr1:+:2010017116:11 chr1:+:2080441079:11 chr1:+:2280652784:12 chr1:+:2359754844:-1 chr1:+:2396387767:11 chr1:+:2687282664:10 chr1:+:2703771537:-1 chr1:+:2773053181:8 chr1:+:2937389286:10 chr1:+:2953896564:9 chr1:+:2984954642:8 chr1:+:2996215890:9 chr1:+:3006357068:8 chr1:+:3006401305:7 chr1:+:3030272202:12 chr1:+:3039203308:12 chr1:+:3046252983:10 +GTTCCAACTTGGTTCCATTCTCCCCATCATTTTCAGATACACCAAACAGATGTAGATTTGGTCTTTTCACATAGTCCCGTATTTCCTGGAGGATTTGCTC chr1:+:175976060:7 chr1:+:177645514:12 chr1:+:440007154:13 chr1:+:994377739:10 chr1:+:1149308067:9 chr1:+:1393334347:12 chr1:+:1450519401:10 chr1:+:1712380321:9 chr1:+:2649138373:11 +TTCTGTGAAGTATTTTATTTATCCTTCACTTAGGAAGCTTAGTTTGGCTGGATATGAAATTCTGGGTTGAAAATTCTTTTCTTTAAGAATGTTGAATATT chr1:+:193988710:5 chr1:+:285380774:6 chr1:+:305270076:3 chr1:+:329574958:6 chr1:+:347146200:4 chr1:+:374605545:3 chr1:+:384662943:3 chr1:+:403119111:3 chr1:+:403362806:3 chr1:+:415843003:4 chr1:+:521601797:3 chr1:+:614214964:4 chr1:+:633289952:3 chr1:+:633308376:3 chr1:+:637424607:4 chr1:+:644538985:10 chr1:+:790662388:4 chr1:+:810671884:3 chr1:+:818460361:4 chr1:+:825131721:4 chr1:+:886127364:4 chr1:+:906744750:3 chr1:+:933023541:5 chr1:+:971589332:3 chr1:+:971850353:4 chr1:+:998304857:3 chr1:+:1004203208:4 chr1:+:1004217516:4 chr1:+:1017749397:4 chr1:+:1025523012:2 chr1:+:1139155609:4 chr1:+:1140156087:4 chr1:+:1195984958:5 chr1:+:1264115328:4 chr1:+:1276281402:3 chr1:+:1324346946:6 chr1:+:1348469046:5 chr1:+:1355020622:4 chr1:+:1358477239:4 chr1:+:1360126988:4 chr1:+:1428185459:4 chr1:+:1445013468:-1 chr1:+:1497415124:4 chr1:+:1556448923:3 chr1:+:1561253733:3 chr1:+:1651926226:4 chr1:+:1664516341:5 chr1:+:1702790190:3 chr1:+:1866124423:5 chr1:+:1914107723:4 chr1:+:1918151993:3 chr1:+:2015599742:3 chr1:+:2028485781:3 chr1:+:2104448344:4 chr1:+:2121352870:3 chr1:+:2256395289:3 chr1:+:2256421118:3 chr1:+:2500667699:8 chr1:+:2702721765:3 chr1:+:2744271800:4 chr1:+:2932771888:6 chr1:+:2950080034:6 chr1:+:2950467736:4 chr1:+:2960353535:7 chr1:+:2975836374:4 chr1:+:3012327652:5 chr1:+:3032441957:5 chr1:+:3043746138:4 chr1:+:3050283824:5 chr1:+:3058457800:5 +AATATTCAACATTCTTAAAGAAAAGAATTTTCAACCCAGAATTTCATATCCAGCCAAACTAAGCTTCCTAAGTGAAGGATAAATAAAATACTTCACAGAA chr1:+:387370244:4 chr1:+:387564553:4 chr1:+:1426015296:5 chr1:+:1514157985:4 chr1:+:1773884198:4 chr1:+:1890508159:4 chr1:+:1923142108:3 chr1:+:1923153056:3 chr1:+:3019552934:4 +AATATTCAACATTCTTAAAGAAAAGAATTTTCAACCCAGAATTTCATATCCAGCCAAACTAAGCTTCCTAAGTGAAGGATAAATAAAATACTTCACAGAA chr1:+:931291100:3 chr1:+:1084305291:-1 +TAACTTCAAAGACAGCTTAAGGATTCAGATCTTCACATGTACACAAGAGACAAGATTTGCAGATTTGAGTGAAAGGCTATGCACGATTTTAAGCCTTTCA chr1:+:207777204:0 +TACAAATTTGAAGACAAACCACAGAGGAAAAATAATAAAAACAACTCTTATACATCAATTATAAAAAGGCAAACACCCAAGTAGAAAAATGGTAAAGAAT chr1:+:219707383:-1 chr1:+:306403857:-1 chr1:+:511196900:-1 chr1:+:556022086:-1 chr1:+:697822432:-1 chr1:+:802193726:-1 chr1:+:853601527:-1 chr1:+:856874591:-1 chr1:+:945470400:-1 chr1:+:1255552027:-1 chr1:+:1322567813:-1 chr1:+:1341948571:-1 chr1:+:1502757221:-1 chr1:+:1565623446:-1 chr1:+:1639609014:-1 chr1:+:1874689237:-1 chr1:+:2244302630:-1 chr1:+:2618021370:-1 chr1:+:2893702730:-1 chr1:+:2919682387:-1 +TACAAATTTGAAGACAAACCACAGAGGAAAAATAATAAAAACAACTCTTATACATCAATTATAAAAAGGCAAACACCCAAGTAGAAAAATGGTAAAGAAT chr1:+:15986230:-1 chr1:+:77585156:-1 chr1:+:199010450:-1 chr1:+:412260158:-1 chr1:+:442399711:-1 chr1:+:589313770:-1 chr1:+:645168411:-1 chr1:+:773529044:-1 chr1:+:787633985:-1 chr1:+:796537200:-1 chr1:+:845490410:-1 chr1:+:894106960:-1 chr1:+:1147462744:-1 chr1:+:1199880841:-1 chr1:+:1203714692:-1 chr1:+:1212073822:-1 chr1:+:1307504218:-1 chr1:+:1337356033:-1 chr1:+:1363242448:-1 chr1:+:1656622722:-1 chr1:+:1829104356:-1 chr1:+:2028363354:-1 chr1:+:2065027428:-1 chr1:+:2189871000:-1 chr1:+:2241805347:-1 chr1:+:2282164785:-1 chr1:+:2355236740:-1 chr1:+:2386840736:-1 chr1:+:2400203135:-1 chr1:+:2462196641:-1 chr1:+:2589250809:-1 chr1:+:2613307792:-1 chr1:+:2629906094:-1 chr1:+:2639693151:-1 chr1:+:2640429381:-1 chr1:+:2723399770:-1 chr1:+:2800983483:-1 chr1:+:2976392467:-1 chr1:+:3006774356:-1 chr1:+:3007621027:-1 +TACAAATTTGAAGACAAACCACAGAGGAAAAATAATAAAAACAACTCTTATACATCAATTATAAAAAGGCAAACACCCAAGTAGAAAAATGGTAAAGAAT chr1:+:356594586:-1 chr1:+:573202963:-1 chr1:+:768748244:-1 chr1:+:1016910178:-1 chr1:+:1393109789:-1 chr1:+:1474838814:-1 chr1:+:1532138190:-1 chr1:+:2774303958:-1 +ATTCTTTACCATTTTTCTACTTGGGTGTTTGCCTTTTTATAATTGATGTATAAGAGTTGTTTTTATTATTTTTCCTCTGTGGTTTGTCTTCAAATTTGTA chr1:+:207777544:0 +TGTACACAGCATATTTCTAGGTGGTGTTATTTATCCACTCAATCTTTGTCTTTAATTCATGTATTTAACACATTTATACTCATTATAAATACAGTTGGAT chr1:+:434788642:-1 chr1:+:851097698:-1 chr1:+:878836530:-1 chr1:+:1075277767:-1 chr1:+:1321440074:-1 chr1:+:2594184811:-1 +TGTACACAGCATATTTCTAGGTGGTGTTATTTATCCACTCAATCTTTGTCTTTAATTCATGTATTTAACACATTTATACTCATTATAAATACAGTTGGAT chr1:+:104221939:-1 chr1:+:237704277:-1 chr1:+:263592624:-1 chr1:+:580910101:-1 chr1:+:603883599:-1 chr1:+:797146899:-1 chr1:+:946321799:-1 chr1:+:1459160056:-1 chr1:+:1630742954:-1 chr1:+:1766084896:-1 chr1:+:1792347457:-1 chr1:+:1960808388:-1 chr1:+:2038344110:-1 chr1:+:2619185762:-1 chr1:+:2637778326:-1 +TGTACACAGCATATTTCTAGGTGGTGTTATTTATCCACTCAATCTTTGTCTTTAATTCATGTATTTAACACATTTATACTCATTATAAATACAGTTGGAT chr1:+:520331606:-1 chr1:+:554353881:-1 chr1:+:694763565:-1 chr1:+:778369728:-1 chr1:+:967302782:-1 chr1:+:1427358417:-1 chr1:+:1514910766:-1 chr1:+:1912959409:-1 chr1:+:2124511760:-1 +ATCCAACTGTATTTATAATGAGTATAAATGTGTTAAATACATGAATTAAAGACAAAGATTGAGTGGATAAATAACACCACCTAGAAATATGCTGTGTACA chr1:+:1564172694:0 +CACCAGCAGAACTGCTTCAAAAGAAATGTTAGATGTTATTCAGGCAAAGTAGAATTATATAGGTCAGAAACTTGTATCTACATTAAAAAAGGCAGAGCAT chr1:+:1564172316:1 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chr1:+:3098583886:10 chr1:+:3098585078:10 chr1:+:3098586950:10 chr1:+:3098588142:8 chr1:+:3098589334:10 chr1:+:3098590526:9 chr1:+:3098591206:9 chr1:+:3098592396:10 chr1:+:3098593589:11 chr1:+:3098595459:11 chr1:+:3098596138:10 chr1:+:3098598010:10 chr1:+:3098599202:10 chr1:+:3098601074:11 chr1:+:3098603456:8 chr1:+:3098605326:9 chr1:+:3098606004:9 chr1:+:3098607194:9 chr1:+:3098608384:8 chr1:+:3098610252:10 chr1:+:3098611442:10 chr1:+:3098612122:10 chr1:+:3098614506:11 chr1:+:3098615184:11 chr1:+:3098615864:9 chr1:+:3098616544:10 chr1:+:3098617736:10 chr1:+:3098618584:11 chr1:+:3098618925:12 chr1:+:3098619604:10 chr1:+:3098621473:9 chr1:+:3098622153:9 chr1:+:3098623343:8 chr1:+:3098625214:10 chr1:+:3098627086:10 chr1:+:3098628958:10 chr1:+:3098630830:8 chr1:+:3098632020:9 chr1:+:3098634576:10 chr1:+:3098635256:10 chr1:+:3098638657:10 chr1:+:3098640529:10 chr1:+:3098642401:10 chr1:+:3098644273:10 chr1:+:3098644952:9 chr1:+:3098650055:8 chr1:+:3098651245:8 chr1:+:3098656180:9 chr1:+:3098658048:11 chr1:+:3098658386:8 chr1:+:3098658726:11 chr1:+:3098661451:10 chr1:+:3098662130:11 chr1:+:3098662808:9 chr1:+:3098663486:10 chr1:+:3098664676:10 chr1:+:3098665356:9 chr1:+:3098668419:8 chr1:+:3098670291:10 chr1:+:3098673350:9 chr1:+:3098674030:9 chr1:+:3098674880:9 chr1:+:3098677262:9 chr1:+:3098678452:9 chr1:+:3098681001:10 chr1:+:3098685593:10 chr1:+:3098687461:10 chr1:+:3098689329:11 +CTGTTAGTTGAGGGCGCACATCACAAATAAGTTTCTGAGAATGCTTCTGTCTAGTTTTCAGGGGAAGATATTTCCTTTTTCACCATAGGCCTGAAAGCGC chr1:+:2218945678:14 chr1:+:3098600394:8 +CTGTTAGTTGAGGGCGCACATCACAAATAAGTTTCTGAGAATGCTTCTGTCTAGTTTTCAGGGGAAGATATTTCCTTTTTCACCATAGGCCTGAAAGCGC chr1:+:172550206:-1 chr1:+:214547228:-1 chr1:+:521571143:-1 chr1:+:748557158:-1 chr1:+:927983092:16 chr1:+:931057558:16 chr1:+:931060112:14 chr1:+:931062667:14 chr1:+:931067947:17 chr1:+:996148488:-1 chr1:+:1192070914:-1 chr1:+:1216406654:-1 chr1:+:1337848583:-1 chr1:+:1354592508:-1 chr1:+:1414477820:-1 chr1:+:1643381924:-1 chr1:+:1733653725:-1 chr1:+:1864673313:15 chr1:+:1864865242:14 chr1:+:1989256825:18 chr1:+:2011479516:-1 chr1:+:2044513360:-1 chr1:+:2359814962:-1 chr1:+:2515023823:-1 chr1:+:2662581409:-1 chr1:+:2878330021:-1 chr1:+:2896179500:-1 chr1:+:2998976548:-1 chr1:+:3046391039:18 chr1:+:3046399722:18 chr1:+:3049414805:18 chr1:+:3049420758:18 chr1:+:3049426720:18 chr1:+:3049434204:19 chr1:+:3097049971:16 +CTGTTAGTTGAGGGCGCACATCACAAATAAGTTTCTGAGAATGCTTCTGTCTAGTTTTCAGGGGAAGATATTTCCTTTTTCACCATAGGCCTGAAAGCGC chr1:+:2687334453:12 chr1:+:2795937175:19 chr1:+:3098689667:11 +GCGCTTTCAGGCCTATGGTGAAAAAGGAAATATCTTCCCCTGAAAACTAGACAGAAGCATTCTCAGAAACTTATTTGTGATGTGCGCCCTCAACTAACAG chr1:+:341548640:0 chr1:+:341551711:2 chr1:+:341555813:9 chr1:+:341558190:2 chr1:+:341558870:2 chr1:+:341559212:0 chr1:+:341560568:0 chr1:+:341561248:0 chr1:+:341563455:1 chr1:+:341563793:0 chr1:+:341564473:0 chr1:+:341567018:0 chr1:+:341568716:1 chr1:+:341575174:0 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chr1:+:2668629743:-1 chr1:+:2694763774:-1 chr1:+:2864021489:-1 +CAAATACATTCATATCCTTGTTCCAAGGAAGATGTCATCTTGGTGGTTTCTTTTTTGCTTTCATTCTCAATATTTCATCATAAGGAAAAGCGTGAAAATC chr1:+:1190436078:0 +CAGGATCCAGGTGTTTGGGGCAGCACACAGTAAAACCCCTCATCTCATCAGCTCTTAGTTGTATTATCTGGTGACTTCCCCTTCTTTTCCCTCCTTTACC chr1:+:1190435698:0 +GAAAATAGAATAAAGTGAAAGCATCTCAGCAGCACAGAGCTGTCTCCAGGCCTCAGAATCAGTACTGCACTCTATTCACAGACCCTACCTCAAACCTGCT chr1:+:626237624:-1 chr1:+:1696045069:-1 chr1:+:1761399093:-1 chr1:+:2290845315:-1 chr1:+:2396318576:-1 +GAAAATAGAATAAAGTGAAAGCATCTCAGCAGCACAGAGCTGTCTCCAGGCCTCAGAATCAGTACTGCACTCTATTCACAGACCCTACCTCAAACCTGCT chr1:+:52329526:-1 chr1:+:165132688:-1 chr1:+:187085130:-1 chr1:+:274735833:-1 chr1:+:321093601:-1 chr1:+:626065161:-1 chr1:+:733827217:-1 chr1:+:902952193:-1 chr1:+:969164859:-1 chr1:+:975123704:-1 chr1:+:1033765072:-1 chr1:+:1119039352:-1 chr1:+:1174850093:-1 chr1:+:1388494722:-1 chr1:+:1476850628:-1 chr1:+:1512311748:-1 chr1:+:1527733814:-1 chr1:+:1760680829:-1 chr1:+:1887686515:-1 chr1:+:2113922183:-1 chr1:+:2173572288:-1 chr1:+:2265230271:-1 chr1:+:2279581925:-1 chr1:+:2382229856:-1 chr1:+:2595035925:-1 chr1:+:2645964103:-1 chr1:+:2654985316:-1 chr1:+:2655904139:-1 chr1:+:2694438041:-1 chr1:+:2760307030:-1 chr1:+:2903594772:-1 chr1:+:2944009138:-1 chr1:+:2949774564:-1 chr1:+:2949888455:-1 chr1:+:3024714241:-1 +GAAAATAGAATAAAGTGAAAGCATCTCAGCAGCACAGAGCTGTCTCCAGGCCTCAGAATCAGTACTGCACTCTATTCACAGACCCTACCTCAAACCTGCT chr1:+:185669990:-1 chr1:+:1007272256:-1 chr1:+:1160881889:-1 chr1:+:1503314434:-1 chr1:+:2341363324:-1 chr1:+:2938188070:-1 +AGCAGGTTTGAGGTAGGGTCTGTGAATAGAGTGCAGTACTGATTCTGAGGCCTGGAGACAGCTCTGTGCTGCTGAGATGCTTTCACTTTATTCTATTTTC chr1:+:295231905:0 +GAAATATTCTAAAGCCAATCCCAGACATCCTAACATTCCCCTCCAGGCATCCTAACATTCCCCTCCCAAATATTTCTGACTGCATCTCCAAAAAAATAAA chr1:+:8738646:-1 chr1:+:215372544:-1 chr1:+:278232899:-1 chr1:+:295231520:0 chr1:+:409925073:-1 chr1:+:419066957:-1 chr1:+:504501481:-1 chr1:+:691106103:-1 chr1:+:697425335:-1 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chr1:+:1297634753:-1 chr1:+:2960792408:0 +AATTCTGTTTATTTGGTGAATCACACTTATTGACTTGTGTATGTTGAACCATTCCTTCATTTCTGGGATGAAACTCATTTGAGCATAATGAATAACGTTT chr1:+:51083076:-1 chr1:+:51405452:-1 chr1:+:71149514:-1 chr1:+:101322748:-1 chr1:+:101812500:-1 chr1:+:160631805:-1 chr1:+:178726682:-1 chr1:+:190027437:-1 chr1:+:190823482:-1 chr1:+:191323742:-1 chr1:+:209448882:-1 chr1:+:266129838:18 chr1:+:271838331:-1 chr1:+:317016645:18 chr1:+:326714525:-1 chr1:+:352944554:19 chr1:+:360021996:-1 chr1:+:410815892:-1 chr1:+:434911321:-1 chr1:+:471993579:-1 chr1:+:478215935:-1 chr1:+:478402515:-1 chr1:+:511999485:-1 chr1:+:561208679:-1 chr1:+:573201586:-1 chr1:+:605235021:-1 chr1:+:618334015:-1 chr1:+:654461304:-1 chr1:+:654525078:-1 chr1:+:657600296:-1 chr1:+:677407814:-1 chr1:+:713264285:-1 chr1:+:726181907:-1 chr1:+:728875166:-1 chr1:+:735432411:-1 chr1:+:739996737:-1 chr1:+:756425371:-1 chr1:+:772734163:-1 chr1:+:787049239:-1 chr1:+:792885225:-1 chr1:+:862398995:-1 chr1:+:887281318:-1 chr1:+:902972499:-1 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chr1:+:2230749821:-1 chr1:+:2264308956:-1 chr1:+:2282819129:-1 chr1:+:2287216811:-1 chr1:+:2358600484:-1 chr1:+:2363146763:-1 chr1:+:2364573958:-1 chr1:+:2442292875:18 chr1:+:2549945145:-1 chr1:+:2567852592:-1 chr1:+:2588659768:-1 chr1:+:2596248411:20 chr1:+:2613902363:-1 chr1:+:2613965103:-1 chr1:+:2772396242:-1 chr1:+:2791483356:-1 chr1:+:2799934376:-1 chr1:+:2947564050:-1 chr1:+:2956206795:-1 chr1:+:2964096052:-1 chr1:+:2965548441:-1 chr1:+:2966518507:19 chr1:+:2979338361:-1 chr1:+:3008211155:-1 chr1:+:3025417451:-1 chr1:+:3049565211:-1 chr1:+:3100885521:-1 +AATTCTGTTTATTTGGTGAATCACACTTATTGACTTGTGTATGTTGAACCATTCCTTCATTTCTGGGATGAAACTCATTTGAGCATAATGAATAACGTTT chr1:+:33674777:-1 chr1:+:74275107:-1 chr1:+:213882150:-1 chr1:+:500019462:-1 chr1:+:510106626:-1 chr1:+:522458431:19 chr1:+:526609808:-1 chr1:+:529115242:-1 chr1:+:588558198:-1 chr1:+:650364540:-1 chr1:+:763215043:-1 chr1:+:826296904:-1 chr1:+:989950448:-1 chr1:+:1026382413:-1 chr1:+:1029335022:-1 chr1:+:1081490729:-1 chr1:+:1147368422:-1 chr1:+:1180670353:-1 chr1:+:1212757054:-1 chr1:+:1242007210:20 chr1:+:1278052448:-1 chr1:+:1442863342:-1 chr1:+:1450713287:20 chr1:+:1465874861:-1 chr1:+:1471034098:-1 chr1:+:1566712433:-1 chr1:+:1725098367:-1 chr1:+:1791498027:-1 chr1:+:2141518365:-1 chr1:+:2143341122:-1 chr1:+:2154602205:-1 chr1:+:2182017477:-1 chr1:+:2233276435:-1 chr1:+:2234600661:-1 chr1:+:2242370455:-1 chr1:+:2407511494:-1 chr1:+:2418136891:-1 chr1:+:2655269812:-1 chr1:+:2681144318:-1 chr1:+:2723245469:-1 chr1:+:2828333037:-1 chr1:+:2938078640:-1 chr1:+:2956566926:14 chr1:+:2960492779:-1 chr1:+:2965099590:-1 chr1:+:3008023335:-1 +AATTCTGTTTATTTGGTGAATCACACTTATTGACTTGTGTATGTTGAACCATTCCTTCATTTCTGGGATGAAACTCATTTGAGCATAATGAATAACGTTT chr1:+:607052592:-1 chr1:+:1447409437:-1 chr1:+:1573663264:-1 chr1:+:2565969801:-1 chr1:+:2692976321:-1 chr1:+:2997747728:-1 +AATTCTGTTTATTTGGTGAATCACACTTATTGACTTGTGTATGTTGAACCATTCCTTCATTTCTGGGATGAAACTCATTTGAGCATAATGAATAACGTTT chr1:+:238910801:-1 chr1:+:255291466:-1 chr1:+:268339220:-1 chr1:+:364502504:-1 chr1:+:781930318:-1 chr1:+:811001792:-1 chr1:+:865865899:-1 chr1:+:866364075:-1 chr1:+:899272341:18 chr1:+:1014816822:-1 chr1:+:1072124244:-1 chr1:+:1346730261:-1 chr1:+:1752965453:-1 chr1:+:2012193618:-1 chr1:+:2704505028:-1 chr1:+:2725734458:-1 chr1:+:2911585543:-1 chr1:+:2975542544:-1 chr1:+:3018434128:-1 +AAACGTTATTCATTATGCTCAAATGAGTTTCATCCCAGAAATGAAGGAATGGTTCAACATACACAAGTCAATAAGTGTGATTCACCAAATAAACAGAATT chr1:+:2960792775:0 +ACTAAGTGGTGTAACCCTTGTCCAAGCTCTGCCTACAGGGGCGTTTTCACATATCCCTGAACTGATGACAAAGGAGATGTAAGTTTGCCTAGGCTTTGCC chr1:+:2581478143:-1 chr1:+:3095289208:-1 chr1:+:3095293981:-1 chr1:+:3095822451:-1 chr1:+:3099028020:-1 chr1:+:3101046147:-1 chr1:+:3101070964:-1 chr1:+:3101072665:-1 chr1:+:3101108435:-1 chr1:+:3101116725:-1 chr1:+:3101129718:-1 chr1:+:3101134014:-1 chr1:+:3101145573:-1 chr1:+:3101148802:-1 chr1:+:3101166567:10 +ACTAAGTGGTGTAACCCTTGTCCAAGCTCTGCCTACAGGGGCGTTTTCACATATCCCTGAACTGATGACAAAGGAGATGTAAGTTTGCCTAGGCTTTGCC chr1:+:26823636:-1 chr1:+:1120410473:-1 chr1:+:1121015352:-1 chr1:+:2796978514:-1 chr1:+:3015169269:-1 chr1:+:3101163693:13 +ACTAAGTGGTGTAACCCTTGTCCAAGCTCTGCCTACAGGGGCGTTTTCACATATCCCTGAACTGATGACAAAGGAGATGTAAGTTTGCCTAGGCTTTGCC chr1:+:69141092:-1 chr1:+:98974163:-1 chr1:+:311871369:-1 chr1:+:608659190:-1 chr1:+:649357618:-1 chr1:+:669048790:-1 chr1:+:723944061:-1 chr1:+:789014925:-1 chr1:+:1011877876:-1 chr1:+:1115088559:-1 chr1:+:1247239848:-1 chr1:+:1272376204:-1 chr1:+:1391681893:-1 chr1:+:1444543706:-1 chr1:+:1569654863:-1 chr1:+:2140118480:-1 chr1:+:2180852702:-1 chr1:+:2220165833:-1 chr1:+:2221998480:-1 chr1:+:2329631998:-1 chr1:+:2344346002:-1 chr1:+:2581476297:8 chr1:+:2880009773:-1 chr1:+:2958533070:-1 chr1:+:3002092394:-1 chr1:+:3018229732:-1 chr1:+:3099021074:8 chr1:+:3099024069:16 chr1:+:3099026856:10 chr1:+:3101127064:12 chr1:+:3101128965:14 chr1:+:3101143312:11 chr1:+:3101149210:15 chr1:+:3101166565:10 chr1:+:3101171283:10 chr1:+:3101177098:11 chr1:+:3101177916:9 +ACTAAGTGGTGTAACCCTTGTCCAAGCTCTGCCTACAGGGGCGTTTTCACATATCCCTGAACTGATGACAAAGGAGATGTAAGTTTGCCTAGGCTTTGCC chr1:+:157938339:-1 chr1:+:1665234457:-1 chr1:+:1886256389:-1 chr1:+:1921908694:-1 chr1:+:3101071845:20 chr1:+:3101122396:14 chr1:+:3101132647:12 chr1:+:3101149278:12 chr1:+:3101162469:14 chr1:+:3101169370:12 +ACTAAGTGGTGTAACCCTTGTCCAAGCTCTGCCTACAGGGGCGTTTTCACATATCCCTGAACTGATGACAAAGGAGATGTAAGTTTGCCTAGGCTTTGCC chr1:+:1207148632:-1 chr1:+:1243552718:-1 chr1:+:1435064275:-1 chr1:+:1474961971:-1 chr1:+:1515475903:-1 chr1:+:1817921748:-1 chr1:+:2065037957:-1 chr1:+:2778533362:-1 chr1:+:3101113444:12 chr1:+:3101183505:-1 +GGCAAAGCCTAGGCAAACTTACATCTCCTTTGTCATCAGTTCAGGGATATGTGAAAACGCCCCTGTAGGCAGAGCTTGGACAAGGGTTACACCACTTAGT chr1:+:260611983:-1 chr1:+:1823267286:-1 chr1:+:2923583504:-1 chr1:+:3097402383:7 chr1:+:3098996465:12 chr1:+:3099006175:10 chr1:+:3099006994:10 chr1:+:3099008902:10 chr1:+:3099013687:8 chr1:+:3099030763:11 chr1:+:3099030831:17 chr1:+:3101079385:8 chr1:+:3101095853:13 chr1:+:3101159118:8 +GGCAAAGCCTAGGCAAACTTACATCTCCTTTGTCATCAGTTCAGGGATATGTGAAAACGCCCCTGTAGGCAGAGCTTGGACAAGGGTTACACCACTTAGT chr1:+:251756001:-1 chr1:+:563383261:-1 chr1:+:1015350798:-1 chr1:+:1080376884:-1 chr1:+:1546748191:-1 chr1:+:2381969411:-1 chr1:+:2645105183:-1 chr1:+:2748867919:-1 chr1:+:3049768800:-1 chr1:+:3049769073:-1 chr1:+:3049772283:-1 chr1:+:3049772419:-1 chr1:+:3049773168:-1 chr1:+:3049776878:-1 chr1:+:3049785290:-1 chr1:+:3097400262:-1 chr1:+:3097404290:-1 chr1:+:3099000438:-1 chr1:+:3099005698:-1 chr1:+:3099013275:-1 chr1:+:3099019874:-1 chr1:+:3099032667:-1 chr1:+:3099034468:-1 chr1:+:3101050734:-1 chr1:+:3101051423:10 chr1:+:3101053185:-1 chr1:+:3101061195:-1 chr1:+:3101061603:-1 chr1:+:3101064336:-1 chr1:+:3101065632:-1 chr1:+:3101066111:-1 chr1:+:3101078564:-1 chr1:+:3101087596:-1 chr1:+:3101091306:-1 chr1:+:3101093736:-1 chr1:+:3101094486:-1 chr1:+:3101097621:-1 chr1:+:3101101330:-1 chr1:+:3101101466:-1 chr1:+:3101102896:-1 chr1:+:3101152025:-1 chr1:+:3101157817:-1 chr1:+:3101159392:-1 +GGCAAAGCCTAGGCAAACTTACATCTCCTTTGTCATCAGTTCAGGGATATGTGAAAACGCCCCTGTAGGCAGAGCTTGGACAAGGGTTACACCACTTAGT chr1:+:2618996521:-1 chr1:+:3049769621:-1 chr1:+:3049785702:15 chr1:+:3099000781:-1 chr1:+:3101153189:11 chr1:+:3101156186:17 +GGCAAAGCCTAGGCAAACTTACATCTCCTTTGTCATCAGTTCAGGGATATGTGAAAACGCCCCTGTAGGCAGAGCTTGGACAAGGGTTACACCACTTAGT chr1:+:709636149:-1 chr1:+:802926314:-1 chr1:+:1262917484:-1 chr1:+:1316225799:-1 chr1:+:1915452018:-1 chr1:+:2864279772:-1 chr1:+:3040355070:-1 chr1:+:3049771468:15 chr1:+:3099010952:13 chr1:+:3099017717:14 +AGGGATATGTCACAAAGCACCCTGTAGGCAGATCCTAGAGAAGAGTTATATCACCTGGGTGATCAGTGCAGAGATATGTCACAAGGCCCCTGGAGGCAGA chr1:+:16109743:-1 chr1:+:23694227:-1 chr1:+:319932775:-1 chr1:+:466833584:-1 chr1:+:484320599:-1 chr1:+:1059134265:-1 chr1:+:1394070812:-1 chr1:+:1817867521:-1 chr1:+:1845907482:-1 chr1:+:2736402281:-1 chr1:+:3098996781:17 chr1:+:3101061781:18 +AGGGATATGTCACAAAGCACCCTGTAGGCAGATCCTAGAGAAGAGTTATATCACCTGGGTGATCAGTGCAGAGATATGTCACAAGGCCCCTGGAGGCAGA chr1:+:3049765070:5 chr1:+:3097403446:3 chr1:+:3098999180:10 chr1:+:3099017281:6 chr1:+:3099031892:3 chr1:+:3101096914:3 +AGGGATATGTCACAAAGCACCCTGTAGGCAGATCCTAGAGAAGAGTTATATCACCTGGGTGATCAGTGCAGAGATATGTCACAAGGCCCCTGGAGGCAGA chr1:+:1920053067:-1 chr1:+:2649528038:-1 chr1:+:3049772393:5 chr1:+:3049772800:14 chr1:+:3049789087:8 chr1:+:3049789904:-1 chr1:+:3099017486:4 chr1:+:3101060076:4 chr1:+:3101063763:16 chr1:+:3101064173:14 chr1:+:3101080447:7 chr1:+:3101102120:4 chr1:+:3101154249:4 +TCTGCCTCCAGGGGCCTTGTGACATATCTCTGCACTGATCACCCAGGTGATATAACTCTTCTCTAGGATCTGCCTACAGGGTGCTTTGTGACATATCCCT chr1:+:2581475439:2 chr1:+:3095293191:7 chr1:+:3095295101:6 chr1:+:3095297300:14 chr1:+:3101070854:5 chr1:+:3101071059:8 chr1:+:3101072487:4 chr1:+:3101107506:10 chr1:+:3101112992:8 chr1:+:3101121335:7 chr1:+:3101121540:7 chr1:+:3101127841:6 chr1:+:3101131587:6 chr1:+:3101138427:8 chr1:+:3101138632:7 chr1:+:3101148149:3 chr1:+:3101162904:4 chr1:+:3101176041:4 chr1:+:3101176246:6 chr1:+:3101187573:5 +TCTGCCTCCAGGGGCCTTGTGACATATCTCTGCACTGATCACCCAGGTGATATAACTCTTCTCTAGGATCTGCCTACAGGGTGCTTTGTGACATATCCCT chr1:+:3095297980:9 chr1:+:3095300644:14 chr1:+:3099026001:5 chr1:+:3101114090:6 chr1:+:3101140678:14 chr1:+:3101162699:4 chr1:+:3101187028:13 chr1:+:3101187778:11 +CCAGCTGTCTCTCAGGCATTTCCCCTTCAACTCCTCACACATTCTTTAAACCCTAAATTTTCTAATAAACAACCTTTATTCCCACAATACCTTACCAAGC chr1:+:74476149:1 +ATATTTTCCCATTGACTTTCTTTTCACAGACTTTAAGGTTCTTGAGGGTACAGACCTGCCTTCTTATCATTTTCTCATCAGTAAGCAACGCAGTACTTGA chr1:+:863241729:-1 chr1:+:952707439:-1 chr1:+:1243627618:-1 chr1:+:2019007905:-1 chr1:+:2065553174:-1 chr1:+:2511437158:-1 chr1:+:2743072940:-1 +ATATTTTCCCATTGACTTTCTTTTCACAGACTTTAAGGTTCTTGAGGGTACAGACCTGCCTTCTTATCATTTTCTCATCAGTAAGCAACGCAGTACTTGA chr1:+:53414355:-1 chr1:+:76283254:-1 chr1:+:273057289:-1 chr1:+:437714824:-1 chr1:+:555863843:-1 chr1:+:988622976:-1 chr1:+:1007730579:-1 chr1:+:1445743705:-1 chr1:+:1741358569:-1 chr1:+:1904685619:-1 chr1:+:2463419189:-1 +ATATTTTCCCATTGACTTTCTTTTCACAGACTTTAAGGTTCTTGAGGGTACAGACCTGCCTTCTTATCATTTTCTCATCAGTAAGCAACGCAGTACTTGA chr1:+:12826199:-1 chr1:+:23052173:-1 chr1:+:299388646:-1 chr1:+:403137714:-1 chr1:+:509394698:-1 chr1:+:569512449:-1 chr1:+:660291932:-1 chr1:+:907731631:-1 chr1:+:913489215:-1 chr1:+:947969235:-1 chr1:+:956114478:-1 chr1:+:994566726:-1 chr1:+:1026358830:-1 chr1:+:1194893055:-1 chr1:+:1215652093:-1 chr1:+:1235713518:-1 chr1:+:1457262608:-1 chr1:+:1508724808:-1 chr1:+:1615049325:-1 chr1:+:1664193870:-1 chr1:+:1820408791:-1 chr1:+:1839929549:-1 chr1:+:1928267025:-1 chr1:+:2115616980:-1 chr1:+:2188102261:-1 chr1:+:2228469045:-1 chr1:+:2337782120:-1 chr1:+:2539005487:-1 chr1:+:2792165688:-1 chr1:+:2799675338:-1 chr1:+:2869892311:-1 chr1:+:3001800010:-1 chr1:+:3032215383:-1 +TCAAGTACTGCGTTGCTTACTGATGAGAAAATGATAAGAAGGCAGGTCTGTACCCTCAAGAACCTTAAAGTCTGTGAAAAGAAAGTCAATGGGAAAATAT chr1:+:74476516:0 +TGAATAGACCAATAATGAGTTCTGAAATTAATTAAGGCAGTAATAAATAGCCTAACAACCAGAAAAAGTCCAGGACCAGAAGGATTTATGGCTGAATTCT chr1:+:596190836:0 +TGAAGGTCTTTTCTACATCTATTGAGTTGATCATGTGGTTTTCATCTTTAGTTCTGTTTATATGTTGAATTAAATTTTTCAGTTTGTGTATGTTGAACCA chr1:+:48600742:20 chr1:+:467249956:16 chr1:+:603001901:16 chr1:+:673640617:20 chr1:+:679222288:18 chr1:+:685367180:18 chr1:+:776896502:17 chr1:+:825431608:20 chr1:+:944252775:18 chr1:+:961765630:18 chr1:+:1130676500:19 chr1:+:1154067162:13 chr1:+:1255229634:14 chr1:+:1322896318:18 chr1:+:1379331501:18 chr1:+:1446753627:13 chr1:+:1464336790:17 chr1:+:1501401401:18 chr1:+:1611060351:17 chr1:+:1680015738:15 chr1:+:1845993282:14 chr1:+:1864485217:19 chr1:+:1878805545:17 chr1:+:1904415715:20 chr1:+:1906894216:20 chr1:+:1958484621:19 chr1:+:2024720103:16 chr1:+:2229430968:-1 chr1:+:2232069827:16 chr1:+:2236563846:19 chr1:+:2240030069:16 chr1:+:2243201882:-1 chr1:+:2282720813:17 chr1:+:2305241674:16 chr1:+:2806043282:17 chr1:+:2895511488:16 chr1:+:2956085068:19 chr1:+:3019490352:19 +TGAAGGTCTTTTCTACATCTATTGAGTTGATCATGTGGTTTTCATCTTTAGTTCTGTTTATATGTTGAATTAAATTTTTCAGTTTGTGTATGTTGAACCA chr1:+:715942408:-1 chr1:+:1314465383:19 chr1:+:1612071777:-1 chr1:+:1923842847:-1 chr1:+:2258984996:-1 chr1:+:2880919497:15 chr1:+:2936915810:20 chr1:+:2952457340:-1 +TGAAGGTCTTTTCTACATCTATTGAGTTGATCATGTGGTTTTCATCTTTAGTTCTGTTTATATGTTGAATTAAATTTTTCAGTTTGTGTATGTTGAACCA chr1:+:945872544:-1 chr1:+:2028846950:-1 chr1:+:2554957768:-1 +TGAAGGTCTTTTCTACATCTATTGAGTTGATCATGTGGTTTTCATCTTTAGTTCTGTTTATATGTTGAATTAAATTTTTCAGTTTGTGTATGTTGAACCA chr1:+:1010122598:-1 chr1:+:1073208251:19 chr1:+:1251142889:17 chr1:+:1709005766:18 chr1:+:1851374977:-1 chr1:+:2238850247:18 +TGAAGGTCTTTTCTACATCTATTGAGTTGATCATGTGGTTTTCATCTTTAGTTCTGTTTATATGTTGAATTAAATTTTTCAGTTTGTGTATGTTGAACCA chr1:+:431376547:-1 chr1:+:971026158:18 chr1:+:1530922042:-1 chr1:+:1558546973:-1 chr1:+:2268308999:-1 chr1:+:2476316111:-1 +TGGTTCAACATACACAAACTGAAAAATTTAATTCAACATATAAACAGAACTAAAGATGAAAACCACATGATCAACTCAATAGATGTAGAAAAGACCTTCA chr1:+:596191206:0 +CCACCTGTTTCTTTTTTCCTTTTTCAGTGTGGCATCTAGAAAACTTTCAGTGACACGTGTGGCTTGTGCTTGTGGTTTGCATTCTGTTTCTCTTAAGCAG chr1:+:2548769771:0 +GAAGGACTAAAAATACAGCTTCCCTGTGGCAGCTAGACTCCCGTTCTCCTGTCCTATACCTCCTCAGCAGCCCTACACAAGACTCCTGCAAAATTAGCTT chr1:+:97486390:-1 chr1:+:98857654:-1 chr1:+:303206753:-1 chr1:+:358915357:-1 chr1:+:400214627:-1 chr1:+:404840338:-1 chr1:+:1270646483:-1 chr1:+:1424486557:-1 chr1:+:1432636130:-1 chr1:+:1481332724:-1 chr1:+:1520951593:-1 chr1:+:1648430293:-1 chr1:+:1820914936:-1 chr1:+:1836768375:-1 chr1:+:1850916872:-1 chr1:+:1896071695:-1 chr1:+:1949320733:-1 chr1:+:2383052172:-1 chr1:+:2792782716:-1 chr1:+:2968294909:-1 +GAAGGACTAAAAATACAGCTTCCCTGTGGCAGCTAGACTCCCGTTCTCCTGTCCTATACCTCCTCAGCAGCCCTACACAAGACTCCTGCAAAATTAGCTT chr1:+:48551567:-1 chr1:+:421843704:-1 chr1:+:439324184:-1 chr1:+:605606508:-1 chr1:+:845398780:-1 chr1:+:1682048340:-1 chr1:+:1684890471:-1 chr1:+:2577014099:-1 chr1:+:2581047464:-1 +GAAGGACTAAAAATACAGCTTCCCTGTGGCAGCTAGACTCCCGTTCTCCTGTCCTATACCTCCTCAGCAGCCCTACACAAGACTCCTGCAAAATTAGCTT chr1:+:15277065:-1 chr1:+:228505344:-1 chr1:+:424906762:-1 chr1:+:466136995:-1 chr1:+:475209039:-1 chr1:+:551053135:-1 chr1:+:678287785:-1 chr1:+:685083812:-1 chr1:+:864068939:-1 chr1:+:881738062:-1 chr1:+:984024135:-1 chr1:+:1263531517:-1 chr1:+:1519431309:-1 chr1:+:1546702682:-1 chr1:+:1704754237:-1 chr1:+:1796494488:-1 chr1:+:1805241639:-1 chr1:+:1966664682:-1 chr1:+:2115457060:-1 chr1:+:2333095698:-1 chr1:+:2386422526:-1 chr1:+:2497505264:-1 chr1:+:2591011413:-1 chr1:+:2602089837:-1 chr1:+:2690855819:-1 chr1:+:2824188264:-1 chr1:+:2829221720:-1 chr1:+:2866601430:-1 +AAGCTAATTTTGCAGGAGTCTTGTGTAGGGCTGCTGAGGAGGTATAGGACAGGAGAACGGGAGTCTAGCTGCCACAGGGAAGCTGTATTTTTAGTCCTTC chr1:+:2548770112:1 +AATCTTCAAATTATCAAATAAAAGTAATCTAATTCTTCACAGGATGTAGACTGGAACTTCATTTTGCTTCCATCAAAAAAAAAAACATATTGCTACCTAG chr1:+:2609442387:1 +TGAGTTAAAATAGGAAAATATATATGCAAATCGACATTGAAAAAAGTAGAAACTTGGTGAGTTTCATTACATATCCTTCACTTATCTTTAGAATGATGAC chr1:+:830761421:-1 chr1:+:1008027225:-1 +TGAGTTAAAATAGGAAAATATATATGCAAATCGACATTGAAAAAAGTAGAAACTTGGTGAGTTTCATTACATATCCTTCACTTATCTTTAGAATGATGAC chr1:+:250244589:-1 chr1:+:474715462:-1 chr1:+:750519200:-1 chr1:+:837648520:-1 chr1:+:1019148644:-1 chr1:+:1037364686:-1 chr1:+:1044669613:-1 chr1:+:1841043665:-1 chr1:+:2111989969:-1 chr1:+:2179863727:-1 +TGAGTTAAAATAGGAAAATATATATGCAAATCGACATTGAAAAAAGTAGAAACTTGGTGAGTTTCATTACATATCCTTCACTTATCTTTAGAATGATGAC chr1:+:23403610:-1 chr1:+:33078408:-1 chr1:+:45825900:-1 chr1:+:59526348:-1 chr1:+:75048433:-1 chr1:+:76114685:-1 chr1:+:79497113:-1 chr1:+:173754041:-1 chr1:+:195510093:-1 chr1:+:210868323:-1 chr1:+:219037679:-1 chr1:+:221521914:-1 chr1:+:251481261:-1 chr1:+:258240611:-1 chr1:+:387122065:-1 chr1:+:387411619:-1 chr1:+:397411761:-1 chr1:+:456676535:-1 chr1:+:460918724:-1 chr1:+:493459344:-1 chr1:+:532971855:-1 chr1:+:564985048:-1 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chr1:+:154081056:13 chr1:+:191831840:20 chr1:+:279537018:10 chr1:+:304175666:14 chr1:+:313160838:12 chr1:+:511197164:20 chr1:+:579187890:-1 chr1:+:607180895:11 chr1:+:625507787:19 chr1:+:646920270:14 chr1:+:647636029:14 chr1:+:659880239:10 chr1:+:789488736:18 chr1:+:892468959:20 chr1:+:896803419:17 chr1:+:1001144702:17 chr1:+:1011970556:16 chr1:+:1126394808:18 chr1:+:1146099516:13 chr1:+:1146198575:12 chr1:+:1180560278:10 chr1:+:1249484363:16 chr1:+:1256434678:15 chr1:+:1260712331:18 chr1:+:1490502026:18 chr1:+:1567396992:19 chr1:+:1575338339:9 chr1:+:1776016511:17 chr1:+:1805057834:17 chr1:+:1822091742:13 chr1:+:1926994362:-1 chr1:+:1938260623:10 chr1:+:1980329975:12 chr1:+:1989882529:18 chr1:+:2035000582:-1 chr1:+:2050596931:19 chr1:+:2133689967:15 chr1:+:2232014307:13 chr1:+:2267263773:13 chr1:+:2564273256:14 chr1:+:2636426546:-1 chr1:+:2902073532:-1 chr1:+:2947497812:17 chr1:+:2951142914:13 chr1:+:2959535517:-1 chr1:+:2965522992:14 chr1:+:2982201437:12 chr1:+:2986962272:16 chr1:+:2997214702:17 chr1:+:3015433347:11 chr1:+:3025005210:17 +AATAAAAACAAGAAATTAAATCATACCACCAGAGAAAATCATCTTCGCTAAAAGGAAAACAGAAGGAAGGAAAGAAGGACGAGAAGACCACAAAACAACC chr1:+:164161182:-1 chr1:+:203173095:-1 chr1:+:288299021:-1 chr1:+:823843151:17 chr1:+:1137134587:-1 chr1:+:1156309322:-1 chr1:+:1270040208:-1 chr1:+:1332057951:-1 chr1:+:1640287725:-1 chr1:+:1799223327:-1 chr1:+:1810019349:-1 chr1:+:2070518661:-1 chr1:+:2071202546:-1 chr1:+:2124663091:-1 chr1:+:2689423092:-1 chr1:+:2692124196:-1 +AATAAAAACAAGAAATTAAATCATACCACCAGAGAAAATCATCTTCGCTAAAAGGAAAACAGAAGGAAGGAAAGAAGGACGAGAAGACCACAAAACAACC chr1:+:105034277:15 chr1:+:163485054:15 chr1:+:241801281:-1 chr1:+:257605690:-1 chr1:+:263276988:19 chr1:+:297221553:-1 chr1:+:304677489:9 chr1:+:444003563:15 chr1:+:653489837:19 chr1:+:665502664:-1 chr1:+:818226487:13 chr1:+:829583321:-1 chr1:+:968827509:-1 chr1:+:986055770:-1 chr1:+:1059287552:-1 chr1:+:1331373408:-1 chr1:+:1397640928:-1 chr1:+:1409603299:16 chr1:+:1611666967:-1 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chr1:+:1878645328:-1 chr1:+:1969659683:-1 chr1:+:2242274293:-1 chr1:+:2889264784:-1 +GGGAGTTTAACTGGGGTGGTAGTAATGTTGGAGAGATAATTAGACAAATCAAGGCCATATTTACCTGGTAAACTGACAGGACTTGGTTTTGAAATATATA chr1:+:1657255162:-1 chr1:+:1908393956:-1 +GGGAGTTTAACTGGGGTGGTAGTAATGTTGGAGAGATAATTAGACAAATCAAGGCCATATTTACCTGGTAAACTGACAGGACTTGGTTTTGAAATATATA chr1:+:101336580:-1 chr1:+:152012616:-1 chr1:+:189166718:-1 chr1:+:251153377:-1 chr1:+:317078277:-1 chr1:+:337798706:-1 chr1:+:391648014:-1 chr1:+:407967259:-1 chr1:+:434950726:-1 chr1:+:530744252:-1 chr1:+:554922569:-1 chr1:+:563882210:-1 chr1:+:605392702:-1 chr1:+:625231848:-1 chr1:+:631243716:-1 chr1:+:686195080:-1 chr1:+:702066173:-1 chr1:+:703678325:-1 chr1:+:733348310:-1 chr1:+:777224000:-1 chr1:+:805778332:-1 chr1:+:863753416:-1 chr1:+:1040713931:-1 chr1:+:1240082409:-1 chr1:+:1262866680:-1 chr1:+:1370723841:-1 chr1:+:1381313767:-1 chr1:+:1398001642:-1 chr1:+:1429128419:-1 chr1:+:1494567323:-1 chr1:+:1580521233:-1 chr1:+:1585875962:-1 chr1:+:1604703487:-1 chr1:+:1607595409:-1 chr1:+:1649275714:-1 chr1:+:1714281025:-1 chr1:+:1896337989:-1 chr1:+:2070288935:-1 chr1:+:2126111089:-1 chr1:+:2165969841:-1 chr1:+:2355303177:-1 chr1:+:2370875825:-1 chr1:+:2517632480:-1 chr1:+:2549377421:-1 chr1:+:2649990956:-1 chr1:+:2759575281:-1 chr1:+:2875918634:-1 chr1:+:2975841775:-1 +TATATATTTCAAAACCAAGTCCTGTCAGTTTACCAGGTAAATATGGCCTTGATTTGTCTAATTATCTCTCCAACATTACTACCACCCCAGTTAAACTCCC chr1:+:2368961754:0 +AAAAGATTTGGGCTTCCTAAGCTTGGAGTTCCTCAGCTGTGATGCAAAGCCACTGTGTGTATGGCATGCACCTTAGCCACTCTGTGAATCCCCGTGGGAC chr1:+:1802895642:-1 chr1:+:2368961393:0 +CATCTGCAAAGACTTTTTTTTTCTTTGAGACAAAGTCTCACCCTGTAGCCCATGCTGGAGTGCAGTGGCACAATCTCAGTTCACTGCAACCTCTGCCTCC chr1:+:9012688:-1 chr1:+:21120551:-1 chr1:+:23258445:-1 chr1:+:41805295:-1 chr1:+:54312833:-1 chr1:+:58048931:-1 chr1:+:87181930:-1 chr1:+:153753826:18 chr1:+:156950793:-1 chr1:+:220774207:20 chr1:+:220947380:19 chr1:+:246724742:-1 chr1:+:248324969:-1 chr1:+:268032899:-1 chr1:+:277303720:-1 chr1:+:295058418:-1 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chr1:+:2965223490:-1 chr1:+:2976361134:-1 chr1:+:2982220653:-1 chr1:+:2984051094:-1 chr1:+:3061038848:-1 chr1:+:3064513245:-1 chr1:+:3101452129:19 +CATCTGCAAAGACTTTTTTTTTCTTTGAGACAAAGTCTCACCCTGTAGCCCATGCTGGAGTGCAGTGGCACAATCTCAGTTCACTGCAACCTCTGCCTCC chr1:+:27009848:17 chr1:+:242698327:17 chr1:+:244276428:-1 chr1:+:264480466:17 chr1:+:468531619:-1 chr1:+:484812611:18 chr1:+:486225463:18 chr1:+:547656027:18 chr1:+:934486004:20 chr1:+:1309287811:17 chr1:+:1816725713:-1 chr1:+:2252375959:17 chr1:+:2269154177:18 chr1:+:2350280093:20 chr1:+:2413148011:-1 chr1:+:2540965048:19 chr1:+:2705395424:17 chr1:+:2870765639:19 chr1:+:3051737984:16 +CATCTGCAAAGACTTTTTTTTTCTTTGAGACAAAGTCTCACCCTGTAGCCCATGCTGGAGTGCAGTGGCACAATCTCAGTTCACTGCAACCTCTGCCTCC chr1:+:99634730:17 chr1:+:670142329:19 chr1:+:1207024439:18 chr1:+:1308927808:19 chr1:+:1366254314:18 chr1:+:1435128590:19 chr1:+:2071769787:-1 chr1:+:2424556809:-1 chr1:+:2653209495:20 chr1:+:2688822665:-1 chr1:+:2739208110:18 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chr1:+:953594270:-1 chr1:+:1352590411:-1 chr1:+:1519002080:-1 chr1:+:1540251044:-1 chr1:+:1798620136:-1 chr1:+:1909097393:-1 chr1:+:1942222324:-1 chr1:+:2805983251:-1 +GATGTCATGTGTTTATGCAAAAAAAAAACAAAAACAAAGAATCAACAACAACAAAAAATTCTCATGGAAGTAATAAGTCATCATAGAGAAGCTACCCAAG chr1:+:312899886:-1 chr1:+:368481005:-1 chr1:+:810905603:-1 chr1:+:1265937802:-1 chr1:+:1413943877:-1 chr1:+:2670159705:-1 chr1:+:2761874083:-1 chr1:+:2869574280:-1 +GATGTCATGTGTTTATGCAAAAAAAAAACAAAAACAAAGAATCAACAACAACAAAAAATTCTCATGGAAGTAATAAGTCATCATAGAGAAGCTACCCAAG chr1:+:26370156:-1 chr1:+:111903439:-1 chr1:+:516914637:-1 chr1:+:668585833:-1 chr1:+:1045506678:-1 chr1:+:1281401511:-1 chr1:+:1507215135:-1 chr1:+:1640514566:-1 chr1:+:1847544455:-1 chr1:+:1865396494:-1 chr1:+:2514215977:-1 chr1:+:2574599071:-1 chr1:+:2622206606:-1 chr1:+:2633961401:-1 chr1:+:2637967824:-1 chr1:+:3022431576:-1 +CTTGGGTAGCTTCTCTATGATGACTTATTACTTCCATGAGAATTTTTTGTTGTTGTTGATTCTTTGTTTTTGTTTTTTTTTTGCATAAACACATGACATC chr1:+:212049392:-1 chr1:+:964098047:-1 chr1:+:1283082960:0 chr1:+:1958336883:-1 +AGTGGGCATGTATCAAGCCTTCTATTTAACTCATTAATTGGCAAGAAAGCATGTTATAAACCACTCAAGTGAAAGCAAAATACCAAACAGTTATTGTGAG chr1:+:1756093501:-1 +AGTGGGCATGTATCAAGCCTTCTATTTAACTCATTAATTGGCAAGAAAGCATGTTATAAACCACTCAAGTGAAAGCAAAATACCAAACAGTTATTGTGAG chr1:+:117819392:-1 chr1:+:507587174:-1 chr1:+:1520435148:-1 chr1:+:1941084270:-1 chr1:+:2476325106:-1 +AGTGGGCATGTATCAAGCCTTCTATTTAACTCATTAATTGGCAAGAAAGCATGTTATAAACCACTCAAGTGAAAGCAAAATACCAAACAGTTATTGTGAG chr1:+:108021317:-1 chr1:+:1095137679:-1 chr1:+:1111716046:-1 chr1:+:1158896392:-1 chr1:+:1697630509:-1 chr1:+:1820885175:-1 chr1:+:1897483704:-1 chr1:+:1902732924:-1 chr1:+:1904354889:-1 chr1:+:2006704011:-1 chr1:+:2156715770:-1 chr1:+:2363053917:-1 chr1:+:2483871687:-1 chr1:+:2492590615:-1 chr1:+:2879913674:-1 chr1:+:2895092011:-1 +CTCACAATAACTGTTTGGTATTTTGCTTTCACTTGAGTGGTTTATAACATGCTTTCTTGCCAATTAATGAGTTAAATAGAAGGCTTGATACATGCCCACT chr1:+:1351433635:0 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chr1:+:1179937474:11 chr1:+:1195087845:13 chr1:+:1207988633:9 chr1:+:1209240275:9 chr1:+:1245584584:9 chr1:+:1251339605:10 chr1:+:1271472098:17 chr1:+:1304333517:11 chr1:+:1347655463:15 chr1:+:1349342105:9 chr1:+:1353364367:11 chr1:+:1378629798:13 chr1:+:1380166180:8 chr1:+:1450530319:8 chr1:+:1452210612:12 chr1:+:1477174273:10 chr1:+:1490488562:14 chr1:+:1505346698:13 chr1:+:1506938567:14 chr1:+:1530927848:20 chr1:+:1543143117:18 chr1:+:1545895483:10 chr1:+:1551606935:16 chr1:+:1561872128:11 chr1:+:1570137300:9 chr1:+:1574739278:14 chr1:+:1578691833:12 chr1:+:1580019371:12 chr1:+:1580836847:12 chr1:+:1645071548:12 chr1:+:1657745709:14 chr1:+:1662038628:9 chr1:+:1736758661:10 chr1:+:1770459047:12 chr1:+:1837144853:14 chr1:+:1854039468:-1 chr1:+:1895388496:14 chr1:+:1906334243:15 chr1:+:1971727696:14 chr1:+:2006320835:1 chr1:+:2012572699:10 chr1:+:2064843558:10 chr1:+:2070969271:8 chr1:+:2116695051:11 chr1:+:2132912189:9 chr1:+:2136509519:15 chr1:+:2152865763:14 chr1:+:2156149614:15 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chr1:+:682463036:0 +TATGACTTCCTTTGTCTTTCAGTCAAAGTCAGTGTTGTGCTTAAAGGAAATAAATGCTTGTGAGAAGTAAAACACAAAACTTCATGATAATAAGGGGAAC chr1:+:458906150:1 +ATAAAACTCACTTTAAAAAATTCTCTAATCAGTTTAAAGATTGTATAGAAGGAGATTTTAAGAGGAGCTGAAAAAACAGTGGCTTGGGAAACAAAAAAGA chr1:+:23634229:-1 chr1:+:272143600:-1 chr1:+:277213366:-1 chr1:+:1038492642:-1 chr1:+:1668744626:-1 chr1:+:1886557336:-1 chr1:+:1947956844:-1 chr1:+:2353134540:-1 chr1:+:2781472474:-1 +ATAAAACTCACTTTAAAAAATTCTCTAATCAGTTTAAAGATTGTATAGAAGGAGATTTTAAGAGGAGCTGAAAAAACAGTGGCTTGGGAAACAAAAAAGA chr1:+:1036053344:-1 chr1:+:1683703142:-1 +ATAAAACTCACTTTAAAAAATTCTCTAATCAGTTTAAAGATTGTATAGAAGGAGATTTTAAGAGGAGCTGAAAAAACAGTGGCTTGGGAAACAAAAAAGA chr1:+:433580568:-1 chr1:+:752487353:-1 chr1:+:945696352:-1 chr1:+:1140232812:-1 chr1:+:1302787247:-1 chr1:+:1443616094:-1 chr1:+:1508987374:-1 chr1:+:1857781832:-1 chr1:+:2339001127:-1 chr1:+:2545431497:-1 chr1:+:2651122525:-1 chr1:+:2736846110:-1 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+TTATCCTTTGTGAAAAACTTAGTGTAAGAGAAGTAGAAGAGAGGGTGCAAGTGGACCGATGGAACAGTGTCTGTGTTCTTGTGTCTCAGTCACACACAGC chr1:+:1362593064:-1 chr1:+:1523513683:-1 chr1:+:1676745508:-1 chr1:+:1778490096:-1 chr1:+:2252461713:-1 chr1:+:2336329754:-1 +TTATCCTTTGTGAAAAACTTAGTGTAAGAGAAGTAGAAGAGAGGGTGCAAGTGGACCGATGGAACAGTGTCTGTGTTCTTGTGTCTCAGTCACACACAGC chr1:+:838067100:-1 chr1:+:1148639095:-1 chr1:+:1859305923:-1 chr1:+:2561822436:-1 +GCTGTGTGTGACTGAGACACAAGAACACAGACACTGTTCCATCGGTCCACTTGCACCCTCTCTTCTACTTCTCTTACACTAAGTTTTTCACAAAGGATAA chr1:+:839663852:0 +GACATAATGTAACTTTTCCCCCTTTAATATTATCCTTACATTAAGATACAGACTTAGATGCTGATACAGATGGCATGAGACGCTGAGGACTGATGGGTAC chr1:+:839663480:0 +TTTTTGTATTAATTATGTAATTATTTCTTCTGTGTGTACATGTAGCTCAATAGTAGTGCCTATGGTATGAATATTTGATTTCTAAAACGTACAGAAACCT chr1:+:581351630:0 chr1:+:1068260414:-1 +AGGACACTGCTGAGATTGAAAAGGTCAGACAAAATGACAGTAACTAATTCAGAAATGAGATGTCAAGAATTGAAGTTCTAAAGCAGGGATTAACCTATAA chr1:+:95075827:-1 chr1:+:110437309:-1 chr1:+:306553922:-1 chr1:+:332835478:-1 chr1:+:355190696:-1 chr1:+:451948874:-1 chr1:+:521999476:-1 chr1:+:718051818:-1 chr1:+:759430532:-1 chr1:+:792561745:-1 chr1:+:826097658:-1 chr1:+:916429676:-1 chr1:+:999409676:-1 chr1:+:1634143350:-1 chr1:+:1940872249:-1 chr1:+:2039352452:-1 chr1:+:2171128173:-1 chr1:+:2551417540:-1 chr1:+:2739203771:-1 +AGGACACTGCTGAGATTGAAAAGGTCAGACAAAATGACAGTAACTAATTCAGAAATGAGATGTCAAGAATTGAAGTTCTAAAGCAGGGATTAACCTATAA chr1:+:517337567:-1 chr1:+:608186264:-1 chr1:+:1401491308:-1 chr1:+:1441687278:-1 chr1:+:1534785308:-1 chr1:+:1571497741:-1 chr1:+:1875701926:-1 chr1:+:2229442855:-1 chr1:+:2779145744:-1 +AGGACACTGCTGAGATTGAAAAGGTCAGACAAAATGACAGTAACTAATTCAGAAATGAGATGTCAAGAATTGAAGTTCTAAAGCAGGGATTAACCTATAA chr1:+:1297613:-1 chr1:+:22530626:-1 chr1:+:265620308:-1 chr1:+:499036734:-1 chr1:+:763137609:-1 chr1:+:898677517:-1 chr1:+:1151449357:-1 chr1:+:1626706081:-1 chr1:+:1677054532:-1 chr1:+:1733053695:-1 chr1:+:1779225003:-1 chr1:+:1867339055:-1 chr1:+:1906727390:-1 chr1:+:2107564801:-1 chr1:+:2555356181:-1 chr1:+:2620543528:-1 +TTATAGGTTAATCCCTGCTTTAGAACTTCAATTCTTGACATCTCATTTCTGAATTAGTTACTGTCATTTTGTCTGACCTTTTCAATCTCAGCAGTGTCCT chr1:+:581351986:0 +TTGCCAGAGTTCTTGCCTGATTATTTTTCATCTGAGAGGGCTGGTGTTCTTTTATCTTTTTGAAATTGTTGTTGCTTGGGTGGGGCTTTTTATTTTTTTA chr1:+:968044754:-1 chr1:+:1375537931:20 chr1:+:1427602276:-1 chr1:+:1922281437:-1 chr1:+:3016960481:-1 +TTGCCAGAGTTCTTGCCTGATTATTTTTCATCTGAGAGGGCTGGTGTTCTTTTATCTTTTTGAAATTGTTGTTGCTTGGGTGGGGCTTTTTATTTTTTTA chr1:+:17674593:-1 chr1:+:212097993:-1 chr1:+:565627800:-1 chr1:+:615466732:-1 chr1:+:622876935:-1 chr1:+:660230078:-1 chr1:+:707858527:-1 chr1:+:944840857:-1 chr1:+:960441734:-1 chr1:+:1013615450:-1 chr1:+:1019377280:-1 chr1:+:1219144446:-1 chr1:+:1397825112:-1 chr1:+:1632062095:-1 chr1:+:1740409545:-1 chr1:+:1804168133:-1 chr1:+:2021810323:-1 chr1:+:2105422334:-1 chr1:+:2123807475:-1 chr1:+:2291524572:-1 chr1:+:2478509793:-1 chr1:+:2864399322:-1 chr1:+:2903003035:-1 +TTGCCAGAGTTCTTGCCTGATTATTTTTCATCTGAGAGGGCTGGTGTTCTTTTATCTTTTTGAAATTGTTGTTGCTTGGGTGGGGCTTTTTATTTTTTTA chr1:+:330340406:17 chr1:+:976111149:-1 chr1:+:1348343895:-1 chr1:+:1415938572:-1 chr1:+:1503761482:-1 chr1:+:1549909013:-1 chr1:+:1565553135:17 chr1:+:1639019218:-1 chr1:+:1718579617:-1 chr1:+:1912516534:15 chr1:+:2034312632:14 chr1:+:2267012892:-1 chr1:+:2572350550:-1 chr1:+:2951357299:-1 +TAAAAAAATAAAAAGCCCCACCCAAGCAACAACAATTTCAAAAAGATAAAAGAACACCAGCCCTCTCAGATGAAAAATAATCAGGCAAGAACTCTGGCAA chr1:+:2124694787:0 +TTCAAAATATCCCAGGAGGCCATCTTGATGCTTCCAAAGTCACCAGAGCAGCACTGCAGTGGGTGGGACCAGTATTTCCTCTCAAGAACTGCAGCTCTCC chr1:+:2124694412:0 +AACTGGCAAAAATGAGTAAATTAGACTGGAGATTAAGAAATGATTAGTACTATGGAGAAAAATAAAGCAGAGAATGGAGATGGGGGTGAATGGGTCAAAA chr1:+:746458027:-1 chr1:+:873136117:-1 chr1:+:1273239236:-1 chr1:+:1475435376:-1 chr1:+:2033725883:-1 chr1:+:2589575441:-1 chr1:+:2792593400:-1 +AACTGGCAAAAATGAGTAAATTAGACTGGAGATTAAGAAATGATTAGTACTATGGAGAAAAATAAAGCAGAGAATGGAGATGGGGGTGAATGGGTCAAAA chr1:+:194713909:-1 chr1:+:1338434409:-1 chr1:+:1881590250:-1 chr1:+:1932357725:-1 chr1:+:2733279219:-1 +AACTGGCAAAAATGAGTAAATTAGACTGGAGATTAAGAAATGATTAGTACTATGGAGAAAAATAAAGCAGAGAATGGAGATGGGGGTGAATGGGTCAAAA chr1:+:28918658:-1 chr1:+:58933116:-1 chr1:+:582044825:-1 chr1:+:938681930:-1 chr1:+:1116147347:-1 chr1:+:1348635679:-1 chr1:+:1478821546:-1 chr1:+:1531303836:-1 chr1:+:3020425577:-1 +TTTTGACCCATTCACCCCCATCTCCATTCTCTGCTTTATTTTTCTCCATAGTACTAATCATTTCTTAATCTCCAGTCTAATTTACTCATTTTTGCCAGTT chr1:+:466898144:-1 chr1:+:927336189:-1 chr1:+:1139838323:0 chr1:+:1341623031:-1 chr1:+:1500759051:-1 chr1:+:1865051763:-1 chr1:+:2588002275:-1 chr1:+:2749714618:-1 chr1:+:2766089610:-1 +ATTCAGGAACTATCCAGTCGATGCTGGTGTGGGTTTATCATATTACTTACTAAATACTTATATGTGTCCCTATTTGTCAATGGCTGATTTATTCGGCTCA chr1:+:1139837946:0 +GGCCCAGCCTAGTGCAAAAATTCTAATCGCTACACTGCTGCATACAATATGATCTCCATAAATATGTGTTGAATGATGTCACAATGTTACTATAACCTAA chr1:+:867154938:0 +CCTGGGCAACAAGAGTGAAACTCAATCTCAAAAAAAAAAAAAAGTTTATTATTTGGCTGGTGAGAAACTGTTGATGTTATTTATCACGTTCCTAGACTAG chr1:+:459792446:-1 chr1:+:776912642:-1 chr1:+:786967347:-1 chr1:+:874546725:-1 chr1:+:924114572:-1 chr1:+:1166522410:-1 chr1:+:1177355717:-1 chr1:+:1471726290:-1 chr1:+:1920845868:-1 chr1:+:1920875785:-1 chr1:+:2147427109:-1 chr1:+:2232540125:-1 chr1:+:2384520563:-1 chr1:+:2470000724:-1 chr1:+:2925135476:-1 chr1:+:2996912513:-1 +CCTGGGCAACAAGAGTGAAACTCAATCTCAAAAAAAAAAAAAAGTTTATTATTTGGCTGGTGAGAAACTGTTGATGTTATTTATCACGTTCCTAGACTAG chr1:+:63828438:-1 chr1:+:369921269:-1 chr1:+:404184672:-1 chr1:+:541407818:-1 chr1:+:674653982:-1 chr1:+:685116972:-1 chr1:+:719605150:-1 chr1:+:890063869:-1 chr1:+:1025316972:-1 chr1:+:1104018607:-1 chr1:+:1231134442:-1 chr1:+:1519364341:-1 chr1:+:1959843957:-1 chr1:+:1979796591:-1 chr1:+:2500884043:-1 chr1:+:2512891328:-1 chr1:+:2515027092:-1 chr1:+:2634032383:-1 chr1:+:2656916585:-1 +CCTGGGCAACAAGAGTGAAACTCAATCTCAAAAAAAAAAAAAAGTTTATTATTTGGCTGGTGAGAAACTGTTGATGTTATTTATCACGTTCCTAGACTAG chr1:+:581722594:-1 chr1:+:704719804:-1 chr1:+:788062559:-1 chr1:+:1574396728:-1 chr1:+:1640697288:-1 chr1:+:1820019049:-1 chr1:+:1921004220:-1 chr1:+:2108132925:-1 chr1:+:2164915551:-1 chr1:+:2281184879:-1 chr1:+:2522378556:-1 +CCTGGGCAACAAGAGTGAAACTCAATCTCAAAAAAAAAAAAAAGTTTATTATTTGGCTGGTGAGAAACTGTTGATGTTATTTATCACGTTCCTAGACTAG chr1:+:24098493:-1 chr1:+:27776062:-1 chr1:+:278240519:-1 chr1:+:417987267:-1 chr1:+:429429395:-1 chr1:+:811469344:-1 chr1:+:1203936998:-1 chr1:+:1260429728:-1 chr1:+:1312486905:-1 chr1:+:1417576543:-1 chr1:+:1803879367:-1 chr1:+:2133427434:-1 chr1:+:2269879244:-1 chr1:+:2363064645:-1 chr1:+:2404312896:-1 chr1:+:2549590322:-1 chr1:+:2921108010:-1 +CCTGGGCAACAAGAGTGAAACTCAATCTCAAAAAAAAAAAAAAGTTTATTATTTGGCTGGTGAGAAACTGTTGATGTTATTTATCACGTTCCTAGACTAG chr1:+:461799749:-1 chr1:+:539928858:-1 chr1:+:731357980:-1 chr1:+:798352370:-1 chr1:+:1022027131:-1 chr1:+:1443166326:-1 chr1:+:1938584082:-1 chr1:+:2223102159:-1 chr1:+:2603803174:-1 chr1:+:2636727966:-1 +CTAGTCTAGGAACGTGATAAATAACATCAACAGTTTCTCACCAGCCAAATAATAAACTTTTTTTTTTTTTTGAGATTGAGTTTCACTCTTGTTGCCCAGG chr1:+:430911497:-1 chr1:+:1272921727:-1 chr1:+:2500608871:-1 +CTAGTCTAGGAACGTGATAAATAACATCAACAGTTTCTCACCAGCCAAATAATAAACTTTTTTTTTTTTTTGAGATTGAGTTTCACTCTTGTTGCCCAGG chr1:+:867155297:2 +AATCTGCAAGTGGACGTTTGGAGGGCTTTGAGGCCTGTGGTGGAAAAGGAAATATCTTCACATAAAAACTAGATAGAAGCATTCTCAGAAACTACTTTGT chr1:+:382227603:13 chr1:+:382231911:11 chr1:+:928007554:10 chr1:+:1291640152:10 chr1:+:1439684489:13 chr1:+:1605936073:11 chr1:+:2942904112:4 +AATCTGCAAGTGGACGTTTGGAGGGCTTTGAGGCCTGTGGTGGAAAAGGAAATATCTTCACATAAAAACTAGATAGAAGCATTCTCAGAAACTACTTTGT chr1:+:1436568075:9 chr1:+:1864773812:15 chr1:+:2687204204:10 chr1:+:2744881819:19 chr1:+:2942860258:11 chr1:+:2942861964:11 +AATCTGCAAGTGGACGTTTGGAGGGCTTTGAGGCCTGTGGTGGAAAAGGAAATATCTTCACATAAAAACTAGATAGAAGCATTCTCAGAAACTACTTTGT chr1:+:1294749271:-1 chr1:+:1295027704:6 chr1:+:1295646182:8 chr1:+:1436561216:10 chr1:+:1605928900:8 chr1:+:1609120166:7 chr1:+:1864735616:11 chr1:+:1866603017:9 chr1:+:2445033357:9 chr1:+:2687322899:16 chr1:+:2687323410:11 +ACAAAGTAGTTTCTGAGAATGCTTCTATCTAGTTTTTATGTGAAGATATTTCCTTTTCCACCACAGGCCTCAAAGCCCTCCAAACGTCCACTTGCAGATT chr1:+:1867478001:4 chr1:+:1867480385:3 chr1:+:2939597702:1 chr1:+:2939599760:1 chr1:+:2939601817:1 chr1:+:2939603874:1 chr1:+:2939605931:1 chr1:+:2939607988:1 chr1:+:2939610045:1 chr1:+:2939612102:1 chr1:+:2939614159:1 chr1:+:2942717118:2 chr1:+:2942719175:1 chr1:+:2942721233:2 chr1:+:2942723290:1 chr1:+:2942725346:1 chr1:+:2942727402:2 chr1:+:2942729458:2 chr1:+:2942731515:3 chr1:+:2942733572:3 chr1:+:2942735629:2 chr1:+:2942739742:1 chr1:+:2942741799:3 chr1:+:2942743856:0 chr1:+:2942745913:0 chr1:+:2942747970:2 chr1:+:2942752084:2 chr1:+:2942754141:2 chr1:+:2942756196:2 +AACTCTCAAAGGCAGGTTCATCTCTGCGAGTTAAATGCATTCATCATGAAGAACTTTCTCAGAGTGTTTGTGTTTAGTTATGGGAAATTATTCCCGTTTC chr1:+:2939597318:3 chr1:+:2939599376:3 chr1:+:2939603490:1 chr1:+:2939607604:1 chr1:+:2939609661:1 chr1:+:2939613775:1 chr1:+:2942724962:0 chr1:+:2942731131:0 chr1:+:2942733188:0 chr1:+:2942735245:0 chr1:+:2942737301:0 chr1:+:2942739358:0 chr1:+:2942743472:1 chr1:+:2942745529:1 chr1:+:2942747586:2 chr1:+:2942749643:3 chr1:+:2942751700:0 chr1:+:2942753757:1 +ATGGGAAGGCGTACTGCTTTAATCCGTCACTTTCCACATGGTAAGCAAGCTGACCCCCAGTCCTATTCCCTGGAAGAGTGTCTGTCTGCTCTAGACAGCA chr1:+:1076623529:-1 chr1:+:2465328657:-1 chr1:+:2860111700:-1 +ATGGGAAGGCGTACTGCTTTAATCCGTCACTTTCCACATGGTAAGCAAGCTGACCCCCAGTCCTATTCCCTGGAAGAGTGTCTGTCTGCTCTAGACAGCA chr1:+:103434718:-1 chr1:+:457448842:-1 chr1:+:617260384:-1 chr1:+:749118748:-1 chr1:+:887277328:-1 chr1:+:944183023:-1 chr1:+:971080043:-1 chr1:+:2481510666:-1 chr1:+:2677466144:-1 chr1:+:2801335843:-1 chr1:+:2848711856:-1 chr1:+:3056092530:-1 +ATGGGAAGGCGTACTGCTTTAATCCGTCACTTTCCACATGGTAAGCAAGCTGACCCCCAGTCCTATTCCCTGGAAGAGTGTCTGTCTGCTCTAGACAGCA chr1:+:29439973:-1 chr1:+:116848159:-1 chr1:+:1065166288:-1 chr1:+:1782905650:-1 chr1:+:1903070415:-1 chr1:+:2105029528:-1 chr1:+:2152052186:-1 chr1:+:2867943136:-1 chr1:+:3035532382:-1 +TGCTGTCTAGAGCAGACAGACACTCTTCCAGGGAATAGGACTGGGGGTCAGCTTGCTTACCATGTGGAAAGTGACGGATTAAAGCAGTACGCCTTCCCAT chr1:+:2849071923:0 +GCTCATGGTGGCTAAGGGGGCCACAGCAAAAACCATAAAAATTTTGGGGCTTTTTCAAAAAGTGCCTCCTGAAAATAATGCAGGAGGACAGTGCTCCTGC chr1:+:2849071675:0 +AAACATTTCTTATAGTCCCATTATAAAAAAGATATTGTGGCTACATATTTAGGATGAGATTTAATCAGATTCTTTATAAGTAATTCTAAGCCATATTAAG chr1:+:2164654460:0 +AGCCACTGAAAATAATTTTGAATAGATGATAAAGTACTTTTTTATGTACTGTAATAGCTTGTGCATTTCTTCTGAATATACTTTCTGATGTTGCCAAGGT chr1:+:167146581:-1 chr1:+:188552962:-1 chr1:+:521571231:-1 chr1:+:597327024:-1 chr1:+:1126712572:-1 chr1:+:1164093644:-1 chr1:+:1295511479:-1 chr1:+:1494328787:-1 chr1:+:2139803905:-1 chr1:+:2909107282:-1 +AGCCACTGAAAATAATTTTGAATAGATGATAAAGTACTTTTTTATGTACTGTAATAGCTTGTGCATTTCTTCTGAATATACTTTCTGATGTTGCCAAGGT chr1:+:424766652:-1 chr1:+:621877768:-1 chr1:+:711225445:-1 chr1:+:721006108:-1 chr1:+:755110622:-1 chr1:+:791516486:-1 chr1:+:943369001:-1 chr1:+:945125208:-1 chr1:+:971982428:-1 chr1:+:1173069455:-1 chr1:+:1318724129:-1 chr1:+:1411286952:-1 chr1:+:1488845263:-1 chr1:+:1646709137:-1 chr1:+:1733697017:-1 chr1:+:1849231318:-1 chr1:+:1917526060:-1 chr1:+:2236442924:-1 chr1:+:2353668530:-1 chr1:+:2988885830:-1 +AGCCACTGAAAATAATTTTGAATAGATGATAAAGTACTTTTTTATGTACTGTAATAGCTTGTGCATTTCTTCTGAATATACTTTCTGATGTTGCCAAGGT chr1:+:5476917:-1 chr1:+:34763609:-1 chr1:+:74809011:-1 chr1:+:156902589:-1 chr1:+:161416720:-1 chr1:+:161424100:-1 chr1:+:161431511:-1 chr1:+:161438891:-1 chr1:+:168302595:-1 chr1:+:198205278:-1 chr1:+:216048288:-1 chr1:+:295578050:-1 chr1:+:297528953:-1 chr1:+:300800804:-1 chr1:+:318417449:-1 chr1:+:351356037:-1 chr1:+:363255879:-1 chr1:+:434678993:-1 chr1:+:492800576:-1 chr1:+:521742581:-1 chr1:+:556824441:-1 chr1:+:640718892:-1 chr1:+:650442029:-1 chr1:+:675615430:-1 chr1:+:842105404:-1 chr1:+:863070048:-1 chr1:+:914146097:-1 chr1:+:972220387:-1 chr1:+:991222517:-1 chr1:+:1045768901:-1 chr1:+:1149280934:-1 chr1:+:1225997912:-1 chr1:+:1229354478:-1 chr1:+:1305747945:-1 chr1:+:1341862196:-1 chr1:+:1343146217:-1 chr1:+:1362576557:-1 chr1:+:1392072531:-1 chr1:+:1473659171:-1 chr1:+:1486530038:-1 chr1:+:1491056984:-1 chr1:+:1523706647:-1 chr1:+:1530839953:-1 chr1:+:1568816778:-1 chr1:+:1649765811:-1 chr1:+:1680525926:-1 chr1:+:1699693695:-1 chr1:+:1726522157:-1 chr1:+:1767317361:-1 chr1:+:1788683250:-1 chr1:+:1803521067:-1 chr1:+:1856657484:-1 chr1:+:1960605964:-1 chr1:+:1963406379:-1 chr1:+:2052650904:-1 chr1:+:2063929468:-1 chr1:+:2081425216:-1 chr1:+:2084616726:-1 chr1:+:2198624774:-1 chr1:+:2255527178:-1 chr1:+:2281561896:-1 chr1:+:2396906346:-1 chr1:+:2400698142:-1 chr1:+:2444784704:-1 chr1:+:2467172921:-1 chr1:+:2500319365:-1 chr1:+:2502997918:-1 chr1:+:2531931681:-1 chr1:+:2677153376:-1 chr1:+:2687605522:-1 chr1:+:2712109933:-1 chr1:+:2826802772:-1 chr1:+:2896252647:-1 chr1:+:2909319733:-1 chr1:+:2954303235:-1 +ACCTTGGCAACATCAGAAAGTATATTCAGAAGAAATGCACAAGCTATTACAGTACATAAAAAAGTACTTTATCATCTATTCAAAATTATTTTCAGTGGCT chr1:+:2164654835:0 +CATTCAAAAGTTGAAAGGTGCCTGCTTAGCTGCTTTCCTCTCTAGAGGAGCAGGGTCAGAACACACAGAGGCGGCCAGGAATACAACACAGGCAGAAGGT chr1:+:1471689523:-1 chr1:+:1774277712:-1 chr1:+:1873174070:-1 chr1:+:2055733125:-1 +CATTCAAAAGTTGAAAGGTGCCTGCTTAGCTGCTTTCCTCTCTAGAGGAGCAGGGTCAGAACACACAGAGGCGGCCAGGAATACAACACAGGCAGAAGGT chr1:+:749241356:-1 chr1:+:1880356646:-1 chr1:+:2193859369:-1 chr1:+:2505691026:-1 chr1:+:2716146077:-1 chr1:+:2716177825:-1 chr1:+:2863749018:-1 +CATTCAAAAGTTGAAAGGTGCCTGCTTAGCTGCTTTCCTCTCTAGAGGAGCAGGGTCAGAACACACAGAGGCGGCCAGGAATACAACACAGGCAGAAGGT chr1:+:182310393:-1 chr1:+:1691664346:-1 chr1:+:2141609120:-1 chr1:+:2480563916:-1 chr1:+:2935108567:-1 +ACCTTCTGCCTGTGTTGTATTCCTGGCCGCCTCTGTGTGTTCTGACCCTGCTCCTCTAGAGAGGAAAGCAGCTAAGCAGGCACCTTTCAACTTTTGAATG chr1:+:2820429123:0 +ATCAGTGTTTTAATTAGAATCACAAAGCCAAATGATTGCCTCATTGGATAATTTTAAGTATTATGCTGCAATTCAATATAGGTACCAAGTACTTAACTAG chr1:+:2820428728:0 +TATCTTTATAAAATCTTAACCAATGATAGGATAATTCCTACTCCCTGGTTCTTTTTTAGGACAATCTTGGCTATTGAGTCTTTTCTATATGGATTTAAGA chr1:+:987786258:0 +AATGAATGACAACTCAATCTATGATCAATTCTGTTTGATATAGGGTAATGAGCAGATGAAACTCACTAGTTCCTCACTGAAGAAATATATTCCCCAAATA chr1:+:116409269:-1 chr1:+:264310719:-1 chr1:+:790964556:-1 chr1:+:1398456875:-1 chr1:+:1689769808:-1 +AATGAATGACAACTCAATCTATGATCAATTCTGTTTGATATAGGGTAATGAGCAGATGAAACTCACTAGTTCCTCACTGAAGAAATATATTCCCCAAATA chr1:+:241297982:-1 +AATGAATGACAACTCAATCTATGATCAATTCTGTTTGATATAGGGTAATGAGCAGATGAAACTCACTAGTTCCTCACTGAAGAAATATATTCCCCAAATA chr1:+:29648085:-1 chr1:+:454654051:-1 chr1:+:503975399:-1 chr1:+:728027445:-1 chr1:+:1129542286:-1 chr1:+:1188759488:-1 chr1:+:1238893789:-1 chr1:+:1359504542:-1 chr1:+:1465657759:-1 chr1:+:1761386147:-1 chr1:+:2033725941:-1 +TATTTGGGGAATATATTTCTTCAGTGAGGAACTAGTGAGTTTCATCTGCTCATTACCCTATATCAAACAGAATTGATCATAGATTGAGTTGTCATTCATT chr1:+:987786626:0 +ACACAAAACATTTCATACACACCATCATCAAACAAGGCTATTCTATGACCATGATGGATCAAGACAAAAACAAGACTACTCTGAATTCACATCTGAAAAC chr1:+:1643133247:0 +AAGAAGAAAGTTACTCCTTCTGTCCAAAAGACTAAAATCTTTTCATCATATGAGCCCATTAATAATAAATCTCCCAGAAGAACTGAAGTCACAGAGAGGG chr1:+:683764852:-1 chr1:+:813190926:-1 chr1:+:824564863:-1 chr1:+:899363420:-1 chr1:+:1164678664:-1 chr1:+:1330892913:-1 chr1:+:1959204754:-1 chr1:+:2403718142:-1 chr1:+:2912348890:-1 +AAGAAGAAAGTTACTCCTTCTGTCCAAAAGACTAAAATCTTTTCATCATATGAGCCCATTAATAATAAATCTCCCAGAAGAACTGAAGTCACAGAGAGGG chr1:+:114462836:-1 chr1:+:170749092:-1 chr1:+:207659628:-1 chr1:+:296314203:-1 chr1:+:393179126:-1 chr1:+:403519527:-1 chr1:+:535502950:-1 chr1:+:535507409:-1 chr1:+:535507432:-1 chr1:+:535508588:-1 chr1:+:686875853:-1 chr1:+:748567948:-1 chr1:+:1007707652:-1 chr1:+:1223139993:-1 chr1:+:1760571464:-1 chr1:+:1813878081:-1 chr1:+:1932192983:-1 chr1:+:2075568950:-1 chr1:+:2495002868:-1 chr1:+:2743048302:-1 chr1:+:2754816681:-1 chr1:+:2766983863:-1 chr1:+:2869571485:-1 chr1:+:3057355577:-1 +AAGAAGAAAGTTACTCCTTCTGTCCAAAAGACTAAAATCTTTTCATCATATGAGCCCATTAATAATAAATCTCCCAGAAGAACTGAAGTCACAGAGAGGG chr1:+:15685243:-1 chr1:+:31674009:-1 chr1:+:182618922:-1 chr1:+:219226901:-1 chr1:+:386282438:-1 chr1:+:494761093:-1 chr1:+:506592026:-1 chr1:+:727889122:-1 chr1:+:823363777:-1 chr1:+:911966044:-1 chr1:+:974806083:-1 chr1:+:993864052:-1 chr1:+:1017080663:-1 chr1:+:1139235207:-1 chr1:+:1148645356:-1 chr1:+:1177308760:-1 chr1:+:1228782751:-1 chr1:+:1281129534:-1 chr1:+:1284774130:-1 chr1:+:1358790844:-1 chr1:+:1543296144:-1 chr1:+:1581405340:-1 chr1:+:1607453328:-1 chr1:+:1609800179:-1 chr1:+:1728163556:-1 chr1:+:1728671884:-1 chr1:+:1757954044:-1 chr1:+:1790139278:-1 chr1:+:1851954432:-1 chr1:+:2004652411:-1 chr1:+:2073805964:-1 chr1:+:2076811140:-1 chr1:+:2154484454:-1 chr1:+:2265196535:-1 chr1:+:2280128912:-1 chr1:+:2364583126:-1 chr1:+:2404597019:-1 chr1:+:2419443286:-1 chr1:+:2437392765:-1 chr1:+:2438422335:-1 chr1:+:2470555599:-1 chr1:+:2539382493:-1 chr1:+:2585758091:-1 chr1:+:2591217076:-1 chr1:+:2603593867:-1 chr1:+:2604805220:-1 chr1:+:2760606354:-1 chr1:+:2792190368:-1 chr1:+:2922892524:-1 chr1:+:3028074455:-1 +CCCTCTCTGTGACTTCAGTTCTTCTGGGAGATTTATTATTAATGGGCTCATATGATGAAAAGATTTTAGTCTTTTGGACAGAAGGAGTAACTTTCTTCTT chr1:+:1643133636:0 +CTTTTCTGGGAAATCCAAAAGTCAAGTCTGGTAGAATTTAGGGCACCACTCTGCTCCCTGATAAAGAAGTTCAGACTGAGCTCCACTGCCTGCCCAATTG chr1:+:1271383634:0 +AGAGGGATACTGCACAGGCTCACTGTATAATTGTATCCCAAAGCAAATAGTATATTTCTATTTCCTAACAGCTTCTGAGATGAGAGGAAGACAAGAGGAG chr1:+:105613679:-1 chr1:+:902616349:-1 chr1:+:1255980253:-1 chr1:+:1403094551:-1 chr1:+:1660055116:-1 chr1:+:2006698156:-1 chr1:+:2154592688:-1 chr1:+:2756970780:-1 chr1:+:2892140570:-1 +AGAGGGATACTGCACAGGCTCACTGTATAATTGTATCCCAAAGCAAATAGTATATTTCTATTTCCTAACAGCTTCTGAGATGAGAGGAAGACAAGAGGAG chr1:+:487482824:-1 chr1:+:509771891:-1 chr1:+:606327763:-1 chr1:+:752537986:-1 chr1:+:800269801:-1 chr1:+:855621115:-1 chr1:+:986602586:-1 chr1:+:1686486939:-1 chr1:+:1786180123:-1 chr1:+:1822543038:-1 chr1:+:1894501340:-1 chr1:+:1917087377:-1 chr1:+:1966253789:-1 chr1:+:1973239833:-1 chr1:+:2030917657:-1 chr1:+:2177457579:-1 chr1:+:2428469209:-1 chr1:+:2719513863:-1 chr1:+:2847453496:-1 chr1:+:2884440522:-1 +AGAGGGATACTGCACAGGCTCACTGTATAATTGTATCCCAAAGCAAATAGTATATTTCTATTTCCTAACAGCTTCTGAGATGAGAGGAAGACAAGAGGAG chr1:+:963178610:-1 chr1:+:2000926679:-1 chr1:+:2015092863:-1 chr1:+:2186999515:-1 chr1:+:2334652139:-1 chr1:+:2441012089:-1 chr1:+:2621050889:-1 chr1:+:2930739399:-1 +CTCCTCTTGTCTTCCTCTCATCTCAGAAGCTGTTAGGAAATAGAAATATACTATTTGCTTTGGGATACAATTATACAGTGAGCCTGTGCAGTATCCCTCT chr1:+:1271384010:3 +GATGATTCCATATGAGTCAATTCGATGATGATTCCATACGAGTCCGTTGGATGATAATTCCATTTGATTTCATTCAATCCTTCTATTCGATTCCATTTGA chr1:+:2444000979:-1 chr1:+:2456209434:8 chr1:+:2456215248:9 chr1:+:2456221354:9 +GATGATTCCATATGAGTCAATTCGATGATGATTCCATACGAGTCCGTTGGATGATAATTCCATTTGATTTCATTCAATCCTTCTATTCGATTCCATTTGA chr1:+:341520006:18 chr1:+:2443997947:-1 chr1:+:2444000010:19 chr1:+:2444000411:-1 chr1:+:2456228879:-1 chr1:+:2456232912:-1 chr1:+:3049948480:-1 +GATGATTCCATATGAGTCAATTCGATGATGATTCCATACGAGTCCGTTGGATGATAATTCCATTTGATTTCATTCAATCCTTCTATTCGATTCCATTTGA chr1:+:107971789:-1 chr1:+:219854203:-1 chr1:+:339624006:-1 chr1:+:339630668:-1 chr1:+:339642860:-1 chr1:+:340852156:-1 chr1:+:340864348:-1 chr1:+:752870076:-1 chr1:+:755773324:-1 chr1:+:846208064:-1 chr1:+:1001908986:-1 chr1:+:1088018190:-1 chr1:+:1199294263:-1 chr1:+:1258539921:-1 chr1:+:1539306274:-1 chr1:+:1608389787:-1 chr1:+:1609366352:-1 chr1:+:1609617262:-1 chr1:+:1802836320:-1 chr1:+:1831530963:-1 chr1:+:1924425718:-1 chr1:+:2443703496:-1 chr1:+:2443997872:18 chr1:+:2444000359:-1 chr1:+:2607528467:-1 chr1:+:2880036941:-1 chr1:+:2931196966:-1 chr1:+:3019316845:-1 chr1:+:3098372040:-1 +GATGATTCCATATGAGTCAATTCGATGATGATTCCATACGAGTCCGTTGGATGATAATTCCATTTGATTTCATTCAATCCTTCTATTCGATTCCATTTGA chr1:+:229385217:-1 chr1:+:248116405:-1 chr1:+:293947172:-1 chr1:+:438833217:-1 chr1:+:522604330:-1 chr1:+:700538078:-1 chr1:+:779887983:-1 chr1:+:884090587:-1 chr1:+:1082007030:-1 chr1:+:1259706501:-1 chr1:+:1269086560:-1 chr1:+:1491741878:-1 chr1:+:1693619527:-1 chr1:+:1920919676:-1 chr1:+:1924937230:-1 chr1:+:1966305102:-1 chr1:+:2296332918:-1 chr1:+:2502630074:-1 chr1:+:3009921965:-1 chr1:+:3049947070:-1 +TCAAATGGAATCGAATAGAAGGATTGAATGAAATCAAATGGAATTATCATCCAACGGACTCGTATGGAATCATCATCGAATTGACTCATATGGAATCATC chr1:+:339094422:-1 chr1:+:1291205659:-1 chr1:+:1291207088:-1 chr1:+:1291207361:-1 chr1:+:1291207794:20 chr1:+:1291209169:-1 chr1:+:1291210798:-1 chr1:+:1291210824:-1 chr1:+:1291210850:19 chr1:+:1291210876:18 chr1:+:1291210902:18 chr1:+:1291210954:19 chr1:+:1291711334:-1 chr1:+:1295399476:-1 chr1:+:1295400806:-1 chr1:+:1295402421:-1 chr1:+:1295402640:-1 chr1:+:1295404034:-1 chr1:+:1295405023:-1 chr1:+:1295405953:20 chr1:+:1295406202:-1 chr1:+:1295409131:-1 chr1:+:1295409979:-1 chr1:+:1295410285:-1 chr1:+:1295413758:-1 chr1:+:1295416262:-1 chr1:+:1295439343:-1 chr1:+:1295444616:19 chr1:+:1295444737:-1 chr1:+:1295445111:-1 chr1:+:1295447182:-1 chr1:+:1295448115:-1 chr1:+:1295448350:-1 chr1:+:1295450344:-1 chr1:+:1295451534:-1 chr1:+:1295455190:14 chr1:+:1295455849:-1 chr1:+:1295458807:-1 chr1:+:1295459973:-1 chr1:+:1719248497:-1 chr1:+:1719249418:16 chr1:+:1719254163:-1 chr1:+:1722975070:-1 chr1:+:2443685950:-1 chr1:+:2443689027:19 chr1:+:2443689183:18 chr1:+:2443689739:-1 chr1:+:2443689817:20 chr1:+:2443689921:19 chr1:+:2443689999:20 chr1:+:2443690048:19 chr1:+:2443690152:18 chr1:+:2443690333:20 chr1:+:2443691774:-1 chr1:+:2456236184:-1 chr1:+:2456238882:-1 chr1:+:2456242586:-1 chr1:+:2456244717:2 chr1:+:2456245360:-1 chr1:+:2456246216:-1 chr1:+:2456248244:-1 chr1:+:2456250218:18 chr1:+:2456250927:-1 chr1:+:2456254799:-1 chr1:+:2456255781:19 chr1:+:2456256424:-1 chr1:+:2456260137:-1 chr1:+:2456260209:-1 chr1:+:2456265535:-1 chr1:+:2456271203:-1 chr1:+:2456271252:-1 chr1:+:2456273540:-1 chr1:+:2456316948:-1 chr1:+:2456317118:-1 chr1:+:2846580739:-1 chr1:+:2846581358:-1 chr1:+:2846582894:-1 chr1:+:2846583881:-1 chr1:+:2846591015:-1 +CACATGGAATGGAATTGAATTGAATCATTCAATGGACTCCAATGGAATCATCATCGAATGGAATCAAATGAAATCATCATCAGATGGAATCAAATGGAAT chr1:+:339094444:14 chr1:+:1291203346:18 chr1:+:1291711356:17 chr1:+:1294712650:19 chr1:+:1294712709:16 chr1:+:1295399498:16 chr1:+:1295401549:15 chr1:+:1295405975:16 chr1:+:1295406224:-1 chr1:+:1295410001:14 chr1:+:1295410111:20 chr1:+:1295416284:17 chr1:+:1295440378:16 chr1:+:1295441044:16 chr1:+:1295444315:15 chr1:+:1295444638:19 chr1:+:1295445133:15 chr1:+:1295455264:18 chr1:+:1719248519:-1 chr1:+:1719249440:19 chr1:+:1719261158:19 chr1:+:1722975092:17 chr1:+:2443690021:20 chr1:+:2456235049:3 chr1:+:2456235716:-1 chr1:+:2456238195:19 chr1:+:2456238904:17 chr1:+:2456242608:-1 chr1:+:2456244370:2 chr1:+:2456245949:-1 chr1:+:2456247776:-1 chr1:+:2456250240:19 chr1:+:2456250949:18 chr1:+:2456254821:18 chr1:+:2456260159:17 chr1:+:2456260231:17 chr1:+:2456268880:20 chr1:+:2456271225:14 chr1:+:2456273562:18 chr1:+:2456317042:17 chr1:+:2846578070:14 chr1:+:2846580761:20 chr1:+:2846582867:19 +AATTTAAAAGCTGTGGATAGTGTATAGATAAACCAAAAGGGATAATTCTGTATGTACCCTGCAACTGTTACCTTCTCTAGGCCTGAAGGGATGAAGGGCA chr1:+:2354625352:3 +TGCCCTTCATCCCTTCAGGCCTAGAGAAGGTAACAGTTGCAGGGTACATACAGAATTATCCCTTTTGGTTTATCTATACACTATCCACAGCTTTTAAATT chr1:+:2744508525:1 +TGCCCTTCATCCCTTCAGGCCTAGAGAAGGTAACAGTTGCAGGGTACATACAGAATTATCCCTTTTGGTTTATCTATACACTATCCACAGCTTTTAAATT chr1:+:1291457573:2 +AAAGGTGTGTTCTACATCTTTCACAGTCTCCAGCATGACTGAACCCTAGCTGCCCACAGTAGAAACCAGGTTATTCATGTGCACTTCATTGCCTTTCATT chr1:+:1291457193:5 chr1:+:1988818818:5 chr1:+:2744508145:4 chr1:+:2748058578:3 +AAAGGTGTGTTCTACATCTTTCACAGTCTCCAGCATGACTGAACCCTAGCTGCCCACAGTAGAAACCAGGTTATTCATGTGCACTTCATTGCCTTTCATT chr1:+:381297911:-1 +CTGATGGGTAAAAAAAAAATCGGTTGCTTAGATTGCAGTGGTAGTCTGATTACTGGTAGCTTTGAGCTAATGGGTAGTCTAGAACAACTAAGTTTCCGAC chr1:+:2381678920:0 +GTCGGAAACTTAGTTGTTCTAGACTACCCATTAGCTCAAAGCTACCAGTAATCAGACTACCACTGCAATCTAAGCAACCGATTTTTTTTTTACCCATCAG chr1:+:2380214317:0 +AACTATGGTCAGCCTTCTGTATCCTCGGGTTCTGGGTCCTTGGATTTAACAAACTGTGCATCAAAAATCTTTGGAAAAAGTAAAACAATAAAAAAATACA chr1:+:2380213916:3 +AACTATGGTCAGCCTTCTGTATCCTCGGGTTCTGGGTCCTTGGATTTAACAAACTGTGCATCAAAAATCTTTGGAAAAAGTAAAACAATAAAAAAATACA chr1:+:782246826:-1 +TGTATTTTTTTATTGTTTTACTTTTTCCAAAGATTTTTGATGCACAGTTTGTTAAATCCAAGGACCCAGAACCCGAGGATACAGAAGGCTGACCATAGTT chr1:+:2381679321:3 +AATCGTTGGTCTTCTTCAATTAGGGCATGAGCAAGATAATTTTTTCCCTTGAAAATTGACGTGGATATTCTTCCATTGCAGGCTTTATCTTCAACATCGA chr1:+:436991164:20 chr1:+:857028701:-1 chr1:+:1741619318:-1 chr1:+:1794149267:20 chr1:+:2924183029:-1 chr1:+:2990040155:-1 chr1:+:2990356200:-1 +AATCGTTGGTCTTCTTCAATTAGGGCATGAGCAAGATAATTTTTTCCCTTGAAAATTGACGTGGATATTCTTCCATTGCAGGCTTTATCTTCAACATCGA chr1:+:1003845038:-1 chr1:+:1386570003:-1 chr1:+:1620513362:-1 chr1:+:2013544876:-1 chr1:+:2066749504:-1 +AATCGTTGGTCTTCTTCAATTAGGGCATGAGCAAGATAATTTTTTCCCTTGAAAATTGACGTGGATATTCTTCCATTGCAGGCTTTATCTTCAACATCGA chr1:+:103402036:-1 chr1:+:192314473:-1 chr1:+:631680507:-1 chr1:+:651863001:-1 chr1:+:749296066:-1 chr1:+:829405004:-1 chr1:+:941358292:-1 chr1:+:1064006522:-1 chr1:+:1078614591:-1 chr1:+:1099770787:-1 chr1:+:1205329482:-1 chr1:+:1280277927:-1 chr1:+:1301160258:-1 chr1:+:1319717850:-1 chr1:+:1349463940:-1 chr1:+:1388039902:-1 chr1:+:1411481429:-1 chr1:+:1668366419:-1 chr1:+:1985356690:-1 chr1:+:2123713735:-1 chr1:+:2177790379:-1 chr1:+:2180112870:-1 chr1:+:2292084539:-1 chr1:+:2425403262:-1 chr1:+:2691817496:-1 chr1:+:2767840909:-1 chr1:+:2921387623:-1 +AATCGTTGGTCTTCTTCAATTAGGGCATGAGCAAGATAATTTTTTCCCTTGAAAATTGACGTGGATATTCTTCCATTGCAGGCTTTATCTTCAACATCGA chr1:+:384567449:-1 chr1:+:711411197:-1 chr1:+:917280039:-1 chr1:+:1400999077:-1 chr1:+:1725361728:-1 chr1:+:2150372454:-1 chr1:+:2463515073:-1 chr1:+:2600263300:-1 chr1:+:2877801471:-1 chr1:+:2980185037:-1 chr1:+:3016949226:-1 +TCGATGTTGAAGATAAAGCCTGCAATGGAAGAATATCCACGTCAATTTTCAAGGGAAAAAATTATCTTGCTCATGCCCTAATTGAAGAAGACCAACGATT chr1:+:1145760319:0 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+GGTGCTGAGCAAGGGGTGTATTTCAGCTGCGTTTGTGTTACAGCTCTTTAGTCCCACCATTTGGCTGGTCCTGAGTTCTTGTCCTGCATCCAGAAAGAAT chr1:+:519057273:-1 chr1:+:2037164324:20 +CCTGGCAGGCTGCACTTGGCTTGCGCCACTGGCAAGTCAGGGGCCAGCCAGGAATGGCGCGGAGAGGGTTGGTTGAGTTAGGGGAGGGTATGGCCGTTTC chr1:+:38697760:-1 chr1:+:348806235:-1 chr1:+:1235169533:-1 chr1:+:1535797732:-1 chr1:+:2392800054:-1 chr1:+:2856925184:-1 +CCTGGCAGGCTGCACTTGGCTTGCGCCACTGGCAAGTCAGGGGCCAGCCAGGAATGGCGCGGAGAGGGTTGGTTGAGTTAGGGGAGGGTATGGCCGTTTC chr1:+:17524161:-1 chr1:+:18987250:-1 chr1:+:21861103:-1 chr1:+:420033143:-1 chr1:+:852647294:-1 chr1:+:919325850:-1 chr1:+:952958789:-1 chr1:+:1113690730:-1 chr1:+:1115110931:-1 chr1:+:1308321678:-1 chr1:+:1308535853:-1 chr1:+:1333531384:-1 chr1:+:1385894184:-1 chr1:+:1496624019:-1 chr1:+:1567649781:-1 chr1:+:1725427355:-1 chr1:+:1920914334:-1 chr1:+:1931351127:-1 chr1:+:1995268416:-1 chr1:+:2179879616:-1 chr1:+:2270239784:-1 chr1:+:2366067631:-1 chr1:+:2426070238:-1 chr1:+:2467605662:-1 chr1:+:2553407523:-1 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chr1:+:1989343619:9 chr1:+:2011048746:7 chr1:+:2065437546:8 chr1:+:2146054050:8 chr1:+:2229399718:10 chr1:+:2245229842:13 chr1:+:2254640760:7 chr1:+:2549558165:8 chr1:+:2759412091:7 chr1:+:2811652047:7 chr1:+:2902394964:8 chr1:+:2907389380:6 chr1:+:2936613292:8 chr1:+:2945536488:7 chr1:+:2945563164:9 chr1:+:2946710955:9 chr1:+:2976476786:13 chr1:+:3022244777:10 chr1:+:3039619303:9 chr1:+:3052701866:8 chr1:+:3059746615:0 chr1:+:3061308791:7 +ACTGCCTGACTTAATAGTAAAACAATAGAACTAACCCATACAAGGATGGAAACAAGATTATGATGCTAATTCATATTTTGCTGAAAGGTTTAGCCCAGGA chr1:+:102855526:-1 chr1:+:531164875:-1 chr1:+:719086100:-1 chr1:+:765106218:-1 chr1:+:1459770393:-1 chr1:+:1711282790:-1 chr1:+:2438199298:-1 chr1:+:2762957008:-1 +ACTGCCTGACTTAATAGTAAAACAATAGAACTAACCCATACAAGGATGGAAACAAGATTATGATGCTAATTCATATTTTGCTGAAAGGTTTAGCCCAGGA chr1:+:613475266:-1 chr1:+:1180326509:-1 chr1:+:1576526802:-1 chr1:+:1611651684:-1 chr1:+:1634167642:-1 chr1:+:1649475602:-1 chr1:+:2069160648:-1 chr1:+:2627094672:-1 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chr1:+:2199265062:-1 chr1:+:2199265409:-1 chr1:+:2199265485:-1 chr1:+:2240263079:-1 chr1:+:2347415485:-1 chr1:+:2418086901:-1 chr1:+:2436810329:-1 chr1:+:2485977214:-1 chr1:+:2550971756:-1 chr1:+:2749728835:-1 chr1:+:2953815751:-1 chr1:+:3014007829:-1 chr1:+:3030126510:-1 +CATTTGGAGGGTGATTGGATGCACGAAATTCAGCCAGGATGCAGGAGATGGGGGTAAATCTTAAAGCGCGGCCCTTTCAGCACTGTGCTAAGTGCTCTGT chr1:+:2298955460:0 +TTCTAGTAATAAAAATTTTGTTCTTAGATACCACTGAGAGTATTTGGATCTATACCAAGGCTTCAGACATTGTCTTCTATATTCAAAAGTGTTATTTCTT chr1:+:1181764622:0 +GTACTAAGGCTAGGAAACCAAGATTCTAAATTCTGTATTTAGGACAGGGGAGGGAAAGGTAGCAGCTCTAGAGATGGCATGTGTCTAAGTGATTCTTTGC chr1:+:33623725:-1 chr1:+:709580299:-1 chr1:+:713587850:-1 chr1:+:1375242516:-1 chr1:+:2283012929:-1 +GTACTAAGGCTAGGAAACCAAGATTCTAAATTCTGTATTTAGGACAGGGGAGGGAAAGGTAGCAGCTCTAGAGATGGCATGTGTCTAAGTGATTCTTTGC chr1:+:167295463:-1 chr1:+:326037181:-1 chr1:+:375142621:-1 chr1:+:785858293:-1 chr1:+:850662736:-1 chr1:+:1243264009:-1 chr1:+:1397964210:-1 chr1:+:1619631073:-1 chr1:+:1969300455:-1 chr1:+:2007745114:-1 chr1:+:2029663067:-1 chr1:+:2133480400:-1 chr1:+:2222451517:-1 chr1:+:2557700099:-1 chr1:+:2775050905:-1 +GTACTAAGGCTAGGAAACCAAGATTCTAAATTCTGTATTTAGGACAGGGGAGGGAAAGGTAGCAGCTCTAGAGATGGCATGTGTCTAAGTGATTCTTTGC chr1:+:11174985:-1 chr1:+:41510275:-1 chr1:+:192050677:-1 chr1:+:205762221:-1 chr1:+:363090038:-1 chr1:+:581472761:-1 chr1:+:595495780:-1 chr1:+:689682252:-1 chr1:+:818680517:-1 chr1:+:838882430:-1 chr1:+:974324261:-1 chr1:+:1085808829:-1 chr1:+:1100089078:-1 chr1:+:1386904362:-1 chr1:+:1724640473:-1 chr1:+:1949752892:-1 chr1:+:2007511486:-1 chr1:+:2158728278:-1 chr1:+:2295326884:-1 chr1:+:2442176664:-1 chr1:+:2443173850:-1 chr1:+:2492275751:-1 chr1:+:2509774895:-1 chr1:+:2978037512:-1 chr1:+:3033617057:-1 +GCAAAGAATCACTTAGACACATGCCATCTCTAGAGCTGCTACCTTTCCCTCCCCTGTCCTAAATACAGAATTTAGAATCTTGGTTTCCTAGCCTTAGTAC chr1:+:1181765026:0 +CTTGCATGGATGGGTCTCTCCTTTCTAGTGAAAGAACCTAGGCAGTTCTTTCACTGTGAATTGTACATAAAGTACATACCGTGTGCCAGGAGATATGGAA chr1:+:1978320741:5 +ACACTTTCTTACAAAAGCTCAGAGTGCTAAAGCTGGATAAACATAAATAGACAGCAAATAAAAGTTCATTGCTCCTGTCCAGCATCACGGCAACAATTCT chr1:+:328090645:-1 chr1:+:493527495:-1 chr1:+:781372175:-1 chr1:+:1197951431:-1 chr1:+:1894051205:-1 chr1:+:1915477768:-1 chr1:+:2231247036:-1 chr1:+:2436178257:-1 chr1:+:2655579014:-1 +ACACTTTCTTACAAAAGCTCAGAGTGCTAAAGCTGGATAAACATAAATAGACAGCAAATAAAAGTTCATTGCTCCTGTCCAGCATCACGGCAACAATTCT chr1:+:13535831:-1 chr1:+:13756691:-1 chr1:+:95716213:-1 chr1:+:254152093:-1 chr1:+:369604520:-1 chr1:+:391176769:-1 chr1:+:564423520:-1 chr1:+:619820791:-1 chr1:+:847000661:-1 chr1:+:977075197:-1 chr1:+:1475722125:-1 chr1:+:1487751352:-1 chr1:+:1827375216:-1 chr1:+:1829097783:-1 chr1:+:1946689164:-1 chr1:+:1990907653:-1 chr1:+:2643604526:-1 chr1:+:3026024662:-1 +ACACTTTCTTACAAAAGCTCAGAGTGCTAAAGCTGGATAAACATAAATAGACAGCAAATAAAAGTTCATTGCTCCTGTCCAGCATCACGGCAACAATTCT chr1:+:34152630:-1 chr1:+:170316509:-1 chr1:+:194455091:-1 chr1:+:311275893:-1 chr1:+:399133138:-1 chr1:+:435205451:-1 chr1:+:454506812:-1 chr1:+:513995265:-1 chr1:+:575422774:-1 chr1:+:608884213:-1 chr1:+:766146622:-1 chr1:+:817601287:-1 chr1:+:873159771:-1 chr1:+:969722206:-1 chr1:+:983253334:-1 chr1:+:1001948105:-1 chr1:+:1287498079:-1 chr1:+:1440912509:-1 chr1:+:1690096299:-1 chr1:+:1719439880:-1 chr1:+:1726546628:-1 chr1:+:1728080802:-1 chr1:+:1728588185:-1 chr1:+:1770740687:-1 chr1:+:1846684124:-1 chr1:+:1896887093:-1 chr1:+:1908808529:-1 chr1:+:2043426072:-1 chr1:+:2105762772:-1 chr1:+:2151101936:-1 chr1:+:2153558420:-1 chr1:+:2186669346:-1 chr1:+:2281408245:-1 chr1:+:2495040200:-1 chr1:+:2905601374:-1 chr1:+:3018801367:-1 chr1:+:3061105905:-1 chr1:+:3064580334:-1 +AGAATTGTTGCCGTGATGCTGGACAGGAGCAATGAACTTTTATTTGCTGTCTATTTATGTTTATCCAGCTTTAGCACTCTGAGCTTTTGTAAGAAAGTGT chr1:+:1978321133:1 +TGGTCTATTTTGAAATCTCTCTAGCTATGACAGCCTGCCTCATGATATAGCTTTAGAGAACGCCTGCCATCAATCAACCTGACCATTTCTTTTAAAGTTT chr1:+:1192010383:0 +TTACAATATTTGAGAAAAAAAATCTGTGGCCCGATTTACATTCACTGATCTTACTATTCAATGTATTTTTCCATATACTATACAGGAGATGAGTTTGAAT chr1:+:12125585:-1 chr1:+:565375234:-1 chr1:+:700314015:-1 chr1:+:761159419:-1 chr1:+:1338087307:-1 chr1:+:1518026252:-1 chr1:+:1556792056:-1 chr1:+:2130534720:-1 chr1:+:2192366362:-1 chr1:+:2922465100:-1 +TTACAATATTTGAGAAAAAAAATCTGTGGCCCGATTTACATTCACTGATCTTACTATTCAATGTATTTTTCCATATACTATACAGGAGATGAGTTTGAAT chr1:+:57050034:-1 chr1:+:1258556686:-1 chr1:+:2020686483:-1 +TTACAATATTTGAGAAAAAAAATCTGTGGCCCGATTTACATTCACTGATCTTACTATTCAATGTATTTTTCCATATACTATACAGGAGATGAGTTTGAAT chr1:+:66679498:-1 chr1:+:72396366:-1 chr1:+:184055315:-1 chr1:+:261818135:-1 chr1:+:310803697:-1 chr1:+:345669219:-1 chr1:+:398497952:-1 chr1:+:424736459:-1 chr1:+:484731192:-1 chr1:+:513024649:-1 chr1:+:531175275:-1 chr1:+:569797751:-1 chr1:+:581599984:-1 chr1:+:615810927:-1 chr1:+:636741121:-1 chr1:+:641372114:-1 chr1:+:666893595:-1 chr1:+:723839937:-1 chr1:+:765802656:-1 chr1:+:884409386:-1 chr1:+:923159738:-1 chr1:+:942966866:-1 chr1:+:985442809:-1 chr1:+:1305280283:-1 chr1:+:1381772572:-1 chr1:+:1499033815:-1 chr1:+:1501519658:-1 chr1:+:1516434679:-1 chr1:+:1699561377:-1 chr1:+:1708104308:-1 chr1:+:1857134309:-1 chr1:+:1882310226:-1 chr1:+:1937524448:-1 chr1:+:1951302553:-1 chr1:+:1995277067:-1 chr1:+:2047068953:-1 chr1:+:2048938454:-1 chr1:+:2149998190:-1 chr1:+:2165519315:-1 chr1:+:2219640261:-1 chr1:+:2221570927:-1 chr1:+:2233152500:-1 chr1:+:2262589195:-1 chr1:+:2435960975:-1 chr1:+:2535856884:-1 chr1:+:2543883341:-1 chr1:+:2567776829:-1 chr1:+:2587451788:-1 chr1:+:2705285932:-1 chr1:+:2781528584:-1 chr1:+:2801874452:-1 chr1:+:2868650202:-1 chr1:+:2894298036:-1 chr1:+:3027032668:-1 +ATTCAAACTCATCTCCTGTATAGTATATGGAAAAATACATTGAATAGTAAGATCAGTGAATGTAAATCGGGCCACAGATTTTTTTTCTCAAATATTGTAA chr1:+:1192010761:0 +CAACAGCAGGTCCAACAATTTTTGTCCTTCAGTGTTTTATAATTCAAAGTTGAGTCACAATGTCCCTTGCCTAGGTATTGCAAAGCAAGTTTATAGTAGT chr1:+:989589463:0 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chr1:+:325998663:-1 chr1:+:332984914:-1 chr1:+:333478079:-1 chr1:+:384023893:-1 chr1:+:395324300:-1 chr1:+:405687326:-1 chr1:+:448858887:-1 chr1:+:457399841:-1 chr1:+:460013477:-1 chr1:+:470560478:-1 chr1:+:514439127:-1 chr1:+:540543201:-1 chr1:+:549361814:-1 chr1:+:575003588:-1 chr1:+:596831913:-1 chr1:+:616941565:-1 chr1:+:657900123:-1 chr1:+:771765423:-1 chr1:+:799678988:-1 chr1:+:813218394:-1 chr1:+:817522966:-1 chr1:+:832241851:-1 chr1:+:891320402:-1 chr1:+:963226848:-1 chr1:+:997245034:-1 chr1:+:999594231:-1 chr1:+:1043399459:-1 chr1:+:1059513637:-1 chr1:+:1078937441:-1 chr1:+:1085148393:-1 chr1:+:1093794442:-1 chr1:+:1127494383:-1 chr1:+:1140426659:-1 chr1:+:1173483385:-1 chr1:+:1193858991:-1 chr1:+:1195051832:-1 chr1:+:1217544844:-1 chr1:+:1257848333:-1 chr1:+:1278227072:-1 chr1:+:1321245142:-1 chr1:+:1321751358:-1 chr1:+:1324549054:-1 chr1:+:1340855063:-1 chr1:+:1353759960:-1 chr1:+:1380476983:-1 chr1:+:1401424764:-1 chr1:+:1417204578:-1 chr1:+:1462249804:-1 chr1:+:1471224676:-1 chr1:+:1495659946:-1 chr1:+:1522454752:-1 chr1:+:1529990927:-1 chr1:+:1541348033:-1 chr1:+:1550052697:-1 chr1:+:1555799117:-1 chr1:+:1568066749:-1 chr1:+:1569235681:-1 chr1:+:1642470206:-1 chr1:+:1643016182:-1 chr1:+:1754967027:-1 chr1:+:1814161367:-1 chr1:+:1833976706:-1 chr1:+:1913526922:-1 chr1:+:1951734602:-1 chr1:+:2039371614:-1 chr1:+:2042467852:-1 chr1:+:2182444857:-1 chr1:+:2226470064:-1 chr1:+:2248258976:-1 chr1:+:2349319424:-1 chr1:+:2403426429:-1 chr1:+:2409280961:-1 chr1:+:2444111598:-1 chr1:+:2584923597:-1 chr1:+:2591691051:-1 chr1:+:2600379365:-1 chr1:+:2630951259:-1 chr1:+:2635659516:-1 chr1:+:2636483038:-1 chr1:+:2658110656:-1 chr1:+:2680210852:-1 chr1:+:2695896441:-1 chr1:+:2726307874:-1 chr1:+:2765622499:-1 chr1:+:2851480497:-1 chr1:+:2852657368:-1 chr1:+:2852742654:-1 chr1:+:2852808243:-1 chr1:+:2852832389:-1 chr1:+:2917013116:-1 chr1:+:2947472678:-1 chr1:+:2971069687:-1 chr1:+:2985808402:-1 chr1:+:2985813564:-1 chr1:+:3019547434:-1 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chr1:+:180809649:-1 chr1:+:182899785:-1 chr1:+:192265778:-1 chr1:+:195512406:-1 chr1:+:205502012:-1 chr1:+:206662655:-1 chr1:+:218894235:-1 chr1:+:239441645:-1 chr1:+:276404639:20 chr1:+:286537157:-1 chr1:+:299807323:-1 chr1:+:323382472:-1 chr1:+:327209605:-1 chr1:+:371943009:-1 chr1:+:380793283:-1 chr1:+:393681895:-1 chr1:+:407962388:-1 chr1:+:447620942:-1 chr1:+:455333160:-1 chr1:+:464866409:-1 chr1:+:490997115:-1 chr1:+:504747715:-1 chr1:+:541465839:-1 chr1:+:623970237:-1 chr1:+:632658871:-1 chr1:+:636932409:-1 chr1:+:655454887:-1 chr1:+:701016677:-1 chr1:+:709847120:-1 chr1:+:735891922:-1 chr1:+:738002901:-1 chr1:+:793380427:-1 chr1:+:808585589:-1 chr1:+:814401134:-1 chr1:+:835911047:-1 chr1:+:885572325:-1 chr1:+:901587343:-1 chr1:+:915683206:20 chr1:+:916379501:-1 chr1:+:937251053:-1 chr1:+:954663857:-1 chr1:+:961199499:-1 chr1:+:971184889:-1 chr1:+:971898786:-1 chr1:+:974668004:-1 chr1:+:975810034:-1 chr1:+:1003320545:-1 chr1:+:1006382494:-1 chr1:+:1031034751:-1 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chr1:+:2198046215:-1 chr1:+:2228142288:-1 chr1:+:2248166520:-1 chr1:+:2259244731:-1 chr1:+:2269428396:-1 chr1:+:2270203522:-1 chr1:+:2295404156:-1 chr1:+:2299897276:-1 chr1:+:2334785369:-1 chr1:+:2336274828:-1 chr1:+:2338054929:-1 chr1:+:2338926699:-1 chr1:+:2390692962:-1 chr1:+:2413297780:-1 chr1:+:2422859474:-1 chr1:+:2430351979:-1 chr1:+:2432715701:-1 chr1:+:2435822245:-1 chr1:+:2466172966:-1 chr1:+:2468630368:-1 chr1:+:2468639073:-1 chr1:+:2470521172:-1 chr1:+:2495370796:-1 chr1:+:2514793677:-1 chr1:+:2521298318:-1 chr1:+:2551079071:-1 chr1:+:2571442018:-1 chr1:+:2591179015:-1 chr1:+:2608091906:-1 chr1:+:2617258911:-1 chr1:+:2622532923:-1 chr1:+:2638140968:-1 chr1:+:2640491055:-1 chr1:+:2651273471:-1 chr1:+:2651814134:-1 chr1:+:2690687248:-1 chr1:+:2698990404:-1 chr1:+:2727010647:-1 chr1:+:2734438736:-1 chr1:+:2755591608:-1 chr1:+:2803156181:-1 chr1:+:2809226431:-1 chr1:+:2819133180:-1 chr1:+:2856034880:-1 chr1:+:2869737164:-1 chr1:+:2873619386:-1 chr1:+:2909346113:-1 chr1:+:2923017932:-1 chr1:+:2926750355:-1 chr1:+:2931066534:-1 chr1:+:2967064484:-1 chr1:+:2977908523:-1 chr1:+:3032939602:-1 chr1:+:3032958833:-1 chr1:+:3032974493:-1 chr1:+:3035501469:-1 +CACAGTCCTGGAGTCTGGGAAGTTTAAGATTAAGGTGCTGGCAGATTCGGCATCTAGTGAGGGCCCACCTTCTAGCTGTGTCTTCCCATAGGGGAAGGAC chr1:+:612554229:-1 chr1:+:655133058:-1 chr1:+:1004966266:-1 chr1:+:1075994635:-1 chr1:+:2057626734:-1 chr1:+:2067693421:-1 chr1:+:2513623359:-1 chr1:+:2896729899:-1 +GTCCTTCCCCTATGGGAAGACACAGCTAGAAGGTGGGCCCTCACTAGATGCCGAATCTGCCAGCACCTTAATCTTAAACTTCCCAGACTCCAGGACTGTG chr1:+:162271118:0 +GTGCTAGTGTTGTCCCAATTGAAATTCTAAAATTGCATATATTGATCAAAATAAGAAAACTGGATTATTCCATCACCCTATGCTAACAATTTCCCACAGT chr1:+:162270749:0 +ACGGACCTTGTTTATCATGACTAAAACAATATGCTGGAAAGCCTGATGTAGGTTTAAGGTTCAGGTTTTCTAATGAATGTACTGTAATAAATCTTTGCCT chr1:+:3045068955:0 +ATGATGTGGATTAAATATCTTATAATTAATAATATATGCAAATGTGATTATACTTATGCCTTGAACTGTAATATTAAAAATATGAACCTCATTTTTTTAG chr1:+:3060395663:7 chr1:+:3062005456:7 +ATGATGTGGATTAAATATCTTATAATTAATAATATATGCAAATGTGATTATACTTATGCCTTGAACTGTAATATTAAAAATATGAACCTCATTTTTTTAG chr1:+:450049621:-1 chr1:+:631972505:-1 chr1:+:1364428677:-1 chr1:+:1645711080:-1 +CTAAAAAAATGAGGTTCATATTTTTAATATTACAGTTCAAGGCATAAGTATAATCACATTTGCATATATTATTAATTATAAGATATTTAATCCACATCAT chr1:+:1900050644:-1 chr1:+:2179512181:-1 chr1:+:2531347754:-1 chr1:+:2551699689:-1 chr1:+:3045069346:0 +AGCCCCAGTCGCCTATCTGGGCTCATTTCCTAGCATCACTCATATGATGTCATTCACTTTAAATCTCCAAGCATTCTATTAAGACTCTTCCTGCCGCCTG chr1:+:1641491350:0 +GACTAGAAAATCTGTACAAGCCTGTCTCACCATGTGAATTTACAATACCGCACCAGAGGAAATCACTACTGTCCACACATGTTTGGGAATCGCTGAAGAA chr1:+:1811510865:-1 diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-200nt.prof b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-200nt.prof new file mode 100644 index 0000000000000000000000000000000000000000..f683573d4bec2d4fb5ad7120b160f640230d2fc0 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-200nt.prof @@ -0,0 +1,1000 @@ +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTC chm1:+:534962123:-1 chm1:+:885569722:-1 chm1:+:1407539900:-1 chm1:+:2402770771:-1 chm1:+:2657300692:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTC chm1:+:199634264:-1 chm1:+:1843823169:-1 chm1:+:2345506255:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTC chm1:+:1740197716:-1 chm1:+:2647349155:-1 chm1:+:2905901998:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTC chm1:+:4614163:-1 chm1:+:309402065:-1 chm1:+:825273869:-1 chm1:+:2479408344:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTC chm1:+:150230484:-1 chm1:+:177305884:-1 chm1:+:480520513:-1 chm1:+:526068555:-1 chm1:+:526941207:-1 chm1:+:665813870:-1 chm1:+:791207152:-1 chm1:+:878582066:-1 chm1:+:1098355560:-1 chm1:+:1244727203:-1 chm1:+:1514987491:-1 chm1:+:1516580096:-1 chm1:+:1892977306:-1 chm1:+:2024728185:-1 chm1:+:2225021771:-1 chm1:+:2572183227:-1 chm1:+:2613975474:-1 chm1:+:2706071907:-1 chm1:+:2720992645:-1 chm1:+:2751022517:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTC chm1:+:592785631:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTC chm1:+:647089841:-1 chm1:+:1380334431:-1 chm1:+:1492882929:-1 chm1:+:1504978898:-1 +GAATCGGAGCCAATTAAATCTCTTTTCATTATAAATTATTCCAGCCTCCAGTTACTTCTTTTATTGCAGTGCAAGAATAGCCTTAACGACACAGGTCGTTACCCTTGAGTCACGGTCTGCAGCATGTCTTTTACCATGTAAGGTATATGTTCAGTGGCTGTGGGGGTTAGGATGTGGACTTCTTTGGGGGGACTTTATTT chm1:+:176283927:-1 chm1:+:217702903:-1 chm1:+:330225003:-1 chm1:+:357186543:-1 chm1:+:404214276:-1 chm1:+:435462106:-1 chm1:+:467888511:-1 chm1:+:581177016:-1 chm1:+:598236858:-1 chm1:+:723019410:-1 chm1:+:732364213:-1 chm1:+:760302286:-1 chm1:+:791158604:-1 chm1:+:811200124:-1 chm1:+:818717689:-1 chm1:+:917643624:-1 chm1:+:1016490209:-1 chm1:+:1158472872:-1 chm1:+:1223503679:-1 chm1:+:1422222376:-1 chm1:+:1472860088:-1 chm1:+:1476143516:-1 chm1:+:1486141920:-1 chm1:+:1532439045:-1 chm1:+:1646471131:-1 chm1:+:1743058095:-1 chm1:+:1814446295:-1 chm1:+:1879293529:-1 chm1:+:2057870015:-1 chm1:+:2119796883:-1 chm1:+:2133033153:-1 chm1:+:2243116812:-1 chm1:+:2298863904:-1 chm1:+:2345107243:-1 chm1:+:2472219280:-1 chm1:+:2488261200:11 chm1:+:2648008649:-1 chm1:+:2667265990:-1 chm1:+:2681699299:-1 chm1:+:2761780585:-1 chm1:+:2765580759:-1 chm1:+:2804890855:-1 chm1:+:2878106080:-1 chm1:+:2911671991:-1 chm1:+:2989425673:-1 chm1:+:3009899573:-1 chm1:+:3025688650:-1 +GAATCGGAGCCAATTAAATCTCTTTTCATTATAAATTATTCCAGCCTCCAGTTACTTCTTTTATTGCAGTGCAAGAATAGCCTTAACGACACAGGTCGTTACCCTTGAGTCACGGTCTGCAGCATGTCTTTTACCATGTAAGGTATATGTTCAGTGGCTGTGGGGGTTAGGATGTGGACTTCTTTGGGGGGACTTTATTT chm1:+:2488261194:11 +GAATCGGAGCCAATTAAATCTCTTTTCATTATAAATTATTCCAGCCTCCAGTTACTTCTTTTATTGCAGTGCAAGAATAGCCTTAACGACACAGGTCGTTACCCTTGAGTCACGGTCTGCAGCATGTCTTTTACCATGTAAGGTATATGTTCAGTGGCTGTGGGGGTTAGGATGTGGACTTCTTTGGGGGGACTTTATTT chm1:+:2488261195:11 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGAC chm1:+:1127594751:8 chm1:+:1127702053:11 chm1:+:1559264750:13 chm1:+:1960239671:26 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGAC chm1:+:431715908:-1 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGAC chm1:+:248462681:17 chm1:+:818868589:15 chm1:+:821412722:14 chm1:+:848099830:-1 chm1:+:868087901:15 chm1:+:943742020:13 chm1:+:986561857:14 chm1:+:1082162912:15 chm1:+:1492070390:12 chm1:+:1716138049:19 chm1:+:1916433323:12 chm1:+:1929004886:19 chm1:+:2284044036:13 chm1:+:2428438807:14 chm1:+:2935998303:16 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGAC chm1:+:30998791:-1 chm1:+:75944279:13 chm1:+:588549060:-1 chm1:+:764187260:17 chm1:+:838579790:30 chm1:+:855959010:17 chm1:+:934727644:12 chm1:+:994039396:12 chm1:+:1050653036:-1 chm1:+:1101966449:14 chm1:+:1510685344:-1 chm1:+:1624498798:-1 chm1:+:1718561249:15 chm1:+:2116592993:25 chm1:+:2976962755:-1 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGAC chm1:+:347805454:15 chm1:+:703609706:27 chm1:+:711214960:19 chm1:+:900059503:-1 chm1:+:1376940853:28 chm1:+:1564019838:13 chm1:+:1718357234:23 chm1:+:1903118967:-1 chm1:+:2106931653:38 chm1:+:2245819133:19 +GTCTAATGTTGACAGTGGGTGTTAAAGTCTCCATTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTAAACTAGTACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGTGCATATATATTTAGGATAGTTAGTTCTTCTTTGTTGAATTGATCCCTTTACCATTATGTAATGGCCCTTCTTTGTCTCTTTTTGATGT chm1:+:160357932:21 chm1:+:419726543:19 chm1:+:449358479:20 chm1:+:486546469:12 chm1:+:633467910:16 chm1:+:777805019:17 chm1:+:1133750680:18 chm1:+:1442650886:22 chm1:+:1486192139:-1 chm1:+:2457273988:15 chm1:+:2947960310:17 +GTCTAATGTTGACAGTGGGTGTTAAAGTCTCCATTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTAAACTAGTACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGTGCATATATATTTAGGATAGTTAGTTCTTCTTTGTTGAATTGATCCCTTTACCATTATGTAATGGCCCTTCTTTGTCTCTTTTTGATGT chm1:+:1139979107:16 chm1:+:1469581843:19 +GTCTAATGTTGACAGTGGGTGTTAAAGTCTCCATTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTAAACTAGTACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGTGCATATATATTTAGGATAGTTAGTTCTTCTTTGTTGAATTGATCCCTTTACCATTATGTAATGGCCCTTCTTTGTCTCTTTTTGATGT chm1:+:2495733149:-1 +GTCTAATGTTGACAGTGGGTGTTAAAGTCTCCATTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTAAACTAGTACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGTGCATATATATTTAGGATAGTTAGTTCTTCTTTGTTGAATTGATCCCTTTACCATTATGTAATGGCCCTTCTTTGTCTCTTTTTGATGT chm1:+:1010170786:30 +GTCTAATGTTGACAGTGGGTGTTAAAGTCTCCATTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTAAACTAGTACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGTGCATATATATTTAGGATAGTTAGTTCTTCTTTGTTGAATTGATCCCTTTACCATTATGTAATGGCCCTTCTTTGTCTCTTTTTGATGT chm1:+:78210649:16 chm1:+:539266917:15 chm1:+:695474053:25 chm1:+:925831978:31 chm1:+:1561666116:18 chm1:+:1561898032:16 chm1:+:1739682718:28 chm1:+:1968770258:13 chm1:+:2063184913:13 chm1:+:2569013174:17 chm1:+:3046106600:15 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTG chm1:+:72892176:-1 chm1:+:86239038:-1 chm1:+:95677727:-1 chm1:+:117990527:-1 chm1:+:210216183:-1 chm1:+:248053106:-1 chm1:+:305616377:-1 chm1:+:322959310:-1 chm1:+:326254991:-1 chm1:+:331424414:-1 chm1:+:398158616:-1 chm1:+:422304101:-1 chm1:+:431883466:-1 chm1:+:432885648:-1 chm1:+:435632819:-1 chm1:+:532107964:-1 chm1:+:551110747:-1 chm1:+:559554279:35 chm1:+:592787540:-1 chm1:+:593598016:-1 chm1:+:598268861:-1 chm1:+:699533162:-1 chm1:+:728414053:-1 chm1:+:797374128:-1 chm1:+:812391106:-1 chm1:+:829308072:-1 chm1:+:834036330:-1 chm1:+:897439425:38 chm1:+:919302521:-1 chm1:+:927502558:-1 chm1:+:942118871:36 chm1:+:943722983:-1 chm1:+:947404211:-1 chm1:+:968123201:-1 chm1:+:977002261:-1 chm1:+:977267339:-1 chm1:+:987734869:-1 chm1:+:1009257713:-1 chm1:+:1009906963:-1 chm1:+:1025596192:-1 chm1:+:1026426480:-1 chm1:+:1093765699:-1 chm1:+:1103639749:-1 chm1:+:1124591541:-1 chm1:+:1133610944:-1 chm1:+:1137470474:-1 chm1:+:1142504460:-1 chm1:+:1144252938:-1 chm1:+:1165794728:-1 chm1:+:1177779244:-1 chm1:+:1177787807:-1 chm1:+:1183230638:-1 chm1:+:1223831129:-1 chm1:+:1254581553:-1 chm1:+:1295032418:-1 chm1:+:1296291556:-1 chm1:+:1314464660:-1 chm1:+:1339983339:-1 chm1:+:1387221247:-1 chm1:+:1399499781:-1 chm1:+:1404779392:-1 chm1:+:1450060923:-1 chm1:+:1451372196:-1 chm1:+:1468105766:-1 chm1:+:1479359809:-1 chm1:+:1479568032:-1 chm1:+:1479580226:-1 chm1:+:1479595501:-1 chm1:+:1479607694:-1 chm1:+:1479619888:-1 chm1:+:1479632075:-1 chm1:+:1498720600:-1 chm1:+:1620848755:-1 chm1:+:1636392712:-1 chm1:+:1685499897:-1 chm1:+:1701100294:-1 chm1:+:1770484589:-1 chm1:+:1873816134:-1 chm1:+:1875058494:-1 chm1:+:1992469884:-1 chm1:+:1995991093:-1 chm1:+:2030814773:-1 chm1:+:2033582530:-1 chm1:+:2035138714:-1 chm1:+:2035315571:-1 chm1:+:2106620172:-1 chm1:+:2125190194:-1 chm1:+:2135636244:-1 chm1:+:2229344768:-1 chm1:+:2272813942:-1 chm1:+:2462751539:-1 chm1:+:2643301852:-1 chm1:+:2772073495:-1 chm1:+:2888968913:-1 chm1:+:2936729534:-1 chm1:+:2937048406:-1 chm1:+:2944733020:-1 chm1:+:2989369895:-1 chm1:+:2989481334:-1 chm1:+:3003173424:-1 chm1:+:3018646231:-1 chm1:+:3055856898:-1 chm1:+:3059092742:-1 chm1:+:3060643565:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTG chm1:+:172229500:-1 chm1:+:1288129430:-1 chm1:+:2964696827:-1 chm1:+:2997032021:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTG chm1:+:781984358:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTG chm1:+:74814149:-1 chm1:+:432676871:-1 chm1:+:434396054:-1 chm1:+:975280134:-1 chm1:+:1254620467:-1 chm1:+:2741386026:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTG chm1:+:367574853:-1 chm1:+:461595340:-1 chm1:+:1453731918:-1 chm1:+:1563795767:-1 chm1:+:1906658213:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTG chm1:+:1109358248:-1 chm1:+:1444084649:-1 chm1:+:1786386923:-1 chm1:+:2422915277:-1 chm1:+:2464579552:-1 chm1:+:2514494161:-1 chm1:+:2532222762:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTG chm1:+:96797162:-1 chm1:+:147059517:-1 chm1:+:209831360:-1 chm1:+:291676805:-1 chm1:+:310086530:-1 chm1:+:317549644:-1 chm1:+:330025787:-1 chm1:+:388514099:-1 chm1:+:388726322:-1 chm1:+:419633262:-1 chm1:+:432827150:-1 chm1:+:459546788:-1 chm1:+:469465067:-1 chm1:+:507468155:-1 chm1:+:522286522:-1 chm1:+:623252584:-1 chm1:+:927028738:-1 chm1:+:1110646425:-1 chm1:+:1249285639:-1 chm1:+:1250446623:-1 chm1:+:1271362028:-1 chm1:+:1314905831:-1 chm1:+:1348767070:-1 chm1:+:1371257989:-1 chm1:+:1735934076:-1 chm1:+:1757639063:-1 chm1:+:1784492457:-1 chm1:+:1798177945:-1 chm1:+:1899109390:-1 chm1:+:1926903580:-1 chm1:+:2033415561:-1 chm1:+:2044746317:-1 chm1:+:2147209043:-1 chm1:+:2147209188:-1 chm1:+:2183811533:-1 chm1:+:2254820305:-1 chm1:+:2259249284:-1 chm1:+:2279277238:-1 chm1:+:2417691967:-1 chm1:+:2519594494:-1 chm1:+:2561131396:-1 chm1:+:2607727916:-1 chm1:+:2615084705:-1 chm1:+:2650838546:-1 chm1:+:2769237230:-1 chm1:+:2879371775:-1 chm1:+:2923578358:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTG chm1:+:2256486:-1 chm1:+:3349709:-1 chm1:+:19568205:-1 chm1:+:41496256:-1 chm1:+:53937711:-1 chm1:+:60504139:-1 chm1:+:76374148:-1 chm1:+:86349370:-1 chm1:+:87430734:-1 chm1:+:89780082:-1 chm1:+:96814746:-1 chm1:+:97155073:-1 chm1:+:106602687:-1 chm1:+:113537625:-1 chm1:+:159099383:-1 chm1:+:169643869:-1 chm1:+:244833112:-1 chm1:+:248040110:-1 chm1:+:256550713:-1 chm1:+:268517502:-1 chm1:+:274607522:-1 chm1:+:280285264:-1 chm1:+:296983697:-1 chm1:+:378323216:-1 chm1:+:390339738:-1 chm1:+:401886477:-1 chm1:+:426909750:-1 chm1:+:435914024:-1 chm1:+:439848010:-1 chm1:+:458248016:-1 chm1:+:469933494:-1 chm1:+:471694794:-1 chm1:+:472724225:-1 chm1:+:474021732:-1 chm1:+:579767085:-1 chm1:+:600654152:-1 chm1:+:619856028:-1 chm1:+:622472910:-1 chm1:+:629313392:-1 chm1:+:643490299:-1 chm1:+:677812146:-1 chm1:+:685796549:-1 chm1:+:694618896:-1 chm1:+:762462503:-1 chm1:+:797418189:-1 chm1:+:798981378:-1 chm1:+:805088859:-1 chm1:+:824321693:-1 chm1:+:847482306:-1 chm1:+:862972310:-1 chm1:+:923794653:-1 chm1:+:927381546:-1 chm1:+:1009825357:-1 chm1:+:1053346020:-1 chm1:+:1064949803:-1 chm1:+:1068534296:-1 chm1:+:1077399256:-1 chm1:+:1078151236:-1 chm1:+:1104586922:-1 chm1:+:1105568118:-1 chm1:+:1173342262:-1 chm1:+:1180631251:-1 chm1:+:1197074413:-1 chm1:+:1234295814:-1 chm1:+:1238423182:-1 chm1:+:1239068095:-1 chm1:+:1248141617:-1 chm1:+:1270463433:-1 chm1:+:1280588417:-1 chm1:+:1289994058:-1 chm1:+:1353463242:-1 chm1:+:1354739200:-1 chm1:+:1362441387:-1 chm1:+:1374318954:-1 chm1:+:1402306844:-1 chm1:+:1409356126:-1 chm1:+:1420104050:-1 chm1:+:1432513001:-1 chm1:+:1488331770:-1 chm1:+:1520686117:-1 chm1:+:1536535490:-1 chm1:+:1536812588:-1 chm1:+:1539433942:-1 chm1:+:1618086240:-1 chm1:+:1631336976:-1 chm1:+:1635164739:-1 chm1:+:1692860435:-1 chm1:+:1696897707:-1 chm1:+:1698053117:-1 chm1:+:1759067039:-1 chm1:+:1782862996:-1 chm1:+:1799279325:-1 chm1:+:1804197402:-1 chm1:+:1807598201:-1 chm1:+:1851986701:-1 chm1:+:1857848333:-1 chm1:+:1883388342:-1 chm1:+:1883668199:-1 chm1:+:1902312475:-1 chm1:+:1911755272:-1 chm1:+:1946354998:-1 chm1:+:1952399117:-1 chm1:+:1964420317:-1 chm1:+:1965118748:-1 chm1:+:2001507935:-1 chm1:+:2018040213:-1 chm1:+:2020689378:-1 chm1:+:2117025192:-1 chm1:+:2122980525:-1 chm1:+:2141241544:-1 chm1:+:2149379344:-1 chm1:+:2196684868:-1 chm1:+:2221512683:-1 chm1:+:2248733285:-1 chm1:+:2291568505:-1 chm1:+:2334796599:-1 chm1:+:2369662484:-1 chm1:+:2429567044:-1 chm1:+:2482304232:-1 chm1:+:2492543095:-1 chm1:+:2507286393:-1 chm1:+:2508805148:-1 chm1:+:2526185623:-1 chm1:+:2534446228:-1 chm1:+:2535134153:-1 chm1:+:2608115753:-1 chm1:+:2612509334:-1 chm1:+:2703974874:-1 chm1:+:2704390804:-1 chm1:+:2725968487:-1 chm1:+:2763081677:-1 chm1:+:2763126464:-1 chm1:+:2767291113:-1 chm1:+:2815082879:-1 chm1:+:2848227090:-1 chm1:+:2881462188:-1 chm1:+:2893284308:-1 chm1:+:2915207782:-1 chm1:+:2915612399:-1 chm1:+:2918407993:-1 chm1:+:2938132810:-1 chm1:+:2956374276:-1 chm1:+:2962747383:-1 chm1:+:3007440634:-1 chm1:+:3016305584:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTG chm1:+:248270344:-1 chm1:+:551328021:-1 chm1:+:748899348:-1 chm1:+:781598235:-1 chm1:+:850962363:-1 chm1:+:991091178:-1 chm1:+:1998283456:-1 chm1:+:2561549475:39 chm1:+:2975066942:-1 +CAAGAGATGTGAAGGAACCTCTTCAAGGAGAACTACAAACCACTACTCCAAGGAACAAGAGCGAACACAAACAAATGGAAAATAGGAAGAATCAATATCATGAAAATGGCCATACTGCTCAAAGTAATTTATAGAATCAATAGCTATTCCCCATCAAACCATCACTGACTATTCCTCAAAGAATTAGAAAAACTATTTAA chm1:+:328136951:7 +GGGTTGTGCAGTTGATATTTCCTCGGGAGGGGTGCTTTCAATGTCATTAACATTGGGAGTCATGGGCTAGCAGGCCAGTCCAGGATCCGCAGTAGATTTTAGTCATGGGCTGCATCTGGGCTCCATTGAGGAACTATTTAGTAGCTTTACAGCTTCAATTCTGGAAGAGACAAACTTAACAAAGAGGTTAATATACAGGG chm1:+:588836040:11 chm1:+:912736443:-1 chm1:+:1044587827:-1 chm1:+:1151666248:27 chm1:+:1456303977:30 chm1:+:1902452793:26 chm1:+:2291628556:26 +GGGTTGTGCAGTTGATATTTCCTCGGGAGGGGTGCTTTCAATGTCATTAACATTGGGAGTCATGGGCTAGCAGGCCAGTCCAGGATCCGCAGTAGATTTTAGTCATGGGCTGCATCTGGGCTCCATTGAGGAACTATTTAGTAGCTTTACAGCTTCAATTCTGGAAGAGACAAACTTAACAAAGAGGTTAATATACAGGG chm1:+:588836039:11 +GGGTTGTGCAGTTGATATTTCCTCGGGAGGGGTGCTTTCAATGTCATTAACATTGGGAGTCATGGGCTAGCAGGCCAGTCCAGGATCCGCAGTAGATTTTAGTCATGGGCTGCATCTGGGCTCCATTGAGGAACTATTTAGTAGCTTTACAGCTTCAATTCTGGAAGAGACAAACTTAACAAAGAGGTTAATATACAGGG chm1:+:40758011:-1 chm1:+:57676850:-1 chm1:+:327429488:-1 chm1:+:530781715:29 chm1:+:591794605:-1 chm1:+:697419823:-1 chm1:+:783445694:-1 chm1:+:830016165:26 chm1:+:1026012217:-1 chm1:+:1027198744:-1 chm1:+:1726930403:-1 chm1:+:1729117299:-1 chm1:+:2956151781:36 +GGGTTGTGCAGTTGATATTTCCTCGGGAGGGGTGCTTTCAATGTCATTAACATTGGGAGTCATGGGCTAGCAGGCCAGTCCAGGATCCGCAGTAGATTTTAGTCATGGGCTGCATCTGGGCTCCATTGAGGAACTATTTAGTAGCTTTACAGCTTCAATTCTGGAAGAGACAAACTTAACAAAGAGGTTAATATACAGGG chm1:+:55377490:32 chm1:+:571502802:-1 chm1:+:623366086:26 chm1:+:641924619:22 chm1:+:764264615:27 chm1:+:1151666247:27 chm1:+:1347676548:31 chm1:+:1441944567:24 chm1:+:1574800831:29 chm1:+:1743167404:26 chm1:+:1776967844:26 chm1:+:1923760078:27 chm1:+:2002211494:28 chm1:+:2700937304:32 chm1:+:2774369007:-1 chm1:+:2946550581:28 chm1:+:2987329015:25 +GGGTTGTGCAGTTGATATTTCCTCGGGAGGGGTGCTTTCAATGTCATTAACATTGGGAGTCATGGGCTAGCAGGCCAGTCCAGGATCCGCAGTAGATTTTAGTCATGGGCTGCATCTGGGCTCCATTGAGGAACTATTTAGTAGCTTTACAGCTTCAATTCTGGAAGAGACAAACTTAACAAAGAGGTTAATATACAGGG chm1:+:46851825:31 chm1:+:56249669:32 chm1:+:445450400:27 chm1:+:989537335:23 +CCCTGTATATTAACCTCTTTGTTAAGTTTGTCTCTTCCAGAATTGAAGCTGTAAAGCTACTAAATAGTTCCTCAATGGAGCCCAGATGCAGCCCATGACTAAAATCTACTGCGGATCCTGGACTGGCCTGCTAGCCCATGACTCCCAATGTTAATGACATTGAAAGCACCCCTCCCGAGGAAATATCAACTGCACAACCC chm1:+:266777494:26 chm1:+:281109106:32 chm1:+:325356148:32 chm1:+:532150906:28 chm1:+:647146435:29 chm1:+:1076425258:25 chm1:+:1169224989:29 chm1:+:1229853047:27 chm1:+:1367933701:25 chm1:+:1746177863:30 chm1:+:2253765247:27 chm1:+:2586058469:22 chm1:+:2639747369:27 chm1:+:2960251224:25 +CCCTGTATATTAACCTCTTTGTTAAGTTTGTCTCTTCCAGAATTGAAGCTGTAAAGCTACTAAATAGTTCCTCAATGGAGCCCAGATGCAGCCCATGACTAAAATCTACTGCGGATCCTGGACTGGCCTGCTAGCCCATGACTCCCAATGTTAATGACATTGAAAGCACCCCTCCCGAGGAAATATCAACTGCACAACCC chm1:+:773872585:28 chm1:+:2400130496:31 +CCCTGTATATTAACCTCTTTGTTAAGTTTGTCTCTTCCAGAATTGAAGCTGTAAAGCTACTAAATAGTTCCTCAATGGAGCCCAGATGCAGCCCATGACTAAAATCTACTGCGGATCCTGGACTGGCCTGCTAGCCCATGACTCCCAATGTTAATGACATTGAAAGCACCCCTCCCGAGGAAATATCAACTGCACAACCC chm1:+:2334053644:-1 +CCCTGTATATTAACCTCTTTGTTAAGTTTGTCTCTTCCAGAATTGAAGCTGTAAAGCTACTAAATAGTTCCTCAATGGAGCCCAGATGCAGCCCATGACTAAAATCTACTGCGGATCCTGGACTGGCCTGCTAGCCCATGACTCCCAATGTTAATGACATTGAAAGCACCCCTCCCGAGGAAATATCAACTGCACAACCC chm1:+:393711551:-1 chm1:+:425441223:26 chm1:+:633989710:30 chm1:+:773872584:28 chm1:+:925740768:24 chm1:+:1146701426:29 chm1:+:1174000580:32 chm1:+:1383030229:29 chm1:+:1412812175:28 chm1:+:1467529874:24 chm1:+:1633903418:31 chm1:+:1653259518:28 chm1:+:1838504504:-1 chm1:+:2122298768:29 chm1:+:2253765246:27 +AGTATTAACTTATTTAGAACTCACATAATTCCTATGGAGAAGGTCCTTTTATTAGGCCAACTTTACAGATTGGGAAACTGAAGGTTTGGAGGTGGGTTAAAAAGTTGCCCGACATCAATACAGCTAGGAAGTGGCAGATGGCAAGAGTTGGCTCCCCAGATTCCACGTCTCCTACAAACACACTATACTGTAGCTCAGAT chm1:+:1168367560:11 +AGTATTAACTTATTTAGAACTCACATAATTCCTATGGAGAAGGTCCTTTTATTAGGCCAACTTTACAGATTGGGAAACTGAAGGTTTGGAGGTGGGTTAAAAAGTTGCCCGACATCAATACAGCTAGGAAGTGGCAGATGGCAAGAGTTGGCTCCCCAGATTCCACGTCTCCTACAAACACACTATACTGTAGCTCAGAT chm1:+:1168367553:11 +AGTATTAACTTATTTAGAACTCACATAATTCCTATGGAGAAGGTCCTTTTATTAGGCCAACTTTACAGATTGGGAAACTGAAGGTTTGGAGGTGGGTTAAAAAGTTGCCCGACATCAATACAGCTAGGAAGTGGCAGATGGCAAGAGTTGGCTCCCCAGATTCCACGTCTCCTACAAACACACTATACTGTAGCTCAGAT chm1:+:883797885:-1 chm1:+:2486066555:-1 +AGTATTAACTTATTTAGAACTCACATAATTCCTATGGAGAAGGTCCTTTTATTAGGCCAACTTTACAGATTGGGAAACTGAAGGTTTGGAGGTGGGTTAAAAAGTTGCCCGACATCAATACAGCTAGGAAGTGGCAGATGGCAAGAGTTGGCTCCCCAGATTCCACGTCTCCTACAAACACACTATACTGTAGCTCAGAT chm1:+:1168367557:11 +ATCTGAGCTACAGTATAGTGTGTTTGTAGGAGACGTGGAATCTGGGGAGCCAACTCTTGCCATCTGCCACTTCCTAGCTGTATTGATGTCGGGCAACTTTTTAACCCACCTCCAAACCTTCAGTTTCCCAATCTGTAAAGTTGGCCTAATAAAAGGACCTTCTCCATAGGAATTATGTGAGTTCTAAATAAGTTAATACT chm1:+:481689226:-1 +CATAGTTTTAGGTAAATAAGTGGGAATCTAGAATAGACTCCAACATTAAGTCCCAAATTGCAAACTTTACATTTTTTACATATACTTCAGGAAAACATTCAAAACTTTGTTACAGTTTGCCAAGTAAATAAATTTATTTATCTTATATTCCTAAAATCCTGATTAAATTTAATTTGCGTCTAGAAGCTTTTACGCATGCC chm1:+:824308337:11 +CATAGTTTTAGGTAAATAAGTGGGAATCTAGAATAGACTCCAACATTAAGTCCCAAATTGCAAACTTTACATTTTTTACATATACTTCAGGAAAACATTCAAAACTTTGTTACAGTTTGCCAAGTAAATAAATTTATTTATCTTATATTCCTAAAATCCTGATTAAATTTAATTTGCGTCTAGAAGCTTTTACGCATGCC chm1:+:824308336:11 +CATAGTTTTAGGTAAATAAGTGGGAATCTAGAATAGACTCCAACATTAAGTCCCAAATTGCAAACTTTACATTTTTTACATATACTTCAGGAAAACATTCAAAACTTTGTTACAGTTTGCCAAGTAAATAAATTTATTTATCTTATATTCCTAAAATCCTGATTAAATTTAATTTGCGTCTAGAAGCTTTTACGCATGCC chm1:+:824308335:11 +GGCATGCGTAAAAGCTTCTAGACGCAAATTAAATTTAATCAGGATTTTAGGAATATAAGATAAATAAATTTATTTACTTGGCAAACTGTAACAAAGTTTTGAATGTTTTCCTGAAGTATATGTAAAAAATGTAAAGTTTGCAATTTGGGACTTAATGTTGGAGTCTATTCTAGATTCCCACTTATTTACCTAAAACTATG chm1:+:1040095943:-1 +AGTTGAGAGTCCCTATTGTTTGACTAGCCTTACCCCATGGCTACAAAATGAACTGCAAGAGCCCTAAACATCATGTTTCCCATTTACACATTCAGAGGCATAAAGCAAGGGGAAGGGTTTTGCCCAGAGAGAAATATACAAATTGTTTCACAATTACTGAAAAGTAAAAATTCTTTCTATCGAGTCACTCGAAACATTTC chm1:+:2381543163:-1 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+AGTTGAGAGTCCCTATTGTTTGACTAGCCTTACCCCATGGCTACAAAATGAACTGCAAGAGCCCTAAACATCATGTTTCCCATTTACACATTCAGAGGCATAAAGCAAGGGGAAGGGTTTTGCCCAGAGAGAAATATACAAATTGTTTCACAATTACTGAAAAGTAAAAATTCTTTCTATCGAGTCACTCGAAACATTTC chm1:+:43985993:-1 chm1:+:56136431:-1 chm1:+:1846790546:-1 chm1:+:1955552822:-1 chm1:+:1991403842:-1 chm1:+:2266379249:-1 +AGTTGAGAGTCCCTATTGTTTGACTAGCCTTACCCCATGGCTACAAAATGAACTGCAAGAGCCCTAAACATCATGTTTCCCATTTACACATTCAGAGGCATAAAGCAAGGGGAAGGGTTTTGCCCAGAGAGAAATATACAAATTGTTTCACAATTACTGAAAAGTAAAAATTCTTTCTATCGAGTCACTCGAAACATTTC chm1:+:185319846:-1 chm1:+:1291257609:-1 chm1:+:1673977255:-1 chm1:+:2979900857:-1 +AGTTGAGAGTCCCTATTGTTTGACTAGCCTTACCCCATGGCTACAAAATGAACTGCAAGAGCCCTAAACATCATGTTTCCCATTTACACATTCAGAGGCATAAAGCAAGGGGAAGGGTTTTGCCCAGAGAGAAATATACAAATTGTTTCACAATTACTGAAAAGTAAAAATTCTTTCTATCGAGTCACTCGAAACATTTC chm1:+:41668779:-1 chm1:+:50150483:-1 chm1:+:80548912:-1 chm1:+:86533489:-1 chm1:+:104716331:-1 chm1:+:200521345:-1 chm1:+:216328077:-1 chm1:+:354533699:-1 chm1:+:362972820:-1 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+AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAG chm1:+:79663234:-1 chm1:+:206964045:-1 chm1:+:388209593:-1 chm1:+:486664863:-1 chm1:+:575057435:-1 chm1:+:603152618:-1 chm1:+:614909570:-1 chm1:+:657264769:-1 chm1:+:932555404:-1 chm1:+:1083605943:-1 chm1:+:1095871894:-1 chm1:+:1391928760:-1 chm1:+:1412077426:-1 chm1:+:1533231517:-1 chm1:+:1629577733:-1 chm1:+:1806674734:-1 chm1:+:1967220324:-1 chm1:+:2065222571:-1 chm1:+:2494239739:-1 chm1:+:2602708395:-1 chm1:+:2871219067:-1 chm1:+:3013534554:-1 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAG chm1:+:67509286:-1 chm1:+:211379678:-1 chm1:+:469530658:-1 chm1:+:474120881:-1 chm1:+:560607434:-1 chm1:+:756064034:-1 chm1:+:760964471:-1 chm1:+:778082201:-1 chm1:+:795364705:-1 chm1:+:828508291:-1 chm1:+:843735344:-1 chm1:+:865839557:-1 chm1:+:1062981111:-1 chm1:+:1109833044:-1 chm1:+:1134859021:-1 chm1:+:1181454666:-1 chm1:+:1271716013:-1 chm1:+:1359417709:-1 chm1:+:1367344733:-1 chm1:+:1485750087:-1 chm1:+:1536855401:-1 chm1:+:1786312062:-1 chm1:+:1847070150:-1 chm1:+:1993247849:-1 chm1:+:2047108819:-1 chm1:+:2071872980:-1 chm1:+:2156349420:-1 chm1:+:2166482821:-1 chm1:+:2229729051:-1 chm1:+:2342681589:-1 chm1:+:2348972740:-1 chm1:+:2351077056:-1 chm1:+:2468735070:-1 chm1:+:2716298304:-1 chm1:+:2973005305:36 chm1:+:2974283871:-1 chm1:+:3042005599:35 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAG chm1:+:56556642:35 chm1:+:85555705:-1 chm1:+:438979057:-1 chm1:+:1978108831:34 chm1:+:2813459436:-1 +CTGATGATTATGTGTCTTGGGGTTGCTCTTCTCAAGGATGTCCTTTGTGGTTTTCTCTGTATTTCCTGAATTTGAATGTTGGTCCTGCCTTAGGTTGAGGAAATTCTCTTGGATAATATCCTGAAGAGTGGTTTCCCAACTTGATTCCATTCTCCTTGTTACTTCATGTACACCATTCAAACATAAGATTTTAAGTCTTT chm1:+:121327389:40 chm1:+:153291184:29 chm1:+:245760855:31 chm1:+:306082997:-1 chm1:+:354495197:32 chm1:+:385946103:31 chm1:+:386273366:38 chm1:+:388949566:31 chm1:+:473407372:31 chm1:+:594138663:33 chm1:+:597477555:35 chm1:+:610489548:-1 chm1:+:735222854:33 chm1:+:744642842:36 chm1:+:812382693:35 chm1:+:851021725:38 chm1:+:865011216:35 chm1:+:939880035:36 chm1:+:969544387:30 chm1:+:995239658:36 chm1:+:1012859703:35 chm1:+:1114328109:29 chm1:+:1147365681:31 chm1:+:1178342606:40 chm1:+:1179962816:38 chm1:+:1200752907:30 chm1:+:1206908709:29 chm1:+:1221145291:31 chm1:+:1328042394:32 chm1:+:1332946969:35 chm1:+:1345985678:32 chm1:+:1354522483:32 chm1:+:1370324639:34 chm1:+:1441876035:33 chm1:+:1545221785:33 chm1:+:1563024740:34 chm1:+:1776889751:40 chm1:+:1778065704:34 chm1:+:1878789349:34 chm1:+:1901166342:31 chm1:+:1960426419:32 chm1:+:2036625042:38 chm1:+:2116634672:36 chm1:+:2240229832:36 chm1:+:2382664360:36 chm1:+:2383553836:33 chm1:+:2394039189:30 chm1:+:2442244642:33 chm1:+:2506922794:34 chm1:+:2552841679:31 chm1:+:2656368802:29 chm1:+:2723177691:33 chm1:+:2898624509:34 chm1:+:2948782029:31 chm1:+:2952095485:35 chm1:+:2952154627:40 chm1:+:2953082666:32 chm1:+:2989610759:38 chm1:+:3019075881:-1 chm1:+:3022889957:29 chm1:+:3059312844:8 +CTGATGATTATGTGTCTTGGGGTTGCTCTTCTCAAGGATGTCCTTTGTGGTTTTCTCTGTATTTCCTGAATTTGAATGTTGGTCCTGCCTTAGGTTGAGGAAATTCTCTTGGATAATATCCTGAAGAGTGGTTTCCCAACTTGATTCCATTCTCCTTGTTACTTCATGTACACCATTCAAACATAAGATTTTAAGTCTTT chm1:+:3059312843:8 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAG chm1:+:205815970:-1 chm1:+:414694693:-1 chm1:+:451846370:-1 chm1:+:489496036:-1 chm1:+:917302853:-1 chm1:+:1102309633:-1 chm1:+:1280807176:-1 chm1:+:1338204568:-1 chm1:+:1345790954:-1 chm1:+:1484403466:-1 chm1:+:1623098849:-1 chm1:+:1699733236:-1 chm1:+:1764966769:-1 chm1:+:1816725586:-1 chm1:+:2150042719:-1 chm1:+:2160497487:-1 chm1:+:2362186303:-1 chm1:+:2459086781:-1 chm1:+:2805481317:-1 chm1:+:2818412185:-1 chm1:+:2929822747:-1 chm1:+:2957465204:-1 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAG chm1:+:331210469:-1 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAG chm1:+:448188532:-1 chm1:+:1483736103:-1 chm1:+:1519844207:-1 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAG chm1:+:521150659:-1 chm1:+:529786911:-1 chm1:+:552291006:-1 chm1:+:1041776999:-1 chm1:+:1322806277:-1 chm1:+:1572548178:-1 chm1:+:1606434857:-1 chm1:+:1608796792:-1 chm1:+:1640085339:-1 chm1:+:1824489720:-1 chm1:+:2279968314:-1 chm1:+:2534054568:-1 chm1:+:2571289306:-1 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAG chm1:+:68510105:-1 chm1:+:196575451:-1 chm1:+:268627132:-1 chm1:+:320719148:-1 chm1:+:552481138:-1 chm1:+:552929407:-1 chm1:+:655492909:-1 chm1:+:673132435:-1 chm1:+:761524721:-1 chm1:+:782315547:-1 chm1:+:914517330:-1 chm1:+:992658611:-1 chm1:+:1035415515:-1 chm1:+:1126530607:-1 chm1:+:1170792609:-1 chm1:+:1319408770:-1 chm1:+:1458070375:-1 chm1:+:1491422512:-1 chm1:+:1638329792:-1 chm1:+:1668060062:-1 chm1:+:1743343319:-1 chm1:+:1904581482:-1 chm1:+:1953687523:-1 chm1:+:1968231303:-1 chm1:+:2039294699:-1 chm1:+:2171156587:-1 chm1:+:2226577796:-1 chm1:+:2227239550:-1 chm1:+:2363878094:-1 chm1:+:2627813151:-1 chm1:+:2732719754:-1 chm1:+:2797999672:-1 chm1:+:3005912898:-1 chm1:+:3011420103:-1 +CTTTAATCCTTATTGCACCAAGTGGGGGAAAATAATTCATGAGCACATAACCAATTTTATGTTCCATTAAAAAAAAGGTAGGATTTCTGAAAAAATAAAAATGAGTGTATTATGACTACTGTATATTGTGGATGACAATTACACATAGTTAAGTAACAATAGCACATAATTACTTATGGATTTTGAATATAAATTACCAT chm1:+:74672771:-1 chm1:+:173979173:-1 chm1:+:881953469:-1 chm1:+:1247679363:7 chm1:+:1810358787:-1 chm1:+:1898194880:-1 chm1:+:2033091382:-1 chm1:+:2297516312:-1 chm1:+:2803807284:-1 chm1:+:2812133421:-1 chm1:+:2934811287:-1 +CTTTAATCCTTATTGCACCAAGTGGGGGAAAATAATTCATGAGCACATAACCAATTTTATGTTCCATTAAAAAAAAGGTAGGATTTCTGAAAAAATAAAAATGAGTGTATTATGACTACTGTATATTGTGGATGACAATTACACATAGTTAAGTAACAATAGCACATAATTACTTATGGATTTTGAATATAAATTACCAT chm1:+:1247679361:7 +CCTGCCCACACTCTGCTAGCGGGTCAGCATCAGACCTGACCAGTCCAATTAGCCCTCCAGTGGGGAGGAGTGGTGGGCTCAGCGCCACCTAGAGGTCATAAATTCCTATCACCCTGACCTCTTGAGAGCAGAGTGGACCAATCTTCTCCATTCCTTGGCCTTGCCAGCACCCTGGCTAGCTGGTTTTTGGGCCCTACATG chm1:+:73245641:-1 chm1:+:170917045:-1 chm1:+:193634326:-1 chm1:+:1793231084:11 +CCTGCCCACACTCTGCTAGCGGGTCAGCATCAGACCTGACCAGTCCAATTAGCCCTCCAGTGGGGAGGAGTGGTGGGCTCAGCGCCACCTAGAGGTCATAAATTCCTATCACCCTGACCTCTTGAGAGCAGAGTGGACCAATCTTCTCCATTCCTTGGCCTTGCCAGCACCCTGGCTAGCTGGTTTTTGGGCCCTACATG chm1:+:1793231083:11 +CCTGCCCACACTCTGCTAGCGGGTCAGCATCAGACCTGACCAGTCCAATTAGCCCTCCAGTGGGGAGGAGTGGTGGGCTCAGCGCCACCTAGAGGTCATAAATTCCTATCACCCTGACCTCTTGAGAGCAGAGTGGACCAATCTTCTCCATTCCTTGGCCTTGCCAGCACCCTGGCTAGCTGGTTTTTGGGCCCTACATG chm1:+:1793231086:11 +CATGTAGGGCCCAAAAACCAGCTAGCCAGGGTGCTGGCAAGGCCAAGGAATGGAGAAGATTGGTCCACTCTGCTCTCAAGAGGTCAGGGTGATAGGAATTTATGACCTCTAGGTGGCGCTGAGCCCACCACTCCTCCCCACTGGAGGGCTAATTGGACTGGTCAGGTCTGATGCTGACCCGCTAGCAGAGTGTGGGCAGG chm1:+:612316168:-1 +AATTAGTGGAAATAGAAAAAGTCACCATTTGGCAAACAACATAATCCATTGAAGGTAAGAATCATCACAGGATTCGTGAGAGAAAGGACGATTGAGACAGAACCATTTACTTAAGTCTCAAAGCTCCTCCCGACAGACATTCATTTAAACACAGAGGAAAACTTTTTAGTGGAGCAGCCTGGCAGACACCACCTGACCAC chm1:+:1424132067:-1 chm1:+:1533858829:9 chm1:+:2915187524:-1 chm1:+:2918440989:-1 +AATTAGTGGAAATAGAAAAAGTCACCATTTGGCAAACAACATAATCCATTGAAGGTAAGAATCATCACAGGATTCGTGAGAGAAAGGACGATTGAGACAGAACCATTTACTTAAGTCTCAAAGCTCCTCCCGACAGACATTCATTTAAACACAGAGGAAAACTTTTTAGTGGAGCAGCCTGGCAGACACCACCTGACCAC chm1:+:1533858834:9 +GCAGAACTGGTGCACTCTGCTGGAGAGTCCCCCTTGTTAGGGTCAGCTGCTCTCTTCCGAGCCAGCAGACAGGAAGATTAAATCCGCTGACCCTGCGACTGGCAGCTGCCTTCTCCCTTCAGGTGCTCTGTCGCCAGGGAGTTGAGAGTCCTGTCTGTAAGCCCCTGACTGGTAGCTTGCTGATTTCCTGCAGAGATGCC chm1:+:108974429:-1 chm1:+:382546713:39 chm1:+:432296876:9 chm1:+:751372119:39 chm1:+:1161146458:-1 chm1:+:1781068659:-1 chm1:+:1960740530:-1 +GCAGAACTGGTGCACTCTGCTGGAGAGTCCCCCTTGTTAGGGTCAGCTGCTCTCTTCCGAGCCAGCAGACAGGAAGATTAAATCCGCTGACCCTGCGACTGGCAGCTGCCTTCTCCCTTCAGGTGCTCTGTCGCCAGGGAGTTGAGAGTCCTGTCTGTAAGCCCCTGACTGGTAGCTTGCTGATTTCCTGCAGAGATGCC chm1:+:432296877:9 +GCAGAACTGGTGCACTCTGCTGGAGAGTCCCCCTTGTTAGGGTCAGCTGCTCTCTTCCGAGCCAGCAGACAGGAAGATTAAATCCGCTGACCCTGCGACTGGCAGCTGCCTTCTCCCTTCAGGTGCTCTGTCGCCAGGGAGTTGAGAGTCCTGTCTGTAAGCCCCTGACTGGTAGCTTGCTGATTTCCTGCAGAGATGCC chm1:+:432296879:9 +GGCATCTCTGCAGGAAATCAGCAAGCTACCAGTCAGGGGCTTACAGACAGGACTCTCAACTCCCTGGCGACAGAGCACCTGAAGGGAGAAGGCAGCTGCCAGTCGCAGGGTCAGCGGATTTAATCTTCCTGTCTGCTGGCTCGGAAGAGAGCAGCTGACCCTAACAAGGGGGACTCTCCAGCAGAGTGCACCAGTTCTGC chm1:+:2438692622:-1 +GAAATGGGAGAGTTCTCGTTACCACCCTCAGAGGACGTTTGACAGGGGTGTGGACTCACTCCTTCTAGCCACCCTGCTGCCTCAAACCCTTAGAGGGAGTGTGCAGATGGGCAGGTACAGAGCCCATGGGGGCACCTCGGGCTCCAAGCGCCACAGCAGCGTCTAGGAAGTTGGGTGCTGCACTTCCAAAGCCCAAGTGG chm1:+:473855942:10 +GAAATGGGAGAGTTCTCGTTACCACCCTCAGAGGACGTTTGACAGGGGTGTGGACTCACTCCTTCTAGCCACCCTGCTGCCTCAAACCCTTAGAGGGAGTGTGCAGATGGGCAGGTACAGAGCCCATGGGGGCACCTCGGGCTCCAAGCGCCACAGCAGCGTCTAGGAAGTTGGGTGCTGCACTTCCAAAGCCCAAGTGG chm1:+:2878274637:-1 +GAAATGGGAGAGTTCTCGTTACCACCCTCAGAGGACGTTTGACAGGGGTGTGGACTCACTCCTTCTAGCCACCCTGCTGCCTCAAACCCTTAGAGGGAGTGTGCAGATGGGCAGGTACAGAGCCCATGGGGGCACCTCGGGCTCCAAGCGCCACAGCAGCGTCTAGGAAGTTGGGTGCTGCACTTCCAAAGCCCAAGTGG chm1:+:2272148151:-1 +GAAATGGGAGAGTTCTCGTTACCACCCTCAGAGGACGTTTGACAGGGGTGTGGACTCACTCCTTCTAGCCACCCTGCTGCCTCAAACCCTTAGAGGGAGTGTGCAGATGGGCAGGTACAGAGCCCATGGGGGCACCTCGGGCTCCAAGCGCCACAGCAGCGTCTAGGAAGTTGGGTGCTGCACTTCCAAAGCCCAAGTGG chm1:+:473855945:10 +CCACTTGGGCTTTGGAAGTGCAGCACCCAACTTCCTAGACGCTGCTGTGGCGCTTGGAGCCCGAGGTGCCCCCATGGGCTCTGTACCTGCCCATCTGCACACTCCCTCTAAGGGTTTGAGGCAGCAGGGTGGCTAGAAGGAGTGAGTCCACACCCCTGTCAAACGTCCTCTGAGGGTGGTAACGAGAACTCTCCCATTTC chm1:+:487562008:-1 +CCACTTGGGCTTTGGAAGTGCAGCACCCAACTTCCTAGACGCTGCTGTGGCGCTTGGAGCCCGAGGTGCCCCCATGGGCTCTGTACCTGCCCATCTGCACACTCCCTCTAAGGGTTTGAGGCAGCAGGGTGGCTAGAAGGAGTGAGTCCACACCCCTGTCAAACGTCCTCTGAGGGTGGTAACGAGAACTCTCCCATTTC chm1:+:200170007:-1 chm1:+:923687266:-1 chm1:+:1127254303:-1 chm1:+:1357977910:-1 chm1:+:1477008898:-1 chm1:+:2118743472:-1 chm1:+:2194297300:-1 +TTTCAGTAGAGACAGGGTTTTCACTACCTGACCTCAAGCAATCCACCCGCCTCGGTCCTCCCAAACTGCTGGATTACAGGGAACAACGCCACTGCTCCAGCCACATTGTCTTGATTTTAGTTCTAAACACACGTTTGTAATAAATATAATTCTACAAACTAACATTTAATGAATGTTGGCTCTACGTCAGGCTCTGTAAC chm1:+:67149518:-1 chm1:+:87499362:-1 chm1:+:155577102:-1 chm1:+:288416871:-1 chm1:+:970686333:-1 chm1:+:1046577957:-1 chm1:+:1423534964:-1 chm1:+:1935566506:-1 chm1:+:2074303933:-1 chm1:+:2126247057:-1 chm1:+:2850760247:-1 +TTTCAGTAGAGACAGGGTTTTCACTACCTGACCTCAAGCAATCCACCCGCCTCGGTCCTCCCAAACTGCTGGATTACAGGGAACAACGCCACTGCTCCAGCCACATTGTCTTGATTTTAGTTCTAAACACACGTTTGTAATAAATATAATTCTACAAACTAACATTTAATGAATGTTGGCTCTACGTCAGGCTCTGTAAC chm1:+:11201585:-1 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chm1:+:2337364463:-1 chm1:+:2410398349:-1 chm1:+:2492983200:-1 chm1:+:2708469215:-1 chm1:+:2718370919:-1 chm1:+:2804693602:-1 chm1:+:2982208479:-1 +GCCCTTAACCTCCTGGGCCTAGTGAGCCTCTCACCTAAGCCTCCTGAGTAACTGGGACTACAGGTGGCACACTACCAATACCCAGCTAATTTTTGCATTTTTTTGTAGACGAAGGGAATTTTGGCTAGGCTAGTCTCAAAGTCTTAGCCGAAGCCATCCTCCCACCTCAGCCTCCAAAGTGCTGGGATTAGTAAGAGGCA chm1:+:431833860:-1 chm1:+:453043183:-1 chm1:+:824976960:-1 chm1:+:1177277444:-1 chm1:+:1890618122:-1 chm1:+:2609293222:-1 chm1:+:2766974128:-1 chm1:+:2934086019:-1 chm1:+:2995752380:-1 +TGCCTCTTACTAATCCCAGCACTTTGGAGGCTGAGGTGGGAGGATGGCTTCGGCTAAGACTTTGAGACTAGCCTAGCCAAAATTCCCTTCGTCTACAAAAAAATGCAAAAATTAGCTGGGTATTGGTAGTGTGCCACCTGTAGTCCCAGTTACTCAGGAGGCTTAGGTGAGAGGCTCACTAGGCCCAGGAGGTTAAGGGC chm1:+:2516065984:-1 chm1:+:2569733708:-1 +TGCCTCTTACTAATCCCAGCACTTTGGAGGCTGAGGTGGGAGGATGGCTTCGGCTAAGACTTTGAGACTAGCCTAGCCAAAATTCCCTTCGTCTACAAAAAAATGCAAAAATTAGCTGGGTATTGGTAGTGTGCCACCTGTAGTCCCAGTTACTCAGGAGGCTTAGGTGAGAGGCTCACTAGGCCCAGGAGGTTAAGGGC chm1:+:447482639:-1 chm1:+:1374250660:-1 chm1:+:1399132177:-1 chm1:+:1474017842:-1 chm1:+:1713382864:-1 chm1:+:1955813496:-1 chm1:+:2264007023:-1 chm1:+:2558787851:-1 chm1:+:2698495025:-1 chm1:+:2826014313:-1 +TGCCTCTTACTAATCCCAGCACTTTGGAGGCTGAGGTGGGAGGATGGCTTCGGCTAAGACTTTGAGACTAGCCTAGCCAAAATTCCCTTCGTCTACAAAAAAATGCAAAAATTAGCTGGGTATTGGTAGTGTGCCACCTGTAGTCCCAGTTACTCAGGAGGCTTAGGTGAGAGGCTCACTAGGCCCAGGAGGTTAAGGGC chm1:+:421504344:-1 chm1:+:2647518982:-1 chm1:+:2713577831:11 +TGCCTCTTACTAATCCCAGCACTTTGGAGGCTGAGGTGGGAGGATGGCTTCGGCTAAGACTTTGAGACTAGCCTAGCCAAAATTCCCTTCGTCTACAAAAAAATGCAAAAATTAGCTGGGTATTGGTAGTGTGCCACCTGTAGTCCCAGTTACTCAGGAGGCTTAGGTGAGAGGCTCACTAGGCCCAGGAGGTTAAGGGC chm1:+:2915996600:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGG chm1:+:170153707:-1 chm1:+:388607918:-1 chm1:+:880651511:-1 chm1:+:981118951:-1 chm1:+:1623096786:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGG chm1:+:219352576:-1 chm1:+:927087870:-1 chm1:+:1306496912:-1 chm1:+:1737647804:-1 chm1:+:1821779330:-1 chm1:+:2028470490:-1 chm1:+:2247437482:-1 chm1:+:2470190442:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGG chm1:+:300569358:-1 chm1:+:1288025944:-1 chm1:+:1974963909:-1 chm1:+:2969882593:-1 chm1:+:3039422232:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGG chm1:+:308126217:-1 chm1:+:326272530:-1 chm1:+:626255934:-1 chm1:+:1113265135:-1 chm1:+:1176186223:-1 chm1:+:1474808411:-1 chm1:+:1492491706:-1 chm1:+:1960630211:-1 chm1:+:2050110515:-1 chm1:+:2359670880:-1 chm1:+:3029118976:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGG chm1:+:818739277:-1 chm1:+:863797627:-1 chm1:+:1000920925:-1 chm1:+:1142397105:-1 chm1:+:1227856555:-1 chm1:+:1230253981:-1 chm1:+:1641074757:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGG chm1:+:258239665:-1 chm1:+:2138407472:-1 chm1:+:2281987156:-1 chm1:+:2432720666:-1 chm1:+:2552555494:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGG chm1:+:1063955700:-1 chm1:+:1485908678:-1 +CCTTTAAAGTTGTAATAAAAGTCAGAAAGTACTTCACTGCTTAATTTTCCTCCTTACTACAGAATATGGATCATTACTAAAGAGAATCAACAGTTATTTCAATTTCCTTTGTTATTATAACTAATAGAACTGTGGTTCTTAATCTAAAGAAATGATAAATGATAATCTCTCTATATATATTTTGAAATTTATAATTCTGT chm1:+:256729184:-1 chm1:+:616985686:-1 chm1:+:752288389:-1 chm1:+:753247898:10 chm1:+:781880282:-1 chm1:+:899022175:-1 chm1:+:995648173:-1 chm1:+:1040445303:-1 chm1:+:1375858039:-1 chm1:+:1803310291:-1 chm1:+:2681567492:-1 +CCTTTAAAGTTGTAATAAAAGTCAGAAAGTACTTCACTGCTTAATTTTCCTCCTTACTACAGAATATGGATCATTACTAAAGAGAATCAACAGTTATTTCAATTTCCTTTGTTATTATAACTAATAGAACTGTGGTTCTTAATCTAAAGAAATGATAAATGATAATCTCTCTATATATATTTTGAAATTTATAATTCTGT chm1:+:753247902:10 +AGAACGGAGAATTTCTCAAGACACACAAATAGTAACTACCATATGATCCAGAATCCCGGTATCTACTCAAAGGAAAGAAATCATTGTATTCAATAAATACTTTGCACTTATATGTTTATTTGCTAGCACTATTTACAATAGTAATGATATGGGAATCAATCTAAGTGTCCATAAATGGGAATTGGATAAGGAAAATGTGA chm1:+:199469515:11 +AGAACGGAGAATTTCTCAAGACACACAAATAGTAACTACCATATGATCCAGAATCCCGGTATCTACTCAAAGGAAAGAAATCATTGTATTCAATAAATACTTTGCACTTATATGTTTATTTGCTAGCACTATTTACAATAGTAATGATATGGGAATCAATCTAAGTGTCCATAAATGGGAATTGGATAAGGAAAATGTGA chm1:+:199469518:11 +AGAACGGAGAATTTCTCAAGACACACAAATAGTAACTACCATATGATCCAGAATCCCGGTATCTACTCAAAGGAAAGAAATCATTGTATTCAATAAATACTTTGCACTTATATGTTTATTTGCTAGCACTATTTACAATAGTAATGATATGGGAATCAATCTAAGTGTCCATAAATGGGAATTGGATAAGGAAAATGTGA chm1:+:199469514:11 +TCACATTTTCCTTATCCAATTCCCATTTATGGACACTTAGATTGATTCCCATATCATTACTATTGTAAATAGTGCTAGCAAATAAACATATAAGTGCAAAGTATTTATTGAATACAATGATTTCTTTCCTTTGAGTAGATACCGGGATTCTGGATCATATGGTAGTTACTATTTGTGTGTCTTGAGAAATTCTCCGTTCT chm1:+:74589332:-1 chm1:+:94922145:-1 chm1:+:103106293:-1 chm1:+:152355700:-1 chm1:+:170817270:-1 chm1:+:254558667:-1 chm1:+:327114361:-1 chm1:+:396823650:-1 chm1:+:414248152:-1 chm1:+:419095586:-1 chm1:+:549079589:-1 chm1:+:567384451:-1 chm1:+:608388136:-1 chm1:+:787097061:-1 chm1:+:819578596:-1 chm1:+:820387933:-1 chm1:+:839197353:-1 chm1:+:994918755:-1 chm1:+:1011947127:-1 chm1:+:1018470216:-1 chm1:+:1075003568:-1 chm1:+:1201014608:-1 chm1:+:1281991494:-1 chm1:+:1314255345:-1 chm1:+:1378734749:-1 chm1:+:1395455827:-1 chm1:+:1540710982:-1 chm1:+:1555175661:-1 chm1:+:1561824124:-1 chm1:+:1563791704:-1 chm1:+:1702811070:-1 chm1:+:1758639702:-1 chm1:+:1788130748:-1 chm1:+:1819949259:-1 chm1:+:2016713617:-1 chm1:+:2147414348:-1 chm1:+:2253006183:-1 chm1:+:2300430415:-1 chm1:+:2333132872:-1 chm1:+:2606470998:-1 chm1:+:2616802377:-1 chm1:+:2621057180:-1 chm1:+:2762730360:-1 chm1:+:2903307462:-1 chm1:+:2937093076:-1 chm1:+:2958340740:-1 chm1:+:2958853309:-1 chm1:+:2992211325:-1 +TCACATTTTCCTTATCCAATTCCCATTTATGGACACTTAGATTGATTCCCATATCATTACTATTGTAAATAGTGCTAGCAAATAAACATATAAGTGCAAAGTATTTATTGAATACAATGATTTCTTTCCTTTGAGTAGATACCGGGATTCTGGATCATATGGTAGTTACTATTTGTGTGTCTTGAGAAATTCTCCGTTCT chm1:+:1712810076:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCT chm1:+:23949818:-1 chm1:+:34483579:-1 chm1:+:291653544:-1 chm1:+:402474669:-1 chm1:+:422813321:-1 chm1:+:780932517:-1 chm1:+:1053157255:-1 chm1:+:1971444552:-1 chm1:+:2888474820:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCT chm1:+:103346332:-1 chm1:+:950361555:-1 chm1:+:1462616755:-1 chm1:+:2153549957:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCT chm1:+:353736426:-1 chm1:+:1389997378:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCT chm1:+:56665001:-1 chm1:+:320244501:-1 chm1:+:609040934:-1 chm1:+:792789354:-1 chm1:+:961964537:-1 chm1:+:1080672347:-1 chm1:+:1143322702:-1 chm1:+:1929856429:-1 chm1:+:1992922201:-1 chm1:+:2050376565:-1 chm1:+:2174022185:-1 chm1:+:2344952995:-1 chm1:+:2380178139:-1 chm1:+:2617944739:-1 chm1:+:2770369509:-1 chm1:+:2808639523:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCT chm1:+:64476028:-1 chm1:+:174457096:-1 chm1:+:211934150:-1 chm1:+:213248914:-1 chm1:+:237537834:-1 chm1:+:286895626:-1 chm1:+:391712640:-1 chm1:+:417694660:-1 chm1:+:460702413:-1 chm1:+:547456141:-1 chm1:+:727367078:-1 chm1:+:771367503:-1 chm1:+:833078299:-1 chm1:+:874677040:-1 chm1:+:876449563:-1 chm1:+:897317656:-1 chm1:+:898850266:-1 chm1:+:1160071657:-1 chm1:+:1199576881:-1 chm1:+:1223895829:-1 chm1:+:1351761294:-1 chm1:+:1522809170:-1 chm1:+:1718678460:-1 chm1:+:1857168962:-1 chm1:+:1887114117:-1 chm1:+:1970578722:-1 chm1:+:2154063564:-1 chm1:+:2252309152:-1 chm1:+:2391637505:-1 chm1:+:2419378076:-1 chm1:+:2568935905:-1 chm1:+:2735761126:-1 chm1:+:2770568168:-1 chm1:+:2874442311:-1 chm1:+:2906900402:-1 chm1:+:2973814939:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCT chm1:+:75016087:-1 chm1:+:87857017:-1 chm1:+:195622473:-1 chm1:+:195951496:-1 chm1:+:277382920:-1 chm1:+:297659063:-1 chm1:+:400652478:-1 chm1:+:406670383:-1 chm1:+:426816663:-1 chm1:+:433746502:-1 chm1:+:470151905:-1 chm1:+:604184278:-1 chm1:+:641262743:-1 chm1:+:655994706:-1 chm1:+:701190361:-1 chm1:+:751844851:-1 chm1:+:754082045:-1 chm1:+:777763678:-1 chm1:+:801882463:-1 chm1:+:829550974:-1 chm1:+:838228329:-1 chm1:+:842865764:-1 chm1:+:861729625:-1 chm1:+:871291162:-1 chm1:+:935588366:-1 chm1:+:949635797:-1 chm1:+:966560062:-1 chm1:+:1006411166:-1 chm1:+:1010635850:-1 chm1:+:1160150364:-1 chm1:+:1190103949:-1 chm1:+:1250199563:-1 chm1:+:1253476659:-1 chm1:+:1296326943:-1 chm1:+:1310980425:-1 chm1:+:1316391088:-1 chm1:+:1319548989:-1 chm1:+:1485522180:-1 chm1:+:1559588143:-1 chm1:+:1786116987:-1 chm1:+:1866055255:-1 chm1:+:1945055486:-1 chm1:+:2017631799:-1 chm1:+:2037042618:-1 chm1:+:2052356328:-1 chm1:+:2147887178:-1 chm1:+:2181859695:-1 chm1:+:2355878335:-1 chm1:+:2486669502:-1 chm1:+:2625932024:-1 chm1:+:2632089585:-1 chm1:+:2758549935:-1 chm1:+:2962991587:-1 chm1:+:2994958440:-1 chm1:+:3016604606:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCT chm1:+:80440247:-1 chm1:+:1234462155:-1 chm1:+:1511808906:-1 chm1:+:1584255459:-1 chm1:+:2231444185:-1 chm1:+:2661346228:-1 chm1:+:2666907071:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCT chm1:+:88405276:-1 chm1:+:1088763286:-1 chm1:+:1449601833:-1 chm1:+:1513431351:-1 chm1:+:1645491943:-1 chm1:+:2705215054:-1 chm1:+:2854410126:-1 +AGACCGTCTCAAAAAACAAAAAAACAAAACAAAACAACAAAAAAAAACCAGAATGCAAAATAAAGTACAAACTCAGTAAAAAACTGGCATTTATCTCTCAAATTTTTTCAAGTAAAACGGAACAATACGTTATACTCAATTCTAGAAGTCATCAGGACAAAGTTTTCCCAGTAGATTTTCTTAAATGTCCTCTTGGAAGC chm1:+:103436504:11 chm1:+:192980852:-1 chm1:+:920545986:-1 chm1:+:1004344847:-1 chm1:+:2044124555:-1 +AGACCGTCTCAAAAAACAAAAAAACAAAACAAAACAACAAAAAAAAACCAGAATGCAAAATAAAGTACAAACTCAGTAAAAAACTGGCATTTATCTCTCAAATTTTTTCAAGTAAAACGGAACAATACGTTATACTCAATTCTAGAAGTCATCAGGACAAAGTTTTCCCAGTAGATTTTCTTAAATGTCCTCTTGGAAGC chm1:+:103436503:11 +ATTACAGAGACAGCCCACACCAGCACTGCCTGAATTACAGAGATGACAGGTCCACACCCAGCACTGCCTTGGAATTACAGAGATGACAGTCCACACCAGACATCATCATAATCACAGAGATATTCTACACCAGCATCATCTTAATTACAGAGACAGCCCACACCAGCGCTGCCTGAATTACAGAGATGACAGTCCACAGC chm1:+:369095755:-1 chm1:+:490448390:-1 chm1:+:647582591:-1 chm1:+:2224811607:-1 chm1:+:2497140261:-1 chm1:+:2570696412:-1 chm1:+:2602487124:-1 +ATTACAGAGACAGCCCACACCAGCACTGCCTGAATTACAGAGATGACAGGTCCACACCCAGCACTGCCTTGGAATTACAGAGATGACAGTCCACACCAGACATCATCATAATCACAGAGATATTCTACACCAGCATCATCTTAATTACAGAGACAGCCCACACCAGCGCTGCCTGAATTACAGAGATGACAGTCCACAGC chm1:+:89174302:-1 chm1:+:202251727:-1 chm1:+:345424266:-1 chm1:+:357581427:-1 chm1:+:414898510:-1 chm1:+:523230418:-1 chm1:+:530200340:-1 chm1:+:616300833:-1 chm1:+:643396384:-1 chm1:+:705041554:-1 chm1:+:840731607:-1 chm1:+:847879858:-1 chm1:+:1041732766:-1 chm1:+:1070460023:-1 chm1:+:1108883484:-1 chm1:+:1201210041:-1 chm1:+:1256719594:-1 chm1:+:1265784839:-1 chm1:+:1655452154:-1 chm1:+:1974366269:-1 chm1:+:2156026785:-1 chm1:+:2457822235:-1 chm1:+:2984819908:-1 chm1:+:3034223294:-1 chm1:+:3034359196:-1 +ATTACAGAGACAGCCCACACCAGCACTGCCTGAATTACAGAGATGACAGGTCCACACCCAGCACTGCCTTGGAATTACAGAGATGACAGTCCACACCAGACATCATCATAATCACAGAGATATTCTACACCAGCATCATCTTAATTACAGAGACAGCCCACACCAGCGCTGCCTGAATTACAGAGATGACAGTCCACAGC chm1:+:368688152:-1 chm1:+:636332734:-1 chm1:+:644940805:-1 chm1:+:862442860:-1 chm1:+:1451278594:-1 chm1:+:1476932375:-1 chm1:+:1567815865:-1 chm1:+:1763718065:-1 chm1:+:1801095575:-1 chm1:+:1908853165:-1 chm1:+:2002307599:-1 chm1:+:2266857091:-1 chm1:+:2700981733:-1 chm1:+:3014449746:-1 +ATTACAGAGACAGCCCACACCAGCACTGCCTGAATTACAGAGATGACAGGTCCACACCCAGCACTGCCTTGGAATTACAGAGATGACAGTCCACACCAGACATCATCATAATCACAGAGATATTCTACACCAGCATCATCTTAATTACAGAGACAGCCCACACCAGCGCTGCCTGAATTACAGAGATGACAGTCCACAGC chm1:+:191248357:-1 chm1:+:408407412:-1 chm1:+:457457974:-1 chm1:+:486420160:-1 chm1:+:520830214:-1 chm1:+:752483736:-1 chm1:+:851954434:-1 chm1:+:880349485:-1 chm1:+:1119368980:-1 chm1:+:1167786849:-1 chm1:+:1200593834:-1 chm1:+:1269367225:-1 chm1:+:1497227274:-1 chm1:+:1555377657:-1 chm1:+:1560492897:-1 chm1:+:1764574538:-1 chm1:+:1770267202:-1 chm1:+:1789546998:-1 chm1:+:1980050474:-1 chm1:+:2157574664:-1 chm1:+:2197947039:-1 chm1:+:2368555944:-1 chm1:+:2562117271:-1 chm1:+:2562154909:-1 chm1:+:2759173897:-1 chm1:+:2803664541:-1 chm1:+:2814755000:-1 chm1:+:2814755090:-1 chm1:+:2814755192:-1 chm1:+:2869945793:-1 chm1:+:2998066325:-1 chm1:+:3005251519:-1 +ATTACAGAGACAGCCCACACCAGCACTGCCTGAATTACAGAGATGACAGGTCCACACCCAGCACTGCCTTGGAATTACAGAGATGACAGTCCACACCAGACATCATCATAATCACAGAGATATTCTACACCAGCATCATCTTAATTACAGAGACAGCCCACACCAGCGCTGCCTGAATTACAGAGATGACAGTCCACAGC chm1:+:1376392226:-1 chm1:+:1537490143:-1 chm1:+:1694955421:-1 chm1:+:2062740714:-1 chm1:+:2444608274:-1 chm1:+:2827797504:-1 chm1:+:2944624151:-1 chm1:+:3007160489:-1 +GCTGTGGACTGTCATCTCTGTAATTCAGGCAGCGCTGGTGTGGGCTGTCTCTGTAATTAAGATGATGCTGGTGTAGAATATCTCTGTGATTATGATGATGTCTGGTGTGGACTGTCATCTCTGTAATTCCAAGGCAGTGCTGGGTGTGGACCTGTCATCTCTGTAATTCAGGCAGTGCTGGTGTGGGCTGTCTCTGTAAT chm1:+:1523960172:-1 chm1:+:2157577406:-1 chm1:+:2498164219:32 chm1:+:2498164255:32 chm1:+:2498164291:32 chm1:+:2498164327:36 chm1:+:2498164429:21 chm1:+:2498164531:23 chm1:+:2498164633:12 chm1:+:2498164669:12 chm1:+:2498164705:12 chm1:+:2498164843:10 chm1:+:2498164945:5 chm1:+:2498164981:5 chm1:+:2498165083:14 chm1:+:2498165155:14 chm1:+:2498165257:22 chm1:+:2498165359:22 chm1:+:2498165461:22 +GCTGTGGACTGTCATCTCTGTAATTCAGGCAGCGCTGGTGTGGGCTGTCTCTGTAATTAAGATGATGCTGGTGTAGAATATCTCTGTGATTATGATGATGTCTGGTGTGGACTGTCATCTCTGTAATTCCAAGGCAGTGCTGGGTGTGGACCTGTCATCTCTGTAATTCAGGCAGTGCTGGTGTGGGCTGTCTCTGTAAT chm1:+:2498164986:5 +ATCTACTGTTCATCCAAAACTCAAGGAGCTAGATGTGACTATTTTCCCTGGCATAAACATATTTAACTCTGGGAAGATTTGAGTTATGCATAGAAAGTTTAGTTTTATATTTAACTTGGTATTTATGTTATTTATAAATTTTAAAGTACAATAGGCTTATCAGAGCATATAGTTCGATTTAAAATGTAAATACGAATAAC chm1:+:1082768830:-1 chm1:+:1150470056:-1 chm1:+:1208004084:-1 chm1:+:1248919575:-1 chm1:+:1322242726:-1 chm1:+:2031958068:-1 chm1:+:2808104186:-1 chm1:+:2913035952:-1 +ATCTACTGTTCATCCAAAACTCAAGGAGCTAGATGTGACTATTTTCCCTGGCATAAACATATTTAACTCTGGGAAGATTTGAGTTATGCATAGAAAGTTTAGTTTTATATTTAACTTGGTATTTATGTTATTTATAAATTTTAAAGTACAATAGGCTTATCAGAGCATATAGTTCGATTTAAAATGTAAATACGAATAAC chm1:+:78059138:-1 chm1:+:1919288620:12 chm1:+:2775246562:-1 +ATCTACTGTTCATCCAAAACTCAAGGAGCTAGATGTGACTATTTTCCCTGGCATAAACATATTTAACTCTGGGAAGATTTGAGTTATGCATAGAAAGTTTAGTTTTATATTTAACTTGGTATTTATGTTATTTATAAATTTTAAAGTACAATAGGCTTATCAGAGCATATAGTTCGATTTAAAATGTAAATACGAATAAC chm1:+:927080725:-1 +ATCTACTGTTCATCCAAAACTCAAGGAGCTAGATGTGACTATTTTCCCTGGCATAAACATATTTAACTCTGGGAAGATTTGAGTTATGCATAGAAAGTTTAGTTTTATATTTAACTTGGTATTTATGTTATTTATAAATTTTAAAGTACAATAGGCTTATCAGAGCATATAGTTCGATTTAAAATGTAAATACGAATAAC chm1:+:1974470114:-1 +GTTATTCGTATTTACATTTTAAATCGAACTATATGCTCTGATAAGCCTATTGTACTTTAAAATTTATAAATAACATAAATACCAAGTTAAATATAAAACTAAACTTTCTATGCATAACTCAAATCTTCCCAGAGTTAAATATGTTTATGCCAGGGAAAATAGTCACATCTAGCTCCTTGAGTTTTGGATGAACAGTAGAT chm1:+:43943839:-1 chm1:+:514885614:-1 chm1:+:794748703:-1 chm1:+:1841368600:-1 +ATCTCCGCCCTCAATGCAACTCCCTTTACCTCATAACAGTGCTTTCGTATTGTTTTCTTACTGAGAAAGTTACCTGTGTGTTTTAATGTTTTTAGAGAATCACAGATTGGAATCTGCCGTATTCAGAACCATCTAATTCTGAAAAGTTTTTACGTGGTTAAGTACAGCGTTTTATGTACAAATCCTATTTTATGAAACTG chm1:+:1167117889:-1 chm1:+:1369050296:-1 chm1:+:1456222401:-1 chm1:+:2331625401:-1 chm1:+:2331895885:-1 chm1:+:2331950831:-1 chm1:+:2332000728:-1 chm1:+:2778374505:-1 +ATCTCCGCCCTCAATGCAACTCCCTTTACCTCATAACAGTGCTTTCGTATTGTTTTCTTACTGAGAAAGTTACCTGTGTGTTTTAATGTTTTTAGAGAATCACAGATTGGAATCTGCCGTATTCAGAACCATCTAATTCTGAAAAGTTTTTACGTGGTTAAGTACAGCGTTTTATGTACAAATCCTATTTTATGAAACTG chm1:+:80527831:-1 chm1:+:1803902931:-1 +ATCTCCGCCCTCAATGCAACTCCCTTTACCTCATAACAGTGCTTTCGTATTGTTTTCTTACTGAGAAAGTTACCTGTGTGTTTTAATGTTTTTAGAGAATCACAGATTGGAATCTGCCGTATTCAGAACCATCTAATTCTGAAAAGTTTTTACGTGGTTAAGTACAGCGTTTTATGTACAAATCCTATTTTATGAAACTG chm1:+:146676266:-1 chm1:+:192530847:-1 chm1:+:330991877:-1 chm1:+:444613168:-1 chm1:+:601910789:-1 chm1:+:836259704:-1 chm1:+:1151246328:-1 chm1:+:1606426453:-1 chm1:+:1608788374:-1 chm1:+:1736690243:-1 chm1:+:1778281889:-1 chm1:+:2107980435:-1 +ATCTCCGCCCTCAATGCAACTCCCTTTACCTCATAACAGTGCTTTCGTATTGTTTTCTTACTGAGAAAGTTACCTGTGTGTTTTAATGTTTTTAGAGAATCACAGATTGGAATCTGCCGTATTCAGAACCATCTAATTCTGAAAAGTTTTTACGTGGTTAAGTACAGCGTTTTATGTACAAATCCTATTTTATGAAACTG chm1:+:1454999385:-1 chm1:+:2238078600:-1 chm1:+:2295820212:-1 +ATCTCCGCCCTCAATGCAACTCCCTTTACCTCATAACAGTGCTTTCGTATTGTTTTCTTACTGAGAAAGTTACCTGTGTGTTTTAATGTTTTTAGAGAATCACAGATTGGAATCTGCCGTATTCAGAACCATCTAATTCTGAAAAGTTTTTACGTGGTTAAGTACAGCGTTTTATGTACAAATCCTATTTTATGAAACTG chm1:+:475598696:-1 chm1:+:1314030034:-1 chm1:+:1350961394:-1 chm1:+:1610450894:-1 chm1:+:2650500937:-1 chm1:+:2812337317:-1 +CAGTTTCATAAAATAGGATTTGTACATAAAACGCTGTACTTAACCACGTAAAAACTTTTCAGAATTAGATGGTTCTGAATACGGCAGATTCCAATCTGTGATTCTCTAAAAACATTAAAACACACAGGTAACTTTCTCAGTAAGAAAACAATACGAAAGCACTGTTATGAGGTAAAGGGAGTTGCATTGAGGGCGGAGAT chm1:+:403666789:-1 chm1:+:480618222:-1 chm1:+:773021761:-1 chm1:+:1273621527:-1 chm1:+:1405905664:-1 chm1:+:1459509860:-1 chm1:+:1921346296:-1 chm1:+:2401890084:-1 chm1:+:2778031030:-1 +CAGTTTCATAAAATAGGATTTGTACATAAAACGCTGTACTTAACCACGTAAAAACTTTTCAGAATTAGATGGTTCTGAATACGGCAGATTCCAATCTGTGATTCTCTAAAAACATTAAAACACACAGGTAACTTTCTCAGTAAGAAAACAATACGAAAGCACTGTTATGAGGTAAAGGGAGTTGCATTGAGGGCGGAGAT chm1:+:97809767:-1 chm1:+:536066205:11 +CAGTTTCATAAAATAGGATTTGTACATAAAACGCTGTACTTAACCACGTAAAAACTTTTCAGAATTAGATGGTTCTGAATACGGCAGATTCCAATCTGTGATTCTCTAAAAACATTAAAACACACAGGTAACTTTCTCAGTAAGAAAACAATACGAAAGCACTGTTATGAGGTAAAGGGAGTTGCATTGAGGGCGGAGAT chm1:+:536066206:11 +CAGTTTCATAAAATAGGATTTGTACATAAAACGCTGTACTTAACCACGTAAAAACTTTTCAGAATTAGATGGTTCTGAATACGGCAGATTCCAATCTGTGATTCTCTAAAAACATTAAAACACACAGGTAACTTTCTCAGTAAGAAAACAATACGAAAGCACTGTTATGAGGTAAAGGGAGTTGCATTGAGGGCGGAGAT chm1:+:536066204:11 +CAGTTTCATAAAATAGGATTTGTACATAAAACGCTGTACTTAACCACGTAAAAACTTTTCAGAATTAGATGGTTCTGAATACGGCAGATTCCAATCTGTGATTCTCTAAAAACATTAAAACACACAGGTAACTTTCTCAGTAAGAAAACAATACGAAAGCACTGTTATGAGGTAAAGGGAGTTGCATTGAGGGCGGAGAT chm1:+:536066208:11 +GTAAGCTCATCTGGATAATCCAGGATACTTTCCCTATTTTAAAATCAGCTGATTAGCAATTGTAATTCCACCTTACAACCTCAAATTCTCCTTTCGTCACGCAACCTCAACATCTTCACAGGTTCTGGGGGATTAGGGATGTAAGCAAGCTTTGTTGGGGGCATTATCCTCCTCTGCCACAAGCTGTATGTTTAAAATTT chm1:+:216907580:-1 chm1:+:798489557:-1 chm1:+:1715158901:-1 chm1:+:1905329302:-1 chm1:+:2815684968:-1 chm1:+:2860298661:-1 +GTAAGCTCATCTGGATAATCCAGGATACTTTCCCTATTTTAAAATCAGCTGATTAGCAATTGTAATTCCACCTTACAACCTCAAATTCTCCTTTCGTCACGCAACCTCAACATCTTCACAGGTTCTGGGGGATTAGGGATGTAAGCAAGCTTTGTTGGGGGCATTATCCTCCTCTGCCACAAGCTGTATGTTTAAAATTT chm1:+:9041709:-1 chm1:+:193140738:-1 chm1:+:256436255:-1 chm1:+:449034594:-1 chm1:+:630033883:-1 chm1:+:660622565:-1 chm1:+:802311981:-1 chm1:+:817226683:-1 chm1:+:835188460:-1 chm1:+:835319054:-1 chm1:+:835429333:-1 chm1:+:1182002024:-1 chm1:+:1234016438:-1 chm1:+:1251717252:-1 chm1:+:1536003994:-1 chm1:+:1666130417:-1 chm1:+:1761370480:-1 chm1:+:1772661889:-1 chm1:+:1793568981:-1 chm1:+:1848035790:-1 chm1:+:2048528673:-1 chm1:+:2067028792:-1 chm1:+:2237818854:-1 chm1:+:2346366564:-1 chm1:+:2378802843:-1 chm1:+:2382030275:-1 chm1:+:2678647235:-1 chm1:+:2696905196:-1 chm1:+:2819969785:-1 chm1:+:2857828621:-1 chm1:+:2901785733:-1 chm1:+:2980714986:-1 chm1:+:3009189045:-1 chm1:+:3030441342:-1 chm1:+:3033782896:-1 chm1:+:3057558322:-1 +GTAAGCTCATCTGGATAATCCAGGATACTTTCCCTATTTTAAAATCAGCTGATTAGCAATTGTAATTCCACCTTACAACCTCAAATTCTCCTTTCGTCACGCAACCTCAACATCTTCACAGGTTCTGGGGGATTAGGGATGTAAGCAAGCTTTGTTGGGGGCATTATCCTCCTCTGCCACAAGCTGTATGTTTAAAATTT chm1:+:93860770:-1 chm1:+:314052716:-1 chm1:+:389073033:-1 chm1:+:843931557:-1 chm1:+:1769050950:-1 +GTAAGCTCATCTGGATAATCCAGGATACTTTCCCTATTTTAAAATCAGCTGATTAGCAATTGTAATTCCACCTTACAACCTCAAATTCTCCTTTCGTCACGCAACCTCAACATCTTCACAGGTTCTGGGGGATTAGGGATGTAAGCAAGCTTTGTTGGGGGCATTATCCTCCTCTGCCACAAGCTGTATGTTTAAAATTT chm1:+:38655978:-1 chm1:+:176472413:-1 chm1:+:272400552:-1 chm1:+:432632197:-1 chm1:+:515883597:-1 chm1:+:643057186:-1 chm1:+:767832831:-1 chm1:+:799978031:-1 chm1:+:855153816:-1 chm1:+:908572295:-1 chm1:+:965391940:-1 chm1:+:1267399779:-1 chm1:+:1272857215:-1 chm1:+:1321284968:-1 chm1:+:1329012929:-1 chm1:+:1337726603:-1 chm1:+:1340930136:-1 chm1:+:1433522052:-1 chm1:+:1785226172:-1 chm1:+:1854316422:-1 chm1:+:1966150101:-1 chm1:+:1998193078:-1 chm1:+:2157629849:-1 chm1:+:2177438713:-1 chm1:+:2284871592:-1 chm1:+:2464737971:-1 chm1:+:2468305083:-1 chm1:+:2551199018:-1 chm1:+:2568957769:-1 chm1:+:2663783686:-1 chm1:+:2691094511:-1 chm1:+:2722970645:-1 chm1:+:2873990831:-1 chm1:+:2913830156:-1 chm1:+:2926721566:-1 +GTAAGCTCATCTGGATAATCCAGGATACTTTCCCTATTTTAAAATCAGCTGATTAGCAATTGTAATTCCACCTTACAACCTCAAATTCTCCTTTCGTCACGCAACCTCAACATCTTCACAGGTTCTGGGGGATTAGGGATGTAAGCAAGCTTTGTTGGGGGCATTATCCTCCTCTGCCACAAGCTGTATGTTTAAAATTT chm1:+:54043332:-1 chm1:+:82670947:-1 chm1:+:147767354:-1 chm1:+:153583027:-1 chm1:+:160923572:-1 chm1:+:192278167:-1 chm1:+:254021401:-1 chm1:+:262159720:-1 chm1:+:273017655:-1 chm1:+:501167806:-1 chm1:+:501169513:-1 chm1:+:501172025:-1 chm1:+:541826589:-1 chm1:+:594107168:-1 chm1:+:605626140:-1 chm1:+:610506160:-1 chm1:+:654895080:-1 chm1:+:699443393:-1 chm1:+:699925037:-1 chm1:+:700233070:-1 chm1:+:712398657:-1 chm1:+:749979552:-1 chm1:+:753544864:-1 chm1:+:885844451:-1 chm1:+:1055999508:-1 chm1:+:1101533645:-1 chm1:+:1179142125:-1 chm1:+:1183370541:-1 chm1:+:1219599173:-1 chm1:+:1229569393:-1 chm1:+:1412203334:-1 chm1:+:1471443636:-1 chm1:+:1476184728:-1 chm1:+:1550122875:-1 chm1:+:1554133252:-1 chm1:+:1608337843:-1 chm1:+:1608346569:-1 chm1:+:1647741237:-1 chm1:+:1679308224:-1 chm1:+:1731278226:-1 chm1:+:1781756426:-1 chm1:+:1793515751:-1 chm1:+:1819668783:-1 chm1:+:1845412230:-1 chm1:+:1848521362:-1 chm1:+:1887219685:-1 chm1:+:1903811802:-1 chm1:+:1927104383:-1 chm1:+:1934806397:-1 chm1:+:1941122952:-1 chm1:+:1943112259:-1 chm1:+:1947512358:-1 chm1:+:1960474961:-1 chm1:+:1982189131:-1 chm1:+:2004197232:-1 chm1:+:2054703191:-1 chm1:+:2069590531:-1 chm1:+:2137272791:-1 chm1:+:2139654223:-1 chm1:+:2146565923:-1 chm1:+:2153255398:-1 chm1:+:2223115987:-1 chm1:+:2277194017:-1 chm1:+:2284658307:-1 chm1:+:2295299153:-1 chm1:+:2335253873:-1 chm1:+:2377227400:-1 chm1:+:2401878982:-1 chm1:+:2436599171:-1 chm1:+:2737814470:-1 chm1:+:2767578920:-1 chm1:+:2808515870:-1 chm1:+:2867078594:-1 chm1:+:2926144660:-1 chm1:+:3031790750:-1 chm1:+:3100430335:-1 +AAATTTTAAACATACAGCTTGTGGCAGAGGAGGATAATGCCCCCAACAAAGCTTGCTTACATCCCTAATCCCCCAGAACCTGTGAAGATGTTGAGGTTGCGTGACGAAAGGAGAATTTGAGGTTGTAAGGTGGAATTACAATTGCTAATCAGCTGATTTTAAAATAGGGAAAGTATCCTGGATTATCCAGATGAGCTTAC chm1:+:593091063:7 +AAATTTTAAACATACAGCTTGTGGCAGAGGAGGATAATGCCCCCAACAAAGCTTGCTTACATCCCTAATCCCCCAGAACCTGTGAAGATGTTGAGGTTGCGTGACGAAAGGAGAATTTGAGGTTGTAAGGTGGAATTACAATTGCTAATCAGCTGATTTTAAAATAGGGAAAGTATCCTGGATTATCCAGATGAGCTTAC chm1:+:593091056:7 +AAATTTTAAACATACAGCTTGTGGCAGAGGAGGATAATGCCCCCAACAAAGCTTGCTTACATCCCTAATCCCCCAGAACCTGTGAAGATGTTGAGGTTGCGTGACGAAAGGAGAATTTGAGGTTGTAAGGTGGAATTACAATTGCTAATCAGCTGATTTTAAAATAGGGAAAGTATCCTGGATTATCCAGATGAGCTTAC chm1:+:2592693902:-1 +AAATTTTAAACATACAGCTTGTGGCAGAGGAGGATAATGCCCCCAACAAAGCTTGCTTACATCCCTAATCCCCCAGAACCTGTGAAGATGTTGAGGTTGCGTGACGAAAGGAGAATTTGAGGTTGTAAGGTGGAATTACAATTGCTAATCAGCTGATTTTAAAATAGGGAAAGTATCCTGGATTATCCAGATGAGCTTAC chm1:+:593091062:7 +CTCTAAATCTCGGGAGACATGGAGAACCATCAGCTTGTCTGTTATGCCTGAAGCCTAGGAGACAACAGAGAAGGAAAGTGGAAACTAGAACTTAAGGTGAAAGGCTGCCAGGAGGTTGATCAGGAGGGAAACTATAAGTCTGCTTAAGAGGAATGGAAAGATTATAAAAGTAGGGGAGCAAACATGATCAAACATGTAAA chm1:+:345777300:-1 chm1:+:347383895:-1 chm1:+:846977159:-1 chm1:+:1125625155:-1 chm1:+:1427562204:-1 chm1:+:1719494780:-1 chm1:+:1913863182:-1 chm1:+:2512374213:-1 chm1:+:2636789434:-1 +CTCTAAATCTCGGGAGACATGGAGAACCATCAGCTTGTCTGTTATGCCTGAAGCCTAGGAGACAACAGAGAAGGAAAGTGGAAACTAGAACTTAAGGTGAAAGGCTGCCAGGAGGTTGATCAGGAGGGAAACTATAAGTCTGCTTAAGAGGAATGGAAAGATTATAAAAGTAGGGGAGCAAACATGATCAAACATGTAAA chm1:+:74363205:-1 chm1:+:159644543:-1 chm1:+:1013658211:-1 chm1:+:2056413329:-1 chm1:+:2115906533:-1 +CTCTAAATCTCGGGAGACATGGAGAACCATCAGCTTGTCTGTTATGCCTGAAGCCTAGGAGACAACAGAGAAGGAAAGTGGAAACTAGAACTTAAGGTGAAAGGCTGCCAGGAGGTTGATCAGGAGGGAAACTATAAGTCTGCTTAAGAGGAATGGAAAGATTATAAAAGTAGGGGAGCAAACATGATCAAACATGTAAA chm1:+:1691614685:-1 chm1:+:2132270050:-1 +CTCTAAATCTCGGGAGACATGGAGAACCATCAGCTTGTCTGTTATGCCTGAAGCCTAGGAGACAACAGAGAAGGAAAGTGGAAACTAGAACTTAAGGTGAAAGGCTGCCAGGAGGTTGATCAGGAGGGAAACTATAAGTCTGCTTAAGAGGAATGGAAAGATTATAAAAGTAGGGGAGCAAACATGATCAAACATGTAAA chm1:+:261940537:-1 chm1:+:433028239:-1 chm1:+:561307952:-1 chm1:+:593943800:-1 chm1:+:611907509:-1 chm1:+:836859496:-1 chm1:+:1063086432:-1 chm1:+:1112610763:-1 chm1:+:1135112026:-1 chm1:+:1162463548:-1 chm1:+:1201520192:-1 chm1:+:1486195542:-1 chm1:+:1783533417:-1 chm1:+:1921758630:-1 chm1:+:1974264058:-1 chm1:+:2001704647:-1 chm1:+:2139868638:-1 chm1:+:2156452092:-1 chm1:+:2395352845:-1 chm1:+:2566044800:-1 chm1:+:2583923527:-1 chm1:+:2613435020:-1 chm1:+:2648328545:-1 chm1:+:2751033474:-1 chm1:+:2763331561:-1 chm1:+:2777086363:-1 chm1:+:2935866305:-1 chm1:+:2943819898:-1 chm1:+:2962561774:-1 chm1:+:2969499119:-1 chm1:+:3013081988:-1 chm1:+:3042712025:-1 chm1:+:3053263197:-1 +CTCTAAATCTCGGGAGACATGGAGAACCATCAGCTTGTCTGTTATGCCTGAAGCCTAGGAGACAACAGAGAAGGAAAGTGGAAACTAGAACTTAAGGTGAAAGGCTGCCAGGAGGTTGATCAGGAGGGAAACTATAAGTCTGCTTAAGAGGAATGGAAAGATTATAAAAGTAGGGGAGCAAACATGATCAAACATGTAAA chm1:+:279137551:-1 chm1:+:306338696:-1 chm1:+:439219394:-1 chm1:+:442185634:-1 chm1:+:751824635:-1 chm1:+:994139788:-1 chm1:+:1712853195:-1 chm1:+:1800507572:-1 chm1:+:2432605031:-1 chm1:+:2468963241:-1 chm1:+:2558085057:-1 chm1:+:2583526385:-1 +TTTACATGTTTGATCATGTTTGCTCCCCTACTTTTATAATCTTTCCATTCCTCTTAAGCAGACTTATAGTTTCCCTCCTGATCAACCTCCTGGCAGCCTTTCACCTTAAGTTCTAGTTTCCACTTTCCTTCTCTGTTGTCTCCTAGGCTTCAGGCATAACAGACAAGCTGATGGTTCTCCATGTCTCCCGAGATTTAGAG chm1:+:1311612229:6 chm1:+:1517863433:-1 +TTTACATGTTTGATCATGTTTGCTCCCCTACTTTTATAATCTTTCCATTCCTCTTAAGCAGACTTATAGTTTCCCTCCTGATCAACCTCCTGGCAGCCTTTCACCTTAAGTTCTAGTTTCCACTTTCCTTCTCTGTTGTCTCCTAGGCTTCAGGCATAACAGACAAGCTGATGGTTCTCCATGTCTCCCGAGATTTAGAG chm1:+:1311612228:6 +AGGGCCTAGCATCCCGAGGCTCGTTTGTGTTTAACCGTCCGCCTAAATGGCTTCGTCTGGCTCCGGGCGGCGCGGGGGGTAACCTGCGAGGCGAAGCGTAGGCCTAGGCCACCCTGTCCCGCCGGGGGGCCCACTCCATTGCGCCGCGCGGGGTGCGCGTAGACCTGACCTCCCCTCGGGCATAAAAAGCGCCCTGCGGG chm1:+:2478493657:9 +AGGGCCTAGCATCCCGAGGCTCGTTTGTGTTTAACCGTCCGCCTAAATGGCTTCGTCTGGCTCCGGGCGGCGCGGGGGGTAACCTGCGAGGCGAAGCGTAGGCCTAGGCCACCCTGTCCCGCCGGGGGGCCCACTCCATTGCGCCGCGCGGGGTGCGCGTAGACCTGACCTCCCCTCGGGCATAAAAAGCGCCCTGCGGG chm1:+:2699090518:-1 +AGGGCCTAGCATCCCGAGGCTCGTTTGTGTTTAACCGTCCGCCTAAATGGCTTCGTCTGGCTCCGGGCGGCGCGGGGGGTAACCTGCGAGGCGAAGCGTAGGCCTAGGCCACCCTGTCCCGCCGGGGGGCCCACTCCATTGCGCCGCGCGGGGTGCGCGTAGACCTGACCTCCCCTCGGGCATAAAAAGCGCCCTGCGGG chm1:+:2478493658:9 +TGACAGTGAGCCAGGAGCAGCGTCAGCATCCTAGTACAGCGGGTTCATCAAACACCAGAAGATGTGACAGAGACAGGCTTGACCTTCTATGGGAACTCGGTTCCTGATGTCCGTTGTAATATTGGTAATAAAGTTAAACAAAAATAATAGATGAAATGAAGTCAGAAAGACATGTTAAAATAGTTACTGTGAAGCACAAG chm1:+:72789195:-1 chm1:+:183433887:-1 chm1:+:251215531:-1 chm1:+:320073469:-1 chm1:+:397937395:-1 chm1:+:553526261:-1 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chm1:+:671663519:-1 chm1:+:704425527:-1 chm1:+:841331493:-1 chm1:+:865226527:-1 chm1:+:1029947396:-1 chm1:+:1113772358:-1 chm1:+:1121294305:-1 chm1:+:1124750723:-1 chm1:+:1124760262:-1 chm1:+:1291623370:-1 chm1:+:1295815674:-1 chm1:+:1295831080:-1 chm1:+:1376303238:-1 chm1:+:1397802846:-1 chm1:+:1439878208:-1 chm1:+:1440017325:-1 chm1:+:1440070112:-1 chm1:+:1440156278:-1 chm1:+:1561891469:-1 chm1:+:1644398329:-1 chm1:+:1722870978:-1 chm1:+:1722881955:-1 chm1:+:1833334398:-1 chm1:+:1865980460:-1 chm1:+:1866412495:-1 chm1:+:1866579111:-1 chm1:+:1867197105:-1 chm1:+:1867277329:-1 chm1:+:1870708433:-1 chm1:+:1870715239:38 chm1:+:1870745894:-1 chm1:+:1893971352:-1 chm1:+:1956282578:-1 chm1:+:1985475209:-1 chm1:+:1985604232:-1 chm1:+:2366954679:-1 chm1:+:2444823129:-1 chm1:+:2444829867:-1 chm1:+:2492329685:-1 chm1:+:2521156909:-1 chm1:+:2585999418:-1 chm1:+:2627111508:-1 chm1:+:2683882106:-1 chm1:+:2712923869:-1 chm1:+:2744519799:-1 chm1:+:2874129983:-1 chm1:+:2904399290:-1 chm1:+:2939594038:-1 chm1:+:2942979437:-1 chm1:+:2942984609:-1 chm1:+:2943044906:-1 chm1:+:2985765298:-1 chm1:+:3030973299:-1 chm1:+:3056068121:-1 chm1:+:3056069275:-1 chm1:+:3056093273:-1 chm1:+:3056555983:-1 +CCAAACTGCTGAATGAAAAAGATGCTTTAACTCTCGTGAGATGATGCACACAACACAAGTGGTTTTACCAGATAGCTTTCTTCTTTGTTTTTATCCTGGGATATTTTGCTTTTTTTGCCCTTTGACCTCAATGAGCTCAAAAATGTTCATTCAAGAAATGGACAAAAACAATGTTTCTAAACTGGCTGAATCAAAAGGAA chm1:+:91831636:-1 chm1:+:229401336:-1 chm1:+:486689388:-1 chm1:+:587936851:-1 chm1:+:709728183:-1 chm1:+:825594066:-1 chm1:+:845511066:-1 chm1:+:888813395:-1 chm1:+:1016461890:-1 chm1:+:1139179307:-1 chm1:+:1243583638:-1 chm1:+:1266460064:-1 chm1:+:1295527020:-1 chm1:+:1460050654:-1 chm1:+:1481127552:-1 chm1:+:1682358697:-1 chm1:+:1718113198:-1 chm1:+:1768141633:-1 chm1:+:1865587800:-1 chm1:+:1866382212:-1 chm1:+:1866436297:-1 chm1:+:1867144007:-1 chm1:+:1867195549:-1 chm1:+:1906160955:-1 chm1:+:1985580032:-1 chm1:+:1985598672:15 chm1:+:1985641083:39 chm1:+:1985655549:-1 chm1:+:2037478308:-1 chm1:+:2295418925:-1 chm1:+:2337955905:-1 chm1:+:2339997236:-1 chm1:+:2355125433:-1 chm1:+:2376695042:-1 chm1:+:2442336170:-1 chm1:+:2442350245:-1 chm1:+:2458282686:-1 chm1:+:2603836979:-1 chm1:+:2609854137:-1 chm1:+:2642574484:-1 chm1:+:2649547192:-1 chm1:+:2655789739:-1 chm1:+:2658656477:-1 chm1:+:2717922175:-1 chm1:+:2778745960:-1 chm1:+:2817551938:-1 chm1:+:2818590978:-1 chm1:+:2902953807:-1 chm1:+:2906491339:-1 chm1:+:2954986694:-1 chm1:+:3001505761:-1 chm1:+:3024764476:-1 chm1:+:3026994269:-1 +TTCCTTTTGATTCAGCCAGTTTAGAAACATTGTTTTTGTCCATTTCTTGAATGAACATTTTTGAGCTCATTGAGGTCAAAGGGCAAAAAAAGCAAAATATCCCAGGATAAAAACAAAGAAGAAAGCTATCTGGTAAAACCACTTGTGTTGTGTGCATCATCTCACGAGAGTTAAAGCATCTTTTTCATTCAGCAGTTTGG chm1:+:1295802150:-1 chm1:+:1295876530:-1 chm1:+:1295907792:-1 chm1:+:1296003443:-1 chm1:+:1296071510:-1 chm1:+:1866240606:-1 chm1:+:1867230004:39 chm1:+:1870771246:-1 chm1:+:1989327345:-1 +TTCCTTTTGATTCAGCCAGTTTAGAAACATTGTTTTTGTCCATTTCTTGAATGAACATTTTTGAGCTCATTGAGGTCAAAGGGCAAAAAAAGCAAAATATCCCAGGATAAAAACAAAGAAGAAAGCTATCTGGTAAAACCACTTGTGTTGTGTGCATCATCTCACGAGAGTTAAAGCATCTTTTTCATTCAGCAGTTTGG chm1:+:1295530078:-1 chm1:+:1866496086:-1 chm1:+:2939226078:-1 +TTCCTTTTGATTCAGCCAGTTTAGAAACATTGTTTTTGTCCATTTCTTGAATGAACATTTTTGAGCTCATTGAGGTCAAAGGGCAAAAAAAGCAAAATATCCCAGGATAAAAACAAAGAAGAAAGCTATCTGGTAAAACCACTTGTGTTGTGTGCATCATCTCACGAGAGTTAAAGCATCTTTTTCATTCAGCAGTTTGG chm1:+:927535377:38 chm1:+:927578585:-1 chm1:+:927810858:-1 chm1:+:927845291:-1 chm1:+:927848316:-1 chm1:+:927856694:-1 chm1:+:1121305595:-1 chm1:+:1295810786:-1 chm1:+:1295838132:-1 chm1:+:1295862005:-1 chm1:+:1295964632:-1 chm1:+:1295965489:-1 chm1:+:1296044300:-1 chm1:+:1296077518:-1 chm1:+:1296105021:-1 chm1:+:1866294133:-1 chm1:+:1866333201:-1 chm1:+:1866390276:-1 chm1:+:1866396970:40 chm1:+:1866473620:-1 chm1:+:1867082529:-1 chm1:+:1867235271:35 chm1:+:1870646542:-1 chm1:+:1870778499:-1 chm1:+:2442326405:-1 chm1:+:2442413148:38 chm1:+:2939405108:37 +TTCCTTTTGATTCAGCCAGTTTAGAAACATTGTTTTTGTCCATTTCTTGAATGAACATTTTTGAGCTCATTGAGGTCAAAGGGCAAAAAAAGCAAAATATCCCAGGATAAAAACAAAGAAGAAAGCTATCTGGTAAAACCACTTGTGTTGTGTGCATCATCTCACGAGAGTTAAAGCATCTTTTTCATTCAGCAGTTTGG chm1:+:512487961:-1 chm1:+:515502780:-1 chm1:+:645072929:-1 chm1:+:757860432:-1 chm1:+:770462019:-1 chm1:+:783350340:-1 chm1:+:828405943:-1 chm1:+:1073923207:-1 chm1:+:1112370807:-1 chm1:+:1143121766:-1 chm1:+:1164818639:-1 chm1:+:1228784159:-1 chm1:+:1235917315:-1 chm1:+:1248811555:-1 chm1:+:1340630644:-1 chm1:+:1460836858:-1 chm1:+:1463144577:-1 chm1:+:1793494767:-1 chm1:+:2058518721:-1 chm1:+:2221902338:-1 chm1:+:2391229828:-1 chm1:+:2537209810:-1 chm1:+:2758039886:-1 chm1:+:2862781387:-1 chm1:+:3096157961:-1 +TTCCTTTTGATTCAGCCAGTTTAGAAACATTGTTTTTGTCCATTTCTTGAATGAACATTTTTGAGCTCATTGAGGTCAAAGGGCAAAAAAAGCAAAATATCCCAGGATAAAAACAAAGAAGAAAGCTATCTGGTAAAACCACTTGTGTTGTGTGCATCATCTCACGAGAGTTAAAGCATCTTTTTCATTCAGCAGTTTGG chm1:+:79392527:-1 chm1:+:927817378:-1 chm1:+:1436410369:-1 chm1:+:1611077425:-1 chm1:+:1960691731:-1 chm1:+:1989312752:-1 chm1:+:2442311606:-1 chm1:+:2442370478:-1 +TTTTTGTGGTTACAATGTTAAGTCAAACTAAATAAGCAAATCTTCATGCCAGGGTCTTAGTTAATGTCATTTGGCTTGGCTGAGAAAAATCTGAAACTTCTCTGAGCAGACATATTTTAAGAGAAGCATTAGGACATGCATATTTTAGGATGCTAATAGAGCCTCTCACCCTTTTTGGTTTTTAGCTGCCAGAAAGTTAT chm1:+:394761677:10 +TTTTTGTGGTTACAATGTTAAGTCAAACTAAATAAGCAAATCTTCATGCCAGGGTCTTAGTTAATGTCATTTGGCTTGGCTGAGAAAAATCTGAAACTTCTCTGAGCAGACATATTTTAAGAGAAGCATTAGGACATGCATATTTTAGGATGCTAATAGAGCCTCTCACCCTTTTTGGTTTTTAGCTGCCAGAAAGTTAT chm1:+:394761678:10 +TTTTTGTGGTTACAATGTTAAGTCAAACTAAATAAGCAAATCTTCATGCCAGGGTCTTAGTTAATGTCATTTGGCTTGGCTGAGAAAAATCTGAAACTTCTCTGAGCAGACATATTTTAAGAGAAGCATTAGGACATGCATATTTTAGGATGCTAATAGAGCCTCTCACCCTTTTTGGTTTTTAGCTGCCAGAAAGTTAT chm1:+:394761679:10 +ATAACTTTCTGGCAGCTAAAAACCAAAAAGGGTGAGAGGCTCTATTAGCATCCTAAAATATGCATGTCCTAATGCTTCTCTTAAAATATGTCTGCTCAGAGAAGTTTCAGATTTTTCTCAGCCAAGCCAAATGACATTAACTAAGACCCTGGCATGAAGATTTGCTTATTTAGTTTGACTTAACATTGTAACCACAAAAA chm1:+:594197479:-1 +ATAACTTTCTGGCAGCTAAAAACCAAAAAGGGTGAGAGGCTCTATTAGCATCCTAAAATATGCATGTCCTAATGCTTCTCTTAAAATATGTCTGCTCAGAGAAGTTTCAGATTTTTCTCAGCCAAGCCAAATGACATTAACTAAGACCCTGGCATGAAGATTTGCTTATTTAGTTTGACTTAACATTGTAACCACAAAAA chm1:+:765261209:-1 +AAAACTGTAGGTTTTTTTCTCAAGATTTAAGAATGTTCTAGCTCCTCCCACAATGAAAAACTTAGCTTAGATCCACTCCTGTCAAGAAGCTGCAGAGTTCCTTCCTTCCATCCCTCCCTCGCTGGGTTAGGTGAGCCTCTGAGGTGCTCTCATGGATTGCTGTGCATATCGCTTTGCTGCTCTTAATGCATCCCTGGAGT chm1:+:345090867:10 chm1:+:2228552973:-1 chm1:+:2611723882:-1 +TGAATGTTGGCCTGGTCTTTTCTCTGTTGGGGAAGTTACTCCTGGATGAGTATACTTAAGTATGTTTTGCAACCTTGGTTCCATTCTCCCCATCTCTTTCAGGTACCCTAAGTGAGTCTTAGGTTCTGTCTTTTTAAATAATTTCATATTTTTTGGAGGTTTTGTCAATGCCTTTCATCTTTTTTTTTTTTCTTTCTGTT chm1:+:253210383:-1 chm1:+:1497457348:10 chm1:+:1810136504:-1 chm1:+:2398179415:-1 chm1:+:2495973892:-1 chm1:+:2696127012:-1 chm1:+:2969367713:-1 +TGAATGTTGGCCTGGTCTTTTCTCTGTTGGGGAAGTTACTCCTGGATGAGTATACTTAAGTATGTTTTGCAACCTTGGTTCCATTCTCCCCATCTCTTTCAGGTACCCTAAGTGAGTCTTAGGTTCTGTCTTTTTAAATAATTTCATATTTTTTGGAGGTTTTGTCAATGCCTTTCATCTTTTTTTTTTTTCTTTCTGTT chm1:+:1497457346:10 +TGAATGTTGGCCTGGTCTTTTCTCTGTTGGGGAAGTTACTCCTGGATGAGTATACTTAAGTATGTTTTGCAACCTTGGTTCCATTCTCCCCATCTCTTTCAGGTACCCTAAGTGAGTCTTAGGTTCTGTCTTTTTAAATAATTTCATATTTTTTGGAGGTTTTGTCAATGCCTTTCATCTTTTTTTTTTTTCTTTCTGTT chm1:+:1780811486:-1 chm1:+:1924380353:-1 chm1:+:2166004178:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCT chm1:+:277478709:-1 chm1:+:793251287:-1 chm1:+:839873655:-1 chm1:+:1058113291:-1 chm1:+:1570032595:-1 chm1:+:1780323372:-1 chm1:+:2051001780:-1 chm1:+:2136610068:-1 chm1:+:2306317777:-1 chm1:+:2419007062:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCT chm1:+:60997487:-1 chm1:+:1907804770:-1 chm1:+:2037483288:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCT chm1:+:2461732158:-1 chm1:+:2632993883:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCT chm1:+:65288954:-1 chm1:+:290308799:-1 chm1:+:424584927:-1 chm1:+:475269653:-1 chm1:+:495943000:-1 chm1:+:630928211:-1 chm1:+:651575956:-1 chm1:+:754560203:-1 chm1:+:792775098:-1 chm1:+:812448927:-1 chm1:+:819423722:-1 chm1:+:868140784:-1 chm1:+:1109252998:-1 chm1:+:1185248738:-1 chm1:+:1257391300:-1 chm1:+:1280327042:-1 chm1:+:1324980251:-1 chm1:+:1332602463:-1 chm1:+:1442090865:-1 chm1:+:1448834192:-1 chm1:+:1510503568:-1 chm1:+:1575716944:-1 chm1:+:1614379186:-1 chm1:+:1652838348:-1 chm1:+:1744918008:-1 chm1:+:1781517868:-1 chm1:+:1857609126:-1 chm1:+:1862461405:-1 chm1:+:1862839661:-1 chm1:+:1895541996:-1 chm1:+:1958288885:-1 chm1:+:1995272914:-1 chm1:+:2012695767:-1 chm1:+:2105281129:-1 chm1:+:2142787594:-1 chm1:+:2166493897:-1 chm1:+:2172139645:-1 chm1:+:2260818809:-1 chm1:+:2268933565:-1 chm1:+:2283399483:-1 chm1:+:2667319788:-1 chm1:+:2822171581:-1 chm1:+:2954270296:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCT chm1:+:99528405:-1 chm1:+:163950088:-1 chm1:+:187688928:-1 chm1:+:329051413:-1 chm1:+:429608274:-1 chm1:+:556198758:-1 chm1:+:793205870:-1 chm1:+:932218597:-1 chm1:+:947957328:-1 chm1:+:1126597176:-1 chm1:+:1129926954:-1 chm1:+:1146385736:-1 chm1:+:1153074885:-1 chm1:+:1198063783:-1 chm1:+:1348901453:-1 chm1:+:1469199235:-1 chm1:+:1518803262:-1 chm1:+:1702964336:-1 chm1:+:2192853878:-1 chm1:+:2472930484:-1 +AGAATTATAGGGTCCTGATTAAGATGTACAAATTCTGCCCACAGACATAGAAAAGTCCAAAAAATACTTTTAACTAATTTATTTCTGTAACTCCCAGTCTCTTTATTACTATTTGCATATATCGTTATCGAATTACACCTTTAGTCCAACAAGAAGATACTATTATTTTAGATGGTAAAACATTCACTTATAATTAGTGT chm1:+:1962075844:8 chm1:+:2006731893:-1 chm1:+:2590690469:-1 chm1:+:3001720357:-1 +AGAATTATAGGGTCCTGATTAAGATGTACAAATTCTGCCCACAGACATAGAAAAGTCCAAAAAATACTTTTAACTAATTTATTTCTGTAACTCCCAGTCTCTTTATTACTATTTGCATATATCGTTATCGAATTACACCTTTAGTCCAACAAGAAGATACTATTATTTTAGATGGTAAAACATTCACTTATAATTAGTGT chm1:+:1962075846:8 +AGAATTATAGGGTCCTGATTAAGATGTACAAATTCTGCCCACAGACATAGAAAAGTCCAAAAAATACTTTTAACTAATTTATTTCTGTAACTCCCAGTCTCTTTATTACTATTTGCATATATCGTTATCGAATTACACCTTTAGTCCAACAAGAAGATACTATTATTTTAGATGGTAAAACATTCACTTATAATTAGTGT chm1:+:1962075847:8 +ATTAGTAATTTATTACCTATCATTCAAGCCTGCCCTGGACTGAAATGCAATCCCTGGCCCACTTTTTGTTCTTCTCAGGGTATTCCGGCCCAGTTCCTATGTATGCTCGACCAGACACGCCCACAAGGCTTCATTGGCCCTTTCAGTGCAGGGGCCTTGGCTGTGGCATCTACAAGGGCATTTCCTTTTACACTAGGTCA chm1:+:613776774:-1 chm1:+:940607289:-1 chm1:+:943179592:-1 chm1:+:1680469374:18 chm1:+:2581417681:15 chm1:+:2813158582:-1 chm1:+:3055935784:-1 +ATTAGTAATTTATTACCTATCATTCAAGCCTGCCCTGGACTGAAATGCAATCCCTGGCCCACTTTTTGTTCTTCTCAGGGTATTCCGGCCCAGTTCCTATGTATGCTCGACCAGACACGCCCACAAGGCTTCATTGGCCCTTTCAGTGCAGGGGCCTTGGCTGTGGCATCTACAAGGGCATTTCCTTTTACACTAGGTCA chm1:+:6012300:-1 chm1:+:314335399:-1 chm1:+:482445519:-1 chm1:+:670004853:-1 chm1:+:1985235344:28 chm1:+:2573694288:-1 chm1:+:2848122432:-1 chm1:+:2853507190:-1 +TGACCTAGTGTAAAAGGAAATGCCCTTGTAGATGCCACAGCCAAGGCCCCTGCACTGAAAGGGCCAATGAAGCCTTGTGGGCGTGTCTGGTCGAGCATACATAGGAACTGGGCCGGAATACCCTGAGAAGAACAAAAAGTGGGCCAGGGATTGCATTTCAGTCCAGGGCAGGCTTGAATGATAGGTAATAAATTACTAAT chm1:+:2956869244:-1 +TGACCTAGTGTAAAAGGAAATGCCCTTGTAGATGCCACAGCCAAGGCCCCTGCACTGAAAGGGCCAATGAAGCCTTGTGGGCGTGTCTGGTCGAGCATACATAGGAACTGGGCCGGAATACCCTGAGAAGAACAAAAAGTGGGCCAGGGATTGCATTTCAGTCCAGGGCAGGCTTGAATGATAGGTAATAAATTACTAAT chm1:+:1680227873:18 chm1:+:2499976216:19 +TGACCTAGTGTAAAAGGAAATGCCCTTGTAGATGCCACAGCCAAGGCCCCTGCACTGAAAGGGCCAATGAAGCCTTGTGGGCGTGTCTGGTCGAGCATACATAGGAACTGGGCCGGAATACCCTGAGAAGAACAAAAAGTGGGCCAGGGATTGCATTTCAGTCCAGGGCAGGCTTGAATGATAGGTAATAAATTACTAAT chm1:+:355502410:-1 chm1:+:1092364511:-1 chm1:+:1680227869:18 chm1:+:1948082710:-1 chm1:+:2499976212:19 chm1:+:3096317810:30 chm1:+:3096369583:23 +TGACCTAGTGTAAAAGGAAATGCCCTTGTAGATGCCACAGCCAAGGCCCCTGCACTGAAAGGGCCAATGAAGCCTTGTGGGCGTGTCTGGTCGAGCATACATAGGAACTGGGCCGGAATACCCTGAGAAGAACAAAAAGTGGGCCAGGGATTGCATTTCAGTCCAGGGCAGGCTTGAATGATAGGTAATAAATTACTAAT chm1:+:3096317814:30 chm1:+:3096369587:23 +TGACCTAGTGTAAAAGGAAATGCCCTTGTAGATGCCACAGCCAAGGCCCCTGCACTGAAAGGGCCAATGAAGCCTTGTGGGCGTGTCTGGTCGAGCATACATAGGAACTGGGCCGGAATACCCTGAGAAGAACAAAAAGTGGGCCAGGGATTGCATTTCAGTCCAGGGCAGGCTTGAATGATAGGTAATAAATTACTAAT chm1:+:54777493:-1 chm1:+:387393200:-1 chm1:+:1235007441:-1 chm1:+:1989508537:30 chm1:+:3046270539:32 +TCGGAAGCTAAATCTCACTCGCGGGGAGGATGGGACGCGTGGGGACTGAAGGCGGCATCTGCCTGAATTAAAGCCCCTCGCGCGCTCTGAGCCTCCCACTCTGTCCTGGAGGCCTGACCTCGCGAGTAGAGCCTGGCGCTTTTCCTCCCCGGGAGCACGACGGATAGAATGCGCGGGTCGAGACGGTGTCGGTAGCGGGG chm1:+:864902791:4 +TCGGAAGCTAAATCTCACTCGCGGGGAGGATGGGACGCGTGGGGACTGAAGGCGGCATCTGCCTGAATTAAAGCCCCTCGCGCGCTCTGAGCCTCCCACTCTGTCCTGGAGGCCTGACCTCGCGAGTAGAGCCTGGCGCTTTTCCTCCCCGGGAGCACGACGGATAGAATGCGCGGGTCGAGACGGTGTCGGTAGCGGGG chm1:+:864902790:4 +TAACGTCAAAATTAAAAAGAACTAGAAAAGCAAGAGGAAACACATTCAAAAAGCTAGCAGAAGGCAAGAAATACCTAAAATCAGAGCAGGAACTGAAGGAAATAGAGACACAAAAACCCTTCAAAAAATTAATGAATCCAGGTTAGCTGGTTTTTTGAAAAGAGTCAACAAAATCGATAGACCGCTAGGCAACGACTAAT chm1:+:2037372778:29 +TAACGTCAAAATTAAAAAGAACTAGAAAAGCAAGAGGAAACACATTCAAAAAGCTAGCAGAAGGCAAGAAATACCTAAAATCAGAGCAGGAACTGAAGGAAATAGAGACACAAAAACCCTTCAAAAAATTAATGAATCCAGGTTAGCTGGTTTTTTGAAAAGAGTCAACAAAATCGATAGACCGCTAGGCAACGACTAAT chm1:+:2362644780:36 chm1:+:2762856403:22 +TAACGTCAAAATTAAAAAGAACTAGAAAAGCAAGAGGAAACACATTCAAAAAGCTAGCAGAAGGCAAGAAATACCTAAAATCAGAGCAGGAACTGAAGGAAATAGAGACACAAAAACCCTTCAAAAAATTAATGAATCCAGGTTAGCTGGTTTTTTGAAAAGAGTCAACAAAATCGATAGACCGCTAGGCAACGACTAAT chm1:+:978183595:-1 chm1:+:1440652771:-1 chm1:+:3055871591:38 +TAACGTCAAAATTAAAAAGAACTAGAAAAGCAAGAGGAAACACATTCAAAAAGCTAGCAGAAGGCAAGAAATACCTAAAATCAGAGCAGGAACTGAAGGAAATAGAGACACAAAAACCCTTCAAAAAATTAATGAATCCAGGTTAGCTGGTTTTTTGAAAAGAGTCAACAAAATCGATAGACCGCTAGGCAACGACTAAT chm1:+:58031973:23 chm1:+:105363394:20 chm1:+:118894392:24 chm1:+:159295620:18 chm1:+:180728276:18 chm1:+:185558544:23 chm1:+:187109862:22 chm1:+:189179538:18 chm1:+:258432092:16 chm1:+:298779256:23 chm1:+:298792210:20 chm1:+:347742828:29 chm1:+:458902636:16 chm1:+:520908363:-1 chm1:+:581058330:23 chm1:+:708206259:16 chm1:+:736128638:20 chm1:+:812044583:18 chm1:+:849827219:16 chm1:+:858664039:19 chm1:+:904447070:-1 chm1:+:925347645:22 chm1:+:926384733:17 chm1:+:939141442:20 chm1:+:1138158455:18 chm1:+:1142226078:16 chm1:+:1148190698:24 chm1:+:1295721694:18 chm1:+:1449187675:17 chm1:+:1462834575:21 chm1:+:1481458975:25 chm1:+:1554197159:16 chm1:+:1571261209:27 chm1:+:1622385422:19 chm1:+:1647488168:23 chm1:+:1718357913:33 chm1:+:1766032965:19 chm1:+:1826895706:30 chm1:+:1877965063:19 chm1:+:1905388135:17 chm1:+:1907716600:17 chm1:+:1925352545:19 chm1:+:1992469779:12 chm1:+:2022174246:17 chm1:+:2039711777:23 chm1:+:2165183117:20 chm1:+:2167452538:23 chm1:+:2239425571:17 chm1:+:2327442193:24 chm1:+:2630636968:15 chm1:+:2729373292:-1 chm1:+:2736889897:9 chm1:+:2748215631:19 chm1:+:2892573667:17 chm1:+:2901808844:17 chm1:+:2956181148:23 chm1:+:2976888932:21 chm1:+:2979525911:21 chm1:+:3006629417:15 chm1:+:3035687939:17 chm1:+:3050359422:20 +ATTAGTCGTTGCCTAGCGGTCTATCGATTTTGTTGACTCTTTTCAAAAAACCAGCTAACCTGGATTCATTAATTTTTTGAAGGGTTTTTGTGTCTCTATTTCCTTCAGTTCCTGCTCTGATTTTAGGTATTTCTTGCCTTCTGCTAGCTTTTTGAATGTGTTTCCTCTTGCTTTTCTAGTTCTTTTTAATTTTGACGTTA chm1:+:934585206:-1 +ATTAGTCGTTGCCTAGCGGTCTATCGATTTTGTTGACTCTTTTCAAAAAACCAGCTAACCTGGATTCATTAATTTTTTGAAGGGTTTTTGTGTCTCTATTTCCTTCAGTTCCTGCTCTGATTTTAGGTATTTCTTGCCTTCTGCTAGCTTTTTGAATGTGTTTCCTCTTGCTTTTCTAGTTCTTTTTAATTTTGACGTTA chm1:+:152406545:19 chm1:+:194283311:17 chm1:+:545852173:16 chm1:+:546408624:16 chm1:+:651562957:17 chm1:+:704684000:20 chm1:+:784985486:18 chm1:+:838843688:16 chm1:+:982021019:17 chm1:+:1288033604:17 chm1:+:1288226308:16 chm1:+:1864857150:18 chm1:+:2735671590:16 chm1:+:3007967284:-1 +ATTAGTCGTTGCCTAGCGGTCTATCGATTTTGTTGACTCTTTTCAAAAAACCAGCTAACCTGGATTCATTAATTTTTTGAAGGGTTTTTGTGTCTCTATTTCCTTCAGTTCCTGCTCTGATTTTAGGTATTTCTTGCCTTCTGCTAGCTTTTTGAATGTGTTTCCTCTTGCTTTTCTAGTTCTTTTTAATTTTGACGTTA chm1:+:63971038:19 chm1:+:185859298:19 chm1:+:406881362:18 chm1:+:407072323:17 chm1:+:1003596042:23 chm1:+:1369438832:15 chm1:+:1369758816:16 chm1:+:1454149735:26 chm1:+:1864485874:24 chm1:+:2012102970:23 chm1:+:2055880755:27 chm1:+:2056824890:19 chm1:+:2164919171:37 chm1:+:2938209334:22 chm1:+:3063563261:31 +ATTAGTCGTTGCCTAGCGGTCTATCGATTTTGTTGACTCTTTTCAAAAAACCAGCTAACCTGGATTCATTAATTTTTTGAAGGGTTTTTGTGTCTCTATTTCCTTCAGTTCCTGCTCTGATTTTAGGTATTTCTTGCCTTCTGCTAGCTTTTTGAATGTGTTTCCTCTTGCTTTTCTAGTTCTTTTTAATTTTGACGTTA chm1:+:55962601:16 chm1:+:68471621:21 chm1:+:157312940:17 chm1:+:702054285:17 chm1:+:804820954:22 chm1:+:933022194:26 chm1:+:1017906690:20 chm1:+:1025832467:18 chm1:+:1063024317:20 chm1:+:1148080966:17 chm1:+:1246968200:18 chm1:+:1717557887:19 chm1:+:1777028672:17 chm1:+:1990874696:20 chm1:+:2012531927:16 chm1:+:2165160350:20 chm1:+:2643488347:19 chm1:+:2656614034:24 chm1:+:2958757868:16 chm1:+:2966042869:19 +ATTAGTCGTTGCCTAGCGGTCTATCGATTTTGTTGACTCTTTTCAAAAAACCAGCTAACCTGGATTCATTAATTTTTTGAAGGGTTTTTGTGTCTCTATTTCCTTCAGTTCCTGCTCTGATTTTAGGTATTTCTTGCCTTCTGCTAGCTTTTTGAATGTGTTTCCTCTTGCTTTTCTAGTTCTTTTTAATTTTGACGTTA chm1:+:433047735:-1 chm1:+:948769485:-1 chm1:+:1167700091:-1 +ATTATAAAATGTGTTTTAAAAAAAGCTCAATAATTAACATACTAATGTGTTTTTTCAATTATTTATAAACGTGTGAATGCCTCCACTTACTAAAGAACATTGTAATTCTAACAAGTTTTATTGTGTTTTTAAGAAAGAGAATCAGGGGGGTCTTCAGGAACACTATTTTCGGAATCCGTCTAGGACTTTTGATGACAGAA chm1:+:213170809:13 chm1:+:2005199090:-1 +ATTATAAAATGTGTTTTAAAAAAAGCTCAATAATTAACATACTAATGTGTTTTTTCAATTATTTATAAACGTGTGAATGCCTCCACTTACTAAAGAACATTGTAATTCTAACAAGTTTTATTGTGTTTTTAAGAAAGAGAATCAGGGGGGTCTTCAGGAACACTATTTTCGGAATCCGTCTAGGACTTTTGATGACAGAA chm1:+:213170813:13 +ATTATAAAATGTGTTTTAAAAAAAGCTCAATAATTAACATACTAATGTGTTTTTTCAATTATTTATAAACGTGTGAATGCCTCCACTTACTAAAGAACATTGTAATTCTAACAAGTTTTATTGTGTTTTTAAGAAAGAGAATCAGGGGGGTCTTCAGGAACACTATTTTCGGAATCCGTCTAGGACTTTTGATGACAGAA chm1:+:425924971:-1 +ATTATAAAATGTGTTTTAAAAAAAGCTCAATAATTAACATACTAATGTGTTTTTTCAATTATTTATAAACGTGTGAATGCCTCCACTTACTAAAGAACATTGTAATTCTAACAAGTTTTATTGTGTTTTTAAGAAAGAGAATCAGGGGGGTCTTCAGGAACACTATTTTCGGAATCCGTCTAGGACTTTTGATGACAGAA chm1:+:213170811:13 +TTCTGTCATCAAAAGTCCTAGACGGATTCCGAAAATAGTGTTCCTGAAGACCCCCCTGATTCTCTTTCTTAAAAACACAATAAAACTTGTTAGAATTACAATGTTCTTTAGTAAGTGGAGGCATTCACACGTTTATAAATAATTGAAAAAACACATTAGTATGTTAATTATTGAGCTTTTTTTAAAACACATTTTATAAT chm1:+:499707873:-1 chm1:+:560868018:-1 chm1:+:1505161466:-1 chm1:+:2292362215:-1 chm1:+:2599948647:-1 chm1:+:2605051629:-1 chm1:+:2643805100:-1 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCA chm1:+:203045737:10 chm1:+:799952721:-1 chm1:+:2365713781:-1 chm1:+:2702359529:-1 chm1:+:2809864912:-1 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCA chm1:+:203045733:10 chm1:+:1919770677:-1 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCA chm1:+:203045735:10 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCA chm1:+:2296751826:-1 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCA chm1:+:203045731:10 +TCTGTGGGACAGCCAAGGAACTCTGAGTCGAGGCTTGTTTTCTCAGTGGGGAGGCCTTGTAGCCTGGGGCAAGTTCTCAGCCTCCTCACTGGTTGCCCTGGAAATCAGCGTCTGTGTTGTTGGTGGGGTGGGGGCAGGGGCACAGTGGGAGTGGGACCAGGCCTTTTGGGCTAGTGGGATGCATTGGGAAGCTGTGTGAG chm1:+:117327660:-1 chm1:+:181849268:-1 chm1:+:248714201:-1 chm1:+:315563083:-1 chm1:+:436887294:-1 chm1:+:733242201:-1 chm1:+:776726908:-1 chm1:+:781401107:-1 chm1:+:825520348:-1 chm1:+:846945757:-1 chm1:+:854258380:-1 chm1:+:926230371:-1 chm1:+:1026267070:-1 chm1:+:1276502341:-1 chm1:+:1427090679:-1 chm1:+:1632939342:-1 chm1:+:1723771661:-1 chm1:+:1852660256:-1 chm1:+:1941479733:-1 chm1:+:2239913945:-1 chm1:+:2384844883:11 chm1:+:2705996841:-1 chm1:+:2988272718:-1 +TCTGTGGGACAGCCAAGGAACTCTGAGTCGAGGCTTGTTTTCTCAGTGGGGAGGCCTTGTAGCCTGGGGCAAGTTCTCAGCCTCCTCACTGGTTGCCCTGGAAATCAGCGTCTGTGTTGTTGGTGGGGTGGGGGCAGGGGCACAGTGGGAGTGGGACCAGGCCTTTTGGGCTAGTGGGATGCATTGGGAAGCTGTGTGAG chm1:+:2384844884:11 +TCTGTGGGACAGCCAAGGAACTCTGAGTCGAGGCTTGTTTTCTCAGTGGGGAGGCCTTGTAGCCTGGGGCAAGTTCTCAGCCTCCTCACTGGTTGCCCTGGAAATCAGCGTCTGTGTTGTTGGTGGGGTGGGGGCAGGGGCACAGTGGGAGTGGGACCAGGCCTTTTGGGCTAGTGGGATGCATTGGGAAGCTGTGTGAG chm1:+:288673747:-1 chm1:+:1522085353:-1 chm1:+:2384844886:11 +CTCACACAGCTTCCCAATGCATCCCACTAGCCCAAAAGGCCTGGTCCCACTCCCACTGTGCCCCTGCCCCCACCCCACCAACAACACAGACGCTGATTTCCAGGGCAACCAGTGAGGAGGCTGAGAACTTGCCCCAGGCTACAAGGCCTCCCCACTGAGAAAACAAGCCTCGACTCAGAGTTCCTTGGCTGTCCCACAGA chm1:+:698752686:-1 chm1:+:1139200039:-1 chm1:+:1351164516:-1 chm1:+:2460680977:-1 +CTCACACAGCTTCCCAATGCATCCCACTAGCCCAAAAGGCCTGGTCCCACTCCCACTGTGCCCCTGCCCCCACCCCACCAACAACACAGACGCTGATTTCCAGGGCAACCAGTGAGGAGGCTGAGAACTTGCCCCAGGCTACAAGGCCTCCCCACTGAGAAAACAAGCCTCGACTCAGAGTTCCTTGGCTGTCCCACAGA chm1:+:492123042:-1 +CTCACACAGCTTCCCAATGCATCCCACTAGCCCAAAAGGCCTGGTCCCACTCCCACTGTGCCCCTGCCCCCACCCCACCAACAACACAGACGCTGATTTCCAGGGCAACCAGTGAGGAGGCTGAGAACTTGCCCCAGGCTACAAGGCCTCCCCACTGAGAAAACAAGCCTCGACTCAGAGTTCCTTGGCTGTCCCACAGA chm1:+:2897330453:-1 chm1:+:2979549372:-1 +CTCACACAGCTTCCCAATGCATCCCACTAGCCCAAAAGGCCTGGTCCCACTCCCACTGTGCCCCTGCCCCCACCCCACCAACAACACAGACGCTGATTTCCAGGGCAACCAGTGAGGAGGCTGAGAACTTGCCCCAGGCTACAAGGCCTCCCCACTGAGAAAACAAGCCTCGACTCAGAGTTCCTTGGCTGTCCCACAGA chm1:+:723083308:-1 chm1:+:1242068459:-1 +CTCACACAGCTTCCCAATGCATCCCACTAGCCCAAAAGGCCTGGTCCCACTCCCACTGTGCCCCTGCCCCCACCCCACCAACAACACAGACGCTGATTTCCAGGGCAACCAGTGAGGAGGCTGAGAACTTGCCCCAGGCTACAAGGCCTCCCCACTGAGAAAACAAGCCTCGACTCAGAGTTCCTTGGCTGTCCCACAGA chm1:+:1744636125:-1 +GAGGCCCGAGGAGGGGTGGATCACCTGAGGTTGGGAGTTGGAGGACCAGCCTGACCAACATGGATAAACCCCTTACTCTACTAAAATGCAAAAATTAGCCGGGGTTGGTGGTGCATGCCTGTAATCTCAGCTACTCGAAGGAGGCTGAGGCAGGAAGAATCGCCTGAACAGGGTGGCGGAGGTTGCGGTGAGCCGAGATC chm1:+:23278041:-1 chm1:+:275515109:34 chm1:+:371503573:38 chm1:+:705951065:28 chm1:+:869297269:35 chm1:+:1375470673:38 chm1:+:1678757202:32 chm1:+:2512736989:10 chm1:+:2600199307:30 chm1:+:2705750972:37 chm1:+:2710940806:39 +GAGGCCCGAGGAGGGGTGGATCACCTGAGGTTGGGAGTTGGAGGACCAGCCTGACCAACATGGATAAACCCCTTACTCTACTAAAATGCAAAAATTAGCCGGGGTTGGTGGTGCATGCCTGTAATCTCAGCTACTCGAAGGAGGCTGAGGCAGGAAGAATCGCCTGAACAGGGTGGCGGAGGTTGCGGTGAGCCGAGATC chm1:+:617690664:-1 +GAGGCCCGAGGAGGGGTGGATCACCTGAGGTTGGGAGTTGGAGGACCAGCCTGACCAACATGGATAAACCCCTTACTCTACTAAAATGCAAAAATTAGCCGGGGTTGGTGGTGCATGCCTGTAATCTCAGCTACTCGAAGGAGGCTGAGGCAGGAAGAATCGCCTGAACAGGGTGGCGGAGGTTGCGGTGAGCCGAGATC chm1:+:942261650:-1 chm1:+:2073804738:-1 chm1:+:2566933491:-1 chm1:+:2636442594:-1 +GATCTCGGCTCACCGCAACCTCCGCCACCCTGTTCAGGCGATTCTTCCTGCCTCAGCCTCCTTCGAGTAGCTGAGATTACAGGCATGCACCACCAACCCCGGCTAATTTTTGCATTTTAGTAGAGTAAGGGGTTTATCCATGTTGGTCAGGCTGGTCCTCCAACTCCCAACCTCAGGTGATCCACCCCTCCTCGGGCCTC chm1:+:53690679:28 chm1:+:61619849:-1 chm1:+:504411546:35 chm1:+:1049392138:35 chm1:+:1532156089:30 chm1:+:1572145066:30 chm1:+:2298717351:-1 chm1:+:2388331622:-1 chm1:+:2668128859:-1 chm1:+:3021101418:31 +GATCTCGGCTCACCGCAACCTCCGCCACCCTGTTCAGGCGATTCTTCCTGCCTCAGCCTCCTTCGAGTAGCTGAGATTACAGGCATGCACCACCAACCCCGGCTAATTTTTGCATTTTAGTAGAGTAAGGGGTTTATCCATGTTGGTCAGGCTGGTCCTCCAACTCCCAACCTCAGGTGATCCACCCCTCCTCGGGCCTC chm1:+:1705715:-1 chm1:+:10275255:31 chm1:+:16153008:33 chm1:+:29503815:-1 chm1:+:36737216:33 chm1:+:39466043:37 chm1:+:53200722:32 chm1:+:56765811:31 chm1:+:68172364:39 chm1:+:161178111:33 chm1:+:184720908:31 chm1:+:201909896:34 chm1:+:256305307:35 chm1:+:297932924:-1 chm1:+:314257610:29 chm1:+:341022364:-1 chm1:+:401518557:34 chm1:+:403590571:35 chm1:+:447676803:31 chm1:+:473977990:39 chm1:+:483074931:35 chm1:+:611674229:29 chm1:+:698823346:35 chm1:+:857740765:31 chm1:+:864980659:-1 chm1:+:961188738:31 chm1:+:1014036691:29 chm1:+:1032651400:31 chm1:+:1073392495:40 chm1:+:1099755559:34 chm1:+:1100952425:33 chm1:+:1136482589:39 chm1:+:1153064640:30 chm1:+:1173626599:33 chm1:+:1192710900:30 chm1:+:1226809311:36 chm1:+:1238341317:33 chm1:+:1238351557:32 chm1:+:1281326922:34 chm1:+:1281342283:33 chm1:+:1299563053:38 chm1:+:1301589010:34 chm1:+:1309405983:-1 chm1:+:1332765115:32 chm1:+:1344344292:34 chm1:+:1462510046:33 chm1:+:1517218238:36 chm1:+:1518248081:30 chm1:+:1566053565:31 chm1:+:1575798015:34 chm1:+:1646869576:32 chm1:+:1664823943:29 chm1:+:1686242433:-1 chm1:+:1726680892:38 chm1:+:1731584523:38 chm1:+:1734286669:30 chm1:+:1741344300:38 chm1:+:1750113054:-1 chm1:+:1782636355:29 chm1:+:1784316942:35 chm1:+:1786400605:30 chm1:+:1825849190:38 chm1:+:1882366199:29 chm1:+:1884528635:32 chm1:+:1887351376:38 chm1:+:1909314570:39 chm1:+:1957943990:34 chm1:+:1976474560:37 chm1:+:2105012606:37 chm1:+:2112594982:-1 chm1:+:2169779120:35 chm1:+:2186060063:35 chm1:+:2223138917:28 chm1:+:2274431611:-1 chm1:+:2283831885:39 chm1:+:2305255271:34 chm1:+:2359610622:37 chm1:+:2372165679:-1 chm1:+:2376913324:32 chm1:+:2380024363:34 chm1:+:2389972360:32 chm1:+:2390348895:32 chm1:+:2412968828:31 chm1:+:2431151208:29 chm1:+:2439298694:40 chm1:+:2440038038:40 chm1:+:2440981409:-1 chm1:+:2474709885:35 chm1:+:2482380218:35 chm1:+:2506075423:34 chm1:+:2516588319:33 chm1:+:2517530730:34 chm1:+:2517821834:30 chm1:+:2580337671:-1 chm1:+:2641442700:31 chm1:+:2670790899:30 chm1:+:2673208775:32 chm1:+:2679724261:-1 chm1:+:2681185540:-1 chm1:+:2689874227:36 chm1:+:2710839170:36 chm1:+:2711617333:33 chm1:+:2712981412:31 chm1:+:2716957178:33 chm1:+:2752007439:-1 chm1:+:2758224600:32 chm1:+:2851750186:29 chm1:+:2854715787:37 chm1:+:2868891502:37 chm1:+:2875234077:39 chm1:+:2880245161:37 chm1:+:2924291151:32 chm1:+:2925591441:28 chm1:+:2934102726:33 chm1:+:2993798229:34 chm1:+:3021068806:33 chm1:+:3021726737:32 chm1:+:3052256542:33 +GATCTCGGCTCACCGCAACCTCCGCCACCCTGTTCAGGCGATTCTTCCTGCCTCAGCCTCCTTCGAGTAGCTGAGATTACAGGCATGCACCACCAACCCCGGCTAATTTTTGCATTTTAGTAGAGTAAGGGGTTTATCCATGTTGGTCAGGCTGGTCCTCCAACTCCCAACCTCAGGTGATCCACCCCTCCTCGGGCCTC chm1:+:144303411:-1 chm1:+:144483640:-1 chm1:+:1034383941:-1 chm1:+:1694642415:37 chm1:+:1797188819:34 chm1:+:1842195893:-1 chm1:+:1884569660:-1 chm1:+:1976717777:-1 chm1:+:2043352062:-1 chm1:+:2151634851:39 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAA chm1:+:219351798:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAA chm1:+:602218947:-1 chm1:+:758970515:-1 chm1:+:911025777:-1 chm1:+:1139729787:-1 chm1:+:1168840940:-1 chm1:+:1571155635:-1 chm1:+:1710381738:-1 chm1:+:2287082458:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAA chm1:+:515169787:-1 chm1:+:570348891:-1 chm1:+:642068072:-1 chm1:+:721864594:-1 chm1:+:853042117:-1 chm1:+:853662680:-1 chm1:+:1137925210:-1 chm1:+:1254687300:-1 chm1:+:1352050727:-1 chm1:+:1458252924:-1 chm1:+:1781586712:-1 chm1:+:1840116194:-1 chm1:+:1879253044:-1 chm1:+:1888086576:-1 chm1:+:2140532069:-1 chm1:+:2164194312:-1 chm1:+:2194368226:-1 chm1:+:2401829897:-1 chm1:+:2809593058:-1 chm1:+:2936025327:-1 chm1:+:2984376756:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAA chm1:+:428407523:-1 chm1:+:719684479:-1 chm1:+:822032869:-1 chm1:+:901025550:-1 chm1:+:1129318968:-1 chm1:+:1190493094:-1 chm1:+:1196647008:-1 chm1:+:1317709272:-1 chm1:+:1509985122:-1 chm1:+:1797399678:-1 chm1:+:1969219285:-1 chm1:+:1984292686:-1 chm1:+:2024154140:-1 chm1:+:2038957202:-1 chm1:+:2344802932:-1 chm1:+:2605690003:-1 chm1:+:2859237956:-1 chm1:+:3002589505:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAA chm1:+:166008928:-1 chm1:+:644577890:-1 chm1:+:1823085208:-1 chm1:+:2022290494:-1 chm1:+:2140735565:-1 chm1:+:2364850418:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAA chm1:+:1460072103:-1 +TTGAGTTAATTGCCATTGTGTAATTTTATTTTAACTTAAATGTAAGAAATTACCATATATTGACGCACCTTCTGTTGTAGACACTTTATTGCATTATTTTTTTTAATTTTTTTTAAACTTTCTTTATATTAAAATATTAATCACTGTACAAGAATGTATGTATTATACACATTACAGTTTAAAGAACGTAATAAAACACA chm1:+:1348261309:-1 chm1:+:2553260322:16 +TTGAGTTAATTGCCATTGTGTAATTTTATTTTAACTTAAATGTAAGAAATTACCATATATTGACGCACCTTCTGTTGTAGACACTTTATTGCATTATTTTTTTTAATTTTTTTTAAACTTTCTTTATATTAAAATATTAATCACTGTACAAGAATGTATGTATTATACACATTACAGTTTAAAGAACGTAATAAAACACA chm1:+:565899579:-1 chm1:+:772078373:-1 chm1:+:1152124905:-1 chm1:+:1907762588:-1 chm1:+:2469273955:-1 chm1:+:2553260320:16 chm1:+:2967246051:-1 +TTGAGTTAATTGCCATTGTGTAATTTTATTTTAACTTAAATGTAAGAAATTACCATATATTGACGCACCTTCTGTTGTAGACACTTTATTGCATTATTTTTTTTAATTTTTTTTAAACTTTCTTTATATTAAAATATTAATCACTGTACAAGAATGTATGTATTATACACATTACAGTTTAAAGAACGTAATAAAACACA chm1:+:120352675:-1 chm1:+:282043736:-1 chm1:+:460008346:-1 chm1:+:828360563:-1 chm1:+:938563447:-1 chm1:+:1351607202:-1 chm1:+:1514320803:-1 chm1:+:2228842791:-1 chm1:+:2344458770:-1 chm1:+:2616011139:-1 chm1:+:2652590615:-1 +TTGAGTTAATTGCCATTGTGTAATTTTATTTTAACTTAAATGTAAGAAATTACCATATATTGACGCACCTTCTGTTGTAGACACTTTATTGCATTATTTTTTTTAATTTTTTTTAAACTTTCTTTATATTAAAATATTAATCACTGTACAAGAATGTATGTATTATACACATTACAGTTTAAAGAACGTAATAAAACACA chm1:+:170613903:-1 chm1:+:192160618:-1 chm1:+:427864599:-1 chm1:+:457193661:-1 chm1:+:494463888:-1 chm1:+:706431331:-1 chm1:+:941136008:-1 chm1:+:970323295:-1 chm1:+:996488676:-1 chm1:+:1097533532:-1 chm1:+:1137949340:-1 chm1:+:1142955725:-1 chm1:+:1203864398:-1 chm1:+:1257821366:-1 chm1:+:1262473016:-1 chm1:+:1288712380:-1 chm1:+:1348554305:-1 chm1:+:1418138500:-1 chm1:+:1742173367:-1 chm1:+:1971606487:-1 chm1:+:1972889401:-1 chm1:+:2024461691:-1 chm1:+:2031168655:-1 chm1:+:2374695567:-1 chm1:+:2400826035:-1 chm1:+:2465786546:-1 chm1:+:2493607083:-1 chm1:+:2551718688:-1 chm1:+:2735438616:-1 chm1:+:2848013567:-1 chm1:+:2995570603:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGA chm1:+:14183717:40 chm1:+:61189089:-1 chm1:+:74148391:-1 chm1:+:92733414:-1 chm1:+:106124628:-1 chm1:+:158728418:-1 chm1:+:184073737:-1 chm1:+:185765945:-1 chm1:+:217474492:-1 chm1:+:283165477:-1 chm1:+:395437534:-1 chm1:+:513120158:-1 chm1:+:523891730:-1 chm1:+:526033292:-1 chm1:+:543726352:-1 chm1:+:576628315:-1 chm1:+:607695935:-1 chm1:+:610541917:-1 chm1:+:612778739:-1 chm1:+:705969749:-1 chm1:+:712750804:-1 chm1:+:720998154:-1 chm1:+:762821782:-1 chm1:+:823647322:-1 chm1:+:903584191:-1 chm1:+:950890035:-1 chm1:+:951765106:-1 chm1:+:1002137138:-1 chm1:+:1008426032:-1 chm1:+:1044961438:-1 chm1:+:1045610362:-1 chm1:+:1045899525:-1 chm1:+:1083283969:-1 chm1:+:1133243207:-1 chm1:+:1164132915:-1 chm1:+:1167207917:-1 chm1:+:1182990659:-1 chm1:+:1194123370:-1 chm1:+:1244963050:-1 chm1:+:1258355953:-1 chm1:+:1286005796:-1 chm1:+:1301109456:-1 chm1:+:1323089032:-1 chm1:+:1477384285:-1 chm1:+:1478275600:-1 chm1:+:1641681223:-1 chm1:+:1789476943:-1 chm1:+:1842361311:-1 chm1:+:1844938852:-1 chm1:+:1900390020:-1 chm1:+:1971794509:-1 chm1:+:2054503446:-1 chm1:+:2232127794:-1 chm1:+:2363835178:-1 chm1:+:2701020321:-1 chm1:+:2742108464:-1 chm1:+:2743147447:-1 chm1:+:2821164560:-1 chm1:+:2958506897:-1 chm1:+:2975182628:-1 chm1:+:2981699446:-1 chm1:+:3006083332:-1 chm1:+:3025107865:-1 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chm1:+:434422007:-1 chm1:+:434823092:-1 chm1:+:455767697:-1 chm1:+:463848178:-1 chm1:+:478213277:-1 chm1:+:513124229:-1 chm1:+:513592436:-1 chm1:+:515128666:-1 chm1:+:517227221:-1 chm1:+:523179984:-1 chm1:+:578251550:-1 chm1:+:587942072:-1 chm1:+:591536786:-1 chm1:+:681845337:-1 chm1:+:726507153:-1 chm1:+:747149044:-1 chm1:+:796886130:-1 chm1:+:812956081:-1 chm1:+:819815824:-1 chm1:+:873357953:-1 chm1:+:901006800:-1 chm1:+:903143998:-1 chm1:+:917134261:-1 chm1:+:1062911862:-1 chm1:+:1084668967:-1 chm1:+:1084671819:-1 chm1:+:1129256911:-1 chm1:+:1132574161:-1 chm1:+:1161089826:-1 chm1:+:1172382725:-1 chm1:+:1183173642:-1 chm1:+:1188831576:-1 chm1:+:1203322671:-1 chm1:+:1207555445:-1 chm1:+:1213614263:-1 chm1:+:1214199629:-1 chm1:+:1250545907:-1 chm1:+:1255021774:-1 chm1:+:1261674964:-1 chm1:+:1304072273:-1 chm1:+:1341551769:-1 chm1:+:1349069514:-1 chm1:+:1357817196:-1 chm1:+:1408675349:-1 chm1:+:1427896293:-1 chm1:+:1432039828:-1 chm1:+:1441778617:-1 chm1:+:1451036822:-1 chm1:+:1478754029:-1 chm1:+:1562064039:-1 chm1:+:1615606717:-1 chm1:+:1734353761:-1 chm1:+:1737057305:-1 chm1:+:1738195373:-1 chm1:+:1743216628:-1 chm1:+:1798626645:-1 chm1:+:1839836988:-1 chm1:+:1856875844:-1 chm1:+:1919544712:-1 chm1:+:1920043922:-1 chm1:+:1921804343:-1 chm1:+:1971969465:-1 chm1:+:1993015665:-1 chm1:+:2024798031:-1 chm1:+:2044036883:-1 chm1:+:2174206027:-1 chm1:+:2219454698:-1 chm1:+:2219477726:-1 chm1:+:2219483066:-1 chm1:+:2247200749:-1 chm1:+:2272223099:-1 chm1:+:2342358493:-1 chm1:+:2346012163:-1 chm1:+:2363144742:-1 chm1:+:2386923668:-1 chm1:+:2387434035:-1 chm1:+:2391199535:-1 chm1:+:2486691630:-1 chm1:+:2490830326:-1 chm1:+:2559247530:-1 chm1:+:2618756107:-1 chm1:+:2621548018:-1 chm1:+:2639273525:-1 chm1:+:2649177126:-1 chm1:+:2679422786:-1 chm1:+:2679461123:-1 chm1:+:2679639578:-1 chm1:+:2679844300:-1 chm1:+:2680409459:-1 chm1:+:2726499374:-1 chm1:+:2736934251:-1 chm1:+:2848613747:-1 chm1:+:2902338953:-1 chm1:+:2908700669:-1 chm1:+:2914476651:-1 chm1:+:2938450499:-1 chm1:+:2946195747:-1 chm1:+:2979122071:-1 chm1:+:2996850425:-1 chm1:+:2997465459:-1 chm1:+:3026008963:-1 chm1:+:3061859705:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGA chm1:+:34842056:-1 chm1:+:142695464:-1 chm1:+:272259968:-1 chm1:+:290800249:-1 chm1:+:410443026:-1 chm1:+:462362532:-1 chm1:+:498227255:-1 chm1:+:676334010:-1 chm1:+:792778411:-1 chm1:+:919845002:-1 chm1:+:938050812:-1 chm1:+:947715566:-1 chm1:+:1182269750:-1 chm1:+:1321622756:-1 chm1:+:1615170816:-1 chm1:+:1724984927:-1 chm1:+:1764266632:-1 chm1:+:1797367085:-1 chm1:+:1929445603:-1 chm1:+:1938658756:-1 chm1:+:2012291920:-1 chm1:+:2368587747:-1 chm1:+:2485233075:-1 chm1:+:2529205404:-1 chm1:+:2541663878:-1 chm1:+:2619698923:-1 chm1:+:2702650912:-1 chm1:+:2907810887:-1 chm1:+:2967539298:-1 chm1:+:3020354223:-1 chm1:+:3058221644:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGA chm1:+:111668016:-1 chm1:+:158682611:-1 chm1:+:222094317:-1 chm1:+:350965489:-1 chm1:+:396837714:-1 chm1:+:411137649:-1 chm1:+:456873538:-1 chm1:+:761029627:-1 chm1:+:834997271:-1 chm1:+:1185303814:-1 chm1:+:1475380267:-1 chm1:+:1495520738:-1 chm1:+:2036695688:-1 chm1:+:2060128303:-1 chm1:+:2120685299:-1 chm1:+:2170885696:-1 chm1:+:2198221245:-1 chm1:+:2271500171:-1 chm1:+:2583624465:-1 chm1:+:2604305021:-1 chm1:+:2861024323:-1 chm1:+:2986232090:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGA chm1:+:104992840:-1 chm1:+:194695136:-1 chm1:+:1114591977:-1 chm1:+:2119390538:-1 chm1:+:2265934993:-1 chm1:+:2406029373:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGA chm1:+:302037912:-1 chm1:+:377868335:-1 chm1:+:822791674:-1 chm1:+:995723490:-1 chm1:+:1091747315:34 chm1:+:1400635617:-1 chm1:+:1442156023:-1 chm1:+:1711985854:-1 chm1:+:1714415482:-1 chm1:+:1974203668:-1 chm1:+:2490090986:-1 chm1:+:2640215039:-1 chm1:+:2916383208:-1 +TCAGAATGGCTATTTGTTGACAGTCACGTATCTGTCAACAAATAACAGATGCTGGCGAGGTTGCAAGAGAAAAGGGAACACAACTTATACACTGTTGAATTGGGAGTGTAAAATTAGTTCAACCATGTTGGAAACCAGTATGGCTATTCCTCAAAGAGCTAAAAGCAGAACTACCATTTAACCGCAATCCCATTACTGGG chm1:+:111953163:11 chm1:+:2955298302:-1 +TCAGAATGGCTATTTGTTGACAGTCACGTATCTGTCAACAAATAACAGATGCTGGCGAGGTTGCAAGAGAAAAGGGAACACAACTTATACACTGTTGAATTGGGAGTGTAAAATTAGTTCAACCATGTTGGAAACCAGTATGGCTATTCCTCAAAGAGCTAAAAGCAGAACTACCATTTAACCGCAATCCCATTACTGGG chm1:+:111953157:11 chm1:+:239333465:-1 chm1:+:391201181:-1 chm1:+:982989201:-1 chm1:+:1365357298:-1 chm1:+:2035374495:-1 chm1:+:2513205305:-1 +TCAGAATGGCTATTTGTTGACAGTCACGTATCTGTCAACAAATAACAGATGCTGGCGAGGTTGCAAGAGAAAAGGGAACACAACTTATACACTGTTGAATTGGGAGTGTAAAATTAGTTCAACCATGTTGGAAACCAGTATGGCTATTCCTCAAAGAGCTAAAAGCAGAACTACCATTTAACCGCAATCCCATTACTGGG chm1:+:530267072:-1 chm1:+:1183495756:-1 chm1:+:2221580564:-1 chm1:+:2260054987:-1 chm1:+:2432468639:-1 chm1:+:2444938178:-1 chm1:+:2923314696:-1 +TCAGTATAATCACATTAGGAGGTTACATGTCAATTTGTGGCATTTACTGGTGATATTAACTTTTTTTTAAGTTCTTGCAGAGAGATTTAGATGTTAGAGTGAACATCACTTTTAAAAAAATTATTTTTCTTTAAATTGATGAATAAAAATAGATATATTTTATGTGTCTAACATGTTTTTATATTTGTAGTGCCTTGCCA chm1:+:61329709:-1 chm1:+:528435166:-1 chm1:+:587505437:-1 chm1:+:1182972258:-1 chm1:+:1299904671:-1 chm1:+:1540175753:-1 chm1:+:1864306731:-1 chm1:+:2115279305:-1 chm1:+:2351821875:-1 chm1:+:2532319419:-1 chm1:+:2988988242:-1 +TCAGTATAATCACATTAGGAGGTTACATGTCAATTTGTGGCATTTACTGGTGATATTAACTTTTTTTTAAGTTCTTGCAGAGAGATTTAGATGTTAGAGTGAACATCACTTTTAAAAAAATTATTTTTCTTTAAATTGATGAATAAAAATAGATATATTTTATGTGTCTAACATGTTTTTATATTTGTAGTGCCTTGCCA chm1:+:33062208:-1 chm1:+:159107290:-1 chm1:+:408069957:-1 chm1:+:1466744249:-1 chm1:+:2744073227:-1 +TCAGTATAATCACATTAGGAGGTTACATGTCAATTTGTGGCATTTACTGGTGATATTAACTTTTTTTTAAGTTCTTGCAGAGAGATTTAGATGTTAGAGTGAACATCACTTTTAAAAAAATTATTTTTCTTTAAATTGATGAATAAAAATAGATATATTTTATGTGTCTAACATGTTTTTATATTTGTAGTGCCTTGCCA chm1:+:88546316:-1 chm1:+:99522656:-1 chm1:+:611116157:-1 chm1:+:923787289:-1 chm1:+:2077487049:-1 +TCAGTATAATCACATTAGGAGGTTACATGTCAATTTGTGGCATTTACTGGTGATATTAACTTTTTTTTAAGTTCTTGCAGAGAGATTTAGATGTTAGAGTGAACATCACTTTTAAAAAAATTATTTTTCTTTAAATTGATGAATAAAAATAGATATATTTTATGTGTCTAACATGTTTTTATATTTGTAGTGCCTTGCCA chm1:+:194634535:-1 chm1:+:479642964:-1 chm1:+:604045315:-1 chm1:+:605057523:-1 chm1:+:628537578:-1 chm1:+:779130959:-1 chm1:+:804546230:-1 chm1:+:922443477:-1 chm1:+:1115435748:-1 chm1:+:1180947264:-1 chm1:+:1187644096:-1 chm1:+:1251280266:-1 chm1:+:1283688220:-1 chm1:+:1412231593:-1 chm1:+:1647474366:-1 chm1:+:2062385671:-1 chm1:+:2077578795:-1 chm1:+:2552055073:-1 chm1:+:2755721652:-1 chm1:+:2758525322:-1 chm1:+:3055662792:-1 +TCAGTATAATCACATTAGGAGGTTACATGTCAATTTGTGGCATTTACTGGTGATATTAACTTTTTTTTAAGTTCTTGCAGAGAGATTTAGATGTTAGAGTGAACATCACTTTTAAAAAAATTATTTTTCTTTAAATTGATGAATAAAAATAGATATATTTTATGTGTCTAACATGTTTTTATATTTGTAGTGCCTTGCCA chm1:+:170666586:-1 chm1:+:176778178:-1 chm1:+:177258145:-1 chm1:+:192055448:-1 chm1:+:382319907:-1 chm1:+:448201851:-1 chm1:+:454464248:-1 chm1:+:478321985:-1 chm1:+:497151528:-1 chm1:+:545158615:-1 chm1:+:589873488:-1 chm1:+:608261679:-1 chm1:+:650696774:-1 chm1:+:655166674:-1 chm1:+:656268530:-1 chm1:+:659939277:-1 chm1:+:696550579:-1 chm1:+:820432698:-1 chm1:+:833813660:-1 chm1:+:872946752:-1 chm1:+:899655235:-1 chm1:+:1111647622:-1 chm1:+:1130033632:-1 chm1:+:1191914489:-1 chm1:+:1219362942:-1 chm1:+:1227486786:-1 chm1:+:1245902613:-1 chm1:+:1247526211:-1 chm1:+:1272740828:-1 chm1:+:1285855430:-1 chm1:+:1339311196:-1 chm1:+:1469587337:-1 chm1:+:1474140933:-1 chm1:+:1482001630:-1 chm1:+:1541374934:-1 chm1:+:1763294798:-1 chm1:+:1772200082:-1 chm1:+:1780828935:-1 chm1:+:1790449401:-1 chm1:+:1790449610:-1 chm1:+:1856783973:-1 chm1:+:1917767687:-1 chm1:+:1923386762:-1 chm1:+:1924610560:-1 chm1:+:2028494729:-1 chm1:+:2071050799:-1 chm1:+:2158304924:-1 chm1:+:2173790525:-1 chm1:+:2241338658:-1 chm1:+:2273426076:-1 chm1:+:2305537830:-1 chm1:+:2306466986:-1 chm1:+:2327896370:-1 chm1:+:2404958099:-1 chm1:+:2405423126:-1 chm1:+:2471029721:-1 chm1:+:2558930557:-1 chm1:+:2731156867:-1 chm1:+:2762173766:-1 chm1:+:2811903344:-1 chm1:+:2826675395:-1 chm1:+:2884292094:-1 chm1:+:2884892190:-1 chm1:+:2962110958:-1 chm1:+:2979136083:-1 +TGGCAAGGCACTACAAATATAAAAACATGTTAGACACATAAAATATATCTATTTTTATTCATCAATTTAAAGAAAAATAATTTTTTTAAAAGTGATGTTCACTCTAACATCTAAATCTCTCTGCAAGAACTTAAAAAAAAGTTAATATCACCAGTAAATGCCACAAATTGACATGTAACCTCCTAATGTGATTATACTGA chm1:+:685577033:-1 chm1:+:890132785:-1 chm1:+:1206881645:8 chm1:+:1648868540:-1 +AAATTCCATACACTTCTTTTTTATAAAGCTGATCTGCCTGAGGATATGCCTGTGGTGCTGTTTATAATCTCTTTTCTCCCTCCCACAAAAAGATAGGCAAACTTTTTACCCAATCCAGGAATCTTACCCTAGTTTGTGGCCCACAAATGGTCAAAACTTTCTGGGGCACCAAACAAAGCAACATTTTCAAATATCAGTAT chm1:+:149944951:-1 chm1:+:216040710:-1 chm1:+:389691132:-1 chm1:+:914909345:11 chm1:+:1373801407:-1 chm1:+:2193612198:-1 chm1:+:2643814707:-1 chm1:+:2798169920:-1 chm1:+:2995769281:-1 +AAATTCCATACACTTCTTTTTTATAAAGCTGATCTGCCTGAGGATATGCCTGTGGTGCTGTTTATAATCTCTTTTCTCCCTCCCACAAAAAGATAGGCAAACTTTTTACCCAATCCAGGAATCTTACCCTAGTTTGTGGCCCACAAATGGTCAAAACTTTCTGGGGCACCAAACAAAGCAACATTTTCAAATATCAGTAT chm1:+:2219313189:-1 +AAATTCCATACACTTCTTTTTTATAAAGCTGATCTGCCTGAGGATATGCCTGTGGTGCTGTTTATAATCTCTTTTCTCCCTCCCACAAAAAGATAGGCAAACTTTTTACCCAATCCAGGAATCTTACCCTAGTTTGTGGCCCACAAATGGTCAAAACTTTCTGGGGCACCAAACAAAGCAACATTTTCAAATATCAGTAT chm1:+:914909347:11 +AAATTCCATACACTTCTTTTTTATAAAGCTGATCTGCCTGAGGATATGCCTGTGGTGCTGTTTATAATCTCTTTTCTCCCTCCCACAAAAAGATAGGCAAACTTTTTACCCAATCCAGGAATCTTACCCTAGTTTGTGGCCCACAAATGGTCAAAACTTTCTGGGGCACCAAACAAAGCAACATTTTCAAATATCAGTAT chm1:+:914909349:11 +AAATTCCATACACTTCTTTTTTATAAAGCTGATCTGCCTGAGGATATGCCTGTGGTGCTGTTTATAATCTCTTTTCTCCCTCCCACAAAAAGATAGGCAAACTTTTTACCCAATCCAGGAATCTTACCCTAGTTTGTGGCCCACAAATGGTCAAAACTTTCTGGGGCACCAAACAAAGCAACATTTTCAAATATCAGTAT chm1:+:914909350:11 +AAGTTGTTTATTCTCTCAAACAATAAAATATGTGTGTACAATCCCAAGACATTTTTGAAAGGAATAAAACCTTGCATCTCTGAATTCCTGTGGGGCCTAGCAACAATGGACGATATACTACGTTGCAGTGTCATTTCCCTAAAATCTAGCTTGTGTGTTACAATCACCATTGATGTATCTTCCCCCACGAACCTAGAGAA chm1:+:84647811:-1 chm1:+:447840134:-1 chm1:+:573082694:-1 chm1:+:2012495033:-1 chm1:+:3018664714:-1 +AAGTTGTTTATTCTCTCAAACAATAAAATATGTGTGTACAATCCCAAGACATTTTTGAAAGGAATAAAACCTTGCATCTCTGAATTCCTGTGGGGCCTAGCAACAATGGACGATATACTACGTTGCAGTGTCATTTCCCTAAAATCTAGCTTGTGTGTTACAATCACCATTGATGTATCTTCCCCCACGAACCTAGAGAA chm1:+:1002845959:-1 chm1:+:1153907107:-1 +AAGTTGTTTATTCTCTCAAACAATAAAATATGTGTGTACAATCCCAAGACATTTTTGAAAGGAATAAAACCTTGCATCTCTGAATTCCTGTGGGGCCTAGCAACAATGGACGATATACTACGTTGCAGTGTCATTTCCCTAAAATCTAGCTTGTGTGTTACAATCACCATTGATGTATCTTCCCCCACGAACCTAGAGAA chm1:+:181298162:-1 chm1:+:230733432:-1 chm1:+:319571711:-1 chm1:+:838577786:-1 chm1:+:1169715645:-1 chm1:+:2066332489:-1 chm1:+:2260501839:-1 +AAGTTGTTTATTCTCTCAAACAATAAAATATGTGTGTACAATCCCAAGACATTTTTGAAAGGAATAAAACCTTGCATCTCTGAATTCCTGTGGGGCCTAGCAACAATGGACGATATACTACGTTGCAGTGTCATTTCCCTAAAATCTAGCTTGTGTGTTACAATCACCATTGATGTATCTTCCCCCACGAACCTAGAGAA chm1:+:2144856399:-1 chm1:+:2189910078:-1 +AAGTTGTTTATTCTCTCAAACAATAAAATATGTGTGTACAATCCCAAGACATTTTTGAAAGGAATAAAACCTTGCATCTCTGAATTCCTGTGGGGCCTAGCAACAATGGACGATATACTACGTTGCAGTGTCATTTCCCTAAAATCTAGCTTGTGTGTTACAATCACCATTGATGTATCTTCCCCCACGAACCTAGAGAA chm1:+:43664904:-1 chm1:+:208438226:-1 chm1:+:477275922:-1 chm1:+:763193375:-1 chm1:+:966503960:-1 chm1:+:1043187287:-1 chm1:+:1046144077:-1 chm1:+:1118293269:-1 chm1:+:1318789706:-1 chm1:+:1326781471:-1 chm1:+:1842607297:-1 chm1:+:2018246550:-1 chm1:+:2019037080:-1 chm1:+:2187722198:-1 chm1:+:2605808102:-1 chm1:+:2736764323:-1 chm1:+:2876265023:-1 +TTCTCTAGGTTCGTGGGGGAAGATACATCAATGGTGATTGTAACACACAAGCTAGATTTTAGGGAAATGACACTGCAACGTAGTATATCGTCCATTGTTGCTAGGCCCCACAGGAATTCAGAGATGCAAGGTTTTATTCCTTTCAAAAATGTCTTGGGATTGTACACACATATTTTATTGTTTGAGAGAATAAACAACTT chm1:+:719181044:-1 chm1:+:873339296:-1 +TTCTCTAGGTTCGTGGGGGAAGATACATCAATGGTGATTGTAACACACAAGCTAGATTTTAGGGAAATGACACTGCAACGTAGTATATCGTCCATTGTTGCTAGGCCCCACAGGAATTCAGAGATGCAAGGTTTTATTCCTTTCAAAAATGTCTTGGGATTGTACACACATATTTTATTGTTTGAGAGAATAAACAACTT chm1:+:705874038:12 chm1:+:815184987:-1 chm1:+:1262485047:-1 chm1:+:1704459224:-1 chm1:+:1725388755:-1 chm1:+:2079450250:-1 +TTCTCTAGGTTCGTGGGGGAAGATACATCAATGGTGATTGTAACACACAAGCTAGATTTTAGGGAAATGACACTGCAACGTAGTATATCGTCCATTGTTGCTAGGCCCCACAGGAATTCAGAGATGCAAGGTTTTATTCCTTTCAAAAATGTCTTGGGATTGTACACACATATTTTATTGTTTGAGAGAATAAACAACTT chm1:+:705874041:12 chm1:+:709093992:-1 +TTCTCTAGGTTCGTGGGGGAAGATACATCAATGGTGATTGTAACACACAAGCTAGATTTTAGGGAAATGACACTGCAACGTAGTATATCGTCCATTGTTGCTAGGCCCCACAGGAATTCAGAGATGCAAGGTTTTATTCCTTTCAAAAATGTCTTGGGATTGTACACACATATTTTATTGTTTGAGAGAATAAACAACTT chm1:+:705874042:12 +TTCTCTAGGTTCGTGGGGGAAGATACATCAATGGTGATTGTAACACACAAGCTAGATTTTAGGGAAATGACACTGCAACGTAGTATATCGTCCATTGTTGCTAGGCCCCACAGGAATTCAGAGATGCAAGGTTTTATTCCTTTCAAAAATGTCTTGGGATTGTACACACATATTTTATTGTTTGAGAGAATAAACAACTT chm1:+:1427288980:-1 +TTCTCTAGGTTCGTGGGGGAAGATACATCAATGGTGATTGTAACACACAAGCTAGATTTTAGGGAAATGACACTGCAACGTAGTATATCGTCCATTGTTGCTAGGCCCCACAGGAATTCAGAGATGCAAGGTTTTATTCCTTTCAAAAATGTCTTGGGATTGTACACACATATTTTATTGTTTGAGAGAATAAACAACTT chm1:+:570239641:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGA chm1:+:289241959:-1 chm1:+:654196420:-1 chm1:+:758580440:-1 chm1:+:1923021001:-1 chm1:+:2895286778:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGA chm1:+:1317671998:-1 chm1:+:1481624631:-1 chm1:+:1832563194:-1 chm1:+:2112411793:-1 chm1:+:2978834370:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGA chm1:+:18023973:-1 chm1:+:73238164:-1 chm1:+:91386841:-1 chm1:+:118427897:-1 chm1:+:217593585:-1 chm1:+:263729768:-1 chm1:+:404578203:-1 chm1:+:440882949:-1 chm1:+:446962428:-1 chm1:+:593910267:-1 chm1:+:714592258:-1 chm1:+:718409121:-1 chm1:+:778656894:-1 chm1:+:842359664:-1 chm1:+:1053526896:-1 chm1:+:1194908773:-1 chm1:+:1325467516:-1 chm1:+:1399034610:-1 chm1:+:1460469582:-1 chm1:+:1626032183:-1 chm1:+:1732946510:-1 chm1:+:1774506418:-1 chm1:+:2063483864:-1 chm1:+:2068626187:-1 chm1:+:2069671318:-1 chm1:+:2125932710:-1 chm1:+:2255579272:-1 chm1:+:2284221095:-1 chm1:+:2339229016:-1 chm1:+:2380323370:-1 chm1:+:2390571102:-1 chm1:+:2402058455:-1 chm1:+:2406365175:-1 chm1:+:2580695240:-1 chm1:+:2582499821:-1 chm1:+:2966203191:-1 chm1:+:2986271117:-1 chm1:+:3059049235:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGA chm1:+:40010167:-1 chm1:+:271153134:-1 chm1:+:314195933:-1 chm1:+:392235249:-1 chm1:+:424032042:-1 chm1:+:499243880:-1 chm1:+:728879482:-1 chm1:+:736806714:-1 chm1:+:918446813:-1 chm1:+:1029713135:-1 chm1:+:1047792291:-1 chm1:+:1354036142:-1 chm1:+:1558172642:-1 chm1:+:1757391417:-1 chm1:+:1836355977:-1 chm1:+:1928510241:-1 chm1:+:1949449306:-1 chm1:+:1958534485:-1 chm1:+:2006181347:-1 chm1:+:2022712701:-1 chm1:+:2029310841:-1 chm1:+:2142619337:-1 chm1:+:2406293767:-1 chm1:+:2490398339:-1 chm1:+:2608534187:-1 chm1:+:2720102595:-1 chm1:+:2766886001:-1 chm1:+:2802841240:-1 chm1:+:2930599862:-1 chm1:+:2957359216:-1 chm1:+:2993267789:-1 chm1:+:3015755044:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGA chm1:+:72575025:-1 chm1:+:313222562:-1 chm1:+:684617927:-1 chm1:+:693078612:-1 chm1:+:754074254:-1 chm1:+:1046972135:-1 chm1:+:1058674352:-1 chm1:+:1193590537:-1 chm1:+:1872673384:-1 chm1:+:1984510209:-1 chm1:+:2187508262:-1 chm1:+:2253688901:-1 chm1:+:2351552560:-1 chm1:+:2889571110:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGA chm1:+:113343561:-1 chm1:+:488057509:-1 chm1:+:960392473:-1 chm1:+:1354500521:-1 chm1:+:2280728205:-1 chm1:+:2410117369:-1 chm1:+:2528140326:-1 chm1:+:2623783230:-1 chm1:+:2797802855:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGA chm1:+:36694874:-1 chm1:+:200024366:-1 chm1:+:283828103:-1 chm1:+:336112099:-1 chm1:+:414914014:-1 chm1:+:503710298:-1 chm1:+:591004565:-1 chm1:+:690129536:-1 chm1:+:708122578:-1 chm1:+:1908568925:-1 chm1:+:1949031272:-1 chm1:+:1957908963:-1 chm1:+:1983849612:-1 chm1:+:2074630102:-1 chm1:+:2511537986:-1 chm1:+:2601025328:-1 chm1:+:2808565561:-1 chm1:+:3015108695:-1 chm1:+:3025769226:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGA chm1:+:447487589:-1 chm1:+:711750429:-1 chm1:+:808437633:-1 chm1:+:832580160:-1 chm1:+:1211421607:-1 chm1:+:1332766619:-1 chm1:+:1420980900:-1 chm1:+:1499799836:-1 chm1:+:1541829800:-1 chm1:+:2232343939:-1 chm1:+:2295191639:-1 chm1:+:2423525694:-1 chm1:+:2508447574:-1 chm1:+:2627278304:-1 chm1:+:2716689403:-1 chm1:+:2847493786:-1 +TCAAGTCTATTTAGTCTATTAAAAGGATCTGCAGGGACAATACTTAAAAAATATTATTATAACTCTGCATTGTTTTATAGTCCTACTGGGTTTTTTGCTTTTAATAACTAGGGAAAAGGCCAGTCACGGTGGACTCACGCTATAATCCCAGCACTTTGGGAGGCTGAGGCAGGTGGATCACTAGGTCGAGGAGTTCAAAG chm1:+:1319361083:-1 chm1:+:1469626949:-1 chm1:+:1760919318:10 +TCAAGTCTATTTAGTCTATTAAAAGGATCTGCAGGGACAATACTTAAAAAATATTATTATAACTCTGCATTGTTTTATAGTCCTACTGGGTTTTTTGCTTTTAATAACTAGGGAAAAGGCCAGTCACGGTGGACTCACGCTATAATCCCAGCACTTTGGGAGGCTGAGGCAGGTGGATCACTAGGTCGAGGAGTTCAAAG chm1:+:1760919313:10 +TCAAGTCTATTTAGTCTATTAAAAGGATCTGCAGGGACAATACTTAAAAAATATTATTATAACTCTGCATTGTTTTATAGTCCTACTGGGTTTTTTGCTTTTAATAACTAGGGAAAAGGCCAGTCACGGTGGACTCACGCTATAATCCCAGCACTTTGGGAGGCTGAGGCAGGTGGATCACTAGGTCGAGGAGTTCAAAG chm1:+:1760919319:10 +TCAAGTCTATTTAGTCTATTAAAAGGATCTGCAGGGACAATACTTAAAAAATATTATTATAACTCTGCATTGTTTTATAGTCCTACTGGGTTTTTTGCTTTTAATAACTAGGGAAAAGGCCAGTCACGGTGGACTCACGCTATAATCCCAGCACTTTGGGAGGCTGAGGCAGGTGGATCACTAGGTCGAGGAGTTCAAAG chm1:+:1387776352:-1 +TCAAGTCTATTTAGTCTATTAAAAGGATCTGCAGGGACAATACTTAAAAAATATTATTATAACTCTGCATTGTTTTATAGTCCTACTGGGTTTTTTGCTTTTAATAACTAGGGAAAAGGCCAGTCACGGTGGACTCACGCTATAATCCCAGCACTTTGGGAGGCTGAGGCAGGTGGATCACTAGGTCGAGGAGTTCAAAG chm1:+:67901216:-1 chm1:+:242199941:-1 chm1:+:277212663:-1 chm1:+:359637572:-1 chm1:+:401049674:-1 chm1:+:1229408209:-1 chm1:+:1266182119:-1 chm1:+:1268379644:-1 chm1:+:1943768120:-1 chm1:+:1977091857:-1 chm1:+:2007398383:-1 chm1:+:2051520751:-1 chm1:+:2347951185:-1 chm1:+:2380892520:-1 chm1:+:2444935148:-1 chm1:+:2586698068:-1 chm1:+:2884313335:-1 chm1:+:2912879630:-1 +CTTTTAGTTAGCAGGCTTTCGATTCCAAATGTTCTATTGAGTCTCCCCTTGTCGTCAATCCTTTCCAATAAGTACCTGGAAAATTTCTTTCTGTGGATATTAGAGCTCTACTTGCAAGAGTTAAGAACTGGACTCTCTATTTGGAATGAGAATGCATACATTTACTTAGTTTTCAAGCACTATTTATTATGTATTATTCT chm1:+:163095163:-1 chm1:+:318954072:-1 chm1:+:695517322:7 chm1:+:1315559560:-1 chm1:+:1319368250:-1 chm1:+:1725906444:-1 chm1:+:1936158194:-1 chm1:+:2048614471:-1 chm1:+:2228003128:-1 chm1:+:2457484906:-1 chm1:+:2640785292:-1 chm1:+:2757814446:-1 chm1:+:2996127698:-1 +CTTTTAGTTAGCAGGCTTTCGATTCCAAATGTTCTATTGAGTCTCCCCTTGTCGTCAATCCTTTCCAATAAGTACCTGGAAAATTTCTTTCTGTGGATATTAGAGCTCTACTTGCAAGAGTTAAGAACTGGACTCTCTATTTGGAATGAGAATGCATACATTTACTTAGTTTTCAAGCACTATTTATTATGTATTATTCT chm1:+:695517323:7 +CTTTTAGTTAGCAGGCTTTCGATTCCAAATGTTCTATTGAGTCTCCCCTTGTCGTCAATCCTTTCCAATAAGTACCTGGAAAATTTCTTTCTGTGGATATTAGAGCTCTACTTGCAAGAGTTAAGAACTGGACTCTCTATTTGGAATGAGAATGCATACATTTACTTAGTTTTCAAGCACTATTTATTATGTATTATTCT chm1:+:236598737:-1 +AGAATAATACATAATAAATAGTGCTTGAAAACTAAGTAAATGTATGCATTCTCATTCCAAATAGAGAGTCCAGTTCTTAACTCTTGCAAGTAGAGCTCTAATATCCACAGAAAGAAATTTTCCAGGTACTTATTGGAAAGGATTGACGACAAGGGGAGACTCAATAGAACATTTGGAATCGAAAGCCTGCTAACTAAAAG chm1:+:2983383881:-1 +AAACAGTTGGCCAGGCGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGAAGGCCAAGCAGAGAGAATTAGCCTGAGCCCAGGGAGTTCGAGACCAGTCTGGACAATATAGGGAGACCCTGTTTAAAACTAAAAAATACAATTAGCCAGGCAATGGTGGCACTGCCTGTGGTCCGAGTTACTCAGGAGGCTGAGGTGAG chm1:+:1250049678:5 chm1:+:2990463538:-1 +AAACAGTTGGCCAGGCGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGAAGGCCAAGCAGAGAGAATTAGCCTGAGCCCAGGGAGTTCGAGACCAGTCTGGACAATATAGGGAGACCCTGTTTAAAACTAAAAAATACAATTAGCCAGGCAATGGTGGCACTGCCTGTGGTCCGAGTTACTCAGGAGGCTGAGGTGAG chm1:+:1250049674:5 +AAACAGTTGGCCAGGCGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGAAGGCCAAGCAGAGAGAATTAGCCTGAGCCCAGGGAGTTCGAGACCAGTCTGGACAATATAGGGAGACCCTGTTTAAAACTAAAAAATACAATTAGCCAGGCAATGGTGGCACTGCCTGTGGTCCGAGTTACTCAGGAGGCTGAGGTGAG chm1:+:1250049675:5 +CTCACCTCAGCCTCCTGAGTAACTCGGACCACAGGCAGTGCCACCATTGCCTGGCTAATTGTATTTTTTAGTTTTAAACAGGGTCTCCCTATATTGTCCAGACTGGTCTCGAACTCCCTGGGCTCAGGCTAATTCTCTCTGCTTGGCCTTCCAAAGTGCTGGGATTACAGGTGTGAGCCACCACGCCTGGCCAACTGTTT chm1:+:155746414:-1 chm1:+:1148969041:-1 chm1:+:1202298976:-1 chm1:+:1785550142:-1 chm1:+:2008373759:-1 chm1:+:2303680680:-1 chm1:+:2365444653:-1 chm1:+:2881812821:-1 chm1:+:2986976473:-1 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTT chm1:+:146697407:-1 chm1:+:161374057:25 chm1:+:161380344:22 chm1:+:249848315:27 chm1:+:290358023:-1 chm1:+:388248607:-1 chm1:+:730850416:-1 chm1:+:750186002:-1 chm1:+:809099509:-1 chm1:+:816174125:-1 chm1:+:852454747:-1 chm1:+:1004772343:-1 chm1:+:1164672254:-1 chm1:+:1325515371:-1 chm1:+:1469322488:-1 chm1:+:1677731976:24 chm1:+:1890747892:30 chm1:+:2080328915:-1 chm1:+:2183364508:-1 chm1:+:2714236573:23 chm1:+:2800786473:-1 chm1:+:2855947398:28 chm1:+:3017046374:30 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTT chm1:+:1760296719:-1 chm1:+:2431899807:-1 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTT chm1:+:272571884:-1 chm1:+:2194930213:-1 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTT chm1:+:8198903:-1 chm1:+:177770205:-1 chm1:+:179501413:-1 chm1:+:279830414:-1 chm1:+:287678512:-1 chm1:+:295734460:-1 chm1:+:301234396:-1 chm1:+:302583373:-1 chm1:+:320620677:-1 chm1:+:381675176:-1 chm1:+:405861546:-1 chm1:+:427957106:-1 chm1:+:434609962:-1 chm1:+:492595085:-1 chm1:+:554981063:-1 chm1:+:562463451:-1 chm1:+:663304728:-1 chm1:+:675493668:-1 chm1:+:728773446:-1 chm1:+:810311409:-1 chm1:+:918921414:-1 chm1:+:991649060:-1 chm1:+:1017047922:-1 chm1:+:1027980297:-1 chm1:+:1075012022:-1 chm1:+:1075622920:-1 chm1:+:1076211485:-1 chm1:+:1117753317:-1 chm1:+:1248586163:-1 chm1:+:1312578851:-1 chm1:+:1332393941:-1 chm1:+:1348371912:-1 chm1:+:1352553533:-1 chm1:+:1433323583:-1 chm1:+:1450542883:-1 chm1:+:1484937276:-1 chm1:+:1517195544:-1 chm1:+:1523610646:-1 chm1:+:1547538628:-1 chm1:+:1555768012:-1 chm1:+:1614658676:-1 chm1:+:1616363771:-1 chm1:+:1663837509:-1 chm1:+:1665203387:-1 chm1:+:1673085567:-1 chm1:+:1716055839:-1 chm1:+:1726475176:-1 chm1:+:1749924331:-1 chm1:+:1783858567:-1 chm1:+:1791150149:-1 chm1:+:1794598701:-1 chm1:+:1799606943:-1 chm1:+:1806423167:-1 chm1:+:1836678560:-1 chm1:+:1838029040:-1 chm1:+:1845535153:-1 chm1:+:1853210792:-1 chm1:+:1903032496:-1 chm1:+:1911553282:-1 chm1:+:1941391092:-1 chm1:+:2036724415:-1 chm1:+:2062591339:-1 chm1:+:2104315545:-1 chm1:+:2132668208:-1 chm1:+:2155981345:-1 chm1:+:2157005515:-1 chm1:+:2179693245:-1 chm1:+:2183594598:-1 chm1:+:2219571821:-1 chm1:+:2237330621:-1 chm1:+:2249224283:-1 chm1:+:2280050383:-1 chm1:+:2291132327:-1 chm1:+:2376328642:-1 chm1:+:2401347116:-1 chm1:+:2413387366:-1 chm1:+:2479428326:-1 chm1:+:2556961483:-1 chm1:+:2562833221:-1 chm1:+:2577900834:-1 chm1:+:2601674976:-1 chm1:+:2609357625:-1 chm1:+:2649158400:-1 chm1:+:2657410024:-1 chm1:+:2660620090:-1 chm1:+:2678644359:-1 chm1:+:2776205598:-1 chm1:+:2796660761:-1 chm1:+:2826110466:-1 chm1:+:2868776843:-1 chm1:+:2877653523:-1 chm1:+:2895245159:-1 chm1:+:2907656188:-1 chm1:+:2950848651:-1 chm1:+:2967325891:-1 chm1:+:3099068515:-1 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTT chm1:+:176438050:-1 chm1:+:313171596:-1 chm1:+:703948949:-1 chm1:+:768186583:-1 chm1:+:1352916302:-1 chm1:+:1359377292:-1 chm1:+:1562900463:-1 chm1:+:1573697436:-1 chm1:+:1615810739:-1 chm1:+:1637857684:-1 chm1:+:1711463839:-1 chm1:+:1744246477:-1 chm1:+:2363448571:-1 chm1:+:2401730963:-1 chm1:+:2596078701:-1 chm1:+:2652678960:-1 chm1:+:2954078791:-1 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTT chm1:+:35607123:26 chm1:+:146697410:-1 chm1:+:161374060:25 chm1:+:161380347:22 chm1:+:246753432:33 chm1:+:477921120:29 chm1:+:1038202091:24 chm1:+:1538875999:-1 chm1:+:1677731979:24 chm1:+:1841397228:31 chm1:+:1859713525:32 chm1:+:1883684846:28 chm1:+:1890747895:30 chm1:+:2194558255:32 chm1:+:2438573029:30 chm1:+:2528739307:31 chm1:+:2625907967:39 chm1:+:2855947401:28 chm1:+:3017046380:30 chm1:+:3017051706:31 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTT chm1:+:35612259:33 chm1:+:105002492:-1 chm1:+:146697440:-1 chm1:+:181448944:-1 chm1:+:218922396:-1 chm1:+:1960378784:-1 chm1:+:2261517361:-1 chm1:+:2261524164:-1 chm1:+:2714236572:23 chm1:+:2772039917:-1 chm1:+:2854175520:-1 chm1:+:3027297960:-1 +AAAAAGTCATAATAATAACATCAACCCCCTTCGACCTAAACTACTTGTGTTATCTGTAAATCCAGACACTGTATGAAAGCATTGTAAAACTTTTTTGTTCTTTTAGCTGATGGCATGTAGCCCCCACGTCACGTTTCCCAAGCTTGCTTGATGTATCACGACCCTTTCACGTGGACCCCTAAGTTCGTAAGCCTTTAAAA chm1:+:698914107:25 +AAAAAGTCATAATAATAACATCAACCCCCTTCGACCTAAACTACTTGTGTTATCTGTAAATCCAGACACTGTATGAAAGCATTGTAAAACTTTTTTGTTCTTTTAGCTGATGGCATGTAGCCCCCACGTCACGTTTCCCAAGCTTGCTTGATGTATCACGACCCTTTCACGTGGACCCCTAAGTTCGTAAGCCTTTAAAA chm1:+:1183785127:-1 chm1:+:1234494153:26 chm1:+:1297906714:21 chm1:+:1479200115:24 chm1:+:1666105920:-1 chm1:+:2430615704:-1 chm1:+:2502860584:22 chm1:+:2742376920:26 chm1:+:2934084328:14 +AGAAAGGAGAAATTTGCCTTCGAACCCGGAGGCGGAGGTTGCACGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAAGAGGAAATGACGAGAAGTCCAACAGGTTAGAGAAGTCGGTGGTATTCTGACCATAGATAATAGAAATTGCAGTCATTGAATCATA chm1:+:1619192:-1 chm1:+:1666645:-1 chm1:+:64181596:-1 chm1:+:65905543:-1 chm1:+:82734292:-1 chm1:+:157933389:-1 chm1:+:160233287:-1 chm1:+:179015989:-1 chm1:+:222624131:-1 chm1:+:224703875:-1 chm1:+:243649362:-1 chm1:+:259046944:-1 chm1:+:260134590:-1 chm1:+:288851989:-1 chm1:+:291791548:-1 chm1:+:295173390:-1 chm1:+:314923426:-1 chm1:+:335656664:-1 chm1:+:336488509:-1 chm1:+:357769760:-1 chm1:+:384572102:-1 chm1:+:411217155:-1 chm1:+:540205706:-1 chm1:+:540458678:-1 chm1:+:629030186:-1 chm1:+:745392005:-1 chm1:+:747311480:-1 chm1:+:747775446:-1 chm1:+:790321089:-1 chm1:+:887453366:-1 chm1:+:896163530:-1 chm1:+:903985076:-1 chm1:+:958014025:-1 chm1:+:1041627999:-1 chm1:+:1067935709:-1 chm1:+:1080846338:-1 chm1:+:1227217811:-1 chm1:+:1236392529:-1 chm1:+:1296616462:-1 chm1:+:1302551116:-1 chm1:+:1309523610:-1 chm1:+:1325753518:-1 chm1:+:1366975357:-1 chm1:+:1473285932:-1 chm1:+:1491447015:-1 chm1:+:1627050525:-1 chm1:+:1653718085:-1 chm1:+:1662441023:-1 chm1:+:1694476452:-1 chm1:+:1697842105:-1 chm1:+:1699071229:-1 chm1:+:1756529715:-1 chm1:+:1757048922:-1 chm1:+:1775575920:-1 chm1:+:1863249291:-1 chm1:+:1887804095:-1 chm1:+:1923321810:-1 chm1:+:1944509647:-1 chm1:+:1962071369:-1 chm1:+:2005553839:-1 chm1:+:2069726453:-1 chm1:+:2072104425:-1 chm1:+:2072487406:-1 chm1:+:2105861402:-1 chm1:+:2162870795:-1 chm1:+:2255282897:-1 chm1:+:2283747149:-1 chm1:+:2290750687:-1 chm1:+:2359547616:-1 chm1:+:2384780689:-1 chm1:+:2389202812:-1 chm1:+:2407560168:-1 chm1:+:2415217836:-1 chm1:+:2430822723:-1 chm1:+:2433467809:-1 chm1:+:2440945660:-1 chm1:+:2478486260:-1 chm1:+:2516288529:-1 chm1:+:2521397991:-1 chm1:+:2573999921:-1 chm1:+:2666983405:-1 chm1:+:2708898265:-1 chm1:+:2712839800:-1 chm1:+:2715118135:-1 chm1:+:2781085877:-1 chm1:+:2829352204:-1 chm1:+:2846037047:-1 chm1:+:2861235968:-1 chm1:+:2935299881:-1 chm1:+:2935961531:-1 chm1:+:3064650964:-1 +AGAAAGGAGAAATTTGCCTTCGAACCCGGAGGCGGAGGTTGCACGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAAGAGGAAATGACGAGAAGTCCAACAGGTTAGAGAAGTCGGTGGTATTCTGACCATAGATAATAGAAATTGCAGTCATTGAATCATA chm1:+:652747956:12 chm1:+:1512796999:-1 chm1:+:2158913592:-1 +AGAAAGGAGAAATTTGCCTTCGAACCCGGAGGCGGAGGTTGCACGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAAGAGGAAATGACGAGAAGTCCAACAGGTTAGAGAAGTCGGTGGTATTCTGACCATAGATAATAGAAATTGCAGTCATTGAATCATA chm1:+:987375083:-1 chm1:+:1570610204:-1 chm1:+:2142803124:-1 +AGAAAGGAGAAATTTGCCTTCGAACCCGGAGGCGGAGGTTGCACGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAAGAGGAAATGACGAGAAGTCCAACAGGTTAGAGAAGTCGGTGGTATTCTGACCATAGATAATAGAAATTGCAGTCATTGAATCATA chm1:+:618182258:-1 chm1:+:652747960:12 chm1:+:1970205771:-1 chm1:+:2883072644:-1 chm1:+:3003865869:-1 +TATGATTCAATGACTGCAATTTCTATTATCTATGGTCAGAATACCACCGACTTCTCTAACCTGTTGGACTTCTCGTCATTTCCTCTTTTTTTTTTTTTGAGACAGAGTCTTACTCTGTCACCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACGTGCAACCTCCGCCTCCGGGTTCGAAGGCAAATTTCTCCTTTCT chm1:+:52185878:-1 chm1:+:60628813:-1 chm1:+:230357653:-1 chm1:+:247213658:-1 chm1:+:273952763:-1 chm1:+:353276773:-1 chm1:+:380368906:-1 chm1:+:489734565:-1 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chm1:+:2880733959:-1 chm1:+:2893588738:-1 chm1:+:2906290989:-1 +TATGATTCAATGACTGCAATTTCTATTATCTATGGTCAGAATACCACCGACTTCTCTAACCTGTTGGACTTCTCGTCATTTCCTCTTTTTTTTTTTTTGAGACAGAGTCTTACTCTGTCACCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACGTGCAACCTCCGCCTCCGGGTTCGAAGGCAAATTTCTCCTTTCT chm1:+:69002660:-1 chm1:+:182537897:-1 chm1:+:474782039:-1 chm1:+:1019498864:-1 chm1:+:1083409983:-1 chm1:+:1095038078:-1 chm1:+:2146853229:-1 chm1:+:2267583826:-1 +TATGATTCAATGACTGCAATTTCTATTATCTATGGTCAGAATACCACCGACTTCTCTAACCTGTTGGACTTCTCGTCATTTCCTCTTTTTTTTTTTTTGAGACAGAGTCTTACTCTGTCACCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACGTGCAACCTCCGCCTCCGGGTTCGAAGGCAAATTTCTCCTTTCT chm1:+:1026669358:-1 +TATGATTCAATGACTGCAATTTCTATTATCTATGGTCAGAATACCACCGACTTCTCTAACCTGTTGGACTTCTCGTCATTTCCTCTTTTTTTTTTTTTGAGACAGAGTCTTACTCTGTCACCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACGTGCAACCTCCGCCTCCGGGTTCGAAGGCAAATTTCTCCTTTCT chm1:+:221484602:-1 chm1:+:232056533:-1 chm1:+:311378583:-1 chm1:+:374065360:-1 chm1:+:1286164720:-1 chm1:+:1298460812:-1 chm1:+:1402734570:-1 chm1:+:1694614340:-1 chm1:+:1751977972:-1 chm1:+:1934292926:-1 chm1:+:1957922267:-1 chm1:+:1993012956:-1 chm1:+:1996748309:-1 chm1:+:2429644595:-1 chm1:+:2539089152:-1 chm1:+:2572461667:-1 chm1:+:2675648208:-1 chm1:+:2722496305:-1 chm1:+:2798590072:-1 chm1:+:2952632514:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATA chm1:+:439868840:-1 chm1:+:672058388:-1 chm1:+:2024006907:-1 chm1:+:2150459484:-1 chm1:+:2385600511:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATA chm1:+:324388916:-1 chm1:+:443070768:-1 chm1:+:932027630:-1 chm1:+:1252672952:-1 chm1:+:1740140011:-1 chm1:+:2533754325:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATA chm1:+:82053461:-1 chm1:+:250898464:-1 chm1:+:324285609:-1 chm1:+:683769357:-1 chm1:+:809977586:-1 chm1:+:826750215:-1 chm1:+:1424119638:-1 chm1:+:1574683936:-1 chm1:+:1784049212:-1 chm1:+:1835634532:-1 chm1:+:1963623988:-1 chm1:+:2084433077:-1 chm1:+:2139982115:-1 chm1:+:2566724809:-1 chm1:+:2572990816:-1 chm1:+:2576599888:-1 chm1:+:2636482619:-1 chm1:+:2673338264:-1 chm1:+:2682034775:-1 chm1:+:2855722437:-1 chm1:+:3031530530:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATA chm1:+:115643484:-1 chm1:+:233896749:-1 chm1:+:333753002:-1 chm1:+:475755220:-1 chm1:+:602665247:-1 chm1:+:608302797:-1 chm1:+:661582543:-1 chm1:+:952075636:-1 chm1:+:1129908991:-1 chm1:+:1248698726:-1 chm1:+:1280288951:-1 chm1:+:2009231361:-1 chm1:+:2529305170:-1 chm1:+:2630108308:-1 chm1:+:2956413810:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATA chm1:+:83875171:-1 chm1:+:169816426:-1 chm1:+:965737403:-1 chm1:+:981992418:-1 chm1:+:1310152319:-1 chm1:+:1398166205:-1 chm1:+:1502112202:-1 chm1:+:1870865867:-1 chm1:+:1900510811:-1 chm1:+:2028122874:-1 chm1:+:2032011885:-1 chm1:+:2117061897:-1 chm1:+:2127987792:-1 chm1:+:2167940321:-1 chm1:+:2483227814:-1 chm1:+:2637103946:-1 chm1:+:2740354438:-1 +TATCCCAAAATGAAATAAGACAATCTACAGATGTATAAGACATTGTCCAAACATTCACTAATAGTGAACTCCTGTCATTTTCAGGTTATGTTTCTGAAAAACTTGAATTCTAAGCAGCCAGTTTTTTGGCCTCTAAGTTGCCAGGTTTGTTTTGTTTGTTTGTTTGTTTTTTTAATAAGGTGGTGGGTGTAGGGGTCTAC chm1:+:41035140:-1 chm1:+:198297408:-1 chm1:+:910928567:-1 chm1:+:2680788579:-1 +TATCCCAAAATGAAATAAGACAATCTACAGATGTATAAGACATTGTCCAAACATTCACTAATAGTGAACTCCTGTCATTTTCAGGTTATGTTTCTGAAAAACTTGAATTCTAAGCAGCCAGTTTTTTGGCCTCTAAGTTGCCAGGTTTGTTTTGTTTGTTTGTTTGTTTTTTTAATAAGGTGGTGGGTGTAGGGGTCTAC chm1:+:218811472:-1 chm1:+:403113673:-1 chm1:+:570420341:-1 chm1:+:1219331877:-1 chm1:+:2155051050:10 +TATCCCAAAATGAAATAAGACAATCTACAGATGTATAAGACATTGTCCAAACATTCACTAATAGTGAACTCCTGTCATTTTCAGGTTATGTTTCTGAAAAACTTGAATTCTAAGCAGCCAGTTTTTTGGCCTCTAAGTTGCCAGGTTTGTTTTGTTTGTTTGTTTGTTTTTTTAATAAGGTGGTGGGTGTAGGGGTCTAC chm1:+:2155051046:10 +TATCCCAAAATGAAATAAGACAATCTACAGATGTATAAGACATTGTCCAAACATTCACTAATAGTGAACTCCTGTCATTTTCAGGTTATGTTTCTGAAAAACTTGAATTCTAAGCAGCCAGTTTTTTGGCCTCTAAGTTGCCAGGTTTGTTTTGTTTGTTTGTTTGTTTTTTTAATAAGGTGGTGGGTGTAGGGGTCTAC chm1:+:1187889153:-1 +TATCCCAAAATGAAATAAGACAATCTACAGATGTATAAGACATTGTCCAAACATTCACTAATAGTGAACTCCTGTCATTTTCAGGTTATGTTTCTGAAAAACTTGAATTCTAAGCAGCCAGTTTTTTGGCCTCTAAGTTGCCAGGTTTGTTTTGTTTGTTTGTTTGTTTTTTTAATAAGGTGGTGGGTGTAGGGGTCTAC chm1:+:2155051051:10 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCT chm1:+:40473003:-1 chm1:+:960332189:-1 chm1:+:2065892864:-1 chm1:+:2885127001:-1 chm1:+:3008404765:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCT chm1:+:1372626462:-1 chm1:+:1845342981:-1 chm1:+:1905880970:-1 chm1:+:1932840537:-1 chm1:+:2083453821:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCT chm1:+:210444702:-1 chm1:+:469527216:-1 chm1:+:767805942:-1 chm1:+:1890867956:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCT chm1:+:50313589:-1 chm1:+:153355895:-1 chm1:+:182662408:-1 chm1:+:365031495:-1 chm1:+:386237378:-1 chm1:+:500886122:-1 chm1:+:531353526:-1 chm1:+:723422995:-1 chm1:+:900703070:-1 chm1:+:1134494782:-1 chm1:+:1165384007:-1 chm1:+:1238707037:-1 chm1:+:1374970269:-1 chm1:+:1382343354:-1 chm1:+:1419516037:-1 chm1:+:1544702194:-1 chm1:+:1644388680:-1 chm1:+:1901012060:-1 chm1:+:2035374389:-1 chm1:+:2507806701:-1 chm1:+:2921425054:-1 chm1:+:2995234052:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCT chm1:+:348961632:-1 chm1:+:439138551:-1 chm1:+:1937778850:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCT chm1:+:62935394:-1 chm1:+:106645155:-1 chm1:+:199713471:-1 chm1:+:533898590:-1 chm1:+:632787532:-1 chm1:+:848592737:-1 chm1:+:1406035030:-1 chm1:+:1835919261:-1 chm1:+:1866457934:-1 chm1:+:1997292125:-1 chm1:+:2368162477:-1 chm1:+:2469873233:-1 chm1:+:2623517316:-1 chm1:+:2739200585:-1 chm1:+:2944747185:-1 chm1:+:2964711482:-1 chm1:+:3025433751:-1 chm1:+:3039103429:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCT chm1:+:17244188:-1 chm1:+:76600372:-1 chm1:+:380746224:-1 chm1:+:383906455:-1 chm1:+:427800597:-1 chm1:+:519687598:-1 chm1:+:599886668:-1 chm1:+:721423017:-1 chm1:+:1054957399:-1 chm1:+:1077173666:-1 chm1:+:1161517524:-1 chm1:+:1253408029:-1 chm1:+:1834034242:-1 chm1:+:1883838115:-1 chm1:+:2016302516:-1 chm1:+:2196168879:-1 chm1:+:2221643817:-1 chm1:+:2278738241:-1 chm1:+:2634991958:-1 chm1:+:2636937843:-1 chm1:+:2648210238:-1 chm1:+:2815630638:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCT chm1:+:85452360:-1 chm1:+:187104591:-1 chm1:+:209355257:-1 chm1:+:364013775:-1 chm1:+:399339381:-1 chm1:+:533128384:-1 chm1:+:596498141:-1 chm1:+:630724396:-1 chm1:+:793854041:-1 chm1:+:826139151:-1 chm1:+:1051515979:-1 chm1:+:1287488211:-1 chm1:+:1386553845:-1 chm1:+:1462423344:-1 chm1:+:2120316157:-1 chm1:+:2335656804:-1 chm1:+:2464878433:-1 chm1:+:2549778966:-1 chm1:+:2737615729:-1 chm1:+:2864671831:-1 +AGAAGTATTCCCTTTTTCACCACAATCCAATGCCAACAACTATTATTTTTTTGATTATGGCCATTTCTTGCAGAGTGAGGTGGTATCACATTGTGGTTTTGATTTGCATTTCCTTGATGTTAGTCCCATGTCCGGGCTATTTAAAAAAAAAAAATCCATAGACAGGGCTTTTCATGATGCCCTAGGCTGATCTCAAACTC chm1:+:795699795:-1 chm1:+:2160130119:-1 +AGAAGTATTCCCTTTTTCACCACAATCCAATGCCAACAACTATTATTTTTTTGATTATGGCCATTTCTTGCAGAGTGAGGTGGTATCACATTGTGGTTTTGATTTGCATTTCCTTGATGTTAGTCCCATGTCCGGGCTATTTAAAAAAAAAAAATCCATAGACAGGGCTTTTCATGATGCCCTAGGCTGATCTCAAACTC chm1:+:549656605:11 +AGAAGTATTCCCTTTTTCACCACAATCCAATGCCAACAACTATTATTTTTTTGATTATGGCCATTTCTTGCAGAGTGAGGTGGTATCACATTGTGGTTTTGATTTGCATTTCCTTGATGTTAGTCCCATGTCCGGGCTATTTAAAAAAAAAAAATCCATAGACAGGGCTTTTCATGATGCCCTAGGCTGATCTCAAACTC chm1:+:1455079326:-1 chm1:+:2611194658:-1 +AGAAGTATTCCCTTTTTCACCACAATCCAATGCCAACAACTATTATTTTTTTGATTATGGCCATTTCTTGCAGAGTGAGGTGGTATCACATTGTGGTTTTGATTTGCATTTCCTTGATGTTAGTCCCATGTCCGGGCTATTTAAAAAAAAAAAATCCATAGACAGGGCTTTTCATGATGCCCTAGGCTGATCTCAAACTC chm1:+:2886151782:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCC chm1:+:325535486:-1 chm1:+:1040417486:-1 chm1:+:1343465041:-1 chm1:+:1880966881:-1 chm1:+:2075559995:-1 chm1:+:2108569615:-1 chm1:+:2662289655:-1 chm1:+:2861677255:-1 chm1:+:3039349375:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCC chm1:+:348243848:-1 chm1:+:424063375:-1 chm1:+:768738082:-1 chm1:+:1492706684:-1 chm1:+:1636289525:-1 chm1:+:2988460877:-1 chm1:+:3021518568:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCC chm1:+:4304819:-1 chm1:+:50850677:-1 chm1:+:63388801:-1 chm1:+:118306969:-1 chm1:+:120234089:-1 chm1:+:189131780:-1 chm1:+:189414678:-1 chm1:+:223540251:-1 chm1:+:270056200:-1 chm1:+:280652923:-1 chm1:+:300257499:-1 chm1:+:316095226:-1 chm1:+:416613102:-1 chm1:+:421562517:-1 chm1:+:430898131:-1 chm1:+:451654383:-1 chm1:+:496132434:-1 chm1:+:515802729:-1 chm1:+:532631821:-1 chm1:+:546960301:-1 chm1:+:582243779:-1 chm1:+:613514222:-1 chm1:+:649515909:-1 chm1:+:679071687:-1 chm1:+:695470924:-1 chm1:+:776554600:-1 chm1:+:778948579:-1 chm1:+:788521485:-1 chm1:+:812654111:-1 chm1:+:822970996:-1 chm1:+:848878278:-1 chm1:+:921591068:-1 chm1:+:941966254:-1 chm1:+:947232842:-1 chm1:+:959333043:-1 chm1:+:969086728:-1 chm1:+:974789374:-1 chm1:+:984181747:-1 chm1:+:986012006:-1 chm1:+:990507504:-1 chm1:+:1002607440:-1 chm1:+:1078423236:-1 chm1:+:1082614248:-1 chm1:+:1087586471:-1 chm1:+:1171592804:-1 chm1:+:1185877139:-1 chm1:+:1209576214:-1 chm1:+:1234284098:-1 chm1:+:1245082743:-1 chm1:+:1261097771:-1 chm1:+:1276277564:-1 chm1:+:1283076620:-1 chm1:+:1413975344:-1 chm1:+:1557431258:-1 chm1:+:1616665665:-1 chm1:+:1633623745:-1 chm1:+:1658040045:-1 chm1:+:1716697520:-1 chm1:+:1855237022:-1 chm1:+:1857841880:-1 chm1:+:1924994697:-1 chm1:+:1941629699:-1 chm1:+:2035095900:-1 chm1:+:2041009897:-1 chm1:+:2042169683:-1 chm1:+:2055803377:-1 chm1:+:2062709188:-1 chm1:+:2182288056:-1 chm1:+:2194431987:-1 chm1:+:2268493970:-1 chm1:+:2272079742:-1 chm1:+:2293886426:-1 chm1:+:2380019125:-1 chm1:+:2462999251:-1 chm1:+:2469259239:-1 chm1:+:2570370244:-1 chm1:+:2639852942:-1 chm1:+:2742341135:-1 chm1:+:2754864697:-1 chm1:+:2770614782:-1 chm1:+:2902314296:-1 chm1:+:2907579111:-1 chm1:+:2913612207:-1 chm1:+:2914608501:-1 chm1:+:2938870364:-1 chm1:+:2947014555:-1 chm1:+:2956129161:-1 chm1:+:2962480993:-1 chm1:+:2970785479:-1 chm1:+:3003269220:-1 chm1:+:3026403571:-1 chm1:+:3031342713:-1 chm1:+:3040246876:-1 chm1:+:3050934554:-1 chm1:+:3051679873:-1 chm1:+:3060769218:-1 chm1:+:3095736564:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCC chm1:+:225220157:-1 chm1:+:262629548:-1 chm1:+:390552886:-1 chm1:+:475508707:-1 chm1:+:548511216:-1 chm1:+:632046665:-1 chm1:+:647562908:-1 chm1:+:767130794:-1 chm1:+:811092970:-1 chm1:+:1115893657:-1 chm1:+:1376025331:-1 chm1:+:1586448231:-1 chm1:+:1739269765:-1 chm1:+:1743422905:-1 chm1:+:1771995817:-1 chm1:+:2138111869:-1 chm1:+:2242469744:-1 chm1:+:2496020811:-1 chm1:+:2615696593:-1 chm1:+:2666534234:-1 chm1:+:2694815040:-1 chm1:+:2900821820:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCC chm1:+:1455116817:-1 chm1:+:2161435371:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCC chm1:+:1073463448:-1 chm1:+:1352661161:-1 chm1:+:2713365077:-1 chm1:+:2732197870:-1 chm1:+:2762264248:-1 chm1:+:2821164457:39 chm1:+:2897309174:-1 chm1:+:2922346337:-1 +GGAGTGTGAACTTTGTCAACCCATTGTGGAAAGCAGTGTGGTGGTCCCTCAAAGGAACTAAAAACAGAACCTCCATTCGACCCAGCAGGCCCATTACTGGGGTATATGCCTAAAGGAATATAAATTGCTCTTACCGAATAAAAGACAGATACATCTATACTGTAATTGCAGCACTATTCACAATAGCCAAAAGACATGGA chm1:+:59767836:-1 chm1:+:408508188:-1 chm1:+:764023226:-1 chm1:+:803490586:-1 chm1:+:979433395:-1 chm1:+:1138827084:-1 chm1:+:1456402306:-1 chm1:+:1571247064:-1 chm1:+:1629140660:-1 chm1:+:2168369656:-1 chm1:+:2176237238:-1 chm1:+:2238712019:-1 chm1:+:2430309510:-1 chm1:+:2534552914:-1 chm1:+:2642714958:-1 chm1:+:2689298279:-1 chm1:+:2943560079:-1 chm1:+:2960827482:-1 chm1:+:3055104441:-1 +GGAGTGTGAACTTTGTCAACCCATTGTGGAAAGCAGTGTGGTGGTCCCTCAAAGGAACTAAAAACAGAACCTCCATTCGACCCAGCAGGCCCATTACTGGGGTATATGCCTAAAGGAATATAAATTGCTCTTACCGAATAAAAGACAGATACATCTATACTGTAATTGCAGCACTATTCACAATAGCCAAAAGACATGGA chm1:+:390170216:-1 chm1:+:574934505:-1 chm1:+:588309386:-1 chm1:+:597261470:-1 chm1:+:674508992:-1 chm1:+:680798257:-1 chm1:+:894100151:13 chm1:+:973208710:39 chm1:+:1108581292:-1 chm1:+:1149088641:-1 chm1:+:1410840405:37 chm1:+:1507485666:-1 chm1:+:1551092540:-1 chm1:+:1856292355:-1 chm1:+:2022019084:-1 chm1:+:2713448853:-1 +GGAGTGTGAACTTTGTCAACCCATTGTGGAAAGCAGTGTGGTGGTCCCTCAAAGGAACTAAAAACAGAACCTCCATTCGACCCAGCAGGCCCATTACTGGGGTATATGCCTAAAGGAATATAAATTGCTCTTACCGAATAAAAGACAGATACATCTATACTGTAATTGCAGCACTATTCACAATAGCCAAAAGACATGGA chm1:+:153026708:-1 chm1:+:232111078:-1 chm1:+:894100152:13 chm1:+:1041683620:-1 chm1:+:1174298689:-1 chm1:+:1237329292:-1 chm1:+:2114796535:-1 +GGAGTGTGAACTTTGTCAACCCATTGTGGAAAGCAGTGTGGTGGTCCCTCAAAGGAACTAAAAACAGAACCTCCATTCGACCCAGCAGGCCCATTACTGGGGTATATGCCTAAAGGAATATAAATTGCTCTTACCGAATAAAAGACAGATACATCTATACTGTAATTGCAGCACTATTCACAATAGCCAAAAGACATGGA chm1:+:894100153:13 chm1:+:2990760319:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAG chm1:+:1206936806:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAG chm1:+:308345391:-1 chm1:+:518216569:-1 chm1:+:613999696:-1 chm1:+:1202062502:-1 chm1:+:1463069745:-1 chm1:+:1892487580:-1 chm1:+:1939562812:-1 chm1:+:2234663046:-1 chm1:+:2336840291:-1 chm1:+:2382518867:-1 chm1:+:2425803528:-1 chm1:+:2429168951:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAG chm1:+:1710747459:-1 chm1:+:2333456015:-1 chm1:+:2507091790:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAG chm1:+:2912783407:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAG chm1:+:219170181:-1 chm1:+:275935767:-1 chm1:+:315203247:-1 chm1:+:548816613:-1 chm1:+:598545035:-1 chm1:+:1074469530:-1 chm1:+:1271042662:-1 chm1:+:1274378640:-1 chm1:+:1332575316:-1 chm1:+:1513715933:-1 chm1:+:1730162314:-1 chm1:+:1742815461:-1 chm1:+:2135889442:-1 chm1:+:2423394583:-1 chm1:+:2515024067:-1 chm1:+:2819006419:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAG chm1:+:314850291:-1 chm1:+:531608689:-1 chm1:+:893809612:-1 chm1:+:959620729:-1 chm1:+:1135578184:-1 chm1:+:1759161987:-1 chm1:+:2060171245:-1 chm1:+:3000648827:-1 +CTAAGATATGGGGGGAAGGGACACACAGCTTCCATGCCCCTCTCTGGGAACCTCCATTGTTCAGCCTATCAGGGAAGCTCTCTGAACCCGTCCTCTTAGATTTTTAAGGAGGGCTTCATTACACTAGGCATGATTAACCATGTAGAAATGTGACTGGACCCAAAGCACATGATCGAAATCCAGCAAAGCCTGTCTGCTCA chm1:+:229007732:10 chm1:+:410315824:-1 chm1:+:421342243:-1 chm1:+:779722375:-1 chm1:+:1019656529:-1 chm1:+:1151125484:-1 chm1:+:1556550680:-1 +CTAAGATATGGGGGGAAGGGACACACAGCTTCCATGCCCCTCTCTGGGAACCTCCATTGTTCAGCCTATCAGGGAAGCTCTCTGAACCCGTCCTCTTAGATTTTTAAGGAGGGCTTCATTACACTAGGCATGATTAACCATGTAGAAATGTGACTGGACCCAAAGCACATGATCGAAATCCAGCAAAGCCTGTCTGCTCA chm1:+:229007734:10 +GTGGGGCTGTCTGACTGTCTGTCTGTCTGGTGGATGACTCTCTCTTTCCACAGTAGGGAGTAATGCTGTAGTGACAGTGTGGCTGAATCTAGAACTTGGGGAGGTGTCTGGAGGATGAGGGCCTGTGGAAAGTGGGCTGAGTGGCCGTCCCTAAGCTCCAGCCCTCTACCCCTTTGTTTCCCCCAGTGGCTACATCTTTG chm1:+:2751234707:9 +GTGGGGCTGTCTGACTGTCTGTCTGTCTGGTGGATGACTCTCTCTTTCCACAGTAGGGAGTAATGCTGTAGTGACAGTGTGGCTGAATCTAGAACTTGGGGAGGTGTCTGGAGGATGAGGGCCTGTGGAAAGTGGGCTGAGTGGCCGTCCCTAAGCTCCAGCCCTCTACCCCTTTGTTTCCCCCAGTGGCTACATCTTTG chm1:+:205444477:-1 +GTGGGGCTGTCTGACTGTCTGTCTGTCTGGTGGATGACTCTCTCTTTCCACAGTAGGGAGTAATGCTGTAGTGACAGTGTGGCTGAATCTAGAACTTGGGGAGGTGTCTGGAGGATGAGGGCCTGTGGAAAGTGGGCTGAGTGGCCGTCCCTAAGCTCCAGCCCTCTACCCCTTTGTTTCCCCCAGTGGCTACATCTTTG chm1:+:2751234706:9 +GTGGGGCTGTCTGACTGTCTGTCTGTCTGGTGGATGACTCTCTCTTTCCACAGTAGGGAGTAATGCTGTAGTGACAGTGTGGCTGAATCTAGAACTTGGGGAGGTGTCTGGAGGATGAGGGCCTGTGGAAAGTGGGCTGAGTGGCCGTCCCTAAGCTCCAGCCCTCTACCCCTTTGTTTCCCCCAGTGGCTACATCTTTG chm1:+:2751234704:9 +GTGGGGCTGTCTGACTGTCTGTCTGTCTGGTGGATGACTCTCTCTTTCCACAGTAGGGAGTAATGCTGTAGTGACAGTGTGGCTGAATCTAGAACTTGGGGAGGTGTCTGGAGGATGAGGGCCTGTGGAAAGTGGGCTGAGTGGCCGTCCCTAAGCTCCAGCCCTCTACCCCTTTGTTTCCCCCAGTGGCTACATCTTTG chm1:+:2693577109:-1 +GACATTTGAAAATGAGTTTCATCTTTAGCTCATCCTTTTACAAATTTCTAGTTCCTTGTGCATGATTGAAGTGTACACATTTTTAGTTAAATATAAGCATATAGAAGGCACAAGTTCAATATTTTTCATGATAAGGATGTGTAATTAAACTGGTTAGGAGACTCATCGACTAGAGGGGGACATAGGTGGCCCCAGGCTGT chm1:+:625914203:4 +TTCCAGACTGAGCTGGGGTCCATTGACACGGACTCCTCCCGACTCGTCAGGAGATACTTTGCCTCTCCAGTTTTGGTGTCTGAGTGATCATTCAACGGGTGCATATTAATGTTTAGTTTGTTTTATTTATTTATTTTGATGAGACAGTCTTGCTCTGTCACCCAGGCTGGGGGTGCAGTGTACGTACCTCAGCTCCACTG chm1:+:1041758466:-1 chm1:+:2080864474:-1 chm1:+:2883885207:15 +TTCCAGACTGAGCTGGGGTCCATTGACACGGACTCCTCCCGACTCGTCAGGAGATACTTTGCCTCTCCAGTTTTGGTGTCTGAGTGATCATTCAACGGGTGCATATTAATGTTTAGTTTGTTTTATTTATTTATTTTGATGAGACAGTCTTGCTCTGTCACCCAGGCTGGGGGTGCAGTGTACGTACCTCAGCTCCACTG chm1:+:2883885212:15 +TTCCAGACTGAGCTGGGGTCCATTGACACGGACTCCTCCCGACTCGTCAGGAGATACTTTGCCTCTCCAGTTTTGGTGTCTGAGTGATCATTCAACGGGTGCATATTAATGTTTAGTTTGTTTTATTTATTTATTTTGATGAGACAGTCTTGCTCTGTCACCCAGGCTGGGGGTGCAGTGTACGTACCTCAGCTCCACTG chm1:+:35551747:-1 chm1:+:53205122:-1 chm1:+:155587811:-1 chm1:+:162501751:-1 chm1:+:163874976:-1 chm1:+:181131243:-1 chm1:+:239412697:-1 chm1:+:240415049:-1 chm1:+:262980338:-1 chm1:+:311141121:-1 chm1:+:327000306:-1 chm1:+:335726001:-1 chm1:+:378057053:-1 chm1:+:398166750:-1 chm1:+:399083220:-1 chm1:+:432079885:-1 chm1:+:441173478:-1 chm1:+:444480031:-1 chm1:+:448689903:-1 chm1:+:676255018:-1 chm1:+:680041011:-1 chm1:+:684412895:-1 chm1:+:713467230:-1 chm1:+:868328409:-1 chm1:+:908715653:-1 chm1:+:960688458:-1 chm1:+:966091513:-1 chm1:+:973698532:-1 chm1:+:998728223:-1 chm1:+:1030885160:-1 chm1:+:1099095674:-1 chm1:+:1136911338:-1 chm1:+:1137601233:-1 chm1:+:1170501199:-1 chm1:+:1199517381:-1 chm1:+:1238732292:-1 chm1:+:1304136274:-1 chm1:+:1308990422:-1 chm1:+:1314634186:-1 chm1:+:1390804710:-1 chm1:+:1422096812:-1 chm1:+:1517933455:-1 chm1:+:1520407277:-1 chm1:+:1575343582:-1 chm1:+:1661353785:-1 chm1:+:1669878239:-1 chm1:+:1686824240:-1 chm1:+:1715946924:-1 chm1:+:1750973289:-1 chm1:+:1792568751:-1 chm1:+:1863749821:-1 chm1:+:1872027320:-1 chm1:+:1893476347:-1 chm1:+:1909749978:-1 chm1:+:1933345014:-1 chm1:+:2040747627:-1 chm1:+:2058960920:-1 chm1:+:2073846801:-1 chm1:+:2078953333:-1 chm1:+:2188627749:-1 chm1:+:2248147081:-1 chm1:+:2348992298:-1 chm1:+:2350436829:-1 chm1:+:2357343760:-1 chm1:+:2508270200:-1 chm1:+:2509653577:-1 chm1:+:2542763659:-1 chm1:+:2654021762:-1 chm1:+:2668767067:-1 chm1:+:2680593714:-1 chm1:+:2692855538:-1 chm1:+:2701833683:-1 chm1:+:2714357665:-1 chm1:+:2731040770:-1 chm1:+:2805031979:-1 chm1:+:2861117893:-1 chm1:+:2861503989:-1 chm1:+:2930684120:-1 chm1:+:2932676840:-1 chm1:+:2937915304:-1 chm1:+:2984768698:-1 +TTCCAGACTGAGCTGGGGTCCATTGACACGGACTCCTCCCGACTCGTCAGGAGATACTTTGCCTCTCCAGTTTTGGTGTCTGAGTGATCATTCAACGGGTGCATATTAATGTTTAGTTTGTTTTATTTATTTATTTTGATGAGACAGTCTTGCTCTGTCACCCAGGCTGGGGGTGCAGTGTACGTACCTCAGCTCCACTG chm1:+:646352493:-1 chm1:+:1367576829:-1 +TTCCAGACTGAGCTGGGGTCCATTGACACGGACTCCTCCCGACTCGTCAGGAGATACTTTGCCTCTCCAGTTTTGGTGTCTGAGTGATCATTCAACGGGTGCATATTAATGTTTAGTTTGTTTTATTTATTTATTTTGATGAGACAGTCTTGCTCTGTCACCCAGGCTGGGGGTGCAGTGTACGTACCTCAGCTCCACTG chm1:+:882301660:-1 chm1:+:882301838:-1 chm1:+:882301948:-1 chm1:+:1382325428:-1 chm1:+:1580462866:-1 chm1:+:1604645027:-1 chm1:+:2920959004:-1 +TTCCAGACTGAGCTGGGGTCCATTGACACGGACTCCTCCCGACTCGTCAGGAGATACTTTGCCTCTCCAGTTTTGGTGTCTGAGTGATCATTCAACGGGTGCATATTAATGTTTAGTTTGTTTTATTTATTTATTTTGATGAGACAGTCTTGCTCTGTCACCCAGGCTGGGGGTGCAGTGTACGTACCTCAGCTCCACTG chm1:+:394253425:-1 chm1:+:846956064:-1 chm1:+:1435465114:-1 chm1:+:2883885208:15 +CAGTGGAGCTGAGGTACGTACACTGCACCCCCAGCCTGGGTGACAGAGCAAGACTGTCTCATCAAAATAAATAAATAAAACAAACTAAACATTAATATGCACCCGTTGAATGATCACTCAGACACCAAAACTGGAGAGGCAAAGTATCTCCTGACGAGTCGGGAGGAGTCCGTGTCAATGGACCCCAGCTCAGTCTGGAA chm1:+:44936997:-1 chm1:+:111700874:-1 chm1:+:226089912:-1 chm1:+:474994995:-1 chm1:+:633546913:-1 chm1:+:674569238:-1 chm1:+:771414626:-1 chm1:+:960384621:-1 chm1:+:1175211035:-1 chm1:+:1201583805:-1 chm1:+:1307796187:-1 chm1:+:1450191253:-1 chm1:+:1693580917:-1 chm1:+:1888101856:-1 chm1:+:2251352221:-1 chm1:+:2337197214:-1 chm1:+:2552305989:-1 chm1:+:2650428181:-1 chm1:+:2871810591:-1 chm1:+:2889001914:-1 +CAGTGGAGCTGAGGTACGTACACTGCACCCCCAGCCTGGGTGACAGAGCAAGACTGTCTCATCAAAATAAATAAATAAAACAAACTAAACATTAATATGCACCCGTTGAATGATCACTCAGACACCAAAACTGGAGAGGCAAAGTATCTCCTGACGAGTCGGGAGGAGTCCGTGTCAATGGACCCCAGCTCAGTCTGGAA chm1:+:4345137:-1 chm1:+:6254163:-1 chm1:+:7953461:-1 chm1:+:53120762:-1 chm1:+:56988247:-1 chm1:+:190989695:-1 chm1:+:203524051:-1 chm1:+:217685569:-1 chm1:+:229610753:-1 chm1:+:231268433:-1 chm1:+:242540852:-1 chm1:+:297097439:-1 chm1:+:390106009:-1 chm1:+:404921672:-1 chm1:+:422777920:-1 chm1:+:443458878:-1 chm1:+:531607053:-1 chm1:+:559212341:-1 chm1:+:613727735:-1 chm1:+:643827622:-1 chm1:+:730356075:-1 chm1:+:765732254:-1 chm1:+:905071406:-1 chm1:+:908571363:-1 chm1:+:911454649:-1 chm1:+:932624678:-1 chm1:+:954193958:-1 chm1:+:961166188:-1 chm1:+:990861975:-1 chm1:+:1022475742:-1 chm1:+:1029699017:-1 chm1:+:1146910185:-1 chm1:+:1155724819:-1 chm1:+:1171115131:-1 chm1:+:1212362713:-1 chm1:+:1232034767:-1 chm1:+:1259743387:-1 chm1:+:1308334767:-1 chm1:+:1308549024:-1 chm1:+:1331841497:-1 chm1:+:1344780948:-1 chm1:+:1355533644:-1 chm1:+:1357198915:-1 chm1:+:1360988530:-1 chm1:+:1372816434:-1 chm1:+:1377921080:-1 chm1:+:1390160621:-1 chm1:+:1394434112:-1 chm1:+:1406134529:-1 chm1:+:1501196255:-1 chm1:+:1507210196:-1 chm1:+:1518761115:-1 chm1:+:1551830109:-1 chm1:+:1855099813:-1 chm1:+:1856409707:-1 chm1:+:1934560671:-1 chm1:+:1957750083:-1 chm1:+:2024393688:-1 chm1:+:2118107356:-1 chm1:+:2126446267:-1 chm1:+:2130201704:-1 chm1:+:2147631075:-1 chm1:+:2170685911:-1 chm1:+:2174235225:-1 chm1:+:2181436971:-1 chm1:+:2184648926:-1 chm1:+:2270201671:-1 chm1:+:2380034283:-1 chm1:+:2527273742:-1 chm1:+:2533623316:-1 chm1:+:2562728102:-1 chm1:+:2606523276:-1 chm1:+:2643232153:-1 chm1:+:2648620678:-1 chm1:+:2669514390:-1 chm1:+:2704659317:-1 chm1:+:2721786562:-1 chm1:+:2739388819:-1 chm1:+:2752377206:-1 chm1:+:2968254923:-1 chm1:+:2969506447:-1 chm1:+:2991709007:-1 chm1:+:3013163538:-1 chm1:+:3023744562:-1 chm1:+:3042719016:-1 +CAGTGGAGCTGAGGTACGTACACTGCACCCCCAGCCTGGGTGACAGAGCAAGACTGTCTCATCAAAATAAATAAATAAAACAAACTAAACATTAATATGCACCCGTTGAATGATCACTCAGACACCAAAACTGGAGAGGCAAAGTATCTCCTGACGAGTCGGGAGGAGTCCGTGTCAATGGACCCCAGCTCAGTCTGGAA chm1:+:2349886236:-1 chm1:+:3050772725:35 +CAGTGGAGCTGAGGTACGTACACTGCACCCCCAGCCTGGGTGACAGAGCAAGACTGTCTCATCAAAATAAATAAATAAAACAAACTAAACATTAATATGCACCCGTTGAATGATCACTCAGACACCAAAACTGGAGAGGCAAAGTATCTCCTGACGAGTCGGGAGGAGTCCGTGTCAATGGACCCCAGCTCAGTCTGGAA chm1:+:227390529:-1 chm1:+:307620252:-1 chm1:+:1147297339:-1 chm1:+:1171732568:-1 chm1:+:1254411378:-1 chm1:+:1305599121:-1 chm1:+:1474088770:-1 chm1:+:2013099204:-1 chm1:+:2584797125:-1 chm1:+:2588620020:-1 chm1:+:2653129079:-1 chm1:+:2672679434:-1 chm1:+:2750870306:-1 chm1:+:2816473632:-1 chm1:+:3027921811:-1 +AAAGATAAAGGAATATGCACATCATTTTGCTAAGACACGAAATATCATCTGATTTTCAGCTATTTCACATTTCCTATTTTTTCCCCCTTACTACATTTTCAGCACTTTGGTTTTGAAAAGCAGAAAATGAACGTCAAACTGGTCTTAAACAGAAAAGAAGATTGAATTTATTGGTGCACTATAACTAAACTAATCCATGG chm1:+:170184723:-1 chm1:+:692439295:-1 chm1:+:1566240952:-1 chm1:+:1829008143:-1 chm1:+:1875047161:-1 chm1:+:2291170060:-1 chm1:+:2588173337:-1 +AAAGATAAAGGAATATGCACATCATTTTGCTAAGACACGAAATATCATCTGATTTTCAGCTATTTCACATTTCCTATTTTTTCCCCCTTACTACATTTTCAGCACTTTGGTTTTGAAAAGCAGAAAATGAACGTCAAACTGGTCTTAAACAGAAAAGAAGATTGAATTTATTGGTGCACTATAACTAAACTAATCCATGG chm1:+:110262246:-1 chm1:+:566637319:10 chm1:+:797595158:-1 chm1:+:2595482647:-1 +AAAGATAAAGGAATATGCACATCATTTTGCTAAGACACGAAATATCATCTGATTTTCAGCTATTTCACATTTCCTATTTTTTCCCCCTTACTACATTTTCAGCACTTTGGTTTTGAAAAGCAGAAAATGAACGTCAAACTGGTCTTAAACAGAAAAGAAGATTGAATTTATTGGTGCACTATAACTAAACTAATCCATGG chm1:+:566637318:10 +CCATGGATTAGTTTAGTTATAGTGCACCAATAAATTCAATCTTCTTTTCTGTTTAAGACCAGTTTGACGTTCATTTTCTGCTTTTCAAAACCAAAGTGCTGAAAATGTAGTAAGGGGGAAAAAATAGGAAATGTGAAATAGCTGAAAATCAGATGATATTTCGTGTCTTAGCAAAATGATGTGCATATTCCTTTATCTTT chm1:+:65380846:-1 chm1:+:1335498510:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGA chm1:+:227443614:-1 chm1:+:264856330:-1 chm1:+:431102775:-1 chm1:+:604422653:-1 chm1:+:864934598:-1 chm1:+:911897337:-1 chm1:+:932772802:-1 chm1:+:1081393075:-1 chm1:+:1134916286:-1 chm1:+:1166884345:-1 chm1:+:1329848632:-1 chm1:+:1468223115:-1 chm1:+:1487317224:-1 chm1:+:1549404483:-1 chm1:+:1660689317:-1 chm1:+:1992342045:-1 chm1:+:2107229113:-1 chm1:+:2190354200:-1 chm1:+:2253484554:-1 chm1:+:2430387962:-1 chm1:+:2910578102:-1 chm1:+:3012893413:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGA chm1:+:108415778:-1 chm1:+:560237832:-1 chm1:+:735756530:-1 chm1:+:746791307:-1 chm1:+:1767699650:-1 chm1:+:1944518187:-1 chm1:+:2025628962:-1 chm1:+:2336303218:-1 chm1:+:2553007236:-1 chm1:+:2648265947:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGA chm1:+:620102426:-1 chm1:+:1116035237:-1 chm1:+:1872940734:-1 chm1:+:2932715326:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGA chm1:+:97233203:-1 chm1:+:856768338:-1 chm1:+:1071353830:-1 chm1:+:1073500036:-1 chm1:+:1074691793:-1 chm1:+:1095387918:-1 chm1:+:1180281849:-1 chm1:+:1212538974:-1 chm1:+:1713623976:-1 chm1:+:1750310887:-1 chm1:+:1990198529:-1 chm1:+:2177201142:-1 chm1:+:2348275233:-1 chm1:+:2714611133:-1 chm1:+:2806522403:-1 chm1:+:2899833227:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGA chm1:+:395842285:-1 chm1:+:625277926:-1 chm1:+:680734927:-1 chm1:+:709692811:-1 chm1:+:781120726:-1 chm1:+:1034417726:-1 chm1:+:1181451625:-1 chm1:+:1248270337:-1 chm1:+:1663117989:-1 chm1:+:1741601737:-1 chm1:+:2132608143:-1 chm1:+:2245307905:-1 +TCATTATTTTTTCATTTTTATACAAGTTATAGAGTATCTACTTATTTTTCATTTAACATTATGCTATTAACAGGTTTTAAAGGTTAGGCCAGTAAGTCTTCCAGTGAAAAGGAAAAGACTGAACATGAAAAGGTTACGAGGCATTACTAATTGGATTGGAATGATGCCTACCAGGCAGCCCATGTCAGTTTTAAGGGAGC chm1:+:1173992119:11 chm1:+:2050637327:-1 +TCATTATTTTTTCATTTTTATACAAGTTATAGAGTATCTACTTATTTTTCATTTAACATTATGCTATTAACAGGTTTTAAAGGTTAGGCCAGTAAGTCTTCCAGTGAAAAGGAAAAGACTGAACATGAAAAGGTTACGAGGCATTACTAATTGGATTGGAATGATGCCTACCAGGCAGCCCATGTCAGTTTTAAGGGAGC chm1:+:1173992117:11 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTG chm1:+:49712056:-1 chm1:+:158578042:-1 chm1:+:287156056:-1 chm1:+:434067335:-1 chm1:+:517395473:-1 chm1:+:557927576:-1 chm1:+:715597709:-1 chm1:+:733252378:-1 chm1:+:794821022:-1 chm1:+:816312514:-1 chm1:+:1044208855:-1 chm1:+:1067526699:-1 chm1:+:1085683180:-1 chm1:+:1244796185:-1 chm1:+:1436093170:-1 chm1:+:1547294911:-1 chm1:+:1698150687:-1 chm1:+:1698347702:-1 chm1:+:2046610673:-1 chm1:+:2165436203:-1 chm1:+:2223852391:-1 chm1:+:2420255981:-1 chm1:+:2912172545:-1 chm1:+:2914680053:-1 chm1:+:2919913997:-1 chm1:+:3055673970:-1 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTG chm1:+:1226837356:-1 chm1:+:1331772770:-1 chm1:+:2414504680:-1 chm1:+:2584002070:-1 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTG chm1:+:231739879:-1 chm1:+:385650019:-1 chm1:+:821435292:-1 chm1:+:962181799:-1 chm1:+:1322063052:-1 chm1:+:2006545488:-1 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTG chm1:+:552401777:-1 chm1:+:885881564:-1 chm1:+:1029446525:-1 chm1:+:1182111224:-1 chm1:+:1419854872:-1 chm1:+:1775257939:-1 chm1:+:2518700283:-1 chm1:+:2920208179:-1 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTG chm1:+:193315912:-1 chm1:+:582717229:-1 chm1:+:586057981:-1 chm1:+:668841759:-1 chm1:+:952799460:-1 chm1:+:1190618489:-1 chm1:+:2427090330:-1 chm1:+:2491667028:-1 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTG chm1:+:85100520:-1 chm1:+:423107078:-1 chm1:+:640998908:-1 chm1:+:821054740:-1 chm1:+:889173699:-1 chm1:+:976552580:-1 chm1:+:993032498:-1 chm1:+:1034245296:-1 chm1:+:1309239683:-1 chm1:+:1999768113:-1 chm1:+:2037459166:-1 chm1:+:2461761349:-1 chm1:+:2729258658:-1 chm1:+:2860179496:-1 +CAGTGGTACTTGGGGTACTCCAAACTCGTGCACATTTTAAAGATAAGACTGGCCCTTGACCATCCTGGAGATAACCTATAAGTCCTTTGGAATACCTAGCCTGATACAAATGTCTTTGTGTATCTGGGTCTTGGGATATGCCAGATAGTTATGTCAAAACAATGTGGATTTATGGTGAATGCCTGTTTTTGTTTCACCTG chm1:+:816188505:-1 chm1:+:996831465:-1 chm1:+:1780080696:-1 chm1:+:2125035670:-1 +CAGTGGTACTTGGGGTACTCCAAACTCGTGCACATTTTAAAGATAAGACTGGCCCTTGACCATCCTGGAGATAACCTATAAGTCCTTTGGAATACCTAGCCTGATACAAATGTCTTTGTGTATCTGGGTCTTGGGATATGCCAGATAGTTATGTCAAAACAATGTGGATTTATGGTGAATGCCTGTTTTTGTTTCACCTG chm1:+:1567892834:-1 chm1:+:2379308496:-1 chm1:+:2492168888:-1 chm1:+:2759833710:13 +CAGTGGTACTTGGGGTACTCCAAACTCGTGCACATTTTAAAGATAAGACTGGCCCTTGACCATCCTGGAGATAACCTATAAGTCCTTTGGAATACCTAGCCTGATACAAATGTCTTTGTGTATCTGGGTCTTGGGATATGCCAGATAGTTATGTCAAAACAATGTGGATTTATGGTGAATGCCTGTTTTTGTTTCACCTG chm1:+:2759833711:13 +CAGTGGTACTTGGGGTACTCCAAACTCGTGCACATTTTAAAGATAAGACTGGCCCTTGACCATCCTGGAGATAACCTATAAGTCCTTTGGAATACCTAGCCTGATACAAATGTCTTTGTGTATCTGGGTCTTGGGATATGCCAGATAGTTATGTCAAAACAATGTGGATTTATGGTGAATGCCTGTTTTTGTTTCACCTG chm1:+:878092966:-1 +AAACCCAAAATGAATTCCCTAACATTTTCACCCTAAAAGCTGTAAGCCAGGCTCAGCAGGGATGTGTTTTCACTCTCAGGTAGAAAGATGTTAGGGATCTAGCACAACTTTCTTCCTCCCCAAATTCTCTTTCAGAACACTTCTGGGAGAACCTTCGAGCAAGGGTGAGGGCCTTCGCCAGCACCCAGCCAGCACCCATG chm1:+:590494382:-1 chm1:+:834637502:-1 chm1:+:1823012817:-1 chm1:+:2163077126:-1 chm1:+:2688767222:11 +AAACCCAAAATGAATTCCCTAACATTTTCACCCTAAAAGCTGTAAGCCAGGCTCAGCAGGGATGTGTTTTCACTCTCAGGTAGAAAGATGTTAGGGATCTAGCACAACTTTCTTCCTCCCCAAATTCTCTTTCAGAACACTTCTGGGAGAACCTTCGAGCAAGGGTGAGGGCCTTCGCCAGCACCCAGCCAGCACCCATG chm1:+:2688767223:11 +AAACCCAAAATGAATTCCCTAACATTTTCACCCTAAAAGCTGTAAGCCAGGCTCAGCAGGGATGTGTTTTCACTCTCAGGTAGAAAGATGTTAGGGATCTAGCACAACTTTCTTCCTCCCCAAATTCTCTTTCAGAACACTTCTGGGAGAACCTTCGAGCAAGGGTGAGGGCCTTCGCCAGCACCCAGCCAGCACCCATG chm1:+:54844690:-1 +CATGGGTGCTGGCTGGGTGCTGGCGAAGGCCCTCACCCTTGCTCGAAGGTTCTCCCAGAAGTGTTCTGAAAGAGAATTTGGGGAGGAAGAAAGTTGTGCTAGATCCCTAACATCTTTCTACCTGAGAGTGAAAACACATCCCTGCTGAGCCTGGCTTACAGCTTTTAGGGTGAAAATGTTAGGGAATTCATTTTGGGTTT chm1:+:2009554141:-1 +CATGGGTGCTGGCTGGGTGCTGGCGAAGGCCCTCACCCTTGCTCGAAGGTTCTCCCAGAAGTGTTCTGAAAGAGAATTTGGGGAGGAAGAAAGTTGTGCTAGATCCCTAACATCTTTCTACCTGAGAGTGAAAACACATCCCTGCTGAGCCTGGCTTACAGCTTTTAGGGTGAAAATGTTAGGGAATTCATTTTGGGTTT chm1:+:228927789:-1 +ATTTCCAGCTAACAACTTTTTTGTGTATGGTGTAAGGACAAGGGCCCTGTTTCAATATTTTGCATGTAGATATCCAGTTTTCCCAACACCATTTATTAAAGAGAACTTTATTTCCCCCTGGTGTATTTCTTGGTCAACCTGTCAAAGATAGTTGACTCTATATGCATGAATTGTATCTGGGTTTTATTCCATTGGTTTGT chm1:+:73000985:-1 chm1:+:108797108:-1 chm1:+:162715226:-1 chm1:+:290870475:-1 chm1:+:377017325:-1 chm1:+:561066036:-1 chm1:+:627645706:-1 chm1:+:858347990:-1 chm1:+:883988095:-1 chm1:+:886016206:6 chm1:+:943927282:-1 chm1:+:1185274644:-1 chm1:+:1214826876:-1 chm1:+:1257670681:-1 chm1:+:1344201444:-1 chm1:+:1427270960:-1 chm1:+:1452183938:-1 chm1:+:1547463406:-1 chm1:+:1578506473:-1 chm1:+:1579035727:-1 chm1:+:1579851355:-1 chm1:+:1580651438:-1 chm1:+:1581173899:-1 chm1:+:1583556749:-1 chm1:+:1585998650:-1 chm1:+:1842853401:-1 chm1:+:1900770433:-1 chm1:+:1952251336:-1 chm1:+:1954812123:-1 chm1:+:2030527642:-1 chm1:+:2057224228:-1 chm1:+:2164143366:-1 chm1:+:2169449077:-1 chm1:+:2246792346:-1 chm1:+:2266663946:-1 chm1:+:2272483525:-1 chm1:+:2332848824:-1 chm1:+:2429983308:-1 chm1:+:2433679625:-1 chm1:+:2615170238:-1 chm1:+:2714779975:-1 chm1:+:2714814029:-1 chm1:+:2824709816:-1 chm1:+:2854962731:-1 chm1:+:3003314628:-1 chm1:+:3014783002:-1 chm1:+:3097785652:-1 chm1:+:3097862892:-1 +ATTTCCAGCTAACAACTTTTTTGTGTATGGTGTAAGGACAAGGGCCCTGTTTCAATATTTTGCATGTAGATATCCAGTTTTCCCAACACCATTTATTAAAGAGAACTTTATTTCCCCCTGGTGTATTTCTTGGTCAACCTGTCAAAGATAGTTGACTCTATATGCATGAATTGTATCTGGGTTTTATTCCATTGGTTTGT chm1:+:886016207:6 +ATTTCCAGCTAACAACTTTTTTGTGTATGGTGTAAGGACAAGGGCCCTGTTTCAATATTTTGCATGTAGATATCCAGTTTTCCCAACACCATTTATTAAAGAGAACTTTATTTCCCCCTGGTGTATTTCTTGGTCAACCTGTCAAAGATAGTTGACTCTATATGCATGAATTGTATCTGGGTTTTATTCCATTGGTTTGT chm1:+:886016205:6 chm1:+:1492862621:-1 +ACAAACCAATGGAATAAAACCCAGATACAATTCATGCATATAGAGTCAACTATCTTTGACAGGTTGACCAAGAAATACACCAGGGGGAAATAAAGTTCTCTTTAATAAATGGTGTTGGGAAAACTGGATATCTACATGCAAAATATTGAAACAGGGCCCTTGTCCTTACACCATACACAAAAAAGTTGTTAGCTGGAAAT chm1:+:146845196:-1 chm1:+:414307074:-1 chm1:+:481981996:-1 chm1:+:672030742:-1 chm1:+:878779680:-1 chm1:+:1258615929:-1 chm1:+:1410997538:-1 chm1:+:1559144365:-1 chm1:+:1568754084:-1 chm1:+:1702680809:-1 chm1:+:1880092201:-1 chm1:+:2729862331:-1 chm1:+:2991144711:-1 +ACCTAGGCAAAAATGGATCAGTCCCTTGATAAATACTTTAAATCTTTGTATAGGCATCTATAGCATGCAGAGCGCTTCTATGCTCGACTGTTTTTGACTGAGCTCCCAGGGGGCACTCTGAAACTTGGATAAAAAGTGTCACCCAGTCCGCCTTTGGGACAAAGAAGCTGAATCTTGGAATGTTTAAAAGTATACATTCA chm1:+:73134039:-1 chm1:+:115525227:-1 chm1:+:218536523:-1 chm1:+:734152475:-1 chm1:+:1147207201:-1 chm1:+:1188287716:-1 chm1:+:2001744060:-1 chm1:+:2114454627:-1 chm1:+:2172666907:-1 chm1:+:2371205682:-1 +ACCTAGGCAAAAATGGATCAGTCCCTTGATAAATACTTTAAATCTTTGTATAGGCATCTATAGCATGCAGAGCGCTTCTATGCTCGACTGTTTTTGACTGAGCTCCCAGGGGGCACTCTGAAACTTGGATAAAAAGTGTCACCCAGTCCGCCTTTGGGACAAAGAAGCTGAATCTTGGAATGTTTAAAAGTATACATTCA chm1:+:1010973222:-1 chm1:+:1227810970:-1 chm1:+:1322687095:-1 chm1:+:1465603147:-1 chm1:+:2619637567:-1 +ACCTAGGCAAAAATGGATCAGTCCCTTGATAAATACTTTAAATCTTTGTATAGGCATCTATAGCATGCAGAGCGCTTCTATGCTCGACTGTTTTTGACTGAGCTCCCAGGGGGCACTCTGAAACTTGGATAAAAAGTGTCACCCAGTCCGCCTTTGGGACAAAGAAGCTGAATCTTGGAATGTTTAAAAGTATACATTCA chm1:+:105195285:-1 chm1:+:172190094:-1 chm1:+:219438161:-1 chm1:+:223327781:-1 chm1:+:235103120:-1 chm1:+:331772298:-1 chm1:+:332185309:-1 chm1:+:367149147:-1 chm1:+:394515010:-1 chm1:+:433042033:-1 chm1:+:438266658:-1 chm1:+:443132500:-1 chm1:+:452778166:-1 chm1:+:460008177:-1 chm1:+:460826704:-1 chm1:+:463934134:-1 chm1:+:475627185:-1 chm1:+:483027542:-1 chm1:+:536900391:-1 chm1:+:579030826:-1 chm1:+:597508622:-1 chm1:+:623573763:-1 chm1:+:660887040:-1 chm1:+:664954592:-1 chm1:+:708790698:-1 chm1:+:748696075:-1 chm1:+:778915760:-1 chm1:+:780865175:-1 chm1:+:804590490:-1 chm1:+:817670516:-1 chm1:+:824975667:-1 chm1:+:847868013:-1 chm1:+:850574351:-1 chm1:+:857582044:-1 chm1:+:861076429:-1 chm1:+:875868972:-1 chm1:+:894346486:-1 chm1:+:934180037:-1 chm1:+:969852990:-1 chm1:+:971926288:-1 chm1:+:1037790601:-1 chm1:+:1146081675:-1 chm1:+:1151581728:-1 chm1:+:1161124719:-1 chm1:+:1258584474:-1 chm1:+:1269583697:-1 chm1:+:1269647871:-1 chm1:+:1269913266:-1 chm1:+:1275921375:-1 chm1:+:1338150884:-1 chm1:+:1382876236:-1 chm1:+:1465090276:-1 chm1:+:1551315738:-1 chm1:+:1554204358:-1 chm1:+:1566098466:-1 chm1:+:1650220914:-1 chm1:+:1655625284:-1 chm1:+:1690742825:-1 chm1:+:1702582279:-1 chm1:+:1705815945:-1 chm1:+:1771423962:-1 chm1:+:1774677625:-1 chm1:+:1835834263:-1 chm1:+:1862000310:-1 chm1:+:1898854228:-1 chm1:+:1914853716:-1 chm1:+:1932875380:-1 chm1:+:2023096723:-1 chm1:+:2043845227:-1 chm1:+:2146999880:-1 chm1:+:2166624781:-1 chm1:+:2167458907:-1 chm1:+:2175173837:-1 chm1:+:2220979811:-1 chm1:+:2222189124:-1 chm1:+:2271994299:-1 chm1:+:2366631159:-1 chm1:+:2506440479:-1 chm1:+:2551816752:-1 chm1:+:2556475387:-1 chm1:+:2584601067:-1 chm1:+:2657086945:-1 chm1:+:2755554686:-1 chm1:+:2803814525:-1 chm1:+:2885647412:-1 chm1:+:2926052150:-1 chm1:+:3010056293:-1 +ACCTAGGCAAAAATGGATCAGTCCCTTGATAAATACTTTAAATCTTTGTATAGGCATCTATAGCATGCAGAGCGCTTCTATGCTCGACTGTTTTTGACTGAGCTCCCAGGGGGCACTCTGAAACTTGGATAAAAAGTGTCACCCAGTCCGCCTTTGGGACAAAGAAGCTGAATCTTGGAATGTTTAAAAGTATACATTCA chm1:+:21825926:-1 chm1:+:271461143:-1 chm1:+:641629830:-1 chm1:+:697034723:-1 chm1:+:790830326:-1 chm1:+:818181464:-1 chm1:+:948468751:-1 chm1:+:1048290159:-1 chm1:+:1526476476:-1 chm1:+:1845686085:-1 chm1:+:1914030456:-1 chm1:+:1936135895:-1 chm1:+:2285040010:-1 chm1:+:2776485185:-1 chm1:+:3010607601:-1 +ACCTAGGCAAAAATGGATCAGTCCCTTGATAAATACTTTAAATCTTTGTATAGGCATCTATAGCATGCAGAGCGCTTCTATGCTCGACTGTTTTTGACTGAGCTCCCAGGGGGCACTCTGAAACTTGGATAAAAAGTGTCACCCAGTCCGCCTTTGGGACAAAGAAGCTGAATCTTGGAATGTTTAAAAGTATACATTCA chm1:+:95838728:-1 chm1:+:201649740:-1 chm1:+:378843243:-1 chm1:+:399351183:-1 chm1:+:673345294:-1 chm1:+:674501600:-1 chm1:+:901783721:-1 chm1:+:1141551771:-1 chm1:+:1414799351:-1 chm1:+:1848986779:-1 chm1:+:2465788540:-1 chm1:+:2482595519:-1 chm1:+:2531661717:-1 chm1:+:2538034587:-1 chm1:+:2549630886:-1 chm1:+:2579676294:-1 chm1:+:2624661951:-1 chm1:+:2847482143:-1 chm1:+:2926116186:-1 chm1:+:2964982886:-1 +TGAATGTATACTTTTAAACATTCCAAGATTCAGCTTCTTTGTCCCAAAGGCGGACTGGGTGACACTTTTTATCCAAGTTTCAGAGTGCCCCCTGGGAGCTCAGTCAAAAACAGTCGAGCATAGAAGCGCTCTGCATGCTATAGATGCCTATACAAAGATTTAAAGTATTTATCAAGGGACTGATCCATTTTTGCCTAGGT chm1:+:1517954868:11 +TGAATGTATACTTTTAAACATTCCAAGATTCAGCTTCTTTGTCCCAAAGGCGGACTGGGTGACACTTTTTATCCAAGTTTCAGAGTGCCCCCTGGGAGCTCAGTCAAAAACAGTCGAGCATAGAAGCGCTCTGCATGCTATAGATGCCTATACAAAGATTTAAAGTATTTATCAAGGGACTGATCCATTTTTGCCTAGGT chm1:+:1517954867:11 +CTTGGGTTTCCTGACATAACCTGTAACTGCTTGGTGCTCTTCAGCTTAGCAGGGCCACAGGCAATTTGGTTTCATGCGCCATCGCCCGAAGTGCAGACAGAGGCCCCACGCTGCACTTTCAGTCACGTGACCTGGTCGACTCAGGCCCTTCTGGTTCCTGCTTGTCAGGGTATGGGAAGGTGAGAACTACTTTGCAGTGG chm1:+:493501085:-1 chm1:+:1964232870:13 +CTTGGGTTTCCTGACATAACCTGTAACTGCTTGGTGCTCTTCAGCTTAGCAGGGCCACAGGCAATTTGGTTTCATGCGCCATCGCCCGAAGTGCAGACAGAGGCCCCACGCTGCACTTTCAGTCACGTGACCTGGTCGACTCAGGCCCTTCTGGTTCCTGCTTGTCAGGGTATGGGAAGGTGAGAACTACTTTGCAGTGG chm1:+:1964232866:13 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTA chm1:+:330409511:-1 chm1:+:559798155:-1 chm1:+:579589709:-1 chm1:+:720771402:-1 chm1:+:775059439:-1 chm1:+:818584556:-1 chm1:+:853547233:-1 chm1:+:933190206:-1 chm1:+:1036038927:-1 chm1:+:1036038994:-1 chm1:+:1191185708:-1 chm1:+:1222614809:-1 chm1:+:1245652359:-1 chm1:+:1582904247:-1 chm1:+:1584579723:-1 chm1:+:1584579750:-1 chm1:+:1584579777:-1 chm1:+:1697740116:-1 chm1:+:1700788902:-1 chm1:+:1918933833:-1 chm1:+:2242389339:-1 chm1:+:2409720895:-1 chm1:+:2415525865:-1 chm1:+:2432838155:-1 chm1:+:2639458884:-1 chm1:+:2661998265:-1 chm1:+:2770123409:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTA chm1:+:4883368:-1 chm1:+:66082038:-1 chm1:+:193173173:-1 chm1:+:225523051:-1 chm1:+:259682208:-1 chm1:+:270957989:-1 chm1:+:326776858:-1 chm1:+:330409959:-1 chm1:+:330409993:-1 chm1:+:330410027:-1 chm1:+:330410061:-1 chm1:+:330410095:-1 chm1:+:330410129:-1 chm1:+:330410163:-1 chm1:+:330410197:-1 chm1:+:355268957:-1 chm1:+:447588627:-1 chm1:+:494199652:-1 chm1:+:494199781:-1 chm1:+:568177675:-1 chm1:+:578268463:-1 chm1:+:578268489:-1 chm1:+:578268515:-1 chm1:+:694542669:-1 chm1:+:694542713:-1 chm1:+:694542745:-1 chm1:+:694542777:-1 chm1:+:694542809:-1 chm1:+:694542841:-1 chm1:+:738594472:-1 chm1:+:757965504:-1 chm1:+:762714020:-1 chm1:+:921071475:-1 chm1:+:1076070116:-1 chm1:+:1107590556:-1 chm1:+:1130876689:-1 chm1:+:1167376906:-1 chm1:+:1227886601:-1 chm1:+:1243304855:-1 chm1:+:1243304897:-1 chm1:+:1333427177:-1 chm1:+:1347777617:-1 chm1:+:1357956809:-1 chm1:+:1405213454:-1 chm1:+:1516268467:-1 chm1:+:1524025211:-1 chm1:+:1549322225:-1 chm1:+:1573471224:-1 chm1:+:1652966076:-1 chm1:+:1911273968:-1 chm1:+:1991020855:-1 chm1:+:2004455738:-1 chm1:+:2012009968:-1 chm1:+:2029896698:-1 chm1:+:2171418450:-1 chm1:+:2171418484:-1 chm1:+:2244685473:-1 chm1:+:2244685509:-1 chm1:+:2379503171:-1 chm1:+:2428791720:-1 chm1:+:2491321681:-1 chm1:+:2501357098:-1 chm1:+:2512426320:-1 chm1:+:2548272411:-1 chm1:+:2569273104:-1 chm1:+:2594237282:-1 chm1:+:2645727230:-1 chm1:+:2700221286:-1 chm1:+:2811759181:-1 chm1:+:2888166204:-1 chm1:+:2967268425:-1 chm1:+:2989833063:-1 chm1:+:2989833155:-1 chm1:+:3032432833:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTA chm1:+:56130223:-1 chm1:+:372152405:-1 chm1:+:475326303:-1 chm1:+:673318396:-1 chm1:+:705388649:-1 chm1:+:723115615:-1 chm1:+:754540735:-1 chm1:+:754540768:-1 chm1:+:754540801:-1 chm1:+:754540834:-1 chm1:+:754540929:-1 chm1:+:825014593:-1 chm1:+:858854299:-1 chm1:+:868478043:-1 chm1:+:894053278:-1 chm1:+:894053302:-1 chm1:+:894053326:-1 chm1:+:894053348:-1 chm1:+:978226479:-1 chm1:+:1154215784:-1 chm1:+:1154216289:-1 chm1:+:1327480189:-1 chm1:+:1341364236:-1 chm1:+:1426033036:-1 chm1:+:1426033060:-1 chm1:+:1742359195:-1 chm1:+:1742359239:-1 chm1:+:1742359266:-1 chm1:+:1742359293:-1 chm1:+:1765717830:-1 chm1:+:1965247123:-1 chm1:+:1968741326:-1 chm1:+:2066383396:-1 chm1:+:2154589653:-1 chm1:+:2426955027:-1 chm1:+:2653252832:-1 chm1:+:2665872660:-1 chm1:+:2945626974:-1 chm1:+:3057689885:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTA chm1:+:832174499:-1 chm1:+:832174593:-1 chm1:+:851743787:-1 chm1:+:1001403432:-1 chm1:+:1256428639:-1 chm1:+:2358411836:-1 chm1:+:2425126836:-1 chm1:+:2428038458:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTA chm1:+:17176547:-1 chm1:+:416308240:-1 chm1:+:416308257:-1 chm1:+:576343479:-1 chm1:+:636813329:-1 chm1:+:663521113:-1 chm1:+:1304338408:-1 chm1:+:1367758848:-1 chm1:+:1547698214:-1 chm1:+:2189572900:-1 chm1:+:2407727578:-1 chm1:+:2565243273:-1 chm1:+:2704341588:-1 chm1:+:2800304902:-1 chm1:+:2810009458:-1 chm1:+:2810009621:-1 chm1:+:2885394564:-1 chm1:+:2982378039:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTA chm1:+:255509844:-1 chm1:+:548998789:-1 chm1:+:548998831:-1 chm1:+:548998873:-1 chm1:+:548998915:-1 chm1:+:558046651:-1 chm1:+:868914801:-1 chm1:+:1032963410:-1 chm1:+:1070796335:-1 chm1:+:1070796365:-1 chm1:+:1070796395:-1 chm1:+:1070796425:-1 chm1:+:1070796455:-1 chm1:+:1070796485:-1 chm1:+:1326231865:-1 chm1:+:1503925934:-1 chm1:+:1581455846:-1 chm1:+:1609851050:-1 chm1:+:1926669438:-1 chm1:+:2146806249:-1 chm1:+:2194045386:-1 chm1:+:2647249235:-1 chm1:+:2734861764:-1 chm1:+:2878232547:-1 chm1:+:2983325565:-1 chm1:+:2988214235:-1 chm1:+:2995898332:-1 chm1:+:2995898374:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTA chm1:+:1367758761:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTA chm1:+:294004885:-1 chm1:+:345950152:-1 chm1:+:345950195:-1 chm1:+:647769064:-1 chm1:+:1410310978:-1 chm1:+:1695246471:-1 chm1:+:1862681506:-1 chm1:+:2756588632:-1 chm1:+:2950870356:-1 +TAGTATACGTATATATAGTATATATGTATTATATATGTATATACGTGTATATGTACATATATAGTATGTATATATACTATATATGTATAGTATACGTATATATACGTGTATAATATACATATATAGTATATATACGTATTACGTACGTAATATATGTATACATATATACATATATTATATTAAAAGCCAGGAGGCTGGGG chm1:+:193040889:-1 chm1:+:647475171:-1 chm1:+:676376587:-1 chm1:+:1131560920:-1 chm1:+:1541103918:-1 chm1:+:1701208276:9 chm1:+:1930410774:-1 chm1:+:2602562896:-1 chm1:+:2885394709:-1 chm1:+:2955859303:-1 +TAGTATACGTATATATAGTATATATGTATTATATATGTATATACGTGTATATGTACATATATAGTATGTATATATACTATATATGTATAGTATACGTATATATACGTGTATAATATACATATATAGTATATATACGTATTACGTACGTAATATATGTATACATATATACATATATTATATTAAAAGCCAGGAGGCTGGGG chm1:+:1076070280:-1 +TAGTATACGTATATATAGTATATATGTATTATATATGTATATACGTGTATATGTACATATATAGTATGTATATATACTATATATGTATAGTATACGTATATATACGTGTATAATATACATATATAGTATATATACGTATTACGTACGTAATATATGTATACATATATACATATATTATATTAAAAGCCAGGAGGCTGGGG chm1:+:375901283:-1 chm1:+:935341556:-1 +TAGTATACGTATATATAGTATATATGTATTATATATGTATATACGTGTATATGTACATATATAGTATGTATATATACTATATATGTATAGTATACGTATATATACGTGTATAATATACATATATAGTATATATACGTATTACGTACGTAATATATGTATACATATATACATATATTATATTAAAAGCCAGGAGGCTGGGG chm1:+:512510228:-1 chm1:+:739084900:-1 chm1:+:1897991673:-1 chm1:+:2107360947:-1 +CTACACCTTTTAAAAGTAAGTCGAATCCAGCTGGTTTTCACTACCTCTTCCACTGCCATCTTTATTCAAACTCTTATCTCTTAGCCTCGATTACCCGTGTAGTAGCCTCCTAATGGCCCAGACCCGTCACTTCCTAAGACTTTCTATAATCTAGTCTCGAGCACAGCAACCAAAGTGATACTGTTACAGAGTGATACCAG chm1:+:1410687787:13 +CTACACCTTTTAAAAGTAAGTCGAATCCAGCTGGTTTTCACTACCTCTTCCACTGCCATCTTTATTCAAACTCTTATCTCTTAGCCTCGATTACCCGTGTAGTAGCCTCCTAATGGCCCAGACCCGTCACTTCCTAAGACTTTCTATAATCTAGTCTCGAGCACAGCAACCAAAGTGATACTGTTACAGAGTGATACCAG chm1:+:1410687783:13 +CTACACCTTTTAAAAGTAAGTCGAATCCAGCTGGTTTTCACTACCTCTTCCACTGCCATCTTTATTCAAACTCTTATCTCTTAGCCTCGATTACCCGTGTAGTAGCCTCCTAATGGCCCAGACCCGTCACTTCCTAAGACTTTCTATAATCTAGTCTCGAGCACAGCAACCAAAGTGATACTGTTACAGAGTGATACCAG chm1:+:1410687786:13 +CTACACCTTTTAAAAGTAAGTCGAATCCAGCTGGTTTTCACTACCTCTTCCACTGCCATCTTTATTCAAACTCTTATCTCTTAGCCTCGATTACCCGTGTAGTAGCCTCCTAATGGCCCAGACCCGTCACTTCCTAAGACTTTCTATAATCTAGTCTCGAGCACAGCAACCAAAGTGATACTGTTACAGAGTGATACCAG chm1:+:1410687785:13 +GAAGAAGTGGCCATGGTTGAGTTTCTCAAAGTTTCCTTTCAAATGTACAGGTCTAAATGGGAGTGTGAGTCCATGTGTGTGACAGCCTTCCCAGCAGGGGAGATGGCACATCATTACCTATTAAATCTCATTCAAAGCAAGATGGCACATCACCTACCTATTAAAATCTCATTCAATCAGCCCTTAGAATACAATATAAT chm1:+:632449835:6 chm1:+:1764760247:-1 chm1:+:2164658873:-1 chm1:+:2675676328:-1 +ATTATATTGTATTCTAAGGGCTGATTGAATGAGATTTTAATAGGTAGGTGATGTGCCATCTTGCTTTGAATGAGATTTAATAGGTAATGATGTGCCATCTCCCCTGCTGGGAAGGCTGTCACACACATGGACTCACACTCCCATTTAGACCTGTACATTTGAAAGGAAACTTTGAGAAACTCAACCATGGCCACTTCTTC chm1:+:1096250374:-1 +TAGACCCTTCAACTTATTGAGGGATGAGAGTGGTGGGTGTTGTACCGAGGCTTCCTCATCCCTGGGTCAGTTCTGTATTCTAACATTAGTATCCGAGAGGGTCCCAGTGGGATTGAGCCCCTATGCCCGACAGGGCAGGATGTGCTCGCTCACCAACATTCCCTTTTCCTTATTCCTTCTCTGACCTTGTTCCACTGCTC chm1:+:2724793796:16 +TAGACCCTTCAACTTATTGAGGGATGAGAGTGGTGGGTGTTGTACCGAGGCTTCCTCATCCCTGGGTCAGTTCTGTATTCTAACATTAGTATCCGAGAGGGTCCCAGTGGGATTGAGCCCCTATGCCCGACAGGGCAGGATGTGCTCGCTCACCAACATTCCCTTTTCCTTATTCCTTCTCTGACCTTGTTCCACTGCTC chm1:+:727185235:-1 chm1:+:851929248:-1 chm1:+:969274889:-1 chm1:+:986113991:-1 chm1:+:2534376416:-1 chm1:+:2724793789:16 +TAGACCCTTCAACTTATTGAGGGATGAGAGTGGTGGGTGTTGTACCGAGGCTTCCTCATCCCTGGGTCAGTTCTGTATTCTAACATTAGTATCCGAGAGGGTCCCAGTGGGATTGAGCCCCTATGCCCGACAGGGCAGGATGTGCTCGCTCACCAACATTCCCTTTTCCTTATTCCTTCTCTGACCTTGTTCCACTGCTC chm1:+:2724793790:16 +TAGACCCTTCAACTTATTGAGGGATGAGAGTGGTGGGTGTTGTACCGAGGCTTCCTCATCCCTGGGTCAGTTCTGTATTCTAACATTAGTATCCGAGAGGGTCCCAGTGGGATTGAGCCCCTATGCCCGACAGGGCAGGATGTGCTCGCTCACCAACATTCCCTTTTCCTTATTCCTTCTCTGACCTTGTTCCACTGCTC chm1:+:2724793798:16 +GAGCAGTGGAACAAGGTCAGAGAAGGAATAAGGAAAAGGGAATGTTGGTGAGCGAGCACATCCTGCCCTGTCGGGCATAGGGGCTCAATCCCACTGGGACCCTCTCGGATACTAATGTTAGAATACAGAACTGACCCAGGGATGAGGAAGCCTCGGTACAACACCCACCACTCTCATCCCTCAATAAGTTGAAGGGTCTA chm1:+:542653301:-1 chm1:+:2116463761:-1 chm1:+:2264190951:-1 chm1:+:2533077026:-1 chm1:+:2653239537:-1 chm1:+:2776739329:-1 +GAGCAGTGGAACAAGGTCAGAGAAGGAATAAGGAAAAGGGAATGTTGGTGAGCGAGCACATCCTGCCCTGTCGGGCATAGGGGCTCAATCCCACTGGGACCCTCTCGGATACTAATGTTAGAATACAGAACTGACCCAGGGATGAGGAAGCCTCGGTACAACACCCACCACTCTCATCCCTCAATAAGTTGAAGGGTCTA chm1:+:314784690:-1 chm1:+:1882189239:-1 +GAGCAGTGGAACAAGGTCAGAGAAGGAATAAGGAAAAGGGAATGTTGGTGAGCGAGCACATCCTGCCCTGTCGGGCATAGGGGCTCAATCCCACTGGGACCCTCTCGGATACTAATGTTAGAATACAGAACTGACCCAGGGATGAGGAAGCCTCGGTACAACACCCACCACTCTCATCCCTCAATAAGTTGAAGGGTCTA chm1:+:184753731:-1 chm1:+:347730772:-1 chm1:+:620609538:-1 chm1:+:926067469:-1 chm1:+:1653983775:-1 chm1:+:1683894563:-1 chm1:+:2107135623:-1 chm1:+:2241706452:-1 chm1:+:2492351548:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCG chm1:+:21316305:-1 chm1:+:24837437:-1 chm1:+:33096248:-1 chm1:+:46825535:-1 chm1:+:155805670:-1 chm1:+:161154445:-1 chm1:+:180879397:-1 chm1:+:184565639:-1 chm1:+:193063147:-1 chm1:+:195508218:-1 chm1:+:198560651:-1 chm1:+:210353145:-1 chm1:+:224671766:-1 chm1:+:225350474:-1 chm1:+:236373589:-1 chm1:+:260247762:-1 chm1:+:297999880:-1 chm1:+:310207332:-1 chm1:+:310864180:-1 chm1:+:311391186:-1 chm1:+:332460075:-1 chm1:+:350637652:-1 chm1:+:439902034:-1 chm1:+:456015576:-1 chm1:+:466052129:-1 chm1:+:469061328:-1 chm1:+:508328235:-1 chm1:+:525232889:-1 chm1:+:537267200:-1 chm1:+:539931988:-1 chm1:+:540365587:-1 chm1:+:540397112:-1 chm1:+:540681228:-1 chm1:+:541322702:-1 chm1:+:573945177:-1 chm1:+:622364941:-1 chm1:+:675932223:-1 chm1:+:688230737:-1 chm1:+:694674260:-1 chm1:+:697372261:-1 chm1:+:705915703:-1 chm1:+:712268560:-1 chm1:+:721584595:-1 chm1:+:730358941:-1 chm1:+:732956378:-1 chm1:+:738322964:-1 chm1:+:762173218:-1 chm1:+:764644282:-1 chm1:+:770608011:-1 chm1:+:774412848:-1 chm1:+:785019124:-1 chm1:+:810018227:-1 chm1:+:830273726:-1 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chm1:+:1493320561:-1 chm1:+:1504712514:-1 chm1:+:1515620181:-1 chm1:+:1574427962:-1 chm1:+:1578771925:-1 chm1:+:1580087923:-1 chm1:+:1580916976:-1 chm1:+:1638833067:-1 chm1:+:1642342717:-1 chm1:+:1644827686:-1 chm1:+:1653749731:-1 chm1:+:1671331495:-1 chm1:+:1671925548:-1 chm1:+:1686365881:-1 chm1:+:1699151019:-1 chm1:+:1709382292:-1 chm1:+:1712231442:-1 chm1:+:1715123311:-1 chm1:+:1725520906:-1 chm1:+:1741235733:-1 chm1:+:1743037985:-1 chm1:+:1750589668:-1 chm1:+:1755237946:-1 chm1:+:1755700207:-1 chm1:+:1789812551:-1 chm1:+:1801667179:-1 chm1:+:1804103802:-1 chm1:+:1805984062:-1 chm1:+:1825449863:-1 chm1:+:1826545376:-1 chm1:+:1838668644:-1 chm1:+:1854855273:-1 chm1:+:1919110312:-1 chm1:+:1958847992:-1 chm1:+:1964993927:-1 chm1:+:1972830058:-1 chm1:+:2059112471:-1 chm1:+:2075352365:-1 chm1:+:2078905905:-1 chm1:+:2105540881:-1 chm1:+:2113425047:-1 chm1:+:2196313866:-1 chm1:+:2197917235:-1 chm1:+:2273432039:-1 chm1:+:2327480733:-1 chm1:+:2334171017:-1 chm1:+:2347731629:-1 chm1:+:2363481376:-1 chm1:+:2367620808:-1 chm1:+:2369962083:-1 chm1:+:2396431521:-1 chm1:+:2398340865:-1 chm1:+:2411160587:-1 chm1:+:2413313276:-1 chm1:+:2418837924:-1 chm1:+:2421668085:-1 chm1:+:2421740008:-1 chm1:+:2428550997:-1 chm1:+:2434199840:-1 chm1:+:2437746725:-1 chm1:+:2492363371:-1 chm1:+:2507774237:-1 chm1:+:2530823716:-1 chm1:+:2560613640:-1 chm1:+:2564030204:-1 chm1:+:2576321064:-1 chm1:+:2585806828:-1 chm1:+:2614632740:-1 chm1:+:2639607670:-1 chm1:+:2660791480:-1 chm1:+:2672953033:-1 chm1:+:2682030978:-1 chm1:+:2699871746:-1 chm1:+:2702770514:-1 chm1:+:2717529361:-1 chm1:+:2717833490:-1 chm1:+:2825747570:-1 chm1:+:2847772912:-1 chm1:+:2849521659:-1 chm1:+:2854506206:-1 chm1:+:2861605095:-1 chm1:+:2871743422:-1 chm1:+:2899179727:-1 chm1:+:2899646222:-1 chm1:+:2903683677:-1 chm1:+:2921835250:-1 chm1:+:2925341872:-1 chm1:+:2929994561:-1 chm1:+:2944918365:-1 chm1:+:2976057386:-1 chm1:+:2984526196:-1 chm1:+:3000787083:-1 chm1:+:3002317169:-1 chm1:+:3013626771:-1 chm1:+:3038954785:-1 chm1:+:3060376219:-1 chm1:+:3061986002:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCG chm1:+:26618624:-1 chm1:+:31593969:-1 chm1:+:89305083:-1 chm1:+:111999685:-1 chm1:+:176982932:-1 chm1:+:435079388:-1 chm1:+:462776162:-1 chm1:+:474365325:-1 chm1:+:558500080:-1 chm1:+:621343118:-1 chm1:+:687327583:-1 chm1:+:752633712:-1 chm1:+:801506420:-1 chm1:+:839057504:-1 chm1:+:1096887186:-1 chm1:+:1168040891:-1 chm1:+:1341698627:-1 chm1:+:1435273519:-1 chm1:+:1630045319:-1 chm1:+:1641971019:-1 chm1:+:1653401205:-1 chm1:+:1673366623:-1 chm1:+:1779758896:-1 chm1:+:1839828307:-1 chm1:+:1928376977:-1 chm1:+:1945374980:-1 chm1:+:1945618283:-1 chm1:+:1995618443:-1 chm1:+:2034158866:-1 chm1:+:2162195662:-1 chm1:+:2231639485:-1 chm1:+:2263805939:-1 chm1:+:2275543557:-1 chm1:+:2295086950:-1 chm1:+:2411169728:-1 chm1:+:2418788496:-1 chm1:+:2468172817:-1 chm1:+:2493641649:-1 chm1:+:2510720231:-1 chm1:+:2565456565:-1 chm1:+:2576236354:-1 chm1:+:2697937722:-1 chm1:+:2768976554:-1 chm1:+:2856774214:-1 chm1:+:2985374912:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCG chm1:+:823405482:-1 chm1:+:2336130335:-1 chm1:+:2806715386:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCG chm1:+:370426625:-1 chm1:+:454899548:-1 chm1:+:1327825576:-1 chm1:+:1549228114:-1 chm1:+:1817240930:-1 chm1:+:2933061320:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCG chm1:+:244488580:-1 chm1:+:310613458:-1 chm1:+:333121516:-1 chm1:+:355210442:-1 chm1:+:437943878:-1 chm1:+:451971484:-1 chm1:+:865246596:-1 chm1:+:885378858:-1 chm1:+:896538473:-1 chm1:+:906828111:-1 chm1:+:919385338:-1 chm1:+:1011895774:-1 chm1:+:1029310839:-1 chm1:+:1077256472:-1 chm1:+:1185267740:-1 chm1:+:1618355033:-1 chm1:+:1685803086:-1 chm1:+:1697677189:-1 chm1:+:1758040507:-1 chm1:+:1990373999:-1 chm1:+:1993957686:-1 chm1:+:2154292079:-1 chm1:+:2350797115:-1 chm1:+:2436983875:-1 chm1:+:2521177611:-1 chm1:+:2687726262:-1 chm1:+:2767943556:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCG chm1:+:47050049:-1 chm1:+:118500132:-1 chm1:+:159645250:-1 chm1:+:167585904:-1 chm1:+:213244039:-1 chm1:+:246617009:-1 chm1:+:387208511:-1 chm1:+:499333850:-1 chm1:+:553545465:-1 chm1:+:812670450:-1 chm1:+:916687262:-1 chm1:+:973385221:-1 chm1:+:1139581997:-1 chm1:+:1142756261:-1 chm1:+:1219872028:-1 chm1:+:1234923763:-1 chm1:+:1299424197:-1 chm1:+:1460122764:-1 chm1:+:1464358065:-1 chm1:+:1477278122:-1 chm1:+:1478292926:-1 chm1:+:1524793483:-1 chm1:+:1578758340:-1 chm1:+:1580074657:-1 chm1:+:1580903376:-1 chm1:+:1756970242:-1 chm1:+:1785759766:-1 chm1:+:1822020521:-1 chm1:+:1841916052:-1 chm1:+:1921910440:-1 chm1:+:1962761399:-1 chm1:+:2022759463:-1 chm1:+:2234760354:-1 chm1:+:2248493073:-1 chm1:+:2286497587:-1 chm1:+:2295079050:-1 chm1:+:2439717173:-1 chm1:+:2441372613:-1 chm1:+:2464148629:-1 chm1:+:2764776637:-1 chm1:+:2765377550:-1 chm1:+:2824425063:-1 chm1:+:2857658076:-1 chm1:+:2860443400:-1 chm1:+:2958358796:-1 chm1:+:2961688894:-1 chm1:+:3032055618:-1 chm1:+:3054341248:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCG chm1:+:186664525:-1 chm1:+:1402655177:-1 chm1:+:1627819612:-1 chm1:+:1819230380:-1 chm1:+:1847894477:-1 chm1:+:1876721302:-1 chm1:+:2155959971:-1 chm1:+:2433622646:-1 chm1:+:2467087825:-1 chm1:+:2662891253:-1 chm1:+:2699452867:-1 chm1:+:2802154767:-1 chm1:+:2904724793:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCG chm1:+:101107925:-1 chm1:+:228719721:-1 chm1:+:313165795:-1 chm1:+:452271843:-1 chm1:+:819435390:-1 chm1:+:1361266419:-1 chm1:+:1529530739:-1 chm1:+:2264176845:-1 chm1:+:2347537697:-1 chm1:+:2513733980:-1 chm1:+:2545978115:-1 chm1:+:2630161368:-1 chm1:+:2662127166:-1 chm1:+:2691058233:-1 chm1:+:2805397959:-1 chm1:+:2806428002:-1 +CGCCCACCACCACGCCCGGGTAATTTTTTGTATTTTTAGTATAGCCAGGCTGGTCTCGATCTCCTGACCTCGTGATCTGCCCGCCTCGCCTCTTCAAAGTGCCTGGAATTACAGGCGGTGAGCCACTGTGCCCTGCCCGCCTCCCTACGTATTTTAAAGGTTGGCCTAAAAGTTTTTTCTTTACATCGTGAACTATAACA chm1:+:29320808:-1 chm1:+:156599042:-1 chm1:+:232060527:-1 chm1:+:422121835:-1 chm1:+:480938040:-1 chm1:+:483076952:-1 chm1:+:1049361440:-1 chm1:+:1171885702:-1 chm1:+:1198209423:-1 chm1:+:1261706254:-1 chm1:+:1524269683:-1 chm1:+:1550251686:-1 chm1:+:1702113111:-1 chm1:+:1876151545:6 chm1:+:1972076945:-1 chm1:+:2045008737:-1 chm1:+:2291654020:-1 chm1:+:2391698446:-1 chm1:+:2477421580:-1 chm1:+:2481815474:-1 chm1:+:2568788838:-1 chm1:+:2625544929:-1 chm1:+:2681991507:-1 chm1:+:2858553473:-1 chm1:+:2868028620:-1 +CGCCCACCACCACGCCCGGGTAATTTTTTGTATTTTTAGTATAGCCAGGCTGGTCTCGATCTCCTGACCTCGTGATCTGCCCGCCTCGCCTCTTCAAAGTGCCTGGAATTACAGGCGGTGAGCCACTGTGCCCTGCCCGCCTCCCTACGTATTTTAAAGGTTGGCCTAAAAGTTTTTTCTTTACATCGTGAACTATAACA chm1:+:2007846348:-1 +CGCCCACCACCACGCCCGGGTAATTTTTTGTATTTTTAGTATAGCCAGGCTGGTCTCGATCTCCTGACCTCGTGATCTGCCCGCCTCGCCTCTTCAAAGTGCCTGGAATTACAGGCGGTGAGCCACTGTGCCCTGCCCGCCTCCCTACGTATTTTAAAGGTTGGCCTAAAAGTTTTTTCTTTACATCGTGAACTATAACA chm1:+:1876151542:6 +CTAACACTCAGATACGAACACATAGCAATCCTATATCAATGCTATCCTATTCCTGGATAGCGATCGTGCCATAAGGAACCCAGTTTGCAGGACTCATCATTGAAGTTTGGGCATTTCAGAAAGAGAAAGATTAATGCCTTCCTTTTTTATATAAAACAACCAGCCGTTATAGAGTTTCCATCTAAAAATAATTTCTTCAT chm1:+:330830766:10 chm1:+:783333143:9 +CTAACACTCAGATACGAACACATAGCAATCCTATATCAATGCTATCCTATTCCTGGATAGCGATCGTGCCATAAGGAACCCAGTTTGCAGGACTCATCATTGAAGTTTGGGCATTTCAGAAAGAGAAAGATTAATGCCTTCCTTTTTTATATAAAACAACCAGCCGTTATAGAGTTTCCATCTAAAAATAATTTCTTCAT chm1:+:330830761:10 chm1:+:783333138:9 +CTAACACTCAGATACGAACACATAGCAATCCTATATCAATGCTATCCTATTCCTGGATAGCGATCGTGCCATAAGGAACCCAGTTTGCAGGACTCATCATTGAAGTTTGGGCATTTCAGAAAGAGAAAGATTAATGCCTTCCTTTTTTATATAAAACAACCAGCCGTTATAGAGTTTCCATCTAAAAATAATTTCTTCAT chm1:+:330830763:10 chm1:+:783333140:9 +CTAACACTCAGATACGAACACATAGCAATCCTATATCAATGCTATCCTATTCCTGGATAGCGATCGTGCCATAAGGAACCCAGTTTGCAGGACTCATCATTGAAGTTTGGGCATTTCAGAAAGAGAAAGATTAATGCCTTCCTTTTTTATATAAAACAACCAGCCGTTATAGAGTTTCCATCTAAAAATAATTTCTTCAT chm1:+:330830765:10 chm1:+:783333142:9 +CTAACACTCAGATACGAACACATAGCAATCCTATATCAATGCTATCCTATTCCTGGATAGCGATCGTGCCATAAGGAACCCAGTTTGCAGGACTCATCATTGAAGTTTGGGCATTTCAGAAAGAGAAAGATTAATGCCTTCCTTTTTTATATAAAACAACCAGCCGTTATAGAGTTTCCATCTAAAAATAATTTCTTCAT chm1:+:330830767:10 chm1:+:783333144:9 +ATGAAGAAATTATTTTTAGATGGAAACTCTATAACGGCTGGTTGTTTTATATAAAAAAGGAAGGCATTAATCTTTCTCTTTCTGAAATGCCCAAACTTCAATGATGAGTCCTGCAAACTGGGTTCCTTATGGCACGATCGCTATCCAGGAATAGGATAGCATTGATATAGGATTGCTATGTGTTCGTATCTGAGTGTTAG chm1:+:430696055:13 +ATGAAGAAATTATTTTTAGATGGAAACTCTATAACGGCTGGTTGTTTTATATAAAAAAGGAAGGCATTAATCTTTCTCTTTCTGAAATGCCCAAACTTCAATGATGAGTCCTGCAAACTGGGTTCCTTATGGCACGATCGCTATCCAGGAATAGGATAGCATTGATATAGGATTGCTATGTGTTCGTATCTGAGTGTTAG chm1:+:430696052:13 +ATGAAGAAATTATTTTTAGATGGAAACTCTATAACGGCTGGTTGTTTTATATAAAAAAGGAAGGCATTAATCTTTCTCTTTCTGAAATGCCCAAACTTCAATGATGAGTCCTGCAAACTGGGTTCCTTATGGCACGATCGCTATCCAGGAATAGGATAGCATTGATATAGGATTGCTATGTGTTCGTATCTGAGTGTTAG chm1:+:430696051:13 +ATGAAGAAATTATTTTTAGATGGAAACTCTATAACGGCTGGTTGTTTTATATAAAAAAGGAAGGCATTAATCTTTCTCTTTCTGAAATGCCCAAACTTCAATGATGAGTCCTGCAAACTGGGTTCCTTATGGCACGATCGCTATCCAGGAATAGGATAGCATTGATATAGGATTGCTATGTGTTCGTATCTGAGTGTTAG chm1:+:430696053:13 +TCTGACTGTCCCAGATCACTCCCAGGGTAGGCACGGTACTTTCGCTCGGGAGAGAGGCAGGCTCCAGAGGAGGGACACAGAGCAGGTAGGGAGGGCTTTGAGACATCCCCACCTGGCTCTGCCCAGGGCACATGGCCTTTTCTGGGAGGGAGCCCTTTCTCAGGGGGATCAGGGACCCACGGTCAGGAACCTCAGGACAG chm1:+:321635742:-1 chm1:+:478668996:-1 chm1:+:541079284:-1 chm1:+:632921212:-1 chm1:+:1005640946:-1 chm1:+:2521350734:-1 chm1:+:2688946347:-1 +TCTGACTGTCCCAGATCACTCCCAGGGTAGGCACGGTACTTTCGCTCGGGAGAGAGGCAGGCTCCAGAGGAGGGACACAGAGCAGGTAGGGAGGGCTTTGAGACATCCCCACCTGGCTCTGCCCAGGGCACATGGCCTTTTCTGGGAGGGAGCCCTTTCTCAGGGGGATCAGGGACCCACGGTCAGGAACCTCAGGACAG chm1:+:55047101:-1 chm1:+:62689801:-1 chm1:+:212802800:-1 chm1:+:234794883:-1 chm1:+:271924475:-1 chm1:+:336301585:-1 chm1:+:812171430:-1 chm1:+:817371359:-1 chm1:+:939340026:-1 chm1:+:1007504594:-1 chm1:+:1096434223:-1 chm1:+:1277461057:-1 chm1:+:1376307969:-1 chm1:+:2160694980:-1 chm1:+:2195937422:-1 chm1:+:2305377394:-1 chm1:+:2343789322:-1 chm1:+:2527745611:-1 chm1:+:2827569359:-1 chm1:+:3020574927:-1 +TCTGACTGTCCCAGATCACTCCCAGGGTAGGCACGGTACTTTCGCTCGGGAGAGAGGCAGGCTCCAGAGGAGGGACACAGAGCAGGTAGGGAGGGCTTTGAGACATCCCCACCTGGCTCTGCCCAGGGCACATGGCCTTTTCTGGGAGGGAGCCCTTTCTCAGGGGGATCAGGGACCCACGGTCAGGAACCTCAGGACAG chm1:+:18056017:-1 chm1:+:182368600:-1 chm1:+:239962868:-1 chm1:+:400481718:-1 chm1:+:413981165:-1 chm1:+:622761176:-1 chm1:+:745187490:-1 chm1:+:791967802:-1 chm1:+:1062074172:-1 chm1:+:1134607706:-1 chm1:+:1278320919:-1 chm1:+:2002628834:-1 chm1:+:2012355436:-1 chm1:+:2249886712:-1 chm1:+:2299927137:-1 chm1:+:2510454307:-1 chm1:+:2650018890:-1 chm1:+:2771961720:-1 +TCTGACTGTCCCAGATCACTCCCAGGGTAGGCACGGTACTTTCGCTCGGGAGAGAGGCAGGCTCCAGAGGAGGGACACAGAGCAGGTAGGGAGGGCTTTGAGACATCCCCACCTGGCTCTGCCCAGGGCACATGGCCTTTTCTGGGAGGGAGCCCTTTCTCAGGGGGATCAGGGACCCACGGTCAGGAACCTCAGGACAG chm1:+:223602520:-1 chm1:+:283841638:-1 chm1:+:316267988:-1 chm1:+:769941686:-1 chm1:+:829351645:-1 chm1:+:1053549016:-1 chm1:+:1153071373:-1 chm1:+:1383616375:-1 chm1:+:1403380182:-1 chm1:+:1429536508:-1 chm1:+:1559824846:-1 chm1:+:1575938197:-1 chm1:+:1627800778:-1 chm1:+:1816118390:-1 chm1:+:1952650548:-1 chm1:+:2128671292:-1 chm1:+:2335401558:-1 chm1:+:2348515297:-1 chm1:+:2385793854:-1 chm1:+:2423392506:-1 chm1:+:2498387258:-1 chm1:+:2659185757:-1 chm1:+:2717557736:-1 chm1:+:2724473267:-1 chm1:+:2815575787:-1 chm1:+:2873595452:-1 +CTGTCCTGAGGTTCCTGACCGTGGGTCCCTGATCCCCCTGAGAAAGGGCTCCCTCCCAGAAAAGGCCATGTGCCCTGGGCAGAGCCAGGTGGGGATGTCTCAAAGCCCTCCCTACCTGCTCTGTGTCCCTCCTCTGGAGCCTGCCTCTCTCCCGAGCGAAAGTACCGTGCCTACCCTGGGAGTGATCTGGGACAGTCAGA chm1:+:69571848:-1 chm1:+:1733792002:-1 chm1:+:1818682450:16 chm1:+:2533057612:-1 +CTGTCCTGAGGTTCCTGACCGTGGGTCCCTGATCCCCCTGAGAAAGGGCTCCCTCCCAGAAAAGGCCATGTGCCCTGGGCAGAGCCAGGTGGGGATGTCTCAAAGCCCTCCCTACCTGCTCTGTGTCCCTCCTCTGGAGCCTGCCTCTCTCCCGAGCGAAAGTACCGTGCCTACCCTGGGAGTGATCTGGGACAGTCAGA chm1:+:1818682454:16 +CTGTCCTGAGGTTCCTGACCGTGGGTCCCTGATCCCCCTGAGAAAGGGCTCCCTCCCAGAAAAGGCCATGTGCCCTGGGCAGAGCCAGGTGGGGATGTCTCAAAGCCCTCCCTACCTGCTCTGTGTCCCTCCTCTGGAGCCTGCCTCTCTCCCGAGCGAAAGTACCGTGCCTACCCTGGGAGTGATCTGGGACAGTCAGA chm1:+:1818682449:16 +ATGGGGGCGCTGCAGGCATCAGGGCCGGCGCCGCGGGGCCTCTCGCGCCTCCTTCTAGGGCCCGCTTCCCGCCCGCACTGTTTTCCTTCCGGTTGTTCCGGAAGTCGGGTCCTCGAGGGCGGTGAGATCGGTTTCCGATTCCGGGGTGACCGGGGTGGCGGCGGCGGCGCTCCGGTCGCGATGGGCCAGAGGTAAGTGAG chm1:+:507439332:-1 chm1:+:538514419:-1 chm1:+:1511919456:-1 chm1:+:1656533330:-1 chm1:+:2693308729:-1 +ATGGGGGCGCTGCAGGCATCAGGGCCGGCGCCGCGGGGCCTCTCGCGCCTCCTTCTAGGGCCCGCTTCCCGCCCGCACTGTTTTCCTTCCGGTTGTTCCGGAAGTCGGGTCCTCGAGGGCGGTGAGATCGGTTTCCGATTCCGGGGTGACCGGGGTGGCGGCGGCGGCGCTCCGGTCGCGATGGGCCAGAGGTAAGTGAG chm1:+:729519092:-1 chm1:+:2548286678:-1 +ATGGGGGCGCTGCAGGCATCAGGGCCGGCGCCGCGGGGCCTCTCGCGCCTCCTTCTAGGGCCCGCTTCCCGCCCGCACTGTTTTCCTTCCGGTTGTTCCGGAAGTCGGGTCCTCGAGGGCGGTGAGATCGGTTTCCGATTCCGGGGTGACCGGGGTGGCGGCGGCGGCGCTCCGGTCGCGATGGGCCAGAGGTAAGTGAG chm1:+:19584713:-1 chm1:+:34347672:-1 chm1:+:531120526:-1 chm1:+:669714023:-1 chm1:+:1382520788:-1 chm1:+:2424163240:-1 chm1:+:2457894473:-1 chm1:+:2756322245:-1 +ATGGGGGCGCTGCAGGCATCAGGGCCGGCGCCGCGGGGCCTCTCGCGCCTCCTTCTAGGGCCCGCTTCCCGCCCGCACTGTTTTCCTTCCGGTTGTTCCGGAAGTCGGGTCCTCGAGGGCGGTGAGATCGGTTTCCGATTCCGGGGTGACCGGGGTGGCGGCGGCGGCGCTCCGGTCGCGATGGGCCAGAGGTAAGTGAG chm1:+:214996856:-1 chm1:+:2565134256:-1 chm1:+:2673507485:-1 +CTCACTTACCTCTGGCCCATCGCGACCGGAGCGCCGCCGCCGCCACCCCGGTCACCCCGGAATCGGAAACCGATCTCACCGCCCTCGAGGACCCGACTTCCGGAACAACCGGAAGGAAAACAGTGCGGGCGGGAAGCGGGCCCTAGAAGGAGGCGCGAGAGGCCCCGCGGCGCCGGCCCTGATGCCTGCAGCGCCCCCAT chm1:+:1235200937:7 +CTCACTTACCTCTGGCCCATCGCGACCGGAGCGCCGCCGCCGCCACCCCGGTCACCCCGGAATCGGAAACCGATCTCACCGCCCTCGAGGACCCGACTTCCGGAACAACCGGAAGGAAAACAGTGCGGGCGGGAAGCGGGCCCTAGAAGGAGGCGCGAGAGGCCCCGCGGCGCCGGCCCTGATGCCTGCAGCGCCCCCAT chm1:+:1235200936:7 chm1:+:1699960987:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAAC chm1:+:1872033682:-1 chm1:+:1895155139:-1 chm1:+:1941566124:-1 chm1:+:2145659438:-1 chm1:+:2267137347:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAAC chm1:+:243636126:-1 chm1:+:1962352689:-1 chm1:+:1962475669:-1 chm1:+:2078815520:-1 chm1:+:2335941263:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAAC chm1:+:828285369:-1 chm1:+:1559354580:-1 chm1:+:1711929977:-1 chm1:+:1796903210:-1 chm1:+:2226605428:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAAC chm1:+:1221413956:-1 chm1:+:1253849555:-1 chm1:+:1620732651:-1 chm1:+:1626588101:-1 chm1:+:1705577602:-1 chm1:+:1874157283:-1 chm1:+:2640832826:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAAC chm1:+:478853168:-1 chm1:+:626563839:-1 chm1:+:708911769:-1 chm1:+:2191799424:-1 +GTTCAACTGGGGCAATAGGAGCAACCAGGGAATGACTGGGGAAGAAAACTGAGGGTGAGAAACAGCTGGGAGTGTACATTATGCTGGGGCAAGCTCTTTGATGCAATCATTTGGGACAAGGACTACAAACCTCCTGAGAGGGAGAAAATAAGTTAAATGTTTGTAGAAAATATATATAGCTCATCTTGTGTCCAATTTAT chm1:+:80316668:10 +GTTCAACTGGGGCAATAGGAGCAACCAGGGAATGACTGGGGAAGAAAACTGAGGGTGAGAAACAGCTGGGAGTGTACATTATGCTGGGGCAAGCTCTTTGATGCAATCATTTGGGACAAGGACTACAAACCTCCTGAGAGGGAGAAAATAAGTTAAATGTTTGTAGAAAATATATATAGCTCATCTTGTGTCCAATTTAT chm1:+:80316665:10 +GTTCAACTGGGGCAATAGGAGCAACCAGGGAATGACTGGGGAAGAAAACTGAGGGTGAGAAACAGCTGGGAGTGTACATTATGCTGGGGCAAGCTCTTTGATGCAATCATTTGGGACAAGGACTACAAACCTCCTGAGAGGGAGAAAATAAGTTAAATGTTTGTAGAAAATATATATAGCTCATCTTGTGTCCAATTTAT chm1:+:80316667:10 +TTGAAAAGCAATAAGATATTTACAAAAGAAACTAATGGCGCTGAGCTATCCACGTCAAAAGAGCCCTTGTGTAAATATTTTTGAAAAAGTAAAGAGATCGTAATAATGTCGAATAACTAAAATGCTGTTTATGTGTATTGTGAGGACATATTCTTATGTATAAGGGTTTGCTGGGTTTTTGCAATATCAGAAGAGCCTAC chm1:+:106325992:-1 chm1:+:1521838168:-1 +TTGAAAAGCAATAAGATATTTACAAAAGAAACTAATGGCGCTGAGCTATCCACGTCAAAAGAGCCCTTGTGTAAATATTTTTGAAAAAGTAAAGAGATCGTAATAATGTCGAATAACTAAAATGCTGTTTATGTGTATTGTGAGGACATATTCTTATGTATAAGGGTTTGCTGGGTTTTTGCAATATCAGAAGAGCCTAC chm1:+:3016857834:12 +TTGAAAAGCAATAAGATATTTACAAAAGAAACTAATGGCGCTGAGCTATCCACGTCAAAAGAGCCCTTGTGTAAATATTTTTGAAAAAGTAAAGAGATCGTAATAATGTCGAATAACTAAAATGCTGTTTATGTGTATTGTGAGGACATATTCTTATGTATAAGGGTTTGCTGGGTTTTTGCAATATCAGAAGAGCCTAC chm1:+:3016857835:12 +TTGAAAAGCAATAAGATATTTACAAAAGAAACTAATGGCGCTGAGCTATCCACGTCAAAAGAGCCCTTGTGTAAATATTTTTGAAAAAGTAAAGAGATCGTAATAATGTCGAATAACTAAAATGCTGTTTATGTGTATTGTGAGGACATATTCTTATGTATAAGGGTTTGCTGGGTTTTTGCAATATCAGAAGAGCCTAC chm1:+:3016857836:12 +TTGAAAAGCAATAAGATATTTACAAAAGAAACTAATGGCGCTGAGCTATCCACGTCAAAAGAGCCCTTGTGTAAATATTTTTGAAAAAGTAAAGAGATCGTAATAATGTCGAATAACTAAAATGCTGTTTATGTGTATTGTGAGGACATATTCTTATGTATAAGGGTTTGCTGGGTTTTTGCAATATCAGAAGAGCCTAC chm1:+:1780041973:-1 +GTAGGCTCTTCTGATATTGCAAAAACCCAGCAAACCCTTATACATAAGAATATGTCCTCACAATACACATAAACAGCATTTTAGTTATTCGACATTATTACGATCTCTTTACTTTTTCAAAAATATTTACACAAGGGCTCTTTTGACGTGGATAGCTCAGCGCCATTAGTTTCTTTTGTAAATATCTTATTGCTTTTCAA chm1:+:579651788:-1 chm1:+:732742565:-1 chm1:+:1977183112:-1 +GTAGGCTCTTCTGATATTGCAAAAACCCAGCAAACCCTTATACATAAGAATATGTCCTCACAATACACATAAACAGCATTTTAGTTATTCGACATTATTACGATCTCTTTACTTTTTCAAAAATATTTACACAAGGGCTCTTTTGACGTGGATAGCTCAGCGCCATTAGTTTCTTTTGTAAATATCTTATTGCTTTTCAA chm1:+:2393363546:-1 +GTGGCTCACACCTGTAATCCATCAATGAGAGGGCCTGAGGTGGGCGGATCTCTTGAGGTCAAGAGTTTGAGACAAGCCTGGCCAATATGACAAAACCCTGACTCCTACTAAAAATAAAAAAATTAGACGGGGTGTGTTGGCACGCACCTGTAGTCCCAGCTACTCGAGAAGGCTGAGATCAGAGAATTGTTTGAACCTGG chm1:+:106553612:6 +CCAGGTTCAAACAATTCTCTGATCTCAGCCTTCTCGAGTAGCTGGGACTACAGGTGCGTGCCAACACACCCCGTCTAATTTTTTTATTTTTAGTAGGAGTCAGGGTTTTGTCATATTGGCCAGGCTTGTCTCAAACTCTTGACCTCAAGAGATCCGCCCACCTCAGGCCCTCTCATTGATGGATTACAGGTGTGAGCCAC chm1:+:2071905342:-1 +CCAGGTTCAAACAATTCTCTGATCTCAGCCTTCTCGAGTAGCTGGGACTACAGGTGCGTGCCAACACACCCCGTCTAATTTTTTTATTTTTAGTAGGAGTCAGGGTTTTGTCATATTGGCCAGGCTTGTCTCAAACTCTTGACCTCAAGAGATCCGCCCACCTCAGGCCCTCTCATTGATGGATTACAGGTGTGAGCCAC chm1:+:2792519150:39 +TATATGTGGAAGTGATGAAAACAGGAGAAAATCTATAGCTCAAAAAGGCAACTTATGAACCACCCCATATTTTATGTTTTGCAAGAGCAACCCCTGCATTACCCTACATTGCTCTATGAAGGAGTGTCGACCTGGAATGTAAGCAAAACTGGGATTAAAAAAACAATGCTCTCAGACCTAATCTGTAACCCATCCCTGCA chm1:+:734065289:-1 chm1:+:1247219779:-1 chm1:+:1451096833:-1 chm1:+:2262806461:-1 +TATATGTGGAAGTGATGAAAACAGGAGAAAATCTATAGCTCAAAAAGGCAACTTATGAACCACCCCATATTTTATGTTTTGCAAGAGCAACCCCTGCATTACCCTACATTGCTCTATGAAGGAGTGTCGACCTGGAATGTAAGCAAAACTGGGATTAAAAAAACAATGCTCTCAGACCTAATCTGTAACCCATCCCTGCA chm1:+:570751583:-1 chm1:+:773223774:-1 chm1:+:1016546934:-1 chm1:+:1060971204:-1 chm1:+:1171859604:-1 chm1:+:1354089779:-1 chm1:+:1373547601:-1 chm1:+:1550347444:-1 chm1:+:1735796269:-1 chm1:+:2148375773:-1 chm1:+:2408699069:-1 chm1:+:2409291789:-1 chm1:+:2650860178:-1 chm1:+:2915478300:-1 chm1:+:3096024734:-1 +TATATGTGGAAGTGATGAAAACAGGAGAAAATCTATAGCTCAAAAAGGCAACTTATGAACCACCCCATATTTTATGTTTTGCAAGAGCAACCCCTGCATTACCCTACATTGCTCTATGAAGGAGTGTCGACCTGGAATGTAAGCAAAACTGGGATTAAAAAAACAATGCTCTCAGACCTAATCTGTAACCCATCCCTGCA chm1:+:216289789:-1 chm1:+:771775682:-1 chm1:+:824624811:-1 chm1:+:947319477:-1 chm1:+:1275440866:-1 chm1:+:1418394791:-1 chm1:+:1466843961:-1 chm1:+:1845977182:-1 chm1:+:2156617235:-1 chm1:+:2259109294:-1 +TATATGTGGAAGTGATGAAAACAGGAGAAAATCTATAGCTCAAAAAGGCAACTTATGAACCACCCCATATTTTATGTTTTGCAAGAGCAACCCCTGCATTACCCTACATTGCTCTATGAAGGAGTGTCGACCTGGAATGTAAGCAAAACTGGGATTAAAAAAACAATGCTCTCAGACCTAATCTGTAACCCATCCCTGCA chm1:+:2674884945:-1 chm1:+:3000601389:-1 chm1:+:3013337396:-1 chm1:+:3040931457:-1 +TATATGTGGAAGTGATGAAAACAGGAGAAAATCTATAGCTCAAAAAGGCAACTTATGAACCACCCCATATTTTATGTTTTGCAAGAGCAACCCCTGCATTACCCTACATTGCTCTATGAAGGAGTGTCGACCTGGAATGTAAGCAAAACTGGGATTAAAAAAACAATGCTCTCAGACCTAATCTGTAACCCATCCCTGCA chm1:+:2798927:-1 chm1:+:74450802:-1 chm1:+:181603754:-1 chm1:+:512991812:-1 chm1:+:555464170:-1 chm1:+:594455578:-1 chm1:+:696032942:-1 chm1:+:820865330:-1 chm1:+:885853377:-1 chm1:+:890429472:-1 chm1:+:952700561:-1 chm1:+:1053817187:-1 chm1:+:1365773718:-1 chm1:+:1369247205:-1 chm1:+:1388306448:-1 chm1:+:1433693640:-1 chm1:+:1435747589:-1 chm1:+:1470340127:-1 chm1:+:1723154336:-1 chm1:+:1753726639:-1 chm1:+:1834909465:-1 chm1:+:2137157623:-1 chm1:+:2378601860:-1 chm1:+:2442273685:-1 chm1:+:2535677798:-1 chm1:+:2607178680:-1 chm1:+:2617714736:-1 chm1:+:2714800728:-1 chm1:+:3098044435:-1 +TGCAGGGATGGGTTACAGATTAGGTCTGAGAGCATTGTTTTTTTAATCCCAGTTTTGCTTACATTCCAGGTCGACACTCCTTCATAGAGCAATGTAGGGTAATGCAGGGGTTGCTCTTGCAAAACATAAAATATGGGGTGGTTCATAAGTTGCCTTTTTGAGCTATAGATTTTCTCCTGTTTTCATCACTTCCACATATA chm1:+:304236497:8 +TGCAGGGATGGGTTACAGATTAGGTCTGAGAGCATTGTTTTTTTAATCCCAGTTTTGCTTACATTCCAGGTCGACACTCCTTCATAGAGCAATGTAGGGTAATGCAGGGGTTGCTCTTGCAAAACATAAAATATGGGGTGGTTCATAAGTTGCCTTTTTGAGCTATAGATTTTCTCCTGTTTTCATCACTTCCACATATA chm1:+:304236500:8 +TGCAGGGATGGGTTACAGATTAGGTCTGAGAGCATTGTTTTTTTAATCCCAGTTTTGCTTACATTCCAGGTCGACACTCCTTCATAGAGCAATGTAGGGTAATGCAGGGGTTGCTCTTGCAAAACATAAAATATGGGGTGGTTCATAAGTTGCCTTTTTGAGCTATAGATTTTCTCCTGTTTTCATCACTTCCACATATA chm1:+:304236502:8 +TGCAGGGATGGGTTACAGATTAGGTCTGAGAGCATTGTTTTTTTAATCCCAGTTTTGCTTACATTCCAGGTCGACACTCCTTCATAGAGCAATGTAGGGTAATGCAGGGGTTGCTCTTGCAAAACATAAAATATGGGGTGGTTCATAAGTTGCCTTTTTGAGCTATAGATTTTCTCCTGTTTTCATCACTTCCACATATA chm1:+:304236496:8 +AAAGCAATAGCTGGGTTTTACCAAATGGTTTTCTGCATCTATTAACATGAGTCAAATAACTTTGGTTTTTAATCTCTTTATGTGATGTTTCACATTTATTGGACTTGCATATGTGAACCATCTCTGCATCTGTGGTATCCCACTTGATCATGATAGTATTATCTTTTTGATATGCTATTGGATTTGATCAGCTAGCATTT chm1:+:1064822662:-1 chm1:+:2655255365:-1 chm1:+:2934882983:-1 chm1:+:2972277193:-1 chm1:+:2991880991:-1 chm1:+:3051409413:-1 +AAAGCAATAGCTGGGTTTTACCAAATGGTTTTCTGCATCTATTAACATGAGTCAAATAACTTTGGTTTTTAATCTCTTTATGTGATGTTTCACATTTATTGGACTTGCATATGTGAACCATCTCTGCATCTGTGGTATCCCACTTGATCATGATAGTATTATCTTTTTGATATGCTATTGGATTTGATCAGCTAGCATTT chm1:+:323788219:-1 chm1:+:410694688:-1 chm1:+:1106349285:-1 chm1:+:1110894490:12 chm1:+:1860661061:-1 +AAAGCAATAGCTGGGTTTTACCAAATGGTTTTCTGCATCTATTAACATGAGTCAAATAACTTTGGTTTTTAATCTCTTTATGTGATGTTTCACATTTATTGGACTTGCATATGTGAACCATCTCTGCATCTGTGGTATCCCACTTGATCATGATAGTATTATCTTTTTGATATGCTATTGGATTTGATCAGCTAGCATTT chm1:+:1110894487:12 +AAATGCTAGCTGATCAAATCCAATAGCATATCAAAAAGATAATACTATCATGATCAAGTGGGATACCACAGATGCAGAGATGGTTCACATATGCAAGTCCAATAAATGTGAAACATCACATAAAGAGATTAAAAACCAAAGTTATTTGACTCATGTTAATAGATGCAGAAAACCATTTGGTAAAACCCAGCTATTGCTTT chm1:+:2909287857:-1 +GTTTCTAGCTGTAATTAAATAAAGCCATTGAGCCTTTCATTTAATCTGATAAACCGTCATAGATATCTACTTTTTGATACTGTTTTTATGTCACGTTACCCTCATGTGTGTTGTGCAAGACCGTGGGGTATCGGGTTTAGAGGAAGATGTTCCCCCACCAGCTCTCTATCGTTTCTGCCACTGGCCCGTCTGCCACATTA chm1:+:356450393:-1 chm1:+:1015179833:-1 chm1:+:1218780162:-1 chm1:+:1959843470:-1 chm1:+:2380073878:-1 chm1:+:2421919911:-1 chm1:+:2637256027:-1 chm1:+:3015741416:-1 +GTTTCTAGCTGTAATTAAATAAAGCCATTGAGCCTTTCATTTAATCTGATAAACCGTCATAGATATCTACTTTTTGATACTGTTTTTATGTCACGTTACCCTCATGTGTGTTGTGCAAGACCGTGGGGTATCGGGTTTAGAGGAAGATGTTCCCCCACCAGCTCTCTATCGTTTCTGCCACTGGCCCGTCTGCCACATTA chm1:+:36629301:-1 chm1:+:95662513:-1 chm1:+:266963668:-1 chm1:+:497910768:-1 chm1:+:600689555:-1 chm1:+:879861723:-1 chm1:+:892837228:-1 chm1:+:1039287286:-1 chm1:+:1151880147:-1 chm1:+:1224395161:-1 chm1:+:1627702054:-1 chm1:+:1825943260:-1 chm1:+:1931121127:-1 chm1:+:2032441641:-1 chm1:+:2159036557:-1 chm1:+:2284355644:-1 chm1:+:2753130511:-1 +GTTTCTAGCTGTAATTAAATAAAGCCATTGAGCCTTTCATTTAATCTGATAAACCGTCATAGATATCTACTTTTTGATACTGTTTTTATGTCACGTTACCCTCATGTGTGTTGTGCAAGACCGTGGGGTATCGGGTTTAGAGGAAGATGTTCCCCCACCAGCTCTCTATCGTTTCTGCCACTGGCCCGTCTGCCACATTA chm1:+:3839900:-1 chm1:+:331403959:-1 chm1:+:499189463:-1 chm1:+:689727518:-1 chm1:+:947113770:-1 chm1:+:1042539586:-1 chm1:+:1949759142:-1 chm1:+:1985523296:-1 chm1:+:2767880296:-1 chm1:+:2769562487:-1 chm1:+:2852468810:-1 +GTTTCTAGCTGTAATTAAATAAAGCCATTGAGCCTTTCATTTAATCTGATAAACCGTCATAGATATCTACTTTTTGATACTGTTTTTATGTCACGTTACCCTCATGTGTGTTGTGCAAGACCGTGGGGTATCGGGTTTAGAGGAAGATGTTCCCCCACCAGCTCTCTATCGTTTCTGCCACTGGCCCGTCTGCCACATTA chm1:+:175551365:-1 chm1:+:278178611:-1 chm1:+:373381222:-1 chm1:+:575397882:-1 chm1:+:1097872592:-1 chm1:+:1445710001:-1 chm1:+:2291490417:-1 chm1:+:2461749514:-1 chm1:+:2474061874:-1 chm1:+:2603774620:-1 chm1:+:3026704824:-1 +TAATGTGGCAGACGGGCCAGTGGCAGAAACGATAGAGAGCTGGTGGGGGAACATCTTCCTCTAAACCCGATACCCCACGGTCTTGCACAACACACATGAGGGTAACGTGACATAAAAACAGTATCAAAAAGTAGATATCTATGACGGTTTATCAGATTAAATGAAAGGCTCAATGGCTTTATTTAATTACAGCTAGAAAC chm1:+:305880317:-1 chm1:+:682280048:11 chm1:+:1845854099:-1 chm1:+:2601535516:-1 chm1:+:2607857090:-1 +TAATGTGGCAGACGGGCCAGTGGCAGAAACGATAGAGAGCTGGTGGGGGAACATCTTCCTCTAAACCCGATACCCCACGGTCTTGCACAACACACATGAGGGTAACGTGACATAAAAACAGTATCAAAAAGTAGATATCTATGACGGTTTATCAGATTAAATGAAAGGCTCAATGGCTTTATTTAATTACAGCTAGAAAC chm1:+:1800044362:-1 +GAGAATCTTTAGGATACCCAGTCTATGATAAAACAAAAAACAAACAAAAAATTTCAAAGACATAACCATTAAGAAATCGGTAAAACAATAAATGGTCCCTTACAAAAAAAAAAAATCGAATACCACTGGCCCAGCCACCAGGCAGTAAAATGGAATGTGGTGATTAGTGCATCCTATTTCATGCTACTACCCACCTCATA chm1:+:3057218200:17 +GAGAATCTTTAGGATACCCAGTCTATGATAAAACAAAAAACAAACAAAAAATTTCAAAGACATAACCATTAAGAAATCGGTAAAACAATAAATGGTCCCTTACAAAAAAAAAAAATCGAATACCACTGGCCCAGCCACCAGGCAGTAAAATGGAATGTGGTGATTAGTGCATCCTATTTCATGCTACTACCCACCTCATA chm1:+:552780525:-1 chm1:+:940372619:-1 chm1:+:1009788975:-1 +GAGAATCTTTAGGATACCCAGTCTATGATAAAACAAAAAACAAACAAAAAATTTCAAAGACATAACCATTAAGAAATCGGTAAAACAATAAATGGTCCCTTACAAAAAAAAAAAATCGAATACCACTGGCCCAGCCACCAGGCAGTAAAATGGAATGTGGTGATTAGTGCATCCTATTTCATGCTACTACCCACCTCATA chm1:+:12214232:-1 chm1:+:28617912:-1 chm1:+:31584599:-1 chm1:+:40987711:-1 chm1:+:61730183:-1 chm1:+:64841768:-1 chm1:+:89462780:-1 chm1:+:153676224:-1 chm1:+:166825261:-1 chm1:+:173777407:-1 chm1:+:175091212:-1 chm1:+:178241926:-1 chm1:+:178575847:-1 chm1:+:228669180:-1 chm1:+:230095396:-1 chm1:+:286174257:-1 chm1:+:292991681:-1 chm1:+:296265439:-1 chm1:+:323186950:-1 chm1:+:331378578:-1 chm1:+:351667064:-1 chm1:+:387768376:-1 chm1:+:401866701:-1 chm1:+:450401873:-1 chm1:+:463882707:-1 chm1:+:501932584:-1 chm1:+:529645356:-1 chm1:+:541359972:-1 chm1:+:582348435:-1 chm1:+:601348999:-1 chm1:+:637904302:-1 chm1:+:639487278:-1 chm1:+:646092431:-1 chm1:+:695294216:-1 chm1:+:706646261:-1 chm1:+:720529823:-1 chm1:+:774349194:-1 chm1:+:779504247:-1 chm1:+:838514421:-1 chm1:+:866708967:-1 chm1:+:872200342:-1 chm1:+:893090524:-1 chm1:+:907514379:-1 chm1:+:969807174:-1 chm1:+:996066826:-1 chm1:+:1035794863:-1 chm1:+:1043357926:-1 chm1:+:1057170013:-1 chm1:+:1059103080:-1 chm1:+:1074620658:-1 chm1:+:1090300775:-1 chm1:+:1100925454:-1 chm1:+:1101063450:-1 chm1:+:1144931171:-1 chm1:+:1162537180:-1 chm1:+:1197331635:-1 chm1:+:1210089252:-1 chm1:+:1238376917:-1 chm1:+:1244248212:-1 chm1:+:1288642048:-1 chm1:+:1311718410:-1 chm1:+:1314010585:-1 chm1:+:1359185979:-1 chm1:+:1362257274:-1 chm1:+:1389971107:-1 chm1:+:1411365373:-1 chm1:+:1417262582:-1 chm1:+:1418562472:-1 chm1:+:1431924527:-1 chm1:+:1469923786:-1 chm1:+:1528162533:-1 chm1:+:1543899630:-1 chm1:+:1558020078:-1 chm1:+:1610393592:-1 chm1:+:1624518934:-1 chm1:+:1636459133:-1 chm1:+:1715348367:-1 chm1:+:1735562524:-1 chm1:+:1760263296:-1 chm1:+:1776685566:-1 chm1:+:1801815157:-1 chm1:+:1888539866:-1 chm1:+:1893291374:-1 chm1:+:1904723265:-1 chm1:+:1958942367:-1 chm1:+:1966774754:-1 chm1:+:1969985252:-1 chm1:+:1970282079:-1 chm1:+:1997484405:-1 chm1:+:2020902018:-1 chm1:+:2047630535:-1 chm1:+:2049770031:-1 chm1:+:2073680345:-1 chm1:+:2113186969:-1 chm1:+:2151075918:-1 chm1:+:2180412926:-1 chm1:+:2185258667:-1 chm1:+:2233577984:-1 chm1:+:2270508537:-1 chm1:+:2273156755:-1 chm1:+:2288922793:-1 chm1:+:2289808631:-1 chm1:+:2352082483:-1 chm1:+:2364240896:-1 chm1:+:2391361306:-1 chm1:+:2394756233:-1 chm1:+:2404096110:-1 chm1:+:2405455237:-1 chm1:+:2441279575:-1 chm1:+:2456710299:-1 chm1:+:2475687281:-1 chm1:+:2490827817:-1 chm1:+:2541716575:-1 chm1:+:2546781190:-1 chm1:+:2546898959:-1 chm1:+:2549359471:-1 chm1:+:2556321751:-1 chm1:+:2569369785:-1 chm1:+:2581632740:-1 chm1:+:2610881078:-1 chm1:+:2612240392:-1 chm1:+:2647703379:-1 chm1:+:2648907651:-1 chm1:+:2662137432:-1 chm1:+:2665637900:-1 chm1:+:2692027497:-1 chm1:+:2724310097:-1 chm1:+:2731811523:-1 chm1:+:2735099712:-1 chm1:+:2761867198:-1 chm1:+:2768388835:-1 chm1:+:2770109950:-1 chm1:+:2796163032:-1 chm1:+:2813850283:-1 chm1:+:2814698787:-1 chm1:+:2815198387:-1 chm1:+:2904621977:-1 chm1:+:2924014518:-1 chm1:+:2935146967:-1 chm1:+:2954334349:-1 chm1:+:3013202032:-1 chm1:+:3015126759:-1 chm1:+:3057218202:17 +GAGAATCTTTAGGATACCCAGTCTATGATAAAACAAAAAACAAACAAAAAATTTCAAAGACATAACCATTAAGAAATCGGTAAAACAATAAATGGTCCCTTACAAAAAAAAAAAATCGAATACCACTGGCCCAGCCACCAGGCAGTAAAATGGAATGTGGTGATTAGTGCATCCTATTTCATGCTACTACCCACCTCATA chm1:+:9043454:-1 chm1:+:32582573:-1 chm1:+:70329994:-1 chm1:+:147339816:-1 chm1:+:160542870:-1 chm1:+:176688421:-1 chm1:+:204475162:-1 chm1:+:245069203:-1 chm1:+:261639588:-1 chm1:+:264261802:-1 chm1:+:390238021:-1 chm1:+:392192074:-1 chm1:+:392773635:-1 chm1:+:408995813:-1 chm1:+:433826872:-1 chm1:+:459628906:-1 chm1:+:465504141:-1 chm1:+:602419945:-1 chm1:+:644276786:-1 chm1:+:660475593:-1 chm1:+:673962788:-1 chm1:+:692668775:-1 chm1:+:773813305:-1 chm1:+:797107275:-1 chm1:+:801151473:-1 chm1:+:817939623:-1 chm1:+:823906002:-1 chm1:+:828583768:-1 chm1:+:851587893:-1 chm1:+:861772426:-1 chm1:+:920642949:-1 chm1:+:1032925461:-1 chm1:+:1041468638:-1 chm1:+:1127252441:-1 chm1:+:1153707556:-1 chm1:+:1165225112:-1 chm1:+:1173879690:-1 chm1:+:1236555048:-1 chm1:+:1243762219:-1 chm1:+:1309682395:-1 chm1:+:1346922418:-1 chm1:+:1351011011:-1 chm1:+:1366562354:-1 chm1:+:1425859520:-1 chm1:+:1449412926:-1 chm1:+:1450160478:-1 chm1:+:1466213358:-1 chm1:+:1473453374:-1 chm1:+:1496106413:-1 chm1:+:1514026856:-1 chm1:+:1549135951:-1 chm1:+:1651945871:-1 chm1:+:1918761845:-1 chm1:+:1968949459:-1 chm1:+:2072434905:-1 chm1:+:2118420228:-1 chm1:+:2162619877:-1 chm1:+:2239827584:-1 chm1:+:2240384408:-1 chm1:+:2240629538:-1 chm1:+:2268324547:-1 chm1:+:2297022152:-1 chm1:+:2348643285:-1 chm1:+:2354667979:-1 chm1:+:2460118063:-1 chm1:+:2461589168:-1 chm1:+:2465224493:-1 chm1:+:2532312170:-1 chm1:+:2546035291:-1 chm1:+:2583550572:-1 chm1:+:2594170463:-1 chm1:+:2623458912:-1 chm1:+:2679660057:-1 chm1:+:2693927128:-1 chm1:+:2742004465:-1 chm1:+:2821174894:-1 chm1:+:2894134492:-1 chm1:+:2944324873:-1 chm1:+:2963878717:-1 chm1:+:2986175998:-1 chm1:+:2989275228:-1 chm1:+:3006738013:-1 chm1:+:3015763480:-1 +GAGAATCTTTAGGATACCCAGTCTATGATAAAACAAAAAACAAACAAAAAATTTCAAAGACATAACCATTAAGAAATCGGTAAAACAATAAATGGTCCCTTACAAAAAAAAAAAATCGAATACCACTGGCCCAGCCACCAGGCAGTAAAATGGAATGTGGTGATTAGTGCATCCTATTTCATGCTACTACCCACCTCATA chm1:+:473311430:-1 chm1:+:676599831:-1 chm1:+:2351343901:-1 chm1:+:2564736924:-1 chm1:+:2618244470:-1 +GAGAATCTTTAGGATACCCAGTCTATGATAAAACAAAAAACAAACAAAAAATTTCAAAGACATAACCATTAAGAAATCGGTAAAACAATAAATGGTCCCTTACAAAAAAAAAAAATCGAATACCACTGGCCCAGCCACCAGGCAGTAAAATGGAATGTGGTGATTAGTGCATCCTATTTCATGCTACTACCCACCTCATA chm1:+:62175984:-1 chm1:+:190117978:-1 chm1:+:247766239:-1 chm1:+:1231067482:-1 chm1:+:1526802997:-1 chm1:+:1712041831:-1 chm1:+:1787369628:-1 chm1:+:1790897098:-1 chm1:+:1832846788:-1 chm1:+:2301190552:-1 chm1:+:2376631124:-1 chm1:+:2427392410:-1 chm1:+:2467093217:-1 chm1:+:2819423648:-1 chm1:+:2827312604:-1 +TATGAGGTGGGTAGTAGCATGAAATAGGATGCACTAATCACCACATTCCATTTTACTGCCTGGTGGCTGGGCCAGTGGTATTCGATTTTTTTTTTTTGTAAGGGACCATTTATTGTTTTACCGATTTCTTAATGGTTATGTCTTTGAAATTTTTTGTTTGTTTTTTGTTTTATCATAGACTGGGTATCCTAAAGATTCTC chm1:+:35106902:-1 chm1:+:75622833:-1 chm1:+:182013544:-1 chm1:+:309286623:-1 chm1:+:438164495:-1 chm1:+:605953620:-1 chm1:+:681862946:-1 chm1:+:688331753:-1 chm1:+:712770653:-1 chm1:+:887362110:-1 chm1:+:1106951344:-1 chm1:+:1273111455:-1 chm1:+:1281542024:-1 chm1:+:1342182287:-1 chm1:+:1362068172:-1 chm1:+:1426376518:-1 chm1:+:1675036882:-1 chm1:+:1778930936:-1 chm1:+:1823300858:-1 chm1:+:1929669109:-1 chm1:+:2078955030:-1 chm1:+:2083374629:-1 chm1:+:2128393897:-1 chm1:+:2231446332:-1 chm1:+:2543592885:-1 chm1:+:2552179087:-1 chm1:+:2698586472:-1 chm1:+:2749506836:-1 chm1:+:2825749673:-1 +TATGAGGTGGGTAGTAGCATGAAATAGGATGCACTAATCACCACATTCCATTTTACTGCCTGGTGGCTGGGCCAGTGGTATTCGATTTTTTTTTTTTGTAAGGGACCATTTATTGTTTTACCGATTTCTTAATGGTTATGTCTTTGAAATTTTTTGTTTGTTTTTTGTTTTATCATAGACTGGGTATCCTAAAGATTCTC chm1:+:340967959:-1 chm1:+:1175965174:-1 chm1:+:2327607292:-1 chm1:+:2328613911:-1 chm1:+:2852342185:-1 chm1:+:3057033386:17 +TATGAGGTGGGTAGTAGCATGAAATAGGATGCACTAATCACCACATTCCATTTTACTGCCTGGTGGCTGGGCCAGTGGTATTCGATTTTTTTTTTTTGTAAGGGACCATTTATTGTTTTACCGATTTCTTAATGGTTATGTCTTTGAAATTTTTTGTTTGTTTTTTGTTTTATCATAGACTGGGTATCCTAAAGATTCTC chm1:+:108749629:-1 chm1:+:1905941302:-1 chm1:+:1908257124:-1 chm1:+:2937235408:-1 chm1:+:3057033388:17 +TATGAGGTGGGTAGTAGCATGAAATAGGATGCACTAATCACCACATTCCATTTTACTGCCTGGTGGCTGGGCCAGTGGTATTCGATTTTTTTTTTTTGTAAGGGACCATTTATTGTTTTACCGATTTCTTAATGGTTATGTCTTTGAAATTTTTTGTTTGTTTTTTGTTTTATCATAGACTGGGTATCCTAAAGATTCTC chm1:+:476487680:-1 +TATGAGGTGGGTAGTAGCATGAAATAGGATGCACTAATCACCACATTCCATTTTACTGCCTGGTGGCTGGGCCAGTGGTATTCGATTTTTTTTTTTTGTAAGGGACCATTTATTGTTTTACCGATTTCTTAATGGTTATGTCTTTGAAATTTTTTGTTTGTTTTTTGTTTTATCATAGACTGGGTATCCTAAAGATTCTC chm1:+:335383743:-1 chm1:+:694190110:-1 chm1:+:919483741:-1 chm1:+:1482220804:-1 chm1:+:1526931984:-1 chm1:+:2081307916:-1 chm1:+:2507933233:-1 chm1:+:2624248012:-1 chm1:+:2816120104:-1 chm1:+:2871639231:-1 +GTAGGAGACCTGGCCACGCCCTACTACCTTCCCACAGACACACCCCCACCATGTTCCAGAAGCCAGTCAATGGGGGCAGGGGGCATGCTCCTTACTATCGAGTTCAGGAACAATCTCCAAACATAGACACCAAGGGCCCAGGATGCATTTGTTAAGTTTCAAAGTATCAAACCCTTACCCTTCCAACACGGTTTCCACTC chm1:+:1565964270:-1 chm1:+:2141078353:-1 chm1:+:2602292729:-1 chm1:+:2691074860:6 +GTAGGAGACCTGGCCACGCCCTACTACCTTCCCACAGACACACCCCCACCATGTTCCAGAAGCCAGTCAATGGGGGCAGGGGGCATGCTCCTTACTATCGAGTTCAGGAACAATCTCCAAACATAGACACCAAGGGCCCAGGATGCATTTGTTAAGTTTCAAAGTATCAAACCCTTACCCTTCCAACACGGTTTCCACTC chm1:+:2691074862:6 +GTAGGAGACCTGGCCACGCCCTACTACCTTCCCACAGACACACCCCCACCATGTTCCAGAAGCCAGTCAATGGGGGCAGGGGGCATGCTCCTTACTATCGAGTTCAGGAACAATCTCCAAACATAGACACCAAGGGCCCAGGATGCATTTGTTAAGTTTCAAAGTATCAAACCCTTACCCTTCCAACACGGTTTCCACTC chm1:+:2691074859:6 +GTAGGAGACCTGGCCACGCCCTACTACCTTCCCACAGACACACCCCCACCATGTTCCAGAAGCCAGTCAATGGGGGCAGGGGGCATGCTCCTTACTATCGAGTTCAGGAACAATCTCCAAACATAGACACCAAGGGCCCAGGATGCATTTGTTAAGTTTCAAAGTATCAAACCCTTACCCTTCCAACACGGTTTCCACTC chm1:+:2691074861:6 +AGGCGGTCTGCTAGGTGGGAAAGGGCACATCCACGGCCCACATCCCCGAGGCATCTGCTAGGTGGGGAAAGGGCAGCCTCGTCCTCACACCTGATGCAACGGGCCCCGTACTGACCAACTCGCTTAGTAGGTGCACCTGCGCCTCCCTGAGCCGGCACATCACTCTGTTGGGCAGGCCTGGGAAGGGAGCATCATTTCAT chm1:+:2278681785:-1 chm1:+:2858138413:13 +AGGCGGTCTGCTAGGTGGGAAAGGGCACATCCACGGCCCACATCCCCGAGGCATCTGCTAGGTGGGGAAAGGGCAGCCTCGTCCTCACACCTGATGCAACGGGCCCCGTACTGACCAACTCGCTTAGTAGGTGCACCTGCGCCTCCCTGAGCCGGCACATCACTCTGTTGGGCAGGCCTGGGAAGGGAGCATCATTTCAT chm1:+:2858138414:13 +AGGCGGTCTGCTAGGTGGGAAAGGGCACATCCACGGCCCACATCCCCGAGGCATCTGCTAGGTGGGGAAAGGGCAGCCTCGTCCTCACACCTGATGCAACGGGCCCCGTACTGACCAACTCGCTTAGTAGGTGCACCTGCGCCTCCCTGAGCCGGCACATCACTCTGTTGGGCAGGCCTGGGAAGGGAGCATCATTTCAT chm1:+:2858138421:13 +AGGCGGTCTGCTAGGTGGGAAAGGGCACATCCACGGCCCACATCCCCGAGGCATCTGCTAGGTGGGGAAAGGGCAGCCTCGTCCTCACACCTGATGCAACGGGCCCCGTACTGACCAACTCGCTTAGTAGGTGCACCTGCGCCTCCCTGAGCCGGCACATCACTCTGTTGGGCAGGCCTGGGAAGGGAGCATCATTTCAT chm1:+:2858138423:13 +ATGAAATGATGCTCCCTTCCCAGGCCTGCCCAACAGAGTGATGTGCCGGCTCAGGGAGGCGCAGGTGCACCTACTAAGCGAGTTGGTCAGTACGGGGCCCGTTGCATCAGGTGTGAGGACGAGGCTGCCCTTTCCCCACCTAGCAGATGCCTCGGGGATGTGGGCCGTGGATGTGCCCTTTCCCACCTAGCAGACCGCCT chm1:+:2395987218:-1 chm1:+:2706689606:-1 +AGGAACTCTTTTTTTTTCTTTTTCTTTTTTGAGACAGTCTCACTCTGTCACCCAGGTAGAGGTGTCTGTGGTGCGATCTTGGCTGACTGCAGCCTCTGTCCTACCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGAATTACAGGCACTCGCCACCACACCCGGCTAATTTTGTATTTTTAGTAGAGA chm1:+:28718064:36 chm1:+:204134047:37 chm1:+:282338653:40 chm1:+:452482982:-1 chm1:+:955503776:36 chm1:+:1169923609:-1 chm1:+:1336494003:8 chm1:+:1524214365:40 chm1:+:2257061575:-1 chm1:+:2348277008:40 chm1:+:2350067042:-1 chm1:+:2572556170:40 chm1:+:2580636761:-1 chm1:+:2584744414:34 chm1:+:2998086220:-1 +AGGAACTCTTTTTTTTTCTTTTTCTTTTTTGAGACAGTCTCACTCTGTCACCCAGGTAGAGGTGTCTGTGGTGCGATCTTGGCTGACTGCAGCCTCTGTCCTACCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGAATTACAGGCACTCGCCACCACACCCGGCTAATTTTGTATTTTTAGTAGAGA chm1:+:47792566:38 chm1:+:204507945:36 chm1:+:245043343:34 chm1:+:1362361390:38 chm1:+:1704395033:-1 chm1:+:1769072858:38 chm1:+:1878160099:-1 chm1:+:2078503961:-1 chm1:+:2414005248:36 chm1:+:2438436367:-1 chm1:+:2501402251:40 chm1:+:2508670562:32 chm1:+:2516429228:37 chm1:+:2660224908:-1 chm1:+:2696377352:-1 chm1:+:2880378800:37 chm1:+:2882454043:38 chm1:+:3043296346:-1 +TCTCTACTAAAAATACAAAATTAGCCGGGTGTGGTGGCGAGTGCCTGTAATTCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGTAGGACAGAGGCTGCAGTCAGCCAAGATCGCACCACAGACACCTCTACCTGGGTGACAGAGTGAGACTGTCTCAAAAAAGAAAAAGAAAAAAAAAGAGTTCCT chm1:+:12647516:-1 chm1:+:458221103:-1 chm1:+:1784019199:40 chm1:+:1797814983:-1 chm1:+:2384644422:37 chm1:+:2680823597:-1 chm1:+:2857239478:-1 +TCTCTACTAAAAATACAAAATTAGCCGGGTGTGGTGGCGAGTGCCTGTAATTCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGTAGGACAGAGGCTGCAGTCAGCCAAGATCGCACCACAGACACCTCTACCTGGGTGACAGAGTGAGACTGTCTCAAAAAAGAAAAAGAAAAAAAAAGAGTTCCT chm1:+:20913230:-1 chm1:+:413695547:-1 chm1:+:721911957:-1 chm1:+:1015248300:-1 chm1:+:1238931770:39 chm1:+:1544955278:28 chm1:+:1620193415:39 chm1:+:1660826766:36 chm1:+:1686855881:-1 chm1:+:1833134402:-1 chm1:+:1935372830:-1 chm1:+:2009008072:32 chm1:+:2156789547:36 chm1:+:2278646740:38 chm1:+:2629811204:-1 chm1:+:2651775926:-1 chm1:+:2681346260:32 chm1:+:2722648346:38 chm1:+:2867591575:-1 +TCTCTACTAAAAATACAAAATTAGCCGGGTGTGGTGGCGAGTGCCTGTAATTCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGTAGGACAGAGGCTGCAGTCAGCCAAGATCGCACCACAGACACCTCTACCTGGGTGACAGAGTGAGACTGTCTCAAAAAAGAAAAAGAAAAAAAAAGAGTTCCT chm1:+:101691824:38 chm1:+:458180564:-1 chm1:+:684720465:-1 chm1:+:725467148:-1 chm1:+:1302017696:-1 chm1:+:1754335160:-1 chm1:+:1774803423:-1 chm1:+:1891832980:31 chm1:+:1939210946:40 chm1:+:2059853939:-1 chm1:+:2479357534:-1 chm1:+:2481636380:38 chm1:+:2696674484:-1 chm1:+:2800392019:-1 chm1:+:2882622485:-1 +GAATCTTTATGTGTGCCAGGTACTGTCCAAGTGCTCCTCAGGGCATCCAATGATCTCATTTAGATTCCACAACCACACAAGGACATAAGGGTGCTATTATTTATCTGCATATGGTAGCTGAGGAAACAAGAAGCTCAGAGAAGCGAGGTAACTTTCTCAAGAGCACACAGCTTAGGAAATATAGTGCAGGAGTTTCCCCC chm1:+:34184623:-1 chm1:+:257512657:-1 chm1:+:972020482:-1 chm1:+:1105938800:-1 chm1:+:1158400903:-1 chm1:+:1346992283:-1 chm1:+:1523869558:-1 chm1:+:1657730326:-1 chm1:+:2771159092:-1 chm1:+:2813258262:-1 +GAATCTTTATGTGTGCCAGGTACTGTCCAAGTGCTCCTCAGGGCATCCAATGATCTCATTTAGATTCCACAACCACACAAGGACATAAGGGTGCTATTATTTATCTGCATATGGTAGCTGAGGAAACAAGAAGCTCAGAGAAGCGAGGTAACTTTCTCAAGAGCACACAGCTTAGGAAATATAGTGCAGGAGTTTCCCCC chm1:+:187501170:-1 chm1:+:225090917:-1 chm1:+:376277567:-1 chm1:+:783098767:-1 chm1:+:1324043576:-1 chm1:+:1347107030:-1 chm1:+:1402812114:-1 chm1:+:1524767799:-1 chm1:+:1651616359:-1 chm1:+:1653821094:-1 chm1:+:1840621380:-1 chm1:+:2463044699:-1 chm1:+:2567304709:-1 chm1:+:2751668942:-1 chm1:+:2891026946:-1 +GAATCTTTATGTGTGCCAGGTACTGTCCAAGTGCTCCTCAGGGCATCCAATGATCTCATTTAGATTCCACAACCACACAAGGACATAAGGGTGCTATTATTTATCTGCATATGGTAGCTGAGGAAACAAGAAGCTCAGAGAAGCGAGGTAACTTTCTCAAGAGCACACAGCTTAGGAAATATAGTGCAGGAGTTTCCCCC chm1:+:644312058:-1 chm1:+:1419972920:-1 chm1:+:1682107396:-1 chm1:+:2695095283:-1 chm1:+:2872605637:-1 chm1:+:2872655098:-1 chm1:+:2938765259:-1 chm1:+:3032334068:-1 chm1:+:3032966924:-1 +GAATCTTTATGTGTGCCAGGTACTGTCCAAGTGCTCCTCAGGGCATCCAATGATCTCATTTAGATTCCACAACCACACAAGGACATAAGGGTGCTATTATTTATCTGCATATGGTAGCTGAGGAAACAAGAAGCTCAGAGAAGCGAGGTAACTTTCTCAAGAGCACACAGCTTAGGAAATATAGTGCAGGAGTTTCCCCC chm1:+:39208840:-1 chm1:+:64057807:-1 chm1:+:118845267:-1 chm1:+:164954625:-1 chm1:+:207497047:-1 chm1:+:242632063:-1 chm1:+:430346434:-1 chm1:+:718053318:-1 chm1:+:733101899:-1 chm1:+:784901084:-1 chm1:+:849803306:-1 chm1:+:851961775:-1 chm1:+:872732718:-1 chm1:+:940636593:-1 chm1:+:999011110:-1 chm1:+:1002053568:-1 chm1:+:1163415654:-1 chm1:+:1194697947:-1 chm1:+:1475511032:-1 chm1:+:1512465906:-1 chm1:+:1574449139:-1 chm1:+:1610720176:-1 chm1:+:1700353543:-1 chm1:+:1767594195:-1 chm1:+:1777607583:-1 chm1:+:1864075875:-1 chm1:+:1896057402:-1 chm1:+:1896141897:-1 chm1:+:1897716427:-1 chm1:+:1921703381:-1 chm1:+:1922206866:-1 chm1:+:1936469896:-1 chm1:+:2016419704:-1 chm1:+:2131047357:-1 chm1:+:2160706567:-1 chm1:+:2289972239:-1 chm1:+:2353664773:-1 chm1:+:2353960816:-1 chm1:+:2480932160:-1 chm1:+:2588319205:-1 chm1:+:2735716681:-1 chm1:+:2888939198:-1 chm1:+:2896595614:-1 chm1:+:3018794672:-1 chm1:+:3021863711:-1 chm1:+:3101582439:-1 +GAATCTTTATGTGTGCCAGGTACTGTCCAAGTGCTCCTCAGGGCATCCAATGATCTCATTTAGATTCCACAACCACACAAGGACATAAGGGTGCTATTATTTATCTGCATATGGTAGCTGAGGAAACAAGAAGCTCAGAGAAGCGAGGTAACTTTCTCAAGAGCACACAGCTTAGGAAATATAGTGCAGGAGTTTCCCCC chm1:+:305399621:-1 chm1:+:334000836:-1 chm1:+:413508162:-1 chm1:+:486296056:-1 chm1:+:640468371:-1 chm1:+:669228439:-1 chm1:+:725889181:-1 chm1:+:817094528:-1 chm1:+:1115486429:-1 chm1:+:1160501224:-1 chm1:+:1228545085:-1 chm1:+:1242852368:-1 chm1:+:1300129022:-1 chm1:+:1357313622:-1 chm1:+:1409907758:-1 chm1:+:1485170406:-1 chm1:+:1860047654:-1 chm1:+:1900396953:-1 chm1:+:2129110957:-1 chm1:+:2163068897:-1 chm1:+:2236695351:-1 chm1:+:2696858664:-1 chm1:+:2855178371:-1 chm1:+:3096645838:-1 +GGGGGAAACTCCTGCACTATATTTCCTAAGCTGTGTGCTCTTGAGAAAGTTACCTCGCTTCTCTGAGCTTCTTGTTTCCTCAGCTACCATATGCAGATAAATAATAGCACCCTTATGTCCTTGTGTGGTTGTGGAATCTAAATGAGATCATTGGATGCCCTGAGGAGCACTTGGACAGTACCTGGCACACATAAAGATTC chm1:+:1957300827:10 chm1:+:2344506040:-1 +GGGGGAAACTCCTGCACTATATTTCCTAAGCTGTGTGCTCTTGAGAAAGTTACCTCGCTTCTCTGAGCTTCTTGTTTCCTCAGCTACCATATGCAGATAAATAATAGCACCCTTATGTCCTTGTGTGGTTGTGGAATCTAAATGAGATCATTGGATGCCCTGAGGAGCACTTGGACAGTACCTGGCACACATAAAGATTC chm1:+:1957300828:10 +AGTTTAATTCGGAACAGTTGGGCAGAATCTTTTCGGCCGCAACGGTTGCATGAAGAATCACCTGGAAACCTTGTTCAGGTGCTGATTCAGAGTCTGGGGTAGGTCTGGGGTGGGGTCTGAGAGTCTTGCAGCTACTCCCAGGCCTCCTCTCGCTGGCGGGTCTGAGGCCACCTTCTAAGCAGCAGGCTGTAAGAGTTATC chm1:+:1958955268:-1 chm1:+:2704746538:-1 chm1:+:3051904618:-1 +AGTTTAATTCGGAACAGTTGGGCAGAATCTTTTCGGCCGCAACGGTTGCATGAAGAATCACCTGGAAACCTTGTTCAGGTGCTGATTCAGAGTCTGGGGTAGGTCTGGGGTGGGGTCTGAGAGTCTTGCAGCTACTCCCAGGCCTCCTCTCGCTGGCGGGTCTGAGGCCACCTTCTAAGCAGCAGGCTGTAAGAGTTATC chm1:+:92140634:-1 chm1:+:485875987:-1 chm1:+:503678514:-1 chm1:+:515491322:-1 chm1:+:616948310:-1 chm1:+:819784967:-1 chm1:+:889260407:-1 chm1:+:1489509490:-1 chm1:+:2287342479:-1 chm1:+:2423182169:-1 chm1:+:2509404631:-1 +AGTTTAATTCGGAACAGTTGGGCAGAATCTTTTCGGCCGCAACGGTTGCATGAAGAATCACCTGGAAACCTTGTTCAGGTGCTGATTCAGAGTCTGGGGTAGGTCTGGGGTGGGGTCTGAGAGTCTTGCAGCTACTCCCAGGCCTCCTCTCGCTGGCGGGTCTGAGGCCACCTTCTAAGCAGCAGGCTGTAAGAGTTATC chm1:+:1916830:-1 chm1:+:66730395:-1 chm1:+:431438644:-1 chm1:+:879751998:-1 chm1:+:1068079437:-1 chm1:+:1068079465:-1 chm1:+:1068079493:-1 chm1:+:1068079521:-1 chm1:+:1068079549:-1 chm1:+:1233280484:-1 chm1:+:1393931928:-1 chm1:+:1751622779:-1 chm1:+:1798215802:-1 chm1:+:1982656988:-1 chm1:+:2269008281:-1 chm1:+:2868306441:-1 chm1:+:3013662794:-1 +AGTTTAATTCGGAACAGTTGGGCAGAATCTTTTCGGCCGCAACGGTTGCATGAAGAATCACCTGGAAACCTTGTTCAGGTGCTGATTCAGAGTCTGGGGTAGGTCTGGGGTGGGGTCTGAGAGTCTTGCAGCTACTCCCAGGCCTCCTCTCGCTGGCGGGTCTGAGGCCACCTTCTAAGCAGCAGGCTGTAAGAGTTATC chm1:+:63345973:-1 chm1:+:211687312:-1 chm1:+:225587824:-1 chm1:+:354545094:-1 chm1:+:380528098:-1 chm1:+:532243492:-1 chm1:+:575386327:-1 chm1:+:1272192976:-1 chm1:+:1464161089:-1 chm1:+:1522011170:-1 chm1:+:1695357143:-1 chm1:+:1695439152:-1 chm1:+:2040799573:-1 chm1:+:2110842823:-1 chm1:+:2129240947:-1 chm1:+:2151354506:-1 chm1:+:2360693077:-1 chm1:+:2437447804:-1 chm1:+:2497684214:-1 chm1:+:2497785566:-1 chm1:+:2541777475:-1 chm1:+:2666666280:-1 chm1:+:2677922232:-1 chm1:+:2869509425:-1 chm1:+:2915449952:-1 chm1:+:3023418504:-1 chm1:+:3046048462:-1 +AGTTTAATTCGGAACAGTTGGGCAGAATCTTTTCGGCCGCAACGGTTGCATGAAGAATCACCTGGAAACCTTGTTCAGGTGCTGATTCAGAGTCTGGGGTAGGTCTGGGGTGGGGTCTGAGAGTCTTGCAGCTACTCCCAGGCCTCCTCTCGCTGGCGGGTCTGAGGCCACCTTCTAAGCAGCAGGCTGTAAGAGTTATC chm1:+:268169658:-1 chm1:+:502874554:-1 chm1:+:625641826:-1 chm1:+:687286974:-1 chm1:+:1024574292:-1 chm1:+:1024741342:-1 chm1:+:1072516231:-1 chm1:+:1336744963:-1 chm1:+:1576593190:-1 chm1:+:1631473719:-1 chm1:+:1799834598:-1 chm1:+:1910172545:-1 chm1:+:2397904859:-1 chm1:+:2399126330:-1 chm1:+:2632441274:-1 chm1:+:2642523013:-1 chm1:+:2723366430:-1 chm1:+:2900657986:-1 +GATAACTCTTACAGCCTGCTGCTTAGAAGGTGGCCTCAGACCCGCCAGCGAGAGGAGGCCTGGGAGTAGCTGCAAGACTCTCAGACCCCACCCCAGACCTACCCCAGACTCTGAATCAGCACCTGAACAAGGTTTCCAGGTGATTCTTCATGCAACCGTTGCGGCCGAAAAGATTCTGCCCAACTGTTCCGAATTAAACT chm1:+:606912360:-1 chm1:+:2519592407:10 +GATAACTCTTACAGCCTGCTGCTTAGAAGGTGGCCTCAGACCCGCCAGCGAGAGGAGGCCTGGGAGTAGCTGCAAGACTCTCAGACCCCACCCCAGACCTACCCCAGACTCTGAATCAGCACCTGAACAAGGTTTCCAGGTGATTCTTCATGCAACCGTTGCGGCCGAAAAGATTCTGCCCAACTGTTCCGAATTAAACT chm1:+:2519592404:10 +GATAACTCTTACAGCCTGCTGCTTAGAAGGTGGCCTCAGACCCGCCAGCGAGAGGAGGCCTGGGAGTAGCTGCAAGACTCTCAGACCCCACCCCAGACCTACCCCAGACTCTGAATCAGCACCTGAACAAGGTTTCCAGGTGATTCTTCATGCAACCGTTGCGGCCGAAAAGATTCTGCCCAACTGTTCCGAATTAAACT chm1:+:2041011979:-1 +AGCTGAAAGGCCCCCGAGGCGGCCCCCCTCCCGTCTCAGTTTGGAGGTCAGTAGAGGACCACCCCCTGGTCATTCGTGGGCCCAAGGAGGGGCCCCATCCTAGTCAGTTTGAAACGTGCCGGGGCCTCATCCCAACCAGTTTGAAGGACCCAGAGCCAAGCGCCTAACTTTTATGCCAGGTCCCAGGGCATTCAGCCTCA chm1:+:175079662:-1 chm1:+:291149660:-1 chm1:+:546834197:-1 chm1:+:1068396544:-1 chm1:+:1363288874:-1 chm1:+:1396270086:-1 chm1:+:1445095426:-1 chm1:+:1488174904:-1 chm1:+:1746240462:-1 chm1:+:1938877423:-1 chm1:+:2137160128:-1 chm1:+:2534205089:-1 chm1:+:2538844422:-1 +AGCTGAAAGGCCCCCGAGGCGGCCCCCCTCCCGTCTCAGTTTGGAGGTCAGTAGAGGACCACCCCCTGGTCATTCGTGGGCCCAAGGAGGGGCCCCATCCTAGTCAGTTTGAAACGTGCCGGGGCCTCATCCCAACCAGTTTGAAGGACCCAGAGCCAAGCGCCTAACTTTTATGCCAGGTCCCAGGGCATTCAGCCTCA chm1:+:59100675:-1 chm1:+:73267136:-1 chm1:+:366783634:-1 chm1:+:392405794:-1 chm1:+:573151945:-1 chm1:+:697590323:-1 chm1:+:855075304:-1 chm1:+:926465230:-1 chm1:+:1088776622:-1 chm1:+:1314466352:-1 chm1:+:1433370227:-1 chm1:+:1466698198:-1 chm1:+:1524745138:-1 chm1:+:1746925039:-1 chm1:+:1845007234:-1 chm1:+:2277683786:-1 chm1:+:2673820147:-1 chm1:+:2884366142:-1 chm1:+:2960746016:-1 chm1:+:2967687555:-1 +AGCTGAAAGGCCCCCGAGGCGGCCCCCCTCCCGTCTCAGTTTGGAGGTCAGTAGAGGACCACCCCCTGGTCATTCGTGGGCCCAAGGAGGGGCCCCATCCTAGTCAGTTTGAAACGTGCCGGGGCCTCATCCCAACCAGTTTGAAGGACCCAGAGCCAAGCGCCTAACTTTTATGCCAGGTCCCAGGGCATTCAGCCTCA chm1:+:814948961:-1 chm1:+:1050327660:-1 chm1:+:1104232842:-1 chm1:+:1334324720:-1 chm1:+:1750225948:-1 chm1:+:1760337977:-1 chm1:+:1888820844:-1 chm1:+:1890337262:-1 chm1:+:2661559263:-1 +AGCTGAAAGGCCCCCGAGGCGGCCCCCCTCCCGTCTCAGTTTGGAGGTCAGTAGAGGACCACCCCCTGGTCATTCGTGGGCCCAAGGAGGGGCCCCATCCTAGTCAGTTTGAAACGTGCCGGGGCCTCATCCCAACCAGTTTGAAGGACCCAGAGCCAAGCGCCTAACTTTTATGCCAGGTCCCAGGGCATTCAGCCTCA chm1:+:286520034:-1 chm1:+:626102634:-1 chm1:+:697208321:-1 chm1:+:1166290134:-1 chm1:+:2161201737:-1 chm1:+:3027553918:-1 +TGAGGCTGAATGCCCTGGGACCTGGCATAAAAGTTAGGCGCTTGGCTCTGGGTCCTTCAAACTGGTTGGGATGAGGCCCCGGCACGTTTCAAACTGACTAGGATGGGGCCCCTCCTTGGGCCCACGAATGACCAGGGGGTGGTCCTCTACTGACCTCCAAACTGAGACGGGAGGGGGGCCGCCTCGGGGGCCTTTCAGCT chm1:+:1837179570:-1 chm1:+:2780084678:11 +TGAGGCTGAATGCCCTGGGACCTGGCATAAAAGTTAGGCGCTTGGCTCTGGGTCCTTCAAACTGGTTGGGATGAGGCCCCGGCACGTTTCAAACTGACTAGGATGGGGCCCCTCCTTGGGCCCACGAATGACCAGGGGGTGGTCCTCTACTGACCTCCAAACTGAGACGGGAGGGGGGCCGCCTCGGGGGCCTTTCAGCT chm1:+:2780084680:11 +ATGAGCCACTGCGCCCCAGCCGAAAACAGGTATTTATGAGTTCCTGAATGTGAATAACTGAAAGAGCCTGTGTGAACGTTAATAGTGCACGCACATCATTTGTCCATTCACTCACAGGTATTTATGCTAGAGAAATTTTTAGACACAATGGACAGACAGTCCTACAGGGATACCCATTCGCAGCAGCATTTGTAACAGGG chm1:+:1491588683:-1 chm1:+:2500861753:6 chm1:+:2605001254:-1 chm1:+:2856003408:-1 +ATGAGCCACTGCGCCCCAGCCGAAAACAGGTATTTATGAGTTCCTGAATGTGAATAACTGAAAGAGCCTGTGTGAACGTTAATAGTGCACGCACATCATTTGTCCATTCACTCACAGGTATTTATGCTAGAGAAATTTTTAGACACAATGGACAGACAGTCCTACAGGGATACCCATTCGCAGCAGCATTTGTAACAGGG chm1:+:2500861751:6 +ATGAGCCACTGCGCCCCAGCCGAAAACAGGTATTTATGAGTTCCTGAATGTGAATAACTGAAAGAGCCTGTGTGAACGTTAATAGTGCACGCACATCATTTGTCCATTCACTCACAGGTATTTATGCTAGAGAAATTTTTAGACACAATGGACAGACAGTCCTACAGGGATACCCATTCGCAGCAGCATTTGTAACAGGG chm1:+:2500861752:6 +ATGCTGAGAGGATGTCGGAGAAAATAGGAACGCTTTACACTGTTGGTGGGAGTGTAAAATTAGCGTCAACCATTGTGGAAGACAGTGTGGCGATTCTTCAAGGATCTAGAACCAGAAAGTACCACTTGACCCAGCAATCGCATTACTGGGTATATACCCAAAGGATATAAATCGTGCTACTATAAAGACACATGCACACG chm1:+:91237832:22 chm1:+:104380863:26 chm1:+:108262143:24 chm1:+:108280289:22 chm1:+:177479524:31 chm1:+:193773214:26 chm1:+:216620334:-1 chm1:+:348087498:-1 chm1:+:407331445:-1 chm1:+:459191861:24 chm1:+:485466570:21 chm1:+:499083899:25 chm1:+:733616408:-1 chm1:+:745177397:20 chm1:+:757215744:23 chm1:+:812966344:29 chm1:+:844854969:30 chm1:+:848044977:27 chm1:+:849425389:-1 chm1:+:858960616:33 chm1:+:952976934:17 chm1:+:959609904:35 chm1:+:991633611:20 chm1:+:995805652:27 chm1:+:1074231425:35 chm1:+:1116584264:31 chm1:+:1131804301:28 chm1:+:1137658279:24 chm1:+:1144963505:-1 chm1:+:1188473519:22 chm1:+:1214150621:32 chm1:+:1328021921:39 chm1:+:1342340017:23 chm1:+:1347807750:21 chm1:+:1497195172:24 chm1:+:1516010039:21 chm1:+:1744921004:20 chm1:+:1798436628:23 chm1:+:1823700106:24 chm1:+:1841546363:24 chm1:+:1858496750:35 chm1:+:1990830201:21 chm1:+:1992446907:28 chm1:+:2040118247:20 chm1:+:2118763844:20 chm1:+:2160276753:31 chm1:+:2161548278:-1 chm1:+:2228054812:27 chm1:+:2249586018:26 chm1:+:2266648856:37 chm1:+:2340798595:25 chm1:+:2342911506:-1 chm1:+:2352896540:23 chm1:+:2463129844:21 chm1:+:2469435658:-1 chm1:+:2490487524:22 chm1:+:2552340297:33 chm1:+:2552960449:25 chm1:+:2635167609:23 chm1:+:2733365840:21 chm1:+:2799201168:24 chm1:+:2868490680:24 chm1:+:2935736333:-1 chm1:+:2943316162:26 chm1:+:2945434880:24 chm1:+:2947098025:32 chm1:+:2951038917:23 chm1:+:2956274272:26 chm1:+:2986273983:27 chm1:+:2989885372:25 chm1:+:3032642089:23 +ATGCTGAGAGGATGTCGGAGAAAATAGGAACGCTTTACACTGTTGGTGGGAGTGTAAAATTAGCGTCAACCATTGTGGAAGACAGTGTGGCGATTCTTCAAGGATCTAGAACCAGAAAGTACCACTTGACCCAGCAATCGCATTACTGGGTATATACCCAAAGGATATAAATCGTGCTACTATAAAGACACATGCACACG chm1:+:305559157:38 chm1:+:307084991:30 chm1:+:582320017:39 chm1:+:926783153:-1 chm1:+:1098116407:-1 chm1:+:1424564251:-1 chm1:+:1620235649:24 chm1:+:1832006706:-1 chm1:+:1876340639:-1 chm1:+:1975564850:36 chm1:+:2552660359:35 +ATGCTGAGAGGATGTCGGAGAAAATAGGAACGCTTTACACTGTTGGTGGGAGTGTAAAATTAGCGTCAACCATTGTGGAAGACAGTGTGGCGATTCTTCAAGGATCTAGAACCAGAAAGTACCACTTGACCCAGCAATCGCATTACTGGGTATATACCCAAAGGATATAAATCGTGCTACTATAAAGACACATGCACACG chm1:+:144948673:-1 chm1:+:366240625:-1 chm1:+:373129956:-1 chm1:+:758017247:-1 chm1:+:841194778:-1 chm1:+:1003755331:-1 chm1:+:1005573500:20 chm1:+:1043319705:-1 chm1:+:1246541674:32 chm1:+:1286306583:20 chm1:+:1310583876:-1 chm1:+:1323689111:-1 chm1:+:1427387980:-1 chm1:+:1531526396:-1 chm1:+:2039312544:-1 chm1:+:2051019843:-1 chm1:+:2967941728:33 chm1:+:3002731893:-1 chm1:+:3046129524:30 chm1:+:3058179343:35 +ATGCTGAGAGGATGTCGGAGAAAATAGGAACGCTTTACACTGTTGGTGGGAGTGTAAAATTAGCGTCAACCATTGTGGAAGACAGTGTGGCGATTCTTCAAGGATCTAGAACCAGAAAGTACCACTTGACCCAGCAATCGCATTACTGGGTATATACCCAAAGGATATAAATCGTGCTACTATAAAGACACATGCACACG chm1:+:310517804:19 chm1:+:379997312:23 chm1:+:1155676779:31 chm1:+:1735508436:25 chm1:+:2044102374:17 chm1:+:2368924787:38 chm1:+:3011633869:23 +ATGCTGAGAGGATGTCGGAGAAAATAGGAACGCTTTACACTGTTGGTGGGAGTGTAAAATTAGCGTCAACCATTGTGGAAGACAGTGTGGCGATTCTTCAAGGATCTAGAACCAGAAAGTACCACTTGACCCAGCAATCGCATTACTGGGTATATACCCAAAGGATATAAATCGTGCTACTATAAAGACACATGCACACG chm1:+:146711424:-1 chm1:+:629550076:34 chm1:+:815566515:39 chm1:+:838159221:-1 chm1:+:1111013040:25 chm1:+:1216163125:28 chm1:+:1265321725:26 chm1:+:2012766988:27 chm1:+:2029087219:-1 chm1:+:2158801609:-1 chm1:+:2564329126:22 chm1:+:2610759952:21 chm1:+:2950252911:-1 chm1:+:2957593161:25 chm1:+:3058972271:27 chm1:+:3058999376:25 +ATGCTGAGAGGATGTCGGAGAAAATAGGAACGCTTTACACTGTTGGTGGGAGTGTAAAATTAGCGTCAACCATTGTGGAAGACAGTGTGGCGATTCTTCAAGGATCTAGAACCAGAAAGTACCACTTGACCCAGCAATCGCATTACTGGGTATATACCCAAAGGATATAAATCGTGCTACTATAAAGACACATGCACACG chm1:+:74916392:39 chm1:+:188597565:30 chm1:+:522219153:18 chm1:+:581576522:23 chm1:+:760080278:-1 chm1:+:1128105914:26 chm1:+:1257496690:25 chm1:+:1280271695:-1 chm1:+:1326347223:-1 chm1:+:1560288130:23 chm1:+:1792380557:21 chm1:+:1861767919:27 chm1:+:1914524623:25 chm1:+:2148221197:-1 chm1:+:2191334249:35 chm1:+:2592429794:23 chm1:+:2919865123:-1 chm1:+:2943501143:25 +ATGCTGAGAGGATGTCGGAGAAAATAGGAACGCTTTACACTGTTGGTGGGAGTGTAAAATTAGCGTCAACCATTGTGGAAGACAGTGTGGCGATTCTTCAAGGATCTAGAACCAGAAAGTACCACTTGACCCAGCAATCGCATTACTGGGTATATACCCAAAGGATATAAATCGTGCTACTATAAAGACACATGCACACG chm1:+:147339193:22 chm1:+:247301219:20 chm1:+:515102250:22 chm1:+:1011189200:28 chm1:+:1074384844:26 chm1:+:1404981164:26 chm1:+:1781313782:25 chm1:+:2225137337:27 chm1:+:2341341811:24 chm1:+:2346890306:23 chm1:+:2552403414:19 chm1:+:2612887052:19 chm1:+:2863524120:-1 chm1:+:2959394554:31 chm1:+:2996645930:23 chm1:+:2996957913:25 chm1:+:3017913196:29 +ATGCTGAGAGGATGTCGGAGAAAATAGGAACGCTTTACACTGTTGGTGGGAGTGTAAAATTAGCGTCAACCATTGTGGAAGACAGTGTGGCGATTCTTCAAGGATCTAGAACCAGAAAGTACCACTTGACCCAGCAATCGCATTACTGGGTATATACCCAAAGGATATAAATCGTGCTACTATAAAGACACATGCACACG chm1:+:50175576:20 chm1:+:533920698:34 chm1:+:575611056:25 chm1:+:671211818:19 chm1:+:1044132333:33 chm1:+:1356774985:23 chm1:+:1570261505:30 chm1:+:3032642091:23 +CGTGTGCATGTGTCTTTATAGTAGCACGATTTATATCCTTTGGGTATATACCCAGTAATGCGATTGCTGGGTCAAGTGGTACTTTCTGGTTCTAGATCCTTGAAGAATCGCCACACTGTCTTCCACAATGGTTGACGCTAATTTTACACTCCCACCAACAGTGTAAAGCGTTCCTATTTTCTCCGACATCCTCTCAGCAT chm1:+:704895023:25 chm1:+:754542548:24 +CGTGTGCATGTGTCTTTATAGTAGCACGATTTATATCCTTTGGGTATATACCCAGTAATGCGATTGCTGGGTCAAGTGGTACTTTCTGGTTCTAGATCCTTGAAGAATCGCCACACTGTCTTCCACAATGGTTGACGCTAATTTTACACTCCCACCAACAGTGTAAAGCGTTCCTATTTTCTCCGACATCCTCTCAGCAT chm1:+:104992786:-1 chm1:+:311603948:27 chm1:+:1010196354:25 chm1:+:1139544962:26 chm1:+:1527679411:-1 chm1:+:2016706215:22 chm1:+:2119390484:29 chm1:+:2126047597:26 chm1:+:2179201804:38 chm1:+:2265934939:-1 chm1:+:2406029319:-1 chm1:+:2980164019:-1 +CGTGTGCATGTGTCTTTATAGTAGCACGATTTATATCCTTTGGGTATATACCCAGTAATGCGATTGCTGGGTCAAGTGGTACTTTCTGGTTCTAGATCCTTGAAGAATCGCCACACTGTCTTCCACAATGGTTGACGCTAATTTTACACTCCCACCAACAGTGTAAAGCGTTCCTATTTTCTCCGACATCCTCTCAGCAT chm1:+:265679602:-1 chm1:+:393052442:22 chm1:+:1653766110:-1 chm1:+:1902031916:-1 chm1:+:2136823093:16 chm1:+:2287147969:23 chm1:+:2478571965:-1 chm1:+:3053708191:-1 +CGTGTGCATGTGTCTTTATAGTAGCACGATTTATATCCTTTGGGTATATACCCAGTAATGCGATTGCTGGGTCAAGTGGTACTTTCTGGTTCTAGATCCTTGAAGAATCGCCACACTGTCTTCCACAATGGTTGACGCTAATTTTACACTCCCACCAACAGTGTAAAGCGTTCCTATTTTCTCCGACATCCTCTCAGCAT chm1:+:58517141:21 chm1:+:69341886:19 chm1:+:108890961:24 chm1:+:143426848:31 chm1:+:193840126:37 chm1:+:213687994:26 chm1:+:213799194:25 chm1:+:225001937:27 chm1:+:232731516:-1 chm1:+:241059009:25 chm1:+:247755854:22 chm1:+:258321704:-1 chm1:+:301017988:26 chm1:+:303010848:19 chm1:+:321217081:36 chm1:+:325823322:25 chm1:+:327938183:-1 chm1:+:374267477:28 chm1:+:375035258:23 chm1:+:378951926:23 chm1:+:383755281:20 chm1:+:388538444:-1 chm1:+:404105199:24 chm1:+:430826666:40 chm1:+:433411155:-1 chm1:+:463422952:35 chm1:+:477820755:-1 chm1:+:483658697:36 chm1:+:512247168:22 chm1:+:514472475:-1 chm1:+:536710949:-1 chm1:+:551927588:23 chm1:+:571696604:21 chm1:+:581134931:28 chm1:+:604236092:24 chm1:+:656147657:25 chm1:+:661888172:28 chm1:+:665422087:24 chm1:+:677427019:27 chm1:+:710198849:-1 chm1:+:713381983:22 chm1:+:723102607:26 chm1:+:733987576:25 chm1:+:752442725:27 chm1:+:756844413:23 chm1:+:769355578:26 chm1:+:769652706:24 chm1:+:803890694:23 chm1:+:812037196:25 chm1:+:826050304:-1 chm1:+:830858388:22 chm1:+:861232535:26 chm1:+:862697867:22 chm1:+:899831462:32 chm1:+:903169882:35 chm1:+:910345475:-1 chm1:+:911163393:22 chm1:+:933089779:24 chm1:+:933115425:23 chm1:+:933888741:26 chm1:+:944893623:32 chm1:+:964660057:26 chm1:+:967137583:24 chm1:+:978174162:32 chm1:+:981153394:-1 chm1:+:981477065:25 chm1:+:990595717:31 chm1:+:1001384028:25 chm1:+:1006834848:25 chm1:+:1009612804:29 chm1:+:1036164276:26 chm1:+:1074447395:40 chm1:+:1099401152:-1 chm1:+:1117226218:25 chm1:+:1125024927:23 chm1:+:1135255954:24 chm1:+:1135360785:29 chm1:+:1137513648:25 chm1:+:1139438210:21 chm1:+:1151604926:23 chm1:+:1151700498:24 chm1:+:1154460879:23 chm1:+:1155043236:31 chm1:+:1160494775:-1 chm1:+:1161896429:23 chm1:+:1188470827:24 chm1:+:1214830701:17 chm1:+:1223127913:23 chm1:+:1278253748:39 chm1:+:1314463607:22 chm1:+:1321725815:21 chm1:+:1328238716:25 chm1:+:1330409756:20 chm1:+:1345938604:25 chm1:+:1348189497:27 chm1:+:1360189639:27 chm1:+:1365018923:-1 chm1:+:1394961378:26 chm1:+:1418308564:24 chm1:+:1432293659:39 chm1:+:1444197447:22 chm1:+:1451907238:25 chm1:+:1458025387:30 chm1:+:1497174132:22 chm1:+:1554763384:28 chm1:+:1560359486:29 chm1:+:1560363889:33 chm1:+:1560374626:29 chm1:+:1560396725:37 chm1:+:1569845706:-1 chm1:+:1648918228:26 chm1:+:1663749784:-1 chm1:+:1685209348:26 chm1:+:1725447822:21 chm1:+:1749642514:23 chm1:+:1763008337:29 chm1:+:1791669941:25 chm1:+:1798185475:23 chm1:+:1802367376:23 chm1:+:1839576127:31 chm1:+:1849145350:22 chm1:+:1851674430:-1 chm1:+:1866427776:-1 chm1:+:1871434711:32 chm1:+:1915741201:25 chm1:+:1960771835:-1 chm1:+:2029560635:26 chm1:+:2030802161:19 chm1:+:2034744781:26 chm1:+:2035085309:24 chm1:+:2036901611:35 chm1:+:2079353363:-1 chm1:+:2121427330:25 chm1:+:2146908837:22 chm1:+:2150444769:22 chm1:+:2165880073:-1 chm1:+:2225023188:23 chm1:+:2238848614:-1 chm1:+:2306690289:29 chm1:+:2329771149:25 chm1:+:2335970431:26 chm1:+:2360713781:25 chm1:+:2402037653:29 chm1:+:2420198116:24 chm1:+:2439760479:29 chm1:+:2471694669:25 chm1:+:2478031940:24 chm1:+:2512862581:35 chm1:+:2552317112:24 chm1:+:2553016169:28 chm1:+:2560649875:39 chm1:+:2616962967:-1 chm1:+:2624344125:-1 chm1:+:2636303154:23 chm1:+:2638559304:33 chm1:+:2651591612:-1 chm1:+:2653830823:29 chm1:+:2720095010:23 chm1:+:2742333345:25 chm1:+:2759003664:23 chm1:+:2777122176:40 chm1:+:2853418757:37 chm1:+:2854425083:35 chm1:+:2854802801:36 chm1:+:2864268065:37 chm1:+:2904475123:25 chm1:+:2906386952:30 chm1:+:2912837275:21 chm1:+:2924943824:-1 chm1:+:2937408401:22 chm1:+:2937484200:26 chm1:+:2948112651:26 chm1:+:2959226519:29 chm1:+:2964584691:31 chm1:+:2969063895:-1 chm1:+:2974436396:32 chm1:+:3013624089:23 chm1:+:3015861688:39 chm1:+:3019786179:22 chm1:+:3020139910:25 chm1:+:3024074402:-1 chm1:+:3042671880:30 chm1:+:3045845401:25 chm1:+:3058300253:27 chm1:+:3063898443:26 chm1:+:3064409884:30 chm1:+:3095893945:32 chm1:+:3098991689:34 +CGTGTGCATGTGTCTTTATAGTAGCACGATTTATATCCTTTGGGTATATACCCAGTAATGCGATTGCTGGGTCAAGTGGTACTTTCTGGTTCTAGATCCTTGAAGAATCGCCACACTGTCTTCCACAATGGTTGACGCTAATTTTACACTCCCACCAACAGTGTAAAGCGTTCCTATTTTCTCCGACATCCTCTCAGCAT chm1:+:216668748:-1 chm1:+:498308352:-1 chm1:+:591880947:-1 chm1:+:645370556:-1 chm1:+:669067499:-1 chm1:+:1560613138:-1 chm1:+:1967413210:-1 chm1:+:2331538850:-1 chm1:+:2585760447:-1 chm1:+:2865921223:-1 +CGTGTGCATGTGTCTTTATAGTAGCACGATTTATATCCTTTGGGTATATACCCAGTAATGCGATTGCTGGGTCAAGTGGTACTTTCTGGTTCTAGATCCTTGAAGAATCGCCACACTGTCTTCCACAATGGTTGACGCTAATTTTACACTCCCACCAACAGTGTAAAGCGTTCCTATTTTCTCCGACATCCTCTCAGCAT chm1:+:294421681:-1 chm1:+:333326620:18 chm1:+:437164113:-1 chm1:+:505825100:-1 chm1:+:578431999:-1 chm1:+:769355577:26 chm1:+:802185224:-1 chm1:+:819110988:31 chm1:+:888814148:29 chm1:+:1006264613:-1 chm1:+:1034144620:-1 chm1:+:1093245456:-1 chm1:+:1107032136:-1 chm1:+:1138187818:-1 chm1:+:1141335124:-1 chm1:+:1267148941:-1 chm1:+:1387723764:-1 chm1:+:1481720580:-1 chm1:+:1525495411:-1 chm1:+:1632560820:-1 chm1:+:1656137248:-1 chm1:+:1694050459:36 chm1:+:1764565783:32 chm1:+:1849055077:-1 chm1:+:2036083860:-1 chm1:+:2143004439:-1 chm1:+:2166861436:-1 chm1:+:2284318274:-1 chm1:+:2361268640:-1 chm1:+:2390615419:-1 chm1:+:2404118549:-1 chm1:+:2420048154:-1 chm1:+:2658104846:-1 chm1:+:2959097124:-1 chm1:+:2961735931:-1 chm1:+:3027013041:-1 +CGTGTGCATGTGTCTTTATAGTAGCACGATTTATATCCTTTGGGTATATACCCAGTAATGCGATTGCTGGGTCAAGTGGTACTTTCTGGTTCTAGATCCTTGAAGAATCGCCACACTGTCTTCCACAATGGTTGACGCTAATTTTACACTCCCACCAACAGTGTAAAGCGTTCCTATTTTCTCCGACATCCTCTCAGCAT chm1:+:526650144:8 chm1:+:854448652:21 chm1:+:1003140561:20 chm1:+:1887465417:27 chm1:+:1919825780:22 chm1:+:2948778037:40 +CTTCCTTGTGTAAACGCTCCAGAAACATTCCTCATTTGGAATGCTAGGTGCTGTTCTGTCCTCTGCATGTTTGGTAGAATGGATACAACTTAGTGTTAGCTCCAGGCCCAAGCTCTTTGGATTATTAGCAAGTCATTTTACTCTCTGATACGTGTCTAGGAAAAAGGGCCTACAGTAATTCCTTACCTCACAAGTGACAA chm1:+:56750966:-1 chm1:+:426260494:-1 chm1:+:1000285089:-1 chm1:+:1306941264:-1 chm1:+:1365191727:-1 chm1:+:1655707356:-1 chm1:+:1884962734:-1 chm1:+:1941263999:-1 chm1:+:2000955296:-1 chm1:+:2349597735:-1 chm1:+:2469479338:-1 +CTTCCTTGTGTAAACGCTCCAGAAACATTCCTCATTTGGAATGCTAGGTGCTGTTCTGTCCTCTGCATGTTTGGTAGAATGGATACAACTTAGTGTTAGCTCCAGGCCCAAGCTCTTTGGATTATTAGCAAGTCATTTTACTCTCTGATACGTGTCTAGGAAAAAGGGCCTACAGTAATTCCTTACCTCACAAGTGACAA chm1:+:163369641:-1 chm1:+:175683113:-1 chm1:+:232652160:-1 chm1:+:550535239:-1 chm1:+:619869292:-1 chm1:+:887138232:-1 chm1:+:907386883:-1 chm1:+:1075471463:-1 chm1:+:1100419317:-1 chm1:+:1526724210:-1 chm1:+:1706071239:-1 chm1:+:1824144755:-1 chm1:+:1946983465:-1 +CTTCCTTGTGTAAACGCTCCAGAAACATTCCTCATTTGGAATGCTAGGTGCTGTTCTGTCCTCTGCATGTTTGGTAGAATGGATACAACTTAGTGTTAGCTCCAGGCCCAAGCTCTTTGGATTATTAGCAAGTCATTTTACTCTCTGATACGTGTCTAGGAAAAAGGGCCTACAGTAATTCCTTACCTCACAAGTGACAA chm1:+:177910395:-1 chm1:+:246698256:-1 chm1:+:470691782:-1 chm1:+:574074908:-1 chm1:+:646854157:-1 chm1:+:703944338:-1 chm1:+:776553295:-1 chm1:+:1193671682:-1 chm1:+:1265176742:-1 chm1:+:1754309490:-1 chm1:+:1845272937:-1 chm1:+:2265432825:-1 chm1:+:2356544651:-1 +CTTCCTTGTGTAAACGCTCCAGAAACATTCCTCATTTGGAATGCTAGGTGCTGTTCTGTCCTCTGCATGTTTGGTAGAATGGATACAACTTAGTGTTAGCTCCAGGCCCAAGCTCTTTGGATTATTAGCAAGTCATTTTACTCTCTGATACGTGTCTAGGAAAAAGGGCCTACAGTAATTCCTTACCTCACAAGTGACAA chm1:+:167469325:-1 chm1:+:328999749:-1 chm1:+:531290543:-1 chm1:+:715635663:-1 chm1:+:1038291511:-1 chm1:+:1578479572:-1 chm1:+:1579008818:-1 chm1:+:1579824491:-1 chm1:+:1847471714:-1 chm1:+:2126293503:-1 chm1:+:2188220063:-1 chm1:+:2287689141:-1 chm1:+:2693137060:-1 +CTTCCTTGTGTAAACGCTCCAGAAACATTCCTCATTTGGAATGCTAGGTGCTGTTCTGTCCTCTGCATGTTTGGTAGAATGGATACAACTTAGTGTTAGCTCCAGGCCCAAGCTCTTTGGATTATTAGCAAGTCATTTTACTCTCTGATACGTGTCTAGGAAAAAGGGCCTACAGTAATTCCTTACCTCACAAGTGACAA chm1:+:95388766:-1 chm1:+:96307605:-1 chm1:+:176615552:-1 chm1:+:362029692:-1 chm1:+:440292599:-1 chm1:+:787481905:-1 chm1:+:820508720:-1 chm1:+:967311138:-1 chm1:+:1188794365:-1 chm1:+:1192884611:-1 chm1:+:1299249598:-1 chm1:+:1539218946:-1 chm1:+:1607955345:-1 chm1:+:1608293450:-1 chm1:+:1920500457:-1 chm1:+:2131732227:-1 chm1:+:2170006013:-1 chm1:+:2173413819:-1 chm1:+:2184744105:-1 chm1:+:2364385425:-1 chm1:+:2506411176:-1 chm1:+:2591973901:-1 chm1:+:2682833828:-1 chm1:+:2796287123:-1 chm1:+:2802629166:-1 chm1:+:2810998070:-1 chm1:+:2913722746:-1 chm1:+:3016307992:-1 +TTGTCACTTGTGAGGTAAGGAATTACTGTAGGCCCTTTTTCCTAGACACGTATCAGAGAGTAAAATGACTTGCTAATAATCCAAAGAGCTTGGGCCTGGAGCTAACACTAAGTTGTATCCATTCTACCAAACATGCAGAGGACAGAACAGCACCTAGCATTCCAAATGAGGAATGTTTCTGGAGCGTTTACACAAGGAAG chm1:+:761953631:-1 chm1:+:1064075343:-1 chm1:+:2269534401:10 chm1:+:2893304235:-1 +TTGTCACTTGTGAGGTAAGGAATTACTGTAGGCCCTTTTTCCTAGACACGTATCAGAGAGTAAAATGACTTGCTAATAATCCAAAGAGCTTGGGCCTGGAGCTAACACTAAGTTGTATCCATTCTACCAAACATGCAGAGGACAGAACAGCACCTAGCATTCCAAATGAGGAATGTTTCTGGAGCGTTTACACAAGGAAG chm1:+:2269534402:10 +AAATTTGACCCCATAGTCCTAGCAGCGCAGACCAACCTATAGATGGCAATTTTACCTTGTGGGTCATTAAACGGAGCCTCTCCTTCTAGCTTTATCCAGCCAGACACTGCCTACGCGTGTCTACAATCAACCTGAAATGTGCTGCACACGTGCATCTTGCTGCCTTAATTAAAGTACACCAATACAGTCCAATTACACTG chm1:+:1168887155:-1 chm1:+:1311099249:-1 chm1:+:1958042979:-1 chm1:+:2364081322:-1 chm1:+:2417547421:-1 +AAATTTGACCCCATAGTCCTAGCAGCGCAGACCAACCTATAGATGGCAATTTTACCTTGTGGGTCATTAAACGGAGCCTCTCCTTCTAGCTTTATCCAGCCAGACACTGCCTACGCGTGTCTACAATCAACCTGAAATGTGCTGCACACGTGCATCTTGCTGCCTTAATTAAAGTACACCAATACAGTCCAATTACACTG chm1:+:2022835913:-1 chm1:+:3024439200:-1 +AAATTTGACCCCATAGTCCTAGCAGCGCAGACCAACCTATAGATGGCAATTTTACCTTGTGGGTCATTAAACGGAGCCTCTCCTTCTAGCTTTATCCAGCCAGACACTGCCTACGCGTGTCTACAATCAACCTGAAATGTGCTGCACACGTGCATCTTGCTGCCTTAATTAAAGTACACCAATACAGTCCAATTACACTG chm1:+:991071456:-1 chm1:+:1276526312:-1 chm1:+:1820776897:-1 chm1:+:1867048235:-1 +AAATTTGACCCCATAGTCCTAGCAGCGCAGACCAACCTATAGATGGCAATTTTACCTTGTGGGTCATTAAACGGAGCCTCTCCTTCTAGCTTTATCCAGCCAGACACTGCCTACGCGTGTCTACAATCAACCTGAAATGTGCTGCACACGTGCATCTTGCTGCCTTAATTAAAGTACACCAATACAGTCCAATTACACTG chm1:+:2068321688:-1 +AAATTTGACCCCATAGTCCTAGCAGCGCAGACCAACCTATAGATGGCAATTTTACCTTGTGGGTCATTAAACGGAGCCTCTCCTTCTAGCTTTATCCAGCCAGACACTGCCTACGCGTGTCTACAATCAACCTGAAATGTGCTGCACACGTGCATCTTGCTGCCTTAATTAAAGTACACCAATACAGTCCAATTACACTG chm1:+:223878866:-1 chm1:+:489535512:-1 chm1:+:672585908:-1 chm1:+:725887425:-1 chm1:+:801054411:-1 chm1:+:1186874981:-1 chm1:+:1395883602:-1 chm1:+:1478832616:-1 chm1:+:1822106302:-1 chm1:+:2232485142:-1 chm1:+:2392489669:-1 chm1:+:2570652857:-1 chm1:+:2633138830:-1 chm1:+:2726967242:-1 chm1:+:2828747467:-1 +AAATTTGACCCCATAGTCCTAGCAGCGCAGACCAACCTATAGATGGCAATTTTACCTTGTGGGTCATTAAACGGAGCCTCTCCTTCTAGCTTTATCCAGCCAGACACTGCCTACGCGTGTCTACAATCAACCTGAAATGTGCTGCACACGTGCATCTTGCTGCCTTAATTAAAGTACACCAATACAGTCCAATTACACTG chm1:+:214917096:-1 chm1:+:1076266247:-1 chm1:+:1422188075:-1 chm1:+:1874941177:-1 +CAGTGTAATTGGACTGTATTGGTGTACTTTAATTAAGGCAGCAAGATGCACGTGTGCAGCACATTTCAGGTTGATTGTAGACACGCGTAGGCAGTGTCTGGCTGGATAAAGCTAGAAGGAGAGGCTCCGTTTAATGACCCACAAGGTAAAATTGCCATCTATAGGTTGGTCTGCGCTGCTAGGACTATGGGGTCAAATTT chm1:+:2457579591:9 +CAGTGTAATTGGACTGTATTGGTGTACTTTAATTAAGGCAGCAAGATGCACGTGTGCAGCACATTTCAGGTTGATTGTAGACACGCGTAGGCAGTGTCTGGCTGGATAAAGCTAGAAGGAGAGGCTCCGTTTAATGACCCACAAGGTAAAATTGCCATCTATAGGTTGGTCTGCGCTGCTAGGACTATGGGGTCAAATTT chm1:+:2457579593:9 +CAGTGTAATTGGACTGTATTGGTGTACTTTAATTAAGGCAGCAAGATGCACGTGTGCAGCACATTTCAGGTTGATTGTAGACACGCGTAGGCAGTGTCTGGCTGGATAAAGCTAGAAGGAGAGGCTCCGTTTAATGACCCACAAGGTAAAATTGCCATCTATAGGTTGGTCTGCGCTGCTAGGACTATGGGGTCAAATTT chm1:+:2457579592:9 +CTCTTTACAGATGGACTAAGTGGCACATCTCATTGACAAAAAATTGTCTTGAACTTGATGCCATTTTAATATTGAGAATAAAGCTTATATTTCTTTTTATCCTTTAATTCCATTTTTTCCATGAACTTTTTGAATTCCTCTTATATACTAGAAATGGATGAGGTTTTTGGTATGTAAATGACCCTTTGAGTAAAGCTGTT chm1:+:1096634463:-1 chm1:+:2593666340:9 +CTCTTTACAGATGGACTAAGTGGCACATCTCATTGACAAAAAATTGTCTTGAACTTGATGCCATTTTAATATTGAGAATAAAGCTTATATTTCTTTTTATCCTTTAATTCCATTTTTTCCATGAACTTTTTGAATTCCTCTTATATACTAGAAATGGATGAGGTTTTTGGTATGTAAATGACCCTTTGAGTAAAGCTGTT chm1:+:2593666338:9 +CTCTTTACAGATGGACTAAGTGGCACATCTCATTGACAAAAAATTGTCTTGAACTTGATGCCATTTTAATATTGAGAATAAAGCTTATATTTCTTTTTATCCTTTAATTCCATTTTTTCCATGAACTTTTTGAATTCCTCTTATATACTAGAAATGGATGAGGTTTTTGGTATGTAAATGACCCTTTGAGTAAAGCTGTT chm1:+:2593666339:9 +AACAGCTTTACTCAAAGGGTCATTTACATACCAAAAACCTCATCCATTTCTAGTATATAAGAGGAATTCAAAAAGTTCATGGAAAAAATGGAATTAAAGGATAAAAAGAAATATAAGCTTTATTCTCAATATTAAAATGGCATCAAGTTCAAGACAATTTTTTGTCAATGAGATGTGCCACTTAGTCCATCTGTAAAGAG chm1:+:99742052:-1 chm1:+:590060200:-1 +TGAAGGATGGGGCTTTCAAAAATGACAAATAAAACACTGATAAACTGATAAACAATTTGTTTTGGCATTACTTTAGGGCAGCATCATGAATGAGTGGCATTTGGCCATCTGTGTATTAGGGCCTGGGGTTGATGAGGGTAAAGAACAGAAACACCCCCACCCACCTTCAGCCTGTACCTCCTGCCACCCTACCACCAGGA chm1:+:373193929:-1 chm1:+:1920756609:-1 chm1:+:2147521719:-1 +TGAAGGATGGGGCTTTCAAAAATGACAAATAAAACACTGATAAACTGATAAACAATTTGTTTTGGCATTACTTTAGGGCAGCATCATGAATGAGTGGCATTTGGCCATCTGTGTATTAGGGCCTGGGGTTGATGAGGGTAAAGAACAGAAACACCCCCACCCACCTTCAGCCTGTACCTCCTGCCACCCTACCACCAGGA chm1:+:38955628:-1 chm1:+:229969045:-1 chm1:+:1457026362:-1 +TGAAGGATGGGGCTTTCAAAAATGACAAATAAAACACTGATAAACTGATAAACAATTTGTTTTGGCATTACTTTAGGGCAGCATCATGAATGAGTGGCATTTGGCCATCTGTGTATTAGGGCCTGGGGTTGATGAGGGTAAAGAACAGAAACACCCCCACCCACCTTCAGCCTGTACCTCCTGCCACCCTACCACCAGGA chm1:+:65990556:-1 chm1:+:112282215:-1 chm1:+:259145794:-1 chm1:+:1270193173:-1 chm1:+:1442258704:-1 chm1:+:1658599394:-1 chm1:+:2550093865:-1 +TGAAGGATGGGGCTTTCAAAAATGACAAATAAAACACTGATAAACTGATAAACAATTTGTTTTGGCATTACTTTAGGGCAGCATCATGAATGAGTGGCATTTGGCCATCTGTGTATTAGGGCCTGGGGTTGATGAGGGTAAAGAACAGAAACACCCCCACCCACCTTCAGCCTGTACCTCCTGCCACCCTACCACCAGGA chm1:+:1303988188:-1 chm1:+:1759152097:-1 chm1:+:2022138170:-1 chm1:+:2569266766:-1 +TGAAGGATGGGGCTTTCAAAAATGACAAATAAAACACTGATAAACTGATAAACAATTTGTTTTGGCATTACTTTAGGGCAGCATCATGAATGAGTGGCATTTGGCCATCTGTGTATTAGGGCCTGGGGTTGATGAGGGTAAAGAACAGAAACACCCCCACCCACCTTCAGCCTGTACCTCCTGCCACCCTACCACCAGGA chm1:+:1421923112:-1 +TCCTGGTGGTAGGGTGGCAGGAGGTACAGGCTGAAGGTGGGTGGGGGTGTTTCTGTTCTTTACCCTCATCAACCCCAGGCCCTAATACACAGATGGCCAAATGCCACTCATTCATGATGCTGCCCTAAAGTAATGCCAAAACAAATTGTTTATCAGTTTATCAGTGTTTTATTTGTCATTTTTGAAAGCCCCATCCTTCA chm1:+:220675646:6 +TCCTGGTGGTAGGGTGGCAGGAGGTACAGGCTGAAGGTGGGTGGGGGTGTTTCTGTTCTTTACCCTCATCAACCCCAGGCCCTAATACACAGATGGCCAAATGCCACTCATTCATGATGCTGCCCTAAAGTAATGCCAAAACAAATTGTTTATCAGTTTATCAGTGTTTTATTTGTCATTTTTGAAAGCCCCATCCTTCA chm1:+:220675647:6 +TCCTGGTGGTAGGGTGGCAGGAGGTACAGGCTGAAGGTGGGTGGGGGTGTTTCTGTTCTTTACCCTCATCAACCCCAGGCCCTAATACACAGATGGCCAAATGCCACTCATTCATGATGCTGCCCTAAAGTAATGCCAAAACAAATTGTTTATCAGTTTATCAGTGTTTTATTTGTCATTTTTGAAAGCCCCATCCTTCA chm1:+:220675648:6 +AATAGGAAATATATAATATACATATATAATATATAGGAAATATATATATACATATATAATATATAGGGAAATATAATATACATATATATATATAGGAAATATATATATACACATATACACACACACACACACCCCTAGGAATATATTAATATATGGAAGGATGAATAGATAGATGTAGATGATACGATAGATAGATAGAT chm1:+:579319672:10 chm1:+:1346402062:-1 +AATAGGAAATATATAATATACATATATAATATATAGGAAATATATATATACATATATAATATATAGGGAAATATAATATACATATATATATATAGGAAATATATATATACACATATACACACACACACACACCCCTAGGAATATATTAATATATGGAAGGATGAATAGATAGATGTAGATGATACGATAGATAGATAGAT chm1:+:1301250488:-1 +AATAGGAAATATATAATATACATATATAATATATAGGAAATATATATATACATATATAATATATAGGGAAATATAATATACATATATATATATAGGAAATATATATATACACATATACACACACACACACACCCCTAGGAATATATTAATATATGGAAGGATGAATAGATAGATGTAGATGATACGATAGATAGATAGAT chm1:+:579319673:10 +AATAGGAAATATATAATATACATATATAATATATAGGAAATATATATATACATATATAATATATAGGGAAATATAATATACATATATATATATAGGAAATATATATATACACATATACACACACACACACACCCCTAGGAATATATTAATATATGGAAGGATGAATAGATAGATGTAGATGATACGATAGATAGATAGAT chm1:+:113672002:-1 chm1:+:435073750:-1 chm1:+:513270642:-1 chm1:+:673028462:-1 chm1:+:935179781:-1 chm1:+:1052311693:-1 chm1:+:1387581172:-1 chm1:+:1428466491:-1 chm1:+:1490532273:-1 chm1:+:1544526609:-1 chm1:+:1835178831:-1 chm1:+:1837996122:-1 chm1:+:2036668423:-1 chm1:+:2907140058:-1 chm1:+:2918615498:-1 +ATCTATCTATCTATCGTATCATCTACATCTATCTATTCATCCTTCCATATATTAATATATTCCTAGGGGTGTGTGTGTGTGTGTATATGTGTATATATATATTTCCTATATATATATATGTATATTATATTTCCCTATATATTATATATGTATATATATATTTCCTATATATTATATATGTATATTATATATTTCCTATT chm1:+:1543258:-1 chm1:+:60321457:-1 chm1:+:186511528:-1 chm1:+:189605651:-1 chm1:+:258834709:-1 chm1:+:291490856:-1 chm1:+:367106987:-1 chm1:+:371115757:-1 chm1:+:385212758:-1 chm1:+:394141351:-1 chm1:+:419988927:-1 chm1:+:419989309:-1 chm1:+:420585904:-1 chm1:+:449623105:-1 chm1:+:481920563:-1 chm1:+:494199032:-1 chm1:+:509029181:-1 chm1:+:526109238:-1 chm1:+:536790196:-1 chm1:+:594944369:-1 chm1:+:599038178:-1 chm1:+:711053931:-1 chm1:+:732678203:-1 chm1:+:783686656:-1 chm1:+:784052260:-1 chm1:+:852502674:-1 chm1:+:871784387:-1 chm1:+:898141574:-1 chm1:+:909858276:-1 chm1:+:1023635961:-1 chm1:+:1025458228:-1 chm1:+:1036038591:-1 chm1:+:1073854704:-1 chm1:+:1120918305:-1 chm1:+:1149221773:-1 chm1:+:1246853291:-1 chm1:+:1247067282:-1 chm1:+:1248114727:-1 chm1:+:1425060300:-1 chm1:+:1430328956:-1 chm1:+:1467589259:-1 chm1:+:1468888100:-1 chm1:+:1490646830:-1 chm1:+:1530410769:-1 chm1:+:1543658561:-1 chm1:+:1549420560:-1 chm1:+:1549420579:-1 chm1:+:1558381920:-1 chm1:+:1581364464:-1 chm1:+:1607932560:-1 chm1:+:1620028077:-1 chm1:+:1755394796:-1 chm1:+:1757751231:-1 chm1:+:1815682260:-1 chm1:+:1977635108:-1 chm1:+:1977635136:-1 chm1:+:2028036477:-1 chm1:+:2037284695:-1 chm1:+:2037874614:-1 chm1:+:2043727140:-1 chm1:+:2044738761:-1 chm1:+:2074352155:-1 chm1:+:2135405574:-1 chm1:+:2135405619:-1 chm1:+:2140623440:-1 chm1:+:2194429425:-1 chm1:+:2222049554:-1 chm1:+:2222558259:-1 chm1:+:2222558278:-1 chm1:+:2222558301:-1 chm1:+:2222558324:-1 chm1:+:2227224736:-1 chm1:+:2229754844:-1 chm1:+:2235274171:-1 chm1:+:2282617488:-1 chm1:+:2302219283:-1 chm1:+:2327599565:-1 chm1:+:2328606175:-1 chm1:+:2333601342:-1 chm1:+:2339331443:-1 chm1:+:2361764572:-1 chm1:+:2366562407:-1 chm1:+:2465983907:-1 chm1:+:2555130382:-1 chm1:+:2555130419:-1 chm1:+:2558598668:-1 chm1:+:2567055749:-1 chm1:+:2584431425:-1 chm1:+:2644772659:-1 chm1:+:2645951719:-1 chm1:+:2717042470:-1 chm1:+:2735718487:-1 chm1:+:2737262114:-1 chm1:+:2778075486:-1 chm1:+:2854363320:-1 chm1:+:2888128605:-1 chm1:+:2974511775:-1 chm1:+:2995534400:-1 chm1:+:3003869580:-1 chm1:+:3016042283:-1 chm1:+:3052418330:-1 +ATCTATCTATCTATCGTATCATCTACATCTATCTATTCATCCTTCCATATATTAATATATTCCTAGGGGTGTGTGTGTGTGTGTATATGTGTATATATATATTTCCTATATATATATATGTATATTATATTTCCCTATATATTATATATGTATATATATATTTCCTATATATTATATATGTATATTATATATTTCCTATT chm1:+:28652138:-1 chm1:+:106307660:-1 chm1:+:162869853:-1 chm1:+:516174562:-1 chm1:+:579129230:-1 chm1:+:905844326:-1 chm1:+:906451847:-1 chm1:+:1222680797:-1 chm1:+:1517387021:-1 chm1:+:1796081599:-1 chm1:+:1951672973:-1 chm1:+:1970612890:-1 chm1:+:1981429654:-1 chm1:+:2405279893:-1 chm1:+:2725138826:-1 +GTTAGTTTCCCATTTTTAACATGTCTTTTTTTCCCCTTTTCGTTTCTTTGATTGGAATCTAGCAACTACATGCGATTATAGCAGCATCTGTCTCTATAAAGTCGTCCCAAAAACTCAAGAAAATTCTGGAGGCAAGTGCAGTTTTTCTTGTAGGTATGAAGGACTACTTCAGCTGACGTTCAGTGACCTGATCGTGCTGT chm1:+:402736690:7 +GTTAGTTTCCCATTTTTAACATGTCTTTTTTTCCCCTTTTCGTTTCTTTGATTGGAATCTAGCAACTACATGCGATTATAGCAGCATCTGTCTCTATAAAGTCGTCCCAAAAACTCAAGAAAATTCTGGAGGCAAGTGCAGTTTTTCTTGTAGGTATGAAGGACTACTTCAGCTGACGTTCAGTGACCTGATCGTGCTGT chm1:+:402736689:7 +AATACACCCTTAAAGAACTAAGAACAGTAGCTCTGAACCGCTACAGGGAGTGTTTTAAAATGACAGTGAAACCCACATAGAGCACTATTTCCAGCTCTGTGCCAAAGACCCATTTGTCTTACAAATCCATTTAATCTGTATCCTCCTTGACATTAGGACCACACTTTCTAAACCTACCAAGATGATGGAAGAAGTGGGCC chm1:+:366201975:-1 chm1:+:645129904:-1 chm1:+:1479014405:-1 chm1:+:1484289107:-1 chm1:+:1563041837:-1 chm1:+:2014785667:-1 chm1:+:2073409424:-1 chm1:+:2340323321:-1 chm1:+:2371684438:-1 chm1:+:2388310673:-1 chm1:+:2416265551:-1 chm1:+:2980958210:-1 +AATACACCCTTAAAGAACTAAGAACAGTAGCTCTGAACCGCTACAGGGAGTGTTTTAAAATGACAGTGAAACCCACATAGAGCACTATTTCCAGCTCTGTGCCAAAGACCCATTTGTCTTACAAATCCATTTAATCTGTATCCTCCTTGACATTAGGACCACACTTTCTAAACCTACCAAGATGATGGAAGAAGTGGGCC chm1:+:520715479:-1 chm1:+:1369041560:-1 chm1:+:2183934387:5 chm1:+:2978080829:-1 +ACAGGCAACCTACTGGGAGAAAATGTTTGCAATCTTATCCATCTGACGAAGGGCCTAATATCCAGAATCTACAAGGAATTTAAACAAATTTACAAGAAAAAAAAACCCCATCAAAAAAGTGGGCGAAGGATATGAAACAGACACTTCTCAAAAGAAGACACTTATTGTGGCCAACAAACATATGAAAAAAAGCTCTATCA chm1:+:34957272:37 chm1:+:71120262:25 chm1:+:72869916:31 chm1:+:90990216:37 chm1:+:91066575:26 chm1:+:93000504:39 chm1:+:357105649:28 chm1:+:362867142:23 chm1:+:448805270:24 chm1:+:528111644:-1 chm1:+:599027076:30 chm1:+:637633085:-1 chm1:+:820426087:27 chm1:+:854792576:27 chm1:+:855053148:25 chm1:+:870942705:30 chm1:+:894077317:25 chm1:+:905226544:32 chm1:+:965022267:30 chm1:+:1128385640:-1 chm1:+:1135110768:23 chm1:+:1145183661:23 chm1:+:1166636716:20 chm1:+:1178560174:31 chm1:+:1229142434:27 chm1:+:1450818279:34 chm1:+:1522002032:-1 chm1:+:1563156571:28 chm1:+:1619403535:27 chm1:+:1734818690:24 chm1:+:1828524406:25 chm1:+:2069098812:34 chm1:+:2104622338:28 chm1:+:2109805252:27 chm1:+:2457554215:-1 chm1:+:2470946883:26 chm1:+:2506819915:-1 chm1:+:2559914967:20 chm1:+:2802855693:39 chm1:+:2954028726:29 chm1:+:2960208277:30 +ACAGGCAACCTACTGGGAGAAAATGTTTGCAATCTTATCCATCTGACGAAGGGCCTAATATCCAGAATCTACAAGGAATTTAAACAAATTTACAAGAAAAAAAAACCCCATCAAAAAAGTGGGCGAAGGATATGAAACAGACACTTCTCAAAAGAAGACACTTATTGTGGCCAACAAACATATGAAAAAAAGCTCTATCA chm1:+:1072504878:-1 chm1:+:1117196246:34 chm1:+:2994465140:30 +ACAGGCAACCTACTGGGAGAAAATGTTTGCAATCTTATCCATCTGACGAAGGGCCTAATATCCAGAATCTACAAGGAATTTAAACAAATTTACAAGAAAAAAAAACCCCATCAAAAAAGTGGGCGAAGGATATGAAACAGACACTTCTCAAAAGAAGACACTTATTGTGGCCAACAAACATATGAAAAAAAGCTCTATCA chm1:+:145784076:31 chm1:+:245793066:33 chm1:+:661587559:23 chm1:+:666914881:36 chm1:+:739385916:25 chm1:+:762959098:-1 chm1:+:849876636:30 chm1:+:850485527:36 chm1:+:907259458:37 chm1:+:1139432072:-1 chm1:+:1167193338:40 chm1:+:1311598739:-1 chm1:+:1475099187:24 chm1:+:1484526433:22 chm1:+:1872596123:30 chm1:+:2022877514:32 chm1:+:2025736514:32 chm1:+:2044869555:37 chm1:+:2104595241:-1 chm1:+:2349883046:32 chm1:+:2378612113:25 chm1:+:2487381134:27 chm1:+:2729642558:30 chm1:+:2873683634:21 chm1:+:2955752417:-1 chm1:+:2973787592:36 chm1:+:3011656433:-1 chm1:+:3035587384:32 +ACAGGCAACCTACTGGGAGAAAATGTTTGCAATCTTATCCATCTGACGAAGGGCCTAATATCCAGAATCTACAAGGAATTTAAACAAATTTACAAGAAAAAAAAACCCCATCAAAAAAGTGGGCGAAGGATATGAAACAGACACTTCTCAAAAGAAGACACTTATTGTGGCCAACAAACATATGAAAAAAAGCTCTATCA chm1:+:460449821:29 chm1:+:797258846:29 chm1:+:1291662161:30 chm1:+:1484526438:22 chm1:+:2642980115:30 chm1:+:2651450277:34 chm1:+:2975627827:-1 +ACAGGCAACCTACTGGGAGAAAATGTTTGCAATCTTATCCATCTGACGAAGGGCCTAATATCCAGAATCTACAAGGAATTTAAACAAATTTACAAGAAAAAAAAACCCCATCAAAAAAGTGGGCGAAGGATATGAAACAGACACTTCTCAAAAGAAGACACTTATTGTGGCCAACAAACATATGAAAAAAAGCTCTATCA chm1:+:425413338:25 chm1:+:690528481:-1 chm1:+:719805674:29 chm1:+:806980665:-1 chm1:+:1160398132:22 chm1:+:1164625356:22 chm1:+:1285374749:-1 chm1:+:1420467845:-1 chm1:+:1799979751:-1 chm1:+:1977970316:25 chm1:+:2907606900:35 chm1:+:2979645660:-1 +ACAGGCAACCTACTGGGAGAAAATGTTTGCAATCTTATCCATCTGACGAAGGGCCTAATATCCAGAATCTACAAGGAATTTAAACAAATTTACAAGAAAAAAAAACCCCATCAAAAAAGTGGGCGAAGGATATGAAACAGACACTTCTCAAAAGAAGACACTTATTGTGGCCAACAAACATATGAAAAAAAGCTCTATCA chm1:+:65859517:-1 chm1:+:297924974:-1 chm1:+:385327505:-1 chm1:+:1039698703:-1 chm1:+:1422093740:-1 chm1:+:1550112896:-1 chm1:+:1684368891:33 chm1:+:1702463227:-1 chm1:+:1993162639:33 chm1:+:2022025517:-1 chm1:+:2667286470:-1 chm1:+:3055698227:-1 +TGATAGAGCTTTTTTTCATATGTTTGTTGGCCACAATAAGTGTCTTCTTTTGAGAAGTGTCTGTTTCATATCCTTCGCCCACTTTTTTGATGGGGTTTTTTTTTCTTGTAAATTTGTTTAAATTCCTTGTAGATTCTGGATATTAGGCCCTTCGTCAGATGGATAAGATTGCAAACATTTTCTCCCAGTAGGTTGCCTGT chm1:+:475163003:27 chm1:+:2119390746:22 +TGATAGAGCTTTTTTTCATATGTTTGTTGGCCACAATAAGTGTCTTCTTTTGAGAAGTGTCTGTTTCATATCCTTCGCCCACTTTTTTGATGGGGTTTTTTTTTCTTGTAAATTTGTTTAAATTCCTTGTAGATTCTGGATATTAGGCCCTTCGTCAGATGGATAAGATTGCAAACATTTTCTCCCAGTAGGTTGCCTGT chm1:+:297531355:26 chm1:+:1503020658:25 chm1:+:2648231843:33 +TGATAGAGCTTTTTTTCATATGTTTGTTGGCCACAATAAGTGTCTTCTTTTGAGAAGTGTCTGTTTCATATCCTTCGCCCACTTTTTTGATGGGGTTTTTTTTTCTTGTAAATTTGTTTAAATTCCTTGTAGATTCTGGATATTAGGCCCTTCGTCAGATGGATAAGATTGCAAACATTTTCTCCCAGTAGGTTGCCTGT chm1:+:1313039079:-1 chm1:+:1442973779:-1 chm1:+:1717707314:37 chm1:+:1773043666:-1 chm1:+:2126047887:25 +TGATAGAGCTTTTTTTCATATGTTTGTTGGCCACAATAAGTGTCTTCTTTTGAGAAGTGTCTGTTTCATATCCTTCGCCCACTTTTTTGATGGGGTTTTTTTTTCTTGTAAATTTGTTTAAATTCCTTGTAGATTCTGGATATTAGGCCCTTCGTCAGATGGATAAGATTGCAAACATTTTCTCCCAGTAGGTTGCCTGT chm1:+:1342313835:-1 chm1:+:1490559268:37 chm1:+:2981058292:21 +TGATAGAGCTTTTTTTCATATGTTTGTTGGCCACAATAAGTGTCTTCTTTTGAGAAGTGTCTGTTTCATATCCTTCGCCCACTTTTTTGATGGGGTTTTTTTTTCTTGTAAATTTGTTTAAATTCCTTGTAGATTCTGGATATTAGGCCCTTCGTCAGATGGATAAGATTGCAAACATTTTCTCCCAGTAGGTTGCCTGT chm1:+:24595969:31 chm1:+:86816490:26 chm1:+:103017567:30 chm1:+:105804441:37 chm1:+:170578086:23 chm1:+:249995445:25 chm1:+:433411442:30 chm1:+:457010273:29 chm1:+:465054016:29 chm1:+:478899864:-1 chm1:+:484207750:-1 chm1:+:720746857:34 chm1:+:780478401:33 chm1:+:781597480:31 chm1:+:812379011:31 chm1:+:945387998:40 chm1:+:1019965284:-1 chm1:+:1021206117:26 chm1:+:1091749432:30 chm1:+:1264035624:34 chm1:+:1285255994:34 chm1:+:1360817789:11 chm1:+:1441713977:28 chm1:+:1451801212:32 chm1:+:1648121048:24 chm1:+:1724699859:25 chm1:+:1749630548:33 chm1:+:1843198038:30 chm1:+:2140055213:32 chm1:+:2284031316:27 chm1:+:2306690579:40 chm1:+:2360051024:29 chm1:+:2924815145:26 chm1:+:2955602284:26 chm1:+:3054762595:33 +TAGAATGTCGCATCAACGCCGCCAACATCGCCACAGACGATGAGCGAGACAAGTTCGGCCGGCCGCGGTGGCCTTCAAACTCCGCATCAACAAAACCCTGAGGCCCCTTCCTCCCACCCCATCTCTCTCCCTTGTGGATGCTCCTGGAATGTCCCTGACCCGTGCCTGATCCCTCCCTCACCCCACCCCAAAGGTATTTT chm1:+:2507730940:7 +TAGAATGTCGCATCAACGCCGCCAACATCGCCACAGACGATGAGCGAGACAAGTTCGGCCGGCCGCGGTGGCCTTCAAACTCCGCATCAACAAAACCCTGAGGCCCCTTCCTCCCACCCCATCTCTCTCCCTTGTGGATGCTCCTGGAATGTCCCTGACCCGTGCCTGATCCCTCCCTCACCCCACCCCAAAGGTATTTT chm1:+:1893169273:-1 +TAGAATGTCGCATCAACGCCGCCAACATCGCCACAGACGATGAGCGAGACAAGTTCGGCCGGCCGCGGTGGCCTTCAAACTCCGCATCAACAAAACCCTGAGGCCCCTTCCTCCCACCCCATCTCTCTCCCTTGTGGATGCTCCTGGAATGTCCCTGACCCGTGCCTGATCCCTCCCTCACCCCACCCCAAAGGTATTTT chm1:+:382690656:-1 chm1:+:2507730933:7 +TAGAATGTCGCATCAACGCCGCCAACATCGCCACAGACGATGAGCGAGACAAGTTCGGCCGGCCGCGGTGGCCTTCAAACTCCGCATCAACAAAACCCTGAGGCCCCTTCCTCCCACCCCATCTCTCTCCCTTGTGGATGCTCCTGGAATGTCCCTGACCCGTGCCTGATCCCTCCCTCACCCCACCCCAAAGGTATTTT chm1:+:2507730934:7 +TAGAATGTCGCATCAACGCCGCCAACATCGCCACAGACGATGAGCGAGACAAGTTCGGCCGGCCGCGGTGGCCTTCAAACTCCGCATCAACAAAACCCTGAGGCCCCTTCCTCCCACCCCATCTCTCTCCCTTGTGGATGCTCCTGGAATGTCCCTGACCCGTGCCTGATCCCTCCCTCACCCCACCCCAAAGGTATTTT chm1:+:2507730938:7 +AAAATACCTTTGGGGTGGGGTGAGGGAGGGATCAGGCACGGGTCAGGGACATTCCAGGAGCATCCACAAGGGAGAGAGATGGGGTGGGAGGAAGGGGCCTCAGGGTTTTGTTGATGCGGAGTTTGAAGGCCACCGCGGCCGGCCGAACTTGTCTCGCTCATCGTCTGTGGCGATGTTGGCGGCGTTGATGCGACATTCTA chm1:+:303885986:-1 +CTCTTTATACGAGAATAAACGAAATCTTTAGTATTCCTTTCTGTGACCCTGGACAAGTTTTCTTTCTTAGCTTTTTCTTCTCTCCATGTTTATAGAAAGTGGCAATCTGTTTTTGATCACAGGCTTGTTCATGGGATGAATCAGATAATGCACATAGAGCTCTGAGCCAGTGCTCAGCACATTCGGTAATTCAAGAAATG chm1:+:181921885:-1 chm1:+:554202006:-1 chm1:+:1134312606:-1 chm1:+:1358663189:-1 chm1:+:2187416398:-1 chm1:+:2733976344:11 +CTCTTTATACGAGAATAAACGAAATCTTTAGTATTCCTTTCTGTGACCCTGGACAAGTTTTCTTTCTTAGCTTTTTCTTCTCTCCATGTTTATAGAAAGTGGCAATCTGTTTTTGATCACAGGCTTGTTCATGGGATGAATCAGATAATGCACATAGAGCTCTGAGCCAGTGCTCAGCACATTCGGTAATTCAAGAAATG chm1:+:2733976347:11 +CTCTTTATACGAGAATAAACGAAATCTTTAGTATTCCTTTCTGTGACCCTGGACAAGTTTTCTTTCTTAGCTTTTTCTTCTCTCCATGTTTATAGAAAGTGGCAATCTGTTTTTGATCACAGGCTTGTTCATGGGATGAATCAGATAATGCACATAGAGCTCTGAGCCAGTGCTCAGCACATTCGGTAATTCAAGAAATG chm1:+:2733976345:11 +TAGGTGATGCAGGAGGGAAAGCTGGATTGGAACAGGGAGAGTTTTGTAGACGGGCTATGCTCATTAGTGCCCTTTGAAAGAGCAGAGCTGGCAGCCTGTAGTCATCATTTGGATATACAGAACTAGAGCATGAAGTCTGATGTAGAGCTACAGAATGAAGAGCAACAGCAGCTGTTTAAATACCGAGAAAGTGTGTAGTA chm1:+:1718862322:21 chm1:+:1726570432:6 chm1:+:1728104693:12 chm1:+:1728612048:10 chm1:+:1732144700:9 chm1:+:1769144424:11 chm1:+:1981222925:-1 chm1:+:2894210823:-1 chm1:+:3012369331:-1 +TACTACACACTTTCTCGGTATTTAAACAGCTGCTGTTGCTCTTCATTCTGTAGCTCTACATCAGACTTCATGCTCTAGTTCTGTATATCCAAATGATGACTACAGGCTGCCAGCTCTGCTCTTTCAAAGGGCACTAATGAGCATAGCCCGTCTACAAAACTCTCCCTGTTCCAATCCAGCTTTCCCTCCTGCATCACCTA chm1:+:1723292793:26 chm1:+:1726692610:12 chm1:+:1727086121:11 chm1:+:1727563309:10 chm1:+:1729272654:9 chm1:+:1729589443:10 chm1:+:1731596238:12 chm1:+:1731835711:9 chm1:+:1755805589:12 chm1:+:2408765172:-1 chm1:+:2634343585:-1 +TACTACACACTTTCTCGGTATTTAAACAGCTGCTGTTGCTCTTCATTCTGTAGCTCTACATCAGACTTCATGCTCTAGTTCTGTATATCCAAATGATGACTACAGGCTGCCAGCTCTGCTCTTTCAAAGGGCACTAATGAGCATAGCCCGTCTACAAAACTCTCCCTGTTCCAATCCAGCTTTCCCTCCTGCATCACCTA chm1:+:108171521:-1 chm1:+:374199943:-1 chm1:+:925859900:-1 chm1:+:1531392147:-1 chm1:+:2153359999:-1 +AATAACATGAAAGTAGCTCAGCCTTCAGACACGCACAAACGTGGCATGTGCATGTGTGTCACACAAAACAATTTTCTGCAATCATATGTGTGGAATGTTTTTATTGGAGAGGCTATTTTTAGATACTGGACTGGCTGCCTACATGGCAACAAATGGTATGTTATTTGCAAAGGAGAATGACACACTAAGAAATGCAAAGT chm1:+:898446345:7 chm1:+:2953293136:-1 +AATAACATGAAAGTAGCTCAGCCTTCAGACACGCACAAACGTGGCATGTGCATGTGTGTCACACAAAACAATTTTCTGCAATCATATGTGTGGAATGTTTTTATTGGAGAGGCTATTTTTAGATACTGGACTGGCTGCCTACATGGCAACAAATGGTATGTTATTTGCAAAGGAGAATGACACACTAAGAAATGCAAAGT chm1:+:898446343:7 +AATAACATGAAAGTAGCTCAGCCTTCAGACACGCACAAACGTGGCATGTGCATGTGTGTCACACAAAACAATTTTCTGCAATCATATGTGTGGAATGTTTTTATTGGAGAGGCTATTTTTAGATACTGGACTGGCTGCCTACATGGCAACAAATGGTATGTTATTTGCAAAGGAGAATGACACACTAAGAAATGCAAAGT chm1:+:898446344:7 +AATAACATGAAAGTAGCTCAGCCTTCAGACACGCACAAACGTGGCATGTGCATGTGTGTCACACAAAACAATTTTCTGCAATCATATGTGTGGAATGTTTTTATTGGAGAGGCTATTTTTAGATACTGGACTGGCTGCCTACATGGCAACAAATGGTATGTTATTTGCAAAGGAGAATGACACACTAAGAAATGCAAAGT chm1:+:2075240316:-1 +ACTTTGCATTTCTTAGTGTGTCATTCTCCTTTGCAAATAACATACCATTTGTTGCCATGTAGGCAGCCAGTCCAGTATCTAAAAATAGCCTCTCCAATAAAAACATTCCACACATATGATTGCAGAAAATTGTTTTGTGTGACACACATGCACATGCCACGTTTGTGCGTGTCTGAAGGCTGAGCTACTTTCATGTTATT chm1:+:1379136442:-1 +ACTTTGCATTTCTTAGTGTGTCATTCTCCTTTGCAAATAACATACCATTTGTTGCCATGTAGGCAGCCAGTCCAGTATCTAAAAATAGCCTCTCCAATAAAAACATTCCACACATATGATTGCAGAAAATTGTTTTGTGTGACACACATGCACATGCCACGTTTGTGCGTGTCTGAAGGCTGAGCTACTTTCATGTTATT chm1:+:1161153416:-1 +CCTGGCCGTACATCTGAGAAAGCTGATAAGAAAAGTCCAGTCATGCCCTTTTTTGACACTGGCAGAAGTTAAACCTTGCAAGCCTTGTCCTATGCCTGCATGCATGAATGCTCAATTGAGCCTACTCCCTAACCACCGTAATAAAACTCCAGGCTGGTCTCTTTTCTCTGCTATCACAAGCTATTTTTTGACCTGCTCAG chm1:+:866544140:-1 chm1:+:1472719001:-1 chm1:+:1710960766:-1 chm1:+:1980617380:-1 chm1:+:2347531259:-1 +CCTGGCCGTACATCTGAGAAAGCTGATAAGAAAAGTCCAGTCATGCCCTTTTTTGACACTGGCAGAAGTTAAACCTTGCAAGCCTTGTCCTATGCCTGCATGCATGAATGCTCAATTGAGCCTACTCCCTAACCACCGTAATAAAACTCCAGGCTGGTCTCTTTTCTCTGCTATCACAAGCTATTTTTTGACCTGCTCAG chm1:+:65155043:-1 chm1:+:94678138:-1 chm1:+:97412604:-1 chm1:+:177677573:-1 chm1:+:299218599:-1 chm1:+:507968862:-1 chm1:+:609083721:-1 chm1:+:907572820:-1 chm1:+:1034524336:-1 chm1:+:1085227570:-1 chm1:+:1100587432:-1 chm1:+:1315855071:-1 chm1:+:1362688594:-1 chm1:+:1649803829:-1 chm1:+:1815259268:-1 chm1:+:2138941273:-1 chm1:+:2399726526:-1 chm1:+:2406936885:-1 chm1:+:2895113582:-1 +CCTGGCCGTACATCTGAGAAAGCTGATAAGAAAAGTCCAGTCATGCCCTTTTTTGACACTGGCAGAAGTTAAACCTTGCAAGCCTTGTCCTATGCCTGCATGCATGAATGCTCAATTGAGCCTACTCCCTAACCACCGTAATAAAACTCCAGGCTGGTCTCTTTTCTCTGCTATCACAAGCTATTTTTTGACCTGCTCAG chm1:+:92657263:-1 chm1:+:399227043:-1 chm1:+:781030082:-1 chm1:+:855034550:-1 chm1:+:855970383:-1 chm1:+:1024982230:-1 chm1:+:1106679229:-1 chm1:+:1112141923:-1 chm1:+:1268294033:-1 chm1:+:1278258965:-1 chm1:+:1468931970:-1 chm1:+:1570940287:-1 chm1:+:2465959394:-1 chm1:+:2477253214:-1 chm1:+:2910542436:-1 +CCTGGCCGTACATCTGAGAAAGCTGATAAGAAAAGTCCAGTCATGCCCTTTTTTGACACTGGCAGAAGTTAAACCTTGCAAGCCTTGTCCTATGCCTGCATGCATGAATGCTCAATTGAGCCTACTCCCTAACCACCGTAATAAAACTCCAGGCTGGTCTCTTTTCTCTGCTATCACAAGCTATTTTTTGACCTGCTCAG chm1:+:31312144:-1 chm1:+:48815120:-1 chm1:+:51735155:-1 chm1:+:149268518:-1 chm1:+:149654114:-1 chm1:+:311841327:-1 chm1:+:416912277:-1 chm1:+:440159835:-1 chm1:+:531113956:-1 chm1:+:594445973:-1 chm1:+:643312148:-1 chm1:+:872208489:-1 chm1:+:887494902:-1 chm1:+:951017522:-1 chm1:+:951892967:-1 chm1:+:1059694475:-1 chm1:+:1060993940:-1 chm1:+:1088675947:-1 chm1:+:1219657364:-1 chm1:+:1314558668:-1 chm1:+:1494732398:-1 chm1:+:1558403543:-1 chm1:+:1571164276:-1 chm1:+:1621462134:-1 chm1:+:1763024416:-1 chm1:+:1818135980:-1 chm1:+:1825694162:-1 chm1:+:1834738449:-1 chm1:+:1858669978:-1 chm1:+:1864267031:-1 chm1:+:2040235423:-1 chm1:+:2046342218:-1 chm1:+:2073309949:-1 chm1:+:2126107613:-1 chm1:+:2375951599:-1 chm1:+:2425564717:-1 chm1:+:2557432168:-1 chm1:+:2563594958:-1 chm1:+:2572942354:-1 chm1:+:2574222926:-1 chm1:+:2683384014:-1 chm1:+:2691483567:-1 chm1:+:2698795555:-1 chm1:+:2729544726:-1 chm1:+:2857859625:-1 chm1:+:2900051604:-1 +CCTGGCCGTACATCTGAGAAAGCTGATAAGAAAAGTCCAGTCATGCCCTTTTTTGACACTGGCAGAAGTTAAACCTTGCAAGCCTTGTCCTATGCCTGCATGCATGAATGCTCAATTGAGCCTACTCCCTAACCACCGTAATAAAACTCCAGGCTGGTCTCTTTTCTCTGCTATCACAAGCTATTTTTTGACCTGCTCAG chm1:+:325077458:-1 chm1:+:372594452:-1 chm1:+:1489780677:-1 chm1:+:2240025299:-1 chm1:+:2876211346:-1 chm1:+:2947827453:-1 +CTGAGCAGGTCAAAAAATAGCTTGTGATAGCAGAGAAAAGAGACCAGCCTGGAGTTTTATTACGGTGGTTAGGGAGTAGGCTCAATTGAGCATTCATGCATGCAGGCATAGGACAAGGCTTGCAAGGTTTAACTTCTGCCAGTGTCAAAAAAGGGCATGACTGGACTTTTCTTATCAGCTTTCTCAGATGTACGGCCAGG chm1:+:894943089:7 +CTGAGCAGGTCAAAAAATAGCTTGTGATAGCAGAGAAAAGAGACCAGCCTGGAGTTTTATTACGGTGGTTAGGGAGTAGGCTCAATTGAGCATTCATGCATGCAGGCATAGGACAAGGCTTGCAAGGTTTAACTTCTGCCAGTGTCAAAAAAGGGCATGACTGGACTTTTCTTATCAGCTTTCTCAGATGTACGGCCAGG chm1:+:894943090:7 +CTGAGCAGGTCAAAAAATAGCTTGTGATAGCAGAGAAAAGAGACCAGCCTGGAGTTTTATTACGGTGGTTAGGGAGTAGGCTCAATTGAGCATTCATGCATGCAGGCATAGGACAAGGCTTGCAAGGTTTAACTTCTGCCAGTGTCAAAAAAGGGCATGACTGGACTTTTCTTATCAGCTTTCTCAGATGTACGGCCAGG chm1:+:2456501873:-1 +CTGAGCAGGTCAAAAAATAGCTTGTGATAGCAGAGAAAAGAGACCAGCCTGGAGTTTTATTACGGTGGTTAGGGAGTAGGCTCAATTGAGCATTCATGCATGCAGGCATAGGACAAGGCTTGCAAGGTTTAACTTCTGCCAGTGTCAAAAAAGGGCATGACTGGACTTTTCTTATCAGCTTTCTCAGATGTACGGCCAGG chm1:+:894943091:7 +TAGCTTCAATCCCCTGAAGGCAATTGCAATACTCCCAGTAAATACAAAATGAAGGCCTGCACAATAAACCCAGAATGATTGTTAATGGTAGAGTTCCAAAGACATTAAATATGCTTTATTCCAGCCTGTCAGAGGCCGATTGTTTATTCGATTTTCACAGCCTGCCCTAACTTCAGTCCTGATCAACATTTGTTCATTGG chm1:+:1622920873:8 +TAGCTTCAATCCCCTGAAGGCAATTGCAATACTCCCAGTAAATACAAAATGAAGGCCTGCACAATAAACCCAGAATGATTGTTAATGGTAGAGTTCCAAAGACATTAAATATGCTTTATTCCAGCCTGTCAGAGGCCGATTGTTTATTCGATTTTCACAGCCTGCCCTAACTTCAGTCCTGATCAACATTTGTTCATTGG chm1:+:1622920867:8 +TAGCTTCAATCCCCTGAAGGCAATTGCAATACTCCCAGTAAATACAAAATGAAGGCCTGCACAATAAACCCAGAATGATTGTTAATGGTAGAGTTCCAAAGACATTAAATATGCTTTATTCCAGCCTGTCAGAGGCCGATTGTTTATTCGATTTTCACAGCCTGCCCTAACTTCAGTCCTGATCAACATTTGTTCATTGG chm1:+:1622920869:8 +TAGCTTCAATCCCCTGAAGGCAATTGCAATACTCCCAGTAAATACAAAATGAAGGCCTGCACAATAAACCCAGAATGATTGTTAATGGTAGAGTTCCAAAGACATTAAATATGCTTTATTCCAGCCTGTCAGAGGCCGATTGTTTATTCGATTTTCACAGCCTGCCCTAACTTCAGTCCTGATCAACATTTGTTCATTGG chm1:+:1903450628:-1 +TAGCTTCAATCCCCTGAAGGCAATTGCAATACTCCCAGTAAATACAAAATGAAGGCCTGCACAATAAACCCAGAATGATTGTTAATGGTAGAGTTCCAAAGACATTAAATATGCTTTATTCCAGCCTGTCAGAGGCCGATTGTTTATTCGATTTTCACAGCCTGCCCTAACTTCAGTCCTGATCAACATTTGTTCATTGG chm1:+:1622920872:8 +CCAATGAACAAATGTTGATCAGGACTGAAGTTAGGGCAGGCTGTGAAAATCGAATAAACAATCGGCCTCTGACAGGCTGGAATAAAGCATATTTAATGTCTTTGGAACTCTACCATTAACAATCATTCTGGGTTTATTGTGCAGGCCTTCATTTTGTATTTACTGGGAGTATTGCAATTGCCTTCAGGGGATTGAAGCTA chm1:+:879307812:-1 +GAAGGCGTCATAAAAGACATCCGGTACAATTTTACTTCCATTTGTGAGAATTTGCTCTTCAACAGGTAATTTTACAGATTTTGGAGGGCACTACCTCTTTTTATGGCTAAGGCCATTTCACAGTTGTACTATTTCCTATTAGAAACACTTCCCTTATATTTTGTCAAAAGCTATTTCTCAATTGGTTCCAGTTCTCTCTT chm1:+:571828080:9 +GAAGGCGTCATAAAAGACATCCGGTACAATTTTACTTCCATTTGTGAGAATTTGCTCTTCAACAGGTAATTTTACAGATTTTGGAGGGCACTACCTCTTTTTATGGCTAAGGCCATTTCACAGTTGTACTATTTCCTATTAGAAACACTTCCCTTATATTTTGTCAAAAGCTATTTCTCAATTGGTTCCAGTTCTCTCTT chm1:+:571828083:9 +GAAGGCGTCATAAAAGACATCCGGTACAATTTTACTTCCATTTGTGAGAATTTGCTCTTCAACAGGTAATTTTACAGATTTTGGAGGGCACTACCTCTTTTTATGGCTAAGGCCATTTCACAGTTGTACTATTTCCTATTAGAAACACTTCCCTTATATTTTGTCAAAAGCTATTTCTCAATTGGTTCCAGTTCTCTCTT chm1:+:571828084:9 +AAGAGAGAACTGGAACCAATTGAGAAATAGCTTTTGACAAAATATAAGGGAAGTGTTTCTAATAGGAAATAGTACAACTGTGAAATGGCCTTAGCCATAAAAAGAGGTAGTGCCCTCCAAAATCTGTAAAATTACCTGTTGAAGAGCAAATTCTCACAAATGGAAGTAAAATTGTACCGGATGTCTTTTATGACGCCTTC chm1:+:2399538644:-1 +AAGAGAGAACTGGAACCAATTGAGAAATAGCTTTTGACAAAATATAAGGGAAGTGTTTCTAATAGGAAATAGTACAACTGTGAAATGGCCTTAGCCATAAAAAGAGGTAGTGCCCTCCAAAATCTGTAAAATTACCTGTTGAAGAGCAAATTCTCACAAATGGAAGTAAAATTGTACCGGATGTCTTTTATGACGCCTTC chm1:+:888759492:-1 +ACTTTGGAGGCTGAGATGGGCAGATCACTTGAGGCCAGGAGTTCGAAACCAGCCTGGCAACATGGTGAAACCCCATCTCTACTAAAAACGCAAAAATTAATTGGGCATGGTGGCACATGCCTGTCCAGACTACTCCGGAGGTCTGAGGCAAGAAAATCACTTGAACCTGGAAGGTGGACCCTCCAGCCTGGCTAAGAGAG chm1:+:624539381:-1 chm1:+:2429783046:-1 +ACTTTGGAGGCTGAGATGGGCAGATCACTTGAGGCCAGGAGTTCGAAACCAGCCTGGCAACATGGTGAAACCCCATCTCTACTAAAAACGCAAAAATTAATTGGGCATGGTGGCACATGCCTGTCCAGACTACTCCGGAGGTCTGAGGCAAGAAAATCACTTGAACCTGGAAGGTGGACCCTCCAGCCTGGCTAAGAGAG chm1:+:7954754:-1 chm1:+:9645554:-1 chm1:+:17228543:-1 chm1:+:24247948:-1 chm1:+:26174151:-1 chm1:+:29081048:-1 chm1:+:113874786:-1 chm1:+:150755074:-1 chm1:+:153524335:-1 chm1:+:174398592:-1 chm1:+:177825459:-1 chm1:+:179821130:-1 chm1:+:203629953:-1 chm1:+:211480545:-1 chm1:+:218737326:-1 chm1:+:222352130:-1 chm1:+:249351037:-1 chm1:+:250179698:-1 chm1:+:252750008:-1 chm1:+:292295305:-1 chm1:+:299442053:-1 chm1:+:311017906:-1 chm1:+:358451943:-1 chm1:+:402749857:-1 chm1:+:409053003:-1 chm1:+:419668144:-1 chm1:+:420783311:-1 chm1:+:455101159:-1 chm1:+:485534255:-1 chm1:+:530592655:-1 chm1:+:544684462:-1 chm1:+:548109104:-1 chm1:+:549427913:-1 chm1:+:580689897:-1 chm1:+:623029822:-1 chm1:+:629281394:-1 chm1:+:633847536:-1 chm1:+:634750812:-1 chm1:+:648216143:-1 chm1:+:662326098:-1 chm1:+:666174567:-1 chm1:+:686548024:-1 chm1:+:687727883:-1 chm1:+:695097755:-1 chm1:+:726420787:-1 chm1:+:762138739:-1 chm1:+:765355733:-1 chm1:+:765853263:-1 chm1:+:801901270:-1 chm1:+:838560309:-1 chm1:+:842170104:-1 chm1:+:860752174:-1 chm1:+:924774571:-1 chm1:+:1013820229:-1 chm1:+:1019853864:-1 chm1:+:1039183147:-1 chm1:+:1041050666:-1 chm1:+:1049549799:-1 chm1:+:1060587396:-1 chm1:+:1069827583:-1 chm1:+:1071495179:-1 chm1:+:1080784277:-1 chm1:+:1086851227:-1 chm1:+:1089114611:-1 chm1:+:1093297277:-1 chm1:+:1170676241:-1 chm1:+:1188162204:-1 chm1:+:1239533781:-1 chm1:+:1254515713:-1 chm1:+:1296558956:-1 chm1:+:1300310049:-1 chm1:+:1305836617:-1 chm1:+:1311221006:-1 chm1:+:1315809047:-1 chm1:+:1331274245:-1 chm1:+:1341213859:-1 chm1:+:1343570184:-1 chm1:+:1352492111:-1 chm1:+:1361724260:-1 chm1:+:1363748491:-1 chm1:+:1374002979:-1 chm1:+:1397581996:-1 chm1:+:1415102366:-1 chm1:+:1435200644:-1 chm1:+:1488814513:-1 chm1:+:1488824375:-1 chm1:+:1498986595:-1 chm1:+:1513425593:-1 chm1:+:1514248251:-1 chm1:+:1634183017:-1 chm1:+:1634593533:-1 chm1:+:1662644905:-1 chm1:+:1663875338:-1 chm1:+:1668695375:-1 chm1:+:1678515985:-1 chm1:+:1678667483:-1 chm1:+:1689616561:-1 chm1:+:1692573587:-1 chm1:+:1771159767:-1 chm1:+:1774022042:-1 chm1:+:1779695018:-1 chm1:+:1781371774:-1 chm1:+:1797091752:-1 chm1:+:1876872169:-1 chm1:+:1876881074:-1 chm1:+:1876899903:-1 chm1:+:1876918729:-1 chm1:+:1879253359:-1 chm1:+:1880349115:-1 chm1:+:1886372006:-1 chm1:+:1934950264:-1 chm1:+:1935867098:-1 chm1:+:1961283090:-1 chm1:+:2007687075:-1 chm1:+:2040598785:-1 chm1:+:2046414792:-1 chm1:+:2048722292:-1 chm1:+:2062562718:-1 chm1:+:2063421429:-1 chm1:+:2076325791:-1 chm1:+:2106452754:-1 chm1:+:2130452768:-1 chm1:+:2185647167:-1 chm1:+:2238635830:-1 chm1:+:2274747329:-1 chm1:+:2278135981:-1 chm1:+:2289449496:-1 chm1:+:2345130581:-1 chm1:+:2389199620:-1 chm1:+:2391775260:-1 chm1:+:2408394762:-1 chm1:+:2410615792:-1 chm1:+:2411830442:-1 chm1:+:2421643939:-1 chm1:+:2429210400:-1 chm1:+:2435265076:-1 chm1:+:2437873822:-1 chm1:+:2439784493:-1 chm1:+:2458273967:-1 chm1:+:2466818393:-1 chm1:+:2467061755:-1 chm1:+:2477114513:-1 chm1:+:2485252017:-1 chm1:+:2502246147:-1 chm1:+:2507682215:-1 chm1:+:2513076388:-1 chm1:+:2517345049:-1 chm1:+:2520606012:-1 chm1:+:2526786110:-1 chm1:+:2556126826:-1 chm1:+:2562819269:-1 chm1:+:2580631637:-1 chm1:+:2581579393:-1 chm1:+:2582659039:-1 chm1:+:2591107499:-1 chm1:+:2601043022:-1 chm1:+:2660479958:-1 chm1:+:2661239292:-1 chm1:+:2663885351:-1 chm1:+:2666685671:-1 chm1:+:2667738246:-1 chm1:+:2668388701:-1 chm1:+:2672459849:-1 chm1:+:2676059026:-1 chm1:+:2676125944:-1 chm1:+:2682319722:-1 chm1:+:2721668613:-1 chm1:+:2737130330:-1 chm1:+:2748578168:-1 chm1:+:2755508604:-1 chm1:+:2763071177:-1 chm1:+:2765891768:-1 chm1:+:2773705832:-1 chm1:+:2848197721:-1 chm1:+:2851536398:-1 chm1:+:2873896954:-1 chm1:+:2875406321:-1 chm1:+:2925696076:-1 chm1:+:2926454767:-1 chm1:+:2928369456:-1 chm1:+:3021371950:-1 chm1:+:3034372292:-1 chm1:+:3035985184:40 chm1:+:3057668983:-1 +ACTTTGGAGGCTGAGATGGGCAGATCACTTGAGGCCAGGAGTTCGAAACCAGCCTGGCAACATGGTGAAACCCCATCTCTACTAAAAACGCAAAAATTAATTGGGCATGGTGGCACATGCCTGTCCAGACTACTCCGGAGGTCTGAGGCAAGAAAATCACTTGAACCTGGAAGGTGGACCCTCCAGCCTGGCTAAGAGAG chm1:+:469434271:39 chm1:+:934322122:-1 chm1:+:1030340890:9 chm1:+:2478630586:-1 chm1:+:2670111716:-1 +ACTTTGGAGGCTGAGATGGGCAGATCACTTGAGGCCAGGAGTTCGAAACCAGCCTGGCAACATGGTGAAACCCCATCTCTACTAAAAACGCAAAAATTAATTGGGCATGGTGGCACATGCCTGTCCAGACTACTCCGGAGGTCTGAGGCAAGAAAATCACTTGAACCTGGAAGGTGGACCCTCCAGCCTGGCTAAGAGAG chm1:+:1413761686:-1 chm1:+:2668604479:-1 +CTCTCTTAGCCAGGCTGGAGGGTCCACCTTCCAGGTTCAAGTGATTTTCTTGCCTCAGACCTCCGGAGTAGTCTGGACAGGCATGTGCCACCATGCCCAATTAATTTTTGCGTTTTTAGTAGAGATGGGGTTTCACCATGTTGCCAGGCTGGTTTCGAACTCCTGGCCTCAAGTGATCTGCCCATCTCAGCCTCCAAAGT chm1:+:154329558:-1 chm1:+:524738971:-1 chm1:+:527126068:-1 chm1:+:569429176:-1 chm1:+:647229468:-1 chm1:+:676004547:-1 chm1:+:692447027:-1 chm1:+:892314752:-1 chm1:+:997765805:-1 chm1:+:1015323501:-1 chm1:+:1054171737:-1 chm1:+:1120830053:-1 chm1:+:1143411859:-1 chm1:+:1188969275:-1 chm1:+:1199497689:-1 chm1:+:1201044565:-1 chm1:+:1335750609:-1 chm1:+:1646990941:-1 chm1:+:1663173211:-1 chm1:+:1692190280:-1 chm1:+:1752559200:-1 chm1:+:1837839681:-1 chm1:+:1880364456:-1 chm1:+:2008589699:-1 chm1:+:2185584878:-1 chm1:+:2250344685:-1 chm1:+:2386386321:-1 chm1:+:2428798138:-1 chm1:+:2478419717:-1 chm1:+:2525909213:-1 chm1:+:2674648579:-1 chm1:+:2865063398:-1 chm1:+:2870141412:-1 chm1:+:2905303718:-1 chm1:+:2928411855:39 chm1:+:2935446884:-1 chm1:+:2999395271:-1 +CTCTCTTAGCCAGGCTGGAGGGTCCACCTTCCAGGTTCAAGTGATTTTCTTGCCTCAGACCTCCGGAGTAGTCTGGACAGGCATGTGCCACCATGCCCAATTAATTTTTGCGTTTTTAGTAGAGATGGGGTTTCACCATGTTGCCAGGCTGGTTTCGAACTCCTGGCCTCAAGTGATCTGCCCATCTCAGCCTCCAAAGT chm1:+:421844572:-1 +CTCTCTTAGCCAGGCTGGAGGGTCCACCTTCCAGGTTCAAGTGATTTTCTTGCCTCAGACCTCCGGAGTAGTCTGGACAGGCATGTGCCACCATGCCCAATTAATTTTTGCGTTTTTAGTAGAGATGGGGTTTCACCATGTTGCCAGGCTGGTTTCGAACTCCTGGCCTCAAGTGATCTGCCCATCTCAGCCTCCAAAGT chm1:+:1633404521:-1 +CTCTCTTAGCCAGGCTGGAGGGTCCACCTTCCAGGTTCAAGTGATTTTCTTGCCTCAGACCTCCGGAGTAGTCTGGACAGGCATGTGCCACCATGCCCAATTAATTTTTGCGTTTTTAGTAGAGATGGGGTTTCACCATGTTGCCAGGCTGGTTTCGAACTCCTGGCCTCAAGTGATCTGCCCATCTCAGCCTCCAAAGT chm1:+:2397235907:-1 +CTCTCTTAGCCAGGCTGGAGGGTCCACCTTCCAGGTTCAAGTGATTTTCTTGCCTCAGACCTCCGGAGTAGTCTGGACAGGCATGTGCCACCATGCCCAATTAATTTTTGCGTTTTTAGTAGAGATGGGGTTTCACCATGTTGCCAGGCTGGTTTCGAACTCCTGGCCTCAAGTGATCTGCCCATCTCAGCCTCCAAAGT chm1:+:32562085:-1 chm1:+:56214537:-1 chm1:+:253708003:-1 chm1:+:1105181754:-1 chm1:+:1309041220:-1 chm1:+:1401101781:-1 chm1:+:1560044031:-1 chm1:+:1990603936:-1 chm1:+:2000755451:-1 chm1:+:2365045630:-1 chm1:+:2440626959:-1 chm1:+:2504203950:-1 chm1:+:2534067750:-1 chm1:+:2728904593:-1 +AAAACACATGTACTTAATAATTAAATAATCTTTATTGTTTCATCTAAGAAACATTCTTTAAGTAAAACTGGCTATTATTTTTACTGCGAGTGCACCGGCAGCTACTGGTATGTTTCCATGCCTTGATGCGTGCTAAGACGCTAGCAGTTTTCCATCACAGTTGCCTTTTGTATTAATTTAATGCAAATGTCCAAACAGGG chm1:+:363955920:-1 chm1:+:796457330:-1 chm1:+:1071826260:-1 chm1:+:1803942083:12 +AAAACACATGTACTTAATAATTAAATAATCTTTATTGTTTCATCTAAGAAACATTCTTTAAGTAAAACTGGCTATTATTTTTACTGCGAGTGCACCGGCAGCTACTGGTATGTTTCCATGCCTTGATGCGTGCTAAGACGCTAGCAGTTTTCCATCACAGTTGCCTTTTGTATTAATTTAATGCAAATGTCCAAACAGGG chm1:+:660669557:-1 +AAAACACATGTACTTAATAATTAAATAATCTTTATTGTTTCATCTAAGAAACATTCTTTAAGTAAAACTGGCTATTATTTTTACTGCGAGTGCACCGGCAGCTACTGGTATGTTTCCATGCCTTGATGCGTGCTAAGACGCTAGCAGTTTTCCATCACAGTTGCCTTTTGTATTAATTTAATGCAAATGTCCAAACAGGG chm1:+:1803942078:12 +AAAACACATGTACTTAATAATTAAATAATCTTTATTGTTTCATCTAAGAAACATTCTTTAAGTAAAACTGGCTATTATTTTTACTGCGAGTGCACCGGCAGCTACTGGTATGTTTCCATGCCTTGATGCGTGCTAAGACGCTAGCAGTTTTCCATCACAGTTGCCTTTTGTATTAATTTAATGCAAATGTCCAAACAGGG chm1:+:1803942079:12 +CCCTGTTTGGACATTTGCATTAAATTAATACAAAAGGCAACTGTGATGGAAAACTGCTAGCGTCTTAGCACGCATCAAGGCATGGAAACATACCAGTAGCTGCCGGTGCACTCGCAGTAAAAATAATAGCCAGTTTTACTTAAAGAATGTTTCTTAGATGAAACAATAAAGATTATTTAATTATTAAGTACATGTGTTTT chm1:+:601856204:-1 chm1:+:752580756:-1 chm1:+:771622871:-1 chm1:+:777211375:-1 chm1:+:931956458:-1 chm1:+:1029307488:-1 chm1:+:1120589339:-1 chm1:+:1174138706:-1 chm1:+:1207966866:-1 chm1:+:1228234883:-1 chm1:+:1899102465:-1 chm1:+:2369299946:-1 chm1:+:2620637177:-1 chm1:+:2624997452:-1 +TAAAGTATTTGTAGTCATCTTTTGTGTCTGTTATTACTTACAAGGACAGGGGAAAAAAACTTTTCGTGATGGCGTCGTAGAATCCCAGGAATGGCCTTTTATCTCCTTTTCCTGTATCCCCATCAGTTAGTCTGCAATTTACTCTTCCAATCATCAGAACAGAAAAAAATAGAGACCATAGTGCTATAGTGTTCTATGAG chm1:+:2220440195:12 +TAAAGTATTTGTAGTCATCTTTTGTGTCTGTTATTACTTACAAGGACAGGGGAAAAAAACTTTTCGTGATGGCGTCGTAGAATCCCAGGAATGGCCTTTTATCTCCTTTTCCTGTATCCCCATCAGTTAGTCTGCAATTTACTCTTCCAATCATCAGAACAGAAAAAAATAGAGACCATAGTGCTATAGTGTTCTATGAG chm1:+:2220440196:12 +CAATCCATCTTTTCTGAACAACGTTACCTAGAAAATTTCTTTAACTAAACAGTATGAATTTCAGACTAAATTTTAAAGTGACATTCTGATTATAAAGAAAAAAAAAAAGCAATTCCCTAAATGAAAATACTTGGAGTTTGCCTGGGAACTGAAAATTTTGTCACTGTGGAAAGTGTGAGGAAAAGATCTAGTGTTGGCAA chm1:+:188136780:-1 chm1:+:209327096:-1 chm1:+:245684510:-1 chm1:+:312133233:-1 chm1:+:345331659:-1 chm1:+:478802543:-1 chm1:+:520226104:-1 chm1:+:581814629:-1 chm1:+:640918050:-1 chm1:+:690794422:-1 chm1:+:755505914:-1 chm1:+:779675410:-1 chm1:+:894791690:-1 chm1:+:903345836:-1 chm1:+:915635433:-1 chm1:+:945478782:-1 chm1:+:1063765481:-1 chm1:+:1217887614:-1 chm1:+:1228499890:-1 chm1:+:1258345421:-1 chm1:+:1289736177:-1 chm1:+:1377199454:-1 chm1:+:1385861516:-1 chm1:+:1452033568:-1 chm1:+:1553262212:-1 chm1:+:1795517725:-1 chm1:+:1811263701:-1 chm1:+:1827584499:-1 chm1:+:1929671174:-1 chm1:+:2042150545:-1 chm1:+:2166277128:-1 chm1:+:2187001933:-1 chm1:+:2187766524:-1 chm1:+:2387147933:-1 chm1:+:2479652064:-1 chm1:+:2486465962:-1 chm1:+:2691161221:-1 chm1:+:2730490645:-1 chm1:+:2759121218:-1 chm1:+:2822549866:-1 chm1:+:2822557342:-1 chm1:+:2853951905:-1 chm1:+:2926267952:-1 +CAATCCATCTTTTCTGAACAACGTTACCTAGAAAATTTCTTTAACTAAACAGTATGAATTTCAGACTAAATTTTAAAGTGACATTCTGATTATAAAGAAAAAAAAAAAGCAATTCCCTAAATGAAAATACTTGGAGTTTGCCTGGGAACTGAAAATTTTGTCACTGTGGAAAGTGTGAGGAAAAGATCTAGTGTTGGCAA chm1:+:1468115787:-1 +CAATCCATCTTTTCTGAACAACGTTACCTAGAAAATTTCTTTAACTAAACAGTATGAATTTCAGACTAAATTTTAAAGTGACATTCTGATTATAAAGAAAAAAAAAAAGCAATTCCCTAAATGAAAATACTTGGAGTTTGCCTGGGAACTGAAAATTTTGTCACTGTGGAAAGTGTGAGGAAAAGATCTAGTGTTGGCAA chm1:+:105599423:-1 chm1:+:193106514:-1 chm1:+:453878221:-1 chm1:+:510058881:-1 chm1:+:571048795:-1 chm1:+:577522195:-1 chm1:+:611177907:-1 chm1:+:662560460:-1 chm1:+:692190008:-1 chm1:+:971931916:-1 chm1:+:1131845905:-1 chm1:+:1182576267:-1 chm1:+:1340767893:-1 chm1:+:1353803951:-1 chm1:+:1445017452:-1 chm1:+:1637702590:-1 chm1:+:1738723125:-1 chm1:+:1778829143:-1 chm1:+:2142020890:-1 chm1:+:2465500826:-1 chm1:+:2650870196:-1 chm1:+:3062212385:-1 chm1:+:3062417104:-1 +CAATCCATCTTTTCTGAACAACGTTACCTAGAAAATTTCTTTAACTAAACAGTATGAATTTCAGACTAAATTTTAAAGTGACATTCTGATTATAAAGAAAAAAAAAAAGCAATTCCCTAAATGAAAATACTTGGAGTTTGCCTGGGAACTGAAAATTTTGTCACTGTGGAAAGTGTGAGGAAAAGATCTAGTGTTGGCAA chm1:+:60013451:-1 chm1:+:83414508:-1 chm1:+:264209618:-1 chm1:+:775922947:-1 chm1:+:1390184328:-1 chm1:+:2469046649:-1 chm1:+:2587987400:-1 chm1:+:2643231400:-1 +CAATCCATCTTTTCTGAACAACGTTACCTAGAAAATTTCTTTAACTAAACAGTATGAATTTCAGACTAAATTTTAAAGTGACATTCTGATTATAAAGAAAAAAAAAAAGCAATTCCCTAAATGAAAATACTTGGAGTTTGCCTGGGAACTGAAAATTTTGTCACTGTGGAAAGTGTGAGGAAAAGATCTAGTGTTGGCAA chm1:+:82956551:-1 chm1:+:114537688:-1 chm1:+:117293667:-1 chm1:+:169598140:-1 chm1:+:476425582:-1 chm1:+:477967458:-1 chm1:+:527383122:-1 chm1:+:530945956:-1 chm1:+:629918253:-1 chm1:+:641948824:-1 chm1:+:690768245:-1 chm1:+:792482589:-1 chm1:+:812853989:-1 chm1:+:831930849:-1 chm1:+:852148592:-1 chm1:+:858536026:-1 chm1:+:868851957:-1 chm1:+:957248544:-1 chm1:+:1086891729:-1 chm1:+:1203891190:-1 chm1:+:1296905437:-1 chm1:+:1319936810:-1 chm1:+:1346070992:-1 chm1:+:1413095255:-1 chm1:+:1564767609:-1 chm1:+:1611100445:-1 chm1:+:1685353828:-1 chm1:+:1802642196:-1 chm1:+:1899558206:-1 chm1:+:1933097644:-1 chm1:+:1937742945:-1 chm1:+:1992073533:-1 chm1:+:2051335139:-1 chm1:+:2077156878:-1 chm1:+:2151803146:-1 chm1:+:2158511954:-1 chm1:+:2185368080:-1 chm1:+:2276608546:-1 chm1:+:2369417582:-1 chm1:+:2438093089:-1 chm1:+:2565788193:-1 chm1:+:2596134007:-1 chm1:+:2751296492:-1 chm1:+:2806690850:-1 chm1:+:2856359296:-1 chm1:+:2912956888:-1 chm1:+:2919395360:-1 chm1:+:2936875399:-1 chm1:+:3019982817:-1 chm1:+:3025492127:-1 +TTGCCAACACTAGATCTTTTCCTCACACTTTCCACAGTGACAAAATTTTCAGTTCCCAGGCAAACTCCAAGTATTTTCATTTAGGGAATTGCTTTTTTTTTTTCTTTATAATCAGAATGTCACTTTAAAATTTAGTCTGAAATTCATACTGTTTAGTTAAAGAAATTTTCTAGGTAACGTTGTTCAGAAAAGATGGATTG chm1:+:2406457368:15 +TTGCCAACACTAGATCTTTTCCTCACACTTTCCACAGTGACAAAATTTTCAGTTCCCAGGCAAACTCCAAGTATTTTCATTTAGGGAATTGCTTTTTTTTTTTCTTTATAATCAGAATGTCACTTTAAAATTTAGTCTGAAATTCATACTGTTTAGTTAAAGAAATTTTCTAGGTAACGTTGTTCAGAAAAGATGGATTG chm1:+:41741268:-1 chm1:+:68276712:-1 chm1:+:142559066:-1 chm1:+:300885946:-1 chm1:+:414194211:-1 chm1:+:448810256:-1 chm1:+:455388633:-1 chm1:+:486072233:-1 chm1:+:602973906:-1 chm1:+:626341464:-1 chm1:+:820381824:-1 chm1:+:1001667803:-1 chm1:+:1157031832:-1 chm1:+:1910798465:-1 chm1:+:2144097701:-1 chm1:+:2406457367:15 chm1:+:2552395471:-1 chm1:+:2662777172:-1 chm1:+:2690539659:-1 chm1:+:2791702874:-1 chm1:+:3095826868:-1 chm1:+:3095933676:-1 +TTGCCAACACTAGATCTTTTCCTCACACTTTCCACAGTGACAAAATTTTCAGTTCCCAGGCAAACTCCAAGTATTTTCATTTAGGGAATTGCTTTTTTTTTTTCTTTATAATCAGAATGTCACTTTAAAATTTAGTCTGAAATTCATACTGTTTAGTTAAAGAAATTTTCTAGGTAACGTTGTTCAGAAAAGATGGATTG chm1:+:42379867:-1 chm1:+:50960447:-1 chm1:+:90200304:-1 chm1:+:109547207:-1 chm1:+:284365131:-1 chm1:+:300247812:-1 chm1:+:517477825:-1 chm1:+:619412005:-1 chm1:+:638215038:-1 chm1:+:650064387:-1 chm1:+:652908147:-1 chm1:+:676516779:-1 chm1:+:719576337:-1 chm1:+:900150310:-1 chm1:+:936191650:-1 chm1:+:953591678:-1 chm1:+:962066500:-1 chm1:+:1030759599:-1 chm1:+:1088742477:-1 chm1:+:1170855830:-1 chm1:+:1176794426:-1 chm1:+:1227584623:-1 chm1:+:1242692266:-1 chm1:+:1254456175:-1 chm1:+:1299432827:-1 chm1:+:1400652549:-1 chm1:+:1632615074:-1 chm1:+:1688357704:-1 chm1:+:1855039970:-1 chm1:+:1884584318:-1 chm1:+:1928039646:-1 chm1:+:1959275516:-1 chm1:+:2033492461:-1 chm1:+:2080302794:-1 chm1:+:2109245575:-1 chm1:+:2185904814:-1 chm1:+:2248700265:-1 chm1:+:2265436634:-1 chm1:+:2389990503:-1 chm1:+:2424080660:-1 chm1:+:2465990826:-1 chm1:+:2614873018:-1 chm1:+:2683422136:-1 chm1:+:2706063891:-1 chm1:+:2713280463:-1 chm1:+:2810666115:-1 chm1:+:2925922649:-1 chm1:+:2958338793:-1 chm1:+:2972463596:-1 chm1:+:3001538999:-1 +TTGCCAACACTAGATCTTTTCCTCACACTTTCCACAGTGACAAAATTTTCAGTTCCCAGGCAAACTCCAAGTATTTTCATTTAGGGAATTGCTTTTTTTTTTTCTTTATAATCAGAATGTCACTTTAAAATTTAGTCTGAAATTCATACTGTTTAGTTAAAGAAATTTTCTAGGTAACGTTGTTCAGAAAAGATGGATTG chm1:+:19539422:-1 chm1:+:62977839:-1 chm1:+:299396990:-1 chm1:+:332219280:-1 chm1:+:434615310:-1 chm1:+:472204278:-1 chm1:+:515823840:-1 chm1:+:521931925:-1 chm1:+:576630294:-1 chm1:+:592336057:-1 chm1:+:638048862:-1 chm1:+:647850924:-1 chm1:+:736207224:-1 chm1:+:776373266:-1 chm1:+:824749630:-1 chm1:+:827172163:-1 chm1:+:870298630:-1 chm1:+:996209357:-1 chm1:+:1010636063:-1 chm1:+:1069136785:-1 chm1:+:1082089360:-1 chm1:+:1138683730:-1 chm1:+:1142885965:-1 chm1:+:1223945282:-1 chm1:+:1253033306:-1 chm1:+:1288008777:-1 chm1:+:1333070592:-1 chm1:+:1378694088:-1 chm1:+:1582926465:-1 chm1:+:1734666201:-1 chm1:+:2280235045:-1 chm1:+:2359485968:-1 chm1:+:2488667541:-1 chm1:+:2530494633:-1 chm1:+:2581724479:-1 chm1:+:2728475958:-1 chm1:+:2732317208:-1 chm1:+:2804343909:-1 chm1:+:2807664294:-1 +ACTGGTGTAAATTGTAAAATCCTTGAACCGATAATCAGTGCATTTCCTCTGTATTGGACATGCTTCCTGGATCCAAAGTCTTTGGTGACCGAAAGTAAAAAGAACGCAAAGACTGAAAGCAAAATCTTCTAATAAAATAGGAATTTTGAAGTTTAATATGTAGTCCTATTATTTTAGAAATCGAGTGCCCAGGAAAAAAG chm1:+:301385456:11 +ACTGGTGTAAATTGTAAAATCCTTGAACCGATAATCAGTGCATTTCCTCTGTATTGGACATGCTTCCTGGATCCAAAGTCTTTGGTGACCGAAAGTAAAAAGAACGCAAAGACTGAAAGCAAAATCTTCTAATAAAATAGGAATTTTGAAGTTTAATATGTAGTCCTATTATTTTAGAAATCGAGTGCCCAGGAAAAAAG chm1:+:301385454:11 +ACTGGTGTAAATTGTAAAATCCTTGAACCGATAATCAGTGCATTTCCTCTGTATTGGACATGCTTCCTGGATCCAAAGTCTTTGGTGACCGAAAGTAAAAAGAACGCAAAGACTGAAAGCAAAATCTTCTAATAAAATAGGAATTTTGAAGTTTAATATGTAGTCCTATTATTTTAGAAATCGAGTGCCCAGGAAAAAAG chm1:+:301385453:11 +GCTGTTAGAAATAGAAATTTAAATCAGGTATGGTGGTATGTGCGGGTAGTCTCAGCTAACTTCGGAAGCTGAGGTGAGAGGATTGCTTGAGGCCAGGAGTCAAGGCTGCCCGTTGAGCTATGATCACACCACTGTATGCCAGGCCTGGGCGACAGAGTAAGATCTCATCTTCTTAACAGTAACAGATCAACTTAGAGGAA chm1:+:183798367:-1 chm1:+:525295420:-1 chm1:+:549548082:-1 chm1:+:852071425:-1 chm1:+:898873785:-1 chm1:+:1019244393:-1 chm1:+:1031431082:-1 chm1:+:1075598383:-1 chm1:+:1171128866:-1 chm1:+:1184324533:-1 chm1:+:1314979286:-1 chm1:+:1334365330:-1 chm1:+:1415113813:-1 chm1:+:1446300386:-1 chm1:+:1480438583:-1 chm1:+:1726493379:-1 chm1:+:1892606665:-1 chm1:+:1975979861:-1 chm1:+:2158322666:-1 chm1:+:2167039665:-1 chm1:+:2256221010:-1 chm1:+:2434630772:-1 chm1:+:2534020548:-1 chm1:+:2562383461:-1 chm1:+:2665971062:-1 chm1:+:2720629323:-1 chm1:+:2749871842:-1 chm1:+:3057633544:-1 +GCTGTTAGAAATAGAAATTTAAATCAGGTATGGTGGTATGTGCGGGTAGTCTCAGCTAACTTCGGAAGCTGAGGTGAGAGGATTGCTTGAGGCCAGGAGTCAAGGCTGCCCGTTGAGCTATGATCACACCACTGTATGCCAGGCCTGGGCGACAGAGTAAGATCTCATCTTCTTAACAGTAACAGATCAACTTAGAGGAA chm1:+:12216731:-1 chm1:+:12286975:-1 chm1:+:26328568:-1 chm1:+:149244702:-1 chm1:+:416209421:-1 chm1:+:452504660:-1 chm1:+:494134278:-1 chm1:+:615188219:-1 chm1:+:638300746:-1 chm1:+:673376258:-1 chm1:+:693813421:-1 chm1:+:814766845:-1 chm1:+:1013971795:-1 chm1:+:1058273452:-1 chm1:+:1076247388:-1 chm1:+:1202462202:-1 chm1:+:1235903529:-1 chm1:+:1306800753:-1 chm1:+:1307665047:-1 chm1:+:1366370461:-1 chm1:+:1461090984:-1 chm1:+:1560966664:-1 chm1:+:1610637209:-1 chm1:+:1612768202:-1 chm1:+:1625705355:-1 chm1:+:1633631749:-1 chm1:+:1673094084:-1 chm1:+:1694892311:-1 chm1:+:1705254597:-1 chm1:+:1707224658:-1 chm1:+:1750885560:-1 chm1:+:1784833098:-1 chm1:+:1928582360:-1 chm1:+:2016637623:-1 chm1:+:2381156842:-1 chm1:+:2391286142:-1 chm1:+:2391907066:-1 chm1:+:2467200129:-1 chm1:+:2468426602:-1 chm1:+:2528063629:-1 chm1:+:2543864476:-1 chm1:+:2555149401:-1 chm1:+:2557085470:-1 chm1:+:2564419172:-1 chm1:+:2586409382:-1 chm1:+:2668585532:-1 chm1:+:2676153259:-1 chm1:+:2708351861:-1 chm1:+:2709446118:-1 chm1:+:2711211123:-1 chm1:+:2736288818:-1 chm1:+:2744634721:-1 chm1:+:2763221589:-1 chm1:+:2800689034:-1 chm1:+:2802302412:-1 chm1:+:2806122703:-1 chm1:+:2815060490:-1 chm1:+:2820330737:-1 chm1:+:2913898198:-1 chm1:+:2927705734:-1 chm1:+:2930689330:-1 chm1:+:3016970395:-1 +GCTGTTAGAAATAGAAATTTAAATCAGGTATGGTGGTATGTGCGGGTAGTCTCAGCTAACTTCGGAAGCTGAGGTGAGAGGATTGCTTGAGGCCAGGAGTCAAGGCTGCCCGTTGAGCTATGATCACACCACTGTATGCCAGGCCTGGGCGACAGAGTAAGATCTCATCTTCTTAACAGTAACAGATCAACTTAGAGGAA chm1:+:1550733365:-1 chm1:+:2343240144:-1 +GCTGTTAGAAATAGAAATTTAAATCAGGTATGGTGGTATGTGCGGGTAGTCTCAGCTAACTTCGGAAGCTGAGGTGAGAGGATTGCTTGAGGCCAGGAGTCAAGGCTGCCCGTTGAGCTATGATCACACCACTGTATGCCAGGCCTGGGCGACAGAGTAAGATCTCATCTTCTTAACAGTAACAGATCAACTTAGAGGAA chm1:+:22242334:-1 chm1:+:25101352:-1 chm1:+:39673595:-1 chm1:+:45519739:-1 chm1:+:154896716:-1 chm1:+:201828877:-1 chm1:+:210449517:-1 chm1:+:226201016:-1 chm1:+:281786356:-1 chm1:+:284466295:-1 chm1:+:292292398:-1 chm1:+:293772053:-1 chm1:+:302988941:-1 chm1:+:311109939:-1 chm1:+:311541593:-1 chm1:+:319518377:-1 chm1:+:423346135:-1 chm1:+:443959413:-1 chm1:+:452636701:-1 chm1:+:463544227:-1 chm1:+:476898127:-1 chm1:+:532625012:-1 chm1:+:556751184:-1 chm1:+:599449116:-1 chm1:+:612485514:-1 chm1:+:641787194:-1 chm1:+:762046989:-1 chm1:+:872145380:-1 chm1:+:965104764:-1 chm1:+:979523503:-1 chm1:+:1078658178:-1 chm1:+:1106717734:-1 chm1:+:1109939971:-1 chm1:+:1112937673:-1 chm1:+:1128926094:-1 chm1:+:1158967550:-1 chm1:+:1197597883:-1 chm1:+:1236043372:-1 chm1:+:1300901891:-1 chm1:+:1302481438:-1 chm1:+:1322026053:-1 chm1:+:1328828196:-1 chm1:+:1338577687:-1 chm1:+:1344425698:-1 chm1:+:1367645960:-1 chm1:+:1423387940:-1 chm1:+:1447702385:-1 chm1:+:1494108361:-1 chm1:+:1500456913:-1 chm1:+:1518634599:-1 chm1:+:1629982070:-1 chm1:+:1631265987:-1 chm1:+:1635351859:-1 chm1:+:1638685881:-1 chm1:+:1639955003:-1 chm1:+:1681001456:-1 chm1:+:1692232140:-1 chm1:+:1709910731:-1 chm1:+:1712667995:-1 chm1:+:1759991329:-1 chm1:+:1762565330:-1 chm1:+:1769679620:-1 chm1:+:1796819205:-1 chm1:+:1823958239:-1 chm1:+:1883899079:-1 chm1:+:1893163855:-1 chm1:+:1893985312:-1 chm1:+:1917820792:-1 chm1:+:1938894956:-1 chm1:+:1941270544:-1 chm1:+:1983477615:-1 chm1:+:2001613340:-1 chm1:+:2033092157:-1 chm1:+:2060430600:-1 chm1:+:2252040969:-1 chm1:+:2335161448:-1 chm1:+:2358233696:-1 chm1:+:2359143918:-1 chm1:+:2360269541:-1 chm1:+:2416610645:-1 chm1:+:2425499546:-1 chm1:+:2426478396:-1 chm1:+:2429746147:-1 chm1:+:2431563363:-1 chm1:+:2432379488:-1 chm1:+:2435100806:-1 chm1:+:2438421233:-1 chm1:+:2463660754:-1 chm1:+:2496834102:-1 chm1:+:2497596777:-1 chm1:+:2529190313:-1 chm1:+:2535849102:-1 chm1:+:2536161355:-1 chm1:+:2544405919:-1 chm1:+:2585806674:-1 chm1:+:2677090825:-1 chm1:+:2692878643:-1 chm1:+:2702674128:-1 chm1:+:2702852157:-1 chm1:+:2702960155:-1 chm1:+:2703120236:-1 chm1:+:2703203355:-1 chm1:+:2711647619:-1 chm1:+:2723599145:-1 chm1:+:2736962055:-1 chm1:+:2750741755:-1 chm1:+:2755784135:-1 chm1:+:2826856335:-1 chm1:+:2827097442:-1 chm1:+:2853956052:-1 chm1:+:2859583055:-1 chm1:+:2921632809:-1 chm1:+:2944967177:-1 chm1:+:2966995994:-1 chm1:+:2970739400:-1 chm1:+:3040199937:-1 +GCTGTTAGAAATAGAAATTTAAATCAGGTATGGTGGTATGTGCGGGTAGTCTCAGCTAACTTCGGAAGCTGAGGTGAGAGGATTGCTTGAGGCCAGGAGTCAAGGCTGCCCGTTGAGCTATGATCACACCACTGTATGCCAGGCCTGGGCGACAGAGTAAGATCTCATCTTCTTAACAGTAACAGATCAACTTAGAGGAA chm1:+:349906432:-1 chm1:+:354930140:-1 chm1:+:402246483:-1 chm1:+:936635708:-1 chm1:+:1075417366:-1 chm1:+:1752726263:-1 chm1:+:1832803735:-1 chm1:+:2046643481:-1 chm1:+:2373767830:-1 chm1:+:2568363783:-1 chm1:+:2593203011:-1 chm1:+:2627662141:-1 chm1:+:2678614722:-1 chm1:+:2751036091:-1 +GCTGTTAGAAATAGAAATTTAAATCAGGTATGGTGGTATGTGCGGGTAGTCTCAGCTAACTTCGGAAGCTGAGGTGAGAGGATTGCTTGAGGCCAGGAGTCAAGGCTGCCCGTTGAGCTATGATCACACCACTGTATGCCAGGCCTGGGCGACAGAGTAAGATCTCATCTTCTTAACAGTAACAGATCAACTTAGAGGAA chm1:+:284605949:-1 chm1:+:1291318165:-1 chm1:+:1922332574:-1 chm1:+:2519677216:-1 +TTCCTCTAAGTTGATCTGTTACTGTTAAGAAGATGAGATCTTACTCTGTCGCCCAGGCCTGGCATACAGTGGTGTGATCATAGCTCAACGGGCAGCCTTGACTCCTGGCCTCAAGCAATCCTCTCACCTCAGCTTCCGAAGTTAGCTGAGACTACCCGCACATACCACCATACCTGATTTAAATTTCTATTTCTAACAGC chm1:+:310433035:-1 chm1:+:958605066:-1 chm1:+:1373984299:-1 chm1:+:1688408234:-1 chm1:+:2534961541:-1 chm1:+:2557818042:-1 chm1:+:2695994774:-1 chm1:+:2739878526:10 +TTCCTCTAAGTTGATCTGTTACTGTTAAGAAGATGAGATCTTACTCTGTCGCCCAGGCCTGGCATACAGTGGTGTGATCATAGCTCAACGGGCAGCCTTGACTCCTGGCCTCAAGCAATCCTCTCACCTCAGCTTCCGAAGTTAGCTGAGACTACCCGCACATACCACCATACCTGATTTAAATTTCTATTTCTAACAGC chm1:+:2739878524:10 +TTCCTCTAAGTTGATCTGTTACTGTTAAGAAGATGAGATCTTACTCTGTCGCCCAGGCCTGGCATACAGTGGTGTGATCATAGCTCAACGGGCAGCCTTGACTCCTGGCCTCAAGCAATCCTCTCACCTCAGCTTCCGAAGTTAGCTGAGACTACCCGCACATACCACCATACCTGATTTAAATTTCTATTTCTAACAGC chm1:+:2739878523:10 +TTCCTCTAAGTTGATCTGTTACTGTTAAGAAGATGAGATCTTACTCTGTCGCCCAGGCCTGGCATACAGTGGTGTGATCATAGCTCAACGGGCAGCCTTGACTCCTGGCCTCAAGCAATCCTCTCACCTCAGCTTCCGAAGTTAGCTGAGACTACCCGCACATACCACCATACCTGATTTAAATTTCTATTTCTAACAGC chm1:+:19988496:-1 chm1:+:233792446:-1 chm1:+:277160374:-1 chm1:+:524318481:-1 chm1:+:621945554:-1 chm1:+:684794473:-1 chm1:+:860819041:-1 chm1:+:1018876019:-1 chm1:+:1143920476:-1 chm1:+:1210967993:-1 chm1:+:1640625569:-1 chm1:+:1649766295:-1 chm1:+:2469469795:-1 chm1:+:2627615748:-1 chm1:+:2627771248:-1 chm1:+:2756462692:-1 chm1:+:2757712377:-1 chm1:+:2884614249:-1 chm1:+:2887117505:-1 +AATTCACCAAAAGAGATGTCTTTTAAAGGTGGGGTGAACACAACTTAAATATTATTTTCCAAGCCAACTCGGATACCATCCCATGGAGTCTAAAAAGACCAACAAAAATGGCATAAAGGATTAATGCCTGGTTTTCAAAATGAAATGAAGTACATTGTTTTTAAAGACTCAATGTAATAAAATGCCTCTGGGACCCTTAG chm1:+:519212243:8 chm1:+:1139284923:-1 +AATTCACCAAAAGAGATGTCTTTTAAAGGTGGGGTGAACACAACTTAAATATTATTTTCCAAGCCAACTCGGATACCATCCCATGGAGTCTAAAAAGACCAACAAAAATGGCATAAAGGATTAATGCCTGGTTTTCAAAATGAAATGAAGTACATTGTTTTTAAAGACTCAATGTAATAAAATGCCTCTGGGACCCTTAG chm1:+:519212244:8 +AATTCACCAAAAGAGATGTCTTTTAAAGGTGGGGTGAACACAACTTAAATATTATTTTCCAAGCCAACTCGGATACCATCCCATGGAGTCTAAAAAGACCAACAAAAATGGCATAAAGGATTAATGCCTGGTTTTCAAAATGAAATGAAGTACATTGTTTTTAAAGACTCAATGTAATAAAATGCCTCTGGGACCCTTAG chm1:+:519212247:8 +CTAAGGGTCCCAGAGGCATTTTATTACATTGAGTCTTTAAAAACAATGTACTTCATTTCATTTTGAAAACCAGGCATTAATCCTTTATGCCATTTTTGTTGGTCTTTTTAGACTCCATGGGATGGTATCCGAGTTGGCTTGGAAAATAATATTTAAGTTGTGTTCACCCCACCTTTAAAAGACATCTCTTTTGGTGAATT chm1:+:448504919:-1 +TAGTTTGAAATCTTGTACCTTAATTTCTTTTCTTTACATTTTTATTTACTTTAAACCTTATCTTTGTTTTTCTGCATCTTTCTCTTCTTGTTCCGAGTAATCCTAGCCCTGATGCCAGTAATATGAGATGCCACTTGGGGCTGTTTTGTTACCTTCTATCATCTCATTTAATAGAATCACTGTGAGAATAAAATGTGTTA chm1:+:641379216:-1 chm1:+:972634830:-1 chm1:+:1500488876:8 chm1:+:2897052504:-1 chm1:+:3027490301:-1 +TAGTTTGAAATCTTGTACCTTAATTTCTTTTCTTTACATTTTTATTTACTTTAAACCTTATCTTTGTTTTTCTGCATCTTTCTCTTCTTGTTCCGAGTAATCCTAGCCCTGATGCCAGTAATATGAGATGCCACTTGGGGCTGTTTTGTTACCTTCTATCATCTCATTTAATAGAATCACTGTGAGAATAAAATGTGTTA chm1:+:1500488875:8 +TAGTTTGAAATCTTGTACCTTAATTTCTTTTCTTTACATTTTTATTTACTTTAAACCTTATCTTTGTTTTTCTGCATCTTTCTCTTCTTGTTCCGAGTAATCCTAGCCCTGATGCCAGTAATATGAGATGCCACTTGGGGCTGTTTTGTTACCTTCTATCATCTCATTTAATAGAATCACTGTGAGAATAAAATGTGTTA chm1:+:1469649347:-1 +GAGTCTTTTTTTTTTTTTTTGAGACAGAGTCCTCCCTCTTGTTGCTCAGGCTGGGGGTGCAGTGTGCGATCTCAGCTCACTACAACCTCCACCTTCCGGGTTCTAAGTGACTTCTCCTGCCTCAGCCTCCTAGAGTAGCTGAAATTACAGGACACCTGCCACCACAACTGGCTATATTTTTTTTGTATTTTTAGTAGAGA chm1:+:113012192:40 chm1:+:771991221:-1 +GAGTCTTTTTTTTTTTTTTTGAGACAGAGTCCTCCCTCTTGTTGCTCAGGCTGGGGGTGCAGTGTGCGATCTCAGCTCACTACAACCTCCACCTTCCGGGTTCTAAGTGACTTCTCCTGCCTCAGCCTCCTAGAGTAGCTGAAATTACAGGACACCTGCCACCACAACTGGCTATATTTTTTTTGTATTTTTAGTAGAGA chm1:+:32494056:-1 chm1:+:57728741:-1 chm1:+:65707129:40 chm1:+:200617104:-1 chm1:+:303269622:-1 chm1:+:452501977:38 chm1:+:477592895:39 chm1:+:502089606:35 chm1:+:621379794:-1 chm1:+:692972287:-1 chm1:+:697715038:38 chm1:+:706624242:-1 chm1:+:716035695:-1 chm1:+:874016540:39 chm1:+:877618962:-1 chm1:+:937284454:-1 chm1:+:1022684166:40 chm1:+:1088042900:-1 chm1:+:1109665485:-1 chm1:+:1233985252:-1 chm1:+:1240213665:-1 chm1:+:1288114886:-1 chm1:+:1300088300:-1 chm1:+:1372559527:38 chm1:+:1407226349:-1 chm1:+:1416329999:-1 chm1:+:1469196151:-1 chm1:+:1480895334:38 chm1:+:1485564596:37 chm1:+:1541054510:-1 chm1:+:1663856898:-1 chm1:+:1665960537:40 chm1:+:1676550840:37 chm1:+:1700649586:-1 chm1:+:1709363950:-1 chm1:+:1748741913:-1 chm1:+:1751563018:-1 chm1:+:1751845766:-1 chm1:+:1756155490:36 chm1:+:1788309427:-1 chm1:+:1801338052:-1 chm1:+:1808771709:40 chm1:+:1814734499:-1 chm1:+:1878547227:-1 chm1:+:1909021409:-1 chm1:+:1930601072:-1 chm1:+:1954029021:39 chm1:+:2016480864:36 chm1:+:2055517542:-1 chm1:+:2070850496:36 chm1:+:2183727674:-1 chm1:+:2221676030:-1 chm1:+:2223975712:37 chm1:+:2234379859:37 chm1:+:2236840186:-1 chm1:+:2240514345:39 chm1:+:2240526348:-1 chm1:+:2330357791:37 chm1:+:2404525231:-1 chm1:+:2430125789:-1 chm1:+:2514452922:-1 chm1:+:2541566362:32 chm1:+:2568162836:-1 chm1:+:2573362163:36 chm1:+:2669368452:36 chm1:+:2678504511:37 chm1:+:2700660425:39 chm1:+:2717414556:35 chm1:+:2723176993:-1 chm1:+:2736794494:-1 chm1:+:2738567717:-1 chm1:+:2753035151:-1 chm1:+:2768054233:34 chm1:+:2850959528:-1 chm1:+:2879499934:-1 +GAGTCTTTTTTTTTTTTTTTGAGACAGAGTCCTCCCTCTTGTTGCTCAGGCTGGGGGTGCAGTGTGCGATCTCAGCTCACTACAACCTCCACCTTCCGGGTTCTAAGTGACTTCTCCTGCCTCAGCCTCCTAGAGTAGCTGAAATTACAGGACACCTGCCACCACAACTGGCTATATTTTTTTTGTATTTTTAGTAGAGA chm1:+:8567422:-1 chm1:+:19823454:-1 chm1:+:26577388:-1 chm1:+:70673971:-1 chm1:+:146864071:-1 chm1:+:205141039:-1 chm1:+:206851049:-1 chm1:+:303319150:-1 chm1:+:303671752:-1 chm1:+:529856709:-1 chm1:+:540168981:-1 chm1:+:687114470:-1 chm1:+:696621065:-1 chm1:+:767147615:-1 chm1:+:795442366:-1 chm1:+:796402253:-1 chm1:+:797353345:-1 chm1:+:871616988:-1 chm1:+:1010192233:-1 chm1:+:1019801544:-1 chm1:+:1020294184:-1 chm1:+:1035551477:36 chm1:+:1129284175:-1 chm1:+:1197264552:-1 chm1:+:1213858718:-1 chm1:+:1216495433:-1 chm1:+:1234902035:-1 chm1:+:1238410439:-1 chm1:+:1260017034:-1 chm1:+:1286745409:-1 chm1:+:1369008941:-1 chm1:+:1409614101:-1 chm1:+:1612929901:-1 chm1:+:1670717158:40 chm1:+:1694665057:-1 chm1:+:1825440503:-1 chm1:+:1864024977:-1 chm1:+:1959022966:-1 chm1:+:2004619406:-1 chm1:+:2046452825:34 chm1:+:2063496435:-1 chm1:+:2066134707:-1 chm1:+:2074903948:-1 chm1:+:2076079293:-1 chm1:+:2082568251:-1 chm1:+:2133498953:-1 chm1:+:2185788594:-1 chm1:+:2231936470:-1 chm1:+:2305833533:-1 chm1:+:2331863780:-1 chm1:+:2349927520:39 chm1:+:2350094202:40 chm1:+:2352167678:38 chm1:+:2383857291:-1 chm1:+:2417795436:-1 chm1:+:2435972142:-1 chm1:+:2456678912:-1 chm1:+:2467088690:-1 chm1:+:2508173376:-1 chm1:+:2527722140:-1 chm1:+:2538473245:-1 chm1:+:2547305725:-1 chm1:+:2594235282:-1 chm1:+:2646786678:-1 chm1:+:2681141677:-1 chm1:+:2692237645:39 chm1:+:2700779648:-1 chm1:+:2821432683:-1 chm1:+:2922290865:35 chm1:+:2925444556:-1 chm1:+:2998851476:35 chm1:+:3098283528:-1 +GAGTCTTTTTTTTTTTTTTTGAGACAGAGTCCTCCCTCTTGTTGCTCAGGCTGGGGGTGCAGTGTGCGATCTCAGCTCACTACAACCTCCACCTTCCGGGTTCTAAGTGACTTCTCCTGCCTCAGCCTCCTAGAGTAGCTGAAATTACAGGACACCTGCCACCACAACTGGCTATATTTTTTTTGTATTTTTAGTAGAGA chm1:+:5057278:-1 chm1:+:115504557:-1 chm1:+:236471838:-1 chm1:+:279758271:-1 chm1:+:381137652:-1 chm1:+:462732037:-1 chm1:+:486414361:-1 chm1:+:534533811:-1 chm1:+:574709995:-1 chm1:+:701799989:-1 chm1:+:751464673:-1 chm1:+:818283265:-1 chm1:+:844380526:-1 chm1:+:869860570:-1 chm1:+:916247816:40 chm1:+:986235520:-1 chm1:+:1106834363:-1 chm1:+:1237895426:39 chm1:+:1298011363:-1 chm1:+:1316452635:-1 chm1:+:1339023007:-1 chm1:+:1382605256:-1 chm1:+:1460646832:-1 chm1:+:1468600032:-1 chm1:+:1551662427:-1 chm1:+:1617309064:36 chm1:+:1693775939:40 chm1:+:1701958847:37 chm1:+:1834350444:40 chm1:+:2015146679:-1 chm1:+:2034072276:-1 chm1:+:2066211954:-1 chm1:+:2113730787:-1 chm1:+:2138796477:-1 chm1:+:2304228314:-1 chm1:+:2360246787:-1 chm1:+:2467681206:-1 chm1:+:2505271630:-1 chm1:+:2507675334:-1 chm1:+:2631608697:-1 chm1:+:2669903006:-1 chm1:+:2712670259:-1 chm1:+:2720840030:-1 chm1:+:2861828457:-1 chm1:+:2870814245:-1 chm1:+:2934496705:39 +GAGTCTTTTTTTTTTTTTTTGAGACAGAGTCCTCCCTCTTGTTGCTCAGGCTGGGGGTGCAGTGTGCGATCTCAGCTCACTACAACCTCCACCTTCCGGGTTCTAAGTGACTTCTCCTGCCTCAGCCTCCTAGAGTAGCTGAAATTACAGGACACCTGCCACCACAACTGGCTATATTTTTTTTGTATTTTTAGTAGAGA chm1:+:3724792:-1 chm1:+:24737884:-1 chm1:+:46529136:-1 chm1:+:171719824:-1 chm1:+:205047576:37 chm1:+:348047228:-1 chm1:+:464083490:-1 chm1:+:464083502:-1 chm1:+:541038595:35 chm1:+:614425411:-1 chm1:+:616406156:-1 chm1:+:629053509:36 chm1:+:634259349:39 chm1:+:667664810:-1 chm1:+:731138650:-1 chm1:+:796730915:39 chm1:+:803617397:-1 chm1:+:804073486:-1 chm1:+:859827798:-1 chm1:+:884413670:-1 chm1:+:1086862472:-1 chm1:+:1109071672:36 chm1:+:1237355226:-1 chm1:+:1318595821:-1 chm1:+:1423293864:-1 chm1:+:1473081528:39 chm1:+:1500512268:-1 chm1:+:1519355949:-1 chm1:+:1577961680:-1 chm1:+:1584322253:40 chm1:+:1639812729:-1 chm1:+:1677784580:-1 chm1:+:1677784878:-1 chm1:+:1679706842:35 chm1:+:1715849283:39 chm1:+:1749545594:-1 chm1:+:1881184922:-1 chm1:+:1979757326:-1 chm1:+:2136967758:-1 chm1:+:2301957470:-1 chm1:+:2477452830:40 chm1:+:2557729260:-1 chm1:+:2566634369:-1 chm1:+:2573484848:37 chm1:+:2696713343:-1 chm1:+:2736795630:38 chm1:+:2780972656:-1 chm1:+:2880895524:-1 +GAGTCTTTTTTTTTTTTTTTGAGACAGAGTCCTCCCTCTTGTTGCTCAGGCTGGGGGTGCAGTGTGCGATCTCAGCTCACTACAACCTCCACCTTCCGGGTTCTAAGTGACTTCTCCTGCCTCAGCCTCCTAGAGTAGCTGAAATTACAGGACACCTGCCACCACAACTGGCTATATTTTTTTTGTATTTTTAGTAGAGA chm1:+:281693657:-1 chm1:+:398428872:-1 chm1:+:436571996:-1 chm1:+:486313180:-1 chm1:+:662624925:-1 chm1:+:700504505:-1 chm1:+:808174498:-1 chm1:+:842832342:-1 chm1:+:958706481:-1 chm1:+:1022816162:-1 chm1:+:1538563966:-1 chm1:+:1971517002:-1 chm1:+:2076484724:-1 chm1:+:2138278899:-1 chm1:+:2143403271:-1 chm1:+:2358392490:-1 chm1:+:2382639861:-1 chm1:+:2458487255:-1 chm1:+:2542684602:39 chm1:+:2577039914:-1 chm1:+:2600186631:-1 chm1:+:2648917100:-1 chm1:+:2701331374:-1 chm1:+:2743894682:-1 chm1:+:2754280375:-1 +GAGTCTTTTTTTTTTTTTTTGAGACAGAGTCCTCCCTCTTGTTGCTCAGGCTGGGGGTGCAGTGTGCGATCTCAGCTCACTACAACCTCCACCTTCCGGGTTCTAAGTGACTTCTCCTGCCTCAGCCTCCTAGAGTAGCTGAAATTACAGGACACCTGCCACCACAACTGGCTATATTTTTTTTGTATTTTTAGTAGAGA chm1:+:264682676:-1 chm1:+:500988072:-1 chm1:+:503545296:-1 chm1:+:1267556668:-1 chm1:+:1623432493:39 chm1:+:1677485655:-1 chm1:+:1762363756:-1 chm1:+:1999168108:-1 chm1:+:2304203770:-1 chm1:+:2417648890:-1 chm1:+:2479719858:-1 chm1:+:2600135731:37 chm1:+:2763117673:37 +TCTCTACTAAAAATACAAAAAAAATATAGCCAGTTGTGGTGGCAGGTGTCCTGTAATTTCAGCTACTCTAGGAGGCTGAGGCAGGAGAAGTCACTTAGAACCCGGAAGGTGGAGGTTGTAGTGAGCTGAGATCGCACACTGCACCCCCAGCCTGAGCAACAAGAGGGAGGACTCTGTCTCAAAAAAAAAAAAAAAGACTC chm1:+:421991692:-1 chm1:+:689532900:8 chm1:+:893424860:-1 chm1:+:902652975:38 chm1:+:993176949:-1 chm1:+:1054334706:34 chm1:+:1792893783:36 chm1:+:2605160666:-1 chm1:+:2980535770:-1 +TCTCTACTAAAAATACAAAAAAAATATAGCCAGTTGTGGTGGCAGGTGTCCTGTAATTTCAGCTACTCTAGGAGGCTGAGGCAGGAGAAGTCACTTAGAACCCGGAAGGTGGAGGTTGTAGTGAGCTGAGATCGCACACTGCACCCCCAGCCTGAGCAACAAGAGGGAGGACTCTGTCTCAAAAAAAAAAAAAAAGACTC chm1:+:550302684:-1 +TCTCTACTAAAAATACAAAAAAAATATAGCCAGTTGTGGTGGCAGGTGTCCTGTAATTTCAGCTACTCTAGGAGGCTGAGGCAGGAGAAGTCACTTAGAACCCGGAAGGTGGAGGTTGTAGTGAGCTGAGATCGCACACTGCACCCCCAGCCTGAGCAACAAGAGGGAGGACTCTGTCTCAAAAAAAAAAAAAAAGACTC chm1:+:280139514:-1 +TCTCTACTAAAAATACAAAAAAAATATAGCCAGTTGTGGTGGCAGGTGTCCTGTAATTTCAGCTACTCTAGGAGGCTGAGGCAGGAGAAGTCACTTAGAACCCGGAAGGTGGAGGTTGTAGTGAGCTGAGATCGCACACTGCACCCCCAGCCTGAGCAACAAGAGGGAGGACTCTGTCTCAAAAAAAAAAAAAAAGACTC chm1:+:87242458:-1 chm1:+:150247098:40 chm1:+:689532895:8 chm1:+:1120323775:-1 chm1:+:1540598929:-1 chm1:+:1649328796:38 chm1:+:1754810410:36 chm1:+:1768308021:-1 chm1:+:2239188791:-1 chm1:+:2264172346:38 chm1:+:2387940522:37 chm1:+:2414663609:35 chm1:+:2564383929:-1 chm1:+:2602198904:39 chm1:+:2640365500:-1 chm1:+:2662455630:38 chm1:+:2669799121:38 chm1:+:2722434013:-1 +ACTCACAAGAAGCCATAGAAAATTTTAAACTAAATAACTGGCAACAAATTTATTCATAAGACTCTTCTCCCAAGTGGGTAATCTCCTGTGACTTTCACATCAGGAATGTTTATGCAGGGAGTTTCCTACCAATGTAACCTCAGACACTCAGTATTCCCTCTGGTAAACACAAAGAATCAGGCAACTTTTAACACTATAGT chm1:+:533045525:-1 chm1:+:813062097:8 chm1:+:1208242507:-1 chm1:+:1443487206:-1 +ACTCACAAGAAGCCATAGAAAATTTTAAACTAAATAACTGGCAACAAATTTATTCATAAGACTCTTCTCCCAAGTGGGTAATCTCCTGTGACTTTCACATCAGGAATGTTTATGCAGGGAGTTTCCTACCAATGTAACCTCAGACACTCAGTATTCCCTCTGGTAAACACAAAGAATCAGGCAACTTTTAACACTATAGT chm1:+:813062098:8 +ACTCACAAGAAGCCATAGAAAATTTTAAACTAAATAACTGGCAACAAATTTATTCATAAGACTCTTCTCCCAAGTGGGTAATCTCCTGTGACTTTCACATCAGGAATGTTTATGCAGGGAGTTTCCTACCAATGTAACCTCAGACACTCAGTATTCCCTCTGGTAAACACAAAGAATCAGGCAACTTTTAACACTATAGT chm1:+:813062099:8 +ACTCACAAGAAGCCATAGAAAATTTTAAACTAAATAACTGGCAACAAATTTATTCATAAGACTCTTCTCCCAAGTGGGTAATCTCCTGTGACTTTCACATCAGGAATGTTTATGCAGGGAGTTTCCTACCAATGTAACCTCAGACACTCAGTATTCCCTCTGGTAAACACAAAGAATCAGGCAACTTTTAACACTATAGT chm1:+:813062100:8 +ACTCACAAGAAGCCATAGAAAATTTTAAACTAAATAACTGGCAACAAATTTATTCATAAGACTCTTCTCCCAAGTGGGTAATCTCCTGTGACTTTCACATCAGGAATGTTTATGCAGGGAGTTTCCTACCAATGTAACCTCAGACACTCAGTATTCCCTCTGGTAAACACAAAGAATCAGGCAACTTTTAACACTATAGT chm1:+:1253682694:-1 +ACTATAGTGTTAAAAGTTGCCTGATTCTTTGTGTTTACCAGAGGGAATACTGAGTGTCTGAGGTTACATTGGTAGGAAACTCCCTGCATAAACATTCCTGATGTGAAAGTCACAGGAGATTACCCACTTGGGAGAAGAGTCTTATGAATAAATTTGTTGCCAGTTATTTAGTTTAAAATTTTCTATGGCTTCTTGTGAGT chm1:+:348574910:-1 +ACTATAGTGTTAAAAGTTGCCTGATTCTTTGTGTTTACCAGAGGGAATACTGAGTGTCTGAGGTTACATTGGTAGGAAACTCCCTGCATAAACATTCCTGATGTGAAAGTCACAGGAGATTACCCACTTGGGAGAAGAGTCTTATGAATAAATTTGTTGCCAGTTATTTAGTTTAAAATTTTCTATGGCTTCTTGTGAGT chm1:+:227518514:-1 +TTACAAGCTTTACAAGCTTGGTGCTGGTGCTTCTTCATCTTATCAGAAGATGATGACAGAAGTTTTCAGATTCATAGGTCTTTCCTCAAACTCTCCTAAATGATTCATTGAGTGAAGACCTGGAGGGCTGGCCTTCCATGAATCACACCCAACTGTATTACTTTTCAGGCAACCTATTCTTTATTCAGATACACGCTCTC chm1:+:1833218705:8 chm1:+:3063724089:-1 +TTACAAGCTTTACAAGCTTGGTGCTGGTGCTTCTTCATCTTATCAGAAGATGATGACAGAAGTTTTCAGATTCATAGGTCTTTCCTCAAACTCTCCTAAATGATTCATTGAGTGAAGACCTGGAGGGCTGGCCTTCCATGAATCACACCCAACTGTATTACTTTTCAGGCAACCTATTCTTTATTCAGATACACGCTCTC chm1:+:2808615179:-1 +TTACAAGCTTTACAAGCTTGGTGCTGGTGCTTCTTCATCTTATCAGAAGATGATGACAGAAGTTTTCAGATTCATAGGTCTTTCCTCAAACTCTCCTAAATGATTCATTGAGTGAAGACCTGGAGGGCTGGCCTTCCATGAATCACACCCAACTGTATTACTTTTCAGGCAACCTATTCTTTATTCAGATACACGCTCTC chm1:+:1833218706:8 +GAGAGCGTGTATCTGAATAAAGAATAGGTTGCCTGAAAAGTAATACAGTTGGGTGTGATTCATGGAAGGCCAGCCCTCCAGGTCTTCACTCAATGAATCATTTAGGAGAGTTTGAGGAAAGACCTATGAATCTGAAAACTTCTGTCATCATCTTCTGATAAGATGAAGAAGCACCAGCACCAAGCTTGTAAAGCTTGTAA chm1:+:735837697:-1 +CACTGGAAAGGGAATGTAAAGGGAATTCTAGGGGGATTGATAATGTTCTTTTTTAAAAATCTGGGTGCTCATTACAAGAGTATTGGTTTTCGTTGAAAATTCATTGAGTTATATACTTATGATACGTACATATCCTGTATACACATGTTGTACTTACAATAAAAAGTTTAAAAAAATACTCTGCCTACCCAAGATCTTCT chm1:+:877200661:-1 chm1:+:1110834037:-1 chm1:+:2048544217:-1 chm1:+:2636711433:7 +CACTGGAAAGGGAATGTAAAGGGAATTCTAGGGGGATTGATAATGTTCTTTTTTAAAAATCTGGGTGCTCATTACAAGAGTATTGGTTTTCGTTGAAAATTCATTGAGTTATATACTTATGATACGTACATATCCTGTATACACATGTTGTACTTACAATAAAAAGTTTAAAAAAATACTCTGCCTACCCAAGATCTTCT chm1:+:2636711430:7 +CACTGGAAAGGGAATGTAAAGGGAATTCTAGGGGGATTGATAATGTTCTTTTTTAAAAATCTGGGTGCTCATTACAAGAGTATTGGTTTTCGTTGAAAATTCATTGAGTTATATACTTATGATACGTACATATCCTGTATACACATGTTGTACTTACAATAAAAAGTTTAAAAAAATACTCTGCCTACCCAAGATCTTCT chm1:+:2636711429:7 +AGAAAAACATATGTTGCCCCAGGTGTCACTTGCCTTTTCTTTTGTGAGTCATTAGAATGAAAGGCCAAGTTCTTCTCAAGAGAAGATAGCAAGATCCACGGATATTAAGCCAAGCAAGAAGTAAATCATTGGAGTCAATTTCTTTCTGTTCTTAGGAGAAAAGTAGATAAGCACTGGCTAATTGGATGGCAACATATTTT chm1:+:1026278112:-1 chm1:+:1472100957:-1 +AGAAAAACATATGTTGCCCCAGGTGTCACTTGCCTTTTCTTTTGTGAGTCATTAGAATGAAAGGCCAAGTTCTTCTCAAGAGAAGATAGCAAGATCCACGGATATTAAGCCAAGCAAGAAGTAAATCATTGGAGTCAATTTCTTTCTGTTCTTAGGAGAAAAGTAGATAAGCACTGGCTAATTGGATGGCAACATATTTT chm1:+:275148545:-1 chm1:+:538521543:-1 chm1:+:836133903:8 chm1:+:1472398888:-1 chm1:+:1507675635:-1 chm1:+:1850423902:-1 chm1:+:2113988384:-1 +AGAAAAACATATGTTGCCCCAGGTGTCACTTGCCTTTTCTTTTGTGAGTCATTAGAATGAAAGGCCAAGTTCTTCTCAAGAGAAGATAGCAAGATCCACGGATATTAAGCCAAGCAAGAAGTAAATCATTGGAGTCAATTTCTTTCTGTTCTTAGGAGAAAAGTAGATAAGCACTGGCTAATTGGATGGCAACATATTTT chm1:+:836133901:8 +CCACTGCACTCCAGCCTGGGTGACTGTAGCAAGAACTCCATCTCAAAAAAACAAACAAAACAAAACAAAAAACTTTTGTTACTTAATTCCTCATTTTTAGTAAAAGCATCTGATTCCCACCTTTGGTTGTTCCCGGGCCCTTTGGAGCTTTAGGCCCTCCTAAGATTCAGCCTCCACAGAAGAGATATCTCCTGCCTTCT chm1:+:1056660578:-1 chm1:+:2660000166:-1 +CCACTGCACTCCAGCCTGGGTGACTGTAGCAAGAACTCCATCTCAAAAAAACAAACAAAACAAAACAAAAAACTTTTGTTACTTAATTCCTCATTTTTAGTAAAAGCATCTGATTCCCACCTTTGGTTGTTCCCGGGCCCTTTGGAGCTTTAGGCCCTCCTAAGATTCAGCCTCCACAGAAGAGATATCTCCTGCCTTCT chm1:+:1819695411:-1 +CCACTGCACTCCAGCCTGGGTGACTGTAGCAAGAACTCCATCTCAAAAAAACAAACAAAACAAAACAAAAAACTTTTGTTACTTAATTCCTCATTTTTAGTAAAAGCATCTGATTCCCACCTTTGGTTGTTCCCGGGCCCTTTGGAGCTTTAGGCCCTCCTAAGATTCAGCCTCCACAGAAGAGATATCTCCTGCCTTCT chm1:+:710308779:-1 chm1:+:846957898:-1 chm1:+:1299038972:-1 chm1:+:1413288275:-1 chm1:+:2118696017:-1 +CCACTGCACTCCAGCCTGGGTGACTGTAGCAAGAACTCCATCTCAAAAAAACAAACAAAACAAAACAAAAAACTTTTGTTACTTAATTCCTCATTTTTAGTAAAAGCATCTGATTCCCACCTTTGGTTGTTCCCGGGCCCTTTGGAGCTTTAGGCCCTCCTAAGATTCAGCCTCCACAGAAGAGATATCTCCTGCCTTCT chm1:+:34643952:-1 chm1:+:208770426:-1 chm1:+:222253818:-1 chm1:+:807502373:-1 chm1:+:1057695310:-1 chm1:+:1396648268:-1 chm1:+:1407103339:-1 chm1:+:1502225905:-1 chm1:+:1704011858:-1 chm1:+:1954605112:-1 chm1:+:2059696914:-1 chm1:+:2183598323:10 chm1:+:2517641106:-1 chm1:+:2542174762:-1 chm1:+:2864923314:-1 +CCACTGCACTCCAGCCTGGGTGACTGTAGCAAGAACTCCATCTCAAAAAAACAAACAAAACAAAACAAAAAACTTTTGTTACTTAATTCCTCATTTTTAGTAAAAGCATCTGATTCCCACCTTTGGTTGTTCCCGGGCCCTTTGGAGCTTTAGGCCCTCCTAAGATTCAGCCTCCACAGAAGAGATATCTCCTGCCTTCT chm1:+:2183598326:10 +AGAAGGCAGGAGATATCTCTTCTGTGGAGGCTGAATCTTAGGAGGGCCTAAAGCTCCAAAGGGCCCGGGAACAACCAAAGGTGGGAATCAGATGCTTTTACTAAAAATGAGGAATTAAGTAACAAAAGTTTTTTGTTTTGTTTTGTTTGTTTTTTTGAGATGGAGTTCTTGCTACAGTCACCCAGGCTGGAGTGCAGTGG chm1:+:147831579:-1 chm1:+:2574470649:-1 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+CGCATTGGCTCACACTTGTAATCCCAGCACTTGGGAGGCCAAGGCAAAGTGGGATCACTTGTGGCCAGGAGCTCGAGACCCAGTCCGTGGCCAACGTGGTGAAACCCCGTCTCTACTAAAATACGAAAATTAGCCTGGGTCGTTGGTGGCGCACATCTGTAGTCCCAATTACTGGGGAGGCTGAGGCACAAGAATCATTT chm1:+:65694761:-1 chm1:+:337958851:-1 chm1:+:512822608:-1 chm1:+:711486310:-1 chm1:+:731539406:-1 chm1:+:734185250:-1 chm1:+:970324266:-1 chm1:+:1002002130:-1 chm1:+:1201730316:-1 chm1:+:1214690102:-1 chm1:+:2184425326:-1 chm1:+:2190463437:-1 chm1:+:2220740409:-1 chm1:+:2353833798:-1 chm1:+:2410465532:-1 chm1:+:2415172847:-1 chm1:+:2432321765:-1 chm1:+:2651314432:-1 chm1:+:2797022024:-1 +CGCATTGGCTCACACTTGTAATCCCAGCACTTGGGAGGCCAAGGCAAAGTGGGATCACTTGTGGCCAGGAGCTCGAGACCCAGTCCGTGGCCAACGTGGTGAAACCCCGTCTCTACTAAAATACGAAAATTAGCCTGGGTCGTTGGTGGCGCACATCTGTAGTCCCAATTACTGGGGAGGCTGAGGCACAAGAATCATTT chm1:+:456963352:-1 chm1:+:501958698:-1 chm1:+:606492349:-1 chm1:+:643992840:-1 chm1:+:733483469:-1 chm1:+:850448965:-1 chm1:+:1136869599:40 chm1:+:1182062718:-1 chm1:+:1183780672:-1 chm1:+:1335819516:-1 chm1:+:1335918605:-1 chm1:+:1818376078:-1 chm1:+:2049119962:-1 chm1:+:2115727348:-1 chm1:+:2398069450:-1 chm1:+:2432838542:-1 chm1:+:2501414364:-1 chm1:+:2648304893:-1 +TGTGTGGACTCAGCTCATACAGTCCTCCAGAGCAGGCTGTGTACATCTCTTTTTACCGACTCTGGCCTTCTAGTGAACCTCACCTGGTAGTTGATATCAGCCATAGTGAAAAGTATTTACAGCATGGAAAATTGGCAAACTCTGTACTTACAGGTTTGGTGGAGTTTTTCTTCCTCCCACAAAGAGCCGAGTTGTTAAAC chm1:+:939572037:-1 chm1:+:958545617:-1 chm1:+:1945220931:-1 chm1:+:2230817773:-1 +TGTGTGGACTCAGCTCATACAGTCCTCCAGAGCAGGCTGTGTACATCTCTTTTTACCGACTCTGGCCTTCTAGTGAACCTCACCTGGTAGTTGATATCAGCCATAGTGAAAAGTATTTACAGCATGGAAAATTGGCAAACTCTGTACTTACAGGTTTGGTGGAGTTTTTCTTCCTCCCACAAAGAGCCGAGTTGTTAAAC chm1:+:478732188:-1 chm1:+:1131530852:-1 chm1:+:1268113826:-1 chm1:+:1958339033:-1 chm1:+:2618003657:-1 chm1:+:2908446438:-1 chm1:+:2912147570:-1 chm1:+:3001167907:-1 +TGTGTGGACTCAGCTCATACAGTCCTCCAGAGCAGGCTGTGTACATCTCTTTTTACCGACTCTGGCCTTCTAGTGAACCTCACCTGGTAGTTGATATCAGCCATAGTGAAAAGTATTTACAGCATGGAAAATTGGCAAACTCTGTACTTACAGGTTTGGTGGAGTTTTTCTTCCTCCCACAAAGAGCCGAGTTGTTAAAC chm1:+:279869371:-1 chm1:+:659190089:-1 chm1:+:2036010184:-1 chm1:+:2144096960:-1 chm1:+:2355663139:-1 +TGTGTGGACTCAGCTCATACAGTCCTCCAGAGCAGGCTGTGTACATCTCTTTTTACCGACTCTGGCCTTCTAGTGAACCTCACCTGGTAGTTGATATCAGCCATAGTGAAAAGTATTTACAGCATGGAAAATTGGCAAACTCTGTACTTACAGGTTTGGTGGAGTTTTTCTTCCTCCCACAAAGAGCCGAGTTGTTAAAC chm1:+:168822160:-1 chm1:+:533759049:-1 chm1:+:595800933:-1 chm1:+:1137446968:-1 chm1:+:1476141417:-1 chm1:+:2638369902:-1 +TGTGTGGACTCAGCTCATACAGTCCTCCAGAGCAGGCTGTGTACATCTCTTTTTACCGACTCTGGCCTTCTAGTGAACCTCACCTGGTAGTTGATATCAGCCATAGTGAAAAGTATTTACAGCATGGAAAATTGGCAAACTCTGTACTTACAGGTTTGGTGGAGTTTTTCTTCCTCCCACAAAGAGCCGAGTTGTTAAAC chm1:+:15996597:-1 chm1:+:154031183:-1 chm1:+:165906597:-1 chm1:+:168831460:-1 chm1:+:195404891:-1 chm1:+:440780213:-1 chm1:+:444321151:-1 chm1:+:707122465:-1 chm1:+:850175846:-1 chm1:+:1134515128:-1 chm1:+:1236854990:-1 chm1:+:1712743368:-1 chm1:+:2357391811:-1 chm1:+:2372099841:-1 chm1:+:2481656993:-1 chm1:+:3026312921:-1 +TGTGTGGACTCAGCTCATACAGTCCTCCAGAGCAGGCTGTGTACATCTCTTTTTACCGACTCTGGCCTTCTAGTGAACCTCACCTGGTAGTTGATATCAGCCATAGTGAAAAGTATTTACAGCATGGAAAATTGGCAAACTCTGTACTTACAGGTTTGGTGGAGTTTTTCTTCCTCCCACAAAGAGCCGAGTTGTTAAAC chm1:+:1439767774:-1 chm1:+:1989326635:-1 chm1:+:1989331608:-1 chm1:+:3101761236:-1 +GTTTAACAACTCGGCTCTTTGTGGGAGGAAGAAAAACTCCACCAAACCTGTAAGTACAGAGTTTGCCAATTTTCCATGCTGTAAATACTTTTCACTATGGCTGATATCAACTACCAGGTGAGGTTCACTAGAAGGCCAGAGTCGGTAAAAAGAGATGTACACAGCCTGCTCTGGAGGACTGTATGAGCTGAGTCCACACA chm1:+:531070777:-1 chm1:+:1387345619:-1 chm1:+:1439861056:-1 chm1:+:1439875823:-1 chm1:+:1439998353:-1 chm1:+:1440101456:-1 chm1:+:1440102560:-1 chm1:+:1440160873:-1 chm1:+:1440180884:-1 chm1:+:1440182262:-1 chm1:+:1440183980:-1 chm1:+:1440186152:-1 chm1:+:1440189198:-1 chm1:+:1440200971:-1 chm1:+:1440201487:-1 chm1:+:1440205262:-1 chm1:+:1440206801:-1 chm1:+:1440206983:-1 chm1:+:1440210988:-1 chm1:+:1440211330:-1 chm1:+:1440214446:-1 chm1:+:1440215132:-1 chm1:+:1440217018:-1 chm1:+:1440218216:-1 chm1:+:1440218385:-1 chm1:+:1985348851:-1 chm1:+:3056076058:-1 +GTTTAACAACTCGGCTCTTTGTGGGAGGAAGAAAAACTCCACCAAACCTGTAAGTACAGAGTTTGCCAATTTTCCATGCTGTAAATACTTTTCACTATGGCTGATATCAACTACCAGGTGAGGTTCACTAGAAGGCCAGAGTCGGTAAAAAGAGATGTACACAGCCTGCTCTGGAGGACTGTATGAGCTGAGTCCACACA chm1:+:170652354:-1 chm1:+:940787242:-1 chm1:+:2180865626:-1 chm1:+:2297753387:12 chm1:+:2460778009:-1 chm1:+:2573138110:-1 +AACCAACTCTTCATCAAAATTTCGTCCTGAGCAAGCCACCACAGTAGGCATCTGATCTTTTTTTTTTTTTTTGATTTACTAAGAATGCAGGTGGGAAAGGGACATGAAAGAACTAATCACACTATTCAGCCAACTGTGGGAAACAGGAAAAAGAGCAGGGAGCAAAGAAAGAGAATTGGCTTGATGCTACCTGAGGAGGA chm1:+:1018806288:-1 chm1:+:1282117259:-1 chm1:+:1877306280:-1 chm1:+:2550599142:-1 +AACCAACTCTTCATCAAAATTTCGTCCTGAGCAAGCCACCACAGTAGGCATCTGATCTTTTTTTTTTTTTTTGATTTACTAAGAATGCAGGTGGGAAAGGGACATGAAAGAACTAATCACACTATTCAGCCAACTGTGGGAAACAGGAAAAAGAGCAGGGAGCAAAGAAAGAGAATTGGCTTGATGCTACCTGAGGAGGA chm1:+:1709383891:-1 chm1:+:1924422628:-1 chm1:+:2709826154:-1 +AACCAACTCTTCATCAAAATTTCGTCCTGAGCAAGCCACCACAGTAGGCATCTGATCTTTTTTTTTTTTTTTGATTTACTAAGAATGCAGGTGGGAAAGGGACATGAAAGAACTAATCACACTATTCAGCCAACTGTGGGAAACAGGAAAAAGAGCAGGGAGCAAAGAAAGAGAATTGGCTTGATGCTACCTGAGGAGGA chm1:+:161099761:-1 chm1:+:759332115:-1 chm1:+:917479246:-1 chm1:+:1177482890:-1 chm1:+:1260253981:-1 chm1:+:1487898104:-1 chm1:+:1552062900:-1 chm1:+:1957483528:-1 chm1:+:2270548457:-1 chm1:+:2275534599:-1 chm1:+:2646337518:-1 chm1:+:2914118619:-1 +AACCAACTCTTCATCAAAATTTCGTCCTGAGCAAGCCACCACAGTAGGCATCTGATCTTTTTTTTTTTTTTTGATTTACTAAGAATGCAGGTGGGAAAGGGACATGAAAGAACTAATCACACTATTCAGCCAACTGTGGGAAACAGGAAAAAGAGCAGGGAGCAAAGAAAGAGAATTGGCTTGATGCTACCTGAGGAGGA chm1:+:18015477:-1 chm1:+:298854648:-1 chm1:+:847465681:-1 chm1:+:897180656:-1 chm1:+:1154691501:-1 chm1:+:1338932197:-1 chm1:+:1661037962:-1 chm1:+:1665750232:-1 chm1:+:1760943124:-1 chm1:+:1803779618:-1 chm1:+:1899738745:-1 chm1:+:1937061945:-1 +AACCAACTCTTCATCAAAATTTCGTCCTGAGCAAGCCACCACAGTAGGCATCTGATCTTTTTTTTTTTTTTTGATTTACTAAGAATGCAGGTGGGAAAGGGACATGAAAGAACTAATCACACTATTCAGCCAACTGTGGGAAACAGGAAAAAGAGCAGGGAGCAAAGAAAGAGAATTGGCTTGATGCTACCTGAGGAGGA chm1:+:67984081:-1 chm1:+:226223178:-1 chm1:+:227057211:-1 chm1:+:489901817:-1 chm1:+:1176645580:-1 chm1:+:1355334533:-1 chm1:+:1624869491:-1 chm1:+:1909662109:-1 +TCCTCCTCAGGTAGCATCAAGCCAATTCTCTTTCTTTGCTCCCTGCTCTTTTTCCTGTTTCCCACAGTTGGCTGAATAGTGTGATTAGTTCTTTCATGTCCCTTTCCCACCTGCATTCTTAGTAAATCAAAAAAAAAAAAAAAGATCAGATGCCTACTGTGGTGGCTTGCTCAGGACGAAATTTTGATGAAGAGTTGGTT chm1:+:1101344888:14 chm1:+:2434194395:-1 chm1:+:2705633201:-1 chm1:+:2777995761:-1 +TCCTCCTCAGGTAGCATCAAGCCAATTCTCTTTCTTTGCTCCCTGCTCTTTTTCCTGTTTCCCACAGTTGGCTGAATAGTGTGATTAGTTCTTTCATGTCCCTTTCCCACCTGCATTCTTAGTAAATCAAAAAAAAAAAAAAAGATCAGATGCCTACTGTGGTGGCTTGCTCAGGACGAAATTTTGATGAAGAGTTGGTT chm1:+:412178219:-1 chm1:+:579153902:-1 chm1:+:1101344887:14 chm1:+:1118452875:-1 chm1:+:1417672575:-1 chm1:+:1970541728:-1 chm1:+:2354952806:-1 chm1:+:2730232080:-1 +TCCTCCTCAGGTAGCATCAAGCCAATTCTCTTTCTTTGCTCCCTGCTCTTTTTCCTGTTTCCCACAGTTGGCTGAATAGTGTGATTAGTTCTTTCATGTCCCTTTCCCACCTGCATTCTTAGTAAATCAAAAAAAAAAAAAAAGATCAGATGCCTACTGTGGTGGCTTGCTCAGGACGAAATTTTGATGAAGAGTTGGTT chm1:+:28348470:-1 chm1:+:116144179:-1 chm1:+:698316243:-1 chm1:+:1113102372:-1 chm1:+:1231281247:-1 chm1:+:1336659752:-1 chm1:+:1612344141:-1 chm1:+:1617146805:-1 chm1:+:1843494801:-1 chm1:+:2252314678:-1 chm1:+:2341714484:-1 chm1:+:2520032972:-1 chm1:+:2820208752:-1 chm1:+:2918872782:-1 +TCCTCCTCAGGTAGCATCAAGCCAATTCTCTTTCTTTGCTCCCTGCTCTTTTTCCTGTTTCCCACAGTTGGCTGAATAGTGTGATTAGTTCTTTCATGTCCCTTTCCCACCTGCATTCTTAGTAAATCAAAAAAAAAAAAAAAGATCAGATGCCTACTGTGGTGGCTTGCTCAGGACGAAATTTTGATGAAGAGTTGGTT chm1:+:284662654:-1 chm1:+:328145560:-1 chm1:+:573365385:-1 chm1:+:781983986:-1 chm1:+:833652783:-1 chm1:+:967810435:-1 chm1:+:1420111023:-1 chm1:+:1534742185:-1 chm1:+:1543843180:-1 chm1:+:1689304517:-1 chm1:+:1757765344:-1 chm1:+:1955192008:-1 chm1:+:2305253967:-1 chm1:+:2476974950:-1 chm1:+:2698935583:-1 chm1:+:2801321065:-1 chm1:+:2805911749:-1 +TAGATAAAAATAGACCATCACCAAAATGAAAAACTTTTGTGTCTTTTAAAGGACACCATCAAGAAAGTGAAAAGACAGCCCACAGAATGGGAGTGAAATTTTTCGCAAATCAAAAATCTAATTAAGGGATTTGTATCTAAAATATACAATAAGGTATTATAATTCAATAATAAAAAAGACAAATCATTTTTAAATATGAC chm1:+:9286716:-1 chm1:+:270629439:-1 chm1:+:1726267042:-1 chm1:+:1756506172:-1 +TAGATAAAAATAGACCATCACCAAAATGAAAAACTTTTGTGTCTTTTAAAGGACACCATCAAGAAAGTGAAAAGACAGCCCACAGAATGGGAGTGAAATTTTTCGCAAATCAAAAATCTAATTAAGGGATTTGTATCTAAAATATACAATAAGGTATTATAATTCAATAATAAAAAAGACAAATCATTTTTAAATATGAC chm1:+:194964590:-1 chm1:+:414412908:-1 chm1:+:1863758866:-1 chm1:+:1893449455:-1 +TAGATAAAAATAGACCATCACCAAAATGAAAAACTTTTGTGTCTTTTAAAGGACACCATCAAGAAAGTGAAAAGACAGCCCACAGAATGGGAGTGAAATTTTTCGCAAATCAAAAATCTAATTAAGGGATTTGTATCTAAAATATACAATAAGGTATTATAATTCAATAATAAAAAAGACAAATCATTTTTAAATATGAC chm1:+:905415418:-1 chm1:+:956129893:-1 +TAGATAAAAATAGACCATCACCAAAATGAAAAACTTTTGTGTCTTTTAAAGGACACCATCAAGAAAGTGAAAAGACAGCCCACAGAATGGGAGTGAAATTTTTCGCAAATCAAAAATCTAATTAAGGGATTTGTATCTAAAATATACAATAAGGTATTATAATTCAATAATAAAAAAGACAAATCATTTTTAAATATGAC chm1:+:78077599:-1 chm1:+:198084002:-1 chm1:+:262856168:-1 chm1:+:334002491:-1 chm1:+:344800987:-1 chm1:+:553798606:-1 chm1:+:666657215:-1 chm1:+:767170863:-1 chm1:+:811297546:-1 chm1:+:854926052:-1 chm1:+:881876571:-1 chm1:+:912310421:-1 chm1:+:1087152218:12 chm1:+:1094742451:-1 chm1:+:1244156838:-1 chm1:+:1331148226:-1 chm1:+:1374894539:-1 chm1:+:1391792719:-1 chm1:+:1424102732:-1 chm1:+:1523378832:-1 chm1:+:2276354402:-1 chm1:+:2277833640:-1 chm1:+:2488270744:-1 chm1:+:2697656753:-1 chm1:+:2701524959:-1 chm1:+:2754243695:-1 +GTCATATTTAAAAATGATTTGTCTTTTTTATTATTGAATTATAATACCTTATTGTATATTTTAGATACAAATCCCTTAATTAGATTTTTGATTTGCGAAAAATTTCACTCCCATTCTGTGGGCTGTCTTTTCACTTTCTTGATGGTGTCCTTTAAAAGACACAAAAGTTTTTCATTTTGGTGATGGTCTATTTTTATCTA chm1:+:77357056:-1 chm1:+:193032476:-1 chm1:+:212575790:-1 chm1:+:620697342:-1 chm1:+:652685534:-1 chm1:+:653548793:-1 chm1:+:1108645146:-1 chm1:+:1255541655:-1 chm1:+:1256790467:-1 chm1:+:1331146980:-1 chm1:+:1364622618:-1 chm1:+:1711567462:-1 chm1:+:1889663277:-1 chm1:+:1889860698:-1 chm1:+:1892476237:-1 chm1:+:1983381895:-1 chm1:+:1984431788:-1 chm1:+:2001122559:-1 chm1:+:2230685204:-1 chm1:+:2235126819:-1 chm1:+:2628168211:-1 chm1:+:2630227704:-1 chm1:+:2903398633:-1 chm1:+:3030278226:-1 +GTCATATTTAAAAATGATTTGTCTTTTTTATTATTGAATTATAATACCTTATTGTATATTTTAGATACAAATCCCTTAATTAGATTTTTGATTTGCGAAAAATTTCACTCCCATTCTGTGGGCTGTCTTTTCACTTTCTTGATGGTGTCCTTTAAAAGACACAAAAGTTTTTCATTTTGGTGATGGTCTATTTTTATCTA chm1:+:42376446:-1 +CCTTCGTGCTCCAAGGAATAGCACACGCGTCCCTCTCCCTCCCTCTCCTTCCTAGATGTGCATCATTAGGGAGACGCTACGGATCAGAATGTAGAGTTGTTCACACATGTCTAGTGAAGTTCCCACAGTCCCTGGAGCTCAGGATTTTTCAGACTTGGCAGAGATGAGGTGACAGTAACAGGGCAGAGCGAGGCAGAGAC chm1:+:27965954:-1 chm1:+:872217065:-1 chm1:+:872217075:-1 chm1:+:872217099:-1 chm1:+:872217109:-1 chm1:+:872217119:-1 chm1:+:872217129:-1 chm1:+:872217139:-1 chm1:+:872217169:-1 chm1:+:872217207:-1 chm1:+:872217231:-1 chm1:+:1043868519:-1 chm1:+:1528343364:-1 chm1:+:1675693041:-1 chm1:+:1675693051:-1 chm1:+:1880913858:-1 chm1:+:2377061947:-1 chm1:+:2710257696:-1 chm1:+:2882834078:-1 chm1:+:2906866853:-1 chm1:+:3021170660:-1 +CCTTCGTGCTCCAAGGAATAGCACACGCGTCCCTCTCCCTCCCTCTCCTTCCTAGATGTGCATCATTAGGGAGACGCTACGGATCAGAATGTAGAGTTGTTCACACATGTCTAGTGAAGTTCCCACAGTCCCTGGAGCTCAGGATTTTTCAGACTTGGCAGAGATGAGGTGACAGTAACAGGGCAGAGCGAGGCAGAGAC chm1:+:1090755848:-1 +CCTTCGTGCTCCAAGGAATAGCACACGCGTCCCTCTCCCTCCCTCTCCTTCCTAGATGTGCATCATTAGGGAGACGCTACGGATCAGAATGTAGAGTTGTTCACACATGTCTAGTGAAGTTCCCACAGTCCCTGGAGCTCAGGATTTTTCAGACTTGGCAGAGATGAGGTGACAGTAACAGGGCAGAGCGAGGCAGAGAC chm1:+:926179062:-1 chm1:+:1424423919:-1 chm1:+:1759708442:-1 chm1:+:1902394844:-1 chm1:+:2025420329:-1 chm1:+:2080392049:-1 chm1:+:2990069200:-1 +CCTTCGTGCTCCAAGGAATAGCACACGCGTCCCTCTCCCTCCCTCTCCTTCCTAGATGTGCATCATTAGGGAGACGCTACGGATCAGAATGTAGAGTTGTTCACACATGTCTAGTGAAGTTCCCACAGTCCCTGGAGCTCAGGATTTTTCAGACTTGGCAGAGATGAGGTGACAGTAACAGGGCAGAGCGAGGCAGAGAC chm1:+:93694146:-1 chm1:+:102495417:-1 chm1:+:156446716:-1 chm1:+:351990789:-1 chm1:+:422629475:-1 chm1:+:484030259:-1 chm1:+:547222969:-1 chm1:+:647037084:-1 chm1:+:678788527:-1 chm1:+:692523503:-1 chm1:+:769847696:-1 chm1:+:843492045:-1 chm1:+:959620783:-1 chm1:+:1154439599:-1 chm1:+:1207342777:-1 chm1:+:1354332235:-1 chm1:+:1667881358:-1 chm1:+:1676596035:-1 chm1:+:1765949653:-1 chm1:+:1930535393:-1 chm1:+:2149431494:-1 chm1:+:2221853615:-1 chm1:+:2263480918:-1 chm1:+:2717649733:-1 chm1:+:2915125474:-1 +CCTTCGTGCTCCAAGGAATAGCACACGCGTCCCTCTCCCTCCCTCTCCTTCCTAGATGTGCATCATTAGGGAGACGCTACGGATCAGAATGTAGAGTTGTTCACACATGTCTAGTGAAGTTCCCACAGTCCCTGGAGCTCAGGATTTTTCAGACTTGGCAGAGATGAGGTGACAGTAACAGGGCAGAGCGAGGCAGAGAC chm1:+:792824163:-1 chm1:+:1260383812:-1 chm1:+:1329001611:-1 chm1:+:1443072993:-1 chm1:+:1748125623:-1 chm1:+:2030500132:-1 chm1:+:2035850893:-1 chm1:+:2504327240:-1 +CCTTCGTGCTCCAAGGAATAGCACACGCGTCCCTCTCCCTCCCTCTCCTTCCTAGATGTGCATCATTAGGGAGACGCTACGGATCAGAATGTAGAGTTGTTCACACATGTCTAGTGAAGTTCCCACAGTCCCTGGAGCTCAGGATTTTTCAGACTTGGCAGAGATGAGGTGACAGTAACAGGGCAGAGCGAGGCAGAGAC chm1:+:635941074:-1 chm1:+:2972323623:-1 +GTCTCTGCCTCGCTCTGCCCTGTTACTGTCACCTCATCTCTGCCAAGTCTGAAAAATCCTGAGCTCCAGGGACTGTGGGAACTTCACTAGACATGTGTGAACAACTCTACATTCTGATCCGTAGCGTCTCCCTAATGATGCACATCTAGGAAGGAGAGGGAGGGAGAGGGACGCGTGTGCTATTCCTTGGAGCACGAAGG chm1:+:5807553:-1 chm1:+:27600161:-1 chm1:+:496196951:-1 chm1:+:1768727086:-1 chm1:+:1790862522:-1 chm1:+:2105661454:8 chm1:+:2487787592:-1 chm1:+:2495914057:-1 chm1:+:2495914147:-1 chm1:+:2495914187:-1 +GTCTCTGCCTCGCTCTGCCCTGTTACTGTCACCTCATCTCTGCCAAGTCTGAAAAATCCTGAGCTCCAGGGACTGTGGGAACTTCACTAGACATGTGTGAACAACTCTACATTCTGATCCGTAGCGTCTCCCTAATGATGCACATCTAGGAAGGAGAGGGAGGGAGAGGGACGCGTGTGCTATTCCTTGGAGCACGAAGG chm1:+:1198849642:-1 +CAAGCAGGTGAGGTAGATGTGGTAAAGAAATATCCTGATTTGTTCCTCTTGCTCAGGTGCTCTGCCTCTCCCCTACTTTGCCCATCTGAGAGAGGGTAAAAAGGAGGAGTATTGGAGATTTGTCAAAATATGAAGGAGTTCATCAGGAAGGTTGGGAGAGTGAATGAATTAGGGAAATATGGTAGGATACCAAGCAGCAC chm1:+:2245639831:5 chm1:+:2283891879:-1 +CAAGCAGGTGAGGTAGATGTGGTAAAGAAATATCCTGATTTGTTCCTCTTGCTCAGGTGCTCTGCCTCTCCCCTACTTTGCCCATCTGAGAGAGGGTAAAAAGGAGGAGTATTGGAGATTTGTCAAAATATGAAGGAGTTCATCAGGAAGGTTGGGAGAGTGAATGAATTAGGGAAATATGGTAGGATACCAAGCAGCAC chm1:+:806101721:-1 chm1:+:2245639830:5 +TACATCTAACTGGGGATAAATTAGCATAATGATTGAAAGAATGCGCCTTGAGTCTGCCAGCCTGTTACTGAAAGGCTTGGCTTCATCATTTGCCAACTTTGTGATCATGAAAAGTTTCTAATATCCACTGACTCTTAAGTTCTCTTCACCCGAAAAATGGGCATATAGAAAAACACAAAAACAGCCTGTAATTCTTAGCA chm1:+:911448360:-1 chm1:+:984029802:-1 chm1:+:1007762123:-1 chm1:+:1660063834:10 chm1:+:2011183684:-1 +TACATCTAACTGGGGATAAATTAGCATAATGATTGAAAGAATGCGCCTTGAGTCTGCCAGCCTGTTACTGAAAGGCTTGGCTTCATCATTTGCCAACTTTGTGATCATGAAAAGTTTCTAATATCCACTGACTCTTAAGTTCTCTTCACCCGAAAAATGGGCATATAGAAAAACACAAAAACAGCCTGTAATTCTTAGCA chm1:+:1660063833:10 +TGCTAAGAATTACAGGCTGTTTTTGTGTTTTTCTATATGCCCATTTTTCGGGTGAAGAGAACTTAAGAGTCAGTGGATATTAGAAACTTTTCATGATCACAAAGTTGGCAAATGATGAAGCCAAGCCTTTCAGTAACAGGCTGGCAGACTCAAGGCGCATTCTTTCAATCATTATGCTAATTTATCCCCAGTTAGATGTA chm1:+:1773784364:-1 +TGTTAAGGTATTTTACCCATTTTTAAATCACGTAGCTTCTTTTCTTATTATGGAACTTTAATAGTCTTTTATATAATTTGGATAATAGTCCTGTATTCAGATAAGTCTTGCAAATAATTTTCTCCAAACCTGCTGCTTGTCTTTTCATTCTCTTGACATTGCCTTAAGAGAAGAAATTTTTTTTTTCTTATTTTTTTTAT chm1:+:33304:-1 chm1:+:29366565:-1 chm1:+:53351379:-1 chm1:+:65263381:-1 chm1:+:71807629:-1 chm1:+:92738949:-1 chm1:+:117894922:-1 chm1:+:154362499:-1 chm1:+:159654570:-1 chm1:+:167251155:-1 chm1:+:169220573:-1 chm1:+:171561621:-1 chm1:+:174559248:-1 chm1:+:184277769:-1 chm1:+:185063047:-1 chm1:+:190177027:-1 chm1:+:212854548:-1 chm1:+:218466141:-1 chm1:+:239246949:-1 chm1:+:301537618:-1 chm1:+:304871489:-1 chm1:+:334037973:-1 chm1:+:365682381:-1 chm1:+:376013833:-1 chm1:+:402639517:-1 chm1:+:404995887:-1 chm1:+:445379607:-1 chm1:+:453127314:-1 chm1:+:454861100:-1 chm1:+:473532740:-1 chm1:+:479621632:-1 chm1:+:484654189:-1 chm1:+:545849091:-1 chm1:+:582684276:-1 chm1:+:644327619:-1 chm1:+:721563243:-1 chm1:+:787760925:-1 chm1:+:787794637:-1 chm1:+:790724247:-1 chm1:+:811342081:-1 chm1:+:855986846:-1 chm1:+:909389640:-1 chm1:+:914043493:-1 chm1:+:914449109:-1 chm1:+:939458426:-1 chm1:+:957906146:-1 chm1:+:1025334547:-1 chm1:+:1033039350:-1 chm1:+:1105201267:-1 chm1:+:1110467052:-1 chm1:+:1120312967:-1 chm1:+:1132385314:-1 chm1:+:1134804940:-1 chm1:+:1178441733:-1 chm1:+:1241641800:-1 chm1:+:1247963905:-1 chm1:+:1315450938:-1 chm1:+:1328149498:-1 chm1:+:1361664907:-1 chm1:+:1372731794:-1 chm1:+:1419904789:-1 chm1:+:1423381440:-1 chm1:+:1433320127:-1 chm1:+:1440397617:-1 chm1:+:1462223081:-1 chm1:+:1489177774:-1 chm1:+:1508528604:-1 chm1:+:1529721990:-1 chm1:+:1541883494:-1 chm1:+:1543643722:-1 chm1:+:1610953375:-1 chm1:+:1621196183:-1 chm1:+:1647698824:-1 chm1:+:1653846658:-1 chm1:+:1668825875:-1 chm1:+:1701633293:-1 chm1:+:1708975710:-1 chm1:+:1713302721:-1 chm1:+:1819193748:-1 chm1:+:1819239576:-1 chm1:+:1834172294:-1 chm1:+:1843215522:-1 chm1:+:1860004038:-1 chm1:+:1870873483:-1 chm1:+:1911110419:-1 chm1:+:1932908225:-1 chm1:+:1953769529:-1 chm1:+:1965341547:-1 chm1:+:2016280465:-1 chm1:+:2110018972:-1 chm1:+:2129553818:-1 chm1:+:2136401885:-1 chm1:+:2143745803:-1 chm1:+:2145483132:-1 chm1:+:2146157667:-1 chm1:+:2168010676:-1 chm1:+:2172358460:-1 chm1:+:2220124140:-1 chm1:+:2222707713:-1 chm1:+:2227649389:-1 chm1:+:2233516822:-1 chm1:+:2250241749:-1 chm1:+:2261457789:-1 chm1:+:2263619756:-1 chm1:+:2267092942:-1 chm1:+:2328360160:-1 chm1:+:2329371318:-1 chm1:+:2337578819:-1 chm1:+:2381401227:-1 chm1:+:2384664696:-1 chm1:+:2406124174:-1 chm1:+:2429269524:-1 chm1:+:2433936376:-1 chm1:+:2456300208:-1 chm1:+:2501014831:-1 chm1:+:2503401486:-1 chm1:+:2514516112:-1 chm1:+:2519701996:-1 chm1:+:2608559089:-1 chm1:+:2622171157:-1 chm1:+:2625151752:-1 chm1:+:2637405122:-1 chm1:+:2659519235:-1 chm1:+:2667730528:-1 chm1:+:2706570330:-1 chm1:+:2754177199:-1 chm1:+:2797875126:-1 chm1:+:2799025652:-1 chm1:+:2812305010:-1 chm1:+:2820181578:-1 chm1:+:2849246175:-1 chm1:+:2859361279:-1 chm1:+:2870897141:-1 chm1:+:2923317172:-1 chm1:+:2954820774:-1 chm1:+:2955808054:-1 chm1:+:2956987722:-1 chm1:+:2967562118:-1 chm1:+:2971145209:-1 chm1:+:2973678584:-1 chm1:+:2984314496:-1 chm1:+:3013047714:-1 chm1:+:3057224022:-1 +TGTTAAGGTATTTTACCCATTTTTAAATCACGTAGCTTCTTTTCTTATTATGGAACTTTAATAGTCTTTTATATAATTTGGATAATAGTCCTGTATTCAGATAAGTCTTGCAAATAATTTTCTCCAAACCTGCTGCTTGTCTTTTCATTCTCTTGACATTGCCTTAAGAGAAGAAATTTTTTTTTTCTTATTTTTTTTAT chm1:+:300882409:-1 chm1:+:312590881:-1 chm1:+:418018193:-1 chm1:+:464511412:-1 chm1:+:661129476:-1 chm1:+:672530190:-1 chm1:+:682920830:-1 chm1:+:811929439:-1 chm1:+:870708661:-1 chm1:+:908370483:-1 chm1:+:1354928948:-1 chm1:+:1490469974:-1 chm1:+:1551458446:-1 chm1:+:1560054313:-1 chm1:+:2255914268:-1 chm1:+:2257849488:-1 chm1:+:2432238298:-1 chm1:+:2911131276:-1 +TGTTAAGGTATTTTACCCATTTTTAAATCACGTAGCTTCTTTTCTTATTATGGAACTTTAATAGTCTTTTATATAATTTGGATAATAGTCCTGTATTCAGATAAGTCTTGCAAATAATTTTCTCCAAACCTGCTGCTTGTCTTTTCATTCTCTTGACATTGCCTTAAGAGAAGAAATTTTTTTTTTCTTATTTTTTTTAT chm1:+:437968939:-1 chm1:+:455774473:-1 chm1:+:610513748:-1 chm1:+:681544585:-1 chm1:+:687919139:-1 chm1:+:847427183:-1 chm1:+:942003156:-1 chm1:+:1024274026:-1 chm1:+:1044083030:-1 chm1:+:1166550920:-1 chm1:+:1216883830:-1 chm1:+:1256463559:-1 chm1:+:1464139107:-1 chm1:+:2737153828:-1 chm1:+:2811502221:-1 +TGTTAAGGTATTTTACCCATTTTTAAATCACGTAGCTTCTTTTCTTATTATGGAACTTTAATAGTCTTTTATATAATTTGGATAATAGTCCTGTATTCAGATAAGTCTTGCAAATAATTTTCTCCAAACCTGCTGCTTGTCTTTTCATTCTCTTGACATTGCCTTAAGAGAAGAAATTTTTTTTTTCTTATTTTTTTTAT chm1:+:154233162:-1 chm1:+:624826485:-1 chm1:+:666708322:-1 chm1:+:1567546209:-1 chm1:+:2560310316:-1 +TGTTAAGGTATTTTACCCATTTTTAAATCACGTAGCTTCTTTTCTTATTATGGAACTTTAATAGTCTTTTATATAATTTGGATAATAGTCCTGTATTCAGATAAGTCTTGCAAATAATTTTCTCCAAACCTGCTGCTTGTCTTTTCATTCTCTTGACATTGCCTTAAGAGAAGAAATTTTTTTTTTCTTATTTTTTTTAT chm1:+:35878311:-1 chm1:+:376263361:-1 chm1:+:515304960:-1 chm1:+:521903055:-1 chm1:+:750504179:-1 chm1:+:788579041:-1 chm1:+:817035537:-1 chm1:+:902774087:-1 chm1:+:995341263:-1 chm1:+:1055207774:-1 chm1:+:1180582424:-1 chm1:+:1233300570:-1 chm1:+:1298083427:-1 chm1:+:1351251693:-1 chm1:+:1401480692:-1 chm1:+:1401532721:-1 chm1:+:1477124370:-1 chm1:+:1486696265:-1 chm1:+:1522536935:-1 chm1:+:1647688366:-1 chm1:+:1653149436:-1 chm1:+:1764665968:-1 chm1:+:1766565401:-1 chm1:+:1852086220:-1 chm1:+:1903351648:-1 chm1:+:1924466169:-1 chm1:+:2349262980:-1 chm1:+:2657501262:-1 chm1:+:2697136709:-1 chm1:+:2915685239:-1 chm1:+:3022654825:-1 +TGTTAAGGTATTTTACCCATTTTTAAATCACGTAGCTTCTTTTCTTATTATGGAACTTTAATAGTCTTTTATATAATTTGGATAATAGTCCTGTATTCAGATAAGTCTTGCAAATAATTTTCTCCAAACCTGCTGCTTGTCTTTTCATTCTCTTGACATTGCCTTAAGAGAAGAAATTTTTTTTTTCTTATTTTTTTTAT chm1:+:300291550:-1 chm1:+:392111401:-1 chm1:+:851361417:-1 chm1:+:911703233:-1 chm1:+:964388846:-1 chm1:+:1059649211:-1 chm1:+:1061930536:-1 chm1:+:1247313881:-1 chm1:+:1462863130:-1 chm1:+:1506381744:-1 chm1:+:1530802388:-1 chm1:+:1841904553:-1 chm1:+:1851815489:-1 chm1:+:2470222262:-1 chm1:+:2567241930:-1 chm1:+:2706038553:-1 +TGTTAAGGTATTTTACCCATTTTTAAATCACGTAGCTTCTTTTCTTATTATGGAACTTTAATAGTCTTTTATATAATTTGGATAATAGTCCTGTATTCAGATAAGTCTTGCAAATAATTTTCTCCAAACCTGCTGCTTGTCTTTTCATTCTCTTGACATTGCCTTAAGAGAAGAAATTTTTTTTTTCTTATTTTTTTTAT chm1:+:2156334344:-1 +TGTTAAGGTATTTTACCCATTTTTAAATCACGTAGCTTCTTTTCTTATTATGGAACTTTAATAGTCTTTTATATAATTTGGATAATAGTCCTGTATTCAGATAAGTCTTGCAAATAATTTTCTCCAAACCTGCTGCTTGTCTTTTCATTCTCTTGACATTGCCTTAAGAGAAGAAATTTTTTTTTTCTTATTTTTTTTAT chm1:+:216445222:-1 chm1:+:1521156148:-1 chm1:+:2600308076:-1 +ATAAAAAAAATAAGAAAAAAAAAATTTCTTCTCTTAAGGCAATGTCAAGAGAATGAAAAGACAAGCAGCAGGTTTGGAGAAAATTATTTGCAAGACTTATCTGAATACAGGACTATTATCCAAATTATATAAAAGACTATTAAAGTTCCATAATAAGAAAAGAAGCTACGTGATTTAAAAATGGGTAAAATACCTTAACA chm1:+:872801447:-1 chm1:+:894993242:-1 chm1:+:1468938993:6 chm1:+:1838411262:-1 chm1:+:2108945360:-1 chm1:+:3027390137:-1 chm1:+:3064746904:-1 +ATAAAAAAAATAAGAAAAAAAAAATTTCTTCTCTTAAGGCAATGTCAAGAGAATGAAAAGACAAGCAGCAGGTTTGGAGAAAATTATTTGCAAGACTTATCTGAATACAGGACTATTATCCAAATTATATAAAAGACTATTAAAGTTCCATAATAAGAAAAGAAGCTACGTGATTTAAAAATGGGTAAAATACCTTAACA chm1:+:1468938994:6 +ATAAAAAAAATAAGAAAAAAAAAATTTCTTCTCTTAAGGCAATGTCAAGAGAATGAAAAGACAAGCAGCAGGTTTGGAGAAAATTATTTGCAAGACTTATCTGAATACAGGACTATTATCCAAATTATATAAAAGACTATTAAAGTTCCATAATAAGAAAAGAAGCTACGTGATTTAAAAATGGGTAAAATACCTTAACA chm1:+:1468938996:6 +TTTTAGTATAACATAGATAATACGTAAGTTAGTACAATTAACGTAATGACTTATACTCTCAATTAGTTATGCCTCCTAATCCTCATCCTGCCCCTTTGTTTTGTATTTTTCTTTTTTCAAAGTATTTCCAGTTGTTATCTCAGTCCTACTATTATAATAAACTTATCTTGTTTATTTTCACATACATCACTTTAGGAAGT chm1:+:59888326:-1 chm1:+:725981008:-1 +TTTTAGTATAACATAGATAATACGTAAGTTAGTACAATTAACGTAATGACTTATACTCTCAATTAGTTATGCCTCCTAATCCTCATCCTGCCCCTTTGTTTTGTATTTTTCTTTTTTCAAAGTATTTCCAGTTGTTATCTCAGTCCTACTATTATAATAAACTTATCTTGTTTATTTTCACATACATCACTTTAGGAAGT chm1:+:58285520:-1 chm1:+:71229567:-1 chm1:+:1092519450:-1 chm1:+:1102664102:-1 chm1:+:2436117925:-1 chm1:+:2811664933:-1 +TTTTAGTATAACATAGATAATACGTAAGTTAGTACAATTAACGTAATGACTTATACTCTCAATTAGTTATGCCTCCTAATCCTCATCCTGCCCCTTTGTTTTGTATTTTTCTTTTTTCAAAGTATTTCCAGTTGTTATCTCAGTCCTACTATTATAATAAACTTATCTTGTTTATTTTCACATACATCACTTTAGGAAGT chm1:+:348129721:-1 chm1:+:551451139:-1 chm1:+:678860295:-1 chm1:+:1047849230:-1 chm1:+:1177649377:-1 chm1:+:1194419535:-1 chm1:+:1313845643:-1 chm1:+:1398166270:-1 chm1:+:2052061497:-1 +TTTTAGTATAACATAGATAATACGTAAGTTAGTACAATTAACGTAATGACTTATACTCTCAATTAGTTATGCCTCCTAATCCTCATCCTGCCCCTTTGTTTTGTATTTTTCTTTTTTCAAAGTATTTCCAGTTGTTATCTCAGTCCTACTATTATAATAAACTTATCTTGTTTATTTTCACATACATCACTTTAGGAAGT chm1:+:218460934:-1 chm1:+:299564478:-1 chm1:+:455199023:-1 chm1:+:622690106:-1 chm1:+:653629077:-1 chm1:+:743874232:-1 chm1:+:1013802041:-1 chm1:+:1383418543:-1 chm1:+:1624953500:-1 chm1:+:1711914687:-1 chm1:+:1899552947:-1 chm1:+:2171990303:-1 chm1:+:2237076212:-1 chm1:+:2457736808:-1 chm1:+:2479743510:-1 chm1:+:2601094827:-1 chm1:+:2672136617:-1 chm1:+:2742743984:-1 +TTTTAGTATAACATAGATAATACGTAAGTTAGTACAATTAACGTAATGACTTATACTCTCAATTAGTTATGCCTCCTAATCCTCATCCTGCCCCTTTGTTTTGTATTTTTCTTTTTTCAAAGTATTTCCAGTTGTTATCTCAGTCCTACTATTATAATAAACTTATCTTGTTTATTTTCACATACATCACTTTAGGAAGT chm1:+:68369645:-1 chm1:+:70882411:-1 chm1:+:71494111:-1 chm1:+:168944917:-1 chm1:+:193169450:-1 chm1:+:225686744:-1 chm1:+:237003266:-1 chm1:+:244233791:-1 chm1:+:314757214:-1 chm1:+:316786737:-1 chm1:+:332776513:-1 chm1:+:363501275:-1 chm1:+:472814870:-1 chm1:+:498353251:-1 chm1:+:509167399:-1 chm1:+:518392909:-1 chm1:+:551909611:-1 chm1:+:560173136:-1 chm1:+:580723094:-1 chm1:+:637912431:-1 chm1:+:658448706:-1 chm1:+:668448307:-1 chm1:+:710260217:-1 chm1:+:759997929:-1 chm1:+:813117147:-1 chm1:+:822899069:-1 chm1:+:823452208:-1 chm1:+:844189345:-1 chm1:+:869696716:-1 chm1:+:870288653:-1 chm1:+:938391253:-1 chm1:+:967230159:-1 chm1:+:981409861:-1 chm1:+:985351788:-1 chm1:+:1020129367:-1 chm1:+:1041316951:-1 chm1:+:1078362457:-1 chm1:+:1112455903:-1 chm1:+:1119575241:-1 chm1:+:1156083177:-1 chm1:+:1167119890:-1 chm1:+:1187746141:-1 chm1:+:1210757078:-1 chm1:+:1211870550:-1 chm1:+:1220563281:-1 chm1:+:1221431910:-1 chm1:+:1239297479:-1 chm1:+:1241785534:-1 chm1:+:1277484327:-1 chm1:+:1290187706:-1 chm1:+:1291592038:-1 chm1:+:1300220293:-1 chm1:+:1343764746:-1 chm1:+:1482436727:-1 chm1:+:1544687572:-1 chm1:+:1554054216:-1 chm1:+:1561877295:-1 chm1:+:1564330771:-1 chm1:+:1574216512:-1 chm1:+:1575609626:-1 chm1:+:1581871581:-1 chm1:+:1610071529:-1 chm1:+:1628130010:-1 chm1:+:1628785840:-1 chm1:+:1641129824:-1 chm1:+:1663469068:-1 chm1:+:1666764141:-1 chm1:+:1674701978:-1 chm1:+:1699929664:-1 chm1:+:1708458401:-1 chm1:+:1769934725:-1 chm1:+:1825440905:-1 chm1:+:1826433017:-1 chm1:+:1835109699:-1 chm1:+:1836544543:-1 chm1:+:1881040604:-1 chm1:+:1881750470:-1 chm1:+:1883025999:-1 chm1:+:1891685259:-1 chm1:+:1908736476:-1 chm1:+:1914072690:-1 chm1:+:1917166567:-1 chm1:+:1968980678:-1 chm1:+:1971266540:-1 chm1:+:1982451397:-1 chm1:+:2037786772:-1 chm1:+:2109624421:-1 chm1:+:2166016400:-1 chm1:+:2174471965:-1 chm1:+:2188628933:-1 chm1:+:2248904985:-1 chm1:+:2262880004:-1 chm1:+:2457905098:-1 chm1:+:2477639437:-1 chm1:+:2544213284:-1 chm1:+:2567725476:-1 chm1:+:2673677231:-1 chm1:+:2681572428:-1 chm1:+:2682570236:-1 chm1:+:2682833842:-1 chm1:+:2713572021:-1 chm1:+:2740269163:-1 chm1:+:2756403606:-1 chm1:+:2772423326:-1 chm1:+:2818359256:-1 chm1:+:2825915252:-1 chm1:+:2855228211:-1 chm1:+:2868396217:-1 chm1:+:2871845669:-1 chm1:+:2905169703:-1 chm1:+:3053437759:-1 +ACTTCCTAAAGTGATGTATGTGAAAATAAACAAGATAAGTTTATTATAATAGTAGGACTGAGATAACAACTGGAAATACTTTGAAAAAAGAAAAATACAAAACAAAGGGGCAGGATGAGGATTAGGAGGCATAACTAATTGAGAGTATAAGTCATTACGTTAATTGTACTAACTTACGTATTATCTATGTTATACTAAAA chm1:+:2472676469:-1 +ACTTCCTAAAGTGATGTATGTGAAAATAAACAAGATAAGTTTATTATAATAGTAGGACTGAGATAACAACTGGAAATACTTTGAAAAAAGAAAAATACAAAACAAAGGGGCAGGATGAGGATTAGGAGGCATAACTAATTGAGAGTATAAGTCATTACGTTAATTGTACTAACTTACGTATTATCTATGTTATACTAAAA chm1:+:1185115:-1 chm1:+:1440388:-1 chm1:+:223730301:-1 chm1:+:465884219:13 chm1:+:589187140:-1 chm1:+:660866248:-1 chm1:+:850709048:-1 chm1:+:1335537997:-1 chm1:+:1436187117:-1 chm1:+:1643471073:-1 chm1:+:1651335430:-1 chm1:+:1678089578:-1 chm1:+:1815683577:-1 chm1:+:1927908903:-1 chm1:+:2059107187:-1 chm1:+:2124525420:-1 chm1:+:2185995184:-1 chm1:+:2220620867:-1 chm1:+:2521182659:-1 chm1:+:2530633989:-1 chm1:+:2687737109:-1 chm1:+:2702813471:-1 chm1:+:2702871146:-1 chm1:+:2703035770:-1 chm1:+:2703139724:-1 chm1:+:2703158809:-1 chm1:+:2703222754:-1 chm1:+:2713132249:-1 chm1:+:2716351395:-1 chm1:+:2716674264:-1 +ACTTCCTAAAGTGATGTATGTGAAAATAAACAAGATAAGTTTATTATAATAGTAGGACTGAGATAACAACTGGAAATACTTTGAAAAAAGAAAAATACAAAACAAAGGGGCAGGATGAGGATTAGGAGGCATAACTAATTGAGAGTATAAGTCATTACGTTAATTGTACTAACTTACGTATTATCTATGTTATACTAAAA chm1:+:465884218:13 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chm1:+:2986079620:14 chm1:+:2987033677:11 chm1:+:2991917022:13 chm1:+:3011672003:11 chm1:+:3029556063:12 chm1:+:3030223708:12 chm1:+:3042804103:17 chm1:+:3059534910:19 +CATTTAGACCCAGCCATCCCATTACTCGGGTATATAACCCAAAAGGACTAATAAATCATGCTGCTATAAAGACCACATGCACACGTATGTTTATTGTGGCATTATTCACAATAGCAAAGACTTGGAACCACCAAATGTACCAACAATGATAGACTGGAGTTAAGAAAATGGTGGCACATATACACCATGGAATACTATGC chm1:+:77130628:19 chm1:+:301713043:17 chm1:+:1215681106:31 chm1:+:1368981409:-1 +CATTTAGACCCAGCCATCCCATTACTCGGGTATATAACCCAAAAGGACTAATAAATCATGCTGCTATAAAGACCACATGCACACGTATGTTTATTGTGGCATTATTCACAATAGCAAAGACTTGGAACCACCAAATGTACCAACAATGATAGACTGGAGTTAAGAAAATGGTGGCACATATACACCATGGAATACTATGC chm1:+:98436890:31 chm1:+:298963657:21 chm1:+:301212336:35 chm1:+:505132284:22 chm1:+:595788333:38 chm1:+:832776921:17 chm1:+:1100785663:18 chm1:+:1186894947:20 chm1:+:1252306629:38 chm1:+:2014204864:19 chm1:+:2077662514:-1 chm1:+:2232323658:37 chm1:+:3099403361:21 +TAGTTGATAACTTTGCTTTTTTCCTTTGAGTCCTGGAGAATGGGAGGTAATACCATAGCTTCTTTTCTCTTTAATATATAAATAATAATTTATGGTACCTTATAAGAGTTAGATTTATTTTAACTTTTAAAGTCTAAGTTTATGCTTAAATTTTTTTGATACCAAAAATTATGAATTCATATTTAATTGTATTTTTGTTG chm1:+:317980177:8 +TAGTTGATAACTTTGCTTTTTTCCTTTGAGTCCTGGAGAATGGGAGGTAATACCATAGCTTCTTTTCTCTTTAATATATAAATAATAATTTATGGTACCTTATAAGAGTTAGATTTATTTTAACTTTTAAAGTCTAAGTTTATGCTTAAATTTTTTTGATACCAAAAATTATGAATTCATATTTAATTGTATTTTTGTTG chm1:+:317980173:8 +TAGTTGATAACTTTGCTTTTTTCCTTTGAGTCCTGGAGAATGGGAGGTAATACCATAGCTTCTTTTCTCTTTAATATATAAATAATAATTTATGGTACCTTATAAGAGTTAGATTTATTTTAACTTTTAAAGTCTAAGTTTATGCTTAAATTTTTTTGATACCAAAAATTATGAATTCATATTTAATTGTATTTTTGTTG chm1:+:317980172:8 +TAATACACCTAAGCTTACTAAACATCATAGCTTAGCCTAGTCTACCTTAAACACACTCAAAACACTCAACTAGCCTACACTTCGGCAAAATCATCTAACACACAGCCTATTTTTATAATAAGGTATTGAATATCTCATGTAACTTATTAAATACTGTACTGAAAATGGAAAGCAAAATGGTATATGGACACTCAAAGTTA chm1:+:8806396:-1 chm1:+:27207690:-1 chm1:+:232341729:-1 chm1:+:297972616:-1 chm1:+:615940509:-1 chm1:+:622875044:40 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+CCAATTAAACAGCAAGGAAGACTGTATTTAAGGCTATTGCAATTAGGATAGATGTATAGCAATAGAAGAGAGACGCTGAACTCAACTTGCTGAAACAAAAGGCTAAGGAGCATTACAAGCACTGAGGTGAGCTAGTGATGGAGAAAGTAGTACCAGAAGATATTAGGGGGAGAGATTGGTCTGTTGGGACGAGGCCCTCT chm1:+:173239011:-1 chm1:+:261699365:-1 chm1:+:1569114605:-1 chm1:+:2736126885:-1 +CCAATTAAACAGCAAGGAAGACTGTATTTAAGGCTATTGCAATTAGGATAGATGTATAGCAATAGAAGAGAGACGCTGAACTCAACTTGCTGAAACAAAAGGCTAAGGAGCATTACAAGCACTGAGGTGAGCTAGTGATGGAGAAAGTAGTACCAGAAGATATTAGGGGGAGAGATTGGTCTGTTGGGACGAGGCCCTCT chm1:+:620160453:-1 chm1:+:2041587104:-1 chm1:+:3043447269:-1 +CCAATTAAACAGCAAGGAAGACTGTATTTAAGGCTATTGCAATTAGGATAGATGTATAGCAATAGAAGAGAGACGCTGAACTCAACTTGCTGAAACAAAAGGCTAAGGAGCATTACAAGCACTGAGGTGAGCTAGTGATGGAGAAAGTAGTACCAGAAGATATTAGGGGGAGAGATTGGTCTGTTGGGACGAGGCCCTCT chm1:+:116017438:-1 chm1:+:181409446:-1 chm1:+:445857305:-1 chm1:+:477070126:-1 chm1:+:860783782:-1 chm1:+:905441028:-1 chm1:+:1442553909:-1 chm1:+:1519438836:-1 chm1:+:2179644643:-1 chm1:+:2262337338:-1 chm1:+:2530993169:-1 chm1:+:2569049063:-1 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chm1:+:412366662:-1 chm1:+:435159142:-1 chm1:+:507915704:-1 chm1:+:557618584:-1 chm1:+:614361994:-1 chm1:+:637905373:-1 chm1:+:667751756:-1 chm1:+:737544413:-1 chm1:+:1015865450:-1 chm1:+:1049593211:-1 chm1:+:1076359603:-1 chm1:+:1111963917:-1 chm1:+:1235377962:-1 chm1:+:1311880738:-1 chm1:+:1323986371:-1 chm1:+:1447287730:-1 chm1:+:1496837587:-1 chm1:+:1705407416:-1 chm1:+:2046887443:-1 chm1:+:2250206359:-1 chm1:+:2397114879:-1 chm1:+:2521381595:-1 chm1:+:2549588743:-1 chm1:+:2564899708:-1 chm1:+:2687723611:-1 chm1:+:2712685389:-1 chm1:+:2763240068:-1 chm1:+:2822929197:-1 chm1:+:2870265866:-1 chm1:+:2958017462:-1 chm1:+:2976823349:-1 +ATAATGAGGAAGACATTCCACCCCCTAACCCACCCCCGAGACGGAGTCTCACTCTGTCGCCCAGGCTGGAGTGCAATAGCGGCAGTCTTGGCGTCACTGTAACCTCTGCCTCCTAGATTCAAAGTGAATTCTCCTGCCTCAGCCTCCCAAGTAAGCTGGGATTACAGTCAAGCACCACCATGCCCAGCTGATTTTTGTAT chm1:+:27258115:-1 chm1:+:70673954:-1 chm1:+:165726672:-1 chm1:+:205141022:-1 chm1:+:303671735:-1 chm1:+:390138150:-1 chm1:+:934495112:-1 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chm1:+:509105188:-1 chm1:+:580361900:-1 chm1:+:593890668:-1 chm1:+:623258216:-1 chm1:+:643845952:-1 chm1:+:690785268:-1 chm1:+:700201128:-1 chm1:+:700968445:-1 chm1:+:706521191:-1 chm1:+:745168400:-1 chm1:+:767931424:-1 chm1:+:850126975:-1 chm1:+:891253146:-1 chm1:+:916396471:-1 chm1:+:962442443:-1 chm1:+:969532680:-1 chm1:+:1020300038:-1 chm1:+:1023761014:-1 chm1:+:1054211057:-1 chm1:+:1056562280:-1 chm1:+:1061469094:-1 chm1:+:1063546795:-1 chm1:+:1065731230:-1 chm1:+:1090135867:-1 chm1:+:1094242222:-1 chm1:+:1126762478:-1 chm1:+:1140882078:-1 chm1:+:1170176456:-1 chm1:+:1189695776:-1 chm1:+:1199294555:-1 chm1:+:1207117279:-1 chm1:+:1332628206:-1 chm1:+:1362429040:-1 chm1:+:1373895590:-1 chm1:+:1418917285:-1 chm1:+:1421281800:-1 chm1:+:1485719295:-1 chm1:+:1499394280:-1 chm1:+:1513796352:-1 chm1:+:1633611460:-1 chm1:+:1636457391:-1 chm1:+:1639830888:-1 chm1:+:1689000617:-1 chm1:+:1755315055:-1 chm1:+:1785402484:-1 chm1:+:1792991713:-1 chm1:+:1801660625:-1 chm1:+:1819775384:-1 chm1:+:1888117223:-1 chm1:+:1903324309:-1 chm1:+:2002607968:-1 chm1:+:2005555970:-1 chm1:+:2026313614:-1 chm1:+:2026891118:-1 chm1:+:2028628672:-1 chm1:+:2053042719:-1 chm1:+:2062170229:-1 chm1:+:2069190318:-1 chm1:+:2106450608:-1 chm1:+:2125946687:-1 chm1:+:2133530067:-1 chm1:+:2183582203:-1 chm1:+:2186755900:-1 chm1:+:2193426817:-1 chm1:+:2263612796:-1 chm1:+:2300328740:-1 chm1:+:2340513487:-1 chm1:+:2351045640:-1 chm1:+:2358745081:-1 chm1:+:2373389567:-1 chm1:+:2386235025:-1 chm1:+:2388140074:-1 chm1:+:2390762223:-1 chm1:+:2391740254:-1 chm1:+:2396427651:-1 chm1:+:2409343065:-1 chm1:+:2414083323:-1 chm1:+:2416628559:-1 chm1:+:2426614823:-1 chm1:+:2478682493:-1 chm1:+:2513276484:-1 chm1:+:2529256579:-1 chm1:+:2530463229:-1 chm1:+:2553991585:-1 chm1:+:2571411471:-1 chm1:+:2670499552:-1 chm1:+:2672059193:-1 chm1:+:2698297940:-1 chm1:+:2710140918:-1 chm1:+:2736460591:-1 chm1:+:2758766980:-1 chm1:+:2819365794:-1 chm1:+:2824362078:-1 chm1:+:2853715131:-1 chm1:+:2859902237:-1 chm1:+:2861660149:-1 chm1:+:2928194705:-1 chm1:+:2934789040:-1 chm1:+:2984515736:-1 chm1:+:3014635061:-1 +ATAATGAGGAAGACATTCCACCCCCTAACCCACCCCCGAGACGGAGTCTCACTCTGTCGCCCAGGCTGGAGTGCAATAGCGGCAGTCTTGGCGTCACTGTAACCTCTGCCTCCTAGATTCAAAGTGAATTCTCCTGCCTCAGCCTCCCAAGTAAGCTGGGATTACAGTCAAGCACCACCATGCCCAGCTGATTTTTGTAT chm1:+:89335252:-1 chm1:+:151145050:-1 chm1:+:221393871:-1 chm1:+:274565980:-1 chm1:+:299807374:-1 chm1:+:501909105:-1 chm1:+:526332455:-1 chm1:+:622238376:-1 chm1:+:1088869169:-1 chm1:+:1309397919:-1 chm1:+:1423030090:-1 chm1:+:1477452980:-1 chm1:+:1833474126:-1 chm1:+:1926217763:-1 chm1:+:2061432400:-1 chm1:+:2231134171:-1 chm1:+:2497882860:-1 chm1:+:2859407413:-1 chm1:+:2870184489:-1 +ATAATGAGGAAGACATTCCACCCCCTAACCCACCCCCGAGACGGAGTCTCACTCTGTCGCCCAGGCTGGAGTGCAATAGCGGCAGTCTTGGCGTCACTGTAACCTCTGCCTCCTAGATTCAAAGTGAATTCTCCTGCCTCAGCCTCCCAAGTAAGCTGGGATTACAGTCAAGCACCACCATGCCCAGCTGATTTTTGTAT chm1:+:36917381:-1 chm1:+:112126440:-1 chm1:+:120001942:-1 chm1:+:145406551:-1 chm1:+:194748684:-1 chm1:+:241091846:-1 chm1:+:254623040:-1 chm1:+:327481364:-1 chm1:+:409614939:-1 chm1:+:520876035:-1 chm1:+:580723903:-1 chm1:+:605954615:-1 chm1:+:645258165:-1 chm1:+:716462674:-1 chm1:+:748293054:-1 chm1:+:777991658:-1 chm1:+:811883844:-1 chm1:+:865967758:-1 chm1:+:1018678497:-1 chm1:+:1043806950:-1 chm1:+:1082299674:-1 chm1:+:1116206946:-1 chm1:+:1116549900:-1 chm1:+:1129491439:-1 chm1:+:1248184191:-1 chm1:+:1263372125:-1 chm1:+:1385334132:-1 chm1:+:1475042158:-1 chm1:+:1518126243:-1 chm1:+:1575719421:-1 chm1:+:1577642028:-1 chm1:+:1636258654:-1 chm1:+:1796414842:-1 chm1:+:1833451202:-1 chm1:+:1875473629:-1 chm1:+:1961198608:-1 chm1:+:2223047656:-1 chm1:+:2278176944:-1 chm1:+:2306888250:-1 chm1:+:2342301053:-1 chm1:+:2480669865:-1 chm1:+:2502625452:-1 chm1:+:2653650111:-1 chm1:+:2661918271:-1 chm1:+:2678558009:-1 chm1:+:2708950100:-1 chm1:+:2810249416:-1 chm1:+:2932531700:-1 chm1:+:2958136331:-1 +ATAATGAGGAAGACATTCCACCCCCTAACCCACCCCCGAGACGGAGTCTCACTCTGTCGCCCAGGCTGGAGTGCAATAGCGGCAGTCTTGGCGTCACTGTAACCTCTGCCTCCTAGATTCAAAGTGAATTCTCCTGCCTCAGCCTCCCAAGTAAGCTGGGATTACAGTCAAGCACCACCATGCCCAGCTGATTTTTGTAT chm1:+:39404869:-1 chm1:+:209438034:-1 chm1:+:374813842:-1 chm1:+:648940661:-1 chm1:+:766027996:-1 chm1:+:840042190:-1 chm1:+:887803396:-1 chm1:+:937986365:-1 chm1:+:960682112:-1 chm1:+:1014677264:-1 chm1:+:1016394467:-1 chm1:+:1060966751:-1 chm1:+:1115240827:-1 chm1:+:1384687031:-1 chm1:+:1484477759:-1 chm1:+:1501904191:-1 chm1:+:1517378939:-1 chm1:+:1636947073:-1 chm1:+:1668912867:-1 chm1:+:1703789980:-1 chm1:+:1718151306:-1 chm1:+:1728576324:-1 chm1:+:1732108901:-1 chm1:+:1940850377:-1 chm1:+:2002607680:-1 chm1:+:2084125841:-1 chm1:+:2420587097:-1 chm1:+:2440725343:-1 chm1:+:2544168264:-1 chm1:+:2572988853:-1 chm1:+:2576856745:-1 chm1:+:2580258203:-1 chm1:+:2719249202:-1 chm1:+:2754617490:-1 chm1:+:2874386594:-1 chm1:+:3001916859:-1 chm1:+:3023506887:-1 +ATAATGAGGAAGACATTCCACCCCCTAACCCACCCCCGAGACGGAGTCTCACTCTGTCGCCCAGGCTGGAGTGCAATAGCGGCAGTCTTGGCGTCACTGTAACCTCTGCCTCCTAGATTCAAAGTGAATTCTCCTGCCTCAGCCTCCCAAGTAAGCTGGGATTACAGTCAAGCACCACCATGCCCAGCTGATTTTTGTAT chm1:+:43720208:-1 chm1:+:345041189:-1 chm1:+:375111771:-1 chm1:+:901696163:-1 chm1:+:1126644974:-1 chm1:+:1307875554:-1 chm1:+:2059754163:-1 chm1:+:2277674283:-1 chm1:+:2444043453:-1 chm1:+:2527334483:-1 chm1:+:2585044674:-1 chm1:+:2593410196:-1 chm1:+:2661721821:-1 chm1:+:2905512057:-1 +ATACAAAAATCAGCTGGGCATGGTGGTGCTTGACTGTAATCCCAGCTTACTTGGGAGGCTGAGGCAGGAGAATTCACTTTGAATCTAGGAGGCAGAGGTTACAGTGACGCCAAGACTGCCGCTATTGCACTCCAGCCTGGGCGACAGAGTGAGACTCCGTCTCGGGGGTGGGTTAGGGGGTGGAATGTCTTCCTCATTAT chm1:+:171312685:-1 chm1:+:208361856:-1 chm1:+:233054388:-1 chm1:+:357664933:-1 chm1:+:428975683:-1 chm1:+:441199411:-1 chm1:+:515328737:-1 chm1:+:617177438:-1 chm1:+:739332397:-1 chm1:+:748314023:-1 chm1:+:1184700520:-1 chm1:+:1306728827:-1 chm1:+:1353876485:-1 chm1:+:1478533595:-1 chm1:+:1549281822:-1 chm1:+:1754449693:-1 chm1:+:2281956735:-1 chm1:+:2291209232:-1 chm1:+:2482188184:-1 chm1:+:2502350382:-1 chm1:+:2563468707:-1 chm1:+:2590033117:-1 chm1:+:2628569221:-1 chm1:+:2699396054:7 +ATACAAAAATCAGCTGGGCATGGTGGTGCTTGACTGTAATCCCAGCTTACTTGGGAGGCTGAGGCAGGAGAATTCACTTTGAATCTAGGAGGCAGAGGTTACAGTGACGCCAAGACTGCCGCTATTGCACTCCAGCCTGGGCGACAGAGTGAGACTCCGTCTCGGGGGTGGGTTAGGGGGTGGAATGTCTTCCTCATTAT chm1:+:2699396047:7 +TAGAAAAGACTCAATTCATCTGCACTGAATGAACCCACTGATGAGTATTTATCCAGAAATCACTTCATGTTTTCCAATCAATCTTCTGTGCCAGTGAACAATGAACTGCAGATAATTTACCAGAACAGGCTCTCTGTGTTGGAATAAGCTGGAGCCCCTTGAAACTATTCATTAGAACAGTAAAAAAATATAAGTATTCT chm1:+:198351051:-1 chm1:+:300785303:-1 chm1:+:412950958:-1 chm1:+:463218237:-1 chm1:+:512596119:-1 chm1:+:815533044:-1 chm1:+:1093986784:-1 chm1:+:1399089611:-1 chm1:+:1475083679:-1 chm1:+:1939844479:-1 chm1:+:2153922108:-1 chm1:+:2229624486:-1 chm1:+:2603306516:-1 chm1:+:2965189130:-1 +TAGAAAAGACTCAATTCATCTGCACTGAATGAACCCACTGATGAGTATTTATCCAGAAATCACTTCATGTTTTCCAATCAATCTTCTGTGCCAGTGAACAATGAACTGCAGATAATTTACCAGAACAGGCTCTCTGTGTTGGAATAAGCTGGAGCCCCTTGAAACTATTCATTAGAACAGTAAAAAAATATAAGTATTCT chm1:+:465868098:-1 chm1:+:997151858:-1 chm1:+:1216266303:-1 chm1:+:1459450455:-1 chm1:+:2502560872:-1 +TAGAAAAGACTCAATTCATCTGCACTGAATGAACCCACTGATGAGTATTTATCCAGAAATCACTTCATGTTTTCCAATCAATCTTCTGTGCCAGTGAACAATGAACTGCAGATAATTTACCAGAACAGGCTCTCTGTGTTGGAATAAGCTGGAGCCCCTTGAAACTATTCATTAGAACAGTAAAAAAATATAAGTATTCT chm1:+:377514654:-1 chm1:+:844415793:-1 chm1:+:1219038428:-1 chm1:+:1775929231:-1 chm1:+:2331772164:-1 chm1:+:2479134965:-1 chm1:+:2946797908:-1 +TAGAAAAGACTCAATTCATCTGCACTGAATGAACCCACTGATGAGTATTTATCCAGAAATCACTTCATGTTTTCCAATCAATCTTCTGTGCCAGTGAACAATGAACTGCAGATAATTTACCAGAACAGGCTCTCTGTGTTGGAATAAGCTGGAGCCCCTTGAAACTATTCATTAGAACAGTAAAAAAATATAAGTATTCT chm1:+:17497916:-1 chm1:+:31640155:-1 chm1:+:158642182:-1 chm1:+:323220190:-1 chm1:+:327477995:-1 chm1:+:421492037:-1 chm1:+:436066630:-1 chm1:+:521010996:-1 chm1:+:649099313:-1 chm1:+:811006580:-1 chm1:+:887514567:-1 chm1:+:1067978979:-1 chm1:+:1446384506:-1 chm1:+:1472134585:-1 chm1:+:1555609881:-1 chm1:+:1709530237:-1 chm1:+:1839506716:-1 chm1:+:1854541885:-1 chm1:+:1939717701:-1 chm1:+:2222622283:-1 chm1:+:2229435946:-1 chm1:+:2658592939:-1 chm1:+:2731673876:-1 chm1:+:2958727154:-1 chm1:+:2966120154:-1 +TAGAAAAGACTCAATTCATCTGCACTGAATGAACCCACTGATGAGTATTTATCCAGAAATCACTTCATGTTTTCCAATCAATCTTCTGTGCCAGTGAACAATGAACTGCAGATAATTTACCAGAACAGGCTCTCTGTGTTGGAATAAGCTGGAGCCCCTTGAAACTATTCATTAGAACAGTAAAAAAATATAAGTATTCT chm1:+:55745952:-1 chm1:+:192597661:-1 chm1:+:297413801:-1 chm1:+:319579706:-1 chm1:+:556548999:-1 chm1:+:586611505:-1 chm1:+:629194223:-1 chm1:+:748250462:-1 chm1:+:1042477451:-1 chm1:+:1058731336:-1 chm1:+:1129205230:-1 chm1:+:1220777181:-1 chm1:+:1230962834:-1 chm1:+:1338397375:-1 chm1:+:1492865531:-1 chm1:+:1691768501:-1 chm1:+:1701396347:-1 chm1:+:1783107935:-1 chm1:+:1853695449:-1 chm1:+:1954283815:-1 chm1:+:2025429791:-1 chm1:+:2059878829:-1 chm1:+:2075044497:-1 chm1:+:2220452805:-1 chm1:+:2512838825:-1 chm1:+:2520533781:-1 chm1:+:2817951728:-1 chm1:+:2910168456:-1 +AGAATACTTATATTTTTTTACTGTTCTAATGAATAGTTTCAAGGGGCTCCAGCTTATTCCAACACAGAGAGCCTGTTCTGGTAAATTATCTGCAGTTCATTGTTCACTGGCACAGAAGATTGATTGGAAAACATGAAGTGATTTCTGGATAAATACTCATCAGTGGGTTCATTCAGTGCAGATGAATTGAGTCTTTTCTA chm1:+:1029798504:-1 chm1:+:1211710776:7 chm1:+:1337156084:-1 +AGAATACTTATATTTTTTTACTGTTCTAATGAATAGTTTCAAGGGGCTCCAGCTTATTCCAACACAGAGAGCCTGTTCTGGTAAATTATCTGCAGTTCATTGTTCACTGGCACAGAAGATTGATTGGAAAACATGAAGTGATTTCTGGATAAATACTCATCAGTGGGTTCATTCAGTGCAGATGAATTGAGTCTTTTCTA chm1:+:1211710775:7 +TAGCATGTTTTATAGTCCACCAAATAACTTGGGAATTTAATTAACTACCATCAATTCATTCATATTTTCCATTTTCGTTAGGAATCAAGCCAGGTTTGAGACCTAGCTGGTAATCAGGAAGCTTGGGAAATGCCTTCTTAACAAAAGAGATATGGACGAAACATGTTTTGTATATAATGACTACACCAAAGTCATTTGCC chm1:+:601885583:-1 +TAGCATGTTTTATAGTCCACCAAATAACTTGGGAATTTAATTAACTACCATCAATTCATTCATATTTTCCATTTTCGTTAGGAATCAAGCCAGGTTTGAGACCTAGCTGGTAATCAGGAAGCTTGGGAAATGCCTTCTTAACAAAAGAGATATGGACGAAACATGTTTTGTATATAATGACTACACCAAAGTCATTTGCC chm1:+:485832647:-1 chm1:+:669307159:-1 chm1:+:795883035:-1 chm1:+:851999440:-1 chm1:+:900899109:-1 chm1:+:1256522450:-1 chm1:+:1569791468:-1 chm1:+:1764571871:-1 chm1:+:2010708029:-1 chm1:+:2049473578:-1 chm1:+:2124741450:-1 chm1:+:2222241163:-1 chm1:+:2428657717:-1 chm1:+:2461663136:-1 chm1:+:2852462821:-1 chm1:+:2852513917:-1 chm1:+:2888501172:-1 +TAGCATGTTTTATAGTCCACCAAATAACTTGGGAATTTAATTAACTACCATCAATTCATTCATATTTTCCATTTTCGTTAGGAATCAAGCCAGGTTTGAGACCTAGCTGGTAATCAGGAAGCTTGGGAAATGCCTTCTTAACAAAAGAGATATGGACGAAACATGTTTTGTATATAATGACTACACCAAAGTCATTTGCC chm1:+:71669143:-1 chm1:+:247867322:-1 chm1:+:300625447:-1 chm1:+:373443628:-1 chm1:+:381147299:-1 chm1:+:400488665:-1 chm1:+:504533485:-1 chm1:+:505497310:-1 chm1:+:527056521:-1 chm1:+:569451795:-1 chm1:+:654426829:-1 chm1:+:658431760:-1 chm1:+:759573690:-1 chm1:+:785695854:-1 chm1:+:804193214:-1 chm1:+:912833315:-1 chm1:+:1000966902:-1 chm1:+:1038084257:-1 chm1:+:1217314080:-1 chm1:+:1316362184:-1 chm1:+:1431348769:-1 chm1:+:1483372134:-1 chm1:+:1511059193:-1 chm1:+:1571019930:-1 chm1:+:1638761220:-1 chm1:+:1655634245:-1 chm1:+:1822761690:-1 chm1:+:1911675134:-1 chm1:+:2020255602:-1 chm1:+:2053851756:-1 chm1:+:2132984206:-1 chm1:+:2219312850:-1 chm1:+:2456537211:-1 chm1:+:2485928047:-1 chm1:+:2529706961:-1 chm1:+:2557052405:-1 chm1:+:2646997149:-1 chm1:+:2653772774:-1 chm1:+:2991033880:-1 +TAGCATGTTTTATAGTCCACCAAATAACTTGGGAATTTAATTAACTACCATCAATTCATTCATATTTTCCATTTTCGTTAGGAATCAAGCCAGGTTTGAGACCTAGCTGGTAATCAGGAAGCTTGGGAAATGCCTTCTTAACAAAAGAGATATGGACGAAACATGTTTTGTATATAATGACTACACCAAAGTCATTTGCC chm1:+:52297505:-1 chm1:+:75160092:-1 chm1:+:88257114:-1 chm1:+:101516589:-1 chm1:+:240702660:-1 chm1:+:328233900:-1 chm1:+:405533646:-1 chm1:+:520885065:-1 chm1:+:599051785:-1 chm1:+:675509400:-1 chm1:+:734364197:-1 chm1:+:736513964:-1 chm1:+:761130250:-1 chm1:+:897755316:-1 chm1:+:902821452:-1 chm1:+:927142152:-1 chm1:+:987867512:-1 chm1:+:1027374735:-1 chm1:+:1100292547:-1 chm1:+:1131600414:-1 chm1:+:1379132052:-1 chm1:+:1434634054:-1 chm1:+:1478356589:-1 chm1:+:1665142031:-1 chm1:+:1789086496:-1 chm1:+:1834843626:-1 chm1:+:2023034113:-1 chm1:+:2032329255:-1 chm1:+:2046380720:-1 chm1:+:2337101128:-1 chm1:+:2619035624:-1 chm1:+:2780402935:-1 chm1:+:2955325264:-1 chm1:+:3051998643:-1 chm1:+:3058196207:-1 +TAGCATGTTTTATAGTCCACCAAATAACTTGGGAATTTAATTAACTACCATCAATTCATTCATATTTTCCATTTTCGTTAGGAATCAAGCCAGGTTTGAGACCTAGCTGGTAATCAGGAAGCTTGGGAAATGCCTTCTTAACAAAAGAGATATGGACGAAACATGTTTTGTATATAATGACTACACCAAAGTCATTTGCC chm1:+:190108728:-1 chm1:+:407567966:-1 chm1:+:516287118:-1 chm1:+:705467187:-1 chm1:+:1290364057:-1 chm1:+:1315851478:-1 chm1:+:1565406626:-1 chm1:+:1716969814:-1 chm1:+:1938686433:-1 chm1:+:1978528109:-1 chm1:+:2162431403:-1 chm1:+:2359212254:-1 chm1:+:2432120155:-1 chm1:+:2496896975:-1 chm1:+:2567287065:-1 chm1:+:3027902224:-1 +GGCAAATGACTTTGGTGTAGTCATTATATACAAAACATGTTTCGTCCATATCTCTTTTGTTAAGAAGGCATTTCCCAAGCTTCCTGATTACCAGCTAGGTCTCAAACCTGGCTTGATTCCTAACGAAAATGGAAAATATGAATGAATTGATGGTAGTTAATTAAATTCCCAAGTTATTTGGTGGACTATAAAACATGCTA chm1:+:805276308:9 +GGCAAATGACTTTGGTGTAGTCATTATATACAAAACATGTTTCGTCCATATCTCTTTTGTTAAGAAGGCATTTCCCAAGCTTCCTGATTACCAGCTAGGTCTCAAACCTGGCTTGATTCCTAACGAAAATGGAAAATATGAATGAATTGATGGTAGTTAATTAAATTCCCAAGTTATTTGGTGGACTATAAAACATGCTA chm1:+:1304336337:-1 +GGCAAATGACTTTGGTGTAGTCATTATATACAAAACATGTTTCGTCCATATCTCTTTTGTTAAGAAGGCATTTCCCAAGCTTCCTGATTACCAGCTAGGTCTCAAACCTGGCTTGATTCCTAACGAAAATGGAAAATATGAATGAATTGATGGTAGTTAATTAAATTCCCAAGTTATTTGGTGGACTATAAAACATGCTA chm1:+:805276307:9 +CATGGATAGTTTTTGCTGTATCTCCTAATTCAACGTATAAACTCGCTTAGGAAATATAACCCAGTTTGAATTTTCTTTGTATAGGTGTAAAAGATCTTAACCCACATATAATGTGTCAGTTATGGAACAAATTATCCATGTTATCCCGTGCATGTTCTTTGTGTCTTGACCTCTGTTATTATTTCAAGTTGGGTTTGGAT chm1:+:703866219:-1 chm1:+:1113606626:-1 chm1:+:2643374489:-1 +CATGGATAGTTTTTGCTGTATCTCCTAATTCAACGTATAAACTCGCTTAGGAAATATAACCCAGTTTGAATTTTCTTTGTATAGGTGTAAAAGATCTTAACCCACATATAATGTGTCAGTTATGGAACAAATTATCCATGTTATCCCGTGCATGTTCTTTGTGTCTTGACCTCTGTTATTATTTCAAGTTGGGTTTGGAT chm1:+:35547538:-1 chm1:+:327546352:-1 chm1:+:569894098:-1 chm1:+:1690380351:-1 chm1:+:2380808130:-1 chm1:+:3025731154:-1 +CATGGATAGTTTTTGCTGTATCTCCTAATTCAACGTATAAACTCGCTTAGGAAATATAACCCAGTTTGAATTTTCTTTGTATAGGTGTAAAAGATCTTAACCCACATATAATGTGTCAGTTATGGAACAAATTATCCATGTTATCCCGTGCATGTTCTTTGTGTCTTGACCTCTGTTATTATTTCAAGTTGGGTTTGGAT chm1:+:906181415:-1 chm1:+:957445394:-1 chm1:+:1393603080:-1 chm1:+:2343138639:-1 +CATGGATAGTTTTTGCTGTATCTCCTAATTCAACGTATAAACTCGCTTAGGAAATATAACCCAGTTTGAATTTTCTTTGTATAGGTGTAAAAGATCTTAACCCACATATAATGTGTCAGTTATGGAACAAATTATCCATGTTATCCCGTGCATGTTCTTTGTGTCTTGACCTCTGTTATTATTTCAAGTTGGGTTTGGAT chm1:+:438662562:-1 chm1:+:669162892:-1 +CATGGATAGTTTTTGCTGTATCTCCTAATTCAACGTATAAACTCGCTTAGGAAATATAACCCAGTTTGAATTTTCTTTGTATAGGTGTAAAAGATCTTAACCCACATATAATGTGTCAGTTATGGAACAAATTATCCATGTTATCCCGTGCATGTTCTTTGTGTCTTGACCTCTGTTATTATTTCAAGTTGGGTTTGGAT chm1:+:74464728:-1 chm1:+:174585273:-1 chm1:+:380304597:-1 chm1:+:389274204:-1 chm1:+:427201120:-1 chm1:+:612512197:-1 chm1:+:614805280:-1 chm1:+:651309482:-1 chm1:+:730194374:-1 chm1:+:821634983:-1 chm1:+:852424916:-1 chm1:+:911055361:-1 chm1:+:1052990498:-1 chm1:+:1200386680:-1 chm1:+:1284211148:-1 chm1:+:1350783303:-1 chm1:+:1354680307:-1 chm1:+:1462533494:-1 chm1:+:1488229885:-1 chm1:+:1495226386:-1 chm1:+:1514653249:-1 chm1:+:1622568030:-1 chm1:+:1716587458:-1 chm1:+:1832112718:-1 chm1:+:1897612872:-1 chm1:+:2186304853:-1 chm1:+:2564079104:-1 chm1:+:2593999678:-1 chm1:+:2632531130:-1 chm1:+:2937875411:-1 +ATCCAAACCCAACTTGAAATAATAACAGAGGTCAAGACACAAAGAACATGCACGGGATAACATGGATAATTTGTTCCATAACTGACACATTATATGTGGGTTAAGATCTTTTACACCTATACAAAGAAAATTCAAACTGGGTTATATTTCCTAAGCGAGTTTATACGTTGAATTAGGAGATACAGCAAAAACTATCCATG chm1:+:185760752:-1 chm1:+:647482794:-1 chm1:+:890879176:12 +ATCCAAACCCAACTTGAAATAATAACAGAGGTCAAGACACAAAGAACATGCACGGGATAACATGGATAATTTGTTCCATAACTGACACATTATATGTGGGTTAAGATCTTTTACACCTATACAAAGAAAATTCAAACTGGGTTATATTTCCTAAGCGAGTTTATACGTTGAATTAGGAGATACAGCAAAAACTATCCATG chm1:+:890879178:12 +ATCGTTCCTAAAATCACAGAGCTACGAGGGGCAGAGACAGGTTTCACCCAGGACTGTCTGGCTCCTAAAAGCCCACAATACCTCTCCTCAGCATCAAGGTCTGGTATCAATGAGACATATTCTAAGGTACCATTTGGGATTATTTTCTTACAAAGATACAGCATGTCCTGATGATAAACCATCTTACATAAGACTCACCT chm1:+:25421131:-1 chm1:+:118362533:-1 chm1:+:242150505:-1 chm1:+:281993382:-1 chm1:+:387670388:-1 chm1:+:410531263:-1 chm1:+:453436434:-1 chm1:+:500334172:-1 chm1:+:534498856:-1 chm1:+:557476177:-1 chm1:+:670086918:-1 chm1:+:675511264:-1 chm1:+:1021386187:-1 chm1:+:1058209518:-1 chm1:+:1092121862:-1 chm1:+:1174665704:-1 chm1:+:1237958809:-1 chm1:+:1283806110:-1 chm1:+:1300274727:-1 chm1:+:1510022444:-1 chm1:+:1574276946:-1 chm1:+:1703503558:-1 chm1:+:1780784783:-1 chm1:+:1816371985:-1 chm1:+:1845202020:-1 chm1:+:1923302330:-1 chm1:+:1952644387:-1 chm1:+:1962410827:-1 chm1:+:2000987822:-1 chm1:+:2075162628:-1 chm1:+:2282691395:-1 chm1:+:2437166128:-1 chm1:+:2499413777:-1 chm1:+:2517366458:-1 chm1:+:2610600596:-1 chm1:+:2743924738:-1 chm1:+:2756078033:-1 chm1:+:2770955815:-1 chm1:+:2825813141:-1 chm1:+:2875344304:-1 chm1:+:2911081021:-1 chm1:+:2985386421:-1 +ATCGTTCCTAAAATCACAGAGCTACGAGGGGCAGAGACAGGTTTCACCCAGGACTGTCTGGCTCCTAAAAGCCCACAATACCTCTCCTCAGCATCAAGGTCTGGTATCAATGAGACATATTCTAAGGTACCATTTGGGATTATTTTCTTACAAAGATACAGCATGTCCTGATGATAAACCATCTTACATAAGACTCACCT chm1:+:68054461:-1 chm1:+:194434013:-1 chm1:+:240327600:-1 chm1:+:280796943:-1 chm1:+:304234253:-1 chm1:+:386932954:-1 chm1:+:407475059:-1 chm1:+:461851014:-1 chm1:+:575257001:-1 chm1:+:753680155:-1 chm1:+:805174816:-1 chm1:+:806958204:-1 chm1:+:828269139:-1 chm1:+:844171836:-1 chm1:+:883222073:-1 chm1:+:961624163:-1 chm1:+:995858991:-1 chm1:+:1076483983:-1 chm1:+:1111349867:-1 chm1:+:1129868713:-1 chm1:+:1187621026:-1 chm1:+:1214138630:-1 chm1:+:1279062472:-1 chm1:+:1389125267:-1 chm1:+:1476685618:-1 chm1:+:1486037917:-1 chm1:+:1491785861:-1 chm1:+:1510141976:-1 chm1:+:1530366556:-1 chm1:+:1646274282:-1 chm1:+:1691910931:-1 chm1:+:1755047902:-1 chm1:+:1770614193:-1 chm1:+:1971715804:-1 chm1:+:1972176713:-1 chm1:+:2137792252:-1 chm1:+:2151383411:-1 chm1:+:2151920557:-1 chm1:+:2246719820:-1 chm1:+:2362401706:-1 chm1:+:2371119821:-1 chm1:+:2614753057:-1 chm1:+:2702654916:-1 chm1:+:2702947015:-1 chm1:+:2703106973:-1 chm1:+:2816665402:-1 chm1:+:2909677143:-1 +ATCGTTCCTAAAATCACAGAGCTACGAGGGGCAGAGACAGGTTTCACCCAGGACTGTCTGGCTCCTAAAAGCCCACAATACCTCTCCTCAGCATCAAGGTCTGGTATCAATGAGACATATTCTAAGGTACCATTTGGGATTATTTTCTTACAAAGATACAGCATGTCCTGATGATAAACCATCTTACATAAGACTCACCT chm1:+:405290913:-1 chm1:+:957081103:-1 chm1:+:1264472748:-1 chm1:+:1682484846:-1 chm1:+:2502353885:-1 +ATCGTTCCTAAAATCACAGAGCTACGAGGGGCAGAGACAGGTTTCACCCAGGACTGTCTGGCTCCTAAAAGCCCACAATACCTCTCCTCAGCATCAAGGTCTGGTATCAATGAGACATATTCTAAGGTACCATTTGGGATTATTTTCTTACAAAGATACAGCATGTCCTGATGATAAACCATCTTACATAAGACTCACCT chm1:+:70061968:-1 chm1:+:109997399:-1 chm1:+:263036641:-1 chm1:+:325984656:-1 chm1:+:450842198:-1 chm1:+:512940947:-1 chm1:+:525950581:-1 chm1:+:537262362:-1 chm1:+:660467571:-1 chm1:+:714048551:-1 chm1:+:846258866:-1 chm1:+:846343581:-1 chm1:+:848918448:-1 chm1:+:978766355:-1 chm1:+:1079730047:-1 chm1:+:1174025961:-1 chm1:+:1232333808:-1 chm1:+:1509365917:-1 chm1:+:1520028074:-1 chm1:+:1527700028:-1 chm1:+:1558516820:-1 chm1:+:1686436507:-1 chm1:+:1931500309:-1 chm1:+:1947861750:-1 chm1:+:1960579465:-1 chm1:+:1980209010:-1 chm1:+:2174661992:-1 chm1:+:2584714365:-1 chm1:+:2615196741:-1 chm1:+:2681738738:-1 chm1:+:2803749684:-1 chm1:+:2937446677:-1 chm1:+:2949841377:-1 chm1:+:2997696433:-1 chm1:+:3006101064:-1 chm1:+:3051111291:-1 chm1:+:3058865875:-1 +ATCGTTCCTAAAATCACAGAGCTACGAGGGGCAGAGACAGGTTTCACCCAGGACTGTCTGGCTCCTAAAAGCCCACAATACCTCTCCTCAGCATCAAGGTCTGGTATCAATGAGACATATTCTAAGGTACCATTTGGGATTATTTTCTTACAAAGATACAGCATGTCCTGATGATAAACCATCTTACATAAGACTCACCT chm1:+:14338481:-1 chm1:+:290677882:-1 chm1:+:555720044:-1 chm1:+:753031339:-1 chm1:+:923602579:-1 chm1:+:979593127:-1 chm1:+:1138723646:-1 chm1:+:1268715114:-1 chm1:+:1509256047:-1 chm1:+:1625674128:-1 chm1:+:1647896294:-1 chm1:+:1715957864:-1 chm1:+:1746191513:-1 chm1:+:2050884686:-1 chm1:+:2511660290:-1 chm1:+:2531094494:-1 chm1:+:2802484951:-1 chm1:+:2828067927:-1 chm1:+:2967156655:-1 chm1:+:2967255006:-1 chm1:+:3035869326:-1 +ATCGTTCCTAAAATCACAGAGCTACGAGGGGCAGAGACAGGTTTCACCCAGGACTGTCTGGCTCCTAAAAGCCCACAATACCTCTCCTCAGCATCAAGGTCTGGTATCAATGAGACATATTCTAAGGTACCATTTGGGATTATTTTCTTACAAAGATACAGCATGTCCTGATGATAAACCATCTTACATAAGACTCACCT chm1:+:877096739:-1 chm1:+:1286300206:-1 chm1:+:2334250277:-1 chm1:+:2531694991:-1 +AGGTGAGTCTTATGTAAGATGGTTTATCATCAGGACATGCTGTATCTTTGTAAGAAAATAATCCCAAATGGTACCTTAGAATATGTCTCATTGATACCAGACCTTGATGCTGAGGAGAGGTATTGTGGGCTTTTAGGAGCCAGACAGTCCTGGGTGAAACCTGTCTCTGCCCCTCGTAGCTCTGTGATTTTAGGAACGAT chm1:+:2399725730:6 +AGGTGAGTCTTATGTAAGATGGTTTATCATCAGGACATGCTGTATCTTTGTAAGAAAATAATCCCAAATGGTACCTTAGAATATGTCTCATTGATACCAGACCTTGATGCTGAGGAGAGGTATTGTGGGCTTTTAGGAGCCAGACAGTCCTGGGTGAAACCTGTCTCTGCCCCTCGTAGCTCTGTGATTTTAGGAACGAT chm1:+:2399725725:6 +AGGTGAGTCTTATGTAAGATGGTTTATCATCAGGACATGCTGTATCTTTGTAAGAAAATAATCCCAAATGGTACCTTAGAATATGTCTCATTGATACCAGACCTTGATGCTGAGGAGAGGTATTGTGGGCTTTTAGGAGCCAGACAGTCCTGGGTGAAACCTGTCTCTGCCCCTCGTAGCTCTGTGATTTTAGGAACGAT chm1:+:2399725726:6 +GCCTGGCCCTATTTTTCTTTATATGAGTAGTAACTTTTATTTAAAATGATTTTTTAAAAATGCCTTTTTTTCTTTTAGTTCTAGTTCACCATTGACTTTACAAGCAGATTTGAAGTAACATACTTGGAGAAACAGTTTTCTAAATCTTCCAGAGCTGACACACCAGGTAATGGAGAAGACTTTTTCCTAATGGAAAAGCA chm1:+:989428902:-1 chm1:+:1298518074:-1 chm1:+:1735739316:-1 chm1:+:2914564555:-1 +GCCTGGCCCTATTTTTCTTTATATGAGTAGTAACTTTTATTTAAAATGATTTTTTAAAAATGCCTTTTTTTCTTTTAGTTCTAGTTCACCATTGACTTTACAAGCAGATTTGAAGTAACATACTTGGAGAAACAGTTTTCTAAATCTTCCAGAGCTGACACACCAGGTAATGGAGAAGACTTTTTCCTAATGGAAAAGCA chm1:+:937867428:-1 chm1:+:1307400004:-1 chm1:+:1991478207:-1 chm1:+:2999583362:-1 +GCCTGGCCCTATTTTTCTTTATATGAGTAGTAACTTTTATTTAAAATGATTTTTTAAAAATGCCTTTTTTTCTTTTAGTTCTAGTTCACCATTGACTTTACAAGCAGATTTGAAGTAACATACTTGGAGAAACAGTTTTCTAAATCTTCCAGAGCTGACACACCAGGTAATGGAGAAGACTTTTTCCTAATGGAAAAGCA chm1:+:2180316796:-1 chm1:+:2820103687:13 +GCCTGGCCCTATTTTTCTTTATATGAGTAGTAACTTTTATTTAAAATGATTTTTTAAAAATGCCTTTTTTTCTTTTAGTTCTAGTTCACCATTGACTTTACAAGCAGATTTGAAGTAACATACTTGGAGAAACAGTTTTCTAAATCTTCCAGAGCTGACACACCAGGTAATGGAGAAGACTTTTTCCTAATGGAAAAGCA chm1:+:2820103689:13 +GCCTGGCCCTATTTTTCTTTATATGAGTAGTAACTTTTATTTAAAATGATTTTTTAAAAATGCCTTTTTTTCTTTTAGTTCTAGTTCACCATTGACTTTACAAGCAGATTTGAAGTAACATACTTGGAGAAACAGTTTTCTAAATCTTCCAGAGCTGACACACCAGGTAATGGAGAAGACTTTTTCCTAATGGAAAAGCA chm1:+:1330625261:-1 chm1:+:2410308308:-1 +TGCTTTTCCATTAGGAAAAAGTCTTCTCCATTACCTGGTGTGTCAGCTCTGGAAGATTTAGAAAACTGTTTCTCCAAGTATGTTACTTCAAATCTGCTTGTAAAGTCAATGGTGAACTAGAACTAAAAGAAAAAAAGGCATTTTTAAAAAATCATTTTAAATAAAAGTTACTACTCATATAAAGAAAAATAGGGCCAGGC chm1:+:1099764697:-1 chm1:+:2415143383:-1 chm1:+:2538302026:-1 chm1:+:2539174168:-1 chm1:+:2732156669:-1 +TGCTTTTCCATTAGGAAAAAGTCTTCTCCATTACCTGGTGTGTCAGCTCTGGAAGATTTAGAAAACTGTTTCTCCAAGTATGTTACTTCAAATCTGCTTGTAAAGTCAATGGTGAACTAGAACTAAAAGAAAAAAAGGCATTTTTAAAAAATCATTTTAAATAAAAGTTACTACTCATATAAAGAAAAATAGGGCCAGGC chm1:+:112810396:-1 chm1:+:120681400:-1 chm1:+:219886120:-1 chm1:+:263038727:-1 chm1:+:285666443:-1 chm1:+:314285384:-1 chm1:+:506129609:-1 chm1:+:521957687:-1 chm1:+:564553416:-1 chm1:+:605781458:-1 chm1:+:658890942:-1 chm1:+:660709978:-1 chm1:+:668518841:-1 chm1:+:689455938:-1 chm1:+:726724613:-1 chm1:+:757029174:-1 chm1:+:846345422:-1 chm1:+:875035227:-1 chm1:+:880428258:-1 chm1:+:884682187:-1 chm1:+:913967553:-1 chm1:+:921840681:-1 chm1:+:921896934:-1 chm1:+:984160110:-1 chm1:+:1051244974:-1 chm1:+:1077188647:-1 chm1:+:1098204069:-1 chm1:+:1116742391:-1 chm1:+:1174028508:-1 chm1:+:1218544629:-1 chm1:+:1243702708:-1 chm1:+:1247068406:-1 chm1:+:1258531536:-1 chm1:+:1315442304:-1 chm1:+:1347652899:-1 chm1:+:1403319221:-1 chm1:+:1443616806:-1 chm1:+:1552713802:-1 chm1:+:1685305709:-1 chm1:+:1768015505:-1 chm1:+:1772398094:-1 chm1:+:1845117749:-1 chm1:+:1894033944:-1 chm1:+:1996987977:-1 chm1:+:2156240295:-1 chm1:+:2481260671:-1 chm1:+:2551214739:-1 chm1:+:2610182327:-1 chm1:+:2725920880:-1 chm1:+:2868889459:-1 chm1:+:2897055851:-1 chm1:+:3025918557:-1 +TGCTTTTCCATTAGGAAAAAGTCTTCTCCATTACCTGGTGTGTCAGCTCTGGAAGATTTAGAAAACTGTTTCTCCAAGTATGTTACTTCAAATCTGCTTGTAAAGTCAATGGTGAACTAGAACTAAAAGAAAAAAAGGCATTTTTAAAAAATCATTTTAAATAAAAGTTACTACTCATATAAAGAAAAATAGGGCCAGGC chm1:+:767399310:-1 chm1:+:990024063:-1 chm1:+:1379981822:-1 chm1:+:1549689739:-1 chm1:+:2955998518:-1 +TGCTTTTCCATTAGGAAAAAGTCTTCTCCATTACCTGGTGTGTCAGCTCTGGAAGATTTAGAAAACTGTTTCTCCAAGTATGTTACTTCAAATCTGCTTGTAAAGTCAATGGTGAACTAGAACTAAAAGAAAAAAAGGCATTTTTAAAAAATCATTTTAAATAAAAGTTACTACTCATATAAAGAAAAATAGGGCCAGGC chm1:+:24996053:-1 chm1:+:379584770:-1 chm1:+:1762910082:-1 chm1:+:1970935303:-1 +ACAGTAGCTTAAAGCTGAGCACTTTCCTTGCCCAGCACTGTGCCTTGGTGCTTTTTTGATCTCACACCAAGCTCTCTCGTGTGTTATTCTTATTCCCATTTTCTAGACGAGCAACCTGAGGCTAATAGAGATCAAGAAACTTGCCAGGGATCCCATGGACAAAGCAACCAGAAGTCTAGACTCAGATCTGACTCCAGAGA chm1:+:1862816357:15 +ACAGTAGCTTAAAGCTGAGCACTTTCCTTGCCCAGCACTGTGCCTTGGTGCTTTTTTGATCTCACACCAAGCTCTCTCGTGTGTTATTCTTATTCCCATTTTCTAGACGAGCAACCTGAGGCTAATAGAGATCAAGAAACTTGCCAGGGATCCCATGGACAAAGCAACCAGAAGTCTAGACTCAGATCTGACTCCAGAGA chm1:+:1862816356:15 chm1:+:2032536361:-1 chm1:+:2416570066:-1 +ACAGTAGCTTAAAGCTGAGCACTTTCCTTGCCCAGCACTGTGCCTTGGTGCTTTTTTGATCTCACACCAAGCTCTCTCGTGTGTTATTCTTATTCCCATTTTCTAGACGAGCAACCTGAGGCTAATAGAGATCAAGAAACTTGCCAGGGATCCCATGGACAAAGCAACCAGAAGTCTAGACTCAGATCTGACTCCAGAGA chm1:+:63580379:-1 chm1:+:543018597:-1 chm1:+:2874759580:-1 +ACAGTAGCTTAAAGCTGAGCACTTTCCTTGCCCAGCACTGTGCCTTGGTGCTTTTTTGATCTCACACCAAGCTCTCTCGTGTGTTATTCTTATTCCCATTTTCTAGACGAGCAACCTGAGGCTAATAGAGATCAAGAAACTTGCCAGGGATCCCATGGACAAAGCAACCAGAAGTCTAGACTCAGATCTGACTCCAGAGA chm1:+:1862816355:15 +ACAGTAGCTTAAAGCTGAGCACTTTCCTTGCCCAGCACTGTGCCTTGGTGCTTTTTTGATCTCACACCAAGCTCTCTCGTGTGTTATTCTTATTCCCATTTTCTAGACGAGCAACCTGAGGCTAATAGAGATCAAGAAACTTGCCAGGGATCCCATGGACAAAGCAACCAGAAGTCTAGACTCAGATCTGACTCCAGAGA chm1:+:3007052448:-1 +TCTCTGGAGTCAGATCTGAGTCTAGACTTCTGGTTGCTTTGTCCATGGGATCCCTGGCAAGTTTCTTGATCTCTATTAGCCTCAGGTTGCTCGTCTAGAAAATGGGAATAAGAATAACACACGAGAGAGCTTGGTGTGAGATCAAAAAAGCACCAAGGCACAGTGCTGGGCAAGGAAAGTGCTCAGCTTTAAGCTACTGT chm1:+:186914738:-1 chm1:+:533340263:-1 chm1:+:553573606:-1 chm1:+:673939522:-1 chm1:+:912512403:-1 chm1:+:999248231:-1 chm1:+:1029880962:-1 chm1:+:1270585088:-1 chm1:+:1285247954:-1 chm1:+:1523297508:-1 chm1:+:1862149833:-1 chm1:+:1940421869:-1 chm1:+:2064147858:-1 chm1:+:2066860802:-1 chm1:+:2261644559:-1 chm1:+:2569057141:-1 chm1:+:2619681436:-1 chm1:+:2706639602:-1 +TCTCTGGAGTCAGATCTGAGTCTAGACTTCTGGTTGCTTTGTCCATGGGATCCCTGGCAAGTTTCTTGATCTCTATTAGCCTCAGGTTGCTCGTCTAGAAAATGGGAATAAGAATAACACACGAGAGAGCTTGGTGTGAGATCAAAAAAGCACCAAGGCACAGTGCTGGGCAAGGAAAGTGCTCAGCTTTAAGCTACTGT chm1:+:269842641:-1 chm1:+:486450278:-1 chm1:+:516825418:-1 chm1:+:800648402:-1 chm1:+:1033333407:-1 chm1:+:1078342036:-1 chm1:+:1370991056:-1 chm1:+:1800474993:-1 chm1:+:2123975955:-1 chm1:+:2762501062:-1 +TCTCTGGAGTCAGATCTGAGTCTAGACTTCTGGTTGCTTTGTCCATGGGATCCCTGGCAAGTTTCTTGATCTCTATTAGCCTCAGGTTGCTCGTCTAGAAAATGGGAATAAGAATAACACACGAGAGAGCTTGGTGTGAGATCAAAAAAGCACCAAGGCACAGTGCTGGGCAAGGAAAGTGCTCAGCTTTAAGCTACTGT chm1:+:386515839:-1 chm1:+:687565066:-1 chm1:+:1783178287:-1 chm1:+:1891980235:-1 chm1:+:2159667112:-1 chm1:+:2160065008:-1 +TCTCTGGAGTCAGATCTGAGTCTAGACTTCTGGTTGCTTTGTCCATGGGATCCCTGGCAAGTTTCTTGATCTCTATTAGCCTCAGGTTGCTCGTCTAGAAAATGGGAATAAGAATAACACACGAGAGAGCTTGGTGTGAGATCAAAAAAGCACCAAGGCACAGTGCTGGGCAAGGAAAGTGCTCAGCTTTAAGCTACTGT chm1:+:615516994:-1 +AGAAAAAACAGTAAACGACCCTGAATGGTAACAGTATGGATCCAAAGGAGAGGGTTGGCAGGCATGAGAGGTGGGTTAGATCTAGCAGGATATAACACTTTGGGGACCCAAAATAAACAACCCTATAAGGGAGGGGCTTGAGAGATACATGACTTAAGCAGCAGCACACAGAAATGCTCGTGTGTTCATCAACAGGAAAA chm1:+:864338060:-1 chm1:+:1642307239:-1 chm1:+:1805787734:-1 chm1:+:1931382608:-1 chm1:+:2270397726:-1 chm1:+:2665522528:-1 chm1:+:2801377805:-1 chm1:+:2956957138:-1 chm1:+:2966243874:-1 +AGAAAAAACAGTAAACGACCCTGAATGGTAACAGTATGGATCCAAAGGAGAGGGTTGGCAGGCATGAGAGGTGGGTTAGATCTAGCAGGATATAACACTTTGGGGACCCAAAATAAACAACCCTATAAGGGAGGGGCTTGAGAGATACATGACTTAAGCAGCAGCACACAGAAATGCTCGTGTGTTCATCAACAGGAAAA chm1:+:720802975:-1 chm1:+:1511081291:-1 chm1:+:1543205998:10 chm1:+:1882410070:-1 chm1:+:1903103110:-1 +AGAAAAAACAGTAAACGACCCTGAATGGTAACAGTATGGATCCAAAGGAGAGGGTTGGCAGGCATGAGAGGTGGGTTAGATCTAGCAGGATATAACACTTTGGGGACCCAAAATAAACAACCCTATAAGGGAGGGGCTTGAGAGATACATGACTTAAGCAGCAGCACACAGAAATGCTCGTGTGTTCATCAACAGGAAAA chm1:+:1543206002:10 +AATCCAAATTTGGGCAAGATGAGAGTTTTCTACTATTTTAATGTTCACATAGTGAAAAAGAAAAGTTAATTAAAAATGCTTGAAATGTCCAGTGCATTTGATCTGTATACTATCTTTACTTCTTAAAATTGCTATACATTAAGTCAATATAATCATATAAATGCAATTCTAAATACGTTCGTTACAAACACATTTGGAGG chm1:+:821084135:-1 chm1:+:1998275839:-1 chm1:+:2644227288:9 chm1:+:2883316736:-1 +AATCCAAATTTGGGCAAGATGAGAGTTTTCTACTATTTTAATGTTCACATAGTGAAAAAGAAAAGTTAATTAAAAATGCTTGAAATGTCCAGTGCATTTGATCTGTATACTATCTTTACTTCTTAAAATTGCTATACATTAAGTCAATATAATCATATAAATGCAATTCTAAATACGTTCGTTACAAACACATTTGGAGG chm1:+:2644227289:9 +AATCCAAATTTGGGCAAGATGAGAGTTTTCTACTATTTTAATGTTCACATAGTGAAAAAGAAAAGTTAATTAAAAATGCTTGAAATGTCCAGTGCATTTGATCTGTATACTATCTTTACTTCTTAAAATTGCTATACATTAAGTCAATATAATCATATAAATGCAATTCTAAATACGTTCGTTACAAACACATTTGGAGG chm1:+:1615280661:-1 chm1:+:2644227290:9 +GGCCAACATGGTGAAACCCTATCTCTACTAAAAAATACAAAAATAGCCGGGTGTGGTGATGCACGCCTTGTATCCCAGCTACTTGGGAGGCTGAGGGGCAGGTAGAATCGCTTGAACCCAGGAAGGCGGAGATTGACAGTGAGCCAAGATCACGCCACTGCACTCCAGCTGGGTGACGAGACGCGAGACTCCATCTCAAA chm1:+:403207933:-1 chm1:+:845137767:30 chm1:+:1816692536:29 chm1:+:2062045524:28 chm1:+:2434145743:35 chm1:+:2699015969:28 chm1:+:3032335459:37 chm1:+:3051000647:39 +GGCCAACATGGTGAAACCCTATCTCTACTAAAAAATACAAAAATAGCCGGGTGTGGTGATGCACGCCTTGTATCCCAGCTACTTGGGAGGCTGAGGGGCAGGTAGAATCGCTTGAACCCAGGAAGGCGGAGATTGACAGTGAGCCAAGATCACGCCACTGCACTCCAGCTGGGTGACGAGACGCGAGACTCCATCTCAAA chm1:+:25644573:-1 chm1:+:114511411:37 chm1:+:214752320:-1 chm1:+:237237386:-1 chm1:+:313362433:-1 chm1:+:315206091:-1 chm1:+:334618374:-1 chm1:+:393401689:35 chm1:+:488547116:-1 chm1:+:502077682:34 chm1:+:545365481:36 chm1:+:586557610:37 chm1:+:896019625:36 chm1:+:1044115071:38 chm1:+:1224913305:-1 chm1:+:1421062056:-1 chm1:+:1496427511:39 chm1:+:1677692967:30 chm1:+:1679559121:32 chm1:+:1760535337:-1 chm1:+:1769016439:37 chm1:+:1855932741:36 chm1:+:1878619748:32 chm1:+:1879320212:-1 chm1:+:1907537519:33 chm1:+:2013752449:30 chm1:+:2061442672:-1 chm1:+:2104889330:-1 chm1:+:2293804571:34 chm1:+:2383681329:-1 chm1:+:2431000647:36 chm1:+:2487048173:34 chm1:+:2516375627:40 chm1:+:2576259040:-1 chm1:+:2663775417:-1 chm1:+:2676104413:-1 chm1:+:2759022379:34 chm1:+:2801623173:36 chm1:+:2912867970:-1 +GGCCAACATGGTGAAACCCTATCTCTACTAAAAAATACAAAAATAGCCGGGTGTGGTGATGCACGCCTTGTATCCCAGCTACTTGGGAGGCTGAGGGGCAGGTAGAATCGCTTGAACCCAGGAAGGCGGAGATTGACAGTGAGCCAAGATCACGCCACTGCACTCCAGCTGGGTGACGAGACGCGAGACTCCATCTCAAA chm1:+:149777914:40 chm1:+:695989506:38 chm1:+:2716134638:-1 +GGCCAACATGGTGAAACCCTATCTCTACTAAAAAATACAAAAATAGCCGGGTGTGGTGATGCACGCCTTGTATCCCAGCTACTTGGGAGGCTGAGGGGCAGGTAGAATCGCTTGAACCCAGGAAGGCGGAGATTGACAGTGAGCCAAGATCACGCCACTGCACTCCAGCTGGGTGACGAGACGCGAGACTCCATCTCAAA chm1:+:17853164:-1 chm1:+:24573856:-1 chm1:+:35278310:33 chm1:+:52237952:39 chm1:+:59623295:-1 chm1:+:90355511:-1 chm1:+:144307251:35 chm1:+:144487480:35 chm1:+:208600697:33 chm1:+:220123745:-1 chm1:+:232871782:32 chm1:+:237584303:35 chm1:+:242058821:33 chm1:+:293068169:-1 chm1:+:425502485:39 chm1:+:560763178:-1 chm1:+:615442414:32 chm1:+:655366862:36 chm1:+:668582446:35 chm1:+:676320561:33 chm1:+:761648313:-1 chm1:+:852638637:34 chm1:+:883063830:36 chm1:+:893455106:38 chm1:+:1019911964:-1 chm1:+:1029198650:-1 chm1:+:1058377357:33 chm1:+:1128530806:-1 chm1:+:1138774842:-1 chm1:+:1175583844:-1 chm1:+:1289766708:38 chm1:+:1289845778:39 chm1:+:1313299049:40 chm1:+:1331937871:34 chm1:+:1387009000:-1 chm1:+:1398823233:35 chm1:+:1427055547:40 chm1:+:1429502562:30 chm1:+:1431150521:-1 chm1:+:1496070769:37 chm1:+:1636586568:-1 chm1:+:1745528145:35 chm1:+:1809692329:33 chm1:+:1825380142:38 chm1:+:1861045135:34 chm1:+:2062963548:32 chm1:+:2064205803:37 chm1:+:2070298250:-1 chm1:+:2118097329:-1 chm1:+:2172386962:34 chm1:+:2231918705:-1 chm1:+:2265941582:33 chm1:+:2279864659:25 chm1:+:2289475967:-1 chm1:+:2292600892:35 chm1:+:2295105985:-1 chm1:+:2337262677:-1 chm1:+:2379416647:-1 chm1:+:2410882920:35 chm1:+:2433453994:-1 chm1:+:2478630631:-1 chm1:+:2481713253:38 chm1:+:2484433593:31 chm1:+:2498486907:38 chm1:+:2512760245:-1 chm1:+:2547070182:36 chm1:+:2547571875:34 chm1:+:2579366553:39 chm1:+:2593927690:40 chm1:+:2679957420:-1 chm1:+:2680026581:-1 chm1:+:2706248004:40 chm1:+:2724287454:36 chm1:+:2753454014:36 chm1:+:2764472186:-1 chm1:+:2813851034:31 chm1:+:2870638739:-1 chm1:+:2903986564:37 chm1:+:2954003426:31 +GGCCAACATGGTGAAACCCTATCTCTACTAAAAAATACAAAAATAGCCGGGTGTGGTGATGCACGCCTTGTATCCCAGCTACTTGGGAGGCTGAGGGGCAGGTAGAATCGCTTGAACCCAGGAAGGCGGAGATTGACAGTGAGCCAAGATCACGCCACTGCACTCCAGCTGGGTGACGAGACGCGAGACTCCATCTCAAA chm1:+:2074119697:29 chm1:+:2510617221:39 +GGCCAACATGGTGAAACCCTATCTCTACTAAAAAATACAAAAATAGCCGGGTGTGGTGATGCACGCCTTGTATCCCAGCTACTTGGGAGGCTGAGGGGCAGGTAGAATCGCTTGAACCCAGGAAGGCGGAGATTGACAGTGAGCCAAGATCACGCCACTGCACTCCAGCTGGGTGACGAGACGCGAGACTCCATCTCAAA chm1:+:155711434:-1 chm1:+:217717500:-1 chm1:+:229609062:-1 chm1:+:310923635:-1 chm1:+:549144278:31 chm1:+:730417988:37 chm1:+:1181969283:36 chm1:+:1300850896:31 chm1:+:1403239187:31 chm1:+:1464418394:32 chm1:+:1620508811:-1 chm1:+:1824987991:-1 chm1:+:1880459938:39 chm1:+:2002395131:-1 chm1:+:2117774134:-1 chm1:+:2291807402:-1 chm1:+:2366310392:33 chm1:+:2600655457:-1 chm1:+:2643915587:34 chm1:+:2708519858:38 chm1:+:2872853036:38 chm1:+:2991491819:-1 +GGCCAACATGGTGAAACCCTATCTCTACTAAAAAATACAAAAATAGCCGGGTGTGGTGATGCACGCCTTGTATCCCAGCTACTTGGGAGGCTGAGGGGCAGGTAGAATCGCTTGAACCCAGGAAGGCGGAGATTGACAGTGAGCCAAGATCACGCCACTGCACTCCAGCTGGGTGACGAGACGCGAGACTCCATCTCAAA chm1:+:36965359:-1 chm1:+:288185828:-1 chm1:+:977639222:-1 chm1:+:1496194658:29 chm1:+:1673991479:36 chm1:+:2052962155:40 chm1:+:2151922830:35 chm1:+:2369955160:32 chm1:+:2461228915:-1 chm1:+:2509150427:29 chm1:+:2851421829:35 chm1:+:3016884621:33 +GGCCAACATGGTGAAACCCTATCTCTACTAAAAAATACAAAAATAGCCGGGTGTGGTGATGCACGCCTTGTATCCCAGCTACTTGGGAGGCTGAGGGGCAGGTAGAATCGCTTGAACCCAGGAAGGCGGAGATTGACAGTGAGCCAAGATCACGCCACTGCACTCCAGCTGGGTGACGAGACGCGAGACTCCATCTCAAA chm1:+:226882700:35 chm1:+:707926989:39 chm1:+:726904941:-1 chm1:+:1030838341:-1 chm1:+:1574194462:-1 chm1:+:1708981817:-1 chm1:+:2253293110:27 chm1:+:2499654747:-1 chm1:+:2547335117:-1 +TTTGAGATGGAGTCTCGCGTCTCGTCACCCAGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGTCAATCTCCGCCTTCCTGGGTTCAAGCGATTCTACCTGCCCCTCAGCCTCCCAAGTAGCTGGGATACAAGGCGTGCATCACCACACCCGGCTATTTTTGTATTTTTTAGTAGAGATAGGGTTTCACCATGTTGGCC chm1:+:202855831:39 chm1:+:213012013:-1 chm1:+:310959461:40 chm1:+:631051408:-1 chm1:+:657516245:-1 chm1:+:791309689:-1 chm1:+:955475119:-1 chm1:+:1038165655:-1 chm1:+:1203103450:-1 chm1:+:1330450253:-1 chm1:+:1332436168:-1 chm1:+:1377589038:-1 chm1:+:1576635536:-1 chm1:+:1623737612:-1 chm1:+:1656473356:-1 chm1:+:1816246464:-1 chm1:+:1882371067:-1 chm1:+:1936494812:-1 chm1:+:2017580581:-1 chm1:+:2053013879:-1 chm1:+:2076443371:36 chm1:+:2079460979:-1 chm1:+:2117856145:39 chm1:+:2122864517:-1 chm1:+:2358340618:38 chm1:+:2367292107:36 chm1:+:2427712711:38 chm1:+:2478601688:-1 chm1:+:2549379860:35 chm1:+:2604429238:38 chm1:+:2672978618:-1 chm1:+:2673233228:-1 chm1:+:2679863844:-1 chm1:+:2707959672:-1 chm1:+:2750641886:38 chm1:+:2796696124:-1 chm1:+:2829389920:-1 chm1:+:2995561100:-1 chm1:+:3099103953:-1 +TTTGAGATGGAGTCTCGCGTCTCGTCACCCAGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGTCAATCTCCGCCTTCCTGGGTTCAAGCGATTCTACCTGCCCCTCAGCCTCCCAAGTAGCTGGGATACAAGGCGTGCATCACCACACCCGGCTATTTTTGTATTTTTTAGTAGAGATAGGGTTTCACCATGTTGGCC chm1:+:358288227:39 chm1:+:731527182:39 chm1:+:2771420356:33 chm1:+:2850234703:36 chm1:+:2851236506:34 +TTTGAGATGGAGTCTCGCGTCTCGTCACCCAGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGTCAATCTCCGCCTTCCTGGGTTCAAGCGATTCTACCTGCCCCTCAGCCTCCCAAGTAGCTGGGATACAAGGCGTGCATCACCACACCCGGCTATTTTTGTATTTTTTAGTAGAGATAGGGTTTCACCATGTTGGCC chm1:+:12078524:-1 chm1:+:345610326:35 chm1:+:505242749:35 chm1:+:524374701:-1 chm1:+:711400996:38 chm1:+:946878877:-1 chm1:+:1261671506:36 chm1:+:1301108992:40 chm1:+:1385591585:33 chm1:+:1575402422:-1 chm1:+:1698223399:39 chm1:+:1698470389:39 chm1:+:1934726051:36 chm1:+:2561771496:39 chm1:+:2663440805:-1 chm1:+:2771921226:37 chm1:+:2881802824:35 chm1:+:3000929508:-1 +TTTGAGATGGAGTCTCGCGTCTCGTCACCCAGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGTCAATCTCCGCCTTCCTGGGTTCAAGCGATTCTACCTGCCCCTCAGCCTCCCAAGTAGCTGGGATACAAGGCGTGCATCACCACACCCGGCTATTTTTGTATTTTTTAGTAGAGATAGGGTTTCACCATGTTGGCC chm1:+:36514279:-1 chm1:+:594376603:-1 chm1:+:1687786198:35 chm1:+:2075854797:-1 chm1:+:2748690323:-1 chm1:+:2925436116:-1 +TTTGAGATGGAGTCTCGCGTCTCGTCACCCAGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGTCAATCTCCGCCTTCCTGGGTTCAAGCGATTCTACCTGCCCCTCAGCCTCCCAAGTAGCTGGGATACAAGGCGTGCATCACCACACCCGGCTATTTTTGTATTTTTTAGTAGAGATAGGGTTTCACCATGTTGGCC chm1:+:31587508:36 chm1:+:39500812:33 chm1:+:55202017:-1 chm1:+:55239277:-1 chm1:+:95304918:40 chm1:+:97173420:39 chm1:+:116226734:39 chm1:+:202842130:-1 chm1:+:218705889:-1 chm1:+:273898486:35 chm1:+:310964713:-1 chm1:+:317636994:-1 chm1:+:404757913:-1 chm1:+:433688517:-1 chm1:+:438281269:-1 chm1:+:468729767:-1 chm1:+:541413952:37 chm1:+:550321479:32 chm1:+:581045477:29 chm1:+:622253770:-1 chm1:+:690711414:-1 chm1:+:694059304:36 chm1:+:710498835:-1 chm1:+:713700888:-1 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chm1:+:2736784546:-1 chm1:+:2754041542:38 chm1:+:2807917412:35 chm1:+:2814839788:29 chm1:+:2815639172:-1 chm1:+:2849253062:37 chm1:+:2866172466:-1 chm1:+:2869059138:36 chm1:+:2905117888:-1 chm1:+:2929156843:-1 chm1:+:2929535455:36 chm1:+:2954179262:35 chm1:+:2954237012:36 chm1:+:2980904960:36 chm1:+:3015122967:37 chm1:+:3096337450:-1 +TTTGAGATGGAGTCTCGCGTCTCGTCACCCAGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGTCAATCTCCGCCTTCCTGGGTTCAAGCGATTCTACCTGCCCCTCAGCCTCCCAAGTAGCTGGGATACAAGGCGTGCATCACCACACCCGGCTATTTTTGTATTTTTTAGTAGAGATAGGGTTTCACCATGTTGGCC chm1:+:34089742:-1 chm1:+:57286847:-1 chm1:+:87336274:38 chm1:+:204382743:37 chm1:+:295186963:-1 chm1:+:368597254:34 chm1:+:443579854:35 chm1:+:1067128407:-1 chm1:+:1197878956:35 chm1:+:1264343670:-1 chm1:+:1628484173:-1 chm1:+:1716953417:40 chm1:+:1753448181:-1 chm1:+:1761353494:-1 chm1:+:1766513566:37 chm1:+:1792261290:36 chm1:+:1876819304:34 chm1:+:1957361825:-1 chm1:+:1993722218:-1 chm1:+:2128201937:32 chm1:+:2274896345:-1 chm1:+:2350993098:-1 chm1:+:2404378518:-1 chm1:+:2546522616:40 chm1:+:2585148399:37 chm1:+:2664130395:-1 chm1:+:2708445866:-1 chm1:+:2731727780:-1 chm1:+:2758283295:-1 chm1:+:3011880173:-1 +TTTGAGATGGAGTCTCGCGTCTCGTCACCCAGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGTCAATCTCCGCCTTCCTGGGTTCAAGCGATTCTACCTGCCCCTCAGCCTCCCAAGTAGCTGGGATACAAGGCGTGCATCACCACACCCGGCTATTTTTGTATTTTTTAGTAGAGATAGGGTTTCACCATGTTGGCC chm1:+:13941752:34 chm1:+:341394787:-1 chm1:+:353395822:30 chm1:+:459569651:32 chm1:+:1203106895:38 chm1:+:1368299168:31 chm1:+:1387523805:38 chm1:+:1447628979:38 chm1:+:1497545074:39 chm1:+:1673846366:39 chm1:+:1750585771:35 chm1:+:1996911681:40 chm1:+:2477888402:39 chm1:+:2604435074:-1 chm1:+:2659324571:33 chm1:+:2822380314:35 +TTTGAGATGGAGTCTCGCGTCTCGTCACCCAGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGTCAATCTCCGCCTTCCTGGGTTCAAGCGATTCTACCTGCCCCTCAGCCTCCCAAGTAGCTGGGATACAAGGCGTGCATCACCACACCCGGCTATTTTTGTATTTTTTAGTAGAGATAGGGTTTCACCATGTTGGCC chm1:+:10501341:-1 chm1:+:42607115:35 chm1:+:44790719:32 chm1:+:531085734:-1 chm1:+:762310325:-1 chm1:+:901392658:33 chm1:+:1096072538:-1 chm1:+:1613735510:-1 chm1:+:1766580662:-1 chm1:+:1816493721:33 chm1:+:1863587421:-1 chm1:+:2245314022:-1 chm1:+:2422341790:38 chm1:+:2461363650:32 chm1:+:2513378735:32 chm1:+:2648722802:36 chm1:+:2741819666:35 chm1:+:2748905240:37 chm1:+:3015707955:-1 +ATAGTTTGATGTAAATGTTTCTTATGATTATCAAATTAAACACAGGCTATTGTGTGGTGGCTCATGCTTGTAATTCCAGTGATTGGAAGGCCAAGGCAGGAGTAATTACTTGGGGCCCAGAAGTTTGGGACCAACCTTGGCAACATACGCAAGACCCCCTGTCTACCAAAAATTTTTTTTTTGACGATCGGACGTTTTGC chm1:+:43069523:-1 chm1:+:64377590:-1 chm1:+:70661865:-1 chm1:+:93747531:-1 chm1:+:113142459:11 chm1:+:173515304:-1 chm1:+:350012755:-1 chm1:+:489390041:-1 chm1:+:491709186:-1 chm1:+:496228315:-1 chm1:+:548155992:-1 chm1:+:550596334:-1 chm1:+:558490435:-1 chm1:+:577518260:-1 chm1:+:652604766:-1 chm1:+:676591651:-1 chm1:+:737977970:-1 chm1:+:748106373:-1 chm1:+:769485357:-1 chm1:+:774866488:-1 chm1:+:790279921:-1 chm1:+:813576547:-1 chm1:+:850695063:-1 chm1:+:971199449:-1 chm1:+:1010370497:-1 chm1:+:1031450921:-1 chm1:+:1038735304:-1 chm1:+:1060116893:-1 chm1:+:1173608762:-1 chm1:+:1180414880:-1 chm1:+:1180944386:-1 chm1:+:1214062588:-1 chm1:+:1369244682:-1 chm1:+:1404319310:-1 chm1:+:1415601432:-1 chm1:+:1461337024:-1 chm1:+:1499260298:-1 chm1:+:1516857906:-1 chm1:+:1573628168:-1 chm1:+:1669880288:-1 chm1:+:1703024445:-1 chm1:+:1714120848:-1 chm1:+:1714971262:-1 chm1:+:1715278643:-1 chm1:+:1754886408:-1 chm1:+:1924012096:-1 chm1:+:1951475634:-1 chm1:+:1970397049:-1 chm1:+:2001295013:-1 chm1:+:2061745571:-1 chm1:+:2069322035:-1 chm1:+:2105137528:-1 chm1:+:2297828272:-1 chm1:+:2350657015:-1 chm1:+:2351086207:-1 chm1:+:2379841714:-1 chm1:+:2383053831:-1 chm1:+:2434665896:-1 chm1:+:2460214710:-1 chm1:+:2468445451:-1 chm1:+:2477584011:-1 chm1:+:2518945618:-1 chm1:+:2527303872:-1 chm1:+:2528500285:-1 chm1:+:2584372730:-1 chm1:+:2622059575:-1 chm1:+:2680976707:-1 chm1:+:2692210371:-1 chm1:+:2692331644:-1 chm1:+:2749290233:-1 chm1:+:2750938057:-1 chm1:+:2752838391:-1 chm1:+:2769687796:-1 chm1:+:2934878896:-1 chm1:+:2998641100:-1 +ATAGTTTGATGTAAATGTTTCTTATGATTATCAAATTAAACACAGGCTATTGTGTGGTGGCTCATGCTTGTAATTCCAGTGATTGGAAGGCCAAGGCAGGAGTAATTACTTGGGGCCCAGAAGTTTGGGACCAACCTTGGCAACATACGCAAGACCCCCTGTCTACCAAAAATTTTTTTTTTGACGATCGGACGTTTTGC chm1:+:113142461:11 +GCAAAACGTCCGATCGTCAAAAAAAAAATTTTTGGTAGACAGGGGGTCTTGCGTATGTTGCCAAGGTTGGTCCCAAACTTCTGGGCCCCAAGTAATTACTCCTGCCTTGGCCTTCCAATCACTGGAATTACAAGCATGAGCCACCACACAATAGCCTGTGTTTAATTTGATAATCATAAGAAACATTTACATCAAACTAT chm1:+:247108246:-1 chm1:+:1015735001:-1 chm1:+:2666582810:-1 +GCAAAACGTCCGATCGTCAAAAAAAAAATTTTTGGTAGACAGGGGGTCTTGCGTATGTTGCCAAGGTTGGTCCCAAACTTCTGGGCCCCAAGTAATTACTCCTGCCTTGGCCTTCCAATCACTGGAATTACAAGCATGAGCCACCACACAATAGCCTGTGTTTAATTTGATAATCATAAGAAACATTTACATCAAACTAT chm1:+:310327234:-1 chm1:+:654290450:-1 chm1:+:1941735730:-1 chm1:+:2236981798:-1 chm1:+:2400629194:-1 chm1:+:2682058616:-1 chm1:+:2938203304:-1 +GGCCGTTGTATTTCAAAACCATGGCCCTTCTATTTCCTCTTTCTTATTGTTTTTTCTCTTCCATGTTCACTTCTGCCTTCTTAATTTCTTTTCCCTTCCTTTACTCTCATTTCTTTCACAGAGTGAGTGATTTCTGTTGAAAGCAAGGTAAGTGTCTCATGGGGTCCAGCTAAGGATGCAACCCACCAAAGGCAAGATCA chm1:+:1904167663:-1 chm1:+:2589313386:-1 +GGCCGTTGTATTTCAAAACCATGGCCCTTCTATTTCCTCTTTCTTATTGTTTTTTCTCTTCCATGTTCACTTCTGCCTTCTTAATTTCTTTTCCCTTCCTTTACTCTCATTTCTTTCACAGAGTGAGTGATTTCTGTTGAAAGCAAGGTAAGTGTCTCATGGGGTCCAGCTAAGGATGCAACCCACCAAAGGCAAGATCA chm1:+:42602335:-1 chm1:+:315248926:-1 chm1:+:527000853:-1 chm1:+:3044059323:-1 +GGCCGTTGTATTTCAAAACCATGGCCCTTCTATTTCCTCTTTCTTATTGTTTTTTCTCTTCCATGTTCACTTCTGCCTTCTTAATTTCTTTTCCCTTCCTTTACTCTCATTTCTTTCACAGAGTGAGTGATTTCTGTTGAAAGCAAGGTAAGTGTCTCATGGGGTCCAGCTAAGGATGCAACCCACCAAAGGCAAGATCA chm1:+:830310077:-1 chm1:+:1304182817:-1 chm1:+:1830661465:-1 chm1:+:2144929768:-1 +GGCCGTTGTATTTCAAAACCATGGCCCTTCTATTTCCTCTTTCTTATTGTTTTTTCTCTTCCATGTTCACTTCTGCCTTCTTAATTTCTTTTCCCTTCCTTTACTCTCATTTCTTTCACAGAGTGAGTGATTTCTGTTGAAAGCAAGGTAAGTGTCTCATGGGGTCCAGCTAAGGATGCAACCCACCAAAGGCAAGATCA chm1:+:94989155:-1 chm1:+:107863802:-1 chm1:+:210729297:-1 chm1:+:224819051:-1 chm1:+:268607007:-1 chm1:+:434564849:-1 chm1:+:473461557:-1 chm1:+:511044688:-1 chm1:+:542432078:-1 chm1:+:647005422:-1 chm1:+:762344217:-1 chm1:+:765560834:-1 chm1:+:771371236:-1 chm1:+:835555739:-1 chm1:+:865243643:-1 chm1:+:905011677:-1 chm1:+:1130698069:-1 chm1:+:1208825350:-1 chm1:+:1259144289:-1 chm1:+:1343861276:-1 chm1:+:1354801775:-1 chm1:+:1551856269:-1 chm1:+:1562332033:-1 chm1:+:1627872522:-1 chm1:+:1688475701:-1 chm1:+:1798075051:-1 chm1:+:1904046732:-1 chm1:+:1907786283:-1 chm1:+:1920720295:-1 chm1:+:1929445957:-1 chm1:+:2024812275:-1 chm1:+:2026345054:-1 chm1:+:2029127496:-1 chm1:+:2147206585:-1 chm1:+:2287061057:-1 chm1:+:2400944465:-1 chm1:+:2473448980:-1 chm1:+:2697035021:-1 chm1:+:2707242499:-1 chm1:+:2897130285:-1 chm1:+:2927279580:-1 chm1:+:2963890130:-1 +GGCCGTTGTATTTCAAAACCATGGCCCTTCTATTTCCTCTTTCTTATTGTTTTTTCTCTTCCATGTTCACTTCTGCCTTCTTAATTTCTTTTCCCTTCCTTTACTCTCATTTCTTTCACAGAGTGAGTGATTTCTGTTGAAAGCAAGGTAAGTGTCTCATGGGGTCCAGCTAAGGATGCAACCCACCAAAGGCAAGATCA chm1:+:10306145:-1 chm1:+:47775783:-1 chm1:+:107123915:-1 chm1:+:158965536:-1 chm1:+:172722558:-1 chm1:+:203998571:-1 chm1:+:239827737:-1 chm1:+:351963554:-1 chm1:+:573667742:-1 chm1:+:627256791:-1 chm1:+:672353712:-1 chm1:+:757947034:-1 chm1:+:762996934:-1 chm1:+:1067386194:-1 chm1:+:1072952836:-1 chm1:+:1354286222:-1 chm1:+:1425312907:-1 chm1:+:1500272354:-1 chm1:+:1619664219:-1 chm1:+:1714090754:-1 chm1:+:1780790819:-1 chm1:+:1794783845:-1 chm1:+:1842910720:-1 chm1:+:1843818690:-1 chm1:+:1847456271:-1 chm1:+:1940028190:-1 chm1:+:1947028674:-1 chm1:+:1969368084:-1 chm1:+:1974314898:-1 chm1:+:1983606385:-1 chm1:+:1994398111:-1 chm1:+:2038725719:-1 chm1:+:2134474226:-1 chm1:+:2144790270:-1 chm1:+:2153832018:-1 chm1:+:2161594343:-1 chm1:+:2261275332:-1 chm1:+:2290483104:-1 chm1:+:2357026149:-1 chm1:+:2507241844:-1 chm1:+:2514960254:-1 chm1:+:2531072052:-1 chm1:+:2714968258:-1 chm1:+:2908287090:-1 chm1:+:2917930290:-1 chm1:+:2945831343:-1 chm1:+:2965405710:-1 chm1:+:2978631196:-1 chm1:+:3003778490:-1 +TGATCTTGCCTTTGGTGGGTTGCATCCTTAGCTGGACCCCATGAGACACTTACCTTGCTTTCAACAGAAATCACTCACTCTGTGAAAGAAATGAGAGTAAAGGAAGGGAAAAGAAATTAAGAAGGCAGAAGTGAACATGGAAGAGAAAAAACAATAAGAAAGAGGAAATAGAAGGGCCATGGTTTTGAAATACAACGGCC chm1:+:324167249:-1 chm1:+:355341719:-1 chm1:+:573735172:-1 chm1:+:664206736:-1 chm1:+:1656311129:-1 chm1:+:1735892063:-1 chm1:+:2136232770:7 chm1:+:2143372424:-1 chm1:+:2757618711:-1 chm1:+:3057663026:-1 +TGATCTTGCCTTTGGTGGGTTGCATCCTTAGCTGGACCCCATGAGACACTTACCTTGCTTTCAACAGAAATCACTCACTCTGTGAAAGAAATGAGAGTAAAGGAAGGGAAAAGAAATTAAGAAGGCAGAAGTGAACATGGAAGAGAAAAAACAATAAGAAAGAGGAAATAGAAGGGCCATGGTTTTGAAATACAACGGCC chm1:+:2136232771:7 +TGATCTTGCCTTTGGTGGGTTGCATCCTTAGCTGGACCCCATGAGACACTTACCTTGCTTTCAACAGAAATCACTCACTCTGTGAAAGAAATGAGAGTAAAGGAAGGGAAAAGAAATTAAGAAGGCAGAAGTGAACATGGAAGAGAAAAAACAATAAGAAAGAGGAAATAGAAGGGCCATGGTTTTGAAATACAACGGCC chm1:+:1897451550:-1 chm1:+:2361961652:-1 +TGATCTTGCCTTTGGTGGGTTGCATCCTTAGCTGGACCCCATGAGACACTTACCTTGCTTTCAACAGAAATCACTCACTCTGTGAAAGAAATGAGAGTAAAGGAAGGGAAAAGAAATTAAGAAGGCAGAAGTGAACATGGAAGAGAAAAAACAATAAGAAAGAGGAAATAGAAGGGCCATGGTTTTGAAATACAACGGCC chm1:+:695060231:-1 +ATTCGTAGCTTTTCTTATAACAGAAGTTAAGCTTATACAGAGGGGGAAAAAACTGAAAGAGATGTGAAAGGCAGTCAGCCCAGTGATGGGAGAGAAAGTATGGGAGTTACAGTAGGGACAAACAGATTATAATAGTCTAGTGAATTTTACTCTCAGAGATTTTAAGAAAAAATGCTTGCAAATGTAAAGACATGGAGTAG chm1:+:1669880544:-1 chm1:+:1858368314:-1 chm1:+:2943561968:-1 +ATTCGTAGCTTTTCTTATAACAGAAGTTAAGCTTATACAGAGGGGGAAAAAACTGAAAGAGATGTGAAAGGCAGTCAGCCCAGTGATGGGAGAGAAAGTATGGGAGTTACAGTAGGGACAAACAGATTATAATAGTCTAGTGAATTTTACTCTCAGAGATTTTAAGAAAAAATGCTTGCAAATGTAAAGACATGGAGTAG chm1:+:420391195:-1 chm1:+:451528750:-1 chm1:+:2382521647:-1 chm1:+:2464641525:-1 +ATTCGTAGCTTTTCTTATAACAGAAGTTAAGCTTATACAGAGGGGGAAAAAACTGAAAGAGATGTGAAAGGCAGTCAGCCCAGTGATGGGAGAGAAAGTATGGGAGTTACAGTAGGGACAAACAGATTATAATAGTCTAGTGAATTTTACTCTCAGAGATTTTAAGAAAAAATGCTTGCAAATGTAAAGACATGGAGTAG chm1:+:981646792:-1 chm1:+:1452808032:-1 chm1:+:1681725936:-1 chm1:+:1690442197:-1 chm1:+:2164167439:-1 +ATTCGTAGCTTTTCTTATAACAGAAGTTAAGCTTATACAGAGGGGGAAAAAACTGAAAGAGATGTGAAAGGCAGTCAGCCCAGTGATGGGAGAGAAAGTATGGGAGTTACAGTAGGGACAAACAGATTATAATAGTCTAGTGAATTTTACTCTCAGAGATTTTAAGAAAAAATGCTTGCAAATGTAAAGACATGGAGTAG chm1:+:190637398:-1 chm1:+:193203829:-1 chm1:+:269866513:-1 chm1:+:312480294:-1 chm1:+:434556454:-1 chm1:+:604450210:-1 chm1:+:634277187:-1 chm1:+:660709934:-1 chm1:+:736682589:-1 chm1:+:750793788:-1 chm1:+:804541830:-1 chm1:+:943544982:-1 chm1:+:994765207:-1 chm1:+:1103821826:-1 chm1:+:1177950017:-1 chm1:+:1823323781:-1 chm1:+:2111685558:-1 chm1:+:2364291174:-1 chm1:+:2948006011:-1 +ATTCGTAGCTTTTCTTATAACAGAAGTTAAGCTTATACAGAGGGGGAAAAAACTGAAAGAGATGTGAAAGGCAGTCAGCCCAGTGATGGGAGAGAAAGTATGGGAGTTACAGTAGGGACAAACAGATTATAATAGTCTAGTGAATTTTACTCTCAGAGATTTTAAGAAAAAATGCTTGCAAATGTAAAGACATGGAGTAG chm1:+:193418882:-1 chm1:+:514166736:-1 chm1:+:1717798114:-1 chm1:+:1893047033:-1 chm1:+:1951357926:-1 chm1:+:2034520216:-1 +CTACTCCATGTCTTTACATTTGCAAGCATTTTTTCTTAAAATCTCTGAGAGTAAAATTCACTAGACTATTATAATCTGTTTGTCCCTACTGTAACTCCCATACTTTCTCTCCCATCACTGGGCTGACTGCCTTTCACATCTCTTTCAGTTTTTTCCCCCTCTGTATAAGCTTAACTTCTGTTATAAGAAAAGCTACGAAT chm1:+:2585527281:10 +CTACTCCATGTCTTTACATTTGCAAGCATTTTTTCTTAAAATCTCTGAGAGTAAAATTCACTAGACTATTATAATCTGTTTGTCCCTACTGTAACTCCCATACTTTCTCTCCCATCACTGGGCTGACTGCCTTTCACATCTCTTTCAGTTTTTTCCCCCTCTGTATAAGCTTAACTTCTGTTATAAGAAAAGCTACGAAT chm1:+:2585527282:10 +CTACTCCATGTCTTTACATTTGCAAGCATTTTTTCTTAAAATCTCTGAGAGTAAAATTCACTAGACTATTATAATCTGTTTGTCCCTACTGTAACTCCCATACTTTCTCTCCCATCACTGGGCTGACTGCCTTTCACATCTCTTTCAGTTTTTTCCCCCTCTGTATAAGCTTAACTTCTGTTATAAGAAAAGCTACGAAT chm1:+:65845771:-1 +CTCCCTCCTGGCTCCCTACTTGAACTAGCCTGTGTGACCTCGGCAAGAGGTATCCCCCGTAGCCTGTGCCTTTTTCCGATGTCCTTCATGTGTAACATGGGAATAGTAAGAGTTCCTACCTTTTGGGCTGTTGCGAGAATTCAGTGAGGGTAATAGCACATGAAGCACTGAGCTAACAGGTAATAGGAGATGCCTGTATA chm1:+:4466099:-1 chm1:+:2179487375:-1 +CTCCCTCCTGGCTCCCTACTTGAACTAGCCTGTGTGACCTCGGCAAGAGGTATCCCCCGTAGCCTGTGCCTTTTTCCGATGTCCTTCATGTGTAACATGGGAATAGTAAGAGTTCCTACCTTTTGGGCTGTTGCGAGAATTCAGTGAGGGTAATAGCACATGAAGCACTGAGCTAACAGGTAATAGGAGATGCCTGTATA chm1:+:88141839:-1 chm1:+:888349824:-1 chm1:+:1046550836:-1 chm1:+:1851802139:-1 chm1:+:2409658261:-1 chm1:+:2669141086:-1 +CTCCCTCCTGGCTCCCTACTTGAACTAGCCTGTGTGACCTCGGCAAGAGGTATCCCCCGTAGCCTGTGCCTTTTTCCGATGTCCTTCATGTGTAACATGGGAATAGTAAGAGTTCCTACCTTTTGGGCTGTTGCGAGAATTCAGTGAGGGTAATAGCACATGAAGCACTGAGCTAACAGGTAATAGGAGATGCCTGTATA chm1:+:435128524:-1 chm1:+:600485130:-1 chm1:+:953483586:-1 chm1:+:1051010873:-1 chm1:+:1585934543:-1 chm1:+:2121005005:-1 chm1:+:2596244375:-1 chm1:+:2907809248:-1 +CTCCCTCCTGGCTCCCTACTTGAACTAGCCTGTGTGACCTCGGCAAGAGGTATCCCCCGTAGCCTGTGCCTTTTTCCGATGTCCTTCATGTGTAACATGGGAATAGTAAGAGTTCCTACCTTTTGGGCTGTTGCGAGAATTCAGTGAGGGTAATAGCACATGAAGCACTGAGCTAACAGGTAATAGGAGATGCCTGTATA chm1:+:109951119:-1 chm1:+:614255738:-1 chm1:+:631948799:-1 chm1:+:1050929235:-1 chm1:+:1463966565:-1 chm1:+:1543428729:-1 chm1:+:2224370881:-1 chm1:+:2224405982:-1 chm1:+:2376936505:-1 chm1:+:2500804144:-1 chm1:+:2742972513:-1 +CTCCCTCCTGGCTCCCTACTTGAACTAGCCTGTGTGACCTCGGCAAGAGGTATCCCCCGTAGCCTGTGCCTTTTTCCGATGTCCTTCATGTGTAACATGGGAATAGTAAGAGTTCCTACCTTTTGGGCTGTTGCGAGAATTCAGTGAGGGTAATAGCACATGAAGCACTGAGCTAACAGGTAATAGGAGATGCCTGTATA chm1:+:292067482:-1 chm1:+:324485735:-1 chm1:+:503453973:-1 chm1:+:1004025927:-1 chm1:+:1026513419:-1 chm1:+:1165763796:-1 chm1:+:1344207753:-1 chm1:+:1844199229:-1 chm1:+:2127460641:-1 chm1:+:2761548490:-1 +TATACAGGCATCTCCTATTACCTGTTAGCTCAGTGCTTCATGTGCTATTACCCTCACTGAATTCTCGCAACAGCCCAAAAGGTAGGAACTCTTACTATTCCCATGTTACACATGAAGGACATCGGAAAAAGGCACAGGCTACGGGGGATACCTCTTGCCGAGGTCACACAGGCTAGTTCAAGTAGGGAGCCAGGAGGGAG chm1:+:17416664:-1 chm1:+:684845869:-1 chm1:+:1403130978:9 chm1:+:1513919850:-1 chm1:+:2771627043:-1 +TATACAGGCATCTCCTATTACCTGTTAGCTCAGTGCTTCATGTGCTATTACCCTCACTGAATTCTCGCAACAGCCCAAAAGGTAGGAACTCTTACTATTCCCATGTTACACATGAAGGACATCGGAAAAAGGCACAGGCTACGGGGGATACCTCTTGCCGAGGTCACACAGGCTAGTTCAAGTAGGGAGCCAGGAGGGAG chm1:+:1403130975:9 +TATACAGGCATCTCCTATTACCTGTTAGCTCAGTGCTTCATGTGCTATTACCCTCACTGAATTCTCGCAACAGCCCAAAAGGTAGGAACTCTTACTATTCCCATGTTACACATGAAGGACATCGGAAAAAGGCACAGGCTACGGGGGATACCTCTTGCCGAGGTCACACAGGCTAGTTCAAGTAGGGAGCCAGGAGGGAG chm1:+:1403130979:9 diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-400nt.prof b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-400nt.prof new file mode 100644 index 0000000000000000000000000000000000000000..2dcf136efb07d606563849be34091afd0b9fc9f3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-400nt.prof @@ -0,0 +1,1000 @@ +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTCTGCAGACTCTACAGAAGCATGTGCCTTGGCTTCCGGTGAGGCCTAGGGAGGCTTACAGTCATGGCGGAAGGCAAAAGGGGAGTAGGCAGCTAACATTGGTGTAGGGCAAGAGCAACAGAGGAAGGAAGGTGCCAGATATCATGTGAACTCACTTATCACCAAAGGGATGGTCCGTAAGTCATGCAATGAGGGTTCCACCC HG:+:113758346:-1 HG:+:223050313:-1 HG:+:690209126:-1 HG:+:878859642:-1 HG:+:975568927:-1 HG:+:1059983333:-1 HG:+:1073903244:-1 HG:+:1130341280:-1 HG:+:1207854317:-1 HG:+:1271880743:-1 HG:+:1463231956:-1 HG:+:2574824748:-1 HG:+:2883155519:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTCTGCAGACTCTACAGAAGCATGTGCCTTGGCTTCCGGTGAGGCCTAGGGAGGCTTACAGTCATGGCGGAAGGCAAAAGGGGAGTAGGCAGCTAACATTGGTGTAGGGCAAGAGCAACAGAGGAAGGAAGGTGCCAGATATCATGTGAACTCACTTATCACCAAAGGGATGGTCCGTAAGTCATGCAATGAGGGTTCCACCC HG:+:15806706:-1 HG:+:30617388:-1 HG:+:105160260:-1 HG:+:182464934:-1 HG:+:192172336:-1 HG:+:196924740:-1 HG:+:292345569:-1 HG:+:325792882:-1 HG:+:327213249:-1 HG:+:360934968:-1 HG:+:407032333:-1 HG:+:408523771:-1 HG:+:531967238:-1 HG:+:587913923:-1 HG:+:591326824:-1 HG:+:591328828:-1 HG:+:654664626:-1 HG:+:668083689:-1 HG:+:668265487:-1 HG:+:702350840:-1 HG:+:712800142:-1 HG:+:763437341:-1 HG:+:765541381:-1 HG:+:784953635:-1 HG:+:787346831:-1 HG:+:794266240:-1 HG:+:809337280:-1 HG:+:842892966:-1 HG:+:855622980:-1 HG:+:870492883:-1 HG:+:907964238:-1 HG:+:975333569:-1 HG:+:981626702:-1 HG:+:1056704953:-1 HG:+:1110814170:-1 HG:+:1129957304:-1 HG:+:1144150753:-1 HG:+:1160012433:-1 HG:+:1206910289:-1 HG:+:1281811381:-1 HG:+:1358870773:-1 HG:+:1419570989:-1 HG:+:1508816949:-1 HG:+:1567090932:-1 HG:+:1626845023:-1 HG:+:1645130728:-1 HG:+:1645562649:-1 HG:+:1672681660:-1 HG:+:1700195342:-1 HG:+:1740234906:-1 HG:+:1790848225:-1 HG:+:1809804651:-1 HG:+:1854197972:-1 HG:+:1954735683:-1 HG:+:1955866942:-1 HG:+:1991697420:-1 HG:+:1995388161:-1 HG:+:2014715533:-1 HG:+:2065555609:-1 HG:+:2113218438:-1 HG:+:2148349295:-1 HG:+:2259205431:-1 HG:+:2265710785:-1 HG:+:2302729565:-1 HG:+:2384415147:-1 HG:+:2468069698:-1 HG:+:2510558868:-1 HG:+:2639528926:-1 HG:+:2737217384:-1 HG:+:2743649381:-1 HG:+:2803211551:-1 HG:+:2889965426:-1 HG:+:2907312541:-1 HG:+:2908807071:-1 HG:+:2969794702:-1 HG:+:2979039186:-1 HG:+:3030724671:-1 HG:+:3039334192:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTCTGCAGACTCTACAGAAGCATGTGCCTTGGCTTCCGGTGAGGCCTAGGGAGGCTTACAGTCATGGCGGAAGGCAAAAGGGGAGTAGGCAGCTAACATTGGTGTAGGGCAAGAGCAACAGAGGAAGGAAGGTGCCAGATATCATGTGAACTCACTTATCACCAAAGGGATGGTCCGTAAGTCATGCAATGAGGGTTCCACCC HG:+:534962083:-1 HG:+:885569682:-1 HG:+:1407539860:-1 HG:+:2402770731:-1 HG:+:2657300652:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTCTGCAGACTCTACAGAAGCATGTGCCTTGGCTTCCGGTGAGGCCTAGGGAGGCTTACAGTCATGGCGGAAGGCAAAAGGGGAGTAGGCAGCTAACATTGGTGTAGGGCAAGAGCAACAGAGGAAGGAAGGTGCCAGATATCATGTGAACTCACTTATCACCAAAGGGATGGTCCGTAAGTCATGCAATGAGGGTTCCACCC HG:+:199634224:-1 HG:+:1843823129:-1 HG:+:2345506215:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTCTGCAGACTCTACAGAAGCATGTGCCTTGGCTTCCGGTGAGGCCTAGGGAGGCTTACAGTCATGGCGGAAGGCAAAAGGGGAGTAGGCAGCTAACATTGGTGTAGGGCAAGAGCAACAGAGGAAGGAAGGTGCCAGATATCATGTGAACTCACTTATCACCAAAGGGATGGTCCGTAAGTCATGCAATGAGGGTTCCACCC HG:+:1740197676:-1 HG:+:2647349115:-1 HG:+:2905901958:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTCTGCAGACTCTACAGAAGCATGTGCCTTGGCTTCCGGTGAGGCCTAGGGAGGCTTACAGTCATGGCGGAAGGCAAAAGGGGAGTAGGCAGCTAACATTGGTGTAGGGCAAGAGCAACAGAGGAAGGAAGGTGCCAGATATCATGTGAACTCACTTATCACCAAAGGGATGGTCCGTAAGTCATGCAATGAGGGTTCCACCC HG:+:251902238:-1 HG:+:371812211:-1 HG:+:407408357:-1 HG:+:454132014:-1 HG:+:696370954:-1 HG:+:743828567:-1 HG:+:867565995:-1 HG:+:1014661153:-1 HG:+:1051393684:-1 HG:+:1101638143:-1 HG:+:1159539700:-1 HG:+:1259273080:-1 HG:+:1326837638:-1 HG:+:1374749880:-1 HG:+:1435157875:-1 HG:+:1465473261:-1 HG:+:1495054063:-1 HG:+:1777982370:-1 HG:+:1813232781:-1 HG:+:2527112819:-1 HG:+:2863419866:-1 HG:+:3004974659:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTCTGCAGACTCTACAGAAGCATGTGCCTTGGCTTCCGGTGAGGCCTAGGGAGGCTTACAGTCATGGCGGAAGGCAAAAGGGGAGTAGGCAGCTAACATTGGTGTAGGGCAAGAGCAACAGAGGAAGGAAGGTGCCAGATATCATGTGAACTCACTTATCACCAAAGGGATGGTCCGTAAGTCATGCAATGAGGGTTCCACCC HG:+:72997319:-1 HG:+:231609712:-1 HG:+:244295108:-1 HG:+:305719817:-1 HG:+:362037949:-1 HG:+:446766901:-1 HG:+:460878887:-1 HG:+:470790834:-1 HG:+:494234443:-1 HG:+:586132141:-1 HG:+:686485173:-1 HG:+:703292975:-1 HG:+:723292179:-1 HG:+:751728225:-1 HG:+:757970838:-1 HG:+:789390595:-1 HG:+:796757812:-1 HG:+:997186559:-1 HG:+:1025387457:-1 HG:+:1038294044:-1 HG:+:1071722660:-1 HG:+:1085244664:-1 HG:+:1244517639:-1 HG:+:1285708971:-1 HG:+:1449989412:-1 HG:+:1492617579:-1 HG:+:1559724018:-1 HG:+:1718784809:-1 HG:+:1753117180:-1 HG:+:1770088110:-1 HG:+:1779968399:-1 HG:+:1793359174:-1 HG:+:1803589536:-1 HG:+:1814805043:-1 HG:+:1829129161:-1 HG:+:1842083761:-1 HG:+:1858704026:-1 HG:+:1861451756:-1 HG:+:1912075820:-1 HG:+:1914987658:-1 HG:+:2047530745:-1 HG:+:2129439572:-1 HG:+:2168225706:-1 HG:+:2198667329:-1 HG:+:2222637225:-1 HG:+:2376648659:-1 HG:+:2422961841:-1 HG:+:2437682336:-1 HG:+:2464925694:-1 HG:+:2486799833:-1 HG:+:2777052855:-1 HG:+:2817210792:-1 HG:+:3018622825:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTCTGCAGACTCTACAGAAGCATGTGCCTTGGCTTCCGGTGAGGCCTAGGGAGGCTTACAGTCATGGCGGAAGGCAAAAGGGGAGTAGGCAGCTAACATTGGTGTAGGGCAAGAGCAACAGAGGAAGGAAGGTGCCAGATATCATGTGAACTCACTTATCACCAAAGGGATGGTCCGTAAGTCATGCAATGAGGGTTCCACCC HG:+:5579328:-1 HG:+:25353412:-1 HG:+:79704985:-1 HG:+:80184387:-1 HG:+:81151485:-1 HG:+:197507504:-1 HG:+:260257729:-1 HG:+:268773627:-1 HG:+:402893356:-1 HG:+:408065824:-1 HG:+:577872307:-1 HG:+:587593689:-1 HG:+:675247076:-1 HG:+:702954313:-1 HG:+:775623597:-1 HG:+:817549550:-1 HG:+:920692415:-1 HG:+:961385257:-1 HG:+:1004618123:-1 HG:+:1040846038:-1 HG:+:1149059369:-1 HG:+:1153585089:-1 HG:+:1185735430:-1 HG:+:1216085978:-1 HG:+:1223266247:-1 HG:+:1346181514:-1 HG:+:1482259609:-1 HG:+:1510307027:-1 HG:+:1627194639:-1 HG:+:1631050121:-1 HG:+:1710705614:-1 HG:+:1885242676:-1 HG:+:1941574871:-1 HG:+:1974312820:-1 HG:+:1985245867:-1 HG:+:2009626329:-1 HG:+:2025867353:-1 HG:+:2031311343:-1 HG:+:2115692889:-1 HG:+:2166174117:-1 HG:+:2179296358:-1 HG:+:2196283520:-1 HG:+:2273951631:-1 HG:+:2273983816:-1 HG:+:2357096880:-1 HG:+:2512201321:-1 HG:+:2622974321:-1 HG:+:2805848244:-1 HG:+:2807863158:-1 HG:+:2902624393:-1 HG:+:2911733894:-1 HG:+:2958342656:-1 HG:+:2993415333:-1 HG:+:3002351373:-1 HG:+:3025238809:-1 HG:+:3029730565:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTCTGCAGACTCTACAGAAGCATGTGCCTTGGCTTCCGGTGAGGCCTAGGGAGGCTTACAGTCATGGCGGAAGGCAAAAGGGGAGTAGGCAGCTAACATTGGTGTAGGGCAAGAGCAACAGAGGAAGGAAGGTGCCAGATATCATGTGAACTCACTTATCACCAAAGGGATGGTCCGTAAGTCATGCAATGAGGGTTCCACCC HG:+:55617136:-1 HG:+:185944160:-1 HG:+:256774735:-1 HG:+:314562083:-1 HG:+:334527076:-1 HG:+:369192550:-1 HG:+:605858969:-1 HG:+:664784909:-1 HG:+:681411965:-1 HG:+:771107172:-1 HG:+:783154757:-1 HG:+:817488759:-1 HG:+:880552127:-1 HG:+:883316034:-1 HG:+:885886368:-1 HG:+:1024779056:-1 HG:+:1056639984:-1 HG:+:1124740318:-1 HG:+:1134413991:-1 HG:+:1194628009:-1 HG:+:1302493189:-1 HG:+:1348834239:-1 HG:+:1350081240:-1 HG:+:1444839115:-1 HG:+:1550212840:-1 HG:+:1611092908:-1 HG:+:1754114981:-1 HG:+:1776274645:-1 HG:+:1866383826:-1 HG:+:1925381911:-1 HG:+:1972315242:-1 HG:+:1988940468:-1 HG:+:2181452524:-1 HG:+:2330225809:-1 HG:+:2443815518:-1 HG:+:2491903793:-1 HG:+:2550610466:-1 HG:+:2623091954:-1 HG:+:2696147170:-1 HG:+:2712826094:-1 HG:+:2792323909:-1 HG:+:2808520701:-1 HG:+:3049412952:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTCTGCAGACTCTACAGAAGCATGTGCCTTGGCTTCCGGTGAGGCCTAGGGAGGCTTACAGTCATGGCGGAAGGCAAAAGGGGAGTAGGCAGCTAACATTGGTGTAGGGCAAGAGCAACAGAGGAAGGAAGGTGCCAGATATCATGTGAACTCACTTATCACCAAAGGGATGGTCCGTAAGTCATGCAATGAGGGTTCCACCC HG:+:2479408304:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTCTGCAGACTCTACAGAAGCATGTGCCTTGGCTTCCGGTGAGGCCTAGGGAGGCTTACAGTCATGGCGGAAGGCAAAAGGGGAGTAGGCAGCTAACATTGGTGTAGGGCAAGAGCAACAGAGGAAGGAAGGTGCCAGATATCATGTGAACTCACTTATCACCAAAGGGATGGTCCGTAAGTCATGCAATGAGGGTTCCACCC HG:+:592785591:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTCTGCAGACTCTACAGAAGCATGTGCCTTGGCTTCCGGTGAGGCCTAGGGAGGCTTACAGTCATGGCGGAAGGCAAAAGGGGAGTAGGCAGCTAACATTGGTGTAGGGCAAGAGCAACAGAGGAAGGAAGGTGCCAGATATCATGTGAACTCACTTATCACCAAAGGGATGGTCCGTAAGTCATGCAATGAGGGTTCCACCC HG:+:242927288:-1 HG:+:403950087:-1 HG:+:467393807:-1 HG:+:635489035:-1 HG:+:1120519380:-1 HG:+:1339134186:-1 HG:+:1517547180:-1 HG:+:1553651920:-1 HG:+:1577397941:-1 HG:+:1787947407:-1 HG:+:1838695039:-1 HG:+:2246322425:-1 HG:+:2513118025:-1 HG:+:2595142764:-1 HG:+:2603847168:-1 HG:+:2926287161:-1 HG:+:3006904052:-1 +AAATAAAGTCCCCCCAAAGAAGTCCACATCCTAACCCCCACAGCCACTGAACATATACCTTACATGGTAAAAGACATGCTGCAGACCGTGACTCAAGGGTAACGACCTGTGTCGTTAAGGCTATTCTTGCACTGCAATAAAAGAAGTAACTGGAGGCTGGAATAATTTATAATGAAAAGAGATTTAATTGGCTCCGATTCTGCAGACTCTACAGAAGCATGTGCCTTGGCTTCCGGTGAGGCCTAGGGAGGCTTACAGTCATGGCGGAAGGCAAAAGGGGAGTAGGCAGCTAACATTGGTGTAGGGCAAGAGCAACAGAGGAAGGAAGGTGCCAGATATCATGTGAACTCACTTATCACCAAAGGGATGGTCCGTAAGTCATGCAATGAGGGTTCCACCC HG:+:270646406:-1 HG:+:417522869:-1 HG:+:437434410:-1 HG:+:647089801:-1 HG:+:754562995:-1 HG:+:1380334391:-1 HG:+:1492882889:-1 HG:+:1504978858:-1 HG:+:1930835540:-1 HG:+:1995700189:-1 HG:+:2015435364:-1 HG:+:2472476163:-1 HG:+:2621256507:-1 HG:+:3005453431:-1 HG:+:3007942060:-1 HG:+:3052752558:-1 +GGGTGGAACCCTCATTGCATGACTTACGGACCATCCCTTTGGTGATAAGTGAGTTCACATGATATCTGGCACCTTCCTTCCTCTGTTGCTCTTGCCCTACACCAATGTTAGCTGCCTACTCCCCTTTTGCCTTCCGCCATGACTGTAAGCCTCCCTAGGCCTCACCGGAAGCCAAGGCACATGCTTCTGTAGAGTCTGCAGAATCGGAGCCAATTAAATCTCTTTTCATTATAAATTATTCCAGCCTCCAGTTACTTCTTTTATTGCAGTGCAAGAATAGCCTTAACGACACAGGTCGTTACCCTTGAGTCACGGTCTGCAGCATGTCTTTTACCATGTAAGGTATATGTTCAGTGGCTGTGGGGGTTAGGATGTGGACTTCTTTGGGGGGACTTTATTT HG:+:176283687:-1 HG:+:217702663:-1 HG:+:330224763:-1 HG:+:357186303:-1 HG:+:404214036:-1 HG:+:435461866:-1 HG:+:467888271:-1 HG:+:581176776:-1 HG:+:598236618:-1 HG:+:723019170:-1 HG:+:732363973:-1 HG:+:760302046:-1 HG:+:791158364:-1 HG:+:811199884:-1 HG:+:818717449:-1 HG:+:917643384:-1 HG:+:1016489969:-1 HG:+:1158472632:-1 HG:+:1223503439:-1 HG:+:1422222136:-1 HG:+:1472859848:-1 HG:+:1476143276:-1 HG:+:1486141680:-1 HG:+:1532438805:-1 HG:+:1646470891:-1 HG:+:1743057855:-1 HG:+:1814446055:-1 HG:+:1879293289:-1 HG:+:2057869775:-1 HG:+:2119796643:-1 HG:+:2133032913:-1 HG:+:2243116572:-1 HG:+:2298863664:-1 HG:+:2345107003:-1 HG:+:2472219040:-1 HG:+:2488260960:19 HG:+:2648008409:-1 HG:+:2667265750:-1 HG:+:2681699059:-1 HG:+:2761780345:-1 HG:+:2765580519:-1 HG:+:2804890615:-1 HG:+:2878105840:-1 HG:+:2911671751:-1 HG:+:2989425433:-1 HG:+:3009899333:-1 HG:+:3025688410:-1 +GGGTGGAACCCTCATTGCATGACTTACGGACCATCCCTTTGGTGATAAGTGAGTTCACATGATATCTGGCACCTTCCTTCCTCTGTTGCTCTTGCCCTACACCAATGTTAGCTGCCTACTCCCCTTTTGCCTTCCGCCATGACTGTAAGCCTCCCTAGGCCTCACCGGAAGCCAAGGCACATGCTTCTGTAGAGTCTGCAGAATCGGAGCCAATTAAATCTCTTTTCATTATAAATTATTCCAGCCTCCAGTTACTTCTTTTATTGCAGTGCAAGAATAGCCTTAACGACACAGGTCGTTACCCTTGAGTCACGGTCTGCAGCATGTCTTTTACCATGTAAGGTATATGTTCAGTGGCTGTGGGGGTTAGGATGTGGACTTCTTTGGGGGGACTTTATTT HG:+:2488260954:19 +GGGTGGAACCCTCATTGCATGACTTACGGACCATCCCTTTGGTGATAAGTGAGTTCACATGATATCTGGCACCTTCCTTCCTCTGTTGCTCTTGCCCTACACCAATGTTAGCTGCCTACTCCCCTTTTGCCTTCCGCCATGACTGTAAGCCTCCCTAGGCCTCACCGGAAGCCAAGGCACATGCTTCTGTAGAGTCTGCAGAATCGGAGCCAATTAAATCTCTTTTCATTATAAATTATTCCAGCCTCCAGTTACTTCTTTTATTGCAGTGCAAGAATAGCCTTAACGACACAGGTCGTTACCCTTGAGTCACGGTCTGCAGCATGTCTTTTACCATGTAAGGTATATGTTCAGTGGCTGTGGGGGTTAGGATGTGGACTTCTTTGGGGGGACTTTATTT HG:+:2488260962:19 +GGGTGGAACCCTCATTGCATGACTTACGGACCATCCCTTTGGTGATAAGTGAGTTCACATGATATCTGGCACCTTCCTTCCTCTGTTGCTCTTGCCCTACACCAATGTTAGCTGCCTACTCCCCTTTTGCCTTCCGCCATGACTGTAAGCCTCCCTAGGCCTCACCGGAAGCCAAGGCACATGCTTCTGTAGAGTCTGCAGAATCGGAGCCAATTAAATCTCTTTTCATTATAAATTATTCCAGCCTCCAGTTACTTCTTTTATTGCAGTGCAAGAATAGCCTTAACGACACAGGTCGTTACCCTTGAGTCACGGTCTGCAGCATGTCTTTTACCATGTAAGGTATATGTTCAGTGGCTGTGGGGGTTAGGATGTGGACTTCTTTGGGGGGACTTTATTT HG:+:2122074147:-1 +GGGTGGAACCCTCATTGCATGACTTACGGACCATCCCTTTGGTGATAAGTGAGTTCACATGATATCTGGCACCTTCCTTCCTCTGTTGCTCTTGCCCTACACCAATGTTAGCTGCCTACTCCCCTTTTGCCTTCCGCCATGACTGTAAGCCTCCCTAGGCCTCACCGGAAGCCAAGGCACATGCTTCTGTAGAGTCTGCAGAATCGGAGCCAATTAAATCTCTTTTCATTATAAATTATTCCAGCCTCCAGTTACTTCTTTTATTGCAGTGCAAGAATAGCCTTAACGACACAGGTCGTTACCCTTGAGTCACGGTCTGCAGCATGTCTTTTACCATGTAAGGTATATGTTCAGTGGCTGTGGGGGTTAGGATGTGGACTTCTTTGGGGGGACTTTATTT HG:+:2488260955:19 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGACAGATAAATGAGACAGAAGTTAACAAACAAATACCAGGAATTGAACGTCAGCTCTGCACCAAGCGACCCTAATAGTACATCGTACCAGAACTCTCCACCCCAAATCAACAGAATATACATTTTTTTTCAGCACACACCACCACCTATTCCAAAATTGACCGACATAGTTGGAAGTAAAGCTCTCCTCAGCCAAATGTAAAA HG:+:299838172:59 HG:+:303066943:41 HG:+:330686338:57 HG:+:670746456:69 HG:+:708966753:37 HG:+:925541321:58 HG:+:1041929392:34 HG:+:1042127217:34 HG:+:1117994462:38 HG:+:1129225137:46 HG:+:1131538047:42 HG:+:1138266278:44 HG:+:1162439169:63 HG:+:1843253184:60 HG:+:1901046861:44 HG:+:2045374752:56 HG:+:2122592949:37 HG:+:2586682574:-1 HG:+:2937698022:43 HG:+:2992868933:39 HG:+:2992997287:37 HG:+:3011631056:-1 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGACAGATAAATGAGACAGAAGTTAACAAACAAATACCAGGAATTGAACGTCAGCTCTGCACCAAGCGACCCTAATAGTACATCGTACCAGAACTCTCCACCCCAAATCAACAGAATATACATTTTTTTTCAGCACACACCACCACCTATTCCAAAATTGACCGACATAGTTGGAAGTAAAGCTCTCCTCAGCCAAATGTAAAA HG:+:1127594711:22 HG:+:1127702013:39 HG:+:1559264710:36 HG:+:1960239631:77 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGACAGATAAATGAGACAGAAGTTAACAAACAAATACCAGGAATTGAACGTCAGCTCTGCACCAAGCGACCCTAATAGTACATCGTACCAGAACTCTCCACCCCAAATCAACAGAATATACATTTTTTTTCAGCACACACCACCACCTATTCCAAAATTGACCGACATAGTTGGAAGTAAAGCTCTCCTCAGCCAAATGTAAAA HG:+:48756321:46 HG:+:50402814:36 HG:+:75020464:55 HG:+:83731455:43 HG:+:93856723:47 HG:+:298219754:37 HG:+:323201446:47 HG:+:367011617:49 HG:+:367166385:41 HG:+:387494486:36 HG:+:410240343:46 HG:+:543942226:43 HG:+:605537730:61 HG:+:646117848:35 HG:+:709869268:40 HG:+:746547062:-1 HG:+:836187455:42 HG:+:928000337:48 HG:+:1011696653:37 HG:+:1034389938:38 HG:+:1140212813:38 HG:+:1178040516:42 HG:+:1184150411:50 HG:+:1426015781:53 HG:+:1466031187:50 HG:+:1523133877:38 HG:+:1525072335:46 HG:+:1525581002:37 HG:+:1540911540:41 HG:+:1543628650:43 HG:+:1548587926:54 HG:+:1643215099:35 HG:+:1743189389:40 HG:+:1761705532:47 HG:+:1790639580:50 HG:+:1910027535:51 HG:+:1955366608:52 HG:+:2006769803:52 HG:+:2136324659:40 HG:+:2234557749:41 HG:+:2250479036:42 HG:+:2362279025:44 HG:+:2363979212:64 HG:+:2701438891:35 HG:+:2926998873:46 HG:+:2933940259:45 HG:+:2937609231:51 HG:+:2938619381:44 HG:+:2942997246:53 HG:+:2989079639:59 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGACAGATAAATGAGACAGAAGTTAACAAACAAATACCAGGAATTGAACGTCAGCTCTGCACCAAGCGACCCTAATAGTACATCGTACCAGAACTCTCCACCCCAAATCAACAGAATATACATTTTTTTTCAGCACACACCACCACCTATTCCAAAATTGACCGACATAGTTGGAAGTAAAGCTCTCCTCAGCCAAATGTAAAA HG:+:1449171026:36 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGACAGATAAATGAGACAGAAGTTAACAAACAAATACCAGGAATTGAACGTCAGCTCTGCACCAAGCGACCCTAATAGTACATCGTACCAGAACTCTCCACCCCAAATCAACAGAATATACATTTTTTTTCAGCACACACCACCACCTATTCCAAAATTGACCGACATAGTTGGAAGTAAAGCTCTCCTCAGCCAAATGTAAAA HG:+:115477327:44 HG:+:175963680:39 HG:+:180727551:-1 HG:+:282647991:38 HG:+:526165228:40 HG:+:668186068:38 HG:+:702566316:39 HG:+:775522523:41 HG:+:866415461:38 HG:+:875603963:39 HG:+:1453243377:35 HG:+:1499765866:50 HG:+:1522153745:36 HG:+:1551495878:39 HG:+:1821304731:37 HG:+:2393265066:34 HG:+:2718686074:39 HG:+:2962082143:46 HG:+:3028282779:49 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGACAGATAAATGAGACAGAAGTTAACAAACAAATACCAGGAATTGAACGTCAGCTCTGCACCAAGCGACCCTAATAGTACATCGTACCAGAACTCTCCACCCCAAATCAACAGAATATACATTTTTTTTCAGCACACACCACCACCTATTCCAAAATTGACCGACATAGTTGGAAGTAAAGCTCTCCTCAGCCAAATGTAAAA HG:+:431715868:-1 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGACAGATAAATGAGACAGAAGTTAACAAACAAATACCAGGAATTGAACGTCAGCTCTGCACCAAGCGACCCTAATAGTACATCGTACCAGAACTCTCCACCCCAAATCAACAGAATATACATTTTTTTTCAGCACACACCACCACCTATTCCAAAATTGACCGACATAGTTGGAAGTAAAGCTCTCCTCAGCCAAATGTAAAA HG:+:515843022:35 HG:+:739544587:39 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGACAGATAAATGAGACAGAAGTTAACAAACAAATACCAGGAATTGAACGTCAGCTCTGCACCAAGCGACCCTAATAGTACATCGTACCAGAACTCTCCACCCCAAATCAACAGAATATACATTTTTTTTCAGCACACACCACCACCTATTCCAAAATTGACCGACATAGTTGGAAGTAAAGCTCTCCTCAGCCAAATGTAAAA HG:+:51479295:-1 HG:+:322122844:49 HG:+:432992137:60 HG:+:624134367:56 HG:+:635561585:42 HG:+:710616743:73 HG:+:1033760515:69 HG:+:1127594713:22 HG:+:1178800754:63 HG:+:1660779884:-1 HG:+:1854214966:-1 HG:+:2033895641:64 HG:+:2367817381:65 HG:+:2937352969:45 HG:+:2946974036:66 HG:+:2955654665:-1 HG:+:3041040543:38 HG:+:3056989016:80 HG:+:3057903074:61 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGACAGATAAATGAGACAGAAGTTAACAAACAAATACCAGGAATTGAACGTCAGCTCTGCACCAAGCGACCCTAATAGTACATCGTACCAGAACTCTCCACCCCAAATCAACAGAATATACATTTTTTTTCAGCACACACCACCACCTATTCCAAAATTGACCGACATAGTTGGAAGTAAAGCTCTCCTCAGCCAAATGTAAAA HG:+:248462641:39 HG:+:818868549:36 HG:+:821412682:34 HG:+:848099790:-1 HG:+:868087861:40 HG:+:943741980:33 HG:+:986561817:41 HG:+:1082162872:41 HG:+:1492070350:36 HG:+:1716138009:41 HG:+:1916433283:32 HG:+:1929004846:50 HG:+:2284043996:35 HG:+:2428438767:34 HG:+:2935998263:42 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGACAGATAAATGAGACAGAAGTTAACAAACAAATACCAGGAATTGAACGTCAGCTCTGCACCAAGCGACCCTAATAGTACATCGTACCAGAACTCTCCACCCCAAATCAACAGAATATACATTTTTTTTCAGCACACACCACCACCTATTCCAAAATTGACCGACATAGTTGGAAGTAAAGCTCTCCTCAGCCAAATGTAAAA HG:+:30998751:-1 HG:+:75944239:35 HG:+:588549020:-1 HG:+:764187220:46 HG:+:838579750:78 HG:+:855958970:41 HG:+:934727604:35 HG:+:994039356:44 HG:+:1050652996:-1 HG:+:1101966409:34 HG:+:1510685304:-1 HG:+:1624498758:-1 HG:+:1718561209:38 HG:+:2116592953:60 HG:+:2976962715:-1 +ACATCAAAAAGAGACAAAGAAGGGCCATTACATAATGGTAAAGGGATCAATTCAACAAAGAAGAACTAACTATCCTAAATATATATGCACCAATACAGGAGCACCCAGATTCATAAAGCAAGTACTAGTTTACCTACAAAGAGACTTAGACTCCCACACAATAATAATGGAGACTTTAACACCCACTGTCAACATTAGACAGATAAATGAGACAGAAGTTAACAAACAAATACCAGGAATTGAACGTCAGCTCTGCACCAAGCGACCCTAATAGTACATCGTACCAGAACTCTCCACCCCAAATCAACAGAATATACATTTTTTTTCAGCACACACCACCACCTATTCCAAAATTGACCGACATAGTTGGAAGTAAAGCTCTCCTCAGCCAAATGTAAAA HG:+:347805414:42 HG:+:703609666:77 HG:+:711214920:45 HG:+:900059463:-1 HG:+:1376940813:-1 HG:+:1564019798:41 HG:+:1718357194:51 HG:+:1903118927:-1 HG:+:2106931613:-1 HG:+:2245819093:47 +TTTTACATTTGGCTGAGGAGAGCTTTACTTCCAACTATGTCGGTCAATTTTGGAATAGGTGGTGGTGTGTGCTGAAAAAAAATGTATATTCTGTTGATTTGGGGTGGAGAGTTCTGGTACGATGTACTATTAGGGTCGCTTGGTGCAGAGCTGACGTTCAATTCCTGGTATTTGTTTGTTAACTTCTGTCTCATTTATCTGTCTAATGTTGACAGTGGGTGTTAAAGTCTCCATTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTAAACTAGTACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGTGCATATATATTTAGGATAGTTAGTTCTTCTTTGTTGAATTGATCCCTTTACCATTATGTAATGGCCCTTCTTTGTCTCTTTTTGATGT HG:+:65919268:33 HG:+:79314437:35 HG:+:238203719:35 HG:+:392619279:34 HG:+:504522678:34 HG:+:539266681:36 HG:+:753281381:34 HG:+:772252292:39 HG:+:773504704:32 HG:+:879955147:37 HG:+:939478100:36 HG:+:1052115171:39 HG:+:1118992658:34 HG:+:1230289696:-1 HG:+:1380677500:-1 HG:+:1428851770:33 HG:+:1485333319:35 HG:+:1520124299:36 HG:+:1611976987:38 HG:+:1645531577:36 HG:+:1992350429:-1 HG:+:1993355005:33 HG:+:2031386167:33 HG:+:2052572591:36 HG:+:2132565343:36 HG:+:2257744291:38 HG:+:2389249844:36 HG:+:2443835720:36 HG:+:2596554202:37 HG:+:2737507224:35 HG:+:2762893085:36 HG:+:2936143944:41 HG:+:2997927734:34 HG:+:3017193474:33 HG:+:3052443205:36 HG:+:3054205217:43 HG:+:3057842322:39 HG:+:3061711386:40 HG:+:3063329443:38 HG:+:3063628692:38 HG:+:3064412744:33 +TTTTACATTTGGCTGAGGAGAGCTTTACTTCCAACTATGTCGGTCAATTTTGGAATAGGTGGTGGTGTGTGCTGAAAAAAAATGTATATTCTGTTGATTTGGGGTGGAGAGTTCTGGTACGATGTACTATTAGGGTCGCTTGGTGCAGAGCTGACGTTCAATTCCTGGTATTTGTTTGTTAACTTCTGTCTCATTTATCTGTCTAATGTTGACAGTGGGTGTTAAAGTCTCCATTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTAAACTAGTACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGTGCATATATATTTAGGATAGTTAGTTCTTCTTTGTTGAATTGATCCCTTTACCATTATGTAATGGCCCTTCTTTGTCTCTTTTTGATGT HG:+:160357692:52 HG:+:419726303:56 HG:+:449358239:46 HG:+:486546229:38 HG:+:633467670:43 HG:+:777804779:51 HG:+:1133750440:61 HG:+:1442650646:56 HG:+:1486191899:-1 HG:+:2457273748:53 HG:+:2947960070:53 +TTTTACATTTGGCTGAGGAGAGCTTTACTTCCAACTATGTCGGTCAATTTTGGAATAGGTGGTGGTGTGTGCTGAAAAAAAATGTATATTCTGTTGATTTGGGGTGGAGAGTTCTGGTACGATGTACTATTAGGGTCGCTTGGTGCAGAGCTGACGTTCAATTCCTGGTATTTGTTTGTTAACTTCTGTCTCATTTATCTGTCTAATGTTGACAGTGGGTGTTAAAGTCTCCATTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTAAACTAGTACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGTGCATATATATTTAGGATAGTTAGTTCTTCTTTGTTGAATTGATCCCTTTACCATTATGTAATGGCCCTTCTTTGTCTCTTTTTGATGT HG:+:97322069:38 HG:+:387404657:35 HG:+:392619277:34 HG:+:443151156:37 HG:+:467792781:56 HG:+:518733850:38 HG:+:536434799:34 HG:+:664700738:-1 HG:+:683181628:48 HG:+:759851253:39 HG:+:768855458:49 HG:+:797464980:56 HG:+:815405277:53 HG:+:862750129:72 HG:+:1114501008:32 HG:+:1124805665:-1 HG:+:1172111689:37 HG:+:1205895627:60 HG:+:1206717845:60 HG:+:1231917398:72 HG:+:1499923184:45 HG:+:1558124762:64 HG:+:1571374840:40 HG:+:1780313253:64 HG:+:2035317386:34 HG:+:2123627918:-1 HG:+:2140057787:75 HG:+:2241124128:33 HG:+:2248978915:45 HG:+:2407205763:49 HG:+:2735672037:39 HG:+:2915651137:-1 HG:+:2956290026:72 HG:+:2965352972:-1 +TTTTACATTTGGCTGAGGAGAGCTTTACTTCCAACTATGTCGGTCAATTTTGGAATAGGTGGTGGTGTGTGCTGAAAAAAAATGTATATTCTGTTGATTTGGGGTGGAGAGTTCTGGTACGATGTACTATTAGGGTCGCTTGGTGCAGAGCTGACGTTCAATTCCTGGTATTTGTTTGTTAACTTCTGTCTCATTTATCTGTCTAATGTTGACAGTGGGTGTTAAAGTCTCCATTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTAAACTAGTACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGTGCATATATATTTAGGATAGTTAGTTCTTCTTTGTTGAATTGATCCCTTTACCATTATGTAATGGCCCTTCTTTGTCTCTTTTTGATGT HG:+:408440451:71 HG:+:761773145:66 HG:+:857724616:68 HG:+:970555739:51 HG:+:1139978867:-1 HG:+:1469581603:46 HG:+:1765473572:45 HG:+:2033940680:60 HG:+:2474668710:-1 +TTTTACATTTGGCTGAGGAGAGCTTTACTTCCAACTATGTCGGTCAATTTTGGAATAGGTGGTGGTGTGTGCTGAAAAAAAATGTATATTCTGTTGATTTGGGGTGGAGAGTTCTGGTACGATGTACTATTAGGGTCGCTTGGTGCAGAGCTGACGTTCAATTCCTGGTATTTGTTTGTTAACTTCTGTCTCATTTATCTGTCTAATGTTGACAGTGGGTGTTAAAGTCTCCATTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTAAACTAGTACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGTGCATATATATTTAGGATAGTTAGTTCTTCTTTGTTGAATTGATCCCTTTACCATTATGTAATGGCCCTTCTTTGTCTCTTTTTGATGT HG:+:2495732909:-1 +TTTTACATTTGGCTGAGGAGAGCTTTACTTCCAACTATGTCGGTCAATTTTGGAATAGGTGGTGGTGTGTGCTGAAAAAAAATGTATATTCTGTTGATTTGGGGTGGAGAGTTCTGGTACGATGTACTATTAGGGTCGCTTGGTGCAGAGCTGACGTTCAATTCCTGGTATTTGTTTGTTAACTTCTGTCTCATTTATCTGTCTAATGTTGACAGTGGGTGTTAAAGTCTCCATTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTAAACTAGTACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGTGCATATATATTTAGGATAGTTAGTTCTTCTTTGTTGAATTGATCCCTTTACCATTATGTAATGGCCCTTCTTTGTCTCTTTTTGATGT HG:+:1010170546:71 +TTTTACATTTGGCTGAGGAGAGCTTTACTTCCAACTATGTCGGTCAATTTTGGAATAGGTGGTGGTGTGTGCTGAAAAAAAATGTATATTCTGTTGATTTGGGGTGGAGAGTTCTGGTACGATGTACTATTAGGGTCGCTTGGTGCAGAGCTGACGTTCAATTCCTGGTATTTGTTTGTTAACTTCTGTCTCATTTATCTGTCTAATGTTGACAGTGGGTGTTAAAGTCTCCATTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTAAACTAGTACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGTGCATATATATTTAGGATAGTTAGTTCTTCTTTGTTGAATTGATCCCTTTACCATTATGTAATGGCCCTTCTTTGTCTCTTTTTGATGT HG:+:78210409:74 HG:+:539266677:36 HG:+:695473813:73 HG:+:925831738:73 HG:+:1561665876:44 HG:+:1561897792:40 HG:+:1574408365:46 HG:+:1739682478:62 HG:+:1968770018:35 HG:+:2063184673:36 HG:+:2569012934:60 HG:+:3046106360:36 +TTTTACATTTGGCTGAGGAGAGCTTTACTTCCAACTATGTCGGTCAATTTTGGAATAGGTGGTGGTGTGTGCTGAAAAAAAATGTATATTCTGTTGATTTGGGGTGGAGAGTTCTGGTACGATGTACTATTAGGGTCGCTTGGTGCAGAGCTGACGTTCAATTCCTGGTATTTGTTTGTTAACTTCTGTCTCATTTATCTGTCTAATGTTGACAGTGGGTGTTAAAGTCTCCATTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTAAACTAGTACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGTGCATATATATTTAGGATAGTTAGTTCTTCTTTGTTGAATTGATCCCTTTACCATTATGTAATGGCCCTTCTTTGTCTCTTTTTGATGT HG:+:236352913:62 HG:+:498519202:72 HG:+:586720019:42 HG:+:705520903:-1 HG:+:878797421:-1 HG:+:1137472262:58 HG:+:1222241464:-1 HG:+:1501402499:53 HG:+:1514043844:53 HG:+:1608974660:46 HG:+:1968970707:60 HG:+:2051948307:35 HG:+:2286501763:41 HG:+:2937890392:-1 HG:+:2947401507:-1 HG:+:2953732723:73 HG:+:2996956455:62 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:72892136:-1 HG:+:86238998:-1 HG:+:95677687:-1 HG:+:117990487:-1 HG:+:210216143:-1 HG:+:248053066:79 HG:+:305616337:-1 HG:+:322959270:-1 HG:+:326254951:-1 HG:+:331424374:-1 HG:+:398158576:-1 HG:+:422304061:-1 HG:+:431883426:-1 HG:+:432885608:-1 HG:+:435632779:-1 HG:+:532107924:-1 HG:+:551110707:-1 HG:+:559554239:-1 HG:+:592787500:-1 HG:+:593597976:-1 HG:+:598268821:-1 HG:+:699533122:-1 HG:+:728414013:-1 HG:+:797374088:-1 HG:+:812391066:-1 HG:+:829308032:-1 HG:+:834036290:-1 HG:+:897439385:76 HG:+:919302481:-1 HG:+:927502518:-1 HG:+:942118831:72 HG:+:943722943:-1 HG:+:947404171:-1 HG:+:968123161:-1 HG:+:977002221:-1 HG:+:977267299:80 HG:+:987734829:-1 HG:+:1009257673:-1 HG:+:1009906923:-1 HG:+:1025596152:-1 HG:+:1026426440:-1 HG:+:1093765659:80 HG:+:1103639709:-1 HG:+:1124591501:-1 HG:+:1133610904:-1 HG:+:1137470434:-1 HG:+:1142504420:-1 HG:+:1144252898:-1 HG:+:1165794688:-1 HG:+:1177779204:-1 HG:+:1177787767:-1 HG:+:1183230598:-1 HG:+:1223831089:-1 HG:+:1254581513:-1 HG:+:1295032378:-1 HG:+:1296291516:-1 HG:+:1314464620:-1 HG:+:1339983299:-1 HG:+:1387221207:-1 HG:+:1399499741:-1 HG:+:1404779352:-1 HG:+:1450060883:-1 HG:+:1451372156:-1 HG:+:1468105726:-1 HG:+:1479359769:-1 HG:+:1479567992:-1 HG:+:1479580186:-1 HG:+:1479595461:-1 HG:+:1479607654:-1 HG:+:1479619848:-1 HG:+:1479632035:-1 HG:+:1498720560:79 HG:+:1620848715:-1 HG:+:1636392672:-1 HG:+:1685499857:-1 HG:+:1701100254:-1 HG:+:1770484549:-1 HG:+:1873816094:-1 HG:+:1875058454:-1 HG:+:1992469844:-1 HG:+:1995991053:-1 HG:+:2030814733:-1 HG:+:2033582490:-1 HG:+:2035138674:-1 HG:+:2035315531:-1 HG:+:2106620132:-1 HG:+:2125190154:-1 HG:+:2135636204:-1 HG:+:2229344728:-1 HG:+:2272813902:-1 HG:+:2462751499:-1 HG:+:2643301812:-1 HG:+:2772073455:-1 HG:+:2888968873:-1 HG:+:2936729494:-1 HG:+:2937048366:-1 HG:+:2944732980:-1 HG:+:2989369855:-1 HG:+:2989481294:-1 HG:+:3003173384:-1 HG:+:3018646191:-1 HG:+:3055856858:-1 HG:+:3059092702:-1 HG:+:3060643525:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:49583341:-1 HG:+:83994305:-1 HG:+:99086233:-1 HG:+:99557930:-1 HG:+:113955949:-1 HG:+:121324410:-1 HG:+:153080180:-1 HG:+:162071179:-1 HG:+:186515883:-1 HG:+:193609993:-1 HG:+:195787992:78 HG:+:225256098:-1 HG:+:225321377:-1 HG:+:259319058:-1 HG:+:331315770:-1 HG:+:345957781:-1 HG:+:354822130:-1 HG:+:365638051:-1 HG:+:389356068:-1 HG:+:390167790:-1 HG:+:395218952:-1 HG:+:395529106:-1 HG:+:397525668:-1 HG:+:399630385:-1 HG:+:425635264:-1 HG:+:444414655:-1 HG:+:446853721:-1 HG:+:449837916:-1 HG:+:455320243:-1 HG:+:460390999:-1 HG:+:479784699:-1 HG:+:483791551:-1 HG:+:492999264:79 HG:+:504385159:-1 HG:+:544059307:-1 HG:+:560038925:-1 HG:+:593464350:80 HG:+:635350527:-1 HG:+:673639857:-1 HG:+:679072762:-1 HG:+:681179364:-1 HG:+:749438567:-1 HG:+:759315729:-1 HG:+:786344305:-1 HG:+:802951625:-1 HG:+:859555087:-1 HG:+:865280118:-1 HG:+:871717837:-1 HG:+:886949264:-1 HG:+:904047447:-1 HG:+:906373745:-1 HG:+:921753332:-1 HG:+:926935616:-1 HG:+:933259601:-1 HG:+:952874202:-1 HG:+:977148203:-1 HG:+:985812340:-1 HG:+:989959112:-1 HG:+:994374617:-1 HG:+:997970121:-1 HG:+:1004728387:-1 HG:+:1034919806:-1 HG:+:1037631075:-1 HG:+:1046668314:-1 HG:+:1068657830:-1 HG:+:1085303958:-1 HG:+:1110067471:79 HG:+:1113888574:-1 HG:+:1143658980:-1 HG:+:1150056714:-1 HG:+:1199710892:-1 HG:+:1200749915:-1 HG:+:1206905720:-1 HG:+:1257471924:79 HG:+:1279187543:-1 HG:+:1289015100:-1 HG:+:1290178052:-1 HG:+:1297791462:-1 HG:+:1298468046:80 HG:+:1313045136:-1 HG:+:1354519486:-1 HG:+:1369809639:-1 HG:+:1453956958:-1 HG:+:1482307535:-1 HG:+:1486100182:-1 HG:+:1514041695:-1 HG:+:1519005572:-1 HG:+:1541558874:-1 HG:+:1564219308:-1 HG:+:1639258606:-1 HG:+:1642746888:-1 HG:+:1701315794:-1 HG:+:1734503583:-1 HG:+:1839338711:80 HG:+:1871200769:-1 HG:+:1904505178:-1 HG:+:1911989943:75 HG:+:1974888213:-1 HG:+:1992123306:-1 HG:+:2010656012:-1 HG:+:2016270359:-1 HG:+:2028400097:-1 HG:+:2034546559:-1 HG:+:2114252906:-1 HG:+:2133791064:-1 HG:+:2172829873:-1 HG:+:2230362211:-1 HG:+:2245836777:-1 HG:+:2285770906:78 HG:+:2342913746:-1 HG:+:2346376841:-1 HG:+:2349876426:-1 HG:+:2361523612:-1 HG:+:2361822337:-1 HG:+:2554309104:79 HG:+:2583091225:-1 HG:+:2592841706:-1 HG:+:2656365825:-1 HG:+:2656507424:-1 HG:+:2730978074:-1 HG:+:2818155354:-1 HG:+:2895510730:-1 HG:+:2895819517:-1 HG:+:2938083253:-1 HG:+:2949897185:-1 HG:+:2953730878:-1 HG:+:2957581577:-1 HG:+:2964372948:-1 HG:+:2966470914:-1 HG:+:2975128929:-1 HG:+:2984818903:-1 HG:+:2989350754:-1 HG:+:2992080815:-1 HG:+:2993847235:-1 HG:+:2997420980:-1 HG:+:3002205277:-1 HG:+:3008022532:-1 HG:+:3023072034:-1 HG:+:3035745774:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:172229460:-1 HG:+:1288129390:-1 HG:+:2964696787:-1 HG:+:2997031981:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:328098873:-1 HG:+:998878407:-1 HG:+:1717934527:-1 HG:+:2140614445:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:1324068203:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:781984318:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:74814109:-1 HG:+:432676831:-1 HG:+:434396014:-1 HG:+:975280094:-1 HG:+:1254620427:75 HG:+:2741385986:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:1080856114:-1 HG:+:1873585074:-1 HG:+:1992200462:-1 HG:+:2398026360:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:1349512422:-1 HG:+:1500236123:-1 HG:+:2243381347:-1 HG:+:2668882506:-1 HG:+:2925781919:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:367574813:-1 HG:+:461595300:-1 HG:+:1453731878:77 HG:+:1563795727:-1 HG:+:1906658173:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:964030983:-1 HG:+:1428400390:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:1109358208:-1 HG:+:1444084609:-1 HG:+:1786386883:-1 HG:+:2422915237:-1 HG:+:2464579512:-1 HG:+:2514494121:-1 HG:+:2532222722:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:96797122:-1 HG:+:147059477:-1 HG:+:209831320:-1 HG:+:291676765:-1 HG:+:310086490:-1 HG:+:317549604:-1 HG:+:330025747:-1 HG:+:388514059:-1 HG:+:388726282:-1 HG:+:419633222:-1 HG:+:432827110:-1 HG:+:459546748:-1 HG:+:469465027:-1 HG:+:507468115:-1 HG:+:522286482:-1 HG:+:623252544:-1 HG:+:927028698:-1 HG:+:1110646385:-1 HG:+:1249285599:-1 HG:+:1250446583:-1 HG:+:1271361988:-1 HG:+:1314905791:-1 HG:+:1348767030:-1 HG:+:1371257949:-1 HG:+:1735934036:-1 HG:+:1757639023:-1 HG:+:1784492417:-1 HG:+:1798177905:-1 HG:+:1899109350:-1 HG:+:1926903540:-1 HG:+:2033415521:-1 HG:+:2044746277:-1 HG:+:2147209003:-1 HG:+:2147209148:-1 HG:+:2183811493:-1 HG:+:2254820265:-1 HG:+:2259249244:-1 HG:+:2279277198:-1 HG:+:2417691927:-1 HG:+:2519594454:-1 HG:+:2561131356:-1 HG:+:2607727876:-1 HG:+:2615084665:-1 HG:+:2650838506:-1 HG:+:2769237190:-1 HG:+:2879371735:-1 HG:+:2923578318:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:454333741:-1 HG:+:521539717:-1 HG:+:821110501:-1 HG:+:944287767:-1 HG:+:1183421708:-1 HG:+:1287008485:78 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:443121863:-1 HG:+:552423742:-1 HG:+:588542304:72 HG:+:636166590:-1 HG:+:907985968:-1 HG:+:1409301873:-1 HG:+:1710369159:-1 HG:+:2072214397:-1 HG:+:2114252905:-1 HG:+:2222007181:-1 HG:+:2405496136:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:575202007:-1 HG:+:1400636598:-1 HG:+:1404797061:-1 HG:+:1405039376:-1 HG:+:1734670972:-1 HG:+:2477959538:-1 HG:+:2997785427:-1 HG:+:3038975089:-1 +TTAAATAGTTTTTCTAATTCTTTGAGGAATAGTCAGTGATGGTTTGATGGGGAATAGCTATTGATTCTATAAATTACTTTGAGCAGTATGGCCATTTTCATGATATTGATTCTTCCTATTTTCCATTTGTTTGTGTTCGCTCTTGTTCCTTGGAGTAGTGGTTTGTAGTTCTCCTTGAAGAGGTTCCTTCACATCTCTTGTTAACTGTTCTTCCTAGGATTCCTTTTGTAGCAATTGTGAATGGGAGTTCATTCTTGATTTGGCTCTTTGTCTTGTCTATTGTTGGTTTATAGGAATGCTTATCATGTTTGCTACATTCGATTTTGTATACCTGAGACTTTGCTGAAATTGCTTTATCAGCTTAAGGAGTTTTTGGGGCTCGAGATGATGGGGTTTTTCT HG:+:248270304:-1 HG:+:551327981:-1 HG:+:748899308:-1 HG:+:781598195:-1 HG:+:850962323:-1 HG:+:991091138:-1 HG:+:1998283416:-1 HG:+:2561549435:77 HG:+:2975066902:-1 +AGAAAAACCCCATCATCTCGAGCCCCAAAAACTCCTTAAGCTGATAAAGCAATTTCAGCAAAGTCTCAGGTATACAAAATCGAATGTAGCAAACATGATAAGCATTCCTATAAACCAACAATAGACAAGACAAAGAGCCAAATCAAGAATGAACTCCCATTCACAATTGCTACAAAAGGAATCCTAGGAAGAACAGTTAACAAGAGATGTGAAGGAACCTCTTCAAGGAGAACTACAAACCACTACTCCAAGGAACAAGAGCGAACACAAACAAATGGAAAATAGGAAGAATCAATATCATGAAAATGGCCATACTGCTCAAAGTAATTTATAGAATCAATAGCTATTCCCCATCAAACCATCACTGACTATTCCTCAAAGAATTAGAAAAACTATTTAA HG:+:51855146:-1 HG:+:56515350:-1 HG:+:159590322:-1 HG:+:281227158:-1 HG:+:289918697:-1 HG:+:459282383:-1 HG:+:496358556:-1 HG:+:509226353:-1 HG:+:516142812:-1 HG:+:535353505:-1 HG:+:553482806:-1 HG:+:568717467:-1 HG:+:579520369:-1 HG:+:582000609:76 HG:+:642783139:-1 HG:+:650985041:-1 HG:+:659461486:-1 HG:+:673297636:-1 HG:+:711712434:-1 HG:+:746138928:-1 HG:+:746167521:-1 HG:+:761645780:-1 HG:+:772493300:-1 HG:+:782475147:-1 HG:+:789175662:-1 HG:+:789363392:-1 HG:+:793875623:-1 HG:+:802472285:-1 HG:+:808667318:-1 HG:+:812965042:-1 HG:+:815980833:-1 HG:+:907933390:-1 HG:+:919374449:-1 HG:+:956743311:-1 HG:+:981465992:-1 HG:+:981592621:-1 HG:+:983418665:-1 HG:+:1003170953:-1 HG:+:1006587329:-1 HG:+:1025890661:-1 HG:+:1033217588:79 HG:+:1126202424:-1 HG:+:1140774250:-1 HG:+:1145799647:-1 HG:+:1149285500:-1 HG:+:1155225918:80 HG:+:1156207689:-1 HG:+:1165256567:-1 HG:+:1165449460:-1 HG:+:1216731141:-1 HG:+:1223015084:-1 HG:+:1246148771:-1 HG:+:1249170362:-1 HG:+:1328071290:77 HG:+:1417433877:-1 HG:+:1433787135:-1 HG:+:1443159369:-1 HG:+:1463572904:-1 HG:+:1477675248:-1 HG:+:1483490435:-1 HG:+:1493920667:-1 HG:+:1497471209:-1 HG:+:1500373054:-1 HG:+:1525062420:-1 HG:+:1569498949:-1 HG:+:1660781760:-1 HG:+:1716936988:-1 HG:+:1755158519:-1 HG:+:1768013682:-1 HG:+:1791683351:-1 HG:+:1812821969:-1 HG:+:1837958533:-1 HG:+:1840587019:-1 HG:+:1865798496:-1 HG:+:1878992498:-1 HG:+:1925093373:-1 HG:+:1925181930:-1 HG:+:1941486905:-1 HG:+:1946766071:-1 HG:+:1958599646:-1 HG:+:1981673911:-1 HG:+:1998936483:-1 HG:+:2006212716:-1 HG:+:2011894395:-1 HG:+:2018715881:-1 HG:+:2051352942:-1 HG:+:2159834215:-1 HG:+:2167201157:-1 HG:+:2246095868:-1 HG:+:2248997275:-1 HG:+:2258147132:-1 HG:+:2349773247:-1 HG:+:2364143480:-1 HG:+:2377351275:-1 HG:+:2384469383:-1 HG:+:2564327833:-1 HG:+:2569814939:-1 HG:+:2731880922:-1 HG:+:2893593652:-1 HG:+:2900282793:74 HG:+:2915219838:-1 HG:+:2933072358:-1 HG:+:2957153168:-1 HG:+:2957483054:-1 HG:+:2957648102:-1 HG:+:3013233197:-1 HG:+:3021147974:-1 HG:+:3059176325:-1 +AGAAAAACCCCATCATCTCGAGCCCCAAAAACTCCTTAAGCTGATAAAGCAATTTCAGCAAAGTCTCAGGTATACAAAATCGAATGTAGCAAACATGATAAGCATTCCTATAAACCAACAATAGACAAGACAAAGAGCCAAATCAAGAATGAACTCCCATTCACAATTGCTACAAAAGGAATCCTAGGAAGAACAGTTAACAAGAGATGTGAAGGAACCTCTTCAAGGAGAACTACAAACCACTACTCCAAGGAACAAGAGCGAACACAAACAAATGGAAAATAGGAAGAATCAATATCATGAAAATGGCCATACTGCTCAAAGTAATTTATAGAATCAATAGCTATTCCCCATCAAACCATCACTGACTATTCCTCAAAGAATTAGAAAAACTATTTAA HG:+:328136711:18 +AGAAAAACCCCATCATCTCGAGCCCCAAAAACTCCTTAAGCTGATAAAGCAATTTCAGCAAAGTCTCAGGTATACAAAATCGAATGTAGCAAACATGATAAGCATTCCTATAAACCAACAATAGACAAGACAAAGAGCCAAATCAAGAATGAACTCCCATTCACAATTGCTACAAAAGGAATCCTAGGAAGAACAGTTAACAAGAGATGTGAAGGAACCTCTTCAAGGAGAACTACAAACCACTACTCCAAGGAACAAGAGCGAACACAAACAAATGGAAAATAGGAAGAATCAATATCATGAAAATGGCCATACTGCTCAAAGTAATTTATAGAATCAATAGCTATTCCCCATCAAACCATCACTGACTATTCCTCAAAGAATTAGAAAAACTATTTAA HG:+:328136712:18 HG:+:777566203:-1 +AGAAAAACCCCATCATCTCGAGCCCCAAAAACTCCTTAAGCTGATAAAGCAATTTCAGCAAAGTCTCAGGTATACAAAATCGAATGTAGCAAACATGATAAGCATTCCTATAAACCAACAATAGACAAGACAAAGAGCCAAATCAAGAATGAACTCCCATTCACAATTGCTACAAAAGGAATCCTAGGAAGAACAGTTAACAAGAGATGTGAAGGAACCTCTTCAAGGAGAACTACAAACCACTACTCCAAGGAACAAGAGCGAACACAAACAAATGGAAAATAGGAAGAATCAATATCATGAAAATGGCCATACTGCTCAAAGTAATTTATAGAATCAATAGCTATTCCCCATCAAACCATCACTGACTATTCCTCAAAGAATTAGAAAAACTATTTAA HG:+:328136714:18 HG:+:2241900631:-1 +AGAAAAACCCCATCATCTCGAGCCCCAAAAACTCCTTAAGCTGATAAAGCAATTTCAGCAAAGTCTCAGGTATACAAAATCGAATGTAGCAAACATGATAAGCATTCCTATAAACCAACAATAGACAAGACAAAGAGCCAAATCAAGAATGAACTCCCATTCACAATTGCTACAAAAGGAATCCTAGGAAGAACAGTTAACAAGAGATGTGAAGGAACCTCTTCAAGGAGAACTACAAACCACTACTCCAAGGAACAAGAGCGAACACAAACAAATGGAAAATAGGAAGAATCAATATCATGAAAATGGCCATACTGCTCAAAGTAATTTATAGAATCAATAGCTATTCCCCATCAAACCATCACTGACTATTCCTCAAAGAATTAGAAAAACTATTTAA HG:+:1533225235:-1 +GGGTTGTGCAGTTGATATTTCCTCGGGAGGGGTGCTTTCAATGTCATTAACATTGGGAGTCATGGGCTAGCAGGCCAGTCCAGGATCCGCAGTAGATTTTAGTCATGGGCTGCATCTGGGCTCCATTGAGGAACTATTTAGTAGCTTTACAGCTTCAATTCTGGAAGAGACAAACTTAACAAAGAGGTTAATATACAGGGATCCCAAAGAGTTGTAACAATATTATAGCTGCTAGAGGTTCTAAGAAGGGGGAGAATCCAGGGGCATCCATTGGCTGAGGAGGCCCCAGGGGTCCAGTGTTTTGAAGCTCCCTCTGCTCTATGGTTGTATTCTAATTCTTGAACTTTCTTTAACTTTCTCGGTGACAATTCCCAGATTCGATTAAACATAATAACAAGCA HG:+:588836000:24 HG:+:912736403:-1 HG:+:1044587787:-1 HG:+:1151666208:-1 HG:+:1456303937:-1 HG:+:1902452753:-1 HG:+:2291628516:-1 +GGGTTGTGCAGTTGATATTTCCTCGGGAGGGGTGCTTTCAATGTCATTAACATTGGGAGTCATGGGCTAGCAGGCCAGTCCAGGATCCGCAGTAGATTTTAGTCATGGGCTGCATCTGGGCTCCATTGAGGAACTATTTAGTAGCTTTACAGCTTCAATTCTGGAAGAGACAAACTTAACAAAGAGGTTAATATACAGGGATCCCAAAGAGTTGTAACAATATTATAGCTGCTAGAGGTTCTAAGAAGGGGGAGAATCCAGGGGCATCCATTGGCTGAGGAGGCCCCAGGGGTCCAGTGTTTTGAAGCTCCCTCTGCTCTATGGTTGTATTCTAATTCTTGAACTTTCTTTAACTTTCTCGGTGACAATTCCCAGATTCGATTAAACATAATAACAAGCA HG:+:8410044:-1 HG:+:1365670896:-1 HG:+:1995681203:-1 HG:+:2878872557:-1 +GGGTTGTGCAGTTGATATTTCCTCGGGAGGGGTGCTTTCAATGTCATTAACATTGGGAGTCATGGGCTAGCAGGCCAGTCCAGGATCCGCAGTAGATTTTAGTCATGGGCTGCATCTGGGCTCCATTGAGGAACTATTTAGTAGCTTTACAGCTTCAATTCTGGAAGAGACAAACTTAACAAAGAGGTTAATATACAGGGATCCCAAAGAGTTGTAACAATATTATAGCTGCTAGAGGTTCTAAGAAGGGGGAGAATCCAGGGGCATCCATTGGCTGAGGAGGCCCCAGGGGTCCAGTGTTTTGAAGCTCCCTCTGCTCTATGGTTGTATTCTAATTCTTGAACTTTCTTTAACTTTCTCGGTGACAATTCCCAGATTCGATTAAACATAATAACAAGCA HG:+:59292175:-1 HG:+:212029425:57 HG:+:386210412:51 HG:+:501896117:-1 HG:+:588835999:24 HG:+:830016124:58 HG:+:938442883:58 HG:+:989537295:59 HG:+:1325755046:64 HG:+:1933815701:72 HG:+:1989336813:63 HG:+:2002211453:57 HG:+:2245425204:63 HG:+:2607012597:-1 HG:+:2987328974:54 +GGGTTGTGCAGTTGATATTTCCTCGGGAGGGGTGCTTTCAATGTCATTAACATTGGGAGTCATGGGCTAGCAGGCCAGTCCAGGATCCGCAGTAGATTTTAGTCATGGGCTGCATCTGGGCTCCATTGAGGAACTATTTAGTAGCTTTACAGCTTCAATTCTGGAAGAGACAAACTTAACAAAGAGGTTAATATACAGGGATCCCAAAGAGTTGTAACAATATTATAGCTGCTAGAGGTTCTAAGAAGGGGGAGAATCCAGGGGCATCCATTGGCTGAGGAGGCCCCAGGGGTCCAGTGTTTTGAAGCTCCCTCTGCTCTATGGTTGTATTCTAATTCTTGAACTTTCTTTAACTTTCTCGGTGACAATTCCCAGATTCGATTAAACATAATAACAAGCA HG:+:588835991:24 +GGGTTGTGCAGTTGATATTTCCTCGGGAGGGGTGCTTTCAATGTCATTAACATTGGGAGTCATGGGCTAGCAGGCCAGTCCAGGATCCGCAGTAGATTTTAGTCATGGGCTGCATCTGGGCTCCATTGAGGAACTATTTAGTAGCTTTACAGCTTCAATTCTGGAAGAGACAAACTTAACAAAGAGGTTAATATACAGGGATCCCAAAGAGTTGTAACAATATTATAGCTGCTAGAGGTTCTAAGAAGGGGGAGAATCCAGGGGCATCCATTGGCTGAGGAGGCCCCAGGGGTCCAGTGTTTTGAAGCTCCCTCTGCTCTATGGTTGTATTCTAATTCTTGAACTTTCTTTAACTTTCTCGGTGACAATTCCCAGATTCGATTAAACATAATAACAAGCA HG:+:55377447:63 HG:+:78938765:-1 HG:+:297418286:-1 HG:+:386210410:51 HG:+:588835997:24 HG:+:764264572:54 HG:+:938442881:58 HG:+:989537293:59 HG:+:1325755044:64 HG:+:1825277576:56 HG:+:1933815699:72 HG:+:2362883131:54 HG:+:2460486008:-1 HG:+:2888650827:51 HG:+:2987328972:54 HG:+:3026197935:-1 +GGGTTGTGCAGTTGATATTTCCTCGGGAGGGGTGCTTTCAATGTCATTAACATTGGGAGTCATGGGCTAGCAGGCCAGTCCAGGATCCGCAGTAGATTTTAGTCATGGGCTGCATCTGGGCTCCATTGAGGAACTATTTAGTAGCTTTACAGCTTCAATTCTGGAAGAGACAAACTTAACAAAGAGGTTAATATACAGGGATCCCAAAGAGTTGTAACAATATTATAGCTGCTAGAGGTTCTAAGAAGGGGGAGAATCCAGGGGCATCCATTGGCTGAGGAGGCCCCAGGGGTCCAGTGTTTTGAAGCTCCCTCTGCTCTATGGTTGTATTCTAATTCTTGAACTTTCTTTAACTTTCTCGGTGACAATTCCCAGATTCGATTAAACATAATAACAAGCA HG:+:55377450:63 HG:+:623366046:-1 HG:+:641924579:-1 HG:+:764264575:54 HG:+:1151666207:-1 HG:+:1347676508:-1 HG:+:1574800791:-1 HG:+:1743167364:-1 HG:+:1923760038:-1 HG:+:2002211454:57 HG:+:2700937264:-1 HG:+:2822710357:-1 HG:+:2987328975:54 +TGCTTGTTATTATGTTTAATCGAATCTGGGAATTGTCACCGAGAAAGTTAAAGAAAGTTCAAGAATTAGAATACAACCATAGAGCAGAGGGAGCTTCAAAACACTGGACCCCTGGGGCCTCCTCAGCCAATGGATGCCCCTGGATTCTCCCCCTTCTTAGAACCTCTAGCAGCTATAATATTGTTACAACTCTTTGGGATCCCTGTATATTAACCTCTTTGTTAAGTTTGTCTCTTCCAGAATTGAAGCTGTAAAGCTACTAAATAGTTCCTCAATGGAGCCCAGATGCAGCCCATGACTAAAATCTACTGCGGATCCTGGACTGGCCTGCTAGCCCATGACTCCCAATGTTAATGACATTGAAAGCACCCCTCCCGAGGAAATATCAACTGCACAACCC HG:+:89396685:-1 HG:+:91645803:-1 HG:+:266777254:-1 HG:+:279992418:-1 HG:+:283139265:-1 HG:+:303238287:-1 HG:+:356081846:-1 HG:+:430353310:-1 HG:+:628106847:-1 HG:+:633989470:57 HG:+:634611594:-1 HG:+:647146195:-1 HG:+:671227040:-1 HG:+:683832479:-1 HG:+:698900603:-1 HG:+:805444501:-1 HG:+:824281821:-1 HG:+:856050846:55 HG:+:874397081:-1 HG:+:941587655:-1 HG:+:993412553:-1 HG:+:1076425018:-1 HG:+:1128262924:-1 HG:+:1148196092:-1 HG:+:1169224749:59 HG:+:1229852807:-1 HG:+:1352867023:-1 HG:+:1367933461:-1 HG:+:1467529634:-1 HG:+:1474450223:-1 HG:+:1561982657:-1 HG:+:1633903178:58 HG:+:1746177623:-1 HG:+:1854535334:-1 HG:+:1958252642:-1 HG:+:1985169405:-1 HG:+:1991696442:-1 HG:+:2074955791:-1 HG:+:2122298528:-1 HG:+:2226665012:60 HG:+:2400130255:-1 HG:+:2534050581:75 HG:+:2586058229:-1 HG:+:2595024014:-1 HG:+:2639747129:-1 HG:+:2641516510:-1 HG:+:2679655256:-1 HG:+:2682378302:-1 HG:+:2683574385:-1 HG:+:2772542000:57 HG:+:2960250984:-1 HG:+:2986280510:-1 +TGCTTGTTATTATGTTTAATCGAATCTGGGAATTGTCACCGAGAAAGTTAAAGAAAGTTCAAGAATTAGAATACAACCATAGAGCAGAGGGAGCTTCAAAACACTGGACCCCTGGGGCCTCCTCAGCCAATGGATGCCCCTGGATTCTCCCCCTTCTTAGAACCTCTAGCAGCTATAATATTGTTACAACTCTTTGGGATCCCTGTATATTAACCTCTTTGTTAAGTTTGTCTCTTCCAGAATTGAAGCTGTAAAGCTACTAAATAGTTCCTCAATGGAGCCCAGATGCAGCCCATGACTAAAATCTACTGCGGATCCTGGACTGGCCTGCTAGCCCATGACTCCCAATGTTAATGACATTGAAAGCACCCCTCCCGAGGAAATATCAACTGCACAACCC HG:+:281108866:-1 HG:+:325355908:-1 HG:+:532150666:-1 HG:+:2253765007:-1 +TGCTTGTTATTATGTTTAATCGAATCTGGGAATTGTCACCGAGAAAGTTAAAGAAAGTTCAAGAATTAGAATACAACCATAGAGCAGAGGGAGCTTCAAAACACTGGACCCCTGGGGCCTCCTCAGCCAATGGATGCCCCTGGATTCTCCCCCTTCTTAGAACCTCTAGCAGCTATAATATTGTTACAACTCTTTGGGATCCCTGTATATTAACCTCTTTGTTAAGTTTGTCTCTTCCAGAATTGAAGCTGTAAAGCTACTAAATAGTTCCTCAATGGAGCCCAGATGCAGCCCATGACTAAAATCTACTGCGGATCCTGGACTGGCCTGCTAGCCCATGACTCCCAATGTTAATGACATTGAAAGCACCCCTCCCGAGGAAATATCAACTGCACAACCC HG:+:773872345:59 HG:+:2400130256:-1 +TGCTTGTTATTATGTTTAATCGAATCTGGGAATTGTCACCGAGAAAGTTAAAGAAAGTTCAAGAATTAGAATACAACCATAGAGCAGAGGGAGCTTCAAAACACTGGACCCCTGGGGCCTCCTCAGCCAATGGATGCCCCTGGATTCTCCCCCTTCTTAGAACCTCTAGCAGCTATAATATTGTTACAACTCTTTGGGATCCCTGTATATTAACCTCTTTGTTAAGTTTGTCTCTTCCAGAATTGAAGCTGTAAAGCTACTAAATAGTTCCTCAATGGAGCCCAGATGCAGCCCATGACTAAAATCTACTGCGGATCCTGGACTGGCCTGCTAGCCCATGACTCCCAATGTTAATGACATTGAAAGCACCCCTCCCGAGGAAATATCAACTGCACAACCC HG:+:2334053404:-1 +TGCTTGTTATTATGTTTAATCGAATCTGGGAATTGTCACCGAGAAAGTTAAAGAAAGTTCAAGAATTAGAATACAACCATAGAGCAGAGGGAGCTTCAAAACACTGGACCCCTGGGGCCTCCTCAGCCAATGGATGCCCCTGGATTCTCCCCCTTCTTAGAACCTCTAGCAGCTATAATATTGTTACAACTCTTTGGGATCCCTGTATATTAACCTCTTTGTTAAGTTTGTCTCTTCCAGAATTGAAGCTGTAAAGCTACTAAATAGTTCCTCAATGGAGCCCAGATGCAGCCCATGACTAAAATCTACTGCGGATCCTGGACTGGCCTGCTAGCCCATGACTCCCAATGTTAATGACATTGAAAGCACCCCTCCCGAGGAAATATCAACTGCACAACCC HG:+:1653259287:52 +TGCTTGTTATTATGTTTAATCGAATCTGGGAATTGTCACCGAGAAAGTTAAAGAAAGTTCAAGAATTAGAATACAACCATAGAGCAGAGGGAGCTTCAAAACACTGGACCCCTGGGGCCTCCTCAGCCAATGGATGCCCCTGGATTCTCCCCCTTCTTAGAACCTCTAGCAGCTATAATATTGTTACAACTCTTTGGGATCCCTGTATATTAACCTCTTTGTTAAGTTTGTCTCTTCCAGAATTGAAGCTGTAAAGCTACTAAATAGTTCCTCAATGGAGCCCAGATGCAGCCCATGACTAAAATCTACTGCGGATCCTGGACTGGCCTGCTAGCCCATGACTCCCAATGTTAATGACATTGAAAGCACCCCTCCCGAGGAAATATCAACTGCACAACCC HG:+:309094206:-1 +TGCTTGTTATTATGTTTAATCGAATCTGGGAATTGTCACCGAGAAAGTTAAAGAAAGTTCAAGAATTAGAATACAACCATAGAGCAGAGGGAGCTTCAAAACACTGGACCCCTGGGGCCTCCTCAGCCAATGGATGCCCCTGGATTCTCCCCCTTCTTAGAACCTCTAGCAGCTATAATATTGTTACAACTCTTTGGGATCCCTGTATATTAACCTCTTTGTTAAGTTTGTCTCTTCCAGAATTGAAGCTGTAAAGCTACTAAATAGTTCCTCAATGGAGCCCAGATGCAGCCCATGACTAAAATCTACTGCGGATCCTGGACTGGCCTGCTAGCCCATGACTCCCAATGTTAATGACATTGAAAGCACCCCTCCCGAGGAAATATCAACTGCACAACCC HG:+:393711311:-1 HG:+:425440983:52 HG:+:773872344:59 HG:+:925740528:56 HG:+:1146701186:-1 HG:+:1174000340:-1 HG:+:1383029989:-1 HG:+:1412811935:-1 HG:+:1653259278:52 HG:+:1838504264:-1 HG:+:2253765006:-1 +TGCTTGTTATTATGTTTAATCGAATCTGGGAATTGTCACCGAGAAAGTTAAAGAAAGTTCAAGAATTAGAATACAACCATAGAGCAGAGGGAGCTTCAAAACACTGGACCCCTGGGGCCTCCTCAGCCAATGGATGCCCCTGGATTCTCCCCCTTCTTAGAACCTCTAGCAGCTATAATATTGTTACAACTCTTTGGGATCCCTGTATATTAACCTCTTTGTTAAGTTTGTCTCTTCCAGAATTGAAGCTGTAAAGCTACTAAATAGTTCCTCAATGGAGCCCAGATGCAGCCCATGACTAAAATCTACTGCGGATCCTGGACTGGCCTGCTAGCCCATGACTCCCAATGTTAATGACATTGAAAGCACCCCTCCCGAGGAAATATCAACTGCACAACCC HG:+:42415096:52 HG:+:425440984:52 HG:+:466964550:-1 HG:+:576252698:-1 HG:+:856050847:55 HG:+:925740529:56 HG:+:1739103237:-1 HG:+:2056251333:61 HG:+:2079538755:-1 HG:+:2534050551:75 HG:+:2535864591:56 HG:+:2681261062:-1 HG:+:2772542001:57 HG:+:3020195373:65 +TGCTTGTTATTATGTTTAATCGAATCTGGGAATTGTCACCGAGAAAGTTAAAGAAAGTTCAAGAATTAGAATACAACCATAGAGCAGAGGGAGCTTCAAAACACTGGACCCCTGGGGCCTCCTCAGCCAATGGATGCCCCTGGATTCTCCCCCTTCTTAGAACCTCTAGCAGCTATAATATTGTTACAACTCTTTGGGATCCCTGTATATTAACCTCTTTGTTAAGTTTGTCTCTTCCAGAATTGAAGCTGTAAAGCTACTAAATAGTTCCTCAATGGAGCCCAGATGCAGCCCATGACTAAAATCTACTGCGGATCCTGGACTGGCCTGCTAGCCCATGACTCCCAATGTTAATGACATTGAAAGCACCCCTCCCGAGGAAATATCAACTGCACAACCC HG:+:42415098:52 HG:+:181247525:-1 HG:+:425440986:52 HG:+:545718178:-1 HG:+:773872347:59 HG:+:856050849:55 HG:+:925740531:56 HG:+:1072749094:-1 HG:+:1081147331:-1 HG:+:1169224752:59 HG:+:1633903181:58 HG:+:1653259281:52 HG:+:2056251335:61 HG:+:2116369543:-1 HG:+:2226665015:60 HG:+:2534050553:75 HG:+:2535864593:56 HG:+:2681261064:-1 HG:+:2748814770:-1 HG:+:2809831851:55 +TGCTTGTTATTATGTTTAATCGAATCTGGGAATTGTCACCGAGAAAGTTAAAGAAAGTTCAAGAATTAGAATACAACCATAGAGCAGAGGGAGCTTCAAAACACTGGACCCCTGGGGCCTCCTCAGCCAATGGATGCCCCTGGATTCTCCCCCTTCTTAGAACCTCTAGCAGCTATAATATTGTTACAACTCTTTGGGATCCCTGTATATTAACCTCTTTGTTAAGTTTGTCTCTTCCAGAATTGAAGCTGTAAAGCTACTAAATAGTTCCTCAATGGAGCCCAGATGCAGCCCATGACTAAAATCTACTGCGGATCCTGGACTGGCCTGCTAGCCCATGACTCCCAATGTTAATGACATTGAAAGCACCCCTCCCGAGGAAATATCAACTGCACAACCC HG:+:744958381:-1 HG:+:1006460888:-1 HG:+:1521483238:-1 HG:+:1756182054:-1 +AGTATTAACTTATTTAGAACTCACATAATTCCTATGGAGAAGGTCCTTTTATTAGGCCAACTTTACAGATTGGGAAACTGAAGGTTTGGAGGTGGGTTAAAAAGTTGCCCGACATCAATACAGCTAGGAAGTGGCAGATGGCAAGAGTTGGCTCCCCAGATTCCACGTCTCCTACAAACACACTATACTGTAGCTCAGATCACACACTGCCAATAATCTGCATTTACGCAGTTGCCATGGTTCCGGGATTCTTATTCAGCACCTGGCCATCCAAGAGAAGTCAGAGTCAAAGAGAGAAAGTTAGGGATACCCAGGCGCTATTTTATCGATTTTGGCTTTGTAAGACCTACTACCATGTTAATTTCAATCAGAGAACTTTGCTAAAATTTGCAACCAAAAG HG:+:1168367520:14 +AGTATTAACTTATTTAGAACTCACATAATTCCTATGGAGAAGGTCCTTTTATTAGGCCAACTTTACAGATTGGGAAACTGAAGGTTTGGAGGTGGGTTAAAAAGTTGCCCGACATCAATACAGCTAGGAAGTGGCAGATGGCAAGAGTTGGCTCCCCAGATTCCACGTCTCCTACAAACACACTATACTGTAGCTCAGATCACACACTGCCAATAATCTGCATTTACGCAGTTGCCATGGTTCCGGGATTCTTATTCAGCACCTGGCCATCCAAGAGAAGTCAGAGTCAAAGAGAGAAAGTTAGGGATACCCAGGCGCTATTTTATCGATTTTGGCTTTGTAAGACCTACTACCATGTTAATTTCAATCAGAGAACTTTGCTAAAATTTGCAACCAAAAG HG:+:1168367513:14 +AGTATTAACTTATTTAGAACTCACATAATTCCTATGGAGAAGGTCCTTTTATTAGGCCAACTTTACAGATTGGGAAACTGAAGGTTTGGAGGTGGGTTAAAAAGTTGCCCGACATCAATACAGCTAGGAAGTGGCAGATGGCAAGAGTTGGCTCCCCAGATTCCACGTCTCCTACAAACACACTATACTGTAGCTCAGATCACACACTGCCAATAATCTGCATTTACGCAGTTGCCATGGTTCCGGGATTCTTATTCAGCACCTGGCCATCCAAGAGAAGTCAGAGTCAAAGAGAGAAAGTTAGGGATACCCAGGCGCTATTTTATCGATTTTGGCTTTGTAAGACCTACTACCATGTTAATTTCAATCAGAGAACTTTGCTAAAATTTGCAACCAAAAG HG:+:1168367516:14 HG:+:2525880902:-1 +AGTATTAACTTATTTAGAACTCACATAATTCCTATGGAGAAGGTCCTTTTATTAGGCCAACTTTACAGATTGGGAAACTGAAGGTTTGGAGGTGGGTTAAAAAGTTGCCCGACATCAATACAGCTAGGAAGTGGCAGATGGCAAGAGTTGGCTCCCCAGATTCCACGTCTCCTACAAACACACTATACTGTAGCTCAGATCACACACTGCCAATAATCTGCATTTACGCAGTTGCCATGGTTCCGGGATTCTTATTCAGCACCTGGCCATCCAAGAGAAGTCAGAGTCAAAGAGAGAAAGTTAGGGATACCCAGGCGCTATTTTATCGATTTTGGCTTTGTAAGACCTACTACCATGTTAATTTCAATCAGAGAACTTTGCTAAAATTTGCAACCAAAAG HG:+:97539239:-1 +AGTATTAACTTATTTAGAACTCACATAATTCCTATGGAGAAGGTCCTTTTATTAGGCCAACTTTACAGATTGGGAAACTGAAGGTTTGGAGGTGGGTTAAAAAGTTGCCCGACATCAATACAGCTAGGAAGTGGCAGATGGCAAGAGTTGGCTCCCCAGATTCCACGTCTCCTACAAACACACTATACTGTAGCTCAGATCACACACTGCCAATAATCTGCATTTACGCAGTTGCCATGGTTCCGGGATTCTTATTCAGCACCTGGCCATCCAAGAGAAGTCAGAGTCAAAGAGAGAAAGTTAGGGATACCCAGGCGCTATTTTATCGATTTTGGCTTTGTAAGACCTACTACCATGTTAATTTCAATCAGAGAACTTTGCTAAAATTTGCAACCAAAAG HG:+:457285824:-1 HG:+:1567674439:-1 +AGTATTAACTTATTTAGAACTCACATAATTCCTATGGAGAAGGTCCTTTTATTAGGCCAACTTTACAGATTGGGAAACTGAAGGTTTGGAGGTGGGTTAAAAAGTTGCCCGACATCAATACAGCTAGGAAGTGGCAGATGGCAAGAGTTGGCTCCCCAGATTCCACGTCTCCTACAAACACACTATACTGTAGCTCAGATCACACACTGCCAATAATCTGCATTTACGCAGTTGCCATGGTTCCGGGATTCTTATTCAGCACCTGGCCATCCAAGAGAAGTCAGAGTCAAAGAGAGAAAGTTAGGGATACCCAGGCGCTATTTTATCGATTTTGGCTTTGTAAGACCTACTACCATGTTAATTTCAATCAGAGAACTTTGCTAAAATTTGCAACCAAAAG HG:+:1168367512:14 +CTTTTGGTTGCAAATTTTAGCAAAGTTCTCTGATTGAAATTAACATGGTAGTAGGTCTTACAAAGCCAAAATCGATAAAATAGCGCCTGGGTATCCCTAACTTTCTCTCTTTGACTCTGACTTCTCTTGGATGGCCAGGTGCTGAATAAGAATCCCGGAACCATGGCAACTGCGTAAATGCAGATTATTGGCAGTGTGTGATCTGAGCTACAGTATAGTGTGTTTGTAGGAGACGTGGAATCTGGGGAGCCAACTCTTGCCATCTGCCACTTCCTAGCTGTATTGATGTCGGGCAACTTTTTAACCCACCTCCAAACCTTCAGTTTCCCAATCTGTAAAGTTGGCCTAATAAAAGGACCTTCTCCATAGGAATTATGTGAGTTCTAAATAAGTTAATACT HG:+:481688986:-1 +CATAGTTTTAGGTAAATAAGTGGGAATCTAGAATAGACTCCAACATTAAGTCCCAAATTGCAAACTTTACATTTTTTACATATACTTCAGGAAAACATTCAAAACTTTGTTACAGTTTGCCAAGTAAATAAATTTATTTATCTTATATTCCTAAAATCCTGATTAAATTTAATTTGCGTCTAGAAGCTTTTACGCATGCCTCCCAACCCCATCCTCCTAAGATGGTATTATGCATTTTCGTTATAATTTATATTGCCTTAATTTATGCATTTTCATTATAATTTACTATTTTATAATTTATACTTTTTGTAATGGTTATGAAGGAACATTGAAATATTAAAAGGAGGTTATTTGTACTCTTGATATATAAAATGCCAAAATGGCTATTGCGTTGTTTTTC HG:+:824308297:21 +CATAGTTTTAGGTAAATAAGTGGGAATCTAGAATAGACTCCAACATTAAGTCCCAAATTGCAAACTTTACATTTTTTACATATACTTCAGGAAAACATTCAAAACTTTGTTACAGTTTGCCAAGTAAATAAATTTATTTATCTTATATTCCTAAAATCCTGATTAAATTTAATTTGCGTCTAGAAGCTTTTACGCATGCCTCCCAACCCCATCCTCCTAAGATGGTATTATGCATTTTCGTTATAATTTATATTGCCTTAATTTATGCATTTTCATTATAATTTACTATTTTATAATTTATACTTTTTGTAATGGTTATGAAGGAACATTGAAATATTAAAAGGAGGTTATTTGTACTCTTGATATATAAAATGCCAAAATGGCTATTGCGTTGTTTTTC HG:+:824308292:21 +CATAGTTTTAGGTAAATAAGTGGGAATCTAGAATAGACTCCAACATTAAGTCCCAAATTGCAAACTTTACATTTTTTACATATACTTCAGGAAAACATTCAAAACTTTGTTACAGTTTGCCAAGTAAATAAATTTATTTATCTTATATTCCTAAAATCCTGATTAAATTTAATTTGCGTCTAGAAGCTTTTACGCATGCCTCCCAACCCCATCCTCCTAAGATGGTATTATGCATTTTCGTTATAATTTATATTGCCTTAATTTATGCATTTTCATTATAATTTACTATTTTATAATTTATACTTTTTGTAATGGTTATGAAGGAACATTGAAATATTAAAAGGAGGTTATTTGTACTCTTGATATATAAAATGCCAAAATGGCTATTGCGTTGTTTTTC HG:+:824308296:21 +CATAGTTTTAGGTAAATAAGTGGGAATCTAGAATAGACTCCAACATTAAGTCCCAAATTGCAAACTTTACATTTTTTACATATACTTCAGGAAAACATTCAAAACTTTGTTACAGTTTGCCAAGTAAATAAATTTATTTATCTTATATTCCTAAAATCCTGATTAAATTTAATTTGCGTCTAGAAGCTTTTACGCATGCCTCCCAACCCCATCCTCCTAAGATGGTATTATGCATTTTCGTTATAATTTATATTGCCTTAATTTATGCATTTTCATTATAATTTACTATTTTATAATTTATACTTTTTGTAATGGTTATGAAGGAACATTGAAATATTAAAAGGAGGTTATTTGTACTCTTGATATATAAAATGCCAAAATGGCTATTGCGTTGTTTTTC HG:+:824308295:21 +GAAAAACAACGCAATAGCCATTTTGGCATTTTATATATCAAGAGTACAAATAACCTCCTTTTAATATTTCAATGTTCCTTCATAACCATTACAAAAAGTATAAATTATAAAATAGTAAATTATAATGAAAATGCATAAATTAAGGCAATATAAATTATAACGAAAATGCATAATACCATCTTAGGAGGATGGGGTTGGGAGGCATGCGTAAAAGCTTCTAGACGCAAATTAAATTTAATCAGGATTTTAGGAATATAAGATAAATAAATTTATTTACTTGGCAAACTGTAACAAAGTTTTGAATGTTTTCCTGAAGTATATGTAAAAAATGTAAAGTTTGCAATTTGGGACTTAATGTTGGAGTCTATTCTAGATTCCCACTTATTTACCTAAAACTATG HG:+:1040095703:-1 +AGTTGAGAGTCCCTATTGTTTGACTAGCCTTACCCCATGGCTACAAAATGAACTGCAAGAGCCCTAAACATCATGTTTCCCATTTACACATTCAGAGGCATAAAGCAAGGGGAAGGGTTTTGCCCAGAGAGAAATATACAAATTGTTTCACAATTACTGAAAAGTAAAAATTCTTTCTATCGAGTCACTCGAAACATTTCTGCTTAATTTTATTACCTTAGAATCACATCAATGACCACCCCTTAGCTGAAAGGCTAAGTAGGCAAAAAAATAAGAAGGGGTTAAAAATGGCTTTGGGGTAAGCAAATAAATACTTCTTAGTGCCATGTAATTTTCATAAATGTAACATCTGTACTGTCCTTACTCATAGCTCTATTTTGCACTTGGTACTTTTATTTTT HG:+:1461380785:-1 HG:+:1731163790:-1 +AGTTGAGAGTCCCTATTGTTTGACTAGCCTTACCCCATGGCTACAAAATGAACTGCAAGAGCCCTAAACATCATGTTTCCCATTTACACATTCAGAGGCATAAAGCAAGGGGAAGGGTTTTGCCCAGAGAGAAATATACAAATTGTTTCACAATTACTGAAAAGTAAAAATTCTTTCTATCGAGTCACTCGAAACATTTCTGCTTAATTTTATTACCTTAGAATCACATCAATGACCACCCCTTAGCTGAAAGGCTAAGTAGGCAAAAAAATAAGAAGGGGTTAAAAATGGCTTTGGGGTAAGCAAATAAATACTTCTTAGTGCCATGTAATTTTCATAAATGTAACATCTGTACTGTCCTTACTCATAGCTCTATTTTGCACTTGGTACTTTTATTTTT HG:+:2762782390:-1 +AGTTGAGAGTCCCTATTGTTTGACTAGCCTTACCCCATGGCTACAAAATGAACTGCAAGAGCCCTAAACATCATGTTTCCCATTTACACATTCAGAGGCATAAAGCAAGGGGAAGGGTTTTGCCCAGAGAGAAATATACAAATTGTTTCACAATTACTGAAAAGTAAAAATTCTTTCTATCGAGTCACTCGAAACATTTCTGCTTAATTTTATTACCTTAGAATCACATCAATGACCACCCCTTAGCTGAAAGGCTAAGTAGGCAAAAAAATAAGAAGGGGTTAAAAATGGCTTTGGGGTAAGCAAATAAATACTTCTTAGTGCCATGTAATTTTCATAAATGTAACATCTGTACTGTCCTTACTCATAGCTCTATTTTGCACTTGGTACTTTTATTTTT HG:+:1327506450:-1 HG:+:2112978444:-1 HG:+:2506370816:-1 HG:+:2779047893:-1 +AGTTGAGAGTCCCTATTGTTTGACTAGCCTTACCCCATGGCTACAAAATGAACTGCAAGAGCCCTAAACATCATGTTTCCCATTTACACATTCAGAGGCATAAAGCAAGGGGAAGGGTTTTGCCCAGAGAGAAATATACAAATTGTTTCACAATTACTGAAAAGTAAAAATTCTTTCTATCGAGTCACTCGAAACATTTCTGCTTAATTTTATTACCTTAGAATCACATCAATGACCACCCCTTAGCTGAAAGGCTAAGTAGGCAAAAAAATAAGAAGGGGTTAAAAATGGCTTTGGGGTAAGCAAATAAATACTTCTTAGTGCCATGTAATTTTCATAAATGTAACATCTGTACTGTCCTTACTCATAGCTCTATTTTGCACTTGGTACTTTTATTTTT HG:+:83495187:-1 HG:+:90032326:-1 HG:+:328233999:-1 HG:+:385091182:-1 HG:+:447337081:-1 HG:+:563721088:-1 HG:+:824075836:-1 HG:+:870895731:-1 HG:+:983405303:-1 HG:+:991072075:-1 HG:+:1048534094:-1 HG:+:1168996968:-1 HG:+:1170518929:-1 HG:+:1177429159:-1 HG:+:1321859228:-1 HG:+:1375987411:-1 HG:+:1544225763:-1 HG:+:1572773690:-1 HG:+:1668184345:-1 HG:+:1818687760:-1 HG:+:1936239927:-1 HG:+:1945871050:-1 HG:+:2081573375:-1 HG:+:2105880768:-1 HG:+:2107423650:-1 HG:+:2118428426:-1 HG:+:2169318683:-1 HG:+:2170508998:-1 HG:+:2178957779:-1 HG:+:2271831746:-1 HG:+:2276785305:-1 HG:+:2286546929:-1 HG:+:2335179048:-1 HG:+:2479339560:-1 HG:+:2561395280:-1 HG:+:2629686025:-1 HG:+:2758935585:-1 HG:+:2805756377:-1 HG:+:2866542724:-1 HG:+:2902748323:-1 HG:+:2965917602:-1 HG:+:3020916324:-1 +AGTTGAGAGTCCCTATTGTTTGACTAGCCTTACCCCATGGCTACAAAATGAACTGCAAGAGCCCTAAACATCATGTTTCCCATTTACACATTCAGAGGCATAAAGCAAGGGGAAGGGTTTTGCCCAGAGAGAAATATACAAATTGTTTCACAATTACTGAAAAGTAAAAATTCTTTCTATCGAGTCACTCGAAACATTTCTGCTTAATTTTATTACCTTAGAATCACATCAATGACCACCCCTTAGCTGAAAGGCTAAGTAGGCAAAAAAATAAGAAGGGGTTAAAAATGGCTTTGGGGTAAGCAAATAAATACTTCTTAGTGCCATGTAATTTTCATAAATGTAACATCTGTACTGTCCTTACTCATAGCTCTATTTTGCACTTGGTACTTTTATTTTT HG:+:191236971:-1 HG:+:234782894:-1 HG:+:376004351:-1 HG:+:390014186:-1 HG:+:432525977:-1 HG:+:600561290:-1 HG:+:723334236:-1 HG:+:727922972:-1 HG:+:781901150:-1 HG:+:911754260:-1 HG:+:940240309:-1 HG:+:1002294370:-1 HG:+:1151690239:-1 HG:+:1177769739:-1 HG:+:1204887841:-1 HG:+:1342707869:-1 HG:+:1359990569:-1 HG:+:1407023156:-1 HG:+:1408507724:-1 HG:+:1473653217:-1 HG:+:1504603344:-1 HG:+:1613084197:-1 HG:+:1689250560:-1 HG:+:1774213582:-1 HG:+:1898652449:-1 HG:+:2264154705:-1 HG:+:2264154734:-1 HG:+:2264154763:-1 HG:+:2264154792:-1 HG:+:2264154821:-1 HG:+:2264154850:-1 HG:+:2378356920:-1 HG:+:2430212997:-1 HG:+:2461284921:-1 HG:+:2619183278:-1 HG:+:2629832358:-1 HG:+:2768130455:-1 HG:+:2899372766:-1 HG:+:2928120047:-1 +AGTTGAGAGTCCCTATTGTTTGACTAGCCTTACCCCATGGCTACAAAATGAACTGCAAGAGCCCTAAACATCATGTTTCCCATTTACACATTCAGAGGCATAAAGCAAGGGGAAGGGTTTTGCCCAGAGAGAAATATACAAATTGTTTCACAATTACTGAAAAGTAAAAATTCTTTCTATCGAGTCACTCGAAACATTTCTGCTTAATTTTATTACCTTAGAATCACATCAATGACCACCCCTTAGCTGAAAGGCTAAGTAGGCAAAAAAATAAGAAGGGGTTAAAAATGGCTTTGGGGTAAGCAAATAAATACTTCTTAGTGCCATGTAATTTTCATAAATGTAACATCTGTACTGTCCTTACTCATAGCTCTATTTTGCACTTGGTACTTTTATTTTT HG:+:1051673918:-1 HG:+:1429934740:-1 HG:+:2179727441:-1 +AGTTGAGAGTCCCTATTGTTTGACTAGCCTTACCCCATGGCTACAAAATGAACTGCAAGAGCCCTAAACATCATGTTTCCCATTTACACATTCAGAGGCATAAAGCAAGGGGAAGGGTTTTGCCCAGAGAGAAATATACAAATTGTTTCACAATTACTGAAAAGTAAAAATTCTTTCTATCGAGTCACTCGAAACATTTCTGCTTAATTTTATTACCTTAGAATCACATCAATGACCACCCCTTAGCTGAAAGGCTAAGTAGGCAAAAAAATAAGAAGGGGTTAAAAATGGCTTTGGGGTAAGCAAATAAATACTTCTTAGTGCCATGTAATTTTCATAAATGTAACATCTGTACTGTCCTTACTCATAGCTCTATTTTGCACTTGGTACTTTTATTTTT HG:+:36453006:-1 HG:+:103532331:-1 HG:+:210980847:-1 HG:+:235670733:-1 HG:+:397242591:-1 HG:+:499817508:-1 HG:+:730634835:-1 HG:+:749806829:-1 HG:+:793482847:-1 HG:+:847307033:-1 HG:+:1144111347:-1 HG:+:1371958811:-1 HG:+:1402774021:-1 HG:+:1419089316:-1 HG:+:1581264097:-1 HG:+:1619218071:-1 HG:+:1663709626:-1 HG:+:1794660334:-1 HG:+:1799748377:-1 HG:+:2680879019:-1 HG:+:2792050263:-1 HG:+:2848423172:-1 +AGTTGAGAGTCCCTATTGTTTGACTAGCCTTACCCCATGGCTACAAAATGAACTGCAAGAGCCCTAAACATCATGTTTCCCATTTACACATTCAGAGGCATAAAGCAAGGGGAAGGGTTTTGCCCAGAGAGAAATATACAAATTGTTTCACAATTACTGAAAAGTAAAAATTCTTTCTATCGAGTCACTCGAAACATTTCTGCTTAATTTTATTACCTTAGAATCACATCAATGACCACCCCTTAGCTGAAAGGCTAAGTAGGCAAAAAAATAAGAAGGGGTTAAAAATGGCTTTGGGGTAAGCAAATAAATACTTCTTAGTGCCATGTAATTTTCATAAATGTAACATCTGTACTGTCCTTACTCATAGCTCTATTTTGCACTTGGTACTTTTATTTTT HG:+:1318257859:-1 +AGTTGAGAGTCCCTATTGTTTGACTAGCCTTACCCCATGGCTACAAAATGAACTGCAAGAGCCCTAAACATCATGTTTCCCATTTACACATTCAGAGGCATAAAGCAAGGGGAAGGGTTTTGCCCAGAGAGAAATATACAAATTGTTTCACAATTACTGAAAAGTAAAAATTCTTTCTATCGAGTCACTCGAAACATTTCTGCTTAATTTTATTACCTTAGAATCACATCAATGACCACCCCTTAGCTGAAAGGCTAAGTAGGCAAAAAAATAAGAAGGGGTTAAAAATGGCTTTGGGGTAAGCAAATAAATACTTCTTAGTGCCATGTAATTTTCATAAATGTAACATCTGTACTGTCCTTACTCATAGCTCTATTTTGCACTTGGTACTTTTATTTTT HG:+:71978533:-1 HG:+:148897754:-1 HG:+:187691498:-1 HG:+:332434317:-1 HG:+:332677753:-1 HG:+:428635858:-1 HG:+:704759959:-1 HG:+:725653663:-1 HG:+:965722818:-1 HG:+:1316473067:-1 HG:+:1505407665:-1 HG:+:1915442910:-1 HG:+:1926372427:-1 HG:+:1967897552:-1 HG:+:2125294220:-1 HG:+:2173474253:-1 HG:+:2250346666:-1 HG:+:2391009240:-1 HG:+:2727228607:-1 HG:+:2889804910:-1 HG:+:2979094310:-1 HG:+:3100287330:-1 +AGTTGAGAGTCCCTATTGTTTGACTAGCCTTACCCCATGGCTACAAAATGAACTGCAAGAGCCCTAAACATCATGTTTCCCATTTACACATTCAGAGGCATAAAGCAAGGGGAAGGGTTTTGCCCAGAGAGAAATATACAAATTGTTTCACAATTACTGAAAAGTAAAAATTCTTTCTATCGAGTCACTCGAAACATTTCTGCTTAATTTTATTACCTTAGAATCACATCAATGACCACCCCTTAGCTGAAAGGCTAAGTAGGCAAAAAAATAAGAAGGGGTTAAAAATGGCTTTGGGGTAAGCAAATAAATACTTCTTAGTGCCATGTAATTTTCATAAATGTAACATCTGTACTGTCCTTACTCATAGCTCTATTTTGCACTTGGTACTTTTATTTTT HG:+:189746015:-1 HG:+:266932403:-1 HG:+:297310405:-1 HG:+:438369970:-1 HG:+:563886939:-1 HG:+:618338457:-1 HG:+:659474272:-1 HG:+:704941978:-1 HG:+:717425028:-1 HG:+:750318587:-1 HG:+:802343696:-1 HG:+:993359444:-1 HG:+:1181714538:-1 HG:+:1198011813:-1 HG:+:1283735654:-1 HG:+:1311298183:-1 HG:+:1408562621:-1 HG:+:1423302908:-1 HG:+:1447353944:-1 HG:+:1521132942:-1 HG:+:1553808400:-1 HG:+:1736624441:-1 HG:+:1742158669:-1 HG:+:1778831899:-1 HG:+:1790252843:-1 HG:+:1897988231:-1 HG:+:1983002112:-1 HG:+:2026364981:-1 HG:+:2131343274:-1 HG:+:2159887396:-1 HG:+:2379062471:-1 HG:+:2405755553:-1 HG:+:2461552517:-1 HG:+:2482323128:-1 HG:+:2502642963:-1 HG:+:2653577679:-1 +AAAAATAAAAGTACCAAGTGCAAAATAGAGCTATGAGTAAGGACAGTACAGATGTTACATTTATGAAAATTACATGGCACTAAGAAGTATTTATTTGCTTACCCCAAAGCCATTTTTAACCCCTTCTTATTTTTTTGCCTACTTAGCCTTTCAGCTAAGGGGTGGTCATTGATGTGATTCTAAGGTAATAAAATTAAGCAGAAATGTTTCGAGTGACTCGATAGAAAGAATTTTTACTTTTCAGTAATTGTGAAACAATTTGTATATTTCTCTCTGGGCAAAACCCTTCCCCTTGCTTTATGCCTCTGAATGTGTAAATGGGAAACATGATGTTTAGGGCTCTTGCAGTTCATTTTGTAGCCATGGGGTAAGGCTAGTCAAACAATAGGGACTCTCAACT HG:+:731479926:-1 HG:+:816456301:23 HG:+:2671506003:-1 +AAAAATAAAAGTACCAAGTGCAAAATAGAGCTATGAGTAAGGACAGTACAGATGTTACATTTATGAAAATTACATGGCACTAAGAAGTATTTATTTGCTTACCCCAAAGCCATTTTTAACCCCTTCTTATTTTTTTGCCTACTTAGCCTTTCAGCTAAGGGGTGGTCATTGATGTGATTCTAAGGTAATAAAATTAAGCAGAAATGTTTCGAGTGACTCGATAGAAAGAATTTTTACTTTTCAGTAATTGTGAAACAATTTGTATATTTCTCTCTGGGCAAAACCCTTCCCCTTGCTTTATGCCTCTGAATGTGTAAATGGGAAACATGATGTTTAGGGCTCTTGCAGTTCATTTTGTAGCCATGGGGTAAGGCTAGTCAAACAATAGGGACTCTCAACT HG:+:816456306:23 +AAAAATAAAAGTACCAAGTGCAAAATAGAGCTATGAGTAAGGACAGTACAGATGTTACATTTATGAAAATTACATGGCACTAAGAAGTATTTATTTGCTTACCCCAAAGCCATTTTTAACCCCTTCTTATTTTTTTGCCTACTTAGCCTTTCAGCTAAGGGGTGGTCATTGATGTGATTCTAAGGTAATAAAATTAAGCAGAAATGTTTCGAGTGACTCGATAGAAAGAATTTTTACTTTTCAGTAATTGTGAAACAATTTGTATATTTCTCTCTGGGCAAAACCCTTCCCCTTGCTTTATGCCTCTGAATGTGTAAATGGGAAACATGATGTTTAGGGCTCTTGCAGTTCATTTTGTAGCCATGGGGTAAGGCTAGTCAAACAATAGGGACTCTCAACT HG:+:816456298:23 +AAAAATAAAAGTACCAAGTGCAAAATAGAGCTATGAGTAAGGACAGTACAGATGTTACATTTATGAAAATTACATGGCACTAAGAAGTATTTATTTGCTTACCCCAAAGCCATTTTTAACCCCTTCTTATTTTTTTGCCTACTTAGCCTTTCAGCTAAGGGGTGGTCATTGATGTGATTCTAAGGTAATAAAATTAAGCAGAAATGTTTCGAGTGACTCGATAGAAAGAATTTTTACTTTTCAGTAATTGTGAAACAATTTGTATATTTCTCTCTGGGCAAAACCCTTCCCCTTGCTTTATGCCTCTGAATGTGTAAATGGGAAACATGATGTTTAGGGCTCTTGCAGTTCATTTTGTAGCCATGGGGTAAGGCTAGTCAAACAATAGGGACTCTCAACT HG:+:816456299:23 +AAAAATAAAAGTACCAAGTGCAAAATAGAGCTATGAGTAAGGACAGTACAGATGTTACATTTATGAAAATTACATGGCACTAAGAAGTATTTATTTGCTTACCCCAAAGCCATTTTTAACCCCTTCTTATTTTTTTGCCTACTTAGCCTTTCAGCTAAGGGGTGGTCATTGATGTGATTCTAAGGTAATAAAATTAAGCAGAAATGTTTCGAGTGACTCGATAGAAAGAATTTTTACTTTTCAGTAATTGTGAAACAATTTGTATATTTCTCTCTGGGCAAAACCCTTCCCCTTGCTTTATGCCTCTGAATGTGTAAATGGGAAACATGATGTTTAGGGCTCTTGCAGTTCATTTTGTAGCCATGGGGTAAGGCTAGTCAAACAATAGGGACTCTCAACT HG:+:816456303:23 +AAAAATAAAAGTACCAAGTGCAAAATAGAGCTATGAGTAAGGACAGTACAGATGTTACATTTATGAAAATTACATGGCACTAAGAAGTATTTATTTGCTTACCCCAAAGCCATTTTTAACCCCTTCTTATTTTTTTGCCTACTTAGCCTTTCAGCTAAGGGGTGGTCATTGATGTGATTCTAAGGTAATAAAATTAAGCAGAAATGTTTCGAGTGACTCGATAGAAAGAATTTTTACTTTTCAGTAATTGTGAAACAATTTGTATATTTCTCTCTGGGCAAAACCCTTCCCCTTGCTTTATGCCTCTGAATGTGTAAATGGGAAACATGATGTTTAGGGCTCTTGCAGTTCATTTTGTAGCCATGGGGTAAGGCTAGTCAAACAATAGGGACTCTCAACT HG:+:1782099401:-1 +CTGTTCCCAATTCTATTCCCAAGCTCTGTCTTCGGTGGAGGTTCTTCCAAGGGCTACCTCTGCTGCTTGGCCTTTGAATTCAGATGCGTGCTTCCCCTATCCTGCTCGGGGTCTAATTGTGCTATTGCACTCCTCCTTTAGGTGTTTTCTGTTTTGTTTTCGTTTTGTTTTTTCTTGAGACAGGGTCTCATTTCTGTCGCCCAGGCTGGAGTGCGATAGCACACCTCTTGGCTCACTGCAACTCCGCCTCCTGGGTTCAAGTGAGTTCTCCTGCCTCAGCCTCCCGAGTAGCTGGATTACAGGCATGTGTATTTTTTTTTTTTAGTAGAGATGGGCTTTTGCCATGTTGGCCAGGCTGGTGTTGAACTCCTGACCTCCAAGTGATCCACCCTCCTGAGCC HG:+:24339043:-1 HG:+:117609102:-1 HG:+:156058545:-1 HG:+:156185257:-1 HG:+:168843599:-1 HG:+:192456575:-1 HG:+:288655228:-1 HG:+:402582411:-1 HG:+:447692839:-1 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+CTGTTCCCAATTCTATTCCCAAGCTCTGTCTTCGGTGGAGGTTCTTCCAAGGGCTACCTCTGCTGCTTGGCCTTTGAATTCAGATGCGTGCTTCCCCTATCCTGCTCGGGGTCTAATTGTGCTATTGCACTCCTCCTTTAGGTGTTTTCTGTTTTGTTTTCGTTTTGTTTTTTCTTGAGACAGGGTCTCATTTCTGTCGCCCAGGCTGGAGTGCGATAGCACACCTCTTGGCTCACTGCAACTCCGCCTCCTGGGTTCAAGTGAGTTCTCCTGCCTCAGCCTCCCGAGTAGCTGGATTACAGGCATGTGTATTTTTTTTTTTTAGTAGAGATGGGCTTTTGCCATGTTGGCCAGGCTGGTGTTGAACTCCTGACCTCCAAGTGATCCACCCTCCTGAGCC HG:+:662076518:-1 HG:+:1537246958:-1 HG:+:1681841833:-1 HG:+:2864028747:-1 +CTGTTCCCAATTCTATTCCCAAGCTCTGTCTTCGGTGGAGGTTCTTCCAAGGGCTACCTCTGCTGCTTGGCCTTTGAATTCAGATGCGTGCTTCCCCTATCCTGCTCGGGGTCTAATTGTGCTATTGCACTCCTCCTTTAGGTGTTTTCTGTTTTGTTTTCGTTTTGTTTTTTCTTGAGACAGGGTCTCATTTCTGTCGCCCAGGCTGGAGTGCGATAGCACACCTCTTGGCTCACTGCAACTCCGCCTCCTGGGTTCAAGTGAGTTCTCCTGCCTCAGCCTCCCGAGTAGCTGGATTACAGGCATGTGTATTTTTTTTTTTTAGTAGAGATGGGCTTTTGCCATGTTGGCCAGGCTGGTGTTGAACTCCTGACCTCCAAGTGATCCACCCTCCTGAGCC HG:+:22150232:-1 HG:+:358543899:-1 HG:+:376869156:-1 HG:+:380410289:-1 HG:+:423697588:-1 HG:+:472578514:-1 HG:+:559887151:-1 HG:+:611906331:-1 HG:+:679365101:-1 HG:+:703464101:-1 HG:+:961789672:-1 HG:+:1165272157:-1 HG:+:1264771431:-1 HG:+:1487034661:-1 HG:+:1506980744:-1 HG:+:1566990444:-1 HG:+:1572855338:-1 HG:+:1755893201:-1 HG:+:1800661744:-1 HG:+:1823734674:-1 HG:+:1897018077:-1 HG:+:1999074021:-1 HG:+:2010101159:-1 HG:+:2139537864:-1 HG:+:2195105041:-1 HG:+:2237603113:-1 HG:+:2573062031:-1 HG:+:2577278093:-1 HG:+:2667070136:-1 HG:+:2906502684:-1 HG:+:2912676685:-1 +CTGTTCCCAATTCTATTCCCAAGCTCTGTCTTCGGTGGAGGTTCTTCCAAGGGCTACCTCTGCTGCTTGGCCTTTGAATTCAGATGCGTGCTTCCCCTATCCTGCTCGGGGTCTAATTGTGCTATTGCACTCCTCCTTTAGGTGTTTTCTGTTTTGTTTTCGTTTTGTTTTTTCTTGAGACAGGGTCTCATTTCTGTCGCCCAGGCTGGAGTGCGATAGCACACCTCTTGGCTCACTGCAACTCCGCCTCCTGGGTTCAAGTGAGTTCTCCTGCCTCAGCCTCCCGAGTAGCTGGATTACAGGCATGTGTATTTTTTTTTTTTAGTAGAGATGGGCTTTTGCCATGTTGGCCAGGCTGGTGTTGAACTCCTGACCTCCAAGTGATCCACCCTCCTGAGCC HG:+:5257648:-1 HG:+:18552132:-1 HG:+:32131581:-1 HG:+:115365591:-1 HG:+:154141071:-1 HG:+:205143626:-1 HG:+:206236610:-1 HG:+:207080489:-1 HG:+:265089520:-1 HG:+:295214717:-1 HG:+:385198170:-1 HG:+:423194813:-1 HG:+:444792863:-1 HG:+:467816888:-1 HG:+:477425390:-1 HG:+:477880134:-1 HG:+:481160615:-1 HG:+:500663340:-1 HG:+:592743260:-1 HG:+:627539858:-1 HG:+:715813675:-1 HG:+:726538537:-1 HG:+:862822088:-1 HG:+:872411854:-1 HG:+:920839106:-1 HG:+:951987551:-1 HG:+:1004950714:-1 HG:+:1015027492:-1 HG:+:1027588461:-1 HG:+:1041193330:-1 HG:+:1054526588:-1 HG:+:1137042254:-1 HG:+:1141460837:-1 HG:+:1162448142:-1 HG:+:1172932654:-1 HG:+:1333493442:-1 HG:+:1338698635:-1 HG:+:1424397324:-1 HG:+:1425820365:-1 HG:+:1428702022:-1 HG:+:1497564113:-1 HG:+:1535295544:-1 HG:+:1637333146:-1 HG:+:1705501755:-1 HG:+:1717915479:-1 HG:+:1770571370:-1 HG:+:1775874805:-1 HG:+:1796484485:-1 HG:+:1796903493:-1 HG:+:1817453441:-1 HG:+:1819328068:-1 HG:+:1831053482:-1 HG:+:1836912385:-1 HG:+:1837035136:-1 HG:+:1855661216:-1 HG:+:1935464044:-1 HG:+:1950814610:-1 HG:+:1999621100:-1 HG:+:2012286647:-1 HG:+:2063116787:-1 HG:+:2069433297:-1 HG:+:2116761508:-1 HG:+:2122507851:-1 HG:+:2130378230:-1 HG:+:2138689294:-1 HG:+:2145638258:-1 HG:+:2151886032:-1 HG:+:2194784711:-1 HG:+:2333086959:-1 HG:+:2338827241:-1 HG:+:2441006483:-1 HG:+:2474424178:-1 HG:+:2478194742:-1 HG:+:2487170210:-1 HG:+:2556162867:-1 HG:+:2578179624:-1 HG:+:2646465130:-1 HG:+:2693671022:-1 HG:+:2717847680:-1 HG:+:2721096403:-1 HG:+:2721645158:-1 HG:+:2729488579:-1 HG:+:2739617124:-1 HG:+:2743545271:-1 HG:+:2819325188:-1 HG:+:2825031112:-1 HG:+:2828070260:-1 HG:+:2849299803:-1 HG:+:2858379737:-1 HG:+:2866769645:-1 HG:+:2872722737:-1 HG:+:2873205402:-1 HG:+:2875331060:-1 HG:+:2896136016:-1 HG:+:2978322682:-1 HG:+:2985447258:-1 HG:+:2993875505:-1 +CTGTTCCCAATTCTATTCCCAAGCTCTGTCTTCGGTGGAGGTTCTTCCAAGGGCTACCTCTGCTGCTTGGCCTTTGAATTCAGATGCGTGCTTCCCCTATCCTGCTCGGGGTCTAATTGTGCTATTGCACTCCTCCTTTAGGTGTTTTCTGTTTTGTTTTCGTTTTGTTTTTTCTTGAGACAGGGTCTCATTTCTGTCGCCCAGGCTGGAGTGCGATAGCACACCTCTTGGCTCACTGCAACTCCGCCTCCTGGGTTCAAGTGAGTTCTCCTGCCTCAGCCTCCCGAGTAGCTGGATTACAGGCATGTGTATTTTTTTTTTTTAGTAGAGATGGGCTTTTGCCATGTTGGCCAGGCTGGTGTTGAACTCCTGACCTCCAAGTGATCCACCCTCCTGAGCC HG:+:10017139:-1 HG:+:43297799:-1 HG:+:590707514:-1 HG:+:779997356:-1 HG:+:831673455:-1 HG:+:913018422:-1 HG:+:1077527978:-1 HG:+:1382238856:-1 HG:+:1410069746:-1 HG:+:1801781680:-1 HG:+:1898862674:-1 HG:+:2074644771:-1 HG:+:2516077117:-1 HG:+:2662700649:-1 HG:+:2696730751:-1 HG:+:2708493448:-1 HG:+:2869330467:-1 +CTGTTCCCAATTCTATTCCCAAGCTCTGTCTTCGGTGGAGGTTCTTCCAAGGGCTACCTCTGCTGCTTGGCCTTTGAATTCAGATGCGTGCTTCCCCTATCCTGCTCGGGGTCTAATTGTGCTATTGCACTCCTCCTTTAGGTGTTTTCTGTTTTGTTTTCGTTTTGTTTTTTCTTGAGACAGGGTCTCATTTCTGTCGCCCAGGCTGGAGTGCGATAGCACACCTCTTGGCTCACTGCAACTCCGCCTCCTGGGTTCAAGTGAGTTCTCCTGCCTCAGCCTCCCGAGTAGCTGGATTACAGGCATGTGTATTTTTTTTTTTTAGTAGAGATGGGCTTTTGCCATGTTGGCCAGGCTGGTGTTGAACTCCTGACCTCCAAGTGATCCACCCTCCTGAGCC HG:+:46880435:-1 HG:+:87840503:-1 HG:+:203614480:-1 HG:+:307124429:-1 HG:+:396429738:-1 HG:+:514013587:-1 HG:+:525447689:-1 HG:+:1066521967:-1 HG:+:1301136571:-1 HG:+:1334744484:-1 HG:+:1762810260:-1 HG:+:2133511719:-1 HG:+:2363214325:-1 HG:+:2505473234:-1 HG:+:2538284164:-1 HG:+:2776816822:-1 HG:+:2878467432:-1 HG:+:2919695049:-1 HG:+:2952568601:-1 +CTGTTCCCAATTCTATTCCCAAGCTCTGTCTTCGGTGGAGGTTCTTCCAAGGGCTACCTCTGCTGCTTGGCCTTTGAATTCAGATGCGTGCTTCCCCTATCCTGCTCGGGGTCTAATTGTGCTATTGCACTCCTCCTTTAGGTGTTTTCTGTTTTGTTTTCGTTTTGTTTTTTCTTGAGACAGGGTCTCATTTCTGTCGCCCAGGCTGGAGTGCGATAGCACACCTCTTGGCTCACTGCAACTCCGCCTCCTGGGTTCAAGTGAGTTCTCCTGCCTCAGCCTCCCGAGTAGCTGGATTACAGGCATGTGTATTTTTTTTTTTTAGTAGAGATGGGCTTTTGCCATGTTGGCCAGGCTGGTGTTGAACTCCTGACCTCCAAGTGATCCACCCTCCTGAGCC HG:+:298451043:-1 HG:+:879382168:-1 HG:+:1150389591:-1 HG:+:1429618649:-1 HG:+:1645492473:-1 HG:+:2047392928:-1 HG:+:2072829548:-1 HG:+:2193309532:-1 HG:+:2237559788:-1 HG:+:2666879880:-1 HG:+:2923010283:-1 +CTGTTCCCAATTCTATTCCCAAGCTCTGTCTTCGGTGGAGGTTCTTCCAAGGGCTACCTCTGCTGCTTGGCCTTTGAATTCAGATGCGTGCTTCCCCTATCCTGCTCGGGGTCTAATTGTGCTATTGCACTCCTCCTTTAGGTGTTTTCTGTTTTGTTTTCGTTTTGTTTTTTCTTGAGACAGGGTCTCATTTCTGTCGCCCAGGCTGGAGTGCGATAGCACACCTCTTGGCTCACTGCAACTCCGCCTCCTGGGTTCAAGTGAGTTCTCCTGCCTCAGCCTCCCGAGTAGCTGGATTACAGGCATGTGTATTTTTTTTTTTTAGTAGAGATGGGCTTTTGCCATGTTGGCCAGGCTGGTGTTGAACTCCTGACCTCCAAGTGATCCACCCTCCTGAGCC HG:+:245611272:-1 HG:+:335065497:-1 HG:+:462231556:-1 HG:+:1309253077:-1 HG:+:1364505660:-1 HG:+:1428972840:-1 HG:+:1909465986:-1 HG:+:2076747041:-1 +CTGTTCCCAATTCTATTCCCAAGCTCTGTCTTCGGTGGAGGTTCTTCCAAGGGCTACCTCTGCTGCTTGGCCTTTGAATTCAGATGCGTGCTTCCCCTATCCTGCTCGGGGTCTAATTGTGCTATTGCACTCCTCCTTTAGGTGTTTTCTGTTTTGTTTTCGTTTTGTTTTTTCTTGAGACAGGGTCTCATTTCTGTCGCCCAGGCTGGAGTGCGATAGCACACCTCTTGGCTCACTGCAACTCCGCCTCCTGGGTTCAAGTGAGTTCTCCTGCCTCAGCCTCCCGAGTAGCTGGATTACAGGCATGTGTATTTTTTTTTTTTAGTAGAGATGGGCTTTTGCCATGTTGGCCAGGCTGGTGTTGAACTCCTGACCTCCAAGTGATCCACCCTCCTGAGCC HG:+:172943733:-1 HG:+:1053827654:-1 HG:+:2295353764:-1 +GGCTCAGGAGGGTGGATCACTTGGAGGTCAGGAGTTCAACACCAGCCTGGCCAACATGGCAAAAGCCCATCTCTACTAAAAAAAAAAAATACACATGCCTGTAATCCAGCTACTCGGGAGGCTGAGGCAGGAGAACTCACTTGAACCCAGGAGGCGGAGTTGCAGTGAGCCAAGAGGTGTGCTATCGCACTCCAGCCTGGGCGACAGAAATGAGACCCTGTCTCAAGAAAAAACAAAACGAAAACAAAACAGAAAACACCTAAAGGAGGAGTGCAATAGCACAATTAGACCCCGAGCAGGATAGGGGAAGCACGCATCTGAATTCAAAGGCCAAGCAGCAGAGGTAGCCCTTGGAAGAACCTCCACCGAAGACAGAGCTTGGGAATAGAATTGGGAACAG HG:+:29121797:-1 HG:+:165591102:-1 HG:+:292628535:-1 HG:+:293620464:-1 HG:+:564382669:-1 HG:+:603256175:-1 HG:+:769224730:-1 HG:+:876392318:-1 HG:+:1077487421:-1 HG:+:1333266564:-1 HG:+:1388454925:-1 HG:+:1467433403:-1 HG:+:1545719208:-1 HG:+:1734209141:-1 HG:+:1925757715:-1 HG:+:2432218681:-1 HG:+:2482780909:-1 HG:+:2678074620:-1 HG:+:2694096500:-1 HG:+:2701910044:20 +GGCTCAGGAGGGTGGATCACTTGGAGGTCAGGAGTTCAACACCAGCCTGGCCAACATGGCAAAAGCCCATCTCTACTAAAAAAAAAAAATACACATGCCTGTAATCCAGCTACTCGGGAGGCTGAGGCAGGAGAACTCACTTGAACCCAGGAGGCGGAGTTGCAGTGAGCCAAGAGGTGTGCTATCGCACTCCAGCCTGGGCGACAGAAATGAGACCCTGTCTCAAGAAAAAACAAAACGAAAACAAAACAGAAAACACCTAAAGGAGGAGTGCAATAGCACAATTAGACCCCGAGCAGGATAGGGGAAGCACGCATCTGAATTCAAAGGCCAAGCAGCAGAGGTAGCCCTTGGAAGAACCTCCACCGAAGACAGAGCTTGGGAATAGAATTGGGAACAG HG:+:991642496:-1 HG:+:1631169749:-1 HG:+:2588450844:-1 +GGCTCAGGAGGGTGGATCACTTGGAGGTCAGGAGTTCAACACCAGCCTGGCCAACATGGCAAAAGCCCATCTCTACTAAAAAAAAAAAATACACATGCCTGTAATCCAGCTACTCGGGAGGCTGAGGCAGGAGAACTCACTTGAACCCAGGAGGCGGAGTTGCAGTGAGCCAAGAGGTGTGCTATCGCACTCCAGCCTGGGCGACAGAAATGAGACCCTGTCTCAAGAAAAAACAAAACGAAAACAAAACAGAAAACACCTAAAGGAGGAGTGCAATAGCACAATTAGACCCCGAGCAGGATAGGGGAAGCACGCATCTGAATTCAAAGGCCAAGCAGCAGAGGTAGCCCTTGGAAGAACCTCCACCGAAGACAGAGCTTGGGAATAGAATTGGGAACAG HG:+:2701910040:20 +GGCTCAGGAGGGTGGATCACTTGGAGGTCAGGAGTTCAACACCAGCCTGGCCAACATGGCAAAAGCCCATCTCTACTAAAAAAAAAAAATACACATGCCTGTAATCCAGCTACTCGGGAGGCTGAGGCAGGAGAACTCACTTGAACCCAGGAGGCGGAGTTGCAGTGAGCCAAGAGGTGTGCTATCGCACTCCAGCCTGGGCGACAGAAATGAGACCCTGTCTCAAGAAAAAACAAAACGAAAACAAAACAGAAAACACCTAAAGGAGGAGTGCAATAGCACAATTAGACCCCGAGCAGGATAGGGGAAGCACGCATCTGAATTCAAAGGCCAAGCAGCAGAGGTAGCCCTTGGAAGAACCTCCACCGAAGACAGAGCTTGGGAATAGAATTGGGAACAG HG:+:1045031017:-1 HG:+:2701910045:20 +GGCTCAGGAGGGTGGATCACTTGGAGGTCAGGAGTTCAACACCAGCCTGGCCAACATGGCAAAAGCCCATCTCTACTAAAAAAAAAAAATACACATGCCTGTAATCCAGCTACTCGGGAGGCTGAGGCAGGAGAACTCACTTGAACCCAGGAGGCGGAGTTGCAGTGAGCCAAGAGGTGTGCTATCGCACTCCAGCCTGGGCGACAGAAATGAGACCCTGTCTCAAGAAAAAACAAAACGAAAACAAAACAGAAAACACCTAAAGGAGGAGTGCAATAGCACAATTAGACCCCGAGCAGGATAGGGGAAGCACGCATCTGAATTCAAAGGCCAAGCAGCAGAGGTAGCCCTTGGAAGAACCTCCACCGAAGACAGAGCTTGGGAATAGAATTGGGAACAG HG:+:1126769716:-1 HG:+:1238595254:-1 HG:+:1430773030:-1 HG:+:1693705944:-1 HG:+:2546407100:-1 HG:+:2557504665:-1 HG:+:2610582552:-1 HG:+:2616264121:-1 HG:+:2701910043:20 HG:+:2826131109:-1 +GGCTCAGGAGGGTGGATCACTTGGAGGTCAGGAGTTCAACACCAGCCTGGCCAACATGGCAAAAGCCCATCTCTACTAAAAAAAAAAAATACACATGCCTGTAATCCAGCTACTCGGGAGGCTGAGGCAGGAGAACTCACTTGAACCCAGGAGGCGGAGTTGCAGTGAGCCAAGAGGTGTGCTATCGCACTCCAGCCTGGGCGACAGAAATGAGACCCTGTCTCAAGAAAAAACAAAACGAAAACAAAACAGAAAACACCTAAAGGAGGAGTGCAATAGCACAATTAGACCCCGAGCAGGATAGGGGAAGCACGCATCTGAATTCAAAGGCCAAGCAGCAGAGGTAGCCCTTGGAAGAACCTCCACCGAAGACAGAGCTTGGGAATAGAATTGGGAACAG HG:+:53060371:-1 HG:+:278327924:-1 HG:+:295234765:-1 HG:+:334567806:-1 HG:+:365879921:-1 HG:+:427033787:-1 HG:+:598306794:-1 HG:+:738460545:-1 HG:+:913793311:-1 HG:+:1138917400:-1 HG:+:1356469400:-1 HG:+:1527650296:-1 HG:+:1665137473:-1 HG:+:1782107957:-1 HG:+:2194178167:-1 HG:+:2235253685:-1 HG:+:2392031348:-1 HG:+:2700339251:-1 HG:+:2753600598:-1 HG:+:3002288651:-1 +ATTTGAAGGTCAAGATTCGTGACCAGCTGGCCAACAGGGTGAAACTCTGTGTTTACCTAAAATACAAAAATTAGACCAGGGCATGGTGGCACATGCCTGTATCCCAGCTACGAGGGAGACTGAGGCACGGAGAATCGCTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCCAAGGATTGCACCACTTGCACTCCAGCCTTGGGGTGACAGAGGAGACTCCATATCGAAAAAAAAAAGAAAGAAAAGAGAAATTTCAAACCATAAAGAATAGAGCAAAGATATGATTCATACGTTAATTATATGAATATGCAAATTCAGTAAATATTTTAACAAACTCGCAATCTAGACCTGAGATTTGTCTGATAAAGTGTTAATCACAATGAACTACACAAGACTCTCTC HG:+:8996429:-1 HG:+:10329272:-1 HG:+:26957900:-1 HG:+:28885871:-1 HG:+:33093657:-1 HG:+:35957814:-1 HG:+:38168323:-1 HG:+:40468330:-1 HG:+:46022561:-1 HG:+:47920240:-1 HG:+:110534731:-1 HG:+:117230582:-1 HG:+:151271865:-1 HG:+:151711782:-1 HG:+:174913113:-1 HG:+:178271851:-1 HG:+:199106861:-1 HG:+:201928481:-1 HG:+:211243863:-1 HG:+:238949880:-1 HG:+:270296623:-1 HG:+:273805431:-1 HG:+:283423189:-1 HG:+:314230760:-1 HG:+:322009434:-1 HG:+:336614191:-1 HG:+:337262378:-1 HG:+:348807917:-1 HG:+:351156962:-1 HG:+:372276429:-1 HG:+:375456085:-1 HG:+:398626375:-1 HG:+:410496529:-1 HG:+:436805857:-1 HG:+:439984863:-1 HG:+:446455640:-1 HG:+:457815911:-1 HG:+:473709321:-1 HG:+:507175076:-1 HG:+:512428053:-1 HG:+:534379006:-1 HG:+:540600298:-1 HG:+:541923044:-1 HG:+:546004486:-1 HG:+:561544302:-1 HG:+:568221658:-1 HG:+:595790060:-1 HG:+:612250087:-1 HG:+:612753948:-1 HG:+:624438019:-1 HG:+:630177138:-1 HG:+:630478562:-1 HG:+:634091188:-1 HG:+:663750090:-1 HG:+:669240545:-1 HG:+:792083946:-1 HG:+:830356206:-1 HG:+:855443550:-1 HG:+:868113336:-1 HG:+:898626651:-1 HG:+:912520798:-1 HG:+:960454573:-1 HG:+:974607679:-1 HG:+:982797463:-1 HG:+:1000164945:-1 HG:+:1007980462:-1 HG:+:1008715779:-1 HG:+:1014432836:-1 HG:+:1015177665:-1 HG:+:1024058434:-1 HG:+:1040418756:-1 HG:+:1060975196:-1 HG:+:1072038589:-1 HG:+:1076112393:-1 HG:+:1092125814:-1 HG:+:1094257440:-1 HG:+:1098067315:-1 HG:+:1098206983:-1 HG:+:1101161460:-1 HG:+:1118674214:-1 HG:+:1134749915:-1 HG:+:1151253184:-1 HG:+:1153038303:-1 HG:+:1167029947:-1 HG:+:1181254463:-1 HG:+:1181896489:-1 HG:+:1192849635:-1 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HG:+:1742473073:-1 HG:+:1807828607:-1 HG:+:1959150502:-1 HG:+:2136652846:-1 HG:+:2502800914:-1 HG:+:2710181155:-1 HG:+:2820438117:-1 HG:+:2871917786:-1 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAGATTCACCAAGGGTTGTAATGAAGAAAGAAATCTTAAGGGGCAGACAGAGAGAAAAGATTGGGTTATGCACAAAGGAAGTCCATCAAACTAATGCCAGATCTCTCAGCAGAAACCCTGCAAGTCAGGAAGACTGTGGGAGCCAATATTCAACATTCTTAAATAAAACACTTTTCAACCTAGGAAATTTCATATTCAGCCAA HG:+:51472320:69 HG:+:91598209:-1 HG:+:378833305:-1 HG:+:420234461:66 HG:+:923981393:68 HG:+:944014256:68 HG:+:960834915:71 HG:+:1025912767:69 HG:+:1071128121:72 HG:+:1147793919:70 HG:+:1515860709:69 HG:+:1554210580:71 HG:+:1564049896:79 HG:+:1773778483:76 HG:+:1837625637:78 HG:+:1844572116:67 HG:+:1860368180:73 HG:+:1919040742:73 HG:+:1994017783:80 HG:+:2024980994:68 HG:+:2145846239:80 HG:+:2226715724:-1 HG:+:2254202491:67 HG:+:2532777340:75 HG:+:2906935159:76 HG:+:2945273125:70 HG:+:2984881695:69 HG:+:3002229612:78 HG:+:3054956626:72 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAGATTCACCAAGGGTTGTAATGAAGAAAGAAATCTTAAGGGGCAGACAGAGAGAAAAGATTGGGTTATGCACAAAGGAAGTCCATCAAACTAATGCCAGATCTCTCAGCAGAAACCCTGCAAGTCAGGAAGACTGTGGGAGCCAATATTCAACATTCTTAAATAAAACACTTTTCAACCTAGGAAATTTCATATTCAGCCAA HG:+:91825096:-1 HG:+:99250717:-1 HG:+:172272438:72 HG:+:172284797:73 HG:+:179664886:77 HG:+:285787034:-1 HG:+:307650811:72 HG:+:341341399:75 HG:+:348910533:-1 HG:+:376170405:-1 HG:+:425785084:66 HG:+:445190459:77 HG:+:449008063:-1 HG:+:531797433:75 HG:+:551253279:73 HG:+:581056720:74 HG:+:629920952:66 HG:+:747702727:74 HG:+:779933939:66 HG:+:790887114:70 HG:+:793872894:75 HG:+:801169971:73 HG:+:808210060:73 HG:+:863297988:67 HG:+:922169390:74 HG:+:931310948:75 HG:+:970143844:66 HG:+:983315122:64 HG:+:1000733347:70 HG:+:1011781408:67 HG:+:1085523916:-1 HG:+:1129419772:78 HG:+:1190119551:71 HG:+:1194403078:65 HG:+:1208042464:74 HG:+:1270818186:73 HG:+:1343770707:69 HG:+:1375926822:-1 HG:+:1379322079:74 HG:+:1443918397:70 HG:+:1522569198:79 HG:+:1554186315:70 HG:+:1579269724:-1 HG:+:1579578438:-1 HG:+:1604899719:-1 HG:+:1644737788:-1 HG:+:1754529602:71 HG:+:1781071404:74 HG:+:1840147945:71 HG:+:1841689153:-1 HG:+:1865894330:-1 HG:+:1874426409:69 HG:+:1929436627:72 HG:+:1972071448:-1 HG:+:1989202007:79 HG:+:1998046583:75 HG:+:2012626312:69 HG:+:2014646461:79 HG:+:2137596152:70 HG:+:2256858739:-1 HG:+:2345080986:-1 HG:+:2363728895:71 HG:+:2460195709:69 HG:+:2470943199:-1 HG:+:2512227063:-1 HG:+:2539545682:80 HG:+:2622783935:72 HG:+:2682606405:77 HG:+:2902142000:69 HG:+:2945374970:-1 HG:+:2955514824:-1 HG:+:2957135133:77 HG:+:2962735748:-1 HG:+:2967543260:74 HG:+:2969582193:75 HG:+:2970937044:-1 HG:+:2977489871:80 HG:+:2982740093:73 HG:+:2985361205:-1 HG:+:3002229609:78 HG:+:3006007536:71 HG:+:3040401587:-1 HG:+:3046022693:80 HG:+:3058317113:75 HG:+:3061371183:80 HG:+:3063004936:79 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAGATTCACCAAGGGTTGTAATGAAGAAAGAAATCTTAAGGGGCAGACAGAGAGAAAAGATTGGGTTATGCACAAAGGAAGTCCATCAAACTAATGCCAGATCTCTCAGCAGAAACCCTGCAAGTCAGGAAGACTGTGGGAGCCAATATTCAACATTCTTAAATAAAACACTTTTCAACCTAGGAAATTTCATATTCAGCCAA HG:+:2349880694:80 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAGATTCACCAAGGGTTGTAATGAAGAAAGAAATCTTAAGGGGCAGACAGAGAGAAAAGATTGGGTTATGCACAAAGGAAGTCCATCAAACTAATGCCAGATCTCTCAGCAGAAACCCTGCAAGTCAGGAAGACTGTGGGAGCCAATATTCAACATTCTTAAATAAAACACTTTTCAACCTAGGAAATTTCATATTCAGCCAA HG:+:297452704:68 HG:+:527998033:-1 HG:+:991558097:-1 HG:+:1336405174:-1 HG:+:1762438350:68 HG:+:2377947205:75 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAGATTCACCAAGGGTTGTAATGAAGAAAGAAATCTTAAGGGGCAGACAGAGAGAAAAGATTGGGTTATGCACAAAGGAAGTCCATCAAACTAATGCCAGATCTCTCAGCAGAAACCCTGCAAGTCAGGAAGACTGTGGGAGCCAATATTCAACATTCTTAAATAAAACACTTTTCAACCTAGGAAATTTCATATTCAGCCAA HG:+:58030367:73 HG:+:74563010:72 HG:+:159701643:76 HG:+:227902527:-1 HG:+:248353679:-1 HG:+:300870671:79 HG:+:313034025:-1 HG:+:317068082:63 HG:+:429328768:-1 HG:+:433966151:67 HG:+:491612920:-1 HG:+:511990697:72 HG:+:527596683:71 HG:+:547874151:74 HG:+:588696922:68 HG:+:604381468:74 HG:+:630150086:70 HG:+:646082445:-1 HG:+:672653581:67 HG:+:672729140:67 HG:+:739543705:69 HG:+:743491468:77 HG:+:772868637:80 HG:+:775597614:75 HG:+:809798671:67 HG:+:829309111:-1 HG:+:874392336:-1 HG:+:890900072:72 HG:+:916732449:65 HG:+:1113632519:76 HG:+:1172543539:68 HG:+:1203094614:65 HG:+:1283738718:-1 HG:+:1313976768:71 HG:+:1339657411:78 HG:+:1451958389:-1 HG:+:1505794919:67 HG:+:1615559052:-1 HG:+:1615939677:72 HG:+:1623991960:73 HG:+:1637177957:78 HG:+:1767106263:71 HG:+:1773778482:76 HG:+:1788248920:-1 HG:+:1879107071:73 HG:+:1892101607:67 HG:+:1906811406:-1 HG:+:1920861523:-1 HG:+:1941597146:-1 HG:+:1993372599:72 HG:+:2009735476:74 HG:+:2028833371:79 HG:+:2335171437:-1 HG:+:2459080514:75 HG:+:2518607778:-1 HG:+:2589079863:68 HG:+:2797772649:75 HG:+:2857499138:76 HG:+:2901927424:-1 HG:+:2946834522:-1 HG:+:2959772284:-1 HG:+:2959783997:78 HG:+:2961056786:73 HG:+:2962908516:-1 HG:+:2963441384:-1 HG:+:2997291350:-1 HG:+:3031402999:72 HG:+:3054028016:74 HG:+:3054268861:-1 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HG:+:1957572205:-1 HG:+:3058242675:-1 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAGATTCACCAAGGGTTGTAATGAAGAAAGAAATCTTAAGGGGCAGACAGAGAGAAAAGATTGGGTTATGCACAAAGGAAGTCCATCAAACTAATGCCAGATCTCTCAGCAGAAACCCTGCAAGTCAGGAAGACTGTGGGAGCCAATATTCAACATTCTTAAATAAAACACTTTTCAACCTAGGAAATTTCATATTCAGCCAA HG:+:35278882:-1 HG:+:327876280:-1 HG:+:621536916:-1 HG:+:733008873:-1 HG:+:958466102:-1 HG:+:985980638:-1 HG:+:1086796891:-1 HG:+:1106472611:-1 HG:+:1209444265:-1 HG:+:1305924970:-1 HG:+:1372451835:-1 HG:+:1391369648:-1 HG:+:1551264985:-1 HG:+:1615754921:-1 HG:+:1622622268:-1 HG:+:1681214456:-1 HG:+:1908800821:-1 HG:+:1943538263:-1 HG:+:2060049365:-1 HG:+:2117688401:-1 HG:+:2229924415:-1 HG:+:2558523429:-1 HG:+:2634211753:-1 HG:+:2640571766:-1 HG:+:2934422302:-1 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAGATTCACCAAGGGTTGTAATGAAGAAAGAAATCTTAAGGGGCAGACAGAGAGAAAAGATTGGGTTATGCACAAAGGAAGTCCATCAAACTAATGCCAGATCTCTCAGCAGAAACCCTGCAAGTCAGGAAGACTGTGGGAGCCAATATTCAACATTCTTAAATAAAACACTTTTCAACCTAGGAAATTTCATATTCAGCCAA HG:+:496401880:71 HG:+:695399650:-1 HG:+:871325935:-1 HG:+:1044095994:-1 HG:+:1259833691:-1 HG:+:2638822029:-1 HG:+:2824783524:-1 HG:+:2995940924:-1 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAGATTCACCAAGGGTTGTAATGAAGAAAGAAATCTTAAGGGGCAGACAGAGAGAAAAGATTGGGTTATGCACAAAGGAAGTCCATCAAACTAATGCCAGATCTCTCAGCAGAAACCCTGCAAGTCAGGAAGACTGTGGGAGCCAATATTCAACATTCTTAAATAAAACACTTTTCAACCTAGGAAATTTCATATTCAGCCAA HG:+:263791985:-1 HG:+:290844189:-1 HG:+:539282851:79 HG:+:593636966:76 HG:+:649148818:-1 HG:+:815978070:-1 HG:+:828745864:-1 HG:+:888580347:79 HG:+:1009007724:73 HG:+:1264235538:69 HG:+:1701218901:67 HG:+:2033430698:-1 HG:+:2902381134:-1 HG:+:2973063131:-1 HG:+:3042063377:-1 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAGATTCACCAAGGGTTGTAATGAAGAAAGAAATCTTAAGGGGCAGACAGAGAGAAAAGATTGGGTTATGCACAAAGGAAGTCCATCAAACTAATGCCAGATCTCTCAGCAGAAACCCTGCAAGTCAGGAAGACTGTGGGAGCCAATATTCAACATTCTTAAATAAAACACTTTTCAACCTAGGAAATTTCATATTCAGCCAA HG:+:436928629:79 HG:+:643653002:74 HG:+:1730319920:-1 HG:+:1984746090:-1 HG:+:2071386850:-1 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAGATTCACCAAGGGTTGTAATGAAGAAAGAAATCTTAAGGGGCAGACAGAGAGAAAAGATTGGGTTATGCACAAAGGAAGTCCATCAAACTAATGCCAGATCTCTCAGCAGAAACCCTGCAAGTCAGGAAGACTGTGGGAGCCAATATTCAACATTCTTAAATAAAACACTTTTCAACCTAGGAAATTTCATATTCAGCCAA HG:+:21005171:-1 HG:+:102793544:-1 HG:+:201706648:-1 HG:+:699634061:-1 HG:+:835668103:-1 HG:+:892874879:-1 HG:+:1668750682:-1 HG:+:1883007277:-1 HG:+:2922852526:-1 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAGATTCACCAAGGGTTGTAATGAAGAAAGAAATCTTAAGGGGCAGACAGAGAGAAAAGATTGGGTTATGCACAAAGGAAGTCCATCAAACTAATGCCAGATCTCTCAGCAGAAACCCTGCAAGTCAGGAAGACTGTGGGAGCCAATATTCAACATTCTTAAATAAAACACTTTTCAACCTAGGAAATTTCATATTCAGCCAA HG:+:1146799569:68 HG:+:2393977497:72 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAGATTCACCAAGGGTTGTAATGAAGAAAGAAATCTTAAGGGGCAGACAGAGAGAAAAGATTGGGTTATGCACAAAGGAAGTCCATCAAACTAATGCCAGATCTCTCAGCAGAAACCCTGCAAGTCAGGAAGACTGTGGGAGCCAATATTCAACATTCTTAAATAAAACACTTTTCAACCTAGGAAATTTCATATTCAGCCAA HG:+:114993291:-1 HG:+:183221527:-1 HG:+:261831179:-1 HG:+:723318554:-1 HG:+:830927216:-1 HG:+:845128791:-1 HG:+:906192251:-1 HG:+:1044899486:-1 HG:+:1153771553:-1 HG:+:1303992747:-1 HG:+:1410846159:-1 HG:+:1413560200:-1 HG:+:1491280102:-1 HG:+:1618424193:-1 HG:+:1641035943:-1 HG:+:1664203592:-1 HG:+:1781190195:-1 HG:+:2041690693:-1 HG:+:2078064167:-1 HG:+:2273054003:-1 HG:+:2507259473:-1 HG:+:2602218866:-1 HG:+:2876523182:-1 HG:+:2976394782:-1 HG:+:3050669557:-1 HG:+:3061203746:-1 HG:+:3062837508:-1 +AAAGACTTAAAATCTTATGTTTGAATGGTGTACATGAAGTAACAAGGAGAATGGAATCAAGTTGGGAAACCACTCTTCAGGATATTATCCAAGAGAATTTCCTCAACCTAAGGCAGGACCAACATTCAAATTCAGGAAATACAGAGAAAACCACAAAGGACATCCTTGAGAAGAGCAACCCCAAGACACATAATCATCAGATTCACCAAGGGTTGTAATGAAGAAAGAAATCTTAAGGGGCAGACAGAGAGAAAAGATTGGGTTATGCACAAAGGAAGTCCATCAAACTAATGCCAGATCTCTCAGCAGAAACCCTGCAAGTCAGGAAGACTGTGGGAGCCAATATTCAACATTCTTAAATAAAACACTTTTCAACCTAGGAAATTTCATATTCAGCCAA HG:+:56556602:73 HG:+:85555665:-1 HG:+:438979017:-1 HG:+:1978108791:70 HG:+:2813459396:-1 +TTGGCTGAATATGAAATTTCCTAGGTTGAAAAGTGTTTTATTTAAGAATGTTGAATATTGGCTCCCACAGTCTTCCTGACTTGCAGGGTTTCTGCTGAGAGATCTGGCATTAGTTTGATGGACTTCCTTTGTGCATAACCCAATCTTTTCTCTCTGTCTGCCCCTTAAGATTTCTTTCTTCATTACAACCCTTGGTGAATCTGATGATTATGTGTCTTGGGGTTGCTCTTCTCAAGGATGTCCTTTGTGGTTTTCTCTGTATTTCCTGAATTTGAATGTTGGTCCTGCCTTAGGTTGAGGAAATTCTCTTGGATAATATCCTGAAGAGTGGTTTCCCAACTTGATTCCATTCTCCTTGTTACTTCATGTACACCATTCAAACATAAGATTTTAAGTCTTT HG:+:186479726:-1 HG:+:230792994:80 HG:+:388077709:70 HG:+:551112503:70 HG:+:561183755:74 HG:+:567506210:73 HG:+:934231871:78 HG:+:944282063:-1 HG:+:956487088:76 HG:+:968138591:75 HG:+:999937101:69 HG:+:1131706353:69 HG:+:1189028570:72 HG:+:1245048453:76 HG:+:1282302017:75 HG:+:1433163819:-1 HG:+:1513794139:68 HG:+:1542782226:74 HG:+:1556313046:77 HG:+:1633399825:67 HG:+:1829462280:75 HG:+:1873956851:76 HG:+:1917243590:72 HG:+:1967840572:-1 HG:+:1984265390:77 HG:+:2027476257:62 HG:+:2032787773:-1 HG:+:2056319856:68 HG:+:2056491623:73 HG:+:2114554980:74 HG:+:2229432946:-1 HG:+:2256401142:72 HG:+:2257946171:69 HG:+:2294553378:-1 HG:+:2346149691:74 HG:+:2635049040:67 HG:+:2694501621:66 HG:+:2893888940:72 HG:+:2895785813:72 HG:+:2930187958:71 HG:+:2986768524:72 HG:+:3019179803:-1 HG:+:3052226637:76 HG:+:3059312605:16 +TTGGCTGAATATGAAATTTCCTAGGTTGAAAAGTGTTTTATTTAAGAATGTTGAATATTGGCTCCCACAGTCTTCCTGACTTGCAGGGTTTCTGCTGAGAGATCTGGCATTAGTTTGATGGACTTCCTTTGTGCATAACCCAATCTTTTCTCTCTGTCTGCCCCTTAAGATTTCTTTCTTCATTACAACCCTTGGTGAATCTGATGATTATGTGTCTTGGGGTTGCTCTTCTCAAGGATGTCCTTTGTGGTTTTCTCTGTATTTCCTGAATTTGAATGTTGGTCCTGCCTTAGGTTGAGGAAATTCTCTTGGATAATATCCTGAAGAGTGGTTTCCCAACTTGATTCCATTCTCCTTGTTACTTCATGTACACCATTCAAACATAAGATTTTAAGTCTTT HG:+:1370324399:71 HG:+:3059312604:16 +TTGGCTGAATATGAAATTTCCTAGGTTGAAAAGTGTTTTATTTAAGAATGTTGAATATTGGCTCCCACAGTCTTCCTGACTTGCAGGGTTTCTGCTGAGAGATCTGGCATTAGTTTGATGGACTTCCTTTGTGCATAACCCAATCTTTTCTCTCTGTCTGCCCCTTAAGATTTCTTTCTTCATTACAACCCTTGGTGAATCTGATGATTATGTGTCTTGGGGTTGCTCTTCTCAAGGATGTCCTTTGTGGTTTTCTCTGTATTTCCTGAATTTGAATGTTGGTCCTGCCTTAGGTTGAGGAAATTCTCTTGGATAATATCCTGAAGAGTGGTTTCCCAACTTGATTCCATTCTCCTTGTTACTTCATGTACACCATTCAAACATAAGATTTTAAGTCTTT HG:+:3059312606:16 +TTGGCTGAATATGAAATTTCCTAGGTTGAAAAGTGTTTTATTTAAGAATGTTGAATATTGGCTCCCACAGTCTTCCTGACTTGCAGGGTTTCTGCTGAGAGATCTGGCATTAGTTTGATGGACTTCCTTTGTGCATAACCCAATCTTTTCTCTCTGTCTGCCCCTTAAGATTTCTTTCTTCATTACAACCCTTGGTGAATCTGATGATTATGTGTCTTGGGGTTGCTCTTCTCAAGGATGTCCTTTGTGGTTTTCTCTGTATTTCCTGAATTTGAATGTTGGTCCTGCCTTAGGTTGAGGAAATTCTCTTGGATAATATCCTGAAGAGTGGTTTCCCAACTTGATTCCATTCTCCTTGTTACTTCATGTACACCATTCAAACATAAGATTTTAAGTCTTT HG:+:2759244626:-1 +TTGGCTGAATATGAAATTTCCTAGGTTGAAAAGTGTTTTATTTAAGAATGTTGAATATTGGCTCCCACAGTCTTCCTGACTTGCAGGGTTTCTGCTGAGAGATCTGGCATTAGTTTGATGGACTTCCTTTGTGCATAACCCAATCTTTTCTCTCTGTCTGCCCCTTAAGATTTCTTTCTTCATTACAACCCTTGGTGAATCTGATGATTATGTGTCTTGGGGTTGCTCTTCTCAAGGATGTCCTTTGTGGTTTTCTCTGTATTTCCTGAATTTGAATGTTGGTCCTGCCTTAGGTTGAGGAAATTCTCTTGGATAATATCCTGAAGAGTGGTTTCCCAACTTGATTCCATTCTCCTTGTTACTTCATGTACACCATTCAAACATAAGATTTTAAGTCTTT HG:+:3059312609:16 +TTGGCTGAATATGAAATTTCCTAGGTTGAAAAGTGTTTTATTTAAGAATGTTGAATATTGGCTCCCACAGTCTTCCTGACTTGCAGGGTTTCTGCTGAGAGATCTGGCATTAGTTTGATGGACTTCCTTTGTGCATAACCCAATCTTTTCTCTCTGTCTGCCCCTTAAGATTTCTTTCTTCATTACAACCCTTGGTGAATCTGATGATTATGTGTCTTGGGGTTGCTCTTCTCAAGGATGTCCTTTGTGGTTTTCTCTGTATTTCCTGAATTTGAATGTTGGTCCTGCCTTAGGTTGAGGAAATTCTCTTGGATAATATCCTGAAGAGTGGTTTCCCAACTTGATTCCATTCTCCTTGTTACTTCATGTACACCATTCAAACATAAGATTTTAAGTCTTT HG:+:3059312603:16 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAGGCTTAAAAACGACATTATTTTATGTGGTTACATAAAACATCGAATTTAGAATTAAGCCATTGAATTACAGAACTCCATATAAATCTCTTATAATTGAACAACAAATTTCCATGTGTGGTGTGGGCCGGGGAGAGGATGGGCTAATCACCCCCTCTTTTTGATGTTGCTAGAAAATAATCTAAAATATGAGAGAAAGACTT HG:+:205815930:-1 HG:+:414694653:-1 HG:+:451846330:-1 HG:+:489495996:-1 HG:+:917302813:-1 HG:+:1102309593:-1 HG:+:1280807136:-1 HG:+:1338204528:-1 HG:+:1345790914:-1 HG:+:1484403426:-1 HG:+:1623098809:-1 HG:+:1699733196:-1 HG:+:1764966729:-1 HG:+:1816725546:-1 HG:+:2150042679:-1 HG:+:2160497447:-1 HG:+:2362186263:-1 HG:+:2459086741:-1 HG:+:2805481277:-1 HG:+:2818412145:-1 HG:+:2929822707:-1 HG:+:2957465164:-1 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAGGCTTAAAAACGACATTATTTTATGTGGTTACATAAAACATCGAATTTAGAATTAAGCCATTGAATTACAGAACTCCATATAAATCTCTTATAATTGAACAACAAATTTCCATGTGTGGTGTGGGCCGGGGAGAGGATGGGCTAATCACCCCCTCTTTTTGATGTTGCTAGAAAATAATCTAAAATATGAGAGAAAGACTT HG:+:331210429:-1 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAGGCTTAAAAACGACATTATTTTATGTGGTTACATAAAACATCGAATTTAGAATTAAGCCATTGAATTACAGAACTCCATATAAATCTCTTATAATTGAACAACAAATTTCCATGTGTGGTGTGGGCCGGGGAGAGGATGGGCTAATCACCCCCTCTTTTTGATGTTGCTAGAAAATAATCTAAAATATGAGAGAAAGACTT HG:+:81013544:-1 HG:+:324658626:-1 HG:+:416092857:-1 HG:+:458498543:-1 HG:+:561667347:-1 HG:+:667345214:-1 HG:+:672750900:-1 HG:+:722067345:-1 HG:+:953032890:-1 HG:+:956792591:-1 HG:+:991116138:-1 HG:+:1000349781:-1 HG:+:1020016057:-1 HG:+:1097614440:-1 HG:+:1153635930:-1 HG:+:1160633579:-1 HG:+:1186025940:-1 HG:+:1209510584:-1 HG:+:1323594245:-1 HG:+:1376049437:-1 HG:+:1511933665:-1 HG:+:1634119619:-1 HG:+:1654641790:-1 HG:+:1705859041:-1 HG:+:1779372687:-1 HG:+:1823595826:-1 HG:+:1832562908:-1 HG:+:1892124036:-1 HG:+:1898267226:-1 HG:+:1912837666:-1 HG:+:1944191169:-1 HG:+:1951826599:-1 HG:+:1992422893:-1 HG:+:2044530783:-1 HG:+:2108972615:-1 HG:+:2151544498:-1 HG:+:2167587273:-1 HG:+:2174823531:-1 HG:+:2225228523:-1 HG:+:2250195985:-1 HG:+:2362944760:-1 HG:+:2552200590:-1 HG:+:2619236180:-1 HG:+:2681014783:-1 HG:+:2681283632:-1 HG:+:2750012091:-1 HG:+:2912366164:-1 HG:+:2969408138:-1 HG:+:3034428270:-1 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAGGCTTAAAAACGACATTATTTTATGTGGTTACATAAAACATCGAATTTAGAATTAAGCCATTGAATTACAGAACTCCATATAAATCTCTTATAATTGAACAACAAATTTCCATGTGTGGTGTGGGCCGGGGAGAGGATGGGCTAATCACCCCCTCTTTTTGATGTTGCTAGAAAATAATCTAAAATATGAGAGAAAGACTT HG:+:709140148:-1 HG:+:2709021143:-1 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAGGCTTAAAAACGACATTATTTTATGTGGTTACATAAAACATCGAATTTAGAATTAAGCCATTGAATTACAGAACTCCATATAAATCTCTTATAATTGAACAACAAATTTCCATGTGTGGTGTGGGCCGGGGAGAGGATGGGCTAATCACCCCCTCTTTTTGATGTTGCTAGAAAATAATCTAAAATATGAGAGAAAGACTT HG:+:744979993:-1 HG:+:786062320:-1 HG:+:1312212286:-1 HG:+:1549606306:-1 HG:+:1736701267:-1 HG:+:3004456014:-1 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAGGCTTAAAAACGACATTATTTTATGTGGTTACATAAAACATCGAATTTAGAATTAAGCCATTGAATTACAGAACTCCATATAAATCTCTTATAATTGAACAACAAATTTCCATGTGTGGTGTGGGCCGGGGAGAGGATGGGCTAATCACCCCCTCTTTTTGATGTTGCTAGAAAATAATCTAAAATATGAGAGAAAGACTT HG:+:150009945:-1 HG:+:244618737:-1 HG:+:456638554:-1 HG:+:529786871:-1 HG:+:552290966:-1 HG:+:776861368:-1 HG:+:946884909:-1 HG:+:958752121:-1 HG:+:963922717:-1 HG:+:1055092642:-1 HG:+:1385830754:-1 HG:+:1526264197:-1 HG:+:1611599967:-1 HG:+:1824489680:-1 HG:+:1857251488:-1 HG:+:1948863820:-1 HG:+:2127714564:-1 HG:+:2279968274:-1 HG:+:2370797750:-1 HG:+:2420798974:-1 HG:+:2430324807:-1 HG:+:2552760626:-1 HG:+:2571289266:-1 HG:+:2639541855:-1 HG:+:2876920689:-1 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAGGCTTAAAAACGACATTATTTTATGTGGTTACATAAAACATCGAATTTAGAATTAAGCCATTGAATTACAGAACTCCATATAAATCTCTTATAATTGAACAACAAATTTCCATGTGTGGTGTGGGCCGGGGAGAGGATGGGCTAATCACCCCCTCTTTTTGATGTTGCTAGAAAATAATCTAAAATATGAGAGAAAGACTT HG:+:68510065:-1 HG:+:196575411:-1 HG:+:268627092:-1 HG:+:320719108:-1 HG:+:552481098:-1 HG:+:552929367:-1 HG:+:655492869:-1 HG:+:673132395:-1 HG:+:761524681:-1 HG:+:782315507:-1 HG:+:914517290:-1 HG:+:992658571:-1 HG:+:1035415475:-1 HG:+:1126530567:-1 HG:+:1170792569:-1 HG:+:1319408730:-1 HG:+:1458070335:-1 HG:+:1491422472:-1 HG:+:1638329752:-1 HG:+:1668060022:-1 HG:+:1743343279:-1 HG:+:1904581442:-1 HG:+:1953687483:-1 HG:+:1968231263:-1 HG:+:2039294659:-1 HG:+:2171156547:-1 HG:+:2226577756:-1 HG:+:2227239510:-1 HG:+:2363878054:-1 HG:+:2627813111:-1 HG:+:2732719714:-1 HG:+:2797999632:-1 HG:+:3005912858:-1 HG:+:3011420063:-1 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAGGCTTAAAAACGACATTATTTTATGTGGTTACATAAAACATCGAATTTAGAATTAAGCCATTGAATTACAGAACTCCATATAAATCTCTTATAATTGAACAACAAATTTCCATGTGTGGTGTGGGCCGGGGAGAGGATGGGCTAATCACCCCCTCTTTTTGATGTTGCTAGAAAATAATCTAAAATATGAGAGAAAGACTT HG:+:485148126:-1 HG:+:498123984:-1 HG:+:543484725:-1 HG:+:686461428:-1 HG:+:728338048:-1 HG:+:761016717:-1 HG:+:774783520:-1 HG:+:782553870:-1 HG:+:823863135:-1 HG:+:1039999657:-1 HG:+:1179361940:-1 HG:+:1267730665:-1 HG:+:1290244875:-1 HG:+:1396026052:-1 HG:+:1419354398:-1 HG:+:1464642867:-1 HG:+:1765978368:-1 HG:+:1784386581:-1 HG:+:1795299574:-1 HG:+:1834365836:-1 HG:+:1917286096:-1 HG:+:1948534985:-1 HG:+:1992321961:-1 HG:+:2612051360:-1 HG:+:2723576267:-1 HG:+:2767049063:-1 HG:+:2901863614:-1 HG:+:3035986130:-1 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAGGCTTAAAAACGACATTATTTTATGTGGTTACATAAAACATCGAATTTAGAATTAAGCCATTGAATTACAGAACTCCATATAAATCTCTTATAATTGAACAACAAATTTCCATGTGTGGTGTGGGCCGGGGAGAGGATGGGCTAATCACCCCCTCTTTTTGATGTTGCTAGAAAATAATCTAAAATATGAGAGAAAGACTT HG:+:13912338:-1 HG:+:83903685:-1 HG:+:114915807:-1 HG:+:520721252:-1 HG:+:616397174:-1 HG:+:760190202:-1 HG:+:774844192:-1 HG:+:784514444:-1 HG:+:785400721:-1 HG:+:828606643:-1 HG:+:922447603:-1 HG:+:1098649787:-1 HG:+:1259286711:-1 HG:+:1276933051:-1 HG:+:1310180781:-1 HG:+:1423628005:-1 HG:+:1581337725:-1 HG:+:1609732468:-1 HG:+:1655669764:-1 HG:+:1760794099:-1 HG:+:1817689283:-1 HG:+:1995687556:-1 HG:+:2379903509:-1 HG:+:2482978930:-1 +ATGGTAATTTATATTCAAAATCCATAAGTAATTATGTGCTATTGTTACTTAACTATGTGTAATTGTCATCCACAATATACAGTAGTCATAATACACTCATTTTTATTTTTTCAGAAATCCTACCTTTTTTTTAATGGAACATAAAATTGGTTATGTGCTCATGAATTATTTTCCCCCACTTGGTGCAATAAGGATTAAAGGCTTAAAAACGACATTATTTTATGTGGTTACATAAAACATCGAATTTAGAATTAAGCCATTGAATTACAGAACTCCATATAAATCTCTTATAATTGAACAACAAATTTCCATGTGTGGTGTGGGCCGGGGAGAGGATGGGCTAATCACCCCCTCTTTTTGATGTTGCTAGAAAATAATCTAAAATATGAGAGAAAGACTT HG:+:192969260:-1 HG:+:425552688:-1 +AAGTCTTTCTCTCATATTTTAGATTATTTTCTAGCAACATCAAAAAGAGGGGGTGATTAGCCCATCCTCTCCCCGGCCCACACCACACATGGAAATTTGTTGTTCAATTATAAGAGATTTATATGGAGTTCTGTAATTCAATGGCTTAATTCTAAATTCGATGTTTTATGTAACCACATAAAATAATGTCGTTTTTAAGCCTTTAATCCTTATTGCACCAAGTGGGGGAAAATAATTCATGAGCACATAACCAATTTTATGTTCCATTAAAAAAAAGGTAGGATTTCTGAAAAAATAAAAATGAGTGTATTATGACTACTGTATATTGTGGATGACAATTACACATAGTTAAGTAACAATAGCACATAATTACTTATGGATTTTGAATATAAATTACCAT HG:+:1247679128:20 +AAGTCTTTCTCTCATATTTTAGATTATTTTCTAGCAACATCAAAAAGAGGGGGTGATTAGCCCATCCTCTCCCCGGCCCACACCACACATGGAAATTTGTTGTTCAATTATAAGAGATTTATATGGAGTTCTGTAATTCAATGGCTTAATTCTAAATTCGATGTTTTATGTAACCACATAAAATAATGTCGTTTTTAAGCCTTTAATCCTTATTGCACCAAGTGGGGGAAAATAATTCATGAGCACATAACCAATTTTATGTTCCATTAAAAAAAAGGTAGGATTTCTGAAAAAATAAAAATGAGTGTATTATGACTACTGTATATTGTGGATGACAATTACACATAGTTAAGTAACAATAGCACATAATTACTTATGGATTTTGAATATAAATTACCAT HG:+:1247679123:20 +AAGTCTTTCTCTCATATTTTAGATTATTTTCTAGCAACATCAAAAAGAGGGGGTGATTAGCCCATCCTCTCCCCGGCCCACACCACACATGGAAATTTGTTGTTCAATTATAAGAGATTTATATGGAGTTCTGTAATTCAATGGCTTAATTCTAAATTCGATGTTTTATGTAACCACATAAAATAATGTCGTTTTTAAGCCTTTAATCCTTATTGCACCAAGTGGGGGAAAATAATTCATGAGCACATAACCAATTTTATGTTCCATTAAAAAAAAGGTAGGATTTCTGAAAAAATAAAAATGAGTGTATTATGACTACTGTATATTGTGGATGACAATTACACATAGTTAAGTAACAATAGCACATAATTACTTATGGATTTTGAATATAAATTACCAT HG:+:1247679121:20 +AAGTCTTTCTCTCATATTTTAGATTATTTTCTAGCAACATCAAAAAGAGGGGGTGATTAGCCCATCCTCTCCCCGGCCCACACCACACATGGAAATTTGTTGTTCAATTATAAGAGATTTATATGGAGTTCTGTAATTCAATGGCTTAATTCTAAATTCGATGTTTTATGTAACCACATAAAATAATGTCGTTTTTAAGCCTTTAATCCTTATTGCACCAAGTGGGGGAAAATAATTCATGAGCACATAACCAATTTTATGTTCCATTAAAAAAAAGGTAGGATTTCTGAAAAAATAAAAATGAGTGTATTATGACTACTGTATATTGTGGATGACAATTACACATAGTTAAGTAACAATAGCACATAATTACTTATGGATTTTGAATATAAATTACCAT HG:+:1247679122:20 +CCTGCCCACACTCTGCTAGCGGGTCAGCATCAGACCTGACCAGTCCAATTAGCCCTCCAGTGGGGAGGAGTGGTGGGCTCAGCGCCACCTAGAGGTCATAAATTCCTATCACCCTGACCTCTTGAGAGCAGAGTGGACCAATCTTCTCCATTCCTTGGCCTTGCCAGCACCCTGGCTAGCTGGTTTTTGGGCCCTACATGGAACTTTCTGAGAGAATGTGGGCCCAGTCTCCCCCTCAAACAGAGTATTGATGCCAACCTCGAGTGTGGAAGTACATCATGGAGGCAATGCCAGACGCCTTTTCTTCCTCATCCTCTTCTCCTTCTCCTGCAAAGACACAGGATCCATGACGTCAGCGAAGAAGCTAAAGGACTCTGATGTTATTTGGTACTGACGTTGC HG:+:1060569049:-1 HG:+:1064391898:-1 HG:+:1793231038:21 HG:+:2488953585:-1 HG:+:2732487674:-1 +CCTGCCCACACTCTGCTAGCGGGTCAGCATCAGACCTGACCAGTCCAATTAGCCCTCCAGTGGGGAGGAGTGGTGGGCTCAGCGCCACCTAGAGGTCATAAATTCCTATCACCCTGACCTCTTGAGAGCAGAGTGGACCAATCTTCTCCATTCCTTGGCCTTGCCAGCACCCTGGCTAGCTGGTTTTTGGGCCCTACATGGAACTTTCTGAGAGAATGTGGGCCCAGTCTCCCCCTCAAACAGAGTATTGATGCCAACCTCGAGTGTGGAAGTACATCATGGAGGCAATGCCAGACGCCTTTTCTTCCTCATCCTCTTCTCCTTCTCCTGCAAAGACACAGGATCCATGACGTCAGCGAAGAAGCTAAAGGACTCTGATGTTATTTGGTACTGACGTTGC HG:+:1793231043:21 +CCTGCCCACACTCTGCTAGCGGGTCAGCATCAGACCTGACCAGTCCAATTAGCCCTCCAGTGGGGAGGAGTGGTGGGCTCAGCGCCACCTAGAGGTCATAAATTCCTATCACCCTGACCTCTTGAGAGCAGAGTGGACCAATCTTCTCCATTCCTTGGCCTTGCCAGCACCCTGGCTAGCTGGTTTTTGGGCCCTACATGGAACTTTCTGAGAGAATGTGGGCCCAGTCTCCCCCTCAAACAGAGTATTGATGCCAACCTCGAGTGTGGAAGTACATCATGGAGGCAATGCCAGACGCCTTTTCTTCCTCATCCTCTTCTCCTTCTCCTGCAAAGACACAGGATCCATGACGTCAGCGAAGAAGCTAAAGGACTCTGATGTTATTTGGTACTGACGTTGC HG:+:146658715:-1 HG:+:1793231035:21 +CCTGCCCACACTCTGCTAGCGGGTCAGCATCAGACCTGACCAGTCCAATTAGCCCTCCAGTGGGGAGGAGTGGTGGGCTCAGCGCCACCTAGAGGTCATAAATTCCTATCACCCTGACCTCTTGAGAGCAGAGTGGACCAATCTTCTCCATTCCTTGGCCTTGCCAGCACCCTGGCTAGCTGGTTTTTGGGCCCTACATGGAACTTTCTGAGAGAATGTGGGCCCAGTCTCCCCCTCAAACAGAGTATTGATGCCAACCTCGAGTGTGGAAGTACATCATGGAGGCAATGCCAGACGCCTTTTCTTCCTCATCCTCTTCTCCTTCTCCTGCAAAGACACAGGATCCATGACGTCAGCGAAGAAGCTAAAGGACTCTGATGTTATTTGGTACTGACGTTGC HG:+:2443556624:-1 +CCTGCCCACACTCTGCTAGCGGGTCAGCATCAGACCTGACCAGTCCAATTAGCCCTCCAGTGGGGAGGAGTGGTGGGCTCAGCGCCACCTAGAGGTCATAAATTCCTATCACCCTGACCTCTTGAGAGCAGAGTGGACCAATCTTCTCCATTCCTTGGCCTTGCCAGCACCCTGGCTAGCTGGTTTTTGGGCCCTACATGGAACTTTCTGAGAGAATGTGGGCCCAGTCTCCCCCTCAAACAGAGTATTGATGCCAACCTCGAGTGTGGAAGTACATCATGGAGGCAATGCCAGACGCCTTTTCTTCCTCATCCTCTTCTCCTTCTCCTGCAAAGACACAGGATCCATGACGTCAGCGAAGAAGCTAAAGGACTCTGATGTTATTTGGTACTGACGTTGC HG:+:1793231044:21 +CCTGCCCACACTCTGCTAGCGGGTCAGCATCAGACCTGACCAGTCCAATTAGCCCTCCAGTGGGGAGGAGTGGTGGGCTCAGCGCCACCTAGAGGTCATAAATTCCTATCACCCTGACCTCTTGAGAGCAGAGTGGACCAATCTTCTCCATTCCTTGGCCTTGCCAGCACCCTGGCTAGCTGGTTTTTGGGCCCTACATGGAACTTTCTGAGAGAATGTGGGCCCAGTCTCCCCCTCAAACAGAGTATTGATGCCAACCTCGAGTGTGGAAGTACATCATGGAGGCAATGCCAGACGCCTTTTCTTCCTCATCCTCTTCTCCTTCTCCTGCAAAGACACAGGATCCATGACGTCAGCGAAGAAGCTAAAGGACTCTGATGTTATTTGGTACTGACGTTGC HG:+:1793231046:21 +CCTGCCCACACTCTGCTAGCGGGTCAGCATCAGACCTGACCAGTCCAATTAGCCCTCCAGTGGGGAGGAGTGGTGGGCTCAGCGCCACCTAGAGGTCATAAATTCCTATCACCCTGACCTCTTGAGAGCAGAGTGGACCAATCTTCTCCATTCCTTGGCCTTGCCAGCACCCTGGCTAGCTGGTTTTTGGGCCCTACATGGAACTTTCTGAGAGAATGTGGGCCCAGTCTCCCCCTCAAACAGAGTATTGATGCCAACCTCGAGTGTGGAAGTACATCATGGAGGCAATGCCAGACGCCTTTTCTTCCTCATCCTCTTCTCCTTCTCCTGCAAAGACACAGGATCCATGACGTCAGCGAAGAAGCTAAAGGACTCTGATGTTATTTGGTACTGACGTTGC HG:+:1793231049:21 +CCTGCCCACACTCTGCTAGCGGGTCAGCATCAGACCTGACCAGTCCAATTAGCCCTCCAGTGGGGAGGAGTGGTGGGCTCAGCGCCACCTAGAGGTCATAAATTCCTATCACCCTGACCTCTTGAGAGCAGAGTGGACCAATCTTCTCCATTCCTTGGCCTTGCCAGCACCCTGGCTAGCTGGTTTTTGGGCCCTACATGGAACTTTCTGAGAGAATGTGGGCCCAGTCTCCCCCTCAAACAGAGTATTGATGCCAACCTCGAGTGTGGAAGTACATCATGGAGGCAATGCCAGACGCCTTTTCTTCCTCATCCTCTTCTCCTTCTCCTGCAAAGACACAGGATCCATGACGTCAGCGAAGAAGCTAAAGGACTCTGATGTTATTTGGTACTGACGTTGC HG:+:1793231040:21 +CCTGCCCACACTCTGCTAGCGGGTCAGCATCAGACCTGACCAGTCCAATTAGCCCTCCAGTGGGGAGGAGTGGTGGGCTCAGCGCCACCTAGAGGTCATAAATTCCTATCACCCTGACCTCTTGAGAGCAGAGTGGACCAATCTTCTCCATTCCTTGGCCTTGCCAGCACCCTGGCTAGCTGGTTTTTGGGCCCTACATGGAACTTTCTGAGAGAATGTGGGCCCAGTCTCCCCCTCAAACAGAGTATTGATGCCAACCTCGAGTGTGGAAGTACATCATGGAGGCAATGCCAGACGCCTTTTCTTCCTCATCCTCTTCTCCTTCTCCTGCAAAGACACAGGATCCATGACGTCAGCGAAGAAGCTAAAGGACTCTGATGTTATTTGGTACTGACGTTGC HG:+:2161060713:-1 +GCAACGTCAGTACCAAATAACATCAGAGTCCTTTAGCTTCTTCGCTGACGTCATGGATCCTGTGTCTTTGCAGGAGAAGGAGAAGAGGATGAGGAAGAAAAGGCGTCTGGCATTGCCTCCATGATGTACTTCCACACTCGAGGTTGGCATCAATACTCTGTTTGAGGGGGAGACTGGGCCCACATTCTCTCAGAAAGTTCCATGTAGGGCCCAAAAACCAGCTAGCCAGGGTGCTGGCAAGGCCAAGGAATGGAGAAGATTGGTCCACTCTGCTCTCAAGAGGTCAGGGTGATAGGAATTTATGACCTCTAGGTGGCGCTGAGCCCACCACTCCTCCCCACTGGAGGGCTAATTGGACTGGTCAGGTCTGATGCTGACCCGCTAGCAGAGTGTGGGCAGG HG:+:612315928:-1 +AATTAGTGGAAATAGAAAAAGTCACCATTTGGCAAACAACATAATCCATTGAAGGTAAGAATCATCACAGGATTCGTGAGAGAAAGGACGATTGAGACAGAACCATTTACTTAAGTCTCAAAGCTCCTCCCGACAGACATTCATTTAAACACAGAGGAAAACTTTTTAGTGGAGCAGCCTGGCAGACACCACCTGACCACTGTGACCAAAGCTACCAGCACCAGGATGAGGCTACCCAACTTGTTGTCCAGGAGTGTGCTGCCTAATTGGCACACATTTGTGAACTTTTCCAGTTTTCCTTGTACGAACTGATTTTAGCTTTATTCTACTGGGTTGGAGAAGATACTTGGTACAATTTCAGTCTTTTTAAATTTGGTAAGACTTACCTTTGTGACCCAAT HG:+:180711201:-1 HG:+:720676048:-1 HG:+:751616697:-1 HG:+:772661349:-1 HG:+:834381036:-1 HG:+:895028092:-1 HG:+:1247070254:-1 HG:+:1251775664:-1 HG:+:1516458496:-1 HG:+:1533858788:15 HG:+:1556268863:-1 HG:+:1641922778:-1 HG:+:1645069884:-1 HG:+:1662555513:-1 HG:+:1709117091:-1 HG:+:1853802193:-1 HG:+:2021519540:-1 HG:+:2235137415:-1 HG:+:2378738747:-1 HG:+:2514728900:-1 HG:+:2561327554:-1 HG:+:2938469521:-1 HG:+:2960764401:-1 HG:+:2965715754:-1 +AATTAGTGGAAATAGAAAAAGTCACCATTTGGCAAACAACATAATCCATTGAAGGTAAGAATCATCACAGGATTCGTGAGAGAAAGGACGATTGAGACAGAACCATTTACTTAAGTCTCAAAGCTCCTCCCGACAGACATTCATTTAAACACAGAGGAAAACTTTTTAGTGGAGCAGCCTGGCAGACACCACCTGACCACTGTGACCAAAGCTACCAGCACCAGGATGAGGCTACCCAACTTGTTGTCCAGGAGTGTGCTGCCTAATTGGCACACATTTGTGAACTTTTCCAGTTTTCCTTGTACGAACTGATTTTAGCTTTATTCTACTGGGTTGGAGAAGATACTTGGTACAATTTCAGTCTTTTTAAATTTGGTAAGACTTACCTTTGTGACCCAAT HG:+:1533858789:15 +AATTAGTGGAAATAGAAAAAGTCACCATTTGGCAAACAACATAATCCATTGAAGGTAAGAATCATCACAGGATTCGTGAGAGAAAGGACGATTGAGACAGAACCATTTACTTAAGTCTCAAAGCTCCTCCCGACAGACATTCATTTAAACACAGAGGAAAACTTTTTAGTGGAGCAGCCTGGCAGACACCACCTGACCACTGTGACCAAAGCTACCAGCACCAGGATGAGGCTACCCAACTTGTTGTCCAGGAGTGTGCTGCCTAATTGGCACACATTTGTGAACTTTTCCAGTTTTCCTTGTACGAACTGATTTTAGCTTTATTCTACTGGGTTGGAGAAGATACTTGGTACAATTTCAGTCTTTTTAAATTTGGTAAGACTTACCTTTGTGACCCAAT HG:+:2043984586:-1 +ATTGGGTCACAAAGGTAAGTCTTACCAAATTTAAAAAGACTGAAATTGTACCAAGTATCTTCTCCAACCCAGTAGAATAAAGCTAAAATCAGTTCGTACAAGGAAAACTGGAAAAGTTCACAAATGTGTGCCAATTAGGCAGCACACTCCTGGACAACAAGTTGGGTAGCCTCATCCTGGTGCTGGTAGCTTTGGTCACAGTGGTCAGGTGGTGTCTGCCAGGCTGCTCCACTAAAAAGTTTTCCTCTGTGTTTAAATGAATGTCTGTCGGGAGGAGCTTTGAGACTTAAGTAAATGGTTCTGTCTCAATCGTCCTTTCTCTCACGAATCCTGTGATGATTCTTACCTTCAATGGATTATGTTGTTTGCCAAATGGTGACTTTTTCTATTTCCACTAATT HG:+:1727996456:-1 +GCAGAACTGGTGCACTCTGCTGGAGAGTCCCCCTTGTTAGGGTCAGCTGCTCTCTTCCGAGCCAGCAGACAGGAAGATTAAATCCGCTGACCCTGCGACTGGCAGCTGCCTTCTCCCTTCAGGTGCTCTGTCGCCAGGGAGTTGAGAGTCCTGTCTGTAAGCCCCTGACTGGTAGCTTGCTGATTTCCTGCAGAGATGCCCTGCCCAGTGAGGAGGAATCCTAGAGAAGCAGTCTGGGACACAGCCGCTTTTGCTGTGTTGTGGTGAATTTTGCTTAGTCCAAACCTCTTCAGTCTCCTTCACACTGTCAGGGGAAAACCGCCTACTAAAGCCCAGCAGTTTGCTTATTTTGTGCAACACTGTGTCTTCATTCCTGTGGTGATTAGTTAAATTTTAAACA HG:+:96439921:-1 HG:+:224058284:-1 HG:+:432296835:15 HG:+:435491786:-1 HG:+:551535663:-1 HG:+:647392900:-1 HG:+:965008126:-1 HG:+:1013091228:-1 HG:+:1168223254:-1 HG:+:1193036714:-1 HG:+:1554777646:-1 HG:+:2019284561:-1 HG:+:2025777123:-1 HG:+:2026774726:-1 HG:+:2270602603:-1 HG:+:2534452375:-1 HG:+:2936132201:-1 HG:+:2937718302:-1 HG:+:2955905011:-1 HG:+:2956786526:-1 +GCAGAACTGGTGCACTCTGCTGGAGAGTCCCCCTTGTTAGGGTCAGCTGCTCTCTTCCGAGCCAGCAGACAGGAAGATTAAATCCGCTGACCCTGCGACTGGCAGCTGCCTTCTCCCTTCAGGTGCTCTGTCGCCAGGGAGTTGAGAGTCCTGTCTGTAAGCCCCTGACTGGTAGCTTGCTGATTTCCTGCAGAGATGCCCTGCCCAGTGAGGAGGAATCCTAGAGAAGCAGTCTGGGACACAGCCGCTTTTGCTGTGTTGTGGTGAATTTTGCTTAGTCCAAACCTCTTCAGTCTCCTTCACACTGTCAGGGGAAAACCGCCTACTAAAGCCCAGCAGTTTGCTTATTTTGTGCAACACTGTGTCTTCATTCCTGTGGTGATTAGTTAAATTTTAAACA HG:+:432296836:15 +GCAGAACTGGTGCACTCTGCTGGAGAGTCCCCCTTGTTAGGGTCAGCTGCTCTCTTCCGAGCCAGCAGACAGGAAGATTAAATCCGCTGACCCTGCGACTGGCAGCTGCCTTCTCCCTTCAGGTGCTCTGTCGCCAGGGAGTTGAGAGTCCTGTCTGTAAGCCCCTGACTGGTAGCTTGCTGATTTCCTGCAGAGATGCCCTGCCCAGTGAGGAGGAATCCTAGAGAAGCAGTCTGGGACACAGCCGCTTTTGCTGTGTTGTGGTGAATTTTGCTTAGTCCAAACCTCTTCAGTCTCCTTCACACTGTCAGGGGAAAACCGCCTACTAAAGCCCAGCAGTTTGCTTATTTTGTGCAACACTGTGTCTTCATTCCTGTGGTGATTAGTTAAATTTTAAACA HG:+:432296831:15 +GCAGAACTGGTGCACTCTGCTGGAGAGTCCCCCTTGTTAGGGTCAGCTGCTCTCTTCCGAGCCAGCAGACAGGAAGATTAAATCCGCTGACCCTGCGACTGGCAGCTGCCTTCTCCCTTCAGGTGCTCTGTCGCCAGGGAGTTGAGAGTCCTGTCTGTAAGCCCCTGACTGGTAGCTTGCTGATTTCCTGCAGAGATGCCCTGCCCAGTGAGGAGGAATCCTAGAGAAGCAGTCTGGGACACAGCCGCTTTTGCTGTGTTGTGGTGAATTTTGCTTAGTCCAAACCTCTTCAGTCTCCTTCACACTGTCAGGGGAAAACCGCCTACTAAAGCCCAGCAGTTTGCTTATTTTGTGCAACACTGTGTCTTCATTCCTGTGGTGATTAGTTAAATTTTAAACA HG:+:432296837:15 +GCAGAACTGGTGCACTCTGCTGGAGAGTCCCCCTTGTTAGGGTCAGCTGCTCTCTTCCGAGCCAGCAGACAGGAAGATTAAATCCGCTGACCCTGCGACTGGCAGCTGCCTTCTCCCTTCAGGTGCTCTGTCGCCAGGGAGTTGAGAGTCCTGTCTGTAAGCCCCTGACTGGTAGCTTGCTGATTTCCTGCAGAGATGCCCTGCCCAGTGAGGAGGAATCCTAGAGAAGCAGTCTGGGACACAGCCGCTTTTGCTGTGTTGTGGTGAATTTTGCTTAGTCCAAACCTCTTCAGTCTCCTTCACACTGTCAGGGGAAAACCGCCTACTAAAGCCCAGCAGTTTGCTTATTTTGTGCAACACTGTGTCTTCATTCCTGTGGTGATTAGTTAAATTTTAAACA HG:+:432296832:15 +GCAGAACTGGTGCACTCTGCTGGAGAGTCCCCCTTGTTAGGGTCAGCTGCTCTCTTCCGAGCCAGCAGACAGGAAGATTAAATCCGCTGACCCTGCGACTGGCAGCTGCCTTCTCCCTTCAGGTGCTCTGTCGCCAGGGAGTTGAGAGTCCTGTCTGTAAGCCCCTGACTGGTAGCTTGCTGATTTCCTGCAGAGATGCCCTGCCCAGTGAGGAGGAATCCTAGAGAAGCAGTCTGGGACACAGCCGCTTTTGCTGTGTTGTGGTGAATTTTGCTTAGTCCAAACCTCTTCAGTCTCCTTCACACTGTCAGGGGAAAACCGCCTACTAAAGCCCAGCAGTTTGCTTATTTTGTGCAACACTGTGTCTTCATTCCTGTGGTGATTAGTTAAATTTTAAACA HG:+:432296839:15 +TGTTTAAAATTTAACTAATCACCACAGGAATGAAGACACAGTGTTGCACAAAATAAGCAAACTGCTGGGCTTTAGTAGGCGGTTTTCCCCTGACAGTGTGAAGGAGACTGAAGAGGTTTGGACTAAGCAAAATTCACCACAACACAGCAAAAGCGGCTGTGTCCCAGACTGCTTCTCTAGGATTCCTCCTCACTGGGCAGGGCATCTCTGCAGGAAATCAGCAAGCTACCAGTCAGGGGCTTACAGACAGGACTCTCAACTCCCTGGCGACAGAGCACCTGAAGGGAGAAGGCAGCTGCCAGTCGCAGGGTCAGCGGATTTAATCTTCCTGTCTGCTGGCTCGGAAGAGAGCAGCTGACCCTAACAAGGGGGACTCTCCAGCAGAGTGCACCAGTTCTGC HG:+:2438692382:-1 +TGTTTAAAATTTAACTAATCACCACAGGAATGAAGACACAGTGTTGCACAAAATAAGCAAACTGCTGGGCTTTAGTAGGCGGTTTTCCCCTGACAGTGTGAAGGAGACTGAAGAGGTTTGGACTAAGCAAAATTCACCACAACACAGCAAAAGCGGCTGTGTCCCAGACTGCTTCTCTAGGATTCCTCCTCACTGGGCAGGGCATCTCTGCAGGAAATCAGCAAGCTACCAGTCAGGGGCTTACAGACAGGACTCTCAACTCCCTGGCGACAGAGCACCTGAAGGGAGAAGGCAGCTGCCAGTCGCAGGGTCAGCGGATTTAATCTTCCTGTCTGCTGGCTCGGAAGAGAGCAGCTGACCCTAACAAGGGGGACTCTCCAGCAGAGTGCACCAGTTCTGC HG:+:188738146:-1 HG:+:190923890:-1 HG:+:248292090:-1 HG:+:273696439:-1 HG:+:286031610:-1 HG:+:306624515:-1 HG:+:407688258:-1 HG:+:1251204883:-1 HG:+:1273350669:-1 HG:+:1452040172:-1 HG:+:1945435981:-1 HG:+:2159687206:-1 HG:+:2548589920:-1 HG:+:2612329924:-1 HG:+:2702113523:-1 HG:+:2752031926:-1 HG:+:2811526040:-1 HG:+:2938195035:-1 HG:+:3005173188:-1 HG:+:3057500287:-1 +GAAATGGGAGAGTTCTCGTTACCACCCTCAGAGGACGTTTGACAGGGGTGTGGACTCACTCCTTCTAGCCACCCTGCTGCCTCAAACCCTTAGAGGGAGTGTGCAGATGGGCAGGTACAGAGCCCATGGGGGCACCTCGGGCTCCAAGCGCCACAGCAGCGTCTAGGAAGTTGGGTGCTGCACTTCCAAAGCCCAAGTGGGTGTGTGTTCACAGTGTGCTCTTTTCAGCTTTGCTGTCTGCAGACGAGCTGTGTTAATCAGCTCAATTAGACACTCTGCCTTATCAAGAGGGCAGACCGGGCCAGTGTGACAGCTTTCTGTATCCCAAGTTCTTTGCCCAGTATACTGGAAAATTGGGACTCACACATGGGCTTGAAGGATGAGTGCTAGGTTTTATTCA HG:+:39106958:79 HG:+:92657613:-1 HG:+:97040226:-1 HG:+:330655601:-1 HG:+:496541068:-1 HG:+:498939079:-1 HG:+:536141174:-1 HG:+:553763393:-1 HG:+:671168552:-1 HG:+:886845028:-1 HG:+:924254270:-1 HG:+:1007064084:-1 HG:+:1009677767:-1 HG:+:1024709567:-1 HG:+:1078458692:-1 HG:+:1187485284:-1 HG:+:1232085026:-1 HG:+:1330518357:-1 HG:+:1353021018:-1 HG:+:1379240765:-1 HG:+:1413245472:-1 HG:+:1522496564:-1 HG:+:1572081098:-1 HG:+:1685371369:-1 HG:+:1714644056:-1 HG:+:1763076941:-1 HG:+:1802357340:-1 HG:+:1841444900:-1 HG:+:1961070902:-1 HG:+:1976152142:-1 HG:+:2042810419:-1 HG:+:2131020168:-1 HG:+:2146866649:-1 HG:+:2156379889:-1 HG:+:2160246764:-1 HG:+:2271539357:-1 HG:+:2282833763:-1 HG:+:2618923868:-1 HG:+:2702914913:-1 HG:+:2703070184:-1 HG:+:2806685402:-1 HG:+:2808653421:-1 HG:+:2885749810:-1 HG:+:2887964836:-1 HG:+:2908139573:-1 +GAAATGGGAGAGTTCTCGTTACCACCCTCAGAGGACGTTTGACAGGGGTGTGGACTCACTCCTTCTAGCCACCCTGCTGCCTCAAACCCTTAGAGGGAGTGTGCAGATGGGCAGGTACAGAGCCCATGGGGGCACCTCGGGCTCCAAGCGCCACAGCAGCGTCTAGGAAGTTGGGTGCTGCACTTCCAAAGCCCAAGTGGGTGTGTGTTCACAGTGTGCTCTTTTCAGCTTTGCTGTCTGCAGACGAGCTGTGTTAATCAGCTCAATTAGACACTCTGCCTTATCAAGAGGGCAGACCGGGCCAGTGTGACAGCTTTCTGTATCCCAAGTTCTTTGCCCAGTATACTGGAAAATTGGGACTCACACATGGGCTTGAAGGATGAGTGCTAGGTTTTATTCA HG:+:473855896:20 HG:+:567957957:-1 HG:+:779028255:-1 HG:+:1280822158:-1 HG:+:1793162371:-1 HG:+:2354556755:-1 +GAAATGGGAGAGTTCTCGTTACCACCCTCAGAGGACGTTTGACAGGGGTGTGGACTCACTCCTTCTAGCCACCCTGCTGCCTCAAACCCTTAGAGGGAGTGTGCAGATGGGCAGGTACAGAGCCCATGGGGGCACCTCGGGCTCCAAGCGCCACAGCAGCGTCTAGGAAGTTGGGTGCTGCACTTCCAAAGCCCAAGTGGGTGTGTGTTCACAGTGTGCTCTTTTCAGCTTTGCTGTCTGCAGACGAGCTGTGTTAATCAGCTCAATTAGACACTCTGCCTTATCAAGAGGGCAGACCGGGCCAGTGTGACAGCTTTCTGTATCCCAAGTTCTTTGCCCAGTATACTGGAAAATTGGGACTCACACATGGGCTTGAAGGATGAGTGCTAGGTTTTATTCA HG:+:473855902:20 +GAAATGGGAGAGTTCTCGTTACCACCCTCAGAGGACGTTTGACAGGGGTGTGGACTCACTCCTTCTAGCCACCCTGCTGCCTCAAACCCTTAGAGGGAGTGTGCAGATGGGCAGGTACAGAGCCCATGGGGGCACCTCGGGCTCCAAGCGCCACAGCAGCGTCTAGGAAGTTGGGTGCTGCACTTCCAAAGCCCAAGTGGGTGTGTGTTCACAGTGTGCTCTTTTCAGCTTTGCTGTCTGCAGACGAGCTGTGTTAATCAGCTCAATTAGACACTCTGCCTTATCAAGAGGGCAGACCGGGCCAGTGTGACAGCTTTCTGTATCCCAAGTTCTTTGCCCAGTATACTGGAAAATTGGGACTCACACATGGGCTTGAAGGATGAGTGCTAGGTTTTATTCA HG:+:473855905:20 +GAAATGGGAGAGTTCTCGTTACCACCCTCAGAGGACGTTTGACAGGGGTGTGGACTCACTCCTTCTAGCCACCCTGCTGCCTCAAACCCTTAGAGGGAGTGTGCAGATGGGCAGGTACAGAGCCCATGGGGGCACCTCGGGCTCCAAGCGCCACAGCAGCGTCTAGGAAGTTGGGTGCTGCACTTCCAAAGCCCAAGTGGGTGTGTGTTCACAGTGTGCTCTTTTCAGCTTTGCTGTCTGCAGACGAGCTGTGTTAATCAGCTCAATTAGACACTCTGCCTTATCAAGAGGGCAGACCGGGCCAGTGTGACAGCTTTCTGTATCCCAAGTTCTTTGCCCAGTATACTGGAAAATTGGGACTCACACATGGGCTTGAAGGATGAGTGCTAGGTTTTATTCA HG:+:473855900:20 +GAAATGGGAGAGTTCTCGTTACCACCCTCAGAGGACGTTTGACAGGGGTGTGGACTCACTCCTTCTAGCCACCCTGCTGCCTCAAACCCTTAGAGGGAGTGTGCAGATGGGCAGGTACAGAGCCCATGGGGGCACCTCGGGCTCCAAGCGCCACAGCAGCGTCTAGGAAGTTGGGTGCTGCACTTCCAAAGCCCAAGTGGGTGTGTGTTCACAGTGTGCTCTTTTCAGCTTTGCTGTCTGCAGACGAGCTGTGTTAATCAGCTCAATTAGACACTCTGCCTTATCAAGAGGGCAGACCGGGCCAGTGTGACAGCTTTCTGTATCCCAAGTTCTTTGCCCAGTATACTGGAAAATTGGGACTCACACATGGGCTTGAAGGATGAGTGCTAGGTTTTATTCA HG:+:1007463749:-1 +TGAATAAAACCTAGCACTCATCCTTCAAGCCCATGTGTGAGTCCCAATTTTCCAGTATACTGGGCAAAGAACTTGGGATACAGAAAGCTGTCACACTGGCCCGGTCTGCCCTCTTGATAAGGCAGAGTGTCTAATTGAGCTGATTAACACAGCTCGTCTGCAGACAGCAAAGCTGAAAAGAGCACACTGTGAACACACACCCACTTGGGCTTTGGAAGTGCAGCACCCAACTTCCTAGACGCTGCTGTGGCGCTTGGAGCCCGAGGTGCCCCCATGGGCTCTGTACCTGCCCATCTGCACACTCCCTCTAAGGGTTTGAGGCAGCAGGGTGGCTAGAAGGAGTGAGTCCACACCCCTGTCAAACGTCCTCTGAGGGTGGTAACGAGAACTCTCCCATTTC HG:+:934212939:-1 +TGAATAAAACCTAGCACTCATCCTTCAAGCCCATGTGTGAGTCCCAATTTTCCAGTATACTGGGCAAAGAACTTGGGATACAGAAAGCTGTCACACTGGCCCGGTCTGCCCTCTTGATAAGGCAGAGTGTCTAATTGAGCTGATTAACACAGCTCGTCTGCAGACAGCAAAGCTGAAAAGAGCACACTGTGAACACACACCCACTTGGGCTTTGGAAGTGCAGCACCCAACTTCCTAGACGCTGCTGTGGCGCTTGGAGCCCGAGGTGCCCCCATGGGCTCTGTACCTGCCCATCTGCACACTCCCTCTAAGGGTTTGAGGCAGCAGGGTGGCTAGAAGGAGTGAGTCCACACCCCTGTCAAACGTCCTCTGAGGGTGGTAACGAGAACTCTCCCATTTC HG:+:487561768:-1 +TGAATAAAACCTAGCACTCATCCTTCAAGCCCATGTGTGAGTCCCAATTTTCCAGTATACTGGGCAAAGAACTTGGGATACAGAAAGCTGTCACACTGGCCCGGTCTGCCCTCTTGATAAGGCAGAGTGTCTAATTGAGCTGATTAACACAGCTCGTCTGCAGACAGCAAAGCTGAAAAGAGCACACTGTGAACACACACCCACTTGGGCTTTGGAAGTGCAGCACCCAACTTCCTAGACGCTGCTGTGGCGCTTGGAGCCCGAGGTGCCCCCATGGGCTCTGTACCTGCCCATCTGCACACTCCCTCTAAGGGTTTGAGGCAGCAGGGTGGCTAGAAGGAGTGAGTCCACACCCCTGTCAAACGTCCTCTGAGGGTGGTAACGAGAACTCTCCCATTTC HG:+:200169767:-1 HG:+:923687026:-1 HG:+:1127254063:-1 HG:+:1357977670:-1 HG:+:1477008658:-1 HG:+:2118743232:-1 HG:+:2194297060:-1 +TGAATAAAACCTAGCACTCATCCTTCAAGCCCATGTGTGAGTCCCAATTTTCCAGTATACTGGGCAAAGAACTTGGGATACAGAAAGCTGTCACACTGGCCCGGTCTGCCCTCTTGATAAGGCAGAGTGTCTAATTGAGCTGATTAACACAGCTCGTCTGCAGACAGCAAAGCTGAAAAGAGCACACTGTGAACACACACCCACTTGGGCTTTGGAAGTGCAGCACCCAACTTCCTAGACGCTGCTGTGGCGCTTGGAGCCCGAGGTGCCCCCATGGGCTCTGTACCTGCCCATCTGCACACTCCCTCTAAGGGTTTGAGGCAGCAGGGTGGCTAGAAGGAGTGAGTCCACACCCCTGTCAAACGTCCTCTGAGGGTGGTAACGAGAACTCTCCCATTTC HG:+:299192041:-1 HG:+:608283797:-1 HG:+:678120648:-1 HG:+:770903265:-1 HG:+:847228515:-1 HG:+:907484669:-1 HG:+:1236781764:-1 HG:+:1357977671:-1 HG:+:1872222622:-1 HG:+:1973407277:-1 HG:+:1973415317:-1 HG:+:2174136685:-1 HG:+:2535851618:-1 HG:+:2995308076:-1 +TGAATAAAACCTAGCACTCATCCTTCAAGCCCATGTGTGAGTCCCAATTTTCCAGTATACTGGGCAAAGAACTTGGGATACAGAAAGCTGTCACACTGGCCCGGTCTGCCCTCTTGATAAGGCAGAGTGTCTAATTGAGCTGATTAACACAGCTCGTCTGCAGACAGCAAAGCTGAAAAGAGCACACTGTGAACACACACCCACTTGGGCTTTGGAAGTGCAGCACCCAACTTCCTAGACGCTGCTGTGGCGCTTGGAGCCCGAGGTGCCCCCATGGGCTCTGTACCTGCCCATCTGCACACTCCCTCTAAGGGTTTGAGGCAGCAGGGTGGCTAGAAGGAGTGAGTCCACACCCCTGTCAAACGTCCTCTGAGGGTGGTAACGAGAACTCTCCCATTTC HG:+:709461651:-1 HG:+:850821095:-1 HG:+:897941514:-1 HG:+:2915656442:-1 HG:+:3029266370:-1 +TTTCAGTAGAGACAGGGTTTTCACTACCTGACCTCAAGCAATCCACCCGCCTCGGTCCTCCCAAACTGCTGGATTACAGGGAACAACGCCACTGCTCCAGCCACATTGTCTTGATTTTAGTTCTAAACACACGTTTGTAATAAATATAATTCTACAAACTAACATTTAATGAATGTTGGCTCTACGTCAGGCTCTGTAACGATGGCTTTGTATAGAACGCTTTATTTAAGCCATTTACATGGGAAAAACAGCAACACTCAGATGGGTGCTGGGGCCCTGCCTACATCACACAGTGGGCACTCAGAGGTGGGATTACCAAATAGTGATCTGAGGAAGTGTGTGCTCTAGTCGGGGCACCTTATATTTCTTGTGAGTTTCAGCAGTGAAGGGATTAGGATTA HG:+:67149478:-1 HG:+:87499322:-1 HG:+:155577062:-1 HG:+:288416831:-1 HG:+:970686293:-1 HG:+:1046577917:-1 HG:+:1423534924:-1 HG:+:1935566466:-1 HG:+:2074303893:-1 HG:+:2126247017:-1 HG:+:2850760207:-1 +TTTCAGTAGAGACAGGGTTTTCACTACCTGACCTCAAGCAATCCACCCGCCTCGGTCCTCCCAAACTGCTGGATTACAGGGAACAACGCCACTGCTCCAGCCACATTGTCTTGATTTTAGTTCTAAACACACGTTTGTAATAAATATAATTCTACAAACTAACATTTAATGAATGTTGGCTCTACGTCAGGCTCTGTAACGATGGCTTTGTATAGAACGCTTTATTTAAGCCATTTACATGGGAAAAACAGCAACACTCAGATGGGTGCTGGGGCCCTGCCTACATCACACAGTGGGCACTCAGAGGTGGGATTACCAAATAGTGATCTGAGGAAGTGTGTGCTCTAGTCGGGGCACCTTATATTTCTTGTGAGTTTCAGCAGTGAAGGGATTAGGATTA HG:+:11201545:-1 HG:+:11701411:-1 HG:+:24344501:-1 HG:+:40897976:-1 HG:+:42581973:-1 HG:+:44219982:-1 HG:+:86247890:-1 HG:+:115117935:-1 HG:+:160140494:-1 HG:+:165857839:-1 HG:+:177357415:-1 HG:+:182958065:-1 HG:+:183389463:-1 HG:+:203249693:-1 HG:+:205354450:-1 HG:+:230448301:-1 HG:+:243491698:-1 HG:+:258772853:-1 HG:+:274264534:-1 HG:+:288601239:-1 HG:+:296609006:-1 HG:+:311374705:-1 HG:+:323681781:-1 HG:+:325540643:-1 HG:+:349043530:-1 HG:+:388719451:-1 HG:+:420728139:-1 HG:+:466360492:-1 HG:+:482081620:-1 HG:+:501833296:-1 HG:+:506083639:-1 HG:+:521363683:-1 HG:+:545791092:-1 HG:+:554547891:-1 HG:+:590880070:-1 HG:+:606280741:-1 HG:+:664961367:-1 HG:+:676326677:-1 HG:+:678618741:-1 HG:+:689458023:-1 HG:+:730283649:-1 HG:+:745485164:-1 HG:+:784424079:-1 HG:+:799570893:-1 HG:+:856200136:-1 HG:+:905852446:-1 HG:+:961558638:-1 HG:+:985185016:-1 HG:+:993844288:-1 HG:+:1014951870:-1 HG:+:1021756922:-1 HG:+:1026941257:-1 HG:+:1038023249:-1 HG:+:1038190390:-1 HG:+:1039278591:-1 HG:+:1049406408:-1 HG:+:1055704553:-1 HG:+:1055704581:-1 HG:+:1056620318:-1 HG:+:1078717511:-1 HG:+:1098058980:-1 HG:+:1098291608:-1 HG:+:1108490785:-1 HG:+:1119439381:-1 HG:+:1119846292:-1 HG:+:1125911553:-1 HG:+:1197556637:-1 HG:+:1236463166:-1 HG:+:1236713358:-1 HG:+:1263629642:-1 HG:+:1277272463:-1 HG:+:1277700780:-1 HG:+:1299928777:-1 HG:+:1302477607:-1 HG:+:1305972944:-1 HG:+:1307523431:-1 HG:+:1309583430:-1 HG:+:1330370763:-1 HG:+:1333504432:-1 HG:+:1335124515:-1 HG:+:1373682146:-1 HG:+:1397616531:-1 HG:+:1397788909:-1 HG:+:1409517584:-1 HG:+:1447254553:-1 HG:+:1454209286:-1 HG:+:1463663546:-1 HG:+:1486387480:-1 HG:+:1505005961:-1 HG:+:1537122140:-1 HG:+:1563087340:-1 HG:+:1575658280:-1 HG:+:1581020840:-1 HG:+:1635479243:-1 HG:+:1654087521:-1 HG:+:1661333037:-1 HG:+:1667173517:-1 HG:+:1669941091:-1 HG:+:1670847336:-1 HG:+:1671456511:-1 HG:+:1674416408:-1 HG:+:1675747612:-1 HG:+:1693220631:-1 HG:+:1696877247:-1 HG:+:1705808227:-1 HG:+:1718595131:-1 HG:+:1754479345:-1 HG:+:1784136181:-1 HG:+:1791866299:-1 HG:+:1816843177:-1 HG:+:1838440572:-1 HG:+:1847365988:-1 HG:+:1862827746:-1 HG:+:1879830200:-1 HG:+:1916373585:-1 HG:+:1933048088:-1 HG:+:1937966052:-1 HG:+:1976115756:-1 HG:+:1979416182:-1 HG:+:1981180862:-1 HG:+:1997218218:-1 HG:+:1999941396:-1 HG:+:2004817815:-1 HG:+:2019943760:-1 HG:+:2051381503:-1 HG:+:2056683911:-1 HG:+:2064437380:-1 HG:+:2067543660:-1 HG:+:2067986366:-1 HG:+:2071225609:-1 HG:+:2072164460:-1 HG:+:2073060266:-1 HG:+:2076470928:-1 HG:+:2105159487:-1 HG:+:2108429782:-1 HG:+:2122190936:-1 HG:+:2142349910:-1 HG:+:2158299554:-1 HG:+:2185727000:-1 HG:+:2187551291:-1 HG:+:2188740463:-1 HG:+:2232236547:-1 HG:+:2261107499:-1 HG:+:2273715996:-1 HG:+:2276909425:-1 HG:+:2278831720:-1 HG:+:2290487586:-1 HG:+:2348675082:-1 HG:+:2348754268:-1 HG:+:2367463320:-1 HG:+:2378983066:-1 HG:+:2397268383:-1 HG:+:2412203671:-1 HG:+:2420783210:-1 HG:+:2456916273:-1 HG:+:2481631127:-1 HG:+:2481878260:-1 HG:+:2490905176:-1 HG:+:2496922541:-1 HG:+:2500568693:-1 HG:+:2505891167:-1 HG:+:2527839900:-1 HG:+:2529335180:-1 HG:+:2529739879:-1 HG:+:2539482770:-1 HG:+:2563648062:-1 HG:+:2564430344:-1 HG:+:2571465781:-1 HG:+:2572591496:-1 HG:+:2573465178:-1 HG:+:2584968277:-1 HG:+:2605112066:-1 HG:+:2668927664:-1 HG:+:2675378044:-1 HG:+:2695378621:-1 HG:+:2700992744:-1 HG:+:2701088410:-1 HG:+:2703515905:-1 HG:+:2705839620:-1 HG:+:2706887111:-1 HG:+:2707067810:-1 HG:+:2708300882:-1 HG:+:2732333605:-1 HG:+:2732455733:-1 HG:+:2744291435:-1 HG:+:2749869898:-1 HG:+:2760875009:-1 HG:+:2760877377:-1 HG:+:2769085645:-1 HG:+:2770723736:-1 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HG:+:915727704:-1 HG:+:1526410526:-1 HG:+:2065396473:-1 HG:+:2344480674:-1 +TTTCAGTAGAGACAGGGTTTTCACTACCTGACCTCAAGCAATCCACCCGCCTCGGTCCTCCCAAACTGCTGGATTACAGGGAACAACGCCACTGCTCCAGCCACATTGTCTTGATTTTAGTTCTAAACACACGTTTGTAATAAATATAATTCTACAAACTAACATTTAATGAATGTTGGCTCTACGTCAGGCTCTGTAACGATGGCTTTGTATAGAACGCTTTATTTAAGCCATTTACATGGGAAAAACAGCAACACTCAGATGGGTGCTGGGGCCCTGCCTACATCACACAGTGGGCACTCAGAGGTGGGATTACCAAATAGTGATCTGAGGAAGTGTGTGCTCTAGTCGGGGCACCTTATATTTCTTGTGAGTTTCAGCAGTGAAGGGATTAGGATTA HG:+:356608943:-1 HG:+:575903769:-1 HG:+:834233447:-1 HG:+:1026969302:-1 HG:+:1947121662:-1 +TTTCAGTAGAGACAGGGTTTTCACTACCTGACCTCAAGCAATCCACCCGCCTCGGTCCTCCCAAACTGCTGGATTACAGGGAACAACGCCACTGCTCCAGCCACATTGTCTTGATTTTAGTTCTAAACACACGTTTGTAATAAATATAATTCTACAAACTAACATTTAATGAATGTTGGCTCTACGTCAGGCTCTGTAACGATGGCTTTGTATAGAACGCTTTATTTAAGCCATTTACATGGGAAAAACAGCAACACTCAGATGGGTGCTGGGGCCCTGCCTACATCACACAGTGGGCACTCAGAGGTGGGATTACCAAATAGTGATCTGAGGAAGTGTGTGCTCTAGTCGGGGCACCTTATATTTCTTGTGAGTTTCAGCAGTGAAGGGATTAGGATTA HG:+:88412748:-1 HG:+:264031271:-1 HG:+:1192323168:-1 HG:+:2371433258:-1 +TTTCAGTAGAGACAGGGTTTTCACTACCTGACCTCAAGCAATCCACCCGCCTCGGTCCTCCCAAACTGCTGGATTACAGGGAACAACGCCACTGCTCCAGCCACATTGTCTTGATTTTAGTTCTAAACACACGTTTGTAATAAATATAATTCTACAAACTAACATTTAATGAATGTTGGCTCTACGTCAGGCTCTGTAACGATGGCTTTGTATAGAACGCTTTATTTAAGCCATTTACATGGGAAAAACAGCAACACTCAGATGGGTGCTGGGGCCCTGCCTACATCACACAGTGGGCACTCAGAGGTGGGATTACCAAATAGTGATCTGAGGAAGTGTGTGCTCTAGTCGGGGCACCTTATATTTCTTGTGAGTTTCAGCAGTGAAGGGATTAGGATTA HG:+:769624398:-1 HG:+:920737484:-1 HG:+:1990555232:-1 HG:+:2871330605:-1 +TTTCAGTAGAGACAGGGTTTTCACTACCTGACCTCAAGCAATCCACCCGCCTCGGTCCTCCCAAACTGCTGGATTACAGGGAACAACGCCACTGCTCCAGCCACATTGTCTTGATTTTAGTTCTAAACACACGTTTGTAATAAATATAATTCTACAAACTAACATTTAATGAATGTTGGCTCTACGTCAGGCTCTGTAACGATGGCTTTGTATAGAACGCTTTATTTAAGCCATTTACATGGGAAAAACAGCAACACTCAGATGGGTGCTGGGGCCCTGCCTACATCACACAGTGGGCACTCAGAGGTGGGATTACCAAATAGTGATCTGAGGAAGTGTGTGCTCTAGTCGGGGCACCTTATATTTCTTGTGAGTTTCAGCAGTGAAGGGATTAGGATTA HG:+:336685567:-1 HG:+:354815843:-1 HG:+:403143105:-1 HG:+:447718033:-1 HG:+:802219900:-1 HG:+:939125476:-1 HG:+:1005112904:-1 HG:+:1034226087:-1 HG:+:1270242697:-1 HG:+:1310171996:-1 HG:+:1331251830:-1 HG:+:1344802518:-1 HG:+:1386210286:-1 HG:+:1561924202:-1 HG:+:2005463234:-1 HG:+:2040167143:-1 HG:+:2279336947:-1 HG:+:2377648253:-1 HG:+:2654683465:-1 HG:+:2720846774:-1 HG:+:2757952530:-1 HG:+:2810955765:-1 HG:+:2823845200:-1 HG:+:2826756268:-1 +TTTCAGTAGAGACAGGGTTTTCACTACCTGACCTCAAGCAATCCACCCGCCTCGGTCCTCCCAAACTGCTGGATTACAGGGAACAACGCCACTGCTCCAGCCACATTGTCTTGATTTTAGTTCTAAACACACGTTTGTAATAAATATAATTCTACAAACTAACATTTAATGAATGTTGGCTCTACGTCAGGCTCTGTAACGATGGCTTTGTATAGAACGCTTTATTTAAGCCATTTACATGGGAAAAACAGCAACACTCAGATGGGTGCTGGGGCCCTGCCTACATCACACAGTGGGCACTCAGAGGTGGGATTACCAAATAGTGATCTGAGGAAGTGTGTGCTCTAGTCGGGGCACCTTATATTTCTTGTGAGTTTCAGCAGTGAAGGGATTAGGATTA HG:+:617755759:-1 HG:+:996386389:-1 HG:+:1251395620:-1 HG:+:1613204285:-1 HG:+:1689293204:-1 HG:+:1705230591:-1 HG:+:2469993288:-1 HG:+:2740251844:-1 HG:+:2884410912:-1 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HG:+:258904115:-1 HG:+:278582885:-1 HG:+:284008417:-1 HG:+:351441996:-1 HG:+:726676970:-1 HG:+:949729802:-1 HG:+:1321518382:-1 HG:+:1754587591:-1 HG:+:2128979806:-1 HG:+:2436555169:-1 HG:+:2484453510:-1 HG:+:2510457555:-1 HG:+:2513389327:-1 HG:+:2929935552:-1 HG:+:2930943452:-1 +TAATCCTAATCCCTTCACTGCTGAAACTCACAAGAAATATAAGGTGCCCCGACTAGAGCACACACTTCCTCAGATCACTATTTGGTAATCCCACCTCTGAGTGCCCACTGTGTGATGTAGGCAGGGCCCCAGCACCCATCTGAGTGTTGCTGTTTTTCCCATGTAAATGGCTTAAATAAAGCGTTCTATACAAAGCCATCGTTACAGAGCCTGACGTAGAGCCAACATTCATTAAATGTTAGTTTGTAGAATTATATTTATTACAAACGTGTGTTTAGAACTAAAATCAAGACAATGTGGCTGGAGCAGTGGCGTTGTTCCCTGTAATCCAGCAGTTTGGGAGGACCGAGGCGGGTGGATTGCTTGAGGTCAGGTAGTGAAAACCCTGTCTCTACTGAAA HG:+:327682799:-1 HG:+:709693916:-1 HG:+:2770388685:17 HG:+:2996455575:-1 +TAATCCTAATCCCTTCACTGCTGAAACTCACAAGAAATATAAGGTGCCCCGACTAGAGCACACACTTCCTCAGATCACTATTTGGTAATCCCACCTCTGAGTGCCCACTGTGTGATGTAGGCAGGGCCCCAGCACCCATCTGAGTGTTGCTGTTTTTCCCATGTAAATGGCTTAAATAAAGCGTTCTATACAAAGCCATCGTTACAGAGCCTGACGTAGAGCCAACATTCATTAAATGTTAGTTTGTAGAATTATATTTATTACAAACGTGTGTTTAGAACTAAAATCAAGACAATGTGGCTGGAGCAGTGGCGTTGTTCCCTGTAATCCAGCAGTTTGGGAGGACCGAGGCGGGTGGATTGCTTGAGGTCAGGTAGTGAAAACCCTGTCTCTACTGAAA HG:+:2770388683:17 +TAATCCTAATCCCTTCACTGCTGAAACTCACAAGAAATATAAGGTGCCCCGACTAGAGCACACACTTCCTCAGATCACTATTTGGTAATCCCACCTCTGAGTGCCCACTGTGTGATGTAGGCAGGGCCCCAGCACCCATCTGAGTGTTGCTGTTTTTCCCATGTAAATGGCTTAAATAAAGCGTTCTATACAAAGCCATCGTTACAGAGCCTGACGTAGAGCCAACATTCATTAAATGTTAGTTTGTAGAATTATATTTATTACAAACGTGTGTTTAGAACTAAAATCAAGACAATGTGGCTGGAGCAGTGGCGTTGTTCCCTGTAATCCAGCAGTTTGGGAGGACCGAGGCGGGTGGATTGCTTGAGGTCAGGTAGTGAAAACCCTGTCTCTACTGAAA HG:+:2770388688:17 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HG:+:2484765256:-1 +GCCCTTAACCTCCTGGGCCTAGTGAGCCTCTCACCTAAGCCTCCTGAGTAACTGGGACTACAGGTGGCACACTACCAATACCCAGCTAATTTTTGCATTTTTTTGTAGACGAAGGGAATTTTGGCTAGGCTAGTCTCAAAGTCTTAGCCGAAGCCATCCTCCCACCTCAGCCTCCAAAGTGCTGGGATTAGTAAGAGGCAGTCTGTGTTGCTCAGGGCTTGGAGGCAATTCACAAGCTGATTTCCACTAACTGATCAGCATGAAAGTTTTTTTTTTTTTTTTTGAGATTGGAGACTCACTCTGTCGCCAGGTTAGAGTGCAGTGGCGTGGATCCCGGCCTCACTGCAACCTCTGCCTCCTGGGTTCAAGCAACTCTCCTGCCTCAGCCTCCCAAATAGCT HG:+:1496118:-1 HG:+:12314234:-1 HG:+:12477613:-1 HG:+:16628658:-1 HG:+:20592195:-1 HG:+:26523052:-1 HG:+:29021398:-1 HG:+:32558353:-1 HG:+:39621045:-1 HG:+:46063496:-1 HG:+:55113692:-1 HG:+:62690165:-1 HG:+:83391196:-1 HG:+:101784869:-1 HG:+:114959934:-1 HG:+:115307317:-1 HG:+:152934554:-1 HG:+:162521075:-1 HG:+:164453277:-1 HG:+:169442126:-1 HG:+:178004044:-1 HG:+:179379019:-1 HG:+:181047941:-1 HG:+:182092916:-1 HG:+:182618700:-1 HG:+:194337056:-1 HG:+:197727753:-1 HG:+:200500465:-1 HG:+:223558155:-1 HG:+:225223491:-1 HG:+:242830713:-1 HG:+:260149063:-1 HG:+:286283964:-1 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HG:+:469317703:-1 HG:+:532758690:-1 HG:+:1653419158:-1 HG:+:2124978662:-1 HG:+:2136675225:-1 HG:+:2291519272:-1 HG:+:2637830339:-1 HG:+:2678040923:-1 HG:+:2680359019:-1 HG:+:2713577594:21 HG:+:2897768252:-1 +AGCTATTTGGGAGGCTGAGGCAGGAGAGTTGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGGCCGGGATCCACGCCACTGCACTCTAACCTGGCGACAGAGTGAGTCTCCAATCTCAAAAAAAAAAAAAAAAACTTTCATGCTGATCAGTTAGTGGAAATCAGCTTGTGAATTGCCTCCAAGCCCTGAGCAACACAGACTGCCTCTTACTAATCCCAGCACTTTGGAGGCTGAGGTGGGAGGATGGCTTCGGCTAAGACTTTGAGACTAGCCTAGCCAAAATTCCCTTCGTCTACAAAAAAATGCAAAAATTAGCTGGGTATTGGTAGTGTGCCACCTGTAGTCCCAGTTACTCAGGAGGCTTAGGTGAGAGGCTCACTAGGCCCAGGAGGTTAAGGGC HG:+:1957735458:-1 +AGCTATTTGGGAGGCTGAGGCAGGAGAGTTGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGGCCGGGATCCACGCCACTGCACTCTAACCTGGCGACAGAGTGAGTCTCCAATCTCAAAAAAAAAAAAAAAAACTTTCATGCTGATCAGTTAGTGGAAATCAGCTTGTGAATTGCCTCCAAGCCCTGAGCAACACAGACTGCCTCTTACTAATCCCAGCACTTTGGAGGCTGAGGTGGGAGGATGGCTTCGGCTAAGACTTTGAGACTAGCCTAGCCAAAATTCCCTTCGTCTACAAAAAAATGCAAAAATTAGCTGGGTATTGGTAGTGTGCCACCTGTAGTCCCAGTTACTCAGGAGGCTTAGGTGAGAGGCTCACTAGGCCCAGGAGGTTAAGGGC HG:+:32464426:-1 HG:+:299355818:-1 HG:+:491936727:-1 HG:+:577274211:-1 HG:+:580059702:-1 HG:+:587668823:-1 HG:+:705951153:-1 HG:+:836447936:-1 HG:+:953010776:-1 HG:+:1244321334:-1 HG:+:1265903798:-1 HG:+:1277549078:-1 HG:+:1510074598:-1 HG:+:1519885050:-1 HG:+:1633515167:-1 HG:+:1755231574:-1 HG:+:1815637344:-1 HG:+:1819697344:-1 HG:+:2009595513:-1 HG:+:2123182511:-1 HG:+:2195095209:-1 HG:+:2342526520:-1 HG:+:2518697197:-1 HG:+:2547149079:-1 HG:+:2713577592:21 HG:+:2744463249:-1 HG:+:2792110357:-1 HG:+:2825621355:-1 +AGCTATTTGGGAGGCTGAGGCAGGAGAGTTGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGGCCGGGATCCACGCCACTGCACTCTAACCTGGCGACAGAGTGAGTCTCCAATCTCAAAAAAAAAAAAAAAAACTTTCATGCTGATCAGTTAGTGGAAATCAGCTTGTGAATTGCCTCCAAGCCCTGAGCAACACAGACTGCCTCTTACTAATCCCAGCACTTTGGAGGCTGAGGTGGGAGGATGGCTTCGGCTAAGACTTTGAGACTAGCCTAGCCAAAATTCCCTTCGTCTACAAAAAAATGCAAAAATTAGCTGGGTATTGGTAGTGTGCCACCTGTAGTCCCAGTTACTCAGGAGGCTTAGGTGAGAGGCTCACTAGGCCCAGGAGGTTAAGGGC HG:+:2713577589:21 +AGCTATTTGGGAGGCTGAGGCAGGAGAGTTGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGGCCGGGATCCACGCCACTGCACTCTAACCTGGCGACAGAGTGAGTCTCCAATCTCAAAAAAAAAAAAAAAAACTTTCATGCTGATCAGTTAGTGGAAATCAGCTTGTGAATTGCCTCCAAGCCCTGAGCAACACAGACTGCCTCTTACTAATCCCAGCACTTTGGAGGCTGAGGTGGGAGGATGGCTTCGGCTAAGACTTTGAGACTAGCCTAGCCAAAATTCCCTTCGTCTACAAAAAAATGCAAAAATTAGCTGGGTATTGGTAGTGTGCCACCTGTAGTCCCAGTTACTCAGGAGGCTTAGGTGAGAGGCTCACTAGGCCCAGGAGGTTAAGGGC HG:+:2915996360:-1 +AGCTATTTGGGAGGCTGAGGCAGGAGAGTTGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGGCCGGGATCCACGCCACTGCACTCTAACCTGGCGACAGAGTGAGTCTCCAATCTCAAAAAAAAAAAAAAAAACTTTCATGCTGATCAGTTAGTGGAAATCAGCTTGTGAATTGCCTCCAAGCCCTGAGCAACACAGACTGCCTCTTACTAATCCCAGCACTTTGGAGGCTGAGGTGGGAGGATGGCTTCGGCTAAGACTTTGAGACTAGCCTAGCCAAAATTCCCTTCGTCTACAAAAAAATGCAAAAATTAGCTGGGTATTGGTAGTGTGCCACCTGTAGTCCCAGTTACTCAGGAGGCTTAGGTGAGAGGCTCACTAGGCCCAGGAGGTTAAGGGC HG:+:43188906:-1 HG:+:1054278271:-1 HG:+:2184425105:-1 HG:+:2384986590:-1 HG:+:2695792680:-1 HG:+:2713577586:21 HG:+:2979757924:-1 +AGCTATTTGGGAGGCTGAGGCAGGAGAGTTGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGGCCGGGATCCACGCCACTGCACTCTAACCTGGCGACAGAGTGAGTCTCCAATCTCAAAAAAAAAAAAAAAAACTTTCATGCTGATCAGTTAGTGGAAATCAGCTTGTGAATTGCCTCCAAGCCCTGAGCAACACAGACTGCCTCTTACTAATCCCAGCACTTTGGAGGCTGAGGTGGGAGGATGGCTTCGGCTAAGACTTTGAGACTAGCCTAGCCAAAATTCCCTTCGTCTACAAAAAAATGCAAAAATTAGCTGGGTATTGGTAGTGTGCCACCTGTAGTCCCAGTTACTCAGGAGGCTTAGGTGAGAGGCTCACTAGGCCCAGGAGGTTAAGGGC HG:+:155922861:-1 HG:+:269557641:-1 HG:+:500516686:-1 HG:+:803680388:-1 HG:+:1693149269:-1 HG:+:2055557924:-1 HG:+:2415022449:-1 HG:+:2626039479:-1 HG:+:2767991073:-1 HG:+:2829096960:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGGACACACACACACACACAACACACACACACACACACACACACATAATTAGGGTCCTTACCTTGTTCAAACTCCGGGCAGTCACTATCTTTTCCACCTGGGGTCAAGTTTCCGAAGCTGTACGATCTAGGAGGCCTACCAGCTGGTCCATGGCCCGGACAGAGTAGGTGAGTGTCCCCAGCATTCAAGTGATTTCTTGTCTG HG:+:17827919:-1 HG:+:550151648:-1 HG:+:600596162:-1 HG:+:621699074:-1 HG:+:695048744:-1 HG:+:1207199995:-1 HG:+:2071167019:-1 HG:+:2193812391:-1 HG:+:2370881496:-1 HG:+:2577463956:-1 HG:+:2615695123:-1 HG:+:2691326641:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGGACACACACACACACACAACACACACACACACACACACACACATAATTAGGGTCCTTACCTTGTTCAAACTCCGGGCAGTCACTATCTTTTCCACCTGGGGTCAAGTTTCCGAAGCTGTACGATCTAGGAGGCCTACCAGCTGGTCCATGGCCCGGACAGAGTAGGTGAGTGTCCCCAGCATTCAAGTGATTTCTTGTCTG HG:+:170153667:-1 HG:+:388607878:-1 HG:+:880651471:-1 HG:+:981118911:-1 HG:+:1623096746:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGGACACACACACACACACAACACACACACACACACACACACACATAATTAGGGTCCTTACCTTGTTCAAACTCCGGGCAGTCACTATCTTTTCCACCTGGGGTCAAGTTTCCGAAGCTGTACGATCTAGGAGGCCTACCAGCTGGTCCATGGCCCGGACAGAGTAGGTGAGTGTCCCCAGCATTCAAGTGATTTCTTGTCTG HG:+:219352536:-1 HG:+:927087830:-1 HG:+:1306496872:-1 HG:+:1737647764:-1 HG:+:1821779290:-1 HG:+:2028470450:-1 HG:+:2247437442:-1 HG:+:2470190402:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGGACACACACACACACACAACACACACACACACACACACACACATAATTAGGGTCCTTACCTTGTTCAAACTCCGGGCAGTCACTATCTTTTCCACCTGGGGTCAAGTTTCCGAAGCTGTACGATCTAGGAGGCCTACCAGCTGGTCCATGGCCCGGACAGAGTAGGTGAGTGTCCCCAGCATTCAAGTGATTTCTTGTCTG HG:+:291513300:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGGACACACACACACACACAACACACACACACACACACACACACATAATTAGGGTCCTTACCTTGTTCAAACTCCGGGCAGTCACTATCTTTTCCACCTGGGGTCAAGTTTCCGAAGCTGTACGATCTAGGAGGCCTACCAGCTGGTCCATGGCCCGGACAGAGTAGGTGAGTGTCCCCAGCATTCAAGTGATTTCTTGTCTG HG:+:300569318:-1 HG:+:1288025904:-1 HG:+:1974963869:-1 HG:+:2969882553:-1 HG:+:3039422192:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGGACACACACACACACACAACACACACACACACACACACACACATAATTAGGGTCCTTACCTTGTTCAAACTCCGGGCAGTCACTATCTTTTCCACCTGGGGTCAAGTTTCCGAAGCTGTACGATCTAGGAGGCCTACCAGCTGGTCCATGGCCCGGACAGAGTAGGTGAGTGTCCCCAGCATTCAAGTGATTTCTTGTCTG HG:+:308126177:-1 HG:+:326272490:-1 HG:+:626255894:-1 HG:+:1113265095:-1 HG:+:1176186183:-1 HG:+:1474808371:-1 HG:+:1492491666:-1 HG:+:1960630171:-1 HG:+:2050110475:-1 HG:+:2359670840:-1 HG:+:3029118936:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGGACACACACACACACACAACACACACACACACACACACACACATAATTAGGGTCCTTACCTTGTTCAAACTCCGGGCAGTCACTATCTTTTCCACCTGGGGTCAAGTTTCCGAAGCTGTACGATCTAGGAGGCCTACCAGCTGGTCCATGGCCCGGACAGAGTAGGTGAGTGTCCCCAGCATTCAAGTGATTTCTTGTCTG HG:+:460786759:-1 HG:+:1005711661:-1 HG:+:1151119989:-1 HG:+:1395825130:-1 HG:+:1759376500:-1 HG:+:2107017899:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGGACACACACACACACACAACACACACACACACACACACACACATAATTAGGGTCCTTACCTTGTTCAAACTCCGGGCAGTCACTATCTTTTCCACCTGGGGTCAAGTTTCCGAAGCTGTACGATCTAGGAGGCCTACCAGCTGGTCCATGGCCCGGACAGAGTAGGTGAGTGTCCCCAGCATTCAAGTGATTTCTTGTCTG HG:+:89354237:-1 HG:+:448344241:-1 HG:+:813244482:-1 HG:+:818739237:-1 HG:+:850236129:-1 HG:+:1076185847:-1 HG:+:1142397065:-1 HG:+:1185115824:-1 HG:+:1227856515:-1 HG:+:1230253941:-1 HG:+:1473581385:-1 HG:+:1560776760:-1 HG:+:1623947635:-1 HG:+:1641074717:-1 HG:+:2024924936:-1 HG:+:2028717147:-1 HG:+:2362790867:-1 HG:+:2731803539:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGGACACACACACACACACAACACACACACACACACACACACACATAATTAGGGTCCTTACCTTGTTCAAACTCCGGGCAGTCACTATCTTTTCCACCTGGGGTCAAGTTTCCGAAGCTGTACGATCTAGGAGGCCTACCAGCTGGTCCATGGCCCGGACAGAGTAGGTGAGTGTCCCCAGCATTCAAGTGATTTCTTGTCTG HG:+:12562488:-1 HG:+:367568011:-1 HG:+:462598373:-1 HG:+:500806822:-1 HG:+:561858123:-1 HG:+:607440399:-1 HG:+:665014279:-1 HG:+:718995096:-1 HG:+:818034030:-1 HG:+:979560266:-1 HG:+:1048002524:-1 HG:+:1205813907:-1 HG:+:1506867539:-1 HG:+:1521355729:-1 HG:+:1746244053:-1 HG:+:1850284271:-1 HG:+:2474797008:-1 HG:+:3035062190:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGGACACACACACACACACAACACACACACACACACACACACACATAATTAGGGTCCTTACCTTGTTCAAACTCCGGGCAGTCACTATCTTTTCCACCTGGGGTCAAGTTTCCGAAGCTGTACGATCTAGGAGGCCTACCAGCTGGTCCATGGCCCGGACAGAGTAGGTGAGTGTCCCCAGCATTCAAGTGATTTCTTGTCTG HG:+:159515994:-1 HG:+:1411462969:-1 HG:+:1766627312:-1 HG:+:2166785550:-1 HG:+:2702189685:-1 HG:+:2999842551:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGGACACACACACACACACAACACACACACACACACACACACACATAATTAGGGTCCTTACCTTGTTCAAACTCCGGGCAGTCACTATCTTTTCCACCTGGGGTCAAGTTTCCGAAGCTGTACGATCTAGGAGGCCTACCAGCTGGTCCATGGCCCGGACAGAGTAGGTGAGTGTCCCCAGCATTCAAGTGATTTCTTGTCTG HG:+:69052013:-1 HG:+:218473068:-1 HG:+:305286619:-1 HG:+:397869647:-1 HG:+:412413925:-1 HG:+:809042743:-1 HG:+:896522989:-1 HG:+:1076365171:-1 HG:+:1178593906:-1 HG:+:1222395697:-1 HG:+:1408217055:-1 HG:+:1627952522:-1 HG:+:1685577132:-1 HG:+:1744438983:-1 HG:+:1944105491:-1 HG:+:2179531766:-1 HG:+:2227419412:-1 HG:+:2669141385:-1 HG:+:2669180489:-1 HG:+:2669235812:-1 HG:+:2852450878:-1 HG:+:2856131388:-1 HG:+:2898674622:-1 HG:+:2948462934:-1 +ACAGAATTATAAATTTCAAAATATATATAGAGAGATTATCATTTATCATTTCTTTAGATTAAGAACCACAGTTCTATTAGTTATAATAACAAAGGAAATTGAAATAACTGTTGATTCTCTTTAGTAATGATCCATATTCTGTAGTAAGGAGGAAAATTAAGCAGTGAAGTACTTTCTGACTTTTATTACAACTTTAAAGGACACACACACACACACAACACACACACACACACACACACACATAATTAGGGTCCTTACCTTGTTCAAACTCCGGGCAGTCACTATCTTTTCCACCTGGGGTCAAGTTTCCGAAGCTGTACGATCTAGGAGGCCTACCAGCTGGTCCATGGCCCGGACAGAGTAGGTGAGTGTCCCCAGCATTCAAGTGATTTCTTGTCTG HG:+:1063955660:-1 HG:+:1485908638:-1 +CAGACAAGAAATCACTTGAATGCTGGGGACACTCACCTACTCTGTCCGGGCCATGGACCAGCTGGTAGGCCTCCTAGATCGTACAGCTTCGGAAACTTGACCCCAGGTGGAAAAGATAGTGACTGCCCGGAGTTTGAACAAGGTAAGGACCCTAATTATGTGTGTGTGTGTGTGTGTGTGTGTTGTGTGTGTGTGTGTGTCCTTTAAAGTTGTAATAAAAGTCAGAAAGTACTTCACTGCTTAATTTTCCTCCTTACTACAGAATATGGATCATTACTAAAGAGAATCAACAGTTATTTCAATTTCCTTTGTTATTATAACTAATAGAACTGTGGTTCTTAATCTAAAGAAATGATAAATGATAATCTCTCTATATATATTTTGAAATTTATAATTCTGT HG:+:753247670:15 +CAGACAAGAAATCACTTGAATGCTGGGGACACTCACCTACTCTGTCCGGGCCATGGACCAGCTGGTAGGCCTCCTAGATCGTACAGCTTCGGAAACTTGACCCCAGGTGGAAAAGATAGTGACTGCCCGGAGTTTGAACAAGGTAAGGACCCTAATTATGTGTGTGTGTGTGTGTGTGTGTGTTGTGTGTGTGTGTGTGTCCTTTAAAGTTGTAATAAAAGTCAGAAAGTACTTCACTGCTTAATTTTCCTCCTTACTACAGAATATGGATCATTACTAAAGAGAATCAACAGTTATTTCAATTTCCTTTGTTATTATAACTAATAGAACTGTGGTTCTTAATCTAAAGAAATGATAAATGATAATCTCTCTATATATATTTTGAAATTTATAATTCTGT HG:+:753247658:15 HG:+:899021935:-1 +CAGACAAGAAATCACTTGAATGCTGGGGACACTCACCTACTCTGTCCGGGCCATGGACCAGCTGGTAGGCCTCCTAGATCGTACAGCTTCGGAAACTTGACCCCAGGTGGAAAAGATAGTGACTGCCCGGAGTTTGAACAAGGTAAGGACCCTAATTATGTGTGTGTGTGTGTGTGTGTGTGTTGTGTGTGTGTGTGTGTCCTTTAAAGTTGTAATAAAAGTCAGAAAGTACTTCACTGCTTAATTTTCCTCCTTACTACAGAATATGGATCATTACTAAAGAGAATCAACAGTTATTTCAATTTCCTTTGTTATTATAACTAATAGAACTGTGGTTCTTAATCTAAAGAAATGATAAATGATAATCTCTCTATATATATTTTGAAATTTATAATTCTGT HG:+:753247662:15 +CAGACAAGAAATCACTTGAATGCTGGGGACACTCACCTACTCTGTCCGGGCCATGGACCAGCTGGTAGGCCTCCTAGATCGTACAGCTTCGGAAACTTGACCCCAGGTGGAAAAGATAGTGACTGCCCGGAGTTTGAACAAGGTAAGGACCCTAATTATGTGTGTGTGTGTGTGTGTGTGTGTTGTGTGTGTGTGTGTGTCCTTTAAAGTTGTAATAAAAGTCAGAAAGTACTTCACTGCTTAATTTTCCTCCTTACTACAGAATATGGATCATTACTAAAGAGAATCAACAGTTATTTCAATTTCCTTTGTTATTATAACTAATAGAACTGTGGTTCTTAATCTAAAGAAATGATAAATGATAATCTCTCTATATATATTTTGAAATTTATAATTCTGT HG:+:753247666:15 +CAGACAAGAAATCACTTGAATGCTGGGGACACTCACCTACTCTGTCCGGGCCATGGACCAGCTGGTAGGCCTCCTAGATCGTACAGCTTCGGAAACTTGACCCCAGGTGGAAAAGATAGTGACTGCCCGGAGTTTGAACAAGGTAAGGACCCTAATTATGTGTGTGTGTGTGTGTGTGTGTGTTGTGTGTGTGTGTGTGTCCTTTAAAGTTGTAATAAAAGTCAGAAAGTACTTCACTGCTTAATTTTCCTCCTTACTACAGAATATGGATCATTACTAAAGAGAATCAACAGTTATTTCAATTTCCTTTGTTATTATAACTAATAGAACTGTGGTTCTTAATCTAAAGAAATGATAAATGATAATCTCTCTATATATATTTTGAAATTTATAATTCTGT HG:+:753247667:15 +CAGACAAGAAATCACTTGAATGCTGGGGACACTCACCTACTCTGTCCGGGCCATGGACCAGCTGGTAGGCCTCCTAGATCGTACAGCTTCGGAAACTTGACCCCAGGTGGAAAAGATAGTGACTGCCCGGAGTTTGAACAAGGTAAGGACCCTAATTATGTGTGTGTGTGTGTGTGTGTGTGTTGTGTGTGTGTGTGTGTCCTTTAAAGTTGTAATAAAAGTCAGAAAGTACTTCACTGCTTAATTTTCCTCCTTACTACAGAATATGGATCATTACTAAAGAGAATCAACAGTTATTTCAATTTCCTTTGTTATTATAACTAATAGAACTGTGGTTCTTAATCTAAAGAAATGATAAATGATAATCTCTCTATATATATTTTGAAATTTATAATTCTGT HG:+:753247669:15 +AGAACGGAGAATTTCTCAAGACACACAAATAGTAACTACCATATGATCCAGAATCCCGGTATCTACTCAAAGGAAAGAAATCATTGTATTCAATAAATACTTTGCACTTATATGTTTATTTGCTAGCACTATTTACAATAGTAATGATATGGGAATCAATCTAAGTGTCCATAAATGGGAATTGGATAAGGAAAATGTGATAGTATATTCACCAGTGGGAAACTACTCAGCCATAAAAAAAGAATAAAATCATGTCTTTTGCAGCAACATGGAATAGAACTGGAGGCACTATCTTAAGTGAAACAACTCAGATACAAGAAGACTAAATACCAATATGTTCTCAGTTACAAGTGGGATCTAAATAAACGGTGTATACATGGAGGCAGAGTGTGTAATGGTG HG:+:199469473:20 HG:+:405929896:-1 HG:+:432587413:-1 HG:+:456152933:-1 HG:+:1406781646:-1 HG:+:1629759040:-1 HG:+:2006595390:-1 HG:+:2500451335:-1 HG:+:2517377123:-1 HG:+:2601612783:-1 HG:+:2904483880:-1 HG:+:3002497545:-1 +AGAACGGAGAATTTCTCAAGACACACAAATAGTAACTACCATATGATCCAGAATCCCGGTATCTACTCAAAGGAAAGAAATCATTGTATTCAATAAATACTTTGCACTTATATGTTTATTTGCTAGCACTATTTACAATAGTAATGATATGGGAATCAATCTAAGTGTCCATAAATGGGAATTGGATAAGGAAAATGTGATAGTATATTCACCAGTGGGAAACTACTCAGCCATAAAAAAAGAATAAAATCATGTCTTTTGCAGCAACATGGAATAGAACTGGAGGCACTATCTTAAGTGAAACAACTCAGATACAAGAAGACTAAATACCAATATGTTCTCAGTTACAAGTGGGATCTAAATAAACGGTGTATACATGGAGGCAGAGTGTGTAATGGTG HG:+:199469474:20 +AGAACGGAGAATTTCTCAAGACACACAAATAGTAACTACCATATGATCCAGAATCCCGGTATCTACTCAAAGGAAAGAAATCATTGTATTCAATAAATACTTTGCACTTATATGTTTATTTGCTAGCACTATTTACAATAGTAATGATATGGGAATCAATCTAAGTGTCCATAAATGGGAATTGGATAAGGAAAATGTGATAGTATATTCACCAGTGGGAAACTACTCAGCCATAAAAAAAGAATAAAATCATGTCTTTTGCAGCAACATGGAATAGAACTGGAGGCACTATCTTAAGTGAAACAACTCAGATACAAGAAGACTAAATACCAATATGTTCTCAGTTACAAGTGGGATCTAAATAAACGGTGTATACATGGAGGCAGAGTGTGTAATGGTG HG:+:199469478:20 +AGAACGGAGAATTTCTCAAGACACACAAATAGTAACTACCATATGATCCAGAATCCCGGTATCTACTCAAAGGAAAGAAATCATTGTATTCAATAAATACTTTGCACTTATATGTTTATTTGCTAGCACTATTTACAATAGTAATGATATGGGAATCAATCTAAGTGTCCATAAATGGGAATTGGATAAGGAAAATGTGATAGTATATTCACCAGTGGGAAACTACTCAGCCATAAAAAAAGAATAAAATCATGTCTTTTGCAGCAACATGGAATAGAACTGGAGGCACTATCTTAAGTGAAACAACTCAGATACAAGAAGACTAAATACCAATATGTTCTCAGTTACAAGTGGGATCTAAATAAACGGTGTATACATGGAGGCAGAGTGTGTAATGGTG HG:+:199469468:20 HG:+:2225030898:-1 +AGAACGGAGAATTTCTCAAGACACACAAATAGTAACTACCATATGATCCAGAATCCCGGTATCTACTCAAAGGAAAGAAATCATTGTATTCAATAAATACTTTGCACTTATATGTTTATTTGCTAGCACTATTTACAATAGTAATGATATGGGAATCAATCTAAGTGTCCATAAATGGGAATTGGATAAGGAAAATGTGATAGTATATTCACCAGTGGGAAACTACTCAGCCATAAAAAAAGAATAAAATCATGTCTTTTGCAGCAACATGGAATAGAACTGGAGGCACTATCTTAAGTGAAACAACTCAGATACAAGAAGACTAAATACCAATATGTTCTCAGTTACAAGTGGGATCTAAATAAACGGTGTATACATGGAGGCAGAGTGTGTAATGGTG HG:+:199469470:20 HG:+:790908188:-1 +AGAACGGAGAATTTCTCAAGACACACAAATAGTAACTACCATATGATCCAGAATCCCGGTATCTACTCAAAGGAAAGAAATCATTGTATTCAATAAATACTTTGCACTTATATGTTTATTTGCTAGCACTATTTACAATAGTAATGATATGGGAATCAATCTAAGTGTCCATAAATGGGAATTGGATAAGGAAAATGTGATAGTATATTCACCAGTGGGAAACTACTCAGCCATAAAAAAAGAATAAAATCATGTCTTTTGCAGCAACATGGAATAGAACTGGAGGCACTATCTTAAGTGAAACAACTCAGATACAAGAAGACTAAATACCAATATGTTCTCAGTTACAAGTGGGATCTAAATAAACGGTGTATACATGGAGGCAGAGTGTGTAATGGTG HG:+:199469472:20 +CACCATTACACACTCTGCCTCCATGTATACACCGTTTATTTAGATCCCACTTGTAACTGAGAACATATTGGTATTTAGTCTTCTTGTATCTGAGTTGTTTCACTTAAGATAGTGCCTCCAGTTCTATTCCATGTTGCTGCAAAAGACATGATTTTATTCTTTTTTTATGGCTGAGTAGTTTCCCACTGGTGAATATACTATCACATTTTCCTTATCCAATTCCCATTTATGGACACTTAGATTGATTCCCATATCATTACTATTGTAAATAGTGCTAGCAAATAAACATATAAGTGCAAAGTATTTATTGAATACAATGATTTCTTTCCTTTGAGTAGATACCGGGATTCTGGATCATATGGTAGTTACTATTTGTGTGTCTTGAGAAATTCTCCGTTCT HG:+:1712809836:-1 +CACCATTACACACTCTGCCTCCATGTATACACCGTTTATTTAGATCCCACTTGTAACTGAGAACATATTGGTATTTAGTCTTCTTGTATCTGAGTTGTTTCACTTAAGATAGTGCCTCCAGTTCTATTCCATGTTGCTGCAAAAGACATGATTTTATTCTTTTTTTATGGCTGAGTAGTTTCCCACTGGTGAATATACTATCACATTTTCCTTATCCAATTCCCATTTATGGACACTTAGATTGATTCCCATATCATTACTATTGTAAATAGTGCTAGCAAATAAACATATAAGTGCAAAGTATTTATTGAATACAATGATTTCTTTCCTTTGAGTAGATACCGGGATTCTGGATCATATGGTAGTTACTATTTGTGTGTCTTGAGAAATTCTCCGTTCT HG:+:21655134:-1 HG:+:283956818:-1 HG:+:288543488:-1 HG:+:642423934:-1 HG:+:642441465:-1 HG:+:660599845:-1 HG:+:1142218037:-1 HG:+:1196647054:-1 HG:+:1357655974:-1 HG:+:1359917932:-1 HG:+:1716643721:-1 HG:+:1718087619:-1 HG:+:1791414572:-1 HG:+:2066152964:-1 HG:+:2129094046:-1 HG:+:2658187236:-1 +CACCATTACACACTCTGCCTCCATGTATACACCGTTTATTTAGATCCCACTTGTAACTGAGAACATATTGGTATTTAGTCTTCTTGTATCTGAGTTGTTTCACTTAAGATAGTGCCTCCAGTTCTATTCCATGTTGCTGCAAAAGACATGATTTTATTCTTTTTTTATGGCTGAGTAGTTTCCCACTGGTGAATATACTATCACATTTTCCTTATCCAATTCCCATTTATGGACACTTAGATTGATTCCCATATCATTACTATTGTAAATAGTGCTAGCAAATAAACATATAAGTGCAAAGTATTTATTGAATACAATGATTTCTTTCCTTTGAGTAGATACCGGGATTCTGGATCATATGGTAGTTACTATTTGTGTGTCTTGAGAAATTCTCCGTTCT HG:+:168242074:-1 HG:+:946031452:-1 HG:+:961725190:-1 HG:+:1018121826:-1 HG:+:1225885506:-1 HG:+:1268220994:-1 HG:+:1381101312:-1 HG:+:1741529797:-1 HG:+:1875664288:-1 HG:+:2118788640:-1 HG:+:2245739303:-1 HG:+:2516817330:-1 HG:+:2520447407:-1 HG:+:2582416043:-1 HG:+:2983332555:-1 HG:+:2984906254:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:23949778:-1 HG:+:34483539:-1 HG:+:291653504:-1 HG:+:402474629:-1 HG:+:422813281:-1 HG:+:780932477:-1 HG:+:1053157215:-1 HG:+:1971444512:-1 HG:+:2888474780:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:25012641:-1 HG:+:146695991:-1 HG:+:410668196:-1 HG:+:535280281:-1 HG:+:612332978:-1 HG:+:1080669095:-1 HG:+:1147453960:-1 HG:+:2243562083:-1 HG:+:2626024176:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:103346292:-1 HG:+:950361515:-1 HG:+:1462616715:-1 HG:+:2153549917:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:353736386:-1 HG:+:1389997338:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:28255609:-1 HG:+:164624101:-1 HG:+:230132283:-1 HG:+:242570632:-1 HG:+:368702356:-1 HG:+:589466353:-1 HG:+:629376538:-1 HG:+:687561700:-1 HG:+:715944517:-1 HG:+:752180231:-1 HG:+:794401715:-1 HG:+:801698109:-1 HG:+:938362923:-1 HG:+:1022508873:-1 HG:+:1140614551:-1 HG:+:1297892943:-1 HG:+:1318020019:-1 HG:+:1356344523:-1 HG:+:1414952162:-1 HG:+:1464346416:-1 HG:+:1546896804:-1 HG:+:1650322982:-1 HG:+:1825212972:-1 HG:+:1863728279:-1 HG:+:1899459311:-1 HG:+:1924242730:-1 HG:+:2019457154:-1 HG:+:2142452649:-1 HG:+:2146028335:-1 HG:+:2255927931:-1 HG:+:2270307517:-1 HG:+:2274679708:-1 HG:+:2396004838:-1 HG:+:2402284126:-1 HG:+:2415954516:-1 HG:+:2607980414:-1 HG:+:2630561638:-1 HG:+:2678718849:-1 HG:+:2712925039:-1 HG:+:2871759020:-1 HG:+:2882487348:-1 HG:+:3002902200:-1 HG:+:3009674568:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:30519726:-1 HG:+:203856042:-1 HG:+:283051801:-1 HG:+:288735450:-1 HG:+:293183138:-1 HG:+:293999520:-1 HG:+:323783229:-1 HG:+:399858559:-1 HG:+:417309699:-1 HG:+:451869113:-1 HG:+:481838612:-1 HG:+:537799971:-1 HG:+:540640762:-1 HG:+:565209045:-1 HG:+:610200518:-1 HG:+:730278326:-1 HG:+:810113593:-1 HG:+:912852738:-1 HG:+:913222395:-1 HG:+:1043117145:-1 HG:+:1053776696:-1 HG:+:1077237143:-1 HG:+:1126085351:-1 HG:+:1207215967:-1 HG:+:1236272828:-1 HG:+:1325307536:-1 HG:+:1629963064:-1 HG:+:1638112153:-1 HG:+:1644210490:-1 HG:+:1976181042:-1 HG:+:2072783849:-1 HG:+:2174584725:-1 HG:+:2244872950:-1 HG:+:2251138786:-1 HG:+:2269809503:-1 HG:+:2359608299:-1 HG:+:2378642123:-1 HG:+:2385040590:-1 HG:+:2483148951:-1 HG:+:2485005563:-1 HG:+:2509798521:-1 HG:+:2542303301:-1 HG:+:2610944637:-1 HG:+:2624919497:-1 HG:+:2658457243:-1 HG:+:2708394409:-1 HG:+:2773868236:-1 HG:+:2814917508:-1 HG:+:2885982553:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:56664961:-1 HG:+:320244461:-1 HG:+:609040894:-1 HG:+:792789314:-1 HG:+:961964497:-1 HG:+:1080672307:-1 HG:+:1143322662:-1 HG:+:1929856389:-1 HG:+:1992922161:-1 HG:+:2050376525:-1 HG:+:2174022145:-1 HG:+:2344952955:-1 HG:+:2380178099:-1 HG:+:2617944699:-1 HG:+:2770369469:-1 HG:+:2808639483:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:1287603:-1 HG:+:44930342:-1 HG:+:174059961:-1 HG:+:205754817:-1 HG:+:289519842:-1 HG:+:311120977:-1 HG:+:402594674:-1 HG:+:656978636:-1 HG:+:708110827:-1 HG:+:757148525:-1 HG:+:931529753:-1 HG:+:1013384381:-1 HG:+:1078928614:-1 HG:+:1236989957:-1 HG:+:1279370751:-1 HG:+:1328262432:-1 HG:+:1332445557:-1 HG:+:1335384483:-1 HG:+:1345406579:-1 HG:+:1370556888:-1 HG:+:1431147849:-1 HG:+:1481742204:-1 HG:+:1646237806:-1 HG:+:1707435023:-1 HG:+:1726214523:-1 HG:+:1830117095:-1 HG:+:1834454097:-1 HG:+:1839218975:-1 HG:+:1848971319:-1 HG:+:1856106146:-1 HG:+:1928140149:-1 HG:+:1957452304:-1 HG:+:2044008554:-1 HG:+:2120102070:-1 HG:+:2177018229:-1 HG:+:2274703487:-1 HG:+:2288609450:-1 HG:+:2302632945:-1 HG:+:2544563296:-1 HG:+:2544780880:-1 HG:+:2545286086:-1 HG:+:2556671672:-1 HG:+:2579747661:-1 HG:+:2593767648:-1 HG:+:2656286613:-1 HG:+:2676398727:-1 HG:+:2696502418:-1 HG:+:2718456681:-1 HG:+:2722354132:-1 HG:+:2729149933:-1 HG:+:2742632474:-1 HG:+:2751458160:-1 HG:+:2776505269:-1 HG:+:2860657004:-1 HG:+:2881484949:-1 HG:+:2887266852:-1 HG:+:2904838556:-1 HG:+:2931244894:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:318963173:-1 HG:+:374282144:-1 HG:+:657408405:-1 HG:+:975443563:-1 HG:+:1120342352:-1 HG:+:1120949109:-1 HG:+:1173236159:-1 HG:+:1220391372:-1 HG:+:1907082115:-1 HG:+:2381851651:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:64475988:-1 HG:+:174457056:-1 HG:+:211934110:-1 HG:+:213248874:-1 HG:+:237537794:-1 HG:+:286895586:-1 HG:+:391712600:-1 HG:+:417694620:-1 HG:+:460702373:-1 HG:+:547456101:-1 HG:+:727367038:-1 HG:+:771367463:-1 HG:+:833078259:-1 HG:+:874677000:-1 HG:+:876449523:-1 HG:+:897317616:-1 HG:+:898850226:-1 HG:+:1160071617:-1 HG:+:1199576841:-1 HG:+:1223895789:-1 HG:+:1351761254:-1 HG:+:1522809130:-1 HG:+:1718678420:-1 HG:+:1857168922:-1 HG:+:1887114077:-1 HG:+:1970578682:-1 HG:+:2154063524:-1 HG:+:2252309112:-1 HG:+:2391637465:-1 HG:+:2419378036:-1 HG:+:2568935865:-1 HG:+:2735761086:-1 HG:+:2770568128:-1 HG:+:2874442271:-1 HG:+:2906900362:-1 HG:+:2973814899:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:75016047:-1 HG:+:87856977:-1 HG:+:195622433:-1 HG:+:195951456:-1 HG:+:277382880:-1 HG:+:297659023:-1 HG:+:400652438:-1 HG:+:406670343:-1 HG:+:426816623:-1 HG:+:433746462:-1 HG:+:470151865:-1 HG:+:604184238:-1 HG:+:641262703:-1 HG:+:655994666:-1 HG:+:701190321:-1 HG:+:751844811:-1 HG:+:754082005:-1 HG:+:777763638:-1 HG:+:801882423:-1 HG:+:829550934:-1 HG:+:838228289:-1 HG:+:842865724:-1 HG:+:861729585:-1 HG:+:871291122:-1 HG:+:935588326:-1 HG:+:949635757:-1 HG:+:966560022:-1 HG:+:1006411126:-1 HG:+:1010635810:-1 HG:+:1160150324:-1 HG:+:1190103909:-1 HG:+:1250199523:-1 HG:+:1253476619:-1 HG:+:1296326903:-1 HG:+:1310980385:-1 HG:+:1316391048:-1 HG:+:1319548949:-1 HG:+:1485522140:-1 HG:+:1559588103:-1 HG:+:1786116947:-1 HG:+:1866055215:-1 HG:+:1945055446:-1 HG:+:2017631759:-1 HG:+:2037042578:-1 HG:+:2052356288:-1 HG:+:2147887138:-1 HG:+:2181859655:-1 HG:+:2355878295:-1 HG:+:2486669462:-1 HG:+:2625931984:-1 HG:+:2632089545:-1 HG:+:2758549895:-1 HG:+:2962991547:-1 HG:+:2994958400:-1 HG:+:3016604566:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:691057790:-1 HG:+:722752315:-1 HG:+:775051185:-1 HG:+:987669952:-1 HG:+:1028999715:-1 HG:+:1443878720:-1 HG:+:1470967382:-1 HG:+:1498699416:-1 HG:+:1698087047:-1 HG:+:1889154107:-1 HG:+:2034455911:-1 HG:+:2466181162:-1 HG:+:2503721198:-1 HG:+:2605224714:-1 HG:+:2607960402:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:164760818:-1 HG:+:422404118:-1 HG:+:587421405:-1 HG:+:871681550:-1 HG:+:2412264018:-1 HG:+:2518837251:-1 HG:+:2551357105:-1 HG:+:2654059091:-1 HG:+:2669791548:-1 HG:+:2881996175:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:80440207:-1 HG:+:1234462115:-1 HG:+:1511808866:-1 HG:+:1584255419:-1 HG:+:2231444145:-1 HG:+:2661346188:-1 HG:+:2666907031:-1 +GCTTCCAAGAGGACATTTAAGAAAATCTACTGGGAAAACTTTGTCCTGATGACTTCTAGAATTGAGTATAACGTATTGTTCCGTTTTACTTGAAAAAATTTGAGAGATAAATGCCAGTTTTTTACTGAGTTTGTACTTTATTTTGCATTCTGGTTTTTTTTTGTTGTTTTGTTTTGTTTTTTTGTTTTTTGAGACGGTCTCGCCTCGGAGTTGCTAGTGCGCCATCTTCAGCTCACTAGCAACCTCCCGCCCTTCCCAGGTTCAAGGGATTCCCCTGCCTCAGCCTCCCGAGTAGCTGGCGACTACAGGCGGTGTGCCAACCACGCCCGGCTACTTTTTTGTTTTTTTAGTAGGAGACGGGGTTTCAGCATGGTGGTCAGAATGGTCTTGATCCTCTGAC HG:+:88405236:-1 HG:+:1088763246:-1 HG:+:1449601793:-1 HG:+:1513431311:-1 HG:+:1645491903:-1 HG:+:2705215014:-1 HG:+:2854410086:-1 +GTCAGAGGATCAAGACCATTCTGACCACCATGCTGAAACCCCGTCTCCTACTAAAAAAACAAAAAAGTAGCCGGGCGTGGTTGGCACACCGCCTGTAGTCGCCAGCTACTCGGGAGGCTGAGGCAGGGGAATCCCTTGAACCTGGGAAGGGCGGGAGGTTGCTAGTGAGCTGAAGATGGCGCACTAGCAACTCCGAGGCGAGACCGTCTCAAAAAACAAAAAAACAAAACAAAACAACAAAAAAAAACCAGAATGCAAAATAAAGTACAAACTCAGTAAAAAACTGGCATTTATCTCTCAAATTTTTTCAAGTAAAACGGAACAATACGTTATACTCAATTCTAGAAGTCATCAGGACAAAGTTTTCCCAGTAGATTTTCTTAAATGTCCTCTTGGAAGC HG:+:28004016:-1 HG:+:29426676:-1 HG:+:121238900:-1 HG:+:161025276:-1 HG:+:224006588:-1 HG:+:370498812:-1 HG:+:466401585:-1 HG:+:491322255:-1 HG:+:693040542:-1 HG:+:726525225:-1 HG:+:755502478:-1 HG:+:874933673:-1 HG:+:1035770272:-1 HG:+:1045304459:-1 HG:+:1088752161:-1 HG:+:1255857556:-1 HG:+:1297244032:-1 HG:+:1384280141:-1 HG:+:1385055658:-1 HG:+:1430998819:-1 HG:+:1669626202:-1 HG:+:1671925617:-1 HG:+:1675476426:-1 HG:+:1778637610:-1 HG:+:1779332972:-1 HG:+:1822303137:-1 HG:+:1878239528:-1 HG:+:1934224311:-1 HG:+:2197542493:-1 HG:+:2337456748:-1 HG:+:2559945913:-1 HG:+:2584767072:-1 HG:+:2665843024:-1 HG:+:2677838868:-1 HG:+:2678121302:-1 HG:+:2752549876:-1 HG:+:2753747330:-1 HG:+:2774314630:-1 HG:+:2825999010:-1 HG:+:2851513582:-1 HG:+:2870382440:-1 HG:+:2926728810:-1 HG:+:3012525638:-1 HG:+:3015128642:-1 HG:+:3030956486:-1 +GTCAGAGGATCAAGACCATTCTGACCACCATGCTGAAACCCCGTCTCCTACTAAAAAAACAAAAAAGTAGCCGGGCGTGGTTGGCACACCGCCTGTAGTCGCCAGCTACTCGGGAGGCTGAGGCAGGGGAATCCCTTGAACCTGGGAAGGGCGGGAGGTTGCTAGTGAGCTGAAGATGGCGCACTAGCAACTCCGAGGCGAGACCGTCTCAAAAAACAAAAAAACAAAACAAAACAACAAAAAAAAACCAGAATGCAAAATAAAGTACAAACTCAGTAAAAAACTGGCATTTATCTCTCAAATTTTTTCAAGTAAAACGGAACAATACGTTATACTCAATTCTAGAAGTCATCAGGACAAAGTTTTCCCAGTAGATTTTCTTAAATGTCCTCTTGGAAGC HG:+:17000109:-1 HG:+:23463115:-1 HG:+:39309097:-1 HG:+:71464568:-1 HG:+:103436275:26 HG:+:172919289:-1 HG:+:243037688:-1 HG:+:290267389:-1 HG:+:333430989:-1 HG:+:381307883:-1 HG:+:446864841:-1 HG:+:465150719:-1 HG:+:506936628:-1 HG:+:525332436:-1 HG:+:614466255:-1 HG:+:629032642:-1 HG:+:728680813:-1 HG:+:809897124:-1 HG:+:809954189:-1 HG:+:819228987:-1 HG:+:819361493:-1 HG:+:874614116:-1 HG:+:891918178:-1 HG:+:981785240:-1 HG:+:1013885273:-1 HG:+:1057244315:-1 HG:+:1061718156:-1 HG:+:1064944577:-1 HG:+:1222466695:-1 HG:+:1238933585:-1 HG:+:1258432109:-1 HG:+:1315339300:-1 HG:+:1331621197:-1 HG:+:1388935986:-1 HG:+:1537511783:-1 HG:+:1577238322:-1 HG:+:1717425650:-1 HG:+:1736351883:-1 HG:+:1737072103:-1 HG:+:1795802278:-1 HG:+:1936224502:-1 HG:+:2044895568:-1 HG:+:2045272737:-1 HG:+:2066598867:-1 HG:+:2076700536:-1 HG:+:2110727141:-1 HG:+:2118755511:-1 HG:+:2134988457:-1 HG:+:2180727098:-1 HG:+:2362104366:-1 HG:+:2398432099:-1 HG:+:2399575704:-1 HG:+:2415058008:-1 HG:+:2460035394:-1 HG:+:2516394638:-1 HG:+:2516509351:-1 HG:+:2521262508:-1 HG:+:2527674646:-1 HG:+:2557482442:-1 HG:+:2588488313:-1 HG:+:2662279497:-1 HG:+:2667246938:-1 HG:+:2730057962:-1 HG:+:2762774046:-1 HG:+:2779332424:-1 HG:+:2796314054:-1 HG:+:2815710747:-1 HG:+:2847306185:-1 HG:+:2848933550:-1 HG:+:2868819292:-1 HG:+:2871671318:-1 HG:+:2881667335:-1 HG:+:2999907725:-1 +GTCAGAGGATCAAGACCATTCTGACCACCATGCTGAAACCCCGTCTCCTACTAAAAAAACAAAAAAGTAGCCGGGCGTGGTTGGCACACCGCCTGTAGTCGCCAGCTACTCGGGAGGCTGAGGCAGGGGAATCCCTTGAACCTGGGAAGGGCGGGAGGTTGCTAGTGAGCTGAAGATGGCGCACTAGCAACTCCGAGGCGAGACCGTCTCAAAAAACAAAAAAACAAAACAAAACAACAAAAAAAAACCAGAATGCAAAATAAAGTACAAACTCAGTAAAAAACTGGCATTTATCTCTCAAATTTTTTCAAGTAAAACGGAACAATACGTTATACTCAATTCTAGAAGTCATCAGGACAAAGTTTTCCCAGTAGATTTTCTTAAATGTCCTCTTGGAAGC HG:+:35653055:-1 HG:+:48883209:-1 HG:+:100428070:-1 HG:+:151583237:-1 HG:+:240947202:-1 HG:+:323880828:-1 HG:+:370249636:-1 HG:+:391325911:-1 HG:+:447155294:-1 HG:+:455803892:-1 HG:+:471286160:-1 HG:+:692662471:-1 HG:+:693868869:-1 HG:+:700526076:-1 HG:+:765547029:-1 HG:+:842831794:-1 HG:+:908720851:-1 HG:+:916594739:-1 HG:+:950990256:-1 HG:+:951865680:-1 HG:+:994228895:-1 HG:+:1026964092:-1 HG:+:1028066614:-1 HG:+:1048895684:-1 HG:+:1080564733:-1 HG:+:1097691077:-1 HG:+:1150706234:-1 HG:+:1151548114:-1 HG:+:1153358763:-1 HG:+:1171106247:-1 HG:+:1172299601:-1 HG:+:1175409221:-1 HG:+:1300659886:-1 HG:+:1353784802:-1 HG:+:1361875746:-1 HG:+:1396276889:-1 HG:+:1416378471:-1 HG:+:1469788373:-1 HG:+:1557550203:-1 HG:+:1651091143:-1 HG:+:1664747793:-1 HG:+:1665380677:-1 HG:+:1693703578:-1 HG:+:1716351295:-1 HG:+:1732384366:-1 HG:+:1784376755:-1 HG:+:1845816791:-1 HG:+:1856097205:-1 HG:+:1863314602:-1 HG:+:1909933470:-1 HG:+:1932738836:-1 HG:+:1932897320:-1 HG:+:1956206781:-1 HG:+:2113529663:-1 HG:+:2154741117:-1 HG:+:2159694836:-1 HG:+:2170623415:-1 HG:+:2250885386:-1 HG:+:2260180423:-1 HG:+:2277427055:-1 HG:+:2403967280:-1 HG:+:2530663610:-1 HG:+:2537963028:-1 HG:+:2549475114:-1 HG:+:2564418175:-1 HG:+:2593713910:-1 HG:+:2615137498:-1 HG:+:2663444652:-1 HG:+:2700301168:-1 HG:+:2723460274:-1 HG:+:2743905551:-1 HG:+:2751253481:-1 HG:+:2760844823:-1 HG:+:2804036049:-1 HG:+:2944589669:-1 HG:+:2948307397:-1 HG:+:2954135865:-1 HG:+:2971038276:-1 HG:+:2991141929:-1 +GTCAGAGGATCAAGACCATTCTGACCACCATGCTGAAACCCCGTCTCCTACTAAAAAAACAAAAAAGTAGCCGGGCGTGGTTGGCACACCGCCTGTAGTCGCCAGCTACTCGGGAGGCTGAGGCAGGGGAATCCCTTGAACCTGGGAAGGGCGGGAGGTTGCTAGTGAGCTGAAGATGGCGCACTAGCAACTCCGAGGCGAGACCGTCTCAAAAAACAAAAAAACAAAACAAAACAACAAAAAAAAACCAGAATGCAAAATAAAGTACAAACTCAGTAAAAAACTGGCATTTATCTCTCAAATTTTTTCAAGTAAAACGGAACAATACGTTATACTCAATTCTAGAAGTCATCAGGACAAAGTTTTCCCAGTAGATTTTCTTAAATGTCCTCTTGGAAGC HG:+:103436277:26 HG:+:229344964:-1 HG:+:478478419:-1 HG:+:1625372532:-1 HG:+:1891818444:-1 HG:+:2371877212:-1 HG:+:2544365466:-1 HG:+:2829280179:-1 HG:+:2872908237:-1 +GTCAGAGGATCAAGACCATTCTGACCACCATGCTGAAACCCCGTCTCCTACTAAAAAAACAAAAAAGTAGCCGGGCGTGGTTGGCACACCGCCTGTAGTCGCCAGCTACTCGGGAGGCTGAGGCAGGGGAATCCCTTGAACCTGGGAAGGGCGGGAGGTTGCTAGTGAGCTGAAGATGGCGCACTAGCAACTCCGAGGCGAGACCGTCTCAAAAAACAAAAAAACAAAACAAAACAACAAAAAAAAACCAGAATGCAAAATAAAGTACAAACTCAGTAAAAAACTGGCATTTATCTCTCAAATTTTTTCAAGTAAAACGGAACAATACGTTATACTCAATTCTAGAAGTCATCAGGACAAAGTTTTCCCAGTAGATTTTCTTAAATGTCCTCTTGGAAGC HG:+:103436264:26 HG:+:192980612:-1 HG:+:920545746:-1 HG:+:1004344607:-1 HG:+:2044124315:-1 +GTCAGAGGATCAAGACCATTCTGACCACCATGCTGAAACCCCGTCTCCTACTAAAAAAACAAAAAAGTAGCCGGGCGTGGTTGGCACACCGCCTGTAGTCGCCAGCTACTCGGGAGGCTGAGGCAGGGGAATCCCTTGAACCTGGGAAGGGCGGGAGGTTGCTAGTGAGCTGAAGATGGCGCACTAGCAACTCCGAGGCGAGACCGTCTCAAAAAACAAAAAAACAAAACAAAACAACAAAAAAAAACCAGAATGCAAAATAAAGTACAAACTCAGTAAAAAACTGGCATTTATCTCTCAAATTTTTTCAAGTAAAACGGAACAATACGTTATACTCAATTCTAGAAGTCATCAGGACAAAGTTTTCCCAGTAGATTTTCTTAAATGTCCTCTTGGAAGC HG:+:103436263:26 +GTCAGAGGATCAAGACCATTCTGACCACCATGCTGAAACCCCGTCTCCTACTAAAAAAACAAAAAAGTAGCCGGGCGTGGTTGGCACACCGCCTGTAGTCGCCAGCTACTCGGGAGGCTGAGGCAGGGGAATCCCTTGAACCTGGGAAGGGCGGGAGGTTGCTAGTGAGCTGAAGATGGCGCACTAGCAACTCCGAGGCGAGACCGTCTCAAAAAACAAAAAAACAAAACAAAACAACAAAAAAAAACCAGAATGCAAAATAAAGTACAAACTCAGTAAAAAACTGGCATTTATCTCTCAAATTTTTTCAAGTAAAACGGAACAATACGTTATACTCAATTCTAGAAGTCATCAGGACAAAGTTTTCCCAGTAGATTTTCTTAAATGTCCTCTTGGAAGC HG:+:7714148:-1 +GTCAGAGGATCAAGACCATTCTGACCACCATGCTGAAACCCCGTCTCCTACTAAAAAAACAAAAAAGTAGCCGGGCGTGGTTGGCACACCGCCTGTAGTCGCCAGCTACTCGGGAGGCTGAGGCAGGGGAATCCCTTGAACCTGGGAAGGGCGGGAGGTTGCTAGTGAGCTGAAGATGGCGCACTAGCAACTCCGAGGCGAGACCGTCTCAAAAAACAAAAAAACAAAACAAAACAACAAAAAAAAACCAGAATGCAAAATAAAGTACAAACTCAGTAAAAAACTGGCATTTATCTCTCAAATTTTTTCAAGTAAAACGGAACAATACGTTATACTCAATTCTAGAAGTCATCAGGACAAAGTTTTCCCAGTAGATTTTCTTAAATGTCCTCTTGGAAGC HG:+:2594277059:-1 +GTCAGAGGATCAAGACCATTCTGACCACCATGCTGAAACCCCGTCTCCTACTAAAAAAACAAAAAAGTAGCCGGGCGTGGTTGGCACACCGCCTGTAGTCGCCAGCTACTCGGGAGGCTGAGGCAGGGGAATCCCTTGAACCTGGGAAGGGCGGGAGGTTGCTAGTGAGCTGAAGATGGCGCACTAGCAACTCCGAGGCGAGACCGTCTCAAAAAACAAAAAAACAAAACAAAACAACAAAAAAAAACCAGAATGCAAAATAAAGTACAAACTCAGTAAAAAACTGGCATTTATCTCTCAAATTTTTTCAAGTAAAACGGAACAATACGTTATACTCAATTCTAGAAGTCATCAGGACAAAGTTTTCCCAGTAGATTTTCTTAAATGTCCTCTTGGAAGC HG:+:102536072:-1 HG:+:103436272:26 HG:+:268520395:-1 HG:+:284436067:-1 HG:+:1019555077:-1 HG:+:1077489288:-1 HG:+:1275298189:-1 HG:+:1318432599:-1 HG:+:1857138787:-1 HG:+:1880486587:-1 HG:+:1955422388:-1 HG:+:2259241245:-1 HG:+:2389420884:-1 HG:+:2673572590:-1 HG:+:2707635082:-1 HG:+:2715227454:-1 HG:+:2749482239:-1 HG:+:2860235897:-1 HG:+:3096030769:-1 +GTCAGAGGATCAAGACCATTCTGACCACCATGCTGAAACCCCGTCTCCTACTAAAAAAACAAAAAAGTAGCCGGGCGTGGTTGGCACACCGCCTGTAGTCGCCAGCTACTCGGGAGGCTGAGGCAGGGGAATCCCTTGAACCTGGGAAGGGCGGGAGGTTGCTAGTGAGCTGAAGATGGCGCACTAGCAACTCCGAGGCGAGACCGTCTCAAAAAACAAAAAAACAAAACAAAACAACAAAAAAAAACCAGAATGCAAAATAAAGTACAAACTCAGTAAAAAACTGGCATTTATCTCTCAAATTTTTTCAAGTAAAACGGAACAATACGTTATACTCAATTCTAGAAGTCATCAGGACAAAGTTTTCCCAGTAGATTTTCTTAAATGTCCTCTTGGAAGC HG:+:294665963:-1 HG:+:804037528:-1 HG:+:1101136064:-1 HG:+:1154435570:-1 HG:+:1766124602:-1 HG:+:2336762243:-1 HG:+:2664252850:-1 HG:+:2869323716:-1 +ATTACAGAGACAGCCCACACCAGCACTGCCTGAATTACAGAGATGACAGGTCCACACCCAGCACTGCCTTGGAATTACAGAGATGACAGTCCACACCAGACATCATCATAATCACAGAGATATTCTACACCAGCATCATCTTAATTACAGAGACAGCCCACACCAGCGCTGCCTGAATTACAGAGATGACAGTCCACAGCAGCAACTGCCTGAATTACAGAGATTGATAGTCCACACCAGCATCATCATAATCACAGACGATATTCTACACCAGCCATCATCTTATTACAGAGACAGCCCACACAGCACTGCCTGAATTACAGAGATGACAGTCCACAACCAGCGACTGCCTGATTACAGAGATGACAGTCCACACCAGCTACTGCCCTGAATTACAGAG HG:+:154591560:-1 HG:+:410203476:-1 HG:+:1699012138:-1 +ATTACAGAGACAGCCCACACCAGCACTGCCTGAATTACAGAGATGACAGGTCCACACCCAGCACTGCCTTGGAATTACAGAGATGACAGTCCACACCAGACATCATCATAATCACAGAGATATTCTACACCAGCATCATCTTAATTACAGAGACAGCCCACACCAGCGCTGCCTGAATTACAGAGATGACAGTCCACAGCAGCAACTGCCTGAATTACAGAGATTGATAGTCCACACCAGCATCATCATAATCACAGACGATATTCTACACCAGCCATCATCTTATTACAGAGACAGCCCACACAGCACTGCCTGAATTACAGAGATGACAGTCCACAACCAGCGACTGCCTGATTACAGAGATGACAGTCCACACCAGCTACTGCCCTGAATTACAGAG HG:+:255571724:-1 HG:+:557751972:-1 HG:+:698207639:-1 HG:+:825296378:-1 HG:+:913041177:-1 HG:+:1045604329:-1 HG:+:1358349230:-1 HG:+:1470397644:-1 HG:+:1656743678:-1 HG:+:2197947226:-1 HG:+:2943890096:-1 HG:+:2955481286:-1 HG:+:3013283771:-1 +ATTACAGAGACAGCCCACACCAGCACTGCCTGAATTACAGAGATGACAGGTCCACACCCAGCACTGCCTTGGAATTACAGAGATGACAGTCCACACCAGACATCATCATAATCACAGAGATATTCTACACCAGCATCATCTTAATTACAGAGACAGCCCACACCAGCGCTGCCTGAATTACAGAGATGACAGTCCACAGCAGCAACTGCCTGAATTACAGAGATTGATAGTCCACACCAGCATCATCATAATCACAGACGATATTCTACACCAGCCATCATCTTATTACAGAGACAGCCCACACAGCACTGCCTGAATTACAGAGATGACAGTCCACAACCAGCGACTGCCTGATTACAGAGATGACAGTCCACACCAGCTACTGCCCTGAATTACAGAG HG:+:22695510:-1 HG:+:841049751:-1 HG:+:1532068414:-1 HG:+:2751171598:-1 HG:+:2816507860:-1 +ATTACAGAGACAGCCCACACCAGCACTGCCTGAATTACAGAGATGACAGGTCCACACCCAGCACTGCCTTGGAATTACAGAGATGACAGTCCACACCAGACATCATCATAATCACAGAGATATTCTACACCAGCATCATCTTAATTACAGAGACAGCCCACACCAGCGCTGCCTGAATTACAGAGATGACAGTCCACAGCAGCAACTGCCTGAATTACAGAGATTGATAGTCCACACCAGCATCATCATAATCACAGACGATATTCTACACCAGCCATCATCTTATTACAGAGACAGCCCACACAGCACTGCCTGAATTACAGAGATGACAGTCCACAACCAGCGACTGCCTGATTACAGAGATGACAGTCCACACCAGCTACTGCCCTGAATTACAGAG HG:+:3052581:-1 HG:+:295267327:-1 HG:+:399549151:-1 HG:+:624128205:-1 HG:+:1098362947:-1 HG:+:1525908662:-1 HG:+:1705028186:-1 HG:+:1832714994:-1 HG:+:1890526375:-1 HG:+:2426501464:-1 HG:+:2994741228:-1 +ATTACAGAGACAGCCCACACCAGCACTGCCTGAATTACAGAGATGACAGGTCCACACCCAGCACTGCCTTGGAATTACAGAGATGACAGTCCACACCAGACATCATCATAATCACAGAGATATTCTACACCAGCATCATCTTAATTACAGAGACAGCCCACACCAGCGCTGCCTGAATTACAGAGATGACAGTCCACAGCAGCAACTGCCTGAATTACAGAGATTGATAGTCCACACCAGCATCATCATAATCACAGACGATATTCTACACCAGCCATCATCTTATTACAGAGACAGCCCACACAGCACTGCCTGAATTACAGAGATGACAGTCCACAACCAGCGACTGCCTGATTACAGAGATGACAGTCCACACCAGCTACTGCCCTGAATTACAGAG HG:+:68614491:-1 HG:+:289538259:-1 HG:+:692191752:-1 HG:+:752516301:-1 HG:+:1346097467:-1 HG:+:1754453219:-1 HG:+:2076872150:-1 HG:+:2373516166:-1 HG:+:2491576430:-1 HG:+:2969321246:-1 +ATTACAGAGACAGCCCACACCAGCACTGCCTGAATTACAGAGATGACAGGTCCACACCCAGCACTGCCTTGGAATTACAGAGATGACAGTCCACACCAGACATCATCATAATCACAGAGATATTCTACACCAGCATCATCTTAATTACAGAGACAGCCCACACCAGCGCTGCCTGAATTACAGAGATGACAGTCCACAGCAGCAACTGCCTGAATTACAGAGATTGATAGTCCACACCAGCATCATCATAATCACAGACGATATTCTACACCAGCCATCATCTTATTACAGAGACAGCCCACACAGCACTGCCTGAATTACAGAGATGACAGTCCACAACCAGCGACTGCCTGATTACAGAGATGACAGTCCACACCAGCTACTGCCCTGAATTACAGAG HG:+:112027973:-1 HG:+:179121227:-1 HG:+:366021784:-1 HG:+:659612965:-1 HG:+:674974344:-1 HG:+:879096737:-1 HG:+:879096827:-1 HG:+:879096872:-1 HG:+:879096917:-1 HG:+:1201486378:-1 HG:+:1227049054:-1 HG:+:1288793378:-1 HG:+:1298732486:-1 HG:+:1307294015:-1 HG:+:1380101748:-1 HG:+:1408138830:-1 HG:+:1441774849:-1 HG:+:1516614061:-1 HG:+:1517917258:-1 HG:+:1670391201:-1 HG:+:1798794515:-1 HG:+:1858464805:-1 HG:+:2025727855:-1 HG:+:2047414090:-1 HG:+:2219851009:-1 HG:+:2434386653:-1 HG:+:2488865261:-1 HG:+:2541809952:-1 HG:+:2845911239:-1 HG:+:2901540006:-1 HG:+:2972625511:-1 HG:+:3041623227:-1 +ATTACAGAGACAGCCCACACCAGCACTGCCTGAATTACAGAGATGACAGGTCCACACCCAGCACTGCCTTGGAATTACAGAGATGACAGTCCACACCAGACATCATCATAATCACAGAGATATTCTACACCAGCATCATCTTAATTACAGAGACAGCCCACACCAGCGCTGCCTGAATTACAGAGATGACAGTCCACAGCAGCAACTGCCTGAATTACAGAGATTGATAGTCCACACCAGCATCATCATAATCACAGACGATATTCTACACCAGCCATCATCTTATTACAGAGACAGCCCACACAGCACTGCCTGAATTACAGAGATGACAGTCCACAACCAGCGACTGCCTGATTACAGAGATGACAGTCCACACCAGCTACTGCCCTGAATTACAGAG HG:+:236482819:-1 HG:+:237515402:-1 HG:+:324487365:-1 HG:+:541332119:-1 HG:+:552825686:-1 HG:+:848152098:-1 HG:+:856741806:-1 HG:+:918866224:-1 HG:+:922230082:-1 HG:+:958185323:-1 HG:+:987510550:-1 HG:+:1137984039:-1 HG:+:1226122399:-1 HG:+:1300031959:-1 HG:+:1471326694:-1 HG:+:1566572969:-1 HG:+:1879063176:-1 HG:+:1989559687:-1 HG:+:2300538497:-1 HG:+:2513694361:-1 HG:+:2537025858:-1 HG:+:2654270885:-1 HG:+:2892346220:-1 +ATTACAGAGACAGCCCACACCAGCACTGCCTGAATTACAGAGATGACAGGTCCACACCCAGCACTGCCTTGGAATTACAGAGATGACAGTCCACACCAGACATCATCATAATCACAGAGATATTCTACACCAGCATCATCTTAATTACAGAGACAGCCCACACCAGCGCTGCCTGAATTACAGAGATGACAGTCCACAGCAGCAACTGCCTGAATTACAGAGATTGATAGTCCACACCAGCATCATCATAATCACAGACGATATTCTACACCAGCCATCATCTTATTACAGAGACAGCCCACACAGCACTGCCTGAATTACAGAGATGACAGTCCACAACCAGCGACTGCCTGATTACAGAGATGACAGTCCACACCAGCTACTGCCCTGAATTACAGAG HG:+:768131204:-1 HG:+:1348236226:-1 HG:+:1471451042:-1 HG:+:1792257801:-1 HG:+:1952752123:-1 HG:+:2279557220:-1 HG:+:2281488098:-1 HG:+:2704933673:-1 +ATTACAGAGACAGCCCACACCAGCACTGCCTGAATTACAGAGATGACAGGTCCACACCCAGCACTGCCTTGGAATTACAGAGATGACAGTCCACACCAGACATCATCATAATCACAGAGATATTCTACACCAGCATCATCTTAATTACAGAGACAGCCCACACCAGCGCTGCCTGAATTACAGAGATGACAGTCCACAGCAGCAACTGCCTGAATTACAGAGATTGATAGTCCACACCAGCATCATCATAATCACAGACGATATTCTACACCAGCCATCATCTTATTACAGAGACAGCCCACACAGCACTGCCTGAATTACAGAGATGACAGTCCACAACCAGCGACTGCCTGATTACAGAGATGACAGTCCACACCAGCTACTGCCCTGAATTACAGAG HG:+:368688112:-1 HG:+:636332694:-1 HG:+:644940765:-1 HG:+:862442820:-1 HG:+:1451278554:-1 HG:+:1476932335:-1 HG:+:1567815825:-1 HG:+:1763718025:-1 HG:+:1801095535:-1 HG:+:1908853125:-1 HG:+:2002307559:-1 HG:+:2266857051:-1 HG:+:2700981693:-1 HG:+:3014449706:-1 +CTCTGTAATTCAGGGCAGTAGCTGGTGTGGACTGTCATCTCTGTAATCAGGCAGTCGCTGGTTGTGGACTGTCATCTCTGTAATTCAGGCAGTGCTGTGTGGGCTGTCTCTGTAATAAGATGATGGCTGGTGTAGAATATCGTCTGTGATTATGATGATGCTGGTGTGGACTATCAATCTCTGTAATTCAGGCAGTTGCTGCTGTGGACTGTCATCTCTGTAATTCAGGCAGCGCTGGTGTGGGCTGTCTCTGTAATTAAGATGATGCTGGTGTAGAATATCTCTGTGATTATGATGATGTCTGGTGTGGACTGTCATCTCTGTAATTCCAAGGCAGTGCTGGGTGTGGACCTGTCATCTCTGTAATTCAGGCAGTGCTGGTGTGGGCTGTCTCTGTAAT HG:+:1523959932:-1 HG:+:2157577166:-1 HG:+:2498163979:-1 HG:+:2498164015:-1 HG:+:2498164051:-1 HG:+:2498164087:-1 HG:+:2498164189:74 HG:+:2498164291:60 HG:+:2498164393:60 HG:+:2498164429:62 HG:+:2498164465:62 HG:+:2498164603:55 HG:+:2498164705:16 HG:+:2498164741:16 HG:+:2498164843:28 HG:+:2498164915:35 HG:+:2498165017:51 HG:+:2498165119:57 HG:+:2498165221:65 +CTCTGTAATTCAGGGCAGTAGCTGGTGTGGACTGTCATCTCTGTAATCAGGCAGTCGCTGGTTGTGGACTGTCATCTCTGTAATTCAGGCAGTGCTGTGTGGGCTGTCTCTGTAATAAGATGATGGCTGGTGTAGAATATCGTCTGTGATTATGATGATGCTGGTGTGGACTATCAATCTCTGTAATTCAGGCAGTTGCTGCTGTGGACTGTCATCTCTGTAATTCAGGCAGCGCTGGTGTGGGCTGTCTCTGTAATTAAGATGATGCTGGTGTAGAATATCTCTGTGATTATGATGATGTCTGGTGTGGACTGTCATCTCTGTAATTCCAAGGCAGTGCTGGGTGTGGACCTGTCATCTCTGTAATTCAGGCAGTGCTGGTGTGGGCTGTCTCTGTAAT HG:+:2498164746:16 +CTCTGTAATTCAGGGCAGTAGCTGGTGTGGACTGTCATCTCTGTAATCAGGCAGTCGCTGGTTGTGGACTGTCATCTCTGTAATTCAGGCAGTGCTGTGTGGGCTGTCTCTGTAATAAGATGATGGCTGGTGTAGAATATCGTCTGTGATTATGATGATGCTGGTGTGGACTATCAATCTCTGTAATTCAGGCAGTTGCTGCTGTGGACTGTCATCTCTGTAATTCAGGCAGCGCTGGTGTGGGCTGTCTCTGTAATTAAGATGATGCTGGTGTAGAATATCTCTGTGATTATGATGATGTCTGGTGTGGACTGTCATCTCTGTAATTCCAAGGCAGTGCTGGGTGTGGACCTGTCATCTCTGTAATTCAGGCAGTGCTGGTGTGGGCTGTCTCTGTAAT HG:+:30997685:-1 +CTCTGTAATTCAGGGCAGTAGCTGGTGTGGACTGTCATCTCTGTAATCAGGCAGTCGCTGGTTGTGGACTGTCATCTCTGTAATTCAGGCAGTGCTGTGTGGGCTGTCTCTGTAATAAGATGATGGCTGGTGTAGAATATCGTCTGTGATTATGATGATGCTGGTGTGGACTATCAATCTCTGTAATTCAGGCAGTTGCTGCTGTGGACTGTCATCTCTGTAATTCAGGCAGCGCTGGTGTGGGCTGTCTCTGTAATTAAGATGATGCTGGTGTAGAATATCTCTGTGATTATGATGATGTCTGGTGTGGACTGTCATCTCTGTAATTCCAAGGCAGTGCTGGGTGTGGACCTGTCATCTCTGTAATTCAGGCAGTGCTGGTGTGGGCTGTCTCTGTAAT HG:+:332522607:-1 HG:+:333900832:-1 HG:+:1398668698:-1 HG:+:1993627490:-1 HG:+:2029462136:-1 HG:+:2498163772:-1 HG:+:2611770860:-1 HG:+:3052374041:-1 +ATCTACTGTTCATCCAAAACTCAAGGAGCTAGATGTGACTATTTTCCCTGGCATAAACATATTTAACTCTGGGAAGATTTGAGTTATGCATAGAAAGTTTAGTTTTATATTTAACTTGGTATTTATGTTATTTATAAATTTTAAAGTACAATAGGCTTATCAGAGCATATAGTTCGATTTAAAATGTAAATACGAATAACTGGAGTTCAAATTATGATCTTAAAGTAAAAATCTAAGTTTATAAACAATTTTGAAAACACCTAAGATAACTTCCACTCAACATATTCCTGACTTTGATATTAGCTTGTGAGAGTTAACTTCAGGTCTAGGAAAATTTGGGTGAACTCAGATAACTAATTTAGGAAGAAAATTAAAATGATAGATGTTATTAAATGTAATT HG:+:116572049:-1 HG:+:394377172:-1 HG:+:1562860119:-1 HG:+:1919288581:22 HG:+:2813464542:-1 +ATCTACTGTTCATCCAAAACTCAAGGAGCTAGATGTGACTATTTTCCCTGGCATAAACATATTTAACTCTGGGAAGATTTGAGTTATGCATAGAAAGTTTAGTTTTATATTTAACTTGGTATTTATGTTATTTATAAATTTTAAAGTACAATAGGCTTATCAGAGCATATAGTTCGATTTAAAATGTAAATACGAATAACTGGAGTTCAAATTATGATCTTAAAGTAAAAATCTAAGTTTATAAACAATTTTGAAAACACCTAAGATAACTTCCACTCAACATATTCCTGACTTTGATATTAGCTTGTGAGAGTTAACTTCAGGTCTAGGAAAATTTGGGTGAACTCAGATAACTAATTTAGGAAGAAAATTAAAATGATAGATGTTATTAAATGTAATT HG:+:1919288580:22 +ATCTACTGTTCATCCAAAACTCAAGGAGCTAGATGTGACTATTTTCCCTGGCATAAACATATTTAACTCTGGGAAGATTTGAGTTATGCATAGAAAGTTTAGTTTTATATTTAACTTGGTATTTATGTTATTTATAAATTTTAAAGTACAATAGGCTTATCAGAGCATATAGTTCGATTTAAAATGTAAATACGAATAACTGGAGTTCAAATTATGATCTTAAAGTAAAAATCTAAGTTTATAAACAATTTTGAAAACACCTAAGATAACTTCCACTCAACATATTCCTGACTTTGATATTAGCTTGTGAGAGTTAACTTCAGGTCTAGGAAAATTTGGGTGAACTCAGATAACTAATTTAGGAAGAAAATTAAAATGATAGATGTTATTAAATGTAATT HG:+:927080685:-1 +ATCTACTGTTCATCCAAAACTCAAGGAGCTAGATGTGACTATTTTCCCTGGCATAAACATATTTAACTCTGGGAAGATTTGAGTTATGCATAGAAAGTTTAGTTTTATATTTAACTTGGTATTTATGTTATTTATAAATTTTAAAGTACAATAGGCTTATCAGAGCATATAGTTCGATTTAAAATGTAAATACGAATAACTGGAGTTCAAATTATGATCTTAAAGTAAAAATCTAAGTTTATAAACAATTTTGAAAACACCTAAGATAACTTCCACTCAACATATTCCTGACTTTGATATTAGCTTGTGAGAGTTAACTTCAGGTCTAGGAAAATTTGGGTGAACTCAGATAACTAATTTAGGAAGAAAATTAAAATGATAGATGTTATTAAATGTAATT HG:+:1974470074:-1 +AATTACATTTAATAACATCTATCATTTTAATTTTCTTCCTAAATTAGTTATCTGAGTTCACCCAAATTTTCCTAGACCTGAAGTTAACTCTCACAAGCTAATATCAAAGTCAGGAATATGTTGAGTGGAAGTTATCTTAGGTGTTTTCAAAATTGTTTATAAACTTAGATTTTTACTTTAAGATCATAATTTGAACTCCAGTTATTCGTATTTACATTTTAAATCGAACTATATGCTCTGATAAGCCTATTGTACTTTAAAATTTATAAATAACATAAATACCAAGTTAAATATAAAACTAAACTTTCTATGCATAACTCAAATCTTCCCAGAGTTAAATATGTTTATGCCAGGGAAAATAGTCACATCTAGCTCCTTGAGTTTTGGATGAACAGTAGAT HG:+:514885374:-1 +ATCTCCGCCCTCAATGCAACTCCCTTTACCTCATAACAGTGCTTTCGTATTGTTTTCTTACTGAGAAAGTTACCTGTGTGTTTTAATGTTTTTAGAGAATCACAGATTGGAATCTGCCGTATTCAGAACCATCTAATTCTGAAAAGTTTTTACGTGGTTAAGTACAGCGTTTTATGTACAAATCCTATTTTATGAAACTGGTATATACTACATAATATATAGGAATACAAATATGAAGAGTTGCGTTCTAATCTAAGATATCAATATATTTTGTGCAAATAGGCAAGGATTGATTAATAAATATGTGTACCTCTGTGTTCAGTAAGCCTTTATTACAAACTGTGCATGTGATGTAAGACTTCAAAAATATAGGAGTTAGTATTATAGCCAATTTCCAGTT HG:+:1167117849:-1 HG:+:1369050256:-1 HG:+:1456222361:-1 HG:+:2331625361:-1 HG:+:2331895845:-1 HG:+:2331950791:-1 HG:+:2332000688:-1 HG:+:2778374465:-1 +ATCTCCGCCCTCAATGCAACTCCCTTTACCTCATAACAGTGCTTTCGTATTGTTTTCTTACTGAGAAAGTTACCTGTGTGTTTTAATGTTTTTAGAGAATCACAGATTGGAATCTGCCGTATTCAGAACCATCTAATTCTGAAAAGTTTTTACGTGGTTAAGTACAGCGTTTTATGTACAAATCCTATTTTATGAAACTGGTATATACTACATAATATATAGGAATACAAATATGAAGAGTTGCGTTCTAATCTAAGATATCAATATATTTTGTGCAAATAGGCAAGGATTGATTAATAAATATGTGTACCTCTGTGTTCAGTAAGCCTTTATTACAAACTGTGCATGTGATGTAAGACTTCAAAAATATAGGAGTTAGTATTATAGCCAATTTCCAGTT HG:+:1130969066:-1 HG:+:1212367870:-1 HG:+:1360772689:-1 HG:+:1528008993:-1 HG:+:2954484055:-1 +ATCTCCGCCCTCAATGCAACTCCCTTTACCTCATAACAGTGCTTTCGTATTGTTTTCTTACTGAGAAAGTTACCTGTGTGTTTTAATGTTTTTAGAGAATCACAGATTGGAATCTGCCGTATTCAGAACCATCTAATTCTGAAAAGTTTTTACGTGGTTAAGTACAGCGTTTTATGTACAAATCCTATTTTATGAAACTGGTATATACTACATAATATATAGGAATACAAATATGAAGAGTTGCGTTCTAATCTAAGATATCAATATATTTTGTGCAAATAGGCAAGGATTGATTAATAAATATGTGTACCTCTGTGTTCAGTAAGCCTTTATTACAAACTGTGCATGTGATGTAAGACTTCAAAAATATAGGAGTTAGTATTATAGCCAATTTCCAGTT HG:+:12810143:-1 HG:+:373041940:-1 HG:+:426822537:-1 HG:+:959069365:-1 HG:+:1152765918:-1 HG:+:1170357269:-1 HG:+:1274589258:-1 HG:+:1283722314:-1 HG:+:1359186650:-1 HG:+:2191068079:-1 HG:+:2459992328:-1 +ATCTCCGCCCTCAATGCAACTCCCTTTACCTCATAACAGTGCTTTCGTATTGTTTTCTTACTGAGAAAGTTACCTGTGTGTTTTAATGTTTTTAGAGAATCACAGATTGGAATCTGCCGTATTCAGAACCATCTAATTCTGAAAAGTTTTTACGTGGTTAAGTACAGCGTTTTATGTACAAATCCTATTTTATGAAACTGGTATATACTACATAATATATAGGAATACAAATATGAAGAGTTGCGTTCTAATCTAAGATATCAATATATTTTGTGCAAATAGGCAAGGATTGATTAATAAATATGTGTACCTCTGTGTTCAGTAAGCCTTTATTACAAACTGTGCATGTGATGTAAGACTTCAAAAATATAGGAGTTAGTATTATAGCCAATTTCCAGTT HG:+:22411864:-1 HG:+:383239122:-1 HG:+:549291107:-1 HG:+:611529341:-1 HG:+:666079291:-1 HG:+:822024238:-1 HG:+:890995660:-1 HG:+:1046354308:-1 HG:+:1152067378:-1 HG:+:1320403151:-1 HG:+:1820974836:-1 HG:+:1827196098:-1 HG:+:2249173269:-1 HG:+:2298092933:-1 HG:+:3029384588:-1 +ATCTCCGCCCTCAATGCAACTCCCTTTACCTCATAACAGTGCTTTCGTATTGTTTTCTTACTGAGAAAGTTACCTGTGTGTTTTAATGTTTTTAGAGAATCACAGATTGGAATCTGCCGTATTCAGAACCATCTAATTCTGAAAAGTTTTTACGTGGTTAAGTACAGCGTTTTATGTACAAATCCTATTTTATGAAACTGGTATATACTACATAATATATAGGAATACAAATATGAAGAGTTGCGTTCTAATCTAAGATATCAATATATTTTGTGCAAATAGGCAAGGATTGATTAATAAATATGTGTACCTCTGTGTTCAGTAAGCCTTTATTACAAACTGTGCATGTGATGTAAGACTTCAAAAATATAGGAGTTAGTATTATAGCCAATTTCCAGTT HG:+:1358967459:-1 HG:+:1996950765:-1 HG:+:2006004350:-1 +ATCTCCGCCCTCAATGCAACTCCCTTTACCTCATAACAGTGCTTTCGTATTGTTTTCTTACTGAGAAAGTTACCTGTGTGTTTTAATGTTTTTAGAGAATCACAGATTGGAATCTGCCGTATTCAGAACCATCTAATTCTGAAAAGTTTTTACGTGGTTAAGTACAGCGTTTTATGTACAAATCCTATTTTATGAAACTGGTATATACTACATAATATATAGGAATACAAATATGAAGAGTTGCGTTCTAATCTAAGATATCAATATATTTTGTGCAAATAGGCAAGGATTGATTAATAAATATGTGTACCTCTGTGTTCAGTAAGCCTTTATTACAAACTGTGCATGTGATGTAAGACTTCAAAAATATAGGAGTTAGTATTATAGCCAATTTCCAGTT HG:+:349915678:-1 HG:+:371411821:-1 HG:+:456575899:-1 HG:+:511959407:-1 HG:+:1042684022:-1 HG:+:1232739748:-1 HG:+:1897436785:-1 HG:+:1952329957:-1 HG:+:2473345402:-1 HG:+:2519887452:-1 HG:+:3054544839:-1 +ATCTCCGCCCTCAATGCAACTCCCTTTACCTCATAACAGTGCTTTCGTATTGTTTTCTTACTGAGAAAGTTACCTGTGTGTTTTAATGTTTTTAGAGAATCACAGATTGGAATCTGCCGTATTCAGAACCATCTAATTCTGAAAAGTTTTTACGTGGTTAAGTACAGCGTTTTATGTACAAATCCTATTTTATGAAACTGGTATATACTACATAATATATAGGAATACAAATATGAAGAGTTGCGTTCTAATCTAAGATATCAATATATTTTGTGCAAATAGGCAAGGATTGATTAATAAATATGTGTACCTCTGTGTTCAGTAAGCCTTTATTACAAACTGTGCATGTGATGTAAGACTTCAAAAATATAGGAGTTAGTATTATAGCCAATTTCCAGTT HG:+:146676226:-1 HG:+:263438482:-1 HG:+:423122004:-1 HG:+:562379107:-1 HG:+:1078004971:-1 HG:+:1343067488:-1 HG:+:1387380277:-1 HG:+:1511846880:-1 HG:+:1606426413:-1 HG:+:1608788334:-1 HG:+:1973163500:-1 HG:+:2345893628:-1 +ATCTCCGCCCTCAATGCAACTCCCTTTACCTCATAACAGTGCTTTCGTATTGTTTTCTTACTGAGAAAGTTACCTGTGTGTTTTAATGTTTTTAGAGAATCACAGATTGGAATCTGCCGTATTCAGAACCATCTAATTCTGAAAAGTTTTTACGTGGTTAAGTACAGCGTTTTATGTACAAATCCTATTTTATGAAACTGGTATATACTACATAATATATAGGAATACAAATATGAAGAGTTGCGTTCTAATCTAAGATATCAATATATTTTGTGCAAATAGGCAAGGATTGATTAATAAATATGTGTACCTCTGTGTTCAGTAAGCCTTTATTACAAACTGTGCATGTGATGTAAGACTTCAAAAATATAGGAGTTAGTATTATAGCCAATTTCCAGTT HG:+:1454999345:-1 HG:+:2238078560:-1 HG:+:2295820172:-1 +ATCTCCGCCCTCAATGCAACTCCCTTTACCTCATAACAGTGCTTTCGTATTGTTTTCTTACTGAGAAAGTTACCTGTGTGTTTTAATGTTTTTAGAGAATCACAGATTGGAATCTGCCGTATTCAGAACCATCTAATTCTGAAAAGTTTTTACGTGGTTAAGTACAGCGTTTTATGTACAAATCCTATTTTATGAAACTGGTATATACTACATAATATATAGGAATACAAATATGAAGAGTTGCGTTCTAATCTAAGATATCAATATATTTTGTGCAAATAGGCAAGGATTGATTAATAAATATGTGTACCTCTGTGTTCAGTAAGCCTTTATTACAAACTGTGCATGTGATGTAAGACTTCAAAAATATAGGAGTTAGTATTATAGCCAATTTCCAGTT HG:+:475598656:-1 HG:+:1314029994:-1 HG:+:1350961354:-1 HG:+:1610450854:-1 HG:+:2650500897:-1 HG:+:2812337277:-1 +AACTGGAAATTGGCTATAATACTAACTCCTATATTTTTGAAGTCTTACATCACATGCACAGTTTGTAATAAAGGCTTACTGAACACAGAGGTACACATATTTATTAATCAATCCTTGCCTATTTGCACAAAATATATTGATATCTTAGATTAGAACGCAACTCTTCATATTTGTATTCCTATATATTATGTAGTATATACCAGTTTCATAAAATAGGATTTGTACATAAAACGCTGTACTTAACCACGTAAAAACTTTTCAGAATTAGATGGTTCTGAATACGGCAGATTCCAATCTGTGATTCTCTAAAAACATTAAAACACACAGGTAACTTTCTCAGTAAGAAAACAATACGAAAGCACTGTTATGAGGTAAAGGGAGTTGCATTGAGGGCGGAGAT HG:+:536065979:16 +AACTGGAAATTGGCTATAATACTAACTCCTATATTTTTGAAGTCTTACATCACATGCACAGTTTGTAATAAAGGCTTACTGAACACAGAGGTACACATATTTATTAATCAATCCTTGCCTATTTGCACAAAATATATTGATATCTTAGATTAGAACGCAACTCTTCATATTTGTATTCCTATATATTATGTAGTATATACCAGTTTCATAAAATAGGATTTGTACATAAAACGCTGTACTTAACCACGTAAAAACTTTTCAGAATTAGATGGTTCTGAATACGGCAGATTCCAATCTGTGATTCTCTAAAAACATTAAAACACACAGGTAACTTTCTCAGTAAGAAAACAATACGAAAGCACTGTTATGAGGTAAAGGGAGTTGCATTGAGGGCGGAGAT HG:+:536065975:16 +AACTGGAAATTGGCTATAATACTAACTCCTATATTTTTGAAGTCTTACATCACATGCACAGTTTGTAATAAAGGCTTACTGAACACAGAGGTACACATATTTATTAATCAATCCTTGCCTATTTGCACAAAATATATTGATATCTTAGATTAGAACGCAACTCTTCATATTTGTATTCCTATATATTATGTAGTATATACCAGTTTCATAAAATAGGATTTGTACATAAAACGCTGTACTTAACCACGTAAAAACTTTTCAGAATTAGATGGTTCTGAATACGGCAGATTCCAATCTGTGATTCTCTAAAAACATTAAAACACACAGGTAACTTTCTCAGTAAGAAAACAATACGAAAGCACTGTTATGAGGTAAAGGGAGTTGCATTGAGGGCGGAGAT HG:+:1273621287:-1 +AACTGGAAATTGGCTATAATACTAACTCCTATATTTTTGAAGTCTTACATCACATGCACAGTTTGTAATAAAGGCTTACTGAACACAGAGGTACACATATTTATTAATCAATCCTTGCCTATTTGCACAAAATATATTGATATCTTAGATTAGAACGCAACTCTTCATATTTGTATTCCTATATATTATGTAGTATATACCAGTTTCATAAAATAGGATTTGTACATAAAACGCTGTACTTAACCACGTAAAAACTTTTCAGAATTAGATGGTTCTGAATACGGCAGATTCCAATCTGTGATTCTCTAAAAACATTAAAACACACAGGTAACTTTCTCAGTAAGAAAACAATACGAAAGCACTGTTATGAGGTAAAGGGAGTTGCATTGAGGGCGGAGAT HG:+:536065965:16 +AACTGGAAATTGGCTATAATACTAACTCCTATATTTTTGAAGTCTTACATCACATGCACAGTTTGTAATAAAGGCTTACTGAACACAGAGGTACACATATTTATTAATCAATCCTTGCCTATTTGCACAAAATATATTGATATCTTAGATTAGAACGCAACTCTTCATATTTGTATTCCTATATATTATGTAGTATATACCAGTTTCATAAAATAGGATTTGTACATAAAACGCTGTACTTAACCACGTAAAAACTTTTCAGAATTAGATGGTTCTGAATACGGCAGATTCCAATCTGTGATTCTCTAAAAACATTAAAACACACAGGTAACTTTCTCAGTAAGAAAACAATACGAAAGCACTGTTATGAGGTAAAGGGAGTTGCATTGAGGGCGGAGAT HG:+:536065966:16 +AACTGGAAATTGGCTATAATACTAACTCCTATATTTTTGAAGTCTTACATCACATGCACAGTTTGTAATAAAGGCTTACTGAACACAGAGGTACACATATTTATTAATCAATCCTTGCCTATTTGCACAAAATATATTGATATCTTAGATTAGAACGCAACTCTTCATATTTGTATTCCTATATATTATGTAGTATATACCAGTTTCATAAAATAGGATTTGTACATAAAACGCTGTACTTAACCACGTAAAAACTTTTCAGAATTAGATGGTTCTGAATACGGCAGATTCCAATCTGTGATTCTCTAAAAACATTAAAACACACAGGTAACTTTCTCAGTAAGAAAACAATACGAAAGCACTGTTATGAGGTAAAGGGAGTTGCATTGAGGGCGGAGAT HG:+:536065974:16 +AACTGGAAATTGGCTATAATACTAACTCCTATATTTTTGAAGTCTTACATCACATGCACAGTTTGTAATAAAGGCTTACTGAACACAGAGGTACACATATTTATTAATCAATCCTTGCCTATTTGCACAAAATATATTGATATCTTAGATTAGAACGCAACTCTTCATATTTGTATTCCTATATATTATGTAGTATATACCAGTTTCATAAAATAGGATTTGTACATAAAACGCTGTACTTAACCACGTAAAAACTTTTCAGAATTAGATGGTTCTGAATACGGCAGATTCCAATCTGTGATTCTCTAAAAACATTAAAACACACAGGTAACTTTCTCAGTAAGAAAACAATACGAAAGCACTGTTATGAGGTAAAGGGAGTTGCATTGAGGGCGGAGAT HG:+:536065964:16 +AACTGGAAATTGGCTATAATACTAACTCCTATATTTTTGAAGTCTTACATCACATGCACAGTTTGTAATAAAGGCTTACTGAACACAGAGGTACACATATTTATTAATCAATCCTTGCCTATTTGCACAAAATATATTGATATCTTAGATTAGAACGCAACTCTTCATATTTGTATTCCTATATATTATGTAGTATATACCAGTTTCATAAAATAGGATTTGTACATAAAACGCTGTACTTAACCACGTAAAAACTTTTCAGAATTAGATGGTTCTGAATACGGCAGATTCCAATCTGTGATTCTCTAAAAACATTAAAACACACAGGTAACTTTCTCAGTAAGAAAACAATACGAAAGCACTGTTATGAGGTAAAGGGAGTTGCATTGAGGGCGGAGAT HG:+:536065968:16 +GTAAGCTCATCTGGATAATCCAGGATACTTTCCCTATTTTAAAATCAGCTGATTAGCAATTGTAATTCCACCTTACAACCTCAAATTCTCCTTTCGTCACGCAACCTCAACATCTTCACAGGTTCTGGGGGATTAGGGATGTAAGCAAGCTTTGTTGGGGGCATTATCCTCCTCTGCCACAAGCTGTATGTTTAAAATTTGCATCTCTATTCAATCCCCTTTTCTGATATCTAGTTTACTGGGATGTATTTTTCACAGATACTGCTGTGGTGGTTTAGTGTATTTGTAACTATAAAGTGATGAATTAAAGTCCCTTGAGTACAAAGTCGACTATACAAGAGCAAAAGAATTTTATTCTTCATGGAAAAAAGCATCACTTACAGCTCCTGCTCTTACTTTC HG:+:508319214:-1 HG:+:578751319:-1 HG:+:1554231517:-1 HG:+:1966329877:-1 HG:+:2992681385:-1 +GTAAGCTCATCTGGATAATCCAGGATACTTTCCCTATTTTAAAATCAGCTGATTAGCAATTGTAATTCCACCTTACAACCTCAAATTCTCCTTTCGTCACGCAACCTCAACATCTTCACAGGTTCTGGGGGATTAGGGATGTAAGCAAGCTTTGTTGGGGGCATTATCCTCCTCTGCCACAAGCTGTATGTTTAAAATTTGCATCTCTATTCAATCCCCTTTTCTGATATCTAGTTTACTGGGATGTATTTTTCACAGATACTGCTGTGGTGGTTTAGTGTATTTGTAACTATAAAGTGATGAATTAAAGTCCCTTGAGTACAAAGTCGACTATACAAGAGCAAAAGAATTTTATTCTTCATGGAAAAAAGCATCACTTACAGCTCCTGCTCTTACTTTC HG:+:453708571:-1 HG:+:644515675:-1 HG:+:1346073482:-1 HG:+:1445180252:-1 HG:+:2393559803:-1 HG:+:2473513325:-1 HG:+:2617697272:-1 +GTAAGCTCATCTGGATAATCCAGGATACTTTCCCTATTTTAAAATCAGCTGATTAGCAATTGTAATTCCACCTTACAACCTCAAATTCTCCTTTCGTCACGCAACCTCAACATCTTCACAGGTTCTGGGGGATTAGGGATGTAAGCAAGCTTTGTTGGGGGCATTATCCTCCTCTGCCACAAGCTGTATGTTTAAAATTTGCATCTCTATTCAATCCCCTTTTCTGATATCTAGTTTACTGGGATGTATTTTTCACAGATACTGCTGTGGTGGTTTAGTGTATTTGTAACTATAAAGTGATGAATTAAAGTCCCTTGAGTACAAAGTCGACTATACAAGAGCAAAAGAATTTTATTCTTCATGGAAAAAAGCATCACTTACAGCTCCTGCTCTTACTTTC HG:+:556791062:-1 HG:+:828350481:-1 HG:+:959523843:-1 HG:+:1311971819:-1 HG:+:1687359670:-1 HG:+:2752465708:-1 HG:+:2878224470:-1 HG:+:2955032252:-1 +GTAAGCTCATCTGGATAATCCAGGATACTTTCCCTATTTTAAAATCAGCTGATTAGCAATTGTAATTCCACCTTACAACCTCAAATTCTCCTTTCGTCACGCAACCTCAACATCTTCACAGGTTCTGGGGGATTAGGGATGTAAGCAAGCTTTGTTGGGGGCATTATCCTCCTCTGCCACAAGCTGTATGTTTAAAATTTGCATCTCTATTCAATCCCCTTTTCTGATATCTAGTTTACTGGGATGTATTTTTCACAGATACTGCTGTGGTGGTTTAGTGTATTTGTAACTATAAAGTGATGAATTAAAGTCCCTTGAGTACAAAGTCGACTATACAAGAGCAAAAGAATTTTATTCTTCATGGAAAAAAGCATCACTTACAGCTCCTGCTCTTACTTTC HG:+:179755793:-1 HG:+:261402301:-1 HG:+:562521404:-1 HG:+:728264229:-1 HG:+:1166996884:-1 HG:+:2192007269:-1 +GTAAGCTCATCTGGATAATCCAGGATACTTTCCCTATTTTAAAATCAGCTGATTAGCAATTGTAATTCCACCTTACAACCTCAAATTCTCCTTTCGTCACGCAACCTCAACATCTTCACAGGTTCTGGGGGATTAGGGATGTAAGCAAGCTTTGTTGGGGGCATTATCCTCCTCTGCCACAAGCTGTATGTTTAAAATTTGCATCTCTATTCAATCCCCTTTTCTGATATCTAGTTTACTGGGATGTATTTTTCACAGATACTGCTGTGGTGGTTTAGTGTATTTGTAACTATAAAGTGATGAATTAAAGTCCCTTGAGTACAAAGTCGACTATACAAGAGCAAAAGAATTTTATTCTTCATGGAAAAAAGCATCACTTACAGCTCCTGCTCTTACTTTC HG:+:291360071:-1 HG:+:352202211:-1 HG:+:704892775:-1 HG:+:823507790:-1 HG:+:1011575743:-1 HG:+:1159301296:-1 HG:+:1187306486:-1 HG:+:1247341986:-1 HG:+:1330666391:-1 HG:+:1374167199:-1 HG:+:1380019779:-1 HG:+:1509911243:-1 HG:+:1770123194:-1 HG:+:1872713883:-1 HG:+:2281192609:-1 HG:+:2611973664:-1 +GTAAGCTCATCTGGATAATCCAGGATACTTTCCCTATTTTAAAATCAGCTGATTAGCAATTGTAATTCCACCTTACAACCTCAAATTCTCCTTTCGTCACGCAACCTCAACATCTTCACAGGTTCTGGGGGATTAGGGATGTAAGCAAGCTTTGTTGGGGGCATTATCCTCCTCTGCCACAAGCTGTATGTTTAAAATTTGCATCTCTATTCAATCCCCTTTTCTGATATCTAGTTTACTGGGATGTATTTTTCACAGATACTGCTGTGGTGGTTTAGTGTATTTGTAACTATAAAGTGATGAATTAAAGTCCCTTGAGTACAAAGTCGACTATACAAGAGCAAAAGAATTTTATTCTTCATGGAAAAAAGCATCACTTACAGCTCCTGCTCTTACTTTC HG:+:177347771:-1 HG:+:1335158576:-1 HG:+:1763695904:-1 HG:+:2552781209:-1 +GTAAGCTCATCTGGATAATCCAGGATACTTTCCCTATTTTAAAATCAGCTGATTAGCAATTGTAATTCCACCTTACAACCTCAAATTCTCCTTTCGTCACGCAACCTCAACATCTTCACAGGTTCTGGGGGATTAGGGATGTAAGCAAGCTTTGTTGGGGGCATTATCCTCCTCTGCCACAAGCTGTATGTTTAAAATTTGCATCTCTATTCAATCCCCTTTTCTGATATCTAGTTTACTGGGATGTATTTTTCACAGATACTGCTGTGGTGGTTTAGTGTATTTGTAACTATAAAGTGATGAATTAAAGTCCCTTGAGTACAAAGTCGACTATACAAGAGCAAAAGAATTTTATTCTTCATGGAAAAAAGCATCACTTACAGCTCCTGCTCTTACTTTC HG:+:279017104:-1 HG:+:379005550:-1 HG:+:454943359:-1 HG:+:603645771:-1 HG:+:710403677:-1 HG:+:786058866:-1 HG:+:1052459939:-1 HG:+:1471510291:-1 HG:+:1806929874:-1 HG:+:1874437487:-1 HG:+:1968921212:-1 HG:+:2052220532:-1 HG:+:2236691727:-1 HG:+:2987786861:-1 +GTAAGCTCATCTGGATAATCCAGGATACTTTCCCTATTTTAAAATCAGCTGATTAGCAATTGTAATTCCACCTTACAACCTCAAATTCTCCTTTCGTCACGCAACCTCAACATCTTCACAGGTTCTGGGGGATTAGGGATGTAAGCAAGCTTTGTTGGGGGCATTATCCTCCTCTGCCACAAGCTGTATGTTTAAAATTTGCATCTCTATTCAATCCCCTTTTCTGATATCTAGTTTACTGGGATGTATTTTTCACAGATACTGCTGTGGTGGTTTAGTGTATTTGTAACTATAAAGTGATGAATTAAAGTCCCTTGAGTACAAAGTCGACTATACAAGAGCAAAAGAATTTTATTCTTCATGGAAAAAAGCATCACTTACAGCTCCTGCTCTTACTTTC HG:+:55598388:-1 HG:+:117746231:-1 HG:+:294148244:-1 HG:+:405825042:-1 HG:+:638138209:-1 HG:+:703463616:-1 HG:+:1002011818:-1 HG:+:1017077272:-1 HG:+:1038960811:-1 HG:+:1082196723:-1 HG:+:1113558106:-1 HG:+:1127036609:-1 HG:+:1357076479:-1 HG:+:1625911563:-1 HG:+:1810925854:-1 HG:+:1833969299:-1 HG:+:1838391413:-1 HG:+:1972482281:-1 HG:+:1984675251:-1 HG:+:2002265456:-1 HG:+:2065844859:-1 HG:+:2394655296:-1 HG:+:2421139478:-1 +GTAAGCTCATCTGGATAATCCAGGATACTTTCCCTATTTTAAAATCAGCTGATTAGCAATTGTAATTCCACCTTACAACCTCAAATTCTCCTTTCGTCACGCAACCTCAACATCTTCACAGGTTCTGGGGGATTAGGGATGTAAGCAAGCTTTGTTGGGGGCATTATCCTCCTCTGCCACAAGCTGTATGTTTAAAATTTGCATCTCTATTCAATCCCCTTTTCTGATATCTAGTTTACTGGGATGTATTTTTCACAGATACTGCTGTGGTGGTTTAGTGTATTTGTAACTATAAAGTGATGAATTAAAGTCCCTTGAGTACAAAGTCGACTATACAAGAGCAAAAGAATTTTATTCTTCATGGAAAAAAGCATCACTTACAGCTCCTGCTCTTACTTTC HG:+:276171623:-1 HG:+:704833916:-1 HG:+:1998209869:-1 HG:+:2045041589:-1 HG:+:2587818656:-1 +GAAAGTAAGAGCAGGAGCTGTAAGTGATGCTTTTTTCCATGAAGAATAAAATTCTTTTGCTCTTGTATAGTCGACTTTGTACTCAAGGGACTTTAATTCATCACTTTATAGTTACAAATACACTAAACCACCACAGCAGTATCTGTGAAAAATACATCCCAGTAAACTAGATATCAGAAAAGGGGATTGAATAGAGATGCAAATTTTAAACATACAGCTTGTGGCAGAGGAGGATAATGCCCCCAACAAAGCTTGCTTACATCCCTAATCCCCCAGAACCTGTGAAGATGTTGAGGTTGCGTGACGAAAGGAGAATTTGAGGTTGTAAGGTGGAATTACAATTGCTAATCAGCTGATTTTAAAATAGGGAAAGTATCCTGGATTATCCAGATGAGCTTAC HG:+:593090827:17 +GAAAGTAAGAGCAGGAGCTGTAAGTGATGCTTTTTTCCATGAAGAATAAAATTCTTTTGCTCTTGTATAGTCGACTTTGTACTCAAGGGACTTTAATTCATCACTTTATAGTTACAAATACACTAAACCACCACAGCAGTATCTGTGAAAAATACATCCCAGTAAACTAGATATCAGAAAAGGGGATTGAATAGAGATGCAAATTTTAAACATACAGCTTGTGGCAGAGGAGGATAATGCCCCCAACAAAGCTTGCTTACATCCCTAATCCCCCAGAACCTGTGAAGATGTTGAGGTTGCGTGACGAAAGGAGAATTTGAGGTTGTAAGGTGGAATTACAATTGCTAATCAGCTGATTTTAAAATAGGGAAAGTATCCTGGATTATCCAGATGAGCTTAC HG:+:2189438984:-1 +GAAAGTAAGAGCAGGAGCTGTAAGTGATGCTTTTTTCCATGAAGAATAAAATTCTTTTGCTCTTGTATAGTCGACTTTGTACTCAAGGGACTTTAATTCATCACTTTATAGTTACAAATACACTAAACCACCACAGCAGTATCTGTGAAAAATACATCCCAGTAAACTAGATATCAGAAAAGGGGATTGAATAGAGATGCAAATTTTAAACATACAGCTTGTGGCAGAGGAGGATAATGCCCCCAACAAAGCTTGCTTACATCCCTAATCCCCCAGAACCTGTGAAGATGTTGAGGTTGCGTGACGAAAGGAGAATTTGAGGTTGTAAGGTGGAATTACAATTGCTAATCAGCTGATTTTAAAATAGGGAAAGTATCCTGGATTATCCAGATGAGCTTAC HG:+:593090816:17 +GAAAGTAAGAGCAGGAGCTGTAAGTGATGCTTTTTTCCATGAAGAATAAAATTCTTTTGCTCTTGTATAGTCGACTTTGTACTCAAGGGACTTTAATTCATCACTTTATAGTTACAAATACACTAAACCACCACAGCAGTATCTGTGAAAAATACATCCCAGTAAACTAGATATCAGAAAAGGGGATTGAATAGAGATGCAAATTTTAAACATACAGCTTGTGGCAGAGGAGGATAATGCCCCCAACAAAGCTTGCTTACATCCCTAATCCCCCAGAACCTGTGAAGATGTTGAGGTTGCGTGACGAAAGGAGAATTTGAGGTTGTAAGGTGGAATTACAATTGCTAATCAGCTGATTTTAAAATAGGGAAAGTATCCTGGATTATCCAGATGAGCTTAC HG:+:2592693662:-1 +GAAAGTAAGAGCAGGAGCTGTAAGTGATGCTTTTTTCCATGAAGAATAAAATTCTTTTGCTCTTGTATAGTCGACTTTGTACTCAAGGGACTTTAATTCATCACTTTATAGTTACAAATACACTAAACCACCACAGCAGTATCTGTGAAAAATACATCCCAGTAAACTAGATATCAGAAAAGGGGATTGAATAGAGATGCAAATTTTAAACATACAGCTTGTGGCAGAGGAGGATAATGCCCCCAACAAAGCTTGCTTACATCCCTAATCCCCCAGAACCTGTGAAGATGTTGAGGTTGCGTGACGAAAGGAGAATTTGAGGTTGTAAGGTGGAATTACAATTGCTAATCAGCTGATTTTAAAATAGGGAAAGTATCCTGGATTATCCAGATGAGCTTAC HG:+:593090823:17 +GAAAGTAAGAGCAGGAGCTGTAAGTGATGCTTTTTTCCATGAAGAATAAAATTCTTTTGCTCTTGTATAGTCGACTTTGTACTCAAGGGACTTTAATTCATCACTTTATAGTTACAAATACACTAAACCACCACAGCAGTATCTGTGAAAAATACATCCCAGTAAACTAGATATCAGAAAAGGGGATTGAATAGAGATGCAAATTTTAAACATACAGCTTGTGGCAGAGGAGGATAATGCCCCCAACAAAGCTTGCTTACATCCCTAATCCCCCAGAACCTGTGAAGATGTTGAGGTTGCGTGACGAAAGGAGAATTTGAGGTTGTAAGGTGGAATTACAATTGCTAATCAGCTGATTTTAAAATAGGGAAAGTATCCTGGATTATCCAGATGAGCTTAC HG:+:593090822:17 +CTCTAAATCTCGGGAGACATGGAGAACCATCAGCTTGTCTGTTATGCCTGAAGCCTAGGAGACAACAGAGAAGGAAAGTGGAAACTAGAACTTAAGGTGAAAGGCTGCCAGGAGGTTGATCAGGAGGGAAACTATAAGTCTGCTTAAGAGGAATGGAAAGATTATAAAAGTAGGGGAGCAAACATGATCAAACATGTAAACATTACAAAATGATTTGATCAAAAGATACCTCTGGAGAGAGAGAGAAACAGAAGTCAGAAAAGAAGTTAAGAAATGTGTGGAAATTCAAGTTCATCTTCCTCTCCAGACTCATCCCTTTCTAGTTCTCTTTATTACTGCACCAATGGGACTCCTTGCCCTGTCGGCTTCCACTTGGGTTGGGTCAGTGGAAGAAGTAGCA HG:+:238922378:-1 HG:+:1530972358:-1 HG:+:1879325952:-1 HG:+:1928483782:-1 HG:+:2122443089:-1 +CTCTAAATCTCGGGAGACATGGAGAACCATCAGCTTGTCTGTTATGCCTGAAGCCTAGGAGACAACAGAGAAGGAAAGTGGAAACTAGAACTTAAGGTGAAAGGCTGCCAGGAGGTTGATCAGGAGGGAAACTATAAGTCTGCTTAAGAGGAATGGAAAGATTATAAAAGTAGGGGAGCAAACATGATCAAACATGTAAACATTACAAAATGATTTGATCAAAAGATACCTCTGGAGAGAGAGAGAAACAGAAGTCAGAAAAGAAGTTAAGAAATGTGTGGAAATTCAAGTTCATCTTCCTCTCCAGACTCATCCCTTTCTAGTTCTCTTTATTACTGCACCAATGGGACTCCTTGCCCTGTCGGCTTCCACTTGGGTTGGGTCAGTGGAAGAAGTAGCA HG:+:1563220971:-1 HG:+:1756536864:-1 HG:+:2164675972:-1 HG:+:2462271330:-1 HG:+:2610007255:-1 HG:+:2731926653:-1 +CTCTAAATCTCGGGAGACATGGAGAACCATCAGCTTGTCTGTTATGCCTGAAGCCTAGGAGACAACAGAGAAGGAAAGTGGAAACTAGAACTTAAGGTGAAAGGCTGCCAGGAGGTTGATCAGGAGGGAAACTATAAGTCTGCTTAAGAGGAATGGAAAGATTATAAAAGTAGGGGAGCAAACATGATCAAACATGTAAACATTACAAAATGATTTGATCAAAAGATACCTCTGGAGAGAGAGAGAAACAGAAGTCAGAAAAGAAGTTAAGAAATGTGTGGAAATTCAAGTTCATCTTCCTCTCCAGACTCATCCCTTTCTAGTTCTCTTTATTACTGCACCAATGGGACTCCTTGCCCTGTCGGCTTCCACTTGGGTTGGGTCAGTGGAAGAAGTAGCA HG:+:321224834:-1 HG:+:710476646:-1 HG:+:1278519511:-1 HG:+:1785815513:-1 HG:+:1899286856:-1 HG:+:2250359778:-1 HG:+:2418103494:-1 HG:+:2485089354:-1 HG:+:2554092253:-1 HG:+:3016631369:-1 +CTCTAAATCTCGGGAGACATGGAGAACCATCAGCTTGTCTGTTATGCCTGAAGCCTAGGAGACAACAGAGAAGGAAAGTGGAAACTAGAACTTAAGGTGAAAGGCTGCCAGGAGGTTGATCAGGAGGGAAACTATAAGTCTGCTTAAGAGGAATGGAAAGATTATAAAAGTAGGGGAGCAAACATGATCAAACATGTAAACATTACAAAATGATTTGATCAAAAGATACCTCTGGAGAGAGAGAGAAACAGAAGTCAGAAAAGAAGTTAAGAAATGTGTGGAAATTCAAGTTCATCTTCCTCTCCAGACTCATCCCTTTCTAGTTCTCTTTATTACTGCACCAATGGGACTCCTTGCCCTGTCGGCTTCCACTTGGGTTGGGTCAGTGGAAGAAGTAGCA HG:+:173205286:-1 HG:+:638939455:-1 HG:+:775825701:-1 HG:+:837727548:-1 HG:+:907902074:-1 HG:+:934915246:-1 HG:+:958626903:-1 HG:+:1228215212:-1 HG:+:1356325006:-1 HG:+:1432492292:-1 HG:+:1458764126:-1 HG:+:1691483951:-1 HG:+:1777719040:-1 HG:+:1913313852:-1 HG:+:2146882581:-1 HG:+:2235038420:-1 HG:+:2249586376:-1 HG:+:2297734272:-1 HG:+:2721606635:-1 HG:+:2756172472:-1 +CTCTAAATCTCGGGAGACATGGAGAACCATCAGCTTGTCTGTTATGCCTGAAGCCTAGGAGACAACAGAGAAGGAAAGTGGAAACTAGAACTTAAGGTGAAAGGCTGCCAGGAGGTTGATCAGGAGGGAAACTATAAGTCTGCTTAAGAGGAATGGAAAGATTATAAAAGTAGGGGAGCAAACATGATCAAACATGTAAACATTACAAAATGATTTGATCAAAAGATACCTCTGGAGAGAGAGAGAAACAGAAGTCAGAAAAGAAGTTAAGAAATGTGTGGAAATTCAAGTTCATCTTCCTCTCCAGACTCATCCCTTTCTAGTTCTCTTTATTACTGCACCAATGGGACTCCTTGCCCTGTCGGCTTCCACTTGGGTTGGGTCAGTGGAAGAAGTAGCA HG:+:399572715:-1 HG:+:715352520:-1 HG:+:1128861158:-1 HG:+:1381587914:-1 HG:+:2996510765:-1 HG:+:3024050626:-1 +CTCTAAATCTCGGGAGACATGGAGAACCATCAGCTTGTCTGTTATGCCTGAAGCCTAGGAGACAACAGAGAAGGAAAGTGGAAACTAGAACTTAAGGTGAAAGGCTGCCAGGAGGTTGATCAGGAGGGAAACTATAAGTCTGCTTAAGAGGAATGGAAAGATTATAAAAGTAGGGGAGCAAACATGATCAAACATGTAAACATTACAAAATGATTTGATCAAAAGATACCTCTGGAGAGAGAGAGAAACAGAAGTCAGAAAAGAAGTTAAGAAATGTGTGGAAATTCAAGTTCATCTTCCTCTCCAGACTCATCCCTTTCTAGTTCTCTTTATTACTGCACCAATGGGACTCCTTGCCCTGTCGGCTTCCACTTGGGTTGGGTCAGTGGAAGAAGTAGCA HG:+:30090312:-1 HG:+:235361110:-1 HG:+:272420399:-1 HG:+:287830091:-1 HG:+:391702142:-1 HG:+:441821481:-1 HG:+:528555946:-1 HG:+:836705500:-1 HG:+:1223753292:-1 HG:+:1279611258:-1 HG:+:1337351369:-1 HG:+:1390289133:-1 HG:+:1833246936:-1 HG:+:2039407167:-1 HG:+:2111985851:-1 HG:+:2365126563:-1 HG:+:2637952879:-1 HG:+:2692846728:-1 +CTCTAAATCTCGGGAGACATGGAGAACCATCAGCTTGTCTGTTATGCCTGAAGCCTAGGAGACAACAGAGAAGGAAAGTGGAAACTAGAACTTAAGGTGAAAGGCTGCCAGGAGGTTGATCAGGAGGGAAACTATAAGTCTGCTTAAGAGGAATGGAAAGATTATAAAAGTAGGGGAGCAAACATGATCAAACATGTAAACATTACAAAATGATTTGATCAAAAGATACCTCTGGAGAGAGAGAGAAACAGAAGTCAGAAAAGAAGTTAAGAAATGTGTGGAAATTCAAGTTCATCTTCCTCTCCAGACTCATCCCTTTCTAGTTCTCTTTATTACTGCACCAATGGGACTCCTTGCCCTGTCGGCTTCCACTTGGGTTGGGTCAGTGGAAGAAGTAGCA HG:+:97051826:-1 HG:+:239029684:-1 HG:+:330359746:-1 HG:+:654688088:-1 HG:+:662443203:-1 HG:+:790922900:-1 HG:+:811350961:-1 HG:+:878648025:-1 HG:+:901866818:-1 HG:+:952003308:-1 HG:+:1485482354:-1 HG:+:1497828649:-1 HG:+:1700364898:-1 HG:+:1840067689:-1 HG:+:1898262186:-1 HG:+:1962467088:-1 HG:+:2394330405:-1 HG:+:2517801972:-1 HG:+:2560592604:-1 HG:+:2631187454:-1 HG:+:3022363517:-1 +CTCTAAATCTCGGGAGACATGGAGAACCATCAGCTTGTCTGTTATGCCTGAAGCCTAGGAGACAACAGAGAAGGAAAGTGGAAACTAGAACTTAAGGTGAAAGGCTGCCAGGAGGTTGATCAGGAGGGAAACTATAAGTCTGCTTAAGAGGAATGGAAAGATTATAAAAGTAGGGGAGCAAACATGATCAAACATGTAAACATTACAAAATGATTTGATCAAAAGATACCTCTGGAGAGAGAGAGAAACAGAAGTCAGAAAAGAAGTTAAGAAATGTGTGGAAATTCAAGTTCATCTTCCTCTCCAGACTCATCCCTTTCTAGTTCTCTTTATTACTGCACCAATGGGACTCCTTGCCCTGTCGGCTTCCACTTGGGTTGGGTCAGTGGAAGAAGTAGCA HG:+:1407983129:-1 HG:+:1823630902:-1 HG:+:2914827744:-1 +CTCTAAATCTCGGGAGACATGGAGAACCATCAGCTTGTCTGTTATGCCTGAAGCCTAGGAGACAACAGAGAAGGAAAGTGGAAACTAGAACTTAAGGTGAAAGGCTGCCAGGAGGTTGATCAGGAGGGAAACTATAAGTCTGCTTAAGAGGAATGGAAAGATTATAAAAGTAGGGGAGCAAACATGATCAAACATGTAAACATTACAAAATGATTTGATCAAAAGATACCTCTGGAGAGAGAGAGAAACAGAAGTCAGAAAAGAAGTTAAGAAATGTGTGGAAATTCAAGTTCATCTTCCTCTCCAGACTCATCCCTTTCTAGTTCTCTTTATTACTGCACCAATGGGACTCCTTGCCCTGTCGGCTTCCACTTGGGTTGGGTCAGTGGAAGAAGTAGCA HG:+:588901559:-1 HG:+:963173381:-1 HG:+:1532959245:-1 HG:+:2373806421:-1 HG:+:2433860293:-1 HG:+:2797542059:-1 HG:+:2928253891:-1 HG:+:2930055670:-1 +TGCTACTTCTTCCACTGACCCAACCCAAGTGGAAGCCGACAGGGCAAGGAGTCCCATTGGTGCAGTAATAAAGAGAACTAGAAAGGGATGAGTCTGGAGAGGAAGATGAACTTGAATTTCCACACATTTCTTAACTTCTTTTCTGACTTCTGTTTCTCTCTCTCTCCAGAGGTATCTTTTGATCAAATCATTTTGTAATGTTTACATGTTTGATCATGTTTGCTCCCCTACTTTTATAATCTTTCCATTCCTCTTAAGCAGACTTATAGTTTCCCTCCTGATCAACCTCCTGGCAGCCTTTCACCTTAAGTTCTAGTTTCCACTTTCCTTCTCTGTTGTCTCCTAGGCTTCAGGCATAACAGACAAGCTGATGGTTCTCCATGTCTCCCGAGATTTAGAG HG:+:1311611989:16 HG:+:1517863193:-1 +TGCTACTTCTTCCACTGACCCAACCCAAGTGGAAGCCGACAGGGCAAGGAGTCCCATTGGTGCAGTAATAAAGAGAACTAGAAAGGGATGAGTCTGGAGAGGAAGATGAACTTGAATTTCCACACATTTCTTAACTTCTTTTCTGACTTCTGTTTCTCTCTCTCTCCAGAGGTATCTTTTGATCAAATCATTTTGTAATGTTTACATGTTTGATCATGTTTGCTCCCCTACTTTTATAATCTTTCCATTCCTCTTAAGCAGACTTATAGTTTCCCTCCTGATCAACCTCCTGGCAGCCTTTCACCTTAAGTTCTAGTTTCCACTTTCCTTCTCTGTTGTCTCCTAGGCTTCAGGCATAACAGACAAGCTGATGGTTCTCCATGTCTCCCGAGATTTAGAG HG:+:1311611991:16 HG:+:2486451721:-1 +TGCTACTTCTTCCACTGACCCAACCCAAGTGGAAGCCGACAGGGCAAGGAGTCCCATTGGTGCAGTAATAAAGAGAACTAGAAAGGGATGAGTCTGGAGAGGAAGATGAACTTGAATTTCCACACATTTCTTAACTTCTTTTCTGACTTCTGTTTCTCTCTCTCTCCAGAGGTATCTTTTGATCAAATCATTTTGTAATGTTTACATGTTTGATCATGTTTGCTCCCCTACTTTTATAATCTTTCCATTCCTCTTAAGCAGACTTATAGTTTCCCTCCTGATCAACCTCCTGGCAGCCTTTCACCTTAAGTTCTAGTTTCCACTTTCCTTCTCTGTTGTCTCCTAGGCTTCAGGCATAACAGACAAGCTGATGGTTCTCCATGTCTCCCGAGATTTAGAG HG:+:1311611988:16 +TGCTACTTCTTCCACTGACCCAACCCAAGTGGAAGCCGACAGGGCAAGGAGTCCCATTGGTGCAGTAATAAAGAGAACTAGAAAGGGATGAGTCTGGAGAGGAAGATGAACTTGAATTTCCACACATTTCTTAACTTCTTTTCTGACTTCTGTTTCTCTCTCTCTCCAGAGGTATCTTTTGATCAAATCATTTTGTAATGTTTACATGTTTGATCATGTTTGCTCCCCTACTTTTATAATCTTTCCATTCCTCTTAAGCAGACTTATAGTTTCCCTCCTGATCAACCTCCTGGCAGCCTTTCACCTTAAGTTCTAGTTTCCACTTTCCTTCTCTGTTGTCTCCTAGGCTTCAGGCATAACAGACAAGCTGATGGTTCTCCATGTCTCCCGAGATTTAGAG HG:+:1311611993:16 +AGGGCCTAGCATCCCGAGGCTCGTTTGTGTTTAACCGTCCGCCTAAATGGCTTCGTCTGGCTCCGGGCGGCGCGGGGGGTAACCTGCGAGGCGAAGCGTAGGCCTAGGCCACCCTGTCCCGCCGGGGGGCCCACTCCATTGCGCCGCGCGGGGTGCGCGTAGACCTGACCTCCCCTCGGGCATAAAAAGCGCCCTGCGGGAGATCCAGGCCCGGGAGGGCCGCGGAGCTCAGCGAGCAGCCCCAGGCTTTTCCCAACCGCGTGGTCCACCCCCAGCCTCAGTCCCAGCCCCAGCTGCTGGGCTCACCCGCCGGCTAAGGGAATGCTCCCGAGATACCAGATGCCAGTTGCTCGTTGTACCCTCAGCCATGAAATTGGAGGATTACAACGCTTCTCATTCT HG:+:281277624:-1 HG:+:484418993:-1 HG:+:644065910:-1 HG:+:860224814:-1 HG:+:1016013919:-1 HG:+:2068965215:-1 HG:+:2239586169:-1 HG:+:2478493614:12 HG:+:2536454002:-1 HG:+:2541022343:-1 HG:+:2711511591:-1 HG:+:2856788225:-1 HG:+:2876630779:-1 HG:+:2880714467:-1 HG:+:2929458890:-1 HG:+:2951394134:-1 +TGACAGTGAGCCAGGAGCAGCGTCAGCATCCTAGTACAGCGGGTTCATCAAACACCAGAAGATGTGACAGAGACAGGCTTGACCTTCTATGGGAACTCGGTTCCTGATGTCCGTTGTAATATTGGTAATAAAGTTAAACAAAAATAATAGATGAAATGAAGTCAGAAAGACATGTTAAAATAGTTACTGTGAAGCACAAGCTTTTGAAAATTAGGGTAGGTGGGAAGCCTCAGGGGCCCTCAGAGTGGGGGCTGAACAGACCTTTCCACACAAAAGCTAAGCTGAGTTTGCATGAACATCTTCAAGTGTTCGTGTTTCCTCCTGGTGCTTGTACTTCCGTAAACTCACTTTGCCCCATTTGAAAATTGCCGTGTCAGAATGTAGCTTCTTCCGGGAAGGT HG:+:2551488373:-1 +TGACAGTGAGCCAGGAGCAGCGTCAGCATCCTAGTACAGCGGGTTCATCAAACACCAGAAGATGTGACAGAGACAGGCTTGACCTTCTATGGGAACTCGGTTCCTGATGTCCGTTGTAATATTGGTAATAAAGTTAAACAAAAATAATAGATGAAATGAAGTCAGAAAGACATGTTAAAATAGTTACTGTGAAGCACAAGCTTTTGAAAATTAGGGTAGGTGGGAAGCCTCAGGGGCCCTCAGAGTGGGGGCTGAACAGACCTTTCCACACAAAAGCTAAGCTGAGTTTGCATGAACATCTTCAAGTGTTCGTGTTTCCTCCTGGTGCTTGTACTTCCGTAAACTCACTTTGCCCCATTTGAAAATTGCCGTGTCAGAATGTAGCTTCTTCCGGGAAGGT HG:+:72789155:-1 HG:+:183433847:-1 HG:+:251215491:-1 HG:+:320073429:-1 HG:+:397937355:-1 HG:+:553526221:-1 HG:+:662207754:-1 HG:+:776250905:-1 HG:+:972831622:-1 HG:+:985393530:-1 HG:+:997400166:-1 HG:+:1007140160:-1 HG:+:1115853614:-1 HG:+:1171988710:-1 HG:+:1223778010:-1 HG:+:1304217755:-1 HG:+:1339586030:-1 HG:+:1347580527:-1 HG:+:1440873679:-1 HG:+:1449883587:-1 HG:+:1573295766:-1 HG:+:1852898318:-1 HG:+:1871394516:-1 HG:+:1915501040:-1 HG:+:2042719259:-1 HG:+:2136657711:-1 HG:+:2275011003:-1 HG:+:2418118724:-1 HG:+:2427434413:-1 HG:+:2558563862:-1 HG:+:2630970586:-1 HG:+:2691305660:-1 HG:+:2691869332:-1 HG:+:2773184461:-1 HG:+:2929045883:-1 HG:+:2957597972:-1 HG:+:2988301983:-1 HG:+:3058432751:-1 +TGACAGTGAGCCAGGAGCAGCGTCAGCATCCTAGTACAGCGGGTTCATCAAACACCAGAAGATGTGACAGAGACAGGCTTGACCTTCTATGGGAACTCGGTTCCTGATGTCCGTTGTAATATTGGTAATAAAGTTAAACAAAAATAATAGATGAAATGAAGTCAGAAAGACATGTTAAAATAGTTACTGTGAAGCACAAGCTTTTGAAAATTAGGGTAGGTGGGAAGCCTCAGGGGCCCTCAGAGTGGGGGCTGAACAGACCTTTCCACACAAAAGCTAAGCTGAGTTTGCATGAACATCTTCAAGTGTTCGTGTTTCCTCCTGGTGCTTGTACTTCCGTAAACTCACTTTGCCCCATTTGAAAATTGCCGTGTCAGAATGTAGCTTCTTCCGGGAAGGT HG:+:215097328:-1 HG:+:689878463:-1 HG:+:1053970787:-1 HG:+:1333371245:-1 HG:+:1818746946:-1 HG:+:1892763088:-1 HG:+:2304996799:-1 +TGACAGTGAGCCAGGAGCAGCGTCAGCATCCTAGTACAGCGGGTTCATCAAACACCAGAAGATGTGACAGAGACAGGCTTGACCTTCTATGGGAACTCGGTTCCTGATGTCCGTTGTAATATTGGTAATAAAGTTAAACAAAAATAATAGATGAAATGAAGTCAGAAAGACATGTTAAAATAGTTACTGTGAAGCACAAGCTTTTGAAAATTAGGGTAGGTGGGAAGCCTCAGGGGCCCTCAGAGTGGGGGCTGAACAGACCTTTCCACACAAAAGCTAAGCTGAGTTTGCATGAACATCTTCAAGTGTTCGTGTTTCCTCCTGGTGCTTGTACTTCCGTAAACTCACTTTGCCCCATTTGAAAATTGCCGTGTCAGAATGTAGCTTCTTCCGGGAAGGT HG:+:69783564:-1 HG:+:735935418:-1 HG:+:1778461331:-1 HG:+:1791214378:-1 HG:+:3033029176:-1 +TGACAGTGAGCCAGGAGCAGCGTCAGCATCCTAGTACAGCGGGTTCATCAAACACCAGAAGATGTGACAGAGACAGGCTTGACCTTCTATGGGAACTCGGTTCCTGATGTCCGTTGTAATATTGGTAATAAAGTTAAACAAAAATAATAGATGAAATGAAGTCAGAAAGACATGTTAAAATAGTTACTGTGAAGCACAAGCTTTTGAAAATTAGGGTAGGTGGGAAGCCTCAGGGGCCCTCAGAGTGGGGGCTGAACAGACCTTTCCACACAAAAGCTAAGCTGAGTTTGCATGAACATCTTCAAGTGTTCGTGTTTCCTCCTGGTGCTTGTACTTCCGTAAACTCACTTTGCCCCATTTGAAAATTGCCGTGTCAGAATGTAGCTTCTTCCGGGAAGGT HG:+:79537472:-1 HG:+:92552932:-1 HG:+:158296196:-1 HG:+:352763255:-1 HG:+:496712490:-1 HG:+:686589492:-1 HG:+:711076358:-1 HG:+:755843120:-1 HG:+:823183109:-1 HG:+:985685569:-1 HG:+:1134903107:-1 HG:+:1378926688:-1 HG:+:1385449298:-1 HG:+:1407500992:-1 HG:+:1408737052:-1 HG:+:1481519012:-1 HG:+:1608502445:-1 HG:+:1648411502:-1 HG:+:1767442841:-1 HG:+:1844609359:-1 HG:+:1917306052:-1 HG:+:1981826108:-1 HG:+:2081283002:-1 HG:+:2151958569:-1 HG:+:2241412483:-1 HG:+:2260626223:-1 HG:+:2418817617:-1 HG:+:2479247945:-1 HG:+:2522128624:-1 HG:+:2535500028:-1 HG:+:2569433156:-1 HG:+:2570707506:-1 HG:+:2756168443:-1 HG:+:2792006147:-1 HG:+:2862493547:-1 HG:+:2905978892:-1 HG:+:2934685619:-1 HG:+:2981288995:-1 HG:+:3008338709:-1 +TGACAGTGAGCCAGGAGCAGCGTCAGCATCCTAGTACAGCGGGTTCATCAAACACCAGAAGATGTGACAGAGACAGGCTTGACCTTCTATGGGAACTCGGTTCCTGATGTCCGTTGTAATATTGGTAATAAAGTTAAACAAAAATAATAGATGAAATGAAGTCAGAAAGACATGTTAAAATAGTTACTGTGAAGCACAAGCTTTTGAAAATTAGGGTAGGTGGGAAGCCTCAGGGGCCCTCAGAGTGGGGGCTGAACAGACCTTTCCACACAAAAGCTAAGCTGAGTTTGCATGAACATCTTCAAGTGTTCGTGTTTCCTCCTGGTGCTTGTACTTCCGTAAACTCACTTTGCCCCATTTGAAAATTGCCGTGTCAGAATGTAGCTTCTTCCGGGAAGGT HG:+:159792501:-1 HG:+:1075988244:-1 HG:+:1222268807:-1 HG:+:2175540372:-1 HG:+:2250459175:-1 HG:+:2362866926:-1 HG:+:2456467379:-1 +TGACAGTGAGCCAGGAGCAGCGTCAGCATCCTAGTACAGCGGGTTCATCAAACACCAGAAGATGTGACAGAGACAGGCTTGACCTTCTATGGGAACTCGGTTCCTGATGTCCGTTGTAATATTGGTAATAAAGTTAAACAAAAATAATAGATGAAATGAAGTCAGAAAGACATGTTAAAATAGTTACTGTGAAGCACAAGCTTTTGAAAATTAGGGTAGGTGGGAAGCCTCAGGGGCCCTCAGAGTGGGGGCTGAACAGACCTTTCCACACAAAAGCTAAGCTGAGTTTGCATGAACATCTTCAAGTGTTCGTGTTTCCTCCTGGTGCTTGTACTTCCGTAAACTCACTTTGCCCCATTTGAAAATTGCCGTGTCAGAATGTAGCTTCTTCCGGGAAGGT HG:+:409154039:-1 HG:+:441615508:-1 HG:+:713604962:-1 HG:+:755881240:-1 HG:+:768320530:-1 HG:+:1107016045:-1 HG:+:1184102699:-1 HG:+:1252451665:-1 HG:+:1313862863:-1 HG:+:1442123758:-1 HG:+:1495184049:-1 HG:+:2304673926:-1 HG:+:2336220917:-1 HG:+:2394294456:-1 HG:+:2731572017:-1 +TGACAGTGAGCCAGGAGCAGCGTCAGCATCCTAGTACAGCGGGTTCATCAAACACCAGAAGATGTGACAGAGACAGGCTTGACCTTCTATGGGAACTCGGTTCCTGATGTCCGTTGTAATATTGGTAATAAAGTTAAACAAAAATAATAGATGAAATGAAGTCAGAAAGACATGTTAAAATAGTTACTGTGAAGCACAAGCTTTTGAAAATTAGGGTAGGTGGGAAGCCTCAGGGGCCCTCAGAGTGGGGGCTGAACAGACCTTTCCACACAAAAGCTAAGCTGAGTTTGCATGAACATCTTCAAGTGTTCGTGTTTCCTCCTGGTGCTTGTACTTCCGTAAACTCACTTTGCCCCATTTGAAAATTGCCGTGTCAGAATGTAGCTTCTTCCGGGAAGGT HG:+:352827095:-1 HG:+:436739125:-1 HG:+:592711932:-1 HG:+:888215048:-1 HG:+:957797408:-1 HG:+:1649736664:-1 HG:+:1806328575:-1 HG:+:2638731800:-1 +TGACAGTGAGCCAGGAGCAGCGTCAGCATCCTAGTACAGCGGGTTCATCAAACACCAGAAGATGTGACAGAGACAGGCTTGACCTTCTATGGGAACTCGGTTCCTGATGTCCGTTGTAATATTGGTAATAAAGTTAAACAAAAATAATAGATGAAATGAAGTCAGAAAGACATGTTAAAATAGTTACTGTGAAGCACAAGCTTTTGAAAATTAGGGTAGGTGGGAAGCCTCAGGGGCCCTCAGAGTGGGGGCTGAACAGACCTTTCCACACAAAAGCTAAGCTGAGTTTGCATGAACATCTTCAAGTGTTCGTGTTTCCTCCTGGTGCTTGTACTTCCGTAAACTCACTTTGCCCCATTTGAAAATTGCCGTGTCAGAATGTAGCTTCTTCCGGGAAGGT HG:+:107171594:-1 HG:+:195938201:-1 HG:+:354225620:-1 HG:+:673034651:-1 HG:+:976518549:-1 HG:+:1004834407:-1 HG:+:1035823912:-1 HG:+:1057154313:-1 HG:+:1057159325:-1 HG:+:1057161871:-1 HG:+:1059094957:-1 HG:+:1061736090:-1 HG:+:1218123274:-1 HG:+:1323431736:-1 HG:+:1498090205:-1 HG:+:1774619478:-1 HG:+:1842594159:-1 HG:+:2126491926:-1 HG:+:2268904835:-1 HG:+:2512836323:-1 HG:+:2666649214:-1 HG:+:2888285108:-1 HG:+:2924633801:-1 +ACCTTCCCGGAAGAAGCTACATTCTGACACGGCAATTTTCAAATGGGGCAAAGTGAGTTTACGGAAGTACAAGCACCAGGAGGAAACACGAACACTTGAAGATGTTCATGCAAACTCAGCTTAGCTTTTGTGTGGAAAGGTCTGTTCAGCCCCCACTCTGAGGGCCCCTGAGGCTTCCCACCTACCCTAATTTTCAAAAGCTTGTGCTTCACAGTAACTATTTTAACATGTCTTTCTGACTTCATTTCATCTATTATTTTTGTTTAACTTTATTACCAATATTACAACGGACATCAGGAACCGAGTTCCCATAGAAGGTCAAGCCTGTCTCTGTCACATCTTCTGGTGTTTGATGAACCCGCTGTACTAGGATGCTGACGCTGCTCCTGGCTCACTGTCA HG:+:2076709674:-1 HG:+:2333331364:14 +ACCTTCCCGGAAGAAGCTACATTCTGACACGGCAATTTTCAAATGGGGCAAAGTGAGTTTACGGAAGTACAAGCACCAGGAGGAAACACGAACACTTGAAGATGTTCATGCAAACTCAGCTTAGCTTTTGTGTGGAAAGGTCTGTTCAGCCCCCACTCTGAGGGCCCCTGAGGCTTCCCACCTACCCTAATTTTCAAAAGCTTGTGCTTCACAGTAACTATTTTAACATGTCTTTCTGACTTCATTTCATCTATTATTTTTGTTTAACTTTATTACCAATATTACAACGGACATCAGGAACCGAGTTCCCATAGAAGGTCAAGCCTGTCTCTGTCACATCTTCTGGTGTTTGATGAACCCGCTGTACTAGGATGCTGACGCTGCTCCTGGCTCACTGTCA HG:+:2333331366:14 +ACCTTCCCGGAAGAAGCTACATTCTGACACGGCAATTTTCAAATGGGGCAAAGTGAGTTTACGGAAGTACAAGCACCAGGAGGAAACACGAACACTTGAAGATGTTCATGCAAACTCAGCTTAGCTTTTGTGTGGAAAGGTCTGTTCAGCCCCCACTCTGAGGGCCCCTGAGGCTTCCCACCTACCCTAATTTTCAAAAGCTTGTGCTTCACAGTAACTATTTTAACATGTCTTTCTGACTTCATTTCATCTATTATTTTTGTTTAACTTTATTACCAATATTACAACGGACATCAGGAACCGAGTTCCCATAGAAGGTCAAGCCTGTCTCTGTCACATCTTCTGGTGTTTGATGAACCCGCTGTACTAGGATGCTGACGCTGCTCCTGGCTCACTGTCA HG:+:2333331365:14 +ACCTTCCCGGAAGAAGCTACATTCTGACACGGCAATTTTCAAATGGGGCAAAGTGAGTTTACGGAAGTACAAGCACCAGGAGGAAACACGAACACTTGAAGATGTTCATGCAAACTCAGCTTAGCTTTTGTGTGGAAAGGTCTGTTCAGCCCCCACTCTGAGGGCCCCTGAGGCTTCCCACCTACCCTAATTTTCAAAAGCTTGTGCTTCACAGTAACTATTTTAACATGTCTTTCTGACTTCATTTCATCTATTATTTTTGTTTAACTTTATTACCAATATTACAACGGACATCAGGAACCGAGTTCCCATAGAAGGTCAAGCCTGTCTCTGTCACATCTTCTGGTGTTTGATGAACCCGCTGTACTAGGATGCTGACGCTGCTCCTGGCTCACTGTCA HG:+:2634186680:-1 +TAATTAGAAATTTTTACTATGCCAGATTTAAAACATTCCTATGTAGATTAAAATAATTCTATAACTCCTTTTAAAATAAATGCAGCATTCTGGTTGGAGCATTCTAGTTTATTTGCTCAAGCTACCTGTTATTCTCAACTAGGCCACAAAGAATCATAATGTTTCAATTGGCTTGTGGGCTTAATACAGGACACATTGTATACTTGGGACGTTTATCTTCTTCTGGTGAAGTCATGACCAGGACGGACAACTCTGACTCCAGGGGTAAAATATCCAGTTGCCAGTTTTCACCTCTAACATGATATTGCCTGCCTTGTTCATTGGCTGGATAAAGAAGGATAATTTCTGTTTCCATGGCAAGTTCTCGGACCCTTGTTTCACTGAATGTTCCAGCAGGGCT HG:+:557841558:-1 HG:+:789178528:-1 HG:+:806864367:-1 HG:+:1024193088:-1 HG:+:1076950184:-1 HG:+:1416645162:-1 HG:+:1525733763:-1 HG:+:1703858031:-1 HG:+:1704789190:-1 HG:+:1732512461:-1 HG:+:1740839004:-1 HG:+:2121465771:-1 HG:+:2652738636:-1 HG:+:2880611349:-1 HG:+:2885026674:-1 HG:+:2920403354:-1 HG:+:3003326060:-1 HG:+:3019936537:-1 HG:+:3029931460:-1 +TAATTAGAAATTTTTACTATGCCAGATTTAAAACATTCCTATGTAGATTAAAATAATTCTATAACTCCTTTTAAAATAAATGCAGCATTCTGGTTGGAGCATTCTAGTTTATTTGCTCAAGCTACCTGTTATTCTCAACTAGGCCACAAAGAATCATAATGTTTCAATTGGCTTGTGGGCTTAATACAGGACACATTGTATACTTGGGACGTTTATCTTCTTCTGGTGAAGTCATGACCAGGACGGACAACTCTGACTCCAGGGGTAAAATATCCAGTTGCCAGTTTTCACCTCTAACATGATATTGCCTGCCTTGTTCATTGGCTGGATAAAGAAGGATAATTTCTGTTTCCATGGCAAGTTCTCGGACCCTTGTTTCACTGAATGTTCCAGCAGGGCT HG:+:198626100:-1 +TAATTAGAAATTTTTACTATGCCAGATTTAAAACATTCCTATGTAGATTAAAATAATTCTATAACTCCTTTTAAAATAAATGCAGCATTCTGGTTGGAGCATTCTAGTTTATTTGCTCAAGCTACCTGTTATTCTCAACTAGGCCACAAAGAATCATAATGTTTCAATTGGCTTGTGGGCTTAATACAGGACACATTGTATACTTGGGACGTTTATCTTCTTCTGGTGAAGTCATGACCAGGACGGACAACTCTGACTCCAGGGGTAAAATATCCAGTTGCCAGTTTTCACCTCTAACATGATATTGCCTGCCTTGTTCATTGGCTGGATAAAGAAGGATAATTTCTGTTTCCATGGCAAGTTCTCGGACCCTTGTTTCACTGAATGTTCCAGCAGGGCT HG:+:56203447:-1 HG:+:212700738:-1 HG:+:1247040695:-1 HG:+:1913001104:-1 HG:+:2156333757:-1 HG:+:2642161098:-1 +TAATTAGAAATTTTTACTATGCCAGATTTAAAACATTCCTATGTAGATTAAAATAATTCTATAACTCCTTTTAAAATAAATGCAGCATTCTGGTTGGAGCATTCTAGTTTATTTGCTCAAGCTACCTGTTATTCTCAACTAGGCCACAAAGAATCATAATGTTTCAATTGGCTTGTGGGCTTAATACAGGACACATTGTATACTTGGGACGTTTATCTTCTTCTGGTGAAGTCATGACCAGGACGGACAACTCTGACTCCAGGGGTAAAATATCCAGTTGCCAGTTTTCACCTCTAACATGATATTGCCTGCCTTGTTCATTGGCTGGATAAAGAAGGATAATTTCTGTTTCCATGGCAAGTTCTCGGACCCTTGTTTCACTGAATGTTCCAGCAGGGCT HG:+:778804374:-1 HG:+:959622018:-1 HG:+:972060570:-1 HG:+:1711410504:-1 HG:+:1823481860:-1 HG:+:2224078387:-1 HG:+:2252758516:-1 HG:+:2290526102:-1 +TAATTAGAAATTTTTACTATGCCAGATTTAAAACATTCCTATGTAGATTAAAATAATTCTATAACTCCTTTTAAAATAAATGCAGCATTCTGGTTGGAGCATTCTAGTTTATTTGCTCAAGCTACCTGTTATTCTCAACTAGGCCACAAAGAATCATAATGTTTCAATTGGCTTGTGGGCTTAATACAGGACACATTGTATACTTGGGACGTTTATCTTCTTCTGGTGAAGTCATGACCAGGACGGACAACTCTGACTCCAGGGGTAAAATATCCAGTTGCCAGTTTTCACCTCTAACATGATATTGCCTGCCTTGTTCATTGGCTGGATAAAGAAGGATAATTTCTGTTTCCATGGCAAGTTCTCGGACCCTTGTTTCACTGAATGTTCCAGCAGGGCT HG:+:211313460:-1 HG:+:536731238:-1 HG:+:647564388:-1 HG:+:744727947:-1 HG:+:823229127:-1 HG:+:833436821:-1 HG:+:884477829:-1 HG:+:935821506:-1 HG:+:1048384016:-1 HG:+:1079191710:-1 HG:+:1114652321:-1 HG:+:1249201968:-1 HG:+:1357520052:-1 HG:+:1389119422:-1 HG:+:1407987874:-1 HG:+:1581266002:-1 HG:+:1607314866:-1 HG:+:1697638387:-1 HG:+:1797529576:-1 HG:+:1799784428:-1 HG:+:1994365772:-1 HG:+:2038267597:-1 HG:+:2076902609:-1 HG:+:2158281829:-1 HG:+:2158820827:-1 HG:+:2224174062:-1 HG:+:2539031552:-1 HG:+:2616071195:-1 HG:+:2761085748:-1 HG:+:2777623223:-1 HG:+:2792052168:-1 HG:+:2813272236:-1 HG:+:2985394443:-1 +TAATTAGAAATTTTTACTATGCCAGATTTAAAACATTCCTATGTAGATTAAAATAATTCTATAACTCCTTTTAAAATAAATGCAGCATTCTGGTTGGAGCATTCTAGTTTATTTGCTCAAGCTACCTGTTATTCTCAACTAGGCCACAAAGAATCATAATGTTTCAATTGGCTTGTGGGCTTAATACAGGACACATTGTATACTTGGGACGTTTATCTTCTTCTGGTGAAGTCATGACCAGGACGGACAACTCTGACTCCAGGGGTAAAATATCCAGTTGCCAGTTTTCACCTCTAACATGATATTGCCTGCCTTGTTCATTGGCTGGATAAAGAAGGATAATTTCTGTTTCCATGGCAAGTTCTCGGACCCTTGTTTCACTGAATGTTCCAGCAGGGCT HG:+:102529336:-1 HG:+:370648597:-1 HG:+:400639964:-1 HG:+:404055356:-1 HG:+:616697489:-1 HG:+:835721379:-1 HG:+:1222125920:-1 HG:+:1343149529:-1 HG:+:1354887292:-1 HG:+:1675637052:-1 HG:+:2122328342:-1 HG:+:2346384850:-1 HG:+:2526486210:-1 HG:+:2652470770:-1 HG:+:2956028851:-1 +TAATTAGAAATTTTTACTATGCCAGATTTAAAACATTCCTATGTAGATTAAAATAATTCTATAACTCCTTTTAAAATAAATGCAGCATTCTGGTTGGAGCATTCTAGTTTATTTGCTCAAGCTACCTGTTATTCTCAACTAGGCCACAAAGAATCATAATGTTTCAATTGGCTTGTGGGCTTAATACAGGACACATTGTATACTTGGGACGTTTATCTTCTTCTGGTGAAGTCATGACCAGGACGGACAACTCTGACTCCAGGGGTAAAATATCCAGTTGCCAGTTTTCACCTCTAACATGATATTGCCTGCCTTGTTCATTGGCTGGATAAAGAAGGATAATTTCTGTTTCCATGGCAAGTTCTCGGACCCTTGTTTCACTGAATGTTCCAGCAGGGCT HG:+:118450604:-1 HG:+:171874150:-1 HG:+:174712252:-1 HG:+:268478254:-1 HG:+:398642382:-1 HG:+:610150911:-1 HG:+:648251551:-1 HG:+:904756485:-1 HG:+:956786366:-1 HG:+:997103974:-1 HG:+:1010793758:-1 HG:+:1021998471:-1 HG:+:1172564420:-1 HG:+:1206263260:-1 HG:+:1250150989:-1 HG:+:1648544627:-1 HG:+:1664009859:-1 HG:+:1962248443:-1 HG:+:2178978710:-1 HG:+:2648576238:-1 HG:+:3022719699:-1 +TAATTAGAAATTTTTACTATGCCAGATTTAAAACATTCCTATGTAGATTAAAATAATTCTATAACTCCTTTTAAAATAAATGCAGCATTCTGGTTGGAGCATTCTAGTTTATTTGCTCAAGCTACCTGTTATTCTCAACTAGGCCACAAAGAATCATAATGTTTCAATTGGCTTGTGGGCTTAATACAGGACACATTGTATACTTGGGACGTTTATCTTCTTCTGGTGAAGTCATGACCAGGACGGACAACTCTGACTCCAGGGGTAAAATATCCAGTTGCCAGTTTTCACCTCTAACATGATATTGCCTGCCTTGTTCATTGGCTGGATAAAGAAGGATAATTTCTGTTTCCATGGCAAGTTCTCGGACCCTTGTTTCACTGAATGTTCCAGCAGGGCT HG:+:81299606:-1 HG:+:170159424:-1 HG:+:192710771:-1 HG:+:381153665:-1 HG:+:387810901:-1 HG:+:510328862:-1 HG:+:718930534:-1 HG:+:875143612:-1 HG:+:972062333:-1 HG:+:988077223:-1 HG:+:1116337249:-1 HG:+:1218963641:-1 HG:+:1265795760:-1 HG:+:1380469401:-1 HG:+:1454470396:-1 HG:+:1520185368:-1 HG:+:1654251279:-1 HG:+:1659089692:-1 HG:+:1692077454:-1 HG:+:1702895728:-1 HG:+:1831095986:-1 HG:+:2010797504:-1 HG:+:2112255752:-1 HG:+:2138360894:-1 HG:+:2258247859:-1 HG:+:2405509428:-1 HG:+:2518793187:-1 HG:+:2527198820:-1 HG:+:2560466184:-1 HG:+:2609165702:-1 HG:+:2620592071:-1 HG:+:2812731011:-1 HG:+:2925140235:-1 HG:+:2964979405:-1 HG:+:3000920756:-1 HG:+:3010425798:-1 +TAATTAGAAATTTTTACTATGCCAGATTTAAAACATTCCTATGTAGATTAAAATAATTCTATAACTCCTTTTAAAATAAATGCAGCATTCTGGTTGGAGCATTCTAGTTTATTTGCTCAAGCTACCTGTTATTCTCAACTAGGCCACAAAGAATCATAATGTTTCAATTGGCTTGTGGGCTTAATACAGGACACATTGTATACTTGGGACGTTTATCTTCTTCTGGTGAAGTCATGACCAGGACGGACAACTCTGACTCCAGGGGTAAAATATCCAGTTGCCAGTTTTCACCTCTAACATGATATTGCCTGCCTTGTTCATTGGCTGGATAAAGAAGGATAATTTCTGTTTCCATGGCAAGTTCTCGGACCCTTGTTTCACTGAATGTTCCAGCAGGGCT HG:+:18065763:-1 HG:+:351440771:-1 HG:+:595821279:-1 HG:+:666634413:-1 HG:+:674850854:-1 HG:+:933986233:-1 HG:+:1049385177:-1 HG:+:1733557411:-1 HG:+:2039112455:-1 HG:+:2144557858:-1 HG:+:2248405472:-1 HG:+:2434490957:-1 HG:+:2519539566:-1 HG:+:2719869958:-1 HG:+:2728940565:-1 HG:+:2902511199:-1 HG:+:3016265904:-1 +AGCCCTGCTGGAACATTCAGTGAAACAAGGGTCCGAGAACTTGCCATGGAAACAGAAATTATCCTTCTTTATCCAGCCAATGAACAAGGCAGGCAATATCATGTTAGAGGTGAAAACTGGCAACTGGATATTTTACCCCTGGAGTCAGAGTTGTCCGTCCTGGTCATGACTTCACCAGAAGAAGATAAACGTCCCAAGTATACAATGTGTCCTGTATTAAGCCCACAAGCCAATTGAAACATTATGATTCTTTGTGGCCTAGTTGAGAATAACAGGTAGCTTGAGCAAATAAACTAGAATGCTCCAACCAGAATGCTGCATTTATTTTAAAAGGAGTTATAGAATTATTTTAATCTACATAGGAATGTTTTAAATCTGGCATAGTAAAAATTTCTAATTA HG:+:479028667:20 +AGCCCTGCTGGAACATTCAGTGAAACAAGGGTCCGAGAACTTGCCATGGAAACAGAAATTATCCTTCTTTATCCAGCCAATGAACAAGGCAGGCAATATCATGTTAGAGGTGAAAACTGGCAACTGGATATTTTACCCCTGGAGTCAGAGTTGTCCGTCCTGGTCATGACTTCACCAGAAGAAGATAAACGTCCCAAGTATACAATGTGTCCTGTATTAAGCCCACAAGCCAATTGAAACATTATGATTCTTTGTGGCCTAGTTGAGAATAACAGGTAGCTTGAGCAAATAAACTAGAATGCTCCAACCAGAATGCTGCATTTATTTTAAAAGGAGTTATAGAATTATTTTAATCTACATAGGAATGTTTTAAATCTGGCATAGTAAAAATTTCTAATTA HG:+:479028664:20 +AGCCCTGCTGGAACATTCAGTGAAACAAGGGTCCGAGAACTTGCCATGGAAACAGAAATTATCCTTCTTTATCCAGCCAATGAACAAGGCAGGCAATATCATGTTAGAGGTGAAAACTGGCAACTGGATATTTTACCCCTGGAGTCAGAGTTGTCCGTCCTGGTCATGACTTCACCAGAAGAAGATAAACGTCCCAAGTATACAATGTGTCCTGTATTAAGCCCACAAGCCAATTGAAACATTATGATTCTTTGTGGCCTAGTTGAGAATAACAGGTAGCTTGAGCAAATAAACTAGAATGCTCCAACCAGAATGCTGCATTTATTTTAAAAGGAGTTATAGAATTATTTTAATCTACATAGGAATGTTTTAAATCTGGCATAGTAAAAATTTCTAATTA HG:+:479028666:20 +AGCCCTGCTGGAACATTCAGTGAAACAAGGGTCCGAGAACTTGCCATGGAAACAGAAATTATCCTTCTTTATCCAGCCAATGAACAAGGCAGGCAATATCATGTTAGAGGTGAAAACTGGCAACTGGATATTTTACCCCTGGAGTCAGAGTTGTCCGTCCTGGTCATGACTTCACCAGAAGAAGATAAACGTCCCAAGTATACAATGTGTCCTGTATTAAGCCCACAAGCCAATTGAAACATTATGATTCTTTGTGGCCTAGTTGAGAATAACAGGTAGCTTGAGCAAATAAACTAGAATGCTCCAACCAGAATGCTGCATTTATTTTAAAAGGAGTTATAGAATTATTTTAATCTACATAGGAATGTTTTAAATCTGGCATAGTAAAAATTTCTAATTA HG:+:239114337:-1 +AGCCCTGCTGGAACATTCAGTGAAACAAGGGTCCGAGAACTTGCCATGGAAACAGAAATTATCCTTCTTTATCCAGCCAATGAACAAGGCAGGCAATATCATGTTAGAGGTGAAAACTGGCAACTGGATATTTTACCCCTGGAGTCAGAGTTGTCCGTCCTGGTCATGACTTCACCAGAAGAAGATAAACGTCCCAAGTATACAATGTGTCCTGTATTAAGCCCACAAGCCAATTGAAACATTATGATTCTTTGTGGCCTAGTTGAGAATAACAGGTAGCTTGAGCAAATAAACTAGAATGCTCCAACCAGAATGCTGCATTTATTTTAAAAGGAGTTATAGAATTATTTTAATCTACATAGGAATGTTTTAAATCTGGCATAGTAAAAATTTCTAATTA HG:+:406741050:-1 HG:+:1866560876:-1 +GCTTGTACATTCCTTCCCCATTTTCTTTCAAGATTTCCATTCTACAGGGCTACGAGGAATGAAGCATCCTAGATACAATTCAATAAAGTTTTGGCCTGATAAGGGAGACCTAGTCCTCTCTGCATTCTGAAATTCCTTTTTGGATGAATCCATAGGAGGTCTTACTTTTTTTTCACTTCCCTGCACCCCTGGCCAAGGATATTCAATATCCAAGAAACAAATACCAATTTTACTTGTAGCTTTCACATTCCCATCAACATGACATAGATTAAAGACCAAAAGACTTCTGTTTCCACTTCTGAGAGATGTGGTCCCCATTTCATGTGAAGGAAATCTGACCGTTCCCGATTTACAGCTACTGAGGGGCCTAAAATATTTGTTCTGAGAATTTCTCAGGCCT HG:+:237950748:-1 HG:+:733605788:-1 HG:+:2951944583:-1 HG:+:2951997479:-1 HG:+:2952101410:-1 +GCTTGTACATTCCTTCCCCATTTTCTTTCAAGATTTCCATTCTACAGGGCTACGAGGAATGAAGCATCCTAGATACAATTCAATAAAGTTTTGGCCTGATAAGGGAGACCTAGTCCTCTCTGCATTCTGAAATTCCTTTTTGGATGAATCCATAGGAGGTCTTACTTTTTTTTCACTTCCCTGCACCCCTGGCCAAGGATATTCAATATCCAAGAAACAAATACCAATTTTACTTGTAGCTTTCACATTCCCATCAACATGACATAGATTAAAGACCAAAAGACTTCTGTTTCCACTTCTGAGAGATGTGGTCCCCATTTCATGTGAAGGAAATCTGACCGTTCCCGATTTACAGCTACTGAGGGGCCTAAAATATTTGTTCTGAGAATTTCTCAGGCCT HG:+:371194504:-1 HG:+:544186639:-1 HG:+:632509196:-1 HG:+:1139924991:-1 HG:+:2616401788:-1 +GCTTGTACATTCCTTCCCCATTTTCTTTCAAGATTTCCATTCTACAGGGCTACGAGGAATGAAGCATCCTAGATACAATTCAATAAAGTTTTGGCCTGATAAGGGAGACCTAGTCCTCTCTGCATTCTGAAATTCCTTTTTGGATGAATCCATAGGAGGTCTTACTTTTTTTTCACTTCCCTGCACCCCTGGCCAAGGATATTCAATATCCAAGAAACAAATACCAATTTTACTTGTAGCTTTCACATTCCCATCAACATGACATAGATTAAAGACCAAAAGACTTCTGTTTCCACTTCTGAGAGATGTGGTCCCCATTTCATGTGAAGGAAATCTGACCGTTCCCGATTTACAGCTACTGAGGGGCCTAAAATATTTGTTCTGAGAATTTCTCAGGCCT HG:+:1701289077:-1 HG:+:1898711371:-1 HG:+:2701221270:-1 HG:+:2870983419:-1 +GCTTGTACATTCCTTCCCCATTTTCTTTCAAGATTTCCATTCTACAGGGCTACGAGGAATGAAGCATCCTAGATACAATTCAATAAAGTTTTGGCCTGATAAGGGAGACCTAGTCCTCTCTGCATTCTGAAATTCCTTTTTGGATGAATCCATAGGAGGTCTTACTTTTTTTTCACTTCCCTGCACCCCTGGCCAAGGATATTCAATATCCAAGAAACAAATACCAATTTTACTTGTAGCTTTCACATTCCCATCAACATGACATAGATTAAAGACCAAAAGACTTCTGTTTCCACTTCTGAGAGATGTGGTCCCCATTTCATGTGAAGGAAATCTGACCGTTCCCGATTTACAGCTACTGAGGGGCCTAAAATATTTGTTCTGAGAATTTCTCAGGCCT HG:+:77414540:-1 HG:+:268455919:-1 HG:+:268474421:-1 HG:+:326951931:-1 HG:+:441589276:-1 HG:+:518146052:-1 HG:+:1203716782:-1 HG:+:1304657763:-1 HG:+:1428952616:-1 HG:+:1903718365:-1 HG:+:2225839072:-1 HG:+:2357163966:-1 HG:+:2805821628:-1 HG:+:3014381035:-1 +GCTTGTACATTCCTTCCCCATTTTCTTTCAAGATTTCCATTCTACAGGGCTACGAGGAATGAAGCATCCTAGATACAATTCAATAAAGTTTTGGCCTGATAAGGGAGACCTAGTCCTCTCTGCATTCTGAAATTCCTTTTTGGATGAATCCATAGGAGGTCTTACTTTTTTTTCACTTCCCTGCACCCCTGGCCAAGGATATTCAATATCCAAGAAACAAATACCAATTTTACTTGTAGCTTTCACATTCCCATCAACATGACATAGATTAAAGACCAAAAGACTTCTGTTTCCACTTCTGAGAGATGTGGTCCCCATTTCATGTGAAGGAAATCTGACCGTTCCCGATTTACAGCTACTGAGGGGCCTAAAATATTTGTTCTGAGAATTTCTCAGGCCT HG:+:262584068:-1 HG:+:1027493114:-1 HG:+:1480065182:-1 HG:+:1815059696:-1 HG:+:2022402077:-1 HG:+:2518159159:-1 HG:+:2802056230:-1 HG:+:2823962160:-1 +GCTTGTACATTCCTTCCCCATTTTCTTTCAAGATTTCCATTCTACAGGGCTACGAGGAATGAAGCATCCTAGATACAATTCAATAAAGTTTTGGCCTGATAAGGGAGACCTAGTCCTCTCTGCATTCTGAAATTCCTTTTTGGATGAATCCATAGGAGGTCTTACTTTTTTTTCACTTCCCTGCACCCCTGGCCAAGGATATTCAATATCCAAGAAACAAATACCAATTTTACTTGTAGCTTTCACATTCCCATCAACATGACATAGATTAAAGACCAAAAGACTTCTGTTTCCACTTCTGAGAGATGTGGTCCCCATTTCATGTGAAGGAAATCTGACCGTTCCCGATTTACAGCTACTGAGGGGCCTAAAATATTTGTTCTGAGAATTTCTCAGGCCT HG:+:2955031:-1 HG:+:43365773:-1 HG:+:276560328:-1 HG:+:413501512:-1 HG:+:542644440:-1 HG:+:1106227971:-1 HG:+:1448027031:-1 HG:+:1517482065:-1 HG:+:1628128378:-1 HG:+:1638404400:-1 HG:+:1709167876:-1 HG:+:1802731074:-1 HG:+:1816438869:-1 HG:+:2037216402:-1 HG:+:2295824386:-1 HG:+:2414221764:-1 HG:+:2502084665:-1 HG:+:2516563663:-1 HG:+:2539564049:-1 HG:+:2539575711:-1 HG:+:2539581075:-1 HG:+:2637181360:-1 +GCTTGTACATTCCTTCCCCATTTTCTTTCAAGATTTCCATTCTACAGGGCTACGAGGAATGAAGCATCCTAGATACAATTCAATAAAGTTTTGGCCTGATAAGGGAGACCTAGTCCTCTCTGCATTCTGAAATTCCTTTTTGGATGAATCCATAGGAGGTCTTACTTTTTTTTCACTTCCCTGCACCCCTGGCCAAGGATATTCAATATCCAAGAAACAAATACCAATTTTACTTGTAGCTTTCACATTCCCATCAACATGACATAGATTAAAGACCAAAAGACTTCTGTTTCCACTTCTGAGAGATGTGGTCCCCATTTCATGTGAAGGAAATCTGACCGTTCCCGATTTACAGCTACTGAGGGGCCTAAAATATTTGTTCTGAGAATTTCTCAGGCCT HG:+:839426597:-1 HG:+:1706541538:-1 +GCTTGTACATTCCTTCCCCATTTTCTTTCAAGATTTCCATTCTACAGGGCTACGAGGAATGAAGCATCCTAGATACAATTCAATAAAGTTTTGGCCTGATAAGGGAGACCTAGTCCTCTCTGCATTCTGAAATTCCTTTTTGGATGAATCCATAGGAGGTCTTACTTTTTTTTCACTTCCCTGCACCCCTGGCCAAGGATATTCAATATCCAAGAAACAAATACCAATTTTACTTGTAGCTTTCACATTCCCATCAACATGACATAGATTAAAGACCAAAAGACTTCTGTTTCCACTTCTGAGAGATGTGGTCCCCATTTCATGTGAAGGAAATCTGACCGTTCCCGATTTACAGCTACTGAGGGGCCTAAAATATTTGTTCTGAGAATTTCTCAGGCCT HG:+:866275605:-1 HG:+:899685204:-1 HG:+:1160273731:-1 HG:+:2145467116:-1 HG:+:2173422884:-1 HG:+:2907971214:-1 +GCTTGTACATTCCTTCCCCATTTTCTTTCAAGATTTCCATTCTACAGGGCTACGAGGAATGAAGCATCCTAGATACAATTCAATAAAGTTTTGGCCTGATAAGGGAGACCTAGTCCTCTCTGCATTCTGAAATTCCTTTTTGGATGAATCCATAGGAGGTCTTACTTTTTTTTCACTTCCCTGCACCCCTGGCCAAGGATATTCAATATCCAAGAAACAAATACCAATTTTACTTGTAGCTTTCACATTCCCATCAACATGACATAGATTAAAGACCAAAAGACTTCTGTTTCCACTTCTGAGAGATGTGGTCCCCATTTCATGTGAAGGAAATCTGACCGTTCCCGATTTACAGCTACTGAGGGGCCTAAAATATTTGTTCTGAGAATTTCTCAGGCCT HG:+:271756468:-1 HG:+:347274802:-1 HG:+:590140138:-1 HG:+:1125216105:-1 HG:+:1527665705:-1 HG:+:1530265329:-1 HG:+:1561793576:-1 HG:+:1921911165:-1 HG:+:2369951409:-1 HG:+:3009661605:-1 +AGGCCTGAGAAATTCTCAGAACAAATATTTTAGGCCCCTCAGTAGCTGTAAATCGGGAACGGTCAGATTTCCTTCACATGAAATGGGGACCACATCTCTCAGAAGTGGAAACAGAAGTCTTTTGGTCTTTAATCTATGTCATGTTGATGGGAATGTGAAAGCTACAAGTAAAATTGGTATTTGTTTCTTGGATATTGAATATCCTTGGCCAGGGGTGCAGGGAAGTGAAAAAAAAGTAAGACCTCCTATGGATTCATCCAAAAAGGAATTTCAGAATGCAGAGAGGACTAGGTCTCCCTTATCAGGCCAAAACTTTATTGAATTGTATCTAGGATGCTTCATTCCTCGTAGCCCTGTAGAATGGAAATCTTGAAAGAAAATGGGGAAGGAATGTACAAGC HG:+:612269291:20 +AGGCCTGAGAAATTCTCAGAACAAATATTTTAGGCCCCTCAGTAGCTGTAAATCGGGAACGGTCAGATTTCCTTCACATGAAATGGGGACCACATCTCTCAGAAGTGGAAACAGAAGTCTTTTGGTCTTTAATCTATGTCATGTTGATGGGAATGTGAAAGCTACAAGTAAAATTGGTATTTGTTTCTTGGATATTGAATATCCTTGGCCAGGGGTGCAGGGAAGTGAAAAAAAAGTAAGACCTCCTATGGATTCATCCAAAAAGGAATTTCAGAATGCAGAGAGGACTAGGTCTCCCTTATCAGGCCAAAACTTTATTGAATTGTATCTAGGATGCTTCATTCCTCGTAGCCCTGTAGAATGGAAATCTTGAAAGAAAATGGGGAAGGAATGTACAAGC HG:+:612269289:20 +AGGCCTGAGAAATTCTCAGAACAAATATTTTAGGCCCCTCAGTAGCTGTAAATCGGGAACGGTCAGATTTCCTTCACATGAAATGGGGACCACATCTCTCAGAAGTGGAAACAGAAGTCTTTTGGTCTTTAATCTATGTCATGTTGATGGGAATGTGAAAGCTACAAGTAAAATTGGTATTTGTTTCTTGGATATTGAATATCCTTGGCCAGGGGTGCAGGGAAGTGAAAAAAAAGTAAGACCTCCTATGGATTCATCCAAAAAGGAATTTCAGAATGCAGAGAGGACTAGGTCTCCCTTATCAGGCCAAAACTTTATTGAATTGTATCTAGGATGCTTCATTCCTCGTAGCCCTGTAGAATGGAAATCTTGAAAGAAAATGGGGAAGGAATGTACAAGC HG:+:612269290:20 +CCAAACTGCTGAATGAAAAAGATGCTTTAACTCTCGTGAGATGATGCACACAACACAAGTGGTTTTACCAGATAGCTTTCTTCTTTGTTTTTATCCTGGGATATTTTGCTTTTTTTGCCCTTTGACCTCAATGAGCTCAAAAATGTTCATTCAAGAAATGGACAAAAACAATGTTTCTAAACTGGCTGAATCAAAAGGAATGGTTTCACTCTATGAGATGAATGCCACATATTCACAAAAGGGTTTCTCAGAAAGCTTCTTTCTACTTTTTATCCTGAAGGTATCTTACTTTTTTCCATAGGCCTCAATGTGCTTCCAAATATCCCCTTCGCAGATACTTATAAAAAACTGGTGTTTCCAAAACTATTGAATGAAAGAAAGTTTTAACTCCATGAGATGA HG:+:582789151:-1 HG:+:582793087:-1 HG:+:927747959:-1 HG:+:927886413:-1 HG:+:1866441208:-1 HG:+:1985517226:56 HG:+:1985598628:25 +CCAAACTGCTGAATGAAAAAGATGCTTTAACTCTCGTGAGATGATGCACACAACACAAGTGGTTTTACCAGATAGCTTTCTTCTTTGTTTTTATCCTGGGATATTTTGCTTTTTTTGCCCTTTGACCTCAATGAGCTCAAAAATGTTCATTCAAGAAATGGACAAAAACAATGTTTCTAAACTGGCTGAATCAAAAGGAATGGTTTCACTCTATGAGATGAATGCCACATATTCACAAAAGGGTTTCTCAGAAAGCTTCTTTCTACTTTTTATCCTGAAGGTATCTTACTTTTTTCCATAGGCCTCAATGTGCTTCCAAATATCCCCTTCGCAGATACTTATAAAAAACTGGTGTTTCCAAAACTATTGAATGAAAGAAAGTTTTAACTCCATGAGATGA HG:+:348128803:-1 HG:+:553109454:-1 HG:+:723449667:-1 HG:+:991838605:-1 HG:+:2260432569:-1 HG:+:2728263018:-1 +CCAAACTGCTGAATGAAAAAGATGCTTTAACTCTCGTGAGATGATGCACACAACACAAGTGGTTTTACCAGATAGCTTTCTTCTTTGTTTTTATCCTGGGATATTTTGCTTTTTTTGCCCTTTGACCTCAATGAGCTCAAAAATGTTCATTCAAGAAATGGACAAAAACAATGTTTCTAAACTGGCTGAATCAAAAGGAATGGTTTCACTCTATGAGATGAATGCCACATATTCACAAAAGGGTTTCTCAGAAAGCTTCTTTCTACTTTTTATCCTGAAGGTATCTTACTTTTTTCCATAGGCCTCAATGTGCTTCCAAATATCCCCTTCGCAGATACTTATAAAAAACTGGTGTTTCCAAAACTATTGAATGAAAGAAAGTTTTAACTCCATGAGATGA HG:+:71017090:-1 HG:+:292716841:-1 HG:+:498394824:-1 HG:+:568866766:-1 HG:+:586570403:-1 HG:+:775067185:-1 HG:+:807365924:-1 HG:+:829714710:-1 HG:+:874509529:-1 HG:+:916924197:-1 HG:+:1114812195:-1 HG:+:1170618010:-1 HG:+:1200617870:-1 HG:+:1258053232:-1 HG:+:1463747743:-1 HG:+:1639754571:-1 HG:+:1649742138:-1 HG:+:1866350327:-1 HG:+:1893428844:-1 HG:+:1946338337:-1 HG:+:1972994812:-1 HG:+:2026905810:-1 HG:+:2045665740:-1 HG:+:2051044502:-1 HG:+:2140049095:-1 HG:+:2144595647:-1 HG:+:2226547916:-1 HG:+:2264367301:-1 HG:+:2442346428:-1 HG:+:2563889417:-1 HG:+:2639678933:-1 HG:+:2712334888:-1 HG:+:3015238156:-1 +CCAAACTGCTGAATGAAAAAGATGCTTTAACTCTCGTGAGATGATGCACACAACACAAGTGGTTTTACCAGATAGCTTTCTTCTTTGTTTTTATCCTGGGATATTTTGCTTTTTTTGCCCTTTGACCTCAATGAGCTCAAAAATGTTCATTCAAGAAATGGACAAAAACAATGTTTCTAAACTGGCTGAATCAAAAGGAATGGTTTCACTCTATGAGATGAATGCCACATATTCACAAAAGGGTTTCTCAGAAAGCTTCTTTCTACTTTTTATCCTGAAGGTATCTTACTTTTTTCCATAGGCCTCAATGTGCTTCCAAATATCCCCTTCGCAGATACTTATAAAAAACTGGTGTTTCCAAAACTATTGAATGAAAGAAAGTTTTAACTCCATGAGATGA HG:+:1867070819:-1 HG:+:1985598630:25 +CCAAACTGCTGAATGAAAAAGATGCTTTAACTCTCGTGAGATGATGCACACAACACAAGTGGTTTTACCAGATAGCTTTCTTCTTTGTTTTTATCCTGGGATATTTTGCTTTTTTTGCCCTTTGACCTCAATGAGCTCAAAAATGTTCATTCAAGAAATGGACAAAAACAATGTTTCTAAACTGGCTGAATCAAAAGGAATGGTTTCACTCTATGAGATGAATGCCACATATTCACAAAAGGGTTTCTCAGAAAGCTTCTTTCTACTTTTTATCCTGAAGGTATCTTACTTTTTTCCATAGGCCTCAATGTGCTTCCAAATATCCCCTTCGCAGATACTTATAAAAAACTGGTGTTTCCAAAACTATTGAATGAAAGAAAGTTTTAACTCCATGAGATGA HG:+:1985524162:73 HG:+:1985598622:25 HG:+:1989274739:-1 HG:+:2522356870:-1 +CCAAACTGCTGAATGAAAAAGATGCTTTAACTCTCGTGAGATGATGCACACAACACAAGTGGTTTTACCAGATAGCTTTCTTCTTTGTTTTTATCCTGGGATATTTTGCTTTTTTTGCCCTTTGACCTCAATGAGCTCAAAAATGTTCATTCAAGAAATGGACAAAAACAATGTTTCTAAACTGGCTGAATCAAAAGGAATGGTTTCACTCTATGAGATGAATGCCACATATTCACAAAAGGGTTTCTCAGAAAGCTTCTTTCTACTTTTTATCCTGAAGGTATCTTACTTTTTTCCATAGGCCTCAATGTGCTTCCAAATATCCCCTTCGCAGATACTTATAAAAAACTGGTGTTTCCAAAACTATTGAATGAAAGAAAGTTTTAACTCCATGAGATGA HG:+:1295749264:-1 HG:+:1298609165:-1 HG:+:1985598626:25 +CCAAACTGCTGAATGAAAAAGATGCTTTAACTCTCGTGAGATGATGCACACAACACAAGTGGTTTTACCAGATAGCTTTCTTCTTTGTTTTTATCCTGGGATATTTTGCTTTTTTTGCCCTTTGACCTCAATGAGCTCAAAAATGTTCATTCAAGAAATGGACAAAAACAATGTTTCTAAACTGGCTGAATCAAAAGGAATGGTTTCACTCTATGAGATGAATGCCACATATTCACAAAAGGGTTTCTCAGAAAGCTTCTTTCTACTTTTTATCCTGAAGGTATCTTACTTTTTTCCATAGGCCTCAATGTGCTTCCAAATATCCCCTTCGCAGATACTTATAAAAAACTGGTGTTTCCAAAACTATTGAATGAAAGAAAGTTTTAACTCCATGAGATGA HG:+:927921645:-1 HG:+:1124743105:-1 HG:+:1124746994:-1 HG:+:1295774511:-1 HG:+:1870743599:-1 +CCAAACTGCTGAATGAAAAAGATGCTTTAACTCTCGTGAGATGATGCACACAACACAAGTGGTTTTACCAGATAGCTTTCTTCTTTGTTTTTATCCTGGGATATTTTGCTTTTTTTGCCCTTTGACCTCAATGAGCTCAAAAATGTTCATTCAAGAAATGGACAAAAACAATGTTTCTAAACTGGCTGAATCAAAAGGAATGGTTTCACTCTATGAGATGAATGCCACATATTCACAAAAGGGTTTCTCAGAAAGCTTCTTTCTACTTTTTATCCTGAAGGTATCTTACTTTTTTCCATAGGCCTCAATGTGCTTCCAAATATCCCCTTCGCAGATACTTATAAAAAACTGGTGTTTCCAAAACTATTGAATGAAAGAAAGTTTTAACTCCATGAGATGA HG:+:276286658:-1 HG:+:312544839:-1 HG:+:316771004:-1 HG:+:433053082:-1 HG:+:956110098:-1 HG:+:964625575:-1 HG:+:1155721357:-1 HG:+:1203981754:-1 HG:+:1295776935:-1 HG:+:1395411718:-1 HG:+:1551086237:-1 HG:+:1985484396:-1 HG:+:1985492486:-1 HG:+:1985581015:-1 HG:+:1985598632:25 HG:+:1993170933:-1 HG:+:2009635061:-1 HG:+:2725368491:-1 +TCATCTCATGGAGTTAAAACTTTCTTTCATTCAATAGTTTTGGAAACACCAGTTTTTTATAAGTATCTGCGAAGGGGATATTTGGAAGCACATTGAGGCCTATGGAAAAAAGTAAGATACCTTCAGGATAAAAAGTAGAAAGAAGCTTTCTGAGAAACCCTTTTGTGAATATGTGGCATTCATCTCATAGAGTGAAACCATTCCTTTTGATTCAGCCAGTTTAGAAACATTGTTTTTGTCCATTTCTTGAATGAACATTTTTGAGCTCATTGAGGTCAAAGGGCAAAAAAAGCAAAATATCCCAGGATAAAAACAAAGAAGAAAGCTATCTGGTAAAACCACTTGTGTTGTGTGCATCATCTCACGAGAGTTAAAGCATCTTTTTCATTCAGCAGTTTGG HG:+:927555189:-1 HG:+:927611876:-1 HG:+:927612561:-1 HG:+:927650170:-1 HG:+:1124477504:-1 HG:+:1124479375:-1 HG:+:1124484549:-1 HG:+:1124764713:-1 HG:+:1124766958:-1 HG:+:1124767817:-1 HG:+:1295954097:-1 HG:+:1295998907:-1 HG:+:1296103193:-1 HG:+:1866463238:-1 HG:+:1866506466:-1 HG:+:1870655807:-1 HG:+:1870666826:-1 HG:+:2683925538:-1 HG:+:2683957415:-1 HG:+:2683978592:-1 HG:+:2687425502:-1 HG:+:2687466727:-1 HG:+:2939464916:-1 +TCATCTCATGGAGTTAAAACTTTCTTTCATTCAATAGTTTTGGAAACACCAGTTTTTTATAAGTATCTGCGAAGGGGATATTTGGAAGCACATTGAGGCCTATGGAAAAAAGTAAGATACCTTCAGGATAAAAAGTAGAAAGAAGCTTTCTGAGAAACCCTTTTGTGAATATGTGGCATTCATCTCATAGAGTGAAACCATTCCTTTTGATTCAGCCAGTTTAGAAACATTGTTTTTGTCCATTTCTTGAATGAACATTTTTGAGCTCATTGAGGTCAAAGGGCAAAAAAAGCAAAATATCCCAGGATAAAAACAAAGAAGAAAGCTATCTGGTAAAACCACTTGTGTTGTGTGCATCATCTCACGAGAGTTAAAGCATCTTTTTCATTCAGCAGTTTGG HG:+:1295801910:-1 HG:+:1295876290:-1 HG:+:1295907552:-1 HG:+:1296003203:-1 HG:+:1296071270:-1 HG:+:1866240366:-1 HG:+:1867229764:-1 HG:+:1870771006:-1 HG:+:1989327105:-1 +TCATCTCATGGAGTTAAAACTTTCTTTCATTCAATAGTTTTGGAAACACCAGTTTTTTATAAGTATCTGCGAAGGGGATATTTGGAAGCACATTGAGGCCTATGGAAAAAAGTAAGATACCTTCAGGATAAAAAGTAGAAAGAAGCTTTCTGAGAAACCCTTTTGTGAATATGTGGCATTCATCTCATAGAGTGAAACCATTCCTTTTGATTCAGCCAGTTTAGAAACATTGTTTTTGTCCATTTCTTGAATGAACATTTTTGAGCTCATTGAGGTCAAAGGGCAAAAAAAGCAAAATATCCCAGGATAAAAACAAAGAAGAAAGCTATCTGGTAAAACCACTTGTGTTGTGTGCATCATCTCACGAGAGTTAAAGCATCTTTTTCATTCAGCAGTTTGG HG:+:1295529838:-1 HG:+:1866495846:-1 HG:+:2939225838:-1 +TCATCTCATGGAGTTAAAACTTTCTTTCATTCAATAGTTTTGGAAACACCAGTTTTTTATAAGTATCTGCGAAGGGGATATTTGGAAGCACATTGAGGCCTATGGAAAAAAGTAAGATACCTTCAGGATAAAAAGTAGAAAGAAGCTTTCTGAGAAACCCTTTTGTGAATATGTGGCATTCATCTCATAGAGTGAAACCATTCCTTTTGATTCAGCCAGTTTAGAAACATTGTTTTTGTCCATTTCTTGAATGAACATTTTTGAGCTCATTGAGGTCAAAGGGCAAAAAAAGCAAAATATCCCAGGATAAAAACAAAGAAGAAAGCTATCTGGTAAAACCACTTGTGTTGTGTGCATCATCTCACGAGAGTTAAAGCATCTTTTTCATTCAGCAGTTTGG HG:+:927535137:-1 HG:+:927578345:-1 HG:+:927810618:-1 HG:+:927845051:-1 HG:+:927848076:-1 HG:+:927856454:-1 HG:+:1121305355:-1 HG:+:1295810546:-1 HG:+:1295837892:-1 HG:+:1295861765:-1 HG:+:1295964392:-1 HG:+:1295965249:-1 HG:+:1296044060:-1 HG:+:1296077278:-1 HG:+:1296104781:-1 HG:+:1866293893:-1 HG:+:1866332961:-1 HG:+:1866390036:-1 HG:+:1866396730:-1 HG:+:1866473380:-1 HG:+:1867082289:-1 HG:+:1867235031:-1 HG:+:1870646302:-1 HG:+:1870778259:-1 HG:+:2442326165:-1 HG:+:2442412908:-1 HG:+:2939404868:-1 +TCATCTCATGGAGTTAAAACTTTCTTTCATTCAATAGTTTTGGAAACACCAGTTTTTTATAAGTATCTGCGAAGGGGATATTTGGAAGCACATTGAGGCCTATGGAAAAAAGTAAGATACCTTCAGGATAAAAAGTAGAAAGAAGCTTTCTGAGAAACCCTTTTGTGAATATGTGGCATTCATCTCATAGAGTGAAACCATTCCTTTTGATTCAGCCAGTTTAGAAACATTGTTTTTGTCCATTTCTTGAATGAACATTTTTGAGCTCATTGAGGTCAAAGGGCAAAAAAAGCAAAATATCCCAGGATAAAAACAAAGAAGAAAGCTATCTGGTAAAACCACTTGTGTTGTGTGCATCATCTCACGAGAGTTAAAGCATCTTTTTCATTCAGCAGTTTGG HG:+:1436311119:-1 +TCATCTCATGGAGTTAAAACTTTCTTTCATTCAATAGTTTTGGAAACACCAGTTTTTTATAAGTATCTGCGAAGGGGATATTTGGAAGCACATTGAGGCCTATGGAAAAAAGTAAGATACCTTCAGGATAAAAAGTAGAAAGAAGCTTTCTGAGAAACCCTTTTGTGAATATGTGGCATTCATCTCATAGAGTGAAACCATTCCTTTTGATTCAGCCAGTTTAGAAACATTGTTTTTGTCCATTTCTTGAATGAACATTTTTGAGCTCATTGAGGTCAAAGGGCAAAAAAAGCAAAATATCCCAGGATAAAAACAAAGAAGAAAGCTATCTGGTAAAACCACTTGTGTTGTGTGCATCATCTCACGAGAGTTAAAGCATCTTTTTCATTCAGCAGTTTGG HG:+:79392287:-1 HG:+:927817138:-1 HG:+:1436410129:-1 HG:+:1611077185:-1 HG:+:1960691491:-1 HG:+:1989312512:-1 HG:+:2442311366:-1 HG:+:2442370238:-1 +TTTTTGTGGTTACAATGTTAAGTCAAACTAAATAAGCAAATCTTCATGCCAGGGTCTTAGTTAATGTCATTTGGCTTGGCTGAGAAAAATCTGAAACTTCTCTGAGCAGACATATTTTAAGAGAAGCATTAGGACATGCATATTTTAGGATGCTAATAGAGCCTCTCACCCTTTTTGGTTTTTAGCTGCCAGAAAGTTATGAATTCATAGTTCTTGATAGCATAGAATAGAAAACATTGTAAAGGGGAAAGAAATTCTAACAGATTGCTCAGGAATGATTTCGGAGTGTCAGTTAAATCAAACATTTCTCTTTCATCCCTTTAGGAAAAGTGCACACTTCTGTTTTGAAAAATAAGATCTAGAAAAATTCTTTACTTTTTGCTTCGGAATGCCCATAATT HG:+:376142832:-1 HG:+:394761634:19 HG:+:727879228:-1 +TTTTTGTGGTTACAATGTTAAGTCAAACTAAATAAGCAAATCTTCATGCCAGGGTCTTAGTTAATGTCATTTGGCTTGGCTGAGAAAAATCTGAAACTTCTCTGAGCAGACATATTTTAAGAGAAGCATTAGGACATGCATATTTTAGGATGCTAATAGAGCCTCTCACCCTTTTTGGTTTTTAGCTGCCAGAAAGTTATGAATTCATAGTTCTTGATAGCATAGAATAGAAAACATTGTAAAGGGGAAAGAAATTCTAACAGATTGCTCAGGAATGATTTCGGAGTGTCAGTTAAATCAAACATTTCTCTTTCATCCCTTTAGGAAAAGTGCACACTTCTGTTTTGAAAAATAAGATCTAGAAAAATTCTTTACTTTTTGCTTCGGAATGCCCATAATT HG:+:240319765:-1 +TTTTTGTGGTTACAATGTTAAGTCAAACTAAATAAGCAAATCTTCATGCCAGGGTCTTAGTTAATGTCATTTGGCTTGGCTGAGAAAAATCTGAAACTTCTCTGAGCAGACATATTTTAAGAGAAGCATTAGGACATGCATATTTTAGGATGCTAATAGAGCCTCTCACCCTTTTTGGTTTTTAGCTGCCAGAAAGTTATGAATTCATAGTTCTTGATAGCATAGAATAGAAAACATTGTAAAGGGGAAAGAAATTCTAACAGATTGCTCAGGAATGATTTCGGAGTGTCAGTTAAATCAAACATTTCTCTTTCATCCCTTTAGGAAAAGTGCACACTTCTGTTTTGAAAAATAAGATCTAGAAAAATTCTTTACTTTTTGCTTCGGAATGCCCATAATT HG:+:394761632:19 +TTTTTGTGGTTACAATGTTAAGTCAAACTAAATAAGCAAATCTTCATGCCAGGGTCTTAGTTAATGTCATTTGGCTTGGCTGAGAAAAATCTGAAACTTCTCTGAGCAGACATATTTTAAGAGAAGCATTAGGACATGCATATTTTAGGATGCTAATAGAGCCTCTCACCCTTTTTGGTTTTTAGCTGCCAGAAAGTTATGAATTCATAGTTCTTGATAGCATAGAATAGAAAACATTGTAAAGGGGAAAGAAATTCTAACAGATTGCTCAGGAATGATTTCGGAGTGTCAGTTAAATCAAACATTTCTCTTTCATCCCTTTAGGAAAAGTGCACACTTCTGTTTTGAAAAATAAGATCTAGAAAAATTCTTTACTTTTTGCTTCGGAATGCCCATAATT HG:+:394761633:19 +TTTTTGTGGTTACAATGTTAAGTCAAACTAAATAAGCAAATCTTCATGCCAGGGTCTTAGTTAATGTCATTTGGCTTGGCTGAGAAAAATCTGAAACTTCTCTGAGCAGACATATTTTAAGAGAAGCATTAGGACATGCATATTTTAGGATGCTAATAGAGCCTCTCACCCTTTTTGGTTTTTAGCTGCCAGAAAGTTATGAATTCATAGTTCTTGATAGCATAGAATAGAAAACATTGTAAAGGGGAAAGAAATTCTAACAGATTGCTCAGGAATGATTTCGGAGTGTCAGTTAAATCAAACATTTCTCTTTCATCCCTTTAGGAAAAGTGCACACTTCTGTTTTGAAAAATAAGATCTAGAAAAATTCTTTACTTTTTGCTTCGGAATGCCCATAATT HG:+:394761637:19 +TTTTTGTGGTTACAATGTTAAGTCAAACTAAATAAGCAAATCTTCATGCCAGGGTCTTAGTTAATGTCATTTGGCTTGGCTGAGAAAAATCTGAAACTTCTCTGAGCAGACATATTTTAAGAGAAGCATTAGGACATGCATATTTTAGGATGCTAATAGAGCCTCTCACCCTTTTTGGTTTTTAGCTGCCAGAAAGTTATGAATTCATAGTTCTTGATAGCATAGAATAGAAAACATTGTAAAGGGGAAAGAAATTCTAACAGATTGCTCAGGAATGATTTCGGAGTGTCAGTTAAATCAAACATTTCTCTTTCATCCCTTTAGGAAAAGTGCACACTTCTGTTTTGAAAAATAAGATCTAGAAAAATTCTTTACTTTTTGCTTCGGAATGCCCATAATT HG:+:394761638:19 +TTTTTGTGGTTACAATGTTAAGTCAAACTAAATAAGCAAATCTTCATGCCAGGGTCTTAGTTAATGTCATTTGGCTTGGCTGAGAAAAATCTGAAACTTCTCTGAGCAGACATATTTTAAGAGAAGCATTAGGACATGCATATTTTAGGATGCTAATAGAGCCTCTCACCCTTTTTGGTTTTTAGCTGCCAGAAAGTTATGAATTCATAGTTCTTGATAGCATAGAATAGAAAACATTGTAAAGGGGAAAGAAATTCTAACAGATTGCTCAGGAATGATTTCGGAGTGTCAGTTAAATCAAACATTTCTCTTTCATCCCTTTAGGAAAAGTGCACACTTCTGTTTTGAAAAATAAGATCTAGAAAAATTCTTTACTTTTTGCTTCGGAATGCCCATAATT HG:+:394761639:19 +AATTATGGGCATTCCGAAGCAAAAAGTAAAGAATTTTTCTAGATCTTATTTTTCAAAACAGAAGTGTGCACTTTTCCTAAAGGGATGAAAGAGAAATGTTTGATTTAACTGACACTCCGAAATCATTCCTGAGCAATCTGTTAGAATTTCTTTCCCCTTTACAATGTTTTCTATTCTATGCTATCAAGAACTATGAATTCATAACTTTCTGGCAGCTAAAAACCAAAAAGGGTGAGAGGCTCTATTAGCATCCTAAAATATGCATGTCCTAATGCTTCTCTTAAAATATGTCTGCTCAGAGAAGTTTCAGATTTTTCTCAGCCAAGCCAAATGACATTAACTAAGACCCTGGCATGAAGATTTGCTTATTTAGTTTGACTTAACATTGTAACCACAAAAA HG:+:594197239:-1 +AATTATGGGCATTCCGAAGCAAAAAGTAAAGAATTTTTCTAGATCTTATTTTTCAAAACAGAAGTGTGCACTTTTCCTAAAGGGATGAAAGAGAAATGTTTGATTTAACTGACACTCCGAAATCATTCCTGAGCAATCTGTTAGAATTTCTTTCCCCTTTACAATGTTTTCTATTCTATGCTATCAAGAACTATGAATTCATAACTTTCTGGCAGCTAAAAACCAAAAAGGGTGAGAGGCTCTATTAGCATCCTAAAATATGCATGTCCTAATGCTTCTCTTAAAATATGTCTGCTCAGAGAAGTTTCAGATTTTTCTCAGCCAAGCCAAATGACATTAACTAAGACCCTGGCATGAAGATTTGCTTATTTAGTTTGACTTAACATTGTAACCACAAAAA HG:+:765260969:-1 +AAAACTGTAGGTTTTTTTCTCAAGATTTAAGAATGTTCTAGCTCCTCCCACAATGAAAAACTTAGCTTAGATCCACTCCTGTCAAGAAGCTGCAGAGTTCCTTCCTTCCATCCCTCCCTCGCTGGGTTAGGTGAGCCTCTGAGGTGCTCTCATGGATTGCTGTGCATATCGCTTTGCTGCTCTTAATGCATCCCTGGAGTGAAATATTATCTCATTACTTGTTTGTTCTCTGTGCTAAGCTATAGCTTCTGGAGGACAAAGACAGTGTCTGACAGGTTTTTCTGTGCTTGATGTAAGTAGTTGGTGCTGAATAAATGCTGGTTGAATAGAAGGATGAATGAATGAGTCACAAAGAAGCTAGTGACCATAATCCCCTTGACTGTTGGAGAATGGTCAGTGC HG:+:59457122:-1 HG:+:217146782:-1 HG:+:345090826:15 HG:+:502721484:-1 HG:+:1002885592:-1 HG:+:1170122033:-1 HG:+:1301541732:-1 HG:+:2032058373:-1 HG:+:2391964713:-1 HG:+:2465675788:-1 HG:+:2489316607:-1 +AAAACTGTAGGTTTTTTTCTCAAGATTTAAGAATGTTCTAGCTCCTCCCACAATGAAAAACTTAGCTTAGATCCACTCCTGTCAAGAAGCTGCAGAGTTCCTTCCTTCCATCCCTCCCTCGCTGGGTTAGGTGAGCCTCTGAGGTGCTCTCATGGATTGCTGTGCATATCGCTTTGCTGCTCTTAATGCATCCCTGGAGTGAAATATTATCTCATTACTTGTTTGTTCTCTGTGCTAAGCTATAGCTTCTGGAGGACAAAGACAGTGTCTGACAGGTTTTTCTGTGCTTGATGTAAGTAGTTGGTGCTGAATAAATGCTGGTTGAATAGAAGGATGAATGAATGAGTCACAAAGAAGCTAGTGACCATAATCCCCTTGACTGTTGGAGAATGGTCAGTGC HG:+:345090827:15 +AAAACTGTAGGTTTTTTTCTCAAGATTTAAGAATGTTCTAGCTCCTCCCACAATGAAAAACTTAGCTTAGATCCACTCCTGTCAAGAAGCTGCAGAGTTCCTTCCTTCCATCCCTCCCTCGCTGGGTTAGGTGAGCCTCTGAGGTGCTCTCATGGATTGCTGTGCATATCGCTTTGCTGCTCTTAATGCATCCCTGGAGTGAAATATTATCTCATTACTTGTTTGTTCTCTGTGCTAAGCTATAGCTTCTGGAGGACAAAGACAGTGTCTGACAGGTTTTTCTGTGCTTGATGTAAGTAGTTGGTGCTGAATAAATGCTGGTTGAATAGAAGGATGAATGAATGAGTCACAAAGAAGCTAGTGACCATAATCCCCTTGACTGTTGGAGAATGGTCAGTGC HG:+:1135855062:-1 +AAAACTGTAGGTTTTTTTCTCAAGATTTAAGAATGTTCTAGCTCCTCCCACAATGAAAAACTTAGCTTAGATCCACTCCTGTCAAGAAGCTGCAGAGTTCCTTCCTTCCATCCCTCCCTCGCTGGGTTAGGTGAGCCTCTGAGGTGCTCTCATGGATTGCTGTGCATATCGCTTTGCTGCTCTTAATGCATCCCTGGAGTGAAATATTATCTCATTACTTGTTTGTTCTCTGTGCTAAGCTATAGCTTCTGGAGGACAAAGACAGTGTCTGACAGGTTTTTCTGTGCTTGATGTAAGTAGTTGGTGCTGAATAAATGCTGGTTGAATAGAAGGATGAATGAATGAGTCACAAAGAAGCTAGTGACCATAATCCCCTTGACTGTTGGAGAATGGTCAGTGC HG:+:345090823:15 HG:+:632640843:-1 +AAAACTGTAGGTTTTTTTCTCAAGATTTAAGAATGTTCTAGCTCCTCCCACAATGAAAAACTTAGCTTAGATCCACTCCTGTCAAGAAGCTGCAGAGTTCCTTCCTTCCATCCCTCCCTCGCTGGGTTAGGTGAGCCTCTGAGGTGCTCTCATGGATTGCTGTGCATATCGCTTTGCTGCTCTTAATGCATCCCTGGAGTGAAATATTATCTCATTACTTGTTTGTTCTCTGTGCTAAGCTATAGCTTCTGGAGGACAAAGACAGTGTCTGACAGGTTTTTCTGTGCTTGATGTAAGTAGTTGGTGCTGAATAAATGCTGGTTGAATAGAAGGATGAATGAATGAGTCACAAAGAAGCTAGTGACCATAATCCCCTTGACTGTTGGAGAATGGTCAGTGC HG:+:500155556:-1 +TGAATGTTGGCCTGGTCTTTTCTCTGTTGGGGAAGTTACTCCTGGATGAGTATACTTAAGTATGTTTTGCAACCTTGGTTCCATTCTCCCCATCTCTTTCAGGTACCCTAAGTGAGTCTTAGGTTCTGTCTTTTTAAATAATTTCATATTTTTTGGAGGTTTTGTCAATGCCTTTCATCTTTTTTTTTTTTCTTTCTGTTCTTGTATGCCTGTCTTACGTCAGAAAGACAGTCTTCAAGCTCTGAGATTCTTTTCTCTGCTTGTCTAGTTCTCATGTTGTGTTTTCAGCTCCACTCAGGTTGGTTATATTCCTCTCTAAACTGGCTATCTGGCTATCAGCTCCTGTATTGTTTTTATCATGAGTCTTAGCTTCTTTGCCATTGGGGTTACCACATGCTCC HG:+:1497457308:18 HG:+:2914602082:-1 HG:+:2953975681:-1 +TGAATGTTGGCCTGGTCTTTTCTCTGTTGGGGAAGTTACTCCTGGATGAGTATACTTAAGTATGTTTTGCAACCTTGGTTCCATTCTCCCCATCTCTTTCAGGTACCCTAAGTGAGTCTTAGGTTCTGTCTTTTTAAATAATTTCATATTTTTTGGAGGTTTTGTCAATGCCTTTCATCTTTTTTTTTTTTCTTTCTGTTCTTGTATGCCTGTCTTACGTCAGAAAGACAGTCTTCAAGCTCTGAGATTCTTTTCTCTGCTTGTCTAGTTCTCATGTTGTGTTTTCAGCTCCACTCAGGTTGGTTATATTCCTCTCTAAACTGGCTATCTGGCTATCAGCTCCTGTATTGTTTTTATCATGAGTCTTAGCTTCTTTGCCATTGGGGTTACCACATGCTCC HG:+:1617082060:-1 HG:+:1999922283:-1 +TGAATGTTGGCCTGGTCTTTTCTCTGTTGGGGAAGTTACTCCTGGATGAGTATACTTAAGTATGTTTTGCAACCTTGGTTCCATTCTCCCCATCTCTTTCAGGTACCCTAAGTGAGTCTTAGGTTCTGTCTTTTTAAATAATTTCATATTTTTTGGAGGTTTTGTCAATGCCTTTCATCTTTTTTTTTTTTCTTTCTGTTCTTGTATGCCTGTCTTACGTCAGAAAGACAGTCTTCAAGCTCTGAGATTCTTTTCTCTGCTTGTCTAGTTCTCATGTTGTGTTTTCAGCTCCACTCAGGTTGGTTATATTCCTCTCTAAACTGGCTATCTGGCTATCAGCTCCTGTATTGTTTTTATCATGAGTCTTAGCTTCTTTGCCATTGGGGTTACCACATGCTCC HG:+:1497457306:18 +TGAATGTTGGCCTGGTCTTTTCTCTGTTGGGGAAGTTACTCCTGGATGAGTATACTTAAGTATGTTTTGCAACCTTGGTTCCATTCTCCCCATCTCTTTCAGGTACCCTAAGTGAGTCTTAGGTTCTGTCTTTTTAAATAATTTCATATTTTTTGGAGGTTTTGTCAATGCCTTTCATCTTTTTTTTTTTTCTTTCTGTTCTTGTATGCCTGTCTTACGTCAGAAAGACAGTCTTCAAGCTCTGAGATTCTTTTCTCTGCTTGTCTAGTTCTCATGTTGTGTTTTCAGCTCCACTCAGGTTGGTTATATTCCTCTCTAAACTGGCTATCTGGCTATCAGCTCCTGTATTGTTTTTATCATGAGTCTTAGCTTCTTTGCCATTGGGGTTACCACATGCTCC HG:+:1497457311:18 +GGAGCATGTGGTAACCCCAATGGCAAAGAAGCTAAGACTCATGATAAAAACAATACAGGAGCTGATAGCCAGATAGCCAGTTTAGAGAGGAATATAACCAACCTGAGTGGAGCTGAAAACACAACATGAGAACTAGACAAGCAGAGAAAAGAATCTCAGAGCTTGAAGACTGTCTTTCTGACGTAAGACAGGCATACAAGAACAGAAAGAAAAAAAAAAAAGATGAAAGGCATTGACAAAACCTCCAAAAAATATGAAATTATTTAAAAAGACAGAACCTAAGACTCACTTAGGGTACCTGAAAGAGATGGGGAGAATGGAACCAAGGTTGCAAAACATACTTAAGTATACTCATCCAGGAGTAACTTCCCCAACAGAGAAAAGACCAGGCCAACATTCA HG:+:816050939:-1 +GGAGCATGTGGTAACCCCAATGGCAAAGAAGCTAAGACTCATGATAAAAACAATACAGGAGCTGATAGCCAGATAGCCAGTTTAGAGAGGAATATAACCAACCTGAGTGGAGCTGAAAACACAACATGAGAACTAGACAAGCAGAGAAAAGAATCTCAGAGCTTGAAGACTGTCTTTCTGACGTAAGACAGGCATACAAGAACAGAAAGAAAAAAAAAAAAGATGAAAGGCATTGACAAAACCTCCAAAAAATATGAAATTATTTAAAAAGACAGAACCTAAGACTCACTTAGGGTACCTGAAAGAGATGGGGAGAATGGAACCAAGGTTGCAAAACATACTTAAGTATACTCATCCAGGAGTAACTTCCCCAACAGAGAAAAGACCAGGCCAACATTCA HG:+:101113821:-1 HG:+:813688358:-1 HG:+:897824375:-1 HG:+:1009514958:-1 HG:+:1064521402:-1 HG:+:1112316329:-1 HG:+:1352726362:-1 HG:+:1453709915:-1 HG:+:1473551378:-1 HG:+:1791727642:-1 HG:+:1808650582:-1 HG:+:1827815693:-1 HG:+:1905323844:-1 HG:+:1919198417:-1 HG:+:2024575540:-1 HG:+:2244179092:-1 HG:+:2267065536:-1 HG:+:2538898096:-1 HG:+:2605068647:-1 HG:+:2936939179:-1 +GGAGCATGTGGTAACCCCAATGGCAAAGAAGCTAAGACTCATGATAAAAACAATACAGGAGCTGATAGCCAGATAGCCAGTTTAGAGAGGAATATAACCAACCTGAGTGGAGCTGAAAACACAACATGAGAACTAGACAAGCAGAGAAAAGAATCTCAGAGCTTGAAGACTGTCTTTCTGACGTAAGACAGGCATACAAGAACAGAAAGAAAAAAAAAAAAGATGAAAGGCATTGACAAAACCTCCAAAAAATATGAAATTATTTAAAAAGACAGAACCTAAGACTCACTTAGGGTACCTGAAAGAGATGGGGAGAATGGAACCAAGGTTGCAAAACATACTTAAGTATACTCATCCAGGAGTAACTTCCCCAACAGAGAAAAGACCAGGCCAACATTCA HG:+:302746221:-1 HG:+:367039028:-1 HG:+:494086454:-1 HG:+:531854511:-1 HG:+:591098661:-1 HG:+:602837374:-1 HG:+:1462923095:-1 HG:+:1972251100:-1 HG:+:2016082140:-1 HG:+:2033120989:-1 HG:+:2260137296:-1 HG:+:2513744288:-1 HG:+:3006491353:-1 +GGAGCATGTGGTAACCCCAATGGCAAAGAAGCTAAGACTCATGATAAAAACAATACAGGAGCTGATAGCCAGATAGCCAGTTTAGAGAGGAATATAACCAACCTGAGTGGAGCTGAAAACACAACATGAGAACTAGACAAGCAGAGAAAAGAATCTCAGAGCTTGAAGACTGTCTTTCTGACGTAAGACAGGCATACAAGAACAGAAAGAAAAAAAAAAAAGATGAAAGGCATTGACAAAACCTCCAAAAAATATGAAATTATTTAAAAAGACAGAACCTAAGACTCACTTAGGGTACCTGAAAGAGATGGGGAGAATGGAACCAAGGTTGCAAAACATACTTAAGTATACTCATCCAGGAGTAACTTCCCCAACAGAGAAAAGACCAGGCCAACATTCA HG:+:48796875:-1 HG:+:119332508:-1 HG:+:612483536:-1 HG:+:723384691:-1 HG:+:969510185:-1 HG:+:1148239773:-1 HG:+:1664652669:-1 HG:+:1749537088:-1 HG:+:1916163745:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCTATACCTAGGCATATATGCAAAGGAATTGTAGCAAATGTATATGAAAGAATGCTCATAGTAGCATTATTCACTATAGTTCATAAAAGAAGCTGTCCAAGTATATATCAACTAAGGATTAGATAATTATAGTAAATTCATAAAATTAAACAATATACGAGAAATGAAAAGAAATAAATTCACATGTACATGCATCGTGTCTT HG:+:334678846:-1 HG:+:655286809:-1 HG:+:701639697:-1 HG:+:761115307:-1 HG:+:1187528000:-1 HG:+:1303939640:-1 HG:+:1813335468:-1 HG:+:1841953618:-1 HG:+:1965452940:-1 HG:+:2644594648:-1 HG:+:2650595432:-1 HG:+:2906537789:-1 HG:+:3008146548:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCTATACCTAGGCATATATGCAAAGGAATTGTAGCAAATGTATATGAAAGAATGCTCATAGTAGCATTATTCACTATAGTTCATAAAAGAAGCTGTCCAAGTATATATCAACTAAGGATTAGATAATTATAGTAAATTCATAAAATTAAACAATATACGAGAAATGAAAAGAAATAAATTCACATGTACATGCATCGTGTCTT HG:+:191011700:-1 HG:+:272198396:-1 HG:+:424675409:-1 HG:+:912422369:-1 HG:+:1008935464:-1 HG:+:1063655574:-1 HG:+:1399011442:-1 HG:+:2586152087:-1 HG:+:2993370895:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCTATACCTAGGCATATATGCAAAGGAATTGTAGCAAATGTATATGAAAGAATGCTCATAGTAGCATTATTCACTATAGTTCATAAAAGAAGCTGTCCAAGTATATATCAACTAAGGATTAGATAATTATAGTAAATTCATAAAATTAAACAATATACGAGAAATGAAAAGAAATAAATTCACATGTACATGCATCGTGTCTT HG:+:543773200:-1 HG:+:595163476:-1 HG:+:1004803212:-1 HG:+:1082825177:-1 HG:+:1251354282:-1 HG:+:1274799598:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCTATACCTAGGCATATATGCAAAGGAATTGTAGCAAATGTATATGAAAGAATGCTCATAGTAGCATTATTCACTATAGTTCATAAAAGAAGCTGTCCAAGTATATATCAACTAAGGATTAGATAATTATAGTAAATTCATAAAATTAAACAATATACGAGAAATGAAAAGAAATAAATTCACATGTACATGCATCGTGTCTT HG:+:607453128:-1 HG:+:1193709728:-1 HG:+:2637011097:-1 HG:+:2769652997:-1 HG:+:2914081314:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCTATACCTAGGCATATATGCAAAGGAATTGTAGCAAATGTATATGAAAGAATGCTCATAGTAGCATTATTCACTATAGTTCATAAAAGAAGCTGTCCAAGTATATATCAACTAAGGATTAGATAATTATAGTAAATTCATAAAATTAAACAATATACGAGAAATGAAAAGAAATAAATTCACATGTACATGCATCGTGTCTT HG:+:292856244:-1 HG:+:569418529:-1 HG:+:2181241911:-1 HG:+:2226201855:-1 HG:+:2697962765:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCTATACCTAGGCATATATGCAAAGGAATTGTAGCAAATGTATATGAAAGAATGCTCATAGTAGCATTATTCACTATAGTTCATAAAAGAAGCTGTCCAAGTATATATCAACTAAGGATTAGATAATTATAGTAAATTCATAAAATTAAACAATATACGAGAAATGAAAAGAAATAAATTCACATGTACATGCATCGTGTCTT HG:+:191291664:-1 HG:+:222955215:-1 HG:+:226165738:-1 HG:+:231694083:-1 HG:+:247955022:-1 HG:+:321387223:-1 HG:+:406029434:-1 HG:+:436783927:-1 HG:+:591383270:-1 HG:+:773388856:-1 HG:+:800315830:-1 HG:+:865518289:-1 HG:+:975060342:-1 HG:+:978899210:-1 HG:+:983629426:-1 HG:+:1021022350:-1 HG:+:1156508974:-1 HG:+:1195958267:-1 HG:+:1216643432:-1 HG:+:1244088821:-1 HG:+:1498716500:-1 HG:+:1786282059:-1 HG:+:1852898109:-1 HG:+:1854500494:-1 HG:+:1922726617:-1 HG:+:1999903037:-1 HG:+:2190286892:-1 HG:+:2230017198:-1 HG:+:2237085077:-1 HG:+:2247698686:-1 HG:+:2255244558:-1 HG:+:2344055047:-1 HG:+:2425338875:-1 HG:+:2486327000:-1 HG:+:2754397217:-1 HG:+:2805310514:-1 HG:+:3018142981:-1 HG:+:3053354221:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCTATACCTAGGCATATATGCAAAGGAATTGTAGCAAATGTATATGAAAGAATGCTCATAGTAGCATTATTCACTATAGTTCATAAAAGAAGCTGTCCAAGTATATATCAACTAAGGATTAGATAATTATAGTAAATTCATAAAATTAAACAATATACGAGAAATGAAAAGAAATAAATTCACATGTACATGCATCGTGTCTT HG:+:435068064:-1 HG:+:461419184:-1 HG:+:600734686:-1 HG:+:710273725:-1 HG:+:863511531:-1 HG:+:917409920:-1 HG:+:970899996:-1 HG:+:1181714331:-1 HG:+:1207328424:-1 HG:+:1409671348:-1 HG:+:1481440607:-1 HG:+:1526682930:-1 HG:+:1556194260:-1 HG:+:1803301056:-1 HG:+:2559840693:-1 HG:+:2619624961:-1 HG:+:2620014613:-1 HG:+:3064140711:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCTATACCTAGGCATATATGCAAAGGAATTGTAGCAAATGTATATGAAAGAATGCTCATAGTAGCATTATTCACTATAGTTCATAAAAGAAGCTGTCCAAGTATATATCAACTAAGGATTAGATAATTATAGTAAATTCATAAAATTAAACAATATACGAGAAATGAAAAGAAATAAATTCACATGTACATGCATCGTGTCTT HG:+:20166723:-1 HG:+:182840386:-1 HG:+:242425002:-1 HG:+:245199517:-1 HG:+:245833553:-1 HG:+:260249842:-1 HG:+:292788999:-1 HG:+:335831253:-1 HG:+:351239914:-1 HG:+:453838958:-1 HG:+:482066553:-1 HG:+:551508335:-1 HG:+:611331164:-1 HG:+:614944333:-1 HG:+:702316986:-1 HG:+:706086622:-1 HG:+:773788619:-1 HG:+:806356359:-1 HG:+:856747374:-1 HG:+:869706788:-1 HG:+:869902346:-1 HG:+:891020318:-1 HG:+:891958624:-1 HG:+:968731591:-1 HG:+:1013574132:-1 HG:+:1043817458:-1 HG:+:1090571906:-1 HG:+:1101478244:-1 HG:+:1177022088:-1 HG:+:1211591410:-1 HG:+:1251581370:-1 HG:+:1332340936:-1 HG:+:1341456303:-1 HG:+:1423635693:-1 HG:+:1465320677:-1 HG:+:1507146026:-1 HG:+:1626641063:-1 HG:+:1654170482:-1 HG:+:1654460911:-1 HG:+:1666542063:-1 HG:+:1704606928:-1 HG:+:1755353045:-1 HG:+:1877683435:-1 HG:+:1887463003:-1 HG:+:1955642959:-1 HG:+:1981023613:-1 HG:+:2001035785:-1 HG:+:2171177799:-1 HG:+:2262054168:-1 HG:+:2348790230:-1 HG:+:2366555788:-1 HG:+:2385012666:-1 HG:+:2543617901:-1 HG:+:2546924376:-1 HG:+:2582218307:-1 HG:+:2629140625:-1 HG:+:2666910660:-1 HG:+:2711658838:-1 HG:+:2798449103:-1 HG:+:2859658421:-1 HG:+:2860177953:-1 HG:+:2888182047:-1 HG:+:2901438903:-1 HG:+:2905469989:-1 HG:+:2917055532:-1 HG:+:2994103968:-1 HG:+:2996396876:-1 HG:+:3032268980:-1 HG:+:3032295119:-1 HG:+:3043188482:-1 HG:+:3064836182:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCTATACCTAGGCATATATGCAAAGGAATTGTAGCAAATGTATATGAAAGAATGCTCATAGTAGCATTATTCACTATAGTTCATAAAAGAAGCTGTCCAAGTATATATCAACTAAGGATTAGATAATTATAGTAAATTCATAAAATTAAACAATATACGAGAAATGAAAAGAAATAAATTCACATGTACATGCATCGTGTCTT HG:+:185095339:-1 HG:+:463979236:-1 HG:+:484326337:-1 HG:+:500218868:-1 HG:+:596622688:-1 HG:+:619601337:-1 HG:+:746774863:-1 HG:+:974091326:-1 HG:+:1196176630:-1 HG:+:1214161819:-1 HG:+:1244489212:-1 HG:+:1325508306:-1 HG:+:1523915845:-1 HG:+:1612229790:-1 HG:+:1794801258:-1 HG:+:2173821112:-1 HG:+:2180040773:-1 HG:+:2240743397:-1 HG:+:2246626799:-1 +ACACTAATTATAAGTGAATGTTTTACCATCTAAAATAATAGTATCTTCTTGTTGGACTAAAGGTGTAATTCGATAACGATATATGCAAATAGTAATAAAGAGACTGGGAGTTACAGAAATAAATTAGTTAAAAGTATTTTTTGGACTTTTCTATGTCTGTGGGCAGAATTTGTACATCTTAATCAGGACCCTATAATTCTATACCTAGGCATATATGCAAAGGAATTGTAGCAAATGTATATGAAAGAATGCTCATAGTAGCATTATTCACTATAGTTCATAAAAGAAGCTGTCCAAGTATATATCAACTAAGGATTAGATAATTATAGTAAATTCATAAAATTAAACAATATACGAGAAATGAAAAGAAATAAATTCACATGTACATGCATCGTGTCTT HG:+:11345907:-1 HG:+:90544160:-1 HG:+:183643484:-1 HG:+:800074452:-1 HG:+:1189565959:-1 HG:+:1266981231:-1 HG:+:1561689837:-1 HG:+:1626890177:-1 HG:+:2124559148:-1 HG:+:2136225510:-1 HG:+:2146301806:-1 HG:+:2360467571:-1 HG:+:2379133840:-1 HG:+:2525845330:-1 HG:+:2609636137:-1 HG:+:2647327188:-1 +AAGACACGATGCATGTACATGTGAATTTATTTCTTTTCATTTCTCGTATATTGTTTAATTTTATGAATTTACTATAATTATCTAATCCTTAGTTGATATATACTTGGACAGCTTCTTTTATGAACTATAGTGAATAATGCTACTATGAGCATTCTTTCATATACATTTGCTACAATTCCTTTGCATATATGCCTAGGTATAGAATTATAGGGTCCTGATTAAGATGTACAAATTCTGCCCACAGACATAGAAAAGTCCAAAAAATACTTTTAACTAATTTATTTCTGTAACTCCCAGTCTCTTTATTACTATTTGCATATATCGTTATCGAATTACACCTTTAGTCCAACAAGAAGATACTATTATTTTAGATGGTAAAACATTCACTTATAATTAGTGT HG:+:41017523:-1 HG:+:151501353:-1 HG:+:220770282:-1 HG:+:221416174:-1 HG:+:358390214:-1 HG:+:379563128:-1 HG:+:392229986:-1 HG:+:395326575:-1 HG:+:507006570:-1 HG:+:586289343:-1 HG:+:776092867:-1 HG:+:852117679:-1 HG:+:961413160:-1 HG:+:1374180216:-1 HG:+:1401277651:-1 HG:+:1664000803:-1 HG:+:1778255366:-1 HG:+:1818414892:-1 HG:+:1994395959:-1 HG:+:2020588284:-1 HG:+:2112335958:-1 HG:+:2135207453:-1 HG:+:2139576109:-1 HG:+:2433643669:-1 HG:+:2756003596:-1 HG:+:2958109819:-1 +AAGACACGATGCATGTACATGTGAATTTATTTCTTTTCATTTCTCGTATATTGTTTAATTTTATGAATTTACTATAATTATCTAATCCTTAGTTGATATATACTTGGACAGCTTCTTTTATGAACTATAGTGAATAATGCTACTATGAGCATTCTTTCATATACATTTGCTACAATTCCTTTGCATATATGCCTAGGTATAGAATTATAGGGTCCTGATTAAGATGTACAAATTCTGCCCACAGACATAGAAAAGTCCAAAAAATACTTTTAACTAATTTATTTCTGTAACTCCCAGTCTCTTTATTACTATTTGCATATATCGTTATCGAATTACACCTTTAGTCCAACAAGAAGATACTATTATTTTAGATGGTAAAACATTCACTTATAATTAGTGT HG:+:1962075604:15 HG:+:2006731653:-1 HG:+:2590690229:-1 HG:+:3001720117:-1 +AAGACACGATGCATGTACATGTGAATTTATTTCTTTTCATTTCTCGTATATTGTTTAATTTTATGAATTTACTATAATTATCTAATCCTTAGTTGATATATACTTGGACAGCTTCTTTTATGAACTATAGTGAATAATGCTACTATGAGCATTCTTTCATATACATTTGCTACAATTCCTTTGCATATATGCCTAGGTATAGAATTATAGGGTCCTGATTAAGATGTACAAATTCTGCCCACAGACATAGAAAAGTCCAAAAAATACTTTTAACTAATTTATTTCTGTAACTCCCAGTCTCTTTATTACTATTTGCATATATCGTTATCGAATTACACCTTTAGTCCAACAAGAAGATACTATTATTTTAGATGGTAAAACATTCACTTATAATTAGTGT HG:+:1962075606:15 +AAGACACGATGCATGTACATGTGAATTTATTTCTTTTCATTTCTCGTATATTGTTTAATTTTATGAATTTACTATAATTATCTAATCCTTAGTTGATATATACTTGGACAGCTTCTTTTATGAACTATAGTGAATAATGCTACTATGAGCATTCTTTCATATACATTTGCTACAATTCCTTTGCATATATGCCTAGGTATAGAATTATAGGGTCCTGATTAAGATGTACAAATTCTGCCCACAGACATAGAAAAGTCCAAAAAATACTTTTAACTAATTTATTTCTGTAACTCCCAGTCTCTTTATTACTATTTGCATATATCGTTATCGAATTACACCTTTAGTCCAACAAGAAGATACTATTATTTTAGATGGTAAAACATTCACTTATAATTAGTGT HG:+:1962075607:15 +AAGACACGATGCATGTACATGTGAATTTATTTCTTTTCATTTCTCGTATATTGTTTAATTTTATGAATTTACTATAATTATCTAATCCTTAGTTGATATATACTTGGACAGCTTCTTTTATGAACTATAGTGAATAATGCTACTATGAGCATTCTTTCATATACATTTGCTACAATTCCTTTGCATATATGCCTAGGTATAGAATTATAGGGTCCTGATTAAGATGTACAAATTCTGCCCACAGACATAGAAAAGTCCAAAAAATACTTTTAACTAATTTATTTCTGTAACTCCCAGTCTCTTTATTACTATTTGCATATATCGTTATCGAATTACACCTTTAGTCCAACAAGAAGATACTATTATTTTAGATGGTAAAACATTCACTTATAATTAGTGT HG:+:449353892:-1 +ATTAGTAATTTATTACCTATCATTCAAGCCTGCCCTGGACTGAAATGCAATCCCTGGCCCACTTTTTGTTCTTCTCAGGGTATTCCGGCCCAGTTCCTATGTATGCTCGACCAGACACGCCCACAAGGCTTCATTGGCCCTTTCAGTGCAGGGGCCTTGGCTGTGGCATCTACAAGGGCATTTCCTTTTACACTAGGTCAGTCTCTCTTTTGATTGTCCTCTGCAATTAATTATAGTCACTTTTTTGGCAGCAAAAGCAGCATCTAACAAACGCTCAAAATCTGAATGATGTATGGAAAAGCCCTTTGGGGTCAGGAGTCCCCACCCATTCAAATTGCAGCATAAGCATGAAAGCACTAAAAAAATCATACTTGGAATCAAGTGTAAATGTTAACTTTTA HG:+:227683856:67 HG:+:881379447:43 HG:+:1680469329:34 HG:+:1985235299:50 HG:+:2047622902:-1 HG:+:2581417633:25 +ATTAGTAATTTATTACCTATCATTCAAGCCTGCCCTGGACTGAAATGCAATCCCTGGCCCACTTTTTGTTCTTCTCAGGGTATTCCGGCCCAGTTCCTATGTATGCTCGACCAGACACGCCCACAAGGCTTCATTGGCCCTTTCAGTGCAGGGGCCTTGGCTGTGGCATCTACAAGGGCATTTCCTTTTACACTAGGTCAGTCTCTCTTTTGATTGTCCTCTGCAATTAATTATAGTCACTTTTTTGGCAGCAAAAGCAGCATCTAACAAACGCTCAAAATCTGAATGATGTATGGAAAAGCCCTTTGGGGTCAGGAGTCCCCACCCATTCAAATTGCAGCATAAGCATGAAAGCACTAAAAAAATCATACTTGGAATCAAGTGTAAATGTTAACTTTTA HG:+:2581417635:25 +ATTAGTAATTTATTACCTATCATTCAAGCCTGCCCTGGACTGAAATGCAATCCCTGGCCCACTTTTTGTTCTTCTCAGGGTATTCCGGCCCAGTTCCTATGTATGCTCGACCAGACACGCCCACAAGGCTTCATTGGCCCTTTCAGTGCAGGGGCCTTGGCTGTGGCATCTACAAGGGCATTTCCTTTTACACTAGGTCAGTCTCTCTTTTGATTGTCCTCTGCAATTAATTATAGTCACTTTTTTGGCAGCAAAAGCAGCATCTAACAAACGCTCAAAATCTGAATGATGTATGGAAAAGCCCTTTGGGGTCAGGAGTCCCCACCCATTCAAATTGCAGCATAAGCATGAAAGCACTAAAAAAATCATACTTGGAATCAAGTGTAAATGTTAACTTTTA HG:+:881379450:43 HG:+:2581417638:25 +ATTAGTAATTTATTACCTATCATTCAAGCCTGCCCTGGACTGAAATGCAATCCCTGGCCCACTTTTTGTTCTTCTCAGGGTATTCCGGCCCAGTTCCTATGTATGCTCGACCAGACACGCCCACAAGGCTTCATTGGCCCTTTCAGTGCAGGGGCCTTGGCTGTGGCATCTACAAGGGCATTTCCTTTTACACTAGGTCAGTCTCTCTTTTGATTGTCCTCTGCAATTAATTATAGTCACTTTTTTGGCAGCAAAAGCAGCATCTAACAAACGCTCAAAATCTGAATGATGTATGGAAAAGCCCTTTGGGGTCAGGAGTCCCCACCCATTCAAATTGCAGCATAAGCATGAAAGCACTAAAAAAATCATACTTGGAATCAAGTGTAAATGTTAACTTTTA HG:+:1680469334:34 HG:+:2581417641:25 +ATTAGTAATTTATTACCTATCATTCAAGCCTGCCCTGGACTGAAATGCAATCCCTGGCCCACTTTTTGTTCTTCTCAGGGTATTCCGGCCCAGTTCCTATGTATGCTCGACCAGACACGCCCACAAGGCTTCATTGGCCCTTTCAGTGCAGGGGCCTTGGCTGTGGCATCTACAAGGGCATTTCCTTTTACACTAGGTCAGTCTCTCTTTTGATTGTCCTCTGCAATTAATTATAGTCACTTTTTTGGCAGCAAAAGCAGCATCTAACAAACGCTCAAAATCTGAATGATGTATGGAAAAGCCCTTTGGGGTCAGGAGTCCCCACCCATTCAAATTGCAGCATAAGCATGAAAGCACTAAAAAAATCATACTTGGAATCAAGTGTAAATGTTAACTTTTA HG:+:2581417645:25 +ATTAGTAATTTATTACCTATCATTCAAGCCTGCCCTGGACTGAAATGCAATCCCTGGCCCACTTTTTGTTCTTCTCAGGGTATTCCGGCCCAGTTCCTATGTATGCTCGACCAGACACGCCCACAAGGCTTCATTGGCCCTTTCAGTGCAGGGGCCTTGGCTGTGGCATCTACAAGGGCATTTCCTTTTACACTAGGTCAGTCTCTCTTTTGATTGTCCTCTGCAATTAATTATAGTCACTTTTTTGGCAGCAAAAGCAGCATCTAACAAACGCTCAAAATCTGAATGATGTATGGAAAAGCCCTTTGGGGTCAGGAGTCCCCACCCATTCAAATTGCAGCATAAGCATGAAAGCACTAAAAAAATCATACTTGGAATCAAGTGTAAATGTTAACTTTTA HG:+:8363050:-1 HG:+:227683857:67 HG:+:881379448:43 HG:+:1680469330:34 HG:+:1985235300:50 HG:+:2195644722:-1 HG:+:2581417634:25 +ATTAGTAATTTATTACCTATCATTCAAGCCTGCCCTGGACTGAAATGCAATCCCTGGCCCACTTTTTGTTCTTCTCAGGGTATTCCGGCCCAGTTCCTATGTATGCTCGACCAGACACGCCCACAAGGCTTCATTGGCCCTTTCAGTGCAGGGGCCTTGGCTGTGGCATCTACAAGGGCATTTCCTTTTACACTAGGTCAGTCTCTCTTTTGATTGTCCTCTGCAATTAATTATAGTCACTTTTTTGGCAGCAAAAGCAGCATCTAACAAACGCTCAAAATCTGAATGATGTATGGAAAAGCCCTTTGGGGTCAGGAGTCCCCACCCATTCAAATTGCAGCATAAGCATGAAAGCACTAAAAAAATCATACTTGGAATCAAGTGTAAATGTTAACTTTTA HG:+:881379449:43 HG:+:1680469331:34 +TAAAAGTTAACATTTACACTTGATTCCAAGTATGATTTTTTTAGTGCTTTCATGCTTATGCTGCAATTTGAATGGGTGGGGACTCCTGACCCCAAAGGGCTTTTCCATACATCATTCAGATTTTGAGCGTTTGTTAGATGCTGCTTTTGCTGCCAAAAAAGTGACTATAATTAATTGCAGAGGACAATCAAAAGAGAGACTGACCTAGTGTAAAAGGAAATGCCCTTGTAGATGCCACAGCCAAGGCCCCTGCACTGAAAGGGCCAATGAAGCCTTGTGGGCGTGTCTGGTCGAGCATACATAGGAACTGGGCCGGAATACCCTGAGAAGAACAAAAAGTGGGCCAGGGATTGCATTTCAGTCCAGGGCAGGCTTGAATGATAGGTAATAAATTACTAAT HG:+:2499975979:32 +TAAAAGTTAACATTTACACTTGATTCCAAGTATGATTTTTTTAGTGCTTTCATGCTTATGCTGCAATTTGAATGGGTGGGGACTCCTGACCCCAAAGGGCTTTTCCATACATCATTCAGATTTTGAGCGTTTGTTAGATGCTGCTTTTGCTGCCAAAAAAGTGACTATAATTAATTGCAGAGGACAATCAAAAGAGAGACTGACCTAGTGTAAAAGGAAATGCCCTTGTAGATGCCACAGCCAAGGCCCCTGCACTGAAAGGGCCAATGAAGCCTTGTGGGCGTGTCTGGTCGAGCATACATAGGAACTGGGCCGGAATACCCTGAGAAGAACAAAAAGTGGGCCAGGGATTGCATTTCAGTCCAGGGCAGGCTTGAATGATAGGTAATAAATTACTAAT HG:+:2956869004:-1 +TAAAAGTTAACATTTACACTTGATTCCAAGTATGATTTTTTTAGTGCTTTCATGCTTATGCTGCAATTTGAATGGGTGGGGACTCCTGACCCCAAAGGGCTTTTCCATACATCATTCAGATTTTGAGCGTTTGTTAGATGCTGCTTTTGCTGCCAAAAAAGTGACTATAATTAATTGCAGAGGACAATCAAAAGAGAGACTGACCTAGTGTAAAAGGAAATGCCCTTGTAGATGCCACAGCCAAGGCCCCTGCACTGAAAGGGCCAATGAAGCCTTGTGGGCGTGTCTGGTCGAGCATACATAGGAACTGGGCCGGAATACCCTGAGAAGAACAAAAAGTGGGCCAGGGATTGCATTTCAGTCCAGGGCAGGCTTGAATGATAGGTAATAAATTACTAAT HG:+:1680227633:32 HG:+:2499975976:32 +TAAAAGTTAACATTTACACTTGATTCCAAGTATGATTTTTTTAGTGCTTTCATGCTTATGCTGCAATTTGAATGGGTGGGGACTCCTGACCCCAAAGGGCTTTTCCATACATCATTCAGATTTTGAGCGTTTGTTAGATGCTGCTTTTGCTGCCAAAAAAGTGACTATAATTAATTGCAGAGGACAATCAAAAGAGAGACTGACCTAGTGTAAAAGGAAATGCCCTTGTAGATGCCACAGCCAAGGCCCCTGCACTGAAAGGGCCAATGAAGCCTTGTGGGCGTGTCTGGTCGAGCATACATAGGAACTGGGCCGGAATACCCTGAGAAGAACAAAAAGTGGGCCAGGGATTGCATTTCAGTCCAGGGCAGGCTTGAATGATAGGTAATAAATTACTAAT HG:+:355502170:-1 HG:+:1092364271:-1 HG:+:1680227629:32 HG:+:1948082470:-1 HG:+:2499975972:32 HG:+:3096317570:48 HG:+:3096369343:47 +TAAAAGTTAACATTTACACTTGATTCCAAGTATGATTTTTTTAGTGCTTTCATGCTTATGCTGCAATTTGAATGGGTGGGGACTCCTGACCCCAAAGGGCTTTTCCATACATCATTCAGATTTTGAGCGTTTGTTAGATGCTGCTTTTGCTGCCAAAAAAGTGACTATAATTAATTGCAGAGGACAATCAAAAGAGAGACTGACCTAGTGTAAAAGGAAATGCCCTTGTAGATGCCACAGCCAAGGCCCCTGCACTGAAAGGGCCAATGAAGCCTTGTGGGCGTGTCTGGTCGAGCATACATAGGAACTGGGCCGGAATACCCTGAGAAGAACAAAAAGTGGGCCAGGGATTGCATTTCAGTCCAGGGCAGGCTTGAATGATAGGTAATAAATTACTAAT HG:+:3096317574:48 HG:+:3096369347:47 +TAAAAGTTAACATTTACACTTGATTCCAAGTATGATTTTTTTAGTGCTTTCATGCTTATGCTGCAATTTGAATGGGTGGGGACTCCTGACCCCAAAGGGCTTTTCCATACATCATTCAGATTTTGAGCGTTTGTTAGATGCTGCTTTTGCTGCCAAAAAAGTGACTATAATTAATTGCAGAGGACAATCAAAAGAGAGACTGACCTAGTGTAAAAGGAAATGCCCTTGTAGATGCCACAGCCAAGGCCCCTGCACTGAAAGGGCCAATGAAGCCTTGTGGGCGTGTCTGGTCGAGCATACATAGGAACTGGGCCGGAATACCCTGAGAAGAACAAAAAGTGGGCCAGGGATTGCATTTCAGTCCAGGGCAGGCTTGAATGATAGGTAATAAATTACTAAT HG:+:54777253:-1 HG:+:387392960:-1 HG:+:1235007201:-1 HG:+:1989508297:49 HG:+:3046270299:51 +TAAAAGTTAACATTTACACTTGATTCCAAGTATGATTTTTTTAGTGCTTTCATGCTTATGCTGCAATTTGAATGGGTGGGGACTCCTGACCCCAAAGGGCTTTTCCATACATCATTCAGATTTTGAGCGTTTGTTAGATGCTGCTTTTGCTGCCAAAAAAGTGACTATAATTAATTGCAGAGGACAATCAAAAGAGAGACTGACCTAGTGTAAAAGGAAATGCCCTTGTAGATGCCACAGCCAAGGCCCCTGCACTGAAAGGGCCAATGAAGCCTTGTGGGCGTGTCTGGTCGAGCATACATAGGAACTGGGCCGGAATACCCTGAGAAGAACAAAAAGTGGGCCAGGGATTGCATTTCAGTCCAGGGCAGGCTTGAATGATAGGTAATAAATTACTAAT HG:+:630403304:-1 HG:+:630403335:-1 HG:+:945238729:-1 HG:+:1680227636:32 HG:+:1798446483:-1 HG:+:1989508300:49 HG:+:2605810895:-1 HG:+:3046270302:51 HG:+:3096317577:48 +TCGGAAGCTAAATCTCACTCGCGGGGAGGATGGGACGCGTGGGGACTGAAGGCGGCATCTGCCTGAATTAAAGCCCCTCGCGCGCTCTGAGCCTCCCACTCTGTCCTGGAGGCCTGACCTCGCGAGTAGAGCCTGGCGCTTTTCCTCCCCGGGAGCACGACGGATAGAATGCGCGGGTCGAGACGGTGTCGGTAGCGGGGGGCCGCAGCGCTTTGCAAAGCCGGCCCTCTGCCCCCGGCCTCCTTGGAGGCGGTAGCGGGACCTGCGCTCGCAGCCTCTCCCCCAGGGCTGTGCGCTTCGGCCTGCGGCCTGCCGGGCAAAACCTCATTTATTTCCTTCCTTCCCCGAGTGAGCTCACTTCCTCCCCGCGCCGCTCCCTTCCGTCGGCCGGAACCCGCTC HG:+:864902751:12 +TCGGAAGCTAAATCTCACTCGCGGGGAGGATGGGACGCGTGGGGACTGAAGGCGGCATCTGCCTGAATTAAAGCCCCTCGCGCGCTCTGAGCCTCCCACTCTGTCCTGGAGGCCTGACCTCGCGAGTAGAGCCTGGCGCTTTTCCTCCCCGGGAGCACGACGGATAGAATGCGCGGGTCGAGACGGTGTCGGTAGCGGGGGGCCGCAGCGCTTTGCAAAGCCGGCCCTCTGCCCCCGGCCTCCTTGGAGGCGGTAGCGGGACCTGCGCTCGCAGCCTCTCCCCCAGGGCTGTGCGCTTCGGCCTGCGGCCTGCCGGGCAAAACCTCATTTATTTCCTTCCTTCCCCGAGTGAGCTCACTTCCTCCCCGCGCCGCTCCCTTCCGTCGGCCGGAACCCGCTC HG:+:864902749:12 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+CAACTTCTTTCCTGGTTTAGTCTTGGGAGACGTGTATGTGTCGAGGAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTGTAGTATTCTCTGATGTAGTTGTATTTCTGTGGGATTGGTGGTGATATCCCCTTCATCATTTTTTATTTAGCATCTATTTGATTCTTCTCTCTTTTTCTTCTTTATTAGTCGTTGCCTAGCGGTCTATCGATTTTGTTGACTCTTTTCAAAAAACCAGCTAACCTGGATTCATTAATTTTTTGAAGGGTTTTTGTGTCTCTATTTCCTTCAGTTCCTGCTCTGATTTTAGGTATTTCTTGCCTTCTGCTAGCTTTTTGAATGTGTTTCCTCTTGCTTTTCTAGTTCTTTTTAATTTTGACGTTA HG:+:934584966:-1 +CAACTTCTTTCCTGGTTTAGTCTTGGGAGACGTGTATGTGTCGAGGAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTGTAGTATTCTCTGATGTAGTTGTATTTCTGTGGGATTGGTGGTGATATCCCCTTCATCATTTTTTATTTAGCATCTATTTGATTCTTCTCTCTTTTTCTTCTTTATTAGTCGTTGCCTAGCGGTCTATCGATTTTGTTGACTCTTTTCAAAAAACCAGCTAACCTGGATTCATTAATTTTTTGAAGGGTTTTTGTGTCTCTATTTCCTTCAGTTCCTGCTCTGATTTTAGGTATTTCTTGCCTTCTGCTAGCTTTTTGAATGTGTTTCCTCTTGCTTTTCTAGTTCTTTTTAATTTTGACGTTA HG:+:152406305:36 HG:+:194283071:30 HG:+:545851933:27 HG:+:546408384:31 HG:+:651562717:35 HG:+:704683760:36 HG:+:784985246:32 HG:+:838843448:30 HG:+:982020779:34 HG:+:1288033364:33 HG:+:1288226068:33 HG:+:1864856910:-1 HG:+:2735671350:30 HG:+:3007967044:-1 +CAACTTCTTTCCTGGTTTAGTCTTGGGAGACGTGTATGTGTCGAGGAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTGTAGTATTCTCTGATGTAGTTGTATTTCTGTGGGATTGGTGGTGATATCCCCTTCATCATTTTTTATTTAGCATCTATTTGATTCTTCTCTCTTTTTCTTCTTTATTAGTCGTTGCCTAGCGGTCTATCGATTTTGTTGACTCTTTTCAAAAAACCAGCTAACCTGGATTCATTAATTTTTTGAAGGGTTTTTGTGTCTCTATTTCCTTCAGTTCCTGCTCTGATTTTAGGTATTTCTTGCCTTCTGCTAGCTTTTTGAATGTGTTTCCTCTTGCTTTTCTAGTTCTTTTTAATTTTGACGTTA HG:+:63970798:31 HG:+:185859058:33 HG:+:406881122:31 HG:+:407072083:31 HG:+:1003595802:39 HG:+:1369438592:34 HG:+:1369758576:30 HG:+:1454149495:48 HG:+:1864485634:50 HG:+:2012102730:45 HG:+:2055880515:42 HG:+:2056824650:38 HG:+:2164918931:72 HG:+:2938209094:37 HG:+:3063563021:58 +CAACTTCTTTCCTGGTTTAGTCTTGGGAGACGTGTATGTGTCGAGGAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTGTAGTATTCTCTGATGTAGTTGTATTTCTGTGGGATTGGTGGTGATATCCCCTTCATCATTTTTTATTTAGCATCTATTTGATTCTTCTCTCTTTTTCTTCTTTATTAGTCGTTGCCTAGCGGTCTATCGATTTTGTTGACTCTTTTCAAAAAACCAGCTAACCTGGATTCATTAATTTTTTGAAGGGTTTTTGTGTCTCTATTTCCTTCAGTTCCTGCTCTGATTTTAGGTATTTCTTGCCTTCTGCTAGCTTTTTGAATGTGTTTCCTCTTGCTTTTCTAGTTCTTTTTAATTTTGACGTTA HG:+:55962361:29 HG:+:68471381:46 HG:+:157312700:30 HG:+:702054045:35 HG:+:804820714:38 HG:+:933021954:45 HG:+:1017906450:47 HG:+:1025832227:32 HG:+:1063024077:43 HG:+:1148080726:40 HG:+:1246967960:30 HG:+:1717557647:38 HG:+:1777028432:31 HG:+:1990874456:44 HG:+:2012531687:36 HG:+:2165160110:35 HG:+:2643488107:35 HG:+:2656613794:38 HG:+:2958757628:31 HG:+:2966042629:32 +CAACTTCTTTCCTGGTTTAGTCTTGGGAGACGTGTATGTGTCGAGGAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTGTAGTATTCTCTGATGTAGTTGTATTTCTGTGGGATTGGTGGTGATATCCCCTTCATCATTTTTTATTTAGCATCTATTTGATTCTTCTCTCTTTTTCTTCTTTATTAGTCGTTGCCTAGCGGTCTATCGATTTTGTTGACTCTTTTCAAAAAACCAGCTAACCTGGATTCATTAATTTTTTGAAGGGTTTTTGTGTCTCTATTTCCTTCAGTTCCTGCTCTGATTTTAGGTATTTCTTGCCTTCTGCTAGCTTTTTGAATGTGTTTCCTCTTGCTTTTCTAGTTCTTTTTAATTTTGACGTTA HG:+:168368133:-1 HG:+:433047495:-1 HG:+:636024615:-1 HG:+:948769245:-1 HG:+:1167699851:-1 HG:+:2269216749:-1 +CAACTTCTTTCCTGGTTTAGTCTTGGGAGACGTGTATGTGTCGAGGAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTGTAGTATTCTCTGATGTAGTTGTATTTCTGTGGGATTGGTGGTGATATCCCCTTCATCATTTTTTATTTAGCATCTATTTGATTCTTCTCTCTTTTTCTTCTTTATTAGTCGTTGCCTAGCGGTCTATCGATTTTGTTGACTCTTTTCAAAAAACCAGCTAACCTGGATTCATTAATTTTTTGAAGGGTTTTTGTGTCTCTATTTCCTTCAGTTCCTGCTCTGATTTTAGGTATTTCTTGCCTTCTGCTAGCTTTTTGAATGTGTTTCCTCTTGCTTTTCTAGTTCTTTTTAATTTTGACGTTA HG:+:685136266:44 HG:+:1431780505:77 HG:+:1478007507:-1 HG:+:1647709686:42 +ATTATAAAATGTGTTTTAAAAAAAGCTCAATAATTAACATACTAATGTGTTTTTTCAATTATTTATAAACGTGTGAATGCCTCCACTTACTAAAGAACATTGTAATTCTAACAAGTTTTATTGTGTTTTTAAGAAAGAGAATCAGGGGGGTCTTCAGGAACACTATTTTCGGAATCCGTCTAGGACTTTTGATGACAGAAGAGGCCATATTCTTACTCTAATTTTTCTTGCTATCACATATAATTTTGTACTGCATCTTAAACAGCTTCTTCTAATGGTTTATTATATTTGCCCCATGCACAAATATAATGTGATGTTTATGAGTAAAAGGTTTAAAGACTATTTTTCTAGTGATACTTATGAATCTTAAGGATCTTTTTATGCCTTGAAGGAAAATAAA HG:+:213170769:21 HG:+:2005199050:-1 +ATTATAAAATGTGTTTTAAAAAAAGCTCAATAATTAACATACTAATGTGTTTTTTCAATTATTTATAAACGTGTGAATGCCTCCACTTACTAAAGAACATTGTAATTCTAACAAGTTTTATTGTGTTTTTAAGAAAGAGAATCAGGGGGGTCTTCAGGAACACTATTTTCGGAATCCGTCTAGGACTTTTGATGACAGAAGAGGCCATATTCTTACTCTAATTTTTCTTGCTATCACATATAATTTTGTACTGCATCTTAAACAGCTTCTTCTAATGGTTTATTATATTTGCCCCATGCACAAATATAATGTGATGTTTATGAGTAAAAGGTTTAAAGACTATTTTTCTAGTGATACTTATGAATCTTAAGGATCTTTTTATGCCTTGAAGGAAAATAAA HG:+:213170760:21 +ATTATAAAATGTGTTTTAAAAAAAGCTCAATAATTAACATACTAATGTGTTTTTTCAATTATTTATAAACGTGTGAATGCCTCCACTTACTAAAGAACATTGTAATTCTAACAAGTTTTATTGTGTTTTTAAGAAAGAGAATCAGGGGGGTCTTCAGGAACACTATTTTCGGAATCCGTCTAGGACTTTTGATGACAGAAGAGGCCATATTCTTACTCTAATTTTTCTTGCTATCACATATAATTTTGTACTGCATCTTAAACAGCTTCTTCTAATGGTTTATTATATTTGCCCCATGCACAAATATAATGTGATGTTTATGAGTAAAAGGTTTAAAGACTATTTTTCTAGTGATACTTATGAATCTTAAGGATCTTTTTATGCCTTGAAGGAAAATAAA HG:+:213170763:21 +ATTATAAAATGTGTTTTAAAAAAAGCTCAATAATTAACATACTAATGTGTTTTTTCAATTATTTATAAACGTGTGAATGCCTCCACTTACTAAAGAACATTGTAATTCTAACAAGTTTTATTGTGTTTTTAAGAAAGAGAATCAGGGGGGTCTTCAGGAACACTATTTTCGGAATCCGTCTAGGACTTTTGATGACAGAAGAGGCCATATTCTTACTCTAATTTTTCTTGCTATCACATATAATTTTGTACTGCATCTTAAACAGCTTCTTCTAATGGTTTATTATATTTGCCCCATGCACAAATATAATGTGATGTTTATGAGTAAAAGGTTTAAAGACTATTTTTCTAGTGATACTTATGAATCTTAAGGATCTTTTTATGCCTTGAAGGAAAATAAA HG:+:213170773:21 +ATTATAAAATGTGTTTTAAAAAAAGCTCAATAATTAACATACTAATGTGTTTTTTCAATTATTTATAAACGTGTGAATGCCTCCACTTACTAAAGAACATTGTAATTCTAACAAGTTTTATTGTGTTTTTAAGAAAGAGAATCAGGGGGGTCTTCAGGAACACTATTTTCGGAATCCGTCTAGGACTTTTGATGACAGAAGAGGCCATATTCTTACTCTAATTTTTCTTGCTATCACATATAATTTTGTACTGCATCTTAAACAGCTTCTTCTAATGGTTTATTATATTTGCCCCATGCACAAATATAATGTGATGTTTATGAGTAAAAGGTTTAAAGACTATTTTTCTAGTGATACTTATGAATCTTAAGGATCTTTTTATGCCTTGAAGGAAAATAAA HG:+:425924931:-1 +ATTATAAAATGTGTTTTAAAAAAAGCTCAATAATTAACATACTAATGTGTTTTTTCAATTATTTATAAACGTGTGAATGCCTCCACTTACTAAAGAACATTGTAATTCTAACAAGTTTTATTGTGTTTTTAAGAAAGAGAATCAGGGGGGTCTTCAGGAACACTATTTTCGGAATCCGTCTAGGACTTTTGATGACAGAAGAGGCCATATTCTTACTCTAATTTTTCTTGCTATCACATATAATTTTGTACTGCATCTTAAACAGCTTCTTCTAATGGTTTATTATATTTGCCCCATGCACAAATATAATGTGATGTTTATGAGTAAAAGGTTTAAAGACTATTTTTCTAGTGATACTTATGAATCTTAAGGATCTTTTTATGCCTTGAAGGAAAATAAA HG:+:213170771:21 +TTTATTTTCCTTCAAGGCATAAAAAGATCCTTAAGATTCATAAGTATCACTAGAAAAATAGTCTTTAAACCTTTTACTCATAAACATCACATTATATTTGTGCATGGGGCAAATATAATAAACCATTAGAAGAAGCTGTTTAAGATGCAGTACAAAATTATATGTGATAGCAAGAAAAATTAGAGTAAGAATATGGCCTCTTCTGTCATCAAAAGTCCTAGACGGATTCCGAAAATAGTGTTCCTGAAGACCCCCCTGATTCTCTTTCTTAAAAACACAATAAAACTTGTTAGAATTACAATGTTCTTTAGTAAGTGGAGGCATTCACACGTTTATAAATAATTGAAAAAACACATTAGTATGTTAATTATTGAGCTTTTTTTAAAACACATTTTATAAT HG:+:1505161226:-1 HG:+:2643804860:-1 +TTTATTTTCCTTCAAGGCATAAAAAGATCCTTAAGATTCATAAGTATCACTAGAAAAATAGTCTTTAAACCTTTTACTCATAAACATCACATTATATTTGTGCATGGGGCAAATATAATAAACCATTAGAAGAAGCTGTTTAAGATGCAGTACAAAATTATATGTGATAGCAAGAAAAATTAGAGTAAGAATATGGCCTCTTCTGTCATCAAAAGTCCTAGACGGATTCCGAAAATAGTGTTCCTGAAGACCCCCCTGATTCTCTTTCTTAAAAACACAATAAAACTTGTTAGAATTACAATGTTCTTTAGTAAGTGGAGGCATTCACACGTTTATAAATAATTGAAAAAACACATTAGTATGTTAATTATTGAGCTTTTTTTAAAACACATTTTATAAT HG:+:1645086576:-1 +TTTATTTTCCTTCAAGGCATAAAAAGATCCTTAAGATTCATAAGTATCACTAGAAAAATAGTCTTTAAACCTTTTACTCATAAACATCACATTATATTTGTGCATGGGGCAAATATAATAAACCATTAGAAGAAGCTGTTTAAGATGCAGTACAAAATTATATGTGATAGCAAGAAAAATTAGAGTAAGAATATGGCCTCTTCTGTCATCAAAAGTCCTAGACGGATTCCGAAAATAGTGTTCCTGAAGACCCCCCTGATTCTCTTTCTTAAAAACACAATAAAACTTGTTAGAATTACAATGTTCTTTAGTAAGTGGAGGCATTCACACGTTTATAAATAATTGAAAAAACACATTAGTATGTTAATTATTGAGCTTTTTTTAAAACACATTTTATAAT HG:+:116744289:-1 +TTTATTTTCCTTCAAGGCATAAAAAGATCCTTAAGATTCATAAGTATCACTAGAAAAATAGTCTTTAAACCTTTTACTCATAAACATCACATTATATTTGTGCATGGGGCAAATATAATAAACCATTAGAAGAAGCTGTTTAAGATGCAGTACAAAATTATATGTGATAGCAAGAAAAATTAGAGTAAGAATATGGCCTCTTCTGTCATCAAAAGTCCTAGACGGATTCCGAAAATAGTGTTCCTGAAGACCCCCCTGATTCTCTTTCTTAAAAACACAATAAAACTTGTTAGAATTACAATGTTCTTTAGTAAGTGGAGGCATTCACACGTTTATAAATAATTGAAAAAACACATTAGTATGTTAATTATTGAGCTTTTTTTAAAACACATTTTATAAT HG:+:226862244:-1 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCACGTCTGGCTGTGCCAAATGGTCTGGCAGCTGGTTTTGGCATTCCCCCAGCATCACCACTCTCCCAACCATCACCGTCGACTGCACGTTCCTGCCCCATTCTCTTGGGTCAGGGAGGGGCTGGGAAGGGCTACTGAAGGCCCCATTCTCCCGACAGGATGGTGAGGCTGGGAGGAGGAACGACTGAGGTAGAGATTCCAGG HG:+:2603602195:-1 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCACGTCTGGCTGTGCCAAATGGTCTGGCAGCTGGTTTTGGCATTCCCCCAGCATCACCACTCTCCCAACCATCACCGTCGACTGCACGTTCCTGCCCCATTCTCTTGGGTCAGGGAGGGGCTGGGAAGGGCTACTGAAGGCCCCATTCTCCCGACAGGATGGTGAGGCTGGGAGGAGGAACGACTGAGGTAGAGATTCCAGG HG:+:203045689:19 HG:+:1105956736:-1 HG:+:1884007025:-1 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCACGTCTGGCTGTGCCAAATGGTCTGGCAGCTGGTTTTGGCATTCCCCCAGCATCACCACTCTCCCAACCATCACCGTCGACTGCACGTTCCTGCCCCATTCTCTTGGGTCAGGGAGGGGCTGGGAAGGGCTACTGAAGGCCCCATTCTCCCGACAGGATGGTGAGGCTGGGAGGAGGAACGACTGAGGTAGAGATTCCAGG HG:+:203045688:19 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCACGTCTGGCTGTGCCAAATGGTCTGGCAGCTGGTTTTGGCATTCCCCCAGCATCACCACTCTCCCAACCATCACCGTCGACTGCACGTTCCTGCCCCATTCTCTTGGGTCAGGGAGGGGCTGGGAAGGGCTACTGAAGGCCCCATTCTCCCGACAGGATGGTGAGGCTGGGAGGAGGAACGACTGAGGTAGAGATTCCAGG HG:+:203045695:19 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCACGTCTGGCTGTGCCAAATGGTCTGGCAGCTGGTTTTGGCATTCCCCCAGCATCACCACTCTCCCAACCATCACCGTCGACTGCACGTTCCTGCCCCATTCTCTTGGGTCAGGGAGGGGCTGGGAAGGGCTACTGAAGGCCCCATTCTCCCGACAGGATGGTGAGGCTGGGAGGAGGAACGACTGAGGTAGAGATTCCAGG HG:+:203045697:19 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCACGTCTGGCTGTGCCAAATGGTCTGGCAGCTGGTTTTGGCATTCCCCCAGCATCACCACTCTCCCAACCATCACCGTCGACTGCACGTTCCTGCCCCATTCTCTTGGGTCAGGGAGGGGCTGGGAAGGGCTACTGAAGGCCCCATTCTCCCGACAGGATGGTGAGGCTGGGAGGAGGAACGACTGAGGTAGAGATTCCAGG HG:+:203045696:19 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCACGTCTGGCTGTGCCAAATGGTCTGGCAGCTGGTTTTGGCATTCCCCCAGCATCACCACTCTCCCAACCATCACCGTCGACTGCACGTTCCTGCCCCATTCTCTTGGGTCAGGGAGGGGCTGGGAAGGGCTACTGAAGGCCCCATTCTCCCGACAGGATGGTGAGGCTGGGAGGAGGAACGACTGAGGTAGAGATTCCAGG HG:+:203045687:19 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCACGTCTGGCTGTGCCAAATGGTCTGGCAGCTGGTTTTGGCATTCCCCCAGCATCACCACTCTCCCAACCATCACCGTCGACTGCACGTTCCTGCCCCATTCTCTTGGGTCAGGGAGGGGCTGGGAAGGGCTACTGAAGGCCCCATTCTCCCGACAGGATGGTGAGGCTGGGAGGAGGAACGACTGAGGTAGAGATTCCAGG HG:+:203045690:19 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCACGTCTGGCTGTGCCAAATGGTCTGGCAGCTGGTTTTGGCATTCCCCCAGCATCACCACTCTCCCAACCATCACCGTCGACTGCACGTTCCTGCCCCATTCTCTTGGGTCAGGGAGGGGCTGGGAAGGGCTACTGAAGGCCCCATTCTCCCGACAGGATGGTGAGGCTGGGAGGAGGAACGACTGAGGTAGAGATTCCAGG HG:+:203045693:19 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCACGTCTGGCTGTGCCAAATGGTCTGGCAGCTGGTTTTGGCATTCCCCCAGCATCACCACTCTCCCAACCATCACCGTCGACTGCACGTTCCTGCCCCATTCTCTTGGGTCAGGGAGGGGCTGGGAAGGGCTACTGAAGGCCCCATTCTCCCGACAGGATGGTGAGGCTGGGAGGAGGAACGACTGAGGTAGAGATTCCAGG HG:+:1929905510:-1 +TTCTGGGGGGAAGGAGAGAAGGGCAGCTCAGGGTGATGTGAAGCCACCCTTCCTCTTCTGGACCCAGCCTTGGTCTGCCACTGCAACCTCCACCAGGACCAGGATCCTGGGCCGACAGGCTGGGATGGTCCCTTCCAAGAAAGGGTCATTTCTAGACGCAGCCTTGTCTTGGGCTATTCAATCTTAGGGGTGTCTATCCACGTCTGGCTGTGCCAAATGGTCTGGCAGCTGGTTTTGGCATTCCCCCAGCATCACCACTCTCCCAACCATCACCGTCGACTGCACGTTCCTGCCCCATTCTCTTGGGTCAGGGAGGGGCTGGGAAGGGCTACTGAAGGCCCCATTCTCCCGACAGGATGGTGAGGCTGGGAGGAGGAACGACTGAGGTAGAGATTCCAGG HG:+:538295094:-1 +CCTGGAATCTCTACCTCAGTCGTTCCTCCTCCCAGCCTCACCATCCTGTCGGGAGAATGGGGCCTTCAGTAGCCCTTCCCAGCCCCTCCCTGACCCAAGAGAATGGGGCAGGAACGTGCAGTCGACGGTGATGGTTGGGAGAGTGGTGATGCTGGGGGAATGCCAAAACCAGCTGCCAGACCATTTGGCACAGCCAGACGTGGATAGACACCCCTAAGATTGAATAGCCCAAGACAAGGCTGCGTCTAGAAATGACCCTTTCTTGGAAGGGACCATCCCAGCCTGTCGGCCCAGGATCCTGGTCCTGGTGGAGGTTGCAGTGGCAGACCAAGGCTGGGTCCAGAAGAGGAAGGGTGGCTTCACATCACCCTGAGCTGCCCTTCTCTCCTTCCCCCCAGAA HG:+:2347928745:-1 +TCTGTGGGACAGCCAAGGAACTCTGAGTCGAGGCTTGTTTTCTCAGTGGGGAGGCCTTGTAGCCTGGGGCAAGTTCTCAGCCTCCTCACTGGTTGCCCTGGAAATCAGCGTCTGTGTTGTTGGTGGGGTGGGGGCAGGGGCACAGTGGGAGTGGGACCAGGCCTTTTGGGCTAGTGGGATGCATTGGGAAGCTGTGTGAGGACTCTGGTCTGCCGGCATTTCCTCCACTCCCTGGCAACCTGTGTGATGCAGCAGAGGCAGCCATAATCTTCCTGGGAACATAACTGGGAACATAACTCTTCCCTGGGAACGTAATTGCATTGGCCTGGGAAACACACCCCCAATCCCCTACAGCAGCCACCATCCCCTGCCCAAGGAGAGTCTGGAGACTCAGACACAC HG:+:484284368:-1 HG:+:559804192:-1 HG:+:575366404:-1 HG:+:910431256:-1 HG:+:1016079316:-1 HG:+:1537315493:-1 HG:+:1759634464:-1 HG:+:1991292184:-1 HG:+:2006658098:-1 HG:+:2350613643:-1 HG:+:2389578891:-1 HG:+:2459672074:-1 HG:+:2503350897:-1 +TCTGTGGGACAGCCAAGGAACTCTGAGTCGAGGCTTGTTTTCTCAGTGGGGAGGCCTTGTAGCCTGGGGCAAGTTCTCAGCCTCCTCACTGGTTGCCCTGGAAATCAGCGTCTGTGTTGTTGGTGGGGTGGGGGCAGGGGCACAGTGGGAGTGGGACCAGGCCTTTTGGGCTAGTGGGATGCATTGGGAAGCTGTGTGAGGACTCTGGTCTGCCGGCATTTCCTCCACTCCCTGGCAACCTGTGTGATGCAGCAGAGGCAGCCATAATCTTCCTGGGAACATAACTGGGAACATAACTCTTCCCTGGGAACGTAATTGCATTGGCCTGGGAAACACACCCCCAATCCCCTACAGCAGCCACCATCCCCTGCCCAAGGAGAGTCTGGAGACTCAGACACAC HG:+:70432575:-1 HG:+:181841493:-1 HG:+:252405492:-1 HG:+:263749560:-1 HG:+:331230114:-1 HG:+:450314842:-1 HG:+:464319117:-1 HG:+:513099445:-1 HG:+:733007530:-1 HG:+:749048424:-1 HG:+:749529439:-1 HG:+:938017556:-1 HG:+:1000715358:-1 HG:+:1065419517:-1 HG:+:1134491257:-1 HG:+:1229798271:-1 HG:+:1349372403:-1 HG:+:1627961212:-1 HG:+:1802964843:-1 HG:+:1985115935:-1 HG:+:2148342068:-1 HG:+:2259510336:-1 HG:+:2384844843:22 HG:+:2976228413:-1 HG:+:2981614592:-1 HG:+:2993364518:-1 +TCTGTGGGACAGCCAAGGAACTCTGAGTCGAGGCTTGTTTTCTCAGTGGGGAGGCCTTGTAGCCTGGGGCAAGTTCTCAGCCTCCTCACTGGTTGCCCTGGAAATCAGCGTCTGTGTTGTTGGTGGGGTGGGGGCAGGGGCACAGTGGGAGTGGGACCAGGCCTTTTGGGCTAGTGGGATGCATTGGGAAGCTGTGTGAGGACTCTGGTCTGCCGGCATTTCCTCCACTCCCTGGCAACCTGTGTGATGCAGCAGAGGCAGCCATAATCTTCCTGGGAACATAACTGGGAACATAACTCTTCCCTGGGAACGTAATTGCATTGGCCTGGGAAACACACCCCCAATCCCCTACAGCAGCCACCATCCCCTGCCCAAGGAGAGTCTGGAGACTCAGACACAC HG:+:1458796620:-1 HG:+:2384844844:22 +TCTGTGGGACAGCCAAGGAACTCTGAGTCGAGGCTTGTTTTCTCAGTGGGGAGGCCTTGTAGCCTGGGGCAAGTTCTCAGCCTCCTCACTGGTTGCCCTGGAAATCAGCGTCTGTGTTGTTGGTGGGGTGGGGGCAGGGGCACAGTGGGAGTGGGACCAGGCCTTTTGGGCTAGTGGGATGCATTGGGAAGCTGTGTGAGGACTCTGGTCTGCCGGCATTTCCTCCACTCCCTGGCAACCTGTGTGATGCAGCAGAGGCAGCCATAATCTTCCTGGGAACATAACTGGGAACATAACTCTTCCCTGGGAACGTAATTGCATTGGCCTGGGAAACACACCCCCAATCCCCTACAGCAGCCACCATCCCCTGCCCAAGGAGAGTCTGGAGACTCAGACACAC HG:+:799159559:-1 +TCTGTGGGACAGCCAAGGAACTCTGAGTCGAGGCTTGTTTTCTCAGTGGGGAGGCCTTGTAGCCTGGGGCAAGTTCTCAGCCTCCTCACTGGTTGCCCTGGAAATCAGCGTCTGTGTTGTTGGTGGGGTGGGGGCAGGGGCACAGTGGGAGTGGGACCAGGCCTTTTGGGCTAGTGGGATGCATTGGGAAGCTGTGTGAGGACTCTGGTCTGCCGGCATTTCCTCCACTCCCTGGCAACCTGTGTGATGCAGCAGAGGCAGCCATAATCTTCCTGGGAACATAACTGGGAACATAACTCTTCCCTGGGAACGTAATTGCATTGGCCTGGGAAACACACCCCCAATCCCCTACAGCAGCCACCATCCCCTGCCCAAGGAGAGTCTGGAGACTCAGACACAC HG:+:2384844835:22 +TCTGTGGGACAGCCAAGGAACTCTGAGTCGAGGCTTGTTTTCTCAGTGGGGAGGCCTTGTAGCCTGGGGCAAGTTCTCAGCCTCCTCACTGGTTGCCCTGGAAATCAGCGTCTGTGTTGTTGGTGGGGTGGGGGCAGGGGCACAGTGGGAGTGGGACCAGGCCTTTTGGGCTAGTGGGATGCATTGGGAAGCTGTGTGAGGACTCTGGTCTGCCGGCATTTCCTCCACTCCCTGGCAACCTGTGTGATGCAGCAGAGGCAGCCATAATCTTCCTGGGAACATAACTGGGAACATAACTCTTCCCTGGGAACGTAATTGCATTGGCCTGGGAAACACACCCCCAATCCCCTACAGCAGCCACCATCCCCTGCCCAAGGAGAGTCTGGAGACTCAGACACAC HG:+:298173249:-1 HG:+:2384844837:22 +TCTGTGGGACAGCCAAGGAACTCTGAGTCGAGGCTTGTTTTCTCAGTGGGGAGGCCTTGTAGCCTGGGGCAAGTTCTCAGCCTCCTCACTGGTTGCCCTGGAAATCAGCGTCTGTGTTGTTGGTGGGGTGGGGGCAGGGGCACAGTGGGAGTGGGACCAGGCCTTTTGGGCTAGTGGGATGCATTGGGAAGCTGTGTGAGGACTCTGGTCTGCCGGCATTTCCTCCACTCCCTGGCAACCTGTGTGATGCAGCAGAGGCAGCCATAATCTTCCTGGGAACATAACTGGGAACATAACTCTTCCCTGGGAACGTAATTGCATTGGCCTGGGAAACACACCCCCAATCCCCTACAGCAGCCACCATCCCCTGCCCAAGGAGAGTCTGGAGACTCAGACACAC HG:+:418721433:-1 HG:+:1456390663:-1 HG:+:2045399517:-1 HG:+:2054669620:-1 HG:+:2384844866:22 +GTGTGTCTGAGTCTCCAGACTCTCCTTGGGCAGGGGATGGTGGCTGCTGTAGGGGATTGGGGGTGTGTTTCCCAGGCCAATGCAATTACGTTCCCAGGGAAGAGTTATGTTCCCAGTTATGTTCCCAGGAAGATTATGGCTGCCTCTGCTGCATCACACAGGTTGCCAGGGAGTGGAGGAAATGCCGGCAGACCAGAGTCCTCACACAGCTTCCCAATGCATCCCACTAGCCCAAAAGGCCTGGTCCCACTCCCACTGTGCCCCTGCCCCCACCCCACCAACAACACAGACGCTGATTTCCAGGGCAACCAGTGAGGAGGCTGAGAACTTGCCCCAGGCTACAAGGCCTCCCCACTGAGAAAACAAGCCTCGACTCAGAGTTCCTTGGCTGTCCCACAGA HG:+:492122802:-1 +GTGTGTCTGAGTCTCCAGACTCTCCTTGGGCAGGGGATGGTGGCTGCTGTAGGGGATTGGGGGTGTGTTTCCCAGGCCAATGCAATTACGTTCCCAGGGAAGAGTTATGTTCCCAGTTATGTTCCCAGGAAGATTATGGCTGCCTCTGCTGCATCACACAGGTTGCCAGGGAGTGGAGGAAATGCCGGCAGACCAGAGTCCTCACACAGCTTCCCAATGCATCCCACTAGCCCAAAAGGCCTGGTCCCACTCCCACTGTGCCCCTGCCCCCACCCCACCAACAACACAGACGCTGATTTCCAGGGCAACCAGTGAGGAGGCTGAGAACTTGCCCCAGGCTACAAGGCCTCCCCACTGAGAAAACAAGCCTCGACTCAGAGTTCCTTGGCTGTCCCACAGA HG:+:1213575071:-1 +GTGTGTCTGAGTCTCCAGACTCTCCTTGGGCAGGGGATGGTGGCTGCTGTAGGGGATTGGGGGTGTGTTTCCCAGGCCAATGCAATTACGTTCCCAGGGAAGAGTTATGTTCCCAGTTATGTTCCCAGGAAGATTATGGCTGCCTCTGCTGCATCACACAGGTTGCCAGGGAGTGGAGGAAATGCCGGCAGACCAGAGTCCTCACACAGCTTCCCAATGCATCCCACTAGCCCAAAAGGCCTGGTCCCACTCCCACTGTGCCCCTGCCCCCACCCCACCAACAACACAGACGCTGATTTCCAGGGCAACCAGTGAGGAGGCTGAGAACTTGCCCCAGGCTACAAGGCCTCCCCACTGAGAAAACAAGCCTCGACTCAGAGTTCCTTGGCTGTCCCACAGA HG:+:2104886229:-1 HG:+:2126072781:-1 +GTGTGTCTGAGTCTCCAGACTCTCCTTGGGCAGGGGATGGTGGCTGCTGTAGGGGATTGGGGGTGTGTTTCCCAGGCCAATGCAATTACGTTCCCAGGGAAGAGTTATGTTCCCAGTTATGTTCCCAGGAAGATTATGGCTGCCTCTGCTGCATCACACAGGTTGCCAGGGAGTGGAGGAAATGCCGGCAGACCAGAGTCCTCACACAGCTTCCCAATGCATCCCACTAGCCCAAAAGGCCTGGTCCCACTCCCACTGTGCCCCTGCCCCCACCCCACCAACAACACAGACGCTGATTTCCAGGGCAACCAGTGAGGAGGCTGAGAACTTGCCCCAGGCTACAAGGCCTCCCCACTGAGAAAACAAGCCTCGACTCAGAGTTCCTTGGCTGTCCCACAGA HG:+:2897330213:-1 HG:+:2979549132:-1 +GTGTGTCTGAGTCTCCAGACTCTCCTTGGGCAGGGGATGGTGGCTGCTGTAGGGGATTGGGGGTGTGTTTCCCAGGCCAATGCAATTACGTTCCCAGGGAAGAGTTATGTTCCCAGTTATGTTCCCAGGAAGATTATGGCTGCCTCTGCTGCATCACACAGGTTGCCAGGGAGTGGAGGAAATGCCGGCAGACCAGAGTCCTCACACAGCTTCCCAATGCATCCCACTAGCCCAAAAGGCCTGGTCCCACTCCCACTGTGCCCCTGCCCCCACCCCACCAACAACACAGACGCTGATTTCCAGGGCAACCAGTGAGGAGGCTGAGAACTTGCCCCAGGCTACAAGGCCTCCCCACTGAGAAAACAAGCCTCGACTCAGAGTTCCTTGGCTGTCCCACAGA HG:+:723083068:-1 HG:+:1242068219:-1 +GTGTGTCTGAGTCTCCAGACTCTCCTTGGGCAGGGGATGGTGGCTGCTGTAGGGGATTGGGGGTGTGTTTCCCAGGCCAATGCAATTACGTTCCCAGGGAAGAGTTATGTTCCCAGTTATGTTCCCAGGAAGATTATGGCTGCCTCTGCTGCATCACACAGGTTGCCAGGGAGTGGAGGAAATGCCGGCAGACCAGAGTCCTCACACAGCTTCCCAATGCATCCCACTAGCCCAAAAGGCCTGGTCCCACTCCCACTGTGCCCCTGCCCCCACCCCACCAACAACACAGACGCTGATTTCCAGGGCAACCAGTGAGGAGGCTGAGAACTTGCCCCAGGCTACAAGGCCTCCCCACTGAGAAAACAAGCCTCGACTCAGAGTTCCTTGGCTGTCCCACAGA HG:+:2623478107:-1 +GTGTGTCTGAGTCTCCAGACTCTCCTTGGGCAGGGGATGGTGGCTGCTGTAGGGGATTGGGGGTGTGTTTCCCAGGCCAATGCAATTACGTTCCCAGGGAAGAGTTATGTTCCCAGTTATGTTCCCAGGAAGATTATGGCTGCCTCTGCTGCATCACACAGGTTGCCAGGGAGTGGAGGAAATGCCGGCAGACCAGAGTCCTCACACAGCTTCCCAATGCATCCCACTAGCCCAAAAGGCCTGGTCCCACTCCCACTGTGCCCCTGCCCCCACCCCACCAACAACACAGACGCTGATTTCCAGGGCAACCAGTGAGGAGGCTGAGAACTTGCCCCAGGCTACAAGGCCTCCCCACTGAGAAAACAAGCCTCGACTCAGAGTTCCTTGGCTGTCCCACAGA HG:+:1744635885:-1 +GTGTGTCTGAGTCTCCAGACTCTCCTTGGGCAGGGGATGGTGGCTGCTGTAGGGGATTGGGGGTGTGTTTCCCAGGCCAATGCAATTACGTTCCCAGGGAAGAGTTATGTTCCCAGTTATGTTCCCAGGAAGATTATGGCTGCCTCTGCTGCATCACACAGGTTGCCAGGGAGTGGAGGAAATGCCGGCAGACCAGAGTCCTCACACAGCTTCCCAATGCATCCCACTAGCCCAAAAGGCCTGGTCCCACTCCCACTGTGCCCCTGCCCCCACCCCACCAACAACACAGACGCTGATTTCCAGGGCAACCAGTGAGGAGGCTGAGAACTTGCCCCAGGCTACAAGGCCTCCCCACTGAGAAAACAAGCCTCGACTCAGAGTTCCTTGGCTGTCCCACAGA HG:+:862373117:-1 HG:+:1011670259:-1 HG:+:1139589944:-1 HG:+:1207391916:-1 HG:+:1800795109:-1 HG:+:1971016600:-1 HG:+:2367850925:-1 +GAGGCCCGAGGAGGGGTGGATCACCTGAGGTTGGGAGTTGGAGGACCAGCCTGACCAACATGGATAAACCCCTTACTCTACTAAAATGCAAAAATTAGCCGGGGTTGGTGGTGCATGCCTGTAATCTCAGCTACTCGAAGGAGGCTGAGGCAGGAAGAATCGCCTGAACAGGGTGGCGGAGGTTGCGGTGAGCCGAGATCACGCCATTGCCACTCCGAGCCTGGGCAACAAGAGCAAAACTCTGTCTCAGAAAAGAAAGAAAGAAAAGAAAAAGACATTCTCCTGCTGCCTTGGAAAAAAGCAAGCCATTGTGAGTTCTAACACTTGCAAAGACCTGAATTCTATCAATAACCAAGTGAACTTGGAAGGGGACACTGAGCTTCTCATAGGGACTGCCAAC HG:+:23715820:-1 HG:+:72344493:-1 HG:+:94858872:-1 HG:+:97049144:-1 HG:+:335103780:-1 HG:+:395587005:-1 HG:+:477545519:-1 HG:+:796954660:-1 HG:+:1616507499:-1 HG:+:1784761733:-1 HG:+:1839071960:-1 HG:+:2395031313:-1 HG:+:2512736951:18 HG:+:2668891266:-1 HG:+:2918597051:-1 HG:+:2929116266:-1 +GAGGCCCGAGGAGGGGTGGATCACCTGAGGTTGGGAGTTGGAGGACCAGCCTGACCAACATGGATAAACCCCTTACTCTACTAAAATGCAAAAATTAGCCGGGGTTGGTGGTGCATGCCTGTAATCTCAGCTACTCGAAGGAGGCTGAGGCAGGAAGAATCGCCTGAACAGGGTGGCGGAGGTTGCGGTGAGCCGAGATCACGCCATTGCCACTCCGAGCCTGGGCAACAAGAGCAAAACTCTGTCTCAGAAAAGAAAGAAAGAAAAGAAAAAGACATTCTCCTGCTGCCTTGGAAAAAAGCAAGCCATTGTGAGTTCTAACACTTGCAAAGACCTGAATTCTATCAATAACCAAGTGAACTTGGAAGGGGACACTGAGCTTCTCATAGGGACTGCCAAC HG:+:2512736949:18 +GAGGCCCGAGGAGGGGTGGATCACCTGAGGTTGGGAGTTGGAGGACCAGCCTGACCAACATGGATAAACCCCTTACTCTACTAAAATGCAAAAATTAGCCGGGGTTGGTGGTGCATGCCTGTAATCTCAGCTACTCGAAGGAGGCTGAGGCAGGAAGAATCGCCTGAACAGGGTGGCGGAGGTTGCGGTGAGCCGAGATCACGCCATTGCCACTCCGAGCCTGGGCAACAAGAGCAAAACTCTGTCTCAGAAAAGAAAGAAAGAAAAGAAAAAGACATTCTCCTGCTGCCTTGGAAAAAAGCAAGCCATTGTGAGTTCTAACACTTGCAAAGACCTGAATTCTATCAATAACCAAGTGAACTTGGAAGGGGACACTGAGCTTCTCATAGGGACTGCCAAC HG:+:2512736947:18 +GAGGCCCGAGGAGGGGTGGATCACCTGAGGTTGGGAGTTGGAGGACCAGCCTGACCAACATGGATAAACCCCTTACTCTACTAAAATGCAAAAATTAGCCGGGGTTGGTGGTGCATGCCTGTAATCTCAGCTACTCGAAGGAGGCTGAGGCAGGAAGAATCGCCTGAACAGGGTGGCGGAGGTTGCGGTGAGCCGAGATCACGCCATTGCCACTCCGAGCCTGGGCAACAAGAGCAAAACTCTGTCTCAGAAAAGAAAGAAAGAAAAGAAAAAGACATTCTCCTGCTGCCTTGGAAAAAAGCAAGCCATTGTGAGTTCTAACACTTGCAAAGACCTGAATTCTATCAATAACCAAGTGAACTTGGAAGGGGACACTGAGCTTCTCATAGGGACTGCCAAC HG:+:783763830:-1 HG:+:2682700693:-1 +GAGGCCCGAGGAGGGGTGGATCACCTGAGGTTGGGAGTTGGAGGACCAGCCTGACCAACATGGATAAACCCCTTACTCTACTAAAATGCAAAAATTAGCCGGGGTTGGTGGTGCATGCCTGTAATCTCAGCTACTCGAAGGAGGCTGAGGCAGGAAGAATCGCCTGAACAGGGTGGCGGAGGTTGCGGTGAGCCGAGATCACGCCATTGCCACTCCGAGCCTGGGCAACAAGAGCAAAACTCTGTCTCAGAAAAGAAAGAAAGAAAAGAAAAAGACATTCTCCTGCTGCCTTGGAAAAAAGCAAGCCATTGTGAGTTCTAACACTTGCAAAGACCTGAATTCTATCAATAACCAAGTGAACTTGGAAGGGGACACTGAGCTTCTCATAGGGACTGCCAAC HG:+:617690624:-1 +GAGGCCCGAGGAGGGGTGGATCACCTGAGGTTGGGAGTTGGAGGACCAGCCTGACCAACATGGATAAACCCCTTACTCTACTAAAATGCAAAAATTAGCCGGGGTTGGTGGTGCATGCCTGTAATCTCAGCTACTCGAAGGAGGCTGAGGCAGGAAGAATCGCCTGAACAGGGTGGCGGAGGTTGCGGTGAGCCGAGATCACGCCATTGCCACTCCGAGCCTGGGCAACAAGAGCAAAACTCTGTCTCAGAAAAGAAAGAAAGAAAAGAAAAAGACATTCTCCTGCTGCCTTGGAAAAAAGCAAGCCATTGTGAGTTCTAACACTTGCAAAGACCTGAATTCTATCAATAACCAAGTGAACTTGGAAGGGGACACTGAGCTTCTCATAGGGACTGCCAAC HG:+:2512736945:18 +GAGGCCCGAGGAGGGGTGGATCACCTGAGGTTGGGAGTTGGAGGACCAGCCTGACCAACATGGATAAACCCCTTACTCTACTAAAATGCAAAAATTAGCCGGGGTTGGTGGTGCATGCCTGTAATCTCAGCTACTCGAAGGAGGCTGAGGCAGGAAGAATCGCCTGAACAGGGTGGCGGAGGTTGCGGTGAGCCGAGATCACGCCATTGCCACTCCGAGCCTGGGCAACAAGAGCAAAACTCTGTCTCAGAAAAGAAAGAAAGAAAAGAAAAAGACATTCTCCTGCTGCCTTGGAAAAAAGCAAGCCATTGTGAGTTCTAACACTTGCAAAGACCTGAATTCTATCAATAACCAAGTGAACTTGGAAGGGGACACTGAGCTTCTCATAGGGACTGCCAAC HG:+:2512736946:18 +GAGGCCCGAGGAGGGGTGGATCACCTGAGGTTGGGAGTTGGAGGACCAGCCTGACCAACATGGATAAACCCCTTACTCTACTAAAATGCAAAAATTAGCCGGGGTTGGTGGTGCATGCCTGTAATCTCAGCTACTCGAAGGAGGCTGAGGCAGGAAGAATCGCCTGAACAGGGTGGCGGAGGTTGCGGTGAGCCGAGATCACGCCATTGCCACTCCGAGCCTGGGCAACAAGAGCAAAACTCTGTCTCAGAAAAGAAAGAAAGAAAAGAAAAAGACATTCTCCTGCTGCCTTGGAAAAAAGCAAGCCATTGTGAGTTCTAACACTTGCAAAGACCTGAATTCTATCAATAACCAAGTGAACTTGGAAGGGGACACTGAGCTTCTCATAGGGACTGCCAAC HG:+:1963338572:-1 HG:+:2927719914:-1 +GTTGGCAGTCCCTATGAGAAGCTCAGTGTCCCCTTCCAAGTTCACTTGGTTATTGATAGAATTCAGGTCTTTGCAAGTGTTAGAACTCACAATGGCTTGCTTTTTTCCAAGGCAGCAGGAGAATGTCTTTTTCTTTTCTTTCTTTCTTTTCTGAGACAGAGTTTTGCTCTTGTTGCCCAGGCTCGGAGTGGCAATGGCGTGATCTCGGCTCACCGCAACCTCCGCCACCCTGTTCAGGCGATTCTTCCTGCCTCAGCCTCCTTCGAGTAGCTGAGATTACAGGCATGCACCACCAACCCCGGCTAATTTTTGCATTTTAGTAGAGTAAGGGGTTTATCCATGTTGGTCAGGCTGGTCCTCCAACTCCCAACCTCAGGTGATCCACCCCTCCTCGGGCCTC HG:+:53690439:-1 HG:+:61619609:-1 HG:+:504411306:-1 HG:+:1049391898:-1 HG:+:1532155849:-1 HG:+:1572144826:-1 HG:+:2298717111:-1 HG:+:2388331382:-1 HG:+:2668128619:-1 HG:+:3021101178:-1 +GTTGGCAGTCCCTATGAGAAGCTCAGTGTCCCCTTCCAAGTTCACTTGGTTATTGATAGAATTCAGGTCTTTGCAAGTGTTAGAACTCACAATGGCTTGCTTTTTTCCAAGGCAGCAGGAGAATGTCTTTTTCTTTTCTTTCTTTCTTTTCTGAGACAGAGTTTTGCTCTTGTTGCCCAGGCTCGGAGTGGCAATGGCGTGATCTCGGCTCACCGCAACCTCCGCCACCCTGTTCAGGCGATTCTTCCTGCCTCAGCCTCCTTCGAGTAGCTGAGATTACAGGCATGCACCACCAACCCCGGCTAATTTTTGCATTTTAGTAGAGTAAGGGGTTTATCCATGTTGGTCAGGCTGGTCCTCCAACTCCCAACCTCAGGTGATCCACCCCTCCTCGGGCCTC HG:+:2890636038:-1 +GTTGGCAGTCCCTATGAGAAGCTCAGTGTCCCCTTCCAAGTTCACTTGGTTATTGATAGAATTCAGGTCTTTGCAAGTGTTAGAACTCACAATGGCTTGCTTTTTTCCAAGGCAGCAGGAGAATGTCTTTTTCTTTTCTTTCTTTCTTTTCTGAGACAGAGTTTTGCTCTTGTTGCCCAGGCTCGGAGTGGCAATGGCGTGATCTCGGCTCACCGCAACCTCCGCCACCCTGTTCAGGCGATTCTTCCTGCCTCAGCCTCCTTCGAGTAGCTGAGATTACAGGCATGCACCACCAACCCCGGCTAATTTTTGCATTTTAGTAGAGTAAGGGGTTTATCCATGTTGGTCAGGCTGGTCCTCCAACTCCCAACCTCAGGTGATCCACCCCTCCTCGGGCCTC HG:+:144303171:-1 HG:+:144483400:-1 HG:+:1034383701:-1 HG:+:1694642175:-1 HG:+:1797188579:-1 HG:+:1842195653:-1 HG:+:1884569420:-1 HG:+:1976717537:-1 HG:+:2043351822:-1 HG:+:2151634611:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAAGTGTACTTTGATATAGAGCTAAGCTTAGTAATAATGACAGTTTTTGTTGAAAGTAAAATTCGACACTAGAAGAATAACCACATGTCATGTTTAGGGTAAGCTTCTTAAATTTAAGTTGGAAGTAACTATGTTTTATCAAAAAGTAGGTCTCATATGTAAGCAGAATATGTATGGGAAAAAAAGTAAAAACAAAAAGTTTG HG:+:981749778:-1 HG:+:1913964282:-1 HG:+:2059055137:-1 HG:+:2413078238:-1 HG:+:2421728566:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAAGTGTACTTTGATATAGAGCTAAGCTTAGTAATAATGACAGTTTTTGTTGAAAGTAAAATTCGACACTAGAAGAATAACCACATGTCATGTTTAGGGTAAGCTTCTTAAATTTAAGTTGGAAGTAACTATGTTTTATCAAAAAGTAGGTCTCATATGTAAGCAGAATATGTATGGGAAAAAAAGTAAAAACAAAAAGTTTG HG:+:2608433796:-1 HG:+:2614916135:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAAGTGTACTTTGATATAGAGCTAAGCTTAGTAATAATGACAGTTTTTGTTGAAAGTAAAATTCGACACTAGAAGAATAACCACATGTCATGTTTAGGGTAAGCTTCTTAAATTTAAGTTGGAAGTAACTATGTTTTATCAAAAAGTAGGTCTCATATGTAAGCAGAATATGTATGGGAAAAAAAGTAAAAACAAAAAGTTTG HG:+:428254482:-1 HG:+:504092528:-1 HG:+:656980023:-1 HG:+:799920379:-1 HG:+:1018285655:-1 HG:+:1187876202:-1 HG:+:1193088014:-1 HG:+:1762042887:-1 HG:+:1849626971:-1 HG:+:2117221779:-1 HG:+:2140334069:-1 HG:+:2254142537:-1 HG:+:2468128875:-1 HG:+:2610219906:-1 HG:+:2808388525:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAAGTGTACTTTGATATAGAGCTAAGCTTAGTAATAATGACAGTTTTTGTTGAAAGTAAAATTCGACACTAGAAGAATAACCACATGTCATGTTTAGGGTAAGCTTCTTAAATTTAAGTTGGAAGTAACTATGTTTTATCAAAAAGTAGGTCTCATATGTAAGCAGAATATGTATGGGAAAAAAAGTAAAAACAAAAAGTTTG HG:+:715221019:-1 HG:+:1313424522:-1 HG:+:1348256016:-1 HG:+:2041950437:-1 HG:+:2262195310:-1 HG:+:2872828567:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAAGTGTACTTTGATATAGAGCTAAGCTTAGTAATAATGACAGTTTTTGTTGAAAGTAAAATTCGACACTAGAAGAATAACCACATGTCATGTTTAGGGTAAGCTTCTTAAATTTAAGTTGGAAGTAACTATGTTTTATCAAAAAGTAGGTCTCATATGTAAGCAGAATATGTATGGGAAAAAAAGTAAAAACAAAAAGTTTG HG:+:51248464:-1 HG:+:102229873:-1 HG:+:106379565:-1 HG:+:189393247:-1 HG:+:209777000:-1 HG:+:294935174:-1 HG:+:312296747:-1 HG:+:329268994:-1 HG:+:437041732:-1 HG:+:445153153:-1 HG:+:532754174:-1 HG:+:608522434:-1 HG:+:639870011:-1 HG:+:736246194:-1 HG:+:845872825:-1 HG:+:858675669:-1 HG:+:871774206:-1 HG:+:900925263:-1 HG:+:910194961:-1 HG:+:910459935:-1 HG:+:1133577930:-1 HG:+:1205970248:-1 HG:+:1246318624:-1 HG:+:1280572276:-1 HG:+:1352809327:-1 HG:+:1360673843:-1 HG:+:1424083811:-1 HG:+:1739167500:-1 HG:+:1744943324:-1 HG:+:1746447737:-1 HG:+:1812516185:-1 HG:+:1837296349:-1 HG:+:1940009820:-1 HG:+:1951328701:-1 HG:+:1994274419:-1 HG:+:2104066091:-1 HG:+:2112047006:-1 HG:+:2134233003:-1 HG:+:2247923091:-1 HG:+:2375688184:-1 HG:+:2410167475:-1 HG:+:2726603530:-1 HG:+:2733778946:-1 HG:+:2741305369:-1 HG:+:2798874913:-1 HG:+:2884024769:-1 HG:+:3053667425:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAAGTGTACTTTGATATAGAGCTAAGCTTAGTAATAATGACAGTTTTTGTTGAAAGTAAAATTCGACACTAGAAGAATAACCACATGTCATGTTTAGGGTAAGCTTCTTAAATTTAAGTTGGAAGTAACTATGTTTTATCAAAAAGTAGGTCTCATATGTAAGCAGAATATGTATGGGAAAAAAAGTAAAAACAAAAAGTTTG HG:+:60963926:-1 HG:+:326687735:-1 HG:+:448712682:-1 HG:+:499193651:-1 HG:+:785624192:-1 HG:+:809086760:-1 HG:+:1103102718:-1 HG:+:1119134540:-1 HG:+:1145235786:-1 HG:+:1168470668:-1 HG:+:1207429777:-1 HG:+:1280603487:-1 HG:+:1494115072:-1 HG:+:1500181372:-1 HG:+:1568027108:-1 HG:+:1679951293:-1 HG:+:1739513521:-1 HG:+:1799545569:-1 HG:+:1875144606:-1 HG:+:2016876993:-1 HG:+:2112914990:-1 HG:+:2140408593:-1 HG:+:2353408252:-1 HG:+:2391172961:-1 HG:+:2476447490:-1 HG:+:2703431125:-1 HG:+:2805606948:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAAGTGTACTTTGATATAGAGCTAAGCTTAGTAATAATGACAGTTTTTGTTGAAAGTAAAATTCGACACTAGAAGAATAACCACATGTCATGTTTAGGGTAAGCTTCTTAAATTTAAGTTGGAAGTAACTATGTTTTATCAAAAAGTAGGTCTCATATGTAAGCAGAATATGTATGGGAAAAAAAGTAAAAACAAAAAGTTTG HG:+:32023531:-1 HG:+:97894515:-1 HG:+:188552180:-1 HG:+:346497495:-1 HG:+:701638696:-1 HG:+:939039601:-1 HG:+:1326134197:-1 HG:+:1385555218:-1 HG:+:1455994060:-1 HG:+:1562444950:-1 HG:+:1897405925:-1 HG:+:2026294096:-1 HG:+:2327911922:-1 HG:+:2743986499:-1 HG:+:3014419678:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAAGTGTACTTTGATATAGAGCTAAGCTTAGTAATAATGACAGTTTTTGTTGAAAGTAAAATTCGACACTAGAAGAATAACCACATGTCATGTTTAGGGTAAGCTTCTTAAATTTAAGTTGGAAGTAACTATGTTTTATCAAAAAGTAGGTCTCATATGTAAGCAGAATATGTATGGGAAAAAAAGTAAAAACAAAAAGTTTG HG:+:353928752:-1 HG:+:564683745:-1 HG:+:1635353393:-1 HG:+:2612472606:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAAGTGTACTTTGATATAGAGCTAAGCTTAGTAATAATGACAGTTTTTGTTGAAAGTAAAATTCGACACTAGAAGAATAACCACATGTCATGTTTAGGGTAAGCTTCTTAAATTTAAGTTGGAAGTAACTATGTTTTATCAAAAAGTAGGTCTCATATGTAAGCAGAATATGTATGGGAAAAAAAGTAAAAACAAAAAGTTTG HG:+:104486592:-1 HG:+:293873822:-1 HG:+:472155607:-1 HG:+:699858805:-1 HG:+:749127777:-1 HG:+:892702703:-1 HG:+:1010302355:-1 HG:+:1055469916:-1 HG:+:1168059914:-1 HG:+:1231697213:-1 HG:+:1355844481:-1 HG:+:1360845114:-1 HG:+:1887436089:-1 HG:+:1973975193:-1 HG:+:1981648890:-1 HG:+:2621911224:-1 HG:+:2903298142:-1 HG:+:2948096053:-1 +TGTGTTTTATTACGTTCTTTAAACTGTAATGTGTATAATACATACATTCTTGTACAGTGATTAATATTTTAATATAAAGAAAGTTTAAAAAAAATTAAAAAAAATAATGCAATAAAGTGTCTACAACAGAAGGTGCGTCAATATATGGTAATTTCTTACATTTAAGTTAAAATAAAATTACACAATGGCAATTAACTCAAGTGTACTTTGATATAGAGCTAAGCTTAGTAATAATGACAGTTTTTGTTGAAAGTAAAATTCGACACTAGAAGAATAACCACATGTCATGTTTAGGGTAAGCTTCTTAAATTTAAGTTGGAAGTAACTATGTTTTATCAAAAAGTAGGTCTCATATGTAAGCAGAATATGTATGGGAAAAAAAGTAAAAACAAAAAGTTTG HG:+:195041352:-1 HG:+:272918054:-1 HG:+:300047195:-1 HG:+:353535845:-1 HG:+:386914410:-1 HG:+:393309838:-1 HG:+:544370532:-1 HG:+:572045154:-1 HG:+:575415392:-1 HG:+:575415422:-1 HG:+:575415452:-1 HG:+:575415518:-1 HG:+:575415556:-1 HG:+:575415594:-1 HG:+:575415632:-1 HG:+:575415670:-1 HG:+:575415708:-1 HG:+:575415746:-1 HG:+:575415784:-1 HG:+:575415822:-1 HG:+:575415860:-1 HG:+:575415898:-1 HG:+:575415936:-1 HG:+:575415973:-1 HG:+:575416010:-1 HG:+:575416080:-1 HG:+:651831301:-1 HG:+:682156088:-1 HG:+:696213557:-1 HG:+:743221894:-1 HG:+:749863685:-1 HG:+:750636090:-1 HG:+:820990129:-1 HG:+:853114961:-1 HG:+:855074395:-1 HG:+:860903327:-1 HG:+:911335259:-1 HG:+:1014124235:-1 HG:+:1042600444:-1 HG:+:1120072472:-1 HG:+:1200911907:-1 HG:+:1230617857:-1 HG:+:1261420764:-1 HG:+:1332154113:-1 HG:+:1342790484:-1 HG:+:1353789340:-1 HG:+:1364793360:-1 HG:+:1469028261:-1 HG:+:1503186372:-1 HG:+:1512186833:-1 HG:+:1522906711:-1 HG:+:1563877749:-1 HG:+:1563877774:-1 HG:+:1631304752:-1 HG:+:1641109725:-1 HG:+:1736957021:-1 HG:+:1749305320:-1 HG:+:1903950731:-1 HG:+:1907444578:-1 HG:+:1911274751:-1 HG:+:1919105853:-1 HG:+:1981691973:-1 HG:+:1999749788:-1 HG:+:2034962499:-1 HG:+:2068481574:-1 HG:+:2116489138:-1 HG:+:2174253125:-1 HG:+:2185671582:-1 HG:+:2258497718:-1 HG:+:2483402801:-1 HG:+:2599930332:-1 HG:+:2634447360:-1 HG:+:2642959462:-1 HG:+:2656584688:-1 HG:+:2705493146:-1 HG:+:2777654759:-1 HG:+:2891874931:-1 HG:+:2933624138:-1 +CAAACTTTTTGTTTTTACTTTTTTTCCCATACATATTCTGCTTACATATGAGACCTACTTTTTGATAAAACATAGTTACTTCCAACTTAAATTTAAGAAGCTTACCCTAAACATGACATGTGGTTATTCTTCTAGTGTCGAATTTTACTTTCAACAAAAACTGTCATTATTACTAAGCTTAGCTCTATATCAAAGTACACTTGAGTTAATTGCCATTGTGTAATTTTATTTTAACTTAAATGTAAGAAATTACCATATATTGACGCACCTTCTGTTGTAGACACTTTATTGCATTATTTTTTTTAATTTTTTTTAAACTTTCTTTATATTAAAATATTAATCACTGTACAAGAATGTATGTATTATACACATTACAGTTTAAAGAACGTAATAAAACACA HG:+:1348261069:-1 HG:+:2553260082:27 +CAAACTTTTTGTTTTTACTTTTTTTCCCATACATATTCTGCTTACATATGAGACCTACTTTTTGATAAAACATAGTTACTTCCAACTTAAATTTAAGAAGCTTACCCTAAACATGACATGTGGTTATTCTTCTAGTGTCGAATTTTACTTTCAACAAAAACTGTCATTATTACTAAGCTTAGCTCTATATCAAAGTACACTTGAGTTAATTGCCATTGTGTAATTTTATTTTAACTTAAATGTAAGAAATTACCATATATTGACGCACCTTCTGTTGTAGACACTTTATTGCATTATTTTTTTTAATTTTTTTTAAACTTTCTTTATATTAAAATATTAATCACTGTACAAGAATGTATGTATTATACACATTACAGTTTAAAGAACGTAATAAAACACA HG:+:565899339:-1 HG:+:772078133:-1 HG:+:1152124665:-1 HG:+:1907762348:-1 HG:+:2469273715:-1 HG:+:2553260080:27 HG:+:2967245811:-1 +CAAACTTTTTGTTTTTACTTTTTTTCCCATACATATTCTGCTTACATATGAGACCTACTTTTTGATAAAACATAGTTACTTCCAACTTAAATTTAAGAAGCTTACCCTAAACATGACATGTGGTTATTCTTCTAGTGTCGAATTTTACTTTCAACAAAAACTGTCATTATTACTAAGCTTAGCTCTATATCAAAGTACACTTGAGTTAATTGCCATTGTGTAATTTTATTTTAACTTAAATGTAAGAAATTACCATATATTGACGCACCTTCTGTTGTAGACACTTTATTGCATTATTTTTTTTAATTTTTTTTAAACTTTCTTTATATTAAAATATTAATCACTGTACAAGAATGTATGTATTATACACATTACAGTTTAAAGAACGTAATAAAACACA HG:+:120352435:-1 HG:+:282043496:-1 HG:+:460008106:-1 HG:+:828360323:-1 HG:+:938563207:-1 HG:+:1351606962:-1 HG:+:1514320563:-1 HG:+:2228842551:-1 HG:+:2344458530:-1 HG:+:2616010899:-1 HG:+:2652590375:-1 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HG:+:1490870814:70 HG:+:1566895877:-1 HG:+:1583440235:-1 HG:+:1585882192:-1 HG:+:1838074716:-1 HG:+:1930161406:80 HG:+:1995550864:-1 HG:+:2016201565:-1 HG:+:2253656059:74 HG:+:2350849652:68 HG:+:2711096164:-1 HG:+:2742458157:-1 HG:+:2807232174:-1 HG:+:2932759718:78 HG:+:2960102209:-1 HG:+:3004304311:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGACTGGTGTGTAGATGGTATCTCATTCTGGTTTGATTTGCATTTCTCTGATACCAGTGATGTTGAGTTTTTTTTCATATGCTTATCGGCCACATGTATGTGTTCTTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCGCTTTTTGATGGGGTCGTTTTTCTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGCTCTTA HG:+:1342798341:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGACTGGTGTGTAGATGGTATCTCATTCTGGTTTGATTTGCATTTCTCTGATACCAGTGATGTTGAGTTTTTTTTCATATGCTTATCGGCCACATGTATGTGTTCTTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCGCTTTTTGATGGGGTCGTTTTTCTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGCTCTTA HG:+:105833689:-1 HG:+:163194246:-1 HG:+:199850496:-1 HG:+:251464100:-1 HG:+:316274224:-1 HG:+:439793204:-1 HG:+:463482549:-1 HG:+:498426482:-1 HG:+:519359755:-1 HG:+:568344556:-1 HG:+:656088538:-1 HG:+:680276339:-1 HG:+:713890689:-1 HG:+:763379555:-1 HG:+:768852590:-1 HG:+:788359773:-1 HG:+:834035260:-1 HG:+:859974742:-1 HG:+:901141071:-1 HG:+:921647723:-1 HG:+:1017913528:-1 HG:+:1139505204:-1 HG:+:1261199251:-1 HG:+:1444624596:-1 HG:+:1503319529:-1 HG:+:1620433073:-1 HG:+:1701188200:-1 HG:+:1765708827:-1 HG:+:1766890178:-1 HG:+:1766906371:-1 HG:+:1870843311:-1 HG:+:1903076408:-1 HG:+:1997890465:-1 HG:+:2043288878:-1 HG:+:2133801843:-1 HG:+:2238962754:-1 HG:+:2246566934:-1 HG:+:2415612470:-1 HG:+:2463559461:-1 HG:+:2741423947:-1 HG:+:2741541950:-1 HG:+:2937161085:-1 HG:+:2959263157:-1 HG:+:2959934426:-1 HG:+:2990350393:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGACTGGTGTGTAGATGGTATCTCATTCTGGTTTGATTTGCATTTCTCTGATACCAGTGATGTTGAGTTTTTTTTCATATGCTTATCGGCCACATGTATGTGTTCTTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCGCTTTTTGATGGGGTCGTTTTTCTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGCTCTTA HG:+:69469802:-1 HG:+:109306936:-1 HG:+:202482979:-1 HG:+:219568383:-1 HG:+:381591922:-1 HG:+:434823052:-1 HG:+:463848138:-1 HG:+:513592396:-1 HG:+:515128626:-1 HG:+:587942032:-1 HG:+:591536746:-1 HG:+:681845297:-1 HG:+:726507113:-1 HG:+:747149004:-1 HG:+:796886090:75 HG:+:812956041:-1 HG:+:819815784:-1 HG:+:901006760:-1 HG:+:917134221:-1 HG:+:1161089786:-1 HG:+:1172382685:-1 HG:+:1183173602:-1 HG:+:1207555405:76 HG:+:1214199589:-1 HG:+:1250545867:-1 HG:+:1255021734:-1 HG:+:1304072233:-1 HG:+:1357817156:-1 HG:+:1432039788:-1 HG:+:1441778577:-1 HG:+:1734353721:-1 HG:+:1743216588:-1 HG:+:1798626605:-1 HG:+:1839836948:-1 HG:+:1920043882:-1 HG:+:2219483026:-1 HG:+:2272223059:-1 HG:+:2386923628:-1 HG:+:2387433995:-1 HG:+:2391199495:68 HG:+:2559247490:-1 HG:+:2618756067:-1 HG:+:2649177086:-1 HG:+:2679422746:-1 HG:+:2679461083:-1 HG:+:2679639538:-1 HG:+:2679844260:-1 HG:+:2680409419:-1 HG:+:2726499334:-1 HG:+:2908700629:-1 HG:+:2938450459:-1 HG:+:2979122031:-1 HG:+:2997465419:-1 HG:+:3026008923:-1 HG:+:3061859665:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGACTGGTGTGTAGATGGTATCTCATTCTGGTTTGATTTGCATTTCTCTGATACCAGTGATGTTGAGTTTTTTTTCATATGCTTATCGGCCACATGTATGTGTTCTTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCGCTTTTTGATGGGGTCGTTTTTCTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGCTCTTA HG:+:306371008:-1 HG:+:665193636:-1 HG:+:978312809:-1 HG:+:1950327298:-1 HG:+:2135905061:-1 HG:+:2171230756:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGACTGGTGTGTAGATGGTATCTCATTCTGGTTTGATTTGCATTTCTCTGATACCAGTGATGTTGAGTTTTTTTTCATATGCTTATCGGCCACATGTATGTGTTCTTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCGCTTTTTGATGGGGTCGTTTTTCTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGCTCTTA HG:+:14183677:-1 HG:+:61189049:-1 HG:+:74148351:-1 HG:+:92733374:-1 HG:+:106124588:-1 HG:+:158728378:-1 HG:+:184073697:80 HG:+:185765905:-1 HG:+:217474452:-1 HG:+:283165437:77 HG:+:395437494:-1 HG:+:513120118:-1 HG:+:523891690:-1 HG:+:526033252:-1 HG:+:543726312:-1 HG:+:576628275:-1 HG:+:607695895:-1 HG:+:610541877:-1 HG:+:612778699:-1 HG:+:705969709:-1 HG:+:712750764:-1 HG:+:720998114:-1 HG:+:762821742:73 HG:+:823647282:-1 HG:+:903584151:76 HG:+:950889995:-1 HG:+:951765066:-1 HG:+:1002137098:-1 HG:+:1008425992:76 HG:+:1044961398:-1 HG:+:1045610322:-1 HG:+:1045899485:-1 HG:+:1083283929:-1 HG:+:1133243167:-1 HG:+:1164132875:-1 HG:+:1167207877:-1 HG:+:1182990619:-1 HG:+:1194123330:-1 HG:+:1244963010:-1 HG:+:1258355913:-1 HG:+:1286005756:-1 HG:+:1301109416:-1 HG:+:1323088992:-1 HG:+:1477384245:-1 HG:+:1478275560:-1 HG:+:1641681183:-1 HG:+:1789476903:-1 HG:+:1842361271:-1 HG:+:1844938812:-1 HG:+:1900389980:80 HG:+:1971794469:-1 HG:+:2054503406:-1 HG:+:2232127754:76 HG:+:2363835138:-1 HG:+:2701020281:-1 HG:+:2742108424:-1 HG:+:2743147407:-1 HG:+:2821164520:-1 HG:+:2958506857:-1 HG:+:2975182588:-1 HG:+:2981699406:-1 HG:+:3006083292:-1 HG:+:3025107825:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGACTGGTGTGTAGATGGTATCTCATTCTGGTTTGATTTGCATTTCTCTGATACCAGTGATGTTGAGTTTTTTTTCATATGCTTATCGGCCACATGTATGTGTTCTTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCGCTTTTTGATGGGGTCGTTTTTCTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGCTCTTA HG:+:426920652:-1 HG:+:3021338510:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGACTGGTGTGTAGATGGTATCTCATTCTGGTTTGATTTGCATTTCTCTGATACCAGTGATGTTGAGTTTTTTTTCATATGCTTATCGGCCACATGTATGTGTTCTTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCGCTTTTTGATGGGGTCGTTTTTCTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGCTCTTA HG:+:1983184554:-1 HG:+:2253575932:-1 HG:+:2339503811:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGACTGGTGTGTAGATGGTATCTCATTCTGGTTTGATTTGCATTTCTCTGATACCAGTGATGTTGAGTTTTTTTTCATATGCTTATCGGCCACATGTATGTGTTCTTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCGCTTTTTGATGGGGTCGTTTTTCTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGCTCTTA HG:+:16902052:-1 HG:+:167871717:-1 HG:+:394630392:-1 HG:+:394679965:-1 HG:+:558449586:-1 HG:+:616560623:-1 HG:+:657443126:77 HG:+:674391940:-1 HG:+:862097851:74 HG:+:1049758642:-1 HG:+:1147023387:-1 HG:+:1178244885:-1 HG:+:1996847035:-1 HG:+:2002589130:-1 HG:+:2013748399:-1 HG:+:2034672695:-1 HG:+:2265007936:-1 HG:+:2267172645:-1 HG:+:2390946209:-1 HG:+:2472792957:-1 HG:+:2742501584:-1 HG:+:3064027278:-1 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HG:+:1845801627:80 HG:+:1872638232:-1 HG:+:1913301177:-1 HG:+:2260373246:74 HG:+:2344482559:-1 HG:+:2380019170:77 HG:+:2393680704:-1 HG:+:2503393556:-1 HG:+:2542216446:-1 HG:+:2551404890:-1 HG:+:2700457977:-1 HG:+:2701020580:-1 HG:+:2805914215:-1 HG:+:2856829990:72 HG:+:2906302183:-1 HG:+:2926391102:74 HG:+:2939119285:-1 HG:+:2965346780:-1 HG:+:2985531939:72 HG:+:3005607961:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGACTGGTGTGTAGATGGTATCTCATTCTGGTTTGATTTGCATTTCTCTGATACCAGTGATGTTGAGTTTTTTTTCATATGCTTATCGGCCACATGTATGTGTTCTTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCGCTTTTTGATGGGGTCGTTTTTCTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGCTCTTA HG:+:34842016:-1 HG:+:142695424:-1 HG:+:272259928:-1 HG:+:290800209:-1 HG:+:410442986:-1 HG:+:462362492:-1 HG:+:498227215:-1 HG:+:676333970:-1 HG:+:792778371:-1 HG:+:919844962:-1 HG:+:938050772:-1 HG:+:947715526:-1 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HG:+:2968692061:80 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGACTGGTGTGTAGATGGTATCTCATTCTGGTTTGATTTGCATTTCTCTGATACCAGTGATGTTGAGTTTTTTTTCATATGCTTATCGGCCACATGTATGTGTTCTTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCGCTTTTTGATGGGGTCGTTTTTCTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGCTCTTA HG:+:104992800:-1 HG:+:194695096:-1 HG:+:1114591937:-1 HG:+:2119390498:-1 HG:+:2265934953:-1 HG:+:2406029333:-1 +CCCAGTAATGGGATTGCGGTTAAATGGTAGTTCTGCTTTTAGCTCTTTGAGGAATAGCCATACTGGTTTCCAACATGGTTGAACTAATTTTACACTCCCAATTCAACAGTGTATAAGTTGTGTTCCCTTTTCTCTTGCAACCTCGCCAGCATCTGTTATTTGTTGACAGATACGTGACTGTCAACAAATAGCCATTCTGACTGGTGTGTAGATGGTATCTCATTCTGGTTTGATTTGCATTTCTCTGATACCAGTGATGTTGAGTTTTTTTTCATATGCTTATCGGCCACATGTATGTGTTCTTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCGCTTTTTGATGGGGTCGTTTTTCTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGCTCTTA HG:+:302037872:-1 HG:+:377868295:-1 HG:+:822791634:-1 HG:+:995723450:-1 HG:+:1091747275:60 HG:+:1400635577:-1 HG:+:1442155983:-1 HG:+:1711985814:-1 HG:+:1714415442:-1 HG:+:1974203628:-1 HG:+:2490090946:-1 HG:+:2640214999:-1 HG:+:2916383168:-1 +TAAGAGCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAGAAAAACGACCCCATCAAAAAGCGGGCAAAGGACATGAACAGACACTTTTCAAAAAGAACACATACATGTGGCCGATAAGCATATGAAAAAAAACTCAACATCACTGGTATCAGAGAAATGCAAATCAAACCAGAATGAGATACCATCTACACACCAGTCAGAATGGCTATTTGTTGACAGTCACGTATCTGTCAACAAATAACAGATGCTGGCGAGGTTGCAAGAGAAAAGGGAACACAACTTATACACTGTTGAATTGGGAGTGTAAAATTAGTTCAACCATGTTGGAAACCAGTATGGCTATTCCTCAAAGAGCTAAAAGCAGAACTACCATTTAACCGCAATCCCATTACTGGG HG:+:111952922:16 +TAAGAGCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAGAAAAACGACCCCATCAAAAAGCGGGCAAAGGACATGAACAGACACTTTTCAAAAAGAACACATACATGTGGCCGATAAGCATATGAAAAAAAACTCAACATCACTGGTATCAGAGAAATGCAAATCAAACCAGAATGAGATACCATCTACACACCAGTCAGAATGGCTATTTGTTGACAGTCACGTATCTGTCAACAAATAACAGATGCTGGCGAGGTTGCAAGAGAAAAGGGAACACAACTTATACACTGTTGAATTGGGAGTGTAAAATTAGTTCAACCATGTTGGAAACCAGTATGGCTATTCCTCAAAGAGCTAAAAGCAGAACTACCATTTAACCGCAATCCCATTACTGGG HG:+:2647339843:-1 +TAAGAGCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAGAAAAACGACCCCATCAAAAAGCGGGCAAAGGACATGAACAGACACTTTTCAAAAAGAACACATACATGTGGCCGATAAGCATATGAAAAAAAACTCAACATCACTGGTATCAGAGAAATGCAAATCAAACCAGAATGAGATACCATCTACACACCAGTCAGAATGGCTATTTGTTGACAGTCACGTATCTGTCAACAAATAACAGATGCTGGCGAGGTTGCAAGAGAAAAGGGAACACAACTTATACACTGTTGAATTGGGAGTGTAAAATTAGTTCAACCATGTTGGAAACCAGTATGGCTATTCCTCAAAGAGCTAAAAGCAGAACTACCATTTAACCGCAATCCCATTACTGGG HG:+:111952923:16 +TAAGAGCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAGAAAAACGACCCCATCAAAAAGCGGGCAAAGGACATGAACAGACACTTTTCAAAAAGAACACATACATGTGGCCGATAAGCATATGAAAAAAAACTCAACATCACTGGTATCAGAGAAATGCAAATCAAACCAGAATGAGATACCATCTACACACCAGTCAGAATGGCTATTTGTTGACAGTCACGTATCTGTCAACAAATAACAGATGCTGGCGAGGTTGCAAGAGAAAAGGGAACACAACTTATACACTGTTGAATTGGGAGTGTAAAATTAGTTCAACCATGTTGGAAACCAGTATGGCTATTCCTCAAAGAGCTAAAAGCAGAACTACCATTTAACCGCAATCCCATTACTGGG HG:+:111952921:16 HG:+:2935548793:-1 +TCAGTATAATCACATTAGGAGGTTACATGTCAATTTGTGGCATTTACTGGTGATATTAACTTTTTTTTAAGTTCTTGCAGAGAGATTTAGATGTTAGAGTGAACATCACTTTTAAAAAAATTATTTTTCTTTAAATTGATGAATAAAAATAGATATATTTTATGTGTCTAACATGTTTTTATATTTGTAGTGCCTTGCCAAATGGCTAGATCAAGCTAATTTAACAAATCCCTGATGTCACATACTTATTTTTTGTGGTAAGAATACTTACTAAAATCTGCAATTTTCAAGTATACAATAATTATATTAACGATAGTCACCATAGTGTAACTACTGGAAATCTTGAACTTATTCCTACCTTACTGAAACTTTGTGTCCTTTGACCAAGACCCGCTACCCC HG:+:69143271:-1 HG:+:95854696:-1 HG:+:153238223:-1 HG:+:179626661:-1 HG:+:304818237:-1 HG:+:363661785:-1 HG:+:449120088:-1 HG:+:510673638:-1 HG:+:637594156:-1 HG:+:687646485:-1 HG:+:693763487:-1 HG:+:715771085:-1 HG:+:846579841:-1 HG:+:865101330:-1 HG:+:949408817:-1 HG:+:952950443:-1 HG:+:972435541:-1 HG:+:1011626794:-1 HG:+:1071198016:-1 HG:+:1074529442:-1 HG:+:1092639666:-1 HG:+:1111155658:-1 HG:+:1179089775:-1 HG:+:1195704904:-1 HG:+:1209566132:-1 HG:+:1227281283:-1 HG:+:1241704404:-1 HG:+:1312781762:-1 HG:+:1324781041:-1 HG:+:1372856245:-1 HG:+:1389083412:-1 HG:+:1455048122:-1 HG:+:1475059704:-1 HG:+:1490629496:-1 HG:+:1515116692:-1 HG:+:1568578346:-1 HG:+:1783845467:-1 HG:+:1788130059:-1 HG:+:1875002321:-1 HG:+:1901956627:-1 HG:+:1920500122:-1 HG:+:1939701802:-1 HG:+:1966063219:-1 HG:+:2015834168:-1 HG:+:2122713779:-1 HG:+:2170667479:-1 HG:+:2181902586:-1 HG:+:2264505220:-1 HG:+:2292150917:-1 HG:+:2333327516:-1 HG:+:2352354954:-1 HG:+:2385009381:-1 HG:+:2424483951:-1 HG:+:2436639146:-1 HG:+:2507843396:-1 HG:+:2551887209:-1 HG:+:2589556866:-1 HG:+:2604604450:-1 HG:+:2697931154:-1 HG:+:2714602777:-1 HG:+:2821556738:-1 HG:+:2916768041:-1 HG:+:2953894090:-1 HG:+:2957752153:-1 HG:+:2992557185:-1 HG:+:2996775486:-1 HG:+:2998486765:-1 +TCAGTATAATCACATTAGGAGGTTACATGTCAATTTGTGGCATTTACTGGTGATATTAACTTTTTTTTAAGTTCTTGCAGAGAGATTTAGATGTTAGAGTGAACATCACTTTTAAAAAAATTATTTTTCTTTAAATTGATGAATAAAAATAGATATATTTTATGTGTCTAACATGTTTTTATATTTGTAGTGCCTTGCCAAATGGCTAGATCAAGCTAATTTAACAAATCCCTGATGTCACATACTTATTTTTTGTGGTAAGAATACTTACTAAAATCTGCAATTTTCAAGTATACAATAATTATATTAACGATAGTCACCATAGTGTAACTACTGGAAATCTTGAACTTATTCCTACCTTACTGAAACTTTGTGTCCTTTGACCAAGACCCGCTACCCC HG:+:262760531:-1 HG:+:589359224:-1 HG:+:598754160:-1 HG:+:814963022:-1 HG:+:825052496:-1 HG:+:850029991:-1 HG:+:986486412:-1 HG:+:1095618610:-1 HG:+:1201486282:-1 HG:+:1210631537:-1 HG:+:1246672445:-1 HG:+:1250563826:-1 HG:+:1479918565:-1 HG:+:1821221364:-1 HG:+:1966063212:-1 HG:+:2076783147:-1 HG:+:2456564277:-1 HG:+:2588774000:-1 HG:+:2620790881:-1 HG:+:2906518090:-1 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HG:+:1735052531:-1 HG:+:2013527126:-1 +TCAGTATAATCACATTAGGAGGTTACATGTCAATTTGTGGCATTTACTGGTGATATTAACTTTTTTTTAAGTTCTTGCAGAGAGATTTAGATGTTAGAGTGAACATCACTTTTAAAAAAATTATTTTTCTTTAAATTGATGAATAAAAATAGATATATTTTATGTGTCTAACATGTTTTTATATTTGTAGTGCCTTGCCAAATGGCTAGATCAAGCTAATTTAACAAATCCCTGATGTCACATACTTATTTTTTGTGGTAAGAATACTTACTAAAATCTGCAATTTTCAAGTATACAATAATTATATTAACGATAGTCACCATAGTGTAACTACTGGAAATCTTGAACTTATTCCTACCTTACTGAAACTTTGTGTCCTTTGACCAAGACCCGCTACCCC HG:+:25112903:-1 HG:+:66713397:-1 HG:+:202513142:-1 HG:+:283697288:-1 HG:+:291861394:-1 HG:+:298568515:-1 HG:+:305016173:-1 HG:+:409848730:-1 HG:+:423265722:-1 HG:+:454692168:-1 HG:+:475165411:-1 HG:+:477624744:-1 HG:+:483519332:-1 HG:+:508452730:-1 HG:+:522685653:-1 HG:+:531452995:-1 HG:+:546924306:-1 HG:+:589179288:-1 HG:+:634481221:-1 HG:+:658722781:-1 HG:+:661623602:-1 HG:+:676006987:-1 HG:+:682393399:-1 HG:+:725832704:-1 HG:+:743571186:-1 HG:+:749044110:-1 HG:+:755418517:-1 HG:+:764472791:-1 HG:+:778586455:-1 HG:+:781833288:-1 HG:+:824764432:-1 HG:+:855969244:-1 HG:+:914641022:-1 HG:+:931346172:-1 HG:+:952707774:-1 HG:+:960484428:-1 HG:+:1008205695:-1 HG:+:1036688949:-1 HG:+:1053270986:-1 HG:+:1117222425:-1 HG:+:1188403382:-1 HG:+:1209013314:-1 HG:+:1273636265:-1 HG:+:1315835716:-1 HG:+:1362337491:-1 HG:+:1389318266:-1 HG:+:1402301222:-1 HG:+:1411331423:-1 HG:+:1432128790:-1 HG:+:1491799149:-1 HG:+:1540175713:-1 HG:+:1561400505:-1 HG:+:1612462731:-1 HG:+:1640081029:-1 HG:+:1698628894:-1 HG:+:1733713200:-1 HG:+:1737995983:-1 HG:+:1754979383:-1 HG:+:1819959459:-1 HG:+:1838841042:-1 HG:+:1873747239:-1 HG:+:1893811926:-1 HG:+:1912580655:-1 HG:+:1983198418:-1 HG:+:2023992420:-1 HG:+:2028103517:-1 HG:+:2044908165:-1 HG:+:2076579664:-1 HG:+:2082354531:-1 HG:+:2115279265:-1 HG:+:2132405291:-1 HG:+:2143817194:-1 HG:+:2148931043:-1 HG:+:2190898355:-1 HG:+:2251661657:-1 HG:+:2262316125:-1 HG:+:2392880217:-1 HG:+:2399470885:-1 HG:+:2399770438:-1 HG:+:2413489533:-1 HG:+:2463439013:-1 HG:+:2473720865:-1 HG:+:2477212734:-1 HG:+:2485662916:-1 HG:+:2509447444:-1 HG:+:2587992321:-1 HG:+:2593911055:-1 HG:+:2617165250:-1 HG:+:2649867426:-1 HG:+:2667790082:-1 HG:+:2667804937:-1 HG:+:2707252663:-1 HG:+:2735274222:-1 HG:+:2738661376:-1 HG:+:2764730978:-1 HG:+:2804761648:-1 HG:+:2816532768:-1 HG:+:2817065666:-1 HG:+:2820545155:-1 HG:+:2875531346:-1 HG:+:2899475725:-1 HG:+:2957352262:-1 HG:+:2993426452:-1 HG:+:3002861196:-1 HG:+:3026560184:-1 HG:+:3061889767:-1 +TCAGTATAATCACATTAGGAGGTTACATGTCAATTTGTGGCATTTACTGGTGATATTAACTTTTTTTTAAGTTCTTGCAGAGAGATTTAGATGTTAGAGTGAACATCACTTTTAAAAAAATTATTTTTCTTTAAATTGATGAATAAAAATAGATATATTTTATGTGTCTAACATGTTTTTATATTTGTAGTGCCTTGCCAAATGGCTAGATCAAGCTAATTTAACAAATCCCTGATGTCACATACTTATTTTTTGTGGTAAGAATACTTACTAAAATCTGCAATTTTCAAGTATACAATAATTATATTAACGATAGTCACCATAGTGTAACTACTGGAAATCTTGAACTTATTCCTACCTTACTGAAACTTTGTGTCCTTTGACCAAGACCCGCTACCCC HG:+:26996566:-1 HG:+:374260996:-1 HG:+:395713285:-1 HG:+:443525580:-1 HG:+:596330530:-1 HG:+:598695562:-1 HG:+:735405273:-1 HG:+:833166434:-1 HG:+:1084672556:-1 HG:+:1255263625:-1 HG:+:1321340260:-1 HG:+:1323738530:-1 HG:+:1426181012:-1 HG:+:1458300876:-1 HG:+:1572179843:-1 HG:+:1967172685:-1 HG:+:1997174454:-1 HG:+:2122664111:-1 HG:+:2226868595:-1 HG:+:2400832451:-1 HG:+:2604571815:-1 HG:+:3035733931:-1 +TCAGTATAATCACATTAGGAGGTTACATGTCAATTTGTGGCATTTACTGGTGATATTAACTTTTTTTTAAGTTCTTGCAGAGAGATTTAGATGTTAGAGTGAACATCACTTTTAAAAAAATTATTTTTCTTTAAATTGATGAATAAAAATAGATATATTTTATGTGTCTAACATGTTTTTATATTTGTAGTGCCTTGCCAAATGGCTAGATCAAGCTAATTTAACAAATCCCTGATGTCACATACTTATTTTTTGTGGTAAGAATACTTACTAAAATCTGCAATTTTCAAGTATACAATAATTATATTAACGATAGTCACCATAGTGTAACTACTGGAAATCTTGAACTTATTCCTACCTTACTGAAACTTTGTGTCCTTTGACCAAGACCCGCTACCCC HG:+:448201811:-1 HG:+:656704610:-1 HG:+:1583627747:-1 HG:+:1666845588:-1 HG:+:1984700072:-1 HG:+:2777027864:-1 HG:+:3100493984:-1 +TCAGTATAATCACATTAGGAGGTTACATGTCAATTTGTGGCATTTACTGGTGATATTAACTTTTTTTTAAGTTCTTGCAGAGAGATTTAGATGTTAGAGTGAACATCACTTTTAAAAAAATTATTTTTCTTTAAATTGATGAATAAAAATAGATATATTTTATGTGTCTAACATGTTTTTATATTTGTAGTGCCTTGCCAAATGGCTAGATCAAGCTAATTTAACAAATCCCTGATGTCACATACTTATTTTTTGTGGTAAGAATACTTACTAAAATCTGCAATTTTCAAGTATACAATAATTATATTAACGATAGTCACCATAGTGTAACTACTGGAAATCTTGAACTTATTCCTACCTTACTGAAACTTTGTGTCCTTTGACCAAGACCCGCTACCCC HG:+:1244689602:-1 HG:+:1370841779:-1 HG:+:2624210278:-1 +TCAGTATAATCACATTAGGAGGTTACATGTCAATTTGTGGCATTTACTGGTGATATTAACTTTTTTTTAAGTTCTTGCAGAGAGATTTAGATGTTAGAGTGAACATCACTTTTAAAAAAATTATTTTTCTTTAAATTGATGAATAAAAATAGATATATTTTATGTGTCTAACATGTTTTTATATTTGTAGTGCCTTGCCAAATGGCTAGATCAAGCTAATTTAACAAATCCCTGATGTCACATACTTATTTTTTGTGGTAAGAATACTTACTAAAATCTGCAATTTTCAAGTATACAATAATTATATTAACGATAGTCACCATAGTGTAACTACTGGAAATCTTGAACTTATTCCTACCTTACTGAAACTTTGTGTCCTTTGACCAAGACCCGCTACCCC HG:+:2405139872:-1 +TCAGTATAATCACATTAGGAGGTTACATGTCAATTTGTGGCATTTACTGGTGATATTAACTTTTTTTTAAGTTCTTGCAGAGAGATTTAGATGTTAGAGTGAACATCACTTTTAAAAAAATTATTTTTCTTTAAATTGATGAATAAAAATAGATATATTTTATGTGTCTAACATGTTTTTATATTTGTAGTGCCTTGCCAAATGGCTAGATCAAGCTAATTTAACAAATCCCTGATGTCACATACTTATTTTTTGTGGTAAGAATACTTACTAAAATCTGCAATTTTCAAGTATACAATAATTATATTAACGATAGTCACCATAGTGTAACTACTGGAAATCTTGAACTTATTCCTACCTTACTGAAACTTTGTGTCCTTTGACCAAGACCCGCTACCCC HG:+:674012886:-1 +TCAGTATAATCACATTAGGAGGTTACATGTCAATTTGTGGCATTTACTGGTGATATTAACTTTTTTTTAAGTTCTTGCAGAGAGATTTAGATGTTAGAGTGAACATCACTTTTAAAAAAATTATTTTTCTTTAAATTGATGAATAAAAATAGATATATTTTATGTGTCTAACATGTTTTTATATTTGTAGTGCCTTGCCAAATGGCTAGATCAAGCTAATTTAACAAATCCCTGATGTCACATACTTATTTTTTGTGGTAAGAATACTTACTAAAATCTGCAATTTTCAAGTATACAATAATTATATTAACGATAGTCACCATAGTGTAACTACTGGAAATCTTGAACTTATTCCTACCTTACTGAAACTTTGTGTCCTTTGACCAAGACCCGCTACCCC HG:+:411889579:-1 HG:+:859756002:-1 HG:+:984420324:-1 HG:+:1162753369:-1 HG:+:1195704901:-1 HG:+:1506337684:-1 HG:+:1612550248:-1 HG:+:1632939430:-1 HG:+:1962867417:-1 HG:+:1984695555:-1 HG:+:2132117576:-1 HG:+:2245595499:-1 HG:+:2332928849:-1 HG:+:2361235097:-1 HG:+:2383684561:-1 HG:+:2615205631:-1 +GGGGTAGCGGGTCTTGGTCAAAGGACACAAAGTTTCAGTAAGGTAGGAATAAGTTCAAGATTTCCAGTAGTTACACTATGGTGACTATCGTTAATATAATTATTGTATACTTGAAAATTGCAGATTTTAGTAAGTATTCTTACCACAAAAAATAAGTATGTGACATCAGGGATTTGTTAAATTAGCTTGATCTAGCCATTTGGCAAGGCACTACAAATATAAAAACATGTTAGACACATAAAATATATCTATTTTTATTCATCAATTTAAAGAAAAATAATTTTTTTAAAAGTGATGTTCACTCTAACATCTAAATCTCTCTGCAAGAACTTAAAAAAAAGTTAATATCACCAGTAAATGCCACAAATTGACATGTAACCTCCTAATGTGATTATACTGA HG:+:685576793:-1 HG:+:890132545:-1 HG:+:1206881405:14 HG:+:1648868300:-1 +GGGGTAGCGGGTCTTGGTCAAAGGACACAAAGTTTCAGTAAGGTAGGAATAAGTTCAAGATTTCCAGTAGTTACACTATGGTGACTATCGTTAATATAATTATTGTATACTTGAAAATTGCAGATTTTAGTAAGTATTCTTACCACAAAAAATAAGTATGTGACATCAGGGATTTGTTAAATTAGCTTGATCTAGCCATTTGGCAAGGCACTACAAATATAAAAACATGTTAGACACATAAAATATATCTATTTTTATTCATCAATTTAAAGAAAAATAATTTTTTTAAAAGTGATGTTCACTCTAACATCTAAATCTCTCTGCAAGAACTTAAAAAAAAGTTAATATCACCAGTAAATGCCACAAATTGACATGTAACCTCCTAATGTGATTATACTGA HG:+:1206881407:14 +GGGGTAGCGGGTCTTGGTCAAAGGACACAAAGTTTCAGTAAGGTAGGAATAAGTTCAAGATTTCCAGTAGTTACACTATGGTGACTATCGTTAATATAATTATTGTATACTTGAAAATTGCAGATTTTAGTAAGTATTCTTACCACAAAAAATAAGTATGTGACATCAGGGATTTGTTAAATTAGCTTGATCTAGCCATTTGGCAAGGCACTACAAATATAAAAACATGTTAGACACATAAAATATATCTATTTTTATTCATCAATTTAAAGAAAAATAATTTTTTTAAAAGTGATGTTCACTCTAACATCTAAATCTCTCTGCAAGAACTTAAAAAAAAGTTAATATCACCAGTAAATGCCACAAATTGACATGTAACCTCCTAATGTGATTATACTGA HG:+:1206881409:14 +GGGGTAGCGGGTCTTGGTCAAAGGACACAAAGTTTCAGTAAGGTAGGAATAAGTTCAAGATTTCCAGTAGTTACACTATGGTGACTATCGTTAATATAATTATTGTATACTTGAAAATTGCAGATTTTAGTAAGTATTCTTACCACAAAAAATAAGTATGTGACATCAGGGATTTGTTAAATTAGCTTGATCTAGCCATTTGGCAAGGCACTACAAATATAAAAACATGTTAGACACATAAAATATATCTATTTTTATTCATCAATTTAAAGAAAAATAATTTTTTTAAAAGTGATGTTCACTCTAACATCTAAATCTCTCTGCAAGAACTTAAAAAAAAGTTAATATCACCAGTAAATGCCACAAATTGACATGTAACCTCCTAATGTGATTATACTGA HG:+:1206881406:14 HG:+:1959450704:-1 +AAATTCCATACACTTCTTTTTTATAAAGCTGATCTGCCTGAGGATATGCCTGTGGTGCTGTTTATAATCTCTTTTCTCCCTCCCACAAAAAGATAGGCAAACTTTTTACCCAATCCAGGAATCTTACCCTAGTTTGTGGCCCACAAATGGTCAAAACTTTCTGGGGCACCAAACAAAGCAACATTTTCAAATATCAGTATCAGCTTTTAGAAAATTGAATTTATTCTGACAGGGAGCAAAACCTTTGGAAAATATGATGGTTTTCAAATTCTTTGCTTTTTAGCAAAATTGAAGGAGGAGCCAAAATCAACTTGTACAGCTGATAAATCATTAAAATTAATCTTGATGAAAGTTAACTTACATGAATTTTGGCATTTATTTGCAAAAAAAAAAAGAACTA HG:+:914909300:20 HG:+:1132860267:-1 HG:+:1622461135:-1 +AAATTCCATACACTTCTTTTTTATAAAGCTGATCTGCCTGAGGATATGCCTGTGGTGCTGTTTATAATCTCTTTTCTCCCTCCCACAAAAAGATAGGCAAACTTTTTACCCAATCCAGGAATCTTACCCTAGTTTGTGGCCCACAAATGGTCAAAACTTTCTGGGGCACCAAACAAAGCAACATTTTCAAATATCAGTATCAGCTTTTAGAAAATTGAATTTATTCTGACAGGGAGCAAAACCTTTGGAAAATATGATGGTTTTCAAATTCTTTGCTTTTTAGCAAAATTGAAGGAGGAGCCAAAATCAACTTGTACAGCTGATAAATCATTAAAATTAATCTTGATGAAAGTTAACTTACATGAATTTTGGCATTTATTTGCAAAAAAAAAAAGAACTA HG:+:914909305:20 +AAATTCCATACACTTCTTTTTTATAAAGCTGATCTGCCTGAGGATATGCCTGTGGTGCTGTTTATAATCTCTTTTCTCCCTCCCACAAAAAGATAGGCAAACTTTTTACCCAATCCAGGAATCTTACCCTAGTTTGTGGCCCACAAATGGTCAAAACTTTCTGGGGCACCAAACAAAGCAACATTTTCAAATATCAGTATCAGCTTTTAGAAAATTGAATTTATTCTGACAGGGAGCAAAACCTTTGGAAAATATGATGGTTTTCAAATTCTTTGCTTTTTAGCAAAATTGAAGGAGGAGCCAAAATCAACTTGTACAGCTGATAAATCATTAAAATTAATCTTGATGAAAGTTAACTTACATGAATTTTGGCATTTATTTGCAAAAAAAAAAAGAACTA HG:+:914909309:20 +AAATTCCATACACTTCTTTTTTATAAAGCTGATCTGCCTGAGGATATGCCTGTGGTGCTGTTTATAATCTCTTTTCTCCCTCCCACAAAAAGATAGGCAAACTTTTTACCCAATCCAGGAATCTTACCCTAGTTTGTGGCCCACAAATGGTCAAAACTTTCTGGGGCACCAAACAAAGCAACATTTTCAAATATCAGTATCAGCTTTTAGAAAATTGAATTTATTCTGACAGGGAGCAAAACCTTTGGAAAATATGATGGTTTTCAAATTCTTTGCTTTTTAGCAAAATTGAAGGAGGAGCCAAAATCAACTTGTACAGCTGATAAATCATTAAAATTAATCTTGATGAAAGTTAACTTACATGAATTTTGGCATTTATTTGCAAAAAAAAAAAGAACTA HG:+:914909307:20 +AAATTCCATACACTTCTTTTTTATAAAGCTGATCTGCCTGAGGATATGCCTGTGGTGCTGTTTATAATCTCTTTTCTCCCTCCCACAAAAAGATAGGCAAACTTTTTACCCAATCCAGGAATCTTACCCTAGTTTGTGGCCCACAAATGGTCAAAACTTTCTGGGGCACCAAACAAAGCAACATTTTCAAATATCAGTATCAGCTTTTAGAAAATTGAATTTATTCTGACAGGGAGCAAAACCTTTGGAAAATATGATGGTTTTCAAATTCTTTGCTTTTTAGCAAAATTGAAGGAGGAGCCAAAATCAACTTGTACAGCTGATAAATCATTAAAATTAATCTTGATGAAAGTTAACTTACATGAATTTTGGCATTTATTTGCAAAAAAAAAAAGAACTA HG:+:914909310:20 +AAGTTGTTTATTCTCTCAAACAATAAAATATGTGTGTACAATCCCAAGACATTTTTGAAAGGAATAAAACCTTGCATCTCTGAATTCCTGTGGGGCCTAGCAACAATGGACGATATACTACGTTGCAGTGTCATTTCCCTAAAATCTAGCTTGTGTGTTACAATCACCATTGATGTATCTTCCCCCACGAACCTAGAGAAGCCAGGCTTAAATCTCTGTCCTGGCATTCACTAATGTCATGGCCTCAGAAAAATTGGATAGGACTTTCTGAAACTTGTTTTCTGACCCATAAAAAGTGTGATAACTCGGCAGTAGTCGTTTTTAATCCCACAGGAATATTGGAAGAACCAGATGATTTCATATATCGGGAAAGGGCCCTTGGAGCAATGCCCTGGGCTTC HG:+:2724001427:-1 HG:+:2887973525:-1 +AAGTTGTTTATTCTCTCAAACAATAAAATATGTGTGTACAATCCCAAGACATTTTTGAAAGGAATAAAACCTTGCATCTCTGAATTCCTGTGGGGCCTAGCAACAATGGACGATATACTACGTTGCAGTGTCATTTCCCTAAAATCTAGCTTGTGTGTTACAATCACCATTGATGTATCTTCCCCCACGAACCTAGAGAAGCCAGGCTTAAATCTCTGTCCTGGCATTCACTAATGTCATGGCCTCAGAAAAATTGGATAGGACTTTCTGAAACTTGTTTTCTGACCCATAAAAAGTGTGATAACTCGGCAGTAGTCGTTTTTAATCCCACAGGAATATTGGAAGAACCAGATGATTTCATATATCGGGAAAGGGCCCTTGGAGCAATGCCCTGGGCTTC HG:+:166619398:-1 HG:+:2811682797:-1 +AAGTTGTTTATTCTCTCAAACAATAAAATATGTGTGTACAATCCCAAGACATTTTTGAAAGGAATAAAACCTTGCATCTCTGAATTCCTGTGGGGCCTAGCAACAATGGACGATATACTACGTTGCAGTGTCATTTCCCTAAAATCTAGCTTGTGTGTTACAATCACCATTGATGTATCTTCCCCCACGAACCTAGAGAAGCCAGGCTTAAATCTCTGTCCTGGCATTCACTAATGTCATGGCCTCAGAAAAATTGGATAGGACTTTCTGAAACTTGTTTTCTGACCCATAAAAAGTGTGATAACTCGGCAGTAGTCGTTTTTAATCCCACAGGAATATTGGAAGAACCAGATGATTTCATATATCGGGAAAGGGCCCTTGGAGCAATGCCCTGGGCTTC HG:+:1179183093:-1 HG:+:1796971226:-1 HG:+:2223826457:-1 HG:+:2489562257:-1 +AAGTTGTTTATTCTCTCAAACAATAAAATATGTGTGTACAATCCCAAGACATTTTTGAAAGGAATAAAACCTTGCATCTCTGAATTCCTGTGGGGCCTAGCAACAATGGACGATATACTACGTTGCAGTGTCATTTCCCTAAAATCTAGCTTGTGTGTTACAATCACCATTGATGTATCTTCCCCCACGAACCTAGAGAAGCCAGGCTTAAATCTCTGTCCTGGCATTCACTAATGTCATGGCCTCAGAAAAATTGGATAGGACTTTCTGAAACTTGTTTTCTGACCCATAAAAAGTGTGATAACTCGGCAGTAGTCGTTTTTAATCCCACAGGAATATTGGAAGAACCAGATGATTTCATATATCGGGAAAGGGCCCTTGGAGCAATGCCCTGGGCTTC HG:+:98804197:-1 HG:+:672748376:-1 HG:+:1271781633:-1 HG:+:1660109606:-1 HG:+:2332594157:-1 HG:+:2332966449:-1 HG:+:2609623656:-1 HG:+:2621043259:-1 HG:+:2702618960:-1 +AAGTTGTTTATTCTCTCAAACAATAAAATATGTGTGTACAATCCCAAGACATTTTTGAAAGGAATAAAACCTTGCATCTCTGAATTCCTGTGGGGCCTAGCAACAATGGACGATATACTACGTTGCAGTGTCATTTCCCTAAAATCTAGCTTGTGTGTTACAATCACCATTGATGTATCTTCCCCCACGAACCTAGAGAAGCCAGGCTTAAATCTCTGTCCTGGCATTCACTAATGTCATGGCCTCAGAAAAATTGGATAGGACTTTCTGAAACTTGTTTTCTGACCCATAAAAAGTGTGATAACTCGGCAGTAGTCGTTTTTAATCCCACAGGAATATTGGAAGAACCAGATGATTTCATATATCGGGAAAGGGCCCTTGGAGCAATGCCCTGGGCTTC HG:+:357822240:-1 HG:+:901120959:-1 HG:+:989702126:-1 HG:+:1168878557:-1 HG:+:1572235655:-1 HG:+:1687671005:-1 HG:+:2301204724:-1 HG:+:2382774474:-1 HG:+:2409389313:-1 HG:+:2559749845:-1 HG:+:2976417814:-1 +AAGTTGTTTATTCTCTCAAACAATAAAATATGTGTGTACAATCCCAAGACATTTTTGAAAGGAATAAAACCTTGCATCTCTGAATTCCTGTGGGGCCTAGCAACAATGGACGATATACTACGTTGCAGTGTCATTTCCCTAAAATCTAGCTTGTGTGTTACAATCACCATTGATGTATCTTCCCCCACGAACCTAGAGAAGCCAGGCTTAAATCTCTGTCCTGGCATTCACTAATGTCATGGCCTCAGAAAAATTGGATAGGACTTTCTGAAACTTGTTTTCTGACCCATAAAAAGTGTGATAACTCGGCAGTAGTCGTTTTTAATCCCACAGGAATATTGGAAGAACCAGATGATTTCATATATCGGGAAAGGGCCCTTGGAGCAATGCCCTGGGCTTC HG:+:278861217:-1 HG:+:305462149:-1 HG:+:361180299:-1 HG:+:400958243:-1 HG:+:540819787:-1 HG:+:679972068:-1 HG:+:777203203:-1 HG:+:1162945337:-1 HG:+:1350440046:-1 HG:+:1488937635:-1 HG:+:1752504897:-1 HG:+:1841057861:-1 HG:+:2261868651:-1 HG:+:2774563017:-1 +AAGTTGTTTATTCTCTCAAACAATAAAATATGTGTGTACAATCCCAAGACATTTTTGAAAGGAATAAAACCTTGCATCTCTGAATTCCTGTGGGGCCTAGCAACAATGGACGATATACTACGTTGCAGTGTCATTTCCCTAAAATCTAGCTTGTGTGTTACAATCACCATTGATGTATCTTCCCCCACGAACCTAGAGAAGCCAGGCTTAAATCTCTGTCCTGGCATTCACTAATGTCATGGCCTCAGAAAAATTGGATAGGACTTTCTGAAACTTGTTTTCTGACCCATAAAAAGTGTGATAACTCGGCAGTAGTCGTTTTTAATCCCACAGGAATATTGGAAGAACCAGATGATTTCATATATCGGGAAAGGGCCCTTGGAGCAATGCCCTGGGCTTC HG:+:682834436:-1 HG:+:774054607:-1 HG:+:926317994:-1 HG:+:1342500139:-1 HG:+:1758479990:-1 HG:+:1908219658:-1 HG:+:2006779066:-1 HG:+:2248048788:-1 HG:+:2331754042:-1 HG:+:2331856616:-1 HG:+:2332063966:-1 HG:+:2352322375:-1 HG:+:2375107056:-1 +AAGTTGTTTATTCTCTCAAACAATAAAATATGTGTGTACAATCCCAAGACATTTTTGAAAGGAATAAAACCTTGCATCTCTGAATTCCTGTGGGGCCTAGCAACAATGGACGATATACTACGTTGCAGTGTCATTTCCCTAAAATCTAGCTTGTGTGTTACAATCACCATTGATGTATCTTCCCCCACGAACCTAGAGAAGCCAGGCTTAAATCTCTGTCCTGGCATTCACTAATGTCATGGCCTCAGAAAAATTGGATAGGACTTTCTGAAACTTGTTTTCTGACCCATAAAAAGTGTGATAACTCGGCAGTAGTCGTTTTTAATCCCACAGGAATATTGGAAGAACCAGATGATTTCATATATCGGGAAAGGGCCCTTGGAGCAATGCCCTGGGCTTC HG:+:49142887:-1 HG:+:52730953:-1 HG:+:176607083:-1 HG:+:487218626:-1 HG:+:488963601:-1 HG:+:600455009:-1 HG:+:636862511:-1 HG:+:663776747:-1 HG:+:728339217:-1 HG:+:823846352:-1 HG:+:843499793:-1 HG:+:955075730:-1 HG:+:1003769865:-1 HG:+:1171200185:-1 HG:+:1196232112:-1 HG:+:1371771107:-1 HG:+:1654230458:-1 HG:+:1742129171:-1 HG:+:1853809226:-1 HG:+:1896493188:-1 HG:+:1918247700:-1 HG:+:2189344261:-1 HG:+:2377211740:-1 HG:+:2435947207:-1 HG:+:2590649501:-1 HG:+:2621832682:-1 HG:+:2800142525:-1 HG:+:2877599669:-1 HG:+:2907091718:-1 HG:+:2932214800:-1 HG:+:3061674695:-1 HG:+:3063289081:-1 HG:+:3063299931:-1 HG:+:3064089312:-1 HG:+:3064280502:-1 +AAGTTGTTTATTCTCTCAAACAATAAAATATGTGTGTACAATCCCAAGACATTTTTGAAAGGAATAAAACCTTGCATCTCTGAATTCCTGTGGGGCCTAGCAACAATGGACGATATACTACGTTGCAGTGTCATTTCCCTAAAATCTAGCTTGTGTGTTACAATCACCATTGATGTATCTTCCCCCACGAACCTAGAGAAGCCAGGCTTAAATCTCTGTCCTGGCATTCACTAATGTCATGGCCTCAGAAAAATTGGATAGGACTTTCTGAAACTTGTTTTCTGACCCATAAAAAGTGTGATAACTCGGCAGTAGTCGTTTTTAATCCCACAGGAATATTGGAAGAACCAGATGATTTCATATATCGGGAAAGGGCCCTTGGAGCAATGCCCTGGGCTTC HG:+:62848307:-1 HG:+:63078349:-1 HG:+:106984984:-1 HG:+:219771982:-1 HG:+:261453686:-1 HG:+:294848000:-1 HG:+:392078624:-1 HG:+:419790689:-1 HG:+:451656438:-1 HG:+:461319119:-1 HG:+:679238637:-1 HG:+:735666286:-1 HG:+:888600642:-1 HG:+:902145007:-1 HG:+:932728803:-1 HG:+:1002286263:-1 HG:+:1138470671:-1 HG:+:1169347571:-1 HG:+:1337722573:-1 HG:+:1337833409:-1 HG:+:1355877449:-1 HG:+:1378343662:-1 HG:+:1427124247:-1 HG:+:1489905075:-1 HG:+:1671864854:-1 HG:+:1724114144:-1 HG:+:1746181540:-1 HG:+:1786932706:-1 HG:+:1906157632:-1 HG:+:1919133045:-1 HG:+:1943296027:-1 HG:+:2042314105:-1 HG:+:2126202570:-1 HG:+:2493310883:-1 HG:+:2513033187:-1 HG:+:2692270354:-1 HG:+:2721550564:-1 HG:+:2807263243:-1 HG:+:3028800597:-1 +GAAGCCCAGGGCATTGCTCCAAGGGCCCTTTCCCGATATATGAAATCATCTGGTTCTTCCAATATTCCTGTGGGATTAAAAACGACTACTGCCGAGTTATCACACTTTTTATGGGTCAGAAAACAAGTTTCAGAAAGTCCTATCCAATTTTTCTGAGGCCATGACATTAGTGAATGCCAGGACAGAGATTTAAGCCTGGCTTCTCTAGGTTCGTGGGGGAAGATACATCAATGGTGATTGTAACACACAAGCTAGATTTTAGGGAAATGACACTGCAACGTAGTATATCGTCCATTGTTGCTAGGCCCCACAGGAATTCAGAGATGCAAGGTTTTATTCCTTTCAAAAATGTCTTGGGATTGTACACACATATTTTATTGTTTGAGAGAATAAACAACTT HG:+:719180804:-1 HG:+:873339056:-1 +GAAGCCCAGGGCATTGCTCCAAGGGCCCTTTCCCGATATATGAAATCATCTGGTTCTTCCAATATTCCTGTGGGATTAAAAACGACTACTGCCGAGTTATCACACTTTTTATGGGTCAGAAAACAAGTTTCAGAAAGTCCTATCCAATTTTTCTGAGGCCATGACATTAGTGAATGCCAGGACAGAGATTTAAGCCTGGCTTCTCTAGGTTCGTGGGGGAAGATACATCAATGGTGATTGTAACACACAAGCTAGATTTTAGGGAAATGACACTGCAACGTAGTATATCGTCCATTGTTGCTAGGCCCCACAGGAATTCAGAGATGCAAGGTTTTATTCCTTTCAAAAATGTCTTGGGATTGTACACACATATTTTATTGTTTGAGAGAATAAACAACTT HG:+:705873798:25 HG:+:815184747:-1 HG:+:1262484807:-1 HG:+:1704458984:-1 HG:+:1725388515:-1 HG:+:2079450010:-1 +GAAGCCCAGGGCATTGCTCCAAGGGCCCTTTCCCGATATATGAAATCATCTGGTTCTTCCAATATTCCTGTGGGATTAAAAACGACTACTGCCGAGTTATCACACTTTTTATGGGTCAGAAAACAAGTTTCAGAAAGTCCTATCCAATTTTTCTGAGGCCATGACATTAGTGAATGCCAGGACAGAGATTTAAGCCTGGCTTCTCTAGGTTCGTGGGGGAAGATACATCAATGGTGATTGTAACACACAAGCTAGATTTTAGGGAAATGACACTGCAACGTAGTATATCGTCCATTGTTGCTAGGCCCCACAGGAATTCAGAGATGCAAGGTTTTATTCCTTTCAAAAATGTCTTGGGATTGTACACACATATTTTATTGTTTGAGAGAATAAACAACTT HG:+:180574123:-1 HG:+:289805422:-1 HG:+:705873801:25 HG:+:709093752:-1 HG:+:1781758791:-1 HG:+:2250993527:-1 HG:+:2289685664:-1 +GAAGCCCAGGGCATTGCTCCAAGGGCCCTTTCCCGATATATGAAATCATCTGGTTCTTCCAATATTCCTGTGGGATTAAAAACGACTACTGCCGAGTTATCACACTTTTTATGGGTCAGAAAACAAGTTTCAGAAAGTCCTATCCAATTTTTCTGAGGCCATGACATTAGTGAATGCCAGGACAGAGATTTAAGCCTGGCTTCTCTAGGTTCGTGGGGGAAGATACATCAATGGTGATTGTAACACACAAGCTAGATTTTAGGGAAATGACACTGCAACGTAGTATATCGTCCATTGTTGCTAGGCCCCACAGGAATTCAGAGATGCAAGGTTTTATTCCTTTCAAAAATGTCTTGGGATTGTACACACATATTTTATTGTTTGAGAGAATAAACAACTT HG:+:705873802:25 +GAAGCCCAGGGCATTGCTCCAAGGGCCCTTTCCCGATATATGAAATCATCTGGTTCTTCCAATATTCCTGTGGGATTAAAAACGACTACTGCCGAGTTATCACACTTTTTATGGGTCAGAAAACAAGTTTCAGAAAGTCCTATCCAATTTTTCTGAGGCCATGACATTAGTGAATGCCAGGACAGAGATTTAAGCCTGGCTTCTCTAGGTTCGTGGGGGAAGATACATCAATGGTGATTGTAACACACAAGCTAGATTTTAGGGAAATGACACTGCAACGTAGTATATCGTCCATTGTTGCTAGGCCCCACAGGAATTCAGAGATGCAAGGTTTTATTCCTTTCAAAAATGTCTTGGGATTGTACACACATATTTTATTGTTTGAGAGAATAAACAACTT HG:+:705873806:25 +GAAGCCCAGGGCATTGCTCCAAGGGCCCTTTCCCGATATATGAAATCATCTGGTTCTTCCAATATTCCTGTGGGATTAAAAACGACTACTGCCGAGTTATCACACTTTTTATGGGTCAGAAAACAAGTTTCAGAAAGTCCTATCCAATTTTTCTGAGGCCATGACATTAGTGAATGCCAGGACAGAGATTTAAGCCTGGCTTCTCTAGGTTCGTGGGGGAAGATACATCAATGGTGATTGTAACACACAAGCTAGATTTTAGGGAAATGACACTGCAACGTAGTATATCGTCCATTGTTGCTAGGCCCCACAGGAATTCAGAGATGCAAGGTTTTATTCCTTTCAAAAATGTCTTGGGATTGTACACACATATTTTATTGTTTGAGAGAATAAACAACTT HG:+:705873812:25 +GAAGCCCAGGGCATTGCTCCAAGGGCCCTTTCCCGATATATGAAATCATCTGGTTCTTCCAATATTCCTGTGGGATTAAAAACGACTACTGCCGAGTTATCACACTTTTTATGGGTCAGAAAACAAGTTTCAGAAAGTCCTATCCAATTTTTCTGAGGCCATGACATTAGTGAATGCCAGGACAGAGATTTAAGCCTGGCTTCTCTAGGTTCGTGGGGGAAGATACATCAATGGTGATTGTAACACACAAGCTAGATTTTAGGGAAATGACACTGCAACGTAGTATATCGTCCATTGTTGCTAGGCCCCACAGGAATTCAGAGATGCAAGGTTTTATTCCTTTCAAAAATGTCTTGGGATTGTACACACATATTTTATTGTTTGAGAGAATAAACAACTT HG:+:1427288740:-1 +GAAGCCCAGGGCATTGCTCCAAGGGCCCTTTCCCGATATATGAAATCATCTGGTTCTTCCAATATTCCTGTGGGATTAAAAACGACTACTGCCGAGTTATCACACTTTTTATGGGTCAGAAAACAAGTTTCAGAAAGTCCTATCCAATTTTTCTGAGGCCATGACATTAGTGAATGCCAGGACAGAGATTTAAGCCTGGCTTCTCTAGGTTCGTGGGGGAAGATACATCAATGGTGATTGTAACACACAAGCTAGATTTTAGGGAAATGACACTGCAACGTAGTATATCGTCCATTGTTGCTAGGCCCCACAGGAATTCAGAGATGCAAGGTTTTATTCCTTTCAAAAATGTCTTGGGATTGTACACACATATTTTATTGTTTGAGAGAATAAACAACTT HG:+:570239401:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGAAGGAATATATCAAAAGGTATTAACAATGGTTATCGACGTATGATGAAATGATGAGCTATTTTAATTTTCTTGCATACATTTTTTATGTTAATCTGAATTATCTATAGTAAAACTTATATTATCTTGAACAAATAAACGTATTTTAAAACCCTAAACTAACTCTAGGCAGTAGAAACTGAAGTTACAAAGTCCCTTAGACT HG:+:258193151:-1 HG:+:289584886:-1 HG:+:321924111:-1 HG:+:355774530:-1 HG:+:406728601:-1 HG:+:436856760:-1 HG:+:514363138:-1 HG:+:538900575:-1 HG:+:556611019:-1 HG:+:582444862:-1 HG:+:601435441:-1 HG:+:765027103:-1 HG:+:782598951:-1 HG:+:811419663:-1 HG:+:859692539:-1 HG:+:952886439:-1 HG:+:954988712:-1 HG:+:961334482:-1 HG:+:975041832:-1 HG:+:977417043:-1 HG:+:1030934732:-1 HG:+:1220352466:-1 HG:+:1301589920:-1 HG:+:1487348452:-1 HG:+:1566845360:-1 HG:+:1574116612:-1 HG:+:1620705165:-1 HG:+:1806572516:-1 HG:+:2012867684:-1 HG:+:2057164573:-1 HG:+:2129246312:-1 HG:+:2358196116:-1 HG:+:2375084238:-1 HG:+:2420476803:-1 HG:+:2482144329:-1 HG:+:2763939841:-1 HG:+:2907991380:-1 HG:+:3039354307:-1 HG:+:3042157253:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGAAGGAATATATCAAAAGGTATTAACAATGGTTATCGACGTATGATGAAATGATGAGCTATTTTAATTTTCTTGCATACATTTTTTATGTTAATCTGAATTATCTATAGTAAAACTTATATTATCTTGAACAAATAAACGTATTTTAAAACCCTAAACTAACTCTAGGCAGTAGAAACTGAAGTTACAAAGTCCCTTAGACT HG:+:99397561:-1 HG:+:211071343:-1 HG:+:429117894:-1 HG:+:449408633:-1 HG:+:587723650:-1 HG:+:858981218:-1 HG:+:866689212:-1 HG:+:867340717:-1 HG:+:958499240:-1 HG:+:1011717920:-1 HG:+:1246056807:-1 HG:+:1508279189:-1 HG:+:1765264371:-1 HG:+:1983402011:-1 HG:+:2134483588:-1 HG:+:2177691758:-1 HG:+:2269294335:-1 HG:+:2350069443:-1 HG:+:2619407034:-1 HG:+:2696074376:-1 HG:+:2930839053:-1 HG:+:2990633015:-1 HG:+:3043544088:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGAAGGAATATATCAAAAGGTATTAACAATGGTTATCGACGTATGATGAAATGATGAGCTATTTTAATTTTCTTGCATACATTTTTTATGTTAATCTGAATTATCTATAGTAAAACTTATATTATCTTGAACAAATAAACGTATTTTAAAACCCTAAACTAACTCTAGGCAGTAGAAACTGAAGTTACAAAGTCCCTTAGACT HG:+:648913539:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGAAGGAATATATCAAAAGGTATTAACAATGGTTATCGACGTATGATGAAATGATGAGCTATTTTAATTTTCTTGCATACATTTTTTATGTTAATCTGAATTATCTATAGTAAAACTTATATTATCTTGAACAAATAAACGTATTTTAAAACCCTAAACTAACTCTAGGCAGTAGAAACTGAAGTTACAAAGTCCCTTAGACT HG:+:7087407:-1 HG:+:80667047:-1 HG:+:852582257:-1 HG:+:910955588:-1 HG:+:1830754628:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGAAGGAATATATCAAAAGGTATTAACAATGGTTATCGACGTATGATGAAATGATGAGCTATTTTAATTTTCTTGCATACATTTTTTATGTTAATCTGAATTATCTATAGTAAAACTTATATTATCTTGAACAAATAAACGTATTTTAAAACCCTAAACTAACTCTAGGCAGTAGAAACTGAAGTTACAAAGTCCCTTAGACT HG:+:482061655:-1 HG:+:624723495:-1 HG:+:992133273:-1 HG:+:1495201107:-1 HG:+:1537497224:-1 HG:+:1539596230:-1 HG:+:2249232405:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGAAGGAATATATCAAAAGGTATTAACAATGGTTATCGACGTATGATGAAATGATGAGCTATTTTAATTTTCTTGCATACATTTTTTATGTTAATCTGAATTATCTATAGTAAAACTTATATTATCTTGAACAAATAAACGTATTTTAAAACCCTAAACTAACTCTAGGCAGTAGAAACTGAAGTTACAAAGTCCCTTAGACT HG:+:74389182:-1 HG:+:196073749:-1 HG:+:327483320:-1 HG:+:332713813:-1 HG:+:429666960:-1 HG:+:571617102:-1 HG:+:768031843:-1 HG:+:819382919:-1 HG:+:871650899:-1 HG:+:1028128448:-1 HG:+:1470763174:-1 HG:+:1503950872:-1 HG:+:1577495040:-1 HG:+:1718337542:-1 HG:+:2011028753:-1 HG:+:2143494018:-1 HG:+:2652269292:-1 HG:+:2802521281:-1 HG:+:2892094701:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGAAGGAATATATCAAAAGGTATTAACAATGGTTATCGACGTATGATGAAATGATGAGCTATTTTAATTTTCTTGCATACATTTTTTATGTTAATCTGAATTATCTATAGTAAAACTTATATTATCTTGAACAAATAAACGTATTTTAAAACCCTAAACTAACTCTAGGCAGTAGAAACTGAAGTTACAAAGTCCCTTAGACT HG:+:435590038:-1 HG:+:556900052:-1 HG:+:809104227:-1 HG:+:1110999916:-1 HG:+:1266651494:-1 HG:+:2370442013:-1 HG:+:2741223839:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGAAGGAATATATCAAAAGGTATTAACAATGGTTATCGACGTATGATGAAATGATGAGCTATTTTAATTTTCTTGCATACATTTTTTATGTTAATCTGAATTATCTATAGTAAAACTTATATTATCTTGAACAAATAAACGTATTTTAAAACCCTAAACTAACTCTAGGCAGTAGAAACTGAAGTTACAAAGTCCCTTAGACT HG:+:1446772159:-1 HG:+:1474499018:-1 HG:+:2577391227:-1 HG:+:2851199334:-1 HG:+:2901680865:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGAAGGAATATATCAAAAGGTATTAACAATGGTTATCGACGTATGATGAAATGATGAGCTATTTTAATTTTCTTGCATACATTTTTTATGTTAATCTGAATTATCTATAGTAAAACTTATATTATCTTGAACAAATAAACGTATTTTAAAACCCTAAACTAACTCTAGGCAGTAGAAACTGAAGTTACAAAGTCCCTTAGACT HG:+:47772108:-1 HG:+:52627426:-1 HG:+:58741142:-1 HG:+:73775945:-1 HG:+:194754176:-1 HG:+:304270485:-1 HG:+:427143531:-1 HG:+:552218718:-1 HG:+:556444986:-1 HG:+:653085226:-1 HG:+:734320059:-1 HG:+:811298708:-1 HG:+:867852340:-1 HG:+:907325735:-1 HG:+:909175091:-1 HG:+:967319910:-1 HG:+:979008346:-1 HG:+:1005903408:-1 HG:+:1108854011:-1 HG:+:1198411130:-1 HG:+:1274375333:-1 HG:+:1332016881:-1 HG:+:1419700364:-1 HG:+:1506885080:-1 HG:+:1623842768:-1 HG:+:1633283251:-1 HG:+:1651314383:-1 HG:+:1690055014:-1 HG:+:1888668611:-1 HG:+:1931463308:-1 HG:+:2016318665:-1 HG:+:2032253908:-1 HG:+:2119883657:-1 HG:+:2144912290:-1 HG:+:2177414894:-1 HG:+:2395794073:-1 HG:+:2560760125:-1 HG:+:2627219766:-1 HG:+:2628448851:-1 HG:+:2692849772:-1 HG:+:2711589623:-1 HG:+:2774104535:-1 HG:+:3003007623:-1 HG:+:3023745700:-1 HG:+:3042361653:-1 HG:+:3056651911:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGAAGGAATATATCAAAAGGTATTAACAATGGTTATCGACGTATGATGAAATGATGAGCTATTTTAATTTTCTTGCATACATTTTTTATGTTAATCTGAATTATCTATAGTAAAACTTATATTATCTTGAACAAATAAACGTATTTTAAAACCCTAAACTAACTCTAGGCAGTAGAAACTGAAGTTACAAAGTCCCTTAGACT HG:+:111706356:-1 HG:+:195293310:-1 HG:+:480848822:-1 HG:+:514258973:-1 HG:+:782171339:-1 HG:+:1052518533:-1 HG:+:1118651427:-1 HG:+:1164301334:-1 HG:+:1169548443:-1 HG:+:1176523920:-1 HG:+:1259158763:-1 HG:+:1839419435:-1 HG:+:1889742870:-1 HG:+:2077635943:-1 HG:+:2178890345:-1 HG:+:2332604066:-1 HG:+:2802605237:-1 HG:+:2913151241:-1 HG:+:2990539366:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGAAGGAATATATCAAAAGGTATTAACAATGGTTATCGACGTATGATGAAATGATGAGCTATTTTAATTTTCTTGCATACATTTTTTATGTTAATCTGAATTATCTATAGTAAAACTTATATTATCTTGAACAAATAAACGTATTTTAAAACCCTAAACTAACTCTAGGCAGTAGAAACTGAAGTTACAAAGTCCCTTAGACT HG:+:52742520:-1 HG:+:63186655:-1 HG:+:98201084:-1 HG:+:217955567:-1 HG:+:244590399:-1 HG:+:245681457:-1 HG:+:307311266:-1 HG:+:330875128:-1 HG:+:331987653:-1 HG:+:366219138:-1 HG:+:400761034:-1 HG:+:430553450:-1 HG:+:460050636:-1 HG:+:494339689:-1 HG:+:495235027:-1 HG:+:614272598:-1 HG:+:638811117:-1 HG:+:682421270:-1 HG:+:770009125:-1 HG:+:774697706:-1 HG:+:815576166:-1 HG:+:833805690:-1 HG:+:956147146:-1 HG:+:970516793:-1 HG:+:1035152381:-1 HG:+:1042544549:-1 HG:+:1120026244:-1 HG:+:1244249086:-1 HG:+:1252206986:-1 HG:+:1254560267:-1 HG:+:1287058999:-1 HG:+:1297472035:-1 HG:+:1298581777:-1 HG:+:1355038536:-1 HG:+:1465729807:-1 HG:+:1498935731:-1 HG:+:1515671406:-1 HG:+:1519811374:-1 HG:+:1547083712:-1 HG:+:1551741075:-1 HG:+:1690099991:-1 HG:+:1696011681:-1 HG:+:1707484269:-1 HG:+:1734743462:-1 HG:+:1765635276:-1 HG:+:1937768518:-1 HG:+:1981114123:-1 HG:+:1997628358:-1 HG:+:2061617936:-1 HG:+:2070621150:-1 HG:+:2136774232:-1 HG:+:2161788146:-1 HG:+:2246852786:-1 HG:+:2357634306:-1 HG:+:2470241751:-1 HG:+:2511352429:-1 HG:+:2551774883:-1 HG:+:2607591667:-1 HG:+:2607867929:-1 HG:+:2648508799:-1 HG:+:2682512168:-1 HG:+:2772619606:-1 HG:+:2803519865:-1 HG:+:2878079509:-1 HG:+:3019334568:-1 HG:+:3032702335:-1 +CTTTGAACTCCTCGACCTAGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGCGTGAGTCCACCGTGACTGGCCTTTTCCCTAGTTATTAAAAGCAAAAAACCCAGTAGGACTATAAAACAATGCAGAGTTATAATAATATTTTTTAAGTATTGTCCCTGCAGATCCTTTTAATAGACTAAATAGACTTGAAGGAATATATCAAAAGGTATTAACAATGGTTATCGACGTATGATGAAATGATGAGCTATTTTAATTTTCTTGCATACATTTTTTATGTTAATCTGAATTATCTATAGTAAAACTTATATTATCTTGAACAAATAAACGTATTTTAAAACCCTAAACTAACTCTAGGCAGTAGAAACTGAAGTTACAAAGTCCCTTAGACT HG:+:447487549:-1 HG:+:832580120:-1 HG:+:1332766579:-1 HG:+:1420980860:-1 HG:+:1541829760:-1 HG:+:2232343899:-1 HG:+:2295191599:-1 HG:+:2423525654:-1 HG:+:2627278264:-1 HG:+:2716689363:-1 HG:+:2847493746:-1 +AGTCTAAGGGACTTTGTAACTTCAGTTTCTACTGCCTAGAGTTAGTTTAGGGTTTTAAAATACGTTTATTTGTTCAAGATAATATAAGTTTTACTATAGATAATTCAGATTAACATAAAAAATGTATGCAAGAAAATTAAAATAGCTCATCATTTCATCATACGTCGATAACCATTGTTAATACCTTTTGATATATTCCTTCAAGTCTATTTAGTCTATTAAAAGGATCTGCAGGGACAATACTTAAAAAATATTATTATAACTCTGCATTGTTTTATAGTCCTACTGGGTTTTTTGCTTTTAATAACTAGGGAAAAGGCCAGTCACGGTGGACTCACGCTATAATCCCAGCACTTTGGGAGGCTGAGGCAGGTGGATCACTAGGTCGAGGAGTTCAAAG HG:+:1319360843:-1 HG:+:1469626709:-1 HG:+:1760919078:21 +AGTCTAAGGGACTTTGTAACTTCAGTTTCTACTGCCTAGAGTTAGTTTAGGGTTTTAAAATACGTTTATTTGTTCAAGATAATATAAGTTTTACTATAGATAATTCAGATTAACATAAAAAATGTATGCAAGAAAATTAAAATAGCTCATCATTTCATCATACGTCGATAACCATTGTTAATACCTTTTGATATATTCCTTCAAGTCTATTTAGTCTATTAAAAGGATCTGCAGGGACAATACTTAAAAAATATTATTATAACTCTGCATTGTTTTATAGTCCTACTGGGTTTTTTGCTTTTAATAACTAGGGAAAAGGCCAGTCACGGTGGACTCACGCTATAATCCCAGCACTTTGGGAGGCTGAGGCAGGTGGATCACTAGGTCGAGGAGTTCAAAG HG:+:1760919073:21 +AGTCTAAGGGACTTTGTAACTTCAGTTTCTACTGCCTAGAGTTAGTTTAGGGTTTTAAAATACGTTTATTTGTTCAAGATAATATAAGTTTTACTATAGATAATTCAGATTAACATAAAAAATGTATGCAAGAAAATTAAAATAGCTCATCATTTCATCATACGTCGATAACCATTGTTAATACCTTTTGATATATTCCTTCAAGTCTATTTAGTCTATTAAAAGGATCTGCAGGGACAATACTTAAAAAATATTATTATAACTCTGCATTGTTTTATAGTCCTACTGGGTTTTTTGCTTTTAATAACTAGGGAAAAGGCCAGTCACGGTGGACTCACGCTATAATCCCAGCACTTTGGGAGGCTGAGGCAGGTGGATCACTAGGTCGAGGAGTTCAAAG HG:+:1760919081:21 +AGTCTAAGGGACTTTGTAACTTCAGTTTCTACTGCCTAGAGTTAGTTTAGGGTTTTAAAATACGTTTATTTGTTCAAGATAATATAAGTTTTACTATAGATAATTCAGATTAACATAAAAAATGTATGCAAGAAAATTAAAATAGCTCATCATTTCATCATACGTCGATAACCATTGTTAATACCTTTTGATATATTCCTTCAAGTCTATTTAGTCTATTAAAAGGATCTGCAGGGACAATACTTAAAAAATATTATTATAACTCTGCATTGTTTTATAGTCCTACTGGGTTTTTTGCTTTTAATAACTAGGGAAAAGGCCAGTCACGGTGGACTCACGCTATAATCCCAGCACTTTGGGAGGCTGAGGCAGGTGGATCACTAGGTCGAGGAGTTCAAAG HG:+:1378115314:-1 HG:+:1760919079:21 +AGTCTAAGGGACTTTGTAACTTCAGTTTCTACTGCCTAGAGTTAGTTTAGGGTTTTAAAATACGTTTATTTGTTCAAGATAATATAAGTTTTACTATAGATAATTCAGATTAACATAAAAAATGTATGCAAGAAAATTAAAATAGCTCATCATTTCATCATACGTCGATAACCATTGTTAATACCTTTTGATATATTCCTTCAAGTCTATTTAGTCTATTAAAAGGATCTGCAGGGACAATACTTAAAAAATATTATTATAACTCTGCATTGTTTTATAGTCCTACTGGGTTTTTTGCTTTTAATAACTAGGGAAAAGGCCAGTCACGGTGGACTCACGCTATAATCCCAGCACTTTGGGAGGCTGAGGCAGGTGGATCACTAGGTCGAGGAGTTCAAAG HG:+:1387776112:-1 +AGTCTAAGGGACTTTGTAACTTCAGTTTCTACTGCCTAGAGTTAGTTTAGGGTTTTAAAATACGTTTATTTGTTCAAGATAATATAAGTTTTACTATAGATAATTCAGATTAACATAAAAAATGTATGCAAGAAAATTAAAATAGCTCATCATTTCATCATACGTCGATAACCATTGTTAATACCTTTTGATATATTCCTTCAAGTCTATTTAGTCTATTAAAAGGATCTGCAGGGACAATACTTAAAAAATATTATTATAACTCTGCATTGTTTTATAGTCCTACTGGGTTTTTTGCTTTTAATAACTAGGGAAAAGGCCAGTCACGGTGGACTCACGCTATAATCCCAGCACTTTGGGAGGCTGAGGCAGGTGGATCACTAGGTCGAGGAGTTCAAAG HG:+:75162874:-1 +AGTCTAAGGGACTTTGTAACTTCAGTTTCTACTGCCTAGAGTTAGTTTAGGGTTTTAAAATACGTTTATTTGTTCAAGATAATATAAGTTTTACTATAGATAATTCAGATTAACATAAAAAATGTATGCAAGAAAATTAAAATAGCTCATCATTTCATCATACGTCGATAACCATTGTTAATACCTTTTGATATATTCCTTCAAGTCTATTTAGTCTATTAAAAGGATCTGCAGGGACAATACTTAAAAAATATTATTATAACTCTGCATTGTTTTATAGTCCTACTGGGTTTTTTGCTTTTAATAACTAGGGAAAAGGCCAGTCACGGTGGACTCACGCTATAATCCCAGCACTTTGGGAGGCTGAGGCAGGTGGATCACTAGGTCGAGGAGTTCAAAG HG:+:67900976:-1 HG:+:242199701:-1 HG:+:277212423:-1 HG:+:359637332:-1 HG:+:401049434:-1 HG:+:1229407969:-1 HG:+:1266181879:-1 HG:+:1268379404:-1 HG:+:1943767880:-1 HG:+:1977091617:-1 HG:+:2007398143:-1 HG:+:2051520511:-1 HG:+:2347950945:-1 HG:+:2380892280:-1 HG:+:2444934908:-1 HG:+:2586697828:-1 HG:+:2884313095:-1 HG:+:2912879390:-1 +CTTTTAGTTAGCAGGCTTTCGATTCCAAATGTTCTATTGAGTCTCCCCTTGTCGTCAATCCTTTCCAATAAGTACCTGGAAAATTTCTTTCTGTGGATATTAGAGCTCTACTTGCAAGAGTTAAGAACTGGACTCTCTATTTGGAATGAGAATGCATACATTTACTTAGTTTTCAAGCACTATTTATTATGTATTATTCTGAACTGTGCATATAGTTTTGCTTATATCTCTCATAAATCTAGCTATATGGTTCTCATAGTCCTTGCAACCAAATAATTCCTTTATATAGGACTGGACACCCAGAACACCTGTAAAGCTCCTGCTCTGCTTCCCAGTGATATCTTAGCAGCCTGCTCTCTTTAGGAGGTGGTGACATATACTTACTCCAGGCCAGGAGGGC HG:+:695517279:14 +CTTTTAGTTAGCAGGCTTTCGATTCCAAATGTTCTATTGAGTCTCCCCTTGTCGTCAATCCTTTCCAATAAGTACCTGGAAAATTTCTTTCTGTGGATATTAGAGCTCTACTTGCAAGAGTTAAGAACTGGACTCTCTATTTGGAATGAGAATGCATACATTTACTTAGTTTTCAAGCACTATTTATTATGTATTATTCTGAACTGTGCATATAGTTTTGCTTATATCTCTCATAAATCTAGCTATATGGTTCTCATAGTCCTTGCAACCAAATAATTCCTTTATATAGGACTGGACACCCAGAACACCTGTAAAGCTCCTGCTCTGCTTCCCAGTGATATCTTAGCAGCCTGCTCTCTTTAGGAGGTGGTGACATATACTTACTCCAGGCCAGGAGGGC HG:+:695517283:14 +CTTTTAGTTAGCAGGCTTTCGATTCCAAATGTTCTATTGAGTCTCCCCTTGTCGTCAATCCTTTCCAATAAGTACCTGGAAAATTTCTTTCTGTGGATATTAGAGCTCTACTTGCAAGAGTTAAGAACTGGACTCTCTATTTGGAATGAGAATGCATACATTTACTTAGTTTTCAAGCACTATTTATTATGTATTATTCTGAACTGTGCATATAGTTTTGCTTATATCTCTCATAAATCTAGCTATATGGTTCTCATAGTCCTTGCAACCAAATAATTCCTTTATATAGGACTGGACACCCAGAACACCTGTAAAGCTCCTGCTCTGCTTCCCAGTGATATCTTAGCAGCCTGCTCTCTTTAGGAGGTGGTGACATATACTTACTCCAGGCCAGGAGGGC HG:+:695517275:14 +CTTTTAGTTAGCAGGCTTTCGATTCCAAATGTTCTATTGAGTCTCCCCTTGTCGTCAATCCTTTCCAATAAGTACCTGGAAAATTTCTTTCTGTGGATATTAGAGCTCTACTTGCAAGAGTTAAGAACTGGACTCTCTATTTGGAATGAGAATGCATACATTTACTTAGTTTTCAAGCACTATTTATTATGTATTATTCTGAACTGTGCATATAGTTTTGCTTATATCTCTCATAAATCTAGCTATATGGTTCTCATAGTCCTTGCAACCAAATAATTCCTTTATATAGGACTGGACACCCAGAACACCTGTAAAGCTCCTGCTCTGCTTCCCAGTGATATCTTAGCAGCCTGCTCTCTTTAGGAGGTGGTGACATATACTTACTCCAGGCCAGGAGGGC HG:+:695517282:14 +CTTTTAGTTAGCAGGCTTTCGATTCCAAATGTTCTATTGAGTCTCCCCTTGTCGTCAATCCTTTCCAATAAGTACCTGGAAAATTTCTTTCTGTGGATATTAGAGCTCTACTTGCAAGAGTTAAGAACTGGACTCTCTATTTGGAATGAGAATGCATACATTTACTTAGTTTTCAAGCACTATTTATTATGTATTATTCTGAACTGTGCATATAGTTTTGCTTATATCTCTCATAAATCTAGCTATATGGTTCTCATAGTCCTTGCAACCAAATAATTCCTTTATATAGGACTGGACACCCAGAACACCTGTAAAGCTCCTGCTCTGCTTCCCAGTGATATCTTAGCAGCCTGCTCTCTTTAGGAGGTGGTGACATATACTTACTCCAGGCCAGGAGGGC HG:+:2601501023:-1 +GCCCTCCTGGCCTGGAGTAAGTATATGTCACCACCTCCTAAAGAGAGCAGGCTGCTAAGATATCACTGGGAAGCAGAGCAGGAGCTTTACAGGTGTTCTGGGTGTCCAGTCCTATATAAAGGAATTATTTGGTTGCAAGGACTATGAGAACCATATAGCTAGATTTATGAGAGATATAAGCAAAACTATATGCACAGTTCAGAATAATACATAATAAATAGTGCTTGAAAACTAAGTAAATGTATGCATTCTCATTCCAAATAGAGAGTCCAGTTCTTAACTCTTGCAAGTAGAGCTCTAATATCCACAGAAAGAAATTTTCCAGGTACTTATTGGAAAGGATTGACGACAAGGGGAGACTCAATAGAACATTTGGAATCGAAAGCCTGCTAACTAAAAG HG:+:2819114190:-1 +GCCCTCCTGGCCTGGAGTAAGTATATGTCACCACCTCCTAAAGAGAGCAGGCTGCTAAGATATCACTGGGAAGCAGAGCAGGAGCTTTACAGGTGTTCTGGGTGTCCAGTCCTATATAAAGGAATTATTTGGTTGCAAGGACTATGAGAACCATATAGCTAGATTTATGAGAGATATAAGCAAAACTATATGCACAGTTCAGAATAATACATAATAAATAGTGCTTGAAAACTAAGTAAATGTATGCATTCTCATTCCAAATAGAGAGTCCAGTTCTTAACTCTTGCAAGTAGAGCTCTAATATCCACAGAAAGAAATTTTCCAGGTACTTATTGGAAAGGATTGACGACAAGGGGAGACTCAATAGAACATTTGGAATCGAAAGCCTGCTAACTAAAAG HG:+:2983383641:-1 +AAACAGTTGGCCAGGCGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGAAGGCCAAGCAGAGAGAATTAGCCTGAGCCCAGGGAGTTCGAGACCAGTCTGGACAATATAGGGAGACCCTGTTTAAAACTAAAAAATACAATTAGCCAGGCAATGGTGGCACTGCCTGTGGTCCGAGTTACTCAGGAGGCTGAGGTGAGAAAATTGCTTGAGCCCAGGGAAGTAGAGGGTGCAGTGAGCTATGACTGAGCCACTGTACTCCAGCCTGGTGGCAGAGCAAAGCCCTGTCTCTAAACATTTAAGTAAAAATAAAAACAAAAGTCAAATTCATTGGAAGCAGAGAAAAGAATCGGTGGTTTACCAGAGGCTTGGAAGGGTGAGATGTTGGTTCAAAGGTATA HG:+:1250049638:15 +AAACAGTTGGCCAGGCGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGAAGGCCAAGCAGAGAGAATTAGCCTGAGCCCAGGGAGTTCGAGACCAGTCTGGACAATATAGGGAGACCCTGTTTAAAACTAAAAAATACAATTAGCCAGGCAATGGTGGCACTGCCTGTGGTCCGAGTTACTCAGGAGGCTGAGGTGAGAAAATTGCTTGAGCCCAGGGAAGTAGAGGGTGCAGTGAGCTATGACTGAGCCACTGTACTCCAGCCTGGTGGCAGAGCAAAGCCCTGTCTCTAAACATTTAAGTAAAAATAAAAACAAAAGTCAAATTCATTGGAAGCAGAGAAAAGAATCGGTGGTTTACCAGAGGCTTGGAAGGGTGAGATGTTGGTTCAAAGGTATA HG:+:310934365:-1 HG:+:1250049632:15 +AAACAGTTGGCCAGGCGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGAAGGCCAAGCAGAGAGAATTAGCCTGAGCCCAGGGAGTTCGAGACCAGTCTGGACAATATAGGGAGACCCTGTTTAAAACTAAAAAATACAATTAGCCAGGCAATGGTGGCACTGCCTGTGGTCCGAGTTACTCAGGAGGCTGAGGTGAGAAAATTGCTTGAGCCCAGGGAAGTAGAGGGTGCAGTGAGCTATGACTGAGCCACTGTACTCCAGCCTGGTGGCAGAGCAAAGCCCTGTCTCTAAACATTTAAGTAAAAATAAAAACAAAAGTCAAATTCATTGGAAGCAGAGAAAAGAATCGGTGGTTTACCAGAGGCTTGGAAGGGTGAGATGTTGGTTCAAAGGTATA HG:+:1250049634:15 HG:+:1672083922:-1 +AAACAGTTGGCCAGGCGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGAAGGCCAAGCAGAGAGAATTAGCCTGAGCCCAGGGAGTTCGAGACCAGTCTGGACAATATAGGGAGACCCTGTTTAAAACTAAAAAATACAATTAGCCAGGCAATGGTGGCACTGCCTGTGGTCCGAGTTACTCAGGAGGCTGAGGTGAGAAAATTGCTTGAGCCCAGGGAAGTAGAGGGTGCAGTGAGCTATGACTGAGCCACTGTACTCCAGCCTGGTGGCAGAGCAAAGCCCTGTCTCTAAACATTTAAGTAAAAATAAAAACAAAAGTCAAATTCATTGGAAGCAGAGAAAAGAATCGGTGGTTTACCAGAGGCTTGGAAGGGTGAGATGTTGGTTCAAAGGTATA HG:+:1250049635:15 +AAACAGTTGGCCAGGCGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGAAGGCCAAGCAGAGAGAATTAGCCTGAGCCCAGGGAGTTCGAGACCAGTCTGGACAATATAGGGAGACCCTGTTTAAAACTAAAAAATACAATTAGCCAGGCAATGGTGGCACTGCCTGTGGTCCGAGTTACTCAGGAGGCTGAGGTGAGAAAATTGCTTGAGCCCAGGGAAGTAGAGGGTGCAGTGAGCTATGACTGAGCCACTGTACTCCAGCCTGGTGGCAGAGCAAAGCCCTGTCTCTAAACATTTAAGTAAAAATAAAAACAAAAGTCAAATTCATTGGAAGCAGAGAAAAGAATCGGTGGTTTACCAGAGGCTTGGAAGGGTGAGATGTTGGTTCAAAGGTATA HG:+:1250049633:15 +AAACAGTTGGCCAGGCGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGAAGGCCAAGCAGAGAGAATTAGCCTGAGCCCAGGGAGTTCGAGACCAGTCTGGACAATATAGGGAGACCCTGTTTAAAACTAAAAAATACAATTAGCCAGGCAATGGTGGCACTGCCTGTGGTCCGAGTTACTCAGGAGGCTGAGGTGAGAAAATTGCTTGAGCCCAGGGAAGTAGAGGGTGCAGTGAGCTATGACTGAGCCACTGTACTCCAGCCTGGTGGCAGAGCAAAGCCCTGTCTCTAAACATTTAAGTAAAAATAAAAACAAAAGTCAAATTCATTGGAAGCAGAGAAAAGAATCGGTGGTTTACCAGAGGCTTGGAAGGGTGAGATGTTGGTTCAAAGGTATA HG:+:1250049636:15 HG:+:1826858834:-1 +AAACAGTTGGCCAGGCGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGAAGGCCAAGCAGAGAGAATTAGCCTGAGCCCAGGGAGTTCGAGACCAGTCTGGACAATATAGGGAGACCCTGTTTAAAACTAAAAAATACAATTAGCCAGGCAATGGTGGCACTGCCTGTGGTCCGAGTTACTCAGGAGGCTGAGGTGAGAAAATTGCTTGAGCCCAGGGAAGTAGAGGGTGCAGTGAGCTATGACTGAGCCACTGTACTCCAGCCTGGTGGCAGAGCAAAGCCCTGTCTCTAAACATTTAAGTAAAAATAAAAACAAAAGTCAAATTCATTGGAAGCAGAGAAAAGAATCGGTGGTTTACCAGAGGCTTGGAAGGGTGAGATGTTGGTTCAAAGGTATA HG:+:11816891:-1 HG:+:1879560193:-1 +TATACCTTTGAACCAACATCTCACCCTTCCAAGCCTCTGGTAAACCACCGATTCTTTTCTCTGCTTCCAATGAATTTGACTTTTGTTTTTATTTTTACTTAAATGTTTAGAGACAGGGCTTTGCTCTGCCACCAGGCTGGAGTACAGTGGCTCAGTCATAGCTCACTGCACCCTCTACTTCCCTGGGCTCAAGCAATTTTCTCACCTCAGCCTCCTGAGTAACTCGGACCACAGGCAGTGCCACCATTGCCTGGCTAATTGTATTTTTTAGTTTTAAACAGGGTCTCCCTATATTGTCCAGACTGGTCTCGAACTCCCTGGGCTCAGGCTAATTCTCTCTGCTTGGCCTTCCAAAGTGCTGGGATTACAGGTGTGAGCCACCACGCCTGGCCAACTGTTT HG:+:248393859:-1 HG:+:1258175551:-1 +TATACCTTTGAACCAACATCTCACCCTTCCAAGCCTCTGGTAAACCACCGATTCTTTTCTCTGCTTCCAATGAATTTGACTTTTGTTTTTATTTTTACTTAAATGTTTAGAGACAGGGCTTTGCTCTGCCACCAGGCTGGAGTACAGTGGCTCAGTCATAGCTCACTGCACCCTCTACTTCCCTGGGCTCAAGCAATTTTCTCACCTCAGCCTCCTGAGTAACTCGGACCACAGGCAGTGCCACCATTGCCTGGCTAATTGTATTTTTTAGTTTTAAACAGGGTCTCCCTATATTGTCCAGACTGGTCTCGAACTCCCTGGGCTCAGGCTAATTCTCTCTGCTTGGCCTTCCAAAGTGCTGGGATTACAGGTGTGAGCCACCACGCCTGGCCAACTGTTT HG:+:155746174:-1 HG:+:1148968801:-1 HG:+:1202298736:-1 HG:+:1785549902:-1 HG:+:2008373519:-1 HG:+:2303680440:-1 HG:+:2365444413:-1 HG:+:2881812581:-1 HG:+:2986976233:-1 +TATACCTTTGAACCAACATCTCACCCTTCCAAGCCTCTGGTAAACCACCGATTCTTTTCTCTGCTTCCAATGAATTTGACTTTTGTTTTTATTTTTACTTAAATGTTTAGAGACAGGGCTTTGCTCTGCCACCAGGCTGGAGTACAGTGGCTCAGTCATAGCTCACTGCACCCTCTACTTCCCTGGGCTCAAGCAATTTTCTCACCTCAGCCTCCTGAGTAACTCGGACCACAGGCAGTGCCACCATTGCCTGGCTAATTGTATTTTTTAGTTTTAAACAGGGTCTCCCTATATTGTCCAGACTGGTCTCGAACTCCCTGGGCTCAGGCTAATTCTCTCTGCTTGGCCTTCCAAAGTGCTGGGATTACAGGTGTGAGCCACCACGCCTGGCCAACTGTTT HG:+:1890537:-1 HG:+:72987890:-1 HG:+:171617791:-1 HG:+:282638499:-1 HG:+:433246153:-1 HG:+:497303548:-1 HG:+:663053220:-1 HG:+:685157106:-1 HG:+:1340825393:-1 HG:+:1688941121:-1 HG:+:1848980079:-1 HG:+:2030828965:-1 HG:+:2270686727:-1 HG:+:2501960429:-1 HG:+:2502599790:-1 HG:+:2652641666:-1 HG:+:2814948668:-1 HG:+:2863669977:-1 HG:+:3000046666:-1 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTTTAACTCCTAGGGGCCGGGTGGTGGTGCCAAGGTTATCTCGGCCTATTTATCTTACTTTTGTTTTTTTCCAACGTTTTGCTTTTTCTCTCCTCCTGTCTTGTGAACTAGGCAAAGGTGGGGGGAGGAGGCAGTAGGAGTAGTAGTGGTCTCCCTTCCTTAGTATCAGAATCTTGCTTCTTGTTTAATTGGACTCTGCATGA HG:+:146697367:-1 HG:+:161380304:59 HG:+:249848275:62 HG:+:271282442:-1 HG:+:1677731936:67 HG:+:1890747852:68 HG:+:2194558212:-1 HG:+:2714236533:60 HG:+:2855947358:66 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTTTAACTCCTAGGGGCCGGGTGGTGGTGCCAAGGTTATCTCGGCCTATTTATCTTACTTTTGTTTTTTTCCAACGTTTTGCTTTTTCTCTCCTCCTGTCTTGTGAACTAGGCAAAGGTGGGGGGAGGAGGCAGTAGGAGTAGTAGTGGTCTCCCTTCCTTAGTATCAGAATCTTGCTTCTTGTTTAATTGGACTCTGCATGA HG:+:35612219:69 HG:+:146697400:-1 HG:+:218922356:-1 HG:+:246753392:-1 HG:+:249848284:62 HG:+:336680544:-1 HG:+:560930940:-1 HG:+:967487748:-1 HG:+:967493253:-1 HG:+:1539090496:-1 HG:+:1746864625:-1 HG:+:1841397188:-1 HG:+:1883684806:-1 HG:+:1923033599:-1 HG:+:1933337262:-1 HG:+:2010661610:-1 HG:+:2168239034:-1 HG:+:2714236532:60 HG:+:2828308947:-1 HG:+:2930038277:-1 HG:+:3027297920:-1 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTTTAACTCCTAGGGGCCGGGTGGTGGTGCCAAGGTTATCTCGGCCTATTTATCTTACTTTTGTTTTTTTCCAACGTTTTGCTTTTTCTCTCCTCCTGTCTTGTGAACTAGGCAAAGGTGGGGGGAGGAGGCAGTAGGAGTAGTAGTGGTCTCCCTTCCTTAGTATCAGAATCTTGCTTCTTGTTTAATTGGACTCTGCATGA HG:+:35612200:69 HG:+:146697370:-1 HG:+:371694805:59 HG:+:1073023056:-1 HG:+:2254461076:-1 HG:+:2623856256:-1 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTTTAACTCCTAGGGGCCGGGTGGTGGTGCCAAGGTTATCTCGGCCTATTTATCTTACTTTTGTTTTTTTCCAACGTTTTGCTTTTTCTCTCCTCCTGTCTTGTGAACTAGGCAAAGGTGGGGGGAGGAGGCAGTAGGAGTAGTAGTGGTCTCCCTTCCTTAGTATCAGAATCTTGCTTCTTGTTTAATTGGACTCTGCATGA HG:+:44579313:-1 HG:+:348780844:-1 HG:+:422849725:-1 HG:+:526110651:-1 HG:+:924199278:-1 HG:+:1249718152:-1 HG:+:1259018510:-1 HG:+:1374889677:-1 HG:+:1807963433:-1 HG:+:1809982409:-1 HG:+:1877182997:-1 HG:+:2138076556:-1 HG:+:2611818546:-1 HG:+:2869793123:-1 HG:+:2875957494:-1 HG:+:2985598011:-1 HG:+:3095331084:-1 HG:+:3101216088:-1 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTTTAACTCCTAGGGGCCGGGTGGTGGTGCCAAGGTTATCTCGGCCTATTTATCTTACTTTTGTTTTTTTCCAACGTTTTGCTTTTTCTCTCCTCCTGTCTTGTGAACTAGGCAAAGGTGGGGGGAGGAGGCAGTAGGAGTAGTAGTGGTCTCCCTTCCTTAGTATCAGAATCTTGCTTCTTGTTTAATTGGACTCTGCATGA HG:+:249848273:62 HG:+:491364775:-1 HG:+:1038202043:62 HG:+:1458615486:-1 HG:+:2438353731:70 HG:+:2625907918:-1 HG:+:2714236531:60 HG:+:3017051660:67 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTTTAACTCCTAGGGGCCGGGTGGTGGTGCCAAGGTTATCTCGGCCTATTTATCTTACTTTTGTTTTTTTCCAACGTTTTGCTTTTTCTCTCCTCCTGTCTTGTGAACTAGGCAAAGGTGGGGGGAGGAGGCAGTAGGAGTAGTAGTGGTCTCCCTTCCTTAGTATCAGAATCTTGCTTCTTGTTTAATTGGACTCTGCATGA HG:+:161374020:69 HG:+:1038202051:62 HG:+:1240647122:-1 HG:+:1538875959:-1 HG:+:1679181852:-1 HG:+:1859713485:-1 HG:+:1883520575:-1 HG:+:2194558215:-1 HG:+:2227104985:-1 HG:+:2438572989:75 HG:+:2528739267:-1 HG:+:2565473425:73 HG:+:2625907927:-1 HG:+:2855947361:66 HG:+:3017046340:75 HG:+:3017051666:67 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTTTAACTCCTAGGGGCCGGGTGGTGGTGCCAAGGTTATCTCGGCCTATTTATCTTACTTTTGTTTTTTTCCAACGTTTTGCTTTTTCTCTCCTCCTGTCTTGTGAACTAGGCAAAGGTGGGGGGAGGAGGCAGTAGGAGTAGTAGTGGTCTCCCTTCCTTAGTATCAGAATCTTGCTTCTTGTTTAATTGGACTCTGCATGA HG:+:272571844:-1 HG:+:2194930173:-1 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTTTAACTCCTAGGGGCCGGGTGGTGGTGCCAAGGTTATCTCGGCCTATTTATCTTACTTTTGTTTTTTTCCAACGTTTTGCTTTTTCTCTCCTCCTGTCTTGTGAACTAGGCAAAGGTGGGGGGAGGAGGCAGTAGGAGTAGTAGTGGTCTCCCTTCCTTAGTATCAGAATCTTGCTTCTTGTTTAATTGGACTCTGCATGA HG:+:64710765:-1 HG:+:517576956:-1 HG:+:568526049:-1 HG:+:632076190:-1 HG:+:683053108:-1 HG:+:796019739:-1 HG:+:887272642:-1 HG:+:963001081:-1 HG:+:997892321:-1 HG:+:1113111579:-1 HG:+:1221803832:-1 HG:+:1230239242:-1 HG:+:1360395070:-1 HG:+:1793449441:-1 HG:+:1822548688:-1 HG:+:1831739177:-1 HG:+:2181251039:-1 HG:+:2289736845:-1 HG:+:2638395470:-1 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTTTAACTCCTAGGGGCCGGGTGGTGGTGCCAAGGTTATCTCGGCCTATTTATCTTACTTTTGTTTTTTTCCAACGTTTTGCTTTTTCTCTCCTCCTGTCTTGTGAACTAGGCAAAGGTGGGGGGAGGAGGCAGTAGGAGTAGTAGTGGTCTCCCTTCCTTAGTATCAGAATCTTGCTTCTTGTTTAATTGGACTCTGCATGA HG:+:35607078:64 HG:+:161374013:69 HG:+:161380305:59 HG:+:1038202047:62 HG:+:1612646541:-1 HG:+:1883684801:-1 HG:+:2438353733:70 HG:+:2565473421:73 HG:+:2855947355:66 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTTTAACTCCTAGGGGCCGGGTGGTGGTGCCAAGGTTATCTCGGCCTATTTATCTTACTTTTGTTTTTTTCCAACGTTTTGCTTTTTCTCTCCTCCTGTCTTGTGAACTAGGCAAAGGTGGGGGGAGGAGGCAGTAGGAGTAGTAGTGGTCTCCCTTCCTTAGTATCAGAATCTTGCTTCTTGTTTAATTGGACTCTGCATGA HG:+:999153:-1 HG:+:386076026:-1 HG:+:477921080:73 HG:+:691875168:-1 HG:+:1362179022:-1 HG:+:1817692892:-1 HG:+:2626140256:-1 HG:+:2855947357:66 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTTTAACTCCTAGGGGCCGGGTGGTGGTGCCAAGGTTATCTCGGCCTATTTATCTTACTTTTGTTTTTTTCCAACGTTTTGCTTTTTCTCTCCTCCTGTCTTGTGAACTAGGCAAAGGTGGGGGGAGGAGGCAGTAGGAGTAGTAGTGGTCTCCCTTCCTTAGTATCAGAATCTTGCTTCTTGTTTAATTGGACTCTGCATGA HG:+:161374016:69 HG:+:1677731930:67 HG:+:1890747851:68 HG:+:2438572980:75 HG:+:3017046330:75 HG:+:3054527355:-1 +TTTTAAAGGCTTACGAACTTAGGGGTCCACGTGAAAGGGTCGTGATACATCAAGCAAGCTTGGGAAACGTGACGTGGGGGCTACATGCCATCAGCTAAAAGAACAAAAAAGTTTTACAATGCTTTCATACAGTGTCTGGATTTACAGATAACACAAGTAGTTTAGGTCGAAGGGGGTTGATGTTATTATTATGACTTTTTTAACTCCTAGGGGCCGGGTGGTGGTGCCAAGGTTATCTCGGCCTATTTATCTTACTTTTGTTTTTTTCCAACGTTTTGCTTTTTCTCTCCTCCTGTCTTGTGAACTAGGCAAAGGTGGGGGGAGGAGGCAGTAGGAGTAGTAGTGGTCTCCCTTCCTTAGTATCAGAATCTTGCTTCTTGTTTAATTGGACTCTGCATGA HG:+:1677731938:67 +TCATGCAGAGTCCAATTAAACAAGAAGCAAGATTCTGATACTAAGGAAGGGAGACCACTACTACTCCTACTGCCTCCTCCCCCCACCTTTGCCTAGTTCACAAGACAGGAGGAGAGAAAAAGCAAAACGTTGGAAAAAAACAAAAGTAAGATAAATAGGCCGAGATAACCTTGGCACCACCACCCGGCCCCTAGGAGTTAAAAAAGTCATAATAATAACATCAACCCCCTTCGACCTAAACTACTTGTGTTATCTGTAAATCCAGACACTGTATGAAAGCATTGTAAAACTTTTTTGTTCTTTTAGCTGATGGCATGTAGCCCCCACGTCACGTTTCCCAAGCTTGCTTGATGTATCACGACCCTTTCACGTGGACCCCTAAGTTCGTAAGCCTTTAAAA HG:+:698913867:69 +TCATGCAGAGTCCAATTAAACAAGAAGCAAGATTCTGATACTAAGGAAGGGAGACCACTACTACTCCTACTGCCTCCTCCCCCCACCTTTGCCTAGTTCACAAGACAGGAGGAGAGAAAAAGCAAAACGTTGGAAAAAAACAAAAGTAAGATAAATAGGCCGAGATAACCTTGGCACCACCACCCGGCCCCTAGGAGTTAAAAAAGTCATAATAATAACATCAACCCCCTTCGACCTAAACTACTTGTGTTATCTGTAAATCCAGACACTGTATGAAAGCATTGTAAAACTTTTTTGTTCTTTTAGCTGATGGCATGTAGCCCCCACGTCACGTTTCCCAAGCTTGCTTGATGTATCACGACCCTTTCACGTGGACCCCTAAGTTCGTAAGCCTTTAAAA HG:+:202135957:75 HG:+:851539196:-1 HG:+:873521136:-1 HG:+:1115428504:-1 HG:+:1386373674:65 HG:+:1739501562:-1 HG:+:1923814562:-1 HG:+:2470973109:-1 HG:+:2934084089:24 HG:+:2955132676:-1 +TCATGCAGAGTCCAATTAAACAAGAAGCAAGATTCTGATACTAAGGAAGGGAGACCACTACTACTCCTACTGCCTCCTCCCCCCACCTTTGCCTAGTTCACAAGACAGGAGGAGAGAAAAAGCAAAACGTTGGAAAAAAACAAAAGTAAGATAAATAGGCCGAGATAACCTTGGCACCACCACCCGGCCCCTAGGAGTTAAAAAAGTCATAATAATAACATCAACCCCCTTCGACCTAAACTACTTGTGTTATCTGTAAATCCAGACACTGTATGAAAGCATTGTAAAACTTTTTTGTTCTTTTAGCTGATGGCATGTAGCCCCCACGTCACGTTTCCCAAGCTTGCTTGATGTATCACGACCCTTTCACGTGGACCCCTAAGTTCGTAAGCCTTTAAAA HG:+:2934084088:24 +AGAAAGGAGAAATTTGCCTTCGAACCCGGAGGCGGAGGTTGCACGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAAGAGGAAATGACGAGAAGTCCAACAGGTTAGAGAAGTCGGTGGTATTCTGACCATAGATAATAGAAATTGCAGTCATTGAATCATAAGTTGTAAAAATTAAAATTTCAGAAACCTTTAACAATACTCTGAACTTTAAGAAAAAGGTTTTTCCAGAGACTTTCTAACGGACTTGTTTGCCACCGTTGCTAATAGTATCCAGATGTTGAGAAGTTTTATTTGATTACATCGCAAATAAAGTTACCTCTAAGTCCCTTAGAAAGCCTAGAGAAAAGGGAAAATTGAACA HG:+:477124853:-1 HG:+:652747920:20 HG:+:730998123:-1 HG:+:1113498407:-1 HG:+:1407635175:-1 HG:+:1460468761:-1 HG:+:1742497013:-1 HG:+:1786212646:-1 HG:+:1889174461:-1 HG:+:2072568848:-1 HG:+:2073911498:-1 HG:+:2115781323:-1 HG:+:2696147664:-1 HG:+:2721916999:-1 HG:+:2852261016:-1 HG:+:2878326792:-1 HG:+:3000162869:-1 +AGAAAGGAGAAATTTGCCTTCGAACCCGGAGGCGGAGGTTGCACGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAAGAGGAAATGACGAGAAGTCCAACAGGTTAGAGAAGTCGGTGGTATTCTGACCATAGATAATAGAAATTGCAGTCATTGAATCATAAGTTGTAAAAATTAAAATTTCAGAAACCTTTAACAATACTCTGAACTTTAAGAAAAAGGTTTTTCCAGAGACTTTCTAACGGACTTGTTTGCCACCGTTGCTAATAGTATCCAGATGTTGAGAAGTTTTATTTGATTACATCGCAAATAAAGTTACCTCTAAGTCCCTTAGAAAGCCTAGAGAAAAGGGAAAATTGAACA HG:+:652747912:20 +AGAAAGGAGAAATTTGCCTTCGAACCCGGAGGCGGAGGTTGCACGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAAGAGGAAATGACGAGAAGTCCAACAGGTTAGAGAAGTCGGTGGTATTCTGACCATAGATAATAGAAATTGCAGTCATTGAATCATAAGTTGTAAAAATTAAAATTTCAGAAACCTTTAACAATACTCTGAACTTTAAGAAAAAGGTTTTTCCAGAGACTTTCTAACGGACTTGTTTGCCACCGTTGCTAATAGTATCCAGATGTTGAGAAGTTTTATTTGATTACATCGCAAATAAAGTTACCTCTAAGTCCCTTAGAAAGCCTAGAGAAAAGGGAAAATTGAACA HG:+:652747914:20 +AGAAAGGAGAAATTTGCCTTCGAACCCGGAGGCGGAGGTTGCACGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAAGAGGAAATGACGAGAAGTCCAACAGGTTAGAGAAGTCGGTGGTATTCTGACCATAGATAATAGAAATTGCAGTCATTGAATCATAAGTTGTAAAAATTAAAATTTCAGAAACCTTTAACAATACTCTGAACTTTAAGAAAAAGGTTTTTCCAGAGACTTTCTAACGGACTTGTTTGCCACCGTTGCTAATAGTATCCAGATGTTGAGAAGTTTTATTTGATTACATCGCAAATAAAGTTACCTCTAAGTCCCTTAGAAAGCCTAGAGAAAAGGGAAAATTGAACA HG:+:652747917:20 +AGAAAGGAGAAATTTGCCTTCGAACCCGGAGGCGGAGGTTGCACGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAAGAGGAAATGACGAGAAGTCCAACAGGTTAGAGAAGTCGGTGGTATTCTGACCATAGATAATAGAAATTGCAGTCATTGAATCATAAGTTGTAAAAATTAAAATTTCAGAAACCTTTAACAATACTCTGAACTTTAAGAAAAAGGTTTTTCCAGAGACTTTCTAACGGACTTGTTTGCCACCGTTGCTAATAGTATCCAGATGTTGAGAAGTTTTATTTGATTACATCGCAAATAAAGTTACCTCTAAGTCCCTTAGAAAGCCTAGAGAAAAGGGAAAATTGAACA HG:+:652747916:20 +AGAAAGGAGAAATTTGCCTTCGAACCCGGAGGCGGAGGTTGCACGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAAGAGGAAATGACGAGAAGTCCAACAGGTTAGAGAAGTCGGTGGTATTCTGACCATAGATAATAGAAATTGCAGTCATTGAATCATAAGTTGTAAAAATTAAAATTTCAGAAACCTTTAACAATACTCTGAACTTTAAGAAAAAGGTTTTTCCAGAGACTTTCTAACGGACTTGTTTGCCACCGTTGCTAATAGTATCCAGATGTTGAGAAGTTTTATTTGATTACATCGCAAATAAAGTTACCTCTAAGTCCCTTAGAAAGCCTAGAGAAAAGGGAAAATTGAACA HG:+:652747913:20 +TGTTCAATTTTCCCTTTTCTCTAGGCTTTCTAAGGGACTTAGAGGTAACTTTATTTGCGATGTAATCAAATAAAACTTCTCAACATCTGGATACTATTAGCAACGGTGGCAAACAAGTCCGTTAGAAAGTCTCTGGAAAAACCTTTTTCTTAAAGTTCAGAGTATTGTTAAAGGTTTCTGAAATTTTAATTTTTACAACTTATGATTCAATGACTGCAATTTCTATTATCTATGGTCAGAATACCACCGACTTCTCTAACCTGTTGGACTTCTCGTCATTTCCTCTTTTTTTTTTTTTGAGACAGAGTCTTACTCTGTCACCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACGTGCAACCTCCGCCTCCGGGTTCGAAGGCAAATTTCTCCTTTCT HG:+:1789461666:-1 +TGTTCAATTTTCCCTTTTCTCTAGGCTTTCTAAGGGACTTAGAGGTAACTTTATTTGCGATGTAATCAAATAAAACTTCTCAACATCTGGATACTATTAGCAACGGTGGCAAACAAGTCCGTTAGAAAGTCTCTGGAAAAACCTTTTTCTTAAAGTTCAGAGTATTGTTAAAGGTTTCTGAAATTTTAATTTTTACAACTTATGATTCAATGACTGCAATTTCTATTATCTATGGTCAGAATACCACCGACTTCTCTAACCTGTTGGACTTCTCGTCATTTCCTCTTTTTTTTTTTTTGAGACAGAGTCTTACTCTGTCACCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACGTGCAACCTCCGCCTCCGGGTTCGAAGGCAAATTTCTCCTTTCT HG:+:1026669118:-1 +TGTTCAATTTTCCCTTTTCTCTAGGCTTTCTAAGGGACTTAGAGGTAACTTTATTTGCGATGTAATCAAATAAAACTTCTCAACATCTGGATACTATTAGCAACGGTGGCAAACAAGTCCGTTAGAAAGTCTCTGGAAAAACCTTTTTCTTAAAGTTCAGAGTATTGTTAAAGGTTTCTGAAATTTTAATTTTTACAACTTATGATTCAATGACTGCAATTTCTATTATCTATGGTCAGAATACCACCGACTTCTCTAACCTGTTGGACTTCTCGTCATTTCCTCTTTTTTTTTTTTTGAGACAGAGTCTTACTCTGTCACCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACGTGCAACCTCCGCCTCCGGGTTCGAAGGCAAATTTCTCCTTTCT HG:+:221484362:-1 HG:+:232056293:-1 HG:+:311378343:-1 HG:+:374065120:-1 HG:+:1286164480:-1 HG:+:1298460572:-1 HG:+:1402734330:-1 HG:+:1694614100:-1 HG:+:1751977732:-1 HG:+:1934292686:-1 HG:+:1957922027:-1 HG:+:1993012716:-1 HG:+:1996748069:-1 HG:+:2429644355:-1 HG:+:2539088912:-1 HG:+:2572461427:-1 HG:+:2675647968:-1 HG:+:2722496065:-1 HG:+:2798589832:-1 HG:+:2952632274:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATAATAACTTTGTATGTCCCATGCTGAGAGGTGAATCCCTGAGTTCCTGAATATAGGAAAAATCAATTTAAAGTCATCATTTTAGAGGAACAAGAACAATGGCTACTGGGAGATTTAAATCTGTGTGATCTCGTTCTCTCCTAATATCTGAGTGTGTCTATGTCAGGTCACTCAGATTTGTTTGGTTTGGTTTTACTGGTAAA HG:+:87261797:-1 HG:+:439868800:-1 HG:+:672058348:-1 HG:+:2024006867:-1 HG:+:2150459444:-1 HG:+:2250234158:-1 HG:+:2385600471:-1 HG:+:2852222504:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATAATAACTTTGTATGTCCCATGCTGAGAGGTGAATCCCTGAGTTCCTGAATATAGGAAAAATCAATTTAAAGTCATCATTTTAGAGGAACAAGAACAATGGCTACTGGGAGATTTAAATCTGTGTGATCTCGTTCTCTCCTAATATCTGAGTGTGTCTATGTCAGGTCACTCAGATTTGTTTGGTTTGGTTTTACTGGTAAA HG:+:2167940281:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATAATAACTTTGTATGTCCCATGCTGAGAGGTGAATCCCTGAGTTCCTGAATATAGGAAAAATCAATTTAAAGTCATCATTTTAGAGGAACAAGAACAATGGCTACTGGGAGATTTAAATCTGTGTGATCTCGTTCTCTCCTAATATCTGAGTGTGTCTATGTCAGGTCACTCAGATTTGTTTGGTTTGGTTTTACTGGTAAA HG:+:545487025:-1 HG:+:636911562:-1 HG:+:1372722515:-1 HG:+:1858038162:-1 HG:+:1975680123:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATAATAACTTTGTATGTCCCATGCTGAGAGGTGAATCCCTGAGTTCCTGAATATAGGAAAAATCAATTTAAAGTCATCATTTTAGAGGAACAAGAACAATGGCTACTGGGAGATTTAAATCTGTGTGATCTCGTTCTCTCCTAATATCTGAGTGTGTCTATGTCAGGTCACTCAGATTTGTTTGGTTTGGTTTTACTGGTAAA HG:+:840392718:-1 HG:+:962468230:-1 HG:+:1502728460:-1 HG:+:1732896597:-1 HG:+:1788845813:-1 HG:+:2758469364:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATAATAACTTTGTATGTCCCATGCTGAGAGGTGAATCCCTGAGTTCCTGAATATAGGAAAAATCAATTTAAAGTCATCATTTTAGAGGAACAAGAACAATGGCTACTGGGAGATTTAAATCTGTGTGATCTCGTTCTCTCCTAATATCTGAGTGTGTCTATGTCAGGTCACTCAGATTTGTTTGGTTTGGTTTTACTGGTAAA HG:+:498003615:-1 HG:+:1497116744:-1 HG:+:2041125926:-1 HG:+:2742746647:-1 HG:+:2936615501:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATAATAACTTTGTATGTCCCATGCTGAGAGGTGAATCCCTGAGTTCCTGAATATAGGAAAAATCAATTTAAAGTCATCATTTTAGAGGAACAAGAACAATGGCTACTGGGAGATTTAAATCTGTGTGATCTCGTTCTCTCCTAATATCTGAGTGTGTCTATGTCAGGTCACTCAGATTTGTTTGGTTTGGTTTTACTGGTAAA HG:+:165915458:-1 HG:+:435892836:-1 HG:+:1177187696:-1 HG:+:2592357432:-1 HG:+:2624279020:-1 HG:+:3019570378:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATAATAACTTTGTATGTCCCATGCTGAGAGGTGAATCCCTGAGTTCCTGAATATAGGAAAAATCAATTTAAAGTCATCATTTTAGAGGAACAAGAACAATGGCTACTGGGAGATTTAAATCTGTGTGATCTCGTTCTCTCCTAATATCTGAGTGTGTCTATGTCAGGTCACTCAGATTTGTTTGGTTTGGTTTTACTGGTAAA HG:+:191245416:-1 HG:+:302661951:-1 HG:+:461987734:-1 HG:+:517638869:-1 HG:+:530227754:-1 HG:+:603673043:-1 HG:+:621011770:-1 HG:+:680641969:-1 HG:+:698386316:-1 HG:+:757770013:-1 HG:+:865480289:-1 HG:+:956000712:-1 HG:+:1127981260:-1 HG:+:1134374403:-1 HG:+:1324654555:-1 HG:+:1407474098:-1 HG:+:1422759206:-1 HG:+:1445852448:-1 HG:+:1568909718:-1 HG:+:1632202064:-1 HG:+:1962390415:-1 HG:+:1962430893:-1 HG:+:2056236087:-1 HG:+:2171700798:-1 HG:+:2243141836:-1 HG:+:2287209043:-1 HG:+:2293695725:-1 HG:+:2349241893:-1 HG:+:2431406972:-1 HG:+:2618921263:-1 HG:+:2855566495:-1 HG:+:2904447370:-1 HG:+:2908820856:-1 HG:+:3021277492:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATAATAACTTTGTATGTCCCATGCTGAGAGGTGAATCCCTGAGTTCCTGAATATAGGAAAAATCAATTTAAAGTCATCATTTTAGAGGAACAAGAACAATGGCTACTGGGAGATTTAAATCTGTGTGATCTCGTTCTCTCCTAATATCTGAGTGTGTCTATGTCAGGTCACTCAGATTTGTTTGGTTTGGTTTTACTGGTAAA HG:+:305635261:-1 HG:+:329415307:-1 HG:+:390844097:-1 HG:+:441458898:-1 HG:+:838636696:-1 HG:+:1037162587:-1 HG:+:1125974683:-1 HG:+:1249818805:-1 HG:+:1460048806:-1 HG:+:1496235407:-1 HG:+:1716575642:-1 HG:+:2021760792:-1 HG:+:2066612846:-1 HG:+:2148383358:-1 HG:+:2332516933:-1 HG:+:2615575130:-1 HG:+:2688181445:-1 HG:+:2824702045:-1 HG:+:2894222672:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATAATAACTTTGTATGTCCCATGCTGAGAGGTGAATCCCTGAGTTCCTGAATATAGGAAAAATCAATTTAAAGTCATCATTTTAGAGGAACAAGAACAATGGCTACTGGGAGATTTAAATCTGTGTGATCTCGTTCTCTCCTAATATCTGAGTGTGTCTATGTCAGGTCACTCAGATTTGTTTGGTTTGGTTTTACTGGTAAA HG:+:385751212:-1 HG:+:415968596:-1 HG:+:426315724:-1 HG:+:580614341:-1 HG:+:667588306:-1 HG:+:752450359:-1 HG:+:1135112871:-1 HG:+:1321467028:-1 HG:+:1341523750:-1 HG:+:1370873775:-1 HG:+:2153556613:-1 HG:+:2653012496:-1 HG:+:2807150315:-1 HG:+:2858341466:-1 HG:+:3018181926:-1 HG:+:3025849581:-1 +GTAGACCCCTACACCCACCACCTTATTAAAAAAACAAACAAACAAACAAAACAAACCTGGCAACTTAGAGGCCAAAAAACTGGCTGCTTAGAATTCAAGTTTTTCAGAAACATAACCTGAAAATGACAGGAGTTCACTATTAGTGAATGTTTGGACAATGTCTTATACATCTGTAGATTGTCTTATTTCATTTTGGGATAATAACTTTGTATGTCCCATGCTGAGAGGTGAATCCCTGAGTTCCTGAATATAGGAAAAATCAATTTAAAGTCATCATTTTAGAGGAACAAGAACAATGGCTACTGGGAGATTTAAATCTGTGTGATCTCGTTCTCTCCTAATATCTGAGTGTGTCTATGTCAGGTCACTCAGATTTGTTTGGTTTGGTTTTACTGGTAAA HG:+:39372758:-1 HG:+:482545449:-1 HG:+:492709399:-1 HG:+:612732721:-1 HG:+:628914552:-1 HG:+:870111084:-1 HG:+:911808816:-1 HG:+:1073123194:-1 HG:+:1250931374:-1 HG:+:1260833333:-1 HG:+:1542471502:-1 HG:+:1717990204:-1 HG:+:1773559124:-1 HG:+:1784049172:-1 HG:+:1835634492:-1 HG:+:2069587870:-1 HG:+:2371226631:-1 HG:+:2506241333:-1 HG:+:2758033187:-1 +TTTACCAGTAAAACCAAACCAAACAAATCTGAGTGACCTGACATAGACACACTCAGATATTAGGAGAGAACGAGATCACACAGATTTAAATCTCCCAGTAGCCATTGTTCTTGTTCCTCTAAAATGATGACTTTAAATTGATTTTTCCTATATTCAGGAACTCAGGGATTCACCTCTCAGCATGGGACATACAAAGTTATTATCCCAAAATGAAATAAGACAATCTACAGATGTATAAGACATTGTCCAAACATTCACTAATAGTGAACTCCTGTCATTTTCAGGTTATGTTTCTGAAAAACTTGAATTCTAAGCAGCCAGTTTTTTGGCCTCTAAGTTGCCAGGTTTGTTTTGTTTGTTTGTTTGTTTTTTTAATAAGGTGGTGGGTGTAGGGGTCTAC HG:+:41034900:-1 HG:+:198297168:-1 HG:+:910928327:-1 HG:+:2680788339:-1 +TTTACCAGTAAAACCAAACCAAACAAATCTGAGTGACCTGACATAGACACACTCAGATATTAGGAGAGAACGAGATCACACAGATTTAAATCTCCCAGTAGCCATTGTTCTTGTTCCTCTAAAATGATGACTTTAAATTGATTTTTCCTATATTCAGGAACTCAGGGATTCACCTCTCAGCATGGGACATACAAAGTTATTATCCCAAAATGAAATAAGACAATCTACAGATGTATAAGACATTGTCCAAACATTCACTAATAGTGAACTCCTGTCATTTTCAGGTTATGTTTCTGAAAAACTTGAATTCTAAGCAGCCAGTTTTTTGGCCTCTAAGTTGCCAGGTTTGTTTTGTTTGTTTGTTTGTTTTTTTAATAAGGTGGTGGGTGTAGGGGTCTAC HG:+:2155050811:19 +TTTACCAGTAAAACCAAACCAAACAAATCTGAGTGACCTGACATAGACACACTCAGATATTAGGAGAGAACGAGATCACACAGATTTAAATCTCCCAGTAGCCATTGTTCTTGTTCCTCTAAAATGATGACTTTAAATTGATTTTTCCTATATTCAGGAACTCAGGGATTCACCTCTCAGCATGGGACATACAAAGTTATTATCCCAAAATGAAATAAGACAATCTACAGATGTATAAGACATTGTCCAAACATTCACTAATAGTGAACTCCTGTCATTTTCAGGTTATGTTTCTGAAAAACTTGAATTCTAAGCAGCCAGTTTTTTGGCCTCTAAGTTGCCAGGTTTGTTTTGTTTGTTTGTTTGTTTTTTTAATAAGGTGGTGGGTGTAGGGGTCTAC HG:+:1717087027:-1 HG:+:2155050813:19 +TTTACCAGTAAAACCAAACCAAACAAATCTGAGTGACCTGACATAGACACACTCAGATATTAGGAGAGAACGAGATCACACAGATTTAAATCTCCCAGTAGCCATTGTTCTTGTTCCTCTAAAATGATGACTTTAAATTGATTTTTCCTATATTCAGGAACTCAGGGATTCACCTCTCAGCATGGGACATACAAAGTTATTATCCCAAAATGAAATAAGACAATCTACAGATGTATAAGACATTGTCCAAACATTCACTAATAGTGAACTCCTGTCATTTTCAGGTTATGTTTCTGAAAAACTTGAATTCTAAGCAGCCAGTTTTTTGGCCTCTAAGTTGCCAGGTTTGTTTTGTTTGTTTGTTTGTTTTTTTAATAAGGTGGTGGGTGTAGGGGTCTAC HG:+:2155050810:19 +TTTACCAGTAAAACCAAACCAAACAAATCTGAGTGACCTGACATAGACACACTCAGATATTAGGAGAGAACGAGATCACACAGATTTAAATCTCCCAGTAGCCATTGTTCTTGTTCCTCTAAAATGATGACTTTAAATTGATTTTTCCTATATTCAGGAACTCAGGGATTCACCTCTCAGCATGGGACATACAAAGTTATTATCCCAAAATGAAATAAGACAATCTACAGATGTATAAGACATTGTCCAAACATTCACTAATAGTGAACTCCTGTCATTTTCAGGTTATGTTTCTGAAAAACTTGAATTCTAAGCAGCCAGTTTTTTGGCCTCTAAGTTGCCAGGTTTGTTTTGTTTGTTTGTTTGTTTTTTTAATAAGGTGGTGGGTGTAGGGGTCTAC HG:+:2155050812:19 +TTTACCAGTAAAACCAAACCAAACAAATCTGAGTGACCTGACATAGACACACTCAGATATTAGGAGAGAACGAGATCACACAGATTTAAATCTCCCAGTAGCCATTGTTCTTGTTCCTCTAAAATGATGACTTTAAATTGATTTTTCCTATATTCAGGAACTCAGGGATTCACCTCTCAGCATGGGACATACAAAGTTATTATCCCAAAATGAAATAAGACAATCTACAGATGTATAAGACATTGTCCAAACATTCACTAATAGTGAACTCCTGTCATTTTCAGGTTATGTTTCTGAAAAACTTGAATTCTAAGCAGCCAGTTTTTTGGCCTCTAAGTTGCCAGGTTTGTTTTGTTTGTTTGTTTGTTTTTTTAATAAGGTGGTGGGTGTAGGGGTCTAC HG:+:2155050806:19 +TTTACCAGTAAAACCAAACCAAACAAATCTGAGTGACCTGACATAGACACACTCAGATATTAGGAGAGAACGAGATCACACAGATTTAAATCTCCCAGTAGCCATTGTTCTTGTTCCTCTAAAATGATGACTTTAAATTGATTTTTCCTATATTCAGGAACTCAGGGATTCACCTCTCAGCATGGGACATACAAAGTTATTATCCCAAAATGAAATAAGACAATCTACAGATGTATAAGACATTGTCCAAACATTCACTAATAGTGAACTCCTGTCATTTTCAGGTTATGTTTCTGAAAAACTTGAATTCTAAGCAGCCAGTTTTTTGGCCTCTAAGTTGCCAGGTTTGTTTTGTTTGTTTGTTTGTTTTTTTAATAAGGTGGTGGGTGTAGGGGTCTAC HG:+:1187888913:-1 +TTTACCAGTAAAACCAAACCAAACAAATCTGAGTGACCTGACATAGACACACTCAGATATTAGGAGAGAACGAGATCACACAGATTTAAATCTCCCAGTAGCCATTGTTCTTGTTCCTCTAAAATGATGACTTTAAATTGATTTTTCCTATATTCAGGAACTCAGGGATTCACCTCTCAGCATGGGACATACAAAGTTATTATCCCAAAATGAAATAAGACAATCTACAGATGTATAAGACATTGTCCAAACATTCACTAATAGTGAACTCCTGTCATTTTCAGGTTATGTTTCTGAAAAACTTGAATTCTAAGCAGCCAGTTTTTTGGCCTCTAAGTTGCCAGGTTTGTTTTGTTTGTTTGTTTGTTTTTTTAATAAGGTGGTGGGTGTAGGGGTCTAC HG:+:2155050815:19 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:73307941:-1 HG:+:101282805:-1 HG:+:266715652:-1 HG:+:397948206:-1 HG:+:711327796:-1 HG:+:972639504:-1 HG:+:974729539:-1 HG:+:1127080439:-1 HG:+:1215779424:-1 HG:+:1970938851:-1 HG:+:2193203158:-1 HG:+:2725620516:-1 HG:+:2829609237:-1 HG:+:3055903719:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:82993232:-1 HG:+:247395611:-1 HG:+:318097630:-1 HG:+:379007875:-1 HG:+:456009632:-1 HG:+:550663885:-1 HG:+:623585338:-1 HG:+:625087995:-1 HG:+:633873726:-1 HG:+:653163679:-1 HG:+:692680657:-1 HG:+:816466937:-1 HG:+:849547693:-1 HG:+:1168664031:-1 HG:+:1373613762:-1 HG:+:1398533969:-1 HG:+:2020359324:-1 HG:+:2340665176:-1 HG:+:2513526399:-1 HG:+:2799469350:-1 HG:+:2954895054:-1 HG:+:2958483944:-1 HG:+:2971715356:-1 HG:+:3018583901:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:348961592:-1 HG:+:400777680:-1 HG:+:439138511:-1 HG:+:656017268:-1 HG:+:812480748:-1 HG:+:1268342527:-1 HG:+:1269380300:-1 HG:+:1351318446:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:232812923:-1 HG:+:410128015:-1 HG:+:820896307:-1 HG:+:1317710092:-1 HG:+:1462167191:-1 HG:+:1783479589:-1 HG:+:2236140205:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:439962687:-1 HG:+:2037556454:-1 HG:+:2463686789:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:142942388:-1 HG:+:143518961:-1 HG:+:410534157:-1 HG:+:776342001:-1 HG:+:843797599:-1 HG:+:864639515:-1 HG:+:903337830:-1 HG:+:1118320919:-1 HG:+:1453360563:-1 HG:+:1507162682:-1 HG:+:1855630120:-1 HG:+:1920515221:-1 HG:+:1946711464:-1 HG:+:1992076695:-1 HG:+:2002708532:-1 HG:+:2027173563:-1 HG:+:2155360331:-1 HG:+:2279484076:-1 HG:+:2334838464:-1 HG:+:2334838496:-1 HG:+:2334838528:-1 HG:+:2334838560:-1 HG:+:2387702549:-1 HG:+:2514547753:-1 HG:+:2646851022:-1 HG:+:2791619043:-1 HG:+:2802229707:-1 HG:+:3032132305:-1 HG:+:3049725830:-1 HG:+:3097683328:-1 HG:+:3098015305:-1 HG:+:3101021342:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:632787492:-1 HG:+:1436570271:-1 HG:+:2862373460:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:68009951:-1 HG:+:705695723:-1 HG:+:1262601828:-1 HG:+:1553349380:-1 HG:+:1713935805:-1 HG:+:1836190473:-1 HG:+:2546402421:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:487308054:-1 HG:+:869130535:-1 HG:+:1956575749:-1 HG:+:2569478000:-1 HG:+:2910758454:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:46346643:-1 HG:+:48011926:-1 HG:+:49598746:-1 HG:+:94347306:-1 HG:+:102643655:-1 HG:+:186053207:-1 HG:+:315152069:-1 HG:+:388246988:-1 HG:+:426689399:-1 HG:+:588715131:-1 HG:+:636853033:-1 HG:+:658487052:-1 HG:+:776561081:-1 HG:+:821438266:-1 HG:+:849234195:-1 HG:+:858551267:-1 HG:+:899562953:-1 HG:+:905374965:-1 HG:+:947818795:-1 HG:+:1141234170:-1 HG:+:1244357782:-1 HG:+:1271274602:-1 HG:+:1378341001:-1 HG:+:1403857400:-1 HG:+:1449192156:-1 HG:+:1483963626:-1 HG:+:1642141402:-1 HG:+:1680453854:-1 HG:+:1683578809:-1 HG:+:1876669734:-1 HG:+:1899247079:-1 HG:+:1929613109:-1 HG:+:2037056822:-1 HG:+:2120379635:-1 HG:+:2171489093:-1 HG:+:2226311980:-1 HG:+:2369845582:-1 HG:+:2581402175:-1 HG:+:2600273285:-1 HG:+:2714766365:-1 HG:+:3008500981:-1 HG:+:3097771635:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:591586489:-1 HG:+:783860914:-1 HG:+:938398304:-1 HG:+:1124799754:-1 HG:+:1198274935:-1 HG:+:1210423279:-1 HG:+:1228458846:-1 HG:+:1268076993:-1 HG:+:1477685426:-1 HG:+:1555986174:-1 HG:+:1858130712:-1 HG:+:1969707647:-1 HG:+:2027420794:-1 HG:+:2106616818:-1 HG:+:2279583195:-1 HG:+:2563608635:-1 HG:+:2567427070:-1 HG:+:2674700933:-1 HG:+:2725949254:-1 HG:+:3055259638:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:328884008:-1 HG:+:374674759:-1 HG:+:507776068:-1 HG:+:520895619:-1 HG:+:542974104:-1 HG:+:618645341:-1 HG:+:1029348017:-1 HG:+:1030130697:-1 HG:+:1060467860:-1 HG:+:1183015379:-1 HG:+:1189906328:-1 HG:+:1279982304:-1 HG:+:1652618735:-1 HG:+:1656043986:-1 HG:+:1692695924:-1 HG:+:1800922863:-1 HG:+:2190117442:-1 HG:+:2554274882:-1 HG:+:2606965470:-1 HG:+:2690577064:-1 HG:+:2875983645:-1 HG:+:2990141302:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:331196804:-1 HG:+:570046576:-1 HG:+:840892717:-1 HG:+:869459121:-1 HG:+:1130429298:-1 HG:+:1132441375:-1 HG:+:1353403680:-1 HG:+:1805634954:-1 HG:+:2221529343:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:88927765:-1 HG:+:145676120:-1 HG:+:194648087:-1 HG:+:263877388:-1 HG:+:291950021:-1 HG:+:309224589:-1 HG:+:314635037:-1 HG:+:435562346:-1 HG:+:555661429:-1 HG:+:556754762:-1 HG:+:629908569:-1 HG:+:709721238:-1 HG:+:755881403:-1 HG:+:759503227:-1 HG:+:764834141:-1 HG:+:888019337:-1 HG:+:897403351:-1 HG:+:903076008:-1 HG:+:959081798:-1 HG:+:973836313:-1 HG:+:979503709:-1 HG:+:988766993:-1 HG:+:1057743233:-1 HG:+:1096867735:-1 HG:+:1161847620:-1 HG:+:1178174826:-1 HG:+:1200453673:-1 HG:+:1205558997:-1 HG:+:1306618784:-1 HG:+:1396113390:-1 HG:+:1396724384:-1 HG:+:1443610274:-1 HG:+:1475123279:-1 HG:+:1559974267:-1 HG:+:1612989214:-1 HG:+:1675026986:-1 HG:+:1716759421:-1 HG:+:1774040576:-1 HG:+:1789002090:-1 HG:+:1799127886:-1 HG:+:1851294409:-1 HG:+:1916779819:-1 HG:+:2184175006:-1 HG:+:2298544273:-1 HG:+:2424172252:-1 HG:+:2458250966:-1 HG:+:2545143347:-1 HG:+:2588017169:-1 HG:+:2768951544:-1 HG:+:3007851407:-1 HG:+:3054764260:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:749531958:-1 HG:+:789425400:-1 HG:+:789822025:-1 HG:+:849239286:-1 HG:+:1127080420:-1 HG:+:1363926873:-1 HG:+:1384988739:-1 HG:+:1458846635:-1 HG:+:1551418701:-1 HG:+:2080905921:-1 HG:+:2165923001:-1 HG:+:2346623748:-1 HG:+:2396417633:-1 HG:+:2631534919:-1 HG:+:2829609238:-1 HG:+:3008483483:-1 +GAGTTTGAGATCAGCCTAGGGCATCATGAAAAGCCCTGTCTATGGATTTTTTTTTTTTAAATAGCCCGGACATGGGACTAACATCAAGGAAATGCAAATCAAAACCACAATGTGATACCACCTCACTCTGCAAGAAATGGCCATAATCAAAAAAATAATAGTTGTTGGCATTGGATTGTGGTGAAAAAGGGAATACTTCTACACTGCTGGTGGGAATGTAAACGTAGTACAACCAACTATGGAAAATATGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGAATCCAGCAATCCCACTACTGTGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAGATACTTTGCCACATACATGTAAAACAATACATATATAAACATGTATGTTT HG:+:462483033:-1 HG:+:669062081:-1 HG:+:776912487:-1 HG:+:1365357147:-1 HG:+:1372535411:-1 HG:+:1458846634:-1 HG:+:1828544835:-1 HG:+:2113190190:-1 HG:+:2161616149:-1 HG:+:2293101896:-1 HG:+:2937407250:-1 +AAACATACATGTTTATATATGTATTGTTTTACATGTATGTGGCAAAGTATCTTTTCGTATAATGACTTCTTTTCCTCTGGGTAGATACACAGTAGTGGGATTGCTGGATTCAAATGGTAGTTCTACTTTTAGTTCTTTAAGGAATCTCCACATATTTTCCATAGTTGGTTGTACTACGTTTACATTCCCACCAGCAGTGTAGAAGTATTCCCTTTTTCACCACAATCCAATGCCAACAACTATTATTTTTTTGATTATGGCCATTTCTTGCAGAGTGAGGTGGTATCACATTGTGGTTTTGATTTGCATTTCCTTGATGTTAGTCCCATGTCCGGGCTATTTAAAAAAAAAAAATCCATAGACAGGGCTTTTCATGATGCCCTAGGCTGATCTCAAACTC HG:+:795699555:-1 HG:+:2160129879:-1 +AAACATACATGTTTATATATGTATTGTTTTACATGTATGTGGCAAAGTATCTTTTCGTATAATGACTTCTTTTCCTCTGGGTAGATACACAGTAGTGGGATTGCTGGATTCAAATGGTAGTTCTACTTTTAGTTCTTTAAGGAATCTCCACATATTTTCCATAGTTGGTTGTACTACGTTTACATTCCCACCAGCAGTGTAGAAGTATTCCCTTTTTCACCACAATCCAATGCCAACAACTATTATTTTTTTGATTATGGCCATTTCTTGCAGAGTGAGGTGGTATCACATTGTGGTTTTGATTTGCATTTCCTTGATGTTAGTCCCATGTCCGGGCTATTTAAAAAAAAAAAATCCATAGACAGGGCTTTTCATGATGCCCTAGGCTGATCTCAAACTC HG:+:76915607:-1 HG:+:80614428:-1 HG:+:197173268:-1 HG:+:250718637:-1 HG:+:284876247:-1 HG:+:290276512:-1 HG:+:338291558:-1 HG:+:382396031:-1 HG:+:414666764:-1 HG:+:465239501:-1 HG:+:469004613:-1 HG:+:473540529:-1 HG:+:549656370:20 HG:+:557634396:-1 HG:+:579384122:-1 HG:+:606433994:-1 HG:+:611122083:-1 HG:+:669168145:-1 HG:+:685170946:-1 HG:+:761435256:-1 HG:+:812799298:-1 HG:+:812807253:-1 HG:+:820968156:-1 HG:+:936491049:-1 HG:+:1032984769:-1 HG:+:1082068578:-1 HG:+:1104179666:-1 HG:+:1155491636:-1 HG:+:1199942517:-1 HG:+:1199990994:-1 HG:+:1225901238:-1 HG:+:1243984975:-1 HG:+:1257773676:-1 HG:+:1304310087:-1 HG:+:1370018079:-1 HG:+:1381256940:-1 HG:+:1478478320:-1 HG:+:1538973603:-1 HG:+:1567062953:-1 HG:+:1683376851:-1 HG:+:1741854289:-1 HG:+:1979455072:-1 HG:+:1997648141:-1 HG:+:2135628478:-1 HG:+:2188877334:-1 HG:+:2222019554:-1 HG:+:2345493899:-1 HG:+:2409418805:-1 HG:+:2423187230:-1 HG:+:2480761443:-1 HG:+:2639039513:-1 HG:+:2735341536:-1 HG:+:2919418453:-1 HG:+:3019451089:-1 HG:+:3035411741:-1 HG:+:3101406966:-1 +AAACATACATGTTTATATATGTATTGTTTTACATGTATGTGGCAAAGTATCTTTTCGTATAATGACTTCTTTTCCTCTGGGTAGATACACAGTAGTGGGATTGCTGGATTCAAATGGTAGTTCTACTTTTAGTTCTTTAAGGAATCTCCACATATTTTCCATAGTTGGTTGTACTACGTTTACATTCCCACCAGCAGTGTAGAAGTATTCCCTTTTTCACCACAATCCAATGCCAACAACTATTATTTTTTTGATTATGGCCATTTCTTGCAGAGTGAGGTGGTATCACATTGTGGTTTTGATTTGCATTTCCTTGATGTTAGTCCCATGTCCGGGCTATTTAAAAAAAAAAAATCCATAGACAGGGCTTTTCATGATGCCCTAGGCTGATCTCAAACTC HG:+:1455079086:-1 HG:+:2611194418:-1 +AAACATACATGTTTATATATGTATTGTTTTACATGTATGTGGCAAAGTATCTTTTCGTATAATGACTTCTTTTCCTCTGGGTAGATACACAGTAGTGGGATTGCTGGATTCAAATGGTAGTTCTACTTTTAGTTCTTTAAGGAATCTCCACATATTTTCCATAGTTGGTTGTACTACGTTTACATTCCCACCAGCAGTGTAGAAGTATTCCCTTTTTCACCACAATCCAATGCCAACAACTATTATTTTTTTGATTATGGCCATTTCTTGCAGAGTGAGGTGGTATCACATTGTGGTTTTGATTTGCATTTCCTTGATGTTAGTCCCATGTCCGGGCTATTTAAAAAAAAAAAATCCATAGACAGGGCTTTTCATGATGCCCTAGGCTGATCTCAAACTC HG:+:2886151542:-1 +AAACATACATGTTTATATATGTATTGTTTTACATGTATGTGGCAAAGTATCTTTTCGTATAATGACTTCTTTTCCTCTGGGTAGATACACAGTAGTGGGATTGCTGGATTCAAATGGTAGTTCTACTTTTAGTTCTTTAAGGAATCTCCACATATTTTCCATAGTTGGTTGTACTACGTTTACATTCCCACCAGCAGTGTAGAAGTATTCCCTTTTTCACCACAATCCAATGCCAACAACTATTATTTTTTTGATTATGGCCATTTCTTGCAGAGTGAGGTGGTATCACATTGTGGTTTTGATTTGCATTTCCTTGATGTTAGTCCCATGTCCGGGCTATTTAAAAAAAAAAAATCCATAGACAGGGCTTTTCATGATGCCCTAGGCTGATCTCAAACTC HG:+:434909263:-1 HG:+:515965231:-1 HG:+:520946313:-1 HG:+:549656368:20 HG:+:922757931:-1 HG:+:1432682064:-1 HG:+:1915702040:-1 HG:+:2047447482:-1 HG:+:2066945731:-1 HG:+:2160622409:-1 +AAACATACATGTTTATATATGTATTGTTTTACATGTATGTGGCAAAGTATCTTTTCGTATAATGACTTCTTTTCCTCTGGGTAGATACACAGTAGTGGGATTGCTGGATTCAAATGGTAGTTCTACTTTTAGTTCTTTAAGGAATCTCCACATATTTTCCATAGTTGGTTGTACTACGTTTACATTCCCACCAGCAGTGTAGAAGTATTCCCTTTTTCACCACAATCCAATGCCAACAACTATTATTTTTTTGATTATGGCCATTTCTTGCAGAGTGAGGTGGTATCACATTGTGGTTTTGATTTGCATTTCCTTGATGTTAGTCCCATGTCCGGGCTATTTAAAAAAAAAAAATCCATAGACAGGGCTTTTCATGATGCCCTAGGCTGATCTCAAACTC HG:+:24316741:-1 HG:+:242293598:-1 HG:+:514771117:-1 HG:+:760452073:-1 HG:+:862641287:-1 HG:+:1443394309:-1 HG:+:3027914147:-1 HG:+:3097110477:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCCCACCAACAGCGTAGTAAGTGTTACCCGTTTTCTCTCAAACCTCACTAGCATCTCTTATTTTTTGACCTTCTTAACGAATAGTCAATTGTGACTGGTGTGAGATGATATCTCATTGTGGTTTTGATTTCTAATGATCAATGATATTTGTAGCCTTTTTACATATTGGTTGTTCGGCCATGTGTATGTCTTCTTTTGAGAAG HG:+:43337920:-1 HG:+:95039373:-1 HG:+:165971059:-1 HG:+:197761992:-1 HG:+:249182271:-1 HG:+:306798037:-1 HG:+:386730522:-1 HG:+:394630297:-1 HG:+:425430241:-1 HG:+:447975548:-1 HG:+:485083297:-1 HG:+:518793608:-1 HG:+:547387404:-1 HG:+:600404882:-1 HG:+:637482861:-1 HG:+:649564050:-1 HG:+:817256527:-1 HG:+:819110893:-1 HG:+:820097716:-1 HG:+:825149838:-1 HG:+:893829969:-1 HG:+:935459085:-1 HG:+:937284468:-1 HG:+:1017579745:-1 HG:+:1227485090:-1 HG:+:1279844302:-1 HG:+:1310386665:-1 HG:+:1321114989:-1 HG:+:1364034388:-1 HG:+:1515272114:-1 HG:+:1621612024:-1 HG:+:1631292104:-1 HG:+:1660560501:-1 HG:+:1700212712:-1 HG:+:1700546750:-1 HG:+:1704591785:-1 HG:+:1755049403:-1 HG:+:1840474049:-1 HG:+:1976192285:-1 HG:+:2133691346:-1 HG:+:2135647538:-1 HG:+:2181735944:-1 HG:+:2463952512:-1 HG:+:2482582025:-1 HG:+:2594446034:-1 HG:+:2613187447:-1 HG:+:2741428445:-1 HG:+:2758265209:-1 HG:+:2823188091:-1 HG:+:2924237516:-1 HG:+:2970881652:-1 HG:+:2985950773:-1 HG:+:2996788184:-1 HG:+:3004431949:-1 HG:+:3013290848:-1 HG:+:3040343000:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCCCACCAACAGCGTAGTAAGTGTTACCCGTTTTCTCTCAAACCTCACTAGCATCTCTTATTTTTTGACCTTCTTAACGAATAGTCAATTGTGACTGGTGTGAGATGATATCTCATTGTGGTTTTGATTTCTAATGATCAATGATATTTGTAGCCTTTTTACATATTGGTTGTTCGGCCATGTGTATGTCTTCTTTTGAGAAG HG:+:602954073:-1 HG:+:645582792:-1 HG:+:975159203:-1 HG:+:1114847223:-1 HG:+:1646430013:-1 HG:+:1661663129:-1 HG:+:1695735428:-1 HG:+:1837684009:-1 HG:+:2025935371:-1 HG:+:2042776809:-1 HG:+:2065689740:-1 HG:+:2106614707:-1 HG:+:2257343802:-1 HG:+:2353575896:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCCCACCAACAGCGTAGTAAGTGTTACCCGTTTTCTCTCAAACCTCACTAGCATCTCTTATTTTTTGACCTTCTTAACGAATAGTCAATTGTGACTGGTGTGAGATGATATCTCATTGTGGTTTTGATTTCTAATGATCAATGATATTTGTAGCCTTTTTACATATTGGTTGTTCGGCCATGTGTATGTCTTCTTTTGAGAAG HG:+:561842939:-1 HG:+:1201511703:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCCCACCAACAGCGTAGTAAGTGTTACCCGTTTTCTCTCAAACCTCACTAGCATCTCTTATTTTTTGACCTTCTTAACGAATAGTCAATTGTGACTGGTGTGAGATGATATCTCATTGTGGTTTTGATTTCTAATGATCAATGATATTTGTAGCCTTTTTACATATTGGTTGTTCGGCCATGTGTATGTCTTCTTTTGAGAAG HG:+:461213795:-1 HG:+:954293979:-1 HG:+:2145751906:-1 HG:+:2252953722:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCCCACCAACAGCGTAGTAAGTGTTACCCGTTTTCTCTCAAACCTCACTAGCATCTCTTATTTTTTGACCTTCTTAACGAATAGTCAATTGTGACTGGTGTGAGATGATATCTCATTGTGGTTTTGATTTCTAATGATCAATGATATTTGTAGCCTTTTTACATATTGGTTGTTCGGCCATGTGTATGTCTTCTTTTGAGAAG HG:+:1643262963:-1 HG:+:1795273221:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCCCACCAACAGCGTAGTAAGTGTTACCCGTTTTCTCTCAAACCTCACTAGCATCTCTTATTTTTTGACCTTCTTAACGAATAGTCAATTGTGACTGGTGTGAGATGATATCTCATTGTGGTTTTGATTTCTAATGATCAATGATATTTGTAGCCTTTTTACATATTGGTTGTTCGGCCATGTGTATGTCTTCTTTTGAGAAG HG:+:233567945:-1 HG:+:280100577:-1 HG:+:426492350:-1 HG:+:433261608:-1 HG:+:1159898855:-1 HG:+:1205572488:-1 HG:+:1213894405:-1 HG:+:1316811494:-1 HG:+:1506920633:-1 HG:+:1621962033:-1 HG:+:1785433155:-1 HG:+:2516819215:-1 HG:+:2542123900:-1 HG:+:2863173330:-1 HG:+:3015210008:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCCCACCAACAGCGTAGTAAGTGTTACCCGTTTTCTCTCAAACCTCACTAGCATCTCTTATTTTTTGACCTTCTTAACGAATAGTCAATTGTGACTGGTGTGAGATGATATCTCATTGTGGTTTTGATTTCTAATGATCAATGATATTTGTAGCCTTTTTACATATTGGTTGTTCGGCCATGTGTATGTCTTCTTTTGAGAAG HG:+:19247658:-1 HG:+:63388761:-1 HG:+:223540211:-1 HG:+:406580494:-1 HG:+:788521445:-1 HG:+:921591028:-1 HG:+:1078423196:-1 HG:+:1234284058:-1 HG:+:1616665625:-1 HG:+:2307108061:-1 HG:+:2380019085:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCCCACCAACAGCGTAGTAAGTGTTACCCGTTTTCTCTCAAACCTCACTAGCATCTCTTATTTTTTGACCTTCTTAACGAATAGTCAATTGTGACTGGTGTGAGATGATATCTCATTGTGGTTTTGATTTCTAATGATCAATGATATTTGTAGCCTTTTTACATATTGGTTGTTCGGCCATGTGTATGTCTTCTTTTGAGAAG HG:+:33126677:-1 HG:+:58664934:-1 HG:+:72453298:-1 HG:+:112687018:-1 HG:+:217990108:-1 HG:+:242231663:-1 HG:+:308191151:-1 HG:+:324114045:-1 HG:+:325535446:-1 HG:+:339339431:-1 HG:+:402617962:-1 HG:+:520796735:-1 HG:+:683321818:-1 HG:+:690305078:-1 HG:+:732642106:-1 HG:+:782991434:-1 HG:+:789655725:-1 HG:+:829574412:-1 HG:+:851462830:-1 HG:+:873653649:-1 HG:+:943445507:-1 HG:+:960567523:-1 HG:+:996149066:-1 HG:+:1091675888:-1 HG:+:1113366648:-1 HG:+:1148604030:-1 HG:+:1209159149:-1 HG:+:1214819155:-1 HG:+:1234578671:-1 HG:+:1253174091:-1 HG:+:1284702132:-1 HG:+:1343465001:-1 HG:+:1507345754:-1 HG:+:1558476096:-1 HG:+:1625697135:-1 HG:+:1650398407:-1 HG:+:1680241489:-1 HG:+:1702487376:-1 HG:+:1709662761:-1 HG:+:1714572102:-1 HG:+:1771127372:-1 HG:+:1812389026:-1 HG:+:1908344537:-1 HG:+:1915570770:-1 HG:+:1951861592:-1 HG:+:1995723454:-1 HG:+:2034721788:-1 HG:+:2108569575:-1 HG:+:2169756773:-1 HG:+:2264608765:-1 HG:+:2362201765:-1 HG:+:2436485164:-1 HG:+:2485522222:-1 HG:+:2618280436:-1 HG:+:2635639443:-1 HG:+:2741041091:-1 HG:+:2755593843:-1 HG:+:2969809864:-1 HG:+:2979122872:-1 HG:+:2985456276:-1 HG:+:3002296883:-1 HG:+:3039349335:-1 HG:+:3046277256:-1 HG:+:3056596228:-1 HG:+:3060762438:-1 HG:+:3064193097:-1 HG:+:3064395193:-1 HG:+:3096320975:-1 HG:+:3096372722:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCCCACCAACAGCGTAGTAAGTGTTACCCGTTTTCTCTCAAACCTCACTAGCATCTCTTATTTTTTGACCTTCTTAACGAATAGTCAATTGTGACTGGTGTGAGATGATATCTCATTGTGGTTTTGATTTCTAATGATCAATGATATTTGTAGCCTTTTTACATATTGGTTGTTCGGCCATGTGTATGTCTTCTTTTGAGAAG HG:+:57126832:-1 HG:+:87507111:-1 HG:+:102448056:-1 HG:+:261419324:-1 HG:+:262135018:-1 HG:+:631524204:-1 HG:+:670284065:-1 HG:+:717096353:-1 HG:+:753160438:-1 HG:+:807332683:-1 HG:+:996010052:-1 HG:+:1208915517:-1 HG:+:1232044232:-1 HG:+:1255268589:-1 HG:+:1318938499:-1 HG:+:1407018198:-1 HG:+:1455525353:-1 HG:+:1495164167:-1 HG:+:1559951911:-1 HG:+:1562175538:-1 HG:+:1908824270:-1 HG:+:1912917178:-1 HG:+:1984749488:-1 HG:+:2193848215:-1 HG:+:2232420477:-1 HG:+:2235726038:-1 HG:+:2255793396:-1 HG:+:2257760780:-1 HG:+:2474947677:-1 HG:+:2512631023:-1 HG:+:2534142360:-1 HG:+:2696161311:-1 HG:+:2696648937:-1 HG:+:2810057152:-1 HG:+:2877093628:-1 HG:+:2925412366:-1 HG:+:2935926812:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCCCACCAACAGCGTAGTAAGTGTTACCCGTTTTCTCTCAAACCTCACTAGCATCTCTTATTTTTTGACCTTCTTAACGAATAGTCAATTGTGACTGGTGTGAGATGATATCTCATTGTGGTTTTGATTTCTAATGATCAATGATATTTGTAGCCTTTTTACATATTGGTTGTTCGGCCATGTGTATGTCTTCTTTTGAGAAG HG:+:72419962:-1 HG:+:163956279:-1 HG:+:249958398:-1 HG:+:520425625:-1 HG:+:814092048:-1 HG:+:910523415:-1 HG:+:924174198:-1 HG:+:1094995336:-1 HG:+:1095016082:-1 HG:+:1095081371:-1 HG:+:1102293242:-1 HG:+:1230245840:-1 HG:+:1383334199:-1 HG:+:1613178144:-1 HG:+:1622665486:-1 HG:+:2137918434:-1 HG:+:2153366166:-1 HG:+:2492413299:-1 HG:+:3022403040:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCCCACCAACAGCGTAGTAAGTGTTACCCGTTTTCTCTCAAACCTCACTAGCATCTCTTATTTTTTGACCTTCTTAACGAATAGTCAATTGTGACTGGTGTGAGATGATATCTCATTGTGGTTTTGATTTCTAATGATCAATGATATTTGTAGCCTTTTTACATATTGGTTGTTCGGCCATGTGTATGTCTTCTTTTGAGAAG HG:+:9940369:-1 HG:+:102555428:-1 HG:+:186772175:-1 HG:+:348243808:-1 HG:+:440914411:-1 HG:+:782397066:-1 HG:+:836258664:-1 HG:+:957392628:-1 HG:+:1055912885:-1 HG:+:1491382611:-1 HG:+:1880226342:-1 HG:+:1915467560:-1 HG:+:1927825415:-1 HG:+:2988460837:-1 HG:+:3021518528:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCCCACCAACAGCGTAGTAAGTGTTACCCGTTTTCTCTCAAACCTCACTAGCATCTCTTATTTTTTGACCTTCTTAACGAATAGTCAATTGTGACTGGTGTGAGATGATATCTCATTGTGGTTTTGATTTCTAATGATCAATGATATTTGTAGCCTTTTTACATATTGGTTGTTCGGCCATGTGTATGTCTTCTTTTGAGAAG HG:+:955564175:-1 HG:+:2026257862:-1 +TCCATGTCTTTTGGCTATTGTGAATAGTGCTGCAATTACAGTATAGATGTATCTGTCTTTTATTCGGTAAGAGCAATTTATATTCCTTTAGGCATATACCCCAGTAATGGGCCTGCTGGGTCGAATGGAGGTTCTGTTTTTAGTTCCTTTGAGGGACCACCACACTGCTTTCCACAATGGGTTGACAAAGTTCACACTCCCACCAACAGCGTAGTAAGTGTTACCCGTTTTCTCTCAAACCTCACTAGCATCTCTTATTTTTTGACCTTCTTAACGAATAGTCAATTGTGACTGGTGTGAGATGATATCTCATTGTGGTTTTGATTTCTAATGATCAATGATATTTGTAGCCTTTTTACATATTGGTTGTTCGGCCATGTGTATGTCTTCTTTTGAGAAG HG:+:331422942:-1 HG:+:595005424:-1 HG:+:597677886:-1 HG:+:1073463408:-1 HG:+:1180290484:-1 HG:+:1669068705:-1 HG:+:1838158251:-1 HG:+:1858076880:-1 HG:+:2762264208:-1 HG:+:2821164417:-1 HG:+:2946630659:-1 HG:+:3008836635:-1 HG:+:3050495281:-1 +CTTCTCAAAAGAAGACATACACATGGCCGAACAACCAATATGTAAAAAGGCTACAAATATCATTGATCATTAGAAATCAAAACCACAATGAGATATCATCTCACACCAGTCACAATTGACTATTCGTTAAGAAGGTCAAAAAATAAGAGATGCTAGTGAGGTTTGAGAGAAAACGGGTAACACTTACTACGCTGTTGGTGGGAGTGTGAACTTTGTCAACCCATTGTGGAAAGCAGTGTGGTGGTCCCTCAAAGGAACTAAAAACAGAACCTCCATTCGACCCAGCAGGCCCATTACTGGGGTATATGCCTAAAGGAATATAAATTGCTCTTACCGAATAAAAGACAGATACATCTATACTGTAATTGCAGCACTATTCACAATAGCCAAAAGACATGGA HG:+:79613466:-1 HG:+:268544891:-1 HG:+:294626363:-1 HG:+:739680853:-1 HG:+:1327897115:-1 HG:+:2735693691:-1 HG:+:2939173088:-1 +CTTCTCAAAAGAAGACATACACATGGCCGAACAACCAATATGTAAAAAGGCTACAAATATCATTGATCATTAGAAATCAAAACCACAATGAGATATCATCTCACACCAGTCACAATTGACTATTCGTTAAGAAGGTCAAAAAATAAGAGATGCTAGTGAGGTTTGAGAGAAAACGGGTAACACTTACTACGCTGTTGGTGGGAGTGTGAACTTTGTCAACCCATTGTGGAAAGCAGTGTGGTGGTCCCTCAAAGGAACTAAAAACAGAACCTCCATTCGACCCAGCAGGCCCATTACTGGGGTATATGCCTAAAGGAATATAAATTGCTCTTACCGAATAAAAGACAGATACATCTATACTGTAATTGCAGCACTATTCACAATAGCCAAAAGACATGGA HG:+:59767596:-1 HG:+:408507948:-1 HG:+:764022986:-1 HG:+:803490346:-1 HG:+:979433155:-1 HG:+:1138826844:-1 HG:+:1456402066:-1 HG:+:1571246824:-1 HG:+:1629140420:-1 HG:+:2168369416:-1 HG:+:2176236998:-1 HG:+:2238711779:-1 HG:+:2430309270:-1 HG:+:2534552674:-1 HG:+:2642714718:-1 HG:+:2689298039:-1 HG:+:2943559839:-1 HG:+:2960827242:-1 HG:+:3055104201:-1 +CTTCTCAAAAGAAGACATACACATGGCCGAACAACCAATATGTAAAAAGGCTACAAATATCATTGATCATTAGAAATCAAAACCACAATGAGATATCATCTCACACCAGTCACAATTGACTATTCGTTAAGAAGGTCAAAAAATAAGAGATGCTAGTGAGGTTTGAGAGAAAACGGGTAACACTTACTACGCTGTTGGTGGGAGTGTGAACTTTGTCAACCCATTGTGGAAAGCAGTGTGGTGGTCCCTCAAAGGAACTAAAAACAGAACCTCCATTCGACCCAGCAGGCCCATTACTGGGGTATATGCCTAAAGGAATATAAATTGCTCTTACCGAATAAAAGACAGATACATCTATACTGTAATTGCAGCACTATTCACAATAGCCAAAAGACATGGA HG:+:112037860:-1 HG:+:1458363543:-1 HG:+:1557772697:-1 HG:+:2225714820:-1 +CTTCTCAAAAGAAGACATACACATGGCCGAACAACCAATATGTAAAAAGGCTACAAATATCATTGATCATTAGAAATCAAAACCACAATGAGATATCATCTCACACCAGTCACAATTGACTATTCGTTAAGAAGGTCAAAAAATAAGAGATGCTAGTGAGGTTTGAGAGAAAACGGGTAACACTTACTACGCTGTTGGTGGGAGTGTGAACTTTGTCAACCCATTGTGGAAAGCAGTGTGGTGGTCCCTCAAAGGAACTAAAAACAGAACCTCCATTCGACCCAGCAGGCCCATTACTGGGGTATATGCCTAAAGGAATATAAATTGCTCTTACCGAATAAAAGACAGATACATCTATACTGTAATTGCAGCACTATTCACAATAGCCAAAAGACATGGA HG:+:390169976:-1 HG:+:574934265:-1 HG:+:588309146:-1 HG:+:597261230:-1 HG:+:674508752:-1 HG:+:680798017:-1 HG:+:894099911:26 HG:+:973208470:-1 HG:+:1108581052:-1 HG:+:1149088401:-1 HG:+:1410840165:-1 HG:+:1507485426:-1 HG:+:1551092300:-1 HG:+:1856292115:-1 HG:+:2022018844:-1 HG:+:2713448613:-1 +CTTCTCAAAAGAAGACATACACATGGCCGAACAACCAATATGTAAAAAGGCTACAAATATCATTGATCATTAGAAATCAAAACCACAATGAGATATCATCTCACACCAGTCACAATTGACTATTCGTTAAGAAGGTCAAAAAATAAGAGATGCTAGTGAGGTTTGAGAGAAAACGGGTAACACTTACTACGCTGTTGGTGGGAGTGTGAACTTTGTCAACCCATTGTGGAAAGCAGTGTGGTGGTCCCTCAAAGGAACTAAAAACAGAACCTCCATTCGACCCAGCAGGCCCATTACTGGGGTATATGCCTAAAGGAATATAAATTGCTCTTACCGAATAAAAGACAGATACATCTATACTGTAATTGCAGCACTATTCACAATAGCCAAAAGACATGGA HG:+:153026468:-1 HG:+:232110838:-1 HG:+:894099912:26 HG:+:1041683380:-1 HG:+:1174298449:-1 HG:+:1237329052:-1 HG:+:2114796295:-1 +CTTCTCAAAAGAAGACATACACATGGCCGAACAACCAATATGTAAAAAGGCTACAAATATCATTGATCATTAGAAATCAAAACCACAATGAGATATCATCTCACACCAGTCACAATTGACTATTCGTTAAGAAGGTCAAAAAATAAGAGATGCTAGTGAGGTTTGAGAGAAAACGGGTAACACTTACTACGCTGTTGGTGGGAGTGTGAACTTTGTCAACCCATTGTGGAAAGCAGTGTGGTGGTCCCTCAAAGGAACTAAAAACAGAACCTCCATTCGACCCAGCAGGCCCATTACTGGGGTATATGCCTAAAGGAATATAAATTGCTCTTACCGAATAAAAGACAGATACATCTATACTGTAATTGCAGCACTATTCACAATAGCCAAAAGACATGGA HG:+:894099913:26 HG:+:2990760079:-1 +CTTCTCAAAAGAAGACATACACATGGCCGAACAACCAATATGTAAAAAGGCTACAAATATCATTGATCATTAGAAATCAAAACCACAATGAGATATCATCTCACACCAGTCACAATTGACTATTCGTTAAGAAGGTCAAAAAATAAGAGATGCTAGTGAGGTTTGAGAGAAAACGGGTAACACTTACTACGCTGTTGGTGGGAGTGTGAACTTTGTCAACCCATTGTGGAAAGCAGTGTGGTGGTCCCTCAAAGGAACTAAAAACAGAACCTCCATTCGACCCAGCAGGCCCATTACTGGGGTATATGCCTAAAGGAATATAAATTGCTCTTACCGAATAAAAGACAGATACATCTATACTGTAATTGCAGCACTATTCACAATAGCCAAAAGACATGGA HG:+:406368023:-1 HG:+:894099920:26 HG:+:1029597841:-1 HG:+:1113913808:-1 HG:+:1319824731:-1 HG:+:2220395882:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAGCCTATGCATCTCTTCATCTGTGTCCCTACGTAATATCCCTTTATAATAAACCTGTCAGCGTTTCCCTGAGTCCTGTGAGCCTGCTCCAGCAAATTAATTGACCGAAAGAGGCCGGCTGTGGGAGCCCCAGTTGAAGCTGCTCTGTCAGATGTTCCAGAGGCTCATGACTGGTGTCTGGCAGTGTCAGGGCAAGTCTTGGG HG:+:402160600:-1 HG:+:420587298:-1 HG:+:1494009487:-1 HG:+:1846092301:-1 HG:+:2020925200:-1 HG:+:2026595595:-1 HG:+:2430775475:-1 HG:+:2555396959:-1 HG:+:2857450545:-1 HG:+:2884928285:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAGCCTATGCATCTCTTCATCTGTGTCCCTACGTAATATCCCTTTATAATAAACCTGTCAGCGTTTCCCTGAGTCCTGTGAGCCTGCTCCAGCAAATTAATTGACCGAAAGAGGCCGGCTGTGGGAGCCCCAGTTGAAGCTGCTCTGTCAGATGTTCCAGAGGCTCATGACTGGTGTCTGGCAGTGTCAGGGCAAGTCTTGGG HG:+:1206936766:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAGCCTATGCATCTCTTCATCTGTGTCCCTACGTAATATCCCTTTATAATAAACCTGTCAGCGTTTCCCTGAGTCCTGTGAGCCTGCTCCAGCAAATTAATTGACCGAAAGAGGCCGGCTGTGGGAGCCCCAGTTGAAGCTGCTCTGTCAGATGTTCCAGAGGCTCATGACTGGTGTCTGGCAGTGTCAGGGCAAGTCTTGGG HG:+:308345351:-1 HG:+:518216529:-1 HG:+:613999656:-1 HG:+:1202062462:-1 HG:+:1463069705:-1 HG:+:1892487540:-1 HG:+:1939562772:-1 HG:+:2234663006:-1 HG:+:2336840251:-1 HG:+:2382518827:-1 HG:+:2425803488:-1 HG:+:2429168911:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAGCCTATGCATCTCTTCATCTGTGTCCCTACGTAATATCCCTTTATAATAAACCTGTCAGCGTTTCCCTGAGTCCTGTGAGCCTGCTCCAGCAAATTAATTGACCGAAAGAGGCCGGCTGTGGGAGCCCCAGTTGAAGCTGCTCTGTCAGATGTTCCAGAGGCTCATGACTGGTGTCTGGCAGTGTCAGGGCAAGTCTTGGG HG:+:375358298:-1 HG:+:382133359:-1 HG:+:411803051:-1 HG:+:417014753:-1 HG:+:481540300:-1 HG:+:560974312:-1 HG:+:653082079:-1 HG:+:681451995:-1 HG:+:697309627:-1 HG:+:753505237:-1 HG:+:850577325:-1 HG:+:1227737434:-1 HG:+:1282578968:-1 HG:+:1332660211:-1 HG:+:1457323298:-1 HG:+:1515761845:-1 HG:+:1528115456:-1 HG:+:1802242250:-1 HG:+:2190605618:-1 HG:+:2242259357:-1 HG:+:2486662058:-1 HG:+:2991390147:-1 HG:+:3035443912:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAGCCTATGCATCTCTTCATCTGTGTCCCTACGTAATATCCCTTTATAATAAACCTGTCAGCGTTTCCCTGAGTCCTGTGAGCCTGCTCCAGCAAATTAATTGACCGAAAGAGGCCGGCTGTGGGAGCCCCAGTTGAAGCTGCTCTGTCAGATGTTCCAGAGGCTCATGACTGGTGTCTGGCAGTGTCAGGGCAAGTCTTGGG HG:+:2912783367:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAGCCTATGCATCTCTTCATCTGTGTCCCTACGTAATATCCCTTTATAATAAACCTGTCAGCGTTTCCCTGAGTCCTGTGAGCCTGCTCCAGCAAATTAATTGACCGAAAGAGGCCGGCTGTGGGAGCCCCAGTTGAAGCTGCTCTGTCAGATGTTCCAGAGGCTCATGACTGGTGTCTGGCAGTGTCAGGGCAAGTCTTGGG HG:+:439595691:-1 HG:+:550403933:-1 HG:+:603266335:-1 HG:+:710596011:-1 HG:+:849742174:-1 HG:+:1499424858:-1 HG:+:1844192736:-1 HG:+:2150746390:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAGCCTATGCATCTCTTCATCTGTGTCCCTACGTAATATCCCTTTATAATAAACCTGTCAGCGTTTCCCTGAGTCCTGTGAGCCTGCTCCAGCAAATTAATTGACCGAAAGAGGCCGGCTGTGGGAGCCCCAGTTGAAGCTGCTCTGTCAGATGTTCCAGAGGCTCATGACTGGTGTCTGGCAGTGTCAGGGCAAGTCTTGGG HG:+:473229235:-1 HG:+:593564368:-1 HG:+:785511252:-1 HG:+:1048502167:-1 HG:+:1322219271:-1 HG:+:1762123324:-1 HG:+:2124947797:-1 HG:+:2564119193:-1 HG:+:2591622265:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAGCCTATGCATCTCTTCATCTGTGTCCCTACGTAATATCCCTTTATAATAAACCTGTCAGCGTTTCCCTGAGTCCTGTGAGCCTGCTCCAGCAAATTAATTGACCGAAAGAGGCCGGCTGTGGGAGCCCCAGTTGAAGCTGCTCTGTCAGATGTTCCAGAGGCTCATGACTGGTGTCTGGCAGTGTCAGGGCAAGTCTTGGG HG:+:278768252:-1 HG:+:282586606:-1 HG:+:386650077:-1 HG:+:1208062412:-1 HG:+:1526964830:-1 HG:+:2118808222:-1 HG:+:2344219251:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAGCCTATGCATCTCTTCATCTGTGTCCCTACGTAATATCCCTTTATAATAAACCTGTCAGCGTTTCCCTGAGTCCTGTGAGCCTGCTCCAGCAAATTAATTGACCGAAAGAGGCCGGCTGTGGGAGCCCCAGTTGAAGCTGCTCTGTCAGATGTTCCAGAGGCTCATGACTGGTGTCTGGCAGTGTCAGGGCAAGTCTTGGG HG:+:369111457:-1 HG:+:426229876:-1 HG:+:700608046:-1 HG:+:961821508:-1 HG:+:1062965324:-1 HG:+:1101721841:-1 HG:+:1776280827:-1 HG:+:2130273818:-1 HG:+:2493237924:-1 HG:+:2527616671:-1 HG:+:2739109094:-1 HG:+:2935118520:-1 HG:+:2960538510:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAGCCTATGCATCTCTTCATCTGTGTCCCTACGTAATATCCCTTTATAATAAACCTGTCAGCGTTTCCCTGAGTCCTGTGAGCCTGCTCCAGCAAATTAATTGACCGAAAGAGGCCGGCTGTGGGAGCCCCAGTTGAAGCTGCTCTGTCAGATGTTCCAGAGGCTCATGACTGGTGTCTGGCAGTGTCAGGGCAAGTCTTGGG HG:+:461311781:-1 HG:+:510530084:-1 HG:+:657622366:-1 HG:+:702959370:-1 HG:+:910227321:-1 HG:+:1033534631:-1 HG:+:1380786660:-1 HG:+:1540679337:-1 HG:+:1826752033:-1 HG:+:1828045887:-1 HG:+:1865026208:-1 HG:+:1884610423:-1 HG:+:1936330310:-1 HG:+:2367881431:-1 HG:+:2722450472:-1 HG:+:2779875685:-1 HG:+:2874416032:-1 HG:+:2908026933:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAGCCTATGCATCTCTTCATCTGTGTCCCTACGTAATATCCCTTTATAATAAACCTGTCAGCGTTTCCCTGAGTCCTGTGAGCCTGCTCCAGCAAATTAATTGACCGAAAGAGGCCGGCTGTGGGAGCCCCAGTTGAAGCTGCTCTGTCAGATGTTCCAGAGGCTCATGACTGGTGTCTGGCAGTGTCAGGGCAAGTCTTGGG HG:+:2666299525:-1 +TGAGCAGACAGGCTTTGCTGGATTTCGATCATGTGCTTTGGGTCCAGTCACATTTCTACATGGTTAATCATGCCTAGTGTAATGAAGCCCTCCTTAAAAATCTAAGAGGACGGGTTCAGAGAGCTTCCCTGATAGGCTGAACAATGGAGGTTCCCAGAGAGGGGCATGGAAGCTGTGTGTCCCTTCCCCCCATATCTTAGCCTATGCATCTCTTCATCTGTGTCCCTACGTAATATCCCTTTATAATAAACCTGTCAGCGTTTCCCTGAGTCCTGTGAGCCTGCTCCAGCAAATTAATTGACCGAAAGAGGCCGGCTGTGGGAGCCCCAGTTGAAGCTGCTCTGTCAGATGTTCCAGAGGCTCATGACTGGTGTCTGGCAGTGTCAGGGCAAGTCTTGGG HG:+:46238197:-1 HG:+:280677946:-1 HG:+:1267829844:-1 HG:+:1627386836:-1 HG:+:1942115357:-1 HG:+:2303198581:-1 HG:+:2411164326:-1 HG:+:2481784885:-1 HG:+:2515547742:-1 +CCCAAGACTTGCCCTGACACTGCCAGACACCAGTCATGAGCCTCTGGAACATCTGACAGAGCAGCTTCAACTGGGGCTCCCACAGCCGGCCTCTTTCGGTCAATTAATTTGCTGGAGCAGGCTCACAGGACTCAGGGAAACGCTGACAGGTTTATTATAAAGGGATATTACGTAGGGACACAGATGAAGAGATGCATAGGCTAAGATATGGGGGGAAGGGACACACAGCTTCCATGCCCCTCTCTGGGAACCTCCATTGTTCAGCCTATCAGGGAAGCTCTCTGAACCCGTCCTCTTAGATTTTTAAGGAGGGCTTCATTACACTAGGCATGATTAACCATGTAGAAATGTGACTGGACCCAAAGCACATGATCGAAATCCAGCAAAGCCTGTCTGCTCA HG:+:171960354:-1 HG:+:229007495:19 +CCCAAGACTTGCCCTGACACTGCCAGACACCAGTCATGAGCCTCTGGAACATCTGACAGAGCAGCTTCAACTGGGGCTCCCACAGCCGGCCTCTTTCGGTCAATTAATTTGCTGGAGCAGGCTCACAGGACTCAGGGAAACGCTGACAGGTTTATTATAAAGGGATATTACGTAGGGACACAGATGAAGAGATGCATAGGCTAAGATATGGGGGGAAGGGACACACAGCTTCCATGCCCCTCTCTGGGAACCTCCATTGTTCAGCCTATCAGGGAAGCTCTCTGAACCCGTCCTCTTAGATTTTTAAGGAGGGCTTCATTACACTAGGCATGATTAACCATGTAGAAATGTGACTGGACCCAAAGCACATGATCGAAATCCAGCAAAGCCTGTCTGCTCA HG:+:229007492:19 HG:+:1151125244:-1 +CCCAAGACTTGCCCTGACACTGCCAGACACCAGTCATGAGCCTCTGGAACATCTGACAGAGCAGCTTCAACTGGGGCTCCCACAGCCGGCCTCTTTCGGTCAATTAATTTGCTGGAGCAGGCTCACAGGACTCAGGGAAACGCTGACAGGTTTATTATAAAGGGATATTACGTAGGGACACAGATGAAGAGATGCATAGGCTAAGATATGGGGGGAAGGGACACACAGCTTCCATGCCCCTCTCTGGGAACCTCCATTGTTCAGCCTATCAGGGAAGCTCTCTGAACCCGTCCTCTTAGATTTTTAAGGAGGGCTTCATTACACTAGGCATGATTAACCATGTAGAAATGTGACTGGACCCAAAGCACATGATCGAAATCCAGCAAAGCCTGTCTGCTCA HG:+:229007494:19 +CCCAAGACTTGCCCTGACACTGCCAGACACCAGTCATGAGCCTCTGGAACATCTGACAGAGCAGCTTCAACTGGGGCTCCCACAGCCGGCCTCTTTCGGTCAATTAATTTGCTGGAGCAGGCTCACAGGACTCAGGGAAACGCTGACAGGTTTATTATAAAGGGATATTACGTAGGGACACAGATGAAGAGATGCATAGGCTAAGATATGGGGGGAAGGGACACACAGCTTCCATGCCCCTCTCTGGGAACCTCCATTGTTCAGCCTATCAGGGAAGCTCTCTGAACCCGTCCTCTTAGATTTTTAAGGAGGGCTTCATTACACTAGGCATGATTAACCATGTAGAAATGTGACTGGACCCAAAGCACATGATCGAAATCCAGCAAAGCCTGTCTGCTCA HG:+:229007497:19 +CCCAAGACTTGCCCTGACACTGCCAGACACCAGTCATGAGCCTCTGGAACATCTGACAGAGCAGCTTCAACTGGGGCTCCCACAGCCGGCCTCTTTCGGTCAATTAATTTGCTGGAGCAGGCTCACAGGACTCAGGGAAACGCTGACAGGTTTATTATAAAGGGATATTACGTAGGGACACAGATGAAGAGATGCATAGGCTAAGATATGGGGGGAAGGGACACACAGCTTCCATGCCCCTCTCTGGGAACCTCCATTGTTCAGCCTATCAGGGAAGCTCTCTGAACCCGTCCTCTTAGATTTTTAAGGAGGGCTTCATTACACTAGGCATGATTAACCATGTAGAAATGTGACTGGACCCAAAGCACATGATCGAAATCCAGCAAAGCCTGTCTGCTCA HG:+:229007496:19 +GTGGGGCTGTCTGACTGTCTGTCTGTCTGGTGGATGACTCTCTCTTTCCACAGTAGGGAGTAATGCTGTAGTGACAGTGTGGCTGAATCTAGAACTTGGGGAGGTGTCTGGAGGATGAGGGCCTGTGGAAAGTGGGCTGAGTGGCCGTCCCTAAGCTCCAGCCCTCTACCCCTTTGTTTCCCCCAGTGGCTACATCTTTGACTATGATTACTACCGGGGACGACTTCTAACGACCAGGTGAGCAGGGGAGGGCGTGCCCAGGCATGAAACAAGGCCAAGCTGGAAGGGTCTTGAGAGGATTGTTGGTGCAGCCCACTGAGTTCTCCAAATGAGAACCAAAACCCAGAGGTTTGCCTGGGGTTGCTCCACCAGTCGGTAGCAGAGCTGAGACTGGGGTCCT HG:+:2751234667:16 +GTGGGGCTGTCTGACTGTCTGTCTGTCTGGTGGATGACTCTCTCTTTCCACAGTAGGGAGTAATGCTGTAGTGACAGTGTGGCTGAATCTAGAACTTGGGGAGGTGTCTGGAGGATGAGGGCCTGTGGAAAGTGGGCTGAGTGGCCGTCCCTAAGCTCCAGCCCTCTACCCCTTTGTTTCCCCCAGTGGCTACATCTTTGACTATGATTACTACCGGGGACGACTTCTAACGACCAGGTGAGCAGGGGAGGGCGTGCCCAGGCATGAAACAAGGCCAAGCTGGAAGGGTCTTGAGAGGATTGTTGGTGCAGCCCACTGAGTTCTCCAAATGAGAACCAAAACCCAGAGGTTTGCCTGGGGTTGCTCCACCAGTCGGTAGCAGAGCTGAGACTGGGGTCCT HG:+:2751234659:16 HG:+:2849424594:-1 +GTGGGGCTGTCTGACTGTCTGTCTGTCTGGTGGATGACTCTCTCTTTCCACAGTAGGGAGTAATGCTGTAGTGACAGTGTGGCTGAATCTAGAACTTGGGGAGGTGTCTGGAGGATGAGGGCCTGTGGAAAGTGGGCTGAGTGGCCGTCCCTAAGCTCCAGCCCTCTACCCCTTTGTTTCCCCCAGTGGCTACATCTTTGACTATGATTACTACCGGGGACGACTTCTAACGACCAGGTGAGCAGGGGAGGGCGTGCCCAGGCATGAAACAAGGCCAAGCTGGAAGGGTCTTGAGAGGATTGTTGGTGCAGCCCACTGAGTTCTCCAAATGAGAACCAAAACCCAGAGGTTTGCCTGGGGTTGCTCCACCAGTCGGTAGCAGAGCTGAGACTGGGGTCCT HG:+:2751234660:16 +GTGGGGCTGTCTGACTGTCTGTCTGTCTGGTGGATGACTCTCTCTTTCCACAGTAGGGAGTAATGCTGTAGTGACAGTGTGGCTGAATCTAGAACTTGGGGAGGTGTCTGGAGGATGAGGGCCTGTGGAAAGTGGGCTGAGTGGCCGTCCCTAAGCTCCAGCCCTCTACCCCTTTGTTTCCCCCAGTGGCTACATCTTTGACTATGATTACTACCGGGGACGACTTCTAACGACCAGGTGAGCAGGGGAGGGCGTGCCCAGGCATGAAACAAGGCCAAGCTGGAAGGGTCTTGAGAGGATTGTTGGTGCAGCCCACTGAGTTCTCCAAATGAGAACCAAAACCCAGAGGTTTGCCTGGGGTTGCTCCACCAGTCGGTAGCAGAGCTGAGACTGGGGTCCT HG:+:2751234664:16 +GTGGGGCTGTCTGACTGTCTGTCTGTCTGGTGGATGACTCTCTCTTTCCACAGTAGGGAGTAATGCTGTAGTGACAGTGTGGCTGAATCTAGAACTTGGGGAGGTGTCTGGAGGATGAGGGCCTGTGGAAAGTGGGCTGAGTGGCCGTCCCTAAGCTCCAGCCCTCTACCCCTTTGTTTCCCCCAGTGGCTACATCTTTGACTATGATTACTACCGGGGACGACTTCTAACGACCAGGTGAGCAGGGGAGGGCGTGCCCAGGCATGAAACAAGGCCAAGCTGGAAGGGTCTTGAGAGGATTGTTGGTGCAGCCCACTGAGTTCTCCAAATGAGAACCAAAACCCAGAGGTTTGCCTGGGGTTGCTCCACCAGTCGGTAGCAGAGCTGAGACTGGGGTCCT HG:+:2988928759:-1 +GTGGGGCTGTCTGACTGTCTGTCTGTCTGGTGGATGACTCTCTCTTTCCACAGTAGGGAGTAATGCTGTAGTGACAGTGTGGCTGAATCTAGAACTTGGGGAGGTGTCTGGAGGATGAGGGCCTGTGGAAAGTGGGCTGAGTGGCCGTCCCTAAGCTCCAGCCCTCTACCCCTTTGTTTCCCCCAGTGGCTACATCTTTGACTATGATTACTACCGGGGACGACTTCTAACGACCAGGTGAGCAGGGGAGGGCGTGCCCAGGCATGAAACAAGGCCAAGCTGGAAGGGTCTTGAGAGGATTGTTGGTGCAGCCCACTGAGTTCTCCAAATGAGAACCAAAACCCAGAGGTTTGCCTGGGGTTGCTCCACCAGTCGGTAGCAGAGCTGAGACTGGGGTCCT HG:+:2751234666:16 +GTGGGGCTGTCTGACTGTCTGTCTGTCTGGTGGATGACTCTCTCTTTCCACAGTAGGGAGTAATGCTGTAGTGACAGTGTGGCTGAATCTAGAACTTGGGGAGGTGTCTGGAGGATGAGGGCCTGTGGAAAGTGGGCTGAGTGGCCGTCCCTAAGCTCCAGCCCTCTACCCCTTTGTTTCCCCCAGTGGCTACATCTTTGACTATGATTACTACCGGGGACGACTTCTAACGACCAGGTGAGCAGGGGAGGGCGTGCCCAGGCATGAAACAAGGCCAAGCTGGAAGGGTCTTGAGAGGATTGTTGGTGCAGCCCACTGAGTTCTCCAAATGAGAACCAAAACCCAGAGGTTTGCCTGGGGTTGCTCCACCAGTCGGTAGCAGAGCTGAGACTGGGGTCCT HG:+:829957722:-1 +GACATTTGAAAATGAGTTTCATCTTTAGCTCATCCTTTTACAAATTTCTAGTTCCTTGTGCATGATTGAAGTGTACACATTTTTAGTTAAATATAAGCATATAGAAGGCACAAGTTCAATATTTTTCATGATAAGGATGTGTAATTAAACTGGTTAGGAGACTCATCGACTAGAGGGGGACATAGGTGGCCCCAGGCTGTAAGAACACGGCCACACCGTCCACTGGGCCGCTTGCTTTGTGCTTAAGATGACACTTTGTTCTGAGCCTCACAGTGTCTTGACCATGTCCTGGAACCTTCTTGTTGGAGGGAGTTCATCTTCCCTATGACTTCTGTCCCTAGTCTAAGGTCGTCCCACAGGAAGCTTGAGGGCGGGAAGTTTTTCCACGCCCAGGAGCCTA HG:+:625914162:13 +GACATTTGAAAATGAGTTTCATCTTTAGCTCATCCTTTTACAAATTTCTAGTTCCTTGTGCATGATTGAAGTGTACACATTTTTAGTTAAATATAAGCATATAGAAGGCACAAGTTCAATATTTTTCATGATAAGGATGTGTAATTAAACTGGTTAGGAGACTCATCGACTAGAGGGGGACATAGGTGGCCCCAGGCTGTAAGAACACGGCCACACCGTCCACTGGGCCGCTTGCTTTGTGCTTAAGATGACACTTTGTTCTGAGCCTCACAGTGTCTTGACCATGTCCTGGAACCTTCTTGTTGGAGGGAGTTCATCTTCCCTATGACTTCTGTCCCTAGTCTAAGGTCGTCCCACAGGAAGCTTGAGGGCGGGAAGTTTTTCCACGCCCAGGAGCCTA HG:+:625914160:13 +GACATTTGAAAATGAGTTTCATCTTTAGCTCATCCTTTTACAAATTTCTAGTTCCTTGTGCATGATTGAAGTGTACACATTTTTAGTTAAATATAAGCATATAGAAGGCACAAGTTCAATATTTTTCATGATAAGGATGTGTAATTAAACTGGTTAGGAGACTCATCGACTAGAGGGGGACATAGGTGGCCCCAGGCTGTAAGAACACGGCCACACCGTCCACTGGGCCGCTTGCTTTGTGCTTAAGATGACACTTTGTTCTGAGCCTCACAGTGTCTTGACCATGTCCTGGAACCTTCTTGTTGGAGGGAGTTCATCTTCCCTATGACTTCTGTCCCTAGTCTAAGGTCGTCCCACAGGAAGCTTGAGGGCGGGAAGTTTTTCCACGCCCAGGAGCCTA HG:+:625914161:13 +GACATTTGAAAATGAGTTTCATCTTTAGCTCATCCTTTTACAAATTTCTAGTTCCTTGTGCATGATTGAAGTGTACACATTTTTAGTTAAATATAAGCATATAGAAGGCACAAGTTCAATATTTTTCATGATAAGGATGTGTAATTAAACTGGTTAGGAGACTCATCGACTAGAGGGGGACATAGGTGGCCCCAGGCTGTAAGAACACGGCCACACCGTCCACTGGGCCGCTTGCTTTGTGCTTAAGATGACACTTTGTTCTGAGCCTCACAGTGTCTTGACCATGTCCTGGAACCTTCTTGTTGGAGGGAGTTCATCTTCCCTATGACTTCTGTCCCTAGTCTAAGGTCGTCCCACAGGAAGCTTGAGGGCGGGAAGTTTTTCCACGCCCAGGAGCCTA HG:+:625914163:13 +GACATTTGAAAATGAGTTTCATCTTTAGCTCATCCTTTTACAAATTTCTAGTTCCTTGTGCATGATTGAAGTGTACACATTTTTAGTTAAATATAAGCATATAGAAGGCACAAGTTCAATATTTTTCATGATAAGGATGTGTAATTAAACTGGTTAGGAGACTCATCGACTAGAGGGGGACATAGGTGGCCCCAGGCTGTAAGAACACGGCCACACCGTCCACTGGGCCGCTTGCTTTGTGCTTAAGATGACACTTTGTTCTGAGCCTCACAGTGTCTTGACCATGTCCTGGAACCTTCTTGTTGGAGGGAGTTCATCTTCCCTATGACTTCTGTCCCTAGTCTAAGGTCGTCCCACAGGAAGCTTGAGGGCGGGAAGTTTTTCCACGCCCAGGAGCCTA HG:+:1067870652:-1 +TAGGCTCCTGGGCGTGGAAAAACTTCCCGCCCTCAAGCTTCCTGTGGGACGACCTTAGACTAGGGACAGAAGTCATAGGGAAGATGAACTCCCTCCAACAAGAAGGTTCCAGGACATGGTCAAGACACTGTGAGGCTCAGAACAAAGTGTCATCTTAAGCACAAAGCAAGCGGCCCAGTGGACGGTGTGGCCGTGTTCTTACAGCCTGGGGCCACCTATGTCCCCCTCTAGTCGATGAGTCTCCTAACCAGTTTAATTACACATCCTTATCATGAAAAATATTGAACTTGTGCCTTCTATATGCTTATATTTAACTAAAAATGTGTACACTTCAATCATGCACAAGGAACTAGAAATTTGTAAAAGGATGAGCTAAAGATGAAACTCATTTTCAAATGTC HG:+:1809428913:-1 +TTCCAGACTGAGCTGGGGTCCATTGACACGGACTCCTCCCGACTCGTCAGGAGATACTTTGCCTCTCCAGTTTTGGTGTCTGAGTGATCATTCAACGGGTGCATATTAATGTTTAGTTTGTTTTATTTATTTATTTTGATGAGACAGTCTTGCTCTGTCACCCAGGCTGGGGGTGCAGTGTACGTACCTCAGCTCCACTGCAACCTCCTGCCTCCCGGCTTCAAGCAATTTCTTCTGCCTCAGCCTCCTGAGTAGCTGGCATTATAAGGCGTCGTGCCACCACACCTGGCTGCTGCTGCTCGCTTTTTTTTTTTTTTTTTTTTTGATAGAGACAGGGTTTCACCATGTTGGTTCGGGCTGGTCGTCGAACTCCTGACCTCAAGTGATCTGCCTGCCTCTG HG:+:638205069:-1 HG:+:842417143:-1 HG:+:959858421:-1 HG:+:1934364475:-1 HG:+:2018344291:-1 HG:+:2359380871:-1 HG:+:2374001889:-1 HG:+:2412201715:-1 HG:+:2419843125:-1 HG:+:2432191148:-1 HG:+:2494734336:-1 HG:+:2699363946:-1 HG:+:2883885159:23 HG:+:2888093752:-1 HG:+:2935564748:-1 +TTCCAGACTGAGCTGGGGTCCATTGACACGGACTCCTCCCGACTCGTCAGGAGATACTTTGCCTCTCCAGTTTTGGTGTCTGAGTGATCATTCAACGGGTGCATATTAATGTTTAGTTTGTTTTATTTATTTATTTTGATGAGACAGTCTTGCTCTGTCACCCAGGCTGGGGGTGCAGTGTACGTACCTCAGCTCCACTGCAACCTCCTGCCTCCCGGCTTCAAGCAATTTCTTCTGCCTCAGCCTCCTGAGTAGCTGGCATTATAAGGCGTCGTGCCACCACACCTGGCTGCTGCTGCTCGCTTTTTTTTTTTTTTTTTTTTTGATAGAGACAGGGTTTCACCATGTTGGTTCGGGCTGGTCGTCGAACTCCTGACCTCAAGTGATCTGCCTGCCTCTG HG:+:93210272:-1 HG:+:100829546:-1 HG:+:153422625:-1 HG:+:155555610:-1 HG:+:205608239:-1 HG:+:220549546:-1 HG:+:258402756:-1 HG:+:278047661:-1 HG:+:293113941:-1 HG:+:397688931:-1 HG:+:407992630:-1 HG:+:526202522:-1 HG:+:604541676:-1 HG:+:605554261:-1 HG:+:670858506:-1 HG:+:817243838:-1 HG:+:828854342:-1 HG:+:1306865154:-1 HG:+:1309575065:-1 HG:+:1332049544:-1 HG:+:1390556243:-1 HG:+:1429093481:-1 HG:+:1547382706:-1 HG:+:1623285565:-1 HG:+:1692701086:-1 HG:+:1704454352:-1 HG:+:1886651743:-1 HG:+:2042636972:-1 HG:+:2044822229:-1 HG:+:2152060372:-1 HG:+:2290735259:-1 HG:+:2337826427:-1 HG:+:2343396930:-1 HG:+:2348984266:-1 HG:+:2412820104:-1 HG:+:2531393625:-1 HG:+:2587875448:-1 HG:+:2635375848:-1 HG:+:2735024223:-1 HG:+:2761587578:-1 HG:+:2809834228:-1 HG:+:2867668902:-1 HG:+:2883885161:23 HG:+:2944831504:-1 HG:+:2977533975:-1 HG:+:3015084705:-1 +TTCCAGACTGAGCTGGGGTCCATTGACACGGACTCCTCCCGACTCGTCAGGAGATACTTTGCCTCTCCAGTTTTGGTGTCTGAGTGATCATTCAACGGGTGCATATTAATGTTTAGTTTGTTTTATTTATTTATTTTGATGAGACAGTCTTGCTCTGTCACCCAGGCTGGGGGTGCAGTGTACGTACCTCAGCTCCACTGCAACCTCCTGCCTCCCGGCTTCAAGCAATTTCTTCTGCCTCAGCCTCCTGAGTAGCTGGCATTATAAGGCGTCGTGCCACCACACCTGGCTGCTGCTGCTCGCTTTTTTTTTTTTTTTTTTTTTGATAGAGACAGGGTTTCACCATGTTGGTTCGGGCTGGTCGTCGAACTCCTGACCTCAAGTGATCTGCCTGCCTCTG HG:+:468890950:-1 HG:+:1072696596:-1 HG:+:1363343452:-1 HG:+:1883879770:-1 HG:+:2228156910:-1 HG:+:2231523187:-1 HG:+:2606345675:-1 HG:+:2907505748:-1 +TTCCAGACTGAGCTGGGGTCCATTGACACGGACTCCTCCCGACTCGTCAGGAGATACTTTGCCTCTCCAGTTTTGGTGTCTGAGTGATCATTCAACGGGTGCATATTAATGTTTAGTTTGTTTTATTTATTTATTTTGATGAGACAGTCTTGCTCTGTCACCCAGGCTGGGGGTGCAGTGTACGTACCTCAGCTCCACTGCAACCTCCTGCCTCCCGGCTTCAAGCAATTTCTTCTGCCTCAGCCTCCTGAGTAGCTGGCATTATAAGGCGTCGTGCCACCACACCTGGCTGCTGCTGCTCGCTTTTTTTTTTTTTTTTTTTTTGATAGAGACAGGGTTTCACCATGTTGGTTCGGGCTGGTCGTCGAACTCCTGACCTCAAGTGATCTGCCTGCCTCTG HG:+:2883885172:23 +TTCCAGACTGAGCTGGGGTCCATTGACACGGACTCCTCCCGACTCGTCAGGAGATACTTTGCCTCTCCAGTTTTGGTGTCTGAGTGATCATTCAACGGGTGCATATTAATGTTTAGTTTGTTTTATTTATTTATTTTGATGAGACAGTCTTGCTCTGTCACCCAGGCTGGGGGTGCAGTGTACGTACCTCAGCTCCACTGCAACCTCCTGCCTCCCGGCTTCAAGCAATTTCTTCTGCCTCAGCCTCCTGAGTAGCTGGCATTATAAGGCGTCGTGCCACCACACCTGGCTGCTGCTGCTCGCTTTTTTTTTTTTTTTTTTTTTGATAGAGACAGGGTTTCACCATGTTGGTTCGGGCTGGTCGTCGAACTCCTGACCTCAAGTGATCTGCCTGCCTCTG HG:+:12105903:-1 HG:+:185361645:-1 HG:+:251378483:-1 HG:+:389439859:-1 HG:+:408119195:-1 HG:+:449163845:-1 HG:+:628581493:-1 HG:+:669416617:-1 HG:+:715325103:-1 HG:+:747464156:-1 HG:+:769148589:-1 HG:+:955379663:-1 HG:+:970587025:-1 HG:+:1058864835:-1 HG:+:1077722116:-1 HG:+:1096268130:-1 HG:+:1229919686:-1 HG:+:1247839794:-1 HG:+:1333323261:-1 HG:+:1371761760:-1 HG:+:1416426772:-1 HG:+:1421428337:-1 HG:+:1541360602:-1 HG:+:1548279030:-1 HG:+:1667051249:-1 HG:+:1694470968:-1 HG:+:1694807015:-1 HG:+:1795760884:-1 HG:+:1821212422:-1 HG:+:1880740444:-1 HG:+:1912378092:-1 HG:+:2004971739:-1 HG:+:2007817066:-1 HG:+:2013607092:-1 HG:+:2022596728:-1 HG:+:2027490239:-1 HG:+:2159759629:-1 HG:+:2261157835:-1 HG:+:2267749674:-1 HG:+:2441146570:-1 HG:+:2478180702:-1 HG:+:2478448593:-1 HG:+:2497844108:-1 HG:+:2517631346:-1 HG:+:2520865481:-1 HG:+:2525795850:-1 HG:+:2558887388:-1 HG:+:2562692085:-1 HG:+:2581567670:-1 HG:+:2594194252:-1 HG:+:2595116627:-1 HG:+:2633163404:-1 HG:+:2666114684:-1 HG:+:2681343091:-1 HG:+:2705690896:-1 HG:+:2707085102:-1 HG:+:2753702568:-1 HG:+:2820009638:-1 HG:+:2902870545:-1 +TTCCAGACTGAGCTGGGGTCCATTGACACGGACTCCTCCCGACTCGTCAGGAGATACTTTGCCTCTCCAGTTTTGGTGTCTGAGTGATCATTCAACGGGTGCATATTAATGTTTAGTTTGTTTTATTTATTTATTTTGATGAGACAGTCTTGCTCTGTCACCCAGGCTGGGGGTGCAGTGTACGTACCTCAGCTCCACTGCAACCTCCTGCCTCCCGGCTTCAAGCAATTTCTTCTGCCTCAGCCTCCTGAGTAGCTGGCATTATAAGGCGTCGTGCCACCACACCTGGCTGCTGCTGCTCGCTTTTTTTTTTTTTTTTTTTTTGATAGAGACAGGGTTTCACCATGTTGGTTCGGGCTGGTCGTCGAACTCCTGACCTCAAGTGATCTGCCTGCCTCTG HG:+:2883885168:23 +TTCCAGACTGAGCTGGGGTCCATTGACACGGACTCCTCCCGACTCGTCAGGAGATACTTTGCCTCTCCAGTTTTGGTGTCTGAGTGATCATTCAACGGGTGCATATTAATGTTTAGTTTGTTTTATTTATTTATTTTGATGAGACAGTCTTGCTCTGTCACCCAGGCTGGGGGTGCAGTGTACGTACCTCAGCTCCACTGCAACCTCCTGCCTCCCGGCTTCAAGCAATTTCTTCTGCCTCAGCCTCCTGAGTAGCTGGCATTATAAGGCGTCGTGCCACCACACCTGGCTGCTGCTGCTCGCTTTTTTTTTTTTTTTTTTTTTGATAGAGACAGGGTTTCACCATGTTGGTTCGGGCTGGTCGTCGAACTCCTGACCTCAAGTGATCTGCCTGCCTCTG HG:+:390570611:-1 HG:+:550009930:-1 HG:+:689915251:-1 HG:+:1308844468:-1 HG:+:2133912527:-1 HG:+:2574731876:-1 HG:+:2662362726:-1 HG:+:2748993401:-1 HG:+:2883885167:23 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HG:+:1067272530:-1 HG:+:1197169183:-1 HG:+:1239062391:-1 HG:+:1258463632:-1 HG:+:1278527455:-1 HG:+:1290454088:-1 HG:+:1301597214:-1 HG:+:1302205217:-1 HG:+:1309155696:-1 HG:+:1350154727:-1 HG:+:1415786574:-1 HG:+:1491409999:-1 HG:+:1583974986:-1 HG:+:1585487328:-1 HG:+:1606896272:-1 HG:+:1629942295:-1 HG:+:1658823681:-1 HG:+:1664697868:-1 HG:+:1666681693:-1 HG:+:1671558350:-1 HG:+:1677499565:-1 HG:+:1690563265:-1 HG:+:1707694549:-1 HG:+:1712986264:-1 HG:+:1715220680:-1 HG:+:1755912126:-1 HG:+:1781761383:-1 HG:+:1796862962:-1 HG:+:1862543529:-1 HG:+:1888752393:-1 HG:+:1944574422:-1 HG:+:1971534937:-1 HG:+:2007536044:-1 HG:+:2007694974:-1 HG:+:2008011694:-1 HG:+:2042097585:-1 HG:+:2047133377:-1 HG:+:2063408206:-1 HG:+:2065309440:-1 HG:+:2073920616:-1 HG:+:2110075537:-1 HG:+:2263851348:-1 HG:+:2264056864:-1 HG:+:2273315925:-1 HG:+:2291401393:-1 HG:+:2296851134:-1 HG:+:2332176215:-1 HG:+:2371061030:-1 HG:+:2375056104:-1 HG:+:2389706070:-1 HG:+:2421228680:-1 HG:+:2476235642:-1 HG:+:2479581868:-1 HG:+:2500633761:-1 HG:+:2500784911:-1 HG:+:2505291487:-1 HG:+:2519985166:-1 HG:+:2533536834:-1 HG:+:2553187381:-1 HG:+:2556855915:-1 HG:+:2558536037:-1 HG:+:2568011516:-1 HG:+:2574513074:-1 HG:+:2582148006:-1 HG:+:2636590097:-1 HG:+:2697695446:-1 HG:+:2704973484:-1 HG:+:2705803582:-1 HG:+:2731923060:-1 HG:+:2748521252:-1 HG:+:2817031876:-1 HG:+:2852555169:-1 HG:+:2875092906:-1 HG:+:2876518017:-1 HG:+:2929738671:-1 HG:+:2980566840:-1 HG:+:3055011753:-1 +CAGAGGCAGGCAGATCACTTGAGGTCAGGAGTTCGACGACCAGCCCGAACCAACATGGTGAAACCCTGTCTCTATCAAAAAAAAAAAAAAAAAAAAAGCGAGCAGCAGCAGCCAGGTGTGGTGGCACGACGCCTTATAATGCCAGCTACTCAGGAGGCTGAGGCAGAAGAAATTGCTTGAAGCCGGGAGGCAGGAGGTTGCAGTGGAGCTGAGGTACGTACACTGCACCCCCAGCCTGGGTGACAGAGCAAGACTGTCTCATCAAAATAAATAAATAAAACAAACTAAACATTAATATGCACCCGTTGAATGATCACTCAGACACCAAAACTGGAGAGGCAAAGTATCTCCTGACGAGTCGGGAGGAGTCCGTGTCAATGGACCCCAGCTCAGTCTGGAA HG:+:20458165:-1 HG:+:23489575:-1 HG:+:93922004:-1 HG:+:538716064:-1 HG:+:680449228:-1 HG:+:764552833:-1 HG:+:798628146:-1 HG:+:818382477:-1 HG:+:830368959:-1 HG:+:864184316:-1 HG:+:1096510892:-1 HG:+:1171362584:-1 HG:+:1217294379:-1 HG:+:1307591971:-1 HG:+:1350185604:-1 HG:+:1353632281:-1 HG:+:1392678590:-1 HG:+:1467468635:-1 HG:+:1698279825:-1 HG:+:1769313963:-1 HG:+:1960932030:-1 HG:+:2072786554:-1 HG:+:2221791821:-1 HG:+:2235339974:-1 HG:+:2560417626:-1 HG:+:2573099757:-1 HG:+:2637786767:-1 HG:+:2671100780:-1 HG:+:2851803031:-1 HG:+:2856758717:-1 HG:+:2873136878:-1 +CAGAGGCAGGCAGATCACTTGAGGTCAGGAGTTCGACGACCAGCCCGAACCAACATGGTGAAACCCTGTCTCTATCAAAAAAAAAAAAAAAAAAAAAGCGAGCAGCAGCAGCCAGGTGTGGTGGCACGACGCCTTATAATGCCAGCTACTCAGGAGGCTGAGGCAGAAGAAATTGCTTGAAGCCGGGAGGCAGGAGGTTGCAGTGGAGCTGAGGTACGTACACTGCACCCCCAGCCTGGGTGACAGAGCAAGACTGTCTCATCAAAATAAATAAATAAAACAAACTAAACATTAATATGCACCCGTTGAATGATCACTCAGACACCAAAACTGGAGAGGCAAAGTATCTCCTGACGAGTCGGGAGGAGTCCGTGTCAATGGACCCCAGCTCAGTCTGGAA HG:+:44936757:-1 HG:+:111700634:-1 HG:+:226089672:-1 HG:+:474994755:-1 HG:+:633546673:-1 HG:+:674568998:-1 HG:+:771414386:-1 HG:+:960384381:-1 HG:+:1175210795:-1 HG:+:1201583565:-1 HG:+:1307795947:-1 HG:+:1450191013:-1 HG:+:1693580677:-1 HG:+:1888101616:-1 HG:+:2251351981:-1 HG:+:2337196974:-1 HG:+:2552305749:-1 HG:+:2650427941:-1 HG:+:2871810351:-1 HG:+:2889001674:-1 +CAGAGGCAGGCAGATCACTTGAGGTCAGGAGTTCGACGACCAGCCCGAACCAACATGGTGAAACCCTGTCTCTATCAAAAAAAAAAAAAAAAAAAAAGCGAGCAGCAGCAGCCAGGTGTGGTGGCACGACGCCTTATAATGCCAGCTACTCAGGAGGCTGAGGCAGAAGAAATTGCTTGAAGCCGGGAGGCAGGAGGTTGCAGTGGAGCTGAGGTACGTACACTGCACCCCCAGCCTGGGTGACAGAGCAAGACTGTCTCATCAAAATAAATAAATAAAACAAACTAAACATTAATATGCACCCGTTGAATGATCACTCAGACACCAAAACTGGAGAGGCAAAGTATCTCCTGACGAGTCGGGAGGAGTCCGTGTCAATGGACCCCAGCTCAGTCTGGAA HG:+:9752469:-1 HG:+:15423997:-1 HG:+:45155572:-1 HG:+:61527085:-1 HG:+:62488644:-1 HG:+:179964422:-1 HG:+:213210705:-1 HG:+:226928244:-1 HG:+:241947938:-1 HG:+:245665511:-1 HG:+:289811492:-1 HG:+:327767401:-1 HG:+:441207433:-1 HG:+:523446964:-1 HG:+:535133046:-1 HG:+:621088923:-1 HG:+:621413601:-1 HG:+:716225837:-1 HG:+:768164637:-1 HG:+:779495854:-1 HG:+:791156066:-1 HG:+:804534241:-1 HG:+:832306522:-1 HG:+:874449911:-1 HG:+:975515526:-1 HG:+:993761289:-1 HG:+:1015362112:-1 HG:+:1030350687:-1 HG:+:1054010323:-1 HG:+:1063637336:-1 HG:+:1080190490:-1 HG:+:1096727266:-1 HG:+:1100444255:-1 HG:+:1106622402:-1 HG:+:1107663447:-1 HG:+:1107752573:-1 HG:+:1158568891:-1 HG:+:1158662250:-1 HG:+:1204019245:-1 HG:+:1241331093:-1 HG:+:1298851252:-1 HG:+:1303947628:-1 HG:+:1305832489:-1 HG:+:1385057798:-1 HG:+:1404452827:-1 HG:+:1414932842:-1 HG:+:1516783673:-1 HG:+:1545039906:-1 HG:+:1566370513:-1 HG:+:1578801116:-1 HG:+:1580946144:-1 HG:+:1670822382:-1 HG:+:1699509599:-1 HG:+:1774689205:-1 HG:+:1783616175:-1 HG:+:1787490315:-1 HG:+:1788816921:-1 HG:+:1878570322:-1 HG:+:2062499026:-1 HG:+:2062943974:-1 HG:+:2072233360:-1 HG:+:2106518559:-1 HG:+:2234341298:-1 HG:+:2264891826:-1 HG:+:2265463168:-1 HG:+:2291974953:-1 HG:+:2302709661:-1 HG:+:2354866992:-1 HG:+:2420407309:-1 HG:+:2425557232:-1 HG:+:2428458928:-1 HG:+:2468606234:-1 HG:+:2490399412:-1 HG:+:2517276840:-1 HG:+:2529454271:-1 HG:+:2543374376:-1 HG:+:2583794482:-1 HG:+:2603308727:-1 HG:+:2605104277:-1 HG:+:2637697728:-1 HG:+:2671246012:-1 HG:+:2704743476:-1 HG:+:2705282877:-1 HG:+:2724250432:-1 HG:+:2873190567:-1 HG:+:2975628554:-1 HG:+:2981189957:-1 HG:+:2999693199:-1 HG:+:3000366006:-1 HG:+:3013430037:-1 +CAGAGGCAGGCAGATCACTTGAGGTCAGGAGTTCGACGACCAGCCCGAACCAACATGGTGAAACCCTGTCTCTATCAAAAAAAAAAAAAAAAAAAAAGCGAGCAGCAGCAGCCAGGTGTGGTGGCACGACGCCTTATAATGCCAGCTACTCAGGAGGCTGAGGCAGAAGAAATTGCTTGAAGCCGGGAGGCAGGAGGTTGCAGTGGAGCTGAGGTACGTACACTGCACCCCCAGCCTGGGTGACAGAGCAAGACTGTCTCATCAAAATAAATAAATAAAACAAACTAAACATTAATATGCACCCGTTGAATGATCACTCAGACACCAAAACTGGAGAGGCAAAGTATCTCCTGACGAGTCGGGAGGAGTCCGTGTCAATGGACCCCAGCTCAGTCTGGAA HG:+:2118107116:-1 HG:+:2147630835:-1 +CAGAGGCAGGCAGATCACTTGAGGTCAGGAGTTCGACGACCAGCCCGAACCAACATGGTGAAACCCTGTCTCTATCAAAAAAAAAAAAAAAAAAAAAGCGAGCAGCAGCAGCCAGGTGTGGTGGCACGACGCCTTATAATGCCAGCTACTCAGGAGGCTGAGGCAGAAGAAATTGCTTGAAGCCGGGAGGCAGGAGGTTGCAGTGGAGCTGAGGTACGTACACTGCACCCCCAGCCTGGGTGACAGAGCAAGACTGTCTCATCAAAATAAATAAATAAAACAAACTAAACATTAATATGCACCCGTTGAATGATCACTCAGACACCAAAACTGGAGAGGCAAAGTATCTCCTGACGAGTCGGGAGGAGTCCGTGTCAATGGACCCCAGCTCAGTCTGGAA HG:+:1576565560:-1 +AAAGATAAAGGAATATGCACATCATTTTGCTAAGACACGAAATATCATCTGATTTTCAGCTATTTCACATTTCCTATTTTTTCCCCCTTACTACATTTTCAGCACTTTGGTTTTGAAAAGCAGAAAATGAACGTCAAACTGGTCTTAAACAGAAAAGAAGATTGAATTTATTGGTGCACTATAACTAAACTAATCCATGGGTATCTGACTTCAGGTGCTGCTGGACTCCAGTTGCTCCAATAATGTCAGGACGTTAGTACTTTCTCTTTCGTCCAGACTCTGCTTTTTCCCCTTACTTTCCTAATTTTTAGTTGTTTGTACCCCACAATTGTCAATTATGTCCTAATAAACTTCAAAGTATATATCTCATTGGCCTGATCGGTTTTCATTGCCTGTCTCT HG:+:566637279:22 HG:+:749856565:-1 +AAAGATAAAGGAATATGCACATCATTTTGCTAAGACACGAAATATCATCTGATTTTCAGCTATTTCACATTTCCTATTTTTTCCCCCTTACTACATTTTCAGCACTTTGGTTTTGAAAAGCAGAAAATGAACGTCAAACTGGTCTTAAACAGAAAAGAAGATTGAATTTATTGGTGCACTATAACTAAACTAATCCATGGGTATCTGACTTCAGGTGCTGCTGGACTCCAGTTGCTCCAATAATGTCAGGACGTTAGTACTTTCTCTTTCGTCCAGACTCTGCTTTTTCCCCTTACTTTCCTAATTTTTAGTTGTTTGTACCCCACAATTGTCAATTATGTCCTAATAAACTTCAAAGTATATATCTCATTGGCCTGATCGGTTTTCATTGCCTGTCTCT HG:+:566637268:22 +AAAGATAAAGGAATATGCACATCATTTTGCTAAGACACGAAATATCATCTGATTTTCAGCTATTTCACATTTCCTATTTTTTCCCCCTTACTACATTTTCAGCACTTTGGTTTTGAAAAGCAGAAAATGAACGTCAAACTGGTCTTAAACAGAAAAGAAGATTGAATTTATTGGTGCACTATAACTAAACTAATCCATGGGTATCTGACTTCAGGTGCTGCTGGACTCCAGTTGCTCCAATAATGTCAGGACGTTAGTACTTTCTCTTTCGTCCAGACTCTGCTTTTTCCCCTTACTTTCCTAATTTTTAGTTGTTTGTACCCCACAATTGTCAATTATGTCCTAATAAACTTCAAAGTATATATCTCATTGGCCTGATCGGTTTTCATTGCCTGTCTCT HG:+:566637278:22 +AAAGATAAAGGAATATGCACATCATTTTGCTAAGACACGAAATATCATCTGATTTTCAGCTATTTCACATTTCCTATTTTTTCCCCCTTACTACATTTTCAGCACTTTGGTTTTGAAAAGCAGAAAATGAACGTCAAACTGGTCTTAAACAGAAAAGAAGATTGAATTTATTGGTGCACTATAACTAAACTAATCCATGGGTATCTGACTTCAGGTGCTGCTGGACTCCAGTTGCTCCAATAATGTCAGGACGTTAGTACTTTCTCTTTCGTCCAGACTCTGCTTTTTCCCCTTACTTTCCTAATTTTTAGTTGTTTGTACCCCACAATTGTCAATTATGTCCTAATAAACTTCAAAGTATATATCTCATTGGCCTGATCGGTTTTCATTGCCTGTCTCT HG:+:566637270:22 +AAAGATAAAGGAATATGCACATCATTTTGCTAAGACACGAAATATCATCTGATTTTCAGCTATTTCACATTTCCTATTTTTTCCCCCTTACTACATTTTCAGCACTTTGGTTTTGAAAAGCAGAAAATGAACGTCAAACTGGTCTTAAACAGAAAAGAAGATTGAATTTATTGGTGCACTATAACTAAACTAATCCATGGGTATCTGACTTCAGGTGCTGCTGGACTCCAGTTGCTCCAATAATGTCAGGACGTTAGTACTTTCTCTTTCGTCCAGACTCTGCTTTTTCCCCTTACTTTCCTAATTTTTAGTTGTTTGTACCCCACAATTGTCAATTATGTCCTAATAAACTTCAAAGTATATATCTCATTGGCCTGATCGGTTTTCATTGCCTGTCTCT HG:+:566637273:22 +AAAGATAAAGGAATATGCACATCATTTTGCTAAGACACGAAATATCATCTGATTTTCAGCTATTTCACATTTCCTATTTTTTCCCCCTTACTACATTTTCAGCACTTTGGTTTTGAAAAGCAGAAAATGAACGTCAAACTGGTCTTAAACAGAAAAGAAGATTGAATTTATTGGTGCACTATAACTAAACTAATCCATGGGTATCTGACTTCAGGTGCTGCTGGACTCCAGTTGCTCCAATAATGTCAGGACGTTAGTACTTTCTCTTTCGTCCAGACTCTGCTTTTTCCCCTTACTTTCCTAATTTTTAGTTGTTTGTACCCCACAATTGTCAATTATGTCCTAATAAACTTCAAAGTATATATCTCATTGGCCTGATCGGTTTTCATTGCCTGTCTCT HG:+:566637274:22 +AAAGATAAAGGAATATGCACATCATTTTGCTAAGACACGAAATATCATCTGATTTTCAGCTATTTCACATTTCCTATTTTTTCCCCCTTACTACATTTTCAGCACTTTGGTTTTGAAAAGCAGAAAATGAACGTCAAACTGGTCTTAAACAGAAAAGAAGATTGAATTTATTGGTGCACTATAACTAAACTAATCCATGGGTATCTGACTTCAGGTGCTGCTGGACTCCAGTTGCTCCAATAATGTCAGGACGTTAGTACTTTCTCTTTCGTCCAGACTCTGCTTTTTCCCCTTACTTTCCTAATTTTTAGTTGTTTGTACCCCACAATTGTCAATTATGTCCTAATAAACTTCAAAGTATATATCTCATTGGCCTGATCGGTTTTCATTGCCTGTCTCT HG:+:662664140:-1 +AGAGACAGGCAATGAAAACCGATCAGGCCAATGAGATATATACTTTGAAGTTTATTAGGACATAATTGACAATTGTGGGGTACAAACAACTAAAAATTAGGAAAGTAAGGGGAAAAAGCAGAGTCTGGACGAAAGAGAAAGTACTAACGTCCTGACATTATTGGAGCAACTGGAGTCCAGCAGCACCTGAAGTCAGATACCCATGGATTAGTTTAGTTATAGTGCACCAATAAATTCAATCTTCTTTTCTGTTTAAGACCAGTTTGACGTTCATTTTCTGCTTTTCAAAACCAAAGTGCTGAAAATGTAGTAAGGGGGAAAAAATAGGAAATGTGAAATAGCTGAAAATCAGATGATATTTCGTGTCTTAGCAAAATGATGTGCATATTCCTTTATCTTT HG:+:65380606:-1 HG:+:1335498270:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGAAATATGAAAATATGAAAAAATAAAACATTTGAAATGAATATTGAAAATTGTTTTATTTTTGAATATGAAAAAATAAACAATTGAAATGAATATGAAAATTGTTTTACTTTTTGATATGAAAAAATAAAATGAATATGAAAAAATATGAATATTGAAAAATAATAAAAACAATTTGTTGGGGTAAAGATTTTTTCTTGAAT HG:+:445236573:-1 HG:+:874540770:-1 HG:+:1977683425:-1 HG:+:2172566006:-1 HG:+:2387930185:-1 HG:+:2847539170:-1 HG:+:2896627892:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGAAATATGAAAATATGAAAAAATAAAACATTTGAAATGAATATTGAAAATTGTTTTATTTTTGAATATGAAAAAATAAACAATTGAAATGAATATGAAAATTGTTTTACTTTTTGATATGAAAAAATAAAATGAATATGAAAAAATATGAATATTGAAAAATAATAAAAACAATTTGTTGGGGTAAAGATTTTTTCTTGAAT HG:+:344836866:-1 HG:+:463979142:-1 HG:+:645850725:-1 HG:+:645850898:-1 HG:+:782444441:-1 HG:+:839724464:-1 HG:+:1157917279:-1 HG:+:1355700374:-1 HG:+:1470034430:-1 HG:+:1707769166:-1 HG:+:2158888426:-1 HG:+:2796456260:-1 HG:+:2855315793:-1 HG:+:2861063507:-1 HG:+:2983526494:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGAAATATGAAAATATGAAAAAATAAAACATTTGAAATGAATATTGAAAATTGTTTTATTTTTGAATATGAAAAAATAAACAATTGAAATGAATATGAAAATTGTTTTACTTTTTGATATGAAAAAATAAAATGAATATGAAAAAATATGAATATTGAAAAATAATAAAAACAATTTGTTGGGGTAAAGATTTTTTCTTGAAT HG:+:69551778:-1 HG:+:813277507:-1 HG:+:1624565039:-1 HG:+:1666070575:-1 HG:+:2981026295:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGAAATATGAAAATATGAAAAAATAAAACATTTGAAATGAATATTGAAAATTGTTTTATTTTTGAATATGAAAAAATAAACAATTGAAATGAATATGAAAATTGTTTTACTTTTTGATATGAAAAAATAAAATGAATATGAAAAAATATGAATATTGAAAAATAATAAAAACAATTTGTTGGGGTAAAGATTTTTTCTTGAAT HG:+:960408733:-1 HG:+:1679369456:-1 HG:+:1700760748:-1 HG:+:1826993759:-1 HG:+:2764859760:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGAAATATGAAAATATGAAAAAATAAAACATTTGAAATGAATATTGAAAATTGTTTTATTTTTGAATATGAAAAAATAAACAATTGAAATGAATATGAAAATTGTTTTACTTTTTGATATGAAAAAATAAAATGAATATGAAAAAATATGAATATTGAAAAATAATAAAAACAATTTGTTGGGGTAAAGATTTTTTCTTGAAT HG:+:305091525:-1 HG:+:1200296386:-1 HG:+:2997323631:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGAAATATGAAAATATGAAAAAATAAAACATTTGAAATGAATATTGAAAATTGTTTTATTTTTGAATATGAAAAAATAAACAATTGAAATGAATATGAAAATTGTTTTACTTTTTGATATGAAAAAATAAAATGAATATGAAAAAATATGAATATTGAAAAATAATAAAAACAATTTGTTGGGGTAAAGATTTTTTCTTGAAT HG:+:190343587:-1 HG:+:198180218:-1 HG:+:408363469:-1 HG:+:426692103:-1 HG:+:448513035:-1 HG:+:560496851:-1 HG:+:643999274:-1 HG:+:814357408:-1 HG:+:855781226:-1 HG:+:974047909:-1 HG:+:1174391791:-1 HG:+:1457841618:-1 HG:+:1477234978:-1 HG:+:1567313140:-1 HG:+:1909407753:-1 HG:+:2032073006:-1 HG:+:2042005766:-1 HG:+:2164564683:-1 HG:+:2281341847:-1 HG:+:2297617729:-1 HG:+:2345274880:-1 HG:+:2486107067:-1 HG:+:2629154953:-1 HG:+:2756547436:-1 HG:+:2964391110:-1 HG:+:3056135908:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGAAATATGAAAATATGAAAAAATAAAACATTTGAAATGAATATTGAAAATTGTTTTATTTTTGAATATGAAAAAATAAACAATTGAAATGAATATGAAAATTGTTTTACTTTTTGATATGAAAAAATAAAATGAATATGAAAAAATATGAATATTGAAAAATAATAAAAACAATTTGTTGGGGTAAAGATTTTTTCTTGAAT HG:+:84061412:-1 HG:+:97849802:-1 HG:+:106957604:-1 HG:+:112027468:-1 HG:+:146652312:-1 HG:+:191852003:-1 HG:+:192043482:-1 HG:+:206297780:-1 HG:+:251037944:-1 HG:+:285703273:-1 HG:+:374964448:-1 HG:+:442726407:-1 HG:+:484901382:-1 HG:+:494732451:-1 HG:+:510639176:-1 HG:+:513580540:-1 HG:+:552438249:-1 HG:+:637829855:-1 HG:+:655387166:-1 HG:+:657114004:-1 HG:+:662603105:-1 HG:+:686637890:-1 HG:+:769443521:-1 HG:+:801411578:-1 HG:+:863142841:-1 HG:+:878851377:-1 HG:+:964465307:-1 HG:+:981140974:-1 HG:+:992005182:-1 HG:+:1049615375:-1 HG:+:1075035340:-1 HG:+:1083045428:-1 HG:+:1138302518:-1 HG:+:1148483611:-1 HG:+:1159591010:-1 HG:+:1188735392:-1 HG:+:1249595001:-1 HG:+:1276377399:-1 HG:+:1296540649:-1 HG:+:1385991759:-1 HG:+:1411484575:-1 HG:+:1452421022:-1 HG:+:1483464707:-1 HG:+:1511922597:-1 HG:+:1514580622:-1 HG:+:1560888803:-1 HG:+:1630469936:-1 HG:+:1638198536:-1 HG:+:1703528906:-1 HG:+:1738928260:-1 HG:+:1767200305:-1 HG:+:1772908483:-1 HG:+:1886166158:-1 HG:+:1896026148:-1 HG:+:1954761701:-1 HG:+:2056900033:-1 HG:+:2124061260:-1 HG:+:2229365303:-1 HG:+:2250928508:-1 HG:+:2270203167:-1 HG:+:2280347594:-1 HG:+:2407007687:-1 HG:+:2462515038:-1 HG:+:2559889068:-1 HG:+:2756061434:-1 HG:+:2806230141:-1 HG:+:2962572531:-1 HG:+:2999170656:-1 HG:+:3028848028:-1 HG:+:3059394292:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGAAATATGAAAATATGAAAAAATAAAACATTTGAAATGAATATTGAAAATTGTTTTATTTTTGAATATGAAAAAATAAACAATTGAAATGAATATGAAAATTGTTTTACTTTTTGATATGAAAAAATAAAATGAATATGAAAAAATATGAATATTGAAAAATAATAAAAACAATTTGTTGGGGTAAAGATTTTTTCTTGAAT HG:+:284696777:-1 HG:+:433615493:-1 HG:+:658317194:-1 HG:+:704045727:-1 HG:+:791843523:-1 HG:+:944178851:-1 HG:+:1319267431:-1 HG:+:1328805947:-1 HG:+:1467006092:-1 HG:+:1477442122:-1 HG:+:2000487520:-1 HG:+:2062544803:-1 HG:+:2179692634:-1 HG:+:2930674304:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGAAATATGAAAATATGAAAAAATAAAACATTTGAAATGAATATTGAAAATTGTTTTATTTTTGAATATGAAAAAATAAACAATTGAAATGAATATGAAAATTGTTTTACTTTTTGATATGAAAAAATAAAATGAATATGAAAAAATATGAATATTGAAAAATAATAAAAACAATTTGTTGGGGTAAAGATTTTTTCTTGAAT HG:+:40679084:-1 HG:+:51882055:-1 HG:+:201361625:-1 HG:+:299905717:-1 HG:+:434541585:-1 HG:+:533964338:-1 HG:+:726069882:-1 HG:+:747191680:-1 HG:+:789425689:-1 HG:+:822471198:-1 HG:+:862822735:-1 HG:+:905587069:-1 HG:+:991605757:-1 HG:+:1043157704:-1 HG:+:1064044799:-1 HG:+:1066813444:-1 HG:+:1069934972:-1 HG:+:1179802893:-1 HG:+:1193251562:-1 HG:+:1218255010:-1 HG:+:1273888845:-1 HG:+:1398153915:-1 HG:+:1422978122:-1 HG:+:1484680367:-1 HG:+:1929123186:-1 HG:+:1946652340:-1 HG:+:1966925326:-1 HG:+:2015768048:-1 HG:+:2051713873:-1 HG:+:2121155407:-1 HG:+:2152872220:-1 HG:+:2374498121:-1 HG:+:2442869511:-1 HG:+:2501408082:-1 HG:+:2748046622:-1 HG:+:2754305355:-1 HG:+:2800308171:-1 HG:+:2857901785:-1 HG:+:3039077771:-1 HG:+:3057990254:-1 HG:+:3099994390:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGAAATATGAAAATATGAAAAAATAAAACATTTGAAATGAATATTGAAAATTGTTTTATTTTTGAATATGAAAAAATAAACAATTGAAATGAATATGAAAATTGTTTTACTTTTTGATATGAAAAAATAAAATGAATATGAAAAAATATGAATATTGAAAAATAATAAAAACAATTTGTTGGGGTAAAGATTTTTTCTTGAAT HG:+:19882537:-1 HG:+:274043360:-1 HG:+:283043443:-1 HG:+:298522470:-1 HG:+:304778740:-1 HG:+:391644081:-1 HG:+:404357316:-1 HG:+:463288854:-1 HG:+:475014164:-1 HG:+:514400014:-1 HG:+:559006343:-1 HG:+:559175193:-1 HG:+:675010835:-1 HG:+:730097129:-1 HG:+:738830826:-1 HG:+:871923018:-1 HG:+:956439371:-1 HG:+:985908937:-1 HG:+:1069308792:-1 HG:+:1071578809:-1 HG:+:1089547167:-1 HG:+:1209006488:-1 HG:+:1464399540:-1 HG:+:1518323783:-1 HG:+:1764184083:-1 HG:+:1838859995:-1 HG:+:1936171454:-1 HG:+:2003903362:-1 HG:+:2009503628:-1 HG:+:2013681909:-1 HG:+:2028234288:-1 HG:+:2128396964:-1 HG:+:2177888086:-1 HG:+:2188435529:-1 HG:+:2242865316:-1 HG:+:2275256186:-1 HG:+:2467390027:-1 HG:+:2750754566:-1 HG:+:2894274987:-1 HG:+:2914033240:-1 HG:+:2968374900:-1 HG:+:3030867469:-1 +GCTCCCTTAAAACTGACATGGGCTGCCTGGTAGGCATCATTCCAATCCAATTAGTAATGCCTCGTAACCTTTTCATGTTCAGTCTTTTCCTTTTCACTGGAAGACTTACTGGCCTAACCTTTAAAACCTGTTAATAGCATAATGTTAAATGAAAAATAAGTAGATACTCTATAACTTGTATAAAAATGAAAAAATAATGAAATATGAAAATATGAAAAAATAAAACATTTGAAATGAATATTGAAAATTGTTTTATTTTTGAATATGAAAAAATAAACAATTGAAATGAATATGAAAATTGTTTTACTTTTTGATATGAAAAAATAAAATGAATATGAAAAAATATGAATATTGAAAAATAATAAAAACAATTTGTTGGGGTAAAGATTTTTTCTTGAAT HG:+:266965709:-1 HG:+:305212819:-1 HG:+:483386072:-1 HG:+:819551109:-1 HG:+:825534686:-1 HG:+:922283288:-1 HG:+:954562159:-1 HG:+:1095894067:-1 HG:+:1262699765:-1 HG:+:1409124948:-1 HG:+:1636685140:-1 HG:+:1685108083:-1 HG:+:1786137052:-1 HG:+:1797104360:-1 HG:+:1810435715:-1 HG:+:1813003578:-1 HG:+:1858815282:-1 HG:+:1981374223:-1 HG:+:2017683978:-1 HG:+:2036735513:-1 HG:+:2046990799:-1 HG:+:2149393018:-1 HG:+:2267342578:-1 HG:+:2408523728:-1 HG:+:2530875694:-1 HG:+:2976116703:-1 HG:+:3005690742:-1 HG:+:3023261328:-1 +ATTCAAGAAAAAATCTTTACCCCAACAAATTGTTTTTATTATTTTTCAATATTCATATTTTTTCATATTCATTTTATTTTTTCATATCAAAAAGTAAAACAATTTTCATATTCATTTCAATTGTTTATTTTTTCATATTCAAAAATAAAACAATTTTCAATATTCATTTCAAATGTTTTATTTTTTCATATTTTCATATTTCATTATTTTTTCATTTTTATACAAGTTATAGAGTATCTACTTATTTTTCATTTAACATTATGCTATTAACAGGTTTTAAAGGTTAGGCCAGTAAGTCTTCCAGTGAAAAGGAAAAGACTGAACATGAAAAGGTTACGAGGCATTACTAATTGGATTGGAATGATGCCTACCAGGCAGCCCATGTCAGTTTTAAGGGAGC HG:+:755597388:-1 HG:+:906599301:-1 HG:+:2403168606:-1 HG:+:2903674282:-1 +ATTCAAGAAAAAATCTTTACCCCAACAAATTGTTTTTATTATTTTTCAATATTCATATTTTTTCATATTCATTTTATTTTTTCATATCAAAAAGTAAAACAATTTTCATATTCATTTCAATTGTTTATTTTTTCATATTCAAAAATAAAACAATTTTCAATATTCATTTCAAATGTTTTATTTTTTCATATTTTCATATTTCATTATTTTTTCATTTTTATACAAGTTATAGAGTATCTACTTATTTTTCATTTAACATTATGCTATTAACAGGTTTTAAAGGTTAGGCCAGTAAGTCTTCCAGTGAAAAGGAAAAGACTGAACATGAAAAGGTTACGAGGCATTACTAATTGGATTGGAATGATGCCTACCAGGCAGCCCATGTCAGTTTTAAGGGAGC HG:+:1173991879:20 HG:+:2050637087:-1 +ATTCAAGAAAAAATCTTTACCCCAACAAATTGTTTTTATTATTTTTCAATATTCATATTTTTTCATATTCATTTTATTTTTTCATATCAAAAAGTAAAACAATTTTCATATTCATTTCAATTGTTTATTTTTTCATATTCAAAAATAAAACAATTTTCAATATTCATTTCAAATGTTTTATTTTTTCATATTTTCATATTTCATTATTTTTTCATTTTTATACAAGTTATAGAGTATCTACTTATTTTTCATTTAACATTATGCTATTAACAGGTTTTAAAGGTTAGGCCAGTAAGTCTTCCAGTGAAAAGGAAAAGACTGAACATGAAAAGGTTACGAGGCATTACTAATTGGATTGGAATGATGCCTACCAGGCAGCCCATGTCAGTTTTAAGGGAGC HG:+:1173991828:20 +ATTCAAGAAAAAATCTTTACCCCAACAAATTGTTTTTATTATTTTTCAATATTCATATTTTTTCATATTCATTTTATTTTTTCATATCAAAAAGTAAAACAATTTTCATATTCATTTCAATTGTTTATTTTTTCATATTCAAAAATAAAACAATTTTCAATATTCATTTCAAATGTTTTATTTTTTCATATTTTCATATTTCATTATTTTTTCATTTTTATACAAGTTATAGAGTATCTACTTATTTTTCATTTAACATTATGCTATTAACAGGTTTTAAAGGTTAGGCCAGTAAGTCTTCCAGTGAAAAGGAAAAGACTGAACATGAAAAGGTTACGAGGCATTACTAATTGGATTGGAATGATGCCTACCAGGCAGCCCATGTCAGTTTTAAGGGAGC HG:+:1173991877:20 +ATTCAAGAAAAAATCTTTACCCCAACAAATTGTTTTTATTATTTTTCAATATTCATATTTTTTCATATTCATTTTATTTTTTCATATCAAAAAGTAAAACAATTTTCATATTCATTTCAATTGTTTATTTTTTCATATTCAAAAATAAAACAATTTTCAATATTCATTTCAAATGTTTTATTTTTTCATATTTTCATATTTCATTATTTTTTCATTTTTATACAAGTTATAGAGTATCTACTTATTTTTCATTTAACATTATGCTATTAACAGGTTTTAAAGGTTAGGCCAGTAAGTCTTCCAGTGAAAAGGAAAAGACTGAACATGAAAAGGTTACGAGGCATTACTAATTGGATTGGAATGATGCCTACCAGGCAGCCCATGTCAGTTTTAAGGGAGC HG:+:1173991930:20 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTGGGTTAACTTGCACAAGCTTGCATTCATTCATTCATTCATTCATTTACACAAGCTTCTTCAAGAATCCCTCAGCTTTAGAGAGTTGGCCTTGCCCAAGATTGGGCTCCTTCCTGGGGCAGCCAATGTTCACTGACTCAGAGAATCAAGAGTTTAAATCGTTTTACCATTTCATCCCTAAAACAGGACAACTCACATTCCGA HG:+:30577270:-1 HG:+:33630071:-1 HG:+:41339454:-1 HG:+:48253145:-1 HG:+:49044124:-1 HG:+:54984063:-1 HG:+:82711250:-1 HG:+:92843453:-1 HG:+:104670966:-1 HG:+:111774672:-1 HG:+:121191741:-1 HG:+:169574365:-1 HG:+:175463882:-1 HG:+:203120617:-1 HG:+:203204603:-1 HG:+:223901708:-1 HG:+:258319795:-1 HG:+:258849122:-1 HG:+:293128608:-1 HG:+:335770521:-1 HG:+:376185089:-1 HG:+:411539167:-1 HG:+:457862955:-1 HG:+:461604816:-1 HG:+:502412465:-1 HG:+:523138753:-1 HG:+:552657637:-1 HG:+:554247655:-1 HG:+:652791844:-1 HG:+:652791852:-1 HG:+:681308849:-1 HG:+:694078155:-1 HG:+:696381891:-1 HG:+:710199423:-1 HG:+:739520458:-1 HG:+:744135466:-1 HG:+:776297502:-1 HG:+:776297506:-1 HG:+:790224468:-1 HG:+:814015491:-1 HG:+:814577228:-1 HG:+:923627722:-1 HG:+:934890887:-1 HG:+:943458649:-1 HG:+:993895401:-1 HG:+:999025724:-1 HG:+:1039516352:-1 HG:+:1049620140:-1 HG:+:1077609374:-1 HG:+:1096516145:-1 HG:+:1103183196:-1 HG:+:1147962270:-1 HG:+:1168060407:-1 HG:+:1181990656:-1 HG:+:1190127479:-1 HG:+:1210137045:-1 HG:+:1238000708:-1 HG:+:1256837959:-1 HG:+:1307121663:-1 HG:+:1308015929:-1 HG:+:1312416955:-1 HG:+:1367256725:-1 HG:+:1410096624:-1 HG:+:1412252979:-1 HG:+:1412804700:-1 HG:+:1461789662:-1 HG:+:1497032824:-1 HG:+:1523874260:-1 HG:+:1524221533:-1 HG:+:1533783272:-1 HG:+:1533949972:-1 HG:+:1565071478:-1 HG:+:1640828153:-1 HG:+:1642505330:-1 HG:+:1666928176:-1 HG:+:1671105097:-1 HG:+:1744139947:-1 HG:+:1744298612:-1 HG:+:1768352742:-1 HG:+:1768426356:-1 HG:+:1778334338:-1 HG:+:1789460953:-1 HG:+:1847915839:-1 HG:+:1849877822:-1 HG:+:1861435566:-1 HG:+:1879739915:-1 HG:+:1942881906:-1 HG:+:1943362690:-1 HG:+:1965731893:-1 HG:+:2040785985:-1 HG:+:2045419943:-1 HG:+:2050509808:-1 HG:+:2050575446:-1 HG:+:2054430275:-1 HG:+:2059906718:-1 HG:+:2069890643:-1 HG:+:2070411174:-1 HG:+:2072633425:-1 HG:+:2081665403:-1 HG:+:2132577005:-1 HG:+:2159987185:-1 HG:+:2165417581:-1 HG:+:2178018737:-1 HG:+:2182859062:-1 HG:+:2184970851:-1 HG:+:2185616746:-1 HG:+:2231009972:-1 HG:+:2277244882:-1 HG:+:2288043550:-1 HG:+:2305002803:-1 HG:+:2338363791:-1 HG:+:2368333518:-1 HG:+:2374189630:-1 HG:+:2407171789:-1 HG:+:2408077906:-1 HG:+:2414778336:-1 HG:+:2426588778:-1 HG:+:2429363471:-1 HG:+:2432777179:-1 HG:+:2463386075:-1 HG:+:2465265555:-1 HG:+:2479657683:-1 HG:+:2480751442:-1 HG:+:2491093876:-1 HG:+:2512265644:-1 HG:+:2537237555:-1 HG:+:2542099392:-1 HG:+:2547105566:-1 HG:+:2554871942:-1 HG:+:2554871954:-1 HG:+:2574501496:-1 HG:+:2577328301:-1 HG:+:2581486454:-1 HG:+:2595828984:-1 HG:+:2605406822:-1 HG:+:2635080144:-1 HG:+:2639978450:-1 HG:+:2660952801:-1 HG:+:2661825851:-1 HG:+:2664715745:-1 HG:+:2668234591:-1 HG:+:2677316807:-1 HG:+:2690151574:-1 HG:+:2701926654:-1 HG:+:2713003352:-1 HG:+:2716027857:-1 HG:+:2719640674:-1 HG:+:2766674466:-1 HG:+:2775248932:-1 HG:+:2775525288:-1 HG:+:2853889932:-1 HG:+:2867405838:-1 HG:+:2904671812:-1 HG:+:2906791318:-1 HG:+:2915824941:-1 HG:+:2916765054:-1 HG:+:2922498496:-1 HG:+:2930843856:-1 HG:+:2943467609:-1 HG:+:2949251105:-1 HG:+:2977255388:-1 HG:+:2982543828:-1 HG:+:2993041685:-1 HG:+:2996534386:-1 HG:+:3003814283:-1 HG:+:3035816644:-1 HG:+:3055228164:-1 HG:+:3101396710:-1 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTGGGTTAACTTGCACAAGCTTGCATTCATTCATTCATTCATTCATTTACACAAGCTTCTTCAAGAATCCCTCAGCTTTAGAGAGTTGGCCTTGCCCAAGATTGGGCTCCTTCCTGGGGCAGCCAATGTTCACTGACTCAGAGAATCAAGAGTTTAAATCGTTTTACCATTTCATCCCTAAAACAGGACAACTCACATTCCGA HG:+:34406073:-1 HG:+:620463874:-1 HG:+:1365741185:-1 HG:+:2656027803:-1 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTGGGTTAACTTGCACAAGCTTGCATTCATTCATTCATTCATTCATTTACACAAGCTTCTTCAAGAATCCCTCAGCTTTAGAGAGTTGGCCTTGCCCAAGATTGGGCTCCTTCCTGGGGCAGCCAATGTTCACTGACTCAGAGAATCAAGAGTTTAAATCGTTTTACCATTTCATCCCTAAAACAGGACAACTCACATTCCGA HG:+:252629697:-1 HG:+:859024020:-1 HG:+:1041054434:-1 HG:+:1049733129:-1 HG:+:1164636188:-1 HG:+:1205421065:-1 HG:+:1741484924:-1 HG:+:1795735953:-1 HG:+:1865703073:-1 HG:+:1892817415:-1 HG:+:2536399590:-1 HG:+:2545699829:-1 HG:+:2654915604:-1 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTGGGTTAACTTGCACAAGCTTGCATTCATTCATTCATTCATTCATTTACACAAGCTTCTTCAAGAATCCCTCAGCTTTAGAGAGTTGGCCTTGCCCAAGATTGGGCTCCTTCCTGGGGCAGCCAATGTTCACTGACTCAGAGAATCAAGAGTTTAAATCGTTTTACCATTTCATCCCTAAAACAGGACAACTCACATTCCGA HG:+:298703738:-1 HG:+:333544653:-1 HG:+:917770752:-1 HG:+:2272786501:-1 HG:+:2427685587:-1 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTGGGTTAACTTGCACAAGCTTGCATTCATTCATTCATTCATTCATTTACACAAGCTTCTTCAAGAATCCCTCAGCTTTAGAGAGTTGGCCTTGCCCAAGATTGGGCTCCTTCCTGGGGCAGCCAATGTTCACTGACTCAGAGAATCAAGAGTTTAAATCGTTTTACCATTTCATCCCTAAAACAGGACAACTCACATTCCGA HG:+:36189677:-1 HG:+:350068980:-1 HG:+:489993727:-1 HG:+:717594772:-1 HG:+:2135711400:-1 HG:+:2285121910:-1 HG:+:2336178048:-1 HG:+:2385708463:-1 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTGGGTTAACTTGCACAAGCTTGCATTCATTCATTCATTCATTCATTTACACAAGCTTCTTCAAGAATCCCTCAGCTTTAGAGAGTTGGCCTTGCCCAAGATTGGGCTCCTTCCTGGGGCAGCCAATGTTCACTGACTCAGAGAATCAAGAGTTTAAATCGTTTTACCATTTCATCCCTAAAACAGGACAACTCACATTCCGA HG:+:321805728:-1 HG:+:632477082:-1 HG:+:1288659861:-1 HG:+:1992493564:-1 HG:+:2360891264:-1 HG:+:2396002367:-1 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTGGGTTAACTTGCACAAGCTTGCATTCATTCATTCATTCATTCATTTACACAAGCTTCTTCAAGAATCCCTCAGCTTTAGAGAGTTGGCCTTGCCCAAGATTGGGCTCCTTCCTGGGGCAGCCAATGTTCACTGACTCAGAGAATCAAGAGTTTAAATCGTTTTACCATTTCATCCCTAAAACAGGACAACTCACATTCCGA HG:+:188196009:-1 HG:+:292717205:-1 HG:+:490367731:-1 HG:+:875651343:-1 HG:+:1340201355:-1 HG:+:1695984025:-1 HG:+:1871406505:-1 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTGGGTTAACTTGCACAAGCTTGCATTCATTCATTCATTCATTCATTTACACAAGCTTCTTCAAGAATCCCTCAGCTTTAGAGAGTTGGCCTTGCCCAAGATTGGGCTCCTTCCTGGGGCAGCCAATGTTCACTGACTCAGAGAATCAAGAGTTTAAATCGTTTTACCATTTCATCCCTAAAACAGGACAACTCACATTCCGA HG:+:49712016:-1 HG:+:287156016:-1 HG:+:514001424:-1 HG:+:517395433:-1 HG:+:520145037:-1 HG:+:727256428:-1 HG:+:888912255:-1 HG:+:999174267:-1 HG:+:1042498115:-1 HG:+:1085683140:-1 HG:+:1244796145:-1 HG:+:1553061022:-1 HG:+:1688429173:-1 HG:+:1949920157:-1 HG:+:1983227457:-1 HG:+:2011408894:-1 HG:+:2223852351:-1 HG:+:2336358988:-1 HG:+:2407186006:-1 HG:+:2608744188:-1 HG:+:2619919112:-1 HG:+:2803233866:-1 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTGGGTTAACTTGCACAAGCTTGCATTCATTCATTCATTCATTCATTTACACAAGCTTCTTCAAGAATCCCTCAGCTTTAGAGAGTTGGCCTTGCCCAAGATTGGGCTCCTTCCTGGGGCAGCCAATGTTCACTGACTCAGAGAATCAAGAGTTTAAATCGTTTTACCATTTCATCCCTAAAACAGGACAACTCACATTCCGA HG:+:899273962:-1 HG:+:1105065488:-1 HG:+:1226837316:-1 HG:+:1447964355:-1 HG:+:2414504640:-1 HG:+:2584002030:-1 HG:+:2591209202:-1 +CAGGTGAAACAAAAACAGGCATTCACCATAAATCCACATTGTTTTGACATAACTATCTGGCATATCCCAAGACCCAGATACACAAAGACATTTGTATCAGGCTAGGTATTCCAAAGGACTTATAGGTTATCTCCAGGATGGTCAAGGGCCAGTCTTATCTTTAAAATGTGCACGAGTTTGGAGTACCCCAAGTACCACTGGGTTAACTTGCACAAGCTTGCATTCATTCATTCATTCATTCATTTACACAAGCTTCTTCAAGAATCCCTCAGCTTTAGAGAGTTGGCCTTGCCCAAGATTGGGCTCCTTCCTGGGGCAGCCAATGTTCACTGACTCAGAGAATCAAGAGTTTAAATCGTTTTACCATTTCATCCCTAAAACAGGACAACTCACATTCCGA HG:+:86670450:-1 HG:+:393307552:-1 HG:+:393814856:-1 HG:+:562140751:-1 HG:+:684615036:-1 HG:+:880016468:-1 HG:+:924085545:-1 HG:+:924788058:-1 HG:+:1255561224:-1 HG:+:1343274142:-1 HG:+:1442782086:-1 HG:+:1649172282:-1 HG:+:2982085775:-1 +TCGGAATGTGAGTTGTCCTGTTTTAGGGATGAAATGGTAAAACGATTTAAACTCTTGATTCTCTGAGTCAGTGAACATTGGCTGCCCCAGGAAGGAGCCCAATCTTGGGCAAGGCCAACTCTCTAAAGCTGAGGGATTCTTGAAGAAGCTTGTGTAAATGAATGAATGAATGAATGAATGCAAGCTTGTGCAAGTTAACCCAGTGGTACTTGGGGTACTCCAAACTCGTGCACATTTTAAAGATAAGACTGGCCCTTGACCATCCTGGAGATAACCTATAAGTCCTTTGGAATACCTAGCCTGATACAAATGTCTTTGTGTATCTGGGTCTTGGGATATGCCAGATAGTTATGTCAAAACAATGTGGATTTATGGTGAATGCCTGTTTTTGTTTCACCTG HG:+:2759833471:19 HG:+:3021043667:-1 +TCGGAATGTGAGTTGTCCTGTTTTAGGGATGAAATGGTAAAACGATTTAAACTCTTGATTCTCTGAGTCAGTGAACATTGGCTGCCCCAGGAAGGAGCCCAATCTTGGGCAAGGCCAACTCTCTAAAGCTGAGGGATTCTTGAAGAAGCTTGTGTAAATGAATGAATGAATGAATGAATGCAAGCTTGTGCAAGTTAACCCAGTGGTACTTGGGGTACTCCAAACTCGTGCACATTTTAAAGATAAGACTGGCCCTTGACCATCCTGGAGATAACCTATAAGTCCTTTGGAATACCTAGCCTGATACAAATGTCTTTGTGTATCTGGGTCTTGGGATATGCCAGATAGTTATGTCAAAACAATGTGGATTTATGGTGAATGCCTGTTTTTGTTTCACCTG HG:+:2759833470:19 +TCGGAATGTGAGTTGTCCTGTTTTAGGGATGAAATGGTAAAACGATTTAAACTCTTGATTCTCTGAGTCAGTGAACATTGGCTGCCCCAGGAAGGAGCCCAATCTTGGGCAAGGCCAACTCTCTAAAGCTGAGGGATTCTTGAAGAAGCTTGTGTAAATGAATGAATGAATGAATGAATGCAAGCTTGTGCAAGTTAACCCAGTGGTACTTGGGGTACTCCAAACTCGTGCACATTTTAAAGATAAGACTGGCCCTTGACCATCCTGGAGATAACCTATAAGTCCTTTGGAATACCTAGCCTGATACAAATGTCTTTGTGTATCTGGGTCTTGGGATATGCCAGATAGTTATGTCAAAACAATGTGGATTTATGGTGAATGCCTGTTTTTGTTTCACCTG HG:+:878092726:-1 +AAACCCAAAATGAATTCCCTAACATTTTCACCCTAAAAGCTGTAAGCCAGGCTCAGCAGGGATGTGTTTTCACTCTCAGGTAGAAAGATGTTAGGGATCTAGCACAACTTTCTTCCTCCCCAAATTCTCTTTCAGAACACTTCTGGGAGAACCTTCGAGCAAGGGTGAGGGCCTTCGCCAGCACCCAGCCAGCACCCATGGGCACCCTAGGCCCTCAGGCCGCCAGCCTCCGAGAACAGTGAGAAAATAGAAAAGGGAGTTTCTGTTGTTTCAGCAAAAACAATACCTTGCATGCACATTAGTTTTCTATTCGAGAGCCTAGATATCCCCTCGGGGTTTCTATGTGAGCCACTTGACCATGTGTGAGTAGGAAGGGGTCCTTGCTCAGTGCCCAGGTGTG HG:+:350629910:-1 HG:+:2688767182:23 +AAACCCAAAATGAATTCCCTAACATTTTCACCCTAAAAGCTGTAAGCCAGGCTCAGCAGGGATGTGTTTTCACTCTCAGGTAGAAAGATGTTAGGGATCTAGCACAACTTTCTTCCTCCCCAAATTCTCTTTCAGAACACTTCTGGGAGAACCTTCGAGCAAGGGTGAGGGCCTTCGCCAGCACCCAGCCAGCACCCATGGGCACCCTAGGCCCTCAGGCCGCCAGCCTCCGAGAACAGTGAGAAAATAGAAAAGGGAGTTTCTGTTGTTTCAGCAAAAACAATACCTTGCATGCACATTAGTTTTCTATTCGAGAGCCTAGATATCCCCTCGGGGTTTCTATGTGAGCCACTTGACCATGTGTGAGTAGGAAGGGGTCCTTGCTCAGTGCCCAGGTGTG HG:+:1516819493:-1 +AAACCCAAAATGAATTCCCTAACATTTTCACCCTAAAAGCTGTAAGCCAGGCTCAGCAGGGATGTGTTTTCACTCTCAGGTAGAAAGATGTTAGGGATCTAGCACAACTTTCTTCCTCCCCAAATTCTCTTTCAGAACACTTCTGGGAGAACCTTCGAGCAAGGGTGAGGGCCTTCGCCAGCACCCAGCCAGCACCCATGGGCACCCTAGGCCCTCAGGCCGCCAGCCTCCGAGAACAGTGAGAAAATAGAAAAGGGAGTTTCTGTTGTTTCAGCAAAAACAATACCTTGCATGCACATTAGTTTTCTATTCGAGAGCCTAGATATCCCCTCGGGGTTTCTATGTGAGCCACTTGACCATGTGTGAGTAGGAAGGGGTCCTTGCTCAGTGCCCAGGTGTG HG:+:297293483:-1 HG:+:2688767183:23 +AAACCCAAAATGAATTCCCTAACATTTTCACCCTAAAAGCTGTAAGCCAGGCTCAGCAGGGATGTGTTTTCACTCTCAGGTAGAAAGATGTTAGGGATCTAGCACAACTTTCTTCCTCCCCAAATTCTCTTTCAGAACACTTCTGGGAGAACCTTCGAGCAAGGGTGAGGGCCTTCGCCAGCACCCAGCCAGCACCCATGGGCACCCTAGGCCCTCAGGCCGCCAGCCTCCGAGAACAGTGAGAAAATAGAAAAGGGAGTTTCTGTTGTTTCAGCAAAAACAATACCTTGCATGCACATTAGTTTTCTATTCGAGAGCCTAGATATCCCCTCGGGGTTTCTATGTGAGCCACTTGACCATGTGTGAGTAGGAAGGGGTCCTTGCTCAGTGCCCAGGTGTG HG:+:2688767177:23 +AAACCCAAAATGAATTCCCTAACATTTTCACCCTAAAAGCTGTAAGCCAGGCTCAGCAGGGATGTGTTTTCACTCTCAGGTAGAAAGATGTTAGGGATCTAGCACAACTTTCTTCCTCCCCAAATTCTCTTTCAGAACACTTCTGGGAGAACCTTCGAGCAAGGGTGAGGGCCTTCGCCAGCACCCAGCCAGCACCCATGGGCACCCTAGGCCCTCAGGCCGCCAGCCTCCGAGAACAGTGAGAAAATAGAAAAGGGAGTTTCTGTTGTTTCAGCAAAAACAATACCTTGCATGCACATTAGTTTTCTATTCGAGAGCCTAGATATCCCCTCGGGGTTTCTATGTGAGCCACTTGACCATGTGTGAGTAGGAAGGGGTCCTTGCTCAGTGCCCAGGTGTG HG:+:2879160187:-1 +AAACCCAAAATGAATTCCCTAACATTTTCACCCTAAAAGCTGTAAGCCAGGCTCAGCAGGGATGTGTTTTCACTCTCAGGTAGAAAGATGTTAGGGATCTAGCACAACTTTCTTCCTCCCCAAATTCTCTTTCAGAACACTTCTGGGAGAACCTTCGAGCAAGGGTGAGGGCCTTCGCCAGCACCCAGCCAGCACCCATGGGCACCCTAGGCCCTCAGGCCGCCAGCCTCCGAGAACAGTGAGAAAATAGAAAAGGGAGTTTCTGTTGTTTCAGCAAAAACAATACCTTGCATGCACATTAGTTTTCTATTCGAGAGCCTAGATATCCCCTCGGGGTTTCTATGTGAGCCACTTGACCATGTGTGAGTAGGAAGGGGTCCTTGCTCAGTGCCCAGGTGTG HG:+:2688767176:23 +CACACCTGGGCACTGAGCAAGGACCCCTTCCTACTCACACATGGTCAAGTGGCTCACATAGAAACCCCGAGGGGATATCTAGGCTCTCGAATAGAAAACTAATGTGCATGCAAGGTATTGTTTTTGCTGAAACAACAGAAACTCCCTTTTCTATTTTCTCACTGTTCTCGGAGGCTGGCGGCCTGAGGGCCTAGGGTGCCCATGGGTGCTGGCTGGGTGCTGGCGAAGGCCCTCACCCTTGCTCGAAGGTTCTCCCAGAAGTGTTCTGAAAGAGAATTTGGGGAGGAAGAAAGTTGTGCTAGATCCCTAACATCTTTCTACCTGAGAGTGAAAACACATCCCTGCTGAGCCTGGCTTACAGCTTTTAGGGTGAAAATGTTAGGGAATTCATTTTGGGTTT HG:+:2009553901:-1 +CACACCTGGGCACTGAGCAAGGACCCCTTCCTACTCACACATGGTCAAGTGGCTCACATAGAAACCCCGAGGGGATATCTAGGCTCTCGAATAGAAAACTAATGTGCATGCAAGGTATTGTTTTTGCTGAAACAACAGAAACTCCCTTTTCTATTTTCTCACTGTTCTCGGAGGCTGGCGGCCTGAGGGCCTAGGGTGCCCATGGGTGCTGGCTGGGTGCTGGCGAAGGCCCTCACCCTTGCTCGAAGGTTCTCCCAGAAGTGTTCTGAAAGAGAATTTGGGGAGGAAGAAAGTTGTGCTAGATCCCTAACATCTTTCTACCTGAGAGTGAAAACACATCCCTGCTGAGCCTGGCTTACAGCTTTTAGGGTGAAAATGTTAGGGAATTCATTTTGGGTTT HG:+:469266423:-1 +CACACCTGGGCACTGAGCAAGGACCCCTTCCTACTCACACATGGTCAAGTGGCTCACATAGAAACCCCGAGGGGATATCTAGGCTCTCGAATAGAAAACTAATGTGCATGCAAGGTATTGTTTTTGCTGAAACAACAGAAACTCCCTTTTCTATTTTCTCACTGTTCTCGGAGGCTGGCGGCCTGAGGGCCTAGGGTGCCCATGGGTGCTGGCTGGGTGCTGGCGAAGGCCCTCACCCTTGCTCGAAGGTTCTCCCAGAAGTGTTCTGAAAGAGAATTTGGGGAGGAAGAAAGTTGTGCTAGATCCCTAACATCTTTCTACCTGAGAGTGAAAACACATCCCTGCTGAGCCTGGCTTACAGCTTTTAGGGTGAAAATGTTAGGGAATTCATTTTGGGTTT HG:+:228927549:-1 +ATTTCCAGCTAACAACTTTTTTGTGTATGGTGTAAGGACAAGGGCCCTGTTTCAATATTTTGCATGTAGATATCCAGTTTTCCCAACACCATTTATTAAAGAGAACTTTATTTCCCCCTGGTGTATTTCTTGGTCAACCTGTCAAAGATAGTTGACTCTATATGCATGAATTGTATCTGGGTTTTATTCCATTGGTTTGTATCTGTTTGTATGCAATTACCATAGTCGTTTGATTACTGTAGCTTTGTAACATAGTTTTAAATTAGAAAGTGTGGATGCCCTCTAACAACTTTTTACTGATTGTTTTAATTATTAAGAGTCGTCCTGTAGCTACATATTAATTTAGTTTTTTTCTTTTTTATGAAATTATTTAATATAAAGATATTAATGTTAAGTTTTT HG:+:886016167:16 +ATTTCCAGCTAACAACTTTTTTGTGTATGGTGTAAGGACAAGGGCCCTGTTTCAATATTTTGCATGTAGATATCCAGTTTTCCCAACACCATTTATTAAAGAGAACTTTATTTCCCCCTGGTGTATTTCTTGGTCAACCTGTCAAAGATAGTTGACTCTATATGCATGAATTGTATCTGGGTTTTATTCCATTGGTTTGTATCTGTTTGTATGCAATTACCATAGTCGTTTGATTACTGTAGCTTTGTAACATAGTTTTAAATTAGAAAGTGTGGATGCCCTCTAACAACTTTTTACTGATTGTTTTAATTATTAAGAGTCGTCCTGTAGCTACATATTAATTTAGTTTTTTTCTTTTTTATGAAATTATTTAATATAAAGATATTAATGTTAAGTTTTT HG:+:886016166:16 +ATTTCCAGCTAACAACTTTTTTGTGTATGGTGTAAGGACAAGGGCCCTGTTTCAATATTTTGCATGTAGATATCCAGTTTTCCCAACACCATTTATTAAAGAGAACTTTATTTCCCCCTGGTGTATTTCTTGGTCAACCTGTCAAAGATAGTTGACTCTATATGCATGAATTGTATCTGGGTTTTATTCCATTGGTTTGTATCTGTTTGTATGCAATTACCATAGTCGTTTGATTACTGTAGCTTTGTAACATAGTTTTAAATTAGAAAGTGTGGATGCCCTCTAACAACTTTTTACTGATTGTTTTAATTATTAAGAGTCGTCCTGTAGCTACATATTAATTTAGTTTTTTTCTTTTTTATGAAATTATTTAATATAAAGATATTAATGTTAAGTTTTT HG:+:1461868953:-1 +ATTTCCAGCTAACAACTTTTTTGTGTATGGTGTAAGGACAAGGGCCCTGTTTCAATATTTTGCATGTAGATATCCAGTTTTCCCAACACCATTTATTAAAGAGAACTTTATTTCCCCCTGGTGTATTTCTTGGTCAACCTGTCAAAGATAGTTGACTCTATATGCATGAATTGTATCTGGGTTTTATTCCATTGGTTTGTATCTGTTTGTATGCAATTACCATAGTCGTTTGATTACTGTAGCTTTGTAACATAGTTTTAAATTAGAAAGTGTGGATGCCCTCTAACAACTTTTTACTGATTGTTTTAATTATTAAGAGTCGTCCTGTAGCTACATATTAATTTAGTTTTTTTCTTTTTTATGAAATTATTTAATATAAAGATATTAATGTTAAGTTTTT HG:+:886016164:16 +ATTTCCAGCTAACAACTTTTTTGTGTATGGTGTAAGGACAAGGGCCCTGTTTCAATATTTTGCATGTAGATATCCAGTTTTCCCAACACCATTTATTAAAGAGAACTTTATTTCCCCCTGGTGTATTTCTTGGTCAACCTGTCAAAGATAGTTGACTCTATATGCATGAATTGTATCTGGGTTTTATTCCATTGGTTTGTATCTGTTTGTATGCAATTACCATAGTCGTTTGATTACTGTAGCTTTGTAACATAGTTTTAAATTAGAAAGTGTGGATGCCCTCTAACAACTTTTTACTGATTGTTTTAATTATTAAGAGTCGTCCTGTAGCTACATATTAATTTAGTTTTTTTCTTTTTTATGAAATTATTTAATATAAAGATATTAATGTTAAGTTTTT HG:+:886016165:16 +ATTTCCAGCTAACAACTTTTTTGTGTATGGTGTAAGGACAAGGGCCCTGTTTCAATATTTTGCATGTAGATATCCAGTTTTCCCAACACCATTTATTAAAGAGAACTTTATTTCCCCCTGGTGTATTTCTTGGTCAACCTGTCAAAGATAGTTGACTCTATATGCATGAATTGTATCTGGGTTTTATTCCATTGGTTTGTATCTGTTTGTATGCAATTACCATAGTCGTTTGATTACTGTAGCTTTGTAACATAGTTTTAAATTAGAAAGTGTGGATGCCCTCTAACAACTTTTTACTGATTGTTTTAATTATTAAGAGTCGTCCTGTAGCTACATATTAATTTAGTTTTTTTCTTTTTTATGAAATTATTTAATATAAAGATATTAATGTTAAGTTTTT HG:+:886016159:16 +ATTTCCAGCTAACAACTTTTTTGTGTATGGTGTAAGGACAAGGGCCCTGTTTCAATATTTTGCATGTAGATATCCAGTTTTCCCAACACCATTTATTAAAGAGAACTTTATTTCCCCCTGGTGTATTTCTTGGTCAACCTGTCAAAGATAGTTGACTCTATATGCATGAATTGTATCTGGGTTTTATTCCATTGGTTTGTATCTGTTTGTATGCAATTACCATAGTCGTTTGATTACTGTAGCTTTGTAACATAGTTTTAAATTAGAAAGTGTGGATGCCCTCTAACAACTTTTTACTGATTGTTTTAATTATTAAGAGTCGTCCTGTAGCTACATATTAATTTAGTTTTTTTCTTTTTTATGAAATTATTTAATATAAAGATATTAATGTTAAGTTTTT HG:+:907612792:-1 +AAAAACTTAACATTAATATCTTTATATTAAATAATTTCATAAAAAAGAAAAAAACTAAATTAATATGTAGCTACAGGACGACTCTTAATAATTAAAACAATCAGTAAAAAGTTGTTAGAGGGCATCCACACTTTCTAATTTAAAACTATGTTACAAAGCTACAGTAATCAAACGACTATGGTAATTGCATACAAACAGATACAAACCAATGGAATAAAACCCAGATACAATTCATGCATATAGAGTCAACTATCTTTGACAGGTTGACCAAGAAATACACCAGGGGGAAATAAAGTTCTCTTTAATAAATGGTGTTGGGAAAACTGGATATCTACATGCAAAATATTGAAACAGGGCCCTTGTCCTTACACCATACACAAAAAAGTTGTTAGCTGGAAAT HG:+:176083132:-1 +AAAAACTTAACATTAATATCTTTATATTAAATAATTTCATAAAAAAGAAAAAAACTAAATTAATATGTAGCTACAGGACGACTCTTAATAATTAAAACAATCAGTAAAAAGTTGTTAGAGGGCATCCACACTTTCTAATTTAAAACTATGTTACAAAGCTACAGTAATCAAACGACTATGGTAATTGCATACAAACAGATACAAACCAATGGAATAAAACCCAGATACAATTCATGCATATAGAGTCAACTATCTTTGACAGGTTGACCAAGAAATACACCAGGGGGAAATAAAGTTCTCTTTAATAAATGGTGTTGGGAAAACTGGATATCTACATGCAAAATATTGAAACAGGGCCCTTGTCCTTACACCATACACAAAAAAGTTGTTAGCTGGAAAT HG:+:2366466274:-1 +AAAAACTTAACATTAATATCTTTATATTAAATAATTTCATAAAAAAGAAAAAAACTAAATTAATATGTAGCTACAGGACGACTCTTAATAATTAAAACAATCAGTAAAAAGTTGTTAGAGGGCATCCACACTTTCTAATTTAAAACTATGTTACAAAGCTACAGTAATCAAACGACTATGGTAATTGCATACAAACAGATACAAACCAATGGAATAAAACCCAGATACAATTCATGCATATAGAGTCAACTATCTTTGACAGGTTGACCAAGAAATACACCAGGGGGAAATAAAGTTCTCTTTAATAAATGGTGTTGGGAAAACTGGATATCTACATGCAAAATATTGAAACAGGGCCCTTGTCCTTACACCATACACAAAAAAGTTGTTAGCTGGAAAT HG:+:1858225312:-1 +AAAAACTTAACATTAATATCTTTATATTAAATAATTTCATAAAAAAGAAAAAAACTAAATTAATATGTAGCTACAGGACGACTCTTAATAATTAAAACAATCAGTAAAAAGTTGTTAGAGGGCATCCACACTTTCTAATTTAAAACTATGTTACAAAGCTACAGTAATCAAACGACTATGGTAATTGCATACAAACAGATACAAACCAATGGAATAAAACCCAGATACAATTCATGCATATAGAGTCAACTATCTTTGACAGGTTGACCAAGAAATACACCAGGGGGAAATAAAGTTCTCTTTAATAAATGGTGTTGGGAAAACTGGATATCTACATGCAAAATATTGAAACAGGGCCCTTGTCCTTACACCATACACAAAAAAGTTGTTAGCTGGAAAT HG:+:146844956:-1 HG:+:414306834:-1 HG:+:481981756:-1 HG:+:672030502:-1 HG:+:878779440:-1 HG:+:1258615689:-1 HG:+:1410997298:-1 HG:+:1559144125:-1 HG:+:1568753844:-1 HG:+:1702680569:-1 HG:+:1880091961:-1 HG:+:2729862091:-1 HG:+:2991144471:-1 +ACCTAGGCAAAAATGGATCAGTCCCTTGATAAATACTTTAAATCTTTGTATAGGCATCTATAGCATGCAGAGCGCTTCTATGCTCGACTGTTTTTGACTGAGCTCCCAGGGGGCACTCTGAAACTTGGATAAAAAGTGTCACCCAGTCCGCCTTTGGGACAAAGAAGCTGAATCTTGGAATGTTTAAAAGTATACATTCAGGAAGGTGCTGAATCTGGACCAAGAGTCTGTCTCTTTAGATTTTCTCCTCACTTAGGCAGGTAATGGAGCAAATTCAATCTACCTCCATTCAGGGCAGGGGAGGAGAGAGTTTACTAGAAACCATCACCATGAGAGTGGATTAAGGTCCTTTGCCTGCTATGGAGGAAGATGAATTATCTGGTCCCTGCTTGGCCCCTTG HG:+:1704208507:-1 HG:+:2765621093:-1 +ACCTAGGCAAAAATGGATCAGTCCCTTGATAAATACTTTAAATCTTTGTATAGGCATCTATAGCATGCAGAGCGCTTCTATGCTCGACTGTTTTTGACTGAGCTCCCAGGGGGCACTCTGAAACTTGGATAAAAAGTGTCACCCAGTCCGCCTTTGGGACAAAGAAGCTGAATCTTGGAATGTTTAAAAGTATACATTCAGGAAGGTGCTGAATCTGGACCAAGAGTCTGTCTCTTTAGATTTTCTCCTCACTTAGGCAGGTAATGGAGCAAATTCAATCTACCTCCATTCAGGGCAGGGGAGGAGAGAGTTTACTAGAAACCATCACCATGAGAGTGGATTAAGGTCCTTTGCCTGCTATGGAGGAAGATGAATTATCTGGTCCCTGCTTGGCCCCTTG HG:+:80944078:-1 HG:+:1476494956:-1 HG:+:1483038379:-1 HG:+:1914853676:-1 HG:+:2907477787:-1 +ACCTAGGCAAAAATGGATCAGTCCCTTGATAAATACTTTAAATCTTTGTATAGGCATCTATAGCATGCAGAGCGCTTCTATGCTCGACTGTTTTTGACTGAGCTCCCAGGGGGCACTCTGAAACTTGGATAAAAAGTGTCACCCAGTCCGCCTTTGGGACAAAGAAGCTGAATCTTGGAATGTTTAAAAGTATACATTCAGGAAGGTGCTGAATCTGGACCAAGAGTCTGTCTCTTTAGATTTTCTCCTCACTTAGGCAGGTAATGGAGCAAATTCAATCTACCTCCATTCAGGGCAGGGGAGGAGAGAGTTTACTAGAAACCATCACCATGAGAGTGGATTAAGGTCCTTTGCCTGCTATGGAGGAAGATGAATTATCTGGTCCCTGCTTGGCCCCTTG HG:+:1670929102:-1 HG:+:2263180364:-1 HG:+:2544489414:-1 HG:+:2589035056:-1 HG:+:2634334593:-1 HG:+:2750886657:-1 HG:+:2766554600:-1 HG:+:2827424401:-1 HG:+:2981881933:-1 +ACCTAGGCAAAAATGGATCAGTCCCTTGATAAATACTTTAAATCTTTGTATAGGCATCTATAGCATGCAGAGCGCTTCTATGCTCGACTGTTTTTGACTGAGCTCCCAGGGGGCACTCTGAAACTTGGATAAAAAGTGTCACCCAGTCCGCCTTTGGGACAAAGAAGCTGAATCTTGGAATGTTTAAAAGTATACATTCAGGAAGGTGCTGAATCTGGACCAAGAGTCTGTCTCTTTAGATTTTCTCCTCACTTAGGCAGGTAATGGAGCAAATTCAATCTACCTCCATTCAGGGCAGGGGAGGAGAGAGTTTACTAGAAACCATCACCATGAGAGTGGATTAAGGTCCTTTGCCTGCTATGGAGGAAGATGAATTATCTGGTCCCTGCTTGGCCCCTTG HG:+:20664235:-1 HG:+:193551593:-1 HG:+:290809654:-1 HG:+:487186332:-1 HG:+:1110289838:-1 HG:+:1336953557:-1 HG:+:1351083463:-1 HG:+:1413514775:-1 HG:+:2232189873:-1 HG:+:2488606741:-1 HG:+:2546524819:-1 HG:+:2673866454:-1 HG:+:2869652721:-1 +ACCTAGGCAAAAATGGATCAGTCCCTTGATAAATACTTTAAATCTTTGTATAGGCATCTATAGCATGCAGAGCGCTTCTATGCTCGACTGTTTTTGACTGAGCTCCCAGGGGGCACTCTGAAACTTGGATAAAAAGTGTCACCCAGTCCGCCTTTGGGACAAAGAAGCTGAATCTTGGAATGTTTAAAAGTATACATTCAGGAAGGTGCTGAATCTGGACCAAGAGTCTGTCTCTTTAGATTTTCTCCTCACTTAGGCAGGTAATGGAGCAAATTCAATCTACCTCCATTCAGGGCAGGGGAGGAGAGAGTTTACTAGAAACCATCACCATGAGAGTGGATTAAGGTCCTTTGCCTGCTATGGAGGAAGATGAATTATCTGGTCCCTGCTTGGCCCCTTG HG:+:442882614:-1 HG:+:689479653:-1 HG:+:807307460:-1 HG:+:1155008103:-1 HG:+:1741943152:-1 HG:+:1972250878:-1 HG:+:2273093852:-1 HG:+:2611527412:-1 HG:+:2676704822:-1 HG:+:2955002869:-1 +ACCTAGGCAAAAATGGATCAGTCCCTTGATAAATACTTTAAATCTTTGTATAGGCATCTATAGCATGCAGAGCGCTTCTATGCTCGACTGTTTTTGACTGAGCTCCCAGGGGGCACTCTGAAACTTGGATAAAAAGTGTCACCCAGTCCGCCTTTGGGACAAAGAAGCTGAATCTTGGAATGTTTAAAAGTATACATTCAGGAAGGTGCTGAATCTGGACCAAGAGTCTGTCTCTTTAGATTTTCTCCTCACTTAGGCAGGTAATGGAGCAAATTCAATCTACCTCCATTCAGGGCAGGGGAGGAGAGAGTTTACTAGAAACCATCACCATGAGAGTGGATTAAGGTCCTTTGCCTGCTATGGAGGAAGATGAATTATCTGGTCCCTGCTTGGCCCCTTG HG:+:5254161:-1 HG:+:2274917528:-1 HG:+:2803404145:-1 HG:+:2881835993:-1 HG:+:3013352739:-1 +ACCTAGGCAAAAATGGATCAGTCCCTTGATAAATACTTTAAATCTTTGTATAGGCATCTATAGCATGCAGAGCGCTTCTATGCTCGACTGTTTTTGACTGAGCTCCCAGGGGGCACTCTGAAACTTGGATAAAAAGTGTCACCCAGTCCGCCTTTGGGACAAAGAAGCTGAATCTTGGAATGTTTAAAAGTATACATTCAGGAAGGTGCTGAATCTGGACCAAGAGTCTGTCTCTTTAGATTTTCTCCTCACTTAGGCAGGTAATGGAGCAAATTCAATCTACCTCCATTCAGGGCAGGGGAGGAGAGAGTTTACTAGAAACCATCACCATGAGAGTGGATTAAGGTCCTTTGCCTGCTATGGAGGAAGATGAATTATCTGGTCCCTGCTTGGCCCCTTG HG:+:323437246:-1 HG:+:394584232:-1 HG:+:521131034:-1 HG:+:571587409:-1 HG:+:574011293:-1 HG:+:708285359:-1 HG:+:721374562:-1 HG:+:762143481:-1 HG:+:810614661:-1 HG:+:883234821:-1 HG:+:1038973393:-1 HG:+:1303121453:-1 HG:+:1311724837:-1 HG:+:1343618521:-1 HG:+:1380801928:-1 HG:+:1454634463:-1 HG:+:1529307961:-1 HG:+:1607523153:-1 HG:+:1623094309:-1 HG:+:1716624929:-1 HG:+:2075093781:-1 HG:+:2164989183:-1 HG:+:2195797452:-1 HG:+:2402464311:-1 HG:+:2553812936:-1 HG:+:2674691570:-1 HG:+:2909029664:-1 +ACCTAGGCAAAAATGGATCAGTCCCTTGATAAATACTTTAAATCTTTGTATAGGCATCTATAGCATGCAGAGCGCTTCTATGCTCGACTGTTTTTGACTGAGCTCCCAGGGGGCACTCTGAAACTTGGATAAAAAGTGTCACCCAGTCCGCCTTTGGGACAAAGAAGCTGAATCTTGGAATGTTTAAAAGTATACATTCAGGAAGGTGCTGAATCTGGACCAAGAGTCTGTCTCTTTAGATTTTCTCCTCACTTAGGCAGGTAATGGAGCAAATTCAATCTACCTCCATTCAGGGCAGGGGAGGAGAGAGTTTACTAGAAACCATCACCATGAGAGTGGATTAAGGTCCTTTGCCTGCTATGGAGGAAGATGAATTATCTGGTCCCTGCTTGGCCCCTTG HG:+:153205421:-1 HG:+:218730518:-1 HG:+:464873972:-1 HG:+:1001203769:-1 HG:+:1249785886:-1 HG:+:1360303540:-1 HG:+:1393685308:-1 HG:+:1433282161:-1 HG:+:1441319940:-1 HG:+:1463242668:-1 HG:+:1581180258:-1 HG:+:1583563105:-1 HG:+:1586005004:-1 HG:+:2874903691:-1 +ACCTAGGCAAAAATGGATCAGTCCCTTGATAAATACTTTAAATCTTTGTATAGGCATCTATAGCATGCAGAGCGCTTCTATGCTCGACTGTTTTTGACTGAGCTCCCAGGGGGCACTCTGAAACTTGGATAAAAAGTGTCACCCAGTCCGCCTTTGGGACAAAGAAGCTGAATCTTGGAATGTTTAAAAGTATACATTCAGGAAGGTGCTGAATCTGGACCAAGAGTCTGTCTCTTTAGATTTTCTCCTCACTTAGGCAGGTAATGGAGCAAATTCAATCTACCTCCATTCAGGGCAGGGGAGGAGAGAGTTTACTAGAAACCATCACCATGAGAGTGGATTAAGGTCCTTTGCCTGCTATGGAGGAAGATGAATTATCTGGTCCCTGCTTGGCCCCTTG HG:+:350466089:-1 HG:+:681894520:-1 HG:+:1052654739:-1 HG:+:1700757248:-1 HG:+:2332997283:-1 HG:+:2472269779:-1 +CAAGGGGCCAAGCAGGGACCAGATAATTCATCTTCCTCCATAGCAGGCAAAGGACCTTAATCCACTCTCATGGTGATGGTTTCTAGTAAACTCTCTCCTCCCCTGCCCTGAATGGAGGTAGATTGAATTTGCTCCATTACCTGCCTAAGTGAGGAGAAAATCTAAAGAGACAGACTCTTGGTCCAGATTCAGCACCTTCCTGAATGTATACTTTTAAACATTCCAAGATTCAGCTTCTTTGTCCCAAAGGCGGACTGGGTGACACTTTTTATCCAAGTTTCAGAGTGCCCCCTGGGAGCTCAGTCAAAAACAGTCGAGCATAGAAGCGCTCTGCATGCTATAGATGCCTATACAAAGATTTAAAGTATTTATCAAGGGACTGATCCATTTTTGCCTAGGT HG:+:1517954628:22 +CAAGGGGCCAAGCAGGGACCAGATAATTCATCTTCCTCCATAGCAGGCAAAGGACCTTAATCCACTCTCATGGTGATGGTTTCTAGTAAACTCTCTCCTCCCCTGCCCTGAATGGAGGTAGATTGAATTTGCTCCATTACCTGCCTAAGTGAGGAGAAAATCTAAAGAGACAGACTCTTGGTCCAGATTCAGCACCTTCCTGAATGTATACTTTTAAACATTCCAAGATTCAGCTTCTTTGTCCCAAAGGCGGACTGGGTGACACTTTTTATCCAAGTTTCAGAGTGCCCCCTGGGAGCTCAGTCAAAAACAGTCGAGCATAGAAGCGCTCTGCATGCTATAGATGCCTATACAAAGATTTAAAGTATTTATCAAGGGACTGATCCATTTTTGCCTAGGT HG:+:1517954627:22 +CAAGGGGCCAAGCAGGGACCAGATAATTCATCTTCCTCCATAGCAGGCAAAGGACCTTAATCCACTCTCATGGTGATGGTTTCTAGTAAACTCTCTCCTCCCCTGCCCTGAATGGAGGTAGATTGAATTTGCTCCATTACCTGCCTAAGTGAGGAGAAAATCTAAAGAGACAGACTCTTGGTCCAGATTCAGCACCTTCCTGAATGTATACTTTTAAACATTCCAAGATTCAGCTTCTTTGTCCCAAAGGCGGACTGGGTGACACTTTTTATCCAAGTTTCAGAGTGCCCCCTGGGAGCTCAGTCAAAAACAGTCGAGCATAGAAGCGCTCTGCATGCTATAGATGCCTATACAAAGATTTAAAGTATTTATCAAGGGACTGATCCATTTTTGCCTAGGT HG:+:1517954626:22 +CAAGGGGCCAAGCAGGGACCAGATAATTCATCTTCCTCCATAGCAGGCAAAGGACCTTAATCCACTCTCATGGTGATGGTTTCTAGTAAACTCTCTCCTCCCCTGCCCTGAATGGAGGTAGATTGAATTTGCTCCATTACCTGCCTAAGTGAGGAGAAAATCTAAAGAGACAGACTCTTGGTCCAGATTCAGCACCTTCCTGAATGTATACTTTTAAACATTCCAAGATTCAGCTTCTTTGTCCCAAAGGCGGACTGGGTGACACTTTTTATCCAAGTTTCAGAGTGCCCCCTGGGAGCTCAGTCAAAAACAGTCGAGCATAGAAGCGCTCTGCATGCTATAGATGCCTATACAAAGATTTAAAGTATTTATCAAGGGACTGATCCATTTTTGCCTAGGT HG:+:1517954629:22 +CTTGGGTTTCCTGACATAACCTGTAACTGCTTGGTGCTCTTCAGCTTAGCAGGGCCACAGGCAATTTGGTTTCATGCGCCATCGCCCGAAGTGCAGACAGAGGCCCCACGCTGCACTTTCAGTCACGTGACCTGGTCGACTCAGGCCCTTCTGGTTCCTGCTTGTCAGGGTATGGGAAGGTGAGAACTACTTTGCAGTGGCTCTTTGGGGAGGGTCTAGGGATGAGCAATAGTTTGGTTATATACAGGTTGCCCGTTGAACCCTTTTTATATGAAGCCATAATAAAGTTATCTTATAACCCCTAGAATTGCCGTTTTCAGTTGATGTCTGCAGAGTTGCTGTGTTCATCTCCTTGTCTCCAGAGTAAGCCAAGTCATCTGAGGGGAAAAAAACAATCTAC HG:+:87184659:-1 HG:+:144462690:-1 HG:+:405375042:-1 HG:+:958170715:-1 HG:+:1621076234:-1 HG:+:1964232823:24 +CTTGGGTTTCCTGACATAACCTGTAACTGCTTGGTGCTCTTCAGCTTAGCAGGGCCACAGGCAATTTGGTTTCATGCGCCATCGCCCGAAGTGCAGACAGAGGCCCCACGCTGCACTTTCAGTCACGTGACCTGGTCGACTCAGGCCCTTCTGGTTCCTGCTTGTCAGGGTATGGGAAGGTGAGAACTACTTTGCAGTGGCTCTTTGGGGAGGGTCTAGGGATGAGCAATAGTTTGGTTATATACAGGTTGCCCGTTGAACCCTTTTTATATGAAGCCATAATAAAGTTATCTTATAACCCCTAGAATTGCCGTTTTCAGTTGATGTCTGCAGAGTTGCTGTGTTCATCTCCTTGTCTCCAGAGTAAGCCAAGTCATCTGAGGGGAAAAAAACAATCTAC HG:+:1964232822:24 +CTTGGGTTTCCTGACATAACCTGTAACTGCTTGGTGCTCTTCAGCTTAGCAGGGCCACAGGCAATTTGGTTTCATGCGCCATCGCCCGAAGTGCAGACAGAGGCCCCACGCTGCACTTTCAGTCACGTGACCTGGTCGACTCAGGCCCTTCTGGTTCCTGCTTGTCAGGGTATGGGAAGGTGAGAACTACTTTGCAGTGGCTCTTTGGGGAGGGTCTAGGGATGAGCAATAGTTTGGTTATATACAGGTTGCCCGTTGAACCCTTTTTATATGAAGCCATAATAAAGTTATCTTATAACCCCTAGAATTGCCGTTTTCAGTTGATGTCTGCAGAGTTGCTGTGTTCATCTCCTTGTCTCCAGAGTAAGCCAAGTCATCTGAGGGGAAAAAAACAATCTAC HG:+:1964232828:24 +CTTGGGTTTCCTGACATAACCTGTAACTGCTTGGTGCTCTTCAGCTTAGCAGGGCCACAGGCAATTTGGTTTCATGCGCCATCGCCCGAAGTGCAGACAGAGGCCCCACGCTGCACTTTCAGTCACGTGACCTGGTCGACTCAGGCCCTTCTGGTTCCTGCTTGTCAGGGTATGGGAAGGTGAGAACTACTTTGCAGTGGCTCTTTGGGGAGGGTCTAGGGATGAGCAATAGTTTGGTTATATACAGGTTGCCCGTTGAACCCTTTTTATATGAAGCCATAATAAAGTTATCTTATAACCCCTAGAATTGCCGTTTTCAGTTGATGTCTGCAGAGTTGCTGTGTTCATCTCCTTGTCTCCAGAGTAAGCCAAGTCATCTGAGGGGAAAAAAACAATCTAC HG:+:596314390:-1 +CTTGGGTTTCCTGACATAACCTGTAACTGCTTGGTGCTCTTCAGCTTAGCAGGGCCACAGGCAATTTGGTTTCATGCGCCATCGCCCGAAGTGCAGACAGAGGCCCCACGCTGCACTTTCAGTCACGTGACCTGGTCGACTCAGGCCCTTCTGGTTCCTGCTTGTCAGGGTATGGGAAGGTGAGAACTACTTTGCAGTGGCTCTTTGGGGAGGGTCTAGGGATGAGCAATAGTTTGGTTATATACAGGTTGCCCGTTGAACCCTTTTTATATGAAGCCATAATAAAGTTATCTTATAACCCCTAGAATTGCCGTTTTCAGTTGATGTCTGCAGAGTTGCTGTGTTCATCTCCTTGTCTCCAGAGTAAGCCAAGTCATCTGAGGGGAAAAAAACAATCTAC HG:+:1964232826:24 +CTTGGGTTTCCTGACATAACCTGTAACTGCTTGGTGCTCTTCAGCTTAGCAGGGCCACAGGCAATTTGGTTTCATGCGCCATCGCCCGAAGTGCAGACAGAGGCCCCACGCTGCACTTTCAGTCACGTGACCTGGTCGACTCAGGCCCTTCTGGTTCCTGCTTGTCAGGGTATGGGAAGGTGAGAACTACTTTGCAGTGGCTCTTTGGGGAGGGTCTAGGGATGAGCAATAGTTTGGTTATATACAGGTTGCCCGTTGAACCCTTTTTATATGAAGCCATAATAAAGTTATCTTATAACCCCTAGAATTGCCGTTTTCAGTTGATGTCTGCAGAGTTGCTGTGTTCATCTCCTTGTCTCCAGAGTAAGCCAAGTCATCTGAGGGGAAAAAAACAATCTAC HG:+:1964232830:24 +GTAGATTGTTTTTTTCCCCTCAGATGACTTGGCTTACTCTGGAGACAAGGAGATGAACACAGCAACTCTGCAGACATCAACTGAAAACGGCAATTCTAGGGGTTATAAGATAACTTTATTATGGCTTCATATAAAAAGGGTTCAACGGGCAACCTGTATATAACCAAACTATTGCTCATCCCTAGACCCTCCCCAAAGAGCCACTGCAAAGTAGTTCTCACCTTCCCATACCCTGACAAGCAGGAACCAGAAGGGCCTGAGTCGACCAGGTCACGTGACTGAAAGTGCAGCGTGGGGCCTCTGTCTGCACTTCGGGCGATGGCGCATGAAACCAAATTGCCTGTGGCCCTGCTAAGCTGAAGAGCACCAAGCAGTTACAGGTTATGTCAGGAAACCCAAG HG:+:219294810:-1 +GTAGATTGTTTTTTTCCCCTCAGATGACTTGGCTTACTCTGGAGACAAGGAGATGAACACAGCAACTCTGCAGACATCAACTGAAAACGGCAATTCTAGGGGTTATAAGATAACTTTATTATGGCTTCATATAAAAAGGGTTCAACGGGCAACCTGTATATAACCAAACTATTGCTCATCCCTAGACCCTCCCCAAAGAGCCACTGCAAAGTAGTTCTCACCTTCCCATACCCTGACAAGCAGGAACCAGAAGGGCCTGAGTCGACCAGGTCACGTGACTGAAAGTGCAGCGTGGGGCCTCTGTCTGCACTTCGGGCGATGGCGCATGAAACCAAATTGCCTGTGGCCCTGCTAAGCTGAAGAGCACCAAGCAGTTACAGGTTATGTCAGGAAACCCAAG HG:+:1503274039:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:330409471:-1 HG:+:559798115:-1 HG:+:579589669:-1 HG:+:720771362:-1 HG:+:775059399:-1 HG:+:1036038887:-1 HG:+:1036038954:-1 HG:+:1222614769:-1 HG:+:1245652319:-1 HG:+:1584579683:-1 HG:+:1584579710:-1 HG:+:1584579737:-1 HG:+:1697740076:-1 HG:+:1918933793:-1 HG:+:2242389299:-1 HG:+:2409720855:-1 HG:+:2415525825:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:832174463:-1 HG:+:847555182:-1 HG:+:869760527:-1 HG:+:909417550:-1 HG:+:1197807738:-1 HG:+:1707434114:-1 HG:+:1763503251:-1 HG:+:2241548210:-1 HG:+:2602563298:-1 HG:+:2885394437:-1 HG:+:2945626873:-1 HG:+:2955859102:-1 HG:+:2955859161:-1 HG:+:2955859185:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:578267701:-1 HG:+:578267728:-1 HG:+:578267755:-1 HG:+:578267782:-1 HG:+:578267809:-1 HG:+:578267836:-1 HG:+:578267863:-1 HG:+:578267890:-1 HG:+:578267917:-1 HG:+:578267944:-1 HG:+:578267971:-1 HG:+:578267998:-1 HG:+:578268025:-1 HG:+:578268078:-1 HG:+:578268105:-1 HG:+:578268132:-1 HG:+:578268159:-1 HG:+:578268196:-1 HG:+:578268231:-1 HG:+:578268266:-1 HG:+:578268375:-1 HG:+:578268410:-1 HG:+:868914746:-1 HG:+:909417637:-1 HG:+:962956285:-1 HG:+:1083799580:-1 HG:+:1103092724:-1 HG:+:1567222072:-1 HG:+:2885394524:-1 HG:+:2888547240:-1 HG:+:2908157935:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:708843495:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:149117103:-1 HG:+:267727994:-1 HG:+:267728077:-1 HG:+:285296325:-1 HG:+:477719434:-1 HG:+:685750164:-1 HG:+:847555147:-1 HG:+:909417318:-1 HG:+:1243461110:-1 HG:+:2050616763:-1 HG:+:2132463182:-1 HG:+:2166468925:-1 HG:+:2539377407:-1 HG:+:2627260380:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:85444275:-1 HG:+:199644742:-1 HG:+:294004845:-1 HG:+:345950112:-1 HG:+:345950155:-1 HG:+:783073310:-1 HG:+:927729996:-1 HG:+:1086262973:-1 HG:+:2356685430:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:682576445:-1 HG:+:832174459:-1 HG:+:832174553:-1 HG:+:1036038965:-1 HG:+:1036038990:-1 HG:+:1036039015:-1 HG:+:1036039040:-1 HG:+:1701208180:-1 HG:+:1701208238:-1 HG:+:1930410736:-1 HG:+:2885394671:-1 HG:+:2955859265:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:1203924218:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:78783330:-1 HG:+:93494376:-1 HG:+:328049479:-1 HG:+:353791097:-1 HG:+:998553508:-1 HG:+:998553540:-1 HG:+:1010570208:-1 HG:+:1209698391:-1 HG:+:1687251633:-1 HG:+:1886040733:-1 HG:+:2239657151:-1 HG:+:2424303265:-1 HG:+:2536040954:-1 HG:+:2817410563:-1 HG:+:2938366452:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:722717231:-1 HG:+:726727481:-1 HG:+:980388379:-1 HG:+:980388404:-1 HG:+:980388431:-1 HG:+:980388456:-1 HG:+:980388481:-1 HG:+:980388506:-1 HG:+:980388531:-1 HG:+:980388558:-1 HG:+:980388585:-1 HG:+:980388610:-1 HG:+:980388635:-1 HG:+:980388660:-1 HG:+:980388710:-1 HG:+:1215609958:-1 HG:+:1947042393:-1 HG:+:2588332709:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:268344523:-1 HG:+:268344617:-1 HG:+:405931425:-1 HG:+:572676525:-1 HG:+:645501443:-1 HG:+:719927868:-1 HG:+:885545454:-1 HG:+:967476862:-1 HG:+:1134999420:-1 HG:+:1380404942:-1 HG:+:1514727572:-1 HG:+:1736020842:-1 HG:+:1820765212:-1 HG:+:1879279155:-1 HG:+:2032445892:-1 HG:+:3008256702:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:444914472:-1 HG:+:551709716:-1 HG:+:577581841:-1 HG:+:636823067:-1 HG:+:644694885:-1 HG:+:1090224173:-1 HG:+:1346651587:-1 HG:+:1548481593:-1 HG:+:1882787689:-1 HG:+:1922793343:-1 HG:+:2111002870:-1 HG:+:2114499154:-1 HG:+:2744166648:-1 HG:+:2911545404:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:17850660:-1 HG:+:76367926:-1 HG:+:272203384:-1 HG:+:274011214:-1 HG:+:475133771:-1 HG:+:475133831:-1 HG:+:590856495:-1 HG:+:689373367:-1 HG:+:718584273:-1 HG:+:763634301:-1 HG:+:858432644:-1 HG:+:922755805:-1 HG:+:995549546:-1 HG:+:1284145261:-1 HG:+:1347492117:-1 HG:+:1372893336:-1 HG:+:1556463661:-1 HG:+:1568305213:-1 HG:+:1571547839:-1 HG:+:1734957529:-1 HG:+:1863706929:-1 HG:+:2079561374:-1 HG:+:2169581821:-1 HG:+:2258583382:-1 HG:+:2279263151:-1 HG:+:2285600816:-1 HG:+:2416806065:-1 HG:+:2558329138:-1 HG:+:2615709531:-1 HG:+:2615709754:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:103183276:-1 HG:+:683283253:-1 HG:+:701404693:-1 HG:+:1120332288:-1 HG:+:1359240463:-1 HG:+:1509286344:-1 HG:+:2285612679:-1 HG:+:2606309531:-1 HG:+:2964242498:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:267727959:-1 HG:+:267728042:-1 HG:+:268932835:-1 HG:+:358418576:-1 HG:+:846773520:-1 HG:+:1034843996:-1 HG:+:1243461255:-1 HG:+:1457271136:-1 HG:+:1481776488:-1 HG:+:2177773313:-1 HG:+:2539377422:-1 HG:+:2817239768:-1 HG:+:3053221758:-1 HG:+:3060422125:-1 HG:+:3062031407:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:57923536:-1 HG:+:561936505:-1 HG:+:573194119:-1 HG:+:605588043:-1 HG:+:1701207898:-1 HG:+:2387695831:-1 HG:+:3044398924:-1 HG:+:3044398962:-1 +CCCCAGCCTCCTGGCTTTTAATATAATATATGTATATATGTATACATATATTACGTACGTAATACGTATATATACTATATATGTATATTATACACGTATATATACGTATACTATACATATATAGTATATATACATACTATATATGTACATATACACGTATATACATATATAATACATATATACTATATATACGTATACTATACATATATAGTATATATGTATACATACTATATATAACATATATAGTATATATGTATACAATACTATATATACATATATAGTATATATGTATACATACTATTAATATACATATATAGTATGGTATACATATATACACGTTATATATGTGTATGTTATATACATGTGTTATGTGTATATATGTATGTGTATATATGTATAT HG:+:225522432:-1 HG:+:268933238:-1 HG:+:367049603:-1 HG:+:703122457:-1 HG:+:905528134:-1 HG:+:1103360399:-1 HG:+:1165855964:-1 HG:+:1568007594:-1 HG:+:1568007660:-1 HG:+:1568007748:-1 HG:+:1841532653:-1 HG:+:1922482148:-1 HG:+:1969164648:-1 HG:+:2288920141:-1 HG:+:2358411688:-1 HG:+:2391184781:-1 HG:+:2594182496:-1 HG:+:2806631913:-1 HG:+:2919073271:-1 HG:+:3019824739:-1 +ATATACATATATACACATACATATATACACATAACACATGTATATAACATACACATATATAACGTGTATATATGTATACCATACTATATATGTATATTAATAGTATGTATACATATATACTATATATGTATATATAGTATTGTATACATATATACTATATATGTTATATATAGTATGTATACATATATACTATATATGTATAGTATACGTATATATAGTATATATGTATTATATATGTATATACGTGTATATGTACATATATAGTATGTATATATACTATATATGTATAGTATACGTATATATACGTGTATAATATACATATATAGTATATATACGTATTACGTACGTAATATATGTATACATATATACATATATTATATTAAAAGCCAGGAGGCTGGGG HG:+:193040649:-1 HG:+:647474931:-1 HG:+:676376347:-1 HG:+:1131560680:-1 HG:+:1541103678:-1 HG:+:1701208036:17 HG:+:1930410534:-1 HG:+:2602562656:-1 HG:+:2885394469:-1 HG:+:2955859063:-1 +ATATACATATATACACATACATATATACACATAACACATGTATATAACATACACATATATAACGTGTATATATGTATACCATACTATATATGTATATTAATAGTATGTATACATATATACTATATATGTATATATAGTATTGTATACATATATACTATATATGTTATATATAGTATGTATACATATATACTATATATGTATAGTATACGTATATATAGTATATATGTATTATATATGTATATACGTGTATATGTACATATATAGTATGTATATATACTATATATGTATAGTATACGTATATATACGTGTATAATATACATATATAGTATATATACGTATTACGTACGTAATATATGTATACATATATACATATATTATATTAAAAGCCAGGAGGCTGGGG HG:+:1076070040:-1 +ATATACATATATACACATACATATATACACATAACACATGTATATAACATACACATATATAACGTGTATATATGTATACCATACTATATATGTATATTAATAGTATGTATACATATATACTATATATGTATATATAGTATTGTATACATATATACTATATATGTTATATATAGTATGTATACATATATACTATATATGTATAGTATACGTATATATAGTATATATGTATTATATATGTATATACGTGTATATGTACATATATAGTATGTATATATACTATATATGTATAGTATACGTATATATACGTGTATAATATACATATATAGTATATATACGTATTACGTACGTAATATATGTATACATATATACATATATTATATTAAAAGCCAGGAGGCTGGGG HG:+:375901043:-1 HG:+:935341316:-1 +ATATACATATATACACATACATATATACACATAACACATGTATATAACATACACATATATAACGTGTATATATGTATACCATACTATATATGTATATTAATAGTATGTATACATATATACTATATATGTATATATAGTATTGTATACATATATACTATATATGTTATATATAGTATGTATACATATATACTATATATGTATAGTATACGTATATATAGTATATATGTATTATATATGTATATACGTGTATATGTACATATATAGTATGTATATATACTATATATGTATAGTATACGTATATATACGTGTATAATATACATATATAGTATATATACGTATTACGTACGTAATATATGTATACATATATACATATATTATATTAAAAGCCAGGAGGCTGGGG HG:+:818810249:-1 +ATATACATATATACACATACATATATACACATAACACATGTATATAACATACACATATATAACGTGTATATATGTATACCATACTATATATGTATATTAATAGTATGTATACATATATACTATATATGTATATATAGTATTGTATACATATATACTATATATGTTATATATAGTATGTATACATATATACTATATATGTATAGTATACGTATATATAGTATATATGTATTATATATGTATATACGTGTATATGTACATATATAGTATGTATATATACTATATATGTATAGTATACGTATATATACGTGTATAATATACATATATAGTATATATACGTATTACGTACGTAATATATGTATACATATATACATATATTATATTAAAAGCCAGGAGGCTGGGG HG:+:512509988:-1 HG:+:739084660:-1 HG:+:1897991433:-1 HG:+:2107360707:-1 +CTACACCTTTTAAAAGTAAGTCGAATCCAGCTGGTTTTCACTACCTCTTCCACTGCCATCTTTATTCAAACTCTTATCTCTTAGCCTCGATTACCCGTGTAGTAGCCTCCTAATGGCCCAGACCCGTCACTTCCTAAGACTTTCTATAATCTAGTCTCGAGCACAGCAACCAAAGTGATACTGTTACAGAGTGATACCAGTAGCCTTCCTATTTTACTTCCAAGTAAAAGCAAAAATGACTTCAGAAGGCCCTACAGGACAATTCTCTACCTCTTCCTTTTCTTATTTCCGTGTGCTTCAGTCCACACTGACCTCTTTGCTGTTCAGACCTCGCCAGGCATCATTGCATTGCAGGGCCTTTTTGCATTACTGTTACCTCTACTAGAATGTTCTTTTCCCT HG:+:1410687747:25 +CTACACCTTTTAAAAGTAAGTCGAATCCAGCTGGTTTTCACTACCTCTTCCACTGCCATCTTTATTCAAACTCTTATCTCTTAGCCTCGATTACCCGTGTAGTAGCCTCCTAATGGCCCAGACCCGTCACTTCCTAAGACTTTCTATAATCTAGTCTCGAGCACAGCAACCAAAGTGATACTGTTACAGAGTGATACCAGTAGCCTTCCTATTTTACTTCCAAGTAAAAGCAAAAATGACTTCAGAAGGCCCTACAGGACAATTCTCTACCTCTTCCTTTTCTTATTTCCGTGTGCTTCAGTCCACACTGACCTCTTTGCTGTTCAGACCTCGCCAGGCATCATTGCATTGCAGGGCCTTTTTGCATTACTGTTACCTCTACTAGAATGTTCTTTTCCCT HG:+:1410687739:25 HG:+:1966385539:-1 +CTACACCTTTTAAAAGTAAGTCGAATCCAGCTGGTTTTCACTACCTCTTCCACTGCCATCTTTATTCAAACTCTTATCTCTTAGCCTCGATTACCCGTGTAGTAGCCTCCTAATGGCCCAGACCCGTCACTTCCTAAGACTTTCTATAATCTAGTCTCGAGCACAGCAACCAAAGTGATACTGTTACAGAGTGATACCAGTAGCCTTCCTATTTTACTTCCAAGTAAAAGCAAAAATGACTTCAGAAGGCCCTACAGGACAATTCTCTACCTCTTCCTTTTCTTATTTCCGTGTGCTTCAGTCCACACTGACCTCTTTGCTGTTCAGACCTCGCCAGGCATCATTGCATTGCAGGGCCTTTTTGCATTACTGTTACCTCTACTAGAATGTTCTTTTCCCT HG:+:1410687738:25 +CTACACCTTTTAAAAGTAAGTCGAATCCAGCTGGTTTTCACTACCTCTTCCACTGCCATCTTTATTCAAACTCTTATCTCTTAGCCTCGATTACCCGTGTAGTAGCCTCCTAATGGCCCAGACCCGTCACTTCCTAAGACTTTCTATAATCTAGTCTCGAGCACAGCAACCAAAGTGATACTGTTACAGAGTGATACCAGTAGCCTTCCTATTTTACTTCCAAGTAAAAGCAAAAATGACTTCAGAAGGCCCTACAGGACAATTCTCTACCTCTTCCTTTTCTTATTTCCGTGTGCTTCAGTCCACACTGACCTCTTTGCTGTTCAGACCTCGCCAGGCATCATTGCATTGCAGGGCCTTTTTGCATTACTGTTACCTCTACTAGAATGTTCTTTTCCCT HG:+:1410687746:25 +CTACACCTTTTAAAAGTAAGTCGAATCCAGCTGGTTTTCACTACCTCTTCCACTGCCATCTTTATTCAAACTCTTATCTCTTAGCCTCGATTACCCGTGTAGTAGCCTCCTAATGGCCCAGACCCGTCACTTCCTAAGACTTTCTATAATCTAGTCTCGAGCACAGCAACCAAAGTGATACTGTTACAGAGTGATACCAGTAGCCTTCCTATTTTACTTCCAAGTAAAAGCAAAAATGACTTCAGAAGGCCCTACAGGACAATTCTCTACCTCTTCCTTTTCTTATTTCCGTGTGCTTCAGTCCACACTGACCTCTTTGCTGTTCAGACCTCGCCAGGCATCATTGCATTGCAGGGCCTTTTTGCATTACTGTTACCTCTACTAGAATGTTCTTTTCCCT HG:+:2590080054:-1 +CTACACCTTTTAAAAGTAAGTCGAATCCAGCTGGTTTTCACTACCTCTTCCACTGCCATCTTTATTCAAACTCTTATCTCTTAGCCTCGATTACCCGTGTAGTAGCCTCCTAATGGCCCAGACCCGTCACTTCCTAAGACTTTCTATAATCTAGTCTCGAGCACAGCAACCAAAGTGATACTGTTACAGAGTGATACCAGTAGCCTTCCTATTTTACTTCCAAGTAAAAGCAAAAATGACTTCAGAAGGCCCTACAGGACAATTCTCTACCTCTTCCTTTTCTTATTTCCGTGTGCTTCAGTCCACACTGACCTCTTTGCTGTTCAGACCTCGCCAGGCATCATTGCATTGCAGGGCCTTTTTGCATTACTGTTACCTCTACTAGAATGTTCTTTTCCCT HG:+:1410687745:25 +AGGGAAAAGAACATTCTAGTAGAGGTAACAGTAATGCAAAAAGGCCCTGCAATGCAATGATGCCTGGCGAGGTCTGAACAGCAAAGAGGTCAGTGTGGACTGAAGCACACGGAAATAAGAAAAGGAAGAGGTAGAGAATTGTCCTGTAGGGCCTTCTGAAGTCATTTTTGCTTTTACTTGGAAGTAAAATAGGAAGGCTACTGGTATCACTCTGTAACAGTATCACTTTGGTTGCTGTGCTCGAGACTAGATTATAGAAAGTCTTAGGAAGTGACGGGTCTGGGCCATTAGGAGGCTACTACACGGGTAATCGAGGCTAAGAGATAAGAGTTTGAATAAAGATGGCAGTGGAAGAGGTAGTGAAAACCAGCTGGATTCGACTTACTTTTAAAAGGTGTAG HG:+:2927025576:-1 +GAAGAAGTGGCCATGGTTGAGTTTCTCAAAGTTTCCTTTCAAATGTACAGGTCTAAATGGGAGTGTGAGTCCATGTGTGTGACAGCCTTCCCAGCAGGGGAGATGGCACATCATTACCTATTAAATCTCATTCAAAGCAAGATGGCACATCACCTACCTATTAAAATCTCATTCAATCAGCCCTTAGAATACAATATAATGAATTATTTTCATTTTAACAGATATTTACTTAGTGTCTAAGATGTGGTAGGTATGGTGGGAGATAACAGGAAGGAATGTTCCTGCCTCAGTGAGCTCGATGGAACTTTGAGGCTCTTCAGAAATGAAAACAAAAGCAAAAACAAAAAAAATATTAGCTCACCTTATCTCATCACCTGTGGGGCAGCGTGGTACCTGGGAA HG:+:188294699:-1 HG:+:632449794:13 HG:+:1567813857:-1 HG:+:1914966395:-1 HG:+:2141942563:-1 HG:+:2458054922:-1 +GAAGAAGTGGCCATGGTTGAGTTTCTCAAAGTTTCCTTTCAAATGTACAGGTCTAAATGGGAGTGTGAGTCCATGTGTGTGACAGCCTTCCCAGCAGGGGAGATGGCACATCATTACCTATTAAATCTCATTCAAAGCAAGATGGCACATCACCTACCTATTAAAATCTCATTCAATCAGCCCTTAGAATACAATATAATGAATTATTTTCATTTTAACAGATATTTACTTAGTGTCTAAGATGTGGTAGGTATGGTGGGAGATAACAGGAAGGAATGTTCCTGCCTCAGTGAGCTCGATGGAACTTTGAGGCTCTTCAGAAATGAAAACAAAAGCAAAAACAAAAAAAATATTAGCTCACCTTATCTCATCACCTGTGGGGCAGCGTGGTACCTGGGAA HG:+:632449795:13 +GAAGAAGTGGCCATGGTTGAGTTTCTCAAAGTTTCCTTTCAAATGTACAGGTCTAAATGGGAGTGTGAGTCCATGTGTGTGACAGCCTTCCCAGCAGGGGAGATGGCACATCATTACCTATTAAATCTCATTCAAAGCAAGATGGCACATCACCTACCTATTAAAATCTCATTCAATCAGCCCTTAGAATACAATATAATGAATTATTTTCATTTTAACAGATATTTACTTAGTGTCTAAGATGTGGTAGGTATGGTGGGAGATAACAGGAAGGAATGTTCCTGCCTCAGTGAGCTCGATGGAACTTTGAGGCTCTTCAGAAATGAAAACAAAAGCAAAAACAAAAAAAATATTAGCTCACCTTATCTCATCACCTGTGGGGCAGCGTGGTACCTGGGAA HG:+:1692055700:-1 +TTCCCAGGTACCACGCTGCCCCACAGGTGATGAGATAAGGTGAGCTAATATTTTTTTTGTTTTTGCTTTTGTTTTCATTTCTGAAGAGCCTCAAAGTTCCATCGAGCTCACTGAGGCAGGAACATTCCTTCCTGTTATCTCCCACCATACCTACCACATCTTAGACACTAAGTAAATATCTGTTAAAATGAAAATAATTCATTATATTGTATTCTAAGGGCTGATTGAATGAGATTTTAATAGGTAGGTGATGTGCCATCTTGCTTTGAATGAGATTTAATAGGTAATGATGTGCCATCTCCCCTGCTGGGAAGGCTGTCACACACATGGACTCACACTCCCATTTAGACCTGTACATTTGAAAGGAAACTTTGAGAAACTCAACCATGGCCACTTCTTC HG:+:1096250134:-1 +TAGACCCTTCAACTTATTGAGGGATGAGAGTGGTGGGTGTTGTACCGAGGCTTCCTCATCCCTGGGTCAGTTCTGTATTCTAACATTAGTATCCGAGAGGGTCCCAGTGGGATTGAGCCCCTATGCCCGACAGGGCAGGATGTGCTCGCTCACCAACATTCCCTTTTCCTTATTCCTTCTCTGACCTTGTTCCACTGCTCCTTGTGCTTCCCTGTTTTCACCTCCCAATTCTTGTCTCAGGATCTGTTGCTGGGTAACTCAAACCAAGGCAACATCTCCTATGATAGCCCACCAGGCCGGCCTCCCCCGCTTTGCCAATCTTGCATTCAGTGAATTACTAAGCGCTTTGGCTCTGCTTTCCTAAATAACCCTCCAATTATCTTCCTCTCTATTTCTAGAG HG:+:396153898:-1 HG:+:460063816:-1 HG:+:487150948:-1 HG:+:2509012129:-1 HG:+:2724793745:23 +TAGACCCTTCAACTTATTGAGGGATGAGAGTGGTGGGTGTTGTACCGAGGCTTCCTCATCCCTGGGTCAGTTCTGTATTCTAACATTAGTATCCGAGAGGGTCCCAGTGGGATTGAGCCCCTATGCCCGACAGGGCAGGATGTGCTCGCTCACCAACATTCCCTTTTCCTTATTCCTTCTCTGACCTTGTTCCACTGCTCCTTGTGCTTCCCTGTTTTCACCTCCCAATTCTTGTCTCAGGATCTGTTGCTGGGTAACTCAAACCAAGGCAACATCTCCTATGATAGCCCACCAGGCCGGCCTCCCCCGCTTTGCCAATCTTGCATTCAGTGAATTACTAAGCGCTTTGGCTCTGCTTTCCTAAATAACCCTCCAATTATCTTCCTCTCTATTTCTAGAG HG:+:2701980979:-1 HG:+:2724793749:23 +TAGACCCTTCAACTTATTGAGGGATGAGAGTGGTGGGTGTTGTACCGAGGCTTCCTCATCCCTGGGTCAGTTCTGTATTCTAACATTAGTATCCGAGAGGGTCCCAGTGGGATTGAGCCCCTATGCCCGACAGGGCAGGATGTGCTCGCTCACCAACATTCCCTTTTCCTTATTCCTTCTCTGACCTTGTTCCACTGCTCCTTGTGCTTCCCTGTTTTCACCTCCCAATTCTTGTCTCAGGATCTGTTGCTGGGTAACTCAAACCAAGGCAACATCTCCTATGATAGCCCACCAGGCCGGCCTCCCCCGCTTTGCCAATCTTGCATTCAGTGAATTACTAAGCGCTTTGGCTCTGCTTTCCTAAATAACCCTCCAATTATCTTCCTCTCTATTTCTAGAG HG:+:2724793748:23 +TAGACCCTTCAACTTATTGAGGGATGAGAGTGGTGGGTGTTGTACCGAGGCTTCCTCATCCCTGGGTCAGTTCTGTATTCTAACATTAGTATCCGAGAGGGTCCCAGTGGGATTGAGCCCCTATGCCCGACAGGGCAGGATGTGCTCGCTCACCAACATTCCCTTTTCCTTATTCCTTCTCTGACCTTGTTCCACTGCTCCTTGTGCTTCCCTGTTTTCACCTCCCAATTCTTGTCTCAGGATCTGTTGCTGGGTAACTCAAACCAAGGCAACATCTCCTATGATAGCCCACCAGGCCGGCCTCCCCCGCTTTGCCAATCTTGCATTCAGTGAATTACTAAGCGCTTTGGCTCTGCTTTCCTAAATAACCCTCCAATTATCTTCCTCTCTATTTCTAGAG HG:+:2724793758:23 +TAGACCCTTCAACTTATTGAGGGATGAGAGTGGTGGGTGTTGTACCGAGGCTTCCTCATCCCTGGGTCAGTTCTGTATTCTAACATTAGTATCCGAGAGGGTCCCAGTGGGATTGAGCCCCTATGCCCGACAGGGCAGGATGTGCTCGCTCACCAACATTCCCTTTTCCTTATTCCTTCTCTGACCTTGTTCCACTGCTCCTTGTGCTTCCCTGTTTTCACCTCCCAATTCTTGTCTCAGGATCTGTTGCTGGGTAACTCAAACCAAGGCAACATCTCCTATGATAGCCCACCAGGCCGGCCTCCCCCGCTTTGCCAATCTTGCATTCAGTGAATTACTAAGCGCTTTGGCTCTGCTTTCCTAAATAACCCTCCAATTATCTTCCTCTCTATTTCTAGAG HG:+:2724793756:23 +TAGACCCTTCAACTTATTGAGGGATGAGAGTGGTGGGTGTTGTACCGAGGCTTCCTCATCCCTGGGTCAGTTCTGTATTCTAACATTAGTATCCGAGAGGGTCCCAGTGGGATTGAGCCCCTATGCCCGACAGGGCAGGATGTGCTCGCTCACCAACATTCCCTTTTCCTTATTCCTTCTCTGACCTTGTTCCACTGCTCCTTGTGCTTCCCTGTTTTCACCTCCCAATTCTTGTCTCAGGATCTGTTGCTGGGTAACTCAAACCAAGGCAACATCTCCTATGATAGCCCACCAGGCCGGCCTCCCCCGCTTTGCCAATCTTGCATTCAGTGAATTACTAAGCGCTTTGGCTCTGCTTTCCTAAATAACCCTCCAATTATCTTCCTCTCTATTTCTAGAG HG:+:2724793746:23 +CTCTAGAAATAGAGAGGAAGATAATTGGAGGGTTATTTAGGAAAGCAGAGCCAAAGCGCTTAGTAATTCACTGAATGCAAGATTGGCAAAGCGGGGGAGGCCGGCCTGGTGGGCTATCATAGGAGATGTTGCCTTGGTTTGAGTTACCCAGCAACAGATCCTGAGACAAGAATTGGGAGGTGAAAACAGGGAAGCACAAGGAGCAGTGGAACAAGGTCAGAGAAGGAATAAGGAAAAGGGAATGTTGGTGAGCGAGCACATCCTGCCCTGTCGGGCATAGGGGCTCAATCCCACTGGGACCCTCTCGGATACTAATGTTAGAATACAGAACTGACCCAGGGATGAGGAAGCCTCGGTACAACACCCACCACTCTCATCCCTCAATAAGTTGAAGGGTCTA HG:+:2492351308:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGATGGAGCTTGCAGTGAGCCGAGAACGTGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGATTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTAAGGAGGCAGTCTTTAGGCTAGACCTTGATTTAA HG:+:35713455:-1 HG:+:65259675:-1 HG:+:149978000:-1 HG:+:154663997:-1 HG:+:162503799:-1 HG:+:217627525:-1 HG:+:235744423:-1 HG:+:243696886:-1 HG:+:254974310:-1 HG:+:314888108:-1 HG:+:337818519:-1 HG:+:362478411:-1 HG:+:388211772:-1 HG:+:429639494:-1 HG:+:456932358:-1 HG:+:462210875:-1 HG:+:464195547:-1 HG:+:495423650:-1 HG:+:503887002:-1 HG:+:513082571:-1 HG:+:524725156:-1 HG:+:545822476:-1 HG:+:592465292:-1 HG:+:630315090:-1 HG:+:648144216:-1 HG:+:653132627:-1 HG:+:661994983:-1 HG:+:668991837:-1 HG:+:673772567:-1 HG:+:687000209:-1 HG:+:713584982:-1 HG:+:735319006:-1 HG:+:751649475:-1 HG:+:791860857:-1 HG:+:794915993:-1 HG:+:797184568:-1 HG:+:848075781:-1 HG:+:861065381:-1 HG:+:879570585:-1 HG:+:880087871:-1 HG:+:884767727:-1 HG:+:891918067:-1 HG:+:897930014:-1 HG:+:905743370:-1 HG:+:942353866:-1 HG:+:955406188:-1 HG:+:966906158:-1 HG:+:992548869:-1 HG:+:1012394605:-1 HG:+:1043952396:-1 HG:+:1060019729:-1 HG:+:1061429823:-1 HG:+:1065338456:-1 HG:+:1071298685:-1 HG:+:1071554826:-1 HG:+:1098115991:-1 HG:+:1100974961:-1 HG:+:1103989639:-1 HG:+:1106148087:-1 HG:+:1171696603:-1 HG:+:1187345822:-1 HG:+:1232467185:-1 HG:+:1235724681:-1 HG:+:1236136135:-1 HG:+:1251449196:-1 HG:+:1253631746:-1 HG:+:1260524917:-1 HG:+:1262976621:-1 HG:+:1300192739:-1 HG:+:1333701657:-1 HG:+:1370911096:-1 HG:+:1371321093:-1 HG:+:1378344131:-1 HG:+:1462235091:-1 HG:+:1474759649:-1 HG:+:1502051142:-1 HG:+:1513848099:-1 HG:+:1516641520:-1 HG:+:1527557037:-1 HG:+:1541384281:-1 HG:+:1545891671:-1 HG:+:1565764397:-1 HG:+:1571742355:-1 HG:+:1575417106:-1 HG:+:1577904531:-1 HG:+:1578644659:-1 HG:+:1607556754:-1 HG:+:1627648220:-1 HG:+:1666672345:-1 HG:+:1670621542:-1 HG:+:1673573253:-1 HG:+:1678444313:-1 HG:+:1696548568:-1 HG:+:1750580478:-1 HG:+:1769632818:-1 HG:+:1773623385:-1 HG:+:1774570748:-1 HG:+:1780546208:-1 HG:+:1780695209:-1 HG:+:1784316251:-1 HG:+:1785526074:-1 HG:+:1806966789:-1 HG:+:1816454052:-1 HG:+:1817737363:-1 HG:+:1818041682:-1 HG:+:1819230340:-1 HG:+:1833730226:-1 HG:+:1849991656:-1 HG:+:1861374745:-1 HG:+:1862115479:-1 HG:+:1878414385:-1 HG:+:1890606342:-1 HG:+:1898718967:-1 HG:+:1923631930:-1 HG:+:1954258333:-1 HG:+:2001677907:-1 HG:+:2002638754:-1 HG:+:2003376775:-1 HG:+:2004593493:-1 HG:+:2008385115:-1 HG:+:2032432993:-1 HG:+:2058254108:-1 HG:+:2075100290:-1 HG:+:2112831650:-1 HG:+:2121727662:-1 HG:+:2131517670:-1 HG:+:2178691806:-1 HG:+:2190374162:-1 HG:+:2230224669:-1 HG:+:2255443235:-1 HG:+:2305846485:-1 HG:+:2345948262:-1 HG:+:2348128894:-1 HG:+:2367105673:-1 HG:+:2372845258:-1 HG:+:2387482924:-1 HG:+:2401301534:-1 HG:+:2402642318:-1 HG:+:2407594739:-1 HG:+:2414136199:-1 HG:+:2414819887:-1 HG:+:2429037905:-1 HG:+:2432275734:-1 HG:+:2480126371:-1 HG:+:2490661605:-1 HG:+:2497117182:-1 HG:+:2499324349:-1 HG:+:2516549765:-1 HG:+:2529945760:-1 HG:+:2550630707:-1 HG:+:2551546063:-1 HG:+:2560484932:-1 HG:+:2574509478:-1 HG:+:2576383788:-1 HG:+:2578141042:-1 HG:+:2580601126:-1 HG:+:2582124171:-1 HG:+:2584675878:-1 HG:+:2596706349:-1 HG:+:2601010956:-1 HG:+:2655591701:-1 HG:+:2661338390:-1 HG:+:2661464391:-1 HG:+:2663906962:-1 HG:+:2664048634:-1 HG:+:2668615250:-1 HG:+:2671609036:-1 HG:+:2671804237:-1 HG:+:2672635730:-1 HG:+:2674780133:-1 HG:+:2676685346:-1 HG:+:2696097398:-1 HG:+:2709751714:-1 HG:+:2710527003:-1 HG:+:2711580868:-1 HG:+:2720216858:-1 HG:+:2721750226:-1 HG:+:2756157001:-1 HG:+:2772611056:-1 HG:+:2802154727:-1 HG:+:2825620030:-1 HG:+:2846947400:-1 HG:+:2850888434:-1 HG:+:2851660963:-1 HG:+:2878592263:-1 HG:+:2882475787:-1 HG:+:2897736870:-1 HG:+:2910457386:-1 HG:+:2952504093:-1 HG:+:2970791439:-1 HG:+:2974328200:-1 HG:+:2983358372:-1 HG:+:2997487523:-1 HG:+:3003829319:-1 HG:+:3010100447:-1 HG:+:3024767566:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGATGGAGCTTGCAGTGAGCCGAGAACGTGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGATTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTAAGGAGGCAGTCTTTAGGCTAGACCTTGATTTAA HG:+:26618584:-1 HG:+:31593929:-1 HG:+:89305043:-1 HG:+:111999645:-1 HG:+:176982892:-1 HG:+:435079348:-1 HG:+:462776122:-1 HG:+:474365285:-1 HG:+:558500040:-1 HG:+:621343078:-1 HG:+:687327543:-1 HG:+:752633672:-1 HG:+:801506380:-1 HG:+:839057464:-1 HG:+:1096887146:-1 HG:+:1168040851:-1 HG:+:1341698587:-1 HG:+:1435273479:-1 HG:+:1630045279:-1 HG:+:1641970979:-1 HG:+:1653401165:-1 HG:+:1673366583:-1 HG:+:1779758856:-1 HG:+:1839828267:-1 HG:+:1928376937:-1 HG:+:1945374940:-1 HG:+:1945618243:-1 HG:+:1995618403:-1 HG:+:2034158826:-1 HG:+:2162195622:-1 HG:+:2231639445:-1 HG:+:2263805899:-1 HG:+:2275543517:-1 HG:+:2295086910:-1 HG:+:2411169688:-1 HG:+:2418788456:-1 HG:+:2468172777:-1 HG:+:2493641609:-1 HG:+:2510720191:-1 HG:+:2565456525:-1 HG:+:2576236314:-1 HG:+:2697937682:-1 HG:+:2768976514:-1 HG:+:2856774174:-1 HG:+:2985374872:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGATGGAGCTTGCAGTGAGCCGAGAACGTGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGATTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTAAGGAGGCAGTCTTTAGGCTAGACCTTGATTTAA HG:+:823405442:-1 HG:+:2336130295:-1 HG:+:2806715346:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGATGGAGCTTGCAGTGAGCCGAGAACGTGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGATTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTAAGGAGGCAGTCTTTAGGCTAGACCTTGATTTAA HG:+:370426585:-1 HG:+:454899508:-1 HG:+:1327825536:-1 HG:+:1549228074:-1 HG:+:1817240890:-1 HG:+:2933061280:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGATGGAGCTTGCAGTGAGCCGAGAACGTGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGATTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTAAGGAGGCAGTCTTTAGGCTAGACCTTGATTTAA HG:+:30253762:-1 HG:+:93405434:-1 HG:+:181878368:-1 HG:+:197973328:-1 HG:+:415586882:-1 HG:+:421974481:-1 HG:+:454718520:-1 HG:+:531197263:-1 HG:+:562115152:-1 HG:+:664517998:-1 HG:+:801262577:-1 HG:+:854441352:-1 HG:+:863210731:-1 HG:+:876330860:-1 HG:+:920434602:-1 HG:+:936753468:-1 HG:+:966491907:-1 HG:+:1021669536:-1 HG:+:1100359073:-1 HG:+:1195819479:-1 HG:+:1226759843:-1 HG:+:1243654765:-1 HG:+:1365893595:-1 HG:+:1432858548:-1 HG:+:1518740203:-1 HG:+:1567766416:-1 HG:+:1569104598:-1 HG:+:1740537057:-1 HG:+:1836970665:-1 HG:+:1837315889:-1 HG:+:1840940901:-1 HG:+:1998111422:-1 HG:+:2037824261:-1 HG:+:2068071293:-1 HG:+:2120235339:-1 HG:+:2235603495:-1 HG:+:2303794464:-1 HG:+:2355193597:-1 HG:+:2395285125:-1 HG:+:2478015134:-1 HG:+:2480383095:-1 HG:+:2589465068:-1 HG:+:2717300447:-1 HG:+:2805987394:-1 HG:+:2829352627:-1 HG:+:2892421126:-1 HG:+:3031679546:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGATGGAGCTTGCAGTGAGCCGAGAACGTGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGATTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTAAGGAGGCAGTCTTTAGGCTAGACCTTGATTTAA HG:+:14295462:-1 HG:+:72246768:-1 HG:+:234190403:-1 HG:+:265517381:-1 HG:+:391990170:-1 HG:+:452569517:-1 HG:+:487671596:-1 HG:+:609982786:-1 HG:+:693442352:-1 HG:+:752564020:-1 HG:+:807632354:-1 HG:+:937324436:-1 HG:+:1087856859:-1 HG:+:1095881978:-1 HG:+:1238584890:-1 HG:+:1326085186:-1 HG:+:1342040581:-1 HG:+:1373785772:-1 HG:+:1488746390:-1 HG:+:1574473783:-1 HG:+:1607616282:-1 HG:+:1652121525:-1 HG:+:1761421413:-1 HG:+:1901298172:-1 HG:+:1910268882:-1 HG:+:1929999915:-1 HG:+:2132495091:-1 HG:+:2228916202:-1 HG:+:2335700989:-1 HG:+:2357030072:-1 HG:+:2387748639:-1 HG:+:2578932023:-1 HG:+:2616312590:-1 HG:+:2704939578:-1 HG:+:2721859231:-1 HG:+:2815865224:-1 HG:+:2862944802:-1 HG:+:2875103552:-1 HG:+:2972263762:-1 HG:+:3041371899:-1 HG:+:3056943818:-1 HG:+:3096559932:-1 HG:+:3099482645:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGATGGAGCTTGCAGTGAGCCGAGAACGTGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGATTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTAAGGAGGCAGTCTTTAGGCTAGACCTTGATTTAA HG:+:244488540:-1 HG:+:310613418:-1 HG:+:333121476:-1 HG:+:355210402:-1 HG:+:437943838:-1 HG:+:451971444:-1 HG:+:865246556:-1 HG:+:885378818:-1 HG:+:896538433:-1 HG:+:906828071:-1 HG:+:919385298:-1 HG:+:1011895734:-1 HG:+:1029310799:-1 HG:+:1077256432:-1 HG:+:1185267700:-1 HG:+:1618354993:-1 HG:+:1685803046:-1 HG:+:1697677149:-1 HG:+:1758040467:-1 HG:+:1990373959:-1 HG:+:1993957646:-1 HG:+:2154292039:-1 HG:+:2350797075:-1 HG:+:2436983835:-1 HG:+:2521177571:-1 HG:+:2687726222:-1 HG:+:2767943516:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGATGGAGCTTGCAGTGAGCCGAGAACGTGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGATTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTAAGGAGGCAGTCTTTAGGCTAGACCTTGATTTAA HG:+:47050009:-1 HG:+:118500092:-1 HG:+:159645210:-1 HG:+:167585864:-1 HG:+:213243999:-1 HG:+:246616969:-1 HG:+:387208471:-1 HG:+:499333810:-1 HG:+:553545425:-1 HG:+:812670410:-1 HG:+:916687222:-1 HG:+:973385181:-1 HG:+:1139581957:-1 HG:+:1142756221:-1 HG:+:1219871988:-1 HG:+:1234923723:-1 HG:+:1299424157:-1 HG:+:1460122724:-1 HG:+:1464358025:-1 HG:+:1477278082:-1 HG:+:1478292886:-1 HG:+:1524793443:-1 HG:+:1578758300:-1 HG:+:1580074617:-1 HG:+:1580903336:-1 HG:+:1756970202:-1 HG:+:1785759726:-1 HG:+:1822020481:-1 HG:+:1841916012:-1 HG:+:1921910400:-1 HG:+:1962761359:-1 HG:+:2022759423:-1 HG:+:2234760314:-1 HG:+:2248493033:-1 HG:+:2286497547:-1 HG:+:2295079010:-1 HG:+:2439717133:-1 HG:+:2441372573:-1 HG:+:2464148589:-1 HG:+:2764776597:-1 HG:+:2765377510:-1 HG:+:2824425023:-1 HG:+:2857658036:-1 HG:+:2860443360:-1 HG:+:2958358756:-1 HG:+:2961688854:-1 HG:+:3032055578:-1 HG:+:3054341208:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGATGGAGCTTGCAGTGAGCCGAGAACGTGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGATTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTAAGGAGGCAGTCTTTAGGCTAGACCTTGATTTAA HG:+:74619521:-1 HG:+:336478279:-1 HG:+:416493438:-1 HG:+:500153059:-1 HG:+:959664501:-1 HG:+:1060693258:-1 HG:+:1126448107:-1 HG:+:1196246201:-1 HG:+:1495629383:-1 HG:+:1848963597:-1 HG:+:2275835664:-1 HG:+:2425260976:-1 HG:+:2642984308:-1 HG:+:2987893120:-1 HG:+:3055429865:-1 HG:+:3057190215:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGATGGAGCTTGCAGTGAGCCGAGAACGTGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGATTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTAAGGAGGCAGTCTTTAGGCTAGACCTTGATTTAA HG:+:45766778:-1 HG:+:801520581:-1 HG:+:1152902598:-1 HG:+:1260973787:-1 HG:+:1299131289:-1 HG:+:1331776338:-1 HG:+:1755475705:-1 HG:+:1778859420:-1 HG:+:1806013082:-1 HG:+:1934374266:-1 HG:+:1955373943:-1 HG:+:1958959915:-1 HG:+:2021734074:-1 HG:+:2144378678:-1 HG:+:2181031661:-1 HG:+:2235303972:-1 HG:+:2502917282:-1 HG:+:2506300350:-1 HG:+:2696455678:-1 HG:+:2716091367:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGATGGAGCTTGCAGTGAGCCGAGAACGTGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGATTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTAAGGAGGCAGTCTTTAGGCTAGACCTTGATTTAA HG:+:4152254:-1 HG:+:24364853:-1 HG:+:97651998:-1 HG:+:202918303:-1 HG:+:612474425:-1 HG:+:1059965428:-1 HG:+:1261697592:-1 HG:+:1413546433:-1 HG:+:2067867573:-1 HG:+:2084605979:-1 HG:+:2263490872:-1 HG:+:2299780055:-1 HG:+:2660892759:-1 HG:+:2716011839:-1 HG:+:2868631686:-1 HG:+:2872324962:-1 HG:+:2974326372:-1 HG:+:3026348867:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGATGGAGCTTGCAGTGAGCCGAGAACGTGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGATTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTAAGGAGGCAGTCTTTAGGCTAGACCTTGATTTAA HG:+:288099462:-1 HG:+:351877253:-1 HG:+:380701221:-1 HG:+:381307908:-1 HG:+:639042136:-1 HG:+:893642146:-1 HG:+:1308325328:-1 HG:+:1308539487:-1 HG:+:1951637071:-1 HG:+:2009138168:-1 HG:+:2372549190:-1 HG:+:2396586733:-1 HG:+:2491864559:-1 HG:+:2498640189:-1 HG:+:2527190326:-1 HG:+:2576802994:-1 HG:+:2665152940:-1 HG:+:2800433868:-1 HG:+:2989604849:-1 HG:+:3008751667:-1 +TGTTATAGTTCACGATGTAAAGAAAAAACTTTTAGGCCAACCTTTAAAATACGTAGGGAGGCGGGCAGGGCACAGTGGCTCACCGCCTGTAATTCCAGGCACTTTGAAGAGGCGAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCAGCCTGGCTATACTAAAAATACAAAAAATTACCCGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGATGGAGCTTGCAGTGAGCCGAGAACGTGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGATTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTAAGGAGGCAGTCTTTAGGCTAGACCTTGATTTAA HG:+:101107885:-1 HG:+:228719681:-1 HG:+:313165755:-1 HG:+:452271803:-1 HG:+:819435350:-1 HG:+:1104456491:-1 HG:+:1361266379:-1 HG:+:1529530699:-1 HG:+:2264176805:-1 HG:+:2347537657:-1 HG:+:2513733940:-1 HG:+:2545978075:-1 HG:+:2630161328:-1 HG:+:2662127126:-1 HG:+:2691058193:-1 HG:+:2805397919:-1 HG:+:2806427962:-1 +TTAAATCAAGGTCTAGCCTAAAGACTGCCTCCTTACATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAATCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACGTTCTCGGCTCACTGCAAGCTCCATCTCCTGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCACCACCACGCCCGGGTAATTTTTTGTATTTTTAGTATAGCCAGGCTGGTCTCGATCTCCTGACCTCGTGATCTGCCCGCCTCGCCTCTTCAAAGTGCCTGGAATTACAGGCGGTGAGCCACTGTGCCCTGCCCGCCTCCCTACGTATTTTAAAGGTTGGCCTAAAAGTTTTTTCTTTACATCGTGAACTATAACA HG:+:29320568:-1 HG:+:156598802:-1 HG:+:232060287:-1 HG:+:422121595:-1 HG:+:480937800:-1 HG:+:483076712:-1 HG:+:1049361200:-1 HG:+:1171885462:-1 HG:+:1198209183:-1 HG:+:1261706014:-1 HG:+:1524269443:-1 HG:+:1550251446:-1 HG:+:1702112871:-1 HG:+:1876151305:9 HG:+:1972076705:-1 HG:+:2045008497:-1 HG:+:2291653780:-1 HG:+:2391698206:-1 HG:+:2477421340:-1 HG:+:2481815234:-1 HG:+:2568788598:-1 HG:+:2625544689:-1 HG:+:2681991267:-1 HG:+:2858553233:-1 HG:+:2868028380:-1 +TTAAATCAAGGTCTAGCCTAAAGACTGCCTCCTTACATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAATCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACGTTCTCGGCTCACTGCAAGCTCCATCTCCTGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCACCACCACGCCCGGGTAATTTTTTGTATTTTTAGTATAGCCAGGCTGGTCTCGATCTCCTGACCTCGTGATCTGCCCGCCTCGCCTCTTCAAAGTGCCTGGAATTACAGGCGGTGAGCCACTGTGCCCTGCCCGCCTCCCTACGTATTTTAAAGGTTGGCCTAAAAGTTTTTTCTTTACATCGTGAACTATAACA HG:+:1876151304:9 +TTAAATCAAGGTCTAGCCTAAAGACTGCCTCCTTACATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAATCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACGTTCTCGGCTCACTGCAAGCTCCATCTCCTGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCACCACCACGCCCGGGTAATTTTTTGTATTTTTAGTATAGCCAGGCTGGTCTCGATCTCCTGACCTCGTGATCTGCCCGCCTCGCCTCTTCAAAGTGCCTGGAATTACAGGCGGTGAGCCACTGTGCCCTGCCCGCCTCCCTACGTATTTTAAAGGTTGGCCTAAAAGTTTTTTCTTTACATCGTGAACTATAACA HG:+:2007846108:-1 +TTAAATCAAGGTCTAGCCTAAAGACTGCCTCCTTACATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAATCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACGTTCTCGGCTCACTGCAAGCTCCATCTCCTGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCACCACCACGCCCGGGTAATTTTTTGTATTTTTAGTATAGCCAGGCTGGTCTCGATCTCCTGACCTCGTGATCTGCCCGCCTCGCCTCTTCAAAGTGCCTGGAATTACAGGCGGTGAGCCACTGTGCCCTGCCCGCCTCCCTACGTATTTTAAAGGTTGGCCTAAAAGTTTTTTCTTTACATCGTGAACTATAACA HG:+:1876151302:9 +CTAACACTCAGATACGAACACATAGCAATCCTATATCAATGCTATCCTATTCCTGGATAGCGATCGTGCCATAAGGAACCCAGTTTGCAGGACTCATCATTGAAGTTTGGGCATTTCAGAAAGAGAAAGATTAATGCCTTCCTTTTTTATATAAAACAACCAGCCGTTATAGAGTTTCCATCTAAAAATAATTTCTTCATCAAATATATTCTAAAAAAATTTGCTTACTGGCTTATAGGCTCCCTCTTGAGTATTCAAATATATACTAACATATTAAACAGCTCTGAGAAGTCATATTGCAAAACCCAACTCTTTTAACTTTACTTAACCAGCCATTGCCCAATCTGTTGACCACAAGAGCATTTTTCATGGTGTGTTTCAGTATAACTCTATGGTATAC HG:+:330830721:25 HG:+:783333098:23 HG:+:2190283688:-1 +CTAACACTCAGATACGAACACATAGCAATCCTATATCAATGCTATCCTATTCCTGGATAGCGATCGTGCCATAAGGAACCCAGTTTGCAGGACTCATCATTGAAGTTTGGGCATTTCAGAAAGAGAAAGATTAATGCCTTCCTTTTTTATATAAAACAACCAGCCGTTATAGAGTTTCCATCTAAAAATAATTTCTTCATCAAATATATTCTAAAAAAATTTGCTTACTGGCTTATAGGCTCCCTCTTGAGTATTCAAATATATACTAACATATTAAACAGCTCTGAGAAGTCATATTGCAAAACCCAACTCTTTTAACTTTACTTAACCAGCCATTGCCCAATCTGTTGACCACAAGAGCATTTTTCATGGTGTGTTTCAGTATAACTCTATGGTATAC HG:+:330830717:25 HG:+:783333094:23 +CTAACACTCAGATACGAACACATAGCAATCCTATATCAATGCTATCCTATTCCTGGATAGCGATCGTGCCATAAGGAACCCAGTTTGCAGGACTCATCATTGAAGTTTGGGCATTTCAGAAAGAGAAAGATTAATGCCTTCCTTTTTTATATAAAACAACCAGCCGTTATAGAGTTTCCATCTAAAAATAATTTCTTCATCAAATATATTCTAAAAAAATTTGCTTACTGGCTTATAGGCTCCCTCTTGAGTATTCAAATATATACTAACATATTAAACAGCTCTGAGAAGTCATATTGCAAAACCCAACTCTTTTAACTTTACTTAACCAGCCATTGCCCAATCTGTTGACCACAAGAGCATTTTTCATGGTGTGTTTCAGTATAACTCTATGGTATAC HG:+:330830725:25 HG:+:783333102:23 +CTAACACTCAGATACGAACACATAGCAATCCTATATCAATGCTATCCTATTCCTGGATAGCGATCGTGCCATAAGGAACCCAGTTTGCAGGACTCATCATTGAAGTTTGGGCATTTCAGAAAGAGAAAGATTAATGCCTTCCTTTTTTATATAAAACAACCAGCCGTTATAGAGTTTCCATCTAAAAATAATTTCTTCATCAAATATATTCTAAAAAAATTTGCTTACTGGCTTATAGGCTCCCTCTTGAGTATTCAAATATATACTAACATATTAAACAGCTCTGAGAAGTCATATTGCAAAACCCAACTCTTTTAACTTTACTTAACCAGCCATTGCCCAATCTGTTGACCACAAGAGCATTTTTCATGGTGTGTTTCAGTATAACTCTATGGTATAC HG:+:330830727:25 HG:+:783333104:23 +CTAACACTCAGATACGAACACATAGCAATCCTATATCAATGCTATCCTATTCCTGGATAGCGATCGTGCCATAAGGAACCCAGTTTGCAGGACTCATCATTGAAGTTTGGGCATTTCAGAAAGAGAAAGATTAATGCCTTCCTTTTTTATATAAAACAACCAGCCGTTATAGAGTTTCCATCTAAAAATAATTTCTTCATCAAATATATTCTAAAAAAATTTGCTTACTGGCTTATAGGCTCCCTCTTGAGTATTCAAATATATACTAACATATTAAACAGCTCTGAGAAGTCATATTGCAAAACCCAACTCTTTTAACTTTACTTAACCAGCCATTGCCCAATCTGTTGACCACAAGAGCATTTTTCATGGTGTGTTTCAGTATAACTCTATGGTATAC HG:+:330830726:25 HG:+:783333103:23 +CTAACACTCAGATACGAACACATAGCAATCCTATATCAATGCTATCCTATTCCTGGATAGCGATCGTGCCATAAGGAACCCAGTTTGCAGGACTCATCATTGAAGTTTGGGCATTTCAGAAAGAGAAAGATTAATGCCTTCCTTTTTTATATAAAACAACCAGCCGTTATAGAGTTTCCATCTAAAAATAATTTCTTCATCAAATATATTCTAAAAAAATTTGCTTACTGGCTTATAGGCTCCCTCTTGAGTATTCAAATATATACTAACATATTAAACAGCTCTGAGAAGTCATATTGCAAAACCCAACTCTTTTAACTTTACTTAACCAGCCATTGCCCAATCTGTTGACCACAAGAGCATTTTTCATGGTGTGTTTCAGTATAACTCTATGGTATAC HG:+:682042161:-1 HG:+:1135409265:-1 HG:+:1324381740:-1 HG:+:1423286729:-1 HG:+:1767885000:-1 HG:+:2616064595:-1 +GTATACCATAGAGTTATACTGAAACACACCATGAAAAATGCTCTTGTGGTCAACAGATTGGGCAATGGCTGGTTAAGTAAAGTTAAAAGAGTTGGGTTTTGCAATATGACTTCTCAGAGCTGTTTAATATGTTAGTATATATTTGAATACTCAAGAGGGAGCCTATAAGCCAGTAAGCAAATTTTTTTAGAATATATTTGATGAAGAAATTATTTTTAGATGGAAACTCTATAACGGCTGGTTGTTTTATATAAAAAAGGAAGGCATTAATCTTTCTCTTTCTGAAATGCCCAAACTTCAATGATGAGTCCTGCAAACTGGGTTCCTTATGGCACGATCGCTATCCAGGAATAGGATAGCATTGATATAGGATTGCTATGTGTTCGTATCTGAGTGTTAG HG:+:246866265:-1 HG:+:430695821:29 HG:+:1132493991:-1 HG:+:1624736716:-1 HG:+:2461283616:-1 HG:+:2797697130:-1 +GTATACCATAGAGTTATACTGAAACACACCATGAAAAATGCTCTTGTGGTCAACAGATTGGGCAATGGCTGGTTAAGTAAAGTTAAAAGAGTTGGGTTTTGCAATATGACTTCTCAGAGCTGTTTAATATGTTAGTATATATTTGAATACTCAAGAGGGAGCCTATAAGCCAGTAAGCAAATTTTTTTAGAATATATTTGATGAAGAAATTATTTTTAGATGGAAACTCTATAACGGCTGGTTGTTTTATATAAAAAAGGAAGGCATTAATCTTTCTCTTTCTGAAATGCCCAAACTTCAATGATGAGTCCTGCAAACTGGGTTCCTTATGGCACGATCGCTATCCAGGAATAGGATAGCATTGATATAGGATTGCTATGTGTTCGTATCTGAGTGTTAG HG:+:430695815:29 +GTATACCATAGAGTTATACTGAAACACACCATGAAAAATGCTCTTGTGGTCAACAGATTGGGCAATGGCTGGTTAAGTAAAGTTAAAAGAGTTGGGTTTTGCAATATGACTTCTCAGAGCTGTTTAATATGTTAGTATATATTTGAATACTCAAGAGGGAGCCTATAAGCCAGTAAGCAAATTTTTTTAGAATATATTTGATGAAGAAATTATTTTTAGATGGAAACTCTATAACGGCTGGTTGTTTTATATAAAAAAGGAAGGCATTAATCTTTCTCTTTCTGAAATGCCCAAACTTCAATGATGAGTCCTGCAAACTGGGTTCCTTATGGCACGATCGCTATCCAGGAATAGGATAGCATTGATATAGGATTGCTATGTGTTCGTATCTGAGTGTTAG HG:+:430695822:29 +GTATACCATAGAGTTATACTGAAACACACCATGAAAAATGCTCTTGTGGTCAACAGATTGGGCAATGGCTGGTTAAGTAAAGTTAAAAGAGTTGGGTTTTGCAATATGACTTCTCAGAGCTGTTTAATATGTTAGTATATATTTGAATACTCAAGAGGGAGCCTATAAGCCAGTAAGCAAATTTTTTTAGAATATATTTGATGAAGAAATTATTTTTAGATGGAAACTCTATAACGGCTGGTTGTTTTATATAAAAAAGGAAGGCATTAATCTTTCTCTTTCTGAAATGCCCAAACTTCAATGATGAGTCCTGCAAACTGGGTTCCTTATGGCACGATCGCTATCCAGGAATAGGATAGCATTGATATAGGATTGCTATGTGTTCGTATCTGAGTGTTAG HG:+:430695812:29 +GTATACCATAGAGTTATACTGAAACACACCATGAAAAATGCTCTTGTGGTCAACAGATTGGGCAATGGCTGGTTAAGTAAAGTTAAAAGAGTTGGGTTTTGCAATATGACTTCTCAGAGCTGTTTAATATGTTAGTATATATTTGAATACTCAAGAGGGAGCCTATAAGCCAGTAAGCAAATTTTTTTAGAATATATTTGATGAAGAAATTATTTTTAGATGGAAACTCTATAACGGCTGGTTGTTTTATATAAAAAAGGAAGGCATTAATCTTTCTCTTTCTGAAATGCCCAAACTTCAATGATGAGTCCTGCAAACTGGGTTCCTTATGGCACGATCGCTATCCAGGAATAGGATAGCATTGATATAGGATTGCTATGTGTTCGTATCTGAGTGTTAG HG:+:430695811:29 +GTATACCATAGAGTTATACTGAAACACACCATGAAAAATGCTCTTGTGGTCAACAGATTGGGCAATGGCTGGTTAAGTAAAGTTAAAAGAGTTGGGTTTTGCAATATGACTTCTCAGAGCTGTTTAATATGTTAGTATATATTTGAATACTCAAGAGGGAGCCTATAAGCCAGTAAGCAAATTTTTTTAGAATATATTTGATGAAGAAATTATTTTTAGATGGAAACTCTATAACGGCTGGTTGTTTTATATAAAAAAGGAAGGCATTAATCTTTCTCTTTCTGAAATGCCCAAACTTCAATGATGAGTCCTGCAAACTGGGTTCCTTATGGCACGATCGCTATCCAGGAATAGGATAGCATTGATATAGGATTGCTATGTGTTCGTATCTGAGTGTTAG HG:+:430695813:29 +GTATACCATAGAGTTATACTGAAACACACCATGAAAAATGCTCTTGTGGTCAACAGATTGGGCAATGGCTGGTTAAGTAAAGTTAAAAGAGTTGGGTTTTGCAATATGACTTCTCAGAGCTGTTTAATATGTTAGTATATATTTGAATACTCAAGAGGGAGCCTATAAGCCAGTAAGCAAATTTTTTTAGAATATATTTGATGAAGAAATTATTTTTAGATGGAAACTCTATAACGGCTGGTTGTTTTATATAAAAAAGGAAGGCATTAATCTTTCTCTTTCTGAAATGCCCAAACTTCAATGATGAGTCCTGCAAACTGGGTTCCTTATGGCACGATCGCTATCCAGGAATAGGATAGCATTGATATAGGATTGCTATGTGTTCGTATCTGAGTGTTAG HG:+:430695824:29 +GTATACCATAGAGTTATACTGAAACACACCATGAAAAATGCTCTTGTGGTCAACAGATTGGGCAATGGCTGGTTAAGTAAAGTTAAAAGAGTTGGGTTTTGCAATATGACTTCTCAGAGCTGTTTAATATGTTAGTATATATTTGAATACTCAAGAGGGAGCCTATAAGCCAGTAAGCAAATTTTTTTAGAATATATTTGATGAAGAAATTATTTTTAGATGGAAACTCTATAACGGCTGGTTGTTTTATATAAAAAAGGAAGGCATTAATCTTTCTCTTTCTGAAATGCCCAAACTTCAATGATGAGTCCTGCAAACTGGGTTCCTTATGGCACGATCGCTATCCAGGAATAGGATAGCATTGATATAGGATTGCTATGTGTTCGTATCTGAGTGTTAG HG:+:573858811:-1 +TCTGACTGTCCCAGATCACTCCCAGGGTAGGCACGGTACTTTCGCTCGGGAGAGAGGCAGGCTCCAGAGGAGGGACACAGAGCAGGTAGGGAGGGCTTTGAGACATCCCCACCTGGCTCTGCCCAGGGCACATGGCCTTTTCTGGGAGGGAGCCCTTTCTCAGGGGGATCAGGGACCCACGGTCAGGAACCTCAGGACAGCAGCTGAAGCTGGCCTCCCTCCTTCCCTGGGCAGACACGGACGGCCTCTGAACTCCCTATTTGGGCTCCAGCCTCACCCCTTCCAACCCATCCCCCTGAGTGGGCGGCGGAGGGGCTTTCCGAGGGACAGACTGAAGATCTCGTGACTCCCCCGCCTCAGATACTGTATGGCTTCCTACTGCTCATGTAATGACATCCAC HG:+:159430320:-1 HG:+:1507790846:-1 HG:+:1524542890:-1 HG:+:1739902557:-1 HG:+:1991841827:-1 +TCTGACTGTCCCAGATCACTCCCAGGGTAGGCACGGTACTTTCGCTCGGGAGAGAGGCAGGCTCCAGAGGAGGGACACAGAGCAGGTAGGGAGGGCTTTGAGACATCCCCACCTGGCTCTGCCCAGGGCACATGGCCTTTTCTGGGAGGGAGCCCTTTCTCAGGGGGATCAGGGACCCACGGTCAGGAACCTCAGGACAGCAGCTGAAGCTGGCCTCCCTCCTTCCCTGGGCAGACACGGACGGCCTCTGAACTCCCTATTTGGGCTCCAGCCTCACCCCTTCCAACCCATCCCCCTGAGTGGGCGGCGGAGGGGCTTTCCGAGGGACAGACTGAAGATCTCGTGACTCCCCCGCCTCAGATACTGTATGGCTTCCTACTGCTCATGTAATGACATCCAC HG:+:94506443:-1 HG:+:1056860875:-1 HG:+:1095524788:-1 HG:+:1655814785:-1 HG:+:1881588239:-1 HG:+:2250021588:-1 HG:+:2627183753:-1 +TCTGACTGTCCCAGATCACTCCCAGGGTAGGCACGGTACTTTCGCTCGGGAGAGAGGCAGGCTCCAGAGGAGGGACACAGAGCAGGTAGGGAGGGCTTTGAGACATCCCCACCTGGCTCTGCCCAGGGCACATGGCCTTTTCTGGGAGGGAGCCCTTTCTCAGGGGGATCAGGGACCCACGGTCAGGAACCTCAGGACAGCAGCTGAAGCTGGCCTCCCTCCTTCCCTGGGCAGACACGGACGGCCTCTGAACTCCCTATTTGGGCTCCAGCCTCACCCCTTCCAACCCATCCCCCTGAGTGGGCGGCGGAGGGGCTTTCCGAGGGACAGACTGAAGATCTCGTGACTCCCCCGCCTCAGATACTGTATGGCTTCCTACTGCTCATGTAATGACATCCAC HG:+:279332545:-1 HG:+:728934120:-1 HG:+:1414786427:-1 HG:+:2245385143:-1 +TCTGACTGTCCCAGATCACTCCCAGGGTAGGCACGGTACTTTCGCTCGGGAGAGAGGCAGGCTCCAGAGGAGGGACACAGAGCAGGTAGGGAGGGCTTTGAGACATCCCCACCTGGCTCTGCCCAGGGCACATGGCCTTTTCTGGGAGGGAGCCCTTTCTCAGGGGGATCAGGGACCCACGGTCAGGAACCTCAGGACAGCAGCTGAAGCTGGCCTCCCTCCTTCCCTGGGCAGACACGGACGGCCTCTGAACTCCCTATTTGGGCTCCAGCCTCACCCCTTCCAACCCATCCCCCTGAGTGGGCGGCGGAGGGGCTTTCCGAGGGACAGACTGAAGATCTCGTGACTCCCCCGCCTCAGATACTGTATGGCTTCCTACTGCTCATGTAATGACATCCAC HG:+:321635702:-1 HG:+:478668956:-1 HG:+:541079244:-1 HG:+:632921172:-1 HG:+:1005640906:-1 HG:+:2521350694:-1 HG:+:2688946307:-1 +TCTGACTGTCCCAGATCACTCCCAGGGTAGGCACGGTACTTTCGCTCGGGAGAGAGGCAGGCTCCAGAGGAGGGACACAGAGCAGGTAGGGAGGGCTTTGAGACATCCCCACCTGGCTCTGCCCAGGGCACATGGCCTTTTCTGGGAGGGAGCCCTTTCTCAGGGGGATCAGGGACCCACGGTCAGGAACCTCAGGACAGCAGCTGAAGCTGGCCTCCCTCCTTCCCTGGGCAGACACGGACGGCCTCTGAACTCCCTATTTGGGCTCCAGCCTCACCCCTTCCAACCCATCCCCCTGAGTGGGCGGCGGAGGGGCTTTCCGAGGGACAGACTGAAGATCTCGTGACTCCCCCGCCTCAGATACTGTATGGCTTCCTACTGCTCATGTAATGACATCCAC HG:+:55047061:-1 HG:+:62689761:-1 HG:+:212802760:-1 HG:+:234794843:-1 HG:+:271924435:-1 HG:+:336301545:-1 HG:+:812171390:-1 HG:+:817371319:-1 HG:+:939339986:-1 HG:+:1007504554:-1 HG:+:1096434183:-1 HG:+:1277461017:-1 HG:+:1376307929:-1 HG:+:2160694940:-1 HG:+:2195937382:-1 HG:+:2305377354:-1 HG:+:2343789282:-1 HG:+:2527745571:-1 HG:+:2827569319:-1 HG:+:3020574887:-1 +TCTGACTGTCCCAGATCACTCCCAGGGTAGGCACGGTACTTTCGCTCGGGAGAGAGGCAGGCTCCAGAGGAGGGACACAGAGCAGGTAGGGAGGGCTTTGAGACATCCCCACCTGGCTCTGCCCAGGGCACATGGCCTTTTCTGGGAGGGAGCCCTTTCTCAGGGGGATCAGGGACCCACGGTCAGGAACCTCAGGACAGCAGCTGAAGCTGGCCTCCCTCCTTCCCTGGGCAGACACGGACGGCCTCTGAACTCCCTATTTGGGCTCCAGCCTCACCCCTTCCAACCCATCCCCCTGAGTGGGCGGCGGAGGGGCTTTCCGAGGGACAGACTGAAGATCTCGTGACTCCCCCGCCTCAGATACTGTATGGCTTCCTACTGCTCATGTAATGACATCCAC HG:+:12119198:-1 HG:+:163380142:-1 HG:+:857827613:-1 HG:+:1067233112:-1 HG:+:1363664918:-1 HG:+:2693761640:-1 +TCTGACTGTCCCAGATCACTCCCAGGGTAGGCACGGTACTTTCGCTCGGGAGAGAGGCAGGCTCCAGAGGAGGGACACAGAGCAGGTAGGGAGGGCTTTGAGACATCCCCACCTGGCTCTGCCCAGGGCACATGGCCTTTTCTGGGAGGGAGCCCTTTCTCAGGGGGATCAGGGACCCACGGTCAGGAACCTCAGGACAGCAGCTGAAGCTGGCCTCCCTCCTTCCCTGGGCAGACACGGACGGCCTCTGAACTCCCTATTTGGGCTCCAGCCTCACCCCTTCCAACCCATCCCCCTGAGTGGGCGGCGGAGGGGCTTTCCGAGGGACAGACTGAAGATCTCGTGACTCCCCCGCCTCAGATACTGTATGGCTTCCTACTGCTCATGTAATGACATCCAC HG:+:351285677:-1 HG:+:366807493:-1 HG:+:1259265175:-1 HG:+:2855892720:-1 +TCTGACTGTCCCAGATCACTCCCAGGGTAGGCACGGTACTTTCGCTCGGGAGAGAGGCAGGCTCCAGAGGAGGGACACAGAGCAGGTAGGGAGGGCTTTGAGACATCCCCACCTGGCTCTGCCCAGGGCACATGGCCTTTTCTGGGAGGGAGCCCTTTCTCAGGGGGATCAGGGACCCACGGTCAGGAACCTCAGGACAGCAGCTGAAGCTGGCCTCCCTCCTTCCCTGGGCAGACACGGACGGCCTCTGAACTCCCTATTTGGGCTCCAGCCTCACCCCTTCCAACCCATCCCCCTGAGTGGGCGGCGGAGGGGCTTTCCGAGGGACAGACTGAAGATCTCGTGACTCCCCCGCCTCAGATACTGTATGGCTTCCTACTGCTCATGTAATGACATCCAC HG:+:278963361:-1 HG:+:507075740:-1 HG:+:1489076498:-1 HG:+:1538420672:-1 HG:+:1880363489:-1 HG:+:2053006148:-1 HG:+:2075856503:-1 HG:+:2515824623:-1 HG:+:2576510933:-1 HG:+:2662831930:-1 HG:+:2736968982:-1 HG:+:2880250615:-1 +TCTGACTGTCCCAGATCACTCCCAGGGTAGGCACGGTACTTTCGCTCGGGAGAGAGGCAGGCTCCAGAGGAGGGACACAGAGCAGGTAGGGAGGGCTTTGAGACATCCCCACCTGGCTCTGCCCAGGGCACATGGCCTTTTCTGGGAGGGAGCCCTTTCTCAGGGGGATCAGGGACCCACGGTCAGGAACCTCAGGACAGCAGCTGAAGCTGGCCTCCCTCCTTCCCTGGGCAGACACGGACGGCCTCTGAACTCCCTATTTGGGCTCCAGCCTCACCCCTTCCAACCCATCCCCCTGAGTGGGCGGCGGAGGGGCTTTCCGAGGGACAGACTGAAGATCTCGTGACTCCCCCGCCTCAGATACTGTATGGCTTCCTACTGCTCATGTAATGACATCCAC HG:+:677649844:-1 +GTGGATGTCATTACATGAGCAGTAGGAAGCCATACAGTATCTGAGGCGGGGGAGTCACGAGATCTTCAGTCTGTCCCTCGGAAAGCCCCTCCGCCGCCCACTCAGGGGGATGGGTTGGAAGGGGTGAGGCTGGAGCCCAAATAGGGAGTTCAGAGGCCGTCCGTGTCTGCCCAGGGAAGGAGGGAGGCCAGCTTCAGCTGCTGTCCTGAGGTTCCTGACCGTGGGTCCCTGATCCCCCTGAGAAAGGGCTCCCTCCCAGAAAAGGCCATGTGCCCTGGGCAGAGCCAGGTGGGGATGTCTCAAAGCCCTCCCTACCTGCTCTGTGTCCCTCCTCTGGAGCCTGCCTCTCTCCCGAGCGAAAGTACCGTGCCTACCCTGGGAGTGATCTGGGACAGTCAGA HG:+:1818682211:19 +GTGGATGTCATTACATGAGCAGTAGGAAGCCATACAGTATCTGAGGCGGGGGAGTCACGAGATCTTCAGTCTGTCCCTCGGAAAGCCCCTCCGCCGCCCACTCAGGGGGATGGGTTGGAAGGGGTGAGGCTGGAGCCCAAATAGGGAGTTCAGAGGCCGTCCGTGTCTGCCCAGGGAAGGAGGGAGGCCAGCTTCAGCTGCTGTCCTGAGGTTCCTGACCGTGGGTCCCTGATCCCCCTGAGAAAGGGCTCCCTCCCAGAAAAGGCCATGTGCCCTGGGCAGAGCCAGGTGGGGATGTCTCAAAGCCCTCCCTACCTGCTCTGTGTCCCTCCTCTGGAGCCTGCCTCTCTCCCGAGCGAAAGTACCGTGCCTACCCTGGGAGTGATCTGGGACAGTCAGA HG:+:1818682210:19 +GTGGATGTCATTACATGAGCAGTAGGAAGCCATACAGTATCTGAGGCGGGGGAGTCACGAGATCTTCAGTCTGTCCCTCGGAAAGCCCCTCCGCCGCCCACTCAGGGGGATGGGTTGGAAGGGGTGAGGCTGGAGCCCAAATAGGGAGTTCAGAGGCCGTCCGTGTCTGCCCAGGGAAGGAGGGAGGCCAGCTTCAGCTGCTGTCCTGAGGTTCCTGACCGTGGGTCCCTGATCCCCCTGAGAAAGGGCTCCCTCCCAGAAAAGGCCATGTGCCCTGGGCAGAGCCAGGTGGGGATGTCTCAAAGCCCTCCCTACCTGCTCTGTGTCCCTCCTCTGGAGCCTGCCTCTCTCCCGAGCGAAAGTACCGTGCCTACCCTGGGAGTGATCTGGGACAGTCAGA HG:+:1818682214:19 +GTGGATGTCATTACATGAGCAGTAGGAAGCCATACAGTATCTGAGGCGGGGGAGTCACGAGATCTTCAGTCTGTCCCTCGGAAAGCCCCTCCGCCGCCCACTCAGGGGGATGGGTTGGAAGGGGTGAGGCTGGAGCCCAAATAGGGAGTTCAGAGGCCGTCCGTGTCTGCCCAGGGAAGGAGGGAGGCCAGCTTCAGCTGCTGTCCTGAGGTTCCTGACCGTGGGTCCCTGATCCCCCTGAGAAAGGGCTCCCTCCCAGAAAAGGCCATGTGCCCTGGGCAGAGCCAGGTGGGGATGTCTCAAAGCCCTCCCTACCTGCTCTGTGTCCCTCCTCTGGAGCCTGCCTCTCTCCCGAGCGAAAGTACCGTGCCTACCCTGGGAGTGATCTGGGACAGTCAGA HG:+:1818682209:19 +GTGGATGTCATTACATGAGCAGTAGGAAGCCATACAGTATCTGAGGCGGGGGAGTCACGAGATCTTCAGTCTGTCCCTCGGAAAGCCCCTCCGCCGCCCACTCAGGGGGATGGGTTGGAAGGGGTGAGGCTGGAGCCCAAATAGGGAGTTCAGAGGCCGTCCGTGTCTGCCCAGGGAAGGAGGGAGGCCAGCTTCAGCTGCTGTCCTGAGGTTCCTGACCGTGGGTCCCTGATCCCCCTGAGAAAGGGCTCCCTCCCAGAAAAGGCCATGTGCCCTGGGCAGAGCCAGGTGGGGATGTCTCAAAGCCCTCCCTACCTGCTCTGTGTCCCTCCTCTGGAGCCTGCCTCTCTCCCGAGCGAAAGTACCGTGCCTACCCTGGGAGTGATCTGGGACAGTCAGA HG:+:311166856:-1 +ATGGGGGCGCTGCAGGCATCAGGGCCGGCGCCGCGGGGCCTCTCGCGCCTCCTTCTAGGGCCCGCTTCCCGCCCGCACTGTTTTCCTTCCGGTTGTTCCGGAAGTCGGGTCCTCGAGGGCGGTGAGATCGGTTTCCGATTCCGGGGTGACCGGGGTGGCGGCGGCGGCGCTCCGGTCGCGATGGGCCAGAGGTAAGTGAGCCGCGGCCTGGGCGCTTCCTCCATTCCGGGCGGAGCGCCTGGGTTCTCCCGGCTACCCGCTCCCGGCCTCTGGGCCGTCCCTTTCTGGTTCTGCCGCCTCCAGCCCGGCGTCCGCGTCGCCTGCTCGCCGCCCGACTGAGCCGCTCCCGGGCGGCTGGGAGGCGGGGGTCCCCTGCAGCTCCTGCAGCATCGCCCGCCGG HG:+:177440756:-1 HG:+:202016090:-1 HG:+:696396384:-1 HG:+:1175633718:-1 HG:+:1231261723:-1 HG:+:1538083474:-1 HG:+:1538083510:-1 HG:+:1538083546:-1 HG:+:1538083582:-1 HG:+:1761179934:-1 HG:+:1947649205:-1 HG:+:2225116400:-1 HG:+:2498320794:-1 HG:+:2508627602:-1 HG:+:2510231286:-1 HG:+:2711776008:-1 HG:+:2774341960:-1 HG:+:2796806263:-1 +ATGGGGGCGCTGCAGGCATCAGGGCCGGCGCCGCGGGGCCTCTCGCGCCTCCTTCTAGGGCCCGCTTCCCGCCCGCACTGTTTTCCTTCCGGTTGTTCCGGAAGTCGGGTCCTCGAGGGCGGTGAGATCGGTTTCCGATTCCGGGGTGACCGGGGTGGCGGCGGCGGCGCTCCGGTCGCGATGGGCCAGAGGTAAGTGAGCCGCGGCCTGGGCGCTTCCTCCATTCCGGGCGGAGCGCCTGGGTTCTCCCGGCTACCCGCTCCCGGCCTCTGGGCCGTCCCTTTCTGGTTCTGCCGCCTCCAGCCCGGCGTCCGCGTCGCCTGCTCGCCGCCCGACTGAGCCGCTCCCGGGCGGCTGGGAGGCGGGGGTCCCCTGCAGCTCCTGCAGCATCGCCCGCCGG HG:+:729519052:-1 HG:+:2548286638:-1 +ATGGGGGCGCTGCAGGCATCAGGGCCGGCGCCGCGGGGCCTCTCGCGCCTCCTTCTAGGGCCCGCTTCCCGCCCGCACTGTTTTCCTTCCGGTTGTTCCGGAAGTCGGGTCCTCGAGGGCGGTGAGATCGGTTTCCGATTCCGGGGTGACCGGGGTGGCGGCGGCGGCGCTCCGGTCGCGATGGGCCAGAGGTAAGTGAGCCGCGGCCTGGGCGCTTCCTCCATTCCGGGCGGAGCGCCTGGGTTCTCCCGGCTACCCGCTCCCGGCCTCTGGGCCGTCCCTTTCTGGTTCTGCCGCCTCCAGCCCGGCGTCCGCGTCGCCTGCTCGCCGCCCGACTGAGCCGCTCCCGGGCGGCTGGGAGGCGGGGGTCCCCTGCAGCTCCTGCAGCATCGCCCGCCGG HG:+:2473544:-1 HG:+:62784133:-1 HG:+:152117331:-1 HG:+:206729988:-1 HG:+:259680800:-1 HG:+:451281528:-1 HG:+:688050247:-1 HG:+:805991848:-1 HG:+:957907640:-1 HG:+:1089465944:-1 HG:+:1171423567:-1 HG:+:1278568446:-1 HG:+:1375799537:-1 HG:+:1519313462:-1 HG:+:1702499635:-1 HG:+:1744506608:-1 HG:+:1938467134:-1 HG:+:1940979250:-1 HG:+:1944466985:-1 HG:+:2074770747:-1 HG:+:2396381482:-1 HG:+:2412894206:-1 HG:+:2501666241:-1 HG:+:2532538838:-1 HG:+:2542467941:-1 HG:+:2543869296:-1 HG:+:2545032767:-1 HG:+:2658522511:-1 HG:+:2698299101:-1 HG:+:2749834523:-1 HG:+:2882579935:-1 HG:+:3052416506:-1 +ATGGGGGCGCTGCAGGCATCAGGGCCGGCGCCGCGGGGCCTCTCGCGCCTCCTTCTAGGGCCCGCTTCCCGCCCGCACTGTTTTCCTTCCGGTTGTTCCGGAAGTCGGGTCCTCGAGGGCGGTGAGATCGGTTTCCGATTCCGGGGTGACCGGGGTGGCGGCGGCGGCGCTCCGGTCGCGATGGGCCAGAGGTAAGTGAGCCGCGGCCTGGGCGCTTCCTCCATTCCGGGCGGAGCGCCTGGGTTCTCCCGGCTACCCGCTCCCGGCCTCTGGGCCGTCCCTTTCTGGTTCTGCCGCCTCCAGCCCGGCGTCCGCGTCGCCTGCTCGCCGCCCGACTGAGCCGCTCCCGGGCGGCTGGGAGGCGGGGGTCCCCTGCAGCTCCTGCAGCATCGCCCGCCGG HG:+:1007636:-1 HG:+:64184527:-1 HG:+:92116390:-1 HG:+:1517347922:-1 HG:+:2305726725:-1 HG:+:2480621262:-1 HG:+:2665438375:-1 HG:+:2981910869:-1 +ATGGGGGCGCTGCAGGCATCAGGGCCGGCGCCGCGGGGCCTCTCGCGCCTCCTTCTAGGGCCCGCTTCCCGCCCGCACTGTTTTCCTTCCGGTTGTTCCGGAAGTCGGGTCCTCGAGGGCGGTGAGATCGGTTTCCGATTCCGGGGTGACCGGGGTGGCGGCGGCGGCGCTCCGGTCGCGATGGGCCAGAGGTAAGTGAGCCGCGGCCTGGGCGCTTCCTCCATTCCGGGCGGAGCGCCTGGGTTCTCCCGGCTACCCGCTCCCGGCCTCTGGGCCGTCCCTTTCTGGTTCTGCCGCCTCCAGCCCGGCGTCCGCGTCGCCTGCTCGCCGCCCGACTGAGCCGCTCCCGGGCGGCTGGGAGGCGGGGGTCCCCTGCAGCTCCTGCAGCATCGCCCGCCGG HG:+:6052889:-1 HG:+:620778018:-1 HG:+:1057230793:-1 HG:+:1059569022:-1 HG:+:1386113743:-1 HG:+:1525036083:-1 HG:+:1646849909:-1 HG:+:1653520614:-1 HG:+:1693501541:-1 HG:+:1768653855:-1 HG:+:1815110715:-1 HG:+:1890904525:-1 HG:+:2136792932:-1 HG:+:2409764935:-1 HG:+:2439071291:-1 HG:+:2440399779:-1 HG:+:2517632014:-1 HG:+:2526867437:-1 HG:+:2616201231:-1 HG:+:2764927534:-1 HG:+:2828285407:-1 HG:+:2865679664:-1 +ATGGGGGCGCTGCAGGCATCAGGGCCGGCGCCGCGGGGCCTCTCGCGCCTCCTTCTAGGGCCCGCTTCCCGCCCGCACTGTTTTCCTTCCGGTTGTTCCGGAAGTCGGGTCCTCGAGGGCGGTGAGATCGGTTTCCGATTCCGGGGTGACCGGGGTGGCGGCGGCGGCGCTCCGGTCGCGATGGGCCAGAGGTAAGTGAGCCGCGGCCTGGGCGCTTCCTCCATTCCGGGCGGAGCGCCTGGGTTCTCCCGGCTACCCGCTCCCGGCCTCTGGGCCGTCCCTTTCTGGTTCTGCCGCCTCCAGCCCGGCGTCCGCGTCGCCTGCTCGCCGCCCGACTGAGCCGCTCCCGGGCGGCTGGGAGGCGGGGGTCCCCTGCAGCTCCTGCAGCATCGCCCGCCGG HG:+:35500953:-1 HG:+:260228746:-1 HG:+:502329681:-1 HG:+:765211259:-1 HG:+:915807808:-1 HG:+:981340085:-1 HG:+:1120796665:-1 HG:+:1236504371:-1 HG:+:1277988043:-1 HG:+:1833714630:-1 HG:+:1953427340:-1 HG:+:2702183841:-1 +ATGGGGGCGCTGCAGGCATCAGGGCCGGCGCCGCGGGGCCTCTCGCGCCTCCTTCTAGGGCCCGCTTCCCGCCCGCACTGTTTTCCTTCCGGTTGTTCCGGAAGTCGGGTCCTCGAGGGCGGTGAGATCGGTTTCCGATTCCGGGGTGACCGGGGTGGCGGCGGCGGCGCTCCGGTCGCGATGGGCCAGAGGTAAGTGAGCCGCGGCCTGGGCGCTTCCTCCATTCCGGGCGGAGCGCCTGGGTTCTCCCGGCTACCCGCTCCCGGCCTCTGGGCCGTCCCTTTCTGGTTCTGCCGCCTCCAGCCCGGCGTCCGCGTCGCCTGCTCGCCGCCCGACTGAGCCGCTCCCGGGCGGCTGGGAGGCGGGGGTCCCCTGCAGCTCCTGCAGCATCGCCCGCCGG HG:+:1484792921:-1 HG:+:2411911705:-1 HG:+:2867433513:-1 +ATGGGGGCGCTGCAGGCATCAGGGCCGGCGCCGCGGGGCCTCTCGCGCCTCCTTCTAGGGCCCGCTTCCCGCCCGCACTGTTTTCCTTCCGGTTGTTCCGGAAGTCGGGTCCTCGAGGGCGGTGAGATCGGTTTCCGATTCCGGGGTGACCGGGGTGGCGGCGGCGGCGCTCCGGTCGCGATGGGCCAGAGGTAAGTGAGCCGCGGCCTGGGCGCTTCCTCCATTCCGGGCGGAGCGCCTGGGTTCTCCCGGCTACCCGCTCCCGGCCTCTGGGCCGTCCCTTTCTGGTTCTGCCGCCTCCAGCCCGGCGTCCGCGTCGCCTGCTCGCCGCCCGACTGAGCCGCTCCCGGGCGGCTGGGAGGCGGGGGTCCCCTGCAGCTCCTGCAGCATCGCCCGCCGG HG:+:518155609:-1 +CCGGCGGGCGATGCTGCAGGAGCTGCAGGGGACCCCCGCCTCCCAGCCGCCCGGGAGCGGCTCAGTCGGGCGGCGAGCAGGCGACGCGGACGCCGGGCTGGAGGCGGCAGAACCAGAAAGGGACGGCCCAGAGGCCGGGAGCGGGTAGCCGGGAGAACCCAGGCGCTCCGCCCGGAATGGAGGAAGCGCCCAGGCCGCGGCTCACTTACCTCTGGCCCATCGCGACCGGAGCGCCGCCGCCGCCACCCCGGTCACCCCGGAATCGGAAACCGATCTCACCGCCCTCGAGGACCCGACTTCCGGAACAACCGGAAGGAAAACAGTGCGGGCGGGAAGCGGGCCCTAGAAGGAGGCGCGAGAGGCCCCGCGGCGCCGGCCCTGATGCCTGCAGCGCCCCCAT HG:+:1235200701:17 +CCGGCGGGCGATGCTGCAGGAGCTGCAGGGGACCCCCGCCTCCCAGCCGCCCGGGAGCGGCTCAGTCGGGCGGCGAGCAGGCGACGCGGACGCCGGGCTGGAGGCGGCAGAACCAGAAAGGGACGGCCCAGAGGCCGGGAGCGGGTAGCCGGGAGAACCCAGGCGCTCCGCCCGGAATGGAGGAAGCGCCCAGGCCGCGGCTCACTTACCTCTGGCCCATCGCGACCGGAGCGCCGCCGCCGCCACCCCGGTCACCCCGGAATCGGAAACCGATCTCACCGCCCTCGAGGACCCGACTTCCGGAACAACCGGAAGGAAAACAGTGCGGGCGGGAAGCGGGCCCTAGAAGGAGGCGCGAGAGGCCCCGCGGCGCCGGCCCTGATGCCTGCAGCGCCCCCAT HG:+:1235200697:17 +CCGGCGGGCGATGCTGCAGGAGCTGCAGGGGACCCCCGCCTCCCAGCCGCCCGGGAGCGGCTCAGTCGGGCGGCGAGCAGGCGACGCGGACGCCGGGCTGGAGGCGGCAGAACCAGAAAGGGACGGCCCAGAGGCCGGGAGCGGGTAGCCGGGAGAACCCAGGCGCTCCGCCCGGAATGGAGGAAGCGCCCAGGCCGCGGCTCACTTACCTCTGGCCCATCGCGACCGGAGCGCCGCCGCCGCCACCCCGGTCACCCCGGAATCGGAAACCGATCTCACCGCCCTCGAGGACCCGACTTCCGGAACAACCGGAAGGAAAACAGTGCGGGCGGGAAGCGGGCCCTAGAAGGAGGCGCGAGAGGCCCCGCGGCGCCGGCCCTGATGCCTGCAGCGCCCCCAT HG:+:1235200700:17 +CCGGCGGGCGATGCTGCAGGAGCTGCAGGGGACCCCCGCCTCCCAGCCGCCCGGGAGCGGCTCAGTCGGGCGGCGAGCAGGCGACGCGGACGCCGGGCTGGAGGCGGCAGAACCAGAAAGGGACGGCCCAGAGGCCGGGAGCGGGTAGCCGGGAGAACCCAGGCGCTCCGCCCGGAATGGAGGAAGCGCCCAGGCCGCGGCTCACTTACCTCTGGCCCATCGCGACCGGAGCGCCGCCGCCGCCACCCCGGTCACCCCGGAATCGGAAACCGATCTCACCGCCCTCGAGGACCCGACTTCCGGAACAACCGGAAGGAAAACAGTGCGGGCGGGAAGCGGGCCCTAGAAGGAGGCGCGAGAGGCCCCGCGGCGCCGGCCCTGATGCCTGCAGCGCCCCCAT HG:+:1235200696:17 HG:+:1699960747:-1 +CCGGCGGGCGATGCTGCAGGAGCTGCAGGGGACCCCCGCCTCCCAGCCGCCCGGGAGCGGCTCAGTCGGGCGGCGAGCAGGCGACGCGGACGCCGGGCTGGAGGCGGCAGAACCAGAAAGGGACGGCCCAGAGGCCGGGAGCGGGTAGCCGGGAGAACCCAGGCGCTCCGCCCGGAATGGAGGAAGCGCCCAGGCCGCGGCTCACTTACCTCTGGCCCATCGCGACCGGAGCGCCGCCGCCGCCACCCCGGTCACCCCGGAATCGGAAACCGATCTCACCGCCCTCGAGGACCCGACTTCCGGAACAACCGGAAGGAAAACAGTGCGGGCGGGAAGCGGGCCCTAGAAGGAGGCGCGAGAGGCCCCGCGGCGCCGGCCCTGATGCCTGCAGCGCCCCCAT HG:+:1235200702:17 +CCGGCGGGCGATGCTGCAGGAGCTGCAGGGGACCCCCGCCTCCCAGCCGCCCGGGAGCGGCTCAGTCGGGCGGCGAGCAGGCGACGCGGACGCCGGGCTGGAGGCGGCAGAACCAGAAAGGGACGGCCCAGAGGCCGGGAGCGGGTAGCCGGGAGAACCCAGGCGCTCCGCCCGGAATGGAGGAAGCGCCCAGGCCGCGGCTCACTTACCTCTGGCCCATCGCGACCGGAGCGCCGCCGCCGCCACCCCGGTCACCCCGGAATCGGAAACCGATCTCACCGCCCTCGAGGACCCGACTTCCGGAACAACCGGAAGGAAAACAGTGCGGGCGGGAAGCGGGCCCTAGAAGGAGGCGCGAGAGGCCCCGCGGCGCCGGCCCTGATGCCTGCAGCGCCCCCAT HG:+:1430450014:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAACCCCTAATCCTCTTTTCTGTAATACATAAAAATTATTACTATGGGAAAAACCAAGGACATTATTTTATAAAACTATCTGAAATTTTTTAAGTCAGGATTCGTTAAACCATGTAAACATATCTTTAATGTAATCCAATCTCACTCAATGACATTCAAACCTATTTAGTCTTTGATCTACTCCTTTATTTGAGAGGTTTTCTT HG:+:1023544684:-1 HG:+:1379454348:-1 HG:+:1462137038:-1 HG:+:1469215273:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAACCCCTAATCCTCTTTTCTGTAATACATAAAAATTATTACTATGGGAAAAACCAAGGACATTATTTTATAAAACTATCTGAAATTTTTTAAGTCAGGATTCGTTAAACCATGTAAACATATCTTTAATGTAATCCAATCTCACTCAATGACATTCAAACCTATTTAGTCTTTGATCTACTCCTTTATTTGAGAGGTTTTCTT HG:+:1063553179:-1 HG:+:2288246154:-1 HG:+:2367914322:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAACCCCTAATCCTCTTTTCTGTAATACATAAAAATTATTACTATGGGAAAAACCAAGGACATTATTTTATAAAACTATCTGAAATTTTTTAAGTCAGGATTCGTTAAACCATGTAAACATATCTTTAATGTAATCCAATCTCACTCAATGACATTCAAACCTATTTAGTCTTTGATCTACTCCTTTATTTGAGAGGTTTTCTT HG:+:550784030:-1 HG:+:814307796:-1 HG:+:2616590247:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAACCCCTAATCCTCTTTTCTGTAATACATAAAAATTATTACTATGGGAAAAACCAAGGACATTATTTTATAAAACTATCTGAAATTTTTTAAGTCAGGATTCGTTAAACCATGTAAACATATCTTTAATGTAATCCAATCTCACTCAATGACATTCAAACCTATTTAGTCTTTGATCTACTCCTTTATTTGAGAGGTTTTCTT HG:+:272047590:-1 HG:+:276717791:-1 HG:+:875565674:-1 HG:+:960742218:-1 HG:+:1032963031:-1 HG:+:1155627303:-1 HG:+:1169904263:-1 HG:+:1357719262:-1 HG:+:1445549174:-1 HG:+:1781991226:-1 HG:+:1900301664:-1 HG:+:2025463170:-1 HG:+:2062587022:-1 HG:+:2382373355:-1 HG:+:2668417280:-1 HG:+:2945896944:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAACCCCTAATCCTCTTTTCTGTAATACATAAAAATTATTACTATGGGAAAAACCAAGGACATTATTTTATAAAACTATCTGAAATTTTTTAAGTCAGGATTCGTTAAACCATGTAAACATATCTTTAATGTAATCCAATCTCACTCAATGACATTCAAACCTATTTAGTCTTTGATCTACTCCTTTATTTGAGAGGTTTTCTT HG:+:821196116:-1 HG:+:999129320:-1 HG:+:1187666549:-1 HG:+:1621782759:-1 HG:+:1793975516:-1 HG:+:2543115878:-1 HG:+:2725629121:-1 HG:+:2970181505:-1 HG:+:3039722242:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAACCCCTAATCCTCTTTTCTGTAATACATAAAAATTATTACTATGGGAAAAACCAAGGACATTATTTTATAAAACTATCTGAAATTTTTTAAGTCAGGATTCGTTAAACCATGTAAACATATCTTTAATGTAATCCAATCTCACTCAATGACATTCAAACCTATTTAGTCTTTGATCTACTCCTTTATTTGAGAGGTTTTCTT HG:+:184966278:-1 HG:+:659621686:-1 HG:+:2173288660:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAACCCCTAATCCTCTTTTCTGTAATACATAAAAATTATTACTATGGGAAAAACCAAGGACATTATTTTATAAAACTATCTGAAATTTTTTAAGTCAGGATTCGTTAAACCATGTAAACATATCTTTAATGTAATCCAATCTCACTCAATGACATTCAAACCTATTTAGTCTTTGATCTACTCCTTTATTTGAGAGGTTTTCTT HG:+:303698762:-1 HG:+:378383080:-1 HG:+:399224958:-1 HG:+:522020285:-1 HG:+:682284956:-1 HG:+:820555434:-1 HG:+:909169065:-1 HG:+:985627707:-1 HG:+:1177026456:-1 HG:+:1211281673:-1 HG:+:1319595336:-1 HG:+:1550331600:-1 HG:+:1726391692:-1 HG:+:1760953426:-1 HG:+:2233271882:-1 HG:+:2341088123:-1 HG:+:2351821263:-1 HG:+:2407424062:-1 HG:+:2512399572:-1 HG:+:2595388822:-1 HG:+:2720859923:-1 HG:+:2922076866:-1 HG:+:2987119154:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAACCCCTAATCCTCTTTTCTGTAATACATAAAAATTATTACTATGGGAAAAACCAAGGACATTATTTTATAAAACTATCTGAAATTTTTTAAGTCAGGATTCGTTAAACCATGTAAACATATCTTTAATGTAATCCAATCTCACTCAATGACATTCAAACCTATTTAGTCTTTGATCTACTCCTTTATTTGAGAGGTTTTCTT HG:+:328466354:-1 HG:+:986972555:-1 HG:+:1136371959:-1 HG:+:3017451401:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAACCCCTAATCCTCTTTTCTGTAATACATAAAAATTATTACTATGGGAAAAACCAAGGACATTATTTTATAAAACTATCTGAAATTTTTTAAGTCAGGATTCGTTAAACCATGTAAACATATCTTTAATGTAATCCAATCTCACTCAATGACATTCAAACCTATTTAGTCTTTGATCTACTCCTTTATTTGAGAGGTTTTCTT HG:+:971810043:-1 HG:+:1020664209:-1 HG:+:1030959697:-1 HG:+:1461047187:-1 HG:+:1463073305:-1 HG:+:1616919094:-1 HG:+:1898486629:-1 HG:+:2234035563:-1 HG:+:2460464883:-1 HG:+:2476801588:-1 HG:+:2905913020:-1 +ATAAATTGGACACAAGATGAGCTATATATATTTTCTACAAACATTTAACTTATTTTCTCCCTCTCAGGAGGTTTGTAGTCCTTGTCCCAAATGATTGCATCAAAGAGCTTGCCCCAGCATAATGTACACTCCCAGCTGTTTCTCACCCTCAGTTTTCTTCCCCAGTCATTCCCTGGTTGCTCCTATTGCCCCAGTTGAACCCCTAATCCTCTTTTCTGTAATACATAAAAATTATTACTATGGGAAAAACCAAGGACATTATTTTATAAAACTATCTGAAATTTTTTAAGTCAGGATTCGTTAAACCATGTAAACATATCTTTAATGTAATCCAATCTCACTCAATGACATTCAAACCTATTTAGTCTTTGATCTACTCCTTTATTTGAGAGGTTTTCTT HG:+:315704131:-1 HG:+:515262549:-1 HG:+:925028063:-1 HG:+:1084055883:-1 HG:+:1128027146:-1 HG:+:1198836608:-1 HG:+:2005164467:-1 HG:+:2079348156:-1 HG:+:2256608129:-1 HG:+:2433395627:-1 HG:+:2569479752:-1 HG:+:2600462115:-1 +AAGAAAACCTCTCAAATAAAGGAGTAGATCAAAGACTAAATAGGTTTGAATGTCATTGAGTGAGATTGGATTACATTAAAGATATGTTTACATGGTTTAACGAATCCTGACTTAAAAAATTTCAGATAGTTTTATAAAATAATGTCCTTGGTTTTTCCCATAGTAATAATTTTTATGTATTACAGAAAAGAGGATTAGGGGTTCAACTGGGGCAATAGGAGCAACCAGGGAATGACTGGGGAAGAAAACTGAGGGTGAGAAACAGCTGGGAGTGTACATTATGCTGGGGCAAGCTCTTTGATGCAATCATTTGGGACAAGGACTACAAACCTCCTGAGAGGGAGAAAATAAGTTAAATGTTTGTAGAAAATATATATAGCTCATCTTGTGTCCAATTTAT HG:+:80316425:22 +AAGAAAACCTCTCAAATAAAGGAGTAGATCAAAGACTAAATAGGTTTGAATGTCATTGAGTGAGATTGGATTACATTAAAGATATGTTTACATGGTTTAACGAATCCTGACTTAAAAAATTTCAGATAGTTTTATAAAATAATGTCCTTGGTTTTTCCCATAGTAATAATTTTTATGTATTACAGAAAAGAGGATTAGGGGTTCAACTGGGGCAATAGGAGCAACCAGGGAATGACTGGGGAAGAAAACTGAGGGTGAGAAACAGCTGGGAGTGTACATTATGCTGGGGCAAGCTCTTTGATGCAATCATTTGGGACAAGGACTACAAACCTCCTGAGAGGGAGAAAATAAGTTAAATGTTTGTAGAAAATATATATAGCTCATCTTGTGTCCAATTTAT HG:+:80316427:22 +AAGAAAACCTCTCAAATAAAGGAGTAGATCAAAGACTAAATAGGTTTGAATGTCATTGAGTGAGATTGGATTACATTAAAGATATGTTTACATGGTTTAACGAATCCTGACTTAAAAAATTTCAGATAGTTTTATAAAATAATGTCCTTGGTTTTTCCCATAGTAATAATTTTTATGTATTACAGAAAAGAGGATTAGGGGTTCAACTGGGGCAATAGGAGCAACCAGGGAATGACTGGGGAAGAAAACTGAGGGTGAGAAACAGCTGGGAGTGTACATTATGCTGGGGCAAGCTCTTTGATGCAATCATTTGGGACAAGGACTACAAACCTCCTGAGAGGGAGAAAATAAGTTAAATGTTTGTAGAAAATATATATAGCTCATCTTGTGTCCAATTTAT HG:+:80316428:22 +AAGAAAACCTCTCAAATAAAGGAGTAGATCAAAGACTAAATAGGTTTGAATGTCATTGAGTGAGATTGGATTACATTAAAGATATGTTTACATGGTTTAACGAATCCTGACTTAAAAAATTTCAGATAGTTTTATAAAATAATGTCCTTGGTTTTTCCCATAGTAATAATTTTTATGTATTACAGAAAAGAGGATTAGGGGTTCAACTGGGGCAATAGGAGCAACCAGGGAATGACTGGGGAAGAAAACTGAGGGTGAGAAACAGCTGGGAGTGTACATTATGCTGGGGCAAGCTCTTTGATGCAATCATTTGGGACAAGGACTACAAACCTCCTGAGAGGGAGAAAATAAGTTAAATGTTTGTAGAAAATATATATAGCTCATCTTGTGTCCAATTTAT HG:+:361875002:-1 +AAGAAAACCTCTCAAATAAAGGAGTAGATCAAAGACTAAATAGGTTTGAATGTCATTGAGTGAGATTGGATTACATTAAAGATATGTTTACATGGTTTAACGAATCCTGACTTAAAAAATTTCAGATAGTTTTATAAAATAATGTCCTTGGTTTTTCCCATAGTAATAATTTTTATGTATTACAGAAAAGAGGATTAGGGGTTCAACTGGGGCAATAGGAGCAACCAGGGAATGACTGGGGAAGAAAACTGAGGGTGAGAAACAGCTGGGAGTGTACATTATGCTGGGGCAAGCTCTTTGATGCAATCATTTGGGACAAGGACTACAAACCTCCTGAGAGGGAGAAAATAAGTTAAATGTTTGTAGAAAATATATATAGCTCATCTTGTGTCCAATTTAT HG:+:5869720:-1 HG:+:80316430:22 +TTGAAAAGCAATAAGATATTTACAAAAGAAACTAATGGCGCTGAGCTATCCACGTCAAAAGAGCCCTTGTGTAAATATTTTTGAAAAAGTAAAGAGATCGTAATAATGTCGAATAACTAAAATGCTGTTTATGTGTATTGTGAGGACATATTCTTATGTATAAGGGTTTGCTGGGTTTTTGCAATATCAGAAGAGCCTACCTTCTTAAACAATAAAGGGCAAGTGAATTATCAAAAAAACTCTAAGGAAAAACTACTGAAGTAGTGGCCAGGCACAGTGGCCGTTATGCCCTGTAAATCCCAGCACCGTGGGAGGCCGACACAGGAAGATCACTTGAGCCCAGGAGTTCAAGACCAGCCTGGGCAACACAGGCAGATCCGTCTCTACAAAAAGTTTAAAC HG:+:32599611:-1 HG:+:155553827:-1 HG:+:288130255:-1 HG:+:968728006:-1 HG:+:1053030413:-1 HG:+:1277347992:-1 HG:+:1756687567:-1 HG:+:2104920828:-1 HG:+:2173874017:-1 HG:+:2235322621:-1 HG:+:2251476685:-1 HG:+:2421872537:-1 HG:+:2760269276:-1 HG:+:2860918438:-1 HG:+:2900766047:-1 HG:+:3016857789:18 HG:+:3019575833:-1 +TTGAAAAGCAATAAGATATTTACAAAAGAAACTAATGGCGCTGAGCTATCCACGTCAAAAGAGCCCTTGTGTAAATATTTTTGAAAAAGTAAAGAGATCGTAATAATGTCGAATAACTAAAATGCTGTTTATGTGTATTGTGAGGACATATTCTTATGTATAAGGGTTTGCTGGGTTTTTGCAATATCAGAAGAGCCTACCTTCTTAAACAATAAAGGGCAAGTGAATTATCAAAAAAACTCTAAGGAAAAACTACTGAAGTAGTGGCCAGGCACAGTGGCCGTTATGCCCTGTAAATCCCAGCACCGTGGGAGGCCGACACAGGAAGATCACTTGAGCCCAGGAGTTCAAGACCAGCCTGGGCAACACAGGCAGATCCGTCTCTACAAAAAGTTTAAAC HG:+:2441627074:-1 HG:+:3016857795:18 +TTGAAAAGCAATAAGATATTTACAAAAGAAACTAATGGCGCTGAGCTATCCACGTCAAAAGAGCCCTTGTGTAAATATTTTTGAAAAAGTAAAGAGATCGTAATAATGTCGAATAACTAAAATGCTGTTTATGTGTATTGTGAGGACATATTCTTATGTATAAGGGTTTGCTGGGTTTTTGCAATATCAGAAGAGCCTACCTTCTTAAACAATAAAGGGCAAGTGAATTATCAAAAAAACTCTAAGGAAAAACTACTGAAGTAGTGGCCAGGCACAGTGGCCGTTATGCCCTGTAAATCCCAGCACCGTGGGAGGCCGACACAGGAAGATCACTTGAGCCCAGGAGTTCAAGACCAGCCTGGGCAACACAGGCAGATCCGTCTCTACAAAAAGTTTAAAC HG:+:3016857794:18 +TTGAAAAGCAATAAGATATTTACAAAAGAAACTAATGGCGCTGAGCTATCCACGTCAAAAGAGCCCTTGTGTAAATATTTTTGAAAAAGTAAAGAGATCGTAATAATGTCGAATAACTAAAATGCTGTTTATGTGTATTGTGAGGACATATTCTTATGTATAAGGGTTTGCTGGGTTTTTGCAATATCAGAAGAGCCTACCTTCTTAAACAATAAAGGGCAAGTGAATTATCAAAAAAACTCTAAGGAAAAACTACTGAAGTAGTGGCCAGGCACAGTGGCCGTTATGCCCTGTAAATCCCAGCACCGTGGGAGGCCGACACAGGAAGATCACTTGAGCCCAGGAGTTCAAGACCAGCCTGGGCAACACAGGCAGATCCGTCTCTACAAAAAGTTTAAAC HG:+:3016857796:18 +TTGAAAAGCAATAAGATATTTACAAAAGAAACTAATGGCGCTGAGCTATCCACGTCAAAAGAGCCCTTGTGTAAATATTTTTGAAAAAGTAAAGAGATCGTAATAATGTCGAATAACTAAAATGCTGTTTATGTGTATTGTGAGGACATATTCTTATGTATAAGGGTTTGCTGGGTTTTTGCAATATCAGAAGAGCCTACCTTCTTAAACAATAAAGGGCAAGTGAATTATCAAAAAAACTCTAAGGAAAAACTACTGAAGTAGTGGCCAGGCACAGTGGCCGTTATGCCCTGTAAATCCCAGCACCGTGGGAGGCCGACACAGGAAGATCACTTGAGCCCAGGAGTTCAAGACCAGCCTGGGCAACACAGGCAGATCCGTCTCTACAAAAAGTTTAAAC HG:+:2819017752:-1 +GTTTAAACTTTTTGTAGAGACGGATCTGCCTGTGTTGCCCAGGCTGGTCTTGAACTCCTGGGCTCAAGTGATCTTCCTGTGTCGGCCTCCCACGGTGCTGGGATTTACAGGGCATAACGGCCACTGTGCCTGGCCACTACTTCAGTAGTTTTTCCTTAGAGTTTTTTTGATAATTCACTTGCCCTTTATTGTTTAAGAAGGTAGGCTCTTCTGATATTGCAAAAACCCAGCAAACCCTTATACATAAGAATATGTCCTCACAATACACATAAACAGCATTTTAGTTATTCGACATTATTACGATCTCTTTACTTTTTCAAAAATATTTACACAAGGGCTCTTTTGACGTGGATAGCTCAGCGCCATTAGTTTCTTTTGTAAATATCTTATTGCTTTTCAA HG:+:1977182872:-1 +GTTTAAACTTTTTGTAGAGACGGATCTGCCTGTGTTGCCCAGGCTGGTCTTGAACTCCTGGGCTCAAGTGATCTTCCTGTGTCGGCCTCCCACGGTGCTGGGATTTACAGGGCATAACGGCCACTGTGCCTGGCCACTACTTCAGTAGTTTTTCCTTAGAGTTTTTTTGATAATTCACTTGCCCTTTATTGTTTAAGAAGGTAGGCTCTTCTGATATTGCAAAAACCCAGCAAACCCTTATACATAAGAATATGTCCTCACAATACACATAAACAGCATTTTAGTTATTCGACATTATTACGATCTCTTTACTTTTTCAAAAATATTTACACAAGGGCTCTTTTGACGTGGATAGCTCAGCGCCATTAGTTTCTTTTGTAAATATCTTATTGCTTTTCAA HG:+:2393363306:-1 +GTTTAAACTTTTTGTAGAGACGGATCTGCCTGTGTTGCCCAGGCTGGTCTTGAACTCCTGGGCTCAAGTGATCTTCCTGTGTCGGCCTCCCACGGTGCTGGGATTTACAGGGCATAACGGCCACTGTGCCTGGCCACTACTTCAGTAGTTTTTCCTTAGAGTTTTTTTGATAATTCACTTGCCCTTTATTGTTTAAGAAGGTAGGCTCTTCTGATATTGCAAAAACCCAGCAAACCCTTATACATAAGAATATGTCCTCACAATACACATAAACAGCATTTTAGTTATTCGACATTATTACGATCTCTTTACTTTTTCAAAAATATTTACACAAGGGCTCTTTTGACGTGGATAGCTCAGCGCCATTAGTTTCTTTTGTAAATATCTTATTGCTTTTCAA HG:+:782285529:-1 +GTGGCTCACACCTGTAATCCATCAATGAGAGGGCCTGAGGTGGGCGGATCTCTTGAGGTCAAGAGTTTGAGACAAGCCTGGCCAATATGACAAAACCCTGACTCCTACTAAAAATAAAAAAATTAGACGGGGTGTGTTGGCACGCACCTGTAGTCCCAGCTACTCGAGAAGGCTGAGATCAGAGAATTGTTTGAACCTGGGAGGTAGGAGGCTGCAGTGAGCTGAGCTGAATTCACAACCACTGCCACTCCAGCCTGGGTGGCAGAGTGAGGCTCCGTCTGCTTAAATAAATAAATAAATAAAATAATAATGCTTGATTGGCAAAATGCGATGAGTGTTGTATATCTGTTACTATTGGGAAGCATTCAGCCCTTCACTTATTTAAGTCATTTTACTGATC HG:+:106553569:13 +GTGGCTCACACCTGTAATCCATCAATGAGAGGGCCTGAGGTGGGCGGATCTCTTGAGGTCAAGAGTTTGAGACAAGCCTGGCCAATATGACAAAACCCTGACTCCTACTAAAAATAAAAAAATTAGACGGGGTGTGTTGGCACGCACCTGTAGTCCCAGCTACTCGAGAAGGCTGAGATCAGAGAATTGTTTGAACCTGGGAGGTAGGAGGCTGCAGTGAGCTGAGCTGAATTCACAACCACTGCCACTCCAGCCTGGGTGGCAGAGTGAGGCTCCGTCTGCTTAAATAAATAAATAAATAAAATAATAATGCTTGATTGGCAAAATGCGATGAGTGTTGTATATCTGTTACTATTGGGAAGCATTCAGCCCTTCACTTATTTAAGTCATTTTACTGATC HG:+:106553572:13 +GTGGCTCACACCTGTAATCCATCAATGAGAGGGCCTGAGGTGGGCGGATCTCTTGAGGTCAAGAGTTTGAGACAAGCCTGGCCAATATGACAAAACCCTGACTCCTACTAAAAATAAAAAAATTAGACGGGGTGTGTTGGCACGCACCTGTAGTCCCAGCTACTCGAGAAGGCTGAGATCAGAGAATTGTTTGAACCTGGGAGGTAGGAGGCTGCAGTGAGCTGAGCTGAATTCACAACCACTGCCACTCCAGCCTGGGTGGCAGAGTGAGGCTCCGTCTGCTTAAATAAATAAATAAATAAAATAATAATGCTTGATTGGCAAAATGCGATGAGTGTTGTATATCTGTTACTATTGGGAAGCATTCAGCCCTTCACTTATTTAAGTCATTTTACTGATC HG:+:1715276900:-1 +GTGGCTCACACCTGTAATCCATCAATGAGAGGGCCTGAGGTGGGCGGATCTCTTGAGGTCAAGAGTTTGAGACAAGCCTGGCCAATATGACAAAACCCTGACTCCTACTAAAAATAAAAAAATTAGACGGGGTGTGTTGGCACGCACCTGTAGTCCCAGCTACTCGAGAAGGCTGAGATCAGAGAATTGTTTGAACCTGGGAGGTAGGAGGCTGCAGTGAGCTGAGCTGAATTCACAACCACTGCCACTCCAGCCTGGGTGGCAGAGTGAGGCTCCGTCTGCTTAAATAAATAAATAAATAAAATAATAATGCTTGATTGGCAAAATGCGATGAGTGTTGTATATCTGTTACTATTGGGAAGCATTCAGCCCTTCACTTATTTAAGTCATTTTACTGATC HG:+:106553568:13 +GTGGCTCACACCTGTAATCCATCAATGAGAGGGCCTGAGGTGGGCGGATCTCTTGAGGTCAAGAGTTTGAGACAAGCCTGGCCAATATGACAAAACCCTGACTCCTACTAAAAATAAAAAAATTAGACGGGGTGTGTTGGCACGCACCTGTAGTCCCAGCTACTCGAGAAGGCTGAGATCAGAGAATTGTTTGAACCTGGGAGGTAGGAGGCTGCAGTGAGCTGAGCTGAATTCACAACCACTGCCACTCCAGCCTGGGTGGCAGAGTGAGGCTCCGTCTGCTTAAATAAATAAATAAATAAAATAATAATGCTTGATTGGCAAAATGCGATGAGTGTTGTATATCTGTTACTATTGGGAAGCATTCAGCCCTTCACTTATTTAAGTCATTTTACTGATC HG:+:106553571:13 +GTGGCTCACACCTGTAATCCATCAATGAGAGGGCCTGAGGTGGGCGGATCTCTTGAGGTCAAGAGTTTGAGACAAGCCTGGCCAATATGACAAAACCCTGACTCCTACTAAAAATAAAAAAATTAGACGGGGTGTGTTGGCACGCACCTGTAGTCCCAGCTACTCGAGAAGGCTGAGATCAGAGAATTGTTTGAACCTGGGAGGTAGGAGGCTGCAGTGAGCTGAGCTGAATTCACAACCACTGCCACTCCAGCCTGGGTGGCAGAGTGAGGCTCCGTCTGCTTAAATAAATAAATAAATAAAATAATAATGCTTGATTGGCAAAATGCGATGAGTGTTGTATATCTGTTACTATTGGGAAGCATTCAGCCCTTCACTTATTTAAGTCATTTTACTGATC HG:+:106553575:13 +GTGGCTCACACCTGTAATCCATCAATGAGAGGGCCTGAGGTGGGCGGATCTCTTGAGGTCAAGAGTTTGAGACAAGCCTGGCCAATATGACAAAACCCTGACTCCTACTAAAAATAAAAAAATTAGACGGGGTGTGTTGGCACGCACCTGTAGTCCCAGCTACTCGAGAAGGCTGAGATCAGAGAATTGTTTGAACCTGGGAGGTAGGAGGCTGCAGTGAGCTGAGCTGAATTCACAACCACTGCCACTCCAGCCTGGGTGGCAGAGTGAGGCTCCGTCTGCTTAAATAAATAAATAAATAAAATAATAATGCTTGATTGGCAAAATGCGATGAGTGTTGTATATCTGTTACTATTGGGAAGCATTCAGCCCTTCACTTATTTAAGTCATTTTACTGATC HG:+:469833526:-1 +GATCAGTAAAATGACTTAAATAAGTGAAGGGCTGAATGCTTCCCAATAGTAACAGATATACAACACTCATCGCATTTTGCCAATCAAGCATTATTATTTTATTTATTTATTTATTTAAGCAGACGGAGCCTCACTCTGCCACCCAGGCTGGAGTGGCAGTGGTTGTGAATTCAGCTCAGCTCACTGCAGCCTCCTACCTCCCAGGTTCAAACAATTCTCTGATCTCAGCCTTCTCGAGTAGCTGGGACTACAGGTGCGTGCCAACACACCCCGTCTAATTTTTTTATTTTTAGTAGGAGTCAGGGTTTTGTCATATTGGCCAGGCTTGTCTCAAACTCTTGACCTCAAGAGATCCGCCCACCTCAGGCCCTCTCATTGATGGATTACAGGTGTGAGCCAC HG:+:614359972:-1 +GATCAGTAAAATGACTTAAATAAGTGAAGGGCTGAATGCTTCCCAATAGTAACAGATATACAACACTCATCGCATTTTGCCAATCAAGCATTATTATTTTATTTATTTATTTATTTAAGCAGACGGAGCCTCACTCTGCCACCCAGGCTGGAGTGGCAGTGGTTGTGAATTCAGCTCAGCTCACTGCAGCCTCCTACCTCCCAGGTTCAAACAATTCTCTGATCTCAGCCTTCTCGAGTAGCTGGGACTACAGGTGCGTGCCAACACACCCCGTCTAATTTTTTTATTTTTAGTAGGAGTCAGGGTTTTGTCATATTGGCCAGGCTTGTCTCAAACTCTTGACCTCAAGAGATCCGCCCACCTCAGGCCCTCTCATTGATGGATTACAGGTGTGAGCCAC HG:+:2071905102:-1 +GATCAGTAAAATGACTTAAATAAGTGAAGGGCTGAATGCTTCCCAATAGTAACAGATATACAACACTCATCGCATTTTGCCAATCAAGCATTATTATTTTATTTATTTATTTATTTAAGCAGACGGAGCCTCACTCTGCCACCCAGGCTGGAGTGGCAGTGGTTGTGAATTCAGCTCAGCTCACTGCAGCCTCCTACCTCCCAGGTTCAAACAATTCTCTGATCTCAGCCTTCTCGAGTAGCTGGGACTACAGGTGCGTGCCAACACACCCCGTCTAATTTTTTTATTTTTAGTAGGAGTCAGGGTTTTGTCATATTGGCCAGGCTTGTCTCAAACTCTTGACCTCAAGAGATCCGCCCACCTCAGGCCCTCTCATTGATGGATTACAGGTGTGAGCCAC HG:+:2792518910:-1 +GATCAGTAAAATGACTTAAATAAGTGAAGGGCTGAATGCTTCCCAATAGTAACAGATATACAACACTCATCGCATTTTGCCAATCAAGCATTATTATTTTATTTATTTATTTATTTAAGCAGACGGAGCCTCACTCTGCCACCCAGGCTGGAGTGGCAGTGGTTGTGAATTCAGCTCAGCTCACTGCAGCCTCCTACCTCCCAGGTTCAAACAATTCTCTGATCTCAGCCTTCTCGAGTAGCTGGGACTACAGGTGCGTGCCAACACACCCCGTCTAATTTTTTTATTTTTAGTAGGAGTCAGGGTTTTGTCATATTGGCCAGGCTTGTCTCAAACTCTTGACCTCAAGAGATCCGCCCACCTCAGGCCCTCTCATTGATGGATTACAGGTGTGAGCCAC HG:+:31987088:-1 HG:+:200323552:-1 HG:+:628530258:-1 HG:+:645387338:-1 HG:+:762038240:-1 HG:+:794297449:-1 HG:+:850126846:-1 HG:+:1007790765:-1 HG:+:1162094444:-1 HG:+:1181623942:-1 HG:+:1406705790:-1 HG:+:1938949853:-1 HG:+:2061949108:-1 HG:+:2069643835:-1 HG:+:2074643396:-1 HG:+:2303503229:-1 HG:+:2351605372:-1 HG:+:2553241748:-1 HG:+:2897480289:-1 +TATATGTGGAAGTGATGAAAACAGGAGAAAATCTATAGCTCAAAAAGGCAACTTATGAACCACCCCATATTTTATGTTTTGCAAGAGCAACCCCTGCATTACCCTACATTGCTCTATGAAGGAGTGTCGACCTGGAATGTAAGCAAAACTGGGATTAAAAAAACAATGCTCTCAGACCTAATCTGTAACCCATCCCTGCAAAGCCTCTTAAAAACAAGATATAGCATCATATTCTTTTTATAAAATATTACTGACACCTGGTTTGGGCCAGGTACTTAGGTAGGCACTAGATTATTTAACAGTGAACAAGATAACATGATCCCTGTTCTTCCAATCAGTCACGAAGGGAAGTAGAAGAGACAAACTAAATGGATGATATACTACAGGTAACTAAGTACTA HG:+:2023143281:-1 HG:+:2886616821:-1 +TATATGTGGAAGTGATGAAAACAGGAGAAAATCTATAGCTCAAAAAGGCAACTTATGAACCACCCCATATTTTATGTTTTGCAAGAGCAACCCCTGCATTACCCTACATTGCTCTATGAAGGAGTGTCGACCTGGAATGTAAGCAAAACTGGGATTAAAAAAACAATGCTCTCAGACCTAATCTGTAACCCATCCCTGCAAAGCCTCTTAAAAACAAGATATAGCATCATATTCTTTTTATAAAATATTACTGACACCTGGTTTGGGCCAGGTACTTAGGTAGGCACTAGATTATTTAACAGTGAACAAGATAACATGATCCCTGTTCTTCCAATCAGTCACGAAGGGAAGTAGAAGAGACAAACTAAATGGATGATATACTACAGGTAACTAAGTACTA HG:+:506620126:-1 HG:+:628221204:-1 HG:+:684742481:-1 HG:+:1183593626:-1 HG:+:1255330274:-1 HG:+:1621964617:-1 HG:+:1820133533:-1 HG:+:2167911070:-1 HG:+:2539144439:-1 +TATATGTGGAAGTGATGAAAACAGGAGAAAATCTATAGCTCAAAAAGGCAACTTATGAACCACCCCATATTTTATGTTTTGCAAGAGCAACCCCTGCATTACCCTACATTGCTCTATGAAGGAGTGTCGACCTGGAATGTAAGCAAAACTGGGATTAAAAAAACAATGCTCTCAGACCTAATCTGTAACCCATCCCTGCAAAGCCTCTTAAAAACAAGATATAGCATCATATTCTTTTTATAAAATATTACTGACACCTGGTTTGGGCCAGGTACTTAGGTAGGCACTAGATTATTTAACAGTGAACAAGATAACATGATCCCTGTTCTTCCAATCAGTCACGAAGGGAAGTAGAAGAGACAAACTAAATGGATGATATACTACAGGTAACTAAGTACTA HG:+:27342603:-1 HG:+:1107453390:-1 HG:+:1158094176:-1 HG:+:1511596034:-1 HG:+:1923866671:-1 HG:+:2181274767:-1 HG:+:2968671433:-1 +TATATGTGGAAGTGATGAAAACAGGAGAAAATCTATAGCTCAAAAAGGCAACTTATGAACCACCCCATATTTTATGTTTTGCAAGAGCAACCCCTGCATTACCCTACATTGCTCTATGAAGGAGTGTCGACCTGGAATGTAAGCAAAACTGGGATTAAAAAAACAATGCTCTCAGACCTAATCTGTAACCCATCCCTGCAAAGCCTCTTAAAAACAAGATATAGCATCATATTCTTTTTATAAAATATTACTGACACCTGGTTTGGGCCAGGTACTTAGGTAGGCACTAGATTATTTAACAGTGAACAAGATAACATGATCCCTGTTCTTCCAATCAGTCACGAAGGGAAGTAGAAGAGACAAACTAAATGGATGATATACTACAGGTAACTAAGTACTA HG:+:3614446:-1 HG:+:451239276:-1 HG:+:591445912:-1 HG:+:885760740:-1 HG:+:1361803101:-1 HG:+:1535210466:-1 HG:+:1646861398:-1 HG:+:2378859788:-1 HG:+:2382274389:-1 HG:+:2560702029:-1 HG:+:2576137777:-1 HG:+:2602673242:-1 +TATATGTGGAAGTGATGAAAACAGGAGAAAATCTATAGCTCAAAAAGGCAACTTATGAACCACCCCATATTTTATGTTTTGCAAGAGCAACCCCTGCATTACCCTACATTGCTCTATGAAGGAGTGTCGACCTGGAATGTAAGCAAAACTGGGATTAAAAAAACAATGCTCTCAGACCTAATCTGTAACCCATCCCTGCAAAGCCTCTTAAAAACAAGATATAGCATCATATTCTTTTTATAAAATATTACTGACACCTGGTTTGGGCCAGGTACTTAGGTAGGCACTAGATTATTTAACAGTGAACAAGATAACATGATCCCTGTTCTTCCAATCAGTCACGAAGGGAAGTAGAAGAGACAAACTAAATGGATGATATACTACAGGTAACTAAGTACTA HG:+:30505170:-1 HG:+:40381791:-1 HG:+:43549450:-1 HG:+:47411428:-1 HG:+:71483854:-1 HG:+:73855143:-1 HG:+:198377391:-1 HG:+:258371081:-1 HG:+:260571691:-1 HG:+:261305409:-1 HG:+:280346543:-1 HG:+:332762859:-1 HG:+:413171291:-1 HG:+:425177634:-1 HG:+:425286696:-1 HG:+:453269505:-1 HG:+:460870775:-1 HG:+:628191060:-1 HG:+:634671867:-1 HG:+:654590592:-1 HG:+:675764842:-1 HG:+:756763425:-1 HG:+:788187832:-1 HG:+:824554999:-1 HG:+:849538899:-1 HG:+:876991929:-1 HG:+:906552801:-1 HG:+:908453790:-1 HG:+:1028564848:-1 HG:+:1120620438:-1 HG:+:1180339238:-1 HG:+:1185490616:-1 HG:+:1210534894:-1 HG:+:1228173921:-1 HG:+:1249323488:-1 HG:+:1252539659:-1 HG:+:1338476181:-1 HG:+:1349276187:-1 HG:+:1509605379:-1 HG:+:1551689175:-1 HG:+:1557979765:-1 HG:+:1623752960:-1 HG:+:1657822782:-1 HG:+:1659431370:-1 HG:+:1692186704:-1 HG:+:1772086110:-1 HG:+:1837875555:-1 HG:+:1849244795:-1 HG:+:1853570876:-1 HG:+:1860462344:-1 HG:+:1871039230:-1 HG:+:1959697319:-1 HG:+:2039956104:-1 HG:+:2040782143:-1 HG:+:2042280000:-1 HG:+:2069579120:-1 HG:+:2170218277:-1 HG:+:2170450693:-1 HG:+:2180204883:-1 HG:+:2189976283:-1 HG:+:2222197312:-1 HG:+:2520322517:-1 HG:+:2602240188:-1 HG:+:2618768573:-1 HG:+:2629413103:-1 HG:+:2734693830:-1 HG:+:2803708873:-1 HG:+:2860057351:-1 HG:+:2934764221:-1 HG:+:2986886987:-1 HG:+:2988121642:-1 +TATATGTGGAAGTGATGAAAACAGGAGAAAATCTATAGCTCAAAAAGGCAACTTATGAACCACCCCATATTTTATGTTTTGCAAGAGCAACCCCTGCATTACCCTACATTGCTCTATGAAGGAGTGTCGACCTGGAATGTAAGCAAAACTGGGATTAAAAAAACAATGCTCTCAGACCTAATCTGTAACCCATCCCTGCAAAGCCTCTTAAAAACAAGATATAGCATCATATTCTTTTTATAAAATATTACTGACACCTGGTTTGGGCCAGGTACTTAGGTAGGCACTAGATTATTTAACAGTGAACAAGATAACATGATCCCTGTTCTTCCAATCAGTCACGAAGGGAAGTAGAAGAGACAAACTAAATGGATGATATACTACAGGTAACTAAGTACTA HG:+:64938123:-1 HG:+:389040601:-1 HG:+:537475116:-1 HG:+:537640072:-1 HG:+:549340566:-1 HG:+:570023832:-1 HG:+:597202436:-1 HG:+:628206222:-1 HG:+:652800499:-1 HG:+:686392482:-1 HG:+:701378521:-1 HG:+:719228715:-1 HG:+:733593663:-1 HG:+:773223734:-1 HG:+:774951661:-1 HG:+:833870812:-1 HG:+:933015378:-1 HG:+:1019271377:-1 HG:+:1031967565:-1 HG:+:1036266238:-1 HG:+:1061100449:-1 HG:+:1226386980:-1 HG:+:1263676938:-1 HG:+:1278791074:-1 HG:+:1285151316:-1 HG:+:1388941311:-1 HG:+:1445726338:-1 HG:+:1451779177:-1 HG:+:1502458864:-1 HG:+:1518750467:-1 HG:+:1711711073:-1 HG:+:1723374411:-1 HG:+:1751100213:-1 HG:+:1769485190:-1 HG:+:1872544524:-1 HG:+:1966316487:-1 HG:+:1984085674:-1 HG:+:2005773254:-1 HG:+:2148616487:-1 HG:+:2158917577:-1 HG:+:2191974016:-1 HG:+:2226088885:-1 HG:+:2251045393:-1 HG:+:2266411043:-1 HG:+:2280292323:-1 HG:+:2363196672:-1 HG:+:2545057797:-1 HG:+:2647333830:-1 +TATATGTGGAAGTGATGAAAACAGGAGAAAATCTATAGCTCAAAAAGGCAACTTATGAACCACCCCATATTTTATGTTTTGCAAGAGCAACCCCTGCATTACCCTACATTGCTCTATGAAGGAGTGTCGACCTGGAATGTAAGCAAAACTGGGATTAAAAAAACAATGCTCTCAGACCTAATCTGTAACCCATCCCTGCAAAGCCTCTTAAAAACAAGATATAGCATCATATTCTTTTTATAAAATATTACTGACACCTGGTTTGGGCCAGGTACTTAGGTAGGCACTAGATTATTTAACAGTGAACAAGATAACATGATCCCTGTTCTTCCAATCAGTCACGAAGGGAAGTAGAAGAGACAAACTAAATGGATGATATACTACAGGTAACTAAGTACTA HG:+:721338152:-1 HG:+:1081973553:-1 HG:+:1156664606:-1 HG:+:1199592407:-1 HG:+:1780822137:-1 HG:+:1856729381:-1 HG:+:1901917888:-1 HG:+:2247360402:-1 HG:+:2467088133:-1 HG:+:2640008463:-1 HG:+:2847903067:-1 +TATATGTGGAAGTGATGAAAACAGGAGAAAATCTATAGCTCAAAAAGGCAACTTATGAACCACCCCATATTTTATGTTTTGCAAGAGCAACCCCTGCATTACCCTACATTGCTCTATGAAGGAGTGTCGACCTGGAATGTAAGCAAAACTGGGATTAAAAAAACAATGCTCTCAGACCTAATCTGTAACCCATCCCTGCAAAGCCTCTTAAAAACAAGATATAGCATCATATTCTTTTTATAAAATATTACTGACACCTGGTTTGGGCCAGGTACTTAGGTAGGCACTAGATTATTTAACAGTGAACAAGATAACATGATCCCTGTTCTTCCAATCAGTCACGAAGGGAAGTAGAAGAGACAAACTAAATGGATGATATACTACAGGTAACTAAGTACTA HG:+:589745323:-1 HG:+:778202915:-1 HG:+:963642572:-1 HG:+:1010364858:-1 HG:+:1275504776:-1 HG:+:1498717332:-1 HG:+:1827863311:-1 HG:+:2064150029:-1 HG:+:2121819670:-1 HG:+:2397891447:-1 HG:+:2473161604:-1 HG:+:2479496433:-1 HG:+:2519214337:-1 HG:+:2552157738:-1 HG:+:2732642903:-1 +TATATGTGGAAGTGATGAAAACAGGAGAAAATCTATAGCTCAAAAAGGCAACTTATGAACCACCCCATATTTTATGTTTTGCAAGAGCAACCCCTGCATTACCCTACATTGCTCTATGAAGGAGTGTCGACCTGGAATGTAAGCAAAACTGGGATTAAAAAAACAATGCTCTCAGACCTAATCTGTAACCCATCCCTGCAAAGCCTCTTAAAAACAAGATATAGCATCATATTCTTTTTATAAAATATTACTGACACCTGGTTTGGGCCAGGTACTTAGGTAGGCACTAGATTATTTAACAGTGAACAAGATAACATGATCCCTGTTCTTCCAATCAGTCACGAAGGGAAGTAGAAGAGACAAACTAAATGGATGATATACTACAGGTAACTAAGTACTA HG:+:231128536:-1 HG:+:270178342:-1 HG:+:463681342:-1 HG:+:467224283:-1 HG:+:564222906:-1 HG:+:725689012:-1 HG:+:739162385:-1 HG:+:833748447:-1 HG:+:901940580:-1 HG:+:1053628613:-1 HG:+:1183309432:-1 HG:+:1206615667:-1 HG:+:1356592017:-1 HG:+:1374337329:-1 HG:+:1414727805:-1 HG:+:1518700875:-1 HG:+:1623973433:-1 HG:+:1770721773:-1 HG:+:1944959052:-1 HG:+:1958284262:-1 HG:+:2138224045:-1 HG:+:2151678288:-1 HG:+:2225890742:-1 HG:+:2272531633:-1 HG:+:2419199664:-1 HG:+:2799735930:-1 HG:+:2857161364:-1 diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-600nt.prof b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-600nt.prof new file mode 100644 index 0000000000000000000000000000000000000000..4ee04ffb3c83952c00c0fc520513db510ce882b2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-600nt.prof @@ -0,0 +1,1000 @@ +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:1680513894:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:2042761554:-1 chm1:+:2360117472:-1 chm1:+:2914989066:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:12281889:-1 chm1:+:253489980:-1 chm1:+:264345456:-1 chm1:+:266462525:-1 chm1:+:458677586:-1 chm1:+:460615436:-1 chm1:+:461883015:-1 chm1:+:658931852:-1 chm1:+:672943370:-1 chm1:+:724449292:-1 chm1:+:995923537:-1 chm1:+:1154803125:-1 chm1:+:1791925339:-1 chm1:+:1971971241:-1 chm1:+:2012473751:-1 chm1:+:2043005803:-1 chm1:+:2916449054:-1 chm1:+:2963069500:-1 chm1:+:2973691503:-1 chm1:+:3035174746:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:4961125:-1 chm1:+:28006089:-1 chm1:+:49548175:-1 chm1:+:66492968:-1 chm1:+:101505316:-1 chm1:+:114260365:-1 chm1:+:121214189:-1 chm1:+:158797774:-1 chm1:+:167566566:-1 chm1:+:177343684:-1 chm1:+:183351343:-1 chm1:+:195611921:-1 chm1:+:198999895:-1 chm1:+:210279945:-1 chm1:+:222236456:-1 chm1:+:222780508:-1 chm1:+:224666916:-1 chm1:+:253672967:-1 chm1:+:257035001:-1 chm1:+:294368958:-1 chm1:+:312260381:-1 chm1:+:326499929:-1 chm1:+:369620782:115 chm1:+:381943919:-1 chm1:+:410913104:-1 chm1:+:430972191:-1 chm1:+:433268416:-1 chm1:+:437340658:-1 chm1:+:450031551:-1 chm1:+:473103876:-1 chm1:+:475685892:-1 chm1:+:508572532:-1 chm1:+:518587040:-1 chm1:+:522874204:-1 chm1:+:526486463:-1 chm1:+:527518680:-1 chm1:+:559686209:-1 chm1:+:566733319:-1 chm1:+:575209493:-1 chm1:+:591566766:-1 chm1:+:593476392:-1 chm1:+:598139948:-1 chm1:+:627574273:-1 chm1:+:651923165:-1 chm1:+:653967735:-1 chm1:+:657859747:-1 chm1:+:681347848:-1 chm1:+:683382969:-1 chm1:+:683817825:-1 chm1:+:695651452:-1 chm1:+:710439685:-1 chm1:+:724077792:-1 chm1:+:729288600:-1 chm1:+:749393504:-1 chm1:+:753129026:-1 chm1:+:754890363:-1 chm1:+:757131969:-1 chm1:+:796060733:-1 chm1:+:805747666:-1 chm1:+:815049418:-1 chm1:+:823086380:-1 chm1:+:825164494:-1 chm1:+:835263686:-1 chm1:+:835384481:-1 chm1:+:846640285:-1 chm1:+:867271130:-1 chm1:+:880306769:-1 chm1:+:896063071:-1 chm1:+:898499601:-1 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chm1:+:2354421912:-1 chm1:+:2473411319:-1 chm1:+:2492784044:-1 chm1:+:2515853114:-1 chm1:+:2566685538:-1 chm1:+:2607784367:-1 chm1:+:2610161631:-1 chm1:+:2650892581:-1 chm1:+:2653599412:-1 chm1:+:2804534020:-1 chm1:+:2806974457:-1 chm1:+:2906668740:-1 chm1:+:2914923850:-1 chm1:+:2914986633:-1 chm1:+:2915492592:-1 chm1:+:2937265766:-1 chm1:+:2955270465:-1 chm1:+:2966754565:-1 chm1:+:2969257991:-1 chm1:+:2971052507:-1 chm1:+:2985039281:-1 chm1:+:2989206097:-1 chm1:+:3022928416:-1 chm1:+:3032707393:-1 chm1:+:3040518218:-1 chm1:+:3100807128:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:7850419:-1 chm1:+:78250842:-1 chm1:+:103248565:-1 chm1:+:272193872:-1 chm1:+:443386004:-1 chm1:+:621532725:-1 chm1:+:705559402:-1 chm1:+:709470459:-1 chm1:+:709924080:-1 chm1:+:774768179:-1 chm1:+:949132546:-1 chm1:+:1180833855:-1 chm1:+:1223265886:-1 chm1:+:1339637866:-1 chm1:+:1362956959:-1 chm1:+:1534282333:-1 chm1:+:1563449938:-1 chm1:+:1767185571:-1 chm1:+:1921128697:-1 chm1:+:2189249106:-1 chm1:+:2545517286:-1 chm1:+:2550916714:-1 chm1:+:2584175947:-1 chm1:+:2669369732:-1 chm1:+:2812223450:-1 chm1:+:2912850805:-1 chm1:+:2945880622:-1 chm1:+:2967293925:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:104594420:-1 chm1:+:419766636:-1 chm1:+:429108758:-1 chm1:+:470722414:-1 chm1:+:495809208:-1 chm1:+:721672837:-1 chm1:+:776050507:-1 chm1:+:848796783:-1 chm1:+:1187043477:-1 chm1:+:1505621312:-1 chm1:+:1699649531:-1 chm1:+:1740558505:-1 chm1:+:1832177039:-1 chm1:+:1840119651:-1 chm1:+:1911032393:-1 chm1:+:1977148486:-1 chm1:+:2013820163:-1 chm1:+:2052856571:-1 chm1:+:2228635247:-1 chm1:+:2261546402:-1 chm1:+:2813669963:-1 chm1:+:3005813097:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:580095510:-1 chm1:+:777207613:-1 chm1:+:1477985183:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:483804406:-1 chm1:+:508478770:-1 chm1:+:1064728166:-1 chm1:+:1959736972:-1 chm1:+:2403249457:-1 chm1:+:2479486674:-1 chm1:+:2567865450:-1 chm1:+:2947240420:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:28006077:-1 chm1:+:84802159:-1 chm1:+:102574955:-1 chm1:+:153130363:-1 chm1:+:184995730:-1 chm1:+:191697319:-1 chm1:+:195407948:-1 chm1:+:217502592:-1 chm1:+:222780463:-1 chm1:+:263381977:-1 chm1:+:306743979:-1 chm1:+:366201642:-1 chm1:+:458714358:-1 chm1:+:561491055:-1 chm1:+:644867671:-1 chm1:+:653968013:-1 chm1:+:659226207:-1 chm1:+:668714898:-1 chm1:+:725216209:-1 chm1:+:725299885:-1 chm1:+:756306790:-1 chm1:+:783681011:-1 chm1:+:818289991:-1 chm1:+:823092355:-1 chm1:+:843538295:-1 chm1:+:890096664:-1 chm1:+:907430171:-1 chm1:+:909308838:-1 chm1:+:915920441:-1 chm1:+:918909134:-1 chm1:+:992614954:-1 chm1:+:1012794198:-1 chm1:+:1166647382:-1 chm1:+:1178356725:-1 chm1:+:1375209354:-1 chm1:+:1458754000:-1 chm1:+:1502851699:-1 chm1:+:1585593799:-1 chm1:+:1680514681:-1 chm1:+:1847422778:-1 chm1:+:1911588860:-1 chm1:+:2040097539:-1 chm1:+:2147258390:-1 chm1:+:2172081617:-1 chm1:+:2221068890:-1 chm1:+:2230244200:-1 chm1:+:2268503952:-1 chm1:+:2357381429:-1 chm1:+:2464921872:-1 chm1:+:2585899068:-1 chm1:+:2653599393:-1 chm1:+:2654049088:-1 chm1:+:2760688348:-1 chm1:+:2826582544:-1 chm1:+:2964561731:-1 chm1:+:2965132299:-1 chm1:+:2965730649:-1 chm1:+:2986126502:-1 chm1:+:3003484217:-1 chm1:+:3005813085:-1 chm1:+:3008191039:-1 chm1:+:3100813084:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:87946874:-1 chm1:+:454923113:-1 chm1:+:1685759384:-1 chm1:+:2630954644:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:418674270:-1 chm1:+:554486129:-1 chm1:+:884121360:-1 chm1:+:1000445054:-1 chm1:+:1529677962:-1 chm1:+:1795304416:-1 chm1:+:1825530051:-1 chm1:+:2180146427:-1 chm1:+:2377334132:-1 chm1:+:2429501202:-1 chm1:+:2559574357:-1 chm1:+:2584132713:-1 chm1:+:2877297062:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:262828362:-1 chm1:+:668265882:-1 chm1:+:847809385:-1 chm1:+:900256374:-1 chm1:+:996568883:-1 chm1:+:1071802717:-1 chm1:+:1180008175:-1 chm1:+:1180012969:-1 chm1:+:1193424489:-1 chm1:+:1352590322:-1 chm1:+:1684332043:-1 chm1:+:2153330426:-1 chm1:+:2975625023:-1 chm1:+:2975734777:-1 chm1:+:3006157893:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:321198842:-1 chm1:+:524924192:-1 chm1:+:886080001:-1 chm1:+:1030224906:-1 chm1:+:1685991610:-1 chm1:+:1962958839:-1 chm1:+:2165156149:-1 chm1:+:2441541811:-1 chm1:+:2819381504:-1 chm1:+:2827308637:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:288833645:-1 chm1:+:695651447:-1 chm1:+:986952683:-1 chm1:+:1630504016:-1 chm1:+:1677208915:-1 chm1:+:1681127399:-1 chm1:+:1726780428:-1 chm1:+:1731462150:-1 chm1:+:1731683880:-1 chm1:+:1812829639:-1 chm1:+:1827969209:-1 chm1:+:1862749108:-1 chm1:+:1951354317:-1 chm1:+:2139924654:-1 chm1:+:2161513741:-1 chm1:+:2464730221:-1 chm1:+:2473769862:-1 chm1:+:2914172513:-1 chm1:+:2979823528:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:748984374:-1 chm1:+:997840420:-1 chm1:+:1230258883:-1 chm1:+:1873878647:-1 chm1:+:2276982554:-1 chm1:+:2691268541:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:423391344:-1 chm1:+:457005669:-1 chm1:+:554750792:-1 chm1:+:764812342:-1 chm1:+:949324330:-1 chm1:+:1014662622:-1 chm1:+:1014662673:-1 chm1:+:1187923682:-1 chm1:+:1378479937:-1 chm1:+:1426726584:-1 chm1:+:1627828232:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:356119641:-1 chm1:+:357787176:-1 chm1:+:379866550:-1 chm1:+:490788866:-1 chm1:+:590793872:-1 chm1:+:1017885617:-1 chm1:+:1685562454:-1 chm1:+:1801813553:-1 chm1:+:2796738969:-1 chm1:+:2799873250:-1 chm1:+:3099146801:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:301573574:-1 chm1:+:336230039:-1 chm1:+:633704857:-1 chm1:+:726611002:-1 chm1:+:730967024:-1 chm1:+:807549540:-1 chm1:+:826851433:-1 chm1:+:936288526:-1 chm1:+:1242059702:-1 chm1:+:1462164494:-1 chm1:+:1566839761:-1 chm1:+:1631131659:-1 chm1:+:1732900448:-1 chm1:+:1821716064:-1 chm1:+:1865320907:-1 chm1:+:2009718453:-1 chm1:+:2036316164:-1 chm1:+:2109886537:-1 chm1:+:2291070025:-1 chm1:+:2365565547:-1 chm1:+:2409323055:-1 chm1:+:2628766653:-1 chm1:+:2755482344:-1 chm1:+:2761687771:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:12904945:-1 chm1:+:13176896:-1 chm1:+:34412344:-1 chm1:+:41314531:-1 chm1:+:47365386:-1 chm1:+:235616966:-1 chm1:+:479195893:-1 chm1:+:488442752:-1 chm1:+:550743575:-1 chm1:+:782724665:-1 chm1:+:836546188:-1 chm1:+:1573777023:-1 chm1:+:1622685832:-1 chm1:+:1662441208:-1 chm1:+:1775639211:-1 chm1:+:1794971235:-1 chm1:+:1891012006:-1 chm1:+:2071719930:-1 chm1:+:2270814755:-1 chm1:+:2364136827:-1 chm1:+:2522282262:-1 chm1:+:2569643428:-1 chm1:+:2625481583:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCT chm1:+:581278899:-1 chm1:+:589387342:-1 chm1:+:835263673:-1 chm1:+:835384468:-1 chm1:+:924018846:-1 chm1:+:1170310173:-1 chm1:+:1358526665:-1 chm1:+:1478378570:-1 chm1:+:1739344058:-1 chm1:+:1875591440:-1 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chm1:+:2810473088:-1 chm1:+:2827816123:-1 chm1:+:2848098144:-1 chm1:+:2851648435:-1 chm1:+:2851990090:-1 chm1:+:2852879195:-1 chm1:+:2858226160:-1 chm1:+:2864126910:-1 chm1:+:2887674428:-1 chm1:+:2893317208:-1 chm1:+:2903149873:-1 chm1:+:2903338293:-1 chm1:+:2912908454:-1 chm1:+:2913636773:-1 chm1:+:2915682245:-1 chm1:+:2951877888:-1 chm1:+:2955458176:-1 chm1:+:2958363635:-1 chm1:+:2971467316:-1 chm1:+:2972763118:-1 chm1:+:2979324014:-1 chm1:+:2980176932:-1 chm1:+:2991732759:-1 chm1:+:2998724681:-1 chm1:+:3016191243:-1 chm1:+:3016955400:-1 chm1:+:3017929936:-1 chm1:+:3020210088:-1 chm1:+:3020710860:-1 chm1:+:3023355723:-1 chm1:+:3030883800:-1 chm1:+:3043222052:-1 chm1:+:3057371935:-1 chm1:+:3060105252:-1 chm1:+:3063455292:-1 chm1:+:3095828994:-1 chm1:+:3099115019:21 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+CCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:3098202266:23 +CCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:3098202271:23 +CCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:923180501:-1 +CCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:3098202270:23 +CCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:2979705911:-1 +CCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:634332540:-1 +CCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:1110036587:-1 +CCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:645088469:-1 +CCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:538870195:-1 chm1:+:578822057:-1 chm1:+:866176980:-1 chm1:+:1106856007:-1 chm1:+:1192703614:-1 chm1:+:1898354178:-1 chm1:+:2342955832:-1 chm1:+:2946054657:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTC chm1:+:9000835:-1 chm1:+:15909110:-1 chm1:+:28521567:-1 chm1:+:36531778:-1 chm1:+:39372829:-1 chm1:+:97616848:-1 chm1:+:112218595:-1 chm1:+:167456231:-1 chm1:+:201842190:-1 chm1:+:244661817:-1 chm1:+:269245065:-1 chm1:+:275641475:-1 chm1:+:275765036:-1 chm1:+:287806808:-1 chm1:+:323896546:-1 chm1:+:432793388:-1 chm1:+:455938801:-1 chm1:+:473456652:-1 chm1:+:481143686:-1 chm1:+:540684653:-1 chm1:+:541254523:-1 chm1:+:662331262:-1 chm1:+:687509571:-1 chm1:+:729505545:-1 chm1:+:828770344:-1 chm1:+:875896001:-1 chm1:+:918669947:-1 chm1:+:960598725:-1 chm1:+:1020547502:-1 chm1:+:1024215663:-1 chm1:+:1030461084:-1 chm1:+:1088056352:-1 chm1:+:1150938341:-1 chm1:+:1238834145:-1 chm1:+:1240136327:-1 chm1:+:1335053860:-1 chm1:+:1420564516:-1 chm1:+:1433248910:-1 chm1:+:1631074220:-1 chm1:+:1633915257:-1 chm1:+:1669460553:-1 chm1:+:1670620518:-1 chm1:+:1829870772:-1 chm1:+:1893737169:-1 chm1:+:1993334991:-1 chm1:+:2004566397:-1 chm1:+:2129716829:-1 chm1:+:2183987040:-1 chm1:+:2227638063:-1 chm1:+:2497664505:-1 chm1:+:2544415059:-1 chm1:+:2554561997:-1 chm1:+:2554935863:-1 chm1:+:2574031337:-1 chm1:+:2697973169:-1 chm1:+:2698102966:-1 chm1:+:2748578688:-1 chm1:+:2764020080:-1 chm1:+:2778218233:-1 chm1:+:2816368449:-1 chm1:+:2867586072:-1 chm1:+:2883467426:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTC chm1:+:617788938:-1 chm1:+:620988510:-1 chm1:+:692136246:-1 chm1:+:938022792:-1 chm1:+:1205070800:-1 chm1:+:1396288621:-1 chm1:+:1642082974:-1 chm1:+:1717357637:-1 chm1:+:1871838309:-1 chm1:+:2352736233:-1 chm1:+:2417135771:-1 chm1:+:2436627757:-1 chm1:+:2463467712:-1 chm1:+:2859499674:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTC chm1:+:18877818:-1 chm1:+:188102324:-1 chm1:+:267000813:-1 chm1:+:540458754:-1 chm1:+:558525197:-1 chm1:+:600780424:-1 chm1:+:607844220:-1 chm1:+:661385184:-1 chm1:+:980272586:-1 chm1:+:1136720925:-1 chm1:+:1269682335:-1 chm1:+:1289133004:-1 chm1:+:1519718681:-1 chm1:+:1546526671:-1 chm1:+:1546526806:-1 chm1:+:1735570621:-1 chm1:+:2008628066:-1 chm1:+:2060679575:-1 chm1:+:2069992442:-1 chm1:+:2080291814:-1 chm1:+:2235469390:-1 chm1:+:2265668900:-1 chm1:+:2270010397:-1 chm1:+:2408677272:-1 chm1:+:2468184557:-1 chm1:+:2578390257:-1 chm1:+:2651754770:-1 chm1:+:2661593484:-1 chm1:+:2689798078:-1 chm1:+:2695686162:-1 chm1:+:2719007672:-1 chm1:+:2729663420:-1 chm1:+:2827914199:-1 chm1:+:2860893974:-1 chm1:+:2929666031:-1 chm1:+:3003980369:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTC chm1:+:911208905:32 chm1:+:1931219630:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTC chm1:+:911208902:32 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTC chm1:+:911208901:32 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTC chm1:+:911208907:32 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTC chm1:+:911208920:32 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTC chm1:+:73177653:-1 chm1:+:409773604:-1 chm1:+:548293091:-1 chm1:+:795768790:-1 chm1:+:959626239:-1 chm1:+:1017632804:-1 chm1:+:1288990381:-1 chm1:+:1475772800:-1 chm1:+:2069151329:-1 chm1:+:2272933195:-1 chm1:+:2710492308:-1 chm1:+:2764418062:-1 chm1:+:2764751226:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTC chm1:+:188931754:-1 chm1:+:202806602:-1 chm1:+:384841179:-1 chm1:+:762226367:-1 chm1:+:911208917:32 chm1:+:1285099121:-1 chm1:+:1296898520:-1 chm1:+:1335065430:-1 chm1:+:1644155827:-1 chm1:+:1876816348:-1 chm1:+:2112925177:-1 chm1:+:2340065625:-1 chm1:+:2487221376:-1 chm1:+:2542179596:-1 chm1:+:2579147398:-1 chm1:+:2681839737:-1 chm1:+:2703466042:-1 chm1:+:2774266843:-1 chm1:+:2860943660:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTC chm1:+:1079011772:-1 chm1:+:1287601088:-1 chm1:+:1384818982:-1 chm1:+:2000795295:-1 chm1:+:2050623042:-1 chm1:+:2593991523:-1 +GACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:2698916144:-1 +GACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:10559069:-1 chm1:+:47502511:-1 chm1:+:542435821:-1 chm1:+:551381400:-1 chm1:+:702538602:-1 chm1:+:722023566:-1 chm1:+:985279782:-1 chm1:+:1236553330:-1 chm1:+:1338481015:-1 chm1:+:1369672130:-1 chm1:+:1558304079:-1 chm1:+:1711921834:-1 chm1:+:1927857322:-1 chm1:+:1993462200:-1 chm1:+:2007784347:-1 chm1:+:2053876846:-1 chm1:+:2354087155:-1 chm1:+:2364754749:-1 chm1:+:2401191857:-1 chm1:+:2436962331:-1 chm1:+:2468424059:-1 chm1:+:2487538943:-1 chm1:+:2506902007:-1 chm1:+:2553008139:-1 chm1:+:2571521270:-1 chm1:+:2588779139:-1 chm1:+:2662124458:-1 chm1:+:2672400355:-1 chm1:+:2681741954:-1 chm1:+:2713880440:-1 chm1:+:2865529300:-1 chm1:+:2988985666:-1 +GACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:335369128:-1 chm1:+:746633420:-1 chm1:+:1694922905:-1 chm1:+:2392916531:-1 +GACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:26841704:-1 chm1:+:553060197:-1 chm1:+:1015169501:-1 chm1:+:1653691023:-1 chm1:+:2468600528:-1 +GACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:2012637944:-1 chm1:+:2039268692:-1 +GACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:1756015052:-1 chm1:+:1959968778:-1 +GACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:204331235:-1 chm1:+:542083342:-1 chm1:+:875149070:-1 chm1:+:1627785546:-1 chm1:+:1871995822:-1 chm1:+:2718526926:-1 chm1:+:2760931682:-1 +GACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:33131520:-1 chm1:+:275806873:-1 chm1:+:288697910:-1 chm1:+:428395923:-1 chm1:+:678003726:-1 chm1:+:893141175:-1 chm1:+:1162535365:-1 chm1:+:1432876364:-1 chm1:+:1492659616:-1 chm1:+:1539932813:-1 chm1:+:1898627561:-1 chm1:+:1957911917:-1 chm1:+:2170145927:-1 chm1:+:2268055250:-1 chm1:+:2302440057:-1 chm1:+:2517913528:-1 chm1:+:2567547065:-1 chm1:+:2717219820:-1 chm1:+:2855197944:-1 chm1:+:2889498272:-1 +GACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:161200851:-1 chm1:+:515714065:-1 chm1:+:731186989:-1 chm1:+:1150706161:-1 chm1:+:1362428661:-1 chm1:+:1545125732:-1 chm1:+:1882548689:-1 chm1:+:2336409216:-1 chm1:+:2338097044:-1 chm1:+:2426639958:-1 chm1:+:2505363423:-1 chm1:+:2578048488:-1 chm1:+:2764650664:-1 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAG chm1:+:579649755:-1 chm1:+:587173858:-1 chm1:+:857243065:29 chm1:+:1706060586:-1 chm1:+:2967293282:-1 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAG chm1:+:857243064:29 chm1:+:2619475345:-1 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAG chm1:+:1310506731:-1 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAG chm1:+:857243069:29 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAG chm1:+:857243067:29 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAG chm1:+:2375919617:-1 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAG chm1:+:2005749991:-1 +CTCATGAGATCTGGTTGGTTTAAAAGTGTGTGGCGACCTCCCCTTCACTCTCTTCCTCCTGTTCCAGTCATGTAAGACGTGCCTGACTTCCCCTTCGGCCTGCCGCCATGAATTGAAGGTTTCCTGGAGGCCGTCCCTACCCCATGCTTCCTGTACAGCTGCGGGACTGTGAGCCAATTAAATCTCTTTTCTTTATAAATTATTCAATCTAGGTAGCTCTTCATAGCAGTGTGAGAATGGACTAAGACAACTGGCCTTCGCCTTTAAGTTCCTAAATTCATGTGGGTGTACCTGCTCCTGGATCTACACCTTTTTGGTCTGGGCGTCTGAACCCTTCTCAGTAGGTGGGCCCTAGGCTTTGATCCAGGCCACAGGGAGAAATCCTAGCATTCATTTTTCCCTTCCACTGCTTTCCAACTACTGCTAGTCTAAGGAGAGGTAGATACTATGAACTTGGGAGTTGAATAAGGTGGACACTTTGGGCTTAAAGTTTTCTAGAAAATTAGGCAATCATTAAGTTGTAATATTCATATTGTCCATAAGCATCAAACAACTCTGCTGCGTAACAAAAAGAATAATCTTTTTTCTTGAAGTCTAGTA chm1:+:1224162544:-1 +CTCATGAGATCTGGTTGGTTTAAAAGTGTGTGGCGACCTCCCCTTCACTCTCTTCCTCCTGTTCCAGTCATGTAAGACGTGCCTGACTTCCCCTTCGGCCTGCCGCCATGAATTGAAGGTTTCCTGGAGGCCGTCCCTACCCCATGCTTCCTGTACAGCTGCGGGACTGTGAGCCAATTAAATCTCTTTTCTTTATAAATTATTCAATCTAGGTAGCTCTTCATAGCAGTGTGAGAATGGACTAAGACAACTGGCCTTCGCCTTTAAGTTCCTAAATTCATGTGGGTGTACCTGCTCCTGGATCTACACCTTTTTGGTCTGGGCGTCTGAACCCTTCTCAGTAGGTGGGCCCTAGGCTTTGATCCAGGCCACAGGGAGAAATCCTAGCATTCATTTTTCCCTTCCACTGCTTTCCAACTACTGCTAGTCTAAGGAGAGGTAGATACTATGAACTTGGGAGTTGAATAAGGTGGACACTTTGGGCTTAAAGTTTTCTAGAAAATTAGGCAATCATTAAGTTGTAATATTCATATTGTCCATAAGCATCAAACAACTCTGCTGCGTAACAAAAAGAATAATCTTTTTTCTTGAAGTCTAGTA chm1:+:621487187:-1 +CTCATGAGATCTGGTTGGTTTAAAAGTGTGTGGCGACCTCCCCTTCACTCTCTTCCTCCTGTTCCAGTCATGTAAGACGTGCCTGACTTCCCCTTCGGCCTGCCGCCATGAATTGAAGGTTTCCTGGAGGCCGTCCCTACCCCATGCTTCCTGTACAGCTGCGGGACTGTGAGCCAATTAAATCTCTTTTCTTTATAAATTATTCAATCTAGGTAGCTCTTCATAGCAGTGTGAGAATGGACTAAGACAACTGGCCTTCGCCTTTAAGTTCCTAAATTCATGTGGGTGTACCTGCTCCTGGATCTACACCTTTTTGGTCTGGGCGTCTGAACCCTTCTCAGTAGGTGGGCCCTAGGCTTTGATCCAGGCCACAGGGAGAAATCCTAGCATTCATTTTTCCCTTCCACTGCTTTCCAACTACTGCTAGTCTAAGGAGAGGTAGATACTATGAACTTGGGAGTTGAATAAGGTGGACACTTTGGGCTTAAAGTTTTCTAGAAAATTAGGCAATCATTAAGTTGTAATATTCATATTGTCCATAAGCATCAAACAACTCTGCTGCGTAACAAAAAGAATAATCTTTTTTCTTGAAGTCTAGTA chm1:+:801110430:-1 chm1:+:1098973217:-1 chm1:+:2267756681:-1 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGAT chm1:+:2389033809:-1 chm1:+:3012507099:25 chm1:+:3022098899:-1 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGAT chm1:+:3012507098:25 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGAT chm1:+:238429634:-1 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGAT chm1:+:3012507094:25 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGAT chm1:+:978903484:-1 chm1:+:1280338229:-1 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGAT chm1:+:3012507096:25 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGAT chm1:+:151817270:-1 chm1:+:234028040:-1 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGAT chm1:+:3012507100:25 +ATCAATAAATGTGGATAATCACACAAAAAGACTTAAAGACAAAAACCAATATAATCATCTTAATAGATGCAGAAAAAGCTATTCAATAAAATTCTAGCACCAACTTTGTGATAAAATCCTCAACAAACCTGGTATAAAAGAAACATACCTCAAAATAACATTAGGTAATATTTGACAAAACCCAAGCCAACATCATACTTAACCGAACAGTTGAAAGCATTCCTCTAAGAACTGGAGCAAGATAACAATGCTCATTTTCACCACTGTTATTCAACATAGTACTAGAAGGTCCTTTGCCAGAGCAATCAACAAGAGGAAAAAAAAAAGACATCTAAAGTTGGAAAAGATGAAGTCAAATTATCCTTGTTCACCAATGATAGGATCTGACTATCTTGAAAACACTAGAGACTCCACCAAAAAACTTTCATTTTGGTAAATGAATTCAGTAAAGTTTCAGGATACAAAATTAACTACAGAGATCAGTAACATTTCTGTACACCAATAATGATACCAGCCAGGACCAAATCATAAAATACATAAAAAACATAAAAATACCTTAGGAATATTATTTAACCAAGAAGGTGAATATCTCTCTAAGCC chm1:+:795750629:-1 chm1:+:2963122055:-1 +ATCAATAAATGTGGATAATCACACAAAAAGACTTAAAGACAAAAACCAATATAATCATCTTAATAGATGCAGAAAAAGCTATTCAATAAAATTCTAGCACCAACTTTGTGATAAAATCCTCAACAAACCTGGTATAAAAGAAACATACCTCAAAATAACATTAGGTAATATTTGACAAAACCCAAGCCAACATCATACTTAACCGAACAGTTGAAAGCATTCCTCTAAGAACTGGAGCAAGATAACAATGCTCATTTTCACCACTGTTATTCAACATAGTACTAGAAGGTCCTTTGCCAGAGCAATCAACAAGAGGAAAAAAAAAAGACATCTAAAGTTGGAAAAGATGAAGTCAAATTATCCTTGTTCACCAATGATAGGATCTGACTATCTTGAAAACACTAGAGACTCCACCAAAAAACTTTCATTTTGGTAAATGAATTCAGTAAAGTTTCAGGATACAAAATTAACTACAGAGATCAGTAACATTTCTGTACACCAATAATGATACCAGCCAGGACCAAATCATAAAATACATAAAAAACATAAAAATACCTTAGGAATATTATTTAACCAAGAAGGTGAATATCTCTCTAAGCC chm1:+:2639113393:-1 +ATCAATAAATGTGGATAATCACACAAAAAGACTTAAAGACAAAAACCAATATAATCATCTTAATAGATGCAGAAAAAGCTATTCAATAAAATTCTAGCACCAACTTTGTGATAAAATCCTCAACAAACCTGGTATAAAAGAAACATACCTCAAAATAACATTAGGTAATATTTGACAAAACCCAAGCCAACATCATACTTAACCGAACAGTTGAAAGCATTCCTCTAAGAACTGGAGCAAGATAACAATGCTCATTTTCACCACTGTTATTCAACATAGTACTAGAAGGTCCTTTGCCAGAGCAATCAACAAGAGGAAAAAAAAAAGACATCTAAAGTTGGAAAAGATGAAGTCAAATTATCCTTGTTCACCAATGATAGGATCTGACTATCTTGAAAACACTAGAGACTCCACCAAAAAACTTTCATTTTGGTAAATGAATTCAGTAAAGTTTCAGGATACAAAATTAACTACAGAGATCAGTAACATTTCTGTACACCAATAATGATACCAGCCAGGACCAAATCATAAAATACATAAAAAACATAAAAATACCTTAGGAATATTATTTAACCAAGAAGGTGAATATCTCTCTAAGCC chm1:+:115688084:-1 chm1:+:205825670:-1 chm1:+:291035747:-1 chm1:+:655296333:-1 chm1:+:689377757:-1 chm1:+:968418099:-1 chm1:+:1119449400:-1 chm1:+:2132683235:-1 chm1:+:2791104015:-1 +ATCAATAAATGTGGATAATCACACAAAAAGACTTAAAGACAAAAACCAATATAATCATCTTAATAGATGCAGAAAAAGCTATTCAATAAAATTCTAGCACCAACTTTGTGATAAAATCCTCAACAAACCTGGTATAAAAGAAACATACCTCAAAATAACATTAGGTAATATTTGACAAAACCCAAGCCAACATCATACTTAACCGAACAGTTGAAAGCATTCCTCTAAGAACTGGAGCAAGATAACAATGCTCATTTTCACCACTGTTATTCAACATAGTACTAGAAGGTCCTTTGCCAGAGCAATCAACAAGAGGAAAAAAAAAAGACATCTAAAGTTGGAAAAGATGAAGTCAAATTATCCTTGTTCACCAATGATAGGATCTGACTATCTTGAAAACACTAGAGACTCCACCAAAAAACTTTCATTTTGGTAAATGAATTCAGTAAAGTTTCAGGATACAAAATTAACTACAGAGATCAGTAACATTTCTGTACACCAATAATGATACCAGCCAGGACCAAATCATAAAATACATAAAAAACATAAAAATACCTTAGGAATATTATTTAACCAAGAAGGTGAATATCTCTCTAAGCC chm1:+:250226319:-1 chm1:+:362193616:-1 chm1:+:376736222:-1 chm1:+:512183567:-1 chm1:+:684215220:-1 chm1:+:879038093:-1 chm1:+:907728443:-1 chm1:+:1427689680:-1 chm1:+:1771697141:-1 chm1:+:1840034229:-1 chm1:+:1897316713:-1 chm1:+:2117462707:-1 chm1:+:2263038119:-1 chm1:+:2379427942:-1 chm1:+:2507038854:-1 +ATCAATAAATGTGGATAATCACACAAAAAGACTTAAAGACAAAAACCAATATAATCATCTTAATAGATGCAGAAAAAGCTATTCAATAAAATTCTAGCACCAACTTTGTGATAAAATCCTCAACAAACCTGGTATAAAAGAAACATACCTCAAAATAACATTAGGTAATATTTGACAAAACCCAAGCCAACATCATACTTAACCGAACAGTTGAAAGCATTCCTCTAAGAACTGGAGCAAGATAACAATGCTCATTTTCACCACTGTTATTCAACATAGTACTAGAAGGTCCTTTGCCAGAGCAATCAACAAGAGGAAAAAAAAAAGACATCTAAAGTTGGAAAAGATGAAGTCAAATTATCCTTGTTCACCAATGATAGGATCTGACTATCTTGAAAACACTAGAGACTCCACCAAAAAACTTTCATTTTGGTAAATGAATTCAGTAAAGTTTCAGGATACAAAATTAACTACAGAGATCAGTAACATTTCTGTACACCAATAATGATACCAGCCAGGACCAAATCATAAAATACATAAAAAACATAAAAATACCTTAGGAATATTATTTAACCAAGAAGGTGAATATCTCTCTAAGCC chm1:+:74693099:-1 chm1:+:211194395:-1 chm1:+:211234387:-1 chm1:+:272444779:-1 chm1:+:385979364:-1 chm1:+:706572482:-1 chm1:+:758801159:-1 chm1:+:938211169:-1 chm1:+:1131534663:-1 chm1:+:1136352672:-1 chm1:+:1141664349:-1 chm1:+:1453585462:-1 chm1:+:1569591206:-1 chm1:+:1812168124:-1 chm1:+:1955363222:-1 chm1:+:2223628710:-1 chm1:+:2937029870:-1 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTC chm1:+:156606780:-1 chm1:+:237092404:-1 chm1:+:960281494:-1 chm1:+:1459391083:25 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTC chm1:+:1459391082:25 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTC chm1:+:1459391086:25 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTC chm1:+:913682278:-1 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTC chm1:+:285064143:-1 chm1:+:1459391084:25 +GAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC chm1:+:2717239972:-1 +GAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC chm1:+:540241063:-1 chm1:+:860688725:-1 chm1:+:926165544:-1 chm1:+:1444413926:-1 chm1:+:1448260566:-1 chm1:+:1471629342:-1 chm1:+:1567200205:-1 chm1:+:1750023777:-1 chm1:+:1794730420:-1 chm1:+:2110098659:-1 chm1:+:2345518578:-1 chm1:+:2349312798:-1 chm1:+:2351944856:-1 chm1:+:2544596369:-1 chm1:+:2544814304:-1 chm1:+:2608125960:-1 +GAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC chm1:+:183214449:-1 chm1:+:1184650965:-1 chm1:+:2269285812:-1 +GAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC chm1:+:231018110:-1 chm1:+:778376112:-1 chm1:+:943487158:-1 chm1:+:1234275905:-1 chm1:+:1554528191:-1 chm1:+:1610337683:-1 chm1:+:1753270479:-1 chm1:+:1819711657:-1 chm1:+:2119224888:-1 chm1:+:2162387635:-1 chm1:+:2425722986:-1 chm1:+:2458339231:-1 chm1:+:2568251479:-1 chm1:+:2672462395:-1 chm1:+:2720483477:-1 chm1:+:2824411525:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:9549853:-1 chm1:+:9564239:-1 chm1:+:12322856:-1 chm1:+:38468001:-1 chm1:+:112189256:-1 chm1:+:169945961:-1 chm1:+:179835635:-1 chm1:+:181873717:-1 chm1:+:208959526:-1 chm1:+:212507729:-1 chm1:+:224442666:-1 chm1:+:314427457:-1 chm1:+:370010412:-1 chm1:+:378595228:-1 chm1:+:381583980:-1 chm1:+:389809681:-1 chm1:+:397846621:-1 chm1:+:410565191:-1 chm1:+:445881608:-1 chm1:+:462972220:-1 chm1:+:483083514:-1 chm1:+:620350745:-1 chm1:+:659029247:-1 chm1:+:679497660:-1 chm1:+:845075368:-1 chm1:+:860829574:-1 chm1:+:895182783:-1 chm1:+:910794882:-1 chm1:+:913492213:-1 chm1:+:913537431:-1 chm1:+:915930202:-1 chm1:+:938056635:-1 chm1:+:946210152:-1 chm1:+:949130733:-1 chm1:+:997907533:-1 chm1:+:1061064155:-1 chm1:+:1106141278:-1 chm1:+:1207302694:-1 chm1:+:1218934571:-1 chm1:+:1238018931:-1 chm1:+:1255120786:-1 chm1:+:1301361880:-1 chm1:+:1303640812:-1 chm1:+:1330969127:-1 chm1:+:1334402727:-1 chm1:+:1336587491:-1 chm1:+:1336604328:-1 chm1:+:1432552461:-1 chm1:+:1491562973:-1 chm1:+:1514579894:-1 chm1:+:1520470068:-1 chm1:+:1521334605:-1 chm1:+:1541985287:-1 chm1:+:1567720480:-1 chm1:+:1570551975:-1 chm1:+:1572479315:-1 chm1:+:1579467468:-1 chm1:+:1583050417:-1 chm1:+:1604792024:-1 chm1:+:1613561197:-1 chm1:+:1640012653:-1 chm1:+:1653778265:-1 chm1:+:1656167244:-1 chm1:+:1656688805:-1 chm1:+:1673272267:-1 chm1:+:1696802516:-1 chm1:+:1702311244:-1 chm1:+:1749207346:-1 chm1:+:1754479457:-1 chm1:+:1755872863:-1 chm1:+:1782341101:-1 chm1:+:1783676904:-1 chm1:+:1785813273:-1 chm1:+:1819935629:-1 chm1:+:1834121218:-1 chm1:+:1922151787:-1 chm1:+:1924277542:-1 chm1:+:1927047258:-1 chm1:+:1932995130:-1 chm1:+:2017482071:-1 chm1:+:2061606796:-1 chm1:+:2062343524:-1 chm1:+:2071701403:-1 chm1:+:2076883652:-1 chm1:+:2080316324:-1 chm1:+:2219474951:-1 chm1:+:2359244089:-1 chm1:+:2402091714:-1 chm1:+:2414299230:-1 chm1:+:2429385911:-1 chm1:+:2431219661:-1 chm1:+:2432055750:-1 chm1:+:2439198792:-1 chm1:+:2465399632:-1 chm1:+:2484614362:-1 chm1:+:2485650784:-1 chm1:+:2486453734:-1 chm1:+:2512783667:-1 chm1:+:2521022528:-1 chm1:+:2538492657:-1 chm1:+:2548304126:-1 chm1:+:2559896705:-1 chm1:+:2571242395:-1 chm1:+:2571846034:-1 chm1:+:2574950519:-1 chm1:+:2590186778:-1 chm1:+:2591269046:-1 chm1:+:2627861375:-1 chm1:+:2635027694:-1 chm1:+:2649237599:-1 chm1:+:2650591302:-1 chm1:+:2651886619:-1 chm1:+:2661610827:-1 chm1:+:2662875919:-1 chm1:+:2666132562:-1 chm1:+:2696741397:-1 chm1:+:2699633930:-1 chm1:+:2710983324:-1 chm1:+:2712593610:-1 chm1:+:2740092286:-1 chm1:+:2750076878:-1 chm1:+:2770188107:-1 chm1:+:2872775331:-1 chm1:+:2875369219:-1 chm1:+:2877796577:-1 chm1:+:2886456582:-1 chm1:+:3034334417:-1 chm1:+:3051627962:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:320148745:-1 chm1:+:447322865:-1 chm1:+:1816790161:-1 chm1:+:1823905522:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:2886661849:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:17740298:-1 chm1:+:97579531:-1 chm1:+:1862445109:-1 chm1:+:2869508374:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:363745560:-1 chm1:+:493317169:-1 chm1:+:504872692:-1 chm1:+:725045035:-1 chm1:+:920783740:-1 chm1:+:1136275678:-1 chm1:+:1630140391:-1 chm1:+:2464559388:-1 chm1:+:2577913814:-1 chm1:+:2740918137:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:188003486:-1 chm1:+:2030837287:-1 chm1:+:2144698764:-1 chm1:+:2170131897:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:5002586:-1 chm1:+:37670522:-1 chm1:+:81679836:-1 chm1:+:84452232:-1 chm1:+:268238765:-1 chm1:+:281455214:-1 chm1:+:309560791:-1 chm1:+:327797954:-1 chm1:+:375765041:-1 chm1:+:403502829:-1 chm1:+:407988598:-1 chm1:+:428917447:-1 chm1:+:457553395:-1 chm1:+:467238255:-1 chm1:+:469767504:-1 chm1:+:501819682:-1 chm1:+:501819711:-1 chm1:+:532266329:-1 chm1:+:548461656:-1 chm1:+:576595710:-1 chm1:+:636529208:-1 chm1:+:664987284:-1 chm1:+:716117902:-1 chm1:+:773709779:-1 chm1:+:843862787:-1 chm1:+:861229369:-1 chm1:+:996791398:-1 chm1:+:1037296829:-1 chm1:+:1077108228:-1 chm1:+:1101622076:-1 chm1:+:1111606321:-1 chm1:+:1141106845:-1 chm1:+:1148205271:-1 chm1:+:1160675589:-1 chm1:+:1172370061:-1 chm1:+:1190931078:-1 chm1:+:1406253058:-1 chm1:+:1447170264:-1 chm1:+:1466283051:-1 chm1:+:1501861218:-1 chm1:+:1503619478:-1 chm1:+:1727142047:-1 chm1:+:1729331782:-1 chm1:+:1735753298:-1 chm1:+:1770943266:-1 chm1:+:1834976014:-1 chm1:+:2027267313:-1 chm1:+:2079024696:-1 chm1:+:2080751663:-1 chm1:+:2142373603:-1 chm1:+:2227948672:-1 chm1:+:2244118118:-1 chm1:+:2256709411:-1 chm1:+:2271795581:-1 chm1:+:2274563768:-1 chm1:+:2381034398:-1 chm1:+:2393615893:-1 chm1:+:2395520171:-1 chm1:+:2466163770:-1 chm1:+:2492862507:-1 chm1:+:2513452851:-1 chm1:+:2553299637:-1 chm1:+:2639396811:-1 chm1:+:2691789312:-1 chm1:+:2896880119:-1 chm1:+:2920598934:-1 chm1:+:3034354010:-1 chm1:+:3061815499:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:239518770:-1 chm1:+:358690777:-1 chm1:+:612805645:-1 chm1:+:1005677468:-1 chm1:+:1063645986:-1 chm1:+:1256744616:-1 chm1:+:1392200158:-1 chm1:+:1672883620:-1 chm1:+:1689088097:-1 chm1:+:2405675139:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:353147787:-1 chm1:+:888550155:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:30503253:-1 chm1:+:53692852:-1 chm1:+:80384528:-1 chm1:+:298970876:-1 chm1:+:312984621:-1 chm1:+:328813523:-1 chm1:+:414823312:-1 chm1:+:446792434:-1 chm1:+:498376672:-1 chm1:+:708862460:-1 chm1:+:727379327:-1 chm1:+:855367051:-1 chm1:+:887023884:-1 chm1:+:922320431:-1 chm1:+:939194308:-1 chm1:+:973694555:-1 chm1:+:1012287296:-1 chm1:+:1227109234:-1 chm1:+:1398124095:-1 chm1:+:1470044283:-1 chm1:+:1682104820:-1 chm1:+:1748927006:-1 chm1:+:1776363710:-1 chm1:+:1815297069:-1 chm1:+:2042795683:-1 chm1:+:2156220154:-1 chm1:+:2159404054:-1 chm1:+:2349687775:-1 chm1:+:2403421981:-1 chm1:+:2405283207:-1 chm1:+:2460942695:-1 chm1:+:2463341377:-1 chm1:+:2608170474:-1 chm1:+:2638613340:-1 chm1:+:2963674523:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:54578036:-1 chm1:+:1263016028:-1 chm1:+:1642989528:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:202731457:-1 chm1:+:401919618:-1 chm1:+:411419486:-1 chm1:+:420548665:-1 chm1:+:551642717:-1 chm1:+:575456127:-1 chm1:+:581914558:-1 chm1:+:588095874:-1 chm1:+:593897235:-1 chm1:+:611318707:-1 chm1:+:611540902:-1 chm1:+:673224201:-1 chm1:+:737873125:-1 chm1:+:801713175:-1 chm1:+:855854698:-1 chm1:+:1064378083:-1 chm1:+:1137523031:-1 chm1:+:1160529475:-1 chm1:+:1164653784:-1 chm1:+:1223350943:-1 chm1:+:1244102716:-1 chm1:+:1283499290:-1 chm1:+:1314674279:-1 chm1:+:1355962037:-1 chm1:+:1424128114:-1 chm1:+:1504552115:-1 chm1:+:1514288157:-1 chm1:+:1542220938:-1 chm1:+:1545986378:-1 chm1:+:1772460993:-1 chm1:+:1865730377:-1 chm1:+:2026980586:-1 chm1:+:2048762762:-1 chm1:+:2134062203:-1 chm1:+:2155316455:-1 chm1:+:2226452124:-1 chm1:+:2233372018:-1 chm1:+:2381217758:-1 chm1:+:2440420977:-1 chm1:+:2513923261:-1 chm1:+:2750921394:-1 chm1:+:2889197740:-1 chm1:+:2911436175:-1 chm1:+:2947137482:-1 chm1:+:2949909656:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:45612886:-1 chm1:+:255056148:-1 chm1:+:396981883:-1 chm1:+:412885514:-1 chm1:+:481061663:-1 chm1:+:645261014:-1 chm1:+:756493208:-1 chm1:+:923446728:-1 chm1:+:966676976:-1 chm1:+:973863822:-1 chm1:+:1079660160:-1 chm1:+:1247409139:-1 chm1:+:1355444043:-1 chm1:+:1507731179:-1 chm1:+:1677946176:-1 chm1:+:1767945520:-1 chm1:+:1789323555:-1 chm1:+:1961522343:-1 chm1:+:2051189974:-1 chm1:+:2155743243:-1 chm1:+:2589489571:-1 chm1:+:2715871925:-1 chm1:+:2806601752:-1 chm1:+:2942984498:-1 chm1:+:2977277379:-1 chm1:+:3000454334:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:15117283:-1 chm1:+:174355740:-1 chm1:+:369577410:-1 chm1:+:622186706:-1 chm1:+:688691700:-1 chm1:+:773709217:-1 chm1:+:898688242:-1 chm1:+:1222993929:-1 chm1:+:1396799920:-1 chm1:+:1537236797:-1 chm1:+:1539951688:-1 chm1:+:1834607963:-1 chm1:+:2274355653:-1 chm1:+:2676839610:-1 chm1:+:2693988253:-1 chm1:+:2704961846:-1 chm1:+:2931553069:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGAC chm1:+:286095605:-1 chm1:+:441536511:-1 chm1:+:488672190:-1 chm1:+:1069742556:-1 chm1:+:1760079533:-1 chm1:+:1816507235:-1 chm1:+:1898241275:-1 chm1:+:2068114917:-1 chm1:+:2115138558:-1 chm1:+:2130431834:-1 chm1:+:2371273400:-1 chm1:+:2764387349:-1 chm1:+:2768374676:-1 +GTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:35639679:-1 chm1:+:143900652:-1 chm1:+:149454059:-1 chm1:+:461860845:-1 chm1:+:617876045:-1 chm1:+:898585767:-1 chm1:+:1103597201:-1 chm1:+:1105765520:-1 chm1:+:1202868282:-1 chm1:+:1667137367:-1 chm1:+:1678990494:-1 chm1:+:1757328158:-1 chm1:+:1982896611:-1 chm1:+:2153246501:-1 chm1:+:2373083472:-1 chm1:+:2424304880:-1 chm1:+:2459994268:-1 chm1:+:2493923804:-1 chm1:+:2578880919:-1 chm1:+:2674989445:-1 chm1:+:2709911944:-1 chm1:+:2754282424:-1 chm1:+:2819323891:-1 chm1:+:3012631437:-1 +GTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2045359768:-1 chm1:+:2694373519:33 +GTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2694373520:33 +GTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2694373529:33 +GTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2694373522:33 +GTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:87511580:-1 chm1:+:2694373524:33 +GTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2694373528:33 +GTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2694373530:33 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTC chm1:+:2277191541:-1 chm1:+:2821050440:40 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTC chm1:+:383819783:-1 chm1:+:1270415843:-1 chm1:+:1278428696:-1 chm1:+:1463007856:-1 chm1:+:1876147207:-1 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTC chm1:+:2821050444:40 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTC chm1:+:26555287:-1 chm1:+:98345585:-1 chm1:+:216742464:-1 chm1:+:231649200:-1 chm1:+:263712274:-1 chm1:+:424812722:-1 chm1:+:504172422:-1 chm1:+:923142827:-1 chm1:+:1051941474:-1 chm1:+:1370265979:-1 chm1:+:1466224111:-1 chm1:+:1545101183:-1 chm1:+:2242235762:-1 chm1:+:2953680187:-1 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTC chm1:+:2821050434:40 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTC chm1:+:490610119:-1 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTC chm1:+:2821050437:40 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTC chm1:+:2821050438:40 +GAGGACCTGACTGTCCTTAAATGAAATATTAATACTGAAGAGGAAAAAGTATCAGGCCATGCTTCTACCCGAGTGGGACAGAGGTAAGAAATCTAGAATGCAGCTTTTGGGTAGCCCAACAACTTGAAATTTCTTAACAGGACAAAGAAAGCCCAGCCAACATGAATGAGTTTATTTCCCTTTATTGAGATAAGAAAAGCCACTAACCCTCGAGCCTGAGGATATTTTTTACCTGTTTCTTCTTCCATTAAAGTTAGGGGTTACTCTTACAAGTCCAGTGATTTTAGACACATGGAACCGATCAACTTTGAATCCTGGGAATCCTTTCCTTTAAGAGTGGTGTATTACCTGTCTTTATATTGAACTCTTAGGGACCTTCTGCCTTGCCAGTTATCTCTCCCTTGTCTCTGAAGACCTAGACCTTTCTTTTTCCTTCCTTCCTATTTTACTTCCTGTGAACTGTGTCTTGACTGTATCGTATTAGCTTCTTGTTTCTCAACGTTTTTATCCTCACTACGTGGAGATAAATGTATGTCACTGAAGTTCTTAAATAAGTGGAGTCATAAGAAAAACATGGACTAACTAATCTGAACTACGATA chm1:+:268666008:-1 chm1:+:351811579:-1 chm1:+:1562469553:-1 chm1:+:2036468139:-1 +GAGGACCTGACTGTCCTTAAATGAAATATTAATACTGAAGAGGAAAAAGTATCAGGCCATGCTTCTACCCGAGTGGGACAGAGGTAAGAAATCTAGAATGCAGCTTTTGGGTAGCCCAACAACTTGAAATTTCTTAACAGGACAAAGAAAGCCCAGCCAACATGAATGAGTTTATTTCCCTTTATTGAGATAAGAAAAGCCACTAACCCTCGAGCCTGAGGATATTTTTTACCTGTTTCTTCTTCCATTAAAGTTAGGGGTTACTCTTACAAGTCCAGTGATTTTAGACACATGGAACCGATCAACTTTGAATCCTGGGAATCCTTTCCTTTAAGAGTGGTGTATTACCTGTCTTTATATTGAACTCTTAGGGACCTTCTGCCTTGCCAGTTATCTCTCCCTTGTCTCTGAAGACCTAGACCTTTCTTTTTCCTTCCTTCCTATTTTACTTCCTGTGAACTGTGTCTTGACTGTATCGTATTAGCTTCTTGTTTCTCAACGTTTTTATCCTCACTACGTGGAGATAAATGTATGTCACTGAAGTTCTTAAATAAGTGGAGTCATAAGAAAAACATGGACTAACTAATCTGAACTACGATA chm1:+:220845793:-1 chm1:+:409382449:-1 chm1:+:417695401:-1 chm1:+:499908387:-1 chm1:+:678765002:-1 chm1:+:688642027:-1 chm1:+:709738192:-1 chm1:+:883055708:-1 chm1:+:1027906258:-1 chm1:+:1033100555:-1 chm1:+:1046607986:-1 chm1:+:1058153037:-1 chm1:+:1081860913:-1 chm1:+:1098239009:-1 chm1:+:1136040942:-1 chm1:+:1416305177:-1 chm1:+:1494900068:-1 chm1:+:1500751391:-1 chm1:+:1541471394:-1 chm1:+:1685149851:-1 chm1:+:1821536932:-1 chm1:+:1847265742:-1 chm1:+:1911426632:-1 chm1:+:1995126571:-1 chm1:+:2006326645:-1 chm1:+:2041201984:-1 chm1:+:2221598589:-1 chm1:+:2221706050:-1 chm1:+:2241057292:-1 chm1:+:2270298194:-1 chm1:+:2390722359:-1 chm1:+:2424207396:-1 chm1:+:2439607960:-1 chm1:+:2572170997:-1 chm1:+:2633287253:-1 chm1:+:2656897078:-1 chm1:+:2689985119:-1 chm1:+:2908666742:-1 +GAGGACCTGACTGTCCTTAAATGAAATATTAATACTGAAGAGGAAAAAGTATCAGGCCATGCTTCTACCCGAGTGGGACAGAGGTAAGAAATCTAGAATGCAGCTTTTGGGTAGCCCAACAACTTGAAATTTCTTAACAGGACAAAGAAAGCCCAGCCAACATGAATGAGTTTATTTCCCTTTATTGAGATAAGAAAAGCCACTAACCCTCGAGCCTGAGGATATTTTTTACCTGTTTCTTCTTCCATTAAAGTTAGGGGTTACTCTTACAAGTCCAGTGATTTTAGACACATGGAACCGATCAACTTTGAATCCTGGGAATCCTTTCCTTTAAGAGTGGTGTATTACCTGTCTTTATATTGAACTCTTAGGGACCTTCTGCCTTGCCAGTTATCTCTCCCTTGTCTCTGAAGACCTAGACCTTTCTTTTTCCTTCCTTCCTATTTTACTTCCTGTGAACTGTGTCTTGACTGTATCGTATTAGCTTCTTGTTTCTCAACGTTTTTATCCTCACTACGTGGAGATAAATGTATGTCACTGAAGTTCTTAAATAAGTGGAGTCATAAGAAAAACATGGACTAACTAATCTGAACTACGATA chm1:+:78420454:-1 chm1:+:1852316941:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:1474079854:-1 chm1:+:1520577141:-1 chm1:+:1665632815:-1 chm1:+:1744579539:-1 chm1:+:2010812169:-1 chm1:+:2245363814:-1 chm1:+:2606469707:-1 chm1:+:2609464780:-1 chm1:+:2627262086:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:89442681:-1 chm1:+:337083258:-1 chm1:+:485694564:-1 chm1:+:513678656:-1 chm1:+:605396396:-1 chm1:+:950301980:-1 chm1:+:1115890067:-1 chm1:+:1282884952:-1 chm1:+:1312320107:-1 chm1:+:1390794138:-1 chm1:+:1481780252:-1 chm1:+:2812951717:-1 chm1:+:2872178498:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:57609804:-1 chm1:+:103691975:-1 chm1:+:217016412:-1 chm1:+:266901354:-1 chm1:+:325954729:-1 chm1:+:604571818:-1 chm1:+:679562034:-1 chm1:+:751613918:-1 chm1:+:762007711:-1 chm1:+:1072083179:-1 chm1:+:1142625316:-1 chm1:+:1187924107:-1 chm1:+:1286166032:-1 chm1:+:1359253137:-1 chm1:+:1440253946:-1 chm1:+:1543192006:-1 chm1:+:2155204825:-1 chm1:+:2196750718:-1 chm1:+:2237637659:-1 chm1:+:2242795831:-1 chm1:+:2471669816:-1 chm1:+:2585364002:-1 chm1:+:3035076537:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:1398192757:-1 chm1:+:1956323605:-1 chm1:+:2136679180:-1 chm1:+:2391219206:-1 chm1:+:2983485310:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:115012378:-1 chm1:+:471641022:-1 chm1:+:670830197:-1 chm1:+:705449990:-1 chm1:+:940362608:-1 chm1:+:1325089907:-1 chm1:+:1461881161:-1 chm1:+:1625226138:-1 chm1:+:1684770492:-1 chm1:+:2032731696:-1 chm1:+:2930924082:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:102746050:-1 chm1:+:394710296:-1 chm1:+:938966836:-1 chm1:+:1710286637:-1 chm1:+:1897303516:-1 chm1:+:2253631111:-1 chm1:+:2376424699:-1 chm1:+:2903960287:-1 chm1:+:2918063202:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:606324652:-1 chm1:+:1352565440:-1 chm1:+:1449471821:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:77709573:-1 chm1:+:211842151:-1 chm1:+:1035018873:-1 chm1:+:1059473573:-1 chm1:+:1117593150:-1 chm1:+:1175490857:-1 chm1:+:1476404169:-1 chm1:+:1783545013:-1 chm1:+:1788232228:-1 chm1:+:1828283145:-1 chm1:+:2796733008:-1 chm1:+:2856237055:-1 chm1:+:3099140840:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:146952026:-1 chm1:+:199098268:-1 chm1:+:627792638:-1 chm1:+:654049269:-1 chm1:+:655181763:-1 chm1:+:750847811:-1 chm1:+:853067622:-1 chm1:+:1053122439:-1 chm1:+:1265599131:-1 chm1:+:1684475315:-1 chm1:+:1717879920:-1 chm1:+:1982545956:-1 chm1:+:2006439662:-1 chm1:+:2154588617:-1 chm1:+:2999103980:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:88824172:-1 chm1:+:90892704:-1 chm1:+:174312369:-1 chm1:+:227043826:-1 chm1:+:294900614:-1 chm1:+:449496797:-1 chm1:+:529374743:-1 chm1:+:551720174:-1 chm1:+:683065205:-1 chm1:+:811032963:-1 chm1:+:1265285541:-1 chm1:+:1341458208:-1 chm1:+:1461377971:-1 chm1:+:2248679299:-1 chm1:+:2289476990:-1 chm1:+:2335437472:-1 chm1:+:2351558622:-1 chm1:+:2376837477:-1 chm1:+:2431358367:-1 chm1:+:2439443782:-1 chm1:+:2550877573:-1 chm1:+:2577706216:-1 chm1:+:2920535887:-1 chm1:+:2947990902:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:1024000762:-1 chm1:+:1166069284:-1 chm1:+:1523972091:-1 chm1:+:2252912137:-1 chm1:+:2603173897:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:96101136:-1 chm1:+:2601319990:-1 chm1:+:2689702554:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:2440687:-1 chm1:+:26617194:-1 chm1:+:276316624:-1 chm1:+:370392627:-1 chm1:+:917108855:-1 chm1:+:990121777:-1 chm1:+:1015036596:-1 chm1:+:1061382540:-1 chm1:+:1072960211:-1 chm1:+:1087715049:-1 chm1:+:1096535908:-1 chm1:+:1446515943:-1 chm1:+:1516627442:-1 chm1:+:1677764038:-1 chm1:+:1686060138:-1 chm1:+:1860870701:-1 chm1:+:1962571835:-1 chm1:+:2046584107:-1 chm1:+:2238810902:-1 chm1:+:2495057986:-1 chm1:+:2565144580:-1 chm1:+:2576752052:-1 chm1:+:2672199181:-1 chm1:+:2677178446:-1 chm1:+:2854897199:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:675070794:-1 chm1:+:1457727940:-1 chm1:+:2361464467:-1 chm1:+:2954606292:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCC chm1:+:65048528:-1 chm1:+:189661410:-1 chm1:+:279049068:-1 chm1:+:402028577:-1 chm1:+:416415201:-1 chm1:+:493197055:-1 chm1:+:672369140:-1 chm1:+:774681799:-1 chm1:+:848439542:-1 chm1:+:1517603005:-1 chm1:+:1790625542:-1 chm1:+:1823897543:-1 chm1:+:1831093929:-1 chm1:+:1886253438:-1 chm1:+:2170730554:-1 chm1:+:2290449951:-1 chm1:+:2359024361:-1 +GGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102440:28 +GGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102447:28 +GGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:3025150011:-1 +GGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102451:28 chm1:+:1698150179:-1 +GGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102454:28 +GGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102441:28 chm1:+:1914056323:-1 +GGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102444:28 +GGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102446:28 +GGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:638074396:-1 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGT chm1:+:1535719899:-1 chm1:+:1886862768:-1 chm1:+:2185252501:-1 chm1:+:2677336010:-1 chm1:+:3033653880:29 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGT chm1:+:3033653869:29 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGT chm1:+:3033653874:29 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGT chm1:+:3033653881:29 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGT chm1:+:3033653882:29 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGT chm1:+:3033653886:29 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGT chm1:+:3033653879:29 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGT chm1:+:3033653885:29 +ACAATGCCCATGGGCTCTGTGGCTGGGGCCCCCTGGAGCTGGGGCTGGCCCTAGTCCTGATAGAGTCCTCCCACACCCGTGGACGGATCTGACTCCAATCATCTCCACCACTTCCATCTGGGGGTGCAGGAGGTGAGGGGAGGCCCAGGCCTTAGGCTACATTCTGTCCACCTTGTCCCATCCCCCAACGGACATGGCCCTTGGGGTGGGAGAGCTGATTCCTCTCATGAATTCCAAAAGACATCGTTCATCCAGGGCCCCAGTGTCTGGTGGGGTCCAGGGAGATCTGCCCCACCTTACCTAGGGGGCTCCATGTCTGGGTTGCAGCCCCTCCCAGGCTGTGGGGTCAGGGTCTGGCAAGCACAGGGAGCCCAGGGGAGGAGGGAGGGGCCTCTTCCCGGTTGGGGGCAGGTGTGGTTAGGGCCTTCTCTGTCTGGGCCCCTGTGGCGATCAAGCAGGTGGGTGTTCAAAGGTGAAGGAGACTTCTGTGGGGGGAAACGGGAGACACCTGTAGACACCAATGACAAAACAGCTCAATAAGGGGTGGTGGTGCCAGAAGCCCTTTGGTACTGTAGAGGCCCAGAGGAAACACTCAGGACT chm1:+:2827183226:-1 +ACAATGCCCATGGGCTCTGTGGCTGGGGCCCCCTGGAGCTGGGGCTGGCCCTAGTCCTGATAGAGTCCTCCCACACCCGTGGACGGATCTGACTCCAATCATCTCCACCACTTCCATCTGGGGGTGCAGGAGGTGAGGGGAGGCCCAGGCCTTAGGCTACATTCTGTCCACCTTGTCCCATCCCCCAACGGACATGGCCCTTGGGGTGGGAGAGCTGATTCCTCTCATGAATTCCAAAAGACATCGTTCATCCAGGGCCCCAGTGTCTGGTGGGGTCCAGGGAGATCTGCCCCACCTTACCTAGGGGGCTCCATGTCTGGGTTGCAGCCCCTCCCAGGCTGTGGGGTCAGGGTCTGGCAAGCACAGGGAGCCCAGGGGAGGAGGGAGGGGCCTCTTCCCGGTTGGGGGCAGGTGTGGTTAGGGCCTTCTCTGTCTGGGCCCCTGTGGCGATCAAGCAGGTGGGTGTTCAAAGGTGAAGGAGACTTCTGTGGGGGGAAACGGGAGACACCTGTAGACACCAATGACAAAACAGCTCAATAAGGGGTGGTGGTGCCAGAAGCCCTTTGGTACTGTAGAGGCCCAGAGGAAACACTCAGGACT chm1:+:1676652179:-1 chm1:+:3034241574:-1 +ACAATGCCCATGGGCTCTGTGGCTGGGGCCCCCTGGAGCTGGGGCTGGCCCTAGTCCTGATAGAGTCCTCCCACACCCGTGGACGGATCTGACTCCAATCATCTCCACCACTTCCATCTGGGGGTGCAGGAGGTGAGGGGAGGCCCAGGCCTTAGGCTACATTCTGTCCACCTTGTCCCATCCCCCAACGGACATGGCCCTTGGGGTGGGAGAGCTGATTCCTCTCATGAATTCCAAAAGACATCGTTCATCCAGGGCCCCAGTGTCTGGTGGGGTCCAGGGAGATCTGCCCCACCTTACCTAGGGGGCTCCATGTCTGGGTTGCAGCCCCTCCCAGGCTGTGGGGTCAGGGTCTGGCAAGCACAGGGAGCCCAGGGGAGGAGGGAGGGGCCTCTTCCCGGTTGGGGGCAGGTGTGGTTAGGGCCTTCTCTGTCTGGGCCCCTGTGGCGATCAAGCAGGTGGGTGTTCAAAGGTGAAGGAGACTTCTGTGGGGGGAAACGGGAGACACCTGTAGACACCAATGACAAAACAGCTCAATAAGGGGTGGTGGTGCCAGAAGCCCTTTGGTACTGTAGAGGCCCAGAGGAAACACTCAGGACT chm1:+:1094204773:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTT chm1:+:1484603629:-1 chm1:+:2687796403:-1 chm1:+:2939140283:-1 chm1:+:2939141502:-1 chm1:+:2939147863:-1 chm1:+:2939161206:-1 chm1:+:2939162773:-1 chm1:+:2939165044:-1 chm1:+:2939165636:-1 chm1:+:2939174490:-1 chm1:+:2939175044:-1 chm1:+:2939177134:-1 chm1:+:2939178738:-1 chm1:+:2939181421:-1 chm1:+:2939182585:-1 chm1:+:2939189727:-1 chm1:+:2939191120:-1 chm1:+:2939196460:-1 chm1:+:2939196600:-1 chm1:+:2939197581:-1 chm1:+:2939200491:-1 chm1:+:2939202060:-1 chm1:+:2939245895:-1 chm1:+:2939246149:-1 chm1:+:2939248690:-1 chm1:+:2939253991:-1 chm1:+:2939255941:-1 chm1:+:2939256502:-1 chm1:+:2939258342:-1 chm1:+:2939259320:-1 chm1:+:2939267785:-1 chm1:+:2939268861:-1 chm1:+:2939269628:-1 chm1:+:2939271689:-1 chm1:+:2939272106:-1 chm1:+:2939297069:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTT chm1:+:585966344:-1 chm1:+:927884475:-1 chm1:+:927896089:-1 chm1:+:927901453:-1 chm1:+:1121295041:-1 chm1:+:1121295726:-1 chm1:+:1291676900:-1 chm1:+:1294958798:-1 chm1:+:1295085528:-1 chm1:+:1295761091:-1 chm1:+:1295772648:-1 chm1:+:1295817592:-1 chm1:+:1295923658:-1 chm1:+:1296054925:-1 chm1:+:1359451290:-1 chm1:+:1440171822:-1 chm1:+:1722824848:-1 chm1:+:1722834956:-1 chm1:+:1722840351:-1 chm1:+:1722840867:-1 chm1:+:1722842097:-1 chm1:+:1722843126:-1 chm1:+:1722868809:-1 chm1:+:1722869150:-1 chm1:+:1722874832:-1 chm1:+:1866438263:-1 chm1:+:1866490050:-1 chm1:+:1867010202:-1 chm1:+:1867026379:-1 chm1:+:1867061161:-1 chm1:+:1867252611:-1 chm1:+:1870606169:-1 chm1:+:1870676566:-1 chm1:+:1870676909:-1 chm1:+:1870898310:-1 chm1:+:1985478424:-1 chm1:+:1985505969:-1 chm1:+:1985553121:-1 chm1:+:1985625119:-1 chm1:+:1985626495:-1 chm1:+:1989153661:-1 chm1:+:1989178683:-1 chm1:+:1989232275:-1 chm1:+:1989244386:-1 chm1:+:1989246426:-1 chm1:+:1989250151:-1 chm1:+:2442350847:-1 chm1:+:2442361224:-1 chm1:+:2683856177:-1 chm1:+:2683856693:-1 chm1:+:2683878302:-1 chm1:+:2939472472:-1 chm1:+:2943052239:-1 chm1:+:3056073856:-1 chm1:+:3056090072:-1 chm1:+:3056092669:-1 chm1:+:3056103529:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTT chm1:+:2939146599:-1 chm1:+:2939150237:-1 chm1:+:2939162327:-1 chm1:+:2939164106:-1 chm1:+:2939180387:-1 chm1:+:2939188273:-1 chm1:+:2939191898:-1 chm1:+:2939192634:-1 chm1:+:2939196572:-1 chm1:+:2939203243:-1 chm1:+:2939253823:-1 chm1:+:2939254872:-1 chm1:+:2939255185:-1 chm1:+:2939260206:-1 chm1:+:2939265403:-1 chm1:+:2939266186:-1 chm1:+:2939269183:-1 chm1:+:2939273885:-1 chm1:+:2939274616:-1 chm1:+:2939287849:-1 chm1:+:2939293424:-1 chm1:+:2939295089:-1 chm1:+:2939295890:-1 chm1:+:2939301415:-1 chm1:+:2939304718:-1 chm1:+:2939311236:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTT chm1:+:883888643:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTT chm1:+:22037001:-1 chm1:+:77093963:-1 chm1:+:260186937:-1 chm1:+:391830378:-1 chm1:+:495079202:-1 chm1:+:623667988:-1 chm1:+:973049587:-1 chm1:+:1170087030:-1 chm1:+:1216471090:-1 chm1:+:1244347756:-1 chm1:+:1358347218:-1 chm1:+:1411360805:-1 chm1:+:1573282162:-1 chm1:+:1788913783:-1 chm1:+:2291391697:-1 chm1:+:2582910279:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTT chm1:+:1770418611:-1 chm1:+:2290187888:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTT chm1:+:215178427:-1 chm1:+:523768208:-1 chm1:+:543650218:-1 chm1:+:699959723:-1 chm1:+:798533324:-1 chm1:+:939607329:-1 chm1:+:993905908:-1 chm1:+:1097746730:-1 chm1:+:1413973665:-1 chm1:+:1494808996:-1 chm1:+:1785924779:-1 chm1:+:2252171810:-1 chm1:+:2407875973:-1 chm1:+:2820543365:-1 chm1:+:3051078503:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTT chm1:+:1466729716:-1 chm1:+:1668859135:-1 chm1:+:2192662987:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTT chm1:+:241180847:-1 chm1:+:688428450:-1 chm1:+:767576923:-1 chm1:+:968244009:-1 chm1:+:1036749068:-1 chm1:+:1370920681:-1 chm1:+:1624676039:-1 chm1:+:1750777156:-1 chm1:+:1984674394:-1 chm1:+:2182101219:-1 chm1:+:2582322907:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTT chm1:+:1015979447:-1 chm1:+:1738369518:-1 chm1:+:2818529175:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTT chm1:+:51798099:-1 chm1:+:56045010:-1 chm1:+:657814322:-1 chm1:+:1805957335:-1 chm1:+:2939271978:-1 chm1:+:2939275900:-1 chm1:+:2939289928:-1 chm1:+:2939291610:-1 chm1:+:2939307393:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTT chm1:+:50463959:-1 chm1:+:81252543:-1 chm1:+:86445219:-1 chm1:+:108390242:-1 chm1:+:294556720:-1 chm1:+:368530396:-1 chm1:+:433910110:-1 chm1:+:451470480:-1 chm1:+:454540534:-1 chm1:+:501755248:-1 chm1:+:527442386:-1 chm1:+:536338375:-1 chm1:+:712325903:-1 chm1:+:762437944:-1 chm1:+:780031516:-1 chm1:+:900744649:-1 chm1:+:956140820:-1 chm1:+:974448852:-1 chm1:+:1030087882:-1 chm1:+:1086482453:-1 chm1:+:1129002780:-1 chm1:+:1140531519:-1 chm1:+:1176157321:-1 chm1:+:1183113686:-1 chm1:+:1193958096:-1 chm1:+:1230217401:-1 chm1:+:1247406561:-1 chm1:+:1313309800:-1 chm1:+:1318012593:-1 chm1:+:1360596485:-1 chm1:+:1424659684:-1 chm1:+:1450261288:-1 chm1:+:1459601216:-1 chm1:+:1492497021:-1 chm1:+:1493924529:-1 chm1:+:1703244263:-1 chm1:+:1767972853:-1 chm1:+:1932093967:-1 chm1:+:2010610922:-1 chm1:+:2061338112:-1 chm1:+:2125288618:-1 chm1:+:2357547388:-1 chm1:+:2505645625:-1 chm1:+:2567205922:-1 chm1:+:2694990478:-1 chm1:+:2700866240:-1 chm1:+:2886422810:-1 chm1:+:2945549521:-1 chm1:+:2968267016:-1 chm1:+:2979873359:-1 chm1:+:3003731096:-1 chm1:+:3018141611:-1 chm1:+:3056990377:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTT chm1:+:30649186:-1 chm1:+:77900240:-1 chm1:+:115325486:-1 chm1:+:121111995:-1 chm1:+:206562224:-1 chm1:+:327942067:-1 chm1:+:329048423:-1 chm1:+:470313800:-1 chm1:+:573458093:-1 chm1:+:573460251:-1 chm1:+:619418151:-1 chm1:+:641834216:-1 chm1:+:775437305:-1 chm1:+:784358956:-1 chm1:+:960273368:-1 chm1:+:1037755042:-1 chm1:+:1089620430:-1 chm1:+:1136568091:-1 chm1:+:1312526263:-1 chm1:+:1348617329:-1 chm1:+:1436530604:-1 chm1:+:1509199565:-1 chm1:+:1682381913:-1 chm1:+:1822309636:-1 chm1:+:1899357722:-1 chm1:+:1940909323:-1 chm1:+:1985346039:-1 chm1:+:2006284304:-1 chm1:+:2134733902:-1 chm1:+:2357730954:-1 chm1:+:2521957932:-1 chm1:+:2687405952:-1 chm1:+:2757437116:-1 chm1:+:2762600600:-1 chm1:+:2766113839:-1 chm1:+:2943002557:-1 chm1:+:2943042774:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTT chm1:+:1396086715:-1 +AACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:1436238654:-1 chm1:+:1436280588:-1 chm1:+:1436343489:-1 chm1:+:1436361520:-1 chm1:+:1436459140:-1 chm1:+:1436507276:-1 chm1:+:1436510529:-1 chm1:+:1440230367:-1 chm1:+:1866243742:-1 chm1:+:2442369670:-1 chm1:+:2684006972:-1 chm1:+:2687478283:-1 chm1:+:2687483966:-1 chm1:+:2687569080:25 chm1:+:2939356770:-1 chm1:+:2939357114:-1 chm1:+:3056693964:-1 chm1:+:3056696561:-1 chm1:+:3056712774:-1 +AACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687569070:25 +AACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687569067:25 +AACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687569072:25 +AACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687569078:25 +AACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687569068:25 +AACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:228718292:-1 +AACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687569069:25 chm1:+:2687687942:-1 +AACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687569071:25 +AACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687569073:25 +AACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687569076:25 +AACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:23198858:-1 +AACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:11895396:-1 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTA chm1:+:766905484:31 chm1:+:1057360605:-1 chm1:+:1493650300:-1 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTA chm1:+:766905489:31 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTA chm1:+:766905490:31 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTA chm1:+:766905483:31 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTA chm1:+:766905488:31 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTA chm1:+:2713228394:-1 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTA chm1:+:766905487:31 +TAATAACTATTTAGAATTTTACCTTTGGATTATAAAATATGTTTTATATAAAGTGTTTTATGGGCAACTTGAGGTAGAGAATTGGGATAAATTTTTCTTTGTAAAAATTAGTATTTAAAAATTATCTAAGAAATACAGGTGATTTTATAAAAATTGGAAAAAACAGAAAGTAGAATAATAAAAATAAAATAACCAGAGCCCTAACCACAGACAAGCTACTGTTTGACATGTCGGTGTATAAGGAATATTTTCTTTCTTAAAAATCTCGAGTTATTTTAGATGTATATTAAAGACATGTATGTAAAGTGTGTCTAAAGTACAGTAACAGTGAATAAGCCACGAGTTTAGGAAGGAATGTTACAATACTTGTCAAAGCCAAGTGTTCCGTGTTCAGTCCTTTCTTCTTGTCCTGCTTGGAGGTAATCACTGTCTTGAATATTTTAATCACTTTCTTGCTTTTTTTTGTTTTTTTGTTTTTTTAAAATATAGTTTGTTTTTAAGGAAGGATAACCAACCTACCAAAAGATACAGAAATTATAAGCAAATGATTTTATGATTTAACAAATGACAATGCCTTTGTAAACCACTACCCCAGATCAA chm1:+:561959102:-1 chm1:+:1864500051:-1 +TAATAACTATTTAGAATTTTACCTTTGGATTATAAAATATGTTTTATATAAAGTGTTTTATGGGCAACTTGAGGTAGAGAATTGGGATAAATTTTTCTTTGTAAAAATTAGTATTTAAAAATTATCTAAGAAATACAGGTGATTTTATAAAAATTGGAAAAAACAGAAAGTAGAATAATAAAAATAAAATAACCAGAGCCCTAACCACAGACAAGCTACTGTTTGACATGTCGGTGTATAAGGAATATTTTCTTTCTTAAAAATCTCGAGTTATTTTAGATGTATATTAAAGACATGTATGTAAAGTGTGTCTAAAGTACAGTAACAGTGAATAAGCCACGAGTTTAGGAAGGAATGTTACAATACTTGTCAAAGCCAAGTGTTCCGTGTTCAGTCCTTTCTTCTTGTCCTGCTTGGAGGTAATCACTGTCTTGAATATTTTAATCACTTTCTTGCTTTTTTTTGTTTTTTTGTTTTTTTAAAATATAGTTTGTTTTTAAGGAAGGATAACCAACCTACCAAAAGATACAGAAATTATAAGCAAATGATTTTATGATTTAACAAATGACAATGCCTTTGTAAACCACTACCCCAGATCAA chm1:+:2124270361:-1 +TAATAACTATTTAGAATTTTACCTTTGGATTATAAAATATGTTTTATATAAAGTGTTTTATGGGCAACTTGAGGTAGAGAATTGGGATAAATTTTTCTTTGTAAAAATTAGTATTTAAAAATTATCTAAGAAATACAGGTGATTTTATAAAAATTGGAAAAAACAGAAAGTAGAATAATAAAAATAAAATAACCAGAGCCCTAACCACAGACAAGCTACTGTTTGACATGTCGGTGTATAAGGAATATTTTCTTTCTTAAAAATCTCGAGTTATTTTAGATGTATATTAAAGACATGTATGTAAAGTGTGTCTAAAGTACAGTAACAGTGAATAAGCCACGAGTTTAGGAAGGAATGTTACAATACTTGTCAAAGCCAAGTGTTCCGTGTTCAGTCCTTTCTTCTTGTCCTGCTTGGAGGTAATCACTGTCTTGAATATTTTAATCACTTTCTTGCTTTTTTTTGTTTTTTTGTTTTTTTAAAATATAGTTTGTTTTTAAGGAAGGATAACCAACCTACCAAAAGATACAGAAATTATAAGCAAATGATTTTATGATTTAACAAATGACAATGCCTTTGTAAACCACTACCCCAGATCAA chm1:+:1805463523:-1 +TAATAACTATTTAGAATTTTACCTTTGGATTATAAAATATGTTTTATATAAAGTGTTTTATGGGCAACTTGAGGTAGAGAATTGGGATAAATTTTTCTTTGTAAAAATTAGTATTTAAAAATTATCTAAGAAATACAGGTGATTTTATAAAAATTGGAAAAAACAGAAAGTAGAATAATAAAAATAAAATAACCAGAGCCCTAACCACAGACAAGCTACTGTTTGACATGTCGGTGTATAAGGAATATTTTCTTTCTTAAAAATCTCGAGTTATTTTAGATGTATATTAAAGACATGTATGTAAAGTGTGTCTAAAGTACAGTAACAGTGAATAAGCCACGAGTTTAGGAAGGAATGTTACAATACTTGTCAAAGCCAAGTGTTCCGTGTTCAGTCCTTTCTTCTTGTCCTGCTTGGAGGTAATCACTGTCTTGAATATTTTAATCACTTTCTTGCTTTTTTTTGTTTTTTTGTTTTTTTAAAATATAGTTTGTTTTTAAGGAAGGATAACCAACCTACCAAAAGATACAGAAATTATAAGCAAATGATTTTATGATTTAACAAATGACAATGCCTTTGTAAACCACTACCCCAGATCAA chm1:+:680734893:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:2365479490:-1 chm1:+:2916781825:-1 chm1:+:2917799378:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:67500672:-1 chm1:+:90697534:-1 chm1:+:96427608:-1 chm1:+:114168866:-1 chm1:+:281297491:-1 chm1:+:356914219:-1 chm1:+:418413063:-1 chm1:+:430388780:-1 chm1:+:512041853:-1 chm1:+:772764493:-1 chm1:+:788686185:-1 chm1:+:840876149:-1 chm1:+:978310673:-1 chm1:+:985424524:-1 chm1:+:1203413459:-1 chm1:+:1322015429:-1 chm1:+:1342219125:-1 chm1:+:1348175722:-1 chm1:+:1435644128:-1 chm1:+:1453151111:-1 chm1:+:1499061119:-1 chm1:+:1557752419:-1 chm1:+:1611657815:-1 chm1:+:1913647400:-1 chm1:+:2022397111:-1 chm1:+:2671957865:-1 chm1:+:2671997668:-1 chm1:+:2804752489:-1 chm1:+:2915962870:-1 chm1:+:2924500903:-1 chm1:+:2982500262:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:105610355:-1 chm1:+:295690711:-1 chm1:+:837023377:-1 chm1:+:1833252808:-1 chm1:+:2430601106:-1 chm1:+:2637687474:-1 chm1:+:2959521957:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:428582495:-1 chm1:+:536321846:-1 chm1:+:580177075:-1 chm1:+:658039245:-1 chm1:+:819998950:-1 chm1:+:972966773:-1 chm1:+:1008334296:-1 chm1:+:1149028363:-1 chm1:+:1273437039:-1 chm1:+:1398005723:-1 chm1:+:1738944696:-1 chm1:+:1787424978:-1 chm1:+:1965887077:-1 chm1:+:2576763843:-1 chm1:+:2606422239:-1 chm1:+:2691488176:-1 chm1:+:2771371256:-1 chm1:+:2957021310:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:792972762:-1 chm1:+:1660839133:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:104557518:-1 chm1:+:283927295:-1 chm1:+:971828558:-1 chm1:+:1000582966:-1 chm1:+:1149758062:-1 chm1:+:1435644153:-1 chm1:+:1984924682:-1 chm1:+:2391905799:-1 chm1:+:2512779269:-1 chm1:+:2947319409:-1 chm1:+:2962889707:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:847403703:-1 chm1:+:1424531744:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:43090346:-1 chm1:+:93936768:-1 chm1:+:119929666:-1 chm1:+:184275172:-1 chm1:+:221799778:-1 chm1:+:285170575:-1 chm1:+:389763001:-1 chm1:+:403724466:-1 chm1:+:403857256:-1 chm1:+:552902377:-1 chm1:+:556369746:-1 chm1:+:569110216:-1 chm1:+:576796356:-1 chm1:+:578651022:-1 chm1:+:630122628:-1 chm1:+:718520284:-1 chm1:+:760071076:-1 chm1:+:766494436:-1 chm1:+:779702515:-1 chm1:+:782670561:-1 chm1:+:822926219:-1 chm1:+:848086029:-1 chm1:+:917945727:-1 chm1:+:933034373:-1 chm1:+:991761838:-1 chm1:+:1000428486:-1 chm1:+:1096677590:-1 chm1:+:1124809295:-1 chm1:+:1160783524:-1 chm1:+:1162707500:-1 chm1:+:1237405093:-1 chm1:+:1256830899:-1 chm1:+:1315343717:-1 chm1:+:1316531599:-1 chm1:+:1370568468:-1 chm1:+:1378634212:-1 chm1:+:1413895129:-1 chm1:+:1428643850:-1 chm1:+:1467742344:-1 chm1:+:1477631930:-1 chm1:+:1489595316:-1 chm1:+:1551841910:-1 chm1:+:1625889188:-1 chm1:+:1681434874:-1 chm1:+:1716800946:-1 chm1:+:1777248288:-1 chm1:+:1778048606:-1 chm1:+:1790402442:-1 chm1:+:1838543663:-1 chm1:+:1859632649:-1 chm1:+:1930200171:-1 chm1:+:1941443085:-1 chm1:+:2006144081:-1 chm1:+:2012543407:-1 chm1:+:2040550874:-1 chm1:+:2077029246:-1 chm1:+:2121741754:-1 chm1:+:2189777642:-1 chm1:+:2227193949:-1 chm1:+:2228285318:-1 chm1:+:2241086838:-1 chm1:+:2301617701:-1 chm1:+:2434768612:-1 chm1:+:2589201484:-1 chm1:+:2726021031:-1 chm1:+:2799959052:-1 chm1:+:2811936449:-1 chm1:+:2853036437:-1 chm1:+:2897123086:-1 chm1:+:2914736267:-1 chm1:+:2915741315:-1 chm1:+:2926017419:-1 chm1:+:2937315404:-1 chm1:+:2960417184:-1 chm1:+:2971819615:-1 chm1:+:2976353019:-1 chm1:+:2993320224:-1 chm1:+:3002429926:-1 chm1:+:3005667769:-1 chm1:+:3009342076:-1 chm1:+:3028129433:-1 chm1:+:3040944754:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:82199892:-1 chm1:+:82200649:-1 chm1:+:516981122:-1 chm1:+:775526789:-1 chm1:+:1018121241:-1 chm1:+:1793760448:-1 chm1:+:2271513578:-1 chm1:+:2605800354:-1 chm1:+:2918859760:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:71305349:-1 chm1:+:74081059:-1 chm1:+:154006772:-1 chm1:+:244694932:-1 chm1:+:263185480:-1 chm1:+:368409685:-1 chm1:+:408085343:-1 chm1:+:596291590:-1 chm1:+:641471195:-1 chm1:+:710694975:-1 chm1:+:795385361:-1 chm1:+:946841779:-1 chm1:+:1024864342:-1 chm1:+:1550469129:-1 chm1:+:1930200173:-1 chm1:+:1961065545:-1 chm1:+:1990394773:-1 chm1:+:2287146648:-1 chm1:+:2354298848:-1 chm1:+:2960921838:-1 chm1:+:2974296146:-1 chm1:+:2981608146:-1 chm1:+:2997522087:-1 chm1:+:3001630400:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:763343011:-1 chm1:+:1483059145:-1 chm1:+:2826995465:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:18231312:-1 chm1:+:176352369:-1 chm1:+:235301851:-1 chm1:+:283160718:-1 chm1:+:478634597:-1 chm1:+:563588202:-1 chm1:+:1273065291:-1 chm1:+:1583617639:-1 chm1:+:1605769118:-1 chm1:+:1888074259:-1 chm1:+:2019362049:-1 chm1:+:2258063369:-1 chm1:+:3017900655:-1 chm1:+:3100483876:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:6355209:-1 chm1:+:321454032:-1 chm1:+:330332217:-1 chm1:+:461276189:-1 chm1:+:722006222:-1 chm1:+:894029104:-1 chm1:+:1125818662:-1 chm1:+:1420249892:-1 chm1:+:1441249431:-1 chm1:+:1615538703:-1 chm1:+:1944600031:-1 chm1:+:2015848318:-1 chm1:+:2176780401:-1 chm1:+:2555338784:-1 chm1:+:2580408802:-1 chm1:+:2826818976:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:2353908:-1 chm1:+:23100959:-1 chm1:+:43363349:-1 chm1:+:63882087:-1 chm1:+:105674345:-1 chm1:+:113767109:-1 chm1:+:115461923:-1 chm1:+:153298430:-1 chm1:+:231056031:-1 chm1:+:248361124:-1 chm1:+:255276388:-1 chm1:+:266088695:-1 chm1:+:278250221:-1 chm1:+:295557188:-1 chm1:+:298912152:-1 chm1:+:304963338:-1 chm1:+:327269376:-1 chm1:+:435039209:-1 chm1:+:456894920:-1 chm1:+:470057559:-1 chm1:+:522478041:-1 chm1:+:533539687:-1 chm1:+:580168061:-1 chm1:+:631258874:-1 chm1:+:659430046:-1 chm1:+:662963607:-1 chm1:+:678942460:-1 chm1:+:719171986:-1 chm1:+:746619969:-1 chm1:+:770832902:-1 chm1:+:777134756:-1 chm1:+:791545369:-1 chm1:+:813961111:-1 chm1:+:861044256:-1 chm1:+:861775032:-1 chm1:+:865244981:-1 chm1:+:925062192:-1 chm1:+:936701791:-1 chm1:+:941551575:-1 chm1:+:953593218:-1 chm1:+:958577871:-1 chm1:+:961643362:-1 chm1:+:965813729:-1 chm1:+:996704245:-1 chm1:+:1001064580:-1 chm1:+:1009854241:-1 chm1:+:1054171430:-1 chm1:+:1079745727:-1 chm1:+:1137774728:-1 chm1:+:1146417453:-1 chm1:+:1161164500:-1 chm1:+:1201101681:-1 chm1:+:1250605766:-1 chm1:+:1253870615:-1 chm1:+:1258989203:-1 chm1:+:1310611252:-1 chm1:+:1326276560:-1 chm1:+:1378634211:-1 chm1:+:1389765110:-1 chm1:+:1390098600:-1 chm1:+:1420754615:-1 chm1:+:1445625906:-1 chm1:+:1496326523:-1 chm1:+:1516110391:-1 chm1:+:1543856326:-1 chm1:+:1575467719:-1 chm1:+:1699795825:-1 chm1:+:1709898183:-1 chm1:+:1766962356:-1 chm1:+:1778170969:-1 chm1:+:1787176943:-1 chm1:+:1790392079:-1 chm1:+:1802451663:-1 chm1:+:1876038998:-1 chm1:+:1970845625:-1 chm1:+:2031332664:-1 chm1:+:2053493801:-1 chm1:+:2106809167:-1 chm1:+:2123890649:-1 chm1:+:2197069341:-1 chm1:+:2226333296:-1 chm1:+:2243086325:-1 chm1:+:2256379733:-1 chm1:+:2292563679:-1 chm1:+:2338350842:-1 chm1:+:2407271126:-1 chm1:+:2420891579:-1 chm1:+:2471454117:-1 chm1:+:2482301912:-1 chm1:+:2487119279:-1 chm1:+:2511965207:-1 chm1:+:2551909906:-1 chm1:+:2562184749:-1 chm1:+:2639771116:-1 chm1:+:2726888763:-1 chm1:+:2728525501:-1 chm1:+:2767381699:-1 chm1:+:2874229757:-1 chm1:+:2888209682:-1 chm1:+:2916219252:-1 chm1:+:2982059194:-1 chm1:+:2986694646:-1 chm1:+:2992720823:-1 chm1:+:3005899956:-1 chm1:+:3008942189:-1 chm1:+:3024528334:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:515374935:-1 chm1:+:592052997:-1 chm1:+:710009353:-1 chm1:+:808062121:-1 chm1:+:853774321:-1 chm1:+:927572647:-1 chm1:+:927770685:-1 chm1:+:927839382:-1 chm1:+:1295806566:-1 chm1:+:1295809973:-1 chm1:+:1295836970:-1 chm1:+:1295840778:-1 chm1:+:1295961263:-1 chm1:+:1296007352:-1 chm1:+:1296043482:-1 chm1:+:1313869488:-1 chm1:+:1336201269:-1 chm1:+:1503205557:-1 chm1:+:1632046993:-1 chm1:+:1739104725:-1 chm1:+:1849202576:-1 chm1:+:1853891420:-1 chm1:+:1864598913:-1 chm1:+:1864627388:-1 chm1:+:1866321231:-1 chm1:+:1866327812:-1 chm1:+:1866329356:-1 chm1:+:1866335127:-1 chm1:+:1866390320:-1 chm1:+:1866391573:-1 chm1:+:1866470745:-1 chm1:+:1867078980:-1 chm1:+:1867105097:-1 chm1:+:1867106986:-1 chm1:+:1867111429:-1 chm1:+:1867116785:-1 chm1:+:1867214423:-1 chm1:+:1870674789:-1 chm1:+:1973727767:-1 chm1:+:1989333188:-1 chm1:+:2403325219:-1 chm1:+:2484106498:-1 chm1:+:2551712889:-1 chm1:+:2564582651:-1 chm1:+:2617692279:-1 chm1:+:2624295444:-1 chm1:+:2861325866:-1 chm1:+:2939404346:-1 chm1:+:2939409203:-1 chm1:+:2997649233:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:64241977:-1 chm1:+:66127318:-1 chm1:+:80671385:-1 chm1:+:167689175:-1 chm1:+:330772227:-1 chm1:+:356120591:-1 chm1:+:357788123:-1 chm1:+:643489153:-1 chm1:+:660345539:-1 chm1:+:667880458:-1 chm1:+:809777255:-1 chm1:+:968910469:-1 chm1:+:997050023:-1 chm1:+:1004524048:-1 chm1:+:1093229044:-1 chm1:+:1226021780:-1 chm1:+:1277708796:-1 chm1:+:1300413049:-1 chm1:+:1308363210:-1 chm1:+:1308577475:-1 chm1:+:1308605497:-1 chm1:+:1308633518:-1 chm1:+:1308792703:-1 chm1:+:1333578917:-1 chm1:+:1351934193:-1 chm1:+:1377787013:-1 chm1:+:1404597010:-1 chm1:+:1765460213:-1 chm1:+:1850126759:-1 chm1:+:1914499546:-1 chm1:+:1942875016:-1 chm1:+:2042422706:-1 chm1:+:2131117437:-1 chm1:+:2187691962:-1 chm1:+:2280195804:-1 chm1:+:2347132664:-1 chm1:+:2376244170:-1 chm1:+:2617681980:-1 chm1:+:2632626715:-1 chm1:+:2682052612:-1 chm1:+:2725129323:-1 chm1:+:2797060716:-1 chm1:+:2810640316:-1 chm1:+:2885436744:-1 chm1:+:2896582437:-1 chm1:+:2932641154:-1 chm1:+:2973302279:-1 chm1:+:3025438224:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:520439546:-1 chm1:+:891653646:-1 chm1:+:1408401433:-1 chm1:+:1739693239:-1 chm1:+:3023169046:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:86766197:-1 chm1:+:162647596:-1 chm1:+:298941157:-1 chm1:+:485103330:-1 chm1:+:900899820:-1 chm1:+:910180134:-1 chm1:+:952597775:-1 chm1:+:977181704:-1 chm1:+:1933683686:-1 chm1:+:2166192617:-1 chm1:+:2715972283:-1 chm1:+:2896455904:-1 chm1:+:2926510694:-1 chm1:+:3001416245:-1 chm1:+:3002542732:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:74081050:-1 chm1:+:286274438:-1 chm1:+:352272553:-1 chm1:+:515144463:-1 chm1:+:521699560:-1 chm1:+:592844245:-1 chm1:+:664188663:-1 chm1:+:772514720:-1 chm1:+:853540224:-1 chm1:+:877461545:-1 chm1:+:964778842:-1 chm1:+:1140555773:-1 chm1:+:1222514379:-1 chm1:+:1406462138:-1 chm1:+:2283663714:-1 chm1:+:2482301908:-1 chm1:+:2966464837:-1 chm1:+:2992777094:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:212377578:-1 chm1:+:430145155:-1 chm1:+:660316752:-1 chm1:+:736089367:-1 chm1:+:882931603:-1 chm1:+:939759972:-1 chm1:+:1084504849:-1 chm1:+:1140570983:-1 chm1:+:1319799167:-1 chm1:+:1793161087:-1 chm1:+:1926421335:-1 chm1:+:1937039203:-1 chm1:+:1976624924:-1 chm1:+:2189889720:-1 chm1:+:2272890419:-1 chm1:+:2572676319:-1 chm1:+:2667209149:-1 chm1:+:2965812164:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:885292757:-1 chm1:+:911165256:-1 chm1:+:1029262388:-1 chm1:+:1216379117:-1 chm1:+:1905687128:-1 chm1:+:2016271217:-1 chm1:+:2237770894:-1 chm1:+:2253371843:-1 chm1:+:2266276887:-1 chm1:+:2804752494:-1 chm1:+:2926482489:-1 chm1:+:3022048426:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:358078766:-1 chm1:+:2123890680:-1 chm1:+:2172648964:-1 chm1:+:2340848485:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAA chm1:+:75530155:-1 chm1:+:88008547:-1 chm1:+:513219966:-1 chm1:+:529897951:-1 chm1:+:733722915:-1 chm1:+:772129330:-1 chm1:+:1037102151:-1 chm1:+:1160407502:-1 chm1:+:1285217730:-1 chm1:+:1485506613:-1 chm1:+:1874039148:-1 chm1:+:1900560492:-1 chm1:+:1912910274:-1 chm1:+:2010530817:-1 chm1:+:2121741769:-1 chm1:+:2973374078:-1 chm1:+:2978955087:-1 chm1:+:3006182414:-1 chm1:+:3042371721:-1 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+TTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:2981987726:33 +TTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:2194975426:-1 +TTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:2981987737:33 +TTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:999212953:-1 +TTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:2847029160:-1 chm1:+:2981987730:33 +TTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:2859553890:-1 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chm1:+:1367989401:-1 chm1:+:1384524415:-1 chm1:+:1423333089:-1 chm1:+:1451638113:-1 chm1:+:1452117296:-1 chm1:+:1508702054:-1 chm1:+:1631241646:-1 chm1:+:1695535996:-1 chm1:+:1750915562:-1 chm1:+:1756832631:-1 chm1:+:1824810465:-1 chm1:+:1843056969:-1 chm1:+:1863327968:-1 chm1:+:2041365798:-1 chm1:+:2255091316:-1 chm1:+:2264007844:-1 chm1:+:2414943394:-1 chm1:+:2417495213:-1 chm1:+:2432543835:-1 chm1:+:2439250762:-1 chm1:+:2503626839:-1 chm1:+:2541830916:-1 chm1:+:2649343483:-1 chm1:+:2668073466:22 chm1:+:2668079060:-1 chm1:+:2695587985:-1 chm1:+:2726333434:-1 chm1:+:2769080170:-1 chm1:+:2797056610:-1 chm1:+:2816904416:-1 chm1:+:2819368338:-1 chm1:+:2871621280:-1 chm1:+:2898371636:-1 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGG chm1:+:1497619756:-1 chm1:+:2676923804:-1 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGG chm1:+:11160406:-1 chm1:+:605374573:-1 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGG chm1:+:2668073477:22 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGG chm1:+:2668073470:22 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGG chm1:+:2668073472:22 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGG chm1:+:2668073471:22 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGG chm1:+:2668073474:22 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGG chm1:+:738344808:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:166072450:95 chm1:+:197261058:96 chm1:+:221383485:87 chm1:+:317069661:108 chm1:+:429083941:112 chm1:+:564165100:89 chm1:+:588546928:105 chm1:+:834068436:97 chm1:+:857215465:90 chm1:+:960836484:89 chm1:+:1149006320:-1 chm1:+:1215475102:105 chm1:+:1336805018:78 chm1:+:1510137445:93 chm1:+:1513331950:84 chm1:+:1646638897:89 chm1:+:1699634324:83 chm1:+:1729930813:85 chm1:+:1732960551:-1 chm1:+:2038482619:99 chm1:+:2038705099:89 chm1:+:2111295575:82 chm1:+:2115009023:89 chm1:+:2444718224:-1 chm1:+:2475779420:95 chm1:+:2852273938:88 chm1:+:2974437279:88 chm1:+:3009458209:98 chm1:+:3052700879:94 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:50828103:109 chm1:+:60977826:90 chm1:+:63030233:93 chm1:+:79882833:97 chm1:+:91765352:79 chm1:+:100668515:83 chm1:+:102597185:-1 chm1:+:105461272:-1 chm1:+:111635462:88 chm1:+:117520354:80 chm1:+:163730550:98 chm1:+:170541360:88 chm1:+:173001694:-1 chm1:+:173589807:109 chm1:+:173667819:97 chm1:+:177664650:88 chm1:+:194578315:-1 chm1:+:199604977:84 chm1:+:211061761:81 chm1:+:214955507:90 chm1:+:221383484:87 chm1:+:242335690:-1 chm1:+:254587508:99 chm1:+:284491131:90 chm1:+:290160317:85 chm1:+:305797905:86 chm1:+:305901798:80 chm1:+:327640827:-1 chm1:+:333834571:106 chm1:+:334142854:84 chm1:+:345012083:109 chm1:+:347742812:80 chm1:+:381689513:-1 chm1:+:387371438:96 chm1:+:387630529:91 chm1:+:393017109:89 chm1:+:396084473:83 chm1:+:401664012:82 chm1:+:405990348:89 chm1:+:407814619:74 chm1:+:408543620:91 chm1:+:411120434:86 chm1:+:413607809:85 chm1:+:414398162:81 chm1:+:418975346:85 chm1:+:459487366:89 chm1:+:473130207:92 chm1:+:484937741:77 chm1:+:493972151:93 chm1:+:517127768:-1 chm1:+:518958509:94 chm1:+:534263565:80 chm1:+:538764410:104 chm1:+:550044968:85 chm1:+:557215545:80 chm1:+:557492395:83 chm1:+:581058314:90 chm1:+:600541178:88 chm1:+:601693190:96 chm1:+:610628555:85 chm1:+:614823197:-1 chm1:+:619683398:83 chm1:+:629715480:93 chm1:+:630691069:84 chm1:+:633159360:94 chm1:+:639231584:97 chm1:+:646433363:93 chm1:+:650204922:87 chm1:+:650234894:79 chm1:+:651885022:86 chm1:+:659300121:85 chm1:+:669032055:93 chm1:+:738757348:72 chm1:+:744311619:84 chm1:+:745383249:89 chm1:+:746531085:81 chm1:+:759959912:-1 chm1:+:778047610:-1 chm1:+:789174518:93 chm1:+:789426538:109 chm1:+:790119842:88 chm1:+:795770123:92 chm1:+:798293943:88 chm1:+:814907861:84 chm1:+:815109643:82 chm1:+:829180234:87 chm1:+:829938780:110 chm1:+:832559387:87 chm1:+:836233256:91 chm1:+:836970921:90 chm1:+:839479074:96 chm1:+:846288547:103 chm1:+:857034354:-1 chm1:+:864328866:83 chm1:+:865182475:94 chm1:+:879237448:95 chm1:+:880744639:93 chm1:+:887103814:102 chm1:+:895482816:-1 chm1:+:897500083:82 chm1:+:902444423:85 chm1:+:909631784:103 chm1:+:932562288:-1 chm1:+:942049175:98 chm1:+:948985216:88 chm1:+:959043728:94 chm1:+:959783144:79 chm1:+:974655469:107 chm1:+:975548455:91 chm1:+:980003039:91 chm1:+:986562523:-1 chm1:+:995998164:-1 chm1:+:1003169805:86 chm1:+:1013568378:88 chm1:+:1017254541:82 chm1:+:1025914812:91 chm1:+:1044203452:86 chm1:+:1062064724:82 chm1:+:1068969283:100 chm1:+:1073997017:83 chm1:+:1107391594:91 chm1:+:1118145283:90 chm1:+:1140506193:91 chm1:+:1144833224:88 chm1:+:1149647255:87 chm1:+:1151895540:82 chm1:+:1156286693:-1 chm1:+:1168331233:93 chm1:+:1171276945:86 chm1:+:1180041009:98 chm1:+:1187903058:87 chm1:+:1208539383:100 chm1:+:1216593625:100 chm1:+:1222670121:90 chm1:+:1241571858:-1 chm1:+:1244446738:99 chm1:+:1255627292:91 chm1:+:1261551877:90 chm1:+:1261681608:78 chm1:+:1268275434:95 chm1:+:1270819778:87 chm1:+:1270852813:97 chm1:+:1326397657:85 chm1:+:1327477404:88 chm1:+:1330902872:88 chm1:+:1343419409:-1 chm1:+:1344720744:-1 chm1:+:1346630724:108 chm1:+:1352761660:-1 chm1:+:1353154880:85 chm1:+:1368320779:90 chm1:+:1380262781:90 chm1:+:1384035526:87 chm1:+:1394461699:91 chm1:+:1402494852:95 chm1:+:1432464006:87 chm1:+:1442196829:-1 chm1:+:1469634804:-1 chm1:+:1474533862:84 chm1:+:1484197677:81 chm1:+:1493801045:99 chm1:+:1493840946:119 chm1:+:1501869964:96 chm1:+:1505796489:109 chm1:+:1522612159:96 chm1:+:1528484886:95 chm1:+:1545365242:79 chm1:+:1549093801:97 chm1:+:1549940992:87 chm1:+:1553842756:94 chm1:+:1558161465:84 chm1:+:1566402079:87 chm1:+:1572120531:82 chm1:+:1574040929:85 chm1:+:1577651784:-1 chm1:+:1615560672:86 chm1:+:1619910782:93 chm1:+:1637179535:76 chm1:+:1648734168:95 chm1:+:1702443976:87 chm1:+:1716138717:88 chm1:+:1741606264:105 chm1:+:1747235656:84 chm1:+:1755125479:98 chm1:+:1757711832:86 chm1:+:1760232565:87 chm1:+:1762439933:85 chm1:+:1766863052:96 chm1:+:1771451971:84 chm1:+:1774265928:87 chm1:+:1782590352:87 chm1:+:1793719692:86 chm1:+:1807712222:90 chm1:+:1812264832:-1 chm1:+:1821846460:93 chm1:+:1824448789:82 chm1:+:1826895690:87 chm1:+:1829515074:108 chm1:+:1830794286:-1 chm1:+:1834591201:90 chm1:+:1834875605:97 chm1:+:1850670225:79 chm1:+:1871255526:90 chm1:+:1890509347:82 chm1:+:1890741254:90 chm1:+:1895486638:87 chm1:+:1897777666:88 chm1:+:1907221006:88 chm1:+:1917634109:86 chm1:+:1925246654:89 chm1:+:1930314903:86 chm1:+:1941638125:88 chm1:+:1949882153:91 chm1:+:1977739898:94 chm1:+:2002283690:85 chm1:+:2024883598:-1 chm1:+:2026661192:108 chm1:+:2038842116:89 chm1:+:2049513174:84 chm1:+:2058390889:87 chm1:+:2063312897:81 chm1:+:2106894974:98 chm1:+:2123613349:94 chm1:+:2127260735:98 chm1:+:2133808857:88 chm1:+:2160617410:91 chm1:+:2177251308:80 chm1:+:2184818732:84 chm1:+:2219585023:-1 chm1:+:2223094388:-1 chm1:+:2231071796:84 chm1:+:2252908479:89 chm1:+:2253490569:103 chm1:+:2254458446:-1 chm1:+:2256215702:88 chm1:+:2257045416:93 chm1:+:2259815345:88 chm1:+:2259919075:89 chm1:+:2262345638:81 chm1:+:2280994539:92 chm1:+:2352571046:-1 chm1:+:2359171842:83 chm1:+:2359744609:106 chm1:+:2387290014:88 chm1:+:2389278092:91 chm1:+:2391818096:87 chm1:+:2394251402:95 chm1:+:2458882717:92 chm1:+:2460197302:94 chm1:+:2461183822:85 chm1:+:2485573124:93 chm1:+:2518609369:-1 chm1:+:2549557187:-1 chm1:+:2588069872:87 chm1:+:2595059830:84 chm1:+:2602274097:83 chm1:+:2659360326:88 chm1:+:2676519181:84 chm1:+:2680482197:103 chm1:+:2681607699:97 chm1:+:2689286554:89 chm1:+:2728716031:82 chm1:+:2797753069:93 chm1:+:2808892376:92 chm1:+:2813698813:97 chm1:+:2818758451:92 chm1:+:2823570222:94 chm1:+:2827579551:89 chm1:+:2858164306:85 chm1:+:2884013640:87 chm1:+:2894236047:-1 chm1:+:2900471453:88 chm1:+:2901825576:93 chm1:+:2903663572:88 chm1:+:2903921097:79 chm1:+:2906936696:-1 chm1:+:2907165001:-1 chm1:+:2908353936:99 chm1:+:2912739381:94 chm1:+:2918640751:-1 chm1:+:2920437953:97 chm1:+:2923546240:85 chm1:+:2926982846:87 chm1:+:2935202894:87 chm1:+:2937353680:85 chm1:+:2938336153:98 chm1:+:2938358184:94 chm1:+:2943320103:95 chm1:+:2945064541:89 chm1:+:2945562170:103 chm1:+:2951119037:89 chm1:+:2952086092:75 chm1:+:2961741043:103 chm1:+:2966293564:98 chm1:+:2977491466:81 chm1:+:2986239879:91 chm1:+:3000982311:89 chm1:+:3007272166:95 chm1:+:3012302918:91 chm1:+:3015957386:89 chm1:+:3018191848:88 chm1:+:3018349176:90 chm1:+:3020077377:80 chm1:+:3031323403:84 chm1:+:3035911579:78 chm1:+:3096123397:98 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:190999310:112 chm1:+:221223774:106 chm1:+:603170446:92 chm1:+:775738036:-1 chm1:+:1091872545:88 chm1:+:1499008806:-1 chm1:+:1706284606:104 chm1:+:2632534068:97 chm1:+:3052099186:112 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:45648928:94 chm1:+:289465295:94 chm1:+:391078552:93 chm1:+:433967740:87 chm1:+:766732161:78 chm1:+:795430149:92 chm1:+:819073190:88 chm1:+:946295642:90 chm1:+:948705542:98 chm1:+:1025914805:91 chm1:+:1336257315:-1 chm1:+:1377474288:-1 chm1:+:1463532059:89 chm1:+:1520152385:93 chm1:+:1871255524:90 chm1:+:1944954579:93 chm1:+:2027630724:100 chm1:+:2345051950:91 chm1:+:2723832170:90 chm1:+:2897414471:93 chm1:+:2943133870:100 chm1:+:3045984597:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:50083648:-1 chm1:+:92721319:88 chm1:+:161665954:96 chm1:+:173433302:-1 chm1:+:181821226:107 chm1:+:243112482:-1 chm1:+:254650400:93 chm1:+:263873610:-1 chm1:+:269912017:78 chm1:+:306297206:95 chm1:+:312783505:87 chm1:+:317481593:89 chm1:+:321919012:-1 chm1:+:367483751:106 chm1:+:369630074:77 chm1:+:370078037:103 chm1:+:396819067:97 chm1:+:401338207:-1 chm1:+:413607810:85 chm1:+:426008694:80 chm1:+:430331472:-1 chm1:+:450004941:83 chm1:+:496838220:104 chm1:+:581249052:107 chm1:+:597478122:100 chm1:+:598705894:98 chm1:+:599328117:114 chm1:+:645592584:-1 chm1:+:655134662:111 chm1:+:661542970:87 chm1:+:661585540:-1 chm1:+:673648420:97 chm1:+:709537185:-1 chm1:+:719706693:93 chm1:+:738535262:96 chm1:+:751527767:-1 chm1:+:766225759:83 chm1:+:769364609:-1 chm1:+:771512152:120 chm1:+:777560304:95 chm1:+:795588327:-1 chm1:+:798805838:84 chm1:+:822869740:90 chm1:+:863851798:95 chm1:+:868307614:-1 chm1:+:885105059:-1 chm1:+:931312523:85 chm1:+:956179848:94 chm1:+:1005876581:90 chm1:+:1013082080:117 chm1:+:1014591396:-1 chm1:+:1044989555:83 chm1:+:1062064723:82 chm1:+:1071129707:92 chm1:+:1072235758:-1 chm1:+:1081783881:78 chm1:+:1087752424:104 chm1:+:1088347577:-1 chm1:+:1132815333:82 chm1:+:1138042882:-1 chm1:+:1153877790:76 chm1:+:1184234362:96 chm1:+:1186048562:119 chm1:+:1242950498:98 chm1:+:1244227293:116 chm1:+:1247993217:99 chm1:+:1258324023:83 chm1:+:1283740796:95 chm1:+:1326410678:86 chm1:+:1340677640:78 chm1:+:1407521647:-1 chm1:+:1441174975:-1 chm1:+:1451406386:116 chm1:+:1454159318:95 chm1:+:1501915078:89 chm1:+:1501932322:78 chm1:+:1512663272:-1 chm1:+:1546711408:115 chm1:+:1565440125:82 chm1:+:1623993559:95 chm1:+:1626400777:89 chm1:+:1637179543:76 chm1:+:1653261085:76 chm1:+:1716903628:-1 chm1:+:1725511226:-1 chm1:+:1739192322:-1 chm1:+:1788029339:81 chm1:+:1841690743:90 chm1:+:1852571306:-1 chm1:+:1894101186:86 chm1:+:1925246652:89 chm1:+:1958353583:95 chm1:+:1962043429:-1 chm1:+:1992591078:108 chm1:+:2006447421:-1 chm1:+:2024577996:-1 chm1:+:2104620190:93 chm1:+:2114968206:115 chm1:+:2122738465:-1 chm1:+:2135223169:79 chm1:+:2153238893:106 chm1:+:2186774694:113 chm1:+:2225134895:-1 chm1:+:2242141741:-1 chm1:+:2258357183:96 chm1:+:2289165538:90 chm1:+:2298080378:-1 chm1:+:2340304437:92 chm1:+:2345700651:83 chm1:+:2359086981:83 chm1:+:2361180261:-1 chm1:+:2408114769:-1 chm1:+:2470944720:96 chm1:+:2481059418:-1 chm1:+:2567116809:-1 chm1:+:2594718195:-1 chm1:+:2635463032:-1 chm1:+:2729936501:101 chm1:+:2737522406:95 chm1:+:2799705145:112 chm1:+:2802398311:90 chm1:+:2852416843:90 chm1:+:2889556530:108 chm1:+:2909509592:79 chm1:+:2913601899:-1 chm1:+:2976296349:-1 chm1:+:2980541360:-1 chm1:+:2982241464:90 chm1:+:2991619457:120 chm1:+:3002744482:-1 chm1:+:3013232051:75 chm1:+:3035911575:78 chm1:+:3054714135:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:152661687:-1 chm1:+:170988770:119 chm1:+:191442526:85 chm1:+:228062533:85 chm1:+:306297213:95 chm1:+:328135572:101 chm1:+:346374079:91 chm1:+:397193581:85 chm1:+:402302414:80 chm1:+:453813932:-1 chm1:+:457462806:89 chm1:+:494427181:-1 chm1:+:509225161:-1 chm1:+:551470923:88 chm1:+:598694597:111 chm1:+:599642222:89 chm1:+:603170455:92 chm1:+:670531926:92 chm1:+:710555393:-1 chm1:+:722886400:90 chm1:+:749056041:-1 chm1:+:756140606:106 chm1:+:757607405:117 chm1:+:765467737:75 chm1:+:766732167:78 chm1:+:794881347:87 chm1:+:812340658:87 chm1:+:818206965:91 chm1:+:840572423:92 chm1:+:851398260:84 chm1:+:873323604:86 chm1:+:878917343:93 chm1:+:891721127:87 chm1:+:897500084:82 chm1:+:934641517:96 chm1:+:940974078:89 chm1:+:1018511047:115 chm1:+:1152082126:82 chm1:+:1186048573:119 chm1:+:1187903059:87 chm1:+:1189848590:88 chm1:+:1190651995:91 chm1:+:1192435087:87 chm1:+:1257494268:95 chm1:+:1313309460:117 chm1:+:1318012257:118 chm1:+:1328083722:75 chm1:+:1337084668:95 chm1:+:1383474210:81 chm1:+:1392737275:-1 chm1:+:1449985893:-1 chm1:+:1454888099:103 chm1:+:1455934705:93 chm1:+:1478113144:-1 chm1:+:1495521209:-1 chm1:+:1506522852:115 chm1:+:1541021703:94 chm1:+:1552822843:89 chm1:+:1619401373:95 chm1:+:1760802292:85 chm1:+:1763684023:113 chm1:+:1791529378:111 chm1:+:1839416474:81 chm1:+:1878960576:92 chm1:+:1919755320:110 chm1:+:1941598725:79 chm1:+:1972073030:87 chm1:+:1989691970:90 chm1:+:2017787115:97 chm1:+:2117032108:83 chm1:+:2133759834:85 chm1:+:2153960519:101 chm1:+:2160451611:117 chm1:+:2225837431:117 chm1:+:2232681093:80 chm1:+:2234799899:80 chm1:+:2249648961:85 chm1:+:2254204084:86 chm1:+:2257510695:78 chm1:+:2288775405:84 chm1:+:2334065227:-1 chm1:+:2394251405:95 chm1:+:2567011915:87 chm1:+:2601708431:82 chm1:+:2632700627:103 chm1:+:2649044908:75 chm1:+:2649958274:103 chm1:+:2694641528:-1 chm1:+:2701608292:-1 chm1:+:2733230528:-1 chm1:+:2735487573:114 chm1:+:2743722887:82 chm1:+:2803209258:-1 chm1:+:2805467634:88 chm1:+:2823732722:84 chm1:+:2894236048:-1 chm1:+:2913363838:-1 chm1:+:2918640752:-1 chm1:+:2926982847:87 chm1:+:2932140769:114 chm1:+:2947054915:107 chm1:+:2948244875:119 chm1:+:2970713722:98 chm1:+:2976505813:89 chm1:+:3017551752:96 chm1:+:3022841334:107 chm1:+:3027937215:78 chm1:+:3040174291:100 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:92721315:88 chm1:+:96265738:-1 chm1:+:99508211:-1 chm1:+:170020987:105 chm1:+:264639063:97 chm1:+:308908763:-1 chm1:+:354481577:-1 chm1:+:460563701:83 chm1:+:494423391:105 chm1:+:495902021:94 chm1:+:581820245:-1 chm1:+:596646320:-1 chm1:+:599642211:89 chm1:+:601966603:88 chm1:+:738535258:96 chm1:+:750923033:107 chm1:+:766225755:83 chm1:+:780031171:96 chm1:+:784951665:84 chm1:+:800551086:-1 chm1:+:817289089:-1 chm1:+:902444416:85 chm1:+:944432836:107 chm1:+:970084345:101 chm1:+:979634029:98 chm1:+:1018512324:-1 chm1:+:1074382390:81 chm1:+:1149284362:-1 chm1:+:1155210285:-1 chm1:+:1195501265:-1 chm1:+:1482707836:102 chm1:+:1504628315:-1 chm1:+:1545365241:79 chm1:+:1621508844:98 chm1:+:1765225079:94 chm1:+:1773780067:94 chm1:+:1792449631:-1 chm1:+:1984562967:89 chm1:+:2051034177:94 chm1:+:2139562322:86 chm1:+:2142817222:-1 chm1:+:2234548344:83 chm1:+:2247026869:113 chm1:+:2258931607:85 chm1:+:2281948825:-1 chm1:+:2335114628:-1 chm1:+:2356649475:84 chm1:+:2534025598:96 chm1:+:2549826908:90 chm1:+:2569364726:-1 chm1:+:2623329802:-1 chm1:+:2946745669:86 chm1:+:2967419680:87 chm1:+:3017551729:96 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:258847933:-1 chm1:+:288741667:-1 chm1:+:511023243:-1 chm1:+:2144955242:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:79398118:110 chm1:+:105238752:104 chm1:+:174115400:85 chm1:+:176328012:94 chm1:+:255438699:-1 chm1:+:403354709:97 chm1:+:425621821:89 chm1:+:557558545:-1 chm1:+:749713193:104 chm1:+:764163358:113 chm1:+:789224957:84 chm1:+:835068977:88 chm1:+:870426503:91 chm1:+:897500081:82 chm1:+:971895228:84 chm1:+:1038041135:75 chm1:+:1120048071:90 chm1:+:1428684269:91 chm1:+:1558161464:84 chm1:+:1724962513:96 chm1:+:1761722364:84 chm1:+:1914778054:90 chm1:+:2044100315:93 chm1:+:2126179166:88 chm1:+:2144635132:89 chm1:+:2168514595:93 chm1:+:2231071795:84 chm1:+:2241397882:-1 chm1:+:2249200861:94 chm1:+:2612835916:105 chm1:+:2649751604:82 chm1:+:2741291587:85 chm1:+:2863768127:96 chm1:+:2907388390:85 chm1:+:2926110247:-1 chm1:+:2944341796:101 chm1:+:2957206875:92 chm1:+:2976296356:-1 chm1:+:2987245851:87 chm1:+:2994663561:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:48779662:-1 chm1:+:1527271326:-1 chm1:+:1768576278:-1 chm1:+:1984234410:90 chm1:+:2333724022:-1 chm1:+:2948355510:84 chm1:+:3055871015:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:95951637:102 chm1:+:301372078:95 chm1:+:333877326:104 chm1:+:400900565:103 chm1:+:423678272:87 chm1:+:756880222:109 chm1:+:795240093:109 chm1:+:824902121:106 chm1:+:851398258:84 chm1:+:873698363:-1 chm1:+:926306385:-1 chm1:+:971720451:92 chm1:+:979707739:105 chm1:+:991562572:92 chm1:+:1006126089:102 chm1:+:1147488191:81 chm1:+:1491341097:80 chm1:+:1564926590:100 chm1:+:1718770413:93 chm1:+:1820491452:116 chm1:+:1908156552:-1 chm1:+:2006022638:-1 chm1:+:2020287349:-1 chm1:+:2035327691:104 chm1:+:2117032106:83 chm1:+:2137326360:89 chm1:+:2156471776:91 chm1:+:2172415404:-1 chm1:+:2649958272:103 chm1:+:2730284972:-1 chm1:+:2799753935:95 chm1:+:2858634245:-1 chm1:+:2909509591:79 chm1:+:2944532722:-1 chm1:+:2949501190:-1 chm1:+:2961198488:96 chm1:+:3053282335:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:54942230:-1 chm1:+:89540529:86 chm1:+:146485053:97 chm1:+:250084159:-1 chm1:+:388940529:106 chm1:+:475243362:90 chm1:+:643699469:95 chm1:+:777560303:95 chm1:+:911484848:93 chm1:+:1010172469:82 chm1:+:1180511668:92 chm1:+:1184127030:115 chm1:+:1270400632:-1 chm1:+:1444468632:-1 chm1:+:1540556080:95 chm1:+:1629834031:-1 chm1:+:2037386933:-1 chm1:+:2616890239:81 chm1:+:2989378946:-1 chm1:+:3029225479:95 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:707309552:-1 chm1:+:920371563:-1 chm1:+:920418122:-1 chm1:+:1104491557:-1 chm1:+:1398591979:-1 chm1:+:1937022363:-1 chm1:+:2889586407:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:338352209:-1 chm1:+:926441827:-1 chm1:+:963967649:-1 chm1:+:1627623647:-1 chm1:+:1758322600:-1 chm1:+:2109247836:-1 chm1:+:2359028985:-1 chm1:+:2593494175:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:2663221530:-1 chm1:+:2902407603:-1 chm1:+:2933335317:-1 chm1:+:2933373394:-1 chm1:+:2933629706:-1 chm1:+:2933868796:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:292067904:-1 chm1:+:296197035:-1 chm1:+:386035084:-1 chm1:+:1017869079:-1 chm1:+:1276284477:-1 chm1:+:1347863341:-1 chm1:+:1584724436:-1 chm1:+:1585110682:-1 chm1:+:1585739926:-1 chm1:+:1726230358:-1 chm1:+:1810791209:-1 chm1:+:1848168001:-1 chm1:+:2019291389:-1 chm1:+:2231325777:-1 chm1:+:2341153544:-1 chm1:+:2442693186:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:18248394:-1 chm1:+:61925676:-1 chm1:+:112455038:-1 chm1:+:409084199:-1 chm1:+:494228017:-1 chm1:+:815117962:102 chm1:+:857314032:-1 chm1:+:1049455835:-1 chm1:+:1202646305:-1 chm1:+:1270201927:-1 chm1:+:1701702588:-1 chm1:+:1729933189:-1 chm1:+:2077404048:-1 chm1:+:2117430787:-1 chm1:+:2232706110:-1 chm1:+:2280423846:-1 chm1:+:2400668735:-1 chm1:+:2484683139:-1 chm1:+:2674739319:-1 chm1:+:2688126297:-1 chm1:+:2931566095:-1 chm1:+:2979841996:-1 chm1:+:3064909141:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:443353841:-1 chm1:+:540473365:-1 chm1:+:569032746:-1 chm1:+:594255483:-1 chm1:+:597279497:-1 chm1:+:764296435:-1 chm1:+:775786634:-1 chm1:+:784551891:-1 chm1:+:796195349:-1 chm1:+:823431578:-1 chm1:+:833035779:-1 chm1:+:839498459:-1 chm1:+:1116198838:-1 chm1:+:1185537201:-1 chm1:+:1212504031:-1 chm1:+:1242575460:96 chm1:+:1258227990:-1 chm1:+:1332898661:-1 chm1:+:1519986506:-1 chm1:+:1529984407:-1 chm1:+:1630664153:-1 chm1:+:1874209891:95 chm1:+:1932399702:-1 chm1:+:2197827841:88 chm1:+:2231902919:87 chm1:+:2536098698:-1 chm1:+:2591508476:-1 chm1:+:2715158680:-1 chm1:+:2715161587:-1 chm1:+:2737704610:-1 chm1:+:2962046602:-1 chm1:+:2984276837:-1 chm1:+:2996781050:84 chm1:+:3044273841:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:107858658:-1 chm1:+:111400492:-1 chm1:+:115005583:-1 chm1:+:145014859:-1 chm1:+:150808256:-1 chm1:+:245786552:-1 chm1:+:378903559:-1 chm1:+:403402964:-1 chm1:+:440813029:-1 chm1:+:478990775:-1 chm1:+:510850516:-1 chm1:+:524494982:-1 chm1:+:525615343:-1 chm1:+:577114357:-1 chm1:+:581119196:-1 chm1:+:598640048:-1 chm1:+:632530033:-1 chm1:+:636223630:-1 chm1:+:660966887:-1 chm1:+:665264451:-1 chm1:+:703166429:-1 chm1:+:744866524:-1 chm1:+:756635465:-1 chm1:+:775947004:-1 chm1:+:790897630:-1 chm1:+:801201686:-1 chm1:+:802123049:-1 chm1:+:893881806:-1 chm1:+:954653196:-1 chm1:+:1090540441:-1 chm1:+:1116451328:-1 chm1:+:1162417674:-1 chm1:+:1172006977:-1 chm1:+:1197924188:-1 chm1:+:1226490907:-1 chm1:+:1244072204:103 chm1:+:1248202008:-1 chm1:+:1322230778:-1 chm1:+:1338386618:-1 chm1:+:1342431338:-1 chm1:+:1349387323:-1 chm1:+:1358641316:-1 chm1:+:1363091126:-1 chm1:+:1376123874:-1 chm1:+:1376134448:-1 chm1:+:1441665759:-1 chm1:+:1445316885:-1 chm1:+:1470163081:-1 chm1:+:1479115843:-1 chm1:+:1486675551:-1 chm1:+:1539423054:-1 chm1:+:1539694162:-1 chm1:+:1543527096:-1 chm1:+:1572953860:-1 chm1:+:1643524709:-1 chm1:+:1676971325:-1 chm1:+:1718698516:-1 chm1:+:1768714569:-1 chm1:+:1810498923:-1 chm1:+:1834022032:-1 chm1:+:1950740435:-1 chm1:+:2066301710:-1 chm1:+:2075566934:-1 chm1:+:2148792382:-1 chm1:+:2148986625:-1 chm1:+:2179808251:-1 chm1:+:2190501967:-1 chm1:+:2195354309:-1 chm1:+:2255615562:-1 chm1:+:2278567343:-1 chm1:+:2339002401:-1 chm1:+:2341480610:-1 chm1:+:2361834018:-1 chm1:+:2472299309:-1 chm1:+:2474078355:-1 chm1:+:2511159642:-1 chm1:+:2585394776:-1 chm1:+:2649670993:-1 chm1:+:2688292615:-1 chm1:+:2816279277:-1 chm1:+:2867995759:-1 chm1:+:2871779291:-1 chm1:+:2987360599:-1 chm1:+:3012782773:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:55578559:-1 chm1:+:58975156:-1 chm1:+:146004671:-1 chm1:+:147546458:-1 chm1:+:531799042:90 chm1:+:574997481:-1 chm1:+:746531079:81 chm1:+:1245949103:90 chm1:+:1462991108:84 chm1:+:1706284602:104 chm1:+:1818430169:-1 chm1:+:1893154095:-1 chm1:+:1898471944:-1 chm1:+:1913216960:-1 chm1:+:2776696544:-1 chm1:+:2944295170:-1 chm1:+:2945256751:-1 chm1:+:2946974725:103 chm1:+:2982241455:90 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:162117563:-1 chm1:+:596656792:94 chm1:+:614702633:-1 chm1:+:1120048063:90 chm1:+:1144086027:-1 chm1:+:1190266720:-1 chm1:+:1244361420:-1 chm1:+:1565394855:-1 chm1:+:1914529463:88 chm1:+:2476521343:-1 chm1:+:2580149713:-1 chm1:+:2602780577:-1 chm1:+:2653090539:73 chm1:+:2760590343:-1 chm1:+:3064007323:104 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:733467:-1 chm1:+:80335067:83 chm1:+:184828555:-1 chm1:+:224210692:-1 chm1:+:714001472:-1 chm1:+:780295190:-1 chm1:+:1158464257:90 chm1:+:1179976685:110 chm1:+:1839147048:86 chm1:+:1923233887:-1 chm1:+:3013053373:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:89622896:100 chm1:+:195639823:86 chm1:+:518958512:94 chm1:+:743493070:101 chm1:+:964679000:107 chm1:+:1346897740:101 chm1:+:1571671299:93 chm1:+:2014945403:93 chm1:+:2241899486:102 chm1:+:2576078280:92 chm1:+:2964687366:107 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:308953229:-1 chm1:+:528618284:-1 chm1:+:914752045:94 chm1:+:1244325345:101 chm1:+:1990110724:88 chm1:+:2123610434:-1 chm1:+:2357315579:-1 chm1:+:2360464998:-1 chm1:+:2616769650:88 chm1:+:2742311340:86 chm1:+:2943617751:-1 chm1:+:2976299296:85 chm1:+:3051604791:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:965749292:-1 chm1:+:1007255883:102 chm1:+:1251052533:-1 chm1:+:1450260949:90 chm1:+:1564926593:100 chm1:+:1615560674:86 chm1:+:1638311911:-1 chm1:+:1834875604:97 chm1:+:1852476576:81 chm1:+:2067377224:-1 chm1:+:2363685484:-1 chm1:+:2558619195:-1 chm1:+:2885993852:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCC chm1:+:769884245:90 chm1:+:817288780:-1 chm1:+:1479885242:100 chm1:+:1501932323:78 chm1:+:1565440129:82 +GGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:497872587:99 chm1:+:1135680653:89 chm1:+:1246125299:93 chm1:+:1551068473:95 chm1:+:2236245546:96 chm1:+:2239884011:105 chm1:+:2701585689:28 chm1:+:2971324732:79 +GGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:2701585691:28 +GGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:1874548966:99 chm1:+:2925316172:-1 +GGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:97591228:-1 +GGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:2375187991:-1 +GGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:183716774:94 chm1:+:230659323:106 chm1:+:302067662:80 chm1:+:473405258:94 chm1:+:629485388:107 chm1:+:767680520:-1 chm1:+:925830768:91 chm1:+:1253720594:87 chm1:+:1363976913:78 chm1:+:1542718887:83 chm1:+:1552026839:77 chm1:+:1933179891:79 chm1:+:1946751190:103 chm1:+:2166969819:103 chm1:+:2701585688:28 chm1:+:2946840718:109 +GGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:1030893:-1 chm1:+:433733637:101 chm1:+:948551607:-1 chm1:+:1482176400:-1 chm1:+:2130959107:89 chm1:+:3051681544:-1 +GGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:118410166:-1 chm1:+:367150755:-1 chm1:+:449412928:-1 chm1:+:590472143:-1 chm1:+:753428756:100 chm1:+:756992733:-1 chm1:+:809062541:105 chm1:+:1200750775:88 chm1:+:1287009358:100 chm1:+:1450978145:99 chm1:+:1482102483:-1 chm1:+:1765916272:90 chm1:+:1848593429:95 chm1:+:1879022084:94 chm1:+:2389248855:90 chm1:+:2550467716:-1 chm1:+:2701585687:28 chm1:+:2764280512:-1 chm1:+:3030381618:-1 +GGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:793134791:97 chm1:+:797861448:95 chm1:+:898261731:92 chm1:+:924952004:90 chm1:+:975097169:96 chm1:+:1033029263:105 chm1:+:1139623419:92 chm1:+:1282702542:86 chm1:+:1418480715:112 chm1:+:1557684465:82 chm1:+:2006850632:91 chm1:+:2461102244:90 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTG chm1:+:848980061:-1 chm1:+:999505395:-1 chm1:+:1186797744:-1 chm1:+:1306661181:-1 chm1:+:1315091356:-1 chm1:+:1480821951:-1 chm1:+:1723390893:-1 chm1:+:1749412391:-1 chm1:+:1780900284:-1 chm1:+:2694655179:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTG chm1:+:70722273:-1 chm1:+:197213993:-1 chm1:+:401177851:-1 chm1:+:504795634:-1 chm1:+:1916077106:-1 chm1:+:2020567780:-1 chm1:+:2167735636:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTG chm1:+:211477728:-1 chm1:+:218778032:-1 chm1:+:278044572:-1 chm1:+:297628511:-1 chm1:+:333957189:-1 chm1:+:403885079:-1 chm1:+:578594119:-1 chm1:+:774638664:-1 chm1:+:966482844:-1 chm1:+:1002895445:-1 chm1:+:1052836553:-1 chm1:+:1211309163:-1 chm1:+:1247051131:-1 chm1:+:1319576941:-1 chm1:+:1337807309:-1 chm1:+:1346307835:-1 chm1:+:1355826473:-1 chm1:+:1471376481:-1 chm1:+:1705064425:-1 chm1:+:1834059763:-1 chm1:+:1900891330:-1 chm1:+:1909718063:-1 chm1:+:2049742816:-1 chm1:+:2057276563:-1 chm1:+:2344387291:-1 chm1:+:2346583239:-1 chm1:+:2376340224:-1 chm1:+:2382259105:-1 chm1:+:2384365068:-1 chm1:+:2389814031:-1 chm1:+:2762415867:-1 chm1:+:2903686801:-1 chm1:+:2905124554:-1 chm1:+:2928427546:-1 chm1:+:2946799798:-1 chm1:+:3051063453:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTG chm1:+:176158713:-1 chm1:+:363960932:-1 chm1:+:424307012:-1 chm1:+:648850562:-1 chm1:+:932490785:-1 chm1:+:946964364:-1 chm1:+:1008308642:-1 chm1:+:1073506037:-1 chm1:+:1083088608:-1 chm1:+:1174169476:-1 chm1:+:1189919168:-1 chm1:+:1493702504:-1 chm1:+:1497904501:-1 chm1:+:1546242327:-1 chm1:+:1694962074:-1 chm1:+:1708789758:-1 chm1:+:1710370677:-1 chm1:+:1753015176:-1 chm1:+:1780802736:-1 chm1:+:1847366025:-1 chm1:+:1858730466:-1 chm1:+:1948725045:-1 chm1:+:1991083468:-1 chm1:+:1992548738:-1 chm1:+:2072210776:-1 chm1:+:2227946374:-1 chm1:+:2460655553:-1 chm1:+:2469559139:-1 chm1:+:2549851605:-1 chm1:+:2563124660:-1 chm1:+:2592697504:-1 chm1:+:2606058742:-1 chm1:+:2619927635:-1 chm1:+:2628839071:-1 chm1:+:2689979057:-1 chm1:+:2721707158:-1 chm1:+:2815277396:-1 chm1:+:3009639398:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTG chm1:+:234039466:-1 chm1:+:571859449:-1 chm1:+:1844681733:-1 chm1:+:2185355022:-1 chm1:+:2622317676:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTG chm1:+:91866876:-1 chm1:+:296493467:-1 chm1:+:410630560:-1 chm1:+:848689341:-1 chm1:+:962389639:-1 chm1:+:1075884701:-1 chm1:+:1117797982:-1 chm1:+:1203463053:-1 chm1:+:1309318695:-1 chm1:+:1478795670:-1 chm1:+:1853520069:-1 chm1:+:1966306949:-1 chm1:+:1981366299:-1 chm1:+:2267572504:-1 chm1:+:2368023639:-1 chm1:+:2432196945:-1 chm1:+:2478620258:-1 chm1:+:2633079149:-1 chm1:+:2904472725:-1 chm1:+:2933979718:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTG chm1:+:74717332:-1 chm1:+:297650924:-1 chm1:+:298058463:-1 chm1:+:755343130:-1 chm1:+:950478220:-1 chm1:+:951333366:-1 chm1:+:1214449114:-1 chm1:+:1380532543:-1 chm1:+:1799881317:-1 chm1:+:1913556764:-1 chm1:+:2014203036:-1 chm1:+:2189327213:-1 chm1:+:2851226830:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTG chm1:+:7263932:-1 chm1:+:69196267:-1 chm1:+:416548990:-1 chm1:+:438316332:-1 chm1:+:482896318:-1 chm1:+:508309760:-1 chm1:+:520998704:-1 chm1:+:528093544:-1 chm1:+:575134280:-1 chm1:+:607080874:-1 chm1:+:644035495:-1 chm1:+:664041281:-1 chm1:+:706300439:-1 chm1:+:831152839:-1 chm1:+:844731682:-1 chm1:+:938002490:-1 chm1:+:959354453:-1 chm1:+:997988258:-1 chm1:+:1045157143:-1 chm1:+:1135632790:-1 chm1:+:1180942114:-1 chm1:+:1190136893:-1 chm1:+:1304158036:-1 chm1:+:1346345706:-1 chm1:+:1365941682:-1 chm1:+:1397839061:-1 chm1:+:1497743285:-1 chm1:+:1500350328:-1 chm1:+:1647350847:-1 chm1:+:1716968346:-1 chm1:+:1798318221:-1 chm1:+:1822593580:-1 chm1:+:1920817217:-1 chm1:+:2118529194:-1 chm1:+:2144564816:-1 chm1:+:2255379597:-1 chm1:+:2264978478:-1 chm1:+:2281655466:-1 chm1:+:2366579599:-1 chm1:+:2479617346:-1 chm1:+:2549013326:-1 chm1:+:2604751645:-1 chm1:+:2629939689:-1 chm1:+:2639907786:-1 chm1:+:2799134479:-1 chm1:+:2908686701:-1 chm1:+:2923673824:-1 chm1:+:3000304901:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTG chm1:+:189308548:-1 chm1:+:337445421:-1 chm1:+:425345345:-1 chm1:+:569278281:-1 chm1:+:588423443:-1 chm1:+:752788582:-1 chm1:+:824679058:-1 chm1:+:953906514:-1 chm1:+:1006178001:-1 chm1:+:1146872837:-1 chm1:+:1402895669:-1 chm1:+:1511988080:-1 chm1:+:1572035638:-1 chm1:+:1702610311:-1 chm1:+:1776853338:-1 chm1:+:1783604442:-1 chm1:+:1823251834:-1 chm1:+:1837146839:-1 chm1:+:2115787459:-1 chm1:+:2172438779:-1 chm1:+:2247482071:-1 chm1:+:2426698309:-1 chm1:+:2639293849:-1 chm1:+:2720654624:-1 chm1:+:2821887139:-1 chm1:+:2951677490:-1 chm1:+:3006297150:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTG chm1:+:280848433:-1 chm1:+:422343369:-1 chm1:+:501525241:-1 chm1:+:752590155:-1 chm1:+:1837034821:-1 chm1:+:2180940393:-1 chm1:+:2777774365:-1 chm1:+:2853017777:-1 chm1:+:2916466681:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTG chm1:+:54180301:-1 chm1:+:284617115:-1 chm1:+:455801897:-1 chm1:+:777819368:-1 chm1:+:988868427:-1 chm1:+:1384859251:-1 chm1:+:1848702654:-1 chm1:+:2224806336:-1 chm1:+:2811766091:-1 chm1:+:2944845243:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTG chm1:+:110330096:-1 chm1:+:294375865:-1 chm1:+:392659799:-1 chm1:+:489827285:-1 chm1:+:532581542:-1 chm1:+:575044724:-1 chm1:+:967058144:-1 chm1:+:1000545965:-1 chm1:+:1053976235:-1 chm1:+:1074389669:-1 chm1:+:1099479252:-1 chm1:+:1314955631:-1 chm1:+:1453339693:-1 chm1:+:1748835894:-1 chm1:+:1787602719:-1 chm1:+:1810831124:-1 chm1:+:1937232654:-1 chm1:+:2077058034:-1 chm1:+:2759002353:-1 chm1:+:2770062090:-1 chm1:+:3016821909:-1 chm1:+:3051832097:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTG chm1:+:60540600:-1 chm1:+:408879684:-1 chm1:+:1034539982:-1 chm1:+:1354598338:-1 chm1:+:1465604830:-1 chm1:+:1829244265:-1 chm1:+:1860791409:-1 +CACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT chm1:+:508087449:23 +CACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT chm1:+:508087444:23 +CACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT chm1:+:508087443:23 +CACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT chm1:+:508087450:23 +CACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT chm1:+:508087448:23 chm1:+:2987752913:-1 +CACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT chm1:+:508087446:23 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGA chm1:+:303727724:-1 chm1:+:1096765743:-1 chm1:+:1516782356:-1 chm1:+:1731335920:-1 chm1:+:2374049623:-1 chm1:+:2485083868:-1 chm1:+:2536938937:-1 chm1:+:2695223040:-1 chm1:+:2700659560:-1 chm1:+:2711948015:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGA chm1:+:2064749628:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGA chm1:+:36679943:-1 chm1:+:48127051:-1 chm1:+:50331919:-1 chm1:+:97715309:-1 chm1:+:145400425:-1 chm1:+:154248298:-1 chm1:+:180058201:-1 chm1:+:422948036:-1 chm1:+:569879943:-1 chm1:+:734035580:-1 chm1:+:979718566:-1 chm1:+:1115610369:-1 chm1:+:1181839272:-1 chm1:+:1235990408:-1 chm1:+:1252265180:-1 chm1:+:1362504802:-1 chm1:+:1434657619:-1 chm1:+:1462331680:-1 chm1:+:1497863805:-1 chm1:+:1569858856:-1 chm1:+:1670458927:-1 chm1:+:1717362441:-1 chm1:+:1796959379:-1 chm1:+:1957595181:-1 chm1:+:1975065624:-1 chm1:+:2029680254:-1 chm1:+:2030864179:-1 chm1:+:2061506021:-1 chm1:+:2073809852:-1 chm1:+:2106258859:-1 chm1:+:2255491500:-1 chm1:+:2281667651:-1 chm1:+:2289855566:-1 chm1:+:2344323369:-1 chm1:+:2414819776:-1 chm1:+:2418900633:-1 chm1:+:2427097845:-1 chm1:+:2429058323:-1 chm1:+:2456785820:-1 chm1:+:2458231434:-1 chm1:+:2540959037:-1 chm1:+:2555473356:-1 chm1:+:2564415249:-1 chm1:+:2565225206:-1 chm1:+:2594027864:-1 chm1:+:2714925829:-1 chm1:+:2717519811:-1 chm1:+:2818999847:-1 chm1:+:2867961239:-1 chm1:+:2875724000:-1 chm1:+:2921830054:-1 chm1:+:2977611671:-1 chm1:+:3016539538:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGA chm1:+:9549873:-1 chm1:+:10645463:-1 chm1:+:19574005:-1 chm1:+:26334424:-1 chm1:+:36531190:-1 chm1:+:41151306:-1 chm1:+:90606844:-1 chm1:+:103283012:-1 chm1:+:176173546:-1 chm1:+:180630492:-1 chm1:+:229346043:-1 chm1:+:255576192:-1 chm1:+:269141683:-1 chm1:+:313545468:-1 chm1:+:335641203:-1 chm1:+:351258507:-1 chm1:+:361030037:-1 chm1:+:362176955:-1 chm1:+:394262096:-1 chm1:+:408674953:-1 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chm1:+:223417102:-1 chm1:+:432250842:-1 chm1:+:582641973:-1 chm1:+:606291489:-1 chm1:+:607198642:-1 chm1:+:960850709:-1 chm1:+:1014860875:-1 chm1:+:1026490531:-1 chm1:+:1106402518:-1 chm1:+:1221801210:-1 chm1:+:1507596439:-1 chm1:+:1732968043:-1 chm1:+:1893962413:-1 chm1:+:1992511576:-1 chm1:+:2405804150:-1 chm1:+:2637359898:-1 chm1:+:2718236627:-1 chm1:+:2972240168:-1 chm1:+:3041348430:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGA chm1:+:19953918:-1 chm1:+:214184743:-1 chm1:+:229555569:-1 chm1:+:314089135:-1 chm1:+:590140820:-1 chm1:+:771067508:-1 chm1:+:1068598388:-1 chm1:+:1068954738:-1 chm1:+:1139784036:-1 chm1:+:1142731171:-1 chm1:+:1532691661:-1 chm1:+:1623100359:-1 chm1:+:1782804745:-1 chm1:+:1863234377:-1 chm1:+:1948813294:-1 chm1:+:2007749243:-1 chm1:+:2570026852:-1 chm1:+:2675676230:-1 chm1:+:2860179946:-1 chm1:+:2891162690:-1 chm1:+:2917590350:-1 chm1:+:3045018951:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGA chm1:+:303435427:-1 chm1:+:1074494825:-1 chm1:+:1207285197:-1 chm1:+:1792893480:-1 chm1:+:1833384859:-1 chm1:+:2511230438:-1 chm1:+:2737593167:-1 chm1:+:2858876282:-1 chm1:+:2884579850:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGA chm1:+:150993107:-1 chm1:+:468951588:-1 chm1:+:504214533:-1 chm1:+:728682141:-1 chm1:+:805816277:-1 chm1:+:873489191:-1 chm1:+:1019895007:-1 chm1:+:1218366789:-1 chm1:+:1512123949:-1 chm1:+:1715819191:-1 chm1:+:1723545526:-1 chm1:+:1755488163:-1 chm1:+:1757159524:-1 chm1:+:2369915317:-1 chm1:+:2397850517:-1 chm1:+:2482264233:-1 chm1:+:2543932435:-1 chm1:+:2750513883:-1 chm1:+:2796456670:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGA chm1:+:62142143:-1 chm1:+:421093126:-1 chm1:+:675225145:-1 chm1:+:936985738:-1 chm1:+:1090500740:-1 chm1:+:1309936014:-1 chm1:+:1466688343:-1 chm1:+:1538599407:-1 chm1:+:1577917522:-1 chm1:+:1708802068:-1 chm1:+:1893097193:-1 chm1:+:2006676273:-1 chm1:+:2460939469:-1 chm1:+:2571144337:-1 chm1:+:2711937476:-1 chm1:+:3012523820:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGA chm1:+:8668046:-1 chm1:+:82170814:-1 chm1:+:220148877:-1 chm1:+:457854673:-1 chm1:+:1005740814:-1 chm1:+:1150437245:-1 chm1:+:1265402744:-1 chm1:+:1748684902:-1 chm1:+:2016580829:-1 chm1:+:2576429051:-1 chm1:+:2602576121:-1 chm1:+:2672547684:-1 chm1:+:2970564347:-1 chm1:+:3010727332:-1 chm1:+:3040016024:-1 +TCGCTACCATTGCACTCCAGCCTGGGTGACAAGACGAAACTCCATCTCAAAAAAAAAAACAAAAAAAAAAAAAAGTTATAGAAATGGAAATGAAAAATTCACCAGACTATTTCGAATTCATTAGAGCAGATGGAAGAGAGAGTCATTGAACACAATGAAAGACAGGTAGACTATCCTGTCTACAGTTCTTTTTTTTTTTTTGGATGGAGTTTTCACTCCTTGTTGTCTAAGCTGGGGTGCAATGGCGTGATCTCGGCTCATTGAAACCTCTGCCTACCGGGTTCAAGCAATTCTCCTGGCCTCAGCCTCCCAAGTAGCTGGGACTTACAGGCATGTCGCCACCATGCCCGGCTATTTTTGTATTTTAGTAGAGATTGGGGTTTCACCATGTTGGCCCAGACTGGTCTTGAACTCCTGACCTCAGGTGATCTGCTCCGCCTTGGCCTCCCAAAGTGCTGGGATTATAGCGTGAGACACCGTGCCCCAGCCTGAATTGTAACACTTTAAAATGGTATGTGGACTGGGTGTGGTGGCTCATGCCTATAATCCCAGCACCTTGGGAGGCTGAGGGTAGGAGGATCGCTTGGAGACCTGGAGTTC chm1:+:52381056:-1 chm1:+:54251291:-1 chm1:+:118928823:-1 chm1:+:179168874:-1 chm1:+:214496476:-1 chm1:+:259547470:-1 chm1:+:275520908:-1 chm1:+:281777087:-1 chm1:+:286607559:-1 chm1:+:289938026:-1 chm1:+:351448133:-1 chm1:+:354373236:-1 chm1:+:406903741:-1 chm1:+:451210486:-1 chm1:+:464070993:-1 chm1:+:481599986:-1 chm1:+:486414100:-1 chm1:+:486619712:-1 chm1:+:545937746:-1 chm1:+:568160846:-1 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chm1:+:2920389453:-1 chm1:+:2922340791:-1 chm1:+:2955117522:-1 chm1:+:2981785204:-1 chm1:+:2999075160:-1 +TCGCTACCATTGCACTCCAGCCTGGGTGACAAGACGAAACTCCATCTCAAAAAAAAAAACAAAAAAAAAAAAAAGTTATAGAAATGGAAATGAAAAATTCACCAGACTATTTCGAATTCATTAGAGCAGATGGAAGAGAGAGTCATTGAACACAATGAAAGACAGGTAGACTATCCTGTCTACAGTTCTTTTTTTTTTTTTGGATGGAGTTTTCACTCCTTGTTGTCTAAGCTGGGGTGCAATGGCGTGATCTCGGCTCATTGAAACCTCTGCCTACCGGGTTCAAGCAATTCTCCTGGCCTCAGCCTCCCAAGTAGCTGGGACTTACAGGCATGTCGCCACCATGCCCGGCTATTTTTGTATTTTAGTAGAGATTGGGGTTTCACCATGTTGGCCCAGACTGGTCTTGAACTCCTGACCTCAGGTGATCTGCTCCGCCTTGGCCTCCCAAAGTGCTGGGATTATAGCGTGAGACACCGTGCCCCAGCCTGAATTGTAACACTTTAAAATGGTATGTGGACTGGGTGTGGTGGCTCATGCCTATAATCCCAGCACCTTGGGAGGCTGAGGGTAGGAGGATCGCTTGGAGACCTGGAGTTC chm1:+:1552434151:-1 +TCGCTACCATTGCACTCCAGCCTGGGTGACAAGACGAAACTCCATCTCAAAAAAAAAAACAAAAAAAAAAAAAAGTTATAGAAATGGAAATGAAAAATTCACCAGACTATTTCGAATTCATTAGAGCAGATGGAAGAGAGAGTCATTGAACACAATGAAAGACAGGTAGACTATCCTGTCTACAGTTCTTTTTTTTTTTTTGGATGGAGTTTTCACTCCTTGTTGTCTAAGCTGGGGTGCAATGGCGTGATCTCGGCTCATTGAAACCTCTGCCTACCGGGTTCAAGCAATTCTCCTGGCCTCAGCCTCCCAAGTAGCTGGGACTTACAGGCATGTCGCCACCATGCCCGGCTATTTTTGTATTTTAGTAGAGATTGGGGTTTCACCATGTTGGCCCAGACTGGTCTTGAACTCCTGACCTCAGGTGATCTGCTCCGCCTTGGCCTCCCAAAGTGCTGGGATTATAGCGTGAGACACCGTGCCCCAGCCTGAATTGTAACACTTTAAAATGGTATGTGGACTGGGTGTGGTGGCTCATGCCTATAATCCCAGCACCTTGGGAGGCTGAGGGTAGGAGGATCGCTTGGAGACCTGGAGTTC chm1:+:1308750982:23 +TCGCTACCATTGCACTCCAGCCTGGGTGACAAGACGAAACTCCATCTCAAAAAAAAAAACAAAAAAAAAAAAAAGTTATAGAAATGGAAATGAAAAATTCACCAGACTATTTCGAATTCATTAGAGCAGATGGAAGAGAGAGTCATTGAACACAATGAAAGACAGGTAGACTATCCTGTCTACAGTTCTTTTTTTTTTTTTGGATGGAGTTTTCACTCCTTGTTGTCTAAGCTGGGGTGCAATGGCGTGATCTCGGCTCATTGAAACCTCTGCCTACCGGGTTCAAGCAATTCTCCTGGCCTCAGCCTCCCAAGTAGCTGGGACTTACAGGCATGTCGCCACCATGCCCGGCTATTTTTGTATTTTAGTAGAGATTGGGGTTTCACCATGTTGGCCCAGACTGGTCTTGAACTCCTGACCTCAGGTGATCTGCTCCGCCTTGGCCTCCCAAAGTGCTGGGATTATAGCGTGAGACACCGTGCCCCAGCCTGAATTGTAACACTTTAAAATGGTATGTGGACTGGGTGTGGTGGCTCATGCCTATAATCCCAGCACCTTGGGAGGCTGAGGGTAGGAGGATCGCTTGGAGACCTGGAGTTC chm1:+:1308750980:23 chm1:+:1309935630:-1 +TCGCTACCATTGCACTCCAGCCTGGGTGACAAGACGAAACTCCATCTCAAAAAAAAAAACAAAAAAAAAAAAAAGTTATAGAAATGGAAATGAAAAATTCACCAGACTATTTCGAATTCATTAGAGCAGATGGAAGAGAGAGTCATTGAACACAATGAAAGACAGGTAGACTATCCTGTCTACAGTTCTTTTTTTTTTTTTGGATGGAGTTTTCACTCCTTGTTGTCTAAGCTGGGGTGCAATGGCGTGATCTCGGCTCATTGAAACCTCTGCCTACCGGGTTCAAGCAATTCTCCTGGCCTCAGCCTCCCAAGTAGCTGGGACTTACAGGCATGTCGCCACCATGCCCGGCTATTTTTGTATTTTAGTAGAGATTGGGGTTTCACCATGTTGGCCCAGACTGGTCTTGAACTCCTGACCTCAGGTGATCTGCTCCGCCTTGGCCTCCCAAAGTGCTGGGATTATAGCGTGAGACACCGTGCCCCAGCCTGAATTGTAACACTTTAAAATGGTATGTGGACTGGGTGTGGTGGCTCATGCCTATAATCCCAGCACCTTGGGAGGCTGAGGGTAGGAGGATCGCTTGGAGACCTGGAGTTC chm1:+:1308750978:23 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+GGAGTGGAACCACAGATGCCCTTGAAACAGATTAGCTGGGACCACAAAGGCTGGAAGGCCAGCAAGCAGGAGGCCAAGACTCCTTGAGGCCAAGCTGGGATAAAATGCACCCTTATTCCCACCACAGCTGCTCCTAGCTTCGGATTTGGCATGGTGTGCTGGAGCAGACACCCTTCGCCATCCTCTCCTGTTGCTCAGCTATGTTTGAGTTTGGAGAGCGACAATGGGTGCTTGCTGCTCTCCTCGACCAAAACTACAGCTACAAGCTCAGGGAGATGAAATTTCCCTCAGGCAGCTTCCGTCTGTCTCTTAGGGAGTCATCCTTACTGGAGGAGCCTCGGGGTTCTCAGAGGGCACCTTGTCCGGGCCTTGTCCCTTCATAGCAGGACCTGGATCAGGTAGCTCGCAGAGGTTGGAGCAACCATGACTGTGCTACCTTGGTTGCTTCTCCAGGCCCAGTCCATACTGGGGTTGATTTGAAAGAATATTTACACTAAAAGGGCTTAAGCAGAGGGAAGATTTCACTGCCTCTTATCTTCTCATAGTTTAGAAAAACAACCAACATTTCACTGAACGCGTGACCCTGTGGTGCCTGTGTTT chm1:+:2476908280:-1 +GGAGTGGAACCACAGATGCCCTTGAAACAGATTAGCTGGGACCACAAAGGCTGGAAGGCCAGCAAGCAGGAGGCCAAGACTCCTTGAGGCCAAGCTGGGATAAAATGCACCCTTATTCCCACCACAGCTGCTCCTAGCTTCGGATTTGGCATGGTGTGCTGGAGCAGACACCCTTCGCCATCCTCTCCTGTTGCTCAGCTATGTTTGAGTTTGGAGAGCGACAATGGGTGCTTGCTGCTCTCCTCGACCAAAACTACAGCTACAAGCTCAGGGAGATGAAATTTCCCTCAGGCAGCTTCCGTCTGTCTCTTAGGGAGTCATCCTTACTGGAGGAGCCTCGGGGTTCTCAGAGGGCACCTTGTCCGGGCCTTGTCCCTTCATAGCAGGACCTGGATCAGGTAGCTCGCAGAGGTTGGAGCAACCATGACTGTGCTACCTTGGTTGCTTCTCCAGGCCCAGTCCATACTGGGGTTGATTTGAAAGAATATTTACACTAAAAGGGCTTAAGCAGAGGGAAGATTTCACTGCCTCTTATCTTCTCATAGTTTAGAAAAACAACCAACATTTCACTGAACGCGTGACCCTGTGGTGCCTGTGTTT chm1:+:1812965830:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACA chm1:+:1298269378:48 chm1:+:1298780601:73 chm1:+:1973078738:-1 chm1:+:2007117774:-1 chm1:+:2330374644:-1 chm1:+:2610866739:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACA chm1:+:13785787:-1 chm1:+:15411428:-1 chm1:+:15496409:-1 chm1:+:26842491:-1 chm1:+:33180179:-1 chm1:+:33519963:-1 chm1:+:112427899:-1 chm1:+:151710852:-1 chm1:+:153821711:-1 chm1:+:154072599:-1 chm1:+:167951084:-1 chm1:+:183720966:-1 chm1:+:300755601:-1 chm1:+:328673288:-1 chm1:+:335041807:-1 chm1:+:360418708:-1 chm1:+:367518219:-1 chm1:+:368702209:-1 chm1:+:425365810:-1 chm1:+:468396084:-1 chm1:+:490863124:-1 chm1:+:498229618:-1 chm1:+:515738444:-1 chm1:+:516263467:-1 chm1:+:539017041:-1 chm1:+:572635004:-1 chm1:+:590913476:-1 chm1:+:593878137:-1 chm1:+:601459702:-1 chm1:+:664359561:-1 chm1:+:677148820:-1 chm1:+:685524203:-1 chm1:+:693230678:-1 chm1:+:702103675:-1 chm1:+:707523257:-1 chm1:+:730339763:-1 chm1:+:810743154:-1 chm1:+:830893691:-1 chm1:+:856627795:-1 chm1:+:876035219:-1 chm1:+:894782004:-1 chm1:+:899064097:-1 chm1:+:931876853:-1 chm1:+:972226145:-1 chm1:+:993629724:-1 chm1:+:1015833266:-1 chm1:+:1021732617:-1 chm1:+:1091954348:-1 chm1:+:1115470564:-1 chm1:+:1152256741:-1 chm1:+:1169704429:-1 chm1:+:1201815101:-1 chm1:+:1202056355:-1 chm1:+:1212526508:-1 chm1:+:1221713392:-1 chm1:+:1226415324:-1 chm1:+:1283631626:-1 chm1:+:1298741285:-1 chm1:+:1305638258:-1 chm1:+:1338698479:-1 chm1:+:1347438709:-1 chm1:+:1361781278:-1 chm1:+:1392301444:-1 chm1:+:1394915532:-1 chm1:+:1396956472:-1 chm1:+:1472846654:-1 chm1:+:1485947300:-1 chm1:+:1493213302:-1 chm1:+:1493293748:-1 chm1:+:1503479425:-1 chm1:+:1508152929:-1 chm1:+:1616634591:-1 chm1:+:1641852579:-1 chm1:+:1646970457:-1 chm1:+:1670620629:-1 chm1:+:1672910531:-1 chm1:+:1688516950:-1 chm1:+:1704665656:-1 chm1:+:1712528291:-1 chm1:+:1762680668:-1 chm1:+:1783336792:-1 chm1:+:1825343667:-1 chm1:+:1861967172:-1 chm1:+:1863544679:-1 chm1:+:1916487265:-1 chm1:+:1923270543:-1 chm1:+:1935361289:-1 chm1:+:1957595734:-1 chm1:+:1976947446:-1 chm1:+:2017198514:-1 chm1:+:2021820017:-1 chm1:+:2030897992:-1 chm1:+:2073318502:-1 chm1:+:2080632182:-1 chm1:+:2155100393:-1 chm1:+:2169041098:-1 chm1:+:2183681168:-1 chm1:+:2276132846:-1 chm1:+:2292610680:-1 chm1:+:2299532973:-1 chm1:+:2302971742:-1 chm1:+:2332503358:-1 chm1:+:2343228412:-1 chm1:+:2367095495:-1 chm1:+:2381009256:-1 chm1:+:2381152648:-1 chm1:+:2397490276:-1 chm1:+:2402774886:-1 chm1:+:2422754212:-1 chm1:+:2426614873:-1 chm1:+:2431281155:-1 chm1:+:2431713398:-1 chm1:+:2438251460:-1 chm1:+:2439259857:-1 chm1:+:2439361623:-1 chm1:+:2440101607:-1 chm1:+:2476887517:-1 chm1:+:2495186923:-1 chm1:+:2545320565:-1 chm1:+:2545811866:-1 chm1:+:2553790714:-1 chm1:+:2553963013:-1 chm1:+:2558935355:-1 chm1:+:2560680550:-1 chm1:+:2561714301:-1 chm1:+:2572352092:-1 chm1:+:2603515188:-1 chm1:+:2618625228:-1 chm1:+:2669881369:-1 chm1:+:2674064628:-1 chm1:+:2682358092:-1 chm1:+:2698442776:-1 chm1:+:2700845107:-1 chm1:+:2709594815:-1 chm1:+:2709711387:-1 chm1:+:2710023374:-1 chm1:+:2718231760:-1 chm1:+:2721535646:-1 chm1:+:2735130338:-1 chm1:+:2750243049:-1 chm1:+:2758581951:-1 chm1:+:2761673946:-1 chm1:+:2765883055:-1 chm1:+:2767346631:-1 chm1:+:2815431483:-1 chm1:+:2819374828:-1 chm1:+:2849363319:-1 chm1:+:2853111483:-1 chm1:+:2860097913:-1 chm1:+:2860613551:-1 chm1:+:2861579709:-1 chm1:+:2881533898:-1 chm1:+:2916896271:-1 chm1:+:2921948901:-1 chm1:+:2923090821:-1 chm1:+:2925586241:-1 chm1:+:2949888303:-1 chm1:+:2954871593:-1 chm1:+:2999787474:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACA chm1:+:211800646:-1 chm1:+:247469405:-1 chm1:+:263891301:-1 chm1:+:296848075:-1 chm1:+:541977914:-1 chm1:+:661910058:-1 chm1:+:747426917:-1 chm1:+:844182268:-1 chm1:+:1035741433:-1 chm1:+:1051859748:-1 chm1:+:1058194633:-1 chm1:+:1214415484:-1 chm1:+:1217909031:-1 chm1:+:1376976325:-1 chm1:+:1377055544:-1 chm1:+:1431406764:-1 chm1:+:1678926383:-1 chm1:+:1744052840:-1 chm1:+:1795858299:-1 chm1:+:2003330080:-1 chm1:+:2074071780:-1 chm1:+:2074302861:-1 chm1:+:2519773130:-1 chm1:+:2537555909:-1 chm1:+:2541146738:-1 chm1:+:2541424214:-1 chm1:+:2628709447:-1 chm1:+:2673974641:-1 chm1:+:2677615964:-1 chm1:+:2719585825:-1 chm1:+:2738297878:-1 chm1:+:2767427267:-1 chm1:+:2872498130:-1 chm1:+:2912337770:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACA chm1:+:93321585:-1 chm1:+:202219144:-1 chm1:+:413767981:-1 chm1:+:471736207:-1 chm1:+:841656776:-1 chm1:+:1136872298:-1 chm1:+:1221855830:-1 chm1:+:1222584942:-1 chm1:+:1707183433:-1 chm1:+:1834617528:-1 chm1:+:1941377125:-1 chm1:+:2046038061:-1 chm1:+:2114088855:-1 chm1:+:2275723888:-1 chm1:+:2353105413:-1 chm1:+:2530963613:-1 chm1:+:2535877480:-1 chm1:+:2641932719:-1 chm1:+:2669549527:-1 chm1:+:2849419424:-1 chm1:+:2956820487:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACA chm1:+:35566005:-1 chm1:+:228002257:-1 chm1:+:292328915:-1 chm1:+:314700320:-1 chm1:+:350311720:-1 chm1:+:388643763:-1 chm1:+:395155942:-1 chm1:+:628716551:-1 chm1:+:642733177:-1 chm1:+:662611444:-1 chm1:+:676102885:-1 chm1:+:1011217924:-1 chm1:+:1015631157:-1 chm1:+:1126951040:-1 chm1:+:1148916569:-1 chm1:+:1298184587:-1 chm1:+:1298878724:-1 chm1:+:1335452300:-1 chm1:+:1449532772:-1 chm1:+:1450716945:-1 chm1:+:1543600918:-1 chm1:+:1622189385:-1 chm1:+:1656818494:-1 chm1:+:1779413086:-1 chm1:+:1796241412:-1 chm1:+:1824674093:-1 chm1:+:1880639549:-1 chm1:+:2075739790:-1 chm1:+:2111670244:-1 chm1:+:2476317184:-1 chm1:+:2481664898:-1 chm1:+:2485362251:-1 chm1:+:2547490131:-1 chm1:+:2614917315:-1 chm1:+:2630091776:-1 chm1:+:2707613457:-1 chm1:+:2736060076:-1 chm1:+:2852715674:-1 chm1:+:2853715959:-1 chm1:+:2871843512:-1 chm1:+:3025181155:-1 chm1:+:3031024646:-1 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chm1:+:2871227176:-1 chm1:+:2948741014:-1 chm1:+:2993091290:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACA chm1:+:514292454:-1 chm1:+:1578796685:-1 chm1:+:1580941714:-1 chm1:+:1634553917:-1 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+CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACA chm1:+:593703884:-1 chm1:+:659826079:-1 chm1:+:864761757:-1 chm1:+:864872618:-1 chm1:+:936541752:-1 chm1:+:956866145:-1 chm1:+:963409871:-1 chm1:+:1093376459:-1 chm1:+:1112648865:-1 chm1:+:1192793555:-1 chm1:+:1248443447:-1 chm1:+:1304408706:-1 chm1:+:1540772247:-1 chm1:+:1545893743:-1 chm1:+:1638157402:-1 chm1:+:1770068627:-1 chm1:+:1785568604:-1 chm1:+:2254863702:-1 chm1:+:2773840284:-1 chm1:+:2885116248:-1 chm1:+:2890824171:-1 chm1:+:2958273403:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACA chm1:+:63246163:-1 chm1:+:171612292:-1 chm1:+:1032221826:-1 chm1:+:1036587173:-1 chm1:+:1084296315:-1 chm1:+:1096800846:-1 chm1:+:1097178187:-1 chm1:+:1116279121:-1 chm1:+:1466042117:-1 chm1:+:1506206786:-1 chm1:+:1705130804:-1 chm1:+:1973641084:-1 chm1:+:2036265040:-1 chm1:+:2042013776:-1 chm1:+:2348587111:-1 chm1:+:2540344224:-1 chm1:+:2559007213:-1 chm1:+:2633908119:-1 chm1:+:2677464552:-1 chm1:+:2696897171:-1 chm1:+:2803740503:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACA chm1:+:93673495:-1 chm1:+:306173114:-1 chm1:+:465613999:-1 chm1:+:506309488:-1 chm1:+:786438486:-1 chm1:+:1165072522:-1 chm1:+:1458114969:-1 chm1:+:1499543501:-1 chm1:+:1639944808:-1 chm1:+:1785242179:-1 chm1:+:2568200607:-1 chm1:+:2609385867:-1 chm1:+:2955445267:-1 chm1:+:3002583203:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACA chm1:+:152923719:-1 chm1:+:245957332:-1 chm1:+:355113359:-1 chm1:+:372440652:-1 chm1:+:472072688:-1 chm1:+:482452215:-1 chm1:+:544769348:-1 chm1:+:745485698:-1 chm1:+:823582601:-1 chm1:+:869070830:-1 chm1:+:876269874:-1 chm1:+:978692470:-1 chm1:+:1021026429:-1 chm1:+:1041983998:-1 chm1:+:1055677558:-1 chm1:+:1058033909:-1 chm1:+:1069225004:-1 chm1:+:1185671401:-1 chm1:+:1224307417:-1 chm1:+:1229662794:-1 chm1:+:1240164764:-1 chm1:+:1340349905:-1 chm1:+:1344655987:-1 chm1:+:1691323498:-1 chm1:+:1697079689:-1 chm1:+:1785023215:-1 chm1:+:1796329352:-1 chm1:+:1826579844:-1 chm1:+:1847570506:-1 chm1:+:1888030168:-1 chm1:+:2007179652:-1 chm1:+:2040822920:-1 chm1:+:2059218056:-1 chm1:+:2302309289:-1 chm1:+:2397548351:-1 chm1:+:2509119019:-1 chm1:+:2529823046:-1 chm1:+:2579506410:-1 chm1:+:2600548251:-1 chm1:+:2610600086:-1 chm1:+:2695899102:-1 chm1:+:2828030806:-1 chm1:+:2850342363:-1 chm1:+:2852716360:-1 chm1:+:2854750955:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACA chm1:+:215184238:-1 chm1:+:232462246:-1 chm1:+:471087726:-1 chm1:+:507498231:-1 chm1:+:706117055:-1 chm1:+:759681281:-1 chm1:+:1017687274:-1 chm1:+:1134041406:-1 chm1:+:1248896748:-1 chm1:+:1667244899:-1 chm1:+:1686959328:-1 chm1:+:1785498752:-1 chm1:+:2135271219:-1 chm1:+:2359970912:-1 chm1:+:2514594745:-1 chm1:+:2537556499:-1 chm1:+:2565442802:-1 chm1:+:2603715399:-1 chm1:+:2624723511:-1 chm1:+:2910209381:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACA chm1:+:44080847:-1 chm1:+:338429447:-1 chm1:+:501955714:-1 chm1:+:559467522:-1 chm1:+:1004165221:-1 chm1:+:1100300589:-1 chm1:+:1234979310:-1 chm1:+:1361034907:-1 chm1:+:1530402768:-1 chm1:+:1656859816:-1 chm1:+:1656862049:-1 chm1:+:1780819080:-1 chm1:+:2285486880:-1 chm1:+:2668607644:-1 chm1:+:2692710336:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACA chm1:+:79877982:-1 chm1:+:79996438:-1 chm1:+:400600161:-1 chm1:+:472787877:-1 chm1:+:944078096:-1 chm1:+:1047974732:-1 chm1:+:1053717180:-1 chm1:+:1417101508:-1 chm1:+:1496473161:-1 chm1:+:1560985968:-1 chm1:+:1684301179:-1 chm1:+:1887787523:-1 chm1:+:2362052846:-1 chm1:+:2383371281:-1 chm1:+:2529491570:-1 chm1:+:2708550052:-1 chm1:+:2972193031:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACA chm1:+:294563552:-1 chm1:+:1462584206:-1 chm1:+:1474214567:-1 chm1:+:1710437114:-1 chm1:+:1817534588:-1 chm1:+:2478712891:-1 +TGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:350922631:-1 chm1:+:401546378:-1 chm1:+:642174933:-1 chm1:+:920952148:-1 chm1:+:1057720487:-1 chm1:+:1085513173:-1 chm1:+:1309902774:-1 chm1:+:1334065475:-1 chm1:+:1345431372:-1 chm1:+:1363958062:-1 chm1:+:1885767372:-1 chm1:+:2004170890:-1 chm1:+:2427776070:-1 chm1:+:2476836482:-1 chm1:+:2752904879:-1 chm1:+:2822056906:-1 chm1:+:2923119705:-1 chm1:+:3010114422:-1 +TGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:44146977:-1 chm1:+:191139551:-1 chm1:+:365813109:-1 chm1:+:455138849:-1 chm1:+:478861368:-1 chm1:+:505242112:-1 chm1:+:540301771:-1 chm1:+:1298665095:73 chm1:+:1366387686:-1 chm1:+:1528564287:-1 chm1:+:1554302441:-1 chm1:+:1755365579:-1 chm1:+:1781475203:-1 chm1:+:1882513430:-1 chm1:+:1893575208:28 chm1:+:1999971804:-1 chm1:+:2170424858:-1 chm1:+:2363558293:-1 chm1:+:2392711503:-1 chm1:+:2509388145:-1 chm1:+:2636657646:-1 chm1:+:2721385612:-1 chm1:+:2977293162:-1 +TGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:2171217870:-1 +TGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:1893575209:28 +TGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:1893575210:28 +TGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:1298665096:73 +TGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:389480998:-1 chm1:+:770038824:-1 chm1:+:1144742880:-1 chm1:+:1174128098:-1 chm1:+:1507874291:-1 chm1:+:2045841485:-1 chm1:+:2163304925:-1 chm1:+:2436007470:-1 +TGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:626353134:-1 chm1:+:996752199:-1 chm1:+:1003880002:-1 chm1:+:1313724935:-1 chm1:+:1328563205:-1 chm1:+:1445104551:-1 chm1:+:1511909722:-1 chm1:+:1662146400:-1 chm1:+:1683242588:-1 chm1:+:1738453275:-1 chm1:+:1771644152:-1 chm1:+:1801623647:-1 chm1:+:2105243125:-1 chm1:+:2172984070:-1 chm1:+:2405840421:-1 chm1:+:2882772605:-1 chm1:+:2933073875:-1 chm1:+:3059400757:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCT chm1:+:21000439:-1 chm1:+:32072687:-1 chm1:+:34131045:-1 chm1:+:55855020:-1 chm1:+:116531171:-1 chm1:+:155831426:-1 chm1:+:200690182:-1 chm1:+:209340752:-1 chm1:+:291986111:-1 chm1:+:293541614:-1 chm1:+:319247433:-1 chm1:+:352431744:-1 chm1:+:423961643:-1 chm1:+:426417804:-1 chm1:+:477874059:-1 chm1:+:512599313:-1 chm1:+:624702209:-1 chm1:+:717314145:-1 chm1:+:731451771:-1 chm1:+:765048908:-1 chm1:+:802196184:-1 chm1:+:876079395:-1 chm1:+:922471050:-1 chm1:+:932233477:-1 chm1:+:989311224:-1 chm1:+:1000803228:-1 chm1:+:1012152901:-1 chm1:+:1029111904:-1 chm1:+:1061940606:-1 chm1:+:1105590985:-1 chm1:+:1166744107:-1 chm1:+:1222824329:-1 chm1:+:1391528579:-1 chm1:+:1395835444:-1 chm1:+:1540725703:-1 chm1:+:1565037781:-1 chm1:+:1574562008:-1 chm1:+:1581517800:-1 chm1:+:1608531414:-1 chm1:+:1623989313:-1 chm1:+:1673746168:-1 chm1:+:1842372218:-1 chm1:+:1889210462:-1 chm1:+:2049452000:-1 chm1:+:2071295666:-1 chm1:+:2121285355:-1 chm1:+:2137618343:-1 chm1:+:2277903972:-1 chm1:+:2368949208:-1 chm1:+:2399910334:-1 chm1:+:2431612964:-1 chm1:+:2432429082:-1 chm1:+:2436418274:-1 chm1:+:2493350536:-1 chm1:+:2504398719:-1 chm1:+:2505319840:-1 chm1:+:2520792324:-1 chm1:+:2537750609:-1 chm1:+:2550775221:-1 chm1:+:2560197668:-1 chm1:+:2643411028:-1 chm1:+:2695441910:-1 chm1:+:2712790825:-1 chm1:+:2750058541:-1 chm1:+:2760289326:-1 chm1:+:2768961931:-1 chm1:+:2816972632:-1 chm1:+:2823542359:-1 chm1:+:2905568643:-1 chm1:+:2920704626:-1 chm1:+:3055019253:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCT chm1:+:288905945:-1 chm1:+:409364904:-1 chm1:+:451119473:-1 chm1:+:1723684006:52 chm1:+:2061193969:-1 chm1:+:2327643286:42 chm1:+:2328649883:42 chm1:+:2921700484:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCT chm1:+:483386237:-1 chm1:+:592791463:-1 chm1:+:617895087:-1 chm1:+:687195175:-1 chm1:+:1236657984:-1 chm1:+:1755251810:-1 chm1:+:2251751242:-1 chm1:+:2263664189:-1 chm1:+:2818027729:-1 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chm1:+:2458545006:-1 chm1:+:2547225620:-1 chm1:+:2564643739:-1 chm1:+:2625130890:-1 chm1:+:2707166814:-1 chm1:+:2861313857:-1 chm1:+:2873023873:-1 chm1:+:3017038400:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCT chm1:+:147728094:-1 chm1:+:293559397:-1 chm1:+:301801445:-1 chm1:+:534483994:-1 chm1:+:791508144:-1 chm1:+:1053518223:-1 chm1:+:1201543576:-1 chm1:+:1273890087:-1 chm1:+:1426717570:-1 chm1:+:1568762091:-1 chm1:+:1878538445:-1 chm1:+:2018409389:-1 chm1:+:2046900752:-1 chm1:+:2301834649:-1 chm1:+:2404021581:-1 chm1:+:2899328339:-1 chm1:+:2929429115:-1 chm1:+:2969337054:-1 chm1:+:3009315412:-1 chm1:+:3101734719:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCT chm1:+:235297356:-1 chm1:+:1723684011:52 chm1:+:2327643290:42 chm1:+:2328649887:42 chm1:+:2852385126:45 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+TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCT chm1:+:320649615:-1 chm1:+:1738557616:-1 chm1:+:1752074489:-1 chm1:+:2290160351:-1 chm1:+:2859582236:-1 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+TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCT chm1:+:306679448:-1 chm1:+:1400909136:-1 chm1:+:1702085843:-1 chm1:+:2983862769:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCT chm1:+:9421700:-1 chm1:+:554362974:-1 chm1:+:1021712321:-1 chm1:+:1142346799:-1 chm1:+:1205609723:-1 chm1:+:1723684013:52 chm1:+:1797542121:-1 chm1:+:1802849427:-1 chm1:+:1802849437:-1 chm1:+:2178661826:-1 chm1:+:2327643292:42 chm1:+:2328649889:42 chm1:+:2345540635:-1 chm1:+:2676429540:-1 chm1:+:2852385128:45 chm1:+:2857602593:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCT chm1:+:507377541:-1 chm1:+:831353598:-1 chm1:+:954782954:-1 chm1:+:1655533622:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCT chm1:+:2047369844:-1 chm1:+:2276953620:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCT chm1:+:1728869366:-1 chm1:+:2993580876:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCT chm1:+:12719691:-1 chm1:+:481083631:-1 chm1:+:1422109203:-1 chm1:+:1520459946:-1 chm1:+:1533844860:-1 chm1:+:1618153280:-1 chm1:+:1723684014:52 chm1:+:1778917266:-1 chm1:+:2125434517:-1 chm1:+:2327643294:42 chm1:+:2328649891:42 chm1:+:2739493091:-1 chm1:+:2975674651:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCT chm1:+:643455441:-1 chm1:+:2272833092:-1 chm1:+:2327643296:42 chm1:+:2328649893:42 +AGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:1606495043:47 chm1:+:2443322046:28 +AGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:1325963262:-1 chm1:+:1372845607:-1 +AGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:2443322041:28 +AGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:2443322045:28 +AGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:1606495042:47 +AGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:2443322050:28 +AGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:1273770764:-1 +AGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:1606495041:47 chm1:+:2443322044:28 +AGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:1606495045:47 chm1:+:2443322048:28 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGG chm1:+:1290336205:-1 chm1:+:1440581457:-1 chm1:+:2444616649:-1 chm1:+:2444620560:-1 chm1:+:3063471460:-1 chm1:+:3063496731:-1 chm1:+:3099935209:20 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGG chm1:+:3099935208:20 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGG chm1:+:3099935214:20 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGG chm1:+:3099935219:20 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGG chm1:+:3099935207:20 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGG chm1:+:2683029318:-1 chm1:+:3099935212:20 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGG chm1:+:3099935217:20 +CCAGTGCACCATTGAGACTGTGACTTGTACACTTTACACCCAACAAACACAATGTGTTTGCTCTCACACCTAGATATGGGACATGTGCAGGATTGTCAGTCTCAGCCCCTGGACTTTCTGGAGGGTATAACTGTGAAATATATCTCGGCCCAGCTCGTGAGTGACTTGACTCTTCTGCGTAGCCCAGCCCAGTGATAAAATTGTGACATTATTGACCCAGCACCTATGACCCCCCTCTTCTGCCTGGGTCCTGTCAAAAAAGAGAGACTTGTGACAAATCACTGGGACAAGGCACCCACATGATGTGACTCTCCTCTTTTCCCCTGGGCCCTGCGATATTTTGTATATTGTGACATACTGCTGGGCATAATACCTAGGGAATTGATCGCTACTGCCTGAGCCCTGTTCACAGGGGGCCTTGGGACAATCTCTACTGCATTCACCACCTAAAAAAAGGTGTGTGCACCCTGCCTACAAAGAAGAGGTGTAGCAGATCACTTGTCCTTAGCAACCAAGTCGATGCGAGTCTCTGTCCTGCCTTGGTGCTGCTCACAGGGGACATTATAACATATACTTGGTGCTGGCCCCATGTTTTGTAAT chm1:+:2681760568:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAA chm1:+:281007966:-1 chm1:+:600759177:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAA chm1:+:253247475:-1 chm1:+:399913742:-1 chm1:+:458273639:-1 chm1:+:657903898:-1 chm1:+:690555953:-1 chm1:+:1563597897:-1 chm1:+:1650266857:-1 chm1:+:1855254409:-1 chm1:+:2015742270:-1 chm1:+:2143430754:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAA chm1:+:172018512:-1 chm1:+:252574962:-1 chm1:+:345062119:-1 chm1:+:762379355:-1 chm1:+:865571737:-1 chm1:+:1025526908:-1 chm1:+:1290069861:-1 chm1:+:2144086947:-1 chm1:+:2430405721:-1 chm1:+:2568130191:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAA chm1:+:641672796:-1 chm1:+:2183067802:-1 chm1:+:2998195439:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAA chm1:+:17367228:-1 chm1:+:85346160:-1 chm1:+:1001679362:-1 chm1:+:1085609875:-1 chm1:+:1170669066:-1 chm1:+:1195786964:-1 chm1:+:1614189135:-1 chm1:+:2424388959:-1 chm1:+:2431940051:-1 chm1:+:2890254266:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAA chm1:+:177541012:-1 chm1:+:547104318:-1 chm1:+:1362994908:-1 chm1:+:1894343980:-1 chm1:+:2111107195:-1 chm1:+:2227475160:-1 chm1:+:2689442919:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAA chm1:+:20226059:-1 chm1:+:198213307:-1 chm1:+:283564027:-1 chm1:+:596437857:-1 chm1:+:677005777:-1 chm1:+:1451272241:-1 chm1:+:2469843574:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAA chm1:+:602481563:-1 chm1:+:1016472148:-1 chm1:+:1158967786:-1 chm1:+:1772268325:-1 chm1:+:2649498285:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAA chm1:+:1057945010:-1 chm1:+:2814254168:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAA chm1:+:1472011596:-1 chm1:+:2951323242:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAA chm1:+:166278110:-1 chm1:+:345353975:-1 chm1:+:372250054:-1 chm1:+:383868372:-1 chm1:+:933445778:-1 chm1:+:961674132:-1 chm1:+:998034514:-1 chm1:+:1133441304:-1 chm1:+:1557489780:-1 chm1:+:1820216455:-1 chm1:+:1820267616:-1 chm1:+:1835432769:-1 chm1:+:2077298669:-1 chm1:+:2125488794:-1 chm1:+:2196231071:-1 chm1:+:2594572042:-1 chm1:+:2645663133:-1 chm1:+:2721521822:-1 chm1:+:3058756406:-1 chm1:+:3058802097:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAA chm1:+:99084421:-1 chm1:+:338788045:-1 chm1:+:672144409:-1 chm1:+:723945618:-1 chm1:+:1003783734:-1 chm1:+:1356748575:-1 chm1:+:1442757259:-1 chm1:+:1517612481:-1 chm1:+:1822708964:-1 chm1:+:1850354938:-1 chm1:+:2025481384:-1 chm1:+:2152260768:-1 chm1:+:2387253890:-1 chm1:+:2636571167:-1 chm1:+:2816031642:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAA chm1:+:86122775:-1 chm1:+:111884699:-1 chm1:+:115380215:-1 chm1:+:244215353:-1 chm1:+:299360313:-1 chm1:+:304507249:-1 chm1:+:315884017:-1 chm1:+:318847630:-1 chm1:+:363134442:-1 chm1:+:380137453:-1 chm1:+:423375254:-1 chm1:+:616189594:-1 chm1:+:701963420:-1 chm1:+:714415458:-1 chm1:+:766235847:-1 chm1:+:833086582:-1 chm1:+:1032844696:-1 chm1:+:1173067858:-1 chm1:+:1317159600:-1 chm1:+:1343561166:-1 chm1:+:1424125233:-1 chm1:+:1457428153:-1 chm1:+:1478258974:-1 chm1:+:1574119392:-1 chm1:+:1584789023:-1 chm1:+:1585175216:-1 chm1:+:1643070496:-1 chm1:+:1716036196:-1 chm1:+:1752187898:-1 chm1:+:1822189770:-1 chm1:+:1823291708:-1 chm1:+:1829526120:-1 chm1:+:1904771690:-1 chm1:+:2112822612:-1 chm1:+:2138972983:-1 chm1:+:2181743967:-1 chm1:+:2337854003:-1 chm1:+:2424405199:-1 chm1:+:2590031125:-1 chm1:+:2603230933:-1 chm1:+:2613702368:-1 chm1:+:2626674030:-1 chm1:+:2731303204:-1 chm1:+:2733874988:-1 chm1:+:2802607940:-1 chm1:+:2887263255:-1 chm1:+:2901027125:-1 chm1:+:3056322770:-1 chm1:+:3062526086:-1 +TTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:166119851:-1 chm1:+:239415495:-1 chm1:+:1420499262:-1 chm1:+:2112864221:-1 chm1:+:2804718498:-1 +TTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:221282636:-1 chm1:+:667757790:-1 chm1:+:782389030:-1 chm1:+:1646930871:-1 chm1:+:2697886792:-1 +TTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:109855879:-1 chm1:+:113276502:-1 chm1:+:115529418:-1 chm1:+:211382844:-1 chm1:+:279692029:-1 chm1:+:368174517:-1 chm1:+:463353602:-1 chm1:+:646335873:-1 chm1:+:781125336:-1 chm1:+:1517317163:-1 chm1:+:1651948547:-1 chm1:+:2007703932:-1 chm1:+:2026630200:39 chm1:+:2072603597:-1 chm1:+:2275971901:-1 chm1:+:2301872866:-1 chm1:+:2530936128:-1 chm1:+:2668680408:-1 chm1:+:2702731699:-1 chm1:+:2703229418:-1 chm1:+:2717635509:-1 chm1:+:2724488908:-1 chm1:+:2732280341:-1 chm1:+:2755823531:-1 chm1:+:2757508119:-1 chm1:+:3002135110:-1 +TTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026630197:39 +TTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026630198:39 +TTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026630199:39 +TTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026630201:39 +TTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026630204:39 +TTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026630203:39 +TTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2010493811:-1 +TTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026630205:39 +TTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:155106264:-1 chm1:+:692967077:-1 chm1:+:1534357882:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGA chm1:+:533567777:-1 chm1:+:658619697:-1 chm1:+:1837007300:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGA chm1:+:529156003:-1 chm1:+:733376878:-1 chm1:+:1108242606:-1 chm1:+:1694511848:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGA chm1:+:166250480:-1 chm1:+:413548505:-1 chm1:+:414393826:-1 chm1:+:504939350:-1 chm1:+:704238657:-1 chm1:+:979935302:-1 chm1:+:1051809791:-1 chm1:+:1319640093:-1 chm1:+:1378625353:-1 chm1:+:1913437118:-1 chm1:+:2120180185:-1 chm1:+:2228056606:-1 chm1:+:2392792846:-1 chm1:+:2641518246:-1 chm1:+:2725211418:-1 chm1:+:2753563636:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGA chm1:+:68162040:-1 chm1:+:165288220:-1 chm1:+:207163507:-1 chm1:+:234396611:-1 chm1:+:325986708:-1 chm1:+:517918267:-1 chm1:+:548526637:-1 chm1:+:659809288:-1 chm1:+:1424567286:-1 chm1:+:1646960583:-1 chm1:+:1907167759:-1 chm1:+:2920911489:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGA chm1:+:162576389:-1 chm1:+:513124212:-1 chm1:+:1495569628:-1 chm1:+:2281987026:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGA chm1:+:813990106:-1 chm1:+:899658172:-1 chm1:+:1431574646:-1 chm1:+:2027917123:-1 chm1:+:2042369034:-1 chm1:+:2262126007:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGA chm1:+:172219419:-1 chm1:+:483678049:-1 chm1:+:562688320:-1 chm1:+:1384579516:-1 chm1:+:1809504534:-1 chm1:+:1925467782:-1 chm1:+:2581184012:-1 chm1:+:2859456653:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGA chm1:+:265395056:-1 chm1:+:482445895:-1 chm1:+:482557275:-1 chm1:+:1235549941:-1 chm1:+:1327247043:-1 chm1:+:1661225722:-1 chm1:+:1671016455:-1 chm1:+:1879829267:-1 chm1:+:1885365164:-1 chm1:+:1933329791:-1 chm1:+:2497571305:-1 chm1:+:2633362325:-1 chm1:+:2669670359:-1 chm1:+:2737537192:-1 chm1:+:2756245852:-1 chm1:+:2779463043:-1 chm1:+:2874146436:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGA chm1:+:935830278:-1 chm1:+:1668838811:-1 chm1:+:1828319814:-1 chm1:+:2467663298:-1 chm1:+:2595250263:-1 chm1:+:2906224970:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGA chm1:+:587941148:-1 chm1:+:778176646:-1 chm1:+:983580057:-1 chm1:+:1046342837:-1 chm1:+:1500553760:-1 chm1:+:2162282745:-1 chm1:+:2179268809:-1 chm1:+:2241646344:-1 chm1:+:2264656824:-1 chm1:+:2424163434:-1 chm1:+:2472449772:-1 chm1:+:2476847357:-1 chm1:+:2528779616:-1 chm1:+:2716180601:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGA chm1:+:74091268:-1 chm1:+:454032294:-1 chm1:+:1267636049:-1 chm1:+:2417724467:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGA chm1:+:187047413:-1 chm1:+:371798913:-1 chm1:+:397009497:-1 chm1:+:431173799:-1 chm1:+:760992431:-1 chm1:+:824524361:-1 chm1:+:987062079:-1 chm1:+:1093217524:-1 chm1:+:1129175340:-1 chm1:+:1144790790:-1 chm1:+:1366202996:-1 chm1:+:1367848415:-1 chm1:+:1441766860:-1 chm1:+:1483289762:-1 chm1:+:1512995931:-1 chm1:+:1950275740:-1 chm1:+:2176754291:-1 chm1:+:2536004683:-1 chm1:+:2951406357:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGA chm1:+:79004090:-1 chm1:+:119261859:-1 chm1:+:120505008:-1 chm1:+:171061223:-1 chm1:+:251863413:-1 chm1:+:286519569:-1 chm1:+:307116474:-1 chm1:+:416680781:-1 chm1:+:427851300:-1 chm1:+:510979133:-1 chm1:+:529084124:-1 chm1:+:568592633:-1 chm1:+:703093460:-1 chm1:+:753264888:-1 chm1:+:763836443:-1 chm1:+:807031739:-1 chm1:+:817096880:-1 chm1:+:855799264:-1 chm1:+:957713134:-1 chm1:+:986597454:-1 chm1:+:1036648619:-1 chm1:+:1059504645:-1 chm1:+:1116159672:-1 chm1:+:1192184855:-1 chm1:+:1299632410:-1 chm1:+:1309457771:-1 chm1:+:1340013859:-1 chm1:+:1374291123:-1 chm1:+:1502345451:-1 chm1:+:1661849100:-1 chm1:+:1732389186:-1 chm1:+:1770683032:-1 chm1:+:1845689815:-1 chm1:+:1944896528:-1 chm1:+:1978826420:-1 chm1:+:2059536466:-1 chm1:+:2262721754:-1 chm1:+:2271301022:-1 chm1:+:2390984690:-1 chm1:+:2462560063:-1 chm1:+:2613497080:-1 chm1:+:2650150253:-1 chm1:+:2701494512:-1 chm1:+:2761564337:-1 chm1:+:2944298488:-1 chm1:+:2967151377:-1 chm1:+:3051610592:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGA chm1:+:71246150:-1 chm1:+:85427682:-1 chm1:+:389871805:-1 chm1:+:393118798:-1 chm1:+:593410681:-1 chm1:+:600974223:-1 chm1:+:660304484:-1 chm1:+:732644404:-1 chm1:+:793170110:-1 chm1:+:996444762:-1 chm1:+:1043968727:-1 chm1:+:1143633171:-1 chm1:+:1145414286:-1 chm1:+:1243766377:-1 chm1:+:1312380261:-1 chm1:+:1487826115:-1 chm1:+:1510285067:-1 chm1:+:1634015356:-1 chm1:+:1746727014:-1 chm1:+:1770384543:-1 chm1:+:1781702386:-1 chm1:+:1871458422:-1 chm1:+:1996227895:-1 chm1:+:2066610165:-1 chm1:+:2117771033:-1 chm1:+:2157447907:-1 chm1:+:2286325771:-1 chm1:+:2403043485:-1 chm1:+:2568218250:-1 chm1:+:2614631885:-1 chm1:+:2687937301:-1 chm1:+:3046124160:-1 +TCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:353689283:-1 chm1:+:1100362649:-1 chm1:+:1201272800:21 chm1:+:1395162867:-1 chm1:+:1478068393:-1 chm1:+:1542217272:-1 chm1:+:2944626864:-1 +TCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272808:21 +TCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:378055021:-1 chm1:+:1201272799:21 +TCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272801:21 +TCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272803:21 +TCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272804:21 +TCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272805:21 +TCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272807:21 +TCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1229611996:-1 +TCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272806:21 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:419189665:-1 chm1:+:1377399202:-1 chm1:+:2771433479:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:836838152:-1 chm1:+:2610619240:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:410854012:-1 chm1:+:589636849:-1 chm1:+:920610275:-1 chm1:+:1022049354:-1 chm1:+:1027211449:-1 chm1:+:1391491230:-1 chm1:+:1495650340:-1 chm1:+:1514741736:-1 chm1:+:2195501475:-1 chm1:+:2468072748:-1 chm1:+:2935762664:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:302982751:-1 chm1:+:1243892152:-1 chm1:+:1410387671:-1 chm1:+:1544360712:-1 chm1:+:1613227640:-1 chm1:+:1850354504:-1 chm1:+:2556260380:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:17904196:-1 chm1:+:67931437:-1 chm1:+:220601034:-1 chm1:+:231071427:-1 chm1:+:323833365:-1 chm1:+:413294170:-1 chm1:+:420922600:-1 chm1:+:467821662:-1 chm1:+:554236895:-1 chm1:+:682602369:-1 chm1:+:1118583346:-1 chm1:+:1208943530:-1 chm1:+:1352095417:-1 chm1:+:1360204089:-1 chm1:+:1521260325:-1 chm1:+:1534553193:-1 chm1:+:2066785217:-1 chm1:+:2081097378:-1 chm1:+:2161758568:-1 chm1:+:2180630547:-1 chm1:+:2333341983:-1 chm1:+:2351509552:-1 chm1:+:2415289396:-1 chm1:+:2573511503:-1 chm1:+:2700481498:-1 chm1:+:2967314258:-1 chm1:+:3027812052:-1 chm1:+:3064930566:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:72280261:-1 chm1:+:975371353:-1 chm1:+:1032971597:-1 chm1:+:1361248879:-1 chm1:+:1474781113:-1 chm1:+:1842708378:-1 chm1:+:2189907058:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:1163859924:-1 chm1:+:1290579181:-1 chm1:+:1795430501:-1 chm1:+:1865949041:-1 chm1:+:1932111559:-1 chm1:+:1949948597:-1 chm1:+:2030973116:-1 chm1:+:2189856257:-1 chm1:+:2228762109:-1 chm1:+:2385796200:-1 chm1:+:2584122516:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:1147471849:-1 chm1:+:1248379640:-1 chm1:+:1667779950:-1 chm1:+:2818867890:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:215984507:-1 chm1:+:1278082756:-1 chm1:+:2299255401:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:213296376:-1 chm1:+:488386971:-1 chm1:+:582139507:-1 chm1:+:634517175:-1 chm1:+:1830935346:-1 chm1:+:2380313234:-1 chm1:+:2585978414:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:23105609:-1 chm1:+:85543652:-1 chm1:+:215248578:-1 chm1:+:336028956:-1 chm1:+:466294310:-1 chm1:+:1486327934:-1 chm1:+:1510321464:-1 chm1:+:1637126276:-1 chm1:+:1691330224:-1 chm1:+:1727114307:-1 chm1:+:1729304068:-1 chm1:+:1900084866:-1 chm1:+:1965952404:-1 chm1:+:2278584993:-1 chm1:+:2398742582:-1 chm1:+:2624110439:-1 chm1:+:2632167532:-1 chm1:+:2664861125:-1 chm1:+:2758766676:-1 chm1:+:2760727593:-1 chm1:+:2849756593:-1 chm1:+:2889851255:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:144010548:-1 chm1:+:625549040:-1 chm1:+:767927558:-1 chm1:+:923001158:-1 chm1:+:1392000395:-1 chm1:+:1659559106:-1 chm1:+:1687370240:-1 chm1:+:2060754662:-1 chm1:+:2061789358:-1 chm1:+:2067968682:-1 chm1:+:2262813255:-1 chm1:+:2556786818:-1 chm1:+:2575396899:-1 chm1:+:2675913944:-1 chm1:+:2757840808:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:98237654:-1 chm1:+:684993581:-1 chm1:+:879974635:-1 chm1:+:1135383704:-1 chm1:+:1135384118:-1 chm1:+:1277505486:-1 chm1:+:1354485484:-1 chm1:+:1417227455:-1 chm1:+:1504012462:-1 chm1:+:1626023725:-1 chm1:+:1639716147:-1 chm1:+:1808380819:-1 chm1:+:1871945634:-1 chm1:+:1941657227:-1 chm1:+:2071000455:-1 chm1:+:2145942410:-1 chm1:+:2289151320:-1 chm1:+:2532381772:-1 chm1:+:2871751383:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:224843802:-1 chm1:+:286892440:-1 chm1:+:504680902:-1 chm1:+:582416286:-1 chm1:+:823807361:-1 chm1:+:962461303:-1 chm1:+:1096532997:-1 chm1:+:1725150395:-1 chm1:+:1888447575:-1 chm1:+:2020741783:-1 chm1:+:2192354511:-1 chm1:+:2422115090:-1 chm1:+:2825427034:-1 chm1:+:3031331811:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:1766305532:-1 chm1:+:1845586509:-1 chm1:+:2346035286:-1 chm1:+:2878820672:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGG chm1:+:479258187:-1 chm1:+:529104360:-1 chm1:+:572213646:-1 chm1:+:576937891:-1 chm1:+:696156164:-1 chm1:+:891204118:-1 chm1:+:950119833:-1 chm1:+:1167370084:-1 chm1:+:1337881436:-1 chm1:+:1485544457:-1 chm1:+:1629682370:-1 chm1:+:1846032620:-1 chm1:+:1882139530:-1 chm1:+:2133357733:-1 chm1:+:2163018030:-1 chm1:+:2234119024:-1 chm1:+:2271199832:-1 chm1:+:2384398303:-1 chm1:+:2726873452:-1 chm1:+:3006237702:-1 +CCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:33461041:-1 chm1:+:41851712:-1 chm1:+:114517173:-1 chm1:+:466117640:-1 chm1:+:590848310:-1 chm1:+:687029398:-1 chm1:+:697922894:-1 chm1:+:779505466:-1 chm1:+:796684225:-1 chm1:+:992280803:-1 chm1:+:1157572392:-1 chm1:+:1690480391:-1 chm1:+:1777382012:-1 chm1:+:1833169886:-1 chm1:+:2663352592:-1 chm1:+:3052648166:-1 +CCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:69531028:-1 chm1:+:327600307:-1 chm1:+:769354828:-1 chm1:+:976304731:-1 chm1:+:1322727362:-1 chm1:+:1545215786:-1 chm1:+:1853992315:-1 chm1:+:2222295858:-1 chm1:+:2457593838:-1 chm1:+:2604882725:-1 +CCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1255376179:31 +CCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1255376180:31 +CCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1255376181:31 +CCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1255376183:31 +CCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1255376184:31 +CCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1255376177:31 +CCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:53364269:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:239563418:-1 chm1:+:643915564:-1 chm1:+:663151191:-1 chm1:+:715092277:-1 chm1:+:855792588:-1 chm1:+:1072167377:-1 chm1:+:1091943568:-1 chm1:+:1144136389:-1 chm1:+:1147370031:-1 chm1:+:1383879841:-1 chm1:+:1547168137:-1 chm1:+:1561824771:-1 chm1:+:2539479696:-1 chm1:+:2587519474:-1 chm1:+:2919008144:-1 chm1:+:3017778218:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:56062188:-1 chm1:+:76368375:-1 chm1:+:95039700:-1 chm1:+:116060985:-1 chm1:+:116395539:-1 chm1:+:180479714:-1 chm1:+:198930684:-1 chm1:+:210208413:-1 chm1:+:225320590:-1 chm1:+:248168012:-1 chm1:+:248225562:-1 chm1:+:320076384:-1 chm1:+:362335370:-1 chm1:+:382814614:-1 chm1:+:394630634:-1 chm1:+:397901720:-1 chm1:+:422387705:-1 chm1:+:463846922:-1 chm1:+:466427886:-1 chm1:+:509492501:-1 chm1:+:528486796:-1 chm1:+:549090326:-1 chm1:+:560697665:-1 chm1:+:579259905:-1 chm1:+:579631382:-1 chm1:+:591618295:-1 chm1:+:641469522:-1 chm1:+:649078948:-1 chm1:+:652955058:-1 chm1:+:654009142:-1 chm1:+:727161939:-1 chm1:+:749437781:-1 chm1:+:768523700:-1 chm1:+:782291683:-1 chm1:+:795191818:-1 chm1:+:796064865:-1 chm1:+:808836571:-1 chm1:+:823647513:-1 chm1:+:912629108:-1 chm1:+:950165328:-1 chm1:+:973055329:-1 chm1:+:975398188:-1 chm1:+:976536910:-1 chm1:+:981289992:-1 chm1:+:989873527:-1 chm1:+:1006193739:-1 chm1:+:1039629444:-1 chm1:+:1111735937:-1 chm1:+:1137489585:-1 chm1:+:1137580971:-1 chm1:+:1141528555:-1 chm1:+:1147319227:-1 chm1:+:1154261136:-1 chm1:+:1155864948:-1 chm1:+:1177350640:-1 chm1:+:1212048053:-1 chm1:+:1221388874:-1 chm1:+:1228194428:-1 chm1:+:1246113689:-1 chm1:+:1280363060:-1 chm1:+:1281904078:-1 chm1:+:1285714620:-1 chm1:+:1323539840:-1 chm1:+:1350257553:-1 chm1:+:1378819657:-1 chm1:+:1380783341:-1 chm1:+:1381417511:-1 chm1:+:1389690795:-1 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chm1:+:2575791679:-1 chm1:+:2590595545:-1 chm1:+:2611596113:-1 chm1:+:2621538630:-1 chm1:+:2643093946:-1 chm1:+:2649575265:-1 chm1:+:2675459234:-1 chm1:+:2697291708:-1 chm1:+:2702547004:-1 chm1:+:2724706126:-1 chm1:+:2738701363:-1 chm1:+:2758265518:-1 chm1:+:2796151617:-1 chm1:+:2799957454:-1 chm1:+:2807477429:-1 chm1:+:2825847578:-1 chm1:+:2871064503:-1 chm1:+:2872161333:-1 chm1:+:2916118432:-1 chm1:+:2923300901:-1 chm1:+:2938204939:-1 chm1:+:2947919846:-1 chm1:+:2955191330:-1 chm1:+:2967136515:-1 chm1:+:2971807930:-1 chm1:+:2988237949:-1 chm1:+:2989535117:-1 chm1:+:2993339430:-1 chm1:+:3003116961:-1 chm1:+:3009590741:-1 chm1:+:3019168864:-1 chm1:+:3021560136:-1 chm1:+:3024098597:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:97821652:-1 chm1:+:106880611:-1 chm1:+:160561993:-1 chm1:+:162481054:-1 chm1:+:319828772:-1 chm1:+:319978331:-1 chm1:+:372452723:-1 chm1:+:404495192:-1 chm1:+:404988059:-1 chm1:+:521996213:-1 chm1:+:625653096:-1 chm1:+:651645225:-1 chm1:+:665055696:-1 chm1:+:745466763:-1 chm1:+:749227102:-1 chm1:+:813868101:-1 chm1:+:820579207:-1 chm1:+:995851392:-1 chm1:+:1209229662:-1 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+TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:190492785:-1 chm1:+:198107340:-1 chm1:+:275522138:-1 chm1:+:275899050:-1 chm1:+:312593215:-1 chm1:+:369333939:-1 chm1:+:436224586:-1 chm1:+:448220028:-1 chm1:+:665592795:-1 chm1:+:727992482:-1 chm1:+:789332199:-1 chm1:+:896678045:-1 chm1:+:1176337200:-1 chm1:+:1210617324:-1 chm1:+:1296294739:-1 chm1:+:1321029822:-1 chm1:+:1358001322:-1 chm1:+:1365392074:-1 chm1:+:1498713077:-1 chm1:+:1917508450:-1 chm1:+:1955925177:-1 chm1:+:2016154053:-1 chm1:+:2147075153:-1 chm1:+:2408566416:-1 chm1:+:2771675503:-1 chm1:+:2777366839:-1 chm1:+:2934943610:-1 chm1:+:3010488580:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:69834305:-1 chm1:+:103787587:-1 chm1:+:103927320:-1 chm1:+:151841613:-1 chm1:+:221097434:-1 chm1:+:266810801:-1 chm1:+:315046915:-1 chm1:+:329427745:-1 chm1:+:409769954:-1 chm1:+:430019505:-1 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chm1:+:2720100633:-1 chm1:+:2896928055:-1 chm1:+:2908603366:-1 chm1:+:2909097039:-1 chm1:+:2915788106:-1 chm1:+:2918116418:-1 chm1:+:2926136812:-1 chm1:+:2931221230:-1 chm1:+:2935189715:-1 chm1:+:2963252359:-1 chm1:+:2965052500:-1 chm1:+:2974602320:-1 chm1:+:2982499521:-1 chm1:+:2986798560:-1 chm1:+:3023819805:-1 chm1:+:3032143040:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:369826810:-1 chm1:+:785614697:-1 chm1:+:972813713:-1 chm1:+:2780280955:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:921629839:-1 chm1:+:1388478626:-1 chm1:+:1524920739:-1 chm1:+:2038263033:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:56303996:-1 chm1:+:176616214:-1 chm1:+:351878497:-1 chm1:+:373802901:-1 chm1:+:379480360:-1 chm1:+:399051933:-1 chm1:+:507464297:-1 chm1:+:598630417:-1 chm1:+:692061056:-1 chm1:+:732575096:-1 chm1:+:767847115:-1 chm1:+:817251383:-1 chm1:+:890613580:-1 chm1:+:921764845:-1 chm1:+:1047037742:-1 chm1:+:1065645491:-1 chm1:+:1082493336:-1 chm1:+:1125185830:-1 chm1:+:1136079077:-1 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+TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:388414235:-1 chm1:+:397270499:-1 chm1:+:586698041:-1 chm1:+:668430880:-1 chm1:+:724191352:-1 chm1:+:1219001750:-1 chm1:+:1305638968:-1 chm1:+:1645534692:-1 chm1:+:2404846098:-1 chm1:+:2655147989:-1 chm1:+:2762730732:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:89199028:-1 chm1:+:221161286:-1 chm1:+:225253702:-1 chm1:+:359745945:-1 chm1:+:389112196:-1 chm1:+:433296653:-1 chm1:+:470255847:-1 chm1:+:729495349:-1 chm1:+:746566255:-1 chm1:+:750580093:-1 chm1:+:774890568:-1 chm1:+:778989691:-1 chm1:+:783745757:-1 chm1:+:857761398:-1 chm1:+:862019647:-1 chm1:+:948311728:-1 chm1:+:972027993:-1 chm1:+:1004881874:-1 chm1:+:1005037130:-1 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+TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:394601181:-1 chm1:+:650859857:-1 chm1:+:1021985555:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:281530269:-1 chm1:+:599294177:-1 chm1:+:644892474:-1 chm1:+:958333070:-1 chm1:+:1109262081:-1 chm1:+:1126085218:-1 chm1:+:1444321820:-1 chm1:+:1508457678:-1 chm1:+:1519964569:-1 chm1:+:1622417884:-1 chm1:+:1763760683:-1 chm1:+:1893542552:-1 chm1:+:1906538370:-1 chm1:+:2255113886:-1 chm1:+:2377021626:-1 chm1:+:2457308105:-1 chm1:+:2592540317:-1 chm1:+:2621851126:-1 chm1:+:3023587106:-1 chm1:+:3035513177:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:537505860:-1 chm1:+:1367030187:-1 chm1:+:1689579333:-1 chm1:+:2583145449:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:7325953:-1 chm1:+:231882668:-1 chm1:+:253684686:-1 chm1:+:277093288:-1 chm1:+:436992600:-1 chm1:+:482735413:-1 chm1:+:515137935:-1 chm1:+:586371918:-1 chm1:+:636465858:-1 chm1:+:953335755:-1 chm1:+:1406312912:-1 chm1:+:1456518233:-1 chm1:+:1541610113:-1 chm1:+:1776040537:-1 chm1:+:1866039598:-1 chm1:+:2015356854:-1 chm1:+:2116726563:-1 chm1:+:2170117987:-1 chm1:+:2241622166:-1 chm1:+:2293114250:-1 chm1:+:2363696769:-1 chm1:+:2420559305:-1 chm1:+:2427505487:-1 chm1:+:2797459259:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:49923766:-1 chm1:+:83698675:-1 chm1:+:106594927:-1 chm1:+:221022100:-1 chm1:+:261785111:-1 chm1:+:397271360:-1 chm1:+:498346657:-1 chm1:+:517464977:-1 chm1:+:543362263:-1 chm1:+:613842638:-1 chm1:+:645559527:-1 chm1:+:766549814:-1 chm1:+:900552227:-1 chm1:+:1036249552:-1 chm1:+:1179024941:-1 chm1:+:1309984309:-1 chm1:+:1507061327:-1 chm1:+:1508432327:-1 chm1:+:1544415505:-1 chm1:+:1750324443:-1 chm1:+:2055503664:-1 chm1:+:2358317177:-1 chm1:+:2630966540:-1 chm1:+:2862224579:-1 chm1:+:2900013862:-1 chm1:+:2991216247:-1 chm1:+:3024696508:-1 chm1:+:3098107518:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:69772773:-1 chm1:+:146613165:-1 chm1:+:167913625:-1 chm1:+:419806989:-1 chm1:+:677406235:-1 chm1:+:711578309:-1 chm1:+:718901478:-1 chm1:+:772659083:-1 chm1:+:788818955:-1 chm1:+:795538906:-1 chm1:+:845063581:-1 chm1:+:895296884:-1 chm1:+:1209469165:-1 chm1:+:1224985317:-1 chm1:+:1358184720:-1 chm1:+:1440407245:-1 chm1:+:1548528990:-1 chm1:+:1741252090:-1 chm1:+:1839915496:-1 chm1:+:1911986640:-1 chm1:+:1971795021:-1 chm1:+:2015426760:-1 chm1:+:2141220957:-1 chm1:+:2146689111:-1 chm1:+:2174320874:-1 chm1:+:2235134772:-1 chm1:+:2681783313:-1 chm1:+:2811331253:-1 chm1:+:2901739097:-1 chm1:+:3054531098:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:716997714:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:121101759:-1 chm1:+:144088956:-1 chm1:+:206551961:-1 chm1:+:635713169:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:170378802:-1 chm1:+:178558303:-1 chm1:+:303723278:-1 chm1:+:324087769:-1 chm1:+:411744925:-1 chm1:+:421330746:-1 chm1:+:439499759:-1 chm1:+:483940653:-1 chm1:+:550914928:-1 chm1:+:771693496:-1 chm1:+:923879862:-1 chm1:+:1262040460:-1 chm1:+:1367332895:-1 chm1:+:1464596044:-1 chm1:+:1738050502:-1 chm1:+:1815592827:-1 chm1:+:2595095711:-1 chm1:+:2895488238:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:176549780:-1 chm1:+:186495639:-1 chm1:+:321300425:-1 chm1:+:328785916:-1 chm1:+:375225029:-1 chm1:+:459299086:-1 chm1:+:557401421:-1 chm1:+:611452575:-1 chm1:+:813259465:-1 chm1:+:990527267:-1 chm1:+:1706604675:-1 chm1:+:1713119764:-1 chm1:+:1772696924:-1 chm1:+:1961419000:-1 chm1:+:1972275148:-1 chm1:+:2306182590:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:195757636:-1 chm1:+:578024731:-1 chm1:+:591037948:-1 chm1:+:709718624:-1 chm1:+:915279099:-1 chm1:+:1788006757:-1 chm1:+:1895331484:-1 chm1:+:1963597511:-1 chm1:+:2036956556:-1 chm1:+:2617915858:-1 chm1:+:2619540016:-1 chm1:+:2991975567:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:100720294:-1 chm1:+:440306973:-1 chm1:+:676162742:-1 chm1:+:1111797895:-1 chm1:+:1375534852:-1 chm1:+:1801995471:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:184432549:-1 chm1:+:378853113:-1 chm1:+:400505116:-1 chm1:+:561872564:-1 chm1:+:674143269:-1 chm1:+:790635071:-1 chm1:+:1154959512:-1 chm1:+:1361448481:-1 chm1:+:1467746960:-1 chm1:+:2583824896:-1 chm1:+:2927015090:-1 chm1:+:3031719673:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCAT chm1:+:238794334:-1 chm1:+:314461860:-1 chm1:+:575024497:-1 chm1:+:663151184:-1 chm1:+:1081650903:-1 chm1:+:1086861279:-1 chm1:+:1171977382:-1 chm1:+:1248626034:-1 chm1:+:1323735288:-1 chm1:+:1380091687:-1 chm1:+:1619312363:-1 chm1:+:2041424165:-1 chm1:+:2263548766:-1 chm1:+:2912399281:-1 +ATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:237763409:28 chm1:+:278470108:-1 chm1:+:401129821:-1 chm1:+:532869454:-1 chm1:+:603561107:-1 chm1:+:660115468:-1 chm1:+:829232570:-1 chm1:+:847399160:-1 chm1:+:1481256634:-1 chm1:+:1658552205:-1 chm1:+:1972664056:-1 chm1:+:2220970297:-1 chm1:+:2922882835:-1 chm1:+:2930543459:-1 +ATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:157347355:-1 chm1:+:237763408:28 +ATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:237763407:28 chm1:+:2689113881:-1 +ATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:1913066889:-1 +ATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:1160027517:-1 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+TCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA chm1:+:82550020:-1 chm1:+:197112208:-1 chm1:+:200796812:-1 chm1:+:329993019:-1 chm1:+:338740163:-1 chm1:+:593428339:-1 chm1:+:652515782:-1 chm1:+:681657811:-1 chm1:+:711183969:-1 chm1:+:716440809:-1 chm1:+:758344087:-1 chm1:+:771296396:-1 chm1:+:795440053:-1 chm1:+:810165608:-1 chm1:+:810248441:-1 chm1:+:999018574:-1 chm1:+:1175963781:-1 chm1:+:1312034299:-1 chm1:+:1354680029:-1 chm1:+:1468672205:-1 chm1:+:1902954915:-1 chm1:+:1976637741:-1 chm1:+:2020582164:-1 chm1:+:2153452186:-1 chm1:+:2636332405:-1 +TCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA chm1:+:211683035:-1 chm1:+:943993024:-1 chm1:+:950213098:-1 chm1:+:1237790662:-1 chm1:+:1241639417:-1 chm1:+:1255873117:-1 chm1:+:1527375795:-1 chm1:+:1540877178:-1 chm1:+:2007493609:-1 chm1:+:2059966169:-1 chm1:+:2305460146:-1 chm1:+:2588503739:-1 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGG chm1:+:80940702:-1 chm1:+:212174284:-1 chm1:+:244493497:-1 chm1:+:312196916:-1 chm1:+:401562185:-1 chm1:+:428585062:-1 chm1:+:449520819:-1 chm1:+:474554792:-1 chm1:+:476974128:-1 chm1:+:565064841:-1 chm1:+:569050722:-1 chm1:+:572845922:-1 chm1:+:715060297:-1 chm1:+:853755109:-1 chm1:+:1159698663:-1 chm1:+:1288683726:-1 chm1:+:1911566511:-1 chm1:+:1959990376:-1 chm1:+:2003577150:-1 chm1:+:2013346092:-1 chm1:+:2021617672:-1 chm1:+:2271290800:-1 chm1:+:2377004434:-1 chm1:+:2392888875:-1 chm1:+:2470469327:-1 chm1:+:2471101751:29 chm1:+:2561351600:-1 chm1:+:2628555919:-1 chm1:+:2862912739:-1 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGG chm1:+:2471101750:29 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGG chm1:+:2471101749:29 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGG chm1:+:2001141147:-1 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGG chm1:+:2471101755:29 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGG chm1:+:2471101752:29 +CCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG chm1:+:984700727:-1 chm1:+:1323135689:-1 +CCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG chm1:+:1831911789:-1 chm1:+:2254634943:-1 +CCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG chm1:+:62601906:-1 chm1:+:69595916:-1 chm1:+:95199172:-1 chm1:+:202208040:-1 chm1:+:486752045:-1 chm1:+:543159899:-1 chm1:+:620663451:-1 chm1:+:687281086:-1 chm1:+:694084948:-1 chm1:+:724845410:-1 chm1:+:1032618627:-1 chm1:+:1355344234:-1 chm1:+:1389367782:-1 chm1:+:1541261404:-1 chm1:+:1638079510:-1 chm1:+:1677825365:-1 chm1:+:1820803204:-1 chm1:+:2107223986:-1 chm1:+:2637546691:-1 chm1:+:2662688571:-1 +CCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG chm1:+:84369048:-1 chm1:+:100987492:-1 chm1:+:428821375:-1 chm1:+:918775917:-1 chm1:+:1073991748:-1 chm1:+:1077230480:-1 chm1:+:1106523570:-1 chm1:+:1453279232:-1 chm1:+:1467373586:-1 chm1:+:1474526197:-1 chm1:+:1655456246:-1 chm1:+:1735821656:-1 chm1:+:1743339673:-1 chm1:+:1763377937:-1 chm1:+:2527352179:-1 chm1:+:2711917716:-1 chm1:+:2727539627:-1 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATG chm1:+:69591412:-1 chm1:+:210221216:-1 chm1:+:384672940:-1 chm1:+:395126140:-1 chm1:+:400235346:-1 chm1:+:551677491:-1 chm1:+:683959168:22 chm1:+:693457479:-1 chm1:+:698828350:-1 chm1:+:710431764:-1 chm1:+:759041392:-1 chm1:+:890098027:-1 chm1:+:980824685:-1 chm1:+:1071933727:-1 chm1:+:1131289350:-1 chm1:+:1291430859:-1 chm1:+:1313331603:-1 chm1:+:1355158258:-1 chm1:+:1370709643:-1 chm1:+:1456703946:-1 chm1:+:1546405306:-1 chm1:+:1802758057:-1 chm1:+:1921063572:-1 chm1:+:1932367001:-1 chm1:+:1988792792:-1 chm1:+:2066622985:-1 chm1:+:2170254189:-1 chm1:+:2172010744:-1 chm1:+:2191084851:-1 chm1:+:2302144510:-1 chm1:+:2371393239:-1 chm1:+:2541742792:-1 chm1:+:2651990348:-1 chm1:+:2658078337:-1 chm1:+:2731556440:-1 chm1:+:2748031511:-1 chm1:+:2800380496:-1 chm1:+:2814421320:-1 chm1:+:2903222075:-1 chm1:+:2975559284:-1 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATG chm1:+:683959167:22 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATG chm1:+:683959171:22 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATG chm1:+:2551976713:-1 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATG chm1:+:683959170:22 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATG chm1:+:107426285:-1 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATG chm1:+:210160194:-1 +CATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:2112077826:-1 +CATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:822796325:-1 chm1:+:1921656693:-1 +CATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:2119429258:-1 +CATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:748861307:-1 chm1:+:792866423:-1 +CATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:2569785482:-1 +CATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:75746210:-1 chm1:+:2140364368:-1 +CATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:2623667931:-1 +CATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:190169679:-1 chm1:+:785370185:-1 chm1:+:965017340:-1 chm1:+:1012555386:-1 chm1:+:1248257630:-1 chm1:+:1578503574:-1 chm1:+:1579032828:-1 chm1:+:1579848459:-1 chm1:+:1580648539:-1 chm1:+:1821754405:-1 chm1:+:1871023527:-1 chm1:+:2024741112:-1 chm1:+:2643314568:-1 +CATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:5214663:-1 chm1:+:262486886:-1 chm1:+:298576838:-1 chm1:+:355875479:-1 chm1:+:470585344:-1 chm1:+:779119902:-1 chm1:+:817168956:-1 chm1:+:1142338523:-1 chm1:+:1267655400:-1 chm1:+:1757444298:-1 chm1:+:2422300157:-1 chm1:+:2695137436:-1 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCAC chm1:+:225407541:100 chm1:+:315658475:43 chm1:+:739550459:59 chm1:+:1282385233:58 chm1:+:1317806385:54 chm1:+:1557468579:88 chm1:+:2037097266:62 chm1:+:3099315624:106 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCAC chm1:+:1249640439:34 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCAC chm1:+:758055735:93 chm1:+:1892526716:-1 chm1:+:2961376357:115 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCAC chm1:+:501211295:44 chm1:+:1151966176:-1 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCAC chm1:+:372981443:-1 chm1:+:749300238:96 chm1:+:790156567:46 chm1:+:1543694452:61 chm1:+:1578042407:-1 chm1:+:1584402994:-1 chm1:+:1737205685:45 chm1:+:1888610379:56 chm1:+:2228479611:-1 chm1:+:3015958060:59 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCAC chm1:+:383558485:46 chm1:+:383625040:48 chm1:+:509071864:-1 chm1:+:705651615:42 chm1:+:803291941:42 chm1:+:1166624988:-1 chm1:+:1436609400:61 chm1:+:1439673107:60 chm1:+:1522525853:44 chm1:+:1563950191:96 chm1:+:1824072160:42 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCAC chm1:+:60079853:63 chm1:+:69911660:57 chm1:+:158277307:102 chm1:+:312086658:64 chm1:+:318076401:68 chm1:+:416796599:66 chm1:+:417262410:48 chm1:+:514938580:89 chm1:+:574900133:52 chm1:+:582597037:-1 chm1:+:586803152:77 chm1:+:627994487:48 chm1:+:628396798:53 chm1:+:629585100:54 chm1:+:654623103:-1 chm1:+:723477821:75 chm1:+:751499000:82 chm1:+:800391237:91 chm1:+:956057224:69 chm1:+:983169493:49 chm1:+:1102249807:53 chm1:+:1118145958:61 chm1:+:1256228491:43 chm1:+:1256624514:48 chm1:+:1442907839:-1 chm1:+:1457132685:-1 chm1:+:1466002729:64 chm1:+:1485599364:67 chm1:+:1529687340:41 chm1:+:1529842251:90 chm1:+:1571261867:73 chm1:+:1648530638:64 chm1:+:1776823605:67 chm1:+:1836505883:63 chm1:+:1855814009:46 chm1:+:1867070269:-1 chm1:+:1932919576:76 chm1:+:1993374850:60 chm1:+:2028965826:46 chm1:+:2140261844:85 chm1:+:2226703523:43 chm1:+:2237596870:70 chm1:+:2237702371:55 chm1:+:2239957431:95 chm1:+:2240064935:48 chm1:+:2266607035:66 chm1:+:2362330858:71 chm1:+:2456439879:67 chm1:+:2957525397:68 chm1:+:2964989033:56 chm1:+:2971056932:62 chm1:+:3040522620:68 chm1:+:3046274800:103 chm1:+:3063823235:51 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCAC chm1:+:833463594:74 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCAC chm1:+:633160029:66 chm1:+:996037067:99 chm1:+:2810546893:43 chm1:+:2902409333:-1 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCAC chm1:+:840157001:118 chm1:+:1009519996:116 chm1:+:1157475792:-1 chm1:+:1178088870:68 chm1:+:1266408318:60 chm1:+:1507419705:42 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCAC chm1:+:655248365:101 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCAC chm1:+:2284045379:42 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCAC chm1:+:459012942:40 chm1:+:465371984:57 chm1:+:498429040:63 chm1:+:1069214036:57 chm1:+:1150114721:46 chm1:+:1163348085:40 chm1:+:1295020386:-1 chm1:+:1999786119:57 chm1:+:2052697904:44 chm1:+:2559362996:41 chm1:+:2604667175:49 chm1:+:2950855370:42 chm1:+:2956621905:120 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCAC chm1:+:444588483:53 chm1:+:650068155:54 chm1:+:971134404:45 chm1:+:1120536131:58 chm1:+:1681675039:53 chm1:+:1736489608:59 chm1:+:1821847146:-1 chm1:+:2408402644:59 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:60931863:-1 chm1:+:187727298:65 chm1:+:331035725:-1 chm1:+:435958720:44 chm1:+:784333783:54 chm1:+:1073528183:46 chm1:+:1322956939:88 chm1:+:1444194541:46 chm1:+:1848592756:62 chm1:+:2742452434:46 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:933170883:40 chm1:+:990695393:53 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:416610359:44 chm1:+:435958721:44 chm1:+:982072498:41 chm1:+:1036383115:49 chm1:+:1140335793:50 chm1:+:1259397580:51 chm1:+:1295313840:-1 chm1:+:1692148222:39 chm1:+:1848872311:43 chm1:+:2146141956:52 chm1:+:2158795061:53 chm1:+:2227036297:43 chm1:+:2419597014:44 chm1:+:2522224164:45 chm1:+:2702719202:52 chm1:+:2858513191:52 chm1:+:2937642885:48 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:867336598:87 chm1:+:1355577639:41 chm1:+:2967842649:46 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:78944740:-1 chm1:+:96900657:85 chm1:+:188723012:42 chm1:+:316097359:55 chm1:+:375036465:95 chm1:+:513673697:-1 chm1:+:562952391:70 chm1:+:590972024:60 chm1:+:603081919:46 chm1:+:628102739:-1 chm1:+:757105925:63 chm1:+:792800888:49 chm1:+:873022555:60 chm1:+:959359378:76 chm1:+:967649993:72 chm1:+:1113141342:62 chm1:+:1135069267:96 chm1:+:1141244409:60 chm1:+:1160895584:61 chm1:+:1178339803:86 chm1:+:1318275412:79 chm1:+:1469063868:-1 chm1:+:1475852937:70 chm1:+:1481347804:60 chm1:+:1563800082:68 chm1:+:1717702465:51 chm1:+:1749643734:74 chm1:+:1797887465:77 chm1:+:1836620361:54 chm1:+:1870629879:-1 chm1:+:2048960957:46 chm1:+:2077721259:72 chm1:+:2233258188:64 chm1:+:2240227052:84 chm1:+:2394036404:76 chm1:+:2649890190:43 chm1:+:2687632313:73 chm1:+:2735343424:85 chm1:+:2951002199:44 chm1:+:3005777873:43 chm1:+:3045045058:80 chm1:+:3062746055:51 chm1:+:3097016799:53 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:163611374:43 chm1:+:270683697:48 chm1:+:425806217:-1 chm1:+:574833897:43 chm1:+:861751143:44 chm1:+:1033661855:50 chm1:+:1205286896:38 chm1:+:1520122807:45 chm1:+:1977284543:76 chm1:+:2991094899:42 chm1:+:3004966366:-1 chm1:+:3057840645:49 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:923882682:61 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:1627824120:68 chm1:+:2623198909:97 chm1:+:2923301866:108 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:986477279:48 chm1:+:1493381859:81 chm1:+:1617853932:-1 chm1:+:2470385955:104 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:737197590:-1 chm1:+:812939910:84 chm1:+:820576826:71 chm1:+:826770121:109 chm1:+:858882373:70 chm1:+:886949453:110 chm1:+:927564971:-1 chm1:+:1022119262:53 chm1:+:1041641591:-1 chm1:+:1189882331:-1 chm1:+:1216911946:-1 chm1:+:1408492199:-1 chm1:+:1848171153:-1 chm1:+:2080438150:56 chm1:+:2136990493:56 chm1:+:2151575757:-1 chm1:+:3019489787:94 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:743614659:57 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:499257446:51 chm1:+:1139366081:55 chm1:+:1267963876:47 chm1:+:2567781574:48 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:51372190:78 chm1:+:719327183:67 chm1:+:757738930:56 chm1:+:1051985750:58 chm1:+:1168826877:-1 chm1:+:2956738873:74 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:462887051:-1 chm1:+:824637227:-1 chm1:+:999955966:54 chm1:+:1266380974:61 chm1:+:1390109511:-1 chm1:+:1699572928:-1 chm1:+:1725275937:75 chm1:+:2056837143:-1 +GTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:464389283:76 chm1:+:512758974:96 chm1:+:2068977057:72 chm1:+:2149553130:93 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAG chm1:+:20852965:-1 chm1:+:1561724730:-1 chm1:+:2642309771:27 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAG chm1:+:2642309772:27 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAG chm1:+:2642309776:27 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAG chm1:+:2642309777:27 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAG chm1:+:2642309769:27 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAG chm1:+:2642309770:27 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAG chm1:+:912071008:-1 +CTGCAGAGGGTACCAGGCTGACCTCCTGTCTGTCTCAAAGCTTAAGACTCACCCAGAAGTCTGTCTTTCTACCCAGAAGCACCTAGACCCATCCTATCAGAGGCCTCCCTCTAATGAGGAGTAGGGTGGGGGCAACCCCATGGTGTCCTTTGTGCCTAAACCTTTACAATAACAGGTTGTTGGCTGTCACCTGAAGCAGGTTTTCAACCATCACTCCCTTCCCACCATACACACACTCCCAGCTCATTTTGAGTTCCTTTTCTGCAATAAATAACAGATTCTTGCAAAGTGGTTAGAAGAAATTAGTAAGTTAAGCCTCACACTAGGGTTATTTTGCCAGGAGACCTTCCTTTCCTAGGTTAACCCCCTCCACCCACGTGGGCACCCAGTGGGATCTGCTGCAGTCTGCGCCAGGGTTTGCTTGGCCTGCAAGGGTGGCCATGGCAGATGCCCTTTCCTTGTAACTGGAATCCCCCATAGCCTGGCCTTCCAGTACAGTAGAGAGAATAATTGGATAAACCCTAAACTGGAAATTACAAACAATAACCTACTCTGTTAGTTTACATATGAAACTACTTAAGCAAGTCCTTTTTATTTTAT chm1:+:2571312913:-1 +CTGCAGAGGGTACCAGGCTGACCTCCTGTCTGTCTCAAAGCTTAAGACTCACCCAGAAGTCTGTCTTTCTACCCAGAAGCACCTAGACCCATCCTATCAGAGGCCTCCCTCTAATGAGGAGTAGGGTGGGGGCAACCCCATGGTGTCCTTTGTGCCTAAACCTTTACAATAACAGGTTGTTGGCTGTCACCTGAAGCAGGTTTTCAACCATCACTCCCTTCCCACCATACACACACTCCCAGCTCATTTTGAGTTCCTTTTCTGCAATAAATAACAGATTCTTGCAAAGTGGTTAGAAGAAATTAGTAAGTTAAGCCTCACACTAGGGTTATTTTGCCAGGAGACCTTCCTTTCCTAGGTTAACCCCCTCCACCCACGTGGGCACCCAGTGGGATCTGCTGCAGTCTGCGCCAGGGTTTGCTTGGCCTGCAAGGGTGGCCATGGCAGATGCCCTTTCCTTGTAACTGGAATCCCCCATAGCCTGGCCTTCCAGTACAGTAGAGAGAATAATTGGATAAACCCTAAACTGGAAATTACAAACAATAACCTACTCTGTTAGTTTACATATGAAACTACTTAAGCAAGTCCTTTTTATTTTAT chm1:+:2270541720:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCC chm1:+:32246241:-1 chm1:+:53530891:-1 chm1:+:625377052:-1 chm1:+:637827881:-1 chm1:+:699241522:-1 chm1:+:710780157:-1 chm1:+:831937724:-1 chm1:+:1066847846:-1 chm1:+:1086400256:-1 chm1:+:1142986510:-1 chm1:+:1655402414:-1 chm1:+:1671314586:-1 chm1:+:1727456872:-1 chm1:+:1878687076:-1 chm1:+:2357476521:-1 chm1:+:2872409938:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCC chm1:+:223267486:-1 chm1:+:2124850300:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCC chm1:+:168497361:-1 chm1:+:408013705:-1 chm1:+:416788624:-1 chm1:+:622669985:-1 chm1:+:866509903:-1 chm1:+:906315039:-1 chm1:+:959118324:-1 chm1:+:1138613632:-1 chm1:+:1530594599:-1 chm1:+:1616452124:-1 chm1:+:1951915866:-1 chm1:+:2048823880:-1 chm1:+:2578189570:-1 chm1:+:2592321901:-1 chm1:+:2769137236:-1 chm1:+:2896816381:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCC chm1:+:499781914:-1 chm1:+:772115062:-1 chm1:+:909516721:-1 chm1:+:1083169018:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCC chm1:+:317791114:-1 chm1:+:471351224:-1 chm1:+:618682336:-1 chm1:+:941890666:-1 chm1:+:1244888677:-1 chm1:+:1300789909:-1 chm1:+:1409614121:-1 chm1:+:1502804493:-1 chm1:+:1810474804:-1 chm1:+:1895770980:-1 chm1:+:2160998740:-1 chm1:+:2173945202:-1 chm1:+:2258012330:-1 chm1:+:2260388574:-1 chm1:+:2268435723:-1 chm1:+:2279008274:-1 chm1:+:2644113646:-1 chm1:+:2859032137:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCC chm1:+:457616869:-1 chm1:+:672049029:-1 chm1:+:1565038002:-1 chm1:+:2155806281:-1 chm1:+:2234361525:-1 chm1:+:2635008919:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCC chm1:+:82262836:-1 chm1:+:1064710083:-1 chm1:+:1651177695:-1 chm1:+:2124085420:-1 chm1:+:2928029760:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCC chm1:+:1980284462:-1 chm1:+:2192462422:-1 chm1:+:3058965126:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCC chm1:+:715165642:-1 chm1:+:890560271:-1 chm1:+:987717286:-1 chm1:+:1275672830:-1 chm1:+:1629854451:-1 chm1:+:1689497148:-1 chm1:+:2001376423:-1 chm1:+:2005113980:-1 chm1:+:2375086709:-1 chm1:+:2464157641:-1 chm1:+:2498152112:-1 chm1:+:2664848847:-1 chm1:+:2763722290:-1 chm1:+:2827310541:-1 chm1:+:3010015572:-1 chm1:+:3034726584:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCC chm1:+:222727905:-1 chm1:+:278226230:-1 chm1:+:355323900:-1 chm1:+:618928507:-1 chm1:+:652014667:-1 chm1:+:1265840312:-1 chm1:+:1389503620:-1 chm1:+:1535623712:-1 chm1:+:1863792204:-1 chm1:+:1964252292:-1 chm1:+:2003939184:-1 chm1:+:2278481805:-1 chm1:+:2579375740:-1 chm1:+:2640974992:-1 chm1:+:2862930961:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCC chm1:+:75651780:-1 chm1:+:524899775:-1 chm1:+:639033165:-1 chm1:+:818212269:-1 chm1:+:836327644:-1 chm1:+:942932257:-1 chm1:+:1026024698:-1 chm1:+:1142085303:-1 chm1:+:1303457970:-1 chm1:+:1738489664:-1 chm1:+:1749551861:-1 chm1:+:1797641504:-1 chm1:+:1898951684:-1 chm1:+:2160312440:-1 chm1:+:2174810959:-1 chm1:+:2275910602:-1 chm1:+:2511620531:-1 chm1:+:2698909161:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCC chm1:+:404438933:-1 chm1:+:1901381873:-1 chm1:+:3024284315:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCC chm1:+:82618290:-1 chm1:+:162831580:-1 chm1:+:163695435:-1 chm1:+:178861533:-1 chm1:+:263145084:-1 chm1:+:377613339:-1 chm1:+:435742409:-1 chm1:+:773377031:-1 chm1:+:894717062:-1 chm1:+:1202865148:-1 chm1:+:1269732622:-1 chm1:+:1322276678:-1 chm1:+:1694289169:-1 chm1:+:1763380139:-1 chm1:+:1833179896:-1 chm1:+:1980310392:-1 chm1:+:2274752280:-1 chm1:+:2400353477:-1 chm1:+:2730748285:-1 chm1:+:2750184658:-1 chm1:+:2820749950:-1 chm1:+:2902244737:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCC chm1:+:112529122:-1 chm1:+:360050910:-1 chm1:+:598010886:-1 chm1:+:696288171:-1 chm1:+:725655274:-1 chm1:+:982690836:-1 chm1:+:991293533:-1 chm1:+:1068678255:-1 chm1:+:1230203155:-1 chm1:+:1230361793:-1 chm1:+:1262998015:-1 chm1:+:1384483631:-1 chm1:+:1568407659:-1 chm1:+:1954134225:-1 chm1:+:2076278489:-1 chm1:+:2182848410:-1 chm1:+:2253511154:-1 chm1:+:2542810780:-1 chm1:+:2564989972:-1 chm1:+:3015181103:-1 +GGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549860:25 chm1:+:863136189:-1 chm1:+:1272010716:-1 chm1:+:2039694248:-1 chm1:+:2617447956:-1 +GGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549855:25 +GGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549862:25 +GGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549863:25 +GGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549867:25 +GGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549870:25 +GGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549871:25 +GGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549856:25 +GGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:263919282:-1 +GGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:1446732184:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:1134873602:-1 chm1:+:1962134488:-1 chm1:+:2067352316:-1 chm1:+:2069116489:-1 chm1:+:2964931533:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:726968989:-1 chm1:+:2536431372:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:2536431691:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:182185589:-1 chm1:+:187802273:-1 chm1:+:409102676:-1 chm1:+:624619656:-1 chm1:+:790781947:-1 chm1:+:1009576763:-1 chm1:+:1316012723:-1 chm1:+:1621365045:-1 chm1:+:1660254551:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:794726563:-1 chm1:+:1056068746:-1 chm1:+:1418360432:-1 chm1:+:1466972369:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:98846081:-1 chm1:+:417495344:-1 chm1:+:497754845:-1 chm1:+:517586044:-1 chm1:+:825859972:-1 chm1:+:944327158:-1 chm1:+:1202238430:-1 chm1:+:1323570083:-1 chm1:+:1376497801:-1 chm1:+:1555724060:-1 chm1:+:1730747440:-1 chm1:+:1836019624:-1 chm1:+:1874233560:-1 chm1:+:1896119981:-1 chm1:+:2058058353:-1 chm1:+:2132767154:-1 chm1:+:2173065462:-1 chm1:+:2264199618:-1 chm1:+:2468929024:-1 chm1:+:2527821808:-1 chm1:+:2557151914:-1 chm1:+:2606553870:-1 chm1:+:2725421530:-1 chm1:+:2869957982:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:493529943:-1 chm1:+:2183517494:-1 chm1:+:2657568327:-1 chm1:+:2888575220:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:188904192:-1 chm1:+:750136205:-1 chm1:+:912945486:-1 chm1:+:923972098:-1 chm1:+:2293235765:-1 chm1:+:2536431688:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:455822336:-1 chm1:+:512791339:-1 chm1:+:626900876:-1 chm1:+:719782244:-1 chm1:+:840662377:-1 chm1:+:1298547972:-1 chm1:+:1526939909:-1 chm1:+:1791577943:-1 chm1:+:1806767943:-1 chm1:+:2018522982:-1 chm1:+:2071824127:-1 chm1:+:2282094835:-1 chm1:+:2950631815:-1 chm1:+:3006573940:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:627099507:-1 chm1:+:1651360218:-1 chm1:+:1880811377:-1 chm1:+:2162503261:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:90986695:-1 chm1:+:304232228:-1 chm1:+:351219973:-1 chm1:+:885811261:-1 chm1:+:952981323:-1 chm1:+:1035561381:-1 chm1:+:1081412579:-1 chm1:+:1261140885:-1 chm1:+:1276594654:-1 chm1:+:1379645771:-1 chm1:+:1472728049:-1 chm1:+:1495156571:-1 chm1:+:1782649583:-1 chm1:+:1942283807:-1 chm1:+:2254819350:-1 chm1:+:2333053426:-1 chm1:+:2969485227:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:890721385:-1 chm1:+:1302756084:-1 chm1:+:2283537738:-1 chm1:+:2536431687:-1 chm1:+:2903204670:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:220851093:-1 chm1:+:438479074:-1 chm1:+:577361507:-1 chm1:+:784865891:-1 chm1:+:849578580:-1 chm1:+:918767841:-1 chm1:+:1163135222:-1 chm1:+:1651696753:-1 chm1:+:2645857636:-1 chm1:+:2916331968:-1 chm1:+:2989329902:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:219685195:-1 chm1:+:260852963:-1 chm1:+:307722547:-1 chm1:+:688250337:-1 chm1:+:732672515:-1 chm1:+:753180103:-1 chm1:+:968836016:-1 chm1:+:1050553927:-1 chm1:+:1184536117:-1 chm1:+:1299182818:-1 chm1:+:1421153617:-1 chm1:+:1774323660:-1 chm1:+:2123581181:-1 chm1:+:2138755332:-1 chm1:+:2185713627:-1 chm1:+:2244610940:-1 chm1:+:3050697189:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTA chm1:+:69604705:-1 chm1:+:240729017:-1 chm1:+:286549553:-1 chm1:+:783173724:-1 chm1:+:968180470:-1 chm1:+:1731159860:-1 chm1:+:1787886674:-1 chm1:+:1905146339:-1 chm1:+:2222730520:-1 chm1:+:2225270010:-1 chm1:+:2249803631:-1 chm1:+:2271415984:-1 chm1:+:2489999467:-1 +TAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:324115651:-1 chm1:+:674355428:-1 chm1:+:1702233415:34 +TAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1408311302:-1 +TAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1004063680:-1 +TAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1702233413:34 +TAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1702233416:34 chm1:+:2534952527:-1 +TAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:2534952215:-1 +TAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:2761293171:-1 +TAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1702233417:34 chm1:+:2534952216:-1 +TAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1702233409:34 +TAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1702233414:34 +TAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:86756181:-1 chm1:+:272483808:-1 chm1:+:529129963:-1 chm1:+:582107660:-1 chm1:+:808169023:-1 chm1:+:1154457679:-1 chm1:+:1195067618:-1 chm1:+:1554960163:-1 chm1:+:1696468620:-1 chm1:+:1766661537:-1 chm1:+:1918448169:-1 chm1:+:2080573428:-1 chm1:+:2146116811:-1 chm1:+:2226674247:-1 chm1:+:2803203352:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:174068498:-1 chm1:+:2028516626:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:386596036:-1 chm1:+:465583865:-1 chm1:+:528017740:-1 chm1:+:956982223:-1 chm1:+:1120438471:-1 chm1:+:1121042468:-1 chm1:+:1333447464:-1 chm1:+:1504280749:-1 chm1:+:1763987101:-1 chm1:+:2018029010:-1 chm1:+:2247198506:-1 chm1:+:2255763890:-1 chm1:+:2376824623:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:509253221:-1 chm1:+:563731854:-1 chm1:+:565532977:-1 chm1:+:589249176:-1 chm1:+:863729135:-1 chm1:+:1087314306:-1 chm1:+:1283138158:-1 chm1:+:1353784762:-1 chm1:+:1640378715:-1 chm1:+:1663692213:-1 chm1:+:2474248177:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:709581286:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:906728699:-1 chm1:+:1171366328:-1 chm1:+:2512681637:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:772490577:-1 chm1:+:967637315:-1 chm1:+:1784751329:-1 chm1:+:2585467117:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:69333403:-1 chm1:+:81786029:-1 chm1:+:102060667:-1 chm1:+:176139357:-1 chm1:+:213841429:-1 chm1:+:213949511:-1 chm1:+:214944284:-1 chm1:+:269274816:-1 chm1:+:478243846:-1 chm1:+:510498675:-1 chm1:+:664958293:-1 chm1:+:866682452:-1 chm1:+:868809312:-1 chm1:+:1015853542:-1 chm1:+:1042594204:-1 chm1:+:1082963434:-1 chm1:+:1208295289:-1 chm1:+:1233753402:-1 chm1:+:1305257234:-1 chm1:+:1401765306:-1 chm1:+:1725699790:-1 chm1:+:1746285810:-1 chm1:+:1771738614:-1 chm1:+:1825044123:-1 chm1:+:1831066269:-1 chm1:+:1994340272:-1 chm1:+:1996691572:-1 chm1:+:2181774808:-1 chm1:+:2252487378:-1 chm1:+:2270612644:-1 chm1:+:2296893870:-1 chm1:+:2346503315:-1 chm1:+:2617213380:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:380890656:-1 chm1:+:599361274:-1 chm1:+:873052840:-1 chm1:+:1205831451:-1 chm1:+:1226627585:-1 chm1:+:1344033476:-1 chm1:+:1519025700:-1 chm1:+:1811672176:-1 chm1:+:2013018441:-1 chm1:+:2399063528:-1 chm1:+:2602728464:-1 chm1:+:2774010841:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:866696797:-1 chm1:+:940009921:-1 chm1:+:1259237346:-1 chm1:+:1287493471:-1 chm1:+:2343201810:-1 chm1:+:3006458168:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:208429262:-1 chm1:+:1386657503:-1 chm1:+:1416519344:-1 chm1:+:2985719867:-1 chm1:+:3056966702:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:362690414:-1 chm1:+:636654551:-1 chm1:+:877289806:-1 chm1:+:974248144:-1 chm1:+:1300435074:-1 chm1:+:1624628591:-1 chm1:+:1804360057:-1 chm1:+:2037436858:-1 chm1:+:2061769634:-1 chm1:+:2667272868:-1 chm1:+:2682248443:-1 chm1:+:2967756745:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:57830712:-1 chm1:+:796010544:-1 chm1:+:796526520:-1 chm1:+:1427899703:-1 chm1:+:1559813948:-1 chm1:+:2004424212:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:68762405:-1 chm1:+:286747168:-1 chm1:+:319507854:-1 chm1:+:435993453:-1 chm1:+:444456586:-1 chm1:+:466184301:-1 chm1:+:582468606:-1 chm1:+:606641672:-1 chm1:+:614110012:-1 chm1:+:654077583:-1 chm1:+:705244264:-1 chm1:+:768868234:-1 chm1:+:844993817:-1 chm1:+:866943553:-1 chm1:+:901591628:-1 chm1:+:1095607077:-1 chm1:+:1096887202:-1 chm1:+:1249381091:-1 chm1:+:1349242797:-1 chm1:+:1466914392:-1 chm1:+:1470283365:-1 chm1:+:1492792134:-1 chm1:+:1493385766:-1 chm1:+:1542606869:-1 chm1:+:1694107222:-1 chm1:+:1819119799:-1 chm1:+:1841322008:-1 chm1:+:2147649522:-1 chm1:+:2192237168:-1 chm1:+:2340269642:-1 chm1:+:2349497463:-1 chm1:+:2468161469:-1 chm1:+:2777904463:-1 chm1:+:2947463866:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:77548688:-1 chm1:+:100466348:-1 chm1:+:1063677278:-1 chm1:+:1343315791:-1 chm1:+:1410829499:-1 chm1:+:1994149756:-1 chm1:+:2547293680:-1 chm1:+:2729822422:-1 chm1:+:3052460404:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:24553873:-1 chm1:+:25142981:-1 chm1:+:69670045:-1 chm1:+:150172463:-1 chm1:+:159225886:-1 chm1:+:168175514:-1 chm1:+:212015530:-1 chm1:+:217012845:-1 chm1:+:382494018:-1 chm1:+:383672037:-1 chm1:+:435581493:-1 chm1:+:445666828:-1 chm1:+:470014928:-1 chm1:+:540222900:-1 chm1:+:618893874:-1 chm1:+:646694222:-1 chm1:+:684282271:-1 chm1:+:732651431:-1 chm1:+:823100759:-1 chm1:+:859465617:-1 chm1:+:918387076:-1 chm1:+:972858806:-1 chm1:+:978555787:-1 chm1:+:1087614966:-1 chm1:+:1106170471:-1 chm1:+:1117558398:-1 chm1:+:1126352602:-1 chm1:+:1176013110:-1 chm1:+:1276695491:-1 chm1:+:1360166427:-1 chm1:+:1368370443:-1 chm1:+:1381009395:-1 chm1:+:1443781762:-1 chm1:+:1492940411:-1 chm1:+:1585608638:-1 chm1:+:1607005656:-1 chm1:+:1615854400:-1 chm1:+:1619167998:-1 chm1:+:1819610415:-1 chm1:+:1835420144:-1 chm1:+:1855683938:-1 chm1:+:1904874474:-1 chm1:+:1915785395:-1 chm1:+:1992017170:-1 chm1:+:2002861650:-1 chm1:+:2013721019:-1 chm1:+:2043490767:-1 chm1:+:2131340102:-1 chm1:+:2150180578:-1 chm1:+:2175570472:-1 chm1:+:2241541475:-1 chm1:+:2405014689:-1 chm1:+:2482363093:-1 chm1:+:2495980628:-1 chm1:+:2609165558:-1 chm1:+:2634011916:-1 chm1:+:2724897412:-1 chm1:+:2791966188:-1 chm1:+:2900648371:-1 chm1:+:2916499917:-1 chm1:+:2983136791:-1 chm1:+:3100821447:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:378515775:-1 chm1:+:1331349075:-1 chm1:+:2121854007:-1 chm1:+:2490298686:-1 chm1:+:2540145115:-1 chm1:+:2601078192:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:21625461:-1 chm1:+:102408806:-1 chm1:+:432583944:-1 chm1:+:440079266:-1 chm1:+:796293320:-1 chm1:+:852424326:-1 chm1:+:1223183467:-1 chm1:+:2604274944:-1 chm1:+:2707691706:-1 chm1:+:2752781136:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTT chm1:+:225312428:-1 chm1:+:363456183:-1 chm1:+:449938664:-1 chm1:+:561316590:-1 chm1:+:643317823:-1 chm1:+:784574526:-1 chm1:+:1147843617:-1 chm1:+:1368800677:-1 chm1:+:1480044185:-1 chm1:+:1581826350:-1 chm1:+:1610026400:-1 chm1:+:1742145029:-1 chm1:+:1779061529:-1 chm1:+:1909268295:-1 chm1:+:2182769428:-1 chm1:+:2224368093:-1 chm1:+:2224403215:-1 chm1:+:2224451171:-1 chm1:+:2268352490:-1 chm1:+:2559990592:-1 +AAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:96591514:27 +AAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:96591501:27 +AAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:96591505:27 +AAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:96591510:27 chm1:+:1359879431:-1 +AAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:96591506:27 +AAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:96591511:27 chm1:+:481204433:-1 +AAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:1495610732:-1 +AAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:96591513:27 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATG chm1:+:63600667:34 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATG chm1:+:63600649:34 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATG chm1:+:63600652:34 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATG chm1:+:63600662:34 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATG chm1:+:63600664:34 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATG chm1:+:63600665:34 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATG chm1:+:63600653:34 chm1:+:1246408822:-1 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATG chm1:+:63600656:34 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATG chm1:+:63600658:34 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATG chm1:+:63600659:34 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATG chm1:+:63600655:34 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATG chm1:+:68045976:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTG chm1:+:26727508:-1 chm1:+:495806616:-1 chm1:+:778489759:-1 chm1:+:972828397:-1 chm1:+:1211173827:-1 chm1:+:1480240798:-1 chm1:+:1534499463:-1 chm1:+:1781726126:-1 chm1:+:2063730083:-1 chm1:+:2284382337:-1 chm1:+:2608362653:-1 chm1:+:2733962601:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTG chm1:+:193709386:-1 chm1:+:1397924434:-1 chm1:+:2540843564:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTG chm1:+:728766703:-1 chm1:+:788802124:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTG chm1:+:109755544:-1 chm1:+:1352638964:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTG chm1:+:207414117:-1 chm1:+:212033888:-1 chm1:+:548452766:-1 chm1:+:563202551:-1 chm1:+:1155218258:-1 chm1:+:2024181985:-1 chm1:+:2811674664:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTG chm1:+:20782755:-1 chm1:+:32207715:-1 chm1:+:341256938:-1 chm1:+:380323811:-1 chm1:+:1581911775:-1 chm1:+:1670108817:-1 chm1:+:1723054424:-1 chm1:+:1784272499:-1 chm1:+:1972607861:-1 chm1:+:2439658920:-1 chm1:+:2536764121:-1 chm1:+:2558404981:-1 chm1:+:2661733459:-1 chm1:+:2676142523:-1 chm1:+:2866800868:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTG chm1:+:377085642:-1 chm1:+:541902048:-1 chm1:+:1014467964:-1 chm1:+:1017463608:-1 chm1:+:1041263759:-1 chm1:+:1148123514:-1 chm1:+:1306839779:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTG chm1:+:7341514:-1 chm1:+:29582338:-1 chm1:+:82310919:-1 chm1:+:107134392:-1 chm1:+:222088193:-1 chm1:+:287423004:-1 chm1:+:678385274:-1 chm1:+:796668889:-1 chm1:+:1262874130:-1 chm1:+:1897280942:-1 chm1:+:2256326387:-1 chm1:+:2502140674:-1 chm1:+:2734466076:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTG chm1:+:823053213:-1 chm1:+:845610096:-1 chm1:+:1006189263:-1 chm1:+:1285536033:-1 chm1:+:1340960063:-1 chm1:+:1441936527:-1 chm1:+:2275994942:-1 chm1:+:2437765841:-1 chm1:+:2903465139:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTG chm1:+:337525041:-1 chm1:+:2628964035:-1 chm1:+:2734723050:-1 chm1:+:3028494255:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTG chm1:+:209836672:-1 chm1:+:680955983:-1 chm1:+:747242923:-1 chm1:+:1432984657:-1 chm1:+:1558787965:-1 chm1:+:2696594312:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTG chm1:+:189051892:-1 chm1:+:189568025:-1 chm1:+:369275265:-1 chm1:+:392193815:-1 chm1:+:424744208:-1 chm1:+:622291560:-1 chm1:+:634920264:-1 chm1:+:679043550:-1 chm1:+:699650316:-1 chm1:+:719234289:-1 chm1:+:834357034:-1 chm1:+:981506196:-1 chm1:+:1106550249:-1 chm1:+:1196816189:-1 chm1:+:1377226103:-1 chm1:+:1378519725:-1 chm1:+:1399951232:-1 chm1:+:1400379311:-1 chm1:+:1400386959:-1 chm1:+:1400394606:-1 chm1:+:1400402254:-1 chm1:+:1400409902:-1 chm1:+:1400417550:-1 chm1:+:1400425198:-1 chm1:+:1404869043:-1 chm1:+:1404877544:-1 chm1:+:1405111565:-1 chm1:+:1405120054:-1 chm1:+:1630877189:-1 chm1:+:1798413390:-1 chm1:+:1819375929:-1 chm1:+:1891295808:-1 chm1:+:1908517664:-1 chm1:+:1934786085:-1 chm1:+:1964548795:-1 chm1:+:2024803620:-1 chm1:+:2104459521:-1 chm1:+:2192952379:-1 chm1:+:2259868521:-1 chm1:+:2395673784:-1 chm1:+:2401781164:-1 chm1:+:2501552871:-1 chm1:+:2541152552:-1 chm1:+:2705182229:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTG chm1:+:239593093:-1 chm1:+:569120211:-1 chm1:+:776126924:-1 chm1:+:1130462248:-1 chm1:+:1168978614:-1 chm1:+:1395473832:-1 chm1:+:1655853037:-1 chm1:+:1705515443:-1 chm1:+:1727306543:-1 chm1:+:1727788633:-1 chm1:+:1769318605:-1 chm1:+:2065931396:-1 chm1:+:2232551237:-1 chm1:+:2534067956:-1 chm1:+:2647052417:-1 chm1:+:2756009976:-1 chm1:+:2865887826:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTG chm1:+:976870724:-1 +CAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:1745779:-1 chm1:+:33364529:-1 chm1:+:90787038:-1 chm1:+:150912571:-1 chm1:+:489593063:-1 chm1:+:671679046:-1 chm1:+:952483156:-1 chm1:+:1019691250:-1 chm1:+:1090119629:-1 chm1:+:1299235908:-1 chm1:+:1382226838:-1 chm1:+:1692788949:-1 chm1:+:1939876958:-1 chm1:+:1967022162:-1 chm1:+:2004663538:-1 chm1:+:2026188918:-1 chm1:+:2236375862:-1 chm1:+:2294771758:-1 chm1:+:2436362218:-1 chm1:+:2464782608:-1 chm1:+:2558140422:-1 chm1:+:2593772461:-1 chm1:+:2899817022:-1 chm1:+:2911058029:-1 chm1:+:3064922648:-1 +CAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:697120300:32 +CAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:697120304:32 +CAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:697120312:32 +CAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:697120314:32 +CAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:1471677180:-1 +CAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:697120318:32 +CAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:697120319:32 +CAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:697120303:32 +CAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:1695577152:-1 +CTTAGTTCTCAGAAGTCAGCAATCTTATTTACTCTGCATTTTAATCTTGAGAAAAGGAAGTTTGTAAGACCAGCCCATATTTAAAAGGAAGAGAATTGGAGTCCTACTTCTTGAGGGAGGAATATAAAAAACCTGTGGATACATTTAAAACCATAAATTTACTTTCCCTCTAGGTTTCCAAAACATTCTTCTTTTCTAGTTGGCATATTCCTTCTTCACCTTGTCTCTCAGTACACATAAGCTTCCTCTGTGTTTAGTTGTCTATTCTCAATACACATTTGTGTGGCATGTTTTTGTTTATACCTGTGAGGTGAGCTCAGTATGTTGTAAGAAGTAAGTGTGCTTTAGCATTTATGGTCATGTGTCCACTTATGATCATGTGAAATGAACACATGATTATAAATGCTAGGGCACACATACTTTAATGAGCACAATACAACGTAATGACATGCTTGTGCTGAATTCTGAAAGGATGAGCAGCTGTGTAAGTGACATTGGTGGGAAAGGGCAGCCCGTGTAGTCACAGTTGGTGGAGGTATGCAGACATTCCACTCTGACCTCCTAGTGGTCACAGCAAACTCCTCTTTTCCTTTTTCCCTA chm1:+:3044721966:-1 chm1:+:3044766383:-1 chm1:+:3044795942:-1 chm1:+:3044806258:-1 chm1:+:3045164883:-1 chm1:+:3045174492:-1 chm1:+:3045179427:-1 chm1:+:3045885454:-1 chm1:+:3045898245:-1 chm1:+:3045941164:-1 chm1:+:3060032381:-1 chm1:+:3060880424:-1 chm1:+:3060881856:-1 chm1:+:3060887520:-1 chm1:+:3060933069:-1 +CTTAGTTCTCAGAAGTCAGCAATCTTATTTACTCTGCATTTTAATCTTGAGAAAAGGAAGTTTGTAAGACCAGCCCATATTTAAAAGGAAGAGAATTGGAGTCCTACTTCTTGAGGGAGGAATATAAAAAACCTGTGGATACATTTAAAACCATAAATTTACTTTCCCTCTAGGTTTCCAAAACATTCTTCTTTTCTAGTTGGCATATTCCTTCTTCACCTTGTCTCTCAGTACACATAAGCTTCCTCTGTGTTTAGTTGTCTATTCTCAATACACATTTGTGTGGCATGTTTTTGTTTATACCTGTGAGGTGAGCTCAGTATGTTGTAAGAAGTAAGTGTGCTTTAGCATTTATGGTCATGTGTCCACTTATGATCATGTGAAATGAACACATGATTATAAATGCTAGGGCACACATACTTTAATGAGCACAATACAACGTAATGACATGCTTGTGCTGAATTCTGAAAGGATGAGCAGCTGTGTAAGTGACATTGGTGGGAAAGGGCAGCCCGTGTAGTCACAGTTGGTGGAGGTATGCAGACATTCCACTCTGACCTCCTAGTGGTCACAGCAAACTCCTCTTTTCCTTTTTCCCTA chm1:+:474905431:-1 chm1:+:874511442:-1 +CTTAGTTCTCAGAAGTCAGCAATCTTATTTACTCTGCATTTTAATCTTGAGAAAAGGAAGTTTGTAAGACCAGCCCATATTTAAAAGGAAGAGAATTGGAGTCCTACTTCTTGAGGGAGGAATATAAAAAACCTGTGGATACATTTAAAACCATAAATTTACTTTCCCTCTAGGTTTCCAAAACATTCTTCTTTTCTAGTTGGCATATTCCTTCTTCACCTTGTCTCTCAGTACACATAAGCTTCCTCTGTGTTTAGTTGTCTATTCTCAATACACATTTGTGTGGCATGTTTTTGTTTATACCTGTGAGGTGAGCTCAGTATGTTGTAAGAAGTAAGTGTGCTTTAGCATTTATGGTCATGTGTCCACTTATGATCATGTGAAATGAACACATGATTATAAATGCTAGGGCACACATACTTTAATGAGCACAATACAACGTAATGACATGCTTGTGCTGAATTCTGAAAGGATGAGCAGCTGTGTAAGTGACATTGGTGGGAAAGGGCAGCCCGTGTAGTCACAGTTGGTGGAGGTATGCAGACATTCCACTCTGACCTCCTAGTGGTCACAGCAAACTCCTCTTTTCCTTTTTCCCTA chm1:+:107845454:-1 chm1:+:180742157:-1 chm1:+:226697102:-1 chm1:+:352256407:-1 chm1:+:357459118:-1 chm1:+:391481626:-1 chm1:+:416668103:-1 chm1:+:440485140:-1 chm1:+:459317163:-1 chm1:+:626821941:-1 chm1:+:681350180:-1 chm1:+:853606891:-1 chm1:+:884670978:-1 chm1:+:924406516:-1 chm1:+:941442821:-1 chm1:+:971772471:-1 chm1:+:1049831381:-1 chm1:+:1176519899:-1 chm1:+:1216110496:-1 chm1:+:1255496921:-1 chm1:+:1303093861:-1 chm1:+:1320672180:-1 chm1:+:1368218473:-1 chm1:+:1413031930:-1 chm1:+:1436095381:-1 chm1:+:1506249773:-1 chm1:+:1637892012:-1 chm1:+:1676694344:-1 chm1:+:1735601523:-1 chm1:+:1927442773:-1 chm1:+:1984659501:-1 chm1:+:2005843592:-1 chm1:+:2166751198:-1 chm1:+:2169449701:-1 chm1:+:2173550893:-1 chm1:+:2179242026:-1 chm1:+:2184793639:-1 chm1:+:2185706672:-1 chm1:+:2275688595:-1 chm1:+:2282030261:-1 chm1:+:2356024533:-1 chm1:+:2368819814:-1 chm1:+:2401141966:-1 chm1:+:2606703803:-1 chm1:+:2613227544:-1 chm1:+:2623721834:-1 chm1:+:2650285774:-1 chm1:+:2758317377:-1 chm1:+:2759987066:-1 chm1:+:2819500189:-1 chm1:+:2864150989:-1 chm1:+:2902005458:-1 chm1:+:2989911678:-1 chm1:+:3024602285:-1 chm1:+:3049731521:-1 +CTTAGTTCTCAGAAGTCAGCAATCTTATTTACTCTGCATTTTAATCTTGAGAAAAGGAAGTTTGTAAGACCAGCCCATATTTAAAAGGAAGAGAATTGGAGTCCTACTTCTTGAGGGAGGAATATAAAAAACCTGTGGATACATTTAAAACCATAAATTTACTTTCCCTCTAGGTTTCCAAAACATTCTTCTTTTCTAGTTGGCATATTCCTTCTTCACCTTGTCTCTCAGTACACATAAGCTTCCTCTGTGTTTAGTTGTCTATTCTCAATACACATTTGTGTGGCATGTTTTTGTTTATACCTGTGAGGTGAGCTCAGTATGTTGTAAGAAGTAAGTGTGCTTTAGCATTTATGGTCATGTGTCCACTTATGATCATGTGAAATGAACACATGATTATAAATGCTAGGGCACACATACTTTAATGAGCACAATACAACGTAATGACATGCTTGTGCTGAATTCTGAAAGGATGAGCAGCTGTGTAAGTGACATTGGTGGGAAAGGGCAGCCCGTGTAGTCACAGTTGGTGGAGGTATGCAGACATTCCACTCTGACCTCCTAGTGGTCACAGCAAACTCCTCTTTTCCTTTTTCCCTA chm1:+:1670232954:-1 chm1:+:2689250259:-1 +CTTAGTTCTCAGAAGTCAGCAATCTTATTTACTCTGCATTTTAATCTTGAGAAAAGGAAGTTTGTAAGACCAGCCCATATTTAAAAGGAAGAGAATTGGAGTCCTACTTCTTGAGGGAGGAATATAAAAAACCTGTGGATACATTTAAAACCATAAATTTACTTTCCCTCTAGGTTTCCAAAACATTCTTCTTTTCTAGTTGGCATATTCCTTCTTCACCTTGTCTCTCAGTACACATAAGCTTCCTCTGTGTTTAGTTGTCTATTCTCAATACACATTTGTGTGGCATGTTTTTGTTTATACCTGTGAGGTGAGCTCAGTATGTTGTAAGAAGTAAGTGTGCTTTAGCATTTATGGTCATGTGTCCACTTATGATCATGTGAAATGAACACATGATTATAAATGCTAGGGCACACATACTTTAATGAGCACAATACAACGTAATGACATGCTTGTGCTGAATTCTGAAAGGATGAGCAGCTGTGTAAGTGACATTGGTGGGAAAGGGCAGCCCGTGTAGTCACAGTTGGTGGAGGTATGCAGACATTCCACTCTGACCTCCTAGTGGTCACAGCAAACTCCTCTTTTCCTTTTTCCCTA chm1:+:773677230:-1 chm1:+:1713889307:-1 chm1:+:1894598687:-1 chm1:+:1957878471:-1 chm1:+:2186216997:-1 chm1:+:2249985313:-1 chm1:+:2377473069:-1 chm1:+:2923979041:-1 +CTTAGTTCTCAGAAGTCAGCAATCTTATTTACTCTGCATTTTAATCTTGAGAAAAGGAAGTTTGTAAGACCAGCCCATATTTAAAAGGAAGAGAATTGGAGTCCTACTTCTTGAGGGAGGAATATAAAAAACCTGTGGATACATTTAAAACCATAAATTTACTTTCCCTCTAGGTTTCCAAAACATTCTTCTTTTCTAGTTGGCATATTCCTTCTTCACCTTGTCTCTCAGTACACATAAGCTTCCTCTGTGTTTAGTTGTCTATTCTCAATACACATTTGTGTGGCATGTTTTTGTTTATACCTGTGAGGTGAGCTCAGTATGTTGTAAGAAGTAAGTGTGCTTTAGCATTTATGGTCATGTGTCCACTTATGATCATGTGAAATGAACACATGATTATAAATGCTAGGGCACACATACTTTAATGAGCACAATACAACGTAATGACATGCTTGTGCTGAATTCTGAAAGGATGAGCAGCTGTGTAAGTGACATTGGTGGGAAAGGGCAGCCCGTGTAGTCACAGTTGGTGGAGGTATGCAGACATTCCACTCTGACCTCCTAGTGGTCACAGCAAACTCCTCTTTTCCTTTTTCCCTA chm1:+:111011120:-1 chm1:+:1419602650:-1 chm1:+:2347075485:-1 chm1:+:2736218630:-1 chm1:+:2814135430:-1 chm1:+:3026683401:-1 +CTTAGTTCTCAGAAGTCAGCAATCTTATTTACTCTGCATTTTAATCTTGAGAAAAGGAAGTTTGTAAGACCAGCCCATATTTAAAAGGAAGAGAATTGGAGTCCTACTTCTTGAGGGAGGAATATAAAAAACCTGTGGATACATTTAAAACCATAAATTTACTTTCCCTCTAGGTTTCCAAAACATTCTTCTTTTCTAGTTGGCATATTCCTTCTTCACCTTGTCTCTCAGTACACATAAGCTTCCTCTGTGTTTAGTTGTCTATTCTCAATACACATTTGTGTGGCATGTTTTTGTTTATACCTGTGAGGTGAGCTCAGTATGTTGTAAGAAGTAAGTGTGCTTTAGCATTTATGGTCATGTGTCCACTTATGATCATGTGAAATGAACACATGATTATAAATGCTAGGGCACACATACTTTAATGAGCACAATACAACGTAATGACATGCTTGTGCTGAATTCTGAAAGGATGAGCAGCTGTGTAAGTGACATTGGTGGGAAAGGGCAGCCCGTGTAGTCACAGTTGGTGGAGGTATGCAGACATTCCACTCTGACCTCCTAGTGGTCACAGCAAACTCCTCTTTTCCTTTTTCCCTA chm1:+:1212190749:-1 chm1:+:1218631122:-1 +CTTAGTTCTCAGAAGTCAGCAATCTTATTTACTCTGCATTTTAATCTTGAGAAAAGGAAGTTTGTAAGACCAGCCCATATTTAAAAGGAAGAGAATTGGAGTCCTACTTCTTGAGGGAGGAATATAAAAAACCTGTGGATACATTTAAAACCATAAATTTACTTTCCCTCTAGGTTTCCAAAACATTCTTCTTTTCTAGTTGGCATATTCCTTCTTCACCTTGTCTCTCAGTACACATAAGCTTCCTCTGTGTTTAGTTGTCTATTCTCAATACACATTTGTGTGGCATGTTTTTGTTTATACCTGTGAGGTGAGCTCAGTATGTTGTAAGAAGTAAGTGTGCTTTAGCATTTATGGTCATGTGTCCACTTATGATCATGTGAAATGAACACATGATTATAAATGCTAGGGCACACATACTTTAATGAGCACAATACAACGTAATGACATGCTTGTGCTGAATTCTGAAAGGATGAGCAGCTGTGTAAGTGACATTGGTGGGAAAGGGCAGCCCGTGTAGTCACAGTTGGTGGAGGTATGCAGACATTCCACTCTGACCTCCTAGTGGTCACAGCAAACTCCTCTTTTCCTTTTTCCCTA chm1:+:38374957:-1 chm1:+:702839420:-1 chm1:+:859271454:-1 chm1:+:1079132352:-1 chm1:+:1413307595:-1 chm1:+:1552576856:-1 chm1:+:1627656920:-1 chm1:+:1685887821:-1 chm1:+:1702584448:-1 chm1:+:1706199283:-1 chm1:+:1910284305:-1 chm1:+:1910952216:-1 chm1:+:2136669397:-1 chm1:+:2180835916:-1 chm1:+:2194685624:-1 chm1:+:2360732695:-1 chm1:+:2417683449:-1 chm1:+:2799886740:-1 chm1:+:2976913920:-1 +CTTAGTTCTCAGAAGTCAGCAATCTTATTTACTCTGCATTTTAATCTTGAGAAAAGGAAGTTTGTAAGACCAGCCCATATTTAAAAGGAAGAGAATTGGAGTCCTACTTCTTGAGGGAGGAATATAAAAAACCTGTGGATACATTTAAAACCATAAATTTACTTTCCCTCTAGGTTTCCAAAACATTCTTCTTTTCTAGTTGGCATATTCCTTCTTCACCTTGTCTCTCAGTACACATAAGCTTCCTCTGTGTTTAGTTGTCTATTCTCAATACACATTTGTGTGGCATGTTTTTGTTTATACCTGTGAGGTGAGCTCAGTATGTTGTAAGAAGTAAGTGTGCTTTAGCATTTATGGTCATGTGTCCACTTATGATCATGTGAAATGAACACATGATTATAAATGCTAGGGCACACATACTTTAATGAGCACAATACAACGTAATGACATGCTTGTGCTGAATTCTGAAAGGATGAGCAGCTGTGTAAGTGACATTGGTGGGAAAGGGCAGCCCGTGTAGTCACAGTTGGTGGAGGTATGCAGACATTCCACTCTGACCTCCTAGTGGTCACAGCAAACTCCTCTTTTCCTTTTTCCCTA chm1:+:467435757:-1 chm1:+:1962836194:-1 chm1:+:2502667005:-1 +CTTAGTTCTCAGAAGTCAGCAATCTTATTTACTCTGCATTTTAATCTTGAGAAAAGGAAGTTTGTAAGACCAGCCCATATTTAAAAGGAAGAGAATTGGAGTCCTACTTCTTGAGGGAGGAATATAAAAAACCTGTGGATACATTTAAAACCATAAATTTACTTTCCCTCTAGGTTTCCAAAACATTCTTCTTTTCTAGTTGGCATATTCCTTCTTCACCTTGTCTCTCAGTACACATAAGCTTCCTCTGTGTTTAGTTGTCTATTCTCAATACACATTTGTGTGGCATGTTTTTGTTTATACCTGTGAGGTGAGCTCAGTATGTTGTAAGAAGTAAGTGTGCTTTAGCATTTATGGTCATGTGTCCACTTATGATCATGTGAAATGAACACATGATTATAAATGCTAGGGCACACATACTTTAATGAGCACAATACAACGTAATGACATGCTTGTGCTGAATTCTGAAAGGATGAGCAGCTGTGTAAGTGACATTGGTGGGAAAGGGCAGCCCGTGTAGTCACAGTTGGTGGAGGTATGCAGACATTCCACTCTGACCTCCTAGTGGTCACAGCAAACTCCTCTTTTCCTTTTTCCCTA chm1:+:105927284:-1 chm1:+:222605052:-1 chm1:+:635450910:-1 chm1:+:1135233862:-1 chm1:+:1184692640:-1 chm1:+:1465402865:-1 chm1:+:1797145056:-1 chm1:+:2012660368:-1 chm1:+:2076574342:-1 chm1:+:2194780995:-1 chm1:+:2256578480:-1 chm1:+:2388842089:-1 +CTTAGTTCTCAGAAGTCAGCAATCTTATTTACTCTGCATTTTAATCTTGAGAAAAGGAAGTTTGTAAGACCAGCCCATATTTAAAAGGAAGAGAATTGGAGTCCTACTTCTTGAGGGAGGAATATAAAAAACCTGTGGATACATTTAAAACCATAAATTTACTTTCCCTCTAGGTTTCCAAAACATTCTTCTTTTCTAGTTGGCATATTCCTTCTTCACCTTGTCTCTCAGTACACATAAGCTTCCTCTGTGTTTAGTTGTCTATTCTCAATACACATTTGTGTGGCATGTTTTTGTTTATACCTGTGAGGTGAGCTCAGTATGTTGTAAGAAGTAAGTGTGCTTTAGCATTTATGGTCATGTGTCCACTTATGATCATGTGAAATGAACACATGATTATAAATGCTAGGGCACACATACTTTAATGAGCACAATACAACGTAATGACATGCTTGTGCTGAATTCTGAAAGGATGAGCAGCTGTGTAAGTGACATTGGTGGGAAAGGGCAGCCCGTGTAGTCACAGTTGGTGGAGGTATGCAGACATTCCACTCTGACCTCCTAGTGGTCACAGCAAACTCCTCTTTTCCTTTTTCCCTA chm1:+:316073085:-1 chm1:+:1133683048:-1 chm1:+:2123834754:-1 chm1:+:2229837250:-1 chm1:+:2372813321:-1 chm1:+:2919641542:-1 chm1:+:2978503464:-1 chm1:+:2992181613:-1 +CTTAGTTCTCAGAAGTCAGCAATCTTATTTACTCTGCATTTTAATCTTGAGAAAAGGAAGTTTGTAAGACCAGCCCATATTTAAAAGGAAGAGAATTGGAGTCCTACTTCTTGAGGGAGGAATATAAAAAACCTGTGGATACATTTAAAACCATAAATTTACTTTCCCTCTAGGTTTCCAAAACATTCTTCTTTTCTAGTTGGCATATTCCTTCTTCACCTTGTCTCTCAGTACACATAAGCTTCCTCTGTGTTTAGTTGTCTATTCTCAATACACATTTGTGTGGCATGTTTTTGTTTATACCTGTGAGGTGAGCTCAGTATGTTGTAAGAAGTAAGTGTGCTTTAGCATTTATGGTCATGTGTCCACTTATGATCATGTGAAATGAACACATGATTATAAATGCTAGGGCACACATACTTTAATGAGCACAATACAACGTAATGACATGCTTGTGCTGAATTCTGAAAGGATGAGCAGCTGTGTAAGTGACATTGGTGGGAAAGGGCAGCCCGTGTAGTCACAGTTGGTGGAGGTATGCAGACATTCCACTCTGACCTCCTAGTGGTCACAGCAAACTCCTCTTTTCCTTTTTCCCTA chm1:+:62918273:-1 chm1:+:83532123:-1 chm1:+:417705323:-1 chm1:+:963559972:-1 chm1:+:1295963260:-1 chm1:+:1311600557:-1 chm1:+:1365420229:-1 chm1:+:1708850865:-1 chm1:+:1733701531:-1 chm1:+:2491986348:-1 chm1:+:2594336813:-1 chm1:+:2731363349:-1 +CTTAGTTCTCAGAAGTCAGCAATCTTATTTACTCTGCATTTTAATCTTGAGAAAAGGAAGTTTGTAAGACCAGCCCATATTTAAAAGGAAGAGAATTGGAGTCCTACTTCTTGAGGGAGGAATATAAAAAACCTGTGGATACATTTAAAACCATAAATTTACTTTCCCTCTAGGTTTCCAAAACATTCTTCTTTTCTAGTTGGCATATTCCTTCTTCACCTTGTCTCTCAGTACACATAAGCTTCCTCTGTGTTTAGTTGTCTATTCTCAATACACATTTGTGTGGCATGTTTTTGTTTATACCTGTGAGGTGAGCTCAGTATGTTGTAAGAAGTAAGTGTGCTTTAGCATTTATGGTCATGTGTCCACTTATGATCATGTGAAATGAACACATGATTATAAATGCTAGGGCACACATACTTTAATGAGCACAATACAACGTAATGACATGCTTGTGCTGAATTCTGAAAGGATGAGCAGCTGTGTAAGTGACATTGGTGGGAAAGGGCAGCCCGTGTAGTCACAGTTGGTGGAGGTATGCAGACATTCCACTCTGACCTCCTAGTGGTCACAGCAAACTCCTCTTTTCCTTTTTCCCTA chm1:+:25898142:-1 chm1:+:42149298:-1 chm1:+:309923229:-1 chm1:+:468457925:-1 chm1:+:473082537:-1 chm1:+:485366502:-1 chm1:+:506769487:-1 chm1:+:844455487:-1 chm1:+:1185943854:-1 chm1:+:1234283706:-1 chm1:+:1365494299:-1 chm1:+:1393708066:-1 chm1:+:1713813701:-1 chm1:+:1816931136:-1 chm1:+:1935621781:-1 chm1:+:2057906841:-1 chm1:+:2195572382:-1 chm1:+:2412894570:-1 chm1:+:2533331362:-1 chm1:+:2729691047:-1 chm1:+:2821325495:-1 chm1:+:2848290571:-1 chm1:+:2858137906:-1 +CTTAGTTCTCAGAAGTCAGCAATCTTATTTACTCTGCATTTTAATCTTGAGAAAAGGAAGTTTGTAAGACCAGCCCATATTTAAAAGGAAGAGAATTGGAGTCCTACTTCTTGAGGGAGGAATATAAAAAACCTGTGGATACATTTAAAACCATAAATTTACTTTCCCTCTAGGTTTCCAAAACATTCTTCTTTTCTAGTTGGCATATTCCTTCTTCACCTTGTCTCTCAGTACACATAAGCTTCCTCTGTGTTTAGTTGTCTATTCTCAATACACATTTGTGTGGCATGTTTTTGTTTATACCTGTGAGGTGAGCTCAGTATGTTGTAAGAAGTAAGTGTGCTTTAGCATTTATGGTCATGTGTCCACTTATGATCATGTGAAATGAACACATGATTATAAATGCTAGGGCACACATACTTTAATGAGCACAATACAACGTAATGACATGCTTGTGCTGAATTCTGAAAGGATGAGCAGCTGTGTAAGTGACATTGGTGGGAAAGGGCAGCCCGTGTAGTCACAGTTGGTGGAGGTATGCAGACATTCCACTCTGACCTCCTAGTGGTCACAGCAAACTCCTCTTTTCCTTTTTCCCTA chm1:+:19094894:-1 chm1:+:47204438:-1 chm1:+:90253490:-1 chm1:+:197868966:-1 chm1:+:252114337:-1 chm1:+:272792338:-1 chm1:+:296290089:-1 chm1:+:458080126:-1 chm1:+:605269062:-1 chm1:+:756614575:-1 chm1:+:804401584:-1 chm1:+:814239400:-1 chm1:+:823575502:-1 chm1:+:879042637:-1 chm1:+:903183336:-1 chm1:+:920795059:-1 chm1:+:964481891:-1 chm1:+:1127896558:-1 chm1:+:1136850697:-1 chm1:+:1188356109:-1 chm1:+:1298261485:-1 chm1:+:1298772635:-1 chm1:+:1342746880:-1 chm1:+:1362577181:-1 chm1:+:1389417997:-1 chm1:+:1456783539:-1 chm1:+:1567629048:-1 chm1:+:1680704423:-1 chm1:+:1763037286:-1 chm1:+:1806296954:-1 chm1:+:1836987281:-1 chm1:+:1893182412:-1 chm1:+:1972108936:-1 chm1:+:2038438440:-1 chm1:+:2051178073:-1 chm1:+:2109316854:-1 chm1:+:2232048283:-1 chm1:+:2271673603:-1 chm1:+:2352413102:-1 chm1:+:2643863872:-1 chm1:+:2754909352:-1 chm1:+:2759831937:-1 chm1:+:2893396540:-1 chm1:+:2918882288:-1 chm1:+:2935648319:-1 chm1:+:2943763633:-1 chm1:+:2989655243:-1 chm1:+:3001438635:-1 chm1:+:3031989453:-1 +TAGGGAAAAAGGAAAAGAGGAGTTTGCTGTGACCACTAGGAGGTCAGAGTGGAATGTCTGCATACCTCCACCAACTGTGACTACACGGGCTGCCCTTTCCCACCAATGTCACTTACACAGCTGCTCATCCTTTCAGAATTCAGCACAAGCATGTCATTACGTTGTATTGTGCTCATTAAAGTATGTGTGCCCTAGCATTTATAATCATGTGTTCATTTCACATGATCATAAGTGGACACATGACCATAAATGCTAAAGCACACTTACTTCTTACAACATACTGAGCTCACCTCACAGGTATAAACAAAAACATGCCACACAAATGTGTATTGAGAATAGACAACTAAACACAGAGGAAGCTTATGTGTACTGAGAGACAAGGTGAAGAAGGAATATGCCAACTAGAAAAGAAGAATGTTTTGGAAACCTAGAGGGAAAGTAAATTTATGGTTTTAAATGTATCCACAGGTTTTTTATATTCCTCCCTCAAGAAGTAGGACTCCAATTCTCTTCCTTTTAAATATGGGCTGGTCTTACAAACTTCCTTTTCTCAAGATTAAAATGCAGAGTAAATAAGATTGCTGACTTCTGAGAACTAAG chm1:+:910121559:-1 chm1:+:1665577324:-1 +TAGGGAAAAAGGAAAAGAGGAGTTTGCTGTGACCACTAGGAGGTCAGAGTGGAATGTCTGCATACCTCCACCAACTGTGACTACACGGGCTGCCCTTTCCCACCAATGTCACTTACACAGCTGCTCATCCTTTCAGAATTCAGCACAAGCATGTCATTACGTTGTATTGTGCTCATTAAAGTATGTGTGCCCTAGCATTTATAATCATGTGTTCATTTCACATGATCATAAGTGGACACATGACCATAAATGCTAAAGCACACTTACTTCTTACAACATACTGAGCTCACCTCACAGGTATAAACAAAAACATGCCACACAAATGTGTATTGAGAATAGACAACTAAACACAGAGGAAGCTTATGTGTACTGAGAGACAAGGTGAAGAAGGAATATGCCAACTAGAAAAGAAGAATGTTTTGGAAACCTAGAGGGAAAGTAAATTTATGGTTTTAAATGTATCCACAGGTTTTTTATATTCCTCCCTCAAGAAGTAGGACTCCAATTCTCTTCCTTTTAAATATGGGCTGGTCTTACAAACTTCCTTTTCTCAAGATTAAAATGCAGAGTAAATAAGATTGCTGACTTCTGAGAACTAAG chm1:+:1154773026:22 chm1:+:1842680112:-1 chm1:+:2259120349:-1 +TAGGGAAAAAGGAAAAGAGGAGTTTGCTGTGACCACTAGGAGGTCAGAGTGGAATGTCTGCATACCTCCACCAACTGTGACTACACGGGCTGCCCTTTCCCACCAATGTCACTTACACAGCTGCTCATCCTTTCAGAATTCAGCACAAGCATGTCATTACGTTGTATTGTGCTCATTAAAGTATGTGTGCCCTAGCATTTATAATCATGTGTTCATTTCACATGATCATAAGTGGACACATGACCATAAATGCTAAAGCACACTTACTTCTTACAACATACTGAGCTCACCTCACAGGTATAAACAAAAACATGCCACACAAATGTGTATTGAGAATAGACAACTAAACACAGAGGAAGCTTATGTGTACTGAGAGACAAGGTGAAGAAGGAATATGCCAACTAGAAAAGAAGAATGTTTTGGAAACCTAGAGGGAAAGTAAATTTATGGTTTTAAATGTATCCACAGGTTTTTTATATTCCTCCCTCAAGAAGTAGGACTCCAATTCTCTTCCTTTTAAATATGGGCTGGTCTTACAAACTTCCTTTTCTCAAGATTAAAATGCAGAGTAAATAAGATTGCTGACTTCTGAGAACTAAG chm1:+:1154773028:22 +TAGGGAAAAAGGAAAAGAGGAGTTTGCTGTGACCACTAGGAGGTCAGAGTGGAATGTCTGCATACCTCCACCAACTGTGACTACACGGGCTGCCCTTTCCCACCAATGTCACTTACACAGCTGCTCATCCTTTCAGAATTCAGCACAAGCATGTCATTACGTTGTATTGTGCTCATTAAAGTATGTGTGCCCTAGCATTTATAATCATGTGTTCATTTCACATGATCATAAGTGGACACATGACCATAAATGCTAAAGCACACTTACTTCTTACAACATACTGAGCTCACCTCACAGGTATAAACAAAAACATGCCACACAAATGTGTATTGAGAATAGACAACTAAACACAGAGGAAGCTTATGTGTACTGAGAGACAAGGTGAAGAAGGAATATGCCAACTAGAAAAGAAGAATGTTTTGGAAACCTAGAGGGAAAGTAAATTTATGGTTTTAAATGTATCCACAGGTTTTTTATATTCCTCCCTCAAGAAGTAGGACTCCAATTCTCTTCCTTTTAAATATGGGCTGGTCTTACAAACTTCCTTTTCTCAAGATTAAAATGCAGAGTAAATAAGATTGCTGACTTCTGAGAACTAAG chm1:+:1154773031:22 +TAGGGAAAAAGGAAAAGAGGAGTTTGCTGTGACCACTAGGAGGTCAGAGTGGAATGTCTGCATACCTCCACCAACTGTGACTACACGGGCTGCCCTTTCCCACCAATGTCACTTACACAGCTGCTCATCCTTTCAGAATTCAGCACAAGCATGTCATTACGTTGTATTGTGCTCATTAAAGTATGTGTGCCCTAGCATTTATAATCATGTGTTCATTTCACATGATCATAAGTGGACACATGACCATAAATGCTAAAGCACACTTACTTCTTACAACATACTGAGCTCACCTCACAGGTATAAACAAAAACATGCCACACAAATGTGTATTGAGAATAGACAACTAAACACAGAGGAAGCTTATGTGTACTGAGAGACAAGGTGAAGAAGGAATATGCCAACTAGAAAAGAAGAATGTTTTGGAAACCTAGAGGGAAAGTAAATTTATGGTTTTAAATGTATCCACAGGTTTTTTATATTCCTCCCTCAAGAAGTAGGACTCCAATTCTCTTCCTTTTAAATATGGGCTGGTCTTACAAACTTCCTTTTCTCAAGATTAAAATGCAGAGTAAATAAGATTGCTGACTTCTGAGAACTAAG chm1:+:1154773032:22 +TAGGGAAAAAGGAAAAGAGGAGTTTGCTGTGACCACTAGGAGGTCAGAGTGGAATGTCTGCATACCTCCACCAACTGTGACTACACGGGCTGCCCTTTCCCACCAATGTCACTTACACAGCTGCTCATCCTTTCAGAATTCAGCACAAGCATGTCATTACGTTGTATTGTGCTCATTAAAGTATGTGTGCCCTAGCATTTATAATCATGTGTTCATTTCACATGATCATAAGTGGACACATGACCATAAATGCTAAAGCACACTTACTTCTTACAACATACTGAGCTCACCTCACAGGTATAAACAAAAACATGCCACACAAATGTGTATTGAGAATAGACAACTAAACACAGAGGAAGCTTATGTGTACTGAGAGACAAGGTGAAGAAGGAATATGCCAACTAGAAAAGAAGAATGTTTTGGAAACCTAGAGGGAAAGTAAATTTATGGTTTTAAATGTATCCACAGGTTTTTTATATTCCTCCCTCAAGAAGTAGGACTCCAATTCTCTTCCTTTTAAATATGGGCTGGTCTTACAAACTTCCTTTTCTCAAGATTAAAATGCAGAGTAAATAAGATTGCTGACTTCTGAGAACTAAG chm1:+:1154773033:22 +TAGGGAAAAAGGAAAAGAGGAGTTTGCTGTGACCACTAGGAGGTCAGAGTGGAATGTCTGCATACCTCCACCAACTGTGACTACACGGGCTGCCCTTTCCCACCAATGTCACTTACACAGCTGCTCATCCTTTCAGAATTCAGCACAAGCATGTCATTACGTTGTATTGTGCTCATTAAAGTATGTGTGCCCTAGCATTTATAATCATGTGTTCATTTCACATGATCATAAGTGGACACATGACCATAAATGCTAAAGCACACTTACTTCTTACAACATACTGAGCTCACCTCACAGGTATAAACAAAAACATGCCACACAAATGTGTATTGAGAATAGACAACTAAACACAGAGGAAGCTTATGTGTACTGAGAGACAAGGTGAAGAAGGAATATGCCAACTAGAAAAGAAGAATGTTTTGGAAACCTAGAGGGAAAGTAAATTTATGGTTTTAAATGTATCCACAGGTTTTTTATATTCCTCCCTCAAGAAGTAGGACTCCAATTCTCTTCCTTTTAAATATGGGCTGGTCTTACAAACTTCCTTTTCTCAAGATTAAAATGCAGAGTAAATAAGATTGCTGACTTCTGAGAACTAAG chm1:+:703178076:-1 chm1:+:1154773030:22 +TAGGGAAAAAGGAAAAGAGGAGTTTGCTGTGACCACTAGGAGGTCAGAGTGGAATGTCTGCATACCTCCACCAACTGTGACTACACGGGCTGCCCTTTCCCACCAATGTCACTTACACAGCTGCTCATCCTTTCAGAATTCAGCACAAGCATGTCATTACGTTGTATTGTGCTCATTAAAGTATGTGTGCCCTAGCATTTATAATCATGTGTTCATTTCACATGATCATAAGTGGACACATGACCATAAATGCTAAAGCACACTTACTTCTTACAACATACTGAGCTCACCTCACAGGTATAAACAAAAACATGCCACACAAATGTGTATTGAGAATAGACAACTAAACACAGAGGAAGCTTATGTGTACTGAGAGACAAGGTGAAGAAGGAATATGCCAACTAGAAAAGAAGAATGTTTTGGAAACCTAGAGGGAAAGTAAATTTATGGTTTTAAATGTATCCACAGGTTTTTTATATTCCTCCCTCAAGAAGTAGGACTCCAATTCTCTTCCTTTTAAATATGGGCTGGTCTTACAAACTTCCTTTTCTCAAGATTAAAATGCAGAGTAAATAAGATTGCTGACTTCTGAGAACTAAG chm1:+:1154773034:22 +TAGGGAAAAAGGAAAAGAGGAGTTTGCTGTGACCACTAGGAGGTCAGAGTGGAATGTCTGCATACCTCCACCAACTGTGACTACACGGGCTGCCCTTTCCCACCAATGTCACTTACACAGCTGCTCATCCTTTCAGAATTCAGCACAAGCATGTCATTACGTTGTATTGTGCTCATTAAAGTATGTGTGCCCTAGCATTTATAATCATGTGTTCATTTCACATGATCATAAGTGGACACATGACCATAAATGCTAAAGCACACTTACTTCTTACAACATACTGAGCTCACCTCACAGGTATAAACAAAAACATGCCACACAAATGTGTATTGAGAATAGACAACTAAACACAGAGGAAGCTTATGTGTACTGAGAGACAAGGTGAAGAAGGAATATGCCAACTAGAAAAGAAGAATGTTTTGGAAACCTAGAGGGAAAGTAAATTTATGGTTTTAAATGTATCCACAGGTTTTTTATATTCCTCCCTCAAGAAGTAGGACTCCAATTCTCTTCCTTTTAAATATGGGCTGGTCTTACAAACTTCCTTTTCTCAAGATTAAAATGCAGAGTAAATAAGATTGCTGACTTCTGAGAACTAAG chm1:+:3022402531:-1 +AATATGCAACTAGACTCAGTGATGTGCTACACTCTTATTGTACTGCCTTCATGTTTATACCTGACAAGACACAGGAATTTGGTTTGATACCATTCTATTAAATGAACATCATTAATAAAGCAATGCATTTATGATTGGTTTGAGATACCCTTATCAAGTATATTTCTGACAAGATACATTTCTCATTTTGACTTGGAATTGATTAGAATGAAATCCTCTGCTGATAAATGTACATGTCCATGGACTGGAAAAAACTTTCCACAGTCTAGCTCTGACTCCACATATTTAAACCTATTTAGACTCTTATCACCCACATACCTTACTGTGGCAATAGCTTTGAGACATGTTTATATTATACTTCCACCTCAAGCCGTTGTGTCATGATGCCAGTGAGCTAGCACAACAGGTGGGTAAGAGTGTTCCTAGAAGTTATTCCACCTTCTTGAGCAATAACTTAACACACATGAAGGGACTAATGAGCCACATAAATATGTCCCACTGAACCCAAATTATAAATTATGATGTAAACTTTATATTATGTATATATACTCAACCTCTTCCTTAGCGGATCTAAAAATGCACATGGCCACTCTAAAGTCA chm1:+:253976085:-1 chm1:+:417194654:-1 chm1:+:526997306:25 chm1:+:1513558131:-1 chm1:+:1684781749:-1 chm1:+:1855858335:-1 chm1:+:1914412702:-1 +AATATGCAACTAGACTCAGTGATGTGCTACACTCTTATTGTACTGCCTTCATGTTTATACCTGACAAGACACAGGAATTTGGTTTGATACCATTCTATTAAATGAACATCATTAATAAAGCAATGCATTTATGATTGGTTTGAGATACCCTTATCAAGTATATTTCTGACAAGATACATTTCTCATTTTGACTTGGAATTGATTAGAATGAAATCCTCTGCTGATAAATGTACATGTCCATGGACTGGAAAAAACTTTCCACAGTCTAGCTCTGACTCCACATATTTAAACCTATTTAGACTCTTATCACCCACATACCTTACTGTGGCAATAGCTTTGAGACATGTTTATATTATACTTCCACCTCAAGCCGTTGTGTCATGATGCCAGTGAGCTAGCACAACAGGTGGGTAAGAGTGTTCCTAGAAGTTATTCCACCTTCTTGAGCAATAACTTAACACACATGAAGGGACTAATGAGCCACATAAATATGTCCCACTGAACCCAAATTATAAATTATGATGTAAACTTTATATTATGTATATATACTCAACCTCTTCCTTAGCGGATCTAAAAATGCACATGGCCACTCTAAAGTCA chm1:+:526997308:25 +AATATGCAACTAGACTCAGTGATGTGCTACACTCTTATTGTACTGCCTTCATGTTTATACCTGACAAGACACAGGAATTTGGTTTGATACCATTCTATTAAATGAACATCATTAATAAAGCAATGCATTTATGATTGGTTTGAGATACCCTTATCAAGTATATTTCTGACAAGATACATTTCTCATTTTGACTTGGAATTGATTAGAATGAAATCCTCTGCTGATAAATGTACATGTCCATGGACTGGAAAAAACTTTCCACAGTCTAGCTCTGACTCCACATATTTAAACCTATTTAGACTCTTATCACCCACATACCTTACTGTGGCAATAGCTTTGAGACATGTTTATATTATACTTCCACCTCAAGCCGTTGTGTCATGATGCCAGTGAGCTAGCACAACAGGTGGGTAAGAGTGTTCCTAGAAGTTATTCCACCTTCTTGAGCAATAACTTAACACACATGAAGGGACTAATGAGCCACATAAATATGTCCCACTGAACCCAAATTATAAATTATGATGTAAACTTTATATTATGTATATATACTCAACCTCTTCCTTAGCGGATCTAAAAATGCACATGGCCACTCTAAAGTCA chm1:+:526997305:25 +AATATGCAACTAGACTCAGTGATGTGCTACACTCTTATTGTACTGCCTTCATGTTTATACCTGACAAGACACAGGAATTTGGTTTGATACCATTCTATTAAATGAACATCATTAATAAAGCAATGCATTTATGATTGGTTTGAGATACCCTTATCAAGTATATTTCTGACAAGATACATTTCTCATTTTGACTTGGAATTGATTAGAATGAAATCCTCTGCTGATAAATGTACATGTCCATGGACTGGAAAAAACTTTCCACAGTCTAGCTCTGACTCCACATATTTAAACCTATTTAGACTCTTATCACCCACATACCTTACTGTGGCAATAGCTTTGAGACATGTTTATATTATACTTCCACCTCAAGCCGTTGTGTCATGATGCCAGTGAGCTAGCACAACAGGTGGGTAAGAGTGTTCCTAGAAGTTATTCCACCTTCTTGAGCAATAACTTAACACACATGAAGGGACTAATGAGCCACATAAATATGTCCCACTGAACCCAAATTATAAATTATGATGTAAACTTTATATTATGTATATATACTCAACCTCTTCCTTAGCGGATCTAAAAATGCACATGGCCACTCTAAAGTCA chm1:+:2864828516:-1 +AATATGCAACTAGACTCAGTGATGTGCTACACTCTTATTGTACTGCCTTCATGTTTATACCTGACAAGACACAGGAATTTGGTTTGATACCATTCTATTAAATGAACATCATTAATAAAGCAATGCATTTATGATTGGTTTGAGATACCCTTATCAAGTATATTTCTGACAAGATACATTTCTCATTTTGACTTGGAATTGATTAGAATGAAATCCTCTGCTGATAAATGTACATGTCCATGGACTGGAAAAAACTTTCCACAGTCTAGCTCTGACTCCACATATTTAAACCTATTTAGACTCTTATCACCCACATACCTTACTGTGGCAATAGCTTTGAGACATGTTTATATTATACTTCCACCTCAAGCCGTTGTGTCATGATGCCAGTGAGCTAGCACAACAGGTGGGTAAGAGTGTTCCTAGAAGTTATTCCACCTTCTTGAGCAATAACTTAACACACATGAAGGGACTAATGAGCCACATAAATATGTCCCACTGAACCCAAATTATAAATTATGATGTAAACTTTATATTATGTATATATACTCAACCTCTTCCTTAGCGGATCTAAAAATGCACATGGCCACTCTAAAGTCA chm1:+:668042003:-1 +AATATGCAACTAGACTCAGTGATGTGCTACACTCTTATTGTACTGCCTTCATGTTTATACCTGACAAGACACAGGAATTTGGTTTGATACCATTCTATTAAATGAACATCATTAATAAAGCAATGCATTTATGATTGGTTTGAGATACCCTTATCAAGTATATTTCTGACAAGATACATTTCTCATTTTGACTTGGAATTGATTAGAATGAAATCCTCTGCTGATAAATGTACATGTCCATGGACTGGAAAAAACTTTCCACAGTCTAGCTCTGACTCCACATATTTAAACCTATTTAGACTCTTATCACCCACATACCTTACTGTGGCAATAGCTTTGAGACATGTTTATATTATACTTCCACCTCAAGCCGTTGTGTCATGATGCCAGTGAGCTAGCACAACAGGTGGGTAAGAGTGTTCCTAGAAGTTATTCCACCTTCTTGAGCAATAACTTAACACACATGAAGGGACTAATGAGCCACATAAATATGTCCCACTGAACCCAAATTATAAATTATGATGTAAACTTTATATTATGTATATATACTCAACCTCTTCCTTAGCGGATCTAAAAATGCACATGGCCACTCTAAAGTCA chm1:+:526997311:25 chm1:+:2258201083:-1 +AATATGCAACTAGACTCAGTGATGTGCTACACTCTTATTGTACTGCCTTCATGTTTATACCTGACAAGACACAGGAATTTGGTTTGATACCATTCTATTAAATGAACATCATTAATAAAGCAATGCATTTATGATTGGTTTGAGATACCCTTATCAAGTATATTTCTGACAAGATACATTTCTCATTTTGACTTGGAATTGATTAGAATGAAATCCTCTGCTGATAAATGTACATGTCCATGGACTGGAAAAAACTTTCCACAGTCTAGCTCTGACTCCACATATTTAAACCTATTTAGACTCTTATCACCCACATACCTTACTGTGGCAATAGCTTTGAGACATGTTTATATTATACTTCCACCTCAAGCCGTTGTGTCATGATGCCAGTGAGCTAGCACAACAGGTGGGTAAGAGTGTTCCTAGAAGTTATTCCACCTTCTTGAGCAATAACTTAACACACATGAAGGGACTAATGAGCCACATAAATATGTCCCACTGAACCCAAATTATAAATTATGATGTAAACTTTATATTATGTATATATACTCAACCTCTTCCTTAGCGGATCTAAAAATGCACATGGCCACTCTAAAGTCA chm1:+:2906278465:-1 +AATATGCAACTAGACTCAGTGATGTGCTACACTCTTATTGTACTGCCTTCATGTTTATACCTGACAAGACACAGGAATTTGGTTTGATACCATTCTATTAAATGAACATCATTAATAAAGCAATGCATTTATGATTGGTTTGAGATACCCTTATCAAGTATATTTCTGACAAGATACATTTCTCATTTTGACTTGGAATTGATTAGAATGAAATCCTCTGCTGATAAATGTACATGTCCATGGACTGGAAAAAACTTTCCACAGTCTAGCTCTGACTCCACATATTTAAACCTATTTAGACTCTTATCACCCACATACCTTACTGTGGCAATAGCTTTGAGACATGTTTATATTATACTTCCACCTCAAGCCGTTGTGTCATGATGCCAGTGAGCTAGCACAACAGGTGGGTAAGAGTGTTCCTAGAAGTTATTCCACCTTCTTGAGCAATAACTTAACACACATGAAGGGACTAATGAGCCACATAAATATGTCCCACTGAACCCAAATTATAAATTATGATGTAAACTTTATATTATGTATATATACTCAACCTCTTCCTTAGCGGATCTAAAAATGCACATGGCCACTCTAAAGTCA chm1:+:526997312:25 +TGACTTTAGAGTGGCCATGTGCATTTTTAGATCCGCTAAGGAAGAGGTTGAGTATATATACATAATATAAAGTTTACATCATAATTTATAATTTGGGTTCAGTGGGACATATTTATGTGGCTCATTAGTCCCTTCATGTGTGTTAAGTTATTGCTCAAGAAGGTGGAATAACTTCTAGGAACACTCTTACCCACCTGTTGTGCTAGCTCACTGGCATCATGACACAACGGCTTGAGGTGGAAGTATAATATAAACATGTCTCAAAGCTATTGCCACAGTAAGGTATGTGGGTGATAAGAGTCTAAATAGGTTTAAATATGTGGAGTCAGAGCTAGACTGTGGAAAGTTTTTTCCAGTCCATGGACATGTACATTTATCAGCAGAGGATTTCATTCTAATCAATTCCAAGTCAAAATGAGAAATGTATCTTGTCAGAAATATACTTGATAAGGGTATCTCAAACCAATCATAAATGCATTGCTTTATTAATGATGTTCATTTAATAGAATGGTATCAAACCAAATTCCTGTGTCTTGTCAGGTATAAACATGAAGGCAGTACAATAAGAGTGTAGCACATCACTGAGTCTAGTTGCATATT chm1:+:1463536470:-1 +TGACTTTAGAGTGGCCATGTGCATTTTTAGATCCGCTAAGGAAGAGGTTGAGTATATATACATAATATAAAGTTTACATCATAATTTATAATTTGGGTTCAGTGGGACATATTTATGTGGCTCATTAGTCCCTTCATGTGTGTTAAGTTATTGCTCAAGAAGGTGGAATAACTTCTAGGAACACTCTTACCCACCTGTTGTGCTAGCTCACTGGCATCATGACACAACGGCTTGAGGTGGAAGTATAATATAAACATGTCTCAAAGCTATTGCCACAGTAAGGTATGTGGGTGATAAGAGTCTAAATAGGTTTAAATATGTGGAGTCAGAGCTAGACTGTGGAAAGTTTTTTCCAGTCCATGGACATGTACATTTATCAGCAGAGGATTTCATTCTAATCAATTCCAAGTCAAAATGAGAAATGTATCTTGTCAGAAATATACTTGATAAGGGTATCTCAAACCAATCATAAATGCATTGCTTTATTAATGATGTTCATTTAATAGAATGGTATCAAACCAAATTCCTGTGTCTTGTCAGGTATAAACATGAAGGCAGTACAATAAGAGTGTAGCACATCACTGAGTCTAGTTGCATATT chm1:+:266658000:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:1519656:-1 chm1:+:23079004:-1 chm1:+:28777645:-1 chm1:+:33698732:-1 chm1:+:34615410:-1 chm1:+:92482640:-1 chm1:+:93444519:-1 chm1:+:98913812:-1 chm1:+:110540827:-1 chm1:+:149807862:-1 chm1:+:174855671:-1 chm1:+:181179611:-1 chm1:+:249190371:-1 chm1:+:276812018:-1 chm1:+:288815387:-1 chm1:+:292089290:-1 chm1:+:294506317:-1 chm1:+:308422487:-1 chm1:+:324059405:-1 chm1:+:377337281:-1 chm1:+:406718852:-1 chm1:+:450410440:-1 chm1:+:464270545:-1 chm1:+:510675181:-1 chm1:+:569105926:-1 chm1:+:569105981:-1 chm1:+:569106036:-1 chm1:+:577703889:-1 chm1:+:601396911:-1 chm1:+:613937308:-1 chm1:+:618058659:-1 chm1:+:672177062:-1 chm1:+:676240388:-1 chm1:+:676507836:-1 chm1:+:704047587:-1 chm1:+:793253739:-1 chm1:+:866919995:-1 chm1:+:919346372:-1 chm1:+:952541788:-1 chm1:+:993332149:-1 chm1:+:1019669864:-1 chm1:+:1037413685:-1 chm1:+:1045850311:-1 chm1:+:1050808369:-1 chm1:+:1054052754:-1 chm1:+:1058643476:-1 chm1:+:1105971082:-1 chm1:+:1199835636:-1 chm1:+:1217868161:-1 chm1:+:1277700716:-1 chm1:+:1300461172:-1 chm1:+:1308784530:-1 chm1:+:1323954777:-1 chm1:+:1334362209:-1 chm1:+:1335854891:-1 chm1:+:1335953975:-1 chm1:+:1336815534:-1 chm1:+:1339537024:-1 chm1:+:1383436789:-1 chm1:+:1416051590:-1 chm1:+:1435526137:-1 chm1:+:1460125122:-1 chm1:+:1470887867:-1 chm1:+:1526641996:-1 chm1:+:1543962260:-1 chm1:+:1637564577:-1 chm1:+:1668037610:-1 chm1:+:1691236474:-1 chm1:+:1695609301:-1 chm1:+:1702488090:-1 chm1:+:1767740445:-1 chm1:+:1862687055:-1 chm1:+:1888352783:-1 chm1:+:1893500575:-1 chm1:+:1958958398:-1 chm1:+:1978577199:-1 chm1:+:1990286329:-1 chm1:+:2021742607:-1 chm1:+:2034475428:-1 chm1:+:2060059472:-1 chm1:+:2072292011:-1 chm1:+:2105157114:-1 chm1:+:2134024083:-1 chm1:+:2193990296:-1 chm1:+:2245348824:-1 chm1:+:2263780491:-1 chm1:+:2268378740:-1 chm1:+:2277093604:-1 chm1:+:2298493600:-1 chm1:+:2392746086:-1 chm1:+:2406368855:-1 chm1:+:2424902214:-1 chm1:+:2432689032:-1 chm1:+:2433604132:-1 chm1:+:2459873876:-1 chm1:+:2502678035:-1 chm1:+:2504530838:-1 chm1:+:2517337167:-1 chm1:+:2520080925:-1 chm1:+:2530750133:-1 chm1:+:2556728255:-1 chm1:+:2562025858:-1 chm1:+:2564716517:-1 chm1:+:2594653172:-1 chm1:+:2602807024:-1 chm1:+:2641070274:-1 chm1:+:2649573494:-1 chm1:+:2661998391:-1 chm1:+:2670891034:-1 chm1:+:2674771858:-1 chm1:+:2681266616:-1 chm1:+:2699144677:-1 chm1:+:2709186978:-1 chm1:+:2748829702:-1 chm1:+:2764780882:-1 chm1:+:2797514924:-1 chm1:+:2847691669:-1 chm1:+:2890485058:-1 chm1:+:2891037934:-1 chm1:+:2904457822:-1 chm1:+:2921380798:-1 chm1:+:2928639508:-1 chm1:+:2949364680:-1 chm1:+:2951677488:-1 chm1:+:3000665980:-1 chm1:+:3016704198:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:13402345:-1 chm1:+:13623142:-1 chm1:+:300295768:-1 chm1:+:315988546:-1 chm1:+:402792934:-1 chm1:+:600876713:-1 chm1:+:606472328:-1 chm1:+:727207270:-1 chm1:+:842438358:-1 chm1:+:916342775:-1 chm1:+:1270404151:-1 chm1:+:1334610856:-1 chm1:+:1653821671:-1 chm1:+:1664928639:-1 chm1:+:1702889055:-1 chm1:+:1754184665:-1 chm1:+:1894078766:-1 chm1:+:2005164754:-1 chm1:+:2068701659:-1 chm1:+:2148600046:-1 chm1:+:2220825155:-1 chm1:+:2275702638:-1 chm1:+:2527918653:-1 chm1:+:2575006777:-1 chm1:+:2869412305:-1 chm1:+:2876985299:-1 chm1:+:2902720125:-1 chm1:+:2928631968:-1 chm1:+:2952223644:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:427016362:-1 chm1:+:444906173:-1 chm1:+:538186488:-1 chm1:+:877512547:-1 chm1:+:996334346:-1 chm1:+:1086084561:-1 chm1:+:1170962062:-1 chm1:+:1350424949:-1 chm1:+:1738931490:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:1188885532:-1 chm1:+:1261733334:-1 chm1:+:2520826195:-1 chm1:+:2618065299:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:634362305:-1 chm1:+:634549058:-1 chm1:+:1012116641:-1 chm1:+:2479971698:-1 chm1:+:2819826434:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:369077305:-1 chm1:+:460238567:-1 chm1:+:534628542:-1 chm1:+:878479078:-1 chm1:+:1012880460:-1 chm1:+:1237570803:-1 chm1:+:2187204736:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:260610636:-1 chm1:+:347875969:-1 chm1:+:372177290:-1 chm1:+:472843665:-1 chm1:+:570839235:-1 chm1:+:617575145:-1 chm1:+:795061139:-1 chm1:+:1058825198:-1 chm1:+:1133864379:-1 chm1:+:1183223974:-1 chm1:+:1619501386:-1 chm1:+:1782177351:-1 chm1:+:1957763448:-1 chm1:+:2073238952:-1 chm1:+:2225621612:-1 chm1:+:2424600360:-1 chm1:+:2424639477:-1 chm1:+:2444334254:-1 chm1:+:2444408268:-1 chm1:+:2558429839:-1 chm1:+:2558813978:-1 chm1:+:2584494121:-1 chm1:+:2673756290:-1 chm1:+:2767280628:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:6973890:-1 chm1:+:11720434:-1 chm1:+:150143170:-1 chm1:+:224547363:-1 chm1:+:335457338:-1 chm1:+:367070614:-1 chm1:+:385743741:-1 chm1:+:403293428:-1 chm1:+:715644382:-1 chm1:+:937957501:-1 chm1:+:953510939:-1 chm1:+:1382436743:-1 chm1:+:1415495893:-1 chm1:+:1494855493:-1 chm1:+:1775877386:-1 chm1:+:1787354686:-1 chm1:+:1899791202:-1 chm1:+:2220913113:-1 chm1:+:2756144699:-1 chm1:+:2767748601:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:4290691:-1 chm1:+:9547417:-1 chm1:+:19627910:-1 chm1:+:22765087:-1 chm1:+:24492763:-1 chm1:+:30587769:-1 chm1:+:38485500:-1 chm1:+:85305332:-1 chm1:+:155992864:-1 chm1:+:167924726:-1 chm1:+:179225108:-1 chm1:+:226695782:-1 chm1:+:228039170:-1 chm1:+:281268242:-1 chm1:+:295222095:-1 chm1:+:305147669:-1 chm1:+:314219297:-1 chm1:+:315244100:-1 chm1:+:334603802:-1 chm1:+:356008261:-1 chm1:+:383991270:-1 chm1:+:388634458:-1 chm1:+:405134649:-1 chm1:+:415706147:-1 chm1:+:466770117:-1 chm1:+:482243008:-1 chm1:+:483553236:-1 chm1:+:491592430:-1 chm1:+:501917640:-1 chm1:+:531651442:-1 chm1:+:545786700:-1 chm1:+:555181732:-1 chm1:+:565587784:-1 chm1:+:590885202:-1 chm1:+:623392792:-1 chm1:+:671839941:-1 chm1:+:675315225:-1 chm1:+:682039231:-1 chm1:+:717226566:-1 chm1:+:751732208:-1 chm1:+:754701732:-1 chm1:+:786141924:-1 chm1:+:786472059:-1 chm1:+:800699678:-1 chm1:+:822174537:-1 chm1:+:839755140:-1 chm1:+:861502061:-1 chm1:+:877073448:-1 chm1:+:914571031:-1 chm1:+:918851630:-1 chm1:+:933094777:-1 chm1:+:943490219:-1 chm1:+:976264723:-1 chm1:+:1015784692:-1 chm1:+:1016495130:-1 chm1:+:1019030468:-1 chm1:+:1019697302:-1 chm1:+:1027222046:-1 chm1:+:1031021274:-1 chm1:+:1053900944:-1 chm1:+:1056128578:-1 chm1:+:1070029708:-1 chm1:+:1079871862:-1 chm1:+:1143643396:-1 chm1:+:1180449331:-1 chm1:+:1181228413:-1 chm1:+:1220809821:-1 chm1:+:1240740826:-1 chm1:+:1266100719:-1 chm1:+:1301881846:-1 chm1:+:1302884046:-1 chm1:+:1306531568:-1 chm1:+:1338453701:-1 chm1:+:1341490220:-1 chm1:+:1349585260:-1 chm1:+:1362532617:-1 chm1:+:1364186547:-1 chm1:+:1383799585:-1 chm1:+:1391418555:-1 chm1:+:1392088553:-1 chm1:+:1394770871:-1 chm1:+:1401636053:-1 chm1:+:1426509562:-1 chm1:+:1459591852:-1 chm1:+:1460525004:-1 chm1:+:1491441523:-1 chm1:+:1499266691:-1 chm1:+:1542770067:-1 chm1:+:1616848741:-1 chm1:+:1619334643:-1 chm1:+:1638152948:-1 chm1:+:1638938010:-1 chm1:+:1647235479:-1 chm1:+:1670544774:-1 chm1:+:1673785677:-1 chm1:+:1680876365:-1 chm1:+:1692137684:-1 chm1:+:1712029954:-1 chm1:+:1725740382:-1 chm1:+:1756028773:-1 chm1:+:1848013153:-1 chm1:+:1862697748:-1 chm1:+:1863279292:-1 chm1:+:1863573468:-1 chm1:+:1873432575:-1 chm1:+:1878421627:-1 chm1:+:1880633030:-1 chm1:+:1881149402:-1 chm1:+:1881611076:-1 chm1:+:1884934908:-1 chm1:+:1894327629:-1 chm1:+:1923742639:-1 chm1:+:1934592594:-1 chm1:+:1982458727:-1 chm1:+:2017671153:-1 chm1:+:2020140425:-1 chm1:+:2021759731:-1 chm1:+:2025162377:-1 chm1:+:2051997458:-1 chm1:+:2061247147:-1 chm1:+:2065997923:-1 chm1:+:2066069250:-1 chm1:+:2066154189:-1 chm1:+:2075951367:-1 chm1:+:2076291253:-1 chm1:+:2115270571:-1 chm1:+:2117986169:-1 chm1:+:2130436270:-1 chm1:+:2145828735:-1 chm1:+:2192579253:-1 chm1:+:2195334968:-1 chm1:+:2235410509:-1 chm1:+:2278419566:-1 chm1:+:2328409683:-1 chm1:+:2329420844:-1 chm1:+:2330914239:-1 chm1:+:2340466501:-1 chm1:+:2352162273:-1 chm1:+:2364945727:-1 chm1:+:2406351622:-1 chm1:+:2438043507:-1 chm1:+:2476973852:-1 chm1:+:2479994632:-1 chm1:+:2485062527:-1 chm1:+:2488576960:-1 chm1:+:2502172039:-1 chm1:+:2511191477:-1 chm1:+:2525971520:-1 chm1:+:2549511503:-1 chm1:+:2558674133:-1 chm1:+:2565991834:-1 chm1:+:2566371895:-1 chm1:+:2585098208:-1 chm1:+:2587784713:-1 chm1:+:2591595735:-1 chm1:+:2592442589:-1 chm1:+:2646938418:-1 chm1:+:2652134519:-1 chm1:+:2663991020:-1 chm1:+:2665215308:-1 chm1:+:2670282090:-1 chm1:+:2671032552:-1 chm1:+:2671255338:-1 chm1:+:2675729446:-1 chm1:+:2676549376:-1 chm1:+:2693263789:-1 chm1:+:2696148159:-1 chm1:+:2697946774:-1 chm1:+:2700647065:-1 chm1:+:2702247626:-1 chm1:+:2703779828:-1 chm1:+:2730890965:-1 chm1:+:2738373210:-1 chm1:+:2767966401:-1 chm1:+:2804019223:-1 chm1:+:2816973060:-1 chm1:+:2851006012:-1 chm1:+:2872849006:-1 chm1:+:2884674644:-1 chm1:+:2897034021:-1 chm1:+:2994860711:-1 chm1:+:3000142860:-1 chm1:+:3004414337:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:8839250:-1 chm1:+:446162920:-1 chm1:+:494904430:-1 chm1:+:603531290:-1 chm1:+:611189128:-1 chm1:+:657825404:-1 chm1:+:667712490:-1 chm1:+:1042967201:-1 chm1:+:1211234595:-1 chm1:+:1624968946:-1 chm1:+:1750272140:-1 chm1:+:1925623241:-1 chm1:+:2031521390:-1 chm1:+:2142684367:-1 chm1:+:2260085585:-1 chm1:+:2458541666:-1 chm1:+:2631276878:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:651824290:-1 chm1:+:654730145:-1 chm1:+:674818800:-1 chm1:+:720514878:-1 chm1:+:972001253:-1 chm1:+:977054554:-1 chm1:+:1176603455:-1 chm1:+:1407969348:-1 chm1:+:1904212132:-1 chm1:+:2052048742:-1 chm1:+:2183694616:-1 chm1:+:2504394973:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:389582621:-1 chm1:+:427920253:-1 chm1:+:428765764:-1 chm1:+:457671081:-1 chm1:+:619078343:-1 chm1:+:764524030:-1 chm1:+:1088537449:-1 chm1:+:1095471300:-1 chm1:+:1265580408:-1 chm1:+:1342280544:-1 chm1:+:1374410040:-1 chm1:+:1398782369:-1 chm1:+:1433212868:-1 chm1:+:1673972521:-1 chm1:+:2993721560:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:269354790:-1 chm1:+:526486257:-1 chm1:+:567590323:-1 chm1:+:624561488:-1 chm1:+:707236387:-1 chm1:+:709203926:-1 chm1:+:992122284:-1 chm1:+:1163085303:-1 chm1:+:1216417356:-1 chm1:+:1326923549:-1 chm1:+:1331087318:-1 chm1:+:1571335820:-1 chm1:+:1623731147:-1 chm1:+:1806396238:-1 chm1:+:1809731013:-1 chm1:+:1847897525:-1 chm1:+:1919502075:-1 chm1:+:2298855395:-1 chm1:+:2353450513:-1 chm1:+:2473308219:-1 chm1:+:2667676488:-1 chm1:+:2978315122:-1 chm1:+:2997103835:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:225898186:-1 chm1:+:514950113:-1 chm1:+:544378651:-1 chm1:+:579526134:-1 chm1:+:1096925718:-1 chm1:+:1557908329:-1 chm1:+:1943255858:-1 chm1:+:2011358859:-1 chm1:+:2133782993:-1 chm1:+:2879458737:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:157952262:-1 chm1:+:173705521:-1 chm1:+:352301626:-1 chm1:+:378039240:-1 chm1:+:518665106:-1 chm1:+:618523731:-1 chm1:+:667413883:-1 chm1:+:751135718:-1 chm1:+:919576694:-1 chm1:+:940522261:-1 chm1:+:1049125065:-1 chm1:+:1206467412:-1 chm1:+:1218430556:-1 chm1:+:1222056675:-1 chm1:+:1283518718:-1 chm1:+:1500238165:-1 chm1:+:1516770207:-1 chm1:+:1520545414:-1 chm1:+:1523233437:-1 chm1:+:1634300583:-1 chm1:+:1704018347:-1 chm1:+:1746532662:-1 chm1:+:1947976994:-1 chm1:+:1975849350:-1 chm1:+:2139893139:-1 chm1:+:2141225402:-1 chm1:+:2404462872:-1 chm1:+:2492101120:-1 chm1:+:2593168762:-1 chm1:+:2654389142:-1 chm1:+:2701511851:-1 chm1:+:2765552231:-1 chm1:+:2905131490:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:218386704:-1 chm1:+:297569873:-1 chm1:+:327246612:-1 chm1:+:639877168:-1 chm1:+:679062759:-1 chm1:+:711417730:-1 chm1:+:871304880:-1 chm1:+:1157890695:-1 chm1:+:1397523907:-1 chm1:+:1424053871:-1 chm1:+:1700581736:-1 chm1:+:1737398779:-1 chm1:+:1781178897:-1 chm1:+:1854890176:-1 chm1:+:1858414687:-1 chm1:+:1897610744:-1 chm1:+:2124836581:-1 chm1:+:2267526772:-1 chm1:+:2286352838:-1 chm1:+:2337453170:-1 chm1:+:2539673161:-1 chm1:+:2592345795:-1 chm1:+:2613927355:-1 chm1:+:2768660779:-1 chm1:+:2949282556:-1 chm1:+:3060929460:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:506081228:-1 chm1:+:1523414736:-1 chm1:+:1751506215:-1 chm1:+:1825960904:-1 chm1:+:2360390122:-1 chm1:+:2848697444:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:300060526:-1 chm1:+:738505231:-1 chm1:+:1176734041:-1 chm1:+:1362004833:-1 chm1:+:1432701174:-1 chm1:+:1671371782:-1 chm1:+:1684269544:-1 chm1:+:1881603474:-1 chm1:+:2421769878:-1 chm1:+:2546328446:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:450484230:-1 chm1:+:814804179:-1 chm1:+:1308653696:-1 chm1:+:2484197086:-1 +TTATTGAGATGTTTACGTGAGAAAAGACATATAGTAAGTCCTGGACAGAGCTGGTATATCAAATATTTGATAAAACTAACTGAAGGGGGAAAACCCTTCACTTTTTCCTATAATTAAATGACCCAGAAATAATTTCAGGATTTATATATAATATATTTTTTTGAGGGGGGTAGACAGGATCTCGCTCTGTCACTCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCCCACTGCAGCCTCAACTCCTGGGACTCAAGCAATCTTCTTGCCTCAGCCTCCTGAGTTAGCTGGGACCACAGGTATTCTGCCACATCGCTGGGTTAATTTTTTATTTTTTAGTAGAGACAAGTTCTCCCTATGTTGCCCAGCTGGTCTTGAACTCCTACTTCAGCCGTCCCCTCAAAGTGCTGGGATTAGTAGGCGTGAATCACCACACCTGGGCAATCACTTATTTTCTGACTAGTTCAAGTAGTTTTAATCAGTTACTTTGTTTTATCAAAACTGCCTGAGTGTCCTAACGATTTCTAATCATTATTTTTAAATATTGTGGCATTTCCAAAGACCAATAAAGCTTTTCTTCTTCCACTTGGTGATGTGTTTGA chm1:+:85699915:-1 chm1:+:151081562:-1 chm1:+:762272322:-1 chm1:+:1160305354:-1 chm1:+:3013248338:-1 +TCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA chm1:+:32240161:-1 chm1:+:37586311:-1 chm1:+:44274819:-1 chm1:+:50472890:-1 chm1:+:65305966:-1 chm1:+:81356586:-1 chm1:+:106033303:-1 chm1:+:149828245:-1 chm1:+:153565478:-1 chm1:+:154254871:-1 chm1:+:162512024:-1 chm1:+:202334021:-1 chm1:+:220107256:-1 chm1:+:225844153:-1 chm1:+:240220701:-1 chm1:+:296519713:-1 chm1:+:345144250:-1 chm1:+:401215985:-1 chm1:+:409168822:-1 chm1:+:409841565:-1 chm1:+:449543801:-1 chm1:+:457666838:-1 chm1:+:476872404:-1 chm1:+:487660564:-1 chm1:+:493286777:-1 chm1:+:525168261:-1 chm1:+:527366469:-1 chm1:+:530117620:-1 chm1:+:534496900:-1 chm1:+:564952933:-1 chm1:+:647744494:-1 chm1:+:692480725:-1 chm1:+:714307987:-1 chm1:+:774417980:-1 chm1:+:790225851:-1 chm1:+:850875351:-1 chm1:+:924739566:-1 chm1:+:955388001:-1 chm1:+:956515819:-1 chm1:+:979767699:-1 chm1:+:1015251004:-1 chm1:+:1026881881:-1 chm1:+:1171207201:-1 chm1:+:1174089740:-1 chm1:+:1176680835:-1 chm1:+:1182721095:-1 chm1:+:1226308210:-1 chm1:+:1249028029:-1 chm1:+:1254462459:-1 chm1:+:1277184036:-1 chm1:+:1277733881:-1 chm1:+:1305994257:-1 chm1:+:1309822814:-1 chm1:+:1310341878:-1 chm1:+:1332503640:-1 chm1:+:1335099053:-1 chm1:+:1335648491:-1 chm1:+:1337863276:-1 chm1:+:1380442514:-1 chm1:+:1387371263:-1 chm1:+:1417711373:-1 chm1:+:1435032992:-1 chm1:+:1491297232:-1 chm1:+:1500253987:-1 chm1:+:1543739744:-1 chm1:+:1561293653:-1 chm1:+:1654530347:-1 chm1:+:1690466960:-1 chm1:+:1693709923:-1 chm1:+:1704878555:-1 chm1:+:1724342203:-1 chm1:+:1750642054:-1 chm1:+:1766996716:-1 chm1:+:1820078171:-1 chm1:+:1873257137:-1 chm1:+:1882774644:-1 chm1:+:1940504175:-1 chm1:+:2005206932:-1 chm1:+:2065719997:-1 chm1:+:2112165476:-1 chm1:+:2117083357:-1 chm1:+:2134940276:-1 chm1:+:2157824972:-1 chm1:+:2158381481:-1 chm1:+:2162011377:-1 chm1:+:2183839859:-1 chm1:+:2186014276:34 chm1:+:2221021440:-1 chm1:+:2289252667:-1 chm1:+:2425750113:-1 chm1:+:2458173213:-1 chm1:+:2476709455:-1 chm1:+:2479899639:-1 chm1:+:2494021000:-1 chm1:+:2555100744:-1 chm1:+:2561439016:-1 chm1:+:2666254125:-1 chm1:+:2670994672:-1 chm1:+:2674656792:-1 chm1:+:2681369803:-1 chm1:+:2698361775:-1 chm1:+:2702214401:-1 chm1:+:2709301534:-1 chm1:+:2715484536:-1 chm1:+:2731838694:-1 chm1:+:2751857046:-1 chm1:+:2767854740:-1 chm1:+:2816878406:-1 chm1:+:2828413586:-1 chm1:+:2881108002:-1 chm1:+:2881186737:-1 chm1:+:2908118856:-1 chm1:+:2914662687:-1 chm1:+:2934212638:-1 chm1:+:2986819138:-1 chm1:+:3055680398:-1 +TCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA chm1:+:176416887:-1 chm1:+:210429744:-1 chm1:+:287456043:-1 chm1:+:346833667:-1 chm1:+:492784632:-1 chm1:+:748300870:-1 chm1:+:777904587:-1 chm1:+:960661959:-1 chm1:+:1136515335:-1 chm1:+:1275472734:-1 chm1:+:1306661646:-1 chm1:+:1470526296:-1 chm1:+:1569099857:-1 chm1:+:1638966568:-1 chm1:+:1751225146:-1 chm1:+:1853076137:-1 chm1:+:1925869458:-1 chm1:+:1946070700:-1 chm1:+:2189624464:-1 chm1:+:2413862926:-1 chm1:+:2549387920:-1 chm1:+:2673277832:-1 +TCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA chm1:+:1415160486:-1 +TCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA chm1:+:545453985:-1 +TCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA chm1:+:2186014272:34 +TCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA chm1:+:2186014273:34 +TCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA chm1:+:2186014277:34 +TCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA chm1:+:2186014278:34 +TCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA chm1:+:1259804672:-1 chm1:+:2186014275:34 +TCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA chm1:+:526105916:-1 chm1:+:593730936:-1 chm1:+:1882565280:-1 chm1:+:2195383708:-1 chm1:+:2289298990:-1 +TCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA chm1:+:1306124422:-1 chm1:+:1306490834:-1 chm1:+:1307954696:-1 chm1:+:2479985251:-1 chm1:+:2501824207:-1 chm1:+:2847536400:-1 chm1:+:2904028547:-1 +TCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA chm1:+:36548930:-1 chm1:+:402209007:-1 chm1:+:604769975:-1 chm1:+:1265850350:-1 chm1:+:1335463254:-1 chm1:+:1412338153:-1 chm1:+:1754535398:-1 chm1:+:1779384695:-1 chm1:+:1893735107:-1 chm1:+:1946056896:-1 chm1:+:2073418037:-1 chm1:+:2137479788:-1 chm1:+:2333157016:-1 chm1:+:2601006352:-1 chm1:+:2676258700:-1 chm1:+:2862290796:-1 +TCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA chm1:+:276213121:-1 chm1:+:746647862:-1 chm1:+:947537795:-1 chm1:+:1174442348:-1 chm1:+:1305411543:-1 chm1:+:1543813094:-1 chm1:+:1762206420:-1 chm1:+:1820947731:-1 chm1:+:1890873960:-1 chm1:+:1892606324:-1 chm1:+:1977113628:-1 chm1:+:2003205914:-1 chm1:+:2237535088:-1 chm1:+:2261711633:-1 chm1:+:2261812046:-1 chm1:+:2279086779:-1 chm1:+:2396994155:-1 chm1:+:2541673167:-1 chm1:+:2690069186:-1 chm1:+:2827643787:-1 +TCAAACACATCACCAAGTGGAAGAAGAAAAGCTTTATTGGTCTTTGGAAATGCCACAATATTTAAAAATAATGATTAGAAATCGTTAGGACACTCAGGCAGTTTTGATAAAACAAAGTAACTGATTAAAACTACTTGAACTAGTCAGAAAATAAGTGATTGCCCAGGTGTGGTGATTCACGCCTACTAATCCCAGCACTTTGAGGGGACGGCTGAAGTAGGAGTTCAAGACCAGCTGGGCAACATAGGGAGAACTTGTCTCTACTAAAAAATAAAAAATTAACCCAGCGATGTGGCAGAATACCTGTGGTCCCAGCTAACTCAGGAGGCTGAGGCAAGAAGATTGCTTGAGTCCCAGGAGTTGAGGCTGCAGTGGGCTGAGATCGCACCACTGCACTCCAGCCTGGAGTGACAGAGCGAGATCCTGTCTACCCCCCTCAAAAAAATATATTATATATAAATCCTGAAATTATTTCTGGGTCATTTAATTATAGGAAAAAGTGAAGGGTTTTCCCCCTTCAGTTAGTTTTATCAAATATTTGATATACCAGCTCTGTCCAGGACTTACTATATGTCTTTTCTCACGTAAACATCTCAATAA chm1:+:81751663:-1 chm1:+:564807923:-1 chm1:+:885447278:-1 chm1:+:1005353911:-1 chm1:+:1324434155:-1 chm1:+:1422225591:-1 chm1:+:1696793826:-1 chm1:+:2002928616:-1 chm1:+:2284299695:-1 chm1:+:2540769459:-1 chm1:+:2864169079:-1 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTAT chm1:+:64439546:-1 chm1:+:931738100:-1 chm1:+:2018417889:-1 chm1:+:2481621800:-1 chm1:+:2639847165:-1 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTAT chm1:+:4325082:-1 chm1:+:203716652:-1 chm1:+:306835846:-1 chm1:+:557067114:-1 chm1:+:672874250:-1 chm1:+:860393480:29 chm1:+:1152024710:-1 chm1:+:1557693266:-1 chm1:+:1575341701:-1 chm1:+:1804597469:-1 chm1:+:1916790486:-1 chm1:+:2138699429:-1 chm1:+:2157042562:-1 chm1:+:2192110370:-1 chm1:+:2471055675:-1 chm1:+:2656556067:-1 chm1:+:2802494829:-1 chm1:+:2918672712:-1 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTAT chm1:+:860393489:29 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTAT chm1:+:860393477:29 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTAT chm1:+:860393491:29 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTAT chm1:+:860393478:29 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTAT chm1:+:252318659:-1 chm1:+:860393498:29 +CGAAACCATTCAGCTTTTGTTATTATCATGAACTAAATTAACCCTTCATTACCCACAGTATTCCAATCCTGAAAGAGAAGGAAGCAAATACATGTAGTTCCAAACCACAAAATAATTTTATTCCACCAGATAGTTCATCTAAGGCTAACGCTAAAAAATCCAATCAGCTTGCATAAAGCTATACACAAAGAGAAAACAGTGCTAAGATAACAACAATGCTGCTTCCTGGATTGTTTTTTTCTTTTTCTTTCTCTCCCTACTCCCCAGCAAATAGATGTATCTGAACCACCAGTCACTTATTCAAATATTCATAGATTTTAGAATGGTCTGGAAATGTAGGCTAGTTGCTATGAGAAAAAAAATAAAAGAAAAGAAAAGAATTGAAATAAAGACACACTATAGACCAAAAGGTTAACTAGGATATTTTGATAAATCCCTGATACCTGCTGGCTCAACTTCAGTGCCAAAGAAAACACCAACTGTAAAGGGTCCAAGCTGGAGCCATTAGTGACCGGAAAGGAAAGGTAGCAAAGGTCGTACTTCAGCCCCTCTCTTTCTTACAAAGGACCAGCAAACCAAAATAAACTGCCTTTTCTTTAT chm1:+:860393497:29 +ATAAAGAAAAGGCAGTTTATTTTGGTTTGCTGGTCCTTTGTAAGAAAGAGAGGGGCTGAAGTACGACCTTTGCTACCTTTCCTTTCCGGTCACTAATGGCTCCAGCTTGGACCCTTTACAGTTGGTGTTTTCTTTGGCACTGAAGTTGAGCCAGCAGGTATCAGGGATTTATCAAAATATCCTAGTTAACCTTTTGGTCTATAGTGTGTCTTTATTTCAATTCTTTTCTTTTCTTTTATTTTTTTTCTCATAGCAACTAGCCTACATTTCCAGACCATTCTAAAATCTATGAATATTTGAATAAGTGACTGGTGGTTCAGATACATCTATTTGCTGGGGAGTAGGGAGAGAAAGAAAAAGAAAAAAACAATCCAGGAAGCAGCATTGTTGTTATCTTAGCACTGTTTTCTCTTTGTGTATAGCTTTATGCAAGCTGATTGGATTTTTTAGCGTTAGCCTTAGATGAACTATCTGGTGGAATAAAATTATTTTGTGGTTTGGAACTACATGTATTTGCTTCCTTCTCTTTCAGGATTGGAATACTGTGGGTAATGAAGGGTTAATTTAGTTCATGATAATAACAAAAGCTGAATGGTTTCG chm1:+:447463216:-1 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTAC chm1:+:566211801:25 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTAC chm1:+:566211793:25 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTAC chm1:+:566211794:25 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTAC chm1:+:566211791:25 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTAC chm1:+:566211795:25 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTAC chm1:+:566211796:25 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTAC chm1:+:2552193677:-1 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTAC chm1:+:566211800:25 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTAC chm1:+:1832628578:-1 +TCAGCATCCCACCCATGTTTGTCTGATGCTAAAAACCTTGTTCTCTTACTCCCTACAAACTGCCCTCGCTTTGGTTAAAGCACTTGTTTTGTTAGAAGTTCTGTGAGAAATCTCGCTGCCACCAAGAAACTCACCCTCAAAATGCTTCCCAGAGTCTAAATCATTTCCCTAAGCCTTAACATTCTCGTCTTGTTATTTTTTCCCCAAAACATTGACAATATTTCTCACTGAGGACAGGATGATGTCAGAAGTTACTTAACCCACACTGAAGACATCTAATTATAATATCTGACTCTAAACTGACCTTCCATGGCTTCCCTATATTAGTTCTCCACTCTAGTCAAATTTTCTATTTACAATGGCCTGTTAATTAATTGTGTTTTCTTTTCTTCTGCTTTGCTTTTCTACTTTCATTTAGTTTGGAATGTTTTTTTTCTTTCTCTTCTTGTAAAATCCTGCCATTTCTTAAAGCACATGAGCTAGTGGAGGTTGGAAGGTAGGAGCCATAGGAAGTGGAAACTCCTGTGGGCTCTACCCTTCACTTTATTCAGAATCTGGCTCAAACCCGCTTCCAACAGCTATTACTCAGGTCCCAGCTAC chm1:+:566211799:25 +GTAGCTGGGACCTGAGTAATAGCTGTTGGAAGCGGGTTTGAGCCAGATTCTGAATAAAGTGAAGGGTAGAGCCCACAGGAGTTTCCACTTCCTATGGCTCCTACCTTCCAACCTCCACTAGCTCATGTGCTTTAAGAAATGGCAGGATTTTACAAGAAGAGAAAGAAAAAAAACATTCCAAACTAAATGAAAGTAGAAAAGCAAAGCAGAAGAAAAGAAAACACAATTAATTAACAGGCCATTGTAAATAGAAAATTTGACTAGAGTGGAGAACTAATATAGGGAAGCCATGGAAGGTCAGTTTAGAGTCAGATATTATAATTAGATGTCTTCAGTGTGGGTTAAGTAACTTCTGACATCATCCTGTCCTCAGTGAGAAATATTGTCAATGTTTTGGGGAAAAAATAACAAGACGAGAATGTTAAGGCTTAGGGAAATGATTTAGACTCTGGGAAGCATTTTGAGGGTGAGTTTCTTGGTGGCAGCGAGATTTCTCACAGAACTTCTAACAAAACAAGTGCTTTAACCAAAGCGAGGGCAGTTTGTAGGGAGTAAGAGAACAAGGTTTTTAGCATCAGACAAACATGGGTGGGATGCTGA chm1:+:1816864958:-1 +GTAGCTGGGACCTGAGTAATAGCTGTTGGAAGCGGGTTTGAGCCAGATTCTGAATAAAGTGAAGGGTAGAGCCCACAGGAGTTTCCACTTCCTATGGCTCCTACCTTCCAACCTCCACTAGCTCATGTGCTTTAAGAAATGGCAGGATTTTACAAGAAGAGAAAGAAAAAAAACATTCCAAACTAAATGAAAGTAGAAAAGCAAAGCAGAAGAAAAGAAAACACAATTAATTAACAGGCCATTGTAAATAGAAAATTTGACTAGAGTGGAGAACTAATATAGGGAAGCCATGGAAGGTCAGTTTAGAGTCAGATATTATAATTAGATGTCTTCAGTGTGGGTTAAGTAACTTCTGACATCATCCTGTCCTCAGTGAGAAATATTGTCAATGTTTTGGGGAAAAAATAACAAGACGAGAATGTTAAGGCTTAGGGAAATGATTTAGACTCTGGGAAGCATTTTGAGGGTGAGTTTCTTGGTGGCAGCGAGATTTCTCACAGAACTTCTAACAAAACAAGTGCTTTAACCAAAGCGAGGGCAGTTTGTAGGGAGTAAGAGAACAAGGTTTTTAGCATCAGACAAACATGGGTGGGATGCTGA chm1:+:2306806226:-1 +GTAGCTGGGACCTGAGTAATAGCTGTTGGAAGCGGGTTTGAGCCAGATTCTGAATAAAGTGAAGGGTAGAGCCCACAGGAGTTTCCACTTCCTATGGCTCCTACCTTCCAACCTCCACTAGCTCATGTGCTTTAAGAAATGGCAGGATTTTACAAGAAGAGAAAGAAAAAAAACATTCCAAACTAAATGAAAGTAGAAAAGCAAAGCAGAAGAAAAGAAAACACAATTAATTAACAGGCCATTGTAAATAGAAAATTTGACTAGAGTGGAGAACTAATATAGGGAAGCCATGGAAGGTCAGTTTAGAGTCAGATATTATAATTAGATGTCTTCAGTGTGGGTTAAGTAACTTCTGACATCATCCTGTCCTCAGTGAGAAATATTGTCAATGTTTTGGGGAAAAAATAACAAGACGAGAATGTTAAGGCTTAGGGAAATGATTTAGACTCTGGGAAGCATTTTGAGGGTGAGTTTCTTGGTGGCAGCGAGATTTCTCACAGAACTTCTAACAAAACAAGTGCTTTAACCAAAGCGAGGGCAGTTTGTAGGGAGTAAGAGAACAAGGTTTTTAGCATCAGACAAACATGGGTGGGATGCTGA chm1:+:1390654051:-1 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCA chm1:+:673211764:-1 chm1:+:731863951:-1 chm1:+:1326239427:-1 chm1:+:2601126721:-1 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCA chm1:+:286393809:-1 chm1:+:640830390:30 chm1:+:1014231236:-1 chm1:+:2814732516:-1 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCA chm1:+:640830387:30 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCA chm1:+:640830392:30 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCA chm1:+:640830388:30 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCA chm1:+:640830391:30 +GTTTCTCTTCTAATTGGAGCCTCCTTAAATTGAAGGAGTAAATAATTACATTTTATCAGAAAAGTTGAATCTGCAGAGATTCTAGTTTTATAGGTGGAATACAAATGCTAGAAAACAGCATTGAATCTCAATACAAGCACTTACTAAAATCTCATTTCTCTGGCCATAAAAATTGTTGGGTGAGTTCAAAAATGTACAGAAAATTATTTTTATAATGAACTGTAATTGGCAGTATATTTAACAAACTTCAGTAACTTGCCATATATATAGATAATTGATTCCATTAATTGAGTTGTGATCTCCTTGAGGGCAAGAACTAACTGGTCTCATAACCACCTCCAGAAACTGAGTTTTCCTCTAGAAAAATCCATATTTCCAGTTTTTGTATTTGTCAGCACATGCTGGTTACTAGTCCATTTTTTTTTTAACTGGAAACAACATTTAGAAGCATTAGCATTAATTAGATGATTAATACATATATTTGCAAACAAACATAGAACCTGTTTATTAAAAGAGGAAGCTAAGATATTCCAGAAGAAAGGAACCCCTGCAATGCCATGACAAATGTATGTAACAGTGATTCTCTAAGTTCTTCCCCCA chm1:+:640830397:30 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTT chm1:+:258685761:-1 chm1:+:415612205:-1 chm1:+:767771735:-1 chm1:+:787403702:-1 chm1:+:870957878:-1 chm1:+:903798889:-1 chm1:+:953496471:-1 chm1:+:986820062:-1 chm1:+:1075788353:-1 chm1:+:1447260415:-1 chm1:+:1478367692:-1 chm1:+:1554696196:-1 chm1:+:2342871816:-1 chm1:+:2909934162:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTT chm1:+:417404291:-1 chm1:+:502359753:-1 chm1:+:714260563:-1 chm1:+:855780587:-1 chm1:+:2186314036:-1 chm1:+:2569620761:-1 chm1:+:2824316445:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTT chm1:+:1663236833:-1 chm1:+:1925779784:-1 chm1:+:2775267556:-1 chm1:+:2957488029:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTT chm1:+:65958645:-1 chm1:+:294320471:-1 chm1:+:557857596:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTT chm1:+:607238607:-1 chm1:+:1215309284:-1 chm1:+:1316431748:-1 chm1:+:1459856889:-1 chm1:+:1777507351:-1 chm1:+:2608872848:-1 chm1:+:2608873750:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTT chm1:+:1046768935:-1 chm1:+:1966415992:-1 chm1:+:1995519297:-1 chm1:+:2966502338:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTT chm1:+:283100259:-1 chm1:+:396157472:-1 chm1:+:760176032:-1 chm1:+:845926182:-1 chm1:+:918719224:-1 chm1:+:976497870:-1 chm1:+:1000724093:-1 chm1:+:1340686991:-1 chm1:+:1448394219:-1 chm1:+:1451168948:-1 chm1:+:1841705938:-1 chm1:+:2116846186:-1 chm1:+:2559536698:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTT chm1:+:115176619:-1 chm1:+:301181619:-1 chm1:+:693565187:-1 chm1:+:1064778169:-1 chm1:+:1197334837:-1 chm1:+:1201269854:-1 chm1:+:1283534251:-1 chm1:+:1327182794:-1 chm1:+:1475600990:-1 chm1:+:1613837455:-1 chm1:+:1668854294:-1 chm1:+:2993356998:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTT chm1:+:1033718350:-1 chm1:+:1255224148:-1 chm1:+:1317021823:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTT chm1:+:257914913:-1 chm1:+:379065668:-1 chm1:+:807613991:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTT chm1:+:409577205:-1 chm1:+:527879682:-1 chm1:+:690791077:-1 chm1:+:1207822560:-1 chm1:+:1530401287:-1 chm1:+:1562745538:-1 chm1:+:1762452394:-1 chm1:+:2178637303:-1 chm1:+:2362146014:-1 chm1:+:2393962476:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTT chm1:+:685818828:-1 chm1:+:1687087062:-1 chm1:+:2756323510:-1 chm1:+:2948655717:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTT chm1:+:152415061:-1 chm1:+:593164587:-1 chm1:+:1003338139:-1 chm1:+:1791400641:-1 chm1:+:2530359686:-1 chm1:+:2925401302:-1 +TATAATGAAGGTAACATCCCCCTTCAAAGGCCAAGATCAGGTCAGGTTTGCAATTCATTATAAAAGACTCAGGTCTCTAAGCTTGGCATTTCTCAACTGTGACGACCAACCTACTACCTATGAGACAATCCACCCTTACACCTATTTGTGTCACCCCTGTAGGACATGCTAGAGTGGTGGGAGCCAAAACAAACATAAAGTTCATACTATTGCTGTGCAATGAGTAATATGTGACCAGAGTCTTATGCTTTTGCAGCATCCATGAAACTAACTTGTCAACAACTGACTTAGGGTAAATGCTCAGATTGCTTACCAGTTTCGGTACCAATATTTCTATTTAGTAAGAATTTAAGCAAATTGCTTCCTCCTATATCTAATAGTGATAGAATTAAGTTCCAAAGCACCAACTTAGGGTGGTCAGTCAATTATATGTCATTTTTGTTCCAAGTCTTCAGGACAAATTGACTTTCAAAAACAAGTTTAAGAACGTTTACTATGTACTAATTGTTAAGCAACAAACATCATTCCATGTAAGTAGGTATTCTATAGACAGTCCACGTAGCTCAGGCAAGATACAGTCAAATTCATTTAATTTATCTT chm1:+:107341580:-1 chm1:+:213561357:-1 chm1:+:256359779:-1 chm1:+:378383397:-1 chm1:+:431062374:-1 chm1:+:432193606:-1 chm1:+:533578817:-1 chm1:+:806082382:-1 chm1:+:813071162:-1 chm1:+:1337660031:-1 chm1:+:1577974742:-1 chm1:+:1584335316:-1 chm1:+:1766039520:-1 chm1:+:1850894348:-1 chm1:+:1970167166:-1 chm1:+:2056148906:-1 chm1:+:2261912580:-1 chm1:+:2554017940:-1 chm1:+:3030059607:-1 +AAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA chm1:+:1345769314:-1 +AAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA chm1:+:1318672461:30 +AAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA chm1:+:1318672462:30 +AAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA chm1:+:1318672463:30 +AAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA chm1:+:1318672466:30 +AAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA chm1:+:1318672467:30 +AAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA chm1:+:1318672464:30 +AAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA chm1:+:1318672465:30 +AAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA chm1:+:1801919711:-1 +AAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA chm1:+:1318672471:30 +AAGATAAATTAAATGAATTTGACTGTATCTTGCCTGAGCTACGTGGACTGTCTATAGAATACCTACTTACATGGAATGATGTTTGTTGCTTAACAATTAGTACATAGTAAACGTTCTTAAACTTGTTTTTGAAAGTCAATTTGTCCTGAAGACTTGGAACAAAAATGACATATAATTGACTGACCACCCTAAGTTGGTGCTTTGGAACTTAATTCTATCACTATTAGATATAGGAGGAAGCAATTTGCTTAAATTCTTACTAAATAGAAATATTGGTACCGAAACTGGTAAGCAATCTGAGCATTTACCCTAAGTCAGTTGTTGACAAGTTAGTTTCATGGATGCTGCAAAAGCATAAGACTCTGGTCACATATTACTCATTGCACAGCAATAGTATGAACTTTATGTTTGTTTTGGCTCCCACCACTCTAGCATGTCCTACAGGGGTGACACAAATAGGTGTAAGGGTGGATTGTCTCATAGGTAGTAGGTTGGTCGTCACAGTTGAGAAATGCCAAGCTTAGAGACCTGAGTCTTTTATAATGAATTGCAAACCTGACCTGATCTTGGCCTTTGAAGGGGGATGTTACCTTCATTATA chm1:+:894581891:-1 chm1:+:1318672473:30 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGA chm1:+:436925757:-1 chm1:+:478299777:29 chm1:+:778196210:-1 chm1:+:2260098203:-1 chm1:+:2975540090:-1 chm1:+:2989228790:-1 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGA chm1:+:478299782:29 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGA chm1:+:1797725902:-1 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGA chm1:+:478299775:29 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGA chm1:+:2584477743:-1 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGA chm1:+:478299778:29 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGA chm1:+:478299787:29 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGA chm1:+:1835949411:-1 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGA chm1:+:478299786:29 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGA chm1:+:1713640923:-1 +GAAGACAACTATGAACACAGAATCTTATGTCTAATAAAATACTCATTAGAAATGAAGATGAAAATGGTATAGAATTCCAGCAGAGCTCTCCTAAAGAATGATTAAAGGAAAATTCTCTAGACACCCAATGAAACCTGTCTTTACAGTTTCGAGGCATCTTAGAATATCAGGAAAAGAAGAAAACTAGTAAGAAAAATTTGAAAGATACAACAGAATTTCTTCTTTTGAAGTTTCCTAAACTACACTTTGAAAAGTCAAAAGGAAAGATTATGACTTTCGATATGCTTCTAAATATAGAGAAAGCATTTAAGACATTATATTAAAGGGAGAAGGGGTAAAGGGTGTAACAAGTAAAGTTTACACATTTTGCTCAAACGGCAAATTGACAACACCAATAAACTATAAATTTTATATATACATATACATACATATATACACATACGATACATACCACATATATATAACATGCATAGAAATTATAAGCTATGCACATAGATAGTACTCAAAAATAATACAGGTTAAATCAATCAAATTGGTTTTATTAGATTTTAAAAAATTTTTTTATTTAATCTATTTAAATGATTTTATCCATTTTAAAGA chm1:+:2011290247:-1 +TCTTTAAAATGGATAAAATCATTTAAATAGATTAAATAAAAAAATTTTTTAAAATCTAATAAAACCAATTTGATTGATTTAACCTGTATTATTTTTGAGTACTATCTATGTGCATAGCTTATAATTTCTATGCATGTTATATATATGTGGTATGTATCGTATGTGTATATATGTATGTATATGTATATATAAAATTTATAGTTTATTGGTGTTGTCAATTTGCCGTTTGAGCAAAATGTGTAAACTTTACTTGTTACACCCTTTACCCCTTCTCCCTTTAATATAATGTCTTAAATGCTTTCTCTATATTTAGAAGCATATCGAAAGTCATAATCTTTCCTTTTGACTTTTCAAAGTGTAGTTTAGGAAACTTCAAAAGAAGAAATTCTGTTGTATCTTTCAAATTTTTCTTACTAGTTTTCTTCTTTTCCTGATATTCTAAGATGCCTCGAAACTGTAAAGACAGGTTTCATTGGGTGTCTAGAGAATTTTCCTTTAATCATTCTTTAGGAGAGCTCTGCTGGAATTCTATACCATTTTCATCTTCATTTCTAATGAGTATTTTATTAGACATAAGATTCTGTGTTCATAGTTGTCTTC chm1:+:2824614570:-1 +TCTTTAAAATGGATAAAATCATTTAAATAGATTAAATAAAAAAATTTTTTAAAATCTAATAAAACCAATTTGATTGATTTAACCTGTATTATTTTTGAGTACTATCTATGTGCATAGCTTATAATTTCTATGCATGTTATATATATGTGGTATGTATCGTATGTGTATATATGTATGTATATGTATATATAAAATTTATAGTTTATTGGTGTTGTCAATTTGCCGTTTGAGCAAAATGTGTAAACTTTACTTGTTACACCCTTTACCCCTTCTCCCTTTAATATAATGTCTTAAATGCTTTCTCTATATTTAGAAGCATATCGAAAGTCATAATCTTTCCTTTTGACTTTTCAAAGTGTAGTTTAGGAAACTTCAAAAGAAGAAATTCTGTTGTATCTTTCAAATTTTTCTTACTAGTTTTCTTCTTTTCCTGATATTCTAAGATGCCTCGAAACTGTAAAGACAGGTTTCATTGGGTGTCTAGAGAATTTTCCTTTAATCATTCTTTAGGAGAGCTCTGCTGGAATTCTATACCATTTTCATCTTCATTTCTAATGAGTATTTTATTAGACATAAGATTCTGTGTTCATAGTTGTCTTC chm1:+:1997113040:-1 +TCTTTAAAATGGATAAAATCATTTAAATAGATTAAATAAAAAAATTTTTTAAAATCTAATAAAACCAATTTGATTGATTTAACCTGTATTATTTTTGAGTACTATCTATGTGCATAGCTTATAATTTCTATGCATGTTATATATATGTGGTATGTATCGTATGTGTATATATGTATGTATATGTATATATAAAATTTATAGTTTATTGGTGTTGTCAATTTGCCGTTTGAGCAAAATGTGTAAACTTTACTTGTTACACCCTTTACCCCTTCTCCCTTTAATATAATGTCTTAAATGCTTTCTCTATATTTAGAAGCATATCGAAAGTCATAATCTTTCCTTTTGACTTTTCAAAGTGTAGTTTAGGAAACTTCAAAAGAAGAAATTCTGTTGTATCTTTCAAATTTTTCTTACTAGTTTTCTTCTTTTCCTGATATTCTAAGATGCCTCGAAACTGTAAAGACAGGTTTCATTGGGTGTCTAGAGAATTTTCCTTTAATCATTCTTTAGGAGAGCTCTGCTGGAATTCTATACCATTTTCATCTTCATTTCTAATGAGTATTTTATTAGACATAAGATTCTGTGTTCATAGTTGTCTTC chm1:+:45022485:-1 chm1:+:454069831:-1 chm1:+:751558797:-1 chm1:+:1309153835:-1 chm1:+:2077811147:-1 chm1:+:2194535829:-1 chm1:+:2712762338:-1 chm1:+:2814462924:-1 +CTTTCTTTACAGGTTTCTTAATCGATATCTAACAGAGGAGAGACAGAAACACATCCAATGTCAAAGCTAATAAAAGTTCCAACCTAGACCAGATCTTCTTACTCTTAGACCTGTTCAAGTGCCAATAAACCACATTGTTTCTGCCGAAGGTCAGAAGGGACTAATTGTAAAGTCAAGTCTGGATAAACTCTGCTCTACTATACTTAATTACGAGATTTGCCAGTTACAGGCAAATATTAAGTAACGTTTGAACAAAATACAGAAATATAGTATTACTATAATTTTAGATAGAACCTAGTTATCTTATTAAAATATCGTTTTGTTAGCACATCAATCCATGTACTATAAAGAGTATGTTTTAACAAGTTCTGAAATATTAGTACTTTTTAAGAAAAGGTTACATTTCTGGAAGAATATTTGGGAATGGACTAAATCTCATTTTAATCCTGACCTAAAATGATTATAAATAAATCATAAGTGATAAATATTCTACTTTGAAAATTTATACATATGTTTACAAATGTTACTATAATATAATAGTGCCATTCCGTTTCATAGCCTAAATGTGAATGTGTGGTACAAGCAAAAATAATGAAATAC chm1:+:189980725:-1 chm1:+:336168653:-1 chm1:+:1052198587:-1 chm1:+:1340229932:-1 chm1:+:2037249382:-1 chm1:+:2124255994:-1 chm1:+:2735147326:-1 +CTTTCTTTACAGGTTTCTTAATCGATATCTAACAGAGGAGAGACAGAAACACATCCAATGTCAAAGCTAATAAAAGTTCCAACCTAGACCAGATCTTCTTACTCTTAGACCTGTTCAAGTGCCAATAAACCACATTGTTTCTGCCGAAGGTCAGAAGGGACTAATTGTAAAGTCAAGTCTGGATAAACTCTGCTCTACTATACTTAATTACGAGATTTGCCAGTTACAGGCAAATATTAAGTAACGTTTGAACAAAATACAGAAATATAGTATTACTATAATTTTAGATAGAACCTAGTTATCTTATTAAAATATCGTTTTGTTAGCACATCAATCCATGTACTATAAAGAGTATGTTTTAACAAGTTCTGAAATATTAGTACTTTTTAAGAAAAGGTTACATTTCTGGAAGAATATTTGGGAATGGACTAAATCTCATTTTAATCCTGACCTAAAATGATTATAAATAAATCATAAGTGATAAATATTCTACTTTGAAAATTTATACATATGTTTACAAATGTTACTATAATATAATAGTGCCATTCCGTTTCATAGCCTAAATGTGAATGTGTGGTACAAGCAAAAATAATGAAATAC chm1:+:162975323:-1 chm1:+:863228182:-1 chm1:+:969768789:-1 chm1:+:2133585283:-1 chm1:+:2401537791:-1 chm1:+:2763282801:-1 +CTTTCTTTACAGGTTTCTTAATCGATATCTAACAGAGGAGAGACAGAAACACATCCAATGTCAAAGCTAATAAAAGTTCCAACCTAGACCAGATCTTCTTACTCTTAGACCTGTTCAAGTGCCAATAAACCACATTGTTTCTGCCGAAGGTCAGAAGGGACTAATTGTAAAGTCAAGTCTGGATAAACTCTGCTCTACTATACTTAATTACGAGATTTGCCAGTTACAGGCAAATATTAAGTAACGTTTGAACAAAATACAGAAATATAGTATTACTATAATTTTAGATAGAACCTAGTTATCTTATTAAAATATCGTTTTGTTAGCACATCAATCCATGTACTATAAAGAGTATGTTTTAACAAGTTCTGAAATATTAGTACTTTTTAAGAAAAGGTTACATTTCTGGAAGAATATTTGGGAATGGACTAAATCTCATTTTAATCCTGACCTAAAATGATTATAAATAAATCATAAGTGATAAATATTCTACTTTGAAAATTTATACATATGTTTACAAATGTTACTATAATATAATAGTGCCATTCCGTTTCATAGCCTAAATGTGAATGTGTGGTACAAGCAAAAATAATGAAATAC chm1:+:1205816963:-1 chm1:+:1218639388:-1 chm1:+:1454438921:-1 chm1:+:1501886406:-1 chm1:+:1641695894:-1 +CTTTCTTTACAGGTTTCTTAATCGATATCTAACAGAGGAGAGACAGAAACACATCCAATGTCAAAGCTAATAAAAGTTCCAACCTAGACCAGATCTTCTTACTCTTAGACCTGTTCAAGTGCCAATAAACCACATTGTTTCTGCCGAAGGTCAGAAGGGACTAATTGTAAAGTCAAGTCTGGATAAACTCTGCTCTACTATACTTAATTACGAGATTTGCCAGTTACAGGCAAATATTAAGTAACGTTTGAACAAAATACAGAAATATAGTATTACTATAATTTTAGATAGAACCTAGTTATCTTATTAAAATATCGTTTTGTTAGCACATCAATCCATGTACTATAAAGAGTATGTTTTAACAAGTTCTGAAATATTAGTACTTTTTAAGAAAAGGTTACATTTCTGGAAGAATATTTGGGAATGGACTAAATCTCATTTTAATCCTGACCTAAAATGATTATAAATAAATCATAAGTGATAAATATTCTACTTTGAAAATTTATACATATGTTTACAAATGTTACTATAATATAATAGTGCCATTCCGTTTCATAGCCTAAATGTGAATGTGTGGTACAAGCAAAAATAATGAAATAC chm1:+:1434117311:-1 +CTTTCTTTACAGGTTTCTTAATCGATATCTAACAGAGGAGAGACAGAAACACATCCAATGTCAAAGCTAATAAAAGTTCCAACCTAGACCAGATCTTCTTACTCTTAGACCTGTTCAAGTGCCAATAAACCACATTGTTTCTGCCGAAGGTCAGAAGGGACTAATTGTAAAGTCAAGTCTGGATAAACTCTGCTCTACTATACTTAATTACGAGATTTGCCAGTTACAGGCAAATATTAAGTAACGTTTGAACAAAATACAGAAATATAGTATTACTATAATTTTAGATAGAACCTAGTTATCTTATTAAAATATCGTTTTGTTAGCACATCAATCCATGTACTATAAAGAGTATGTTTTAACAAGTTCTGAAATATTAGTACTTTTTAAGAAAAGGTTACATTTCTGGAAGAATATTTGGGAATGGACTAAATCTCATTTTAATCCTGACCTAAAATGATTATAAATAAATCATAAGTGATAAATATTCTACTTTGAAAATTTATACATATGTTTACAAATGTTACTATAATATAATAGTGCCATTCCGTTTCATAGCCTAAATGTGAATGTGTGGTACAAGCAAAAATAATGAAATAC chm1:+:104707399:-1 chm1:+:1201526843:-1 +CTTTCTTTACAGGTTTCTTAATCGATATCTAACAGAGGAGAGACAGAAACACATCCAATGTCAAAGCTAATAAAAGTTCCAACCTAGACCAGATCTTCTTACTCTTAGACCTGTTCAAGTGCCAATAAACCACATTGTTTCTGCCGAAGGTCAGAAGGGACTAATTGTAAAGTCAAGTCTGGATAAACTCTGCTCTACTATACTTAATTACGAGATTTGCCAGTTACAGGCAAATATTAAGTAACGTTTGAACAAAATACAGAAATATAGTATTACTATAATTTTAGATAGAACCTAGTTATCTTATTAAAATATCGTTTTGTTAGCACATCAATCCATGTACTATAAAGAGTATGTTTTAACAAGTTCTGAAATATTAGTACTTTTTAAGAAAAGGTTACATTTCTGGAAGAATATTTGGGAATGGACTAAATCTCATTTTAATCCTGACCTAAAATGATTATAAATAAATCATAAGTGATAAATATTCTACTTTGAAAATTTATACATATGTTTACAAATGTTACTATAATATAATAGTGCCATTCCGTTTCATAGCCTAAATGTGAATGTGTGGTACAAGCAAAAATAATGAAATAC chm1:+:62742648:-1 chm1:+:93490496:-1 chm1:+:521547174:-1 chm1:+:551672492:-1 chm1:+:1037685689:-1 chm1:+:1201080644:-1 chm1:+:1711259548:-1 chm1:+:1788735912:-1 chm1:+:2182325325:-1 +CTTTCTTTACAGGTTTCTTAATCGATATCTAACAGAGGAGAGACAGAAACACATCCAATGTCAAAGCTAATAAAAGTTCCAACCTAGACCAGATCTTCTTACTCTTAGACCTGTTCAAGTGCCAATAAACCACATTGTTTCTGCCGAAGGTCAGAAGGGACTAATTGTAAAGTCAAGTCTGGATAAACTCTGCTCTACTATACTTAATTACGAGATTTGCCAGTTACAGGCAAATATTAAGTAACGTTTGAACAAAATACAGAAATATAGTATTACTATAATTTTAGATAGAACCTAGTTATCTTATTAAAATATCGTTTTGTTAGCACATCAATCCATGTACTATAAAGAGTATGTTTTAACAAGTTCTGAAATATTAGTACTTTTTAAGAAAAGGTTACATTTCTGGAAGAATATTTGGGAATGGACTAAATCTCATTTTAATCCTGACCTAAAATGATTATAAATAAATCATAAGTGATAAATATTCTACTTTGAAAATTTATACATATGTTTACAAATGTTACTATAATATAATAGTGCCATTCCGTTTCATAGCCTAAATGTGAATGTGTGGTACAAGCAAAAATAATGAAATAC chm1:+:512442160:-1 chm1:+:1740424217:-1 chm1:+:2017149127:-1 chm1:+:2138799435:-1 +CTTTCTTTACAGGTTTCTTAATCGATATCTAACAGAGGAGAGACAGAAACACATCCAATGTCAAAGCTAATAAAAGTTCCAACCTAGACCAGATCTTCTTACTCTTAGACCTGTTCAAGTGCCAATAAACCACATTGTTTCTGCCGAAGGTCAGAAGGGACTAATTGTAAAGTCAAGTCTGGATAAACTCTGCTCTACTATACTTAATTACGAGATTTGCCAGTTACAGGCAAATATTAAGTAACGTTTGAACAAAATACAGAAATATAGTATTACTATAATTTTAGATAGAACCTAGTTATCTTATTAAAATATCGTTTTGTTAGCACATCAATCCATGTACTATAAAGAGTATGTTTTAACAAGTTCTGAAATATTAGTACTTTTTAAGAAAAGGTTACATTTCTGGAAGAATATTTGGGAATGGACTAAATCTCATTTTAATCCTGACCTAAAATGATTATAAATAAATCATAAGTGATAAATATTCTACTTTGAAAATTTATACATATGTTTACAAATGTTACTATAATATAATAGTGCCATTCCGTTTCATAGCCTAAATGTGAATGTGTGGTACAAGCAAAAATAATGAAATAC chm1:+:106332579:-1 chm1:+:253328246:-1 chm1:+:290423180:-1 chm1:+:301543411:-1 chm1:+:302332160:-1 chm1:+:372409961:-1 chm1:+:533926022:-1 chm1:+:576672336:-1 chm1:+:579524289:-1 chm1:+:666088055:-1 chm1:+:705511672:-1 chm1:+:750754119:-1 chm1:+:805758511:-1 chm1:+:858884060:-1 chm1:+:858884096:-1 chm1:+:892954324:-1 chm1:+:924129043:-1 chm1:+:999119992:-1 chm1:+:1059957681:-1 chm1:+:1068681686:-1 chm1:+:1131292940:-1 chm1:+:1167772539:-1 chm1:+:1193359079:-1 chm1:+:1263504991:-1 chm1:+:1285546364:-1 chm1:+:1353242798:-1 chm1:+:1408952614:-1 chm1:+:1557284608:-1 chm1:+:1614611585:-1 chm1:+:1623357736:-1 chm1:+:1694487485:-1 chm1:+:1708803036:-1 chm1:+:1787374553:-1 chm1:+:1790426322:-1 chm1:+:1793533669:-1 chm1:+:1842491661:-1 chm1:+:1852777421:-1 chm1:+:1856264056:-1 chm1:+:2068296433:-1 chm1:+:2120480144:-1 chm1:+:2128780561:-1 chm1:+:2131496999:-1 chm1:+:2164311536:-1 chm1:+:2169633106:-1 chm1:+:2184831278:-1 chm1:+:2258288192:-1 chm1:+:2368386022:-1 chm1:+:2394732859:-1 chm1:+:2652124799:-1 chm1:+:2885272879:-1 chm1:+:2935143939:-1 chm1:+:2982134606:-1 chm1:+:3023462993:-1 +CTTTCTTTACAGGTTTCTTAATCGATATCTAACAGAGGAGAGACAGAAACACATCCAATGTCAAAGCTAATAAAAGTTCCAACCTAGACCAGATCTTCTTACTCTTAGACCTGTTCAAGTGCCAATAAACCACATTGTTTCTGCCGAAGGTCAGAAGGGACTAATTGTAAAGTCAAGTCTGGATAAACTCTGCTCTACTATACTTAATTACGAGATTTGCCAGTTACAGGCAAATATTAAGTAACGTTTGAACAAAATACAGAAATATAGTATTACTATAATTTTAGATAGAACCTAGTTATCTTATTAAAATATCGTTTTGTTAGCACATCAATCCATGTACTATAAAGAGTATGTTTTAACAAGTTCTGAAATATTAGTACTTTTTAAGAAAAGGTTACATTTCTGGAAGAATATTTGGGAATGGACTAAATCTCATTTTAATCCTGACCTAAAATGATTATAAATAAATCATAAGTGATAAATATTCTACTTTGAAAATTTATACATATGTTTACAAATGTTACTATAATATAATAGTGCCATTCCGTTTCATAGCCTAAATGTGAATGTGTGGTACAAGCAAAAATAATGAAATAC chm1:+:25092283:-1 chm1:+:39399060:-1 chm1:+:111612905:-1 chm1:+:152466189:-1 chm1:+:185007213:-1 chm1:+:300936264:-1 chm1:+:313522462:-1 chm1:+:379954776:-1 chm1:+:492578915:-1 chm1:+:504169184:-1 chm1:+:534217794:-1 chm1:+:557923670:-1 chm1:+:725601382:-1 chm1:+:747138699:-1 chm1:+:887358722:-1 chm1:+:919904951:-1 chm1:+:922680442:-1 chm1:+:1021613735:-1 chm1:+:1057769382:-1 chm1:+:1084117015:-1 chm1:+:1106071654:-1 chm1:+:1152886089:-1 chm1:+:1170860412:-1 chm1:+:1211829494:-1 chm1:+:1223372669:-1 chm1:+:1258087920:-1 chm1:+:1275559158:-1 chm1:+:1318253331:-1 chm1:+:1384834457:-1 chm1:+:1390367087:-1 chm1:+:1408150608:-1 chm1:+:1417827127:-1 chm1:+:1443693041:-1 chm1:+:1521717810:-1 chm1:+:1538735990:-1 chm1:+:1717974608:-1 chm1:+:1723990861:-1 chm1:+:1927839857:-1 chm1:+:2058515275:-1 chm1:+:2162026481:-1 chm1:+:2175989524:-1 chm1:+:2183986212:-1 chm1:+:2265009813:-1 chm1:+:2422464454:-1 chm1:+:2507526124:-1 chm1:+:2624720152:-1 chm1:+:2639965522:-1 chm1:+:2648351128:-1 chm1:+:2664254377:-1 chm1:+:2667787921:-1 chm1:+:2667802759:-1 chm1:+:2709070681:-1 chm1:+:2732459487:-1 chm1:+:2741215874:-1 chm1:+:2808146593:-1 chm1:+:2886513994:-1 chm1:+:2890326343:-1 chm1:+:2979539779:-1 chm1:+:3054055260:-1 +CTTTCTTTACAGGTTTCTTAATCGATATCTAACAGAGGAGAGACAGAAACACATCCAATGTCAAAGCTAATAAAAGTTCCAACCTAGACCAGATCTTCTTACTCTTAGACCTGTTCAAGTGCCAATAAACCACATTGTTTCTGCCGAAGGTCAGAAGGGACTAATTGTAAAGTCAAGTCTGGATAAACTCTGCTCTACTATACTTAATTACGAGATTTGCCAGTTACAGGCAAATATTAAGTAACGTTTGAACAAAATACAGAAATATAGTATTACTATAATTTTAGATAGAACCTAGTTATCTTATTAAAATATCGTTTTGTTAGCACATCAATCCATGTACTATAAAGAGTATGTTTTAACAAGTTCTGAAATATTAGTACTTTTTAAGAAAAGGTTACATTTCTGGAAGAATATTTGGGAATGGACTAAATCTCATTTTAATCCTGACCTAAAATGATTATAAATAAATCATAAGTGATAAATATTCTACTTTGAAAATTTATACATATGTTTACAAATGTTACTATAATATAATAGTGCCATTCCGTTTCATAGCCTAAATGTGAATGTGTGGTACAAGCAAAAATAATGAAATAC chm1:+:97976784:-1 chm1:+:211799857:-1 chm1:+:216902916:-1 chm1:+:419758949:-1 chm1:+:434322346:-1 chm1:+:615172795:-1 chm1:+:822385339:-1 chm1:+:948791776:-1 chm1:+:1106043074:-1 chm1:+:1246797241:-1 chm1:+:1263530361:-1 chm1:+:1442386811:-1 chm1:+:1635427763:-1 chm1:+:1636955026:-1 chm1:+:1832079142:-1 chm1:+:2244358599:-1 chm1:+:2263185853:-1 chm1:+:2482979150:-1 chm1:+:2499307642:-1 chm1:+:2670539456:-1 chm1:+:2698976875:-1 chm1:+:2938226385:-1 +CTTTCTTTACAGGTTTCTTAATCGATATCTAACAGAGGAGAGACAGAAACACATCCAATGTCAAAGCTAATAAAAGTTCCAACCTAGACCAGATCTTCTTACTCTTAGACCTGTTCAAGTGCCAATAAACCACATTGTTTCTGCCGAAGGTCAGAAGGGACTAATTGTAAAGTCAAGTCTGGATAAACTCTGCTCTACTATACTTAATTACGAGATTTGCCAGTTACAGGCAAATATTAAGTAACGTTTGAACAAAATACAGAAATATAGTATTACTATAATTTTAGATAGAACCTAGTTATCTTATTAAAATATCGTTTTGTTAGCACATCAATCCATGTACTATAAAGAGTATGTTTTAACAAGTTCTGAAATATTAGTACTTTTTAAGAAAAGGTTACATTTCTGGAAGAATATTTGGGAATGGACTAAATCTCATTTTAATCCTGACCTAAAATGATTATAAATAAATCATAAGTGATAAATATTCTACTTTGAAAATTTATACATATGTTTACAAATGTTACTATAATATAATAGTGCCATTCCGTTTCATAGCCTAAATGTGAATGTGTGGTACAAGCAAAAATAATGAAATAC chm1:+:34170768:-1 chm1:+:66264130:-1 chm1:+:118915653:-1 chm1:+:453370141:-1 chm1:+:507861207:-1 chm1:+:525001864:-1 chm1:+:561522588:-1 chm1:+:588493799:-1 chm1:+:592424359:-1 chm1:+:592424395:-1 chm1:+:646470574:-1 chm1:+:748538661:-1 chm1:+:755415615:-1 chm1:+:755667479:-1 chm1:+:817533436:-1 chm1:+:1005973775:-1 chm1:+:1085196863:-1 chm1:+:1088414550:-1 chm1:+:1160582477:-1 chm1:+:1189455707:-1 chm1:+:1329774263:-1 chm1:+:1473513620:-1 chm1:+:1717892837:-1 chm1:+:1877811562:-1 chm1:+:1900975532:-1 chm1:+:1920911377:-1 chm1:+:1961275718:-1 chm1:+:2032380804:-1 chm1:+:2040088854:-1 chm1:+:2128241558:-1 chm1:+:2169190644:-1 chm1:+:2276792600:-1 chm1:+:2494166593:-1 chm1:+:2696153083:-1 chm1:+:2810909973:-1 chm1:+:3008701074:-1 chm1:+:3011350550:-1 +CTTTCTTTACAGGTTTCTTAATCGATATCTAACAGAGGAGAGACAGAAACACATCCAATGTCAAAGCTAATAAAAGTTCCAACCTAGACCAGATCTTCTTACTCTTAGACCTGTTCAAGTGCCAATAAACCACATTGTTTCTGCCGAAGGTCAGAAGGGACTAATTGTAAAGTCAAGTCTGGATAAACTCTGCTCTACTATACTTAATTACGAGATTTGCCAGTTACAGGCAAATATTAAGTAACGTTTGAACAAAATACAGAAATATAGTATTACTATAATTTTAGATAGAACCTAGTTATCTTATTAAAATATCGTTTTGTTAGCACATCAATCCATGTACTATAAAGAGTATGTTTTAACAAGTTCTGAAATATTAGTACTTTTTAAGAAAAGGTTACATTTCTGGAAGAATATTTGGGAATGGACTAAATCTCATTTTAATCCTGACCTAAAATGATTATAAATAAATCATAAGTGATAAATATTCTACTTTGAAAATTTATACATATGTTTACAAATGTTACTATAATATAATAGTGCCATTCCGTTTCATAGCCTAAATGTGAATGTGTGGTACAAGCAAAAATAATGAAATAC chm1:+:62620369:-1 chm1:+:431405050:-1 chm1:+:706494710:-1 chm1:+:1011387133:-1 chm1:+:1164657356:-1 chm1:+:1337335535:-1 chm1:+:1650585687:-1 chm1:+:2420139324:-1 chm1:+:2909264543:-1 +CTTTCTTTACAGGTTTCTTAATCGATATCTAACAGAGGAGAGACAGAAACACATCCAATGTCAAAGCTAATAAAAGTTCCAACCTAGACCAGATCTTCTTACTCTTAGACCTGTTCAAGTGCCAATAAACCACATTGTTTCTGCCGAAGGTCAGAAGGGACTAATTGTAAAGTCAAGTCTGGATAAACTCTGCTCTACTATACTTAATTACGAGATTTGCCAGTTACAGGCAAATATTAAGTAACGTTTGAACAAAATACAGAAATATAGTATTACTATAATTTTAGATAGAACCTAGTTATCTTATTAAAATATCGTTTTGTTAGCACATCAATCCATGTACTATAAAGAGTATGTTTTAACAAGTTCTGAAATATTAGTACTTTTTAAGAAAAGGTTACATTTCTGGAAGAATATTTGGGAATGGACTAAATCTCATTTTAATCCTGACCTAAAATGATTATAAATAAATCATAAGTGATAAATATTCTACTTTGAAAATTTATACATATGTTTACAAATGTTACTATAATATAATAGTGCCATTCCGTTTCATAGCCTAAATGTGAATGTGTGGTACAAGCAAAAATAATGAAATAC chm1:+:236486466:-1 chm1:+:239612177:-1 chm1:+:326444333:-1 chm1:+:403675976:-1 chm1:+:447837508:-1 chm1:+:507350222:-1 chm1:+:752049585:-1 chm1:+:807593349:-1 chm1:+:999120137:-1 chm1:+:1270160928:-1 chm1:+:1312629285:-1 chm1:+:1444554885:-1 chm1:+:1524738525:-1 chm1:+:2031569945:-1 chm1:+:2404589913:-1 chm1:+:2478645146:-1 chm1:+:2644119982:-1 +CTTTCTTTACAGGTTTCTTAATCGATATCTAACAGAGGAGAGACAGAAACACATCCAATGTCAAAGCTAATAAAAGTTCCAACCTAGACCAGATCTTCTTACTCTTAGACCTGTTCAAGTGCCAATAAACCACATTGTTTCTGCCGAAGGTCAGAAGGGACTAATTGTAAAGTCAAGTCTGGATAAACTCTGCTCTACTATACTTAATTACGAGATTTGCCAGTTACAGGCAAATATTAAGTAACGTTTGAACAAAATACAGAAATATAGTATTACTATAATTTTAGATAGAACCTAGTTATCTTATTAAAATATCGTTTTGTTAGCACATCAATCCATGTACTATAAAGAGTATGTTTTAACAAGTTCTGAAATATTAGTACTTTTTAAGAAAAGGTTACATTTCTGGAAGAATATTTGGGAATGGACTAAATCTCATTTTAATCCTGACCTAAAATGATTATAAATAAATCATAAGTGATAAATATTCTACTTTGAAAATTTATACATATGTTTACAAATGTTACTATAATATAATAGTGCCATTCCGTTTCATAGCCTAAATGTGAATGTGTGGTACAAGCAAAAATAATGAAATAC chm1:+:197961123:-1 chm1:+:406946794:-1 chm1:+:408734400:-1 chm1:+:410459828:-1 chm1:+:437564654:-1 chm1:+:452739083:-1 chm1:+:553134215:-1 chm1:+:557770794:-1 chm1:+:610856444:-1 chm1:+:623368494:-1 chm1:+:669508974:-1 chm1:+:794823753:-1 chm1:+:813221179:-1 chm1:+:871059241:-1 chm1:+:891457889:-1 chm1:+:897139475:-1 chm1:+:900701822:-1 chm1:+:949519729:-1 chm1:+:1026616841:-1 chm1:+:1040647720:-1 chm1:+:1116873861:-1 chm1:+:1154511338:-1 chm1:+:1154713015:-1 chm1:+:1166073917:-1 chm1:+:1166462546:-1 chm1:+:1170295398:-1 chm1:+:1260192398:-1 chm1:+:1298371487:-1 chm1:+:1298371616:-1 chm1:+:1361907450:-1 chm1:+:1370977190:-1 chm1:+:1406064606:-1 chm1:+:1444374951:-1 chm1:+:1447368705:-1 chm1:+:1629445614:-1 chm1:+:1631095458:-1 chm1:+:1644935055:-1 chm1:+:1752396129:-1 chm1:+:1772157777:-1 chm1:+:1918841603:-1 chm1:+:1948331059:-1 chm1:+:1973515593:-1 chm1:+:1984477809:-1 chm1:+:2017437510:-1 chm1:+:2024599902:-1 chm1:+:2053327375:-1 chm1:+:2065560447:-1 chm1:+:2130278479:-1 chm1:+:2170343878:-1 chm1:+:2177189977:-1 chm1:+:2180102556:-1 chm1:+:2226060896:-1 chm1:+:2229989205:-1 chm1:+:2239795029:-1 chm1:+:2400553392:-1 chm1:+:2478019765:-1 chm1:+:2563860590:-1 chm1:+:2612190558:-1 chm1:+:2623846472:-1 chm1:+:2628302021:-1 chm1:+:2637224439:-1 chm1:+:2640006808:-1 chm1:+:2909935310:-1 chm1:+:2937081033:-1 chm1:+:3021290010:-1 chm1:+:3057304058:-1 +GTATTTCATTATTTTTGCTTGTACCACACATTCACATTTAGGCTATGAAACGGAATGGCACTATTATATTATAGTAACATTTGTAAACATATGTATAAATTTTCAAAGTAGAATATTTATCACTTATGATTTATTTATAATCATTTTAGGTCAGGATTAAAATGAGATTTAGTCCATTCCCAAATATTCTTCCAGAAATGTAACCTTTTCTTAAAAAGTACTAATATTTCAGAACTTGTTAAAACATACTCTTTATAGTACATGGATTGATGTGCTAACAAAACGATATTTTAATAAGATAACTAGGTTCTATCTAAAATTATAGTAATACTATATTTCTGTATTTTGTTCAAACGTTACTTAATATTTGCCTGTAACTGGCAAATCTCGTAATTAAGTATAGTAGAGCAGAGTTTATCCAGACTTGACTTTACAATTAGTCCCTTCTGACCTTCGGCAGAAACAATGTGGTTTATTGGCACTTGAACAGGTCTAAGAGTAAGAAGATCTGGTCTAGGTTGGAACTTTTATTAGCTTTGACATTGGATGTGTTTCTGTCTCTCCTCTGTTAGATATCGATTAAGAAACCTGTAAAGAAAG chm1:+:211086714:-1 chm1:+:366105435:-1 chm1:+:581692960:26 chm1:+:1490024232:-1 chm1:+:1797701163:-1 chm1:+:2350704742:-1 chm1:+:2391896444:-1 +GTATTTCATTATTTTTGCTTGTACCACACATTCACATTTAGGCTATGAAACGGAATGGCACTATTATATTATAGTAACATTTGTAAACATATGTATAAATTTTCAAAGTAGAATATTTATCACTTATGATTTATTTATAATCATTTTAGGTCAGGATTAAAATGAGATTTAGTCCATTCCCAAATATTCTTCCAGAAATGTAACCTTTTCTTAAAAAGTACTAATATTTCAGAACTTGTTAAAACATACTCTTTATAGTACATGGATTGATGTGCTAACAAAACGATATTTTAATAAGATAACTAGGTTCTATCTAAAATTATAGTAATACTATATTTCTGTATTTTGTTCAAACGTTACTTAATATTTGCCTGTAACTGGCAAATCTCGTAATTAAGTATAGTAGAGCAGAGTTTATCCAGACTTGACTTTACAATTAGTCCCTTCTGACCTTCGGCAGAAACAATGTGGTTTATTGGCACTTGAACAGGTCTAAGAGTAAGAAGATCTGGTCTAGGTTGGAACTTTTATTAGCTTTGACATTGGATGTGTTTCTGTCTCTCCTCTGTTAGATATCGATTAAGAAACCTGTAAAGAAAG chm1:+:702499233:-1 +GTATTTCATTATTTTTGCTTGTACCACACATTCACATTTAGGCTATGAAACGGAATGGCACTATTATATTATAGTAACATTTGTAAACATATGTATAAATTTTCAAAGTAGAATATTTATCACTTATGATTTATTTATAATCATTTTAGGTCAGGATTAAAATGAGATTTAGTCCATTCCCAAATATTCTTCCAGAAATGTAACCTTTTCTTAAAAAGTACTAATATTTCAGAACTTGTTAAAACATACTCTTTATAGTACATGGATTGATGTGCTAACAAAACGATATTTTAATAAGATAACTAGGTTCTATCTAAAATTATAGTAATACTATATTTCTGTATTTTGTTCAAACGTTACTTAATATTTGCCTGTAACTGGCAAATCTCGTAATTAAGTATAGTAGAGCAGAGTTTATCCAGACTTGACTTTACAATTAGTCCCTTCTGACCTTCGGCAGAAACAATGTGGTTTATTGGCACTTGAACAGGTCTAAGAGTAAGAAGATCTGGTCTAGGTTGGAACTTTTATTAGCTTTGACATTGGATGTGTTTCTGTCTCTCCTCTGTTAGATATCGATTAAGAAACCTGTAAAGAAAG chm1:+:581692962:26 +GTATTTCATTATTTTTGCTTGTACCACACATTCACATTTAGGCTATGAAACGGAATGGCACTATTATATTATAGTAACATTTGTAAACATATGTATAAATTTTCAAAGTAGAATATTTATCACTTATGATTTATTTATAATCATTTTAGGTCAGGATTAAAATGAGATTTAGTCCATTCCCAAATATTCTTCCAGAAATGTAACCTTTTCTTAAAAAGTACTAATATTTCAGAACTTGTTAAAACATACTCTTTATAGTACATGGATTGATGTGCTAACAAAACGATATTTTAATAAGATAACTAGGTTCTATCTAAAATTATAGTAATACTATATTTCTGTATTTTGTTCAAACGTTACTTAATATTTGCCTGTAACTGGCAAATCTCGTAATTAAGTATAGTAGAGCAGAGTTTATCCAGACTTGACTTTACAATTAGTCCCTTCTGACCTTCGGCAGAAACAATGTGGTTTATTGGCACTTGAACAGGTCTAAGAGTAAGAAGATCTGGTCTAGGTTGGAACTTTTATTAGCTTTGACATTGGATGTGTTTCTGTCTCTCCTCTGTTAGATATCGATTAAGAAACCTGTAAAGAAAG chm1:+:581692952:26 +GTATTTCATTATTTTTGCTTGTACCACACATTCACATTTAGGCTATGAAACGGAATGGCACTATTATATTATAGTAACATTTGTAAACATATGTATAAATTTTCAAAGTAGAATATTTATCACTTATGATTTATTTATAATCATTTTAGGTCAGGATTAAAATGAGATTTAGTCCATTCCCAAATATTCTTCCAGAAATGTAACCTTTTCTTAAAAAGTACTAATATTTCAGAACTTGTTAAAACATACTCTTTATAGTACATGGATTGATGTGCTAACAAAACGATATTTTAATAAGATAACTAGGTTCTATCTAAAATTATAGTAATACTATATTTCTGTATTTTGTTCAAACGTTACTTAATATTTGCCTGTAACTGGCAAATCTCGTAATTAAGTATAGTAGAGCAGAGTTTATCCAGACTTGACTTTACAATTAGTCCCTTCTGACCTTCGGCAGAAACAATGTGGTTTATTGGCACTTGAACAGGTCTAAGAGTAAGAAGATCTGGTCTAGGTTGGAACTTTTATTAGCTTTGACATTGGATGTGTTTCTGTCTCTCCTCTGTTAGATATCGATTAAGAAACCTGTAAAGAAAG chm1:+:581692955:26 +GTATTTCATTATTTTTGCTTGTACCACACATTCACATTTAGGCTATGAAACGGAATGGCACTATTATATTATAGTAACATTTGTAAACATATGTATAAATTTTCAAAGTAGAATATTTATCACTTATGATTTATTTATAATCATTTTAGGTCAGGATTAAAATGAGATTTAGTCCATTCCCAAATATTCTTCCAGAAATGTAACCTTTTCTTAAAAAGTACTAATATTTCAGAACTTGTTAAAACATACTCTTTATAGTACATGGATTGATGTGCTAACAAAACGATATTTTAATAAGATAACTAGGTTCTATCTAAAATTATAGTAATACTATATTTCTGTATTTTGTTCAAACGTTACTTAATATTTGCCTGTAACTGGCAAATCTCGTAATTAAGTATAGTAGAGCAGAGTTTATCCAGACTTGACTTTACAATTAGTCCCTTCTGACCTTCGGCAGAAACAATGTGGTTTATTGGCACTTGAACAGGTCTAAGAGTAAGAAGATCTGGTCTAGGTTGGAACTTTTATTAGCTTTGACATTGGATGTGTTTCTGTCTCTCCTCTGTTAGATATCGATTAAGAAACCTGTAAAGAAAG chm1:+:581692958:26 +GTATTTCATTATTTTTGCTTGTACCACACATTCACATTTAGGCTATGAAACGGAATGGCACTATTATATTATAGTAACATTTGTAAACATATGTATAAATTTTCAAAGTAGAATATTTATCACTTATGATTTATTTATAATCATTTTAGGTCAGGATTAAAATGAGATTTAGTCCATTCCCAAATATTCTTCCAGAAATGTAACCTTTTCTTAAAAAGTACTAATATTTCAGAACTTGTTAAAACATACTCTTTATAGTACATGGATTGATGTGCTAACAAAACGATATTTTAATAAGATAACTAGGTTCTATCTAAAATTATAGTAATACTATATTTCTGTATTTTGTTCAAACGTTACTTAATATTTGCCTGTAACTGGCAAATCTCGTAATTAAGTATAGTAGAGCAGAGTTTATCCAGACTTGACTTTACAATTAGTCCCTTCTGACCTTCGGCAGAAACAATGTGGTTTATTGGCACTTGAACAGGTCTAAGAGTAAGAAGATCTGGTCTAGGTTGGAACTTTTATTAGCTTTGACATTGGATGTGTTTCTGTCTCTCCTCTGTTAGATATCGATTAAGAAACCTGTAAAGAAAG chm1:+:581692961:26 +GTATTTCATTATTTTTGCTTGTACCACACATTCACATTTAGGCTATGAAACGGAATGGCACTATTATATTATAGTAACATTTGTAAACATATGTATAAATTTTCAAAGTAGAATATTTATCACTTATGATTTATTTATAATCATTTTAGGTCAGGATTAAAATGAGATTTAGTCCATTCCCAAATATTCTTCCAGAAATGTAACCTTTTCTTAAAAAGTACTAATATTTCAGAACTTGTTAAAACATACTCTTTATAGTACATGGATTGATGTGCTAACAAAACGATATTTTAATAAGATAACTAGGTTCTATCTAAAATTATAGTAATACTATATTTCTGTATTTTGTTCAAACGTTACTTAATATTTGCCTGTAACTGGCAAATCTCGTAATTAAGTATAGTAGAGCAGAGTTTATCCAGACTTGACTTTACAATTAGTCCCTTCTGACCTTCGGCAGAAACAATGTGGTTTATTGGCACTTGAACAGGTCTAAGAGTAAGAAGATCTGGTCTAGGTTGGAACTTTTATTAGCTTTGACATTGGATGTGTTTCTGTCTCTCCTCTGTTAGATATCGATTAAGAAACCTGTAAAGAAAG chm1:+:581692954:26 +GTATTTCATTATTTTTGCTTGTACCACACATTCACATTTAGGCTATGAAACGGAATGGCACTATTATATTATAGTAACATTTGTAAACATATGTATAAATTTTCAAAGTAGAATATTTATCACTTATGATTTATTTATAATCATTTTAGGTCAGGATTAAAATGAGATTTAGTCCATTCCCAAATATTCTTCCAGAAATGTAACCTTTTCTTAAAAAGTACTAATATTTCAGAACTTGTTAAAACATACTCTTTATAGTACATGGATTGATGTGCTAACAAAACGATATTTTAATAAGATAACTAGGTTCTATCTAAAATTATAGTAATACTATATTTCTGTATTTTGTTCAAACGTTACTTAATATTTGCCTGTAACTGGCAAATCTCGTAATTAAGTATAGTAGAGCAGAGTTTATCCAGACTTGACTTTACAATTAGTCCCTTCTGACCTTCGGCAGAAACAATGTGGTTTATTGGCACTTGAACAGGTCTAAGAGTAAGAAGATCTGGTCTAGGTTGGAACTTTTATTAGCTTTGACATTGGATGTGTTTCTGTCTCTCCTCTGTTAGATATCGATTAAGAAACCTGTAAAGAAAG chm1:+:581692968:26 chm1:+:1750264781:-1 +GTATTTCATTATTTTTGCTTGTACCACACATTCACATTTAGGCTATGAAACGGAATGGCACTATTATATTATAGTAACATTTGTAAACATATGTATAAATTTTCAAAGTAGAATATTTATCACTTATGATTTATTTATAATCATTTTAGGTCAGGATTAAAATGAGATTTAGTCCATTCCCAAATATTCTTCCAGAAATGTAACCTTTTCTTAAAAAGTACTAATATTTCAGAACTTGTTAAAACATACTCTTTATAGTACATGGATTGATGTGCTAACAAAACGATATTTTAATAAGATAACTAGGTTCTATCTAAAATTATAGTAATACTATATTTCTGTATTTTGTTCAAACGTTACTTAATATTTGCCTGTAACTGGCAAATCTCGTAATTAAGTATAGTAGAGCAGAGTTTATCCAGACTTGACTTTACAATTAGTCCCTTCTGACCTTCGGCAGAAACAATGTGGTTTATTGGCACTTGAACAGGTCTAAGAGTAAGAAGATCTGGTCTAGGTTGGAACTTTTATTAGCTTTGACATTGGATGTGTTTCTGTCTCTCCTCTGTTAGATATCGATTAAGAAACCTGTAAAGAAAG chm1:+:2081583212:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:1928040:-1 chm1:+:358882515:-1 chm1:+:690959572:-1 chm1:+:804103958:-1 chm1:+:1020312700:-1 chm1:+:1042923953:-1 chm1:+:1210287476:-1 chm1:+:1395890349:-1 chm1:+:1523335505:-1 chm1:+:1533727960:-1 chm1:+:1573271533:-1 chm1:+:1633716792:-1 chm1:+:1686267798:-1 chm1:+:1713919376:-1 chm1:+:1825254558:-1 chm1:+:1967731136:-1 chm1:+:1983032911:-1 chm1:+:2134197242:-1 chm1:+:2192323140:-1 chm1:+:2222983326:-1 chm1:+:2244072957:-1 chm1:+:2285695419:-1 chm1:+:2367905747:-1 chm1:+:2868304180:-1 chm1:+:2936643017:-1 chm1:+:2948722338:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:7917587:-1 chm1:+:19817705:-1 chm1:+:24375270:-1 chm1:+:26411062:-1 chm1:+:109206292:-1 chm1:+:258045294:-1 chm1:+:276396497:-1 chm1:+:362806777:-1 chm1:+:381933056:-1 chm1:+:482186530:-1 chm1:+:486940069:-1 chm1:+:745413377:-1 chm1:+:867373609:-1 chm1:+:960239099:-1 chm1:+:1031447109:-1 chm1:+:1053353869:-1 chm1:+:1096703863:-1 chm1:+:1097813735:-1 chm1:+:1104367006:-1 chm1:+:1299770927:-1 chm1:+:1732637796:-1 chm1:+:1753683137:-1 chm1:+:1784573605:-1 chm1:+:1792589992:-1 chm1:+:1994421802:-1 chm1:+:2059053440:-1 chm1:+:2061869217:-1 chm1:+:2065934556:-1 chm1:+:2066082734:-1 chm1:+:2109654488:-1 chm1:+:2152299861:-1 chm1:+:2160280810:-1 chm1:+:2375062140:-1 chm1:+:2439891250:-1 chm1:+:2499220382:-1 chm1:+:2511192037:-1 chm1:+:2587847010:-1 chm1:+:2592379793:-1 chm1:+:2658430113:-1 chm1:+:2664263285:-1 chm1:+:2664944566:-1 chm1:+:2675615014:-1 chm1:+:2697954732:-1 chm1:+:2705334525:-1 chm1:+:2708607617:-1 chm1:+:2713662100:-1 chm1:+:2730627614:-1 chm1:+:2752728192:-1 chm1:+:2806880562:-1 chm1:+:2817897261:-1 chm1:+:2927944459:-1 chm1:+:3035196399:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:317922090:-1 chm1:+:1037962311:-1 chm1:+:1893499538:-1 chm1:+:2561027586:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:8122958:-1 chm1:+:35483628:-1 chm1:+:1300286305:-1 chm1:+:1511521909:-1 chm1:+:1754244070:-1 chm1:+:1862235628:-1 chm1:+:2236191224:-1 chm1:+:2302949336:-1 chm1:+:2437333030:-1 chm1:+:2484683069:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:265131271:-1 chm1:+:552730147:-1 chm1:+:653547776:-1 chm1:+:1067530406:-1 chm1:+:1385409836:-1 chm1:+:1636580268:-1 chm1:+:1723508858:-1 chm1:+:1929696751:-1 chm1:+:2137986099:-1 chm1:+:2256258142:-1 chm1:+:2257414663:-1 chm1:+:2391420238:-1 chm1:+:2391661815:-1 chm1:+:2890397408:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:191640707:-1 chm1:+:2934962873:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:262482361:-1 chm1:+:323534004:-1 chm1:+:689392028:-1 chm1:+:898256222:-1 chm1:+:1136303813:-1 chm1:+:1228370650:-1 chm1:+:1297097311:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:976803676:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:229653099:-1 chm1:+:278666789:-1 chm1:+:708155688:-1 chm1:+:1270777289:-1 chm1:+:1324299087:-1 chm1:+:1913908896:-1 chm1:+:2889209925:-1 chm1:+:3009366483:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:190837827:-1 chm1:+:412955922:-1 chm1:+:444255260:-1 chm1:+:1008957858:-1 chm1:+:1193006050:-1 chm1:+:1207421519:-1 chm1:+:1219013719:-1 chm1:+:1244882101:-1 chm1:+:1355051140:-1 chm1:+:1358988097:-1 chm1:+:1385604461:-1 chm1:+:1459454917:-1 chm1:+:1622551121:-1 chm1:+:2031937630:-1 chm1:+:2122347658:-1 chm1:+:2198220117:-1 chm1:+:2338683752:-1 chm1:+:2529174899:-1 chm1:+:2534631030:-1 chm1:+:2655293892:-1 chm1:+:2769717691:-1 chm1:+:2876207460:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:860833401:-1 chm1:+:911453328:-1 chm1:+:1022363560:-1 chm1:+:1257903286:-1 chm1:+:1968816949:-1 chm1:+:2267339724:-1 chm1:+:2742513842:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:2963506042:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:93423741:-1 chm1:+:556450343:-1 chm1:+:803237754:-1 chm1:+:848157761:-1 chm1:+:1543737101:-1 chm1:+:1647203382:-1 chm1:+:2948427823:-1 chm1:+:3013902919:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:89073131:-1 chm1:+:657272746:-1 chm1:+:689405900:-1 chm1:+:914785552:-1 chm1:+:923442880:-1 chm1:+:1155191125:-1 chm1:+:1484944015:-1 chm1:+:1556000518:-1 chm1:+:1675304850:-1 chm1:+:1723624714:-1 chm1:+:1915367626:-1 chm1:+:2251848615:-1 chm1:+:2632899195:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:63374843:-1 chm1:+:68447180:-1 chm1:+:163975193:-1 chm1:+:195523393:-1 chm1:+:226329030:-1 chm1:+:235979574:-1 chm1:+:285139085:-1 chm1:+:380114365:-1 chm1:+:471741713:-1 chm1:+:718053320:-1 chm1:+:752085892:-1 chm1:+:987033400:-1 chm1:+:1039445803:-1 chm1:+:1086112447:-1 chm1:+:1301412682:-1 chm1:+:1312183593:-1 chm1:+:1316406677:-1 chm1:+:1352904389:-1 chm1:+:1383797397:-1 chm1:+:1478532321:-1 chm1:+:2436096753:-1 chm1:+:2493923635:-1 chm1:+:2634530429:-1 chm1:+:2970899571:-1 chm1:+:2998329421:-1 chm1:+:3007899458:-1 chm1:+:3023487491:-1 chm1:+:3040360891:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:293587511:-1 chm1:+:326627566:-1 chm1:+:474811880:-1 chm1:+:625300804:-1 chm1:+:716581389:-1 chm1:+:795806841:-1 chm1:+:900477039:-1 chm1:+:916161010:-1 chm1:+:982402086:-1 chm1:+:1034249941:-1 chm1:+:1053320933:-1 chm1:+:1227855116:-1 chm1:+:1228590749:-1 chm1:+:1319055561:-1 chm1:+:1417860310:-1 chm1:+:1457580345:-1 chm1:+:1457610363:-1 chm1:+:1648092534:-1 chm1:+:1661312667:-1 chm1:+:1664166957:-1 chm1:+:1801981721:-1 chm1:+:1859594596:-1 chm1:+:2019776398:-1 chm1:+:2133103802:-1 chm1:+:2379506377:-1 chm1:+:2421424503:-1 chm1:+:2603944621:-1 chm1:+:2732513975:-1 chm1:+:2748845975:-1 chm1:+:2851909428:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:85023307:-1 chm1:+:85920219:-1 chm1:+:393075025:-1 chm1:+:490162927:-1 chm1:+:602527247:-1 chm1:+:724342634:-1 chm1:+:780994096:-1 chm1:+:819137511:-1 chm1:+:819153310:-1 chm1:+:1050223897:-1 chm1:+:1061921596:-1 chm1:+:1177832181:-1 chm1:+:1282082729:-1 chm1:+:1662537829:-1 chm1:+:1740962977:-1 chm1:+:1786861488:-1 chm1:+:1995984629:-1 chm1:+:2122353060:-1 chm1:+:2328315740:-1 chm1:+:2329322413:-1 chm1:+:2374270357:-1 chm1:+:2547842913:-1 chm1:+:2603290227:-1 chm1:+:2805935045:-1 chm1:+:3008354471:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:599602354:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:173986892:-1 chm1:+:524634352:-1 chm1:+:563090281:-1 chm1:+:579423041:-1 chm1:+:1252782635:-1 chm1:+:2018936997:-1 chm1:+:2234854322:-1 chm1:+:2543818035:-1 chm1:+:2563083765:-1 chm1:+:2674620751:-1 chm1:+:2676694552:-1 chm1:+:2708756335:-1 chm1:+:2987132234:-1 +AGCCTGGGGCAACATAGGCGGAAACATCTCTACAAAAAAATACAAAAATTTAGCTAGGTGTGGTGGTGTGCACCTGTAGTGCAGCGTACTCAGGAGCTTGAGGTGGGAGGATCACCTTGAGACTCAGGAGGTGGAGGTTGCAGTGAGCGAGAGGATCACGCCACTGCACTCCAGCCCTGGGCAACAGAGTGAGACCCAGTCGTCAAAACAAGACAAAAAATGATATTATATAAATGGAATCATACCTGTATGTAACGTTTTGACATTTAGCTTTTTTAGCATAATTAACATTTTTTTTTCTGATTATAAAGTAATACGGAAATTAGCCTTAAAGAACTATTGGAACTAATTACTAAGGAGATGGATGTTATATTTACCACACAAAAATGAATAGCTTTCTCTTATTTACCATTAGTAATCAATTTAAAAAATGGTATGGGAGAAAAAGAAGATTCCATTCACAATGATAACAAAAACCTATAAATACTTAGAAATAAACTTAACAAAAAATTACAATTATTAAAACTTTGAATAAAGATTCACAAAGAAGGTGGGAAAGATAAATTGTAAAAATGATTGTGTCAATCTATAATTTCCAGT chm1:+:41006411:-1 chm1:+:100443765:-1 chm1:+:206950434:-1 chm1:+:414671828:-1 chm1:+:418029954:-1 chm1:+:710210596:-1 chm1:+:791595937:-1 chm1:+:878083957:-1 chm1:+:1061457707:-1 chm1:+:1278322281:-1 chm1:+:1463585193:-1 chm1:+:1483707246:-1 chm1:+:1782299002:-1 chm1:+:1945110571:-1 chm1:+:2068266166:-1 chm1:+:2222219979:-1 chm1:+:2516314059:-1 chm1:+:2875072973:-1 chm1:+:2952805598:-1 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:21775462:-1 chm1:+:1116007539:-1 chm1:+:1269625740:-1 chm1:+:1998942539:-1 chm1:+:2750903949:-1 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:18126591:-1 chm1:+:113072537:-1 chm1:+:180984304:-1 chm1:+:292431159:-1 chm1:+:603193510:-1 chm1:+:820023028:-1 chm1:+:1059787096:-1 chm1:+:1126705838:-1 chm1:+:1171314382:-1 chm1:+:1574236975:-1 chm1:+:1661207723:-1 chm1:+:1966426265:-1 chm1:+:2049846036:-1 chm1:+:2084438262:-1 chm1:+:2120045390:-1 chm1:+:2233663699:-1 chm1:+:2491940534:-1 chm1:+:2495887267:-1 chm1:+:2620274452:-1 chm1:+:2876173559:-1 chm1:+:2993805148:-1 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:323646878:-1 chm1:+:2672475801:-1 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:319913238:-1 chm1:+:354918623:-1 chm1:+:488623380:-1 chm1:+:1001300767:-1 chm1:+:1038329364:-1 chm1:+:1726795109:-1 chm1:+:1731476810:-1 chm1:+:1731698572:-1 chm1:+:2380807129:-1 chm1:+:2811921175:35 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:3366069:-1 chm1:+:6025802:-1 chm1:+:8592150:-1 chm1:+:9225411:-1 chm1:+:29244060:-1 chm1:+:32544282:-1 chm1:+:33601466:-1 chm1:+:35465335:-1 chm1:+:35574844:-1 chm1:+:41348800:-1 chm1:+:89676769:-1 chm1:+:150431565:-1 chm1:+:151186689:-1 chm1:+:154353101:-1 chm1:+:195666219:-1 chm1:+:201734019:-1 chm1:+:206925678:-1 chm1:+:212884153:-1 chm1:+:220461495:-1 chm1:+:236019742:-1 chm1:+:274806316:-1 chm1:+:275337808:-1 chm1:+:276620579:-1 chm1:+:276818698:-1 chm1:+:294664408:-1 chm1:+:302068201:-1 chm1:+:305610275:-1 chm1:+:323647382:-1 chm1:+:409041499:-1 chm1:+:411467165:-1 chm1:+:462545282:-1 chm1:+:484017545:-1 chm1:+:508759327:-1 chm1:+:519977813:-1 chm1:+:534469743:-1 chm1:+:553044549:-1 chm1:+:561403811:-1 chm1:+:580191632:-1 chm1:+:593966947:-1 chm1:+:600721464:-1 chm1:+:607093864:-1 chm1:+:616061142:-1 chm1:+:621803128:-1 chm1:+:633429486:-1 chm1:+:639975746:-1 chm1:+:646026112:-1 chm1:+:672753377:-1 chm1:+:680825423:-1 chm1:+:684378705:-1 chm1:+:686180591:-1 chm1:+:690186812:-1 chm1:+:693004992:-1 chm1:+:693385101:-1 chm1:+:730431431:-1 chm1:+:737762200:-1 chm1:+:739397806:-1 chm1:+:775441678:-1 chm1:+:779205896:-1 chm1:+:804669018:-1 chm1:+:819451808:-1 chm1:+:830611262:-1 chm1:+:836921176:-1 chm1:+:880358024:-1 chm1:+:889344458:-1 chm1:+:898397885:-1 chm1:+:900647808:-1 chm1:+:913672545:-1 chm1:+:936667446:-1 chm1:+:1022892162:-1 chm1:+:1031761800:-1 chm1:+:1062031772:-1 chm1:+:1080363729:-1 chm1:+:1098814987:-1 chm1:+:1109385797:-1 chm1:+:1132969044:-1 chm1:+:1141512030:-1 chm1:+:1201937120:-1 chm1:+:1203990587:-1 chm1:+:1232934435:-1 chm1:+:1238588869:-1 chm1:+:1239403880:-1 chm1:+:1256955326:-1 chm1:+:1258020703:-1 chm1:+:1277495595:-1 chm1:+:1301095379:-1 chm1:+:1318090262:-1 chm1:+:1330387841:-1 chm1:+:1364977067:-1 chm1:+:1366366788:-1 chm1:+:1383525424:-1 chm1:+:1436180743:-1 chm1:+:1491069638:-1 chm1:+:1518998299:-1 chm1:+:1531083951:-1 chm1:+:1532085992:-1 chm1:+:1625066282:-1 chm1:+:1638353050:-1 chm1:+:1639980514:-1 chm1:+:1654402134:-1 chm1:+:1666784642:-1 chm1:+:1672785737:-1 chm1:+:1684155913:-1 chm1:+:1717381279:-1 chm1:+:1734312087:-1 chm1:+:1742805748:-1 chm1:+:1742820463:-1 chm1:+:1760193284:-1 chm1:+:1773280976:-1 chm1:+:1810186270:-1 chm1:+:1821528020:-1 chm1:+:1824041227:-1 chm1:+:1852163104:-1 chm1:+:1858143053:-1 chm1:+:1860584524:-1 chm1:+:1877298750:-1 chm1:+:1897431943:-1 chm1:+:1928021619:-1 chm1:+:2006071804:-1 chm1:+:2007536073:-1 chm1:+:2007637016:-1 chm1:+:2019881478:-1 chm1:+:2021881188:-1 chm1:+:2049869723:-1 chm1:+:2058863774:-1 chm1:+:2059940193:-1 chm1:+:2065903578:-1 chm1:+:2074203964:-1 chm1:+:2074717857:-1 chm1:+:2074872334:-1 chm1:+:2081339223:-1 chm1:+:2081614898:-1 chm1:+:2111457009:-1 chm1:+:2113460950:-1 chm1:+:2134959226:-1 chm1:+:2149128200:-1 chm1:+:2160102933:-1 chm1:+:2164512305:-1 chm1:+:2174493889:-1 chm1:+:2177013069:-1 chm1:+:2196199243:-1 chm1:+:2199800977:-1 chm1:+:2237674708:-1 chm1:+:2239595067:-1 chm1:+:2250286805:-1 chm1:+:2264539643:-1 chm1:+:2265986572:-1 chm1:+:2274292175:-1 chm1:+:2275199351:-1 chm1:+:2293770492:-1 chm1:+:2342244406:-1 chm1:+:2352242013:-1 chm1:+:2372124205:-1 chm1:+:2379723307:-1 chm1:+:2389962638:-1 chm1:+:2390339171:-1 chm1:+:2393008645:-1 chm1:+:2440645412:-1 chm1:+:2444923492:-1 chm1:+:2467205190:-1 chm1:+:2468793749:-1 chm1:+:2476733643:-1 chm1:+:2518922791:-1 chm1:+:2528151965:-1 chm1:+:2540186045:-1 chm1:+:2547360349:-1 chm1:+:2558210607:-1 chm1:+:2559395796:-1 chm1:+:2575025928:-1 chm1:+:2580006508:-1 chm1:+:2583898895:-1 chm1:+:2592909065:-1 chm1:+:2593105017:-1 chm1:+:2614917210:-1 chm1:+:2628409498:-1 chm1:+:2634425765:-1 chm1:+:2663737883:-1 chm1:+:2676005110:-1 chm1:+:2719008120:-1 chm1:+:2719603335:-1 chm1:+:2724709119:-1 chm1:+:2754224326:-1 chm1:+:2766268230:-1 chm1:+:2772623680:-1 chm1:+:2796366727:-1 chm1:+:2796453787:-1 chm1:+:2812437859:-1 chm1:+:2825236123:-1 chm1:+:2826735927:-1 chm1:+:2846813769:-1 chm1:+:2925515276:-1 chm1:+:2931493000:-1 chm1:+:2935402064:-1 chm1:+:2935864315:-1 chm1:+:2943669786:-1 chm1:+:2944454499:-1 chm1:+:2964921094:-1 chm1:+:2975470367:-1 chm1:+:2987677270:-1 chm1:+:3013591191:-1 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:2811921165:35 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:1043128763:-1 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:2811921167:35 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:2811921172:35 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:2811921174:35 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:2811921178:35 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:2811921171:35 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:2118246287:-1 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:2187135331:-1 +ACTGGAAATTATAGATTGACACAATCATTTTTACAATTTATCTTTCCCACCTTCTTTGTGAATCTTTATTCAAAGTTTTAATAATTGTAATTTTTTGTTAAGTTTATTTCTAAGTATTTATAGGTTTTTGTTATCATTGTGAATGGAATCTTCTTTTTCTCCCATACCATTTTTTAAATTGATTACTAATGGTAAATAAGAGAAAGCTATTCATTTTTGTGTGGTAAATATAACATCCATCTCCTTAGTAATTAGTTCCAATAGTTCTTTAAGGCTAATTTCCGTATTACTTTATAATCAGAAAAAAAAATGTTAATTATGCTAAAAAAGCTAAATGTCAAAACGTTACATACAGGTATGATTCCATTTATATAATATCATTTTTTGTCTTGTTTTGACGACTGGGTCTCACTCTGTTGCCCAGGGCTGGAGTGCAGTGGCGTGATCCTCTCGCTCACTGCAACCTCCACCTCCTGAGTCTCAAGGTGATCCTCCCACCTCAAGCTCCTGAGTACGCTGCACTACAGGTGCACACCACCACACCTAGCTAAATTTTTGTATTTTTTTGTAGAGATGTTTCCGCCTATGTTGCCCCAGGCT chm1:+:2914221729:-1 +TCCAAAGGTGACTGGCCAATGAATTGTTAATCTCATAGACTCATGGATTAAACACATTAATGTATTTACTACATTGCAGTTACTCTTAGTTGTATTCCCAAAATATCTTGGCCAGTGAAAGGCCCTTCAAATTGCCTTCAAGTAGGTAGTCTCCGGGTGCATTCTTGCTTTCTAGCATAACAACATGTTCCAGGCTCATTTTCATTTCCTGCCTCAGATCTGAAAACCAACCATTTAACGTAAGAAGCTCTGATGCCTTTGAGTGAGAAATAGCATTTAGGGAAGCATAATTTGTATTCTTCTATTTTATTTCTGAAACAAAAAATATCTGAAGCAAGCACGGCATTAGGTTATGAAATGGATAATGGTTGTTGGGGATACTACGAGACATTTGCTATGTTATTCATCCTTTGTGTATGCCAGTGTTTCCAATCCTCCATATATAACAACCCTTGTCGGAAAAATCCTCACAGAGTTTCTCTACAGAAAAATGTTGTTTCTCCTGATGTATTGATAGTAATGATTAGAAAATTAGTCTGTAAATGCCTGTCTACAGTAGCTAATTTTTGTGTTTAATTTATATGATTTATTCTTGTTTTT chm1:+:779569030:28 +TCCAAAGGTGACTGGCCAATGAATTGTTAATCTCATAGACTCATGGATTAAACACATTAATGTATTTACTACATTGCAGTTACTCTTAGTTGTATTCCCAAAATATCTTGGCCAGTGAAAGGCCCTTCAAATTGCCTTCAAGTAGGTAGTCTCCGGGTGCATTCTTGCTTTCTAGCATAACAACATGTTCCAGGCTCATTTTCATTTCCTGCCTCAGATCTGAAAACCAACCATTTAACGTAAGAAGCTCTGATGCCTTTGAGTGAGAAATAGCATTTAGGGAAGCATAATTTGTATTCTTCTATTTTATTTCTGAAACAAAAAATATCTGAAGCAAGCACGGCATTAGGTTATGAAATGGATAATGGTTGTTGGGGATACTACGAGACATTTGCTATGTTATTCATCCTTTGTGTATGCCAGTGTTTCCAATCCTCCATATATAACAACCCTTGTCGGAAAAATCCTCACAGAGTTTCTCTACAGAAAAATGTTGTTTCTCCTGATGTATTGATAGTAATGATTAGAAAATTAGTCTGTAAATGCCTGTCTACAGTAGCTAATTTTTGTGTTTAATTTATATGATTTATTCTTGTTTTT chm1:+:779569027:28 +TCCAAAGGTGACTGGCCAATGAATTGTTAATCTCATAGACTCATGGATTAAACACATTAATGTATTTACTACATTGCAGTTACTCTTAGTTGTATTCCCAAAATATCTTGGCCAGTGAAAGGCCCTTCAAATTGCCTTCAAGTAGGTAGTCTCCGGGTGCATTCTTGCTTTCTAGCATAACAACATGTTCCAGGCTCATTTTCATTTCCTGCCTCAGATCTGAAAACCAACCATTTAACGTAAGAAGCTCTGATGCCTTTGAGTGAGAAATAGCATTTAGGGAAGCATAATTTGTATTCTTCTATTTTATTTCTGAAACAAAAAATATCTGAAGCAAGCACGGCATTAGGTTATGAAATGGATAATGGTTGTTGGGGATACTACGAGACATTTGCTATGTTATTCATCCTTTGTGTATGCCAGTGTTTCCAATCCTCCATATATAACAACCCTTGTCGGAAAAATCCTCACAGAGTTTCTCTACAGAAAAATGTTGTTTCTCCTGATGTATTGATAGTAATGATTAGAAAATTAGTCTGTAAATGCCTGTCTACAGTAGCTAATTTTTGTGTTTAATTTATATGATTTATTCTTGTTTTT chm1:+:779569020:28 +TCCAAAGGTGACTGGCCAATGAATTGTTAATCTCATAGACTCATGGATTAAACACATTAATGTATTTACTACATTGCAGTTACTCTTAGTTGTATTCCCAAAATATCTTGGCCAGTGAAAGGCCCTTCAAATTGCCTTCAAGTAGGTAGTCTCCGGGTGCATTCTTGCTTTCTAGCATAACAACATGTTCCAGGCTCATTTTCATTTCCTGCCTCAGATCTGAAAACCAACCATTTAACGTAAGAAGCTCTGATGCCTTTGAGTGAGAAATAGCATTTAGGGAAGCATAATTTGTATTCTTCTATTTTATTTCTGAAACAAAAAATATCTGAAGCAAGCACGGCATTAGGTTATGAAATGGATAATGGTTGTTGGGGATACTACGAGACATTTGCTATGTTATTCATCCTTTGTGTATGCCAGTGTTTCCAATCCTCCATATATAACAACCCTTGTCGGAAAAATCCTCACAGAGTTTCTCTACAGAAAAATGTTGTTTCTCCTGATGTATTGATAGTAATGATTAGAAAATTAGTCTGTAAATGCCTGTCTACAGTAGCTAATTTTTGTGTTTAATTTATATGATTTATTCTTGTTTTT chm1:+:177385869:-1 +TCCAAAGGTGACTGGCCAATGAATTGTTAATCTCATAGACTCATGGATTAAACACATTAATGTATTTACTACATTGCAGTTACTCTTAGTTGTATTCCCAAAATATCTTGGCCAGTGAAAGGCCCTTCAAATTGCCTTCAAGTAGGTAGTCTCCGGGTGCATTCTTGCTTTCTAGCATAACAACATGTTCCAGGCTCATTTTCATTTCCTGCCTCAGATCTGAAAACCAACCATTTAACGTAAGAAGCTCTGATGCCTTTGAGTGAGAAATAGCATTTAGGGAAGCATAATTTGTATTCTTCTATTTTATTTCTGAAACAAAAAATATCTGAAGCAAGCACGGCATTAGGTTATGAAATGGATAATGGTTGTTGGGGATACTACGAGACATTTGCTATGTTATTCATCCTTTGTGTATGCCAGTGTTTCCAATCCTCCATATATAACAACCCTTGTCGGAAAAATCCTCACAGAGTTTCTCTACAGAAAAATGTTGTTTCTCCTGATGTATTGATAGTAATGATTAGAAAATTAGTCTGTAAATGCCTGTCTACAGTAGCTAATTTTTGTGTTTAATTTATATGATTTATTCTTGTTTTT chm1:+:816366666:-1 +TCCAAAGGTGACTGGCCAATGAATTGTTAATCTCATAGACTCATGGATTAAACACATTAATGTATTTACTACATTGCAGTTACTCTTAGTTGTATTCCCAAAATATCTTGGCCAGTGAAAGGCCCTTCAAATTGCCTTCAAGTAGGTAGTCTCCGGGTGCATTCTTGCTTTCTAGCATAACAACATGTTCCAGGCTCATTTTCATTTCCTGCCTCAGATCTGAAAACCAACCATTTAACGTAAGAAGCTCTGATGCCTTTGAGTGAGAAATAGCATTTAGGGAAGCATAATTTGTATTCTTCTATTTTATTTCTGAAACAAAAAATATCTGAAGCAAGCACGGCATTAGGTTATGAAATGGATAATGGTTGTTGGGGATACTACGAGACATTTGCTATGTTATTCATCCTTTGTGTATGCCAGTGTTTCCAATCCTCCATATATAACAACCCTTGTCGGAAAAATCCTCACAGAGTTTCTCTACAGAAAAATGTTGTTTCTCCTGATGTATTGATAGTAATGATTAGAAAATTAGTCTGTAAATGCCTGTCTACAGTAGCTAATTTTTGTGTTTAATTTATATGATTTATTCTTGTTTTT chm1:+:779569028:28 +TCCAAAGGTGACTGGCCAATGAATTGTTAATCTCATAGACTCATGGATTAAACACATTAATGTATTTACTACATTGCAGTTACTCTTAGTTGTATTCCCAAAATATCTTGGCCAGTGAAAGGCCCTTCAAATTGCCTTCAAGTAGGTAGTCTCCGGGTGCATTCTTGCTTTCTAGCATAACAACATGTTCCAGGCTCATTTTCATTTCCTGCCTCAGATCTGAAAACCAACCATTTAACGTAAGAAGCTCTGATGCCTTTGAGTGAGAAATAGCATTTAGGGAAGCATAATTTGTATTCTTCTATTTTATTTCTGAAACAAAAAATATCTGAAGCAAGCACGGCATTAGGTTATGAAATGGATAATGGTTGTTGGGGATACTACGAGACATTTGCTATGTTATTCATCCTTTGTGTATGCCAGTGTTTCCAATCCTCCATATATAACAACCCTTGTCGGAAAAATCCTCACAGAGTTTCTCTACAGAAAAATGTTGTTTCTCCTGATGTATTGATAGTAATGATTAGAAAATTAGTCTGTAAATGCCTGTCTACAGTAGCTAATTTTTGTGTTTAATTTATATGATTTATTCTTGTTTTT chm1:+:779569029:28 +TCCAAAGGTGACTGGCCAATGAATTGTTAATCTCATAGACTCATGGATTAAACACATTAATGTATTTACTACATTGCAGTTACTCTTAGTTGTATTCCCAAAATATCTTGGCCAGTGAAAGGCCCTTCAAATTGCCTTCAAGTAGGTAGTCTCCGGGTGCATTCTTGCTTTCTAGCATAACAACATGTTCCAGGCTCATTTTCATTTCCTGCCTCAGATCTGAAAACCAACCATTTAACGTAAGAAGCTCTGATGCCTTTGAGTGAGAAATAGCATTTAGGGAAGCATAATTTGTATTCTTCTATTTTATTTCTGAAACAAAAAATATCTGAAGCAAGCACGGCATTAGGTTATGAAATGGATAATGGTTGTTGGGGATACTACGAGACATTTGCTATGTTATTCATCCTTTGTGTATGCCAGTGTTTCCAATCCTCCATATATAACAACCCTTGTCGGAAAAATCCTCACAGAGTTTCTCTACAGAAAAATGTTGTTTCTCCTGATGTATTGATAGTAATGATTAGAAAATTAGTCTGTAAATGCCTGTCTACAGTAGCTAATTTTTGTGTTTAATTTATATGATTTATTCTTGTTTTT chm1:+:779569031:28 +TCCAAAGGTGACTGGCCAATGAATTGTTAATCTCATAGACTCATGGATTAAACACATTAATGTATTTACTACATTGCAGTTACTCTTAGTTGTATTCCCAAAATATCTTGGCCAGTGAAAGGCCCTTCAAATTGCCTTCAAGTAGGTAGTCTCCGGGTGCATTCTTGCTTTCTAGCATAACAACATGTTCCAGGCTCATTTTCATTTCCTGCCTCAGATCTGAAAACCAACCATTTAACGTAAGAAGCTCTGATGCCTTTGAGTGAGAAATAGCATTTAGGGAAGCATAATTTGTATTCTTCTATTTTATTTCTGAAACAAAAAATATCTGAAGCAAGCACGGCATTAGGTTATGAAATGGATAATGGTTGTTGGGGATACTACGAGACATTTGCTATGTTATTCATCCTTTGTGTATGCCAGTGTTTCCAATCCTCCATATATAACAACCCTTGTCGGAAAAATCCTCACAGAGTTTCTCTACAGAAAAATGTTGTTTCTCCTGATGTATTGATAGTAATGATTAGAAAATTAGTCTGTAAATGCCTGTCTACAGTAGCTAATTTTTGTGTTTAATTTATATGATTTATTCTTGTTTTT chm1:+:779569022:28 +TCCAAAGGTGACTGGCCAATGAATTGTTAATCTCATAGACTCATGGATTAAACACATTAATGTATTTACTACATTGCAGTTACTCTTAGTTGTATTCCCAAAATATCTTGGCCAGTGAAAGGCCCTTCAAATTGCCTTCAAGTAGGTAGTCTCCGGGTGCATTCTTGCTTTCTAGCATAACAACATGTTCCAGGCTCATTTTCATTTCCTGCCTCAGATCTGAAAACCAACCATTTAACGTAAGAAGCTCTGATGCCTTTGAGTGAGAAATAGCATTTAGGGAAGCATAATTTGTATTCTTCTATTTTATTTCTGAAACAAAAAATATCTGAAGCAAGCACGGCATTAGGTTATGAAATGGATAATGGTTGTTGGGGATACTACGAGACATTTGCTATGTTATTCATCCTTTGTGTATGCCAGTGTTTCCAATCCTCCATATATAACAACCCTTGTCGGAAAAATCCTCACAGAGTTTCTCTACAGAAAAATGTTGTTTCTCCTGATGTATTGATAGTAATGATTAGAAAATTAGTCTGTAAATGCCTGTCTACAGTAGCTAATTTTTGTGTTTAATTTATATGATTTATTCTTGTTTTT chm1:+:779569023:28 chm1:+:2234266262:-1 +TCCAAAGGTGACTGGCCAATGAATTGTTAATCTCATAGACTCATGGATTAAACACATTAATGTATTTACTACATTGCAGTTACTCTTAGTTGTATTCCCAAAATATCTTGGCCAGTGAAAGGCCCTTCAAATTGCCTTCAAGTAGGTAGTCTCCGGGTGCATTCTTGCTTTCTAGCATAACAACATGTTCCAGGCTCATTTTCATTTCCTGCCTCAGATCTGAAAACCAACCATTTAACGTAAGAAGCTCTGATGCCTTTGAGTGAGAAATAGCATTTAGGGAAGCATAATTTGTATTCTTCTATTTTATTTCTGAAACAAAAAATATCTGAAGCAAGCACGGCATTAGGTTATGAAATGGATAATGGTTGTTGGGGATACTACGAGACATTTGCTATGTTATTCATCCTTTGTGTATGCCAGTGTTTCCAATCCTCCATATATAACAACCCTTGTCGGAAAAATCCTCACAGAGTTTCTCTACAGAAAAATGTTGTTTCTCCTGATGTATTGATAGTAATGATTAGAAAATTAGTCTGTAAATGCCTGTCTACAGTAGCTAATTTTTGTGTTTAATTTATATGATTTATTCTTGTTTTT chm1:+:1635744565:-1 +TCCAAAGGTGACTGGCCAATGAATTGTTAATCTCATAGACTCATGGATTAAACACATTAATGTATTTACTACATTGCAGTTACTCTTAGTTGTATTCCCAAAATATCTTGGCCAGTGAAAGGCCCTTCAAATTGCCTTCAAGTAGGTAGTCTCCGGGTGCATTCTTGCTTTCTAGCATAACAACATGTTCCAGGCTCATTTTCATTTCCTGCCTCAGATCTGAAAACCAACCATTTAACGTAAGAAGCTCTGATGCCTTTGAGTGAGAAATAGCATTTAGGGAAGCATAATTTGTATTCTTCTATTTTATTTCTGAAACAAAAAATATCTGAAGCAAGCACGGCATTAGGTTATGAAATGGATAATGGTTGTTGGGGATACTACGAGACATTTGCTATGTTATTCATCCTTTGTGTATGCCAGTGTTTCCAATCCTCCATATATAACAACCCTTGTCGGAAAAATCCTCACAGAGTTTCTCTACAGAAAAATGTTGTTTCTCCTGATGTATTGATAGTAATGATTAGAAAATTAGTCTGTAAATGCCTGTCTACAGTAGCTAATTTTTGTGTTTAATTTATATGATTTATTCTTGTTTTT chm1:+:779569026:28 +AAAAACAAGAATAAATCATATAAATTAAACACAAAAATTAGCTACTGTAGACAGGCATTTACAGACTAATTTTCTAATCATTACTATCAATACATCAGGAGAAACAACATTTTTCTGTAGAGAAACTCTGTGAGGATTTTTCCGACAAGGGTTGTTATATATGGAGGATTGGAAACACTGGCATACACAAAGGATGAATAACATAGCAAATGTCTCGTAGTATCCCCAACAACCATTATCCATTTCATAACCTAATGCCGTGCTTGCTTCAGATATTTTTTGTTTCAGAAATAAAATAGAAGAATACAAATTATGCTTCCCTAAATGCTATTTCTCACTCAAAGGCATCAGAGCTTCTTACGTTAAATGGTTGGTTTTCAGATCTGAGGCAGGAAATGAAAATGAGCCTGGAACATGTTGTTATGCTAGAAAGCAAGAATGCACCCGGAGACTACCTACTTGAAGGCAATTTGAAGGGCCTTTCACTGGCCAAGATATTTTGGGAATACAACTAAGAGTAACTGCAATGTAGTAAATACATTAATGTGTTTAATCCATGAGTCTATGAGATTAACAATTCATTGGCCAGTCACCTTTGGA chm1:+:1702190497:-1 +AAAAACAAGAATAAATCATATAAATTAAACACAAAAATTAGCTACTGTAGACAGGCATTTACAGACTAATTTTCTAATCATTACTATCAATACATCAGGAGAAACAACATTTTTCTGTAGAGAAACTCTGTGAGGATTTTTCCGACAAGGGTTGTTATATATGGAGGATTGGAAACACTGGCATACACAAAGGATGAATAACATAGCAAATGTCTCGTAGTATCCCCAACAACCATTATCCATTTCATAACCTAATGCCGTGCTTGCTTCAGATATTTTTTGTTTCAGAAATAAAATAGAAGAATACAAATTATGCTTCCCTAAATGCTATTTCTCACTCAAAGGCATCAGAGCTTCTTACGTTAAATGGTTGGTTTTCAGATCTGAGGCAGGAAATGAAAATGAGCCTGGAACATGTTGTTATGCTAGAAAGCAAGAATGCACCCGGAGACTACCTACTTGAAGGCAATTTGAAGGGCCTTTCACTGGCCAAGATATTTTGGGAATACAACTAAGAGTAACTGCAATGTAGTAAATACATTAATGTGTTTAATCCATGAGTCTATGAGATTAACAATTCATTGGCCAGTCACCTTTGGA chm1:+:2946699229:-1 +TCCTTCAGAACAGTTTACCCTTAGGGTTTGAAAGATAAAAGATATCAATCCTATTATTCTAGGAAGATCAGATAAACTGAAACCCAACACCCAATTCCTCCATTTTAAAAACAAACCTAGGCAAGTATGGCTTCTTCATCCCATTTTCACTCATATTTAAACATATCCTTAGAGCAATTATGTTGATGCTAAGGTTCCTCAATAGTAGCTTAGGACATGCCTTGAAATACTGTAACCTGGTCTTTCTATGGCTGAATTTCTTTCAGTTCTCCGTTGAAAATGTCCTCTCCTCCAAGAAACCTTCCCGACTACCCAATCTAGCATAGCCTCCCAGTACATTTCTCTACACTACATCACACTATTTTATTATTTTTATAGTATATATGGACTATTTCGAAGTTGCTAGTACATTTATTTGCTTATTATTATAGTATTTCTCCTTCAACCTTCAAAGTCTCATGAAAGCAGGGACTCATTTTATTCTCCTATATCCTCAAGATAACATCTTCCTTGCTAAAGATCCCAAGTTTTGTTTAGGTAGTCACGTGAGCCAATTATGGTAATCCCATTATATCTAGCATAATTTGTTTACAGGAAGAA chm1:+:108128932:-1 chm1:+:763992152:-1 chm1:+:826150634:-1 chm1:+:906537635:-1 chm1:+:962665471:25 chm1:+:1113327851:-1 chm1:+:1142400711:-1 chm1:+:1178425609:-1 chm1:+:1297981624:-1 chm1:+:1343215532:-1 chm1:+:1424123799:-1 chm1:+:1562337309:-1 chm1:+:1958428734:-1 chm1:+:2105817679:-1 chm1:+:2145518277:-1 chm1:+:2167674512:-1 chm1:+:2252932731:-1 chm1:+:2283449951:-1 chm1:+:2479193187:-1 chm1:+:2889192768:-1 chm1:+:2957078614:-1 +TCCTTCAGAACAGTTTACCCTTAGGGTTTGAAAGATAAAAGATATCAATCCTATTATTCTAGGAAGATCAGATAAACTGAAACCCAACACCCAATTCCTCCATTTTAAAAACAAACCTAGGCAAGTATGGCTTCTTCATCCCATTTTCACTCATATTTAAACATATCCTTAGAGCAATTATGTTGATGCTAAGGTTCCTCAATAGTAGCTTAGGACATGCCTTGAAATACTGTAACCTGGTCTTTCTATGGCTGAATTTCTTTCAGTTCTCCGTTGAAAATGTCCTCTCCTCCAAGAAACCTTCCCGACTACCCAATCTAGCATAGCCTCCCAGTACATTTCTCTACACTACATCACACTATTTTATTATTTTTATAGTATATATGGACTATTTCGAAGTTGCTAGTACATTTATTTGCTTATTATTATAGTATTTCTCCTTCAACCTTCAAAGTCTCATGAAAGCAGGGACTCATTTTATTCTCCTATATCCTCAAGATAACATCTTCCTTGCTAAAGATCCCAAGTTTTGTTTAGGTAGTCACGTGAGCCAATTATGGTAATCCCATTATATCTAGCATAATTTGTTTACAGGAAGAA chm1:+:962665470:25 +TCCTTCAGAACAGTTTACCCTTAGGGTTTGAAAGATAAAAGATATCAATCCTATTATTCTAGGAAGATCAGATAAACTGAAACCCAACACCCAATTCCTCCATTTTAAAAACAAACCTAGGCAAGTATGGCTTCTTCATCCCATTTTCACTCATATTTAAACATATCCTTAGAGCAATTATGTTGATGCTAAGGTTCCTCAATAGTAGCTTAGGACATGCCTTGAAATACTGTAACCTGGTCTTTCTATGGCTGAATTTCTTTCAGTTCTCCGTTGAAAATGTCCTCTCCTCCAAGAAACCTTCCCGACTACCCAATCTAGCATAGCCTCCCAGTACATTTCTCTACACTACATCACACTATTTTATTATTTTTATAGTATATATGGACTATTTCGAAGTTGCTAGTACATTTATTTGCTTATTATTATAGTATTTCTCCTTCAACCTTCAAAGTCTCATGAAAGCAGGGACTCATTTTATTCTCCTATATCCTCAAGATAACATCTTCCTTGCTAAAGATCCCAAGTTTTGTTTAGGTAGTCACGTGAGCCAATTATGGTAATCCCATTATATCTAGCATAATTTGTTTACAGGAAGAA chm1:+:962665469:25 +TCCTTCAGAACAGTTTACCCTTAGGGTTTGAAAGATAAAAGATATCAATCCTATTATTCTAGGAAGATCAGATAAACTGAAACCCAACACCCAATTCCTCCATTTTAAAAACAAACCTAGGCAAGTATGGCTTCTTCATCCCATTTTCACTCATATTTAAACATATCCTTAGAGCAATTATGTTGATGCTAAGGTTCCTCAATAGTAGCTTAGGACATGCCTTGAAATACTGTAACCTGGTCTTTCTATGGCTGAATTTCTTTCAGTTCTCCGTTGAAAATGTCCTCTCCTCCAAGAAACCTTCCCGACTACCCAATCTAGCATAGCCTCCCAGTACATTTCTCTACACTACATCACACTATTTTATTATTTTTATAGTATATATGGACTATTTCGAAGTTGCTAGTACATTTATTTGCTTATTATTATAGTATTTCTCCTTCAACCTTCAAAGTCTCATGAAAGCAGGGACTCATTTTATTCTCCTATATCCTCAAGATAACATCTTCCTTGCTAAAGATCCCAAGTTTTGTTTAGGTAGTCACGTGAGCCAATTATGGTAATCCCATTATATCTAGCATAATTTGTTTACAGGAAGAA chm1:+:962665474:25 +TCCTTCAGAACAGTTTACCCTTAGGGTTTGAAAGATAAAAGATATCAATCCTATTATTCTAGGAAGATCAGATAAACTGAAACCCAACACCCAATTCCTCCATTTTAAAAACAAACCTAGGCAAGTATGGCTTCTTCATCCCATTTTCACTCATATTTAAACATATCCTTAGAGCAATTATGTTGATGCTAAGGTTCCTCAATAGTAGCTTAGGACATGCCTTGAAATACTGTAACCTGGTCTTTCTATGGCTGAATTTCTTTCAGTTCTCCGTTGAAAATGTCCTCTCCTCCAAGAAACCTTCCCGACTACCCAATCTAGCATAGCCTCCCAGTACATTTCTCTACACTACATCACACTATTTTATTATTTTTATAGTATATATGGACTATTTCGAAGTTGCTAGTACATTTATTTGCTTATTATTATAGTATTTCTCCTTCAACCTTCAAAGTCTCATGAAAGCAGGGACTCATTTTATTCTCCTATATCCTCAAGATAACATCTTCCTTGCTAAAGATCCCAAGTTTTGTTTAGGTAGTCACGTGAGCCAATTATGGTAATCCCATTATATCTAGCATAATTTGTTTACAGGAAGAA chm1:+:962665479:25 +TCCTTCAGAACAGTTTACCCTTAGGGTTTGAAAGATAAAAGATATCAATCCTATTATTCTAGGAAGATCAGATAAACTGAAACCCAACACCCAATTCCTCCATTTTAAAAACAAACCTAGGCAAGTATGGCTTCTTCATCCCATTTTCACTCATATTTAAACATATCCTTAGAGCAATTATGTTGATGCTAAGGTTCCTCAATAGTAGCTTAGGACATGCCTTGAAATACTGTAACCTGGTCTTTCTATGGCTGAATTTCTTTCAGTTCTCCGTTGAAAATGTCCTCTCCTCCAAGAAACCTTCCCGACTACCCAATCTAGCATAGCCTCCCAGTACATTTCTCTACACTACATCACACTATTTTATTATTTTTATAGTATATATGGACTATTTCGAAGTTGCTAGTACATTTATTTGCTTATTATTATAGTATTTCTCCTTCAACCTTCAAAGTCTCATGAAAGCAGGGACTCATTTTATTCTCCTATATCCTCAAGATAACATCTTCCTTGCTAAAGATCCCAAGTTTTGTTTAGGTAGTCACGTGAGCCAATTATGGTAATCCCATTATATCTAGCATAATTTGTTTACAGGAAGAA chm1:+:2916356687:-1 +TCCTTCAGAACAGTTTACCCTTAGGGTTTGAAAGATAAAAGATATCAATCCTATTATTCTAGGAAGATCAGATAAACTGAAACCCAACACCCAATTCCTCCATTTTAAAAACAAACCTAGGCAAGTATGGCTTCTTCATCCCATTTTCACTCATATTTAAACATATCCTTAGAGCAATTATGTTGATGCTAAGGTTCCTCAATAGTAGCTTAGGACATGCCTTGAAATACTGTAACCTGGTCTTTCTATGGCTGAATTTCTTTCAGTTCTCCGTTGAAAATGTCCTCTCCTCCAAGAAACCTTCCCGACTACCCAATCTAGCATAGCCTCCCAGTACATTTCTCTACACTACATCACACTATTTTATTATTTTTATAGTATATATGGACTATTTCGAAGTTGCTAGTACATTTATTTGCTTATTATTATAGTATTTCTCCTTCAACCTTCAAAGTCTCATGAAAGCAGGGACTCATTTTATTCTCCTATATCCTCAAGATAACATCTTCCTTGCTAAAGATCCCAAGTTTTGTTTAGGTAGTCACGTGAGCCAATTATGGTAATCCCATTATATCTAGCATAATTTGTTTACAGGAAGAA chm1:+:962665477:25 +TCCTTCAGAACAGTTTACCCTTAGGGTTTGAAAGATAAAAGATATCAATCCTATTATTCTAGGAAGATCAGATAAACTGAAACCCAACACCCAATTCCTCCATTTTAAAAACAAACCTAGGCAAGTATGGCTTCTTCATCCCATTTTCACTCATATTTAAACATATCCTTAGAGCAATTATGTTGATGCTAAGGTTCCTCAATAGTAGCTTAGGACATGCCTTGAAATACTGTAACCTGGTCTTTCTATGGCTGAATTTCTTTCAGTTCTCCGTTGAAAATGTCCTCTCCTCCAAGAAACCTTCCCGACTACCCAATCTAGCATAGCCTCCCAGTACATTTCTCTACACTACATCACACTATTTTATTATTTTTATAGTATATATGGACTATTTCGAAGTTGCTAGTACATTTATTTGCTTATTATTATAGTATTTCTCCTTCAACCTTCAAAGTCTCATGAAAGCAGGGACTCATTTTATTCTCCTATATCCTCAAGATAACATCTTCCTTGCTAAAGATCCCAAGTTTTGTTTAGGTAGTCACGTGAGCCAATTATGGTAATCCCATTATATCTAGCATAATTTGTTTACAGGAAGAA chm1:+:962665478:25 +TCCTTCAGAACAGTTTACCCTTAGGGTTTGAAAGATAAAAGATATCAATCCTATTATTCTAGGAAGATCAGATAAACTGAAACCCAACACCCAATTCCTCCATTTTAAAAACAAACCTAGGCAAGTATGGCTTCTTCATCCCATTTTCACTCATATTTAAACATATCCTTAGAGCAATTATGTTGATGCTAAGGTTCCTCAATAGTAGCTTAGGACATGCCTTGAAATACTGTAACCTGGTCTTTCTATGGCTGAATTTCTTTCAGTTCTCCGTTGAAAATGTCCTCTCCTCCAAGAAACCTTCCCGACTACCCAATCTAGCATAGCCTCCCAGTACATTTCTCTACACTACATCACACTATTTTATTATTTTTATAGTATATATGGACTATTTCGAAGTTGCTAGTACATTTATTTGCTTATTATTATAGTATTTCTCCTTCAACCTTCAAAGTCTCATGAAAGCAGGGACTCATTTTATTCTCCTATATCCTCAAGATAACATCTTCCTTGCTAAAGATCCCAAGTTTTGTTTAGGTAGTCACGTGAGCCAATTATGGTAATCCCATTATATCTAGCATAATTTGTTTACAGGAAGAA chm1:+:962665481:25 +TCCTTCAGAACAGTTTACCCTTAGGGTTTGAAAGATAAAAGATATCAATCCTATTATTCTAGGAAGATCAGATAAACTGAAACCCAACACCCAATTCCTCCATTTTAAAAACAAACCTAGGCAAGTATGGCTTCTTCATCCCATTTTCACTCATATTTAAACATATCCTTAGAGCAATTATGTTGATGCTAAGGTTCCTCAATAGTAGCTTAGGACATGCCTTGAAATACTGTAACCTGGTCTTTCTATGGCTGAATTTCTTTCAGTTCTCCGTTGAAAATGTCCTCTCCTCCAAGAAACCTTCCCGACTACCCAATCTAGCATAGCCTCCCAGTACATTTCTCTACACTACATCACACTATTTTATTATTTTTATAGTATATATGGACTATTTCGAAGTTGCTAGTACATTTATTTGCTTATTATTATAGTATTTCTCCTTCAACCTTCAAAGTCTCATGAAAGCAGGGACTCATTTTATTCTCCTATATCCTCAAGATAACATCTTCCTTGCTAAAGATCCCAAGTTTTGTTTAGGTAGTCACGTGAGCCAATTATGGTAATCCCATTATATCTAGCATAATTTGTTTACAGGAAGAA chm1:+:962665473:25 +TCCTTCAGAACAGTTTACCCTTAGGGTTTGAAAGATAAAAGATATCAATCCTATTATTCTAGGAAGATCAGATAAACTGAAACCCAACACCCAATTCCTCCATTTTAAAAACAAACCTAGGCAAGTATGGCTTCTTCATCCCATTTTCACTCATATTTAAACATATCCTTAGAGCAATTATGTTGATGCTAAGGTTCCTCAATAGTAGCTTAGGACATGCCTTGAAATACTGTAACCTGGTCTTTCTATGGCTGAATTTCTTTCAGTTCTCCGTTGAAAATGTCCTCTCCTCCAAGAAACCTTCCCGACTACCCAATCTAGCATAGCCTCCCAGTACATTTCTCTACACTACATCACACTATTTTATTATTTTTATAGTATATATGGACTATTTCGAAGTTGCTAGTACATTTATTTGCTTATTATTATAGTATTTCTCCTTCAACCTTCAAAGTCTCATGAAAGCAGGGACTCATTTTATTCTCCTATATCCTCAAGATAACATCTTCCTTGCTAAAGATCCCAAGTTTTGTTTAGGTAGTCACGTGAGCCAATTATGGTAATCCCATTATATCTAGCATAATTTGTTTACAGGAAGAA chm1:+:962665475:25 +TTCTTCCTGTAAACAAATTATGCTAGATATAATGGGATTACCATAATTGGCTCACGTGACTACCTAAACAAAACTTGGGATCTTTAGCAAGGAAGATGTTATCTTGAGGATATAGGAGAATAAAATGAGTCCCTGCTTTCATGAGACTTTGAAGGTTGAAGGAGAAATACTATAATAATAAGCAAATAAATGTACTAGCAACTTCGAAATAGTCCATATATACTATAAAAATAATAAAATAGTGTGATGTAGTGTAGAGAAATGTACTGGGAGGCTATGCTAGATTGGGTAGTCGGGAAGGTTTCTTGGAGGAGAGGACATTTTCAACGGAGAACTGAAAGAAATTCAGCCATAGAAAGACCAGGTTACAGTATTTCAAGGCATGTCCTAAGCTACTATTGAGGAACCTTAGCATCAACATAATTGCTCTAAGGATATGTTTAAATATGAGTGAAAATGGGATGAAGAAGCCATACTTGCCTAGGTTTGTTTTTAAAATGGAGGAATTGGGTGTTGGGTTTCAGTTTATCTGATCTTCCTAGAATAATAGGATTGATATCTTTTATCTTTCAAACCCTAAGGGTAAACTGTTCTGAAGGA chm1:+:172127070:-1 +TTTAGCCTTGGAGATCACAGGAGTACCCTATCTCCAACAGGATCATCTCGAAGATTCATAAATGCCTGGCACACACATAGTAAGCACTGTGTCGAATGTGAGCTTTCATTATCATGTCATTATAATCTAAAAAGTGCCTAAGCAAATATTTGTAGAATGAATGAATCAATGAGATTACTCAGAGAAAGTTATACGGGAATGAGAACGACAAGAAGGAATAAGAATAAAACCTGAGTTATTAGTTCCTTAGAATGTTAGTATTCTAGTTCTATAAGAATTTCAGTTGCTTTTGAAAATTTACTTCAAGGAACAAAGATAAATTCAGATCCAAAATATTATTTCTCTAAAAATGTTTTAGTTTATTTTATTTTTTTGTAGAGACAGAGTCTTTGCTATATTGCCCAGGGTGGTCTCAAACTCCGGGCCTCAAGTAATCCTCCCGCCTCTGCCTTCCCAAAGCTCTGAGATTAACAGGCACGAAACAATGCACCCAGCCCCAAACAATATTCTTATCCAGGAGCACAGAAGAGATTCCAATGTTGCCAGGAAAAAGATTAGTTTGAGACCAGATAGGGGTAGTTAATCTTGAACCAATTAGGT chm1:+:13866389:-1 chm1:+:36652418:-1 chm1:+:99076610:-1 chm1:+:110671512:-1 chm1:+:171859494:-1 chm1:+:247031243:-1 chm1:+:271497331:-1 chm1:+:286975094:-1 chm1:+:385314603:-1 chm1:+:401381567:-1 chm1:+:423961325:-1 chm1:+:428217458:-1 chm1:+:510976933:-1 chm1:+:551712910:38 chm1:+:566607593:-1 chm1:+:590825295:-1 chm1:+:669423699:-1 chm1:+:699540039:-1 chm1:+:700070925:-1 chm1:+:716435491:-1 chm1:+:717112784:-1 chm1:+:728120457:-1 chm1:+:784794094:-1 chm1:+:830365643:-1 chm1:+:850076707:-1 chm1:+:879510145:-1 chm1:+:958750318:-1 chm1:+:975978106:-1 chm1:+:1019570723:-1 chm1:+:1057070086:-1 chm1:+:1099483627:-1 chm1:+:1099905863:-1 chm1:+:1152185397:-1 chm1:+:1221491840:-1 chm1:+:1305461771:-1 chm1:+:1331309291:-1 chm1:+:1334644468:-1 chm1:+:1338708804:-1 chm1:+:1362376291:-1 chm1:+:1388157643:-1 chm1:+:1400789061:-1 chm1:+:1435398278:-1 chm1:+:1495326627:-1 chm1:+:1540379723:-1 chm1:+:1559710162:-1 chm1:+:1615602559:-1 chm1:+:1633831032:-1 chm1:+:1636581899:-1 chm1:+:1689474436:-1 chm1:+:1690419956:-1 chm1:+:1700350019:-1 chm1:+:1713048135:-1 chm1:+:1762518090:-1 chm1:+:1796804465:-1 chm1:+:1802345599:-1 chm1:+:1818110168:-1 chm1:+:1825275819:-1 chm1:+:1908638235:-1 chm1:+:1923164316:-1 chm1:+:1934841435:-1 chm1:+:1938852466:-1 chm1:+:1990719431:-1 chm1:+:2057863191:-1 chm1:+:2120407862:-1 chm1:+:2162287890:-1 chm1:+:2162498570:-1 chm1:+:2259714282:-1 chm1:+:2269836367:-1 chm1:+:2285009484:-1 chm1:+:2293350548:-1 chm1:+:2298418118:-1 chm1:+:2351881477:-1 chm1:+:2367184473:-1 chm1:+:2382089351:-1 chm1:+:2404044085:-1 chm1:+:2420165856:-1 chm1:+:2421539462:-1 chm1:+:2436722096:-1 chm1:+:2477855748:-1 chm1:+:2507413416:-1 chm1:+:2537625925:-1 chm1:+:2565298554:-1 chm1:+:2591159835:-1 chm1:+:2615046930:-1 chm1:+:2661436247:-1 chm1:+:2663658172:-1 chm1:+:2670063982:-1 chm1:+:2692603726:-1 chm1:+:2699088231:-1 chm1:+:2711384261:-1 chm1:+:2716498008:-1 chm1:+:2774655984:-1 chm1:+:2819333186:-1 chm1:+:2822335974:-1 chm1:+:2851646401:-1 chm1:+:2859206451:-1 chm1:+:2875101873:-1 chm1:+:2875270096:-1 chm1:+:2898860864:-1 chm1:+:2983416934:-1 chm1:+:3013669210:-1 +TTTAGCCTTGGAGATCACAGGAGTACCCTATCTCCAACAGGATCATCTCGAAGATTCATAAATGCCTGGCACACACATAGTAAGCACTGTGTCGAATGTGAGCTTTCATTATCATGTCATTATAATCTAAAAAGTGCCTAAGCAAATATTTGTAGAATGAATGAATCAATGAGATTACTCAGAGAAAGTTATACGGGAATGAGAACGACAAGAAGGAATAAGAATAAAACCTGAGTTATTAGTTCCTTAGAATGTTAGTATTCTAGTTCTATAAGAATTTCAGTTGCTTTTGAAAATTTACTTCAAGGAACAAAGATAAATTCAGATCCAAAATATTATTTCTCTAAAAATGTTTTAGTTTATTTTATTTTTTTGTAGAGACAGAGTCTTTGCTATATTGCCCAGGGTGGTCTCAAACTCCGGGCCTCAAGTAATCCTCCCGCCTCTGCCTTCCCAAAGCTCTGAGATTAACAGGCACGAAACAATGCACCCAGCCCCAAACAATATTCTTATCCAGGAGCACAGAAGAGATTCCAATGTTGCCAGGAAAAAGATTAGTTTGAGACCAGATAGGGGTAGTTAATCTTGAACCAATTAGGT chm1:+:44574752:-1 chm1:+:47839260:-1 chm1:+:103280279:-1 chm1:+:143444587:-1 chm1:+:395483043:-1 chm1:+:461038193:-1 chm1:+:488130117:-1 chm1:+:523346833:-1 chm1:+:540436942:-1 chm1:+:586190484:-1 chm1:+:593974853:-1 chm1:+:760001227:-1 chm1:+:824024384:-1 chm1:+:835020975:-1 chm1:+:1097202923:-1 chm1:+:1188864237:-1 chm1:+:1197252227:-1 chm1:+:1237427976:-1 chm1:+:1261478407:-1 chm1:+:1301081945:-1 chm1:+:1316017937:-1 chm1:+:1376177588:-1 chm1:+:1413247961:-1 chm1:+:1485620923:-1 chm1:+:1496236194:-1 chm1:+:1523031538:-1 chm1:+:1525965107:-1 chm1:+:1540214771:-1 chm1:+:1561235289:-1 chm1:+:1670960739:-1 chm1:+:1686823918:-1 chm1:+:1687561158:-1 chm1:+:1778237026:-1 chm1:+:1931383498:-1 chm1:+:1971746112:-1 chm1:+:2047622076:-1 chm1:+:2071969325:-1 chm1:+:2081156378:-1 chm1:+:2112550688:-1 chm1:+:2113236780:-1 chm1:+:2144365196:-1 chm1:+:2146123775:-1 chm1:+:2235834301:-1 chm1:+:2273787574:-1 chm1:+:2438433566:-1 chm1:+:2651767888:-1 chm1:+:2671114418:-1 chm1:+:2673693737:-1 chm1:+:2711652795:-1 chm1:+:2712140684:-1 chm1:+:2881403328:-1 chm1:+:2976338047:-1 chm1:+:3043325477:-1 chm1:+:3049651398:-1 chm1:+:3061672828:-1 chm1:+:3063287214:-1 chm1:+:3095911686:-1 chm1:+:3097940811:-1 +TTTAGCCTTGGAGATCACAGGAGTACCCTATCTCCAACAGGATCATCTCGAAGATTCATAAATGCCTGGCACACACATAGTAAGCACTGTGTCGAATGTGAGCTTTCATTATCATGTCATTATAATCTAAAAAGTGCCTAAGCAAATATTTGTAGAATGAATGAATCAATGAGATTACTCAGAGAAAGTTATACGGGAATGAGAACGACAAGAAGGAATAAGAATAAAACCTGAGTTATTAGTTCCTTAGAATGTTAGTATTCTAGTTCTATAAGAATTTCAGTTGCTTTTGAAAATTTACTTCAAGGAACAAAGATAAATTCAGATCCAAAATATTATTTCTCTAAAAATGTTTTAGTTTATTTTATTTTTTTGTAGAGACAGAGTCTTTGCTATATTGCCCAGGGTGGTCTCAAACTCCGGGCCTCAAGTAATCCTCCCGCCTCTGCCTTCCCAAAGCTCTGAGATTAACAGGCACGAAACAATGCACCCAGCCCCAAACAATATTCTTATCCAGGAGCACAGAAGAGATTCCAATGTTGCCAGGAAAAAGATTAGTTTGAGACCAGATAGGGGTAGTTAATCTTGAACCAATTAGGT chm1:+:11816940:-1 chm1:+:551712918:38 chm1:+:818765758:-1 chm1:+:942621224:-1 chm1:+:984277499:-1 chm1:+:1106304280:-1 chm1:+:1364251437:-1 chm1:+:1897409318:-1 chm1:+:1924818471:-1 chm1:+:2300179368:-1 chm1:+:2640920877:-1 +TTTAGCCTTGGAGATCACAGGAGTACCCTATCTCCAACAGGATCATCTCGAAGATTCATAAATGCCTGGCACACACATAGTAAGCACTGTGTCGAATGTGAGCTTTCATTATCATGTCATTATAATCTAAAAAGTGCCTAAGCAAATATTTGTAGAATGAATGAATCAATGAGATTACTCAGAGAAAGTTATACGGGAATGAGAACGACAAGAAGGAATAAGAATAAAACCTGAGTTATTAGTTCCTTAGAATGTTAGTATTCTAGTTCTATAAGAATTTCAGTTGCTTTTGAAAATTTACTTCAAGGAACAAAGATAAATTCAGATCCAAAATATTATTTCTCTAAAAATGTTTTAGTTTATTTTATTTTTTTGTAGAGACAGAGTCTTTGCTATATTGCCCAGGGTGGTCTCAAACTCCGGGCCTCAAGTAATCCTCCCGCCTCTGCCTTCCCAAAGCTCTGAGATTAACAGGCACGAAACAATGCACCCAGCCCCAAACAATATTCTTATCCAGGAGCACAGAAGAGATTCCAATGTTGCCAGGAAAAAGATTAGTTTGAGACCAGATAGGGGTAGTTAATCTTGAACCAATTAGGT chm1:+:438987472:-1 chm1:+:551712911:38 chm1:+:579507163:-1 chm1:+:1328385859:-1 +TTTAGCCTTGGAGATCACAGGAGTACCCTATCTCCAACAGGATCATCTCGAAGATTCATAAATGCCTGGCACACACATAGTAAGCACTGTGTCGAATGTGAGCTTTCATTATCATGTCATTATAATCTAAAAAGTGCCTAAGCAAATATTTGTAGAATGAATGAATCAATGAGATTACTCAGAGAAAGTTATACGGGAATGAGAACGACAAGAAGGAATAAGAATAAAACCTGAGTTATTAGTTCCTTAGAATGTTAGTATTCTAGTTCTATAAGAATTTCAGTTGCTTTTGAAAATTTACTTCAAGGAACAAAGATAAATTCAGATCCAAAATATTATTTCTCTAAAAATGTTTTAGTTTATTTTATTTTTTTGTAGAGACAGAGTCTTTGCTATATTGCCCAGGGTGGTCTCAAACTCCGGGCCTCAAGTAATCCTCCCGCCTCTGCCTTCCCAAAGCTCTGAGATTAACAGGCACGAAACAATGCACCCAGCCCCAAACAATATTCTTATCCAGGAGCACAGAAGAGATTCCAATGTTGCCAGGAAAAAGATTAGTTTGAGACCAGATAGGGGTAGTTAATCTTGAACCAATTAGGT chm1:+:1434854925:-1 chm1:+:1752688903:-1 chm1:+:1755254146:-1 chm1:+:1960745229:-1 chm1:+:2613824702:-1 +TTTAGCCTTGGAGATCACAGGAGTACCCTATCTCCAACAGGATCATCTCGAAGATTCATAAATGCCTGGCACACACATAGTAAGCACTGTGTCGAATGTGAGCTTTCATTATCATGTCATTATAATCTAAAAAGTGCCTAAGCAAATATTTGTAGAATGAATGAATCAATGAGATTACTCAGAGAAAGTTATACGGGAATGAGAACGACAAGAAGGAATAAGAATAAAACCTGAGTTATTAGTTCCTTAGAATGTTAGTATTCTAGTTCTATAAGAATTTCAGTTGCTTTTGAAAATTTACTTCAAGGAACAAAGATAAATTCAGATCCAAAATATTATTTCTCTAAAAATGTTTTAGTTTATTTTATTTTTTTGTAGAGACAGAGTCTTTGCTATATTGCCCAGGGTGGTCTCAAACTCCGGGCCTCAAGTAATCCTCCCGCCTCTGCCTTCCCAAAGCTCTGAGATTAACAGGCACGAAACAATGCACCCAGCCCCAAACAATATTCTTATCCAGGAGCACAGAAGAGATTCCAATGTTGCCAGGAAAAAGATTAGTTTGAGACCAGATAGGGGTAGTTAATCTTGAACCAATTAGGT chm1:+:551712912:38 +TTTAGCCTTGGAGATCACAGGAGTACCCTATCTCCAACAGGATCATCTCGAAGATTCATAAATGCCTGGCACACACATAGTAAGCACTGTGTCGAATGTGAGCTTTCATTATCATGTCATTATAATCTAAAAAGTGCCTAAGCAAATATTTGTAGAATGAATGAATCAATGAGATTACTCAGAGAAAGTTATACGGGAATGAGAACGACAAGAAGGAATAAGAATAAAACCTGAGTTATTAGTTCCTTAGAATGTTAGTATTCTAGTTCTATAAGAATTTCAGTTGCTTTTGAAAATTTACTTCAAGGAACAAAGATAAATTCAGATCCAAAATATTATTTCTCTAAAAATGTTTTAGTTTATTTTATTTTTTTGTAGAGACAGAGTCTTTGCTATATTGCCCAGGGTGGTCTCAAACTCCGGGCCTCAAGTAATCCTCCCGCCTCTGCCTTCCCAAAGCTCTGAGATTAACAGGCACGAAACAATGCACCCAGCCCCAAACAATATTCTTATCCAGGAGCACAGAAGAGATTCCAATGTTGCCAGGAAAAAGATTAGTTTGAGACCAGATAGGGGTAGTTAATCTTGAACCAATTAGGT chm1:+:551712919:38 +TTTAGCCTTGGAGATCACAGGAGTACCCTATCTCCAACAGGATCATCTCGAAGATTCATAAATGCCTGGCACACACATAGTAAGCACTGTGTCGAATGTGAGCTTTCATTATCATGTCATTATAATCTAAAAAGTGCCTAAGCAAATATTTGTAGAATGAATGAATCAATGAGATTACTCAGAGAAAGTTATACGGGAATGAGAACGACAAGAAGGAATAAGAATAAAACCTGAGTTATTAGTTCCTTAGAATGTTAGTATTCTAGTTCTATAAGAATTTCAGTTGCTTTTGAAAATTTACTTCAAGGAACAAAGATAAATTCAGATCCAAAATATTATTTCTCTAAAAATGTTTTAGTTTATTTTATTTTTTTGTAGAGACAGAGTCTTTGCTATATTGCCCAGGGTGGTCTCAAACTCCGGGCCTCAAGTAATCCTCCCGCCTCTGCCTTCCCAAAGCTCTGAGATTAACAGGCACGAAACAATGCACCCAGCCCCAAACAATATTCTTATCCAGGAGCACAGAAGAGATTCCAATGTTGCCAGGAAAAAGATTAGTTTGAGACCAGATAGGGGTAGTTAATCTTGAACCAATTAGGT chm1:+:551712909:38 +TTTAGCCTTGGAGATCACAGGAGTACCCTATCTCCAACAGGATCATCTCGAAGATTCATAAATGCCTGGCACACACATAGTAAGCACTGTGTCGAATGTGAGCTTTCATTATCATGTCATTATAATCTAAAAAGTGCCTAAGCAAATATTTGTAGAATGAATGAATCAATGAGATTACTCAGAGAAAGTTATACGGGAATGAGAACGACAAGAAGGAATAAGAATAAAACCTGAGTTATTAGTTCCTTAGAATGTTAGTATTCTAGTTCTATAAGAATTTCAGTTGCTTTTGAAAATTTACTTCAAGGAACAAAGATAAATTCAGATCCAAAATATTATTTCTCTAAAAATGTTTTAGTTTATTTTATTTTTTTGTAGAGACAGAGTCTTTGCTATATTGCCCAGGGTGGTCTCAAACTCCGGGCCTCAAGTAATCCTCCCGCCTCTGCCTTCCCAAAGCTCTGAGATTAACAGGCACGAAACAATGCACCCAGCCCCAAACAATATTCTTATCCAGGAGCACAGAAGAGATTCCAATGTTGCCAGGAAAAAGATTAGTTTGAGACCAGATAGGGGTAGTTAATCTTGAACCAATTAGGT chm1:+:2539768116:-1 +TTTAGCCTTGGAGATCACAGGAGTACCCTATCTCCAACAGGATCATCTCGAAGATTCATAAATGCCTGGCACACACATAGTAAGCACTGTGTCGAATGTGAGCTTTCATTATCATGTCATTATAATCTAAAAAGTGCCTAAGCAAATATTTGTAGAATGAATGAATCAATGAGATTACTCAGAGAAAGTTATACGGGAATGAGAACGACAAGAAGGAATAAGAATAAAACCTGAGTTATTAGTTCCTTAGAATGTTAGTATTCTAGTTCTATAAGAATTTCAGTTGCTTTTGAAAATTTACTTCAAGGAACAAAGATAAATTCAGATCCAAAATATTATTTCTCTAAAAATGTTTTAGTTTATTTTATTTTTTTGTAGAGACAGAGTCTTTGCTATATTGCCCAGGGTGGTCTCAAACTCCGGGCCTCAAGTAATCCTCCCGCCTCTGCCTTCCCAAAGCTCTGAGATTAACAGGCACGAAACAATGCACCCAGCCCCAAACAATATTCTTATCCAGGAGCACAGAAGAGATTCCAATGTTGCCAGGAAAAAGATTAGTTTGAGACCAGATAGGGGTAGTTAATCTTGAACCAATTAGGT chm1:+:551712908:38 +TTTAGCCTTGGAGATCACAGGAGTACCCTATCTCCAACAGGATCATCTCGAAGATTCATAAATGCCTGGCACACACATAGTAAGCACTGTGTCGAATGTGAGCTTTCATTATCATGTCATTATAATCTAAAAAGTGCCTAAGCAAATATTTGTAGAATGAATGAATCAATGAGATTACTCAGAGAAAGTTATACGGGAATGAGAACGACAAGAAGGAATAAGAATAAAACCTGAGTTATTAGTTCCTTAGAATGTTAGTATTCTAGTTCTATAAGAATTTCAGTTGCTTTTGAAAATTTACTTCAAGGAACAAAGATAAATTCAGATCCAAAATATTATTTCTCTAAAAATGTTTTAGTTTATTTTATTTTTTTGTAGAGACAGAGTCTTTGCTATATTGCCCAGGGTGGTCTCAAACTCCGGGCCTCAAGTAATCCTCCCGCCTCTGCCTTCCCAAAGCTCTGAGATTAACAGGCACGAAACAATGCACCCAGCCCCAAACAATATTCTTATCCAGGAGCACAGAAGAGATTCCAATGTTGCCAGGAAAAAGATTAGTTTGAGACCAGATAGGGGTAGTTAATCTTGAACCAATTAGGT chm1:+:551712915:38 +TTTAGCCTTGGAGATCACAGGAGTACCCTATCTCCAACAGGATCATCTCGAAGATTCATAAATGCCTGGCACACACATAGTAAGCACTGTGTCGAATGTGAGCTTTCATTATCATGTCATTATAATCTAAAAAGTGCCTAAGCAAATATTTGTAGAATGAATGAATCAATGAGATTACTCAGAGAAAGTTATACGGGAATGAGAACGACAAGAAGGAATAAGAATAAAACCTGAGTTATTAGTTCCTTAGAATGTTAGTATTCTAGTTCTATAAGAATTTCAGTTGCTTTTGAAAATTTACTTCAAGGAACAAAGATAAATTCAGATCCAAAATATTATTTCTCTAAAAATGTTTTAGTTTATTTTATTTTTTTGTAGAGACAGAGTCTTTGCTATATTGCCCAGGGTGGTCTCAAACTCCGGGCCTCAAGTAATCCTCCCGCCTCTGCCTTCCCAAAGCTCTGAGATTAACAGGCACGAAACAATGCACCCAGCCCCAAACAATATTCTTATCCAGGAGCACAGAAGAGATTCCAATGTTGCCAGGAAAAAGATTAGTTTGAGACCAGATAGGGGTAGTTAATCTTGAACCAATTAGGT chm1:+:1485750047:-1 +TTTAGCCTTGGAGATCACAGGAGTACCCTATCTCCAACAGGATCATCTCGAAGATTCATAAATGCCTGGCACACACATAGTAAGCACTGTGTCGAATGTGAGCTTTCATTATCATGTCATTATAATCTAAAAAGTGCCTAAGCAAATATTTGTAGAATGAATGAATCAATGAGATTACTCAGAGAAAGTTATACGGGAATGAGAACGACAAGAAGGAATAAGAATAAAACCTGAGTTATTAGTTCCTTAGAATGTTAGTATTCTAGTTCTATAAGAATTTCAGTTGCTTTTGAAAATTTACTTCAAGGAACAAAGATAAATTCAGATCCAAAATATTATTTCTCTAAAAATGTTTTAGTTTATTTTATTTTTTTGTAGAGACAGAGTCTTTGCTATATTGCCCAGGGTGGTCTCAAACTCCGGGCCTCAAGTAATCCTCCCGCCTCTGCCTTCCCAAAGCTCTGAGATTAACAGGCACGAAACAATGCACCCAGCCCCAAACAATATTCTTATCCAGGAGCACAGAAGAGATTCCAATGTTGCCAGGAAAAAGATTAGTTTGAGACCAGATAGGGGTAGTTAATCTTGAACCAATTAGGT chm1:+:551712920:38 +TTTAGCCTTGGAGATCACAGGAGTACCCTATCTCCAACAGGATCATCTCGAAGATTCATAAATGCCTGGCACACACATAGTAAGCACTGTGTCGAATGTGAGCTTTCATTATCATGTCATTATAATCTAAAAAGTGCCTAAGCAAATATTTGTAGAATGAATGAATCAATGAGATTACTCAGAGAAAGTTATACGGGAATGAGAACGACAAGAAGGAATAAGAATAAAACCTGAGTTATTAGTTCCTTAGAATGTTAGTATTCTAGTTCTATAAGAATTTCAGTTGCTTTTGAAAATTTACTTCAAGGAACAAAGATAAATTCAGATCCAAAATATTATTTCTCTAAAAATGTTTTAGTTTATTTTATTTTTTTGTAGAGACAGAGTCTTTGCTATATTGCCCAGGGTGGTCTCAAACTCCGGGCCTCAAGTAATCCTCCCGCCTCTGCCTTCCCAAAGCTCTGAGATTAACAGGCACGAAACAATGCACCCAGCCCCAAACAATATTCTTATCCAGGAGCACAGAAGAGATTCCAATGTTGCCAGGAAAAAGATTAGTTTGAGACCAGATAGGGGTAGTTAATCTTGAACCAATTAGGT chm1:+:59509836:-1 chm1:+:161336251:-1 chm1:+:398328232:-1 chm1:+:642447181:-1 chm1:+:819166048:-1 chm1:+:1100932727:-1 chm1:+:1211435120:-1 chm1:+:1311259955:-1 chm1:+:1513990342:-1 chm1:+:1774606654:-1 chm1:+:1924068162:-1 chm1:+:2044603630:-1 chm1:+:2349834321:-1 chm1:+:2391204284:-1 chm1:+:2487870591:-1 chm1:+:2519961307:-1 chm1:+:2538850264:-1 chm1:+:2717275208:-1 chm1:+:2995444282:-1 +ACCTAATTGGTTCAAGATTAACTACCCCTATCTGGTCTCAAACTAATCTTTTTCCTGGCAACATTGGAATCTCTTCTGTGCTCCTGGATAAGAATATTGTTTGGGGCTGGGTGCATTGTTTCGTGCCTGTTAATCTCAGAGCTTTGGGAAGGCAGAGGCGGGAGGATTACTTGAGGCCCGGAGTTTGAGACCACCCTGGGCAATATAGCAAAGACTCTGTCTCTACAAAAAAATAAAATAAACTAAAACATTTTTAGAGAAATAATATTTTGGATCTGAATTTATCTTTGTTCCTTGAAGTAAATTTTCAAAAGCAACTGAAATTCTTATAGAACTAGAATACTAACATTCTAAGGAACTAATAACTCAGGTTTTATTCTTATTCCTTCTTGTCGTTCTCATTCCCGTATAACTTTCTCTGAGTAATCTCATTGATTCATTCATTCTACAAATATTTGCTTAGGCACTTTTTAGATTATAATGACATGATAATGAAAGCTCACATTCGACACAGTGCTTACTATGTGTGTGCCAGGCATTTATGAATCTTCGAGATGATCCTGTTGGAGATAGGGTACTCCTGTGATCTCCAAGGCTAAA chm1:+:169107439:-1 chm1:+:386152800:-1 chm1:+:539532626:-1 chm1:+:1075877744:-1 chm1:+:1381876617:-1 chm1:+:1545209794:-1 chm1:+:2111379110:-1 chm1:+:2432868801:-1 chm1:+:2504817890:-1 chm1:+:2627416134:-1 chm1:+:2704784229:-1 chm1:+:2705654088:-1 diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-800nt.prof b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-800nt.prof new file mode 100644 index 0000000000000000000000000000000000000000..4ef417232d3c8fc3ab4525b10f14a94179003116 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/data/1K-800nt.prof @@ -0,0 +1,1000 @@ +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:1680513854:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:2042761514:-1 chm1:+:2360117432:-1 chm1:+:2914989026:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:12281849:-1 chm1:+:253489940:-1 chm1:+:264345416:-1 chm1:+:266462485:-1 chm1:+:458677546:-1 chm1:+:460615396:-1 chm1:+:461882975:-1 chm1:+:658931812:-1 chm1:+:672943330:-1 chm1:+:724449252:-1 chm1:+:995923497:-1 chm1:+:1154803085:-1 chm1:+:1791925299:-1 chm1:+:1971971201:-1 chm1:+:2012473711:-1 chm1:+:2043005763:-1 chm1:+:2916449014:-1 chm1:+:2963069460:-1 chm1:+:2973691463:-1 chm1:+:3035174706:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:190584374:-1 chm1:+:301429551:-1 chm1:+:431320963:-1 chm1:+:515342897:-1 chm1:+:592626712:-1 chm1:+:636675381:-1 chm1:+:690564492:-1 chm1:+:783063076:-1 chm1:+:840030091:-1 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+ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:5637150:-1 chm1:+:74377106:-1 chm1:+:174704914:-1 chm1:+:404395275:-1 chm1:+:430972143:-1 chm1:+:512145463:-1 chm1:+:738132134:-1 chm1:+:1050716327:-1 chm1:+:1155716298:-1 chm1:+:1166535650:-1 chm1:+:1210922262:-1 chm1:+:1357199830:-1 chm1:+:1751373540:-1 chm1:+:1917095207:-1 chm1:+:2139372950:-1 chm1:+:2613196022:-1 chm1:+:2801362057:-1 chm1:+:2958304959:-1 chm1:+:2967008239:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:66523309:-1 chm1:+:74065732:-1 chm1:+:77157529:-1 chm1:+:231564558:-1 chm1:+:240106377:-1 chm1:+:263381935:-1 chm1:+:456569577:-1 chm1:+:573237657:-1 chm1:+:576713580:-1 chm1:+:579648372:-1 chm1:+:1002049479:-1 chm1:+:1043686944:-1 chm1:+:1189608743:160 chm1:+:1203175279:-1 chm1:+:1611086861:-1 chm1:+:1854703548:-1 chm1:+:1908993756:-1 chm1:+:1996376372:-1 chm1:+:2141831921:-1 chm1:+:2145646061:-1 chm1:+:2260412234:-1 chm1:+:2377284864:-1 chm1:+:2737340089:-1 chm1:+:2894112783:-1 chm1:+:2962930989:-1 chm1:+:2974960421:-1 chm1:+:2980329120:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:1908879730:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:54224016:-1 chm1:+:107351243:-1 chm1:+:299007024:-1 chm1:+:476133026:-1 chm1:+:587324305:-1 chm1:+:788124438:-1 chm1:+:908827208:-1 chm1:+:1141442702:-1 chm1:+:1524513990:-1 chm1:+:1524558153:-1 chm1:+:1621951696:-1 chm1:+:1764485490:-1 chm1:+:1913923132:-1 chm1:+:2969321061:-1 chm1:+:3024847521:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:7850379:-1 chm1:+:51220471:-1 chm1:+:78250802:-1 chm1:+:103248525:-1 chm1:+:189945731:-1 chm1:+:231888107:-1 chm1:+:272193832:-1 chm1:+:283167812:-1 chm1:+:299209082:-1 chm1:+:302740508:-1 chm1:+:377697957:-1 chm1:+:443385964:-1 chm1:+:595161188:-1 chm1:+:621532685:-1 chm1:+:632873804:-1 chm1:+:682508172:-1 chm1:+:705559362:-1 chm1:+:709470419:-1 chm1:+:709924040:-1 chm1:+:774768139:-1 chm1:+:880706820:-1 chm1:+:949132506:-1 chm1:+:994667216:-1 chm1:+:1119931814:-1 chm1:+:1180833815:-1 chm1:+:1195477083:-1 chm1:+:1205324916:-1 chm1:+:1223265846:-1 chm1:+:1339637826:-1 chm1:+:1359571955:-1 chm1:+:1362956919:-1 chm1:+:1386913219:-1 chm1:+:1534282293:-1 chm1:+:1563449898:-1 chm1:+:1765872920:-1 chm1:+:1767185531:-1 chm1:+:1788920953:-1 chm1:+:1789241318:-1 chm1:+:1866201667:-1 chm1:+:1921128657:-1 chm1:+:1984913184:-1 chm1:+:2171934923:-1 chm1:+:2189249066:-1 chm1:+:2247658328:-1 chm1:+:2307007620:-1 chm1:+:2334906466:-1 chm1:+:2474500923:-1 chm1:+:2545517246:-1 chm1:+:2550916674:-1 chm1:+:2584175907:-1 chm1:+:2621355104:-1 chm1:+:2669369692:-1 chm1:+:2806469330:-1 chm1:+:2812223410:-1 chm1:+:2907194551:-1 chm1:+:2912850765:-1 chm1:+:2945880582:-1 chm1:+:2952114320:-1 chm1:+:2962141049:-1 chm1:+:2967293885:-1 chm1:+:2973293867:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:87946834:-1 chm1:+:454923073:-1 chm1:+:1685759344:-1 chm1:+:2630954604:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:262828322:-1 chm1:+:668265842:-1 chm1:+:847809345:-1 chm1:+:900256334:-1 chm1:+:996568843:-1 chm1:+:1071802677:160 chm1:+:1180008135:-1 chm1:+:1180012929:-1 chm1:+:1193424449:-1 chm1:+:1352590282:-1 chm1:+:1684332003:-1 chm1:+:2153330386:-1 chm1:+:2975624983:-1 chm1:+:2975734737:-1 chm1:+:3006157853:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:321198802:-1 chm1:+:524924152:-1 chm1:+:886079961:-1 chm1:+:1030224866:-1 chm1:+:1685991570:-1 chm1:+:1962958799:-1 chm1:+:2165156109:-1 chm1:+:2441541771:-1 chm1:+:2819381464:-1 chm1:+:2827308597:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:149101901:-1 chm1:+:153334042:-1 chm1:+:689594790:-1 chm1:+:689594853:-1 chm1:+:876196121:-1 chm1:+:883127043:-1 chm1:+:936456585:-1 chm1:+:1035435726:-1 chm1:+:1309276145:-1 chm1:+:1398320929:-1 chm1:+:1423972221:-1 chm1:+:1730424461:-1 chm1:+:1949964096:-1 chm1:+:2190701593:-1 chm1:+:2460421708:-1 chm1:+:2604660213:-1 chm1:+:2690257210:-1 chm1:+:2701144192:-1 chm1:+:2707832450:-1 chm1:+:2824938236:-1 chm1:+:2878241844:-1 chm1:+:2905544501:-1 chm1:+:3061356220:-1 chm1:+:3062989969:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:294467980:-1 chm1:+:612323018:-1 chm1:+:2159216060:-1 chm1:+:2291606852:-1 chm1:+:2461495904:-1 chm1:+:2929613863:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:70252266:-1 chm1:+:163151916:-1 chm1:+:668714857:-1 chm1:+:713019388:-1 chm1:+:1097663107:-1 chm1:+:1163106744:-1 chm1:+:1247693676:-1 chm1:+:1475214621:-1 chm1:+:1717629847:-1 chm1:+:1971297317:-1 chm1:+:2249318907:-1 chm1:+:2359960380:-1 chm1:+:2489347402:-1 chm1:+:2893009019:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:288833605:-1 chm1:+:695651407:-1 chm1:+:986952643:-1 chm1:+:1630503976:-1 chm1:+:1677208875:-1 chm1:+:1681127359:-1 chm1:+:1726780388:-1 chm1:+:1731462110:-1 chm1:+:1731683840:-1 chm1:+:1812829599:-1 chm1:+:1827969169:-1 chm1:+:1862749068:-1 chm1:+:1951354277:-1 chm1:+:2139924614:-1 chm1:+:2161513701:-1 chm1:+:2464730181:-1 chm1:+:2473769822:-1 chm1:+:2914172473:-1 chm1:+:2979823488:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:748984334:-1 chm1:+:997840380:-1 chm1:+:1230258843:-1 chm1:+:1873878607:-1 chm1:+:2276982514:-1 chm1:+:2691268501:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:423391304:-1 chm1:+:457005629:-1 chm1:+:554750752:-1 chm1:+:764812302:-1 chm1:+:949324290:-1 chm1:+:1014662582:-1 chm1:+:1014662633:-1 chm1:+:1187923642:-1 chm1:+:1378479897:-1 chm1:+:1426726544:-1 chm1:+:1627828192:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:4961072:-1 chm1:+:25634364:-1 chm1:+:30477146:-1 chm1:+:56487037:-1 chm1:+:61543149:-1 chm1:+:86842344:-1 chm1:+:88490590:-1 chm1:+:88871338:-1 chm1:+:215496392:-1 chm1:+:253732732:-1 chm1:+:262175728:-1 chm1:+:263381937:-1 chm1:+:294368914:-1 chm1:+:365262425:-1 chm1:+:366201602:-1 chm1:+:379283311:-1 chm1:+:388762677:-1 chm1:+:394079611:-1 chm1:+:405901947:-1 chm1:+:437607587:-1 chm1:+:445093966:-1 chm1:+:456463767:-1 chm1:+:471667039:-1 chm1:+:472606745:-1 chm1:+:478510395:-1 chm1:+:519094295:-1 chm1:+:527882734:-1 chm1:+:558724767:-1 chm1:+:561491015:-1 chm1:+:594679569:-1 chm1:+:725216169:-1 chm1:+:725807319:-1 chm1:+:756306750:-1 chm1:+:756474511:-1 chm1:+:794393673:-1 chm1:+:809392025:-1 chm1:+:855435947:-1 chm1:+:864127561:-1 chm1:+:894893596:-1 chm1:+:932765509:-1 chm1:+:941701010:-1 chm1:+:986724200:-1 chm1:+:995054131:-1 chm1:+:996724393:-1 chm1:+:1011941987:-1 chm1:+:1129147238:-1 chm1:+:1170265864:-1 chm1:+:1195053474:-1 chm1:+:1206735771:-1 chm1:+:1252969255:-1 chm1:+:1269153844:-1 chm1:+:1319677249:-1 chm1:+:1364112273:-1 chm1:+:1487188689:-1 chm1:+:1502851659:-1 chm1:+:1513205896:-1 chm1:+:1523410870:-1 chm1:+:1571819406:-1 chm1:+:1665421667:-1 chm1:+:1677130668:-1 chm1:+:1680514641:-1 chm1:+:1701680994:-1 chm1:+:1808420723:-1 chm1:+:1849598433:-1 chm1:+:1855183839:-1 chm1:+:1919502226:-1 chm1:+:2000027393:-1 chm1:+:2018066428:-1 chm1:+:2032610556:-1 chm1:+:2038473241:-1 chm1:+:2077689989:-1 chm1:+:2113417831:-1 chm1:+:2140344905:-1 chm1:+:2166889655:-1 chm1:+:2230244160:-1 chm1:+:2251096217:-1 chm1:+:2290616344:-1 chm1:+:2303181009:-1 chm1:+:2331565683:-1 chm1:+:2332889080:-1 chm1:+:2359561957:-1 chm1:+:2394659963:-1 chm1:+:2492715198:-1 chm1:+:2521865897:-1 chm1:+:2543345364:-1 chm1:+:2600584716:-1 chm1:+:2653599353:-1 chm1:+:2654049048:-1 chm1:+:2668936467:-1 chm1:+:2691419646:-1 chm1:+:2823898973:-1 chm1:+:2851126383:-1 chm1:+:2899668185:-1 chm1:+:2973397533:-1 chm1:+:2995199434:-1 chm1:+:3015771852:-1 chm1:+:3026425331:-1 chm1:+:3042395206:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:4296667:-1 chm1:+:799360247:-1 chm1:+:968771097:-1 chm1:+:1008743214:-1 chm1:+:1178356685:-1 chm1:+:1198641812:-1 chm1:+:1673908561:-1 chm1:+:2062553803:-1 chm1:+:2193075781:-1 chm1:+:2259082194:-1 chm1:+:2334906468:-1 chm1:+:2336534854:-1 chm1:+:2458064602:-1 chm1:+:2806221511:-1 chm1:+:2934506014:-1 chm1:+:2966692229:-1 chm1:+:2991598953:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:338368:-1 chm1:+:4130809:-1 chm1:+:71254234:-1 chm1:+:78681813:-1 chm1:+:171041344:-1 chm1:+:182060286:-1 chm1:+:432179343:-1 chm1:+:492319372:-1 chm1:+:501442462:-1 chm1:+:525575677:-1 chm1:+:666910337:-1 chm1:+:690409303:-1 chm1:+:760073784:-1 chm1:+:830453392:-1 chm1:+:831826660:-1 chm1:+:877776588:-1 chm1:+:938576043:-1 chm1:+:942350694:-1 chm1:+:958485689:-1 chm1:+:974757562:-1 chm1:+:1062391683:-1 chm1:+:1064056004:-1 chm1:+:1136193573:-1 chm1:+:1164523354:-1 chm1:+:1234561559:-1 chm1:+:1360096791:-1 chm1:+:1859281589:-1 chm1:+:1914439659:-1 chm1:+:1943123261:-1 chm1:+:1985183424:-1 chm1:+:2028266767:-1 chm1:+:2049934264:-1 chm1:+:2112120318:-1 chm1:+:2129752154:-1 chm1:+:2162098207:-1 chm1:+:2236137216:-1 chm1:+:2338315475:-1 chm1:+:2340386099:-1 chm1:+:2357748048:-1 chm1:+:2500065476:-1 chm1:+:2513403877:-1 chm1:+:2535982019:-1 chm1:+:2551806478:-1 chm1:+:2552555205:-1 chm1:+:2635236314:-1 chm1:+:2918326062:-1 chm1:+:2929722628:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:13187142:-1 chm1:+:34446294:-1 chm1:+:58866313:-1 chm1:+:161707422:-1 chm1:+:257991350:-1 chm1:+:488567633:-1 chm1:+:514137549:-1 chm1:+:886535036:-1 chm1:+:1040957368:-1 chm1:+:1041250595:-1 chm1:+:1109483527:-1 chm1:+:1138351203:-1 chm1:+:1214952434:-1 chm1:+:1751952744:-1 chm1:+:1939856506:-1 chm1:+:1978746250:-1 chm1:+:2062763859:-1 chm1:+:2265034812:-1 chm1:+:2341540397:-1 chm1:+:2347626617:-1 chm1:+:2398002781:-1 chm1:+:2402257619:-1 chm1:+:2406601513:-1 chm1:+:2537870869:-1 chm1:+:2652720091:-1 chm1:+:2814859588:-1 chm1:+:2826902514:-1 chm1:+:2944181864:-1 chm1:+:2985035179:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:65075697:-1 chm1:+:219056372:-1 chm1:+:260832482:-1 chm1:+:589554769:-1 chm1:+:610587422:-1 chm1:+:1264529970:-1 chm1:+:1285862860:-1 chm1:+:1418811595:-1 chm1:+:1472887353:-1 chm1:+:1502146250:-1 chm1:+:1510842754:-1 chm1:+:1585852960:-1 chm1:+:2012047401:-1 chm1:+:2256022491:-1 chm1:+:2545517252:-1 chm1:+:2596412283:-1 chm1:+:2651068046:-1 chm1:+:2726712213:-1 chm1:+:2917094425:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:581278859:-1 chm1:+:589387302:-1 chm1:+:835263633:-1 chm1:+:835384428:-1 chm1:+:924018806:-1 chm1:+:1170310133:-1 chm1:+:1358526625:-1 chm1:+:1478378530:-1 chm1:+:1739344018:-1 chm1:+:1875591400:-1 chm1:+:2056842303:-1 chm1:+:2519151983:-1 chm1:+:2519278033:-1 chm1:+:2902042245:160 chm1:+:2963069445:-1 chm1:+:3023618203:-1 +ATAGAACTACAATTCAAGATGAGATTTGGGTGGGACACCACGCCAAACCATTCTGCCCTTGGTCCCCTCCATATCTCATGGTCCACGACATTTCAAAACACAAACATGCCCTATCCAAACAGTCCCCAAAGCCTTAACTCATTCCCAACATTAACTCAAAAGTCCAAGTCCAAAGTCTCATCTGAGACAACGCAAGTCCCTTCCACCTATGAGCCTGTAAAATCAAAATCAAGTTAGTTACTTCCTGGATGAAATGGTATACAAGAAATTTGTAAGTACACTTATTCCAAATGGGAGAAATTGGCCAAAACGAACGGGGCTACAGGCCCCCATGAAAGTTGGAAACCCAAATTGGGCAGTCATCATTAAACCTTAAGTTCCAAAATGCTCTCCTTAACCTCCCCGAATGTTAGTCGCATCCTAGGGCATGCTGATGTAAGAGGTGGGCTCCCACAGTCCTTGGACAGTTCAACCCCTTGTGGCTTTGCAGGGTACAGTCCCTTCCAGCTGCTTTCAGTAGACTGTCATTGAGTGTCTCCAGTTTTCCTGGTGCACGGTTCAAGCTGTCAATGGACCTCCCATTCTAGGATCTGGACGGCTGGTGGCCCTCCACTCACAGCCTCCAAAAGGCAGTGCCCCAGTGGGGGACTCTGTGTGGGGGCTTCCAACCCCACATTTTCATTCTGCACTGCCCTAGCAGAGATTCTCCATGAACTAGCAGAAAACTTCTGCCTGGACATCCAGGTGTTTCCATACATCCTCTGAAATCTAGGCCAGGGGTTCCCAAACCTCAATTCTTG chm1:+:192169769:-1 chm1:+:390046031:-1 chm1:+:512109747:-1 chm1:+:682508188:-1 chm1:+:724183430:-1 chm1:+:733983838:-1 chm1:+:753925922:-1 chm1:+:881281057:-1 chm1:+:1384885460:-1 chm1:+:1607839435:-1 chm1:+:1608178459:-1 chm1:+:1657346215:-1 chm1:+:1667273124:-1 chm1:+:1930376257:-1 chm1:+:2189186191:-1 chm1:+:2275104283:-1 chm1:+:2280735910:-1 chm1:+:2927063327:-1 chm1:+:2958826993:-1 +CAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT chm1:+:168443504:-1 chm1:+:265783231:-1 chm1:+:300419761:-1 chm1:+:376396728:-1 chm1:+:511175568:-1 chm1:+:573481323:-1 chm1:+:591316967:-1 chm1:+:702988641:-1 chm1:+:763381137:-1 chm1:+:767753594:-1 chm1:+:806702136:-1 chm1:+:881695211:150 chm1:+:895141280:-1 chm1:+:911296559:43 chm1:+:993017027:-1 chm1:+:1150011573:-1 chm1:+:1226567466:-1 chm1:+:1248473118:-1 chm1:+:1323750550:160 chm1:+:1377364641:-1 chm1:+:1430748243:-1 chm1:+:1484326639:-1 chm1:+:1565549692:-1 chm1:+:1570961523:-1 chm1:+:1630026455:-1 chm1:+:1635260395:-1 chm1:+:1712617103:-1 chm1:+:1735386386:-1 chm1:+:1916936683:-1 chm1:+:1946284963:-1 chm1:+:2034615280:-1 chm1:+:2045325630:-1 chm1:+:2047395686:-1 chm1:+:2117758634:-1 chm1:+:2140518694:-1 chm1:+:2240764901:-1 chm1:+:2530928438:-1 chm1:+:2657701350:-1 chm1:+:2757262908:-1 chm1:+:2802599993:-1 chm1:+:2814737219:-1 chm1:+:2863296204:-1 chm1:+:2906185881:-1 chm1:+:2925715413:-1 chm1:+:2960510930:-1 chm1:+:2965945570:-1 chm1:+:2974329872:-1 chm1:+:3008461384:-1 chm1:+:3028369212:-1 chm1:+:3042384075:-1 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chm1:+:1406127341:-1 chm1:+:1451571260:-1 chm1:+:1530379171:-1 chm1:+:1581172387:-1 chm1:+:1735386396:-1 chm1:+:1837257651:-1 chm1:+:1972394377:-1 chm1:+:1990865842:-1 chm1:+:2279284465:-1 chm1:+:2293381092:-1 chm1:+:2358472119:-1 chm1:+:2796293946:-1 chm1:+:2975699965:-1 +CAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT chm1:+:272127846:-1 +CAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT chm1:+:2272283391:-1 +CAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT chm1:+:2979001486:-1 +CAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT chm1:+:911296557:43 +CAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT chm1:+:911296569:43 +CAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT chm1:+:911296562:43 +CAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT chm1:+:1352507831:-1 +CAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT chm1:+:181498230:-1 chm1:+:823232155:-1 chm1:+:1904326697:-1 chm1:+:2796197690:-1 chm1:+:2810886456:-1 chm1:+:2864567134:-1 +CAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT chm1:+:969639195:-1 chm1:+:1622565138:-1 chm1:+:1966012545:-1 chm1:+:2643124631:-1 +CAAGAATTGAGGTTTGGGAACCCCTGGCCTAGATTTCAGAGGATGTATGGAAACACCTGGATGTCCAGGCAGAAGTTTTCTGCTAGTTCATGGAGAATCTCTGCTAGGGCAGTGCAGAATGAAAATGTGGGGTTGGAAGCCCCCACACAGAGTCCCCCACTGGGGCACTGCCTTTTGGAGGCTGTGAGTGGAGGGCCACCAGCCGTCCAGATCCTAGAATGGGAGGTCCATTGACAGCTTGAACCGTGCACCAGGAAAACTGGAGACACTCAATGACAGTCTACTGAAAGCAGCTGGAAGGGACTGTACCCTGCAAAGCCACAAGGGGTTGAACTGTCCAAGGACTGTGGGAGCCCACCTCTTACATCAGCATGCCCTAGGATGCGACTAACATTCGGGGAGGTTAAGGAGAGCATTTTGGAACTTAAGGTTTAATGATGACTGCCCAATTTGGGTTTCCAACTTTCATGGGGGCCTGTAGCCCCGTTCGTTTTGGCCAATTTCTCCCATTTGGAATAAGTGTACTTACAAATTTCTTGTATACCATTTCATCCAGGAAGTAACTAACTTGATTTTGATTTTACAGGCTCATAGGTGGAAGGGACTTGCGTTGTCTCAGATGAGACTTTGGACTTGGACTTTTGAGTTAATGTTGGGAATGAGTTAAGGCTTTGGGGACTGTTTGGATAGGGCATGTTTGTGTTTTGAAATGTCGTGGACCATGAGATATGGAGGGGACCAAGGGCAGAATGGTTTGGCGTGGTGTCCCACCCAAATCTCATCTTGAATTGTAGTTCTAT chm1:+:911296574:43 chm1:+:1011709258:-1 chm1:+:1129532281:-1 +CCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATGTTGACATTTGGGTTAGGTTCCCAAGTCTTTGCTATGTGAATAGTGCCACAATAAACATACGTGTGCATGTGTCTTTATAAGCAGCCAATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGTCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAATAGGCACAGAAAGTGAATTTGCCTTGTAAACTTGACTTCTGTGCTGCATAAATATTTTACGTTAATTACAAAAACAAAAAATAAAAAAGCAATTTTTACAAATCTTTGTGTGTTCAGTTAGGAGCACACCTTCACAGAGAGGAACTCTTCCCAATGGCCTTAAGGCGCCAATTGTTGTTGTTTTTAAAAATATCTTAAATAAATTTTTATTTTTATAGATTTAGAGGTACAAGTTGCAGGATTGTTACATGGAATAAATTGTGTGGTAGTGAAATCTGGGGCTTTTAGAAGACACAGTAATTTGACTCTCCATCCCTAGTGCACAAAAAAGAATTAAACAATTTCCAGTATTCAGGATCCAAATGAAGTTTCATACAGTGATTGTTTGAAATAACTTTTAAGTCTCCTTAATAATCCATTATTTCACATTTCCTTTCTTTCCTTTTTTAATTATACATTTTCTGCTTATTGAGGAACGAGAAAACTAGTTATCCTGTAGTTTTTCCCTACAGTCTGAATTTTGCTGTTGCATCACCATAATATAGAAATAAAAATT chm1:+:72890856:-1 chm1:+:82995007:-1 chm1:+:159603629:-1 chm1:+:164987798:-1 chm1:+:200765994:-1 chm1:+:230606574:-1 chm1:+:253751621:-1 chm1:+:347760171:-1 chm1:+:441896346:-1 chm1:+:494405379:-1 chm1:+:576933487:-1 chm1:+:587327758:-1 chm1:+:706287691:-1 chm1:+:719619947:-1 chm1:+:760328890:-1 chm1:+:781920142:-1 chm1:+:820648726:-1 chm1:+:871631507:-1 chm1:+:938571597:-1 chm1:+:978729219:-1 chm1:+:1063715297:-1 chm1:+:1149311676:-1 chm1:+:1166546603:-1 chm1:+:1187570142:-1 chm1:+:1210343558:-1 chm1:+:1237298532:-1 chm1:+:1267866404:-1 chm1:+:1314729348:-1 chm1:+:1383625497:-1 chm1:+:1398360179:-1 chm1:+:1542301851:-1 chm1:+:1632915388:-1 chm1:+:1835056093:-1 chm1:+:1925725971:-1 chm1:+:1956506908:-1 chm1:+:2114589443:-1 chm1:+:2134009910:-1 chm1:+:2181323046:-1 chm1:+:2236482847:-1 chm1:+:2418098431:-1 chm1:+:2528945253:-1 chm1:+:2634750009:-1 chm1:+:2847206449:-1 chm1:+:2898540396:-1 chm1:+:2916184117:-1 chm1:+:2916682001:-1 chm1:+:2956734892:-1 chm1:+:2975078672:-1 chm1:+:3021388830:-1 chm1:+:3063625582:-1 +CCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATGTTGACATTTGGGTTAGGTTCCCAAGTCTTTGCTATGTGAATAGTGCCACAATAAACATACGTGTGCATGTGTCTTTATAAGCAGCCAATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGTCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAATAGGCACAGAAAGTGAATTTGCCTTGTAAACTTGACTTCTGTGCTGCATAAATATTTTACGTTAATTACAAAAACAAAAAATAAAAAAGCAATTTTTACAAATCTTTGTGTGTTCAGTTAGGAGCACACCTTCACAGAGAGGAACTCTTCCCAATGGCCTTAAGGCGCCAATTGTTGTTGTTTTTAAAAATATCTTAAATAAATTTTTATTTTTATAGATTTAGAGGTACAAGTTGCAGGATTGTTACATGGAATAAATTGTGTGGTAGTGAAATCTGGGGCTTTTAGAAGACACAGTAATTTGACTCTCCATCCCTAGTGCACAAAAAAGAATTAAACAATTTCCAGTATTCAGGATCCAAATGAAGTTTCATACAGTGATTGTTTGAAATAACTTTTAAGTCTCCTTAATAATCCATTATTTCACATTTCCTTTCTTTCCTTTTTTAATTATACATTTTCTGCTTATTGAGGAACGAGAAAACTAGTTATCCTGTAGTTTTTCCCTACAGTCTGAATTTTGCTGTTGCATCACCATAATATAGAAATAAAAATT chm1:+:961502881:-1 chm1:+:1541091001:-1 chm1:+:2589823829:-1 chm1:+:2883290894:-1 +CCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATGTTGACATTTGGGTTAGGTTCCCAAGTCTTTGCTATGTGAATAGTGCCACAATAAACATACGTGTGCATGTGTCTTTATAAGCAGCCAATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGTCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAATAGGCACAGAAAGTGAATTTGCCTTGTAAACTTGACTTCTGTGCTGCATAAATATTTTACGTTAATTACAAAAACAAAAAATAAAAAAGCAATTTTTACAAATCTTTGTGTGTTCAGTTAGGAGCACACCTTCACAGAGAGGAACTCTTCCCAATGGCCTTAAGGCGCCAATTGTTGTTGTTTTTAAAAATATCTTAAATAAATTTTTATTTTTATAGATTTAGAGGTACAAGTTGCAGGATTGTTACATGGAATAAATTGTGTGGTAGTGAAATCTGGGGCTTTTAGAAGACACAGTAATTTGACTCTCCATCCCTAGTGCACAAAAAAGAATTAAACAATTTCCAGTATTCAGGATCCAAATGAAGTTTCATACAGTGATTGTTTGAAATAACTTTTAAGTCTCCTTAATAATCCATTATTTCACATTTCCTTTCTTTCCTTTTTTAATTATACATTTTCTGCTTATTGAGGAACGAGAAAACTAGTTATCCTGTAGTTTTTCCCTACAGTCTGAATTTTGCTGTTGCATCACCATAATATAGAAATAAAAATT chm1:+:563201842:-1 chm1:+:2796707146:39 chm1:+:3099114978:38 +CCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATGTTGACATTTGGGTTAGGTTCCCAAGTCTTTGCTATGTGAATAGTGCCACAATAAACATACGTGTGCATGTGTCTTTATAAGCAGCCAATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGTCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAATAGGCACAGAAAGTGAATTTGCCTTGTAAACTTGACTTCTGTGCTGCATAAATATTTTACGTTAATTACAAAAACAAAAAATAAAAAAGCAATTTTTACAAATCTTTGTGTGTTCAGTTAGGAGCACACCTTCACAGAGAGGAACTCTTCCCAATGGCCTTAAGGCGCCAATTGTTGTTGTTTTTAAAAATATCTTAAATAAATTTTTATTTTTATAGATTTAGAGGTACAAGTTGCAGGATTGTTACATGGAATAAATTGTGTGGTAGTGAAATCTGGGGCTTTTAGAAGACACAGTAATTTGACTCTCCATCCCTAGTGCACAAAAAAGAATTAAACAATTTCCAGTATTCAGGATCCAAATGAAGTTTCATACAGTGATTGTTTGAAATAACTTTTAAGTCTCCTTAATAATCCATTATTTCACATTTCCTTTCTTTCCTTTTTTAATTATACATTTTCTGCTTATTGAGGAACGAGAAAACTAGTTATCCTGTAGTTTTTCCCTACAGTCTGAATTTTGCTGTTGCATCACCATAATATAGAAATAAAAATT chm1:+:1528321903:-1 +CCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATGTTGACATTTGGGTTAGGTTCCCAAGTCTTTGCTATGTGAATAGTGCCACAATAAACATACGTGTGCATGTGTCTTTATAAGCAGCCAATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGTCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAATAGGCACAGAAAGTGAATTTGCCTTGTAAACTTGACTTCTGTGCTGCATAAATATTTTACGTTAATTACAAAAACAAAAAATAAAAAAGCAATTTTTACAAATCTTTGTGTGTTCAGTTAGGAGCACACCTTCACAGAGAGGAACTCTTCCCAATGGCCTTAAGGCGCCAATTGTTGTTGTTTTTAAAAATATCTTAAATAAATTTTTATTTTTATAGATTTAGAGGTACAAGTTGCAGGATTGTTACATGGAATAAATTGTGTGGTAGTGAAATCTGGGGCTTTTAGAAGACACAGTAATTTGACTCTCCATCCCTAGTGCACAAAAAAGAATTAAACAATTTCCAGTATTCAGGATCCAAATGAAGTTTCATACAGTGATTGTTTGAAATAACTTTTAAGTCTCCTTAATAATCCATTATTTCACATTTCCTTTCTTTCCTTTTTTAATTATACATTTTCTGCTTATTGAGGAACGAGAAAACTAGTTATCCTGTAGTTTTTCCCTACAGTCTGAATTTTGCTGTTGCATCACCATAATATAGAAATAAAAATT chm1:+:645234892:-1 +CCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATGTTGACATTTGGGTTAGGTTCCCAAGTCTTTGCTATGTGAATAGTGCCACAATAAACATACGTGTGCATGTGTCTTTATAAGCAGCCAATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGTCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAATAGGCACAGAAAGTGAATTTGCCTTGTAAACTTGACTTCTGTGCTGCATAAATATTTTACGTTAATTACAAAAACAAAAAATAAAAAAGCAATTTTTACAAATCTTTGTGTGTTCAGTTAGGAGCACACCTTCACAGAGAGGAACTCTTCCCAATGGCCTTAAGGCGCCAATTGTTGTTGTTTTTAAAAATATCTTAAATAAATTTTTATTTTTATAGATTTAGAGGTACAAGTTGCAGGATTGTTACATGGAATAAATTGTGTGGTAGTGAAATCTGGGGCTTTTAGAAGACACAGTAATTTGACTCTCCATCCCTAGTGCACAAAAAAGAATTAAACAATTTCCAGTATTCAGGATCCAAATGAAGTTTCATACAGTGATTGTTTGAAATAACTTTTAAGTCTCCTTAATAATCCATTATTTCACATTTCCTTTCTTTCCTTTTTTAATTATACATTTTCTGCTTATTGAGGAACGAGAAAACTAGTTATCCTGTAGTTTTTCCCTACAGTCTGAATTTTGCTGTTGCATCACCATAATATAGAAATAAAAATT chm1:+:542715525:-1 chm1:+:554574837:-1 chm1:+:603213554:-1 chm1:+:688792782:-1 chm1:+:898282569:-1 chm1:+:1368214279:-1 chm1:+:1468138148:148 chm1:+:1990018474:-1 chm1:+:2067242567:-1 chm1:+:2137022450:-1 chm1:+:2796707133:39 chm1:+:2920036215:-1 chm1:+:3099114964:38 +CCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATGTTGACATTTGGGTTAGGTTCCCAAGTCTTTGCTATGTGAATAGTGCCACAATAAACATACGTGTGCATGTGTCTTTATAAGCAGCCAATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGTCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAATAGGCACAGAAAGTGAATTTGCCTTGTAAACTTGACTTCTGTGCTGCATAAATATTTTACGTTAATTACAAAAACAAAAAATAAAAAAGCAATTTTTACAAATCTTTGTGTGTTCAGTTAGGAGCACACCTTCACAGAGAGGAACTCTTCCCAATGGCCTTAAGGCGCCAATTGTTGTTGTTTTTAAAAATATCTTAAATAAATTTTTATTTTTATAGATTTAGAGGTACAAGTTGCAGGATTGTTACATGGAATAAATTGTGTGGTAGTGAAATCTGGGGCTTTTAGAAGACACAGTAATTTGACTCTCCATCCCTAGTGCACAAAAAAGAATTAAACAATTTCCAGTATTCAGGATCCAAATGAAGTTTCATACAGTGATTGTTTGAAATAACTTTTAAGTCTCCTTAATAATCCATTATTTCACATTTCCTTTCTTTCCTTTTTTAATTATACATTTTCTGCTTATTGAGGAACGAGAAAACTAGTTATCCTGTAGTTTTTCCCTACAGTCTGAATTTTGCTGTTGCATCACCATAATATAGAAATAAAAATT chm1:+:293455611:-1 chm1:+:511742564:-1 chm1:+:736440128:-1 chm1:+:908217831:-1 chm1:+:1468138149:148 chm1:+:1485144881:-1 chm1:+:2016201259:-1 chm1:+:2361519986:-1 chm1:+:2506341709:-1 chm1:+:2796707134:39 chm1:+:3099114965:38 +CCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATGTTGACATTTGGGTTAGGTTCCCAAGTCTTTGCTATGTGAATAGTGCCACAATAAACATACGTGTGCATGTGTCTTTATAAGCAGCCAATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGTCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAATAGGCACAGAAAGTGAATTTGCCTTGTAAACTTGACTTCTGTGCTGCATAAATATTTTACGTTAATTACAAAAACAAAAAATAAAAAAGCAATTTTTACAAATCTTTGTGTGTTCAGTTAGGAGCACACCTTCACAGAGAGGAACTCTTCCCAATGGCCTTAAGGCGCCAATTGTTGTTGTTTTTAAAAATATCTTAAATAAATTTTTATTTTTATAGATTTAGAGGTACAAGTTGCAGGATTGTTACATGGAATAAATTGTGTGGTAGTGAAATCTGGGGCTTTTAGAAGACACAGTAATTTGACTCTCCATCCCTAGTGCACAAAAAAGAATTAAACAATTTCCAGTATTCAGGATCCAAATGAAGTTTCATACAGTGATTGTTTGAAATAACTTTTAAGTCTCCTTAATAATCCATTATTTCACATTTCCTTTCTTTCCTTTTTTAATTATACATTTTCTGCTTATTGAGGAACGAGAAAACTAGTTATCCTGTAGTTTTTCCCTACAGTCTGAATTTTGCTGTTGCATCACCATAATATAGAAATAAAAATT chm1:+:1468138156:148 chm1:+:2796707141:39 chm1:+:3099114972:38 +CCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATGTTGACATTTGGGTTAGGTTCCCAAGTCTTTGCTATGTGAATAGTGCCACAATAAACATACGTGTGCATGTGTCTTTATAAGCAGCCAATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGTCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAATAGGCACAGAAAGTGAATTTGCCTTGTAAACTTGACTTCTGTGCTGCATAAATATTTTACGTTAATTACAAAAACAAAAAATAAAAAAGCAATTTTTACAAATCTTTGTGTGTTCAGTTAGGAGCACACCTTCACAGAGAGGAACTCTTCCCAATGGCCTTAAGGCGCCAATTGTTGTTGTTTTTAAAAATATCTTAAATAAATTTTTATTTTTATAGATTTAGAGGTACAAGTTGCAGGATTGTTACATGGAATAAATTGTGTGGTAGTGAAATCTGGGGCTTTTAGAAGACACAGTAATTTGACTCTCCATCCCTAGTGCACAAAAAAGAATTAAACAATTTCCAGTATTCAGGATCCAAATGAAGTTTCATACAGTGATTGTTTGAAATAACTTTTAAGTCTCCTTAATAATCCATTATTTCACATTTCCTTTCTTTCCTTTTTTAATTATACATTTTCTGCTTATTGAGGAACGAGAAAACTAGTTATCCTGTAGTTTTTCCCTACAGTCTGAATTTTGCTGTTGCATCACCATAATATAGAAATAAAAATT chm1:+:1468138157:148 chm1:+:2796707142:39 chm1:+:3099114973:38 +CCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATGTTGACATTTGGGTTAGGTTCCCAAGTCTTTGCTATGTGAATAGTGCCACAATAAACATACGTGTGCATGTGTCTTTATAAGCAGCCAATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGTCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAATAGGCACAGAAAGTGAATTTGCCTTGTAAACTTGACTTCTGTGCTGCATAAATATTTTACGTTAATTACAAAAACAAAAAATAAAAAAGCAATTTTTACAAATCTTTGTGTGTTCAGTTAGGAGCACACCTTCACAGAGAGGAACTCTTCCCAATGGCCTTAAGGCGCCAATTGTTGTTGTTTTTAAAAATATCTTAAATAAATTTTTATTTTTATAGATTTAGAGGTACAAGTTGCAGGATTGTTACATGGAATAAATTGTGTGGTAGTGAAATCTGGGGCTTTTAGAAGACACAGTAATTTGACTCTCCATCCCTAGTGCACAAAAAAGAATTAAACAATTTCCAGTATTCAGGATCCAAATGAAGTTTCATACAGTGATTGTTTGAAATAACTTTTAAGTCTCCTTAATAATCCATTATTTCACATTTCCTTTCTTTCCTTTTTTAATTATACATTTTCTGCTTATTGAGGAACGAGAAAACTAGTTATCCTGTAGTTTTTCCCTACAGTCTGAATTTTGCTGTTGCATCACCATAATATAGAAATAAAAATT chm1:+:2240898838:-1 +CCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATGTTGACATTTGGGTTAGGTTCCCAAGTCTTTGCTATGTGAATAGTGCCACAATAAACATACGTGTGCATGTGTCTTTATAAGCAGCCAATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGTCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAATAGGCACAGAAAGTGAATTTGCCTTGTAAACTTGACTTCTGTGCTGCATAAATATTTTACGTTAATTACAAAAACAAAAAATAAAAAAGCAATTTTTACAAATCTTTGTGTGTTCAGTTAGGAGCACACCTTCACAGAGAGGAACTCTTCCCAATGGCCTTAAGGCGCCAATTGTTGTTGTTTTTAAAAATATCTTAAATAAATTTTTATTTTTATAGATTTAGAGGTACAAGTTGCAGGATTGTTACATGGAATAAATTGTGTGGTAGTGAAATCTGGGGCTTTTAGAAGACACAGTAATTTGACTCTCCATCCCTAGTGCACAAAAAAGAATTAAACAATTTCCAGTATTCAGGATCCAAATGAAGTTTCATACAGTGATTGTTTGAAATAACTTTTAAGTCTCCTTAATAATCCATTATTTCACATTTCCTTTCTTTCCTTTTTTAATTATACATTTTCTGCTTATTGAGGAACGAGAAAACTAGTTATCCTGTAGTTTTTCCCTACAGTCTGAATTTTGCTGTTGCATCACCATAATATAGAAATAAAAATT chm1:+:374435275:-1 chm1:+:737976622:-1 chm1:+:1743185079:-1 chm1:+:2370145508:-1 chm1:+:2965184455:-1 +CCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATGTTGACATTTGGGTTAGGTTCCCAAGTCTTTGCTATGTGAATAGTGCCACAATAAACATACGTGTGCATGTGTCTTTATAAGCAGCCAATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGTCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAATAGGCACAGAAAGTGAATTTGCCTTGTAAACTTGACTTCTGTGCTGCATAAATATTTTACGTTAATTACAAAAACAAAAAATAAAAAAGCAATTTTTACAAATCTTTGTGTGTTCAGTTAGGAGCACACCTTCACAGAGAGGAACTCTTCCCAATGGCCTTAAGGCGCCAATTGTTGTTGTTTTTAAAAATATCTTAAATAAATTTTTATTTTTATAGATTTAGAGGTACAAGTTGCAGGATTGTTACATGGAATAAATTGTGTGGTAGTGAAATCTGGGGCTTTTAGAAGACACAGTAATTTGACTCTCCATCCCTAGTGCACAAAAAAGAATTAAACAATTTCCAGTATTCAGGATCCAAATGAAGTTTCATACAGTGATTGTTTGAAATAACTTTTAAGTCTCCTTAATAATCCATTATTTCACATTTCCTTTCTTTCCTTTTTTAATTATACATTTTCTGCTTATTGAGGAACGAGAAAACTAGTTATCCTGTAGTTTTTCCCTACAGTCTGAATTTTGCTGTTGCATCACCATAATATAGAAATAAAAATT chm1:+:51598230:-1 chm1:+:153256018:-1 chm1:+:754276509:-1 chm1:+:940407001:-1 chm1:+:2358704159:-1 +AATTTTTATTTCTATATTATGGTGATGCAACAGCAAAATTCAGACTGTAGGGAAAAACTACAGGATAACTAGTTTTCTCGTTCCTCAATAAGCAGAAAATGTATAATTAAAAAAGGAAAGAAAGGAAATGTGAAATAATGGATTATTAAGGAGACTTAAAAGTTATTTCAAACAATCACTGTATGAAACTTCATTTGGATCCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:3098202029:40 +AATTTTTATTTCTATATTATGGTGATGCAACAGCAAAATTCAGACTGTAGGGAAAAACTACAGGATAACTAGTTTTCTCGTTCCTCAATAAGCAGAAAATGTATAATTAAAAAAGGAAAGAAAGGAAATGTGAAATAATGGATTATTAAGGAGACTTAAAAGTTATTTCAAACAATCACTGTATGAAACTTCATTTGGATCCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:3098202026:40 +AATTTTTATTTCTATATTATGGTGATGCAACAGCAAAATTCAGACTGTAGGGAAAAACTACAGGATAACTAGTTTTCTCGTTCCTCAATAAGCAGAAAATGTATAATTAAAAAAGGAAAGAAAGGAAATGTGAAATAATGGATTATTAAGGAGACTTAAAAGTTATTTCAAACAATCACTGTATGAAACTTCATTTGGATCCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:3098202031:40 +AATTTTTATTTCTATATTATGGTGATGCAACAGCAAAATTCAGACTGTAGGGAAAAACTACAGGATAACTAGTTTTCTCGTTCCTCAATAAGCAGAAAATGTATAATTAAAAAAGGAAAGAAAGGAAATGTGAAATAATGGATTATTAAGGAGACTTAAAAGTTATTTCAAACAATCACTGTATGAAACTTCATTTGGATCCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:923180261:-1 +AATTTTTATTTCTATATTATGGTGATGCAACAGCAAAATTCAGACTGTAGGGAAAAACTACAGGATAACTAGTTTTCTCGTTCCTCAATAAGCAGAAAATGTATAATTAAAAAAGGAAAGAAAGGAAATGTGAAATAATGGATTATTAAGGAGACTTAAAAGTTATTTCAAACAATCACTGTATGAAACTTCATTTGGATCCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:3098202032:40 +AATTTTTATTTCTATATTATGGTGATGCAACAGCAAAATTCAGACTGTAGGGAAAAACTACAGGATAACTAGTTTTCTCGTTCCTCAATAAGCAGAAAATGTATAATTAAAAAAGGAAAGAAAGGAAATGTGAAATAATGGATTATTAAGGAGACTTAAAAGTTATTTCAAACAATCACTGTATGAAACTTCATTTGGATCCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:3098202030:40 +AATTTTTATTTCTATATTATGGTGATGCAACAGCAAAATTCAGACTGTAGGGAAAAACTACAGGATAACTAGTTTTCTCGTTCCTCAATAAGCAGAAAATGTATAATTAAAAAAGGAAAGAAAGGAAATGTGAAATAATGGATTATTAAGGAGACTTAAAAGTTATTTCAAACAATCACTGTATGAAACTTCATTTGGATCCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:2979705671:-1 +AATTTTTATTTCTATATTATGGTGATGCAACAGCAAAATTCAGACTGTAGGGAAAAACTACAGGATAACTAGTTTTCTCGTTCCTCAATAAGCAGAAAATGTATAATTAAAAAAGGAAAGAAAGGAAATGTGAAATAATGGATTATTAAGGAGACTTAAAAGTTATTTCAAACAATCACTGTATGAAACTTCATTTGGATCCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:3098202033:40 +AATTTTTATTTCTATATTATGGTGATGCAACAGCAAAATTCAGACTGTAGGGAAAAACTACAGGATAACTAGTTTTCTCGTTCCTCAATAAGCAGAAAATGTATAATTAAAAAAGGAAAGAAAGGAAATGTGAAATAATGGATTATTAAGGAGACTTAAAAGTTATTTCAAACAATCACTGTATGAAACTTCATTTGGATCCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:634332300:-1 +AATTTTTATTTCTATATTATGGTGATGCAACAGCAAAATTCAGACTGTAGGGAAAAACTACAGGATAACTAGTTTTCTCGTTCCTCAATAAGCAGAAAATGTATAATTAAAAAAGGAAAGAAAGGAAATGTGAAATAATGGATTATTAAGGAGACTTAAAAGTTATTTCAAACAATCACTGTATGAAACTTCATTTGGATCCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:1110036347:-1 +AATTTTTATTTCTATATTATGGTGATGCAACAGCAAAATTCAGACTGTAGGGAAAAACTACAGGATAACTAGTTTTCTCGTTCCTCAATAAGCAGAAAATGTATAATTAAAAAAGGAAAGAAAGGAAATGTGAAATAATGGATTATTAAGGAGACTTAAAAGTTATTTCAAACAATCACTGTATGAAACTTCATTTGGATCCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:645088229:-1 +AATTTTTATTTCTATATTATGGTGATGCAACAGCAAAATTCAGACTGTAGGGAAAAACTACAGGATAACTAGTTTTCTCGTTCCTCAATAAGCAGAAAATGTATAATTAAAAAAGGAAAGAAAGGAAATGTGAAATAATGGATTATTAAGGAGACTTAAAAGTTATTTCAAACAATCACTGTATGAAACTTCATTTGGATCCTGAATACTGGAAATTGTTTAATTCTTTTTTGTGCACTAGGGATGGAGAGTCAAATTACTGTGTCTTCTAAAAGCCCCAGATTTCACTACCACACAATTTATTCCATGTAACAATCCTGCAACTTGTACCTCTAAATCTATAAAAATAAAAATTTATTTAAGATATTTTTAAAAACAACAACAATTGGCGCCTTAAGGCCATTGGGAAGAGTTCCTCTCTGTGAAGGTGTGCTCCTAACTGAACACACAAAGATTTGTAAAAATTGCTTTTTTATTTTTTGTTTTTGTAATTAACGTAAAATATTTATGCAGCACAGAAGTCAAGTTTACAAGGCAAATTCACTTTCTGTGCCTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATTGGCTGCTTATAAAGACACATGCACACGTATGTTTATTGTGGCACTATTCACATAGCAAAGACTTGGGAACCTAACCCAAATGTCAACATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGG chm1:+:538869955:-1 chm1:+:578821817:-1 chm1:+:866176740:-1 chm1:+:1106855767:-1 chm1:+:1192703374:-1 chm1:+:1898353938:-1 chm1:+:2342955592:-1 chm1:+:2946054417:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAA chm1:+:9000795:-1 chm1:+:15909070:-1 chm1:+:28521527:-1 chm1:+:36531738:-1 chm1:+:39372789:-1 chm1:+:97616808:-1 chm1:+:112218555:-1 chm1:+:167456191:-1 chm1:+:201842150:-1 chm1:+:244661777:-1 chm1:+:269245025:-1 chm1:+:275641435:-1 chm1:+:275764996:-1 chm1:+:287806768:-1 chm1:+:323896506:-1 chm1:+:432793348:-1 chm1:+:455938761:-1 chm1:+:473456612:-1 chm1:+:481143646:-1 chm1:+:540684613:-1 chm1:+:541254483:-1 chm1:+:662331222:-1 chm1:+:687509531:-1 chm1:+:729505505:-1 chm1:+:828770304:-1 chm1:+:875895961:-1 chm1:+:918669907:-1 chm1:+:960598685:-1 chm1:+:1020547462:-1 chm1:+:1024215623:-1 chm1:+:1030461044:-1 chm1:+:1088056312:-1 chm1:+:1150938301:-1 chm1:+:1238834105:-1 chm1:+:1240136287:-1 chm1:+:1335053820:-1 chm1:+:1420564476:-1 chm1:+:1433248870:-1 chm1:+:1631074180:-1 chm1:+:1633915217:-1 chm1:+:1669460513:-1 chm1:+:1670620478:-1 chm1:+:1829870732:-1 chm1:+:1893737129:-1 chm1:+:1993334951:-1 chm1:+:2004566357:-1 chm1:+:2129716789:-1 chm1:+:2183987000:-1 chm1:+:2227638023:-1 chm1:+:2497664465:-1 chm1:+:2544415019:-1 chm1:+:2554561957:-1 chm1:+:2554935823:-1 chm1:+:2574031297:-1 chm1:+:2697973129:-1 chm1:+:2698102926:-1 chm1:+:2748578648:-1 chm1:+:2764020040:-1 chm1:+:2778218193:-1 chm1:+:2816368409:-1 chm1:+:2867586032:-1 chm1:+:2883467386:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAA chm1:+:617788898:-1 chm1:+:620988470:-1 chm1:+:692136206:-1 chm1:+:938022752:-1 chm1:+:1205070760:-1 chm1:+:1396288581:-1 chm1:+:1642082934:-1 chm1:+:1717357597:-1 chm1:+:1871838269:-1 chm1:+:2352736193:-1 chm1:+:2417135731:-1 chm1:+:2436627717:-1 chm1:+:2463467672:-1 chm1:+:2859499634:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAA chm1:+:18877778:-1 chm1:+:188102284:-1 chm1:+:267000773:-1 chm1:+:540458714:-1 chm1:+:558525157:-1 chm1:+:600780384:-1 chm1:+:607844180:-1 chm1:+:661385144:-1 chm1:+:980272546:-1 chm1:+:1136720885:-1 chm1:+:1269682295:-1 chm1:+:1289132964:-1 chm1:+:1519718641:-1 chm1:+:1546526631:-1 chm1:+:1546526766:-1 chm1:+:1735570581:-1 chm1:+:2008628026:-1 chm1:+:2060679535:-1 chm1:+:2069992402:-1 chm1:+:2080291774:-1 chm1:+:2235469350:-1 chm1:+:2265668860:-1 chm1:+:2270010357:-1 chm1:+:2408677232:-1 chm1:+:2468184517:-1 chm1:+:2578390217:-1 chm1:+:2651754730:-1 chm1:+:2661593444:-1 chm1:+:2689798038:-1 chm1:+:2695686122:-1 chm1:+:2719007632:-1 chm1:+:2729663380:-1 chm1:+:2827914159:-1 chm1:+:2860893934:-1 chm1:+:2929665991:-1 chm1:+:3003980329:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAA chm1:+:573759728:-1 chm1:+:911208861:38 chm1:+:1503050878:-1 chm1:+:1863820604:-1 chm1:+:2022287976:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAA chm1:+:911208865:38 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAA chm1:+:763635146:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAA chm1:+:1118331315:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAA chm1:+:1791627500:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAA chm1:+:911208862:38 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAA chm1:+:911208864:38 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAA chm1:+:1487300094:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAA chm1:+:911208867:38 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAA chm1:+:1303727833:-1 +CCTGTAAGTCCCAGCACTTTGGGGAGACCGAGGGGGACAGATCACTGAGGTCAGGAGTTTGAGACGAGCCTGGCCTAACATGGTGAAACCTCACCTCGACAAATAATACAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTTCTGGAAGGCTGAGACAGAATTGCTTGAACCTGGGAGGCAGAGGTTACAGTGAGCAGAGATCATGCCACTGTCACTCCAACCTGGGCAACAGAGCGAAGACTTCCATCACAAAAAAAAAAAAAAAAAAAAATTGCAGTTTCCTTTTACTTACATCCAAAATGGTTATCAATTATTTGCTGTCATTTGGGCTATATCACTCTAGGGCTCCTAGACCTTTATTTATATTTGCAGCCCTAGCCCATGCTTGGGAAAGAGTCATACTCAATTAAATGTGATGAAACCATAAATGATAATAACGAATGATCAAATTTTATAGAAAATCTTTCTAGGTCTGAGCATCATATAGATACCAATGAAAGCACGCATTTAACAAAAATATATCAAAGTTTCACATGGCCATGGAGATTATATTGTTAACTAGGACTTAGATATATTAATATGGTCCTGAAAGAGTGAAATTTTATCTCAAGTTATTTTAGTTTTCTGGTAATTGAGGTTTAAAGTAGACTATACTCTTTTCATAATGATGTATATGTCAGTGCATTTCATTCTCAAAAAGCCTAACTTAGATCTAAGCTTGTCAAGTAGTTCAAAATAAATCTGCTTCATACTGTTTAATTATTGTTCAGTCATTTCTGCTTTAA chm1:+:911208880:38 +TTAAAGCAGAAATGACTGAACAATAATTAAACAGTATGAAGCAGATTTATTTTGAACTACTTGACAAGCTTAGATCTAAGTTAGGCTTTTTGAGAATGAAATGCACTGACATATACATCATTATGAAAAGAGTATAGTCTACTTTAAACCTCAATTACCAGAAAACTAAAATAACTTGAGATAAAATTTCACTCTTTCAGGACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:2698915904:-1 +TTAAAGCAGAAATGACTGAACAATAATTAAACAGTATGAAGCAGATTTATTTTGAACTACTTGACAAGCTTAGATCTAAGTTAGGCTTTTTGAGAATGAAATGCACTGACATATACATCATTATGAAAAGAGTATAGTCTACTTTAAACCTCAATTACCAGAAAACTAAAATAACTTGAGATAAAATTTCACTCTTTCAGGACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:2012637704:-1 chm1:+:2039268452:-1 +TTAAAGCAGAAATGACTGAACAATAATTAAACAGTATGAAGCAGATTTATTTTGAACTACTTGACAAGCTTAGATCTAAGTTAGGCTTTTTGAGAATGAAATGCACTGACATATACATCATTATGAAAAGAGTATAGTCTACTTTAAACCTCAATTACCAGAAAACTAAAATAACTTGAGATAAAATTTCACTCTTTCAGGACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:1756014812:-1 chm1:+:1959968538:-1 +TTAAAGCAGAAATGACTGAACAATAATTAAACAGTATGAAGCAGATTTATTTTGAACTACTTGACAAGCTTAGATCTAAGTTAGGCTTTTTGAGAATGAAATGCACTGACATATACATCATTATGAAAAGAGTATAGTCTACTTTAAACCTCAATTACCAGAAAACTAAAATAACTTGAGATAAAATTTCACTCTTTCAGGACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:204330995:-1 chm1:+:542083102:-1 chm1:+:875148830:-1 chm1:+:1627785306:-1 chm1:+:1871995582:-1 chm1:+:2718526686:-1 chm1:+:2760931442:-1 +TTAAAGCAGAAATGACTGAACAATAATTAAACAGTATGAAGCAGATTTATTTTGAACTACTTGACAAGCTTAGATCTAAGTTAGGCTTTTTGAGAATGAAATGCACTGACATATACATCATTATGAAAAGAGTATAGTCTACTTTAAACCTCAATTACCAGAAAACTAAAATAACTTGAGATAAAATTTCACTCTTTCAGGACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:33131280:-1 chm1:+:275806633:-1 chm1:+:288697670:-1 chm1:+:428395683:-1 chm1:+:678003486:-1 chm1:+:893140935:-1 chm1:+:1162535125:-1 chm1:+:1432876124:-1 chm1:+:1492659376:-1 chm1:+:1539932573:-1 chm1:+:1898627321:-1 chm1:+:1957911677:-1 chm1:+:2170145687:-1 chm1:+:2268055010:-1 chm1:+:2302439817:-1 chm1:+:2517913288:-1 chm1:+:2567546825:-1 chm1:+:2717219580:-1 chm1:+:2855197704:-1 chm1:+:2889498032:-1 +TTAAAGCAGAAATGACTGAACAATAATTAAACAGTATGAAGCAGATTTATTTTGAACTACTTGACAAGCTTAGATCTAAGTTAGGCTTTTTGAGAATGAAATGCACTGACATATACATCATTATGAAAAGAGTATAGTCTACTTTAAACCTCAATTACCAGAAAACTAAAATAACTTGAGATAAAATTTCACTCTTTCAGGACCATATTAATATATCTAAGTCCTAGTTAACAATATAATCTCCATGGCCATGTGAAACTTTGATATATTTTTGTTAAATGCGTGCTTTCATTGGTATCTATATGATGCTCAGACCTAGAAAGATTTTCTATAAAATTTGATCATTCGTTATTATCATTTATGGTTTCATCACATTTAATTGAGTATGACTCTTTCCCAAGCATGGGCTAGGGCTGCAAATATAAATAAAGGTCTAGGAGCCCTAGAGTGATATAGCCCAAATGACAGCAAATAATTGATAACCATTTTGGATGTAAGTAAAAGGAAACTGCAATTTTTTTTTTTTTTTTTTTTTGTGATGGAAGTCTTCGCTCTGTTGCCCAGGTTGGAGTGACAGTGGCATGATCTCTGCTCACTGTAACCTCTGCCTCCCAGGTTCAAGCAATTCTGTCTCAGCCTTCCAGAAGTAGCTGGGATTACAGGCGCCCACCACCATGCCTGGCTAATTTTTGTATTATTTGTCGAGGTGAGGTTTCACCATGTTAGGCCAGGCTCGTCTCAAACTCCTGACCTCAGTGATCTGTCCCCCTCGGTCTCCCCAAAGTGCTGGGACTTACAGG chm1:+:161200611:-1 chm1:+:515713825:-1 chm1:+:731186749:-1 chm1:+:1150705921:-1 chm1:+:1362428421:-1 chm1:+:1545125492:-1 chm1:+:1882548449:-1 chm1:+:2336408976:-1 chm1:+:2338096804:-1 chm1:+:2426639718:-1 chm1:+:2505363183:-1 chm1:+:2578048248:-1 chm1:+:2764650424:-1 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAG chm1:+:857243025:38 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAG chm1:+:857243024:38 chm1:+:2619475305:-1 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAG chm1:+:32311091:-1 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAG chm1:+:857243029:38 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAG chm1:+:857243017:38 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAG chm1:+:587769746:-1 chm1:+:857243020:38 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAG chm1:+:857243027:38 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAG chm1:+:857243016:38 +TACTAGACTTCAAGAAAAAAGATTATTCTTTTTGTTACGCAGCAGAGTTGTTTGATGCTTATGGACAATATGAATATTACAACTTAATGATTGCCTAATTTTCTAGAAAACTTTAAGCCCAAAGTGTCCACCTTATTCAACTCCCAAGTTCATAGTATCTACCTCTCCTTAGACTAGCAGTAGTTGGAAAGCAGTGGAAGGGAAAAATGAATGCTAGGATTTCTCCCTGTGGCCTGGATCAAAGCCTAGGGCCCACCTACTGAGAAGGGTTCAGACGCCCAGACCAAAAAGGTGTAGATCCAGGAGCAGGTACACCCACATGAATTTAGGAACTTAAAGGCGAAGGCCAGTTGTCTTAGTCCATTCTCACACTGCTATGAAGAGCTACCTAGATTGAATAATTTATAAAGAAAAGAGATTTAATTGGCTCACAGTCCCGCAGCTGTACAGGAAGCATGGGGTAGGGACGGCCTCCAGGAAACCTTCAATTCATGGCGGCAGGCCGAAGGGGAAGTCAGGCACGTCTTACATGACTGGAACAGGAGGAAGAGAGTGAAGGGGAGGTCGCCACACACTTTTAAACCAACCAGATCTCATGAGAACTCACTCACTATCTTGAGAACAGCAAGGGGGAAATCCCTCCCCCATGATGATCATCTCCTACCAGGCCCTTACCTCCAACATTGGGGATTACAATTCAAAATGAAGATTTCTATGGGTGACACAGAGCCAAACCATATCACCATGTTGGTTGTACCCAAGTGTGTCAGGACTACCTGGGCTCCCGAGGAGACCACAAG chm1:+:2005749951:-1 +CTTGTGGTCTCCTCGGGAGCCCAGGTAGTCCTGACACACTTGGGTACAACCAACATGGTGATATGGTTTGGCTCTGTGTCACCCATAGAAATCTTCATTTTGAATTGTAATCCCCAATGTTGGAGGTAAGGGCCTGGTAGGAGATGATCATCATGGGGGAGGGATTTCCCCCTTGCTGTTCTCAAGATAGTGAGTGAGTTCTCATGAGATCTGGTTGGTTTAAAAGTGTGTGGCGACCTCCCCTTCACTCTCTTCCTCCTGTTCCAGTCATGTAAGACGTGCCTGACTTCCCCTTCGGCCTGCCGCCATGAATTGAAGGTTTCCTGGAGGCCGTCCCTACCCCATGCTTCCTGTACAGCTGCGGGACTGTGAGCCAATTAAATCTCTTTTCTTTATAAATTATTCAATCTAGGTAGCTCTTCATAGCAGTGTGAGAATGGACTAAGACAACTGGCCTTCGCCTTTAAGTTCCTAAATTCATGTGGGTGTACCTGCTCCTGGATCTACACCTTTTTGGTCTGGGCGTCTGAACCCTTCTCAGTAGGTGGGCCCTAGGCTTTGATCCAGGCCACAGGGAGAAATCCTAGCATTCATTTTTCCCTTCCACTGCTTTCCAACTACTGCTAGTCTAAGGAGAGGTAGATACTATGAACTTGGGAGTTGAATAAGGTGGACACTTTGGGCTTAAAGTTTTCTAGAAAATTAGGCAATCATTAAGTTGTAATATTCATATTGTCCATAAGCATCAAACAACTCTGCTGCGTAACAAAAAGAATAATCTTTTTTCTTGAAGTCTAGTA chm1:+:1224162304:-1 +CTTGTGGTCTCCTCGGGAGCCCAGGTAGTCCTGACACACTTGGGTACAACCAACATGGTGATATGGTTTGGCTCTGTGTCACCCATAGAAATCTTCATTTTGAATTGTAATCCCCAATGTTGGAGGTAAGGGCCTGGTAGGAGATGATCATCATGGGGGAGGGATTTCCCCCTTGCTGTTCTCAAGATAGTGAGTGAGTTCTCATGAGATCTGGTTGGTTTAAAAGTGTGTGGCGACCTCCCCTTCACTCTCTTCCTCCTGTTCCAGTCATGTAAGACGTGCCTGACTTCCCCTTCGGCCTGCCGCCATGAATTGAAGGTTTCCTGGAGGCCGTCCCTACCCCATGCTTCCTGTACAGCTGCGGGACTGTGAGCCAATTAAATCTCTTTTCTTTATAAATTATTCAATCTAGGTAGCTCTTCATAGCAGTGTGAGAATGGACTAAGACAACTGGCCTTCGCCTTTAAGTTCCTAAATTCATGTGGGTGTACCTGCTCCTGGATCTACACCTTTTTGGTCTGGGCGTCTGAACCCTTCTCAGTAGGTGGGCCCTAGGCTTTGATCCAGGCCACAGGGAGAAATCCTAGCATTCATTTTTCCCTTCCACTGCTTTCCAACTACTGCTAGTCTAAGGAGAGGTAGATACTATGAACTTGGGAGTTGAATAAGGTGGACACTTTGGGCTTAAAGTTTTCTAGAAAATTAGGCAATCATTAAGTTGTAATATTCATATTGTCCATAAGCATCAAACAACTCTGCTGCGTAACAAAAAGAATAATCTTTTTTCTTGAAGTCTAGTA chm1:+:1377654516:-1 +CTTGTGGTCTCCTCGGGAGCCCAGGTAGTCCTGACACACTTGGGTACAACCAACATGGTGATATGGTTTGGCTCTGTGTCACCCATAGAAATCTTCATTTTGAATTGTAATCCCCAATGTTGGAGGTAAGGGCCTGGTAGGAGATGATCATCATGGGGGAGGGATTTCCCCCTTGCTGTTCTCAAGATAGTGAGTGAGTTCTCATGAGATCTGGTTGGTTTAAAAGTGTGTGGCGACCTCCCCTTCACTCTCTTCCTCCTGTTCCAGTCATGTAAGACGTGCCTGACTTCCCCTTCGGCCTGCCGCCATGAATTGAAGGTTTCCTGGAGGCCGTCCCTACCCCATGCTTCCTGTACAGCTGCGGGACTGTGAGCCAATTAAATCTCTTTTCTTTATAAATTATTCAATCTAGGTAGCTCTTCATAGCAGTGTGAGAATGGACTAAGACAACTGGCCTTCGCCTTTAAGTTCCTAAATTCATGTGGGTGTACCTGCTCCTGGATCTACACCTTTTTGGTCTGGGCGTCTGAACCCTTCTCAGTAGGTGGGCCCTAGGCTTTGATCCAGGCCACAGGGAGAAATCCTAGCATTCATTTTTCCCTTCCACTGCTTTCCAACTACTGCTAGTCTAAGGAGAGGTAGATACTATGAACTTGGGAGTTGAATAAGGTGGACACTTTGGGCTTAAAGTTTTCTAGAAAATTAGGCAATCATTAAGTTGTAATATTCATATTGTCCATAAGCATCAAACAACTCTGCTGCGTAACAAAAAGAATAATCTTTTTTCTTGAAGTCTAGTA chm1:+:281233548:-1 chm1:+:1290201709:-1 +CTTGTGGTCTCCTCGGGAGCCCAGGTAGTCCTGACACACTTGGGTACAACCAACATGGTGATATGGTTTGGCTCTGTGTCACCCATAGAAATCTTCATTTTGAATTGTAATCCCCAATGTTGGAGGTAAGGGCCTGGTAGGAGATGATCATCATGGGGGAGGGATTTCCCCCTTGCTGTTCTCAAGATAGTGAGTGAGTTCTCATGAGATCTGGTTGGTTTAAAAGTGTGTGGCGACCTCCCCTTCACTCTCTTCCTCCTGTTCCAGTCATGTAAGACGTGCCTGACTTCCCCTTCGGCCTGCCGCCATGAATTGAAGGTTTCCTGGAGGCCGTCCCTACCCCATGCTTCCTGTACAGCTGCGGGACTGTGAGCCAATTAAATCTCTTTTCTTTATAAATTATTCAATCTAGGTAGCTCTTCATAGCAGTGTGAGAATGGACTAAGACAACTGGCCTTCGCCTTTAAGTTCCTAAATTCATGTGGGTGTACCTGCTCCTGGATCTACACCTTTTTGGTCTGGGCGTCTGAACCCTTCTCAGTAGGTGGGCCCTAGGCTTTGATCCAGGCCACAGGGAGAAATCCTAGCATTCATTTTTCCCTTCCACTGCTTTCCAACTACTGCTAGTCTAAGGAGAGGTAGATACTATGAACTTGGGAGTTGAATAAGGTGGACACTTTGGGCTTAAAGTTTTCTAGAAAATTAGGCAATCATTAAGTTGTAATATTCATATTGTCCATAAGCATCAAACAACTCTGCTGCGTAACAAAAAGAATAATCTTTTTTCTTGAAGTCTAGTA chm1:+:621486947:-1 +CTTGTGGTCTCCTCGGGAGCCCAGGTAGTCCTGACACACTTGGGTACAACCAACATGGTGATATGGTTTGGCTCTGTGTCACCCATAGAAATCTTCATTTTGAATTGTAATCCCCAATGTTGGAGGTAAGGGCCTGGTAGGAGATGATCATCATGGGGGAGGGATTTCCCCCTTGCTGTTCTCAAGATAGTGAGTGAGTTCTCATGAGATCTGGTTGGTTTAAAAGTGTGTGGCGACCTCCCCTTCACTCTCTTCCTCCTGTTCCAGTCATGTAAGACGTGCCTGACTTCCCCTTCGGCCTGCCGCCATGAATTGAAGGTTTCCTGGAGGCCGTCCCTACCCCATGCTTCCTGTACAGCTGCGGGACTGTGAGCCAATTAAATCTCTTTTCTTTATAAATTATTCAATCTAGGTAGCTCTTCATAGCAGTGTGAGAATGGACTAAGACAACTGGCCTTCGCCTTTAAGTTCCTAAATTCATGTGGGTGTACCTGCTCCTGGATCTACACCTTTTTGGTCTGGGCGTCTGAACCCTTCTCAGTAGGTGGGCCCTAGGCTTTGATCCAGGCCACAGGGAGAAATCCTAGCATTCATTTTTCCCTTCCACTGCTTTCCAACTACTGCTAGTCTAAGGAGAGGTAGATACTATGAACTTGGGAGTTGAATAAGGTGGACACTTTGGGCTTAAAGTTTTCTAGAAAATTAGGCAATCATTAAGTTGTAATATTCATATTGTCCATAAGCATCAAACAACTCTGCTGCGTAACAAAAAGAATAATCTTTTTTCTTGAAGTCTAGTA chm1:+:801110190:-1 chm1:+:1098972977:-1 chm1:+:2267756441:-1 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGATTTGCATAATGCTGCACTATCCTTGCATCTCTGGGAGAATCCCATCTTGACCAAAACAAATAGCCCCATTAAAAAGGGGACAAAGGAGTATGAACAGATATTTTTCAAAAGAAGACATTCAACGTGGCCAATGAACATATGAAAAAAATGACTCAACATCACTAATCATCAGAGAAATGCAAATTAAAATCACAATGAGAA chm1:+:2389033769:-1 chm1:+:3012507059:31 chm1:+:3022098859:-1 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGATTTGCATAATGCTGCACTATCCTTGCATCTCTGGGAGAATCCCATCTTGACCAAAACAAATAGCCCCATTAAAAAGGGGACAAAGGAGTATGAACAGATATTTTTCAAAAGAAGACATTCAACGTGGCCAATGAACATATGAAAAAAATGACTCAACATCACTAATCATCAGAGAAATGCAAATTAAAATCACAATGAGAA chm1:+:3012507058:31 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGATTTGCATAATGCTGCACTATCCTTGCATCTCTGGGAGAATCCCATCTTGACCAAAACAAATAGCCCCATTAAAAAGGGGACAAAGGAGTATGAACAGATATTTTTCAAAAGAAGACATTCAACGTGGCCAATGAACATATGAAAAAAATGACTCAACATCACTAATCATCAGAGAAATGCAAATTAAAATCACAATGAGAA chm1:+:238429594:-1 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGATTTGCATAATGCTGCACTATCCTTGCATCTCTGGGAGAATCCCATCTTGACCAAAACAAATAGCCCCATTAAAAAGGGGACAAAGGAGTATGAACAGATATTTTTCAAAAGAAGACATTCAACGTGGCCAATGAACATATGAAAAAAATGACTCAACATCACTAATCATCAGAGAAATGCAAATTAAAATCACAATGAGAA chm1:+:3012507052:31 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGATTTGCATAATGCTGCACTATCCTTGCATCTCTGGGAGAATCCCATCTTGACCAAAACAAATAGCCCCATTAAAAAGGGGACAAAGGAGTATGAACAGATATTTTTCAAAAGAAGACATTCAACGTGGCCAATGAACATATGAAAAAAATGACTCAACATCACTAATCATCAGAGAAATGCAAATTAAAATCACAATGAGAA chm1:+:3012507054:31 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGATTTGCATAATGCTGCACTATCCTTGCATCTCTGGGAGAATCCCATCTTGACCAAAACAAATAGCCCCATTAAAAAGGGGACAAAGGAGTATGAACAGATATTTTTCAAAAGAAGACATTCAACGTGGCCAATGAACATATGAAAAAAATGACTCAACATCACTAATCATCAGAGAAATGCAAATTAAAATCACAATGAGAA chm1:+:978903444:-1 chm1:+:1280338189:-1 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGATTTGCATAATGCTGCACTATCCTTGCATCTCTGGGAGAATCCCATCTTGACCAAAACAAATAGCCCCATTAAAAAGGGGACAAAGGAGTATGAACAGATATTTTTCAAAAGAAGACATTCAACGTGGCCAATGAACATATGAAAAAAATGACTCAACATCACTAATCATCAGAGAAATGCAAATTAAAATCACAATGAGAA chm1:+:3012507056:31 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGATTTGCATAATGCTGCACTATCCTTGCATCTCTGGGAGAATCCCATCTTGACCAAAACAAATAGCCCCATTAAAAAGGGGACAAAGGAGTATGAACAGATATTTTTCAAAAGAAGACATTCAACGTGGCCAATGAACATATGAAAAAAATGACTCAACATCACTAATCATCAGAGAAATGCAAATTAAAATCACAATGAGAA chm1:+:151817230:-1 chm1:+:234028000:-1 +GGCTTAGAGAGATATTCACCTTCTTGGTTAAATAATATTCCTAAGGTATTTTTATGTTTTTTATGTATTTTATGATTTGGTCCTGGCTGGTATCATTATTGGTGTACAGAAATGTTACTGATCTCTGTAGTTAATTTTGTATCCTGAAACTTTACTGAATTCATTTACCAAAATGAAAGTTTTTTGGTGGAGTCTCTAGTGTTTTCAAGATAGTCAGATCCTATCATTGGTGAACAAGGATAATTTGACTTCATCTTTTCCAACTTTAGATGTCTTTTTTTTTTCCTCTTGTTGATTGCTCTGGCAAAGGACCTTCTAGTACTATGTTGAATAACAGTGGTGAAAATGAGCATTGTTATCTTGCTCCAGTTCTTAGAGGAATGCTTTCAACTGTTCGGTTAAGTATGATGTTGGCTTGGGTTTTGTCAAATATTACCTAATGTTATTTTGAGGTATGTTTCTTTTATACCAGGTTTGTTGAGGATTTTATCACAAAGTTGGTGCTAGAATTTTATTGAATAGCTTTTTCTGCATCTATTAAGATGATTATATTGGTTTTTGTCTTTAAGTCTTTTTGTGTGATTATCCACATTTATTGATTTGCATAATGCTGCACTATCCTTGCATCTCTGGGAGAATCCCATCTTGACCAAAACAAATAGCCCCATTAAAAAGGGGACAAAGGAGTATGAACAGATATTTTTCAAAAGAAGACATTCAACGTGGCCAATGAACATATGAAAAAAATGACTCAACATCACTAATCATCAGAGAAATGCAAATTAAAATCACAATGAGAA chm1:+:3012507060:31 +TTCTCATTGTGATTTTAATTTGCATTTCTCTGATGATTAGTGATGTTGAGTCATTTTTTTCATATGTTCATTGGCCACGTTGAATGTCTTCTTTTGAAAAATATCTGTTCATACTCCTTTGTCCCCTTTTTAATGGGGCTATTTGTTTTGGTCAAGATGGGATTCTCCCAGAGATGCAAGGATAGTGCAGCATTATGCAAATCAATAAATGTGGATAATCACACAAAAAGACTTAAAGACAAAAACCAATATAATCATCTTAATAGATGCAGAAAAAGCTATTCAATAAAATTCTAGCACCAACTTTGTGATAAAATCCTCAACAAACCTGGTATAAAAGAAACATACCTCAAAATAACATTAGGTAATATTTGACAAAACCCAAGCCAACATCATACTTAACCGAACAGTTGAAAGCATTCCTCTAAGAACTGGAGCAAGATAACAATGCTCATTTTCACCACTGTTATTCAACATAGTACTAGAAGGTCCTTTGCCAGAGCAATCAACAAGAGGAAAAAAAAAAGACATCTAAAGTTGGAAAAGATGAAGTCAAATTATCCTTGTTCACCAATGATAGGATCTGACTATCTTGAAAACACTAGAGACTCCACCAAAAAACTTTCATTTTGGTAAATGAATTCAGTAAAGTTTCAGGATACAAAATTAACTACAGAGATCAGTAACATTTCTGTACACCAATAATGATACCAGCCAGGACCAAATCATAAAATACATAAAAAACATAAAAATACCTTAGGAATATTATTTAACCAAGAAGGTGAATATCTCTCTAAGCC chm1:+:795750389:-1 chm1:+:2963121815:-1 +TTCTCATTGTGATTTTAATTTGCATTTCTCTGATGATTAGTGATGTTGAGTCATTTTTTTCATATGTTCATTGGCCACGTTGAATGTCTTCTTTTGAAAAATATCTGTTCATACTCCTTTGTCCCCTTTTTAATGGGGCTATTTGTTTTGGTCAAGATGGGATTCTCCCAGAGATGCAAGGATAGTGCAGCATTATGCAAATCAATAAATGTGGATAATCACACAAAAAGACTTAAAGACAAAAACCAATATAATCATCTTAATAGATGCAGAAAAAGCTATTCAATAAAATTCTAGCACCAACTTTGTGATAAAATCCTCAACAAACCTGGTATAAAAGAAACATACCTCAAAATAACATTAGGTAATATTTGACAAAACCCAAGCCAACATCATACTTAACCGAACAGTTGAAAGCATTCCTCTAAGAACTGGAGCAAGATAACAATGCTCATTTTCACCACTGTTATTCAACATAGTACTAGAAGGTCCTTTGCCAGAGCAATCAACAAGAGGAAAAAAAAAAGACATCTAAAGTTGGAAAAGATGAAGTCAAATTATCCTTGTTCACCAATGATAGGATCTGACTATCTTGAAAACACTAGAGACTCCACCAAAAAACTTTCATTTTGGTAAATGAATTCAGTAAAGTTTCAGGATACAAAATTAACTACAGAGATCAGTAACATTTCTGTACACCAATAATGATACCAGCCAGGACCAAATCATAAAATACATAAAAAACATAAAAATACCTTAGGAATATTATTTAACCAAGAAGGTGAATATCTCTCTAAGCC chm1:+:2639113153:-1 +TTCTCATTGTGATTTTAATTTGCATTTCTCTGATGATTAGTGATGTTGAGTCATTTTTTTCATATGTTCATTGGCCACGTTGAATGTCTTCTTTTGAAAAATATCTGTTCATACTCCTTTGTCCCCTTTTTAATGGGGCTATTTGTTTTGGTCAAGATGGGATTCTCCCAGAGATGCAAGGATAGTGCAGCATTATGCAAATCAATAAATGTGGATAATCACACAAAAAGACTTAAAGACAAAAACCAATATAATCATCTTAATAGATGCAGAAAAAGCTATTCAATAAAATTCTAGCACCAACTTTGTGATAAAATCCTCAACAAACCTGGTATAAAAGAAACATACCTCAAAATAACATTAGGTAATATTTGACAAAACCCAAGCCAACATCATACTTAACCGAACAGTTGAAAGCATTCCTCTAAGAACTGGAGCAAGATAACAATGCTCATTTTCACCACTGTTATTCAACATAGTACTAGAAGGTCCTTTGCCAGAGCAATCAACAAGAGGAAAAAAAAAAGACATCTAAAGTTGGAAAAGATGAAGTCAAATTATCCTTGTTCACCAATGATAGGATCTGACTATCTTGAAAACACTAGAGACTCCACCAAAAAACTTTCATTTTGGTAAATGAATTCAGTAAAGTTTCAGGATACAAAATTAACTACAGAGATCAGTAACATTTCTGTACACCAATAATGATACCAGCCAGGACCAAATCATAAAATACATAAAAAACATAAAAATACCTTAGGAATATTATTTAACCAAGAAGGTGAATATCTCTCTAAGCC chm1:+:115687844:-1 chm1:+:205825430:-1 chm1:+:291035507:-1 chm1:+:655296093:-1 chm1:+:689377517:-1 chm1:+:968417859:-1 chm1:+:1119449160:-1 chm1:+:2132682995:-1 chm1:+:2791103775:-1 +TTCTCATTGTGATTTTAATTTGCATTTCTCTGATGATTAGTGATGTTGAGTCATTTTTTTCATATGTTCATTGGCCACGTTGAATGTCTTCTTTTGAAAAATATCTGTTCATACTCCTTTGTCCCCTTTTTAATGGGGCTATTTGTTTTGGTCAAGATGGGATTCTCCCAGAGATGCAAGGATAGTGCAGCATTATGCAAATCAATAAATGTGGATAATCACACAAAAAGACTTAAAGACAAAAACCAATATAATCATCTTAATAGATGCAGAAAAAGCTATTCAATAAAATTCTAGCACCAACTTTGTGATAAAATCCTCAACAAACCTGGTATAAAAGAAACATACCTCAAAATAACATTAGGTAATATTTGACAAAACCCAAGCCAACATCATACTTAACCGAACAGTTGAAAGCATTCCTCTAAGAACTGGAGCAAGATAACAATGCTCATTTTCACCACTGTTATTCAACATAGTACTAGAAGGTCCTTTGCCAGAGCAATCAACAAGAGGAAAAAAAAAAGACATCTAAAGTTGGAAAAGATGAAGTCAAATTATCCTTGTTCACCAATGATAGGATCTGACTATCTTGAAAACACTAGAGACTCCACCAAAAAACTTTCATTTTGGTAAATGAATTCAGTAAAGTTTCAGGATACAAAATTAACTACAGAGATCAGTAACATTTCTGTACACCAATAATGATACCAGCCAGGACCAAATCATAAAATACATAAAAAACATAAAAATACCTTAGGAATATTATTTAACCAAGAAGGTGAATATCTCTCTAAGCC chm1:+:250226079:-1 chm1:+:362193376:-1 chm1:+:376735982:-1 chm1:+:512183327:-1 chm1:+:684214980:-1 chm1:+:879037853:-1 chm1:+:907728203:-1 chm1:+:1427689440:-1 chm1:+:1771696901:-1 chm1:+:1840033989:-1 chm1:+:1897316473:-1 chm1:+:2117462467:-1 chm1:+:2263037879:-1 chm1:+:2379427702:-1 chm1:+:2507038614:-1 +TTCTCATTGTGATTTTAATTTGCATTTCTCTGATGATTAGTGATGTTGAGTCATTTTTTTCATATGTTCATTGGCCACGTTGAATGTCTTCTTTTGAAAAATATCTGTTCATACTCCTTTGTCCCCTTTTTAATGGGGCTATTTGTTTTGGTCAAGATGGGATTCTCCCAGAGATGCAAGGATAGTGCAGCATTATGCAAATCAATAAATGTGGATAATCACACAAAAAGACTTAAAGACAAAAACCAATATAATCATCTTAATAGATGCAGAAAAAGCTATTCAATAAAATTCTAGCACCAACTTTGTGATAAAATCCTCAACAAACCTGGTATAAAAGAAACATACCTCAAAATAACATTAGGTAATATTTGACAAAACCCAAGCCAACATCATACTTAACCGAACAGTTGAAAGCATTCCTCTAAGAACTGGAGCAAGATAACAATGCTCATTTTCACCACTGTTATTCAACATAGTACTAGAAGGTCCTTTGCCAGAGCAATCAACAAGAGGAAAAAAAAAAGACATCTAAAGTTGGAAAAGATGAAGTCAAATTATCCTTGTTCACCAATGATAGGATCTGACTATCTTGAAAACACTAGAGACTCCACCAAAAAACTTTCATTTTGGTAAATGAATTCAGTAAAGTTTCAGGATACAAAATTAACTACAGAGATCAGTAACATTTCTGTACACCAATAATGATACCAGCCAGGACCAAATCATAAAATACATAAAAAACATAAAAATACCTTAGGAATATTATTTAACCAAGAAGGTGAATATCTCTCTAAGCC chm1:+:74692859:-1 chm1:+:211194155:-1 chm1:+:211234147:-1 chm1:+:272444539:-1 chm1:+:385979124:-1 chm1:+:706572242:-1 chm1:+:758800919:-1 chm1:+:938210929:-1 chm1:+:1131534423:-1 chm1:+:1136352432:-1 chm1:+:1141664109:-1 chm1:+:1453585222:-1 chm1:+:1569590966:-1 chm1:+:1812167884:-1 chm1:+:1955362982:-1 chm1:+:2223628470:-1 chm1:+:2937029630:-1 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTC chm1:+:156606740:-1 chm1:+:237092364:-1 chm1:+:960281454:-1 chm1:+:1459391043:36 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTC chm1:+:1459391042:36 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTC chm1:+:1459391046:36 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTC chm1:+:1459391035:36 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTC chm1:+:913682238:-1 +GGCCAGCGTAATTTTTGTGTTTTAGTACGAGATGGGGTTTTCACCATGTTGGCCAAGGATGGTCTTGGATCTCTTGACCTTGTGATCTGCCTAGTTTCGGCCTTCCAAAGTGCTGGGGATACAGGTGTTGAGCCCACTGTGCCTGGCCCTTGTTTTCTTATTGTTATTATAGTATTAGACATTTATCACATAACTTTGTTCTTTTTTTTTAGCAATTCTTTACGAACCATAATGTAAGAACATTTCAGTTCAACATTGAAATAATATAAAATTCTAACAGATATCTCTGCCACTTTTAAATAATAGATTAACATGTGGAGATGTGGAAGATGTATTTACTCATCATTTAGAATTCAGAAGTGCCCATGTGTACCCGTTTGATAACATGTCATGTCTTAAATCACTCCTCCTGGGTAAATGGAGGTGAAATCTGTTTTCTTTTTCTTTTTTTTTTGGAGACAGAGTCTTGCCCTGTGATCTCAGGTGATCTGCGCATCTCTGCCTCCCTAAGTGCTGGGATTACACGGCGTGAGCCACTGCACCCGGCTGCCTTTTTTCTTTTTTAATAATCAAAATGAAGAAATCTGTGTAGTAAGTCTCTCAAGTACTTTCCTAAGAATTCAATTCATTTTAGACATTGAACTGCTCTTATTTGCAGTTTCCTTCAAATAGAGGCTATTATGTTAACTAAGTTTTATAAACTTTTTTTCTGTATTGTTCAATTCCATCAATGTCTTTCTGGTTAAACTATCTTACCTCCCTCCTAGTTCCAGGAAAATGTGCTTCAGCGTTTGGCATTC chm1:+:285064103:-1 chm1:+:1459391044:36 +GAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC chm1:+:2645246595:-1 +GAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC chm1:+:10314953:-1 +GAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC chm1:+:2167922196:-1 +GAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC chm1:+:2717239732:-1 +GAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC chm1:+:540240823:-1 chm1:+:860688485:-1 chm1:+:926165304:-1 chm1:+:1444413686:-1 chm1:+:1448260326:-1 chm1:+:1471629102:-1 chm1:+:1567199965:-1 chm1:+:1750023537:-1 chm1:+:1794730180:-1 chm1:+:2110098419:-1 chm1:+:2345518338:-1 chm1:+:2349312558:-1 chm1:+:2351944616:-1 chm1:+:2544596129:-1 chm1:+:2544814064:-1 chm1:+:2608125720:-1 +GAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC chm1:+:183214209:-1 chm1:+:1184650725:-1 chm1:+:2269285572:-1 +GAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC chm1:+:231017870:-1 chm1:+:778375872:-1 chm1:+:943486918:-1 chm1:+:1234275665:-1 chm1:+:1554527951:-1 chm1:+:1610337443:-1 chm1:+:1753270239:-1 chm1:+:1819711417:-1 chm1:+:2119224648:-1 chm1:+:2162387395:-1 chm1:+:2425722746:-1 chm1:+:2458338991:-1 chm1:+:2568251239:-1 chm1:+:2672462155:-1 chm1:+:2720483237:-1 chm1:+:2824411285:-1 +GAATGCCAAACGCTGAAGCACATTTTCCTGGAACTAGGAGGGAGGTAAGATAGTTTAACCAGAAAGACATTGATGGAATTGAACAATACAGAAAAAAAGTTTATAAAACTTAGTTAACATAATAGCCTCTATTTGAAGGAAACTGCAAATAAGAGCAGTTCAATGTCTAAAATGAATTGAATTCTTAGGAAAGTACTTGAGAGACTTACTACACAGATTTCTTCATTTTGATTATTAAAAAAGAAAAAAGGCAGCCGGGTGCAGTGGCTCACGCCGTGTAATCCCAGCACTTAGGGAGGCAGAGATGCGCAGATCACCTGAGATCACAGGGCAAGACTCTGTCTCCAAAAAAAAAAGAAAAAGAAAACAGATTTCACCTCCATTTACCCAGGAGGAGTGATTTAAGACATGACATGTTATCAAACGGGTACACATGGGCACTTCTGAATTCTAAATGATGAGTAAATACATCTTCCACATCTCCACATGTTAATCTATTATTTAAAAGTGGCAGAGATATCTGTTAGAATTTTATATTATTTCAATGTTGAACTGAAATGTTCTTACATTATGGTTCGTAAAGAATTGCTAAAAAAAAAGAACAAAGTTATGTGATAAATGTCTAATACTATAATAACAATAAGAAAACAAGGGCCAGGCACAGTGGGCTCAACACCTGTATCCCCAGCACTTTGGAAGGCCGAAACTAGGCAGATCACAAGGTCAAGAGATCCAAGACCATCCTTGGCCAACATGGTGAAAACCCCATCTCGTACTAAAACACAAAAATTACGCTGGCC chm1:+:118409817:-1 chm1:+:661703831:-1 chm1:+:1077695781:-1 chm1:+:1426054729:-1 chm1:+:1677160769:-1 chm1:+:1745328654:-1 chm1:+:1889354859:-1 chm1:+:1966327277:-1 chm1:+:2049834636:-1 chm1:+:2067313671:-1 chm1:+:2372626879:-1 chm1:+:2535941639:-1 chm1:+:2655382502:-1 chm1:+:2732382057:-1 chm1:+:2753982739:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:9549813:-1 chm1:+:9564199:-1 chm1:+:12322816:-1 chm1:+:38467961:-1 chm1:+:112189216:-1 chm1:+:169945921:-1 chm1:+:179835595:-1 chm1:+:181873677:-1 chm1:+:208959486:-1 chm1:+:212507689:-1 chm1:+:224442626:-1 chm1:+:314427417:-1 chm1:+:370010372:-1 chm1:+:378595188:-1 chm1:+:381583940:-1 chm1:+:389809641:-1 chm1:+:397846581:-1 chm1:+:410565151:-1 chm1:+:445881568:-1 chm1:+:462972180:-1 chm1:+:483083474:-1 chm1:+:620350705:-1 chm1:+:659029207:-1 chm1:+:679497620:-1 chm1:+:845075328:-1 chm1:+:860829534:-1 chm1:+:895182743:-1 chm1:+:910794842:-1 chm1:+:913492173:-1 chm1:+:913537391:-1 chm1:+:915930162:-1 chm1:+:938056595:-1 chm1:+:946210112:-1 chm1:+:949130693:-1 chm1:+:997907493:-1 chm1:+:1061064115:-1 chm1:+:1106141238:-1 chm1:+:1207302654:-1 chm1:+:1218934531:-1 chm1:+:1238018891:-1 chm1:+:1255120746:-1 chm1:+:1301361840:-1 chm1:+:1303640772:-1 chm1:+:1330969087:-1 chm1:+:1334402687:-1 chm1:+:1336587451:-1 chm1:+:1336604288:-1 chm1:+:1432552421:-1 chm1:+:1491562933:-1 chm1:+:1514579854:-1 chm1:+:1520470028:-1 chm1:+:1521334565:-1 chm1:+:1541985247:-1 chm1:+:1567720440:-1 chm1:+:1570551935:-1 chm1:+:1572479275:-1 chm1:+:1579467428:-1 chm1:+:1583050377:-1 chm1:+:1604791984:-1 chm1:+:1613561157:-1 chm1:+:1640012613:-1 chm1:+:1653778225:-1 chm1:+:1656167204:-1 chm1:+:1656688765:-1 chm1:+:1673272227:-1 chm1:+:1696802476:-1 chm1:+:1702311204:-1 chm1:+:1749207306:-1 chm1:+:1754479417:-1 chm1:+:1755872823:-1 chm1:+:1782341061:-1 chm1:+:1783676864:-1 chm1:+:1785813233:-1 chm1:+:1819935589:-1 chm1:+:1834121178:-1 chm1:+:1922151747:-1 chm1:+:1924277502:-1 chm1:+:1927047218:-1 chm1:+:1932995090:-1 chm1:+:2017482031:-1 chm1:+:2061606756:-1 chm1:+:2062343484:-1 chm1:+:2071701363:-1 chm1:+:2076883612:-1 chm1:+:2080316284:-1 chm1:+:2219474911:-1 chm1:+:2359244049:-1 chm1:+:2402091674:-1 chm1:+:2414299190:-1 chm1:+:2429385871:-1 chm1:+:2431219621:-1 chm1:+:2432055710:-1 chm1:+:2439198752:-1 chm1:+:2465399592:-1 chm1:+:2484614322:-1 chm1:+:2485650744:-1 chm1:+:2486453694:-1 chm1:+:2512783627:-1 chm1:+:2521022488:-1 chm1:+:2538492617:-1 chm1:+:2548304086:-1 chm1:+:2559896665:-1 chm1:+:2571242355:-1 chm1:+:2571845994:-1 chm1:+:2574950479:-1 chm1:+:2590186738:-1 chm1:+:2591269006:-1 chm1:+:2627861335:-1 chm1:+:2635027654:-1 chm1:+:2649237559:-1 chm1:+:2650591262:-1 chm1:+:2651886579:-1 chm1:+:2661610787:-1 chm1:+:2662875879:-1 chm1:+:2666132522:-1 chm1:+:2696741357:-1 chm1:+:2699633890:-1 chm1:+:2710983284:-1 chm1:+:2712593570:-1 chm1:+:2740092246:-1 chm1:+:2750076838:-1 chm1:+:2770188067:-1 chm1:+:2872775291:-1 chm1:+:2875369179:-1 chm1:+:2877796537:-1 chm1:+:2886456542:-1 chm1:+:3034334377:-1 chm1:+:3051627922:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:60910593:-1 chm1:+:317258873:-1 chm1:+:326354055:-1 chm1:+:365357721:-1 chm1:+:454652923:-1 chm1:+:825438146:-1 chm1:+:1152403500:-1 chm1:+:1653142622:-1 chm1:+:1717212435:-1 chm1:+:2031042275:-1 chm1:+:2858438769:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:84575278:-1 chm1:+:273990537:-1 chm1:+:327795205:-1 chm1:+:481172301:-1 chm1:+:983487990:-1 chm1:+:1002970911:-1 chm1:+:1502439728:-1 chm1:+:2133651101:-1 chm1:+:2237206605:-1 chm1:+:2243126492:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:667615905:-1 chm1:+:673498272:-1 chm1:+:703551795:-1 chm1:+:1126413889:-1 chm1:+:1468155647:-1 chm1:+:1502598074:-1 chm1:+:2604794870:-1 chm1:+:3057676586:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:447322825:-1 chm1:+:524069946:-1 chm1:+:1088404817:-1 chm1:+:1125438656:-1 chm1:+:1816790121:-1 chm1:+:2234425081:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:2886661809:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:17740258:-1 chm1:+:97579491:-1 chm1:+:1862445069:-1 chm1:+:2869508334:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:363745520:-1 chm1:+:493317129:-1 chm1:+:504872652:-1 chm1:+:725044995:-1 chm1:+:920783700:-1 chm1:+:1136275638:-1 chm1:+:1630140351:-1 chm1:+:2464559348:-1 chm1:+:2577913774:-1 chm1:+:2740918097:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:188003446:-1 chm1:+:2030837247:-1 chm1:+:2144698724:-1 chm1:+:2170131857:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:292694867:-1 chm1:+:320682214:-1 chm1:+:992856085:-1 chm1:+:1078369965:-1 chm1:+:1343929604:-1 chm1:+:1871075566:-1 chm1:+:2115509245:-1 chm1:+:2356566189:-1 chm1:+:2584010902:-1 chm1:+:2656840956:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:116306168:-1 chm1:+:205806133:-1 chm1:+:264896008:-1 chm1:+:313739047:-1 chm1:+:466094484:-1 chm1:+:607597831:-1 chm1:+:720955710:-1 chm1:+:756752367:-1 chm1:+:810033467:-1 chm1:+:1197120071:-1 chm1:+:1318912607:-1 chm1:+:1346551139:-1 chm1:+:1486187878:-1 chm1:+:1508220749:-1 chm1:+:1657235495:-1 chm1:+:1670571156:-1 chm1:+:1956889217:-1 chm1:+:2137433914:-1 chm1:+:2160550765:-1 chm1:+:2416917385:-1 chm1:+:2821215324:-1 chm1:+:3005052032:-1 chm1:+:3060184673:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:311663979:-1 chm1:+:523228419:-1 chm1:+:1737063421:-1 chm1:+:2354292723:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:82091187:-1 chm1:+:85593232:-1 chm1:+:544319989:-1 chm1:+:703114673:-1 chm1:+:1365032938:-1 chm1:+:1860254118:-1 chm1:+:1901452235:-1 chm1:+:2188621059:-1 chm1:+:2258638049:-1 chm1:+:2465815807:-1 chm1:+:2474088470:-1 chm1:+:2704721117:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:235284583:-1 chm1:+:372889966:-1 chm1:+:2181980816:-1 chm1:+:3013259518:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:1028516268:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:353147747:-1 chm1:+:888550115:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:30503213:-1 chm1:+:53692812:-1 chm1:+:80384488:-1 chm1:+:298970836:-1 chm1:+:312984581:-1 chm1:+:328813483:-1 chm1:+:414823272:-1 chm1:+:446792394:-1 chm1:+:498376632:-1 chm1:+:708862420:-1 chm1:+:727379287:-1 chm1:+:855367011:-1 chm1:+:887023844:-1 chm1:+:922320391:-1 chm1:+:939194268:-1 chm1:+:973694515:-1 chm1:+:1012287256:-1 chm1:+:1227109194:-1 chm1:+:1398124055:-1 chm1:+:1470044243:-1 chm1:+:1682104780:-1 chm1:+:1748926966:-1 chm1:+:1776363670:-1 chm1:+:1815297029:-1 chm1:+:2042795643:-1 chm1:+:2156220114:-1 chm1:+:2159404014:-1 chm1:+:2349687735:-1 chm1:+:2403421941:-1 chm1:+:2405283167:-1 chm1:+:2460942655:-1 chm1:+:2463341337:-1 chm1:+:2608170434:-1 chm1:+:2638613300:-1 chm1:+:2963674483:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:160221497:-1 chm1:+:252292634:-1 chm1:+:353261983:-1 chm1:+:409695103:-1 chm1:+:459741829:-1 chm1:+:524467545:-1 chm1:+:651671182:-1 chm1:+:818447625:-1 chm1:+:859493328:-1 chm1:+:872920790:-1 chm1:+:1042882681:-1 chm1:+:1120287383:-1 chm1:+:1120894530:-1 chm1:+:1145325436:-1 chm1:+:1168567951:-1 chm1:+:1185087488:-1 chm1:+:1251158473:-1 chm1:+:1565903047:-1 chm1:+:1649213452:-1 chm1:+:1797339916:-1 chm1:+:1891141735:-1 chm1:+:1974696872:-1 chm1:+:2021003242:-1 chm1:+:2036606073:-1 chm1:+:2161842472:-1 chm1:+:2170363334:-1 chm1:+:2386479024:-1 chm1:+:2423823379:-1 chm1:+:2740296915:-1 chm1:+:2876857366:-1 chm1:+:2933159165:-1 chm1:+:2950299094:-1 chm1:+:2964049694:-1 chm1:+:2992675769:-1 chm1:+:3060806663:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:1188954212:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:15117243:-1 chm1:+:174355700:-1 chm1:+:369577370:-1 chm1:+:622186666:-1 chm1:+:688691660:-1 chm1:+:773709177:-1 chm1:+:898688202:-1 chm1:+:1222993889:-1 chm1:+:1396799880:-1 chm1:+:1537236757:-1 chm1:+:1539951648:-1 chm1:+:1834607923:-1 chm1:+:2274355613:-1 chm1:+:2676839570:-1 chm1:+:2693988213:-1 chm1:+:2704961806:-1 chm1:+:2931553029:-1 +TCTCGAAACTCCTCGCGCTCAGGTGATCCGACCACCTCAGTTCCCAAAGTGCCGGGATTACAGGTGTGAGCCACCGCACCGGCCAGCTACATTTAACCTTAAGAAATACTGCAAGAAAGCTACTAAAGCATCCCTTCACCAATATTTAAACATCCTGAGTTCATCTCTTCAAGGTAATTAAATAAAAATGACTCCATTTTCCAATCCATCAGTACCGAAAAGCATTGCCAAGAAATATACACTCTTACTTGAACAAGTACTTTTAGCCCAACGATAGCAATGTATAGGTTCTGAAGGTGTGTTAAGAATTGTACAGCCAGGAAAGGTTTCCTCTGGTCGCTTAGGATGACACTCATAACACTCGGTCACACCCTATGAAGTCAGGATCTATGAGAAAAATTTACTCCGATCGACTGGCAGTTTTCAACATTATAAGGTAATATAAACACTTCATTCATCGTATATTCCAACTACGTTTTACGTGTCAAGGAAAATTTAAAATATTAGTGAACTCCAAAAATGCTTACTTTATGATAAACTAACACAAAAGCTAACTGAATCCTACCAGTCATAGGCTAAGGCTGTGCCAGGACGCCCGACTCCTGGTTTCAGTGAACATGAACTTACAAGCCCAAATAAAAAATACTACACCTGAGGTGTCAAATATGAAGTTTACCTTGATCACACTAAACAGAAAAAACTACTGGAAAGACAAACAGCAGCTTTCCAAGAAATTATTTCGTCAAAGTTGTAAAATGTTATCTAAATATTATTCGCAGCCATTTTCTTACTATGTGTTT chm1:+:286095565:-1 chm1:+:441536471:-1 chm1:+:488672150:-1 chm1:+:1069742516:-1 chm1:+:1760079493:-1 chm1:+:1816507195:-1 chm1:+:1898241235:-1 chm1:+:2068114877:-1 chm1:+:2115138518:-1 chm1:+:2130431794:-1 chm1:+:2371273360:-1 chm1:+:2764387309:-1 chm1:+:2768374636:-1 +AAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:35639439:-1 chm1:+:143900412:-1 chm1:+:149453819:-1 chm1:+:461860605:-1 chm1:+:617875805:-1 chm1:+:898585527:-1 chm1:+:1103596961:-1 chm1:+:1105765280:-1 chm1:+:1202868042:-1 chm1:+:1667137127:-1 chm1:+:1678990254:-1 chm1:+:1757327918:-1 chm1:+:1982896371:-1 chm1:+:2153246261:-1 chm1:+:2373083232:-1 chm1:+:2424304640:-1 chm1:+:2459994028:-1 chm1:+:2493923564:-1 chm1:+:2578880679:-1 chm1:+:2674989205:-1 chm1:+:2709911704:-1 chm1:+:2754282184:-1 chm1:+:2819323651:-1 chm1:+:3012631197:-1 +AAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:1385626986:-1 chm1:+:2792656141:-1 +AAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2045359528:-1 chm1:+:2694373279:42 +AAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2694373280:42 +AAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2694373289:42 +AAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2694373298:42 +AAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2694373300:42 +AAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2694373282:42 +AAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:87511340:-1 chm1:+:2694373284:42 +AAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2694373288:42 +AAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2694373290:42 +AAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2007981869:-1 +AAACACATAGTAAGAAAATGGCTGCGAATAATATTTAGATAACATTTTACAACTTTGACGAAATAATTTCTTGGAAAGCTGCTGTTTGTCTTTCCAGTAGTTTTTTCTGTTTAGTGTGATCAAGGTAAACTTCATATTTGACACCTCAGGTGTAGTATTTTTTATTTGGGCTTGTAAGTTCATGTTCACTGAAACCAGGAGTCGGGCGTCCTGGCACAGCCTTAGCCTATGACTGGTAGGATTCAGTTAGCTTTTGTGTTAGTTTATCATAAAGTAAGCATTTTTGGAGTTCACTAATATTTTAAATTTTCCTTGACACGTAAAACGTAGTTGGAATATACGATGAATGAAGTGTTTATATTACCTTATAATGTTGAAAACTGCCAGTCGATCGGAGTAAATTTTTCTCATAGATCCTGACTTCATAGGGTGTGACCGAGTGTTATGAGTGTCATCCTAAGCGACCAGAGGAAACCTTTCCTGGCTGTACAATTCTTAACACACCTTCAGAACCTATACATTGCTATCGTTGGGCTAAAAGTACTTGTTCAAGTAAGAGTGTATATTTCTTGGCAATGCTTTTCGGTACTGATGGATTGGAAAATGGAGTCATTTTTATTTAATTACCTTGAAGAGATGAACTCAGGATGTTTAAATATTGGTGAAGGGATGCTTTAGTAGCTTTCTTGCAGTATTTCTTAAGGTTAAATGTAGCTGGCCGGTGCGGTGGCTCACACCTGTAATCCCGGCACTTTGGGAACTGAGGTGGTCGGATCACCTGAGCGCGAGGAGTTTCGAGA chm1:+:2694373297:42 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACA chm1:+:2277191501:-1 chm1:+:2821050400:50 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACA chm1:+:383819743:-1 chm1:+:1270415803:-1 chm1:+:1278428656:-1 chm1:+:1463007816:-1 chm1:+:1876147167:-1 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACA chm1:+:2821050404:50 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACA chm1:+:2821050389:50 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACA chm1:+:2821050392:50 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACA chm1:+:2821050393:50 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACA chm1:+:2821050397:50 +TATCGTAGTTCAGATTAGTTAGTCCATGTTTTTCTTATGACTCCACTTATTTAAGAACTTCAGTGACATACATTTATCTCCACGTAGTGAGGATAAAAACGTTGAGAAACAAGAAGCTAATACGATACAGTCAAGACACAGTTCACAGGAAGTAAAATAGGAAGGAAGGAAAAAGAAAGGTCTAGGTCTTCAGAGACAAGGGAGAGATAACTGGCAAGGCAGAAGGTCCCTAAGAGTTCAATATAAAGACAGGTAATACACCACTCTTAAAGGAAAGGATTCCCAGGATTCAAAGTTGATCGGTTCCATGTGTCTAAAATCACTGGACTTGTAAGAGTAACCCCTAACTTTAATGGAAGAAGAAACAGGTAAAAAATATCCTCAGGCTCGAGGGTTAGTGGCTTTTCTTATCTCAATAAAGGGAAATAAACTCATTCATGTTGGCTGGGCTTTCTTTGTCCTGTTAAGAAATTTCAAGTTGTTGGGCTACCCAAAAGCTGCATTCTAGATTTCTTACCTCTGTCCCACTCGGGTAGAAGCATGGCCTGATACTTTTTCCTCTTCAGTATTAATATTTCATTTAAGGACAGTCAGGTCCTCCTTAAATGTGTTATTATTTGGTTCCAGGCTTAAACCGAATAAGCCCGCCAAACATTGATAAAAGCAATGTATCTGAGCTTCCCATATTTACTCGGCACCCAGTGACATTTTGGCTCTTATCTACTGAGAATATGAGAGTGATAACAGTAGGAAACTTAAGTCGAGGAGCCCTGCAGGTTCTTATTTAATATCTATAGACA chm1:+:2821050398:50 +TGTCTATAGATATTAAATAAGAACCTGCAGGGCTCCTCGACTTAAGTTTCCTACTGTTATCACTCTCATATTCTCAGTAGATAAGAGCCAAAATGTCACTGGGTGCCGAGTAAATATGGGAAGCTCAGATACATTGCTTTTATCAATGTTTGGCGGGCTTATTCGGTTTAAGCCTGGAACCAAATAATAACACATTTAAGGAGGACCTGACTGTCCTTAAATGAAATATTAATACTGAAGAGGAAAAAGTATCAGGCCATGCTTCTACCCGAGTGGGACAGAGGTAAGAAATCTAGAATGCAGCTTTTGGGTAGCCCAACAACTTGAAATTTCTTAACAGGACAAAGAAAGCCCAGCCAACATGAATGAGTTTATTTCCCTTTATTGAGATAAGAAAAGCCACTAACCCTCGAGCCTGAGGATATTTTTTACCTGTTTCTTCTTCCATTAAAGTTAGGGGTTACTCTTACAAGTCCAGTGATTTTAGACACATGGAACCGATCAACTTTGAATCCTGGGAATCCTTTCCTTTAAGAGTGGTGTATTACCTGTCTTTATATTGAACTCTTAGGGACCTTCTGCCTTGCCAGTTATCTCTCCCTTGTCTCTGAAGACCTAGACCTTTCTTTTTCCTTCCTTCCTATTTTACTTCCTGTGAACTGTGTCTTGACTGTATCGTATTAGCTTCTTGTTTCTCAACGTTTTTATCCTCACTACGTGGAGATAAATGTATGTCACTGAAGTTCTTAAATAAGTGGAGTCATAAGAAAAACATGGACTAACTAATCTGAACTACGATA chm1:+:268665768:-1 chm1:+:351811339:-1 chm1:+:1562469313:-1 chm1:+:2036467899:-1 +TGTCTATAGATATTAAATAAGAACCTGCAGGGCTCCTCGACTTAAGTTTCCTACTGTTATCACTCTCATATTCTCAGTAGATAAGAGCCAAAATGTCACTGGGTGCCGAGTAAATATGGGAAGCTCAGATACATTGCTTTTATCAATGTTTGGCGGGCTTATTCGGTTTAAGCCTGGAACCAAATAATAACACATTTAAGGAGGACCTGACTGTCCTTAAATGAAATATTAATACTGAAGAGGAAAAAGTATCAGGCCATGCTTCTACCCGAGTGGGACAGAGGTAAGAAATCTAGAATGCAGCTTTTGGGTAGCCCAACAACTTGAAATTTCTTAACAGGACAAAGAAAGCCCAGCCAACATGAATGAGTTTATTTCCCTTTATTGAGATAAGAAAAGCCACTAACCCTCGAGCCTGAGGATATTTTTTACCTGTTTCTTCTTCCATTAAAGTTAGGGGTTACTCTTACAAGTCCAGTGATTTTAGACACATGGAACCGATCAACTTTGAATCCTGGGAATCCTTTCCTTTAAGAGTGGTGTATTACCTGTCTTTATATTGAACTCTTAGGGACCTTCTGCCTTGCCAGTTATCTCTCCCTTGTCTCTGAAGACCTAGACCTTTCTTTTTCCTTCCTTCCTATTTTACTTCCTGTGAACTGTGTCTTGACTGTATCGTATTAGCTTCTTGTTTCTCAACGTTTTTATCCTCACTACGTGGAGATAAATGTATGTCACTGAAGTTCTTAAATAAGTGGAGTCATAAGAAAAACATGGACTAACTAATCTGAACTACGATA chm1:+:220845553:-1 chm1:+:409382209:-1 chm1:+:417695161:-1 chm1:+:499908147:-1 chm1:+:678764762:-1 chm1:+:688641787:-1 chm1:+:709737952:-1 chm1:+:883055468:-1 chm1:+:1027906018:-1 chm1:+:1033100315:-1 chm1:+:1046607746:-1 chm1:+:1058152797:-1 chm1:+:1081860673:-1 chm1:+:1098238769:-1 chm1:+:1136040702:-1 chm1:+:1416304937:-1 chm1:+:1494899828:-1 chm1:+:1500751151:-1 chm1:+:1541471154:-1 chm1:+:1685149611:-1 chm1:+:1821536692:-1 chm1:+:1847265502:-1 chm1:+:1911426392:-1 chm1:+:1995126331:-1 chm1:+:2006326405:-1 chm1:+:2041201744:-1 chm1:+:2221598349:-1 chm1:+:2221705810:-1 chm1:+:2241057052:-1 chm1:+:2270297954:-1 chm1:+:2390722119:-1 chm1:+:2424207156:-1 chm1:+:2439607720:-1 chm1:+:2572170757:-1 chm1:+:2633287013:-1 chm1:+:2656896838:-1 chm1:+:2689984879:-1 chm1:+:2908666502:-1 +TGTCTATAGATATTAAATAAGAACCTGCAGGGCTCCTCGACTTAAGTTTCCTACTGTTATCACTCTCATATTCTCAGTAGATAAGAGCCAAAATGTCACTGGGTGCCGAGTAAATATGGGAAGCTCAGATACATTGCTTTTATCAATGTTTGGCGGGCTTATTCGGTTTAAGCCTGGAACCAAATAATAACACATTTAAGGAGGACCTGACTGTCCTTAAATGAAATATTAATACTGAAGAGGAAAAAGTATCAGGCCATGCTTCTACCCGAGTGGGACAGAGGTAAGAAATCTAGAATGCAGCTTTTGGGTAGCCCAACAACTTGAAATTTCTTAACAGGACAAAGAAAGCCCAGCCAACATGAATGAGTTTATTTCCCTTTATTGAGATAAGAAAAGCCACTAACCCTCGAGCCTGAGGATATTTTTTACCTGTTTCTTCTTCCATTAAAGTTAGGGGTTACTCTTACAAGTCCAGTGATTTTAGACACATGGAACCGATCAACTTTGAATCCTGGGAATCCTTTCCTTTAAGAGTGGTGTATTACCTGTCTTTATATTGAACTCTTAGGGACCTTCTGCCTTGCCAGTTATCTCTCCCTTGTCTCTGAAGACCTAGACCTTTCTTTTTCCTTCCTTCCTATTTTACTTCCTGTGAACTGTGTCTTGACTGTATCGTATTAGCTTCTTGTTTCTCAACGTTTTTATCCTCACTACGTGGAGATAAATGTATGTCACTGAAGTTCTTAAATAAGTGGAGTCATAAGAAAAACATGGACTAACTAATCTGAACTACGATA chm1:+:2063025038:-1 +TGTCTATAGATATTAAATAAGAACCTGCAGGGCTCCTCGACTTAAGTTTCCTACTGTTATCACTCTCATATTCTCAGTAGATAAGAGCCAAAATGTCACTGGGTGCCGAGTAAATATGGGAAGCTCAGATACATTGCTTTTATCAATGTTTGGCGGGCTTATTCGGTTTAAGCCTGGAACCAAATAATAACACATTTAAGGAGGACCTGACTGTCCTTAAATGAAATATTAATACTGAAGAGGAAAAAGTATCAGGCCATGCTTCTACCCGAGTGGGACAGAGGTAAGAAATCTAGAATGCAGCTTTTGGGTAGCCCAACAACTTGAAATTTCTTAACAGGACAAAGAAAGCCCAGCCAACATGAATGAGTTTATTTCCCTTTATTGAGATAAGAAAAGCCACTAACCCTCGAGCCTGAGGATATTTTTTACCTGTTTCTTCTTCCATTAAAGTTAGGGGTTACTCTTACAAGTCCAGTGATTTTAGACACATGGAACCGATCAACTTTGAATCCTGGGAATCCTTTCCTTTAAGAGTGGTGTATTACCTGTCTTTATATTGAACTCTTAGGGACCTTCTGCCTTGCCAGTTATCTCTCCCTTGTCTCTGAAGACCTAGACCTTTCTTTTTCCTTCCTTCCTATTTTACTTCCTGTGAACTGTGTCTTGACTGTATCGTATTAGCTTCTTGTTTCTCAACGTTTTTATCCTCACTACGTGGAGATAAATGTATGTCACTGAAGTTCTTAAATAAGTGGAGTCATAAGAAAAACATGGACTAACTAATCTGAACTACGATA chm1:+:654380223:-1 +TGTCTATAGATATTAAATAAGAACCTGCAGGGCTCCTCGACTTAAGTTTCCTACTGTTATCACTCTCATATTCTCAGTAGATAAGAGCCAAAATGTCACTGGGTGCCGAGTAAATATGGGAAGCTCAGATACATTGCTTTTATCAATGTTTGGCGGGCTTATTCGGTTTAAGCCTGGAACCAAATAATAACACATTTAAGGAGGACCTGACTGTCCTTAAATGAAATATTAATACTGAAGAGGAAAAAGTATCAGGCCATGCTTCTACCCGAGTGGGACAGAGGTAAGAAATCTAGAATGCAGCTTTTGGGTAGCCCAACAACTTGAAATTTCTTAACAGGACAAAGAAAGCCCAGCCAACATGAATGAGTTTATTTCCCTTTATTGAGATAAGAAAAGCCACTAACCCTCGAGCCTGAGGATATTTTTTACCTGTTTCTTCTTCCATTAAAGTTAGGGGTTACTCTTACAAGTCCAGTGATTTTAGACACATGGAACCGATCAACTTTGAATCCTGGGAATCCTTTCCTTTAAGAGTGGTGTATTACCTGTCTTTATATTGAACTCTTAGGGACCTTCTGCCTTGCCAGTTATCTCTCCCTTGTCTCTGAAGACCTAGACCTTTCTTTTTCCTTCCTTCCTATTTTACTTCCTGTGAACTGTGTCTTGACTGTATCGTATTAGCTTCTTGTTTCTCAACGTTTTTATCCTCACTACGTGGAGATAAATGTATGTCACTGAAGTTCTTAAATAAGTGGAGTCATAAGAAAAACATGGACTAACTAATCTGAACTACGATA chm1:+:2296171832:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:1474079814:-1 chm1:+:1520577101:-1 chm1:+:1665632775:-1 chm1:+:1744579499:-1 chm1:+:2010812129:-1 chm1:+:2245363774:-1 chm1:+:2606469667:-1 chm1:+:2609464740:-1 chm1:+:2627262046:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:89442641:-1 chm1:+:337083218:-1 chm1:+:485694524:-1 chm1:+:513678616:-1 chm1:+:605396356:-1 chm1:+:950301940:-1 chm1:+:1115890027:-1 chm1:+:1282884912:-1 chm1:+:1312320067:-1 chm1:+:1390794098:-1 chm1:+:1481780212:-1 chm1:+:2812951677:-1 chm1:+:2872178458:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:57609764:-1 chm1:+:103691935:-1 chm1:+:217016372:-1 chm1:+:266901314:-1 chm1:+:325954689:-1 chm1:+:604571778:-1 chm1:+:679561994:-1 chm1:+:751613878:-1 chm1:+:762007671:-1 chm1:+:1072083139:-1 chm1:+:1142625276:-1 chm1:+:1187924067:-1 chm1:+:1286165992:-1 chm1:+:1359253097:-1 chm1:+:1440253906:-1 chm1:+:1543191966:-1 chm1:+:2155204785:-1 chm1:+:2196750678:-1 chm1:+:2237637619:-1 chm1:+:2242795791:-1 chm1:+:2471669776:-1 chm1:+:2585363962:-1 chm1:+:3035076497:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:425496422:-1 chm1:+:683982816:-1 chm1:+:685714975:-1 chm1:+:826195207:-1 chm1:+:839030589:-1 chm1:+:2798519516:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:1398192717:-1 chm1:+:1956323565:-1 chm1:+:2136679140:-1 chm1:+:2391219166:-1 chm1:+:2983485270:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:115012338:-1 chm1:+:471640982:-1 chm1:+:670830157:-1 chm1:+:705449950:-1 chm1:+:940362568:-1 chm1:+:1325089867:-1 chm1:+:1461881121:-1 chm1:+:1625226098:-1 chm1:+:1684770452:-1 chm1:+:2032731656:-1 chm1:+:2930924042:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:102746010:-1 chm1:+:394710256:-1 chm1:+:938966796:-1 chm1:+:1710286597:-1 chm1:+:1897303476:-1 chm1:+:2253631071:-1 chm1:+:2376424659:-1 chm1:+:2903960247:-1 chm1:+:2918063162:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:606324612:-1 chm1:+:1352565400:-1 chm1:+:1449471781:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:77709533:-1 chm1:+:211842111:-1 chm1:+:1035018833:-1 chm1:+:1059473533:-1 chm1:+:1117593110:-1 chm1:+:1175490817:-1 chm1:+:1476404129:-1 chm1:+:1783544973:-1 chm1:+:1788232188:-1 chm1:+:1828283105:-1 chm1:+:2796732968:-1 chm1:+:2856237015:-1 chm1:+:3099140800:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:7429887:-1 chm1:+:52740633:-1 chm1:+:174899049:-1 chm1:+:195203304:-1 chm1:+:374335718:-1 chm1:+:380096417:-1 chm1:+:380484983:-1 chm1:+:405697893:-1 chm1:+:414700816:-1 chm1:+:527891063:-1 chm1:+:595374748:-1 chm1:+:739321930:-1 chm1:+:758961216:-1 chm1:+:781835440:-1 chm1:+:849723756:-1 chm1:+:871150454:-1 chm1:+:888345015:-1 chm1:+:1185085556:-1 chm1:+:1220648868:-1 chm1:+:1483894188:-1 chm1:+:1789946592:-1 chm1:+:1845052927:-1 chm1:+:2052824407:-1 chm1:+:2078300228:-1 chm1:+:2168556137:-1 chm1:+:2193228837:-1 chm1:+:2226916699:-1 chm1:+:2231125387:-1 chm1:+:2236846364:-1 chm1:+:2556340220:-1 chm1:+:2587663746:-1 chm1:+:2620352205:-1 chm1:+:2627975031:-1 chm1:+:2799551460:-1 chm1:+:2972097721:-1 chm1:+:3041202756:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:548949684:-1 chm1:+:593553828:-1 chm1:+:2436605634:-1 chm1:+:2931855478:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:235795844:-1 chm1:+:455960534:-1 chm1:+:611476203:-1 chm1:+:657828589:-1 chm1:+:1082171106:-1 chm1:+:2193355123:-1 chm1:+:2426745272:-1 chm1:+:2700090499:-1 chm1:+:2722683000:-1 chm1:+:2923219533:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:146951986:-1 chm1:+:199098228:-1 chm1:+:627792598:-1 chm1:+:654049229:-1 chm1:+:655181723:-1 chm1:+:750847771:-1 chm1:+:853067582:-1 chm1:+:1053122399:-1 chm1:+:1265599091:-1 chm1:+:1684475275:-1 chm1:+:1717879880:-1 chm1:+:1982545916:-1 chm1:+:2006439622:-1 chm1:+:2154588577:-1 chm1:+:2999103940:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:88824132:-1 chm1:+:90892664:-1 chm1:+:174312329:-1 chm1:+:227043786:-1 chm1:+:294900574:-1 chm1:+:449496757:-1 chm1:+:529374703:-1 chm1:+:551720134:-1 chm1:+:683065165:-1 chm1:+:811032923:-1 chm1:+:1265285501:-1 chm1:+:1341458168:-1 chm1:+:1461377931:-1 chm1:+:2248679259:-1 chm1:+:2289476950:-1 chm1:+:2335437432:-1 chm1:+:2351558582:-1 chm1:+:2376837437:-1 chm1:+:2431358327:-1 chm1:+:2439443742:-1 chm1:+:2550877533:-1 chm1:+:2577706176:-1 chm1:+:2920535847:-1 chm1:+:2947990862:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:1024000722:-1 chm1:+:1166069244:-1 chm1:+:1523972051:-1 chm1:+:2252912097:-1 chm1:+:2603173857:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:96101096:-1 chm1:+:2601319950:-1 chm1:+:2689702514:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:2440647:-1 chm1:+:26617154:-1 chm1:+:276316584:-1 chm1:+:370392587:-1 chm1:+:917108815:-1 chm1:+:990121737:-1 chm1:+:1015036556:-1 chm1:+:1061382500:-1 chm1:+:1072960171:-1 chm1:+:1087715009:-1 chm1:+:1096535868:-1 chm1:+:1446515903:-1 chm1:+:1516627402:-1 chm1:+:1677763998:-1 chm1:+:1686060098:-1 chm1:+:1860870661:-1 chm1:+:1962571795:-1 chm1:+:2046584067:-1 chm1:+:2238810862:-1 chm1:+:2495057946:-1 chm1:+:2565144540:-1 chm1:+:2576752012:-1 chm1:+:2672199141:-1 chm1:+:2677178406:-1 chm1:+:2854897159:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:675070754:-1 chm1:+:1457727900:-1 chm1:+:2361464427:-1 chm1:+:2954606252:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:221497299:-1 chm1:+:579772397:-1 chm1:+:623978587:-1 chm1:+:738331913:-1 chm1:+:1156390226:-1 chm1:+:1979879388:-1 chm1:+:2172251475:-1 chm1:+:2246267054:-1 chm1:+:2250548282:-1 chm1:+:2691091408:-1 chm1:+:2935560221:-1 chm1:+:3035861803:-1 +GCCAAGTCTTTCTTCATGTACTGTTTTTTTTTCAATATTTTATATATTTTGTTTTCTCAAGTATATTTTGTATTTAAAAAAAAAATCCTCATTGGTTTCTCTTGAAAATAAGGTCAAAATTTGAGTGGATTTAGTAGAAATTGACACTTTACCGTACTGTTGTTATCTTAAATAAAAACTAGTGGTACACTTCTAATGAAATAATTATAGATGGTTTATTAAGTATTATAACTAATATCTATTGGTTAAGCAGAAAAAAGTAAACTGTGGTAAGCAAAACACCCTCACCCATGTTAAGATGTGCCTTCACCCTCCCCAGGCCTCACTCTTCTCTCCTCATAACTTCCAAGCATCTCCAAGGTATGCTCCAAGACAAAGAACTAGTGCACATTCATTTGCTGCAAGTTTTGCTCTCTGAGCAACCTGGGCTAAGACAATAAAAACCCAACAGGGGAAATTGATAAAAGACTTAAAACGTACTTCAGTAGACACCTCAAATTACTAAGAAAACCAATAGCTACCAATAACTTAATAAACTAAAAAATATATACTAAGCCTCACTAATATATATTATCAGGAAAAATGCAACTAAAAACCGCCCTTAGGATACTGTTATAAAAGCTACAGATGACAAACATCAACAAGTGTGGGGGAGAAGGTGGGAATTCTCTCTGCCAAAACTGTAAATTGATACAACCATTTGAAAAATAGTATAGTATTTACTCAGAAATATTTAAAATGTCCCTATCCTATAATCCTACAACCCCTACTGTGAGGTTTATATGTACAAAAATACCACG chm1:+:65048488:-1 chm1:+:189661370:-1 chm1:+:279049028:-1 chm1:+:402028537:-1 chm1:+:416415161:-1 chm1:+:493197015:-1 chm1:+:672369100:-1 chm1:+:774681759:-1 chm1:+:848439502:-1 chm1:+:1517602965:-1 chm1:+:1790625502:-1 chm1:+:1823897503:-1 chm1:+:1831093889:-1 chm1:+:1886253398:-1 chm1:+:2170730514:-1 chm1:+:2290449911:-1 chm1:+:2359024321:-1 +CGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102200:35 +CGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102207:35 +CGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:3025149771:-1 +CGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102215:35 +CGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102211:35 chm1:+:1698149939:-1 +CGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102214:35 +CGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102216:35 +CGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102201:35 chm1:+:1914056083:-1 +CGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102204:35 +CGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:517102206:35 +CGTGGTATTTTTGTACATATAAACCTCACAGTAGGGGTTGTAGGATTATAGGATAGGGACATTTTAAATATTTCTGAGTAAATACTATACTATTTTTCAAATGGTTGTATCAATTTACAGTTTTGGCAGAGAGAATTCCCACCTTCTCCCCCACACTTGTTGATGTTTGTCATCTGTAGCTTTTATAACAGTATCCTAAGGGCGGTTTTTAGTTGCATTTTTCCTGATAATATATATTAGTGAGGCTTAGTATATATTTTTTAGTTTATTAAGTTATTGGTAGCTATTGGTTTTCTTAGTAATTTGAGGTGTCTACTGAAGTACGTTTTAAGTCTTTTATCAATTTCCCCTGTTGGGTTTTTATTGTCTTAGCCCAGGTTGCTCAGAGAGCAAAACTTGCAGCAAATGAATGTGCACTAGTTCTTTGTCTTGGAGCATACCTTGGAGATGCTTGGAAGTTATGAGGAGAGAAGAGTGAGGCCTGGGGAGGGTGAAGGCACATCTTAACATGGGTGAGGGTGTTTTGCTTACCACAGTTTACTTTTTTCTGCTTAACCAATAGATATTAGTTATAATACTTAATAAACCATCTATAATTATTTCATTAGAAGTGTACCACTAGTTTTTATTTAAGATAACAACAGTACGGTAAAGTGTCAATTTCTACTAAATCCACTCAAATTTTGACCTTATTTTCAAGAGAAACCAATGAGGATTTTTTTTTTAAATACAAAATATACTTGAGAAAACAAAATATATAAAATATTGAAAAAAAAACAGTACATGAAGAAAGACTTGGC chm1:+:638074156:-1 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:2347843306:-1 chm1:+:2695010721:-1 chm1:+:3033653829:39 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:3033653841:39 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:3033653840:39 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:3033653822:39 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:3033653827:39 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:1561148569:-1 chm1:+:3033653834:39 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:2527601967:-1 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:3033653839:39 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:1676182175:-1 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:3033653842:39 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:3033653846:39 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:3033653824:39 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:3033653826:39 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:159175314:-1 chm1:+:3033653828:39 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:3033653831:39 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:3033653835:39 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:546247992:-1 +AGTCCTGAGTGTTTCCTCTGGGCCTCTACAGTACCAAAGGGCTTCTGGCACCACCACCCCTTATTGAGCTGTTTTGTCATTGGTGTCTACAGGTGTCTCCCGTTTCCCCCCACAGAAGTCTCCTTCACCTTTGAACACCCACCTGCTTGATCGCCACAGGGGCCCAGACAGAGAAGGCCCTAACCACACCTGCCCCCAACCGGGAAGAGGCCCCTCCCTCCTCCCCTGGGCTCCCTGTGCTTGCCAGACCCTGACCCCACAGCCTGGGAGGGGCTGCAACCCAGACATGGAGCCCCCTAGGTAAGGTGGGGCAGATCTCCCTGGACCCCACCAGACACTGGGGCCCTGGATGAACGATGTCTTTTGGAATTCATGAGAGGAATCAGCTCTCCCACCCCAAGGGCCATGTCCGTTGGGGGATGGGACAAGGTGGACAGAATGTAGCCTAAGGCCTGGGCCTCCCCTCACCTCCTGCACCCCCAGATGGAAGTGGTGGAGATGATTGGAGTCAGATCCGTCCACGGGTGTGGGAGGACTCTATCAGGACTAGGGCCAGCCCCAGCTCCAGGGGGCCCCAGCCACAGAGCCCATGGGCATTGTCCATGATGCTGCTGAACCTGGCAGAGCAGCTCAGGGGAGGCAGACAAGGAACTGGCAGGCAAATACACTAGAGCTGGGGAACTGGTGCACTTGGAAGGATTTCTGCAGCTCATGCAGGTTGGAGGGGCCTGGGGACCTGGCAGCAAGGGGGACCCTCCACCTTCCCAACTCCCCAGGGTGTCCTCGGCTTTACACACCTG chm1:+:3033653845:39 +CAGGTGTGTAAAGCCGAGGACACCCTGGGGAGTTGGGAAGGTGGAGGGTCCCCCTTGCTGCCAGGTCCCCAGGCCCCTCCAACCTGCATGAGCTGCAGAAATCCTTCCAAGTGCACCAGTTCCCCAGCTCTAGTGTATTTGCCTGCCAGTTCCTTGTCTGCCTCCCCTGAGCTGCTCTGCCAGGTTCAGCAGCATCATGGACAATGCCCATGGGCTCTGTGGCTGGGGCCCCCTGGAGCTGGGGCTGGCCCTAGTCCTGATAGAGTCCTCCCACACCCGTGGACGGATCTGACTCCAATCATCTCCACCACTTCCATCTGGGGGTGCAGGAGGTGAGGGGAGGCCCAGGCCTTAGGCTACATTCTGTCCACCTTGTCCCATCCCCCAACGGACATGGCCCTTGGGGTGGGAGAGCTGATTCCTCTCATGAATTCCAAAAGACATCGTTCATCCAGGGCCCCAGTGTCTGGTGGGGTCCAGGGAGATCTGCCCCACCTTACCTAGGGGGCTCCATGTCTGGGTTGCAGCCCCTCCCAGGCTGTGGGGTCAGGGTCTGGCAAGCACAGGGAGCCCAGGGGAGGAGGGAGGGGCCTCTTCCCGGTTGGGGGCAGGTGTGGTTAGGGCCTTCTCTGTCTGGGCCCCTGTGGCGATCAAGCAGGTGGGTGTTCAAAGGTGAAGGAGACTTCTGTGGGGGGAAACGGGAGACACCTGTAGACACCAATGACAAAACAGCTCAATAAGGGGTGGTGGTGCCAGAAGCCCTTTGGTACTGTAGAGGCCCAGAGGAAACACTCAGGACT chm1:+:2827182986:-1 +CAGGTGTGTAAAGCCGAGGACACCCTGGGGAGTTGGGAAGGTGGAGGGTCCCCCTTGCTGCCAGGTCCCCAGGCCCCTCCAACCTGCATGAGCTGCAGAAATCCTTCCAAGTGCACCAGTTCCCCAGCTCTAGTGTATTTGCCTGCCAGTTCCTTGTCTGCCTCCCCTGAGCTGCTCTGCCAGGTTCAGCAGCATCATGGACAATGCCCATGGGCTCTGTGGCTGGGGCCCCCTGGAGCTGGGGCTGGCCCTAGTCCTGATAGAGTCCTCCCACACCCGTGGACGGATCTGACTCCAATCATCTCCACCACTTCCATCTGGGGGTGCAGGAGGTGAGGGGAGGCCCAGGCCTTAGGCTACATTCTGTCCACCTTGTCCCATCCCCCAACGGACATGGCCCTTGGGGTGGGAGAGCTGATTCCTCTCATGAATTCCAAAAGACATCGTTCATCCAGGGCCCCAGTGTCTGGTGGGGTCCAGGGAGATCTGCCCCACCTTACCTAGGGGGCTCCATGTCTGGGTTGCAGCCCCTCCCAGGCTGTGGGGTCAGGGTCTGGCAAGCACAGGGAGCCCAGGGGAGGAGGGAGGGGCCTCTTCCCGGTTGGGGGCAGGTGTGGTTAGGGCCTTCTCTGTCTGGGCCCCTGTGGCGATCAAGCAGGTGGGTGTTCAAAGGTGAAGGAGACTTCTGTGGGGGGAAACGGGAGACACCTGTAGACACCAATGACAAAACAGCTCAATAAGGGGTGGTGGTGCCAGAAGCCCTTTGGTACTGTAGAGGCCCAGAGGAAACACTCAGGACT chm1:+:1676651939:-1 chm1:+:3034241334:-1 +CAGGTGTGTAAAGCCGAGGACACCCTGGGGAGTTGGGAAGGTGGAGGGTCCCCCTTGCTGCCAGGTCCCCAGGCCCCTCCAACCTGCATGAGCTGCAGAAATCCTTCCAAGTGCACCAGTTCCCCAGCTCTAGTGTATTTGCCTGCCAGTTCCTTGTCTGCCTCCCCTGAGCTGCTCTGCCAGGTTCAGCAGCATCATGGACAATGCCCATGGGCTCTGTGGCTGGGGCCCCCTGGAGCTGGGGCTGGCCCTAGTCCTGATAGAGTCCTCCCACACCCGTGGACGGATCTGACTCCAATCATCTCCACCACTTCCATCTGGGGGTGCAGGAGGTGAGGGGAGGCCCAGGCCTTAGGCTACATTCTGTCCACCTTGTCCCATCCCCCAACGGACATGGCCCTTGGGGTGGGAGAGCTGATTCCTCTCATGAATTCCAAAAGACATCGTTCATCCAGGGCCCCAGTGTCTGGTGGGGTCCAGGGAGATCTGCCCCACCTTACCTAGGGGGCTCCATGTCTGGGTTGCAGCCCCTCCCAGGCTGTGGGGTCAGGGTCTGGCAAGCACAGGGAGCCCAGGGGAGGAGGGAGGGGCCTCTTCCCGGTTGGGGGCAGGTGTGGTTAGGGCCTTCTCTGTCTGGGCCCCTGTGGCGATCAAGCAGGTGGGTGTTCAAAGGTGAAGGAGACTTCTGTGGGGGGAAACGGGAGACACCTGTAGACACCAATGACAAAACAGCTCAATAAGGGGTGGTGGTGCCAGAAGCCCTTTGGTACTGTAGAGGCCCAGAGGAAACACTCAGGACT chm1:+:1094204533:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAG chm1:+:2939181703:-1 chm1:+:2939253257:-1 chm1:+:2939257063:-1 chm1:+:2939269143:-1 chm1:+:2939272981:-1 chm1:+:2939274018:-1 chm1:+:2939287809:-1 chm1:+:2939290061:-1 chm1:+:2939304678:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAG chm1:+:506342547:-1 chm1:+:573445766:-1 chm1:+:573453955:-1 chm1:+:1295521242:-1 chm1:+:1436528158:-1 chm1:+:1722874792:-1 chm1:+:1866484697:-1 chm1:+:1867271942:-1 chm1:+:1870676526:-1 chm1:+:1985553081:-1 chm1:+:2327303628:-1 chm1:+:2444820393:-1 chm1:+:2444829561:-1 chm1:+:2444985427:-1 chm1:+:2521956860:-1 chm1:+:2521959765:-1 chm1:+:2683883345:-1 chm1:+:2683900664:-1 chm1:+:2687615717:-1 chm1:+:2943019955:-1 chm1:+:2943069839:-1 chm1:+:3046366614:-1 chm1:+:3056087338:-1 chm1:+:3056090032:-1 chm1:+:3056092629:-1 chm1:+:3056111499:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAG chm1:+:228128506:-1 chm1:+:481477565:-1 chm1:+:981371951:-1 chm1:+:2877219905:-1 chm1:+:2939199374:-1 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chm1:+:2939268753:-1 chm1:+:2939284877:-1 chm1:+:2939301020:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAG chm1:+:898701808:-1 chm1:+:1228299448:-1 chm1:+:1257822632:-1 chm1:+:2303495428:-1 chm1:+:2385757498:-1 chm1:+:2570301180:-1 chm1:+:2798451780:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAG chm1:+:152700380:-1 chm1:+:1445428910:-1 chm1:+:2939138387:-1 chm1:+:2939247122:-1 chm1:+:2939295987:-1 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chm1:+:826142253:-1 chm1:+:866516453:-1 chm1:+:890016133:-1 chm1:+:901313280:-1 chm1:+:910516094:-1 chm1:+:927001111:-1 chm1:+:993015098:-1 chm1:+:999838933:-1 chm1:+:1193407845:-1 chm1:+:1254195824:-1 chm1:+:1261681909:-1 chm1:+:1287959048:-1 chm1:+:1462925244:-1 chm1:+:1535456383:-1 chm1:+:1552790178:-1 chm1:+:1705495229:-1 chm1:+:1717991378:-1 chm1:+:1808088747:-1 chm1:+:1913217265:-1 chm1:+:2157969720:-1 chm1:+:2658014303:-1 chm1:+:2760022668:-1 chm1:+:2802398612:-1 chm1:+:2818094740:-1 chm1:+:2916647481:-1 chm1:+:2965516998:-1 chm1:+:2970799275:-1 chm1:+:2970938935:-1 chm1:+:3040260695:-1 chm1:+:3040403482:-1 chm1:+:3049821621:-1 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chm1:+:1940933236:-1 chm1:+:2032370065:-1 chm1:+:2052026218:-1 chm1:+:2335045835:-1 chm1:+:2806398903:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAG chm1:+:101104549:-1 chm1:+:205865830:-1 chm1:+:216229862:-1 chm1:+:289946574:-1 chm1:+:323862587:-1 chm1:+:346914515:-1 chm1:+:403043231:-1 chm1:+:430497210:-1 chm1:+:440036184:-1 chm1:+:488857005:-1 chm1:+:535917381:-1 chm1:+:575048886:-1 chm1:+:659471131:-1 chm1:+:696574917:-1 chm1:+:702547222:-1 chm1:+:734771181:-1 chm1:+:772163305:-1 chm1:+:795584492:-1 chm1:+:826946372:-1 chm1:+:829422890:-1 chm1:+:832493368:-1 chm1:+:833681502:-1 chm1:+:837765430:-1 chm1:+:846516814:-1 chm1:+:881695981:-1 chm1:+:903729251:-1 chm1:+:923347242:-1 chm1:+:947729339:-1 chm1:+:961084121:-1 chm1:+:965958906:-1 chm1:+:1000533289:-1 chm1:+:1000600614:-1 chm1:+:1027127714:-1 chm1:+:1053654369:-1 chm1:+:1060121278:-1 chm1:+:1070325727:-1 chm1:+:1071469530:-1 chm1:+:1085261409:-1 chm1:+:1140552524:-1 chm1:+:1188494518:-1 chm1:+:1201097073:-1 chm1:+:1213624121:-1 chm1:+:1236603231:-1 chm1:+:1256145110:-1 chm1:+:1301676491:-1 chm1:+:1303131119:-1 chm1:+:1343784127:-1 chm1:+:1362860900:-1 chm1:+:1424065910:-1 chm1:+:1435639763:-1 chm1:+:1451533095:-1 chm1:+:1455247424:-1 chm1:+:1506088001:-1 chm1:+:1524919402:-1 chm1:+:1620787184:-1 chm1:+:1659451029:-1 chm1:+:1660755908:-1 chm1:+:1669169094:-1 chm1:+:1832044556:-1 chm1:+:1847251813:-1 chm1:+:1854923301:-1 chm1:+:1864380626:-1 chm1:+:1880137735:-1 chm1:+:1911407863:-1 chm1:+:1912718543:-1 chm1:+:1926643857:-1 chm1:+:1948242470:-1 chm1:+:1955020178:-1 chm1:+:1955153324:-1 chm1:+:1977139463:-1 chm1:+:2001062751:-1 chm1:+:2019629534:-1 chm1:+:2073661002:-1 chm1:+:2113095993:-1 chm1:+:2144220010:-1 chm1:+:2158701191:-1 chm1:+:2174299032:-1 chm1:+:2242464984:-1 chm1:+:2263246607:-1 chm1:+:2281533075:-1 chm1:+:2331194765:-1 chm1:+:2333538997:-1 chm1:+:2365313696:-1 chm1:+:2367603138:-1 chm1:+:2417662497:-1 chm1:+:2429492935:-1 chm1:+:2436254273:-1 chm1:+:2440979389:-1 chm1:+:2456370672:-1 chm1:+:2534622567:-1 chm1:+:2568204842:-1 chm1:+:2615883957:-1 chm1:+:2634432637:-1 chm1:+:2644939509:-1 chm1:+:2673590106:-1 chm1:+:2822799164:-1 chm1:+:2860673603:-1 chm1:+:2871687370:-1 chm1:+:2887232453:-1 chm1:+:2915375530:-1 chm1:+:2923038204:-1 chm1:+:2935679170:-1 chm1:+:2961669560:-1 chm1:+:2965954000:-1 chm1:+:2989372369:-1 +GGAGAGTACTCCAGCCGACTATAAGCAGCGTAATGTTAGAGACAGCTGGACGATCTCAGGCATTTAATGAAAGAGATTCACAGCTGAACTCAGGCATTCTACTGATAAGAGACAACGTGGGTGACTCTAGGCATTCTAATGGGAGAGACTCTTGGCTGGCCTTTTGGTATTTTATGGTAGAGACTTCTTTGCCCAACACCAGCAATGTAATGATGGAGACACCTTAGCAAACCCGATGCATTCTAGTGGAAGAGTCTCCTGGCTGAACCCTAGGCAGTCTAAGGTTGGTATACCTGGTTGACTTTAGGCATCCTAGTGGGAGAGACTCTCAGGCCAACCCCTGGAAGTCTAACGATGAGAAAAAGTGGGGGTTTAGCAGGGATTCGTAAAGGAAGAAACTCCTGTCTTGACCCAGGAAGTGTAATGATAGAGATACCTTGGGCAACCCTATGCATTTCTAGTGGGAGAGACTCCTGGCTGACCCCAAAGCAGTCTAATGATAAAGACAACAGGCAACCCCAGATATTCTAATAGGAGACTTCTACCAGCCCACACAAGGTTTAACTTCTGTGATATGAATCCACACATCATATAGCAGTTTCACAAATAACATCCTTTCTATTTTTATCTGGGAATAATTCAATTTTTCACCTTTAGGTCTCAAAGAGCTCCCACATATCCCTTTCCTGATTCTACTAAAAGAGTGTTTCCAACCTGCTGAATCATAGAAAAAGTTAAACTCTGTGAGTAGAAGTCTGCACCATCACAAAGTAGTTTCGAACTAAAATTCTTCTTTCTAG chm1:+:1440171094:-1 chm1:+:1865979979:-1 chm1:+:1988847126:-1 chm1:+:2521950875:-1 chm1:+:2748087000:-1 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:228728598:-1 chm1:+:228737801:-1 chm1:+:228740354:-1 chm1:+:2444735371:-1 chm1:+:2444739473:-1 chm1:+:2687568838:35 chm1:+:2687701369:-1 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687568840:35 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687568841:35 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687568830:35 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687568827:35 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687568832:35 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687568843:35 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687568828:35 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:228718052:-1 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687568829:35 chm1:+:2687687702:-1 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687568831:35 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687568833:35 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:2687568836:35 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:23198618:-1 +CTAGAAAGAAGAATTTTAGTTCGAAACTACTTTGTGATGGTGCAGACTTCTACTCACAGAGTTTAACTTTTTCTATGATTCAGCAGGTTGGAAACACTCTTTTAGTAGAATCAGGAAAGGGATATGTGGGAGCTCTTTGAGACCTAAAGGTGAAAAATTGAATTATTCCCAGATAAAAATAGAAAGGATGTTATTTGTGAAACTGCTATATGATGTGTGGATTCATATCACAGAAGTTAAACCTTGTGTGGGCTGGTAGAAGTCTCCTATTAGAATATCTGGGGTTGCCTGTTGTCTTTATCATTAGACTGCTTTGGGGTCAGCCAGGAGTCTCTCCCACTAGAAATGCATAGGGTTGCCCAAGGTATCTCTATCATTACACTTCCTGGGTCAAGACAGGAGTTTCTTCCTTTACGAATCCCTGCTAAACCCCCACTTTTTCTCATCGTTAGACTTCCAGGGGTTGGCCTGAGAGTCTCTCCCACTAGGATGCCTAAAGTCAACCAGGTATACCAACCTTAGACTGCCTAGGGTTCAGCCAGGAGACTCTTCCACTAGAATGCATCGGGTTTGCTAAGGTGTCTCCATCATTACATTGCTGGTGTTGGGCAAAGAAGTCTCTACCATAAAATACCAAAAGGCCAGCCAAGAGTCTCTCCCATTAGAATGCCTAGAGTCACCCACGTTGTCTCTTATCAGTAGAATGCCTGAGTTCAGCTGTGAATCTCTTTCATTAAATGCCTGAGATCGTCCAGCTGTCTCTAACATTACGCTGCTTATAGTCGGCTGGAGTACTCTCC chm1:+:11895156:-1 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTACAATAAATTGATGGGTAAATTAAATTATTAACAAATTATGAATAAACTTTTTAGAATGGATATGTTCTATAGCTTGATTGTGCTGATAGTAAAGAGATACCGGTATTTATCAAACTCACTTAATTGGACACTTAAAATGAATGTATCTTATCAGATGGTAAATTACACCTTAAGTAAAGTTGATTTTAAAAAACTATTAT chm1:+:766905444:37 chm1:+:1057360565:-1 chm1:+:1493650260:-1 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTACAATAAATTGATGGGTAAATTAAATTATTAACAAATTATGAATAAACTTTTTAGAATGGATATGTTCTATAGCTTGATTGTGCTGATAGTAAAGAGATACCGGTATTTATCAAACTCACTTAATTGGACACTTAAAATGAATGTATCTTATCAGATGGTAAATTACACCTTAAGTAAAGTTGATTTTAAAAAACTATTAT chm1:+:766905449:37 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTACAATAAATTGATGGGTAAATTAAATTATTAACAAATTATGAATAAACTTTTTAGAATGGATATGTTCTATAGCTTGATTGTGCTGATAGTAAAGAGATACCGGTATTTATCAAACTCACTTAATTGGACACTTAAAATGAATGTATCTTATCAGATGGTAAATTACACCTTAAGTAAAGTTGATTTTAAAAAACTATTAT chm1:+:766905447:37 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTACAATAAATTGATGGGTAAATTAAATTATTAACAAATTATGAATAAACTTTTTAGAATGGATATGTTCTATAGCTTGATTGTGCTGATAGTAAAGAGATACCGGTATTTATCAAACTCACTTAATTGGACACTTAAAATGAATGTATCTTATCAGATGGTAAATTACACCTTAAGTAAAGTTGATTTTAAAAAACTATTAT chm1:+:766905450:37 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTACAATAAATTGATGGGTAAATTAAATTATTAACAAATTATGAATAAACTTTTTAGAATGGATATGTTCTATAGCTTGATTGTGCTGATAGTAAAGAGATACCGGTATTTATCAAACTCACTTAATTGGACACTTAAAATGAATGTATCTTATCAGATGGTAAATTACACCTTAAGTAAAGTTGATTTTAAAAAACTATTAT chm1:+:766905443:37 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTACAATAAATTGATGGGTAAATTAAATTATTAACAAATTATGAATAAACTTTTTAGAATGGATATGTTCTATAGCTTGATTGTGCTGATAGTAAAGAGATACCGGTATTTATCAAACTCACTTAATTGGACACTTAAAATGAATGTATCTTATCAGATGGTAAATTACACCTTAAGTAAAGTTGATTTTAAAAAACTATTAT chm1:+:766905448:37 +TTGATCTGGGGTAGTGGTTTACAAAGGCATTGTCATTTGTTAAATCATAAAATCATTTGCTTATAATTTCTGTATCTTTTGGTAGGTTGGTTATCCTTCCTTAAAAACAAACTATATTTTAAAAAAACAAAAAAACAAAAAAAAGCAAGAAAGTGATTAAAATATTCAAGACAGTGATTACCTCCAAGCAGGACAAGAAGAAAGGACTGAACACGGAACACTTGGCTTTGACAAGTATTGTAACATTCCTTCCTAAACTCGTGGCTTATTCACTGTTACTGTACTTTAGACACACTTTACATACATGTCTTTAATATACATCTAAAATAACTCGAGATTTTTAAGAAAGAAAATATTCCTTATACACCGACATGTCAAACAGTAGCTTGTCTGTGGTTAGGGCTCTGGTTATTTTATTTTTATTATTCTACTTTCTGTTTTTTCCAATTTTTATAAAATCACCTGTATTTCTTAGATAATTTTTAAATACTAATTTTTACAAAGAAAAATTTATCCCAATTCTCTACCTCAAGTTGCCCATAAAACACTTTATATAAAACATATTTTATAATCCAAAGGTAAAATTCTAAATAGTTATTACAATAAATTGATGGGTAAATTAAATTATTAACAAATTATGAATAAACTTTTTAGAATGGATATGTTCTATAGCTTGATTGTGCTGATAGTAAAGAGATACCGGTATTTATCAAACTCACTTAATTGGACACTTAAAATGAATGTATCTTATCAGATGGTAAATTACACCTTAAGTAAAGTTGATTTTAAAAAACTATTAT chm1:+:2713228354:-1 +ATAATAGTTTTTTAAAATCAACTTTACTTAAGGTGTAATTTACCATCTGATAAGATACATTCATTTTAAGTGTCCAATTAAGTGAGTTTGATAAATACCGGTATCTCTTTACTATCAGCACAATCAAGCTATAGAACATATCCATTCTAAAAAGTTTATTCATAATTTGTTAATAATTTAATTTACCCATCAATTTATTGTAATAACTATTTAGAATTTTACCTTTGGATTATAAAATATGTTTTATATAAAGTGTTTTATGGGCAACTTGAGGTAGAGAATTGGGATAAATTTTTCTTTGTAAAAATTAGTATTTAAAAATTATCTAAGAAATACAGGTGATTTTATAAAAATTGGAAAAAACAGAAAGTAGAATAATAAAAATAAAATAACCAGAGCCCTAACCACAGACAAGCTACTGTTTGACATGTCGGTGTATAAGGAATATTTTCTTTCTTAAAAATCTCGAGTTATTTTAGATGTATATTAAAGACATGTATGTAAAGTGTGTCTAAAGTACAGTAACAGTGAATAAGCCACGAGTTTAGGAAGGAATGTTACAATACTTGTCAAAGCCAAGTGTTCCGTGTTCAGTCCTTTCTTCTTGTCCTGCTTGGAGGTAATCACTGTCTTGAATATTTTAATCACTTTCTTGCTTTTTTTTGTTTTTTTGTTTTTTTAAAATATAGTTTGTTTTTAAGGAAGGATAACCAACCTACCAAAAGATACAGAAATTATAAGCAAATGATTTTATGATTTAACAAATGACAATGCCTTTGTAAACCACTACCCCAGATCAA chm1:+:561958862:-1 chm1:+:1864499811:-1 +ATAATAGTTTTTTAAAATCAACTTTACTTAAGGTGTAATTTACCATCTGATAAGATACATTCATTTTAAGTGTCCAATTAAGTGAGTTTGATAAATACCGGTATCTCTTTACTATCAGCACAATCAAGCTATAGAACATATCCATTCTAAAAAGTTTATTCATAATTTGTTAATAATTTAATTTACCCATCAATTTATTGTAATAACTATTTAGAATTTTACCTTTGGATTATAAAATATGTTTTATATAAAGTGTTTTATGGGCAACTTGAGGTAGAGAATTGGGATAAATTTTTCTTTGTAAAAATTAGTATTTAAAAATTATCTAAGAAATACAGGTGATTTTATAAAAATTGGAAAAAACAGAAAGTAGAATAATAAAAATAAAATAACCAGAGCCCTAACCACAGACAAGCTACTGTTTGACATGTCGGTGTATAAGGAATATTTTCTTTCTTAAAAATCTCGAGTTATTTTAGATGTATATTAAAGACATGTATGTAAAGTGTGTCTAAAGTACAGTAACAGTGAATAAGCCACGAGTTTAGGAAGGAATGTTACAATACTTGTCAAAGCCAAGTGTTCCGTGTTCAGTCCTTTCTTCTTGTCCTGCTTGGAGGTAATCACTGTCTTGAATATTTTAATCACTTTCTTGCTTTTTTTTGTTTTTTTGTTTTTTTAAAATATAGTTTGTTTTTAAGGAAGGATAACCAACCTACCAAAAGATACAGAAATTATAAGCAAATGATTTTATGATTTAACAAATGACAATGCCTTTGTAAACCACTACCCCAGATCAA chm1:+:2124270121:-1 +ATAATAGTTTTTTAAAATCAACTTTACTTAAGGTGTAATTTACCATCTGATAAGATACATTCATTTTAAGTGTCCAATTAAGTGAGTTTGATAAATACCGGTATCTCTTTACTATCAGCACAATCAAGCTATAGAACATATCCATTCTAAAAAGTTTATTCATAATTTGTTAATAATTTAATTTACCCATCAATTTATTGTAATAACTATTTAGAATTTTACCTTTGGATTATAAAATATGTTTTATATAAAGTGTTTTATGGGCAACTTGAGGTAGAGAATTGGGATAAATTTTTCTTTGTAAAAATTAGTATTTAAAAATTATCTAAGAAATACAGGTGATTTTATAAAAATTGGAAAAAACAGAAAGTAGAATAATAAAAATAAAATAACCAGAGCCCTAACCACAGACAAGCTACTGTTTGACATGTCGGTGTATAAGGAATATTTTCTTTCTTAAAAATCTCGAGTTATTTTAGATGTATATTAAAGACATGTATGTAAAGTGTGTCTAAAGTACAGTAACAGTGAATAAGCCACGAGTTTAGGAAGGAATGTTACAATACTTGTCAAAGCCAAGTGTTCCGTGTTCAGTCCTTTCTTCTTGTCCTGCTTGGAGGTAATCACTGTCTTGAATATTTTAATCACTTTCTTGCTTTTTTTTGTTTTTTTGTTTTTTTAAAATATAGTTTGTTTTTAAGGAAGGATAACCAACCTACCAAAAGATACAGAAATTATAAGCAAATGATTTTATGATTTAACAAATGACAATGCCTTTGTAAACCACTACCCCAGATCAA chm1:+:1805463283:-1 +ATAATAGTTTTTTAAAATCAACTTTACTTAAGGTGTAATTTACCATCTGATAAGATACATTCATTTTAAGTGTCCAATTAAGTGAGTTTGATAAATACCGGTATCTCTTTACTATCAGCACAATCAAGCTATAGAACATATCCATTCTAAAAAGTTTATTCATAATTTGTTAATAATTTAATTTACCCATCAATTTATTGTAATAACTATTTAGAATTTTACCTTTGGATTATAAAATATGTTTTATATAAAGTGTTTTATGGGCAACTTGAGGTAGAGAATTGGGATAAATTTTTCTTTGTAAAAATTAGTATTTAAAAATTATCTAAGAAATACAGGTGATTTTATAAAAATTGGAAAAAACAGAAAGTAGAATAATAAAAATAAAATAACCAGAGCCCTAACCACAGACAAGCTACTGTTTGACATGTCGGTGTATAAGGAATATTTTCTTTCTTAAAAATCTCGAGTTATTTTAGATGTATATTAAAGACATGTATGTAAAGTGTGTCTAAAGTACAGTAACAGTGAATAAGCCACGAGTTTAGGAAGGAATGTTACAATACTTGTCAAAGCCAAGTGTTCCGTGTTCAGTCCTTTCTTCTTGTCCTGCTTGGAGGTAATCACTGTCTTGAATATTTTAATCACTTTCTTGCTTTTTTTTGTTTTTTTGTTTTTTTAAAATATAGTTTGTTTTTAAGGAAGGATAACCAACCTACCAAAAGATACAGAAATTATAAGCAAATGATTTTATGATTTAACAAATGACAATGCCTTTGTAAACCACTACCCCAGATCAA chm1:+:680734653:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:2365479450:-1 chm1:+:2916781785:-1 chm1:+:2917799338:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:63851717:-1 chm1:+:67500635:-1 chm1:+:70131751:-1 chm1:+:84055554:-1 chm1:+:97134663:-1 chm1:+:225222354:-1 chm1:+:398231172:-1 chm1:+:405384193:-1 chm1:+:515778671:-1 chm1:+:551612136:-1 chm1:+:724702554:-1 chm1:+:772069783:-1 chm1:+:779629398:-1 chm1:+:779957558:-1 chm1:+:809589676:-1 chm1:+:1001522770:-1 chm1:+:1100824276:-1 chm1:+:1129287985:-1 chm1:+:1149758343:-1 chm1:+:1210267485:-1 chm1:+:1243605674:-1 chm1:+:1267018633:-1 chm1:+:1329912864:-1 chm1:+:1480056317:-1 chm1:+:1493172445:-1 chm1:+:1558423756:-1 chm1:+:1706320169:-1 chm1:+:1706701204:-1 chm1:+:1839845955:-1 chm1:+:1916057673:-1 chm1:+:1924775616:-1 chm1:+:1941590856:-1 chm1:+:2075063358:-1 chm1:+:2129508292:-1 chm1:+:2240351242:-1 chm1:+:2253868762:-1 chm1:+:2469946733:-1 chm1:+:2611550700:-1 chm1:+:2720049765:-1 chm1:+:2737324720:-1 chm1:+:2915752903:-1 chm1:+:2938201082:-1 chm1:+:2943153067:-1 chm1:+:2969419542:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:105610315:-1 chm1:+:295690671:-1 chm1:+:837023337:-1 chm1:+:1833252768:-1 chm1:+:2430601066:-1 chm1:+:2637687434:-1 chm1:+:2959521917:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:653628605:-1 chm1:+:2284918797:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:45539647:-1 chm1:+:52635411:-1 chm1:+:75530086:-1 chm1:+:89784540:-1 chm1:+:151644708:-1 chm1:+:166410030:-1 chm1:+:244694869:-1 chm1:+:253686265:-1 chm1:+:266424862:-1 chm1:+:283927327:-1 chm1:+:298314672:-1 chm1:+:354579807:-1 chm1:+:419766876:-1 chm1:+:429201712:-1 chm1:+:432126223:-1 chm1:+:433218405:-1 chm1:+:438730488:-1 chm1:+:482208446:-1 chm1:+:507185442:-1 chm1:+:509247536:-1 chm1:+:512111822:-1 chm1:+:515144423:-1 chm1:+:520439502:-1 chm1:+:521363269:-1 chm1:+:576834760:-1 chm1:+:589344980:-1 chm1:+:589362163:-1 chm1:+:600869655:-1 chm1:+:628995552:-1 chm1:+:629526227:-1 chm1:+:639172600:-1 chm1:+:657931414:-1 chm1:+:687402368:-1 chm1:+:718520232:-1 chm1:+:733736964:-1 chm1:+:770742120:-1 chm1:+:792279152:-1 chm1:+:807213688:-1 chm1:+:813961063:-1 chm1:+:894035596:-1 chm1:+:911771880:-1 chm1:+:919271039:-1 chm1:+:920523689:-1 chm1:+:938064746:-1 chm1:+:949982027:-1 chm1:+:961607430:-1 chm1:+:978310625:-1 chm1:+:991265473:-1 chm1:+:991812136:-1 chm1:+:1036526639:-1 chm1:+:1102520133:-1 chm1:+:1146991664:-1 chm1:+:1148427082:-1 chm1:+:1155735771:-1 chm1:+:1157905876:-1 chm1:+:1162913499:-1 chm1:+:1180292353:-1 chm1:+:1189077097:-1 chm1:+:1200994563:-1 chm1:+:1203287290:-1 chm1:+:1203413416:-1 chm1:+:1209231675:-1 chm1:+:1215054099:-1 chm1:+:1222514335:-1 chm1:+:1250605718:-1 chm1:+:1266905790:-1 chm1:+:1270427230:-1 chm1:+:1282251690:-1 chm1:+:1285217655:-1 chm1:+:1325024253:-1 chm1:+:1345992053:-1 chm1:+:1356437251:-1 chm1:+:1394757357:-1 chm1:+:1444308305:-1 chm1:+:1450756321:-1 chm1:+:1477297400:-1 chm1:+:1477799597:-1 chm1:+:1518821601:-1 chm1:+:1623060524:-1 chm1:+:1626302908:-1 chm1:+:1713183991:-1 chm1:+:1755313096:-1 chm1:+:1777052782:-1 chm1:+:1834925156:-1 chm1:+:1836163011:-1 chm1:+:1848669369:-1 chm1:+:1859632604:-1 chm1:+:1879065441:-1 chm1:+:1900560421:-1 chm1:+:1903325424:-1 chm1:+:1917092692:-1 chm1:+:1930200120:-1 chm1:+:1941572386:-1 chm1:+:2008252694:-1 chm1:+:2020684617:-1 chm1:+:2045181874:-1 chm1:+:2077029198:-1 chm1:+:2126549477:-1 chm1:+:2156623258:-1 chm1:+:2228285270:-1 chm1:+:2246091156:-1 chm1:+:2254472749:-1 chm1:+:2256567183:-1 chm1:+:2257838450:-1 chm1:+:2334028029:-1 chm1:+:2357126178:-1 chm1:+:2383371431:-1 chm1:+:2391497740:-1 chm1:+:2506962260:-1 chm1:+:2611095611:-1 chm1:+:2611598001:-1 chm1:+:2614368023:-1 chm1:+:2639257435:-1 chm1:+:2651628599:-1 chm1:+:2655371382:-1 chm1:+:2671957819:-1 chm1:+:2671997623:-1 chm1:+:2772594184:-1 chm1:+:2858700937:-1 chm1:+:2901641618:-1 chm1:+:2914736209:-1 chm1:+:2914886480:-1 chm1:+:2926886623:-1 chm1:+:2930511734:-1 chm1:+:2935801509:-1 chm1:+:2935894848:-1 chm1:+:2937267445:-1 chm1:+:2947517588:-1 chm1:+:2954628090:-1 chm1:+:2955246290:-1 chm1:+:2956449677:-1 chm1:+:2960867908:-1 chm1:+:2973233878:-1 chm1:+:2973374010:-1 chm1:+:2973677832:-1 chm1:+:2978390451:-1 chm1:+:2980450562:-1 chm1:+:2982059149:155 chm1:+:2997522046:-1 chm1:+:3001416197:-1 chm1:+:3006801138:-1 chm1:+:3012443750:-1 chm1:+:3016676777:-1 chm1:+:3018237760:-1 chm1:+:3042233295:-1 chm1:+:3042371654:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:163710365:-1 chm1:+:313474710:-1 chm1:+:507185749:-1 chm1:+:1194056396:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:169182059:-1 chm1:+:428943855:-1 chm1:+:819998910:-1 chm1:+:1148152308:-1 chm1:+:1186779717:-1 chm1:+:1738944656:-1 chm1:+:1965887037:-1 chm1:+:2035632049:-1 chm1:+:2284471734:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:114168826:-1 chm1:+:281297451:-1 chm1:+:404630166:-1 chm1:+:420293549:-1 chm1:+:536879493:-1 chm1:+:938064750:-1 chm1:+:958577831:-1 chm1:+:985424484:-1 chm1:+:1137774688:-1 chm1:+:1378634171:-1 chm1:+:1453151071:-1 chm1:+:1454569748:-1 chm1:+:1738467464:-1 chm1:+:1907786000:-1 chm1:+:1913458775:-1 chm1:+:1994861866:-1 chm1:+:2482301872:-1 chm1:+:2972355701:-1 chm1:+:3005695435:-1 chm1:+:3041463893:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:84586455:-1 chm1:+:520439506:-1 chm1:+:891653606:-1 chm1:+:2726020988:-1 chm1:+:2956449683:-1 chm1:+:2966572733:-1 chm1:+:2982059154:155 chm1:+:3023169006:-1 chm1:+:3055655541:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:74081010:-1 chm1:+:184275127:-1 chm1:+:421755605:-1 chm1:+:510347523:-1 chm1:+:588009232:-1 chm1:+:602621824:-1 chm1:+:631179476:-1 chm1:+:667727474:-1 chm1:+:770872505:-1 chm1:+:991812134:-1 chm1:+:1036526637:-1 chm1:+:1039632199:-1 chm1:+:1118052411:-1 chm1:+:1216886894:-1 chm1:+:1222514339:-1 chm1:+:1285217665:-1 chm1:+:1319281879:-1 chm1:+:1476129212:-1 chm1:+:1551448634:-1 chm1:+:2126549479:-1 chm1:+:2139637199:-1 chm1:+:2220552544:-1 chm1:+:2232048788:-1 chm1:+:2261358166:-1 chm1:+:2421198555:-1 chm1:+:2482301868:-1 chm1:+:2623283634:-1 chm1:+:2646427001:-1 chm1:+:2956501450:-1 chm1:+:2982565203:-1 chm1:+:2992777054:-1 chm1:+:2996298337:-1 chm1:+:3013323666:-1 chm1:+:3024458856:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:792972722:-1 chm1:+:1660839093:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:104557478:-1 chm1:+:283927255:-1 chm1:+:971828518:-1 chm1:+:1000582926:-1 chm1:+:1149758022:-1 chm1:+:1435644113:-1 chm1:+:1984924642:-1 chm1:+:2391905759:-1 chm1:+:2512779229:-1 chm1:+:2947319369:-1 chm1:+:2962889667:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:8216631:-1 chm1:+:59898694:-1 chm1:+:176369285:-1 chm1:+:389583913:-1 chm1:+:470502890:-1 chm1:+:495063723:-1 chm1:+:566897200:-1 chm1:+:617098825:-1 chm1:+:641471144:-1 chm1:+:726146194:-1 chm1:+:734767408:-1 chm1:+:748326592:-1 chm1:+:812807617:-1 chm1:+:832778462:-1 chm1:+:837141214:-1 chm1:+:866299097:-1 chm1:+:924860902:-1 chm1:+:1092791147:-1 chm1:+:1129089094:-1 chm1:+:1174745246:-1 chm1:+:1247267824:-1 chm1:+:1395752200:-1 chm1:+:1401942542:-1 chm1:+:1465591817:-1 chm1:+:1473601605:-1 chm1:+:1491532173:-1 chm1:+:1703186107:-1 chm1:+:1736402050:-1 chm1:+:1769053853:-1 chm1:+:1937039147:-1 chm1:+:1956126959:-1 chm1:+:2010206903:-1 chm1:+:2058131359:-1 chm1:+:2140256533:-1 chm1:+:2220552546:-1 chm1:+:2334316442:-1 chm1:+:2344329614:-1 chm1:+:2474385457:-1 chm1:+:2474467660:-1 chm1:+:2552178441:-1 chm1:+:2651474089:-1 chm1:+:2653031802:-1 chm1:+:2915962827:-1 chm1:+:2919460473:-1 chm1:+:2937093403:-1 chm1:+:2946761378:-1 chm1:+:3006588337:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:630365686:-1 chm1:+:1412800574:-1 chm1:+:1678544188:-1 chm1:+:2047090254:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:407082316:-1 chm1:+:488371212:-1 chm1:+:727618496:-1 chm1:+:855867084:-1 chm1:+:938065097:-1 chm1:+:960173748:-1 chm1:+:1253684241:-1 chm1:+:2758177675:-1 chm1:+:2762806382:-1 chm1:+:2809576117:-1 chm1:+:2828748022:-1 chm1:+:2972150146:-1 chm1:+:3041255154:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:44696000:-1 chm1:+:249364082:-1 chm1:+:284828795:-1 chm1:+:307267743:-1 chm1:+:354478580:-1 chm1:+:375999030:-1 chm1:+:383653030:-1 chm1:+:402678182:-1 chm1:+:452828125:-1 chm1:+:499108984:-1 chm1:+:512111825:-1 chm1:+:518281519:-1 chm1:+:526558163:-1 chm1:+:541437996:-1 chm1:+:576648958:-1 chm1:+:602233190:-1 chm1:+:659430006:-1 chm1:+:683615581:-1 chm1:+:760115221:-1 chm1:+:774868609:-1 chm1:+:813463071:-1 chm1:+:818298579:-1 chm1:+:830782970:-1 chm1:+:850354189:-1 chm1:+:853475473:-1 chm1:+:991990602:-1 chm1:+:1007342433:-1 chm1:+:1113915199:-1 chm1:+:1141543348:-1 chm1:+:1165084649:-1 chm1:+:1171264498:-1 chm1:+:1263118022:-1 chm1:+:1273617375:-1 chm1:+:1319451083:-1 chm1:+:1401099110:-1 chm1:+:1499061079:-1 chm1:+:1499625973:-1 chm1:+:1524756811:-1 chm1:+:1555142740:-1 chm1:+:1641188776:-1 chm1:+:1696619299:-1 chm1:+:1798005437:-1 chm1:+:1822856206:-1 chm1:+:1830806365:-1 chm1:+:1838169677:-1 chm1:+:1896286832:-1 chm1:+:1994534687:-1 chm1:+:2012631294:-1 chm1:+:2017702958:-1 chm1:+:2041675125:-1 chm1:+:2048399057:-1 chm1:+:2157263275:-1 chm1:+:2166999589:-1 chm1:+:2238829526:-1 chm1:+:2506428632:-1 chm1:+:2612776357:-1 chm1:+:2620595447:-1 chm1:+:2653724273:-1 chm1:+:2657579922:-1 chm1:+:2713658287:-1 chm1:+:2735936740:-1 chm1:+:2806620735:-1 chm1:+:2829536107:-1 chm1:+:2892097455:-1 chm1:+:2921035166:-1 chm1:+:2931697287:-1 chm1:+:2969527228:-1 chm1:+:3002156458:-1 chm1:+:3042744929:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:82199852:-1 chm1:+:82200609:-1 chm1:+:516981082:-1 chm1:+:775526749:-1 chm1:+:1018121201:-1 chm1:+:1793760408:-1 chm1:+:2271513538:-1 chm1:+:2605800314:-1 chm1:+:2918859720:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:71305309:-1 chm1:+:74081019:-1 chm1:+:154006732:-1 chm1:+:244694892:-1 chm1:+:263185440:-1 chm1:+:368409645:-1 chm1:+:408085303:-1 chm1:+:596291550:-1 chm1:+:641471155:-1 chm1:+:710694935:-1 chm1:+:795385321:-1 chm1:+:946841739:-1 chm1:+:1024864302:-1 chm1:+:1550469089:-1 chm1:+:1930200133:-1 chm1:+:1961065505:-1 chm1:+:1990394733:-1 chm1:+:2287146608:-1 chm1:+:2354298808:-1 chm1:+:2960921798:-1 chm1:+:2974296106:-1 chm1:+:2981608106:-1 chm1:+:2997522047:-1 chm1:+:3001630360:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:763342971:-1 chm1:+:1483059105:-1 chm1:+:2826995425:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:18231272:-1 chm1:+:176352329:-1 chm1:+:235301811:-1 chm1:+:283160678:-1 chm1:+:478634557:-1 chm1:+:563588162:-1 chm1:+:1273065251:-1 chm1:+:1583617599:-1 chm1:+:1605769078:-1 chm1:+:1888074219:-1 chm1:+:2019362009:-1 chm1:+:2258063329:-1 chm1:+:3017900615:-1 chm1:+:3100483836:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:6355169:-1 chm1:+:321453992:-1 chm1:+:330332177:-1 chm1:+:461276149:-1 chm1:+:722006182:-1 chm1:+:894029064:-1 chm1:+:1125818622:-1 chm1:+:1420249852:-1 chm1:+:1441249391:-1 chm1:+:1615538663:-1 chm1:+:1944599991:-1 chm1:+:2015848278:-1 chm1:+:2176780361:-1 chm1:+:2555338744:-1 chm1:+:2580408762:-1 chm1:+:2826818936:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:158370149:-1 chm1:+:256682975:-1 chm1:+:350790431:-1 chm1:+:677132834:-1 chm1:+:778555614:-1 chm1:+:828865251:-1 chm1:+:849035208:-1 chm1:+:969963518:-1 chm1:+:977732989:-1 chm1:+:1319008147:-1 chm1:+:1342818707:-1 chm1:+:1643177327:-1 chm1:+:1856138877:-1 chm1:+:2026753153:-1 chm1:+:2387705908:-1 chm1:+:2570214703:-1 chm1:+:2631966995:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:249989018:-1 chm1:+:308304953:-1 chm1:+:357959013:-1 chm1:+:991761798:-1 chm1:+:1428643810:-1 chm1:+:1433097239:-1 chm1:+:1486727308:-1 chm1:+:1941443045:-1 chm1:+:2040550834:-1 chm1:+:2184578740:-1 chm1:+:2366231383:-1 chm1:+:2614547749:-1 chm1:+:2818511203:-1 chm1:+:2915741275:-1 chm1:+:2937315364:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:430145115:-1 chm1:+:660316712:-1 chm1:+:736089327:-1 chm1:+:882931563:-1 chm1:+:939759932:-1 chm1:+:1319799127:-1 chm1:+:1793161047:-1 chm1:+:1926421295:-1 chm1:+:1976624884:-1 chm1:+:2272890379:-1 chm1:+:2572676279:-1 chm1:+:2667209109:-1 chm1:+:2965812124:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:885292717:-1 chm1:+:911165216:-1 chm1:+:1029262348:-1 chm1:+:1216379077:-1 chm1:+:1905687088:-1 chm1:+:2016271177:-1 chm1:+:2237770854:-1 chm1:+:2253371803:-1 chm1:+:2266276847:-1 chm1:+:2804752454:-1 chm1:+:2926482449:-1 chm1:+:3022048386:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:358078726:-1 chm1:+:2123890640:-1 chm1:+:2172648924:-1 chm1:+:2340848445:-1 +TGGCCTAAAGTTTTCTTTTTTTTTTCTTTTTTTGATGTGTCTTTTTCTGCTTTTGGTATCCACATAATACTGGCCTCAGATAGAATGAGTTTGGAGGTATTCCCTTCCTTTTCTACTTTTGAAACAGTTTGAATAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAATTCTACTGGAAAGCCACTGGGTCCGTGGGCTTTTCTTTACTACGAGACTTTTTATTGTGACTGCAATCTCATTACTTGTTAAAATTGGTCCTGGTTTCAGTTTTGAATTTCGTTTCTCTTTCAATCTTGGTAGATTTAGTGTATGTCTAGGGAATGTGTCCATTTCTTCTAGATTTCCAATTTATTGGCTATATGTTGTCTCATAAGTAGCCTACTAATGATCCTTTGAATTCAGCAGTATCCAGTTGTAATGTCTCCTTTTTCATCTCTGACTTTATTTATTTGGATTTTATCTATTTTTTTCTTAGTTAATCTGGCTAAAGGTCTGTCAATTTTAACTTTTCAAAAAACAACTTTTTGTTTCAGTTGATGTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTGTGTTCTGTAGTCTTTAATATTTCTTTTTTTTCTACTAATTTTGGGTTTGGTTTGCTGTTGCTTTTCTATTTCTTTAAGACGCATCTTTAGGTTGTTTATTTGAAGTTTTGCTTCTTTTTGATGTAGGCACTTATAGCTTATAAGCTTACCCTCTTGGTACTGCTTTTGCTCTATCCAGAGGTATGGTGTGTTGTGTTGCCATTTATCATTTGTTTCA chm1:+:75530115:-1 chm1:+:88008507:-1 chm1:+:513219926:-1 chm1:+:529897911:-1 chm1:+:733722875:-1 chm1:+:772129290:-1 chm1:+:1037102111:-1 chm1:+:1160407462:-1 chm1:+:1285217690:-1 chm1:+:1485506573:-1 chm1:+:1874039108:-1 chm1:+:1900560452:-1 chm1:+:1912910234:-1 chm1:+:2010530777:-1 chm1:+:2121741729:-1 chm1:+:2973374038:-1 chm1:+:2978955047:-1 chm1:+:3006182374:-1 chm1:+:3042371681:-1 +TGAAACAAATGATAAATGGCAACACAACACACCATACCTCTGGATAGAGCAAAAGCAGTACCAAGAGGGTAAGCTTATAAGCTATAAGTGCCTACATCAAAAAGAAGCAAAACTTCAAATAAACAACCTAAAGATGCGTCTTAAAGAAATAGAAAAGCAACAGCAAACCAAACCCAAAATTAGTAGAAAAAAAAGAAATATTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:2981987488:39 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+TGAAACAAATGATAAATGGCAACACAACACACCATACCTCTGGATAGAGCAAAAGCAGTACCAAGAGGGTAAGCTTATAAGCTATAAGTGCCTACATCAAAAAGAAGCAAAACTTCAAATAAACAACCTAAAGATGCGTCTTAAAGAAATAGAAAAGCAACAGCAAACCAAACCCAAAATTAGTAGAAAAAAAAGAAATATTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:2981987486:39 +TGAAACAAATGATAAATGGCAACACAACACACCATACCTCTGGATAGAGCAAAAGCAGTACCAAGAGGGTAAGCTTATAAGCTATAAGTGCCTACATCAAAAAGAAGCAAAACTTCAAATAAACAACCTAAAGATGCGTCTTAAAGAAATAGAAAAGCAACAGCAAACCAAACCCAAAATTAGTAGAAAAAAAAGAAATATTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:2194975186:-1 +TGAAACAAATGATAAATGGCAACACAACACACCATACCTCTGGATAGAGCAAAAGCAGTACCAAGAGGGTAAGCTTATAAGCTATAAGTGCCTACATCAAAAAGAAGCAAAACTTCAAATAAACAACCTAAAGATGCGTCTTAAAGAAATAGAAAAGCAACAGCAAACCAAACCCAAAATTAGTAGAAAAAAAAGAAATATTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:2981987497:39 +TGAAACAAATGATAAATGGCAACACAACACACCATACCTCTGGATAGAGCAAAAGCAGTACCAAGAGGGTAAGCTTATAAGCTATAAGTGCCTACATCAAAAAGAAGCAAAACTTCAAATAAACAACCTAAAGATGCGTCTTAAAGAAATAGAAAAGCAACAGCAAACCAAACCCAAAATTAGTAGAAAAAAAAGAAATATTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:999212713:-1 +TGAAACAAATGATAAATGGCAACACAACACACCATACCTCTGGATAGAGCAAAAGCAGTACCAAGAGGGTAAGCTTATAAGCTATAAGTGCCTACATCAAAAAGAAGCAAAACTTCAAATAAACAACCTAAAGATGCGTCTTAAAGAAATAGAAAAGCAACAGCAAACCAAACCCAAAATTAGTAGAAAAAAAAGAAATATTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:2847028920:-1 chm1:+:2981987490:39 +TGAAACAAATGATAAATGGCAACACAACACACCATACCTCTGGATAGAGCAAAAGCAGTACCAAGAGGGTAAGCTTATAAGCTATAAGTGCCTACATCAAAAAGAAGCAAAACTTCAAATAAACAACCTAAAGATGCGTCTTAAAGAAATAGAAAAGCAACAGCAAACCAAACCCAAAATTAGTAGAAAAAAAAGAAATATTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:2859553650:-1 +TGAAACAAATGATAAATGGCAACACAACACACCATACCTCTGGATAGAGCAAAAGCAGTACCAAGAGGGTAAGCTTATAAGCTATAAGTGCCTACATCAAAAAGAAGCAAAACTTCAAATAAACAACCTAAAGATGCGTCTTAAAGAAATAGAAAAGCAACAGCAAACCAAACCCAAAATTAGTAGAAAAAAAAGAAATATTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:109986058:-1 chm1:+:526190079:-1 chm1:+:808870535:-1 chm1:+:1256881902:-1 chm1:+:1452954256:-1 chm1:+:1890517956:-1 chm1:+:2051099695:-1 chm1:+:2223627140:-1 chm1:+:2241239495:-1 chm1:+:2470657377:-1 chm1:+:2552894276:-1 chm1:+:2956026408:-1 +TGAAACAAATGATAAATGGCAACACAACACACCATACCTCTGGATAGAGCAAAAGCAGTACCAAGAGGGTAAGCTTATAAGCTATAAGTGCCTACATCAAAAAGAAGCAAAACTTCAAATAAACAACCTAAAGATGCGTCTTAAAGAAATAGAAAAGCAACAGCAAACCAAACCCAAAATTAGTAGAAAAAAAAGAAATATTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:544107321:-1 chm1:+:693634277:-1 chm1:+:881221044:-1 chm1:+:1088804527:-1 chm1:+:1290731558:-1 chm1:+:2043825240:-1 chm1:+:2671989152:-1 chm1:+:2902146403:-1 +TGAAACAAATGATAAATGGCAACACAACACACCATACCTCTGGATAGAGCAAAAGCAGTACCAAGAGGGTAAGCTTATAAGCTATAAGTGCCTACATCAAAAAGAAGCAAAACTTCAAATAAACAACCTAAAGATGCGTCTTAAAGAAATAGAAAAGCAACAGCAAACCAAACCCAAAATTAGTAGAAAAAAAAGAAATATTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:85443672:-1 chm1:+:508280929:-1 chm1:+:631321185:-1 chm1:+:805683396:-1 chm1:+:1193499878:-1 chm1:+:1380262553:-1 chm1:+:1905433584:-1 chm1:+:1906698768:-1 chm1:+:1976665472:-1 chm1:+:2043115425:-1 chm1:+:2408239143:-1 chm1:+:2505651091:-1 chm1:+:2649273797:-1 chm1:+:2965386837:-1 chm1:+:2981987496:39 chm1:+:3020509641:-1 chm1:+:3027337388:-1 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chm1:+:1706565637:-1 chm1:+:1777184488:-1 chm1:+:1958534853:-1 chm1:+:2017724227:-1 chm1:+:2132280412:-1 chm1:+:2282776412:-1 chm1:+:2681168088:-1 chm1:+:3007165571:-1 +TGAAACAAATGATAAATGGCAACACAACACACCATACCTCTGGATAGAGCAAAAGCAGTACCAAGAGGGTAAGCTTATAAGCTATAAGTGCCTACATCAAAAAGAAGCAAAACTTCAAATAAACAACCTAAAGATGCGTCTTAAAGAAATAGAAAAGCAACAGCAAACCAAACCCAAAATTAGTAGAAAAAAAAGAAATATTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:520961875:-1 chm1:+:600461685:-1 chm1:+:1061747638:-1 chm1:+:1542876530:-1 chm1:+:1853678128:-1 chm1:+:2139751026:-1 chm1:+:2170441887:-1 chm1:+:2386930242:-1 chm1:+:2457156044:-1 chm1:+:2732115983:-1 chm1:+:2934867008:-1 chm1:+:2954657525:-1 chm1:+:3000765081:-1 chm1:+:3027003725:-1 +TGAAACAAATGATAAATGGCAACACAACACACCATACCTCTGGATAGAGCAAAAGCAGTACCAAGAGGGTAAGCTTATAAGCTATAAGTGCCTACATCAAAAAGAAGCAAAACTTCAAATAAACAACCTAAAGATGCGTCTTAAAGAAATAGAAAAGCAACAGCAAACCAAACCCAAAATTAGTAGAAAAAAAAGAAATATTAAAGACTACAGAACACAAATAAATGAATTTGAAATGAGGAAAACAACACAAAACATCAACTGAAACAAAAAGTTGTTTTTTGAAAAGTTAAAATTGACAGACCTTTAGCCAGATTAACTAAGAAAAAAATAGATAAAATCCAAATAAATAAAGTCAGAGATGAAAAAGGAGACATTACAACTGGATACTGCTGAATTCAAAGGATCATTAGTAGGCTACTTATGAGACAACATATAGCCAATAAATTGGAAATCTAGAAGAAATGGACACATTCCCTAGACATACACTAAATCTACCAAGATTGAAAGAGAAACGAAATTCAAAACTGAAACCAGGACCAATTTTAACAAGTAATGAGATTGCAGTCACAATAAAAAGTCTCGTAGTAAAGAAAAGCCCACGGACCCAGTGGCTTTCCAGTAGAATTTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTATTCAAACTGTTTCAAAAGTAGAAAAGGAAGGGAATACCTCCAAACTCATTCTATCTGAGGCCAGTATTATGTGGATACCAAAAGCAGAAAAAGACACATCAAAAAAAGAAAAAAAAAAGAAAACTTTAGGCCA chm1:+:102495288:-1 chm1:+:328196755:-1 chm1:+:366668198:-1 chm1:+:1432149411:-1 chm1:+:1462385295:-1 chm1:+:3024761515:-1 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chm1:+:1080610514:-1 chm1:+:1142630361:-1 chm1:+:1199697834:-1 chm1:+:1331838586:-1 chm1:+:1337113773:-1 chm1:+:1344178911:-1 chm1:+:1429907530:-1 chm1:+:1508702014:-1 chm1:+:1636351346:-1 chm1:+:1637853507:-1 chm1:+:1826711571:-1 chm1:+:1976426796:-1 chm1:+:2003809027:-1 chm1:+:2072937192:-1 chm1:+:2117700245:-1 chm1:+:2189073448:-1 chm1:+:2191512094:-1 chm1:+:2198705192:-1 chm1:+:2235470524:-1 chm1:+:2250307012:-1 chm1:+:2417495173:-1 chm1:+:2426322972:-1 chm1:+:2668073426:33 chm1:+:2694174018:-1 chm1:+:2867671977:-1 chm1:+:2879460515:-1 chm1:+:2949652762:-1 chm1:+:3034379160:-1 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGG chm1:+:1497619716:-1 chm1:+:2676923764:-1 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGG chm1:+:569447299:-1 chm1:+:873833138:-1 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGG chm1:+:605374533:-1 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGG chm1:+:2668073437:33 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGG chm1:+:2668073430:33 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGG chm1:+:2668073432:33 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGG chm1:+:2668073431:33 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGG chm1:+:2668073434:33 +AAAAAAAGAAGGAGGTGCTGACTGGGATGCACTGAGAGTCCCCTGGGGTGCGTCAGGAGATGACAGAAATCCTGGGGGAGCACGTGGCATGGAGGGTTGAAGTTGACACCCACCACAGACTGGCTGAGTAAGGAACTGCCAGGGGAAGTCAGAGGCAAAACCGGACCAGGCAGGGGGAGGCCCAGATGGGACGAGGGTGGGTTAGGAGCCATCGACTCAACCCTGAAGAGCGTCTGAGCTCACTGGAGACTAAGAGGGGCCCCAGGGTCAGAAGCAGGAGTTGGGAGGCTAGGAGTAATAGACAGGAATGAGGATCTGGCTGACGAAGGGGAAGAGGGAGAGAGGCTGTGGGGGAGAAGTGGGGTCAGGGGAGCCCGTGTTTCCTGTTTTTTTTTTTGTTGTTGTTTTTGAGACAGAGTCTCGCTCTTGTCACCCAGGCTGGAGTGCAGTGGTATGATTTCGGCTCACTGCAACCTCCCGCCTCCCGGGTTCAAGGATTCTCTGCCTCAGCCTCCCAAGTAACGTGGAAATACAGGCGCCCTGCCACCAAGCCAGGCTGATTTTTGTGTTTTTAGTAGAGACAGGATTTCACCACGTTGGACACGCTCATCTCGAACCTCCAACCTACAGGTGATCCGCCCACCTCAGCTCCCACTGTGGCTGGATAACAGGCATGAGCCACTGTGTCCGGCCAGAGGACAGGGATTTCACCATGTTGGCCAGGCTGGTCTGTAACTCCTGACCCTCTAAGTTCAAGTGATCCACCCACCTCAGCCTCCCAAAGTGCCTGGGAGTACAGG chm1:+:738344768:-1 +CCTGTACTCCCAGGCACTTTGGGAGGCTGAGGTGGGTGGATCACTTGAACTTAGAGGGTCAGGAGTTACAGACCAGCCTGGCCAACATGGTGAAATCCCTGTCCTCTGGCCGGACACAGTGGCTCATGCCTGTTATCCAGCCACAGTGGGAGCTGAGGTGGGCGGATCACCTGTAGGTTGGAGGTTCGAGATGAGCGTGTCCAACGTGGTGAAATCCTGTCTCTACTAAAAACACAAAAATCAGCCTGGCTTGGTGGCAGGGCGCCTGTATTTCCACGTTACTTGGGAGGCTGAGGCAGAGAATCCTTGAACCCGGGAGGCGGGAGGTTGCAGTGAGCCGAAATCATACCACTGCACTCCAGCCTGGGTGACAAGAGCGAGACTCTGTCTCAAAAACAACAACAAAAAAAAAAACAGGAAACACGGGCTCCCCTGACCCCACTTCTCCCCCACAGCCTCTCTCCCTCTTCCCCTTCGTCAGCCAGATCCTCATTCCTGTCTATTACTCCTAGCCTCCCAACTCCTGCTTCTGACCCTGGGGCCCCTCTTAGTCTCCAGTGAGCTCAGACGCTCTTCAGGGTTGAGTCGATGGCTCCTAACCCACCCTCGTCCCATCTGGGCCTCCCCCTGCCTGGTCCGGTTTTGCCTCTGACTTCCCCTGGCAGTTCCTTACTCAGCCAGTCTGTGGTGGGTGTCAACTTCAACCCTCCATGCCACGTGCTCCCCCAGGATTTCTGTCATCTCCTGACGCACCCCAGGGGACTCTCAGTGCATCCCAGTCAGCACCTCCTTCTTTTTTT chm1:+:2647527500:-1 +CCTGTACTCCCAGGCACTTTGGGAGGCTGAGGTGGGTGGATCACTTGAACTTAGAGGGTCAGGAGTTACAGACCAGCCTGGCCAACATGGTGAAATCCCTGTCCTCTGGCCGGACACAGTGGCTCATGCCTGTTATCCAGCCACAGTGGGAGCTGAGGTGGGCGGATCACCTGTAGGTTGGAGGTTCGAGATGAGCGTGTCCAACGTGGTGAAATCCTGTCTCTACTAAAAACACAAAAATCAGCCTGGCTTGGTGGCAGGGCGCCTGTATTTCCACGTTACTTGGGAGGCTGAGGCAGAGAATCCTTGAACCCGGGAGGCGGGAGGTTGCAGTGAGCCGAAATCATACCACTGCACTCCAGCCTGGGTGACAAGAGCGAGACTCTGTCTCAAAAACAACAACAAAAAAAAAAACAGGAAACACGGGCTCCCCTGACCCCACTTCTCCCCCACAGCCTCTCTCCCTCTTCCCCTTCGTCAGCCAGATCCTCATTCCTGTCTATTACTCCTAGCCTCCCAACTCCTGCTTCTGACCCTGGGGCCCCTCTTAGTCTCCAGTGAGCTCAGACGCTCTTCAGGGTTGAGTCGATGGCTCCTAACCCACCCTCGTCCCATCTGGGCCTCCCCCTGCCTGGTCCGGTTTTGCCTCTGACTTCCCCTGGCAGTTCCTTACTCAGCCAGTCTGTGGTGGGTGTCAACTTCAACCCTCCATGCCACGTGCTCCCCCAGGATTTCTGTCATCTCCTGACGCACCCCAGGGGACTCTCAGTGCATCCCAGTCAGCACCTCCTTCTTTTTTT chm1:+:2872582304:-1 +CCTGTACTCCCAGGCACTTTGGGAGGCTGAGGTGGGTGGATCACTTGAACTTAGAGGGTCAGGAGTTACAGACCAGCCTGGCCAACATGGTGAAATCCCTGTCCTCTGGCCGGACACAGTGGCTCATGCCTGTTATCCAGCCACAGTGGGAGCTGAGGTGGGCGGATCACCTGTAGGTTGGAGGTTCGAGATGAGCGTGTCCAACGTGGTGAAATCCTGTCTCTACTAAAAACACAAAAATCAGCCTGGCTTGGTGGCAGGGCGCCTGTATTTCCACGTTACTTGGGAGGCTGAGGCAGAGAATCCTTGAACCCGGGAGGCGGGAGGTTGCAGTGAGCCGAAATCATACCACTGCACTCCAGCCTGGGTGACAAGAGCGAGACTCTGTCTCAAAAACAACAACAAAAAAAAAAACAGGAAACACGGGCTCCCCTGACCCCACTTCTCCCCCACAGCCTCTCTCCCTCTTCCCCTTCGTCAGCCAGATCCTCATTCCTGTCTATTACTCCTAGCCTCCCAACTCCTGCTTCTGACCCTGGGGCCCCTCTTAGTCTCCAGTGAGCTCAGACGCTCTTCAGGGTTGAGTCGATGGCTCCTAACCCACCCTCGTCCCATCTGGGCCTCCCCCTGCCTGGTCCGGTTTTGCCTCTGACTTCCCCTGGCAGTTCCTTACTCAGCCAGTCTGTGGTGGGTGTCAACTTCAACCCTCCATGCCACGTGCTCCCCCAGGATTTCTGTCATCTCCTGACGCACCCCAGGGGACTCTCAGTGCATCCCAGTCAGCACCTCCTTCTTTTTTT chm1:+:1495349922:-1 chm1:+:2499489775:-1 +CCTGTACTCCCAGGCACTTTGGGAGGCTGAGGTGGGTGGATCACTTGAACTTAGAGGGTCAGGAGTTACAGACCAGCCTGGCCAACATGGTGAAATCCCTGTCCTCTGGCCGGACACAGTGGCTCATGCCTGTTATCCAGCCACAGTGGGAGCTGAGGTGGGCGGATCACCTGTAGGTTGGAGGTTCGAGATGAGCGTGTCCAACGTGGTGAAATCCTGTCTCTACTAAAAACACAAAAATCAGCCTGGCTTGGTGGCAGGGCGCCTGTATTTCCACGTTACTTGGGAGGCTGAGGCAGAGAATCCTTGAACCCGGGAGGCGGGAGGTTGCAGTGAGCCGAAATCATACCACTGCACTCCAGCCTGGGTGACAAGAGCGAGACTCTGTCTCAAAAACAACAACAAAAAAAAAAACAGGAAACACGGGCTCCCCTGACCCCACTTCTCCCCCACAGCCTCTCTCCCTCTTCCCCTTCGTCAGCCAGATCCTCATTCCTGTCTATTACTCCTAGCCTCCCAACTCCTGCTTCTGACCCTGGGGCCCCTCTTAGTCTCCAGTGAGCTCAGACGCTCTTCAGGGTTGAGTCGATGGCTCCTAACCCACCCTCGTCCCATCTGGGCCTCCCCCTGCCTGGTCCGGTTTTGCCTCTGACTTCCCCTGGCAGTTCCTTACTCAGCCAGTCTGTGGTGGGTGTCAACTTCAACCCTCCATGCCACGTGCTCCCCCAGGATTTCTGTCATCTCCTGACGCACCCCAGGGGACTCTCAGTGCATCCCAGTCAGCACCTCCTTCTTTTTTT chm1:+:155424009:-1 chm1:+:888141937:-1 chm1:+:1010599691:-1 chm1:+:1182031796:-1 chm1:+:1270701774:-1 chm1:+:1547867841:-1 chm1:+:1677653780:-1 chm1:+:1726103812:-1 chm1:+:1849098478:-1 chm1:+:1893744918:-1 chm1:+:1895632228:-1 chm1:+:2359746904:-1 chm1:+:2508400429:-1 chm1:+:2537284155:-1 chm1:+:2662128894:-1 chm1:+:2663725527:-1 chm1:+:2668667911:-1 chm1:+:2872516121:-1 chm1:+:2921888008:-1 chm1:+:3034425920:-1 +CCTGTACTCCCAGGCACTTTGGGAGGCTGAGGTGGGTGGATCACTTGAACTTAGAGGGTCAGGAGTTACAGACCAGCCTGGCCAACATGGTGAAATCCCTGTCCTCTGGCCGGACACAGTGGCTCATGCCTGTTATCCAGCCACAGTGGGAGCTGAGGTGGGCGGATCACCTGTAGGTTGGAGGTTCGAGATGAGCGTGTCCAACGTGGTGAAATCCTGTCTCTACTAAAAACACAAAAATCAGCCTGGCTTGGTGGCAGGGCGCCTGTATTTCCACGTTACTTGGGAGGCTGAGGCAGAGAATCCTTGAACCCGGGAGGCGGGAGGTTGCAGTGAGCCGAAATCATACCACTGCACTCCAGCCTGGGTGACAAGAGCGAGACTCTGTCTCAAAAACAACAACAAAAAAAAAAACAGGAAACACGGGCTCCCCTGACCCCACTTCTCCCCCACAGCCTCTCTCCCTCTTCCCCTTCGTCAGCCAGATCCTCATTCCTGTCTATTACTCCTAGCCTCCCAACTCCTGCTTCTGACCCTGGGGCCCCTCTTAGTCTCCAGTGAGCTCAGACGCTCTTCAGGGTTGAGTCGATGGCTCCTAACCCACCCTCGTCCCATCTGGGCCTCCCCCTGCCTGGTCCGGTTTTGCCTCTGACTTCCCCTGGCAGTTCCTTACTCAGCCAGTCTGTGGTGGGTGTCAACTTCAACCCTCCATGCCACGTGCTCCCCCAGGATTTCTGTCATCTCCTGACGCACCCCAGGGGACTCTCAGTGCATCCCAGTCAGCACCTCCTTCTTTTTTT chm1:+:113381184:-1 chm1:+:541363973:-1 chm1:+:1378323291:-1 chm1:+:1616454181:-1 chm1:+:1701585201:-1 chm1:+:2301812009:-1 chm1:+:2372728852:-1 chm1:+:2419508115:-1 chm1:+:2476181125:-1 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chm1:+:2123610394:-1 chm1:+:2357315539:-1 chm1:+:2360464958:-1 chm1:+:2616769610:115 chm1:+:2742311300:112 chm1:+:2943617711:-1 chm1:+:2976299256:128 chm1:+:3051604751:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGA chm1:+:965749252:-1 chm1:+:1007255843:125 chm1:+:1251052493:-1 chm1:+:1450260909:126 chm1:+:1564926553:129 chm1:+:1615560634:119 chm1:+:1638311871:-1 chm1:+:1834875564:122 chm1:+:1852476536:107 chm1:+:2067377184:-1 chm1:+:2363685444:-1 chm1:+:2558619155:-1 chm1:+:2885993812:-1 +ACAAGAAATAACTAAGATCAGACGCAGTAAATGAGGGAGATAGAGACACAAAAAGCCTTCAAAAAAATCAATGAATCCAGGAGCTGGTTTTAAAAAAGATTAGCAAAATAGATAGACCACTATCCAGACTAATAAAGAAGAAAAGAGAGAAGTCAAATAAACAACAATAAAGAAGGATAAAGGGGATATCACCACTGAATACCACAGAAATACAACTACCAGTCAGAGAATACTATAAACACCTCTATGCAAATAAAGTAGAAAATTCTAGAAGAAATAGATACATTCCTGGACCACATACACCCTCCAAGACTAAACCAGGAAGAAGTCAAATCCTGGAATAGACCAAATAACAAGTTCTGAAACTGGATTCAGTAATTAATAGCCTACAACCAACAAAGCCCAGGACCAGACAGATTCACAGCCTGAATTCTACCAGAGGTACAAAGAGGAAACTGGTACCATTCCTTCTGAAACTCTTTCAATCAATAGAGAAGAGGGAGTCCTCTCTAACTCATTTTTATGTGGCCAGCATCATACCTGATAACAAAACCTGGCAGAAGACACAACAAGAAAAAGAAAATTTCGGGCCAATATCCCTGAGTGAACATCGATGCGAAATCCTCAATAAAATAGTGGCAAACCACATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTCAGCTTCATCCCTGGGATGGCAAAGGCTTGGTTCAACATATGCAAATCACAAACGTAATCCATCGCAATAAAGAAAACCAATGACAAAAACCCACATGATTATCTCAACAGA chm1:+:769884205:118 chm1:+:817288740:-1 chm1:+:1479885202:124 chm1:+:1501932283:109 chm1:+:1565440089:111 +TCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:185166175:125 chm1:+:433291791:130 chm1:+:448901249:-1 chm1:+:496379368:116 chm1:+:504355531:117 chm1:+:511530728:126 chm1:+:613132193:124 chm1:+:629561844:113 chm1:+:638457757:114 chm1:+:709813413:130 chm1:+:810776309:112 chm1:+:856660968:115 chm1:+:922190265:114 chm1:+:1028661046:116 chm1:+:1107274567:106 chm1:+:1171678330:119 chm1:+:1242763626:128 chm1:+:1378569351:101 chm1:+:1381198794:114 chm1:+:1489737884:118 chm1:+:1523524633:-1 chm1:+:1871010909:142 chm1:+:1915934704:125 chm1:+:2278941216:128 chm1:+:2589232337:128 chm1:+:2658207773:134 chm1:+:2694499493:118 chm1:+:2701585454:36 chm1:+:2965692717:114 chm1:+:2969038440:109 chm1:+:2989481918:137 +TCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:2701585449:36 +TCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:2701585451:36 +TCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:1874548726:128 chm1:+:2925315932:-1 +TCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:1002882955:-1 chm1:+:2701585457:36 +TCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:97590988:-1 +TCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:2375187751:-1 +TCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:183716534:142 chm1:+:230659083:136 chm1:+:302067422:112 chm1:+:473405018:127 chm1:+:629485148:133 chm1:+:767680280:-1 chm1:+:925830528:125 chm1:+:1253720354:123 chm1:+:1363976673:104 chm1:+:1542718647:116 chm1:+:1552026599:101 chm1:+:1933179651:113 chm1:+:1946750950:132 chm1:+:2166969579:129 chm1:+:2701585448:36 chm1:+:2946840478:140 +TCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:1030653:-1 chm1:+:433733397:133 chm1:+:948551367:-1 chm1:+:1482176160:-1 chm1:+:2130958867:118 chm1:+:3051681304:-1 +TCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:118409926:-1 chm1:+:367150515:-1 chm1:+:449412688:-1 chm1:+:590471903:-1 chm1:+:753428516:130 chm1:+:756992493:-1 chm1:+:809062301:133 chm1:+:1200750535:114 chm1:+:1287009118:125 chm1:+:1450977905:137 chm1:+:1482102243:-1 chm1:+:1765916032:117 chm1:+:1848593189:120 chm1:+:1879021844:121 chm1:+:2389248615:116 chm1:+:2550467476:-1 chm1:+:2701585447:36 chm1:+:2764280272:-1 chm1:+:3030381378:-1 +TCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:793134551:125 chm1:+:797861208:122 chm1:+:898261491:121 chm1:+:924951764:123 chm1:+:975096929:123 chm1:+:1033029023:137 chm1:+:1139623179:117 chm1:+:1282702302:111 chm1:+:1418480475:138 chm1:+:1557684225:108 chm1:+:2006850392:120 chm1:+:2461102004:116 +TCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:300838527:119 chm1:+:468804986:-1 chm1:+:744436382:-1 chm1:+:1164040075:123 chm1:+:1383944923:123 chm1:+:1408684510:123 chm1:+:1457215071:114 chm1:+:1544076838:124 chm1:+:1791671569:110 chm1:+:1818423534:115 chm1:+:2251102384:-1 chm1:+:2811590989:-1 chm1:+:2924331495:-1 chm1:+:2985952514:-1 chm1:+:3058848371:140 +TCTGTTGAGATAATCATGTGGGTTTTTGTCATTGGTTTTCTTTATTGCGATGGATTACGTTTGTGATTTGCATATGTTGAACCAAGCCTTTGCCATCCCAGGGATGAAGCTGACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATGTGGTTTGCCACTATTTTATTGAGGATTTCGCATCGATGTTCACTCAGGGATATTGGCCCGAAATTTTCTTTTTCTTGTTGTGTCTTCTGCCAGGTTTTGTTATCAGGTATGATGCTGGCCACATAAAAATGAGTTAGAGAGGACTCCCTCTTCTCTATTGATTGAAAGAGTTTCAGAAGGAATGGTACCAGTTTCCTCTTTGTACCTCTGGTAGAATTCAGGCTGTGAATCTGTCTGGTCCTGGGCTTTGTTGGTTGTAGGCTATTAATTACTGAATCCAGTTTCAGAACTTGTTATTTGGTCTATTCCAGGATTTGACTTCTTCCTGGTTTAGTCTTGGAGGGTGTATGTGGTCCAGGAATGTATCTATTTCTTCTAGAATTTTCTACTTTATTTGCATAGAGGTGTTTATAGTATTCTCTGACTGGTAGTTGTATTTCTGTGGTATTCAGTGGTGATATCCCCTTTATCCTTCTTTATTGTTGTTTATTTGACTTCTCTCTTTTCTTCTTTATTAGTCTGGATAGTGGTCTATCTATTTTGCTAATCTTTTTTAAAACCAGCTCCTGGATTCATTGATTTTTTTGAAGGCTTTTTGTGTCTCTATCTCCCTCATTTACTGCGTCTGATCTTAGTTATTTCTTGT chm1:+:96059134:-1 chm1:+:157609315:-1 chm1:+:575202637:156 chm1:+:1190532604:111 chm1:+:1252693889:-1 chm1:+:1469262704:-1 chm1:+:1485181218:-1 chm1:+:1624162874:118 chm1:+:1993283451:124 chm1:+:2006724662:-1 chm1:+:2134293145:-1 chm1:+:2594841454:-1 chm1:+:2701585450:36 chm1:+:3062561724:134 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:23314451:-1 chm1:+:26959148:-1 chm1:+:52436654:-1 chm1:+:59112998:-1 chm1:+:68743452:-1 chm1:+:153684677:-1 chm1:+:190566246:-1 chm1:+:200503038:-1 chm1:+:215753406:-1 chm1:+:240167553:-1 chm1:+:245289741:-1 chm1:+:269518938:-1 chm1:+:310942535:-1 chm1:+:377175581:-1 chm1:+:452672464:-1 chm1:+:476046790:-1 chm1:+:476800160:-1 chm1:+:519897768:-1 chm1:+:590989687:-1 chm1:+:601538565:-1 chm1:+:610252806:-1 chm1:+:615035624:-1 chm1:+:641909551:-1 chm1:+:644981053:-1 chm1:+:645175814:-1 chm1:+:648027805:-1 chm1:+:675258626:-1 chm1:+:730965611:-1 chm1:+:731203571:-1 chm1:+:802510852:-1 chm1:+:805557451:-1 chm1:+:830953870:-1 chm1:+:847847971:-1 chm1:+:861448796:-1 chm1:+:914277340:-1 chm1:+:1015279412:-1 chm1:+:1018302071:-1 chm1:+:1020195008:-1 chm1:+:1049594091:-1 chm1:+:1079885458:-1 chm1:+:1109642644:-1 chm1:+:1152022658:-1 chm1:+:1179507505:-1 chm1:+:1218175277:-1 chm1:+:1255573322:-1 chm1:+:1323672478:-1 chm1:+:1329508928:-1 chm1:+:1338474298:-1 chm1:+:1369334618:-1 chm1:+:1370470913:-1 chm1:+:1417536295:-1 chm1:+:1421259455:-1 chm1:+:1435056733:-1 chm1:+:1463470036:-1 chm1:+:1469204412:-1 chm1:+:1484393672:-1 chm1:+:1489834229:-1 chm1:+:1541864996:-1 chm1:+:1612145323:-1 chm1:+:1629245091:-1 chm1:+:1646050297:-1 chm1:+:1654614868:-1 chm1:+:1674435230:-1 chm1:+:1700889434:-1 chm1:+:1703015884:-1 chm1:+:1741584904:-1 chm1:+:1755487481:-1 chm1:+:1762125794:-1 chm1:+:1862435721:-1 chm1:+:1891700276:-1 chm1:+:1901067863:-1 chm1:+:1902125716:-1 chm1:+:1935071830:-1 chm1:+:1946001273:-1 chm1:+:1951920858:-1 chm1:+:2000380447:-1 chm1:+:2061703018:-1 chm1:+:2064386598:-1 chm1:+:2110942728:-1 chm1:+:2115116112:-1 chm1:+:2127186275:-1 chm1:+:2160735069:-1 chm1:+:2179931343:-1 chm1:+:2183627153:-1 chm1:+:2184896216:-1 chm1:+:2249235550:-1 chm1:+:2270003137:-1 chm1:+:2293068838:-1 chm1:+:2352126488:-1 chm1:+:2374202280:-1 chm1:+:2414456037:-1 chm1:+:2426027675:-1 chm1:+:2431330404:-1 chm1:+:2432966636:-1 chm1:+:2439423520:-1 chm1:+:2439627998:-1 chm1:+:2471860755:-1 chm1:+:2476482898:-1 chm1:+:2479239382:-1 chm1:+:2500085619:-1 chm1:+:2540396120:-1 chm1:+:2548755503:-1 chm1:+:2557543000:-1 chm1:+:2560704102:-1 chm1:+:2599974254:-1 chm1:+:2605593348:-1 chm1:+:2627012872:-1 chm1:+:2629585501:-1 chm1:+:2667824162:-1 chm1:+:2674393347:-1 chm1:+:2680624837:-1 chm1:+:2696538205:-1 chm1:+:2717244494:-1 chm1:+:2736452350:-1 chm1:+:2764720285:-1 chm1:+:2815481352:-1 chm1:+:2861822428:-1 chm1:+:2873140176:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:451700856:-1 chm1:+:492308102:-1 chm1:+:1091739167:-1 chm1:+:1134126170:-1 chm1:+:1227566781:-1 chm1:+:1470570875:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:646706909:-1 chm1:+:1904600844:-1 chm1:+:1970805712:-1 chm1:+:2072351391:-1 chm1:+:2390604900:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:216762973:-1 chm1:+:321919653:-1 chm1:+:683786843:-1 chm1:+:831020718:-1 chm1:+:1637750789:-1 chm1:+:1704282539:-1 chm1:+:1774621851:-1 chm1:+:2343439269:-1 chm1:+:2918067872:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:1149242367:-1 chm1:+:1239831366:-1 chm1:+:1656368756:-1 chm1:+:1898249223:-1 chm1:+:2936789153:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:261632528:-1 chm1:+:705308235:-1 chm1:+:912260060:-1 chm1:+:1006357618:-1 chm1:+:1406005391:-1 chm1:+:1728880198:-1 chm1:+:2251545900:-1 chm1:+:2256330764:-1 chm1:+:2565773932:-1 chm1:+:2608810475:-1 chm1:+:2651613765:-1 chm1:+:2709221352:-1 chm1:+:2926578753:-1 chm1:+:3003032532:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:22632330:-1 chm1:+:189623364:-1 chm1:+:348909714:-1 chm1:+:393564525:-1 chm1:+:629891286:-1 chm1:+:643965472:-1 chm1:+:1423659903:-1 chm1:+:1444688316:-1 chm1:+:1457360714:-1 chm1:+:1628554417:-1 chm1:+:1662591496:-1 chm1:+:2149406015:-1 chm1:+:2190534931:-1 chm1:+:2192598881:-1 chm1:+:2621858558:-1 chm1:+:2887323595:-1 chm1:+:3034050099:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:387280511:-1 chm1:+:468602270:-1 chm1:+:478836320:-1 chm1:+:1102096012:-1 chm1:+:1251546313:-1 chm1:+:1365941642:-1 chm1:+:1946396437:-1 chm1:+:2757340138:-1 chm1:+:2961965860:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:649574256:-1 chm1:+:796770586:-1 chm1:+:918769499:-1 chm1:+:1306544563:-1 chm1:+:1968646006:-1 chm1:+:1998980147:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:807285351:-1 chm1:+:1028140163:-1 chm1:+:1074667870:-1 chm1:+:1151866588:-1 chm1:+:1165356829:-1 chm1:+:1222046695:-1 chm1:+:1231081862:-1 chm1:+:2121303513:-1 chm1:+:2872085510:-1 chm1:+:2887143014:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:79534796:-1 chm1:+:91055511:-1 chm1:+:172986553:-1 chm1:+:189312473:-1 chm1:+:332120283:-1 chm1:+:528919304:-1 chm1:+:608315826:-1 chm1:+:748406203:-1 chm1:+:910890396:-1 chm1:+:1211788532:-1 chm1:+:1452055170:-1 chm1:+:1515224523:-1 chm1:+:1517195245:-1 chm1:+:1542551935:-1 chm1:+:1687066689:-1 chm1:+:1937156333:-1 chm1:+:1945679413:-1 chm1:+:2405000358:-1 chm1:+:2931323939:-1 chm1:+:2971438092:-1 chm1:+:3040785489:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:457624:-1 chm1:+:33702721:-1 chm1:+:36878661:-1 chm1:+:39668747:-1 chm1:+:51475715:-1 chm1:+:65517297:-1 chm1:+:71448871:-1 chm1:+:90319376:-1 chm1:+:92318372:-1 chm1:+:106585093:-1 chm1:+:107790572:-1 chm1:+:119096675:-1 chm1:+:148641102:-1 chm1:+:148803111:-1 chm1:+:149550101:-1 chm1:+:175090328:-1 chm1:+:207736946:-1 chm1:+:229051901:-1 chm1:+:229690923:-1 chm1:+:322174237:-1 chm1:+:351292384:-1 chm1:+:368580393:-1 chm1:+:373394168:-1 chm1:+:378641476:-1 chm1:+:379484470:-1 chm1:+:379958879:-1 chm1:+:394535864:-1 chm1:+:409946504:-1 chm1:+:421874546:-1 chm1:+:439829095:-1 chm1:+:467072649:-1 chm1:+:504547586:-1 chm1:+:561498168:-1 chm1:+:567883393:-1 chm1:+:581319118:-1 chm1:+:621192169:-1 chm1:+:689040072:-1 chm1:+:694389519:-1 chm1:+:716189974:-1 chm1:+:721155478:-1 chm1:+:788214036:-1 chm1:+:807248523:-1 chm1:+:823404535:-1 chm1:+:837787746:-1 chm1:+:845693051:-1 chm1:+:874365750:-1 chm1:+:894567857:-1 chm1:+:896121432:-1 chm1:+:905817965:-1 chm1:+:960404322:-1 chm1:+:1008276969:-1 chm1:+:1012173176:-1 chm1:+:1041262025:-1 chm1:+:1044996883:-1 chm1:+:1062512382:-1 chm1:+:1094909447:-1 chm1:+:1118526355:-1 chm1:+:1168923323:-1 chm1:+:1169527528:-1 chm1:+:1211091033:-1 chm1:+:1233583270:-1 chm1:+:1236508092:-1 chm1:+:1239755353:-1 chm1:+:1239957174:-1 chm1:+:1240589915:-1 chm1:+:1262830544:-1 chm1:+:1303824308:-1 chm1:+:1309300393:-1 chm1:+:1323786811:-1 chm1:+:1329640794:-1 chm1:+:1329873509:-1 chm1:+:1341152247:-1 chm1:+:1367847299:-1 chm1:+:1373828048:-1 chm1:+:1387674696:-1 chm1:+:1417181724:-1 chm1:+:1435514891:-1 chm1:+:1473886056:-1 chm1:+:1477543207:-1 chm1:+:1490952732:-1 chm1:+:1508663554:-1 chm1:+:1509929430:-1 chm1:+:1521878419:-1 chm1:+:1522990250:-1 chm1:+:1545895564:-1 chm1:+:1562373325:-1 chm1:+:1565382077:-1 chm1:+:1607656446:-1 chm1:+:1673275114:-1 chm1:+:1687235049:-1 chm1:+:1718076387:-1 chm1:+:1749548310:-1 chm1:+:1750106892:-1 chm1:+:1768673636:-1 chm1:+:1773341309:-1 chm1:+:1785654309:-1 chm1:+:1812579020:-1 chm1:+:1822220325:-1 chm1:+:1825726208:-1 chm1:+:1826375427:-1 chm1:+:1838530320:-1 chm1:+:1856513173:-1 chm1:+:1857560820:-1 chm1:+:1883424589:-1 chm1:+:1889250517:-1 chm1:+:1895428387:-1 chm1:+:1924330334:-1 chm1:+:1927338776:-1 chm1:+:1983131017:-1 chm1:+:2002544775:-1 chm1:+:2003091545:-1 chm1:+:2013740798:-1 chm1:+:2015907446:-1 chm1:+:2017494634:-1 chm1:+:2017617919:-1 chm1:+:2061311636:-1 chm1:+:2064538773:-1 chm1:+:2112536433:-1 chm1:+:2120236546:-1 chm1:+:2139501187:-1 chm1:+:2166555329:-1 chm1:+:2168453857:-1 chm1:+:2172643844:-1 chm1:+:2228201488:-1 chm1:+:2261196363:-1 chm1:+:2273412153:-1 chm1:+:2276967451:-1 chm1:+:2292827303:-1 chm1:+:2296767147:-1 chm1:+:2299770922:-1 chm1:+:2388891746:-1 chm1:+:2399704055:-1 chm1:+:2414516216:-1 chm1:+:2429242141:-1 chm1:+:2433256996:-1 chm1:+:2467693627:-1 chm1:+:2516598104:-1 chm1:+:2520038870:-1 chm1:+:2540078488:-1 chm1:+:2540528593:-1 chm1:+:2545737906:-1 chm1:+:2556154997:-1 chm1:+:2562101647:-1 chm1:+:2562351521:-1 chm1:+:2567812764:-1 chm1:+:2581344502:-1 chm1:+:2584701894:-1 chm1:+:2600515434:-1 chm1:+:2636713692:-1 chm1:+:2638189438:-1 chm1:+:2660181514:-1 chm1:+:2662220090:-1 chm1:+:2670325862:-1 chm1:+:2677831318:-1 chm1:+:2681054522:-1 chm1:+:2696559103:-1 chm1:+:2736983565:-1 chm1:+:2751592867:-1 chm1:+:2758537411:-1 chm1:+:2763478034:-1 chm1:+:2766181686:-1 chm1:+:2800440969:-1 chm1:+:2848701467:-1 chm1:+:2870722823:-1 chm1:+:2873735198:-1 chm1:+:2882473250:-1 chm1:+:2921795907:-1 chm1:+:2987290099:-1 chm1:+:2990258925:-1 chm1:+:3009879383:-1 chm1:+:3018720649:-1 chm1:+:3056655101:-1 chm1:+:3057418624:-1 chm1:+:3058274015:-1 chm1:+:3061464065:-1 chm1:+:3063097807:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:1300633741:-1 chm1:+:1647538641:-1 chm1:+:1835295634:-1 chm1:+:2052880914:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:803422253:-1 chm1:+:2709016638:-1 chm1:+:2929085411:-1 chm1:+:2929194894:-1 chm1:+:2929245286:-1 chm1:+:2933671441:-1 chm1:+:2933713152:-1 chm1:+:2933765390:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:38291761:-1 chm1:+:236986707:-1 chm1:+:1211006618:-1 chm1:+:1291071927:-1 chm1:+:2380999870:-1 chm1:+:2539465332:-1 chm1:+:2993462675:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:1255477065:-1 chm1:+:1914605642:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:464346463:-1 chm1:+:722699144:-1 chm1:+:782655317:-1 chm1:+:1021076498:-1 chm1:+:1133213957:-1 chm1:+:1168086531:-1 chm1:+:2156578701:-1 chm1:+:2170411902:-1 chm1:+:2884202660:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:937486167:-1 chm1:+:1254011374:-1 chm1:+:2064312657:-1 chm1:+:2285318733:-1 chm1:+:3017295406:-1 +ATTTAAGCAATTGTAAGAGGATGTTTTGAATAACATACATATGAACAAATTCCTGAAAACTAAAATTTAGATAACCATTATTGAAATTTATGTGTAGAACATTTATTACTAAGGTTGGAAATATTTTAATTCTGTCCTTTAACCACTATGTTCTTAGTCTATTATTTAACTAGTTAAGTTGCTGTCATAAATAGTACTTATAAGGATCCCAATATGCTCAGTCCCAGTGTTGTTTTCTCGTAGGCTTGTTATGCTGCCTCGCGATTGGATATCTGACAAGCAGGTAAACTAAAATTTGTTTCACTTCAATTACTTTAATATTTTTGGGTAGAACTATTACGTCTTTCAGCTGAAGGATGGAGTTCATTTTGGAAAGATTATAGAAAAATATATTAAATAACAAAGGATAAAAACATTTAAACTCTCTGAGGACCACGTCAAAAGAATAATGATACCAGAAGTGTTTCAGAGTGGAACACATTGCCATTTTGTAGAGTGATCACTGGGTGATCAGATAAGTGAGTTGATGTATGATACCTTGTCTTGGATCTCAACACTACCCCAGCACACTTAATACAAAAATGCTTGGTTCAAAATGTGACTGTTGAGAGCTGTTTCCACACGTTCTGATTTTTAGTGTGTATTCCATGTTACCTAACTACCACCCCTTTTTATTATAAAATAATACATTTTTAAAATGTCCATTTTGGAAACTTGGAAAAATTATAGAAAGCACAAAAGAAGAAAATGAAAATCGACTTAGGCACGGTGGGTCACGCCTGTAATCCCAGAACCTTTGG chm1:+:94960517:-1 chm1:+:189308508:-1 chm1:+:269138685:-1 chm1:+:659635143:-1 chm1:+:885675389:-1 chm1:+:921053796:-1 chm1:+:984165007:-1 chm1:+:1327041061:-1 chm1:+:1364793371:-1 chm1:+:1408593831:-1 chm1:+:1706784993:-1 chm1:+:2666006757:-1 chm1:+:3024644297:-1 chm1:+:3028468257:-1 +CCAAAGGTTCTGGGATTACAGGCGTGACCCACCGTGCCTAAGTCGATTTTCATTTTCTTCTTTTGTGCTTTCTATAATTTTTCCAAGTTTCCAAAATGGACATTTTAAAAATGTATTATTTTATAATAAAAAGGGGTGGTAGTTAGGTAACATGGAATACACACTAAAAATCAGAACGTGTGGAAACAGCTCTCAACAGTCACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT chm1:+:508087204:37 +CCAAAGGTTCTGGGATTACAGGCGTGACCCACCGTGCCTAAGTCGATTTTCATTTTCTTCTTTTGTGCTTTCTATAATTTTTCCAAGTTTCCAAAATGGACATTTTAAAAATGTATTATTTTATAATAAAAAGGGGTGGTAGTTAGGTAACATGGAATACACACTAAAAATCAGAACGTGTGGAAACAGCTCTCAACAGTCACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT chm1:+:508087206:37 +CCAAAGGTTCTGGGATTACAGGCGTGACCCACCGTGCCTAAGTCGATTTTCATTTTCTTCTTTTGTGCTTTCTATAATTTTTCCAAGTTTCCAAAATGGACATTTTAAAAATGTATTATTTTATAATAAAAAGGGGTGGTAGTTAGGTAACATGGAATACACACTAAAAATCAGAACGTGTGGAAACAGCTCTCAACAGTCACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT chm1:+:508087203:37 +CCAAAGGTTCTGGGATTACAGGCGTGACCCACCGTGCCTAAGTCGATTTTCATTTTCTTCTTTTGTGCTTTCTATAATTTTTCCAAGTTTCCAAAATGGACATTTTAAAAATGTATTATTTTATAATAAAAAGGGGTGGTAGTTAGGTAACATGGAATACACACTAAAAATCAGAACGTGTGGAAACAGCTCTCAACAGTCACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT chm1:+:508087210:37 +CCAAAGGTTCTGGGATTACAGGCGTGACCCACCGTGCCTAAGTCGATTTTCATTTTCTTCTTTTGTGCTTTCTATAATTTTTCCAAGTTTCCAAAATGGACATTTTAAAAATGTATTATTTTATAATAAAAAGGGGTGGTAGTTAGGTAACATGGAATACACACTAAAAATCAGAACGTGTGGAAACAGCTCTCAACAGTCACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT chm1:+:508087208:37 chm1:+:2987752673:-1 +CCAAAGGTTCTGGGATTACAGGCGTGACCCACCGTGCCTAAGTCGATTTTCATTTTCTTCTTTTGTGCTTTCTATAATTTTTCCAAGTTTCCAAAATGGACATTTTAAAAATGTATTATTTTATAATAAAAAGGGGTGGTAGTTAGGTAACATGGAATACACACTAAAAATCAGAACGTGTGGAAACAGCTCTCAACAGTCACATTTTGAACCAAGCATTTTTGTATTAAGTGTGCTGGGGTAGTGTTGAGATCCAAGACAAGGTATCATACATCAACTCACTTATCTGATCACCCAGTGATCACTCTACAAAATGGCAATGTGTTCCACTCTGAAACACTTCTGGTATCATTATTCTTTTGACGTGGTCCTCAGAGAGTTTAAATGTTTTTATCCTTTGTTATTTAATATATTTTTCTATAATCTTTCCAAAATGAACTCCATCCTTCAGCTGAAAGACGTAATAGTTCTACCCAAAAATATTAAAGTAATTGAAGTGAAACAAATTTTAGTTTACCTGCTTGTCAGATATCCAATCGCGAGGCAGCATAACAAGCCTACGAGAAAACAACACTGGGACTGAGCATATTGGGATCCTTATAAGTACTATTTATGACAGCAACTTAACTAGTTAAATAATAGACTAAGAACATAGTGGTTAAAGGACAGAATTAAAATATTTCCAACCTTAGTAATAAATGTTCTACACATAAATTTCAATAATGGTTATCTAAATTTTAGTTTTCAGGAATTTGTTCATATGTATGTTATTCAAAACATCCTCTTACAATTGCTTAAAT chm1:+:508087209:37 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:2922358405:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:303727684:-1 chm1:+:1096765703:-1 chm1:+:1516782316:-1 chm1:+:1731335880:-1 chm1:+:2374049583:-1 chm1:+:2485083828:-1 chm1:+:2536938897:-1 chm1:+:2695223000:-1 chm1:+:2700659520:-1 chm1:+:2711947975:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:2064749588:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:36679903:-1 chm1:+:48127011:-1 chm1:+:50331879:-1 chm1:+:97715269:-1 chm1:+:145400385:-1 chm1:+:154248258:-1 chm1:+:180058161:-1 chm1:+:422947996:-1 chm1:+:569879903:-1 chm1:+:734035540:-1 chm1:+:979718526:-1 chm1:+:1115610329:-1 chm1:+:1181839232:-1 chm1:+:1235990368:-1 chm1:+:1252265140:-1 chm1:+:1362504762:-1 chm1:+:1434657579:-1 chm1:+:1462331640:-1 chm1:+:1497863765:-1 chm1:+:1569858816:-1 chm1:+:1670458887:-1 chm1:+:1717362401:-1 chm1:+:1796959339:-1 chm1:+:1957595141:-1 chm1:+:1975065584:-1 chm1:+:2029680214:-1 chm1:+:2030864139:-1 chm1:+:2061505981:-1 chm1:+:2073809812:-1 chm1:+:2106258819:-1 chm1:+:2255491460:-1 chm1:+:2281667611:-1 chm1:+:2289855526:-1 chm1:+:2344323329:-1 chm1:+:2414819736:-1 chm1:+:2418900593:-1 chm1:+:2427097805:-1 chm1:+:2429058283:-1 chm1:+:2456785780:-1 chm1:+:2458231394:-1 chm1:+:2540958997:-1 chm1:+:2555473316:-1 chm1:+:2564415209:-1 chm1:+:2565225166:-1 chm1:+:2594027824:-1 chm1:+:2714925789:-1 chm1:+:2717519771:-1 chm1:+:2818999807:-1 chm1:+:2867961199:-1 chm1:+:2875723960:-1 chm1:+:2921830014:-1 chm1:+:2977611631:-1 chm1:+:3016539498:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:9549833:-1 chm1:+:10645423:-1 chm1:+:19573965:-1 chm1:+:26334384:-1 chm1:+:36531150:-1 chm1:+:41151266:-1 chm1:+:90606804:-1 chm1:+:103282972:-1 chm1:+:176173506:-1 chm1:+:180630452:-1 chm1:+:229346003:-1 chm1:+:255576152:-1 chm1:+:269141643:-1 chm1:+:313545428:-1 chm1:+:335641163:-1 chm1:+:351258467:-1 chm1:+:361029997:-1 chm1:+:362176915:-1 chm1:+:394262056:-1 chm1:+:408674913:-1 chm1:+:442934584:-1 chm1:+:502036890:-1 chm1:+:503880162:-1 chm1:+:541882586:-1 chm1:+:677597428:-1 chm1:+:691006258:-1 chm1:+:700996068:-1 chm1:+:732320510:-1 chm1:+:748349564:-1 chm1:+:773657886:-1 chm1:+:856059951:-1 chm1:+:867595639:-1 chm1:+:878931914:-1 chm1:+:950223708:-1 chm1:+:1048335150:-1 chm1:+:1057378535:-1 chm1:+:1082561873:-1 chm1:+:1251671983:-1 chm1:+:1301674790:-1 chm1:+:1306029123:97 chm1:+:1309935975:-1 chm1:+:1363351800:-1 chm1:+:1519052660:-1 chm1:+:1534324836:-1 chm1:+:1614443380:-1 chm1:+:1621593747:-1 chm1:+:1668799907:-1 chm1:+:1677882175:-1 chm1:+:1690045136:-1 chm1:+:1704075193:-1 chm1:+:1730267115:-1 chm1:+:1795641803:-1 chm1:+:1800946596:-1 chm1:+:1843072075:-1 chm1:+:1861824507:-1 chm1:+:1863126815:-1 chm1:+:1882771420:-1 chm1:+:1899326049:-1 chm1:+:1933908486:-1 chm1:+:1941460524:-1 chm1:+:1975934791:-1 chm1:+:1982660886:-1 chm1:+:2006979248:-1 chm1:+:2021433801:-1 chm1:+:2030046011:-1 chm1:+:2046748197:-1 chm1:+:2073770820:-1 chm1:+:2112439118:-1 chm1:+:2231760245:-1 chm1:+:2251316840:-1 chm1:+:2267542726:-1 chm1:+:2302449495:-1 chm1:+:2302843639:-1 chm1:+:2337605415:-1 chm1:+:2428340557:-1 chm1:+:2433615967:-1 chm1:+:2494130077:-1 chm1:+:2530620053:-1 chm1:+:2540095961:-1 chm1:+:2541300753:-1 chm1:+:2543083339:-1 chm1:+:2548572497:-1 chm1:+:2552189019:-1 chm1:+:2567200759:-1 chm1:+:2576858072:-1 chm1:+:2593766365:-1 chm1:+:2626540817:-1 chm1:+:2661239318:-1 chm1:+:2669084565:-1 chm1:+:2680176504:-1 chm1:+:2694048712:-1 chm1:+:2695033187:-1 chm1:+:2698825957:-1 chm1:+:2699966196:-1 chm1:+:2704512446:-1 chm1:+:2709517137:-1 chm1:+:2712195904:-1 chm1:+:2713352373:-1 chm1:+:2761224820:-1 chm1:+:2812482580:-1 chm1:+:2858704123:-1 chm1:+:2871319475:-1 chm1:+:2872011204:-1 chm1:+:2876547672:-1 chm1:+:2885221771:-1 chm1:+:2905183938:-1 chm1:+:2949766768:-1 chm1:+:3050869930:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:56591115:-1 chm1:+:92922270:-1 chm1:+:203745613:-1 chm1:+:532779240:-1 chm1:+:732233025:-1 chm1:+:1256975325:-1 chm1:+:1533906638:-1 chm1:+:1693654171:-1 chm1:+:1913996673:-1 chm1:+:2106953008:-1 chm1:+:2293523953:-1 chm1:+:2434671143:-1 chm1:+:2484906942:-1 chm1:+:2903099819:-1 chm1:+:3055438020:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:197177781:-1 chm1:+:590140780:-1 chm1:+:817358521:-1 chm1:+:817572569:-1 chm1:+:1632391843:-1 chm1:+:1775615407:-1 chm1:+:1875380536:-1 chm1:+:2001621663:-1 chm1:+:2424321904:-1 chm1:+:2948769252:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:9154120:-1 chm1:+:20168120:-1 chm1:+:28067081:-1 chm1:+:52646093:-1 chm1:+:84918325:-1 chm1:+:161387247:-1 chm1:+:205243595:-1 chm1:+:225816055:-1 chm1:+:240918203:-1 chm1:+:300161708:-1 chm1:+:317839206:-1 chm1:+:350014741:-1 chm1:+:385253563:-1 chm1:+:461597697:-1 chm1:+:525417654:-1 chm1:+:545065698:-1 chm1:+:635063571:-1 chm1:+:636067802:-1 chm1:+:671769572:-1 chm1:+:745513584:-1 chm1:+:749115821:-1 chm1:+:804020632:-1 chm1:+:819400170:-1 chm1:+:879163120:-1 chm1:+:934927705:-1 chm1:+:945181894:-1 chm1:+:959453384:-1 chm1:+:969130312:-1 chm1:+:976591954:-1 chm1:+:1030519609:-1 chm1:+:1038045559:-1 chm1:+:1084439427:-1 chm1:+:1145348669:-1 chm1:+:1168728770:-1 chm1:+:1304899361:-1 chm1:+:1390817026:-1 chm1:+:1417541590:-1 chm1:+:1521679795:-1 chm1:+:1663249408:-1 chm1:+:1697913729:-1 chm1:+:1755742058:-1 chm1:+:1768872677:-1 chm1:+:1781698153:-1 chm1:+:1882761523:-1 chm1:+:2000623861:-1 chm1:+:2241315776:-1 chm1:+:2250548476:-1 chm1:+:2251174328:-1 chm1:+:2257486835:-1 chm1:+:2302295712:-1 chm1:+:2333069713:-1 chm1:+:2341150340:-1 chm1:+:2371944336:-1 chm1:+:2372304653:-1 chm1:+:2412588653:-1 chm1:+:2414145773:-1 chm1:+:2480238572:-1 chm1:+:2482966576:-1 chm1:+:2496247923:-1 chm1:+:2500196339:-1 chm1:+:2505152319:-1 chm1:+:2507349016:-1 chm1:+:2537698781:-1 chm1:+:2563797804:-1 chm1:+:2600535397:-1 chm1:+:2624970045:-1 chm1:+:2665521759:-1 chm1:+:2670412672:-1 chm1:+:2700723591:-1 chm1:+:2701985379:-1 chm1:+:2705525853:-1 chm1:+:2708698976:-1 chm1:+:2753784434:-1 chm1:+:2760686870:-1 chm1:+:2769240488:-1 chm1:+:2808111511:-1 chm1:+:2812816977:-1 chm1:+:2871017676:-1 chm1:+:2881634043:-1 chm1:+:2981664347:-1 chm1:+:3015015152:-1 chm1:+:3021201286:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:453338536:-1 chm1:+:547896828:-1 chm1:+:820776934:-1 chm1:+:969945662:-1 chm1:+:1299260213:-1 chm1:+:1612674325:-1 chm1:+:2861160413:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:19562316:-1 chm1:+:150243988:-1 chm1:+:344847055:-1 chm1:+:504217716:-1 chm1:+:526109577:-1 chm1:+:656114189:-1 chm1:+:656566081:-1 chm1:+:697101153:-1 chm1:+:917770931:-1 chm1:+:924805207:-1 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chm1:+:1188868474:-1 chm1:+:1529025779:-1 chm1:+:2051890785:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:562802812:-1 chm1:+:1306029132:97 chm1:+:1423434998:-1 chm1:+:2040180674:-1 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chm1:+:2671832479:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:57794060:-1 chm1:+:94852260:-1 chm1:+:160545124:-1 chm1:+:335357370:-1 chm1:+:525893123:-1 chm1:+:531048410:-1 chm1:+:644358088:-1 chm1:+:674528334:-1 chm1:+:1249239337:-1 chm1:+:1320749664:-1 chm1:+:1488548051:-1 chm1:+:1635917342:-1 chm1:+:1726464059:-1 chm1:+:2301026676:-1 chm1:+:2344785665:-1 chm1:+:2668478528:-1 chm1:+:2810159494:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:706017128:-1 chm1:+:917589224:-1 chm1:+:2425711048:-1 chm1:+:2607778785:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:667537985:-1 chm1:+:695097545:-1 chm1:+:860578106:-1 chm1:+:1077850734:-1 chm1:+:1187585859:-1 chm1:+:1516066649:-1 chm1:+:1789757942:-1 chm1:+:1820945999:-1 chm1:+:1971861230:-1 chm1:+:2179405218:-1 chm1:+:2806943256:-1 chm1:+:3012110569:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:1324185:-1 chm1:+:10935571:-1 chm1:+:46015013:-1 chm1:+:61287957:-1 chm1:+:88678603:-1 chm1:+:151146140:-1 chm1:+:178136848:-1 chm1:+:187442694:-1 chm1:+:209970170:-1 chm1:+:237767854:-1 chm1:+:247807133:-1 chm1:+:367770864:-1 chm1:+:420957594:-1 chm1:+:426146022:-1 chm1:+:442256255:-1 chm1:+:447018039:-1 chm1:+:522479712:-1 chm1:+:535125993:-1 chm1:+:541914519:-1 chm1:+:556743482:-1 chm1:+:650629222:-1 chm1:+:665999352:-1 chm1:+:671494543:-1 chm1:+:686606072:-1 chm1:+:771928531:-1 chm1:+:779518638:-1 chm1:+:780070149:-1 chm1:+:861936783:-1 chm1:+:869770237:-1 chm1:+:895048820:-1 chm1:+:898911042:-1 chm1:+:899417251:-1 chm1:+:938080937:-1 chm1:+:961983969:-1 chm1:+:964523080:-1 chm1:+:983588184:-1 chm1:+:988421220:-1 chm1:+:1016237310:-1 chm1:+:1020569657:-1 chm1:+:1023486677:-1 chm1:+:1091411945:-1 chm1:+:1112257924:-1 chm1:+:1134641195:-1 chm1:+:1159820710:-1 chm1:+:1160107899:-1 chm1:+:1175540913:-1 chm1:+:1191279199:-1 chm1:+:1212086435:-1 chm1:+:1216369425:-1 chm1:+:1276495866:-1 chm1:+:1307236465:-1 chm1:+:1344669641:-1 chm1:+:1390751373:-1 chm1:+:1447485577:-1 chm1:+:1468020919:-1 chm1:+:1481985369:-1 chm1:+:1487353833:-1 chm1:+:1493843513:-1 chm1:+:1518095234:-1 chm1:+:1531609515:-1 chm1:+:1552320723:-1 chm1:+:1562195223:-1 chm1:+:1632761996:-1 chm1:+:1666831048:-1 chm1:+:1708911525:-1 chm1:+:1825169589:-1 chm1:+:1886321071:-1 chm1:+:1948271839:-1 chm1:+:1970499811:-1 chm1:+:1983141895:-1 chm1:+:2059181513:-1 chm1:+:2075625945:-1 chm1:+:2255626082:-1 chm1:+:2350755362:-1 chm1:+:2363322875:-1 chm1:+:2429020295:-1 chm1:+:2430963602:-1 chm1:+:2475073626:-1 chm1:+:2508709271:-1 chm1:+:2514385863:-1 chm1:+:2547107728:-1 chm1:+:2584306852:-1 chm1:+:2611347926:-1 chm1:+:2635576907:-1 chm1:+:2689007326:-1 chm1:+:2695314495:-1 chm1:+:2696957810:-1 chm1:+:2704894172:-1 chm1:+:2706504171:-1 chm1:+:2753802654:-1 chm1:+:2797135989:-1 chm1:+:2824209160:-1 chm1:+:2883412979:-1 chm1:+:2892908195:-1 chm1:+:2897617133:-1 chm1:+:2921642699:-1 chm1:+:2947550728:-1 chm1:+:2986286227:-1 chm1:+:2993572522:-1 chm1:+:3001731762:-1 chm1:+:3012611540:-1 chm1:+:3024802878:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:85846353:-1 chm1:+:106007613:-1 chm1:+:113144147:-1 chm1:+:200601014:-1 chm1:+:276775084:-1 chm1:+:466667612:-1 chm1:+:473552558:-1 chm1:+:498357977:-1 chm1:+:578438924:-1 chm1:+:604297210:-1 chm1:+:620156404:-1 chm1:+:646187031:-1 chm1:+:763204672:-1 chm1:+:774368731:-1 chm1:+:859283159:-1 chm1:+:910204311:-1 chm1:+:918771964:-1 chm1:+:946238321:-1 chm1:+:985136626:-1 chm1:+:1059899216:-1 chm1:+:1060692766:-1 chm1:+:1077384821:-1 chm1:+:1128827989:-1 chm1:+:1135688394:-1 chm1:+:1290979828:-1 chm1:+:1335295860:-1 chm1:+:1383092851:-1 chm1:+:1389748915:-1 chm1:+:1408347076:-1 chm1:+:1423262290:-1 chm1:+:1548477325:-1 chm1:+:1638903722:-1 chm1:+:1639517506:-1 chm1:+:1681635001:-1 chm1:+:1817454749:-1 chm1:+:1820134353:-1 chm1:+:1839071724:-1 chm1:+:1892733440:-1 chm1:+:1959007005:-1 chm1:+:1963639528:-1 chm1:+:2106885554:-1 chm1:+:2165625661:-1 chm1:+:2356312403:-1 chm1:+:2365412646:-1 chm1:+:2536968727:-1 chm1:+:2600180514:-1 chm1:+:2610413820:-1 chm1:+:2628359601:-1 chm1:+:2929767854:-1 chm1:+:2954152525:-1 chm1:+:3007686867:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:24626183:-1 chm1:+:203802908:-1 chm1:+:233596347:-1 chm1:+:881029304:-1 chm1:+:1203410483:-1 chm1:+:1259087539:-1 chm1:+:1283605933:-1 chm1:+:1309935976:-1 chm1:+:1658676387:-1 chm1:+:2011551147:-1 chm1:+:2129787898:-1 chm1:+:2159702324:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:1306029125:97 chm1:+:2411620292:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:33616699:-1 chm1:+:180109844:-1 chm1:+:376939214:-1 chm1:+:630972190:-1 chm1:+:874337823:-1 chm1:+:1031336341:-1 chm1:+:1230371044:-1 chm1:+:1303860812:-1 chm1:+:1536343867:-1 chm1:+:1565847081:-1 chm1:+:1612253331:-1 chm1:+:2052661890:-1 chm1:+:2060754426:-1 chm1:+:2579252891:-1 chm1:+:2673769136:-1 chm1:+:2697600154:-1 chm1:+:2749460292:-1 chm1:+:2779932987:-1 chm1:+:2850214819:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:159203258:-1 chm1:+:228836676:-1 chm1:+:299032046:-1 chm1:+:319092591:-1 chm1:+:570159468:-1 chm1:+:658320492:-1 chm1:+:859179916:-1 chm1:+:881442903:-1 chm1:+:1063936861:-1 chm1:+:1133016239:-1 chm1:+:1212451831:-1 chm1:+:1212635319:-1 chm1:+:1215136364:-1 chm1:+:1367915509:-1 chm1:+:1664544664:-1 chm1:+:1815835319:-1 chm1:+:2003755928:-1 chm1:+:2179087803:-1 chm1:+:2261221405:-1 chm1:+:2275093953:-1 chm1:+:2428371853:-1 chm1:+:2445066578:-1 chm1:+:2463718549:-1 chm1:+:2616030466:-1 chm1:+:2620444633:-1 chm1:+:2712315237:-1 chm1:+:2917418122:-1 chm1:+:2936172880:-1 chm1:+:3097339530:-1 chm1:+:3099955654:-1 chm1:+:3100402729:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:80426043:-1 chm1:+:112641718:-1 chm1:+:159454790:-1 chm1:+:251562714:-1 chm1:+:390222456:-1 chm1:+:406417966:-1 chm1:+:411426024:-1 chm1:+:452114538:-1 chm1:+:701082708:-1 chm1:+:1023586775:-1 chm1:+:1098492637:-1 chm1:+:1125942381:-1 chm1:+:1229077861:-1 chm1:+:1279676441:-1 chm1:+:1362859994:-1 chm1:+:1378359587:-1 chm1:+:1478796264:-1 chm1:+:1704682441:-1 chm1:+:1727074863:-1 chm1:+:1727225992:-1 chm1:+:1727706784:-1 chm1:+:1727949307:-1 chm1:+:1729415750:-1 chm1:+:1731824338:-1 chm1:+:1900894630:-1 chm1:+:2024659654:-1 chm1:+:2142681372:-1 chm1:+:2161737603:-1 chm1:+:2259683043:-1 chm1:+:2278574181:-1 chm1:+:2349643334:-1 chm1:+:2423595092:-1 chm1:+:2601646501:-1 chm1:+:2849412712:-1 chm1:+:2876677523:-1 chm1:+:3026564810:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:52782692:-1 chm1:+:217359491:-1 chm1:+:223417062:-1 chm1:+:432250802:-1 chm1:+:582641933:-1 chm1:+:606291449:-1 chm1:+:607198602:-1 chm1:+:960850669:-1 chm1:+:1014860835:-1 chm1:+:1026490491:-1 chm1:+:1106402478:-1 chm1:+:1221801170:-1 chm1:+:1507596399:-1 chm1:+:1732968003:-1 chm1:+:1893962373:-1 chm1:+:1992511536:-1 chm1:+:2405804110:-1 chm1:+:2637359858:-1 chm1:+:2718236587:-1 chm1:+:2972240128:-1 chm1:+:3041348390:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:54227539:-1 chm1:+:76908431:-1 chm1:+:95769147:-1 chm1:+:121208749:-1 chm1:+:151540113:-1 chm1:+:175992327:-1 chm1:+:177803244:-1 chm1:+:189222811:-1 chm1:+:195659607:-1 chm1:+:199775820:-1 chm1:+:229079826:-1 chm1:+:387414765:-1 chm1:+:625727635:-1 chm1:+:812876935:-1 chm1:+:876450218:-1 chm1:+:905148668:-1 chm1:+:908984063:-1 chm1:+:1045286522:-1 chm1:+:1080867595:-1 chm1:+:1081016054:-1 chm1:+:1137450791:-1 chm1:+:1143061198:-1 chm1:+:1318413149:-1 chm1:+:1350138277:-1 chm1:+:1387785678:-1 chm1:+:1401634395:-1 chm1:+:1417532281:-1 chm1:+:1428692200:-1 chm1:+:1460301598:-1 chm1:+:1471670304:-1 chm1:+:1546901610:-1 chm1:+:1620860167:-1 chm1:+:1965580315:-1 chm1:+:2024860202:-1 chm1:+:2082936250:-1 chm1:+:2115474815:-1 chm1:+:2119430019:-1 chm1:+:2184366673:-1 chm1:+:2234433500:-1 chm1:+:2239920230:-1 chm1:+:2283320705:-1 chm1:+:2345819844:-1 chm1:+:2626314489:-1 chm1:+:2727050434:-1 chm1:+:2874591286:-1 chm1:+:3016372245:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:63288272:-1 chm1:+:174956269:-1 chm1:+:276887264:-1 chm1:+:306795892:-1 chm1:+:361787486:-1 chm1:+:490214153:-1 chm1:+:504202976:-1 chm1:+:541862132:-1 chm1:+:548125600:-1 chm1:+:620619667:-1 chm1:+:731655832:-1 chm1:+:990210027:-1 chm1:+:1099288266:-1 chm1:+:1142649793:-1 chm1:+:1151908215:-1 chm1:+:1170474425:-1 chm1:+:1195296906:-1 chm1:+:1258505500:-1 chm1:+:1336437922:-1 chm1:+:1383085821:-1 chm1:+:1386697470:-1 chm1:+:1433629064:-1 chm1:+:1498107340:-1 chm1:+:1514507081:-1 chm1:+:1822962613:-1 chm1:+:1847993286:-1 chm1:+:1863656082:-1 chm1:+:1932437585:-1 chm1:+:1947333454:-1 chm1:+:2111735334:-1 chm1:+:2277420257:-1 chm1:+:2332951762:-1 chm1:+:2374449431:-1 chm1:+:2379647632:-1 chm1:+:2383036748:-1 chm1:+:2440235790:-1 chm1:+:2468372413:-1 chm1:+:2507104736:-1 chm1:+:2583846727:-1 chm1:+:2618964592:-1 chm1:+:2626696059:-1 chm1:+:2739246107:-1 chm1:+:2750429467:-1 chm1:+:2776521677:-1 chm1:+:3045907335:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:509254853:-1 chm1:+:564511965:-1 chm1:+:652931554:-1 chm1:+:1102404277:-1 chm1:+:1146777157:-1 chm1:+:1266438938:-1 chm1:+:2020424157:-1 chm1:+:2530409926:-1 chm1:+:2600657622:-1 chm1:+:2858978038:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:303435387:-1 chm1:+:1074494785:-1 chm1:+:1207285157:-1 chm1:+:1792893440:-1 chm1:+:1833384819:-1 chm1:+:2511230398:-1 chm1:+:2737593127:-1 chm1:+:2858876242:-1 chm1:+:2884579810:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:150993067:-1 chm1:+:468951548:-1 chm1:+:504214493:-1 chm1:+:728682101:-1 chm1:+:805816237:-1 chm1:+:873489151:-1 chm1:+:1019894967:-1 chm1:+:1218366749:-1 chm1:+:1512123909:-1 chm1:+:1715819151:-1 chm1:+:1723545486:-1 chm1:+:1755488123:-1 chm1:+:1757159484:-1 chm1:+:2369915277:-1 chm1:+:2397850477:-1 chm1:+:2482264193:-1 chm1:+:2543932395:-1 chm1:+:2750513843:-1 chm1:+:2796456630:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:62142103:-1 chm1:+:421093086:-1 chm1:+:675225105:-1 chm1:+:936985698:-1 chm1:+:1090500700:-1 chm1:+:1309935974:-1 chm1:+:1466688303:-1 chm1:+:1538599367:-1 chm1:+:1577917482:-1 chm1:+:1708802028:-1 chm1:+:1893097153:-1 chm1:+:2006676233:-1 chm1:+:2460939429:-1 chm1:+:2571144297:-1 chm1:+:2711937436:-1 chm1:+:3012523780:-1 +GAACTCCAGGTCTCCAAGCGATCCTCCTACCCTCAGCCTCCCAAGGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCCACATACCATTTTAAAGTGTTACAATTCAGGCTGGGGCACGGTGTCTCACGCTATAATCCCAGCACTTTGGGAGGCCAAGGCGGAGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGTCTGGGCCAACATGGTGAAACCCCAATCTCTACTAAAATACAAAAATAGCCGGGCATGGTGGCGACATGCCTGTAAGTCCCAGCTACTTGGGAGGCTGAGGCCAGGAGAATTGCTTGAACCCGGTAGGCAGAGGTTTCAATGAGCCGAGATCACGCCATTGCACCCCAGCTTAGACAACAAGGAGTGAAAACTCCATCCAAAAAAAAAAAAAGAACTGTAGACAGGATAGTCTACCTGTCTTTCATTGTGTTCAATGACTCTCTCTTCCATCTGCTCTAATGAATTCGAAATAGTCTGGTGAATTTTTCATTTCCATTTCTATAACTTTTTTTTTTTTTTGTTTTTTTTTTTGAGATGGAGTTTCGTCTTGTCACCCAGGCTGGAGTGCAATGGTAGCGATCTTGGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGCAATTCTCCTGTCTCAGCTCTCGAGTAGCTGGGATTACAGGTGCCCGCCACCATGCCTGGCTAATTTTTGTATACTTTTACAGCTTCAGACTTTGATTCCTTTCAATAATTTCTATTTTTTTTCCCTTTCTTTTTTTTCTCTAAGCTTTTAGTTTGTCTATAA chm1:+:8668006:-1 chm1:+:82170774:-1 chm1:+:220148837:-1 chm1:+:457854633:-1 chm1:+:1005740774:-1 chm1:+:1150437205:-1 chm1:+:1265402704:-1 chm1:+:1748684862:-1 chm1:+:2016580789:-1 chm1:+:2576429011:-1 chm1:+:2602576081:-1 chm1:+:2672547644:-1 chm1:+:2970564307:-1 chm1:+:3010727292:-1 chm1:+:3040015984:-1 +TTATAGACAAACTAAAAGCTTAGAGAAAAAAAAGAAAGGGAAAAAAAATAGAAATTATTGAAAGGAATCAAAGTCTGAAGCTGTAAAAGTATACAAAAATTAGCCAGGCATGGTGGCGGGCACCTGTAATCCCAGCTACTCGAGAGCTGAGACAGGAGAATTGCTTGAACCCAGGAGACAGAGGTTGCAGTGAGCCAAGATCGCTACCATTGCACTCCAGCCTGGGTGACAAGACGAAACTCCATCTCAAAAAAAAAAACAAAAAAAAAAAAAAGTTATAGAAATGGAAATGAAAAATTCACCAGACTATTTCGAATTCATTAGAGCAGATGGAAGAGAGAGTCATTGAACACAATGAAAGACAGGTAGACTATCCTGTCTACAGTTCTTTTTTTTTTTTTGGATGGAGTTTTCACTCCTTGTTGTCTAAGCTGGGGTGCAATGGCGTGATCTCGGCTCATTGAAACCTCTGCCTACCGGGTTCAAGCAATTCTCCTGGCCTCAGCCTCCCAAGTAGCTGGGACTTACAGGCATGTCGCCACCATGCCCGGCTATTTTTGTATTTTAGTAGAGATTGGGGTTTCACCATGTTGGCCCAGACTGGTCTTGAACTCCTGACCTCAGGTGATCTGCTCCGCCTTGGCCTCCCAAAGTGCTGGGATTATAGCGTGAGACACCGTGCCCCAGCCTGAATTGTAACACTTTAAAATGGTATGTGGACTGGGTGTGGTGGCTCATGCCTATAATCCCAGCACCTTGGGAGGCTGAGGGTAGGAGGATCGCTTGGAGACCTGGAGTTC chm1:+:26259288:-1 chm1:+:185825214:-1 chm1:+:204017364:-1 chm1:+:712993837:-1 chm1:+:1308750740:29 chm1:+:1309935396:132 chm1:+:2076100837:-1 chm1:+:2371347366:-1 chm1:+:2397798522:-1 chm1:+:2978502246:-1 +TTATAGACAAACTAAAAGCTTAGAGAAAAAAAAGAAAGGGAAAAAAAATAGAAATTATTGAAAGGAATCAAAGTCTGAAGCTGTAAAAGTATACAAAAATTAGCCAGGCATGGTGGCGGGCACCTGTAATCCCAGCTACTCGAGAGCTGAGACAGGAGAATTGCTTGAACCCAGGAGACAGAGGTTGCAGTGAGCCAAGATCGCTACCATTGCACTCCAGCCTGGGTGACAAGACGAAACTCCATCTCAAAAAAAAAAACAAAAAAAAAAAAAAGTTATAGAAATGGAAATGAAAAATTCACCAGACTATTTCGAATTCATTAGAGCAGATGGAAGAGAGAGTCATTGAACACAATGAAAGACAGGTAGACTATCCTGTCTACAGTTCTTTTTTTTTTTTTGGATGGAGTTTTCACTCCTTGTTGTCTAAGCTGGGGTGCAATGGCGTGATCTCGGCTCATTGAAACCTCTGCCTACCGGGTTCAAGCAATTCTCCTGGCCTCAGCCTCCCAAGTAGCTGGGACTTACAGGCATGTCGCCACCATGCCCGGCTATTTTTGTATTTTAGTAGAGATTGGGGTTTCACCATGTTGGCCCAGACTGGTCTTGAACTCCTGACCTCAGGTGATCTGCTCCGCCTTGGCCTCCCAAAGTGCTGGGATTATAGCGTGAGACACCGTGCCCCAGCCTGAATTGTAACACTTTAAAATGGTATGTGGACTGGGTGTGGTGGCTCATGCCTATAATCCCAGCACCTTGGGAGGCTGAGGGTAGGAGGATCGCTTGGAGACCTGGAGTTC chm1:+:1552433911:-1 +TTATAGACAAACTAAAAGCTTAGAGAAAAAAAAGAAAGGGAAAAAAAATAGAAATTATTGAAAGGAATCAAAGTCTGAAGCTGTAAAAGTATACAAAAATTAGCCAGGCATGGTGGCGGGCACCTGTAATCCCAGCTACTCGAGAGCTGAGACAGGAGAATTGCTTGAACCCAGGAGACAGAGGTTGCAGTGAGCCAAGATCGCTACCATTGCACTCCAGCCTGGGTGACAAGACGAAACTCCATCTCAAAAAAAAAAACAAAAAAAAAAAAAAGTTATAGAAATGGAAATGAAAAATTCACCAGACTATTTCGAATTCATTAGAGCAGATGGAAGAGAGAGTCATTGAACACAATGAAAGACAGGTAGACTATCCTGTCTACAGTTCTTTTTTTTTTTTTGGATGGAGTTTTCACTCCTTGTTGTCTAAGCTGGGGTGCAATGGCGTGATCTCGGCTCATTGAAACCTCTGCCTACCGGGTTCAAGCAATTCTCCTGGCCTCAGCCTCCCAAGTAGCTGGGACTTACAGGCATGTCGCCACCATGCCCGGCTATTTTTGTATTTTAGTAGAGATTGGGGTTTCACCATGTTGGCCCAGACTGGTCTTGAACTCCTGACCTCAGGTGATCTGCTCCGCCTTGGCCTCCCAAAGTGCTGGGATTATAGCGTGAGACACCGTGCCCCAGCCTGAATTGTAACACTTTAAAATGGTATGTGGACTGGGTGTGGTGGCTCATGCCTATAATCCCAGCACCTTGGGAGGCTGAGGGTAGGAGGATCGCTTGGAGACCTGGAGTTC chm1:+:1308750742:29 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chm1:+:2029581096:-1 chm1:+:2068696828:-1 chm1:+:2108818263:-1 chm1:+:2111453810:-1 chm1:+:2220769187:-1 chm1:+:2249523249:-1 chm1:+:2344758118:-1 chm1:+:2373543243:-1 chm1:+:2458928642:-1 chm1:+:2474738741:-1 chm1:+:2485127025:-1 chm1:+:2495402330:-1 chm1:+:2529466854:-1 chm1:+:2537329173:-1 chm1:+:2545899865:-1 chm1:+:2559605895:-1 chm1:+:2584888793:-1 chm1:+:2664623859:-1 chm1:+:2702020628:-1 chm1:+:2714364651:-1 chm1:+:2717321138:-1 chm1:+:2728336463:-1 chm1:+:2741999781:-1 chm1:+:2776628175:-1 chm1:+:2816923482:-1 chm1:+:2865064095:-1 chm1:+:2948740979:-1 chm1:+:3004004775:-1 chm1:+:3017288692:-1 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chm1:+:2698975360:-1 chm1:+:2827098928:-1 chm1:+:2908507317:-1 chm1:+:2924709302:-1 chm1:+:2961648421:-1 +TTTCTTTCTTTCTGTCTGTACTCTTTCTTCTTTCTTTCTTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTCCTACCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTTCTTTTCTTTCTTTCTTTCTTTCTCTCTTTCTCTTCTTCTTCTTTTCTTCGTTACTTTCTTTTTCTTTCTTTCCTCTTTCTCTCTCTCTTTCCTCCCTCCCTTCCTCTTCCTCCATCCCTCCCTTCCTTTCTTGCTTTTTTTTTTTTCTTGCTTCGCTACCCAGGCTGGAGTGCAGTGGCATGGATCATAGCTCACTGCAGCCCTTGAACTTCTGGGCTCAAGCAATCTTCCTGCTTCGGCCACCCCTGGGATTTACAGGTGTAGAACCTGTGGCGCCCAGACCTTGGCCACTTTCTTTATTCTAACTTCTTTGTTCCATACTTTGCTTCTTTCCCTTGGATCCATCCCTACCAGCCTCCCTGTCCACTCCAGTGATAGGACACTCACGTCTTGCCAAGTCAATGTAACCCAGACCCTTCTCATTTAAACCTAGTCTCCTTTGGTTAAACTAGTCAATTCAGGATTCTCACAATCAATCTGAGTTTAAATCTTAATTAGTTGAAAGATTTTCATATCTCTGTCTTTCCACTTTGTCACTAGCTTCCGACTGTCGGTAGCTATACCACTCAGACCTCTTGTTGCAGGACCACCGAGGCCCTCTGTCCCCCAGCTGCTGGGAGACCTGGGCTCGCTAACAGCTCATAGCAAAGTCCTGCCTCTGGCAAGAAGGCACCTGTAG chm1:+:5305814:-1 chm1:+:5305840:-1 chm1:+:5305866:-1 chm1:+:18444979:-1 chm1:+:25380496:-1 chm1:+:161148745:-1 chm1:+:181381829:-1 chm1:+:243395517:-1 chm1:+:278609537:-1 chm1:+:299923883:-1 chm1:+:388135402:-1 chm1:+:475897534:-1 chm1:+:542284298:-1 chm1:+:577480427:-1 chm1:+:622088036:-1 chm1:+:655859400:-1 chm1:+:837351038:-1 chm1:+:899510213:-1 chm1:+:910315139:-1 chm1:+:917483307:-1 chm1:+:931879450:-1 chm1:+:943541438:-1 chm1:+:1083840998:-1 chm1:+:1101780995:-1 chm1:+:1220485355:-1 chm1:+:1237779999:-1 chm1:+:1275958489:-1 chm1:+:1286856292:-1 chm1:+:1363376351:-1 chm1:+:1363376379:-1 chm1:+:1363639805:-1 chm1:+:1499341615:-1 chm1:+:1667898431:-1 chm1:+:1800002383:-1 chm1:+:1802085668:-1 chm1:+:1894347098:-1 chm1:+:2059585565:-1 chm1:+:2070816229:-1 chm1:+:2159553667:-1 chm1:+:2300913682:-1 chm1:+:2377203482:-1 chm1:+:2377203512:-1 chm1:+:2415608998:-1 chm1:+:2426381055:76 chm1:+:2467990182:-1 chm1:+:2621799450:-1 chm1:+:2653597592:-1 chm1:+:2657356308:-1 chm1:+:2713962965:-1 chm1:+:2767207477:-1 chm1:+:2770034785:-1 chm1:+:2770034813:-1 chm1:+:2825403581:-1 chm1:+:2883683545:-1 chm1:+:2906845632:-1 chm1:+:2961037716:-1 chm1:+:3055190340:-1 +TTTCTTTCTTTCTGTCTGTACTCTTTCTTCTTTCTTTCTTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTCCTACCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTTCTTTTCTTTCTTTCTTTCTTTCTCTCTTTCTCTTCTTCTTCTTTTCTTCGTTACTTTCTTTTTCTTTCTTTCCTCTTTCTCTCTCTCTTTCCTCCCTCCCTTCCTCTTCCTCCATCCCTCCCTTCCTTTCTTGCTTTTTTTTTTTTCTTGCTTCGCTACCCAGGCTGGAGTGCAGTGGCATGGATCATAGCTCACTGCAGCCCTTGAACTTCTGGGCTCAAGCAATCTTCCTGCTTCGGCCACCCCTGGGATTTACAGGTGTAGAACCTGTGGCGCCCAGACCTTGGCCACTTTCTTTATTCTAACTTCTTTGTTCCATACTTTGCTTCTTTCCCTTGGATCCATCCCTACCAGCCTCCCTGTCCACTCCAGTGATAGGACACTCACGTCTTGCCAAGTCAATGTAACCCAGACCCTTCTCATTTAAACCTAGTCTCCTTTGGTTAAACTAGTCAATTCAGGATTCTCACAATCAATCTGAGTTTAAATCTTAATTAGTTGAAAGATTTTCATATCTCTGTCTTTCCACTTTGTCACTAGCTTCCGACTGTCGGTAGCTATACCACTCAGACCTCTTGTTGCAGGACCACCGAGGCCCTCTGTCCCCCAGCTGCTGGGAGACCTGGGCTCGCTAACAGCTCATAGCAAAGTCCTGCCTCTGGCAAGAAGGCACCTGTAG chm1:+:31659176:-1 chm1:+:31975141:-1 chm1:+:54875044:-1 chm1:+:155271441:-1 chm1:+:198523655:-1 chm1:+:229713698:-1 chm1:+:238626115:-1 chm1:+:240881498:-1 chm1:+:292890583:-1 chm1:+:474827813:-1 chm1:+:537926713:-1 chm1:+:615810249:-1 chm1:+:676143609:-1 chm1:+:694849314:-1 chm1:+:770368869:-1 chm1:+:1007996146:-1 chm1:+:1019074946:-1 chm1:+:1022679472:-1 chm1:+:1054352801:-1 chm1:+:1281432408:-1 chm1:+:1300326106:-1 chm1:+:1306019831:-1 chm1:+:1415722379:-1 chm1:+:1558633378:-1 chm1:+:1810438811:-1 chm1:+:1852381591:-1 chm1:+:1873429696:-1 chm1:+:1950432402:-1 chm1:+:2003697253:-1 chm1:+:2065079159:-1 chm1:+:2068958098:-1 chm1:+:2182070564:-1 chm1:+:2423893744:-1 chm1:+:2488056614:-1 chm1:+:2634837459:-1 chm1:+:2639126340:-1 chm1:+:2665563257:-1 chm1:+:2710540119:-1 chm1:+:2781175151:-1 chm1:+:2855306618:-1 chm1:+:2855374804:-1 chm1:+:2860344353:-1 chm1:+:2867173946:-1 chm1:+:2882712849:-1 chm1:+:2930926560:-1 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+TTTCTTTCTTTCTGTCTGTACTCTTTCTTCTTTCTTTCTTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTCCTACCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTTCTTTTCTTTCTTTCTTTCTTTCTCTCTTTCTCTTCTTCTTCTTTTCTTCGTTACTTTCTTTTTCTTTCTTTCCTCTTTCTCTCTCTCTTTCCTCCCTCCCTTCCTCTTCCTCCATCCCTCCCTTCCTTTCTTGCTTTTTTTTTTTTCTTGCTTCGCTACCCAGGCTGGAGTGCAGTGGCATGGATCATAGCTCACTGCAGCCCTTGAACTTCTGGGCTCAAGCAATCTTCCTGCTTCGGCCACCCCTGGGATTTACAGGTGTAGAACCTGTGGCGCCCAGACCTTGGCCACTTTCTTTATTCTAACTTCTTTGTTCCATACTTTGCTTCTTTCCCTTGGATCCATCCCTACCAGCCTCCCTGTCCACTCCAGTGATAGGACACTCACGTCTTGCCAAGTCAATGTAACCCAGACCCTTCTCATTTAAACCTAGTCTCCTTTGGTTAAACTAGTCAATTCAGGATTCTCACAATCAATCTGAGTTTAAATCTTAATTAGTTGAAAGATTTTCATATCTCTGTCTTTCCACTTTGTCACTAGCTTCCGACTGTCGGTAGCTATACCACTCAGACCTCTTGTTGCAGGACCACCGAGGCCCTCTGTCCCCCAGCTGCTGGGAGACCTGGGCTCGCTAACAGCTCATAGCAAAGTCCTGCCTCTGGCAAGAAGGCACCTGTAG chm1:+:181963913:-1 chm1:+:855777318:-1 chm1:+:1213229975:-1 chm1:+:1577454814:-1 chm1:+:1884588482:-1 +TTTCTTTCTTTCTGTCTGTACTCTTTCTTCTTTCTTTCTTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTCCTACCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTTCTTTTCTTTCTTTCTTTCTTTCTCTCTTTCTCTTCTTCTTCTTTTCTTCGTTACTTTCTTTTTCTTTCTTTCCTCTTTCTCTCTCTCTTTCCTCCCTCCCTTCCTCTTCCTCCATCCCTCCCTTCCTTTCTTGCTTTTTTTTTTTTCTTGCTTCGCTACCCAGGCTGGAGTGCAGTGGCATGGATCATAGCTCACTGCAGCCCTTGAACTTCTGGGCTCAAGCAATCTTCCTGCTTCGGCCACCCCTGGGATTTACAGGTGTAGAACCTGTGGCGCCCAGACCTTGGCCACTTTCTTTATTCTAACTTCTTTGTTCCATACTTTGCTTCTTTCCCTTGGATCCATCCCTACCAGCCTCCCTGTCCACTCCAGTGATAGGACACTCACGTCTTGCCAAGTCAATGTAACCCAGACCCTTCTCATTTAAACCTAGTCTCCTTTGGTTAAACTAGTCAATTCAGGATTCTCACAATCAATCTGAGTTTAAATCTTAATTAGTTGAAAGATTTTCATATCTCTGTCTTTCCACTTTGTCACTAGCTTCCGACTGTCGGTAGCTATACCACTCAGACCTCTTGTTGCAGGACCACCGAGGCCCTCTGTCCCCCAGCTGCTGGGAGACCTGGGCTCGCTAACAGCTCATAGCAAAGTCCTGCCTCTGGCAAGAAGGCACCTGTAG chm1:+:1696237544:-1 chm1:+:1696895513:-1 chm1:+:1841409764:-1 chm1:+:2025625732:-1 chm1:+:2902829854:-1 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chm1:+:2495028412:-1 +TTTCTTTCTTTCTGTCTGTACTCTTTCTTCTTTCTTTCTTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTCCTACCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTTCTTTTCTTTCTTTCTTTCTTTCTCTCTTTCTCTTCTTCTTCTTTTCTTCGTTACTTTCTTTTTCTTTCTTTCCTCTTTCTCTCTCTCTTTCCTCCCTCCCTTCCTCTTCCTCCATCCCTCCCTTCCTTTCTTGCTTTTTTTTTTTTCTTGCTTCGCTACCCAGGCTGGAGTGCAGTGGCATGGATCATAGCTCACTGCAGCCCTTGAACTTCTGGGCTCAAGCAATCTTCCTGCTTCGGCCACCCCTGGGATTTACAGGTGTAGAACCTGTGGCGCCCAGACCTTGGCCACTTTCTTTATTCTAACTTCTTTGTTCCATACTTTGCTTCTTTCCCTTGGATCCATCCCTACCAGCCTCCCTGTCCACTCCAGTGATAGGACACTCACGTCTTGCCAAGTCAATGTAACCCAGACCCTTCTCATTTAAACCTAGTCTCCTTTGGTTAAACTAGTCAATTCAGGATTCTCACAATCAATCTGAGTTTAAATCTTAATTAGTTGAAAGATTTTCATATCTCTGTCTTTCCACTTTGTCACTAGCTTCCGACTGTCGGTAGCTATACCACTCAGACCTCTTGTTGCAGGACCACCGAGGCCCTCTGTCCCCCAGCTGCTGGGAGACCTGGGCTCGCTAACAGCTCATAGCAAAGTCCTGCCTCTGGCAAGAAGGCACCTGTAG chm1:+:1055691947:-1 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chm1:+:1616251102:-1 chm1:+:2426381048:76 +TTTCTTTCTTTCTGTCTGTACTCTTTCTTCTTTCTTTCTTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTCCTACCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTTCTTTTCTTTCTTTCTTTCTTTCTCTCTTTCTCTTCTTCTTCTTTTCTTCGTTACTTTCTTTTTCTTTCTTTCCTCTTTCTCTCTCTCTTTCCTCCCTCCCTTCCTCTTCCTCCATCCCTCCCTTCCTTTCTTGCTTTTTTTTTTTTCTTGCTTCGCTACCCAGGCTGGAGTGCAGTGGCATGGATCATAGCTCACTGCAGCCCTTGAACTTCTGGGCTCAAGCAATCTTCCTGCTTCGGCCACCCCTGGGATTTACAGGTGTAGAACCTGTGGCGCCCAGACCTTGGCCACTTTCTTTATTCTAACTTCTTTGTTCCATACTTTGCTTCTTTCCCTTGGATCCATCCCTACCAGCCTCCCTGTCCACTCCAGTGATAGGACACTCACGTCTTGCCAAGTCAATGTAACCCAGACCCTTCTCATTTAAACCTAGTCTCCTTTGGTTAAACTAGTCAATTCAGGATTCTCACAATCAATCTGAGTTTAAATCTTAATTAGTTGAAAGATTTTCATATCTCTGTCTTTCCACTTTGTCACTAGCTTCCGACTGTCGGTAGCTATACCACTCAGACCTCTTGTTGCAGGACCACCGAGGCCCTCTGTCCCCCAGCTGCTGGGAGACCTGGGCTCGCTAACAGCTCATAGCAAAGTCCTGCCTCTGGCAAGAAGGCACCTGTAG chm1:+:66081176:-1 chm1:+:621058259:-1 chm1:+:717041568:-1 chm1:+:1105246060:-1 chm1:+:1254917146:-1 chm1:+:1653487115:-1 chm1:+:1674837099:-1 chm1:+:2488272952:-1 chm1:+:2564060160:-1 chm1:+:2627828457:-1 chm1:+:2753268810:-1 chm1:+:2767245108:-1 chm1:+:2865548590:-1 +TTTCTTTCTTTCTGTCTGTACTCTTTCTTCTTTCTTTCTTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTCCTACCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTTCTTTTCTTTCTTTCTTTCTTTCTCTCTTTCTCTTCTTCTTCTTTTCTTCGTTACTTTCTTTTTCTTTCTTTCCTCTTTCTCTCTCTCTTTCCTCCCTCCCTTCCTCTTCCTCCATCCCTCCCTTCCTTTCTTGCTTTTTTTTTTTTCTTGCTTCGCTACCCAGGCTGGAGTGCAGTGGCATGGATCATAGCTCACTGCAGCCCTTGAACTTCTGGGCTCAAGCAATCTTCCTGCTTCGGCCACCCCTGGGATTTACAGGTGTAGAACCTGTGGCGCCCAGACCTTGGCCACTTTCTTTATTCTAACTTCTTTGTTCCATACTTTGCTTCTTTCCCTTGGATCCATCCCTACCAGCCTCCCTGTCCACTCCAGTGATAGGACACTCACGTCTTGCCAAGTCAATGTAACCCAGACCCTTCTCATTTAAACCTAGTCTCCTTTGGTTAAACTAGTCAATTCAGGATTCTCACAATCAATCTGAGTTTAAATCTTAATTAGTTGAAAGATTTTCATATCTCTGTCTTTCCACTTTGTCACTAGCTTCCGACTGTCGGTAGCTATACCACTCAGACCTCTTGTTGCAGGACCACCGAGGCCCTCTGTCCCCCAGCTGCTGGGAGACCTGGGCTCGCTAACAGCTCATAGCAAAGTCCTGCCTCTGGCAAGAAGGCACCTGTAG chm1:+:462851622:-1 chm1:+:1287813386:-1 chm1:+:1430022044:-1 chm1:+:1511579921:-1 chm1:+:2161031476:-1 chm1:+:2185614473:-1 chm1:+:2431981791:-1 chm1:+:2601639949:-1 chm1:+:2759664390:-1 chm1:+:2916522508:-1 +TTTCTTTCTTTCTGTCTGTACTCTTTCTTCTTTCTTTCTTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTCCTACCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTTCTTTTCTTTCTTTCTTTCTTTCTCTCTTTCTCTTCTTCTTCTTTTCTTCGTTACTTTCTTTTTCTTTCTTTCCTCTTTCTCTCTCTCTTTCCTCCCTCCCTTCCTCTTCCTCCATCCCTCCCTTCCTTTCTTGCTTTTTTTTTTTTCTTGCTTCGCTACCCAGGCTGGAGTGCAGTGGCATGGATCATAGCTCACTGCAGCCCTTGAACTTCTGGGCTCAAGCAATCTTCCTGCTTCGGCCACCCCTGGGATTTACAGGTGTAGAACCTGTGGCGCCCAGACCTTGGCCACTTTCTTTATTCTAACTTCTTTGTTCCATACTTTGCTTCTTTCCCTTGGATCCATCCCTACCAGCCTCCCTGTCCACTCCAGTGATAGGACACTCACGTCTTGCCAAGTCAATGTAACCCAGACCCTTCTCATTTAAACCTAGTCTCCTTTGGTTAAACTAGTCAATTCAGGATTCTCACAATCAATCTGAGTTTAAATCTTAATTAGTTGAAAGATTTTCATATCTCTGTCTTTCCACTTTGTCACTAGCTTCCGACTGTCGGTAGCTATACCACTCAGACCTCTTGTTGCAGGACCACCGAGGCCCTCTGTCCCCCAGCTGCTGGGAGACCTGGGCTCGCTAACAGCTCATAGCAAAGTCCTGCCTCTGGCAAGAAGGCACCTGTAG chm1:+:65751791:-1 chm1:+:600383963:-1 chm1:+:758201128:-1 chm1:+:1047623093:-1 chm1:+:1238590949:-1 chm1:+:1298727290:-1 chm1:+:1806456311:-1 chm1:+:2194791518:-1 chm1:+:2388389225:-1 +TTTCTTTCTTTCTGTCTGTACTCTTTCTTCTTTCTTTCTTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTCCTACCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTTCTTTTCTTTCTTTCTTTCTTTCTCTCTTTCTCTTCTTCTTCTTTTCTTCGTTACTTTCTTTTTCTTTCTTTCCTCTTTCTCTCTCTCTTTCCTCCCTCCCTTCCTCTTCCTCCATCCCTCCCTTCCTTTCTTGCTTTTTTTTTTTTCTTGCTTCGCTACCCAGGCTGGAGTGCAGTGGCATGGATCATAGCTCACTGCAGCCCTTGAACTTCTGGGCTCAAGCAATCTTCCTGCTTCGGCCACCCCTGGGATTTACAGGTGTAGAACCTGTGGCGCCCAGACCTTGGCCACTTTCTTTATTCTAACTTCTTTGTTCCATACTTTGCTTCTTTCCCTTGGATCCATCCCTACCAGCCTCCCTGTCCACTCCAGTGATAGGACACTCACGTCTTGCCAAGTCAATGTAACCCAGACCCTTCTCATTTAAACCTAGTCTCCTTTGGTTAAACTAGTCAATTCAGGATTCTCACAATCAATCTGAGTTTAAATCTTAATTAGTTGAAAGATTTTCATATCTCTGTCTTTCCACTTTGTCACTAGCTTCCGACTGTCGGTAGCTATACCACTCAGACCTCTTGTTGCAGGACCACCGAGGCCCTCTGTCCCCCAGCTGCTGGGAGACCTGGGCTCGCTAACAGCTCATAGCAAAGTCCTGCCTCTGGCAAGAAGGCACCTGTAG chm1:+:234425663:-1 chm1:+:302106423:-1 chm1:+:384578237:-1 chm1:+:625939380:-1 chm1:+:991665471:-1 chm1:+:1066178771:-1 chm1:+:1067253027:-1 chm1:+:1160435618:-1 chm1:+:1426050986:-1 chm1:+:1792611952:-1 +TTTCTTTCTTTCTGTCTGTACTCTTTCTTCTTTCTTTCTTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTCCTACCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTTCTTTTCTTTCTTTCTTTCTTTCTCTCTTTCTCTTCTTCTTCTTTTCTTCGTTACTTTCTTTTTCTTTCTTTCCTCTTTCTCTCTCTCTTTCCTCCCTCCCTTCCTCTTCCTCCATCCCTCCCTTCCTTTCTTGCTTTTTTTTTTTTCTTGCTTCGCTACCCAGGCTGGAGTGCAGTGGCATGGATCATAGCTCACTGCAGCCCTTGAACTTCTGGGCTCAAGCAATCTTCCTGCTTCGGCCACCCCTGGGATTTACAGGTGTAGAACCTGTGGCGCCCAGACCTTGGCCACTTTCTTTATTCTAACTTCTTTGTTCCATACTTTGCTTCTTTCCCTTGGATCCATCCCTACCAGCCTCCCTGTCCACTCCAGTGATAGGACACTCACGTCTTGCCAAGTCAATGTAACCCAGACCCTTCTCATTTAAACCTAGTCTCCTTTGGTTAAACTAGTCAATTCAGGATTCTCACAATCAATCTGAGTTTAAATCTTAATTAGTTGAAAGATTTTCATATCTCTGTCTTTCCACTTTGTCACTAGCTTCCGACTGTCGGTAGCTATACCACTCAGACCTCTTGTTGCAGGACCACCGAGGCCCTCTGTCCCCCAGCTGCTGGGAGACCTGGGCTCGCTAACAGCTCATAGCAAAGTCCTGCCTCTGGCAAGAAGGCACCTGTAG chm1:+:288815259:-1 chm1:+:312004172:-1 chm1:+:359694409:-1 chm1:+:523091674:-1 chm1:+:961216566:-1 chm1:+:1019669736:-1 chm1:+:1030939122:-1 chm1:+:1296959932:-1 chm1:+:1688550291:-1 chm1:+:1705969181:-1 chm1:+:1804223132:-1 chm1:+:2069532051:-1 chm1:+:2118916406:-1 chm1:+:2134778008:-1 chm1:+:2276341507:-1 chm1:+:2421224433:-1 chm1:+:2426381052:76 chm1:+:2559146699:-1 chm1:+:2602359641:-1 chm1:+:2890395845:-1 +TTTCTTTCTTTCTGTCTGTACTCTTTCTTCTTTCTTTCTTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTCCTACCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTTCTTTTCTTTCTTTCTTTCTTTCTCTCTTTCTCTTCTTCTTCTTTTCTTCGTTACTTTCTTTTTCTTTCTTTCCTCTTTCTCTCTCTCTTTCCTCCCTCCCTTCCTCTTCCTCCATCCCTCCCTTCCTTTCTTGCTTTTTTTTTTTTCTTGCTTCGCTACCCAGGCTGGAGTGCAGTGGCATGGATCATAGCTCACTGCAGCCCTTGAACTTCTGGGCTCAAGCAATCTTCCTGCTTCGGCCACCCCTGGGATTTACAGGTGTAGAACCTGTGGCGCCCAGACCTTGGCCACTTTCTTTATTCTAACTTCTTTGTTCCATACTTTGCTTCTTTCCCTTGGATCCATCCCTACCAGCCTCCCTGTCCACTCCAGTGATAGGACACTCACGTCTTGCCAAGTCAATGTAACCCAGACCCTTCTCATTTAAACCTAGTCTCCTTTGGTTAAACTAGTCAATTCAGGATTCTCACAATCAATCTGAGTTTAAATCTTAATTAGTTGAAAGATTTTCATATCTCTGTCTTTCCACTTTGTCACTAGCTTCCGACTGTCGGTAGCTATACCACTCAGACCTCTTGTTGCAGGACCACCGAGGCCCTCTGTCCCCCAGCTGCTGGGAGACCTGGGCTCGCTAACAGCTCATAGCAAAGTCCTGCCTCTGGCAAGAAGGCACCTGTAG chm1:+:351770387:-1 chm1:+:440308436:-1 chm1:+:498596467:-1 chm1:+:704212809:-1 chm1:+:909864345:-1 chm1:+:909864562:-1 chm1:+:963566648:-1 chm1:+:1148390395:-1 chm1:+:1526948825:-1 chm1:+:1628269797:-1 chm1:+:1658901492:-1 chm1:+:1772201130:-1 chm1:+:2169200400:-1 chm1:+:2257325837:-1 +TTTCTTTCTTTCTGTCTGTACTCTTTCTTCTTTCTTTCTTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTCCTACCTTCCTTCCTTCCTTCCTTCCTTCTTCCTTTCTTTTCTTTCTTTCTTTCTTTCTCTCTTTCTCTTCTTCTTCTTTTCTTCGTTACTTTCTTTTTCTTTCTTTCCTCTTTCTCTCTCTCTTTCCTCCCTCCCTTCCTCTTCCTCCATCCCTCCCTTCCTTTCTTGCTTTTTTTTTTTTCTTGCTTCGCTACCCAGGCTGGAGTGCAGTGGCATGGATCATAGCTCACTGCAGCCCTTGAACTTCTGGGCTCAAGCAATCTTCCTGCTTCGGCCACCCCTGGGATTTACAGGTGTAGAACCTGTGGCGCCCAGACCTTGGCCACTTTCTTTATTCTAACTTCTTTGTTCCATACTTTGCTTCTTTCCCTTGGATCCATCCCTACCAGCCTCCCTGTCCACTCCAGTGATAGGACACTCACGTCTTGCCAAGTCAATGTAACCCAGACCCTTCTCATTTAAACCTAGTCTCCTTTGGTTAAACTAGTCAATTCAGGATTCTCACAATCAATCTGAGTTTAAATCTTAATTAGTTGAAAGATTTTCATATCTCTGTCTTTCCACTTTGTCACTAGCTTCCGACTGTCGGTAGCTATACCACTCAGACCTCTTGTTGCAGGACCACCGAGGCCCTCTGTCCCCCAGCTGCTGGGAGACCTGGGCTCGCTAACAGCTCATAGCAAAGTCCTGCCTCTGGCAAGAAGGCACCTGTAG chm1:+:116742844:-1 chm1:+:236817873:-1 chm1:+:618459095:-1 chm1:+:681578331:-1 chm1:+:706856564:-1 chm1:+:1063376099:-1 chm1:+:1063376123:-1 chm1:+:1214087972:-1 chm1:+:1387869326:-1 chm1:+:1451235558:-1 chm1:+:1656688404:-1 chm1:+:1687878616:-1 chm1:+:1856475276:-1 chm1:+:2023392791:-1 chm1:+:2170492158:-1 chm1:+:2367452569:-1 chm1:+:2388204786:-1 chm1:+:2514123348:-1 chm1:+:2621331842:-1 chm1:+:2652520964:-1 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+AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACT chm1:+:2817198734:47 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACT chm1:+:2817198740:47 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACT chm1:+:2817198741:47 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACT chm1:+:2817198725:47 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACT chm1:+:2817198726:47 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACT chm1:+:2817198736:47 +AAACACAGGCACCACAGGGTCACGCGTTCAGTGAAATGTTGGTTGTTTTTCTAAACTATGAGAAGATAAGAGGCAGTGAAATCTTCCCTCTGCTTAAGCCCTTTTAGTGTAAATATTCTTTCAAATCAACCCCAGTATGGACTGGGCCTGGAGAAGCAACCAAGGTAGCACAGTCATGGTTGCTCCAACCTCTGCGAGCTACCTGATCCAGGTCCTGCTATGAAGGGACAAGGCCCGGACAAGGTGCCCTCTGAGAACCCCGAGGCTCCTCCAGTAAGGATGACTCCCTAAGAGACAGACGGAAGCTGCCTGAGGGAAATTTCATCTCCCTGAGCTTGTAGCTGTAGTTTTGGTCGAGGAGAGCAGCAAGCACCCATTGTCGCTCTCCAAACTCAAACATAGCTGAGCAACAGGAGAGGATGGCGAAGGGTGTCTGCTCCAGCACACCATGCCAAATCCGAAGCTAGGAGCAGCTGTGGTGGGAATAAGGGTGCATTTTATCCCAGCTTGGCCTCAAGGAGTCTTGGCCTCCTGCTTGCTGGCCTTCCAGCCTTTGTGGTCCCAGCTAATCTGTTTCAAGGGCATCTGTGGTTCCACTCCAACGTTAAGCCTGAAGTTGGTACTGAGTGTCCCCAAGCAGACAGCCACATGGTTGGAAGGTTCATACTTGGTTTCCTAAACTGTATTAGGTCAGGTTCTCAGAGGGGACAGAACTAATAGGCGATATCTATCTATCTATTATCTATCTATCTATCTATCTATACTATCTATCTGGAGTTTATTAAGTATTAACTTACACT chm1:+:3014694430:-1 +AGTGTAAGTTAATACTTAATAAACTCCAGATAGATAGTATAGATAGATAGATAGATAGATAATAGATAGATAGATATCGCCTATTAGTTCTGTCCCCTCTGAGAACCTGACCTAATACAGTTTAGGAAACCAAGTATGAACCTTCCAACCATGTGGCTGTCTGCTTGGGGACACTCAGTACCAACTTCAGGCTTAACGTTGGAGTGGAACCACAGATGCCCTTGAAACAGATTAGCTGGGACCACAAAGGCTGGAAGGCCAGCAAGCAGGAGGCCAAGACTCCTTGAGGCCAAGCTGGGATAAAATGCACCCTTATTCCCACCACAGCTGCTCCTAGCTTCGGATTTGGCATGGTGTGCTGGAGCAGACACCCTTCGCCATCCTCTCCTGTTGCTCAGCTATGTTTGAGTTTGGAGAGCGACAATGGGTGCTTGCTGCTCTCCTCGACCAAAACTACAGCTACAAGCTCAGGGAGATGAAATTTCCCTCAGGCAGCTTCCGTCTGTCTCTTAGGGAGTCATCCTTACTGGAGGAGCCTCGGGGTTCTCAGAGGGCACCTTGTCCGGGCCTTGTCCCTTCATAGCAGGACCTGGATCAGGTAGCTCGCAGAGGTTGGAGCAACCATGACTGTGCTACCTTGGTTGCTTCTCCAGGCCCAGTCCATACTGGGGTTGATTTGAAAGAATATTTACACTAAAAGGGCTTAAGCAGAGGGAAGATTTCACTGCCTCTTATCTTCTCATAGTTTAGAAAAACAACCAACATTTCACTGAACGCGTGACCCTGTGGTGCCTGTGTTT chm1:+:2476908040:-1 +AGTGTAAGTTAATACTTAATAAACTCCAGATAGATAGTATAGATAGATAGATAGATAGATAATAGATAGATAGATATCGCCTATTAGTTCTGTCCCCTCTGAGAACCTGACCTAATACAGTTTAGGAAACCAAGTATGAACCTTCCAACCATGTGGCTGTCTGCTTGGGGACACTCAGTACCAACTTCAGGCTTAACGTTGGAGTGGAACCACAGATGCCCTTGAAACAGATTAGCTGGGACCACAAAGGCTGGAAGGCCAGCAAGCAGGAGGCCAAGACTCCTTGAGGCCAAGCTGGGATAAAATGCACCCTTATTCCCACCACAGCTGCTCCTAGCTTCGGATTTGGCATGGTGTGCTGGAGCAGACACCCTTCGCCATCCTCTCCTGTTGCTCAGCTATGTTTGAGTTTGGAGAGCGACAATGGGTGCTTGCTGCTCTCCTCGACCAAAACTACAGCTACAAGCTCAGGGAGATGAAATTTCCCTCAGGCAGCTTCCGTCTGTCTCTTAGGGAGTCATCCTTACTGGAGGAGCCTCGGGGTTCTCAGAGGGCACCTTGTCCGGGCCTTGTCCCTTCATAGCAGGACCTGGATCAGGTAGCTCGCAGAGGTTGGAGCAACCATGACTGTGCTACCTTGGTTGCTTCTCCAGGCCCAGTCCATACTGGGGTTGATTTGAAAGAATATTTACACTAAAAGGGCTTAAGCAGAGGGAAGATTTCACTGCCTCTTATCTTCTCATAGTTTAGAAAAACAACCAACATTTCACTGAACGCGTGACCCTGTGGTGCCTGTGTTT chm1:+:1019559936:-1 +AGTGTAAGTTAATACTTAATAAACTCCAGATAGATAGTATAGATAGATAGATAGATAGATAATAGATAGATAGATATCGCCTATTAGTTCTGTCCCCTCTGAGAACCTGACCTAATACAGTTTAGGAAACCAAGTATGAACCTTCCAACCATGTGGCTGTCTGCTTGGGGACACTCAGTACCAACTTCAGGCTTAACGTTGGAGTGGAACCACAGATGCCCTTGAAACAGATTAGCTGGGACCACAAAGGCTGGAAGGCCAGCAAGCAGGAGGCCAAGACTCCTTGAGGCCAAGCTGGGATAAAATGCACCCTTATTCCCACCACAGCTGCTCCTAGCTTCGGATTTGGCATGGTGTGCTGGAGCAGACACCCTTCGCCATCCTCTCCTGTTGCTCAGCTATGTTTGAGTTTGGAGAGCGACAATGGGTGCTTGCTGCTCTCCTCGACCAAAACTACAGCTACAAGCTCAGGGAGATGAAATTTCCCTCAGGCAGCTTCCGTCTGTCTCTTAGGGAGTCATCCTTACTGGAGGAGCCTCGGGGTTCTCAGAGGGCACCTTGTCCGGGCCTTGTCCCTTCATAGCAGGACCTGGATCAGGTAGCTCGCAGAGGTTGGAGCAACCATGACTGTGCTACCTTGGTTGCTTCTCCAGGCCCAGTCCATACTGGGGTTGATTTGAAAGAATATTTACACTAAAAGGGCTTAAGCAGAGGGAAGATTTCACTGCCTCTTATCTTCTCATAGTTTAGAAAAACAACCAACATTTCACTGAACGCGTGACCCTGTGGTGCCTGTGTTT chm1:+:1812965590:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:1298269338:66 chm1:+:1298780561:90 chm1:+:1973078698:-1 chm1:+:2007117734:-1 chm1:+:2330374604:-1 chm1:+:2610866699:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:13785747:-1 chm1:+:15411388:-1 chm1:+:15496369:-1 chm1:+:26842451:-1 chm1:+:33180139:-1 chm1:+:33519923:-1 chm1:+:112427859:-1 chm1:+:151710812:-1 chm1:+:153821671:-1 chm1:+:154072559:-1 chm1:+:167951044:-1 chm1:+:183720926:-1 chm1:+:300755561:-1 chm1:+:328673248:-1 chm1:+:335041767:-1 chm1:+:360418668:-1 chm1:+:367518179:-1 chm1:+:368702169:-1 chm1:+:425365770:-1 chm1:+:468396044:-1 chm1:+:490863084:-1 chm1:+:498229578:-1 chm1:+:515738404:-1 chm1:+:516263427:-1 chm1:+:539017001:-1 chm1:+:572634964:-1 chm1:+:590913436:-1 chm1:+:593878097:-1 chm1:+:601459662:-1 chm1:+:664359521:-1 chm1:+:677148780:-1 chm1:+:685524163:-1 chm1:+:693230638:-1 chm1:+:702103635:-1 chm1:+:707523217:-1 chm1:+:730339723:-1 chm1:+:810743114:-1 chm1:+:830893651:-1 chm1:+:856627755:-1 chm1:+:876035179:-1 chm1:+:894781964:-1 chm1:+:899064057:-1 chm1:+:931876813:-1 chm1:+:972226105:-1 chm1:+:993629684:-1 chm1:+:1015833226:-1 chm1:+:1021732577:-1 chm1:+:1091954308:-1 chm1:+:1115470524:-1 chm1:+:1152256701:-1 chm1:+:1169704389:-1 chm1:+:1201815061:-1 chm1:+:1202056315:-1 chm1:+:1212526468:-1 chm1:+:1221713352:-1 chm1:+:1226415284:-1 chm1:+:1283631586:-1 chm1:+:1298741245:-1 chm1:+:1305638218:-1 chm1:+:1338698439:-1 chm1:+:1347438669:-1 chm1:+:1361781238:-1 chm1:+:1392301404:-1 chm1:+:1394915492:-1 chm1:+:1396956432:-1 chm1:+:1472846614:-1 chm1:+:1485947260:-1 chm1:+:1493213262:-1 chm1:+:1493293708:-1 chm1:+:1503479385:-1 chm1:+:1508152889:-1 chm1:+:1616634551:-1 chm1:+:1641852539:-1 chm1:+:1646970417:-1 chm1:+:1670620589:-1 chm1:+:1672910491:-1 chm1:+:1688516910:-1 chm1:+:1704665616:-1 chm1:+:1712528251:-1 chm1:+:1762680628:-1 chm1:+:1783336752:-1 chm1:+:1825343627:-1 chm1:+:1861967132:-1 chm1:+:1863544639:-1 chm1:+:1916487225:-1 chm1:+:1923270503:-1 chm1:+:1935361249:-1 chm1:+:1957595694:-1 chm1:+:1976947406:-1 chm1:+:2017198474:-1 chm1:+:2021819977:-1 chm1:+:2030897952:-1 chm1:+:2073318462:-1 chm1:+:2080632142:-1 chm1:+:2155100353:-1 chm1:+:2169041058:-1 chm1:+:2183681128:-1 chm1:+:2276132806:-1 chm1:+:2292610640:-1 chm1:+:2299532933:-1 chm1:+:2302971702:-1 chm1:+:2332503318:-1 chm1:+:2343228372:-1 chm1:+:2367095455:-1 chm1:+:2381009216:-1 chm1:+:2381152608:-1 chm1:+:2397490236:-1 chm1:+:2402774846:-1 chm1:+:2422754172:-1 chm1:+:2426614833:-1 chm1:+:2431281115:-1 chm1:+:2431713358:-1 chm1:+:2438251420:-1 chm1:+:2439259817:-1 chm1:+:2439361583:-1 chm1:+:2440101567:-1 chm1:+:2476887477:-1 chm1:+:2495186883:-1 chm1:+:2545320525:-1 chm1:+:2545811826:-1 chm1:+:2553790674:-1 chm1:+:2553962973:-1 chm1:+:2558935315:-1 chm1:+:2560680510:-1 chm1:+:2561714261:-1 chm1:+:2572352052:-1 chm1:+:2603515148:-1 chm1:+:2618625188:-1 chm1:+:2669881329:-1 chm1:+:2674064588:-1 chm1:+:2682358052:-1 chm1:+:2698442736:-1 chm1:+:2700845067:-1 chm1:+:2709594775:-1 chm1:+:2709711347:-1 chm1:+:2710023334:-1 chm1:+:2718231720:-1 chm1:+:2721535606:-1 chm1:+:2735130298:-1 chm1:+:2750243009:-1 chm1:+:2758581911:-1 chm1:+:2761673906:-1 chm1:+:2765883015:-1 chm1:+:2767346591:-1 chm1:+:2815431443:-1 chm1:+:2819374788:-1 chm1:+:2849363279:-1 chm1:+:2853111443:-1 chm1:+:2860097873:-1 chm1:+:2860613511:-1 chm1:+:2861579669:-1 chm1:+:2881533858:-1 chm1:+:2916896231:-1 chm1:+:2921948861:-1 chm1:+:2923090781:-1 chm1:+:2925586201:-1 chm1:+:2949888263:-1 chm1:+:2954871553:-1 chm1:+:2999787434:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:211800606:-1 chm1:+:247469365:-1 chm1:+:263891261:-1 chm1:+:296848035:-1 chm1:+:541977874:-1 chm1:+:661910018:-1 chm1:+:747426877:-1 chm1:+:844182228:-1 chm1:+:1035741393:-1 chm1:+:1051859708:-1 chm1:+:1058194593:-1 chm1:+:1214415444:-1 chm1:+:1217908991:-1 chm1:+:1376976285:-1 chm1:+:1377055504:-1 chm1:+:1431406724:-1 chm1:+:1678926343:-1 chm1:+:1744052800:-1 chm1:+:1795858259:-1 chm1:+:2003330040:-1 chm1:+:2074071740:-1 chm1:+:2074302821:-1 chm1:+:2519773090:-1 chm1:+:2537555869:-1 chm1:+:2541146698:-1 chm1:+:2541424174:-1 chm1:+:2628709407:-1 chm1:+:2673974601:-1 chm1:+:2677615924:-1 chm1:+:2719585785:-1 chm1:+:2738297838:-1 chm1:+:2767427227:-1 chm1:+:2872498090:-1 chm1:+:2912337730:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:93321545:-1 chm1:+:202219104:-1 chm1:+:413767941:-1 chm1:+:471736167:-1 chm1:+:841656736:-1 chm1:+:1136872258:-1 chm1:+:1221855790:-1 chm1:+:1222584902:-1 chm1:+:1707183393:-1 chm1:+:1834617488:-1 chm1:+:1941377085:-1 chm1:+:2046038021:-1 chm1:+:2114088815:-1 chm1:+:2275723848:-1 chm1:+:2353105373:-1 chm1:+:2530963573:-1 chm1:+:2535877440:-1 chm1:+:2641932679:-1 chm1:+:2669549487:-1 chm1:+:2849419384:-1 chm1:+:2956820447:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:26760402:-1 chm1:+:28348485:-1 chm1:+:40889649:-1 chm1:+:44382598:-1 chm1:+:150286121:-1 chm1:+:248182347:-1 chm1:+:259074321:-1 chm1:+:860449843:-1 chm1:+:876260487:-1 chm1:+:1022818506:-1 chm1:+:1023160867:-1 chm1:+:1332329027:-1 chm1:+:1345586065:-1 chm1:+:1398852398:-1 chm1:+:1557785949:-1 chm1:+:1752797414:-1 chm1:+:2358031036:-1 chm1:+:2376254087:-1 chm1:+:2480621851:-1 chm1:+:2743995806:-1 chm1:+:2803061238:-1 chm1:+:2925697020:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:19941669:-1 chm1:+:27121609:-1 chm1:+:31371477:-1 chm1:+:957623617:-1 chm1:+:1200314048:-1 chm1:+:1426848379:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:35565965:-1 chm1:+:228002217:-1 chm1:+:292328875:-1 chm1:+:350311680:-1 chm1:+:395155902:-1 chm1:+:628716511:-1 chm1:+:642733137:-1 chm1:+:662611404:-1 chm1:+:676102845:-1 chm1:+:1011217884:-1 chm1:+:1015631117:-1 chm1:+:1126951000:-1 chm1:+:1148916529:-1 chm1:+:1298184547:-1 chm1:+:1298878684:-1 chm1:+:1335452260:-1 chm1:+:1449532732:-1 chm1:+:1450716905:-1 chm1:+:1543600878:-1 chm1:+:1656818454:-1 chm1:+:1779413046:-1 chm1:+:1796241372:-1 chm1:+:1824674053:-1 chm1:+:1880639509:-1 chm1:+:2075739750:-1 chm1:+:2111670204:-1 chm1:+:2476317144:-1 chm1:+:2481664858:-1 chm1:+:2485362211:-1 chm1:+:2547490091:-1 chm1:+:2614917275:-1 chm1:+:2630091736:-1 chm1:+:2707613417:-1 chm1:+:2736060036:-1 chm1:+:2852715634:-1 chm1:+:2853715919:-1 chm1:+:2871843472:-1 chm1:+:3025181115:-1 chm1:+:3031024606:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:77585164:-1 chm1:+:78170443:-1 chm1:+:93289120:-1 chm1:+:95021729:-1 chm1:+:155395120:-1 chm1:+:260232963:-1 chm1:+:281608991:-1 chm1:+:293164821:-1 chm1:+:303491782:-1 chm1:+:320707714:-1 chm1:+:382825406:-1 chm1:+:402393077:-1 chm1:+:416307031:-1 chm1:+:545845503:-1 chm1:+:568576773:-1 chm1:+:593716730:-1 chm1:+:626602693:-1 chm1:+:675193089:-1 chm1:+:679407678:-1 chm1:+:841885821:-1 chm1:+:867068489:-1 chm1:+:903927705:-1 chm1:+:910313932:-1 chm1:+:1034175638:-1 chm1:+:1058624559:-1 chm1:+:1176597027:-1 chm1:+:1332799787:-1 chm1:+:1333604774:-1 chm1:+:1382515414:-1 chm1:+:1688142752:-1 chm1:+:1745494647:-1 chm1:+:1768711624:-1 chm1:+:1770873366:-1 chm1:+:1823907307:-1 chm1:+:1954116699:-1 chm1:+:2053019471:-1 chm1:+:2072198766:-1 chm1:+:2257373215:-1 chm1:+:2348284172:-1 chm1:+:2560757578:-1 chm1:+:2573826566:-1 chm1:+:2625097891:-1 chm1:+:2659017569:-1 chm1:+:2664688886:-1 chm1:+:2726512239:-1 chm1:+:2859585473:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:1269563771:-1 chm1:+:1529641978:-1 chm1:+:1645007038:-1 chm1:+:1701927475:-1 chm1:+:2058489036:-1 chm1:+:2167794024:-1 chm1:+:2764472992:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:181306784:-1 chm1:+:205333892:-1 chm1:+:231497075:-1 chm1:+:310972162:-1 chm1:+:388976318:-1 chm1:+:401679248:-1 chm1:+:403598315:-1 chm1:+:504851067:-1 chm1:+:747430759:-1 chm1:+:961112197:-1 chm1:+:1305412498:-1 chm1:+:2019783701:-1 chm1:+:2061106445:-1 chm1:+:2106478955:-1 chm1:+:2300452826:-1 chm1:+:2466371934:-1 chm1:+:2558618527:-1 chm1:+:2721449043:-1 chm1:+:2847483962:-1 chm1:+:2871227136:-1 chm1:+:2948740974:-1 chm1:+:2993091250:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:514292414:-1 chm1:+:1578796645:-1 chm1:+:1580941674:-1 chm1:+:1634553877:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:433755589:-1 chm1:+:1863629786:-1 chm1:+:1946112109:-1 chm1:+:2025555899:-1 chm1:+:3011481166:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:115994729:-1 chm1:+:789221369:-1 chm1:+:1160282875:-1 chm1:+:1298269337:66 chm1:+:1298780560:90 chm1:+:2106581183:-1 chm1:+:2157757292:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:434749282:-1 chm1:+:729299118:-1 chm1:+:1031674381:-1 chm1:+:1046939646:-1 chm1:+:1617300372:-1 chm1:+:2404091136:-1 chm1:+:2503070937:-1 chm1:+:2807580879:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:593703844:-1 chm1:+:659826039:-1 chm1:+:864761717:-1 chm1:+:864872578:-1 chm1:+:936541712:-1 chm1:+:956866105:-1 chm1:+:963409831:-1 chm1:+:1093376419:-1 chm1:+:1112648825:-1 chm1:+:1192793515:-1 chm1:+:1248443407:-1 chm1:+:1304408666:-1 chm1:+:1540772207:-1 chm1:+:1545893703:-1 chm1:+:1638157362:-1 chm1:+:1770068587:-1 chm1:+:1785568564:-1 chm1:+:2254863662:-1 chm1:+:2773840244:-1 chm1:+:2885116208:-1 chm1:+:2890824131:-1 chm1:+:2958273363:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:63246123:-1 chm1:+:171612252:-1 chm1:+:1032221786:-1 chm1:+:1036587133:-1 chm1:+:1084296275:-1 chm1:+:1096800806:-1 chm1:+:1097178147:-1 chm1:+:1116279081:-1 chm1:+:1466042077:-1 chm1:+:1506206746:-1 chm1:+:1705130764:-1 chm1:+:1973641044:-1 chm1:+:2036265000:-1 chm1:+:2042013736:-1 chm1:+:2348587071:-1 chm1:+:2540344184:-1 chm1:+:2559007173:-1 chm1:+:2633908079:-1 chm1:+:2677464512:-1 chm1:+:2696897131:-1 chm1:+:2803740463:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:93673455:-1 chm1:+:306173074:-1 chm1:+:465613959:-1 chm1:+:506309448:-1 chm1:+:786438446:-1 chm1:+:1165072482:-1 chm1:+:1458114929:-1 chm1:+:1499543461:-1 chm1:+:1639944768:-1 chm1:+:1785242139:-1 chm1:+:2568200567:-1 chm1:+:2609385827:-1 chm1:+:2955445227:-1 chm1:+:3002583163:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:52401288:-1 chm1:+:171711920:-1 chm1:+:375290444:-1 chm1:+:377583210:-1 chm1:+:383293280:-1 chm1:+:455733673:-1 chm1:+:557381030:-1 chm1:+:682126758:-1 chm1:+:715775342:-1 chm1:+:823334296:-1 chm1:+:857538011:-1 chm1:+:880961535:-1 chm1:+:995592183:-1 chm1:+:1088519947:-1 chm1:+:1400461900:-1 chm1:+:1517165369:-1 chm1:+:1581376094:-1 chm1:+:1607422815:-1 chm1:+:1609770937:-1 chm1:+:1671844105:-1 chm1:+:1679311231:-1 chm1:+:1888938990:-1 chm1:+:1931667459:-1 chm1:+:2015320317:-1 chm1:+:2222041157:-1 chm1:+:2239641904:-1 chm1:+:2244470117:-1 chm1:+:2425401211:-1 chm1:+:2434856891:-1 chm1:+:2590429656:-1 chm1:+:2737739373:-1 chm1:+:2792161202:-1 chm1:+:2823718685:-1 chm1:+:2947597961:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:255463285:-1 chm1:+:537434132:-1 chm1:+:885446526:-1 chm1:+:1332024355:-1 chm1:+:1630180180:-1 chm1:+:2386045566:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:165170213:-1 chm1:+:172248212:-1 chm1:+:296489110:-1 chm1:+:591381739:-1 chm1:+:648808653:-1 chm1:+:733917571:-1 chm1:+:915825089:-1 chm1:+:950581637:-1 chm1:+:951161378:-1 chm1:+:951457758:-1 chm1:+:952161716:-1 chm1:+:1089414741:-1 chm1:+:1156353872:-1 chm1:+:1636765780:-1 chm1:+:2132062100:-1 chm1:+:2370060258:-1 chm1:+:2810659402:-1 chm1:+:3024085216:-1 chm1:+:3035338147:-1 chm1:+:3060467893:-1 chm1:+:3062077185:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:21702792:-1 chm1:+:1038900772:-1 chm1:+:1298269315:66 chm1:+:1298780514:90 chm1:+:1796187205:-1 chm1:+:2702517709:-1 chm1:+:2803539502:-1 chm1:+:2861485421:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:1702860:-1 chm1:+:27756128:-1 chm1:+:419093819:-1 chm1:+:452128122:-1 chm1:+:976025259:-1 chm1:+:1036978584:-1 chm1:+:1241328662:-1 chm1:+:1371650445:-1 chm1:+:1536724536:-1 chm1:+:1895320034:-1 chm1:+:1963066235:-1 chm1:+:2070605642:-1 chm1:+:2196581440:-1 chm1:+:2541266534:-1 chm1:+:2611262740:-1 chm1:+:2764208133:-1 chm1:+:2890323406:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:215184198:-1 chm1:+:232462206:-1 chm1:+:471087686:-1 chm1:+:507498191:-1 chm1:+:706117015:-1 chm1:+:759681241:-1 chm1:+:1017687234:-1 chm1:+:1134041366:-1 chm1:+:1248896708:-1 chm1:+:1667244859:-1 chm1:+:1686959288:-1 chm1:+:1785498712:-1 chm1:+:2135271179:-1 chm1:+:2359970872:-1 chm1:+:2514594705:-1 chm1:+:2537556459:-1 chm1:+:2565442762:-1 chm1:+:2603715359:-1 chm1:+:2624723471:-1 chm1:+:2910209341:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:44080807:-1 chm1:+:338429407:-1 chm1:+:501955674:-1 chm1:+:559467482:-1 chm1:+:1004165181:-1 chm1:+:1100300549:-1 chm1:+:1234979270:-1 chm1:+:1361034867:-1 chm1:+:1530402728:-1 chm1:+:1656859776:-1 chm1:+:1656862009:-1 chm1:+:1780819040:-1 chm1:+:2285486840:-1 chm1:+:2668607604:-1 chm1:+:2692710296:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:79877942:-1 chm1:+:79996398:-1 chm1:+:400600121:-1 chm1:+:472787837:-1 chm1:+:944078056:-1 chm1:+:1047974692:-1 chm1:+:1053717140:-1 chm1:+:1417101468:-1 chm1:+:1496473121:-1 chm1:+:1560985928:-1 chm1:+:1684301139:-1 chm1:+:1887787483:-1 chm1:+:2362052806:-1 chm1:+:2383371241:-1 chm1:+:2529491530:-1 chm1:+:2708550012:-1 chm1:+:2972192991:-1 +CTGCACTCCAGCCTGGGCGACAGAAGTGAGACCCTGTCGTCAAAAAAAGCATAATTTTGCAATGCAACTGAAAGAGTTGGTTTGTTACTCCCAGAGTGATTTGTTTATTCCAAACTGTATTTAATCATTCTAGGATTTGAACTATTCAATATCATTTTTGTGTGTGTCAGTCTTCATTGACTGTCTCAGTTTATTGAGCCTGACAGCCTTTACTTACTTATGTATTTATTTGTTTATTATTATTATTATTATTATTATTATTATTAATTATTATTATTATTATTTTTTGAGATGGAAGTCTCGCTCTGTTGCCAGGCTTGGAGTTGTAGGTGGCACTATTCTTGGATCACTGCAACCTCCACCATTCCAGGTTACAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTGCAGACATTGTGTCACCATGCCTGGCTAAATTTTTATATTTTTAGTAGAGAGAGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCTTGCCTCAAGTTATCCCACCTGCCTCAGCCCTCCCCAAGTGCTGGCATTACAGCGTGAGCCCATTGCGCCCAGGACTGTATTTATTTTTCAAGACAGGGTCTTGCTGTAGTCATCCTAGGCTGAGTTGCCGTGGTGTGATCTCAAGCTCACTGCCAACCTTTCACCTCCAGGAGCTAAAGTAATCTTCCCACTTCAGCCTCCCCAAGTAGCTGGGACTATCAGCGCAATGCCACCGCCTAGCTAATTTTTGTATTTTTTTGTAGAGATGAGGTTTTGCCATATTGCTCAGGTTGGT chm1:+:294563512:-1 chm1:+:1462584166:-1 chm1:+:1474214527:-1 chm1:+:1710437074:-1 chm1:+:1817534548:-1 chm1:+:2478712851:-1 +ACCAACCTGAGCAATATGGCAAAACCTCATCTCTACAAAAAAATACAAAAATTAGCTAGGCGGTGGCATTGCGCTGATAGTCCCAGCTACTTGGGGAGGCTGAAGTGGGAAGATTACTTTAGCTCCTGGAGGTGAAAGGTTGGCAGTGAGCTTGAGATCACACCACGGCAACTCAGCCTAGGATGACTACAGCAAGACCCTGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:350922391:-1 chm1:+:401546138:-1 chm1:+:642174693:-1 chm1:+:920951908:-1 chm1:+:1057720247:-1 chm1:+:1085512933:-1 chm1:+:1309902534:-1 chm1:+:1334065235:-1 chm1:+:1345431132:-1 chm1:+:1363957822:-1 chm1:+:1885767132:-1 chm1:+:2004170650:-1 chm1:+:2427775830:-1 chm1:+:2476836242:-1 chm1:+:2752904639:-1 chm1:+:2822056666:-1 chm1:+:2923119465:-1 chm1:+:3010114182:-1 +ACCAACCTGAGCAATATGGCAAAACCTCATCTCTACAAAAAAATACAAAAATTAGCTAGGCGGTGGCATTGCGCTGATAGTCCCAGCTACTTGGGGAGGCTGAAGTGGGAAGATTACTTTAGCTCCTGGAGGTGAAAGGTTGGCAGTGAGCTTGAGATCACACCACGGCAACTCAGCCTAGGATGACTACAGCAAGACCCTGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:1298664902:90 chm1:+:1893574986:41 +ACCAACCTGAGCAATATGGCAAAACCTCATCTCTACAAAAAAATACAAAAATTAGCTAGGCGGTGGCATTGCGCTGATAGTCCCAGCTACTTGGGGAGGCTGAAGTGGGAAGATTACTTTAGCTCCTGGAGGTGAAAGGTTGGCAGTGAGCTTGAGATCACACCACGGCAACTCAGCCTAGGATGACTACAGCAAGACCCTGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:1893574968:41 +ACCAACCTGAGCAATATGGCAAAACCTCATCTCTACAAAAAAATACAAAAATTAGCTAGGCGGTGGCATTGCGCTGATAGTCCCAGCTACTTGGGGAGGCTGAAGTGGGAAGATTACTTTAGCTCCTGGAGGTGAAAGGTTGGCAGTGAGCTTGAGATCACACCACGGCAACTCAGCCTAGGATGACTACAGCAAGACCCTGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:2171217630:-1 +ACCAACCTGAGCAATATGGCAAAACCTCATCTCTACAAAAAAATACAAAAATTAGCTAGGCGGTGGCATTGCGCTGATAGTCCCAGCTACTTGGGGAGGCTGAAGTGGGAAGATTACTTTAGCTCCTGGAGGTGAAAGGTTGGCAGTGAGCTTGAGATCACACCACGGCAACTCAGCCTAGGATGACTACAGCAAGACCCTGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:1298664855:90 chm1:+:1893574969:41 +ACCAACCTGAGCAATATGGCAAAACCTCATCTCTACAAAAAAATACAAAAATTAGCTAGGCGGTGGCATTGCGCTGATAGTCCCAGCTACTTGGGGAGGCTGAAGTGGGAAGATTACTTTAGCTCCTGGAGGTGAAAGGTTGGCAGTGAGCTTGAGATCACACCACGGCAACTCAGCCTAGGATGACTACAGCAAGACCCTGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:1893574970:41 +ACCAACCTGAGCAATATGGCAAAACCTCATCTCTACAAAAAAATACAAAAATTAGCTAGGCGGTGGCATTGCGCTGATAGTCCCAGCTACTTGGGGAGGCTGAAGTGGGAAGATTACTTTAGCTCCTGGAGGTGAAAGGTTGGCAGTGAGCTTGAGATCACACCACGGCAACTCAGCCTAGGATGACTACAGCAAGACCCTGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:1298664856:90 +ACCAACCTGAGCAATATGGCAAAACCTCATCTCTACAAAAAAATACAAAAATTAGCTAGGCGGTGGCATTGCGCTGATAGTCCCAGCTACTTGGGGAGGCTGAAGTGGGAAGATTACTTTAGCTCCTGGAGGTGAAAGGTTGGCAGTGAGCTTGAGATCACACCACGGCAACTCAGCCTAGGATGACTACAGCAAGACCCTGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:389480758:-1 chm1:+:770038584:-1 chm1:+:1144742640:-1 chm1:+:1174127858:-1 chm1:+:1507874051:-1 chm1:+:2045841245:-1 chm1:+:2163304685:-1 chm1:+:2436007230:-1 +ACCAACCTGAGCAATATGGCAAAACCTCATCTCTACAAAAAAATACAAAAATTAGCTAGGCGGTGGCATTGCGCTGATAGTCCCAGCTACTTGGGGAGGCTGAAGTGGGAAGATTACTTTAGCTCCTGGAGGTGAAAGGTTGGCAGTGAGCTTGAGATCACACCACGGCAACTCAGCCTAGGATGACTACAGCAAGACCCTGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:626352894:-1 chm1:+:996751959:-1 chm1:+:1003879762:-1 chm1:+:1313724695:-1 chm1:+:1328562965:-1 chm1:+:1445104311:-1 chm1:+:1511909482:-1 chm1:+:1662146160:-1 chm1:+:1683242348:-1 chm1:+:1738453035:-1 chm1:+:1771643912:-1 chm1:+:1801623407:-1 chm1:+:2105242885:-1 chm1:+:2172983830:-1 chm1:+:2405840181:-1 chm1:+:2882772365:-1 chm1:+:2933073635:-1 chm1:+:3059400517:-1 +ACCAACCTGAGCAATATGGCAAAACCTCATCTCTACAAAAAAATACAAAAATTAGCTAGGCGGTGGCATTGCGCTGATAGTCCCAGCTACTTGGGGAGGCTGAAGTGGGAAGATTACTTTAGCTCCTGGAGGTGAAAGGTTGGCAGTGAGCTTGAGATCACACCACGGCAACTCAGCCTAGGATGACTACAGCAAGACCCTGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:6200671:-1 chm1:+:65140983:-1 chm1:+:235765868:-1 chm1:+:433176211:-1 chm1:+:668699633:-1 chm1:+:1014599653:-1 chm1:+:1342742821:-1 chm1:+:1376694998:-1 chm1:+:1619188674:-1 chm1:+:2005149022:-1 chm1:+:2070546223:-1 chm1:+:2137532351:-1 chm1:+:2433524915:-1 chm1:+:2558528384:-1 chm1:+:2577906179:-1 chm1:+:2656756607:-1 chm1:+:2854354558:-1 +ACCAACCTGAGCAATATGGCAAAACCTCATCTCTACAAAAAAATACAAAAATTAGCTAGGCGGTGGCATTGCGCTGATAGTCCCAGCTACTTGGGGAGGCTGAAGTGGGAAGATTACTTTAGCTCCTGGAGGTGAAAGGTTGGCAGTGAGCTTGAGATCACACCACGGCAACTCAGCCTAGGATGACTACAGCAAGACCCTGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:538327475:-1 chm1:+:1068877503:-1 chm1:+:1100438355:-1 chm1:+:1364918353:-1 chm1:+:1407693150:-1 chm1:+:1540459030:-1 chm1:+:2362924677:-1 chm1:+:2526428387:-1 chm1:+:2704313989:-1 chm1:+:2817899137:-1 +ACCAACCTGAGCAATATGGCAAAACCTCATCTCTACAAAAAAATACAAAAATTAGCTAGGCGGTGGCATTGCGCTGATAGTCCCAGCTACTTGGGGAGGCTGAAGTGGGAAGATTACTTTAGCTCCTGGAGGTGAAAGGTTGGCAGTGAGCTTGAGATCACACCACGGCAACTCAGCCTAGGATGACTACAGCAAGACCCTGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:194538380:-1 chm1:+:889815136:-1 chm1:+:1079778204:-1 chm1:+:1083129624:-1 +ACCAACCTGAGCAATATGGCAAAACCTCATCTCTACAAAAAAATACAAAAATTAGCTAGGCGGTGGCATTGCGCTGATAGTCCCAGCTACTTGGGGAGGCTGAAGTGGGAAGATTACTTTAGCTCCTGGAGGTGAAAGGTTGGCAGTGAGCTTGAGATCACACCACGGCAACTCAGCCTAGGATGACTACAGCAAGACCCTGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:75409681:-1 chm1:+:273246633:-1 chm1:+:721093262:-1 chm1:+:1038735323:-1 chm1:+:1039717334:-1 chm1:+:1697674516:-1 chm1:+:1827403007:-1 chm1:+:1858535762:-1 chm1:+:1893574987:41 chm1:+:1939220034:-1 chm1:+:2410312995:-1 chm1:+:2736577613:-1 chm1:+:2849219050:-1 chm1:+:2966906194:-1 +ACCAACCTGAGCAATATGGCAAAACCTCATCTCTACAAAAAAATACAAAAATTAGCTAGGCGGTGGCATTGCGCTGATAGTCCCAGCTACTTGGGGAGGCTGAAGTGGGAAGATTACTTTAGCTCCTGGAGGTGAAAGGTTGGCAGTGAGCTTGAGATCACACCACGGCAACTCAGCCTAGGATGACTACAGCAAGACCCTGTCTTGAAAAATAAATACAGTCCTGGGCGCAATGGGCTCACGCTGTAATGCCAGCACTTGGGGAGGGCTGAGGCAGGTGGGATAACTTGAGGCAAGAGTTCGAGACCAGCCTGGCCAACATGGCGAAACCTCTCTCTACTAAAAATATAAAAATTTAGCCAGGCATGGTGACACAATGTCTGCAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGTAACCTGGAATGGTGGAGGTTGCAGTGATCCAAGAATAGTGCCACCTACAACTCCAAGCCTGGCAACAGAGCGAGACTTCCATCTCAAAAAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAAACAAATAAATACATAAGTAAGTAAAGGCTGTCAGGCTCAATAAACTGAGACAGTCAATGAAGACTGACACACACAAAAATGATATTGAATAGTTCAAATCCTAGAATGATTAAATACAGTTTGGAATAAACAAATCACTCTGGGAGTAACAAACCAACTCTTTCAGTTGCATTGCAAAATTATGCTTTTTTTGACGACAGGGTCTCACTTCTGTCGCCCAGGCTGGAGTGCAG chm1:+:42997073:-1 chm1:+:220214314:-1 chm1:+:549036881:-1 chm1:+:918939271:-1 chm1:+:1133796044:-1 chm1:+:1146675429:-1 chm1:+:1213615849:-1 chm1:+:1290138716:-1 chm1:+:1692472281:-1 chm1:+:1712541123:-1 chm1:+:1726581885:-1 chm1:+:1805843428:-1 chm1:+:2007694245:-1 chm1:+:2296860753:-1 chm1:+:2338522574:-1 chm1:+:2512117468:-1 chm1:+:2640996823:-1 chm1:+:2848230319:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:1074477244:-1 chm1:+:1580448584:-1 chm1:+:1582751849:-1 chm1:+:1604631012:-1 chm1:+:1893984593:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:94097646:-1 chm1:+:275140050:-1 chm1:+:316394141:-1 chm1:+:346549945:-1 chm1:+:453005186:-1 chm1:+:480638316:-1 chm1:+:631059669:-1 chm1:+:675153862:-1 chm1:+:675503707:-1 chm1:+:687308649:-1 chm1:+:696684683:-1 chm1:+:716115977:-1 chm1:+:773991669:-1 chm1:+:874955958:-1 chm1:+:971353437:-1 chm1:+:1054709994:-1 chm1:+:1333279941:-1 chm1:+:1489685572:-1 chm1:+:1684594132:-1 chm1:+:1712738311:-1 chm1:+:1723683961:75 chm1:+:1752060122:-1 chm1:+:1873011727:-1 chm1:+:1879229061:-1 chm1:+:1890640197:-1 chm1:+:2106132258:-1 chm1:+:2106388348:-1 chm1:+:2127594141:-1 chm1:+:2221468580:-1 chm1:+:2327643517:-1 chm1:+:2328650122:-1 chm1:+:2334101985:-1 chm1:+:2348899923:-1 chm1:+:2382050398:-1 chm1:+:2404690967:-1 chm1:+:2421687760:-1 chm1:+:2515510002:-1 chm1:+:2520848034:-1 chm1:+:2535871657:-1 chm1:+:2546110645:-1 chm1:+:2625829200:-1 chm1:+:2638852200:-1 chm1:+:2664788946:-1 chm1:+:2669634056:-1 chm1:+:2676440252:-1 chm1:+:2715237099:-1 chm1:+:2729312733:-1 chm1:+:2732205570:-1 chm1:+:2751737896:-1 chm1:+:2753898487:-1 chm1:+:2770732613:-1 chm1:+:2852385078:66 chm1:+:2858757059:-1 chm1:+:2869282305:-1 chm1:+:2900066194:-1 chm1:+:2975852597:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:21000399:-1 chm1:+:32072647:-1 chm1:+:34131005:-1 chm1:+:55854980:-1 chm1:+:116531131:-1 chm1:+:155831386:-1 chm1:+:200690142:-1 chm1:+:209340712:-1 chm1:+:291986071:-1 chm1:+:293541574:-1 chm1:+:319247393:-1 chm1:+:352431704:-1 chm1:+:423961603:-1 chm1:+:426417764:-1 chm1:+:477874019:-1 chm1:+:512599273:-1 chm1:+:624702169:-1 chm1:+:717314105:-1 chm1:+:731451731:-1 chm1:+:765048868:-1 chm1:+:802196144:-1 chm1:+:876079355:-1 chm1:+:922471010:-1 chm1:+:932233437:-1 chm1:+:989311184:-1 chm1:+:1000803188:-1 chm1:+:1012152861:-1 chm1:+:1029111864:-1 chm1:+:1061940566:-1 chm1:+:1105590945:-1 chm1:+:1166744067:-1 chm1:+:1222824289:-1 chm1:+:1391528539:-1 chm1:+:1395835404:-1 chm1:+:1540725663:-1 chm1:+:1565037741:-1 chm1:+:1574561968:-1 chm1:+:1581517760:-1 chm1:+:1608531374:-1 chm1:+:1623989273:-1 chm1:+:1673746128:-1 chm1:+:1842372178:-1 chm1:+:1889210422:-1 chm1:+:2049451960:-1 chm1:+:2071295626:-1 chm1:+:2121285315:-1 chm1:+:2137618303:-1 chm1:+:2277903932:-1 chm1:+:2368949168:-1 chm1:+:2399910294:-1 chm1:+:2431612924:-1 chm1:+:2432429042:-1 chm1:+:2436418234:-1 chm1:+:2493350496:-1 chm1:+:2504398679:-1 chm1:+:2505319800:-1 chm1:+:2520792284:-1 chm1:+:2537750569:-1 chm1:+:2550775181:-1 chm1:+:2560197628:-1 chm1:+:2643410988:-1 chm1:+:2695441870:-1 chm1:+:2712790785:-1 chm1:+:2750058501:-1 chm1:+:2760289286:-1 chm1:+:2768961891:-1 chm1:+:2816972592:-1 chm1:+:2823542319:-1 chm1:+:2905568603:-1 chm1:+:2920704586:-1 chm1:+:3055019213:-1 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+TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:7390371:-1 chm1:+:89462646:-1 chm1:+:92519217:-1 chm1:+:304516608:-1 chm1:+:688224592:-1 chm1:+:731171300:-1 chm1:+:820135619:-1 chm1:+:1038586748:-1 chm1:+:1512285015:-1 chm1:+:1528734632:-1 chm1:+:1892814373:-1 chm1:+:1998975456:-1 chm1:+:2001546901:-1 chm1:+:2269830245:-1 chm1:+:2273901435:-1 chm1:+:2535039168:-1 chm1:+:2588802036:-1 chm1:+:2701321645:-1 chm1:+:2711994324:-1 chm1:+:2760727964:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:235297316:-1 chm1:+:1723683971:75 chm1:+:2327643250:133 chm1:+:2328649847:133 chm1:+:2852385086:66 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:2512859:-1 chm1:+:872485849:-1 chm1:+:1276905162:-1 chm1:+:2706961725:-1 chm1:+:2947800270:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:21315743:-1 chm1:+:288905905:-1 chm1:+:409364864:-1 chm1:+:451119433:-1 chm1:+:1723683966:75 chm1:+:2061193929:-1 chm1:+:2327643246:133 chm1:+:2328649843:133 chm1:+:2540345165:-1 chm1:+:2852385082:66 chm1:+:2921700444:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:385026341:-1 chm1:+:402040748:-1 chm1:+:680222061:-1 chm1:+:872303785:-1 chm1:+:885389982:-1 chm1:+:1194227704:-1 chm1:+:1259196342:-1 chm1:+:1390721559:-1 chm1:+:1556533641:-1 chm1:+:1699300637:-1 chm1:+:1707550161:-1 chm1:+:1896302864:-1 chm1:+:2002000097:-1 chm1:+:2332513334:-1 chm1:+:2574198807:-1 chm1:+:2680845293:-1 chm1:+:2764192983:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:84017655:-1 chm1:+:157232342:-1 chm1:+:190805333:-1 chm1:+:1283635626:-1 chm1:+:1656140131:-1 chm1:+:1909181712:-1 chm1:+:2425510514:-1 chm1:+:2802886254:-1 chm1:+:2818943165:-1 chm1:+:3013134942:-1 chm1:+:3043085950:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:315739539:-1 chm1:+:538981406:-1 chm1:+:675707164:-1 chm1:+:789200310:-1 chm1:+:1030896913:-1 chm1:+:1093343658:-1 chm1:+:1639290288:-1 chm1:+:1821883447:-1 chm1:+:2036488671:-1 chm1:+:2053061683:-1 chm1:+:2165891674:-1 chm1:+:2392402505:-1 chm1:+:2396913747:-1 chm1:+:2607246423:-1 chm1:+:2805347875:-1 chm1:+:3031475951:-1 chm1:+:3060707917:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:1723683964:75 chm1:+:2327643523:-1 chm1:+:2328650128:-1 chm1:+:2852385083:66 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:85506627:-1 chm1:+:505941119:-1 chm1:+:548610819:-1 chm1:+:724955470:-1 chm1:+:1017729208:-1 chm1:+:1299178057:-1 chm1:+:1356360565:-1 chm1:+:1795769898:-1 chm1:+:2015642677:-1 chm1:+:2022698695:-1 chm1:+:2421005854:-1 chm1:+:2499368087:-1 chm1:+:2558846141:-1 chm1:+:2716143546:-1 chm1:+:2749513743:-1 chm1:+:2858465572:-1 chm1:+:2943946423:-1 chm1:+:3031007724:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:320649575:-1 chm1:+:1738557576:-1 chm1:+:1752074449:-1 chm1:+:2290160311:-1 chm1:+:2859582196:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:1723683972:75 chm1:+:2327643251:133 chm1:+:2328649848:133 chm1:+:2852385087:66 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:919101071:-1 chm1:+:1174567979:-1 chm1:+:1348239601:-1 chm1:+:1416996220:-1 chm1:+:1671548855:-1 chm1:+:2070060450:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:444099010:-1 chm1:+:934867746:-1 chm1:+:1178208147:-1 chm1:+:1921363029:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:306679408:-1 chm1:+:1400909096:-1 chm1:+:1702085803:-1 chm1:+:2983862729:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:9421660:-1 chm1:+:554362934:-1 chm1:+:1021712281:-1 chm1:+:1142346759:-1 chm1:+:1205609683:-1 chm1:+:1723683973:75 chm1:+:1797542081:-1 chm1:+:1802849387:-1 chm1:+:1802849397:-1 chm1:+:2178661786:-1 chm1:+:2327643252:133 chm1:+:2328649849:133 chm1:+:2345540595:-1 chm1:+:2676429500:-1 chm1:+:2852385088:66 chm1:+:2857602553:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:507377501:-1 chm1:+:831353558:-1 chm1:+:954782914:-1 chm1:+:1655533582:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:2047369804:-1 chm1:+:2276953580:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:1728869326:-1 chm1:+:2993580836:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:12719651:-1 chm1:+:481083591:-1 chm1:+:1422109163:-1 chm1:+:1520459906:-1 chm1:+:1533844820:-1 chm1:+:1618153240:-1 chm1:+:1723683974:75 chm1:+:1778917226:-1 chm1:+:2125434477:-1 chm1:+:2327643254:133 chm1:+:2328649851:133 chm1:+:2739493051:-1 chm1:+:2975674611:-1 +TTTAACTTGCCTCTTTCTTTGTTTTCCTTTTTTTTGAGACCAGGTTCTCACTCTGTCACCCAGGGCTGGAGGTCAGTGATGCAATTATGGCTCCACTTGCAACCTCTGCCTCCCGGGACCCCCAAGTGCCTGGGTTTACAGGTGTGAGCCACTGCACCCAGCCTTACTTGTCTATTCTTCTAAGAGTGGGAACTATAATTGAGCCCAGAGCTCCAAAAACAATGAAGGAATGAATGAGTGAATAAGCTCTTCCCATGGGTTTGGTGTGGTTTGGGGGCTCTACTGTTAATCTAAATGCTATGTTTTATATAATCTAAAATTTCCCCTAGGTGTGTTACATGATTGCGTTGTGTTGAACTTACATTGAGACTCCTTTTCACAATATGCTGGTTATTCAGCATTGGGACTTTTCCATTCACTCTTTCGAATTATTCGCTTTGGGGGACACAGATAGACCTCTGTGTCTTTCATAAAGAGTGTCCATTGGCCGGGTGCAGTGGCTACATGCTGTAATCCAGCACTTTGGAAGGCTGAGGAGGGCAGATCACCGAGGTCAGGAGTTCGTAGACCTAGCCTCGGCCAATATGGTGAAATTTCCCTCTCTACTAAAAATACAAAAATTAGCCAGGCCTGGTGGCGGGTGCCTATAATCCCAGCTACTCGGAGACTGAGGTAGTAGAATTGCTGAACTGGGAGGCAGAGGTTGCTATTGAGCTGAGTTCATGCCACTGCAACTCCAAGCTTGAGTGACAGACGTGAGACTCCATCTCCTAAAAAACAAAAAACAAAAGAGTGTCCAT chm1:+:643455401:-1 chm1:+:2272833052:-1 chm1:+:2327643256:133 chm1:+:2328649853:133 +ATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:5368656:-1 chm1:+:16739935:-1 chm1:+:24275850:-1 chm1:+:25934065:-1 chm1:+:33176240:-1 chm1:+:44823807:-1 chm1:+:47145110:-1 chm1:+:52089416:-1 chm1:+:92452304:-1 chm1:+:95290714:-1 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chm1:+:2951395928:-1 chm1:+:2981563469:-1 chm1:+:2984482229:-1 chm1:+:2987165685:-1 chm1:+:3014926294:-1 chm1:+:3016223383:-1 chm1:+:3028479276:-1 chm1:+:3038995327:-1 chm1:+:3052316765:-1 chm1:+:3097069580:-1 +ATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:1606494803:72 chm1:+:2443321806:36 +ATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:1325963022:-1 chm1:+:1372845367:-1 +ATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:2443321801:36 +ATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:2443321805:36 +ATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:1606494802:72 +ATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:2443321810:36 +ATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:1273770524:-1 +ATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:1606494801:72 chm1:+:2443321804:36 +ATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:1606494805:72 chm1:+:2443321808:36 +ATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:641047939:-1 chm1:+:2443321813:36 +ATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:995071276:-1 +ATGGACACTCTTTTGTTTTTTGTTTTTTAGGAGATGGAGTCTCACGTCTGTCACTCAAGCTTGGAGTTGCAGTGGCATGAACTCAGCTCAATAGCAACCTCTGCCTCCCAGTTCAGCAATTCTACTACCTCAGTCTCCGAGTAGCTGGGATTATAGGCACCCGCCACCAGGCCTGGCTAATTTTTGTATTTTTAGTAGAGAGGGAAATTTCACCATATTGGCCGAGGCTAGGTCTACGAACTCCTGACCTCGGTGATCTGCCCTCCTCAGCCTTCCAAAGTGCTGGATTACAGCATGTAGCCACTGCACCCGGCCAATGGACACTCTTTATGAAAGACACAGAGGTCTATCTGTGTCCCCCAAAGCGAATAATTCGAAAGAGTGAATGGAAAAGTCCCAATGCTGAATAACCAGCATATTGTGAAAAGGAGTCTCAATGTAAGTTCAACACAACGCAATCATGTAACACACCTAGGGGAAATTTTAGATTATATAAAACATAGCATTTAGATTAACAGTAGAGCCCCCAAACCACACCAAACCCATGGGAAGAGCTTATTCACTCATTCATTCCTTCATTGTTTTTGGAGCTCTGGGCTCAATTATAGTTCCCACTCTTAGAAGAATAGACAAGTAAGGCTGGGTGCAGTGGCTCACACCTGTAAACCCAGGCACTTGGGGGTCCCGGGAGGCAGAGGTTGCAAGTGGAGCCATAATTGCATCACTGACCTCCAGCCCTGGGTGACAGAGTGAGAACCTGGTCTCAAAAAAAAGGAAAACAAAGAAAGAGGCAAGTTAAA chm1:+:1750270834:-1 chm1:+:2370610801:-1 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGGATCTGTGCATGGCAGCTTCCTTTCCCGAGGACCGTGGCCCCTTAATGGAGTCCACAGCGTCACGTGTTTTGCTGAATGTTGGTTTTAGAGTCACTGACTCAAACATGGACGCATCCACTTATGAGAGTCAATATTCATCTCTCACCGCTCCAGGTGTTGAGATTTGGAACCTCAACAGTGGGCTGTGTTCATGTGAAAGA chm1:+:315315113:-1 chm1:+:580104117:-1 chm1:+:1668089144:-1 chm1:+:2681666680:-1 chm1:+:2681879402:-1 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGGATCTGTGCATGGCAGCTTCCTTTCCCGAGGACCGTGGCCCCTTAATGGAGTCCACAGCGTCACGTGTTTTGCTGAATGTTGGTTTTAGAGTCACTGACTCAAACATGGACGCATCCACTTATGAGAGTCAATATTCATCTCTCACCGCTCCAGGTGTTGAGATTTGGAACCTCAACAGTGGGCTGTGTTCATGTGAAAGA chm1:+:2681886993:-1 chm1:+:2682681596:-1 chm1:+:3059468233:-1 chm1:+:3099935171:31 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGGATCTGTGCATGGCAGCTTCCTTTCCCGAGGACCGTGGCCCCTTAATGGAGTCCACAGCGTCACGTGTTTTGCTGAATGTTGGTTTTAGAGTCACTGACTCAAACATGGACGCATCCACTTATGAGAGTCAATATTCATCTCTCACCGCTCCAGGTGTTGAGATTTGGAACCTCAACAGTGGGCTGTGTTCATGTGAAAGA chm1:+:3099935168:31 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGGATCTGTGCATGGCAGCTTCCTTTCCCGAGGACCGTGGCCCCTTAATGGAGTCCACAGCGTCACGTGTTTTGCTGAATGTTGGTTTTAGAGTCACTGACTCAAACATGGACGCATCCACTTATGAGAGTCAATATTCATCTCTCACCGCTCCAGGTGTTGAGATTTGGAACCTCAACAGTGGGCTGTGTTCATGTGAAAGA chm1:+:3099935169:31 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGGATCTGTGCATGGCAGCTTCCTTTCCCGAGGACCGTGGCCCCTTAATGGAGTCCACAGCGTCACGTGTTTTGCTGAATGTTGGTTTTAGAGTCACTGACTCAAACATGGACGCATCCACTTATGAGAGTCAATATTCATCTCTCACCGCTCCAGGTGTTGAGATTTGGAACCTCAACAGTGGGCTGTGTTCATGTGAAAGA chm1:+:3099935174:31 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGGATCTGTGCATGGCAGCTTCCTTTCCCGAGGACCGTGGCCCCTTAATGGAGTCCACAGCGTCACGTGTTTTGCTGAATGTTGGTTTTAGAGTCACTGACTCAAACATGGACGCATCCACTTATGAGAGTCAATATTCATCTCTCACCGCTCCAGGTGTTGAGATTTGGAACCTCAACAGTGGGCTGTGTTCATGTGAAAGA chm1:+:3099935179:31 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGGATCTGTGCATGGCAGCTTCCTTTCCCGAGGACCGTGGCCCCTTAATGGAGTCCACAGCGTCACGTGTTTTGCTGAATGTTGGTTTTAGAGTCACTGACTCAAACATGGACGCATCCACTTATGAGAGTCAATATTCATCTCTCACCGCTCCAGGTGTTGAGATTTGGAACCTCAACAGTGGGCTGTGTTCATGTGAAAGA chm1:+:3099935167:31 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGGATCTGTGCATGGCAGCTTCCTTTCCCGAGGACCGTGGCCCCTTAATGGAGTCCACAGCGTCACGTGTTTTGCTGAATGTTGGTTTTAGAGTCACTGACTCAAACATGGACGCATCCACTTATGAGAGTCAATATTCATCTCTCACCGCTCCAGGTGTTGAGATTTGGAACCTCAACAGTGGGCTGTGTTCATGTGAAAGA chm1:+:2683029278:-1 chm1:+:3099935172:31 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGGATCTGTGCATGGCAGCTTCCTTTCCCGAGGACCGTGGCCCCTTAATGGAGTCCACAGCGTCACGTGTTTTGCTGAATGTTGGTTTTAGAGTCACTGACTCAAACATGGACGCATCCACTTATGAGAGTCAATATTCATCTCTCACCGCTCCAGGTGTTGAGATTTGGAACCTCAACAGTGGGCTGTGTTCATGTGAAAGA chm1:+:3099935177:31 +ATTACAAAACATGGGGCCAGCACCAAGTATATGTTATAATGTCCCCTGTGAGCAGCACCAAGGCAGGACAGAGACTCGCATCGACTTGGTTGCTAAGGACAAGTGATCTGCTACACCTCTTCTTTGTAGGCAGGGTGCACACACCTTTTTTTAGGTGGTGAATGCAGTAGAGATTGTCCCAAGGCCCCCTGTGAACAGGGCTCAGGCAGTAGCGATCAATTCCCTAGGTATTATGCCCAGCAGTATGTCACAATATACAAAATATCGCAGGGCCCAGGGGAAAAGAGGAGAGTCACATCATGTGGGTGCCTTGTCCCAGTGATTTGTCACAAGTCTCTCTTTTTTGACAGGACCCAGGCAGAAGAGGGGGGTCATAGGTGCTGGGTCAATAATGTCACAATTTTATCACTGGGCTGGGCTACGCAGAAGAGTCAAGTCACTCACGAGCTGGGCCGAGATATATTTCACAGTTATACCCTCCAGAAAGTCCAGGGGCTGAGACTGACAATCCTGCACATGTCCCATATCTAGGTGTGAGAGCAAACACATTGTGTTTGTTGGGTGTAAAGTGTACAAGTCACAGTCTCAATGGTGCACTGGATCTGTGCATGGCAGCTTCCTTTCCCGAGGACCGTGGCCCCTTAATGGAGTCCACAGCGTCACGTGTTTTGCTGAATGTTGGTTTTAGAGTCACTGACTCAAACATGGACGCATCCACTTATGAGAGTCAATATTCATCTCTCACCGCTCCAGGTGTTGAGATTTGGAACCTCAACAGTGGGCTGTGTTCATGTGAAAGA chm1:+:3099935170:31 +TCTTTCACATGAACACAGCCCACTGTTGAGGTTCCAAATCTCAACACCTGGAGCGGTGAGAGATGAATATTGACTCTCATAAGTGGATGCGTCCATGTTTGAGTCAGTGACTCTAAAACCAACATTCAGCAAAACACGTGACGCTGTGGACTCCATTAAGGGGCCACGGTCCTCGGGAAAGGAAGCTGCCATGCACAGATCCAGTGCACCATTGAGACTGTGACTTGTACACTTTACACCCAACAAACACAATGTGTTTGCTCTCACACCTAGATATGGGACATGTGCAGGATTGTCAGTCTCAGCCCCTGGACTTTCTGGAGGGTATAACTGTGAAATATATCTCGGCCCAGCTCGTGAGTGACTTGACTCTTCTGCGTAGCCCAGCCCAGTGATAAAATTGTGACATTATTGACCCAGCACCTATGACCCCCCTCTTCTGCCTGGGTCCTGTCAAAAAAGAGAGACTTGTGACAAATCACTGGGACAAGGCACCCACATGATGTGACTCTCCTCTTTTCCCCTGGGCCCTGCGATATTTTGTATATTGTGACATACTGCTGGGCATAATACCTAGGGAATTGATCGCTACTGCCTGAGCCCTGTTCACAGGGGGCCTTGGGACAATCTCTACTGCATTCACCACCTAAAAAAAGGTGTGTGCACCCTGCCTACAAAGAAGAGGTGTAGCAGATCACTTGTCCTTAGCAACCAAGTCGATGCGAGTCTCTGTCCTGCCTTGGTGCTGCTCACAGGGGACATTATAACATATACTTGGTGCTGGCCCCATGTTTTGTAAT chm1:+:2681760328:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:92769211:-1 chm1:+:154620655:-1 chm1:+:202327712:-1 chm1:+:397839193:-1 chm1:+:404299466:-1 chm1:+:623461466:-1 chm1:+:726326201:-1 chm1:+:831508774:-1 chm1:+:960558057:-1 chm1:+:1170334343:-1 chm1:+:1198736027:-1 chm1:+:1203220730:-1 chm1:+:1340988397:-1 chm1:+:1432435460:-1 chm1:+:1446867231:-1 chm1:+:1483383524:-1 chm1:+:1511177666:-1 chm1:+:1761865504:-1 chm1:+:1769387680:-1 chm1:+:1830297061:-1 chm1:+:1836227813:-1 chm1:+:1855791743:-1 chm1:+:1964816064:-1 chm1:+:2029737560:-1 chm1:+:2287611718:-1 chm1:+:2464384749:-1 chm1:+:2481006229:-1 chm1:+:2505373292:-1 chm1:+:2911745663:-1 chm1:+:3033056774:-1 chm1:+:3101657328:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:1167872574:-1 chm1:+:1768935856:-1 chm1:+:2152803287:-1 chm1:+:2587731204:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:166558619:-1 chm1:+:799198155:-1 chm1:+:1331007125:-1 chm1:+:2361831181:-1 chm1:+:2692872987:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:207344277:-1 chm1:+:671394188:-1 chm1:+:1192750598:-1 chm1:+:1353294171:-1 chm1:+:1683083008:-1 chm1:+:1905240431:-1 chm1:+:3014167376:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:332211294:-1 chm1:+:859482997:-1 chm1:+:911231918:-1 chm1:+:926056922:-1 chm1:+:1072320790:-1 chm1:+:1130157356:-1 chm1:+:1230418424:-1 chm1:+:1980572484:-1 chm1:+:2362086487:-1 chm1:+:2424936989:-1 chm1:+:2818870547:-1 chm1:+:2896062837:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:281007926:-1 chm1:+:600759137:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:253247435:-1 chm1:+:399913702:-1 chm1:+:458273599:-1 chm1:+:657903858:-1 chm1:+:690555913:-1 chm1:+:1563597857:-1 chm1:+:1650266817:-1 chm1:+:1855254369:-1 chm1:+:2015742230:-1 chm1:+:2143430714:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:172018472:-1 chm1:+:252574922:-1 chm1:+:345062079:-1 chm1:+:762379315:-1 chm1:+:865571697:-1 chm1:+:1025526868:-1 chm1:+:1290069821:-1 chm1:+:2144086907:-1 chm1:+:2430405681:-1 chm1:+:2568130151:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:234850014:-1 chm1:+:391300288:-1 chm1:+:439839289:-1 chm1:+:582723393:-1 chm1:+:586064129:-1 chm1:+:638026303:-1 chm1:+:819001990:-1 chm1:+:965821019:-1 chm1:+:982382495:-1 chm1:+:1409337353:-1 chm1:+:1458227059:-1 chm1:+:1616766579:-1 chm1:+:1655829574:-1 chm1:+:1666747274:-1 chm1:+:2036569715:-1 chm1:+:2694134952:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:199911826:-1 chm1:+:225937973:-1 chm1:+:474245967:-1 chm1:+:515033938:-1 chm1:+:764565789:-1 chm1:+:920929132:-1 chm1:+:932116075:-1 chm1:+:1971698263:-1 chm1:+:2268774318:-1 chm1:+:2799649189:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:17367188:-1 chm1:+:85346120:-1 chm1:+:1001679322:-1 chm1:+:1085609835:-1 chm1:+:1170669026:-1 chm1:+:1195786924:-1 chm1:+:1614189095:-1 chm1:+:2424388919:-1 chm1:+:2431940011:-1 chm1:+:2890254226:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:177540972:-1 chm1:+:547104278:-1 chm1:+:1362994868:-1 chm1:+:1894343940:-1 chm1:+:2111107155:-1 chm1:+:2227475120:-1 chm1:+:2689442879:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:20226019:-1 chm1:+:198213267:-1 chm1:+:283563987:-1 chm1:+:596437817:-1 chm1:+:677005737:-1 chm1:+:1451272201:-1 chm1:+:2469843534:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:602481523:-1 chm1:+:1016472108:-1 chm1:+:1158967746:-1 chm1:+:1772268285:-1 chm1:+:2649498245:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:1057944970:-1 chm1:+:2814254128:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:1472011556:-1 chm1:+:2951323202:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:166278070:-1 chm1:+:345353935:-1 chm1:+:372250014:-1 chm1:+:383868332:-1 chm1:+:933445738:-1 chm1:+:961674092:-1 chm1:+:998034474:-1 chm1:+:1133441264:-1 chm1:+:1557489740:-1 chm1:+:1820216415:-1 chm1:+:1820267576:-1 chm1:+:1835432729:-1 chm1:+:2077298629:-1 chm1:+:2125488754:-1 chm1:+:2196231031:-1 chm1:+:2594572002:-1 chm1:+:2645663093:-1 chm1:+:2721521782:-1 chm1:+:3058756366:-1 chm1:+:3058802057:-1 +GCAAGCTCTTAGATCAGATCTTGCTGCTAAGCCAATGTAAGACTGGTTCTCTTGGAAACTGATTCGACTGCTTTAGGGCTGCTGACTATGGAGTAAGTAGCTTATGCTCATTCCAGATTGTCTTCCTTGAGACATGTTTATGCTTCAACATATCTAGTGTTTTGCTCACTAAATTTGAATATAGATTCTGACTAGTATAGTGTAGGGCTTTTCTGTTTTTGTTAGTCTTTTCATACAGCCTGACTCTATTCATGTTCTTAGTTCATTTTGGAAATTGCATAAATAATACCCTGAAGCTTGCTTCATCCTCTCCTGTGGTTAGACATAGACTATCCTCAACACTTTCAAGGGTTGGGACTGGCTTTATAAAAAGCTCGTTTTGGAGTGCCTGTCCCTCCCTTAGGTCAATACAACTATGCCCTTTGTATTTTGTAGTAACTTTCTTTTAGGTTTCTACTTATCCACTGACTCTTATTATCCTCTCACTCGCATGGAAATGTTGGTAGGGAACCAAATAATATTTCGGTCACTGTAAAGATAGTGGGAAAACAGAATGAAGGTTTCTTGTAAGCACGTACTTTACTGAGTGGCAGGCTAAAAATGGTTCAAAATATTTTTTAAGTAAAACTTTTATTTCCTAATGCAAATTCAAATGAGGACATTTGTTTATTTTTGGTTTAAGAGAAAAACAAATTTTATTTGCAAATATTTCCATGTTTGCAAATTAGATAGAATATATTGATATTCTAGAAATGACAACCAATCCTTCTCAGTATTAATGACTCCTTCATTGCTCTATC chm1:+:48558257:-1 chm1:+:177481726:-1 chm1:+:476788517:-1 chm1:+:656896909:-1 chm1:+:712394385:-1 chm1:+:983371774:-1 chm1:+:1110908697:-1 chm1:+:1451556551:-1 chm1:+:1952644550:-1 chm1:+:2040235897:-1 chm1:+:2272802342:-1 chm1:+:2402252849:-1 chm1:+:2424224491:-1 chm1:+:2530644078:-1 chm1:+:2751994089:-1 chm1:+:2769102484:-1 +GATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026629967:45 +GATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026628121:-1 chm1:+:2026629968:45 +GATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026629960:45 chm1:+:2275971661:-1 +GATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026629957:45 +GATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026629958:45 +GATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026629959:45 +GATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026629961:45 +GATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026629964:45 +GATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:577336299:-1 +GATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026629963:45 +GATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2010493571:-1 +GATAGAGCAATGAAGGAGTCATTAATACTGAGAAGGATTGGTTGTCATTTCTAGAATATCAATATATTCTATCTAATTTGCAAACATGGAAATATTTGCAAATAAAATTTGTTTTTCTCTTAAACCAAAAATAAACAAATGTCCTCATTTGAATTTGCATTAGGAAATAAAAGTTTTACTTAAAAAATATTTTGAACCATTTTTAGCCTGCCACTCAGTAAAGTACGTGCTTACAAGAAACCTTCATTCTGTTTTCCCACTATCTTTACAGTGACCGAAATATTATTTGGTTCCCTACCAACATTTCCATGCGAGTGAGAGGATAATAAGAGTCAGTGGATAAGTAGAAACCTAAAAGAAAGTTACTACAAAATACAAAGGGCATAGTTGTATTGACCTAAGGGAGGGACAGGCACTCCAAAACGAGCTTTTTATAAAGCCAGTCCCAACCCTTGAAAGTGTTGAGGATAGTCTATGTCTAACCACAGGAGAGGATGAAGCAAGCTTCAGGGTATTATTTATGCAATTTCCAAAATGAACTAAGAACATGAATAGAGTCAGGCTGTATGAAAAGACTAACAAAAACAGAAAAGCCCTACACTATACTAGTCAGAATCTATATTCAAATTTAGTGAGCAAAACACTAGATATGTTGAAGCATAAACATGTCTCAAGGAAGACAATCTGGAATGAGCATAAGCTACTTACTCCATAGTCAGCAGCCCTAAAGCAGTCGAATCAGTTTCCAAGAGAACCAGTCTTACATTGGCTTAGCAGCAAGATCTGATCTAAGAGCTTGC chm1:+:2026629965:45 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:533567737:-1 chm1:+:658619657:-1 chm1:+:1837007260:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:529155963:-1 chm1:+:733376838:-1 chm1:+:1108242566:-1 chm1:+:1694511808:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:166250440:-1 chm1:+:413548465:-1 chm1:+:414393786:-1 chm1:+:504939310:-1 chm1:+:704238617:-1 chm1:+:979935262:-1 chm1:+:1051809751:-1 chm1:+:1319640053:-1 chm1:+:1378625313:-1 chm1:+:1913437078:-1 chm1:+:2120180145:-1 chm1:+:2228056566:-1 chm1:+:2392792806:-1 chm1:+:2641518206:-1 chm1:+:2725211378:-1 chm1:+:2753563596:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:68162000:-1 chm1:+:165288180:-1 chm1:+:207163467:-1 chm1:+:234396571:-1 chm1:+:325986668:-1 chm1:+:517918227:-1 chm1:+:548526597:-1 chm1:+:659809248:-1 chm1:+:1424567246:-1 chm1:+:1646960543:-1 chm1:+:1907167719:-1 chm1:+:2920911449:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:292789478:-1 chm1:+:467359467:-1 chm1:+:721705454:-1 chm1:+:868186831:-1 chm1:+:1201268137:-1 chm1:+:1282211334:-1 chm1:+:2187145957:-1 chm1:+:2414124937:-1 chm1:+:2477354650:-1 chm1:+:2774257546:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:162576349:-1 chm1:+:513124172:-1 chm1:+:1495569588:-1 chm1:+:2281986986:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:813990066:-1 chm1:+:899658132:-1 chm1:+:1431574606:-1 chm1:+:2027917083:-1 chm1:+:2042368994:-1 chm1:+:2262125967:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:172219379:-1 chm1:+:483678009:-1 chm1:+:562688280:-1 chm1:+:1384579476:-1 chm1:+:1809504494:-1 chm1:+:1925467742:-1 chm1:+:2581183972:-1 chm1:+:2859456613:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:265395016:-1 chm1:+:482445855:-1 chm1:+:482557235:-1 chm1:+:1235549901:-1 chm1:+:1327247003:-1 chm1:+:1661225682:-1 chm1:+:1671016415:-1 chm1:+:1879829227:-1 chm1:+:1885365124:-1 chm1:+:1933329751:-1 chm1:+:2497571265:-1 chm1:+:2633362285:-1 chm1:+:2669670319:-1 chm1:+:2737537152:-1 chm1:+:2756245812:-1 chm1:+:2779463003:-1 chm1:+:2874146396:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:935830238:-1 chm1:+:1668838771:-1 chm1:+:1828319774:-1 chm1:+:2467663258:-1 chm1:+:2595250223:-1 chm1:+:2906224930:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:587941108:-1 chm1:+:778176606:-1 chm1:+:983580017:-1 chm1:+:1046342797:-1 chm1:+:1500553720:-1 chm1:+:2162282705:-1 chm1:+:2179268769:-1 chm1:+:2241646304:-1 chm1:+:2264656784:-1 chm1:+:2424163394:-1 chm1:+:2472449732:-1 chm1:+:2476847317:-1 chm1:+:2528779576:-1 chm1:+:2716180561:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:74091228:-1 chm1:+:454032254:-1 chm1:+:1267636009:-1 chm1:+:2417724427:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:187047373:-1 chm1:+:371798873:-1 chm1:+:397009457:-1 chm1:+:431173759:-1 chm1:+:760992391:-1 chm1:+:824524321:-1 chm1:+:987062039:-1 chm1:+:1093217484:-1 chm1:+:1129175300:-1 chm1:+:1144790750:-1 chm1:+:1366202956:-1 chm1:+:1367848375:-1 chm1:+:1441766820:-1 chm1:+:1483289722:-1 chm1:+:1512995891:-1 chm1:+:1950275700:-1 chm1:+:2176754251:-1 chm1:+:2536004643:-1 chm1:+:2951406317:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:79004050:-1 chm1:+:119261819:-1 chm1:+:120504968:-1 chm1:+:171061183:-1 chm1:+:251863373:-1 chm1:+:286519529:-1 chm1:+:307116434:-1 chm1:+:416680741:-1 chm1:+:427851260:-1 chm1:+:510979093:-1 chm1:+:529084084:-1 chm1:+:568592593:-1 chm1:+:703093420:-1 chm1:+:753264848:-1 chm1:+:763836403:-1 chm1:+:807031699:-1 chm1:+:817096840:-1 chm1:+:855799224:-1 chm1:+:957713094:-1 chm1:+:986597414:-1 chm1:+:1036648579:-1 chm1:+:1059504605:-1 chm1:+:1116159632:-1 chm1:+:1192184815:-1 chm1:+:1299632370:-1 chm1:+:1309457731:-1 chm1:+:1340013819:-1 chm1:+:1374291083:-1 chm1:+:1502345411:-1 chm1:+:1661849060:-1 chm1:+:1732389146:-1 chm1:+:1770682992:-1 chm1:+:1845689775:-1 chm1:+:1944896488:-1 chm1:+:1978826380:-1 chm1:+:2059536426:-1 chm1:+:2262721714:-1 chm1:+:2271300982:-1 chm1:+:2390984650:-1 chm1:+:2462560023:-1 chm1:+:2613497040:-1 chm1:+:2650150213:-1 chm1:+:2701494472:-1 chm1:+:2761564297:-1 chm1:+:2944298448:-1 chm1:+:2967151337:-1 chm1:+:3051610552:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:46749348:-1 chm1:+:209036881:-1 chm1:+:302045162:-1 chm1:+:328677752:-1 chm1:+:499149840:-1 chm1:+:516895286:-1 chm1:+:526437689:-1 chm1:+:1022063854:-1 chm1:+:1150483251:-1 chm1:+:1175841198:-1 chm1:+:1247396656:-1 chm1:+:1294912358:-1 chm1:+:1295039091:-1 chm1:+:1482529423:-1 chm1:+:1626793266:-1 chm1:+:1750844904:-1 chm1:+:1791122343:-1 chm1:+:1852902247:-1 chm1:+:1898361215:-1 chm1:+:1923823610:-1 chm1:+:1941570747:-1 chm1:+:2012009558:-1 chm1:+:2106289495:-1 chm1:+:2131455288:-1 chm1:+:2180352552:-1 chm1:+:2260707489:-1 chm1:+:2305710785:-1 chm1:+:2361948529:-1 chm1:+:2458736446:-1 chm1:+:2610208204:-1 chm1:+:2649867837:-1 chm1:+:2683320059:-1 chm1:+:2771772183:-1 chm1:+:2873891470:-1 chm1:+:2909349399:-1 chm1:+:3022673913:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:241196545:-1 chm1:+:1382132856:-1 chm1:+:1391754114:-1 chm1:+:1401242586:-1 chm1:+:2070430642:-1 chm1:+:2125943194:-1 chm1:+:2989850030:-1 chm1:+:3033637957:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:207024936:-1 chm1:+:408706903:-1 chm1:+:439809548:-1 chm1:+:798961247:-1 chm1:+:914474545:-1 chm1:+:1023816985:-1 chm1:+:1090801161:-1 chm1:+:1143187637:-1 chm1:+:1194445733:-1 chm1:+:1877744402:-1 chm1:+:1919285603:-1 chm1:+:2020879730:-1 chm1:+:2261834474:-1 chm1:+:2752709691:-1 chm1:+:2908562407:-1 +TTTAGCATGTTCTGCCTAAAAGGAATTTGTTTTCAAATTCATTTTCCCTTAAAATCAAATACTGAACCCTCTAATTAGAAATAAGGCTTTTGTTCTCTGTACTGTGTGTTGTTCACAAGATCTATTCACTGTTTATTCAGAACACAGACAACATATATGGTGCTTGCCTCCCTCACCCCCACCGTGCCTGCCTTGCCAGGGGCCTGGAATATATGGACATAGTAACATGCTTGTCATATTCTTGAAGAATTTCCGTCTATAAATAAGCCACTATTACTTAGAAGGAAGAAGAATAGAAGGGCCCCAAGGACAGAGTACCTAGCTAGGTGGAGAAATTGAAGAAGGCATCACAGAAAAGGTGTCATTTGTCCTGGTAGGGTGGCAATGGGCTCTCCAGGAGAGGAAAAAGAGAGTACTAGTAGCTAGGAATGCTTGATGCTCATGTTCCAAGTTGTTTTACATAAATTAACTCATCCGATCTTCATGGCAACCCGTAGTGAGATAGTAAGTATTATGATCACACCGCATTTTAAAACAGGGAAATTTAGCAAGGAAAAGTGGACTAACGTGCCTGAGGTCAAAGTAACAAGATGTGGAAGAACATTGGCATGTTACATTGAAGGGTGAGAAGCCCAAGTTGGTGGAAGGGAGCTGCGTGAGACAGGGCTGGGCCAGGTCATATGTGGGCACCTGTGCACCGTAGTGAACAATCTGAGCCTTCCCTGGGGAGGCAAGAGGAATCCAACGGAGATTTTTGGGCTTTTGTCTATTGTGGTAAAGAAAAGATGACAGTTCCAGTG chm1:+:3638608:-1 chm1:+:491147711:-1 chm1:+:542119256:-1 chm1:+:862099504:-1 chm1:+:898062440:-1 chm1:+:1062187661:-1 chm1:+:1101638311:-1 chm1:+:1390741213:-1 chm1:+:1419789918:-1 chm1:+:1760694391:-1 chm1:+:1816739098:-1 chm1:+:2041676176:-1 chm1:+:2131265908:-1 chm1:+:2417330485:-1 chm1:+:2638470303:-1 chm1:+:2662917768:-1 chm1:+:2719849242:-1 chm1:+:3033138688:-1 +CACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:353689043:-1 chm1:+:1100362409:-1 chm1:+:1201272560:35 chm1:+:1395162627:-1 chm1:+:1478068153:-1 chm1:+:1542217032:-1 chm1:+:2944626624:-1 +CACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272568:35 +CACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:378054781:-1 chm1:+:1201272559:35 +CACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272561:35 +CACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272563:35 +CACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272564:35 +CACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272565:35 +CACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272567:35 +CACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272572:35 +CACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1229611756:-1 +CACTGGAACTGTCATCTTTTCTTTACCACAATAGACAAAAGCCCAAAAATCTCCGTTGGATTCCTCTTGCCTCCCCAGGGAAGGCTCAGATTGTTCACTACGGTGCACAGGTGCCCACATATGACCTGGCCCAGCCCTGTCTCACGCAGCTCCCTTCCACCAACTTGGGCTTCTCACCCTTCAATGTAACATGCCAATGTTCTTCCACATCTTGTTACTTTGACCTCAGGCACGTTAGTCCACTTTTCCTTGCTAAATTTCCCTGTTTTAAAATGCGGTGTGATCATAATACTTACTATCTCACTACGGGTTGCCATGAAGATCGGATGAGTTAATTTATGTAAAACAACTTGGAACATGAGCATCAAGCATTCCTAGCTACTAGTACTCTCTTTTTCCTCTCCTGGAGAGCCCATTGCCACCCTACCAGGACAAATGACACCTTTTCTGTGATGCCTTCTTCAATTTCTCCACCTAGCTAGGTACTCTGTCCTTGGGGCCCTTCTATTCTTCTTCCTTCTAAGTAATAGTGGCTTATTTATAGACGGAAATTCTTCAAGAATATGACAAGCATGTTACTATGTCCATATATTCCAGGCCCCTGGCAAGGCAGGCACGGTGGGGGTGAGGGAGGCAAGCACCATATATGTTGTCTGTGTTCTGAATAAACAGTGAATAGATCTTGTGAACAACACACAGTACAGAGAACAAAAGCCTTATTTCTAATTAGAGGGTTCAGTATTTGATTTTAAGGGAAAATGAATTTGAAAACAAATTCCTTTTAGGCAGAACATGCTAAA chm1:+:1201272566:35 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:419189625:-1 chm1:+:1377399162:-1 chm1:+:2771433439:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:826128420:-1 chm1:+:942511836:-1 chm1:+:1472734573:-1 chm1:+:1542618257:-1 chm1:+:2441218310:-1 chm1:+:2617209518:-1 chm1:+:2730669846:-1 chm1:+:2902760798:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:836838112:-1 chm1:+:2610619200:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:410853972:-1 chm1:+:589636809:-1 chm1:+:920610235:-1 chm1:+:1022049314:-1 chm1:+:1027211409:-1 chm1:+:1391491190:-1 chm1:+:1495650300:-1 chm1:+:1514741696:-1 chm1:+:2195501435:-1 chm1:+:2468072708:-1 chm1:+:2935762624:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:302982711:-1 chm1:+:1243892112:-1 chm1:+:1410387631:-1 chm1:+:1544360672:-1 chm1:+:1613227600:-1 chm1:+:1850354464:-1 chm1:+:2556260340:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:17904156:-1 chm1:+:67931397:-1 chm1:+:220600994:-1 chm1:+:231071387:-1 chm1:+:323833325:-1 chm1:+:413294130:-1 chm1:+:420922560:-1 chm1:+:467821622:-1 chm1:+:554236855:-1 chm1:+:682602329:-1 chm1:+:1118583306:-1 chm1:+:1208943490:-1 chm1:+:1352095377:-1 chm1:+:1360204049:-1 chm1:+:1521260285:-1 chm1:+:1534553153:-1 chm1:+:2066785177:-1 chm1:+:2081097338:-1 chm1:+:2161758528:-1 chm1:+:2180630507:-1 chm1:+:2333341943:-1 chm1:+:2351509512:-1 chm1:+:2415289356:-1 chm1:+:2573511463:-1 chm1:+:2700481458:-1 chm1:+:2967314218:-1 chm1:+:3027812012:-1 chm1:+:3064930526:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:200901802:-1 chm1:+:243966780:-1 chm1:+:258643672:-1 chm1:+:302628723:-1 chm1:+:330230267:-1 chm1:+:368496833:-1 chm1:+:478040638:-1 chm1:+:523079323:-1 chm1:+:599840254:-1 chm1:+:668600307:-1 chm1:+:687271964:-1 chm1:+:702411000:-1 chm1:+:849105261:-1 chm1:+:878498556:-1 chm1:+:892796295:-1 chm1:+:901617230:-1 chm1:+:938126782:-1 chm1:+:968359470:-1 chm1:+:971653944:-1 chm1:+:995736554:-1 chm1:+:1113587616:-1 chm1:+:1128600482:-1 chm1:+:1185315777:-1 chm1:+:1244921299:-1 chm1:+:1323039813:-1 chm1:+:1355036131:-1 chm1:+:1387122457:-1 chm1:+:1394247220:-1 chm1:+:1420502902:-1 chm1:+:1425228300:-1 chm1:+:1492707524:-1 chm1:+:1617672961:-1 chm1:+:1618299221:-1 chm1:+:1689228756:-1 chm1:+:1713859117:-1 chm1:+:1796556730:-1 chm1:+:1922963987:-1 chm1:+:2021514448:-1 chm1:+:2028223919:-1 chm1:+:2070755146:-1 chm1:+:2139129668:-1 chm1:+:2147779346:-1 chm1:+:2161858389:-1 chm1:+:2273796217:-1 chm1:+:2287408261:-1 chm1:+:2327542742:-1 chm1:+:2328470639:-1 chm1:+:2328549525:-1 chm1:+:2329481867:-1 chm1:+:2329564294:-1 chm1:+:2360758152:-1 chm1:+:2368703250:-1 chm1:+:2462171661:-1 chm1:+:2469330774:-1 chm1:+:2516677637:-1 chm1:+:2691408249:-1 chm1:+:2742819017:-1 chm1:+:2809113666:-1 chm1:+:2862286899:-1 chm1:+:2868431933:-1 chm1:+:2926333948:-1 chm1:+:2972197168:-1 chm1:+:3014389554:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:301655342:-1 chm1:+:635276068:-1 chm1:+:833894884:-1 chm1:+:853421776:-1 chm1:+:933032222:-1 chm1:+:1343130008:-1 chm1:+:1490706060:-1 chm1:+:1706437648:-1 chm1:+:2195438240:-1 chm1:+:2346332553:-1 chm1:+:2488932418:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:118597991:-1 chm1:+:169937372:-1 chm1:+:716729884:-1 chm1:+:893116601:-1 chm1:+:992912515:-1 chm1:+:1350911097:-1 chm1:+:1366761946:-1 chm1:+:1525156581:-1 chm1:+:1738217869:-1 chm1:+:1772869503:-1 chm1:+:2246005596:-1 chm1:+:2329605893:-1 chm1:+:2393651433:-1 chm1:+:2428358408:-1 chm1:+:2756875254:-1 chm1:+:3005040173:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:72280221:-1 chm1:+:975371313:-1 chm1:+:1032971557:-1 chm1:+:1361248839:-1 chm1:+:1474781073:-1 chm1:+:1842708338:-1 chm1:+:2189907018:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:1163859884:-1 chm1:+:1290579141:-1 chm1:+:1795430461:-1 chm1:+:1865949001:-1 chm1:+:1932111519:-1 chm1:+:1949948557:-1 chm1:+:2030973076:-1 chm1:+:2189856217:-1 chm1:+:2228762069:-1 chm1:+:2385796160:-1 chm1:+:2584122476:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:1147471809:-1 chm1:+:1248379600:-1 chm1:+:1667779910:-1 chm1:+:2818867850:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:215984467:-1 chm1:+:1278082716:-1 chm1:+:2299255361:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:213296336:-1 chm1:+:488386931:-1 chm1:+:582139467:-1 chm1:+:634517135:-1 chm1:+:1830935306:-1 chm1:+:2380313194:-1 chm1:+:2585978374:-1 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chm1:+:713137886:-1 chm1:+:739049431:-1 chm1:+:778751189:-1 chm1:+:878042492:-1 chm1:+:1049596527:-1 chm1:+:1050611481:-1 chm1:+:1129525046:-1 chm1:+:1215566916:-1 chm1:+:1319070536:-1 chm1:+:1364192522:-1 chm1:+:1757676783:-1 chm1:+:1815772479:-1 chm1:+:1827386877:-1 chm1:+:1911805719:-1 chm1:+:2035768718:-1 chm1:+:2070593961:-1 chm1:+:2112730519:-1 chm1:+:2129684162:-1 chm1:+:2158545760:-1 chm1:+:2220168450:-1 chm1:+:2329634592:-1 chm1:+:2333903545:-1 chm1:+:2354275860:-1 chm1:+:2361475666:-1 chm1:+:2366731016:-1 chm1:+:2493720558:-1 chm1:+:2513449739:-1 chm1:+:2716564072:-1 chm1:+:2879215249:-1 chm1:+:2992547268:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:337856274:-1 chm1:+:408517539:-1 chm1:+:557312563:-1 chm1:+:713463006:-1 chm1:+:825484266:-1 chm1:+:871196059:-1 chm1:+:1374509766:-1 chm1:+:1550502833:-1 chm1:+:1551811660:-1 chm1:+:1613400822:-1 chm1:+:1810197525:-1 chm1:+:1978451903:-1 chm1:+:2803320786:-1 chm1:+:2962344570:-1 chm1:+:2973712093:-1 chm1:+:2992513769:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:61812558:-1 chm1:+:87270167:-1 chm1:+:191874732:-1 chm1:+:214736420:-1 chm1:+:416839668:-1 chm1:+:475369491:-1 chm1:+:702155318:-1 chm1:+:750635643:-1 chm1:+:806998911:-1 chm1:+:847062161:-1 chm1:+:908566596:-1 chm1:+:960409459:-1 chm1:+:965914799:-1 chm1:+:1009315636:-1 chm1:+:1059819430:-1 chm1:+:1193637361:-1 chm1:+:1230750985:-1 chm1:+:1267682955:-1 chm1:+:1344712630:-1 chm1:+:1449310331:-1 chm1:+:1449900505:-1 chm1:+:1641606115:-1 chm1:+:1756677277:-1 chm1:+:1939790962:-1 chm1:+:1990146869:-1 chm1:+:2120455719:-1 chm1:+:2139850614:-1 chm1:+:2149092784:-1 chm1:+:2190728666:-1 chm1:+:2251010435:-1 chm1:+:2621214479:-1 chm1:+:2656757035:-1 chm1:+:2936712032:-1 chm1:+:3032502336:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:86773615:-1 chm1:+:195364040:-1 chm1:+:221144857:-1 chm1:+:235819134:-1 chm1:+:254889895:-1 chm1:+:271405248:-1 chm1:+:375307457:-1 chm1:+:452410391:-1 chm1:+:456861007:-1 chm1:+:484823790:-1 chm1:+:494013208:-1 chm1:+:545690572:-1 chm1:+:553285898:-1 chm1:+:603060333:-1 chm1:+:777795021:-1 chm1:+:821541947:-1 chm1:+:858818014:-1 chm1:+:897915387:-1 chm1:+:905190389:-1 chm1:+:926879322:-1 chm1:+:969562677:-1 chm1:+:1003612291:-1 chm1:+:1007197046:-1 chm1:+:1043097318:-1 chm1:+:1049821153:-1 chm1:+:1065936058:-1 chm1:+:1174277182:-1 chm1:+:1425921220:-1 chm1:+:1447451831:-1 chm1:+:1461019738:-1 chm1:+:1504529143:-1 chm1:+:1607922802:-1 chm1:+:1608261729:-1 chm1:+:1626799965:-1 chm1:+:1640430451:-1 chm1:+:1748311772:-1 chm1:+:1778416889:-1 chm1:+:1964768421:-1 chm1:+:2034404741:-1 chm1:+:2123716072:-1 chm1:+:2351919871:-1 chm1:+:2480477485:-1 chm1:+:2553550333:-1 chm1:+:2638670078:-1 chm1:+:2693061061:-1 chm1:+:2805437751:-1 chm1:+:2924372638:-1 chm1:+:2957934016:-1 chm1:+:2979612235:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:23105569:-1 chm1:+:85543612:-1 chm1:+:215248538:-1 chm1:+:336028916:-1 chm1:+:466294270:-1 chm1:+:1486327894:-1 chm1:+:1510321424:-1 chm1:+:1637126236:-1 chm1:+:1691330184:-1 chm1:+:1727114267:-1 chm1:+:1729304028:-1 chm1:+:1900084826:-1 chm1:+:1965952364:-1 chm1:+:2278584953:-1 chm1:+:2398742542:-1 chm1:+:2624110399:-1 chm1:+:2632167492:-1 chm1:+:2664861085:-1 chm1:+:2758766636:-1 chm1:+:2760727553:-1 chm1:+:2849756553:-1 chm1:+:2889851215:-1 +AGAACTCAAACCTTTGTAGCTACTGTCAAAATACAGGTCCACTACTGTACTATATTCATGCCCCGGAAAATGCGAAACCCTGCAAACTTTCCCCTGAGATTGCCGTGCGGCTGGAGGCTAGAGAAAGTCATACAGCTGGAATAAGAAGGGAGAAGAAAGGGGAGGAAGAGATAACTGTAACATGTGCAATTTCCATGAAATAAGAACAAAAGAAGGTTCCAGGCACTGACTAAGGCAACGTTGCTGATCTCGATTGCACGTTAATCTTAAATGCTAATGACGAGTGAATGGGTGGCAGCACACCAACGATGGCATATCGTATACATATGTAACAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTTTTTAAAAAGAAAGATATCTGTATCGAACTTGACAGATGAGGAAAATTGAGTCAAAGCCCTATTAACCACATTTGCCAATCCAGGGAGGAGAATTCAAATCCCAACAGTCTGACTTCAGATTTCATCACAAAAGACCCTCTCCAGCCTCCACAAGACCTACCCATCCCTTCAGGGTCTGAGAAACTGTTAGCTGTGGCAAGAAGCATCAGGGACAGACTTACGAGTCAAACACAAAGGAAAGCTGGGCTTAAGAAATAAAAATATTAATATATGTCCCCTAGATATTCAGGAATTACACCGACAGACTTTATAAGCATTTTGCCCTATTTACTCCACCCCCTGGGGCTTTATTGAGGTATGACTGGAAAACAAAAAATTGTATACGTTAAGGTATACAACGTGATATTTTG chm1:+:479258147:-1 chm1:+:529104320:-1 chm1:+:572213606:-1 chm1:+:576937851:-1 chm1:+:696156124:-1 chm1:+:891204078:-1 chm1:+:950119793:-1 chm1:+:1167370044:-1 chm1:+:1337881396:-1 chm1:+:1485544417:-1 chm1:+:1629682330:-1 chm1:+:1846032580:-1 chm1:+:1882139490:-1 chm1:+:2133357693:-1 chm1:+:2163017990:-1 chm1:+:2234118984:-1 chm1:+:2271199792:-1 chm1:+:2384398263:-1 chm1:+:2726873412:-1 chm1:+:3006237662:-1 +CAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1255375955:44 +CAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:796683985:-1 +CAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1322727122:-1 +CAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1255375939:44 +CAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1255375940:44 +CAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1255375941:44 +CAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1255375948:44 +CAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1255375943:44 +CAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1255375944:44 +CAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:1255375937:44 +CAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:53364029:-1 +CAAAATATCACGTTGTATACCTTAACGTATACAATTTTTTGTTTTCCAGTCATACCTCAATAAAGCCCCAGGGGGTGGAGTAAATAGGGCAAAATGCTTATAAAGTCTGTCGGTGTAATTCCTGAATATCTAGGGGACATATATTAATATTTTTATTTCTTAAGCCCAGCTTTCCTTTGTGTTTGACTCGTAAGTCTGTCCCTGATGCTTCTTGCCACAGCTAACAGTTTCTCAGACCCTGAAGGGATGGGTAGGTCTTGTGGAGGCTGGAGAGGGTCTTTTGTGATGAAATCTGAAGTCAGACTGTTGGGATTTGAATTCTCCTCCCTGGATTGGCAAATGTGGTTAATAGGGCTTTGACTCAATTTTCCTCATCTGTCAAGTTCGATACAGATATCTTTCTTTTTAAAAAATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCAGGTTGTTACATATGTATACGATATGCCATCGTTGGTGTGCTGCCACCCATTCACTCGTCATTAGCATTTAAGATTAACGTGCAATCGAGATCAGCAACGTTGCCTTAGTCAGTGCCTGGAACCTTCTTTTGTTCTTATTTCATGGAAATTGCACATGTTACAGTTATCTCTTCCTCCCCTTTCTTCTCCCTTCTTATTCCAGCTGTATGACTTTCTCTAGCCTCCAGCCGCACGGCAATCTCAGGGGAAAGTTTGCAGGGTTTCGCATTTTCCGGGGCATGAATATAGTACAGTAGTGGACCTGTATTTTGACAGTAGCTACAAAGGTTTGAGTTCT chm1:+:159464826:-1 chm1:+:460226508:-1 chm1:+:718171805:-1 chm1:+:747527418:-1 chm1:+:811145895:-1 chm1:+:944654657:-1 chm1:+:978641100:-1 chm1:+:1011212615:-1 chm1:+:1255375945:44 chm1:+:1445749020:-1 chm1:+:2195505805:-1 chm1:+:2232639410:-1 chm1:+:2600829401:-1 chm1:+:2650968471:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:239563378:-1 chm1:+:643915524:-1 chm1:+:663151151:-1 chm1:+:715092237:-1 chm1:+:855792548:-1 chm1:+:1072167337:-1 chm1:+:1091943528:-1 chm1:+:1144136349:-1 chm1:+:1147369991:-1 chm1:+:1383879801:-1 chm1:+:1547168097:-1 chm1:+:1561824731:-1 chm1:+:2539479656:-1 chm1:+:2587519434:-1 chm1:+:2919008104:-1 chm1:+:3017778178:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:56062148:-1 chm1:+:76368335:-1 chm1:+:95039660:-1 chm1:+:116060945:-1 chm1:+:116395499:-1 chm1:+:180479674:-1 chm1:+:198930644:-1 chm1:+:210208373:-1 chm1:+:225320550:-1 chm1:+:248167972:-1 chm1:+:248225522:-1 chm1:+:320076344:-1 chm1:+:362335330:-1 chm1:+:382814574:-1 chm1:+:394630594:-1 chm1:+:397901680:-1 chm1:+:422387665:-1 chm1:+:463846882:-1 chm1:+:466427846:-1 chm1:+:509492461:-1 chm1:+:528486756:-1 chm1:+:549090286:-1 chm1:+:560697625:-1 chm1:+:579259865:-1 chm1:+:579631342:-1 chm1:+:591618255:-1 chm1:+:641469482:-1 chm1:+:649078908:-1 chm1:+:652955018:-1 chm1:+:654009102:-1 chm1:+:727161899:-1 chm1:+:749437741:-1 chm1:+:768523660:-1 chm1:+:782291643:-1 chm1:+:795191778:-1 chm1:+:796064825:-1 chm1:+:808836531:-1 chm1:+:823647473:-1 chm1:+:912629068:-1 chm1:+:950165288:-1 chm1:+:973055289:-1 chm1:+:975398148:-1 chm1:+:976536870:-1 chm1:+:981289952:-1 chm1:+:989873487:-1 chm1:+:1006193699:-1 chm1:+:1039629404:-1 chm1:+:1111735897:-1 chm1:+:1137489545:-1 chm1:+:1137580931:-1 chm1:+:1141528515:-1 chm1:+:1147319187:-1 chm1:+:1154261096:-1 chm1:+:1155864908:-1 chm1:+:1177350600:-1 chm1:+:1212048013:-1 chm1:+:1221388834:-1 chm1:+:1228194388:-1 chm1:+:1246113649:-1 chm1:+:1280363020:-1 chm1:+:1281904038:-1 chm1:+:1285714580:-1 chm1:+:1323539800:-1 chm1:+:1350257513:-1 chm1:+:1378819617:-1 chm1:+:1380783301:-1 chm1:+:1381417471:-1 chm1:+:1389690755:-1 chm1:+:1410647850:-1 chm1:+:1410647885:-1 chm1:+:1421245576:-1 chm1:+:1425642435:-1 chm1:+:1432342025:-1 chm1:+:1464363729:-1 chm1:+:1465353187:-1 chm1:+:1490492767:-1 chm1:+:1517798262:-1 chm1:+:1555090933:-1 chm1:+:1566178481:-1 chm1:+:1574079341:-1 chm1:+:1685313545:-1 chm1:+:1726304464:-1 chm1:+:1776616305:-1 chm1:+:1778238549:-1 chm1:+:1800786304:-1 chm1:+:1831389460:-1 chm1:+:1837305106:-1 chm1:+:1838541990:-1 chm1:+:1844713630:-1 chm1:+:1859746405:-1 chm1:+:1924562930:-1 chm1:+:1928828413:-1 chm1:+:1939463980:-1 chm1:+:1940284281:-1 chm1:+:1975722358:-1 chm1:+:2016154008:-1 chm1:+:2037585201:-1 chm1:+:2041424256:-1 chm1:+:2041614167:-1 chm1:+:2048123368:-1 chm1:+:2113034559:-1 chm1:+:2121089789:-1 chm1:+:2123291607:-1 chm1:+:2154752119:-1 chm1:+:2166165750:-1 chm1:+:2240397772:-1 chm1:+:2243246475:-1 chm1:+:2266005495:-1 chm1:+:2267221596:-1 chm1:+:2269835051:-1 chm1:+:2282817478:-1 chm1:+:2384200928:-1 chm1:+:2391554283:-1 chm1:+:2558496514:-1 chm1:+:2560594788:-1 chm1:+:2575791639:-1 chm1:+:2590595505:-1 chm1:+:2611596073:-1 chm1:+:2621538590:-1 chm1:+:2643093906:-1 chm1:+:2649575225:-1 chm1:+:2675459194:-1 chm1:+:2697291668:-1 chm1:+:2702546964:-1 chm1:+:2724706086:-1 chm1:+:2738701323:-1 chm1:+:2758265478:-1 chm1:+:2796151577:-1 chm1:+:2799957414:-1 chm1:+:2807477389:-1 chm1:+:2825847538:-1 chm1:+:2871064463:-1 chm1:+:2872161293:-1 chm1:+:2916118392:-1 chm1:+:2923300861:-1 chm1:+:2938204899:-1 chm1:+:2947919806:-1 chm1:+:2955191290:-1 chm1:+:2967136475:-1 chm1:+:2971807890:-1 chm1:+:2988237909:-1 chm1:+:2989535077:-1 chm1:+:2993339390:-1 chm1:+:3003116921:-1 chm1:+:3009590701:-1 chm1:+:3019168824:-1 chm1:+:3021560096:-1 chm1:+:3024098557:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:97821612:-1 chm1:+:106880571:-1 chm1:+:160561953:-1 chm1:+:162481014:-1 chm1:+:319828732:-1 chm1:+:319978291:-1 chm1:+:372452683:-1 chm1:+:404495152:-1 chm1:+:404988019:-1 chm1:+:521996173:-1 chm1:+:625653056:-1 chm1:+:651645185:-1 chm1:+:665055656:-1 chm1:+:745466723:-1 chm1:+:749227062:-1 chm1:+:813868061:-1 chm1:+:820579167:-1 chm1:+:995851352:-1 chm1:+:1209229622:-1 chm1:+:1250898656:-1 chm1:+:1257253055:-1 chm1:+:1285657395:-1 chm1:+:1327977928:-1 chm1:+:1365126068:-1 chm1:+:1435444290:-1 chm1:+:1456707509:-1 chm1:+:1552826704:-1 chm1:+:1567840279:-1 chm1:+:1618863957:-1 chm1:+:1629463768:-1 chm1:+:1648927301:-1 chm1:+:1726907411:-1 chm1:+:1729094334:-1 chm1:+:1757460626:-1 chm1:+:1762695973:-1 chm1:+:1774046697:-1 chm1:+:1865411123:-1 chm1:+:1914463594:-1 chm1:+:1918992073:-1 chm1:+:1919146835:-1 chm1:+:1976588179:-1 chm1:+:1994913539:-1 chm1:+:2147415245:-1 chm1:+:2156730926:-1 chm1:+:2225721905:-1 chm1:+:2407030034:-1 chm1:+:2433679172:-1 chm1:+:2534455698:-1 chm1:+:2551705817:-1 chm1:+:2600304142:-1 chm1:+:2603899376:-1 chm1:+:2630965683:-1 chm1:+:2671733059:-1 chm1:+:2903958891:-1 chm1:+:2909120441:-1 chm1:+:2920298166:-1 chm1:+:2955079361:-1 chm1:+:2958246043:-1 chm1:+:2986358715:-1 chm1:+:2993900338:-1 chm1:+:3006133909:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:802525791:-1 chm1:+:883304725:-1 chm1:+:1242856981:-1 chm1:+:1654308172:-1 chm1:+:2166345403:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:190492745:-1 chm1:+:198107300:-1 chm1:+:275522098:-1 chm1:+:275899010:-1 chm1:+:312593175:-1 chm1:+:369333899:-1 chm1:+:436224546:-1 chm1:+:448219988:-1 chm1:+:665592755:-1 chm1:+:727992442:-1 chm1:+:789332159:-1 chm1:+:896678005:-1 chm1:+:1176337160:-1 chm1:+:1210617284:-1 chm1:+:1296294699:-1 chm1:+:1321029782:-1 chm1:+:1358001282:-1 chm1:+:1365392034:-1 chm1:+:1498713037:-1 chm1:+:1917508410:-1 chm1:+:1955925137:-1 chm1:+:2016154013:-1 chm1:+:2147075113:-1 chm1:+:2408566376:-1 chm1:+:2771675463:-1 chm1:+:2777366799:-1 chm1:+:2934943570:-1 chm1:+:3010488540:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:69834265:-1 chm1:+:103787547:-1 chm1:+:103927280:-1 chm1:+:151841573:-1 chm1:+:221097394:-1 chm1:+:266810761:-1 chm1:+:315046875:-1 chm1:+:329427705:-1 chm1:+:409769914:-1 chm1:+:430019465:-1 chm1:+:434823242:-1 chm1:+:437384864:-1 chm1:+:467092383:-1 chm1:+:467461499:-1 chm1:+:474840516:-1 chm1:+:493522222:-1 chm1:+:530849149:-1 chm1:+:543177021:-1 chm1:+:578840354:-1 chm1:+:613158101:-1 chm1:+:623075763:-1 chm1:+:681178186:-1 chm1:+:713728798:-1 chm1:+:733557481:-1 chm1:+:778042424:-1 chm1:+:836318289:-1 chm1:+:946939829:-1 chm1:+:982431376:-1 chm1:+:1158525153:-1 chm1:+:1160023493:-1 chm1:+:1181154301:-1 chm1:+:1313907544:-1 chm1:+:1343333632:-1 chm1:+:1347223392:-1 chm1:+:1432121374:-1 chm1:+:1450339264:-1 chm1:+:1458236831:-1 chm1:+:1462877561:-1 chm1:+:1471504700:-1 chm1:+:1548302649:-1 chm1:+:1570808763:-1 chm1:+:1644011839:-1 chm1:+:1645534657:-1 chm1:+:1698682667:-1 chm1:+:1709310514:-1 chm1:+:1741534649:-1 chm1:+:1755188125:-1 chm1:+:1772587992:-1 chm1:+:1823771341:-1 chm1:+:1857500749:-1 chm1:+:1879030756:-1 chm1:+:1913645769:-1 chm1:+:2189650404:-1 chm1:+:2391713004:-1 chm1:+:2514347276:-1 chm1:+:2593607281:-1 chm1:+:2596318551:-1 chm1:+:2649514565:-1 chm1:+:2720100593:-1 chm1:+:2896928015:-1 chm1:+:2908603326:-1 chm1:+:2909096999:-1 chm1:+:2915788066:-1 chm1:+:2918116378:-1 chm1:+:2926136772:-1 chm1:+:2931221190:-1 chm1:+:2935189675:-1 chm1:+:2963252319:-1 chm1:+:2965052460:-1 chm1:+:2974602280:-1 chm1:+:2982499481:-1 chm1:+:2986798520:-1 chm1:+:3023819765:-1 chm1:+:3032143000:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:668033559:-1 chm1:+:797047849:-1 chm1:+:1472962224:-1 chm1:+:1725872433:-1 chm1:+:1736484594:-1 chm1:+:1913130583:-1 chm1:+:2142094384:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:593191723:-1 chm1:+:665129836:-1 chm1:+:672881431:-1 chm1:+:782378860:-1 chm1:+:918849994:-1 chm1:+:1184862458:-1 chm1:+:1312635228:-1 chm1:+:1489005696:-1 chm1:+:1524883171:-1 chm1:+:1747287111:-1 chm1:+:1937631122:-1 chm1:+:2038215963:-1 chm1:+:2114725598:-1 chm1:+:2609706262:-1 chm1:+:2995579213:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:2035565573:-1 chm1:+:2552637018:-1 chm1:+:2803163398:-1 chm1:+:2971143833:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:369826770:-1 chm1:+:785614657:-1 chm1:+:972813673:-1 chm1:+:2780280915:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:921629799:-1 chm1:+:1388478586:-1 chm1:+:1524920699:-1 chm1:+:2038262993:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:56303956:-1 chm1:+:176616174:-1 chm1:+:351878457:-1 chm1:+:373802861:-1 chm1:+:379480320:-1 chm1:+:399051893:-1 chm1:+:507464257:-1 chm1:+:598630377:-1 chm1:+:692061016:-1 chm1:+:732575056:-1 chm1:+:767847075:-1 chm1:+:817251343:-1 chm1:+:890613540:-1 chm1:+:921764805:-1 chm1:+:1047037702:-1 chm1:+:1065645451:-1 chm1:+:1082493296:-1 chm1:+:1125185790:-1 chm1:+:1136079037:-1 chm1:+:1150045110:-1 chm1:+:1190231812:-1 chm1:+:1228066460:-1 chm1:+:1276878404:-1 chm1:+:1346632105:-1 chm1:+:1446578843:-1 chm1:+:1447371333:-1 chm1:+:1547168096:-1 chm1:+:1571254956:-1 chm1:+:1574943587:-1 chm1:+:1637766156:-1 chm1:+:1739169830:-1 chm1:+:1888726965:-1 chm1:+:1971236637:-1 chm1:+:1984854207:-1 chm1:+:1994130334:-1 chm1:+:2025326420:-1 chm1:+:2029626631:-1 chm1:+:2051240577:-1 chm1:+:2126777216:-1 chm1:+:2167648049:-1 chm1:+:2178577749:-1 chm1:+:2191131251:-1 chm1:+:2346884550:-1 chm1:+:2350278312:-1 chm1:+:2441143339:-1 chm1:+:2555102151:-1 chm1:+:2655267406:-1 chm1:+:2690873890:-1 chm1:+:2935924345:-1 chm1:+:2962509622:-1 chm1:+:2965624714:-1 chm1:+:3006250278:-1 chm1:+:3042370074:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:388414195:-1 chm1:+:397270459:-1 chm1:+:586698001:-1 chm1:+:668430840:-1 chm1:+:724191312:-1 chm1:+:1219001710:-1 chm1:+:1305638928:-1 chm1:+:1645534652:-1 chm1:+:2404846058:-1 chm1:+:2655147949:-1 chm1:+:2762730692:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:89198988:-1 chm1:+:221161246:-1 chm1:+:225253662:-1 chm1:+:359745905:-1 chm1:+:389112156:-1 chm1:+:433296613:-1 chm1:+:470255807:-1 chm1:+:729495309:-1 chm1:+:746566215:-1 chm1:+:750580053:-1 chm1:+:774890528:-1 chm1:+:778989651:-1 chm1:+:783745717:-1 chm1:+:857761358:-1 chm1:+:862019607:-1 chm1:+:948311688:-1 chm1:+:972027953:-1 chm1:+:1004881834:-1 chm1:+:1005037090:-1 chm1:+:1032992348:-1 chm1:+:1033611740:-1 chm1:+:1042053684:-1 chm1:+:1076118477:-1 chm1:+:1107557586:-1 chm1:+:1125346026:-1 chm1:+:1149145003:-1 chm1:+:1251358916:-1 chm1:+:1313840516:-1 chm1:+:1342914811:-1 chm1:+:1386152269:-1 chm1:+:1410893552:-1 chm1:+:1458680165:-1 chm1:+:1483911206:-1 chm1:+:1510879105:-1 chm1:+:1575128561:-1 chm1:+:1641557931:-1 chm1:+:1699767711:-1 chm1:+:1734792986:-1 chm1:+:1763482839:-1 chm1:+:2123331834:-1 chm1:+:2231206473:-1 chm1:+:2403011969:-1 chm1:+:2415721961:-1 chm1:+:2427505453:-1 chm1:+:2461329442:-1 chm1:+:2472181000:-1 chm1:+:2608889667:-1 chm1:+:2613379761:-1 chm1:+:2806415128:-1 chm1:+:2852393810:-1 chm1:+:2926115141:-1 chm1:+:2953882056:-1 chm1:+:2975170656:-1 chm1:+:2999073418:-1 chm1:+:3022820294:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:394601141:-1 chm1:+:650859817:-1 chm1:+:1021985515:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:487789035:-1 chm1:+:1539365724:-1 chm1:+:1762926866:-1 chm1:+:2185158403:-1 chm1:+:2352009181:-1 chm1:+:2769204674:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:870546382:-1 chm1:+:1089335935:-1 chm1:+:1120727373:-1 chm1:+:1415643025:-1 chm1:+:1903329595:-1 chm1:+:2513863398:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:2983173777:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:281530229:-1 chm1:+:599294137:-1 chm1:+:644892434:-1 chm1:+:958333030:-1 chm1:+:1109262041:-1 chm1:+:1126085178:-1 chm1:+:1444321780:-1 chm1:+:1508457638:-1 chm1:+:1519964529:-1 chm1:+:1622417844:-1 chm1:+:1763760643:-1 chm1:+:1893542512:-1 chm1:+:1906538330:-1 chm1:+:2255113846:-1 chm1:+:2377021586:-1 chm1:+:2457308065:-1 chm1:+:2592540277:-1 chm1:+:2621851086:-1 chm1:+:3023587066:-1 chm1:+:3035513137:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:537505820:-1 chm1:+:1367030147:-1 chm1:+:1689579293:-1 chm1:+:2583145409:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:7325913:-1 chm1:+:231882628:-1 chm1:+:253684646:-1 chm1:+:277093248:-1 chm1:+:436992560:-1 chm1:+:482735373:-1 chm1:+:515137895:-1 chm1:+:586371878:-1 chm1:+:636465818:-1 chm1:+:953335715:-1 chm1:+:1406312872:-1 chm1:+:1456518193:-1 chm1:+:1541610073:-1 chm1:+:1776040497:-1 chm1:+:1866039558:-1 chm1:+:2015356814:-1 chm1:+:2116726523:-1 chm1:+:2170117947:-1 chm1:+:2241622126:-1 chm1:+:2293114210:-1 chm1:+:2363696729:-1 chm1:+:2420559265:-1 chm1:+:2427505447:-1 chm1:+:2797459219:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:49923726:-1 chm1:+:83698635:-1 chm1:+:106594887:-1 chm1:+:221022060:-1 chm1:+:261785071:-1 chm1:+:397271320:-1 chm1:+:498346617:-1 chm1:+:517464937:-1 chm1:+:543362223:-1 chm1:+:613842598:-1 chm1:+:645559487:-1 chm1:+:766549774:-1 chm1:+:900552187:-1 chm1:+:1036249512:-1 chm1:+:1179024901:-1 chm1:+:1309984269:-1 chm1:+:1507061287:-1 chm1:+:1508432287:-1 chm1:+:1544415465:-1 chm1:+:1750324403:-1 chm1:+:2055503624:-1 chm1:+:2358317137:-1 chm1:+:2630966500:-1 chm1:+:2862224539:-1 chm1:+:2900013822:-1 chm1:+:2991216207:-1 chm1:+:3024696468:-1 chm1:+:3098107478:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:170817846:-1 chm1:+:271639207:-1 chm1:+:409970973:-1 chm1:+:482116797:-1 chm1:+:689488974:-1 chm1:+:868220231:-1 chm1:+:945097242:-1 chm1:+:1074810107:-1 chm1:+:1161939658:-1 chm1:+:1834743678:-1 chm1:+:2170619458:-1 chm1:+:2254664500:-1 chm1:+:2928148241:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:143476609:-1 chm1:+:297775097:-1 chm1:+:735859859:-1 chm1:+:783809620:-1 chm1:+:1507307031:-1 chm1:+:1605845972:-1 chm1:+:1609028974:-1 chm1:+:1661822752:-1 chm1:+:1788554085:-1 chm1:+:1854845852:-1 chm1:+:2163413825:-1 chm1:+:2394035402:-1 chm1:+:2791576359:-1 chm1:+:3049683487:-1 chm1:+:3097972928:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:121101719:-1 chm1:+:144088916:-1 chm1:+:206551921:-1 chm1:+:635713129:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:170378762:-1 chm1:+:178558263:-1 chm1:+:303723238:-1 chm1:+:324087729:-1 chm1:+:411744885:-1 chm1:+:421330706:-1 chm1:+:439499719:-1 chm1:+:483940613:-1 chm1:+:550914888:-1 chm1:+:771693456:-1 chm1:+:923879822:-1 chm1:+:1262040420:-1 chm1:+:1367332855:-1 chm1:+:1464596004:-1 chm1:+:1738050462:-1 chm1:+:1815592787:-1 chm1:+:2595095671:-1 chm1:+:2895488198:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:176549740:-1 chm1:+:186495599:-1 chm1:+:321300385:-1 chm1:+:328785876:-1 chm1:+:375224989:-1 chm1:+:459299046:-1 chm1:+:557401381:-1 chm1:+:611452535:-1 chm1:+:813259425:-1 chm1:+:990527227:-1 chm1:+:1706604635:-1 chm1:+:1713119724:-1 chm1:+:1772696884:-1 chm1:+:1961418960:-1 chm1:+:1972275108:-1 chm1:+:2306182550:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:195757596:-1 chm1:+:578024691:-1 chm1:+:591037908:-1 chm1:+:709718584:-1 chm1:+:915279059:-1 chm1:+:1788006717:-1 chm1:+:1895331444:-1 chm1:+:1963597471:-1 chm1:+:2036956516:-1 chm1:+:2617915818:-1 chm1:+:2619539976:-1 chm1:+:2991975527:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:100720254:-1 chm1:+:440306933:-1 chm1:+:676162702:-1 chm1:+:1111797855:-1 chm1:+:1375534812:-1 chm1:+:1801995431:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:184432509:-1 chm1:+:378853073:-1 chm1:+:400505076:-1 chm1:+:561872524:-1 chm1:+:674143229:-1 chm1:+:790635031:-1 chm1:+:1154959472:-1 chm1:+:1361448441:-1 chm1:+:1467746920:-1 chm1:+:2583824856:-1 chm1:+:2927015050:-1 chm1:+:3031719633:-1 +TTGGCCATTTGTATGCCTTCTTTTGAGAAATGTTTATTAAGGTCGTTTGCCCCTTTTAAATCACGATTGTTTTTACTATTGTTGTTTGTGTTCCTTATATATTCTGGATTATTCGATCCCTTATCAGATGTATAGTTTACAAATATTTGTCCCATTCTGTAGATTGTCTTTTCACTCTGTTAATTGTTTCCTTGGCTGTGCAGAGGATTTTTAGTTTGATTATAATCCCACTTGTCTATTTTTGCTTTTGTTGCCTGTGCTTTTGAGGTCTCGTCCAAAAAATCCTACCCAGTCCAATGTCATGAAGTGTTCCCCCATGTTTTCTTTCCAGTACTTTCATAGTTTAAGGTCCTACATAAGTCTTTAATCCACTTTTGAGTGATTTTTGTATATGGTGAAAAATAGGGTACCAATTTCATTCTTCTGCATGTGGATATTCAATTTTTCCCTGTACCATTTATTGAAGAAACCTGTCCTTCCCCAAATGTGTCGTTCTTGGCACCTTGTTGAAAAATTAGTTGGGATATGGATAGGTCGTTTTTTTTTCTGGGTTCTCTGTTCTGTTTTTATTTGGTCTATATGTCTCTTTTTGGTTACCATAGCTTGTAGTATAGTTCAAGTCAGGTAGTGTTTGGTTACTATGGCCTTTGTGTAATTTAAACTCAGGTTAGTGTGAATGTTTCCAGCTTTATTCTTTTTGCTCAAGATGCTTTGGCTGCTTGGGGTCTTTGTGATTTCATAAGAAATTTAGAATTAATTTTTTCTATTTCTACTAATAGAATAATAATGTCATTGGTATT chm1:+:238794294:-1 chm1:+:314461820:-1 chm1:+:575024457:-1 chm1:+:663151144:-1 chm1:+:1081650863:-1 chm1:+:1086861239:-1 chm1:+:1171977342:-1 chm1:+:1248625994:-1 chm1:+:1323735248:-1 chm1:+:1380091647:-1 chm1:+:1619312323:-1 chm1:+:2041424125:-1 chm1:+:2263548726:-1 chm1:+:2912399241:-1 +AATACCAATGACATTATTATTCTATTAGTAGAAATAGAAAAAATTAATTCTAAATTTCTTATGAAATCACAAAGACCCCAAGCAGCCAAAGCATCTTGAGCAAAAAGAATAAAGCTGGAAACATTCACACTAACCTGAGTTTAAATTACACAAAGGCCATAGTAACCAAACACTACCTGACTTGAACTATACTACAAGCTATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:237763169:39 chm1:+:278469868:-1 chm1:+:401129581:-1 chm1:+:532869214:-1 chm1:+:603560867:-1 chm1:+:660115228:-1 chm1:+:829232330:-1 chm1:+:847398920:-1 chm1:+:1481256394:-1 chm1:+:1658551965:-1 chm1:+:1972663816:-1 chm1:+:2220970057:-1 chm1:+:2922882595:-1 chm1:+:2930543219:-1 +AATACCAATGACATTATTATTCTATTAGTAGAAATAGAAAAAATTAATTCTAAATTTCTTATGAAATCACAAAGACCCCAAGCAGCCAAAGCATCTTGAGCAAAAAGAATAAAGCTGGAAACATTCACACTAACCTGAGTTTAAATTACACAAAGGCCATAGTAACCAAACACTACCTGACTTGAACTATACTACAAGCTATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:157347115:-1 chm1:+:237763168:39 +AATACCAATGACATTATTATTCTATTAGTAGAAATAGAAAAAATTAATTCTAAATTTCTTATGAAATCACAAAGACCCCAAGCAGCCAAAGCATCTTGAGCAAAAAGAATAAAGCTGGAAACATTCACACTAACCTGAGTTTAAATTACACAAAGGCCATAGTAACCAAACACTACCTGACTTGAACTATACTACAAGCTATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:237763167:39 chm1:+:2689113641:-1 +AATACCAATGACATTATTATTCTATTAGTAGAAATAGAAAAAATTAATTCTAAATTTCTTATGAAATCACAAAGACCCCAAGCAGCCAAAGCATCTTGAGCAAAAAGAATAAAGCTGGAAACATTCACACTAACCTGAGTTTAAATTACACAAAGGCCATAGTAACCAAACACTACCTGACTTGAACTATACTACAAGCTATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:1913066649:-1 +AATACCAATGACATTATTATTCTATTAGTAGAAATAGAAAAAATTAATTCTAAATTTCTTATGAAATCACAAAGACCCCAAGCAGCCAAAGCATCTTGAGCAAAAAGAATAAAGCTGGAAACATTCACACTAACCTGAGTTTAAATTACACAAAGGCCATAGTAACCAAACACTACCTGACTTGAACTATACTACAAGCTATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:1160027277:-1 +AATACCAATGACATTATTATTCTATTAGTAGAAATAGAAAAAATTAATTCTAAATTTCTTATGAAATCACAAAGACCCCAAGCAGCCAAAGCATCTTGAGCAAAAAGAATAAAGCTGGAAACATTCACACTAACCTGAGTTTAAATTACACAAAGGCCATAGTAACCAAACACTACCTGACTTGAACTATACTACAAGCTATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:2775836174:-1 +AATACCAATGACATTATTATTCTATTAGTAGAAATAGAAAAAATTAATTCTAAATTTCTTATGAAATCACAAAGACCCCAAGCAGCCAAAGCATCTTGAGCAAAAAGAATAAAGCTGGAAACATTCACACTAACCTGAGTTTAAATTACACAAAGGCCATAGTAACCAAACACTACCTGACTTGAACTATACTACAAGCTATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:98975362:-1 chm1:+:659146896:-1 +AATACCAATGACATTATTATTCTATTAGTAGAAATAGAAAAAATTAATTCTAAATTTCTTATGAAATCACAAAGACCCCAAGCAGCCAAAGCATCTTGAGCAAAAAGAATAAAGCTGGAAACATTCACACTAACCTGAGTTTAAATTACACAAAGGCCATAGTAACCAAACACTACCTGACTTGAACTATACTACAAGCTATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:3027161793:-1 +AATACCAATGACATTATTATTCTATTAGTAGAAATAGAAAAAATTAATTCTAAATTTCTTATGAAATCACAAAGACCCCAAGCAGCCAAAGCATCTTGAGCAAAAAGAATAAAGCTGGAAACATTCACACTAACCTGAGTTTAAATTACACAAAGGCCATAGTAACCAAACACTACCTGACTTGAACTATACTACAAGCTATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:237763174:39 +AATACCAATGACATTATTATTCTATTAGTAGAAATAGAAAAAATTAATTCTAAATTTCTTATGAAATCACAAAGACCCCAAGCAGCCAAAGCATCTTGAGCAAAAAGAATAAAGCTGGAAACATTCACACTAACCTGAGTTTAAATTACACAAAGGCCATAGTAACCAAACACTACCTGACTTGAACTATACTACAAGCTATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:237763173:39 +AATACCAATGACATTATTATTCTATTAGTAGAAATAGAAAAAATTAATTCTAAATTTCTTATGAAATCACAAAGACCCCAAGCAGCCAAAGCATCTTGAGCAAAAAGAATAAAGCTGGAAACATTCACACTAACCTGAGTTTAAATTACACAAAGGCCATAGTAACCAAACACTACCTGACTTGAACTATACTACAAGCTATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:684806002:-1 +AATACCAATGACATTATTATTCTATTAGTAGAAATAGAAAAAATTAATTCTAAATTTCTTATGAAATCACAAAGACCCCAAGCAGCCAAAGCATCTTGAGCAAAAAGAATAAAGCTGGAAACATTCACACTAACCTGAGTTTAAATTACACAAAGGCCATAGTAACCAAACACTACCTGACTTGAACTATACTACAAGCTATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:89503481:-1 +AATACCAATGACATTATTATTCTATTAGTAGAAATAGAAAAAATTAATTCTAAATTTCTTATGAAATCACAAAGACCCCAAGCAGCCAAAGCATCTTGAGCAAAAAGAATAAAGCTGGAAACATTCACACTAACCTGAGTTTAAATTACACAAAGGCCATAGTAACCAAACACTACCTGACTTGAACTATACTACAAGCTATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:72920742:-1 chm1:+:415374004:-1 chm1:+:421465414:-1 chm1:+:812072322:-1 chm1:+:1109103786:-1 chm1:+:1183933674:-1 chm1:+:1262602838:-1 chm1:+:1315176573:-1 chm1:+:1318838446:-1 chm1:+:1468962545:-1 chm1:+:1739130504:-1 chm1:+:1858622934:-1 chm1:+:1940229789:-1 chm1:+:2407347379:-1 chm1:+:2414918346:-1 chm1:+:2608676205:-1 chm1:+:3003672592:-1 chm1:+:3014486308:-1 chm1:+:3018929074:-1 +AATACCAATGACATTATTATTCTATTAGTAGAAATAGAAAAAATTAATTCTAAATTTCTTATGAAATCACAAAGACCCCAAGCAGCCAAAGCATCTTGAGCAAAAAGAATAAAGCTGGAAACATTCACACTAACCTGAGTTTAAATTACACAAAGGCCATAGTAACCAAACACTACCTGACTTGAACTATACTACAAGCTATGGTAACCAAAAAGAGACATATAGACCAAATAAAAACAGAACAGAGAACCCAGAAAAAAAAACGACCTATCCATATCCCAACTAATTTTTCAACAAGGTGCCAAGAACGACACATTTGGGGAAGGACAGGTTTCTTCAATAAATGGTACAGGGAAAAATTGAATATCCACATGCAGAAGAATGAAATTGGTACCCTATTTTTCACCATATACAAAAATCACTCAAAAGTGGATTAAAGACTTATGTAGGACCTTAAACTATGAAAGTACTGGAAAGAAAACATGGGGGAACACTTCATGACATTGGACTGGGTAGGATTTTTTGGACGAGACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATAATCAAACTAAAAATCCTCTGCACAGCCAAGGAAACAATTAACAGAGTGAAAAGACAATCTACAGAATGGGACAAATATTTGTAAACTATACATCTGATAAGGGATCGAATAATCCAGAATATATAAGGAACACAAACAACAATAGTAAAAACAATCGTGATTTAAAAGGGGCAAACGACCTTAATAAACATTTCTCAAAAGAAGGCATACAAATGGCCAA chm1:+:264407326:-1 chm1:+:397975750:-1 chm1:+:430624810:-1 chm1:+:524379222:-1 chm1:+:705444419:-1 chm1:+:751593664:-1 chm1:+:1223158950:-1 chm1:+:1246158475:-1 chm1:+:1452270345:-1 chm1:+:1922939535:-1 chm1:+:1956751946:-1 chm1:+:2026235561:-1 chm1:+:2892781220:-1 chm1:+:3025871489:-1 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCA chm1:+:12705627:-1 chm1:+:15824638:-1 chm1:+:29826146:-1 chm1:+:154587954:-1 chm1:+:164915495:-1 chm1:+:182194836:-1 chm1:+:293176072:-1 chm1:+:297206474:-1 chm1:+:401234038:-1 chm1:+:508084784:-1 chm1:+:559115157:-1 chm1:+:698530516:-1 chm1:+:778930087:-1 chm1:+:895301676:-1 chm1:+:1026234067:-1 chm1:+:1064216808:-1 chm1:+:1169148032:-1 chm1:+:1226832125:-1 chm1:+:1381268735:-1 chm1:+:1404253366:-1 chm1:+:1539061523:-1 chm1:+:1560637412:-1 chm1:+:1571885556:-1 chm1:+:1573467742:-1 chm1:+:1619779737:-1 chm1:+:1640116484:-1 chm1:+:1670380900:-1 chm1:+:1701895184:-1 chm1:+:1792116280:-1 chm1:+:1969826419:-1 chm1:+:2032302963:-1 chm1:+:2295666615:-1 chm1:+:2300042865:-1 chm1:+:2350704549:-1 chm1:+:2411748746:-1 chm1:+:2535766604:28 chm1:+:2538204100:-1 chm1:+:2546004858:-1 chm1:+:2555123667:-1 chm1:+:2590999870:-1 chm1:+:2697956572:-1 chm1:+:2704052230:-1 chm1:+:2808712334:-1 chm1:+:2811385877:-1 chm1:+:2861550211:-1 chm1:+:2921965431:-1 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCA chm1:+:2535766601:28 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCA chm1:+:2535766597:28 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCA chm1:+:2535766600:28 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCA chm1:+:2535766590:28 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCA chm1:+:2535766595:28 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCA chm1:+:2535766599:28 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCA chm1:+:2535766603:28 +TCCTGGGCTCAAGCAATCTGCCGGCCTTGGCCTCCGAAAGTGCTAGGATTTACAGGCTTTTCAGACTCCCTTATGACGTATTTGATGAACAGAGTTCTTGAGTGGAGTTTAAGTAATCAATCTTTTCTTTTGTAGTTTGTTACTTGCTGTGTCTTATACAACAAAAATCTTCCTATCCTGAGGTTATAACGATATTCTCCTTAACCATTTAACAGCTTCACCTCTTTAGTACATATTTAAGTCTTTATCGGGAATTGATTTTTGTGTATAGGCATAAGATAAGGGAATCCATTTCTTTCTTTCCTCTTTTTTTTTTTTAAATGAATAACCGATTGTGCTGGTATCATTTATTGAAAAAAAAAAAAATCTATCCTTTCCCCATGATCTACAATGCCTCCTCTATTCATAAAATAAGTTTTCATATATGGCTGGATCTGTTTCTGGGTCATTAAGTTCCACTTGATCTATAAATCTATCTCTACACCTATCTCACAATTTCTTTAATTTAATATGGCTTTATATTAAATCTTGATATCTGATTAGGCAAATCTTTTCACCTTGTATTTCTTTGGAAGTATCTTTGGTTATTTGTGAGACTTGTCTTTTATGGAAATTTTATTAATTAGCATTACAAAATACTACTAACCAGAATTTTTATTGAAATGTCAATCTACAGATGAATTTAGGAAGAATCGGCACTAATAGTGTACACTTCCAATTTTAAGACCTTGATAATTTATTAATCTTCTTTTACTATTATAATATTCTTGATTATAACTTTTCCTCAAAAGAGGCTTGCA chm1:+:2535766591:28 +TGCAAGCCTCTTTTGAGGAAAAGTTATAATCAAGAATATTATAATAGTAAAAGAAGATTAATAAATTATCAAGGTCTTAAAATTGGAAGTGTACACTATTAGTGCCGATTCTTCCTAAATTCATCTGTAGATTGACATTTCAATAAAAATTCTGGTTAGTAGTATTTTGTAATGCTAATTAATAAAATTTCCATAAAAGACAAGTCTCACAAATAACCAAAGATACTTCCAAAGAAATACAAGGTGAAAAGATTTGCCTAATCAGATATCAAGATTTAATATAAAGCCATATTAAATTAAAGAAATTGTGAGATAGGTGTAGAGATAGATTTATAGATCAAGTGGAACTTAATGACCCAGAAACAGATCCAGCCATATATGAAAACTTATTTTATGAATAGAGGAGGCATTGTAGATCATGGGGAAAGGATAGATTTTTTTTTTTTTCAATAAATGATACCAGCACAATCGGTTATTCATTTAAAAAAAAAAAAGAGGAAAGAAAGAAATGGATTCCCTTATCTTATGCCTATACACAAAAATCAATTCCCGATAAAGACTTAAATATGTACTAAAGAGGTGAAGCTGTTAAATGGTTAAGGAGAATATCGTTATAACCTCAGGATAGGAAGATTTTTGTTGTATAAGACACAGCAAGTAACAAACTACAAAAGAAAAGATTGATTACTTAAACTCCACTCAAGAACTCTGTTCATCAAATACGTCATAAGGGAGTCTGAAAAGCCTGTAAATCCTAGCACTTTCGGAGGCCAAGGCCGGCAGATTGCTTGAGCCCAGGA chm1:+:630756240:-1 +TGCAAGCCTCTTTTGAGGAAAAGTTATAATCAAGAATATTATAATAGTAAAAGAAGATTAATAAATTATCAAGGTCTTAAAATTGGAAGTGTACACTATTAGTGCCGATTCTTCCTAAATTCATCTGTAGATTGACATTTCAATAAAAATTCTGGTTAGTAGTATTTTGTAATGCTAATTAATAAAATTTCCATAAAAGACAAGTCTCACAAATAACCAAAGATACTTCCAAAGAAATACAAGGTGAAAAGATTTGCCTAATCAGATATCAAGATTTAATATAAAGCCATATTAAATTAAAGAAATTGTGAGATAGGTGTAGAGATAGATTTATAGATCAAGTGGAACTTAATGACCCAGAAACAGATCCAGCCATATATGAAAACTTATTTTATGAATAGAGGAGGCATTGTAGATCATGGGGAAAGGATAGATTTTTTTTTTTTTCAATAAATGATACCAGCACAATCGGTTATTCATTTAAAAAAAAAAAAGAGGAAAGAAAGAAATGGATTCCCTTATCTTATGCCTATACACAAAAATCAATTCCCGATAAAGACTTAAATATGTACTAAAGAGGTGAAGCTGTTAAATGGTTAAGGAGAATATCGTTATAACCTCAGGATAGGAAGATTTTTGTTGTATAAGACACAGCAAGTAACAAACTACAAAAGAAAAGATTGATTACTTAAACTCCACTCAAGAACTCTGTTCATCAAATACGTCATAAGGGAGTCTGAAAAGCCTGTAAATCCTAGCACTTTCGGAGGCCAAGGCCGGCAGATTGCTTGAGCCCAGGA chm1:+:40055021:-1 +TGCAAGCCTCTTTTGAGGAAAAGTTATAATCAAGAATATTATAATAGTAAAAGAAGATTAATAAATTATCAAGGTCTTAAAATTGGAAGTGTACACTATTAGTGCCGATTCTTCCTAAATTCATCTGTAGATTGACATTTCAATAAAAATTCTGGTTAGTAGTATTTTGTAATGCTAATTAATAAAATTTCCATAAAAGACAAGTCTCACAAATAACCAAAGATACTTCCAAAGAAATACAAGGTGAAAAGATTTGCCTAATCAGATATCAAGATTTAATATAAAGCCATATTAAATTAAAGAAATTGTGAGATAGGTGTAGAGATAGATTTATAGATCAAGTGGAACTTAATGACCCAGAAACAGATCCAGCCATATATGAAAACTTATTTTATGAATAGAGGAGGCATTGTAGATCATGGGGAAAGGATAGATTTTTTTTTTTTTCAATAAATGATACCAGCACAATCGGTTATTCATTTAAAAAAAAAAAAGAGGAAAGAAAGAAATGGATTCCCTTATCTTATGCCTATACACAAAAATCAATTCCCGATAAAGACTTAAATATGTACTAAAGAGGTGAAGCTGTTAAATGGTTAAGGAGAATATCGTTATAACCTCAGGATAGGAAGATTTTTGTTGTATAAGACACAGCAAGTAACAAACTACAAAAGAAAAGATTGATTACTTAAACTCCACTCAAGAACTCTGTTCATCAAATACGTCATAAGGGAGTCTGAAAAGCCTGTAAATCCTAGCACTTTCGGAGGCCAAGGCCGGCAGATTGCTTGAGCCCAGGA chm1:+:630584080:-1 chm1:+:694573690:-1 chm1:+:864608518:-1 chm1:+:1959449535:-1 chm1:+:2387332094:-1 chm1:+:2663649769:-1 chm1:+:3005407423:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:23849763:-1 chm1:+:44249377:-1 chm1:+:65145369:-1 chm1:+:67963633:-1 chm1:+:92387826:-1 chm1:+:198090499:-1 chm1:+:323896126:-1 chm1:+:537228197:-1 chm1:+:543666830:-1 chm1:+:649533715:-1 chm1:+:664862925:-1 chm1:+:672741947:-1 chm1:+:676834721:-1 chm1:+:688058920:-1 chm1:+:1041192675:-1 chm1:+:1047769217:-1 chm1:+:1058110635:-1 chm1:+:1063122451:-1 chm1:+:1152313564:-1 chm1:+:1222889696:-1 chm1:+:1235247797:-1 chm1:+:1258874882:-1 chm1:+:1275373463:-1 chm1:+:1304063082:-1 chm1:+:1337113050:-1 chm1:+:1376350705:-1 chm1:+:1411404572:-1 chm1:+:1411409850:-1 chm1:+:1421314284:-1 chm1:+:1448562312:-1 chm1:+:1479344490:-1 chm1:+:1520257313:-1 chm1:+:1626023293:-1 chm1:+:1741420592:-1 chm1:+:1757269638:-1 chm1:+:1757318692:-1 chm1:+:1795863372:-1 chm1:+:1891462091:-1 chm1:+:1908715091:-1 chm1:+:2069348826:-1 chm1:+:2245211417:-1 chm1:+:2295730120:-1 chm1:+:2386168629:55 chm1:+:2394130924:-1 chm1:+:2428756242:-1 chm1:+:2467982911:-1 chm1:+:2557733345:-1 chm1:+:2567389557:-1 chm1:+:2666725895:-1 chm1:+:2672051001:-1 chm1:+:2676252281:-1 chm1:+:2678507514:-1 chm1:+:2679169488:-1 chm1:+:2706741284:-1 chm1:+:2751796849:-1 chm1:+:2819335372:-1 chm1:+:2822577936:-1 chm1:+:2900210646:-1 chm1:+:2929617486:-1 chm1:+:2947545179:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:756910737:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:27340825:-1 chm1:+:53632789:-1 chm1:+:162446301:-1 chm1:+:309924579:-1 chm1:+:346209992:-1 chm1:+:659525913:-1 chm1:+:861727917:-1 chm1:+:873413138:-1 chm1:+:1022547895:-1 chm1:+:1171588225:-1 chm1:+:1258126968:-1 chm1:+:1300123243:-1 chm1:+:1335189274:-1 chm1:+:1467554289:-1 chm1:+:1499240900:-1 chm1:+:1574399959:-1 chm1:+:1657162631:-1 chm1:+:1710416524:-1 chm1:+:1787780590:-1 chm1:+:1801853131:-1 chm1:+:1893683120:-1 chm1:+:1965425722:-1 chm1:+:2027455679:-1 chm1:+:2072463690:-1 chm1:+:2338686817:-1 chm1:+:2341475304:-1 chm1:+:2359941349:-1 chm1:+:2386058265:-1 chm1:+:2413797573:-1 chm1:+:2503049583:-1 chm1:+:2543083627:-1 chm1:+:2547226473:-1 chm1:+:2560173249:-1 chm1:+:2575257158:-1 chm1:+:2600555887:-1 chm1:+:2680052118:-1 chm1:+:2715290934:-1 chm1:+:2879770780:-1 chm1:+:2928297269:-1 chm1:+:3039582723:-1 chm1:+:3060959126:-1 chm1:+:3061367206:-1 chm1:+:3063000955:-1 chm1:+:3064433121:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:278278030:-1 chm1:+:1299068341:-1 chm1:+:1309247413:-1 chm1:+:1452424126:-1 chm1:+:1554769527:-1 chm1:+:1674687782:-1 chm1:+:1863564759:-1 chm1:+:2124253774:-1 chm1:+:2414652079:-1 chm1:+:2499548789:-1 chm1:+:2600297797:-1 chm1:+:3016969795:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:377344524:-1 chm1:+:924751767:-1 chm1:+:1133744902:-1 chm1:+:1508519308:-1 chm1:+:1523946850:-1 chm1:+:1534241320:-1 chm1:+:1545356018:-1 chm1:+:1572300412:-1 chm1:+:1576994633:-1 chm1:+:2268896361:-1 chm1:+:2421805584:-1 chm1:+:2441479793:-1 chm1:+:2537793610:-1 chm1:+:2557203775:-1 chm1:+:2558050610:-1 chm1:+:2605123156:-1 chm1:+:2664938262:-1 chm1:+:2670885478:-1 chm1:+:2693080709:-1 chm1:+:2700371540:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:394437362:-1 chm1:+:527752110:-1 chm1:+:547183593:-1 chm1:+:796774852:-1 chm1:+:1347717346:-1 chm1:+:1876270073:-1 chm1:+:2153976024:-1 chm1:+:2386168616:55 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:17849829:-1 chm1:+:24977918:-1 chm1:+:531883965:-1 chm1:+:616694473:-1 chm1:+:1038096436:-1 chm1:+:1098362171:-1 chm1:+:1212719818:-1 chm1:+:1411568490:-1 chm1:+:1652438649:-1 chm1:+:2382587932:-1 chm1:+:2536974575:-1 chm1:+:2822191849:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:178413690:-1 chm1:+:2031733903:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:1458374095:-1 chm1:+:1723677365:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:495647872:-1 chm1:+:601362028:-1 chm1:+:900080184:-1 chm1:+:926672198:-1 chm1:+:1201632765:-1 chm1:+:1347013979:-1 chm1:+:1442268235:-1 chm1:+:1464492696:-1 chm1:+:1613019340:-1 chm1:+:1767445963:-1 chm1:+:2112998363:-1 chm1:+:2257826158:-1 chm1:+:2386168615:55 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:2386168638:55 chm1:+:2521396403:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:2386168639:55 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:1245000726:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:2386168631:55 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:2391928058:-1 +TAAAGCATAGATTGACGGGGCCAGAATGTTGACATATTTTCTATAAAAGATCTTTACTAAGGCTTGTTTTCAGTTAAAGCACCTGCAAAATGGGGCATTTACCACAATCTCACTTCTCCACTTCCCCCATCAGCTACTCTTGGCTCTAAGAAAATTTAGTGTTATATTCTAACGGGAAATAAGTATCCTGCCATATTTCTTGGCTCTGACCCTGATGAATTTGTTTTAATTTCTTGGGGTTGAGGGCTAGTGGGTGAACTGTTTTAATTTGTGAGGGCTTCAGTAACTTGTTTCTAATTGTGATAATCTGTAGGCAGAACTCCATATAACAGTTAATGGAGTTATCAAAAGTTTCTTTTAGGCTGGGCCAGTGGCTTCTATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTTGAGATCAGTCCTGGTCAACATGTGAAACTCCAATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGGTGGCACATGCCTATAGTCACGAAGCGTTACTTCGGGAGGCTGGGGCAGGAGAATCACTTGAACCCAAGGAGGCGGAGATTTGCAGTGGAGCCGAGAGTCACGCCATTGCACTCCAGCCTGGGCGACCCGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAGTTCTTTTAAAAGAATGAGCCTAATCGTGGAATTTATAAGTATAAATTCAGTCTTGTCACTGTTATTTCTTCTATTGTGTATTATTTTAAACCTATGACTATAGTAATATTTTCATAATTGAAT chm1:+:384632289:-1 chm1:+:542508256:-1 chm1:+:954005608:-1 chm1:+:1080410374:-1 chm1:+:1254832646:-1 chm1:+:1278739443:-1 chm1:+:1575096971:-1 chm1:+:1740427371:-1 chm1:+:1757471847:-1 chm1:+:2075571424:-1 chm1:+:2076791969:-1 chm1:+:2536187051:-1 chm1:+:2541639884:-1 chm1:+:2766385154:-1 +ATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA chm1:+:184460188:-1 +ATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA chm1:+:78163458:-1 chm1:+:302025331:-1 chm1:+:430219315:-1 chm1:+:538149751:-1 chm1:+:541961482:-1 chm1:+:829560439:-1 chm1:+:856310926:-1 chm1:+:1057182461:-1 chm1:+:1496776970:-1 chm1:+:1532707166:-1 chm1:+:1755535435:-1 chm1:+:1796997599:-1 chm1:+:2002790279:-1 chm1:+:2695584412:-1 chm1:+:2701332990:-1 chm1:+:2872089204:-1 chm1:+:3049872015:-1 +ATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA chm1:+:8094784:-1 chm1:+:212336145:-1 chm1:+:328400597:-1 chm1:+:422499024:-1 chm1:+:699905052:-1 chm1:+:976522923:-1 chm1:+:996656622:-1 chm1:+:1305485453:-1 chm1:+:1361669265:-1 chm1:+:1448845539:-1 chm1:+:1490655528:-1 chm1:+:1745479688:-1 chm1:+:2112613845:-1 chm1:+:2235309288:-1 chm1:+:2363476265:-1 chm1:+:2504114516:-1 chm1:+:2508105474:-1 chm1:+:2508849809:-1 chm1:+:2666473840:-1 chm1:+:2678373307:-1 +ATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA chm1:+:262104142:-1 chm1:+:333795224:-1 chm1:+:1019622807:-1 chm1:+:1101762904:-1 chm1:+:1425024899:-1 chm1:+:1430911165:-1 chm1:+:1825511005:-1 chm1:+:2477885071:-1 chm1:+:2589213943:-1 chm1:+:2671456326:-1 chm1:+:2701978637:-1 chm1:+:2760656558:-1 chm1:+:2859979545:-1 chm1:+:2982216321:-1 chm1:+:3051297681:-1 +ATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA chm1:+:881210449:-1 chm1:+:920413175:-1 chm1:+:1103512617:-1 chm1:+:2257202988:-1 chm1:+:2767801367:-1 +ATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA chm1:+:1029804358:-1 chm1:+:1745112630:-1 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chm1:+:2570701026:-1 chm1:+:2749659446:-1 +ATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA chm1:+:312289232:-1 chm1:+:1399531665:-1 chm1:+:2122115118:-1 chm1:+:2438564511:-1 chm1:+:2778110632:-1 chm1:+:2931470320:-1 +ATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA chm1:+:923955574:-1 chm1:+:2387622649:-1 +ATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA chm1:+:211682795:-1 chm1:+:943992784:-1 chm1:+:950212858:-1 chm1:+:1237790422:-1 chm1:+:1241639177:-1 chm1:+:1255872877:-1 chm1:+:1527375555:-1 chm1:+:1540876938:-1 chm1:+:2007493369:-1 chm1:+:2059965929:-1 chm1:+:2305459906:-1 chm1:+:2588503499:-1 +ATTCAATTATGAAAATATTACTATAGTCATAGGTTTAAAATAATACACAATAGAAGAAATAACAGTGACAAGACTGAATTTATACTTATAAATTCCACGATTAGGCTCATTCTTTTAAAAGAACTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCGGGTCGCCCAGGCTGGAGTGCAATGGCGTGACTCTCGGCTCCACTGCAAATCTCCGCCTCCTTGGGTTCAAGTGATTCTCCTGCCCCAGCCTCCCGAAGTAACGCTTCGTGACTATAGGCATGTGCCACCCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAAATTGGAGTTTCACATGTTGACCAGGACTGATCTCAAACTCCTGACCTCAAATGATCCACCCACCTCGGCCTCCCAAAGTGGTGGGATTACAGGCATAGAAGCCACTGGCCCAGCCTAAAAGAAACTTTTGATAACTCCATTAACTGTTATATGGAGTTCTGCCTACAGATTATCACAATTAGAAACAAGTTACTGAAGCCCTCACAAATTAAAACAGTTCACCCACTAGCCCTCAACCCCAAGAAATTAAAACAAATTCATCAGGGTCAGAGCCAAGAAATATGGCAGGATACTTATTTCCCGTTAGAATATAACACTAAATTTTCTTAGAGCCAAGAGTAGCTGATGGGGGAAGTGGAGAAGTGAGATTGTGGTAAATGCCCCATTTTGCAGGTGCTTTAACTGAAAACAAGCCTTAGTAAAGATCTTTTATAGAAAATATGTCAACATTCTGGCCCCGTCAATCTATGCTTTA chm1:+:6241837:-1 chm1:+:8068098:-1 chm1:+:1007525593:-1 chm1:+:2250412283:-1 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTT chm1:+:80940662:-1 chm1:+:212174244:-1 chm1:+:244493457:-1 chm1:+:312196876:-1 chm1:+:401562145:-1 chm1:+:428585022:-1 chm1:+:449520779:-1 chm1:+:474554752:-1 chm1:+:476974088:-1 chm1:+:565064801:-1 chm1:+:569050682:-1 chm1:+:572845882:-1 chm1:+:715060257:-1 chm1:+:853755069:-1 chm1:+:1159698623:-1 chm1:+:1288683686:-1 chm1:+:1911566471:-1 chm1:+:1959990336:-1 chm1:+:2003577110:-1 chm1:+:2013346052:-1 chm1:+:2021617632:-1 chm1:+:2271290760:-1 chm1:+:2377004394:-1 chm1:+:2392888835:-1 chm1:+:2470469287:-1 chm1:+:2471101711:37 chm1:+:2561351560:-1 chm1:+:2628555879:-1 chm1:+:2862912699:-1 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTT chm1:+:2471101710:37 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTT chm1:+:2001141107:-1 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTT chm1:+:2471101707:37 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTT chm1:+:2471101705:37 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTT chm1:+:2471101709:37 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTT chm1:+:2471101715:37 +CACTACTTACTGAACAATATAGAAAATTGGACTAGATGTATAAGTACCAAGCACCTAGCATAGAATACAGGTTATTATCTAAAATTGTGAGCTAATCCAGAAGCTGCAAGCATGTTAGTGCCTGAAGAGTAGAAAAAGAGACAGCATAGGTTTTTATGATGGAATTAGTTGCTAGGATTTAGCAGATGAAATTCAAGGGCAACTTAGTTGAATTTGAATTTCAGATAAATCACACACACAACACACCACACACACACACACACACAAACATATACATGTACACTTGGACCCTCCAATATCTAGTGAGTTAACATCAATGAATTCAACCAACTGTGGATGGAAATATTTGGGGACAAAATGGATGATTGTGTTGTAGTGACATCTACAGACTTTTTTTTCTTGTCATTTATATCCTAGATAATATAGAACAGGCTATTTGCATACCATTACATTGTATTAGATATTATAAGTAATCTAGAGACACTTTAAAGTAAGACAGAGGTATGTACATAGGTTGTATGCAAATACTATACTATTTTATGTAAGGGACTTGGAATATCTGGACATTTTAGTATTCATGAAAAGGGGATAGTGTTCTGGAACCAAGTTCCCATGATGTTGAGGAATGACTGTGTATAGTAATATGTGGTATCCTATATTTTTAAAAGCTCTATCATTTTATAGCTAAAATTTTACATTTAACCAGTATTAAAATGAACTTAGGCATATCTTAAGAAGTGTACTTGAGCACTCAGCAATCTATGAATCCGGCAGCACCAGACTGCAAGCGGTTGGGTGTT chm1:+:2471101712:37 +AACACCCAACCGCTTGCAGTCTGGTGCTGCCGGATTCATAGATTGCTGAGTGCTCAAGTACACTTCTTAAGATATGCCTAAGTTCATTTTAATACTGGTTAAATGTAAAATTTTAGCTATAAAATGATAGAGCTTTTAAAAATATAGGATACCACATATTACTATACACAGTCATTCCTCAACATCATGGGAACTTGGTTCCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG chm1:+:1328108441:-1 chm1:+:2404753494:-1 +AACACCCAACCGCTTGCAGTCTGGTGCTGCCGGATTCATAGATTGCTGAGTGCTCAAGTACACTTCTTAAGATATGCCTAAGTTCATTTTAATACTGGTTAAATGTAAAATTTTAGCTATAAAATGATAGAGCTTTTAAAAATATAGGATACCACATATTACTATACACAGTCATTCCTCAACATCATGGGAACTTGGTTCCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG chm1:+:984700487:-1 chm1:+:1323135449:-1 +AACACCCAACCGCTTGCAGTCTGGTGCTGCCGGATTCATAGATTGCTGAGTGCTCAAGTACACTTCTTAAGATATGCCTAAGTTCATTTTAATACTGGTTAAATGTAAAATTTTAGCTATAAAATGATAGAGCTTTTAAAAATATAGGATACCACATATTACTATACACAGTCATTCCTCAACATCATGGGAACTTGGTTCCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG chm1:+:1831911549:-1 chm1:+:2254634703:-1 +AACACCCAACCGCTTGCAGTCTGGTGCTGCCGGATTCATAGATTGCTGAGTGCTCAAGTACACTTCTTAAGATATGCCTAAGTTCATTTTAATACTGGTTAAATGTAAAATTTTAGCTATAAAATGATAGAGCTTTTAAAAATATAGGATACCACATATTACTATACACAGTCATTCCTCAACATCATGGGAACTTGGTTCCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG chm1:+:62601666:-1 chm1:+:69595676:-1 chm1:+:95198932:-1 chm1:+:202207800:-1 chm1:+:486751805:-1 chm1:+:543159659:-1 chm1:+:620663211:-1 chm1:+:687280846:-1 chm1:+:694084708:-1 chm1:+:724845170:-1 chm1:+:1032618387:-1 chm1:+:1355343994:-1 chm1:+:1389367542:-1 chm1:+:1541261164:-1 chm1:+:1638079270:-1 chm1:+:1677825125:-1 chm1:+:1820802964:-1 chm1:+:2107223746:-1 chm1:+:2637546451:-1 chm1:+:2662688331:-1 +AACACCCAACCGCTTGCAGTCTGGTGCTGCCGGATTCATAGATTGCTGAGTGCTCAAGTACACTTCTTAAGATATGCCTAAGTTCATTTTAATACTGGTTAAATGTAAAATTTTAGCTATAAAATGATAGAGCTTTTAAAAATATAGGATACCACATATTACTATACACAGTCATTCCTCAACATCATGGGAACTTGGTTCCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG chm1:+:84368808:-1 chm1:+:100987252:-1 chm1:+:428821135:-1 chm1:+:918775677:-1 chm1:+:1073991508:-1 chm1:+:1077230240:-1 chm1:+:1106523330:-1 chm1:+:1453278992:-1 chm1:+:1467373346:-1 chm1:+:1474525957:-1 chm1:+:1655456006:-1 chm1:+:1735821416:-1 chm1:+:1743339433:-1 chm1:+:1763377697:-1 chm1:+:2527351939:-1 chm1:+:2711917476:-1 chm1:+:2727539387:-1 +AACACCCAACCGCTTGCAGTCTGGTGCTGCCGGATTCATAGATTGCTGAGTGCTCAAGTACACTTCTTAAGATATGCCTAAGTTCATTTTAATACTGGTTAAATGTAAAATTTTAGCTATAAAATGATAGAGCTTTTAAAAATATAGGATACCACATATTACTATACACAGTCATTCCTCAACATCATGGGAACTTGGTTCCAGAACACTATCCCCTTTTCATGAATACTAAAATGTCCAGATATTCCAAGTCCCTTACATAAAATAGTATAGTATTTGCATACAACCTATGTACATACCTCTGTCTTACTTTAAAGTGTCTCTAGATTACTTATAATATCTAATACAATGTAATGGTATGCAAATAGCCTGTTCTATATTATCTAGGATATAAATGACAAGAAAAAAAAGTCTGTAGATGTCACTACAACACAATCATCCATTTTGTCCCCAAATATTTCCATCCACAGTTGGTTGAATTCATTGATGTTAACTCACTAGATATTGGAGGGTCCAAGTGTACATGTATATGTTTGTGTGTGTGTGTGTGTGTGGTGTGTTGTGTGTGTGATTTATCTGAAATTCAAATTCAACTAAGTTGCCCTTGAATTTCATCTGCTAAATCCTAGCAACTAATTCCATCATAAAAACCTATGCTGTCTCTTTTTCTACTCTTCAGGCACTAACATGCTTGCAGCTTCTGGATTAGCTCACAATTTTAGATAATAACCTGTATTCTATGCTAGGTGCTTGGTACTTATACATCTAGTCCAATTTTCTATATTGTTCAGTAAGTAGTG chm1:+:57744495:-1 chm1:+:214077010:-1 chm1:+:287064779:-1 chm1:+:965136457:-1 chm1:+:1127410558:-1 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCAC chm1:+:69591372:-1 chm1:+:210221176:-1 chm1:+:384672900:-1 chm1:+:395126100:-1 chm1:+:400235306:-1 chm1:+:551677451:-1 chm1:+:683959128:29 chm1:+:693457439:-1 chm1:+:698828310:-1 chm1:+:710431724:-1 chm1:+:759041352:-1 chm1:+:890097987:-1 chm1:+:980824645:-1 chm1:+:1071933687:-1 chm1:+:1131289310:-1 chm1:+:1291430819:-1 chm1:+:1313331563:-1 chm1:+:1355158218:-1 chm1:+:1370709603:-1 chm1:+:1456703906:-1 chm1:+:1546405266:-1 chm1:+:1802758017:-1 chm1:+:1921063532:-1 chm1:+:1932366961:-1 chm1:+:1988792752:-1 chm1:+:2066622945:-1 chm1:+:2170254149:-1 chm1:+:2172010704:-1 chm1:+:2191084811:-1 chm1:+:2302144470:-1 chm1:+:2371393199:-1 chm1:+:2541742752:-1 chm1:+:2651990308:-1 chm1:+:2658078297:-1 chm1:+:2731556400:-1 chm1:+:2748031471:-1 chm1:+:2800380456:-1 chm1:+:2814421280:-1 chm1:+:2903222035:-1 chm1:+:2975559244:-1 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCAC chm1:+:683959127:29 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCAC chm1:+:683959131:29 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCAC chm1:+:683959124:29 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCAC chm1:+:683959123:29 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCAC chm1:+:2551976673:-1 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCAC chm1:+:683959130:29 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCAC chm1:+:107426245:-1 +CAACAAGTTTCTTTATCTTCCATCTGAGACCAACCTTAGCCTGGACTTCATTAGTCATATCACTATCAGCACTTTGGTTAAAGCCATTCAACAAAGTCTCCAGGAAGTTCAAAACTTTCCACAGCTACCTGTCTTCTGAGCCCCCAAGTCTCCATCAAGAATCCAAACCTTCTCACATTTTTCTGTCTTTTTCTGAGCCCTCCAGACTATTCTAACCACTGTCTATTGCCCAGTTCAAAGTCGCCTTCCACATTTTGGGGTATTTTTACAGCAGCACCCAATTCTACCAGTACAATTTACTATATTAATCTGTTCTCACACTGCTAATAAAACTATACCAGAGACAGGTGATTTATAAAGGAAAATGTTTAAATTGACTCAACAGTTCCACATGGCTAGGGGAGGCCTCACAATCATGGCAGAAGGCAAGAGAGCAAAGGCATGCCTAACATGGTGGCAGACAAGACAATGTGTGCAAGGAAACTGCCCCTTTTAAAACCATCAGATCTCATGAGACTTTATTCATTATCAAGAGTACAGCATGGGAAAAACCTACACCATGATTCAGTTACCTCCCACCAGGTCCTTTCACACCACATGGGGGATTATGGGACCTACAATTCAACGATGAGATTTCGGGTAGGGACACAGATAAACCATATCAATTACCAAACTGCAGAAATGTAAACCCGTATTGTGTAAAGAAATTAGGCTGTTTATATTTCTAAGTAATCAAAATCCAGAAATAGACTCCCCGAAGGGTCATGTGATGAGTCCACAATCACAACAGCATCCCGCAC chm1:+:210160154:-1 +GTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:2112077586:-1 +GTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:822796085:-1 chm1:+:1921656453:-1 +GTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:2119429018:-1 +GTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:748861067:-1 chm1:+:792866183:-1 +GTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:2569785242:-1 +GTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:75745970:-1 chm1:+:2140364128:-1 +GTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:2623667691:-1 +GTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:2081460141:-1 +GTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:190169439:-1 chm1:+:785369945:-1 chm1:+:965017100:-1 chm1:+:1012555146:-1 chm1:+:1248257390:-1 chm1:+:1578503334:-1 chm1:+:1579032588:-1 chm1:+:1579848219:-1 chm1:+:1580648299:-1 chm1:+:1821754165:-1 chm1:+:1871023287:-1 chm1:+:2024740872:-1 chm1:+:2643314328:-1 +GTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:5214423:-1 chm1:+:262486646:-1 chm1:+:298576598:-1 chm1:+:355875239:-1 chm1:+:470585104:-1 chm1:+:779119662:-1 chm1:+:817168716:-1 chm1:+:1142338283:-1 chm1:+:1267655160:-1 chm1:+:1757444058:-1 chm1:+:2422299917:-1 chm1:+:2695137196:-1 +GTGCGGGATGCTGTTGTGATTGTGGACTCATCACATGACCCTTCGGGGAGTCTATTTCTGGATTTTGATTACTTAGAAATATAAACAGCCTAATTTCTTTACACAATACGGGTTTACATTTCTGCAGTTTGGTAATTGATATGGTTTATCTGTGTCCCTACCCGAAATCTCATCGTTGAATTGTAGGTCCCATAATCCCCCATGTGGTGTGAAAGGACCTGGTGGGAGGTAACTGAATCATGGTGTAGGTTTTTCCCATGCTGTACTCTTGATAATGAATAAAGTCTCATGAGATCTGATGGTTTTAAAAGGGGCAGTTTCCTTGCACACATTGTCTTGTCTGCCACCATGTTAGGCATGCCTTTGCTCTCTTGCCTTCTGCCATGATTGTGAGGCCTCCCCTAGCCATGTGGAACTGTTGAGTCAATTTAAACATTTTCCTTTATAAATCACCTGTCTCTGGTATAGTTTTATTAGCAGTGTGAGAACAGATTAATATAGTAAATTGTACTGGTAGAATTGGGTGCTGCTGTAAAAATACCCCAAAATGTGGAAGGCGACTTTGAACTGGGCAATAGACAGTGGTTAGAATAGTCTGGAGGGCTCAGAAAAAGACAGAAAAATGTGAGAAGGTTTGGATTCTTGATGGAGACTTGGGGGCTCAGAAGACAGGTAGCTGTGGAAAGTTTTGAACTTCCTGGAGACTTTGTTGAATGGCTTTAACCAAAGTGCTGATAGTGATATGACTAATGAAGTCCAGGCTAAGGTTGGTCTCAGATGGAAGATAAAGAAACTTGTTG chm1:+:720002408:-1 chm1:+:888124525:-1 chm1:+:933016476:-1 chm1:+:1787535345:-1 chm1:+:1827042725:-1 chm1:+:1970876796:-1 chm1:+:1982750485:-1 chm1:+:2644382810:-1 chm1:+:2915734025:-1 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:40834013:47 chm1:+:119566743:62 chm1:+:152928895:-1 chm1:+:207907311:55 chm1:+:254588137:56 chm1:+:271633436:56 chm1:+:312316731:60 chm1:+:398200436:56 chm1:+:465371938:68 chm1:+:482474063:57 chm1:+:511992895:60 chm1:+:519278086:69 chm1:+:535559756:52 chm1:+:536060806:53 chm1:+:556172483:55 chm1:+:597468561:60 chm1:+:627830918:57 chm1:+:703126730:-1 chm1:+:819610860:55 chm1:+:828893343:63 chm1:+:838651678:91 chm1:+:855029308:59 chm1:+:923708581:67 chm1:+:927288745:53 chm1:+:983155385:59 chm1:+:992268133:54 chm1:+:1086349734:67 chm1:+:1125315132:53 chm1:+:1142226688:59 chm1:+:1149899088:55 chm1:+:1167482731:50 chm1:+:1190459879:51 chm1:+:1247464142:54 chm1:+:1247979152:65 chm1:+:1248013424:60 chm1:+:1249640383:43 chm1:+:1327444348:58 chm1:+:1344746280:54 chm1:+:1352887289:60 chm1:+:1493501101:56 chm1:+:1526424869:-1 chm1:+:1644714130:-1 chm1:+:1657350971:122 chm1:+:1661980730:52 chm1:+:1676916683:-1 chm1:+:1681674983:65 chm1:+:1718203641:70 chm1:+:1718441223:56 chm1:+:1726234243:66 chm1:+:1777215618:58 chm1:+:1803047110:58 chm1:+:1826106266:58 chm1:+:1830891849:59 chm1:+:1838217698:59 chm1:+:1851325602:-1 chm1:+:1858873252:59 chm1:+:1923143928:53 chm1:+:1923154868:51 chm1:+:1924042736:60 chm1:+:1924139051:53 chm1:+:1925991091:54 chm1:+:1932352365:58 chm1:+:1958279215:-1 chm1:+:1976607553:59 chm1:+:1995218191:55 chm1:+:2044227416:49 chm1:+:2127768821:50 chm1:+:2130988975:53 chm1:+:2133125826:53 chm1:+:2170467130:54 chm1:+:2226703478:55 chm1:+:2236593555:55 chm1:+:2240340056:-1 chm1:+:2244430096:72 chm1:+:2258993986:80 chm1:+:2327805495:56 chm1:+:2345008573:55 chm1:+:2346364155:62 chm1:+:2362645382:58 chm1:+:2470728471:51 chm1:+:2509694670:56 chm1:+:2553754438:57 chm1:+:2553807491:-1 chm1:+:2581906271:57 chm1:+:2901386813:54 chm1:+:2952697305:62 chm1:+:2960289914:57 chm1:+:2980842050:55 chm1:+:2981832112:57 chm1:+:2995386505:58 chm1:+:2998263815:63 chm1:+:3007392989:87 chm1:+:3027017045:61 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:225407501:121 chm1:+:315658435:56 chm1:+:739550419:74 chm1:+:1282385193:76 chm1:+:1317806345:72 chm1:+:1557468539:116 chm1:+:2037097226:87 chm1:+:3099315584:125 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:1249640399:43 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:166470524:90 chm1:+:422767307:83 chm1:+:496748427:53 chm1:+:498900681:-1 chm1:+:630137598:67 chm1:+:637232959:-1 chm1:+:1454899263:86 chm1:+:1616832673:92 chm1:+:1765572583:86 chm1:+:1777287423:74 chm1:+:2363135404:90 chm1:+:2748216244:80 chm1:+:2997670840:159 chm1:+:3051516950:62 chm1:+:3060494541:95 chm1:+:3062103831:94 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:758055695:120 chm1:+:1892526676:-1 chm1:+:2961376317:144 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:501211255:57 chm1:+:1151966136:147 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:372981403:-1 chm1:+:749300198:110 chm1:+:790156527:60 chm1:+:1543694412:76 chm1:+:1578042367:-1 chm1:+:1584402954:-1 chm1:+:1737205645:126 chm1:+:1888610339:72 chm1:+:2228479571:-1 chm1:+:3015958020:74 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:383558445:61 chm1:+:383625000:62 chm1:+:509071824:-1 chm1:+:705651575:67 chm1:+:803291901:56 chm1:+:1166624948:-1 chm1:+:1436609360:74 chm1:+:1439673067:73 chm1:+:1522525813:58 chm1:+:1563950151:129 chm1:+:1824072120:55 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:60079813:80 chm1:+:69911620:81 chm1:+:158277267:120 chm1:+:312086618:86 chm1:+:318076361:86 chm1:+:416796559:86 chm1:+:417262370:63 chm1:+:514938540:-1 chm1:+:574900093:68 chm1:+:582596997:-1 chm1:+:586803112:103 chm1:+:627994447:61 chm1:+:628396758:70 chm1:+:629585060:71 chm1:+:654623063:-1 chm1:+:723477781:100 chm1:+:751498960:104 chm1:+:800391197:113 chm1:+:956057184:86 chm1:+:983169453:62 chm1:+:1102249767:92 chm1:+:1118145918:77 chm1:+:1256228451:55 chm1:+:1256624474:64 chm1:+:1442907799:-1 chm1:+:1457132645:-1 chm1:+:1466002689:86 chm1:+:1485599324:89 chm1:+:1529687300:53 chm1:+:1529842211:-1 chm1:+:1571261827:104 chm1:+:1648530598:80 chm1:+:1776823565:86 chm1:+:1836505843:84 chm1:+:1855813969:71 chm1:+:1867070229:-1 chm1:+:1932919536:94 chm1:+:1993374810:77 chm1:+:2028965786:62 chm1:+:2140261804:111 chm1:+:2226703483:55 chm1:+:2237596830:97 chm1:+:2237702331:70 chm1:+:2239957391:-1 chm1:+:2240064895:64 chm1:+:2266606995:82 chm1:+:2362330818:87 chm1:+:2456439839:88 chm1:+:2957525357:87 chm1:+:2964988993:72 chm1:+:2971056892:83 chm1:+:3040522580:87 chm1:+:3046274760:125 chm1:+:3063823195:69 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:833463554:95 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:633159989:88 chm1:+:996037027:124 chm1:+:2810546853:56 chm1:+:2902409293:-1 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:1266408278:77 chm1:+:1507419665:55 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:655248325:127 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:2284045339:58 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:169875770:-1 chm1:+:249059467:67 chm1:+:358203282:66 chm1:+:924365026:60 chm1:+:1001797452:66 chm1:+:1295020327:-1 chm1:+:1353370432:-1 chm1:+:1507076367:-1 chm1:+:1531052108:78 chm1:+:2552412755:78 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:63889509:-1 chm1:+:438981249:128 chm1:+:559754455:-1 chm1:+:596100951:94 chm1:+:1081501439:-1 chm1:+:1248175012:-1 chm1:+:1298547486:-1 chm1:+:1465748872:-1 chm1:+:1726987005:-1 chm1:+:1729173932:-1 chm1:+:1729694445:-1 chm1:+:2133760461:120 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:459012902:53 chm1:+:465371944:68 chm1:+:498429000:80 chm1:+:1069213996:74 chm1:+:1150114681:61 chm1:+:1163348045:52 chm1:+:1295020346:-1 chm1:+:1999786079:124 chm1:+:2052697864:64 chm1:+:2559362956:54 chm1:+:2604667135:68 chm1:+:2950855330:55 chm1:+:2956621865:139 +GCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCTAATCAATAATGTAACCAGCATATAACAGAGCCAAAGACAAAAACCACATGGATTATCTCAATAGATGCAGAAAAAGCCTTTGGACAAAATTCAACAACCCTTCATGCTAAAAAACTCTCAATAAAATTAGGTATTGATGGGGACGTATTCAAAAGTAACTAAGAGCTATCCTATGACAAACCCGTCAGCCAATTATCATTACTGAATGGGGCAAAAACTGGTAGCATTCCCTTTGAAAAACTGGCACAAGACAGGGAATGCCCTCTACTCACCACTTCCTATTCAACATAGTGTTGAAGTTCTGGCCAGGGCAATTAGGCAGGAGAAGGAAATAAAGGGTATCGAATTAGGAAAAGAGGAAGTCAAATTTGTCCCCTGTTTGCAGATGACATGATTGTATATTAGAAAACCCCATTGTCTCAGCCCAAATCTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAAATCACAAGCATTCTTATACACCTACAACAAGACAAACAGAGAGCCGAAATCATCGAGTGAACTCCCATTCACAACTTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACACGGGAGTGGAAGGACCCTCTTCAAGGAGAAATACAACCACTGCTCAAGGAAATAAAGAGGATACAAACAAATTGGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAA chm1:+:444588443:66 chm1:+:650068115:68 chm1:+:971134364:56 chm1:+:1120536091:74 chm1:+:1681674999:65 chm1:+:1736489568:72 chm1:+:1821847106:-1 chm1:+:2408402604:75 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:60931623:-1 chm1:+:187727058:82 chm1:+:331035485:-1 chm1:+:435958480:60 chm1:+:784333543:73 chm1:+:1073527943:62 chm1:+:1322956699:112 chm1:+:1444194301:58 chm1:+:1848592516:83 chm1:+:2742452194:66 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:933170643:54 chm1:+:990695153:67 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:416610119:57 chm1:+:435958481:60 chm1:+:982072258:53 chm1:+:1036382875:66 chm1:+:1140335553:65 chm1:+:1259397340:92 chm1:+:1295313600:-1 chm1:+:1692147982:52 chm1:+:1848872071:56 chm1:+:2146141716:65 chm1:+:2158794821:69 chm1:+:2227036057:54 chm1:+:2419596774:59 chm1:+:2522223924:58 chm1:+:2702718962:70 chm1:+:2858512951:68 chm1:+:2937642645:62 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:867336358:115 chm1:+:1355577399:52 chm1:+:2967842409:59 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:78944500:-1 chm1:+:96900417:106 chm1:+:188722772:60 chm1:+:316097119:70 chm1:+:375036225:124 chm1:+:513673457:152 chm1:+:562952151:91 chm1:+:590971784:78 chm1:+:603081679:57 chm1:+:628102499:139 chm1:+:757105685:85 chm1:+:792800648:63 chm1:+:873022315:80 chm1:+:959359138:97 chm1:+:967649753:90 chm1:+:1113141102:80 chm1:+:1135069027:119 chm1:+:1141244169:82 chm1:+:1160895344:84 chm1:+:1178339563:115 chm1:+:1318275172:96 chm1:+:1469063628:-1 chm1:+:1475852697:96 chm1:+:1481347564:79 chm1:+:1563799842:91 chm1:+:1717702225:72 chm1:+:1749643494:93 chm1:+:1797887225:102 chm1:+:1836620121:70 chm1:+:1870629639:-1 chm1:+:2048960717:59 chm1:+:2077721019:102 chm1:+:2233257948:83 chm1:+:2240226812:104 chm1:+:2394036164:99 chm1:+:2649889950:59 chm1:+:2687632073:94 chm1:+:2735343184:106 chm1:+:2951001959:57 chm1:+:3005777633:56 chm1:+:3045044818:99 chm1:+:3062745815:69 chm1:+:3097016559:65 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:163611134:55 chm1:+:270683457:61 chm1:+:425805977:-1 chm1:+:574833657:57 chm1:+:861750903:55 chm1:+:1033661615:62 chm1:+:1205286656:50 chm1:+:1520122567:58 chm1:+:1977284303:88 chm1:+:2991094659:61 chm1:+:3004966126:-1 chm1:+:3057840405:69 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:75364777:78 chm1:+:499380318:68 chm1:+:546407175:53 chm1:+:673754590:111 chm1:+:1426352830:74 chm1:+:1510154611:-1 chm1:+:1864630679:67 chm1:+:2009326739:124 chm1:+:2302148144:84 chm1:+:2329598759:71 chm1:+:2606037889:96 chm1:+:2846207634:91 chm1:+:3021377652:126 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:923882442:77 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:47590027:-1 chm1:+:62040462:93 chm1:+:103395055:61 chm1:+:146663497:67 chm1:+:186694391:118 chm1:+:302326024:147 chm1:+:356542420:-1 chm1:+:390313253:81 chm1:+:407382365:110 chm1:+:503977416:100 chm1:+:506450118:72 chm1:+:507884404:76 chm1:+:508400148:77 chm1:+:717704332:70 chm1:+:751057114:84 chm1:+:763131207:102 chm1:+:768733047:91 chm1:+:807100053:122 chm1:+:825832130:103 chm1:+:846166718:93 chm1:+:850923006:81 chm1:+:854192336:135 chm1:+:863194240:107 chm1:+:879251751:62 chm1:+:910006206:-1 chm1:+:931538188:-1 chm1:+:947233872:-1 chm1:+:957183374:124 chm1:+:994893048:69 chm1:+:995120807:73 chm1:+:996363009:-1 chm1:+:1028385093:-1 chm1:+:1050677287:121 chm1:+:1118990758:69 chm1:+:1133748570:123 chm1:+:1137282763:86 chm1:+:1142615974:89 chm1:+:1147836557:-1 chm1:+:1227933084:-1 chm1:+:1247283113:-1 chm1:+:1429321013:121 chm1:+:1444187883:-1 chm1:+:1453660021:75 chm1:+:1458634648:-1 chm1:+:1459142361:-1 chm1:+:1497560258:82 chm1:+:1561651243:112 chm1:+:1564201085:82 chm1:+:1564219267:126 chm1:+:1606807768:82 chm1:+:1646360241:130 chm1:+:1648009708:147 chm1:+:1864729295:83 chm1:+:1956174075:-1 chm1:+:1960676992:-1 chm1:+:1997655401:83 chm1:+:2080863829:-1 chm1:+:2156468963:-1 chm1:+:2161418052:-1 chm1:+:2163855051:64 chm1:+:2189936468:-1 chm1:+:2287148958:87 chm1:+:2350617002:118 chm1:+:2395087121:112 chm1:+:2653831812:113 chm1:+:2735670145:72 chm1:+:2737491210:125 chm1:+:2828646484:-1 chm1:+:2939514425:-1 chm1:+:2958579146:105 chm1:+:2961989287:132 chm1:+:3050994763:115 chm1:+:3051900553:142 chm1:+:3056106488:-1 chm1:+:3057778872:-1 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:1627823880:84 chm1:+:2623198669:123 chm1:+:2923301626:150 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:986477039:59 chm1:+:1493381619:101 chm1:+:1617853692:-1 chm1:+:2470385715:127 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:737197350:-1 chm1:+:812939670:103 chm1:+:820576586:86 chm1:+:826769881:144 chm1:+:858882133:86 chm1:+:886949213:153 chm1:+:927564731:-1 chm1:+:1022119022:70 chm1:+:1041641351:-1 chm1:+:1189882091:-1 chm1:+:1216911706:-1 chm1:+:1408491959:-1 chm1:+:1848170913:-1 chm1:+:2080437910:72 chm1:+:2136990253:72 chm1:+:2151575517:-1 chm1:+:3019489547:115 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:873036492:-1 chm1:+:2246156797:120 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:743614419:70 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:499257206:66 chm1:+:1139365841:75 chm1:+:1267963636:59 chm1:+:2567781334:69 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:51371950:96 chm1:+:719326943:86 chm1:+:757738690:75 chm1:+:1051985510:74 chm1:+:1168826637:-1 chm1:+:2956738633:95 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:462886811:-1 chm1:+:824636987:-1 chm1:+:999955726:71 chm1:+:1266380734:78 chm1:+:1390109271:-1 chm1:+:1699572688:-1 chm1:+:1725275697:104 chm1:+:2056836903:-1 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:464389043:100 chm1:+:512758734:119 chm1:+:2068976817:102 chm1:+:2149552890:112 +TTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACAATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTTCCAATTTGTTTGTATCCTCTTTATTTCCTTGAGCAGTGGTTGTATTTCTCCTTGAAGAGGGTCCTTCCACTCCCGTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAGTTGTGAATGGGAGTTCACTCGATGATTTCGGCTCTCTGTTTGTCTTGTTGTAGGTGTATAAGAATGCTTGTGATTTTTTGTACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAGATTTGGGCTGAGACAATGGGGTTTTCTAATATACAATCATGTCATCTGCAAACAGGGGACAAATTTGACTTCCTCTTTTCCTAATTCGATACCCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCAACACTATGTTGAATAGGAAGTGGTGAGTAGAGGGCATTCCCTGTCTTGTGCCAGTTTTTCAAAGGGAATGCTACCAGTTTTTGCCCCATTCAGTAATGATAATTGGCTGACGGGTTTGTCATAGGATAGCTCTTAGTTACTTTTGAATACGTCCCCATCAATACCTAATTTTATTGAGAGTTTTTTAGCATGAAGGGTTGTTGAATTTTGTCCAAAGGCTTTTTCTGCATCTATTGAGATAATCCATGTGGTTTTTGTCTTTGGCTCTGTTATATGCTGGTTACATTATTGATTAGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC chm1:+:520857038:82 chm1:+:646131446:-1 chm1:+:934583940:84 chm1:+:1507715631:58 chm1:+:1647466826:88 chm1:+:2056187862:149 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCT chm1:+:1321934916:-1 chm1:+:1937612323:-1 chm1:+:2642309723:35 chm1:+:2967299066:-1 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCT chm1:+:2642309730:35 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCT chm1:+:707937511:-1 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCT chm1:+:1185290999:-1 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCT chm1:+:2642309731:35 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCT chm1:+:1118052451:-1 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCT chm1:+:2642309732:35 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCT chm1:+:2642309736:35 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCT chm1:+:2642309722:35 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCT chm1:+:2642309729:35 +ATAAAATAAAAAGGACTTGCTTAAGTAGTTTCATATGTAAACTAACAGAGTAGGTTATTGTTTGTAATTTCCAGTTTAGGGTTTATCCAATTATTCTCTCTACTGTACTGGAAGGCCAGGCTATGGGGGATTCCAGTTACAAGGAAAGGGCATCTGCCATGGCCACCCTTGCAGGCCAAGCAAACCCTGGCGCAGACTGCAGCAGATCCCACTGGGTGCCCACGTGGGTGGAGGGGGTTAACCTAGGAAAGGAAGGTCTCCTGGCAAAATAACCCTAGTGTGAGGCTTAACTTACTAATTTCTTCTAACCACTTTGCAAGAATCTGTTATTTATTGCAGAAAAGGAACTCAAAATGAGCTGGGAGTGTGTGTATGGTGGGAAGGGAGTGATGGTTGAAAACCTGCTTCAGGTGACAGCCAACAACCTGTTATTGTAAAGGTTTAGGCACAAAGGACACCATGGGGTTGCCCCCACCCTACTCCTCATTAGAGGGAGGCCTCTGATAGGATGGGTCTAGGTGCTTCTGGGTAGAAAGACAGACTTCTGGGTGAGTCTTAAGCTTTGAGACAGACAGGAGGTCAGCCTGGTACCCTCTGCAGCTCACTCTTGGGGGCCGAGTCTTGCGTAAGTGAACACAGAAACCTACAGCCTCCCCTTCATTATTTTTATGAATAGGCAGATCTCTTTAAAACCTAGGTTGGGTCACTTCACTTCCCTGATCCAAACTGTCTGCTGGCTTCTATTACATGCAAACAAAACCCAAAATGCTTGAAAAAGCATCTGGAAAATCCATGGGGCT chm1:+:2642309725:35 +AGCCCCATGGATTTTCCAGATGCTTTTTCAAGCATTTTGGGTTTTGTTTGCATGTAATAGAAGCCAGCAGACAGTTTGGATCAGGGAAGTGAAGTGACCCAACCTAGGTTTTAAAGAGATCTGCCTATTCATAAAAATAATGAAGGGGAGGCTGTAGGTTTCTGTGTTCACTTACGCAAGACTCGGCCCCCAAGAGTGAGCTGCAGAGGGTACCAGGCTGACCTCCTGTCTGTCTCAAAGCTTAAGACTCACCCAGAAGTCTGTCTTTCTACCCAGAAGCACCTAGACCCATCCTATCAGAGGCCTCCCTCTAATGAGGAGTAGGGTGGGGGCAACCCCATGGTGTCCTTTGTGCCTAAACCTTTACAATAACAGGTTGTTGGCTGTCACCTGAAGCAGGTTTTCAACCATCACTCCCTTCCCACCATACACACACTCCCAGCTCATTTTGAGTTCCTTTTCTGCAATAAATAACAGATTCTTGCAAAGTGGTTAGAAGAAATTAGTAAGTTAAGCCTCACACTAGGGTTATTTTGCCAGGAGACCTTCCTTTCCTAGGTTAACCCCCTCCACCCACGTGGGCACCCAGTGGGATCTGCTGCAGTCTGCGCCAGGGTTTGCTTGGCCTGCAAGGGTGGCCATGGCAGATGCCCTTTCCTTGTAACTGGAATCCCCCATAGCCTGGCCTTCCAGTACAGTAGAGAGAATAATTGGATAAACCCTAAACTGGAAATTACAAACAATAACCTACTCTGTTAGTTTACATATGAAACTACTTAAGCAAGTCCTTTTTATTTTAT chm1:+:2571312673:-1 +AGCCCCATGGATTTTCCAGATGCTTTTTCAAGCATTTTGGGTTTTGTTTGCATGTAATAGAAGCCAGCAGACAGTTTGGATCAGGGAAGTGAAGTGACCCAACCTAGGTTTTAAAGAGATCTGCCTATTCATAAAAATAATGAAGGGGAGGCTGTAGGTTTCTGTGTTCACTTACGCAAGACTCGGCCCCCAAGAGTGAGCTGCAGAGGGTACCAGGCTGACCTCCTGTCTGTCTCAAAGCTTAAGACTCACCCAGAAGTCTGTCTTTCTACCCAGAAGCACCTAGACCCATCCTATCAGAGGCCTCCCTCTAATGAGGAGTAGGGTGGGGGCAACCCCATGGTGTCCTTTGTGCCTAAACCTTTACAATAACAGGTTGTTGGCTGTCACCTGAAGCAGGTTTTCAACCATCACTCCCTTCCCACCATACACACACTCCCAGCTCATTTTGAGTTCCTTTTCTGCAATAAATAACAGATTCTTGCAAAGTGGTTAGAAGAAATTAGTAAGTTAAGCCTCACACTAGGGTTATTTTGCCAGGAGACCTTCCTTTCCTAGGTTAACCCCCTCCACCCACGTGGGCACCCAGTGGGATCTGCTGCAGTCTGCGCCAGGGTTTGCTTGGCCTGCAAGGGTGGCCATGGCAGATGCCCTTTCCTTGTAACTGGAATCCCCCATAGCCTGGCCTTCCAGTACAGTAGAGAGAATAATTGGATAAACCCTAAACTGGAAATTACAAACAATAACCTACTCTGTTAGTTTACATATGAAACTACTTAAGCAAGTCCTTTTTATTTTAT chm1:+:2270541480:-1 +AGCCCCATGGATTTTCCAGATGCTTTTTCAAGCATTTTGGGTTTTGTTTGCATGTAATAGAAGCCAGCAGACAGTTTGGATCAGGGAAGTGAAGTGACCCAACCTAGGTTTTAAAGAGATCTGCCTATTCATAAAAATAATGAAGGGGAGGCTGTAGGTTTCTGTGTTCACTTACGCAAGACTCGGCCCCCAAGAGTGAGCTGCAGAGGGTACCAGGCTGACCTCCTGTCTGTCTCAAAGCTTAAGACTCACCCAGAAGTCTGTCTTTCTACCCAGAAGCACCTAGACCCATCCTATCAGAGGCCTCCCTCTAATGAGGAGTAGGGTGGGGGCAACCCCATGGTGTCCTTTGTGCCTAAACCTTTACAATAACAGGTTGTTGGCTGTCACCTGAAGCAGGTTTTCAACCATCACTCCCTTCCCACCATACACACACTCCCAGCTCATTTTGAGTTCCTTTTCTGCAATAAATAACAGATTCTTGCAAAGTGGTTAGAAGAAATTAGTAAGTTAAGCCTCACACTAGGGTTATTTTGCCAGGAGACCTTCCTTTCCTAGGTTAACCCCCTCCACCCACGTGGGCACCCAGTGGGATCTGCTGCAGTCTGCGCCAGGGTTTGCTTGGCCTGCAAGGGTGGCCATGGCAGATGCCCTTTCCTTGTAACTGGAATCCCCCATAGCCTGGCCTTCCAGTACAGTAGAGAGAATAATTGGATAAACCCTAAACTGGAAATTACAAACAATAACCTACTCTGTTAGTTTACATATGAAACTACTTAAGCAAGTCCTTTTTATTTTAT chm1:+:1753725048:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:429144382:-1 chm1:+:832778442:-1 chm1:+:2040089972:-1 chm1:+:2384983283:-1 chm1:+:2666418608:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:1673249956:-1 chm1:+:1682361627:-1 chm1:+:2060597063:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:538125439:-1 chm1:+:711930436:-1 chm1:+:1246206830:-1 chm1:+:1498638385:-1 chm1:+:2683310394:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:168497321:-1 chm1:+:408013665:-1 chm1:+:416788584:-1 chm1:+:622669945:-1 chm1:+:866509863:-1 chm1:+:906314999:-1 chm1:+:959118284:-1 chm1:+:1138613592:-1 chm1:+:1530594559:-1 chm1:+:1616452084:-1 chm1:+:1951915826:-1 chm1:+:2048823840:-1 chm1:+:2578189530:-1 chm1:+:2592321861:-1 chm1:+:2769137196:-1 chm1:+:2896816341:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:499781874:-1 chm1:+:772115022:-1 chm1:+:909516681:-1 chm1:+:1083168978:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:291026329:-1 chm1:+:355636827:-1 chm1:+:386632547:-1 chm1:+:753885119:-1 chm1:+:1106916567:-1 chm1:+:1370125635:-1 chm1:+:1507875113:-1 chm1:+:1548053425:-1 chm1:+:1695263076:-1 chm1:+:1704082934:-1 chm1:+:1717616039:-1 chm1:+:2156768310:-1 chm1:+:2300625981:-1 chm1:+:2739015979:-1 chm1:+:2927188480:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:839743401:-1 chm1:+:1033603558:-1 chm1:+:1757258809:-1 chm1:+:1940345646:-1 chm1:+:2576587669:-1 chm1:+:2739506333:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:75780322:-1 chm1:+:214206806:-1 chm1:+:474768727:-1 chm1:+:532080732:-1 chm1:+:1004902822:-1 chm1:+:1052014652:-1 chm1:+:1068604664:-1 chm1:+:1311280299:-1 chm1:+:1551603276:-1 chm1:+:1852698892:-1 chm1:+:2011708317:-1 chm1:+:2374929993:-1 chm1:+:2529494562:-1 chm1:+:2618753525:-1 chm1:+:2732140090:-1 chm1:+:2791427808:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:467049875:-1 chm1:+:645218277:-1 chm1:+:984700603:-1 chm1:+:1804704268:-1 chm1:+:1977338233:-1 chm1:+:2376704722:-1 chm1:+:2399353796:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:156955472:-1 chm1:+:1518271968:-1 chm1:+:1947190065:-1 chm1:+:2348006682:-1 chm1:+:2758156820:-1 chm1:+:2988700309:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:165043800:-1 chm1:+:173024017:-1 chm1:+:438572615:-1 chm1:+:676868868:-1 chm1:+:1096867238:-1 chm1:+:1104570384:-1 chm1:+:1562563580:-1 chm1:+:1937627282:-1 chm1:+:1959062799:-1 chm1:+:1966098498:-1 chm1:+:1981437339:-1 chm1:+:2025711612:-1 chm1:+:2374467347:-1 chm1:+:2405077308:-1 chm1:+:2527180912:-1 chm1:+:2530641101:-1 chm1:+:2748219282:-1 chm1:+:2914129651:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:501717673:-1 chm1:+:836468174:-1 chm1:+:921454129:-1 chm1:+:1453220111:-1 chm1:+:2898244619:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:281237924:-1 chm1:+:318211070:-1 chm1:+:385532763:-1 chm1:+:833722920:-1 chm1:+:1027609458:-1 chm1:+:1090812153:-1 chm1:+:1249721090:-1 chm1:+:1315766437:-1 chm1:+:1725078555:-1 chm1:+:2990718826:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:66210676:-1 chm1:+:1169187003:-1 chm1:+:1733815206:-1 chm1:+:1838378076:-1 chm1:+:2224007088:-1 chm1:+:2668942849:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:715165602:-1 chm1:+:890560231:-1 chm1:+:987717246:-1 chm1:+:1275672790:-1 chm1:+:1629854411:-1 chm1:+:1689497108:-1 chm1:+:2001376383:-1 chm1:+:2005113940:-1 chm1:+:2375086669:-1 chm1:+:2464157601:-1 chm1:+:2498152072:-1 chm1:+:2664848807:-1 chm1:+:2763722250:-1 chm1:+:2827310501:-1 chm1:+:3010015532:-1 chm1:+:3034726544:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:222727865:-1 chm1:+:278226190:-1 chm1:+:355323860:-1 chm1:+:618928467:-1 chm1:+:652014627:-1 chm1:+:1265840272:-1 chm1:+:1389503580:-1 chm1:+:1535623672:-1 chm1:+:1863792164:-1 chm1:+:1964252252:-1 chm1:+:2003939144:-1 chm1:+:2278481765:-1 chm1:+:2579375700:-1 chm1:+:2640974952:-1 chm1:+:2862930921:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:75651740:-1 chm1:+:524899735:-1 chm1:+:639033125:-1 chm1:+:818212229:-1 chm1:+:836327604:-1 chm1:+:942932217:-1 chm1:+:1026024658:-1 chm1:+:1142085263:-1 chm1:+:1303457930:-1 chm1:+:1738489624:-1 chm1:+:1749551821:-1 chm1:+:1797641464:-1 chm1:+:1898951644:-1 chm1:+:2160312400:-1 chm1:+:2174810919:-1 chm1:+:2275910562:-1 chm1:+:2511620491:-1 chm1:+:2698909121:-1 +GTTTGTTGAACAAAACAGACACAAATGAGTAGGCCTGGTTTGAATAAGTTGAGTCAACCTGACTAAAATTGGAGAGTGGCTAAAAAATCAGGTTGGATAAGTTCAGTTGAAGAGCTATAAGAATACATTTTATAGAGAGAATGGAACAATAAAGACAGGTGGGAAGGCAATGGGGTCAGTGTTAAAGCTGGGGCCCTCAGCGTTTTGTCTCTGCCCAGCTCTCTTCCCATTACTAGTAGAAAAGAGTTTCTAAAATTCAGACCCAATCGACAACTGTCTTCTACTTAAAACTGTTCAGTGGCTTCCCCACTGCCTTTGGGGTAAAATGTCTTAGACACGGTCGTGCAAATGCCCTTCTTCACCTGACACTTTTCCCTTCAGCTTCAACCCAACATCACTTCCCTACAAACAGCCTATGAAGTAAATTTACTTGCATCCCCCAAAACTCACTGTCAACTAGAATCTTGCCTCTGTGCCTTTGCACATATTCTCTTCAGCCTGAGATGCCCTTCCCCTTCACTCTTCTATTTGACCAACTCTTATTCATTCTTTAAGACCCAGCAAGGGCATTGCTCTTCTAGGAAGTCCACCCTCATATCCTCTTCTCTCCCAAGGCTAGCTATGTGTCCCTTCCTCTGGACTCCTAGATTGATCTATACCAACCCTCTCCGATGGTACCTGCTACTTTCTAGTGCAAATTTTTTGTCTTTCTCATCTGCTTAGGGGCAGATAATGTCTTTCATCTCTTCCCTTAGTGTCTGGCACCTACGTAAGTCTCCATAGATATTTAGTAAACTGAA chm1:+:404438893:-1 chm1:+:1901381833:-1 chm1:+:3024284275:-1 +TTCAGTTTACTAAATATCTATGGAGACTTACGTAGGTGCCAGACACTAAGGGAAGAGATGAAAGACATTATCTGCCCCTAAGCAGATGAGAAAGACAAAAAATTTGCACTAGAAAGTAGCAGGTACCATCGGAGAGGGTTGGTATAGATCAATCTAGGAGTCCAGAGGAAGGGACACATAGCTAGCCTTGGGAGAGAAGAGGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549620:33 chm1:+:863135949:-1 chm1:+:1272010476:-1 chm1:+:2039694008:-1 chm1:+:2617447716:-1 +TTCAGTTTACTAAATATCTATGGAGACTTACGTAGGTGCCAGACACTAAGGGAAGAGATGAAAGACATTATCTGCCCCTAAGCAGATGAGAAAGACAAAAAATTTGCACTAGAAAGTAGCAGGTACCATCGGAGAGGGTTGGTATAGATCAATCTAGGAGTCCAGAGGAAGGGACACATAGCTAGCCTTGGGAGAGAAGAGGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549615:33 +TTCAGTTTACTAAATATCTATGGAGACTTACGTAGGTGCCAGACACTAAGGGAAGAGATGAAAGACATTATCTGCCCCTAAGCAGATGAGAAAGACAAAAAATTTGCACTAGAAAGTAGCAGGTACCATCGGAGAGGGTTGGTATAGATCAATCTAGGAGTCCAGAGGAAGGGACACATAGCTAGCCTTGGGAGAGAAGAGGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549622:33 +TTCAGTTTACTAAATATCTATGGAGACTTACGTAGGTGCCAGACACTAAGGGAAGAGATGAAAGACATTATCTGCCCCTAAGCAGATGAGAAAGACAAAAAATTTGCACTAGAAAGTAGCAGGTACCATCGGAGAGGGTTGGTATAGATCAATCTAGGAGTCCAGAGGAAGGGACACATAGCTAGCCTTGGGAGAGAAGAGGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549623:33 +TTCAGTTTACTAAATATCTATGGAGACTTACGTAGGTGCCAGACACTAAGGGAAGAGATGAAAGACATTATCTGCCCCTAAGCAGATGAGAAAGACAAAAAATTTGCACTAGAAAGTAGCAGGTACCATCGGAGAGGGTTGGTATAGATCAATCTAGGAGTCCAGAGGAAGGGACACATAGCTAGCCTTGGGAGAGAAGAGGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549627:33 +TTCAGTTTACTAAATATCTATGGAGACTTACGTAGGTGCCAGACACTAAGGGAAGAGATGAAAGACATTATCTGCCCCTAAGCAGATGAGAAAGACAAAAAATTTGCACTAGAAAGTAGCAGGTACCATCGGAGAGGGTTGGTATAGATCAATCTAGGAGTCCAGAGGAAGGGACACATAGCTAGCCTTGGGAGAGAAGAGGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549630:33 +TTCAGTTTACTAAATATCTATGGAGACTTACGTAGGTGCCAGACACTAAGGGAAGAGATGAAAGACATTATCTGCCCCTAAGCAGATGAGAAAGACAAAAAATTTGCACTAGAAAGTAGCAGGTACCATCGGAGAGGGTTGGTATAGATCAATCTAGGAGTCCAGAGGAAGGGACACATAGCTAGCCTTGGGAGAGAAGAGGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549631:33 +TTCAGTTTACTAAATATCTATGGAGACTTACGTAGGTGCCAGACACTAAGGGAAGAGATGAAAGACATTATCTGCCCCTAAGCAGATGAGAAAGACAAAAAATTTGCACTAGAAAGTAGCAGGTACCATCGGAGAGGGTTGGTATAGATCAATCTAGGAGTCCAGAGGAAGGGACACATAGCTAGCCTTGGGAGAGAAGAGGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549633:33 +TTCAGTTTACTAAATATCTATGGAGACTTACGTAGGTGCCAGACACTAAGGGAAGAGATGAAAGACATTATCTGCCCCTAAGCAGATGAGAAAGACAAAAAATTTGCACTAGAAAGTAGCAGGTACCATCGGAGAGGGTTGGTATAGATCAATCTAGGAGTCCAGAGGAAGGGACACATAGCTAGCCTTGGGAGAGAAGAGGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549616:33 +TTCAGTTTACTAAATATCTATGGAGACTTACGTAGGTGCCAGACACTAAGGGAAGAGATGAAAGACATTATCTGCCCCTAAGCAGATGAGAAAGACAAAAAATTTGCACTAGAAAGTAGCAGGTACCATCGGAGAGGGTTGGTATAGATCAATCTAGGAGTCCAGAGGAAGGGACACATAGCTAGCCTTGGGAGAGAAGAGGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:263919042:-1 +TTCAGTTTACTAAATATCTATGGAGACTTACGTAGGTGCCAGACACTAAGGGAAGAGATGAAAGACATTATCTGCCCCTAAGCAGATGAGAAAGACAAAAAATTTGCACTAGAAAGTAGCAGGTACCATCGGAGAGGGTTGGTATAGATCAATCTAGGAGTCCAGAGGAAGGGACACATAGCTAGCCTTGGGAGAGAAGAGGATATGAGGGTGGACTTCCTAGAAGAGCAATGCCCTTGCTGGGTCTTAAAGAATGAATAAGAGTTGGTCAAATAGAAGAGTGAAGGGGAAGGGCATCTCAGGCTGAAGAGAATATGTGCAAAGGCACAGAGGCAAGATTCTAGTTGACAGTGAGTTTTGGGGGATGCAAGTAAATTTACTTCATAGGCTGTTTGTAGGGAAGTGATGTTGGGTTGAAGCTGAAGGGAAAAGTGTCAGGTGAAGAAGGGCATTTGCACGACCGTGTCTAAGACATTTTACCCCAAAGGCAGTGGGGAAGCCACTGAACAGTTTTAAGTAGAAGACAGTTGTCGATTGGGTCTGAATTTTAGAAACTCTTTTCTACTAGTAATGGGAAGAGAGCTGGGCAGAGACAAAACGCTGAGGGCCCCAGCTTTAACACTGACCCCATTGCCTTCCCACCTGTCTTTATTGTTCCATTCTCTCTATAAAATGTATTCTTATAGCTCTTCAACTGAACTTATCCAACCTGATTTTTTAGCCACTCTCCAATTTTAGTCAGGTTGACTCAACTTATTCAAACCAGGCCTACTCATTTGTGTCTGTTTTGTTCAACAAAC chm1:+:616549632:33 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:87712917:-1 chm1:+:361363588:-1 chm1:+:810884896:-1 chm1:+:1310267267:-1 chm1:+:1479700992:-1 chm1:+:1522486230:-1 chm1:+:1527402174:-1 chm1:+:1750178538:-1 chm1:+:2388349093:-1 chm1:+:2424408292:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:1235986772:-1 chm1:+:1736964339:-1 chm1:+:1941729126:-1 chm1:+:1946420377:-1 chm1:+:2013964154:-1 chm1:+:2879589980:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:724627458:-1 chm1:+:727275497:-1 chm1:+:971452376:-1 chm1:+:1958377589:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:99278670:-1 chm1:+:106407163:-1 chm1:+:208129791:-1 chm1:+:235999254:-1 chm1:+:245199848:-1 chm1:+:377056205:-1 chm1:+:435354532:-1 chm1:+:448819756:-1 chm1:+:482314609:-1 chm1:+:547936138:-1 chm1:+:895723214:-1 chm1:+:908778859:-1 chm1:+:1138001339:-1 chm1:+:1296601365:-1 chm1:+:1352130776:-1 chm1:+:1426907307:-1 chm1:+:1500904332:-1 chm1:+:1750235551:-1 chm1:+:1793705532:-1 chm1:+:1811708586:-1 chm1:+:1850614874:-1 chm1:+:1979013810:-1 chm1:+:2011512681:-1 chm1:+:2057200726:-1 chm1:+:2103997974:-1 chm1:+:2115752215:-1 chm1:+:2239025259:-1 chm1:+:2352670578:-1 chm1:+:2536431647:141 chm1:+:2600405276:-1 chm1:+:2715770823:-1 chm1:+:2796725783:-1 chm1:+:2810872972:-1 chm1:+:3099133615:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:48861269:-1 chm1:+:110826455:-1 chm1:+:166994001:-1 chm1:+:219960035:-1 chm1:+:474238832:-1 chm1:+:579188196:-1 chm1:+:588000491:-1 chm1:+:691652473:-1 chm1:+:737755214:-1 chm1:+:779575632:-1 chm1:+:902254063:-1 chm1:+:918166319:-1 chm1:+:953237350:-1 chm1:+:1050372958:-1 chm1:+:1112928056:-1 chm1:+:1280723406:-1 chm1:+:1394469079:-1 chm1:+:1543414286:-1 chm1:+:1694859079:-1 chm1:+:1737891338:-1 chm1:+:1761931620:-1 chm1:+:1765514988:-1 chm1:+:1769453798:-1 chm1:+:1845200123:-1 chm1:+:1847560542:-1 chm1:+:2188760978:-1 chm1:+:2229111496:-1 chm1:+:2279555407:-1 chm1:+:2284088518:-1 chm1:+:2354935949:-1 chm1:+:2516717574:-1 chm1:+:2522290391:-1 chm1:+:2536431648:141 chm1:+:2552999400:-1 chm1:+:2611390055:-1 chm1:+:2876292764:-1 chm1:+:2897928518:-1 chm1:+:2974639100:-1 chm1:+:3004286552:-1 chm1:+:3027576207:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:356697680:-1 chm1:+:2536431332:-1 chm1:+:2676119607:-1 chm1:+:3036240131:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:178211816:-1 chm1:+:806661382:-1 chm1:+:1651696713:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:84772323:-1 chm1:+:215080370:-1 chm1:+:294362954:-1 chm1:+:391881629:-1 chm1:+:956043291:-1 chm1:+:1135698549:-1 chm1:+:1389807076:-1 chm1:+:1802190609:-1 chm1:+:1866189149:-1 chm1:+:2536431646:141 chm1:+:2952579533:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:44982499:-1 chm1:+:1953554955:-1 chm1:+:2118619476:-1 chm1:+:2536431650:141 chm1:+:2548124594:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:310073271:-1 chm1:+:906877345:-1 chm1:+:1627436902:-1 chm1:+:1766672402:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:1768859375:-1 chm1:+:1965055247:-1 chm1:+:2408073147:-1 chm1:+:2426482372:-1 chm1:+:2536431651:141 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:681309458:-1 chm1:+:1736178599:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:303088622:-1 chm1:+:604890177:-1 chm1:+:617566488:-1 chm1:+:1084550749:-1 chm1:+:1333842297:-1 chm1:+:1402348050:-1 chm1:+:1949014705:-1 chm1:+:2182734941:-1 chm1:+:2536431649:141 chm1:+:2716870722:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:690936884:-1 chm1:+:1802644509:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:349766121:-1 chm1:+:492976108:-1 chm1:+:586756462:-1 chm1:+:746062107:-1 chm1:+:750710366:-1 chm1:+:793673486:-1 chm1:+:947192566:-1 chm1:+:966272450:-1 chm1:+:1065053573:-1 chm1:+:1258663622:-1 chm1:+:1524139029:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:239408782:-1 chm1:+:442497824:-1 chm1:+:557430634:-1 chm1:+:1471609373:-1 chm1:+:1842795790:-1 chm1:+:1948461941:-1 chm1:+:2807761860:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:673740362:-1 chm1:+:1346137160:-1 chm1:+:1412432250:-1 chm1:+:2283537698:-1 chm1:+:2693830597:-1 chm1:+:2976801369:-1 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chm1:+:1259189632:-1 chm1:+:1333061996:-1 chm1:+:1336058099:-1 chm1:+:1657819781:-1 chm1:+:2066335901:-1 chm1:+:2233533181:-1 chm1:+:2332967254:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:1550883502:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:367780057:-1 chm1:+:619576243:-1 chm1:+:626818773:-1 chm1:+:2505484284:-1 +CAAAACCTTTAGAGGAATAAAAGAAATTACCTTCATGACTTCGAGGTTAGGCAAAACTGTCTTAGCTCACTAGTAAGCAATAAACTACAAAGAAAAACACTGACTAAATTTAAACTTATCAGATATAAATAATTTCTCGACTCATCAAAAGGTACAGTTAAAATAAATAGTTAAACCATATAGACTTGGGGAAAGTATTTACAAAACATTTATCAGACACAGGATCAGTATTTAGGACATATAAAACACCTTCTGCAACTCAAATAGATGAAAAAGGAAAACAAATAGCAAAGGCTAATGAACAAACTCATCACAAAGAGAACACACGAATGGTCAACACCACCAAGCTAAAATGTGCTGAATATCATCAGTTATCATGAAAAAAGTAATTTAAAACCACAATGGATACCACTTCTGGTCAGATGGAGTGAATAAAGGGGACCAGGATATAGCCTCCTTGCACGAATAATAAAACCTAATAAATGAATGTAAACAACAGCACTGAAGATATGGACAAGCAACAAAACACAGTCATCCCTGGAAAGACAAAAAACAATGGGCCGCACGTGTGCCCAGCTTACTGCCTTGAGAGAGTTTCTAGGTCGTGGAACAGGAGGAGGAACCCAGGCAGAGCCTGTAGGTCTCCCCAAGTTGAGGGAAATGAAGCTGGAAGTCCAAGGAGGCCAAGGTGCCTAGAGCTCACAAGGGAGACCAGCACTGAGTAGAGAGCTGGAGAGAGAGAGAGAATGAAGAGACTCTACAAAAGGCTTCACCCGTAGAACTTTTTGGTTGAATGACAA chm1:+:107542428:-1 chm1:+:348033834:-1 chm1:+:664894299:-1 chm1:+:1012806075:-1 chm1:+:1089970702:-1 chm1:+:1144802163:-1 chm1:+:1166847116:-1 chm1:+:1225310163:-1 chm1:+:1336092250:-1 chm1:+:1654569483:-1 chm1:+:1713777119:-1 chm1:+:1858661381:-1 chm1:+:2281351005:-1 chm1:+:2378747108:-1 chm1:+:2461541369:-1 chm1:+:2646437120:-1 chm1:+:2755958633:-1 +TTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:80578859:-1 chm1:+:99326882:-1 chm1:+:186676246:-1 chm1:+:321257609:-1 chm1:+:581492584:-1 chm1:+:647693964:-1 chm1:+:797307721:-1 chm1:+:799550515:-1 chm1:+:854398842:-1 chm1:+:904636688:-1 chm1:+:1034737243:-1 chm1:+:1260038414:-1 chm1:+:1269285675:-1 chm1:+:1296629483:-1 chm1:+:1432654166:-1 chm1:+:1452617684:-1 chm1:+:1572553971:-1 chm1:+:1584025119:-1 chm1:+:1585538083:-1 chm1:+:1655248223:-1 chm1:+:2005321981:-1 chm1:+:2014623406:-1 chm1:+:2043057648:-1 chm1:+:2146355700:-1 chm1:+:2337151326:-1 chm1:+:2498918559:-1 chm1:+:2751240787:-1 chm1:+:2780935366:-1 chm1:+:2805741100:-1 chm1:+:2829513769:-1 chm1:+:2859749397:-1 chm1:+:2881934111:-1 chm1:+:2883569619:-1 chm1:+:2949305723:-1 chm1:+:2987696232:-1 +TTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1702233176:43 chm1:+:2534951972:143 +TTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1408311062:-1 +TTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1004063440:-1 +TTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1702233173:43 +TTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:2534952287:-1 +TTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:2534951975:143 +TTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1702233175:43 +TTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:2761292931:-1 +TTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1702233177:43 chm1:+:2534951976:143 +TTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1702233169:43 +TTGTCATTCAACCAAAAAGTTCTACGGGTGAAGCCTTTTGTAGAGTCTCTTCATTCTCTCTCTCTCTCCAGCTCTCTACTCAGTGCTGGTCTCCCTTGTGAGCTCTAGGCACCTTGGCCTCCTTGGACTTCCAGCTTCATTTCCCTCAACTTGGGGAGACCTACAGGCTCTGCCTGGGTTCCTCCTCCTGTTCCACGACCTAGAAACTCTCTCAAGGCAGTAAGCTGGGCACACGTGCGGCCCATTGTTTTTTGTCTTTCCAGGGATGACTGTGTTTTGTTGCTTGTCCATATCTTCAGTGCTGTTGTTTACATTCATTTATTAGGTTTTATTATTCGTGCAAGGAGGCTATATCCTGGTCCCCTTTATTCACTCCATCTGACCAGAAGTGGTATCCATTGTGGTTTTAAATTACTTTTTTCATGATAACTGATGATATTCAGCACATTTTAGCTTGGTGGTGTTGACCATTCGTGTGTTCTCTTTGTGATGAGTTTGTTCATTAGCCTTTGCTATTTGTTTTCCTTTTTCATCTATTTGAGTTGCAGAAGGTGTTTTATATGTCCTAAATACTGATCCTGTGTCTGATAAATGTTTTGTAAATACTTTCCCCAAGTCTATATGGTTTAACTATTTATTTTAACTGTACCTTTTGATGAGTCGAGAAATTATTTATATCTGATAAGTTTAAATTTAGTCAGTGTTTTTCTTTGTAGTTTATTGCTTACTAGTGAGCTAAGACAGTTTTGCCTAACCTCGAAGTCATGAAGGTAATTTCTTTTATTCCTCTAAAGGTTTTG chm1:+:1702233174:43 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:871305639:-1 chm1:+:1097311179:-1 chm1:+:1119943781:-1 chm1:+:1551427777:-1 chm1:+:1800723587:-1 chm1:+:1918092089:-1 chm1:+:2075282223:-1 chm1:+:2277820830:-1 chm1:+:2350829470:-1 chm1:+:2384891666:-1 chm1:+:2484471939:-1 chm1:+:2811177116:-1 chm1:+:2905491958:-1 chm1:+:3011024611:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:20934142:-1 chm1:+:46445983:-1 chm1:+:120619682:-1 chm1:+:148887666:-1 chm1:+:353549742:-1 chm1:+:525216669:-1 chm1:+:540327251:-1 chm1:+:849703318:-1 chm1:+:900275057:-1 chm1:+:1043800496:-1 chm1:+:1087314266:-1 chm1:+:1400974631:-1 chm1:+:1881043165:-1 chm1:+:2033629033:-1 chm1:+:2734802286:-1 chm1:+:3100277350:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:174068458:-1 chm1:+:2028516586:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:386595996:-1 chm1:+:465583825:-1 chm1:+:528017700:-1 chm1:+:956982183:-1 chm1:+:1120438431:-1 chm1:+:1121042428:-1 chm1:+:1333447424:-1 chm1:+:1504280709:-1 chm1:+:1763987061:-1 chm1:+:2018028970:-1 chm1:+:2247198466:-1 chm1:+:2255763850:-1 chm1:+:2376824583:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:17124259:-1 chm1:+:35811845:-1 chm1:+:53482765:-1 chm1:+:203745545:-1 chm1:+:230583162:-1 chm1:+:433210824:-1 chm1:+:540263850:-1 chm1:+:545661194:-1 chm1:+:844960359:-1 chm1:+:981541067:-1 chm1:+:1236110184:-1 chm1:+:1256975257:-1 chm1:+:1335311370:-1 chm1:+:1533906570:-1 chm1:+:1544500198:-1 chm1:+:1662851176:-1 chm1:+:1878424391:-1 chm1:+:1978373321:-1 chm1:+:2005626895:-1 chm1:+:2292470840:-1 chm1:+:2416678724:-1 chm1:+:2542867335:-1 chm1:+:2614894700:-1 chm1:+:2705082601:-1 chm1:+:2717776762:-1 chm1:+:2740005189:-1 chm1:+:2850481819:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:709581246:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:906728659:-1 chm1:+:1171366288:-1 chm1:+:2512681597:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:7329593:-1 chm1:+:26963105:-1 chm1:+:26993975:-1 chm1:+:46615719:-1 chm1:+:46630216:-1 chm1:+:143459439:-1 chm1:+:155268536:-1 chm1:+:156174073:-1 chm1:+:180512045:-1 chm1:+:192741175:-1 chm1:+:224787130:-1 chm1:+:234281476:-1 chm1:+:247175266:-1 chm1:+:285104538:-1 chm1:+:310355920:-1 chm1:+:311098791:-1 chm1:+:365791969:-1 chm1:+:378080019:-1 chm1:+:385964193:-1 chm1:+:401988254:-1 chm1:+:496975385:-1 chm1:+:506878459:-1 chm1:+:531049113:-1 chm1:+:534893984:-1 chm1:+:537792539:-1 chm1:+:538902575:-1 chm1:+:541462879:-1 chm1:+:558438365:-1 chm1:+:592375559:-1 chm1:+:596308855:-1 chm1:+:601552584:-1 chm1:+:614691203:-1 chm1:+:617595111:-1 chm1:+:628983438:-1 chm1:+:642936855:-1 chm1:+:695408411:-1 chm1:+:702354192:-1 chm1:+:715811376:-1 chm1:+:764100980:-1 chm1:+:836082623:-1 chm1:+:865261377:-1 chm1:+:884424461:-1 chm1:+:932384005:-1 chm1:+:977651874:-1 chm1:+:1001975854:-1 chm1:+:1003059677:-1 chm1:+:1003423312:-1 chm1:+:1011235020:-1 chm1:+:1013938959:-1 chm1:+:1015855996:-1 chm1:+:1023678008:-1 chm1:+:1053875470:-1 chm1:+:1055982216:-1 chm1:+:1076497754:-1 chm1:+:1078562414:-1 chm1:+:1096951789:-1 chm1:+:1119828151:-1 chm1:+:1139889292:-1 chm1:+:1173353626:-1 chm1:+:1181730240:-1 chm1:+:1181840327:-1 chm1:+:1194344657:-1 chm1:+:1229349685:-1 chm1:+:1235730117:-1 chm1:+:1256989170:-1 chm1:+:1260735170:-1 chm1:+:1266581786:-1 chm1:+:1278706462:-1 chm1:+:1305262819:-1 chm1:+:1331706245:-1 chm1:+:1344343510:-1 chm1:+:1362190925:-1 chm1:+:1362866175:-1 chm1:+:1366102032:-1 chm1:+:1372674848:-1 chm1:+:1435139313:-1 chm1:+:1469220201:-1 chm1:+:1479903523:-1 chm1:+:1502033351:-1 chm1:+:1534355644:-1 chm1:+:1536887905:-1 chm1:+:1558316441:-1 chm1:+:1558371391:-1 chm1:+:1559064357:-1 chm1:+:1577819968:-1 chm1:+:1611461220:-1 chm1:+:1651317087:-1 chm1:+:1661895751:-1 chm1:+:1717454422:-1 chm1:+:1757405653:-1 chm1:+:1757431071:-1 chm1:+:1776695949:-1 chm1:+:1784316162:-1 chm1:+:1832656105:-1 chm1:+:1835071410:-1 chm1:+:1882636560:-1 chm1:+:1882776245:-1 chm1:+:1884163615:-1 chm1:+:1889400739:-1 chm1:+:1905977502:-1 chm1:+:1909343258:-1 chm1:+:1938351839:-1 chm1:+:1952659526:-1 chm1:+:1960094392:-1 chm1:+:1961000596:-1 chm1:+:1967237611:-1 chm1:+:1990752534:-1 chm1:+:2000029100:-1 chm1:+:2007272054:-1 chm1:+:2015557737:-1 chm1:+:2020672044:-1 chm1:+:2033169459:-1 chm1:+:2049131816:-1 chm1:+:2066566517:-1 chm1:+:2074998503:-1 chm1:+:2083244566:-1 chm1:+:2126824487:-1 chm1:+:2133579881:-1 chm1:+:2134862440:-1 chm1:+:2146934228:-1 chm1:+:2258842467:-1 chm1:+:2267693363:-1 chm1:+:2286131796:-1 chm1:+:2296119180:-1 chm1:+:2363498480:-1 chm1:+:2369048529:-1 chm1:+:2372357568:-1 chm1:+:2383103294:-1 chm1:+:2408465307:-1 chm1:+:2435768836:-1 chm1:+:2437443025:-1 chm1:+:2459049841:-1 chm1:+:2459810684:-1 chm1:+:2470191940:-1 chm1:+:2471281804:-1 chm1:+:2480218525:-1 chm1:+:2483150752:-1 chm1:+:2500902744:-1 chm1:+:2502400009:-1 chm1:+:2511092892:-1 chm1:+:2531060603:-1 chm1:+:2556898521:-1 chm1:+:2560689910:-1 chm1:+:2561907197:-1 chm1:+:2577074218:-1 chm1:+:2579297745:-1 chm1:+:2582195218:-1 chm1:+:2593392346:-1 chm1:+:2666732977:-1 chm1:+:2671013323:-1 chm1:+:2674181750:-1 chm1:+:2680857845:-1 chm1:+:2681624798:-1 chm1:+:2698564877:-1 chm1:+:2713428161:-1 chm1:+:2749930638:-1 chm1:+:2753897043:-1 chm1:+:2755086202:-1 chm1:+:2764592358:-1 chm1:+:2766455977:-1 chm1:+:2791559180:-1 chm1:+:2813686134:-1 chm1:+:2814689881:-1 chm1:+:2821431791:-1 chm1:+:2849078042:-1 chm1:+:2876618364:-1 chm1:+:2883078106:-1 chm1:+:2890432414:-1 chm1:+:2901448834:-1 chm1:+:2935603427:-1 chm1:+:2959584285:-1 chm1:+:2964307722:-1 chm1:+:2983152949:-1 chm1:+:3005960224:-1 chm1:+:3049666354:-1 chm1:+:3060189640:-1 chm1:+:3095926534:-1 chm1:+:3096056631:-1 chm1:+:3097955811:-1 chm1:+:3100961419:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:940009881:-1 chm1:+:1287493431:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:772490537:-1 chm1:+:967637275:-1 chm1:+:1784751289:-1 chm1:+:2585467077:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:69333363:-1 chm1:+:81785989:-1 chm1:+:102060627:-1 chm1:+:176139317:-1 chm1:+:213841389:-1 chm1:+:213949471:-1 chm1:+:214944244:-1 chm1:+:269274776:-1 chm1:+:478243806:-1 chm1:+:510498635:-1 chm1:+:664958253:-1 chm1:+:866682412:-1 chm1:+:868809272:-1 chm1:+:1015853502:-1 chm1:+:1042594164:-1 chm1:+:1082963394:-1 chm1:+:1208295249:-1 chm1:+:1233753362:-1 chm1:+:1305257194:-1 chm1:+:1401765266:-1 chm1:+:1725699750:-1 chm1:+:1746285770:-1 chm1:+:1771738574:-1 chm1:+:1825044083:-1 chm1:+:1831066229:-1 chm1:+:1994340232:-1 chm1:+:1996691532:-1 chm1:+:2181774768:-1 chm1:+:2252487338:-1 chm1:+:2270612604:-1 chm1:+:2296893830:-1 chm1:+:2346503275:-1 chm1:+:2617213340:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:33062574:-1 chm1:+:351151209:-1 chm1:+:451155060:-1 chm1:+:458187274:-1 chm1:+:569633777:-1 chm1:+:593115382:-1 chm1:+:746020247:-1 chm1:+:792588590:-1 chm1:+:956209628:-1 chm1:+:960120377:-1 chm1:+:1328438420:-1 chm1:+:1577870597:-1 chm1:+:1582838977:-1 chm1:+:1664891130:-1 chm1:+:1754936219:-1 chm1:+:2065825743:-1 chm1:+:2270026580:-1 chm1:+:2516504895:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:315150900:-1 chm1:+:339756471:-1 chm1:+:340978137:-1 chm1:+:348877449:-1 chm1:+:360006703:-1 chm1:+:381520758:-1 chm1:+:425165577:-1 chm1:+:556060913:-1 chm1:+:612332456:-1 chm1:+:1054689666:-1 chm1:+:1066781017:-1 chm1:+:1184325949:-1 chm1:+:1188099982:-1 chm1:+:1246829997:-1 chm1:+:1270179563:-1 chm1:+:1271182712:-1 chm1:+:1278507487:-1 chm1:+:1306598127:-1 chm1:+:1311137602:-1 chm1:+:1408864757:-1 chm1:+:1552395226:-1 chm1:+:1702140181:-1 chm1:+:1723084946:-1 chm1:+:1827731651:-1 chm1:+:2059726983:-1 chm1:+:2071677615:-1 chm1:+:2115965116:-1 chm1:+:2234882354:-1 chm1:+:2327617532:-1 chm1:+:2327749804:-1 chm1:+:2328624137:-1 chm1:+:2339716885:-1 chm1:+:2442150078:-1 chm1:+:2443147512:-1 chm1:+:2529866251:-1 chm1:+:2634294096:-1 chm1:+:2649422433:-1 chm1:+:2739773659:-1 chm1:+:2813147084:-1 chm1:+:2852352348:-1 chm1:+:2861551672:-1 chm1:+:2905161172:-1 chm1:+:2933175011:-1 chm1:+:2934079441:-1 chm1:+:2954339151:-1 chm1:+:3098720746:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:10454499:-1 chm1:+:29108306:-1 chm1:+:386338192:-1 chm1:+:435593546:-1 chm1:+:472902967:-1 chm1:+:586568127:-1 chm1:+:587409987:-1 chm1:+:879277978:-1 chm1:+:1272460730:-1 chm1:+:1280368267:-1 chm1:+:1286931009:-1 chm1:+:1296840747:-1 chm1:+:1300018956:-1 chm1:+:1351387405:-1 chm1:+:1454259348:-1 chm1:+:1575786471:-1 chm1:+:1610774761:-1 chm1:+:1866166145:-1 chm1:+:2061587692:-1 chm1:+:2332611455:-1 chm1:+:2432083581:-1 chm1:+:2469806773:-1 chm1:+:2476661055:-1 chm1:+:2530307304:-1 chm1:+:2545123043:-1 chm1:+:2573378621:-1 chm1:+:2660881296:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:650838338:-1 chm1:+:1670514882:-1 chm1:+:2478105052:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:1614394867:-1 chm1:+:1960458332:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:208429222:-1 chm1:+:1386657463:-1 chm1:+:1416519304:-1 chm1:+:2985719827:-1 chm1:+:3056966662:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:362690374:-1 chm1:+:636654511:-1 chm1:+:877289766:-1 chm1:+:974248104:-1 chm1:+:1300435034:-1 chm1:+:1624628551:-1 chm1:+:1804360017:-1 chm1:+:2037436818:-1 chm1:+:2061769594:-1 chm1:+:2667272828:-1 chm1:+:2682248403:-1 chm1:+:2967756705:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:57830672:-1 chm1:+:796010504:-1 chm1:+:796526480:-1 chm1:+:1427899663:-1 chm1:+:1559813908:-1 chm1:+:2004424172:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:68762365:-1 chm1:+:286747128:-1 chm1:+:319507814:-1 chm1:+:435993413:-1 chm1:+:444456546:-1 chm1:+:466184261:-1 chm1:+:582468566:-1 chm1:+:606641632:-1 chm1:+:614109972:-1 chm1:+:654077543:-1 chm1:+:705244224:-1 chm1:+:768868194:-1 chm1:+:844993777:-1 chm1:+:866943513:-1 chm1:+:901591588:-1 chm1:+:1095607037:-1 chm1:+:1096887162:-1 chm1:+:1249381051:-1 chm1:+:1349242757:-1 chm1:+:1466914352:-1 chm1:+:1470283325:-1 chm1:+:1492792094:-1 chm1:+:1493385726:-1 chm1:+:1542606829:-1 chm1:+:1694107182:-1 chm1:+:1819119759:-1 chm1:+:1841321968:-1 chm1:+:2147649482:-1 chm1:+:2192237128:-1 chm1:+:2340269602:-1 chm1:+:2349497423:-1 chm1:+:2468161429:-1 chm1:+:2777904423:-1 chm1:+:2947463826:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:77548648:-1 chm1:+:100466308:-1 chm1:+:1063677238:-1 chm1:+:1343315751:-1 chm1:+:1410829459:-1 chm1:+:1994149716:-1 chm1:+:2547293640:-1 chm1:+:2729822382:-1 chm1:+:3052460364:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:24553833:-1 chm1:+:25142941:-1 chm1:+:69670005:-1 chm1:+:150172423:-1 chm1:+:159225846:-1 chm1:+:168175474:-1 chm1:+:212015490:-1 chm1:+:217012805:-1 chm1:+:382493978:-1 chm1:+:383671997:-1 chm1:+:435581453:-1 chm1:+:445666788:-1 chm1:+:470014888:-1 chm1:+:540222860:-1 chm1:+:618893834:-1 chm1:+:646694182:-1 chm1:+:684282231:-1 chm1:+:732651391:-1 chm1:+:823100719:-1 chm1:+:859465577:-1 chm1:+:918387036:-1 chm1:+:972858766:-1 chm1:+:978555747:-1 chm1:+:1087614926:-1 chm1:+:1106170431:-1 chm1:+:1117558358:-1 chm1:+:1126352562:-1 chm1:+:1176013070:-1 chm1:+:1276695451:-1 chm1:+:1360166387:-1 chm1:+:1368370403:-1 chm1:+:1381009355:-1 chm1:+:1443781722:-1 chm1:+:1492940371:-1 chm1:+:1585608598:-1 chm1:+:1607005616:-1 chm1:+:1615854360:-1 chm1:+:1619167958:-1 chm1:+:1819610375:-1 chm1:+:1835420104:-1 chm1:+:1855683898:-1 chm1:+:1904874434:-1 chm1:+:1915785355:-1 chm1:+:1992017130:-1 chm1:+:2002861610:-1 chm1:+:2013720979:-1 chm1:+:2043490727:-1 chm1:+:2131340062:-1 chm1:+:2150180538:-1 chm1:+:2175570432:-1 chm1:+:2241541435:-1 chm1:+:2405014649:-1 chm1:+:2482363053:-1 chm1:+:2495980588:-1 chm1:+:2609165518:-1 chm1:+:2634011876:-1 chm1:+:2724897372:-1 chm1:+:2791966148:-1 chm1:+:2900648331:-1 chm1:+:2916499877:-1 chm1:+:2983136751:-1 chm1:+:3100821407:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:378515735:-1 chm1:+:1331349035:-1 chm1:+:2121853967:-1 chm1:+:2490298646:-1 chm1:+:2540145075:-1 chm1:+:2601078152:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:478399636:-1 chm1:+:538177383:-1 chm1:+:557903274:-1 chm1:+:728453052:-1 chm1:+:943932115:-1 chm1:+:973094834:-1 chm1:+:1031780420:-1 chm1:+:1064625931:-1 chm1:+:1065232254:-1 chm1:+:1158168195:-1 chm1:+:1336668399:-1 chm1:+:1558386297:-1 chm1:+:2247249495:-1 chm1:+:2504512176:-1 chm1:+:2639513760:-1 chm1:+:2669201972:-1 chm1:+:2863288453:-1 chm1:+:2881976808:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:11434307:-1 chm1:+:154624963:-1 chm1:+:601642700:-1 chm1:+:1301845950:-1 chm1:+:1374334372:-1 chm1:+:1435195605:-1 chm1:+:1467695559:-1 chm1:+:1694885629:-1 chm1:+:1883007033:-1 chm1:+:1923190198:-1 chm1:+:2243166687:-1 chm1:+:2528240758:-1 chm1:+:2630305747:-1 chm1:+:2775299016:-1 chm1:+:2811547098:-1 chm1:+:2819985530:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:21625421:-1 chm1:+:102408766:-1 chm1:+:432583904:-1 chm1:+:440079226:-1 chm1:+:796293280:-1 chm1:+:852424286:-1 chm1:+:1223183427:-1 chm1:+:2604274904:-1 chm1:+:2707691666:-1 chm1:+:2752781096:-1 +GCTATAGCCTATATGTATTTCTAAATGTATTTCGTGAAATACTGTACTCGAAAGTCAAACTCCTTGATTTATGGGCTGCAGATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCTCCATCAGGGATCTTGGGGTGATCAGGTGAATTGTCAAATGAACTGTAATATTTGAAAGGAAGTCTTTTTTTCTGAGCAAATAAAGTCTCAACAGTGGGCTTAAAGTATTTAGTAATTCATGCTCTAAACAGATGTACTGTTATCCAGGGTCTTTGTTGTTCCATTTTATAAAAACACAGGCAAGAGTAGATTTAGCATAATTCTAAAGGGCCCTAAAATTTTCAGAATGTTACATGAGCAAATAAAATAAAGTCATTAGCCCCTAACAAAGAGTCAGCCTGTTCCTTTGAAGCTTGAAAACCAGGAATTGACTTCTCTCTGTCACTATGCAAGTCCCTAGATGACATCTTCTTCTAGTGAAAGACTGTCTTAATCTACTTTGAAAAATTGAGGGTTTAGTGTAACCACTTGCACCAATTTCTTAGTTAGATCTTCTGGAGTAACTTGCTATAGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTGAGATGGAGTCCTTGGGTCTTGTCACCCAGGCTGGAATGCAATGGTGTGATCTACAAGCTCAGTGTACCCTCTGCCTCCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGAATTTTACAGGCATGTTCCACCCATATCCGGCAAATTTTTTTGTATTTTTAAATAGAGA chm1:+:225312388:-1 chm1:+:363456143:-1 chm1:+:449938624:-1 chm1:+:561316550:-1 chm1:+:643317783:-1 chm1:+:784574486:-1 chm1:+:1147843577:-1 chm1:+:1368800637:-1 chm1:+:1480044145:-1 chm1:+:1581826310:-1 chm1:+:1610026360:-1 chm1:+:1742144989:-1 chm1:+:1779061489:-1 chm1:+:1909268255:-1 chm1:+:2182769388:-1 chm1:+:2224368053:-1 chm1:+:2224403175:-1 chm1:+:2224451131:-1 chm1:+:2268352450:-1 chm1:+:2559990552:-1 +TCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:96591274:36 chm1:+:288206105:-1 chm1:+:303208822:-1 chm1:+:424582163:-1 chm1:+:508493626:-1 chm1:+:612238710:-1 chm1:+:1055726994:-1 chm1:+:1094645382:-1 chm1:+:1118795774:-1 chm1:+:1330851188:-1 chm1:+:1424049789:-1 chm1:+:1710978614:-1 chm1:+:1763156006:-1 chm1:+:1784998253:-1 chm1:+:1863334126:-1 chm1:+:1880813422:-1 chm1:+:1894618108:-1 chm1:+:2130423642:-1 chm1:+:2224616226:-1 chm1:+:2247728671:-1 chm1:+:2302694646:-1 chm1:+:2500447004:-1 chm1:+:2815266769:-1 +TCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:96591261:36 +TCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:96591265:36 +TCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:96591270:36 chm1:+:1359879191:-1 +TCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:96591266:36 +TCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:96591271:36 chm1:+:481204193:-1 +TCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:1495610492:-1 +TCTCTATTTAAAAATACAAAAAAATTTGCCGGATATGGGTGGAACATGCCTGTAAAATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGGAGGCAGAGGGTACACTGAGCTTGTAGATCACACCATTGCATTCCAGCCTGGGTGACAAGACCCAAGGACTCCATCTCAAAAAACAAAACAAAACAAAACAAAACAAAACTATAGCAAGTTACTCCAGAAGATCTAACTAAGAAATTGGTGCAAGTGGTTACACTAAACCCTCAATTTTTCAAAGTAGATTAAGACAGTCTTTCACTAGAAGAAGATGTCATCTAGGGACTTGCATAGTGACAGAGAGAAGTCAATTCCTGGTTTTCAAGCTTCAAAGGAACAGGCTGACTCTTTGTTAGGGGCTAATGACTTTATTTTATTTGCTCATGTAACATTCTGAAAATTTTAGGGCCCTTTAGAATTATGCTAAATCTACTCTTGCCTGTGTTTTTATAAAATGGAACAACAAAGACCCTGGATAACAGTACATCTGTTTAGAGCATGAATTACTAAATACTTTAAGCCCACTGTTGAGACTTTATTTGCTCAGAAAAAAAGACTTCCTTTCAAATATTACAGTTCATTTGACAATTCACCTGATCACCCCAAGATCCCTGATGGAGATGTACAAGGAGATTAATGTTGTTTTCATGCCTGCTAACACAACATCCATCTGCAGCCCATAAATCAAGGAGTTTGACTTTCGAGTACAGTATTTCACGAAATACATTTAGAAATACATATAGGCTATAGC chm1:+:96591273:36 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAAT chm1:+:63600627:45 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAAT chm1:+:63600602:45 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAAT chm1:+:63600607:45 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAAT chm1:+:63600609:45 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAAT chm1:+:63600612:45 chm1:+:425504322:-1 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAAT chm1:+:63600622:45 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAAT chm1:+:63600624:45 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAAT chm1:+:63600625:45 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAAT chm1:+:63600613:45 chm1:+:1246408782:-1 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAAT chm1:+:63600616:45 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAAT chm1:+:63600618:45 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAAT chm1:+:63600619:45 +TCCGCTCGTTCAGTTGCAGAGTCGGATATTCACCTTTGTTAGTGCACCCCCCAACAATCGAAGCCTTGTTATGACCTACATTTATTAAGTGAAAGTATTTGGAAACTGATGGTACATTCAAGCTTGGTTGCCATAGGGCAGTAATCATGGCAGAAAGTCATGACCTCCCTGTTATTGCGAGCGAGTAACTAATTGAAATGATACAAATTACTCCGATTCTCTGTCCTGCCAATTTAGAGCCTTGGTTCTGGTCCAAGGGTCAAATGAGCTCCTATTCAATGAAACTATGTTTGAAGTAGCTGCTACCATAGCAACGGGGGTTTGGTGTGGCCATTGGCTGCTCCTTTAGACTTTGCCACATACTGTGGGGAGGCAGTAAGCAGTAAGGTTCCCAAAGCCTACCTTAGCCCAACACAGTCAAAGCTTGTCTGTTGTCACTCGGTTTGTGCCTACTGTCAACAGCACCTGGACTGGTTTGCTAAACTTTACTGGCCAGTAAATAAATGTTGTATTCAGAAGCCATTTAGGGATTCAGCCTCGTTTAGCCCCGCACATTTCATCAGCTCTCTGAGTATGCCCCTCGGCAGAGAAAACCAAATGCCATAAACCTCAATTATTGAATGATTTTCAACTTATCAATTCCCATCAAGTGTCATCCTTTCCAGCTTCTCTCAGCCCCAGCGACCACATACACAGTACCTGCCAAATAAATAAGATAAAATTAAAAGCCTTGAAAGGTACATAACAGTGCAAGCTCTTCGTTCAAAGATAATTAGGATGATTATTTCTGTTTGAGAAAT chm1:+:63600615:45 +ATTTCTCAAACAGAAATAATCATCCTAATTATCTTTGAACGAAGAGCTTGCACTGTTATGTACCTTTCAAGGCTTTTAATTTTATCTTATTTATTTGGCAGGTACTGTGTATGTGGTCGCTGGGGCTGAGAGAAGCTGGAAAGGATGACACTTGATGGGAATTGATAAGTTGAAAATCATTCAATAATTGAGGTTTATGGCATTTGGTTTTCTCTGCCGAGGGGCATACTCAGAGAGCTGATGAAATGTGCGGGGCTAAACGAGGCTGAATCCCTAAATGGCTTCTGAATACAACATTTATTTACTGGCCAGTAAAGTTTAGCAAACCAGTCCAGGTGCTGTTGACAGTAGGCACAAACCGAGTGACAACAGACAAGCTTTGACTGTGTTGGGCTAAGGTAGGCTTTGGGAACCTTACTGCTTACTGCCTCCCCACAGTATGTGGCAAAGTCTAAAGGAGCAGCCAATGGCCACACCAAACCCCCGTTGCTATGGTAGCAGCTACTTCAAACATAGTTTCATTGAATAGGAGCTCATTTGACCCTTGGACCAGAACCAAGGCTCTAAATTGGCAGGACAGAGAATCGGAGTAATTTGTATCATTTCAATTAGTTACTCGCTCGCAATAACAGGGAGGTCATGACTTTCTGCCATGATTACTGCCCTATGGCAACCAAGCTTGAATGTACCATCAGTTTCCAAATACTTTCACTTAATAAATGTAGGTCATAACAAGGCTTCGATTGTTGGGGGGTGCACTAACAAAGGTGAATATCCGACTCTGCAACTGAACGAGCGGA chm1:+:1479202342:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:30772598:-1 chm1:+:43951791:-1 chm1:+:108243905:-1 chm1:+:239695776:-1 chm1:+:440130764:-1 chm1:+:457004711:-1 chm1:+:485304261:-1 chm1:+:485476149:-1 chm1:+:546977915:-1 chm1:+:793808206:-1 chm1:+:898749723:-1 chm1:+:1016043229:-1 chm1:+:1024550321:-1 chm1:+:1028844511:-1 chm1:+:1219475255:-1 chm1:+:1231563376:-1 chm1:+:1422624777:-1 chm1:+:1523409948:-1 chm1:+:1813323330:-1 chm1:+:2172061643:-1 chm1:+:2299322972:-1 chm1:+:2791107000:-1 chm1:+:2799868853:-1 chm1:+:2889964870:-1 chm1:+:2892252177:-1 chm1:+:2932123106:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:2818273708:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:93225510:-1 chm1:+:1172779602:-1 chm1:+:1616873159:-1 chm1:+:2052726360:-1 chm1:+:2270365066:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:428369432:-1 chm1:+:1315618909:-1 chm1:+:1789165121:-1 chm1:+:1817835462:-1 chm1:+:1817835509:-1 chm1:+:1927874234:-1 chm1:+:2283700231:-1 chm1:+:2371589812:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:981083653:-1 chm1:+:2036564556:-1 chm1:+:2159775772:-1 chm1:+:2188570337:-1 chm1:+:2648177111:-1 chm1:+:2896448442:-1 chm1:+:2905426121:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:29750826:-1 chm1:+:1361391525:-1 chm1:+:2536764081:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:3028516763:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:4928190:-1 chm1:+:116058390:-1 chm1:+:302380270:-1 chm1:+:427664650:-1 chm1:+:444882676:-1 chm1:+:539767724:-1 chm1:+:633671057:-1 chm1:+:809690172:-1 chm1:+:875033622:-1 chm1:+:1112790995:-1 chm1:+:1170464204:-1 chm1:+:1186983507:-1 chm1:+:1273549729:-1 chm1:+:1470192097:-1 chm1:+:1565199276:-1 chm1:+:1571705532:-1 chm1:+:1736285652:-1 chm1:+:1780478655:-1 chm1:+:1831460796:-1 chm1:+:2149526081:-1 chm1:+:2291318453:-1 chm1:+:2395546379:-1 chm1:+:2590783505:-1 chm1:+:2610303677:-1 chm1:+:2874953621:-1 chm1:+:2900952081:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:494102222:-1 chm1:+:645102007:-1 chm1:+:753138723:-1 chm1:+:806881599:-1 chm1:+:1020004937:-1 chm1:+:1151983817:-1 chm1:+:1628515241:-1 chm1:+:1746189452:-1 chm1:+:1877483341:-1 chm1:+:2045254182:-1 chm1:+:2281989440:-1 chm1:+:2901542214:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:165981499:-1 chm1:+:603568494:-1 chm1:+:896314924:-1 chm1:+:965268626:-1 chm1:+:1036090695:-1 chm1:+:1499446925:-1 chm1:+:1910715964:-1 chm1:+:1949999685:-1 chm1:+:2268447157:-1 chm1:+:2801463134:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:73920715:-1 chm1:+:444035875:-1 chm1:+:486560634:-1 chm1:+:728766663:-1 chm1:+:793916032:-1 chm1:+:794589505:-1 chm1:+:1189520332:-1 chm1:+:1502573682:-1 chm1:+:2077285575:-1 chm1:+:2147988495:-1 chm1:+:2462865409:-1 chm1:+:2583167617:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:241632572:-1 chm1:+:315523352:-1 chm1:+:646423888:-1 chm1:+:653328455:-1 chm1:+:2225517834:-1 chm1:+:2381871012:-1 chm1:+:2468622739:-1 chm1:+:2550572037:-1 chm1:+:2730858914:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:466678868:-1 chm1:+:650653720:-1 chm1:+:834067148:-1 chm1:+:1642027416:-1 chm1:+:1773808003:-1 chm1:+:2283958467:-1 chm1:+:2297637255:-1 chm1:+:2418288208:-1 chm1:+:2489379019:-1 chm1:+:2632679472:-1 chm1:+:2734195399:-1 chm1:+:2863404502:-1 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chm1:+:1146430364:-1 chm1:+:1420940172:-1 chm1:+:1710581269:-1 chm1:+:2250492039:-1 chm1:+:2473937413:-1 chm1:+:2821183296:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:7341474:-1 chm1:+:29582298:-1 chm1:+:82310879:-1 chm1:+:107134352:-1 chm1:+:222088153:-1 chm1:+:287422964:-1 chm1:+:678385234:-1 chm1:+:796668849:-1 chm1:+:1262874090:-1 chm1:+:1897280902:-1 chm1:+:2256326347:-1 chm1:+:2502140634:-1 chm1:+:2734466036:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:823053173:-1 chm1:+:845610056:-1 chm1:+:1006189223:-1 chm1:+:1285535993:-1 chm1:+:1340960023:-1 chm1:+:1441936487:-1 chm1:+:2275994902:-1 chm1:+:2437765801:-1 chm1:+:2903465099:-1 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chm1:+:1942715513:-1 chm1:+:2232816907:-1 chm1:+:2811611240:-1 chm1:+:2874845678:-1 +TTAATATGAATAAATTGCTTTTCCAATATCAGCCCTCCTATTTTCTGGCCACATCCCATCTTCCAGGTGACACTTTCACCTGTAGGTCACTAACATCGCTGGGATCTCCATTCACTTTACCAGCTAACTTTCCCTATTTGCTCTCCTGCTCTTCACCTCCATACTTCCCCACGTCAGAGTACACTCATGTATTAGTTGCAGTGATGTCCTTGTACAAAAACCCTAAGCCTCTTTTTTTCTTTTTTCATCCTTCTCTTGGCAAAAATGCAGTCCTGAATGAACGCAGTATCTGCCCCAGGCAGTGGGCAAGTGCTGTAAGGAACCACTCACCCAACAAGGCTACAGGGAAGCCCAGGGCTTGGGAAAATCTAGTTTTCAGCTGTTAAGAGTTGGTAAAGAAATGTTCTTTGAAGAGGCAAAGAACGTAATATGGATTAATTTGGGAAATAATGGAATGCAGGATTTTTGTGAACCATGGTATAGAGTTTGAAGGAGGAAGCAATGGGGATATAAACCAGTAAAATAGGTACCACAGAACATTATGGAAATCGAGAGACGGGGAAAAGAGAATTGACTTCAGACGAGGTCTAACATATGCTGGGCTGTGTATTTAGTCTGTTCTCATGCCTGCTATGAAGAAATACCCGAGACTGATTAATTTATTAAAGGGAAAGAGGTTAATTAGACTCCAGTTCCACATGGCTGGGGAGGCCTCAGGAAACTTACAATCATGGCAGAAGGGGAAGCAAACCTGTCCTTCCTTCGTATGGCAGGCAAGGAAGGAGAAGTGCAGAGCAAAG chm1:+:374710178:-1 chm1:+:538424855:-1 chm1:+:939326869:-1 chm1:+:1110245034:-1 chm1:+:1550248724:-1 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chm1:+:1210478954:-1 chm1:+:1746516309:-1 chm1:+:2049191811:-1 chm1:+:2225938522:-1 chm1:+:2464327109:-1 chm1:+:2765244760:-1 chm1:+:2911584122:-1 chm1:+:2961999553:-1 +CTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:697120083:43 chm1:+:1337991124:-1 chm1:+:1492479698:-1 chm1:+:1688017474:-1 chm1:+:2142039689:-1 chm1:+:2923150879:-1 +CTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:2436361978:-1 +CTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:697120060:43 +CTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:697120064:43 +CTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:697120072:43 +CTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:697120074:43 +CTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:1471676940:-1 +CTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:697120078:43 +CTTTGCTCTGCACTTCTCCTTCCTTGCCTGCCATACGAAGGAAGGACAGGTTTGCTTCCCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGCCATGTGGAACTGGAGTCTAATTAACCTCTTTCCCTTTAATAAATTAATCAGTCTCGGGTATTTCTTCATAGCAGGCATGAGAACAGACTAAATACACAGCCCAGCATATGTTAGACCTCGTCTGAAGTCAATTCTCTTTTCCCCGTCTCTCGATTTCCATAATGTTCTGTGGTACCTATTTTACTGGTTTATATCCCCATTGCTTCCTCCTTCAAACTCTATACCATGGTTCACAAAAATCCTGCATTCCATTATTTCCCAAATTAATCCATATTACGTTCTTTGCCTCTTCAAAGAACATTTCTTTACCAACTCTTAACAGCTGAAAACTAGATTTTCCCAAGCCCTGGGCTTCCCTGTAGCCTTGTTGGGTGAGTGGTTCCTTACAGCACTTGCCCACTGCCTGGGGCAGATACTGCGTTCATTCAGGACTGCATTTTTGCCAAGAGAAGGATGAAAAAAGAAAAAAAGAGGCTTAGGGTTTTTGTACAAGGACATCACTGCAACTAATACATGAGTGTACTCTGACGTGGGGAAGTATGGAGGTGAAGAGCAGGAGAGCAAATAGGGAAAGTTAGCTGGTAAAGTGAATGGAGATCCCAGCGATGTTAGTGACCTACAGGTGAAAGTGTCACCTGGAAGATGGGATGTGGCCAGAAAATAGGAGGGCTGATATTGGAAAAGCAATTTATTCATATTAA chm1:+:697120079:43 diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/docs/analysis.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/docs/analysis.txt new file mode 100644 index 0000000000000000000000000000000000000000..ca67e13d5662be912f976c7675ad3784a1a082d3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/docs/analysis.txt @@ -0,0 +1,186 @@ +Computational analysis: + +SW: 2 MIN + 3 ADDS + 1 CMP + {4 LOADS/STORES + 1 ADD + 1 CMP} = 6 OP; {12 OP} +---------------------------------------------------------------------------------------------- + +Task-parallel version SW +------------------------- +512nt x 512nt --> 2048 x 2048 +time: 289 ms +block size 1D: 128th +grid size 1D: 1024th +Registers/thread: 71 +Executed instructions: 8826M +Inter-thread instructions: 0 +Executed IPC: 2.823 + +ISR execution dependency: 32% +ISR Data Request: 19% +ISR Instruction fetch: 4.6% + +# SW: 128*1024 = 128K +Ins per SW = 8826M / 128K = 67337 +Instructions per cell = 67337 / (512 * 512) = 0.25 +Operations per cell = 0.25 * 32 = 8.21 + +Thread-cooperative version SW +----------------------------- +512nt x 512nt --> 2048 x 2048 +time: 1.331 seg --> 21 seg --> 16 times (ok) +block size 1D: 128th +grid size 1D: 32768th +Registers/thread: 29 +Executed instructions: 54682M +Inter-thread instructions: 145467M +Executed IPC: 3.707 + +ISR execution dependency: 31.8% +ISR Data Request: 0.3% +ISR Instruction fetch: 9% + +# SW: 128*1024 = 128K +Ins per SW = 54682M / 128K = 417190 +Instructions per cell = 67337 / (512 * 512) = 1.591 +Operations per cell = 0.25 * 32 = 50.92 + +WORK RATE = 50.92 / 8.21 = 6.20 times more work +SPEEDUP = 1.331 / 0.289 = 4.60 times faster + + +MEMORY PRESSURE ANALISYS +------------------------- + +Task-Parallel +------------- +Best scenario Memory Footprint now: +2 sequences x 512 bases x 2 bits/base = 256 Bytes +1 score column * 512 cells * 4 Bytes/cell = 2048 Bytes +Interest to cache 1 sequence + score column = 2176 Bytes + +SM level: +All in L1 or Shared Mem. = 48K / 2176 = 22 problems fitting on cache +Combination L1 (48K) & Read-Only (64K) = min (48 K / 2048, 64K / 128) = (24, 512) = 24 SW fitting on cache +Die level: +LLC 1.5 MB = 722 SW fitting on cache LLC + +READS: 193.76M - 21.434 GB/s (read 6.2 GB lines of 32 Bytes) +WRITES: 193.21M - 21.364 GB/s (write 6.18 GB lines of 32 Bytes) + +#SW 1024 * 128 = 131072 + + +2048 th/SM * 15 SM = 30720 SW running on fly +30720 SW * 2176 Bytes = 66846720 = 63MB best scenario -> to fit in mem cache. + + +Thread-Cooperative (WARP-Wide) +------------------------------ +Best scenario Memory Footprint now: +2 sequences x 512 bases x 2 bits/base = 256 Bytes +1 score column * 512 cells * 4 Bytes/cell = 2048 Bytes +Interest to cache 1 sequence + score column = 2176 Bytes + +SM level: +All in L1 or Shared Mem. = 48K / 2176 = 22 problems fitting on cache +Combination L1 (48K) & Read-Only (64K) = min (48 K / 2048, 64K / 128) = (24, 512) = 24 SW fitting on cache +Die level: +LLC 1.5 MB = 722 SW fitting on cache LLC + +READS: 3.75M - 90.137 MB/s (read 6.2 GB lines of 32 Bytes) +WRITES: 1468.42M - 35.216 GB/s (write 6.18 GB lines of 32 Bytes) + +#SW 1024 * 128 = 131072 + + +2048 th/SM * 15 SM = 30720 SW running on fly +30720 SW * 2176 Bytes = 66846720 = 63MB best scenario -> to fit in mem cache. + + +SW-GOTOH: 5 SUBS + 1 CMP + 4 MAX + { 8 LOAD/STORES + 1 ADD + 1 CMP } = 10 OP; {20 OP} +---------------------------------------------------------------------------------------------- + +TASK PARALLEL +------------- +512nt x 512nt +time: 416 ms +block size 1D: 128th +grid size 1D: 1024 blocks +Registers/thread: 63 +Executed instructions: 14537M +LD/STORE instructions: 21618M (?) +Executed IPC: 3.28 + +ISR Pipe Busy: 14.6% +ISR Memory Throttle: 19.3% +ISR Execution dependency: 33.9% +ISR Data Request: 13.1% +ISR Instruction fetch: 5.4% + +# SW: 128*1024 = 128K +Ins per SW = 14537M / 128K = 116296 +Instructions per cell = 116296 / (512 * 512) = 0.443 +Operations per cell = 0.443 * 32 = 14.19 + + +WARP WIDE +---------- +512nt x 512nt +time: 1.54 sec +block size 1D: 128th +grid size 1D: 32768 blocks +Registers/thread: 33 +Executed instructions: 66417M +LD/STORE instructions: 5503M (?) +Executed IPC: 3.91 + +ISR Pipe Busy: 37.9% +ISR Memory Throttle: 0% +ISR Execution dependency: 35.1% +ISR Data Request: 0.2% +ISR Instruction fetch: 7.4% + +# SW: 128 * 32768 / 32 = 128K +Ins per SW = 66417M / 128K = 531336 +Instructions per cell = 531336 / (512 * 512) = 2.026885986 +Operations per cell = 0.443 * 32 = 64.86 + + +* The task-parallel version is quite efficient running ~8 op/cell for SW and ~14 op/cell for SWG + + +Matrix score Scalability +------------------------- + +(GLOBAL ALIGNMENTS) + +TASK-PARALLEL (SW) + N = 16 - M = 16 => 81.0 + N = 32 - M = 32 => 99.5 + N = 64 - M = 64 => 105.8 + N = 128 - M = 128 => 106.9 + N = 256 - M = 256 => 108.0 + N = 512 - M = 512 => 108.5 + N = 1024 - M = 1024 => 108.6 + N = 2048 - M = 2048 => 108.5 + + +TASK-PARALLEL (SW-Gotoh) + N = 16 - M = 16 => 60.9 + N = 32 - M = 32 => 67.0 + N = 64 - M = 64 => 69.4 + N = 128 - M = 128 => 70.5 + N = 256 - M = 256 => 70.9 + N = 512 - M = 512 => 71.0 + + +WARP-WIDE (SW-Gotoh) + N = 16 - M = 16 => 4.6 + N = 32 - M = 32 => 48.3 + N = 64 - M = 64 => 24.7 + N = 128 - M = 128 => 22.2 + N = 256 - M = 256 => 22.1 + N = 512 - M = 512 => 22.2 + N = 1024 - M = 1024 => 22.3 + N = 2048 - M = 2048 => 22.4 + N = 4096 - M = 4096 => 22.4 + N = 8192 - M = 8192 => 22.3 \ No newline at end of file diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/docs/profile.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/docs/profile.txt new file mode 100644 index 0000000000000000000000000000000000000000..1468392ea8ccc865e5f20411ad1a6bb18a78a261 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/docs/profile.txt @@ -0,0 +1,37 @@ +NOTES: + +A) Smith & waterman benchmarking + +* Reading the candidates from the reference in gather mode, we can appreciate a performance penalty in TITAN BLACK (~25%) but not in TITAN X. +Next step will be checking if this penalization is related to the "cache hierarchy". +It's very strange that this does not happen in Maxwell. It is interesting to know the performance issue that is happening here. + +* The best performance is: in Kepler, using the implementation that combines interger & video instructions and in Maxwell, using the baseline implementation that just uses the integer instructions. + +* In Kepler the mixing of instructions improves the code 57%, but that needs bigger effort to be integrated. This strategy requires to group in sets of 4 queries with the same or similar size, and designing a pipeline strategy to rerun the failed alignments using higher precision (In section B we give some numbers of this filtering efficiency). + +* The low performance in Maxwell compared to Kepler using video instructions is interesting. We are talking about 111 GCUPS in Kepler compared with 17 GCUPS in Maxwell (it's 15% of the Kepler performance). +There is the suspiction that the compiler could generate better sass code for Maxwell when we use video instructions. With the implementation that simulates the video instructions using integer/logical instructions, we are showing that using a very naive own implementation of the MAX video instruction (that executes 20 op/max op), more performance is achieved than if we rely on the compiler to generate the emulated video instruction. + +The next performance metrics from the implementation that uses video instructions, shows that the compiler is generating 7 times more instructions in Maxwell than in Kepler, and this is one of the reasons for the performance degradation: +​​ GTX Titan Black: GTX Titan X: +Performance 156 GCUPS 41.6 GCUPS +IPC 2.32 2.57 +ICount 418 M 2923 M +Registers/th 64 71 + + +B) Smith & waterman 8 bits filtering efficency + +It has been validated and checked the filtering efficiency of the 8bits/cell representation running all the algorithms against a big dataset, 20M of queries with sizes 100, 200, 400, 600, 800 and 1000. + Percentage of + candidates with errors +100: 0% +200: 0.001% +400: 1.12% +600: 3.21% +800: 14% +1000: 48% + +We used the BWA scores, but this percentage could vary using other scores. +It would be interesting to desing a pipeline strategy to rerun the failed alignments with more resolution per cell. \ No newline at end of file diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_alignments.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_alignments.h new file mode 100644 index 0000000000000000000000000000000000000000..0061b09720c255f558c7e8f28268e00f5c29a223 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_alignments.h @@ -0,0 +1,44 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_alignments + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: API functions to manage the alignments (sink and score) + */ + +#ifndef PSA_ALIGNMENTS_H_ +#define PSA_ALIGNMENTS_H_ + +#include "psa_commons.h" +#include "psa_errors.h" +#include "psa_alignments.h" + + +typedef uint32_t alignmentInfo_t; + +typedef struct { + uint32_t column; + int32_t score; +} alignmentEntry_t; + +typedef struct { + uint32_t num; + uint32_t numReordered; + /* aligment structures */ + alignmentInfo_t *h_info; + alignmentInfo_t *d_info; + alignmentEntry_t *h_results; + alignmentEntry_t *d_results; + /* reorder structures */ + alignmentEntry_t *h_reorderResults; + alignmentEntry_t *d_reorderResults; +} alignments_t; + +psaError_t initAlignments(alignments_t **alignments, uint32_t numAlignments); +psaError_t allocateAlignments(alignments_t *alignments); +psaError_t loadAlignments(FILE *fp, alignments_t *alignments); +psaError_t saveAlignments(FILE *fp, alignments_t *alignments); +psaError_t saveASCIIAlignments(FILE *fp, alignments_t *alignments); +psaError_t freeAlignments(alignments_t **alignments); + + +#endif /* PSA_ALIGNMENTS_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_commons.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_commons.h new file mode 100644 index 0000000000000000000000000000000000000000..9a3d8b0f06ce5954fd9df048e3a30d20fbe47ef1 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_commons.h @@ -0,0 +1,57 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_commons + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Common definitions and functions. + */ + +#ifndef PSA_COMMONS_H_ +#define PSA_COMMONS_H_ + +#include +#include +#include + +/******************************** +Common constants for Device & Host +*********************************/ + +#define UINT32_ZEROS 0x00000000u +#define UINT32_ONES 0xFFFFFFFFu +#define UINT32_LOW_ONE 0x00000001u +#define UINT32_HIGH_ONE 0x80000000u +#define UINT32_SIZE 4 +#define UINT32_LENGTH 32 +#define UINT64_SIZE 8 +#define UINT64_LENGTH 64 + +#define BITPAL_INLINE inline + +/* Functions inline */ +#define DIV_CEIL(NUMERATOR,DENOMINATOR) (((NUMERATOR)+((DENOMINATOR)-1))/(DENOMINATOR)) +#define ROUND(NUM) ((int)((NUM) < 0 ? ((NUM) - 0.5) : ((NUM) + 0.5))) +#define MIN(NUM_A,NUM_B) (((NUM_A) < (NUM_B)) ? (NUM_A) : (NUM_B)) +#define MAX(NUM_A,NUM_B) (((NUM_A) >= (NUM_B)) ? (NUM_A) : (NUM_B)) + +/* Conversion utils */ +#define CONVERT_B_TO_KB(NUM) ((NUM)/(1024)) +#define CONVERT_B_TO_MB(NUM) ((NUM)/(1024*1024)) +#define CONVERT_B_TO_GB(NUM) ((NUM)/(1024*1024*1024)) +#define CONVERT_MB_TO_B(NUM) ((NUM)*1024*1024) + +/* System */ +#define FILE_SIZE_LINES 20000 + +/* Encoded DNA Nucleotides */ +#define NUM_BASES 5 +#define ENC_DNA_CHAR_A 0LL +#define ENC_DNA_CHAR_C 1LL +#define ENC_DNA_CHAR_G 2LL +#define ENC_DNA_CHAR_T 3LL + +#define ENC_DNA_CHAR_N 4LL +#define ENC_DNA_CHAR_SEP 5LL +#define ENC_DNA_CHAR_JUMP 6LL + +#endif /* PSA_COMMONS_H_ */ + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_errors.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_errors.h new file mode 100644 index 0000000000000000000000000000000000000000..a823ef90ef1203bb802149c3917f8cdda7a25200 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_errors.h @@ -0,0 +1,35 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_errors + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: API Interface to manage errors. + */ + +#ifndef PSA_ERRORS_H_ +#define PSA_ERRORS_H_ + +#include "psa_commons.h" + +#define PSA_ERROR(error) (psaError(error, __FILE__, __LINE__ )) + +typedef enum +{ + SUCCESS, + E_OPENING_FILE, + E_READING_FILE, + E_WRITING_FILE, + E_INSUFFICIENT_MEM_GPU, + E_ALLOCATE_MEM, + E_INCOMPATIBLE_GPU, + E_NO_SUPPORTED_GPUS, + E_REFERENCE_CODING, + E_PROGRAM_PARAMETERS, + E_NO_MULTIFASTA_FILE, + E_PARSING_REGPROF +} psaError_t; + +void psaError(psaError_t error, const char *file, int32_t line); +char *psaGetErrorString(psaError_t error); + + +#endif /* PSA_ERRORS_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_pairwise.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_pairwise.h new file mode 100644 index 0000000000000000000000000000000000000000..e70b593379aa5ef54c372002752917b3ff25d6b8 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_pairwise.h @@ -0,0 +1,32 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_pairwise + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: API Interface pairwise definitions for basic operations. + */ + +#ifndef PSA_PAIRWISE_H_ +#define PSA_PAIRWISE_H_ + +#include "psa_commons.h" +#include "psa_regions.h" +#include "psa_sequences.h" +#include "psa_alignments.h" + + +char* buildTag(); +psaError_t printBuildInfo(); +psaError_t transformDataReferences(sequences_t *references); +psaError_t transformDataQueries(sequences_t *queries); +psaError_t transformDataCandidates(sequences_t *candidates); +psaError_t processPairwiseReference(sequences_t* references, sequences_t *candidates, sequences_t *queries, alignments_t *alignments); +psaError_t processPairwiseStream(sequences_t *candidates, sequences_t *queries, alignments_t *alignments); + +#ifdef CUDA +psaError_t transferGPUtoCPU(alignments_t *alignments); +psaError_t transferCPUtoGPUReference(sequences_t* references, sequences_t *queries, sequences_t *candidates, alignments_t *alignments); +psaError_t transferCPUtoGPUStream(sequences_t *queries, sequences_t *candidates, alignments_t *alignments); +#endif + + +#endif /* PSA_PAIRWISE_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_pairwise_gpu.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_pairwise_gpu.h new file mode 100644 index 0000000000000000000000000000000000000000..aaf9729179a0e9ccd3d39c67f632419a9836cf39 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_pairwise_gpu.h @@ -0,0 +1,19 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_pairwise_gpu + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: API Interface pairwise definitions for basic operations exlusive for GPU. + */ + + +#ifndef PSA_PAIRWISE_GPU_H_ +#define PSA_PAIRWISE_GPU_H_ + +#include "psa_commons.h" +#include "psa_sequences.h" +#include "psa_alignments.h" + +psaError_t localProcessPairwiseReference(sequences_t* references, sequences_t *candidates, sequences_t *queries, alignments_t *alignments); +psaError_t processPairwiseStream(sequences_t *candidates, sequences_t *queries, alignments_t *alignments); + +#endif /* PSA_PAIRWISE_GPU_H_ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_profile.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_profile.h new file mode 100644 index 0000000000000000000000000000000000000000..ec710f84484fe7e93d9639e6514954511a9706b6 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_profile.h @@ -0,0 +1,39 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_profile + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Process functions for GEM profile files. + */ + +#ifndef PSA_PROFILE_H_ +#define PSA_PROFILE_H_ + +#include +#include "psa_commons.h" +#include "psa_errors.h" + +psaError_t countCandidates(char* cadena, uint32_t *numberOfCandidates, uint32_t *querySize); +psaError_t countRegionsProfile(FILE *fp, float distance, + uint32_t *retNumQueries, uint32_t *retTotalSizeQueries, + uint32_t *retNumCandidates, uint32_t *retTotalSizeCandidates); +psaError_t processQuery(uint32_t queryNumber, char *textLine, + char *queries, uint32_t *h_PositionCandidates, uint32_t *h_AlignmentInfo, uint32_t *listResults, + uint32_t *retSizeQueries, uint32_t *retNumCandidates); +psaError_t loadRegionsProfile(FILE *fp, char *h_ASCIIQueries, uint32_t *h_ASCIISizeQueries, uint32_t *h_ASCIIPositionQueries, + uint32_t *h_GenomePositionCandidates, uint32_t *h_AlignmentInfo, uint32_t *h_AlignmentScores); + + +#endif /* BP_PROFILE_H_ */ + + + + + + + + + + + + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_regions.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_regions.h new file mode 100644 index 0000000000000000000000000000000000000000..5aad9e156c498c9645c5a593bb5258c92ba9abf2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_regions.h @@ -0,0 +1,48 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_regions + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: API Interface to process GEM regions. + */ + + +#ifndef PSA_REGIONS_H_ +#define PSA_REGIONS_H_ + +#include "psa_commons.h" +#include "psa_sequences.h" +#include "psa_alignments.h" +#include "psa_errors.h" + + +typedef struct { + float distance; + uint32_t averageSizeQuery; + uint32_t averageCandidatesPerQuery; + sequences_t *queries; + sequences_t *candidates; + alignments_t *alignments; +} regions_t; + +psaError_t initRegions(regions_t **regions, uint32_t numQueries, uint32_t numCandidates, uint32_t numAlignments); +psaError_t allocateRegions(regions_t *regions, float distance, + uint32_t totalSizeQueries, seq_format_t QUERIES_ASCII, + uint32_t totalSizeCandidates, seq_format_t CANDIDATES_ASCII); +psaError_t loadRegions(FILE *fp, regions_t *regions); +psaError_t saveRegions(FILE *fp, regions_t *regions); +psaError_t statistics(regions_t *regions); +psaError_t printRegions(regions_t *regions, uint32_t numAlignments, uint32_t reformated); +psaError_t freeRegions(regions_t **regions); + +#endif /* PSA_REGIONS_H_ */ + + + + + + + + + + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_sequences.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_sequences.h new file mode 100644 index 0000000000000000000000000000000000000000..8da874745292210637b6ea402c2b313d5bdd3be3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_sequences.h @@ -0,0 +1,122 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_sequences + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: API Interface to manage / transform string sequence formats. + */ + +#ifndef PSA_SEQUENCES_H_ +#define PSA_SEQUENCES_H_ + +#include +#include "psa_commons.h" +#include "psa_errors.h" + +#define PEQ_ENTRY_LENGTH 128 +#define PEQ_SUB_ENTRIES (PEQ_ENTRY_LENGTH / UINT32_LENGTH) +#define RAW_16B_LENGTH 4 + +#define RAW_4B_LENGTH 2 + + +typedef enum +{ + SEQ_VOID = UINT32_LOW_ONE << 0, + SEQ_PEQ_4x32b = UINT32_LOW_ONE << 1, + SEQ_RAW = UINT32_LOW_ONE << 2, + SEQ_ASCII = UINT32_LOW_ONE << 3, + SEQ_HLF_RAW = UINT32_LOW_ONE << 4, + SEQ_REF_POS = UINT32_LOW_ONE << 5 +} seq_format_t; + +typedef struct { + uint32_t bitmap[NUM_BASES][PEQ_SUB_ENTRIES]; +} PEQEntry_t; + +typedef uint64_t RAWEntry_t; +typedef uint32_t RAWHlfEntry_t; + +typedef char ASCIIEntry_t; + +typedef struct { + /* sequences info */ + uint32_t num; + seq_format_t formats; + /* Reference Positions */ + uint32_t *h_refPosition; + uint32_t *d_refPosition; + /* PEQ structures */ + uint32_t numPEQEntries; + PEQEntry_t *h_PEQ; + PEQEntry_t *d_PEQ; + uint32_t *h_PEQposition; + uint32_t *d_PEQposition; + /* RAW structures */ + uint32_t numRAWEntries; + RAWEntry_t *h_RAW; + RAWEntry_t *d_RAW; + uint32_t *h_RAWposition; + uint32_t *d_RAWposition; + /* Half RAW structures (smaller entries)*/ + uint32_t numRAWHlfEntries; + RAWHlfEntry_t *h_HlfRAW; + RAWHlfEntry_t *d_HlfRAW; + uint32_t *h_HlfRAWposition; + uint32_t *d_HlfRAWposition; + /* ASCII structures (debug) */ + uint32_t numASCIIEntries; + ASCIIEntry_t *h_ASCII; + ASCIIEntry_t *d_ASCII; + uint32_t *h_ASCIIposition; + uint32_t *d_ASCIIposition; + /* Common data to all formats */ + uint32_t *h_size; + uint32_t *d_size; +} sequences_t; + +psaError_t initSequences(sequences_t **sequences, uint32_t numSequences); +psaError_t allocateSequences(sequences_t *sequences, uint32_t numEntries, seq_format_t SEQ_FORMAT); + +uint32_t ASCIIto4bits(char base); +uint32_t ASCIItoIndex(char base); +psaError_t ASCIItoPEQ_32bits(char *h_ASCII, uint32_t idSubPEQ, PEQEntry_t *PEQEntry, int numBases); +psaError_t ASCIItoPEQ_31bits(char *h_ASCII, uint32_t idSubPEQ, PEQEntry_t *PEQEntry, int numBases); +uint64_t ASCIItoRAW_64bits(unsigned char base); +uint32_t ASCIItoRAW_32bits(unsigned char base); +char ASCIItoUpperCase(char base); + +psaError_t sequences_positionASCIItoPEQ_128bits(uint32_t *h_PEQposition, uint32_t *h_size, uint32_t num); +psaError_t sequences_recoverASCII(uint32_t position, uint32_t *h_size, uint32_t num); + +uint32_t sequences_totalEntriesRAW(uint32_t *h_size, uint32_t num, const uint32_t baseSize); +uint32_t sequences_totalEntriesHlfRAW(uint32_t *h_size, uint32_t num, const uint32_t baseSize); +uint32_t sequences_totalEntriesPEQ_128bits(uint32_t *h_size, uint32_t num); +uint32_t sequences_totalEntriesPEQ_4x31bits(uint32_t *h_size, uint32_t num); + +psaError_t sequenceASCIItoPEQ_4x32bits(char *h_ASCII, uint32_t sizeSequence, PEQEntry_t *h_PEQ); +psaError_t sequenceASCIItoPEQ_4x31bits(char *h_ASCII, uint32_t sizeSequence, PEQEntry_t *h_PEQ); +psaError_t sequenceASCIItoRAW_4x64bits(const char *h_ASCII, int32_t size, RAWEntry_t *h_RAW); +psaError_t sequenceASCIItoRAW_2x32bits(const char *h_ASCII, int32_t size, RAWHlfEntry_t *h_HlfRAW); + + +psaError_t loadSequenceRAW_64bits(const char *h_ASCII, int32_t size, char *h_RAW, int32_t numRAWEntries); +psaError_t loadSequenceMFASTA(FILE *fp, uint32_t **h_size, char **h_ASCII, uint32_t **h_ASCIIposition, seq_format_t *formats); + +psaError_t saveSequences(FILE *fp, sequences_t *sequences); +psaError_t loadSequences(FILE *fp, sequences_t *sequences); +psaError_t freeSequences(sequences_t **sequences); + +#endif /* PSA_SEQUENCES_H_ */ + + + + + + + + + + + + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_time.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_time.h new file mode 100644 index 0000000000000000000000000000000000000000..543029ab0ade15566640502689f2fb66d50ff025 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/psa_time.h @@ -0,0 +1,21 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_time + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: API Interface timming definitions for CPU. + */ + +#ifndef PSA_TIME_H_ +#define PSA_TIME_H_ + +#include +#include + +#ifdef __MACH__ +#include +#include +#endif + +double sampleTime(); + +#endif /* PSA_TIME_H_ */ \ No newline at end of file diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/simd_functions.h b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/simd_functions.h new file mode 100644 index 0000000000000000000000000000000000000000..01ad12338ec833cb4b3d549debe3ee264140c353 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/include/simd_functions.h @@ -0,0 +1,2236 @@ +/* + * Copyright (c) 2013 NVIDIA Corporation. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * + * Redistributions of source code must retain the above copyright notice, + * this list of conditions and the following disclaimer. + * + * Redistributions in binary form must reproduce the above copyright notice, + * this list of conditions and the following disclaimer in the documentation + * and/or other materials provided with the distribution. + * + * Neither the name of NVIDIA Corporation nor the names of its contributors + * may be used to endorse or promote products derived from this software + * without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE + * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF + * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS + * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN + * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) + * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE + * POSSIBILITY OF SUCH DAMAGE. + */ + +/* Release 1.1 + * + * (1) Use of incorrect symbol in multiple-inclusion guard has been corrected. + * (2) 44 additional functions were added to the initial set of 38 functions. + * (3) The emulation paths for many existing functions were optimized for sm_2x + */ + +#if !defined (SIMD_FUNCTIONS_H__) +#define SIMD_FUNCTIONS_H__ + +/* + This header file contains inline functions that implement intra-word SIMD + operations, that are hardware accelerated on sm_3x (Kepler) GPUs. Efficient + emulation code paths are provided for earlier architectures (sm_1x, sm_2x) + to make the code portable across all GPUs supported by CUDA. The following + functions are currently implemented: + + vabs2(a) per-halfword absolute value, with wrap-around: |a| + vabsdiffs2(a,b) per-halfword absolute difference of signed integer: |a - b| + vabsdiffu2(a,b) per-halfword absolute difference of unsigned integer: |a - b| + vabsss2(a) per-halfword abs. value, with signed saturation: sat.s16(|a|) + vadd2(a,b) per-halfword (un)signed addition, with wrap-around: a + b + vaddss2(a,b) per-halfword addition with signed saturation: sat.s16 (a + b) + vaddus2(a,b) per-halfword addition with unsigned saturation: sat.u16 (a+b) + vavgs2(a,b) per-halfword signed rounded average: (a+b+((a+b)>=0)) >> 1 + vavgu2(a,b) per-halfword unsigned rounded average: (a + b + 1) / 2 + vcmpeq2(a,b) per-halfword (un)signed comparison: a == b ? 0xffff : 0 + vcmpges2(a,b) per-halfword signed comparison: a >= b ? 0xffff : 0 + vcmpgeu2(a,b) per-halfword unsigned comparison: a >= b ? 0xffff : 0 + vcmpgts2(a,b) per-halfword signed comparison: a > b ? 0xffff : 0 + vcmpgtu2(a,b) per-halfword unsigned comparison: a > b ? 0xffff : 0 + vcmples2(a,b) per-halfword signed comparison: a <= b ? 0xffff : 0 + vcmpleu2(a,b) per-halfword unsigned comparison: a <= b ? 0xffff : 0 + vcmplts2(a,b) per-halfword signed comparison: a < b ? 0xffff : 0 + vcmpltu2(a,b) per-halfword unsigned comparison: a < b ? 0xffff : 0 + vcmpne2(a,b) per-halfword (un)signed comparison: a != b ? 0xffff : 0 + vhaddu2(a,b) per-halfword unsigned average: (a + b) / 2 + vmaxs2(a,b) per-halfword signed maximum: max(a, b) + vmaxu2(a,b) per-halfword unsigned maximum: max(a, b) + vmins2(a,b) per-halfword signed minimum: min(a, b) + vminu2(a,b) per-halfword unsigned minimum: min(a, b) + vneg2(a,b) per-halfword negation, with wrap-around: -a + vnegss2(a,b) per-halfword negation, with signed saturation: sat.s16(-a) + vsads2(a,b) per-halfword sum of abs diff of signed: sum{0,1}(|a-b|) + vsadu2(a,b) per-halfword sum of abs diff of unsigned: sum{0,1}(|a-b|) + vseteq2(a,b) per-halfword (un)signed comparison: a == b ? 1 : 0 + vsetges2(a,b) per-halfword signed comparison: a >= b ? 1 : 0 + vsetgeu2(a,b) per-halfword unsigned comparison: a >= b ? 1 : 0 + vsetgts2(a,b) per-halfword signed comparison: a > b ? 1 : 0 + vsetgtu2(a,b) per-halfword unsigned comparison: a > b ? 1 : 0 + vsetles2(a,b) per-halfword signed comparison: a <= b ? 1 : 0 + vsetleu2(a,b) per-halfword unsigned comparison: a <= b ? 1 : 0 + vsetlts2(a,b) per-halfword signed comparison: a < b ? 1 : 0 + vsetltu2(a,b) per-halfword unsigned comparison: a < b ? 1 : 0 + vsetne2(a,b) per-halfword (un)signed comparison: a != b ? 1 : 0 + vsub2(a,b) per-halfword (un)signed subtraction, with wrap-around: a - b + vsubss2(a,b) per-halfword subtraction with signed saturation: sat.s16(a-b) + vsubus2(a,b) per-halfword subtraction w/ unsigned saturation: sat.u16(a-b) + + vabs4(a) per-byte absolute value, with wrap-around: |a| + vabsdiffs4(a,b) per-byte absolute difference of signed integer: |a - b| + vabsdiffu4(a,b) per-byte absolute difference of unsigned integer: |a - b| + vabsss4(a) per-byte absolute value, with signed saturation: sat.s8(|a|) + vadd4(a,b) per-byte (un)signed addition, with wrap-around: a + b + vaddss4(a,b) per-byte addition with signed saturation: sat.s8 (a + b) + vaddus4(a,b) per-byte addition with unsigned saturation: sat.u8 (a + b) + vavgs4(a,b) per-byte signed rounded average: (a + b + ((a+b) >= 0)) >> 1 + vavgu4(a,b) per-byte unsigned rounded average: (a + b + 1) / 2 + vcmpeq4(a,b) per-byte (un)signed comparison: a == b ? 0xff : 0 + vcmpges4(a,b) per-byte signed comparison: a >= b ? 0xff : 0 + vcmpgeu4(a,b) per-byte unsigned comparison: a >= b ? 0xff : 0 + vcmpgts4(a,b) per-byte signed comparison: a > b ? 0xff : 0 + vcmpgtu4(a,b) per-byte unsigned comparison: a > b ? 0xff : 0 + vcmples4(a,b) per-byte signed comparison: a <= b ? 0xff : 0 + vcmpleu4(a,b) per-byte unsigned comparison: a <= b ? 0xff : 0 + vcmplts4(a,b) per-byte signed comparison: a < b ? 0xff : 0 + vcmpltu4(a,b) per-byte unsigned comparison: a < b ? 0xff : 0 + vcmpne4(a,b) per-byte (un)signed comparison: a != b ? 0xff: 0 + vhaddu4(a,b) per-byte unsigned average: (a + b) / 2 + vmaxs4(a,b) per-byte signed maximum: max(a, b) + vmaxu4(a,b) per-byte unsigned maximum: max(a, b) + vmins4(a,b) per-byte signed minimum: min(a, b) + vminu4(a,b) per-byte unsigned minimum: min(a, b) + vneg4(a,b) per-byte negation, with wrap-around: -a + vnegss4(a,b) per-byte negation, with signed saturation: sat.s8(-a) + vsads4(a,b) per-byte sum of abs difference of signed: sum{0,3}(|a-b|) + vsadu4(a,b) per-byte sum of abs difference of unsigned: sum{0,3}(|a-b|) + vseteq4(a,b) per-byte (un)signed comparison: a == b ? 1 : 0 + vsetges4(a,b) per-byte signed comparison: a >= b ? 1 : 0 + vsetgeu4(a,b) per-byte unsigned comparison: a >= b ? 1 : 0 + vsetgts4(a,b) per-byte signed comparison: a > b ? 1 : 0 + vsetgtu4(a,b) per-byte unsigned comparison: a > b ? 1 : 0 + vsetles4(a,b) per-byte signed comparison: a <= b ? 1 : 0 + vsetleu4(a,b) per-byte unsigned comparison: a <= b ? 1 : 0 + vsetlts4(a,b) per-byte signed comparison: a < b ? 1 : 0 + vsetltu4(a,b) per-byte unsigned comparison: a < b ? 1 : 0 + vsetne4(a,b) per-byte (un)signed comparison: a != b ? 1: 0 + vsub4(a,b) per-byte (un)signed subtraction, with wrap-around: a - b + vsubss4(a,b) per-byte subtraction with signed saturation: sat.s8 (a - b) + vsubus4(a,b) per-byte subtraction with unsigned saturation: sat.u8 (a - b) +*/ + +static __device__ __forceinline__ unsigned int vabs2(unsigned int a) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int b = 0, c = 0; + asm ("vabsdiff2.s32.s32.s32 %0,%1,%2,%3;" : "=r"(r) :"r"(a),"r"(b),"r"(c)); +#elif __CUDA_ARCH__ >= 200 + asm ("{ \n\t" + ".reg .u32 a,m,r; \n\t" + "mov.b32 a,%1; \n\t" + "prmt.b32 m,a,0,0xbb99; \n\t" // msb ? 0xffff : 0000 + "xor.b32 r,a,m; \n\t" // conditionally invert bits + "and.b32 m,m,0x00010001;\n\t" // msb ? 0x1 : 0 + "add.u32 r,r,m; \n\t" // conditionally add 1 + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a)); +#else /* __CUDA_ARCH__ >= 200 */ + asm ("{ \n\t" + ".reg .u32 a,m,r,s; \n\t" + "mov.b32 a,%1; \n\t" + "and.b32 m,a,0x80008000;\n\t" // extract msb + "and.b32 r,a,0x7fff7fff;\n\t" // clear msb + "shr.u32 s,m,15; \n\t" // build lsb mask + "sub.u32 m,m,s; \n\t" // from msb + "xor.b32 r,r,m; \n\t" // conditionally invert lsbs + "add.u32 r,r,s; \n\t" // conditionally add 1 + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a)); +#endif /* __CUDA_ARCH__ >= 200 */ + return r; // halfword-wise absolute value, with wrap-around +} + +static __device__ __forceinline__ unsigned int vabsss2(unsigned int a) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int b = 0, c = 0; + asm("vabsdiff2.s32.s32.s32.sat %0,%1,%2,%3;":"=r"(r):"r"(a),"r"(b),"r"(c)); +#elif __CUDA_ARCH__ >= 200 + asm ("{ \n\t" + ".reg .u32 a,m,r; \n\t" + "mov.b32 a,%1; \n\t" + "prmt.b32 m,a,0,0xbb99; \n\t" // msb ? 0xffff : 0000 + "xor.b32 r,a,m; \n\t" // conditionally invert bits + "and.b32 m,m,0x00010001;\n\t" // msb ? 0x1 : 0 + "add.u32 r,r,m; \n\t" // conditionally add 1 + "prmt.b32 m,r,0,0xbb99; \n\t" // msb ? 0xffff : 0000 + "and.b32 m,m,0x00010001;\n\t" // msb ? 0x1 : 0 + "sub.u32 r,r,m; \n\t" // subtract 1 if result wrapped around + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a)); +#else /* __CUDA_ARCH__ >= 200 */ + asm ("{ \n\t" + ".reg .u32 a,m,r,s; \n\t" + "mov.b32 a,%1; \n\t" + "and.b32 m,a,0x80008000;\n\t" // extract msb + "and.b32 r,a,0x7fff7fff;\n\t" // clear msb + "shr.u32 s,m,15; \n\t" // build lsb mask + "sub.u32 m,m,s; \n\t" // from msb + "xor.b32 r,r,m; \n\t" // conditionally invert lsbs + "add.u32 r,r,s; \n\t" // conditionally add 1 + "and.b32 m,r,0x80008000;\n\t" // extract msb (1 if wrap-around) + "shr.u32 s,m,15; \n\t" // msb ? 1 : 0 + "sub.u32 r,r,s; \n\t" // subtract 1 if result wrapped around + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a)); +#endif /* __CUDA_ARCH__ >= 200 */ + return r; // halfword-wise absolute value with signed saturation +} + +static __device__ __forceinline__ unsigned int vadd2(unsigned int a, unsigned int b) +{ + unsigned int s, t; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm ("vadd2.u32.u32.u32 %0,%1,%2,%3;" : "=r"(t) : "r"(a), "r"(b), "r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + s = a ^ b; // sum bits + t = a + b; // actual sum + s = s ^ t; // determine carry-ins for each bit position + s = s & 0x00010000; // carry-in to high word (= carry-out from low word) + t = t - s; // subtract out carry-out from low word +#endif /* __CUDA_ARCH__ >= 300 */ + return t; // halfword-wise sum, with wrap around +} + +static __device__ __forceinline__ unsigned int vaddss2 (unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vadd2.s32.s32.s32.sat %0,%1,%2,%3;" : "=r"(r):"r"(a),"r"(b),"r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + int ahi, alo, blo, bhi, rhi, rlo; + ahi = (int)((a & 0xffff0000U)); + bhi = (int)((b & 0xffff0000U)); +#if __CUDA_ARCH__ < 200 + alo = (int)(a << 16); + blo = (int)(b << 16); +#elif __CUDA_ARCH__ < 350 + // work around (we would want left shifts at least for sm_2x) + asm ("prmt.b32 %0,%1,0,0x1044;" : "=r"(alo) : "r"(a)); + asm ("prmt.b32 %0,%1,0,0x1044;" : "=r"(blo) : "r"(b)); +#else + asm ("shf.l.clamp.b32 %0,0,%1,16;" : "=r"(alo) : "r"(a)); + asm ("shf.l.clamp.b32 %0,0,%1,16;" : "=r"(blo) : "r"(b)); +#endif + asm ("add.sat.s32 %0,%1,%2;" : "=r"(rlo) : "r"(alo), "r"(blo)); + asm ("add.sat.s32 %0,%1,%2;" : "=r"(rhi) : "r"(ahi), "r"(bhi)); +#if __CUDA_ARCH__ < 200 + r = ((unsigned int)rhi & 0xffff0000U) | ((unsigned int)rlo >> 16); +#else + asm ("prmt.b32 %0,%1,%2,0x7632;" : "=r"(r) : "r"(rlo), "r"(rhi)); +#endif /* __CUDA_ARCH__ < 200 */ +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise sum with signed saturation +} + +static __device__ __forceinline__ unsigned int vaddus2 (unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vadd2.u32.u32.u32.sat %0,%1,%2,%3;" : "=r"(r):"r"(a),"r"(b),"r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + int alo, blo, rlo, ahi, bhi, rhi; + asm ("{ \n\t" + "and.b32 %0, %4, 0xffff; \n\t" + "and.b32 %1, %5, 0xffff; \n\t" +#if __CUDA_ARCH__ < 350 + "shr.u32 %2, %4, 16; \n\t" + "shr.u32 %3, %5, 16; \n\t" +#else /* __CUDA_ARCH__ < 350 */ + "shf.r.clamp.b32 %2, %4, 0, 16;\n\t" + "shf.r.clamp.b32 %3, %5, 0, 16;\n\t" +#endif /* __CUDA_ARCH__ < 350 */ + "}" + : "=r"(alo), "=r"(blo), "=r"(ahi), "=r"(bhi) + : "r"(a), "r"(b)); + rlo = min (alo + blo, 65535); + rhi = min (ahi + bhi, 65535); + r = (rhi << 16) + rlo; +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise sum with unsigned saturation +} + +static __device__ __forceinline__ unsigned int vavgs2(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vavrg2.s32.s32.s32 %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + // avgs (a + b) = ((a + b) < 0) ? ((a + b) >> 1) : ((a + b + 1) >> 1). The + // two expressions can be re-written as follows to avoid needing additional + // intermediate bits: ((a + b) >> 1) = (a >> 1) + (b >> 1) + ((a & b) & 1), + // ((a + b + 1) >> 1) = (a >> 1) + (b >> 1) + ((a | b) & 1). The difference + // between the two is ((a ^ b) & 1). Note that if (a + b) < 0, then also + // ((a + b) >> 1) < 0, since right shift rounds to negative infinity. This + // means we can compute ((a + b) >> 1) then conditionally add ((a ^ b) & 1) + // depending on the sign bit of the shifted sum. By handling the msb sum + // bit of the result separately, we avoid carry-out during summation and + // also can use (potentially faster) logical right shifts. + asm ("{ \n\t" + ".reg .u32 a,b,c,r,s,t,u,v;\n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "and.b32 u,a,0xfffefffe;\n\t" // prevent shift crossing chunk boundary + "and.b32 v,b,0xfffefffe;\n\t" // prevent shift crossing chunk boundary + "xor.b32 s,a,b; \n\t" // a ^ b + "and.b32 t,a,b; \n\t" // a & b + "shr.u32 u,u,1; \n\t" // a >> 1 + "shr.u32 v,v,1; \n\t" // b >> 1 + "and.b32 c,s,0x00010001;\n\t" // (a ^ b) & 1 + "and.b32 s,s,0x80008000;\n\t" // extract msb (a ^ b) + "and.b32 t,t,0x00010001;\n\t" // (a & b) & 1 + "add.u32 r,u,v; \n\t" // (a>>1)+(b>>1) + "add.u32 r,r,t; \n\t" // (a>>1)+(b>>1)+(a&b&1); rec. msb cy-in + "xor.b32 r,r,s; \n\t" // compute msb sum bit: a ^ b ^ cy-in + "shr.u32 t,r,15; \n\t" // sign ((a + b) >> 1) + "not.b32 t,t; \n\t" // ~sign ((a + b) >> 1) + "and.b32 t,t,c; \n\t" // ((a ^ b) & 1) & ~sign ((a + b) >> 1) + "add.u32 r,r,t; \n\t" // conditionally add ((a ^ b) & 1) + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise average of signed integers +} + +static __device__ __forceinline__ unsigned int vavgu2(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vavrg2.u32.u32.u32 %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + // HAKMEM #23: a + b = 2 * (a | b) - (a ^ b) ==> + // (a + b + 1) / 2 = (a | b) - ((a ^ b) >> 1) + c = a ^ b; + r = a | b; + c = c & 0xfffefffe; // ensure shift doesn't cross half-word boundaries + c = c >> 1; + r = r - c; +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise average of unsigned integers +} + +static __device__ __forceinline__ unsigned int vhaddu2(unsigned int a, unsigned int b) +{ + // HAKMEM #23: a + b = 2 * (a & b) + (a ^ b) ==> + // (a + b) / 2 = (a & b) + ((a ^ b) >> 1) + unsigned int r, s; + s = a ^ b; + r = a & b; + s = s & 0xfffefffe; // ensure shift doesn't cross halfword boundaries + s = s >> 1; + r = r + s; + return r; // halfword-wise average of unsigned ints, rounded down +} + +static __device__ __forceinline__ unsigned int vcmpeq2(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset2.u32.u32.eq %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 16; // convert bool + r = c - r; // into mask +#else /* __CUDA_ARCH__ >= 300 */ + // inspired by Alan Mycroft's null-byte detection algorithm: + // null_byte(x) = ((x - 0x01010101) & (~x & 0x80808080)) + r = a ^ b; // 0x0000 if a == b + c = r | 0x80008000; // set msbs, to catch carry out + r = r ^ c; // extract msbs, msb = 1 if r < 0x8000 + c = c - 0x00010001; // msb = 0, if r was 0x0000 or 0x8000 + c = r & ~c; // msb = 1, if r was 0x0000 +#if __CUDA_ARCH__ >= 200 + asm ("prmt.b32 %0,%1,0,0xbb99;" : "=r"(r) : "r"(c));// convert msbs to mask +#else /* __CUDA_ARCH__ >= 200 */ + asm ("shr.u32 %0,%1,15;" : "=r"(r) : "r"(c)); // convert + asm ("sub.u32 %0,%1,%0;" : "+r"(r) : "r"(c)); // msbs to + asm ("or.b32 %0,%1,%0;" : "+r"(r) : "r"(c)); // mask +#endif /* __CUDA_ARCH__ >= 200 */ +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise (un)signed eq comparison, mask result +} + +static __device__ __forceinline__ unsigned int vcmpges2(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset2.s32.s32.ge %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 16; // convert bool + r = c - r; // to mask +#else /* __CUDA_ARCH__ >= 300 */ + asm ("{ \n\t" + ".reg .u32 a, b, r, s, t, u; \n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "and.b32 s,a,0xffff0000;\n\t" // high word of a + "and.b32 t,b,0xffff0000;\n\t" // high word of b + "set.ge.s32.s32 u,s,t; \n\t" // compare two high words + "cvt.s32.s16 s,a; \n\t" // sign-extend low word of a + "cvt.s32.s16 t,b; \n\t" // sign-extend low word of b + "set.ge.s32.s32 s,s,t; \n\t" // compare two low words +#if __CUDA_ARCH__ >= 200 + "prmt.b32 r,s,u,0x7632; \n\t" // combine low and high results +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 u,u,0xffff0000;\n\t" // mask comparison result hi word + "and.b32 s,s,0x0000ffff;\n\t" // mask comparison result lo word + "or.b32 r,s,u; \n\t" // combine the two results +#endif /* __CUDA_ARCH__ >= 200 */ + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise signed gt-eq comparison, mask result +} + +static __device__ __forceinline__ unsigned int vcmpgeu2(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset2.u32.u32.ge %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 16; // convert bool + r = c - r; // into mask +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(b)); + c = vavgu2 (a, b); // (a + ~b + 1) / 2 = (a - b) / 2 +#if __CUDA_ARCH__ >= 200 + asm ("prmt.b32 %0,%1,0,0xbb99;" : "=r"(r) : "r"(c));// build mask from msbs +#else /* __CUDA_ARCH__ >= 200 */ + asm ("and.b32 %0,%0,0x80008000;" : "+r"(c)); // msb = carry-outs + asm ("shr.u32 %0,%1,15;" : "=r"(r) : "r"(c)); // build mask + asm ("sub.u32 %0,%1,%0;" : "+r"(r) : "r"(c)); // from + asm ("or.b32 %0,%1,%0;" : "+r"(r) : "r"(c)); // msbs +#endif /* __CUDA_ARCH__ >= 200 */ +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise unsigned gt-eq comparison, mask result +} + +static __device__ __forceinline__ unsigned int vcmpgts2(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset2.s32.s32.gt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 16; // convert bool + r = c - r; // to mask +#else /* __CUDA_ARCH__ >= 300 */ + asm ("{ \n\t" + ".reg .u32 a, b, r, s, t, u; \n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "and.b32 s,a,0xffff0000;\n\t" // high word of a + "and.b32 t,b,0xffff0000;\n\t" // high word of b + "set.gt.s32.s32 u,s,t; \n\t" // compare two high words + "cvt.s32.s16 s,a; \n\t" // sign-extend low word of a + "cvt.s32.s16 t,b; \n\t" // sign-extend low word of b + "set.gt.s32.s32 s,s,t; \n\t" // compare two low words +#if __CUDA_ARCH__ >= 200 + "prmt.b32 r,s,u,0x7632; \n\t" // combine low and high results +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 u,u,0xffff0000;\n\t" // mask comparison result hi word + "and.b32 s,s,0x0000ffff;\n\t" // mask comparison result lo word + "or.b32 r,s,u; \n\t" // combine the two results +#endif /* __CUDA_ARCH__ >= 200 */ + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise signed gt comparison with mask result +} + +static __device__ __forceinline__ unsigned int vcmpgtu2(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset2.u32.u32.gt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 16; // convert bool + r = c - r; // into mask +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(b)); + c = vhaddu2 (a, b); // (a + ~b) / 2 = (a - b) / 2 [rounded down] +#if __CUDA_ARCH__ >= 200 + asm ("prmt.b32 %0,%1,0,0xbb99;" : "=r"(r) : "r"(c));// build mask from msbs +#else /* __CUDA_ARCH__ >= 200 */ + asm ("and.b32 %0,%0,0x80008000;" : "+r"(c)); // msb = carry-outs + asm ("shr.u32 %0,%1,15;" : "=r"(r) : "r"(c)); // build mask + asm ("sub.u32 %0,%1,%0;" : "+r"(r) : "r"(c)); // from + asm ("or.b32 %0,%1,%0;" : "+r"(r) : "r"(c)); // msbs +#endif /* __CUDA_ARCH__ >= 200 */ +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise unsigned gt comparison, mask result +} + +static __device__ __forceinline__ unsigned int vcmples2(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset2.s32.s32.le %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 16; // convert bool + r = c - r; // to mask +#else /* __CUDA_ARCH__ >= 300 */ + asm ("{ \n\t" + ".reg .u32 a, b, r, s, t, u; \n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "and.b32 s,a,0xffff0000;\n\t" // high word of a + "and.b32 t,b,0xffff0000;\n\t" // high word of b + "set.le.s32.s32 u,s,t; \n\t" // compare two high words + "cvt.s32.s16 s,a; \n\t" // sign-extend low word of a + "cvt.s32.s16 t,b; \n\t" // sign-extend low word of b + "set.le.s32.s32 s,s,t; \n\t" // compare two low words +#if __CUDA_ARCH__ >= 200 + "prmt.b32 r,s,u,0x7632; \n\t" // combine low and high results +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 u,u,0xffff0000;\n\t" // mask comparison result hi word + "and.b32 s,s,0x0000ffff;\n\t" // mask comparison result lo word + "or.b32 r,s,u; \n\t" // combine the two results +#endif /* __CUDA_ARCH__ >= 200 */ + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise signed lt-eq comparison, mask result +} + +static __device__ __forceinline__ unsigned int vcmpleu2(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset2.u32.u32.le %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 16; // convert bool + r = c - r; // into mask +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(a)); + c = vavgu2 (a, b); // (b + ~a + 1) / 2 = (b - a) / 2 +#if __CUDA_ARCH__ >= 200 + asm ("prmt.b32 %0,%1,0,0xbb99;" : "=r"(r) : "r"(c));// build mask from msbs +#else /* __CUDA_ARCH__ >= 200 */ + asm ("and.b32 %0,%0,0x80008000;" : "+r"(c)); // msb = carry-outs + asm ("shr.u32 %0,%1,15;" : "=r"(r) : "r"(c)); // build mask + asm ("sub.u32 %0,%1,%0;" : "+r"(r) : "r"(c)); // from + asm ("or.b32 %0,%1,%0;" : "+r"(r) : "r"(c)); // msbs +#endif /* __CUDA_ARCH__ >= 200 */ +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise unsigned lt-eq comparison, mask result +} + +static __device__ __forceinline__ unsigned int vcmplts2(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset2.s32.s32.lt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 16; // convert bool + r = c - r; // to mask +#else /* __CUDA_ARCH__ >= 300 */ + asm ("{ \n\t" + ".reg .u32 a, b, r, s, t, u; \n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "and.b32 s,a,0xffff0000;\n\t" // high word of a + "and.b32 t,b,0xffff0000;\n\t" // high word of b + "set.lt.s32.s32 u,s,t; \n\t" // compare two high words + "cvt.s32.s16 s,a; \n\t" // sign-extend low word of a + "cvt.s32.s16 t,b; \n\t" // sign-extend low word of b + "set.lt.s32.s32 s,s,t; \n\t" // compare two low words +#if __CUDA_ARCH__ >= 200 + "prmt.b32 r,s,u,0x7632; \n\t" // combine low and high results +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 u,u,0xffff0000;\n\t" // mask comparison result hi word + "and.b32 s,s,0x0000ffff;\n\t" // mask comparison result lo word + "or.b32 r,s,u; \n\t" // combine the two results +#endif /* __CUDA_ARCH__ >= 200 */ + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise signed lt comparison with mask result +} + +static __device__ __forceinline__ unsigned int vcmpltu2(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset2.u32.u32.lt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 16; // convert bool + r = c - r; // into mask +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(a)); + c = vhaddu2 (a, b); // (b + ~a) / 2 = (b - a) / 2 [rounded down] +#if __CUDA_ARCH__ >= 200 + asm ("prmt.b32 %0,%1,0,0xbb99;" : "=r"(r) : "r"(c));// build mask from msbs +#else /* __CUDA_ARCH__ >= 200 */ + asm ("and.b32 %0,%0,0x80008000;" : "+r"(c)); // msb = carry-outs + asm ("shr.u32 %0,%1,15;" : "=r"(r) : "r"(c)); // build mask + asm ("sub.u32 %0,%1,%0;" : "+r"(r) : "r"(c)); // from + asm ("or.b32 %0,%1,%0;" : "+r"(r) : "r"(c)); // msbs +#endif /* __CUDA_ARCH__ >= 200 */ +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise unsigned lt comparison, mask result +} + +static __device__ __forceinline__ unsigned int vcmpne2(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset2.u32.u32.ne %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 16; // convert bool + r = c - r; // into mask +#else /* __CUDA_ARCH__ >= 300 */ + // inspired by Alan Mycroft's null-byte detection algorithm: + // null_byte(x) = ((x - 0x01010101) & (~x & 0x80808080)) + r = a ^ b; // 0x0000 if a == b + c = r | 0x80008000; // set msbs, to catch carry out + c = c - 0x00010001; // msb = 0, if r was 0x0000 or 0x8000 + c = r | c; // msb = 1, if r was not 0x0000 +#if __CUDA_ARCH__ >= 200 + asm ("prmt.b32 %0,%1,0,0xbb99;" : "=r"(r) : "r"(c));// build mask from msbs +#else /* __CUDA_ARCH__ >= 200 */ + asm ("and.b32 %0,%0,0x80008000;" : "+r"(c)); // extract msbs + asm ("shr.u32 %0,%1,15;" : "=r"(r) : "r"(c)); // build mask + asm ("sub.u32 %0,%1,%0;" : "+r"(r) : "r"(c)); // from + asm ("or.b32 %0,%1,%0;" : "+r"(r) : "r"(c)); // msbs +#endif /* __CUDA_ARCH__ >= 200 */ +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise (un)signed ne comparison, mask result +} + +static __device__ __forceinline__ unsigned int vabsdiffu2(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm ("vabsdiff2.u32.u32.u32 %0,%1,%2,%3;" : "=r"(r) :"r"(a),"r"(b),"r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + unsigned int t, u, v; + s = a & 0x0000ffff; // extract low halfword + r = b & 0x0000ffff; // extract low halfword + u = max (r, s); // maximum of low halfwords + v = min (r, s); // minimum of low halfwords + s = a & 0xffff0000; // extract high halfword + r = b & 0xffff0000; // extract high halfword + t = max (r, s); // maximum of high halfwords + s = min (r, s); // minimum of high halfwords + r = u | t; // maximum of both halfwords + s = v | s; // minimum of both halfwords + r = r - s; // |a - b| = max(a,b) - min(a,b); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise absolute difference of unsigned ints +} + +static __device__ __forceinline__ unsigned int vmaxs2(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm ("vmax2.s32.s32.s32 %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + unsigned int t, u; + asm ("cvt.s32.s16 %0,%1;" : "=r"(r) : "r"(a)); // extract low halfword + asm ("cvt.s32.s16 %0,%1;" : "=r"(s) : "r"(b)); // extract low halfword + t = max((int)r,(int)s); // maximum of low halfwords + r = a & 0xffff0000; // extract high halfword + s = b & 0xffff0000; // extract high halfword + u = max((int)r,(int)s); // maximum of high halfwords + r = u | (t & 0xffff); // combine halfword maximums +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise maximum of signed integers +} + +static __device__ __forceinline__ unsigned int vmaxu2(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm ("vmax2.u32.u32.u32 %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + unsigned int t, u; + r = a & 0x0000ffff; // extract low halfword + s = b & 0x0000ffff; // extract low halfword + t = max (r, s); // maximum of low halfwords + r = a & 0xffff0000; // extract high halfword + s = b & 0xffff0000; // extract high halfword + u = max (r, s); // maximum of high halfwords + r = t | u; // combine halfword maximums +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise maximum of unsigned integers +} + +static __device__ __forceinline__ unsigned int vmins2(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm ("vmin2.s32.s32.s32 %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + unsigned int t, u; + asm ("cvt.s32.s16 %0,%1;" : "=r"(r) : "r"(a)); // extract low halfword + asm ("cvt.s32.s16 %0,%1;" : "=r"(s) : "r"(b)); // extract low halfword + t = min((int)r,(int)s); // minimum of low halfwords + r = a & 0xffff0000; // extract high halfword + s = b & 0xffff0000; // extract high halfword + u = min((int)r,(int)s); // minimum of high halfwords + r = u | (t & 0xffff); // combine halfword minimums +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise minimum of signed integers +} + +static __device__ __forceinline__ unsigned int vminu2(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm ("vmin2.u32.u32.u32 %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + unsigned int t, u; + r = a & 0x0000ffff; // extract low halfword + s = b & 0x0000ffff; // extract low halfword + t = min (r, s); // minimum of low halfwords + r = a & 0xffff0000; // extract high halfword + s = b & 0xffff0000; // extract high halfword + u = min (r, s); // minimum of high halfwords + r = t | u; // combine halfword minimums +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise minimum of unsigned integers +} + +static __device__ __forceinline__ unsigned int vseteq2(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset2.u32.u32.eq %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + // inspired by Alan Mycroft's null-byte detection algorithm: + // null_byte(x) = ((x - 0x01010101) & (~x & 0x80808080)) + r = a ^ b; // 0x0000 if a == b + c = r | 0x80008000; // set msbs, to catch carry out + r = r ^ c; // extract msbs, msb = 1 if r < 0x8000 + c = c - 0x00010001; // msb = 0, if r was 0x0000 or 0x8000 + c = r & ~c; // msb = 1, if r was 0x0000 + r = c >> 15; // convert to bool +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise (un)signed eq comparison, bool result +} + +static __device__ __forceinline__ unsigned int vsetges2(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset2.s32.s32.ge %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + asm ("{ \n\t" + ".reg .u32 a, b, r, s, t, u; \n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "and.b32 s,a,0xffff0000;\n\t" // high word of a + "and.b32 t,b,0xffff0000;\n\t" // high word of b + "set.ge.s32.s32 u,s,t; \n\t" // compare two high words + "cvt.s32.s16 s,a; \n\t" // sign-extend low word of a + "cvt.s32.s16 t,b; \n\t" // sign-extend low word of b + "set.ge.s32.s32 s,s,t; \n\t" // compare two low words +#if __CUDA_ARCH__ >= 200 + "prmt.b32 r,s,u,0x7632; \n\t" // combine low and high results + "and.b32 r,r,0x00010001;\n\t" // convert from mask to bool +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 u,u,0x00010000;\n\t" // extract bool result of hi word + "and.b32 s,s,0x00000001;\n\t" // extract bool result of lo word + "or.b32 r,s,u; \n\t" // combine the two results +#endif /* __CUDA_ARCH__ >= 200 */ + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise signed gt-eq comparison, bool result +} + +static __device__ __forceinline__ unsigned int vsetgeu2(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset2.u32.u32.ge %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(b)); + c = vavgu2 (a, b); // (a + ~b + 1) / 2 = (a - b) / 2 + c = c & 0x80008000; // msb = carry-outs + r = c >> 15; // convert to bool +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise unsigned gt-eq comparison, bool result +} + +static __device__ __forceinline__ unsigned int vsetgts2(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset2.s32.s32.gt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + asm ("{ \n\t" + ".reg .u32 a, b, r, s, t, u; \n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "and.b32 s,a,0xffff0000;\n\t" // high word of a + "and.b32 t,b,0xffff0000;\n\t" // high word of b + "set.gt.s32.s32 u,s,t; \n\t" // compare two high words + "cvt.s32.s16 s,a; \n\t" // sign-extend low word of a + "cvt.s32.s16 t,b; \n\t" // sign-extend low word of b + "set.gt.s32.s32 s,s,t; \n\t" // compare two low words +#if __CUDA_ARCH__ >= 200 + "prmt.b32 r,s,u,0x7632; \n\t" // combine low and high results + "and.b32 r,r,0x00010001;\n\t" // convert from mask to bool +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 u,u,0x00010000;\n\t" // extract bool result of hi word + "and.b32 s,s,0x00000001;\n\t" // extract bool result of lo word + "or.b32 r,s,u; \n\t" // combine the two results +#endif /* __CUDA_ARCH__ >= 200 */ + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise signed gt comparison with bool result +} + +static __device__ __forceinline__ unsigned int vsetgtu2(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset2.u32.u32.gt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(b)); + c = vhaddu2 (a, b); // (a + ~b) / 2 = (a - b) / 2 [rounded down] + c = c & 0x80008000; // msbs = carry-outs + r = c >> 15; // convert to bool +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise unsigned gt comparison, bool result +} + +static __device__ __forceinline__ unsigned int vsetles2(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset2.s32.s32.le %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + asm ("{ \n\t" + ".reg .u32 a, b, r, s, t, u; \n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "and.b32 s,a,0xffff0000;\n\t" // high word of a + "and.b32 t,b,0xffff0000;\n\t" // high word of b + "set.le.s32.s32 u,s,t; \n\t" // compare two high words + "cvt.s32.s16 s,a; \n\t" // sign-extend low word of a + "cvt.s32.s16 t,b; \n\t" // sign-extend low word of b + "set.le.s32.s32 s,s,t; \n\t" // compare two low words +#if __CUDA_ARCH__ >= 200 + "prmt.b32 r,s,u,0x7632; \n\t" // combine low and high results + "and.b32 r,r,0x00010001;\n\t" // convert from mask to bool +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 u,u,0x00010000;\n\t" // extract bool result of hi word + "and.b32 s,s,0x00000001;\n\t" // extract bool result of lo word + "or.b32 r,s,u; \n\t" // combine the two results +#endif /* __CUDA_ARCH__ >= 200 */ + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise signed lt-eq comparison, bool result +} + +static __device__ __forceinline__ unsigned int vsetleu2(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset2.u32.u32.le %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(a)); + c = vavgu2 (a, b); // (b + ~a + 1) / 2 = (b - a) / 2 + c = c & 0x80008000; // msb = carry-outs + r = c >> 15; // convert to bool +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise unsigned lt-eq comparison, bool result +} + +static __device__ __forceinline__ unsigned int vsetlts2(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset2.s32.s32.lt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + asm ("{ \n\t" + ".reg .u32 a, b, r, s, t, u; \n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "and.b32 s,a,0xffff0000;\n\t" // high word of a + "and.b32 t,b,0xffff0000;\n\t" // high word of b + "set.lt.s32.s32 u,s,t; \n\t" // compare two high words + "cvt.s32.s16 s,a; \n\t" // sign-extend low word of a + "cvt.s32.s16 t,b; \n\t" // sign-extend low word of b + "set.lt.s32.s32 s,s,t; \n\t" // compare two low words +#if __CUDA_ARCH__ >= 200 + "prmt.b32 r,s,u,0x7632; \n\t" // combine low and high results + "and.b32 r,r,0x00010001;\n\t" // convert from mask to bool +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 u,u,0x00010000;\n\t" // extract bool result of hi word + "and.b32 s,s,0x00000001;\n\t" // extract bool result of lo word + "or.b32 r,s,u; \n\t" // combine the two results +#endif /* __CUDA_ARCH__ >= 200 */ + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise signed lt comparison with bool result +} + +static __device__ __forceinline__ unsigned int vsetltu2(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset2.u32.u32.lt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(a)); + c = vhaddu2 (a, b); // (b + ~a) / 2 = (b - a) / 2 [rounded down] + c = c & 0x80008000; // msb = carry-outs + r = c >> 15; // convert to bool +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise unsigned lt comparison, bool result +} + +static __device__ __forceinline__ unsigned int vsetne2(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset2.u32.u32.ne %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + // inspired by Alan Mycroft's null-byte detection algorithm: + // null_byte(x) = ((x - 0x01010101) & (~x & 0x80808080)) + r = a ^ b; // 0x0000 if a == b + c = r | 0x80008000; // set msbs, to catch carry out + c = c - 0x00010001; // msb = 0, if r was 0x0000 or 0x8000 + c = r | c; // msb = 1, if r was not 0x0000 + c = c & 0x80008000; // extract msbs + r = c >> 15; // convert to bool +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise (un)signed ne comparison, bool result +} + +static __device__ __forceinline__ unsigned int vsadu2(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm("vabsdiff2.u32.u32.u32.add %0,%1,%2,%3;":"=r"(r):"r"(a),"r"(b),"r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + unsigned int t, u, v; + s = a & 0x0000ffff; // extract low halfword + r = b & 0x0000ffff; // extract low halfword + u = max (r, s); // maximum of low halfwords + v = min (r, s); // minimum of low halfwords + s = a & 0xffff0000; // extract high halfword + r = b & 0xffff0000; // extract high halfword + t = max (r, s); // maximum of high halfwords + s = min (r, s); // minimum of high halfwords + u = u - v; // low halfword: |a - b| = max(a,b) - min(a,b); + t = t - s; // high halfword: |a - b| = max(a,b) - min(a,b); +#if __CUDA_ARCH__ < 350 + asm ("shr.u32 %0,%0,16;" : "+r"(t)); +#else /*__CUDA_ARCH__ < 350 */ + asm ("shf.r.clamp.b32 %0,%0,0,16;" : "+r"(t)); +#endif /*__CUDA_ARCH__ < 350 */ + r = t + u; // sum absolute halfword differences +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise sum of abs differences of unsigned int +} + +static __device__ __forceinline__ unsigned int vsub2(unsigned int a, unsigned int b) +{ + unsigned int s, t; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm ("vsub2.u32.u32.u32 %0,%1,%2,%3;" : "=r"(t) : "r"(a), "r"(b), "r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + s = a ^ b; // sum bits + t = a - b; // actual sum + s = s ^ t; // determine carry-ins for each bit position + s = s & 0x00010000; // borrow to high word + t = t + s; // compensate for borrow from low word +#endif /* __CUDA_ARCH__ >= 300 */ + return t; // halfword-wise difference +} + +static __device__ __forceinline__ unsigned int vsubss2 (unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vsub2.s32.s32.s32.sat %0,%1,%2,%3;" : "=r"(r):"r"(a),"r"(b),"r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + int ahi, alo, blo, bhi, rhi, rlo; + ahi = (int)((a & 0xffff0000U)); + bhi = (int)((b & 0xffff0000U)); +#if __CUDA_ARCH__ < 200 + alo = (int)(a << 16); + blo = (int)(b << 16); +#elif __CUDA_ARCH__ < 350 + // work around (we would want left shifts at least for sm_2x) + asm ("prmt.b32 %0,%1,0,0x1044;" : "=r"(alo) : "r"(a)); + asm ("prmt.b32 %0,%1,0,0x1044;" : "=r"(blo) : "r"(b)); +#else /* __CUDA_ARCH__ < 350 */ + asm ("shf.l.clamp.b32 %0,0,%1,16;" : "=r"(alo) : "r"(a)); + asm ("shf.l.clamp.b32 %0,0,%1,16;" : "=r"(blo) : "r"(b)); +#endif /* __CUDA_ARCH__ < 350 */ + asm ("sub.sat.s32 %0,%1,%2;" : "=r"(rlo) : "r"(alo), "r"(blo)); + asm ("sub.sat.s32 %0,%1,%2;" : "=r"(rhi) : "r"(ahi), "r"(bhi)); +#if __CUDA_ARCH__ < 200 + r = ((unsigned int)rhi & 0xffff0000U) | ((unsigned int)rlo >> 16); +#else /* __CUDA_ARCH__ < 200 */ + asm ("prmt.b32 %0,%1,%2,0x7632;" : "=r"(r) : "r"(rlo), "r"(rhi)); +#endif /* __CUDA_ARCH__ < 200 */ +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise difference with signed saturation +} + +static __device__ __forceinline__ unsigned int vsubus2 (unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vsub2.u32.u32.u32.sat %0,%1,%2,%3;" : "=r"(r):"r"(a),"r"(b),"r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + int alo, blo, rlo, ahi, bhi, rhi; + asm ("{ \n\t" + "and.b32 %0, %4, 0xffff; \n\t" + "and.b32 %1, %5, 0xffff; \n\t" +#if __CUDA_ARCH__ < 350 + "shr.u32 %2, %4, 16; \n\t" + "shr.u32 %3, %5, 16; \n\t" +#else /* __CUDA_ARCH__ < 350 */ + "shf.r.clamp.b32 %2, %4, 0, 16;\n\t" + "shf.r.clamp.b32 %3, %5, 0, 16;\n\t" +#endif /* __CUDA_ARCH__ < 350 */ + "}" + : "=r"(alo), "=r"(blo), "=r"(ahi), "=r"(bhi) + : "r"(a), "r"(b)); + rlo = max ((int)(alo - blo), 0); + rhi = max ((int)(ahi - bhi), 0); + r = rhi * 65536 + rlo; +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise difference with unsigned saturation +} + +static __device__ __forceinline__ unsigned int vneg2(unsigned int a) +{ + return vsub2 (0, a);// halfword-wise negation with wrap-around +} + +static __device__ __forceinline__ unsigned int vnegss2(unsigned int a) +{ + return vsubss2(0,a);// halfword-wise negation with signed saturation +} + +static __device__ __forceinline__ unsigned int vabsdiffs2(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm ("vabsdiff2.s32.s32.s32 %0,%1,%2,%3;" : "=r"(r) :"r"(a),"r"(b),"r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + s = vcmpges2 (a, b);// mask = 0xff if a >= b + r = a ^ b; // + s = (r & s) ^ b; // select a when a >= b, else select b => max(a,b) + r = s ^ r; // select a when b >= a, else select b => min(a,b) + r = vsub2 (s, r); // |a - b| = max(a,b) - min(a,b); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise absolute difference of signed integers +} + +static __device__ __forceinline__ unsigned int vsads2(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm("vabsdiff2.s32.s32.s32.add %0,%1,%2,%3;":"=r"(r):"r"(a),"r"(b),"r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + s = vabsdiffs2 (a, b); + r = (s >> 16) + (s & 0x0000ffff); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // halfword-wise sum of abs. differences of signed ints +} + +static __device__ __forceinline__ unsigned int vabs4(unsigned int a) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int b = 0, c = 0; + asm ("vabsdiff4.s32.s32.s32 %0,%1,%2,%3;" : "=r"(r) :"r"(a),"r"(b),"r"(c)); +#elif __CUDA_ARCH__ >= 200 + asm ("{ \n\t" + ".reg .u32 a,m,r; \n\t" + "mov.b32 a,%1; \n\t" + "prmt.b32 m,a,0,0xba98; \n\t" // msb ? 0xff : 00 + "xor.b32 r,a,m; \n\t" // conditionally invert bits + "and.b32 m,m,0x01010101;\n\t" // msb ? 0x1 : 0 + "add.u32 r,r,m; \n\t" // conditionally add 1 + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a)); +#else /* __CUDA_ARCH__ >= 200 */ + asm ("{ \n\t" + ".reg .u32 a,m,r,s; \n\t" + "mov.b32 a,%1; \n\t" + "and.b32 m,a,0x80808080;\n\t" // extract msb + "and.b32 r,a,0x7f7f7f7f;\n\t" // clear msb + "shr.u32 s,m,7; \n\t" // build lsb mask + "sub.u32 m,m,s; \n\t" // from msb + "xor.b32 r,r,m; \n\t" // conditionally invert lsbs + "add.u32 r,r,s; \n\t" // conditionally add 1 + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a)); +#endif /* __CUDA_ARCH__ >= 200 */ + return r; // byte-wise absolute value, with wrap-around +} + +static __device__ __forceinline__ unsigned int vabsss4(unsigned int a) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int b = 0, c = 0; + asm("vabsdiff4.s32.s32.s32.sat %0,%1,%2,%3;":"=r"(r):"r"(a),"r"(b),"r"(c)); +#elif __CUDA_ARCH__ >= 200 + asm ("{ \n\t" + ".reg .u32 a,m,r; \n\t" + "mov.b32 a,%1; \n\t" + "prmt.b32 m,a,0,0xba98; \n\t" // msb ? 0xff : 00 + "xor.b32 r,a,m; \n\t" // conditionally invert bits + "and.b32 m,m,0x01010101;\n\t" // msb ? 0x1 : 0 + "add.u32 r,r,m; \n\t" // conditionally add 1 + "prmt.b32 m,r,0,0xba98; \n\t" // msb ? 0xff : 00 + "and.b32 m,m,0x01010101;\n\t" // msb ? 0x1 : 0 + "sub.u32 r,r,m; \n\t" // subtract 1 if result wrapped around + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a)); +#else /* __CUDA_ARCH__ >= 200 */ + asm ("{ \n\t" + ".reg .u32 a,m,r,s; \n\t" + "mov.b32 a,%1; \n\t" + "and.b32 m,a,0x80808080;\n\t" // extract msb + "and.b32 r,a,0x7f7f7f7f;\n\t" // clear msb + "shr.u32 s,m,7; \n\t" // build lsb mask + "sub.u32 m,m,s; \n\t" // from msb + "xor.b32 r,r,m; \n\t" // conditionally invert lsbs + "add.u32 r,r,s; \n\t" // conditionally add 1 + "and.b32 m,r,0x80808080;\n\t" // extract msb (1 if wrap-around) + "shr.u32 s,m,7; \n\t" // msb ? 1 : 0 + "sub.u32 r,r,s; \n\t" // subtract 1 if result wrapped around + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a)); +#endif /* __CUDA_ARCH__ >= 200 */ + return r; // byte-wise absolute value with signed saturation +} + +static __device__ __forceinline__ unsigned int vadd4(unsigned int a, unsigned int b) +{ +#if __CUDA_ARCH__ >= 300 + unsigned int r, c = 0; + asm ("vadd4.u32.u32.u32 %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + unsigned int r, s, t; + s = a ^ b; // sum bits + r = a & 0x7f7f7f7f; // clear msbs + t = b & 0x7f7f7f7f; // clear msbs + s = s & 0x80808080; // msb sum bits + r = r + t; // add without msbs, record carry-out in msbs + r = r ^ s; // sum of msb sum and carry-in bits, w/o carry-out +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise sum, with wrap-around +} + +static __device__ __forceinline__ unsigned int vaddss4 (unsigned int a, unsigned int b) +{ +#if __CUDA_ARCH__ >= 300 + unsigned int r, c = 0; + asm ("vadd4.sat.s32.s32.s32 %0,%1,%2,%3;" : "=r"(r):"r"(a),"r"(b),"r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + /* + For signed saturation, saturation is controlled by the overflow signal: + ovfl = (carry-in to msb) XOR (carry-out from msb). Overflow can only + occur when the msbs of both inputs are the same. The defined response to + overflow is to deliver 0x7f when the addends are positive (bit 7 clear), + and 0x80 when the addends are negative (bit 7 set). The truth table for + the msb is + + a b cy_in res cy_out ovfl + -------------------------------- + 0 0 0 0 0 0 + 0 0 1 1 0 1 + 0 1 0 1 0 0 + 0 1 1 0 1 0 + 1 0 0 1 0 0 + 1 0 1 0 1 0 + 1 1 0 0 1 1 + 1 1 1 1 1 0 + + The seven low-order bits can be handled by simple wrapping addition with + the carry out from bit 6 recorded in the msb (thus corresponding to the + cy_in in the truth table for the msb above). ovfl can be computed in many + equivalent ways, here we use ovfl = (a ^ carry_in) & ~(a ^ b) since we + already need to compute (a ^ b) for the msb sum bit computation. First we + compute the normal, wrapped addition result. When overflow is detected, + we mask off the msb of the result, then compute a mask covering the seven + low order bits, which are all set to 1. This sets the byte to 0x7f as we + previously cleared the msb. In the overflow case, the sign of the result + matches the sign of either of the inputs, so we extract the sign of a and + add it to the low order bits, which turns 0x7f into 0x80, the correct + result for an overflowed negative result. + */ + unsigned int r; + asm ("{ \n\t" + ".reg .u32 a,b,r,s,t,u; \n\t" + "mov.b32 a, %1; \n\t" + "mov.b32 b, %2; \n\t" + "and.b32 r, a, 0x7f7f7f7f;\n\t" // clear msbs + "and.b32 t, b, 0x7f7f7f7f;\n\t" // clear msbs + "xor.b32 s, a, b; \n\t" // sum bits = (a ^ b) + "add.u32 r, r, t; \n\t" // capture msb carry-in in bit 7 + "xor.b32 t, a, r; \n\t" // a ^ carry_in + "not.b32 u, s; \n\t" // ~(a ^ b) + "and.b32 t, t, u; \n\t" // ovfl = (a ^ carry_in) & ~(a ^ b) + "and.b32 s, s, 0x80808080;\n\t" // msb sum bits + "xor.b32 r, r, s; \n\t" // msb result = (a ^ b ^ carry_in) +#if __CUDA_ARCH__ >= 200 + "prmt.b32 s,a,0,0xba98; \n\t" // sign(a) ? 0xff : 0 + "xor.b32 s,s,0x7f7f7f7f; \n\t" // sign(a) ? 0x80 : 0x7f + "prmt.b32 t,t,0,0xba98; \n\t" // ovfl ? 0xff : 0 + "and.b32 s,s,t; \n\t" // ovfl ? (sign(a) ? 0x80:0x7f) : 0 + "not.b32 t,t; \n\t" // ~ovfl + "and.b32 r,r,t; \n\t" // ovfl ? 0 : a + b + "or.b32 r,r,s; \n\t" // ovfl ? (sign(a) ? 0x80:0x7f) : a+b +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 t, t, 0x80808080;\n\t" // ovfl ? 0x80 : 0 + "shr.u32 s, t, 7; \n\t" // ovfl ? 1 : 0 + "not.b32 u, t; \n\t" // ovfl ? 0x7f : 0xff + "and.b32 r, r, u; \n\t" // ovfl ? (a + b) & 0x7f : a + b + "and.b32 u, a, t; \n\t" // ovfl ? a & 0x80 : 0 + "sub.u32 t, t, s; \n\t" // ovfl ? 0x7f : 0 + "shr.u32 u, u, 7; \n\t" // ovfl ? sign(a) : 0 + "or.b32 r, r, t; \n\t" // ovfl ? 0x7f : a + b + "add.u32 r, r, u; \n\t" // ovfl ? 0x7f+sign(a) : a + b +#endif /* __CUDA_ARCH__ >= 200 */ + "mov.b32 %0, r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise sum with signed saturation +} + +static __device__ __forceinline__ unsigned int vaddus4 (unsigned int a, unsigned int b) +{ +#if __CUDA_ARCH__ >= 300 + unsigned int r, c = 0; + asm ("vadd4.u32.u32.u32.sat %0,%1,%2,%3;" : "=r"(r):"r"(a),"r"(b),"r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + // This code uses the same basic approach used for non-saturating addition. + // The seven low-order bits in each byte are summed by regular addition, + // with the carry-out from bit 6 (= carry-in for the msb) being recorded + // in bit 7, while the msb is handled separately. + // + // The fact that this is a saturating addition simplifies the handling of + // the msb. When carry-out from the msb occurs, the entire byte must be + // written as 0xff, and the computed msb is overwritten in the process. + // The corresponding entries in the truth table for the result msb thus + // become "don't cares": + // + // a b cy-in res cy-out + // ------------------------ + // 0 0 0 0 0 + // 0 0 1 1 0 + // 0 1 0 1 0 + // 0 1 1 X 1 + // 1 0 0 1 0 + // 1 0 1 X 1 + // 1 1 0 X 1 + // 1 1 1 X 1 + // + // As is easily seen, the simplest implementation of the result msb bit is + // simply (a | b | cy-in), with masking needed to isolate the msb. Note + // that this computation also makes the msb handling redundant with the + // clamping to 0xFF, because the msb is already set to 1 when saturation + // occurs. This means we only need to apply saturation to the seven lsb + // bits in each byte, by overwriting with 0x7F. Saturation is controlled + // by carry-out from the msb, which can be represented by various Boolean + // expressions. Since to compute (a | b | cy-in) we need to compute (a | b) + // anyhow, most efficient of these is cy-out = ((a & b) | cy-in) & (a | b). + unsigned int r; + asm ("{ \n\t" + ".reg .u32 a,b,r,s,t,m; \n\t" + "mov.b32 a, %1; \n\t" + "mov.b32 b, %2; \n\t" + "or.b32 m, a, b; \n\t" // (a | b) + "and.b32 r, a, 0x7f7f7f7f;\n\t" // clear msbs + "and.b32 t, b, 0x7f7f7f7f;\n\t" // clear msbs + "and.b32 m, m, 0x80808080;\n\t" // (a | b), isolate msbs + "add.u32 r, r, t; \n\t" // add w/o msbs, record msb-carry-ins + "and.b32 t, a, b; \n\t" // (a & b) + "or.b32 t, t, r; \n\t" // (a & b) | cy-in) + "or.b32 r, r, m; \n\t" // msb = cy-in | (a | b) + "and.b32 t, t, m; \n\t" // cy-out=((a&b)|cy-in)&(a|b),in msbs +#if __CUDA_ARCH__ >= 200 + "prmt.b32 t, t, 0, 0xba98; \n\t" // cy-out ? 0xff : 0 +#else /* __CUDA_ARCH__ >= 200 */ + "shr.u32 s, t, 7; \n\t" // cy-out ? 1 : 0 + "sub.u32 t, t, s; \n\t" // lsb-overwrite: cy-out ? 0x7F : 0 +#endif /* __CUDA_ARCH__ >= 200 */ + "or.b32 r, r, t; \n\t" // conditionally overwrite lsbs + "mov.b32 %0, r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise sum with unsigned saturation +} + +static __device__ __forceinline__ unsigned int vavgs4(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vavrg4.s32.s32.s32 %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + // avgs (a + b) = ((a + b) < 0) ? ((a + b) >> 1) : ((a + b + 1) >> 1). The + // two expressions can be re-written as follows to avoid needing additional + // intermediate bits: ((a + b) >> 1) = (a >> 1) + (b >> 1) + ((a & b) & 1), + // ((a + b + 1) >> 1) = (a >> 1) + (b >> 1) + ((a | b) & 1). The difference + // between the two is ((a ^ b) & 1). Note that if (a + b) < 0, then also + // ((a + b) >> 1) < 0, since right shift rounds to negative infinity. This + // means we can compute ((a + b) >> 1) then conditionally add ((a ^ b) & 1) + // depending on the sign bit of the shifted sum. By handling the msb sum + // bit of the result separately, we avoid carry-out during summation and + // also can use (potentially faster) logical right shifts. + asm ("{ \n\t" + ".reg .u32 a,b,c,r,s,t,u,v;\n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "and.b32 u,a,0xfefefefe;\n\t" // prevent shift crossing chunk boundary + "and.b32 v,b,0xfefefefe;\n\t" // prevent shift crossing chunk boundary + "xor.b32 s,a,b; \n\t" // a ^ b + "and.b32 t,a,b; \n\t" // a & b + "shr.u32 u,u,1; \n\t" // a >> 1 + "shr.u32 v,v,1; \n\t" // b >> 1 + "and.b32 c,s,0x01010101;\n\t" // (a ^ b) & 1 + "and.b32 s,s,0x80808080;\n\t" // extract msb (a ^ b) + "and.b32 t,t,0x01010101;\n\t" // (a & b) & 1 + "add.u32 r,u,v; \n\t" // (a>>1)+(b>>1) + "add.u32 r,r,t; \n\t" // (a>>1)+(b>>1)+(a&b&1); rec. msb cy-in + "xor.b32 r,r,s; \n\t" // compute msb sum bit: a ^ b ^ cy-in + "shr.u32 t,r,7; \n\t" // sign ((a + b) >> 1) + "not.b32 t,t; \n\t" // ~sign ((a + b) >> 1) + "and.b32 t,t,c; \n\t" // ((a ^ b) & 1) & ~sign ((a + b) >> 1) + "add.u32 r,r,t; \n\t" // conditionally add ((a ^ b) & 1) + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise average of signed integers +} + +static __device__ __forceinline__ unsigned int vavgu4(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vavrg4.u32.u32.u32 %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + // HAKMEM #23: a + b = 2 * (a | b) - (a ^ b) ==> + // (a + b + 1) / 2 = (a | b) - ((a ^ b) >> 1) + c = a ^ b; + r = a | b; + c = c & 0xfefefefe; // ensure following shift doesn't cross byte boundaries + c = c >> 1; + r = r - c; +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise average of unsigned integers +} + +static __device__ __forceinline__ unsigned int vhaddu4(unsigned int a, unsigned int b) +{ + // HAKMEM #23: a + b = 2 * (a & b) + (a ^ b) ==> + // (a + b) / 2 = (a & b) + ((a ^ b) >> 1) + unsigned int r, s; + s = a ^ b; + r = a & b; + s = s & 0xfefefefe; // ensure following shift doesn't cross byte boundaries + s = s >> 1; + s = r + s; + return s; // byte-wise average of unsigned integers, rounded down +} + +static __device__ __forceinline__ unsigned int vcmpeq4(unsigned int a, unsigned int b) +{ + unsigned int c, r; +#if __CUDA_ARCH__ >= 300 + r = 0; + asm ("vset4.u32.u32.eq %0,%1,%2,%3;" : "=r"(c) : "r"(a), "r"(b), "r"(r)); + r = c << 8; // convert bool + r = r - c; // to mask +#else /* __CUDA_ARCH__ >= 300 */ + // inspired by Alan Mycroft's null-byte detection algorithm: + // null_byte(x) = ((x - 0x01010101) & (~x & 0x80808080)) + r = a ^ b; // 0x00 if a == b + c = r | 0x80808080; // set msbs, to catch carry out + r = r ^ c; // extract msbs, msb = 1 if r < 0x80 + c = c - 0x01010101; // msb = 0, if r was 0x00 or 0x80 + c = r & ~c; // msb = 1, if r was 0x00 +#if __CUDA_ARCH__ >= 200 + asm ("prmt.b32 %0,%1,0,0xba98;" : "=r"(r) : "r"(c));// convert msbs to mask +#else /* __CUDA_ARCH__ >= 200 */ + asm ("shr.u32 %0,%1,7;" : "=r"(r) : "r"(c)); // convert + asm ("sub.u32 %0,%1,%0;" : "+r"(r) : "r"(c)); // msbs to + asm ("or.b32 %0,%1,%0;" : "+r"(r) : "r"(c)); // mask +#endif /* __CUDA_ARCH__ >= 200 */ +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise (un)signed eq comparison with mask result +} + +static __device__ __forceinline__ unsigned int vcmpges4(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset4.s32.s32.ge %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 8; // convert bool + r = c - r; // to mask +#else /* __CUDA_ARCH__ >= 300 */ + asm ("{ \n\t" + ".reg .u32 a, b, r, s, t, u;\n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "xor.b32 s,a,b; \n\t" // a ^ b + "or.b32 r,a,0x80808080;\n\t" // set msbs + "and.b32 t,b,0x7f7f7f7f;\n\t" // clear msbs + "sub.u32 r,r,t; \n\t" // subtract lsbs, msb: ~borrow-in + "xor.b32 t,r,a; \n\t" // msb: ~borrow-in ^ a + "xor.b32 r,r,s; \n\t" // msb: ~sign(res) = a^b^~borrow-in + "and.b32 t,t,s; \n\t" // msb: ovfl= (~bw-in ^ a) & (a ^ b) + "xor.b32 t,t,r; \n\t" // msb: ge = ovfl != ~sign(res) +#if __CUDA_ARCH__ >= 200 + "prmt.b32 r,t,0,0xba98; \n\t" // build mask from msbs +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 t,t,0x80808080;\n\t" // isolate msbs = ovfl + "shr.u32 r,t,7; \n\t" // build mask + "sub.u32 r,t,r; \n\t" // from + "or.b32 r,r,t; \n\t" // msbs +#endif /* __CUDA_ARCH__ >= 200 */ + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise signed gt-eq comparison with mask result +} + +static __device__ __forceinline__ unsigned int vcmpgeu4(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset4.u32.u32.ge %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 8; // convert bool + r = c - r; // to mask +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(b)); + c = vavgu4 (a, b); // (a + ~b + 1) / 2 = (a - b) / 2 +#if __CUDA_ARCH__ >= 200 + asm ("prmt.b32 %0,%1,0,0xba98;" : "=r"(r) : "r"(c));// build mask from msbs +#else /* __CUDA_ARCH__ >= 200 */ + asm ("and.b32 %0,%0,0x80808080;" : "+r"(c)); // msb = carry-outs + asm ("shr.u32 %0,%1,7;" : "=r"(r) : "r"(c)); // build mask + asm ("sub.u32 %0,%1,%0;" : "+r"(r) : "r"(c)); // from + asm ("or.b32 %0,%1,%0;" : "+r"(r) : "r"(c)); // msbs +#endif /* __CUDA_ARCH__ >= 200 */ +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise unsigned gt-eq comparison with mask result +} + +static __device__ __forceinline__ unsigned int vcmpgts4(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset4.s32.s32.gt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 8; // convert bool + r = c - r; // to mask +#else /* __CUDA_ARCH__ >= 300 */ + /* a <= b <===> a + ~b < 0 */ + asm ("{ \n\t" + ".reg .u32 a,b,r,s,t,u; \n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "not.b32 b,b; \n\t" + "and.b32 r,a,0x7f7f7f7f;\n\t" // clear msbs + "and.b32 t,b,0x7f7f7f7f;\n\t" // clear msbs + "xor.b32 s,a,b; \n\t" // sum bits = (a ^ b) + "add.u32 r,r,t; \n\t" // capture msb carry-in in bit 7 + "xor.b32 t,a,r; \n\t" // a ^ carry_in + "not.b32 u,s; \n\t" // ~(a ^ b) + "and.b32 t,t,u; \n\t" // msb: ovfl = (a ^ carry_in) & ~(a^b) + "xor.b32 r,r,u; \n\t" // msb: ~result = (~(a ^ b) ^ carry_in) + "xor.b32 t,t,r; \n\t" // msb: gt = ovfl != sign(~res) +#if __CUDA_ARCH__ >= 200 + "prmt.b32 r,t,0,0xba98; \n\t" // build mask from msbs +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 t,t,0x80808080;\n\t" // isolate msbs + "shr.u32 r,t,7; \n\t" // build mask + "sub.u32 r,t,r; \n\t" // from + "or.b32 r,r,t; \n\t" // msbs +#endif /* __CUDA_ARCH__ >= 200 */ + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise signed gt comparison with mask result +} + +static __device__ __forceinline__ unsigned int vcmpgtu4(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset4.u32.u32.gt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 8; // convert bool + r = c - r; // to mask +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(b)); + c = vhaddu4 (a, b); // (a + ~b) / 2 = (a - b) / 2 [rounded down] +#if __CUDA_ARCH__ >= 200 + asm ("prmt.b32 %0,%1,0,0xba98;" : "=r"(r) : "r"(c));// build mask from msbs +#else /* __CUDA_ARCH__ >= 200 */ + asm ("and.b32 %0,%0,0x80808080;" : "+r"(c)); // msb = carry-outs + asm ("shr.u32 %0,%1,7;" : "=r"(r) : "r"(c)); // build mask + asm ("sub.u32 %0,%1,%0;" : "+r"(r) : "r"(c)); // from + asm ("or.b32 %0,%1,%0;" : "+r"(r) : "r"(c)); // msbs +#endif /* __CUDA_ARCH__ >= 200 */ +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise unsigned gt comparison with mask result +} + +static __device__ __forceinline__ unsigned int vcmples4(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset4.s32.s32.le %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 8; // convert bool + r = c - r; // to mask +#else /* __CUDA_ARCH__ >= 300 */ + /* a <= b <===> a + ~b < 0 */ + asm ("{ \n\t" + ".reg .u32 a,b,r,s,t,u; \n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "not.b32 u,b; \n\t" // ~b + "and.b32 r,a,0x7f7f7f7f;\n\t" // clear msbs + "and.b32 t,u,0x7f7f7f7f;\n\t" // clear msbs + "xor.b32 u,a,b; \n\t" // sum bits = (a ^ b) + "add.u32 r,r,t; \n\t" // capture msb carry-in in bit 7 + "xor.b32 t,a,r; \n\t" // a ^ carry_in + "not.b32 s,u; \n\t" // ~(a ^ b) + "and.b32 t,t,u; \n\t" // msb: ovfl = (a ^ carry_in) & (a ^ b) + "xor.b32 r,r,s; \n\t" // msb: result = (a ^ ~b ^ carry_in) + "xor.b32 t,t,r; \n\t" // msb: le = ovfl != sign(res) +#if __CUDA_ARCH__ >= 200 + "prmt.b32 r,t,0,0xba98; \n\t" // build mask from msbs +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 t,t,0x80808080;\n\t" // isolate msbs + "shr.u32 r,t,7; \n\t" // build mask + "sub.u32 r,t,r; \n\t" // from + "or.b32 r,r,t; \n\t" // msbs +#endif /* __CUDA_ARCH__ >= 200 */ + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise signed lt-eq comparison with mask result +} + +static __device__ __forceinline__ unsigned int vcmpleu4(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset4.u32.u32.le %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 8; // convert bool + r = c - r; // to mask +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(a)); + c = vavgu4 (a, b); // (b + ~a + 1) / 2 = (b - a) / 2 +#if __CUDA_ARCH__ >= 200 + asm ("prmt.b32 %0,%1,0,0xba98;" : "=r"(r) : "r"(c));// build mask from msbs +#else /* __CUDA_ARCH__ >= 200 */ + asm ("and.b32 %0,%0,0x80808080;" : "+r"(c)); // msb = carry-outs + asm ("shr.u32 %0,%1,7;" : "=r"(r) : "r"(c)); // build mask + asm ("sub.u32 %0,%1,%0;" : "+r"(r) : "r"(c)); // from + asm ("or.b32 %0,%1,%0;" : "+r"(r) : "r"(c)); // msbs +#endif /* __CUDA_ARCH__ >= 200 */ +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise unsigned lt-eq comparison with mask result +} + +static __device__ __forceinline__ unsigned int vcmplts4(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset4.s32.s32.lt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 8; // convert bool + r = c - r; // to mask +#else /* __CUDA_ARCH__ >= 300 */ + asm ("{ \n\t" + ".reg .u32 a, b, r, s, t, u;\n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "not.b32 u,b; \n\t" // ~b + "xor.b32 s,u,a; \n\t" // a ^ ~b + "or.b32 r,a,0x80808080;\n\t" // set msbs + "and.b32 t,b,0x7f7f7f7f;\n\t" // clear msbs + "sub.u32 r,r,t; \n\t" // subtract lsbs, msb: ~borrow-in + "xor.b32 t,r,a; \n\t" // msb: ~borrow-in ^ a + "not.b32 u,s; \n\t" // msb: ~(a^~b) + "xor.b32 r,r,s; \n\t" // msb: res = a ^ ~b ^ ~borrow-in + "and.b32 t,t,u; \n\t" // msb: ovfl= (~bw-in ^ a) & ~(a^~b) + "xor.b32 t,t,r; \n\t" // msb: lt = ovfl != sign(res) +#if __CUDA_ARCH__ >= 200 + "prmt.b32 r,t,0,0xba98; \n\t" // build mask from msbs +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 t,t,0x80808080;\n\t" // isolate msbs + "shr.u32 r,t,7; \n\t" // build mask + "sub.u32 r,t,r; \n\t" // from + "or.b32 r,r,t; \n\t" // msbs +#endif /* __CUDA_ARCH__ >= 200 */ + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise signed lt comparison with mask result +} + +static __device__ __forceinline__ unsigned int vcmpltu4(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset4.u32.u32.lt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 8; // convert bool + r = c - r; // to mask +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(a)); + c = vhaddu4 (a, b); // (b + ~a) / 2 = (b - a) / 2 [rounded down] +#if __CUDA_ARCH__ >= 200 + asm ("prmt.b32 %0,%1,0,0xba98;" : "=r"(r) : "r"(c));// build mask from msbs +#else /* __CUDA_ARCH__ >= 200 */ + asm ("and.b32 %0,%0,0x80808080;" : "+r"(c)); // msb = carry-outs + asm ("shr.u32 %0,%1,7;" : "=r"(r) : "r"(c)); // build mask + asm ("sub.u32 %0,%1,%0;" : "+r"(r) : "r"(c)); // from + asm ("or.b32 %0,%1,%0;" : "+r"(r) : "r"(c)); // msbs +#endif /* __CUDA_ARCH__ >= 200 */ +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise unsigned lt comparison with mask result +} + +static __device__ __forceinline__ unsigned int vcmpne4(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset4.u32.u32.ne %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); + c = r << 8; // convert bool + r = c - r; // to mask +#else /* __CUDA_ARCH__ >= 300 */ + // inspired by Alan Mycroft's null-byte detection algorithm: + // null_byte(x) = ((x - 0x01010101) & (~x & 0x80808080)) + r = a ^ b; // 0x00 if a == b + c = r | 0x80808080; // set msbs, to catch carry out + c = c - 0x01010101; // msb = 0, if r was 0x00 or 0x80 + c = r | c; // msb = 1, if r was not 0x00 +#if __CUDA_ARCH__ >= 200 + asm ("prmt.b32 %0,%1,0,0xba98;" : "=r"(r) : "r"(c));// build mask from msbs +#else /* __CUDA_ARCH__ >= 200 */ + asm ("and.b32 %0,%0,0x80808080;" : "+r"(c)); // extract msbs + asm ("shr.u32 %0,%1,7;" : "=r"(r) : "r"(c)); // build mask + asm ("sub.u32 %0,%1,%0;" : "+r"(r) : "r"(c)); // from + asm ("or.b32 %0,%1,%0;" : "+r"(r) : "r"(c)); // msbs +#endif /* __CUDA_ARCH__ >= 200 */ +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise (un)signed ne comparison with mask result +} + +static __device__ __forceinline__ unsigned int vabsdiffu4(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm ("vabsdiff4.u32.u32.u32 %0,%1,%2,%3;" : "=r"(r) :"r"(a),"r"(b),"r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + s = vcmpgeu4 (a, b);// mask = 0xff if a >= b + r = a ^ b; // + s = (r & s) ^ b; // select a when a >= b, else select b => max(a,b) + r = s ^ r; // select a when b >= a, else select b => min(a,b) + r = s - r; // |a - b| = max(a,b) - min(a,b); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise absolute difference of unsigned integers +} + +static __device__ __forceinline__ unsigned int vmaxs4(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm ("vmax4.s32.s32.s32 %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + s = vcmpges4 (a, b);// mask = 0xff if a >= b + r = a & s; // select a when b >= a + s = b & ~s; // select b when b < a + r = r | s; // combine byte selections +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise maximum of signed integers +} + +static __device__ __forceinline__ unsigned int vmaxu4(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm ("vmax4.u32.u32.u32 %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + s = vcmpgeu4 (a, b);// mask = 0xff if a >= b + r = a & s; // select a when b >= a + s = b & ~s; // select b when b < a + r = r | s; // combine byte selections +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise maximum of unsigned integers +} + +static __device__ __forceinline__ unsigned int vmins4(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm ("vmin4.s32.s32.s32 %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + s = vcmpges4 (b, a);// mask = 0xff if a >= b + r = a & s; // select a when b >= a + s = b & ~s; // select b when b < a + r = r | s; // combine byte selections +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise minimum of signed integers +} + +static __device__ __forceinline__ unsigned int vminu4(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm ("vmin4.u32.u32.u32 %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + s = vcmpgeu4 (b, a);// mask = 0xff if a >= b + r = a & s; // select a when b >= a + s = b & ~s; // select b when b < a + r = r | s; // combine byte selections +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise minimum of unsigned integers +} +static __device__ __forceinline__ unsigned int vseteq4(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset4.u32.u32.eq %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + // inspired by Alan Mycroft's null-byte detection algorithm: + // null_byte(x) = ((x - 0x01010101) & (~x & 0x80808080)) + r = a ^ b; // 0x00 if a == b + c = r | 0x80808080; // set msbs, to catch carry out + r = r ^ c; // extract msbs, msb = 1 if r < 0x80 + c = c - 0x01010101; // msb = 0, if r was 0x00 or 0x80 + c = r & ~c; // msb = 1, if r was 0x00 + r = c >> 7; // convert to bool +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise (un)signed eq comparison with bool result +} + +static __device__ __forceinline__ unsigned int vsetles4(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset4.s32.s32.le %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + /* a <= b <===> a + ~b < 0 */ + asm ("{ \n\t" + ".reg .u32 a,b,r,s,t,u; \n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "not.b32 u,b; \n\t" // ~b + "and.b32 r,a,0x7f7f7f7f;\n\t" // clear msbs + "and.b32 t,u,0x7f7f7f7f;\n\t" // clear msbs + "xor.b32 u,a,b; \n\t" // sum bits = (a ^ b) + "add.u32 r,r,t; \n\t" // capture msb carry-in in bit 7 + "xor.b32 t,a,r; \n\t" // a ^ carry_in + "not.b32 s,u; \n\t" // ~(a ^ b) + "and.b32 t,t,u; \n\t" // msb: ovfl = (a ^ carry_in) & (a ^ b) + "xor.b32 r,r,s; \n\t" // msb: result = (a ^ ~b ^ carry_in) + "xor.b32 t,t,r; \n\t" // msb: le = ovfl != sign(res) + "and.b32 t,t,0x80808080;\n\t" // isolate msbs + "shr.u32 r,t,7; \n\t" // convert to bool + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise signed lt-eq comparison with bool result +} + +static __device__ __forceinline__ unsigned int vsetleu4(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset4.u32.u32.le %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(a)); + c = vavgu4 (a, b); // (b + ~a + 1) / 2 = (b - a) / 2 + c = c & 0x80808080; // msb = carry-outs + r = c >> 7; // convert to bool +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise unsigned lt-eq comparison with bool result +} + +static __device__ __forceinline__ unsigned int vsetlts4(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset4.s32.s32.lt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + asm ("{ \n\t" + ".reg .u32 a, b, r, s, t, u;\n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "not.b32 u,b; \n\t" // ~b + "or.b32 r,a,0x80808080;\n\t" // set msbs + "and.b32 t,b,0x7f7f7f7f;\n\t" // clear msbs + "xor.b32 s,u,a; \n\t" // a ^ ~b + "sub.u32 r,r,t; \n\t" // subtract lsbs, msb: ~borrow-in + "xor.b32 t,r,a; \n\t" // msb: ~borrow-in ^ a + "not.b32 u,s; \n\t" // msb: ~(a^~b) + "xor.b32 r,r,s; \n\t" // msb: res = a ^ ~b ^ ~borrow-in + "and.b32 t,t,u; \n\t" // msb: ovfl= (~bw-in ^ a) & ~(a^~b) + "xor.b32 t,t,r; \n\t" // msb: lt = ovfl != sign(res) + "and.b32 t,t,0x80808080;\n\t" // isolate msbs + "shr.u32 r,t,7; \n\t" // convert to bool + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise signed lt comparison with bool result +} + +static __device__ __forceinline__ unsigned int vsetltu4(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset4.u32.u32.lt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(a)); + c = vhaddu4 (a, b); // (b + ~a) / 2 = (b - a) / 2 [rounded down] + c = c & 0x80808080; // msb = carry-outs + r = c >> 7; // convert to bool +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise unsigned lt comparison with bool result +} + +static __device__ __forceinline__ unsigned int vsetges4(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset4.s32.s32.ge %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + asm ("{ \n\t" + ".reg .u32 a, b, r, s, t, u;\n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "xor.b32 s,a,b; \n\t" // a ^ b + "or.b32 r,a,0x80808080;\n\t" // set msbs + "and.b32 t,b,0x7f7f7f7f;\n\t" // clear msbs + "sub.u32 r,r,t; \n\t" // subtract lsbs, msb: ~borrow-in + "xor.b32 t,r,a; \n\t" // msb: ~borrow-in ^ a + "xor.b32 r,r,s; \n\t" // msb: ~sign(res) = a^b^~borrow-in + "and.b32 t,t,s; \n\t" // msb: ovfl= (~bw-in ^ a) & (a ^ b) + "xor.b32 t,t,r; \n\t" // msb: ge = ovfl != ~sign(res) + "and.b32 t,t,0x80808080;\n\t" // isolate msbs + "shr.u32 r,t,7; \n\t" // convert to bool + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise signed gt-eq comparison with bool result +} + +static __device__ __forceinline__ unsigned int vsetgeu4(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset4.u32.u32.ge %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(b)); + c = vavgu4 (a, b); // (a + ~b + 1) / 2 = (a - b) / 2 + c = c & 0x80808080; // msb = carry-outs + r = c >> 7; // convert to bool +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise unsigned gt-eq comparison with bool result +} + +static __device__ __forceinline__ unsigned int vsetgts4(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vset4.s32.s32.gt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + /* a <= b <===> a + ~b < 0 */ + asm ("{ \n\t" + ".reg .u32 a,b,r,s,t,u; \n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "not.b32 b,b; \n\t" + "and.b32 r,a,0x7f7f7f7f;\n\t" // clear msbs + "and.b32 t,b,0x7f7f7f7f;\n\t" // clear msbs + "xor.b32 s,a,b; \n\t" // sum bits = (a ^ b) + "add.u32 r,r,t; \n\t" // capture msb carry-in in bit 7 + "xor.b32 t,a,r; \n\t" // a ^ carry_in + "not.b32 u,s; \n\t" // ~(a ^ b) + "and.b32 t,t,u; \n\t" // msb: ovfl = (a ^ carry_in) & ~(a^b) + "xor.b32 r,r,u; \n\t" // msb: ~result = (~(a ^ b) ^ carry_in) + "xor.b32 t,t,r; \n\t" // msb: gt = ovfl != sign(~res) + "and.b32 t,t,0x80808080;\n\t" // isolate msbs + "shr.u32 r,t,7; \n\t" // convert to bool + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise signed gt comparison with mask result +} + +static __device__ __forceinline__ unsigned int vsetgtu4(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset4.u32.u32.gt %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + asm ("not.b32 %0,%0;" : "+r"(b)); + c = vhaddu4 (a, b); // (a + ~b) / 2 = (a - b) / 2 [rounded down] + c = c & 0x80808080; // msb = carry-outs + r = c >> 7; // convert to bool +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise unsigned gt comparison with bool result +} + +static __device__ __forceinline__ unsigned int vsetne4(unsigned int a, unsigned int b) +{ + unsigned int r, c; +#if __CUDA_ARCH__ >= 300 + c = 0; + asm ("vset4.u32.u32.ne %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + // inspired by Alan Mycroft's null-byte detection algorithm: + // null_byte(x) = ((x - 0x01010101) & (~x & 0x80808080)) + r = a ^ b; // 0x00 if a == b + c = r | 0x80808080; // set msbs, to catch carry out + c = c - 0x01010101; // msb = 0, if r was 0x00 or 0x80 + c = r | c; // msb = 1, if r was not 0x00 + c = c & 0x80808080; // extract msbs + r = c >> 7; // convert to bool +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise (un)signed ne comparison with bool result +} + +static __device__ __forceinline__ unsigned int vsadu4(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm("vabsdiff4.u32.u32.u32.add %0,%1,%2,%3;":"=r"(r):"r"(a),"r"(b),"r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + r = vabsdiffu4 (a, b); + s = r >> 8; + r = (r & 0x00ff00ff) + (s & 0x00ff00ff); + r = ((r << 16) + r) >> 16; +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise sum of absol. differences of unsigned ints +} + +static __device__ __forceinline__ unsigned int vsub4(unsigned int a, unsigned int b) +{ +#if __CUDA_ARCH__ >= 300 + unsigned int r, c = 0; + asm ("vsub4.u32.u32.u32 %0,%1,%2,%3;" : "=r"(r) : "r"(a), "r"(b), "r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + unsigned int r, s, t; + s = a ^ ~b; // inverted sum bits + r = a | 0x80808080; // set msbs + t = b & 0x7f7f7f7f; // clear msbs + s = s & 0x80808080; // inverted msb sum bits + r = r - t; // subtract w/o msbs, record inverted borrows in msb + r = r ^ s; // combine inverted msb sum bits and borrows +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise difference +} + +static __device__ __forceinline__ unsigned int vsubss4(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vsub4.s32.s32.s32.sat %0,%1,%2,%3;" : "=r"(r) :"r"(a),"r"(b),"r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + /* + For signed saturation, saturation is controlled by the overflow signal: + ovfl = (borrow-in to msb) XOR (borrow-out from msb). Overflow can only + occur when the msbs of both inputs are differemt. The defined response to + overflow is to deliver 0x7f when the addends are positive (bit 7 clear), + and 0x80 when the addends are negative (bit 7 set). The truth table for + the msb is + + a b bw_in res bw_out ovfl a^~bw_in ~(a^~b) (a^~bw_in)&~(a^~b) + --------------------------------------------------------------------- + 0 0 0 0 0 0 1 0 0 + 0 0 1 1 1 0 0 0 0 + 0 1 0 1 1 1 1 1 1 + 0 1 1 0 1 0 0 1 0 + 1 0 0 1 0 0 0 1 0 + 1 0 1 0 0 1 1 1 1 + 1 1 0 0 0 0 0 0 0 + 1 1 1 1 1 0 1 0 0 + + The seven low-order bits can be handled by wrapping subtraction with the + borrow-out from bit 6 recorded in the msb (thus corresponding to the + bw_in in the truth table for the msb above). ovfl can be computed in many + equivalent ways, here we use ovfl = (a ^ ~borrow_in) & ~(a ^~b) since we + already need to compute (a ^~b) and ~borrow-in for the msb result bit + computation. First we compute the normal, wrapped subtraction result. + When overflow is detected, we mask off the result's msb, then compute a + mask covering the seven low order bits, which are all set to 1. This sets + the byte to 0x7f as we previously cleared the msb. In the overflow case, + the sign of the result matches the sign of input a, so we extract the + sign of a and add it to the low order bits, which turns 0x7f into 0x80, + the correct result for an overflowed negative result. + */ + asm ("{ \n\t" + ".reg .u32 a,b,r,s,t,u,v,w; \n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "not.b32 u,b; \n\t" // ~b + "xor.b32 s,u,a; \n\t" // a ^ ~b + "or.b32 r,a,0x80808080;\n\t" // set msbs + "and.b32 t,b,0x7f7f7f7f;\n\t" // clear msbs + "sub.u32 r,r,t; \n\t" // subtract lsbs, msb: ~borrow-in + "xor.b32 t,r,a; \n\t" // msb: ~borrow-in ^ a + "not.b32 u,s; \n\t" // msb: ~(a^~b) + "and.b32 s,s,0x80808080;\n\t" // msb: a ^ ~b + "xor.b32 r,r,s; \n\t" // msb: res = a ^ ~b ^ ~borrow-in + "and.b32 t,t,u; \n\t" // msb: ovfl= (~bw-in ^ a) & ~(a^~b) +#if __CUDA_ARCH__ >= 200 + "prmt.b32 s,a,0,0xba98; \n\t" // sign(a) ? 0xff : 0 + "xor.b32 s,s,0x7f7f7f7f;\n\t" // sign(a) ? 0x80 : 0x7f + "prmt.b32 t,t,0,0xba98; \n\t" // ovfl ? 0xff : 0 + "and.b32 s,s,t; \n\t" // ovfl ? (sign(a) ? 0x80:0x7f) : 0 + "not.b32 t,t; \n\t" // ~ovfl + "and.b32 r,r,t; \n\t" // ovfl ? 0 : a + b + "or.b32 r,r,s; \n\t" // ovfl ? (sign(a) ? 0x80:0x7f) :a+b +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 t,t,0x80808080;\n\t" // ovfl ? 0x80 : 0 + "shr.u32 s,t,7; \n\t" // ovfl ? 1 : 0 + "not.b32 u,t; \n\t" // ovfl ? 0x7f : 0xff + "and.b32 r,r,u; \n\t" // ovfl ? (a - b) & 0x7f : a - b + "and.b32 u,a,t; \n\t" // ovfl ? a & 0x80 : 0 + "sub.u32 t,t,s; \n\t" // ovfl ? 0x7f : 0 + "shr.u32 u,u,7; \n\t" // ovfl ? sign(a) : 0 + "or.b32 r,r,t; \n\t" // ovfl ? 0x7f : a - b + "add.u32 r,r,u; \n\t" // ovfl ? 0x7f+sign(a) : a - b +#endif /* __CUDA_ARCH__ >= 200 */ + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a), "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise difference with signed saturation +} + +static __device__ __forceinline__ unsigned int vsubus4(unsigned int a, unsigned int b) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int c = 0; + asm ("vsub4.u32.u32.u32.sat %0,%1,%2,%3;" : "=r"(r) :"r"(a),"r"(b),"r"(c)); +#else /* __CUDA_ARCH__ >= 300 */ + // This code uses the same basic approach used for the non-saturating + // subtraction. The seven low-order bits in each byte are subtracted by + // regular subtraction with the inverse of the borrow-out from bit 6 (= + // inverse of borrow-in for the msb) being recorded in bit 7, while the + // msb is handled separately. + // + // Clamping to 0 needs happens when there is a borrow-out from the msb. + // This is simply accomplished by ANDing the normal addition result with + // a mask based on the inverted msb borrow-out: ~borrow-out ? 0xff : 0x00. + // The borrow-out information is generated from the msb. Since we already + // have the msb's ~borrow-in and (a^~b) available from the computation of + // the msb result bit, the most efficient way to compute msb ~borrow-out + // is: ((a ^ ~b) & ~borrow-in) | (~b & a). The truth table for the msb is + // + // a b bw-in res ~bw-out a^~b (a^~b)&~bw-in (a&~b) ((a^~b)&~bw-in)|(a&~b) + // + // 0 0 0 0 1 1 1 0 1 + // 0 0 1 1 0 1 0 0 0 + // 0 1 0 1 0 0 0 0 0 + // 0 1 1 0 0 0 0 0 0 + // 1 0 0 1 1 0 0 1 1 + // 1 0 1 0 1 0 0 1 1 + // 1 1 0 0 1 1 1 0 1 + // 1 1 1 1 0 1 0 0 0 + // + asm ("{ \n\t" + ".reg .u32 a,b,r,s,t,u; \n\t" + "mov.b32 a,%1; \n\t" + "mov.b32 b,%2; \n\t" + "not.b32 u,b; \n\t" // ~b + "xor.b32 s,u,a; \n\t" // a ^ ~b + "and.b32 u,u,a; \n\t" // a & ~b + "or.b32 r,a,0x80808080;\n\t" // set msbs + "and.b32 t,b,0x7f7f7f7f;\n\t" // clear msbs + "sub.u32 r,r,t; \n\t" // subtract lsbs, msb: ~borrow-in + "and.b32 t,r,s; \n\t" // msb: (a ^ ~b) & ~borrow-in + "and.b32 s,s,0x80808080;\n\t" // msb: a ^ ~b + "xor.b32 r,r,s; \n\t" // msb: res = a ^ ~b ^ ~borrow-in + "or.b32 t,t,u; \n\t" // msb: bw-out = ((a^~b)&~bw-in)|(a&~b) +#if __CUDA_ARCH__ >= 200 + "prmt.b32 t,t,0,0xba98; \n\t" // ~borrow-out ? 0xff : 0 +#else /* __CUDA_ARCH__ >= 200 */ + "and.b32 t,t,0x80808080;\n\t" // isolate msb: ~borrow-out + "shr.u32 s,t,7; \n\t" // build mask + "sub.u32 s,t,s; \n\t" // from + "or.b32 t,t,s; \n\t" // msb +#endif /* __CUDA_ARCH__ >= 200 */ + "and.b32 r,r,t; \n\t" // cond. clear result if msb borrow-out + "mov.b32 %0,r; \n\t" + "}" + : "=r"(r) : "r"(a) , "r"(b)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise difference with unsigned saturation +} + +static __device__ __forceinline__ unsigned int vneg4(unsigned int a) +{ + return vsub4 (0, a);// byte-wise negation with wrap-around +} + +static __device__ __forceinline__ unsigned int vnegss4(unsigned int a) +{ + unsigned int r; +#if __CUDA_ARCH__ >= 300 + unsigned int s = 0; + asm ("vsub4.s32.s32.s32.sat %0,%1,%2,%3;" : "=r"(r) :"r"(s),"r"(a),"r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + r = vsub4 (0, a); // + asm ("{ \n\t" + ".reg .u32 a, r, s; \n\t" + "mov.b32 r,%0; \n\t" + "mov.b32 a,%1; \n\t" + "and.b32 a,a,0x80808080;\n\t" // extract msb + "and.b32 s,a,r; \n\t" // wrap-around if msb set in a and -a + "shr.u32 s,s,7; \n\t" // msb ? 1 : 0 + "sub.u32 r,r,s; \n\t" // subtract 1 if result wrapped around + "mov.b32 %0,r; \n\t" + "}" + : "+r"(r) : "r"(a)); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise negation with signed saturation +} + +static __device__ __forceinline__ unsigned int vabsdiffs4(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm ("vabsdiff4.s32.s32.s32 %0,%1,%2,%3;" : "=r"(r) :"r"(a),"r"(b),"r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + s = vcmpges4 (a, b);// mask = 0xff if a >= b + r = a ^ b; // + s = (r & s) ^ b; // select a when a >= b, else select b => max(a,b) + r = s ^ r; // select a when b >= a, else select b => min(a,b) + r = vsub4 (s, r); // |a - b| = max(a,b) - min(a,b); +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise absolute difference of signed integers +} + +static __device__ __forceinline__ unsigned int vsads4(unsigned int a, unsigned int b) +{ + unsigned int r, s; +#if __CUDA_ARCH__ >= 300 + s = 0; + asm("vabsdiff4.s32.s32.s32.add %0,%1,%2,%3;":"=r"(r):"r"(a),"r"(b),"r"(s)); +#else /* __CUDA_ARCH__ >= 300 */ + r = vabsdiffs4 (a, b); + s = r >> 8; + r = (r & 0x00ff00ff) + (s & 0x00ff00ff); + r = ((r << 16) + r) >> 16; +#endif /* __CUDA_ARCH__ >= 300 */ + return r; // byte-wise sum of absolute differences of signed ints +} + +#endif /* SIMD_FUNCTIONS_H__ */ diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/makefile b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/makefile new file mode 100644 index 0000000000000000000000000000000000000000..0b29f229d87f33ba8c99c7ae9ae3a1a023539277 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/makefile @@ -0,0 +1,147 @@ +# COMPILATION EXAMPLES +# -------------------- +# make gregions +# make checksum +# make swg_ref_2b_integer_gpu squery=100 scandidate=120 +# +# EXECUTION EXAMPLES: +# --------------------- +# bin/benchmark_swg_cpu data/1K-100nt.prof.1000.100.21.regions +# bin/bench_swg_ref_2b_integer_gpu_100 data/1K-100nt.prof.1000.100.21.ref.regions data/profiles/hsapiens_v37.fa + +squery?=100 +scandidate?=120 + +# Shell interpreter # +##################### +SHELL := /bin/bash + +# Compilers # +############## +NVCC=nvcc +CC=gcc + +# CPU flags # +############## +CFLAGS=-O3 -m64 +LFLAGS= + +# CUDA flags # +############## +CUDA_FLAGS=-O3 -m64 -gencode arch=compute_35,code=sm_35 +CUDA_LIBRARY_FLAGS=-L/usr/local/cuda/lib64 -I/usr/local/cuda/include -lcuda -lcudart + +# DEBUG FLAGS # +############### +GCC_GDB_FLAGS=-g -O0 -m64 +NVCC_GDB_FLAGS=-g -G -O0 -m64 -gencode arch=compute_35,code=sm_35 + +all: gregions checksum \ +benchmark_swg_cpu benchmark_swg_farrar_gpu benchmark_swg_wozniak_gpu benchmark_swg_2b_integer_gpu \ +benchmark_swg_2b_video_gpu benchmark_swg_2b_mixed_gpu benchmark_swg_2b_mixedsim_gpu \ +benchmark_swg_ref_2b_integer_gpu swg_ref_2b_host-dbg swg_ref_2b_integer_gpu-dbg \ +benchmark_swg_ref_2b_integer_gpu-dbg + +# MODULES: +alignments: + $(CC) $(CFLAGS) -c src/psa_alignments.c -o build/psa_alignments.o +errors: + $(CC) $(CFLAGS) -c src/psa_errors.c -o build/psa_errors.o +profile: + $(CC) $(CFLAGS) -c src/psa_profile.c -o build/psa_profile.o +regions: + $(CC) $(CFLAGS) -c src/psa_regions.c -o build/psa_regions.o +sequences: + $(CC) $(CFLAGS) -c src/psa_sequences.c -o build/psa_sequences.o +time: + $(CC) $(CFLAGS) -c src/psa_time.c -o build/psa_time.o -lrt + +# BUILDERS: +gregions: alignments errors profile regions sequences + $(CC) $(CFLAGS) build/psa_alignments.o build/psa_errors.o build/psa_profile.o build/psa_regions.o build/psa_sequences.o tools/genRegions.c -o bin/gregions + +# CHECKERS: +checksum: + $(CC) $(CFLAGS) tools/checksum.c -o bin/checksum + + +# SWG VERSIONS: +swg_cpu: + $(CC) $(CFLAGS) -c src/gotoh/psa_swgotoh_cpu.c -o build/psa_swg_cpu.o +swg_2b_host: + $(CC) $(CFLAGS) -DCUDA -c src/gotoh/psa_swgotoh_2b_gpu.c -o build/psa_swg_2b_host.o $(CUDA_LIBRARY_FLAGS) +swg_ref_2b_host: + $(CC) $(CFLAGS) -DCUDA -c src/gotoh/psa_swgotoh_ref_2b_gpu.c -o build/psa_swg_ref_2b_host.o $(CUDA_LIBRARY_FLAGS) +swfarrar_gpu: + $(CC) $(CFLAGS) -DCUDA -c src/gotoh/misc/psa_swfarrar_gpu.c -o build/psa_swfarrar_host.o $(CUDA_LIBRARY_FLAGS) + $(NVCC) $(CUDA_FLAGS) -DCUDA -DQUERIES_SIZE=$(squery) -DCANDIDATES_SIZE=$(scandidate) -c src/gotoh/misc/psa_swfarrar_gpu.cu -o build/psa_swfarrar_device.o +swwozniak_gpu: + $(CC) $(CFLAGS) -DCUDA -c src/gotoh/misc/psa_swwozniak_gpu.c -o build/psa_swwozniak_host.o $(CUDA_LIBRARY_FLAGS) + $(NVCC) $(CUDA_FLAGS) -DCUDA -DQUERIES_SIZE=$(squery) -DCANDIDATES_SIZE=$(scandidate) -c src/gotoh/misc/psa_swwozniak_gpu.cu -o build/psa_swwozniak_device.o +swg_2b_integer_gpu: + $(NVCC) $(CUDA_FLAGS) -Xptxas -dlcm=ca -DCUDA -DQUERIES_SIZE=$(squery) -DCANDIDATES_SIZE=$(scandidate) -c src/gotoh/psa_swgotoh_2b_integer_gpu.cu -o build/psa_swg_2b_integer_device.o +swg_2b_video_gpu: + $(NVCC) $(CUDA_FLAGS) -Xptxas -dlcm=ca -DCUDA -DQUERIES_SIZE=$(squery) -DCANDIDATES_SIZE=$(scandidate) -c src/gotoh/psa_swgotoh_2b_video_gpu.cu -o build/psa_swg_2b_video_device.o +swg_2b_mixed_gpu: + $(NVCC) $(CUDA_FLAGS) -Xptxas -dlcm=ca -DCUDA -DQUERIES_SIZE=$(squery) -DCANDIDATES_SIZE=$(scandidate) -c src/gotoh/psa_swgotoh_2b_mixed_gpu.cu -o build/psa_swg_2b_mixed_device.o +swg_2b_mixedsim_gpu: + $(NVCC) $(CUDA_FLAGS) -Xptxas -dlcm=ca -DCUDA -DQUERIES_SIZE=$(squery) -DCANDIDATES_SIZE=$(scandidate) -c src/gotoh/psa_swgotoh_2b_mixedsim_gpu.cu -o build/psa_swg_2b_mixedsim_device.o +swg_ref_2b_integer_gpu: + $(NVCC) $(CUDA_FLAGS) -Xptxas -dlcm=ca -DCUDA -DQUERIES_SIZE=$(squery) -DCANDIDATES_SIZE=$(scandidate) -DREFERENCE -c src/gotoh/psa_swgotoh_ref_2b_integer_gpu.cu -o build/psa_swg_ref_2b_integer_device.o + + + +## BENCHMARKS VERSIONS: +benchmark_swg_cpu: alignments errors profile regions sequences swg_cpu time + $(CC) $(CFLAGS) build/psa_alignments.o build/psa_errors.o build/psa_profile.o build/psa_regions.o build/psa_sequences.o build/psa_swg_cpu.o build/psa_time.o tools/benchmark.c -o bin/benchmark_swg_cpu -lrt +benchmark_swg_farrar_gpu: alignments errors profile regions sequences swfarrar_gpu time + $(CC) $(CFLAGS) -DCUDA build/psa_alignments.o build/psa_errors.o build/psa_profile.o build/psa_regions.o build/psa_sequences.o build/psa_swfarrar_host.o build/psa_swfarrar_device.o build/psa_time.o tools/benchmark.c -o bin/benchmark_swfarrar_gpu_$(squery) $(CUDA_LIBRARY_FLAGS) +benchmark_swg_wozniak_gpu: alignments errors profile regions sequences swwozniak_gpu time + $(CC) $(CFLAGS) -DCUDA build/psa_alignments.o build/psa_errors.o build/psa_profile.o build/psa_regions.o build/psa_sequences.o build/psa_swwozniak_host.o build/psa_swwozniak_device.o build/psa_time.o tools/benchmark.c -o bin/benchmark_swwozniak_gpu_$(squery) $(CUDA_LIBRARY_FLAGS) +benchmark_swg_2b_integer_gpu: alignments errors profile regions sequences swg_2b_host swg_2b_integer_gpu time + $(CC) $(CFLAGS) -DCUDA build/psa_alignments.o build/psa_errors.o build/psa_profile.o build/psa_regions.o build/psa_sequences.o build/psa_swg_2b_host.o build/psa_swg_2b_integer_device.o build/psa_time.o tools/benchmark.c -o bin/bench_swg_2b_integer_gpu_$(squery) $(CUDA_LIBRARY_FLAGS) +benchmark_swg_2b_video_gpu: alignments errors profile regions sequences swg_2b_host swg_2b_video_gpu time + $(CC) $(CFLAGS) -DCUDA build/psa_alignments.o build/psa_errors.o build/psa_profile.o build/psa_regions.o build/psa_sequences.o build/psa_swg_2b_host.o build/psa_swg_2b_video_device.o build/psa_time.o tools/benchmark.c -o bin/bench_swg_2b_video_gpu_$(squery) $(CUDA_LIBRARY_FLAGS) +benchmark_swg_2b_mixed_gpu: alignments errors profile regions sequences swg_2b_host swg_2b_mixed_gpu time + $(CC) $(CFLAGS) -DCUDA build/psa_alignments.o build/psa_errors.o build/psa_profile.o build/psa_regions.o build/psa_sequences.o build/psa_swg_2b_host.o build/psa_swg_2b_mixed_device.o build/psa_time.o tools/benchmark.c -o bin/bench_swg_2b_mixed_gpu_$(squery) $(CUDA_LIBRARY_FLAGS) +benchmark_swg_2b_mixedsim_gpu: alignments errors profile regions sequences swg_2b_host swg_2b_mixedsim_gpu time + $(CC) $(CFLAGS) -DCUDA build/psa_alignments.o build/psa_errors.o build/psa_profile.o build/psa_regions.o build/psa_sequences.o build/psa_swg_2b_host.o build/psa_swg_2b_mixedsim_device.o build/psa_time.o tools/benchmark.c -o bin/bench_swg_2b_mixedsim_gpu_$(squery) $(CUDA_LIBRARY_FLAGS) +benchmark_swg_ref_2b_integer_gpu: alignments errors profile regions sequences swg_ref_2b_host swg_ref_2b_integer_gpu time + $(CC) $(CFLAGS) -DCUDA -DREFERENCE build/psa_alignments.o build/psa_errors.o build/psa_profile.o build/psa_regions.o build/psa_sequences.o build/psa_swg_ref_2b_host.o build/psa_swg_ref_2b_integer_device.o build/psa_time.o tools/benchmark.c -o bin/bench_swg_ref_2b_integer_gpu_$(squery) $(CUDA_LIBRARY_FLAGS) + + + +# DEBUG # +###################### + +# DEBUG SWG VERSIONS: +alignments-dbg: + $(CC) $(GCC_GDB_FLAGS) -c src/psa_alignments.c -o build/psa_alignments-dbg.o +errors-dbg: + $(CC) $(GCC_GDB_FLAGS) -c src/psa_errors.c -o build/psa_errors-dbg.o +profile-dbg: + $(CC) $(GCC_GDB_FLAGS) -c src/psa_profile.c -o build/psa_profile-dbg.o +regions-dbg: + $(CC) $(GCC_GDB_FLAGS) -c src/psa_regions.c -o build/psa_regions-dbg.o +sequences-dbg: + $(CC) $(GCC_GDB_FLAGS) -c src/psa_sequences.c -o build/psa_sequences-dbg.o +time-dbg: + $(CC) $(GCC_GDB_FLAGS) -c src/psa_time.c -o build/psa_time-dbg.o -lrt + +## DEBUG BENCHMARKS VERSIONS: +swg_ref_2b_host-dbg: + $(CC) $(GCC_GDB_FLAGS) -DCUDA -c src/gotoh/psa_swgotoh_ref_2b_gpu.c -o build/psa_swg_ref_2b_host-dbg.o $(CUDA_LIBRARY_FLAGS) +swg_ref_2b_integer_gpu-dbg: + $(NVCC) $(NVCC_GDB_FLAGS) -lineinfo -Xptxas -dlcm=ca -DCUDA -DQUERIES_SIZE=$(squery) -DCANDIDATES_SIZE=$(scandidate) -c src/gotoh/psa_swgotoh_ref_2b_integer_gpu.cu -o build/psa_swg_ref_2b_integer_device-dbg.o + +benchmark_swg_ref_2b_integer_gpu-dbg: alignments-dbg errors-dbg profile-dbg regions-dbg sequences-dbg swg_ref_2b_host-dbg swg_ref_2b_integer_gpu-dbg time-dbg + $(CC) $(GCC_GDB_FLAGS) -DCUDA -DREFERENCE build/psa_alignments-dbg.o build/psa_errors-dbg.o build/psa_profile-dbg.o build/psa_regions-dbg.o build/psa_sequences-dbg.o build/psa_swg_ref_2b_host-dbg.o build/psa_swg_ref_2b_integer_device-dbg.o build/psa_time-dbg.o tools/benchmark.c -o bin/bench_swg_ref_2b_integer_gpu_$(squery)-dbg $(CUDA_LIBRARY_FLAGS) + + +# INSTALL # +###################### + +clean: + rm build/* + rm bin/* + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swfarrar_gpu.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swfarrar_gpu.c new file mode 100644 index 0000000000000000000000000000000000000000..7d735c9a80345749ab1cb712abbd305fceb68700 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swfarrar_gpu.c @@ -0,0 +1,119 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swfarrar_gpu + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Host functions for the SW-Gotoh GPU implementation + * using a farrar approach. Paralelizing by columns. + */ + +#include "../../../include/psa_pairwise.h" +#include "../../../include/psa_pairwise_gpu.h" +#include +#include + +#define WORD_SIZE 32 + +#define MATCH_SCORE 2 +#define MISMATCH_SCORE -5 +#define OPEN_INDEL_SCORE -2 +#define EXTEND_INDEL_SCORE -1 + +#define MAX3(a,b,c) ((a >= b) ? ((a >= c) ? a : c) : ((b >= c) ? b : c)) + +#define BUILD_ALGORITHM "SW-GOTOH FARRAR (LOCAL ALIGNMENT)" +#define BUILD_VERSION "GPU VERSION 32bits per cell" +#define BUILD_TAG "farrar.32b.tc.gpu" + +#define CUDA_ERROR(error) (HandleError(error, __FILE__, __LINE__ )) + +static void HandleError( cudaError_t err, const char *file, int32_t line ) { + if (err != cudaSuccess) { + printf( "%s in %s at line %d\n", cudaGetErrorString(err), file, line ); + exit( EXIT_FAILURE ); + } +} + +char* buildTag() +{ + return (BUILD_TAG); +} + +psaError_t printBuildInfo() +{ + printf("%s \n", BUILD_ALGORITHM); + printf("%s \n", BUILD_VERSION); + printf("CONFIG - MATCH: %d, MISMATCH: %d, INDEL_OPEN: %d, INDEL_EXTEND %d\n", + MATCH_SCORE, MISMATCH_SCORE, OPEN_INDEL_SCORE, EXTEND_INDEL_SCORE); + printf("Build: %s - %s \n", __DATE__, __TIME__ ); + + return (SUCCESS); +} + +psaError_t transformDataQueries(sequences_t *queries) +{ + uint32_t idBase; + + for (idBase = 0; idBase < queries->numASCIIEntries; ++idBase) + queries->h_ASCII[idBase] = ASCIItoUpperCase(queries->h_ASCII[idBase]); + + queries->formats |= SEQ_ASCII; + + return (SUCCESS); +} + +psaError_t transformDataCandidates(sequences_t *candidates) +{ + uint32_t idBase; + + for (idBase = 0; idBase < candidates->numASCIIEntries; ++idBase) + candidates->h_ASCII[idBase] = ASCIItoUpperCase(candidates->h_ASCII[idBase]); + + candidates->formats |= SEQ_ASCII; + + return (SUCCESS); +} + +psaError_t transferCPUtoGPUStream(sequences_t *queries, sequences_t *candidates, alignments_t *alignments) +{ + //allocate & transfer Queries to GPU + CUDA_ERROR(cudaMalloc((void**)&queries->d_ASCII, queries->numASCIIEntries * sizeof(ASCIIEntry_t))); + CUDA_ERROR(cudaMemcpy(queries->d_ASCII, queries->h_ASCII, queries->numASCIIEntries * sizeof(ASCIIEntry_t), cudaMemcpyHostToDevice)); + + CUDA_ERROR(cudaMalloc((void**)&queries->d_ASCIIposition, queries->num * sizeof(uint32_t))); + CUDA_ERROR(cudaMemcpy(queries->d_ASCIIposition, queries->h_ASCIIposition, queries->num * sizeof(uint32_t), cudaMemcpyHostToDevice)); + + + //allocate & transfer FMIndex to GPU + CUDA_ERROR(cudaMalloc((void**)&candidates->d_ASCII, candidates->numASCIIEntries * sizeof(ASCIIEntry_t))); + CUDA_ERROR(cudaMemcpy(candidates->d_ASCII, candidates->h_ASCII, candidates->numASCIIEntries * sizeof(ASCIIEntry_t), cudaMemcpyHostToDevice)); + + CUDA_ERROR(cudaMalloc((void**)&candidates->d_ASCIIposition, candidates->num * sizeof(uint32_t))); + CUDA_ERROR(cudaMemcpy(candidates->d_ASCIIposition, candidates->h_ASCIIposition, candidates->num * sizeof(uint32_t), cudaMemcpyHostToDevice)); + + + //allocate & initialize Results + CUDA_ERROR(cudaMalloc((void**)&alignments->d_info, alignments->num * sizeof(alignmentInfo_t))); + CUDA_ERROR(cudaMemcpy(alignments->d_info, alignments->h_info, alignments->num * sizeof(alignmentInfo_t), cudaMemcpyHostToDevice)); + + CUDA_ERROR(cudaMalloc((void**)&alignments->d_results, alignments->num * sizeof(alignmentEntry_t))); + CUDA_ERROR(cudaMemset(alignments->d_results, 0, alignments->num * sizeof(alignmentEntry_t))); + + return (SUCCESS); +} + +psaError_t transferGPUtoCPU(alignments_t *alignments) +{ + CUDA_ERROR(cudaMemcpy(alignments->h_results, alignments->d_results, alignments->num * sizeof(alignmentEntry_t), cudaMemcpyDeviceToHost)); + + return (SUCCESS); +} + +psaError_t processPairwiseStream(sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + return(localProcessPairwiseStream(candidates, queries, alignments)); +} + + + + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swfarrar_gpu.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swfarrar_gpu.cu new file mode 100644 index 0000000000000000000000000000000000000000..9342ae6dade610979e81a5d6ffcd306e4ccc114c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swfarrar_gpu.cu @@ -0,0 +1,200 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swfarrar_gpu + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Device functions for the SW-Gotoh GPU implementation + * using a farrar approach. Paralelizing by columns. + * The implementation is warp-wide using shuffle instructions. + */ + +extern "C" { +#include "../../../include/psa_pairwise_gpu.h" +} +#include +#include + +#define MATCH_SCORE 2 +#define MISMATCH_SCORE -5 +#define OPEN_INDEL_SCORE -2 +#define EXTEND_INDEL_SCORE -1 + +#ifndef QUERIES_SIZE + #define QUERIES_SIZE 100 +#endif + +#ifndef CANDIDATES_SIZE + #define CANDIDATES_SIZE 120 +#endif + +#define MAX3(a,b,c) (MAX(MAX(a, b), c)) + +#define WARP_SIZE 32 +#define MAX_THREADS_PER_SM 128 +#define CUDA_NUM_THREADS 128 + +#define THREADS_PER_SEGMENT 32 +#define NUM_SEGMENTS (DIV_CEIL(QUERIES_SIZE, THREADS_PER_SEGMENT)) +#define NUM_SW_PER_BLOCK (MAX_THREADS_PER_SM / THREADS_PER_SEGMENT) +#define NUM_WARPS (MAX_THREADS_PER_SM / WARP_SIZE) + + + + +//inline __device__ int32_t reduce_max(int32_t values, int32_t localThreadIdx) +inline __device__ int32_t reduce_max(int32_t values) +{ + //TODO: Remember the maximal ROW (reduce using KEY and VALUE) + //const int32_t SEGMENTS_PER_WARP = 1; + for (int i = 1; i < THREADS_PER_SEGMENT; i *= 2){ + int n = __shfl_down(values, i, 32); + values = MAX(n, values); + } + //values = __shfl(values, ((localThreadIdx % SEGMENTS_PER_WARP) * THREADS_PER_SEGMENT)); + return(values); +} + +__global__ +void localProcessSWFarrar(ASCIIEntry_t *d_CandidatesASCII, uint32_t *d_CandidatesASCIIposition, + ASCIIEntry_t *d_QueriesASCII, uint32_t *d_QueriesASCIIposition, + alignmentInfo_t *d_AlignmentsInfo, alignmentEntry_t *d_AlignmentsResults, + uint32_t querySize, uint32_t candidateSize, uint32_t candidatesNum) +{ + const uint32_t idThread = blockIdx.x * MAX_THREADS_PER_SM + threadIdx.x; + const uint32_t idCandidate = idThread / THREADS_PER_SEGMENT; + const uint32_t idThreadLocalSegment = idThread % THREADS_PER_SEGMENT; + + if ((threadIdx.x < MAX_THREADS_PER_SM) && (idCandidate < candidatesNum)) + { + const char* candidate = d_CandidatesASCII + d_CandidatesASCIIposition[idCandidate]; + const char* query = d_QueriesASCII + d_QueriesASCIIposition[d_AlignmentsInfo[idCandidate]]; + + const uint32_t numSegments = DIV_CEIL(querySize, THREADS_PER_SEGMENT); + + int32_t vMaxScore = 0; // Trace the highest score of the whole SW matrix (using a Segment) + int32_t maxScore = 0; // Final maximal score (Scalar value) + int32_t maxColumn = 0; // Final maximal score (Scalar value) + //int32_t maxRow = 0; // Final maximal score (Scalar value) + int32_t tmpMax = 0; + + __shared__ int32_t CTA_pvHStore [THREADS_PER_SEGMENT * NUM_SEGMENTS * NUM_SW_PER_BLOCK]; + __shared__ int32_t CTA_pvHLoad [THREADS_PER_SEGMENT * NUM_SEGMENTS * NUM_SW_PER_BLOCK]; + __shared__ int32_t CTA_pvE [THREADS_PER_SEGMENT * NUM_SEGMENTS * NUM_SW_PER_BLOCK]; + + int32_t *pvHLoad = CTA_pvHLoad + ((THREADS_PER_SEGMENT * NUM_SEGMENTS) * (idCandidate % NUM_SW_PER_BLOCK)); + int32_t *pvHStore = CTA_pvHStore + ((THREADS_PER_SEGMENT * NUM_SEGMENTS) * (idCandidate % NUM_SW_PER_BLOCK)); + int32_t *pvE = CTA_pvE + ((THREADS_PER_SEGMENT * NUM_SEGMENTS) * (idCandidate % NUM_SW_PER_BLOCK)); + + int32_t idColumn, idSegmentCell, idSegment, idColumnCell = idThreadLocalSegment; + + // All is initialized to zero because is local + for (idSegment = 0; idSegment < numSegments; ++idSegment){ + pvHStore[idColumnCell] = 0; + pvHLoad[idColumnCell] = 0; + pvE[idColumnCell] = 0; + idColumnCell += THREADS_PER_SEGMENT; + } + + for (idColumn = 0; idColumn < CANDIDATES_SIZE; ++idColumn) { + const char candidateBase = candidate[idColumn]; + int32_t vE, vF = 0, vW, idColumnCell = idThreadLocalSegment; + //int32_t vRowMax = idThreadLocalSegment; + int32_t *pv = pvHLoad; + vMaxScore = 0; + + // Reads the previous and last vH column value + int32_t vH = pvHStore[(NUM_SEGMENTS - 1) * THREADS_PER_SEGMENT + idThreadLocalSegment]; + + // Shifts the last column value 1 element to the left. + vH = __shfl_down(vH, 1); //ok + vH = (idThreadLocalSegment == THREADS_PER_SEGMENT-1) ? 0 : vH; + + // Swap the 2 H buffers + pvHLoad = pvHStore; + pvHStore = pv; + + // Inner loop to process each query segment + for (idSegment = 0; idSegment < NUM_SEGMENTS; ++idSegment) { + //TODO: discuss include query profile + vW = (candidateBase == query[idColumnCell]) ? MATCH_SCORE : MISMATCH_SCORE; + vW = (idColumnCell < querySize) ? vW : 0; + + //Adds to the vH of the previous column the W(q_i, d_j) value + vH += vW; + + vE = pvE[idColumnCell]; + //Get max from vH, vF and vE + vH = MAX3(vH, vF, vE); + + //Get max from vH, vE and vF + vMaxScore = MAX(vMaxScore, vH); + //vMaxRow = assigned from vMaxScore o vH + + //Save vH values + pvHStore[idColumnCell] = vH; + + // {Calculate new vE_ij value} + vH += OPEN_INDEL_SCORE; + vE += EXTEND_INDEL_SCORE; + pvE[idColumnCell] = MAX(vE, vH); + + //{Calculate new vF_ij value} + vF += EXTEND_INDEL_SCORE; + vF = MAX(vF, vH); + + // Load the next vH value to process + vH = pvHLoad[idColumnCell]; + idColumnCell += THREADS_PER_SEGMENT; + } + + // Lazy_F loop: disallow adjacent insertion and deletion don't update E(i, j) + // Fix all the F dependences contributions (evaluates all the combinations in parallel) + for (idSegmentCell = 0; idSegmentCell < THREADS_PER_SEGMENT; ++idSegmentCell) { + vF = __shfl_down(vF, 1); + vF = (idThreadLocalSegment == THREADS_PER_SEGMENT-1) ? 0 : vF; + idColumnCell = idThreadLocalSegment; + for (idSegment = 0; idSegment < NUM_SEGMENTS; ++idSegment) { + vH = MAX(pvHStore[idColumnCell], vF); + pvHStore[idColumnCell] = vH; + vH += OPEN_INDEL_SCORE; + vF += EXTEND_INDEL_SCORE; + if (__all(vF <= vH)) + goto exit_lazy_f_loop; + //vF += EXTEND_INDEL_SCORE; + idColumnCell += THREADS_PER_SEGMENT; + } + } + + exit_lazy_f_loop: + // Record the max score of current column + tmpMax = reduce_max(vMaxScore); + maxScore = ((idThreadLocalSegment == 0) && (tmpMax >= maxScore)) ? tmpMax : maxScore; + maxColumn = ((idThreadLocalSegment == 0) && (tmpMax >= maxScore)) ? idColumn : maxColumn; + } + + if(idThreadLocalSegment == 0){ + d_AlignmentsResults[idCandidate].score = maxScore; + d_AlignmentsResults[idCandidate].column = 0; + //d_AlignmentsResults[idCandidate].column = maxColumn; + } + } +} + +extern "C" +psaError_t localProcessPairwiseStream(sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + uint32_t alignmentsPerBlock = DIV_CEIL(MAX_THREADS_PER_SM, THREADS_PER_SEGMENT); + uint32_t blocks = DIV_CEIL(candidates->num, alignmentsPerBlock); + uint32_t threads = CUDA_NUM_THREADS; + uint32_t querySize = queries->h_size[0]; + uint32_t candidateSize = candidates->h_size[0]; + + printf("Grid Size: %d, Block Size: %d, Alignments Per Block: %d, Total alignments: %d\n", blocks, threads, alignmentsPerBlock, candidates->num); + localProcessSWFarrar<<>>(candidates->d_ASCII, candidates->d_ASCIIposition, + queries->d_ASCII, queries->d_ASCIIposition, + alignments->d_info, alignments->d_results, + querySize, candidateSize, candidates->num); + + cudaThreadSynchronize(); + + return (SUCCESS); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swgotoh_registers_16b_gpu.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swgotoh_registers_16b_gpu.cu new file mode 100644 index 0000000000000000000000000000000000000000..4248c7bfbb2043739d41d8d763dd378f56bfb47b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swgotoh_registers_16b_gpu.cu @@ -0,0 +1,167 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swgotoh_registers_16b_gpu + * AUTHOR(S): Alejandro Chacon + * Jacopo Pantaleoni + * DESCRIPTION: Device functions for the SW-Gotoh GPU implementation: + * Using a 16 bits of representation per cell and intermediate column. + */ + +extern "C" { +#include "../../../include/psa_pairwise_gpu.h" +} +#include +#include + +#define MATCH_SCORE ((short) 2) +#define MISMATCH_SCORE ((short)-5) +#define OPEN_INDEL_SCORE ((short)-2) +#define EXTEND_INDEL_SCORE ((short)-1) + +#define V4_PACKET1(NUM_A,NUM_B,NUM_C,NUM_D) ((NUM_A << 24) | (NUM_B << 16) | (NUM_C << 8) | NUM_D) +#define V4_PACKET4(NUM) ((NUM << 24) | (NUM << 16) | (NUM << 8) | NUM) + +#ifndef QUERIES_SIZE + #define QUERIES_SIZE 100 +#endif + +#ifndef CANDIDATES_SIZE + #define CANDIDATES_SIZE 120 +#endif + +#define MAX3(a,b,c) (MAX(MAX(a, b), c)) + +#define WARP_SIZE 32 +#define MAX_THREADS_PER_SM 128 +#define CUDA_NUM_THREADS 128 + +#define THREADS_PER_SEGMENT 32 +#define NUM_SW_PER_BLOCK (MAX_THREADS_PER_SM / THREADS_PER_SEGMENT) +#define NUM_WARPS (MAX_THREADS_PER_SM / WARP_SIZE) + +#define BAND_LEN 8 +#define MAX_QUERY_SIZE 200 + +inline __device__ +int32_t max3(const int32_t op1, const int32_t op2, const int32_t op3) +{ + uint32_t r; + asm( " vmax.s32.s32.s32.max %0, %1, %2, %3;" : "=r"(r) : "r"(op1), "r"(op2), "r"(op3) ); + return r; +} + + +inline __device__ +void update_band(int32_t idRow, char q_i, char *ref_cache, int16_t *H_band, int16_t *F_band, + short2 *temp, int16_t *H_maxScore) +{ + int16_t H_diag = H_band[0]; + H_band[0] = temp[idRow].x; + int16_t E = temp[idRow].y; + + #pragma unroll + for (uint32_t j = 1; j <= BAND_LEN; ++j) + { + // update F + const int16_t ftop = F_band[j] + EXTEND_INDEL_SCORE; + const int16_t htop = H_band[j] + OPEN_INDEL_SCORE; + F_band[j] = MAX(ftop, htop); + + // update E + const int16_t eleft = E + EXTEND_INDEL_SCORE; + const int16_t hleft = H_band[j-1] + OPEN_INDEL_SCORE; + E = MAX(eleft, hleft); + + const char r_j = ref_cache[j-1]; + const int16_t W_ij = (r_j == q_i) ? MATCH_SCORE : MISMATCH_SCORE; + const int16_t diagonal = H_diag + W_ij; + const int16_t top = F_band[j]; + const int16_t left = E; + int16_t hi = MAX3(left, top, diagonal); + hi = MAX(hi, (short) 0); + H_diag = H_band[j]; + H_band[j] = hi; + (*H_maxScore) = MAX((*H_maxScore), hi); + } + + // save the last entry of the band + temp[idRow] = make_short2(H_band[BAND_LEN], E); + //(* H_maxScore) = MAX((* H_maxScore), H_band[BAND_LEN]); +} + +__global__ +void localProcessSWTiling(ASCIIEntry_t *d_CandidatesASCII, uint32_t *d_CandidatesASCIIposition, + ASCIIEntry_t *d_QueriesASCII, uint32_t *d_QueriesASCIIposition, + alignmentInfo_t *d_AlignmentsInfo, alignmentEntry_t *d_AlignmentsResults, + uint32_t querySize, uint32_t candidateSize, uint32_t candidatesNum) +{ + const uint32_t idCandidate = blockIdx.x * MAX_THREADS_PER_SM + threadIdx.x; + + if (idCandidate < candidatesNum) + { + const char* candidate = d_CandidatesASCII + d_CandidatesASCIIposition[idCandidate]; + const char* query = d_QueriesASCII + d_QueriesASCIIposition[d_AlignmentsInfo[idCandidate]]; + + short2 temp[MAX_QUERY_SIZE]; + char r_cache[BAND_LEN]; + int16_t H_band[BAND_LEN + 1]; + int16_t F_band[BAND_LEN + 1]; + char q_i; + + const int32_t numRows = querySize, numColumns = candidateSize; + int32_t idColumn, idRow, idBand; + int16_t H_maxScore = 0; + + for(idBand = 0; idBand < MAX_QUERY_SIZE; ++idBand){ + temp[idBand].x = 0; + temp[idBand].y = 0; + } + + // Compute Score SW-GOTOH + for(idColumn = 0; idColumn < numColumns; idColumn += BAND_LEN){ + + // load a block of entries from the reference + #pragma unroll + for (uint32_t idBand = 0; idBand < BAND_LEN; ++idBand) + r_cache[idBand] = candidate[idColumn + idBand]; + + // initialize the first band + #pragma unroll + for (uint32_t idBand = 0; idBand <= BAND_LEN; ++idBand){ + H_band[idBand] = 0; + F_band[idBand] = 0; + } + + for(idRow = 0; idRow < numRows; ++idRow){ + q_i = query[idRow]; + update_band(idRow, q_i, r_cache, H_band, F_band, temp, &H_maxScore); + } + } + + d_AlignmentsResults[idCandidate].score = H_maxScore; + d_AlignmentsResults[idCandidate].column = 0; + //d_AlignmentsResults[idCandidate].column = maxColumn; + } +} + + +extern "C" +psaError_t localProcessPairwiseStream(sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + uint32_t blocks = DIV_CEIL(candidates->num, CUDA_NUM_THREADS); + uint32_t threads = CUDA_NUM_THREADS; + uint32_t querySize = queries->h_size[0]; + uint32_t candidateSize = candidates->h_size[0]; + + cudaThreadSetCacheConfig(cudaFuncCachePreferL1); + + printf("Grid Size: %d, Block Size: %d, Total alignments: %d\n", blocks, threads, candidates->num); + localProcessSWTiling<<>>(candidates->d_ASCII, candidates->d_ASCIIposition, + queries->d_ASCII, queries->d_ASCIIposition, + alignments->d_info, alignments->d_results, + querySize, candidateSize, candidates->num); + + cudaThreadSynchronize(); + + return (SUCCESS); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swgotoh_registers_32b_gpu.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swgotoh_registers_32b_gpu.cu new file mode 100644 index 0000000000000000000000000000000000000000..98306bb4659c401d82ae335116d1d767d4090847 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swgotoh_registers_32b_gpu.cu @@ -0,0 +1,167 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swgotoh_registers_32b_gpu + * AUTHOR(S): Alejandro Chacon + * Jacopo Pantaleoni + * DESCRIPTION: Device functions for the SW-Gotoh GPU implementation: + * Using a 16 bits of representation per cell and intermediate column. + */ + +extern "C" { +#include "../../../include/psa_pairwise_gpu.h" +} +#include +#include + +#define MATCH_SCORE 2 +#define MISMATCH_SCORE -5 +#define OPEN_INDEL_SCORE -2 +#define EXTEND_INDEL_SCORE -1 + +#define V4_PACKET1(NUM_A,NUM_B,NUM_C,NUM_D) ((NUM_A << 24) | (NUM_B << 16) | (NUM_C << 8) | NUM_D) +#define V4_PACKET4(NUM) ((NUM << 24) | (NUM << 16) | (NUM << 8) | NUM) + +#ifndef QUERIES_SIZE + #define QUERIES_SIZE 100 +#endif + +#ifndef CANDIDATES_SIZE + #define CANDIDATES_SIZE 120 +#endif + +#define MAX3(a,b,c) (MAX(MAX(a, b), c)) + +#define WARP_SIZE 32 +#define MAX_THREADS_PER_SM 128 +#define CUDA_NUM_THREADS 128 + +#define THREADS_PER_SEGMENT 32 +#define NUM_SW_PER_BLOCK (MAX_THREADS_PER_SM / THREADS_PER_SEGMENT) +#define NUM_WARPS (MAX_THREADS_PER_SM / WARP_SIZE) + +#define BAND_LEN 8 +#define MAX_QUERY_SIZE 200 + +inline __device__ +int32_t max3(const int32_t op1, const int32_t op2, const int32_t op3) +{ + uint32_t r; + asm( " vmax.s32.s32.s32.max %0, %1, %2, %3;" : "=r"(r) : "r"(op1), "r"(op2), "r"(op3) ); + return r; +} + + +inline __device__ +void update_band(int32_t idRow, char q_i, char *ref_cache, int32_t *H_band, int32_t *F_band, + int2 *temp, int32_t *H_maxScore) +{ + int32_t H_diag = H_band[0]; + H_band[0] = temp[idRow].x; + int32_t E = temp[idRow].y; + + #pragma unroll + for (uint32_t j = 1; j <= BAND_LEN; ++j) + { + // update F + const int32_t ftop = F_band[j] + EXTEND_INDEL_SCORE; + const int32_t htop = H_band[j] + OPEN_INDEL_SCORE; + F_band[j] = MAX(ftop, htop); + + // update E + const int32_t eleft = E + EXTEND_INDEL_SCORE; + const int32_t hleft = H_band[j-1] + OPEN_INDEL_SCORE; + E = MAX(eleft, hleft); + + const int32_t r_j = ref_cache[j-1]; + const int32_t W_ij = (r_j == q_i) ? MATCH_SCORE : MISMATCH_SCORE; + const int32_t diagonal = H_diag + W_ij; + const int32_t top = F_band[j]; + const int32_t left = E; + int32_t hi = MAX3(left, top, diagonal); + hi = MAX(hi, 0); + H_diag = H_band[j]; + H_band[j] = hi; + (*H_maxScore) = MAX((*H_maxScore), hi); + } + + // save the last entry of the band + temp[idRow] = make_int2(H_band[BAND_LEN], E); + //(* H_maxScore) = MAX((* H_maxScore), H_band[BAND_LEN]); +} + +__global__ +void localProcessSWTiling(ASCIIEntry_t *d_CandidatesASCII, uint32_t *d_CandidatesASCIIposition, + ASCIIEntry_t *d_QueriesASCII, uint32_t *d_QueriesASCIIposition, + alignmentInfo_t *d_AlignmentsInfo, alignmentEntry_t *d_AlignmentsResults, + uint32_t querySize, uint32_t candidateSize, uint32_t candidatesNum) +{ + const uint32_t idCandidate = blockIdx.x * MAX_THREADS_PER_SM + threadIdx.x; + + if (idCandidate < candidatesNum) + { + const char* candidate = d_CandidatesASCII + d_CandidatesASCIIposition[idCandidate]; + const char* query = d_QueriesASCII + d_QueriesASCIIposition[d_AlignmentsInfo[idCandidate]]; + + int2 temp[MAX_QUERY_SIZE]; + char r_cache[BAND_LEN]; + int32_t H_band[BAND_LEN + 1]; + int32_t F_band[BAND_LEN + 1]; + char q_i; + + const int32_t numRows = querySize, numColumns = candidateSize; + int32_t idColumn, idRow, idBand; + int32_t H_maxScore = 0; + + for(idBand = 0; idBand < MAX_QUERY_SIZE; ++idBand){ + temp[idBand].x = 0; + temp[idBand].y = 0; + } + + // Compute Score SW-GOTOH + for(idColumn = 0; idColumn < numColumns; idColumn += BAND_LEN){ + + // load a block of entries from the reference + #pragma unroll + for (uint32_t idBand = 0; idBand < BAND_LEN; ++idBand) + r_cache[idBand] = candidate[idColumn + idBand]; + + // initialize the first band + #pragma unroll + for (uint32_t idBand = 0; idBand <= BAND_LEN; ++idBand){ + H_band[idBand] = 0; + F_band[idBand] = 0; /* ? */ + } + + for(idRow = 0; idRow < numRows; ++idRow){ + q_i = query[idRow]; + update_band(idRow, q_i, r_cache, H_band, F_band, temp, &H_maxScore); + } + } + + d_AlignmentsResults[idCandidate].score = H_maxScore; + d_AlignmentsResults[idCandidate].column = 0; + //d_AlignmentsResults[idCandidate].column = maxColumn; + } +} + + +extern "C" +psaError_t localProcessPairwiseStream(sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + uint32_t blocks = DIV_CEIL(candidates->num, CUDA_NUM_THREADS); + uint32_t threads = CUDA_NUM_THREADS; + uint32_t querySize = queries->h_size[0]; + uint32_t candidateSize = candidates->h_size[0]; + + cudaThreadSetCacheConfig(cudaFuncCachePreferL1); + + printf("Grid Size: %d, Block Size: %d, Total alignments: %d\n", blocks, threads, candidates->num); + localProcessSWTiling<<>>(candidates->d_ASCII, candidates->d_ASCIIposition, + queries->d_ASCII, queries->d_ASCIIposition, + alignments->d_info, alignments->d_results, + querySize, candidateSize, candidates->num); + + cudaThreadSynchronize(); + + return (SUCCESS); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swgotoh_registers_tilling_2D_gpu.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swgotoh_registers_tilling_2D_gpu.cu new file mode 100644 index 0000000000000000000000000000000000000000..0f98fac7324f81ca2ec501bc65b5d847e548498a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swgotoh_registers_tilling_2D_gpu.cu @@ -0,0 +1,237 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swgotoh_registers_32b_gpu + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Device functions for the SW-Gotoh GPU implementation: + * (A) Using video instructions to pack 4 SW in the same register + * (B) 2D tilling to reduce the number of accesses (reference / queries / intermediate column) + */ + +extern "C" { +#include "../../../include/psa_pairwise_gpu.h" +} +#include +#include +#include "../../../includes/simd_functions.h" + +#define V4_PACKET1(NUM_A,NUM_B,NUM_C,NUM_D) ((NUM_A << 24) | (NUM_B << 16) | (NUM_C << 8) | NUM_D) +#define V4_PACKET4(NUM) ((NUM << 24) | (NUM << 16) | (NUM << 8) | NUM) + +#ifndef QUERIES_SIZE + #define QUERIES_SIZE 100 +#endif + +#ifndef CANDIDATES_SIZE + #define CANDIDATES_SIZE 120 +#endif + +#define MAX3(a,b,c) (MAX(MAX(a, b), c)) +//#define SCORE(a,b) ((r_j.x == q_i.x) ? MATCH_SCORE : MISMATCH_SCORE) + +#define WARP_SIZE 32 +#define MAX_THREADS_PER_SM 128 +#define CUDA_NUM_THREADS 128 + +#define BAND_LEN 4 +#define VECTOR_ELEMENTS 4 +#define MAX_QUERY_SIZE QUERIES_SIZE + +//typedef char4 score_type; +typedef union { + char4 c4; + uint32_t i; +}score_type; + +typedef char4 score_type2; + + +inline __device__ +int32_t max3(const int32_t op1, const int32_t op2, const int32_t op3) +{ + uint32_t r; + asm( " vmax.s32.s32.s32.max %0, %1, %2, %3;" : "=r"(r) : "r"(op1), "r"(op2), "r"(op3) ); + return r; +} + + +inline __device__ +void update_band(const uint32_t q_i, const uint32_t *ref_cache, uint32_t *H_band, uint32_t *F_band, + uint32_t *H_temp, uint32_t *E_temp, uint32_t *H_maxScore, + const uint32_t MATCH_SCORE, const uint32_t MISMATCH_SCORE, + const uint32_t OPEN_INDEL_SCORE, const uint32_t EXTEND_INDEL_SCORE) +{ + + const uint32_t ZERO = 0; + uint32_t H_diag = H_band[0]; + H_band[0] = (* H_temp); + uint32_t E = (* E_temp); + + #pragma unroll + for (uint32_t j = 1; j <= BAND_LEN; ++j) + { + // update F + const uint32_t ftop = vaddss4(F_band[j], EXTEND_INDEL_SCORE); + const uint32_t htop = vaddss4(H_band[j], OPEN_INDEL_SCORE); + F_band[j] = vmaxs4(ftop, htop); + + // update E + const uint32_t eleft = vaddss4(E, EXTEND_INDEL_SCORE); + + const uint32_t hleft = vaddss4(H_band[j-1], OPEN_INDEL_SCORE); + E = vmaxs4(eleft, hleft); + + // update H + const uint32_t r_j = ref_cache[j-1]; + const uint32_t Eq = vcmpeq4(r_j, q_i); + const uint32_t W_ij = (~Eq & MISMATCH_SCORE) | (Eq & MATCH_SCORE); + const uint32_t diagonal = vaddss4(H_diag, W_ij); + + const uint32_t top = F_band[j]; + const uint32_t left = E; + uint32_t hi = vmaxs4(vmaxs4(left, top), diagonal); + hi = vmaxs4(hi, ZERO); + + H_diag = H_band[j]; + H_band[j] = hi; + (* H_maxScore) = vmaxs4((* H_maxScore), hi); + } + + (* H_temp) = H_band[BAND_LEN]; + (* E_temp) = E; +} + +__global__ +void localProcessSWTiling(ASCIIEntry_t *d_CandidatesASCII, uint32_t *d_CandidatesASCIIposition, + ASCIIEntry_t *d_QueriesASCII, uint32_t *d_QueriesASCIIposition, + alignmentInfo_t *d_AlignmentsInfo, alignmentEntry_t *d_AlignmentsResults, + uint32_t querySize, uint32_t candidateSize, uint32_t candidatesNum) +{ + const uint32_t idCandidate = (blockIdx.x * MAX_THREADS_PER_SM + threadIdx.x) * VECTOR_ELEMENTS; + + //if (idCandidate < candidatesNum) + if (idCandidate < (candidatesNum - 4)) + { + const char* candidate0 = d_CandidatesASCII + d_CandidatesASCIIposition[idCandidate]; + const char* candidate1 = d_CandidatesASCII + d_CandidatesASCIIposition[idCandidate + 1]; + const char* candidate2 = d_CandidatesASCII + d_CandidatesASCIIposition[idCandidate + 2]; + const char* candidate3 = d_CandidatesASCII + d_CandidatesASCIIposition[idCandidate + 3]; + + const char* query0 = d_QueriesASCII + d_QueriesASCIIposition[d_AlignmentsInfo[idCandidate]]; + const char* query1 = d_QueriesASCII + d_QueriesASCIIposition[d_AlignmentsInfo[idCandidate + 1]]; + const char* query2 = d_QueriesASCII + d_QueriesASCIIposition[d_AlignmentsInfo[idCandidate + 2]]; + const char* query3 = d_QueriesASCII + d_QueriesASCIIposition[d_AlignmentsInfo[idCandidate + 3]]; + + const score_type MATCH_SCORE = { 2, 2, 2, 2}; + const score_type MISMATCH_SCORE = {-5,-5,-5,-5}; + const score_type OPEN_INDEL_SCORE = {-2,-2,-2,-2}; + const score_type EXTEND_INDEL_SCORE = {-1,-1,-1,-1}; + const score_type ZERO = { 0, 0, 0, 0}; + + + score_type r_cache[BAND_LEN]; + + score_type H_temp [MAX_QUERY_SIZE]; + score_type E_temp [MAX_QUERY_SIZE]; + + score_type H_band [BAND_LEN + 1]; + score_type F_band [BAND_LEN + 1]; + + const int32_t numRows = querySize, numColumns = candidateSize; + int32_t idColumn, idRow, idBand; + score_type H_maxScore = ZERO; + + for(idBand = 0; idBand < MAX_QUERY_SIZE; ++idBand){ + H_temp[idBand] = ZERO; + E_temp[idBand] = ZERO; + } + + // Compute Score SW-GOTOH + for(idColumn = 0; idColumn < numColumns; idColumn += BAND_LEN){ + + // load a block of entries from the reference + #pragma unroll + for (uint32_t idBand = 0; idBand < BAND_LEN; ++idBand){ + r_cache[idBand].c4.x = candidate0[idColumn + idBand]; + r_cache[idBand].c4.y = candidate1[idColumn + idBand]; + r_cache[idBand].c4.z = candidate2[idColumn + idBand]; + r_cache[idBand].c4.w = candidate3[idColumn + idBand]; + } + + // initialize the first band + #pragma unroll + for (uint32_t idBand = 0; idBand <= BAND_LEN; ++idBand){ + H_band[idBand] = ZERO; + F_band[idBand] = ZERO; + } + + #pragma unroll 1 + for(idRow = 0; idRow < numRows; idRow += 4){ + const uint idTile = idRow / 4; + uint4 H_temp_v4 = ((uint4 *)H_temp)[idTile]; + uint4 E_temp_v4 = ((uint4 *)E_temp)[idTile]; + + const score_type query0_v4 = ((score_type *)query0)[idTile]; + const score_type query1_v4 = ((score_type *)query1)[idTile]; + const score_type query2_v4 = ((score_type *)query2)[idTile]; + const score_type query3_v4 = ((score_type *)query3)[idTile]; + + const score_type q_i0 = {query0_v4.c4.x, query1_v4.c4.x, query2_v4.c4.x, query3_v4.c4.x}; + const score_type q_i1 = {query0_v4.c4.y, query1_v4.c4.y, query2_v4.c4.y, query3_v4.c4.y}; + const score_type q_i2 = {query0_v4.c4.z, query1_v4.c4.z, query2_v4.c4.z, query3_v4.c4.z}; + const score_type q_i3 = {query0_v4.c4.w, query1_v4.c4.w, query2_v4.c4.w, query3_v4.c4.w}; + + { + update_band(q_i0.i, (uint32_t *) r_cache, (uint32_t *) H_band, (uint32_t *) F_band, &H_temp_v4.x, &E_temp_v4.x, &H_maxScore.i, + MATCH_SCORE.i, MISMATCH_SCORE.i, OPEN_INDEL_SCORE.i, EXTEND_INDEL_SCORE.i); + } + { + update_band(q_i1.i, (uint32_t *) r_cache, (uint32_t *) H_band, (uint32_t *) F_band, &H_temp_v4.y, &E_temp_v4.y, &H_maxScore.i, + MATCH_SCORE.i, MISMATCH_SCORE.i, OPEN_INDEL_SCORE.i, EXTEND_INDEL_SCORE.i); + } + { + update_band(q_i2.i, (uint32_t *) r_cache, (uint32_t *) H_band, (uint32_t *) F_band, &H_temp_v4.z, &E_temp_v4.z, &H_maxScore.i, + MATCH_SCORE.i, MISMATCH_SCORE.i, OPEN_INDEL_SCORE.i, EXTEND_INDEL_SCORE.i); + } + { + update_band(q_i3.i, (uint32_t *) r_cache, (uint32_t *) H_band, (uint32_t *) F_band, &H_temp_v4.w, &E_temp_v4.w, &H_maxScore.i, + MATCH_SCORE.i, MISMATCH_SCORE.i, OPEN_INDEL_SCORE.i, EXTEND_INDEL_SCORE.i); + } + + ((uint4 *)H_temp)[idTile] = H_temp_v4; + ((uint4 *)E_temp)[idTile] = E_temp_v4; + } + } + + d_AlignmentsResults[idCandidate].score = H_maxScore.c4.x; + d_AlignmentsResults[idCandidate + 1].score = H_maxScore.c4.y; + d_AlignmentsResults[idCandidate + 2].score = H_maxScore.c4.z; + d_AlignmentsResults[idCandidate + 3].score = H_maxScore.c4.w; + + d_AlignmentsResults[idCandidate].column = 0; + d_AlignmentsResults[idCandidate + 1].column = 0; + d_AlignmentsResults[idCandidate + 2].column = 0; + d_AlignmentsResults[idCandidate + 3].column = 0; + } +} + + +extern "C" +psaError_t localProcessPairwise(sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + uint32_t blocks = DIV_CEIL(DIV_CEIL(candidates->num, VECTOR_ELEMENTS), CUDA_NUM_THREADS); + uint32_t threads = CUDA_NUM_THREADS; + uint32_t querySize = queries->h_size[0]; + uint32_t candidateSize = candidates->h_size[0]; + + cudaThreadSetCacheConfig(cudaFuncCachePreferL1); + + printf("Grid Size: %d, Block Size: %d, Total alignments: %d, BAND_LEN: %d \n", blocks, threads, candidates->num, BAND_LEN); + localProcessSWTiling<<>>(candidates->d_ASCII, candidates->d_ASCIIposition, + queries->d_ASCII, queries->d_ASCIIposition, + alignments->d_info, alignments->d_results, + querySize, candidateSize, candidates->num); + + cudaThreadSynchronize(); + + return (SUCCESS); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swwozniak_gpu.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swwozniak_gpu.c new file mode 100644 index 0000000000000000000000000000000000000000..a81a6166f582173b13ac8e1ec723b95f5e711d59 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swwozniak_gpu.c @@ -0,0 +1,118 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swwozniak_gpu + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Host functions for the SW-Gotoh GPU implementation + * using a wozniak approach. Paralelizing by anti-diagonals. + */ + +#include "../../../include/psa_pairwise.h" +#include "../../../include/psa_pairwise_gpu.h" +#include +#include + +#define WORD_SIZE 32 + +#define MATCH_SCORE 2 +#define MISMATCH_SCORE -5 +#define OPEN_INDEL_SCORE -2 +#define EXTEND_INDEL_SCORE -1 + +#define MAX3(a,b,c) ((a >= b) ? ((a >= c) ? a : c) : ((b >= c) ? b : c)) + +#define BUILD_ALGORITHM "SW-GOTOH WOZNIAK (LOCAL ALIGNMENT)" +#define BUILD_VERSION "GPU VERSION 32bits per cell" +#define BUILD_TAG "wozniak.32b.tc.gpu" + +#define CUDA_ERROR(error) (HandleError(error, __FILE__, __LINE__ )) + +static void HandleError( cudaError_t err, const char *file, int32_t line ) { + if (err != cudaSuccess) { + printf( "%s in %s at line %d\n", cudaGetErrorString(err), file, line ); + exit( EXIT_FAILURE ); + } +} + +char* buildTag() +{ + return (BUILD_TAG); +} + +psaError_t printBuildInfo() +{ + printf("%s \n", BUILD_ALGORITHM); + printf("%s \n", BUILD_VERSION); + printf("CONFIG - MATCH: %d, MISMATCH: %d, INDEL_OPEN: %d, INDEL_EXTEND: %d\n", + MATCH_SCORE, MISMATCH_SCORE, OPEN_INDEL_SCORE, EXTEND_INDEL_SCORE); + printf("Build: %s - %s \n", __DATE__, __TIME__ ); + + return (SUCCESS); +} + +psaError_t transformDataQueries(sequences_t *queries) +{ + uint32_t idBase; + + for (idBase = 0; idBase < queries->numASCIIEntries; ++idBase) + queries->h_ASCII[idBase] = ASCIItoUpperCase(queries->h_ASCII[idBase]); + + queries->formats |= SEQ_ASCII; + + return (SUCCESS); +} + +psaError_t transformDataCandidates(sequences_t *candidates) +{ + uint32_t idBase; + + for (idBase = 0; idBase < candidates->numASCIIEntries; ++idBase) + candidates->h_ASCII[idBase] = ASCIItoUpperCase(candidates->h_ASCII[idBase]); + + candidates->formats |= SEQ_ASCII; + + return (SUCCESS); +} + +psaError_t transferCPUtoGPUStream(sequences_t *queries, sequences_t *candidates, alignments_t *alignments) +{ + //allocate & transfer Queries to GPU + CUDA_ERROR(cudaMalloc((void**)&queries->d_ASCII, queries->numASCIIEntries * sizeof(ASCIIEntry_t))); + CUDA_ERROR(cudaMemcpy(queries->d_ASCII, queries->h_ASCII, queries->numASCIIEntries * sizeof(ASCIIEntry_t), cudaMemcpyHostToDevice)); + + CUDA_ERROR(cudaMalloc((void**)&queries->d_ASCIIposition, queries->num * sizeof(uint32_t))); + CUDA_ERROR(cudaMemcpy(queries->d_ASCIIposition, queries->h_ASCIIposition, queries->num * sizeof(uint32_t), cudaMemcpyHostToDevice)); + + + //allocate & transfer FMIndex to GPU + CUDA_ERROR(cudaMalloc((void**)&candidates->d_ASCII, candidates->numASCIIEntries * sizeof(ASCIIEntry_t))); + CUDA_ERROR(cudaMemcpy(candidates->d_ASCII, candidates->h_ASCII, candidates->numASCIIEntries * sizeof(ASCIIEntry_t), cudaMemcpyHostToDevice)); + + CUDA_ERROR(cudaMalloc((void**)&candidates->d_ASCIIposition, candidates->num * sizeof(uint32_t))); + CUDA_ERROR(cudaMemcpy(candidates->d_ASCIIposition, candidates->h_ASCIIposition, candidates->num * sizeof(uint32_t), cudaMemcpyHostToDevice)); + + + //allocate & initialize Results + CUDA_ERROR(cudaMalloc((void**)&alignments->d_info, alignments->num * sizeof(alignmentInfo_t))); + CUDA_ERROR(cudaMemcpy(alignments->d_info, alignments->h_info, alignments->num * sizeof(alignmentInfo_t), cudaMemcpyHostToDevice)); + + CUDA_ERROR(cudaMalloc((void**)&alignments->d_results, alignments->num * sizeof(alignmentEntry_t))); + CUDA_ERROR(cudaMemset(alignments->d_results, 0, alignments->num * sizeof(alignmentEntry_t))); + + return (SUCCESS); +} + +psaError_t transferGPUtoCPU(alignments_t *alignments) +{ + CUDA_ERROR(cudaMemcpy(alignments->h_results, alignments->d_results, alignments->num * sizeof(alignmentEntry_t), cudaMemcpyDeviceToHost)); + + return (SUCCESS); +} + +psaError_t processPairwiseStream(sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + return(localProcessPairwiseStream(candidates, queries, alignments)); +} + + + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swwozniak_gpu.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swwozniak_gpu.cu new file mode 100644 index 0000000000000000000000000000000000000000..8eb9135ac55ef84a8c0625f8766e76fbaed5a5cc --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/misc/psa_swwozniak_gpu.cu @@ -0,0 +1,231 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swwozniak_gpu + * AUTHOR(S): Alejandro Chacon + * Jacopo Pantaleoni + * DESCRIPTION: Device functions for the SW-Gotoh GPU implementation + * using a wozniak approach. Paralelizing by anti-diagonals. + * The implementation is warp-wide using shuffle instructions. + */ + +extern "C" { +#include "../../../include/psa_pairwise_gpu.h" +} +#include +#include + +#define MATCH_SCORE 2 +#define MISMATCH_SCORE -5 +#define OPEN_INDEL_SCORE -2 +#define EXTEND_INDEL_SCORE -1 + +#ifndef QUERIES_SIZE + #define QUERIES_SIZE 100 +#endif + +#ifndef CANDIDATES_SIZE + #define CANDIDATES_SIZE 120 +#endif + +#define MAX3(a,b,c) ((a >= b) ? ((a >= c) ? a : c) : ((b >= c) ? b : c)) +#define MIN3(a,b,c) ((a < b) ? ((a < c) ? a : c) : ((b < c) ? b : c)) + +#define WARP_SIZE 32 +#define MAX_THREADS_PER_SM 128 +#define CUDA_NUM_THREADS 128 + +#define THREADS_PER_SEGMENT 32 +#define NUM_SEGMENTS (DIV_CEIL(QUERIES_SIZE, THREADS_PER_SEGMENT)) +#define NUM_SW_PER_BLOCK (MAX_THREADS_PER_SM / THREADS_PER_SEGMENT) +#define NUM_WARPS (MAX_THREADS_PER_SM / WARP_SIZE) + + + + +inline __device__ int32_t reduce_max(int32_t values, int32_t column) +{ + //TODO: Remember the maximal ROW (reduce using KEY and VALUE) + for (int i = 1; i < THREADS_PER_SEGMENT; i *= 2){ + //TODO: Pack the 2 values to save 1 SHUFFLE & CMOV ops + int newValue = __shfl_down(values, i, 32); + int newColumn = __shfl_down(column, i, 32); + values = MAX(newValue, values); + column = (newValue >= values) ? newColumn : column; + } + return(values); +} + +__global__ +void localProcessSWWozniak(ASCIIEntry_t *d_CandidatesASCII, uint32_t *d_CandidatesASCIIposition, + ASCIIEntry_t *d_QueriesASCII, uint32_t *d_QueriesASCIIposition, + alignmentInfo_t *d_AlignmentsInfo, alignmentEntry_t *d_AlignmentsResults, + uint32_t querySize, uint32_t candidateSize, uint32_t candidatesNum) +{ + const uint32_t idThread = blockIdx.x * MAX_THREADS_PER_SM + threadIdx.x; + const uint32_t idCandidate = idThread / THREADS_PER_SEGMENT; + const uint32_t idThreadLocalSegment = idThread % THREADS_PER_SEGMENT; + + if ((threadIdx.x < MAX_THREADS_PER_SM) && (idCandidate < candidatesNum)){ + + typedef int32_t score_type; + __shared__ short2 tmpHValues[CANDIDATES_SIZE * NUM_SW_PER_BLOCK]; + short2 *temp = tmpHValues + (CANDIDATES_SIZE * (idCandidate % NUM_WARPS)); + + const char* candidate = d_CandidatesASCII + d_CandidatesASCIIposition[idCandidate]; + const char* query = d_QueriesASCII + d_QueriesASCIIposition[d_AlignmentsInfo[idCandidate]]; + + // local scores + score_type h_top, h_left, h_diag, hi; + score_type e_top, ei; + score_type f_left, fi; + score_type h_maxScore = 0; + uint32_t maxColumn = 0; + + // current reference string character + uint8_t r_j; + + // per-thread cache for temp values and reference string characters + // each thread loads a different value; cache values are shuffled down the warp at each iteration + score_type temp_cache_h, temp_cache_f; + uint8_t reference_cache; + + // width of the current warp-block stripe of the DP matrix (always WARP_SIZE except for the last stripe) + uint32_t warp_block_width; + + // compute warp-block horizontal coordinate in DP matrix for this thread + const uint32_t wi = idThreadLocalSegment + 1; + + // initialize the leftmost matrix column + for(uint32_t i = idThreadLocalSegment; i < CANDIDATES_SIZE; i += WARP_SIZE) + temp[i] = make_short2(0,0); + + for(uint32_t warp_block = 0; warp_block < QUERIES_SIZE; warp_block += WARP_SIZE){ + + // width of this block + warp_block_width = (warp_block + WARP_SIZE >= QUERIES_SIZE ? QUERIES_SIZE % WARP_SIZE : WARP_SIZE); + // compute the horizontal coordinate of the current thread in the DP matrix (including border column) + const uint32_t i = wi + warp_block; + + // set top boundary values + h_top = 0; + e_top = 0; + + // initialize diagonal + h_diag = 0; + + // load the query string character for the current thread + const uint8_t s_i = (i <= QUERIES_SIZE ? query[i - 1] : 0); + + // initialize the best score for this stripe + score_type max_score = 0; + + // loop over all DP anti-diagonals, excluding the border row/column + for(uint32_t block_diag = 2; block_diag <= warp_block_width + CANDIDATES_SIZE; block_diag += WARP_SIZE){ + + // reload caches every WARP_SIZE diagonals + const uint32_t thread_j = (block_diag - 2) + idThreadLocalSegment; + + if (thread_j < CANDIDATES_SIZE){ + temp_cache_h = temp[thread_j].x; + temp_cache_f = temp[thread_j].y; + reference_cache = candidate[(block_diag - 2) + idThreadLocalSegment]; + } else { + temp_cache_h = 0; + temp_cache_f = 0; + reference_cache = 0; + } + + for(uint32_t diag = block_diag; diag < block_diag + WARP_SIZE; diag++){ + + // compute the length of this anti-diagonal (excluding border row/column) + const uint32_t diag_len = MIN3(diag - 1, WARP_SIZE, warp_block_width); + // compute vertical coordinate of the current cell in the DP matrix (including border column) + const uint32_t j = diag - wi; + + // is the current cell inside the DP matrix? + if (wi <= diag_len && j <= CANDIDATES_SIZE){ + if (wi == 1){ + // load new temp and reference values + r_j = reference_cache; + // initialize cell to the left of the current cell + h_left = temp_cache_h; + f_left = temp_cache_f; + } + + // compute the match/mismatch score + const score_type S_ij = (r_j == s_i) ? MATCH_SCORE : MISMATCH_SCORE; + + ei = MAX(e_top + EXTEND_INDEL_SCORE, + h_top + OPEN_INDEL_SCORE); + fi = MAX(f_left + EXTEND_INDEL_SCORE, + h_left + OPEN_INDEL_SCORE); + hi = MAX3(h_diag + S_ij, + ei, + fi); + + // clamp score to zero + hi = MAX(hi, 0); + + // save off the last column + if (wi == WARP_SIZE){ + temp[j - 1] = make_short2( hi, fi ); + // keep track of the best score in this stripe + max_score = MAX( max_score, hi ); + } + + // save the best score across the entire matrix for local scoring + if (hi >= h_maxScore){ + h_maxScore = hi; + maxColumn = j; + //h_alignment = make_uint2(j, i); + } + + // current left becomes diagonal for next iteration on this lane + h_diag = h_left; + + // current value becomes h_top for next iteration on this lane + h_top = hi; + e_top = ei; + } + + // move previous cell reference value across the warp + r_j = __shfl_up(r_j, 1); + // hi becomes h_left on the next lane + h_left = __shfl_up(hi, 1); + f_left = __shfl_up(fi, 1); + + // push temp_cache and reference_cache values down the warp + temp_cache_h = __shfl_down(temp_cache_h, 1); + temp_cache_f = __shfl_down(temp_cache_f, 1); + reference_cache = __shfl_down(reference_cache, 1); + } + } + } + + h_maxScore = reduce_max(h_maxScore, maxColumn); + if(idThreadLocalSegment == 0){ + d_AlignmentsResults[idCandidate].score = h_maxScore; + //d_AlignmentsResults[idCandidate].column = maxColumn; + d_AlignmentsResults[idCandidate].column = 0; //DEBUG + } + } +} + +extern "C" +psaError_t localProcessPairwiseStream(sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + uint32_t alignmentsPerBlock = DIV_CEIL(MAX_THREADS_PER_SM, THREADS_PER_SEGMENT); + uint32_t blocks = DIV_CEIL(candidates->num, alignmentsPerBlock); + uint32_t threads = CUDA_NUM_THREADS; + uint32_t querySize = queries->h_size[0]; + uint32_t candidateSize = candidates->h_size[0]; + + printf("Grid Size: %d, Block Size: %d, Alignments Per Block: %d, Total alignments: %d\n", blocks, threads, alignmentsPerBlock, candidates->num); + localProcessSWWozniak<<>>(candidates->d_ASCII, candidates->d_ASCIIposition, + queries->d_ASCII, queries->d_ASCIIposition, + alignments->d_info, alignments->d_results, + querySize, candidateSize, candidates->num); + cudaThreadSynchronize(); + + return (SUCCESS); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_gpu.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_gpu.c new file mode 100644 index 0000000000000000000000000000000000000000..447f76d7ed11fc13c6374b01037336955d3a54a7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_gpu.c @@ -0,0 +1,150 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swgotoh_2b_gpu + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Host functions for the SW-Gotoh GPU implementation + * Which uses 2 bits per letter. + */ + +#include "../../include/psa_pairwise.h" +#include "../../include/psa_pairwise_gpu.h" +#include +#include + +#define WORD_SIZE 32 + +#define MATCH_SCORE 2 +#define MISMATCH_SCORE -5 +#define OPEN_INDEL_SCORE -2 +#define EXTEND_INDEL_SCORE -1 + +#define MAX3(a,b,c) ((a >= b) ? ((a >= c) ? a : c) : ((b >= c) ? b : c)) + +#define BUILD_ALGORITHM "SW-GOTOH: VIDEO INST. PACKING CANDIDATES (LOCAL ALIGNMENT)" +#define BUILD_VERSION "GPU VERSION 8bits per cell" +#define BUILD_TAG "gotoh.video.8b.gpu" + +#define CUDA_ERROR(error) (HandleError(error, __FILE__, __LINE__ )) + +static void HandleError( cudaError_t err, const char *file, int32_t line ) { + if (err != cudaSuccess) { + printf( "%s in %s at line %d\n", cudaGetErrorString(err), file, line ); + exit( EXIT_FAILURE ); + } +} + +char* buildTag() +{ + return (BUILD_TAG); +} + +psaError_t printBuildInfo() +{ + printf("%s \n", BUILD_ALGORITHM); + printf("%s \n", BUILD_VERSION); + printf("CONFIG - MATCH: %d, MISMATCH: %d, INDEL_OPEN: %d, INDEL_EXTEND %d\n", + MATCH_SCORE, MISMATCH_SCORE, OPEN_INDEL_SCORE, EXTEND_INDEL_SCORE); + printf("Build: %s - %s \n", __DATE__, __TIME__ ); + + return (SUCCESS); +} + +psaError_t transformDataQueries(sequences_t *queries) +{ + uint32_t idQuery, position, size; + uint32_t currentHlfRAWEntry = 0, numHlfRAWEntries; + const uint32_t RAW_BASES_PER_ENTRY = UINT32_LENGTH / RAW_4B_LENGTH; + + queries->numRAWHlfEntries = sequences_totalEntriesHlfRAW(queries->h_size, queries->num, RAW_4B_LENGTH); + + queries->h_HlfRAW = (RAWHlfEntry_t *) malloc(queries->numRAWHlfEntries * sizeof(RAWHlfEntry_t)); + if (queries->h_HlfRAW == NULL) return (E_ALLOCATE_MEM); + + queries->h_HlfRAWposition = (uint32_t *) malloc(queries->num * sizeof(uint32_t)); + if (queries->h_HlfRAWposition == NULL) return (E_ALLOCATE_MEM); + + for (idQuery = 0; idQuery < queries->num; ++idQuery) + { + position = queries->h_ASCIIposition[idQuery]; + size = queries->h_size[idQuery]; + numHlfRAWEntries = DIV_CEIL(size, RAW_BASES_PER_ENTRY); + + sequenceASCIItoRAW_2x32bits(queries->h_ASCII + position, size, queries->h_HlfRAW + currentHlfRAWEntry); + queries->h_HlfRAWposition[idQuery] = currentHlfRAWEntry; + currentHlfRAWEntry += numHlfRAWEntries; + } + + queries->formats |= SEQ_HLF_RAW; + return (SUCCESS); +} + +psaError_t transformDataCandidates(sequences_t *candidates) +{ + uint32_t idCandidate, position, size; + uint32_t currentHlfRAWEntry = 0, numHlfRAWEntries; + const uint32_t RAW_BASES_PER_ENTRY = UINT32_LENGTH / RAW_4B_LENGTH; + + candidates->numRAWHlfEntries = sequences_totalEntriesHlfRAW(candidates->h_size, candidates->num, RAW_4B_LENGTH); + + candidates->h_HlfRAW = (RAWHlfEntry_t *) malloc(candidates->numRAWHlfEntries * sizeof(RAWHlfEntry_t)); + if (candidates->h_HlfRAW == NULL) return (E_ALLOCATE_MEM); + + candidates->h_HlfRAWposition = (uint32_t *) malloc(candidates->num * sizeof(uint32_t)); + if (candidates->h_HlfRAWposition == NULL) return (E_ALLOCATE_MEM); + + for (idCandidate = 0; idCandidate < candidates->num; ++idCandidate) + { + position = candidates->h_ASCIIposition[idCandidate]; + size = candidates->h_size[idCandidate]; + numHlfRAWEntries = DIV_CEIL(size, RAW_BASES_PER_ENTRY); + + sequenceASCIItoRAW_2x32bits(candidates->h_ASCII + position, size, candidates->h_HlfRAW + currentHlfRAWEntry); + candidates->h_HlfRAWposition[idCandidate] = currentHlfRAWEntry; + currentHlfRAWEntry += numHlfRAWEntries; + } + + candidates->formats |= SEQ_HLF_RAW; + return (SUCCESS); +} + +psaError_t transferCPUtoGPUStream(sequences_t *queries, sequences_t *candidates, alignments_t *alignments) +{ + //allocate & transfer Queries to GPU + CUDA_ERROR(cudaMalloc((void**)&queries->d_HlfRAW, queries->numRAWHlfEntries * sizeof(RAWHlfEntry_t))); + CUDA_ERROR(cudaMemcpy(queries->d_HlfRAW, queries->h_HlfRAW, queries->numRAWHlfEntries * sizeof(RAWHlfEntry_t), cudaMemcpyHostToDevice)); + + CUDA_ERROR(cudaMalloc((void**)&queries->d_HlfRAWposition, queries->num * sizeof(uint32_t))); + CUDA_ERROR(cudaMemcpy(queries->d_HlfRAWposition, queries->h_HlfRAWposition, queries->num * sizeof(uint32_t), cudaMemcpyHostToDevice)); + + //allocate & transfer FMIndex to GPU + CUDA_ERROR(cudaMalloc((void**)&candidates->d_HlfRAW, candidates->numRAWHlfEntries * sizeof(RAWHlfEntry_t))); + CUDA_ERROR(cudaMemcpy(candidates->d_HlfRAW, candidates->h_HlfRAW, candidates->numRAWHlfEntries * sizeof(RAWHlfEntry_t), cudaMemcpyHostToDevice)); + + CUDA_ERROR(cudaMalloc((void**)&candidates->d_HlfRAWposition, candidates->num * sizeof(uint32_t))); + CUDA_ERROR(cudaMemcpy(candidates->d_HlfRAWposition, candidates->h_HlfRAWposition, candidates->num * sizeof(uint32_t), cudaMemcpyHostToDevice)); + + //allocate & initialize Results + CUDA_ERROR(cudaMalloc((void**)&alignments->d_info, alignments->num * sizeof(alignmentInfo_t))); + CUDA_ERROR(cudaMemcpy(alignments->d_info, alignments->h_info, alignments->num * sizeof(alignmentInfo_t), cudaMemcpyHostToDevice)); + + CUDA_ERROR(cudaMalloc((void**)&alignments->d_results, alignments->num * sizeof(alignmentEntry_t))); + CUDA_ERROR(cudaMemset(alignments->d_results, 0, alignments->num * sizeof(alignmentEntry_t))); + + return (SUCCESS); +} + +psaError_t transferGPUtoCPU(alignments_t *alignments) +{ + CUDA_ERROR(cudaMemcpy(alignments->h_results, alignments->d_results, alignments->num * sizeof(alignmentEntry_t), cudaMemcpyDeviceToHost)); + + return (SUCCESS); +} + +psaError_t processPairwiseStream(sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + return(localProcessPairwiseStream(candidates, queries, alignments)); +} + + + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_integer_gpu.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_integer_gpu.cu new file mode 100644 index 0000000000000000000000000000000000000000..9c54de271d9561173619084c91307a3d26596172 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_integer_gpu.cu @@ -0,0 +1,177 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swgotoh_2b_integer_gpu + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Device functions for the SW-Gotoh GPU implementation. + * (A) Which uses the 32bit integer resources and store the temporal columns with 8 bits. + * (B) The bases are represented using 2 bits/base. + */ + +extern "C" { +#include "../../include/psa_pairwise_gpu.h" +} +#include +#include + +#ifndef QUERIES_SIZE + #define QUERIES_SIZE 100 +#endif + +#ifndef CANDIDATES_SIZE + #define CANDIDATES_SIZE 120 +#endif + +#define MAX3(a,b,c) (MAX(MAX(a, b), c)) + +#define WARP_SIZE 32 +#define MAX_THREADS_PER_SM 64 +#define CUDA_NUM_THREADS 64 + +#define THREADS_PER_SEGMENT 32 +#define NUM_SW_PER_BLOCK (MAX_THREADS_PER_SM / THREADS_PER_SEGMENT) +#define NUM_WARPS (MAX_THREADS_PER_SM / WARP_SIZE) + +#define BAND_LEN 8 +#define MAX_QUERY_SIZE QUERIES_SIZE +#define RAW_BASES_PER_ENTRY (UINT32_LENGTH / RAW_4B_LENGTH) + +typedef int32_t score_type; +//typedef char2 score_type2; +//typedef int2 score_type2; +typedef short2 score_type2; + +inline __device__ +void update_band(int32_t idRow, char q_i, char *ref_cache, score_type *H_band, score_type *F_band, + score_type2 *temp, score_type *H_maxScore, + const score_type MATCH_SCORE, const score_type MISMATCH_SCORE, + const score_type OPEN_INDEL_SCORE, const score_type EXTEND_INDEL_SCORE) +{ + score_type H_diag = H_band[0]; + H_band[0] = temp[idRow].x; + score_type E = temp[idRow].y; + + #pragma unroll + for (uint32_t j = 1; j <= BAND_LEN; ++j) + { + // update F + const score_type ftop = F_band[j] + EXTEND_INDEL_SCORE; + const score_type htop = H_band[j] + OPEN_INDEL_SCORE; + F_band[j] = MAX(ftop, htop); + + // update E + const score_type eleft = E + EXTEND_INDEL_SCORE; + const score_type hleft = H_band[j-1] + OPEN_INDEL_SCORE; + E = MAX(eleft, hleft); + + const char r_j = ref_cache[j-1]; + const score_type diagonal = (r_j == q_i) ? H_diag + MATCH_SCORE : H_diag + MISMATCH_SCORE; + const score_type top = F_band[j]; + const score_type left = E; + score_type hi = MAX3(left, top, diagonal); + hi = MAX(hi, 0); + H_diag = H_band[j]; + H_band[j] = hi; + (*H_maxScore) = MAX((*H_maxScore), hi); + } + + // save the last entry of the band + temp[idRow] = make_short2(H_band[BAND_LEN], E); +} + +__global__ +void localProcessSWTiling(RAWHlfEntry_t *d_CandidatesHlfRaw, uint32_t *d_CandidatesHlfRAWposition, + RAWHlfEntry_t *d_QueriesHlfRaw, uint32_t *d_QueriesHlfRAWposition, + alignmentInfo_t *d_AlignmentsInfo, alignmentEntry_t *d_AlignmentsResults, + uint32_t querySize, uint32_t candidateSize, uint32_t candidatesNum) +{ + const uint32_t idCandidate = blockIdx.x * MAX_THREADS_PER_SM + threadIdx.x; + + if (idCandidate < candidatesNum) + { + const RAWHlfEntry_t* candidate = d_CandidatesHlfRaw + d_CandidatesHlfRAWposition[idCandidate]; + const RAWHlfEntry_t* query = d_QueriesHlfRaw + d_QueriesHlfRAWposition[d_AlignmentsInfo[idCandidate]]; + + // All the scores have to be absolute numbers: + // Original BWA Scores: Gap_Ex = -1; Gap_Op = -2; Match = 2; Miss = -5; + const score_type MATCH_SCORE = 2; + const score_type MISMATCH_SCORE = -5; + const score_type OPEN_INDEL_SCORE = -2; + const score_type EXTEND_INDEL_SCORE = -1; + const score_type ZERO = 0; + + char r_cache[BAND_LEN]; + score_type2 temp [MAX_QUERY_SIZE]; + score_type H_band [BAND_LEN + 1]; + score_type F_band [BAND_LEN + 1]; + + const int32_t numRows = querySize, numColumns = candidateSize; + int32_t idColumn, idRow, idBand; + score_type H_maxScore = ZERO; + + uint32_t entryCandidate, idCandidateEntry = 0; + + for(idBand = 0; idBand < MAX_QUERY_SIZE; ++idBand){ + temp[idBand].x = ZERO; + temp[idBand].y = ZERO; + } + + // Compute Score SW-GOTOH + for(idColumn = 0; idColumn < numColumns; idColumn += BAND_LEN){ + uint32_t entryQuery, idQueryEntry = 0; + if((idColumn % RAW_BASES_PER_ENTRY) == 0){ + entryCandidate = candidate[idCandidateEntry]; + idCandidateEntry++; + } + + // Load a block of entries from the reference + #pragma unroll + for (uint32_t idBand = 0; idBand < BAND_LEN; ++idBand){ + r_cache[idBand] = entryCandidate & 0x3; + entryCandidate >>= RAW_4B_LENGTH; + } + + // Initialize the first band + #pragma unroll + for (uint32_t idBand = 0; idBand <= BAND_LEN; ++idBand){ + H_band[idBand] = ZERO; + F_band[idBand] = ZERO; + } + + #pragma unroll 4 + for(idRow = 0; idRow < numRows; ++idRow){ + entryQuery >>= RAW_4B_LENGTH; + if((idRow % RAW_BASES_PER_ENTRY) == 0){ + entryQuery = query[idQueryEntry]; + idQueryEntry++; + } + + update_band(idRow, entryQuery & 0x03, r_cache, H_band, F_band, temp, &H_maxScore, + MATCH_SCORE, MISMATCH_SCORE, OPEN_INDEL_SCORE, EXTEND_INDEL_SCORE); + } + } + d_AlignmentsResults[idCandidate].score = H_maxScore; + d_AlignmentsResults[idCandidate].column = 0; + } +} + + +extern "C" +psaError_t localProcessPairwiseStream(sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + uint32_t blocks = DIV_CEIL(candidates->num, CUDA_NUM_THREADS); + uint32_t threads = CUDA_NUM_THREADS; + uint32_t querySize = queries->h_size[0]; + uint32_t candidateSize = candidates->h_size[0]; + + cudaThreadSetCacheConfig(cudaFuncCachePreferL1); + + printf("Grid Size: %d, Block Size: %d, Total alignments: %d, BAND_LEN: %d \n", blocks, threads, candidates->num, BAND_LEN); + localProcessSWTiling<<>>(candidates->d_HlfRAW, candidates->d_HlfRAWposition, + queries->d_HlfRAW, queries->d_HlfRAWposition, + alignments->d_info, alignments->d_results, + querySize, candidateSize, candidates->num); + + cudaThreadSynchronize(); + + return (SUCCESS); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_mixed_gpu.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_mixed_gpu.cu new file mode 100644 index 0000000000000000000000000000000000000000..6804d9b138c7ce85f766e6c5aad6e64b1c1f04d3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_mixed_gpu.cu @@ -0,0 +1,239 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swgotoh_2b_mixed_gpu + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Device functions for the SW-Gotoh GPU implementation using: + * (A) pack 4 SW in the same register mixing integer instructions and video instructions. + * (B) 32bit integer resources + and store the temporal columns with 8 bits. + * (C) bases are represented using 2 bits/base. + */ + +extern "C" { +#include "../../include/psa_pairwise_gpu.h" +} +#include +#include +#include "../../include/simd_functions.h" + +#ifndef QUERIES_SIZE + #define QUERIES_SIZE 100 +#endif + +#ifndef CANDIDATES_SIZE + #define CANDIDATES_SIZE 120 +#endif + +#define MAX3(a,b,c) (MAX(MAX(a, b), c)) + +#define WARP_SIZE 32 +#define MAX_THREADS_PER_SM 64 +#define CUDA_NUM_THREADS 64 + +#define THREADS_PER_SEGMENT 32 +#define NUM_SW_PER_BLOCK (MAX_THREADS_PER_SM / THREADS_PER_SEGMENT) +#define NUM_WARPS (MAX_THREADS_PER_SM / WARP_SIZE) + +#define BAND_LEN 8 +#define VECTOR_ELEMENTS 4 +#define MAX_QUERY_SIZE QUERIES_SIZE +#define BIAS 16 +#define RAW_BASES_PER_ENTRY (UINT32_LENGTH / RAW_4B_LENGTH) + +typedef union { + uchar4 c4; + uint32_t i; +}score_type; + +typedef uchar4 score_type2; + +inline __device__ +uint32_t sim_vmaxu4(uint32_t NUM_A, uint32_t NUM_B){ + return(MAX(NUM_A & 0xFF000000, NUM_B & 0xFF000000) | + MAX(NUM_A & 0x00FF0000, NUM_B & 0x00FF0000) | + MAX(NUM_A & 0x0000FF00, NUM_B & 0x0000FF00) | + MAX(NUM_A & 0x000000FF, NUM_B & 0x000000FF)); +} + + +inline __device__ +void update_band(int32_t idRow, const uint32_t q_i, const uint32_t *ref_cache, uint32_t *H_band, uint32_t *F_band, + uint32_t *H_temp, uint32_t *E_temp, uint32_t *H_maxScore, + const uint32_t MATCH_SCORE, const uint32_t MISMATCH_SCORE, + const uint32_t OPEN_INDEL_SCORE, const uint32_t EXTEND_INDEL_SCORE) +{ + + //Biased Scores to 16 + const uint32_t ZERO = 0x10101010; + uint32_t H_diag = H_band[0]; + H_band[0] = H_temp[idRow]; + uint32_t E = E_temp[idRow]; + + #pragma unroll + for (uint32_t j = 1; j <= BAND_LEN; ++j) + { + // update F + const uint32_t ftop = F_band[j] - EXTEND_INDEL_SCORE; + const uint32_t htop = H_band[j] - OPEN_INDEL_SCORE; + F_band[j] = vmaxu4(ftop, htop); + + // update E + const uint32_t eleft = E - EXTEND_INDEL_SCORE; + const uint32_t hleft = H_band[j-1] - OPEN_INDEL_SCORE; + E = vmaxu4(eleft, hleft); + // update H + const uint32_t r_j = ref_cache[j-1]; + const uint32_t Eq = vcmpeq4(r_j, q_i); + const uint32_t notEq = ~Eq; + const uint32_t diagonal = (notEq & (H_diag - MISMATCH_SCORE)) | (Eq & (H_diag + MATCH_SCORE)); + + const uint32_t top = F_band[j]; + const uint32_t left = E; + uint32_t hi = vmaxu4(vmaxu4(left, top), diagonal); + hi = vmaxu4(hi, ZERO); + + H_diag = H_band[j]; + H_band[j] = hi; + (* H_maxScore) = vmaxu4((* H_maxScore), hi); + } + + H_temp[idRow] = H_band[BAND_LEN]; + E_temp[idRow] = E; +} + +__global__ +void localProcessSWTiling(RAWHlfEntry_t *d_CandidatesHlfRaw, uint32_t *d_CandidatesHlfRAWposition, + RAWHlfEntry_t *d_QueriesHlfRaw, uint32_t *d_QueriesHlfRAWposition, + alignmentInfo_t *d_AlignmentsInfo, alignmentEntry_t *d_AlignmentsResults, + uint32_t querySize, uint32_t candidateSize, uint32_t candidatesNum) +{ + const uint32_t idCandidate = (blockIdx.x * MAX_THREADS_PER_SM + threadIdx.x) * VECTOR_ELEMENTS; + + if (idCandidate < (candidatesNum)) + { + const RAWHlfEntry_t* candidate0 = d_CandidatesHlfRaw + d_CandidatesHlfRAWposition[idCandidate]; + const RAWHlfEntry_t* candidate1 = d_CandidatesHlfRaw + d_CandidatesHlfRAWposition[idCandidate + 1]; + const RAWHlfEntry_t* candidate2 = d_CandidatesHlfRaw + d_CandidatesHlfRAWposition[idCandidate + 2]; + const RAWHlfEntry_t* candidate3 = d_CandidatesHlfRaw + d_CandidatesHlfRAWposition[idCandidate + 3]; + + const RAWHlfEntry_t* query0 = d_QueriesHlfRaw + d_QueriesHlfRAWposition[d_AlignmentsInfo[idCandidate]]; + const RAWHlfEntry_t* query1 = d_QueriesHlfRaw + d_QueriesHlfRAWposition[d_AlignmentsInfo[idCandidate + 1]]; + const RAWHlfEntry_t* query2 = d_QueriesHlfRaw + d_QueriesHlfRAWposition[d_AlignmentsInfo[idCandidate + 2]]; + const RAWHlfEntry_t* query3 = d_QueriesHlfRaw + d_QueriesHlfRAWposition[d_AlignmentsInfo[idCandidate + 3]]; + + // All the scores have to be absolute numbers: + // Original BWA Scores: Gap_Ex = -1; Gap_Op = -2; Match = 2; Miss = -5; + const score_type MATCH_SCORE = { 2, 2, 2, 2}; + const score_type MISMATCH_SCORE = { 5, 5, 5, 5}; + + const score_type OPEN_INDEL_SCORE = { 2, 2, 2, 2}; + const score_type EXTEND_INDEL_SCORE = { 1, 1, 1, 1}; + + //Biased Scores to 16 + const score_type ZERO = { BIAS, BIAS, BIAS, BIAS}; + + score_type r_cache[BAND_LEN]; + score_type H_temp [MAX_QUERY_SIZE]; + score_type E_temp [MAX_QUERY_SIZE]; + score_type H_band [BAND_LEN + 1]; + score_type F_band [BAND_LEN + 1]; + + const int32_t numRows = querySize, numColumns = candidateSize; + int32_t idColumn, idRow, idBand; + score_type H_maxScore = ZERO; + + uint32_t idCandidateEntry = 0; + uint32_t entryCandidate0, entryCandidate1, entryCandidate2, entryCandidate3; + + for(idBand = 0; idBand < MAX_QUERY_SIZE; ++idBand){ + H_temp[idBand].i = ZERO.i; + E_temp[idBand].i = ZERO.i; + } + + // Compute Score SW-GOTOH + for(idColumn = 0; idColumn < numColumns; idColumn += BAND_LEN){ + uint32_t idQueryEntry = 0; + uint32_t entryQuery0, entryQuery1, entryQuery2, entryQuery3; + + if((idColumn % RAW_BASES_PER_ENTRY) == 0){ + entryCandidate0 = candidate0[idCandidateEntry]; + entryCandidate1 = candidate1[idCandidateEntry]; + entryCandidate2 = candidate2[idCandidateEntry]; + entryCandidate3 = candidate3[idCandidateEntry]; + idCandidateEntry++; + } + + // Load a block of entries from the reference + #pragma unroll + for (uint32_t idBand = 0; idBand < BAND_LEN; ++idBand){ + r_cache[idBand].c4 = make_uchar4(entryCandidate0 & 0x3, + entryCandidate1 & 0x3, + entryCandidate2 & 0x3, + entryCandidate3 & 0x3); + entryCandidate0 >>= RAW_4B_LENGTH; + entryCandidate1 >>= RAW_4B_LENGTH; + entryCandidate2 >>= RAW_4B_LENGTH; + entryCandidate3 >>= RAW_4B_LENGTH; + } + + // Initialize the first band + #pragma unroll + for (uint32_t idBand = 0; idBand <= BAND_LEN; ++idBand){ + H_band[idBand].i = ZERO.i; + F_band[idBand].i = ZERO.i; + } + + #pragma unroll 1 + for(idRow = 0; idRow < numRows; ++idRow){ + + entryQuery0 >>= RAW_4B_LENGTH; + entryQuery1 >>= RAW_4B_LENGTH; + entryQuery2 >>= RAW_4B_LENGTH; + entryQuery3 >>= RAW_4B_LENGTH; + + if((idRow % RAW_BASES_PER_ENTRY) == 0){ + entryQuery0 = query0[idQueryEntry]; + entryQuery1 = query1[idQueryEntry]; + entryQuery2 = query2[idQueryEntry]; + entryQuery3 = query3[idQueryEntry]; + idQueryEntry++; + } + + const score_type q_i = {entryQuery0 & 0x03, entryQuery1 & 0x03, entryQuery2 & 0x03, entryQuery3 & 0x03}; + update_band(idRow, q_i.i, (uint32_t *) r_cache, (uint32_t *) H_band, (uint32_t *) F_band, (uint32_t *) H_temp, (uint32_t *) E_temp, + &H_maxScore.i, MATCH_SCORE.i, MISMATCH_SCORE.i, OPEN_INDEL_SCORE.i, EXTEND_INDEL_SCORE.i); + } + } + + d_AlignmentsResults[idCandidate].score = H_maxScore.c4.x - BIAS; + d_AlignmentsResults[idCandidate + 1].score = H_maxScore.c4.y - BIAS; + d_AlignmentsResults[idCandidate + 2].score = H_maxScore.c4.z - BIAS; + d_AlignmentsResults[idCandidate + 3].score = H_maxScore.c4.w - BIAS; + + d_AlignmentsResults[idCandidate].column = 0; + d_AlignmentsResults[idCandidate + 1].column = 0; + d_AlignmentsResults[idCandidate + 2].column = 0; + d_AlignmentsResults[idCandidate + 3].column = 0; + } +} + + +extern "C" +psaError_t localProcessPairwiseStream(sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + uint32_t blocks = DIV_CEIL(DIV_CEIL(candidates->num, VECTOR_ELEMENTS), CUDA_NUM_THREADS); + uint32_t threads = CUDA_NUM_THREADS; + uint32_t querySize = queries->h_size[0]; + uint32_t candidateSize = candidates->h_size[0]; + + cudaThreadSetCacheConfig(cudaFuncCachePreferL1); + + printf("Grid Size: %d, Block Size: %d, Total alignments: %d, BAND_LEN: %d \n", blocks, threads, candidates->num, BAND_LEN); + localProcessSWTiling<<>>(candidates->d_HlfRAW, candidates->d_HlfRAWposition, + queries->d_HlfRAW, queries->d_HlfRAWposition, + alignments->d_info, alignments->d_results, + querySize, candidateSize, candidates->num - VECTOR_ELEMENTS); + + cudaThreadSynchronize(); + + return (SUCCESS); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_mixedsim_gpu.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_mixedsim_gpu.cu new file mode 100644 index 0000000000000000000000000000000000000000..28328a48b644e8e32b2caba54e4cb9b7319f4505 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_mixedsim_gpu.cu @@ -0,0 +1,239 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swgotoh_2b_mixedsim_gpu + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Device functions for the SW-Gotoh GPU implementation using: + * (A) pack 4 SW in the same register emulating video instructions using just integer resources. + * (B) 32bit integer resources + and store the temporal columns with 8 bits. + * (C) bases are represented using 2 bits/base. + */ + +extern "C" { +#include "../../include/psa_pairwise_gpu.h" +} +#include +#include +#include "../../include/simd_functions.h" + +#ifndef QUERIES_SIZE + #define QUERIES_SIZE 100 +#endif + +#ifndef CANDIDATES_SIZE + #define CANDIDATES_SIZE 120 +#endif + +#define MAX3(a,b,c) (MAX(MAX(a, b), c)) + +#define WARP_SIZE 32 +#define MAX_THREADS_PER_SM 64 +#define CUDA_NUM_THREADS 64 + +#define THREADS_PER_SEGMENT 32 +#define NUM_SW_PER_BLOCK (MAX_THREADS_PER_SM / THREADS_PER_SEGMENT) +#define NUM_WARPS (MAX_THREADS_PER_SM / WARP_SIZE) + +#define BAND_LEN 8 +#define VECTOR_ELEMENTS 4 +#define MAX_QUERY_SIZE QUERIES_SIZE +#define BIAS 16 +#define RAW_BASES_PER_ENTRY (UINT32_LENGTH / RAW_4B_LENGTH) + +typedef union { + uchar4 c4; + uint32_t i; +}score_type; + +typedef uchar4 score_type2; + +inline __device__ +uint32_t sim_vmaxu4(uint32_t NUM_A, uint32_t NUM_B){ + return(MAX(NUM_A & 0xFF000000, NUM_B & 0xFF000000) | + MAX(NUM_A & 0x00FF0000, NUM_B & 0x00FF0000) | + MAX(NUM_A & 0x0000FF00, NUM_B & 0x0000FF00) | + MAX(NUM_A & 0x000000FF, NUM_B & 0x000000FF)); +} + + +inline __device__ +void update_band(int32_t idRow, const uint32_t q_i, const uint32_t *ref_cache, uint32_t *H_band, uint32_t *F_band, + uint32_t *H_temp, uint32_t *E_temp, uint32_t *H_maxScore, + const uint32_t MATCH_SCORE, const uint32_t MISMATCH_SCORE, + const uint32_t OPEN_INDEL_SCORE, const uint32_t EXTEND_INDEL_SCORE) +{ + + //Biased Scores to 16 + const uint32_t ZERO = 0x10101010; + uint32_t H_diag = H_band[0]; + H_band[0] = H_temp[idRow]; + uint32_t E = E_temp[idRow]; + + #pragma unroll + for (uint32_t j = 1; j <= BAND_LEN; ++j) + { + // update F + const uint32_t ftop = F_band[j] - EXTEND_INDEL_SCORE; + const uint32_t htop = H_band[j] - OPEN_INDEL_SCORE; + F_band[j] = sim_vmaxu4(ftop, htop); + + // update E + const uint32_t eleft = E - EXTEND_INDEL_SCORE; + const uint32_t hleft = H_band[j-1] - OPEN_INDEL_SCORE; + E = sim_vmaxu4(eleft, hleft); + // update H + const uint32_t r_j = ref_cache[j-1]; + const uint32_t Eq = vcmpeq4(r_j, q_i); + const uint32_t notEq = ~Eq; + const uint32_t diagonal = (notEq & (H_diag - MISMATCH_SCORE)) | (Eq & (H_diag + MATCH_SCORE)); + + const uint32_t top = F_band[j]; + const uint32_t left = E; + uint32_t hi = sim_vmaxu4(vmaxu4(left, top), diagonal); + hi = sim_vmaxu4(hi, ZERO); + + H_diag = H_band[j]; + H_band[j] = hi; + (* H_maxScore) = sim_vmaxu4((* H_maxScore), hi); + } + + H_temp[idRow] = H_band[BAND_LEN]; + E_temp[idRow] = E; +} + +__global__ +void localProcessSWTiling(RAWHlfEntry_t *d_CandidatesHlfRaw, uint32_t *d_CandidatesHlfRAWposition, + RAWHlfEntry_t *d_QueriesHlfRaw, uint32_t *d_QueriesHlfRAWposition, + alignmentInfo_t *d_AlignmentsInfo, alignmentEntry_t *d_AlignmentsResults, + uint32_t querySize, uint32_t candidateSize, uint32_t candidatesNum) +{ + const uint32_t idCandidate = (blockIdx.x * MAX_THREADS_PER_SM + threadIdx.x) * VECTOR_ELEMENTS; + + if (idCandidate < (candidatesNum)) + { + const RAWHlfEntry_t* candidate0 = d_CandidatesHlfRaw + d_CandidatesHlfRAWposition[idCandidate]; + const RAWHlfEntry_t* candidate1 = d_CandidatesHlfRaw + d_CandidatesHlfRAWposition[idCandidate + 1]; + const RAWHlfEntry_t* candidate2 = d_CandidatesHlfRaw + d_CandidatesHlfRAWposition[idCandidate + 2]; + const RAWHlfEntry_t* candidate3 = d_CandidatesHlfRaw + d_CandidatesHlfRAWposition[idCandidate + 3]; + + const RAWHlfEntry_t* query0 = d_QueriesHlfRaw + d_QueriesHlfRAWposition[d_AlignmentsInfo[idCandidate]]; + const RAWHlfEntry_t* query1 = d_QueriesHlfRaw + d_QueriesHlfRAWposition[d_AlignmentsInfo[idCandidate + 1]]; + const RAWHlfEntry_t* query2 = d_QueriesHlfRaw + d_QueriesHlfRAWposition[d_AlignmentsInfo[idCandidate + 2]]; + const RAWHlfEntry_t* query3 = d_QueriesHlfRaw + d_QueriesHlfRAWposition[d_AlignmentsInfo[idCandidate + 3]]; + + // All the scores have to be absolute numbers: + // Original BWA Scores: Gap_Ex = -1; Gap_Op = -2; Match = 2; Miss = -5; + const score_type MATCH_SCORE = { 2, 2, 2, 2}; + const score_type MISMATCH_SCORE = { 5, 5, 5, 5}; + + const score_type OPEN_INDEL_SCORE = { 2, 2, 2, 2}; + const score_type EXTEND_INDEL_SCORE = { 1, 1, 1, 1}; + + //Biased Scores to 16 + const score_type ZERO = { BIAS, BIAS, BIAS, BIAS}; + + score_type r_cache[BAND_LEN]; + score_type H_temp [MAX_QUERY_SIZE]; + score_type E_temp [MAX_QUERY_SIZE]; + score_type H_band [BAND_LEN + 1]; + score_type F_band [BAND_LEN + 1]; + + const int32_t numRows = querySize, numColumns = candidateSize; + int32_t idColumn, idRow, idBand; + score_type H_maxScore = ZERO; + + uint32_t idCandidateEntry = 0; + uint32_t entryCandidate0, entryCandidate1, entryCandidate2, entryCandidate3; + + for(idBand = 0; idBand < MAX_QUERY_SIZE; ++idBand){ + H_temp[idBand].i = ZERO.i; + E_temp[idBand].i = ZERO.i; + } + + // Compute Score SW-GOTOH + for(idColumn = 0; idColumn < numColumns; idColumn += BAND_LEN){ + uint32_t idQueryEntry = 0; + uint32_t entryQuery0, entryQuery1, entryQuery2, entryQuery3; + + if((idColumn % RAW_BASES_PER_ENTRY) == 0){ + entryCandidate0 = candidate0[idCandidateEntry]; + entryCandidate1 = candidate1[idCandidateEntry]; + entryCandidate2 = candidate2[idCandidateEntry]; + entryCandidate3 = candidate3[idCandidateEntry]; + idCandidateEntry++; + } + + // Load a block of entries from the reference + #pragma unroll + for (uint32_t idBand = 0; idBand < BAND_LEN; ++idBand){ + r_cache[idBand].c4 = make_uchar4(entryCandidate0 & 0x3, + entryCandidate1 & 0x3, + entryCandidate2 & 0x3, + entryCandidate3 & 0x3); + entryCandidate0 >>= RAW_4B_LENGTH; + entryCandidate1 >>= RAW_4B_LENGTH; + entryCandidate2 >>= RAW_4B_LENGTH; + entryCandidate3 >>= RAW_4B_LENGTH; + } + + // Initialize the first band + #pragma unroll + for (uint32_t idBand = 0; idBand <= BAND_LEN; ++idBand){ + H_band[idBand].i = ZERO.i; + F_band[idBand].i = ZERO.i; + } + + #pragma unroll 1 + for(idRow = 0; idRow < numRows; ++idRow){ + + entryQuery0 >>= RAW_4B_LENGTH; + entryQuery1 >>= RAW_4B_LENGTH; + entryQuery2 >>= RAW_4B_LENGTH; + entryQuery3 >>= RAW_4B_LENGTH; + + if((idRow % RAW_BASES_PER_ENTRY) == 0){ + entryQuery0 = query0[idQueryEntry]; + entryQuery1 = query1[idQueryEntry]; + entryQuery2 = query2[idQueryEntry]; + entryQuery3 = query3[idQueryEntry]; + idQueryEntry++; + } + + const score_type q_i = {entryQuery0 & 0x03, entryQuery1 & 0x03, entryQuery2 & 0x03, entryQuery3 & 0x03}; + update_band(idRow, q_i.i, (uint32_t *) r_cache, (uint32_t *) H_band, (uint32_t *) F_band, (uint32_t *) H_temp, (uint32_t *) E_temp, + &H_maxScore.i, MATCH_SCORE.i, MISMATCH_SCORE.i, OPEN_INDEL_SCORE.i, EXTEND_INDEL_SCORE.i); + } + } + + d_AlignmentsResults[idCandidate].score = H_maxScore.c4.x - BIAS; + d_AlignmentsResults[idCandidate + 1].score = H_maxScore.c4.y - BIAS; + d_AlignmentsResults[idCandidate + 2].score = H_maxScore.c4.z - BIAS; + d_AlignmentsResults[idCandidate + 3].score = H_maxScore.c4.w - BIAS; + + d_AlignmentsResults[idCandidate].column = 0; + d_AlignmentsResults[idCandidate + 1].column = 0; + d_AlignmentsResults[idCandidate + 2].column = 0; + d_AlignmentsResults[idCandidate + 3].column = 0; + } +} + + +extern "C" +psaError_t localProcessPairwiseStream(sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + uint32_t blocks = DIV_CEIL(DIV_CEIL(candidates->num, VECTOR_ELEMENTS), CUDA_NUM_THREADS); + uint32_t threads = CUDA_NUM_THREADS; + uint32_t querySize = queries->h_size[0]; + uint32_t candidateSize = candidates->h_size[0]; + + cudaThreadSetCacheConfig(cudaFuncCachePreferL1); + + printf("Grid Size: %d, Block Size: %d, Total alignments: %d, BAND_LEN: %d \n", blocks, threads, candidates->num, BAND_LEN); + localProcessSWTiling<<>>(candidates->d_HlfRAW, candidates->d_HlfRAWposition, + queries->d_HlfRAW, queries->d_HlfRAWposition, + alignments->d_info, alignments->d_results, + querySize, candidateSize, candidates->num - VECTOR_ELEMENTS); + + cudaThreadSynchronize(); + + return (SUCCESS); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_video_gpu.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_video_gpu.cu new file mode 100644 index 0000000000000000000000000000000000000000..71bdfb688b4c705342df88dccfa828770a081513 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_2b_video_gpu.cu @@ -0,0 +1,226 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swgotoh_2b_mixedsim_gpu + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Device functions for the SW-Gotoh GPU implementation using: + * (A) pack 4 SW in the same register using native video instructions. + * (B) 32bit video resources + and store the temporal columns with 8 bits. + * (C) bases are represented using 2 bits/base. + */ + +extern "C" { +#include "../../include/psa_pairwise_gpu.h" +} +#include +#include +#include "../../include/simd_functions.h" + +#ifndef QUERIES_SIZE + #define QUERIES_SIZE 100 +#endif + +#ifndef CANDIDATES_SIZE + #define CANDIDATES_SIZE 120 +#endif + +#define MAX3(a,b,c) (MAX(MAX(a, b), c)) + +#define WARP_SIZE 32 +#define MAX_THREADS_PER_SM 64 +#define CUDA_NUM_THREADS 64 + +#define THREADS_PER_SEGMENT 32 +#define NUM_SW_PER_BLOCK (MAX_THREADS_PER_SM / THREADS_PER_SEGMENT) +#define NUM_WARPS (MAX_THREADS_PER_SM / WARP_SIZE) + +#define BAND_LEN 8 +#define VECTOR_ELEMENTS 4 +#define MAX_QUERY_SIZE QUERIES_SIZE +#define BIAS 16 +#define RAW_BASES_PER_ENTRY (UINT32_LENGTH / RAW_4B_LENGTH) + +typedef union { + char4 c4; + uint32_t i; +}score_type; + +typedef uchar4 score_type2; + +inline __device__ +void update_band(int32_t idRow, const uint32_t q_i, const uint32_t *ref_cache, uint32_t *H_band, uint32_t *F_band, + uint32_t *H_temp, uint32_t *E_temp, uint32_t *H_maxScore, + const uint32_t MATCH_SCORE, const uint32_t MISMATCH_SCORE, + const uint32_t OPEN_INDEL_SCORE, const uint32_t EXTEND_INDEL_SCORE) +{ + const uint32_t ZERO = 0x00000000; + uint32_t H_diag = H_band[0]; + H_band[0] = H_temp[idRow]; + uint32_t E = E_temp[idRow]; + + #pragma unroll + for (uint32_t j = 1; j <= BAND_LEN; ++j) + { + // update F + const uint32_t ftop = vaddss4(F_band[j], EXTEND_INDEL_SCORE); + const uint32_t htop = vaddss4(H_band[j], OPEN_INDEL_SCORE); + F_band[j] = vmaxs4(ftop, htop); + + // update E + const uint32_t eleft = vaddss4(E, EXTEND_INDEL_SCORE); + const uint32_t hleft = vaddss4(H_band[j-1], OPEN_INDEL_SCORE); + E = vmaxs4(eleft, hleft); + // update H + const uint32_t r_j = ref_cache[j-1]; + const uint32_t Eq = vcmpeq4(r_j, q_i); + const uint32_t W_ij = (~Eq & MISMATCH_SCORE) | (Eq & MATCH_SCORE); + const uint32_t diagonal = vaddss4(H_diag, W_ij); + + const uint32_t top = F_band[j]; + const uint32_t left = E; + uint32_t hi = vmaxs4(vmaxs4(left, top), diagonal); + hi = vmaxs4(hi, ZERO); + + H_diag = H_band[j]; + H_band[j] = hi; + (* H_maxScore) = vmaxu4((* H_maxScore), hi); + } + + H_temp[idRow] = H_band[BAND_LEN]; + E_temp[idRow] = E; +} + +__global__ +void localProcessSWTiling(RAWHlfEntry_t *d_CandidatesHlfRaw, uint32_t *d_CandidatesHlfRAWposition, + RAWHlfEntry_t *d_QueriesHlfRaw, uint32_t *d_QueriesHlfRAWposition, + alignmentInfo_t *d_AlignmentsInfo, alignmentEntry_t *d_AlignmentsResults, + uint32_t querySize, uint32_t candidateSize, uint32_t candidatesNum) +{ + const uint32_t idCandidate = (blockIdx.x * MAX_THREADS_PER_SM + threadIdx.x) * VECTOR_ELEMENTS; + + if (idCandidate < (candidatesNum)) + { + const RAWHlfEntry_t* candidate0 = d_CandidatesHlfRaw + d_CandidatesHlfRAWposition[idCandidate]; + const RAWHlfEntry_t* candidate1 = d_CandidatesHlfRaw + d_CandidatesHlfRAWposition[idCandidate + 1]; + const RAWHlfEntry_t* candidate2 = d_CandidatesHlfRaw + d_CandidatesHlfRAWposition[idCandidate + 2]; + const RAWHlfEntry_t* candidate3 = d_CandidatesHlfRaw + d_CandidatesHlfRAWposition[idCandidate + 3]; + + const RAWHlfEntry_t* query0 = d_QueriesHlfRaw + d_QueriesHlfRAWposition[d_AlignmentsInfo[idCandidate]]; + const RAWHlfEntry_t* query1 = d_QueriesHlfRaw + d_QueriesHlfRAWposition[d_AlignmentsInfo[idCandidate + 1]]; + const RAWHlfEntry_t* query2 = d_QueriesHlfRaw + d_QueriesHlfRAWposition[d_AlignmentsInfo[idCandidate + 2]]; + const RAWHlfEntry_t* query3 = d_QueriesHlfRaw + d_QueriesHlfRAWposition[d_AlignmentsInfo[idCandidate + 3]]; + + // All the scores have to be absolute numbers: + // Original BWA Scores: Gap_Ex = -1; Gap_Op = -2; Match = 2; Miss = -5; + const score_type MATCH_SCORE = { 2, 2, 2, 2}; + const score_type MISMATCH_SCORE = { -5, -5, -5, -5}; + const score_type OPEN_INDEL_SCORE = { -2, -2, -2, -2}; + const score_type EXTEND_INDEL_SCORE = { -1, -1, -1, -1}; + const score_type ZERO = { 0, 0, 0, 0}; + + score_type r_cache[BAND_LEN]; + score_type H_temp [MAX_QUERY_SIZE]; + score_type E_temp [MAX_QUERY_SIZE]; + score_type H_band [BAND_LEN + 1]; + score_type F_band [BAND_LEN + 1]; + + const int32_t numRows = querySize, numColumns = candidateSize; + int32_t idColumn, idRow, idBand; + score_type H_maxScore = ZERO; + + uint32_t idCandidateEntry = 0; + uint32_t entryCandidate0, entryCandidate1, entryCandidate2, entryCandidate3; + + for(idBand = 0; idBand < MAX_QUERY_SIZE; ++idBand){ + H_temp[idBand].i = ZERO.i; + E_temp[idBand].i = ZERO.i; + } + + // Compute Score SW-GOTOH + for(idColumn = 0; idColumn < numColumns; idColumn += BAND_LEN){ + uint32_t idQueryEntry = 0; + uint32_t entryQuery0, entryQuery1, entryQuery2, entryQuery3; + + if((idColumn % RAW_BASES_PER_ENTRY) == 0){ + entryCandidate0 = candidate0[idCandidateEntry]; + entryCandidate1 = candidate1[idCandidateEntry]; + entryCandidate2 = candidate2[idCandidateEntry]; + entryCandidate3 = candidate3[idCandidateEntry]; + idCandidateEntry++; + } + + // Load a block of entries from the reference + #pragma unroll + for (uint32_t idBand = 0; idBand < BAND_LEN; ++idBand){ + r_cache[idBand].c4 = make_char4(entryCandidate0 & 0x3, + entryCandidate1 & 0x3, + entryCandidate2 & 0x3, + entryCandidate3 & 0x3); + entryCandidate0 >>= RAW_4B_LENGTH; + entryCandidate1 >>= RAW_4B_LENGTH; + entryCandidate2 >>= RAW_4B_LENGTH; + entryCandidate3 >>= RAW_4B_LENGTH; + } + + // Initialize the first band + #pragma unroll + for (uint32_t idBand = 0; idBand <= BAND_LEN; ++idBand){ + H_band[idBand].i = ZERO.i; + F_band[idBand].i = ZERO.i; + } + + #pragma unroll 1 + for(idRow = 0; idRow < numRows; ++idRow){ + + entryQuery0 >>= RAW_4B_LENGTH; + entryQuery1 >>= RAW_4B_LENGTH; + entryQuery2 >>= RAW_4B_LENGTH; + entryQuery3 >>= RAW_4B_LENGTH; + + if((idRow % RAW_BASES_PER_ENTRY) == 0){ + entryQuery0 = query0[idQueryEntry]; + entryQuery1 = query1[idQueryEntry]; + entryQuery2 = query2[idQueryEntry]; + entryQuery3 = query3[idQueryEntry]; + idQueryEntry++; + } + + const score_type q_i = {entryQuery0 & 0x03, entryQuery1 & 0x03, entryQuery2 & 0x03, entryQuery3 & 0x03}; + update_band(idRow, q_i.i, (uint32_t *) r_cache, (uint32_t *) H_band, (uint32_t *) F_band, + (uint32_t *) H_temp, (uint32_t *) E_temp, &H_maxScore.i, + MATCH_SCORE.i, MISMATCH_SCORE.i, OPEN_INDEL_SCORE.i, EXTEND_INDEL_SCORE.i); + } + } + + d_AlignmentsResults[idCandidate].score = H_maxScore.c4.x; + d_AlignmentsResults[idCandidate + 1].score = H_maxScore.c4.y; + d_AlignmentsResults[idCandidate + 2].score = H_maxScore.c4.z; + d_AlignmentsResults[idCandidate + 3].score = H_maxScore.c4.w; + + d_AlignmentsResults[idCandidate].column = 0; + d_AlignmentsResults[idCandidate + 1].column = 0; + d_AlignmentsResults[idCandidate + 2].column = 0; + d_AlignmentsResults[idCandidate + 3].column = 0; + } +} + + +extern "C" +psaError_t localProcessPairwiseStream(sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + uint32_t blocks = DIV_CEIL(DIV_CEIL(candidates->num, VECTOR_ELEMENTS), CUDA_NUM_THREADS); + uint32_t threads = CUDA_NUM_THREADS; + uint32_t querySize = queries->h_size[0]; + uint32_t candidateSize = candidates->h_size[0]; + + cudaThreadSetCacheConfig(cudaFuncCachePreferL1); + + printf("Grid Size: %d, Block Size: %d, Total alignments: %d, BAND_LEN: %d \n", blocks, threads, candidates->num, BAND_LEN); + localProcessSWTiling<<>>(candidates->d_HlfRAW, candidates->d_HlfRAWposition, + queries->d_HlfRAW, queries->d_HlfRAWposition, + alignments->d_info, alignments->d_results, + querySize, candidateSize, candidates->num - VECTOR_ELEMENTS); + + cudaThreadSynchronize(); + + return (SUCCESS); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_cpu.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_cpu.c new file mode 100644 index 0000000000000000000000000000000000000000..cbf03e725bd1f9047b9838a6fc579b3442e694ad --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_cpu.c @@ -0,0 +1,224 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swgotoh_cpu + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Functions for the SW-Gotoh CPU implementation using: + * (A) LOCAL / GLOBAL alignments + * (B) 8 bits per base and 32bits per cell + * (C) validation purposes + */ + +#include "../../include/psa_pairwise.h" + +#define WORD_SIZE 32 + +#define MATCH_SCORE 2 +#define MISMATCH_SCORE -5 +#define OPEN_INDEL_SCORE -2 +#define EXTEND_INDEL_SCORE -1 +#define LOCAL + + +#define MAX3(a,b,c) ((a >= b) ? ((a >= c) ? a : c) : ((b >= c) ? b : c)) + +#define BUILD_ALGORITHM "SMITH & WATERMAN GOTOH" +#define BUILD_VERSION "CPU VERSION WHOLE MATRIX" +#define BUILD_TAG "sw-gotoh.32b.cpu" + +char* buildTag() +{ + return (BUILD_TAG); +} + +psaError_t printBuildInfo() +{ + printf("%s \n", BUILD_ALGORITHM); + printf("%s \n", BUILD_VERSION); + printf("CONFIG - MATCH: %d, MISMATCH: %d, OPEN_INDEL: %d, EXTEND_INDEL: %d \n", + MATCH_SCORE, MISMATCH_SCORE, OPEN_INDEL_SCORE, EXTEND_INDEL_SCORE); + printf("Build: %s - %s \n", __DATE__, __TIME__ ); + + return (SUCCESS); +} + +psaError_t transformDataQueries(sequences_t *queries) +{ + uint32_t idBase; + + for (idBase = 0; idBase < queries->numASCIIEntries; ++idBase) + queries->h_ASCII[idBase] = ASCIItoUpperCase(queries->h_ASCII[idBase]); + + queries->formats |= SEQ_ASCII; + + return (SUCCESS); +} + +psaError_t transformDataCandidates(sequences_t *candidates) +{ + uint32_t idBase; + + for (idBase = 0; idBase < candidates->numASCIIEntries; ++idBase) + candidates->h_ASCII[idBase] = ASCIItoUpperCase(candidates->h_ASCII[idBase]); + + candidates->formats |= SEQ_ASCII; + + return (SUCCESS); +} + +psaError_t localProcessSWG(alignments_t *alignments, uint32_t idCandidate, char *candidate, uint32_t candidateSize, + char *query, uint32_t querySize, int32_t *H, int32_t *E, int32_t *F) +{ + int32_t sizeColumn = querySize + 1, numColumns = candidateSize + 1; + int32_t idColumn, i, y, j; + int32_t H_cellLeft, H_cellTop, H_cellDiag, H_cellScore; + int32_t E_cellTop, E_cellScore; + int32_t F_cellLeft, F_cellScore; + int32_t W_cellScore; + int32_t maxColumn = 0; + char base; + + #if defined(LOCAL) + int32_t H_maxScore = INT32_MIN; + #else + int32_t H_maxScore = OPEN_INDEL_SCORE + (EXTEND_INDEL_SCORE * querySize); // GLOBAL + #endif + + #if defined(DEBUG) + int32_t idRow; + #endif + + // Horizontal initialization + for(i = 0; i < numColumns; i++){ + #if defined(LOCAL) //LOCAL + H[i] = 0; + F[i] = 0; + #else //GLOBAL + H[i] = OPEN_INDEL_SCORE + (EXTEND_INDEL_SCORE * i); + F[i] = INT32_MIN; + #endif + } + // Vertical initialization + for(i = 0; i < sizeColumn; i++){ + #if defined(LOCAL) //LOCAL + H[i * numColumns] = 0; + E[i * numColumns] = 0; + #else //GLOBAL + E[i * numColumns] = INT32_MIN; + H[i * numColumns] = OPEN_INDEL_SCORE + (EXTEND_INDEL_SCORE * i); + #endif + } + H[0] = 0; + + // Compute Score SW-GOTOH + for(idColumn = 1; idColumn < numColumns; idColumn++){ + base = candidate[idColumn - 1]; + #if defined(DEBUG) + int32_t H_maxColumn = 0; + #endif + for(y = 1; y < sizeColumn; y++){ + W_cellScore = (base == query[y - 1]) ? MATCH_SCORE : MISMATCH_SCORE; + + H_cellLeft = H[y * numColumns + (idColumn - 1)]; + H_cellTop = H[(y - 1) * numColumns + idColumn]; + H_cellDiag = H[(y - 1) * numColumns + (idColumn - 1)]; + + E_cellTop = E[(y - 1) * numColumns + idColumn]; + F_cellLeft = F[y * numColumns + (idColumn - 1)]; + + E_cellScore = MAX(E_cellTop + EXTEND_INDEL_SCORE, + H_cellTop + OPEN_INDEL_SCORE); + F_cellScore = MAX(F_cellLeft + EXTEND_INDEL_SCORE, + H_cellLeft + OPEN_INDEL_SCORE); + H_cellScore = MAX3(E_cellScore, F_cellScore, H_cellDiag + W_cellScore); + H_cellScore = MAX(H_cellScore, 0); + + E[y * numColumns + idColumn] = E_cellScore; + F[y * numColumns + idColumn] = F_cellScore; + H[y * numColumns + idColumn] = H_cellScore; + + #if defined(DEBUG) + H_maxColumn = MAX(H_cellScore, H_maxColumn); + #endif + + if(H_cellScore >= H_maxScore){ + H_maxScore = H_cellScore; + maxColumn = idColumn - 1; + } + } + } + + #if defined(DEBUG) + if(idCandidate == 0){ + printf("\n E (D): \n"); + for(idColumn = 0; idColumn < sizeColumn; idColumn++){ + if(idColumn != 0) printf("\t %c:", query[idColumn - 1]); + for(idRow = 0; idRow < numColumns; idRow++){ + printf("%4d,", E[(idColumn * numColumns) + idRow]); + } + printf("\n"); + } + printf("\n F (I): \n"); + for(idColumn = 0; idColumn < sizeColumn; idColumn++){ + if(idColumn != 0) printf("\t %c:", query[idColumn - 1]); + for(idRow = 0; idRow < numColumns; idRow++){ + printf("%4d,", F[(idColumn * numColumns) + idRow]); + } + printf("\n"); + } + printf("\n H (M): \n"); + for(idColumn = 0; idColumn < sizeColumn; idColumn++){ + if(idColumn != 0) printf("\t %c:", query[idColumn - 1]); + for(idRow = 0; idRow < numColumns; idRow++){ + printf("%4d,", H[(idColumn * numColumns) + idRow]); + } + printf("\n"); + } + } + #endif + + //alignments->h_results[idCandidate].column = maxColumn; + alignments->h_results[idCandidate].column = 0; + alignments->h_results[idCandidate].score = H_maxScore; + + return(SUCCESS); +} + +psaError_t processPairwiseStream(sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + uint32_t idCandidate, words; + uint32_t scoreBP, scoreSW; + char *S1, *S2; + uint32_t candidateSize, querySize; + int32_t *H, *E, *F; + + words = DIV_CEIL(candidates->h_size[0], UINT32_LENGTH); + H = (int32_t *) malloc((candidates->h_size[0] + 1) * (queries->h_size[0] + 1) * sizeof(int32_t)); + if (H == NULL) return (E_ALLOCATE_MEM); + E = (int32_t *) malloc((candidates->h_size[0] + 1) * (queries->h_size[0] + 1) * sizeof(int32_t)); + if (E == NULL) return (E_ALLOCATE_MEM); + F = (int32_t *) malloc((candidates->h_size[0] + 1) * (queries->h_size[0] + 1) * sizeof(int32_t)); + if (F == NULL) return (E_ALLOCATE_MEM); + + for (idCandidate = 0; idCandidate < candidates->num; ++idCandidate) + { + S1 = &candidates->h_ASCII[candidates->h_ASCIIposition[idCandidate]]; + S2 = &queries->h_ASCII[queries->h_ASCIIposition[alignments->h_info[idCandidate]]]; + candidateSize = candidates->h_size[idCandidate]; + querySize = queries->h_size[alignments->h_info[idCandidate]]; + + localProcessSWG(alignments, idCandidate, S1, candidateSize, S2, querySize, H, E, F); + } + + free(H); + free(F); + free(E); + + return (SUCCESS); +} + + + + + + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_ref_2b_gpu.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_ref_2b_gpu.c new file mode 100644 index 0000000000000000000000000000000000000000..b532738e8a28928fa4ffefec26f0a6787652dd3a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_ref_2b_gpu.c @@ -0,0 +1,184 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swgotoh_ref_2b_gpu + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Host functions for the SW-Gotoh GPU implementation using: + * (A) pack 4 SW in the same register using native video instructions. + * (B) 32bit video resources + and store the temporal columns with 8 bits. + * (C) bases are represented using 2 bits/base. + * (D) reads the candidates from the reference (check the impact of random accesses) + */ + +#include "../../include/psa_pairwise.h" +#include "../../include/psa_pairwise_gpu.h" +#include +#include + +#define WORD_SIZE 32 + +#define MATCH_SCORE 2 +#define MISMATCH_SCORE -5 +#define OPEN_INDEL_SCORE -2 +#define EXTEND_INDEL_SCORE -1 + +#define MAX3(a,b,c) ((a >= b) ? ((a >= c) ? a : c) : ((b >= c) ? b : c)) + +#define BUILD_ALGORITHM "SW-GOTOH: VIDEO INST USING REFERENCE POS (LOCAL ALIGNMENT)" +#define BUILD_VERSION "GPU VERSION 8bits per cell" +#define BUILD_TAG "gotoh.video.ref.8b.gpu" + +#define CUDA_ERROR(error) (HandleError(error, __FILE__, __LINE__ )) + +static void HandleError( cudaError_t err, const char *file, int32_t line ) { + if (err != cudaSuccess) { + printf( "%s in %s at line %d\n", cudaGetErrorString(err), file, line ); + exit( EXIT_FAILURE ); + } +} + +char* buildTag() +{ + return (BUILD_TAG); +} + +psaError_t printBuildInfo() +{ + printf("%s \n", BUILD_ALGORITHM); + printf("%s \n", BUILD_VERSION); + printf("CONFIG - MATCH: %d, MISMATCH: %d, INDEL_OPEN: %d, INDEL_EXTEND %d\n", + MATCH_SCORE, MISMATCH_SCORE, OPEN_INDEL_SCORE, EXTEND_INDEL_SCORE); + printf("Build: %s - %s \n", __DATE__, __TIME__ ); + + return (SUCCESS); +} + +psaError_t transformDataReferences(sequences_t *references) +{ + uint32_t idReference, position, size; + uint32_t currentHlfRAWEntry = 0, numHlfRAWEntries; + const uint32_t RAW_BASES_PER_ENTRY = UINT32_LENGTH / RAW_4B_LENGTH; + + references->numRAWHlfEntries = sequences_totalEntriesHlfRAW(references->h_size, references->num, RAW_4B_LENGTH); + + references->h_HlfRAW = (RAWHlfEntry_t *) malloc(references->numRAWHlfEntries * sizeof(RAWHlfEntry_t)); + if (references->h_HlfRAW == NULL) return (E_ALLOCATE_MEM); + + references->h_HlfRAWposition = (uint32_t *) malloc(references->num * sizeof(uint32_t)); + if (references->h_HlfRAWposition == NULL) return (E_ALLOCATE_MEM); + + for (idReference = 0; idReference < references->num; ++idReference) + { + position = references->h_ASCIIposition[idReference]; + size = references->h_size[idReference]; + numHlfRAWEntries = DIV_CEIL(size, RAW_BASES_PER_ENTRY); + + sequenceASCIItoRAW_2x32bits(references->h_ASCII + position, size, references->h_HlfRAW + currentHlfRAWEntry); + references->h_HlfRAWposition[idReference] = currentHlfRAWEntry; + currentHlfRAWEntry += numHlfRAWEntries; + } + + references->formats |= SEQ_HLF_RAW; + return (SUCCESS); +} + +psaError_t transformDataQueries(sequences_t *queries) +{ + uint32_t idQuery, position, size; + uint32_t currentHlfRAWEntry = 0, numHlfRAWEntries; + const uint32_t RAW_BASES_PER_ENTRY = UINT32_LENGTH / RAW_4B_LENGTH; + + queries->numRAWHlfEntries = sequences_totalEntriesHlfRAW(queries->h_size, queries->num, RAW_4B_LENGTH); + + queries->h_HlfRAW = (RAWHlfEntry_t *) malloc(queries->numRAWHlfEntries * sizeof(RAWHlfEntry_t)); + if (queries->h_HlfRAW == NULL) return (E_ALLOCATE_MEM); + + queries->h_HlfRAWposition = (uint32_t *) malloc(queries->num * sizeof(uint32_t)); + if (queries->h_HlfRAWposition == NULL) return (E_ALLOCATE_MEM); + + for (idQuery = 0; idQuery < queries->num; ++idQuery) + { + position = queries->h_ASCIIposition[idQuery]; + size = queries->h_size[idQuery]; + numHlfRAWEntries = DIV_CEIL(size, RAW_BASES_PER_ENTRY); + + sequenceASCIItoRAW_2x32bits(queries->h_ASCII + position, size, queries->h_HlfRAW + currentHlfRAWEntry); + queries->h_HlfRAWposition[idQuery] = currentHlfRAWEntry; + currentHlfRAWEntry += numHlfRAWEntries; + } + + queries->formats |= SEQ_HLF_RAW; + return (SUCCESS); +} + +psaError_t transformDataCandidates(sequences_t *candidates) +{ + uint32_t idCandidate, position, size; + uint32_t currentHlfRAWEntry = 0, numHlfRAWEntries; + const uint32_t RAW_BASES_PER_ENTRY = UINT32_LENGTH / RAW_4B_LENGTH; + + candidates->numRAWHlfEntries = sequences_totalEntriesHlfRAW(candidates->h_size, candidates->num, RAW_4B_LENGTH); + + candidates->h_HlfRAW = (RAWHlfEntry_t *) malloc(candidates->numRAWHlfEntries * sizeof(RAWHlfEntry_t)); + if (candidates->h_HlfRAW == NULL) return (E_ALLOCATE_MEM); + + candidates->h_HlfRAWposition = (uint32_t *) malloc(candidates->num * sizeof(uint32_t)); + if (candidates->h_HlfRAWposition == NULL) return (E_ALLOCATE_MEM); + + for (idCandidate = 0; idCandidate < candidates->num; ++idCandidate) + { + position = candidates->h_ASCIIposition[idCandidate]; + size = candidates->h_size[idCandidate]; + numHlfRAWEntries = DIV_CEIL(size, RAW_BASES_PER_ENTRY); + + sequenceASCIItoRAW_2x32bits(candidates->h_ASCII + position, size, candidates->h_HlfRAW + currentHlfRAWEntry); + candidates->h_HlfRAWposition[idCandidate] = currentHlfRAWEntry; + currentHlfRAWEntry += numHlfRAWEntries; + } + + candidates->formats |= SEQ_HLF_RAW; + return (SUCCESS); +} + +psaError_t transferCPUtoGPUReference(sequences_t *references, sequences_t *queries, sequences_t *candidates, alignments_t *alignments) +{ + //allocate & transfer References to GPU + CUDA_ERROR(cudaMalloc((void**)&references->d_HlfRAW, references->numRAWHlfEntries * sizeof(RAWHlfEntry_t))); + CUDA_ERROR(cudaMemcpy(references->d_HlfRAW, references->h_HlfRAW, references->numRAWHlfEntries * sizeof(RAWHlfEntry_t), cudaMemcpyHostToDevice)); + + //allocate & transfer Queries to GPU + CUDA_ERROR(cudaMalloc((void**)&queries->d_HlfRAW, queries->numRAWHlfEntries * sizeof(RAWHlfEntry_t))); + CUDA_ERROR(cudaMemcpy(queries->d_HlfRAW, queries->h_HlfRAW, queries->numRAWHlfEntries * sizeof(RAWHlfEntry_t), cudaMemcpyHostToDevice)); + + CUDA_ERROR(cudaMalloc((void**)&queries->d_HlfRAWposition, queries->num * sizeof(uint32_t))); + CUDA_ERROR(cudaMemcpy(queries->d_HlfRAWposition, queries->h_HlfRAWposition, queries->num * sizeof(uint32_t), cudaMemcpyHostToDevice)); + + //allocate & transfer Candidates to GPU + CUDA_ERROR(cudaMalloc((void**)&candidates->d_refPosition, candidates->num * sizeof(uint32_t))); + CUDA_ERROR(cudaMemcpy(candidates->d_refPosition, candidates->h_refPosition, candidates->num * sizeof(uint32_t), cudaMemcpyHostToDevice)); + + //allocate & initialize Results + CUDA_ERROR(cudaMalloc((void**)&alignments->d_info, alignments->num * sizeof(alignmentInfo_t))); + CUDA_ERROR(cudaMemcpy(alignments->d_info, alignments->h_info, alignments->num * sizeof(alignmentInfo_t), cudaMemcpyHostToDevice)); + + CUDA_ERROR(cudaMalloc((void**)&alignments->d_results, alignments->num * sizeof(alignmentEntry_t))); + CUDA_ERROR(cudaMemset(alignments->d_results, 0, alignments->num * sizeof(alignmentEntry_t))); + + return (SUCCESS); +} + +psaError_t transferGPUtoCPU(alignments_t *alignments) +{ + CUDA_ERROR(cudaMemcpy(alignments->h_results, alignments->d_results, alignments->num * sizeof(alignmentEntry_t), cudaMemcpyDeviceToHost)); + + return (SUCCESS); +} + +psaError_t processPairwiseReference(sequences_t* references, sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + return(localProcessPairwiseReference(references, candidates, queries, alignments)); +} + + + + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_ref_2b_integer_gpu.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_ref_2b_integer_gpu.cu new file mode 100644 index 0000000000000000000000000000000000000000..a48f6ed1c8951e4ca3e3dac9f2e615d0590f5c13 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/gotoh/psa_swgotoh_ref_2b_integer_gpu.cu @@ -0,0 +1,185 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_swgotoh_ref_2b_gpu + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Device functions for the SW-Gotoh GPU implementation using: + * (A) pack 4 SW in the same register using native video instructions. + * (B) 32bit video resources + and store the temporal columns with 8 bits. + * (C) bases are represented using 2 bits/base. + * (D) reads the candidates from the reference (check the impact of random accesses) + */ + +extern "C" { +#include "../../include/psa_pairwise_gpu.h" +} +#include +#include + +#ifndef QUERIES_SIZE + #define QUERIES_SIZE 100 +#endif + +#ifndef CANDIDATES_SIZE + #define CANDIDATES_SIZE 120 +#endif + +#define MAX3(a,b,c) (MAX(MAX(a, b), c)) + +#define WARP_SIZE 32 +#define MAX_THREADS_PER_SM 64 +#define CUDA_NUM_THREADS 64 + +#define THREADS_PER_SEGMENT 32 +#define NUM_SW_PER_BLOCK (MAX_THREADS_PER_SM / THREADS_PER_SEGMENT) +#define NUM_WARPS (MAX_THREADS_PER_SM / WARP_SIZE) + +#define BAND_LEN 8 +#define MAX_QUERY_SIZE QUERIES_SIZE +#define RAW_BASES_PER_ENTRY (UINT32_LENGTH / RAW_4B_LENGTH) + +typedef int32_t score_type; +//typedef char2 score_type2; +//typedef int2 score_type2; +typedef short2 score_type2; + +inline __device__ +void update_band(int32_t idRow, char q_i, char *ref_cache, score_type *H_band, score_type *F_band, + score_type2 *temp, score_type *H_maxScore, + const score_type MATCH_SCORE, const score_type MISMATCH_SCORE, + const score_type OPEN_INDEL_SCORE, const score_type EXTEND_INDEL_SCORE) +{ + score_type H_diag = H_band[0]; + H_band[0] = temp[idRow].x; + score_type E = temp[idRow].y; + + #pragma unroll + for (uint32_t j = 1; j <= BAND_LEN; ++j) + { + // update F + const score_type ftop = F_band[j] + EXTEND_INDEL_SCORE; + const score_type htop = H_band[j] + OPEN_INDEL_SCORE; + F_band[j] = MAX(ftop, htop); + + // update E + const score_type eleft = E + EXTEND_INDEL_SCORE; + const score_type hleft = H_band[j-1] + OPEN_INDEL_SCORE; + E = MAX(eleft, hleft); + + const char r_j = ref_cache[j-1]; + const score_type diagonal = (r_j == q_i) ? H_diag + MATCH_SCORE : H_diag + MISMATCH_SCORE; + const score_type top = F_band[j]; + const score_type left = E; + score_type hi = MAX3(left, top, diagonal); + hi = MAX(hi, 0); + H_diag = H_band[j]; + H_band[j] = hi; + (*H_maxScore) = MAX((*H_maxScore), hi); + } + + // save the last entry of the band + temp[idRow] = make_short2(H_band[BAND_LEN], E); +} + +__global__ +void localProcessSWTiling(RAWHlfEntry_t *d_refHlfRaw, uint32_t *d_refPosition, + RAWHlfEntry_t *d_QueriesHlfRaw, uint32_t *d_QueriesHlfRAWposition, + alignmentInfo_t *d_AlignmentsInfo, alignmentEntry_t *d_AlignmentsResults, + uint32_t querySize, uint32_t candidateSize, uint32_t candidatesNum) +{ + const uint32_t idCandidate = blockIdx.x * MAX_THREADS_PER_SM + threadIdx.x; + + if (idCandidate < candidatesNum) + { + const uint32_t refPosition = d_refPosition[idCandidate]; + const RAWHlfEntry_t* candidate = d_refHlfRaw + (refPosition / RAW_BASES_PER_ENTRY); + const RAWHlfEntry_t* query = d_QueriesHlfRaw + d_QueriesHlfRAWposition[d_AlignmentsInfo[idCandidate]]; + + // All the scores have to be absolute numbers: + // Original BWA Scores: Gap_Ex = -1; Gap_Op = -2; Match = 2; Miss = -5; + const score_type MATCH_SCORE = 2; + const score_type MISMATCH_SCORE = -5; + const score_type OPEN_INDEL_SCORE = -2; + const score_type EXTEND_INDEL_SCORE = -1; + const score_type ZERO = 0; + + char r_cache[BAND_LEN]; + score_type2 temp [MAX_QUERY_SIZE]; + score_type H_band [BAND_LEN + 1]; + score_type F_band [BAND_LEN + 1]; + + const int32_t numRows = querySize, numColumns = candidateSize; + int32_t idColumn, idRow, idBand; + score_type H_maxScore = ZERO; + + uint32_t entryCandidate, actualEntryCandidate, lastEntryCandidate, idCandidateEntry = 0; + + for(idBand = 0; idBand < MAX_QUERY_SIZE; ++idBand){ + temp[idBand].x = ZERO; + temp[idBand].y = ZERO; + } + + lastEntryCandidate = candidate[idCandidateEntry]; + // Compute Score SW-GOTOH + for(idColumn = 0; idColumn < numColumns; idColumn += BAND_LEN){ + uint32_t entryQuery, idQueryEntry = 0; + if((idColumn % RAW_BASES_PER_ENTRY) == 0){ + const uint32_t alignment = refPosition % RAW_BASES_PER_ENTRY; + idCandidateEntry++; + actualEntryCandidate = candidate[idCandidateEntry]; + entryCandidate = actualEntryCandidate << (RAW_4B_LENGTH * (RAW_BASES_PER_ENTRY - alignment)) + | lastEntryCandidate >> (RAW_4B_LENGTH * alignment); + lastEntryCandidate = actualEntryCandidate; + } + + // Load a block of entries from the reference + #pragma unroll + for (uint32_t idBand = 0; idBand < BAND_LEN; ++idBand){ + r_cache[idBand] = entryCandidate & 0x3; + entryCandidate >>= RAW_4B_LENGTH; + } + + // Initialize the first band + #pragma unroll + for (uint32_t idBand = 0; idBand <= BAND_LEN; ++idBand){ + H_band[idBand] = ZERO; + F_band[idBand] = ZERO; + } + + #pragma unroll 4 + for(idRow = 0; idRow < numRows; ++idRow){ + entryQuery >>= RAW_4B_LENGTH; + if((idRow % RAW_BASES_PER_ENTRY) == 0){ + entryQuery = query[idQueryEntry]; + idQueryEntry++; + } + + update_band(idRow, entryQuery & 0x03, r_cache, H_band, F_band, temp, &H_maxScore, + MATCH_SCORE, MISMATCH_SCORE, OPEN_INDEL_SCORE, EXTEND_INDEL_SCORE); + } + } + d_AlignmentsResults[idCandidate].score = H_maxScore; + d_AlignmentsResults[idCandidate].column = 0; + } +} + + +extern "C" +psaError_t localProcessPairwiseReference(sequences_t* references, sequences_t *candidates, sequences_t *queries, alignments_t *alignments) +{ + uint32_t blocks = DIV_CEIL(candidates->num, CUDA_NUM_THREADS); + uint32_t threads = CUDA_NUM_THREADS; + uint32_t querySize = queries->h_size[0]; + uint32_t candidateSize = candidates->h_size[0]; + + cudaThreadSetCacheConfig(cudaFuncCachePreferL1); + + printf("Grid Size: %d, Block Size: %d, Total alignments: %d, BAND_LEN: %d \n", blocks, threads, candidates->num, BAND_LEN); + localProcessSWTiling<<>>(references->d_HlfRAW, candidates->d_refPosition, + queries->d_HlfRAW, queries->d_HlfRAWposition, + alignments->d_info, alignments->d_results, + querySize, candidateSize, candidates->num); + + cudaThreadSynchronize(); + + return (SUCCESS); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_alignments.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_alignments.c new file mode 100644 index 0000000000000000000000000000000000000000..ee843b1b2f0fe7e308d8e234a7d2310889dff7f9 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_alignments.c @@ -0,0 +1,117 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_alignments + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: API functions to manage the alignments (sink and score) + */ + +#include "../include/psa_alignments.h" + +psaError_t initAlignments(alignments_t **alignments, uint32_t numAlignments) +{ + (* alignments) = (alignments_t *) malloc(sizeof(alignments_t)); + if((* alignments) == NULL) return (E_ALLOCATE_MEM); + + /* Alignment data */ + (* alignments)->num = numAlignments; + (* alignments)->numReordered = 0; + /* Alignment structures */ + (* alignments)->h_info = 0; + (* alignments)->d_info = 0; + (* alignments)->h_results = NULL; + (* alignments)->d_results = NULL; + /* Binning by size structures */ + (* alignments)->h_reorderResults = NULL; + (* alignments)->d_reorderResults = NULL; + + return (SUCCESS); +} + +psaError_t allocateAlignments(alignments_t *alignments) +{ + if (alignments == NULL) return (E_ALLOCATE_MEM); + + alignments->h_info = (alignmentInfo_t *) malloc(alignments->num * sizeof(alignmentInfo_t)); + if (alignments->h_info == NULL) return (E_ALLOCATE_MEM); + + alignments->h_results = (alignmentEntry_t *) malloc(alignments->num * sizeof(alignmentEntry_t)); + if (alignments->h_results == NULL) return (E_ALLOCATE_MEM); + + return (SUCCESS); +} + +psaError_t loadAlignments(FILE *fp, alignments_t *alignments) +{ + uint32_t result; + + result = fread(&alignments->num, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_WRITING_FILE); + + alignments->h_info = (alignmentInfo_t *) malloc(alignments->num * sizeof(alignmentInfo_t)); + if (alignments->h_info == NULL) return (E_ALLOCATE_MEM); + result = fread(alignments->h_info, sizeof(alignmentInfo_t), alignments->num, fp); + if (result != alignments->num) return(E_WRITING_FILE); + + alignments->h_results = (alignmentEntry_t *) malloc(alignments->num * sizeof(alignmentEntry_t)); + if (alignments->h_results == NULL) return (E_ALLOCATE_MEM); + result = fread(alignments->h_results, sizeof(alignmentEntry_t), alignments->num, fp); + if (result != alignments->num) return(E_WRITING_FILE); + + return (SUCCESS); +} + +psaError_t saveAlignments(FILE *fp, alignments_t *alignments) +{ + uint32_t result; + + result = fwrite(&alignments->num, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_WRITING_FILE); + result = fwrite(alignments->h_info, sizeof(alignmentInfo_t), alignments->num, fp); + if (result != alignments->num) return(E_WRITING_FILE); + result = fwrite(alignments->h_results, sizeof(alignmentEntry_t), alignments->num, fp); + if (result != alignments->num) return(E_WRITING_FILE); + + return (SUCCESS); +} + +psaError_t saveASCIIAlignments(FILE *fp, alignments_t *alignments) +{ + char textLine[256]; + uint32_t error, idAlignment; + + sprintf(textLine, "%u\n", alignments->num); + fputs(textLine, fp); + for(idAlignment = 0; idAlignment < alignments->num; idAlignment++){ + sprintf(textLine, "%u %d %u\n", idAlignment, alignments->h_results[idAlignment].score, alignments->h_results[idAlignment].column); + fputs(textLine, fp); + } + + return(SUCCESS); +} + +psaError_t freeAlignments(alignments_t **alignments) +{ + if((* alignments) != NULL){ + + if((* alignments)->h_info != NULL){ + free((* alignments)->h_info); + (* alignments)->h_info = NULL; + } + + if((* alignments)->h_results != NULL){ + free((* alignments)->h_results); + (* alignments)->h_results = NULL; + } + + if((* alignments)->h_reorderResults != NULL){ + free((* alignments)->h_reorderResults); + (* alignments)->h_reorderResults = NULL; + } + + free((* alignments)); + (* alignments) = NULL; + } + + return(SUCCESS); +} + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_errors.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_errors.c new file mode 100644 index 0000000000000000000000000000000000000000..31250d9cff7e2da57d69dd6792b9f8e46964d4d6 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_errors.c @@ -0,0 +1,32 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_errors + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: API Interface to manage errors. + */ + +#include "../include/psa_errors.h" + +char *psaGetErrorString(psaError_t error) +{ + switch(error) { + case E_OPENING_FILE: return "PSA - Error: opening file"; break; + case E_READING_FILE: return "PSA - Error: reading file"; break; + case E_WRITING_FILE: return "PSA - Error: reading file"; break; + case E_INSUFFICIENT_MEM_GPU: return "PSA - Error: there aren't enough GPU memory space"; break; + case E_ALLOCATE_MEM: return "PSA - Error: allocating data"; break; + case E_INCOMPATIBLE_GPU: return "PSA - Error: incompatible GPU (old CC version)"; break; + case E_REFERENCE_CODING: return "PSA - Error: reference coding not supported"; break; + case E_NO_MULTIFASTA_FILE: return "PSA - Error: reference file isn't multifasta format"; break; + case E_PARSING_REGPROF: return "PSA - Error: parsing a candidate from GEM regions profile"; break; + default: return "PSA - Unknown error"; + } +} + +void psaError(psaError_t error, const char *file, int32_t line) +{ + if (error != 0) { + fprintf(stderr, "%s in %s at line %d\n", psaGetErrorString(error), file, line); + exit(EXIT_FAILURE); + } +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_profile.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_profile.c new file mode 100644 index 0000000000000000000000000000000000000000..fd6943eb36344dba528ec47807eca31d320b5969 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_profile.c @@ -0,0 +1,169 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_profile + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Process functions for GEM profile files. + */ + +#include "../include/psa_profile.h" + +psaError_t countCandidates(char* cadena, uint32_t *numberOfCandidates, uint32_t *querySize) +{ + int localNumCandidates = 0, i = 0, flagQueryMesured = 0; + + while(cadena[i] != '\n'){ + if(cadena[i] == '\t'){ + if(flagQueryMesured == 0){ + (* querySize) = i; + flagQueryMesured = 1; + } + localNumCandidates++; + } + i++; + } + (* numberOfCandidates) = localNumCandidates; + return (SUCCESS); +} + +psaError_t countRegionsProfile(FILE *fp, float distance, + uint32_t *retNumQueries, uint32_t *retTotalSizeQueries, + uint32_t *retNumCandidates, uint32_t *retTotalSizeCandidates) +{ + //Read all the file and return the number of candidates and queries + char cadena[FILE_SIZE_LINES]; + uint32_t numCandidates = 0, numQueries = 0; + uint32_t totalSizeCandidates = 0, totalSizeQueries = 0; + uint32_t localCandidates = 0, currentQuerySize = 0; + + if (fgets(cadena, FILE_SIZE_LINES, fp) == NULL) return (E_READING_FILE); + + PSA_ERROR(countCandidates(cadena, &localCandidates, ¤tQuerySize)); + numCandidates += localCandidates; + totalSizeQueries += currentQuerySize; + totalSizeCandidates += ((distance * currentQuerySize) * localCandidates); + numQueries++; + + while((!feof(fp)) && (fgets(cadena, FILE_SIZE_LINES, fp) != NULL)){ + PSA_ERROR(countCandidates(cadena, &localCandidates, ¤tQuerySize)); + + numCandidates += localCandidates; + totalSizeQueries += currentQuerySize; + totalSizeCandidates += ((distance * currentQuerySize) * localCandidates); + numQueries++; + } + + (* retNumQueries) = numQueries; + (* retNumCandidates) = numCandidates; + (* retTotalSizeQueries) = totalSizeQueries; + (* retTotalSizeCandidates) = totalSizeCandidates; + + return (SUCCESS); +} + +psaError_t parseCandidate(char *candidate, uint32_t *retPosition, uint32_t *retScore) +{ + char area[50]; + char symbol[10]; + char position[15]; + char score[500]; + int tokenCount; + + tokenCount = sscanf(candidate,"%49[^:]:%9[^:]:%14[^:]:%s", area, symbol, position, score); + if (tokenCount != 4) return (E_PARSING_REGPROF); + + (* retPosition) = (uint32_t) atoi(position); + (* retScore) = (uint32_t) atoi(score); + + return (SUCCESS); +} + +psaError_t processQuery(uint32_t queryNumber, char *textLine, + char *queries, uint32_t *h_PositionCandidates, uint32_t *h_AlignmentInfo, uint32_t *listResults, + uint32_t *retSizeQueries, uint32_t *retNumCandidates) +{ + uint32_t position, + numCandidates = 0, + sizeQuery, + result, + tokenCount; + + int32_t sizeLastCandidates, + sizeCurrentCandidate; + + char *pLastCandidates; + + char query[FILE_SIZE_LINES], + lastCandidates[FILE_SIZE_LINES], + currentCandidate[500]; + + pLastCandidates = &lastCandidates[0]; + + sscanf(textLine, "%s\t%[^\n]", query, pLastCandidates); + sizeQuery = strlen(query); + sizeLastCandidates = strlen(pLastCandidates); + memcpy(queries, query, sizeQuery); + + while (sizeLastCandidates > 0){ + tokenCount = sscanf(pLastCandidates,"%s", currentCandidate); + if (tokenCount < 1) return (E_PARSING_REGPROF); + + PSA_ERROR(parseCandidate(currentCandidate, &position, &result)); + h_AlignmentInfo[numCandidates] = queryNumber; + h_PositionCandidates[numCandidates] = position; + listResults[numCandidates] = result; + numCandidates++; + + //update values next iteration + sizeCurrentCandidate = strlen(currentCandidate) + 1; + pLastCandidates += sizeCurrentCandidate; + sizeLastCandidates -= sizeCurrentCandidate; + } + + //return the number of data used + (* retSizeQueries) = sizeQuery; + (* retNumCandidates) = numCandidates; + + return (SUCCESS); +} + +psaError_t loadRegionsProfile(FILE *fp, char *h_ASCIIQueries, uint32_t *h_ASCIISizeQueries, uint32_t *h_ASCIIPositionQueries, + uint32_t *h_GenomePositionCandidates, uint32_t *h_AlignmentInfo, uint32_t *h_AlignmentScores) +{ + char textLine[FILE_SIZE_LINES]; + uint32_t queryNumber = 0, + sizeCurrentQuery, + numQueryCandidates, + processedCandidates = 0, + processedBases = 0, + totalSizeQueries = 0; + + if (fgets(textLine, FILE_SIZE_LINES, fp) == NULL) + return (E_READING_FILE); + + PSA_ERROR(processQuery(queryNumber, textLine, + h_ASCIIQueries, h_GenomePositionCandidates, h_AlignmentInfo, h_AlignmentScores, + &sizeCurrentQuery, &numQueryCandidates)); + + h_ASCIISizeQueries[queryNumber] = sizeCurrentQuery; + h_ASCIIPositionQueries[queryNumber] = 0; + processedBases = sizeCurrentQuery; + processedCandidates += numQueryCandidates; + queryNumber++; + + while((!feof(fp)) && (fgets(textLine, FILE_SIZE_LINES, fp) != NULL)){ + PSA_ERROR(processQuery(queryNumber, textLine, + h_ASCIIQueries + processedBases, + h_GenomePositionCandidates + processedCandidates, + h_AlignmentInfo + processedCandidates, + h_AlignmentScores + processedCandidates, + &sizeCurrentQuery, &numQueryCandidates)); + + h_ASCIISizeQueries[queryNumber] = sizeCurrentQuery; + h_ASCIIPositionQueries[queryNumber] = processedBases; + processedBases += sizeCurrentQuery; + processedCandidates += numQueryCandidates; + queryNumber++; + } + + return (SUCCESS); +} \ No newline at end of file diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_regions.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_regions.c new file mode 100644 index 0000000000000000000000000000000000000000..d7a61badb3effc5a7d6b3a511bb87306b86c97f9 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_regions.c @@ -0,0 +1,168 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_regions + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: API Interface to process GEM regions. + */ + +#include "../include/psa_regions.h" + +psaError_t initRegions(regions_t **regions, uint32_t numQueries, uint32_t numCandidates, uint32_t numAlignments) +{ + (* regions) = (regions_t *) malloc(sizeof(regions_t)); + if((* regions) == NULL) + + (* regions)->distance = 0.0; + (* regions)->averageSizeQuery = 0; + (* regions)->averageCandidatesPerQuery = 0; + + PSA_ERROR(initSequences(&((* regions)->candidates), numCandidates)); + PSA_ERROR(initSequences(&((* regions)->queries), numQueries)); + PSA_ERROR(initAlignments(&((* regions)->alignments), numAlignments)); + + return (SUCCESS); +} + +psaError_t allocateRegions(regions_t *regions, float distance, + uint32_t totalSizeQueries, seq_format_t QUERIES_ASCII, + uint32_t totalSizeCandidates, seq_format_t CANDIDATES_ASCII) +{ + if (regions == NULL) return (E_ALLOCATE_MEM); + + regions->distance = distance; + regions->averageSizeQuery = totalSizeQueries / regions->queries->num; + regions->averageCandidatesPerQuery = regions->candidates->num / regions->queries->num; + + PSA_ERROR(allocateSequences(regions->queries, totalSizeQueries, QUERIES_ASCII)); + PSA_ERROR(allocateSequences(regions->candidates, totalSizeCandidates, CANDIDATES_ASCII)); + PSA_ERROR(allocateAlignments(regions->alignments)); + + return (SUCCESS); +} + +psaError_t loadRegions(FILE *fp, regions_t *regions) +{ + uint32_t result; + + result = fread(®ions->distance, sizeof(float), 1, fp); + if (result != 1) return(E_WRITING_FILE); + result = fread(®ions->averageCandidatesPerQuery, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_WRITING_FILE); + result = fread(®ions->averageSizeQuery, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_WRITING_FILE); + + PSA_ERROR(loadSequences(fp, regions->queries)); + PSA_ERROR(loadSequences(fp, regions->candidates)); + PSA_ERROR(loadAlignments(fp, regions->alignments)); + + return (SUCCESS); +} + +psaError_t saveRegions(FILE *fp, regions_t *regions) +{ + uint32_t result; + + result = fwrite(®ions->distance, sizeof(float), 1, fp); + if (result != 1) return(E_WRITING_FILE); + result = fwrite(®ions->averageCandidatesPerQuery, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_WRITING_FILE); + result = fwrite(®ions->averageSizeQuery, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_WRITING_FILE); + + PSA_ERROR(saveSequences(fp, regions->queries)); + PSA_ERROR(saveSequences(fp, regions->candidates)); + PSA_ERROR(saveAlignments(fp, regions->alignments)); + + return (SUCCESS); +} + + +psaError_t statistics(regions_t *regions) +{ + const uint32_t RANGE_SIZE = 10000; + uint32_t idHistogram, idQuery; + uint32_t queryHistogram[RANGE_SIZE]; + uint32_t numElements = RANGE_SIZE; + + uint32_t minQueryLong = regions->queries->h_size[0]; + uint32_t maxQueryLong = regions->queries->h_size[0]; + + for(idHistogram = 0; idHistogram < numElements; idHistogram++) + queryHistogram[idHistogram] = 0; + + for(idQuery = 0; idQuery < regions->queries->num; idQuery++){ + maxQueryLong = MAX(regions->queries->h_size[idQuery], maxQueryLong); + minQueryLong = MIN(regions->queries->h_size[idQuery], minQueryLong); + } + + for(idQuery = 0; idQuery < regions->queries->num; idQuery++) + queryHistogram[regions->queries->h_size[idQuery]]++; + + printf("Number of queries: %d\n", regions->queries->num); + printf("Number of candidates: %d\n", regions->candidates->num); + printf("Ratio: %.2f\n", (float)regions->candidates->num/(float)regions->queries->num); + printf("Minimum Query Longitud %d - Maximum Query Longitud %d\n", minQueryLong, maxQueryLong); + + for(idHistogram = 0; idHistogram < maxQueryLong; idHistogram++){ + printf("%d\n",queryHistogram[idHistogram]); + } + + return (SUCCESS); +} + +psaError_t printRegions(regions_t *regions, uint32_t numAlignments, uint32_t reformated) +{ + uint32_t i, idAlignment; + char ASCIIBase; + + printf("REGIONS: \n"); + printf("distance: %f \n", regions->distance); + printf("averageSizeQuery: %d \n", regions->averageSizeQuery); + printf("averageCandidatesPerQuery: %d \n", regions->averageCandidatesPerQuery); + + printf("QUERIES: \n"); + printf("formats: %d \n", regions->queries->formats); + printf("num: %d \n", regions->queries->num); + printf("numASCIIEntries: %d \n", regions->queries->numASCIIEntries); + + for(idAlignment = 0; idAlignment < numAlignments; ++idAlignment){ + printf("Queries %d: ", idAlignment); + for(i = regions->queries->h_ASCIIposition[idAlignment]; i < regions->queries->h_ASCIIposition[idAlignment+1]; ++i){ + if(reformated) ASCIIBase = ASCIItoUpperCase(regions->queries->h_ASCII[i]); + printf("%c", ASCIIBase); + } + printf("\n"); + printf("Query %d size: %d \n", idAlignment, regions->queries->h_size[0]); + } + + printf("CANDIDATES: \n"); + printf("formats: %d \n", regions->candidates->formats); + printf("num: %d \n", regions->candidates->num); + printf("numASCIIEntries: %d \n", regions->candidates->numASCIIEntries); + + for(idAlignment = 0; idAlignment < numAlignments; ++idAlignment){ + printf("Candidate %d: ", idAlignment); + for(i = regions->candidates->h_ASCIIposition[idAlignment]; i < regions->candidates->h_ASCIIposition[idAlignment+1]; ++i){ + if(reformated) ASCIIBase = ASCIItoUpperCase(regions->candidates->h_ASCII[i]); + printf("%c", ASCIIBase); + } + printf("\n"); + printf("Candidate %d size: %d \n", idAlignment, regions->candidates->h_size[0]); + } + + return (SUCCESS); +} + +psaError_t freeRegions(regions_t **regions) +{ + if((* regions) != NULL){ + PSA_ERROR(freeSequences(&(* regions)->queries)); + PSA_ERROR(freeSequences(&(* regions)->candidates)); + PSA_ERROR(freeAlignments(&(* regions)->alignments)); + + free((* regions)); + (* regions) = NULL; + } + + return (SUCCESS); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_sequences.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_sequences.c new file mode 100644 index 0000000000000000000000000000000000000000..478b0ae9b42dbd76b12ca429cd3b9c34c29823d9 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_sequences.c @@ -0,0 +1,677 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_sequences + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: API Interface to manage / transform string sequence formats. + */ + +#include "../include/psa_sequences.h" + +psaError_t initSequences(sequences_t **sequences, uint32_t numSequences) +{ + (* sequences) = (sequences_t *) malloc(sizeof(sequences_t)); + if((* sequences) == NULL) return (E_ALLOCATE_MEM); + + /* sequences info */ + (* sequences)->num = numSequences; + (* sequences)->formats = SEQ_VOID; + /* Ref absolute position */ + (* sequences)->h_refPosition = NULL; + (* sequences)->d_refPosition = NULL; + /* PEQ structures */ + (* sequences)->numPEQEntries = 0; + (* sequences)->h_PEQ = NULL; + (* sequences)->d_PEQ = NULL; + (* sequences)->h_PEQposition = NULL; + (* sequences)->d_PEQposition = NULL; + /* RAW structures */ + (* sequences)->numRAWEntries = 0; + (* sequences)->h_RAW = NULL; + (* sequences)->d_RAW = NULL; + (* sequences)->h_RAWposition = NULL; + (* sequences)->d_RAWposition = NULL; + /* ASCII structures (debug) */ + (* sequences)->numASCIIEntries = 0; + (* sequences)->h_ASCII = NULL; + (* sequences)->d_ASCII = NULL; + (* sequences)->h_ASCIIposition = NULL; + (* sequences)->d_ASCIIposition = NULL; + /* Common data to all formats */ + (* sequences)->h_size = NULL; + (* sequences)->d_size = NULL; + + return (SUCCESS); +} + +psaError_t allocateSequences(sequences_t *sequences, uint32_t numEntries, seq_format_t SEQ_FORMAT) +{ + if (sequences == NULL) + return (E_ALLOCATE_MEM); + + if(SEQ_REF_POS & SEQ_FORMAT){ + sequences->h_refPosition = (uint32_t *) malloc(sequences->num * sizeof(uint32_t)); + if (sequences->h_refPosition == NULL) PSA_ERROR(E_ALLOCATE_MEM); + } + + if(SEQ_PEQ_4x32b & SEQ_FORMAT){ + /* PEQ structures */ + sequences->numPEQEntries = numEntries; + + if(sequences->h_PEQ != NULL) free(sequences->h_PEQ); + sequences->h_PEQ = (PEQEntry_t *) malloc(sequences->numPEQEntries * sizeof(PEQEntry_t)); + if (sequences->h_PEQ == NULL) return (E_ALLOCATE_MEM); + + if(sequences->h_PEQposition != NULL) free(sequences->h_PEQposition); + sequences->h_PEQposition = (uint32_t *) malloc(sequences->num * sizeof(uint32_t)); + if (sequences->h_PEQposition == NULL) return (E_ALLOCATE_MEM); + } + + if(SEQ_RAW & SEQ_FORMAT){ + /* RAW structures */ + sequences->numRAWEntries = numEntries; + + if(sequences->h_RAW != NULL) free(sequences->h_RAW); + sequences->h_RAW = (RAWEntry_t *) malloc(sequences->numRAWEntries * sizeof(RAWEntry_t)); + if (sequences->h_RAW == NULL) return (E_ALLOCATE_MEM); + + if(sequences->h_RAWposition != NULL) free(sequences->h_RAWposition); + sequences->h_RAWposition = (uint32_t *) malloc(sequences->num * sizeof(uint32_t)); + if (sequences->h_RAWposition == NULL) return (E_ALLOCATE_MEM); + } + + if(SEQ_ASCII & SEQ_FORMAT){ + /* ASCII structures (debug) */ + sequences->numASCIIEntries = numEntries; + + if(sequences->h_ASCII != NULL) free(sequences->h_ASCII); + sequences->h_ASCII = (ASCIIEntry_t *) malloc(sequences->numASCIIEntries * sizeof(ASCIIEntry_t)); + if (sequences->h_ASCII == NULL) return (E_ALLOCATE_MEM); + + if(sequences->h_ASCIIposition != NULL) free(sequences->h_ASCIIposition); + sequences->h_ASCIIposition = (uint32_t *) malloc(sequences->num * sizeof(uint32_t)); + if (sequences->h_ASCIIposition == NULL) return (E_ALLOCATE_MEM); + } + + if(sequences->formats == SEQ_VOID){ + /* Common data to all formats */ + if(sequences->h_size != NULL) free(sequences->h_size); + sequences->h_size = (uint32_t *) malloc(sequences->num * sizeof(uint32_t)); + if (sequences->h_size == NULL) return (E_ALLOCATE_MEM); + } + + /* sequences info */ + sequences->formats |= SEQ_FORMAT; + + return (SUCCESS); +} + +uint32_t ASCIIto4bits(char base) +{ + switch(base) + { + case 'A': + case 'a': + return(1); + case 'C': + case 'c': + return(2); + case 'G': + case 'g': + return(4); + case 'T': + case 't': + return(8); + default : + return(16); + } +} + +uint32_t ASCIItoIndex(char base) +{ + switch(base) + { + case 'A': + case 'a': + return(0); + case 'C': + case 'c': + return(1); + case 'G': + case 'g': + return(2); + case 'T': + case 't': + return(3); + default : + return(4); + } +} + +char ASCIItoUpperCase(char base) +{ + switch(base) + { + case 'A': + case 'a': + return('A'); + case 'C': + case 'c': + return('C'); + case 'G': + case 'g': + return('G'); + case 'T': + case 't': + return('T'); + default : + return('A'); + } +} + +psaError_t ASCIItoPEQ_32bits(char *h_ASCII, uint32_t idSubPEQ, PEQEntry_t *PEQEntry, int numBases) +{ + int i; + uint32_t indexBase; + uint32_t bitmapA = 0; + uint32_t bitmapC = 0; + uint32_t bitmapG = 0; + uint32_t bitmapT = 0; + uint32_t bitmapN = 0; + + for(i = 0; i < numBases; i++){ + indexBase = ASCIIto4bits(h_ASCII[i]); + bitmapA |= ((indexBase & 1 ) ) << i; + bitmapC |= ((indexBase & 2 ) >> 1) << i; + bitmapG |= ((indexBase & 4 ) >> 2) << i; + bitmapT |= ((indexBase & 8 ) >> 3) << i; + bitmapN |= ((indexBase & 16) >> 4) << i; + } + + PEQEntry->bitmap[0][idSubPEQ] = bitmapA; + PEQEntry->bitmap[1][idSubPEQ] = bitmapC; + PEQEntry->bitmap[2][idSubPEQ] = bitmapG; + PEQEntry->bitmap[3][idSubPEQ] = bitmapT; + PEQEntry->bitmap[4][idSubPEQ] = bitmapN; + + return (SUCCESS); +} + +psaError_t ASCIItoPEQ_31bits(char *h_ASCII, uint32_t idSubPEQ, PEQEntry_t *PEQEntry, int numBases) +{ + int i; + uint32_t indexBase; + uint32_t bitmap[5] = {0,0,0,0,0}; + uint32_t bitmask = 1; + + for(i = 0; i < numBases; i++){ + indexBase = ASCIItoIndex(h_ASCII[i]); + bitmask <<= 1; + bitmap[indexBase] |= bitmask; + } + + PEQEntry->bitmap[0][idSubPEQ] = bitmap[0] >> 1; + PEQEntry->bitmap[1][idSubPEQ] = bitmap[1] >> 1; + PEQEntry->bitmap[2][idSubPEQ] = bitmap[2] >> 1; + PEQEntry->bitmap[3][idSubPEQ] = bitmap[3] >> 1; + PEQEntry->bitmap[4][idSubPEQ] = bitmap[4] >> 1; + + return (SUCCESS); +} + +psaError_t sequences_positionASCIItoPEQ_128bits(uint32_t *h_PEQposition, uint32_t *h_size, uint32_t num) +{ + uint32_t idSequence, sizeSequence, totalEntriesPEQ = 0; + + const uint32_t BASES_PER_PEQ_ENTRY = PEQ_SUB_ENTRIES * UINT32_LENGTH; + + for(idSequence = 0; idSequence < num; ++idSequence){ + h_PEQposition[idSequence] = totalEntriesPEQ; + sizeSequence = h_size[idSequence]; + totalEntriesPEQ += DIV_CEIL(sizeSequence, BASES_PER_PEQ_ENTRY); + } + + return (SUCCESS); +} + +uint32_t sequences_totalEntriesPEQ_4x31bits(uint32_t *h_size, uint32_t num) +{ + uint32_t sizeSequence, idSequence, totalEntriesPEQ = 0; + + const uint32_t BASES_PER_PEQ_ENTRY = PEQ_SUB_ENTRIES * (UINT32_LENGTH - 1); + + for(idSequence = 0; idSequence < num; ++idSequence){ + sizeSequence = h_size[idSequence]; + totalEntriesPEQ += DIV_CEIL(sizeSequence, BASES_PER_PEQ_ENTRY); + } + + return (totalEntriesPEQ); +} + +uint32_t sequences_totalEntriesRAW(uint32_t *h_size, uint32_t num, const uint32_t baseSize) +{ + uint32_t sizeSequence, idSequence, totalEntriesRAW = 0; + + const uint32_t RAW_BASES_PER_ENTRY = UINT64_LENGTH / baseSize; + + for(idSequence = 0; idSequence < num; ++idSequence){ + sizeSequence = h_size[idSequence]; + totalEntriesRAW += DIV_CEIL(sizeSequence, RAW_BASES_PER_ENTRY); + } + + return (totalEntriesRAW); +} + +uint32_t sequences_totalEntriesHlfRAW(uint32_t *h_size, uint32_t num, const uint32_t baseSize) +{ + uint32_t sizeSequence, idSequence, totalEntriesHlfRAW = 0; + + const uint32_t RAW_BASES_PER_ENTRY = UINT32_LENGTH / baseSize; + + for(idSequence = 0; idSequence < num; ++idSequence){ + sizeSequence = h_size[idSequence]; + totalEntriesHlfRAW += DIV_CEIL(sizeSequence, RAW_BASES_PER_ENTRY); + } + + return (totalEntriesHlfRAW); +} + + +psaError_t sequenceASCIItoPEQ_4x32bits(char *h_ASCII, uint32_t sizeSequence, PEQEntry_t *h_PEQ) +{ + int32_t pos, idSequence, intraSequence = 0; + int32_t processedBases = 0; + int32_t idSubPEQ; + int32_t intraBasesProcessed, numBases; + + //const uint32_t PEQ_SUB_ENTRIES = 4; + const uint32_t BASES_PER_PEQ_ENTRY = PEQ_SUB_ENTRIES * UINT32_LENGTH; + + for(pos = 0; pos < sizeSequence; pos += BASES_PER_PEQ_ENTRY){ + for(idSubPEQ = 0; idSubPEQ < PEQ_SUB_ENTRIES; ++idSubPEQ){ + intraBasesProcessed = UINT32_LENGTH * idSubPEQ; + numBases = MIN(sizeSequence - (pos + intraBasesProcessed), UINT32_LENGTH); + numBases = (numBases < 0) ? 0 : numBases; + ASCIItoPEQ_32bits(h_ASCII + processedBases + pos + intraBasesProcessed, idSubPEQ, h_PEQ + intraSequence, numBases); + } + intraSequence++; + } + + return (SUCCESS); +} + +psaError_t sequenceASCIItoPEQ_4x31bits(char *h_ASCII, uint32_t sizeSequence, PEQEntry_t *h_PEQ) +{ + int32_t pos, idSequence, intraSequence = 0; + int32_t processedBases = 0; + int32_t idSubPEQ; + int32_t intraBasesProcessed, numBases; + + //const uint32_t PEQ_SUB_ENTRIES = 4; + const uint32_t BASES_PER_PEQ_ENTRY = PEQ_SUB_ENTRIES * (UINT32_LENGTH - 1); + + for(pos = 0; pos < sizeSequence; pos += BASES_PER_PEQ_ENTRY){ + for(idSubPEQ = 0; idSubPEQ < PEQ_SUB_ENTRIES; ++idSubPEQ){ + intraBasesProcessed = (UINT32_LENGTH - 1) * idSubPEQ; + numBases = MIN(sizeSequence - (pos + intraBasesProcessed), (UINT32_LENGTH - 1)); + numBases = (numBases < 0) ? 0 : numBases; + ASCIItoPEQ_31bits(h_ASCII + processedBases + pos + intraBasesProcessed, idSubPEQ, h_PEQ + intraSequence, numBases); + } + intraSequence++; + } + + return (SUCCESS); +} + + +/* +psaError_t sequences_ASCIItoPEQ_4x32bits(char *h_ASCII, PEQEntry_t *h_PEQ, uint32_t *h_PEQposition, uint32_t *h_size, uint32_t num) +{ + int32_t pos, idSequence, intraSequence; + int32_t processedBases = 0; + int32_t startSequenceEntry, idSubPEQ; + int32_t intraBasesProcessed, sizeSequence, numBases; + + //const uint32_t PEQ_SUB_ENTRIES = 4; + const uint32_t BASES_PER_PEQ_ENTRY = PEQ_SUB_ENTRIES * UINT32_LENGTH; + + for(idSequence = 0; idSequence < num; ++idSequence){ + intraSequence = 0; + startSequenceEntry = h_PEQposition[idSequence]; + sizeSequence = h_size[idSequence]; + for(pos = 0; pos < sizeSequence; pos += BASES_PER_PEQ_ENTRY){ + for(idSubPEQ = 0; idSubPEQ < PEQ_SUB_ENTRIES; ++idSubPEQ){ + intraBasesProcessed = UINT32_LENGTH * idSubPEQ; + numBases = MIN(sizeSequence - (pos + intraBasesProcessed), UINT32_LENGTH); + numBases = (numBases < 0) ? 0 : numBases; + ASCIItoPEQ_32bits(h_ASCII + processedBases + pos + intraBasesProcessed, idSubPEQ, h_PEQ + startSequenceEntry + intraSequence, numBases); + } + intraSequence++; + } + processedBases += sizeSequence; + } + + return (SUCCESS); +}*/ + +uint64_t ASCIItoRAW_64bits(unsigned char base) +{ + switch(base) + { + case 'A': + case 'a': + return(ENC_DNA_CHAR_A); + case 'C': + case 'c': + return(ENC_DNA_CHAR_C << (UINT64_LENGTH - RAW_16B_LENGTH)); + case 'G': + case 'g': + return(ENC_DNA_CHAR_G << (UINT64_LENGTH - RAW_16B_LENGTH)); + case 'T': + case 't': + return(ENC_DNA_CHAR_T << (UINT64_LENGTH - RAW_16B_LENGTH)); + default : + return(ENC_DNA_CHAR_N << (UINT64_LENGTH - RAW_16B_LENGTH)); + } +} + +uint32_t ASCIItoRAW_32bits(unsigned char base) +{ + switch(base) + { + case 'A': + case 'a': + return(ENC_DNA_CHAR_A); + case 'C': + case 'c': + return(ENC_DNA_CHAR_C << (UINT32_LENGTH - RAW_4B_LENGTH)); + case 'G': + case 'g': + return(ENC_DNA_CHAR_G << (UINT32_LENGTH - RAW_4B_LENGTH)); + case 'T': + case 't': + return(ENC_DNA_CHAR_T << (UINT32_LENGTH - RAW_4B_LENGTH)); + default : + return(ENC_DNA_CHAR_A << (UINT32_LENGTH - RAW_4B_LENGTH)); + } +} + +psaError_t sequenceASCIItoRAW_4x64bits(const char *h_ASCII, int32_t size, RAWEntry_t *h_RAW) +{ + RAWEntry_t indexBase, bitmap; + uint32_t idEntry, i, sequencePosition; + unsigned char base; + + //4 bits per character using 64 bits + const uint32_t RAW_BASES_PER_ENTRY = UINT64_LENGTH / RAW_16B_LENGTH; + const uint32_t numRAWEntries = DIV_CEIL(size, RAW_BASES_PER_ENTRY); + + for(idEntry = 0; idEntry < numRAWEntries; ++idEntry){ + bitmap = 0; + for(i = 0; i < RAW_BASES_PER_ENTRY; ++i){ + sequencePosition = (idEntry * RAW_BASES_PER_ENTRY) + i; + if (sequencePosition < size) base = h_ASCII[sequencePosition]; + else base = 'N'; //filling reference padding + indexBase = ASCIItoRAW_64bits(base); + bitmap = (bitmap >> RAW_16B_LENGTH) | indexBase; + } + h_RAW[sequencePosition / RAW_BASES_PER_ENTRY] = bitmap; + } + return (SUCCESS); +} + +psaError_t sequenceASCIItoRAW_2x32bits(const char *h_ASCII, int32_t size, RAWHlfEntry_t *h_HlfRAW) +{ + RAWHlfEntry_t indexBase, bitmap; + uint32_t idEntry, i, sequencePosition; + unsigned char base; + + //2 bits per character using 32 bits + const uint32_t RAW_BASES_PER_ENTRY = UINT32_LENGTH / RAW_4B_LENGTH; + const uint32_t numRAWEntries = DIV_CEIL(size, RAW_BASES_PER_ENTRY); + + for(idEntry = 0; idEntry < numRAWEntries; ++idEntry){ + bitmap = 0; + for(i = 0; i < RAW_BASES_PER_ENTRY; ++i){ + sequencePosition = (idEntry * RAW_BASES_PER_ENTRY) + i; + if (sequencePosition < size) base = h_ASCII[sequencePosition]; + else base = 'A'; //filling reference padding + indexBase = ASCIItoRAW_32bits(base); + bitmap = (bitmap >> RAW_4B_LENGTH) | indexBase; + } + h_HlfRAW[sequencePosition / RAW_BASES_PER_ENTRY] = bitmap; + } + return (SUCCESS); +} + + + +psaError_t loadSequenceMFASTA(FILE *fp, uint32_t **h_size, char **h_ASCII, uint32_t **h_ASCIIposition, seq_format_t *formats) +{ + char lineFile[FILE_SIZE_LINES]; + uint32_t sizeFile = 0, position = 0, numGenomes = 1; + int32_t charsRead = 0; + + fseek(fp, 0L, SEEK_END); + sizeFile = ftell(fp); + rewind(fp); + + (* h_ASCII) = (char *) malloc(sizeFile * sizeof(char)); + if ((* h_ASCII) == NULL) return (E_ALLOCATE_MEM); + + (* h_size) = (uint32_t *) malloc(numGenomes * sizeof(uint32_t)); + if ((* h_size) == NULL) return (E_ALLOCATE_MEM); + + (* h_ASCIIposition) = (uint32_t *) malloc(numGenomes * sizeof(uint32_t)); + if ((* h_ASCIIposition) == NULL) return (E_ALLOCATE_MEM); + + if ((fgets(lineFile, FILE_SIZE_LINES, fp) == NULL) || (lineFile[0] != '>')) + return (E_NO_MULTIFASTA_FILE); + + while((!feof(fp)) && (fgets(lineFile, FILE_SIZE_LINES, fp) != NULL)){ + if (lineFile[0] != '>'){ + charsRead = strlen(lineFile); + if(charsRead) charsRead--; + memcpy(((* h_ASCII) + position), lineFile, charsRead); + position += charsRead; + } + } + + (* formats) |= SEQ_ASCII; + (* h_size)[0] = position; + (* h_ASCIIposition)[0] = 0; + + return (SUCCESS); +} + +psaError_t saveSequences(FILE *fp, sequences_t *sequences) +{ + uint32_t result; + + if(sequences->formats != SEQ_VOID){ + + result = fwrite(&sequences->num, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_WRITING_FILE); + result = fwrite(&sequences->formats, sizeof(seq_format_t), 1, fp); + if (result != 1) return(E_WRITING_FILE); + + result = fwrite(sequences->h_size, sizeof(uint32_t), sequences->num, fp); + if (result != sequences->num) return(E_WRITING_FILE); + + if(sequences->formats & SEQ_REF_POS){ + result = fwrite(sequences->h_refPosition, sizeof(uint32_t), sequences->num, fp); + if (result != sequences->num) return(E_WRITING_FILE); + } + if(sequences->formats & SEQ_PEQ_4x32b){ + result = fwrite(&sequences->numPEQEntries, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_WRITING_FILE); + result = fwrite(sequences->h_PEQ, sizeof(PEQEntry_t), sequences->numPEQEntries, fp); + if (result != sequences->numPEQEntries) return(E_WRITING_FILE); + result = fwrite(sequences->h_PEQposition, sizeof(uint32_t), sequences->num, fp); + if (result != sequences->num) return(E_WRITING_FILE); + } + if(sequences->formats & SEQ_RAW){ + result = fwrite(&sequences->numRAWEntries, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_WRITING_FILE); + result = fwrite(sequences->h_RAW, sizeof(RAWEntry_t), sequences->numRAWEntries, fp); + if (result != sequences->numRAWEntries) return(E_WRITING_FILE); + result = fwrite(sequences->h_RAWposition, sizeof(uint32_t), sequences->num, fp); + if (result != sequences->num) return(E_WRITING_FILE); + } + if(sequences->formats & SEQ_HLF_RAW){ + result = fwrite(&sequences->numRAWHlfEntries, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_WRITING_FILE); + result = fwrite(sequences->h_HlfRAW, sizeof(RAWHlfEntry_t), sequences->numRAWHlfEntries, fp); + if (result != sequences->numRAWHlfEntries) return(E_WRITING_FILE); + result = fwrite(sequences->h_HlfRAWposition, sizeof(uint32_t), sequences->num, fp); + if (result != sequences->num) return(E_WRITING_FILE); + } + if(sequences->formats & SEQ_ASCII){ + result = fwrite(&sequences->numASCIIEntries, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_WRITING_FILE); + result = fwrite(sequences->h_ASCII, sizeof(ASCIIEntry_t), sequences->numASCIIEntries, fp); + if (result != sequences->numASCIIEntries) return(E_WRITING_FILE); + result = fwrite(sequences->h_ASCIIposition, sizeof(uint32_t), sequences->num, fp); + if (result != sequences->num) return(E_WRITING_FILE); + } + } + + return (SUCCESS); +} + +psaError_t loadSequences(FILE *fp, sequences_t *sequences) +{ + uint32_t result; + + if(sequences->formats == SEQ_VOID){ + + result = fread(&sequences->num, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_READING_FILE); + result = fread(&sequences->formats, sizeof(seq_format_t), 1, fp); + if (result != 1) return(E_READING_FILE); + + sequences->h_size = (uint32_t *) malloc(sequences->num * sizeof(uint32_t)); + if (sequences->h_size == NULL) return (E_ALLOCATE_MEM); + result = fread(sequences->h_size, sizeof(uint32_t), sequences->num, fp); + if (result != sequences->num) return(E_READING_FILE); + + if(sequences->formats & SEQ_REF_POS){ + sequences->h_refPosition = (uint32_t *) malloc(sequences->num * sizeof(uint32_t)); + if (sequences->h_refPosition == NULL) return (E_ALLOCATE_MEM); + result = fread(sequences->h_refPosition, sizeof(uint32_t), sequences->num, fp); + if (result != sequences->num) return(E_WRITING_FILE); + } + if(sequences->formats & SEQ_PEQ_4x32b){ + result = fread(&sequences->numPEQEntries, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_READING_FILE); + + sequences->h_PEQ = (PEQEntry_t *) malloc(sequences->numPEQEntries * sizeof(PEQEntry_t)); + if (sequences->h_PEQ == NULL) return (E_ALLOCATE_MEM); + result = fread(sequences->h_PEQ, sizeof(PEQEntry_t), sequences->numPEQEntries, fp); + if (result != sequences->numPEQEntries) return(E_READING_FILE); + + sequences->h_PEQposition = (uint32_t *) malloc(sequences->num * sizeof(uint32_t)); + if (sequences->h_PEQposition == NULL) return (E_ALLOCATE_MEM); + result = fread(sequences->h_PEQposition, sizeof(uint32_t), sequences->num, fp); + if (result != sequences->num) return(E_READING_FILE); + } + if(sequences->formats & SEQ_RAW){ + result = fread(&sequences->numRAWEntries, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_READING_FILE); + + sequences->h_RAW = (RAWEntry_t *) malloc(sequences->numRAWEntries * sizeof(RAWEntry_t)); + if (sequences->h_RAW == NULL) return (E_ALLOCATE_MEM); + result = fread(sequences->h_RAW, sizeof(RAWEntry_t), sequences->numRAWEntries, fp); + if (result != sequences->numRAWEntries) return(E_READING_FILE); + + sequences->h_RAWposition = (uint32_t *) malloc(sequences->num * sizeof(uint32_t)); + if (sequences->h_RAWposition == NULL) return (E_ALLOCATE_MEM); + result = fread(sequences->h_RAWposition, sizeof(uint32_t), sequences->num, fp); + if (result != sequences->num) return(E_READING_FILE); + } + if(sequences->formats & SEQ_HLF_RAW){ + result = fread(&sequences->numRAWHlfEntries, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_READING_FILE); + + sequences->h_HlfRAW = (RAWHlfEntry_t *) malloc(sequences->numRAWHlfEntries * sizeof(RAWHlfEntry_t)); + if (sequences->h_HlfRAW == NULL) return (E_ALLOCATE_MEM); + result = fread(sequences->h_HlfRAW, sizeof(RAWHlfEntry_t), sequences->numRAWHlfEntries, fp); + if (result != sequences->numRAWHlfEntries) return(E_READING_FILE); + + sequences->h_HlfRAWposition = (uint32_t *) malloc(sequences->num * sizeof(uint32_t)); + if (sequences->h_HlfRAWposition == NULL) return (E_ALLOCATE_MEM); + result = fread(sequences->h_HlfRAWposition, sizeof(uint32_t), sequences->num, fp); + if (result != sequences->num) return(E_READING_FILE); + } + if(sequences->formats & SEQ_ASCII){ + result = fread(&sequences->numASCIIEntries, sizeof(uint32_t), 1, fp); + if (result != 1) return(E_READING_FILE); + + sequences->h_ASCII = (ASCIIEntry_t *) malloc(sequences->numASCIIEntries * sizeof(ASCIIEntry_t)); + if (sequences->h_ASCII == NULL) return (E_ALLOCATE_MEM); + result = fread(sequences->h_ASCII, sizeof(ASCIIEntry_t), sequences->numASCIIEntries, fp); + if (result != sequences->numASCIIEntries) return(E_READING_FILE); + + sequences->h_ASCIIposition = (uint32_t *) malloc(sequences->num * sizeof(uint32_t)); + if (sequences->h_ASCIIposition == NULL) return (E_ALLOCATE_MEM); + result = fread(sequences->h_ASCIIposition, sizeof(uint32_t), sequences->num, fp); + if (result != sequences->num) return(E_READING_FILE); + } + } + + return (SUCCESS); +} + +psaError_t freeSequences(sequences_t **sequences) +{ + if((* sequences) != NULL){ + if((* sequences)->h_PEQ != NULL){ + free((* sequences)->h_PEQ); + (* sequences)->h_PEQ = NULL; + } + + if((* sequences)->h_PEQposition != NULL){ + free((* sequences)->h_PEQposition); + (* sequences)->h_PEQposition = NULL; + } + + if((* sequences)->h_RAW != NULL){ + free((* sequences)->h_RAW); + (* sequences)->h_RAW = NULL; + } + + if((* sequences)->h_RAWposition != NULL){ + free((* sequences)->h_RAWposition); + (* sequences)->h_RAWposition = NULL; + } + + if((* sequences)->h_HlfRAW != NULL){ + free((* sequences)->h_HlfRAW); + (* sequences)->h_HlfRAW = NULL; + } + + if((* sequences)->h_HlfRAWposition != NULL){ + free((* sequences)->h_HlfRAWposition); + (* sequences)->h_HlfRAWposition = NULL; + } + + if((* sequences)->h_ASCII != NULL){ + free((* sequences)->h_ASCII); + (* sequences)->h_ASCII = NULL; + } + + if((* sequences)->h_ASCIIposition != NULL){ + free((* sequences)->h_ASCIIposition); + (* sequences)->h_ASCIIposition = NULL; + } + + if((* sequences)->h_size != NULL){ + free((* sequences)->h_size); + (* sequences)->h_size = NULL; + } + + free((* sequences)); + (* sequences) = NULL; + } + + return (SUCCESS); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_time.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_time.c new file mode 100644 index 0000000000000000000000000000000000000000..288498759784395e26df95ba8e648431e3d8e457 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/src/psa_time.c @@ -0,0 +1,30 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: psa_time + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: API Interface timming definitions for CPU. + */ + +#include "../include/psa_time.h" + +double sampleTime() +{ + struct timespec tv; + + #ifdef __MACH__ // OS X does not have clock_gettime, use clock_get_time + clock_serv_t cclock; + mach_timespec_t mts; + host_get_clock_service(mach_host_self(), CALENDAR_CLOCK, &cclock); + clock_get_time(cclock, &mts); + mach_port_deallocate(mach_task_self(), cclock); + tv.tv_sec = mts.tv_sec; + tv.tv_nsec = mts.tv_nsec; + + #else + clock_gettime(CLOCK_REALTIME, &tv); + #endif + + return((tv.tv_sec+tv.tv_nsec/1000000000.0)); +} + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/tools/benchmark.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/tools/benchmark.c new file mode 100644 index 0000000000000000000000000000000000000000..e28af0a7c02ade049acd7ce7410dee416c92422c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/tools/benchmark.c @@ -0,0 +1,111 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: benchmark + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Code example of using the PSA GPU interface + * in compiler time link with the appropiate pairwise algorithm. + * This example: (A) extract the candidates from a reference positions + * or + * (B) replicates and packs the candidates in an stream + */ + +#include "../include/psa_commons.h" +#include "../include/psa_errors.h" +#include "../include/psa_pairwise.h" +#include "../include/psa_regions.h" +#include "../include/psa_sequences.h" +#include "../include/psa_time.h" + +#include +#include +#include + +int main(int32_t argc, char *argv[]) +{ + if(argc < 2) { + printBuildInfo(); + printf("Usage: psa-benchmark regionsfile.regions \n"); + printf("Usage: or \n"); + printf("Usage: psa-benchmark regionsfile.regions genome.fasta\n"); + printf("example: bin/psa-benchmark input/regions.1M.prof.1000.400.12.regions \n"); + exit(E_PROGRAM_PARAMETERS); + } + + regions_t *regions = NULL; + sequences_t *genome; + const uint32_t numGenomes = 1; + float workPerCandidate; + char resultsFile[512]; + char *regionsFile = argv[1], *genomeFile; + FILE *fp = NULL; + + /* Measure definitions */ + double ts, ts1, segTime; + int32_t iter = 1, n; + + PSA_ERROR(printBuildInfo()); + + fp = fopen(regionsFile, "rb"); + if (fp == NULL) return(E_OPENING_FILE); + PSA_ERROR(initRegions(®ions, 0, 0, 0)); + PSA_ERROR(loadRegions(fp, regions)); + fclose(fp); + + if(regions->candidates->formats & SEQ_REF_POS){ + genomeFile = argv[2]; + fp = fopen(genomeFile, "rb"); + if (fp == NULL) return(E_OPENING_FILE); + PSA_ERROR(initSequences(&genome, numGenomes)); + PSA_ERROR(loadSequenceMFASTA(fp, &genome->h_size, &genome->h_ASCII, &genome->h_ASCIIposition, &genome->formats)); + fclose(fp); + } + + /* DEBUG REGIONS*/ + //PSA_ERROR(printRegions(regions, 4, 1)); + + #ifdef REFERENCE + PSA_ERROR(transformDataReferences(genome)); + #endif + + PSA_ERROR(transformDataQueries(regions->queries)); + PSA_ERROR(transformDataCandidates(regions->candidates)); + + #if defined(CUDA) && defined(REFERENCE) + PSA_ERROR(transferCPUtoGPUReference(genome, regions->queries, regions->candidates, regions->alignments)); + #endif + #if defined(CUDA) && !defined(REFERENCE) + PSA_ERROR(transferCPUtoGPUStream(regions->queries, regions->candidates, regions->alignments)); + #endif + + ts = sampleTime(); + + #ifdef REFERENCE + for(n = 0; n < iter; ++n) + processPairwiseReference(genome, regions->candidates, regions->queries, regions->alignments); + #else + for(n = 0; n < iter; ++n) + processPairwiseStream(regions->candidates, regions->queries, regions->alignments); + #endif + + ts1 = sampleTime(); + workPerCandidate = regions->averageSizeQuery * (regions->distance * regions->averageSizeQuery); + segTime = (ts1 - ts) / iter; + printf("TIME: \t %f \t GCUPS: \t %f \n", segTime, (workPerCandidate * regions->candidates->num) / 1000000000 / segTime); + printf("AVERAGE_QUERY_SIZE: \t %d, \t AVERAGE_CANDIDATES_PER_QUERY: \t %d, \t NUM_CANDIDATES: \t %d \n", + regions->averageSizeQuery, regions->averageCandidatesPerQuery, regions->candidates->num); + + #ifdef CUDA + PSA_ERROR(transferGPUtoCPU(regions->alignments)); + #endif + + + sprintf(resultsFile, "%s.%s", regionsFile, buildTag()); + fp = fopen(resultsFile, "wb"); + if (fp == NULL) return(E_OPENING_FILE); + PSA_ERROR(saveASCIIAlignments(fp, regions->alignments)); + fclose(fp); + + PSA_ERROR(freeRegions(®ions)); + + return (SUCCESS); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/tools/checksum.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/tools/checksum.c new file mode 100644 index 0000000000000000000000000000000000000000..e7e41ed921db2e635b181571e1e6a95f19ea48b4 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/tools/checksum.c @@ -0,0 +1,261 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: checksum + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: This tool process the outputs of two alignment sets and + * process the differences with stadistics + * (ideal to analize the required precision of the data) + */ + +#include +#include +#include +#include + +#define DIV_CEIL(NUMERATOR,DENOMINATOR) (((NUMERATOR)+((DENOMINATOR)-1))/(DENOMINATOR)) +#define CATCH_ERROR(error) {{if (error) { fprintf(stderr, "%s\n", processError(error)); exit(EXIT_FAILURE); }}} +#ifndef MIN + #define MIN(_a, _b) (((_a) < (_b)) ? (_a) : (_b)) +#endif + +#ifndef TRUE + #define TRUE 1 +#endif + +#ifndef FALSE + #define FALSE 0 +#endif + +#ifndef MATCH_SCORE + #define MATCH_SCORE 2 +#endif + +typedef struct { + uint32_t column; + uint32_t score; +} resEntry_t; + +typedef struct { + uint32_t numResults; + resEntry_t* h_results; + char *h_verified; +} res_t; + +int loadResults(const char *fn, void **results) +{ + FILE *fp = NULL; + res_t *res = (res_t *) malloc(sizeof(res_t)); + uint32_t idResult, column, score, idCandidate; + size_t result; + + fp = fopen(fn, "r"); + if (fp == NULL) return (2); + + res->h_results = NULL; + fscanf(fp, "%u", &res->numResults); + //DEBUG + res->numResults -= 4; + + res->h_results = (resEntry_t *) malloc(res->numResults * sizeof(resEntry_t)); + if (res->h_results == NULL) return (45); + res->h_verified = (char *) malloc(res->numResults * sizeof(char)); + if (res->h_verified == NULL) return (45); + + for(idResult = 0; idResult < res->numResults; idResult++){ + fscanf(fp, "%u %u %u", &idCandidate, &score, &column); + res->h_results[idResult].column = column; + res->h_results[idResult].score = score; + res->h_verified[idResult] = TRUE; + } + + fclose(fp); + (* results) = res; + return (0); +} + +int checkResults(void *newResults) +{ + res_t *newRes = (res_t *) newResults; + + uint biasedNumber = 16; + uint maxScoring = 255 - biasedNumber - MATCH_SCORE; + uint sizeOfGroup = 4; + + uint idCandidate = 0, idGroup, numResults = newRes->numResults; + uint newCandidateScore, idIntraGroup; + uint numGroups = DIV_CEIL(numResults, sizeOfGroup); + + uint totalFalsePositives = 0, totalGroupsFalsePositives = 0; + + for(idGroup = 0; idGroup < numGroups; ++idGroup){ + uint correctness = TRUE; + + for(idIntraGroup = 0; idIntraGroup < sizeOfGroup; ++idIntraGroup){ + idCandidate = idGroup * sizeOfGroup + idIntraGroup; + newCandidateScore = newRes->h_results[idCandidate].score; + if(newCandidateScore >= maxScoring) correctness = FALSE; + } + + if(correctness == FALSE){ + totalGroupsFalsePositives++; + totalFalsePositives += sizeOfGroup; + } + + for(idIntraGroup = 0; idIntraGroup < sizeOfGroup; ++idIntraGroup){ + idCandidate = idGroup * sizeOfGroup + idIntraGroup; + newRes->h_verified[idCandidate] = correctness; + } + } + + printf("Number of candidates benchmarked: \t\t [ %d ]\n", numResults); + printf("Total 'False positives' REPORTED: \t\t %d \t\t(%3.2f \%)\n", totalFalsePositives, (float)totalFalsePositives/numResults * 100); + printf("\t => Groups REPORTED: \t\t\t %d \t\t(%3.2f \%)\n", totalGroupsFalsePositives, (float)totalGroupsFalsePositives/numResults * 100); + + return(0); +} + +int compareResults(void *oldResults, void *newResults) +{ + res_t *oldRes = (res_t *) oldResults; + res_t *newRes = (res_t *) newResults; + + uint idCandidate, numResults; + uint biasedNumber = 16; + uint maxScoring = 255 - biasedNumber - MATCH_SCORE; + uint oldCandidateScore, newCandidateScore; + + uint totalMaxScoring = 0; + uint totalUnderMaxScoring = 0; + uint diffScores = 0; + + numResults = MIN(oldRes->numResults, newRes->numResults); + for(idCandidate = 0; idCandidate < numResults; idCandidate++){ + + oldCandidateScore = oldRes->h_results[idCandidate].score; + newCandidateScore = newRes->h_results[idCandidate].score; + if (oldCandidateScore != newCandidateScore){ + oldRes->h_verified[idCandidate] = FALSE; + diffScores++; + + if(newCandidateScore >= maxScoring) totalMaxScoring++; + if(newCandidateScore < maxScoring) totalUnderMaxScoring++; + } + } + + printf("\t => Total with maxScoring: \t\t %d \t\t(%3.2f \%)\n", totalMaxScoring, (float)totalMaxScoring/numResults * 100); + printf("\t => Total under maxScoring: \t\t %d \t\t(%3.2f \%)\n", totalUnderMaxScoring, (float)totalUnderMaxScoring/numResults * 100); + + printf("TOTAL DIFFERENT RESULTS: \t\t\t %d \t\t(%3.2f \%)\n", diffScores, (float)diffScores/numResults * 100); + return(0); +} + +int intersectResults(void *oldResults, void *newResults) +{ + res_t *oldRes = (res_t *) oldResults; + res_t *newRes = (res_t *) newResults; + + uint idCandidate, numResults; + uint biasedNumber = 16; + uint maxScoring = 255 - biasedNumber - MATCH_SCORE; + + uint oldCandidateChecksum, newCandidateChecksum; + + uint overheadAlignments = 0; + uint detectedAlignments = 0; + uint undetectedAlignments = 0; + + numResults = MIN(oldRes->numResults, newRes->numResults); + for(idCandidate = 0; idCandidate < numResults; idCandidate++){ + oldCandidateChecksum = oldRes->h_verified[idCandidate]; + newCandidateChecksum = newRes->h_verified[idCandidate]; + if ((oldCandidateChecksum == FALSE) && (newCandidateChecksum == FALSE)) detectedAlignments++; + if ((oldCandidateChecksum == FALSE) && (newCandidateChecksum == TRUE)) undetectedAlignments++; + if ((oldCandidateChecksum == TRUE) && (newCandidateChecksum == FALSE)) overheadAlignments++; + } + + printf("Intersection results:\n"); + printf("\t => Total detected alignments: \t\t %d \t\t(%3.2f \%)\n", detectedAlignments, (float)detectedAlignments/numResults * 100); + printf("\t => Total undetected alignments: \t %d \t\t(%3.2f \%)\n", undetectedAlignments, (float)undetectedAlignments/numResults * 100); + printf("\t => Total overhead alignments: \t\t %d \t\t(%3.2f \%)\n", overheadAlignments, (float)overheadAlignments/numResults * 100); + + return(0); +} + +char *processError(int e){ + printf("ERROR: %d\n", e); + switch(e) { + case 0: return "No error"; break; + case 1: return "Error opening reference file"; break; + case 2: return "Error opening queries file"; break; + case 5: return "Error reading candidates"; break; + case 6: return "Error reading original results"; break; + case 30: return "Cannot open reference file"; break; + case 31: return "Cannot allocate reference"; break; + case 33: return "Cannot allocate queries"; break; + case 34: return "Cannot allocate candidates"; break; + case 32: return "Reference file isn't multifasta format"; break; + case 37: return "Cannot open reference file on write mode"; break; + case 42: return "Cannot open queries file"; break; + case 43: return "Cannot allocate queries"; break; + case 45: return "Cannot allocate results"; break; + case 47: return "Cannot open results file for save intervals"; break; + case 48: return "Cannot open results file for load intervals"; break; + case 99: return "Not implemented"; break; + default: return "Unknown error"; + } +} + +int freeResults(void *results) +{ + res_t *res = (res_t *) results; + + if(res->h_results != NULL){ + free(res->h_results); + res->h_results = NULL; + } + + if(res->h_verified != NULL){ + free(res->h_verified); + res->h_verified = NULL; + } + + return(0); +} + +int main(int argc, char *argv[]) +{ + void *oldResults, *newResults; + int32_t error; + unsigned char *oldFile = argv[1]; + unsigned char *newFile = argv[2]; + + if(argc != 3){ + printf("[INFO] This program check the correctness of the SW results \n"); + printf("Usage: ./checksum oldFile newFileToCheck\n"); + return (0); + } + + printf("[INFO] Loading results: %s ...\n", oldFile); + error = loadResults(oldFile, &oldResults); + CATCH_ERROR(error); + + printf("[INFO] Loading results: %s ...\n", newFile); + error = loadResults(newFile, &newResults); + CATCH_ERROR(error); + + printf("[INFO] Checking results ...\n"); + checkResults(newResults); + + printf("[INFO] Comparing results ...\n"); + compareResults(oldResults, newResults); + + printf("[INFO] Intersecting results ...\n"); + intersectResults(oldResults, newResults); + + error = freeResults(oldResults); + CATCH_ERROR(error); + error = freeResults(newResults); + CATCH_ERROR(error); + + return (0); +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/tools/genRegions.c b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/tools/genRegions.c new file mode 100644 index 0000000000000000000000000000000000000000..1231a6d058e13772fc5cac33e18488f58d440562 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/prototypes/psa/tools/genRegions.c @@ -0,0 +1,138 @@ +/* + * PROJECT: Pairwise sequence alignments on GPU + * FILE: genRegions + * AUTHOR(S): Alejandro Chacon + * DESCRIPTION: Generate candidates from *.profile + */ + +#include "../include/psa_sequences.h" +#include "../include/psa_regions.h" +#include "../include/psa_profile.h" +#include "../include/psa_alignments.h" + +psaError_t gatherCandidatesASCIIStream(regions_t *regions, uint32_t *h_genomePositionCandidates, sequences_t *genome) +{ + sequences_t *queries = regions->queries; + sequences_t *candidates = regions->candidates; + alignments_t *alignments = regions->alignments; + + uint32_t idRecoveredSequence, sizeRecoveredSequence, startPositionSequence, idSequenceBase, recoveredBases = 0; + const uint32_t numCandidates = candidates->num; + + for(idRecoveredSequence = 0; idRecoveredSequence < numCandidates; ++idRecoveredSequence){ + sizeRecoveredSequence = regions->distance * queries->h_size[alignments->h_info[idRecoveredSequence]]; + candidates->h_ASCIIposition[idRecoveredSequence] = recoveredBases; + candidates->h_size[idRecoveredSequence] = sizeRecoveredSequence; + startPositionSequence = h_genomePositionCandidates[idRecoveredSequence]; + + for(idSequenceBase = 0; idSequenceBase < sizeRecoveredSequence; ++idSequenceBase) + candidates->h_ASCII[recoveredBases + idSequenceBase] = genome->h_ASCII[startPositionSequence + idSequenceBase]; + + recoveredBases += sizeRecoveredSequence; + + } + + return (SUCCESS); +} + +psaError_t gatherCandidatesASCIIReference(regions_t *regions, sequences_t* genome) +{ + sequences_t *queries = regions->queries; + sequences_t *candidates = regions->candidates; + alignments_t *alignments = regions->alignments; + + uint32_t idRecoveredSequence, sizeRecoveredSequence, startPositionSequence, idSequenceBase, recoveredBases = 0; + const uint32_t numCandidates = candidates->num; + + for(idRecoveredSequence = 0; idRecoveredSequence < numCandidates; ++idRecoveredSequence){ + sizeRecoveredSequence = regions->distance * queries->h_size[alignments->h_info[idRecoveredSequence]]; + candidates->h_ASCIIposition[idRecoveredSequence] = recoveredBases; + candidates->h_size[idRecoveredSequence] = sizeRecoveredSequence; + startPositionSequence = candidates->h_refPosition[idRecoveredSequence]; + + for(idSequenceBase = 0; idSequenceBase < sizeRecoveredSequence; ++idSequenceBase) + candidates->h_ASCII[recoveredBases + idSequenceBase] = genome->h_ASCII[startPositionSequence + idSequenceBase]; + + recoveredBases += sizeRecoveredSequence; + } + + return (SUCCESS); +} + + +int main(int argc, char *argv[]) +{ + + if(argc != 5){ + printf("Usage: gregions mode distance regionsfile.prof \n"); + printf("\t mode = 0 -> ASCII candidates \n"); + printf("\t mode = 1 -> Reference Candidates \n"); + printf("example: bin/gregions 1 1.2 input/regions-score.1M.prof input/human_genome.fasta \n"); + exit(0); + } + + regions_t *regions; + sequences_t *genome; + seq_format_t candidatesMode = SEQ_ASCII, queriesMode = SEQ_ASCII; + uint32_t mode = atof(argv[1]); + float distance = atof(argv[2]); + char *profileFile = argv[3], *genomeFile = argv[4]; + char regionsFile[512]; + FILE *fp = NULL; + + const uint32_t numGenomes = 1; + uint32_t *h_genomePositionCandidates = NULL, *h_regionsProfiledScores = NULL; + uint32_t numQueries = 0, totalSizeQueries = 0, numCandidates = 0, totalSizeCandidates = 0; + + if(mode == 1) candidatesMode |= SEQ_REF_POS; + + fp = fopen(profileFile, "rb"); + if (fp == NULL) return(E_OPENING_FILE); + PSA_ERROR(countRegionsProfile(fp, distance, &numQueries, &totalSizeQueries, &numCandidates, &totalSizeCandidates)); + PSA_ERROR(initRegions(®ions, numQueries, numCandidates, numCandidates)); + PSA_ERROR(allocateRegions(regions, distance, totalSizeQueries, queriesMode, totalSizeCandidates, candidatesMode)); + + h_genomePositionCandidates = (uint32_t *) malloc(numCandidates * sizeof(uint32_t)); + if (h_genomePositionCandidates == NULL) PSA_ERROR(E_ALLOCATE_MEM); + h_regionsProfiledScores = (uint32_t *) malloc(numCandidates * sizeof(uint32_t)); + if (h_regionsProfiledScores == NULL) PSA_ERROR(E_ALLOCATE_MEM); + + rewind(fp); + if(mode == 1) PSA_ERROR(loadRegionsProfile(fp, regions->queries->h_ASCII, regions->queries->h_size, regions->queries->h_ASCIIposition, + regions->candidates->h_refPosition, regions->alignments->h_info, h_regionsProfiledScores)); + else PSA_ERROR(loadRegionsProfile(fp, regions->queries->h_ASCII, regions->queries->h_size, regions->queries->h_ASCIIposition, + h_genomePositionCandidates, regions->alignments->h_info, h_regionsProfiledScores)); + regions->queries->formats |= queriesMode; + fclose(fp); + + fp = fopen(genomeFile, "rb"); + if (fp == NULL) return(E_OPENING_FILE); + PSA_ERROR(initSequences(&genome, numGenomes)); + PSA_ERROR(loadSequenceMFASTA(fp, &genome->h_size, &genome->h_ASCII, &genome->h_ASCIIposition, &genome->formats)); + fclose(fp); + + /* recover the candidates from genome in ASCII rep */ + if (mode == 1) PSA_ERROR(gatherCandidatesASCIIReference(regions, genome)); + else PSA_ERROR(gatherCandidatesASCIIStream(regions, h_genomePositionCandidates, genome)); + regions->candidates->formats |= candidatesMode; + + /* DEBUG REGIONS*/ + #if defined(DEBUG) + PSA_ERROR(printRegions(regions, 4, 1)); + #endif + + if (mode == 1) sprintf(regionsFile, "%s.%u.%u.%u.ref.regions", profileFile, regions->queries->num, regions->averageSizeQuery, regions->averageCandidatesPerQuery);\ + else sprintf(regionsFile, "%s.%u.%u.%u.regions", profileFile, regions->queries->num, regions->averageSizeQuery, regions->averageCandidatesPerQuery); + + fp = fopen(regionsFile, "wb"); + if (fp == NULL) return(E_OPENING_FILE); + PSA_ERROR(saveRegions(fp, regions)); + fclose(fp); + + PSA_ERROR(freeRegions(®ions)); + free(h_genomePositionCandidates); + free(h_regionsProfiledScores); + + return (SUCCESS); +} + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/sw-benchmark/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/nvbio/sw-benchmark/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..4c5904eb4588f8dd07702ef163adbb8d3d9a51ce --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/sw-benchmark/CMakeLists.txt @@ -0,0 +1,21 @@ +nvbio_module(sw-benchmark) + +option(SSWLIB + "Enable SSW" + OFF) + +addsources( +sw-benchmark.cu +) + +if (SSWLIB) +add_definitions(-DSSWLIB) +addsources( +ssw.c +ssw.h +) +endif() + +cuda_add_executable(sw-benchmark ${sw-benchmark_srcs}) +target_link_libraries(sw-benchmark nvbio zlibstatic lz4 crcstatic ${SYSTEM_LINK_LIBRARIES}) + diff --git a/methods/ring/utils/fast_gicp/thirdparty/nvbio/sw-benchmark/sw-benchmark.cu b/methods/ring/utils/fast_gicp/thirdparty/nvbio/sw-benchmark/sw-benchmark.cu new file mode 100644 index 0000000000000000000000000000000000000000..fd7f83c1a9508dd086f3fe857691dd46873de1bc --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/nvbio/sw-benchmark/sw-benchmark.cu @@ -0,0 +1,716 @@ +/* + * nvbio + * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * * Neither the name of the NVIDIA CORPORATION nor the + * names of its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY + * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ + +// sw-benchmark.cu +// + +// +// This project supports comparisons against multi-core SSE-enabled CPUs using +// conditional compilation of the SSW library: +// +// https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library +// +// In order to perform these additional tests, the user must download ssw.h and ssw.c +// from the above repository, copy them in the sw-benchmark directory, and run cmake with +// the option -DSSWLIB=ON. +// +#if defined(SSWLIB) +#include "ssw.h" +#include +#endif + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +enum { MAX_READ_LENGTH = 1024 }; + +using namespace nvbio; + +enum { CACHE_SIZE = 64 }; +typedef nvbio::lmem_cache_tag lmem_cache_tag_type; +typedef nvbio::uncached_tag uncached_tag_type; + +enum { REF_BITS = 2 }; +enum { REF_BIG_ENDIAN = false }; + +// +// An alignment stream class to be used in conjunction with the BatchAlignmentScore class +// +template +struct AlignmentStream +{ + typedef t_aligner_type aligner_type; + + typedef nvbio::cuda::ldg_pointer storage_iterator; + + typedef nvbio::PackedStringLoader< + storage_iterator, + io::SequenceDataTraits::SEQUENCE_BITS, + io::SequenceDataTraits::SEQUENCE_BIG_ENDIAN,cache_type> pattern_loader_type; + typedef typename pattern_loader_type::input_iterator uncached_pattern_iterator; + typedef typename pattern_loader_type::iterator pattern_iterator; + typedef nvbio::vector_view pattern_string; + + typedef nvbio::PackedStringLoader< + storage_iterator, + REF_BITS, + REF_BIG_ENDIAN,uncached_tag_type> text_loader_type; + typedef typename text_loader_type::input_iterator uncached_text_iterator; + typedef typename text_loader_type::iterator text_iterator; + typedef nvbio::vector_view text_string; + + // an alignment context + struct context_type + { + int32 min_score; + aln::BestSink sink; + }; + // a container for the strings to be aligned + struct strings_type + { + pattern_loader_type pattern_loader; + text_loader_type text_loader; + pattern_string pattern; + aln::trivial_quality_string quals; + text_string text; + }; + + // constructor + AlignmentStream( + aligner_type _aligner, + const uint32 _count, + const uint32* _offsets, + const uint32* _patterns, + const uint32 _max_pattern_len, + const uint32 _total_pattern_len, + const uint32* _text, + const uint32 _text_len, + int16* _scores) : + m_aligner ( _aligner ), + m_count (_count), + m_max_pattern_len (_max_pattern_len), + m_total_pattern_len (_total_pattern_len), + m_text_len (_text_len), + m_offsets (_offsets), + m_patterns (storage_iterator(_patterns)), + m_text (storage_iterator(_text)), + m_scores (_scores) {} + + // get the aligner + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + const aligner_type& aligner() const { return m_aligner; }; + + // return the maximum pattern length + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 max_pattern_length() const { return m_max_pattern_len; } + + // return the maximum text length + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 max_text_length() const { return m_text_len; } + + // return the stream size + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 size() const { return m_count; } + + // return the i-th pattern's length + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 pattern_length(const uint32 i, context_type* context) const { return m_offsets[i+1] - m_offsets[i]; } + + // return the i-th text's length + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + uint32 text_length(const uint32 i, context_type* context) const { return m_text_len; } + + // return the total number of cells + uint64 cells() const { return uint64( m_total_pattern_len ) * uint64( m_text_len ); } + + // initialize the i-th context + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + bool init_context( + const uint32 i, + context_type* context) const + { + context->min_score = Field_traits::min(); + return true; + } + + // initialize the i-th context + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void load_strings( + const uint32 i, + const uint32 window_begin, + const uint32 window_end, + const context_type* context, + strings_type* strings) const + { + const uint32 offset = m_offsets[i]; + const uint32 length = m_offsets[i+1] - offset; + + strings->text = text_string( m_text_len, + strings->text_loader.load( + m_text, + m_text_len, + make_uint2( window_begin, window_end ), + false ) ); + + strings->pattern = pattern_string( length, + strings->pattern_loader.load( m_patterns + offset, length ) ); + } + + // handle the output + NVBIO_FORCEINLINE NVBIO_HOST_DEVICE + void output( + const uint32 i, + const context_type* context) const + { + // copy the output score + m_scores[i] = context->sink.score; + } + + aligner_type m_aligner; + uint32 m_count; + uint32 m_max_pattern_len; + uint32 m_total_pattern_len; + uint32 m_text_len; + const uint32* m_offsets; + uncached_pattern_iterator m_patterns; + uncached_text_iterator m_text; + int16* m_scores; +}; + +// A simple kernel to test the speed of alignment without the possible overheads of the BatchAlignmentScore interface +// +template +__global__ void alignment_test_kernel( + const aligner_type aligner, + const uint32 N_probs, + const uint32* offsets, + const uint32* pattern_ptr, + const uint32 text_len, + const uint32* text_ptr, + score_type* score) +{ + const uint32 tid = blockIdx.x * BLOCKDIM + threadIdx.x; + + typedef lmem_cache_tag_type lmem_cache_type; + typedef nvbio::cuda::ldg_pointer storage_iterator; + + typedef nvbio::PackedStringLoader< + storage_iterator, + io::SequenceDataTraits::SEQUENCE_BITS, + io::SequenceDataTraits::SEQUENCE_BIG_ENDIAN,lmem_cache_type> pattern_loader_type; + typedef typename pattern_loader_type::input_iterator uncached_pattern_iterator; + typedef typename pattern_loader_type::iterator pattern_iterator; + typedef nvbio::vector_view pattern_string; + + typedef nvbio::PackedStringLoader< + storage_iterator, + REF_BITS, + REF_BIG_ENDIAN,uncached_tag_type> text_loader_type; + typedef typename text_loader_type::input_iterator uncached_text_iterator; + typedef typename text_loader_type::iterator text_iterator; + typedef nvbio::vector_view text_string; + + if (tid >= N_probs) + return; + + const uint32 pattern_off = offsets[tid]; + const uint32 pattern_len = offsets[tid+1] - pattern_off; + + pattern_loader_type pattern_loader; + pattern_string pattern = pattern_string( pattern_len, pattern_loader.load( uncached_pattern_iterator( pattern_ptr ) + pattern_off, pattern_len ) ); + + text_loader_type text_loader; + text_string text = text_string( text_len, text_loader.load( uncached_text_iterator( text_ptr ), text_len ) ); + + aln::BestSink sink; + + aln::alignment_score( + aligner, + pattern, + aln::trivial_quality_string(), + text, + Field_traits::min(), + sink ); + + score[tid] = sink.score; +} + +unsigned char nst_nt4_table[256] = { + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5 /*'-'*/, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 +}; + +struct ReferenceCounter +{ + ReferenceCounter() : m_size(0) {} + + void begin_read() {} + void end_read() {} + + void id(const uint8 c) {} + void read(const uint8 c) { ++m_size; } + + uint32 m_size; +}; +struct ReferenceCoder +{ + typedef PackedStream stream_type; + + ReferenceCoder(uint32* storage) : + m_size(0), m_stream( storage ) + {} + + void begin_read() {} + void end_read() {} + + void id(const uint8 c) {} + + void read(const uint8 s) + { + const uint8 c = nst_nt4_table[s]; + + m_stream[ m_size++ ] = c < 4 ? c : 0; + } + + uint32 m_size; + stream_type m_stream; +}; + + +// execute a given batch alignment type on a given stream +// +// \tparam batch_type a \ref BatchAlignment "Batch Alignment" +// \tparam stream_type a stream compatible to the given batch_type +// +// \return average time +// +template +float enact_batch( + batch_type& batch, + const stream_type& stream) +{ + // allow to alloc all the needed temporary storage + const uint64 temp_size = batch_type::max_temp_storage( + stream.max_pattern_length(), + stream.max_text_length(), + stream.size() ); + + Timer timer; + timer.start(); + + // enact the batch + batch.enact( stream, temp_size, NULL ); + + cudaDeviceSynchronize(); + + timer.stop(); + + return timer.seconds(); +} + +// execute and time a batch of full DP alignments using BatchAlignmentScore +// +template +void batch_score_profile( + const stream_type stream) +{ + typedef aln::BatchedAlignmentScore batch_type; // our batch type + + // setup a batch + batch_type batch; + + const float time = enact_batch( + batch, + stream ); + + fprintf(stderr," %5.1f", 1.0e-9f * float(stream.cells())/time ); +} + +// execute and time the batch_score algorithm for all possible schedulers +// +template +void batch_score_profile_all( + const aligner_type aligner, + const uint32 n_tasks, + const uint32* offsets_dvec, + const uint32* pattern_dvec, + const uint32 max_pattern_len, + const uint32 total_pattern_len, + const uint32* text_dvec, + const uint32 text_len, + int16* score_dvec) +{ + { + typedef AlignmentStream stream_type; + + // create a stream + stream_type stream( + aligner, + n_tasks, + offsets_dvec, + pattern_dvec, + max_pattern_len, + total_pattern_len, + text_dvec, + text_len, + score_dvec ); + + // test the DeviceThreadScheduler + batch_score_profile( stream ); + + // test the DeviceStagedThreadScheduler + //batch_score_profile( stream ); + } + { + const uint32 BLOCKDIM = 128; + const uint32 N_BLOCKS = (n_tasks + BLOCKDIM-1) / BLOCKDIM; + + Timer timer; + timer.start(); + + // enact the batch + alignment_test_kernel <<>>( + aligner, + n_tasks, + offsets_dvec, + pattern_dvec, + text_len, + text_dvec, + score_dvec ); + + cudaDeviceSynchronize(); + + timer.stop(); + + const float time = timer.seconds(); + + fprintf(stderr," %5.1f", 1.0e-9f * float(uint64(total_pattern_len)*uint64(text_len))/time ); + } + fprintf(stderr, " GCUPS\n"); +} + +enum AlignmentTest +{ + ALL = 0xFFFFFFFFu, + ED = 1u, + SW = 2u, + GOTOH = 4u, + ED_BANDED = 8u, + SW_BANDED = 16u, + GOTOH_BANDED = 32u, + SSW = 64u +}; + +int main(int argc, char* argv[]) +{ + uint32 TEST_MASK = 0xFFFFFFFFu; + + const char* reads_name = argv[argc-2]; + const char* ref_name = argv[argc-1]; + uint32 threads = omp_get_num_procs(); + io::QualityEncoding qencoding = io::Phred33; + + for (int i = 0; i < argc-2; ++i) + { + if (strcmp( argv[i], "-tests" ) == 0) + { + const std::string tests_string( argv[++i] ); + + char temp[256]; + const char* begin = tests_string.c_str(); + const char* end = begin; + + TEST_MASK = 0u; + + while (1) + { + while (*end != ':' && *end != '\0') + { + temp[end - begin] = *end; + end++; + } + + temp[end - begin] = '\0'; + + if (strcmp( temp, "ed" ) == 0) + TEST_MASK |= ED; + else if (strcmp( temp, "sw" ) == 0) + TEST_MASK |= SW; + else if (strcmp( temp, "gotoh" ) == 0) + TEST_MASK |= GOTOH; + else if (strcmp( temp, "ssw" ) == 0) + TEST_MASK |= SSW; + + if (*end == '\0') + break; + + ++end; begin = end; + } + } + else if (strcmp( argv[i], "-threads" ) == 0) + threads = atoi( argv[++i] ); + } + + fprintf(stderr,"sw-benchmark... started\n"); + + log_visible(stderr, "opening read file \"%s\"\n", reads_name); + SharedPointer read_data_file( + nvbio::io::open_sequence_file(reads_name, + qencoding) + ); + + log_visible(stderr, "reading reference file \"%s\"... started\n", ref_name); + + // read the reference + thrust::host_vector h_ref_storage; + uint32 ref_length; + uint32 ref_words; + { + ReferenceCounter counter; + + FASTA_inc_reader fasta( ref_name ); + if (fasta.valid() == false) + { + fprintf(stderr, " error: unable to open reference file \"%s\"\n", ref_name); + exit(1); + } + while (fasta.read( 1024, counter ) == 1024); + + ref_length = counter.m_size; + ref_words = (ref_length + 15)/16; // # of words at 2 bits per symbol + } + { + h_ref_storage.resize( ref_words ); + ReferenceCoder coder( &h_ref_storage[0] ); + + FASTA_inc_reader fasta( ref_name ); + if (fasta.valid() == false) + { + fprintf(stderr, " error: unable to open reference file \"%s\"\n", ref_name); + exit(1); + } + while (fasta.read( 1024, coder ) == 1024); + } + log_visible(stderr, "reading reference file \"%s\"... done (%u bps)\n", ref_name, ref_length); + + typedef PackedStream ref_stream_type; + + thrust::device_vector d_ref_storage( h_ref_storage ); + ref_stream_type d_ref_stream( nvbio::raw_pointer( d_ref_storage ) ); + + const uint32 batch_size = 256*1024; + + thrust::device_vector score_dvec( batch_size, 0 ); + + #if defined(SSWLIB) + std::vector unpacked_ref( ref_length ); + { + ref_stream_type h_ref_stream( nvbio::raw_pointer( h_ref_storage ) ); + for (uint32 i = 0; i < ref_length; ++i) + unpacked_ref[i] = h_ref_stream[i]; + } + + // Now set the number of threads + omp_set_num_threads( threads ); + + #pragma omp parallel + { + fprintf(stderr, " running on multiple threads\n"); + } + #endif + + io::SequenceDataHost h_read_data; + + while (io::next( DNA_N, &h_read_data, read_data_file.get(), batch_size )) + { + // build the device side representation + const io::SequenceDataDevice d_read_data( h_read_data ); + + const uint32 n_read_symbols = h_read_data.bps(); + + fprintf(stderr," %u reads, avg: %u bps, max: %u bps\n", + h_read_data.size(), + h_read_data.avg_sequence_len(), + h_read_data.max_sequence_len()); + + if (TEST_MASK & GOTOH) + { + aln::SimpleGotohScheme scoring; + scoring.m_match = 2; + scoring.m_mismatch = -1; + scoring.m_gap_open = -2; + scoring.m_gap_ext = -1; + + fprintf(stderr," testing Gotoh scoring speed...\n"); + fprintf(stderr," %15s : ", "global"); + { + batch_score_profile_all( + aln::make_gotoh_aligner( scoring ), + d_read_data.size(), + nvbio::plain_view( d_read_data ).sequence_index(), + nvbio::plain_view( d_read_data ).sequence_storage(), + d_read_data.max_sequence_len(), + n_read_symbols, + nvbio::raw_pointer( d_ref_storage ), + ref_length, + nvbio::raw_pointer( score_dvec ) ); + } + + fprintf(stderr," %15s : ", "semi-global"); + { + batch_score_profile_all( + aln::make_gotoh_aligner( scoring ), + d_read_data.size(), + nvbio::plain_view( d_read_data ).sequence_index(), + nvbio::plain_view( d_read_data ).sequence_storage(), + d_read_data.max_sequence_len(), + n_read_symbols, + nvbio::raw_pointer( d_ref_storage ), + ref_length, + nvbio::raw_pointer( score_dvec ) ); + } + fprintf(stderr," %15s : ", "local"); + { + batch_score_profile_all( + aln::make_gotoh_aligner( scoring ), + d_read_data.size(), + nvbio::plain_view( d_read_data ).sequence_index(), + nvbio::plain_view( d_read_data ).sequence_storage(), + d_read_data.max_sequence_len(), + n_read_symbols, + nvbio::raw_pointer( d_ref_storage ), + ref_length, + nvbio::raw_pointer( score_dvec ) ); + } + } + if (TEST_MASK & ED) + { + fprintf(stderr," testing Edit Distance scoring speed...\n"); + fprintf(stderr," %15s : ", "semi-global"); + { + batch_score_profile_all( + aln::make_edit_distance_aligner(), + d_read_data.size(), + nvbio::plain_view( d_read_data ).sequence_index(), + nvbio::plain_view( d_read_data ).sequence_storage(), + d_read_data.max_sequence_len(), + n_read_symbols, + nvbio::raw_pointer( d_ref_storage ), + ref_length, + nvbio::raw_pointer( score_dvec ) ); + } + } + + #if defined(SSWLIB) + if (TEST_MASK & SSW) + { + fprintf(stderr," testing SSW scoring speed...\n"); + fprintf(stderr," %15s : ", "local"); + + const int8_t mat[4*4] = {2, -1, -1, -1, -1, 2, -1, -1, -1, -1, 2, -1, -1, -1, -1, 2}; + + std::vector unpacked_reads( n_read_symbols ); + + typedef io::SequenceDataAccess read_access_type; + typedef read_access_type::sequence_stream_type read_stream_type; + + const read_access_type reads_access( h_read_data ); + + const read_stream_type packed_reads( reads_access.sequence_stream() ); + + #pragma omp parallel for + for (int i = 0; i < int( n_read_symbols ); ++i) + unpacked_reads[i] = packed_reads[i]; + + Timer timer; + timer.start(); + + #pragma omp parallel for + for (int i = 0; i < int( h_read_data.size() ); ++i) + { + const uint32 read_off = reads_access.sequence_index()[i]; + const uint32 read_len = reads_access.sequence_index()[i+1] - read_off; + + s_profile* prof = ssw_init( &unpacked_reads[read_off], read_len, mat, 4, 2 ); + + s_align* align = ssw_align( + prof, + &unpacked_ref[0], + ref_length, + 2, + 2, + 0u, + 0u, + 0, + 15 ); + + align_destroy( align ); + + init_destroy( prof ); + } + + timer.stop(); + const float time = timer.seconds(); + + fprintf(stderr," %5.1f", 1.0e-9f * float(uint64(n_read_symbols)*uint64(ref_length))/time ); + fprintf(stderr, " GCUPS\n"); + } + #endif + } + fprintf(stderr,"sw-benchmark... done\n"); + return 0; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.appveyor.yml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.appveyor.yml new file mode 100644 index 0000000000000000000000000000000000000000..85445d41a2b2e06576d9a428d7b2ac7d23095ded --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.appveyor.yml @@ -0,0 +1,37 @@ +version: 1.0.{build} +image: +- Visual Studio 2015 +test: off +skip_branch_with_pr: true +build: + parallel: true +platform: +- x86 +environment: + matrix: + - PYTHON: 36 + CONFIG: Debug + - PYTHON: 27 + CONFIG: Debug +install: +- ps: | + $env:CMAKE_GENERATOR = "Visual Studio 14 2015" + if ($env:PLATFORM -eq "x64") { $env:PYTHON = "$env:PYTHON-x64" } + $env:PATH = "C:\Python$env:PYTHON\;C:\Python$env:PYTHON\Scripts\;$env:PATH" + python -W ignore -m pip install --upgrade pip wheel + python -W ignore -m pip install pytest numpy --no-warn-script-location pytest-timeout +- ps: | + Start-FileDownload 'https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.zip' + 7z x eigen-3.3.7.zip -y > $null + $env:CMAKE_INCLUDE_PATH = "eigen-3.3.7;$env:CMAKE_INCLUDE_PATH" +build_script: +- cmake -G "%CMAKE_GENERATOR%" -A "%CMAKE_ARCH%" + -DCMAKE_CXX_STANDARD=14 + -DPYBIND11_WERROR=ON + -DDOWNLOAD_CATCH=ON + -DCMAKE_SUPPRESS_REGENERATION=1 + . +- set MSBuildLogger="C:\Program Files\AppVeyor\BuildAgent\Appveyor.MSBuildLogger.dll" +- cmake --build . --config %CONFIG% --target pytest -- /m /v:m /logger:%MSBuildLogger% +- cmake --build . --config %CONFIG% --target cpptest -- /m /v:m /logger:%MSBuildLogger% +on_failure: if exist "tests\test_cmake_build" type tests\test_cmake_build\*.log* diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.clang-format b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.clang-format new file mode 100644 index 0000000000000000000000000000000000000000..8700fca84d2f3d292c58897f24a4cf0770ed26ca --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.clang-format @@ -0,0 +1,21 @@ +--- +# See all possible options and defaults with: +# clang-format --style=llvm --dump-config +BasedOnStyle: LLVM +AccessModifierOffset: -4 +AlignConsecutiveAssignments: true +AlwaysBreakTemplateDeclarations: Yes +BinPackArguments: false +BinPackParameters: false +BreakBeforeBinaryOperators: All +BreakConstructorInitializers: BeforeColon +ColumnLimit: 99 +IndentCaseLabels: true +IndentPPDirectives: AfterHash +IndentWidth: 4 +Language: Cpp +SpaceAfterCStyleCast: true +# SpaceInEmptyBlock: true # too new +Standard: Cpp11 +TabWidth: 4 +... diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.clang-tidy b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.clang-tidy new file mode 100644 index 0000000000000000000000000000000000000000..e29d929897bd06c6c1c3b1e4a9d54688fa245c12 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.clang-tidy @@ -0,0 +1,13 @@ +FormatStyle: file + +Checks: ' +llvm-namespace-comment, +modernize-use-override, +readability-container-size-empty, +modernize-use-using, +modernize-use-equals-default, +modernize-use-auto, +modernize-use-emplace, +' + +HeaderFilterRegex: 'pybind11/.*h' diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.cmake-format.yaml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.cmake-format.yaml new file mode 100644 index 0000000000000000000000000000000000000000..a2a69f3f897da990a4255b593dc3fcdf4b89a764 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.cmake-format.yaml @@ -0,0 +1,73 @@ +parse: + additional_commands: + pybind11_add_module: + flags: + - THIN_LTO + - MODULE + - SHARED + - NO_EXTRAS + - EXCLUDE_FROM_ALL + - SYSTEM + +format: + line_width: 99 + tab_size: 2 + + # If an argument group contains more than this many sub-groups + # (parg or kwarg groups) then force it to a vertical layout. + max_subgroups_hwrap: 2 + + # If a positional argument group contains more than this many + # arguments, then force it to a vertical layout. + max_pargs_hwrap: 6 + + # If a cmdline positional group consumes more than this many + # lines without nesting, then invalidate the layout (and nest) + max_rows_cmdline: 2 + separate_ctrl_name_with_space: false + separate_fn_name_with_space: false + dangle_parens: false + + # If the trailing parenthesis must be 'dangled' on its on + # 'line, then align it to this reference: `prefix`: the start' + # 'of the statement, `prefix-indent`: the start of the' + # 'statement, plus one indentation level, `child`: align to' + # the column of the arguments + dangle_align: prefix + # If the statement spelling length (including space and + # parenthesis) is smaller than this amount, then force reject + # nested layouts. + min_prefix_chars: 4 + + # If the statement spelling length (including space and + # parenthesis) is larger than the tab width by more than this + # amount, then force reject un-nested layouts. + max_prefix_chars: 10 + + # If a candidate layout is wrapped horizontally but it exceeds + # this many lines, then reject the layout. + max_lines_hwrap: 2 + + line_ending: unix + + # Format command names consistently as 'lower' or 'upper' case + command_case: canonical + + # Format keywords consistently as 'lower' or 'upper' case + # unchanged is valid too + keyword_case: 'upper' + + # A list of command names which should always be wrapped + always_wrap: [] + + # If true, the argument lists which are known to be sortable + # will be sorted lexicographically + enable_sort: true + + # If true, the parsers may infer whether or not an argument + # list is sortable (without annotation). + autosort: false + +# Causes a few issues - can be solved later, possibly. +markup: + enable_markup: false diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/CONTRIBUTING.md b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/CONTRIBUTING.md new file mode 100644 index 0000000000000000000000000000000000000000..08d9e7cb93ae95e44498cbcb26c64570aa88930f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/CONTRIBUTING.md @@ -0,0 +1,358 @@ +Thank you for your interest in this project! Please refer to the following +sections on how to contribute code and bug reports. + +### Reporting bugs + +Before submitting a question or bug report, please take a moment of your time +and ensure that your issue isn't already discussed in the project documentation +provided at [pybind11.readthedocs.org][] or in the [issue tracker][]. You can +also check [gitter][] to see if it came up before. + +Assuming that you have identified a previously unknown problem or an important +question, it's essential that you submit a self-contained and minimal piece of +code that reproduces the problem. In other words: no external dependencies, +isolate the function(s) that cause breakage, submit matched and complete C++ +and Python snippets that can be easily compiled and run in isolation; or +ideally make a small PR with a failing test case that can be used as a starting +point. + +## Pull requests + +Contributions are submitted, reviewed, and accepted using GitHub pull requests. +Please refer to [this article][using pull requests] for details and adhere to +the following rules to make the process as smooth as possible: + +* Make a new branch for every feature you're working on. +* Make small and clean pull requests that are easy to review but make sure they + do add value by themselves. +* Add tests for any new functionality and run the test suite (`cmake --build + build --target pytest`) to ensure that no existing features break. +* Please run [`pre-commit`][pre-commit] to check your code matches the + project style. (Note that `gawk` is required.) Use `pre-commit run + --all-files` before committing (or use installed-mode, check pre-commit docs) + to verify your code passes before pushing to save time. +* This project has a strong focus on providing general solutions using a + minimal amount of code, thus small pull requests are greatly preferred. + +### Licensing of contributions + +pybind11 is provided under a BSD-style license that can be found in the +``LICENSE`` file. By using, distributing, or contributing to this project, you +agree to the terms and conditions of this license. + +You are under no obligation whatsoever to provide any bug fixes, patches, or +upgrades to the features, functionality or performance of the source code +("Enhancements") to anyone; however, if you choose to make your Enhancements +available either publicly, or directly to the author of this software, without +imposing a separate written license agreement for such Enhancements, then you +hereby grant the following license: a non-exclusive, royalty-free perpetual +license to install, use, modify, prepare derivative works, incorporate into +other computer software, distribute, and sublicense such enhancements or +derivative works thereof, in binary and source code form. + + +## Development of pybind11 + +To setup an ideal development environment, run the following commands on a +system with CMake 3.14+: + +```bash +python3 -m venv venv +source venv/bin/activate +pip install -r tests/requirements.txt +cmake -S . -B build -DDOWNLOAD_CATCH=ON -DDOWNLOAD_EIGEN=ON +cmake --build build -j4 +``` + +Tips: + +* You can use `virtualenv` (from PyPI) instead of `venv` (which is Python 3 + only). +* You can select any name for your environment folder; if it contains "env" it + will be ignored by git. +* If you don’t have CMake 3.14+, just add “cmake” to the pip install command. +* You can use `-DPYBIND11_FINDPYTHON=ON` to use FindPython on CMake 3.12+ +* In classic mode, you may need to set `-DPYTHON_EXECUTABLE=/path/to/python`. + FindPython uses `-DPython_ROOT_DIR=/path/to` or + `-DPython_EXECUTABLE=/path/to/python`. + +### Configuration options + +In CMake, configuration options are given with “-D”. Options are stored in the +build directory, in the `CMakeCache.txt` file, so they are remembered for each +build directory. Two selections are special - the generator, given with `-G`, +and the compiler, which is selected based on environment variables `CXX` and +similar, or `-DCMAKE_CXX_COMPILER=`. Unlike the others, these cannot be changed +after the initial run. + +The valid options are: + +* `-DCMAKE_BUILD_TYPE`: Release, Debug, MinSizeRel, RelWithDebInfo +* `-DPYBIND11_FINDPYTHON=ON`: Use CMake 3.12+’s FindPython instead of the + classic, deprecated, custom FindPythonLibs +* `-DPYBIND11_NOPYTHON=ON`: Disable all Python searching (disables tests) +* `-DBUILD_TESTING=ON`: Enable the tests +* `-DDOWNLOAD_CATCH=ON`: Download catch to build the C++ tests +* `-DOWNLOAD_EIGEN=ON`: Download Eigen for the NumPy tests +* `-DPYBIND11_INSTALL=ON/OFF`: Enable the install target (on by default for the + master project) +* `-DUSE_PYTHON_INSTALL_DIR=ON`: Try to install into the python dir + + +
A few standard CMake tricks: (click to expand)

+ +* Use `cmake --build build -v` to see the commands used to build the files. +* Use `cmake build -LH` to list the CMake options with help. +* Use `ccmake` if available to see a curses (terminal) gui, or `cmake-gui` for + a completely graphical interface (not present in the PyPI package). +* Use `cmake --build build -j12` to build with 12 cores (for example). +* Use `-G` and the name of a generator to use something different. `cmake + --help` lists the generators available. + - On Unix, setting `CMAKE_GENERATER=Ninja` in your environment will give + you automatic mulithreading on all your CMake projects! +* Open the `CMakeLists.txt` with QtCreator to generate for that IDE. +* You can use `-DCMAKE_EXPORT_COMPILE_COMMANDS=ON` to generate the `.json` file + that some tools expect. + +

+ + +To run the tests, you can "build" the check target: + +```bash +cmake --build build --target check +``` + +`--target` can be spelled `-t` in CMake 3.15+. You can also run individual +tests with these targets: + +* `pytest`: Python tests only, using the +[pytest](https://docs.pytest.org/en/stable/) framework +* `cpptest`: C++ tests only +* `test_cmake_build`: Install / subdirectory tests + +If you want to build just a subset of tests, use +`-DPYBIND11_TEST_OVERRIDE="test_callbacks.cpp;test_pickling.cpp"`. If this is +empty, all tests will be built. + +You may also pass flags to the `pytest` target by editing `tests/pytest.ini` or +by using the `PYTEST_ADDOPTS` environment variable +(see [`pytest` docs](https://docs.pytest.org/en/2.7.3/customize.html#adding-default-options)). As an example: + +```bash +env PYTEST_ADDOPTS="--capture=no --exitfirst" \ + cmake --build build --target pytest +# Or using abbreviated flags +env PYTEST_ADDOPTS="-s -x" cmake --build build --target pytest +``` + +### Formatting + +All formatting is handled by pre-commit. + +Install with brew (macOS) or pip (any OS): + +```bash +# Any OS +python3 -m pip install pre-commit + +# OR macOS with homebrew: +brew install pre-commit +``` + +Then, you can run it on the items you've added to your staging area, or all +files: + +```bash +pre-commit run +# OR +pre-commit run --all-files +``` + +And, if you want to always use it, you can install it as a git hook (hence the +name, pre-commit): + +```bash +pre-commit install +``` + +### Clang-Format + +As of v2.6.2, pybind11 ships with a [`clang-format`][clang-format] +configuration file at the top level of the repo (the filename is +`.clang-format`). Currently, formatting is NOT applied automatically, but +manually using `clang-format` for newly developed files is highly encouraged. +To check if a file needs formatting: + +```bash +clang-format -style=file --dry-run some.cpp +``` + +The output will show things to be fixed, if any. To actually format the file: + +```bash +clang-format -style=file -i some.cpp +``` + +Note that the `-style-file` option searches the parent directories for the +`.clang-format` file, i.e. the commands above can be run in any subdirectory +of the pybind11 repo. + +### Clang-Tidy + +[`clang-tidy`][clang-tidy] performs deeper static code analyses and is +more complex to run, compared to `clang-format`, but support for `clang-tidy` +is built into the pybind11 CMake configuration. To run `clang-tidy`, the +following recipe should work. Files will be modified in place, so you can +use git to monitor the changes. + +```bash +docker run --rm -v $PWD:/pybind11 -it silkeh/clang:10 +apt-get update && apt-get install python3-dev python3-pytest +cmake -S pybind11/ -B build -DCMAKE_CXX_CLANG_TIDY="$(which clang-tidy);-fix" +cmake --build build +``` + +### Include what you use + +To run include what you use, install (`brew install include-what-you-use` on +macOS), then run: + +```bash +cmake -S . -B build-iwyu -DCMAKE_CXX_INCLUDE_WHAT_YOU_USE=$(which include-what-you-use) +cmake --build build +``` + +The report is sent to stderr; you can pipe it into a file if you wish. + +### Build recipes + +This builds with the Intel compiler (assuming it is in your path, along with a +recent CMake and Python 3): + +```bash +python3 -m venv venv +. venv/bin/activate +pip install pytest +cmake -S . -B build-intel -DCMAKE_CXX_COMPILER=$(which icpc) -DDOWNLOAD_CATCH=ON -DDOWNLOAD_EIGEN=ON -DPYBIND11_WERROR=ON +``` + +This will test the PGI compilers: + +```bash +docker run --rm -it -v $PWD:/pybind11 nvcr.io/hpc/pgi-compilers:ce +apt-get update && apt-get install -y python3-dev python3-pip python3-pytest +wget -qO- "https://cmake.org/files/v3.18/cmake-3.18.2-Linux-x86_64.tar.gz" | tar --strip-components=1 -xz -C /usr/local +cmake -S pybind11/ -B build +cmake --build build +``` + +### Explanation of the SDist/wheel building design + +> These details below are _only_ for packaging the Python sources from git. The +> SDists and wheels created do not have any extra requirements at all and are +> completely normal. + +The main objective of the packaging system is to create SDists (Python's source +distribution packages) and wheels (Python's binary distribution packages) that +include everything that is needed to work with pybind11, and which can be +installed without any additional dependencies. This is more complex than it +appears: in order to support CMake as a first class language even when using +the PyPI package, they must include the _generated_ CMake files (so as not to +require CMake when installing the `pybind11` package itself). They should also +provide the option to install to the "standard" location +(`/include/pybind11` and `/share/cmake/pybind11`) so they are +easy to find with CMake, but this can cause problems if you are not an +environment or using ``pyproject.toml`` requirements. This was solved by having +two packages; the "nice" pybind11 package that stores the includes and CMake +files inside the package, that you get access to via functions in the package, +and a `pybind11-global` package that can be included via `pybind11[global]` if +you want the more invasive but discoverable file locations. + +If you want to install or package the GitHub source, it is best to have Pip 10 +or newer on Windows, macOS, or Linux (manylinux1 compatible, includes most +distributions). You can then build the SDists, or run any procedure that makes +SDists internally, like making wheels or installing. + + +```bash +# Editable development install example +python3 -m pip install -e . +``` + +Since Pip itself does not have an `sdist` command (it does have `wheel` and +`install`), you may want to use the upcoming `build` package: + +```bash +python3 -m pip install build + +# Normal package +python3 -m build -s . + +# Global extra +PYBIND11_GLOBAL_SDIST=1 python3 -m build -s . +``` + +If you want to use the classic "direct" usage of `python setup.py`, you will +need CMake 3.15+ and either `make` or `ninja` preinstalled (possibly via `pip +install cmake ninja`), since directly running Python on `setup.py` cannot pick +up and install `pyproject.toml` requirements. As long as you have those two +things, though, everything works the way you would expect: + +```bash +# Normal package +python3 setup.py sdist + +# Global extra +PYBIND11_GLOBAL_SDIST=1 python3 setup.py sdist +``` + +A detailed explanation of the build procedure design for developers wanting to +work on or maintain the packaging system is as follows: + +#### 1. Building from the source directory + +When you invoke any `setup.py` command from the source directory, including +`pip wheel .` and `pip install .`, you will activate a full source build. This +is made of the following steps: + +1. If the tool is PEP 518 compliant, like Pip 10+, it will create a temporary + virtual environment and install the build requirements (mostly CMake) into + it. (if you are not on Windows, macOS, or a manylinux compliant system, you + can disable this with `--no-build-isolation` as long as you have CMake 3.15+ + installed) +2. The environment variable `PYBIND11_GLOBAL_SDIST` is checked - if it is set + and truthy, this will be make the accessory `pybind11-global` package, + instead of the normal `pybind11` package. This package is used for + installing the files directly to your environment root directory, using + `pybind11[global]`. +2. `setup.py` reads the version from `pybind11/_version.py` and verifies it + matches `includes/pybind11/detail/common.h`. +3. CMake is run with `-DCMAKE_INSTALL_PREIFX=pybind11`. Since the CMake install + procedure uses only relative paths and is identical on all platforms, these + files are valid as long as they stay in the correct relative position to the + includes. `pybind11/share/cmake/pybind11` has the CMake files, and + `pybind11/include` has the includes. The build directory is discarded. +4. Simpler files are placed in the SDist: `tools/setup_*.py.in`, + `tools/pyproject.toml` (`main` or `global`) +5. The package is created by running the setup function in the + `tools/setup_*.py`. `setup_main.py` fills in Python packages, and + `setup_global.py` fills in only the data/header slots. +6. A context manager cleans up the temporary CMake install directory (even if + an error is thrown). + +### 2. Building from SDist + +Since the SDist has the rendered template files in `tools` along with the +includes and CMake files in the correct locations, the builds are completely +trivial and simple. No extra requirements are required. You can even use Pip 9 +if you really want to. + + +[pre-commit]: https://pre-commit.com +[clang-format]: https://clang.llvm.org/docs/ClangFormat.html +[clang-tidy]: https://clang.llvm.org/extra/clang-tidy/ +[pybind11.readthedocs.org]: http://pybind11.readthedocs.org/en/latest +[issue tracker]: https://github.com/pybind/pybind11/issues +[gitter]: https://gitter.im/pybind/Lobby +[using pull requests]: https://help.github.com/articles/using-pull-requests diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/ISSUE_TEMPLATE/bug-report.md b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/ISSUE_TEMPLATE/bug-report.md new file mode 100644 index 0000000000000000000000000000000000000000..ae36ea65083643dfc6f252249141b94c7ecb65e7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/ISSUE_TEMPLATE/bug-report.md @@ -0,0 +1,28 @@ +--- +name: Bug Report +about: File an issue about a bug +title: "[BUG] " +--- + + +Make sure you've completed the following steps before submitting your issue -- thank you! + +1. Make sure you've read the [documentation][]. Your issue may be addressed there. +2. Search the [issue tracker][] to verify that this hasn't already been reported. +1 or comment there if it has. +3. Consider asking first in the [Gitter chat room][]. +4. Include a self-contained and minimal piece of code that reproduces the problem. If that's not possible, try to make the description as clear as possible. + a. If possible, make a PR with a new, failing test to give us a starting point to work on! + +[documentation]: https://pybind11.readthedocs.io +[issue tracker]: https://github.com/pybind/pybind11/issues +[Gitter chat room]: https://gitter.im/pybind/Lobby + +*After reading, remove this checklist and the template text in parentheses below.* + +## Issue description + +(Provide a short description, state the expected behavior and what actually happens.) + +## Reproducible example code + +(The code should be minimal, have no external dependencies, isolate the function(s) that cause breakage. Submit matched and complete C++ and Python snippets that can be easily compiled and run to diagnose the issue.) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/ISSUE_TEMPLATE/config.yml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/ISSUE_TEMPLATE/config.yml new file mode 100644 index 0000000000000000000000000000000000000000..20e743136f3f2efea7deadf3e08c5b104c22a7f3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/ISSUE_TEMPLATE/config.yml @@ -0,0 +1,5 @@ +blank_issues_enabled: false +contact_links: + - name: Gitter room + url: https://gitter.im/pybind/Lobby + about: A room for discussing pybind11 with an active community diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/ISSUE_TEMPLATE/feature-request.md b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/ISSUE_TEMPLATE/feature-request.md new file mode 100644 index 0000000000000000000000000000000000000000..5f6ec81ec972b13e38520ef2e37d85022c2642c9 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/ISSUE_TEMPLATE/feature-request.md @@ -0,0 +1,16 @@ +--- +name: Feature Request +about: File an issue about adding a feature +title: "[FEAT] " +--- + + +Make sure you've completed the following steps before submitting your issue -- thank you! + +1. Check if your feature has already been mentioned / rejected / planned in other issues. +2. If those resources didn't help, consider asking in the [Gitter chat room][] to see if this is interesting / useful to a larger audience and possible to implement reasonably, +4. If you have a useful feature that passes the previous items (or not suitable for chat), please fill in the details below. + +[Gitter chat room]: https://gitter.im/pybind/Lobby + +*After reading, remove this checklist.* diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/ISSUE_TEMPLATE/question.md b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/ISSUE_TEMPLATE/question.md new file mode 100644 index 0000000000000000000000000000000000000000..b199b6ee8ad446994aed54f67b0d1c22049d53c1 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/ISSUE_TEMPLATE/question.md @@ -0,0 +1,21 @@ +--- +name: Question +about: File an issue about unexplained behavior +title: "[QUESTION] " +--- + +If you have a question, please check the following first: + +1. Check if your question has already been answered in the [FAQ][] section. +2. Make sure you've read the [documentation][]. Your issue may be addressed there. +3. If those resources didn't help and you only have a short question (not a bug report), consider asking in the [Gitter chat room][] +4. Search the [issue tracker][], including the closed issues, to see if your question has already been asked/answered. +1 or comment if it has been asked but has no answer. +5. If you have a more complex question which is not answered in the previous items (or not suitable for chat), please fill in the details below. +6. Include a self-contained and minimal piece of code that illustrates your question. If that's not possible, try to make the description as clear as possible. + +[FAQ]: http://pybind11.readthedocs.io/en/latest/faq.html +[documentation]: https://pybind11.readthedocs.io +[issue tracker]: https://github.com/pybind/pybind11/issues +[Gitter chat room]: https://gitter.im/pybind/Lobby + +*After reading, remove this checklist.* diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/dependabot.yml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/dependabot.yml new file mode 100644 index 0000000000000000000000000000000000000000..73273365c0dd0de34754b26f08c0f4d16a5a535c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/dependabot.yml @@ -0,0 +1,16 @@ +version: 2 +updates: + # Maintain dependencies for GitHub Actions + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "daily" + ignore: + # Official actions have moving tags like v1 + # that are used, so they don't need updates here + - dependency-name: "actions/checkout" + - dependency-name: "actions/setup-python" + - dependency-name: "actions/cache" + - dependency-name: "actions/upload-artifact" + - dependency-name: "actions/download-artifact" + - dependency-name: "actions/labeler" diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/labeler.yml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/labeler.yml new file mode 100644 index 0000000000000000000000000000000000000000..abb0d05aaa3f1ce86f027249b47ce2bc5f7f2e7b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/labeler.yml @@ -0,0 +1,8 @@ +docs: +- any: + - 'docs/**/*.rst' + - '!docs/changelog.rst' + - '!docs/upgrade.rst' + +ci: +- '.github/workflows/*.yml' diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/labeler_merged.yml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/labeler_merged.yml new file mode 100644 index 0000000000000000000000000000000000000000..2374ad42e4597965da5a0aecb2afeb213da10445 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/labeler_merged.yml @@ -0,0 +1,3 @@ +needs changelog: +- all: + - '!docs/changelog.rst' diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/pull_request_template.md b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/pull_request_template.md new file mode 100644 index 0000000000000000000000000000000000000000..97a6ff7dda9b44e18a0ec0e87b5eae45c4d6dddb --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/pull_request_template.md @@ -0,0 +1,15 @@ +## Description + + + + +## Suggested changelog entry: + + + +```rst + +``` + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/ci.yml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..a1bdec7bd70833cce0b7bd8211be796970e3ac25 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/ci.yml @@ -0,0 +1,846 @@ +name: CI + +on: + workflow_dispatch: + pull_request: + push: + branches: + - master + - stable + - v* + +jobs: + # This is the "main" test suite, which tests a large number of different + # versions of default compilers and Python versions in GitHub Actions. + standard: + strategy: + fail-fast: false + matrix: + runs-on: [ubuntu-latest, windows-latest, macos-latest] + python: + - 2.7 + - 3.5 + - 3.6 + - 3.9 + - 3.10-dev + - pypy2 + - pypy3 + + # Items in here will either be added to the build matrix (if not + # present), or add new keys to an existing matrix element if all the + # existing keys match. + # + # We support three optional keys: args (both build), args1 (first + # build), and args2 (second build). + include: + # Just add a key + - runs-on: ubuntu-latest + python: 3.6 + args: > + -DPYBIND11_FINDPYTHON=ON + - runs-on: windows-latest + python: 3.6 + args: > + -DPYBIND11_FINDPYTHON=ON + + # These items will be removed from the build matrix, keys must match. + exclude: + # Currently 32bit only, and we build 64bit + - runs-on: windows-latest + python: pypy2 + - runs-on: windows-latest + python: pypy3 + + # TODO: PyPy2 7.3.3 segfaults, while 7.3.2 was fine. + - runs-on: ubuntu-latest + python: pypy2 + + name: "🐍 ${{ matrix.python }} • ${{ matrix.runs-on }} • x64 ${{ matrix.args }}" + runs-on: ${{ matrix.runs-on }} + + steps: + - uses: actions/checkout@v2 + + - name: Setup Python ${{ matrix.python }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python }} + + - name: Setup Boost (Windows / Linux latest) + shell: bash + run: echo "BOOST_ROOT=$BOOST_ROOT_1_72_0" >> $GITHUB_ENV + + - name: Update CMake + uses: jwlawson/actions-setup-cmake@v1.8 + + - name: Cache wheels + if: runner.os == 'macOS' + uses: actions/cache@v2 + with: + # This path is specific to macOS - we really only need it for PyPy NumPy wheels + # See https://github.com/actions/cache/blob/master/examples.md#python---pip + # for ways to do this more generally + path: ~/Library/Caches/pip + # Look to see if there is a cache hit for the corresponding requirements file + key: ${{ runner.os }}-pip-${{ matrix.python }}-x64-${{ hashFiles('tests/requirements.txt') }} + + - name: Prepare env + run: python -m pip install -r tests/requirements.txt --prefer-binary + + - name: Setup annotations on Linux + if: runner.os == 'Linux' + run: python -m pip install pytest-github-actions-annotate-failures + + # First build - C++11 mode and inplace + - name: Configure C++11 ${{ matrix.args }} + run: > + cmake -S . -B . + -DPYBIND11_WERROR=ON + -DDOWNLOAD_CATCH=ON + -DDOWNLOAD_EIGEN=ON + -DCMAKE_CXX_STANDARD=11 + ${{ matrix.args }} + + - name: Build C++11 + run: cmake --build . -j 2 + + - name: Python tests C++11 + run: cmake --build . --target pytest -j 2 + + - name: C++11 tests + # TODO: Figure out how to load the DLL on Python 3.8+ + if: "!(runner.os == 'Windows' && (matrix.python == 3.8 || matrix.python == 3.9 || matrix.python == '3.10-dev'))" + run: cmake --build . --target cpptest -j 2 + + - name: Interface test C++11 + run: cmake --build . --target test_cmake_build + + - name: Clean directory + run: git clean -fdx + + # Second build - C++17 mode and in a build directory + - name: Configure ${{ matrix.args2 }} + run: > + cmake -S . -B build2 + -DPYBIND11_WERROR=ON + -DDOWNLOAD_CATCH=ON + -DDOWNLOAD_EIGEN=ON + -DCMAKE_CXX_STANDARD=17 + ${{ matrix.args }} + ${{ matrix.args2 }} + + - name: Build + run: cmake --build build2 -j 2 + + - name: Python tests + run: cmake --build build2 --target pytest + + - name: C++ tests + # TODO: Figure out how to load the DLL on Python 3.8+ + if: "!(runner.os == 'Windows' && (matrix.python == 3.8 || matrix.python == 3.9 || matrix.python == '3.10-dev'))" + run: cmake --build build2 --target cpptest + + - name: Interface test + run: cmake --build build2 --target test_cmake_build + + # Eventually Microsoft might have an action for setting up + # MSVC, but for now, this action works: + - name: Prepare compiler environment for Windows 🐍 2.7 + if: matrix.python == 2.7 && runner.os == 'Windows' + uses: ilammy/msvc-dev-cmd@v1 + with: + arch: x64 + + # This makes two environment variables available in the following step(s) + - name: Set Windows 🐍 2.7 environment variables + if: matrix.python == 2.7 && runner.os == 'Windows' + shell: bash + run: | + echo "DISTUTILS_USE_SDK=1" >> $GITHUB_ENV + echo "MSSdk=1" >> $GITHUB_ENV + + # This makes sure the setup_helpers module can build packages using + # setuptools + - name: Setuptools helpers test + run: pytest tests/extra_setuptools + + + deadsnakes: + strategy: + fail-fast: false + matrix: + include: + - python-version: 3.9 + python-debug: true + valgrind: true + - python-version: 3.10-dev + python-debug: false + + name: "🐍 ${{ matrix.python-version }}${{ matrix.python-debug && '-dbg' || '' }} (deadsnakes)${{ matrix.valgrind && ' • Valgrind' || '' }} • x64" + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + + - name: Setup Python ${{ matrix.python-version }} (deadsnakes) + uses: deadsnakes/action@v2.1.1 + with: + python-version: ${{ matrix.python-version }} + debug: ${{ matrix.python-debug }} + + - name: Update CMake + uses: jwlawson/actions-setup-cmake@v1.8 + + - name: Valgrind cache + if: matrix.valgrind + uses: actions/cache@v2 + id: cache-valgrind + with: + path: valgrind + key: 3.16.1 # Valgrind version + + - name: Compile Valgrind + if: matrix.valgrind && steps.cache-valgrind.outputs.cache-hit != 'true' + run: | + VALGRIND_VERSION=3.16.1 + curl https://sourceware.org/pub/valgrind/valgrind-$VALGRIND_VERSION.tar.bz2 -o - | tar xj + mv valgrind-$VALGRIND_VERSION valgrind + cd valgrind + ./configure + make -j 2 > /dev/null + + - name: Install Valgrind + if: matrix.valgrind + working-directory: valgrind + run: | + sudo make install + sudo apt-get update + sudo apt-get install libc6-dbg # Needed by Valgrind + + - name: Prepare env + run: python -m pip install -r tests/requirements.txt --prefer-binary + + - name: Configure + run: > + cmake -S . -B build + -DCMAKE_BUILD_TYPE=Debug + -DPYBIND11_WERROR=ON + -DDOWNLOAD_CATCH=ON + -DDOWNLOAD_EIGEN=ON + -DCMAKE_CXX_STANDARD=17 + + - name: Build + run: cmake --build build -j 2 + + - name: Python tests + run: cmake --build build --target pytest + + - name: C++ tests + run: cmake --build build --target cpptest + + - name: Run Valgrind on Python tests + if: matrix.valgrind + run: cmake --build build --target memcheck + + + # Testing on clang using the excellent silkeh clang docker images + clang: + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + clang: + - 3.6 + - 3.7 + - 3.9 + - 7 + - 9 + - dev + std: + - 11 + include: + - clang: 5 + std: 14 + - clang: 10 + std: 20 + - clang: 10 + std: 17 + + name: "🐍 3 • Clang ${{ matrix.clang }} • C++${{ matrix.std }} • x64" + container: "silkeh/clang:${{ matrix.clang }}" + + steps: + - uses: actions/checkout@v2 + + - name: Add wget and python3 + run: apt-get update && apt-get install -y python3-dev python3-numpy python3-pytest libeigen3-dev + + - name: Configure + shell: bash + run: > + cmake -S . -B build + -DPYBIND11_WERROR=ON + -DDOWNLOAD_CATCH=ON + -DCMAKE_CXX_STANDARD=${{ matrix.std }} + -DPYTHON_EXECUTABLE=$(python3 -c "import sys; print(sys.executable)") + + - name: Build + run: cmake --build build -j 2 + + - name: Python tests + run: cmake --build build --target pytest + + - name: C++ tests + run: cmake --build build --target cpptest + + - name: Interface test + run: cmake --build build --target test_cmake_build + + + # Testing NVCC; forces sources to behave like .cu files + cuda: + runs-on: ubuntu-latest + name: "🐍 3.8 • CUDA 11 • Ubuntu 20.04" + container: nvidia/cuda:11.0-devel-ubuntu20.04 + + steps: + - uses: actions/checkout@v2 + + # tzdata will try to ask for the timezone, so set the DEBIAN_FRONTEND + - name: Install 🐍 3 + run: apt-get update && DEBIAN_FRONTEND="noninteractive" apt-get install -y cmake git python3-dev python3-pytest python3-numpy + + - name: Configure + run: cmake -S . -B build -DPYBIND11_CUDA_TESTS=ON -DPYBIND11_WERROR=ON -DDOWNLOAD_CATCH=ON + + - name: Build + run: cmake --build build -j2 --verbose + + - name: Python tests + run: cmake --build build --target pytest + + +# TODO: Internal compiler error - report to NVidia +# # Testing CentOS 8 + PGI compilers +# centos-nvhpc8: +# runs-on: ubuntu-latest +# name: "🐍 3 • CentOS8 / PGI 20.11 • x64" +# container: centos:8 +# +# steps: +# - uses: actions/checkout@v2 +# +# - name: Add Python 3 and a few requirements +# run: yum update -y && yum install -y git python3-devel python3-numpy python3-pytest make environment-modules +# +# - name: Install CMake with pip +# run: | +# python3 -m pip install --upgrade pip +# python3 -m pip install cmake --prefer-binary +# +# - name: Install NVidia HPC SDK +# run: > +# yum -y install +# https://developer.download.nvidia.com/hpc-sdk/20.11/nvhpc-20-11-20.11-1.x86_64.rpm +# https://developer.download.nvidia.com/hpc-sdk/20.11/nvhpc-2020-20.11-1.x86_64.rpm +# +# - name: Configure +# shell: bash +# run: | +# source /etc/profile.d/modules.sh +# module load /opt/nvidia/hpc_sdk/modulefiles/nvhpc/20.11 +# cmake -S . -B build -DDOWNLOAD_CATCH=ON -DCMAKE_CXX_STANDARD=14 -DPYTHON_EXECUTABLE=$(python3 -c "import sys; print(sys.executable)") +# +# - name: Build +# run: cmake --build build -j 2 --verbose +# +# - name: Python tests +# run: cmake --build build --target pytest +# +# - name: C++ tests +# run: cmake --build build --target cpptest +# +# - name: Interface test +# run: cmake --build build --target test_cmake_build + + + # Testing on CentOS 7 + PGI compilers, which seems to require more workarounds + centos-nvhpc7: + runs-on: ubuntu-latest + name: "🐍 3 • CentOS7 / PGI 20.9 • x64" + container: centos:7 + + steps: + - uses: actions/checkout@v2 + + - name: Add Python 3 and a few requirements + run: yum update -y && yum install -y epel-release && yum install -y git python3-devel make environment-modules cmake3 + + - name: Install NVidia HPC SDK + run: yum -y install https://developer.download.nvidia.com/hpc-sdk/20.9/nvhpc-20-9-20.9-1.x86_64.rpm https://developer.download.nvidia.com/hpc-sdk/20.9/nvhpc-2020-20.9-1.x86_64.rpm + + # On CentOS 7, we have to filter a few tests (compiler internal error) + # and allow deeper templete recursion (not needed on CentOS 8 with a newer + # standard library). On some systems, you many need further workarounds: + # https://github.com/pybind/pybind11/pull/2475 + - name: Configure + shell: bash + run: | + source /etc/profile.d/modules.sh + module load /opt/nvidia/hpc_sdk/modulefiles/nvhpc/20.9 + cmake3 -S . -B build -DDOWNLOAD_CATCH=ON \ + -DCMAKE_CXX_STANDARD=11 \ + -DPYTHON_EXECUTABLE=$(python3 -c "import sys; print(sys.executable)") \ + -DCMAKE_CXX_FLAGS="-Wc,--pending_instantiations=0" \ + -DPYBIND11_TEST_FILTER="test_smart_ptr.cpp;test_virtual_functions.cpp" + + # Building before installing Pip should produce a warning but not an error + - name: Build + run: cmake3 --build build -j 2 --verbose + + - name: Install CMake with pip + run: | + python3 -m pip install --upgrade pip + python3 -m pip install pytest + + - name: Python tests + run: cmake3 --build build --target pytest + + - name: C++ tests + run: cmake3 --build build --target cpptest + + - name: Interface test + run: cmake3 --build build --target test_cmake_build + + + # Testing on GCC using the GCC docker images (only recent images supported) + gcc: + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + gcc: + - 7 + - latest + std: + - 11 + include: + - gcc: 10 + std: 20 + + name: "🐍 3 • GCC ${{ matrix.gcc }} • C++${{ matrix.std }}• x64" + container: "gcc:${{ matrix.gcc }}" + + steps: + - uses: actions/checkout@v1 + + - name: Add Python 3 + run: apt-get update; apt-get install -y python3-dev python3-numpy python3-pytest python3-pip libeigen3-dev + + - name: Update pip + run: python3 -m pip install --upgrade pip + + - name: Update CMake + uses: jwlawson/actions-setup-cmake@v1.8 + + - name: Configure + shell: bash + run: > + cmake -S . -B build + -DPYBIND11_WERROR=ON + -DDOWNLOAD_CATCH=ON + -DCMAKE_CXX_STANDARD=${{ matrix.std }} + -DPYTHON_EXECUTABLE=$(python3 -c "import sys; print(sys.executable)") + + - name: Build + run: cmake --build build -j 2 + + - name: Python tests + run: cmake --build build --target pytest + + - name: C++ tests + run: cmake --build build --target cpptest + + - name: Interface test + run: cmake --build build --target test_cmake_build + + + # Testing on ICC using the oneAPI apt repo + icc: + runs-on: ubuntu-20.04 + strategy: + fail-fast: false + + name: "🐍 3 • ICC latest • x64" + + steps: + - uses: actions/checkout@v2 + + - name: Add apt repo + run: | + sudo apt-get update + sudo apt-get install -y wget build-essential pkg-config cmake ca-certificates gnupg + wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB + sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB + echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list + + - name: Add ICC & Python 3 + run: sudo apt-get update; sudo apt-get install -y intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic cmake python3-dev python3-numpy python3-pytest python3-pip + + - name: Update pip + run: | + set +e; source /opt/intel/oneapi/setvars.sh; set -e + python3 -m pip install --upgrade pip + + - name: Install dependencies + run: | + set +e; source /opt/intel/oneapi/setvars.sh; set -e + python3 -m pip install -r tests/requirements.txt --prefer-binary + + - name: Configure C++11 + run: | + set +e; source /opt/intel/oneapi/setvars.sh; set -e + cmake -S . -B build-11 \ + -DPYBIND11_WERROR=ON \ + -DDOWNLOAD_CATCH=ON \ + -DDOWNLOAD_EIGEN=OFF \ + -DCMAKE_CXX_STANDARD=11 \ + -DCMAKE_CXX_COMPILER=$(which icpc) \ + -DPYTHON_EXECUTABLE=$(python3 -c "import sys; print(sys.executable)") + + - name: Build C++11 + run: | + set +e; source /opt/intel/oneapi/setvars.sh; set -e + cmake --build build-11 -j 2 -v + + - name: Python tests C++11 + run: | + set +e; source /opt/intel/oneapi/setvars.sh; set -e + sudo service apport stop + cmake --build build-11 --target check + + - name: C++ tests C++11 + run: | + set +e; source /opt/intel/oneapi/setvars.sh; set -e + cmake --build build-11 --target cpptest + + - name: Interface test C++11 + run: | + set +e; source /opt/intel/oneapi/setvars.sh; set -e + cmake --build build-11 --target test_cmake_build + + - name: Configure C++17 + run: | + set +e; source /opt/intel/oneapi/setvars.sh; set -e + cmake -S . -B build-17 \ + -DPYBIND11_WERROR=ON \ + -DDOWNLOAD_CATCH=ON \ + -DDOWNLOAD_EIGEN=OFF \ + -DCMAKE_CXX_STANDARD=17 \ + -DCMAKE_CXX_COMPILER=$(which icpc) \ + -DPYTHON_EXECUTABLE=$(python3 -c "import sys; print(sys.executable)") + + - name: Build C++17 + run: | + set +e; source /opt/intel/oneapi/setvars.sh; set -e + cmake --build build-17 -j 2 -v + + - name: Python tests C++17 + run: | + set +e; source /opt/intel/oneapi/setvars.sh; set -e + sudo service apport stop + cmake --build build-17 --target check + + - name: C++ tests C++17 + run: | + set +e; source /opt/intel/oneapi/setvars.sh; set -e + cmake --build build-17 --target cpptest + + - name: Interface test C++17 + run: | + set +e; source /opt/intel/oneapi/setvars.sh; set -e + cmake --build build-17 --target test_cmake_build + + + # Testing on CentOS (manylinux uses a centos base, and this is an easy way + # to get GCC 4.8, which is the manylinux1 compiler). + centos: + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + centos: + - 7 # GCC 4.8 + - 8 + + name: "🐍 3 • CentOS ${{ matrix.centos }} • x64" + container: "centos:${{ matrix.centos }}" + + steps: + - uses: actions/checkout@v2 + + - name: Add Python 3 + run: yum update -y && yum install -y python3-devel gcc-c++ make git + + - name: Update pip + run: python3 -m pip install --upgrade pip + + - name: Install dependencies + run: python3 -m pip install cmake -r tests/requirements.txt --prefer-binary + + - name: Configure + shell: bash + run: > + cmake -S . -B build + -DPYBIND11_WERROR=ON + -DDOWNLOAD_CATCH=ON + -DDOWNLOAD_EIGEN=ON + -DCMAKE_CXX_STANDARD=11 + -DPYTHON_EXECUTABLE=$(python3 -c "import sys; print(sys.executable)") + + - name: Build + run: cmake --build build -j 2 + + - name: Python tests + run: cmake --build build --target pytest + + - name: C++ tests + run: cmake --build build --target cpptest + + - name: Interface test + run: cmake --build build --target test_cmake_build + + + # This tests an "install" with the CMake tools + install-classic: + name: "🐍 3.5 • Debian • x86 • Install" + runs-on: ubuntu-latest + container: i386/debian:stretch + + steps: + - uses: actions/checkout@v1 + + - name: Install requirements + run: | + apt-get update + apt-get install -y git make cmake g++ libeigen3-dev python3-dev python3-pip + pip3 install "pytest==3.1.*" + + - name: Configure for install + run: > + cmake . + -DPYBIND11_INSTALL=1 -DPYBIND11_TEST=0 + -DPYTHON_EXECUTABLE=$(python3 -c "import sys; print(sys.executable)") + + - name: Make and install + run: make install + + - name: Copy tests to new directory + run: cp -a tests /pybind11-tests + + - name: Make a new test directory + run: mkdir /build-tests + + - name: Configure tests + run: > + cmake ../pybind11-tests + -DDOWNLOAD_CATCH=ON + -DPYBIND11_WERROR=ON + -DPYTHON_EXECUTABLE=$(python3 -c "import sys; print(sys.executable)") + working-directory: /build-tests + + - name: Run tests + run: make pytest -j 2 + working-directory: /build-tests + + + # This verifies that the documentation is not horribly broken, and does a + # basic sanity check on the SDist. + doxygen: + name: "Documentation build test" + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + + - uses: actions/setup-python@v2 + + - name: Install Doxygen + run: sudo apt-get install -y doxygen librsvg2-bin # Changed to rsvg-convert in 20.04 + + - name: Install docs & setup requirements + run: python3 -m pip install -r docs/requirements.txt + + - name: Build docs + run: python3 -m sphinx -W -b html docs docs/.build + + - name: Make SDist + run: python3 setup.py sdist + + - run: git status --ignored + + - name: Check local include dir + run: > + ls pybind11; + python3 -c "import pybind11, pathlib; assert (a := pybind11.get_include()) == (b := str(pathlib.Path('include').resolve())), f'{a} != {b}'" + + - name: Compare Dists (headers only) + working-directory: include + run: | + python3 -m pip install --user -U ../dist/* + installed=$(python3 -c "import pybind11; print(pybind11.get_include() + '/pybind11')") + diff -rq $installed ./pybind11 + + win32: + strategy: + fail-fast: false + matrix: + python: + - 3.5 + - 3.6 + - 3.7 + - 3.8 + - 3.9 + - pypy3 + # TODO: fix hang on pypy2 + + include: + - python: 3.9 + args: -DCMAKE_CXX_STANDARD=20 -DDOWNLOAD_EIGEN=OFF + - python: 3.8 + args: -DCMAKE_CXX_STANDARD=17 + + name: "🐍 ${{ matrix.python }} • MSVC 2019 • x86 ${{ matrix.args }}" + runs-on: windows-latest + + steps: + - uses: actions/checkout@v2 + + - name: Setup Python ${{ matrix.python }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python }} + architecture: x86 + + - name: Update CMake + uses: jwlawson/actions-setup-cmake@v1.8 + + - name: Prepare MSVC + uses: ilammy/msvc-dev-cmd@v1 + with: + arch: x86 + + - name: Prepare env + run: python -m pip install -r tests/requirements.txt --prefer-binary + + # First build - C++11 mode and inplace + - name: Configure ${{ matrix.args }} + run: > + cmake -S . -B build + -G "Visual Studio 16 2019" -A Win32 + -DPYBIND11_WERROR=ON + -DDOWNLOAD_CATCH=ON + -DDOWNLOAD_EIGEN=ON + ${{ matrix.args }} + - name: Build C++11 + run: cmake --build build -j 2 + + - name: Run tests + run: cmake --build build -t pytest + + win32-msvc2015: + name: "🐍 ${{ matrix.python }} • MSVC 2015 • x64" + runs-on: windows-latest + strategy: + fail-fast: false + matrix: + python: + - 2.7 + - 3.6 + - 3.7 + # todo: check/cpptest does not support 3.8+ yet + + steps: + - uses: actions/checkout@v2 + + - name: Setup 🐍 ${{ matrix.python }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python }} + + - name: Update CMake + uses: jwlawson/actions-setup-cmake@v1.8 + + - name: Prepare MSVC + uses: ilammy/msvc-dev-cmd@v1 + with: + toolset: 14.0 + + - name: Prepare env + run: python -m pip install -r tests/requirements.txt --prefer-binary + + # First build - C++11 mode and inplace + - name: Configure + run: > + cmake -S . -B build + -G "Visual Studio 14 2015" -A x64 + -DPYBIND11_WERROR=ON + -DDOWNLOAD_CATCH=ON + -DDOWNLOAD_EIGEN=ON + + - name: Build C++14 + run: cmake --build build -j 2 + + - name: Run all checks + run: cmake --build build -t check + + + win32-msvc2017: + name: "🐍 ${{ matrix.python }} • MSVC 2017 • x64" + runs-on: windows-2016 + strategy: + fail-fast: false + matrix: + python: + - 2.7 + - 3.5 + - 3.7 + std: + - 14 + + include: + - python: 2.7 + std: 17 + args: > + -DCMAKE_CXX_FLAGS="/permissive- /EHsc /GR" + + steps: + - uses: actions/checkout@v2 + + - name: Setup 🐍 ${{ matrix.python }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python }} + + - name: Update CMake + uses: jwlawson/actions-setup-cmake@v1.8 + + - name: Prepare env + run: python -m pip install -r tests/requirements.txt --prefer-binary + + # First build - C++11 mode and inplace + - name: Configure + run: > + cmake -S . -B build + -G "Visual Studio 15 2017" -A x64 + -DPYBIND11_WERROR=ON + -DDOWNLOAD_CATCH=ON + -DDOWNLOAD_EIGEN=ON + -DCMAKE_CXX_STANDARD=${{ matrix.std }} + ${{ matrix.args }} + + - name: Build ${{ matrix.std }} + run: cmake --build build -j 2 + + - name: Run all checks + run: cmake --build build -t check diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/configure.yml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/configure.yml new file mode 100644 index 0000000000000000000000000000000000000000..0f3117be99419028a1aa7078c7a7d3ed0c107ea4 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/configure.yml @@ -0,0 +1,84 @@ +name: Config + +on: + workflow_dispatch: + pull_request: + push: + branches: + - master + - stable + - v* + +jobs: + # This tests various versions of CMake in various combinations, to make sure + # the configure step passes. + cmake: + strategy: + fail-fast: false + matrix: + runs-on: [ubuntu-latest, macos-latest, windows-latest] + arch: [x64] + cmake: [3.18] + + include: + - runs-on: ubuntu-latest + arch: x64 + cmake: 3.4 + + - runs-on: macos-latest + arch: x64 + cmake: 3.7 + + - runs-on: windows-2016 + arch: x86 + cmake: 3.8 + + - runs-on: windows-2016 + arch: x86 + cmake: 3.18 + + name: 🐍 3.7 • CMake ${{ matrix.cmake }} • ${{ matrix.runs-on }} + runs-on: ${{ matrix.runs-on }} + + steps: + - uses: actions/checkout@v2 + + - name: Setup Python 3.7 + uses: actions/setup-python@v2 + with: + python-version: 3.7 + architecture: ${{ matrix.arch }} + + - name: Prepare env + run: python -m pip install -r tests/requirements.txt + + # An action for adding a specific version of CMake: + # https://github.com/jwlawson/actions-setup-cmake + - name: Setup CMake ${{ matrix.cmake }} + uses: jwlawson/actions-setup-cmake@v1.8 + with: + cmake-version: ${{ matrix.cmake }} + + # These steps use a directory with a space in it intentionally + - name: Make build directories + run: mkdir "build dir" + + - name: Configure + working-directory: build dir + shell: bash + run: > + cmake .. + -DPYBIND11_WERROR=ON + -DDOWNLOAD_CATCH=ON + -DPYTHON_EXECUTABLE=$(python -c "import sys; print(sys.executable)") + + # Only build and test if this was manually triggered in the GitHub UI + - name: Build + working-directory: build dir + if: github.event_name == 'workflow_dispatch' + run: cmake --build . --config Release + + - name: Test + working-directory: build dir + if: github.event_name == 'workflow_dispatch' + run: cmake --build . --config Release --target check diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/format.yml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/format.yml new file mode 100644 index 0000000000000000000000000000000000000000..5cebed17da0cee13cee124e816833e88cb2dcfa5 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/format.yml @@ -0,0 +1,46 @@ +# This is a format job. Pre-commit has a first-party GitHub action, so we use +# that: https://github.com/pre-commit/action + +name: Format + +on: + workflow_dispatch: + pull_request: + push: + branches: + - master + - stable + - "v*" + +jobs: + pre-commit: + name: Format + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - uses: actions/setup-python@v2 + - uses: pre-commit/action@v2.0.0 + with: + # Slow hooks are marked with manual - slow is okay here, run them too + extra_args: --hook-stage manual --all-files + + clang-tidy: + name: Clang-Tidy + runs-on: ubuntu-latest + container: silkeh/clang:10 + steps: + - uses: actions/checkout@v2 + + - name: Install requirements + run: apt-get update && apt-get install -y python3-dev python3-pytest + + - name: Configure + run: > + cmake -S . -B build + -DCMAKE_CXX_CLANG_TIDY="$(which clang-tidy);--warnings-as-errors=*" + -DDOWNLOAD_EIGEN=ON + -DDOWNLOAD_CATCH=ON + -DCMAKE_CXX_STANDARD=17 + + - name: Build + run: cmake --build build -j 2 diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/labeler.yml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/labeler.yml new file mode 100644 index 0000000000000000000000000000000000000000..d2b59796819ea3a9ea01f60cf583876b654b1ad4 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/labeler.yml @@ -0,0 +1,16 @@ +name: Labeler +on: + pull_request_target: + types: [closed] + +jobs: + label: + name: Labeler + runs-on: ubuntu-latest + steps: + + - uses: actions/labeler@main + if: github.event.pull_request.merged == true + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} + configuration-path: .github/labeler_merged.yml diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/pip.yml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/pip.yml new file mode 100644 index 0000000000000000000000000000000000000000..5547a5e285b344a9b03c83af31c947d167254665 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.github/workflows/pip.yml @@ -0,0 +1,103 @@ +name: Pip + +on: + workflow_dispatch: + pull_request: + push: + branches: + - master + - stable + - v* + release: + types: + - published + +jobs: + # This builds the sdists and wheels and makes sure the files are exactly as + # expected. Using Windows and Python 2.7, since that is often the most + # challenging matrix element. + test-packaging: + name: 🐍 2.7 • 📦 tests • windows-latest + runs-on: windows-latest + + steps: + - uses: actions/checkout@v2 + + - name: Setup 🐍 2.7 + uses: actions/setup-python@v2 + with: + python-version: 2.7 + + - name: Prepare env + run: python -m pip install -r tests/requirements.txt --prefer-binary + + - name: Python Packaging tests + run: pytest tests/extra_python_package/ + + + # This runs the packaging tests and also builds and saves the packages as + # artifacts. + packaging: + name: 🐍 3.8 • 📦 & 📦 tests • ubuntu-latest + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + + - name: Setup 🐍 3.8 + uses: actions/setup-python@v2 + with: + python-version: 3.8 + + - name: Prepare env + run: python -m pip install -r tests/requirements.txt build twine --prefer-binary + + - name: Python Packaging tests + run: pytest tests/extra_python_package/ + + - name: Build SDist and wheels + run: | + python -m build + PYBIND11_GLOBAL_SDIST=1 python -m build + + - name: Check metadata + run: twine check dist/* + + - name: Save standard package + uses: actions/upload-artifact@v2 + with: + name: standard + path: dist/pybind11-* + + - name: Save global package + uses: actions/upload-artifact@v2 + with: + name: global + path: dist/pybind11_global-* + + + + # When a GitHub release is made, upload the artifacts to PyPI + upload: + name: Upload to PyPI + runs-on: ubuntu-latest + if: github.event_name == 'release' && github.event.action == 'published' + needs: [packaging] + + steps: + - uses: actions/setup-python@v2 + + # Downloads all to directories matching the artifact names + - uses: actions/download-artifact@v2 + + - name: Publish standard package + uses: pypa/gh-action-pypi-publish@v1.4.2 + with: + password: ${{ secrets.pypi_password }} + packages_dir: standard/ + + - name: Publish global package + uses: pypa/gh-action-pypi-publish@v1.4.2 + with: + password: ${{ secrets.pypi_password_global }} + packages_dir: global/ diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.gitignore b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..3f36b89e0cb8b1c18539ba2bfe5bd286f1403b97 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.gitignore @@ -0,0 +1,43 @@ +CMakeCache.txt +CMakeFiles +Makefile +cmake_install.cmake +cmake_uninstall.cmake +.DS_Store +*.so +*.pyd +*.dll +*.sln +*.sdf +*.opensdf +*.vcxproj +*.vcxproj.user +*.filters +example.dir +Win32 +x64 +Release +Debug +.vs +CTestTestfile.cmake +Testing +autogen +MANIFEST +/.ninja_* +/*.ninja +/docs/.build +*.py[co] +*.egg-info +*~ +.*.swp +.DS_Store +/dist +/*build* +.cache/ +sosize-*.txt +pybind11Config*.cmake +pybind11Targets.cmake +/*env* +/.vscode +/pybind11/include/* +/pybind11/share/* diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.pre-commit-config.yaml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.pre-commit-config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..6781ac4f11ed18b5453e7a7ccaaf5b5358e9fbff --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.pre-commit-config.yaml @@ -0,0 +1,100 @@ +# To use: +# +# pre-commit run -a +# +# Or: +# +# pre-commit install # (runs every time you commit in git) +# +# To update this file: +# +# pre-commit autoupdate +# +# See https://github.com/pre-commit/pre-commit + +repos: +# Standard hooks +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v3.4.0 + hooks: + - id: check-added-large-files + - id: check-case-conflict + - id: check-merge-conflict + - id: check-symlinks + - id: check-yaml + - id: debug-statements + - id: end-of-file-fixer + - id: mixed-line-ending + - id: requirements-txt-fixer + - id: trailing-whitespace + - id: fix-encoding-pragma + +# Black, the code formatter, natively supports pre-commit +- repo: https://github.com/psf/black + rev: 20.8b1 + hooks: + - id: black + # By default, this ignores pyi files, though black supports them + types: [text] + files: \.pyi?$ + +# Changes tabs to spaces +- repo: https://github.com/Lucas-C/pre-commit-hooks + rev: v1.1.9 + hooks: + - id: remove-tabs + +# Flake8 also supports pre-commit natively (same author) +- repo: https://gitlab.com/pycqa/flake8 + rev: 3.8.4 + hooks: + - id: flake8 + additional_dependencies: [flake8-bugbear, pep8-naming] + exclude: ^(docs/.*|tools/.*)$ + +# CMake formatting +- repo: https://github.com/cheshirekow/cmake-format-precommit + rev: v0.6.13 + hooks: + - id: cmake-format + additional_dependencies: [pyyaml] + types: [file] + files: (\.cmake|CMakeLists.txt)(.in)?$ + +# Check static types with mypy +- repo: https://github.com/pre-commit/mirrors-mypy + rev: v0.800 + hooks: + - id: mypy + # The default Python type ignores .pyi files, so let's rerun if detected + types: [text] + files: ^pybind11.*\.pyi?$ + # Running per-file misbehaves a bit, so just run on all files, it's fast + pass_filenames: false + +# Checks the manifest for missing files (native support) +- repo: https://github.com/mgedmin/check-manifest + rev: "0.46" + hooks: + - id: check-manifest + # This is a slow hook, so only run this if --hook-stage manual is passed + stages: [manual] + additional_dependencies: [cmake, ninja] + +# The original pybind11 checks for a few C++ style items +- repo: local + hooks: + - id: disallow-caps + name: Disallow improper capitalization + language: pygrep + entry: PyBind|Numpy|Cmake|CCache + exclude: .pre-commit-config.yaml + +- repo: local + hooks: + - id: check-style + name: Classic check-style + language: system + types: + - c++ + entry: ./tools/check-style.sh diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/.readthedocs.yml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.readthedocs.yml new file mode 100644 index 0000000000000000000000000000000000000000..c9c61617ca9b13a3e31d33226c52ba9529872a0d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/.readthedocs.yml @@ -0,0 +1,3 @@ +python: + version: 3 +requirements_file: docs/requirements.txt diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/CMakeLists.txt b/methods/ring/utils/fast_gicp/thirdparty/pybind11/CMakeLists.txt new file mode 100644 index 0000000000000000000000000000000000000000..152763eb42f8e8c4529957dd7e2f3fcedfd8f183 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/CMakeLists.txt @@ -0,0 +1,283 @@ +# CMakeLists.txt -- Build system for the pybind11 modules +# +# Copyright (c) 2015 Wenzel Jakob +# +# All rights reserved. Use of this source code is governed by a +# BSD-style license that can be found in the LICENSE file. + +cmake_minimum_required(VERSION 3.4) + +# The `cmake_minimum_required(VERSION 3.4...3.18)` syntax does not work with +# some versions of VS that have a patched CMake 3.11. This forces us to emulate +# the behavior using the following workaround: +if(${CMAKE_VERSION} VERSION_LESS 3.18) + cmake_policy(VERSION ${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}) +else() + cmake_policy(VERSION 3.18) +endif() + +# Extract project version from source +file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/include/pybind11/detail/common.h" + pybind11_version_defines REGEX "#define PYBIND11_VERSION_(MAJOR|MINOR|PATCH) ") + +foreach(ver ${pybind11_version_defines}) + if(ver MATCHES [[#define PYBIND11_VERSION_(MAJOR|MINOR|PATCH) +([^ ]+)$]]) + set(PYBIND11_VERSION_${CMAKE_MATCH_1} "${CMAKE_MATCH_2}") + endif() +endforeach() + +if(PYBIND11_VERSION_PATCH MATCHES [[\.([a-zA-Z0-9]+)$]]) + set(pybind11_VERSION_TYPE "${CMAKE_MATCH_1}") +endif() +string(REGEX MATCH "^[0-9]+" PYBIND11_VERSION_PATCH "${PYBIND11_VERSION_PATCH}") + +project( + pybind11 + LANGUAGES CXX + VERSION "${PYBIND11_VERSION_MAJOR}.${PYBIND11_VERSION_MINOR}.${PYBIND11_VERSION_PATCH}") + +# Standard includes +include(GNUInstallDirs) +include(CMakePackageConfigHelpers) +include(CMakeDependentOption) + +if(NOT pybind11_FIND_QUIETLY) + message(STATUS "pybind11 v${pybind11_VERSION} ${pybind11_VERSION_TYPE}") +endif() + +# Avoid infinite recursion if tests include this as a subdirectory +if(DEFINED PYBIND11_MASTER_PROJECT) + set(PYBIND11_TEST OFF) +endif() + +# Check if pybind11 is being used directly or via add_subdirectory +if(CMAKE_SOURCE_DIR STREQUAL PROJECT_SOURCE_DIR AND NOT DEFINED PYBIND11_MASTER_PROJECT) + ### Warn if not an out-of-source builds + if(CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR) + set(lines + "You are building in-place. If that is not what you intended to " + "do, you can clean the source directory with:\n" + "rm -r CMakeCache.txt CMakeFiles/ cmake_uninstall.cmake pybind11Config.cmake " + "pybind11ConfigVersion.cmake tests/CMakeFiles/\n") + message(AUTHOR_WARNING ${lines}) + endif() + + set(PYBIND11_MASTER_PROJECT ON) + + if(OSX AND CMAKE_VERSION VERSION_LESS 3.7) + # Bug in macOS CMake < 3.7 is unable to download catch + message(WARNING "CMAKE 3.7+ needed on macOS to download catch, and newer HIGHLY recommended") + elseif(WINDOWS AND CMAKE_VERSION VERSION_LESS 3.8) + # Only tested with 3.8+ in CI. + message(WARNING "CMAKE 3.8+ tested on Windows, previous versions untested") + endif() + + message(STATUS "CMake ${CMAKE_VERSION}") + + if(CMAKE_CXX_STANDARD) + set(CMAKE_CXX_EXTENSIONS OFF) + set(CMAKE_CXX_STANDARD_REQUIRED ON) + endif() + + set(pybind11_system "") +else() + set(PYBIND11_MASTER_PROJECT OFF) + set(pybind11_system SYSTEM) +endif() + +# Options +option(PYBIND11_INSTALL "Install pybind11 header files?" ${PYBIND11_MASTER_PROJECT}) +option(PYBIND11_TEST "Build pybind11 test suite?" ${PYBIND11_MASTER_PROJECT}) +option(PYBIND11_NOPYTHON "Disable search for Python" OFF) + +cmake_dependent_option( + USE_PYTHON_INCLUDE_DIR + "Install pybind11 headers in Python include directory instead of default installation prefix" + OFF "PYBIND11_INSTALL" OFF) + +cmake_dependent_option(PYBIND11_FINDPYTHON "Force new FindPython" OFF + "NOT CMAKE_VERSION VERSION_LESS 3.12" OFF) + +# NB: when adding a header don't forget to also add it to setup.py +set(PYBIND11_HEADERS + include/pybind11/detail/class.h + include/pybind11/detail/common.h + include/pybind11/detail/descr.h + include/pybind11/detail/init.h + include/pybind11/detail/internals.h + include/pybind11/detail/type_caster_base.h + include/pybind11/detail/typeid.h + include/pybind11/attr.h + include/pybind11/buffer_info.h + include/pybind11/cast.h + include/pybind11/chrono.h + include/pybind11/common.h + include/pybind11/complex.h + include/pybind11/options.h + include/pybind11/eigen.h + include/pybind11/embed.h + include/pybind11/eval.h + include/pybind11/gil.h + include/pybind11/iostream.h + include/pybind11/functional.h + include/pybind11/numpy.h + include/pybind11/operators.h + include/pybind11/pybind11.h + include/pybind11/pytypes.h + include/pybind11/stl.h + include/pybind11/stl_bind.h) + +# Compare with grep and warn if mismatched +if(PYBIND11_MASTER_PROJECT AND NOT CMAKE_VERSION VERSION_LESS 3.12) + file( + GLOB_RECURSE _pybind11_header_check + LIST_DIRECTORIES false + RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" + CONFIGURE_DEPENDS "include/pybind11/*.h") + set(_pybind11_here_only ${PYBIND11_HEADERS}) + set(_pybind11_disk_only ${_pybind11_header_check}) + list(REMOVE_ITEM _pybind11_here_only ${_pybind11_header_check}) + list(REMOVE_ITEM _pybind11_disk_only ${PYBIND11_HEADERS}) + if(_pybind11_here_only) + message(AUTHOR_WARNING "PYBIND11_HEADERS has extra files:" ${_pybind11_here_only}) + endif() + if(_pybind11_disk_only) + message(AUTHOR_WARNING "PYBIND11_HEADERS is missing files:" ${_pybind11_disk_only}) + endif() +endif() + +# CMake 3.12 added list(TRANSFORM PREPEND +# But we can't use it yet +string(REPLACE "include/" "${CMAKE_CURRENT_SOURCE_DIR}/include/" PYBIND11_HEADERS + "${PYBIND11_HEADERS}") + +# Cache variable so this can be used in parent projects +set(pybind11_INCLUDE_DIR + "${CMAKE_CURRENT_LIST_DIR}/include" + CACHE INTERNAL "Directory where pybind11 headers are located") + +# Backward compatible variable for add_subdirectory mode +if(NOT PYBIND11_MASTER_PROJECT) + set(PYBIND11_INCLUDE_DIR + "${pybind11_INCLUDE_DIR}" + CACHE INTERNAL "") +endif() + +# Note: when creating targets, you cannot use if statements at configure time - +# you need generator expressions, because those will be placed in the target file. +# You can also place ifs *in* the Config.in, but not here. + +# This section builds targets, but does *not* touch Python +# Non-IMPORT targets cannot be defined twice +if(NOT TARGET pybind11_headers) + # Build the headers-only target (no Python included): + # (long name used here to keep this from clashing in subdirectory mode) + add_library(pybind11_headers INTERFACE) + add_library(pybind11::pybind11_headers ALIAS pybind11_headers) # to match exported target + add_library(pybind11::headers ALIAS pybind11_headers) # easier to use/remember + + target_include_directories( + pybind11_headers ${pybind11_system} INTERFACE $ + $) + + target_compile_features(pybind11_headers INTERFACE cxx_inheriting_constructors cxx_user_literals + cxx_right_angle_brackets) +else() + # It is invalid to install a target twice, too. + set(PYBIND11_INSTALL OFF) +endif() + +include("${CMAKE_CURRENT_SOURCE_DIR}/tools/pybind11Common.cmake") + +# Relative directory setting +if(USE_PYTHON_INCLUDE_DIR AND DEFINED Python_INCLUDE_DIRS) + file(RELATIVE_PATH CMAKE_INSTALL_INCLUDEDIR ${CMAKE_INSTALL_PREFIX} ${Python_INCLUDE_DIRS}) +elseif(USE_PYTHON_INCLUDE_DIR AND DEFINED PYTHON_INCLUDE_DIR) + file(RELATIVE_PATH CMAKE_INSTALL_INCLUDEDIR ${CMAKE_INSTALL_PREFIX} ${PYTHON_INCLUDE_DIRS}) +endif() + +if(PYBIND11_INSTALL) + install(DIRECTORY ${pybind11_INCLUDE_DIR}/pybind11 DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) + set(PYBIND11_CMAKECONFIG_INSTALL_DIR + "${CMAKE_INSTALL_DATAROOTDIR}/cmake/${PROJECT_NAME}" + CACHE STRING "install path for pybind11Config.cmake") + + configure_package_config_file( + tools/${PROJECT_NAME}Config.cmake.in "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake" + INSTALL_DESTINATION ${PYBIND11_CMAKECONFIG_INSTALL_DIR}) + + if(CMAKE_VERSION VERSION_LESS 3.14) + # Remove CMAKE_SIZEOF_VOID_P from ConfigVersion.cmake since the library does + # not depend on architecture specific settings or libraries. + set(_PYBIND11_CMAKE_SIZEOF_VOID_P ${CMAKE_SIZEOF_VOID_P}) + unset(CMAKE_SIZEOF_VOID_P) + + write_basic_package_version_file( + ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake + VERSION ${PROJECT_VERSION} + COMPATIBILITY AnyNewerVersion) + + set(CMAKE_SIZEOF_VOID_P ${_PYBIND11_CMAKE_SIZEOF_VOID_P}) + else() + # CMake 3.14+ natively supports header-only libraries + write_basic_package_version_file( + ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake + VERSION ${PROJECT_VERSION} + COMPATIBILITY AnyNewerVersion ARCH_INDEPENDENT) + endif() + + install( + FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake + ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake + tools/FindPythonLibsNew.cmake + tools/pybind11Common.cmake + tools/pybind11Tools.cmake + tools/pybind11NewTools.cmake + DESTINATION ${PYBIND11_CMAKECONFIG_INSTALL_DIR}) + + if(NOT PYBIND11_EXPORT_NAME) + set(PYBIND11_EXPORT_NAME "${PROJECT_NAME}Targets") + endif() + + install(TARGETS pybind11_headers EXPORT "${PYBIND11_EXPORT_NAME}") + + install( + EXPORT "${PYBIND11_EXPORT_NAME}" + NAMESPACE "pybind11::" + DESTINATION ${PYBIND11_CMAKECONFIG_INSTALL_DIR}) + + # Uninstall target + if(PYBIND11_MASTER_PROJECT) + configure_file("${CMAKE_CURRENT_SOURCE_DIR}/tools/cmake_uninstall.cmake.in" + "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake" IMMEDIATE @ONLY) + + add_custom_target(uninstall COMMAND ${CMAKE_COMMAND} -P + ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake) + endif() +endif() + +# BUILD_TESTING takes priority, but only if this is the master project +if(PYBIND11_MASTER_PROJECT AND DEFINED BUILD_TESTING) + if(BUILD_TESTING) + if(_pybind11_nopython) + message(FATAL_ERROR "Cannot activate tests in NOPYTHON mode") + else() + add_subdirectory(tests) + endif() + endif() +else() + if(PYBIND11_TEST) + if(_pybind11_nopython) + message(FATAL_ERROR "Cannot activate tests in NOPYTHON mode") + else() + add_subdirectory(tests) + endif() + endif() +endif() + +# Better symmetry with find_package(pybind11 CONFIG) mode. +if(NOT PYBIND11_MASTER_PROJECT) + set(pybind11_FOUND + TRUE + CACHE INTERNAL "True if pybind11 and all required components found on the system") +endif() diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/LICENSE b/methods/ring/utils/fast_gicp/thirdparty/pybind11/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..e466b0dfda14f3a7c8ece512937eb99c8b7b6d68 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/LICENSE @@ -0,0 +1,29 @@ +Copyright (c) 2016 Wenzel Jakob , All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its contributors + may be used to endorse or promote products derived from this software + without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +Please also refer to the file .github/CONTRIBUTING.md, which clarifies licensing of +external contributions to this project including patches, pull requests, etc. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/MANIFEST.in b/methods/ring/utils/fast_gicp/thirdparty/pybind11/MANIFEST.in new file mode 100644 index 0000000000000000000000000000000000000000..aed183e874749089ab5d89ab43523bdde8a9a34c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/MANIFEST.in @@ -0,0 +1,6 @@ +recursive-include pybind11/include/pybind11 *.h +recursive-include pybind11 *.py +recursive-include pybind11 py.typed +recursive-include pybind11 *.pyi +include pybind11/share/cmake/pybind11/*.cmake +include LICENSE README.rst pyproject.toml setup.py setup.cfg diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/README.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/README.rst new file mode 100644 index 0000000000000000000000000000000000000000..6c2a2551096a456036cced3c1caf70ed89d3dc4a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/README.rst @@ -0,0 +1,191 @@ +.. figure:: https://github.com/pybind/pybind11/raw/master/docs/pybind11-logo.png + :alt: pybind11 logo + +**pybind11 — Seamless operability between C++11 and Python** + +|Latest Documentation Status| |Stable Documentation Status| |Gitter chat| |CI| |Build status| + +|Repology| |PyPI package| |Conda-forge| |Python Versions| + +`Setuptools example `_ +• `Scikit-build example `_ +• `CMake example `_ + +.. start + +.. warning:: + + Combining older versions of pybind11 (< 2.6.0) with Python 3.9.0 will + trigger undefined behavior that typically manifests as crashes during + interpreter shutdown (but could also destroy your data. **You have been + warned.**) + + We recommend that you update to the latest patch release of Python (3.9.1), + which includes a `fix `_ + that resolves this problem. If you do use Python 3.9.0, please update to + the latest version of pybind11 (2.6.0 or newer), which includes a temporary + workaround specifically when Python 3.9.0 is detected at runtime. + + +**pybind11** is a lightweight header-only library that exposes C++ types +in Python and vice versa, mainly to create Python bindings of existing +C++ code. Its goals and syntax are similar to the excellent +`Boost.Python `_ +library by David Abrahams: to minimize boilerplate code in traditional +extension modules by inferring type information using compile-time +introspection. + +The main issue with Boost.Python—and the reason for creating such a +similar project—is Boost. Boost is an enormously large and complex suite +of utility libraries that works with almost every C++ compiler in +existence. This compatibility has its cost: arcane template tricks and +workarounds are necessary to support the oldest and buggiest of compiler +specimens. Now that C++11-compatible compilers are widely available, +this heavy machinery has become an excessively large and unnecessary +dependency. + +Think of this library as a tiny self-contained version of Boost.Python +with everything stripped away that isn’t relevant for binding +generation. Without comments, the core header files only require ~4K +lines of code and depend on Python (2.7 or 3.5+, or PyPy) and the C++ +standard library. This compact implementation was possible thanks to +some of the new C++11 language features (specifically: tuples, lambda +functions and variadic templates). Since its creation, this library has +grown beyond Boost.Python in many ways, leading to dramatically simpler +binding code in many common situations. + +Tutorial and reference documentation is provided at +`pybind11.readthedocs.io `_. +A PDF version of the manual is available +`here `_. +And the source code is always available at +`github.com/pybind/pybind11 `_. + + +Core features +------------- + + +pybind11 can map the following core C++ features to Python: + +- Functions accepting and returning custom data structures per value, + reference, or pointer +- Instance methods and static methods +- Overloaded functions +- Instance attributes and static attributes +- Arbitrary exception types +- Enumerations +- Callbacks +- Iterators and ranges +- Custom operators +- Single and multiple inheritance +- STL data structures +- Smart pointers with reference counting like ``std::shared_ptr`` +- Internal references with correct reference counting +- C++ classes with virtual (and pure virtual) methods can be extended + in Python + +Goodies +------- + +In addition to the core functionality, pybind11 provides some extra +goodies: + +- Python 2.7, 3.5+, and PyPy/PyPy3 7.3 are supported with an + implementation-agnostic interface. + +- It is possible to bind C++11 lambda functions with captured + variables. The lambda capture data is stored inside the resulting + Python function object. + +- pybind11 uses C++11 move constructors and move assignment operators + whenever possible to efficiently transfer custom data types. + +- It’s easy to expose the internal storage of custom data types through + Pythons’ buffer protocols. This is handy e.g. for fast conversion + between C++ matrix classes like Eigen and NumPy without expensive + copy operations. + +- pybind11 can automatically vectorize functions so that they are + transparently applied to all entries of one or more NumPy array + arguments. + +- Python’s slice-based access and assignment operations can be + supported with just a few lines of code. + +- Everything is contained in just a few header files; there is no need + to link against any additional libraries. + +- Binaries are generally smaller by a factor of at least 2 compared to + equivalent bindings generated by Boost.Python. A recent pybind11 + conversion of PyRosetta, an enormous Boost.Python binding project, + `reported `_ + a binary size reduction of **5.4x** and compile time reduction by + **5.8x**. + +- Function signatures are precomputed at compile time (using + ``constexpr``), leading to smaller binaries. + +- With little extra effort, C++ types can be pickled and unpickled + similar to regular Python objects. + +Supported compilers +------------------- + +1. Clang/LLVM 3.3 or newer (for Apple Xcode’s clang, this is 5.0.0 or + newer) +2. GCC 4.8 or newer +3. Microsoft Visual Studio 2015 Update 3 or newer +4. Intel classic C++ compiler 18 or newer (ICC 20.2 tested in CI) +5. Cygwin/GCC (previously tested on 2.5.1) +6. NVCC (CUDA 11.0 tested in CI) +7. NVIDIA PGI (20.9 tested in CI) + +About +----- + +This project was created by `Wenzel +Jakob `_. Significant features and/or +improvements to the code were contributed by Jonas Adler, Lori A. Burns, +Sylvain Corlay, Eric Cousineau, Ralf Grosse-Kunstleve, Trent Houliston, Axel +Huebl, @hulucc, Yannick Jadoul, Sergey Lyskov Johan Mabille, Tomasz Miąsko, +Dean Moldovan, Ben Pritchard, Jason Rhinelander, Boris Schäling, Pim +Schellart, Henry Schreiner, Ivan Smirnov, Boris Staletic, and Patrick Stewart. + +We thank Google for a generous financial contribution to the continuous +integration infrastructure used by this project. + + +Contributing +~~~~~~~~~~~~ + +See the `contributing +guide `_ +for information on building and contributing to pybind11. + +License +~~~~~~~ + +pybind11 is provided under a BSD-style license that can be found in the +`LICENSE `_ +file. By using, distributing, or contributing to this project, you agree +to the terms and conditions of this license. + +.. |Latest Documentation Status| image:: https://readthedocs.org/projects/pybind11/badge?version=latest + :target: http://pybind11.readthedocs.org/en/latest +.. |Stable Documentation Status| image:: https://img.shields.io/badge/docs-stable-blue.svg + :target: http://pybind11.readthedocs.org/en/stable +.. |Gitter chat| image:: https://img.shields.io/gitter/room/gitterHQ/gitter.svg + :target: https://gitter.im/pybind/Lobby +.. |CI| image:: https://github.com/pybind/pybind11/workflows/CI/badge.svg + :target: https://github.com/pybind/pybind11/actions +.. |Build status| image:: https://ci.appveyor.com/api/projects/status/riaj54pn4h08xy40?svg=true + :target: https://ci.appveyor.com/project/wjakob/pybind11 +.. |PyPI package| image:: https://img.shields.io/pypi/v/pybind11.svg + :target: https://pypi.org/project/pybind11/ +.. |Conda-forge| image:: https://img.shields.io/conda/vn/conda-forge/pybind11.svg + :target: https://github.com/conda-forge/pybind11-feedstock +.. |Repology| image:: https://repology.org/badge/latest-versions/python:pybind11.svg + :target: https://repology.org/project/python:pybind11/versions +.. |Python Versions| image:: https://img.shields.io/pypi/pyversions/pybind11.svg + :target: https://pypi.org/project/pybind11/ diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/Doxyfile b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/Doxyfile new file mode 100644 index 0000000000000000000000000000000000000000..c8562952ef426d3fc13485a7fa98b32f0bc97b75 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/Doxyfile @@ -0,0 +1,23 @@ +PROJECT_NAME = pybind11 +INPUT = ../include/pybind11/ +RECURSIVE = YES + +GENERATE_HTML = NO +GENERATE_LATEX = NO +GENERATE_XML = YES +XML_OUTPUT = .build/doxygenxml +XML_PROGRAMLISTING = YES + +MACRO_EXPANSION = YES +EXPAND_ONLY_PREDEF = YES +EXPAND_AS_DEFINED = PYBIND11_RUNTIME_EXCEPTION + +ALIASES = "rst=\verbatim embed:rst" +ALIASES += "endrst=\endverbatim" + +QUIET = YES +WARNINGS = YES +WARN_IF_UNDOCUMENTED = NO +PREDEFINED = DOXYGEN_SHOULD_SKIP_THIS \ + PY_MAJOR_VERSION=3 \ + PYBIND11_NOINLINE diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/_static/theme_overrides.css b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/_static/theme_overrides.css new file mode 100644 index 0000000000000000000000000000000000000000..1071809fa0fecf7c28d3356f37363266e9128b81 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/_static/theme_overrides.css @@ -0,0 +1,11 @@ +.wy-table-responsive table td, +.wy-table-responsive table th { + white-space: initial !important; +} +.rst-content table.docutils td { + vertical-align: top !important; +} +div[class^='highlight'] pre { + white-space: pre; + white-space: pre-wrap; +} diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/chrono.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/chrono.rst new file mode 100644 index 0000000000000000000000000000000000000000..fbd46057aa392c86ae3747c2b21768367205ea49 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/chrono.rst @@ -0,0 +1,81 @@ +Chrono +====== + +When including the additional header file :file:`pybind11/chrono.h` conversions +from C++11 chrono datatypes to python datetime objects are automatically enabled. +This header also enables conversions of python floats (often from sources such +as ``time.monotonic()``, ``time.perf_counter()`` and ``time.process_time()``) +into durations. + +An overview of clocks in C++11 +------------------------------ + +A point of confusion when using these conversions is the differences between +clocks provided in C++11. There are three clock types defined by the C++11 +standard and users can define their own if needed. Each of these clocks have +different properties and when converting to and from python will give different +results. + +The first clock defined by the standard is ``std::chrono::system_clock``. This +clock measures the current date and time. However, this clock changes with to +updates to the operating system time. For example, if your time is synchronised +with a time server this clock will change. This makes this clock a poor choice +for timing purposes but good for measuring the wall time. + +The second clock defined in the standard is ``std::chrono::steady_clock``. +This clock ticks at a steady rate and is never adjusted. This makes it excellent +for timing purposes, however the value in this clock does not correspond to the +current date and time. Often this clock will be the amount of time your system +has been on, although it does not have to be. This clock will never be the same +clock as the system clock as the system clock can change but steady clocks +cannot. + +The third clock defined in the standard is ``std::chrono::high_resolution_clock``. +This clock is the clock that has the highest resolution out of the clocks in the +system. It is normally a typedef to either the system clock or the steady clock +but can be its own independent clock. This is important as when using these +conversions as the types you get in python for this clock might be different +depending on the system. +If it is a typedef of the system clock, python will get datetime objects, but if +it is a different clock they will be timedelta objects. + +Provided conversions +-------------------- + +.. rubric:: C++ to Python + +- ``std::chrono::system_clock::time_point`` → ``datetime.datetime`` + System clock times are converted to python datetime instances. They are + in the local timezone, but do not have any timezone information attached + to them (they are naive datetime objects). + +- ``std::chrono::duration`` → ``datetime.timedelta`` + Durations are converted to timedeltas, any precision in the duration + greater than microseconds is lost by rounding towards zero. + +- ``std::chrono::[other_clocks]::time_point`` → ``datetime.timedelta`` + Any clock time that is not the system clock is converted to a time delta. + This timedelta measures the time from the clocks epoch to now. + +.. rubric:: Python to C++ + +- ``datetime.datetime`` or ``datetime.date`` or ``datetime.time`` → ``std::chrono::system_clock::time_point`` + Date/time objects are converted into system clock timepoints. Any + timezone information is ignored and the type is treated as a naive + object. + +- ``datetime.timedelta`` → ``std::chrono::duration`` + Time delta are converted into durations with microsecond precision. + +- ``datetime.timedelta`` → ``std::chrono::[other_clocks]::time_point`` + Time deltas that are converted into clock timepoints are treated as + the amount of time from the start of the clocks epoch. + +- ``float`` → ``std::chrono::duration`` + Floats that are passed to C++ as durations be interpreted as a number of + seconds. These will be converted to the duration using ``duration_cast`` + from the float. + +- ``float`` → ``std::chrono::[other_clocks]::time_point`` + Floats that are passed to C++ as time points will be interpreted as the + number of seconds from the start of the clocks epoch. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/custom.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/custom.rst new file mode 100644 index 0000000000000000000000000000000000000000..a779444c24a2fc6ee0d928b766a14dce8d7aec14 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/custom.rst @@ -0,0 +1,91 @@ +Custom type casters +=================== + +In very rare cases, applications may require custom type casters that cannot be +expressed using the abstractions provided by pybind11, thus requiring raw +Python C API calls. This is fairly advanced usage and should only be pursued by +experts who are familiar with the intricacies of Python reference counting. + +The following snippets demonstrate how this works for a very simple ``inty`` +type that that should be convertible from Python types that provide a +``__int__(self)`` method. + +.. code-block:: cpp + + struct inty { long long_value; }; + + void print(inty s) { + std::cout << s.long_value << std::endl; + } + +The following Python snippet demonstrates the intended usage from the Python side: + +.. code-block:: python + + class A: + def __int__(self): + return 123 + + from example import print + print(A()) + +To register the necessary conversion routines, it is necessary to add an +instantiation of the ``pybind11::detail::type_caster`` template. +Although this is an implementation detail, adding an instantiation of this +type is explicitly allowed. + +.. code-block:: cpp + + namespace pybind11 { namespace detail { + template <> struct type_caster { + public: + /** + * This macro establishes the name 'inty' in + * function signatures and declares a local variable + * 'value' of type inty + */ + PYBIND11_TYPE_CASTER(inty, _("inty")); + + /** + * Conversion part 1 (Python->C++): convert a PyObject into a inty + * instance or return false upon failure. The second argument + * indicates whether implicit conversions should be applied. + */ + bool load(handle src, bool) { + /* Extract PyObject from handle */ + PyObject *source = src.ptr(); + /* Try converting into a Python integer value */ + PyObject *tmp = PyNumber_Long(source); + if (!tmp) + return false; + /* Now try to convert into a C++ int */ + value.long_value = PyLong_AsLong(tmp); + Py_DECREF(tmp); + /* Ensure return code was OK (to avoid out-of-range errors etc) */ + return !(value.long_value == -1 && !PyErr_Occurred()); + } + + /** + * Conversion part 2 (C++ -> Python): convert an inty instance into + * a Python object. The second and third arguments are used to + * indicate the return value policy and parent object (for + * ``return_value_policy::reference_internal``) and are generally + * ignored by implicit casters. + */ + static handle cast(inty src, return_value_policy /* policy */, handle /* parent */) { + return PyLong_FromLong(src.long_value); + } + }; + }} // namespace pybind11::detail + +.. note:: + + A ``type_caster`` defined with ``PYBIND11_TYPE_CASTER(T, ...)`` requires + that ``T`` is default-constructible (``value`` is first default constructed + and then ``load()`` assigns to it). + +.. warning:: + + When using custom type casters, it's important to declare them consistently + in every compilation unit of the Python extension module. Otherwise, + undefined behavior can ensue. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/eigen.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/eigen.rst new file mode 100644 index 0000000000000000000000000000000000000000..e01472d5aeaccc5c59a187f5ca9bf00eaf4fddba --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/eigen.rst @@ -0,0 +1,310 @@ +Eigen +##### + +`Eigen `_ is C++ header-based library for dense and +sparse linear algebra. Due to its popularity and widespread adoption, pybind11 +provides transparent conversion and limited mapping support between Eigen and +Scientific Python linear algebra data types. + +To enable the built-in Eigen support you must include the optional header file +:file:`pybind11/eigen.h`. + +Pass-by-value +============= + +When binding a function with ordinary Eigen dense object arguments (for +example, ``Eigen::MatrixXd``), pybind11 will accept any input value that is +already (or convertible to) a ``numpy.ndarray`` with dimensions compatible with +the Eigen type, copy its values into a temporary Eigen variable of the +appropriate type, then call the function with this temporary variable. + +Sparse matrices are similarly copied to or from +``scipy.sparse.csr_matrix``/``scipy.sparse.csc_matrix`` objects. + +Pass-by-reference +================= + +One major limitation of the above is that every data conversion implicitly +involves a copy, which can be both expensive (for large matrices) and disallows +binding functions that change their (Matrix) arguments. Pybind11 allows you to +work around this by using Eigen's ``Eigen::Ref`` class much as you +would when writing a function taking a generic type in Eigen itself (subject to +some limitations discussed below). + +When calling a bound function accepting a ``Eigen::Ref`` +type, pybind11 will attempt to avoid copying by using an ``Eigen::Map`` object +that maps into the source ``numpy.ndarray`` data: this requires both that the +data types are the same (e.g. ``dtype='float64'`` and ``MatrixType::Scalar`` is +``double``); and that the storage is layout compatible. The latter limitation +is discussed in detail in the section below, and requires careful +consideration: by default, numpy matrices and Eigen matrices are *not* storage +compatible. + +If the numpy matrix cannot be used as is (either because its types differ, e.g. +passing an array of integers to an Eigen parameter requiring doubles, or +because the storage is incompatible), pybind11 makes a temporary copy and +passes the copy instead. + +When a bound function parameter is instead ``Eigen::Ref`` (note the +lack of ``const``), pybind11 will only allow the function to be called if it +can be mapped *and* if the numpy array is writeable (that is +``a.flags.writeable`` is true). Any access (including modification) made to +the passed variable will be transparently carried out directly on the +``numpy.ndarray``. + +This means you can can write code such as the following and have it work as +expected: + +.. code-block:: cpp + + void scale_by_2(Eigen::Ref v) { + v *= 2; + } + +Note, however, that you will likely run into limitations due to numpy and +Eigen's difference default storage order for data; see the below section on +:ref:`storage_orders` for details on how to bind code that won't run into such +limitations. + +.. note:: + + Passing by reference is not supported for sparse types. + +Returning values to Python +========================== + +When returning an ordinary dense Eigen matrix type to numpy (e.g. +``Eigen::MatrixXd`` or ``Eigen::RowVectorXf``) pybind11 keeps the matrix and +returns a numpy array that directly references the Eigen matrix: no copy of the +data is performed. The numpy array will have ``array.flags.owndata`` set to +``False`` to indicate that it does not own the data, and the lifetime of the +stored Eigen matrix will be tied to the returned ``array``. + +If you bind a function with a non-reference, ``const`` return type (e.g. +``const Eigen::MatrixXd``), the same thing happens except that pybind11 also +sets the numpy array's ``writeable`` flag to false. + +If you return an lvalue reference or pointer, the usual pybind11 rules apply, +as dictated by the binding function's return value policy (see the +documentation on :ref:`return_value_policies` for full details). That means, +without an explicit return value policy, lvalue references will be copied and +pointers will be managed by pybind11. In order to avoid copying, you should +explicitly specify an appropriate return value policy, as in the following +example: + +.. code-block:: cpp + + class MyClass { + Eigen::MatrixXd big_mat = Eigen::MatrixXd::Zero(10000, 10000); + public: + Eigen::MatrixXd &getMatrix() { return big_mat; } + const Eigen::MatrixXd &viewMatrix() { return big_mat; } + }; + + // Later, in binding code: + py::class_(m, "MyClass") + .def(py::init<>()) + .def("copy_matrix", &MyClass::getMatrix) // Makes a copy! + .def("get_matrix", &MyClass::getMatrix, py::return_value_policy::reference_internal) + .def("view_matrix", &MyClass::viewMatrix, py::return_value_policy::reference_internal) + ; + +.. code-block:: python + + a = MyClass() + m = a.get_matrix() # flags.writeable = True, flags.owndata = False + v = a.view_matrix() # flags.writeable = False, flags.owndata = False + c = a.copy_matrix() # flags.writeable = True, flags.owndata = True + # m[5,6] and v[5,6] refer to the same element, c[5,6] does not. + +Note in this example that ``py::return_value_policy::reference_internal`` is +used to tie the life of the MyClass object to the life of the returned arrays. + +You may also return an ``Eigen::Ref``, ``Eigen::Map`` or other map-like Eigen +object (for example, the return value of ``matrix.block()`` and related +methods) that map into a dense Eigen type. When doing so, the default +behaviour of pybind11 is to simply reference the returned data: you must take +care to ensure that this data remains valid! You may ask pybind11 to +explicitly *copy* such a return value by using the +``py::return_value_policy::copy`` policy when binding the function. You may +also use ``py::return_value_policy::reference_internal`` or a +``py::keep_alive`` to ensure the data stays valid as long as the returned numpy +array does. + +When returning such a reference of map, pybind11 additionally respects the +readonly-status of the returned value, marking the numpy array as non-writeable +if the reference or map was itself read-only. + +.. note:: + + Sparse types are always copied when returned. + +.. _storage_orders: + +Storage orders +============== + +Passing arguments via ``Eigen::Ref`` has some limitations that you must be +aware of in order to effectively pass matrices by reference. First and +foremost is that the default ``Eigen::Ref`` class requires +contiguous storage along columns (for column-major types, the default in Eigen) +or rows if ``MatrixType`` is specifically an ``Eigen::RowMajor`` storage type. +The former, Eigen's default, is incompatible with ``numpy``'s default row-major +storage, and so you will not be able to pass numpy arrays to Eigen by reference +without making one of two changes. + +(Note that this does not apply to vectors (or column or row matrices): for such +types the "row-major" and "column-major" distinction is meaningless). + +The first approach is to change the use of ``Eigen::Ref`` to the +more general ``Eigen::Ref>`` (or similar type with a fully dynamic stride type in the +third template argument). Since this is a rather cumbersome type, pybind11 +provides a ``py::EigenDRef`` type alias for your convenience (along +with EigenDMap for the equivalent Map, and EigenDStride for just the stride +type). + +This type allows Eigen to map into any arbitrary storage order. This is not +the default in Eigen for performance reasons: contiguous storage allows +vectorization that cannot be done when storage is not known to be contiguous at +compile time. The default ``Eigen::Ref`` stride type allows non-contiguous +storage along the outer dimension (that is, the rows of a column-major matrix +or columns of a row-major matrix), but not along the inner dimension. + +This type, however, has the added benefit of also being able to map numpy array +slices. For example, the following (contrived) example uses Eigen with a numpy +slice to multiply by 2 all coefficients that are both on even rows (0, 2, 4, +...) and in columns 2, 5, or 8: + +.. code-block:: cpp + + m.def("scale", [](py::EigenDRef m, double c) { m *= c; }); + +.. code-block:: python + + # a = np.array(...) + scale_by_2(myarray[0::2, 2:9:3]) + +The second approach to avoid copying is more intrusive: rearranging the +underlying data types to not run into the non-contiguous storage problem in the +first place. In particular, that means using matrices with ``Eigen::RowMajor`` +storage, where appropriate, such as: + +.. code-block:: cpp + + using RowMatrixXd = Eigen::Matrix; + // Use RowMatrixXd instead of MatrixXd + +Now bound functions accepting ``Eigen::Ref`` arguments will be +callable with numpy's (default) arrays without involving a copying. + +You can, alternatively, change the storage order that numpy arrays use by +adding the ``order='F'`` option when creating an array: + +.. code-block:: python + + myarray = np.array(source, order='F') + +Such an object will be passable to a bound function accepting an +``Eigen::Ref`` (or similar column-major Eigen type). + +One major caveat with this approach, however, is that it is not entirely as +easy as simply flipping all Eigen or numpy usage from one to the other: some +operations may alter the storage order of a numpy array. For example, ``a2 = +array.transpose()`` results in ``a2`` being a view of ``array`` that references +the same data, but in the opposite storage order! + +While this approach allows fully optimized vectorized calculations in Eigen, it +cannot be used with array slices, unlike the first approach. + +When *returning* a matrix to Python (either a regular matrix, a reference via +``Eigen::Ref<>``, or a map/block into a matrix), no special storage +consideration is required: the created numpy array will have the required +stride that allows numpy to properly interpret the array, whatever its storage +order. + +Failing rather than copying +=========================== + +The default behaviour when binding ``Eigen::Ref`` Eigen +references is to copy matrix values when passed a numpy array that does not +conform to the element type of ``MatrixType`` or does not have a compatible +stride layout. If you want to explicitly avoid copying in such a case, you +should bind arguments using the ``py::arg().noconvert()`` annotation (as +described in the :ref:`nonconverting_arguments` documentation). + +The following example shows an example of arguments that don't allow data +copying to take place: + +.. code-block:: cpp + + // The method and function to be bound: + class MyClass { + // ... + double some_method(const Eigen::Ref &matrix) { /* ... */ } + }; + float some_function(const Eigen::Ref &big, + const Eigen::Ref &small) { + // ... + } + + // The associated binding code: + using namespace pybind11::literals; // for "arg"_a + py::class_(m, "MyClass") + // ... other class definitions + .def("some_method", &MyClass::some_method, py::arg().noconvert()); + + m.def("some_function", &some_function, + "big"_a.noconvert(), // <- Don't allow copying for this arg + "small"_a // <- This one can be copied if needed + ); + +With the above binding code, attempting to call the the ``some_method(m)`` +method on a ``MyClass`` object, or attempting to call ``some_function(m, m2)`` +will raise a ``RuntimeError`` rather than making a temporary copy of the array. +It will, however, allow the ``m2`` argument to be copied into a temporary if +necessary. + +Note that explicitly specifying ``.noconvert()`` is not required for *mutable* +Eigen references (e.g. ``Eigen::Ref`` without ``const`` on the +``MatrixXd``): mutable references will never be called with a temporary copy. + +Vectors versus column/row matrices +================================== + +Eigen and numpy have fundamentally different notions of a vector. In Eigen, a +vector is simply a matrix with the number of columns or rows set to 1 at +compile time (for a column vector or row vector, respectively). NumPy, in +contrast, has comparable 2-dimensional 1xN and Nx1 arrays, but *also* has +1-dimensional arrays of size N. + +When passing a 2-dimensional 1xN or Nx1 array to Eigen, the Eigen type must +have matching dimensions: That is, you cannot pass a 2-dimensional Nx1 numpy +array to an Eigen value expecting a row vector, or a 1xN numpy array as a +column vector argument. + +On the other hand, pybind11 allows you to pass 1-dimensional arrays of length N +as Eigen parameters. If the Eigen type can hold a column vector of length N it +will be passed as such a column vector. If not, but the Eigen type constraints +will accept a row vector, it will be passed as a row vector. (The column +vector takes precedence when both are supported, for example, when passing a +1D numpy array to a MatrixXd argument). Note that the type need not be +explicitly a vector: it is permitted to pass a 1D numpy array of size 5 to an +Eigen ``Matrix``: you would end up with a 1x5 Eigen matrix. +Passing the same to an ``Eigen::MatrixXd`` would result in a 5x1 Eigen matrix. + +When returning an Eigen vector to numpy, the conversion is ambiguous: a row +vector of length 4 could be returned as either a 1D array of length 4, or as a +2D array of size 1x4. When encountering such a situation, pybind11 compromises +by considering the returned Eigen type: if it is a compile-time vector--that +is, the type has either the number of rows or columns set to 1 at compile +time--pybind11 converts to a 1D numpy array when returning the value. For +instances that are a vector only at run-time (e.g. ``MatrixXd``, +``Matrix``), pybind11 returns the vector as a 2D array to +numpy. If this isn't want you want, you can use ``array.reshape(...)`` to get +a view of the same data in the desired dimensions. + +.. seealso:: + + The file :file:`tests/test_eigen.cpp` contains a complete example that + shows how to pass Eigen sparse and dense data types in more detail. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/functional.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/functional.rst new file mode 100644 index 0000000000000000000000000000000000000000..d9b46057598f0d182422accd088fbff9785b0b53 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/functional.rst @@ -0,0 +1,109 @@ +Functional +########## + +The following features must be enabled by including :file:`pybind11/functional.h`. + + +Callbacks and passing anonymous functions +========================================= + +The C++11 standard brought lambda functions and the generic polymorphic +function wrapper ``std::function<>`` to the C++ programming language, which +enable powerful new ways of working with functions. Lambda functions come in +two flavors: stateless lambda function resemble classic function pointers that +link to an anonymous piece of code, while stateful lambda functions +additionally depend on captured variables that are stored in an anonymous +*lambda closure object*. + +Here is a simple example of a C++ function that takes an arbitrary function +(stateful or stateless) with signature ``int -> int`` as an argument and runs +it with the value 10. + +.. code-block:: cpp + + int func_arg(const std::function &f) { + return f(10); + } + +The example below is more involved: it takes a function of signature ``int -> int`` +and returns another function of the same kind. The return value is a stateful +lambda function, which stores the value ``f`` in the capture object and adds 1 to +its return value upon execution. + +.. code-block:: cpp + + std::function func_ret(const std::function &f) { + return [f](int i) { + return f(i) + 1; + }; + } + +This example demonstrates using python named parameters in C++ callbacks which +requires using ``py::cpp_function`` as a wrapper. Usage is similar to defining +methods of classes: + +.. code-block:: cpp + + py::cpp_function func_cpp() { + return py::cpp_function([](int i) { return i+1; }, + py::arg("number")); + } + +After including the extra header file :file:`pybind11/functional.h`, it is almost +trivial to generate binding code for all of these functions. + +.. code-block:: cpp + + #include + + PYBIND11_MODULE(example, m) { + m.def("func_arg", &func_arg); + m.def("func_ret", &func_ret); + m.def("func_cpp", &func_cpp); + } + +The following interactive session shows how to call them from Python. + +.. code-block:: pycon + + $ python + >>> import example + >>> def square(i): + ... return i * i + ... + >>> example.func_arg(square) + 100L + >>> square_plus_1 = example.func_ret(square) + >>> square_plus_1(4) + 17L + >>> plus_1 = func_cpp() + >>> plus_1(number=43) + 44L + +.. warning:: + + Keep in mind that passing a function from C++ to Python (or vice versa) + will instantiate a piece of wrapper code that translates function + invocations between the two languages. Naturally, this translation + increases the computational cost of each function call somewhat. A + problematic situation can arise when a function is copied back and forth + between Python and C++ many times in a row, in which case the underlying + wrappers will accumulate correspondingly. The resulting long sequence of + C++ -> Python -> C++ -> ... roundtrips can significantly decrease + performance. + + There is one exception: pybind11 detects case where a stateless function + (i.e. a function pointer or a lambda function without captured variables) + is passed as an argument to another C++ function exposed in Python. In this + case, there is no overhead. Pybind11 will extract the underlying C++ + function pointer from the wrapped function to sidestep a potential C++ -> + Python -> C++ roundtrip. This is demonstrated in :file:`tests/test_callbacks.cpp`. + +.. note:: + + This functionality is very useful when generating bindings for callbacks in + C++ libraries (e.g. GUI libraries, asynchronous networking libraries, etc.). + + The file :file:`tests/test_callbacks.cpp` contains a complete example + that demonstrates how to work with callbacks and anonymous functions in + more detail. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/index.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/index.rst new file mode 100644 index 0000000000000000000000000000000000000000..3ce9ea0286e9dbd5fc795e60ae77a3c9afa356b8 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/index.rst @@ -0,0 +1,43 @@ +.. _type-conversions: + +Type conversions +################ + +Apart from enabling cross-language function calls, a fundamental problem +that a binding tool like pybind11 must address is to provide access to +native Python types in C++ and vice versa. There are three fundamentally +different ways to do this—which approach is preferable for a particular type +depends on the situation at hand. + +1. Use a native C++ type everywhere. In this case, the type must be wrapped + using pybind11-generated bindings so that Python can interact with it. + +2. Use a native Python type everywhere. It will need to be wrapped so that + C++ functions can interact with it. + +3. Use a native C++ type on the C++ side and a native Python type on the + Python side. pybind11 refers to this as a *type conversion*. + + Type conversions are the most "natural" option in the sense that native + (non-wrapped) types are used everywhere. The main downside is that a copy + of the data must be made on every Python ↔ C++ transition: this is + needed since the C++ and Python versions of the same type generally won't + have the same memory layout. + + pybind11 can perform many kinds of conversions automatically. An overview + is provided in the table ":ref:`conversion_table`". + +The following subsections discuss the differences between these options in more +detail. The main focus in this section is on type conversions, which represent +the last case of the above list. + +.. toctree:: + :maxdepth: 1 + + overview + strings + stl + functional + chrono + eigen + custom diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/overview.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/overview.rst new file mode 100644 index 0000000000000000000000000000000000000000..b0e32a52f9c8bb2945e230416216c38e3c3a4a9b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/overview.rst @@ -0,0 +1,165 @@ +Overview +######## + +.. rubric:: 1. Native type in C++, wrapper in Python + +Exposing a custom C++ type using :class:`py::class_` was covered in detail +in the :doc:`/classes` section. There, the underlying data structure is +always the original C++ class while the :class:`py::class_` wrapper provides +a Python interface. Internally, when an object like this is sent from C++ to +Python, pybind11 will just add the outer wrapper layer over the native C++ +object. Getting it back from Python is just a matter of peeling off the +wrapper. + +.. rubric:: 2. Wrapper in C++, native type in Python + +This is the exact opposite situation. Now, we have a type which is native to +Python, like a ``tuple`` or a ``list``. One way to get this data into C++ is +with the :class:`py::object` family of wrappers. These are explained in more +detail in the :doc:`/advanced/pycpp/object` section. We'll just give a quick +example here: + +.. code-block:: cpp + + void print_list(py::list my_list) { + for (auto item : my_list) + std::cout << item << " "; + } + +.. code-block:: pycon + + >>> print_list([1, 2, 3]) + 1 2 3 + +The Python ``list`` is not converted in any way -- it's just wrapped in a C++ +:class:`py::list` class. At its core it's still a Python object. Copying a +:class:`py::list` will do the usual reference-counting like in Python. +Returning the object to Python will just remove the thin wrapper. + +.. rubric:: 3. Converting between native C++ and Python types + +In the previous two cases we had a native type in one language and a wrapper in +the other. Now, we have native types on both sides and we convert between them. + +.. code-block:: cpp + + void print_vector(const std::vector &v) { + for (auto item : v) + std::cout << item << "\n"; + } + +.. code-block:: pycon + + >>> print_vector([1, 2, 3]) + 1 2 3 + +In this case, pybind11 will construct a new ``std::vector`` and copy each +element from the Python ``list``. The newly constructed object will be passed +to ``print_vector``. The same thing happens in the other direction: a new +``list`` is made to match the value returned from C++. + +Lots of these conversions are supported out of the box, as shown in the table +below. They are very convenient, but keep in mind that these conversions are +fundamentally based on copying data. This is perfectly fine for small immutable +types but it may become quite expensive for large data structures. This can be +avoided by overriding the automatic conversion with a custom wrapper (i.e. the +above-mentioned approach 1). This requires some manual effort and more details +are available in the :ref:`opaque` section. + +.. _conversion_table: + +List of all builtin conversions +------------------------------- + +The following basic data types are supported out of the box (some may require +an additional extension header to be included). To pass other data structures +as arguments and return values, refer to the section on binding :ref:`classes`. + ++------------------------------------+---------------------------+-------------------------------+ +| Data type | Description | Header file | ++====================================+===========================+===============================+ +| ``int8_t``, ``uint8_t`` | 8-bit integers | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``int16_t``, ``uint16_t`` | 16-bit integers | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``int32_t``, ``uint32_t`` | 32-bit integers | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``int64_t``, ``uint64_t`` | 64-bit integers | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``ssize_t``, ``size_t`` | Platform-dependent size | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``float``, ``double`` | Floating point types | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``bool`` | Two-state Boolean type | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``char`` | Character literal | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``char16_t`` | UTF-16 character literal | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``char32_t`` | UTF-32 character literal | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``wchar_t`` | Wide character literal | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``const char *`` | UTF-8 string literal | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``const char16_t *`` | UTF-16 string literal | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``const char32_t *`` | UTF-32 string literal | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``const wchar_t *`` | Wide string literal | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::string`` | STL dynamic UTF-8 string | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::u16string`` | STL dynamic UTF-16 string | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::u32string`` | STL dynamic UTF-32 string | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::wstring`` | STL dynamic wide string | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::string_view``, | STL C++17 string views | :file:`pybind11/pybind11.h` | +| ``std::u16string_view``, etc. | | | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::pair`` | Pair of two custom types | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::tuple<...>`` | Arbitrary tuple of types | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::reference_wrapper<...>`` | Reference type wrapper | :file:`pybind11/pybind11.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::complex`` | Complex numbers | :file:`pybind11/complex.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::array`` | STL static array | :file:`pybind11/stl.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::vector`` | STL dynamic array | :file:`pybind11/stl.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::deque`` | STL double-ended queue | :file:`pybind11/stl.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::valarray`` | STL value array | :file:`pybind11/stl.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::list`` | STL linked list | :file:`pybind11/stl.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::map`` | STL ordered map | :file:`pybind11/stl.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::unordered_map`` | STL unordered map | :file:`pybind11/stl.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::set`` | STL ordered set | :file:`pybind11/stl.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::unordered_set`` | STL unordered set | :file:`pybind11/stl.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::optional`` | STL optional type (C++17) | :file:`pybind11/stl.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::experimental::optional`` | STL optional type (exp.) | :file:`pybind11/stl.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::variant<...>`` | Type-safe union (C++17) | :file:`pybind11/stl.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::function<...>`` | STL polymorphic function | :file:`pybind11/functional.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::chrono::duration<...>`` | STL time duration | :file:`pybind11/chrono.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``std::chrono::time_point<...>`` | STL date/time | :file:`pybind11/chrono.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``Eigen::Matrix<...>`` | Eigen: dense matrix | :file:`pybind11/eigen.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``Eigen::Map<...>`` | Eigen: mapped memory | :file:`pybind11/eigen.h` | ++------------------------------------+---------------------------+-------------------------------+ +| ``Eigen::SparseMatrix<...>`` | Eigen: sparse matrix | :file:`pybind11/eigen.h` | ++------------------------------------+---------------------------+-------------------------------+ diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/stl.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/stl.rst new file mode 100644 index 0000000000000000000000000000000000000000..b8622ee095799b31235ba5b01f52ac3fc6be9a22 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/stl.rst @@ -0,0 +1,251 @@ +STL containers +############## + +Automatic conversion +==================== + +When including the additional header file :file:`pybind11/stl.h`, conversions +between ``std::vector<>``/``std::deque<>``/``std::list<>``/``std::array<>``/``std::valarray<>``, +``std::set<>``/``std::unordered_set<>``, and +``std::map<>``/``std::unordered_map<>`` and the Python ``list``, ``set`` and +``dict`` data structures are automatically enabled. The types ``std::pair<>`` +and ``std::tuple<>`` are already supported out of the box with just the core +:file:`pybind11/pybind11.h` header. + +The major downside of these implicit conversions is that containers must be +converted (i.e. copied) on every Python->C++ and C++->Python transition, which +can have implications on the program semantics and performance. Please read the +next sections for more details and alternative approaches that avoid this. + +.. note:: + + Arbitrary nesting of any of these types is possible. + +.. seealso:: + + The file :file:`tests/test_stl.cpp` contains a complete + example that demonstrates how to pass STL data types in more detail. + +.. _cpp17_container_casters: + +C++17 library containers +======================== + +The :file:`pybind11/stl.h` header also includes support for ``std::optional<>`` +and ``std::variant<>``. These require a C++17 compiler and standard library. +In C++14 mode, ``std::experimental::optional<>`` is supported if available. + +Various versions of these containers also exist for C++11 (e.g. in Boost). +pybind11 provides an easy way to specialize the ``type_caster`` for such +types: + +.. code-block:: cpp + + // `boost::optional` as an example -- can be any `std::optional`-like container + namespace pybind11 { namespace detail { + template + struct type_caster> : optional_caster> {}; + }} + +The above should be placed in a header file and included in all translation units +where automatic conversion is needed. Similarly, a specialization can be provided +for custom variant types: + +.. code-block:: cpp + + // `boost::variant` as an example -- can be any `std::variant`-like container + namespace pybind11 { namespace detail { + template + struct type_caster> : variant_caster> {}; + + // Specifies the function used to visit the variant -- `apply_visitor` instead of `visit` + template <> + struct visit_helper { + template + static auto call(Args &&...args) -> decltype(boost::apply_visitor(args...)) { + return boost::apply_visitor(args...); + } + }; + }} // namespace pybind11::detail + +The ``visit_helper`` specialization is not required if your ``name::variant`` provides +a ``name::visit()`` function. For any other function name, the specialization must be +included to tell pybind11 how to visit the variant. + +.. warning:: + + When converting a ``variant`` type, pybind11 follows the same rules as when + determining which function overload to call (:ref:`overload_resolution`), and + so the same caveats hold. In particular, the order in which the ``variant``'s + alternatives are listed is important, since pybind11 will try conversions in + this order. This means that, for example, when converting ``variant``, + the ``bool`` variant will never be selected, as any Python ``bool`` is already + an ``int`` and is convertible to a C++ ``int``. Changing the order of alternatives + (and using ``variant``, in this example) provides a solution. + +.. note:: + + pybind11 only supports the modern implementation of ``boost::variant`` + which makes use of variadic templates. This requires Boost 1.56 or newer. + Additionally, on Windows, MSVC 2017 is required because ``boost::variant`` + falls back to the old non-variadic implementation on MSVC 2015. + +.. _opaque: + +Making opaque types +=================== + +pybind11 heavily relies on a template matching mechanism to convert parameters +and return values that are constructed from STL data types such as vectors, +linked lists, hash tables, etc. This even works in a recursive manner, for +instance to deal with lists of hash maps of pairs of elementary and custom +types, etc. + +However, a fundamental limitation of this approach is that internal conversions +between Python and C++ types involve a copy operation that prevents +pass-by-reference semantics. What does this mean? + +Suppose we bind the following function + +.. code-block:: cpp + + void append_1(std::vector &v) { + v.push_back(1); + } + +and call it from Python, the following happens: + +.. code-block:: pycon + + >>> v = [5, 6] + >>> append_1(v) + >>> print(v) + [5, 6] + +As you can see, when passing STL data structures by reference, modifications +are not propagated back the Python side. A similar situation arises when +exposing STL data structures using the ``def_readwrite`` or ``def_readonly`` +functions: + +.. code-block:: cpp + + /* ... definition ... */ + + class MyClass { + std::vector contents; + }; + + /* ... binding code ... */ + + py::class_(m, "MyClass") + .def(py::init<>()) + .def_readwrite("contents", &MyClass::contents); + +In this case, properties can be read and written in their entirety. However, an +``append`` operation involving such a list type has no effect: + +.. code-block:: pycon + + >>> m = MyClass() + >>> m.contents = [5, 6] + >>> print(m.contents) + [5, 6] + >>> m.contents.append(7) + >>> print(m.contents) + [5, 6] + +Finally, the involved copy operations can be costly when dealing with very +large lists. To deal with all of the above situations, pybind11 provides a +macro named ``PYBIND11_MAKE_OPAQUE(T)`` that disables the template-based +conversion machinery of types, thus rendering them *opaque*. The contents of +opaque objects are never inspected or extracted, hence they *can* be passed by +reference. For instance, to turn ``std::vector`` into an opaque type, add +the declaration + +.. code-block:: cpp + + PYBIND11_MAKE_OPAQUE(std::vector); + +before any binding code (e.g. invocations to ``class_::def()``, etc.). This +macro must be specified at the top level (and outside of any namespaces), since +it adds a template instantiation of ``type_caster``. If your binding code consists of +multiple compilation units, it must be present in every file (typically via a +common header) preceding any usage of ``std::vector``. Opaque types must +also have a corresponding ``class_`` declaration to associate them with a name +in Python, and to define a set of available operations, e.g.: + +.. code-block:: cpp + + py::class_>(m, "IntVector") + .def(py::init<>()) + .def("clear", &std::vector::clear) + .def("pop_back", &std::vector::pop_back) + .def("__len__", [](const std::vector &v) { return v.size(); }) + .def("__iter__", [](std::vector &v) { + return py::make_iterator(v.begin(), v.end()); + }, py::keep_alive<0, 1>()) /* Keep vector alive while iterator is used */ + // .... + +.. seealso:: + + The file :file:`tests/test_opaque_types.cpp` contains a complete + example that demonstrates how to create and expose opaque types using + pybind11 in more detail. + +.. _stl_bind: + +Binding STL containers +====================== + +The ability to expose STL containers as native Python objects is a fairly +common request, hence pybind11 also provides an optional header file named +:file:`pybind11/stl_bind.h` that does exactly this. The mapped containers try +to match the behavior of their native Python counterparts as much as possible. + +The following example showcases usage of :file:`pybind11/stl_bind.h`: + +.. code-block:: cpp + + // Don't forget this + #include + + PYBIND11_MAKE_OPAQUE(std::vector); + PYBIND11_MAKE_OPAQUE(std::map); + + // ... + + // later in binding code: + py::bind_vector>(m, "VectorInt"); + py::bind_map>(m, "MapStringDouble"); + +When binding STL containers pybind11 considers the types of the container's +elements to decide whether the container should be confined to the local module +(via the :ref:`module_local` feature). If the container element types are +anything other than already-bound custom types bound without +``py::module_local()`` the container binding will have ``py::module_local()`` +applied. This includes converting types such as numeric types, strings, Eigen +types; and types that have not yet been bound at the time of the stl container +binding. This module-local binding is designed to avoid potential conflicts +between module bindings (for example, from two separate modules each attempting +to bind ``std::vector`` as a python type). + +It is possible to override this behavior to force a definition to be either +module-local or global. To do so, you can pass the attributes +``py::module_local()`` (to make the binding module-local) or +``py::module_local(false)`` (to make the binding global) into the +``py::bind_vector`` or ``py::bind_map`` arguments: + +.. code-block:: cpp + + py::bind_vector>(m, "VectorInt", py::module_local(false)); + +Note, however, that such a global binding would make it impossible to load this +module at the same time as any other pybind module that also attempts to bind +the same container type (``std::vector`` in the above example). + +See :ref:`module_local` for more details on module-local bindings. + +.. seealso:: + + The file :file:`tests/test_stl_binders.cpp` shows how to use the + convenience STL container wrappers. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/strings.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/strings.rst new file mode 100644 index 0000000000000000000000000000000000000000..e25701ecabd80142f4fd705f5419ef7c10cc6c56 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/cast/strings.rst @@ -0,0 +1,305 @@ +Strings, bytes and Unicode conversions +###################################### + +.. note:: + + This section discusses string handling in terms of Python 3 strings. For + Python 2.7, replace all occurrences of ``str`` with ``unicode`` and + ``bytes`` with ``str``. Python 2.7 users may find it best to use ``from + __future__ import unicode_literals`` to avoid unintentionally using ``str`` + instead of ``unicode``. + +Passing Python strings to C++ +============================= + +When a Python ``str`` is passed from Python to a C++ function that accepts +``std::string`` or ``char *`` as arguments, pybind11 will encode the Python +string to UTF-8. All Python ``str`` can be encoded in UTF-8, so this operation +does not fail. + +The C++ language is encoding agnostic. It is the responsibility of the +programmer to track encodings. It's often easiest to simply `use UTF-8 +everywhere `_. + +.. code-block:: c++ + + m.def("utf8_test", + [](const std::string &s) { + cout << "utf-8 is icing on the cake.\n"; + cout << s; + } + ); + m.def("utf8_charptr", + [](const char *s) { + cout << "My favorite food is\n"; + cout << s; + } + ); + +.. code-block:: python + + >>> utf8_test('🎂') + utf-8 is icing on the cake. + 🎂 + + >>> utf8_charptr('🍕') + My favorite food is + 🍕 + +.. note:: + + Some terminal emulators do not support UTF-8 or emoji fonts and may not + display the example above correctly. + +The results are the same whether the C++ function accepts arguments by value or +reference, and whether or not ``const`` is used. + +Passing bytes to C++ +-------------------- + +A Python ``bytes`` object will be passed to C++ functions that accept +``std::string`` or ``char*`` *without* conversion. On Python 3, in order to +make a function *only* accept ``bytes`` (and not ``str``), declare it as taking +a ``py::bytes`` argument. + + +Returning C++ strings to Python +=============================== + +When a C++ function returns a ``std::string`` or ``char*`` to a Python caller, +**pybind11 will assume that the string is valid UTF-8** and will decode it to a +native Python ``str``, using the same API as Python uses to perform +``bytes.decode('utf-8')``. If this implicit conversion fails, pybind11 will +raise a ``UnicodeDecodeError``. + +.. code-block:: c++ + + m.def("std_string_return", + []() { + return std::string("This string needs to be UTF-8 encoded"); + } + ); + +.. code-block:: python + + >>> isinstance(example.std_string_return(), str) + True + + +Because UTF-8 is inclusive of pure ASCII, there is never any issue with +returning a pure ASCII string to Python. If there is any possibility that the +string is not pure ASCII, it is necessary to ensure the encoding is valid +UTF-8. + +.. warning:: + + Implicit conversion assumes that a returned ``char *`` is null-terminated. + If there is no null terminator a buffer overrun will occur. + +Explicit conversions +-------------------- + +If some C++ code constructs a ``std::string`` that is not a UTF-8 string, one +can perform a explicit conversion and return a ``py::str`` object. Explicit +conversion has the same overhead as implicit conversion. + +.. code-block:: c++ + + // This uses the Python C API to convert Latin-1 to Unicode + m.def("str_output", + []() { + std::string s = "Send your r\xe9sum\xe9 to Alice in HR"; // Latin-1 + py::str py_s = PyUnicode_DecodeLatin1(s.data(), s.length()); + return py_s; + } + ); + +.. code-block:: python + + >>> str_output() + 'Send your résumé to Alice in HR' + +The `Python C API +`_ provides +several built-in codecs. + + +One could also use a third party encoding library such as libiconv to transcode +to UTF-8. + +Return C++ strings without conversion +------------------------------------- + +If the data in a C++ ``std::string`` does not represent text and should be +returned to Python as ``bytes``, then one can return the data as a +``py::bytes`` object. + +.. code-block:: c++ + + m.def("return_bytes", + []() { + std::string s("\xba\xd0\xba\xd0"); // Not valid UTF-8 + return py::bytes(s); // Return the data without transcoding + } + ); + +.. code-block:: python + + >>> example.return_bytes() + b'\xba\xd0\xba\xd0' + + +Note the asymmetry: pybind11 will convert ``bytes`` to ``std::string`` without +encoding, but cannot convert ``std::string`` back to ``bytes`` implicitly. + +.. code-block:: c++ + + m.def("asymmetry", + [](std::string s) { // Accepts str or bytes from Python + return s; // Looks harmless, but implicitly converts to str + } + ); + +.. code-block:: python + + >>> isinstance(example.asymmetry(b"have some bytes"), str) + True + + >>> example.asymmetry(b"\xba\xd0\xba\xd0") # invalid utf-8 as bytes + UnicodeDecodeError: 'utf-8' codec can't decode byte 0xba in position 0: invalid start byte + + +Wide character strings +====================== + +When a Python ``str`` is passed to a C++ function expecting ``std::wstring``, +``wchar_t*``, ``std::u16string`` or ``std::u32string``, the ``str`` will be +encoded to UTF-16 or UTF-32 depending on how the C++ compiler implements each +type, in the platform's native endianness. When strings of these types are +returned, they are assumed to contain valid UTF-16 or UTF-32, and will be +decoded to Python ``str``. + +.. code-block:: c++ + + #define UNICODE + #include + + m.def("set_window_text", + [](HWND hwnd, std::wstring s) { + // Call SetWindowText with null-terminated UTF-16 string + ::SetWindowText(hwnd, s.c_str()); + } + ); + m.def("get_window_text", + [](HWND hwnd) { + const int buffer_size = ::GetWindowTextLength(hwnd) + 1; + auto buffer = std::make_unique< wchar_t[] >(buffer_size); + + ::GetWindowText(hwnd, buffer.data(), buffer_size); + + std::wstring text(buffer.get()); + + // wstring will be converted to Python str + return text; + } + ); + +.. warning:: + + Wide character strings may not work as described on Python 2.7 or Python + 3.3 compiled with ``--enable-unicode=ucs2``. + +Strings in multibyte encodings such as Shift-JIS must transcoded to a +UTF-8/16/32 before being returned to Python. + + +Character literals +================== + +C++ functions that accept character literals as input will receive the first +character of a Python ``str`` as their input. If the string is longer than one +Unicode character, trailing characters will be ignored. + +When a character literal is returned from C++ (such as a ``char`` or a +``wchar_t``), it will be converted to a ``str`` that represents the single +character. + +.. code-block:: c++ + + m.def("pass_char", [](char c) { return c; }); + m.def("pass_wchar", [](wchar_t w) { return w; }); + +.. code-block:: python + + >>> example.pass_char('A') + 'A' + +While C++ will cast integers to character types (``char c = 0x65;``), pybind11 +does not convert Python integers to characters implicitly. The Python function +``chr()`` can be used to convert integers to characters. + +.. code-block:: python + + >>> example.pass_char(0x65) + TypeError + + >>> example.pass_char(chr(0x65)) + 'A' + +If the desire is to work with an 8-bit integer, use ``int8_t`` or ``uint8_t`` +as the argument type. + +Grapheme clusters +----------------- + +A single grapheme may be represented by two or more Unicode characters. For +example 'é' is usually represented as U+00E9 but can also be expressed as the +combining character sequence U+0065 U+0301 (that is, the letter 'e' followed by +a combining acute accent). The combining character will be lost if the +two-character sequence is passed as an argument, even though it renders as a +single grapheme. + +.. code-block:: python + + >>> example.pass_wchar('é') + 'é' + + >>> combining_e_acute = 'e' + '\u0301' + + >>> combining_e_acute + 'é' + + >>> combining_e_acute == 'é' + False + + >>> example.pass_wchar(combining_e_acute) + 'e' + +Normalizing combining characters before passing the character literal to C++ +may resolve *some* of these issues: + +.. code-block:: python + + >>> example.pass_wchar(unicodedata.normalize('NFC', combining_e_acute)) + 'é' + +In some languages (Thai for example), there are `graphemes that cannot be +expressed as a single Unicode code point +`_, so there is +no way to capture them in a C++ character type. + + +C++17 string views +================== + +C++17 string views are automatically supported when compiling in C++17 mode. +They follow the same rules for encoding and decoding as the corresponding STL +string type (for example, a ``std::u16string_view`` argument will be passed +UTF-16-encoded data, and a returned ``std::string_view`` will be decoded as +UTF-8). + +References +========== + +* `The Absolute Minimum Every Software Developer Absolutely, Positively Must Know About Unicode and Character Sets (No Excuses!) `_ +* `C++ - Using STL Strings at Win32 API Boundaries `_ diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/classes.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/classes.rst new file mode 100644 index 0000000000000000000000000000000000000000..49279020694704249a718d5acf3827fb806ef05a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/classes.rst @@ -0,0 +1,1261 @@ +Classes +####### + +This section presents advanced binding code for classes and it is assumed +that you are already familiar with the basics from :doc:`/classes`. + +.. _overriding_virtuals: + +Overriding virtual functions in Python +====================================== + +Suppose that a C++ class or interface has a virtual function that we'd like to +to override from within Python (we'll focus on the class ``Animal``; ``Dog`` is +given as a specific example of how one would do this with traditional C++ +code). + +.. code-block:: cpp + + class Animal { + public: + virtual ~Animal() { } + virtual std::string go(int n_times) = 0; + }; + + class Dog : public Animal { + public: + std::string go(int n_times) override { + std::string result; + for (int i=0; igo(3); + } + +Normally, the binding code for these classes would look as follows: + +.. code-block:: cpp + + PYBIND11_MODULE(example, m) { + py::class_(m, "Animal") + .def("go", &Animal::go); + + py::class_(m, "Dog") + .def(py::init<>()); + + m.def("call_go", &call_go); + } + +However, these bindings are impossible to extend: ``Animal`` is not +constructible, and we clearly require some kind of "trampoline" that +redirects virtual calls back to Python. + +Defining a new type of ``Animal`` from within Python is possible but requires a +helper class that is defined as follows: + +.. code-block:: cpp + + class PyAnimal : public Animal { + public: + /* Inherit the constructors */ + using Animal::Animal; + + /* Trampoline (need one for each virtual function) */ + std::string go(int n_times) override { + PYBIND11_OVERRIDE_PURE( + std::string, /* Return type */ + Animal, /* Parent class */ + go, /* Name of function in C++ (must match Python name) */ + n_times /* Argument(s) */ + ); + } + }; + +The macro :c:macro:`PYBIND11_OVERRIDE_PURE` should be used for pure virtual +functions, and :c:macro:`PYBIND11_OVERRIDE` should be used for functions which have +a default implementation. There are also two alternate macros +:c:macro:`PYBIND11_OVERRIDE_PURE_NAME` and :c:macro:`PYBIND11_OVERRIDE_NAME` which +take a string-valued name argument between the *Parent class* and *Name of the +function* slots, which defines the name of function in Python. This is required +when the C++ and Python versions of the +function have different names, e.g. ``operator()`` vs ``__call__``. + +The binding code also needs a few minor adaptations (highlighted): + +.. code-block:: cpp + :emphasize-lines: 2,3 + + PYBIND11_MODULE(example, m) { + py::class_(m, "Animal") + .def(py::init<>()) + .def("go", &Animal::go); + + py::class_(m, "Dog") + .def(py::init<>()); + + m.def("call_go", &call_go); + } + +Importantly, pybind11 is made aware of the trampoline helper class by +specifying it as an extra template argument to :class:`class_`. (This can also +be combined with other template arguments such as a custom holder type; the +order of template types does not matter). Following this, we are able to +define a constructor as usual. + +Bindings should be made against the actual class, not the trampoline helper class. + +.. code-block:: cpp + :emphasize-lines: 3 + + py::class_(m, "Animal"); + .def(py::init<>()) + .def("go", &PyAnimal::go); /* <--- THIS IS WRONG, use &Animal::go */ + +Note, however, that the above is sufficient for allowing python classes to +extend ``Animal``, but not ``Dog``: see :ref:`virtual_and_inheritance` for the +necessary steps required to providing proper overriding support for inherited +classes. + +The Python session below shows how to override ``Animal::go`` and invoke it via +a virtual method call. + +.. code-block:: pycon + + >>> from example import * + >>> d = Dog() + >>> call_go(d) + u'woof! woof! woof! ' + >>> class Cat(Animal): + ... def go(self, n_times): + ... return "meow! " * n_times + ... + >>> c = Cat() + >>> call_go(c) + u'meow! meow! meow! ' + +If you are defining a custom constructor in a derived Python class, you *must* +ensure that you explicitly call the bound C++ constructor using ``__init__``, +*regardless* of whether it is a default constructor or not. Otherwise, the +memory for the C++ portion of the instance will be left uninitialized, which +will generally leave the C++ instance in an invalid state and cause undefined +behavior if the C++ instance is subsequently used. + +.. versionchanged:: 2.6 + The default pybind11 metaclass will throw a ``TypeError`` when it detects + that ``__init__`` was not called by a derived class. + +Here is an example: + +.. code-block:: python + + class Dachshund(Dog): + def __init__(self, name): + Dog.__init__(self) # Without this, a TypeError is raised. + self.name = name + def bark(self): + return "yap!" + +Note that a direct ``__init__`` constructor *should be called*, and ``super()`` +should not be used. For simple cases of linear inheritance, ``super()`` +may work, but once you begin mixing Python and C++ multiple inheritance, +things will fall apart due to differences between Python's MRO and C++'s +mechanisms. + +Please take a look at the :ref:`macro_notes` before using this feature. + +.. note:: + + When the overridden type returns a reference or pointer to a type that + pybind11 converts from Python (for example, numeric values, std::string, + and other built-in value-converting types), there are some limitations to + be aware of: + + - because in these cases there is no C++ variable to reference (the value + is stored in the referenced Python variable), pybind11 provides one in + the PYBIND11_OVERRIDE macros (when needed) with static storage duration. + Note that this means that invoking the overridden method on *any* + instance will change the referenced value stored in *all* instances of + that type. + + - Attempts to modify a non-const reference will not have the desired + effect: it will change only the static cache variable, but this change + will not propagate to underlying Python instance, and the change will be + replaced the next time the override is invoked. + +.. warning:: + + The :c:macro:`PYBIND11_OVERRIDE` and accompanying macros used to be called + ``PYBIND11_OVERLOAD`` up until pybind11 v2.5.0, and :func:`get_override` + used to be called ``get_overload``. This naming was corrected and the older + macro and function names may soon be deprecated, in order to reduce + confusion with overloaded functions and methods and ``py::overload_cast`` + (see :ref:`classes`). + +.. seealso:: + + The file :file:`tests/test_virtual_functions.cpp` contains a complete + example that demonstrates how to override virtual functions using pybind11 + in more detail. + +.. _virtual_and_inheritance: + +Combining virtual functions and inheritance +=========================================== + +When combining virtual methods with inheritance, you need to be sure to provide +an override for each method for which you want to allow overrides from derived +python classes. For example, suppose we extend the above ``Animal``/``Dog`` +example as follows: + +.. code-block:: cpp + + class Animal { + public: + virtual std::string go(int n_times) = 0; + virtual std::string name() { return "unknown"; } + }; + class Dog : public Animal { + public: + std::string go(int n_times) override { + std::string result; + for (int i=0; i class PyAnimal : public AnimalBase { + public: + using AnimalBase::AnimalBase; // Inherit constructors + std::string go(int n_times) override { PYBIND11_OVERRIDE_PURE(std::string, AnimalBase, go, n_times); } + std::string name() override { PYBIND11_OVERRIDE(std::string, AnimalBase, name, ); } + }; + template class PyDog : public PyAnimal { + public: + using PyAnimal::PyAnimal; // Inherit constructors + // Override PyAnimal's pure virtual go() with a non-pure one: + std::string go(int n_times) override { PYBIND11_OVERRIDE(std::string, DogBase, go, n_times); } + std::string bark() override { PYBIND11_OVERRIDE(std::string, DogBase, bark, ); } + }; + +This technique has the advantage of requiring just one trampoline method to be +declared per virtual method and pure virtual method override. It does, +however, require the compiler to generate at least as many methods (and +possibly more, if both pure virtual and overridden pure virtual methods are +exposed, as above). + +The classes are then registered with pybind11 using: + +.. code-block:: cpp + + py::class_> animal(m, "Animal"); + py::class_> dog(m, "Dog"); + py::class_> husky(m, "Husky"); + // ... add animal, dog, husky definitions + +Note that ``Husky`` did not require a dedicated trampoline template class at +all, since it neither declares any new virtual methods nor provides any pure +virtual method implementations. + +With either the repeated-virtuals or templated trampoline methods in place, you +can now create a python class that inherits from ``Dog``: + +.. code-block:: python + + class ShihTzu(Dog): + def bark(self): + return "yip!" + +.. seealso:: + + See the file :file:`tests/test_virtual_functions.cpp` for complete examples + using both the duplication and templated trampoline approaches. + +.. _extended_aliases: + +Extended trampoline class functionality +======================================= + +.. _extended_class_functionality_forced_trampoline: + +Forced trampoline class initialisation +-------------------------------------- +The trampoline classes described in the previous sections are, by default, only +initialized when needed. More specifically, they are initialized when a python +class actually inherits from a registered type (instead of merely creating an +instance of the registered type), or when a registered constructor is only +valid for the trampoline class but not the registered class. This is primarily +for performance reasons: when the trampoline class is not needed for anything +except virtual method dispatching, not initializing the trampoline class +improves performance by avoiding needing to do a run-time check to see if the +inheriting python instance has an overridden method. + +Sometimes, however, it is useful to always initialize a trampoline class as an +intermediate class that does more than just handle virtual method dispatching. +For example, such a class might perform extra class initialization, extra +destruction operations, and might define new members and methods to enable a +more python-like interface to a class. + +In order to tell pybind11 that it should *always* initialize the trampoline +class when creating new instances of a type, the class constructors should be +declared using ``py::init_alias()`` instead of the usual +``py::init()``. This forces construction via the trampoline class, +ensuring member initialization and (eventual) destruction. + +.. seealso:: + + See the file :file:`tests/test_virtual_functions.cpp` for complete examples + showing both normal and forced trampoline instantiation. + +Different method signatures +--------------------------- +The macro's introduced in :ref:`overriding_virtuals` cover most of the standard +use cases when exposing C++ classes to Python. Sometimes it is hard or unwieldy +to create a direct one-on-one mapping between the arguments and method return +type. + +An example would be when the C++ signature contains output arguments using +references (See also :ref:`faq_reference_arguments`). Another way of solving +this is to use the method body of the trampoline class to do conversions to the +input and return of the Python method. + +The main building block to do so is the :func:`get_override`, this function +allows retrieving a method implemented in Python from within the trampoline's +methods. Consider for example a C++ method which has the signature +``bool myMethod(int32_t& value)``, where the return indicates whether +something should be done with the ``value``. This can be made convenient on the +Python side by allowing the Python function to return ``None`` or an ``int``: + +.. code-block:: cpp + + bool MyClass::myMethod(int32_t& value) + { + pybind11::gil_scoped_acquire gil; // Acquire the GIL while in this scope. + // Try to look up the overridden method on the Python side. + pybind11::function override = pybind11::get_override(this, "myMethod"); + if (override) { // method is found + auto obj = override(value); // Call the Python function. + if (py::isinstance(obj)) { // check if it returned a Python integer type + value = obj.cast(); // Cast it and assign it to the value. + return true; // Return true; value should be used. + } else { + return false; // Python returned none, return false. + } + } + return false; // Alternatively return MyClass::myMethod(value); + } + + +.. _custom_constructors: + +Custom constructors +=================== + +The syntax for binding constructors was previously introduced, but it only +works when a constructor of the appropriate arguments actually exists on the +C++ side. To extend this to more general cases, pybind11 makes it possible +to bind factory functions as constructors. For example, suppose you have a +class like this: + +.. code-block:: cpp + + class Example { + private: + Example(int); // private constructor + public: + // Factory function: + static Example create(int a) { return Example(a); } + }; + + py::class_(m, "Example") + .def(py::init(&Example::create)); + +While it is possible to create a straightforward binding of the static +``create`` method, it may sometimes be preferable to expose it as a constructor +on the Python side. This can be accomplished by calling ``.def(py::init(...))`` +with the function reference returning the new instance passed as an argument. +It is also possible to use this approach to bind a function returning a new +instance by raw pointer or by the holder (e.g. ``std::unique_ptr``). + +The following example shows the different approaches: + +.. code-block:: cpp + + class Example { + private: + Example(int); // private constructor + public: + // Factory function - returned by value: + static Example create(int a) { return Example(a); } + + // These constructors are publicly callable: + Example(double); + Example(int, int); + Example(std::string); + }; + + py::class_(m, "Example") + // Bind the factory function as a constructor: + .def(py::init(&Example::create)) + // Bind a lambda function returning a pointer wrapped in a holder: + .def(py::init([](std::string arg) { + return std::unique_ptr(new Example(arg)); + })) + // Return a raw pointer: + .def(py::init([](int a, int b) { return new Example(a, b); })) + // You can mix the above with regular C++ constructor bindings as well: + .def(py::init()) + ; + +When the constructor is invoked from Python, pybind11 will call the factory +function and store the resulting C++ instance in the Python instance. + +When combining factory functions constructors with :ref:`virtual function +trampolines ` there are two approaches. The first is to +add a constructor to the alias class that takes a base value by +rvalue-reference. If such a constructor is available, it will be used to +construct an alias instance from the value returned by the factory function. +The second option is to provide two factory functions to ``py::init()``: the +first will be invoked when no alias class is required (i.e. when the class is +being used but not inherited from in Python), and the second will be invoked +when an alias is required. + +You can also specify a single factory function that always returns an alias +instance: this will result in behaviour similar to ``py::init_alias<...>()``, +as described in the :ref:`extended trampoline class documentation +`. + +The following example shows the different factory approaches for a class with +an alias: + +.. code-block:: cpp + + #include + class Example { + public: + // ... + virtual ~Example() = default; + }; + class PyExample : public Example { + public: + using Example::Example; + PyExample(Example &&base) : Example(std::move(base)) {} + }; + py::class_(m, "Example") + // Returns an Example pointer. If a PyExample is needed, the Example + // instance will be moved via the extra constructor in PyExample, above. + .def(py::init([]() { return new Example(); })) + // Two callbacks: + .def(py::init([]() { return new Example(); } /* no alias needed */, + []() { return new PyExample(); } /* alias needed */)) + // *Always* returns an alias instance (like py::init_alias<>()) + .def(py::init([]() { return new PyExample(); })) + ; + +Brace initialization +-------------------- + +``pybind11::init<>`` internally uses C++11 brace initialization to call the +constructor of the target class. This means that it can be used to bind +*implicit* constructors as well: + +.. code-block:: cpp + + struct Aggregate { + int a; + std::string b; + }; + + py::class_(m, "Aggregate") + .def(py::init()); + +.. note:: + + Note that brace initialization preferentially invokes constructor overloads + taking a ``std::initializer_list``. In the rare event that this causes an + issue, you can work around it by using ``py::init(...)`` with a lambda + function that constructs the new object as desired. + +.. _classes_with_non_public_destructors: + +Non-public destructors +====================== + +If a class has a private or protected destructor (as might e.g. be the case in +a singleton pattern), a compile error will occur when creating bindings via +pybind11. The underlying issue is that the ``std::unique_ptr`` holder type that +is responsible for managing the lifetime of instances will reference the +destructor even if no deallocations ever take place. In order to expose classes +with private or protected destructors, it is possible to override the holder +type via a holder type argument to ``class_``. Pybind11 provides a helper class +``py::nodelete`` that disables any destructor invocations. In this case, it is +crucial that instances are deallocated on the C++ side to avoid memory leaks. + +.. code-block:: cpp + + /* ... definition ... */ + + class MyClass { + private: + ~MyClass() { } + }; + + /* ... binding code ... */ + + py::class_>(m, "MyClass") + .def(py::init<>()) + +.. _destructors_that_call_python: + +Destructors that call Python +============================ + +If a Python function is invoked from a C++ destructor, an exception may be thrown +of type :class:`error_already_set`. If this error is thrown out of a class destructor, +``std::terminate()`` will be called, terminating the process. Class destructors +must catch all exceptions of type :class:`error_already_set` to discard the Python +exception using :func:`error_already_set::discard_as_unraisable`. + +Every Python function should be treated as *possibly throwing*. When a Python generator +stops yielding items, Python will throw a ``StopIteration`` exception, which can pass +though C++ destructors if the generator's stack frame holds the last reference to C++ +objects. + +For more information, see :ref:`the documentation on exceptions `. + +.. code-block:: cpp + + class MyClass { + public: + ~MyClass() { + try { + py::print("Even printing is dangerous in a destructor"); + py::exec("raise ValueError('This is an unraisable exception')"); + } catch (py::error_already_set &e) { + // error_context should be information about where/why the occurred, + // e.g. use __func__ to get the name of the current function + e.discard_as_unraisable(__func__); + } + } + }; + +.. note:: + + pybind11 does not support C++ destructors marked ``noexcept(false)``. + +.. versionadded:: 2.6 + +.. _implicit_conversions: + +Implicit conversions +==================== + +Suppose that instances of two types ``A`` and ``B`` are used in a project, and +that an ``A`` can easily be converted into an instance of type ``B`` (examples of this +could be a fixed and an arbitrary precision number type). + +.. code-block:: cpp + + py::class_(m, "A") + /// ... members ... + + py::class_(m, "B") + .def(py::init()) + /// ... members ... + + m.def("func", + [](const B &) { /* .... */ } + ); + +To invoke the function ``func`` using a variable ``a`` containing an ``A`` +instance, we'd have to write ``func(B(a))`` in Python. On the other hand, C++ +will automatically apply an implicit type conversion, which makes it possible +to directly write ``func(a)``. + +In this situation (i.e. where ``B`` has a constructor that converts from +``A``), the following statement enables similar implicit conversions on the +Python side: + +.. code-block:: cpp + + py::implicitly_convertible(); + +.. note:: + + Implicit conversions from ``A`` to ``B`` only work when ``B`` is a custom + data type that is exposed to Python via pybind11. + + To prevent runaway recursion, implicit conversions are non-reentrant: an + implicit conversion invoked as part of another implicit conversion of the + same type (i.e. from ``A`` to ``B``) will fail. + +.. _static_properties: + +Static properties +================= + +The section on :ref:`properties` discussed the creation of instance properties +that are implemented in terms of C++ getters and setters. + +Static properties can also be created in a similar way to expose getters and +setters of static class attributes. Note that the implicit ``self`` argument +also exists in this case and is used to pass the Python ``type`` subclass +instance. This parameter will often not be needed by the C++ side, and the +following example illustrates how to instantiate a lambda getter function +that ignores it: + +.. code-block:: cpp + + py::class_(m, "Foo") + .def_property_readonly_static("foo", [](py::object /* self */) { return Foo(); }); + +Operator overloading +==================== + +Suppose that we're given the following ``Vector2`` class with a vector addition +and scalar multiplication operation, all implemented using overloaded operators +in C++. + +.. code-block:: cpp + + class Vector2 { + public: + Vector2(float x, float y) : x(x), y(y) { } + + Vector2 operator+(const Vector2 &v) const { return Vector2(x + v.x, y + v.y); } + Vector2 operator*(float value) const { return Vector2(x * value, y * value); } + Vector2& operator+=(const Vector2 &v) { x += v.x; y += v.y; return *this; } + Vector2& operator*=(float v) { x *= v; y *= v; return *this; } + + friend Vector2 operator*(float f, const Vector2 &v) { + return Vector2(f * v.x, f * v.y); + } + + std::string toString() const { + return "[" + std::to_string(x) + ", " + std::to_string(y) + "]"; + } + private: + float x, y; + }; + +The following snippet shows how the above operators can be conveniently exposed +to Python. + +.. code-block:: cpp + + #include + + PYBIND11_MODULE(example, m) { + py::class_(m, "Vector2") + .def(py::init()) + .def(py::self + py::self) + .def(py::self += py::self) + .def(py::self *= float()) + .def(float() * py::self) + .def(py::self * float()) + .def(-py::self) + .def("__repr__", &Vector2::toString); + } + +Note that a line like + +.. code-block:: cpp + + .def(py::self * float()) + +is really just short hand notation for + +.. code-block:: cpp + + .def("__mul__", [](const Vector2 &a, float b) { + return a * b; + }, py::is_operator()) + +This can be useful for exposing additional operators that don't exist on the +C++ side, or to perform other types of customization. The ``py::is_operator`` +flag marker is needed to inform pybind11 that this is an operator, which +returns ``NotImplemented`` when invoked with incompatible arguments rather than +throwing a type error. + +.. note:: + + To use the more convenient ``py::self`` notation, the additional + header file :file:`pybind11/operators.h` must be included. + +.. seealso:: + + The file :file:`tests/test_operator_overloading.cpp` contains a + complete example that demonstrates how to work with overloaded operators in + more detail. + +.. _pickling: + +Pickling support +================ + +Python's ``pickle`` module provides a powerful facility to serialize and +de-serialize a Python object graph into a binary data stream. To pickle and +unpickle C++ classes using pybind11, a ``py::pickle()`` definition must be +provided. Suppose the class in question has the following signature: + +.. code-block:: cpp + + class Pickleable { + public: + Pickleable(const std::string &value) : m_value(value) { } + const std::string &value() const { return m_value; } + + void setExtra(int extra) { m_extra = extra; } + int extra() const { return m_extra; } + private: + std::string m_value; + int m_extra = 0; + }; + +Pickling support in Python is enabled by defining the ``__setstate__`` and +``__getstate__`` methods [#f3]_. For pybind11 classes, use ``py::pickle()`` +to bind these two functions: + +.. code-block:: cpp + + py::class_(m, "Pickleable") + .def(py::init()) + .def("value", &Pickleable::value) + .def("extra", &Pickleable::extra) + .def("setExtra", &Pickleable::setExtra) + .def(py::pickle( + [](const Pickleable &p) { // __getstate__ + /* Return a tuple that fully encodes the state of the object */ + return py::make_tuple(p.value(), p.extra()); + }, + [](py::tuple t) { // __setstate__ + if (t.size() != 2) + throw std::runtime_error("Invalid state!"); + + /* Create a new C++ instance */ + Pickleable p(t[0].cast()); + + /* Assign any additional state */ + p.setExtra(t[1].cast()); + + return p; + } + )); + +The ``__setstate__`` part of the ``py::picke()`` definition follows the same +rules as the single-argument version of ``py::init()``. The return type can be +a value, pointer or holder type. See :ref:`custom_constructors` for details. + +An instance can now be pickled as follows: + +.. code-block:: python + + try: + import cPickle as pickle # Use cPickle on Python 2.7 + except ImportError: + import pickle + + p = Pickleable("test_value") + p.setExtra(15) + data = pickle.dumps(p, 2) + + +.. note:: + Note that only the cPickle module is supported on Python 2.7. + + The second argument to ``dumps`` is also crucial: it selects the pickle + protocol version 2, since the older version 1 is not supported. Newer + versions are also fine—for instance, specify ``-1`` to always use the + latest available version. Beware: failure to follow these instructions + will cause important pybind11 memory allocation routines to be skipped + during unpickling, which will likely lead to memory corruption and/or + segmentation faults. + +.. seealso:: + + The file :file:`tests/test_pickling.cpp` contains a complete example + that demonstrates how to pickle and unpickle types using pybind11 in more + detail. + +.. [#f3] http://docs.python.org/3/library/pickle.html#pickling-class-instances + +Deepcopy support +================ + +Python normally uses references in assignments. Sometimes a real copy is needed +to prevent changing all copies. The ``copy`` module [#f5]_ provides these +capabilities. + +On Python 3, a class with pickle support is automatically also (deep)copy +compatible. However, performance can be improved by adding custom +``__copy__`` and ``__deepcopy__`` methods. With Python 2.7, these custom methods +are mandatory for (deep)copy compatibility, because pybind11 only supports +cPickle. + +For simple classes (deep)copy can be enabled by using the copy constructor, +which should look as follows: + +.. code-block:: cpp + + py::class_(m, "Copyable") + .def("__copy__", [](const Copyable &self) { + return Copyable(self); + }) + .def("__deepcopy__", [](const Copyable &self, py::dict) { + return Copyable(self); + }, "memo"_a); + +.. note:: + + Dynamic attributes will not be copied in this example. + +.. [#f5] https://docs.python.org/3/library/copy.html + +Multiple Inheritance +==================== + +pybind11 can create bindings for types that derive from multiple base types +(aka. *multiple inheritance*). To do so, specify all bases in the template +arguments of the ``class_`` declaration: + +.. code-block:: cpp + + py::class_(m, "MyType") + ... + +The base types can be specified in arbitrary order, and they can even be +interspersed with alias types and holder types (discussed earlier in this +document)---pybind11 will automatically find out which is which. The only +requirement is that the first template argument is the type to be declared. + +It is also permitted to inherit multiply from exported C++ classes in Python, +as well as inheriting from multiple Python and/or pybind11-exported classes. + +There is one caveat regarding the implementation of this feature: + +When only one base type is specified for a C++ type that actually has multiple +bases, pybind11 will assume that it does not participate in multiple +inheritance, which can lead to undefined behavior. In such cases, add the tag +``multiple_inheritance`` to the class constructor: + +.. code-block:: cpp + + py::class_(m, "MyType", py::multiple_inheritance()); + +The tag is redundant and does not need to be specified when multiple base types +are listed. + +.. _module_local: + +Module-local class bindings +=========================== + +When creating a binding for a class, pybind11 by default makes that binding +"global" across modules. What this means is that a type defined in one module +can be returned from any module resulting in the same Python type. For +example, this allows the following: + +.. code-block:: cpp + + // In the module1.cpp binding code for module1: + py::class_(m, "Pet") + .def(py::init()) + .def_readonly("name", &Pet::name); + +.. code-block:: cpp + + // In the module2.cpp binding code for module2: + m.def("create_pet", [](std::string name) { return new Pet(name); }); + +.. code-block:: pycon + + >>> from module1 import Pet + >>> from module2 import create_pet + >>> pet1 = Pet("Kitty") + >>> pet2 = create_pet("Doggy") + >>> pet2.name() + 'Doggy' + +When writing binding code for a library, this is usually desirable: this +allows, for example, splitting up a complex library into multiple Python +modules. + +In some cases, however, this can cause conflicts. For example, suppose two +unrelated modules make use of an external C++ library and each provide custom +bindings for one of that library's classes. This will result in an error when +a Python program attempts to import both modules (directly or indirectly) +because of conflicting definitions on the external type: + +.. code-block:: cpp + + // dogs.cpp + + // Binding for external library class: + py::class(m, "Pet") + .def("name", &pets::Pet::name); + + // Binding for local extension class: + py::class(m, "Dog") + .def(py::init()); + +.. code-block:: cpp + + // cats.cpp, in a completely separate project from the above dogs.cpp. + + // Binding for external library class: + py::class(m, "Pet") + .def("get_name", &pets::Pet::name); + + // Binding for local extending class: + py::class(m, "Cat") + .def(py::init()); + +.. code-block:: pycon + + >>> import cats + >>> import dogs + Traceback (most recent call last): + File "", line 1, in + ImportError: generic_type: type "Pet" is already registered! + +To get around this, you can tell pybind11 to keep the external class binding +localized to the module by passing the ``py::module_local()`` attribute into +the ``py::class_`` constructor: + +.. code-block:: cpp + + // Pet binding in dogs.cpp: + py::class(m, "Pet", py::module_local()) + .def("name", &pets::Pet::name); + +.. code-block:: cpp + + // Pet binding in cats.cpp: + py::class(m, "Pet", py::module_local()) + .def("get_name", &pets::Pet::name); + +This makes the Python-side ``dogs.Pet`` and ``cats.Pet`` into distinct classes, +avoiding the conflict and allowing both modules to be loaded. C++ code in the +``dogs`` module that casts or returns a ``Pet`` instance will result in a +``dogs.Pet`` Python instance, while C++ code in the ``cats`` module will result +in a ``cats.Pet`` Python instance. + +This does come with two caveats, however: First, external modules cannot return +or cast a ``Pet`` instance to Python (unless they also provide their own local +bindings). Second, from the Python point of view they are two distinct classes. + +Note that the locality only applies in the C++ -> Python direction. When +passing such a ``py::module_local`` type into a C++ function, the module-local +classes are still considered. This means that if the following function is +added to any module (including but not limited to the ``cats`` and ``dogs`` +modules above) it will be callable with either a ``dogs.Pet`` or ``cats.Pet`` +argument: + +.. code-block:: cpp + + m.def("pet_name", [](const pets::Pet &pet) { return pet.name(); }); + +For example, suppose the above function is added to each of ``cats.cpp``, +``dogs.cpp`` and ``frogs.cpp`` (where ``frogs.cpp`` is some other module that +does *not* bind ``Pets`` at all). + +.. code-block:: pycon + + >>> import cats, dogs, frogs # No error because of the added py::module_local() + >>> mycat, mydog = cats.Cat("Fluffy"), dogs.Dog("Rover") + >>> (cats.pet_name(mycat), dogs.pet_name(mydog)) + ('Fluffy', 'Rover') + >>> (cats.pet_name(mydog), dogs.pet_name(mycat), frogs.pet_name(mycat)) + ('Rover', 'Fluffy', 'Fluffy') + +It is possible to use ``py::module_local()`` registrations in one module even +if another module registers the same type globally: within the module with the +module-local definition, all C++ instances will be cast to the associated bound +Python type. In other modules any such values are converted to the global +Python type created elsewhere. + +.. note:: + + STL bindings (as provided via the optional :file:`pybind11/stl_bind.h` + header) apply ``py::module_local`` by default when the bound type might + conflict with other modules; see :ref:`stl_bind` for details. + +.. note:: + + The localization of the bound types is actually tied to the shared object + or binary generated by the compiler/linker. For typical modules created + with ``PYBIND11_MODULE()``, this distinction is not significant. It is + possible, however, when :ref:`embedding` to embed multiple modules in the + same binary (see :ref:`embedding_modules`). In such a case, the + localization will apply across all embedded modules within the same binary. + +.. seealso:: + + The file :file:`tests/test_local_bindings.cpp` contains additional examples + that demonstrate how ``py::module_local()`` works. + +Binding protected member functions +================================== + +It's normally not possible to expose ``protected`` member functions to Python: + +.. code-block:: cpp + + class A { + protected: + int foo() const { return 42; } + }; + + py::class_(m, "A") + .def("foo", &A::foo); // error: 'foo' is a protected member of 'A' + +On one hand, this is good because non-``public`` members aren't meant to be +accessed from the outside. But we may want to make use of ``protected`` +functions in derived Python classes. + +The following pattern makes this possible: + +.. code-block:: cpp + + class A { + protected: + int foo() const { return 42; } + }; + + class Publicist : public A { // helper type for exposing protected functions + public: + using A::foo; // inherited with different access modifier + }; + + py::class_(m, "A") // bind the primary class + .def("foo", &Publicist::foo); // expose protected methods via the publicist + +This works because ``&Publicist::foo`` is exactly the same function as +``&A::foo`` (same signature and address), just with a different access +modifier. The only purpose of the ``Publicist`` helper class is to make +the function name ``public``. + +If the intent is to expose ``protected`` ``virtual`` functions which can be +overridden in Python, the publicist pattern can be combined with the previously +described trampoline: + +.. code-block:: cpp + + class A { + public: + virtual ~A() = default; + + protected: + virtual int foo() const { return 42; } + }; + + class Trampoline : public A { + public: + int foo() const override { PYBIND11_OVERRIDE(int, A, foo, ); } + }; + + class Publicist : public A { + public: + using A::foo; + }; + + py::class_(m, "A") // <-- `Trampoline` here + .def("foo", &Publicist::foo); // <-- `Publicist` here, not `Trampoline`! + +.. note:: + + MSVC 2015 has a compiler bug (fixed in version 2017) which + requires a more explicit function binding in the form of + ``.def("foo", static_cast(&Publicist::foo));`` + where ``int (A::*)() const`` is the type of ``A::foo``. + +Binding final classes +===================== + +Some classes may not be appropriate to inherit from. In C++11, classes can +use the ``final`` specifier to ensure that a class cannot be inherited from. +The ``py::is_final`` attribute can be used to ensure that Python classes +cannot inherit from a specified type. The underlying C++ type does not need +to be declared final. + +.. code-block:: cpp + + class IsFinal final {}; + + py::class_(m, "IsFinal", py::is_final()); + +When you try to inherit from such a class in Python, you will now get this +error: + +.. code-block:: pycon + + >>> class PyFinalChild(IsFinal): + ... pass + TypeError: type 'IsFinal' is not an acceptable base type + +.. note:: This attribute is currently ignored on PyPy + +.. versionadded:: 2.6 + +Custom automatic downcasters +============================ + +As explained in :ref:`inheritance`, pybind11 comes with built-in +understanding of the dynamic type of polymorphic objects in C++; that +is, returning a Pet to Python produces a Python object that knows it's +wrapping a Dog, if Pet has virtual methods and pybind11 knows about +Dog and this Pet is in fact a Dog. Sometimes, you might want to +provide this automatic downcasting behavior when creating bindings for +a class hierarchy that does not use standard C++ polymorphism, such as +LLVM [#f4]_. As long as there's some way to determine at runtime +whether a downcast is safe, you can proceed by specializing the +``pybind11::polymorphic_type_hook`` template: + +.. code-block:: cpp + + enum class PetKind { Cat, Dog, Zebra }; + struct Pet { // Not polymorphic: has no virtual methods + const PetKind kind; + int age = 0; + protected: + Pet(PetKind _kind) : kind(_kind) {} + }; + struct Dog : Pet { + Dog() : Pet(PetKind::Dog) {} + std::string sound = "woof!"; + std::string bark() const { return sound; } + }; + + namespace pybind11 { + template<> struct polymorphic_type_hook { + static const void *get(const Pet *src, const std::type_info*& type) { + // note that src may be nullptr + if (src && src->kind == PetKind::Dog) { + type = &typeid(Dog); + return static_cast(src); + } + return src; + } + }; + } // namespace pybind11 + +When pybind11 wants to convert a C++ pointer of type ``Base*`` to a +Python object, it calls ``polymorphic_type_hook::get()`` to +determine if a downcast is possible. The ``get()`` function should use +whatever runtime information is available to determine if its ``src`` +parameter is in fact an instance of some class ``Derived`` that +inherits from ``Base``. If it finds such a ``Derived``, it sets ``type += &typeid(Derived)`` and returns a pointer to the ``Derived`` object +that contains ``src``. Otherwise, it just returns ``src``, leaving +``type`` at its default value of nullptr. If you set ``type`` to a +type that pybind11 doesn't know about, no downcasting will occur, and +the original ``src`` pointer will be used with its static type +``Base*``. + +It is critical that the returned pointer and ``type`` argument of +``get()`` agree with each other: if ``type`` is set to something +non-null, the returned pointer must point to the start of an object +whose type is ``type``. If the hierarchy being exposed uses only +single inheritance, a simple ``return src;`` will achieve this just +fine, but in the general case, you must cast ``src`` to the +appropriate derived-class pointer (e.g. using +``static_cast(src)``) before allowing it to be returned as a +``void*``. + +.. [#f4] https://llvm.org/docs/HowToSetUpLLVMStyleRTTI.html + +.. note:: + + pybind11's standard support for downcasting objects whose types + have virtual methods is implemented using + ``polymorphic_type_hook`` too, using the standard C++ ability to + determine the most-derived type of a polymorphic object using + ``typeid()`` and to cast a base pointer to that most-derived type + (even if you don't know what it is) using ``dynamic_cast``. + +.. seealso:: + + The file :file:`tests/test_tagbased_polymorphic.cpp` contains a + more complete example, including a demonstration of how to provide + automatic downcasting for an entire class hierarchy without + writing one get() function for each class. + +Accessing the type object +========================= + +You can get the type object from a C++ class that has already been registered using: + +.. code-block:: python + + py::type T_py = py::type::of(); + +You can directly use ``py::type::of(ob)`` to get the type object from any python +object, just like ``type(ob)`` in Python. + +.. note:: + + Other types, like ``py::type::of()``, do not work, see :ref:`type-conversions`. + +.. versionadded:: 2.6 diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/embedding.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/embedding.rst new file mode 100644 index 0000000000000000000000000000000000000000..dfdaad2d7f08f899237d69db2749b12a3c58c438 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/embedding.rst @@ -0,0 +1,261 @@ +.. _embedding: + +Embedding the interpreter +######################### + +While pybind11 is mainly focused on extending Python using C++, it's also +possible to do the reverse: embed the Python interpreter into a C++ program. +All of the other documentation pages still apply here, so refer to them for +general pybind11 usage. This section will cover a few extra things required +for embedding. + +Getting started +=============== + +A basic executable with an embedded interpreter can be created with just a few +lines of CMake and the ``pybind11::embed`` target, as shown below. For more +information, see :doc:`/compiling`. + +.. code-block:: cmake + + cmake_minimum_required(VERSION 3.4) + project(example) + + find_package(pybind11 REQUIRED) # or `add_subdirectory(pybind11)` + + add_executable(example main.cpp) + target_link_libraries(example PRIVATE pybind11::embed) + +The essential structure of the ``main.cpp`` file looks like this: + +.. code-block:: cpp + + #include // everything needed for embedding + namespace py = pybind11; + + int main() { + py::scoped_interpreter guard{}; // start the interpreter and keep it alive + + py::print("Hello, World!"); // use the Python API + } + +The interpreter must be initialized before using any Python API, which includes +all the functions and classes in pybind11. The RAII guard class `scoped_interpreter` +takes care of the interpreter lifetime. After the guard is destroyed, the interpreter +shuts down and clears its memory. No Python functions can be called after this. + +Executing Python code +===================== + +There are a few different ways to run Python code. One option is to use `eval`, +`exec` or `eval_file`, as explained in :ref:`eval`. Here is a quick example in +the context of an executable with an embedded interpreter: + +.. code-block:: cpp + + #include + namespace py = pybind11; + + int main() { + py::scoped_interpreter guard{}; + + py::exec(R"( + kwargs = dict(name="World", number=42) + message = "Hello, {name}! The answer is {number}".format(**kwargs) + print(message) + )"); + } + +Alternatively, similar results can be achieved using pybind11's API (see +:doc:`/advanced/pycpp/index` for more details). + +.. code-block:: cpp + + #include + namespace py = pybind11; + using namespace py::literals; + + int main() { + py::scoped_interpreter guard{}; + + auto kwargs = py::dict("name"_a="World", "number"_a=42); + auto message = "Hello, {name}! The answer is {number}"_s.format(**kwargs); + py::print(message); + } + +The two approaches can also be combined: + +.. code-block:: cpp + + #include + #include + + namespace py = pybind11; + using namespace py::literals; + + int main() { + py::scoped_interpreter guard{}; + + auto locals = py::dict("name"_a="World", "number"_a=42); + py::exec(R"( + message = "Hello, {name}! The answer is {number}".format(**locals()) + )", py::globals(), locals); + + auto message = locals["message"].cast(); + std::cout << message; + } + +Importing modules +================= + +Python modules can be imported using `module_::import()`: + +.. code-block:: cpp + + py::module_ sys = py::module_::import("sys"); + py::print(sys.attr("path")); + +For convenience, the current working directory is included in ``sys.path`` when +embedding the interpreter. This makes it easy to import local Python files: + +.. code-block:: python + + """calc.py located in the working directory""" + + def add(i, j): + return i + j + + +.. code-block:: cpp + + py::module_ calc = py::module_::import("calc"); + py::object result = calc.attr("add")(1, 2); + int n = result.cast(); + assert(n == 3); + +Modules can be reloaded using `module_::reload()` if the source is modified e.g. +by an external process. This can be useful in scenarios where the application +imports a user defined data processing script which needs to be updated after +changes by the user. Note that this function does not reload modules recursively. + +.. _embedding_modules: + +Adding embedded modules +======================= + +Embedded binary modules can be added using the `PYBIND11_EMBEDDED_MODULE` macro. +Note that the definition must be placed at global scope. They can be imported +like any other module. + +.. code-block:: cpp + + #include + namespace py = pybind11; + + PYBIND11_EMBEDDED_MODULE(fast_calc, m) { + // `m` is a `py::module_` which is used to bind functions and classes + m.def("add", [](int i, int j) { + return i + j; + }); + } + + int main() { + py::scoped_interpreter guard{}; + + auto fast_calc = py::module_::import("fast_calc"); + auto result = fast_calc.attr("add")(1, 2).cast(); + assert(result == 3); + } + +Unlike extension modules where only a single binary module can be created, on +the embedded side an unlimited number of modules can be added using multiple +`PYBIND11_EMBEDDED_MODULE` definitions (as long as they have unique names). + +These modules are added to Python's list of builtins, so they can also be +imported in pure Python files loaded by the interpreter. Everything interacts +naturally: + +.. code-block:: python + + """py_module.py located in the working directory""" + import cpp_module + + a = cpp_module.a + b = a + 1 + + +.. code-block:: cpp + + #include + namespace py = pybind11; + + PYBIND11_EMBEDDED_MODULE(cpp_module, m) { + m.attr("a") = 1; + } + + int main() { + py::scoped_interpreter guard{}; + + auto py_module = py::module_::import("py_module"); + + auto locals = py::dict("fmt"_a="{} + {} = {}", **py_module.attr("__dict__")); + assert(locals["a"].cast() == 1); + assert(locals["b"].cast() == 2); + + py::exec(R"( + c = a + b + message = fmt.format(a, b, c) + )", py::globals(), locals); + + assert(locals["c"].cast() == 3); + assert(locals["message"].cast() == "1 + 2 = 3"); + } + + +Interpreter lifetime +==================== + +The Python interpreter shuts down when `scoped_interpreter` is destroyed. After +this, creating a new instance will restart the interpreter. Alternatively, the +`initialize_interpreter` / `finalize_interpreter` pair of functions can be used +to directly set the state at any time. + +Modules created with pybind11 can be safely re-initialized after the interpreter +has been restarted. However, this may not apply to third-party extension modules. +The issue is that Python itself cannot completely unload extension modules and +there are several caveats with regard to interpreter restarting. In short, not +all memory may be freed, either due to Python reference cycles or user-created +global data. All the details can be found in the CPython documentation. + +.. warning:: + + Creating two concurrent `scoped_interpreter` guards is a fatal error. So is + calling `initialize_interpreter` for a second time after the interpreter + has already been initialized. + + Do not use the raw CPython API functions ``Py_Initialize`` and + ``Py_Finalize`` as these do not properly handle the lifetime of + pybind11's internal data. + + +Sub-interpreter support +======================= + +Creating multiple copies of `scoped_interpreter` is not possible because it +represents the main Python interpreter. Sub-interpreters are something different +and they do permit the existence of multiple interpreters. This is an advanced +feature of the CPython API and should be handled with care. pybind11 does not +currently offer a C++ interface for sub-interpreters, so refer to the CPython +documentation for all the details regarding this feature. + +We'll just mention a couple of caveats the sub-interpreters support in pybind11: + + 1. Sub-interpreters will not receive independent copies of embedded modules. + Instead, these are shared and modifications in one interpreter may be + reflected in another. + + 2. Managing multiple threads, multiple interpreters and the GIL can be + challenging and there are several caveats here, even within the pure + CPython API (please refer to the Python docs for details). As for + pybind11, keep in mind that `gil_scoped_release` and `gil_scoped_acquire` + do not take sub-interpreters into account. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/exceptions.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/exceptions.rst new file mode 100644 index 0000000000000000000000000000000000000000..7a4d6cbc6e0beebf6f430b81af7301366f5d2233 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/exceptions.rst @@ -0,0 +1,306 @@ +Exceptions +########## + +Built-in C++ to Python exception translation +============================================ + +When Python calls C++ code through pybind11, pybind11 provides a C++ exception handler +that will trap C++ exceptions, translate them to the corresponding Python exception, +and raise them so that Python code can handle them. + +pybind11 defines translations for ``std::exception`` and its standard +subclasses, and several special exception classes that translate to specific +Python exceptions. Note that these are not actually Python exceptions, so they +cannot be examined using the Python C API. Instead, they are pure C++ objects +that pybind11 will translate the corresponding Python exception when they arrive +at its exception handler. + +.. tabularcolumns:: |p{0.5\textwidth}|p{0.45\textwidth}| + ++--------------------------------------+--------------------------------------+ +| Exception thrown by C++ | Translated to Python exception type | ++======================================+======================================+ +| :class:`std::exception` | ``RuntimeError`` | ++--------------------------------------+--------------------------------------+ +| :class:`std::bad_alloc` | ``MemoryError`` | ++--------------------------------------+--------------------------------------+ +| :class:`std::domain_error` | ``ValueError`` | ++--------------------------------------+--------------------------------------+ +| :class:`std::invalid_argument` | ``ValueError`` | ++--------------------------------------+--------------------------------------+ +| :class:`std::length_error` | ``ValueError`` | ++--------------------------------------+--------------------------------------+ +| :class:`std::out_of_range` | ``IndexError`` | ++--------------------------------------+--------------------------------------+ +| :class:`std::range_error` | ``ValueError`` | ++--------------------------------------+--------------------------------------+ +| :class:`std::overflow_error` | ``OverflowError`` | ++--------------------------------------+--------------------------------------+ +| :class:`pybind11::stop_iteration` | ``StopIteration`` (used to implement | +| | custom iterators) | ++--------------------------------------+--------------------------------------+ +| :class:`pybind11::index_error` | ``IndexError`` (used to indicate out | +| | of bounds access in ``__getitem__``, | +| | ``__setitem__``, etc.) | ++--------------------------------------+--------------------------------------+ +| :class:`pybind11::key_error` | ``KeyError`` (used to indicate out | +| | of bounds access in ``__getitem__``, | +| | ``__setitem__`` in dict-like | +| | objects, etc.) | ++--------------------------------------+--------------------------------------+ +| :class:`pybind11::value_error` | ``ValueError`` (used to indicate | +| | wrong value passed in | +| | ``container.remove(...)``) | ++--------------------------------------+--------------------------------------+ +| :class:`pybind11::type_error` | ``TypeError`` | ++--------------------------------------+--------------------------------------+ +| :class:`pybind11::buffer_error` | ``BufferError`` | ++--------------------------------------+--------------------------------------+ +| :class:`pybind11::import_error` | ``import_error`` | ++--------------------------------------+--------------------------------------+ +| Any other exception | ``RuntimeError`` | ++--------------------------------------+--------------------------------------+ + +Exception translation is not bidirectional. That is, *catching* the C++ +exceptions defined above above will not trap exceptions that originate from +Python. For that, catch :class:`pybind11::error_already_set`. See :ref:`below +` for further details. + +There is also a special exception :class:`cast_error` that is thrown by +:func:`handle::call` when the input arguments cannot be converted to Python +objects. + +Registering custom translators +============================== + +If the default exception conversion policy described above is insufficient, +pybind11 also provides support for registering custom exception translators. +To register a simple exception conversion that translates a C++ exception into +a new Python exception using the C++ exception's ``what()`` method, a helper +function is available: + +.. code-block:: cpp + + py::register_exception(module, "PyExp"); + +This call creates a Python exception class with the name ``PyExp`` in the given +module and automatically converts any encountered exceptions of type ``CppExp`` +into Python exceptions of type ``PyExp``. + +It is possible to specify base class for the exception using the third +parameter, a `handle`: + +.. code-block:: cpp + + py::register_exception(module, "PyExp", PyExc_RuntimeError); + +Then `PyExp` can be caught both as `PyExp` and `RuntimeError`. + +The class objects of the built-in Python exceptions are listed in the Python +documentation on `Standard Exceptions `_. +The default base class is `PyExc_Exception`. + +When more advanced exception translation is needed, the function +``py::register_exception_translator(translator)`` can be used to register +functions that can translate arbitrary exception types (and which may include +additional logic to do so). The function takes a stateless callable (e.g. a +function pointer or a lambda function without captured variables) with the call +signature ``void(std::exception_ptr)``. + +When a C++ exception is thrown, the registered exception translators are tried +in reverse order of registration (i.e. the last registered translator gets the +first shot at handling the exception). + +Inside the translator, ``std::rethrow_exception`` should be used within +a try block to re-throw the exception. One or more catch clauses to catch +the appropriate exceptions should then be used with each clause using +``PyErr_SetString`` to set a Python exception or ``ex(string)`` to set +the python exception to a custom exception type (see below). + +To declare a custom Python exception type, declare a ``py::exception`` variable +and use this in the associated exception translator (note: it is often useful +to make this a static declaration when using it inside a lambda expression +without requiring capturing). + +The following example demonstrates this for a hypothetical exception classes +``MyCustomException`` and ``OtherException``: the first is translated to a +custom python exception ``MyCustomError``, while the second is translated to a +standard python RuntimeError: + +.. code-block:: cpp + + static py::exception exc(m, "MyCustomError"); + py::register_exception_translator([](std::exception_ptr p) { + try { + if (p) std::rethrow_exception(p); + } catch (const MyCustomException &e) { + exc(e.what()); + } catch (const OtherException &e) { + PyErr_SetString(PyExc_RuntimeError, e.what()); + } + }); + +Multiple exceptions can be handled by a single translator, as shown in the +example above. If the exception is not caught by the current translator, the +previously registered one gets a chance. + +If none of the registered exception translators is able to handle the +exception, it is handled by the default converter as described in the previous +section. + +.. seealso:: + + The file :file:`tests/test_exceptions.cpp` contains examples + of various custom exception translators and custom exception types. + +.. note:: + + Call either ``PyErr_SetString`` or a custom exception's call + operator (``exc(string)``) for every exception caught in a custom exception + translator. Failure to do so will cause Python to crash with ``SystemError: + error return without exception set``. + + Exceptions that you do not plan to handle should simply not be caught, or + may be explicitly (re-)thrown to delegate it to the other, + previously-declared existing exception translators. + +.. _handling_python_exceptions_cpp: + +Handling exceptions from Python in C++ +====================================== + +When C++ calls Python functions, such as in a callback function or when +manipulating Python objects, and Python raises an ``Exception``, pybind11 +converts the Python exception into a C++ exception of type +:class:`pybind11::error_already_set` whose payload contains a C++ string textual +summary and the actual Python exception. ``error_already_set`` is used to +propagate Python exception back to Python (or possibly, handle them in C++). + +.. tabularcolumns:: |p{0.5\textwidth}|p{0.45\textwidth}| + ++--------------------------------------+--------------------------------------+ +| Exception raised in Python | Thrown as C++ exception type | ++======================================+======================================+ +| Any Python ``Exception`` | :class:`pybind11::error_already_set` | ++--------------------------------------+--------------------------------------+ + +For example: + +.. code-block:: cpp + + try { + // open("missing.txt", "r") + auto file = py::module_::import("io").attr("open")("missing.txt", "r"); + auto text = file.attr("read")(); + file.attr("close")(); + } catch (py::error_already_set &e) { + if (e.matches(PyExc_FileNotFoundError)) { + py::print("missing.txt not found"); + } else if (e.matches(PyExc_PermissionError)) { + py::print("missing.txt found but not accessible"); + } else { + throw; + } + } + +Note that C++ to Python exception translation does not apply here, since that is +a method for translating C++ exceptions to Python, not vice versa. The error raised +from Python is always ``error_already_set``. + +This example illustrates this behavior: + +.. code-block:: cpp + + try { + py::eval("raise ValueError('The Ring')"); + } catch (py::value_error &boromir) { + // Boromir never gets the ring + assert(false); + } catch (py::error_already_set &frodo) { + // Frodo gets the ring + py::print("I will take the ring"); + } + + try { + // py::value_error is a request for pybind11 to raise a Python exception + throw py::value_error("The ball"); + } catch (py::error_already_set &cat) { + // cat won't catch the ball since + // py::value_error is not a Python exception + assert(false); + } catch (py::value_error &dog) { + // dog will catch the ball + py::print("Run Spot run"); + throw; // Throw it again (pybind11 will raise ValueError) + } + +Handling errors from the Python C API +===================================== + +Where possible, use :ref:`pybind11 wrappers ` instead of calling +the Python C API directly. When calling the Python C API directly, in +addition to manually managing reference counts, one must follow the pybind11 +error protocol, which is outlined here. + +After calling the Python C API, if Python returns an error, +``throw py::error_already_set();``, which allows pybind11 to deal with the +exception and pass it back to the Python interpreter. This includes calls to +the error setting functions such as ``PyErr_SetString``. + +.. code-block:: cpp + + PyErr_SetString(PyExc_TypeError, "C API type error demo"); + throw py::error_already_set(); + + // But it would be easier to simply... + throw py::type_error("pybind11 wrapper type error"); + +Alternately, to ignore the error, call `PyErr_Clear +`_. + +Any Python error must be thrown or cleared, or Python/pybind11 will be left in +an invalid state. + +.. _unraisable_exceptions: + +Handling unraisable exceptions +============================== + +If a Python function invoked from a C++ destructor or any function marked +``noexcept(true)`` (collectively, "noexcept functions") throws an exception, there +is no way to propagate the exception, as such functions may not throw. +Should they throw or fail to catch any exceptions in their call graph, +the C++ runtime calls ``std::terminate()`` to abort immediately. + +Similarly, Python exceptions raised in a class's ``__del__`` method do not +propagate, but are logged by Python as an unraisable error. In Python 3.8+, a +`system hook is triggered +`_ +and an auditing event is logged. + +Any noexcept function should have a try-catch block that traps +class:`error_already_set` (or any other exception that can occur). Note that +pybind11 wrappers around Python exceptions such as +:class:`pybind11::value_error` are *not* Python exceptions; they are C++ +exceptions that pybind11 catches and converts to Python exceptions. Noexcept +functions cannot propagate these exceptions either. A useful approach is to +convert them to Python exceptions and then ``discard_as_unraisable`` as shown +below. + +.. code-block:: cpp + + void nonthrowing_func() noexcept(true) { + try { + // ... + } catch (py::error_already_set &eas) { + // Discard the Python error using Python APIs, using the C++ magic + // variable __func__. Python already knows the type and value and of the + // exception object. + eas.discard_as_unraisable(__func__); + } catch (const std::exception &e) { + // Log and discard C++ exceptions. + third_party::log(e); + } + } + +.. versionadded:: 2.6 diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/functions.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/functions.rst new file mode 100644 index 0000000000000000000000000000000000000000..6a93ab9da8c75fb0262be6d051312b4418e3698f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/functions.rst @@ -0,0 +1,563 @@ +Functions +######### + +Before proceeding with this section, make sure that you are already familiar +with the basics of binding functions and classes, as explained in :doc:`/basics` +and :doc:`/classes`. The following guide is applicable to both free and member +functions, i.e. *methods* in Python. + +.. _return_value_policies: + +Return value policies +===================== + +Python and C++ use fundamentally different ways of managing the memory and +lifetime of objects managed by them. This can lead to issues when creating +bindings for functions that return a non-trivial type. Just by looking at the +type information, it is not clear whether Python should take charge of the +returned value and eventually free its resources, or if this is handled on the +C++ side. For this reason, pybind11 provides a several *return value policy* +annotations that can be passed to the :func:`module_::def` and +:func:`class_::def` functions. The default policy is +:enum:`return_value_policy::automatic`. + +Return value policies are tricky, and it's very important to get them right. +Just to illustrate what can go wrong, consider the following simple example: + +.. code-block:: cpp + + /* Function declaration */ + Data *get_data() { return _data; /* (pointer to a static data structure) */ } + ... + + /* Binding code */ + m.def("get_data", &get_data); // <-- KABOOM, will cause crash when called from Python + +What's going on here? When ``get_data()`` is called from Python, the return +value (a native C++ type) must be wrapped to turn it into a usable Python type. +In this case, the default return value policy (:enum:`return_value_policy::automatic`) +causes pybind11 to assume ownership of the static ``_data`` instance. + +When Python's garbage collector eventually deletes the Python +wrapper, pybind11 will also attempt to delete the C++ instance (via ``operator +delete()``) due to the implied ownership. At this point, the entire application +will come crashing down, though errors could also be more subtle and involve +silent data corruption. + +In the above example, the policy :enum:`return_value_policy::reference` should have +been specified so that the global data instance is only *referenced* without any +implied transfer of ownership, i.e.: + +.. code-block:: cpp + + m.def("get_data", &get_data, py::return_value_policy::reference); + +On the other hand, this is not the right policy for many other situations, +where ignoring ownership could lead to resource leaks. +As a developer using pybind11, it's important to be familiar with the different +return value policies, including which situation calls for which one of them. +The following table provides an overview of available policies: + +.. tabularcolumns:: |p{0.5\textwidth}|p{0.45\textwidth}| + ++--------------------------------------------------+----------------------------------------------------------------------------+ +| Return value policy | Description | ++==================================================+============================================================================+ +| :enum:`return_value_policy::take_ownership` | Reference an existing object (i.e. do not create a new copy) and take | +| | ownership. Python will call the destructor and delete operator when the | +| | object's reference count reaches zero. Undefined behavior ensues when the | +| | C++ side does the same, or when the data was not dynamically allocated. | ++--------------------------------------------------+----------------------------------------------------------------------------+ +| :enum:`return_value_policy::copy` | Create a new copy of the returned object, which will be owned by Python. | +| | This policy is comparably safe because the lifetimes of the two instances | +| | are decoupled. | ++--------------------------------------------------+----------------------------------------------------------------------------+ +| :enum:`return_value_policy::move` | Use ``std::move`` to move the return value contents into a new instance | +| | that will be owned by Python. This policy is comparably safe because the | +| | lifetimes of the two instances (move source and destination) are decoupled.| ++--------------------------------------------------+----------------------------------------------------------------------------+ +| :enum:`return_value_policy::reference` | Reference an existing object, but do not take ownership. The C++ side is | +| | responsible for managing the object's lifetime and deallocating it when | +| | it is no longer used. Warning: undefined behavior will ensue when the C++ | +| | side deletes an object that is still referenced and used by Python. | ++--------------------------------------------------+----------------------------------------------------------------------------+ +| :enum:`return_value_policy::reference_internal` | Indicates that the lifetime of the return value is tied to the lifetime | +| | of a parent object, namely the implicit ``this``, or ``self`` argument of | +| | the called method or property. Internally, this policy works just like | +| | :enum:`return_value_policy::reference` but additionally applies a | +| | ``keep_alive<0, 1>`` *call policy* (described in the next section) that | +| | prevents the parent object from being garbage collected as long as the | +| | return value is referenced by Python. This is the default policy for | +| | property getters created via ``def_property``, ``def_readwrite``, etc. | ++--------------------------------------------------+----------------------------------------------------------------------------+ +| :enum:`return_value_policy::automatic` | **Default policy.** This policy falls back to the policy | +| | :enum:`return_value_policy::take_ownership` when the return value is a | +| | pointer. Otherwise, it uses :enum:`return_value_policy::move` or | +| | :enum:`return_value_policy::copy` for rvalue and lvalue references, | +| | respectively. See above for a description of what all of these different | +| | policies do. | ++--------------------------------------------------+----------------------------------------------------------------------------+ +| :enum:`return_value_policy::automatic_reference` | As above, but use policy :enum:`return_value_policy::reference` when the | +| | return value is a pointer. This is the default conversion policy for | +| | function arguments when calling Python functions manually from C++ code | +| | (i.e. via handle::operator()). You probably won't need to use this. | ++--------------------------------------------------+----------------------------------------------------------------------------+ + +Return value policies can also be applied to properties: + +.. code-block:: cpp + + class_(m, "MyClass") + .def_property("data", &MyClass::getData, &MyClass::setData, + py::return_value_policy::copy); + +Technically, the code above applies the policy to both the getter and the +setter function, however, the setter doesn't really care about *return* +value policies which makes this a convenient terse syntax. Alternatively, +targeted arguments can be passed through the :class:`cpp_function` constructor: + +.. code-block:: cpp + + class_(m, "MyClass") + .def_property("data" + py::cpp_function(&MyClass::getData, py::return_value_policy::copy), + py::cpp_function(&MyClass::setData) + ); + +.. warning:: + + Code with invalid return value policies might access uninitialized memory or + free data structures multiple times, which can lead to hard-to-debug + non-determinism and segmentation faults, hence it is worth spending the + time to understand all the different options in the table above. + +.. note:: + + One important aspect of the above policies is that they only apply to + instances which pybind11 has *not* seen before, in which case the policy + clarifies essential questions about the return value's lifetime and + ownership. When pybind11 knows the instance already (as identified by its + type and address in memory), it will return the existing Python object + wrapper rather than creating a new copy. + +.. note:: + + The next section on :ref:`call_policies` discusses *call policies* that can be + specified *in addition* to a return value policy from the list above. Call + policies indicate reference relationships that can involve both return values + and parameters of functions. + +.. note:: + + As an alternative to elaborate call policies and lifetime management logic, + consider using smart pointers (see the section on :ref:`smart_pointers` for + details). Smart pointers can tell whether an object is still referenced from + C++ or Python, which generally eliminates the kinds of inconsistencies that + can lead to crashes or undefined behavior. For functions returning smart + pointers, it is not necessary to specify a return value policy. + +.. _call_policies: + +Additional call policies +======================== + +In addition to the above return value policies, further *call policies* can be +specified to indicate dependencies between parameters or ensure a certain state +for the function call. + +Keep alive +---------- + +In general, this policy is required when the C++ object is any kind of container +and another object is being added to the container. ``keep_alive`` +indicates that the argument with index ``Patient`` should be kept alive at least +until the argument with index ``Nurse`` is freed by the garbage collector. Argument +indices start at one, while zero refers to the return value. For methods, index +``1`` refers to the implicit ``this`` pointer, while regular arguments begin at +index ``2``. Arbitrarily many call policies can be specified. When a ``Nurse`` +with value ``None`` is detected at runtime, the call policy does nothing. + +When the nurse is not a pybind11-registered type, the implementation internally +relies on the ability to create a *weak reference* to the nurse object. When +the nurse object is not a pybind11-registered type and does not support weak +references, an exception will be thrown. + +Consider the following example: here, the binding code for a list append +operation ties the lifetime of the newly added element to the underlying +container: + +.. code-block:: cpp + + py::class_(m, "List") + .def("append", &List::append, py::keep_alive<1, 2>()); + +For consistency, the argument indexing is identical for constructors. Index +``1`` still refers to the implicit ``this`` pointer, i.e. the object which is +being constructed. Index ``0`` refers to the return type which is presumed to +be ``void`` when a constructor is viewed like a function. The following example +ties the lifetime of the constructor element to the constructed object: + +.. code-block:: cpp + + py::class_(m, "Nurse") + .def(py::init(), py::keep_alive<1, 2>()); + +.. note:: + + ``keep_alive`` is analogous to the ``with_custodian_and_ward`` (if Nurse, + Patient != 0) and ``with_custodian_and_ward_postcall`` (if Nurse/Patient == + 0) policies from Boost.Python. + +Call guard +---------- + +The ``call_guard`` policy allows any scope guard type ``T`` to be placed +around the function call. For example, this definition: + +.. code-block:: cpp + + m.def("foo", foo, py::call_guard()); + +is equivalent to the following pseudocode: + +.. code-block:: cpp + + m.def("foo", [](args...) { + T scope_guard; + return foo(args...); // forwarded arguments + }); + +The only requirement is that ``T`` is default-constructible, but otherwise any +scope guard will work. This is very useful in combination with `gil_scoped_release`. +See :ref:`gil`. + +Multiple guards can also be specified as ``py::call_guard``. The +constructor order is left to right and destruction happens in reverse. + +.. seealso:: + + The file :file:`tests/test_call_policies.cpp` contains a complete example + that demonstrates using `keep_alive` and `call_guard` in more detail. + +.. _python_objects_as_args: + +Python objects as arguments +=========================== + +pybind11 exposes all major Python types using thin C++ wrapper classes. These +wrapper classes can also be used as parameters of functions in bindings, which +makes it possible to directly work with native Python types on the C++ side. +For instance, the following statement iterates over a Python ``dict``: + +.. code-block:: cpp + + void print_dict(py::dict dict) { + /* Easily interact with Python types */ + for (auto item : dict) + std::cout << "key=" << std::string(py::str(item.first)) << ", " + << "value=" << std::string(py::str(item.second)) << std::endl; + } + +It can be exported: + +.. code-block:: cpp + + m.def("print_dict", &print_dict); + +And used in Python as usual: + +.. code-block:: pycon + + >>> print_dict({'foo': 123, 'bar': 'hello'}) + key=foo, value=123 + key=bar, value=hello + +For more information on using Python objects in C++, see :doc:`/advanced/pycpp/index`. + +Accepting \*args and \*\*kwargs +=============================== + +Python provides a useful mechanism to define functions that accept arbitrary +numbers of arguments and keyword arguments: + +.. code-block:: python + + def generic(*args, **kwargs): + ... # do something with args and kwargs + +Such functions can also be created using pybind11: + +.. code-block:: cpp + + void generic(py::args args, py::kwargs kwargs) { + /// .. do something with args + if (kwargs) + /// .. do something with kwargs + } + + /// Binding code + m.def("generic", &generic); + +The class ``py::args`` derives from ``py::tuple`` and ``py::kwargs`` derives +from ``py::dict``. + +You may also use just one or the other, and may combine these with other +arguments as long as the ``py::args`` and ``py::kwargs`` arguments are the last +arguments accepted by the function. + +Please refer to the other examples for details on how to iterate over these, +and on how to cast their entries into C++ objects. A demonstration is also +available in ``tests/test_kwargs_and_defaults.cpp``. + +.. note:: + + When combining \*args or \*\*kwargs with :ref:`keyword_args` you should + *not* include ``py::arg`` tags for the ``py::args`` and ``py::kwargs`` + arguments. + +Default arguments revisited +=========================== + +The section on :ref:`default_args` previously discussed basic usage of default +arguments using pybind11. One noteworthy aspect of their implementation is that +default arguments are converted to Python objects right at declaration time. +Consider the following example: + +.. code-block:: cpp + + py::class_("MyClass") + .def("myFunction", py::arg("arg") = SomeType(123)); + +In this case, pybind11 must already be set up to deal with values of the type +``SomeType`` (via a prior instantiation of ``py::class_``), or an +exception will be thrown. + +Another aspect worth highlighting is that the "preview" of the default argument +in the function signature is generated using the object's ``__repr__`` method. +If not available, the signature may not be very helpful, e.g.: + +.. code-block:: pycon + + FUNCTIONS + ... + | myFunction(...) + | Signature : (MyClass, arg : SomeType = ) -> NoneType + ... + +The first way of addressing this is by defining ``SomeType.__repr__``. +Alternatively, it is possible to specify the human-readable preview of the +default argument manually using the ``arg_v`` notation: + +.. code-block:: cpp + + py::class_("MyClass") + .def("myFunction", py::arg_v("arg", SomeType(123), "SomeType(123)")); + +Sometimes it may be necessary to pass a null pointer value as a default +argument. In this case, remember to cast it to the underlying type in question, +like so: + +.. code-block:: cpp + + py::class_("MyClass") + .def("myFunction", py::arg("arg") = static_cast(nullptr)); + +Keyword-only arguments +====================== + +Python 3 introduced keyword-only arguments by specifying an unnamed ``*`` +argument in a function definition: + +.. code-block:: python + + def f(a, *, b): # a can be positional or via keyword; b must be via keyword + pass + + f(a=1, b=2) # good + f(b=2, a=1) # good + f(1, b=2) # good + f(1, 2) # TypeError: f() takes 1 positional argument but 2 were given + +Pybind11 provides a ``py::kw_only`` object that allows you to implement +the same behaviour by specifying the object between positional and keyword-only +argument annotations when registering the function: + +.. code-block:: cpp + + m.def("f", [](int a, int b) { /* ... */ }, + py::arg("a"), py::kw_only(), py::arg("b")); + +Note that you currently cannot combine this with a ``py::args`` argument. This +feature does *not* require Python 3 to work. + +.. versionadded:: 2.6 + +Positional-only arguments +========================= + +Python 3.8 introduced a new positional-only argument syntax, using ``/`` in the +function definition (note that this has been a convention for CPython +positional arguments, such as in ``pow()``, since Python 2). You can +do the same thing in any version of Python using ``py::pos_only()``: + +.. code-block:: cpp + + m.def("f", [](int a, int b) { /* ... */ }, + py::arg("a"), py::pos_only(), py::arg("b")); + +You now cannot give argument ``a`` by keyword. This can be combined with +keyword-only arguments, as well. + +.. versionadded:: 2.6 + +.. _nonconverting_arguments: + +Non-converting arguments +======================== + +Certain argument types may support conversion from one type to another. Some +examples of conversions are: + +* :ref:`implicit_conversions` declared using ``py::implicitly_convertible()`` +* Calling a method accepting a double with an integer argument +* Calling a ``std::complex`` argument with a non-complex python type + (for example, with a float). (Requires the optional ``pybind11/complex.h`` + header). +* Calling a function taking an Eigen matrix reference with a numpy array of the + wrong type or of an incompatible data layout. (Requires the optional + ``pybind11/eigen.h`` header). + +This behaviour is sometimes undesirable: the binding code may prefer to raise +an error rather than convert the argument. This behaviour can be obtained +through ``py::arg`` by calling the ``.noconvert()`` method of the ``py::arg`` +object, such as: + +.. code-block:: cpp + + m.def("floats_only", [](double f) { return 0.5 * f; }, py::arg("f").noconvert()); + m.def("floats_preferred", [](double f) { return 0.5 * f; }, py::arg("f")); + +Attempting the call the second function (the one without ``.noconvert()``) with +an integer will succeed, but attempting to call the ``.noconvert()`` version +will fail with a ``TypeError``: + +.. code-block:: pycon + + >>> floats_preferred(4) + 2.0 + >>> floats_only(4) + Traceback (most recent call last): + File "", line 1, in + TypeError: floats_only(): incompatible function arguments. The following argument types are supported: + 1. (f: float) -> float + + Invoked with: 4 + +You may, of course, combine this with the :var:`_a` shorthand notation (see +:ref:`keyword_args`) and/or :ref:`default_args`. It is also permitted to omit +the argument name by using the ``py::arg()`` constructor without an argument +name, i.e. by specifying ``py::arg().noconvert()``. + +.. note:: + + When specifying ``py::arg`` options it is necessary to provide the same + number of options as the bound function has arguments. Thus if you want to + enable no-convert behaviour for just one of several arguments, you will + need to specify a ``py::arg()`` annotation for each argument with the + no-convert argument modified to ``py::arg().noconvert()``. + +.. _none_arguments: + +Allow/Prohibiting None arguments +================================ + +When a C++ type registered with :class:`py::class_` is passed as an argument to +a function taking the instance as pointer or shared holder (e.g. ``shared_ptr`` +or a custom, copyable holder as described in :ref:`smart_pointers`), pybind +allows ``None`` to be passed from Python which results in calling the C++ +function with ``nullptr`` (or an empty holder) for the argument. + +To explicitly enable or disable this behaviour, using the +``.none`` method of the :class:`py::arg` object: + +.. code-block:: cpp + + py::class_(m, "Dog").def(py::init<>()); + py::class_(m, "Cat").def(py::init<>()); + m.def("bark", [](Dog *dog) -> std::string { + if (dog) return "woof!"; /* Called with a Dog instance */ + else return "(no dog)"; /* Called with None, dog == nullptr */ + }, py::arg("dog").none(true)); + m.def("meow", [](Cat *cat) -> std::string { + // Can't be called with None argument + return "meow"; + }, py::arg("cat").none(false)); + +With the above, the Python call ``bark(None)`` will return the string ``"(no +dog)"``, while attempting to call ``meow(None)`` will raise a ``TypeError``: + +.. code-block:: pycon + + >>> from animals import Dog, Cat, bark, meow + >>> bark(Dog()) + 'woof!' + >>> meow(Cat()) + 'meow' + >>> bark(None) + '(no dog)' + >>> meow(None) + Traceback (most recent call last): + File "", line 1, in + TypeError: meow(): incompatible function arguments. The following argument types are supported: + 1. (cat: animals.Cat) -> str + + Invoked with: None + +The default behaviour when the tag is unspecified is to allow ``None``. + +.. note:: + + Even when ``.none(true)`` is specified for an argument, ``None`` will be converted to a + ``nullptr`` *only* for custom and :ref:`opaque ` types. Pointers to built-in types + (``double *``, ``int *``, ...) and STL types (``std::vector *``, ...; if ``pybind11/stl.h`` + is included) are copied when converted to C++ (see :doc:`/advanced/cast/overview`) and will + not allow ``None`` as argument. To pass optional argument of these copied types consider + using ``std::optional`` + +.. _overload_resolution: + +Overload resolution order +========================= + +When a function or method with multiple overloads is called from Python, +pybind11 determines which overload to call in two passes. The first pass +attempts to call each overload without allowing argument conversion (as if +every argument had been specified as ``py::arg().noconvert()`` as described +above). + +If no overload succeeds in the no-conversion first pass, a second pass is +attempted in which argument conversion is allowed (except where prohibited via +an explicit ``py::arg().noconvert()`` attribute in the function definition). + +If the second pass also fails a ``TypeError`` is raised. + +Within each pass, overloads are tried in the order they were registered with +pybind11. If the ``py::prepend()`` tag is added to the definition, a function +can be placed at the beginning of the overload sequence instead, allowing user +overloads to proceed built in functions. + +What this means in practice is that pybind11 will prefer any overload that does +not require conversion of arguments to an overload that does, but otherwise +prefers earlier-defined overloads to later-defined ones. + +.. note:: + + pybind11 does *not* further prioritize based on the number/pattern of + overloaded arguments. That is, pybind11 does not prioritize a function + requiring one conversion over one requiring three, but only prioritizes + overloads requiring no conversion at all to overloads that require + conversion of at least one argument. + +.. versionadded:: 2.6 + + The ``py::prepend()`` tag. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/misc.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/misc.rst new file mode 100644 index 0000000000000000000000000000000000000000..b3f3b2265a4fbed9fbd11ed736b6bbd72d999af7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/misc.rst @@ -0,0 +1,337 @@ +Miscellaneous +############# + +.. _macro_notes: + +General notes regarding convenience macros +========================================== + +pybind11 provides a few convenience macros such as +:func:`PYBIND11_DECLARE_HOLDER_TYPE` and ``PYBIND11_OVERRIDE_*``. Since these +are "just" macros that are evaluated in the preprocessor (which has no concept +of types), they *will* get confused by commas in a template argument; for +example, consider: + +.. code-block:: cpp + + PYBIND11_OVERRIDE(MyReturnType, Class, func) + +The limitation of the C preprocessor interprets this as five arguments (with new +arguments beginning after each comma) rather than three. To get around this, +there are two alternatives: you can use a type alias, or you can wrap the type +using the ``PYBIND11_TYPE`` macro: + +.. code-block:: cpp + + // Version 1: using a type alias + using ReturnType = MyReturnType; + using ClassType = Class; + PYBIND11_OVERRIDE(ReturnType, ClassType, func); + + // Version 2: using the PYBIND11_TYPE macro: + PYBIND11_OVERRIDE(PYBIND11_TYPE(MyReturnType), + PYBIND11_TYPE(Class), func) + +The ``PYBIND11_MAKE_OPAQUE`` macro does *not* require the above workarounds. + +.. _gil: + +Global Interpreter Lock (GIL) +============================= + +When calling a C++ function from Python, the GIL is always held. +The classes :class:`gil_scoped_release` and :class:`gil_scoped_acquire` can be +used to acquire and release the global interpreter lock in the body of a C++ +function call. In this way, long-running C++ code can be parallelized using +multiple Python threads. Taking :ref:`overriding_virtuals` as an example, this +could be realized as follows (important changes highlighted): + +.. code-block:: cpp + :emphasize-lines: 8,9,31,32 + + class PyAnimal : public Animal { + public: + /* Inherit the constructors */ + using Animal::Animal; + + /* Trampoline (need one for each virtual function) */ + std::string go(int n_times) { + /* Acquire GIL before calling Python code */ + py::gil_scoped_acquire acquire; + + PYBIND11_OVERRIDE_PURE( + std::string, /* Return type */ + Animal, /* Parent class */ + go, /* Name of function */ + n_times /* Argument(s) */ + ); + } + }; + + PYBIND11_MODULE(example, m) { + py::class_ animal(m, "Animal"); + animal + .def(py::init<>()) + .def("go", &Animal::go); + + py::class_(m, "Dog", animal) + .def(py::init<>()); + + m.def("call_go", [](Animal *animal) -> std::string { + /* Release GIL before calling into (potentially long-running) C++ code */ + py::gil_scoped_release release; + return call_go(animal); + }); + } + +The ``call_go`` wrapper can also be simplified using the `call_guard` policy +(see :ref:`call_policies`) which yields the same result: + +.. code-block:: cpp + + m.def("call_go", &call_go, py::call_guard()); + + +Binding sequence data types, iterators, the slicing protocol, etc. +================================================================== + +Please refer to the supplemental example for details. + +.. seealso:: + + The file :file:`tests/test_sequences_and_iterators.cpp` contains a + complete example that shows how to bind a sequence data type, including + length queries (``__len__``), iterators (``__iter__``), the slicing + protocol and other kinds of useful operations. + + +Partitioning code over multiple extension modules +================================================= + +It's straightforward to split binding code over multiple extension modules, +while referencing types that are declared elsewhere. Everything "just" works +without any special precautions. One exception to this rule occurs when +extending a type declared in another extension module. Recall the basic example +from Section :ref:`inheritance`. + +.. code-block:: cpp + + py::class_ pet(m, "Pet"); + pet.def(py::init()) + .def_readwrite("name", &Pet::name); + + py::class_(m, "Dog", pet /* <- specify parent */) + .def(py::init()) + .def("bark", &Dog::bark); + +Suppose now that ``Pet`` bindings are defined in a module named ``basic``, +whereas the ``Dog`` bindings are defined somewhere else. The challenge is of +course that the variable ``pet`` is not available anymore though it is needed +to indicate the inheritance relationship to the constructor of ``class_``. +However, it can be acquired as follows: + +.. code-block:: cpp + + py::object pet = (py::object) py::module_::import("basic").attr("Pet"); + + py::class_(m, "Dog", pet) + .def(py::init()) + .def("bark", &Dog::bark); + +Alternatively, you can specify the base class as a template parameter option to +``class_``, which performs an automated lookup of the corresponding Python +type. Like the above code, however, this also requires invoking the ``import`` +function once to ensure that the pybind11 binding code of the module ``basic`` +has been executed: + +.. code-block:: cpp + + py::module_::import("basic"); + + py::class_(m, "Dog") + .def(py::init()) + .def("bark", &Dog::bark); + +Naturally, both methods will fail when there are cyclic dependencies. + +Note that pybind11 code compiled with hidden-by-default symbol visibility (e.g. +via the command line flag ``-fvisibility=hidden`` on GCC/Clang), which is +required for proper pybind11 functionality, can interfere with the ability to +access types defined in another extension module. Working around this requires +manually exporting types that are accessed by multiple extension modules; +pybind11 provides a macro to do just this: + +.. code-block:: cpp + + class PYBIND11_EXPORT Dog : public Animal { + ... + }; + +Note also that it is possible (although would rarely be required) to share arbitrary +C++ objects between extension modules at runtime. Internal library data is shared +between modules using capsule machinery [#f6]_ which can be also utilized for +storing, modifying and accessing user-defined data. Note that an extension module +will "see" other extensions' data if and only if they were built with the same +pybind11 version. Consider the following example: + +.. code-block:: cpp + + auto data = reinterpret_cast(py::get_shared_data("mydata")); + if (!data) + data = static_cast(py::set_shared_data("mydata", new MyData(42))); + +If the above snippet was used in several separately compiled extension modules, +the first one to be imported would create a ``MyData`` instance and associate +a ``"mydata"`` key with a pointer to it. Extensions that are imported later +would be then able to access the data behind the same pointer. + +.. [#f6] https://docs.python.org/3/extending/extending.html#using-capsules + +Module Destructors +================== + +pybind11 does not provide an explicit mechanism to invoke cleanup code at +module destruction time. In rare cases where such functionality is required, it +is possible to emulate it using Python capsules or weak references with a +destruction callback. + +.. code-block:: cpp + + auto cleanup_callback = []() { + // perform cleanup here -- this function is called with the GIL held + }; + + m.add_object("_cleanup", py::capsule(cleanup_callback)); + +This approach has the potential downside that instances of classes exposed +within the module may still be alive when the cleanup callback is invoked +(whether this is acceptable will generally depend on the application). + +Alternatively, the capsule may also be stashed within a type object, which +ensures that it not called before all instances of that type have been +collected: + +.. code-block:: cpp + + auto cleanup_callback = []() { /* ... */ }; + m.attr("BaseClass").attr("_cleanup") = py::capsule(cleanup_callback); + +Both approaches also expose a potentially dangerous ``_cleanup`` attribute in +Python, which may be undesirable from an API standpoint (a premature explicit +call from Python might lead to undefined behavior). Yet another approach that +avoids this issue involves weak reference with a cleanup callback: + +.. code-block:: cpp + + // Register a callback function that is invoked when the BaseClass object is collected + py::cpp_function cleanup_callback( + [](py::handle weakref) { + // perform cleanup here -- this function is called with the GIL held + + weakref.dec_ref(); // release weak reference + } + ); + + // Create a weak reference with a cleanup callback and initially leak it + (void) py::weakref(m.attr("BaseClass"), cleanup_callback).release(); + +.. note:: + + PyPy does not garbage collect objects when the interpreter exits. An alternative + approach (which also works on CPython) is to use the :py:mod:`atexit` module [#f7]_, + for example: + + .. code-block:: cpp + + auto atexit = py::module_::import("atexit"); + atexit.attr("register")(py::cpp_function([]() { + // perform cleanup here -- this function is called with the GIL held + })); + + .. [#f7] https://docs.python.org/3/library/atexit.html + + +Generating documentation using Sphinx +===================================== + +Sphinx [#f4]_ has the ability to inspect the signatures and documentation +strings in pybind11-based extension modules to automatically generate beautiful +documentation in a variety formats. The python_example repository [#f5]_ contains a +simple example repository which uses this approach. + +There are two potential gotchas when using this approach: first, make sure that +the resulting strings do not contain any :kbd:`TAB` characters, which break the +docstring parsing routines. You may want to use C++11 raw string literals, +which are convenient for multi-line comments. Conveniently, any excess +indentation will be automatically be removed by Sphinx. However, for this to +work, it is important that all lines are indented consistently, i.e.: + +.. code-block:: cpp + + // ok + m.def("foo", &foo, R"mydelimiter( + The foo function + + Parameters + ---------- + )mydelimiter"); + + // *not ok* + m.def("foo", &foo, R"mydelimiter(The foo function + + Parameters + ---------- + )mydelimiter"); + +By default, pybind11 automatically generates and prepends a signature to the docstring of a function +registered with ``module_::def()`` and ``class_::def()``. Sometimes this +behavior is not desirable, because you want to provide your own signature or remove +the docstring completely to exclude the function from the Sphinx documentation. +The class ``options`` allows you to selectively suppress auto-generated signatures: + +.. code-block:: cpp + + PYBIND11_MODULE(example, m) { + py::options options; + options.disable_function_signatures(); + + m.def("add", [](int a, int b) { return a + b; }, "A function which adds two numbers"); + } + +Note that changes to the settings affect only function bindings created during the +lifetime of the ``options`` instance. When it goes out of scope at the end of the module's init function, +the default settings are restored to prevent unwanted side effects. + +.. [#f4] http://www.sphinx-doc.org +.. [#f5] http://github.com/pybind/python_example + +.. _avoiding-cpp-types-in-docstrings: + +Avoiding C++ types in docstrings +================================ + +Docstrings are generated at the time of the declaration, e.g. when ``.def(...)`` is called. +At this point parameter and return types should be known to pybind11. +If a custom type is not exposed yet through a ``py::class_`` constructor or a custom type caster, +its C++ type name will be used instead to generate the signature in the docstring: + +.. code-block:: text + + | __init__(...) + | __init__(self: example.Foo, arg0: ns::Bar) -> None + ^^^^^^^ + + +This limitation can be circumvented by ensuring that C++ classes are registered with pybind11 +before they are used as a parameter or return type of a function: + +.. code-block:: cpp + + PYBIND11_MODULE(example, m) { + + auto pyFoo = py::class_(m, "Foo"); + auto pyBar = py::class_(m, "Bar"); + + pyFoo.def(py::init()); + pyBar.def(py::init()); + } diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/pycpp/index.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/pycpp/index.rst new file mode 100644 index 0000000000000000000000000000000000000000..6885bdcff1b56bbab5605873ccb1e0676864bb03 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/pycpp/index.rst @@ -0,0 +1,13 @@ +Python C++ interface +#################### + +pybind11 exposes Python types and functions using thin C++ wrappers, which +makes it possible to conveniently call Python code from C++ without resorting +to Python's C API. + +.. toctree:: + :maxdepth: 2 + + object + numpy + utilities diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/pycpp/numpy.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/pycpp/numpy.rst new file mode 100644 index 0000000000000000000000000000000000000000..0a81aa8fd54b94928d5748a04134967e8a5d8875 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/pycpp/numpy.rst @@ -0,0 +1,438 @@ +.. _numpy: + +NumPy +##### + +Buffer protocol +=============== + +Python supports an extremely general and convenient approach for exchanging +data between plugin libraries. Types can expose a buffer view [#f2]_, which +provides fast direct access to the raw internal data representation. Suppose we +want to bind the following simplistic Matrix class: + +.. code-block:: cpp + + class Matrix { + public: + Matrix(size_t rows, size_t cols) : m_rows(rows), m_cols(cols) { + m_data = new float[rows*cols]; + } + float *data() { return m_data; } + size_t rows() const { return m_rows; } + size_t cols() const { return m_cols; } + private: + size_t m_rows, m_cols; + float *m_data; + }; + +The following binding code exposes the ``Matrix`` contents as a buffer object, +making it possible to cast Matrices into NumPy arrays. It is even possible to +completely avoid copy operations with Python expressions like +``np.array(matrix_instance, copy = False)``. + +.. code-block:: cpp + + py::class_(m, "Matrix", py::buffer_protocol()) + .def_buffer([](Matrix &m) -> py::buffer_info { + return py::buffer_info( + m.data(), /* Pointer to buffer */ + sizeof(float), /* Size of one scalar */ + py::format_descriptor::format(), /* Python struct-style format descriptor */ + 2, /* Number of dimensions */ + { m.rows(), m.cols() }, /* Buffer dimensions */ + { sizeof(float) * m.cols(), /* Strides (in bytes) for each index */ + sizeof(float) } + ); + }); + +Supporting the buffer protocol in a new type involves specifying the special +``py::buffer_protocol()`` tag in the ``py::class_`` constructor and calling the +``def_buffer()`` method with a lambda function that creates a +``py::buffer_info`` description record on demand describing a given matrix +instance. The contents of ``py::buffer_info`` mirror the Python buffer protocol +specification. + +.. code-block:: cpp + + struct buffer_info { + void *ptr; + py::ssize_t itemsize; + std::string format; + py::ssize_t ndim; + std::vector shape; + std::vector strides; + }; + +To create a C++ function that can take a Python buffer object as an argument, +simply use the type ``py::buffer`` as one of its arguments. Buffers can exist +in a great variety of configurations, hence some safety checks are usually +necessary in the function body. Below, you can see a basic example on how to +define a custom constructor for the Eigen double precision matrix +(``Eigen::MatrixXd``) type, which supports initialization from compatible +buffer objects (e.g. a NumPy matrix). + +.. code-block:: cpp + + /* Bind MatrixXd (or some other Eigen type) to Python */ + typedef Eigen::MatrixXd Matrix; + + typedef Matrix::Scalar Scalar; + constexpr bool rowMajor = Matrix::Flags & Eigen::RowMajorBit; + + py::class_(m, "Matrix", py::buffer_protocol()) + .def(py::init([](py::buffer b) { + typedef Eigen::Stride Strides; + + /* Request a buffer descriptor from Python */ + py::buffer_info info = b.request(); + + /* Some sanity checks ... */ + if (info.format != py::format_descriptor::format()) + throw std::runtime_error("Incompatible format: expected a double array!"); + + if (info.ndim != 2) + throw std::runtime_error("Incompatible buffer dimension!"); + + auto strides = Strides( + info.strides[rowMajor ? 0 : 1] / (py::ssize_t)sizeof(Scalar), + info.strides[rowMajor ? 1 : 0] / (py::ssize_t)sizeof(Scalar)); + + auto map = Eigen::Map( + static_cast(info.ptr), info.shape[0], info.shape[1], strides); + + return Matrix(map); + })); + +For reference, the ``def_buffer()`` call for this Eigen data type should look +as follows: + +.. code-block:: cpp + + .def_buffer([](Matrix &m) -> py::buffer_info { + return py::buffer_info( + m.data(), /* Pointer to buffer */ + sizeof(Scalar), /* Size of one scalar */ + py::format_descriptor::format(), /* Python struct-style format descriptor */ + 2, /* Number of dimensions */ + { m.rows(), m.cols() }, /* Buffer dimensions */ + { sizeof(Scalar) * (rowMajor ? m.cols() : 1), + sizeof(Scalar) * (rowMajor ? 1 : m.rows()) } + /* Strides (in bytes) for each index */ + ); + }) + +For a much easier approach of binding Eigen types (although with some +limitations), refer to the section on :doc:`/advanced/cast/eigen`. + +.. seealso:: + + The file :file:`tests/test_buffers.cpp` contains a complete example + that demonstrates using the buffer protocol with pybind11 in more detail. + +.. [#f2] http://docs.python.org/3/c-api/buffer.html + +Arrays +====== + +By exchanging ``py::buffer`` with ``py::array`` in the above snippet, we can +restrict the function so that it only accepts NumPy arrays (rather than any +type of Python object satisfying the buffer protocol). + +In many situations, we want to define a function which only accepts a NumPy +array of a certain data type. This is possible via the ``py::array_t`` +template. For instance, the following function requires the argument to be a +NumPy array containing double precision values. + +.. code-block:: cpp + + void f(py::array_t array); + +When it is invoked with a different type (e.g. an integer or a list of +integers), the binding code will attempt to cast the input into a NumPy array +of the requested type. This feature requires the :file:`pybind11/numpy.h` +header to be included. Note that :file:`pybind11/numpy.h` does not depend on +the NumPy headers, and thus can be used without declaring a build-time +dependency on NumPy; NumPy>=1.7.0 is a runtime dependency. + +Data in NumPy arrays is not guaranteed to packed in a dense manner; +furthermore, entries can be separated by arbitrary column and row strides. +Sometimes, it can be useful to require a function to only accept dense arrays +using either the C (row-major) or Fortran (column-major) ordering. This can be +accomplished via a second template argument with values ``py::array::c_style`` +or ``py::array::f_style``. + +.. code-block:: cpp + + void f(py::array_t array); + +The ``py::array::forcecast`` argument is the default value of the second +template parameter, and it ensures that non-conforming arguments are converted +into an array satisfying the specified requirements instead of trying the next +function overload. + +Structured types +================ + +In order for ``py::array_t`` to work with structured (record) types, we first +need to register the memory layout of the type. This can be done via +``PYBIND11_NUMPY_DTYPE`` macro, called in the plugin definition code, which +expects the type followed by field names: + +.. code-block:: cpp + + struct A { + int x; + double y; + }; + + struct B { + int z; + A a; + }; + + // ... + PYBIND11_MODULE(test, m) { + // ... + + PYBIND11_NUMPY_DTYPE(A, x, y); + PYBIND11_NUMPY_DTYPE(B, z, a); + /* now both A and B can be used as template arguments to py::array_t */ + } + +The structure should consist of fundamental arithmetic types, ``std::complex``, +previously registered substructures, and arrays of any of the above. Both C++ +arrays and ``std::array`` are supported. While there is a static assertion to +prevent many types of unsupported structures, it is still the user's +responsibility to use only "plain" structures that can be safely manipulated as +raw memory without violating invariants. + +Vectorizing functions +===================== + +Suppose we want to bind a function with the following signature to Python so +that it can process arbitrary NumPy array arguments (vectors, matrices, general +N-D arrays) in addition to its normal arguments: + +.. code-block:: cpp + + double my_func(int x, float y, double z); + +After including the ``pybind11/numpy.h`` header, this is extremely simple: + +.. code-block:: cpp + + m.def("vectorized_func", py::vectorize(my_func)); + +Invoking the function like below causes 4 calls to be made to ``my_func`` with +each of the array elements. The significant advantage of this compared to +solutions like ``numpy.vectorize()`` is that the loop over the elements runs +entirely on the C++ side and can be crunched down into a tight, optimized loop +by the compiler. The result is returned as a NumPy array of type +``numpy.dtype.float64``. + +.. code-block:: pycon + + >>> x = np.array([[1, 3],[5, 7]]) + >>> y = np.array([[2, 4],[6, 8]]) + >>> z = 3 + >>> result = vectorized_func(x, y, z) + +The scalar argument ``z`` is transparently replicated 4 times. The input +arrays ``x`` and ``y`` are automatically converted into the right types (they +are of type ``numpy.dtype.int64`` but need to be ``numpy.dtype.int32`` and +``numpy.dtype.float32``, respectively). + +.. note:: + + Only arithmetic, complex, and POD types passed by value or by ``const &`` + reference are vectorized; all other arguments are passed through as-is. + Functions taking rvalue reference arguments cannot be vectorized. + +In cases where the computation is too complicated to be reduced to +``vectorize``, it will be necessary to create and access the buffer contents +manually. The following snippet contains a complete example that shows how this +works (the code is somewhat contrived, since it could have been done more +simply using ``vectorize``). + +.. code-block:: cpp + + #include + #include + + namespace py = pybind11; + + py::array_t add_arrays(py::array_t input1, py::array_t input2) { + py::buffer_info buf1 = input1.request(), buf2 = input2.request(); + + if (buf1.ndim != 1 || buf2.ndim != 1) + throw std::runtime_error("Number of dimensions must be one"); + + if (buf1.size != buf2.size) + throw std::runtime_error("Input shapes must match"); + + /* No pointer is passed, so NumPy will allocate the buffer */ + auto result = py::array_t(buf1.size); + + py::buffer_info buf3 = result.request(); + + double *ptr1 = static_cast(buf1.ptr); + double *ptr2 = static_cast(buf2.ptr); + double *ptr3 = static_cast(buf3.ptr); + + for (size_t idx = 0; idx < buf1.shape[0]; idx++) + ptr3[idx] = ptr1[idx] + ptr2[idx]; + + return result; + } + + PYBIND11_MODULE(test, m) { + m.def("add_arrays", &add_arrays, "Add two NumPy arrays"); + } + +.. seealso:: + + The file :file:`tests/test_numpy_vectorize.cpp` contains a complete + example that demonstrates using :func:`vectorize` in more detail. + +Direct access +============= + +For performance reasons, particularly when dealing with very large arrays, it +is often desirable to directly access array elements without internal checking +of dimensions and bounds on every access when indices are known to be already +valid. To avoid such checks, the ``array`` class and ``array_t`` template +class offer an unchecked proxy object that can be used for this unchecked +access through the ``unchecked`` and ``mutable_unchecked`` methods, +where ``N`` gives the required dimensionality of the array: + +.. code-block:: cpp + + m.def("sum_3d", [](py::array_t x) { + auto r = x.unchecked<3>(); // x must have ndim = 3; can be non-writeable + double sum = 0; + for (py::ssize_t i = 0; i < r.shape(0); i++) + for (py::ssize_t j = 0; j < r.shape(1); j++) + for (py::ssize_t k = 0; k < r.shape(2); k++) + sum += r(i, j, k); + return sum; + }); + m.def("increment_3d", [](py::array_t x) { + auto r = x.mutable_unchecked<3>(); // Will throw if ndim != 3 or flags.writeable is false + for (py::ssize_t i = 0; i < r.shape(0); i++) + for (py::ssize_t j = 0; j < r.shape(1); j++) + for (py::ssize_t k = 0; k < r.shape(2); k++) + r(i, j, k) += 1.0; + }, py::arg().noconvert()); + +To obtain the proxy from an ``array`` object, you must specify both the data +type and number of dimensions as template arguments, such as ``auto r = +myarray.mutable_unchecked()``. + +If the number of dimensions is not known at compile time, you can omit the +dimensions template parameter (i.e. calling ``arr_t.unchecked()`` or +``arr.unchecked()``. This will give you a proxy object that works in the +same way, but results in less optimizable code and thus a small efficiency +loss in tight loops. + +Note that the returned proxy object directly references the array's data, and +only reads its shape, strides, and writeable flag when constructed. You must +take care to ensure that the referenced array is not destroyed or reshaped for +the duration of the returned object, typically by limiting the scope of the +returned instance. + +The returned proxy object supports some of the same methods as ``py::array`` so +that it can be used as a drop-in replacement for some existing, index-checked +uses of ``py::array``: + +- ``r.ndim()`` returns the number of dimensions + +- ``r.data(1, 2, ...)`` and ``r.mutable_data(1, 2, ...)``` returns a pointer to + the ``const T`` or ``T`` data, respectively, at the given indices. The + latter is only available to proxies obtained via ``a.mutable_unchecked()``. + +- ``itemsize()`` returns the size of an item in bytes, i.e. ``sizeof(T)``. + +- ``ndim()`` returns the number of dimensions. + +- ``shape(n)`` returns the size of dimension ``n`` + +- ``size()`` returns the total number of elements (i.e. the product of the shapes). + +- ``nbytes()`` returns the number of bytes used by the referenced elements + (i.e. ``itemsize()`` times ``size()``). + +.. seealso:: + + The file :file:`tests/test_numpy_array.cpp` contains additional examples + demonstrating the use of this feature. + +Ellipsis +======== + +Python 3 provides a convenient ``...`` ellipsis notation that is often used to +slice multidimensional arrays. For instance, the following snippet extracts the +middle dimensions of a tensor with the first and last index set to zero. +In Python 2, the syntactic sugar ``...`` is not available, but the singleton +``Ellipsis`` (of type ``ellipsis``) can still be used directly. + +.. code-block:: python + + a = # a NumPy array + b = a[0, ..., 0] + +The function ``py::ellipsis()`` function can be used to perform the same +operation on the C++ side: + +.. code-block:: cpp + + py::array a = /* A NumPy array */; + py::array b = a[py::make_tuple(0, py::ellipsis(), 0)]; + +.. versionchanged:: 2.6 + ``py::ellipsis()`` is now also avaliable in Python 2. + +Memory view +=========== + +For a case when we simply want to provide a direct accessor to C/C++ buffer +without a concrete class object, we can return a ``memoryview`` object. Suppose +we wish to expose a ``memoryview`` for 2x4 uint8_t array, we can do the +following: + +.. code-block:: cpp + + const uint8_t buffer[] = { + 0, 1, 2, 3, + 4, 5, 6, 7 + }; + m.def("get_memoryview2d", []() { + return py::memoryview::from_buffer( + buffer, // buffer pointer + { 2, 4 }, // shape (rows, cols) + { sizeof(uint8_t) * 4, sizeof(uint8_t) } // strides in bytes + ); + }) + +This approach is meant for providing a ``memoryview`` for a C/C++ buffer not +managed by Python. The user is responsible for managing the lifetime of the +buffer. Using a ``memoryview`` created in this way after deleting the buffer in +C++ side results in undefined behavior. + +We can also use ``memoryview::from_memory`` for a simple 1D contiguous buffer: + +.. code-block:: cpp + + m.def("get_memoryview1d", []() { + return py::memoryview::from_memory( + buffer, // buffer pointer + sizeof(uint8_t) * 8 // buffer size + ); + }) + +.. note:: + + ``memoryview::from_memory`` is not available in Python 2. + +.. versionchanged:: 2.6 + ``memoryview::from_memory`` added. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/pycpp/object.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/pycpp/object.rst new file mode 100644 index 0000000000000000000000000000000000000000..6c7525ceaf1842f73e8990aceacfae75a7bbe3b2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/pycpp/object.rst @@ -0,0 +1,251 @@ +Python types +############ + +.. _wrappers: + +Available wrappers +================== + +All major Python types are available as thin C++ wrapper classes. These +can also be used as function parameters -- see :ref:`python_objects_as_args`. + +Available types include :class:`handle`, :class:`object`, :class:`bool_`, +:class:`int_`, :class:`float_`, :class:`str`, :class:`bytes`, :class:`tuple`, +:class:`list`, :class:`dict`, :class:`slice`, :class:`none`, :class:`capsule`, +:class:`iterable`, :class:`iterator`, :class:`function`, :class:`buffer`, +:class:`array`, and :class:`array_t`. + +.. warning:: + + Be sure to review the :ref:`pytypes_gotchas` before using this heavily in + your C++ API. + +.. _casting_back_and_forth: + +Casting back and forth +====================== + +In this kind of mixed code, it is often necessary to convert arbitrary C++ +types to Python, which can be done using :func:`py::cast`: + +.. code-block:: cpp + + MyClass *cls = ..; + py::object obj = py::cast(cls); + +The reverse direction uses the following syntax: + +.. code-block:: cpp + + py::object obj = ...; + MyClass *cls = obj.cast(); + +When conversion fails, both directions throw the exception :class:`cast_error`. + +.. _python_libs: + +Accessing Python libraries from C++ +=================================== + +It is also possible to import objects defined in the Python standard +library or available in the current Python environment (``sys.path``) and work +with these in C++. + +This example obtains a reference to the Python ``Decimal`` class. + +.. code-block:: cpp + + // Equivalent to "from decimal import Decimal" + py::object Decimal = py::module_::import("decimal").attr("Decimal"); + +.. code-block:: cpp + + // Try to import scipy + py::object scipy = py::module_::import("scipy"); + return scipy.attr("__version__"); + + +.. _calling_python_functions: + +Calling Python functions +======================== + +It is also possible to call Python classes, functions and methods +via ``operator()``. + +.. code-block:: cpp + + // Construct a Python object of class Decimal + py::object pi = Decimal("3.14159"); + +.. code-block:: cpp + + // Use Python to make our directories + py::object os = py::module_::import("os"); + py::object makedirs = os.attr("makedirs"); + makedirs("/tmp/path/to/somewhere"); + +One can convert the result obtained from Python to a pure C++ version +if a ``py::class_`` or type conversion is defined. + +.. code-block:: cpp + + py::function f = <...>; + py::object result_py = f(1234, "hello", some_instance); + MyClass &result = result_py.cast(); + +.. _calling_python_methods: + +Calling Python methods +======================== + +To call an object's method, one can again use ``.attr`` to obtain access to the +Python method. + +.. code-block:: cpp + + // Calculate e^π in decimal + py::object exp_pi = pi.attr("exp")(); + py::print(py::str(exp_pi)); + +In the example above ``pi.attr("exp")`` is a *bound method*: it will always call +the method for that same instance of the class. Alternately one can create an +*unbound method* via the Python class (instead of instance) and pass the ``self`` +object explicitly, followed by other arguments. + +.. code-block:: cpp + + py::object decimal_exp = Decimal.attr("exp"); + + // Compute the e^n for n=0..4 + for (int n = 0; n < 5; n++) { + py::print(decimal_exp(Decimal(n)); + } + +Keyword arguments +================= + +Keyword arguments are also supported. In Python, there is the usual call syntax: + +.. code-block:: python + + def f(number, say, to): + ... # function code + + f(1234, say="hello", to=some_instance) # keyword call in Python + +In C++, the same call can be made using: + +.. code-block:: cpp + + using namespace pybind11::literals; // to bring in the `_a` literal + f(1234, "say"_a="hello", "to"_a=some_instance); // keyword call in C++ + +Unpacking arguments +=================== + +Unpacking of ``*args`` and ``**kwargs`` is also possible and can be mixed with +other arguments: + +.. code-block:: cpp + + // * unpacking + py::tuple args = py::make_tuple(1234, "hello", some_instance); + f(*args); + + // ** unpacking + py::dict kwargs = py::dict("number"_a=1234, "say"_a="hello", "to"_a=some_instance); + f(**kwargs); + + // mixed keywords, * and ** unpacking + py::tuple args = py::make_tuple(1234); + py::dict kwargs = py::dict("to"_a=some_instance); + f(*args, "say"_a="hello", **kwargs); + +Generalized unpacking according to PEP448_ is also supported: + +.. code-block:: cpp + + py::dict kwargs1 = py::dict("number"_a=1234); + py::dict kwargs2 = py::dict("to"_a=some_instance); + f(**kwargs1, "say"_a="hello", **kwargs2); + +.. seealso:: + + The file :file:`tests/test_pytypes.cpp` contains a complete + example that demonstrates passing native Python types in more detail. The + file :file:`tests/test_callbacks.cpp` presents a few examples of calling + Python functions from C++, including keywords arguments and unpacking. + +.. _PEP448: https://www.python.org/dev/peps/pep-0448/ + +.. _implicit_casting: + +Implicit casting +================ + +When using the C++ interface for Python types, or calling Python functions, +objects of type :class:`object` are returned. It is possible to invoke implicit +conversions to subclasses like :class:`dict`. The same holds for the proxy objects +returned by ``operator[]`` or ``obj.attr()``. +Casting to subtypes improves code readability and allows values to be passed to +C++ functions that require a specific subtype rather than a generic :class:`object`. + +.. code-block:: cpp + + #include + using namespace pybind11::literals; + + py::module_ os = py::module_::import("os"); + py::module_ path = py::module_::import("os.path"); // like 'import os.path as path' + py::module_ np = py::module_::import("numpy"); // like 'import numpy as np' + + py::str curdir_abs = path.attr("abspath")(path.attr("curdir")); + py::print(py::str("Current directory: ") + curdir_abs); + py::dict environ = os.attr("environ"); + py::print(environ["HOME"]); + py::array_t arr = np.attr("ones")(3, "dtype"_a="float32"); + py::print(py::repr(arr + py::int_(1))); + +These implicit conversions are available for subclasses of :class:`object`; there +is no need to call ``obj.cast()`` explicitly as for custom classes, see +:ref:`casting_back_and_forth`. + +.. note:: + If a trivial conversion via move constructor is not possible, both implicit and + explicit casting (calling ``obj.cast()``) will attempt a "rich" conversion. + For instance, ``py::list env = os.attr("environ");`` will succeed and is + equivalent to the Python code ``env = list(os.environ)`` that produces a + list of the dict keys. + +.. TODO: Adapt text once PR #2349 has landed + +Handling exceptions +=================== + +Python exceptions from wrapper classes will be thrown as a ``py::error_already_set``. +See :ref:`Handling exceptions from Python in C++ +` for more information on handling exceptions +raised when calling C++ wrapper classes. + +.. _pytypes_gotchas: + +Gotchas +======= + +Default-Constructed Wrappers +---------------------------- + +When a wrapper type is default-constructed, it is **not** a valid Python object (i.e. it is not ``py::none()``). It is simply the same as +``PyObject*`` null pointer. To check for this, use +``static_cast(my_wrapper)``. + +Assigning py::none() to wrappers +-------------------------------- + +You may be tempted to use types like ``py::str`` and ``py::dict`` in C++ +signatures (either pure C++, or in bound signatures), and assign them default +values of ``py::none()``. However, in a best case scenario, it will fail fast +because ``None`` is not convertible to that type (e.g. ``py::dict``), or in a +worse case scenario, it will silently work but corrupt the types you want to +work with (e.g. ``py::str(py::none())`` will yield ``"None"`` in Python). diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/pycpp/utilities.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/pycpp/utilities.rst new file mode 100644 index 0000000000000000000000000000000000000000..c15051fb96ac0d2bfe74e027d6c127e112f04aa2 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/pycpp/utilities.rst @@ -0,0 +1,144 @@ +Utilities +######### + +Using Python's print function in C++ +==================================== + +The usual way to write output in C++ is using ``std::cout`` while in Python one +would use ``print``. Since these methods use different buffers, mixing them can +lead to output order issues. To resolve this, pybind11 modules can use the +:func:`py::print` function which writes to Python's ``sys.stdout`` for consistency. + +Python's ``print`` function is replicated in the C++ API including optional +keyword arguments ``sep``, ``end``, ``file``, ``flush``. Everything works as +expected in Python: + +.. code-block:: cpp + + py::print(1, 2.0, "three"); // 1 2.0 three + py::print(1, 2.0, "three", "sep"_a="-"); // 1-2.0-three + + auto args = py::make_tuple("unpacked", true); + py::print("->", *args, "end"_a="<-"); // -> unpacked True <- + +.. _ostream_redirect: + +Capturing standard output from ostream +====================================== + +Often, a library will use the streams ``std::cout`` and ``std::cerr`` to print, +but this does not play well with Python's standard ``sys.stdout`` and ``sys.stderr`` +redirection. Replacing a library's printing with `py::print ` may not +be feasible. This can be fixed using a guard around the library function that +redirects output to the corresponding Python streams: + +.. code-block:: cpp + + #include + + ... + + // Add a scoped redirect for your noisy code + m.def("noisy_func", []() { + py::scoped_ostream_redirect stream( + std::cout, // std::ostream& + py::module_::import("sys").attr("stdout") // Python output + ); + call_noisy_func(); + }); + +This method respects flushes on the output streams and will flush if needed +when the scoped guard is destroyed. This allows the output to be redirected in +real time, such as to a Jupyter notebook. The two arguments, the C++ stream and +the Python output, are optional, and default to standard output if not given. An +extra type, `py::scoped_estream_redirect `, is identical +except for defaulting to ``std::cerr`` and ``sys.stderr``; this can be useful with +`py::call_guard`, which allows multiple items, but uses the default constructor: + +.. code-block:: py + + // Alternative: Call single function using call guard + m.def("noisy_func", &call_noisy_function, + py::call_guard()); + +The redirection can also be done in Python with the addition of a context +manager, using the `py::add_ostream_redirect() ` function: + +.. code-block:: cpp + + py::add_ostream_redirect(m, "ostream_redirect"); + +The name in Python defaults to ``ostream_redirect`` if no name is passed. This +creates the following context manager in Python: + +.. code-block:: python + + with ostream_redirect(stdout=True, stderr=True): + noisy_function() + +It defaults to redirecting both streams, though you can use the keyword +arguments to disable one of the streams if needed. + +.. note:: + + The above methods will not redirect C-level output to file descriptors, such + as ``fprintf``. For those cases, you'll need to redirect the file + descriptors either directly in C or with Python's ``os.dup2`` function + in an operating-system dependent way. + +.. _eval: + +Evaluating Python expressions from strings and files +==================================================== + +pybind11 provides the `eval`, `exec` and `eval_file` functions to evaluate +Python expressions and statements. The following example illustrates how they +can be used. + +.. code-block:: cpp + + // At beginning of file + #include + + ... + + // Evaluate in scope of main module + py::object scope = py::module_::import("__main__").attr("__dict__"); + + // Evaluate an isolated expression + int result = py::eval("my_variable + 10", scope).cast(); + + // Evaluate a sequence of statements + py::exec( + "print('Hello')\n" + "print('world!');", + scope); + + // Evaluate the statements in an separate Python file on disk + py::eval_file("script.py", scope); + +C++11 raw string literals are also supported and quite handy for this purpose. +The only requirement is that the first statement must be on a new line following +the raw string delimiter ``R"(``, ensuring all lines have common leading indent: + +.. code-block:: cpp + + py::exec(R"( + x = get_answer() + if x == 42: + print('Hello World!') + else: + print('Bye!') + )", scope + ); + +.. note:: + + `eval` and `eval_file` accept a template parameter that describes how the + string/file should be interpreted. Possible choices include ``eval_expr`` + (isolated expression), ``eval_single_statement`` (a single statement, return + value is always ``none``), and ``eval_statements`` (sequence of statements, + return value is always ``none``). `eval` defaults to ``eval_expr``, + `eval_file` defaults to ``eval_statements`` and `exec` is just a shortcut + for ``eval``. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/smart_ptrs.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/smart_ptrs.rst new file mode 100644 index 0000000000000000000000000000000000000000..da57748ca585a92000198a6c607a087704b1f07c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/advanced/smart_ptrs.rst @@ -0,0 +1,173 @@ +Smart pointers +############## + +std::unique_ptr +=============== + +Given a class ``Example`` with Python bindings, it's possible to return +instances wrapped in C++11 unique pointers, like so + +.. code-block:: cpp + + std::unique_ptr create_example() { return std::unique_ptr(new Example()); } + +.. code-block:: cpp + + m.def("create_example", &create_example); + +In other words, there is nothing special that needs to be done. While returning +unique pointers in this way is allowed, it is *illegal* to use them as function +arguments. For instance, the following function signature cannot be processed +by pybind11. + +.. code-block:: cpp + + void do_something_with_example(std::unique_ptr ex) { ... } + +The above signature would imply that Python needs to give up ownership of an +object that is passed to this function, which is generally not possible (for +instance, the object might be referenced elsewhere). + +std::shared_ptr +=============== + +The binding generator for classes, :class:`class_`, can be passed a template +type that denotes a special *holder* type that is used to manage references to +the object. If no such holder type template argument is given, the default for +a type named ``Type`` is ``std::unique_ptr``, which means that the object +is deallocated when Python's reference count goes to zero. + +It is possible to switch to other types of reference counting wrappers or smart +pointers, which is useful in codebases that rely on them. For instance, the +following snippet causes ``std::shared_ptr`` to be used instead. + +.. code-block:: cpp + + py::class_ /* <- holder type */> obj(m, "Example"); + +Note that any particular class can only be associated with a single holder type. + +One potential stumbling block when using holder types is that they need to be +applied consistently. Can you guess what's broken about the following binding +code? + +.. code-block:: cpp + + class Child { }; + + class Parent { + public: + Parent() : child(std::make_shared()) { } + Child *get_child() { return child.get(); } /* Hint: ** DON'T DO THIS ** */ + private: + std::shared_ptr child; + }; + + PYBIND11_MODULE(example, m) { + py::class_>(m, "Child"); + + py::class_>(m, "Parent") + .def(py::init<>()) + .def("get_child", &Parent::get_child); + } + +The following Python code will cause undefined behavior (and likely a +segmentation fault). + +.. code-block:: python + + from example import Parent + print(Parent().get_child()) + +The problem is that ``Parent::get_child()`` returns a pointer to an instance of +``Child``, but the fact that this instance is already managed by +``std::shared_ptr<...>`` is lost when passing raw pointers. In this case, +pybind11 will create a second independent ``std::shared_ptr<...>`` that also +claims ownership of the pointer. In the end, the object will be freed **twice** +since these shared pointers have no way of knowing about each other. + +There are two ways to resolve this issue: + +1. For types that are managed by a smart pointer class, never use raw pointers + in function arguments or return values. In other words: always consistently + wrap pointers into their designated holder types (such as + ``std::shared_ptr<...>``). In this case, the signature of ``get_child()`` + should be modified as follows: + +.. code-block:: cpp + + std::shared_ptr get_child() { return child; } + +2. Adjust the definition of ``Child`` by specifying + ``std::enable_shared_from_this`` (see cppreference_ for details) as a + base class. This adds a small bit of information to ``Child`` that allows + pybind11 to realize that there is already an existing + ``std::shared_ptr<...>`` and communicate with it. In this case, the + declaration of ``Child`` should look as follows: + +.. _cppreference: http://en.cppreference.com/w/cpp/memory/enable_shared_from_this + +.. code-block:: cpp + + class Child : public std::enable_shared_from_this { }; + +.. _smart_pointers: + +Custom smart pointers +===================== + +pybind11 supports ``std::unique_ptr`` and ``std::shared_ptr`` right out of the +box. For any other custom smart pointer, transparent conversions can be enabled +using a macro invocation similar to the following. It must be declared at the +top namespace level before any binding code: + +.. code-block:: cpp + + PYBIND11_DECLARE_HOLDER_TYPE(T, SmartPtr); + +The first argument of :func:`PYBIND11_DECLARE_HOLDER_TYPE` should be a +placeholder name that is used as a template parameter of the second argument. +Thus, feel free to use any identifier, but use it consistently on both sides; +also, don't use the name of a type that already exists in your codebase. + +The macro also accepts a third optional boolean parameter that is set to false +by default. Specify + +.. code-block:: cpp + + PYBIND11_DECLARE_HOLDER_TYPE(T, SmartPtr, true); + +if ``SmartPtr`` can always be initialized from a ``T*`` pointer without the +risk of inconsistencies (such as multiple independent ``SmartPtr`` instances +believing that they are the sole owner of the ``T*`` pointer). A common +situation where ``true`` should be passed is when the ``T`` instances use +*intrusive* reference counting. + +Please take a look at the :ref:`macro_notes` before using this feature. + +By default, pybind11 assumes that your custom smart pointer has a standard +interface, i.e. provides a ``.get()`` member function to access the underlying +raw pointer. If this is not the case, pybind11's ``holder_helper`` must be +specialized: + +.. code-block:: cpp + + // Always needed for custom holder types + PYBIND11_DECLARE_HOLDER_TYPE(T, SmartPtr); + + // Only needed if the type's `.get()` goes by another name + namespace pybind11 { namespace detail { + template + struct holder_helper> { // <-- specialization + static const T *get(const SmartPtr &p) { return p.getPointer(); } + }; + }} + +The above specialization informs pybind11 that the custom ``SmartPtr`` class +provides ``.get()`` functionality via ``.getPointer()``. + +.. seealso:: + + The file :file:`tests/test_smart_ptr.cpp` contains a complete example + that demonstrates how to work with custom reference-counting holder types + in more detail. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/basics.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/basics.rst new file mode 100644 index 0000000000000000000000000000000000000000..0b1d85cfd3984f448fd9b07b4dc67bc3709be390 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/basics.rst @@ -0,0 +1,308 @@ +.. _basics: + +First steps +########### + +This sections demonstrates the basic features of pybind11. Before getting +started, make sure that development environment is set up to compile the +included set of test cases. + + +Compiling the test cases +======================== + +Linux/macOS +----------- + +On Linux you'll need to install the **python-dev** or **python3-dev** packages as +well as **cmake**. On macOS, the included python version works out of the box, +but **cmake** must still be installed. + +After installing the prerequisites, run + +.. code-block:: bash + + mkdir build + cd build + cmake .. + make check -j 4 + +The last line will both compile and run the tests. + +Windows +------- + +On Windows, only **Visual Studio 2015** and newer are supported since pybind11 relies +on various C++11 language features that break older versions of Visual Studio. + +.. Note:: + + To use the C++17 in Visual Studio 2017 (MSVC 14.1), pybind11 requires the flag + ``/permissive-`` to be passed to the compiler `to enforce standard conformance`_. When + building with Visual Studio 2019, this is not strictly necessary, but still advised. + +.. _`to enforce standard conformance`: https://docs.microsoft.com/en-us/cpp/build/reference/permissive-standards-conformance?view=vs-2017 + +To compile and run the tests: + +.. code-block:: batch + + mkdir build + cd build + cmake .. + cmake --build . --config Release --target check + +This will create a Visual Studio project, compile and run the target, all from the +command line. + +.. Note:: + + If all tests fail, make sure that the Python binary and the testcases are compiled + for the same processor type and bitness (i.e. either **i386** or **x86_64**). You + can specify **x86_64** as the target architecture for the generated Visual Studio + project using ``cmake -A x64 ..``. + +.. seealso:: + + Advanced users who are already familiar with Boost.Python may want to skip + the tutorial and look at the test cases in the :file:`tests` directory, + which exercise all features of pybind11. + +Header and namespace conventions +================================ + +For brevity, all code examples assume that the following two lines are present: + +.. code-block:: cpp + + #include + + namespace py = pybind11; + +Some features may require additional headers, but those will be specified as needed. + +.. _simple_example: + +Creating bindings for a simple function +======================================= + +Let's start by creating Python bindings for an extremely simple function, which +adds two numbers and returns their result: + +.. code-block:: cpp + + int add(int i, int j) { + return i + j; + } + +For simplicity [#f1]_, we'll put both this function and the binding code into +a file named :file:`example.cpp` with the following contents: + +.. code-block:: cpp + + #include + + int add(int i, int j) { + return i + j; + } + + PYBIND11_MODULE(example, m) { + m.doc() = "pybind11 example plugin"; // optional module docstring + + m.def("add", &add, "A function which adds two numbers"); + } + +.. [#f1] In practice, implementation and binding code will generally be located + in separate files. + +The :func:`PYBIND11_MODULE` macro creates a function that will be called when an +``import`` statement is issued from within Python. The module name (``example``) +is given as the first macro argument (it should not be in quotes). The second +argument (``m``) defines a variable of type :class:`py::module_ ` which +is the main interface for creating bindings. The method :func:`module_::def` +generates binding code that exposes the ``add()`` function to Python. + +.. note:: + + Notice how little code was needed to expose our function to Python: all + details regarding the function's parameters and return value were + automatically inferred using template metaprogramming. This overall + approach and the used syntax are borrowed from Boost.Python, though the + underlying implementation is very different. + +pybind11 is a header-only library, hence it is not necessary to link against +any special libraries and there are no intermediate (magic) translation steps. +On Linux, the above example can be compiled using the following command: + +.. code-block:: bash + + $ c++ -O3 -Wall -shared -std=c++11 -fPIC $(python3 -m pybind11 --includes) example.cpp -o example$(python3-config --extension-suffix) + +.. note:: + + If you used :ref:`include_as_a_submodule` to get the pybind11 source, then + use ``$(python3-config --includes) -Iextern/pybind11/include`` instead of + ``$(python3 -m pybind11 --includes)`` in the above compilation, as + explained in :ref:`building_manually`. + +For more details on the required compiler flags on Linux and macOS, see +:ref:`building_manually`. For complete cross-platform compilation instructions, +refer to the :ref:`compiling` page. + +The `python_example`_ and `cmake_example`_ repositories are also a good place +to start. They are both complete project examples with cross-platform build +systems. The only difference between the two is that `python_example`_ uses +Python's ``setuptools`` to build the module, while `cmake_example`_ uses CMake +(which may be preferable for existing C++ projects). + +.. _python_example: https://github.com/pybind/python_example +.. _cmake_example: https://github.com/pybind/cmake_example + +Building the above C++ code will produce a binary module file that can be +imported to Python. Assuming that the compiled module is located in the +current directory, the following interactive Python session shows how to +load and execute the example: + +.. code-block:: pycon + + $ python + Python 2.7.10 (default, Aug 22 2015, 20:33:39) + [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.1)] on darwin + Type "help", "copyright", "credits" or "license" for more information. + >>> import example + >>> example.add(1, 2) + 3L + >>> + +.. _keyword_args: + +Keyword arguments +================= + +With a simple code modification, it is possible to inform Python about the +names of the arguments ("i" and "j" in this case). + +.. code-block:: cpp + + m.def("add", &add, "A function which adds two numbers", + py::arg("i"), py::arg("j")); + +:class:`arg` is one of several special tag classes which can be used to pass +metadata into :func:`module_::def`. With this modified binding code, we can now +call the function using keyword arguments, which is a more readable alternative +particularly for functions taking many parameters: + +.. code-block:: pycon + + >>> import example + >>> example.add(i=1, j=2) + 3L + +The keyword names also appear in the function signatures within the documentation. + +.. code-block:: pycon + + >>> help(example) + + .... + + FUNCTIONS + add(...) + Signature : (i: int, j: int) -> int + + A function which adds two numbers + +A shorter notation for named arguments is also available: + +.. code-block:: cpp + + // regular notation + m.def("add1", &add, py::arg("i"), py::arg("j")); + // shorthand + using namespace pybind11::literals; + m.def("add2", &add, "i"_a, "j"_a); + +The :var:`_a` suffix forms a C++11 literal which is equivalent to :class:`arg`. +Note that the literal operator must first be made visible with the directive +``using namespace pybind11::literals``. This does not bring in anything else +from the ``pybind11`` namespace except for literals. + +.. _default_args: + +Default arguments +================= + +Suppose now that the function to be bound has default arguments, e.g.: + +.. code-block:: cpp + + int add(int i = 1, int j = 2) { + return i + j; + } + +Unfortunately, pybind11 cannot automatically extract these parameters, since they +are not part of the function's type information. However, they are simple to specify +using an extension of :class:`arg`: + +.. code-block:: cpp + + m.def("add", &add, "A function which adds two numbers", + py::arg("i") = 1, py::arg("j") = 2); + +The default values also appear within the documentation. + +.. code-block:: pycon + + >>> help(example) + + .... + + FUNCTIONS + add(...) + Signature : (i: int = 1, j: int = 2) -> int + + A function which adds two numbers + +The shorthand notation is also available for default arguments: + +.. code-block:: cpp + + // regular notation + m.def("add1", &add, py::arg("i") = 1, py::arg("j") = 2); + // shorthand + m.def("add2", &add, "i"_a=1, "j"_a=2); + +Exporting variables +=================== + +To expose a value from C++, use the ``attr`` function to register it in a +module as shown below. Built-in types and general objects (more on that later) +are automatically converted when assigned as attributes, and can be explicitly +converted using the function ``py::cast``. + +.. code-block:: cpp + + PYBIND11_MODULE(example, m) { + m.attr("the_answer") = 42; + py::object world = py::cast("World"); + m.attr("what") = world; + } + +These are then accessible from Python: + +.. code-block:: pycon + + >>> import example + >>> example.the_answer + 42 + >>> example.what + 'World' + +.. _supported_types: + +Supported data types +==================== + +A large number of data types are supported out of the box and can be used +seamlessly as functions arguments, return values or with ``py::cast`` in general. +For a full overview, see the :doc:`advanced/cast/index` section. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/benchmark.py b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/benchmark.py new file mode 100644 index 0000000000000000000000000000000000000000..33d78fb4e6dc7bd1b99ed5647d33660c80d064b0 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/benchmark.py @@ -0,0 +1,92 @@ +# -*- coding: utf-8 -*- +import random +import os +import time +import datetime as dt + +nfns = 4 # Functions per class +nargs = 4 # Arguments per function + + +def generate_dummy_code_pybind11(nclasses=10): + decl = "" + bindings = "" + + for cl in range(nclasses): + decl += "class cl%03i;\n" % cl + decl += "\n" + + for cl in range(nclasses): + decl += "class cl%03i {\n" % cl + decl += "public:\n" + bindings += ' py::class_(m, "cl%03i")\n' % (cl, cl) + for fn in range(nfns): + ret = random.randint(0, nclasses - 1) + params = [random.randint(0, nclasses - 1) for i in range(nargs)] + decl += " cl%03i *fn_%03i(" % (ret, fn) + decl += ", ".join("cl%03i *" % p for p in params) + decl += ");\n" + bindings += ' .def("fn_%03i", &cl%03i::fn_%03i)\n' % (fn, cl, fn) + decl += "};\n\n" + bindings += " ;\n" + + result = "#include \n\n" + result += "namespace py = pybind11;\n\n" + result += decl + "\n" + result += "PYBIND11_MODULE(example, m) {\n" + result += bindings + result += "}" + return result + + +def generate_dummy_code_boost(nclasses=10): + decl = "" + bindings = "" + + for cl in range(nclasses): + decl += "class cl%03i;\n" % cl + decl += "\n" + + for cl in range(nclasses): + decl += "class cl%03i {\n" % cl + decl += "public:\n" + bindings += ' py::class_("cl%03i")\n' % (cl, cl) + for fn in range(nfns): + ret = random.randint(0, nclasses - 1) + params = [random.randint(0, nclasses - 1) for i in range(nargs)] + decl += " cl%03i *fn_%03i(" % (ret, fn) + decl += ", ".join("cl%03i *" % p for p in params) + decl += ");\n" + bindings += ( + ' .def("fn_%03i", &cl%03i::fn_%03i, py::return_value_policy())\n' + % (fn, cl, fn) + ) + decl += "};\n\n" + bindings += " ;\n" + + result = "#include \n\n" + result += "namespace py = boost::python;\n\n" + result += decl + "\n" + result += "BOOST_PYTHON_MODULE(example) {\n" + result += bindings + result += "}" + return result + + +for codegen in [generate_dummy_code_pybind11, generate_dummy_code_boost]: + print("{") + for i in range(0, 10): + nclasses = 2 ** i + with open("test.cpp", "w") as f: + f.write(codegen(nclasses)) + n1 = dt.datetime.now() + os.system( + "g++ -Os -shared -rdynamic -undefined dynamic_lookup " + "-fvisibility=hidden -std=c++14 test.cpp -I include " + "-I /System/Library/Frameworks/Python.framework/Headers -o test.so" + ) + n2 = dt.datetime.now() + elapsed = (n2 - n1).total_seconds() + size = os.stat("test.so").st_size + print(" {%i, %f, %i}," % (nclasses * nfns, elapsed, size)) + print("}") diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/benchmark.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/benchmark.rst new file mode 100644 index 0000000000000000000000000000000000000000..02c2ccde7dc00db1e57b73a7523521f9c39a5639 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/benchmark.rst @@ -0,0 +1,95 @@ +Benchmark +========= + +The following is the result of a synthetic benchmark comparing both compilation +time and module size of pybind11 against Boost.Python. A detailed report about a +Boost.Python to pybind11 conversion of a real project is available here: [#f1]_. + +.. [#f1] http://graylab.jhu.edu/RosettaCon2016/PyRosetta-4.pdf + +Setup +----- + +A python script (see the ``docs/benchmark.py`` file) was used to generate a set +of files with dummy classes whose count increases for each successive benchmark +(between 1 and 2048 classes in powers of two). Each class has four methods with +a randomly generated signature with a return value and four arguments. (There +was no particular reason for this setup other than the desire to generate many +unique function signatures whose count could be controlled in a simple way.) + +Here is an example of the binding code for one class: + +.. code-block:: cpp + + ... + class cl034 { + public: + cl279 *fn_000(cl084 *, cl057 *, cl065 *, cl042 *); + cl025 *fn_001(cl098 *, cl262 *, cl414 *, cl121 *); + cl085 *fn_002(cl445 *, cl297 *, cl145 *, cl421 *); + cl470 *fn_003(cl200 *, cl323 *, cl332 *, cl492 *); + }; + ... + + PYBIND11_MODULE(example, m) { + ... + py::class_(m, "cl034") + .def("fn_000", &cl034::fn_000) + .def("fn_001", &cl034::fn_001) + .def("fn_002", &cl034::fn_002) + .def("fn_003", &cl034::fn_003) + ... + } + +The Boost.Python version looks almost identical except that a return value +policy had to be specified as an argument to ``def()``. For both libraries, +compilation was done with + +.. code-block:: bash + + Apple LLVM version 7.0.2 (clang-700.1.81) + +and the following compilation flags + +.. code-block:: bash + + g++ -Os -shared -rdynamic -undefined dynamic_lookup -fvisibility=hidden -std=c++14 + +Compilation time +---------------- + +The following log-log plot shows how the compilation time grows for an +increasing number of class and function declarations. pybind11 includes many +fewer headers, which initially leads to shorter compilation times, but the +performance is ultimately fairly similar (pybind11 is 19.8 seconds faster for +the largest largest file with 2048 classes and a total of 8192 methods -- a +modest **1.2x** speedup relative to Boost.Python, which required 116.35 +seconds). + +.. only:: not latex + + .. image:: pybind11_vs_boost_python1.svg + +.. only:: latex + + .. image:: pybind11_vs_boost_python1.png + +Module size +----------- + +Differences between the two libraries become much more pronounced when +considering the file size of the generated Python plugin: for the largest file, +the binary generated by Boost.Python required 16.8 MiB, which was **2.17 +times** / **9.1 megabytes** larger than the output generated by pybind11. For +very small inputs, Boost.Python has an edge in the plot below -- however, note +that it stores many definitions in an external library, whose size was not +included here, hence the comparison is slightly shifted in Boost.Python's +favor. + +.. only:: not latex + + .. image:: pybind11_vs_boost_python2.svg + +.. only:: latex + + .. image:: pybind11_vs_boost_python2.png diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/changelog.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/changelog.rst new file mode 100644 index 0000000000000000000000000000000000000000..84f1352fb9d581281664cb0a640144b9b452c540 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/changelog.rst @@ -0,0 +1,1679 @@ +.. _changelog: + +Changelog +######### + +Starting with version 1.8.0, pybind11 releases use a `semantic versioning +`_ policy. + +v2.7.0 (TBA, not yet released) +------------------------------ + +* ``py::str`` changed to exclusively hold `PyUnicodeObject`. Previously + ``py::str`` could also hold `bytes`, which is probably surprising, was + never documented, and can mask bugs (e.g. accidental use of ``py::str`` + instead of ``py::bytes``). + `#2409 `_ + + +v2.6.2 (Jan 26, 2021) +--------------------- + +Minor missing functionality added: + +* enum: add missing Enum.value property. + `#2739 `_ + +* Allow thread termination to be avoided during shutdown for CPython 3.7+ via + ``.disarm`` for ``gil_scoped_acquire``/``gil_scoped_release``. + `#2657 `_ + +Fixed or improved behavior in a few special cases: + +* Fix bug where the constructor of ``object`` subclasses would not throw on + being passed a Python object of the wrong type. + `#2701 `_ + +* The ``type_caster`` for integers does not convert Python objects with + ``__int__`` anymore with ``noconvert`` or during the first round of trying + overloads. + `#2698 `_ + +* When casting to a C++ integer, ``__index__`` is always called and not + considered as conversion, consistent with Python 3.8+. + `#2801 `_ + +Build improvements: + +* Setup helpers: ``extra_compile_args`` and ``extra_link_args`` automatically set by + Pybind11Extension are now prepended, which allows them to be overridden + by user-set ``extra_compile_args`` and ``extra_link_args``. + `#2808 `_ + +* Setup helpers: Don't trigger unused parameter warning. + `#2735 `_ + +* CMake: Support running with ``--warn-uninitialized`` active. + `#2806 `_ + +* CMake: Avoid error if included from two submodule directories. + `#2804 `_ + +* CMake: Fix ``STATIC`` / ``SHARED`` being ignored in FindPython mode. + `#2796 `_ + +* CMake: Respect the setting for ``CMAKE_CXX_VISIBILITY_PRESET`` if defined. + `#2793 `_ + +* CMake: Fix issue with FindPython2/FindPython3 not working with ``pybind11::embed``. + `#2662 `_ + +* CMake: mixing local and installed pybind11's would prioritize the installed + one over the local one (regression in 2.6.0). + `#2716 `_ + + +Bug fixes: + +* Fixed segfault in multithreaded environments when using + ``scoped_ostream_redirect``. + `#2675 `_ + +* Leave docstring unset when all docstring-related options are disabled, rather + than set an empty string. + `#2745 `_ + +* The module key in builtins that pybind11 uses to store its internals changed + from std::string to a python str type (more natural on Python 2, no change on + Python 3). + `#2814 `_ + +* Fixed assertion error related to unhandled (later overwritten) exception in + CPython 3.8 and 3.9 debug builds. + `#2685 `_ + +* Fix ``py::gil_scoped_acquire`` assert with CPython 3.9 debug build. + `#2683 `_ + +* Fix issue with a test failing on PyTest 6.2. + `#2741 `_ + +Warning fixes: + +* Fix warning modifying constructor parameter 'flag' that shadows a field of + 'set_flag' ``[-Wshadow-field-in-constructor-modified]``. + `#2780 `_ + +* Suppressed some deprecation warnings about old-style + ``__init__``/``__setstate__`` in the tests. + `#2759 `_ + +Valgrind work: + +* Fix invalid access when calling a pybind11 ``__init__`` on a non-pybind11 + class instance. + `#2755 `_ + +* Fixed various minor memory leaks in pybind11's test suite. + `#2758 `_ + +* Resolved memory leak in cpp_function initialization when exceptions occurred. + `#2756 `_ + +* Added a Valgrind build, checking for leaks and memory-related UB, to CI. + `#2746 `_ + +Compiler support: + +* Intel compiler was not activating C++14 support due to a broken define. + `#2679 `_ + +* Support ICC and NVIDIA HPC SDK in C++17 mode. + `#2729 `_ + +* Support Intel OneAPI compiler (ICC 20.2) and add to CI. + `#2573 `_ + + + +v2.6.1 (Nov 11, 2020) +--------------------- + +* ``py::exec``, ``py::eval``, and ``py::eval_file`` now add the builtins module + as ``"__builtins__"`` to their ``globals`` argument, better matching ``exec`` + and ``eval`` in pure Python. + `#2616 `_ + +* ``setup_helpers`` will no longer set a minimum macOS version higher than the + current version. + `#2622 `_ + +* Allow deleting static properties. + `#2629 `_ + +* Seal a leak in ``def_buffer``, cleaning up the ``capture`` object after the + ``class_`` object goes out of scope. + `#2634 `_ + +* ``pybind11_INCLUDE_DIRS`` was incorrect, potentially causing a regression if + it was expected to include ``PYTHON_INCLUDE_DIRS`` (please use targets + instead). + `#2636 `_ + +* Added parameter names to the ``py::enum_`` constructor and methods, avoiding + ``arg0`` in the generated docstrings. + `#2637 `_ + +* Added ``needs_recompile`` optional function to the ``ParallelCompiler`` + helper, to allow a recompile to be skipped based on a user-defined function. + `#2643 `_ + + +v2.6.0 (Oct 21, 2020) +--------------------- + +See :ref:`upgrade-guide-2.6` for help upgrading to the new version. + +New features: + +* Keyword-only arguments supported in Python 2 or 3 with ``py::kw_only()``. + `#2100 `_ + +* Positional-only arguments supported in Python 2 or 3 with ``py::pos_only()``. + `#2459 `_ + +* ``py::is_final()`` class modifier to block subclassing (CPython only). + `#2151 `_ + +* Added ``py::prepend()``, allowing a function to be placed at the beginning of + the overload chain. + `#1131 `_ + +* Access to the type object now provided with ``py::type::of()`` and + ``py::type::of(h)``. + `#2364 `_ + +* Perfect forwarding support for methods. + `#2048 `_ + +* Added ``py::error_already_set::discard_as_unraisable()``. + `#2372 `_ + +* ``py::hash`` is now public. + `#2217 `_ + +* ``py::class_`` is now supported. Note that writing to one data + member of the union and reading another (type punning) is UB in C++. Thus + pybind11-bound enums should never be used for such conversions. + `#2320 `_. + +* Classes now check local scope when registering members, allowing a subclass + to have a member with the same name as a parent (such as an enum). + `#2335 `_ + +Code correctness features: + +* Error now thrown when ``__init__`` is forgotten on subclasses. + `#2152 `_ + +* Throw error if conversion to a pybind11 type if the Python object isn't a + valid instance of that type, such as ``py::bytes(o)`` when ``py::object o`` + isn't a bytes instance. + `#2349 `_ + +* Throw if conversion to ``str`` fails. + `#2477 `_ + + +API changes: + +* ``py::module`` was renamed ``py::module_`` to avoid issues with C++20 when + used unqualified, but an alias ``py::module`` is provided for backward + compatibility. + `#2489 `_ + +* Public constructors for ``py::module_`` have been deprecated; please use + ``pybind11::module_::create_extension_module`` if you were using the public + constructor (fairly rare after ``PYBIND11_MODULE`` was introduced). + `#2552 `_ + +* ``PYBIND11_OVERLOAD*`` macros and ``get_overload`` function replaced by + correctly-named ``PYBIND11_OVERRIDE*`` and ``get_override``, fixing + inconsistencies in the presence of a closing ``;`` in these macros. + ``get_type_overload`` is deprecated. + `#2325 `_ + +Packaging / building improvements: + +* The Python package was reworked to be more powerful and useful. + `#2433 `_ + + * :ref:`build-setuptools` is easier thanks to a new + ``pybind11.setup_helpers`` module, which provides utilities to use + setuptools with pybind11. It can be used via PEP 518, ``setup_requires``, + or by directly importing or copying ``setup_helpers.py`` into your project. + + * CMake configuration files are now included in the Python package. Use + ``pybind11.get_cmake_dir()`` or ``python -m pybind11 --cmakedir`` to get + the directory with the CMake configuration files, or include the + site-packages location in your ``CMAKE_MODULE_PATH``. Or you can use the + new ``pybind11[global]`` extra when you install ``pybind11``, which + installs the CMake files and headers into your base environment in the + standard location. + + * ``pybind11-config`` is another way to write ``python -m pybind11`` if you + have your PATH set up. + + * Added external typing support to the helper module, code from + ``import pybind11`` can now be type checked. + `#2588 `_ + +* Minimum CMake required increased to 3.4. + `#2338 `_ and + `#2370 `_ + + * Full integration with CMake’s C++ standard system and compile features + replaces ``PYBIND11_CPP_STANDARD``. + + * Generated config file is now portable to different Python/compiler/CMake + versions. + + * Virtual environments prioritized if ``PYTHON_EXECUTABLE`` is not set + (``venv``, ``virtualenv``, and ``conda``) (similar to the new FindPython + mode). + + * Other CMake features now natively supported, like + ``CMAKE_INTERPROCEDURAL_OPTIMIZATION``, ``set(CMAKE_CXX_VISIBILITY_PRESET + hidden)``. + + * ``CUDA`` as a language is now supported. + + * Helper functions ``pybind11_strip``, ``pybind11_extension``, + ``pybind11_find_import`` added, see :doc:`cmake/index`. + + * Optional :ref:`find-python-mode` and :ref:`nopython-mode` with CMake. + `#2370 `_ + +* Uninstall target added. + `#2265 `_ and + `#2346 `_ + +* ``pybind11_add_module()`` now accepts an optional ``OPT_SIZE`` flag that + switches the binding target to size-based optimization if the global build + type can not always be fixed to ``MinSizeRel`` (except in debug mode, where + optimizations remain disabled). ``MinSizeRel`` or this flag reduces binary + size quite substantially (~25% on some platforms). + `#2463 `_ + +Smaller or developer focused features and fixes: + +* Moved ``mkdoc.py`` to a new repo, `pybind11-mkdoc`_. There are no longer + submodules in the main repo. + +* ``py::memoryview`` segfault fix and update, with new + ``py::memoryview::from_memory`` in Python 3, and documentation. + `#2223 `_ + +* Fix for ``buffer_info`` on Python 2. + `#2503 `_ + +* If ``__eq__`` defined but not ``__hash__``, ``__hash__`` is now set to + ``None``. + `#2291 `_ + +* ``py::ellipsis`` now also works on Python 2. + `#2360 `_ + +* Pointer to ``std::tuple`` & ``std::pair`` supported in cast. + `#2334 `_ + +* Small fixes in NumPy support. ``py::array`` now uses ``py::ssize_t`` as first + argument type. + `#2293 `_ + +* Added missing signature for ``py::array``. + `#2363 `_ + +* ``unchecked_mutable_reference`` has access to operator ``()`` and ``[]`` when + const. + `#2514 `_ + +* ``py::vectorize`` is now supported on functions that return void. + `#1969 `_ + +* ``py::capsule`` supports ``get_pointer`` and ``set_pointer``. + `#1131 `_ + +* Fix crash when different instances share the same pointer of the same type. + `#2252 `_ + +* Fix for ``py::len`` not clearing Python's error state when it fails and throws. + `#2575 `_ + +* Bugfixes related to more extensive testing, new GitHub Actions CI. + `#2321 `_ + +* Bug in timezone issue in Eastern hemisphere midnight fixed. + `#2438 `_ + +* ``std::chrono::time_point`` now works when the resolution is not the same as + the system. + `#2481 `_ + +* Bug fixed where ``py::array_t`` could accept arrays that did not match the + requested ordering. + `#2484 `_ + +* Avoid a segfault on some compilers when types are removed in Python. + `#2564 `_ + +* ``py::arg::none()`` is now also respected when passing keyword arguments. + `#2611 `_ + +* PyPy fixes, PyPy 7.3.x now supported, including PyPy3. (Known issue with + PyPy2 and Windows `#2596 `_). + `#2146 `_ + +* CPython 3.9.0 workaround for undefined behavior (macOS segfault). + `#2576 `_ + +* CPython 3.9 warning fixes. + `#2253 `_ + +* Improved C++20 support, now tested in CI. + `#2489 `_ + `#2599 `_ + +* Improved but still incomplete debug Python interpreter support. + `#2025 `_ + +* NVCC (CUDA 11) now supported and tested in CI. + `#2461 `_ + +* NVIDIA PGI compilers now supported and tested in CI. + `#2475 `_ + +* At least Intel 18 now explicitly required when compiling with Intel. + `#2577 `_ + +* Extensive style checking in CI, with `pre-commit`_ support. Code + modernization, checked by clang-tidy. + +* Expanded docs, including new main page, new installing section, and CMake + helpers page, along with over a dozen new sections on existing pages. + +* In GitHub, new docs for contributing and new issue templates. + +.. _pre-commit: https://pre-commit.com + +.. _pybind11-mkdoc: https://github.com/pybind/pybind11-mkdoc + +v2.5.0 (Mar 31, 2020) +----------------------------------------------------- + +* Use C++17 fold expressions in type casters, if available. This can + improve performance during overload resolution when functions have + multiple arguments. + `#2043 `_. + +* Changed include directory resolution in ``pybind11/__init__.py`` + and installation in ``setup.py``. This fixes a number of open issues + where pybind11 headers could not be found in certain environments. + `#1995 `_. + +* C++20 ``char8_t`` and ``u8string`` support. `#2026 + `_. + +* CMake: search for Python 3.9. `bb9c91 + `_. + +* Fixes for MSYS-based build environments. + `#2087 `_, + `#2053 `_. + +* STL bindings for ``std::vector<...>::clear``. `#2074 + `_. + +* Read-only flag for ``py::buffer``. `#1466 + `_. + +* Exception handling during module initialization. + `bf2b031 `_. + +* Support linking against a CPython debug build. + `#2025 `_. + +* Fixed issues involving the availability and use of aligned ``new`` and + ``delete``. `#1988 `_, + `759221 `_. + +* Fixed a resource leak upon interpreter shutdown. + `#2020 `_. + +* Fixed error handling in the boolean caster. + `#1976 `_. + +v2.4.3 (Oct 15, 2019) +----------------------------------------------------- + +* Adapt pybind11 to a C API convention change in Python 3.8. `#1950 + `_. + +v2.4.2 (Sep 21, 2019) +----------------------------------------------------- + +* Replaced usage of a C++14 only construct. `#1929 + `_. + +* Made an ifdef future-proof for Python >= 4. `f3109d + `_. + +v2.4.1 (Sep 20, 2019) +----------------------------------------------------- + +* Fixed a problem involving implicit conversion from enumerations to integers + on Python 3.8. `#1780 `_. + +v2.4.0 (Sep 19, 2019) +----------------------------------------------------- + +* Try harder to keep pybind11-internal data structures separate when there + are potential ABI incompatibilities. Fixes crashes that occurred when loading + multiple pybind11 extensions that were e.g. compiled by GCC (libstdc++) + and Clang (libc++). + `#1588 `_ and + `c9f5a `_. + +* Added support for ``__await__``, ``__aiter__``, and ``__anext__`` protocols. + `#1842 `_. + +* ``pybind11_add_module()``: don't strip symbols when compiling in + ``RelWithDebInfo`` mode. `#1980 + `_. + +* ``enum_``: Reproduce Python behavior when comparing against invalid values + (e.g. ``None``, strings, etc.). Add back support for ``__invert__()``. + `#1912 `_, + `#1907 `_. + +* List insertion operation for ``py::list``. + Added ``.empty()`` to all collection types. + Added ``py::set::contains()`` and ``py::dict::contains()``. + `#1887 `_, + `#1884 `_, + `#1888 `_. + +* ``py::details::overload_cast_impl`` is available in C++11 mode, can be used + like ``overload_cast`` with an additional set of parantheses. + `#1581 `_. + +* Fixed ``get_include()`` on Conda. + `#1877 `_. + +* ``stl_bind.h``: negative indexing support. + `#1882 `_. + +* Minor CMake fix to add MinGW compatibility. + `#1851 `_. + +* GIL-related fixes. + `#1836 `_, + `8b90b `_. + +* Other very minor/subtle fixes and improvements. + `#1329 `_, + `#1910 `_, + `#1863 `_, + `#1847 `_, + `#1890 `_, + `#1860 `_, + `#1848 `_, + `#1821 `_, + `#1837 `_, + `#1833 `_, + `#1748 `_, + `#1852 `_. + +v2.3.0 (June 11, 2019) +----------------------------------------------------- + +* Significantly reduced module binary size (10-20%) when compiled in C++11 mode + with GCC/Clang, or in any mode with MSVC. Function signatures are now always + precomputed at compile time (this was previously only available in C++14 mode + for non-MSVC compilers). + `#934 `_. + +* Add basic support for tag-based static polymorphism, where classes + provide a method to returns the desired type of an instance. + `#1326 `_. + +* Python type wrappers (``py::handle``, ``py::object``, etc.) + now support map Python's number protocol onto C++ arithmetic + operators such as ``operator+``, ``operator/=``, etc. + `#1511 `_. + +* A number of improvements related to enumerations: + + 1. The ``enum_`` implementation was rewritten from scratch to reduce + code bloat. Rather than instantiating a full implementation for each + enumeration, most code is now contained in a generic base class. + `#1511 `_. + + 2. The ``value()`` method of ``py::enum_`` now accepts an optional + docstring that will be shown in the documentation of the associated + enumeration. `#1160 `_. + + 3. check for already existing enum value and throw an error if present. + `#1453 `_. + +* Support for over-aligned type allocation via C++17's aligned ``new`` + statement. `#1582 `_. + +* Added ``py::ellipsis()`` method for slicing of multidimensional NumPy arrays + `#1502 `_. + +* Numerous Improvements to the ``mkdoc.py`` script for extracting documentation + from C++ header files. + `#1788 `_. + +* ``pybind11_add_module()``: allow including Python as a ``SYSTEM`` include path. + `#1416 `_. + +* ``pybind11/stl.h`` does not convert strings to ``vector`` anymore. + `#1258 `_. + +* Mark static methods as such to fix auto-generated Sphinx documentation. + `#1732 `_. + +* Re-throw forced unwind exceptions (e.g. during pthread termination). + `#1208 `_. + +* Added ``__contains__`` method to the bindings of maps (``std::map``, + ``std::unordered_map``). + `#1767 `_. + +* Improvements to ``gil_scoped_acquire``. + `#1211 `_. + +* Type caster support for ``std::deque``. + `#1609 `_. + +* Support for ``std::unique_ptr`` holders, whose deleters differ between a base and derived + class. `#1353 `_. + +* Construction of STL array/vector-like data structures from + iterators. Added an ``extend()`` operation. + `#1709 `_, + +* CMake build system improvements for projects that include non-C++ + files (e.g. plain C, CUDA) in ``pybind11_add_module`` et al. + `#1678 `_. + +* Fixed asynchronous invocation and deallocation of Python functions + wrapped in ``std::function``. + `#1595 `_. + +* Fixes regarding return value policy propagation in STL type casters. + `#1603 `_. + +* Fixed scoped enum comparisons. + `#1571 `_. + +* Fixed iostream redirection for code that releases the GIL. + `#1368 `_, + +* A number of CI-related fixes. + `#1757 `_, + `#1744 `_, + `#1670 `_. + +v2.2.4 (September 11, 2018) +----------------------------------------------------- + +* Use new Python 3.7 Thread Specific Storage (TSS) implementation if available. + `#1454 `_, + `#1517 `_. + +* Fixes for newer MSVC versions and C++17 mode. + `#1347 `_, + `#1462 `_. + +* Propagate return value policies to type-specific casters + when casting STL containers. + `#1455 `_. + +* Allow ostream-redirection of more than 1024 characters. + `#1479 `_. + +* Set ``Py_DEBUG`` define when compiling against a debug Python build. + `#1438 `_. + +* Untangle integer logic in number type caster to work for custom + types that may only be castable to a restricted set of builtin types. + `#1442 `_. + +* CMake build system: Remember Python version in cache file. + `#1434 `_. + +* Fix for custom smart pointers: use ``std::addressof`` to obtain holder + address instead of ``operator&``. + `#1435 `_. + +* Properly report exceptions thrown during module initialization. + `#1362 `_. + +* Fixed a segmentation fault when creating empty-shaped NumPy array. + `#1371 `_. + +* The version of Intel C++ compiler must be >= 2017, and this is now checked by + the header files. `#1363 `_. + +* A few minor typo fixes and improvements to the test suite, and + patches that silence compiler warnings. + +* Vectors now support construction from generators, as well as ``extend()`` from a + list or generator. + `#1496 `_. + + +v2.2.3 (April 29, 2018) +----------------------------------------------------- + +* The pybind11 header location detection was replaced by a new implementation + that no longer depends on ``pip`` internals (the recently released ``pip`` + 10 has restricted access to this API). + `#1190 `_. + +* Small adjustment to an implementation detail to work around a compiler segmentation fault in Clang 3.3/3.4. + `#1350 `_. + +* The minimal supported version of the Intel compiler was >= 17.0 since + pybind11 v2.1. This check is now explicit, and a compile-time error is raised + if the compiler meet the requirement. + `#1363 `_. + +* Fixed an endianness-related fault in the test suite. + `#1287 `_. + +v2.2.2 (February 7, 2018) +----------------------------------------------------- + +* Fixed a segfault when combining embedded interpreter + shutdown/reinitialization with external loaded pybind11 modules. + `#1092 `_. + +* Eigen support: fixed a bug where Nx1/1xN numpy inputs couldn't be passed as + arguments to Eigen vectors (which for Eigen are simply compile-time fixed + Nx1/1xN matrices). + `#1106 `_. + +* Clarified to license by moving the licensing of contributions from + ``LICENSE`` into ``CONTRIBUTING.md``: the licensing of contributions is not + actually part of the software license as distributed. This isn't meant to be + a substantial change in the licensing of the project, but addresses concerns + that the clause made the license non-standard. + `#1109 `_. + +* Fixed a regression introduced in 2.1 that broke binding functions with lvalue + character literal arguments. + `#1128 `_. + +* MSVC: fix for compilation failures under /permissive-, and added the flag to + the appveyor test suite. + `#1155 `_. + +* Fixed ``__qualname__`` generation, and in turn, fixes how class names + (especially nested class names) are shown in generated docstrings. + `#1171 `_. + +* Updated the FAQ with a suggested project citation reference. + `#1189 `_. + +* Added fixes for deprecation warnings when compiled under C++17 with + ``-Wdeprecated`` turned on, and add ``-Wdeprecated`` to the test suite + compilation flags. + `#1191 `_. + +* Fixed outdated PyPI URLs in ``setup.py``. + `#1213 `_. + +* Fixed a refcount leak for arguments that end up in a ``py::args`` argument + for functions with both fixed positional and ``py::args`` arguments. + `#1216 `_. + +* Fixed a potential segfault resulting from possible premature destruction of + ``py::args``/``py::kwargs`` arguments with overloaded functions. + `#1223 `_. + +* Fixed ``del map[item]`` for a ``stl_bind.h`` bound stl map. + `#1229 `_. + +* Fixed a regression from v2.1.x where the aggregate initialization could + unintentionally end up at a constructor taking a templated + ``std::initializer_list`` argument. + `#1249 `_. + +* Fixed an issue where calling a function with a keep_alive policy on the same + nurse/patient pair would cause the internal patient storage to needlessly + grow (unboundedly, if the nurse is long-lived). + `#1251 `_. + +* Various other minor fixes. + +v2.2.1 (September 14, 2017) +----------------------------------------------------- + +* Added ``py::module_::reload()`` member function for reloading a module. + `#1040 `_. + +* Fixed a reference leak in the number converter. + `#1078 `_. + +* Fixed compilation with Clang on host GCC < 5 (old libstdc++ which isn't fully + C++11 compliant). `#1062 `_. + +* Fixed a regression where the automatic ``std::vector`` caster would + fail to compile. The same fix also applies to any container which returns + element proxies instead of references. + `#1053 `_. + +* Fixed a regression where the ``py::keep_alive`` policy could not be applied + to constructors. `#1065 `_. + +* Fixed a nullptr dereference when loading a ``py::module_local`` type + that's only registered in an external module. + `#1058 `_. + +* Fixed implicit conversion of accessors to types derived from ``py::object``. + `#1076 `_. + +* The ``name`` in ``PYBIND11_MODULE(name, variable)`` can now be a macro. + `#1082 `_. + +* Relaxed overly strict ``py::pickle()`` check for matching get and set types. + `#1064 `_. + +* Conversion errors now try to be more informative when it's likely that + a missing header is the cause (e.g. forgetting ````). + `#1077 `_. + +v2.2.0 (August 31, 2017) +----------------------------------------------------- + +* Support for embedding the Python interpreter. See the + :doc:`documentation page ` for a + full overview of the new features. + `#774 `_, + `#889 `_, + `#892 `_, + `#920 `_. + + .. code-block:: cpp + + #include + namespace py = pybind11; + + int main() { + py::scoped_interpreter guard{}; // start the interpreter and keep it alive + + py::print("Hello, World!"); // use the Python API + } + +* Support for inheriting from multiple C++ bases in Python. + `#693 `_. + + .. code-block:: python + + from cpp_module import CppBase1, CppBase2 + + class PyDerived(CppBase1, CppBase2): + def __init__(self): + CppBase1.__init__(self) # C++ bases must be initialized explicitly + CppBase2.__init__(self) + +* ``PYBIND11_MODULE`` is now the preferred way to create module entry points. + ``PYBIND11_PLUGIN`` is deprecated. See :ref:`macros` for details. + `#879 `_. + + .. code-block:: cpp + + // new + PYBIND11_MODULE(example, m) { + m.def("add", [](int a, int b) { return a + b; }); + } + + // old + PYBIND11_PLUGIN(example) { + py::module m("example"); + m.def("add", [](int a, int b) { return a + b; }); + return m.ptr(); + } + +* pybind11's headers and build system now more strictly enforce hidden symbol + visibility for extension modules. This should be seamless for most users, + but see the :doc:`upgrade` if you use a custom build system. + `#995 `_. + +* Support for ``py::module_local`` types which allow multiple modules to + export the same C++ types without conflicts. This is useful for opaque + types like ``std::vector``. ``py::bind_vector`` and ``py::bind_map`` + now default to ``py::module_local`` if their elements are builtins or + local types. See :ref:`module_local` for details. + `#949 `_, + `#981 `_, + `#995 `_, + `#997 `_. + +* Custom constructors can now be added very easily using lambdas or factory + functions which return a class instance by value, pointer or holder. This + supersedes the old placement-new ``__init__`` technique. + See :ref:`custom_constructors` for details. + `#805 `_, + `#1014 `_. + + .. code-block:: cpp + + struct Example { + Example(std::string); + }; + + py::class_(m, "Example") + .def(py::init()) // existing constructor + .def(py::init([](int n) { // custom constructor + return std::make_unique(std::to_string(n)); + })); + +* Similarly to custom constructors, pickling support functions are now bound + using the ``py::pickle()`` adaptor which improves type safety. See the + :doc:`upgrade` and :ref:`pickling` for details. + `#1038 `_. + +* Builtin support for converting C++17 standard library types and general + conversion improvements: + + 1. C++17 ``std::variant`` is supported right out of the box. C++11/14 + equivalents (e.g. ``boost::variant``) can also be added with a simple + user-defined specialization. See :ref:`cpp17_container_casters` for details. + `#811 `_, + `#845 `_, + `#989 `_. + + 2. Out-of-the-box support for C++17 ``std::string_view``. + `#906 `_. + + 3. Improved compatibility of the builtin ``optional`` converter. + `#874 `_. + + 4. The ``bool`` converter now accepts ``numpy.bool_`` and types which + define ``__bool__`` (Python 3.x) or ``__nonzero__`` (Python 2.7). + `#925 `_. + + 5. C++-to-Python casters are now more efficient and move elements out + of rvalue containers whenever possible. + `#851 `_, + `#936 `_, + `#938 `_. + + 6. Fixed ``bytes`` to ``std::string/char*`` conversion on Python 3. + `#817 `_. + + 7. Fixed lifetime of temporary C++ objects created in Python-to-C++ conversions. + `#924 `_. + +* Scope guard call policy for RAII types, e.g. ``py::call_guard()``, + ``py::call_guard()``. See :ref:`call_policies` for details. + `#740 `_. + +* Utility for redirecting C++ streams to Python (e.g. ``std::cout`` -> + ``sys.stdout``). Scope guard ``py::scoped_ostream_redirect`` in C++ and + a context manager in Python. See :ref:`ostream_redirect`. + `#1009 `_. + +* Improved handling of types and exceptions across module boundaries. + `#915 `_, + `#951 `_, + `#995 `_. + +* Fixed destruction order of ``py::keep_alive`` nurse/patient objects + in reference cycles. + `#856 `_. + +* NumPy and buffer protocol related improvements: + + 1. Support for negative strides in Python buffer objects/numpy arrays. This + required changing integers from unsigned to signed for the related C++ APIs. + Note: If you have compiler warnings enabled, you may notice some new conversion + warnings after upgrading. These can be resolved with ``static_cast``. + `#782 `_. + + 2. Support ``std::complex`` and arrays inside ``PYBIND11_NUMPY_DTYPE``. + `#831 `_, + `#832 `_. + + 3. Support for constructing ``py::buffer_info`` and ``py::arrays`` using + arbitrary containers or iterators instead of requiring a ``std::vector``. + `#788 `_, + `#822 `_, + `#860 `_. + + 4. Explicitly check numpy version and require >= 1.7.0. + `#819 `_. + +* Support for allowing/prohibiting ``None`` for specific arguments and improved + ``None`` overload resolution order. See :ref:`none_arguments` for details. + `#843 `_. + `#859 `_. + +* Added ``py::exec()`` as a shortcut for ``py::eval()`` + and support for C++11 raw string literals as input. See :ref:`eval`. + `#766 `_, + `#827 `_. + +* ``py::vectorize()`` ignores non-vectorizable arguments and supports + member functions. + `#762 `_. + +* Support for bound methods as callbacks (``pybind11/functional.h``). + `#815 `_. + +* Allow aliasing pybind11 methods: ``cls.attr("foo") = cls.attr("bar")``. + `#802 `_. + +* Don't allow mixed static/non-static overloads. + `#804 `_. + +* Fixed overriding static properties in derived classes. + `#784 `_. + +* Added support for write only properties. + `#1144 `_. + +* Improved deduction of member functions of a derived class when its bases + aren't registered with pybind11. + `#855 `_. + + .. code-block:: cpp + + struct Base { + int foo() { return 42; } + } + + struct Derived : Base {} + + // Now works, but previously required also binding `Base` + py::class_(m, "Derived") + .def("foo", &Derived::foo); // function is actually from `Base` + +* The implementation of ``py::init<>`` now uses C++11 brace initialization + syntax to construct instances, which permits binding implicit constructors of + aggregate types. `#1015 `_. + + .. code-block:: cpp + + struct Aggregate { + int a; + std::string b; + }; + + py::class_(m, "Aggregate") + .def(py::init()); + +* Fixed issues with multiple inheritance with offset base/derived pointers. + `#812 `_, + `#866 `_, + `#960 `_. + +* Fixed reference leak of type objects. + `#1030 `_. + +* Improved support for the ``/std:c++14`` and ``/std:c++latest`` modes + on MSVC 2017. + `#841 `_, + `#999 `_. + +* Fixed detection of private operator new on MSVC. + `#893 `_, + `#918 `_. + +* Intel C++ compiler compatibility fixes. + `#937 `_. + +* Fixed implicit conversion of `py::enum_` to integer types on Python 2.7. + `#821 `_. + +* Added ``py::hash`` to fetch the hash value of Python objects, and + ``.def(hash(py::self))`` to provide the C++ ``std::hash`` as the Python + ``__hash__`` method. + `#1034 `_. + +* Fixed ``__truediv__`` on Python 2 and ``__itruediv__`` on Python 3. + `#867 `_. + +* ``py::capsule`` objects now support the ``name`` attribute. This is useful + for interfacing with ``scipy.LowLevelCallable``. + `#902 `_. + +* Fixed ``py::make_iterator``'s ``__next__()`` for past-the-end calls. + `#897 `_. + +* Added ``error_already_set::matches()`` for checking Python exceptions. + `#772 `_. + +* Deprecated ``py::error_already_set::clear()``. It's no longer needed + following a simplification of the ``py::error_already_set`` class. + `#954 `_. + +* Deprecated ``py::handle::operator==()`` in favor of ``py::handle::is()`` + `#825 `_. + +* Deprecated ``py::object::borrowed``/``py::object::stolen``. + Use ``py::object::borrowed_t{}``/``py::object::stolen_t{}`` instead. + `#771 `_. + +* Changed internal data structure versioning to avoid conflicts between + modules compiled with different revisions of pybind11. + `#1012 `_. + +* Additional compile-time and run-time error checking and more informative messages. + `#786 `_, + `#794 `_, + `#803 `_. + +* Various minor improvements and fixes. + `#764 `_, + `#791 `_, + `#795 `_, + `#840 `_, + `#844 `_, + `#846 `_, + `#849 `_, + `#858 `_, + `#862 `_, + `#871 `_, + `#872 `_, + `#881 `_, + `#888 `_, + `#899 `_, + `#928 `_, + `#931 `_, + `#944 `_, + `#950 `_, + `#952 `_, + `#962 `_, + `#965 `_, + `#970 `_, + `#978 `_, + `#979 `_, + `#986 `_, + `#1020 `_, + `#1027 `_, + `#1037 `_. + +* Testing improvements. + `#798 `_, + `#882 `_, + `#898 `_, + `#900 `_, + `#921 `_, + `#923 `_, + `#963 `_. + +v2.1.1 (April 7, 2017) +----------------------------------------------------- + +* Fixed minimum version requirement for MSVC 2015u3 + `#773 `_. + +v2.1.0 (March 22, 2017) +----------------------------------------------------- + +* pybind11 now performs function overload resolution in two phases. The first + phase only considers exact type matches, while the second allows for implicit + conversions to take place. A special ``noconvert()`` syntax can be used to + completely disable implicit conversions for specific arguments. + `#643 `_, + `#634 `_, + `#650 `_. + +* Fixed a regression where static properties no longer worked with classes + using multiple inheritance. The ``py::metaclass`` attribute is no longer + necessary (and deprecated as of this release) when binding classes with + static properties. + `#679 `_, + +* Classes bound using ``pybind11`` can now use custom metaclasses. + `#679 `_, + +* ``py::args`` and ``py::kwargs`` can now be mixed with other positional + arguments when binding functions using pybind11. + `#611 `_. + +* Improved support for C++11 unicode string and character types; added + extensive documentation regarding pybind11's string conversion behavior. + `#624 `_, + `#636 `_, + `#715 `_. + +* pybind11 can now avoid expensive copies when converting Eigen arrays to NumPy + arrays (and vice versa). `#610 `_. + +* The "fast path" in ``py::vectorize`` now works for any full-size group of C or + F-contiguous arrays. The non-fast path is also faster since it no longer performs + copies of the input arguments (except when type conversions are necessary). + `#610 `_. + +* Added fast, unchecked access to NumPy arrays via a proxy object. + `#746 `_. + +* Transparent support for class-specific ``operator new`` and + ``operator delete`` implementations. + `#755 `_. + +* Slimmer and more efficient STL-compatible iterator interface for sequence types. + `#662 `_. + +* Improved custom holder type support. + `#607 `_. + +* ``nullptr`` to ``None`` conversion fixed in various builtin type casters. + `#732 `_. + +* ``enum_`` now exposes its members via a special ``__members__`` attribute. + `#666 `_. + +* ``std::vector`` bindings created using ``stl_bind.h`` can now optionally + implement the buffer protocol. `#488 `_. + +* Automated C++ reference documentation using doxygen and breathe. + `#598 `_. + +* Added minimum compiler version assertions. + `#727 `_. + +* Improved compatibility with C++1z. + `#677 `_. + +* Improved ``py::capsule`` API. Can be used to implement cleanup + callbacks that are involved at module destruction time. + `#752 `_. + +* Various minor improvements and fixes. + `#595 `_, + `#588 `_, + `#589 `_, + `#603 `_, + `#619 `_, + `#648 `_, + `#695 `_, + `#720 `_, + `#723 `_, + `#729 `_, + `#724 `_, + `#742 `_, + `#753 `_. + +v2.0.1 (Jan 4, 2017) +----------------------------------------------------- + +* Fix pointer to reference error in type_caster on MSVC + `#583 `_. + +* Fixed a segmentation in the test suite due to a typo + `cd7eac `_. + +v2.0.0 (Jan 1, 2017) +----------------------------------------------------- + +* Fixed a reference counting regression affecting types with custom metaclasses + (introduced in v2.0.0-rc1). + `#571 `_. + +* Quenched a CMake policy warning. + `#570 `_. + +v2.0.0-rc1 (Dec 23, 2016) +----------------------------------------------------- + +The pybind11 developers are excited to issue a release candidate of pybind11 +with a subsequent v2.0.0 release planned in early January next year. + +An incredible amount of effort by went into pybind11 over the last ~5 months, +leading to a release that is jam-packed with exciting new features and numerous +usability improvements. The following list links PRs or individual commits +whenever applicable. + +Happy Christmas! + +* Support for binding C++ class hierarchies that make use of multiple + inheritance. `#410 `_. + +* PyPy support: pybind11 now supports nightly builds of PyPy and will + interoperate with the future 5.7 release. No code changes are necessary, + everything "just" works as usual. Note that we only target the Python 2.7 + branch for now; support for 3.x will be added once its ``cpyext`` extension + support catches up. A few minor features remain unsupported for the time + being (notably dynamic attributes in custom types). + `#527 `_. + +* Significant work on the documentation -- in particular, the monolithic + ``advanced.rst`` file was restructured into a easier to read hierarchical + organization. `#448 `_. + +* Many NumPy-related improvements: + + 1. Object-oriented API to access and modify NumPy ``ndarray`` instances, + replicating much of the corresponding NumPy C API functionality. + `#402 `_. + + 2. NumPy array ``dtype`` array descriptors are now first-class citizens and + are exposed via a new class ``py::dtype``. + + 3. Structured dtypes can be registered using the ``PYBIND11_NUMPY_DTYPE()`` + macro. Special ``array`` constructors accepting dtype objects were also + added. + + One potential caveat involving this change: format descriptor strings + should now be accessed via ``format_descriptor::format()`` (however, for + compatibility purposes, the old syntax ``format_descriptor::value`` will + still work for non-structured data types). `#308 + `_. + + 4. Further improvements to support structured dtypes throughout the system. + `#472 `_, + `#474 `_, + `#459 `_, + `#453 `_, + `#452 `_, and + `#505 `_. + + 5. Fast access operators. `#497 `_. + + 6. Constructors for arrays whose storage is owned by another object. + `#440 `_. + + 7. Added constructors for ``array`` and ``array_t`` explicitly accepting shape + and strides; if strides are not provided, they are deduced assuming + C-contiguity. Also added simplified constructors for 1-dimensional case. + + 8. Added buffer/NumPy support for ``char[N]`` and ``std::array`` types. + + 9. Added ``memoryview`` wrapper type which is constructible from ``buffer_info``. + +* Eigen: many additional conversions and support for non-contiguous + arrays/slices. + `#427 `_, + `#315 `_, + `#316 `_, + `#312 `_, and + `#267 `_ + +* Incompatible changes in ``class_<...>::class_()``: + + 1. Declarations of types that provide access via the buffer protocol must + now include the ``py::buffer_protocol()`` annotation as an argument to + the ``class_`` constructor. + + 2. Declarations of types that require a custom metaclass (i.e. all classes + which include static properties via commands such as + ``def_readwrite_static()``) must now include the ``py::metaclass()`` + annotation as an argument to the ``class_`` constructor. + + These two changes were necessary to make type definitions in pybind11 + future-proof, and to support PyPy via its cpyext mechanism. `#527 + `_. + + + 3. This version of pybind11 uses a redesigned mechanism for instantiating + trampoline classes that are used to override virtual methods from within + Python. This led to the following user-visible syntax change: instead of + + .. code-block:: cpp + + py::class_("MyClass") + .alias() + .... + + write + + .. code-block:: cpp + + py::class_("MyClass") + .... + + Importantly, both the original and the trampoline class are now + specified as an arguments (in arbitrary order) to the ``py::class_`` + template, and the ``alias<..>()`` call is gone. The new scheme has zero + overhead in cases when Python doesn't override any functions of the + underlying C++ class. `rev. 86d825 + `_. + +* Added ``eval`` and ``eval_file`` functions for evaluating expressions and + statements from a string or file. `rev. 0d3fc3 + `_. + +* pybind11 can now create types with a modifiable dictionary. + `#437 `_ and + `#444 `_. + +* Support for translation of arbitrary C++ exceptions to Python counterparts. + `#296 `_ and + `#273 `_. + +* Report full backtraces through mixed C++/Python code, better reporting for + import errors, fixed GIL management in exception processing. + `#537 `_, + `#494 `_, + `rev. e72d95 `_, and + `rev. 099d6e `_. + +* Support for bit-level operations, comparisons, and serialization of C++ + enumerations. `#503 `_, + `#508 `_, + `#380 `_, + `#309 `_. + `#311 `_. + +* The ``class_`` constructor now accepts its template arguments in any order. + `#385 `_. + +* Attribute and item accessors now have a more complete interface which makes + it possible to chain attributes as in + ``obj.attr("a")[key].attr("b").attr("method")(1, 2, 3)``. `#425 + `_. + +* Major redesign of the default and conversion constructors in ``pytypes.h``. + `#464 `_. + +* Added built-in support for ``std::shared_ptr`` holder type. It is no longer + necessary to to include a declaration of the form + ``PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr)`` (though continuing to + do so won't cause an error). + `#454 `_. + +* New ``py::overload_cast`` casting operator to select among multiple possible + overloads of a function. An example: + + .. code-block:: cpp + + py::class_(m, "Pet") + .def("set", py::overload_cast(&Pet::set), "Set the pet's age") + .def("set", py::overload_cast(&Pet::set), "Set the pet's name"); + + This feature only works on C++14-capable compilers. + `#541 `_. + +* C++ types are automatically cast to Python types, e.g. when assigning + them as an attribute. For instance, the following is now legal: + + .. code-block:: cpp + + py::module m = /* ... */ + m.attr("constant") = 123; + + (Previously, a ``py::cast`` call was necessary to avoid a compilation error.) + `#551 `_. + +* Redesigned ``pytest``-based test suite. `#321 `_. + +* Instance tracking to detect reference leaks in test suite. `#324 `_ + +* pybind11 can now distinguish between multiple different instances that are + located at the same memory address, but which have different types. + `#329 `_. + +* Improved logic in ``move`` return value policy. + `#510 `_, + `#297 `_. + +* Generalized unpacking API to permit calling Python functions from C++ using + notation such as ``foo(a1, a2, *args, "ka"_a=1, "kb"_a=2, **kwargs)``. `#372 `_. + +* ``py::print()`` function whose behavior matches that of the native Python + ``print()`` function. `#372 `_. + +* Added ``py::dict`` keyword constructor:``auto d = dict("number"_a=42, + "name"_a="World");``. `#372 `_. + +* Added ``py::str::format()`` method and ``_s`` literal: ``py::str s = "1 + 2 + = {}"_s.format(3);``. `#372 `_. + +* Added ``py::repr()`` function which is equivalent to Python's builtin + ``repr()``. `#333 `_. + +* Improved construction and destruction logic for holder types. It is now + possible to reference instances with smart pointer holder types without + constructing the holder if desired. The ``PYBIND11_DECLARE_HOLDER_TYPE`` + macro now accepts an optional second parameter to indicate whether the holder + type uses intrusive reference counting. + `#533 `_ and + `#561 `_. + +* Mapping a stateless C++ function to Python and back is now "for free" (i.e. + no extra indirections or argument conversion overheads). `rev. 954b79 + `_. + +* Bindings for ``std::valarray``. + `#545 `_. + +* Improved support for C++17 capable compilers. + `#562 `_. + +* Bindings for ``std::optional``. + `#475 `_, + `#476 `_, + `#479 `_, + `#499 `_, and + `#501 `_. + +* ``stl_bind.h``: general improvements and support for ``std::map`` and + ``std::unordered_map``. + `#490 `_, + `#282 `_, + `#235 `_. + +* The ``std::tuple``, ``std::pair``, ``std::list``, and ``std::vector`` type + casters now accept any Python sequence type as input. `rev. 107285 + `_. + +* Improved CMake Python detection on multi-architecture Linux. + `#532 `_. + +* Infrastructure to selectively disable or enable parts of the automatically + generated docstrings. `#486 `_. + +* ``reference`` and ``reference_internal`` are now the default return value + properties for static and non-static properties, respectively. `#473 + `_. (the previous defaults + were ``automatic``). `#473 `_. + +* Support for ``std::unique_ptr`` with non-default deleters or no deleter at + all (``py::nodelete``). `#384 `_. + +* Deprecated ``handle::call()`` method. The new syntax to call Python + functions is simply ``handle()``. It can also be invoked explicitly via + ``handle::operator()``, where ``X`` is an optional return value policy. + +* Print more informative error messages when ``make_tuple()`` or ``cast()`` + fail. `#262 `_. + +* Creation of holder types for classes deriving from + ``std::enable_shared_from_this<>`` now also works for ``const`` values. + `#260 `_. + +* ``make_iterator()`` improvements for better compatibility with various + types (now uses prefix increment operator); it now also accepts iterators + with different begin/end types as long as they are equality comparable. + `#247 `_. + +* ``arg()`` now accepts a wider range of argument types for default values. + `#244 `_. + +* Support ``keep_alive`` where the nurse object may be ``None``. `#341 + `_. + +* Added constructors for ``str`` and ``bytes`` from zero-terminated char + pointers, and from char pointers and length. Added constructors for ``str`` + from ``bytes`` and for ``bytes`` from ``str``, which will perform UTF-8 + decoding/encoding as required. + +* Many other improvements of library internals without user-visible changes + + +1.8.1 (July 12, 2016) +---------------------- +* Fixed a rare but potentially very severe issue when the garbage collector ran + during pybind11 type creation. + +1.8.0 (June 14, 2016) +---------------------- +* Redesigned CMake build system which exports a convenient + ``pybind11_add_module`` function to parent projects. +* ``std::vector<>`` type bindings analogous to Boost.Python's ``indexing_suite`` +* Transparent conversion of sparse and dense Eigen matrices and vectors (``eigen.h``) +* Added an ``ExtraFlags`` template argument to the NumPy ``array_t<>`` wrapper + to disable an enforced cast that may lose precision, e.g. to create overloads + for different precisions and complex vs real-valued matrices. +* Prevent implicit conversion of floating point values to integral types in + function arguments +* Fixed incorrect default return value policy for functions returning a shared + pointer +* Don't allow registering a type via ``class_`` twice +* Don't allow casting a ``None`` value into a C++ lvalue reference +* Fixed a crash in ``enum_::operator==`` that was triggered by the ``help()`` command +* Improved detection of whether or not custom C++ types can be copy/move-constructed +* Extended ``str`` type to also work with ``bytes`` instances +* Added a ``"name"_a`` user defined string literal that is equivalent to ``py::arg("name")``. +* When specifying function arguments via ``py::arg``, the test that verifies + the number of arguments now runs at compile time. +* Added ``[[noreturn]]`` attribute to ``pybind11_fail()`` to quench some + compiler warnings +* List function arguments in exception text when the dispatch code cannot find + a matching overload +* Added ``PYBIND11_OVERLOAD_NAME`` and ``PYBIND11_OVERLOAD_PURE_NAME`` macros which + can be used to override virtual methods whose name differs in C++ and Python + (e.g. ``__call__`` and ``operator()``) +* Various minor ``iterator`` and ``make_iterator()`` improvements +* Transparently support ``__bool__`` on Python 2.x and Python 3.x +* Fixed issue with destructor of unpickled object not being called +* Minor CMake build system improvements on Windows +* New ``pybind11::args`` and ``pybind11::kwargs`` types to create functions which + take an arbitrary number of arguments and keyword arguments +* New syntax to call a Python function from C++ using ``*args`` and ``*kwargs`` +* The functions ``def_property_*`` now correctly process docstring arguments (these + formerly caused a segmentation fault) +* Many ``mkdoc.py`` improvements (enumerations, template arguments, ``DOC()`` + macro accepts more arguments) +* Cygwin support +* Documentation improvements (pickling support, ``keep_alive``, macro usage) + +1.7 (April 30, 2016) +---------------------- +* Added a new ``move`` return value policy that triggers C++11 move semantics. + The automatic return value policy falls back to this case whenever a rvalue + reference is encountered +* Significantly more general GIL state routines that are used instead of + Python's troublesome ``PyGILState_Ensure`` and ``PyGILState_Release`` API +* Redesign of opaque types that drastically simplifies their usage +* Extended ability to pass values of type ``[const] void *`` +* ``keep_alive`` fix: don't fail when there is no patient +* ``functional.h``: acquire the GIL before calling a Python function +* Added Python RAII type wrappers ``none`` and ``iterable`` +* Added ``*args`` and ``*kwargs`` pass-through parameters to + ``pybind11.get_include()`` function +* Iterator improvements and fixes +* Documentation on return value policies and opaque types improved + +1.6 (April 30, 2016) +---------------------- +* Skipped due to upload to PyPI gone wrong and inability to recover + (https://github.com/pypa/packaging-problems/issues/74) + +1.5 (April 21, 2016) +---------------------- +* For polymorphic types, use RTTI to try to return the closest type registered with pybind11 +* Pickling support for serializing and unserializing C++ instances to a byte stream in Python +* Added a convenience routine ``make_iterator()`` which turns a range indicated + by a pair of C++ iterators into a iterable Python object +* Added ``len()`` and a variadic ``make_tuple()`` function +* Addressed a rare issue that could confuse the current virtual function + dispatcher and another that could lead to crashes in multi-threaded + applications +* Added a ``get_include()`` function to the Python module that returns the path + of the directory containing the installed pybind11 header files +* Documentation improvements: import issues, symbol visibility, pickling, limitations +* Added casting support for ``std::reference_wrapper<>`` + +1.4 (April 7, 2016) +-------------------------- +* Transparent type conversion for ``std::wstring`` and ``wchar_t`` +* Allow passing ``nullptr``-valued strings +* Transparent passing of ``void *`` pointers using capsules +* Transparent support for returning values wrapped in ``std::unique_ptr<>`` +* Improved docstring generation for compatibility with Sphinx +* Nicer debug error message when default parameter construction fails +* Support for "opaque" types that bypass the transparent conversion layer for STL containers +* Redesigned type casting interface to avoid ambiguities that could occasionally cause compiler errors +* Redesigned property implementation; fixes crashes due to an unfortunate default return value policy +* Anaconda package generation support + +1.3 (March 8, 2016) +-------------------------- + +* Added support for the Intel C++ compiler (v15+) +* Added support for the STL unordered set/map data structures +* Added support for the STL linked list data structure +* NumPy-style broadcasting support in ``pybind11::vectorize`` +* pybind11 now displays more verbose error messages when ``arg::operator=()`` fails +* pybind11 internal data structures now live in a version-dependent namespace to avoid ABI issues +* Many, many bugfixes involving corner cases and advanced usage + +1.2 (February 7, 2016) +-------------------------- + +* Optional: efficient generation of function signatures at compile time using C++14 +* Switched to a simpler and more general way of dealing with function default + arguments. Unused keyword arguments in function calls are now detected and + cause errors as expected +* New ``keep_alive`` call policy analogous to Boost.Python's ``with_custodian_and_ward`` +* New ``pybind11::base<>`` attribute to indicate a subclass relationship +* Improved interface for RAII type wrappers in ``pytypes.h`` +* Use RAII type wrappers consistently within pybind11 itself. This + fixes various potential refcount leaks when exceptions occur +* Added new ``bytes`` RAII type wrapper (maps to ``string`` in Python 2.7) +* Made handle and related RAII classes const correct, using them more + consistently everywhere now +* Got rid of the ugly ``__pybind11__`` attributes on the Python side---they are + now stored in a C++ hash table that is not visible in Python +* Fixed refcount leaks involving NumPy arrays and bound functions +* Vastly improved handling of shared/smart pointers +* Removed an unnecessary copy operation in ``pybind11::vectorize`` +* Fixed naming clashes when both pybind11 and NumPy headers are included +* Added conversions for additional exception types +* Documentation improvements (using multiple extension modules, smart pointers, + other minor clarifications) +* unified infrastructure for parsing variadic arguments in ``class_`` and cpp_function +* Fixed license text (was: ZLIB, should have been: 3-clause BSD) +* Python 3.2 compatibility +* Fixed remaining issues when accessing types in another plugin module +* Added enum comparison and casting methods +* Improved SFINAE-based detection of whether types are copy-constructible +* Eliminated many warnings about unused variables and the use of ``offsetof()`` +* Support for ``std::array<>`` conversions + +1.1 (December 7, 2015) +-------------------------- + +* Documentation improvements (GIL, wrapping functions, casting, fixed many typos) +* Generalized conversion of integer types +* Improved support for casting function objects +* Improved support for ``std::shared_ptr<>`` conversions +* Initial support for ``std::set<>`` conversions +* Fixed type resolution issue for types defined in a separate plugin module +* CMake build system improvements +* Factored out generic functionality to non-templated code (smaller code size) +* Added a code size / compile time benchmark vs Boost.Python +* Added an appveyor CI script + +1.0 (October 15, 2015) +------------------------ +* Initial release diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/classes.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/classes.rst new file mode 100644 index 0000000000000000000000000000000000000000..f3610ef367d0cbb19dcb8c790ede6b1bf6c4dc3c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/classes.rst @@ -0,0 +1,532 @@ +.. _classes: + +Object-oriented code +#################### + +Creating bindings for a custom type +=================================== + +Let's now look at a more complex example where we'll create bindings for a +custom C++ data structure named ``Pet``. Its definition is given below: + +.. code-block:: cpp + + struct Pet { + Pet(const std::string &name) : name(name) { } + void setName(const std::string &name_) { name = name_; } + const std::string &getName() const { return name; } + + std::string name; + }; + +The binding code for ``Pet`` looks as follows: + +.. code-block:: cpp + + #include + + namespace py = pybind11; + + PYBIND11_MODULE(example, m) { + py::class_(m, "Pet") + .def(py::init()) + .def("setName", &Pet::setName) + .def("getName", &Pet::getName); + } + +:class:`class_` creates bindings for a C++ *class* or *struct*-style data +structure. :func:`init` is a convenience function that takes the types of a +constructor's parameters as template arguments and wraps the corresponding +constructor (see the :ref:`custom_constructors` section for details). An +interactive Python session demonstrating this example is shown below: + +.. code-block:: pycon + + % python + >>> import example + >>> p = example.Pet('Molly') + >>> print(p) + + >>> p.getName() + u'Molly' + >>> p.setName('Charly') + >>> p.getName() + u'Charly' + +.. seealso:: + + Static member functions can be bound in the same way using + :func:`class_::def_static`. + +Keyword and default arguments +============================= +It is possible to specify keyword and default arguments using the syntax +discussed in the previous chapter. Refer to the sections :ref:`keyword_args` +and :ref:`default_args` for details. + +Binding lambda functions +======================== + +Note how ``print(p)`` produced a rather useless summary of our data structure in the example above: + +.. code-block:: pycon + + >>> print(p) + + +To address this, we could bind a utility function that returns a human-readable +summary to the special method slot named ``__repr__``. Unfortunately, there is no +suitable functionality in the ``Pet`` data structure, and it would be nice if +we did not have to change it. This can easily be accomplished by binding a +Lambda function instead: + +.. code-block:: cpp + + py::class_(m, "Pet") + .def(py::init()) + .def("setName", &Pet::setName) + .def("getName", &Pet::getName) + .def("__repr__", + [](const Pet &a) { + return ""; + } + ); + +Both stateless [#f1]_ and stateful lambda closures are supported by pybind11. +With the above change, the same Python code now produces the following output: + +.. code-block:: pycon + + >>> print(p) + + +.. [#f1] Stateless closures are those with an empty pair of brackets ``[]`` as the capture object. + +.. _properties: + +Instance and static fields +========================== + +We can also directly expose the ``name`` field using the +:func:`class_::def_readwrite` method. A similar :func:`class_::def_readonly` +method also exists for ``const`` fields. + +.. code-block:: cpp + + py::class_(m, "Pet") + .def(py::init()) + .def_readwrite("name", &Pet::name) + // ... remainder ... + +This makes it possible to write + +.. code-block:: pycon + + >>> p = example.Pet('Molly') + >>> p.name + u'Molly' + >>> p.name = 'Charly' + >>> p.name + u'Charly' + +Now suppose that ``Pet::name`` was a private internal variable +that can only be accessed via setters and getters. + +.. code-block:: cpp + + class Pet { + public: + Pet(const std::string &name) : name(name) { } + void setName(const std::string &name_) { name = name_; } + const std::string &getName() const { return name; } + private: + std::string name; + }; + +In this case, the method :func:`class_::def_property` +(:func:`class_::def_property_readonly` for read-only data) can be used to +provide a field-like interface within Python that will transparently call +the setter and getter functions: + +.. code-block:: cpp + + py::class_(m, "Pet") + .def(py::init()) + .def_property("name", &Pet::getName, &Pet::setName) + // ... remainder ... + +Write only properties can be defined by passing ``nullptr`` as the +input for the read function. + +.. seealso:: + + Similar functions :func:`class_::def_readwrite_static`, + :func:`class_::def_readonly_static` :func:`class_::def_property_static`, + and :func:`class_::def_property_readonly_static` are provided for binding + static variables and properties. Please also see the section on + :ref:`static_properties` in the advanced part of the documentation. + +Dynamic attributes +================== + +Native Python classes can pick up new attributes dynamically: + +.. code-block:: pycon + + >>> class Pet: + ... name = 'Molly' + ... + >>> p = Pet() + >>> p.name = 'Charly' # overwrite existing + >>> p.age = 2 # dynamically add a new attribute + +By default, classes exported from C++ do not support this and the only writable +attributes are the ones explicitly defined using :func:`class_::def_readwrite` +or :func:`class_::def_property`. + +.. code-block:: cpp + + py::class_(m, "Pet") + .def(py::init<>()) + .def_readwrite("name", &Pet::name); + +Trying to set any other attribute results in an error: + +.. code-block:: pycon + + >>> p = example.Pet() + >>> p.name = 'Charly' # OK, attribute defined in C++ + >>> p.age = 2 # fail + AttributeError: 'Pet' object has no attribute 'age' + +To enable dynamic attributes for C++ classes, the :class:`py::dynamic_attr` tag +must be added to the :class:`py::class_` constructor: + +.. code-block:: cpp + + py::class_(m, "Pet", py::dynamic_attr()) + .def(py::init<>()) + .def_readwrite("name", &Pet::name); + +Now everything works as expected: + +.. code-block:: pycon + + >>> p = example.Pet() + >>> p.name = 'Charly' # OK, overwrite value in C++ + >>> p.age = 2 # OK, dynamically add a new attribute + >>> p.__dict__ # just like a native Python class + {'age': 2} + +Note that there is a small runtime cost for a class with dynamic attributes. +Not only because of the addition of a ``__dict__``, but also because of more +expensive garbage collection tracking which must be activated to resolve +possible circular references. Native Python classes incur this same cost by +default, so this is not anything to worry about. By default, pybind11 classes +are more efficient than native Python classes. Enabling dynamic attributes +just brings them on par. + +.. _inheritance: + +Inheritance and automatic downcasting +===================================== + +Suppose now that the example consists of two data structures with an +inheritance relationship: + +.. code-block:: cpp + + struct Pet { + Pet(const std::string &name) : name(name) { } + std::string name; + }; + + struct Dog : Pet { + Dog(const std::string &name) : Pet(name) { } + std::string bark() const { return "woof!"; } + }; + +There are two different ways of indicating a hierarchical relationship to +pybind11: the first specifies the C++ base class as an extra template +parameter of the :class:`class_`: + +.. code-block:: cpp + + py::class_(m, "Pet") + .def(py::init()) + .def_readwrite("name", &Pet::name); + + // Method 1: template parameter: + py::class_(m, "Dog") + .def(py::init()) + .def("bark", &Dog::bark); + +Alternatively, we can also assign a name to the previously bound ``Pet`` +:class:`class_` object and reference it when binding the ``Dog`` class: + +.. code-block:: cpp + + py::class_ pet(m, "Pet"); + pet.def(py::init()) + .def_readwrite("name", &Pet::name); + + // Method 2: pass parent class_ object: + py::class_(m, "Dog", pet /* <- specify Python parent type */) + .def(py::init()) + .def("bark", &Dog::bark); + +Functionality-wise, both approaches are equivalent. Afterwards, instances will +expose fields and methods of both types: + +.. code-block:: pycon + + >>> p = example.Dog('Molly') + >>> p.name + u'Molly' + >>> p.bark() + u'woof!' + +The C++ classes defined above are regular non-polymorphic types with an +inheritance relationship. This is reflected in Python: + +.. code-block:: cpp + + // Return a base pointer to a derived instance + m.def("pet_store", []() { return std::unique_ptr(new Dog("Molly")); }); + +.. code-block:: pycon + + >>> p = example.pet_store() + >>> type(p) # `Dog` instance behind `Pet` pointer + Pet # no pointer downcasting for regular non-polymorphic types + >>> p.bark() + AttributeError: 'Pet' object has no attribute 'bark' + +The function returned a ``Dog`` instance, but because it's a non-polymorphic +type behind a base pointer, Python only sees a ``Pet``. In C++, a type is only +considered polymorphic if it has at least one virtual function and pybind11 +will automatically recognize this: + +.. code-block:: cpp + + struct PolymorphicPet { + virtual ~PolymorphicPet() = default; + }; + + struct PolymorphicDog : PolymorphicPet { + std::string bark() const { return "woof!"; } + }; + + // Same binding code + py::class_(m, "PolymorphicPet"); + py::class_(m, "PolymorphicDog") + .def(py::init<>()) + .def("bark", &PolymorphicDog::bark); + + // Again, return a base pointer to a derived instance + m.def("pet_store2", []() { return std::unique_ptr(new PolymorphicDog); }); + +.. code-block:: pycon + + >>> p = example.pet_store2() + >>> type(p) + PolymorphicDog # automatically downcast + >>> p.bark() + u'woof!' + +Given a pointer to a polymorphic base, pybind11 performs automatic downcasting +to the actual derived type. Note that this goes beyond the usual situation in +C++: we don't just get access to the virtual functions of the base, we get the +concrete derived type including functions and attributes that the base type may +not even be aware of. + +.. seealso:: + + For more information about polymorphic behavior see :ref:`overriding_virtuals`. + + +Overloaded methods +================== + +Sometimes there are several overloaded C++ methods with the same name taking +different kinds of input arguments: + +.. code-block:: cpp + + struct Pet { + Pet(const std::string &name, int age) : name(name), age(age) { } + + void set(int age_) { age = age_; } + void set(const std::string &name_) { name = name_; } + + std::string name; + int age; + }; + +Attempting to bind ``Pet::set`` will cause an error since the compiler does not +know which method the user intended to select. We can disambiguate by casting +them to function pointers. Binding multiple functions to the same Python name +automatically creates a chain of function overloads that will be tried in +sequence. + +.. code-block:: cpp + + py::class_(m, "Pet") + .def(py::init()) + .def("set", static_cast(&Pet::set), "Set the pet's age") + .def("set", static_cast(&Pet::set), "Set the pet's name"); + +The overload signatures are also visible in the method's docstring: + +.. code-block:: pycon + + >>> help(example.Pet) + + class Pet(__builtin__.object) + | Methods defined here: + | + | __init__(...) + | Signature : (Pet, str, int) -> NoneType + | + | set(...) + | 1. Signature : (Pet, int) -> NoneType + | + | Set the pet's age + | + | 2. Signature : (Pet, str) -> NoneType + | + | Set the pet's name + +If you have a C++14 compatible compiler [#cpp14]_, you can use an alternative +syntax to cast the overloaded function: + +.. code-block:: cpp + + py::class_(m, "Pet") + .def("set", py::overload_cast(&Pet::set), "Set the pet's age") + .def("set", py::overload_cast(&Pet::set), "Set the pet's name"); + +Here, ``py::overload_cast`` only requires the parameter types to be specified. +The return type and class are deduced. This avoids the additional noise of +``void (Pet::*)()`` as seen in the raw cast. If a function is overloaded based +on constness, the ``py::const_`` tag should be used: + +.. code-block:: cpp + + struct Widget { + int foo(int x, float y); + int foo(int x, float y) const; + }; + + py::class_(m, "Widget") + .def("foo_mutable", py::overload_cast(&Widget::foo)) + .def("foo_const", py::overload_cast(&Widget::foo, py::const_)); + +If you prefer the ``py::overload_cast`` syntax but have a C++11 compatible compiler only, +you can use ``py::detail::overload_cast_impl`` with an additional set of parentheses: + +.. code-block:: cpp + + template + using overload_cast_ = pybind11::detail::overload_cast_impl; + + py::class_(m, "Pet") + .def("set", overload_cast_()(&Pet::set), "Set the pet's age") + .def("set", overload_cast_()(&Pet::set), "Set the pet's name"); + +.. [#cpp14] A compiler which supports the ``-std=c++14`` flag + or Visual Studio 2015 Update 2 and newer. + +.. note:: + + To define multiple overloaded constructors, simply declare one after the + other using the ``.def(py::init<...>())`` syntax. The existing machinery + for specifying keyword and default arguments also works. + +Enumerations and internal types +=============================== + +Let's now suppose that the example class contains an internal enumeration type, +e.g.: + +.. code-block:: cpp + + struct Pet { + enum Kind { + Dog = 0, + Cat + }; + + Pet(const std::string &name, Kind type) : name(name), type(type) { } + + std::string name; + Kind type; + }; + +The binding code for this example looks as follows: + +.. code-block:: cpp + + py::class_ pet(m, "Pet"); + + pet.def(py::init()) + .def_readwrite("name", &Pet::name) + .def_readwrite("type", &Pet::type); + + py::enum_(pet, "Kind") + .value("Dog", Pet::Kind::Dog) + .value("Cat", Pet::Kind::Cat) + .export_values(); + +To ensure that the ``Kind`` type is created within the scope of ``Pet``, the +``pet`` :class:`class_` instance must be supplied to the :class:`enum_`. +constructor. The :func:`enum_::export_values` function exports the enum entries +into the parent scope, which should be skipped for newer C++11-style strongly +typed enums. + +.. code-block:: pycon + + >>> p = Pet('Lucy', Pet.Cat) + >>> p.type + Kind.Cat + >>> int(p.type) + 1L + +The entries defined by the enumeration type are exposed in the ``__members__`` property: + +.. code-block:: pycon + + >>> Pet.Kind.__members__ + {'Dog': Kind.Dog, 'Cat': Kind.Cat} + +The ``name`` property returns the name of the enum value as a unicode string. + +.. note:: + + It is also possible to use ``str(enum)``, however these accomplish different + goals. The following shows how these two approaches differ. + + .. code-block:: pycon + + >>> p = Pet( "Lucy", Pet.Cat ) + >>> pet_type = p.type + >>> pet_type + Pet.Cat + >>> str(pet_type) + 'Pet.Cat' + >>> pet_type.name + 'Cat' + +.. note:: + + When the special tag ``py::arithmetic()`` is specified to the ``enum_`` + constructor, pybind11 creates an enumeration that also supports rudimentary + arithmetic and bit-level operations like comparisons, and, or, xor, negation, + etc. + + .. code-block:: cpp + + py::enum_(pet, "Kind", py::arithmetic()) + ... + + By default, these are omitted to conserve space. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/cmake/index.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/cmake/index.rst new file mode 100644 index 0000000000000000000000000000000000000000..eaf66d70f31fadc25bc6810aa458854893b9db6e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/cmake/index.rst @@ -0,0 +1,8 @@ +CMake helpers +------------- + +Pybind11 can be used with ``add_subdirectory(extern/pybind11)``, or from an +install with ``find_package(pybind11 CONFIG)``. The interface provided in +either case is functionally identical. + +.. cmake-module:: ../../tools/pybind11Config.cmake.in diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/compiling.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/compiling.rst new file mode 100644 index 0000000000000000000000000000000000000000..3a8a270d582c04e240856ff769efc251ee45e41e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/compiling.rst @@ -0,0 +1,642 @@ +.. _compiling: + +Build systems +############# + +.. _build-setuptools: + +Building with setuptools +======================== + +For projects on PyPI, building with setuptools is the way to go. Sylvain Corlay +has kindly provided an example project which shows how to set up everything, +including automatic generation of documentation using Sphinx. Please refer to +the [python_example]_ repository. + +.. [python_example] https://github.com/pybind/python_example + +A helper file is provided with pybind11 that can simplify usage with setuptools. + +To use pybind11 inside your ``setup.py``, you have to have some system to +ensure that ``pybind11`` is installed when you build your package. There are +four possible ways to do this, and pybind11 supports all four: You can ask all +users to install pybind11 beforehand (bad), you can use +:ref:`setup_helpers-pep518` (good, but very new and requires Pip 10), +:ref:`setup_helpers-setup_requires` (discouraged by Python packagers now that +PEP 518 is available, but it still works everywhere), or you can +:ref:`setup_helpers-copy-manually` (always works but you have to manually sync +your copy to get updates). + +An example of a ``setup.py`` using pybind11's helpers: + +.. code-block:: python + + from glob import glob + from setuptools import setup + from pybind11.setup_helpers import Pybind11Extension + + ext_modules = [ + Pybind11Extension( + "python_example", + sorted(glob("src/*.cpp")), # Sort source files for reproducibility + ), + ] + + setup( + ..., + ext_modules=ext_modules + ) + +If you want to do an automatic search for the highest supported C++ standard, +that is supported via a ``build_ext`` command override; it will only affect +``Pybind11Extensions``: + +.. code-block:: python + + from glob import glob + from setuptools import setup + from pybind11.setup_helpers import Pybind11Extension, build_ext + + ext_modules = [ + Pybind11Extension( + "python_example", + sorted(glob("src/*.cpp")), + ), + ] + + setup( + ..., + cmdclass={"build_ext": build_ext}, + ext_modules=ext_modules + ) + +Since pybind11 does not require NumPy when building, a light-weight replacement +for NumPy's parallel compilation distutils tool is included. Use it like this: + +.. code-block:: python + + from pybind11.setup_helpers import ParallelCompile + + # Optional multithreaded build + ParallelCompile("NPY_NUM_BUILD_JOBS").install() + + setup(...) + +The argument is the name of an environment variable to control the number of +threads, such as ``NPY_NUM_BUILD_JOBS`` (as used by NumPy), though you can set +something different if you want; ``CMAKE_BUILD_PARALLEL_LEVEL`` is another choice +a user might expect. You can also pass ``default=N`` to set the default number +of threads (0 will take the number of threads available) and ``max=N``, the +maximum number of threads; if you have a large extension you may want set this +to a memory dependent number. + +If you are developing rapidly and have a lot of C++ files, you may want to +avoid rebuilding files that have not changed. For simple cases were you are +using ``pip install -e .`` and do not have local headers, you can skip the +rebuild if a object file is newer than it's source (headers are not checked!) +with the following: + +.. code-block:: python + + from pybind11.setup_helpers import ParallelCompile, naive_recompile + + SmartCompile("NPY_NUM_BUILD_JOBS", needs_recompile=naive_recompile).install() + + +If you have a more complex build, you can implement a smarter function and pass +it to ``needs_recompile``, or you can use [Ccache]_ instead. ``CXX="cache g++" +pip install -e .`` would be the way to use it with GCC, for example. Unlike the +simple solution, this even works even when not compiling in editable mode, but +it does require Ccache to be installed. + +Keep in mind that Pip will not even attempt to rebuild if it thinks it has +already built a copy of your code, which it deduces from the version number. +One way to avoid this is to use [setuptools_scm]_, which will generate a +version number that includes the number of commits since your last tag and a +hash for a dirty directory. Another way to force a rebuild is purge your cache +or use Pip's ``--no-cache-dir`` option. + +.. [Ccache] https://ccache.dev + +.. [setuptools_scm] https://github.com/pypa/setuptools_scm + +.. _setup_helpers-pep518: + +PEP 518 requirements (Pip 10+ required) +--------------------------------------- + +If you use `PEP 518's `_ +``pyproject.toml`` file, you can ensure that ``pybind11`` is available during +the compilation of your project. When this file exists, Pip will make a new +virtual environment, download just the packages listed here in ``requires=``, +and build a wheel (binary Python package). It will then throw away the +environment, and install your wheel. + +Your ``pyproject.toml`` file will likely look something like this: + +.. code-block:: toml + + [build-system] + requires = ["setuptools>=42", "wheel", "pybind11~=2.6.1"] + build-backend = "setuptools.build_meta" + +.. note:: + + The main drawback to this method is that a `PEP 517`_ compliant build tool, + such as Pip 10+, is required for this approach to work; older versions of + Pip completely ignore this file. If you distribute binaries (called wheels + in Python) using something like `cibuildwheel`_, remember that ``setup.py`` + and ``pyproject.toml`` are not even contained in the wheel, so this high + Pip requirement is only for source builds, and will not affect users of + your binary wheels. If you are building SDists and wheels, then + `pypa-build`_ is the recommended offical tool. + +.. _PEP 517: https://www.python.org/dev/peps/pep-0517/ +.. _cibuildwheel: https://cibuildwheel.readthedocs.io +.. _pypa-build: https://pypa-build.readthedocs.io/en/latest/ + +.. _setup_helpers-setup_requires: + +Classic ``setup_requires`` +-------------------------- + +If you want to support old versions of Pip with the classic +``setup_requires=["pybind11"]`` keyword argument to setup, which triggers a +two-phase ``setup.py`` run, then you will need to use something like this to +ensure the first pass works (which has not yet installed the ``setup_requires`` +packages, since it can't install something it does not know about): + +.. code-block:: python + + try: + from pybind11.setup_helpers import Pybind11Extension + except ImportError: + from setuptools import Extension as Pybind11Extension + + +It doesn't matter that the Extension class is not the enhanced subclass for the +first pass run; and the second pass will have the ``setup_requires`` +requirements. + +This is obviously more of a hack than the PEP 518 method, but it supports +ancient versions of Pip. + +.. _setup_helpers-copy-manually: + +Copy manually +------------- + +You can also copy ``setup_helpers.py`` directly to your project; it was +designed to be usable standalone, like the old example ``setup.py``. You can +set ``include_pybind11=False`` to skip including the pybind11 package headers, +so you can use it with git submodules and a specific git version. If you use +this, you will need to import from a local file in ``setup.py`` and ensure the +helper file is part of your MANIFEST. + + +Closely related, if you include pybind11 as a subproject, you can run the +``setup_helpers.py`` inplace. If loaded correctly, this should even pick up +the correct include for pybind11, though you can turn it off as shown above if +you want to input it manually. + +Suggested usage if you have pybind11 as a submodule in ``extern/pybind11``: + +.. code-block:: python + + DIR = os.path.abspath(os.path.dirname(__file__)) + + sys.path.append(os.path.join(DIR, "extern", "pybind11")) + from pybind11.setup_helpers import Pybind11Extension # noqa: E402 + + del sys.path[-1] + + +.. versionchanged:: 2.6 + + Added ``setup_helpers`` file. + +Building with cppimport +======================== + +[cppimport]_ is a small Python import hook that determines whether there is a C++ +source file whose name matches the requested module. If there is, the file is +compiled as a Python extension using pybind11 and placed in the same folder as +the C++ source file. Python is then able to find the module and load it. + +.. [cppimport] https://github.com/tbenthompson/cppimport + +.. _cmake: + +Building with CMake +=================== + +For C++ codebases that have an existing CMake-based build system, a Python +extension module can be created with just a few lines of code: + +.. code-block:: cmake + + cmake_minimum_required(VERSION 3.4...3.18) + project(example LANGUAGES CXX) + + add_subdirectory(pybind11) + pybind11_add_module(example example.cpp) + +This assumes that the pybind11 repository is located in a subdirectory named +:file:`pybind11` and that the code is located in a file named :file:`example.cpp`. +The CMake command ``add_subdirectory`` will import the pybind11 project which +provides the ``pybind11_add_module`` function. It will take care of all the +details needed to build a Python extension module on any platform. + +A working sample project, including a way to invoke CMake from :file:`setup.py` for +PyPI integration, can be found in the [cmake_example]_ repository. + +.. [cmake_example] https://github.com/pybind/cmake_example + +.. versionchanged:: 2.6 + CMake 3.4+ is required. + +Further information can be found at :doc:`cmake/index`. + +pybind11_add_module +------------------- + +To ease the creation of Python extension modules, pybind11 provides a CMake +function with the following signature: + +.. code-block:: cmake + + pybind11_add_module( [MODULE | SHARED] [EXCLUDE_FROM_ALL] + [NO_EXTRAS] [THIN_LTO] [OPT_SIZE] source1 [source2 ...]) + +This function behaves very much like CMake's builtin ``add_library`` (in fact, +it's a wrapper function around that command). It will add a library target +called ```` to be built from the listed source files. In addition, it +will take care of all the Python-specific compiler and linker flags as well +as the OS- and Python-version-specific file extension. The produced target +```` can be further manipulated with regular CMake commands. + +``MODULE`` or ``SHARED`` may be given to specify the type of library. If no +type is given, ``MODULE`` is used by default which ensures the creation of a +Python-exclusive module. Specifying ``SHARED`` will create a more traditional +dynamic library which can also be linked from elsewhere. ``EXCLUDE_FROM_ALL`` +removes this target from the default build (see CMake docs for details). + +Since pybind11 is a template library, ``pybind11_add_module`` adds compiler +flags to ensure high quality code generation without bloat arising from long +symbol names and duplication of code in different translation units. It +sets default visibility to *hidden*, which is required for some pybind11 +features and functionality when attempting to load multiple pybind11 modules +compiled under different pybind11 versions. It also adds additional flags +enabling LTO (Link Time Optimization) and strip unneeded symbols. See the +:ref:`FAQ entry ` for a more detailed explanation. These +latter optimizations are never applied in ``Debug`` mode. If ``NO_EXTRAS`` is +given, they will always be disabled, even in ``Release`` mode. However, this +will result in code bloat and is generally not recommended. + +As stated above, LTO is enabled by default. Some newer compilers also support +different flavors of LTO such as `ThinLTO`_. Setting ``THIN_LTO`` will cause +the function to prefer this flavor if available. The function falls back to +regular LTO if ``-flto=thin`` is not available. If +``CMAKE_INTERPROCEDURAL_OPTIMIZATION`` is set (either ``ON`` or ``OFF``), then +that will be respected instead of the built-in flag search. + +.. note:: + + If you want to set the property form on targets or the + ``CMAKE_INTERPROCEDURAL_OPTIMIZATION_`` versions of this, you should + still use ``set(CMAKE_INTERPROCEDURAL_OPTIMIZATION OFF)`` (otherwise a + no-op) to disable pybind11's ipo flags. + +The ``OPT_SIZE`` flag enables size-based optimization equivalent to the +standard ``/Os`` or ``-Os`` compiler flags and the ``MinSizeRel`` build type, +which avoid optimizations that that can substantially increase the size of the +resulting binary. This flag is particularly useful in projects that are split +into performance-critical parts and associated bindings. In this case, we can +compile the project in release mode (and hence, optimize performance globally), +and specify ``OPT_SIZE`` for the binding target, where size might be the main +concern as performance is often less critical here. A ~25% size reduction has +been observed in practice. This flag only changes the optimization behavior at +a per-target level and takes precedence over the global CMake build type +(``Release``, ``RelWithDebInfo``) except for ``Debug`` builds, where +optimizations remain disabled. + +.. _ThinLTO: http://clang.llvm.org/docs/ThinLTO.html + +Configuration variables +----------------------- + +By default, pybind11 will compile modules with the compiler default or the +minimum standard required by pybind11, whichever is higher. You can set the +standard explicitly with +`CMAKE_CXX_STANDARD `_: + +.. code-block:: cmake + + set(CMAKE_CXX_STANDARD 14 CACHE STRING "C++ version selection") # or 11, 14, 17, 20 + set(CMAKE_CXX_STANDARD_REQUIRED ON) # optional, ensure standard is supported + set(CMAKE_CXX_EXTENSIONS OFF) # optional, keep compiler extensionsn off + +The variables can also be set when calling CMake from the command line using +the ``-D=`` flag. You can also manually set ``CXX_STANDARD`` +on a target or use ``target_compile_features`` on your targets - anything that +CMake supports. + +Classic Python support: The target Python version can be selected by setting +``PYBIND11_PYTHON_VERSION`` or an exact Python installation can be specified +with ``PYTHON_EXECUTABLE``. For example: + +.. code-block:: bash + + cmake -DPYBIND11_PYTHON_VERSION=3.6 .. + + # Another method: + cmake -DPYTHON_EXECUTABLE=/path/to/python .. + + # This often is a good way to get the current Python, works in environments: + cmake -DPYTHON_EXECUTABLE=$(python3 -c "import sys; print(sys.executable)") .. + + +find_package vs. add_subdirectory +--------------------------------- + +For CMake-based projects that don't include the pybind11 repository internally, +an external installation can be detected through ``find_package(pybind11)``. +See the `Config file`_ docstring for details of relevant CMake variables. + +.. code-block:: cmake + + cmake_minimum_required(VERSION 3.4...3.18) + project(example LANGUAGES CXX) + + find_package(pybind11 REQUIRED) + pybind11_add_module(example example.cpp) + +Note that ``find_package(pybind11)`` will only work correctly if pybind11 +has been correctly installed on the system, e. g. after downloading or cloning +the pybind11 repository : + +.. code-block:: bash + + # Classic CMake + cd pybind11 + mkdir build + cd build + cmake .. + make install + + # CMake 3.15+ + cd pybind11 + cmake -S . -B build + cmake --build build -j 2 # Build on 2 cores + cmake --install build + +Once detected, the aforementioned ``pybind11_add_module`` can be employed as +before. The function usage and configuration variables are identical no matter +if pybind11 is added as a subdirectory or found as an installed package. You +can refer to the same [cmake_example]_ repository for a full sample project +-- just swap out ``add_subdirectory`` for ``find_package``. + +.. _Config file: https://github.com/pybind/pybind11/blob/master/tools/pybind11Config.cmake.in + + +.. _find-python-mode: + +FindPython mode +--------------- + +CMake 3.12+ (3.15+ recommended, 3.18.2+ ideal) added a new module called +FindPython that had a highly improved search algorithm and modern targets +and tools. If you use FindPython, pybind11 will detect this and use the +existing targets instead: + +.. code-block:: cmake + + cmake_minumum_required(VERSION 3.15...3.19) + project(example LANGUAGES CXX) + + find_package(Python COMPONENTS Interpreter Development REQUIRED) + find_package(pybind11 CONFIG REQUIRED) + # or add_subdirectory(pybind11) + + pybind11_add_module(example example.cpp) + +You can also use the targets (as listed below) with FindPython. If you define +``PYBIND11_FINDPYTHON``, pybind11 will perform the FindPython step for you +(mostly useful when building pybind11's own tests, or as a way to change search +algorithms from the CMake invocation, with ``-DPYBIND11_FINDPYTHON=ON``. + +.. warning:: + + If you use FindPython2 and FindPython3 to dual-target Python, use the + individual targets listed below, and avoid targets that directly include + Python parts. + +There are `many ways to hint or force a discovery of a specific Python +installation `_), +setting ``Python_ROOT_DIR`` may be the most common one (though with +virtualenv/venv support, and Conda support, this tends to find the correct +Python version more often than the old system did). + +.. warning:: + + When the Python libraries (i.e. ``libpythonXX.a`` and ``libpythonXX.so`` + on Unix) are not available, as is the case on a manylinux image, the + ``Development`` component will not be resolved by ``FindPython``. When not + using the embedding functionality, CMake 3.18+ allows you to specify + ``Development.Module`` instead of ``Development`` to resolve this issue. + +.. versionadded:: 2.6 + +Advanced: interface library targets +----------------------------------- + +Pybind11 supports modern CMake usage patterns with a set of interface targets, +available in all modes. The targets provided are: + + ``pybind11::headers`` + Just the pybind11 headers and minimum compile requirements + + ``pybind11::python2_no_register`` + Quiets the warning/error when mixing C++14 or higher and Python 2 + + ``pybind11::pybind11`` + Python headers + ``pybind11::headers`` + ``pybind11::python2_no_register`` (Python 2 only) + + ``pybind11::python_link_helper`` + Just the "linking" part of pybind11:module + + ``pybind11::module`` + Everything for extension modules - ``pybind11::pybind11`` + ``Python::Module`` (FindPython CMake 3.15+) or ``pybind11::python_link_helper`` + + ``pybind11::embed`` + Everything for embedding the Python interpreter - ``pybind11::pybind11`` + ``Python::Embed`` (FindPython) or Python libs + + ``pybind11::lto`` / ``pybind11::thin_lto`` + An alternative to `INTERPROCEDURAL_OPTIMIZATION` for adding link-time optimization. + + ``pybind11::windows_extras`` + ``/bigobj`` and ``/mp`` for MSVC. + + ``pybind11::opt_size`` + ``/Os`` for MSVC, ``-Os`` for other compilers. Does nothing for debug builds. + +Two helper functions are also provided: + + ``pybind11_strip(target)`` + Strips a target (uses ``CMAKE_STRIP`` after the target is built) + + ``pybind11_extension(target)`` + Sets the correct extension (with SOABI) for a target. + +You can use these targets to build complex applications. For example, the +``add_python_module`` function is identical to: + +.. code-block:: cmake + + cmake_minimum_required(VERSION 3.4) + project(example LANGUAGES CXX) + + find_package(pybind11 REQUIRED) # or add_subdirectory(pybind11) + + add_library(example MODULE main.cpp) + + target_link_libraries(example PRIVATE pybind11::module pybind11::lto pybind11::windows_extras) + + pybind11_extension(example) + pybind11_strip(example) + + set_target_properties(example PROPERTIES CXX_VISIBILITY_PRESET "hidden" + CUDA_VISIBILITY_PRESET "hidden") + +Instead of setting properties, you can set ``CMAKE_*`` variables to initialize these correctly. + +.. warning:: + + Since pybind11 is a metatemplate library, it is crucial that certain + compiler flags are provided to ensure high quality code generation. In + contrast to the ``pybind11_add_module()`` command, the CMake interface + provides a *composable* set of targets to ensure that you retain flexibility. + It can be expecially important to provide or set these properties; the + :ref:`FAQ ` contains an explanation on why these are needed. + +.. versionadded:: 2.6 + +.. _nopython-mode: + +Advanced: NOPYTHON mode +----------------------- + +If you want complete control, you can set ``PYBIND11_NOPYTHON`` to completely +disable Python integration (this also happens if you run ``FindPython2`` and +``FindPython3`` without running ``FindPython``). This gives you complete +freedom to integrate into an existing system (like `Scikit-Build's +`_ ``PythonExtensions``). +``pybind11_add_module`` and ``pybind11_extension`` will be unavailable, and the +targets will be missing any Python specific behavior. + +.. versionadded:: 2.6 + +Embedding the Python interpreter +-------------------------------- + +In addition to extension modules, pybind11 also supports embedding Python into +a C++ executable or library. In CMake, simply link with the ``pybind11::embed`` +target. It provides everything needed to get the interpreter running. The Python +headers and libraries are attached to the target. Unlike ``pybind11::module``, +there is no need to manually set any additional properties here. For more +information about usage in C++, see :doc:`/advanced/embedding`. + +.. code-block:: cmake + + cmake_minimum_required(VERSION 3.4...3.18) + project(example LANGUAGES CXX) + + find_package(pybind11 REQUIRED) # or add_subdirectory(pybind11) + + add_executable(example main.cpp) + target_link_libraries(example PRIVATE pybind11::embed) + +.. _building_manually: + +Building manually +================= + +pybind11 is a header-only library, hence it is not necessary to link against +any special libraries and there are no intermediate (magic) translation steps. + +On Linux, you can compile an example such as the one given in +:ref:`simple_example` using the following command: + +.. code-block:: bash + + $ c++ -O3 -Wall -shared -std=c++11 -fPIC $(python3 -m pybind11 --includes) example.cpp -o example$(python3-config --extension-suffix) + +The flags given here assume that you're using Python 3. For Python 2, just +change the executable appropriately (to ``python`` or ``python2``). + +The ``python3 -m pybind11 --includes`` command fetches the include paths for +both pybind11 and Python headers. This assumes that pybind11 has been installed +using ``pip`` or ``conda``. If it hasn't, you can also manually specify +``-I /include`` together with the Python includes path +``python3-config --includes``. + +Note that Python 2.7 modules don't use a special suffix, so you should simply +use ``example.so`` instead of ``example$(python3-config --extension-suffix)``. +Besides, the ``--extension-suffix`` option may or may not be available, depending +on the distribution; in the latter case, the module extension can be manually +set to ``.so``. + +On macOS: the build command is almost the same but it also requires passing +the ``-undefined dynamic_lookup`` flag so as to ignore missing symbols when +building the module: + +.. code-block:: bash + + $ c++ -O3 -Wall -shared -std=c++11 -undefined dynamic_lookup $(python3 -m pybind11 --includes) example.cpp -o example$(python3-config --extension-suffix) + +In general, it is advisable to include several additional build parameters +that can considerably reduce the size of the created binary. Refer to section +:ref:`cmake` for a detailed example of a suitable cross-platform CMake-based +build system that works on all platforms including Windows. + +.. note:: + + On Linux and macOS, it's better to (intentionally) not link against + ``libpython``. The symbols will be resolved when the extension library + is loaded into a Python binary. This is preferable because you might + have several different installations of a given Python version (e.g. the + system-provided Python, and one that ships with a piece of commercial + software). In this way, the plugin will work with both versions, instead + of possibly importing a second Python library into a process that already + contains one (which will lead to a segfault). + + +Building with Bazel +=================== + +You can build with the Bazel build system using the `pybind11_bazel +`_ repository. + +Generating binding code automatically +===================================== + +The ``Binder`` project is a tool for automatic generation of pybind11 binding +code by introspecting existing C++ codebases using LLVM/Clang. See the +[binder]_ documentation for details. + +.. [binder] http://cppbinder.readthedocs.io/en/latest/about.html + +[AutoWIG]_ is a Python library that wraps automatically compiled libraries into +high-level languages. It parses C++ code using LLVM/Clang technologies and +generates the wrappers using the Mako templating engine. The approach is automatic, +extensible, and applies to very complex C++ libraries, composed of thousands of +classes or incorporating modern meta-programming constructs. + +.. [AutoWIG] https://github.com/StatisKit/AutoWIG + +[robotpy-build]_ is a is a pure python, cross platform build tool that aims to +simplify creation of python wheels for pybind11 projects, and provide +cross-project dependency management. Additionally, it is able to autogenerate +customizable pybind11-based wrappers by parsing C++ header files. + +.. [robotpy-build] https://robotpy-build.readthedocs.io diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/conf.py b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/conf.py new file mode 100644 index 0000000000000000000000000000000000000000..6ac054c6b88bdf36a6e75950fae5ae05540ab26f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/conf.py @@ -0,0 +1,382 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +# +# pybind11 documentation build configuration file, created by +# sphinx-quickstart on Sun Oct 11 19:23:48 2015. +# +# This file is execfile()d with the current directory set to its +# containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys +import os +import shlex +import subprocess +from pathlib import Path +import re + +DIR = Path(__file__).parent.resolve() + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# sys.path.insert(0, os.path.abspath('.')) + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +# needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + "breathe", + "sphinxcontrib.rsvgconverter", + "sphinxcontrib.moderncmakedomain", +] + +breathe_projects = {"pybind11": ".build/doxygenxml/"} +breathe_default_project = "pybind11" +breathe_domain_by_extension = {"h": "cpp"} + +# Add any paths that contain templates here, relative to this directory. +templates_path = [".templates"] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# source_suffix = ['.rst', '.md'] +source_suffix = ".rst" + +# The encoding of source files. +# source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = "index" + +# General information about the project. +project = "pybind11" +copyright = "2017, Wenzel Jakob" +author = "Wenzel Jakob" + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. + +# Read the listed version +with open("../pybind11/_version.py") as f: + code = compile(f.read(), "../pybind11/_version.py", "exec") +loc = {} +exec(code, loc) + +# The full version, including alpha/beta/rc tags. +version = loc["__version__"] + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# +# This is also used if you do content translation via gettext catalogs. +# Usually you set "language" from the command line for these cases. +language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +# today = '' +# Else, today_fmt is used as the format for a strftime call. +# today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = [".build", "release.rst"] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +default_role = "any" + +# If true, '()' will be appended to :func: etc. cross-reference text. +# add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +# add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +# show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +# pygments_style = 'monokai' + +# A list of ignored prefixes for module index sorting. +# modindex_common_prefix = [] + +# If true, keep warnings as "system message" paragraphs in the built documents. +# keep_warnings = False + +# If true, `todo` and `todoList` produce output, else they produce nothing. +todo_include_todos = False + + +# -- Options for HTML output ---------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. + +on_rtd = os.environ.get("READTHEDOCS", None) == "True" + +if not on_rtd: # only import and set the theme if we're building docs locally + import sphinx_rtd_theme + + html_theme = "sphinx_rtd_theme" + html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] + + html_context = {"css_files": ["_static/theme_overrides.css"]} +else: + html_context = { + "css_files": [ + "//media.readthedocs.org/css/sphinx_rtd_theme.css", + "//media.readthedocs.org/css/readthedocs-doc-embed.css", + "_static/theme_overrides.css", + ] + } + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +# html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +# html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +# html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +# html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +# html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +# html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ["_static"] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +# html_extra_path = [] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +# html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +# html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +# html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +# html_additional_pages = {} + +# If false, no module index is generated. +# html_domain_indices = True + +# If false, no index is generated. +# html_use_index = True + +# If true, the index is split into individual pages for each letter. +# html_split_index = False + +# If true, links to the reST sources are added to the pages. +# html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +# html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +# html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +# html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +# html_file_suffix = None + +# Language to be used for generating the HTML full-text search index. +# Sphinx supports the following languages: +# 'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja' +# 'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr' +# html_search_language = 'en' + +# A dictionary with options for the search language support, empty by default. +# Now only 'ja' uses this config value +# html_search_options = {'type': 'default'} + +# The name of a javascript file (relative to the configuration directory) that +# implements a search results scorer. If empty, the default will be used. +# html_search_scorer = 'scorer.js' + +# Output file base name for HTML help builder. +htmlhelp_basename = "pybind11doc" + +# -- Options for LaTeX output --------------------------------------------- + +latex_engine = "pdflatex" + +latex_elements = { + # The paper size ('letterpaper' or 'a4paper'). + # 'papersize': 'letterpaper', + # + # The font size ('10pt', '11pt' or '12pt'). + # 'pointsize': '10pt', + # + # Additional stuff for the LaTeX preamble. + # remove blank pages (between the title page and the TOC, etc.) + "classoptions": ",openany,oneside", + "preamble": r""" +\usepackage{fontawesome} +\usepackage{textgreek} +\DeclareUnicodeCharacter{00A0}{} +\DeclareUnicodeCharacter{2194}{\faArrowsH} +\DeclareUnicodeCharacter{1F382}{\faBirthdayCake} +\DeclareUnicodeCharacter{1F355}{\faAdjust} +\DeclareUnicodeCharacter{0301}{'} +\DeclareUnicodeCharacter{03C0}{\textpi} + +""", + # Latex figure (float) alignment + # 'figure_align': 'htbp', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + (master_doc, "pybind11.tex", "pybind11 Documentation", "Wenzel Jakob", "manual"), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +# latex_logo = 'pybind11-logo.png' + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +# latex_use_parts = False + +# If true, show page references after internal links. +# latex_show_pagerefs = False + +# If true, show URL addresses after external links. +# latex_show_urls = False + +# Documents to append as an appendix to all manuals. +# latex_appendices = [] + +# If false, no module index is generated. +# latex_domain_indices = True + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [(master_doc, "pybind11", "pybind11 Documentation", [author], 1)] + +# If true, show URL addresses after external links. +# man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ( + master_doc, + "pybind11", + "pybind11 Documentation", + author, + "pybind11", + "One line description of project.", + "Miscellaneous", + ), +] + +# Documents to append as an appendix to all manuals. +# texinfo_appendices = [] + +# If false, no module index is generated. +# texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +# texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +# texinfo_no_detailmenu = False + +primary_domain = "cpp" +highlight_language = "cpp" + + +def generate_doxygen_xml(app): + build_dir = os.path.join(app.confdir, ".build") + if not os.path.exists(build_dir): + os.mkdir(build_dir) + + try: + subprocess.call(["doxygen", "--version"]) + retcode = subprocess.call(["doxygen"], cwd=app.confdir) + if retcode < 0: + sys.stderr.write("doxygen error code: {}\n".format(-retcode)) + except OSError as e: + sys.stderr.write("doxygen execution failed: {}\n".format(e)) + + +def prepare(app): + with open(DIR.parent / "README.rst") as f: + contents = f.read() + + if app.builder.name == "latex": + # Remove badges and stuff from start + contents = contents[contents.find(r".. start") :] + + # Filter out section titles for index.rst for LaTeX + contents = re.sub(r"^(.*)\n[-~]{3,}$", r"**\1**", contents, flags=re.MULTILINE) + + with open(DIR / "readme.rst", "w") as f: + f.write(contents) + + +def clean_up(app, exception): + (DIR / "readme.rst").unlink() + + +def setup(app): + + # Add hook for building doxygen xml when needed + app.connect("builder-inited", generate_doxygen_xml) + + # Copy the readme in + app.connect("builder-inited", prepare) + + # Clean up the generated readme + app.connect("build-finished", clean_up) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/faq.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/faq.rst new file mode 100644 index 0000000000000000000000000000000000000000..8c0b0f9fc22df57a6ef57282182b5fa5d63a228a --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/faq.rst @@ -0,0 +1,343 @@ +Frequently asked questions +########################## + +"ImportError: dynamic module does not define init function" +=========================================================== + +1. Make sure that the name specified in PYBIND11_MODULE is identical to the +filename of the extension library (without suffixes such as .so) + +2. If the above did not fix the issue, you are likely using an incompatible +version of Python (for instance, the extension library was compiled against +Python 2, while the interpreter is running on top of some version of Python +3, or vice versa). + +"Symbol not found: ``__Py_ZeroStruct`` / ``_PyInstanceMethod_Type``" +======================================================================== + +See the first answer. + +"SystemError: dynamic module not initialized properly" +====================================================== + +See the first answer. + +The Python interpreter immediately crashes when importing my module +=================================================================== + +See the first answer. + +.. _faq_reference_arguments: + +Limitations involving reference arguments +========================================= + +In C++, it's fairly common to pass arguments using mutable references or +mutable pointers, which allows both read and write access to the value +supplied by the caller. This is sometimes done for efficiency reasons, or to +realize functions that have multiple return values. Here are two very basic +examples: + +.. code-block:: cpp + + void increment(int &i) { i++; } + void increment_ptr(int *i) { (*i)++; } + +In Python, all arguments are passed by reference, so there is no general +issue in binding such code from Python. + +However, certain basic Python types (like ``str``, ``int``, ``bool``, +``float``, etc.) are **immutable**. This means that the following attempt +to port the function to Python doesn't have the same effect on the value +provided by the caller -- in fact, it does nothing at all. + +.. code-block:: python + + def increment(i): + i += 1 # nope.. + +pybind11 is also affected by such language-level conventions, which means that +binding ``increment`` or ``increment_ptr`` will also create Python functions +that don't modify their arguments. + +Although inconvenient, one workaround is to encapsulate the immutable types in +a custom type that does allow modifications. + +An other alternative involves binding a small wrapper lambda function that +returns a tuple with all output arguments (see the remainder of the +documentation for examples on binding lambda functions). An example: + +.. code-block:: cpp + + int foo(int &i) { i++; return 123; } + +and the binding code + +.. code-block:: cpp + + m.def("foo", [](int i) { int rv = foo(i); return std::make_tuple(rv, i); }); + + +How can I reduce the build time? +================================ + +It's good practice to split binding code over multiple files, as in the +following example: + +:file:`example.cpp`: + +.. code-block:: cpp + + void init_ex1(py::module_ &); + void init_ex2(py::module_ &); + /* ... */ + + PYBIND11_MODULE(example, m) { + init_ex1(m); + init_ex2(m); + /* ... */ + } + +:file:`ex1.cpp`: + +.. code-block:: cpp + + void init_ex1(py::module_ &m) { + m.def("add", [](int a, int b) { return a + b; }); + } + +:file:`ex2.cpp`: + +.. code-block:: cpp + + void init_ex2(py::module_ &m) { + m.def("sub", [](int a, int b) { return a - b; }); + } + +:command:`python`: + +.. code-block:: pycon + + >>> import example + >>> example.add(1, 2) + 3 + >>> example.sub(1, 1) + 0 + +As shown above, the various ``init_ex`` functions should be contained in +separate files that can be compiled independently from one another, and then +linked together into the same final shared object. Following this approach +will: + +1. reduce memory requirements per compilation unit. + +2. enable parallel builds (if desired). + +3. allow for faster incremental builds. For instance, when a single class + definition is changed, only a subset of the binding code will generally need + to be recompiled. + +"recursive template instantiation exceeded maximum depth of 256" +================================================================ + +If you receive an error about excessive recursive template evaluation, try +specifying a larger value, e.g. ``-ftemplate-depth=1024`` on GCC/Clang. The +culprit is generally the generation of function signatures at compile time +using C++14 template metaprogramming. + +.. _`faq:hidden_visibility`: + +"‘SomeClass’ declared with greater visibility than the type of its field ‘SomeClass::member’ [-Wattributes]" +============================================================================================================ + +This error typically indicates that you are compiling without the required +``-fvisibility`` flag. pybind11 code internally forces hidden visibility on +all internal code, but if non-hidden (and thus *exported*) code attempts to +include a pybind type (for example, ``py::object`` or ``py::list``) you can run +into this warning. + +To avoid it, make sure you are specifying ``-fvisibility=hidden`` when +compiling pybind code. + +As to why ``-fvisibility=hidden`` is necessary, because pybind modules could +have been compiled under different versions of pybind itself, it is also +important that the symbols defined in one module do not clash with the +potentially-incompatible symbols defined in another. While Python extension +modules are usually loaded with localized symbols (under POSIX systems +typically using ``dlopen`` with the ``RTLD_LOCAL`` flag), this Python default +can be changed, but even if it isn't it is not always enough to guarantee +complete independence of the symbols involved when not using +``-fvisibility=hidden``. + +Additionally, ``-fvisibility=hidden`` can deliver considerably binary size +savings. (See the following section for more details). + + +.. _`faq:symhidden`: + +How can I create smaller binaries? +================================== + +To do its job, pybind11 extensively relies on a programming technique known as +*template metaprogramming*, which is a way of performing computation at compile +time using type information. Template metaprogamming usually instantiates code +involving significant numbers of deeply nested types that are either completely +removed or reduced to just a few instructions during the compiler's optimization +phase. However, due to the nested nature of these types, the resulting symbol +names in the compiled extension library can be extremely long. For instance, +the included test suite contains the following symbol: + +.. only:: html + + .. code-block:: none + + _​_​Z​N​8​p​y​b​i​n​d​1​1​1​2​c​p​p​_​f​u​n​c​t​i​o​n​C​1​I​v​8​E​x​a​m​p​l​e​2​J​R​N​S​t​3​_​_​1​6​v​e​c​t​o​r​I​N​S​3​_​1​2​b​a​s​i​c​_​s​t​r​i​n​g​I​w​N​S​3​_​1​1​c​h​a​r​_​t​r​a​i​t​s​I​w​E​E​N​S​3​_​9​a​l​l​o​c​a​t​o​r​I​w​E​E​E​E​N​S​8​_​I​S​A​_​E​E​E​E​E​J​N​S​_​4​n​a​m​e​E​N​S​_​7​s​i​b​l​i​n​g​E​N​S​_​9​i​s​_​m​e​t​h​o​d​E​A​2​8​_​c​E​E​E​M​T​0​_​F​T​_​D​p​T​1​_​E​D​p​R​K​T​2​_ + +.. only:: not html + + .. code-block:: cpp + + __ZN8pybind1112cpp_functionC1Iv8Example2JRNSt3__16vectorINS3_12basic_stringIwNS3_11char_traitsIwEENS3_9allocatorIwEEEENS8_ISA_EEEEEJNS_4nameENS_7siblingENS_9is_methodEA28_cEEEMT0_FT_DpT1_EDpRKT2_ + +which is the mangled form of the following function type: + +.. code-block:: cpp + + pybind11::cpp_function::cpp_function, std::__1::allocator >, std::__1::allocator, std::__1::allocator > > >&, pybind11::name, pybind11::sibling, pybind11::is_method, char [28]>(void (Example2::*)(std::__1::vector, std::__1::allocator >, std::__1::allocator, std::__1::allocator > > >&), pybind11::name const&, pybind11::sibling const&, pybind11::is_method const&, char const (&) [28]) + +The memory needed to store just the mangled name of this function (196 bytes) +is larger than the actual piece of code (111 bytes) it represents! On the other +hand, it's silly to even give this function a name -- after all, it's just a +tiny cog in a bigger piece of machinery that is not exposed to the outside +world. So we'll generally only want to export symbols for those functions which +are actually called from the outside. + +This can be achieved by specifying the parameter ``-fvisibility=hidden`` to GCC +and Clang, which sets the default symbol visibility to *hidden*, which has a +tremendous impact on the final binary size of the resulting extension library. +(On Visual Studio, symbols are already hidden by default, so nothing needs to +be done there.) + +In addition to decreasing binary size, ``-fvisibility=hidden`` also avoids +potential serious issues when loading multiple modules and is required for +proper pybind operation. See the previous FAQ entry for more details. + +Working with ancient Visual Studio 2008 builds on Windows +========================================================= + +The official Windows distributions of Python are compiled using truly +ancient versions of Visual Studio that lack good C++11 support. Some users +implicitly assume that it would be impossible to load a plugin built with +Visual Studio 2015 into a Python distribution that was compiled using Visual +Studio 2008. However, no such issue exists: it's perfectly legitimate to +interface DLLs that are built with different compilers and/or C libraries. +Common gotchas to watch out for involve not ``free()``-ing memory region +that that were ``malloc()``-ed in another shared library, using data +structures with incompatible ABIs, and so on. pybind11 is very careful not +to make these types of mistakes. + +How can I properly handle Ctrl-C in long-running functions? +=========================================================== + +Ctrl-C is received by the Python interpreter, and holds it until the GIL +is released, so a long-running function won't be interrupted. + +To interrupt from inside your function, you can use the ``PyErr_CheckSignals()`` +function, that will tell if a signal has been raised on the Python side. This +function merely checks a flag, so its impact is negligible. When a signal has +been received, you must either explicitly interrupt execution by throwing +``py::error_already_set`` (which will propagate the existing +``KeyboardInterrupt``), or clear the error (which you usually will not want): + +.. code-block:: cpp + + PYBIND11_MODULE(example, m) + { + m.def("long running_func", []() + { + for (;;) { + if (PyErr_CheckSignals() != 0) + throw py::error_already_set(); + // Long running iteration + } + }); + } + +CMake doesn't detect the right Python version +============================================= + +The CMake-based build system will try to automatically detect the installed +version of Python and link against that. When this fails, or when there are +multiple versions of Python and it finds the wrong one, delete +``CMakeCache.txt`` and then add ``-DPYTHON_EXECUTABLE=$(which python)`` to your +CMake configure line. (Replace ``$(which python)`` with a path to python if +your prefer.) + +You can alternatively try ``-DPYBIND11_FINDPYTHON=ON``, which will activate the +new CMake FindPython support instead of pybind11's custom search. Requires +CMake 3.12+, and 3.15+ or 3.18.2+ are even better. You can set this in your +``CMakeLists.txt`` before adding or finding pybind11, as well. + +Inconsistent detection of Python version in CMake and pybind11 +============================================================== + +The functions ``find_package(PythonInterp)`` and ``find_package(PythonLibs)`` +provided by CMake for Python version detection are modified by pybind11 due to +unreliability and limitations that make them unsuitable for pybind11's needs. +Instead pybind11 provides its own, more reliable Python detection CMake code. +Conflicts can arise, however, when using pybind11 in a project that *also* uses +the CMake Python detection in a system with several Python versions installed. + +This difference may cause inconsistencies and errors if *both* mechanisms are +used in the same project. Consider the following CMake code executed in a +system with Python 2.7 and 3.x installed: + +.. code-block:: cmake + + find_package(PythonInterp) + find_package(PythonLibs) + find_package(pybind11) + +It will detect Python 2.7 and pybind11 will pick it as well. + +In contrast this code: + +.. code-block:: cmake + + find_package(pybind11) + find_package(PythonInterp) + find_package(PythonLibs) + +will detect Python 3.x for pybind11 and may crash on +``find_package(PythonLibs)`` afterwards. + +There are three possible solutions: + +1. Avoid using ``find_package(PythonInterp)`` and ``find_package(PythonLibs)`` + from CMake and rely on pybind11 in detecting Python version. If this is not + possible, the CMake machinery should be called *before* including pybind11. +2. Set ``PYBIND11_FINDPYTHON`` to ``True`` or use ``find_package(Python + COMPONENTS Interpreter Development)`` on modern CMake (3.12+, 3.15+ better, + 3.18.2+ best). Pybind11 in these cases uses the new CMake FindPython instead + of the old, deprecated search tools, and these modules are much better at + finding the correct Python. +3. Set ``PYBIND11_NOPYTHON`` to ``TRUE``. Pybind11 will not search for Python. + However, you will have to use the target-based system, and do more setup + yourself, because it does not know about or include things that depend on + Python, like ``pybind11_add_module``. This might be ideal for integrating + into an existing system, like scikit-build's Python helpers. + +How to cite this project? +========================= + +We suggest the following BibTeX template to cite pybind11 in scientific +discourse: + +.. code-block:: bash + + @misc{pybind11, + author = {Wenzel Jakob and Jason Rhinelander and Dean Moldovan}, + year = {2017}, + note = {https://github.com/pybind/pybind11}, + title = {pybind11 -- Seamless operability between C++11 and Python} + } diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/index.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/index.rst new file mode 100644 index 0000000000000000000000000000000000000000..4e2e8ca3a04a072d9adfdfa4bb98f5c221be10ea --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/index.rst @@ -0,0 +1,48 @@ +.. only:: latex + + Intro + ===== + +.. include:: readme.rst + +.. only:: not latex + + Contents: + +.. toctree:: + :maxdepth: 1 + + changelog + upgrade + +.. toctree:: + :caption: The Basics + :maxdepth: 2 + + installing + basics + classes + compiling + +.. toctree:: + :caption: Advanced Topics + :maxdepth: 2 + + advanced/functions + advanced/classes + advanced/exceptions + advanced/smart_ptrs + advanced/cast/index + advanced/pycpp/index + advanced/embedding + advanced/misc + +.. toctree:: + :caption: Extra Information + :maxdepth: 1 + + faq + benchmark + limitations + reference + cmake/index diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/installing.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/installing.rst new file mode 100644 index 0000000000000000000000000000000000000000..30b9f1853d7edf9b90f88ff347be63648056f99f --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/installing.rst @@ -0,0 +1,105 @@ +.. _installing: + +Installing the library +###################### + +There are several ways to get the pybind11 source, which lives at +`pybind/pybind11 on GitHub `_. The pybind11 +developers recommend one of the first three ways listed here, submodule, PyPI, +or conda-forge, for obtaining pybind11. + +.. _include_as_a_submodule: + +Include as a submodule +====================== + +When you are working on a project in Git, you can use the pybind11 repository +as a submodule. From your git repository, use: + +.. code-block:: bash + + git submodule add -b stable ../../pybind/pybind11 extern/pybind11 + git submodule update --init + +This assumes you are placing your dependencies in ``extern/``, and that you are +using GitHub; if you are not using GitHub, use the full https or ssh URL +instead of the relative URL ``../../pybind/pybind11`` above. Some other servers +also require the ``.git`` extension (GitHub does not). + +From here, you can now include ``extern/pybind11/include``, or you can use +the various integration tools (see :ref:`compiling`) pybind11 provides directly +from the local folder. + +Include with PyPI +================= + +You can download the sources and CMake files as a Python package from PyPI +using Pip. Just use: + +.. code-block:: bash + + pip install pybind11 + +This will provide pybind11 in a standard Python package format. If you want +pybind11 available directly in your environment root, you can use: + +.. code-block:: bash + + pip install "pybind11[global]" + +This is not recommended if you are installing with your system Python, as it +will add files to ``/usr/local/include/pybind11`` and +``/usr/local/share/cmake/pybind11``, so unless that is what you want, it is +recommended only for use in virtual environments or your ``pyproject.toml`` +file (see :ref:`compiling`). + +Include with conda-forge +======================== + +You can use pybind11 with conda packaging via `conda-forge +`_: + +.. code-block:: bash + + conda install -c conda-forge pybind11 + + +Include with vcpkg +================== +You can download and install pybind11 using the Microsoft `vcpkg +`_ dependency manager: + +.. code-block:: bash + + git clone https://github.com/Microsoft/vcpkg.git + cd vcpkg + ./bootstrap-vcpkg.sh + ./vcpkg integrate install + vcpkg install pybind11 + +The pybind11 port in vcpkg is kept up to date by Microsoft team members and +community contributors. If the version is out of date, please `create an issue +or pull request `_ on the vcpkg +repository. + +Global install with brew +======================== + +The brew package manager (Homebrew on macOS, or Linuxbrew on Linux) has a +`pybind11 package +`_. +To install: + +.. code-block:: bash + + brew install pybind11 + +.. We should list Conan, and possibly a few other C++ package managers (hunter, +.. perhaps). Conan has a very clean CMake integration that would be good to show. + +Other options +============= + +Other locations you can find pybind11 are `listed here +`_; these are maintained +by various packagers and the community. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/limitations.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/limitations.rst new file mode 100644 index 0000000000000000000000000000000000000000..be7300cdb6f5e2fcbb487bf17c6ee7abc46959df --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/limitations.rst @@ -0,0 +1,72 @@ +Limitations +########### + +Design choices +^^^^^^^^^^^^^^ + +pybind11 strives to be a general solution to binding generation, but it also has +certain limitations: + +- pybind11 casts away ``const``-ness in function arguments and return values. + This is in line with the Python language, which has no concept of ``const`` + values. This means that some additional care is needed to avoid bugs that + would be caught by the type checker in a traditional C++ program. + +- The NumPy interface ``pybind11::array`` greatly simplifies accessing + numerical data from C++ (and vice versa), but it's not a full-blown array + class like ``Eigen::Array`` or ``boost.multi_array``. ``Eigen`` objects are + directly supported, however, with ``pybind11/eigen.h``. + +Large but useful features could be implemented in pybind11 but would lead to a +significant increase in complexity. Pybind11 strives to be simple and compact. +Users who require large new features are encouraged to write an extension to +pybind11; see `pybind11_json `_ for an +example. + + +Known bugs +^^^^^^^^^^ + +These are issues that hopefully will one day be fixed, but currently are +unsolved. If you know how to help with one of these issues, contributions +are welcome! + +- Intel 20.2 is currently having an issue with the test suite. + `#2573 `_ + +- Debug mode Python does not support 1-5 tests in the test suite currently. + `#2422 `_ + +- PyPy3 7.3.1 and 7.3.2 have issues with several tests on 32-bit Windows. + +Known limitations +^^^^^^^^^^^^^^^^^ + +These are issues that are probably solvable, but have not been fixed yet. A +clean, well written patch would likely be accepted to solve them. + +- Type casters are not kept alive recursively. + `#2527 `_ + One consequence is that containers of ``char *`` are currently not supported. + `#2245 `_ + +- The ``cpptest`` does not run on Windows with Python 3.8 or newer, due to DLL + loader changes. User code that is correctly installed should not be affected. + `#2560 `_ + +Python 3.9.0 warning +^^^^^^^^^^^^^^^^^^^^ + +Combining older versions of pybind11 (< 2.6.0) with Python on 3.9.0 will +trigger undefined behavior that typically manifests as crashes during +interpreter shutdown (but could also destroy your data. **You have been +warned**). + +This issue has been +`fixed in Python `_. As a +mitigation until 3.9.1 is released and commonly used, pybind11 (2.6.0 or newer) +includes a temporary workaround specifically when Python 3.9.0 is detected at +runtime, leaking about 50 bytes of memory when a callback function is garbage +collected. For reference; the pybind11 test suite has about 2,000 such +callbacks, but only 49 are garbage collected before the end-of-process. Wheels +built with Python 3.9.0 will correctly avoid the leak when run in Python 3.9.1. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/pybind11_vs_boost_python1.svg b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/pybind11_vs_boost_python1.svg new file mode 100644 index 0000000000000000000000000000000000000000..5bf950e6fdc81676d9a9774926a623b4f6a2e2a8 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/pybind11_vs_boost_python1.svg @@ -0,0 +1,427 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/pybind11_vs_boost_python2.svg b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/pybind11_vs_boost_python2.svg new file mode 100644 index 0000000000000000000000000000000000000000..5ed6530ca112cbe643d5dd6d6fde385c4edea6b5 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/pybind11_vs_boost_python2.svg @@ -0,0 +1,427 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/reference.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/reference.rst new file mode 100644 index 0000000000000000000000000000000000000000..a678d41c885f45f439671622951ded8476a6cf84 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/reference.rst @@ -0,0 +1,127 @@ +.. _reference: + +.. warning:: + + Please be advised that the reference documentation discussing pybind11 + internals is currently incomplete. Please refer to the previous sections + and the pybind11 header files for the nitty gritty details. + +Reference +######### + +.. _macros: + +Macros +====== + +.. doxygendefine:: PYBIND11_MODULE + +.. _core_types: + +Convenience classes for arbitrary Python types +============================================== + +Common member functions +----------------------- + +.. doxygenclass:: object_api + :members: + +Without reference counting +-------------------------- + +.. doxygenclass:: handle + :members: + +With reference counting +----------------------- + +.. doxygenclass:: object + :members: + +.. doxygenfunction:: reinterpret_borrow + +.. doxygenfunction:: reinterpret_steal + +Convenience classes for specific Python types +============================================= + +.. doxygenclass:: module_ + :members: + +.. doxygengroup:: pytypes + :members: + +Convenience functions converting to Python types +================================================ + +.. doxygenfunction:: make_tuple(Args&&...) + +.. doxygenfunction:: make_iterator(Iterator, Sentinel, Extra &&...) +.. doxygenfunction:: make_iterator(Type &, Extra&&...) + +.. doxygenfunction:: make_key_iterator(Iterator, Sentinel, Extra &&...) +.. doxygenfunction:: make_key_iterator(Type &, Extra&&...) + +.. _extras: + +Passing extra arguments to ``def`` or ``class_`` +================================================ + +.. doxygengroup:: annotations + :members: + +Embedding the interpreter +========================= + +.. doxygendefine:: PYBIND11_EMBEDDED_MODULE + +.. doxygenfunction:: initialize_interpreter + +.. doxygenfunction:: finalize_interpreter + +.. doxygenclass:: scoped_interpreter + +Redirecting C++ streams +======================= + +.. doxygenclass:: scoped_ostream_redirect + +.. doxygenclass:: scoped_estream_redirect + +.. doxygenfunction:: add_ostream_redirect + +Python built-in functions +========================= + +.. doxygengroup:: python_builtins + :members: + +Inheritance +=========== + +See :doc:`/classes` and :doc:`/advanced/classes` for more detail. + +.. doxygendefine:: PYBIND11_OVERRIDE + +.. doxygendefine:: PYBIND11_OVERRIDE_PURE + +.. doxygendefine:: PYBIND11_OVERRIDE_NAME + +.. doxygendefine:: PYBIND11_OVERRIDE_PURE_NAME + +.. doxygenfunction:: get_override + +Exceptions +========== + +.. doxygenclass:: error_already_set + :members: + +.. doxygenclass:: builtin_exception + :members: + +Literals +======== + +.. doxygennamespace:: literals diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/release.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/release.rst new file mode 100644 index 0000000000000000000000000000000000000000..9dbff0383893042e86048bce87a170c50ff37e6e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/release.rst @@ -0,0 +1,92 @@ +On version numbers +^^^^^^^^^^^^^^^^^^ + +The two version numbers (C++ and Python) must match when combined (checked when +you build the PyPI package), and must be a valid `PEP 440 +`_ version when combined. + +For example: + +.. code-block:: C++ + + #define PYBIND11_VERSION_MAJOR X + #define PYBIND11_VERSION_MINOR Y + #define PYBIND11_VERSION_PATCH Z.dev1 + +For beta, ``PYBIND11_VERSION_PATCH`` should be ``Z.b1``. RC's can be ``Z.rc1``. +Always include the dot (even though PEP 440 allows it to be dropped). For a +final release, this must be a simple integer. + + +To release a new version of pybind11: +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +- Update the version number + - Update ``PYBIND11_VERSION_MAJOR`` etc. in + ``include/pybind11/detail/common.h``. PATCH should be a simple integer. + - Update ``pybind11/_version.py`` (match above) + - Ensure that all the information in ``setup.cfg`` is up-to-date, like + supported Python versions. + - Add release date in ``docs/changelog.rst``. + - Check to make sure + `needs-changelog `_ + issues are entered in the changelog (clear the label when done). + - ``git add`` and ``git commit``, ``git push``. **Ensure CI passes**. (If it + fails due to a known flake issue, either ignore or restart CI.) +- Add a release branch if this is a new minor version, or update the existing release branch if it is a patch version + - New branch: ``git checkout -b vX.Y``, ``git push -u origin vX.Y`` + - Update branch: ``git checkout vX.Y``, ``git merge ``, ``git push`` +- Update tags (optional; if you skip this, the GitHub release makes a + non-annotated tag for you) + - ``git tag -a vX.Y.Z -m 'vX.Y.Z release'``. + - ``git push --tags``. +- Update stable + - ``git checkout stable`` + - ``git merge master`` + - ``git push`` +- Make a GitHub release (this shows up in the UI, sends new release + notifications to users watching releases, and also uploads PyPI packages). + (Note: if you do not use an existing tag, this creates a new lightweight tag + for you, so you could skip the above step). + - GUI method: click "Create a new release" on the far right, fill in the tag + name (if you didn't tag above, it will be made here), fill in a release + name like "Version X.Y.Z", and optionally copy-and-paste the changelog into + the description (processed as markdown by Pandoc). Check "pre-release" if + this is a beta/RC. You can get partway there with + ``cat docs/changelog.rst | pandsoc -f rst -t markdown``. + - CLI method: with ``gh`` installed, run ``gh release create vX.Y.Z -t "Version X.Y.Z"`` + If this is a pre-release, add ``-p``. + +- Get back to work + - Make sure you are on master, not somewhere else: ``git checkout master`` + - Update version macros in ``include/pybind11/detail/common.h`` (set PATCH to + ``0.dev1`` and increment MINOR). + - Update ``_version.py`` to match + - Add a spot for in-development updates in ``docs/changelog.rst``. + - ``git add``, ``git commit``, ``git push`` + +If a version branch is updated, remember to set PATCH to ``1.dev1``. + +If you'd like to bump homebrew, run: + +.. code-block:: + + brew bump-formula-pr --url https://github.com/pybind/pybind11/archive/vX.Y.Z.tar.gz + +Conda-forge should automatically make a PR in a few hours, and automatically +merge it if there are no issues. + + +Manual packaging +^^^^^^^^^^^^^^^^ + +If you need to manually upload releases, you can download the releases from the job artifacts and upload them with twine. You can also make the files locally (not recommended in general, as your local directory is more likely to be "dirty" and SDists love picking up random unrelated/hidden files); this is the procedure: + +.. code-block:: bash + + python3 -m pip install build + python3 -m build + PYBIND11_SDIST_GLOBAL=1 python3 -m build + twine upload dist/* + +This makes SDists and wheels, and the final line uploads them. diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/requirements.txt b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..a1276a65d924247df765140918424fd0da3ed897 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/requirements.txt @@ -0,0 +1,7 @@ +breathe==4.26.1 +commonmark==0.9.1 +recommonmark==0.7.1 +sphinx==3.3.1 +sphinx_rtd_theme==0.5.0 +sphinxcontrib-moderncmakedomain==3.17 +sphinxcontrib-svg2pdfconverter==1.1.0 diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/upgrade.rst b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/upgrade.rst new file mode 100644 index 0000000000000000000000000000000000000000..5691879c858bd0ef51ebcec2be00e2328d859768 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/docs/upgrade.rst @@ -0,0 +1,537 @@ +Upgrade guide +############# + +This is a companion guide to the :doc:`changelog`. While the changelog briefly +lists all of the new features, improvements and bug fixes, this upgrade guide +focuses only the subset which directly impacts your experience when upgrading +to a new version. But it goes into more detail. This includes things like +deprecated APIs and their replacements, build system changes, general code +modernization and other useful information. + +.. _upgrade-guide-2.6: + +v2.7 +==== + +*Before* v2.7, ``py::str`` can hold ``PyUnicodeObject`` or ``PyBytesObject``, +and ``py::isinstance()`` is ``true`` for both ``py::str`` and +``py::bytes``. Starting with v2.7, ``py::str`` exclusively holds +``PyUnicodeObject`` (`#2409 `_), +and ``py::isinstance()`` is ``true`` only for ``py::str``. To help in +the transition of user code, the ``PYBIND11_STR_LEGACY_PERMISSIVE`` macro +is provided as an escape hatch to go back to the legacy behavior. This macro +will be removed in future releases. Two types of required fixes are expected +to be common: + +* Accidental use of ``py::str`` instead of ``py::bytes``, masked by the legacy + behavior. These are probably very easy to fix, by changing from + ``py::str`` to ``py::bytes``. + +* Reliance on py::isinstance(obj) being ``true`` for + ``py::bytes``. This is likely to be easy to fix in most cases by adding + ``|| py::isinstance(obj)``, but a fix may be more involved, e.g. if + ``py::isinstance`` appears in a template. Such situations will require + careful review and custom fixes. + + + +v2.6 +==== + +Usage of the ``PYBIND11_OVERLOAD*`` macros and ``get_overload`` function should +be replaced by ``PYBIND11_OVERRIDE*`` and ``get_override``. In the future, the +old macros may be deprecated and removed. + +``py::module`` has been renamed ``py::module_``, but a backward compatible +typedef has been included. This change was to avoid a language change in C++20 +that requires unqualified ``module`` not be placed at the start of a logical +line. Qualified usage is unaffected and the typedef will remain unless the +C++ language rules change again. + +The public constructors of ``py::module_`` have been deprecated. Use +``PYBIND11_MODULE`` or ``module_::create_extension_module`` instead. + +An error is now thrown when ``__init__`` is forgotten on subclasses. This was +incorrect before, but was not checked. Add a call to ``__init__`` if it is +missing. + +A ``py::type_error`` is now thrown when casting to a subclass (like +``py::bytes`` from ``py::object``) if the conversion is not valid. Make a valid +conversion instead. + +The undocumented ``h.get_type()`` method has been deprecated and replaced by +``py::type::of(h)``. + +Enums now have a ``__str__`` method pre-defined; if you want to override it, +the simplest fix is to add the new ``py::prepend()`` tag when defining +``"__str__"``. + +If ``__eq__`` defined but not ``__hash__``, ``__hash__`` is now set to +``None``, as in normal CPython. You should add ``__hash__`` if you intended the +class to be hashable, possibly using the new ``py::hash`` shortcut. + +The constructors for ``py::array`` now always take signed integers for size, +for consistency. This may lead to compiler warnings on some systems. Cast to +``py::ssize_t`` instead of ``std::size_t``. + +The ``tools/clang`` submodule and ``tools/mkdoc.py`` have been moved to a +standalone package, `pybind11-mkdoc`_. If you were using those tools, please +use them via a pip install from the new location. + +The ``pybind11`` package on PyPI no longer fills the wheel "headers" slot - if +you were using the headers from this slot, they are available by requesting the +``global`` extra, that is, ``pip install "pybind11[global]"``. (Most users will +be unaffected, as the ``pybind11/include`` location is reported by ``python -m +pybind11 --includes`` and ``pybind11.get_include()`` is still correct and has +not changed since 2.5). + +.. _pybind11-mkdoc: https://github.com/pybind/pybind11-mkdoc + +CMake support: +-------------- + +The minimum required version of CMake is now 3.4. Several details of the CMake +support have been deprecated; warnings will be shown if you need to change +something. The changes are: + +* ``PYBIND11_CPP_STANDARD=`` is deprecated, please use + ``CMAKE_CXX_STANDARD=`` instead, or any other valid CMake CXX or CUDA + standard selection method, like ``target_compile_features``. + +* If you do not request a standard, pybind11 targets will compile with the + compiler default, but not less than C++11, instead of forcing C++14 always. + If you depend on the old behavior, please use ``set(CMAKE_CXX_STANDARD 14 CACHE STRING "")`` + instead. + +* Direct ``pybind11::module`` usage should always be accompanied by at least + ``set(CMAKE_CXX_VISIBILITY_PRESET hidden)`` or similar - it used to try to + manually force this compiler flag (but not correctly on all compilers or with + CUDA). + +* ``pybind11_add_module``'s ``SYSTEM`` argument is deprecated and does nothing; + linking now behaves like other imported libraries consistently in both + config and submodule mode, and behaves like a ``SYSTEM`` library by + default. + +* If ``PYTHON_EXECUTABLE`` is not set, virtual environments (``venv``, + ``virtualenv``, and ``conda``) are prioritized over the standard search + (similar to the new FindPython mode). + +In addition, the following changes may be of interest: + +* ``CMAKE_INTERPROCEDURAL_OPTIMIZATION`` will be respected by + ``pybind11_add_module`` if set instead of linking to ``pybind11::lto`` or + ``pybind11::thin_lto``. + +* Using ``find_package(Python COMPONENTS Interpreter Development)`` before + pybind11 will cause pybind11 to use the new Python mechanisms instead of its + own custom search, based on a patched version of classic ``FindPythonInterp`` + / ``FindPythonLibs``. In the future, this may become the default. A recent + (3.15+ or 3.18.2+) version of CMake is recommended. + + + +v2.5 +==== + +The Python package now includes the headers as data in the package itself, as +well as in the "headers" wheel slot. ``pybind11 --includes`` and +``pybind11.get_include()`` report the new location, which is always correct +regardless of how pybind11 was installed, making the old ``user=`` argument +meaningless. If you are not using the function to get the location already, you +are encouraged to switch to the package location. + + +v2.2 +==== + +Deprecation of the ``PYBIND11_PLUGIN`` macro +-------------------------------------------- + +``PYBIND11_MODULE`` is now the preferred way to create module entry points. +The old macro emits a compile-time deprecation warning. + +.. code-block:: cpp + + // old + PYBIND11_PLUGIN(example) { + py::module m("example", "documentation string"); + + m.def("add", [](int a, int b) { return a + b; }); + + return m.ptr(); + } + + // new + PYBIND11_MODULE(example, m) { + m.doc() = "documentation string"; // optional + + m.def("add", [](int a, int b) { return a + b; }); + } + + +New API for defining custom constructors and pickling functions +--------------------------------------------------------------- + +The old placement-new custom constructors have been deprecated. The new approach +uses ``py::init()`` and factory functions to greatly improve type safety. + +Placement-new can be called accidentally with an incompatible type (without any +compiler errors or warnings), or it can initialize the same object multiple times +if not careful with the Python-side ``__init__`` calls. The new-style custom +constructors prevent such mistakes. See :ref:`custom_constructors` for details. + +.. code-block:: cpp + + // old -- deprecated (runtime warning shown only in debug mode) + py::class(m, "Foo") + .def("__init__", [](Foo &self, ...) { + new (&self) Foo(...); // uses placement-new + }); + + // new + py::class(m, "Foo") + .def(py::init([](...) { // Note: no `self` argument + return new Foo(...); // return by raw pointer + // or: return std::make_unique(...); // return by holder + // or: return Foo(...); // return by value (move constructor) + })); + +Mirroring the custom constructor changes, ``py::pickle()`` is now the preferred +way to get and set object state. See :ref:`pickling` for details. + +.. code-block:: cpp + + // old -- deprecated (runtime warning shown only in debug mode) + py::class(m, "Foo") + ... + .def("__getstate__", [](const Foo &self) { + return py::make_tuple(self.value1(), self.value2(), ...); + }) + .def("__setstate__", [](Foo &self, py::tuple t) { + new (&self) Foo(t[0].cast(), ...); + }); + + // new + py::class(m, "Foo") + ... + .def(py::pickle( + [](const Foo &self) { // __getstate__ + return py::make_tuple(self.value1(), self.value2(), ...); // unchanged + }, + [](py::tuple t) { // __setstate__, note: no `self` argument + return new Foo(t[0].cast(), ...); + // or: return std::make_unique(...); // return by holder + // or: return Foo(...); // return by value (move constructor) + } + )); + +For both the constructors and pickling, warnings are shown at module +initialization time (on import, not when the functions are called). +They're only visible when compiled in debug mode. Sample warning: + +.. code-block:: none + + pybind11-bound class 'mymodule.Foo' is using an old-style placement-new '__init__' + which has been deprecated. See the upgrade guide in pybind11's docs. + + +Stricter enforcement of hidden symbol visibility for pybind11 modules +--------------------------------------------------------------------- + +pybind11 now tries to actively enforce hidden symbol visibility for modules. +If you're using either one of pybind11's :doc:`CMake or Python build systems +` (the two example repositories) and you haven't been exporting any +symbols, there's nothing to be concerned about. All the changes have been done +transparently in the background. If you were building manually or relied on +specific default visibility, read on. + +Setting default symbol visibility to *hidden* has always been recommended for +pybind11 (see :ref:`faq:symhidden`). On Linux and macOS, hidden symbol +visibility (in conjunction with the ``strip`` utility) yields much smaller +module binaries. `CPython's extension docs`_ also recommend hiding symbols +by default, with the goal of avoiding symbol name clashes between modules. +Starting with v2.2, pybind11 enforces this more strictly: (1) by declaring +all symbols inside the ``pybind11`` namespace as hidden and (2) by including +the ``-fvisibility=hidden`` flag on Linux and macOS (only for extension +modules, not for embedding the interpreter). + +.. _CPython's extension docs: https://docs.python.org/3/extending/extending.html#providing-a-c-api-for-an-extension-module + +The namespace-scope hidden visibility is done automatically in pybind11's +headers and it's generally transparent to users. It ensures that: + +* Modules compiled with different pybind11 versions don't clash with each other. + +* Some new features, like ``py::module_local`` bindings, can work as intended. + +The ``-fvisibility=hidden`` flag applies the same visibility to user bindings +outside of the ``pybind11`` namespace. It's now set automatic by pybind11's +CMake and Python build systems, but this needs to be done manually by users +of other build systems. Adding this flag: + +* Minimizes the chances of symbol conflicts between modules. E.g. if two + unrelated modules were statically linked to different (ABI-incompatible) + versions of the same third-party library, a symbol clash would be likely + (and would end with unpredictable results). + +* Produces smaller binaries on Linux and macOS, as pointed out previously. + +Within pybind11's CMake build system, ``pybind11_add_module`` has always been +setting the ``-fvisibility=hidden`` flag in release mode. From now on, it's +being applied unconditionally, even in debug mode and it can no longer be opted +out of with the ``NO_EXTRAS`` option. The ``pybind11::module`` target now also +adds this flag to it's interface. The ``pybind11::embed`` target is unchanged. + +The most significant change here is for the ``pybind11::module`` target. If you +were previously relying on default visibility, i.e. if your Python module was +doubling as a shared library with dependents, you'll need to either export +symbols manually (recommended for cross-platform libraries) or factor out the +shared library (and have the Python module link to it like the other +dependents). As a temporary workaround, you can also restore default visibility +using the CMake code below, but this is not recommended in the long run: + +.. code-block:: cmake + + target_link_libraries(mymodule PRIVATE pybind11::module) + + add_library(restore_default_visibility INTERFACE) + target_compile_options(restore_default_visibility INTERFACE -fvisibility=default) + target_link_libraries(mymodule PRIVATE restore_default_visibility) + + +Local STL container bindings +---------------------------- + +Previous pybind11 versions could only bind types globally -- all pybind11 +modules, even unrelated ones, would have access to the same exported types. +However, this would also result in a conflict if two modules exported the +same C++ type, which is especially problematic for very common types, e.g. +``std::vector``. :ref:`module_local` were added to resolve this (see +that section for a complete usage guide). + +``py::class_`` still defaults to global bindings (because these types are +usually unique across modules), however in order to avoid clashes of opaque +types, ``py::bind_vector`` and ``py::bind_map`` will now bind STL containers +as ``py::module_local`` if their elements are: builtins (``int``, ``float``, +etc.), not bound using ``py::class_``, or bound as ``py::module_local``. For +example, this change allows multiple modules to bind ``std::vector`` +without causing conflicts. See :ref:`stl_bind` for more details. + +When upgrading to this version, if you have multiple modules which depend on +a single global binding of an STL container, note that all modules can still +accept foreign ``py::module_local`` types in the direction of Python-to-C++. +The locality only affects the C++-to-Python direction. If this is needed in +multiple modules, you'll need to either: + +* Add a copy of the same STL binding to all of the modules which need it. + +* Restore the global status of that single binding by marking it + ``py::module_local(false)``. + +The latter is an easy workaround, but in the long run it would be best to +localize all common type bindings in order to avoid conflicts with +third-party modules. + + +Negative strides for Python buffer objects and numpy arrays +----------------------------------------------------------- + +Support for negative strides required changing the integer type from unsigned +to signed in the interfaces of ``py::buffer_info`` and ``py::array``. If you +have compiler warnings enabled, you may notice some new conversion warnings +after upgrading. These can be resolved using ``static_cast``. + + +Deprecation of some ``py::object`` APIs +--------------------------------------- + +To compare ``py::object`` instances by pointer, you should now use +``obj1.is(obj2)`` which is equivalent to ``obj1 is obj2`` in Python. +Previously, pybind11 used ``operator==`` for this (``obj1 == obj2``), but +that could be confusing and is now deprecated (so that it can eventually +be replaced with proper rich object comparison in a future release). + +For classes which inherit from ``py::object``, ``borrowed`` and ``stolen`` +were previously available as protected constructor tags. Now the types +should be used directly instead: ``borrowed_t{}`` and ``stolen_t{}`` +(`#771 `_). + + +Stricter compile-time error checking +------------------------------------ + +Some error checks have been moved from run time to compile time. Notably, +automatic conversion of ``std::shared_ptr`` is not possible when ``T`` is +not directly registered with ``py::class_`` (e.g. ``std::shared_ptr`` +or ``std::shared_ptr>`` are not automatically convertible). +Attempting to bind a function with such arguments now results in a compile-time +error instead of waiting to fail at run time. + +``py::init<...>()`` constructor definitions are also stricter and now prevent +bindings which could cause unexpected behavior: + +.. code-block:: cpp + + struct Example { + Example(int &); + }; + + py::class_(m, "Example") + .def(py::init()); // OK, exact match + // .def(py::init()); // compile-time error, mismatch + +A non-``const`` lvalue reference is not allowed to bind to an rvalue. However, +note that a constructor taking ``const T &`` can still be registered using +``py::init()`` because a ``const`` lvalue reference can bind to an rvalue. + +v2.1 +==== + +Minimum compiler versions are enforced at compile time +------------------------------------------------------ + +The minimums also apply to v2.0 but the check is now explicit and a compile-time +error is raised if the compiler does not meet the requirements: + +* GCC >= 4.8 +* clang >= 3.3 (appleclang >= 5.0) +* MSVC >= 2015u3 +* Intel C++ >= 15.0 + + +The ``py::metaclass`` attribute is not required for static properties +--------------------------------------------------------------------- + +Binding classes with static properties is now possible by default. The +zero-parameter version of ``py::metaclass()`` is deprecated. However, a new +one-parameter ``py::metaclass(python_type)`` version was added for rare +cases when a custom metaclass is needed to override pybind11's default. + +.. code-block:: cpp + + // old -- emits a deprecation warning + py::class_(m, "Foo", py::metaclass()) + .def_property_readonly_static("foo", ...); + + // new -- static properties work without the attribute + py::class_(m, "Foo") + .def_property_readonly_static("foo", ...); + + // new -- advanced feature, override pybind11's default metaclass + py::class_(m, "Bar", py::metaclass(custom_python_type)) + ... + + +v2.0 +==== + +Breaking changes in ``py::class_`` +---------------------------------- + +These changes were necessary to make type definitions in pybind11 +future-proof, to support PyPy via its ``cpyext`` mechanism (`#527 +`_), and to improve efficiency +(`rev. 86d825 `_). + +1. Declarations of types that provide access via the buffer protocol must + now include the ``py::buffer_protocol()`` annotation as an argument to + the ``py::class_`` constructor. + + .. code-block:: cpp + + py::class_("Matrix", py::buffer_protocol()) + .def(py::init<...>()) + .def_buffer(...); + +2. Classes which include static properties (e.g. ``def_readwrite_static()``) + must now include the ``py::metaclass()`` attribute. Note: this requirement + has since been removed in v2.1. If you're upgrading from 1.x, it's + recommended to skip directly to v2.1 or newer. + +3. This version of pybind11 uses a redesigned mechanism for instantiating + trampoline classes that are used to override virtual methods from within + Python. This led to the following user-visible syntax change: + + .. code-block:: cpp + + // old v1.x syntax + py::class_("MyClass") + .alias() + ... + + // new v2.x syntax + py::class_("MyClass") + ... + + Importantly, both the original and the trampoline class are now specified + as arguments to the ``py::class_`` template, and the ``alias<..>()`` call + is gone. The new scheme has zero overhead in cases when Python doesn't + override any functions of the underlying C++ class. + `rev. 86d825 `_. + + The class type must be the first template argument given to ``py::class_`` + while the trampoline can be mixed in arbitrary order with other arguments + (see the following section). + + +Deprecation of the ``py::base()`` attribute +---------------------------------------------- + +``py::base()`` was deprecated in favor of specifying ``T`` as a template +argument to ``py::class_``. This new syntax also supports multiple inheritance. +Note that, while the type being exported must be the first argument in the +``py::class_`` template, the order of the following types (bases, +holder and/or trampoline) is not important. + +.. code-block:: cpp + + // old v1.x + py::class_("Derived", py::base()); + + // new v2.x + py::class_("Derived"); + + // new -- multiple inheritance + py::class_("Derived"); + + // new -- apart from `Derived` the argument order can be arbitrary + py::class_("Derived"); + + +Out-of-the-box support for ``std::shared_ptr`` +---------------------------------------------- + +The relevant type caster is now built in, so it's no longer necessary to +include a declaration of the form: + +.. code-block:: cpp + + PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr) + +Continuing to do so won’t cause an error or even a deprecation warning, +but it's completely redundant. + + +Deprecation of a few ``py::object`` APIs +---------------------------------------- + +All of the old-style calls emit deprecation warnings. + ++---------------------------------------+---------------------------------------------+ +| Old syntax | New syntax | ++=======================================+=============================================+ +| ``obj.call(args...)`` | ``obj(args...)`` | ++---------------------------------------+---------------------------------------------+ +| ``obj.str()`` | ``py::str(obj)`` | ++---------------------------------------+---------------------------------------------+ +| ``auto l = py::list(obj); l.check()`` | ``py::isinstance(obj)`` | ++---------------------------------------+---------------------------------------------+ +| ``py::object(ptr, true)`` | ``py::reinterpret_borrow(ptr)`` | ++---------------------------------------+---------------------------------------------+ +| ``py::object(ptr, false)`` | ``py::reinterpret_steal(ptr)`` | ++---------------------------------------+---------------------------------------------+ +| ``if (obj.attr("foo"))`` | ``if (py::hasattr(obj, "foo"))`` | ++---------------------------------------+---------------------------------------------+ +| ``if (obj["bar"])`` | ``if (obj.contains("bar"))`` | ++---------------------------------------+---------------------------------------------+ diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/attr.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/attr.h new file mode 100644 index 0000000000000000000000000000000000000000..50efdc7cec1a3f7a2c47685d95f313ceac8aaf8e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/attr.h @@ -0,0 +1,551 @@ +/* + pybind11/attr.h: Infrastructure for processing custom + type and function attributes + + Copyright (c) 2016 Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "cast.h" + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) + +/// \addtogroup annotations +/// @{ + +/// Annotation for methods +struct is_method { handle class_; is_method(const handle &c) : class_(c) { } }; + +/// Annotation for operators +struct is_operator { }; + +/// Annotation for classes that cannot be subclassed +struct is_final { }; + +/// Annotation for parent scope +struct scope { handle value; scope(const handle &s) : value(s) { } }; + +/// Annotation for documentation +struct doc { const char *value; doc(const char *value) : value(value) { } }; + +/// Annotation for function names +struct name { const char *value; name(const char *value) : value(value) { } }; + +/// Annotation indicating that a function is an overload associated with a given "sibling" +struct sibling { handle value; sibling(const handle &value) : value(value.ptr()) { } }; + +/// Annotation indicating that a class derives from another given type +template struct base { + + PYBIND11_DEPRECATED("base() was deprecated in favor of specifying 'T' as a template argument to class_") + base() { } // NOLINT(modernize-use-equals-default): breaks MSVC 2015 when adding an attribute +}; + +/// Keep patient alive while nurse lives +template struct keep_alive { }; + +/// Annotation indicating that a class is involved in a multiple inheritance relationship +struct multiple_inheritance { }; + +/// Annotation which enables dynamic attributes, i.e. adds `__dict__` to a class +struct dynamic_attr { }; + +/// Annotation which enables the buffer protocol for a type +struct buffer_protocol { }; + +/// Annotation which requests that a special metaclass is created for a type +struct metaclass { + handle value; + + PYBIND11_DEPRECATED("py::metaclass() is no longer required. It's turned on by default now.") + metaclass() { } // NOLINT(modernize-use-equals-default): breaks MSVC 2015 when adding an attribute + + /// Override pybind11's default metaclass + explicit metaclass(handle value) : value(value) { } +}; + +/// Annotation that marks a class as local to the module: +struct module_local { const bool value; constexpr module_local(bool v = true) : value(v) { } }; + +/// Annotation to mark enums as an arithmetic type +struct arithmetic { }; + +/// Mark a function for addition at the beginning of the existing overload chain instead of the end +struct prepend { }; + +/** \rst + A call policy which places one or more guard variables (``Ts...``) around the function call. + + For example, this definition: + + .. code-block:: cpp + + m.def("foo", foo, py::call_guard()); + + is equivalent to the following pseudocode: + + .. code-block:: cpp + + m.def("foo", [](args...) { + T scope_guard; + return foo(args...); // forwarded arguments + }); + \endrst */ +template struct call_guard; + +template <> struct call_guard<> { using type = detail::void_type; }; + +template +struct call_guard { + static_assert(std::is_default_constructible::value, + "The guard type must be default constructible"); + + using type = T; +}; + +template +struct call_guard { + struct type { + T guard{}; // Compose multiple guard types with left-to-right default-constructor order + typename call_guard::type next{}; + }; +}; + +/// @} annotations + +PYBIND11_NAMESPACE_BEGIN(detail) +/* Forward declarations */ +enum op_id : int; +enum op_type : int; +struct undefined_t; +template struct op_; +inline void keep_alive_impl(size_t Nurse, size_t Patient, function_call &call, handle ret); + +/// Internal data structure which holds metadata about a keyword argument +struct argument_record { + const char *name; ///< Argument name + const char *descr; ///< Human-readable version of the argument value + handle value; ///< Associated Python object + bool convert : 1; ///< True if the argument is allowed to convert when loading + bool none : 1; ///< True if None is allowed when loading + + argument_record(const char *name, const char *descr, handle value, bool convert, bool none) + : name(name), descr(descr), value(value), convert(convert), none(none) { } +}; + +/// Internal data structure which holds metadata about a bound function (signature, overloads, etc.) +struct function_record { + function_record() + : is_constructor(false), is_new_style_constructor(false), is_stateless(false), + is_operator(false), is_method(false), has_args(false), + has_kwargs(false), has_kw_only_args(false), prepend(false) { } + + /// Function name + char *name = nullptr; /* why no C++ strings? They generate heavier code.. */ + + // User-specified documentation string + char *doc = nullptr; + + /// Human-readable version of the function signature + char *signature = nullptr; + + /// List of registered keyword arguments + std::vector args; + + /// Pointer to lambda function which converts arguments and performs the actual call + handle (*impl) (function_call &) = nullptr; + + /// Storage for the wrapped function pointer and captured data, if any + void *data[3] = { }; + + /// Pointer to custom destructor for 'data' (if needed) + void (*free_data) (function_record *ptr) = nullptr; + + /// Return value policy associated with this function + return_value_policy policy = return_value_policy::automatic; + + /// True if name == '__init__' + bool is_constructor : 1; + + /// True if this is a new-style `__init__` defined in `detail/init.h` + bool is_new_style_constructor : 1; + + /// True if this is a stateless function pointer + bool is_stateless : 1; + + /// True if this is an operator (__add__), etc. + bool is_operator : 1; + + /// True if this is a method + bool is_method : 1; + + /// True if the function has a '*args' argument + bool has_args : 1; + + /// True if the function has a '**kwargs' argument + bool has_kwargs : 1; + + /// True once a 'py::kw_only' is encountered (any following args are keyword-only) + bool has_kw_only_args : 1; + + /// True if this function is to be inserted at the beginning of the overload resolution chain + bool prepend : 1; + + /// Number of arguments (including py::args and/or py::kwargs, if present) + std::uint16_t nargs; + + /// Number of trailing arguments (counted in `nargs`) that are keyword-only + std::uint16_t nargs_kw_only = 0; + + /// Number of leading arguments (counted in `nargs`) that are positional-only + std::uint16_t nargs_pos_only = 0; + + /// Python method object + PyMethodDef *def = nullptr; + + /// Python handle to the parent scope (a class or a module) + handle scope; + + /// Python handle to the sibling function representing an overload chain + handle sibling; + + /// Pointer to next overload + function_record *next = nullptr; +}; + +/// Special data structure which (temporarily) holds metadata about a bound class +struct type_record { + PYBIND11_NOINLINE type_record() + : multiple_inheritance(false), dynamic_attr(false), buffer_protocol(false), + default_holder(true), module_local(false), is_final(false) { } + + /// Handle to the parent scope + handle scope; + + /// Name of the class + const char *name = nullptr; + + // Pointer to RTTI type_info data structure + const std::type_info *type = nullptr; + + /// How large is the underlying C++ type? + size_t type_size = 0; + + /// What is the alignment of the underlying C++ type? + size_t type_align = 0; + + /// How large is the type's holder? + size_t holder_size = 0; + + /// The global operator new can be overridden with a class-specific variant + void *(*operator_new)(size_t) = nullptr; + + /// Function pointer to class_<..>::init_instance + void (*init_instance)(instance *, const void *) = nullptr; + + /// Function pointer to class_<..>::dealloc + void (*dealloc)(detail::value_and_holder &) = nullptr; + + /// List of base classes of the newly created type + list bases; + + /// Optional docstring + const char *doc = nullptr; + + /// Custom metaclass (optional) + handle metaclass; + + /// Multiple inheritance marker + bool multiple_inheritance : 1; + + /// Does the class manage a __dict__? + bool dynamic_attr : 1; + + /// Does the class implement the buffer protocol? + bool buffer_protocol : 1; + + /// Is the default (unique_ptr) holder type used? + bool default_holder : 1; + + /// Is the class definition local to the module shared object? + bool module_local : 1; + + /// Is the class inheritable from python classes? + bool is_final : 1; + + PYBIND11_NOINLINE void add_base(const std::type_info &base, void *(*caster)(void *)) { + auto base_info = detail::get_type_info(base, false); + if (!base_info) { + std::string tname(base.name()); + detail::clean_type_id(tname); + pybind11_fail("generic_type: type \"" + std::string(name) + + "\" referenced unknown base type \"" + tname + "\""); + } + + if (default_holder != base_info->default_holder) { + std::string tname(base.name()); + detail::clean_type_id(tname); + pybind11_fail("generic_type: type \"" + std::string(name) + "\" " + + (default_holder ? "does not have" : "has") + + " a non-default holder type while its base \"" + tname + "\" " + + (base_info->default_holder ? "does not" : "does")); + } + + bases.append((PyObject *) base_info->type); + + if (base_info->type->tp_dictoffset != 0) + dynamic_attr = true; + + if (caster) + base_info->implicit_casts.emplace_back(type, caster); + } +}; + +inline function_call::function_call(const function_record &f, handle p) : + func(f), parent(p) { + args.reserve(f.nargs); + args_convert.reserve(f.nargs); +} + +/// Tag for a new-style `__init__` defined in `detail/init.h` +struct is_new_style_constructor { }; + +/** + * Partial template specializations to process custom attributes provided to + * cpp_function_ and class_. These are either used to initialize the respective + * fields in the type_record and function_record data structures or executed at + * runtime to deal with custom call policies (e.g. keep_alive). + */ +template struct process_attribute; + +template struct process_attribute_default { + /// Default implementation: do nothing + static void init(const T &, function_record *) { } + static void init(const T &, type_record *) { } + static void precall(function_call &) { } + static void postcall(function_call &, handle) { } +}; + +/// Process an attribute specifying the function's name +template <> struct process_attribute : process_attribute_default { + static void init(const name &n, function_record *r) { r->name = const_cast(n.value); } +}; + +/// Process an attribute specifying the function's docstring +template <> struct process_attribute : process_attribute_default { + static void init(const doc &n, function_record *r) { r->doc = const_cast(n.value); } +}; + +/// Process an attribute specifying the function's docstring (provided as a C-style string) +template <> struct process_attribute : process_attribute_default { + static void init(const char *d, function_record *r) { r->doc = const_cast(d); } + static void init(const char *d, type_record *r) { r->doc = const_cast(d); } +}; +template <> struct process_attribute : process_attribute { }; + +/// Process an attribute indicating the function's return value policy +template <> struct process_attribute : process_attribute_default { + static void init(const return_value_policy &p, function_record *r) { r->policy = p; } +}; + +/// Process an attribute which indicates that this is an overloaded function associated with a given sibling +template <> struct process_attribute : process_attribute_default { + static void init(const sibling &s, function_record *r) { r->sibling = s.value; } +}; + +/// Process an attribute which indicates that this function is a method +template <> struct process_attribute : process_attribute_default { + static void init(const is_method &s, function_record *r) { r->is_method = true; r->scope = s.class_; } +}; + +/// Process an attribute which indicates the parent scope of a method +template <> struct process_attribute : process_attribute_default { + static void init(const scope &s, function_record *r) { r->scope = s.value; } +}; + +/// Process an attribute which indicates that this function is an operator +template <> struct process_attribute : process_attribute_default { + static void init(const is_operator &, function_record *r) { r->is_operator = true; } +}; + +template <> struct process_attribute : process_attribute_default { + static void init(const is_new_style_constructor &, function_record *r) { r->is_new_style_constructor = true; } +}; + +inline void process_kw_only_arg(const arg &a, function_record *r) { + if (!a.name || strlen(a.name) == 0) + pybind11_fail("arg(): cannot specify an unnamed argument after an kw_only() annotation"); + ++r->nargs_kw_only; +} + +/// Process a keyword argument attribute (*without* a default value) +template <> struct process_attribute : process_attribute_default { + static void init(const arg &a, function_record *r) { + if (r->is_method && r->args.empty()) + r->args.emplace_back("self", nullptr, handle(), true /*convert*/, false /*none not allowed*/); + r->args.emplace_back(a.name, nullptr, handle(), !a.flag_noconvert, a.flag_none); + + if (r->has_kw_only_args) process_kw_only_arg(a, r); + } +}; + +/// Process a keyword argument attribute (*with* a default value) +template <> struct process_attribute : process_attribute_default { + static void init(const arg_v &a, function_record *r) { + if (r->is_method && r->args.empty()) + r->args.emplace_back("self", nullptr /*descr*/, handle() /*parent*/, true /*convert*/, false /*none not allowed*/); + + if (!a.value) { +#if !defined(NDEBUG) + std::string descr("'"); + if (a.name) descr += std::string(a.name) + ": "; + descr += a.type + "'"; + if (r->is_method) { + if (r->name) + descr += " in method '" + (std::string) str(r->scope) + "." + (std::string) r->name + "'"; + else + descr += " in method of '" + (std::string) str(r->scope) + "'"; + } else if (r->name) { + descr += " in function '" + (std::string) r->name + "'"; + } + pybind11_fail("arg(): could not convert default argument " + + descr + " into a Python object (type not registered yet?)"); +#else + pybind11_fail("arg(): could not convert default argument " + "into a Python object (type not registered yet?). " + "Compile in debug mode for more information."); +#endif + } + r->args.emplace_back(a.name, a.descr, a.value.inc_ref(), !a.flag_noconvert, a.flag_none); + + if (r->has_kw_only_args) process_kw_only_arg(a, r); + } +}; + +/// Process a keyword-only-arguments-follow pseudo argument +template <> struct process_attribute : process_attribute_default { + static void init(const kw_only &, function_record *r) { + r->has_kw_only_args = true; + } +}; + +/// Process a positional-only-argument maker +template <> struct process_attribute : process_attribute_default { + static void init(const pos_only &, function_record *r) { + r->nargs_pos_only = static_cast(r->args.size()); + } +}; + +/// Process a parent class attribute. Single inheritance only (class_ itself already guarantees that) +template +struct process_attribute::value>> : process_attribute_default { + static void init(const handle &h, type_record *r) { r->bases.append(h); } +}; + +/// Process a parent class attribute (deprecated, does not support multiple inheritance) +template +struct process_attribute> : process_attribute_default> { + static void init(const base &, type_record *r) { r->add_base(typeid(T), nullptr); } +}; + +/// Process a multiple inheritance attribute +template <> +struct process_attribute : process_attribute_default { + static void init(const multiple_inheritance &, type_record *r) { r->multiple_inheritance = true; } +}; + +template <> +struct process_attribute : process_attribute_default { + static void init(const dynamic_attr &, type_record *r) { r->dynamic_attr = true; } +}; + +template <> +struct process_attribute : process_attribute_default { + static void init(const is_final &, type_record *r) { r->is_final = true; } +}; + +template <> +struct process_attribute : process_attribute_default { + static void init(const buffer_protocol &, type_record *r) { r->buffer_protocol = true; } +}; + +template <> +struct process_attribute : process_attribute_default { + static void init(const metaclass &m, type_record *r) { r->metaclass = m.value; } +}; + +template <> +struct process_attribute : process_attribute_default { + static void init(const module_local &l, type_record *r) { r->module_local = l.value; } +}; + +/// Process a 'prepend' attribute, putting this at the beginning of the overload chain +template <> +struct process_attribute : process_attribute_default { + static void init(const prepend &, function_record *r) { r->prepend = true; } +}; + +/// Process an 'arithmetic' attribute for enums (does nothing here) +template <> +struct process_attribute : process_attribute_default {}; + +template +struct process_attribute> : process_attribute_default> { }; + +/** + * Process a keep_alive call policy -- invokes keep_alive_impl during the + * pre-call handler if both Nurse, Patient != 0 and use the post-call handler + * otherwise + */ +template struct process_attribute> : public process_attribute_default> { + template = 0> + static void precall(function_call &call) { keep_alive_impl(Nurse, Patient, call, handle()); } + template = 0> + static void postcall(function_call &, handle) { } + template = 0> + static void precall(function_call &) { } + template = 0> + static void postcall(function_call &call, handle ret) { keep_alive_impl(Nurse, Patient, call, ret); } +}; + +/// Recursively iterate over variadic template arguments +template struct process_attributes { + static void init(const Args&... args, function_record *r) { + int unused[] = { 0, (process_attribute::type>::init(args, r), 0) ... }; + ignore_unused(unused); + } + static void init(const Args&... args, type_record *r) { + int unused[] = { 0, (process_attribute::type>::init(args, r), 0) ... }; + ignore_unused(unused); + } + static void precall(function_call &call) { + int unused[] = { 0, (process_attribute::type>::precall(call), 0) ... }; + ignore_unused(unused); + } + static void postcall(function_call &call, handle fn_ret) { + int unused[] = { 0, (process_attribute::type>::postcall(call, fn_ret), 0) ... }; + ignore_unused(unused); + } +}; + +template +using is_call_guard = is_instantiation; + +/// Extract the ``type`` from the first `call_guard` in `Extras...` (or `void_type` if none found) +template +using extract_guard_t = typename exactly_one_t, Extra...>::type; + +/// Check the number of named arguments at compile time +template ::value...), + size_t self = constexpr_sum(std::is_same::value...)> +constexpr bool expected_num_args(size_t nargs, bool has_args, bool has_kwargs) { + return named == 0 || (self + named + size_t(has_args) + size_t(has_kwargs)) == nargs; +} + +PYBIND11_NAMESPACE_END(detail) +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/buffer_info.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/buffer_info.h new file mode 100644 index 0000000000000000000000000000000000000000..d803004a102f4150778f0f7a70b8b0865bd4c245 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/buffer_info.h @@ -0,0 +1,146 @@ +/* + pybind11/buffer_info.h: Python buffer object interface + + Copyright (c) 2016 Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "detail/common.h" + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) + +PYBIND11_NAMESPACE_BEGIN(detail) + +// Default, C-style strides +inline std::vector c_strides(const std::vector &shape, ssize_t itemsize) { + auto ndim = shape.size(); + std::vector strides(ndim, itemsize); + if (ndim > 0) + for (size_t i = ndim - 1; i > 0; --i) + strides[i - 1] = strides[i] * shape[i]; + return strides; +} + +// F-style strides; default when constructing an array_t with `ExtraFlags & f_style` +inline std::vector f_strides(const std::vector &shape, ssize_t itemsize) { + auto ndim = shape.size(); + std::vector strides(ndim, itemsize); + for (size_t i = 1; i < ndim; ++i) + strides[i] = strides[i - 1] * shape[i - 1]; + return strides; +} + +PYBIND11_NAMESPACE_END(detail) + +/// Information record describing a Python buffer object +struct buffer_info { + void *ptr = nullptr; // Pointer to the underlying storage + ssize_t itemsize = 0; // Size of individual items in bytes + ssize_t size = 0; // Total number of entries + std::string format; // For homogeneous buffers, this should be set to format_descriptor::format() + ssize_t ndim = 0; // Number of dimensions + std::vector shape; // Shape of the tensor (1 entry per dimension) + std::vector strides; // Number of bytes between adjacent entries (for each per dimension) + bool readonly = false; // flag to indicate if the underlying storage may be written to + + buffer_info() = default; + + buffer_info(void *ptr, ssize_t itemsize, const std::string &format, ssize_t ndim, + detail::any_container shape_in, detail::any_container strides_in, bool readonly=false) + : ptr(ptr), itemsize(itemsize), size(1), format(format), ndim(ndim), + shape(std::move(shape_in)), strides(std::move(strides_in)), readonly(readonly) { + if (ndim != (ssize_t) shape.size() || ndim != (ssize_t) strides.size()) + pybind11_fail("buffer_info: ndim doesn't match shape and/or strides length"); + for (size_t i = 0; i < (size_t) ndim; ++i) + size *= shape[i]; + } + + template + buffer_info(T *ptr, detail::any_container shape_in, detail::any_container strides_in, bool readonly=false) + : buffer_info(private_ctr_tag(), ptr, sizeof(T), format_descriptor::format(), static_cast(shape_in->size()), std::move(shape_in), std::move(strides_in), readonly) { } + + buffer_info(void *ptr, ssize_t itemsize, const std::string &format, ssize_t size, bool readonly=false) + : buffer_info(ptr, itemsize, format, 1, {size}, {itemsize}, readonly) { } + + template + buffer_info(T *ptr, ssize_t size, bool readonly=false) + : buffer_info(ptr, sizeof(T), format_descriptor::format(), size, readonly) { } + + template + buffer_info(const T *ptr, ssize_t size, bool readonly=true) + : buffer_info(const_cast(ptr), sizeof(T), format_descriptor::format(), size, readonly) { } + + explicit buffer_info(Py_buffer *view, bool ownview = true) + : buffer_info(view->buf, view->itemsize, view->format, view->ndim, + {view->shape, view->shape + view->ndim}, + /* Though buffer::request() requests PyBUF_STRIDES, ctypes objects + * ignore this flag and return a view with NULL strides. + * When strides are NULL, build them manually. */ + view->strides + ? std::vector(view->strides, view->strides + view->ndim) + : detail::c_strides({view->shape, view->shape + view->ndim}, view->itemsize), + view->readonly) { + this->m_view = view; + this->ownview = ownview; + } + + buffer_info(const buffer_info &) = delete; + buffer_info& operator=(const buffer_info &) = delete; + + buffer_info(buffer_info &&other) { + (*this) = std::move(other); + } + + buffer_info& operator=(buffer_info &&rhs) { + ptr = rhs.ptr; + itemsize = rhs.itemsize; + size = rhs.size; + format = std::move(rhs.format); + ndim = rhs.ndim; + shape = std::move(rhs.shape); + strides = std::move(rhs.strides); + std::swap(m_view, rhs.m_view); + std::swap(ownview, rhs.ownview); + readonly = rhs.readonly; + return *this; + } + + ~buffer_info() { + if (m_view && ownview) { PyBuffer_Release(m_view); delete m_view; } + } + + Py_buffer *view() const { return m_view; } + Py_buffer *&view() { return m_view; } +private: + struct private_ctr_tag { }; + + buffer_info(private_ctr_tag, void *ptr, ssize_t itemsize, const std::string &format, ssize_t ndim, + detail::any_container &&shape_in, detail::any_container &&strides_in, bool readonly) + : buffer_info(ptr, itemsize, format, ndim, std::move(shape_in), std::move(strides_in), readonly) { } + + Py_buffer *m_view = nullptr; + bool ownview = false; +}; + +PYBIND11_NAMESPACE_BEGIN(detail) + +template struct compare_buffer_info { + static bool compare(const buffer_info& b) { + return b.format == format_descriptor::format() && b.itemsize == (ssize_t) sizeof(T); + } +}; + +template struct compare_buffer_info::value>> { + static bool compare(const buffer_info& b) { + return (size_t) b.itemsize == sizeof(T) && (b.format == format_descriptor::value || + ((sizeof(T) == sizeof(long)) && b.format == (std::is_unsigned::value ? "L" : "l")) || + ((sizeof(T) == sizeof(size_t)) && b.format == (std::is_unsigned::value ? "N" : "n"))); + } +}; + +PYBIND11_NAMESPACE_END(detail) +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/cast.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/cast.h new file mode 100644 index 0000000000000000000000000000000000000000..0ad10e9a9329a3de956d74c3f21300d8a6d0be05 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/cast.h @@ -0,0 +1,1383 @@ +/* + pybind11/cast.h: Partial template specializations to cast between + C++ and Python types + + Copyright (c) 2016 Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "pytypes.h" +#include "detail/common.h" +#include "detail/descr.h" +#include "detail/type_caster_base.h" +#include "detail/typeid.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#if defined(PYBIND11_CPP17) +# if defined(__has_include) +# if __has_include() +# define PYBIND11_HAS_STRING_VIEW +# endif +# elif defined(_MSC_VER) +# define PYBIND11_HAS_STRING_VIEW +# endif +#endif +#ifdef PYBIND11_HAS_STRING_VIEW +#include +#endif + +#if defined(__cpp_lib_char8_t) && __cpp_lib_char8_t >= 201811L +# define PYBIND11_HAS_U8STRING +#endif + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) +PYBIND11_NAMESPACE_BEGIN(detail) + +template class type_caster : public type_caster_base { }; +template using make_caster = type_caster>; + +// Shortcut for calling a caster's `cast_op_type` cast operator for casting a type_caster to a T +template typename make_caster::template cast_op_type cast_op(make_caster &caster) { + return caster.operator typename make_caster::template cast_op_type(); +} +template typename make_caster::template cast_op_type::type> +cast_op(make_caster &&caster) { + return std::move(caster).operator + typename make_caster::template cast_op_type::type>(); +} + +template class type_caster> { +private: + using caster_t = make_caster; + caster_t subcaster; + using reference_t = type&; + using subcaster_cast_op_type = + typename caster_t::template cast_op_type; + + static_assert(std::is_same::type &, subcaster_cast_op_type>::value || + std::is_same::value, + "std::reference_wrapper caster requires T to have a caster with an " + "`operator T &()` or `operator const T &()`"); +public: + bool load(handle src, bool convert) { return subcaster.load(src, convert); } + static constexpr auto name = caster_t::name; + static handle cast(const std::reference_wrapper &src, return_value_policy policy, handle parent) { + // It is definitely wrong to take ownership of this pointer, so mask that rvp + if (policy == return_value_policy::take_ownership || policy == return_value_policy::automatic) + policy = return_value_policy::automatic_reference; + return caster_t::cast(&src.get(), policy, parent); + } + template using cast_op_type = std::reference_wrapper; + operator std::reference_wrapper() { return cast_op(subcaster); } +}; + +#define PYBIND11_TYPE_CASTER(type, py_name) \ + protected: \ + type value; \ + public: \ + static constexpr auto name = py_name; \ + template >::value, int> = 0> \ + static handle cast(T_ *src, return_value_policy policy, handle parent) { \ + if (!src) return none().release(); \ + if (policy == return_value_policy::take_ownership) { \ + auto h = cast(std::move(*src), policy, parent); delete src; return h; \ + } else { \ + return cast(*src, policy, parent); \ + } \ + } \ + operator type*() { return &value; } \ + operator type&() { return value; } \ + operator type&&() && { return std::move(value); } \ + template using cast_op_type = pybind11::detail::movable_cast_op_type + + +template using is_std_char_type = any_of< + std::is_same, /* std::string */ +#if defined(PYBIND11_HAS_U8STRING) + std::is_same, /* std::u8string */ +#endif + std::is_same, /* std::u16string */ + std::is_same, /* std::u32string */ + std::is_same /* std::wstring */ +>; + + +template +struct type_caster::value && !is_std_char_type::value>> { + using _py_type_0 = conditional_t; + using _py_type_1 = conditional_t::value, _py_type_0, typename std::make_unsigned<_py_type_0>::type>; + using py_type = conditional_t::value, double, _py_type_1>; +public: + + bool load(handle src, bool convert) { + py_type py_value; + + if (!src) + return false; + +#if !defined(PYPY_VERSION) + auto index_check = [](PyObject *o) { return PyIndex_Check(o); }; +#else + // In PyPy 7.3.3, `PyIndex_Check` is implemented by calling `__index__`, + // while CPython only considers the existence of `nb_index`/`__index__`. + auto index_check = [](PyObject *o) { return hasattr(o, "__index__"); }; +#endif + + if (std::is_floating_point::value) { + if (convert || PyFloat_Check(src.ptr())) + py_value = (py_type) PyFloat_AsDouble(src.ptr()); + else + return false; + } else if (PyFloat_Check(src.ptr())) { + return false; + } else if (!convert && !PYBIND11_LONG_CHECK(src.ptr()) && !index_check(src.ptr())) { + return false; + } else { + handle src_or_index = src; +#if PY_VERSION_HEX < 0x03080000 + object index; + if (!PYBIND11_LONG_CHECK(src.ptr())) { // So: index_check(src.ptr()) + index = reinterpret_steal(PyNumber_Index(src.ptr())); + if (!index) { + PyErr_Clear(); + if (!convert) + return false; + } + else { + src_or_index = index; + } + } +#endif + if (std::is_unsigned::value) { + py_value = as_unsigned(src_or_index.ptr()); + } else { // signed integer: + py_value = sizeof(T) <= sizeof(long) + ? (py_type) PyLong_AsLong(src_or_index.ptr()) + : (py_type) PYBIND11_LONG_AS_LONGLONG(src_or_index.ptr()); + } + } + + // Python API reported an error + bool py_err = py_value == (py_type) -1 && PyErr_Occurred(); + + // Check to see if the conversion is valid (integers should match exactly) + // Signed/unsigned checks happen elsewhere + if (py_err || (std::is_integral::value && sizeof(py_type) != sizeof(T) && py_value != (py_type) (T) py_value)) { + PyErr_Clear(); + if (py_err && convert && PyNumber_Check(src.ptr())) { + auto tmp = reinterpret_steal(std::is_floating_point::value + ? PyNumber_Float(src.ptr()) + : PyNumber_Long(src.ptr())); + PyErr_Clear(); + return load(tmp, false); + } + return false; + } + + value = (T) py_value; + return true; + } + + template + static typename std::enable_if::value, handle>::type + cast(U src, return_value_policy /* policy */, handle /* parent */) { + return PyFloat_FromDouble((double) src); + } + + template + static typename std::enable_if::value && std::is_signed::value && (sizeof(U) <= sizeof(long)), handle>::type + cast(U src, return_value_policy /* policy */, handle /* parent */) { + return PYBIND11_LONG_FROM_SIGNED((long) src); + } + + template + static typename std::enable_if::value && std::is_unsigned::value && (sizeof(U) <= sizeof(unsigned long)), handle>::type + cast(U src, return_value_policy /* policy */, handle /* parent */) { + return PYBIND11_LONG_FROM_UNSIGNED((unsigned long) src); + } + + template + static typename std::enable_if::value && std::is_signed::value && (sizeof(U) > sizeof(long)), handle>::type + cast(U src, return_value_policy /* policy */, handle /* parent */) { + return PyLong_FromLongLong((long long) src); + } + + template + static typename std::enable_if::value && std::is_unsigned::value && (sizeof(U) > sizeof(unsigned long)), handle>::type + cast(U src, return_value_policy /* policy */, handle /* parent */) { + return PyLong_FromUnsignedLongLong((unsigned long long) src); + } + + PYBIND11_TYPE_CASTER(T, _::value>("int", "float")); +}; + +template struct void_caster { +public: + bool load(handle src, bool) { + if (src && src.is_none()) + return true; + return false; + } + static handle cast(T, return_value_policy /* policy */, handle /* parent */) { + return none().inc_ref(); + } + PYBIND11_TYPE_CASTER(T, _("None")); +}; + +template <> class type_caster : public void_caster {}; + +template <> class type_caster : public type_caster { +public: + using type_caster::cast; + + bool load(handle h, bool) { + if (!h) { + return false; + } else if (h.is_none()) { + value = nullptr; + return true; + } + + /* Check if this is a capsule */ + if (isinstance(h)) { + value = reinterpret_borrow(h); + return true; + } + + /* Check if this is a C++ type */ + auto &bases = all_type_info((PyTypeObject *) type::handle_of(h).ptr()); + if (bases.size() == 1) { // Only allowing loading from a single-value type + value = values_and_holders(reinterpret_cast(h.ptr())).begin()->value_ptr(); + return true; + } + + /* Fail */ + return false; + } + + static handle cast(const void *ptr, return_value_policy /* policy */, handle /* parent */) { + if (ptr) + return capsule(ptr).release(); + else + return none().inc_ref(); + } + + template using cast_op_type = void*&; + operator void *&() { return value; } + static constexpr auto name = _("capsule"); +private: + void *value = nullptr; +}; + +template <> class type_caster : public void_caster { }; + +template <> class type_caster { +public: + bool load(handle src, bool convert) { + if (!src) return false; + else if (src.ptr() == Py_True) { value = true; return true; } + else if (src.ptr() == Py_False) { value = false; return true; } + else if (convert || !std::strcmp("numpy.bool_", Py_TYPE(src.ptr())->tp_name)) { + // (allow non-implicit conversion for numpy booleans) + + Py_ssize_t res = -1; + if (src.is_none()) { + res = 0; // None is implicitly converted to False + } + #if defined(PYPY_VERSION) + // On PyPy, check that "__bool__" (or "__nonzero__" on Python 2.7) attr exists + else if (hasattr(src, PYBIND11_BOOL_ATTR)) { + res = PyObject_IsTrue(src.ptr()); + } + #else + // Alternate approach for CPython: this does the same as the above, but optimized + // using the CPython API so as to avoid an unneeded attribute lookup. + else if (auto tp_as_number = src.ptr()->ob_type->tp_as_number) { + if (PYBIND11_NB_BOOL(tp_as_number)) { + res = (*PYBIND11_NB_BOOL(tp_as_number))(src.ptr()); + } + } + #endif + if (res == 0 || res == 1) { + value = (bool) res; + return true; + } else { + PyErr_Clear(); + } + } + return false; + } + static handle cast(bool src, return_value_policy /* policy */, handle /* parent */) { + return handle(src ? Py_True : Py_False).inc_ref(); + } + PYBIND11_TYPE_CASTER(bool, _("bool")); +}; + +// Helper class for UTF-{8,16,32} C++ stl strings: +template struct string_caster { + using CharT = typename StringType::value_type; + + // Simplify life by being able to assume standard char sizes (the standard only guarantees + // minimums, but Python requires exact sizes) + static_assert(!std::is_same::value || sizeof(CharT) == 1, "Unsupported char size != 1"); +#if defined(PYBIND11_HAS_U8STRING) + static_assert(!std::is_same::value || sizeof(CharT) == 1, "Unsupported char8_t size != 1"); +#endif + static_assert(!std::is_same::value || sizeof(CharT) == 2, "Unsupported char16_t size != 2"); + static_assert(!std::is_same::value || sizeof(CharT) == 4, "Unsupported char32_t size != 4"); + // wchar_t can be either 16 bits (Windows) or 32 (everywhere else) + static_assert(!std::is_same::value || sizeof(CharT) == 2 || sizeof(CharT) == 4, + "Unsupported wchar_t size != 2/4"); + static constexpr size_t UTF_N = 8 * sizeof(CharT); + + bool load(handle src, bool) { +#if PY_MAJOR_VERSION < 3 + object temp; +#endif + handle load_src = src; + if (!src) { + return false; + } else if (!PyUnicode_Check(load_src.ptr())) { +#if PY_MAJOR_VERSION >= 3 + return load_bytes(load_src); +#else + if (std::is_same::value) { + return load_bytes(load_src); + } + + // The below is a guaranteed failure in Python 3 when PyUnicode_Check returns false + if (!PYBIND11_BYTES_CHECK(load_src.ptr())) + return false; + + temp = reinterpret_steal(PyUnicode_FromObject(load_src.ptr())); + if (!temp) { PyErr_Clear(); return false; } + load_src = temp; +#endif + } + + auto utfNbytes = reinterpret_steal(PyUnicode_AsEncodedString( + load_src.ptr(), UTF_N == 8 ? "utf-8" : UTF_N == 16 ? "utf-16" : "utf-32", nullptr)); + if (!utfNbytes) { PyErr_Clear(); return false; } + + const auto *buffer = reinterpret_cast(PYBIND11_BYTES_AS_STRING(utfNbytes.ptr())); + size_t length = (size_t) PYBIND11_BYTES_SIZE(utfNbytes.ptr()) / sizeof(CharT); + if (UTF_N > 8) { buffer++; length--; } // Skip BOM for UTF-16/32 + value = StringType(buffer, length); + + // If we're loading a string_view we need to keep the encoded Python object alive: + if (IsView) + loader_life_support::add_patient(utfNbytes); + + return true; + } + + static handle cast(const StringType &src, return_value_policy /* policy */, handle /* parent */) { + const char *buffer = reinterpret_cast(src.data()); + auto nbytes = ssize_t(src.size() * sizeof(CharT)); + handle s = decode_utfN(buffer, nbytes); + if (!s) throw error_already_set(); + return s; + } + + PYBIND11_TYPE_CASTER(StringType, _(PYBIND11_STRING_NAME)); + +private: + static handle decode_utfN(const char *buffer, ssize_t nbytes) { +#if !defined(PYPY_VERSION) + return + UTF_N == 8 ? PyUnicode_DecodeUTF8(buffer, nbytes, nullptr) : + UTF_N == 16 ? PyUnicode_DecodeUTF16(buffer, nbytes, nullptr, nullptr) : + PyUnicode_DecodeUTF32(buffer, nbytes, nullptr, nullptr); +#else + // PyPy segfaults when on PyUnicode_DecodeUTF16 (and possibly on PyUnicode_DecodeUTF32 as well), + // so bypass the whole thing by just passing the encoding as a string value, which works properly: + return PyUnicode_Decode(buffer, nbytes, UTF_N == 8 ? "utf-8" : UTF_N == 16 ? "utf-16" : "utf-32", nullptr); +#endif + } + + // When loading into a std::string or char*, accept a bytes object as-is (i.e. + // without any encoding/decoding attempt). For other C++ char sizes this is a no-op. + // which supports loading a unicode from a str, doesn't take this path. + template + bool load_bytes(enable_if_t::value, handle> src) { + if (PYBIND11_BYTES_CHECK(src.ptr())) { + // We were passed a Python 3 raw bytes; accept it into a std::string or char* + // without any encoding attempt. + const char *bytes = PYBIND11_BYTES_AS_STRING(src.ptr()); + if (bytes) { + value = StringType(bytes, (size_t) PYBIND11_BYTES_SIZE(src.ptr())); + return true; + } + } + + return false; + } + + template + bool load_bytes(enable_if_t::value, handle>) { return false; } +}; + +template +struct type_caster, enable_if_t::value>> + : string_caster> {}; + +#ifdef PYBIND11_HAS_STRING_VIEW +template +struct type_caster, enable_if_t::value>> + : string_caster, true> {}; +#endif + +// Type caster for C-style strings. We basically use a std::string type caster, but also add the +// ability to use None as a nullptr char* (which the string caster doesn't allow). +template struct type_caster::value>> { + using StringType = std::basic_string; + using StringCaster = type_caster; + StringCaster str_caster; + bool none = false; + CharT one_char = 0; +public: + bool load(handle src, bool convert) { + if (!src) return false; + if (src.is_none()) { + // Defer accepting None to other overloads (if we aren't in convert mode): + if (!convert) return false; + none = true; + return true; + } + return str_caster.load(src, convert); + } + + static handle cast(const CharT *src, return_value_policy policy, handle parent) { + if (src == nullptr) return pybind11::none().inc_ref(); + return StringCaster::cast(StringType(src), policy, parent); + } + + static handle cast(CharT src, return_value_policy policy, handle parent) { + if (std::is_same::value) { + handle s = PyUnicode_DecodeLatin1((const char *) &src, 1, nullptr); + if (!s) throw error_already_set(); + return s; + } + return StringCaster::cast(StringType(1, src), policy, parent); + } + + operator CharT*() { return none ? nullptr : const_cast(static_cast(str_caster).c_str()); } + operator CharT&() { + if (none) + throw value_error("Cannot convert None to a character"); + + auto &value = static_cast(str_caster); + size_t str_len = value.size(); + if (str_len == 0) + throw value_error("Cannot convert empty string to a character"); + + // If we're in UTF-8 mode, we have two possible failures: one for a unicode character that + // is too high, and one for multiple unicode characters (caught later), so we need to figure + // out how long the first encoded character is in bytes to distinguish between these two + // errors. We also allow want to allow unicode characters U+0080 through U+00FF, as those + // can fit into a single char value. + if (StringCaster::UTF_N == 8 && str_len > 1 && str_len <= 4) { + auto v0 = static_cast(value[0]); + size_t char0_bytes = !(v0 & 0x80) ? 1 : // low bits only: 0-127 + (v0 & 0xE0) == 0xC0 ? 2 : // 0b110xxxxx - start of 2-byte sequence + (v0 & 0xF0) == 0xE0 ? 3 : // 0b1110xxxx - start of 3-byte sequence + 4; // 0b11110xxx - start of 4-byte sequence + + if (char0_bytes == str_len) { + // If we have a 128-255 value, we can decode it into a single char: + if (char0_bytes == 2 && (v0 & 0xFC) == 0xC0) { // 0x110000xx 0x10xxxxxx + one_char = static_cast(((v0 & 3) << 6) + (static_cast(value[1]) & 0x3F)); + return one_char; + } + // Otherwise we have a single character, but it's > U+00FF + throw value_error("Character code point not in range(0x100)"); + } + } + + // UTF-16 is much easier: we can only have a surrogate pair for values above U+FFFF, thus a + // surrogate pair with total length 2 instantly indicates a range error (but not a "your + // string was too long" error). + else if (StringCaster::UTF_N == 16 && str_len == 2) { + one_char = static_cast(value[0]); + if (one_char >= 0xD800 && one_char < 0xE000) + throw value_error("Character code point not in range(0x10000)"); + } + + if (str_len != 1) + throw value_error("Expected a character, but multi-character string found"); + + one_char = value[0]; + return one_char; + } + + static constexpr auto name = _(PYBIND11_STRING_NAME); + template using cast_op_type = pybind11::detail::cast_op_type<_T>; +}; + +// Base implementation for std::tuple and std::pair +template class Tuple, typename... Ts> class tuple_caster { + using type = Tuple; + static constexpr auto size = sizeof...(Ts); + using indices = make_index_sequence; +public: + + bool load(handle src, bool convert) { + if (!isinstance(src)) + return false; + const auto seq = reinterpret_borrow(src); + if (seq.size() != size) + return false; + return load_impl(seq, convert, indices{}); + } + + template + static handle cast(T &&src, return_value_policy policy, handle parent) { + return cast_impl(std::forward(src), policy, parent, indices{}); + } + + // copied from the PYBIND11_TYPE_CASTER macro + template + static handle cast(T *src, return_value_policy policy, handle parent) { + if (!src) return none().release(); + if (policy == return_value_policy::take_ownership) { + auto h = cast(std::move(*src), policy, parent); delete src; return h; + } else { + return cast(*src, policy, parent); + } + } + + static constexpr auto name = _("Tuple[") + concat(make_caster::name...) + _("]"); + + template using cast_op_type = type; + + operator type() & { return implicit_cast(indices{}); } + operator type() && { return std::move(*this).implicit_cast(indices{}); } + +protected: + template + type implicit_cast(index_sequence) & { return type(cast_op(std::get(subcasters))...); } + template + type implicit_cast(index_sequence) && { return type(cast_op(std::move(std::get(subcasters)))...); } + + static constexpr bool load_impl(const sequence &, bool, index_sequence<>) { return true; } + + template + bool load_impl(const sequence &seq, bool convert, index_sequence) { +#ifdef __cpp_fold_expressions + if ((... || !std::get(subcasters).load(seq[Is], convert))) + return false; +#else + for (bool r : {std::get(subcasters).load(seq[Is], convert)...}) + if (!r) + return false; +#endif + return true; + } + + /* Implementation: Convert a C++ tuple into a Python tuple */ + template + static handle cast_impl(T &&src, return_value_policy policy, handle parent, index_sequence) { + std::array entries{{ + reinterpret_steal(make_caster::cast(std::get(std::forward(src)), policy, parent))... + }}; + for (const auto &entry: entries) + if (!entry) + return handle(); + tuple result(size); + int counter = 0; + for (auto & entry: entries) + PyTuple_SET_ITEM(result.ptr(), counter++, entry.release().ptr()); + return result.release(); + } + + Tuple...> subcasters; +}; + +template class type_caster> + : public tuple_caster {}; + +template class type_caster> + : public tuple_caster {}; + +/// Helper class which abstracts away certain actions. Users can provide specializations for +/// custom holders, but it's only necessary if the type has a non-standard interface. +template +struct holder_helper { + static auto get(const T &p) -> decltype(p.get()) { return p.get(); } +}; + +/// Type caster for holder types like std::shared_ptr, etc. +/// The SFINAE hook is provided to help work around the current lack of support +/// for smart-pointer interoperability. Please consider it an implementation +/// detail that may change in the future, as formal support for smart-pointer +/// interoperability is added into pybind11. +template +struct copyable_holder_caster : public type_caster_base { +public: + using base = type_caster_base; + static_assert(std::is_base_of>::value, + "Holder classes are only supported for custom types"); + using base::base; + using base::cast; + using base::typeinfo; + using base::value; + + bool load(handle src, bool convert) { + return base::template load_impl>(src, convert); + } + + explicit operator type*() { return this->value; } + // static_cast works around compiler error with MSVC 17 and CUDA 10.2 + // see issue #2180 + explicit operator type&() { return *(static_cast(this->value)); } + explicit operator holder_type*() { return std::addressof(holder); } + explicit operator holder_type&() { return holder; } + + static handle cast(const holder_type &src, return_value_policy, handle) { + const auto *ptr = holder_helper::get(src); + return type_caster_base::cast_holder(ptr, &src); + } + +protected: + friend class type_caster_generic; + void check_holder_compat() { + if (typeinfo->default_holder) + throw cast_error("Unable to load a custom holder type from a default-holder instance"); + } + + bool load_value(value_and_holder &&v_h) { + if (v_h.holder_constructed()) { + value = v_h.value_ptr(); + holder = v_h.template holder(); + return true; + } else { + throw cast_error("Unable to cast from non-held to held instance (T& to Holder) " +#if defined(NDEBUG) + "(compile in debug mode for type information)"); +#else + "of type '" + type_id() + "''"); +#endif + } + } + + template ::value, int> = 0> + bool try_implicit_casts(handle, bool) { return false; } + + template ::value, int> = 0> + bool try_implicit_casts(handle src, bool convert) { + for (auto &cast : typeinfo->implicit_casts) { + copyable_holder_caster sub_caster(*cast.first); + if (sub_caster.load(src, convert)) { + value = cast.second(sub_caster.value); + holder = holder_type(sub_caster.holder, (type *) value); + return true; + } + } + return false; + } + + static bool try_direct_conversions(handle) { return false; } + + + holder_type holder; +}; + +/// Specialize for the common std::shared_ptr, so users don't need to +template +class type_caster> : public copyable_holder_caster> { }; + +/// Type caster for holder types like std::unique_ptr. +/// Please consider the SFINAE hook an implementation detail, as explained +/// in the comment for the copyable_holder_caster. +template +struct move_only_holder_caster { + static_assert(std::is_base_of, type_caster>::value, + "Holder classes are only supported for custom types"); + + static handle cast(holder_type &&src, return_value_policy, handle) { + auto *ptr = holder_helper::get(src); + return type_caster_base::cast_holder(ptr, std::addressof(src)); + } + static constexpr auto name = type_caster_base::name; +}; + +template +class type_caster> + : public move_only_holder_caster> { }; + +template +using type_caster_holder = conditional_t::value, + copyable_holder_caster, + move_only_holder_caster>; + +template struct always_construct_holder { static constexpr bool value = Value; }; + +/// Create a specialization for custom holder types (silently ignores std::shared_ptr) +#define PYBIND11_DECLARE_HOLDER_TYPE(type, holder_type, ...) \ + namespace pybind11 { namespace detail { \ + template \ + struct always_construct_holder : always_construct_holder { }; \ + template \ + class type_caster::value>> \ + : public type_caster_holder { }; \ + }} + +// PYBIND11_DECLARE_HOLDER_TYPE holder types: +template struct is_holder_type : + std::is_base_of, detail::type_caster> {}; +// Specialization for always-supported unique_ptr holders: +template struct is_holder_type> : + std::true_type {}; + +template struct handle_type_name { static constexpr auto name = _(); }; +template <> struct handle_type_name { static constexpr auto name = _(PYBIND11_BYTES_NAME); }; +template <> struct handle_type_name { static constexpr auto name = _("int"); }; +template <> struct handle_type_name { static constexpr auto name = _("Iterable"); }; +template <> struct handle_type_name { static constexpr auto name = _("Iterator"); }; +template <> struct handle_type_name { static constexpr auto name = _("None"); }; +template <> struct handle_type_name { static constexpr auto name = _("*args"); }; +template <> struct handle_type_name { static constexpr auto name = _("**kwargs"); }; + +template +struct pyobject_caster { + template ::value, int> = 0> + bool load(handle src, bool /* convert */) { value = src; return static_cast(value); } + + template ::value, int> = 0> + bool load(handle src, bool /* convert */) { +#if PY_MAJOR_VERSION < 3 && !defined(PYBIND11_STR_LEGACY_PERMISSIVE) + // For Python 2, without this implicit conversion, Python code would + // need to be cluttered with six.ensure_text() or similar, only to be + // un-cluttered later after Python 2 support is dropped. + if (std::is_same::value && isinstance(src)) { + PyObject *str_from_bytes = PyUnicode_FromEncodedObject(src.ptr(), "utf-8", nullptr); + if (!str_from_bytes) throw error_already_set(); + value = reinterpret_steal(str_from_bytes); + return true; + } +#endif + if (!isinstance(src)) + return false; + value = reinterpret_borrow(src); + return true; + } + + static handle cast(const handle &src, return_value_policy /* policy */, handle /* parent */) { + return src.inc_ref(); + } + PYBIND11_TYPE_CASTER(type, handle_type_name::name); +}; + +template +class type_caster::value>> : public pyobject_caster { }; + +// Our conditions for enabling moving are quite restrictive: +// At compile time: +// - T needs to be a non-const, non-pointer, non-reference type +// - type_caster::operator T&() must exist +// - the type must be move constructible (obviously) +// At run-time: +// - if the type is non-copy-constructible, the object must be the sole owner of the type (i.e. it +// must have ref_count() == 1)h +// If any of the above are not satisfied, we fall back to copying. +template using move_is_plain_type = satisfies_none_of; +template struct move_always : std::false_type {}; +template struct move_always, + negation>, + std::is_move_constructible, + std::is_same>().operator T&()), T&> +>::value>> : std::true_type {}; +template struct move_if_unreferenced : std::false_type {}; +template struct move_if_unreferenced, + negation>, + std::is_move_constructible, + std::is_same>().operator T&()), T&> +>::value>> : std::true_type {}; +template using move_never = none_of, move_if_unreferenced>; + +// Detect whether returning a `type` from a cast on type's type_caster is going to result in a +// reference or pointer to a local variable of the type_caster. Basically, only +// non-reference/pointer `type`s and reference/pointers from a type_caster_generic are safe; +// everything else returns a reference/pointer to a local variable. +template using cast_is_temporary_value_reference = bool_constant< + (std::is_reference::value || std::is_pointer::value) && + !std::is_base_of>::value && + !std::is_same, void>::value +>; + +// When a value returned from a C++ function is being cast back to Python, we almost always want to +// force `policy = move`, regardless of the return value policy the function/method was declared +// with. +template struct return_value_policy_override { + static return_value_policy policy(return_value_policy p) { return p; } +}; + +template struct return_value_policy_override>::value, void>> { + static return_value_policy policy(return_value_policy p) { + return !std::is_lvalue_reference::value && + !std::is_pointer::value + ? return_value_policy::move : p; + } +}; + +// Basic python -> C++ casting; throws if casting fails +template type_caster &load_type(type_caster &conv, const handle &handle) { + if (!conv.load(handle, true)) { +#if defined(NDEBUG) + throw cast_error("Unable to cast Python instance to C++ type (compile in debug mode for details)"); +#else + throw cast_error("Unable to cast Python instance of type " + + (std::string) str(type::handle_of(handle)) + " to C++ type '" + type_id() + "'"); +#endif + } + return conv; +} +// Wrapper around the above that also constructs and returns a type_caster +template make_caster load_type(const handle &handle) { + make_caster conv; + load_type(conv, handle); + return conv; +} + +PYBIND11_NAMESPACE_END(detail) + +// pytype -> C++ type +template ::value, int> = 0> +T cast(const handle &handle) { + using namespace detail; + static_assert(!cast_is_temporary_value_reference::value, + "Unable to cast type to reference: value is local to type caster"); + return cast_op(load_type(handle)); +} + +// pytype -> pytype (calls converting constructor) +template ::value, int> = 0> +T cast(const handle &handle) { return T(reinterpret_borrow(handle)); } + +// C++ type -> py::object +template ::value, int> = 0> +object cast(T &&value, return_value_policy policy = return_value_policy::automatic_reference, + handle parent = handle()) { + using no_ref_T = typename std::remove_reference::type; + if (policy == return_value_policy::automatic) + policy = std::is_pointer::value ? return_value_policy::take_ownership : + std::is_lvalue_reference::value ? return_value_policy::copy : return_value_policy::move; + else if (policy == return_value_policy::automatic_reference) + policy = std::is_pointer::value ? return_value_policy::reference : + std::is_lvalue_reference::value ? return_value_policy::copy : return_value_policy::move; + return reinterpret_steal(detail::make_caster::cast(std::forward(value), policy, parent)); +} + +template T handle::cast() const { return pybind11::cast(*this); } +template <> inline void handle::cast() const { return; } + +template +detail::enable_if_t::value, T> move(object &&obj) { + if (obj.ref_count() > 1) +#if defined(NDEBUG) + throw cast_error("Unable to cast Python instance to C++ rvalue: instance has multiple references" + " (compile in debug mode for details)"); +#else + throw cast_error("Unable to move from Python " + (std::string) str(type::handle_of(obj)) + + " instance to C++ " + type_id() + " instance: instance has multiple references"); +#endif + + // Move into a temporary and return that, because the reference may be a local value of `conv` + T ret = std::move(detail::load_type(obj).operator T&()); + return ret; +} + +// Calling cast() on an rvalue calls pybind11::cast with the object rvalue, which does: +// - If we have to move (because T has no copy constructor), do it. This will fail if the moved +// object has multiple references, but trying to copy will fail to compile. +// - If both movable and copyable, check ref count: if 1, move; otherwise copy +// - Otherwise (not movable), copy. +template detail::enable_if_t::value, T> cast(object &&object) { + return move(std::move(object)); +} +template detail::enable_if_t::value, T> cast(object &&object) { + if (object.ref_count() > 1) + return cast(object); + else + return move(std::move(object)); +} +template detail::enable_if_t::value, T> cast(object &&object) { + return cast(object); +} + +template T object::cast() const & { return pybind11::cast(*this); } +template T object::cast() && { return pybind11::cast(std::move(*this)); } +template <> inline void object::cast() const & { return; } +template <> inline void object::cast() && { return; } + +PYBIND11_NAMESPACE_BEGIN(detail) + +// Declared in pytypes.h: +template ::value, int>> +object object_or_cast(T &&o) { return pybind11::cast(std::forward(o)); } + +struct override_unused {}; // Placeholder type for the unneeded (and dead code) static variable in the PYBIND11_OVERRIDE_OVERRIDE macro +template using override_caster_t = conditional_t< + cast_is_temporary_value_reference::value, make_caster, override_unused>; + +// Trampoline use: for reference/pointer types to value-converted values, we do a value cast, then +// store the result in the given variable. For other types, this is a no-op. +template enable_if_t::value, T> cast_ref(object &&o, make_caster &caster) { + return cast_op(load_type(caster, o)); +} +template enable_if_t::value, T> cast_ref(object &&, override_unused &) { + pybind11_fail("Internal error: cast_ref fallback invoked"); } + +// Trampoline use: Having a pybind11::cast with an invalid reference type is going to static_assert, even +// though if it's in dead code, so we provide a "trampoline" to pybind11::cast that only does anything in +// cases where pybind11::cast is valid. +template enable_if_t::value, T> cast_safe(object &&o) { + return pybind11::cast(std::move(o)); } +template enable_if_t::value, T> cast_safe(object &&) { + pybind11_fail("Internal error: cast_safe fallback invoked"); } +template <> inline void cast_safe(object &&) {} + +PYBIND11_NAMESPACE_END(detail) + +template +tuple make_tuple() { return tuple(0); } + +template tuple make_tuple(Args&&... args_) { + constexpr size_t size = sizeof...(Args); + std::array args { + { reinterpret_steal(detail::make_caster::cast( + std::forward(args_), policy, nullptr))... } + }; + for (size_t i = 0; i < args.size(); i++) { + if (!args[i]) { +#if defined(NDEBUG) + throw cast_error("make_tuple(): unable to convert arguments to Python object (compile in debug mode for details)"); +#else + std::array argtypes { {type_id()...} }; + throw cast_error("make_tuple(): unable to convert argument of type '" + + argtypes[i] + "' to Python object"); +#endif + } + } + tuple result(size); + int counter = 0; + for (auto &arg_value : args) + PyTuple_SET_ITEM(result.ptr(), counter++, arg_value.release().ptr()); + return result; +} + +/// \ingroup annotations +/// Annotation for arguments +struct arg { + /// Constructs an argument with the name of the argument; if null or omitted, this is a positional argument. + constexpr explicit arg(const char *name = nullptr) : name(name), flag_noconvert(false), flag_none(true) { } + /// Assign a value to this argument + template arg_v operator=(T &&value) const; + /// Indicate that the type should not be converted in the type caster + arg &noconvert(bool flag = true) { flag_noconvert = flag; return *this; } + /// Indicates that the argument should/shouldn't allow None (e.g. for nullable pointer args) + arg &none(bool flag = true) { flag_none = flag; return *this; } + + const char *name; ///< If non-null, this is a named kwargs argument + bool flag_noconvert : 1; ///< If set, do not allow conversion (requires a supporting type caster!) + bool flag_none : 1; ///< If set (the default), allow None to be passed to this argument +}; + +/// \ingroup annotations +/// Annotation for arguments with values +struct arg_v : arg { +private: + template + arg_v(arg &&base, T &&x, const char *descr = nullptr) + : arg(base), + value(reinterpret_steal( + detail::make_caster::cast(x, return_value_policy::automatic, {}) + )), + descr(descr) +#if !defined(NDEBUG) + , type(type_id()) +#endif + { + // Workaround! See: + // https://github.com/pybind/pybind11/issues/2336 + // https://github.com/pybind/pybind11/pull/2685#issuecomment-731286700 + if (PyErr_Occurred()) { + PyErr_Clear(); + } + } + +public: + /// Direct construction with name, default, and description + template + arg_v(const char *name, T &&x, const char *descr = nullptr) + : arg_v(arg(name), std::forward(x), descr) { } + + /// Called internally when invoking `py::arg("a") = value` + template + arg_v(const arg &base, T &&x, const char *descr = nullptr) + : arg_v(arg(base), std::forward(x), descr) { } + + /// Same as `arg::noconvert()`, but returns *this as arg_v&, not arg& + arg_v &noconvert(bool flag = true) { arg::noconvert(flag); return *this; } + + /// Same as `arg::nonone()`, but returns *this as arg_v&, not arg& + arg_v &none(bool flag = true) { arg::none(flag); return *this; } + + /// The default value + object value; + /// The (optional) description of the default value + const char *descr; +#if !defined(NDEBUG) + /// The C++ type name of the default value (only available when compiled in debug mode) + std::string type; +#endif +}; + +/// \ingroup annotations +/// Annotation indicating that all following arguments are keyword-only; the is the equivalent of an +/// unnamed '*' argument (in Python 3) +struct kw_only {}; + +/// \ingroup annotations +/// Annotation indicating that all previous arguments are positional-only; the is the equivalent of an +/// unnamed '/' argument (in Python 3.8) +struct pos_only {}; + +template +arg_v arg::operator=(T &&value) const { return {std::move(*this), std::forward(value)}; } + +/// Alias for backward compatibility -- to be removed in version 2.0 +template using arg_t = arg_v; + +inline namespace literals { +/** \rst + String literal version of `arg` + \endrst */ +constexpr arg operator"" _a(const char *name, size_t) { return arg(name); } +} // namespace literals + +PYBIND11_NAMESPACE_BEGIN(detail) + +// forward declaration (definition in attr.h) +struct function_record; + +/// Internal data associated with a single function call +struct function_call { + function_call(const function_record &f, handle p); // Implementation in attr.h + + /// The function data: + const function_record &func; + + /// Arguments passed to the function: + std::vector args; + + /// The `convert` value the arguments should be loaded with + std::vector args_convert; + + /// Extra references for the optional `py::args` and/or `py::kwargs` arguments (which, if + /// present, are also in `args` but without a reference). + object args_ref, kwargs_ref; + + /// The parent, if any + handle parent; + + /// If this is a call to an initializer, this argument contains `self` + handle init_self; +}; + + +/// Helper class which loads arguments for C++ functions called from Python +template +class argument_loader { + using indices = make_index_sequence; + + template using argument_is_args = std::is_same, args>; + template using argument_is_kwargs = std::is_same, kwargs>; + // Get args/kwargs argument positions relative to the end of the argument list: + static constexpr auto args_pos = constexpr_first() - (int) sizeof...(Args), + kwargs_pos = constexpr_first() - (int) sizeof...(Args); + + static constexpr bool args_kwargs_are_last = kwargs_pos >= - 1 && args_pos >= kwargs_pos - 1; + + static_assert(args_kwargs_are_last, "py::args/py::kwargs are only permitted as the last argument(s) of a function"); + +public: + static constexpr bool has_kwargs = kwargs_pos < 0; + static constexpr bool has_args = args_pos < 0; + + static constexpr auto arg_names = concat(type_descr(make_caster::name)...); + + bool load_args(function_call &call) { + return load_impl_sequence(call, indices{}); + } + + template + enable_if_t::value, Return> call(Func &&f) && { + return std::move(*this).template call_impl(std::forward(f), indices{}, Guard{}); + } + + template + enable_if_t::value, void_type> call(Func &&f) && { + std::move(*this).template call_impl(std::forward(f), indices{}, Guard{}); + return void_type(); + } + +private: + + static bool load_impl_sequence(function_call &, index_sequence<>) { return true; } + + template + bool load_impl_sequence(function_call &call, index_sequence) { +#ifdef __cpp_fold_expressions + if ((... || !std::get(argcasters).load(call.args[Is], call.args_convert[Is]))) + return false; +#else + for (bool r : {std::get(argcasters).load(call.args[Is], call.args_convert[Is])...}) + if (!r) + return false; +#endif + return true; + } + + template + Return call_impl(Func &&f, index_sequence, Guard &&) && { + return std::forward(f)(cast_op(std::move(std::get(argcasters)))...); + } + + std::tuple...> argcasters; +}; + +/// Helper class which collects only positional arguments for a Python function call. +/// A fancier version below can collect any argument, but this one is optimal for simple calls. +template +class simple_collector { +public: + template + explicit simple_collector(Ts &&...values) + : m_args(pybind11::make_tuple(std::forward(values)...)) { } + + const tuple &args() const & { return m_args; } + dict kwargs() const { return {}; } + + tuple args() && { return std::move(m_args); } + + /// Call a Python function and pass the collected arguments + object call(PyObject *ptr) const { + PyObject *result = PyObject_CallObject(ptr, m_args.ptr()); + if (!result) + throw error_already_set(); + return reinterpret_steal(result); + } + +private: + tuple m_args; +}; + +/// Helper class which collects positional, keyword, * and ** arguments for a Python function call +template +class unpacking_collector { +public: + template + explicit unpacking_collector(Ts &&...values) { + // Tuples aren't (easily) resizable so a list is needed for collection, + // but the actual function call strictly requires a tuple. + auto args_list = list(); + int _[] = { 0, (process(args_list, std::forward(values)), 0)... }; + ignore_unused(_); + + m_args = std::move(args_list); + } + + const tuple &args() const & { return m_args; } + const dict &kwargs() const & { return m_kwargs; } + + tuple args() && { return std::move(m_args); } + dict kwargs() && { return std::move(m_kwargs); } + + /// Call a Python function and pass the collected arguments + object call(PyObject *ptr) const { + PyObject *result = PyObject_Call(ptr, m_args.ptr(), m_kwargs.ptr()); + if (!result) + throw error_already_set(); + return reinterpret_steal(result); + } + +private: + template + void process(list &args_list, T &&x) { + auto o = reinterpret_steal(detail::make_caster::cast(std::forward(x), policy, {})); + if (!o) { +#if defined(NDEBUG) + argument_cast_error(); +#else + argument_cast_error(std::to_string(args_list.size()), type_id()); +#endif + } + args_list.append(o); + } + + void process(list &args_list, detail::args_proxy ap) { + for (auto a : ap) + args_list.append(a); + } + + void process(list &/*args_list*/, arg_v a) { + if (!a.name) +#if defined(NDEBUG) + nameless_argument_error(); +#else + nameless_argument_error(a.type); +#endif + + if (m_kwargs.contains(a.name)) { +#if defined(NDEBUG) + multiple_values_error(); +#else + multiple_values_error(a.name); +#endif + } + if (!a.value) { +#if defined(NDEBUG) + argument_cast_error(); +#else + argument_cast_error(a.name, a.type); +#endif + } + m_kwargs[a.name] = a.value; + } + + void process(list &/*args_list*/, detail::kwargs_proxy kp) { + if (!kp) + return; + for (auto k : reinterpret_borrow(kp)) { + if (m_kwargs.contains(k.first)) { +#if defined(NDEBUG) + multiple_values_error(); +#else + multiple_values_error(str(k.first)); +#endif + } + m_kwargs[k.first] = k.second; + } + } + + [[noreturn]] static void nameless_argument_error() { + throw type_error("Got kwargs without a name; only named arguments " + "may be passed via py::arg() to a python function call. " + "(compile in debug mode for details)"); + } + [[noreturn]] static void nameless_argument_error(std::string type) { + throw type_error("Got kwargs without a name of type '" + type + "'; only named " + "arguments may be passed via py::arg() to a python function call. "); + } + [[noreturn]] static void multiple_values_error() { + throw type_error("Got multiple values for keyword argument " + "(compile in debug mode for details)"); + } + + [[noreturn]] static void multiple_values_error(std::string name) { + throw type_error("Got multiple values for keyword argument '" + name + "'"); + } + + [[noreturn]] static void argument_cast_error() { + throw cast_error("Unable to convert call argument to Python object " + "(compile in debug mode for details)"); + } + + [[noreturn]] static void argument_cast_error(std::string name, std::string type) { + throw cast_error("Unable to convert call argument '" + name + + "' of type '" + type + "' to Python object"); + } + +private: + tuple m_args; + dict m_kwargs; +}; + +// [workaround(intel)] Separate function required here +// We need to put this into a separate function because the Intel compiler +// fails to compile enable_if_t...>::value> +// (tested with ICC 2021.1 Beta 20200827). +template +constexpr bool args_are_all_positional() +{ + return all_of...>::value; +} + +/// Collect only positional arguments for a Python function call +template ()>> +simple_collector collect_arguments(Args &&...args) { + return simple_collector(std::forward(args)...); +} + +/// Collect all arguments, including keywords and unpacking (only instantiated when needed) +template ()>> +unpacking_collector collect_arguments(Args &&...args) { + // Following argument order rules for generalized unpacking according to PEP 448 + static_assert( + constexpr_last() < constexpr_first() + && constexpr_last() < constexpr_first(), + "Invalid function call: positional args must precede keywords and ** unpacking; " + "* unpacking must precede ** unpacking" + ); + return unpacking_collector(std::forward(args)...); +} + +template +template +object object_api::operator()(Args &&...args) const { + return detail::collect_arguments(std::forward(args)...).call(derived().ptr()); +} + +template +template +object object_api::call(Args &&...args) const { + return operator()(std::forward(args)...); +} + +PYBIND11_NAMESPACE_END(detail) + + +template +handle type::handle_of() { + static_assert( + std::is_base_of>::value, + "py::type::of only supports the case where T is a registered C++ types." + ); + + return detail::get_type_handle(typeid(T), true); +} + + +#define PYBIND11_MAKE_OPAQUE(...) \ + namespace pybind11 { namespace detail { \ + template<> class type_caster<__VA_ARGS__> : public type_caster_base<__VA_ARGS__> { }; \ + }} + +/// Lets you pass a type containing a `,` through a macro parameter without needing a separate +/// typedef, e.g.: `PYBIND11_OVERRIDE(PYBIND11_TYPE(ReturnType), PYBIND11_TYPE(Parent), f, arg)` +#define PYBIND11_TYPE(...) __VA_ARGS__ + +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/chrono.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/chrono.h new file mode 100644 index 0000000000000000000000000000000000000000..317afd183770f415debce24b876c6f35bb648195 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/chrono.h @@ -0,0 +1,198 @@ +/* + pybind11/chrono.h: Transparent conversion between std::chrono and python's datetime + + Copyright (c) 2016 Trent Houliston and + Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "pybind11.h" +#include +#include +#include +#include + +// Backport the PyDateTime_DELTA functions from Python3.3 if required +#ifndef PyDateTime_DELTA_GET_DAYS +#define PyDateTime_DELTA_GET_DAYS(o) (((PyDateTime_Delta*)o)->days) +#endif +#ifndef PyDateTime_DELTA_GET_SECONDS +#define PyDateTime_DELTA_GET_SECONDS(o) (((PyDateTime_Delta*)o)->seconds) +#endif +#ifndef PyDateTime_DELTA_GET_MICROSECONDS +#define PyDateTime_DELTA_GET_MICROSECONDS(o) (((PyDateTime_Delta*)o)->microseconds) +#endif + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) +PYBIND11_NAMESPACE_BEGIN(detail) + +template class duration_caster { +public: + using rep = typename type::rep; + using period = typename type::period; + + using days = std::chrono::duration>; // signed 25 bits required by the standard. + + bool load(handle src, bool) { + using namespace std::chrono; + + // Lazy initialise the PyDateTime import + if (!PyDateTimeAPI) { PyDateTime_IMPORT; } + + if (!src) return false; + // If invoked with datetime.delta object + if (PyDelta_Check(src.ptr())) { + value = type(duration_cast>( + days(PyDateTime_DELTA_GET_DAYS(src.ptr())) + + seconds(PyDateTime_DELTA_GET_SECONDS(src.ptr())) + + microseconds(PyDateTime_DELTA_GET_MICROSECONDS(src.ptr())))); + return true; + } + // If invoked with a float we assume it is seconds and convert + else if (PyFloat_Check(src.ptr())) { + value = type(duration_cast>(duration(PyFloat_AsDouble(src.ptr())))); + return true; + } + else return false; + } + + // If this is a duration just return it back + static const std::chrono::duration& get_duration(const std::chrono::duration &src) { + return src; + } + + // If this is a time_point get the time_since_epoch + template static std::chrono::duration get_duration(const std::chrono::time_point> &src) { + return src.time_since_epoch(); + } + + static handle cast(const type &src, return_value_policy /* policy */, handle /* parent */) { + using namespace std::chrono; + + // Use overloaded function to get our duration from our source + // Works out if it is a duration or time_point and get the duration + auto d = get_duration(src); + + // Lazy initialise the PyDateTime import + if (!PyDateTimeAPI) { PyDateTime_IMPORT; } + + // Declare these special duration types so the conversions happen with the correct primitive types (int) + using dd_t = duration>; + using ss_t = duration>; + using us_t = duration; + + auto dd = duration_cast(d); + auto subd = d - dd; + auto ss = duration_cast(subd); + auto us = duration_cast(subd - ss); + return PyDelta_FromDSU(dd.count(), ss.count(), us.count()); + } + + PYBIND11_TYPE_CASTER(type, _("datetime.timedelta")); +}; + +// This is for casting times on the system clock into datetime.datetime instances +template class type_caster> { +public: + using type = std::chrono::time_point; + bool load(handle src, bool) { + using namespace std::chrono; + + // Lazy initialise the PyDateTime import + if (!PyDateTimeAPI) { PyDateTime_IMPORT; } + + if (!src) return false; + + std::tm cal; + microseconds msecs; + + if (PyDateTime_Check(src.ptr())) { + cal.tm_sec = PyDateTime_DATE_GET_SECOND(src.ptr()); + cal.tm_min = PyDateTime_DATE_GET_MINUTE(src.ptr()); + cal.tm_hour = PyDateTime_DATE_GET_HOUR(src.ptr()); + cal.tm_mday = PyDateTime_GET_DAY(src.ptr()); + cal.tm_mon = PyDateTime_GET_MONTH(src.ptr()) - 1; + cal.tm_year = PyDateTime_GET_YEAR(src.ptr()) - 1900; + cal.tm_isdst = -1; + msecs = microseconds(PyDateTime_DATE_GET_MICROSECOND(src.ptr())); + } else if (PyDate_Check(src.ptr())) { + cal.tm_sec = 0; + cal.tm_min = 0; + cal.tm_hour = 0; + cal.tm_mday = PyDateTime_GET_DAY(src.ptr()); + cal.tm_mon = PyDateTime_GET_MONTH(src.ptr()) - 1; + cal.tm_year = PyDateTime_GET_YEAR(src.ptr()) - 1900; + cal.tm_isdst = -1; + msecs = microseconds(0); + } else if (PyTime_Check(src.ptr())) { + cal.tm_sec = PyDateTime_TIME_GET_SECOND(src.ptr()); + cal.tm_min = PyDateTime_TIME_GET_MINUTE(src.ptr()); + cal.tm_hour = PyDateTime_TIME_GET_HOUR(src.ptr()); + cal.tm_mday = 1; // This date (day, month, year) = (1, 0, 70) + cal.tm_mon = 0; // represents 1-Jan-1970, which is the first + cal.tm_year = 70; // earliest available date for Python's datetime + cal.tm_isdst = -1; + msecs = microseconds(PyDateTime_TIME_GET_MICROSECOND(src.ptr())); + } + else return false; + + value = time_point_cast(system_clock::from_time_t(std::mktime(&cal)) + msecs); + return true; + } + + static handle cast(const std::chrono::time_point &src, return_value_policy /* policy */, handle /* parent */) { + using namespace std::chrono; + + // Lazy initialise the PyDateTime import + if (!PyDateTimeAPI) { PyDateTime_IMPORT; } + + // Get out microseconds, and make sure they are positive, to avoid bug in eastern hemisphere time zones + // (cfr. https://github.com/pybind/pybind11/issues/2417) + using us_t = duration; + auto us = duration_cast(src.time_since_epoch() % seconds(1)); + if (us.count() < 0) + us += seconds(1); + + // Subtract microseconds BEFORE `system_clock::to_time_t`, because: + // > If std::time_t has lower precision, it is implementation-defined whether the value is rounded or truncated. + // (https://en.cppreference.com/w/cpp/chrono/system_clock/to_time_t) + std::time_t tt = system_clock::to_time_t(time_point_cast(src - us)); + + // std::localtime returns a pointer to a static internal std::tm object on success, + // or null pointer otherwise + std::tm *localtime_ptr = std::localtime(&tt); + if (!localtime_ptr) + throw cast_error("Unable to represent system_clock in local time"); + + // this function uses static memory so it's best to copy it out asap just in case + // otherwise other code that is using localtime may break this (not just python code) + std::tm localtime = *localtime_ptr; + + return PyDateTime_FromDateAndTime(localtime.tm_year + 1900, + localtime.tm_mon + 1, + localtime.tm_mday, + localtime.tm_hour, + localtime.tm_min, + localtime.tm_sec, + us.count()); + } + PYBIND11_TYPE_CASTER(type, _("datetime.datetime")); +}; + +// Other clocks that are not the system clock are not measured as datetime.datetime objects +// since they are not measured on calendar time. So instead we just make them timedeltas +// Or if they have passed us a time as a float we convert that +template class type_caster> +: public duration_caster> { +}; + +template class type_caster> +: public duration_caster> { +}; + +PYBIND11_NAMESPACE_END(detail) +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/common.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/common.h new file mode 100644 index 0000000000000000000000000000000000000000..6c8a4f1e88e493ee08d24e668639c8d495fd49b1 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/common.h @@ -0,0 +1,2 @@ +#include "detail/common.h" +#warning "Including 'common.h' is deprecated. It will be removed in v3.0. Use 'pybind11.h'." diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/complex.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/complex.h new file mode 100644 index 0000000000000000000000000000000000000000..f8327eb37307490b658becf3d151132ddb5df531 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/complex.h @@ -0,0 +1,65 @@ +/* + pybind11/complex.h: Complex number support + + Copyright (c) 2016 Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "pybind11.h" +#include + +/// glibc defines I as a macro which breaks things, e.g., boost template names +#ifdef I +# undef I +#endif + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) + +template struct format_descriptor, detail::enable_if_t::value>> { + static constexpr const char c = format_descriptor::c; + static constexpr const char value[3] = { 'Z', c, '\0' }; + static std::string format() { return std::string(value); } +}; + +#ifndef PYBIND11_CPP17 + +template constexpr const char format_descriptor< + std::complex, detail::enable_if_t::value>>::value[3]; + +#endif + +PYBIND11_NAMESPACE_BEGIN(detail) + +template struct is_fmt_numeric, detail::enable_if_t::value>> { + static constexpr bool value = true; + static constexpr int index = is_fmt_numeric::index + 3; +}; + +template class type_caster> { +public: + bool load(handle src, bool convert) { + if (!src) + return false; + if (!convert && !PyComplex_Check(src.ptr())) + return false; + Py_complex result = PyComplex_AsCComplex(src.ptr()); + if (result.real == -1.0 && PyErr_Occurred()) { + PyErr_Clear(); + return false; + } + value = std::complex((T) result.real, (T) result.imag); + return true; + } + + static handle cast(const std::complex &src, return_value_policy /* policy */, handle /* parent */) { + return PyComplex_FromDoubles((double) src.real(), (double) src.imag()); + } + + PYBIND11_TYPE_CASTER(std::complex, _("complex")); +}; +PYBIND11_NAMESPACE_END(detail) +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/eigen.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/eigen.h new file mode 100644 index 0000000000000000000000000000000000000000..e8c6f63391afd51a7eda841d512237ee6fa43518 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/eigen.h @@ -0,0 +1,607 @@ +/* + pybind11/eigen.h: Transparent conversion for dense and sparse Eigen matrices + + Copyright (c) 2016 Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "numpy.h" + +#if defined(__INTEL_COMPILER) +# pragma warning(disable: 1682) // implicit conversion of a 64-bit integral type to a smaller integral type (potential portability problem) +#elif defined(__GNUG__) || defined(__clang__) +# pragma GCC diagnostic push +# pragma GCC diagnostic ignored "-Wconversion" +# pragma GCC diagnostic ignored "-Wdeprecated-declarations" +# ifdef __clang__ +// Eigen generates a bunch of implicit-copy-constructor-is-deprecated warnings with -Wdeprecated +// under Clang, so disable that warning here: +# pragma GCC diagnostic ignored "-Wdeprecated" +# endif +# if __GNUC__ >= 7 +# pragma GCC diagnostic ignored "-Wint-in-bool-context" +# endif +#endif + +#if defined(_MSC_VER) +# pragma warning(push) +# pragma warning(disable: 4127) // warning C4127: Conditional expression is constant +# pragma warning(disable: 4996) // warning C4996: std::unary_negate is deprecated in C++17 +#endif + +#include +#include + +// Eigen prior to 3.2.7 doesn't have proper move constructors--but worse, some classes get implicit +// move constructors that break things. We could detect this an explicitly copy, but an extra copy +// of matrices seems highly undesirable. +static_assert(EIGEN_VERSION_AT_LEAST(3,2,7), "Eigen support in pybind11 requires Eigen >= 3.2.7"); + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) + +// Provide a convenience alias for easier pass-by-ref usage with fully dynamic strides: +using EigenDStride = Eigen::Stride; +template using EigenDRef = Eigen::Ref; +template using EigenDMap = Eigen::Map; + +PYBIND11_NAMESPACE_BEGIN(detail) + +#if EIGEN_VERSION_AT_LEAST(3,3,0) +using EigenIndex = Eigen::Index; +#else +using EigenIndex = EIGEN_DEFAULT_DENSE_INDEX_TYPE; +#endif + +// Matches Eigen::Map, Eigen::Ref, blocks, etc: +template using is_eigen_dense_map = all_of, std::is_base_of, T>>; +template using is_eigen_mutable_map = std::is_base_of, T>; +template using is_eigen_dense_plain = all_of>, is_template_base_of>; +template using is_eigen_sparse = is_template_base_of; +// Test for objects inheriting from EigenBase that aren't captured by the above. This +// basically covers anything that can be assigned to a dense matrix but that don't have a typical +// matrix data layout that can be copied from their .data(). For example, DiagonalMatrix and +// SelfAdjointView fall into this category. +template using is_eigen_other = all_of< + is_template_base_of, + negation, is_eigen_dense_plain, is_eigen_sparse>> +>; + +// Captures numpy/eigen conformability status (returned by EigenProps::conformable()): +template struct EigenConformable { + bool conformable = false; + EigenIndex rows = 0, cols = 0; + EigenDStride stride{0, 0}; // Only valid if negativestrides is false! + bool negativestrides = false; // If true, do not use stride! + + EigenConformable(bool fits = false) : conformable{fits} {} + // Matrix type: + EigenConformable(EigenIndex r, EigenIndex c, + EigenIndex rstride, EigenIndex cstride) : + conformable{true}, rows{r}, cols{c} { + // TODO: when Eigen bug #747 is fixed, remove the tests for non-negativity. http://eigen.tuxfamily.org/bz/show_bug.cgi?id=747 + if (rstride < 0 || cstride < 0) { + negativestrides = true; + } else { + stride = {EigenRowMajor ? rstride : cstride /* outer stride */, + EigenRowMajor ? cstride : rstride /* inner stride */ }; + } + } + // Vector type: + EigenConformable(EigenIndex r, EigenIndex c, EigenIndex stride) + : EigenConformable(r, c, r == 1 ? c*stride : stride, c == 1 ? r : r*stride) {} + + template bool stride_compatible() const { + // To have compatible strides, we need (on both dimensions) one of fully dynamic strides, + // matching strides, or a dimension size of 1 (in which case the stride value is irrelevant) + return + !negativestrides && + (props::inner_stride == Eigen::Dynamic || props::inner_stride == stride.inner() || + (EigenRowMajor ? cols : rows) == 1) && + (props::outer_stride == Eigen::Dynamic || props::outer_stride == stride.outer() || + (EigenRowMajor ? rows : cols) == 1); + } + operator bool() const { return conformable; } +}; + +template struct eigen_extract_stride { using type = Type; }; +template +struct eigen_extract_stride> { using type = StrideType; }; +template +struct eigen_extract_stride> { using type = StrideType; }; + +// Helper struct for extracting information from an Eigen type +template struct EigenProps { + using Type = Type_; + using Scalar = typename Type::Scalar; + using StrideType = typename eigen_extract_stride::type; + static constexpr EigenIndex + rows = Type::RowsAtCompileTime, + cols = Type::ColsAtCompileTime, + size = Type::SizeAtCompileTime; + static constexpr bool + row_major = Type::IsRowMajor, + vector = Type::IsVectorAtCompileTime, // At least one dimension has fixed size 1 + fixed_rows = rows != Eigen::Dynamic, + fixed_cols = cols != Eigen::Dynamic, + fixed = size != Eigen::Dynamic, // Fully-fixed size + dynamic = !fixed_rows && !fixed_cols; // Fully-dynamic size + + template using if_zero = std::integral_constant; + static constexpr EigenIndex inner_stride = if_zero::value, + outer_stride = if_zero::value; + static constexpr bool dynamic_stride = inner_stride == Eigen::Dynamic && outer_stride == Eigen::Dynamic; + static constexpr bool requires_row_major = !dynamic_stride && !vector && (row_major ? inner_stride : outer_stride) == 1; + static constexpr bool requires_col_major = !dynamic_stride && !vector && (row_major ? outer_stride : inner_stride) == 1; + + // Takes an input array and determines whether we can make it fit into the Eigen type. If + // the array is a vector, we attempt to fit it into either an Eigen 1xN or Nx1 vector + // (preferring the latter if it will fit in either, i.e. for a fully dynamic matrix type). + static EigenConformable conformable(const array &a) { + const auto dims = a.ndim(); + if (dims < 1 || dims > 2) + return false; + + if (dims == 2) { // Matrix type: require exact match (or dynamic) + + EigenIndex + np_rows = a.shape(0), + np_cols = a.shape(1), + np_rstride = a.strides(0) / static_cast(sizeof(Scalar)), + np_cstride = a.strides(1) / static_cast(sizeof(Scalar)); + if ((fixed_rows && np_rows != rows) || (fixed_cols && np_cols != cols)) + return false; + + return {np_rows, np_cols, np_rstride, np_cstride}; + } + + // Otherwise we're storing an n-vector. Only one of the strides will be used, but whichever + // is used, we want the (single) numpy stride value. + const EigenIndex n = a.shape(0), + stride = a.strides(0) / static_cast(sizeof(Scalar)); + + if (vector) { // Eigen type is a compile-time vector + if (fixed && size != n) + return false; // Vector size mismatch + return {rows == 1 ? 1 : n, cols == 1 ? 1 : n, stride}; + } + else if (fixed) { + // The type has a fixed size, but is not a vector: abort + return false; + } + else if (fixed_cols) { + // Since this isn't a vector, cols must be != 1. We allow this only if it exactly + // equals the number of elements (rows is Dynamic, and so 1 row is allowed). + if (cols != n) return false; + return {1, n, stride}; + } + else { + // Otherwise it's either fully dynamic, or column dynamic; both become a column vector + if (fixed_rows && rows != n) return false; + return {n, 1, stride}; + } + } + + static constexpr bool show_writeable = is_eigen_dense_map::value && is_eigen_mutable_map::value; + static constexpr bool show_order = is_eigen_dense_map::value; + static constexpr bool show_c_contiguous = show_order && requires_row_major; + static constexpr bool show_f_contiguous = !show_c_contiguous && show_order && requires_col_major; + + static constexpr auto descriptor = + _("numpy.ndarray[") + npy_format_descriptor::name + + _("[") + _(_<(size_t) rows>(), _("m")) + + _(", ") + _(_<(size_t) cols>(), _("n")) + + _("]") + + // For a reference type (e.g. Ref) we have other constraints that might need to be + // satisfied: writeable=True (for a mutable reference), and, depending on the map's stride + // options, possibly f_contiguous or c_contiguous. We include them in the descriptor output + // to provide some hint as to why a TypeError is occurring (otherwise it can be confusing to + // see that a function accepts a 'numpy.ndarray[float64[3,2]]' and an error message that you + // *gave* a numpy.ndarray of the right type and dimensions. + _(", flags.writeable", "") + + _(", flags.c_contiguous", "") + + _(", flags.f_contiguous", "") + + _("]"); +}; + +// Casts an Eigen type to numpy array. If given a base, the numpy array references the src data, +// otherwise it'll make a copy. writeable lets you turn off the writeable flag for the array. +template handle eigen_array_cast(typename props::Type const &src, handle base = handle(), bool writeable = true) { + constexpr ssize_t elem_size = sizeof(typename props::Scalar); + array a; + if (props::vector) + a = array({ src.size() }, { elem_size * src.innerStride() }, src.data(), base); + else + a = array({ src.rows(), src.cols() }, { elem_size * src.rowStride(), elem_size * src.colStride() }, + src.data(), base); + + if (!writeable) + array_proxy(a.ptr())->flags &= ~detail::npy_api::NPY_ARRAY_WRITEABLE_; + + return a.release(); +} + +// Takes an lvalue ref to some Eigen type and a (python) base object, creating a numpy array that +// reference the Eigen object's data with `base` as the python-registered base class (if omitted, +// the base will be set to None, and lifetime management is up to the caller). The numpy array is +// non-writeable if the given type is const. +template +handle eigen_ref_array(Type &src, handle parent = none()) { + // none here is to get past array's should-we-copy detection, which currently always + // copies when there is no base. Setting the base to None should be harmless. + return eigen_array_cast(src, parent, !std::is_const::value); +} + +// Takes a pointer to some dense, plain Eigen type, builds a capsule around it, then returns a numpy +// array that references the encapsulated data with a python-side reference to the capsule to tie +// its destruction to that of any dependent python objects. Const-ness is determined by whether or +// not the Type of the pointer given is const. +template ::value>> +handle eigen_encapsulate(Type *src) { + capsule base(src, [](void *o) { delete static_cast(o); }); + return eigen_ref_array(*src, base); +} + +// Type caster for regular, dense matrix types (e.g. MatrixXd), but not maps/refs/etc. of dense +// types. +template +struct type_caster::value>> { + using Scalar = typename Type::Scalar; + using props = EigenProps; + + bool load(handle src, bool convert) { + // If we're in no-convert mode, only load if given an array of the correct type + if (!convert && !isinstance>(src)) + return false; + + // Coerce into an array, but don't do type conversion yet; the copy below handles it. + auto buf = array::ensure(src); + + if (!buf) + return false; + + auto dims = buf.ndim(); + if (dims < 1 || dims > 2) + return false; + + auto fits = props::conformable(buf); + if (!fits) + return false; + + // Allocate the new type, then build a numpy reference into it + value = Type(fits.rows, fits.cols); + auto ref = reinterpret_steal(eigen_ref_array(value)); + if (dims == 1) ref = ref.squeeze(); + else if (ref.ndim() == 1) buf = buf.squeeze(); + + int result = detail::npy_api::get().PyArray_CopyInto_(ref.ptr(), buf.ptr()); + + if (result < 0) { // Copy failed! + PyErr_Clear(); + return false; + } + + return true; + } + +private: + + // Cast implementation + template + static handle cast_impl(CType *src, return_value_policy policy, handle parent) { + switch (policy) { + case return_value_policy::take_ownership: + case return_value_policy::automatic: + return eigen_encapsulate(src); + case return_value_policy::move: + return eigen_encapsulate(new CType(std::move(*src))); + case return_value_policy::copy: + return eigen_array_cast(*src); + case return_value_policy::reference: + case return_value_policy::automatic_reference: + return eigen_ref_array(*src); + case return_value_policy::reference_internal: + return eigen_ref_array(*src, parent); + default: + throw cast_error("unhandled return_value_policy: should not happen!"); + }; + } + +public: + + // Normal returned non-reference, non-const value: + static handle cast(Type &&src, return_value_policy /* policy */, handle parent) { + return cast_impl(&src, return_value_policy::move, parent); + } + // If you return a non-reference const, we mark the numpy array readonly: + static handle cast(const Type &&src, return_value_policy /* policy */, handle parent) { + return cast_impl(&src, return_value_policy::move, parent); + } + // lvalue reference return; default (automatic) becomes copy + static handle cast(Type &src, return_value_policy policy, handle parent) { + if (policy == return_value_policy::automatic || policy == return_value_policy::automatic_reference) + policy = return_value_policy::copy; + return cast_impl(&src, policy, parent); + } + // const lvalue reference return; default (automatic) becomes copy + static handle cast(const Type &src, return_value_policy policy, handle parent) { + if (policy == return_value_policy::automatic || policy == return_value_policy::automatic_reference) + policy = return_value_policy::copy; + return cast(&src, policy, parent); + } + // non-const pointer return + static handle cast(Type *src, return_value_policy policy, handle parent) { + return cast_impl(src, policy, parent); + } + // const pointer return + static handle cast(const Type *src, return_value_policy policy, handle parent) { + return cast_impl(src, policy, parent); + } + + static constexpr auto name = props::descriptor; + + operator Type*() { return &value; } + operator Type&() { return value; } + operator Type&&() && { return std::move(value); } + template using cast_op_type = movable_cast_op_type; + +private: + Type value; +}; + +// Base class for casting reference/map/block/etc. objects back to python. +template struct eigen_map_caster { +private: + using props = EigenProps; + +public: + + // Directly referencing a ref/map's data is a bit dangerous (whatever the map/ref points to has + // to stay around), but we'll allow it under the assumption that you know what you're doing (and + // have an appropriate keep_alive in place). We return a numpy array pointing directly at the + // ref's data (The numpy array ends up read-only if the ref was to a const matrix type.) Note + // that this means you need to ensure you don't destroy the object in some other way (e.g. with + // an appropriate keep_alive, or with a reference to a statically allocated matrix). + static handle cast(const MapType &src, return_value_policy policy, handle parent) { + switch (policy) { + case return_value_policy::copy: + return eigen_array_cast(src); + case return_value_policy::reference_internal: + return eigen_array_cast(src, parent, is_eigen_mutable_map::value); + case return_value_policy::reference: + case return_value_policy::automatic: + case return_value_policy::automatic_reference: + return eigen_array_cast(src, none(), is_eigen_mutable_map::value); + default: + // move, take_ownership don't make any sense for a ref/map: + pybind11_fail("Invalid return_value_policy for Eigen Map/Ref/Block type"); + } + } + + static constexpr auto name = props::descriptor; + + // Explicitly delete these: support python -> C++ conversion on these (i.e. these can be return + // types but not bound arguments). We still provide them (with an explicitly delete) so that + // you end up here if you try anyway. + bool load(handle, bool) = delete; + operator MapType() = delete; + template using cast_op_type = MapType; +}; + +// We can return any map-like object (but can only load Refs, specialized next): +template struct type_caster::value>> + : eigen_map_caster {}; + +// Loader for Ref<...> arguments. See the documentation for info on how to make this work without +// copying (it requires some extra effort in many cases). +template +struct type_caster< + Eigen::Ref, + enable_if_t>::value> +> : public eigen_map_caster> { +private: + using Type = Eigen::Ref; + using props = EigenProps; + using Scalar = typename props::Scalar; + using MapType = Eigen::Map; + using Array = array_t; + static constexpr bool need_writeable = is_eigen_mutable_map::value; + // Delay construction (these have no default constructor) + std::unique_ptr map; + std::unique_ptr ref; + // Our array. When possible, this is just a numpy array pointing to the source data, but + // sometimes we can't avoid copying (e.g. input is not a numpy array at all, has an incompatible + // layout, or is an array of a type that needs to be converted). Using a numpy temporary + // (rather than an Eigen temporary) saves an extra copy when we need both type conversion and + // storage order conversion. (Note that we refuse to use this temporary copy when loading an + // argument for a Ref with M non-const, i.e. a read-write reference). + Array copy_or_ref; +public: + bool load(handle src, bool convert) { + // First check whether what we have is already an array of the right type. If not, we can't + // avoid a copy (because the copy is also going to do type conversion). + bool need_copy = !isinstance(src); + + EigenConformable fits; + if (!need_copy) { + // We don't need a converting copy, but we also need to check whether the strides are + // compatible with the Ref's stride requirements + auto aref = reinterpret_borrow(src); + + if (aref && (!need_writeable || aref.writeable())) { + fits = props::conformable(aref); + if (!fits) return false; // Incompatible dimensions + if (!fits.template stride_compatible()) + need_copy = true; + else + copy_or_ref = std::move(aref); + } + else { + need_copy = true; + } + } + + if (need_copy) { + // We need to copy: If we need a mutable reference, or we're not supposed to convert + // (either because we're in the no-convert overload pass, or because we're explicitly + // instructed not to copy (via `py::arg().noconvert()`) we have to fail loading. + if (!convert || need_writeable) return false; + + Array copy = Array::ensure(src); + if (!copy) return false; + fits = props::conformable(copy); + if (!fits || !fits.template stride_compatible()) + return false; + copy_or_ref = std::move(copy); + loader_life_support::add_patient(copy_or_ref); + } + + ref.reset(); + map.reset(new MapType(data(copy_or_ref), fits.rows, fits.cols, make_stride(fits.stride.outer(), fits.stride.inner()))); + ref.reset(new Type(*map)); + + return true; + } + + operator Type*() { return ref.get(); } + operator Type&() { return *ref; } + template using cast_op_type = pybind11::detail::cast_op_type<_T>; + +private: + template ::value, int> = 0> + Scalar *data(Array &a) { return a.mutable_data(); } + + template ::value, int> = 0> + const Scalar *data(Array &a) { return a.data(); } + + // Attempt to figure out a constructor of `Stride` that will work. + // If both strides are fixed, use a default constructor: + template using stride_ctor_default = bool_constant< + S::InnerStrideAtCompileTime != Eigen::Dynamic && S::OuterStrideAtCompileTime != Eigen::Dynamic && + std::is_default_constructible::value>; + // Otherwise, if there is a two-index constructor, assume it is (outer,inner) like + // Eigen::Stride, and use it: + template using stride_ctor_dual = bool_constant< + !stride_ctor_default::value && std::is_constructible::value>; + // Otherwise, if there is a one-index constructor, and just one of the strides is dynamic, use + // it (passing whichever stride is dynamic). + template using stride_ctor_outer = bool_constant< + !any_of, stride_ctor_dual>::value && + S::OuterStrideAtCompileTime == Eigen::Dynamic && S::InnerStrideAtCompileTime != Eigen::Dynamic && + std::is_constructible::value>; + template using stride_ctor_inner = bool_constant< + !any_of, stride_ctor_dual>::value && + S::InnerStrideAtCompileTime == Eigen::Dynamic && S::OuterStrideAtCompileTime != Eigen::Dynamic && + std::is_constructible::value>; + + template ::value, int> = 0> + static S make_stride(EigenIndex, EigenIndex) { return S(); } + template ::value, int> = 0> + static S make_stride(EigenIndex outer, EigenIndex inner) { return S(outer, inner); } + template ::value, int> = 0> + static S make_stride(EigenIndex outer, EigenIndex) { return S(outer); } + template ::value, int> = 0> + static S make_stride(EigenIndex, EigenIndex inner) { return S(inner); } + +}; + +// type_caster for special matrix types (e.g. DiagonalMatrix), which are EigenBase, but not +// EigenDense (i.e. they don't have a data(), at least not with the usual matrix layout). +// load() is not supported, but we can cast them into the python domain by first copying to a +// regular Eigen::Matrix, then casting that. +template +struct type_caster::value>> { +protected: + using Matrix = Eigen::Matrix; + using props = EigenProps; +public: + static handle cast(const Type &src, return_value_policy /* policy */, handle /* parent */) { + handle h = eigen_encapsulate(new Matrix(src)); + return h; + } + static handle cast(const Type *src, return_value_policy policy, handle parent) { return cast(*src, policy, parent); } + + static constexpr auto name = props::descriptor; + + // Explicitly delete these: support python -> C++ conversion on these (i.e. these can be return + // types but not bound arguments). We still provide them (with an explicitly delete) so that + // you end up here if you try anyway. + bool load(handle, bool) = delete; + operator Type() = delete; + template using cast_op_type = Type; +}; + +template +struct type_caster::value>> { + using Scalar = typename Type::Scalar; + using StorageIndex = remove_reference_t().outerIndexPtr())>; + using Index = typename Type::Index; + static constexpr bool rowMajor = Type::IsRowMajor; + + bool load(handle src, bool) { + if (!src) + return false; + + auto obj = reinterpret_borrow(src); + object sparse_module = module_::import("scipy.sparse"); + object matrix_type = sparse_module.attr( + rowMajor ? "csr_matrix" : "csc_matrix"); + + if (!type::handle_of(obj).is(matrix_type)) { + try { + obj = matrix_type(obj); + } catch (const error_already_set &) { + return false; + } + } + + auto values = array_t((object) obj.attr("data")); + auto innerIndices = array_t((object) obj.attr("indices")); + auto outerIndices = array_t((object) obj.attr("indptr")); + auto shape = pybind11::tuple((pybind11::object) obj.attr("shape")); + auto nnz = obj.attr("nnz").cast(); + + if (!values || !innerIndices || !outerIndices) + return false; + + value = Eigen::MappedSparseMatrix( + shape[0].cast(), shape[1].cast(), nnz, + outerIndices.mutable_data(), innerIndices.mutable_data(), values.mutable_data()); + + return true; + } + + static handle cast(const Type &src, return_value_policy /* policy */, handle /* parent */) { + const_cast(src).makeCompressed(); + + object matrix_type = module_::import("scipy.sparse").attr( + rowMajor ? "csr_matrix" : "csc_matrix"); + + array data(src.nonZeros(), src.valuePtr()); + array outerIndices((rowMajor ? src.rows() : src.cols()) + 1, src.outerIndexPtr()); + array innerIndices(src.nonZeros(), src.innerIndexPtr()); + + return matrix_type( + std::make_tuple(data, innerIndices, outerIndices), + std::make_pair(src.rows(), src.cols()) + ).release(); + } + + PYBIND11_TYPE_CASTER(Type, _<(Type::IsRowMajor) != 0>("scipy.sparse.csr_matrix[", "scipy.sparse.csc_matrix[") + + npy_format_descriptor::name + _("]")); +}; + +PYBIND11_NAMESPACE_END(detail) +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) + +#if defined(__GNUG__) || defined(__clang__) +# pragma GCC diagnostic pop +#elif defined(_MSC_VER) +# pragma warning(pop) +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/embed.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/embed.h new file mode 100644 index 0000000000000000000000000000000000000000..204aaf989ff6225543efa7b9fb85fb7dbe817b1b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/embed.h @@ -0,0 +1,201 @@ +/* + pybind11/embed.h: Support for embedding the interpreter + + Copyright (c) 2017 Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "pybind11.h" +#include "eval.h" + +#if defined(PYPY_VERSION) +# error Embedding the interpreter is not supported with PyPy +#endif + +#if PY_MAJOR_VERSION >= 3 +# define PYBIND11_EMBEDDED_MODULE_IMPL(name) \ + extern "C" PyObject *pybind11_init_impl_##name(); \ + extern "C" PyObject *pybind11_init_impl_##name() { \ + return pybind11_init_wrapper_##name(); \ + } +#else +# define PYBIND11_EMBEDDED_MODULE_IMPL(name) \ + extern "C" void pybind11_init_impl_##name(); \ + extern "C" void pybind11_init_impl_##name() { \ + pybind11_init_wrapper_##name(); \ + } +#endif + +/** \rst + Add a new module to the table of builtins for the interpreter. Must be + defined in global scope. The first macro parameter is the name of the + module (without quotes). The second parameter is the variable which will + be used as the interface to add functions and classes to the module. + + .. code-block:: cpp + + PYBIND11_EMBEDDED_MODULE(example, m) { + // ... initialize functions and classes here + m.def("foo", []() { + return "Hello, World!"; + }); + } + \endrst */ +#define PYBIND11_EMBEDDED_MODULE(name, variable) \ + static ::pybind11::module_::module_def \ + PYBIND11_CONCAT(pybind11_module_def_, name); \ + static void PYBIND11_CONCAT(pybind11_init_, name)(::pybind11::module_ &); \ + static PyObject PYBIND11_CONCAT(*pybind11_init_wrapper_, name)() { \ + auto m = ::pybind11::module_::create_extension_module( \ + PYBIND11_TOSTRING(name), nullptr, \ + &PYBIND11_CONCAT(pybind11_module_def_, name)); \ + try { \ + PYBIND11_CONCAT(pybind11_init_, name)(m); \ + return m.ptr(); \ + } PYBIND11_CATCH_INIT_EXCEPTIONS \ + } \ + PYBIND11_EMBEDDED_MODULE_IMPL(name) \ + ::pybind11::detail::embedded_module PYBIND11_CONCAT(pybind11_module_, name) \ + (PYBIND11_TOSTRING(name), \ + PYBIND11_CONCAT(pybind11_init_impl_, name)); \ + void PYBIND11_CONCAT(pybind11_init_, name)(::pybind11::module_ &variable) + + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) +PYBIND11_NAMESPACE_BEGIN(detail) + +/// Python 2.7/3.x compatible version of `PyImport_AppendInittab` and error checks. +struct embedded_module { +#if PY_MAJOR_VERSION >= 3 + using init_t = PyObject *(*)(); +#else + using init_t = void (*)(); +#endif + embedded_module(const char *name, init_t init) { + if (Py_IsInitialized()) + pybind11_fail("Can't add new modules after the interpreter has been initialized"); + + auto result = PyImport_AppendInittab(name, init); + if (result == -1) + pybind11_fail("Insufficient memory to add a new module"); + } +}; + +PYBIND11_NAMESPACE_END(detail) + +/** \rst + Initialize the Python interpreter. No other pybind11 or CPython API functions can be + called before this is done; with the exception of `PYBIND11_EMBEDDED_MODULE`. The + optional parameter can be used to skip the registration of signal handlers (see the + `Python documentation`_ for details). Calling this function again after the interpreter + has already been initialized is a fatal error. + + If initializing the Python interpreter fails, then the program is terminated. (This + is controlled by the CPython runtime and is an exception to pybind11's normal behavior + of throwing exceptions on errors.) + + .. _Python documentation: https://docs.python.org/3/c-api/init.html#c.Py_InitializeEx + \endrst */ +inline void initialize_interpreter(bool init_signal_handlers = true) { + if (Py_IsInitialized()) + pybind11_fail("The interpreter is already running"); + + Py_InitializeEx(init_signal_handlers ? 1 : 0); + + // Make .py files in the working directory available by default + module_::import("sys").attr("path").cast().append("."); +} + +/** \rst + Shut down the Python interpreter. No pybind11 or CPython API functions can be called + after this. In addition, pybind11 objects must not outlive the interpreter: + + .. code-block:: cpp + + { // BAD + py::initialize_interpreter(); + auto hello = py::str("Hello, World!"); + py::finalize_interpreter(); + } // <-- BOOM, hello's destructor is called after interpreter shutdown + + { // GOOD + py::initialize_interpreter(); + { // scoped + auto hello = py::str("Hello, World!"); + } // <-- OK, hello is cleaned up properly + py::finalize_interpreter(); + } + + { // BETTER + py::scoped_interpreter guard{}; + auto hello = py::str("Hello, World!"); + } + + .. warning:: + + The interpreter can be restarted by calling `initialize_interpreter` again. + Modules created using pybind11 can be safely re-initialized. However, Python + itself cannot completely unload binary extension modules and there are several + caveats with regard to interpreter restarting. All the details can be found + in the CPython documentation. In short, not all interpreter memory may be + freed, either due to reference cycles or user-created global data. + + \endrst */ +inline void finalize_interpreter() { + handle builtins(PyEval_GetBuiltins()); + const char *id = PYBIND11_INTERNALS_ID; + + // Get the internals pointer (without creating it if it doesn't exist). It's possible for the + // internals to be created during Py_Finalize() (e.g. if a py::capsule calls `get_internals()` + // during destruction), so we get the pointer-pointer here and check it after Py_Finalize(). + detail::internals **internals_ptr_ptr = detail::get_internals_pp(); + // It could also be stashed in builtins, so look there too: + if (builtins.contains(id) && isinstance(builtins[id])) + internals_ptr_ptr = capsule(builtins[id]); + + Py_Finalize(); + + if (internals_ptr_ptr) { + delete *internals_ptr_ptr; + *internals_ptr_ptr = nullptr; + } +} + +/** \rst + Scope guard version of `initialize_interpreter` and `finalize_interpreter`. + This a move-only guard and only a single instance can exist. + + .. code-block:: cpp + + #include + + int main() { + py::scoped_interpreter guard{}; + py::print(Hello, World!); + } // <-- interpreter shutdown + \endrst */ +class scoped_interpreter { +public: + scoped_interpreter(bool init_signal_handlers = true) { + initialize_interpreter(init_signal_handlers); + } + + scoped_interpreter(const scoped_interpreter &) = delete; + scoped_interpreter(scoped_interpreter &&other) noexcept { other.is_valid = false; } + scoped_interpreter &operator=(const scoped_interpreter &) = delete; + scoped_interpreter &operator=(scoped_interpreter &&) = delete; + + ~scoped_interpreter() { + if (is_valid) + finalize_interpreter(); + } + +private: + bool is_valid = true; +}; + +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/eval.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/eval.h new file mode 100644 index 0000000000000000000000000000000000000000..fa6b8af4791ee5245dacda19d5678991eb1442cc --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/eval.h @@ -0,0 +1,152 @@ +/* + pybind11/exec.h: Support for evaluating Python expressions and statements + from strings and files + + Copyright (c) 2016 Klemens Morgenstern and + Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "pybind11.h" + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) +PYBIND11_NAMESPACE_BEGIN(detail) + +inline void ensure_builtins_in_globals(object &global) { + #if PY_VERSION_HEX < 0x03080000 + // Running exec and eval on Python 2 and 3 adds `builtins` module under + // `__builtins__` key to globals if not yet present. + // Python 3.8 made PyRun_String behave similarly. Let's also do that for + // older versions, for consistency. + if (!global.contains("__builtins__")) + global["__builtins__"] = module_::import(PYBIND11_BUILTINS_MODULE); + #else + (void) global; + #endif +} + +PYBIND11_NAMESPACE_END(detail) + +enum eval_mode { + /// Evaluate a string containing an isolated expression + eval_expr, + + /// Evaluate a string containing a single statement. Returns \c none + eval_single_statement, + + /// Evaluate a string containing a sequence of statement. Returns \c none + eval_statements +}; + +template +object eval(str expr, object global = globals(), object local = object()) { + if (!local) + local = global; + + detail::ensure_builtins_in_globals(global); + + /* PyRun_String does not accept a PyObject / encoding specifier, + this seems to be the only alternative */ + std::string buffer = "# -*- coding: utf-8 -*-\n" + (std::string) expr; + + int start; + switch (mode) { + case eval_expr: start = Py_eval_input; break; + case eval_single_statement: start = Py_single_input; break; + case eval_statements: start = Py_file_input; break; + default: pybind11_fail("invalid evaluation mode"); + } + + PyObject *result = PyRun_String(buffer.c_str(), start, global.ptr(), local.ptr()); + if (!result) + throw error_already_set(); + return reinterpret_steal(result); +} + +template +object eval(const char (&s)[N], object global = globals(), object local = object()) { + /* Support raw string literals by removing common leading whitespace */ + auto expr = (s[0] == '\n') ? str(module_::import("textwrap").attr("dedent")(s)) + : str(s); + return eval(expr, global, local); +} + +inline void exec(str expr, object global = globals(), object local = object()) { + eval(expr, global, local); +} + +template +void exec(const char (&s)[N], object global = globals(), object local = object()) { + eval(s, global, local); +} + +#if defined(PYPY_VERSION) && PY_VERSION_HEX >= 0x03000000 +template +object eval_file(str, object, object) { + pybind11_fail("eval_file not supported in PyPy3. Use eval"); +} +template +object eval_file(str, object) { + pybind11_fail("eval_file not supported in PyPy3. Use eval"); +} +template +object eval_file(str) { + pybind11_fail("eval_file not supported in PyPy3. Use eval"); +} +#else +template +object eval_file(str fname, object global = globals(), object local = object()) { + if (!local) + local = global; + + detail::ensure_builtins_in_globals(global); + + int start; + switch (mode) { + case eval_expr: start = Py_eval_input; break; + case eval_single_statement: start = Py_single_input; break; + case eval_statements: start = Py_file_input; break; + default: pybind11_fail("invalid evaluation mode"); + } + + int closeFile = 1; + std::string fname_str = (std::string) fname; +#if PY_VERSION_HEX >= 0x03040000 + FILE *f = _Py_fopen_obj(fname.ptr(), "r"); +#elif PY_VERSION_HEX >= 0x03000000 + FILE *f = _Py_fopen(fname.ptr(), "r"); +#else + /* No unicode support in open() :( */ + auto fobj = reinterpret_steal(PyFile_FromString( + const_cast(fname_str.c_str()), + const_cast("r"))); + FILE *f = nullptr; + if (fobj) + f = PyFile_AsFile(fobj.ptr()); + closeFile = 0; +#endif + if (!f) { + PyErr_Clear(); + pybind11_fail("File \"" + fname_str + "\" could not be opened!"); + } + +#if PY_VERSION_HEX < 0x03000000 && defined(PYPY_VERSION) + PyObject *result = PyRun_File(f, fname_str.c_str(), start, global.ptr(), + local.ptr()); + (void) closeFile; +#else + PyObject *result = PyRun_FileEx(f, fname_str.c_str(), start, global.ptr(), + local.ptr(), closeFile); +#endif + + if (!result) + throw error_already_set(); + return reinterpret_steal(result); +} +#endif + +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/functional.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/functional.h new file mode 100644 index 0000000000000000000000000000000000000000..92c17dc2255cacacee6b03ad3b73109a5bbcacc3 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/functional.h @@ -0,0 +1,104 @@ +/* + pybind11/functional.h: std::function<> support + + Copyright (c) 2016 Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "pybind11.h" +#include + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) +PYBIND11_NAMESPACE_BEGIN(detail) + +template +struct type_caster> { + using type = std::function; + using retval_type = conditional_t::value, void_type, Return>; + using function_type = Return (*) (Args...); + +public: + bool load(handle src, bool convert) { + if (src.is_none()) { + // Defer accepting None to other overloads (if we aren't in convert mode): + if (!convert) return false; + return true; + } + + if (!isinstance(src)) + return false; + + auto func = reinterpret_borrow(src); + + /* + When passing a C++ function as an argument to another C++ + function via Python, every function call would normally involve + a full C++ -> Python -> C++ roundtrip, which can be prohibitive. + Here, we try to at least detect the case where the function is + stateless (i.e. function pointer or lambda function without + captured variables), in which case the roundtrip can be avoided. + */ + if (auto cfunc = func.cpp_function()) { + auto c = reinterpret_borrow(PyCFunction_GET_SELF(cfunc.ptr())); + auto rec = (function_record *) c; + + if (rec && rec->is_stateless && + same_type(typeid(function_type), *reinterpret_cast(rec->data[1]))) { + struct capture { function_type f; }; + value = ((capture *) &rec->data)->f; + return true; + } + } + + // ensure GIL is held during functor destruction + struct func_handle { + function f; + func_handle(function&& f_) : f(std::move(f_)) {} + func_handle(const func_handle& f_) { + gil_scoped_acquire acq; + f = f_.f; + } + ~func_handle() { + gil_scoped_acquire acq; + function kill_f(std::move(f)); + } + }; + + // to emulate 'move initialization capture' in C++11 + struct func_wrapper { + func_handle hfunc; + func_wrapper(func_handle&& hf): hfunc(std::move(hf)) {} + Return operator()(Args... args) const { + gil_scoped_acquire acq; + object retval(hfunc.f(std::forward(args)...)); + /* Visual studio 2015 parser issue: need parentheses around this expression */ + return (retval.template cast()); + } + }; + + value = func_wrapper(func_handle(std::move(func))); + return true; + } + + template + static handle cast(Func &&f_, return_value_policy policy, handle /* parent */) { + if (!f_) + return none().inc_ref(); + + auto result = f_.template target(); + if (result) + return cpp_function(*result, policy).release(); + else + return cpp_function(std::forward(f_), policy).release(); + } + + PYBIND11_TYPE_CASTER(type, _("Callable[[") + concat(make_caster::name...) + _("], ") + + make_caster::name + _("]")); +}; + +PYBIND11_NAMESPACE_END(detail) +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/iostream.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/iostream.h new file mode 100644 index 0000000000000000000000000000000000000000..9dee7554314f4715d77212aa8561ccd216df35ed --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/iostream.h @@ -0,0 +1,220 @@ +/* + pybind11/iostream.h -- Tools to assist with redirecting cout and cerr to Python + + Copyright (c) 2017 Henry F. Schreiner + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "pybind11.h" + +#include +#include +#include +#include +#include + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) +PYBIND11_NAMESPACE_BEGIN(detail) + +// Buffer that writes to Python instead of C++ +class pythonbuf : public std::streambuf { +private: + using traits_type = std::streambuf::traits_type; + + const size_t buf_size; + std::unique_ptr d_buffer; + object pywrite; + object pyflush; + + int overflow(int c) override { + if (!traits_type::eq_int_type(c, traits_type::eof())) { + *pptr() = traits_type::to_char_type(c); + pbump(1); + } + return sync() == 0 ? traits_type::not_eof(c) : traits_type::eof(); + } + + // This function must be non-virtual to be called in a destructor. If the + // rare MSVC test failure shows up with this version, then this should be + // simplified to a fully qualified call. + int _sync() { + if (pbase() != pptr()) { + + { + gil_scoped_acquire tmp; + + // This subtraction cannot be negative, so dropping the sign. + str line(pbase(), static_cast(pptr() - pbase())); + + pywrite(line); + pyflush(); + + // Placed inside gil_scoped_aquire as a mutex to avoid a race + setp(pbase(), epptr()); + } + + } + return 0; + } + + int sync() override { + return _sync(); + } + +public: + + pythonbuf(object pyostream, size_t buffer_size = 1024) + : buf_size(buffer_size), + d_buffer(new char[buf_size]), + pywrite(pyostream.attr("write")), + pyflush(pyostream.attr("flush")) { + setp(d_buffer.get(), d_buffer.get() + buf_size - 1); + } + + pythonbuf(pythonbuf&&) = default; + + /// Sync before destroy + ~pythonbuf() override { + _sync(); + } +}; + +PYBIND11_NAMESPACE_END(detail) + + +/** \rst + This a move-only guard that redirects output. + + .. code-block:: cpp + + #include + + ... + + { + py::scoped_ostream_redirect output; + std::cout << "Hello, World!"; // Python stdout + } // <-- return std::cout to normal + + You can explicitly pass the c++ stream and the python object, + for example to guard stderr instead. + + .. code-block:: cpp + + { + py::scoped_ostream_redirect output{std::cerr, py::module::import("sys").attr("stderr")}; + std::cout << "Hello, World!"; + } + \endrst */ +class scoped_ostream_redirect { +protected: + std::streambuf *old; + std::ostream &costream; + detail::pythonbuf buffer; + +public: + scoped_ostream_redirect( + std::ostream &costream = std::cout, + object pyostream = module_::import("sys").attr("stdout")) + : costream(costream), buffer(pyostream) { + old = costream.rdbuf(&buffer); + } + + ~scoped_ostream_redirect() { + costream.rdbuf(old); + } + + scoped_ostream_redirect(const scoped_ostream_redirect &) = delete; + scoped_ostream_redirect(scoped_ostream_redirect &&other) = default; + scoped_ostream_redirect &operator=(const scoped_ostream_redirect &) = delete; + scoped_ostream_redirect &operator=(scoped_ostream_redirect &&) = delete; +}; + + +/** \rst + Like `scoped_ostream_redirect`, but redirects cerr by default. This class + is provided primary to make ``py::call_guard`` easier to make. + + .. code-block:: cpp + + m.def("noisy_func", &noisy_func, + py::call_guard()); + +\endrst */ +class scoped_estream_redirect : public scoped_ostream_redirect { +public: + scoped_estream_redirect( + std::ostream &costream = std::cerr, + object pyostream = module_::import("sys").attr("stderr")) + : scoped_ostream_redirect(costream,pyostream) {} +}; + + +PYBIND11_NAMESPACE_BEGIN(detail) + +// Class to redirect output as a context manager. C++ backend. +class OstreamRedirect { + bool do_stdout_; + bool do_stderr_; + std::unique_ptr redirect_stdout; + std::unique_ptr redirect_stderr; + +public: + OstreamRedirect(bool do_stdout = true, bool do_stderr = true) + : do_stdout_(do_stdout), do_stderr_(do_stderr) {} + + void enter() { + if (do_stdout_) + redirect_stdout.reset(new scoped_ostream_redirect()); + if (do_stderr_) + redirect_stderr.reset(new scoped_estream_redirect()); + } + + void exit() { + redirect_stdout.reset(); + redirect_stderr.reset(); + } +}; + +PYBIND11_NAMESPACE_END(detail) + +/** \rst + This is a helper function to add a C++ redirect context manager to Python + instead of using a C++ guard. To use it, add the following to your binding code: + + .. code-block:: cpp + + #include + + ... + + py::add_ostream_redirect(m, "ostream_redirect"); + + You now have a Python context manager that redirects your output: + + .. code-block:: python + + with m.ostream_redirect(): + m.print_to_cout_function() + + This manager can optionally be told which streams to operate on: + + .. code-block:: python + + with m.ostream_redirect(stdout=true, stderr=true): + m.noisy_function_with_error_printing() + + \endrst */ +inline class_ add_ostream_redirect(module_ m, std::string name = "ostream_redirect") { + return class_(m, name.c_str(), module_local()) + .def(init(), arg("stdout")=true, arg("stderr")=true) + .def("__enter__", &detail::OstreamRedirect::enter) + .def("__exit__", [](detail::OstreamRedirect &self_, args) { self_.exit(); }); +} + +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/numpy.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/numpy.h new file mode 100644 index 0000000000000000000000000000000000000000..d1ddc4a9db195aeb4629f3659b2fb12e0b228c1b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/numpy.h @@ -0,0 +1,1703 @@ +/* + pybind11/numpy.h: Basic NumPy support, vectorize() wrapper + + Copyright (c) 2016 Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "pybind11.h" +#include "complex.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#if defined(_MSC_VER) +# pragma warning(push) +# pragma warning(disable: 4127) // warning C4127: Conditional expression is constant +#endif + +/* This will be true on all flat address space platforms and allows us to reduce the + whole npy_intp / ssize_t / Py_intptr_t business down to just ssize_t for all size + and dimension types (e.g. shape, strides, indexing), instead of inflicting this + upon the library user. */ +static_assert(sizeof(::pybind11::ssize_t) == sizeof(Py_intptr_t), "ssize_t != Py_intptr_t"); +static_assert(std::is_signed::value, "Py_intptr_t must be signed"); +// We now can reinterpret_cast between py::ssize_t and Py_intptr_t (MSVC + PyPy cares) + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) + +class array; // Forward declaration + +PYBIND11_NAMESPACE_BEGIN(detail) + +template <> struct handle_type_name { static constexpr auto name = _("numpy.ndarray"); }; + +template struct npy_format_descriptor; + +struct PyArrayDescr_Proxy { + PyObject_HEAD + PyObject *typeobj; + char kind; + char type; + char byteorder; + char flags; + int type_num; + int elsize; + int alignment; + char *subarray; + PyObject *fields; + PyObject *names; +}; + +struct PyArray_Proxy { + PyObject_HEAD + char *data; + int nd; + ssize_t *dimensions; + ssize_t *strides; + PyObject *base; + PyObject *descr; + int flags; +}; + +struct PyVoidScalarObject_Proxy { + PyObject_VAR_HEAD + char *obval; + PyArrayDescr_Proxy *descr; + int flags; + PyObject *base; +}; + +struct numpy_type_info { + PyObject* dtype_ptr; + std::string format_str; +}; + +struct numpy_internals { + std::unordered_map registered_dtypes; + + numpy_type_info *get_type_info(const std::type_info& tinfo, bool throw_if_missing = true) { + auto it = registered_dtypes.find(std::type_index(tinfo)); + if (it != registered_dtypes.end()) + return &(it->second); + if (throw_if_missing) + pybind11_fail(std::string("NumPy type info missing for ") + tinfo.name()); + return nullptr; + } + + template numpy_type_info *get_type_info(bool throw_if_missing = true) { + return get_type_info(typeid(typename std::remove_cv::type), throw_if_missing); + } +}; + +inline PYBIND11_NOINLINE void load_numpy_internals(numpy_internals* &ptr) { + ptr = &get_or_create_shared_data("_numpy_internals"); +} + +inline numpy_internals& get_numpy_internals() { + static numpy_internals* ptr = nullptr; + if (!ptr) + load_numpy_internals(ptr); + return *ptr; +} + +template struct same_size { + template using as = bool_constant; +}; + +template constexpr int platform_lookup() { return -1; } + +// Lookup a type according to its size, and return a value corresponding to the NumPy typenum. +template +constexpr int platform_lookup(int I, Ints... Is) { + return sizeof(Concrete) == sizeof(T) ? I : platform_lookup(Is...); +} + +struct npy_api { + enum constants { + NPY_ARRAY_C_CONTIGUOUS_ = 0x0001, + NPY_ARRAY_F_CONTIGUOUS_ = 0x0002, + NPY_ARRAY_OWNDATA_ = 0x0004, + NPY_ARRAY_FORCECAST_ = 0x0010, + NPY_ARRAY_ENSUREARRAY_ = 0x0040, + NPY_ARRAY_ALIGNED_ = 0x0100, + NPY_ARRAY_WRITEABLE_ = 0x0400, + NPY_BOOL_ = 0, + NPY_BYTE_, NPY_UBYTE_, + NPY_SHORT_, NPY_USHORT_, + NPY_INT_, NPY_UINT_, + NPY_LONG_, NPY_ULONG_, + NPY_LONGLONG_, NPY_ULONGLONG_, + NPY_FLOAT_, NPY_DOUBLE_, NPY_LONGDOUBLE_, + NPY_CFLOAT_, NPY_CDOUBLE_, NPY_CLONGDOUBLE_, + NPY_OBJECT_ = 17, + NPY_STRING_, NPY_UNICODE_, NPY_VOID_, + // Platform-dependent normalization + NPY_INT8_ = NPY_BYTE_, + NPY_UINT8_ = NPY_UBYTE_, + NPY_INT16_ = NPY_SHORT_, + NPY_UINT16_ = NPY_USHORT_, + // `npy_common.h` defines the integer aliases. In order, it checks: + // NPY_BITSOF_LONG, NPY_BITSOF_LONGLONG, NPY_BITSOF_INT, NPY_BITSOF_SHORT, NPY_BITSOF_CHAR + // and assigns the alias to the first matching size, so we should check in this order. + NPY_INT32_ = platform_lookup( + NPY_LONG_, NPY_INT_, NPY_SHORT_), + NPY_UINT32_ = platform_lookup( + NPY_ULONG_, NPY_UINT_, NPY_USHORT_), + NPY_INT64_ = platform_lookup( + NPY_LONG_, NPY_LONGLONG_, NPY_INT_), + NPY_UINT64_ = platform_lookup( + NPY_ULONG_, NPY_ULONGLONG_, NPY_UINT_), + }; + + typedef struct { + Py_intptr_t *ptr; + int len; + } PyArray_Dims; + + static npy_api& get() { + static npy_api api = lookup(); + return api; + } + + bool PyArray_Check_(PyObject *obj) const { + return (bool) PyObject_TypeCheck(obj, PyArray_Type_); + } + bool PyArrayDescr_Check_(PyObject *obj) const { + return (bool) PyObject_TypeCheck(obj, PyArrayDescr_Type_); + } + + unsigned int (*PyArray_GetNDArrayCFeatureVersion_)(); + PyObject *(*PyArray_DescrFromType_)(int); + PyObject *(*PyArray_NewFromDescr_) + (PyTypeObject *, PyObject *, int, Py_intptr_t const *, + Py_intptr_t const *, void *, int, PyObject *); + // Unused. Not removed because that affects ABI of the class. + PyObject *(*PyArray_DescrNewFromType_)(int); + int (*PyArray_CopyInto_)(PyObject *, PyObject *); + PyObject *(*PyArray_NewCopy_)(PyObject *, int); + PyTypeObject *PyArray_Type_; + PyTypeObject *PyVoidArrType_Type_; + PyTypeObject *PyArrayDescr_Type_; + PyObject *(*PyArray_DescrFromScalar_)(PyObject *); + PyObject *(*PyArray_FromAny_) (PyObject *, PyObject *, int, int, int, PyObject *); + int (*PyArray_DescrConverter_) (PyObject *, PyObject **); + bool (*PyArray_EquivTypes_) (PyObject *, PyObject *); + int (*PyArray_GetArrayParamsFromObject_)(PyObject *, PyObject *, unsigned char, PyObject **, int *, + Py_intptr_t *, PyObject **, PyObject *); + PyObject *(*PyArray_Squeeze_)(PyObject *); + // Unused. Not removed because that affects ABI of the class. + int (*PyArray_SetBaseObject_)(PyObject *, PyObject *); + PyObject* (*PyArray_Resize_)(PyObject*, PyArray_Dims*, int, int); +private: + enum functions { + API_PyArray_GetNDArrayCFeatureVersion = 211, + API_PyArray_Type = 2, + API_PyArrayDescr_Type = 3, + API_PyVoidArrType_Type = 39, + API_PyArray_DescrFromType = 45, + API_PyArray_DescrFromScalar = 57, + API_PyArray_FromAny = 69, + API_PyArray_Resize = 80, + API_PyArray_CopyInto = 82, + API_PyArray_NewCopy = 85, + API_PyArray_NewFromDescr = 94, + API_PyArray_DescrNewFromType = 96, + API_PyArray_DescrConverter = 174, + API_PyArray_EquivTypes = 182, + API_PyArray_GetArrayParamsFromObject = 278, + API_PyArray_Squeeze = 136, + API_PyArray_SetBaseObject = 282 + }; + + static npy_api lookup() { + module_ m = module_::import("numpy.core.multiarray"); + auto c = m.attr("_ARRAY_API"); +#if PY_MAJOR_VERSION >= 3 + void **api_ptr = (void **) PyCapsule_GetPointer(c.ptr(), NULL); +#else + void **api_ptr = (void **) PyCObject_AsVoidPtr(c.ptr()); +#endif + npy_api api; +#define DECL_NPY_API(Func) api.Func##_ = (decltype(api.Func##_)) api_ptr[API_##Func]; + DECL_NPY_API(PyArray_GetNDArrayCFeatureVersion); + if (api.PyArray_GetNDArrayCFeatureVersion_() < 0x7) + pybind11_fail("pybind11 numpy support requires numpy >= 1.7.0"); + DECL_NPY_API(PyArray_Type); + DECL_NPY_API(PyVoidArrType_Type); + DECL_NPY_API(PyArrayDescr_Type); + DECL_NPY_API(PyArray_DescrFromType); + DECL_NPY_API(PyArray_DescrFromScalar); + DECL_NPY_API(PyArray_FromAny); + DECL_NPY_API(PyArray_Resize); + DECL_NPY_API(PyArray_CopyInto); + DECL_NPY_API(PyArray_NewCopy); + DECL_NPY_API(PyArray_NewFromDescr); + DECL_NPY_API(PyArray_DescrNewFromType); + DECL_NPY_API(PyArray_DescrConverter); + DECL_NPY_API(PyArray_EquivTypes); + DECL_NPY_API(PyArray_GetArrayParamsFromObject); + DECL_NPY_API(PyArray_Squeeze); + DECL_NPY_API(PyArray_SetBaseObject); +#undef DECL_NPY_API + return api; + } +}; + +inline PyArray_Proxy* array_proxy(void* ptr) { + return reinterpret_cast(ptr); +} + +inline const PyArray_Proxy* array_proxy(const void* ptr) { + return reinterpret_cast(ptr); +} + +inline PyArrayDescr_Proxy* array_descriptor_proxy(PyObject* ptr) { + return reinterpret_cast(ptr); +} + +inline const PyArrayDescr_Proxy* array_descriptor_proxy(const PyObject* ptr) { + return reinterpret_cast(ptr); +} + +inline bool check_flags(const void* ptr, int flag) { + return (flag == (array_proxy(ptr)->flags & flag)); +} + +template struct is_std_array : std::false_type { }; +template struct is_std_array> : std::true_type { }; +template struct is_complex : std::false_type { }; +template struct is_complex> : std::true_type { }; + +template struct array_info_scalar { + using type = T; + static constexpr bool is_array = false; + static constexpr bool is_empty = false; + static constexpr auto extents = _(""); + static void append_extents(list& /* shape */) { } +}; +// Computes underlying type and a comma-separated list of extents for array +// types (any mix of std::array and built-in arrays). An array of char is +// treated as scalar because it gets special handling. +template struct array_info : array_info_scalar { }; +template struct array_info> { + using type = typename array_info::type; + static constexpr bool is_array = true; + static constexpr bool is_empty = (N == 0) || array_info::is_empty; + static constexpr size_t extent = N; + + // appends the extents to shape + static void append_extents(list& shape) { + shape.append(N); + array_info::append_extents(shape); + } + + static constexpr auto extents = _::is_array>( + concat(_(), array_info::extents), _() + ); +}; +// For numpy we have special handling for arrays of characters, so we don't include +// the size in the array extents. +template struct array_info : array_info_scalar { }; +template struct array_info> : array_info_scalar> { }; +template struct array_info : array_info> { }; +template using remove_all_extents_t = typename array_info::type; + +template using is_pod_struct = all_of< + std::is_standard_layout, // since we're accessing directly in memory we need a standard layout type +#if !defined(__GNUG__) || defined(_LIBCPP_VERSION) || defined(_GLIBCXX_USE_CXX11_ABI) + // _GLIBCXX_USE_CXX11_ABI indicates that we're using libstdc++ from GCC 5 or newer, independent + // of the actual compiler (Clang can also use libstdc++, but it always defines __GNUC__ == 4). + std::is_trivially_copyable, +#else + // GCC 4 doesn't implement is_trivially_copyable, so approximate it + std::is_trivially_destructible, + satisfies_any_of, +#endif + satisfies_none_of +>; + +// Replacement for std::is_pod (deprecated in C++20) +template using is_pod = all_of< + std::is_standard_layout, + std::is_trivial +>; + +template ssize_t byte_offset_unsafe(const Strides &) { return 0; } +template +ssize_t byte_offset_unsafe(const Strides &strides, ssize_t i, Ix... index) { + return i * strides[Dim] + byte_offset_unsafe(strides, index...); +} + +/** + * Proxy class providing unsafe, unchecked const access to array data. This is constructed through + * the `unchecked()` method of `array` or the `unchecked()` method of `array_t`. `Dims` + * will be -1 for dimensions determined at runtime. + */ +template +class unchecked_reference { +protected: + static constexpr bool Dynamic = Dims < 0; + const unsigned char *data_; + // Storing the shape & strides in local variables (i.e. these arrays) allows the compiler to + // make large performance gains on big, nested loops, but requires compile-time dimensions + conditional_t> + shape_, strides_; + const ssize_t dims_; + + friend class pybind11::array; + // Constructor for compile-time dimensions: + template + unchecked_reference(const void *data, const ssize_t *shape, const ssize_t *strides, enable_if_t) + : data_{reinterpret_cast(data)}, dims_{Dims} { + for (size_t i = 0; i < (size_t) dims_; i++) { + shape_[i] = shape[i]; + strides_[i] = strides[i]; + } + } + // Constructor for runtime dimensions: + template + unchecked_reference(const void *data, const ssize_t *shape, const ssize_t *strides, enable_if_t dims) + : data_{reinterpret_cast(data)}, shape_{shape}, strides_{strides}, dims_{dims} {} + +public: + /** + * Unchecked const reference access to data at the given indices. For a compile-time known + * number of dimensions, this requires the correct number of arguments; for run-time + * dimensionality, this is not checked (and so is up to the caller to use safely). + */ + template const T &operator()(Ix... index) const { + static_assert(ssize_t{sizeof...(Ix)} == Dims || Dynamic, + "Invalid number of indices for unchecked array reference"); + return *reinterpret_cast(data_ + byte_offset_unsafe(strides_, ssize_t(index)...)); + } + /** + * Unchecked const reference access to data; this operator only participates if the reference + * is to a 1-dimensional array. When present, this is exactly equivalent to `obj(index)`. + */ + template > + const T &operator[](ssize_t index) const { return operator()(index); } + + /// Pointer access to the data at the given indices. + template const T *data(Ix... ix) const { return &operator()(ssize_t(ix)...); } + + /// Returns the item size, i.e. sizeof(T) + constexpr static ssize_t itemsize() { return sizeof(T); } + + /// Returns the shape (i.e. size) of dimension `dim` + ssize_t shape(ssize_t dim) const { return shape_[(size_t) dim]; } + + /// Returns the number of dimensions of the array + ssize_t ndim() const { return dims_; } + + /// Returns the total number of elements in the referenced array, i.e. the product of the shapes + template + enable_if_t size() const { + return std::accumulate(shape_.begin(), shape_.end(), (ssize_t) 1, std::multiplies()); + } + template + enable_if_t size() const { + return std::accumulate(shape_, shape_ + ndim(), (ssize_t) 1, std::multiplies()); + } + + /// Returns the total number of bytes used by the referenced data. Note that the actual span in + /// memory may be larger if the referenced array has non-contiguous strides (e.g. for a slice). + ssize_t nbytes() const { + return size() * itemsize(); + } +}; + +template +class unchecked_mutable_reference : public unchecked_reference { + friend class pybind11::array; + using ConstBase = unchecked_reference; + using ConstBase::ConstBase; + using ConstBase::Dynamic; +public: + // Bring in const-qualified versions from base class + using ConstBase::operator(); + using ConstBase::operator[]; + + /// Mutable, unchecked access to data at the given indices. + template T& operator()(Ix... index) { + static_assert(ssize_t{sizeof...(Ix)} == Dims || Dynamic, + "Invalid number of indices for unchecked array reference"); + return const_cast(ConstBase::operator()(index...)); + } + /** + * Mutable, unchecked access data at the given index; this operator only participates if the + * reference is to a 1-dimensional array (or has runtime dimensions). When present, this is + * exactly equivalent to `obj(index)`. + */ + template > + T &operator[](ssize_t index) { return operator()(index); } + + /// Mutable pointer access to the data at the given indices. + template T *mutable_data(Ix... ix) { return &operator()(ssize_t(ix)...); } +}; + +template +struct type_caster> { + static_assert(Dim == 0 && Dim > 0 /* always fail */, "unchecked array proxy object is not castable"); +}; +template +struct type_caster> : type_caster> {}; + +PYBIND11_NAMESPACE_END(detail) + +class dtype : public object { +public: + PYBIND11_OBJECT_DEFAULT(dtype, object, detail::npy_api::get().PyArrayDescr_Check_); + + explicit dtype(const buffer_info &info) { + dtype descr(_dtype_from_pep3118()(PYBIND11_STR_TYPE(info.format))); + // If info.itemsize == 0, use the value calculated from the format string + m_ptr = descr.strip_padding(info.itemsize ? info.itemsize : descr.itemsize()).release().ptr(); + } + + explicit dtype(const std::string &format) { + m_ptr = from_args(pybind11::str(format)).release().ptr(); + } + + dtype(const char *format) : dtype(std::string(format)) { } + + dtype(list names, list formats, list offsets, ssize_t itemsize) { + dict args; + args["names"] = names; + args["formats"] = formats; + args["offsets"] = offsets; + args["itemsize"] = pybind11::int_(itemsize); + m_ptr = from_args(args).release().ptr(); + } + + /// This is essentially the same as calling numpy.dtype(args) in Python. + static dtype from_args(object args) { + PyObject *ptr = nullptr; + if (!detail::npy_api::get().PyArray_DescrConverter_(args.ptr(), &ptr) || !ptr) + throw error_already_set(); + return reinterpret_steal(ptr); + } + + /// Return dtype associated with a C++ type. + template static dtype of() { + return detail::npy_format_descriptor::type>::dtype(); + } + + /// Size of the data type in bytes. + ssize_t itemsize() const { + return detail::array_descriptor_proxy(m_ptr)->elsize; + } + + /// Returns true for structured data types. + bool has_fields() const { + return detail::array_descriptor_proxy(m_ptr)->names != nullptr; + } + + /// Single-character code for dtype's kind. + /// For example, floating point types are 'f' and integral types are 'i'. + char kind() const { + return detail::array_descriptor_proxy(m_ptr)->kind; + } + + /// Single-character for dtype's type. + /// For example, ``float`` is 'f', ``double`` 'd', ``int`` 'i', and ``long`` 'd'. + char char_() const { + // Note: The signature, `dtype::char_` follows the naming of NumPy's + // public Python API (i.e., ``dtype.char``), rather than its internal + // C API (``PyArray_Descr::type``). + return detail::array_descriptor_proxy(m_ptr)->type; + } + +private: + static object _dtype_from_pep3118() { + static PyObject *obj = module_::import("numpy.core._internal") + .attr("_dtype_from_pep3118").cast().release().ptr(); + return reinterpret_borrow(obj); + } + + dtype strip_padding(ssize_t itemsize) { + // Recursively strip all void fields with empty names that are generated for + // padding fields (as of NumPy v1.11). + if (!has_fields()) + return *this; + + struct field_descr { PYBIND11_STR_TYPE name; object format; pybind11::int_ offset; }; + std::vector field_descriptors; + + for (auto field : attr("fields").attr("items")()) { + auto spec = field.cast(); + auto name = spec[0].cast(); + auto format = spec[1].cast()[0].cast(); + auto offset = spec[1].cast()[1].cast(); + if (!len(name) && format.kind() == 'V') + continue; + field_descriptors.push_back({(PYBIND11_STR_TYPE) name, format.strip_padding(format.itemsize()), offset}); + } + + std::sort(field_descriptors.begin(), field_descriptors.end(), + [](const field_descr& a, const field_descr& b) { + return a.offset.cast() < b.offset.cast(); + }); + + list names, formats, offsets; + for (auto& descr : field_descriptors) { + names.append(descr.name); + formats.append(descr.format); + offsets.append(descr.offset); + } + return dtype(names, formats, offsets, itemsize); + } +}; + +class array : public buffer { +public: + PYBIND11_OBJECT_CVT(array, buffer, detail::npy_api::get().PyArray_Check_, raw_array) + + enum { + c_style = detail::npy_api::NPY_ARRAY_C_CONTIGUOUS_, + f_style = detail::npy_api::NPY_ARRAY_F_CONTIGUOUS_, + forcecast = detail::npy_api::NPY_ARRAY_FORCECAST_ + }; + + array() : array(0, static_cast(nullptr)) {} + + using ShapeContainer = detail::any_container; + using StridesContainer = detail::any_container; + + // Constructs an array taking shape/strides from arbitrary container types + array(const pybind11::dtype &dt, ShapeContainer shape, StridesContainer strides, + const void *ptr = nullptr, handle base = handle()) { + + if (strides->empty()) + *strides = detail::c_strides(*shape, dt.itemsize()); + + auto ndim = shape->size(); + if (ndim != strides->size()) + pybind11_fail("NumPy: shape ndim doesn't match strides ndim"); + auto descr = dt; + + int flags = 0; + if (base && ptr) { + if (isinstance(base)) + /* Copy flags from base (except ownership bit) */ + flags = reinterpret_borrow(base).flags() & ~detail::npy_api::NPY_ARRAY_OWNDATA_; + else + /* Writable by default, easy to downgrade later on if needed */ + flags = detail::npy_api::NPY_ARRAY_WRITEABLE_; + } + + auto &api = detail::npy_api::get(); + auto tmp = reinterpret_steal(api.PyArray_NewFromDescr_( + api.PyArray_Type_, descr.release().ptr(), (int) ndim, + // Use reinterpret_cast for PyPy on Windows (remove if fixed, checked on 7.3.1) + reinterpret_cast(shape->data()), + reinterpret_cast(strides->data()), + const_cast(ptr), flags, nullptr)); + if (!tmp) + throw error_already_set(); + if (ptr) { + if (base) { + api.PyArray_SetBaseObject_(tmp.ptr(), base.inc_ref().ptr()); + } else { + tmp = reinterpret_steal(api.PyArray_NewCopy_(tmp.ptr(), -1 /* any order */)); + } + } + m_ptr = tmp.release().ptr(); + } + + array(const pybind11::dtype &dt, ShapeContainer shape, const void *ptr = nullptr, handle base = handle()) + : array(dt, std::move(shape), {}, ptr, base) { } + + template ::value && !std::is_same::value>> + array(const pybind11::dtype &dt, T count, const void *ptr = nullptr, handle base = handle()) + : array(dt, {{count}}, ptr, base) { } + + template + array(ShapeContainer shape, StridesContainer strides, const T *ptr, handle base = handle()) + : array(pybind11::dtype::of(), std::move(shape), std::move(strides), ptr, base) { } + + template + array(ShapeContainer shape, const T *ptr, handle base = handle()) + : array(std::move(shape), {}, ptr, base) { } + + template + explicit array(ssize_t count, const T *ptr, handle base = handle()) : array({count}, {}, ptr, base) { } + + explicit array(const buffer_info &info, handle base = handle()) + : array(pybind11::dtype(info), info.shape, info.strides, info.ptr, base) { } + + /// Array descriptor (dtype) + pybind11::dtype dtype() const { + return reinterpret_borrow(detail::array_proxy(m_ptr)->descr); + } + + /// Total number of elements + ssize_t size() const { + return std::accumulate(shape(), shape() + ndim(), (ssize_t) 1, std::multiplies()); + } + + /// Byte size of a single element + ssize_t itemsize() const { + return detail::array_descriptor_proxy(detail::array_proxy(m_ptr)->descr)->elsize; + } + + /// Total number of bytes + ssize_t nbytes() const { + return size() * itemsize(); + } + + /// Number of dimensions + ssize_t ndim() const { + return detail::array_proxy(m_ptr)->nd; + } + + /// Base object + object base() const { + return reinterpret_borrow(detail::array_proxy(m_ptr)->base); + } + + /// Dimensions of the array + const ssize_t* shape() const { + return detail::array_proxy(m_ptr)->dimensions; + } + + /// Dimension along a given axis + ssize_t shape(ssize_t dim) const { + if (dim >= ndim()) + fail_dim_check(dim, "invalid axis"); + return shape()[dim]; + } + + /// Strides of the array + const ssize_t* strides() const { + return detail::array_proxy(m_ptr)->strides; + } + + /// Stride along a given axis + ssize_t strides(ssize_t dim) const { + if (dim >= ndim()) + fail_dim_check(dim, "invalid axis"); + return strides()[dim]; + } + + /// Return the NumPy array flags + int flags() const { + return detail::array_proxy(m_ptr)->flags; + } + + /// If set, the array is writeable (otherwise the buffer is read-only) + bool writeable() const { + return detail::check_flags(m_ptr, detail::npy_api::NPY_ARRAY_WRITEABLE_); + } + + /// If set, the array owns the data (will be freed when the array is deleted) + bool owndata() const { + return detail::check_flags(m_ptr, detail::npy_api::NPY_ARRAY_OWNDATA_); + } + + /// Pointer to the contained data. If index is not provided, points to the + /// beginning of the buffer. May throw if the index would lead to out of bounds access. + template const void* data(Ix... index) const { + return static_cast(detail::array_proxy(m_ptr)->data + offset_at(index...)); + } + + /// Mutable pointer to the contained data. If index is not provided, points to the + /// beginning of the buffer. May throw if the index would lead to out of bounds access. + /// May throw if the array is not writeable. + template void* mutable_data(Ix... index) { + check_writeable(); + return static_cast(detail::array_proxy(m_ptr)->data + offset_at(index...)); + } + + /// Byte offset from beginning of the array to a given index (full or partial). + /// May throw if the index would lead to out of bounds access. + template ssize_t offset_at(Ix... index) const { + if ((ssize_t) sizeof...(index) > ndim()) + fail_dim_check(sizeof...(index), "too many indices for an array"); + return byte_offset(ssize_t(index)...); + } + + ssize_t offset_at() const { return 0; } + + /// Item count from beginning of the array to a given index (full or partial). + /// May throw if the index would lead to out of bounds access. + template ssize_t index_at(Ix... index) const { + return offset_at(index...) / itemsize(); + } + + /** + * Returns a proxy object that provides access to the array's data without bounds or + * dimensionality checking. Will throw if the array is missing the `writeable` flag. Use with + * care: the array must not be destroyed or reshaped for the duration of the returned object, + * and the caller must take care not to access invalid dimensions or dimension indices. + */ + template detail::unchecked_mutable_reference mutable_unchecked() & { + if (Dims >= 0 && ndim() != Dims) + throw std::domain_error("array has incorrect number of dimensions: " + std::to_string(ndim()) + + "; expected " + std::to_string(Dims)); + return detail::unchecked_mutable_reference(mutable_data(), shape(), strides(), ndim()); + } + + /** + * Returns a proxy object that provides const access to the array's data without bounds or + * dimensionality checking. Unlike `mutable_unchecked()`, this does not require that the + * underlying array have the `writable` flag. Use with care: the array must not be destroyed or + * reshaped for the duration of the returned object, and the caller must take care not to access + * invalid dimensions or dimension indices. + */ + template detail::unchecked_reference unchecked() const & { + if (Dims >= 0 && ndim() != Dims) + throw std::domain_error("array has incorrect number of dimensions: " + std::to_string(ndim()) + + "; expected " + std::to_string(Dims)); + return detail::unchecked_reference(data(), shape(), strides(), ndim()); + } + + /// Return a new view with all of the dimensions of length 1 removed + array squeeze() { + auto& api = detail::npy_api::get(); + return reinterpret_steal(api.PyArray_Squeeze_(m_ptr)); + } + + /// Resize array to given shape + /// If refcheck is true and more that one reference exist to this array + /// then resize will succeed only if it makes a reshape, i.e. original size doesn't change + void resize(ShapeContainer new_shape, bool refcheck = true) { + detail::npy_api::PyArray_Dims d = { + // Use reinterpret_cast for PyPy on Windows (remove if fixed, checked on 7.3.1) + reinterpret_cast(new_shape->data()), + int(new_shape->size()) + }; + // try to resize, set ordering param to -1 cause it's not used anyway + auto new_array = reinterpret_steal( + detail::npy_api::get().PyArray_Resize_(m_ptr, &d, int(refcheck), -1) + ); + if (!new_array) throw error_already_set(); + if (isinstance(new_array)) { *this = std::move(new_array); } + } + + /// Ensure that the argument is a NumPy array + /// In case of an error, nullptr is returned and the Python error is cleared. + static array ensure(handle h, int ExtraFlags = 0) { + auto result = reinterpret_steal(raw_array(h.ptr(), ExtraFlags)); + if (!result) + PyErr_Clear(); + return result; + } + +protected: + template friend struct detail::npy_format_descriptor; + + void fail_dim_check(ssize_t dim, const std::string& msg) const { + throw index_error(msg + ": " + std::to_string(dim) + + " (ndim = " + std::to_string(ndim()) + ")"); + } + + template ssize_t byte_offset(Ix... index) const { + check_dimensions(index...); + return detail::byte_offset_unsafe(strides(), ssize_t(index)...); + } + + void check_writeable() const { + if (!writeable()) + throw std::domain_error("array is not writeable"); + } + + template void check_dimensions(Ix... index) const { + check_dimensions_impl(ssize_t(0), shape(), ssize_t(index)...); + } + + void check_dimensions_impl(ssize_t, const ssize_t*) const { } + + template void check_dimensions_impl(ssize_t axis, const ssize_t* shape, ssize_t i, Ix... index) const { + if (i >= *shape) { + throw index_error(std::string("index ") + std::to_string(i) + + " is out of bounds for axis " + std::to_string(axis) + + " with size " + std::to_string(*shape)); + } + check_dimensions_impl(axis + 1, shape + 1, index...); + } + + /// Create array from any object -- always returns a new reference + static PyObject *raw_array(PyObject *ptr, int ExtraFlags = 0) { + if (ptr == nullptr) { + PyErr_SetString(PyExc_ValueError, "cannot create a pybind11::array from a nullptr"); + return nullptr; + } + return detail::npy_api::get().PyArray_FromAny_( + ptr, nullptr, 0, 0, detail::npy_api::NPY_ARRAY_ENSUREARRAY_ | ExtraFlags, nullptr); + } +}; + +template class array_t : public array { +private: + struct private_ctor {}; + // Delegating constructor needed when both moving and accessing in the same constructor + array_t(private_ctor, ShapeContainer &&shape, StridesContainer &&strides, const T *ptr, handle base) + : array(std::move(shape), std::move(strides), ptr, base) {} +public: + static_assert(!detail::array_info::is_array, "Array types cannot be used with array_t"); + + using value_type = T; + + array_t() : array(0, static_cast(nullptr)) {} + array_t(handle h, borrowed_t) : array(h, borrowed_t{}) { } + array_t(handle h, stolen_t) : array(h, stolen_t{}) { } + + PYBIND11_DEPRECATED("Use array_t::ensure() instead") + array_t(handle h, bool is_borrowed) : array(raw_array_t(h.ptr()), stolen_t{}) { + if (!m_ptr) PyErr_Clear(); + if (!is_borrowed) Py_XDECREF(h.ptr()); + } + + array_t(const object &o) : array(raw_array_t(o.ptr()), stolen_t{}) { + if (!m_ptr) throw error_already_set(); + } + + explicit array_t(const buffer_info& info, handle base = handle()) : array(info, base) { } + + array_t(ShapeContainer shape, StridesContainer strides, const T *ptr = nullptr, handle base = handle()) + : array(std::move(shape), std::move(strides), ptr, base) { } + + explicit array_t(ShapeContainer shape, const T *ptr = nullptr, handle base = handle()) + : array_t(private_ctor{}, std::move(shape), + ExtraFlags & f_style + ? detail::f_strides(*shape, itemsize()) + : detail::c_strides(*shape, itemsize()), + ptr, base) { } + + explicit array_t(ssize_t count, const T *ptr = nullptr, handle base = handle()) + : array({count}, {}, ptr, base) { } + + constexpr ssize_t itemsize() const { + return sizeof(T); + } + + template ssize_t index_at(Ix... index) const { + return offset_at(index...) / itemsize(); + } + + template const T* data(Ix... index) const { + return static_cast(array::data(index...)); + } + + template T* mutable_data(Ix... index) { + return static_cast(array::mutable_data(index...)); + } + + // Reference to element at a given index + template const T& at(Ix... index) const { + if ((ssize_t) sizeof...(index) != ndim()) + fail_dim_check(sizeof...(index), "index dimension mismatch"); + return *(static_cast(array::data()) + byte_offset(ssize_t(index)...) / itemsize()); + } + + // Mutable reference to element at a given index + template T& mutable_at(Ix... index) { + if ((ssize_t) sizeof...(index) != ndim()) + fail_dim_check(sizeof...(index), "index dimension mismatch"); + return *(static_cast(array::mutable_data()) + byte_offset(ssize_t(index)...) / itemsize()); + } + + /** + * Returns a proxy object that provides access to the array's data without bounds or + * dimensionality checking. Will throw if the array is missing the `writeable` flag. Use with + * care: the array must not be destroyed or reshaped for the duration of the returned object, + * and the caller must take care not to access invalid dimensions or dimension indices. + */ + template detail::unchecked_mutable_reference mutable_unchecked() & { + return array::mutable_unchecked(); + } + + /** + * Returns a proxy object that provides const access to the array's data without bounds or + * dimensionality checking. Unlike `unchecked()`, this does not require that the underlying + * array have the `writable` flag. Use with care: the array must not be destroyed or reshaped + * for the duration of the returned object, and the caller must take care not to access invalid + * dimensions or dimension indices. + */ + template detail::unchecked_reference unchecked() const & { + return array::unchecked(); + } + + /// Ensure that the argument is a NumPy array of the correct dtype (and if not, try to convert + /// it). In case of an error, nullptr is returned and the Python error is cleared. + static array_t ensure(handle h) { + auto result = reinterpret_steal(raw_array_t(h.ptr())); + if (!result) + PyErr_Clear(); + return result; + } + + static bool check_(handle h) { + const auto &api = detail::npy_api::get(); + return api.PyArray_Check_(h.ptr()) + && api.PyArray_EquivTypes_(detail::array_proxy(h.ptr())->descr, dtype::of().ptr()) + && detail::check_flags(h.ptr(), ExtraFlags & (array::c_style | array::f_style)); + } + +protected: + /// Create array from any object -- always returns a new reference + static PyObject *raw_array_t(PyObject *ptr) { + if (ptr == nullptr) { + PyErr_SetString(PyExc_ValueError, "cannot create a pybind11::array_t from a nullptr"); + return nullptr; + } + return detail::npy_api::get().PyArray_FromAny_( + ptr, dtype::of().release().ptr(), 0, 0, + detail::npy_api::NPY_ARRAY_ENSUREARRAY_ | ExtraFlags, nullptr); + } +}; + +template +struct format_descriptor::value>> { + static std::string format() { + return detail::npy_format_descriptor::type>::format(); + } +}; + +template struct format_descriptor { + static std::string format() { return std::to_string(N) + "s"; } +}; +template struct format_descriptor> { + static std::string format() { return std::to_string(N) + "s"; } +}; + +template +struct format_descriptor::value>> { + static std::string format() { + return format_descriptor< + typename std::remove_cv::type>::type>::format(); + } +}; + +template +struct format_descriptor::is_array>> { + static std::string format() { + using namespace detail; + static constexpr auto extents = _("(") + array_info::extents + _(")"); + return extents.text + format_descriptor>::format(); + } +}; + +PYBIND11_NAMESPACE_BEGIN(detail) +template +struct pyobject_caster> { + using type = array_t; + + bool load(handle src, bool convert) { + if (!convert && !type::check_(src)) + return false; + value = type::ensure(src); + return static_cast(value); + } + + static handle cast(const handle &src, return_value_policy /* policy */, handle /* parent */) { + return src.inc_ref(); + } + PYBIND11_TYPE_CASTER(type, handle_type_name::name); +}; + +template +struct compare_buffer_info::value>> { + static bool compare(const buffer_info& b) { + return npy_api::get().PyArray_EquivTypes_(dtype::of().ptr(), dtype(b).ptr()); + } +}; + +template +struct npy_format_descriptor_name; + +template +struct npy_format_descriptor_name::value>> { + static constexpr auto name = _::value>( + _("bool"), _::value>("numpy.int", "numpy.uint") + _() + ); +}; + +template +struct npy_format_descriptor_name::value>> { + static constexpr auto name = _::value || std::is_same::value>( + _("numpy.float") + _(), _("numpy.longdouble") + ); +}; + +template +struct npy_format_descriptor_name::value>> { + static constexpr auto name = _::value + || std::is_same::value>( + _("numpy.complex") + _(), _("numpy.longcomplex") + ); +}; + +template +struct npy_format_descriptor::value>> + : npy_format_descriptor_name { +private: + // NB: the order here must match the one in common.h + constexpr static const int values[15] = { + npy_api::NPY_BOOL_, + npy_api::NPY_BYTE_, npy_api::NPY_UBYTE_, npy_api::NPY_INT16_, npy_api::NPY_UINT16_, + npy_api::NPY_INT32_, npy_api::NPY_UINT32_, npy_api::NPY_INT64_, npy_api::NPY_UINT64_, + npy_api::NPY_FLOAT_, npy_api::NPY_DOUBLE_, npy_api::NPY_LONGDOUBLE_, + npy_api::NPY_CFLOAT_, npy_api::NPY_CDOUBLE_, npy_api::NPY_CLONGDOUBLE_ + }; + +public: + static constexpr int value = values[detail::is_fmt_numeric::index]; + + static pybind11::dtype dtype() { + if (auto ptr = npy_api::get().PyArray_DescrFromType_(value)) + return reinterpret_steal(ptr); + pybind11_fail("Unsupported buffer format!"); + } +}; + +#define PYBIND11_DECL_CHAR_FMT \ + static constexpr auto name = _("S") + _(); \ + static pybind11::dtype dtype() { return pybind11::dtype(std::string("S") + std::to_string(N)); } +template struct npy_format_descriptor { PYBIND11_DECL_CHAR_FMT }; +template struct npy_format_descriptor> { PYBIND11_DECL_CHAR_FMT }; +#undef PYBIND11_DECL_CHAR_FMT + +template struct npy_format_descriptor::is_array>> { +private: + using base_descr = npy_format_descriptor::type>; +public: + static_assert(!array_info::is_empty, "Zero-sized arrays are not supported"); + + static constexpr auto name = _("(") + array_info::extents + _(")") + base_descr::name; + static pybind11::dtype dtype() { + list shape; + array_info::append_extents(shape); + return pybind11::dtype::from_args(pybind11::make_tuple(base_descr::dtype(), shape)); + } +}; + +template struct npy_format_descriptor::value>> { +private: + using base_descr = npy_format_descriptor::type>; +public: + static constexpr auto name = base_descr::name; + static pybind11::dtype dtype() { return base_descr::dtype(); } +}; + +struct field_descriptor { + const char *name; + ssize_t offset; + ssize_t size; + std::string format; + dtype descr; +}; + +inline PYBIND11_NOINLINE void register_structured_dtype( + any_container fields, + const std::type_info& tinfo, ssize_t itemsize, + bool (*direct_converter)(PyObject *, void *&)) { + + auto& numpy_internals = get_numpy_internals(); + if (numpy_internals.get_type_info(tinfo, false)) + pybind11_fail("NumPy: dtype is already registered"); + + // Use ordered fields because order matters as of NumPy 1.14: + // https://docs.scipy.org/doc/numpy/release.html#multiple-field-indexing-assignment-of-structured-arrays + std::vector ordered_fields(std::move(fields)); + std::sort(ordered_fields.begin(), ordered_fields.end(), + [](const field_descriptor &a, const field_descriptor &b) { return a.offset < b.offset; }); + + list names, formats, offsets; + for (auto& field : ordered_fields) { + if (!field.descr) + pybind11_fail(std::string("NumPy: unsupported field dtype: `") + + field.name + "` @ " + tinfo.name()); + names.append(PYBIND11_STR_TYPE(field.name)); + formats.append(field.descr); + offsets.append(pybind11::int_(field.offset)); + } + auto dtype_ptr = pybind11::dtype(names, formats, offsets, itemsize).release().ptr(); + + // There is an existing bug in NumPy (as of v1.11): trailing bytes are + // not encoded explicitly into the format string. This will supposedly + // get fixed in v1.12; for further details, see these: + // - https://github.com/numpy/numpy/issues/7797 + // - https://github.com/numpy/numpy/pull/7798 + // Because of this, we won't use numpy's logic to generate buffer format + // strings and will just do it ourselves. + ssize_t offset = 0; + std::ostringstream oss; + // mark the structure as unaligned with '^', because numpy and C++ don't + // always agree about alignment (particularly for complex), and we're + // explicitly listing all our padding. This depends on none of the fields + // overriding the endianness. Putting the ^ in front of individual fields + // isn't guaranteed to work due to https://github.com/numpy/numpy/issues/9049 + oss << "^T{"; + for (auto& field : ordered_fields) { + if (field.offset > offset) + oss << (field.offset - offset) << 'x'; + oss << field.format << ':' << field.name << ':'; + offset = field.offset + field.size; + } + if (itemsize > offset) + oss << (itemsize - offset) << 'x'; + oss << '}'; + auto format_str = oss.str(); + + // Sanity check: verify that NumPy properly parses our buffer format string + auto& api = npy_api::get(); + auto arr = array(buffer_info(nullptr, itemsize, format_str, 1)); + if (!api.PyArray_EquivTypes_(dtype_ptr, arr.dtype().ptr())) + pybind11_fail("NumPy: invalid buffer descriptor!"); + + auto tindex = std::type_index(tinfo); + numpy_internals.registered_dtypes[tindex] = { dtype_ptr, format_str }; + get_internals().direct_conversions[tindex].push_back(direct_converter); +} + +template struct npy_format_descriptor { + static_assert(is_pod_struct::value, "Attempt to use a non-POD or unimplemented POD type as a numpy dtype"); + + static constexpr auto name = make_caster::name; + + static pybind11::dtype dtype() { + return reinterpret_borrow(dtype_ptr()); + } + + static std::string format() { + static auto format_str = get_numpy_internals().get_type_info(true)->format_str; + return format_str; + } + + static void register_dtype(any_container fields) { + register_structured_dtype(std::move(fields), typeid(typename std::remove_cv::type), + sizeof(T), &direct_converter); + } + +private: + static PyObject* dtype_ptr() { + static PyObject* ptr = get_numpy_internals().get_type_info(true)->dtype_ptr; + return ptr; + } + + static bool direct_converter(PyObject *obj, void*& value) { + auto& api = npy_api::get(); + if (!PyObject_TypeCheck(obj, api.PyVoidArrType_Type_)) + return false; + if (auto descr = reinterpret_steal(api.PyArray_DescrFromScalar_(obj))) { + if (api.PyArray_EquivTypes_(dtype_ptr(), descr.ptr())) { + value = ((PyVoidScalarObject_Proxy *) obj)->obval; + return true; + } + } + return false; + } +}; + +#ifdef __CLION_IDE__ // replace heavy macro with dummy code for the IDE (doesn't affect code) +# define PYBIND11_NUMPY_DTYPE(Type, ...) ((void)0) +# define PYBIND11_NUMPY_DTYPE_EX(Type, ...) ((void)0) +#else + +#define PYBIND11_FIELD_DESCRIPTOR_EX(T, Field, Name) \ + ::pybind11::detail::field_descriptor { \ + Name, offsetof(T, Field), sizeof(decltype(std::declval().Field)), \ + ::pybind11::format_descriptor().Field)>::format(), \ + ::pybind11::detail::npy_format_descriptor().Field)>::dtype() \ + } + +// Extract name, offset and format descriptor for a struct field +#define PYBIND11_FIELD_DESCRIPTOR(T, Field) PYBIND11_FIELD_DESCRIPTOR_EX(T, Field, #Field) + +// The main idea of this macro is borrowed from https://github.com/swansontec/map-macro +// (C) William Swanson, Paul Fultz +#define PYBIND11_EVAL0(...) __VA_ARGS__ +#define PYBIND11_EVAL1(...) PYBIND11_EVAL0 (PYBIND11_EVAL0 (PYBIND11_EVAL0 (__VA_ARGS__))) +#define PYBIND11_EVAL2(...) PYBIND11_EVAL1 (PYBIND11_EVAL1 (PYBIND11_EVAL1 (__VA_ARGS__))) +#define PYBIND11_EVAL3(...) PYBIND11_EVAL2 (PYBIND11_EVAL2 (PYBIND11_EVAL2 (__VA_ARGS__))) +#define PYBIND11_EVAL4(...) PYBIND11_EVAL3 (PYBIND11_EVAL3 (PYBIND11_EVAL3 (__VA_ARGS__))) +#define PYBIND11_EVAL(...) PYBIND11_EVAL4 (PYBIND11_EVAL4 (PYBIND11_EVAL4 (__VA_ARGS__))) +#define PYBIND11_MAP_END(...) +#define PYBIND11_MAP_OUT +#define PYBIND11_MAP_COMMA , +#define PYBIND11_MAP_GET_END() 0, PYBIND11_MAP_END +#define PYBIND11_MAP_NEXT0(test, next, ...) next PYBIND11_MAP_OUT +#define PYBIND11_MAP_NEXT1(test, next) PYBIND11_MAP_NEXT0 (test, next, 0) +#define PYBIND11_MAP_NEXT(test, next) PYBIND11_MAP_NEXT1 (PYBIND11_MAP_GET_END test, next) +#if defined(_MSC_VER) && !defined(__clang__) // MSVC is not as eager to expand macros, hence this workaround +#define PYBIND11_MAP_LIST_NEXT1(test, next) \ + PYBIND11_EVAL0 (PYBIND11_MAP_NEXT0 (test, PYBIND11_MAP_COMMA next, 0)) +#else +#define PYBIND11_MAP_LIST_NEXT1(test, next) \ + PYBIND11_MAP_NEXT0 (test, PYBIND11_MAP_COMMA next, 0) +#endif +#define PYBIND11_MAP_LIST_NEXT(test, next) \ + PYBIND11_MAP_LIST_NEXT1 (PYBIND11_MAP_GET_END test, next) +#define PYBIND11_MAP_LIST0(f, t, x, peek, ...) \ + f(t, x) PYBIND11_MAP_LIST_NEXT (peek, PYBIND11_MAP_LIST1) (f, t, peek, __VA_ARGS__) +#define PYBIND11_MAP_LIST1(f, t, x, peek, ...) \ + f(t, x) PYBIND11_MAP_LIST_NEXT (peek, PYBIND11_MAP_LIST0) (f, t, peek, __VA_ARGS__) +// PYBIND11_MAP_LIST(f, t, a1, a2, ...) expands to f(t, a1), f(t, a2), ... +#define PYBIND11_MAP_LIST(f, t, ...) \ + PYBIND11_EVAL (PYBIND11_MAP_LIST1 (f, t, __VA_ARGS__, (), 0)) + +#define PYBIND11_NUMPY_DTYPE(Type, ...) \ + ::pybind11::detail::npy_format_descriptor::register_dtype \ + (::std::vector<::pybind11::detail::field_descriptor> \ + {PYBIND11_MAP_LIST (PYBIND11_FIELD_DESCRIPTOR, Type, __VA_ARGS__)}) + +#if defined(_MSC_VER) && !defined(__clang__) +#define PYBIND11_MAP2_LIST_NEXT1(test, next) \ + PYBIND11_EVAL0 (PYBIND11_MAP_NEXT0 (test, PYBIND11_MAP_COMMA next, 0)) +#else +#define PYBIND11_MAP2_LIST_NEXT1(test, next) \ + PYBIND11_MAP_NEXT0 (test, PYBIND11_MAP_COMMA next, 0) +#endif +#define PYBIND11_MAP2_LIST_NEXT(test, next) \ + PYBIND11_MAP2_LIST_NEXT1 (PYBIND11_MAP_GET_END test, next) +#define PYBIND11_MAP2_LIST0(f, t, x1, x2, peek, ...) \ + f(t, x1, x2) PYBIND11_MAP2_LIST_NEXT (peek, PYBIND11_MAP2_LIST1) (f, t, peek, __VA_ARGS__) +#define PYBIND11_MAP2_LIST1(f, t, x1, x2, peek, ...) \ + f(t, x1, x2) PYBIND11_MAP2_LIST_NEXT (peek, PYBIND11_MAP2_LIST0) (f, t, peek, __VA_ARGS__) +// PYBIND11_MAP2_LIST(f, t, a1, a2, ...) expands to f(t, a1, a2), f(t, a3, a4), ... +#define PYBIND11_MAP2_LIST(f, t, ...) \ + PYBIND11_EVAL (PYBIND11_MAP2_LIST1 (f, t, __VA_ARGS__, (), 0)) + +#define PYBIND11_NUMPY_DTYPE_EX(Type, ...) \ + ::pybind11::detail::npy_format_descriptor::register_dtype \ + (::std::vector<::pybind11::detail::field_descriptor> \ + {PYBIND11_MAP2_LIST (PYBIND11_FIELD_DESCRIPTOR_EX, Type, __VA_ARGS__)}) + +#endif // __CLION_IDE__ + +class common_iterator { +public: + using container_type = std::vector; + using value_type = container_type::value_type; + using size_type = container_type::size_type; + + common_iterator() : p_ptr(0), m_strides() {} + + common_iterator(void* ptr, const container_type& strides, const container_type& shape) + : p_ptr(reinterpret_cast(ptr)), m_strides(strides.size()) { + m_strides.back() = static_cast(strides.back()); + for (size_type i = m_strides.size() - 1; i != 0; --i) { + size_type j = i - 1; + auto s = static_cast(shape[i]); + m_strides[j] = strides[j] + m_strides[i] - strides[i] * s; + } + } + + void increment(size_type dim) { + p_ptr += m_strides[dim]; + } + + void* data() const { + return p_ptr; + } + +private: + char* p_ptr; + container_type m_strides; +}; + +template class multi_array_iterator { +public: + using container_type = std::vector; + + multi_array_iterator(const std::array &buffers, + const container_type &shape) + : m_shape(shape.size()), m_index(shape.size(), 0), + m_common_iterator() { + + // Manual copy to avoid conversion warning if using std::copy + for (size_t i = 0; i < shape.size(); ++i) + m_shape[i] = shape[i]; + + container_type strides(shape.size()); + for (size_t i = 0; i < N; ++i) + init_common_iterator(buffers[i], shape, m_common_iterator[i], strides); + } + + multi_array_iterator& operator++() { + for (size_t j = m_index.size(); j != 0; --j) { + size_t i = j - 1; + if (++m_index[i] != m_shape[i]) { + increment_common_iterator(i); + break; + } else { + m_index[i] = 0; + } + } + return *this; + } + + template T* data() const { + return reinterpret_cast(m_common_iterator[K].data()); + } + +private: + + using common_iter = common_iterator; + + void init_common_iterator(const buffer_info &buffer, + const container_type &shape, + common_iter &iterator, + container_type &strides) { + auto buffer_shape_iter = buffer.shape.rbegin(); + auto buffer_strides_iter = buffer.strides.rbegin(); + auto shape_iter = shape.rbegin(); + auto strides_iter = strides.rbegin(); + + while (buffer_shape_iter != buffer.shape.rend()) { + if (*shape_iter == *buffer_shape_iter) + *strides_iter = *buffer_strides_iter; + else + *strides_iter = 0; + + ++buffer_shape_iter; + ++buffer_strides_iter; + ++shape_iter; + ++strides_iter; + } + + std::fill(strides_iter, strides.rend(), 0); + iterator = common_iter(buffer.ptr, strides, shape); + } + + void increment_common_iterator(size_t dim) { + for (auto &iter : m_common_iterator) + iter.increment(dim); + } + + container_type m_shape; + container_type m_index; + std::array m_common_iterator; +}; + +enum class broadcast_trivial { non_trivial, c_trivial, f_trivial }; + +// Populates the shape and number of dimensions for the set of buffers. Returns a broadcast_trivial +// enum value indicating whether the broadcast is "trivial"--that is, has each buffer being either a +// singleton or a full-size, C-contiguous (`c_trivial`) or Fortran-contiguous (`f_trivial`) storage +// buffer; returns `non_trivial` otherwise. +template +broadcast_trivial broadcast(const std::array &buffers, ssize_t &ndim, std::vector &shape) { + ndim = std::accumulate(buffers.begin(), buffers.end(), ssize_t(0), [](ssize_t res, const buffer_info &buf) { + return std::max(res, buf.ndim); + }); + + shape.clear(); + shape.resize((size_t) ndim, 1); + + // Figure out the output size, and make sure all input arrays conform (i.e. are either size 1 or + // the full size). + for (size_t i = 0; i < N; ++i) { + auto res_iter = shape.rbegin(); + auto end = buffers[i].shape.rend(); + for (auto shape_iter = buffers[i].shape.rbegin(); shape_iter != end; ++shape_iter, ++res_iter) { + const auto &dim_size_in = *shape_iter; + auto &dim_size_out = *res_iter; + + // Each input dimension can either be 1 or `n`, but `n` values must match across buffers + if (dim_size_out == 1) + dim_size_out = dim_size_in; + else if (dim_size_in != 1 && dim_size_in != dim_size_out) + pybind11_fail("pybind11::vectorize: incompatible size/dimension of inputs!"); + } + } + + bool trivial_broadcast_c = true; + bool trivial_broadcast_f = true; + for (size_t i = 0; i < N && (trivial_broadcast_c || trivial_broadcast_f); ++i) { + if (buffers[i].size == 1) + continue; + + // Require the same number of dimensions: + if (buffers[i].ndim != ndim) + return broadcast_trivial::non_trivial; + + // Require all dimensions be full-size: + if (!std::equal(buffers[i].shape.cbegin(), buffers[i].shape.cend(), shape.cbegin())) + return broadcast_trivial::non_trivial; + + // Check for C contiguity (but only if previous inputs were also C contiguous) + if (trivial_broadcast_c) { + ssize_t expect_stride = buffers[i].itemsize; + auto end = buffers[i].shape.crend(); + for (auto shape_iter = buffers[i].shape.crbegin(), stride_iter = buffers[i].strides.crbegin(); + trivial_broadcast_c && shape_iter != end; ++shape_iter, ++stride_iter) { + if (expect_stride == *stride_iter) + expect_stride *= *shape_iter; + else + trivial_broadcast_c = false; + } + } + + // Check for Fortran contiguity (if previous inputs were also F contiguous) + if (trivial_broadcast_f) { + ssize_t expect_stride = buffers[i].itemsize; + auto end = buffers[i].shape.cend(); + for (auto shape_iter = buffers[i].shape.cbegin(), stride_iter = buffers[i].strides.cbegin(); + trivial_broadcast_f && shape_iter != end; ++shape_iter, ++stride_iter) { + if (expect_stride == *stride_iter) + expect_stride *= *shape_iter; + else + trivial_broadcast_f = false; + } + } + } + + return + trivial_broadcast_c ? broadcast_trivial::c_trivial : + trivial_broadcast_f ? broadcast_trivial::f_trivial : + broadcast_trivial::non_trivial; +} + +template +struct vectorize_arg { + static_assert(!std::is_rvalue_reference::value, "Functions with rvalue reference arguments cannot be vectorized"); + // The wrapped function gets called with this type: + using call_type = remove_reference_t; + // Is this a vectorized argument? + static constexpr bool vectorize = + satisfies_any_of::value && + satisfies_none_of::value && + (!std::is_reference::value || + (std::is_lvalue_reference::value && std::is_const::value)); + // Accept this type: an array for vectorized types, otherwise the type as-is: + using type = conditional_t, array::forcecast>, T>; +}; + + +// py::vectorize when a return type is present +template +struct vectorize_returned_array { + using Type = array_t; + + static Type create(broadcast_trivial trivial, const std::vector &shape) { + if (trivial == broadcast_trivial::f_trivial) + return array_t(shape); + else + return array_t(shape); + } + + static Return *mutable_data(Type &array) { + return array.mutable_data(); + } + + static Return call(Func &f, Args &... args) { + return f(args...); + } + + static void call(Return *out, size_t i, Func &f, Args &... args) { + out[i] = f(args...); + } +}; + +// py::vectorize when a return type is not present +template +struct vectorize_returned_array { + using Type = none; + + static Type create(broadcast_trivial, const std::vector &) { + return none(); + } + + static void *mutable_data(Type &) { + return nullptr; + } + + static detail::void_type call(Func &f, Args &... args) { + f(args...); + return {}; + } + + static void call(void *, size_t, Func &f, Args &... args) { + f(args...); + } +}; + + +template +struct vectorize_helper { + +// NVCC for some reason breaks if NVectorized is private +#ifdef __CUDACC__ +public: +#else +private: +#endif + + static constexpr size_t N = sizeof...(Args); + static constexpr size_t NVectorized = constexpr_sum(vectorize_arg::vectorize...); + static_assert(NVectorized >= 1, + "pybind11::vectorize(...) requires a function with at least one vectorizable argument"); + +public: + template + explicit vectorize_helper(T &&f) : f(std::forward(f)) { } + + object operator()(typename vectorize_arg::type... args) { + return run(args..., + make_index_sequence(), + select_indices::vectorize...>(), + make_index_sequence()); + } + +private: + remove_reference_t f; + + // Internal compiler error in MSVC 19.16.27025.1 (Visual Studio 2017 15.9.4), when compiling with "/permissive-" flag + // when arg_call_types is manually inlined. + using arg_call_types = std::tuple::call_type...>; + template using param_n_t = typename std::tuple_element::type; + + using returned_array = vectorize_returned_array; + + // Runs a vectorized function given arguments tuple and three index sequences: + // - Index is the full set of 0 ... (N-1) argument indices; + // - VIndex is the subset of argument indices with vectorized parameters, letting us access + // vectorized arguments (anything not in this sequence is passed through) + // - BIndex is a incremental sequence (beginning at 0) of the same size as VIndex, so that + // we can store vectorized buffer_infos in an array (argument VIndex has its buffer at + // index BIndex in the array). + template object run( + typename vectorize_arg::type &...args, + index_sequence i_seq, index_sequence vi_seq, index_sequence bi_seq) { + + // Pointers to values the function was called with; the vectorized ones set here will start + // out as array_t pointers, but they will be changed them to T pointers before we make + // call the wrapped function. Non-vectorized pointers are left as-is. + std::array params{{ &args... }}; + + // The array of `buffer_info`s of vectorized arguments: + std::array buffers{{ reinterpret_cast(params[VIndex])->request()... }}; + + /* Determine dimensions parameters of output array */ + ssize_t nd = 0; + std::vector shape(0); + auto trivial = broadcast(buffers, nd, shape); + auto ndim = (size_t) nd; + + size_t size = std::accumulate(shape.begin(), shape.end(), (size_t) 1, std::multiplies()); + + // If all arguments are 0-dimension arrays (i.e. single values) return a plain value (i.e. + // not wrapped in an array). + if (size == 1 && ndim == 0) { + PYBIND11_EXPAND_SIDE_EFFECTS(params[VIndex] = buffers[BIndex].ptr); + return cast(returned_array::call(f, *reinterpret_cast *>(params[Index])...)); + } + + auto result = returned_array::create(trivial, shape); + + if (size == 0) return std::move(result); + + /* Call the function */ + auto mutable_data = returned_array::mutable_data(result); + if (trivial == broadcast_trivial::non_trivial) + apply_broadcast(buffers, params, mutable_data, size, shape, i_seq, vi_seq, bi_seq); + else + apply_trivial(buffers, params, mutable_data, size, i_seq, vi_seq, bi_seq); + + return std::move(result); + } + + template + void apply_trivial(std::array &buffers, + std::array ¶ms, + Return *out, + size_t size, + index_sequence, index_sequence, index_sequence) { + + // Initialize an array of mutable byte references and sizes with references set to the + // appropriate pointer in `params`; as we iterate, we'll increment each pointer by its size + // (except for singletons, which get an increment of 0). + std::array, NVectorized> vecparams{{ + std::pair( + reinterpret_cast(params[VIndex] = buffers[BIndex].ptr), + buffers[BIndex].size == 1 ? 0 : sizeof(param_n_t) + )... + }}; + + for (size_t i = 0; i < size; ++i) { + returned_array::call(out, i, f, *reinterpret_cast *>(params[Index])...); + for (auto &x : vecparams) x.first += x.second; + } + } + + template + void apply_broadcast(std::array &buffers, + std::array ¶ms, + Return *out, + size_t size, + const std::vector &output_shape, + index_sequence, index_sequence, index_sequence) { + + multi_array_iterator input_iter(buffers, output_shape); + + for (size_t i = 0; i < size; ++i, ++input_iter) { + PYBIND11_EXPAND_SIDE_EFFECTS(( + params[VIndex] = input_iter.template data() + )); + returned_array::call(out, i, f, *reinterpret_cast *>(std::get(params))...); + } + } +}; + +template +vectorize_helper +vectorize_extractor(const Func &f, Return (*) (Args ...)) { + return detail::vectorize_helper(f); +} + +template struct handle_type_name> { + static constexpr auto name = _("numpy.ndarray[") + npy_format_descriptor::name + _("]"); +}; + +PYBIND11_NAMESPACE_END(detail) + +// Vanilla pointer vectorizer: +template +detail::vectorize_helper +vectorize(Return (*f) (Args ...)) { + return detail::vectorize_helper(f); +} + +// lambda vectorizer: +template ::value, int> = 0> +auto vectorize(Func &&f) -> decltype( + detail::vectorize_extractor(std::forward(f), (detail::function_signature_t *) nullptr)) { + return detail::vectorize_extractor(std::forward(f), (detail::function_signature_t *) nullptr); +} + +// Vectorize a class method (non-const): +template ())), Return, Class *, Args...>> +Helper vectorize(Return (Class::*f)(Args...)) { + return Helper(std::mem_fn(f)); +} + +// Vectorize a class method (const): +template ())), Return, const Class *, Args...>> +Helper vectorize(Return (Class::*f)(Args...) const) { + return Helper(std::mem_fn(f)); +} + +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) + +#if defined(_MSC_VER) +#pragma warning(pop) +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/operators.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/operators.h new file mode 100644 index 0000000000000000000000000000000000000000..086cb4cfd838797767dd3b3caa275bdb4348fc8e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/operators.h @@ -0,0 +1,173 @@ +/* + pybind11/operator.h: Metatemplates for operator overloading + + Copyright (c) 2016 Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "pybind11.h" + +#if defined(__clang__) && !defined(__INTEL_COMPILER) +# pragma clang diagnostic ignored "-Wunsequenced" // multiple unsequenced modifications to 'self' (when using def(py::self OP Type())) +#elif defined(_MSC_VER) +# pragma warning(push) +# pragma warning(disable: 4127) // warning C4127: Conditional expression is constant +#endif + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) +PYBIND11_NAMESPACE_BEGIN(detail) + +/// Enumeration with all supported operator types +enum op_id : int { + op_add, op_sub, op_mul, op_div, op_mod, op_divmod, op_pow, op_lshift, + op_rshift, op_and, op_xor, op_or, op_neg, op_pos, op_abs, op_invert, + op_int, op_long, op_float, op_str, op_cmp, op_gt, op_ge, op_lt, op_le, + op_eq, op_ne, op_iadd, op_isub, op_imul, op_idiv, op_imod, op_ilshift, + op_irshift, op_iand, op_ixor, op_ior, op_complex, op_bool, op_nonzero, + op_repr, op_truediv, op_itruediv, op_hash +}; + +enum op_type : int { + op_l, /* base type on left */ + op_r, /* base type on right */ + op_u /* unary operator */ +}; + +struct self_t { }; +static const self_t self = self_t(); + +/// Type for an unused type slot +struct undefined_t { }; + +/// Don't warn about an unused variable +inline self_t __self() { return self; } + +/// base template of operator implementations +template struct op_impl { }; + +/// Operator implementation generator +template struct op_ { + template void execute(Class &cl, const Extra&... extra) const { + using Base = typename Class::type; + using L_type = conditional_t::value, Base, L>; + using R_type = conditional_t::value, Base, R>; + using op = op_impl; + cl.def(op::name(), &op::execute, is_operator(), extra...); + #if PY_MAJOR_VERSION < 3 + if (id == op_truediv || id == op_itruediv) + cl.def(id == op_itruediv ? "__idiv__" : ot == op_l ? "__div__" : "__rdiv__", + &op::execute, is_operator(), extra...); + #endif + } + template void execute_cast(Class &cl, const Extra&... extra) const { + using Base = typename Class::type; + using L_type = conditional_t::value, Base, L>; + using R_type = conditional_t::value, Base, R>; + using op = op_impl; + cl.def(op::name(), &op::execute_cast, is_operator(), extra...); + #if PY_MAJOR_VERSION < 3 + if (id == op_truediv || id == op_itruediv) + cl.def(id == op_itruediv ? "__idiv__" : ot == op_l ? "__div__" : "__rdiv__", + &op::execute, is_operator(), extra...); + #endif + } +}; + +#define PYBIND11_BINARY_OPERATOR(id, rid, op, expr) \ +template struct op_impl { \ + static char const* name() { return "__" #id "__"; } \ + static auto execute(const L &l, const R &r) -> decltype(expr) { return (expr); } \ + static B execute_cast(const L &l, const R &r) { return B(expr); } \ +}; \ +template struct op_impl { \ + static char const* name() { return "__" #rid "__"; } \ + static auto execute(const R &r, const L &l) -> decltype(expr) { return (expr); } \ + static B execute_cast(const R &r, const L &l) { return B(expr); } \ +}; \ +inline op_ op(const self_t &, const self_t &) { \ + return op_(); \ +} \ +template op_ op(const self_t &, const T &) { \ + return op_(); \ +} \ +template op_ op(const T &, const self_t &) { \ + return op_(); \ +} + +#define PYBIND11_INPLACE_OPERATOR(id, op, expr) \ +template struct op_impl { \ + static char const* name() { return "__" #id "__"; } \ + static auto execute(L &l, const R &r) -> decltype(expr) { return expr; } \ + static B execute_cast(L &l, const R &r) { return B(expr); } \ +}; \ +template op_ op(const self_t &, const T &) { \ + return op_(); \ +} + +#define PYBIND11_UNARY_OPERATOR(id, op, expr) \ +template struct op_impl { \ + static char const* name() { return "__" #id "__"; } \ + static auto execute(const L &l) -> decltype(expr) { return expr; } \ + static B execute_cast(const L &l) { return B(expr); } \ +}; \ +inline op_ op(const self_t &) { \ + return op_(); \ +} + +PYBIND11_BINARY_OPERATOR(sub, rsub, operator-, l - r) +PYBIND11_BINARY_OPERATOR(add, radd, operator+, l + r) +PYBIND11_BINARY_OPERATOR(mul, rmul, operator*, l * r) +PYBIND11_BINARY_OPERATOR(truediv, rtruediv, operator/, l / r) +PYBIND11_BINARY_OPERATOR(mod, rmod, operator%, l % r) +PYBIND11_BINARY_OPERATOR(lshift, rlshift, operator<<, l << r) +PYBIND11_BINARY_OPERATOR(rshift, rrshift, operator>>, l >> r) +PYBIND11_BINARY_OPERATOR(and, rand, operator&, l & r) +PYBIND11_BINARY_OPERATOR(xor, rxor, operator^, l ^ r) +PYBIND11_BINARY_OPERATOR(eq, eq, operator==, l == r) +PYBIND11_BINARY_OPERATOR(ne, ne, operator!=, l != r) +PYBIND11_BINARY_OPERATOR(or, ror, operator|, l | r) +PYBIND11_BINARY_OPERATOR(gt, lt, operator>, l > r) +PYBIND11_BINARY_OPERATOR(ge, le, operator>=, l >= r) +PYBIND11_BINARY_OPERATOR(lt, gt, operator<, l < r) +PYBIND11_BINARY_OPERATOR(le, ge, operator<=, l <= r) +//PYBIND11_BINARY_OPERATOR(pow, rpow, pow, std::pow(l, r)) +PYBIND11_INPLACE_OPERATOR(iadd, operator+=, l += r) +PYBIND11_INPLACE_OPERATOR(isub, operator-=, l -= r) +PYBIND11_INPLACE_OPERATOR(imul, operator*=, l *= r) +PYBIND11_INPLACE_OPERATOR(itruediv, operator/=, l /= r) +PYBIND11_INPLACE_OPERATOR(imod, operator%=, l %= r) +PYBIND11_INPLACE_OPERATOR(ilshift, operator<<=, l <<= r) +PYBIND11_INPLACE_OPERATOR(irshift, operator>>=, l >>= r) +PYBIND11_INPLACE_OPERATOR(iand, operator&=, l &= r) +PYBIND11_INPLACE_OPERATOR(ixor, operator^=, l ^= r) +PYBIND11_INPLACE_OPERATOR(ior, operator|=, l |= r) +PYBIND11_UNARY_OPERATOR(neg, operator-, -l) +PYBIND11_UNARY_OPERATOR(pos, operator+, +l) +// WARNING: This usage of `abs` should only be done for existing STL overloads. +// Adding overloads directly in to the `std::` namespace is advised against: +// https://en.cppreference.com/w/cpp/language/extending_std +PYBIND11_UNARY_OPERATOR(abs, abs, std::abs(l)) +PYBIND11_UNARY_OPERATOR(hash, hash, std::hash()(l)) +PYBIND11_UNARY_OPERATOR(invert, operator~, (~l)) +PYBIND11_UNARY_OPERATOR(bool, operator!, !!l) +PYBIND11_UNARY_OPERATOR(int, int_, (int) l) +PYBIND11_UNARY_OPERATOR(float, float_, (double) l) + +#undef PYBIND11_BINARY_OPERATOR +#undef PYBIND11_INPLACE_OPERATOR +#undef PYBIND11_UNARY_OPERATOR +PYBIND11_NAMESPACE_END(detail) + +using detail::self; +// Add named operators so that they are accessible via `py::`. +using detail::hash; + +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) + +#if defined(_MSC_VER) +# pragma warning(pop) +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/options.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/options.h new file mode 100644 index 0000000000000000000000000000000000000000..d74db1c68dddb3436cc0fb2674a6ef32ac77d5fd --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/options.h @@ -0,0 +1,65 @@ +/* + pybind11/options.h: global settings that are configurable at runtime. + + Copyright (c) 2016 Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "detail/common.h" + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) + +class options { +public: + + // Default RAII constructor, which leaves settings as they currently are. + options() : previous_state(global_state()) {} + + // Class is non-copyable. + options(const options&) = delete; + options& operator=(const options&) = delete; + + // Destructor, which restores settings that were in effect before. + ~options() { + global_state() = previous_state; + } + + // Setter methods (affect the global state): + + options& disable_user_defined_docstrings() & { global_state().show_user_defined_docstrings = false; return *this; } + + options& enable_user_defined_docstrings() & { global_state().show_user_defined_docstrings = true; return *this; } + + options& disable_function_signatures() & { global_state().show_function_signatures = false; return *this; } + + options& enable_function_signatures() & { global_state().show_function_signatures = true; return *this; } + + // Getter methods (return the global state): + + static bool show_user_defined_docstrings() { return global_state().show_user_defined_docstrings; } + + static bool show_function_signatures() { return global_state().show_function_signatures; } + + // This type is not meant to be allocated on the heap. + void* operator new(size_t) = delete; + +private: + + struct state { + bool show_user_defined_docstrings = true; //< Include user-supplied texts in docstrings. + bool show_function_signatures = true; //< Include auto-generated function signatures in docstrings. + }; + + static state &global_state() { + static state instance; + return instance; + } + + state previous_state; +}; + +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/pybind11.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/pybind11.h new file mode 100644 index 0000000000000000000000000000000000000000..648300eef264bf136eadeb803b370f25fb227b40 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/pybind11.h @@ -0,0 +1,2288 @@ +/* + pybind11/pybind11.h: Main header file of the C++11 python + binding generator library + + Copyright (c) 2016 Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#if defined(__INTEL_COMPILER) +# pragma warning push +# pragma warning disable 68 // integer conversion resulted in a change of sign +# pragma warning disable 186 // pointless comparison of unsigned integer with zero +# pragma warning disable 878 // incompatible exception specifications +# pragma warning disable 1334 // the "template" keyword used for syntactic disambiguation may only be used within a template +# pragma warning disable 1682 // implicit conversion of a 64-bit integral type to a smaller integral type (potential portability problem) +# pragma warning disable 1786 // function "strdup" was declared deprecated +# pragma warning disable 1875 // offsetof applied to non-POD (Plain Old Data) types is nonstandard +# pragma warning disable 2196 // warning #2196: routine is both "inline" and "noinline" +#elif defined(_MSC_VER) +# pragma warning(push) +# pragma warning(disable: 4100) // warning C4100: Unreferenced formal parameter +# pragma warning(disable: 4127) // warning C4127: Conditional expression is constant +# pragma warning(disable: 4512) // warning C4512: Assignment operator was implicitly defined as deleted +# pragma warning(disable: 4800) // warning C4800: 'int': forcing value to bool 'true' or 'false' (performance warning) +# pragma warning(disable: 4996) // warning C4996: The POSIX name for this item is deprecated. Instead, use the ISO C and C++ conformant name +# pragma warning(disable: 4702) // warning C4702: unreachable code +# pragma warning(disable: 4522) // warning C4522: multiple assignment operators specified +# pragma warning(disable: 4505) // warning C4505: 'PySlice_GetIndicesEx': unreferenced local function has been removed (PyPy only) +#elif defined(__GNUG__) && !defined(__clang__) +# pragma GCC diagnostic push +# pragma GCC diagnostic ignored "-Wunused-but-set-parameter" +# pragma GCC diagnostic ignored "-Wunused-but-set-variable" +# pragma GCC diagnostic ignored "-Wmissing-field-initializers" +# pragma GCC diagnostic ignored "-Wstrict-aliasing" +# pragma GCC diagnostic ignored "-Wattributes" +# if __GNUC__ >= 7 +# pragma GCC diagnostic ignored "-Wnoexcept-type" +# endif +#endif + +#include "attr.h" +#include "gil.h" +#include "options.h" +#include "detail/class.h" +#include "detail/init.h" + +#include +#include +#include +#include + +#if defined(__GNUG__) && !defined(__clang__) +# include +#endif + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) + +/// Wraps an arbitrary C++ function/method/lambda function/.. into a callable Python object +class cpp_function : public function { +public: + cpp_function() = default; + cpp_function(std::nullptr_t) { } + + /// Construct a cpp_function from a vanilla function pointer + template + cpp_function(Return (*f)(Args...), const Extra&... extra) { + initialize(f, f, extra...); + } + + /// Construct a cpp_function from a lambda function (possibly with internal state) + template ::value>> + cpp_function(Func &&f, const Extra&... extra) { + initialize(std::forward(f), + (detail::function_signature_t *) nullptr, extra...); + } + + /// Construct a cpp_function from a class method (non-const, no ref-qualifier) + template + cpp_function(Return (Class::*f)(Arg...), const Extra&... extra) { + initialize([f](Class *c, Arg... args) -> Return { return (c->*f)(std::forward(args)...); }, + (Return (*) (Class *, Arg...)) nullptr, extra...); + } + + /// Construct a cpp_function from a class method (non-const, lvalue ref-qualifier) + /// A copy of the overload for non-const functions without explicit ref-qualifier + /// but with an added `&`. + template + cpp_function(Return (Class::*f)(Arg...)&, const Extra&... extra) { + initialize([f](Class *c, Arg... args) -> Return { return (c->*f)(args...); }, + (Return (*) (Class *, Arg...)) nullptr, extra...); + } + + /// Construct a cpp_function from a class method (const, no ref-qualifier) + template + cpp_function(Return (Class::*f)(Arg...) const, const Extra&... extra) { + initialize([f](const Class *c, Arg... args) -> Return { return (c->*f)(std::forward(args)...); }, + (Return (*)(const Class *, Arg ...)) nullptr, extra...); + } + + /// Construct a cpp_function from a class method (const, lvalue ref-qualifier) + /// A copy of the overload for const functions without explicit ref-qualifier + /// but with an added `&`. + template + cpp_function(Return (Class::*f)(Arg...) const&, const Extra&... extra) { + initialize([f](const Class *c, Arg... args) -> Return { return (c->*f)(args...); }, + (Return (*)(const Class *, Arg ...)) nullptr, extra...); + } + + /// Return the function name + object name() const { return attr("__name__"); } + +protected: + struct InitializingFunctionRecordDeleter { + // `destruct(function_record, false)`: `initialize_generic` copies strings and + // takes care of cleaning up in case of exceptions. So pass `false` to `free_strings`. + void operator()(detail::function_record * rec) { destruct(rec, false); } + }; + using unique_function_record = std::unique_ptr; + + /// Space optimization: don't inline this frequently instantiated fragment + PYBIND11_NOINLINE unique_function_record make_function_record() { + return unique_function_record(new detail::function_record()); + } + + /// Special internal constructor for functors, lambda functions, etc. + template + void initialize(Func &&f, Return (*)(Args...), const Extra&... extra) { + using namespace detail; + struct capture { remove_reference_t f; }; + + /* Store the function including any extra state it might have (e.g. a lambda capture object) */ + // The unique_ptr makes sure nothing is leaked in case of an exception. + auto unique_rec = make_function_record(); + auto rec = unique_rec.get(); + + /* Store the capture object directly in the function record if there is enough space */ + if (sizeof(capture) <= sizeof(rec->data)) { + /* Without these pragmas, GCC warns that there might not be + enough space to use the placement new operator. However, the + 'if' statement above ensures that this is the case. */ +#if defined(__GNUG__) && !defined(__clang__) && __GNUC__ >= 6 +# pragma GCC diagnostic push +# pragma GCC diagnostic ignored "-Wplacement-new" +#endif + new ((capture *) &rec->data) capture { std::forward(f) }; +#if defined(__GNUG__) && !defined(__clang__) && __GNUC__ >= 6 +# pragma GCC diagnostic pop +#endif + if (!std::is_trivially_destructible::value) + rec->free_data = [](function_record *r) { ((capture *) &r->data)->~capture(); }; + } else { + rec->data[0] = new capture { std::forward(f) }; + rec->free_data = [](function_record *r) { delete ((capture *) r->data[0]); }; + } + + /* Type casters for the function arguments and return value */ + using cast_in = argument_loader; + using cast_out = make_caster< + conditional_t::value, void_type, Return> + >; + + static_assert(expected_num_args(sizeof...(Args), cast_in::has_args, cast_in::has_kwargs), + "The number of argument annotations does not match the number of function arguments"); + + /* Dispatch code which converts function arguments and performs the actual function call */ + rec->impl = [](function_call &call) -> handle { + cast_in args_converter; + + /* Try to cast the function arguments into the C++ domain */ + if (!args_converter.load_args(call)) + return PYBIND11_TRY_NEXT_OVERLOAD; + + /* Invoke call policy pre-call hook */ + process_attributes::precall(call); + + /* Get a pointer to the capture object */ + auto data = (sizeof(capture) <= sizeof(call.func.data) + ? &call.func.data : call.func.data[0]); + auto *cap = const_cast(reinterpret_cast(data)); + + /* Override policy for rvalues -- usually to enforce rvp::move on an rvalue */ + return_value_policy policy = return_value_policy_override::policy(call.func.policy); + + /* Function scope guard -- defaults to the compile-to-nothing `void_type` */ + using Guard = extract_guard_t; + + /* Perform the function call */ + handle result = cast_out::cast( + std::move(args_converter).template call(cap->f), policy, call.parent); + + /* Invoke call policy post-call hook */ + process_attributes::postcall(call, result); + + return result; + }; + + /* Process any user-provided function attributes */ + process_attributes::init(extra..., rec); + + { + constexpr bool has_kw_only_args = any_of...>::value, + has_pos_only_args = any_of...>::value, + has_args = any_of...>::value, + has_arg_annotations = any_of...>::value; + static_assert(has_arg_annotations || !has_kw_only_args, "py::kw_only requires the use of argument annotations"); + static_assert(has_arg_annotations || !has_pos_only_args, "py::pos_only requires the use of argument annotations (for docstrings and aligning the annotations to the argument)"); + static_assert(!(has_args && has_kw_only_args), "py::kw_only cannot be combined with a py::args argument"); + } + + /* Generate a readable signature describing the function's arguments and return value types */ + static constexpr auto signature = _("(") + cast_in::arg_names + _(") -> ") + cast_out::name; + PYBIND11_DESCR_CONSTEXPR auto types = decltype(signature)::types(); + + /* Register the function with Python from generic (non-templated) code */ + // Pass on the ownership over the `unique_rec` to `initialize_generic`. `rec` stays valid. + initialize_generic(std::move(unique_rec), signature.text, types.data(), sizeof...(Args)); + + if (cast_in::has_args) rec->has_args = true; + if (cast_in::has_kwargs) rec->has_kwargs = true; + + /* Stash some additional information used by an important optimization in 'functional.h' */ + using FunctionType = Return (*)(Args...); + constexpr bool is_function_ptr = + std::is_convertible::value && + sizeof(capture) == sizeof(void *); + if (is_function_ptr) { + rec->is_stateless = true; + rec->data[1] = const_cast(reinterpret_cast(&typeid(FunctionType))); + } + } + + // Utility class that keeps track of all duplicated strings, and cleans them up in its destructor, + // unless they are released. Basically a RAII-solution to deal with exceptions along the way. + class strdup_guard { + public: + ~strdup_guard() { + for (auto s : strings) + std::free(s); + } + char *operator()(const char *s) { + auto t = strdup(s); + strings.push_back(t); + return t; + } + void release() { + strings.clear(); + } + private: + std::vector strings; + }; + + /// Register a function call with Python (generic non-templated code goes here) + void initialize_generic(unique_function_record &&unique_rec, const char *text, + const std::type_info *const *types, size_t args) { + // Do NOT receive `unique_rec` by value. If this function fails to move out the unique_ptr, + // we do not want this to destuct the pointer. `initialize` (the caller) still relies on the + // pointee being alive after this call. Only move out if a `capsule` is going to keep it alive. + auto rec = unique_rec.get(); + + // Keep track of strdup'ed strings, and clean them up as long as the function's capsule + // has not taken ownership yet (when `unique_rec.release()` is called). + // Note: This cannot easily be fixed by a `unique_ptr` with custom deleter, because the strings + // are only referenced before strdup'ing. So only *after* the following block could `destruct` + // safely be called, but even then, `repr` could still throw in the middle of copying all strings. + strdup_guard guarded_strdup; + + /* Create copies of all referenced C-style strings */ + rec->name = guarded_strdup(rec->name ? rec->name : ""); + if (rec->doc) rec->doc = guarded_strdup(rec->doc); + for (auto &a: rec->args) { + if (a.name) + a.name = guarded_strdup(a.name); + if (a.descr) + a.descr = guarded_strdup(a.descr); + else if (a.value) + a.descr = guarded_strdup(repr(a.value).cast().c_str()); + } + + rec->is_constructor = !strcmp(rec->name, "__init__") || !strcmp(rec->name, "__setstate__"); + +#if !defined(NDEBUG) && !defined(PYBIND11_DISABLE_NEW_STYLE_INIT_WARNING) + if (rec->is_constructor && !rec->is_new_style_constructor) { + const auto class_name = detail::get_fully_qualified_tp_name((PyTypeObject *) rec->scope.ptr()); + const auto func_name = std::string(rec->name); + PyErr_WarnEx( + PyExc_FutureWarning, + ("pybind11-bound class '" + class_name + "' is using an old-style " + "placement-new '" + func_name + "' which has been deprecated. See " + "the upgrade guide in pybind11's docs. This message is only visible " + "when compiled in debug mode.").c_str(), 0 + ); + } +#endif + + /* Generate a proper function signature */ + std::string signature; + size_t type_index = 0, arg_index = 0; + for (auto *pc = text; *pc != '\0'; ++pc) { + const auto c = *pc; + + if (c == '{') { + // Write arg name for everything except *args and **kwargs. + if (*(pc + 1) == '*') + continue; + // Separator for keyword-only arguments, placed before the kw + // arguments start + if (rec->nargs_kw_only > 0 && arg_index + rec->nargs_kw_only == args) + signature += "*, "; + if (arg_index < rec->args.size() && rec->args[arg_index].name) { + signature += rec->args[arg_index].name; + } else if (arg_index == 0 && rec->is_method) { + signature += "self"; + } else { + signature += "arg" + std::to_string(arg_index - (rec->is_method ? 1 : 0)); + } + signature += ": "; + } else if (c == '}') { + // Write default value if available. + if (arg_index < rec->args.size() && rec->args[arg_index].descr) { + signature += " = "; + signature += rec->args[arg_index].descr; + } + // Separator for positional-only arguments (placed after the + // argument, rather than before like * + if (rec->nargs_pos_only > 0 && (arg_index + 1) == rec->nargs_pos_only) + signature += ", /"; + arg_index++; + } else if (c == '%') { + const std::type_info *t = types[type_index++]; + if (!t) + pybind11_fail("Internal error while parsing type signature (1)"); + if (auto tinfo = detail::get_type_info(*t)) { + handle th((PyObject *) tinfo->type); + signature += + th.attr("__module__").cast() + "." + + th.attr("__qualname__").cast(); // Python 3.3+, but we backport it to earlier versions + } else if (rec->is_new_style_constructor && arg_index == 0) { + // A new-style `__init__` takes `self` as `value_and_holder`. + // Rewrite it to the proper class type. + signature += + rec->scope.attr("__module__").cast() + "." + + rec->scope.attr("__qualname__").cast(); + } else { + std::string tname(t->name()); + detail::clean_type_id(tname); + signature += tname; + } + } else { + signature += c; + } + } + + if (arg_index != args || types[type_index] != nullptr) + pybind11_fail("Internal error while parsing type signature (2)"); + +#if PY_MAJOR_VERSION < 3 + if (strcmp(rec->name, "__next__") == 0) { + std::free(rec->name); + rec->name = guarded_strdup("next"); + } else if (strcmp(rec->name, "__bool__") == 0) { + std::free(rec->name); + rec->name = guarded_strdup("__nonzero__"); + } +#endif + rec->signature = guarded_strdup(signature.c_str()); + rec->args.shrink_to_fit(); + rec->nargs = (std::uint16_t) args; + + if (rec->sibling && PYBIND11_INSTANCE_METHOD_CHECK(rec->sibling.ptr())) + rec->sibling = PYBIND11_INSTANCE_METHOD_GET_FUNCTION(rec->sibling.ptr()); + + detail::function_record *chain = nullptr, *chain_start = rec; + if (rec->sibling) { + if (PyCFunction_Check(rec->sibling.ptr())) { + auto rec_capsule = reinterpret_borrow(PyCFunction_GET_SELF(rec->sibling.ptr())); + chain = (detail::function_record *) rec_capsule; + /* Never append a method to an overload chain of a parent class; + instead, hide the parent's overloads in this case */ + if (!chain->scope.is(rec->scope)) + chain = nullptr; + } + // Don't trigger for things like the default __init__, which are wrapper_descriptors that we are intentionally replacing + else if (!rec->sibling.is_none() && rec->name[0] != '_') + pybind11_fail("Cannot overload existing non-function object \"" + std::string(rec->name) + + "\" with a function of the same name"); + } + + if (!chain) { + /* No existing overload was found, create a new function object */ + rec->def = new PyMethodDef(); + std::memset(rec->def, 0, sizeof(PyMethodDef)); + rec->def->ml_name = rec->name; + rec->def->ml_meth = reinterpret_cast(reinterpret_cast(*dispatcher)); + rec->def->ml_flags = METH_VARARGS | METH_KEYWORDS; + + capsule rec_capsule(unique_rec.release(), [](void *ptr) { + destruct((detail::function_record *) ptr); + }); + guarded_strdup.release(); + + object scope_module; + if (rec->scope) { + if (hasattr(rec->scope, "__module__")) { + scope_module = rec->scope.attr("__module__"); + } else if (hasattr(rec->scope, "__name__")) { + scope_module = rec->scope.attr("__name__"); + } + } + + m_ptr = PyCFunction_NewEx(rec->def, rec_capsule.ptr(), scope_module.ptr()); + if (!m_ptr) + pybind11_fail("cpp_function::cpp_function(): Could not allocate function object"); + } else { + /* Append at the beginning or end of the overload chain */ + m_ptr = rec->sibling.ptr(); + inc_ref(); + if (chain->is_method != rec->is_method) + pybind11_fail("overloading a method with both static and instance methods is not supported; " + #if defined(NDEBUG) + "compile in debug mode for more details" + #else + "error while attempting to bind " + std::string(rec->is_method ? "instance" : "static") + " method " + + std::string(pybind11::str(rec->scope.attr("__name__"))) + "." + std::string(rec->name) + signature + #endif + ); + + if (rec->prepend) { + // Beginning of chain; we need to replace the capsule's current head-of-the-chain + // pointer with this one, then make this one point to the previous head of the + // chain. + chain_start = rec; + rec->next = chain; + auto rec_capsule = reinterpret_borrow(((PyCFunctionObject *) m_ptr)->m_self); + rec_capsule.set_pointer(unique_rec.release()); + guarded_strdup.release(); + } else { + // Or end of chain (normal behavior) + chain_start = chain; + while (chain->next) + chain = chain->next; + chain->next = unique_rec.release(); + guarded_strdup.release(); + } + } + + std::string signatures; + int index = 0; + /* Create a nice pydoc rec including all signatures and + docstrings of the functions in the overload chain */ + if (chain && options::show_function_signatures()) { + // First a generic signature + signatures += rec->name; + signatures += "(*args, **kwargs)\n"; + signatures += "Overloaded function.\n\n"; + } + // Then specific overload signatures + bool first_user_def = true; + for (auto it = chain_start; it != nullptr; it = it->next) { + if (options::show_function_signatures()) { + if (index > 0) signatures += "\n"; + if (chain) + signatures += std::to_string(++index) + ". "; + signatures += rec->name; + signatures += it->signature; + signatures += "\n"; + } + if (it->doc && strlen(it->doc) > 0 && options::show_user_defined_docstrings()) { + // If we're appending another docstring, and aren't printing function signatures, we + // need to append a newline first: + if (!options::show_function_signatures()) { + if (first_user_def) first_user_def = false; + else signatures += "\n"; + } + if (options::show_function_signatures()) signatures += "\n"; + signatures += it->doc; + if (options::show_function_signatures()) signatures += "\n"; + } + } + + /* Install docstring */ + auto *func = (PyCFunctionObject *) m_ptr; + std::free(const_cast(func->m_ml->ml_doc)); + // Install docstring if it's non-empty (when at least one option is enabled) + func->m_ml->ml_doc = signatures.empty() ? nullptr : strdup(signatures.c_str()); + + if (rec->is_method) { + m_ptr = PYBIND11_INSTANCE_METHOD_NEW(m_ptr, rec->scope.ptr()); + if (!m_ptr) + pybind11_fail("cpp_function::cpp_function(): Could not allocate instance method object"); + Py_DECREF(func); + } + } + + /// When a cpp_function is GCed, release any memory allocated by pybind11 + static void destruct(detail::function_record *rec, bool free_strings = true) { + // If on Python 3.9, check the interpreter "MICRO" (patch) version. + // If this is running on 3.9.0, we have to work around a bug. + #if !defined(PYPY_VERSION) && PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 9 + static bool is_zero = Py_GetVersion()[4] == '0'; + #endif + + while (rec) { + detail::function_record *next = rec->next; + if (rec->free_data) + rec->free_data(rec); + // During initialization, these strings might not have been copied yet, + // so they cannot be freed. Once the function has been created, they can. + // Check `make_function_record` for more details. + if (free_strings) { + std::free((char *) rec->name); + std::free((char *) rec->doc); + std::free((char *) rec->signature); + for (auto &arg: rec->args) { + std::free(const_cast(arg.name)); + std::free(const_cast(arg.descr)); + } + } + for (auto &arg: rec->args) + arg.value.dec_ref(); + if (rec->def) { + std::free(const_cast(rec->def->ml_doc)); + // Python 3.9.0 decref's these in the wrong order; rec->def + // If loaded on 3.9.0, let these leak (use Python 3.9.1 at runtime to fix) + // See https://github.com/python/cpython/pull/22670 + #if !defined(PYPY_VERSION) && PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 9 + if (!is_zero) + delete rec->def; + #else + delete rec->def; + #endif + } + delete rec; + rec = next; + } + } + + /// Main dispatch logic for calls to functions bound using pybind11 + static PyObject *dispatcher(PyObject *self, PyObject *args_in, PyObject *kwargs_in) { + using namespace detail; + + /* Iterator over the list of potentially admissible overloads */ + const function_record *overloads = (function_record *) PyCapsule_GetPointer(self, nullptr), + *it = overloads; + + /* Need to know how many arguments + keyword arguments there are to pick the right overload */ + const auto n_args_in = (size_t) PyTuple_GET_SIZE(args_in); + + handle parent = n_args_in > 0 ? PyTuple_GET_ITEM(args_in, 0) : nullptr, + result = PYBIND11_TRY_NEXT_OVERLOAD; + + auto self_value_and_holder = value_and_holder(); + if (overloads->is_constructor) { + if (!PyObject_TypeCheck(parent.ptr(), (PyTypeObject *) overloads->scope.ptr())) { + PyErr_SetString(PyExc_TypeError, "__init__(self, ...) called with invalid `self` argument"); + return nullptr; + } + + const auto tinfo = get_type_info((PyTypeObject *) overloads->scope.ptr()); + const auto pi = reinterpret_cast(parent.ptr()); + self_value_and_holder = pi->get_value_and_holder(tinfo, true); + + // If this value is already registered it must mean __init__ is invoked multiple times; + // we really can't support that in C++, so just ignore the second __init__. + if (self_value_and_holder.instance_registered()) + return none().release().ptr(); + } + + try { + // We do this in two passes: in the first pass, we load arguments with `convert=false`; + // in the second, we allow conversion (except for arguments with an explicit + // py::arg().noconvert()). This lets us prefer calls without conversion, with + // conversion as a fallback. + std::vector second_pass; + + // However, if there are no overloads, we can just skip the no-convert pass entirely + const bool overloaded = it != nullptr && it->next != nullptr; + + for (; it != nullptr; it = it->next) { + + /* For each overload: + 1. Copy all positional arguments we were given, also checking to make sure that + named positional arguments weren't *also* specified via kwarg. + 2. If we weren't given enough, try to make up the omitted ones by checking + whether they were provided by a kwarg matching the `py::arg("name")` name. If + so, use it (and remove it from kwargs; if not, see if the function binding + provided a default that we can use. + 3. Ensure that either all keyword arguments were "consumed", or that the function + takes a kwargs argument to accept unconsumed kwargs. + 4. Any positional arguments still left get put into a tuple (for args), and any + leftover kwargs get put into a dict. + 5. Pack everything into a vector; if we have py::args or py::kwargs, they are an + extra tuple or dict at the end of the positional arguments. + 6. Call the function call dispatcher (function_record::impl) + + If one of these fail, move on to the next overload and keep trying until we get a + result other than PYBIND11_TRY_NEXT_OVERLOAD. + */ + + const function_record &func = *it; + size_t num_args = func.nargs; // Number of positional arguments that we need + if (func.has_args) --num_args; // (but don't count py::args + if (func.has_kwargs) --num_args; // or py::kwargs) + size_t pos_args = num_args - func.nargs_kw_only; + + if (!func.has_args && n_args_in > pos_args) + continue; // Too many positional arguments for this overload + + if (n_args_in < pos_args && func.args.size() < pos_args) + continue; // Not enough positional arguments given, and not enough defaults to fill in the blanks + + function_call call(func, parent); + + size_t args_to_copy = (std::min)(pos_args, n_args_in); // Protect std::min with parentheses + size_t args_copied = 0; + + // 0. Inject new-style `self` argument + if (func.is_new_style_constructor) { + // The `value` may have been preallocated by an old-style `__init__` + // if it was a preceding candidate for overload resolution. + if (self_value_and_holder) + self_value_and_holder.type->dealloc(self_value_and_holder); + + call.init_self = PyTuple_GET_ITEM(args_in, 0); + call.args.emplace_back(reinterpret_cast(&self_value_and_holder)); + call.args_convert.push_back(false); + ++args_copied; + } + + // 1. Copy any position arguments given. + bool bad_arg = false; + for (; args_copied < args_to_copy; ++args_copied) { + const argument_record *arg_rec = args_copied < func.args.size() ? &func.args[args_copied] : nullptr; + if (kwargs_in && arg_rec && arg_rec->name && PyDict_GetItemString(kwargs_in, arg_rec->name)) { + bad_arg = true; + break; + } + + handle arg(PyTuple_GET_ITEM(args_in, args_copied)); + if (arg_rec && !arg_rec->none && arg.is_none()) { + bad_arg = true; + break; + } + call.args.push_back(arg); + call.args_convert.push_back(arg_rec ? arg_rec->convert : true); + } + if (bad_arg) + continue; // Maybe it was meant for another overload (issue #688) + + // We'll need to copy this if we steal some kwargs for defaults + dict kwargs = reinterpret_borrow(kwargs_in); + + // 1.5. Fill in any missing pos_only args from defaults if they exist + if (args_copied < func.nargs_pos_only) { + for (; args_copied < func.nargs_pos_only; ++args_copied) { + const auto &arg_rec = func.args[args_copied]; + handle value; + + if (arg_rec.value) { + value = arg_rec.value; + } + if (value) { + call.args.push_back(value); + call.args_convert.push_back(arg_rec.convert); + } else + break; + } + + if (args_copied < func.nargs_pos_only) + continue; // Not enough defaults to fill the positional arguments + } + + // 2. Check kwargs and, failing that, defaults that may help complete the list + if (args_copied < num_args) { + bool copied_kwargs = false; + + for (; args_copied < num_args; ++args_copied) { + const auto &arg_rec = func.args[args_copied]; + + handle value; + if (kwargs_in && arg_rec.name) + value = PyDict_GetItemString(kwargs.ptr(), arg_rec.name); + + if (value) { + // Consume a kwargs value + if (!copied_kwargs) { + kwargs = reinterpret_steal(PyDict_Copy(kwargs.ptr())); + copied_kwargs = true; + } + PyDict_DelItemString(kwargs.ptr(), arg_rec.name); + } else if (arg_rec.value) { + value = arg_rec.value; + } + + if (!arg_rec.none && value.is_none()) { + break; + } + + if (value) { + call.args.push_back(value); + call.args_convert.push_back(arg_rec.convert); + } + else + break; + } + + if (args_copied < num_args) + continue; // Not enough arguments, defaults, or kwargs to fill the positional arguments + } + + // 3. Check everything was consumed (unless we have a kwargs arg) + if (kwargs && !kwargs.empty() && !func.has_kwargs) + continue; // Unconsumed kwargs, but no py::kwargs argument to accept them + + // 4a. If we have a py::args argument, create a new tuple with leftovers + if (func.has_args) { + tuple extra_args; + if (args_to_copy == 0) { + // We didn't copy out any position arguments from the args_in tuple, so we + // can reuse it directly without copying: + extra_args = reinterpret_borrow(args_in); + } else if (args_copied >= n_args_in) { + extra_args = tuple(0); + } else { + size_t args_size = n_args_in - args_copied; + extra_args = tuple(args_size); + for (size_t i = 0; i < args_size; ++i) { + extra_args[i] = PyTuple_GET_ITEM(args_in, args_copied + i); + } + } + call.args.push_back(extra_args); + call.args_convert.push_back(false); + call.args_ref = std::move(extra_args); + } + + // 4b. If we have a py::kwargs, pass on any remaining kwargs + if (func.has_kwargs) { + if (!kwargs.ptr()) + kwargs = dict(); // If we didn't get one, send an empty one + call.args.push_back(kwargs); + call.args_convert.push_back(false); + call.kwargs_ref = std::move(kwargs); + } + + // 5. Put everything in a vector. Not technically step 5, we've been building it + // in `call.args` all along. + #if !defined(NDEBUG) + if (call.args.size() != func.nargs || call.args_convert.size() != func.nargs) + pybind11_fail("Internal error: function call dispatcher inserted wrong number of arguments!"); + #endif + + std::vector second_pass_convert; + if (overloaded) { + // We're in the first no-convert pass, so swap out the conversion flags for a + // set of all-false flags. If the call fails, we'll swap the flags back in for + // the conversion-allowed call below. + second_pass_convert.resize(func.nargs, false); + call.args_convert.swap(second_pass_convert); + } + + // 6. Call the function. + try { + loader_life_support guard{}; + result = func.impl(call); + } catch (reference_cast_error &) { + result = PYBIND11_TRY_NEXT_OVERLOAD; + } + + if (result.ptr() != PYBIND11_TRY_NEXT_OVERLOAD) + break; + + if (overloaded) { + // The (overloaded) call failed; if the call has at least one argument that + // permits conversion (i.e. it hasn't been explicitly specified `.noconvert()`) + // then add this call to the list of second pass overloads to try. + for (size_t i = func.is_method ? 1 : 0; i < pos_args; i++) { + if (second_pass_convert[i]) { + // Found one: swap the converting flags back in and store the call for + // the second pass. + call.args_convert.swap(second_pass_convert); + second_pass.push_back(std::move(call)); + break; + } + } + } + } + + if (overloaded && !second_pass.empty() && result.ptr() == PYBIND11_TRY_NEXT_OVERLOAD) { + // The no-conversion pass finished without success, try again with conversion allowed + for (auto &call : second_pass) { + try { + loader_life_support guard{}; + result = call.func.impl(call); + } catch (reference_cast_error &) { + result = PYBIND11_TRY_NEXT_OVERLOAD; + } + + if (result.ptr() != PYBIND11_TRY_NEXT_OVERLOAD) { + // The error reporting logic below expects 'it' to be valid, as it would be + // if we'd encountered this failure in the first-pass loop. + if (!result) + it = &call.func; + break; + } + } + } + } catch (error_already_set &e) { + e.restore(); + return nullptr; +#ifdef __GLIBCXX__ + } catch ( abi::__forced_unwind& ) { + throw; +#endif + } catch (...) { + /* When an exception is caught, give each registered exception + translator a chance to translate it to a Python exception + in reverse order of registration. + + A translator may choose to do one of the following: + + - catch the exception and call PyErr_SetString or PyErr_SetObject + to set a standard (or custom) Python exception, or + - do nothing and let the exception fall through to the next translator, or + - delegate translation to the next translator by throwing a new type of exception. */ + + auto last_exception = std::current_exception(); + auto ®istered_exception_translators = get_internals().registered_exception_translators; + for (auto& translator : registered_exception_translators) { + try { + translator(last_exception); + } catch (...) { + last_exception = std::current_exception(); + continue; + } + return nullptr; + } + PyErr_SetString(PyExc_SystemError, "Exception escaped from default exception translator!"); + return nullptr; + } + + auto append_note_if_missing_header_is_suspected = [](std::string &msg) { + if (msg.find("std::") != std::string::npos) { + msg += "\n\n" + "Did you forget to `#include `? Or ,\n" + ", , etc. Some automatic\n" + "conversions are optional and require extra headers to be included\n" + "when compiling your pybind11 module."; + } + }; + + if (result.ptr() == PYBIND11_TRY_NEXT_OVERLOAD) { + if (overloads->is_operator) + return handle(Py_NotImplemented).inc_ref().ptr(); + + std::string msg = std::string(overloads->name) + "(): incompatible " + + std::string(overloads->is_constructor ? "constructor" : "function") + + " arguments. The following argument types are supported:\n"; + + int ctr = 0; + for (const function_record *it2 = overloads; it2 != nullptr; it2 = it2->next) { + msg += " "+ std::to_string(++ctr) + ". "; + + bool wrote_sig = false; + if (overloads->is_constructor) { + // For a constructor, rewrite `(self: Object, arg0, ...) -> NoneType` as `Object(arg0, ...)` + std::string sig = it2->signature; + size_t start = sig.find('(') + 7; // skip "(self: " + if (start < sig.size()) { + // End at the , for the next argument + size_t end = sig.find(", "), next = end + 2; + size_t ret = sig.rfind(" -> "); + // Or the ), if there is no comma: + if (end >= sig.size()) next = end = sig.find(')'); + if (start < end && next < sig.size()) { + msg.append(sig, start, end - start); + msg += '('; + msg.append(sig, next, ret - next); + wrote_sig = true; + } + } + } + if (!wrote_sig) msg += it2->signature; + + msg += "\n"; + } + msg += "\nInvoked with: "; + auto args_ = reinterpret_borrow(args_in); + bool some_args = false; + for (size_t ti = overloads->is_constructor ? 1 : 0; ti < args_.size(); ++ti) { + if (!some_args) some_args = true; + else msg += ", "; + try { + msg += pybind11::repr(args_[ti]); + } catch (const error_already_set&) { + msg += ""; + } + } + if (kwargs_in) { + auto kwargs = reinterpret_borrow(kwargs_in); + if (!kwargs.empty()) { + if (some_args) msg += "; "; + msg += "kwargs: "; + bool first = true; + for (auto kwarg : kwargs) { + if (first) first = false; + else msg += ", "; + msg += pybind11::str("{}=").format(kwarg.first); + try { + msg += pybind11::repr(kwarg.second); + } catch (const error_already_set&) { + msg += ""; + } + } + } + } + + append_note_if_missing_header_is_suspected(msg); + PyErr_SetString(PyExc_TypeError, msg.c_str()); + return nullptr; + } else if (!result) { + std::string msg = "Unable to convert function return value to a " + "Python type! The signature was\n\t"; + msg += it->signature; + append_note_if_missing_header_is_suspected(msg); + PyErr_SetString(PyExc_TypeError, msg.c_str()); + return nullptr; + } else { + if (overloads->is_constructor && !self_value_and_holder.holder_constructed()) { + auto *pi = reinterpret_cast(parent.ptr()); + self_value_and_holder.type->init_instance(pi, nullptr); + } + return result.ptr(); + } + } +}; + +/// Wrapper for Python extension modules +class module_ : public object { +public: + PYBIND11_OBJECT_DEFAULT(module_, object, PyModule_Check) + + /// Create a new top-level Python module with the given name and docstring + PYBIND11_DEPRECATED("Use PYBIND11_MODULE or module_::create_extension_module instead") + explicit module_(const char *name, const char *doc = nullptr) { +#if PY_MAJOR_VERSION >= 3 + *this = create_extension_module(name, doc, new PyModuleDef()); +#else + *this = create_extension_module(name, doc, nullptr); +#endif + } + + /** \rst + Create Python binding for a new function within the module scope. ``Func`` + can be a plain C++ function, a function pointer, or a lambda function. For + details on the ``Extra&& ... extra`` argument, see section :ref:`extras`. + \endrst */ + template + module_ &def(const char *name_, Func &&f, const Extra& ... extra) { + cpp_function func(std::forward(f), name(name_), scope(*this), + sibling(getattr(*this, name_, none())), extra...); + // NB: allow overwriting here because cpp_function sets up a chain with the intention of + // overwriting (and has already checked internally that it isn't overwriting non-functions). + add_object(name_, func, true /* overwrite */); + return *this; + } + + /** \rst + Create and return a new Python submodule with the given name and docstring. + This also works recursively, i.e. + + .. code-block:: cpp + + py::module_ m("example", "pybind11 example plugin"); + py::module_ m2 = m.def_submodule("sub", "A submodule of 'example'"); + py::module_ m3 = m2.def_submodule("subsub", "A submodule of 'example.sub'"); + \endrst */ + module_ def_submodule(const char *name, const char *doc = nullptr) { + std::string full_name = std::string(PyModule_GetName(m_ptr)) + + std::string(".") + std::string(name); + auto result = reinterpret_borrow(PyImport_AddModule(full_name.c_str())); + if (doc && options::show_user_defined_docstrings()) + result.attr("__doc__") = pybind11::str(doc); + attr(name) = result; + return result; + } + + /// Import and return a module or throws `error_already_set`. + static module_ import(const char *name) { + PyObject *obj = PyImport_ImportModule(name); + if (!obj) + throw error_already_set(); + return reinterpret_steal(obj); + } + + /// Reload the module or throws `error_already_set`. + void reload() { + PyObject *obj = PyImport_ReloadModule(ptr()); + if (!obj) + throw error_already_set(); + *this = reinterpret_steal(obj); + } + + /** \rst + Adds an object to the module using the given name. Throws if an object with the given name + already exists. + + ``overwrite`` should almost always be false: attempting to overwrite objects that pybind11 has + established will, in most cases, break things. + \endrst */ + PYBIND11_NOINLINE void add_object(const char *name, handle obj, bool overwrite = false) { + if (!overwrite && hasattr(*this, name)) + pybind11_fail("Error during initialization: multiple incompatible definitions with name \"" + + std::string(name) + "\""); + + PyModule_AddObject(ptr(), name, obj.inc_ref().ptr() /* steals a reference */); + } + +#if PY_MAJOR_VERSION >= 3 + using module_def = PyModuleDef; +#else + struct module_def {}; +#endif + + /** \rst + Create a new top-level module that can be used as the main module of a C extension. + + For Python 3, ``def`` should point to a statically allocated module_def. + For Python 2, ``def`` can be a nullptr and is completely ignored. + \endrst */ + static module_ create_extension_module(const char *name, const char *doc, module_def *def) { +#if PY_MAJOR_VERSION >= 3 + // module_def is PyModuleDef + def = new (def) PyModuleDef { // Placement new (not an allocation). + /* m_base */ PyModuleDef_HEAD_INIT, + /* m_name */ name, + /* m_doc */ options::show_user_defined_docstrings() ? doc : nullptr, + /* m_size */ -1, + /* m_methods */ nullptr, + /* m_slots */ nullptr, + /* m_traverse */ nullptr, + /* m_clear */ nullptr, + /* m_free */ nullptr + }; + auto m = PyModule_Create(def); +#else + // Ignore module_def *def; only necessary for Python 3 + (void) def; + auto m = Py_InitModule3(name, nullptr, options::show_user_defined_docstrings() ? doc : nullptr); +#endif + if (m == nullptr) { + if (PyErr_Occurred()) + throw error_already_set(); + pybind11_fail("Internal error in module_::create_extension_module()"); + } + // TODO: Should be reinterpret_steal for Python 3, but Python also steals it again when returned from PyInit_... + // For Python 2, reinterpret_borrow is correct. + return reinterpret_borrow(m); + } +}; + +// When inside a namespace (or anywhere as long as it's not the first item on a line), +// C++20 allows "module" to be used. This is provided for backward compatibility, and for +// simplicity, if someone wants to use py::module for example, that is perfectly safe. +using module = module_; + +/// \ingroup python_builtins +/// Return a dictionary representing the global variables in the current execution frame, +/// or ``__main__.__dict__`` if there is no frame (usually when the interpreter is embedded). +inline dict globals() { + PyObject *p = PyEval_GetGlobals(); + return reinterpret_borrow(p ? p : module_::import("__main__").attr("__dict__").ptr()); +} + +PYBIND11_NAMESPACE_BEGIN(detail) +/// Generic support for creating new Python heap types +class generic_type : public object { +public: + PYBIND11_OBJECT_DEFAULT(generic_type, object, PyType_Check) +protected: + void initialize(const type_record &rec) { + if (rec.scope && hasattr(rec.scope, "__dict__") && rec.scope.attr("__dict__").contains(rec.name)) + pybind11_fail("generic_type: cannot initialize type \"" + std::string(rec.name) + + "\": an object with that name is already defined"); + + if (rec.module_local ? get_local_type_info(*rec.type) : get_global_type_info(*rec.type)) + pybind11_fail("generic_type: type \"" + std::string(rec.name) + + "\" is already registered!"); + + m_ptr = make_new_python_type(rec); + + /* Register supplemental type information in C++ dict */ + auto *tinfo = new detail::type_info(); + tinfo->type = (PyTypeObject *) m_ptr; + tinfo->cpptype = rec.type; + tinfo->type_size = rec.type_size; + tinfo->type_align = rec.type_align; + tinfo->operator_new = rec.operator_new; + tinfo->holder_size_in_ptrs = size_in_ptrs(rec.holder_size); + tinfo->init_instance = rec.init_instance; + tinfo->dealloc = rec.dealloc; + tinfo->simple_type = true; + tinfo->simple_ancestors = true; + tinfo->default_holder = rec.default_holder; + tinfo->module_local = rec.module_local; + + auto &internals = get_internals(); + auto tindex = std::type_index(*rec.type); + tinfo->direct_conversions = &internals.direct_conversions[tindex]; + if (rec.module_local) + registered_local_types_cpp()[tindex] = tinfo; + else + internals.registered_types_cpp[tindex] = tinfo; + internals.registered_types_py[(PyTypeObject *) m_ptr] = { tinfo }; + + if (rec.bases.size() > 1 || rec.multiple_inheritance) { + mark_parents_nonsimple(tinfo->type); + tinfo->simple_ancestors = false; + } + else if (rec.bases.size() == 1) { + auto parent_tinfo = get_type_info((PyTypeObject *) rec.bases[0].ptr()); + tinfo->simple_ancestors = parent_tinfo->simple_ancestors; + } + + if (rec.module_local) { + // Stash the local typeinfo and loader so that external modules can access it. + tinfo->module_local_load = &type_caster_generic::local_load; + setattr(m_ptr, PYBIND11_MODULE_LOCAL_ID, capsule(tinfo)); + } + } + + /// Helper function which tags all parents of a type using mult. inheritance + void mark_parents_nonsimple(PyTypeObject *value) { + auto t = reinterpret_borrow(value->tp_bases); + for (handle h : t) { + auto tinfo2 = get_type_info((PyTypeObject *) h.ptr()); + if (tinfo2) + tinfo2->simple_type = false; + mark_parents_nonsimple((PyTypeObject *) h.ptr()); + } + } + + void install_buffer_funcs( + buffer_info *(*get_buffer)(PyObject *, void *), + void *get_buffer_data) { + auto *type = (PyHeapTypeObject*) m_ptr; + auto tinfo = detail::get_type_info(&type->ht_type); + + if (!type->ht_type.tp_as_buffer) + pybind11_fail( + "To be able to register buffer protocol support for the type '" + + get_fully_qualified_tp_name(tinfo->type) + + "' the associated class<>(..) invocation must " + "include the pybind11::buffer_protocol() annotation!"); + + tinfo->get_buffer = get_buffer; + tinfo->get_buffer_data = get_buffer_data; + } + + // rec_func must be set for either fget or fset. + void def_property_static_impl(const char *name, + handle fget, handle fset, + detail::function_record *rec_func) { + const auto is_static = rec_func && !(rec_func->is_method && rec_func->scope); + const auto has_doc = rec_func && rec_func->doc && pybind11::options::show_user_defined_docstrings(); + auto property = handle((PyObject *) (is_static ? get_internals().static_property_type + : &PyProperty_Type)); + attr(name) = property(fget.ptr() ? fget : none(), + fset.ptr() ? fset : none(), + /*deleter*/none(), + pybind11::str(has_doc ? rec_func->doc : "")); + } +}; + +/// Set the pointer to operator new if it exists. The cast is needed because it can be overloaded. +template (T::operator new))>> +void set_operator_new(type_record *r) { r->operator_new = &T::operator new; } + +template void set_operator_new(...) { } + +template struct has_operator_delete : std::false_type { }; +template struct has_operator_delete(T::operator delete))>> + : std::true_type { }; +template struct has_operator_delete_size : std::false_type { }; +template struct has_operator_delete_size(T::operator delete))>> + : std::true_type { }; +/// Call class-specific delete if it exists or global otherwise. Can also be an overload set. +template ::value, int> = 0> +void call_operator_delete(T *p, size_t, size_t) { T::operator delete(p); } +template ::value && has_operator_delete_size::value, int> = 0> +void call_operator_delete(T *p, size_t s, size_t) { T::operator delete(p, s); } + +inline void call_operator_delete(void *p, size_t s, size_t a) { + (void)s; (void)a; + #if defined(__cpp_aligned_new) && (!defined(_MSC_VER) || _MSC_VER >= 1912) + if (a > __STDCPP_DEFAULT_NEW_ALIGNMENT__) { + #ifdef __cpp_sized_deallocation + ::operator delete(p, s, std::align_val_t(a)); + #else + ::operator delete(p, std::align_val_t(a)); + #endif + return; + } + #endif + #ifdef __cpp_sized_deallocation + ::operator delete(p, s); + #else + ::operator delete(p); + #endif +} + +inline void add_class_method(object& cls, const char *name_, const cpp_function &cf) { + cls.attr(cf.name()) = cf; + if (strcmp(name_, "__eq__") == 0 && !cls.attr("__dict__").contains("__hash__")) { + cls.attr("__hash__") = none(); + } +} + +PYBIND11_NAMESPACE_END(detail) + +/// Given a pointer to a member function, cast it to its `Derived` version. +/// Forward everything else unchanged. +template +auto method_adaptor(F &&f) -> decltype(std::forward(f)) { return std::forward(f); } + +template +auto method_adaptor(Return (Class::*pmf)(Args...)) -> Return (Derived::*)(Args...) { + static_assert(detail::is_accessible_base_of::value, + "Cannot bind an inaccessible base class method; use a lambda definition instead"); + return pmf; +} + +template +auto method_adaptor(Return (Class::*pmf)(Args...) const) -> Return (Derived::*)(Args...) const { + static_assert(detail::is_accessible_base_of::value, + "Cannot bind an inaccessible base class method; use a lambda definition instead"); + return pmf; +} + +template +class class_ : public detail::generic_type { + template using is_holder = detail::is_holder_type; + template using is_subtype = detail::is_strict_base_of; + template using is_base = detail::is_strict_base_of; + // struct instead of using here to help MSVC: + template struct is_valid_class_option : + detail::any_of, is_subtype, is_base> {}; + +public: + using type = type_; + using type_alias = detail::exactly_one_t; + constexpr static bool has_alias = !std::is_void::value; + using holder_type = detail::exactly_one_t, options...>; + + static_assert(detail::all_of...>::value, + "Unknown/invalid class_ template parameters provided"); + + static_assert(!has_alias || std::is_polymorphic::value, + "Cannot use an alias class with a non-polymorphic type"); + + PYBIND11_OBJECT(class_, generic_type, PyType_Check) + + template + class_(handle scope, const char *name, const Extra &... extra) { + using namespace detail; + + // MI can only be specified via class_ template options, not constructor parameters + static_assert( + none_of...>::value || // no base class arguments, or: + ( constexpr_sum(is_pyobject::value...) == 1 && // Exactly one base + constexpr_sum(is_base::value...) == 0 && // no template option bases + none_of...>::value), // no multiple_inheritance attr + "Error: multiple inheritance bases must be specified via class_ template options"); + + type_record record; + record.scope = scope; + record.name = name; + record.type = &typeid(type); + record.type_size = sizeof(conditional_t); + record.type_align = alignof(conditional_t&); + record.holder_size = sizeof(holder_type); + record.init_instance = init_instance; + record.dealloc = dealloc; + record.default_holder = detail::is_instantiation::value; + + set_operator_new(&record); + + /* Register base classes specified via template arguments to class_, if any */ + PYBIND11_EXPAND_SIDE_EFFECTS(add_base(record)); + + /* Process optional arguments, if any */ + process_attributes::init(extra..., &record); + + generic_type::initialize(record); + + if (has_alias) { + auto &instances = record.module_local ? registered_local_types_cpp() : get_internals().registered_types_cpp; + instances[std::type_index(typeid(type_alias))] = instances[std::type_index(typeid(type))]; + } + } + + template ::value, int> = 0> + static void add_base(detail::type_record &rec) { + rec.add_base(typeid(Base), [](void *src) -> void * { + return static_cast(reinterpret_cast(src)); + }); + } + + template ::value, int> = 0> + static void add_base(detail::type_record &) { } + + template + class_ &def(const char *name_, Func&& f, const Extra&... extra) { + cpp_function cf(method_adaptor(std::forward(f)), name(name_), is_method(*this), + sibling(getattr(*this, name_, none())), extra...); + add_class_method(*this, name_, cf); + return *this; + } + + template class_ & + def_static(const char *name_, Func &&f, const Extra&... extra) { + static_assert(!std::is_member_function_pointer::value, + "def_static(...) called with a non-static member function pointer"); + cpp_function cf(std::forward(f), name(name_), scope(*this), + sibling(getattr(*this, name_, none())), extra...); + attr(cf.name()) = staticmethod(cf); + return *this; + } + + template + class_ &def(const detail::op_ &op, const Extra&... extra) { + op.execute(*this, extra...); + return *this; + } + + template + class_ & def_cast(const detail::op_ &op, const Extra&... extra) { + op.execute_cast(*this, extra...); + return *this; + } + + template + class_ &def(const detail::initimpl::constructor &init, const Extra&... extra) { + init.execute(*this, extra...); + return *this; + } + + template + class_ &def(const detail::initimpl::alias_constructor &init, const Extra&... extra) { + init.execute(*this, extra...); + return *this; + } + + template + class_ &def(detail::initimpl::factory &&init, const Extra&... extra) { + std::move(init).execute(*this, extra...); + return *this; + } + + template + class_ &def(detail::initimpl::pickle_factory &&pf, const Extra &...extra) { + std::move(pf).execute(*this, extra...); + return *this; + } + + template + class_& def_buffer(Func &&func) { + struct capture { Func func; }; + auto *ptr = new capture { std::forward(func) }; + install_buffer_funcs([](PyObject *obj, void *ptr) -> buffer_info* { + detail::make_caster caster; + if (!caster.load(obj, false)) + return nullptr; + return new buffer_info(((capture *) ptr)->func(caster)); + }, ptr); + weakref(m_ptr, cpp_function([ptr](handle wr) { + delete ptr; + wr.dec_ref(); + })).release(); + return *this; + } + + template + class_ &def_buffer(Return (Class::*func)(Args...)) { + return def_buffer([func] (type &obj) { return (obj.*func)(); }); + } + + template + class_ &def_buffer(Return (Class::*func)(Args...) const) { + return def_buffer([func] (const type &obj) { return (obj.*func)(); }); + } + + template + class_ &def_readwrite(const char *name, D C::*pm, const Extra&... extra) { + static_assert(std::is_same::value || std::is_base_of::value, "def_readwrite() requires a class member (or base class member)"); + cpp_function fget([pm](const type &c) -> const D &{ return c.*pm; }, is_method(*this)), + fset([pm](type &c, const D &value) { c.*pm = value; }, is_method(*this)); + def_property(name, fget, fset, return_value_policy::reference_internal, extra...); + return *this; + } + + template + class_ &def_readonly(const char *name, const D C::*pm, const Extra& ...extra) { + static_assert(std::is_same::value || std::is_base_of::value, "def_readonly() requires a class member (or base class member)"); + cpp_function fget([pm](const type &c) -> const D &{ return c.*pm; }, is_method(*this)); + def_property_readonly(name, fget, return_value_policy::reference_internal, extra...); + return *this; + } + + template + class_ &def_readwrite_static(const char *name, D *pm, const Extra& ...extra) { + cpp_function fget([pm](object) -> const D &{ return *pm; }, scope(*this)), + fset([pm](object, const D &value) { *pm = value; }, scope(*this)); + def_property_static(name, fget, fset, return_value_policy::reference, extra...); + return *this; + } + + template + class_ &def_readonly_static(const char *name, const D *pm, const Extra& ...extra) { + cpp_function fget([pm](object) -> const D &{ return *pm; }, scope(*this)); + def_property_readonly_static(name, fget, return_value_policy::reference, extra...); + return *this; + } + + /// Uses return_value_policy::reference_internal by default + template + class_ &def_property_readonly(const char *name, const Getter &fget, const Extra& ...extra) { + return def_property_readonly(name, cpp_function(method_adaptor(fget)), + return_value_policy::reference_internal, extra...); + } + + /// Uses cpp_function's return_value_policy by default + template + class_ &def_property_readonly(const char *name, const cpp_function &fget, const Extra& ...extra) { + return def_property(name, fget, nullptr, extra...); + } + + /// Uses return_value_policy::reference by default + template + class_ &def_property_readonly_static(const char *name, const Getter &fget, const Extra& ...extra) { + return def_property_readonly_static(name, cpp_function(fget), return_value_policy::reference, extra...); + } + + /// Uses cpp_function's return_value_policy by default + template + class_ &def_property_readonly_static(const char *name, const cpp_function &fget, const Extra& ...extra) { + return def_property_static(name, fget, nullptr, extra...); + } + + /// Uses return_value_policy::reference_internal by default + template + class_ &def_property(const char *name, const Getter &fget, const Setter &fset, const Extra& ...extra) { + return def_property(name, fget, cpp_function(method_adaptor(fset)), extra...); + } + template + class_ &def_property(const char *name, const Getter &fget, const cpp_function &fset, const Extra& ...extra) { + return def_property(name, cpp_function(method_adaptor(fget)), fset, + return_value_policy::reference_internal, extra...); + } + + /// Uses cpp_function's return_value_policy by default + template + class_ &def_property(const char *name, const cpp_function &fget, const cpp_function &fset, const Extra& ...extra) { + return def_property_static(name, fget, fset, is_method(*this), extra...); + } + + /// Uses return_value_policy::reference by default + template + class_ &def_property_static(const char *name, const Getter &fget, const cpp_function &fset, const Extra& ...extra) { + return def_property_static(name, cpp_function(fget), fset, return_value_policy::reference, extra...); + } + + /// Uses cpp_function's return_value_policy by default + template + class_ &def_property_static(const char *name, const cpp_function &fget, const cpp_function &fset, const Extra& ...extra) { + static_assert( 0 == detail::constexpr_sum(std::is_base_of::value...), + "Argument annotations are not allowed for properties"); + auto rec_fget = get_function_record(fget), rec_fset = get_function_record(fset); + auto *rec_active = rec_fget; + if (rec_fget) { + char *doc_prev = rec_fget->doc; /* 'extra' field may include a property-specific documentation string */ + detail::process_attributes::init(extra..., rec_fget); + if (rec_fget->doc && rec_fget->doc != doc_prev) { + free(doc_prev); + rec_fget->doc = strdup(rec_fget->doc); + } + } + if (rec_fset) { + char *doc_prev = rec_fset->doc; + detail::process_attributes::init(extra..., rec_fset); + if (rec_fset->doc && rec_fset->doc != doc_prev) { + free(doc_prev); + rec_fset->doc = strdup(rec_fset->doc); + } + if (! rec_active) rec_active = rec_fset; + } + def_property_static_impl(name, fget, fset, rec_active); + return *this; + } + +private: + /// Initialize holder object, variant 1: object derives from enable_shared_from_this + template + static void init_holder(detail::instance *inst, detail::value_and_holder &v_h, + const holder_type * /* unused */, const std::enable_shared_from_this * /* dummy */) { + + auto sh = std::dynamic_pointer_cast( + detail::try_get_shared_from_this(v_h.value_ptr())); + if (sh) { + new (std::addressof(v_h.holder())) holder_type(std::move(sh)); + v_h.set_holder_constructed(); + } + + if (!v_h.holder_constructed() && inst->owned) { + new (std::addressof(v_h.holder())) holder_type(v_h.value_ptr()); + v_h.set_holder_constructed(); + } + } + + static void init_holder_from_existing(const detail::value_and_holder &v_h, + const holder_type *holder_ptr, std::true_type /*is_copy_constructible*/) { + new (std::addressof(v_h.holder())) holder_type(*reinterpret_cast(holder_ptr)); + } + + static void init_holder_from_existing(const detail::value_and_holder &v_h, + const holder_type *holder_ptr, std::false_type /*is_copy_constructible*/) { + new (std::addressof(v_h.holder())) holder_type(std::move(*const_cast(holder_ptr))); + } + + /// Initialize holder object, variant 2: try to construct from existing holder object, if possible + static void init_holder(detail::instance *inst, detail::value_and_holder &v_h, + const holder_type *holder_ptr, const void * /* dummy -- not enable_shared_from_this) */) { + if (holder_ptr) { + init_holder_from_existing(v_h, holder_ptr, std::is_copy_constructible()); + v_h.set_holder_constructed(); + } else if (inst->owned || detail::always_construct_holder::value) { + new (std::addressof(v_h.holder())) holder_type(v_h.value_ptr()); + v_h.set_holder_constructed(); + } + } + + /// Performs instance initialization including constructing a holder and registering the known + /// instance. Should be called as soon as the `type` value_ptr is set for an instance. Takes an + /// optional pointer to an existing holder to use; if not specified and the instance is + /// `.owned`, a new holder will be constructed to manage the value pointer. + static void init_instance(detail::instance *inst, const void *holder_ptr) { + auto v_h = inst->get_value_and_holder(detail::get_type_info(typeid(type))); + if (!v_h.instance_registered()) { + register_instance(inst, v_h.value_ptr(), v_h.type); + v_h.set_instance_registered(); + } + init_holder(inst, v_h, (const holder_type *) holder_ptr, v_h.value_ptr()); + } + + /// Deallocates an instance; via holder, if constructed; otherwise via operator delete. + static void dealloc(detail::value_and_holder &v_h) { + // We could be deallocating because we are cleaning up after a Python exception. + // If so, the Python error indicator will be set. We need to clear that before + // running the destructor, in case the destructor code calls more Python. + // If we don't, the Python API will exit with an exception, and pybind11 will + // throw error_already_set from the C++ destructor which is forbidden and triggers + // std::terminate(). + error_scope scope; + if (v_h.holder_constructed()) { + v_h.holder().~holder_type(); + v_h.set_holder_constructed(false); + } + else { + detail::call_operator_delete(v_h.value_ptr(), + v_h.type->type_size, + v_h.type->type_align + ); + } + v_h.value_ptr() = nullptr; + } + + static detail::function_record *get_function_record(handle h) { + h = detail::get_function(h); + return h ? (detail::function_record *) reinterpret_borrow(PyCFunction_GET_SELF(h.ptr())) + : nullptr; + } +}; + +/// Binds an existing constructor taking arguments Args... +template detail::initimpl::constructor init() { return {}; } +/// Like `init()`, but the instance is always constructed through the alias class (even +/// when not inheriting on the Python side). +template detail::initimpl::alias_constructor init_alias() { return {}; } + +/// Binds a factory function as a constructor +template > +Ret init(Func &&f) { return {std::forward(f)}; } + +/// Dual-argument factory function: the first function is called when no alias is needed, the second +/// when an alias is needed (i.e. due to python-side inheritance). Arguments must be identical. +template > +Ret init(CFunc &&c, AFunc &&a) { + return {std::forward(c), std::forward(a)}; +} + +/// Binds pickling functions `__getstate__` and `__setstate__` and ensures that the type +/// returned by `__getstate__` is the same as the argument accepted by `__setstate__`. +template +detail::initimpl::pickle_factory pickle(GetState &&g, SetState &&s) { + return {std::forward(g), std::forward(s)}; +} + +PYBIND11_NAMESPACE_BEGIN(detail) + +inline str enum_name(handle arg) { + dict entries = arg.get_type().attr("__entries"); + for (auto kv : entries) { + if (handle(kv.second[int_(0)]).equal(arg)) + return pybind11::str(kv.first); + } + return "???"; +} + +struct enum_base { + enum_base(handle base, handle parent) : m_base(base), m_parent(parent) { } + + PYBIND11_NOINLINE void init(bool is_arithmetic, bool is_convertible) { + m_base.attr("__entries") = dict(); + auto property = handle((PyObject *) &PyProperty_Type); + auto static_property = handle((PyObject *) get_internals().static_property_type); + + m_base.attr("__repr__") = cpp_function( + [](object arg) -> str { + handle type = type::handle_of(arg); + object type_name = type.attr("__name__"); + return pybind11::str("<{}.{}: {}>").format(type_name, enum_name(arg), int_(arg)); + }, name("__repr__"), is_method(m_base) + ); + + m_base.attr("name") = property(cpp_function(&enum_name, name("name"), is_method(m_base))); + + m_base.attr("__str__") = cpp_function( + [](handle arg) -> str { + object type_name = type::handle_of(arg).attr("__name__"); + return pybind11::str("{}.{}").format(type_name, enum_name(arg)); + }, name("name"), is_method(m_base) + ); + + m_base.attr("__doc__") = static_property(cpp_function( + [](handle arg) -> std::string { + std::string docstring; + dict entries = arg.attr("__entries"); + if (((PyTypeObject *) arg.ptr())->tp_doc) + docstring += std::string(((PyTypeObject *) arg.ptr())->tp_doc) + "\n\n"; + docstring += "Members:"; + for (auto kv : entries) { + auto key = std::string(pybind11::str(kv.first)); + auto comment = kv.second[int_(1)]; + docstring += "\n\n " + key; + if (!comment.is_none()) + docstring += " : " + (std::string) pybind11::str(comment); + } + return docstring; + }, name("__doc__") + ), none(), none(), ""); + + m_base.attr("__members__") = static_property(cpp_function( + [](handle arg) -> dict { + dict entries = arg.attr("__entries"), m; + for (auto kv : entries) + m[kv.first] = kv.second[int_(0)]; + return m; + }, name("__members__")), none(), none(), "" + ); + + #define PYBIND11_ENUM_OP_STRICT(op, expr, strict_behavior) \ + m_base.attr(op) = cpp_function( \ + [](object a, object b) { \ + if (!type::handle_of(a).is(type::handle_of(b))) \ + strict_behavior; \ + return expr; \ + }, \ + name(op), is_method(m_base), arg("other")) + + #define PYBIND11_ENUM_OP_CONV(op, expr) \ + m_base.attr(op) = cpp_function( \ + [](object a_, object b_) { \ + int_ a(a_), b(b_); \ + return expr; \ + }, \ + name(op), is_method(m_base), arg("other")) + + #define PYBIND11_ENUM_OP_CONV_LHS(op, expr) \ + m_base.attr(op) = cpp_function( \ + [](object a_, object b) { \ + int_ a(a_); \ + return expr; \ + }, \ + name(op), is_method(m_base), arg("other")) + + if (is_convertible) { + PYBIND11_ENUM_OP_CONV_LHS("__eq__", !b.is_none() && a.equal(b)); + PYBIND11_ENUM_OP_CONV_LHS("__ne__", b.is_none() || !a.equal(b)); + + if (is_arithmetic) { + PYBIND11_ENUM_OP_CONV("__lt__", a < b); + PYBIND11_ENUM_OP_CONV("__gt__", a > b); + PYBIND11_ENUM_OP_CONV("__le__", a <= b); + PYBIND11_ENUM_OP_CONV("__ge__", a >= b); + PYBIND11_ENUM_OP_CONV("__and__", a & b); + PYBIND11_ENUM_OP_CONV("__rand__", a & b); + PYBIND11_ENUM_OP_CONV("__or__", a | b); + PYBIND11_ENUM_OP_CONV("__ror__", a | b); + PYBIND11_ENUM_OP_CONV("__xor__", a ^ b); + PYBIND11_ENUM_OP_CONV("__rxor__", a ^ b); + m_base.attr("__invert__") = cpp_function( + [](object arg) { return ~(int_(arg)); }, name("__invert__"), is_method(m_base)); + } + } else { + PYBIND11_ENUM_OP_STRICT("__eq__", int_(a).equal(int_(b)), return false); + PYBIND11_ENUM_OP_STRICT("__ne__", !int_(a).equal(int_(b)), return true); + + if (is_arithmetic) { + #define PYBIND11_THROW throw type_error("Expected an enumeration of matching type!"); + PYBIND11_ENUM_OP_STRICT("__lt__", int_(a) < int_(b), PYBIND11_THROW); + PYBIND11_ENUM_OP_STRICT("__gt__", int_(a) > int_(b), PYBIND11_THROW); + PYBIND11_ENUM_OP_STRICT("__le__", int_(a) <= int_(b), PYBIND11_THROW); + PYBIND11_ENUM_OP_STRICT("__ge__", int_(a) >= int_(b), PYBIND11_THROW); + #undef PYBIND11_THROW + } + } + + #undef PYBIND11_ENUM_OP_CONV_LHS + #undef PYBIND11_ENUM_OP_CONV + #undef PYBIND11_ENUM_OP_STRICT + + m_base.attr("__getstate__") = cpp_function( + [](object arg) { return int_(arg); }, name("__getstate__"), is_method(m_base)); + + m_base.attr("__hash__") = cpp_function( + [](object arg) { return int_(arg); }, name("__hash__"), is_method(m_base)); + } + + PYBIND11_NOINLINE void value(char const* name_, object value, const char *doc = nullptr) { + dict entries = m_base.attr("__entries"); + str name(name_); + if (entries.contains(name)) { + std::string type_name = (std::string) str(m_base.attr("__name__")); + throw value_error(type_name + ": element \"" + std::string(name_) + "\" already exists!"); + } + + entries[name] = std::make_pair(value, doc); + m_base.attr(name) = value; + } + + PYBIND11_NOINLINE void export_values() { + dict entries = m_base.attr("__entries"); + for (auto kv : entries) + m_parent.attr(kv.first) = kv.second[int_(0)]; + } + + handle m_base; + handle m_parent; +}; + +PYBIND11_NAMESPACE_END(detail) + +/// Binds C++ enumerations and enumeration classes to Python +template class enum_ : public class_ { +public: + using Base = class_; + using Base::def; + using Base::attr; + using Base::def_property_readonly; + using Base::def_property_readonly_static; + using Scalar = typename std::underlying_type::type; + + template + enum_(const handle &scope, const char *name, const Extra&... extra) + : class_(scope, name, extra...), m_base(*this, scope) { + constexpr bool is_arithmetic = detail::any_of...>::value; + constexpr bool is_convertible = std::is_convertible::value; + m_base.init(is_arithmetic, is_convertible); + + def(init([](Scalar i) { return static_cast(i); }), arg("value")); + def_property_readonly("value", [](Type value) { return (Scalar) value; }); + def("__int__", [](Type value) { return (Scalar) value; }); + #if PY_MAJOR_VERSION < 3 + def("__long__", [](Type value) { return (Scalar) value; }); + #endif + #if PY_MAJOR_VERSION > 3 || (PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION >= 8) + def("__index__", [](Type value) { return (Scalar) value; }); + #endif + + attr("__setstate__") = cpp_function( + [](detail::value_and_holder &v_h, Scalar arg) { + detail::initimpl::setstate(v_h, static_cast(arg), + Py_TYPE(v_h.inst) != v_h.type->type); }, + detail::is_new_style_constructor(), + pybind11::name("__setstate__"), is_method(*this), arg("state")); + } + + /// Export enumeration entries into the parent scope + enum_& export_values() { + m_base.export_values(); + return *this; + } + + /// Add an enumeration entry + enum_& value(char const* name, Type value, const char *doc = nullptr) { + m_base.value(name, pybind11::cast(value, return_value_policy::copy), doc); + return *this; + } + +private: + detail::enum_base m_base; +}; + +PYBIND11_NAMESPACE_BEGIN(detail) + + +inline void keep_alive_impl(handle nurse, handle patient) { + if (!nurse || !patient) + pybind11_fail("Could not activate keep_alive!"); + + if (patient.is_none() || nurse.is_none()) + return; /* Nothing to keep alive or nothing to be kept alive by */ + + auto tinfo = all_type_info(Py_TYPE(nurse.ptr())); + if (!tinfo.empty()) { + /* It's a pybind-registered type, so we can store the patient in the + * internal list. */ + add_patient(nurse.ptr(), patient.ptr()); + } + else { + /* Fall back to clever approach based on weak references taken from + * Boost.Python. This is not used for pybind-registered types because + * the objects can be destroyed out-of-order in a GC pass. */ + cpp_function disable_lifesupport( + [patient](handle weakref) { patient.dec_ref(); weakref.dec_ref(); }); + + weakref wr(nurse, disable_lifesupport); + + patient.inc_ref(); /* reference patient and leak the weak reference */ + (void) wr.release(); + } +} + +PYBIND11_NOINLINE inline void keep_alive_impl(size_t Nurse, size_t Patient, function_call &call, handle ret) { + auto get_arg = [&](size_t n) { + if (n == 0) + return ret; + else if (n == 1 && call.init_self) + return call.init_self; + else if (n <= call.args.size()) + return call.args[n - 1]; + return handle(); + }; + + keep_alive_impl(get_arg(Nurse), get_arg(Patient)); +} + +inline std::pair all_type_info_get_cache(PyTypeObject *type) { + auto res = get_internals().registered_types_py +#ifdef __cpp_lib_unordered_map_try_emplace + .try_emplace(type); +#else + .emplace(type, std::vector()); +#endif + if (res.second) { + // New cache entry created; set up a weak reference to automatically remove it if the type + // gets destroyed: + weakref((PyObject *) type, cpp_function([type](handle wr) { + get_internals().registered_types_py.erase(type); + wr.dec_ref(); + })).release(); + } + + return res; +} + +template +struct iterator_state { + Iterator it; + Sentinel end; + bool first_or_done; +}; + +PYBIND11_NAMESPACE_END(detail) + +/// Makes a python iterator from a first and past-the-end C++ InputIterator. +template ()), +#endif + typename... Extra> +iterator make_iterator(Iterator first, Sentinel last, Extra &&... extra) { + using state = detail::iterator_state; + + if (!detail::get_type_info(typeid(state), false)) { + class_(handle(), "iterator", pybind11::module_local()) + .def("__iter__", [](state &s) -> state& { return s; }) + .def("__next__", [](state &s) -> ValueType { + if (!s.first_or_done) + ++s.it; + else + s.first_or_done = false; + if (s.it == s.end) { + s.first_or_done = true; + throw stop_iteration(); + } + return *s.it; + }, std::forward(extra)..., Policy); + } + + return cast(state{first, last, true}); +} + +/// Makes an python iterator over the keys (`.first`) of a iterator over pairs from a +/// first and past-the-end InputIterator. +template ()).first), +#endif + typename... Extra> +iterator make_key_iterator(Iterator first, Sentinel last, Extra &&... extra) { + using state = detail::iterator_state; + + if (!detail::get_type_info(typeid(state), false)) { + class_(handle(), "iterator", pybind11::module_local()) + .def("__iter__", [](state &s) -> state& { return s; }) + .def("__next__", [](state &s) -> KeyType { + if (!s.first_or_done) + ++s.it; + else + s.first_or_done = false; + if (s.it == s.end) { + s.first_or_done = true; + throw stop_iteration(); + } + return (*s.it).first; + }, std::forward(extra)..., Policy); + } + + return cast(state{first, last, true}); +} + +/// Makes an iterator over values of an stl container or other container supporting +/// `std::begin()`/`std::end()` +template iterator make_iterator(Type &value, Extra&&... extra) { + return make_iterator(std::begin(value), std::end(value), extra...); +} + +/// Makes an iterator over the keys (`.first`) of a stl map-like container supporting +/// `std::begin()`/`std::end()` +template iterator make_key_iterator(Type &value, Extra&&... extra) { + return make_key_iterator(std::begin(value), std::end(value), extra...); +} + +template void implicitly_convertible() { + struct set_flag { + bool &flag; + set_flag(bool &flag_) : flag(flag_) { flag_ = true; } + ~set_flag() { flag = false; } + }; + auto implicit_caster = [](PyObject *obj, PyTypeObject *type) -> PyObject * { + static bool currently_used = false; + if (currently_used) // implicit conversions are non-reentrant + return nullptr; + set_flag flag_helper(currently_used); + if (!detail::make_caster().load(obj, false)) + return nullptr; + tuple args(1); + args[0] = obj; + PyObject *result = PyObject_Call((PyObject *) type, args.ptr(), nullptr); + if (result == nullptr) + PyErr_Clear(); + return result; + }; + + if (auto tinfo = detail::get_type_info(typeid(OutputType))) + tinfo->implicit_conversions.push_back(implicit_caster); + else + pybind11_fail("implicitly_convertible: Unable to find type " + type_id()); +} + +template +void register_exception_translator(ExceptionTranslator&& translator) { + detail::get_internals().registered_exception_translators.push_front( + std::forward(translator)); +} + +/** + * Wrapper to generate a new Python exception type. + * + * This should only be used with PyErr_SetString for now. + * It is not (yet) possible to use as a py::base. + * Template type argument is reserved for future use. + */ +template +class exception : public object { +public: + exception() = default; + exception(handle scope, const char *name, handle base = PyExc_Exception) { + std::string full_name = scope.attr("__name__").cast() + + std::string(".") + name; + m_ptr = PyErr_NewException(const_cast(full_name.c_str()), base.ptr(), NULL); + if (hasattr(scope, "__dict__") && scope.attr("__dict__").contains(name)) + pybind11_fail("Error during initialization: multiple incompatible " + "definitions with name \"" + std::string(name) + "\""); + scope.attr(name) = *this; + } + + // Sets the current python exception to this exception object with the given message + void operator()(const char *message) { + PyErr_SetString(m_ptr, message); + } +}; + +PYBIND11_NAMESPACE_BEGIN(detail) +// Returns a reference to a function-local static exception object used in the simple +// register_exception approach below. (It would be simpler to have the static local variable +// directly in register_exception, but that makes clang <3.5 segfault - issue #1349). +template +exception &get_exception_object() { static exception ex; return ex; } +PYBIND11_NAMESPACE_END(detail) + +/** + * Registers a Python exception in `m` of the given `name` and installs an exception translator to + * translate the C++ exception to the created Python exception using the exceptions what() method. + * This is intended for simple exception translations; for more complex translation, register the + * exception object and translator directly. + */ +template +exception ®ister_exception(handle scope, + const char *name, + handle base = PyExc_Exception) { + auto &ex = detail::get_exception_object(); + if (!ex) ex = exception(scope, name, base); + + register_exception_translator([](std::exception_ptr p) { + if (!p) return; + try { + std::rethrow_exception(p); + } catch (const CppException &e) { + detail::get_exception_object()(e.what()); + } + }); + return ex; +} + +PYBIND11_NAMESPACE_BEGIN(detail) +PYBIND11_NOINLINE inline void print(tuple args, dict kwargs) { + auto strings = tuple(args.size()); + for (size_t i = 0; i < args.size(); ++i) { + strings[i] = str(args[i]); + } + auto sep = kwargs.contains("sep") ? kwargs["sep"] : cast(" "); + auto line = sep.attr("join")(strings); + + object file; + if (kwargs.contains("file")) { + file = kwargs["file"].cast(); + } else { + try { + file = module_::import("sys").attr("stdout"); + } catch (const error_already_set &) { + /* If print() is called from code that is executed as + part of garbage collection during interpreter shutdown, + importing 'sys' can fail. Give up rather than crashing the + interpreter in this case. */ + return; + } + } + + auto write = file.attr("write"); + write(line); + write(kwargs.contains("end") ? kwargs["end"] : cast("\n")); + + if (kwargs.contains("flush") && kwargs["flush"].cast()) + file.attr("flush")(); +} +PYBIND11_NAMESPACE_END(detail) + +template +void print(Args &&...args) { + auto c = detail::collect_arguments(std::forward(args)...); + detail::print(c.args(), c.kwargs()); +} + +error_already_set::~error_already_set() { + if (m_type) { + gil_scoped_acquire gil; + error_scope scope; + m_type.release().dec_ref(); + m_value.release().dec_ref(); + m_trace.release().dec_ref(); + } +} + +PYBIND11_NAMESPACE_BEGIN(detail) +inline function get_type_override(const void *this_ptr, const type_info *this_type, const char *name) { + handle self = get_object_handle(this_ptr, this_type); + if (!self) + return function(); + handle type = type::handle_of(self); + auto key = std::make_pair(type.ptr(), name); + + /* Cache functions that aren't overridden in Python to avoid + many costly Python dictionary lookups below */ + auto &cache = get_internals().inactive_override_cache; + if (cache.find(key) != cache.end()) + return function(); + + function override = getattr(self, name, function()); + if (override.is_cpp_function()) { + cache.insert(key); + return function(); + } + + /* Don't call dispatch code if invoked from overridden function. + Unfortunately this doesn't work on PyPy. */ +#if !defined(PYPY_VERSION) + PyFrameObject *frame = PyThreadState_Get()->frame; + if (frame && (std::string) str(frame->f_code->co_name) == name && + frame->f_code->co_argcount > 0) { + PyFrame_FastToLocals(frame); + PyObject *self_caller = PyDict_GetItem( + frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); + if (self_caller == self.ptr()) + return function(); + } +#else + /* PyPy currently doesn't provide a detailed cpyext emulation of + frame objects, so we have to emulate this using Python. This + is going to be slow..*/ + dict d; d["self"] = self; d["name"] = pybind11::str(name); + PyObject *result = PyRun_String( + "import inspect\n" + "frame = inspect.currentframe()\n" + "if frame is not None:\n" + " frame = frame.f_back\n" + " if frame is not None and str(frame.f_code.co_name) == name and " + "frame.f_code.co_argcount > 0:\n" + " self_caller = frame.f_locals[frame.f_code.co_varnames[0]]\n" + " if self_caller == self:\n" + " self = None\n", + Py_file_input, d.ptr(), d.ptr()); + if (result == nullptr) + throw error_already_set(); + if (d["self"].is_none()) + return function(); + Py_DECREF(result); +#endif + + return override; +} +PYBIND11_NAMESPACE_END(detail) + +/** \rst + Try to retrieve a python method by the provided name from the instance pointed to by the this_ptr. + + :this_ptr: The pointer to the object the overridden method should be retrieved for. This should be + the first non-trampoline class encountered in the inheritance chain. + :name: The name of the overridden Python method to retrieve. + :return: The Python method by this name from the object or an empty function wrapper. + \endrst */ +template function get_override(const T *this_ptr, const char *name) { + auto tinfo = detail::get_type_info(typeid(T)); + return tinfo ? detail::get_type_override(this_ptr, tinfo, name) : function(); +} + +#define PYBIND11_OVERRIDE_IMPL(ret_type, cname, name, ...) \ + do { \ + pybind11::gil_scoped_acquire gil; \ + pybind11::function override = pybind11::get_override(static_cast(this), name); \ + if (override) { \ + auto o = override(__VA_ARGS__); \ + if (pybind11::detail::cast_is_temporary_value_reference::value) { \ + static pybind11::detail::override_caster_t caster; \ + return pybind11::detail::cast_ref(std::move(o), caster); \ + } \ + else return pybind11::detail::cast_safe(std::move(o)); \ + } \ + } while (false) + +/** \rst + Macro to populate the virtual method in the trampoline class. This macro tries to look up a method named 'fn' + from the Python side, deals with the :ref:`gil` and necessary argument conversions to call this method and return + the appropriate type. See :ref:`overriding_virtuals` for more information. This macro should be used when the method + name in C is not the same as the method name in Python. For example with `__str__`. + + .. code-block:: cpp + + std::string toString() override { + PYBIND11_OVERRIDE_NAME( + std::string, // Return type (ret_type) + Animal, // Parent class (cname) + "__str__", // Name of method in Python (name) + toString, // Name of function in C++ (fn) + ); + } +\endrst */ +#define PYBIND11_OVERRIDE_NAME(ret_type, cname, name, fn, ...) \ + do { \ + PYBIND11_OVERRIDE_IMPL(PYBIND11_TYPE(ret_type), PYBIND11_TYPE(cname), name, __VA_ARGS__); \ + return cname::fn(__VA_ARGS__); \ + } while (false) + +/** \rst + Macro for pure virtual functions, this function is identical to :c:macro:`PYBIND11_OVERRIDE_NAME`, except that it + throws if no override can be found. +\endrst */ +#define PYBIND11_OVERRIDE_PURE_NAME(ret_type, cname, name, fn, ...) \ + do { \ + PYBIND11_OVERRIDE_IMPL(PYBIND11_TYPE(ret_type), PYBIND11_TYPE(cname), name, __VA_ARGS__); \ + pybind11::pybind11_fail("Tried to call pure virtual function \"" PYBIND11_STRINGIFY(cname) "::" name "\""); \ + } while (false) + +/** \rst + Macro to populate the virtual method in the trampoline class. This macro tries to look up the method + from the Python side, deals with the :ref:`gil` and necessary argument conversions to call this method and return + the appropriate type. This macro should be used if the method name in C and in Python are identical. + See :ref:`overriding_virtuals` for more information. + + .. code-block:: cpp + + class PyAnimal : public Animal { + public: + // Inherit the constructors + using Animal::Animal; + + // Trampoline (need one for each virtual function) + std::string go(int n_times) override { + PYBIND11_OVERRIDE_PURE( + std::string, // Return type (ret_type) + Animal, // Parent class (cname) + go, // Name of function in C++ (must match Python name) (fn) + n_times // Argument(s) (...) + ); + } + }; +\endrst */ +#define PYBIND11_OVERRIDE(ret_type, cname, fn, ...) \ + PYBIND11_OVERRIDE_NAME(PYBIND11_TYPE(ret_type), PYBIND11_TYPE(cname), #fn, fn, __VA_ARGS__) + +/** \rst + Macro for pure virtual functions, this function is identical to :c:macro:`PYBIND11_OVERRIDE`, except that it throws + if no override can be found. +\endrst */ +#define PYBIND11_OVERRIDE_PURE(ret_type, cname, fn, ...) \ + PYBIND11_OVERRIDE_PURE_NAME(PYBIND11_TYPE(ret_type), PYBIND11_TYPE(cname), #fn, fn, __VA_ARGS__) + + +// Deprecated versions + +PYBIND11_DEPRECATED("get_type_overload has been deprecated") +inline function get_type_overload(const void *this_ptr, const detail::type_info *this_type, const char *name) { + return detail::get_type_override(this_ptr, this_type, name); +} + +template +inline function get_overload(const T *this_ptr, const char *name) { + return get_override(this_ptr, name); +} + +#define PYBIND11_OVERLOAD_INT(ret_type, cname, name, ...) \ + PYBIND11_OVERRIDE_IMPL(PYBIND11_TYPE(ret_type), PYBIND11_TYPE(cname), name, __VA_ARGS__) +#define PYBIND11_OVERLOAD_NAME(ret_type, cname, name, fn, ...) \ + PYBIND11_OVERRIDE_NAME(PYBIND11_TYPE(ret_type), PYBIND11_TYPE(cname), name, fn, __VA_ARGS__) +#define PYBIND11_OVERLOAD_PURE_NAME(ret_type, cname, name, fn, ...) \ + PYBIND11_OVERRIDE_PURE_NAME(PYBIND11_TYPE(ret_type), PYBIND11_TYPE(cname), name, fn, __VA_ARGS__); +#define PYBIND11_OVERLOAD(ret_type, cname, fn, ...) \ + PYBIND11_OVERRIDE(PYBIND11_TYPE(ret_type), PYBIND11_TYPE(cname), fn, __VA_ARGS__) +#define PYBIND11_OVERLOAD_PURE(ret_type, cname, fn, ...) \ + PYBIND11_OVERRIDE_PURE(PYBIND11_TYPE(ret_type), PYBIND11_TYPE(cname), fn, __VA_ARGS__); + +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) + +#if defined(_MSC_VER) && !defined(__INTEL_COMPILER) +# pragma warning(pop) +#elif defined(__GNUG__) && !defined(__clang__) +# pragma GCC diagnostic pop +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/pytypes.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/pytypes.h new file mode 100644 index 0000000000000000000000000000000000000000..6f0e6067efebe74644c9e6d42cf4566010e2f1d1 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/pytypes.h @@ -0,0 +1,1712 @@ +/* + pybind11/pytypes.h: Convenience wrapper classes for basic Python types + + Copyright (c) 2016 Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "detail/common.h" +#include "buffer_info.h" +#include +#include + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) + +/* A few forward declarations */ +class handle; class object; +class str; class iterator; +class type; +struct arg; struct arg_v; + +PYBIND11_NAMESPACE_BEGIN(detail) +class args_proxy; +inline bool isinstance_generic(handle obj, const std::type_info &tp); + +// Accessor forward declarations +template class accessor; +namespace accessor_policies { + struct obj_attr; + struct str_attr; + struct generic_item; + struct sequence_item; + struct list_item; + struct tuple_item; +} // namespace accessor_policies +using obj_attr_accessor = accessor; +using str_attr_accessor = accessor; +using item_accessor = accessor; +using sequence_accessor = accessor; +using list_accessor = accessor; +using tuple_accessor = accessor; + +/// Tag and check to identify a class which implements the Python object API +class pyobject_tag { }; +template using is_pyobject = std::is_base_of>; + +/** \rst + A mixin class which adds common functions to `handle`, `object` and various accessors. + The only requirement for `Derived` is to implement ``PyObject *Derived::ptr() const``. +\endrst */ +template +class object_api : public pyobject_tag { + const Derived &derived() const { return static_cast(*this); } + +public: + /** \rst + Return an iterator equivalent to calling ``iter()`` in Python. The object + must be a collection which supports the iteration protocol. + \endrst */ + iterator begin() const; + /// Return a sentinel which ends iteration. + iterator end() const; + + /** \rst + Return an internal functor to invoke the object's sequence protocol. Casting + the returned ``detail::item_accessor`` instance to a `handle` or `object` + subclass causes a corresponding call to ``__getitem__``. Assigning a `handle` + or `object` subclass causes a call to ``__setitem__``. + \endrst */ + item_accessor operator[](handle key) const; + /// See above (the only difference is that they key is provided as a string literal) + item_accessor operator[](const char *key) const; + + /** \rst + Return an internal functor to access the object's attributes. Casting the + returned ``detail::obj_attr_accessor`` instance to a `handle` or `object` + subclass causes a corresponding call to ``getattr``. Assigning a `handle` + or `object` subclass causes a call to ``setattr``. + \endrst */ + obj_attr_accessor attr(handle key) const; + /// See above (the only difference is that they key is provided as a string literal) + str_attr_accessor attr(const char *key) const; + + /** \rst + Matches * unpacking in Python, e.g. to unpack arguments out of a ``tuple`` + or ``list`` for a function call. Applying another * to the result yields + ** unpacking, e.g. to unpack a dict as function keyword arguments. + See :ref:`calling_python_functions`. + \endrst */ + args_proxy operator*() const; + + /// Check if the given item is contained within this object, i.e. ``item in obj``. + template bool contains(T &&item) const; + + /** \rst + Assuming the Python object is a function or implements the ``__call__`` + protocol, ``operator()`` invokes the underlying function, passing an + arbitrary set of parameters. The result is returned as a `object` and + may need to be converted back into a Python object using `handle::cast()`. + + When some of the arguments cannot be converted to Python objects, the + function will throw a `cast_error` exception. When the Python function + call fails, a `error_already_set` exception is thrown. + \endrst */ + template + object operator()(Args &&...args) const; + template + PYBIND11_DEPRECATED("call(...) was deprecated in favor of operator()(...)") + object call(Args&&... args) const; + + /// Equivalent to ``obj is other`` in Python. + bool is(object_api const& other) const { return derived().ptr() == other.derived().ptr(); } + /// Equivalent to ``obj is None`` in Python. + bool is_none() const { return derived().ptr() == Py_None; } + /// Equivalent to obj == other in Python + bool equal(object_api const &other) const { return rich_compare(other, Py_EQ); } + bool not_equal(object_api const &other) const { return rich_compare(other, Py_NE); } + bool operator<(object_api const &other) const { return rich_compare(other, Py_LT); } + bool operator<=(object_api const &other) const { return rich_compare(other, Py_LE); } + bool operator>(object_api const &other) const { return rich_compare(other, Py_GT); } + bool operator>=(object_api const &other) const { return rich_compare(other, Py_GE); } + + object operator-() const; + object operator~() const; + object operator+(object_api const &other) const; + object operator+=(object_api const &other) const; + object operator-(object_api const &other) const; + object operator-=(object_api const &other) const; + object operator*(object_api const &other) const; + object operator*=(object_api const &other) const; + object operator/(object_api const &other) const; + object operator/=(object_api const &other) const; + object operator|(object_api const &other) const; + object operator|=(object_api const &other) const; + object operator&(object_api const &other) const; + object operator&=(object_api const &other) const; + object operator^(object_api const &other) const; + object operator^=(object_api const &other) const; + object operator<<(object_api const &other) const; + object operator<<=(object_api const &other) const; + object operator>>(object_api const &other) const; + object operator>>=(object_api const &other) const; + + PYBIND11_DEPRECATED("Use py::str(obj) instead") + pybind11::str str() const; + + /// Get or set the object's docstring, i.e. ``obj.__doc__``. + str_attr_accessor doc() const; + + /// Return the object's current reference count + int ref_count() const { return static_cast(Py_REFCNT(derived().ptr())); } + + // TODO PYBIND11_DEPRECATED("Call py::type::handle_of(h) or py::type::of(h) instead of h.get_type()") + handle get_type() const; + +private: + bool rich_compare(object_api const &other, int value) const; +}; + +PYBIND11_NAMESPACE_END(detail) + +/** \rst + Holds a reference to a Python object (no reference counting) + + The `handle` class is a thin wrapper around an arbitrary Python object (i.e. a + ``PyObject *`` in Python's C API). It does not perform any automatic reference + counting and merely provides a basic C++ interface to various Python API functions. + + .. seealso:: + The `object` class inherits from `handle` and adds automatic reference + counting features. +\endrst */ +class handle : public detail::object_api { +public: + /// The default constructor creates a handle with a ``nullptr``-valued pointer + handle() = default; + /// Creates a ``handle`` from the given raw Python object pointer + handle(PyObject *ptr) : m_ptr(ptr) { } // Allow implicit conversion from PyObject* + + /// Return the underlying ``PyObject *`` pointer + PyObject *ptr() const { return m_ptr; } + PyObject *&ptr() { return m_ptr; } + + /** \rst + Manually increase the reference count of the Python object. Usually, it is + preferable to use the `object` class which derives from `handle` and calls + this function automatically. Returns a reference to itself. + \endrst */ + const handle& inc_ref() const & { Py_XINCREF(m_ptr); return *this; } + + /** \rst + Manually decrease the reference count of the Python object. Usually, it is + preferable to use the `object` class which derives from `handle` and calls + this function automatically. Returns a reference to itself. + \endrst */ + const handle& dec_ref() const & { Py_XDECREF(m_ptr); return *this; } + + /** \rst + Attempt to cast the Python object into the given C++ type. A `cast_error` + will be throw upon failure. + \endrst */ + template T cast() const; + /// Return ``true`` when the `handle` wraps a valid Python object + explicit operator bool() const { return m_ptr != nullptr; } + /** \rst + Deprecated: Check that the underlying pointers are the same. + Equivalent to ``obj1 is obj2`` in Python. + \endrst */ + PYBIND11_DEPRECATED("Use obj1.is(obj2) instead") + bool operator==(const handle &h) const { return m_ptr == h.m_ptr; } + PYBIND11_DEPRECATED("Use !obj1.is(obj2) instead") + bool operator!=(const handle &h) const { return m_ptr != h.m_ptr; } + PYBIND11_DEPRECATED("Use handle::operator bool() instead") + bool check() const { return m_ptr != nullptr; } +protected: + PyObject *m_ptr = nullptr; +}; + +/** \rst + Holds a reference to a Python object (with reference counting) + + Like `handle`, the `object` class is a thin wrapper around an arbitrary Python + object (i.e. a ``PyObject *`` in Python's C API). In contrast to `handle`, it + optionally increases the object's reference count upon construction, and it + *always* decreases the reference count when the `object` instance goes out of + scope and is destructed. When using `object` instances consistently, it is much + easier to get reference counting right at the first attempt. +\endrst */ +class object : public handle { +public: + object() = default; + PYBIND11_DEPRECATED("Use reinterpret_borrow() or reinterpret_steal()") + object(handle h, bool is_borrowed) : handle(h) { if (is_borrowed) inc_ref(); } + /// Copy constructor; always increases the reference count + object(const object &o) : handle(o) { inc_ref(); } + /// Move constructor; steals the object from ``other`` and preserves its reference count + object(object &&other) noexcept { m_ptr = other.m_ptr; other.m_ptr = nullptr; } + /// Destructor; automatically calls `handle::dec_ref()` + ~object() { dec_ref(); } + + /** \rst + Resets the internal pointer to ``nullptr`` without decreasing the + object's reference count. The function returns a raw handle to the original + Python object. + \endrst */ + handle release() { + PyObject *tmp = m_ptr; + m_ptr = nullptr; + return handle(tmp); + } + + object& operator=(const object &other) { + other.inc_ref(); + dec_ref(); + m_ptr = other.m_ptr; + return *this; + } + + object& operator=(object &&other) noexcept { + if (this != &other) { + handle temp(m_ptr); + m_ptr = other.m_ptr; + other.m_ptr = nullptr; + temp.dec_ref(); + } + return *this; + } + + // Calling cast() on an object lvalue just copies (via handle::cast) + template T cast() const &; + // Calling on an object rvalue does a move, if needed and/or possible + template T cast() &&; + +protected: + // Tags for choosing constructors from raw PyObject * + struct borrowed_t { }; + struct stolen_t { }; + +#ifndef DOXYGEN_SHOULD_SKIP_THIS // Issue in breathe 4.26.1 + template friend T reinterpret_borrow(handle); + template friend T reinterpret_steal(handle); +#endif + +public: + // Only accessible from derived classes and the reinterpret_* functions + object(handle h, borrowed_t) : handle(h) { inc_ref(); } + object(handle h, stolen_t) : handle(h) { } +}; + +/** \rst + Declare that a `handle` or ``PyObject *`` is a certain type and borrow the reference. + The target type ``T`` must be `object` or one of its derived classes. The function + doesn't do any conversions or checks. It's up to the user to make sure that the + target type is correct. + + .. code-block:: cpp + + PyObject *p = PyList_GetItem(obj, index); + py::object o = reinterpret_borrow(p); + // or + py::tuple t = reinterpret_borrow(p); // <-- `p` must be already be a `tuple` +\endrst */ +template T reinterpret_borrow(handle h) { return {h, object::borrowed_t{}}; } + +/** \rst + Like `reinterpret_borrow`, but steals the reference. + + .. code-block:: cpp + + PyObject *p = PyObject_Str(obj); + py::str s = reinterpret_steal(p); // <-- `p` must be already be a `str` +\endrst */ +template T reinterpret_steal(handle h) { return {h, object::stolen_t{}}; } + +PYBIND11_NAMESPACE_BEGIN(detail) +inline std::string error_string(); +PYBIND11_NAMESPACE_END(detail) + +/// Fetch and hold an error which was already set in Python. An instance of this is typically +/// thrown to propagate python-side errors back through C++ which can either be caught manually or +/// else falls back to the function dispatcher (which then raises the captured error back to +/// python). +class error_already_set : public std::runtime_error { +public: + /// Constructs a new exception from the current Python error indicator, if any. The current + /// Python error indicator will be cleared. + error_already_set() : std::runtime_error(detail::error_string()) { + PyErr_Fetch(&m_type.ptr(), &m_value.ptr(), &m_trace.ptr()); + } + + error_already_set(const error_already_set &) = default; + error_already_set(error_already_set &&) = default; + + inline ~error_already_set() override; + + /// Give the currently-held error back to Python, if any. If there is currently a Python error + /// already set it is cleared first. After this call, the current object no longer stores the + /// error variables (but the `.what()` string is still available). + void restore() { PyErr_Restore(m_type.release().ptr(), m_value.release().ptr(), m_trace.release().ptr()); } + + /// If it is impossible to raise the currently-held error, such as in destructor, we can write + /// it out using Python's unraisable hook (sys.unraisablehook). The error context should be + /// some object whose repr() helps identify the location of the error. Python already knows the + /// type and value of the error, so there is no need to repeat that. For example, __func__ could + /// be helpful. After this call, the current object no longer stores the error variables, + /// and neither does Python. + void discard_as_unraisable(object err_context) { + restore(); + PyErr_WriteUnraisable(err_context.ptr()); + } + void discard_as_unraisable(const char *err_context) { + discard_as_unraisable(reinterpret_steal(PYBIND11_FROM_STRING(err_context))); + } + + // Does nothing; provided for backwards compatibility. + PYBIND11_DEPRECATED("Use of error_already_set.clear() is deprecated") + void clear() {} + + /// Check if the currently trapped error type matches the given Python exception class (or a + /// subclass thereof). May also be passed a tuple to search for any exception class matches in + /// the given tuple. + bool matches(handle exc) const { return PyErr_GivenExceptionMatches(m_type.ptr(), exc.ptr()); } + + const object& type() const { return m_type; } + const object& value() const { return m_value; } + const object& trace() const { return m_trace; } + +private: + object m_type, m_value, m_trace; +}; + +/** \defgroup python_builtins _ + Unless stated otherwise, the following C++ functions behave the same + as their Python counterparts. + */ + +/** \ingroup python_builtins + \rst + Return true if ``obj`` is an instance of ``T``. Type ``T`` must be a subclass of + `object` or a class which was exposed to Python as ``py::class_``. +\endrst */ +template ::value, int> = 0> +bool isinstance(handle obj) { return T::check_(obj); } + +template ::value, int> = 0> +bool isinstance(handle obj) { return detail::isinstance_generic(obj, typeid(T)); } + +template <> inline bool isinstance(handle) = delete; +template <> inline bool isinstance(handle obj) { return obj.ptr() != nullptr; } + +/// \ingroup python_builtins +/// Return true if ``obj`` is an instance of the ``type``. +inline bool isinstance(handle obj, handle type) { + const auto result = PyObject_IsInstance(obj.ptr(), type.ptr()); + if (result == -1) + throw error_already_set(); + return result != 0; +} + +/// \addtogroup python_builtins +/// @{ +inline bool hasattr(handle obj, handle name) { + return PyObject_HasAttr(obj.ptr(), name.ptr()) == 1; +} + +inline bool hasattr(handle obj, const char *name) { + return PyObject_HasAttrString(obj.ptr(), name) == 1; +} + +inline void delattr(handle obj, handle name) { + if (PyObject_DelAttr(obj.ptr(), name.ptr()) != 0) { throw error_already_set(); } +} + +inline void delattr(handle obj, const char *name) { + if (PyObject_DelAttrString(obj.ptr(), name) != 0) { throw error_already_set(); } +} + +inline object getattr(handle obj, handle name) { + PyObject *result = PyObject_GetAttr(obj.ptr(), name.ptr()); + if (!result) { throw error_already_set(); } + return reinterpret_steal(result); +} + +inline object getattr(handle obj, const char *name) { + PyObject *result = PyObject_GetAttrString(obj.ptr(), name); + if (!result) { throw error_already_set(); } + return reinterpret_steal(result); +} + +inline object getattr(handle obj, handle name, handle default_) { + if (PyObject *result = PyObject_GetAttr(obj.ptr(), name.ptr())) { + return reinterpret_steal(result); + } else { + PyErr_Clear(); + return reinterpret_borrow(default_); + } +} + +inline object getattr(handle obj, const char *name, handle default_) { + if (PyObject *result = PyObject_GetAttrString(obj.ptr(), name)) { + return reinterpret_steal(result); + } else { + PyErr_Clear(); + return reinterpret_borrow(default_); + } +} + +inline void setattr(handle obj, handle name, handle value) { + if (PyObject_SetAttr(obj.ptr(), name.ptr(), value.ptr()) != 0) { throw error_already_set(); } +} + +inline void setattr(handle obj, const char *name, handle value) { + if (PyObject_SetAttrString(obj.ptr(), name, value.ptr()) != 0) { throw error_already_set(); } +} + +inline ssize_t hash(handle obj) { + auto h = PyObject_Hash(obj.ptr()); + if (h == -1) { throw error_already_set(); } + return h; +} + +/// @} python_builtins + +PYBIND11_NAMESPACE_BEGIN(detail) +inline handle get_function(handle value) { + if (value) { +#if PY_MAJOR_VERSION >= 3 + if (PyInstanceMethod_Check(value.ptr())) + value = PyInstanceMethod_GET_FUNCTION(value.ptr()); + else +#endif + if (PyMethod_Check(value.ptr())) + value = PyMethod_GET_FUNCTION(value.ptr()); + } + return value; +} + +// Helper aliases/functions to support implicit casting of values given to python accessors/methods. +// When given a pyobject, this simply returns the pyobject as-is; for other C++ type, the value goes +// through pybind11::cast(obj) to convert it to an `object`. +template ::value, int> = 0> +auto object_or_cast(T &&o) -> decltype(std::forward(o)) { return std::forward(o); } +// The following casting version is implemented in cast.h: +template ::value, int> = 0> +object object_or_cast(T &&o); +// Match a PyObject*, which we want to convert directly to handle via its converting constructor +inline handle object_or_cast(PyObject *ptr) { return ptr; } + +template +class accessor : public object_api> { + using key_type = typename Policy::key_type; + +public: + accessor(handle obj, key_type key) : obj(obj), key(std::move(key)) { } + accessor(const accessor &) = default; + accessor(accessor &&) = default; + + // accessor overload required to override default assignment operator (templates are not allowed + // to replace default compiler-generated assignments). + void operator=(const accessor &a) && { std::move(*this).operator=(handle(a)); } + void operator=(const accessor &a) & { operator=(handle(a)); } + + template void operator=(T &&value) && { + Policy::set(obj, key, object_or_cast(std::forward(value))); + } + template void operator=(T &&value) & { + get_cache() = reinterpret_borrow(object_or_cast(std::forward(value))); + } + + template + PYBIND11_DEPRECATED("Use of obj.attr(...) as bool is deprecated in favor of pybind11::hasattr(obj, ...)") + explicit operator enable_if_t::value || + std::is_same::value, bool>() const { + return hasattr(obj, key); + } + template + PYBIND11_DEPRECATED("Use of obj[key] as bool is deprecated in favor of obj.contains(key)") + explicit operator enable_if_t::value, bool>() const { + return obj.contains(key); + } + + operator object() const { return get_cache(); } + PyObject *ptr() const { return get_cache().ptr(); } + template T cast() const { return get_cache().template cast(); } + +private: + object &get_cache() const { + if (!cache) { cache = Policy::get(obj, key); } + return cache; + } + +private: + handle obj; + key_type key; + mutable object cache; +}; + +PYBIND11_NAMESPACE_BEGIN(accessor_policies) +struct obj_attr { + using key_type = object; + static object get(handle obj, handle key) { return getattr(obj, key); } + static void set(handle obj, handle key, handle val) { setattr(obj, key, val); } +}; + +struct str_attr { + using key_type = const char *; + static object get(handle obj, const char *key) { return getattr(obj, key); } + static void set(handle obj, const char *key, handle val) { setattr(obj, key, val); } +}; + +struct generic_item { + using key_type = object; + + static object get(handle obj, handle key) { + PyObject *result = PyObject_GetItem(obj.ptr(), key.ptr()); + if (!result) { throw error_already_set(); } + return reinterpret_steal(result); + } + + static void set(handle obj, handle key, handle val) { + if (PyObject_SetItem(obj.ptr(), key.ptr(), val.ptr()) != 0) { throw error_already_set(); } + } +}; + +struct sequence_item { + using key_type = size_t; + + static object get(handle obj, size_t index) { + PyObject *result = PySequence_GetItem(obj.ptr(), static_cast(index)); + if (!result) { throw error_already_set(); } + return reinterpret_steal(result); + } + + static void set(handle obj, size_t index, handle val) { + // PySequence_SetItem does not steal a reference to 'val' + if (PySequence_SetItem(obj.ptr(), static_cast(index), val.ptr()) != 0) { + throw error_already_set(); + } + } +}; + +struct list_item { + using key_type = size_t; + + static object get(handle obj, size_t index) { + PyObject *result = PyList_GetItem(obj.ptr(), static_cast(index)); + if (!result) { throw error_already_set(); } + return reinterpret_borrow(result); + } + + static void set(handle obj, size_t index, handle val) { + // PyList_SetItem steals a reference to 'val' + if (PyList_SetItem(obj.ptr(), static_cast(index), val.inc_ref().ptr()) != 0) { + throw error_already_set(); + } + } +}; + +struct tuple_item { + using key_type = size_t; + + static object get(handle obj, size_t index) { + PyObject *result = PyTuple_GetItem(obj.ptr(), static_cast(index)); + if (!result) { throw error_already_set(); } + return reinterpret_borrow(result); + } + + static void set(handle obj, size_t index, handle val) { + // PyTuple_SetItem steals a reference to 'val' + if (PyTuple_SetItem(obj.ptr(), static_cast(index), val.inc_ref().ptr()) != 0) { + throw error_already_set(); + } + } +}; +PYBIND11_NAMESPACE_END(accessor_policies) + +/// STL iterator template used for tuple, list, sequence and dict +template +class generic_iterator : public Policy { + using It = generic_iterator; + +public: + using difference_type = ssize_t; + using iterator_category = typename Policy::iterator_category; + using value_type = typename Policy::value_type; + using reference = typename Policy::reference; + using pointer = typename Policy::pointer; + + generic_iterator() = default; + generic_iterator(handle seq, ssize_t index) : Policy(seq, index) { } + + reference operator*() const { return Policy::dereference(); } + reference operator[](difference_type n) const { return *(*this + n); } + pointer operator->() const { return **this; } + + It &operator++() { Policy::increment(); return *this; } + It operator++(int) { auto copy = *this; Policy::increment(); return copy; } + It &operator--() { Policy::decrement(); return *this; } + It operator--(int) { auto copy = *this; Policy::decrement(); return copy; } + It &operator+=(difference_type n) { Policy::advance(n); return *this; } + It &operator-=(difference_type n) { Policy::advance(-n); return *this; } + + friend It operator+(const It &a, difference_type n) { auto copy = a; return copy += n; } + friend It operator+(difference_type n, const It &b) { return b + n; } + friend It operator-(const It &a, difference_type n) { auto copy = a; return copy -= n; } + friend difference_type operator-(const It &a, const It &b) { return a.distance_to(b); } + + friend bool operator==(const It &a, const It &b) { return a.equal(b); } + friend bool operator!=(const It &a, const It &b) { return !(a == b); } + friend bool operator< (const It &a, const It &b) { return b - a > 0; } + friend bool operator> (const It &a, const It &b) { return b < a; } + friend bool operator>=(const It &a, const It &b) { return !(a < b); } + friend bool operator<=(const It &a, const It &b) { return !(a > b); } +}; + +PYBIND11_NAMESPACE_BEGIN(iterator_policies) +/// Quick proxy class needed to implement ``operator->`` for iterators which can't return pointers +template +struct arrow_proxy { + T value; + + arrow_proxy(T &&value) : value(std::move(value)) { } + T *operator->() const { return &value; } +}; + +/// Lightweight iterator policy using just a simple pointer: see ``PySequence_Fast_ITEMS`` +class sequence_fast_readonly { +protected: + using iterator_category = std::random_access_iterator_tag; + using value_type = handle; + using reference = const handle; + using pointer = arrow_proxy; + + sequence_fast_readonly(handle obj, ssize_t n) : ptr(PySequence_Fast_ITEMS(obj.ptr()) + n) { } + + reference dereference() const { return *ptr; } + void increment() { ++ptr; } + void decrement() { --ptr; } + void advance(ssize_t n) { ptr += n; } + bool equal(const sequence_fast_readonly &b) const { return ptr == b.ptr; } + ssize_t distance_to(const sequence_fast_readonly &b) const { return ptr - b.ptr; } + +private: + PyObject **ptr; +}; + +/// Full read and write access using the sequence protocol: see ``detail::sequence_accessor`` +class sequence_slow_readwrite { +protected: + using iterator_category = std::random_access_iterator_tag; + using value_type = object; + using reference = sequence_accessor; + using pointer = arrow_proxy; + + sequence_slow_readwrite(handle obj, ssize_t index) : obj(obj), index(index) { } + + reference dereference() const { return {obj, static_cast(index)}; } + void increment() { ++index; } + void decrement() { --index; } + void advance(ssize_t n) { index += n; } + bool equal(const sequence_slow_readwrite &b) const { return index == b.index; } + ssize_t distance_to(const sequence_slow_readwrite &b) const { return index - b.index; } + +private: + handle obj; + ssize_t index; +}; + +/// Python's dictionary protocol permits this to be a forward iterator +class dict_readonly { +protected: + using iterator_category = std::forward_iterator_tag; + using value_type = std::pair; + using reference = const value_type; + using pointer = arrow_proxy; + + dict_readonly() = default; + dict_readonly(handle obj, ssize_t pos) : obj(obj), pos(pos) { increment(); } + + reference dereference() const { return {key, value}; } + void increment() { if (!PyDict_Next(obj.ptr(), &pos, &key, &value)) { pos = -1; } } + bool equal(const dict_readonly &b) const { return pos == b.pos; } + +private: + handle obj; + PyObject *key = nullptr, *value = nullptr; + ssize_t pos = -1; +}; +PYBIND11_NAMESPACE_END(iterator_policies) + +#if !defined(PYPY_VERSION) +using tuple_iterator = generic_iterator; +using list_iterator = generic_iterator; +#else +using tuple_iterator = generic_iterator; +using list_iterator = generic_iterator; +#endif + +using sequence_iterator = generic_iterator; +using dict_iterator = generic_iterator; + +inline bool PyIterable_Check(PyObject *obj) { + PyObject *iter = PyObject_GetIter(obj); + if (iter) { + Py_DECREF(iter); + return true; + } else { + PyErr_Clear(); + return false; + } +} + +inline bool PyNone_Check(PyObject *o) { return o == Py_None; } +inline bool PyEllipsis_Check(PyObject *o) { return o == Py_Ellipsis; } + +#ifdef PYBIND11_STR_LEGACY_PERMISSIVE +inline bool PyUnicode_Check_Permissive(PyObject *o) { return PyUnicode_Check(o) || PYBIND11_BYTES_CHECK(o); } +#define PYBIND11_STR_CHECK_FUN detail::PyUnicode_Check_Permissive +#else +#define PYBIND11_STR_CHECK_FUN PyUnicode_Check +#endif + +inline bool PyStaticMethod_Check(PyObject *o) { return o->ob_type == &PyStaticMethod_Type; } + +class kwargs_proxy : public handle { +public: + explicit kwargs_proxy(handle h) : handle(h) { } +}; + +class args_proxy : public handle { +public: + explicit args_proxy(handle h) : handle(h) { } + kwargs_proxy operator*() const { return kwargs_proxy(*this); } +}; + +/// Python argument categories (using PEP 448 terms) +template using is_keyword = std::is_base_of; +template using is_s_unpacking = std::is_same; // * unpacking +template using is_ds_unpacking = std::is_same; // ** unpacking +template using is_positional = satisfies_none_of; +template using is_keyword_or_ds = satisfies_any_of; + +// Call argument collector forward declarations +template +class simple_collector; +template +class unpacking_collector; + +PYBIND11_NAMESPACE_END(detail) + +// TODO: After the deprecated constructors are removed, this macro can be simplified by +// inheriting ctors: `using Parent::Parent`. It's not an option right now because +// the `using` statement triggers the parent deprecation warning even if the ctor +// isn't even used. +#define PYBIND11_OBJECT_COMMON(Name, Parent, CheckFun) \ + public: \ + PYBIND11_DEPRECATED("Use reinterpret_borrow<"#Name">() or reinterpret_steal<"#Name">()") \ + Name(handle h, bool is_borrowed) : Parent(is_borrowed ? Parent(h, borrowed_t{}) : Parent(h, stolen_t{})) { } \ + Name(handle h, borrowed_t) : Parent(h, borrowed_t{}) { } \ + Name(handle h, stolen_t) : Parent(h, stolen_t{}) { } \ + PYBIND11_DEPRECATED("Use py::isinstance(obj) instead") \ + bool check() const { return m_ptr != nullptr && (bool) CheckFun(m_ptr); } \ + static bool check_(handle h) { return h.ptr() != nullptr && CheckFun(h.ptr()); } \ + template \ + Name(const ::pybind11::detail::accessor &a) : Name(object(a)) { } + +#define PYBIND11_OBJECT_CVT(Name, Parent, CheckFun, ConvertFun) \ + PYBIND11_OBJECT_COMMON(Name, Parent, CheckFun) \ + /* This is deliberately not 'explicit' to allow implicit conversion from object: */ \ + Name(const object &o) \ + : Parent(check_(o) ? o.inc_ref().ptr() : ConvertFun(o.ptr()), stolen_t{}) \ + { if (!m_ptr) throw error_already_set(); } \ + Name(object &&o) \ + : Parent(check_(o) ? o.release().ptr() : ConvertFun(o.ptr()), stolen_t{}) \ + { if (!m_ptr) throw error_already_set(); } + +#define PYBIND11_OBJECT_CVT_DEFAULT(Name, Parent, CheckFun, ConvertFun) \ + PYBIND11_OBJECT_CVT(Name, Parent, CheckFun, ConvertFun) \ + Name() : Parent() { } + +#define PYBIND11_OBJECT_CHECK_FAILED(Name, o_ptr) \ + ::pybind11::type_error("Object of type '" + \ + ::pybind11::detail::get_fully_qualified_tp_name(Py_TYPE(o_ptr)) + \ + "' is not an instance of '" #Name "'") + +#define PYBIND11_OBJECT(Name, Parent, CheckFun) \ + PYBIND11_OBJECT_COMMON(Name, Parent, CheckFun) \ + /* This is deliberately not 'explicit' to allow implicit conversion from object: */ \ + Name(const object &o) : Parent(o) \ + { if (m_ptr && !check_(m_ptr)) throw PYBIND11_OBJECT_CHECK_FAILED(Name, m_ptr); } \ + Name(object &&o) : Parent(std::move(o)) \ + { if (m_ptr && !check_(m_ptr)) throw PYBIND11_OBJECT_CHECK_FAILED(Name, m_ptr); } + +#define PYBIND11_OBJECT_DEFAULT(Name, Parent, CheckFun) \ + PYBIND11_OBJECT(Name, Parent, CheckFun) \ + Name() : Parent() { } + +/// \addtogroup pytypes +/// @{ + +/** \rst + Wraps a Python iterator so that it can also be used as a C++ input iterator + + Caveat: copying an iterator does not (and cannot) clone the internal + state of the Python iterable. This also applies to the post-increment + operator. This iterator should only be used to retrieve the current + value using ``operator*()``. +\endrst */ +class iterator : public object { +public: + using iterator_category = std::input_iterator_tag; + using difference_type = ssize_t; + using value_type = handle; + using reference = const handle; + using pointer = const handle *; + + PYBIND11_OBJECT_DEFAULT(iterator, object, PyIter_Check) + + iterator& operator++() { + advance(); + return *this; + } + + iterator operator++(int) { + auto rv = *this; + advance(); + return rv; + } + + reference operator*() const { + if (m_ptr && !value.ptr()) { + auto& self = const_cast(*this); + self.advance(); + } + return value; + } + + pointer operator->() const { operator*(); return &value; } + + /** \rst + The value which marks the end of the iteration. ``it == iterator::sentinel()`` + is equivalent to catching ``StopIteration`` in Python. + + .. code-block:: cpp + + void foo(py::iterator it) { + while (it != py::iterator::sentinel()) { + // use `*it` + ++it; + } + } + \endrst */ + static iterator sentinel() { return {}; } + + friend bool operator==(const iterator &a, const iterator &b) { return a->ptr() == b->ptr(); } + friend bool operator!=(const iterator &a, const iterator &b) { return a->ptr() != b->ptr(); } + +private: + void advance() { + value = reinterpret_steal(PyIter_Next(m_ptr)); + if (PyErr_Occurred()) { throw error_already_set(); } + } + +private: + object value = {}; +}; + + + +class type : public object { +public: + PYBIND11_OBJECT(type, object, PyType_Check) + + /// Return a type handle from a handle or an object + static handle handle_of(handle h) { return handle((PyObject*) Py_TYPE(h.ptr())); } + + /// Return a type object from a handle or an object + static type of(handle h) { return type(type::handle_of(h), borrowed_t{}); } + + // Defined in pybind11/cast.h + /// Convert C++ type to handle if previously registered. Does not convert + /// standard types, like int, float. etc. yet. + /// See https://github.com/pybind/pybind11/issues/2486 + template + static handle handle_of(); + + /// Convert C++ type to type if previously registered. Does not convert + /// standard types, like int, float. etc. yet. + /// See https://github.com/pybind/pybind11/issues/2486 + template + static type of() {return type(type::handle_of(), borrowed_t{}); } +}; + +class iterable : public object { +public: + PYBIND11_OBJECT_DEFAULT(iterable, object, detail::PyIterable_Check) +}; + +class bytes; + +class str : public object { +public: + PYBIND11_OBJECT_CVT(str, object, PYBIND11_STR_CHECK_FUN, raw_str) + + str(const char *c, size_t n) + : object(PyUnicode_FromStringAndSize(c, (ssize_t) n), stolen_t{}) { + if (!m_ptr) pybind11_fail("Could not allocate string object!"); + } + + // 'explicit' is explicitly omitted from the following constructors to allow implicit conversion to py::str from C++ string-like objects + str(const char *c = "") + : object(PyUnicode_FromString(c), stolen_t{}) { + if (!m_ptr) pybind11_fail("Could not allocate string object!"); + } + + str(const std::string &s) : str(s.data(), s.size()) { } + + explicit str(const bytes &b); + + /** \rst + Return a string representation of the object. This is analogous to + the ``str()`` function in Python. + \endrst */ + explicit str(handle h) : object(raw_str(h.ptr()), stolen_t{}) { if (!m_ptr) throw error_already_set(); } + + operator std::string() const { + object temp = *this; + if (PyUnicode_Check(m_ptr)) { + temp = reinterpret_steal(PyUnicode_AsUTF8String(m_ptr)); + if (!temp) + pybind11_fail("Unable to extract string contents! (encoding issue)"); + } + char *buffer; + ssize_t length; + if (PYBIND11_BYTES_AS_STRING_AND_SIZE(temp.ptr(), &buffer, &length)) + pybind11_fail("Unable to extract string contents! (invalid type)"); + return std::string(buffer, (size_t) length); + } + + template + str format(Args &&...args) const { + return attr("format")(std::forward(args)...); + } + +private: + /// Return string representation -- always returns a new reference, even if already a str + static PyObject *raw_str(PyObject *op) { + PyObject *str_value = PyObject_Str(op); +#if PY_MAJOR_VERSION < 3 + if (!str_value) throw error_already_set(); + PyObject *unicode = PyUnicode_FromEncodedObject(str_value, "utf-8", nullptr); + Py_XDECREF(str_value); str_value = unicode; +#endif + return str_value; + } +}; +/// @} pytypes + +inline namespace literals { +/** \rst + String literal version of `str` + \endrst */ +inline str operator"" _s(const char *s, size_t size) { return {s, size}; } +} // namespace literals + +/// \addtogroup pytypes +/// @{ +class bytes : public object { +public: + PYBIND11_OBJECT(bytes, object, PYBIND11_BYTES_CHECK) + + // Allow implicit conversion: + bytes(const char *c = "") + : object(PYBIND11_BYTES_FROM_STRING(c), stolen_t{}) { + if (!m_ptr) pybind11_fail("Could not allocate bytes object!"); + } + + bytes(const char *c, size_t n) + : object(PYBIND11_BYTES_FROM_STRING_AND_SIZE(c, (ssize_t) n), stolen_t{}) { + if (!m_ptr) pybind11_fail("Could not allocate bytes object!"); + } + + // Allow implicit conversion: + bytes(const std::string &s) : bytes(s.data(), s.size()) { } + + explicit bytes(const pybind11::str &s); + + operator std::string() const { + char *buffer; + ssize_t length; + if (PYBIND11_BYTES_AS_STRING_AND_SIZE(m_ptr, &buffer, &length)) + pybind11_fail("Unable to extract bytes contents!"); + return std::string(buffer, (size_t) length); + } +}; +// Note: breathe >= 4.17.0 will fail to build docs if the below two constructors +// are included in the doxygen group; close here and reopen after as a workaround +/// @} pytypes + +inline bytes::bytes(const pybind11::str &s) { + object temp = s; + if (PyUnicode_Check(s.ptr())) { + temp = reinterpret_steal(PyUnicode_AsUTF8String(s.ptr())); + if (!temp) + pybind11_fail("Unable to extract string contents! (encoding issue)"); + } + char *buffer; + ssize_t length; + if (PYBIND11_BYTES_AS_STRING_AND_SIZE(temp.ptr(), &buffer, &length)) + pybind11_fail("Unable to extract string contents! (invalid type)"); + auto obj = reinterpret_steal(PYBIND11_BYTES_FROM_STRING_AND_SIZE(buffer, length)); + if (!obj) + pybind11_fail("Could not allocate bytes object!"); + m_ptr = obj.release().ptr(); +} + +inline str::str(const bytes& b) { + char *buffer; + ssize_t length; + if (PYBIND11_BYTES_AS_STRING_AND_SIZE(b.ptr(), &buffer, &length)) + pybind11_fail("Unable to extract bytes contents!"); + auto obj = reinterpret_steal(PyUnicode_FromStringAndSize(buffer, (ssize_t) length)); + if (!obj) + pybind11_fail("Could not allocate string object!"); + m_ptr = obj.release().ptr(); +} + +/// \addtogroup pytypes +/// @{ +class bytearray : public object { +public: + PYBIND11_OBJECT_CVT(bytearray, object, PyByteArray_Check, PyByteArray_FromObject) + + bytearray(const char *c, size_t n) + : object(PyByteArray_FromStringAndSize(c, (ssize_t) n), stolen_t{}) { + if (!m_ptr) pybind11_fail("Could not allocate bytearray object!"); + } + + bytearray() + : bytearray("", 0) {} + + explicit bytearray(const std::string &s) : bytearray(s.data(), s.size()) { } + + size_t size() const { return static_cast(PyByteArray_Size(m_ptr)); } + + explicit operator std::string() const { + char *buffer = PyByteArray_AS_STRING(m_ptr); + ssize_t size = PyByteArray_GET_SIZE(m_ptr); + return std::string(buffer, static_cast(size)); + } +}; +// Note: breathe >= 4.17.0 will fail to build docs if the below two constructors +// are included in the doxygen group; close here and reopen after as a workaround +/// @} pytypes + +/// \addtogroup pytypes +/// @{ +class none : public object { +public: + PYBIND11_OBJECT(none, object, detail::PyNone_Check) + none() : object(Py_None, borrowed_t{}) { } +}; + +class ellipsis : public object { +public: + PYBIND11_OBJECT(ellipsis, object, detail::PyEllipsis_Check) + ellipsis() : object(Py_Ellipsis, borrowed_t{}) { } +}; + +class bool_ : public object { +public: + PYBIND11_OBJECT_CVT(bool_, object, PyBool_Check, raw_bool) + bool_() : object(Py_False, borrowed_t{}) { } + // Allow implicit conversion from and to `bool`: + bool_(bool value) : object(value ? Py_True : Py_False, borrowed_t{}) { } + operator bool() const { return m_ptr && PyLong_AsLong(m_ptr) != 0; } + +private: + /// Return the truth value of an object -- always returns a new reference + static PyObject *raw_bool(PyObject *op) { + const auto value = PyObject_IsTrue(op); + if (value == -1) return nullptr; + return handle(value ? Py_True : Py_False).inc_ref().ptr(); + } +}; + +PYBIND11_NAMESPACE_BEGIN(detail) +// Converts a value to the given unsigned type. If an error occurs, you get back (Unsigned) -1; +// otherwise you get back the unsigned long or unsigned long long value cast to (Unsigned). +// (The distinction is critically important when casting a returned -1 error value to some other +// unsigned type: (A)-1 != (B)-1 when A and B are unsigned types of different sizes). +template +Unsigned as_unsigned(PyObject *o) { + if (sizeof(Unsigned) <= sizeof(unsigned long) +#if PY_VERSION_HEX < 0x03000000 + || PyInt_Check(o) +#endif + ) { + unsigned long v = PyLong_AsUnsignedLong(o); + return v == (unsigned long) -1 && PyErr_Occurred() ? (Unsigned) -1 : (Unsigned) v; + } + else { + unsigned long long v = PyLong_AsUnsignedLongLong(o); + return v == (unsigned long long) -1 && PyErr_Occurred() ? (Unsigned) -1 : (Unsigned) v; + } +} +PYBIND11_NAMESPACE_END(detail) + +class int_ : public object { +public: + PYBIND11_OBJECT_CVT(int_, object, PYBIND11_LONG_CHECK, PyNumber_Long) + int_() : object(PyLong_FromLong(0), stolen_t{}) { } + // Allow implicit conversion from C++ integral types: + template ::value, int> = 0> + int_(T value) { + if (sizeof(T) <= sizeof(long)) { + if (std::is_signed::value) + m_ptr = PyLong_FromLong((long) value); + else + m_ptr = PyLong_FromUnsignedLong((unsigned long) value); + } else { + if (std::is_signed::value) + m_ptr = PyLong_FromLongLong((long long) value); + else + m_ptr = PyLong_FromUnsignedLongLong((unsigned long long) value); + } + if (!m_ptr) pybind11_fail("Could not allocate int object!"); + } + + template ::value, int> = 0> + operator T() const { + return std::is_unsigned::value + ? detail::as_unsigned(m_ptr) + : sizeof(T) <= sizeof(long) + ? (T) PyLong_AsLong(m_ptr) + : (T) PYBIND11_LONG_AS_LONGLONG(m_ptr); + } +}; + +class float_ : public object { +public: + PYBIND11_OBJECT_CVT(float_, object, PyFloat_Check, PyNumber_Float) + // Allow implicit conversion from float/double: + float_(float value) : object(PyFloat_FromDouble((double) value), stolen_t{}) { + if (!m_ptr) pybind11_fail("Could not allocate float object!"); + } + float_(double value = .0) : object(PyFloat_FromDouble((double) value), stolen_t{}) { + if (!m_ptr) pybind11_fail("Could not allocate float object!"); + } + operator float() const { return (float) PyFloat_AsDouble(m_ptr); } + operator double() const { return (double) PyFloat_AsDouble(m_ptr); } +}; + +class weakref : public object { +public: + PYBIND11_OBJECT_CVT_DEFAULT(weakref, object, PyWeakref_Check, raw_weakref) + explicit weakref(handle obj, handle callback = {}) + : object(PyWeakref_NewRef(obj.ptr(), callback.ptr()), stolen_t{}) { + if (!m_ptr) pybind11_fail("Could not allocate weak reference!"); + } + +private: + static PyObject *raw_weakref(PyObject *o) { + return PyWeakref_NewRef(o, nullptr); + } +}; + +class slice : public object { +public: + PYBIND11_OBJECT_DEFAULT(slice, object, PySlice_Check) + slice(ssize_t start_, ssize_t stop_, ssize_t step_) { + int_ start(start_), stop(stop_), step(step_); + m_ptr = PySlice_New(start.ptr(), stop.ptr(), step.ptr()); + if (!m_ptr) pybind11_fail("Could not allocate slice object!"); + } + bool compute(size_t length, size_t *start, size_t *stop, size_t *step, + size_t *slicelength) const { + return PySlice_GetIndicesEx((PYBIND11_SLICE_OBJECT *) m_ptr, + (ssize_t) length, (ssize_t *) start, + (ssize_t *) stop, (ssize_t *) step, + (ssize_t *) slicelength) == 0; + } + bool compute(ssize_t length, ssize_t *start, ssize_t *stop, ssize_t *step, + ssize_t *slicelength) const { + return PySlice_GetIndicesEx((PYBIND11_SLICE_OBJECT *) m_ptr, + length, start, + stop, step, + slicelength) == 0; + } +}; + +class capsule : public object { +public: + PYBIND11_OBJECT_DEFAULT(capsule, object, PyCapsule_CheckExact) + PYBIND11_DEPRECATED("Use reinterpret_borrow() or reinterpret_steal()") + capsule(PyObject *ptr, bool is_borrowed) : object(is_borrowed ? object(ptr, borrowed_t{}) : object(ptr, stolen_t{})) { } + + explicit capsule(const void *value, const char *name = nullptr, void (*destructor)(PyObject *) = nullptr) + : object(PyCapsule_New(const_cast(value), name, destructor), stolen_t{}) { + if (!m_ptr) + pybind11_fail("Could not allocate capsule object!"); + } + + PYBIND11_DEPRECATED("Please pass a destructor that takes a void pointer as input") + capsule(const void *value, void (*destruct)(PyObject *)) + : object(PyCapsule_New(const_cast(value), nullptr, destruct), stolen_t{}) { + if (!m_ptr) + pybind11_fail("Could not allocate capsule object!"); + } + + capsule(const void *value, void (*destructor)(void *)) { + m_ptr = PyCapsule_New(const_cast(value), nullptr, [](PyObject *o) { + auto destructor = reinterpret_cast(PyCapsule_GetContext(o)); + void *ptr = PyCapsule_GetPointer(o, nullptr); + destructor(ptr); + }); + + if (!m_ptr) + pybind11_fail("Could not allocate capsule object!"); + + if (PyCapsule_SetContext(m_ptr, (void *) destructor) != 0) + pybind11_fail("Could not set capsule context!"); + } + + capsule(void (*destructor)()) { + m_ptr = PyCapsule_New(reinterpret_cast(destructor), nullptr, [](PyObject *o) { + auto destructor = reinterpret_cast(PyCapsule_GetPointer(o, nullptr)); + destructor(); + }); + + if (!m_ptr) + pybind11_fail("Could not allocate capsule object!"); + } + + template operator T *() const { + return get_pointer(); + } + + /// Get the pointer the capsule holds. + template + T* get_pointer() const { + auto name = this->name(); + T *result = static_cast(PyCapsule_GetPointer(m_ptr, name)); + if (!result) pybind11_fail("Unable to extract capsule contents!"); + return result; + } + + /// Replaces a capsule's pointer *without* calling the destructor on the existing one. + void set_pointer(const void *value) { + if (PyCapsule_SetPointer(m_ptr, const_cast(value)) != 0) + pybind11_fail("Could not set capsule pointer"); + } + + const char *name() const { return PyCapsule_GetName(m_ptr); } +}; + +class tuple : public object { +public: + PYBIND11_OBJECT_CVT(tuple, object, PyTuple_Check, PySequence_Tuple) + explicit tuple(size_t size = 0) : object(PyTuple_New((ssize_t) size), stolen_t{}) { + if (!m_ptr) pybind11_fail("Could not allocate tuple object!"); + } + size_t size() const { return (size_t) PyTuple_Size(m_ptr); } + bool empty() const { return size() == 0; } + detail::tuple_accessor operator[](size_t index) const { return {*this, index}; } + detail::item_accessor operator[](handle h) const { return object::operator[](h); } + detail::tuple_iterator begin() const { return {*this, 0}; } + detail::tuple_iterator end() const { return {*this, PyTuple_GET_SIZE(m_ptr)}; } +}; + +// We need to put this into a separate function because the Intel compiler +// fails to compile enable_if_t...>::value> part below +// (tested with ICC 2021.1 Beta 20200827). +template +constexpr bool args_are_all_keyword_or_ds() +{ + return detail::all_of...>::value; +} + +class dict : public object { +public: + PYBIND11_OBJECT_CVT(dict, object, PyDict_Check, raw_dict) + dict() : object(PyDict_New(), stolen_t{}) { + if (!m_ptr) pybind11_fail("Could not allocate dict object!"); + } + template ()>, + // MSVC workaround: it can't compile an out-of-line definition, so defer the collector + typename collector = detail::deferred_t, Args...>> + explicit dict(Args &&...args) : dict(collector(std::forward(args)...).kwargs()) { } + + size_t size() const { return (size_t) PyDict_Size(m_ptr); } + bool empty() const { return size() == 0; } + detail::dict_iterator begin() const { return {*this, 0}; } + detail::dict_iterator end() const { return {}; } + void clear() const { PyDict_Clear(ptr()); } + template bool contains(T &&key) const { + return PyDict_Contains(m_ptr, detail::object_or_cast(std::forward(key)).ptr()) == 1; + } + +private: + /// Call the `dict` Python type -- always returns a new reference + static PyObject *raw_dict(PyObject *op) { + if (PyDict_Check(op)) + return handle(op).inc_ref().ptr(); + return PyObject_CallFunctionObjArgs((PyObject *) &PyDict_Type, op, nullptr); + } +}; + +class sequence : public object { +public: + PYBIND11_OBJECT_DEFAULT(sequence, object, PySequence_Check) + size_t size() const { + ssize_t result = PySequence_Size(m_ptr); + if (result == -1) + throw error_already_set(); + return (size_t) result; + } + bool empty() const { return size() == 0; } + detail::sequence_accessor operator[](size_t index) const { return {*this, index}; } + detail::item_accessor operator[](handle h) const { return object::operator[](h); } + detail::sequence_iterator begin() const { return {*this, 0}; } + detail::sequence_iterator end() const { return {*this, PySequence_Size(m_ptr)}; } +}; + +class list : public object { +public: + PYBIND11_OBJECT_CVT(list, object, PyList_Check, PySequence_List) + explicit list(size_t size = 0) : object(PyList_New((ssize_t) size), stolen_t{}) { + if (!m_ptr) pybind11_fail("Could not allocate list object!"); + } + size_t size() const { return (size_t) PyList_Size(m_ptr); } + bool empty() const { return size() == 0; } + detail::list_accessor operator[](size_t index) const { return {*this, index}; } + detail::item_accessor operator[](handle h) const { return object::operator[](h); } + detail::list_iterator begin() const { return {*this, 0}; } + detail::list_iterator end() const { return {*this, PyList_GET_SIZE(m_ptr)}; } + template void append(T &&val) const { + PyList_Append(m_ptr, detail::object_or_cast(std::forward(val)).ptr()); + } + template void insert(size_t index, T &&val) const { + PyList_Insert(m_ptr, static_cast(index), + detail::object_or_cast(std::forward(val)).ptr()); + } +}; + +class args : public tuple { PYBIND11_OBJECT_DEFAULT(args, tuple, PyTuple_Check) }; +class kwargs : public dict { PYBIND11_OBJECT_DEFAULT(kwargs, dict, PyDict_Check) }; + +class set : public object { +public: + PYBIND11_OBJECT_CVT(set, object, PySet_Check, PySet_New) + set() : object(PySet_New(nullptr), stolen_t{}) { + if (!m_ptr) pybind11_fail("Could not allocate set object!"); + } + size_t size() const { return (size_t) PySet_Size(m_ptr); } + bool empty() const { return size() == 0; } + template bool add(T &&val) const { + return PySet_Add(m_ptr, detail::object_or_cast(std::forward(val)).ptr()) == 0; + } + void clear() const { PySet_Clear(m_ptr); } + template bool contains(T &&val) const { + return PySet_Contains(m_ptr, detail::object_or_cast(std::forward(val)).ptr()) == 1; + } +}; + +class function : public object { +public: + PYBIND11_OBJECT_DEFAULT(function, object, PyCallable_Check) + handle cpp_function() const { + handle fun = detail::get_function(m_ptr); + if (fun && PyCFunction_Check(fun.ptr())) + return fun; + return handle(); + } + bool is_cpp_function() const { return (bool) cpp_function(); } +}; + +class staticmethod : public object { +public: + PYBIND11_OBJECT_CVT(staticmethod, object, detail::PyStaticMethod_Check, PyStaticMethod_New) +}; + +class buffer : public object { +public: + PYBIND11_OBJECT_DEFAULT(buffer, object, PyObject_CheckBuffer) + + buffer_info request(bool writable = false) const { + int flags = PyBUF_STRIDES | PyBUF_FORMAT; + if (writable) flags |= PyBUF_WRITABLE; + auto *view = new Py_buffer(); + if (PyObject_GetBuffer(m_ptr, view, flags) != 0) { + delete view; + throw error_already_set(); + } + return buffer_info(view); + } +}; + +class memoryview : public object { +public: + PYBIND11_OBJECT_CVT(memoryview, object, PyMemoryView_Check, PyMemoryView_FromObject) + + /** \rst + Creates ``memoryview`` from ``buffer_info``. + + ``buffer_info`` must be created from ``buffer::request()``. Otherwise + throws an exception. + + For creating a ``memoryview`` from objects that support buffer protocol, + use ``memoryview(const object& obj)`` instead of this constructor. + \endrst */ + explicit memoryview(const buffer_info& info) { + if (!info.view()) + pybind11_fail("Prohibited to create memoryview without Py_buffer"); + // Note: PyMemoryView_FromBuffer never increments obj reference. + m_ptr = (info.view()->obj) ? + PyMemoryView_FromObject(info.view()->obj) : + PyMemoryView_FromBuffer(info.view()); + if (!m_ptr) + pybind11_fail("Unable to create memoryview from buffer descriptor"); + } + + /** \rst + Creates ``memoryview`` from static buffer. + + This method is meant for providing a ``memoryview`` for C/C++ buffer not + managed by Python. The caller is responsible for managing the lifetime + of ``ptr`` and ``format``, which MUST outlive the memoryview constructed + here. + + See also: Python C API documentation for `PyMemoryView_FromBuffer`_. + + .. _PyMemoryView_FromBuffer: https://docs.python.org/c-api/memoryview.html#c.PyMemoryView_FromBuffer + + :param ptr: Pointer to the buffer. + :param itemsize: Byte size of an element. + :param format: Pointer to the null-terminated format string. For + homogeneous Buffers, this should be set to + ``format_descriptor::value``. + :param shape: Shape of the tensor (1 entry per dimension). + :param strides: Number of bytes between adjacent entries (for each + per dimension). + :param readonly: Flag to indicate if the underlying storage may be + written to. + \endrst */ + static memoryview from_buffer( + void *ptr, ssize_t itemsize, const char *format, + detail::any_container shape, + detail::any_container strides, bool readonly = false); + + static memoryview from_buffer( + const void *ptr, ssize_t itemsize, const char *format, + detail::any_container shape, + detail::any_container strides) { + return memoryview::from_buffer( + const_cast(ptr), itemsize, format, shape, strides, true); + } + + template + static memoryview from_buffer( + T *ptr, detail::any_container shape, + detail::any_container strides, bool readonly = false) { + return memoryview::from_buffer( + reinterpret_cast(ptr), sizeof(T), + format_descriptor::value, shape, strides, readonly); + } + + template + static memoryview from_buffer( + const T *ptr, detail::any_container shape, + detail::any_container strides) { + return memoryview::from_buffer( + const_cast(ptr), shape, strides, true); + } + +#if PY_MAJOR_VERSION >= 3 + /** \rst + Creates ``memoryview`` from static memory. + + This method is meant for providing a ``memoryview`` for C/C++ buffer not + managed by Python. The caller is responsible for managing the lifetime + of ``mem``, which MUST outlive the memoryview constructed here. + + This method is not available in Python 2. + + See also: Python C API documentation for `PyMemoryView_FromBuffer`_. + + .. _PyMemoryView_FromMemory: https://docs.python.org/c-api/memoryview.html#c.PyMemoryView_FromMemory + \endrst */ + static memoryview from_memory(void *mem, ssize_t size, bool readonly = false) { + PyObject* ptr = PyMemoryView_FromMemory( + reinterpret_cast(mem), size, + (readonly) ? PyBUF_READ : PyBUF_WRITE); + if (!ptr) + pybind11_fail("Could not allocate memoryview object!"); + return memoryview(object(ptr, stolen_t{})); + } + + static memoryview from_memory(const void *mem, ssize_t size) { + return memoryview::from_memory(const_cast(mem), size, true); + } +#endif +}; + +#ifndef DOXYGEN_SHOULD_SKIP_THIS +inline memoryview memoryview::from_buffer( + void *ptr, ssize_t itemsize, const char* format, + detail::any_container shape, + detail::any_container strides, bool readonly) { + size_t ndim = shape->size(); + if (ndim != strides->size()) + pybind11_fail("memoryview: shape length doesn't match strides length"); + ssize_t size = ndim ? 1 : 0; + for (size_t i = 0; i < ndim; ++i) + size *= (*shape)[i]; + Py_buffer view; + view.buf = ptr; + view.obj = nullptr; + view.len = size * itemsize; + view.readonly = static_cast(readonly); + view.itemsize = itemsize; + view.format = const_cast(format); + view.ndim = static_cast(ndim); + view.shape = shape->data(); + view.strides = strides->data(); + view.suboffsets = nullptr; + view.internal = nullptr; + PyObject* obj = PyMemoryView_FromBuffer(&view); + if (!obj) + throw error_already_set(); + return memoryview(object(obj, stolen_t{})); +} +#endif // DOXYGEN_SHOULD_SKIP_THIS +/// @} pytypes + +/// \addtogroup python_builtins +/// @{ + +/// Get the length of a Python object. +inline size_t len(handle h) { + ssize_t result = PyObject_Length(h.ptr()); + if (result < 0) + throw error_already_set(); + return (size_t) result; +} + +/// Get the length hint of a Python object. +/// Returns 0 when this cannot be determined. +inline size_t len_hint(handle h) { +#if PY_VERSION_HEX >= 0x03040000 + ssize_t result = PyObject_LengthHint(h.ptr(), 0); +#else + ssize_t result = PyObject_Length(h.ptr()); +#endif + if (result < 0) { + // Sometimes a length can't be determined at all (eg generators) + // In which case simply return 0 + PyErr_Clear(); + return 0; + } + return (size_t) result; +} + +inline str repr(handle h) { + PyObject *str_value = PyObject_Repr(h.ptr()); + if (!str_value) throw error_already_set(); +#if PY_MAJOR_VERSION < 3 + PyObject *unicode = PyUnicode_FromEncodedObject(str_value, "utf-8", nullptr); + Py_XDECREF(str_value); str_value = unicode; + if (!str_value) throw error_already_set(); +#endif + return reinterpret_steal(str_value); +} + +inline iterator iter(handle obj) { + PyObject *result = PyObject_GetIter(obj.ptr()); + if (!result) { throw error_already_set(); } + return reinterpret_steal(result); +} +/// @} python_builtins + +PYBIND11_NAMESPACE_BEGIN(detail) +template iterator object_api::begin() const { return iter(derived()); } +template iterator object_api::end() const { return iterator::sentinel(); } +template item_accessor object_api::operator[](handle key) const { + return {derived(), reinterpret_borrow(key)}; +} +template item_accessor object_api::operator[](const char *key) const { + return {derived(), pybind11::str(key)}; +} +template obj_attr_accessor object_api::attr(handle key) const { + return {derived(), reinterpret_borrow(key)}; +} +template str_attr_accessor object_api::attr(const char *key) const { + return {derived(), key}; +} +template args_proxy object_api::operator*() const { + return args_proxy(derived().ptr()); +} +template template bool object_api::contains(T &&item) const { + return attr("__contains__")(std::forward(item)).template cast(); +} + +template +pybind11::str object_api::str() const { return pybind11::str(derived()); } + +template +str_attr_accessor object_api::doc() const { return attr("__doc__"); } + +template +handle object_api::get_type() const { return type::handle_of(derived()); } + +template +bool object_api::rich_compare(object_api const &other, int value) const { + int rv = PyObject_RichCompareBool(derived().ptr(), other.derived().ptr(), value); + if (rv == -1) + throw error_already_set(); + return rv == 1; +} + +#define PYBIND11_MATH_OPERATOR_UNARY(op, fn) \ + template object object_api::op() const { \ + object result = reinterpret_steal(fn(derived().ptr())); \ + if (!result.ptr()) \ + throw error_already_set(); \ + return result; \ + } + +#define PYBIND11_MATH_OPERATOR_BINARY(op, fn) \ + template \ + object object_api::op(object_api const &other) const { \ + object result = reinterpret_steal( \ + fn(derived().ptr(), other.derived().ptr())); \ + if (!result.ptr()) \ + throw error_already_set(); \ + return result; \ + } + +PYBIND11_MATH_OPERATOR_UNARY (operator~, PyNumber_Invert) +PYBIND11_MATH_OPERATOR_UNARY (operator-, PyNumber_Negative) +PYBIND11_MATH_OPERATOR_BINARY(operator+, PyNumber_Add) +PYBIND11_MATH_OPERATOR_BINARY(operator+=, PyNumber_InPlaceAdd) +PYBIND11_MATH_OPERATOR_BINARY(operator-, PyNumber_Subtract) +PYBIND11_MATH_OPERATOR_BINARY(operator-=, PyNumber_InPlaceSubtract) +PYBIND11_MATH_OPERATOR_BINARY(operator*, PyNumber_Multiply) +PYBIND11_MATH_OPERATOR_BINARY(operator*=, PyNumber_InPlaceMultiply) +PYBIND11_MATH_OPERATOR_BINARY(operator/, PyNumber_TrueDivide) +PYBIND11_MATH_OPERATOR_BINARY(operator/=, PyNumber_InPlaceTrueDivide) +PYBIND11_MATH_OPERATOR_BINARY(operator|, PyNumber_Or) +PYBIND11_MATH_OPERATOR_BINARY(operator|=, PyNumber_InPlaceOr) +PYBIND11_MATH_OPERATOR_BINARY(operator&, PyNumber_And) +PYBIND11_MATH_OPERATOR_BINARY(operator&=, PyNumber_InPlaceAnd) +PYBIND11_MATH_OPERATOR_BINARY(operator^, PyNumber_Xor) +PYBIND11_MATH_OPERATOR_BINARY(operator^=, PyNumber_InPlaceXor) +PYBIND11_MATH_OPERATOR_BINARY(operator<<, PyNumber_Lshift) +PYBIND11_MATH_OPERATOR_BINARY(operator<<=, PyNumber_InPlaceLshift) +PYBIND11_MATH_OPERATOR_BINARY(operator>>, PyNumber_Rshift) +PYBIND11_MATH_OPERATOR_BINARY(operator>>=, PyNumber_InPlaceRshift) + +#undef PYBIND11_MATH_OPERATOR_UNARY +#undef PYBIND11_MATH_OPERATOR_BINARY + +PYBIND11_NAMESPACE_END(detail) +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/stl.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/stl.h new file mode 100644 index 0000000000000000000000000000000000000000..18fbafb1e2e9ec999bc665027c88f7f1011e5ec7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/stl.h @@ -0,0 +1,388 @@ +/* + pybind11/stl.h: Transparent conversion for STL data types + + Copyright (c) 2016 Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "pybind11.h" +#include +#include +#include +#include +#include +#include +#include +#include + +#if defined(_MSC_VER) +#pragma warning(push) +#pragma warning(disable: 4127) // warning C4127: Conditional expression is constant +#endif + +#ifdef __has_include +// std::optional (but including it in c++14 mode isn't allowed) +# if defined(PYBIND11_CPP17) && __has_include() +# include +# define PYBIND11_HAS_OPTIONAL 1 +# endif +// std::experimental::optional (but not allowed in c++11 mode) +# if defined(PYBIND11_CPP14) && (__has_include() && \ + !__has_include()) +# include +# define PYBIND11_HAS_EXP_OPTIONAL 1 +# endif +// std::variant +# if defined(PYBIND11_CPP17) && __has_include() +# include +# define PYBIND11_HAS_VARIANT 1 +# endif +#elif defined(_MSC_VER) && defined(PYBIND11_CPP17) +# include +# include +# define PYBIND11_HAS_OPTIONAL 1 +# define PYBIND11_HAS_VARIANT 1 +#endif + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) +PYBIND11_NAMESPACE_BEGIN(detail) + +/// Extracts an const lvalue reference or rvalue reference for U based on the type of T (e.g. for +/// forwarding a container element). Typically used indirect via forwarded_type(), below. +template +using forwarded_type = conditional_t< + std::is_lvalue_reference::value, remove_reference_t &, remove_reference_t &&>; + +/// Forwards a value U as rvalue or lvalue according to whether T is rvalue or lvalue; typically +/// used for forwarding a container's elements. +template +forwarded_type forward_like(U &&u) { + return std::forward>(std::forward(u)); +} + +template struct set_caster { + using type = Type; + using key_conv = make_caster; + + bool load(handle src, bool convert) { + if (!isinstance(src)) + return false; + auto s = reinterpret_borrow(src); + value.clear(); + for (auto entry : s) { + key_conv conv; + if (!conv.load(entry, convert)) + return false; + value.insert(cast_op(std::move(conv))); + } + return true; + } + + template + static handle cast(T &&src, return_value_policy policy, handle parent) { + if (!std::is_lvalue_reference::value) + policy = return_value_policy_override::policy(policy); + pybind11::set s; + for (auto &&value : src) { + auto value_ = reinterpret_steal(key_conv::cast(forward_like(value), policy, parent)); + if (!value_ || !s.add(value_)) + return handle(); + } + return s.release(); + } + + PYBIND11_TYPE_CASTER(type, _("Set[") + key_conv::name + _("]")); +}; + +template struct map_caster { + using key_conv = make_caster; + using value_conv = make_caster; + + bool load(handle src, bool convert) { + if (!isinstance(src)) + return false; + auto d = reinterpret_borrow(src); + value.clear(); + for (auto it : d) { + key_conv kconv; + value_conv vconv; + if (!kconv.load(it.first.ptr(), convert) || + !vconv.load(it.second.ptr(), convert)) + return false; + value.emplace(cast_op(std::move(kconv)), cast_op(std::move(vconv))); + } + return true; + } + + template + static handle cast(T &&src, return_value_policy policy, handle parent) { + dict d; + return_value_policy policy_key = policy; + return_value_policy policy_value = policy; + if (!std::is_lvalue_reference::value) { + policy_key = return_value_policy_override::policy(policy_key); + policy_value = return_value_policy_override::policy(policy_value); + } + for (auto &&kv : src) { + auto key = reinterpret_steal(key_conv::cast(forward_like(kv.first), policy_key, parent)); + auto value = reinterpret_steal(value_conv::cast(forward_like(kv.second), policy_value, parent)); + if (!key || !value) + return handle(); + d[key] = value; + } + return d.release(); + } + + PYBIND11_TYPE_CASTER(Type, _("Dict[") + key_conv::name + _(", ") + value_conv::name + _("]")); +}; + +template struct list_caster { + using value_conv = make_caster; + + bool load(handle src, bool convert) { + if (!isinstance(src) || isinstance(src) || isinstance(src)) + return false; + auto s = reinterpret_borrow(src); + value.clear(); + reserve_maybe(s, &value); + for (auto it : s) { + value_conv conv; + if (!conv.load(it, convert)) + return false; + value.push_back(cast_op(std::move(conv))); + } + return true; + } + +private: + template ().reserve(0)), void>::value, int> = 0> + void reserve_maybe(sequence s, Type *) { value.reserve(s.size()); } + void reserve_maybe(sequence, void *) { } + +public: + template + static handle cast(T &&src, return_value_policy policy, handle parent) { + if (!std::is_lvalue_reference::value) + policy = return_value_policy_override::policy(policy); + list l(src.size()); + size_t index = 0; + for (auto &&value : src) { + auto value_ = reinterpret_steal(value_conv::cast(forward_like(value), policy, parent)); + if (!value_) + return handle(); + PyList_SET_ITEM(l.ptr(), (ssize_t) index++, value_.release().ptr()); // steals a reference + } + return l.release(); + } + + PYBIND11_TYPE_CASTER(Type, _("List[") + value_conv::name + _("]")); +}; + +template struct type_caster> + : list_caster, Type> { }; + +template struct type_caster> + : list_caster, Type> { }; + +template struct type_caster> + : list_caster, Type> { }; + +template struct array_caster { + using value_conv = make_caster; + +private: + template + bool require_size(enable_if_t size) { + if (value.size() != size) + value.resize(size); + return true; + } + template + bool require_size(enable_if_t size) { + return size == Size; + } + +public: + bool load(handle src, bool convert) { + if (!isinstance(src)) + return false; + auto l = reinterpret_borrow(src); + if (!require_size(l.size())) + return false; + size_t ctr = 0; + for (auto it : l) { + value_conv conv; + if (!conv.load(it, convert)) + return false; + value[ctr++] = cast_op(std::move(conv)); + } + return true; + } + + template + static handle cast(T &&src, return_value_policy policy, handle parent) { + list l(src.size()); + size_t index = 0; + for (auto &&value : src) { + auto value_ = reinterpret_steal(value_conv::cast(forward_like(value), policy, parent)); + if (!value_) + return handle(); + PyList_SET_ITEM(l.ptr(), (ssize_t) index++, value_.release().ptr()); // steals a reference + } + return l.release(); + } + + PYBIND11_TYPE_CASTER(ArrayType, _("List[") + value_conv::name + _(_(""), _("[") + _() + _("]")) + _("]")); +}; + +template struct type_caster> + : array_caster, Type, false, Size> { }; + +template struct type_caster> + : array_caster, Type, true> { }; + +template struct type_caster> + : set_caster, Key> { }; + +template struct type_caster> + : set_caster, Key> { }; + +template struct type_caster> + : map_caster, Key, Value> { }; + +template struct type_caster> + : map_caster, Key, Value> { }; + +// This type caster is intended to be used for std::optional and std::experimental::optional +template struct optional_caster { + using value_conv = make_caster; + + template + static handle cast(T_ &&src, return_value_policy policy, handle parent) { + if (!src) + return none().inc_ref(); + if (!std::is_lvalue_reference::value) { + policy = return_value_policy_override::policy(policy); + } + return value_conv::cast(*std::forward(src), policy, parent); + } + + bool load(handle src, bool convert) { + if (!src) { + return false; + } else if (src.is_none()) { + return true; // default-constructed value is already empty + } + value_conv inner_caster; + if (!inner_caster.load(src, convert)) + return false; + + value.emplace(cast_op(std::move(inner_caster))); + return true; + } + + PYBIND11_TYPE_CASTER(T, _("Optional[") + value_conv::name + _("]")); +}; + +#if defined(PYBIND11_HAS_OPTIONAL) +template struct type_caster> + : public optional_caster> {}; + +template<> struct type_caster + : public void_caster {}; +#endif + +#if defined(PYBIND11_HAS_EXP_OPTIONAL) +template struct type_caster> + : public optional_caster> {}; + +template<> struct type_caster + : public void_caster {}; +#endif + +/// Visit a variant and cast any found type to Python +struct variant_caster_visitor { + return_value_policy policy; + handle parent; + + using result_type = handle; // required by boost::variant in C++11 + + template + result_type operator()(T &&src) const { + return make_caster::cast(std::forward(src), policy, parent); + } +}; + +/// Helper class which abstracts away variant's `visit` function. `std::variant` and similar +/// `namespace::variant` types which provide a `namespace::visit()` function are handled here +/// automatically using argument-dependent lookup. Users can provide specializations for other +/// variant-like classes, e.g. `boost::variant` and `boost::apply_visitor`. +template class Variant> +struct visit_helper { + template + static auto call(Args &&...args) -> decltype(visit(std::forward(args)...)) { + return visit(std::forward(args)...); + } +}; + +/// Generic variant caster +template struct variant_caster; + +template class V, typename... Ts> +struct variant_caster> { + static_assert(sizeof...(Ts) > 0, "Variant must consist of at least one alternative."); + + template + bool load_alternative(handle src, bool convert, type_list) { + auto caster = make_caster(); + if (caster.load(src, convert)) { + value = cast_op(caster); + return true; + } + return load_alternative(src, convert, type_list{}); + } + + bool load_alternative(handle, bool, type_list<>) { return false; } + + bool load(handle src, bool convert) { + // Do a first pass without conversions to improve constructor resolution. + // E.g. `py::int_(1).cast>()` needs to fill the `int` + // slot of the variant. Without two-pass loading `double` would be filled + // because it appears first and a conversion is possible. + if (convert && load_alternative(src, false, type_list{})) + return true; + return load_alternative(src, convert, type_list{}); + } + + template + static handle cast(Variant &&src, return_value_policy policy, handle parent) { + return visit_helper::call(variant_caster_visitor{policy, parent}, + std::forward(src)); + } + + using Type = V; + PYBIND11_TYPE_CASTER(Type, _("Union[") + detail::concat(make_caster::name...) + _("]")); +}; + +#if defined(PYBIND11_HAS_VARIANT) +template +struct type_caster> : variant_caster> { }; +#endif + +PYBIND11_NAMESPACE_END(detail) + +inline std::ostream &operator<<(std::ostream &os, const handle &obj) { + os << (std::string) str(obj); + return os; +} + +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) + +#if defined(_MSC_VER) +#pragma warning(pop) +#endif diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/stl_bind.h b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/stl_bind.h new file mode 100644 index 0000000000000000000000000000000000000000..83195ee49639c17fe413bf09bac77a8a420219d9 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/include/pybind11/stl_bind.h @@ -0,0 +1,676 @@ +/* + pybind11/std_bind.h: Binding generators for STL data types + + Copyright (c) 2016 Sergey Lyskov and Wenzel Jakob + + All rights reserved. Use of this source code is governed by a + BSD-style license that can be found in the LICENSE file. +*/ + +#pragma once + +#include "detail/common.h" +#include "operators.h" + +#include +#include + +PYBIND11_NAMESPACE_BEGIN(PYBIND11_NAMESPACE) +PYBIND11_NAMESPACE_BEGIN(detail) + +/* SFINAE helper class used by 'is_comparable */ +template struct container_traits { + template static std::true_type test_comparable(decltype(std::declval() == std::declval())*); + template static std::false_type test_comparable(...); + template static std::true_type test_value(typename T2::value_type *); + template static std::false_type test_value(...); + template static std::true_type test_pair(typename T2::first_type *, typename T2::second_type *); + template static std::false_type test_pair(...); + + static constexpr const bool is_comparable = std::is_same(nullptr))>::value; + static constexpr const bool is_pair = std::is_same(nullptr, nullptr))>::value; + static constexpr const bool is_vector = std::is_same(nullptr))>::value; + static constexpr const bool is_element = !is_pair && !is_vector; +}; + +/* Default: is_comparable -> std::false_type */ +template +struct is_comparable : std::false_type { }; + +/* For non-map data structures, check whether operator== can be instantiated */ +template +struct is_comparable< + T, enable_if_t::is_element && + container_traits::is_comparable>> + : std::true_type { }; + +/* For a vector/map data structure, recursively check the value type (which is std::pair for maps) */ +template +struct is_comparable::is_vector>> { + static constexpr const bool value = + is_comparable::value; +}; + +/* For pairs, recursively check the two data types */ +template +struct is_comparable::is_pair>> { + static constexpr const bool value = + is_comparable::value && + is_comparable::value; +}; + +/* Fallback functions */ +template void vector_if_copy_constructible(const Args &...) { } +template void vector_if_equal_operator(const Args &...) { } +template void vector_if_insertion_operator(const Args &...) { } +template void vector_modifiers(const Args &...) { } + +template +void vector_if_copy_constructible(enable_if_t::value, Class_> &cl) { + cl.def(init(), "Copy constructor"); +} + +template +void vector_if_equal_operator(enable_if_t::value, Class_> &cl) { + using T = typename Vector::value_type; + + cl.def(self == self); + cl.def(self != self); + + cl.def("count", + [](const Vector &v, const T &x) { + return std::count(v.begin(), v.end(), x); + }, + arg("x"), + "Return the number of times ``x`` appears in the list" + ); + + cl.def("remove", [](Vector &v, const T &x) { + auto p = std::find(v.begin(), v.end(), x); + if (p != v.end()) + v.erase(p); + else + throw value_error(); + }, + arg("x"), + "Remove the first item from the list whose value is x. " + "It is an error if there is no such item." + ); + + cl.def("__contains__", + [](const Vector &v, const T &x) { + return std::find(v.begin(), v.end(), x) != v.end(); + }, + arg("x"), + "Return true the container contains ``x``" + ); +} + +// Vector modifiers -- requires a copyable vector_type: +// (Technically, some of these (pop and __delitem__) don't actually require copyability, but it seems +// silly to allow deletion but not insertion, so include them here too.) +template +void vector_modifiers(enable_if_t::value, Class_> &cl) { + using T = typename Vector::value_type; + using SizeType = typename Vector::size_type; + using DiffType = typename Vector::difference_type; + + auto wrap_i = [](DiffType i, SizeType n) { + if (i < 0) + i += n; + if (i < 0 || (SizeType)i >= n) + throw index_error(); + return i; + }; + + cl.def("append", + [](Vector &v, const T &value) { v.push_back(value); }, + arg("x"), + "Add an item to the end of the list"); + + cl.def(init([](iterable it) { + auto v = std::unique_ptr(new Vector()); + v->reserve(len_hint(it)); + for (handle h : it) + v->push_back(h.cast()); + return v.release(); + })); + + cl.def("clear", + [](Vector &v) { + v.clear(); + }, + "Clear the contents" + ); + + cl.def("extend", + [](Vector &v, const Vector &src) { + v.insert(v.end(), src.begin(), src.end()); + }, + arg("L"), + "Extend the list by appending all the items in the given list" + ); + + cl.def("extend", + [](Vector &v, iterable it) { + const size_t old_size = v.size(); + v.reserve(old_size + len_hint(it)); + try { + for (handle h : it) { + v.push_back(h.cast()); + } + } catch (const cast_error &) { + v.erase(v.begin() + static_cast(old_size), v.end()); + try { + v.shrink_to_fit(); + } catch (const std::exception &) { + // Do nothing + } + throw; + } + }, + arg("L"), + "Extend the list by appending all the items in the given list" + ); + + cl.def("insert", + [](Vector &v, DiffType i, const T &x) { + // Can't use wrap_i; i == v.size() is OK + if (i < 0) + i += v.size(); + if (i < 0 || (SizeType)i > v.size()) + throw index_error(); + v.insert(v.begin() + i, x); + }, + arg("i") , arg("x"), + "Insert an item at a given position." + ); + + cl.def("pop", + [](Vector &v) { + if (v.empty()) + throw index_error(); + T t = v.back(); + v.pop_back(); + return t; + }, + "Remove and return the last item" + ); + + cl.def("pop", + [wrap_i](Vector &v, DiffType i) { + i = wrap_i(i, v.size()); + T t = v[(SizeType) i]; + v.erase(v.begin() + i); + return t; + }, + arg("i"), + "Remove and return the item at index ``i``" + ); + + cl.def("__setitem__", + [wrap_i](Vector &v, DiffType i, const T &t) { + i = wrap_i(i, v.size()); + v[(SizeType)i] = t; + } + ); + + /// Slicing protocol + cl.def("__getitem__", + [](const Vector &v, slice slice) -> Vector * { + size_t start, stop, step, slicelength; + + if (!slice.compute(v.size(), &start, &stop, &step, &slicelength)) + throw error_already_set(); + + auto *seq = new Vector(); + seq->reserve((size_t) slicelength); + + for (size_t i=0; ipush_back(v[start]); + start += step; + } + return seq; + }, + arg("s"), + "Retrieve list elements using a slice object" + ); + + cl.def("__setitem__", + [](Vector &v, slice slice, const Vector &value) { + size_t start, stop, step, slicelength; + if (!slice.compute(v.size(), &start, &stop, &step, &slicelength)) + throw error_already_set(); + + if (slicelength != value.size()) + throw std::runtime_error("Left and right hand size of slice assignment have different sizes!"); + + for (size_t i=0; i), +// we have to access by copying; otherwise we return by reference. +template using vector_needs_copy = negation< + std::is_same()[typename Vector::size_type()]), typename Vector::value_type &>>; + +// The usual case: access and iterate by reference +template +void vector_accessor(enable_if_t::value, Class_> &cl) { + using T = typename Vector::value_type; + using SizeType = typename Vector::size_type; + using DiffType = typename Vector::difference_type; + using ItType = typename Vector::iterator; + + auto wrap_i = [](DiffType i, SizeType n) { + if (i < 0) + i += n; + if (i < 0 || (SizeType)i >= n) + throw index_error(); + return i; + }; + + cl.def("__getitem__", + [wrap_i](Vector &v, DiffType i) -> T & { + i = wrap_i(i, v.size()); + return v[(SizeType)i]; + }, + return_value_policy::reference_internal // ref + keepalive + ); + + cl.def("__iter__", + [](Vector &v) { + return make_iterator< + return_value_policy::reference_internal, ItType, ItType, T&>( + v.begin(), v.end()); + }, + keep_alive<0, 1>() /* Essential: keep list alive while iterator exists */ + ); +} + +// The case for special objects, like std::vector, that have to be returned-by-copy: +template +void vector_accessor(enable_if_t::value, Class_> &cl) { + using T = typename Vector::value_type; + using SizeType = typename Vector::size_type; + using DiffType = typename Vector::difference_type; + using ItType = typename Vector::iterator; + cl.def("__getitem__", + [](const Vector &v, DiffType i) -> T { + if (i < 0 && (i += v.size()) < 0) + throw index_error(); + if ((SizeType)i >= v.size()) + throw index_error(); + return v[(SizeType)i]; + } + ); + + cl.def("__iter__", + [](Vector &v) { + return make_iterator< + return_value_policy::copy, ItType, ItType, T>( + v.begin(), v.end()); + }, + keep_alive<0, 1>() /* Essential: keep list alive while iterator exists */ + ); +} + +template auto vector_if_insertion_operator(Class_ &cl, std::string const &name) + -> decltype(std::declval() << std::declval(), void()) { + using size_type = typename Vector::size_type; + + cl.def("__repr__", + [name](Vector &v) { + std::ostringstream s; + s << name << '['; + for (size_type i=0; i < v.size(); ++i) { + s << v[i]; + if (i != v.size() - 1) + s << ", "; + } + s << ']'; + return s.str(); + }, + "Return the canonical string representation of this list." + ); +} + +// Provide the buffer interface for vectors if we have data() and we have a format for it +// GCC seems to have "void std::vector::data()" - doing SFINAE on the existence of data() is insufficient, we need to check it returns an appropriate pointer +template +struct vector_has_data_and_format : std::false_type {}; +template +struct vector_has_data_and_format::format(), std::declval().data()), typename Vector::value_type*>::value>> : std::true_type {}; + +// [workaround(intel)] Separate function required here +// Workaround as the Intel compiler does not compile the enable_if_t part below +// (tested with icc (ICC) 2021.1 Beta 20200827) +template +constexpr bool args_any_are_buffer() { + return detail::any_of...>::value; +} + +// [workaround(intel)] Separate function required here +// [workaround(msvc)] Can't use constexpr bool in return type + +// Add the buffer interface to a vector +template +void vector_buffer_impl(Class_& cl, std::true_type) { + using T = typename Vector::value_type; + + static_assert(vector_has_data_and_format::value, "There is not an appropriate format descriptor for this vector"); + + // numpy.h declares this for arbitrary types, but it may raise an exception and crash hard at runtime if PYBIND11_NUMPY_DTYPE hasn't been called, so check here + format_descriptor::format(); + + cl.def_buffer([](Vector& v) -> buffer_info { + return buffer_info(v.data(), static_cast(sizeof(T)), format_descriptor::format(), 1, {v.size()}, {sizeof(T)}); + }); + + cl.def(init([](buffer buf) { + auto info = buf.request(); + if (info.ndim != 1 || info.strides[0] % static_cast(sizeof(T))) + throw type_error("Only valid 1D buffers can be copied to a vector"); + if (!detail::compare_buffer_info::compare(info) || (ssize_t) sizeof(T) != info.itemsize) + throw type_error("Format mismatch (Python: " + info.format + " C++: " + format_descriptor::format() + ")"); + + T *p = static_cast(info.ptr); + ssize_t step = info.strides[0] / static_cast(sizeof(T)); + T *end = p + info.shape[0] * step; + if (step == 1) { + return Vector(p, end); + } + else { + Vector vec; + vec.reserve((size_t) info.shape[0]); + for (; p != end; p += step) + vec.push_back(*p); + return vec; + } + })); + + return; +} + +template +void vector_buffer_impl(Class_&, std::false_type) {} + +template +void vector_buffer(Class_& cl) { + vector_buffer_impl(cl, detail::any_of...>{}); +} + +PYBIND11_NAMESPACE_END(detail) + +// +// std::vector +// +template , typename... Args> +class_ bind_vector(handle scope, std::string const &name, Args&&... args) { + using Class_ = class_; + + // If the value_type is unregistered (e.g. a converting type) or is itself registered + // module-local then make the vector binding module-local as well: + using vtype = typename Vector::value_type; + auto vtype_info = detail::get_type_info(typeid(vtype)); + bool local = !vtype_info || vtype_info->module_local; + + Class_ cl(scope, name.c_str(), pybind11::module_local(local), std::forward(args)...); + + // Declare the buffer interface if a buffer_protocol() is passed in + detail::vector_buffer(cl); + + cl.def(init<>()); + + // Register copy constructor (if possible) + detail::vector_if_copy_constructible(cl); + + // Register comparison-related operators and functions (if possible) + detail::vector_if_equal_operator(cl); + + // Register stream insertion operator (if possible) + detail::vector_if_insertion_operator(cl, name); + + // Modifiers require copyable vector value type + detail::vector_modifiers(cl); + + // Accessor and iterator; return by value if copyable, otherwise we return by ref + keep-alive + detail::vector_accessor(cl); + + cl.def("__bool__", + [](const Vector &v) -> bool { + return !v.empty(); + }, + "Check whether the list is nonempty" + ); + + cl.def("__len__", &Vector::size); + + + + +#if 0 + // C++ style functions deprecated, leaving it here as an example + cl.def(init()); + + cl.def("resize", + (void (Vector::*) (size_type count)) & Vector::resize, + "changes the number of elements stored"); + + cl.def("erase", + [](Vector &v, SizeType i) { + if (i >= v.size()) + throw index_error(); + v.erase(v.begin() + i); + }, "erases element at index ``i``"); + + cl.def("empty", &Vector::empty, "checks whether the container is empty"); + cl.def("size", &Vector::size, "returns the number of elements"); + cl.def("push_back", (void (Vector::*)(const T&)) &Vector::push_back, "adds an element to the end"); + cl.def("pop_back", &Vector::pop_back, "removes the last element"); + + cl.def("max_size", &Vector::max_size, "returns the maximum possible number of elements"); + cl.def("reserve", &Vector::reserve, "reserves storage"); + cl.def("capacity", &Vector::capacity, "returns the number of elements that can be held in currently allocated storage"); + cl.def("shrink_to_fit", &Vector::shrink_to_fit, "reduces memory usage by freeing unused memory"); + + cl.def("clear", &Vector::clear, "clears the contents"); + cl.def("swap", &Vector::swap, "swaps the contents"); + + cl.def("front", [](Vector &v) { + if (v.size()) return v.front(); + else throw index_error(); + }, "access the first element"); + + cl.def("back", [](Vector &v) { + if (v.size()) return v.back(); + else throw index_error(); + }, "access the last element "); + +#endif + + return cl; +} + + + +// +// std::map, std::unordered_map +// + +PYBIND11_NAMESPACE_BEGIN(detail) + +/* Fallback functions */ +template void map_if_insertion_operator(const Args &...) { } +template void map_assignment(const Args &...) { } + +// Map assignment when copy-assignable: just copy the value +template +void map_assignment(enable_if_t::value, Class_> &cl) { + using KeyType = typename Map::key_type; + using MappedType = typename Map::mapped_type; + + cl.def("__setitem__", + [](Map &m, const KeyType &k, const MappedType &v) { + auto it = m.find(k); + if (it != m.end()) it->second = v; + else m.emplace(k, v); + } + ); +} + +// Not copy-assignable, but still copy-constructible: we can update the value by erasing and reinserting +template +void map_assignment(enable_if_t< + !is_copy_assignable::value && + is_copy_constructible::value, + Class_> &cl) { + using KeyType = typename Map::key_type; + using MappedType = typename Map::mapped_type; + + cl.def("__setitem__", + [](Map &m, const KeyType &k, const MappedType &v) { + // We can't use m[k] = v; because value type might not be default constructable + auto r = m.emplace(k, v); + if (!r.second) { + // value type is not copy assignable so the only way to insert it is to erase it first... + m.erase(r.first); + m.emplace(k, v); + } + } + ); +} + + +template auto map_if_insertion_operator(Class_ &cl, std::string const &name) +-> decltype(std::declval() << std::declval() << std::declval(), void()) { + + cl.def("__repr__", + [name](Map &m) { + std::ostringstream s; + s << name << '{'; + bool f = false; + for (auto const &kv : m) { + if (f) + s << ", "; + s << kv.first << ": " << kv.second; + f = true; + } + s << '}'; + return s.str(); + }, + "Return the canonical string representation of this map." + ); +} + + +PYBIND11_NAMESPACE_END(detail) + +template , typename... Args> +class_ bind_map(handle scope, const std::string &name, Args&&... args) { + using KeyType = typename Map::key_type; + using MappedType = typename Map::mapped_type; + using Class_ = class_; + + // If either type is a non-module-local bound type then make the map binding non-local as well; + // otherwise (e.g. both types are either module-local or converting) the map will be + // module-local. + auto tinfo = detail::get_type_info(typeid(MappedType)); + bool local = !tinfo || tinfo->module_local; + if (local) { + tinfo = detail::get_type_info(typeid(KeyType)); + local = !tinfo || tinfo->module_local; + } + + Class_ cl(scope, name.c_str(), pybind11::module_local(local), std::forward(args)...); + + cl.def(init<>()); + + // Register stream insertion operator (if possible) + detail::map_if_insertion_operator(cl, name); + + cl.def("__bool__", + [](const Map &m) -> bool { return !m.empty(); }, + "Check whether the map is nonempty" + ); + + cl.def("__iter__", + [](Map &m) { return make_key_iterator(m.begin(), m.end()); }, + keep_alive<0, 1>() /* Essential: keep list alive while iterator exists */ + ); + + cl.def("items", + [](Map &m) { return make_iterator(m.begin(), m.end()); }, + keep_alive<0, 1>() /* Essential: keep list alive while iterator exists */ + ); + + cl.def("__getitem__", + [](Map &m, const KeyType &k) -> MappedType & { + auto it = m.find(k); + if (it == m.end()) + throw key_error(); + return it->second; + }, + return_value_policy::reference_internal // ref + keepalive + ); + + cl.def("__contains__", + [](Map &m, const KeyType &k) -> bool { + auto it = m.find(k); + if (it == m.end()) + return false; + return true; + } + ); + + // Assignment provided only if the type is copyable + detail::map_assignment(cl); + + cl.def("__delitem__", + [](Map &m, const KeyType &k) { + auto it = m.find(k); + if (it == m.end()) + throw key_error(); + m.erase(it); + } + ); + + cl.def("__len__", &Map::size); + + return cl; +} + +PYBIND11_NAMESPACE_END(PYBIND11_NAMESPACE) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/__init__.py b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..ad65420893d6fdfb9625d42bc326565866a6c9c8 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/__init__.py @@ -0,0 +1,12 @@ +# -*- coding: utf-8 -*- + +from ._version import version_info, __version__ +from .commands import get_include, get_cmake_dir + + +__all__ = ( + "version_info", + "__version__", + "get_include", + "get_cmake_dir", +) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/__main__.py b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/__main__.py new file mode 100644 index 0000000000000000000000000000000000000000..020988c6713d99ec0188be147084ccd21379c7b6 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/__main__.py @@ -0,0 +1,52 @@ +# -*- coding: utf-8 -*- +from __future__ import print_function + +import argparse +import sys +import sysconfig + +from .commands import get_include, get_cmake_dir + + +def print_includes(): + # type: () -> None + dirs = [ + sysconfig.get_path("include"), + sysconfig.get_path("platinclude"), + get_include(), + ] + + # Make unique but preserve order + unique_dirs = [] + for d in dirs: + if d and d not in unique_dirs: + unique_dirs.append(d) + + print(" ".join("-I" + d for d in unique_dirs)) + + +def main(): + # type: () -> None + + parser = argparse.ArgumentParser() + parser.add_argument( + "--includes", + action="store_true", + help="Include flags for both pybind11 and Python headers.", + ) + parser.add_argument( + "--cmakedir", + action="store_true", + help="Print the CMake module directory, ideal for setting -Dpybind11_ROOT in CMake.", + ) + args = parser.parse_args() + if not sys.argv[1:]: + parser.print_help() + if args.includes: + print_includes() + if args.cmakedir: + print(get_cmake_dir()) + + +if __name__ == "__main__": + main() diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/_version.py b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/_version.py new file mode 100644 index 0000000000000000000000000000000000000000..ffadcca5a8ab4cdc5ad211c150a238f381a1b531 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/_version.py @@ -0,0 +1,12 @@ +# -*- coding: utf-8 -*- + + +def _to_int(s): + try: + return int(s) + except ValueError: + return s + + +__version__ = "2.6.3.dev1" +version_info = tuple(_to_int(s) for s in __version__.split(".")) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/_version.pyi b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/_version.pyi new file mode 100644 index 0000000000000000000000000000000000000000..970184c7707167c8a612182d663d5034f476b370 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/_version.pyi @@ -0,0 +1,6 @@ +from typing import Union, Tuple + +def _to_int(s: str) -> Union[int, str]: ... + +__version__: str +version_info: Tuple[Union[int, str], ...] diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/commands.py b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/commands.py new file mode 100644 index 0000000000000000000000000000000000000000..34dbaf8a89621fb1bfdc4eec584c67fd5b526e1d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/commands.py @@ -0,0 +1,22 @@ +# -*- coding: utf-8 -*- +import os + + +DIR = os.path.abspath(os.path.dirname(__file__)) + + +def get_include(user=False): + # type: (bool) -> str + installed_path = os.path.join(DIR, "include") + source_path = os.path.join(os.path.dirname(DIR), "include") + return installed_path if os.path.exists(installed_path) else source_path + + +def get_cmake_dir(): + # type: () -> str + cmake_installed_path = os.path.join(DIR, "share", "cmake", "pybind11") + if os.path.exists(cmake_installed_path): + return cmake_installed_path + else: + msg = "pybind11 not installed, installation required to access the CMake files" + raise ImportError(msg) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/py.typed b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/py.typed new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/setup_helpers.py b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/setup_helpers.py new file mode 100644 index 0000000000000000000000000000000000000000..c69064ca502790d0dc2e42d1f266e471819fbdea --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/setup_helpers.py @@ -0,0 +1,444 @@ +# -*- coding: utf-8 -*- + +""" +This module provides helpers for C++11+ projects using pybind11. + +LICENSE: + +Copyright (c) 2016 Wenzel Jakob , All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its contributors + may be used to endorse or promote products derived from this software + without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +""" + +# IMPORTANT: If you change this file in the pybind11 repo, also review +# setup_helpers.pyi for matching changes. +# +# If you copy this file in, you don't +# need the .pyi file; it's just an interface file for static type checkers. + +import contextlib +import os +import shutil +import sys +import tempfile +import threading +import platform +import warnings + +try: + from setuptools.command.build_ext import build_ext as _build_ext + from setuptools import Extension as _Extension +except ImportError: + from distutils.command.build_ext import build_ext as _build_ext + from distutils.extension import Extension as _Extension + +import distutils.errors +import distutils.ccompiler + + +WIN = sys.platform.startswith("win32") +PY2 = sys.version_info[0] < 3 +MACOS = sys.platform.startswith("darwin") +STD_TMPL = "/std:c++{}" if WIN else "-std=c++{}" + + +# It is recommended to use PEP 518 builds if using this module. However, this +# file explicitly supports being copied into a user's project directory +# standalone, and pulling pybind11 with the deprecated setup_requires feature. +# If you copy the file, remember to add it to your MANIFEST.in, and add the current +# directory into your path if it sits beside your setup.py. + + +class Pybind11Extension(_Extension): + """ + Build a C++11+ Extension module with pybind11. This automatically adds the + recommended flags when you init the extension and assumes C++ sources - you + can further modify the options yourself. + + The customizations are: + + * ``/EHsc`` and ``/bigobj`` on Windows + * ``stdlib=libc++`` on macOS + * ``visibility=hidden`` and ``-g0`` on Unix + + Finally, you can set ``cxx_std`` via constructor or afterwords to enable + flags for C++ std, and a few extra helper flags related to the C++ standard + level. It is _highly_ recommended you either set this, or use the provided + ``build_ext``, which will search for the highest supported extension for + you if the ``cxx_std`` property is not set. Do not set the ``cxx_std`` + property more than once, as flags are added when you set it. Set the + property to None to disable the addition of C++ standard flags. + + If you want to add pybind11 headers manually, for example for an exact + git checkout, then set ``include_pybind11=False``. + + Warning: do not use property-based access to the instance on Python 2 - + this is an ugly old-style class due to Distutils. + """ + + # flags are prepended, so that they can be further overridden, e.g. by + # ``extra_compile_args=["-g"]``. + + def _add_cflags(self, flags): + self.extra_compile_args[:0] = flags + + def _add_ldflags(self, flags): + self.extra_link_args[:0] = flags + + def __init__(self, *args, **kwargs): + + self._cxx_level = 0 + cxx_std = kwargs.pop("cxx_std", 0) + + if "language" not in kwargs: + kwargs["language"] = "c++" + + include_pybind11 = kwargs.pop("include_pybind11", True) + + # Can't use super here because distutils has old-style classes in + # Python 2! + _Extension.__init__(self, *args, **kwargs) + + # Include the installed package pybind11 headers + if include_pybind11: + # If using setup_requires, this fails the first time - that's okay + try: + import pybind11 + + pyinc = pybind11.get_include() + + if pyinc not in self.include_dirs: + self.include_dirs.append(pyinc) + except ImportError: + pass + + # Have to use the accessor manually to support Python 2 distutils + Pybind11Extension.cxx_std.__set__(self, cxx_std) + + cflags = [] + ldflags = [] + if WIN: + cflags += ["/EHsc", "/bigobj"] + else: + cflags += ["-fvisibility=hidden", "-g0"] + if MACOS: + cflags += ["-stdlib=libc++"] + ldflags += ["-stdlib=libc++"] + self._add_cflags(cflags) + self._add_ldflags(ldflags) + + @property + def cxx_std(self): + """ + The CXX standard level. If set, will add the required flags. If left + at 0, it will trigger an automatic search when pybind11's build_ext + is used. If None, will have no effect. Besides just the flags, this + may add a register warning/error fix for Python 2 or macos-min 10.9 + or 10.14. + """ + return self._cxx_level + + @cxx_std.setter + def cxx_std(self, level): + + if self._cxx_level: + warnings.warn("You cannot safely change the cxx_level after setting it!") + + # MSVC 2015 Update 3 and later only have 14 (and later 17) modes, so + # force a valid flag here. + if WIN and level == 11: + level = 14 + + self._cxx_level = level + + if not level: + return + + cflags = [STD_TMPL.format(level)] + ldflags = [] + + if MACOS and "MACOSX_DEPLOYMENT_TARGET" not in os.environ: + # C++17 requires a higher min version of macOS. An earlier version + # (10.12 or 10.13) can be set manually via environment variable if + # you are careful in your feature usage, but 10.14 is the safest + # setting for general use. However, never set higher than the + # current macOS version! + current_macos = tuple(int(x) for x in platform.mac_ver()[0].split(".")[:2]) + desired_macos = (10, 9) if level < 17 else (10, 14) + macos_string = ".".join(str(x) for x in min(current_macos, desired_macos)) + macosx_min = "-mmacosx-version-min=" + macos_string + cflags += [macosx_min] + ldflags += [macosx_min] + + if PY2: + if WIN: + # Will be ignored on MSVC 2015, where C++17 is not supported so + # this flag is not valid. + cflags += ["/wd5033"] + elif level >= 17: + cflags += ["-Wno-register"] + elif level >= 14: + cflags += ["-Wno-deprecated-register"] + + self._add_cflags(cflags) + self._add_ldflags(ldflags) + + +# Just in case someone clever tries to multithread +tmp_chdir_lock = threading.Lock() +cpp_cache_lock = threading.Lock() + + +@contextlib.contextmanager +def tmp_chdir(): + "Prepare and enter a temporary directory, cleanup when done" + + # Threadsafe + with tmp_chdir_lock: + olddir = os.getcwd() + try: + tmpdir = tempfile.mkdtemp() + os.chdir(tmpdir) + yield tmpdir + finally: + os.chdir(olddir) + shutil.rmtree(tmpdir) + + +# cf http://bugs.python.org/issue26689 +def has_flag(compiler, flag): + """ + Return the flag if a flag name is supported on the + specified compiler, otherwise None (can be used as a boolean). + If multiple flags are passed, return the first that matches. + """ + + with tmp_chdir(): + fname = "flagcheck.cpp" + with open(fname, "w") as f: + # Don't trigger -Wunused-parameter. + f.write("int main (int, char **) { return 0; }") + + try: + compiler.compile([fname], extra_postargs=[flag]) + except distutils.errors.CompileError: + return False + return True + + +# Every call will cache the result +cpp_flag_cache = None + + +def auto_cpp_level(compiler): + """ + Return the max supported C++ std level (17, 14, or 11). Returns latest on Windows. + """ + + if WIN: + return "latest" + + global cpp_flag_cache + + # If this has been previously calculated with the same args, return that + with cpp_cache_lock: + if cpp_flag_cache: + return cpp_flag_cache + + levels = [17, 14, 11] + + for level in levels: + if has_flag(compiler, STD_TMPL.format(level)): + with cpp_cache_lock: + cpp_flag_cache = level + return level + + msg = "Unsupported compiler -- at least C++11 support is needed!" + raise RuntimeError(msg) + + +class build_ext(_build_ext): # noqa: N801 + """ + Customized build_ext that allows an auto-search for the highest supported + C++ level for Pybind11Extension. This is only needed for the auto-search + for now, and is completely optional otherwise. + """ + + def build_extensions(self): + """ + Build extensions, injecting C++ std for Pybind11Extension if needed. + """ + + for ext in self.extensions: + if hasattr(ext, "_cxx_level") and ext._cxx_level == 0: + # Python 2 syntax - old-style distutils class + ext.__class__.cxx_std.__set__(ext, auto_cpp_level(self.compiler)) + + # Python 2 doesn't allow super here, since distutils uses old-style + # classes! + _build_ext.build_extensions(self) + + +def naive_recompile(obj, src): + """ + This will recompile only if the source file changes. It does not check + header files, so a more advanced function or Ccache is better if you have + editable header files in your package. + """ + return os.stat(obj).st_mtime < os.stat(src).st_mtime + + +def no_recompile(obg, src): + """ + This is the safest but slowest choice (and is the default) - will always + recompile sources. + """ + return True + + +# Optional parallel compile utility +# inspired by: http://stackoverflow.com/questions/11013851/speeding-up-build-process-with-distutils +# and: https://github.com/tbenthompson/cppimport/blob/stable/cppimport/build_module.py +# and NumPy's parallel distutils module: +# https://github.com/numpy/numpy/blob/master/numpy/distutils/ccompiler.py +class ParallelCompile(object): + """ + Make a parallel compile function. Inspired by + numpy.distutils.ccompiler.CCompiler_compile and cppimport. + + This takes several arguments that allow you to customize the compile + function created: + + envvar: + Set an environment variable to control the compilation threads, like + NPY_NUM_BUILD_JOBS + default: + 0 will automatically multithread, or 1 will only multithread if the + envvar is set. + max: + The limit for automatic multithreading if non-zero + needs_recompile: + A function of (obj, src) that returns True when recompile is needed. No + effect in isolated mode; use ccache instead, see + https://github.com/matplotlib/matplotlib/issues/1507/ + + To use:: + + ParallelCompile("NPY_NUM_BUILD_JOBS").install() + + or:: + + with ParallelCompile("NPY_NUM_BUILD_JOBS"): + setup(...) + + By default, this assumes all files need to be recompiled. A smarter + function can be provided via needs_recompile. If the output has not yet + been generated, the compile will always run, and this function is not + called. + """ + + __slots__ = ("envvar", "default", "max", "_old", "needs_recompile") + + def __init__(self, envvar=None, default=0, max=0, needs_recompile=no_recompile): + self.envvar = envvar + self.default = default + self.max = max + self.needs_recompile = needs_recompile + self._old = [] + + def function(self): + """ + Builds a function object usable as distutils.ccompiler.CCompiler.compile. + """ + + def compile_function( + compiler, + sources, + output_dir=None, + macros=None, + include_dirs=None, + debug=0, + extra_preargs=None, + extra_postargs=None, + depends=None, + ): + + # These lines are directly from distutils.ccompiler.CCompiler + macros, objects, extra_postargs, pp_opts, build = compiler._setup_compile( + output_dir, macros, include_dirs, sources, depends, extra_postargs + ) + cc_args = compiler._get_cc_args(pp_opts, debug, extra_preargs) + + # The number of threads; start with default. + threads = self.default + + # Determine the number of compilation threads, unless set by an environment variable. + if self.envvar is not None: + threads = int(os.environ.get(self.envvar, self.default)) + + def _single_compile(obj): + try: + src, ext = build[obj] + except KeyError: + return + + if not os.path.exists(obj) or self.needs_recompile(obj, src): + compiler._compile(obj, src, ext, cc_args, extra_postargs, pp_opts) + + try: + import multiprocessing + from multiprocessing.pool import ThreadPool + except ImportError: + threads = 1 + + if threads == 0: + try: + threads = multiprocessing.cpu_count() + threads = self.max if self.max and self.max < threads else threads + except NotImplementedError: + threads = 1 + + if threads > 1: + for _ in ThreadPool(threads).imap_unordered(_single_compile, objects): + pass + else: + for ob in objects: + _single_compile(ob) + + return objects + + return compile_function + + def install(self): + distutils.ccompiler.CCompiler.compile = self.function() + return self + + def __enter__(self): + self._old.append(distutils.ccompiler.CCompiler.compile) + return self.install() + + def __exit__(self, *args): + distutils.ccompiler.CCompiler.compile = self._old.pop() diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/setup_helpers.pyi b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/setup_helpers.pyi new file mode 100644 index 0000000000000000000000000000000000000000..23232e1fdaed10aa8e6e7e8083d278403ac041f4 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pybind11/setup_helpers.pyi @@ -0,0 +1,61 @@ +# IMPORTANT: Should stay in sync with setup_helpers.py (mostly checked by CI / +# pre-commit). + +from typing import Any, Callable, Iterator, Optional, Type, TypeVar, Union +from types import TracebackType + +from distutils.command.build_ext import build_ext as _build_ext # type: ignore +from distutils.extension import Extension as _Extension +import distutils.ccompiler +import contextlib + +WIN: bool +PY2: bool +MACOS: bool +STD_TMPL: str + +class Pybind11Extension(_Extension): + def _add_cflags(self, *flags: str) -> None: ... + def _add_lflags(self, *flags: str) -> None: ... + def __init__( + self, *args: Any, cxx_std: int = 0, language: str = "c++", **kwargs: Any + ) -> None: ... + @property + def cxx_std(self) -> int: ... + @cxx_std.setter + def cxx_std(self, level: int) -> None: ... + +@contextlib.contextmanager +def tmp_chdir() -> Iterator[str]: ... +def has_flag(compiler: distutils.ccompiler.CCompiler, flag: str) -> bool: ... +def auto_cpp_level(compiler: distutils.ccompiler.CCompiler) -> Union[int, str]: ... + +class build_ext(_build_ext): # type: ignore + def build_extensions(self) -> None: ... + +def no_recompile(obj: str, src: str) -> bool: ... +def naive_recompile(obj: str, src: str) -> bool: ... + +T = TypeVar("T", bound="ParallelCompile") + +class ParallelCompile: + envvar: Optional[str] + default: int + max: int + needs_recompile: Callable[[str, str], bool] + def __init__( + self, + envvar: Optional[str] = None, + default: int = 0, + max: int = 0, + needs_recompile: Callable[[str, str], bool] = no_recompile, + ) -> None: ... + def function(self) -> Any: ... + def install(self: T) -> T: ... + def __enter__(self: T) -> T: ... + def __exit__( + self, + exc_type: Optional[Type[BaseException]], + exc_value: Optional[BaseException], + traceback: Optional[TracebackType], + ) -> None: ... diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/pyproject.toml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pyproject.toml new file mode 100644 index 0000000000000000000000000000000000000000..5c9d15354123e736255c67c3777ab6b5a24d052b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/pyproject.toml @@ -0,0 +1,3 @@ +[build-system] +requires = ["setuptools>=42", "wheel", "cmake>=3.18", "ninja"] +build-backend = "setuptools.build_meta" diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/setup.cfg b/methods/ring/utils/fast_gicp/thirdparty/pybind11/setup.cfg new file mode 100644 index 0000000000000000000000000000000000000000..041e62dae69e3ef9c100ba500d72986df2155eac --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/setup.cfg @@ -0,0 +1,85 @@ +[metadata] +long_description = file: README.rst +long_description_content_type = text/x-rst +description = Seamless operability between C++11 and Python +author = Wenzel Jakob +author_email = wenzel.jakob@epfl.ch +url = https://github.com/pybind/pybind11 +license = BSD + +classifiers = + Development Status :: 5 - Production/Stable + Intended Audience :: Developers + Topic :: Software Development :: Libraries :: Python Modules + Topic :: Utilities + Programming Language :: C++ + Programming Language :: Python :: 2.7 + Programming Language :: Python :: 3 + Programming Language :: Python :: 3.5 + Programming Language :: Python :: 3.6 + Programming Language :: Python :: 3.7 + Programming Language :: Python :: 3.8 + Programming Language :: Python :: 3.9 + License :: OSI Approved :: BSD License + Programming Language :: Python :: Implementation :: PyPy + Programming Language :: Python :: Implementation :: CPython + Programming Language :: C++ + Topic :: Software Development :: Libraries :: Python Modules + +keywords = + C++11 + Python bindings + +[options] +python_requires = >=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4 +zip_safe = False + +[bdist_wheel] +universal=1 + +[check-manifest] +ignore = + tests/** + docs/** + tools/** + include/** + .* + pybind11/include/** + pybind11/share/** + CMakeLists.txt + + +[flake8] +max-line-length = 99 +show_source = True +exclude = .git, __pycache__, build, dist, docs, tools, venv +ignore = + # required for pretty matrix formatting: multiple spaces after `,` and `[` + E201, E241, W504, + # camelcase 'cPickle' imported as lowercase 'pickle' + N813 + # Black conflict + W503, E203 + +[mypy] +files = pybind11 +python_version = 2.7 +warn_unused_configs = True + +# Currently (0.800) identical to --strict +disallow_any_generics = True +disallow_subclassing_any = True +disallow_untyped_calls = True +disallow_untyped_defs = True +disallow_incomplete_defs = True +check_untyped_defs = True +disallow_untyped_decorators = True +no_implicit_optional = True +warn_redundant_casts = True +warn_unused_ignores = True +warn_return_any = True +no_implicit_reexport = True +strict_equality = True + +[tool:pytest] +timeout = 300 diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/setup.py b/methods/ring/utils/fast_gicp/thirdparty/pybind11/setup.py new file mode 100644 index 0000000000000000000000000000000000000000..3a0327982adc1a37cf3f5a073aa025a45f97ec78 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/setup.py @@ -0,0 +1,115 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +# Setup script for PyPI; use CMakeFile.txt to build extension modules + +import contextlib +import os +import re +import shutil +import string +import subprocess +import sys +import tempfile + +import setuptools.command.sdist + +DIR = os.path.abspath(os.path.dirname(__file__)) +VERSION_REGEX = re.compile( + r"^\s*#\s*define\s+PYBIND11_VERSION_([A-Z]+)\s+(.*)$", re.MULTILINE +) + +# PYBIND11_GLOBAL_SDIST will build a different sdist, with the python-headers +# files, and the sys.prefix files (CMake and headers). + +global_sdist = os.environ.get("PYBIND11_GLOBAL_SDIST", False) + +setup_py = "tools/setup_global.py.in" if global_sdist else "tools/setup_main.py.in" +extra_cmd = 'cmdclass["sdist"] = SDist\n' + +to_src = ( + ("pyproject.toml", "tools/pyproject.toml"), + ("setup.py", setup_py), +) + +# Read the listed version +with open("pybind11/_version.py") as f: + code = compile(f.read(), "pybind11/_version.py", "exec") +loc = {} +exec(code, loc) +version = loc["__version__"] + +# Verify that the version matches the one in C++ +with open("include/pybind11/detail/common.h") as f: + matches = dict(VERSION_REGEX.findall(f.read())) +cpp_version = "{MAJOR}.{MINOR}.{PATCH}".format(**matches) +if version != cpp_version: + msg = "Python version {} does not match C++ version {}!".format( + version, cpp_version + ) + raise RuntimeError(msg) + + +def get_and_replace(filename, binary=False, **opts): + with open(filename, "rb" if binary else "r") as f: + contents = f.read() + # Replacement has to be done on text in Python 3 (both work in Python 2) + if binary: + return string.Template(contents.decode()).substitute(opts).encode() + else: + return string.Template(contents).substitute(opts) + + +# Use our input files instead when making the SDist (and anything that depends +# on it, like a wheel) +class SDist(setuptools.command.sdist.sdist): + def make_release_tree(self, base_dir, files): + setuptools.command.sdist.sdist.make_release_tree(self, base_dir, files) + + for to, src in to_src: + txt = get_and_replace(src, binary=True, version=version, extra_cmd="") + + dest = os.path.join(base_dir, to) + + # This is normally linked, so unlink before writing! + os.unlink(dest) + with open(dest, "wb") as f: + f.write(txt) + + +# Backport from Python 3 +@contextlib.contextmanager +def TemporaryDirectory(): # noqa: N802 + "Prepare a temporary directory, cleanup when done" + try: + tmpdir = tempfile.mkdtemp() + yield tmpdir + finally: + shutil.rmtree(tmpdir) + + +# Remove the CMake install directory when done +@contextlib.contextmanager +def remove_output(*sources): + try: + yield + finally: + for src in sources: + shutil.rmtree(src) + + +with remove_output("pybind11/include", "pybind11/share"): + # Generate the files if they are not present. + with TemporaryDirectory() as tmpdir: + cmd = ["cmake", "-S", ".", "-B", tmpdir] + [ + "-DCMAKE_INSTALL_PREFIX=pybind11", + "-DBUILD_TESTING=OFF", + "-DPYBIND11_NOPYTHON=ON", + ] + cmake_opts = dict(cwd=DIR, stdout=sys.stdout, stderr=sys.stderr) + subprocess.check_call(cmd, **cmake_opts) + subprocess.check_call(["cmake", "--install", tmpdir], **cmake_opts) + + txt = get_and_replace(setup_py, version=version, extra_cmd=extra_cmd) + code = compile(txt, setup_py, "exec") + exec(code, {"SDist": SDist}) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/FindCatch.cmake b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/FindCatch.cmake new file mode 100644 index 0000000000000000000000000000000000000000..4d6bffcf6810c5caa2ed424392f3c45216d1356b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/FindCatch.cmake @@ -0,0 +1,70 @@ +# - Find the Catch test framework or download it (single header) +# +# This is a quick module for internal use. It assumes that Catch is +# REQUIRED and that a minimum version is provided (not EXACT). If +# a suitable version isn't found locally, the single header file +# will be downloaded and placed in the build dir: PROJECT_BINARY_DIR. +# +# This code sets the following variables: +# CATCH_INCLUDE_DIR - path to catch.hpp +# CATCH_VERSION - version number + +if(NOT Catch_FIND_VERSION) + message(FATAL_ERROR "A version number must be specified.") +elseif(Catch_FIND_REQUIRED) + message(FATAL_ERROR "This module assumes Catch is not required.") +elseif(Catch_FIND_VERSION_EXACT) + message(FATAL_ERROR "Exact version numbers are not supported, only minimum.") +endif() + +# Extract the version number from catch.hpp +function(_get_catch_version) + file( + STRINGS "${CATCH_INCLUDE_DIR}/catch.hpp" version_line + REGEX "Catch v.*" + LIMIT_COUNT 1) + if(version_line MATCHES "Catch v([0-9]+)\\.([0-9]+)\\.([0-9]+)") + set(CATCH_VERSION + "${CMAKE_MATCH_1}.${CMAKE_MATCH_2}.${CMAKE_MATCH_3}" + PARENT_SCOPE) + endif() +endfunction() + +# Download the single-header version of Catch +function(_download_catch version destination_dir) + message(STATUS "Downloading catch v${version}...") + set(url https://github.com/philsquared/Catch/releases/download/v${version}/catch.hpp) + file(DOWNLOAD ${url} "${destination_dir}/catch.hpp" STATUS status) + list(GET status 0 error) + if(error) + message(FATAL_ERROR "Could not download ${url}") + endif() + set(CATCH_INCLUDE_DIR + "${destination_dir}" + CACHE INTERNAL "") +endfunction() + +# Look for catch locally +find_path( + CATCH_INCLUDE_DIR + NAMES catch.hpp + PATH_SUFFIXES catch2) +if(CATCH_INCLUDE_DIR) + _get_catch_version() +endif() + +# Download the header if it wasn't found or if it's outdated +if(NOT CATCH_VERSION OR CATCH_VERSION VERSION_LESS ${Catch_FIND_VERSION}) + if(DOWNLOAD_CATCH) + _download_catch(${Catch_FIND_VERSION} "${PROJECT_BINARY_DIR}/catch/") + _get_catch_version() + else() + set(CATCH_FOUND FALSE) + return() + endif() +endif() + +add_library(Catch2::Catch2 IMPORTED INTERFACE) +set_property(TARGET Catch2::Catch2 PROPERTY INTERFACE_INCLUDE_DIRECTORIES "${CATCH_INCLUDE_DIR}") + +set(CATCH_FOUND TRUE) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/FindEigen3.cmake b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/FindEigen3.cmake new file mode 100644 index 0000000000000000000000000000000000000000..83625d92e071abdda3e1e066d2d3770dd1a4e38c --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/FindEigen3.cmake @@ -0,0 +1,86 @@ +# - Try to find Eigen3 lib +# +# This module supports requiring a minimum version, e.g. you can do +# find_package(Eigen3 3.1.2) +# to require version 3.1.2 or newer of Eigen3. +# +# Once done this will define +# +# EIGEN3_FOUND - system has eigen lib with correct version +# EIGEN3_INCLUDE_DIR - the eigen include directory +# EIGEN3_VERSION - eigen version + +# Copyright (c) 2006, 2007 Montel Laurent, +# Copyright (c) 2008, 2009 Gael Guennebaud, +# Copyright (c) 2009 Benoit Jacob +# Redistribution and use is allowed according to the terms of the 2-clause BSD license. + +if(NOT Eigen3_FIND_VERSION) + if(NOT Eigen3_FIND_VERSION_MAJOR) + set(Eigen3_FIND_VERSION_MAJOR 2) + endif(NOT Eigen3_FIND_VERSION_MAJOR) + if(NOT Eigen3_FIND_VERSION_MINOR) + set(Eigen3_FIND_VERSION_MINOR 91) + endif(NOT Eigen3_FIND_VERSION_MINOR) + if(NOT Eigen3_FIND_VERSION_PATCH) + set(Eigen3_FIND_VERSION_PATCH 0) + endif(NOT Eigen3_FIND_VERSION_PATCH) + + set(Eigen3_FIND_VERSION + "${Eigen3_FIND_VERSION_MAJOR}.${Eigen3_FIND_VERSION_MINOR}.${Eigen3_FIND_VERSION_PATCH}") +endif(NOT Eigen3_FIND_VERSION) + +macro(_eigen3_check_version) + file(READ "${EIGEN3_INCLUDE_DIR}/Eigen/src/Core/util/Macros.h" _eigen3_version_header) + + string(REGEX MATCH "define[ \t]+EIGEN_WORLD_VERSION[ \t]+([0-9]+)" _eigen3_world_version_match + "${_eigen3_version_header}") + set(EIGEN3_WORLD_VERSION "${CMAKE_MATCH_1}") + string(REGEX MATCH "define[ \t]+EIGEN_MAJOR_VERSION[ \t]+([0-9]+)" _eigen3_major_version_match + "${_eigen3_version_header}") + set(EIGEN3_MAJOR_VERSION "${CMAKE_MATCH_1}") + string(REGEX MATCH "define[ \t]+EIGEN_MINOR_VERSION[ \t]+([0-9]+)" _eigen3_minor_version_match + "${_eigen3_version_header}") + set(EIGEN3_MINOR_VERSION "${CMAKE_MATCH_1}") + + set(EIGEN3_VERSION ${EIGEN3_WORLD_VERSION}.${EIGEN3_MAJOR_VERSION}.${EIGEN3_MINOR_VERSION}) + if(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION}) + set(EIGEN3_VERSION_OK FALSE) + else(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION}) + set(EIGEN3_VERSION_OK TRUE) + endif(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION}) + + if(NOT EIGEN3_VERSION_OK) + + message(STATUS "Eigen3 version ${EIGEN3_VERSION} found in ${EIGEN3_INCLUDE_DIR}, " + "but at least version ${Eigen3_FIND_VERSION} is required") + endif(NOT EIGEN3_VERSION_OK) +endmacro(_eigen3_check_version) + +if(EIGEN3_INCLUDE_DIR) + + # in cache already + _eigen3_check_version() + set(EIGEN3_FOUND ${EIGEN3_VERSION_OK}) + +else(EIGEN3_INCLUDE_DIR) + if(NOT DEFINED KDE4_INCLUDE_DIR) + set(KDE4_INCLUDE_DIR "") + endif() + + find_path( + EIGEN3_INCLUDE_DIR + NAMES signature_of_eigen3_matrix_library + PATHS ${CMAKE_INSTALL_PREFIX}/include ${KDE4_INCLUDE_DIR} + PATH_SUFFIXES eigen3 eigen) + + if(EIGEN3_INCLUDE_DIR) + _eigen3_check_version() + endif(EIGEN3_INCLUDE_DIR) + + include(FindPackageHandleStandardArgs) + find_package_handle_standard_args(Eigen3 DEFAULT_MSG EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) + + mark_as_advanced(EIGEN3_INCLUDE_DIR) + +endif(EIGEN3_INCLUDE_DIR) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/FindPythonLibsNew.cmake b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/FindPythonLibsNew.cmake new file mode 100644 index 0000000000000000000000000000000000000000..3605aebcf354218aace7cc95f33da300b02615f1 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/FindPythonLibsNew.cmake @@ -0,0 +1,257 @@ +# - Find python libraries +# This module finds the libraries corresponding to the Python interpreter +# FindPythonInterp provides. +# This code sets the following variables: +# +# PYTHONLIBS_FOUND - have the Python libs been found +# PYTHON_PREFIX - path to the Python installation +# PYTHON_LIBRARIES - path to the python library +# PYTHON_INCLUDE_DIRS - path to where Python.h is found +# PYTHON_MODULE_EXTENSION - lib extension, e.g. '.so' or '.pyd' +# PYTHON_MODULE_PREFIX - lib name prefix: usually an empty string +# PYTHON_SITE_PACKAGES - path to installation site-packages +# PYTHON_IS_DEBUG - whether the Python interpreter is a debug build +# +# Thanks to talljimbo for the patch adding the 'LDVERSION' config +# variable usage. + +#============================================================================= +# Copyright 2001-2009 Kitware, Inc. +# Copyright 2012 Continuum Analytics, Inc. +# +# All rights reserved. +# +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions +# are met: +# +# * Redistributions of source code must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# * Redistributions in binary form must reproduce the above copyright +# notice, this list of conditions and the following disclaimer in the +# documentation and/or other materials provided with the distribution. +# +# * Neither the names of Kitware, Inc., the Insight Software Consortium, +# nor the names of their contributors may be used to endorse or promote +# products derived from this software without specific prior written +# permission. +# +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +# # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +#============================================================================= + +# Checking for the extension makes sure that `LibsNew` was found and not just `Libs`. +if(PYTHONLIBS_FOUND AND PYTHON_MODULE_EXTENSION) + return() +endif() + +if(PythonLibsNew_FIND_QUIETLY) + set(_pythonlibs_quiet QUIET) +else() + set(_pythonlibs_quiet "") +endif() + +if(PythonLibsNew_FIND_REQUIRED) + set(_pythonlibs_required REQUIRED) +endif() + +# Check to see if the `python` command is present and from a virtual +# environment, conda, or GHA activation - if it is, try to use that. + +if(NOT DEFINED PYTHON_EXECUTABLE) + if(DEFINED ENV{VIRTUAL_ENV}) + find_program( + PYTHON_EXECUTABLE python + PATHS "$ENV{VIRTUAL_ENV}" "$ENV{VIRTUAL_ENV}/bin" + NO_DEFAULT_PATH) + elseif(DEFINED ENV{CONDA_PREFIX}) + find_program( + PYTHON_EXECUTABLE python + PATHS "$ENV{CONDA_PREFIX}" "$ENV{CONDA_PREFIX}/bin" + NO_DEFAULT_PATH) + elseif(DEFINED ENV{pythonLocation}) + find_program( + PYTHON_EXECUTABLE python + PATHS "$ENV{pythonLocation}" "$ENV{pythonLocation}/bin" + NO_DEFAULT_PATH) + endif() + if(NOT PYTHON_EXECUTABLE) + unset(PYTHON_EXECUTABLE) + endif() +endif() + +# Use the Python interpreter to find the libs. +if(NOT PythonLibsNew_FIND_VERSION) + set(PythonLibsNew_FIND_VERSION "") +endif() + +find_package(PythonInterp ${PythonLibsNew_FIND_VERSION} ${_pythonlibs_required} + ${_pythonlibs_quiet}) + +if(NOT PYTHONINTERP_FOUND) + set(PYTHONLIBS_FOUND FALSE) + set(PythonLibsNew_FOUND FALSE) + return() +endif() + +# According to https://stackoverflow.com/questions/646518/python-how-to-detect-debug-interpreter +# testing whether sys has the gettotalrefcount function is a reliable, cross-platform +# way to detect a CPython debug interpreter. +# +# The library suffix is from the config var LDVERSION sometimes, otherwise +# VERSION. VERSION will typically be like "2.7" on unix, and "27" on windows. +execute_process( + COMMAND + "${PYTHON_EXECUTABLE}" "-c" "from distutils import sysconfig as s;import sys;import struct; +print('.'.join(str(v) for v in sys.version_info)); +print(sys.prefix); +print(s.get_python_inc(plat_specific=True)); +print(s.get_python_lib(plat_specific=True)); +print(s.get_config_var('EXT_SUFFIX') or s.get_config_var('SO')); +print(hasattr(sys, 'gettotalrefcount')+0); +print(struct.calcsize('@P')); +print(s.get_config_var('LDVERSION') or s.get_config_var('VERSION')); +print(s.get_config_var('LIBDIR') or ''); +print(s.get_config_var('MULTIARCH') or ''); +" + RESULT_VARIABLE _PYTHON_SUCCESS + OUTPUT_VARIABLE _PYTHON_VALUES + ERROR_VARIABLE _PYTHON_ERROR_VALUE) + +if(NOT _PYTHON_SUCCESS MATCHES 0) + if(PythonLibsNew_FIND_REQUIRED) + message(FATAL_ERROR "Python config failure:\n${_PYTHON_ERROR_VALUE}") + endif() + set(PYTHONLIBS_FOUND FALSE) + set(PythonLibsNew_FOUND FALSE) + return() +endif() + +# Convert the process output into a list +if(WIN32) + string(REGEX REPLACE "\\\\" "/" _PYTHON_VALUES ${_PYTHON_VALUES}) +endif() +string(REGEX REPLACE ";" "\\\\;" _PYTHON_VALUES ${_PYTHON_VALUES}) +string(REGEX REPLACE "\n" ";" _PYTHON_VALUES ${_PYTHON_VALUES}) +list(GET _PYTHON_VALUES 0 _PYTHON_VERSION_LIST) +list(GET _PYTHON_VALUES 1 PYTHON_PREFIX) +list(GET _PYTHON_VALUES 2 PYTHON_INCLUDE_DIR) +list(GET _PYTHON_VALUES 3 PYTHON_SITE_PACKAGES) +list(GET _PYTHON_VALUES 4 PYTHON_MODULE_EXTENSION) +list(GET _PYTHON_VALUES 5 PYTHON_IS_DEBUG) +list(GET _PYTHON_VALUES 6 PYTHON_SIZEOF_VOID_P) +list(GET _PYTHON_VALUES 7 PYTHON_LIBRARY_SUFFIX) +list(GET _PYTHON_VALUES 8 PYTHON_LIBDIR) +list(GET _PYTHON_VALUES 9 PYTHON_MULTIARCH) + +# Make sure the Python has the same pointer-size as the chosen compiler +# Skip if CMAKE_SIZEOF_VOID_P is not defined +if(CMAKE_SIZEOF_VOID_P AND (NOT "${PYTHON_SIZEOF_VOID_P}" STREQUAL "${CMAKE_SIZEOF_VOID_P}")) + if(PythonLibsNew_FIND_REQUIRED) + math(EXPR _PYTHON_BITS "${PYTHON_SIZEOF_VOID_P} * 8") + math(EXPR _CMAKE_BITS "${CMAKE_SIZEOF_VOID_P} * 8") + message(FATAL_ERROR "Python config failure: Python is ${_PYTHON_BITS}-bit, " + "chosen compiler is ${_CMAKE_BITS}-bit") + endif() + set(PYTHONLIBS_FOUND FALSE) + set(PythonLibsNew_FOUND FALSE) + return() +endif() + +# The built-in FindPython didn't always give the version numbers +string(REGEX REPLACE "\\." ";" _PYTHON_VERSION_LIST ${_PYTHON_VERSION_LIST}) +list(GET _PYTHON_VERSION_LIST 0 PYTHON_VERSION_MAJOR) +list(GET _PYTHON_VERSION_LIST 1 PYTHON_VERSION_MINOR) +list(GET _PYTHON_VERSION_LIST 2 PYTHON_VERSION_PATCH) +set(PYTHON_VERSION "${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}.${PYTHON_VERSION_PATCH}") + +# Make sure all directory separators are '/' +string(REGEX REPLACE "\\\\" "/" PYTHON_PREFIX "${PYTHON_PREFIX}") +string(REGEX REPLACE "\\\\" "/" PYTHON_INCLUDE_DIR "${PYTHON_INCLUDE_DIR}") +string(REGEX REPLACE "\\\\" "/" PYTHON_SITE_PACKAGES "${PYTHON_SITE_PACKAGES}") + +if(CMAKE_HOST_WIN32) + set(PYTHON_LIBRARY "${PYTHON_PREFIX}/libs/python${PYTHON_LIBRARY_SUFFIX}.lib") + + # when run in a venv, PYTHON_PREFIX points to it. But the libraries remain in the + # original python installation. They may be found relative to PYTHON_INCLUDE_DIR. + if(NOT EXISTS "${PYTHON_LIBRARY}") + get_filename_component(_PYTHON_ROOT ${PYTHON_INCLUDE_DIR} DIRECTORY) + set(PYTHON_LIBRARY "${_PYTHON_ROOT}/libs/python${PYTHON_LIBRARY_SUFFIX}.lib") + endif() + + # if we are in MSYS & MINGW, and we didn't find windows python lib, look for system python lib + if(DEFINED ENV{MSYSTEM} + AND MINGW + AND NOT EXISTS "${PYTHON_LIBRARY}") + if(PYTHON_MULTIARCH) + set(_PYTHON_LIBS_SEARCH "${PYTHON_LIBDIR}/${PYTHON_MULTIARCH}" "${PYTHON_LIBDIR}") + else() + set(_PYTHON_LIBS_SEARCH "${PYTHON_LIBDIR}") + endif() + unset(PYTHON_LIBRARY) + find_library( + PYTHON_LIBRARY + NAMES "python${PYTHON_LIBRARY_SUFFIX}" + PATHS ${_PYTHON_LIBS_SEARCH} + NO_DEFAULT_PATH) + endif() + + # raise an error if the python libs are still not found. + if(NOT EXISTS "${PYTHON_LIBRARY}") + message(FATAL_ERROR "Python libraries not found") + endif() + +else() + if(PYTHON_MULTIARCH) + set(_PYTHON_LIBS_SEARCH "${PYTHON_LIBDIR}/${PYTHON_MULTIARCH}" "${PYTHON_LIBDIR}") + else() + set(_PYTHON_LIBS_SEARCH "${PYTHON_LIBDIR}") + endif() + #message(STATUS "Searching for Python libs in ${_PYTHON_LIBS_SEARCH}") + # Probably this needs to be more involved. It would be nice if the config + # information the python interpreter itself gave us were more complete. + find_library( + PYTHON_LIBRARY + NAMES "python${PYTHON_LIBRARY_SUFFIX}" + PATHS ${_PYTHON_LIBS_SEARCH} + NO_DEFAULT_PATH) + + # If all else fails, just set the name/version and let the linker figure out the path. + if(NOT PYTHON_LIBRARY) + set(PYTHON_LIBRARY python${PYTHON_LIBRARY_SUFFIX}) + endif() +endif() + +mark_as_advanced(PYTHON_LIBRARY PYTHON_INCLUDE_DIR) + +# We use PYTHON_INCLUDE_DIR, PYTHON_LIBRARY and PYTHON_DEBUG_LIBRARY for the +# cache entries because they are meant to specify the location of a single +# library. We now set the variables listed by the documentation for this +# module. +set(PYTHON_INCLUDE_DIRS "${PYTHON_INCLUDE_DIR}") +set(PYTHON_LIBRARIES "${PYTHON_LIBRARY}") +if(NOT PYTHON_DEBUG_LIBRARY) + set(PYTHON_DEBUG_LIBRARY "") +endif() +set(PYTHON_DEBUG_LIBRARIES "${PYTHON_DEBUG_LIBRARY}") + +find_package_message(PYTHON "Found PythonLibs: ${PYTHON_LIBRARY}" + "${PYTHON_EXECUTABLE}${PYTHON_VERSION_STRING}") + +set(PYTHONLIBS_FOUND TRUE) +set(PythonLibsNew_FOUND TRUE) + +if(NOT PYTHON_MODULE_PREFIX) + set(PYTHON_MODULE_PREFIX "") +endif() diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/check-style.sh b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/check-style.sh new file mode 100644 index 0000000000000000000000000000000000000000..f7af2a4169744334af0b9c28823e98a502b813be --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/check-style.sh @@ -0,0 +1,44 @@ +#!/bin/bash +# +# Script to check include/test code for common pybind11 code style errors. +# +# This script currently checks for +# +# 1. missing space between keyword and parenthesis, e.g.: for(, if(, while( +# 2. Missing space between right parenthesis and brace, e.g. 'for (...){' +# 3. opening brace on its own line. It should always be on the same line as the +# if/while/for/do statement. +# +# Invoke as: tools/check-style.sh +# + +check_style_errors=0 +IFS=$'\n' + + +found="$(grep '\<\(if\|for\|while\|catch\)(\|){' $@ -rn --color=always)" +if [ -n "$found" ]; then + echo -e '\033[31;01mError: found the following coding style problems:\033[0m' + check_style_errors=1 + echo "$found" | sed -e 's/^/ /' +fi + +found="$(awk ' +function prefix(filename, lineno) { + return " \033[35m" filename "\033[36m:\033[32m" lineno "\033[36m:\033[0m" +} +function mark(pattern, string) { sub(pattern, "\033[01;31m&\033[0m", string); return string } +last && /^\s*{/ { + print prefix(FILENAME, FNR-1) mark("\\)\\s*$", last) + print prefix(FILENAME, FNR) mark("^\\s*{", $0) + last="" +} +{ last = /(if|for|while|catch|switch)\s*\(.*\)\s*$/ ? $0 : "" } +' $(find include -type f) $@)" +if [ -n "$found" ]; then + check_style_errors=1 + echo -e '\033[31;01mError: braces should occur on the same line as the if/while/.. statement. Found issues in the following files:\033[0m' + echo "$found" +fi + +exit $check_style_errors diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/cmake_uninstall.cmake.in b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/cmake_uninstall.cmake.in new file mode 100644 index 0000000000000000000000000000000000000000..1e5d2bb876d17f24b88b19ddb525d4146869944b --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/cmake_uninstall.cmake.in @@ -0,0 +1,23 @@ +# Source: https://gitlab.kitware.com/cmake/community/-/wikis/FAQ#can-i-do-make-uninstall-with-cmake + +if(NOT EXISTS "@CMAKE_BINARY_DIR@/install_manifest.txt") + message(FATAL_ERROR "Cannot find install manifest: @CMAKE_BINARY_DIR@/install_manifest.txt") +endif() + +file(READ "@CMAKE_BINARY_DIR@/install_manifest.txt" files) +string(REGEX REPLACE "\n" ";" files "${files}") +foreach(file ${files}) + message(STATUS "Uninstalling $ENV{DESTDIR}${file}") + if(IS_SYMLINK "$ENV{DESTDIR}${file}" OR EXISTS "$ENV{DESTDIR}${file}") + exec_program( + "@CMAKE_COMMAND@" ARGS + "-E remove \"$ENV{DESTDIR}${file}\"" + OUTPUT_VARIABLE rm_out + RETURN_VALUE rm_retval) + if(NOT "${rm_retval}" STREQUAL 0) + message(FATAL_ERROR "Problem when removing $ENV{DESTDIR}${file}") + endif() + else(IS_SYMLINK "$ENV{DESTDIR}${file}" OR EXISTS "$ENV{DESTDIR}${file}") + message(STATUS "File $ENV{DESTDIR}${file} does not exist.") + endif() +endforeach() diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/libsize.py b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/libsize.py new file mode 100644 index 0000000000000000000000000000000000000000..589c317f0dc2c5fe5a7ad945137d38410d8d5c3e --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/libsize.py @@ -0,0 +1,38 @@ +# -*- coding: utf-8 -*- +from __future__ import print_function, division +import os +import sys + +# Internal build script for generating debugging test .so size. +# Usage: +# python libsize.py file.so save.txt -- displays the size of file.so and, if save.txt exists, compares it to the +# size in it, then overwrites save.txt with the new size for future runs. + +if len(sys.argv) != 3: + sys.exit("Invalid arguments: usage: python libsize.py file.so save.txt") + +lib = sys.argv[1] +save = sys.argv[2] + +if not os.path.exists(lib): + sys.exit("Error: requested file ({}) does not exist".format(lib)) + +libsize = os.path.getsize(lib) + +print("------", os.path.basename(lib), "file size:", libsize, end="") + +if os.path.exists(save): + with open(save) as sf: + oldsize = int(sf.readline()) + + if oldsize > 0: + change = libsize - oldsize + if change == 0: + print(" (no change)") + else: + print(" (change of {:+} bytes = {:+.2%})".format(change, change / oldsize)) +else: + print() + +with open(save, "w") as sf: + sf.write(str(libsize)) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/make_changelog.py b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/make_changelog.py new file mode 100644 index 0000000000000000000000000000000000000000..609ce2f194fccdec754f10456daadebbb61ca8c7 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/make_changelog.py @@ -0,0 +1,63 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- + +import re + +import ghapi.all + +from rich import print +from rich.syntax import Syntax + + +ENTRY = re.compile( + r""" + Suggested \s changelog \s entry: + .* + ```rst + \s* + (.*?) + \s* + ``` +""", + re.DOTALL | re.VERBOSE, +) + +print() + + +api = ghapi.all.GhApi(owner="pybind", repo="pybind11") + +issues = api.issues.list_for_repo(labels="needs changelog", state="closed") +missing = [] + +for issue in issues: + changelog = ENTRY.findall(issue.body) + if changelog: + (msg,) = changelog + if not msg.startswith("* "): + msg = "* " + msg + if not msg.endswith("."): + msg += "." + + msg += f"\n `#{issue.number} <{issue.html_url}>`_" + + print(Syntax(msg, "rst", theme="ansi_light")) + print() + + else: + missing.append(issue) + +if missing: + print() + print("[blue]" + "-" * 30) + print() + + for issue in missing: + print(f"[red bold]Missing:[/red bold][red] {issue.title}") + print(f"[red] {issue.html_url}\n") + + print("[bold]Template:\n") + msg = "## Suggested changelog entry:\n\n```rst\n\n```" + print(Syntax(msg, "md", theme="ansi_light")) + +print() diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pybind11Common.cmake b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pybind11Common.cmake new file mode 100644 index 0000000000000000000000000000000000000000..57e42536e1fc6c4f5594ecbdde7c185f5dd25367 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pybind11Common.cmake @@ -0,0 +1,397 @@ +#[======================================================[.rst + +Adds the following targets:: + + pybind11::pybind11 - link to headers and pybind11 + pybind11::module - Adds module links + pybind11::embed - Adds embed links + pybind11::lto - Link time optimizations (manual selection) + pybind11::thin_lto - Link time optimizations (manual selection) + pybind11::python_link_helper - Adds link to Python libraries + pybind11::python2_no_register - Avoid warning/error with Python 2 + C++14/7 + pybind11::windows_extras - MSVC bigobj and mp for building multithreaded + pybind11::opt_size - avoid optimizations that increase code size + +Adds the following functions:: + + pybind11_strip(target) - strip target after building on linux/macOS + pybind11_find_import(module) - See if a module is installed. + +#]======================================================] + +# CMake 3.10 has an include_guard command, but we can't use that yet +if(TARGET pybind11::lto) + return() +endif() + +# If we are in subdirectory mode, all IMPORTED targets must be GLOBAL. If we +# are in CONFIG mode, they should be "normal" targets instead. +# In CMake 3.11+ you can promote a target to global after you create it, +# which might be simpler than this check. +get_property( + is_config + TARGET pybind11::headers + PROPERTY IMPORTED) +if(NOT is_config) + set(optional_global GLOBAL) +endif() + +# If not run in Python mode, we still would like this to at least +# include pybind11's include directory: +set(pybind11_INCLUDE_DIRS + "${pybind11_INCLUDE_DIR}" + CACHE INTERNAL "Include directory for pybind11 (Python not requested)") + +# --------------------- Shared targets ---------------------------- + +# Build an interface library target: +add_library(pybind11::pybind11 IMPORTED INTERFACE ${optional_global}) +set_property( + TARGET pybind11::pybind11 + APPEND + PROPERTY INTERFACE_LINK_LIBRARIES pybind11::headers) + +# Build a module target: +add_library(pybind11::module IMPORTED INTERFACE ${optional_global}) +set_property( + TARGET pybind11::module + APPEND + PROPERTY INTERFACE_LINK_LIBRARIES pybind11::pybind11) + +# Build an embed library target: +add_library(pybind11::embed IMPORTED INTERFACE ${optional_global}) +set_property( + TARGET pybind11::embed + APPEND + PROPERTY INTERFACE_LINK_LIBRARIES pybind11::pybind11) + +# ----------------------- no register ---------------------- + +# Workaround for Python 2.7 and C++17 (C++14 as a warning) incompatibility +# This adds the flags -Wno-register and -Wno-deprecated-register if the compiler +# is Clang 3.9+ or AppleClang and the compile language is CXX, or /wd5033 for MSVC (all languages, +# since MSVC didn't recognize COMPILE_LANGUAGE until CMake 3.11+). + +add_library(pybind11::python2_no_register INTERFACE IMPORTED ${optional_global}) +set(clang_4plus + "$,$,3.9>>>") +set(no_register "$>") + +if(MSVC AND CMAKE_VERSION VERSION_LESS 3.11) + set(cxx_no_register "${no_register}") +else() + set(cxx_no_register "$,${no_register}>") +endif() + +set(msvc "$") + +set_property( + TARGET pybind11::python2_no_register + PROPERTY INTERFACE_COMPILE_OPTIONS + "$<${cxx_no_register}:-Wno-register;-Wno-deprecated-register>" "$<${msvc}:/wd5033>") + +# --------------------------- link helper --------------------------- + +add_library(pybind11::python_link_helper IMPORTED INTERFACE ${optional_global}) + +if(CMAKE_VERSION VERSION_LESS 3.13) + # In CMake 3.11+, you can set INTERFACE properties via the normal methods, and + # this would be simpler. + set_property( + TARGET pybind11::python_link_helper + APPEND + PROPERTY INTERFACE_LINK_LIBRARIES "$<$:-undefined dynamic_lookup>") +else() + # link_options was added in 3.13+ + # This is safer, because you are ensured the deduplication pass in CMake will not consider + # these separate and remove one but not the other. + set_property( + TARGET pybind11::python_link_helper + APPEND + PROPERTY INTERFACE_LINK_OPTIONS "$<$:LINKER:-undefined,dynamic_lookup>") +endif() + +# ------------------------ Windows extras ------------------------- + +add_library(pybind11::windows_extras IMPORTED INTERFACE ${optional_global}) + +if(MSVC) # That's also clang-cl + # /bigobj is needed for bigger binding projects due to the limit to 64k + # addressable sections + set_property( + TARGET pybind11::windows_extras + APPEND + PROPERTY INTERFACE_COMPILE_OPTIONS /bigobj) + + # /MP enables multithreaded builds (relevant when there are many files) for MSVC + if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC") # no Clang no Intel + if(CMAKE_VERSION VERSION_LESS 3.11) + set_property( + TARGET pybind11::windows_extras + APPEND + PROPERTY INTERFACE_COMPILE_OPTIONS $<$>:/MP>) + else() + # Only set these options for C++ files. This is important so that, for + # instance, projects that include other types of source files like CUDA + # .cu files don't get these options propagated to nvcc since that would + # cause the build to fail. + set_property( + TARGET pybind11::windows_extras + APPEND + PROPERTY INTERFACE_COMPILE_OPTIONS + $<$>:$<$:/MP>>) + endif() + endif() +endif() + +# ----------------------- Optimize binary size -------------------------- + +add_library(pybind11::opt_size IMPORTED INTERFACE ${optional_global}) + +if(MSVC) + set(PYBIND11_OPT_SIZE /Os) +else() + set(PYBIND11_OPT_SIZE -Os) +endif() + +set_property( + TARGET pybind11::opt_size + APPEND + PROPERTY INTERFACE_COMPILE_OPTIONS $<$:${PYBIND11_OPT_SIZE}> + $<$:${PYBIND11_OPT_SIZE}> + $<$:${PYBIND11_OPT_SIZE}>) + +# ----------------------- Legacy option -------------------------- + +# Warn or error if old variable name used +if(PYBIND11_CPP_STANDARD) + string(REGEX MATCH [[..$]] VAL "${PYBIND11_CPP_STANDARD}") + if(CMAKE_CXX_STANDARD) + if(NOT CMAKE_CXX_STANDARD STREQUAL VAL) + message(WARNING "CMAKE_CXX_STANDARD=${CMAKE_CXX_STANDARD} does not match " + "PYBIND11_CPP_STANDARD=${PYBIND11_CPP_STANDARD}, " + "please remove PYBIND11_CPP_STANDARD from your cache") + endif() + else() + set(supported_standards 11 14 17 20) + if("${VAL}" IN_LIST supported_standards) + message(WARNING "USE -DCMAKE_CXX_STANDARD=${VAL} instead of PYBIND11_CPP_STANDARD") + set(CMAKE_CXX_STANDARD + ${VAL} + CACHE STRING "From PYBIND11_CPP_STANDARD") + else() + message(FATAL_ERROR "PYBIND11_CPP_STANDARD should be replaced with CMAKE_CXX_STANDARD " + "(last two chars: ${VAL} not understood as a valid CXX std)") + endif() + endif() +endif() + +# --------------------- Python specifics ------------------------- + +# Check to see which Python mode we are in, new, old, or no python +if(PYBIND11_NOPYTHON) + set(_pybind11_nopython ON) +elseif( + PYBIND11_FINDPYTHON + OR Python_FOUND + OR Python2_FOUND + OR Python3_FOUND) + # New mode + include("${CMAKE_CURRENT_LIST_DIR}/pybind11NewTools.cmake") + +else() + + # Classic mode + include("${CMAKE_CURRENT_LIST_DIR}/pybind11Tools.cmake") + +endif() + +# --------------------- pybind11_find_import ------------------------------- + +if(NOT _pybind11_nopython) + # Check to see if modules are importable. Use REQUIRED to force an error if + # one of the modules is not found. _FOUND will be set if the + # package was found (underscores replace dashes if present). QUIET will hide + # the found message, and VERSION will require a minimum version. A successful + # find will cache the result. + function(pybind11_find_import PYPI_NAME) + # CMake variables need underscores (PyPI doesn't care) + string(REPLACE "-" "_" NORM_PYPI_NAME "${PYPI_NAME}") + + # Return if found previously + if(${NORM_PYPI_NAME}_FOUND) + return() + endif() + + set(options "REQUIRED;QUIET") + set(oneValueArgs "VERSION") + cmake_parse_arguments(ARG "${options}" "${oneValueArgs}" "" ${ARGN}) + + if(ARG_REQUIRED) + set(status_level FATAL_ERROR) + else() + set(status_level WARNING) + endif() + + execute_process( + COMMAND + ${${_Python}_EXECUTABLE} -c + "from pkg_resources import get_distribution; print(get_distribution('${PYPI_NAME}').version)" + RESULT_VARIABLE RESULT_PRESENT + OUTPUT_VARIABLE PKG_VERSION + ERROR_QUIET) + + string(STRIP "${PKG_VERSION}" PKG_VERSION) + + # If a result is present, this failed + if(RESULT_PRESENT) + set(${NORM_PYPI_NAME}_FOUND + ${NORM_PYPI_NAME}-NOTFOUND + CACHE INTERNAL "") + # Always warn or error + message( + ${status_level} + "Missing: ${PYPI_NAME} ${ARG_VERSION}\nTry: ${${_Python}_EXECUTABLE} -m pip install ${PYPI_NAME}" + ) + else() + if(ARG_VERSION AND PKG_VERSION VERSION_LESS ARG_VERSION) + message( + ${status_level} + "Version incorrect: ${PYPI_NAME} ${PKG_VERSION} found, ${ARG_VERSION} required - try upgrading" + ) + else() + set(${NORM_PYPI_NAME}_FOUND + YES + CACHE INTERNAL "") + set(${NORM_PYPI_NAME}_VERSION + ${PKG_VERSION} + CACHE INTERNAL "") + endif() + if(NOT ARG_QUIET) + message(STATUS "Found ${PYPI_NAME} ${PKG_VERSION}") + endif() + endif() + if(NOT ARG_VERSION OR (NOT PKG_VERSION VERSION_LESS ARG_VERSION)) + # We have successfully found a good version, cache to avoid calling again. + endif() + endfunction() +endif() + +# --------------------- LTO ------------------------------- + +include(CheckCXXCompilerFlag) + +# Checks whether the given CXX/linker flags can compile and link a cxx file. +# cxxflags and linkerflags are lists of flags to use. The result variable is a +# unique variable name for each set of flags: the compilation result will be +# cached base on the result variable. If the flags work, sets them in +# cxxflags_out/linkerflags_out internal cache variables (in addition to +# ${result}). +function(_pybind11_return_if_cxx_and_linker_flags_work result cxxflags linkerflags cxxflags_out + linkerflags_out) + set(CMAKE_REQUIRED_LIBRARIES ${linkerflags}) + check_cxx_compiler_flag("${cxxflags}" ${result}) + if(${result}) + set(${cxxflags_out} + "${cxxflags}" + PARENT_SCOPE) + set(${linkerflags_out} + "${linkerflags}" + PARENT_SCOPE) + endif() +endfunction() + +function(_pybind11_generate_lto target prefer_thin_lto) + if(CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang") + set(cxx_append "") + set(linker_append "") + if(CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND NOT APPLE) + # Clang Gold plugin does not support -Os; append -O3 to MinSizeRel builds to override it + set(linker_append ";$<$:-O3>") + elseif(CMAKE_CXX_COMPILER_ID MATCHES "GNU") + set(cxx_append ";-fno-fat-lto-objects") + endif() + + if(CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND prefer_thin_lto) + _pybind11_return_if_cxx_and_linker_flags_work( + HAS_FLTO_THIN "-flto=thin${cxx_append}" "-flto=thin${linker_append}" + PYBIND11_LTO_CXX_FLAGS PYBIND11_LTO_LINKER_FLAGS) + endif() + + if(NOT HAS_FLTO_THIN) + _pybind11_return_if_cxx_and_linker_flags_work( + HAS_FLTO "-flto${cxx_append}" "-flto${linker_append}" PYBIND11_LTO_CXX_FLAGS + PYBIND11_LTO_LINKER_FLAGS) + endif() + elseif(CMAKE_CXX_COMPILER_ID MATCHES "Intel") + # Intel equivalent to LTO is called IPO + _pybind11_return_if_cxx_and_linker_flags_work(HAS_INTEL_IPO "-ipo" "-ipo" + PYBIND11_LTO_CXX_FLAGS PYBIND11_LTO_LINKER_FLAGS) + elseif(MSVC) + # cmake only interprets libraries as linker flags when they start with a - (otherwise it + # converts /LTCG to \LTCG as if it was a Windows path). Luckily MSVC supports passing flags + # with - instead of /, even if it is a bit non-standard: + _pybind11_return_if_cxx_and_linker_flags_work(HAS_MSVC_GL_LTCG "/GL" "-LTCG" + PYBIND11_LTO_CXX_FLAGS PYBIND11_LTO_LINKER_FLAGS) + endif() + + # Enable LTO flags if found, except for Debug builds + if(PYBIND11_LTO_CXX_FLAGS) + # CONFIG takes multiple values in CMake 3.19+, until then we have to use OR + set(is_debug "$,$>") + set(not_debug "$") + set(cxx_lang "$") + if(MSVC AND CMAKE_VERSION VERSION_LESS 3.11) + set(genex "${not_debug}") + else() + set(genex "$") + endif() + set_property( + TARGET ${target} + APPEND + PROPERTY INTERFACE_COMPILE_OPTIONS "$<${genex}:${PYBIND11_LTO_CXX_FLAGS}>") + if(CMAKE_PROJECT_NAME STREQUAL "pybind11") + message(STATUS "${target} enabled") + endif() + else() + if(CMAKE_PROJECT_NAME STREQUAL "pybind11") + message(STATUS "${target} disabled (not supported by the compiler and/or linker)") + endif() + endif() + + if(PYBIND11_LTO_LINKER_FLAGS) + if(CMAKE_VERSION VERSION_LESS 3.11) + set_property( + TARGET ${target} + APPEND + PROPERTY INTERFACE_LINK_LIBRARIES "$<${not_debug}:${PYBIND11_LTO_LINKER_FLAGS}>") + else() + set_property( + TARGET ${target} + APPEND + PROPERTY INTERFACE_LINK_OPTIONS "$<${not_debug}:${PYBIND11_LTO_LINKER_FLAGS}>") + endif() + endif() +endfunction() + +add_library(pybind11::lto IMPORTED INTERFACE ${optional_global}) +_pybind11_generate_lto(pybind11::lto FALSE) + +add_library(pybind11::thin_lto IMPORTED INTERFACE ${optional_global}) +_pybind11_generate_lto(pybind11::thin_lto TRUE) + +# ---------------------- pybind11_strip ----------------------------- + +function(pybind11_strip target_name) + # Strip unnecessary sections of the binary on Linux/macOS + if(CMAKE_STRIP) + if(APPLE) + set(x_opt -x) + endif() + + add_custom_command( + TARGET ${target_name} + POST_BUILD + COMMAND ${CMAKE_STRIP} ${x_opt} $) + endif() +endfunction() diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pybind11Config.cmake.in b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pybind11Config.cmake.in new file mode 100644 index 0000000000000000000000000000000000000000..9921aeb3552af198c72bde6e0e75bc23ca6cea31 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pybind11Config.cmake.in @@ -0,0 +1,232 @@ +#[=============================================================================[.rst: + +pybind11Config.cmake +#################### + +Exported variables +================== + +This module sets the following variables in your project: + +``pybind11_FOUND`` + true if pybind11 and all required components found on the system +``pybind11_VERSION`` + pybind11 version in format Major.Minor.Release +``pybind11_VERSION_TYPE`` + pybind11 version type (dev, release) +``pybind11_INCLUDE_DIRS`` + Directories where pybind11 and python headers are located. +``pybind11_INCLUDE_DIR`` + Directory where pybind11 headers are located. +``pybind11_DEFINITIONS`` + Definitions necessary to use pybind11, namely USING_pybind11. +``pybind11_LIBRARIES`` + Compile flags and python libraries (as needed) to link against. +``pybind11_LIBRARY`` + Empty. + +Available components: None + + +Exported targets +================ + +If pybind11 is found, this module defines the following ``IMPORTED`` +interface library targets: + +``pybind11::module`` + for extension modules. +``pybind11::embed`` + for embedding the Python interpreter. + +Python headers, libraries (as needed by platform), and the C++ standard +are attached to the target. + +Advanced targets are also supplied - these are primary for users building +complex applications, and they are available in all modes: + +``pybind11::headers`` + Just the pybind11 headers and minimum compile requirements. +``pybind11::pybind11`` + Python headers too. +``pybind11::python_link_helper`` + Just the "linking" part of ``pybind11:module``, for CMake < 3.15. +``pybind11::python2_no_register`` + Quiets the warning/error when mixing C++14+ and Python 2, also included in ``pybind11::module``. +``pybind11::thin_lto`` + An alternative to ``INTERPROCEDURAL_OPTIMIZATION``. +``pybind11::lto`` + An alternative to ``INTERPROCEDURAL_OPTIMIZATION`` (also avoids thin LTO on clang). +``pybind11::windows_extras`` + Adds bigobj and mp for MSVC. + +Modes +===== + +There are two modes provided; classic, which is built on the old Python +discovery packages in CMake, or the new FindPython mode, which uses FindPython +from 3.12+ forward (3.15+ _highly_ recommended). + +New FindPython mode +^^^^^^^^^^^^^^^^^^^ + +To activate this mode, either call ``find_package(Python COMPONENTS Interpreter Development)`` +before finding this package, or set the ``PYBIND11_FINDPYTHON`` variable to ON. In this mode, +you can either use the basic targets, or use the FindPython tools: + +.. code-block:: cmake + + find_package(Python COMPONENTS Interpreter Development) + find_package(pybind11 CONFIG) + + # pybind11 method: + pybind11_add_module(MyModule1 src1.cpp) + + # Python method: + Python_add_library(MyModule2 src2.cpp) + target_link_libraries(MyModule2 pybind11::headers) + set_target_properties(MyModule2 PROPERTIES + INTERPROCEDURAL_OPTIMIZATION ON + CXX_VISIBILITY_PRESET ON + VISIBLITY_INLINES_HIDDEN ON) + +If you build targets yourself, you may be interested in stripping the output +for reduced size; this is the one other feature that the helper function gives you. + +Classic mode +^^^^^^^^^^^^ + +Set PythonLibsNew variables to influence python detection and +CMAKE_CXX_STANDARD to influence standard setting. + +.. code-block:: cmake + + find_package(pybind11 CONFIG REQUIRED) + + # Create an extension module + add_library(mylib MODULE main.cpp) + target_link_libraries(mylib PUBLIC pybind11::module) + + # Or embed the Python interpreter into an executable + add_executable(myexe main.cpp) + target_link_libraries(myexe PUBLIC pybind11::embed) + + +Hints +===== + +The following variables can be set to guide the search for this package: + +``pybind11_DIR`` + CMake variable, set to directory containing this Config file. +``CMAKE_PREFIX_PATH`` + CMake variable, set to root directory of this package. +``PATH`` + Environment variable, set to bin directory of this package. +``CMAKE_DISABLE_FIND_PACKAGE_pybind11`` + CMake variable, disables ``find_package(pybind11)`` when not ``REQUIRED``, + perhaps to force internal build. + +Commands +======== + +pybind11_add_module +^^^^^^^^^^^^^^^^^^^ + +This module defines the following commands to assist with creating Python modules: + +.. code-block:: cmake + + pybind11_add_module( + [STATIC|SHARED|MODULE] + [THIN_LTO] [OPT_SIZE] [NO_EXTRAS] [WITHOUT_SOBAI] + ... + ) + +Add a module and setup all helpers. You can select the type of the library; the +default is ``MODULE``. There are several options: + +``OPT_SIZE`` + Optimize for size, even if the ``CMAKE_BUILD_TYPE`` is not ``RelSize``. +``THIN_LTO`` + Use thin TLO instead of regular if there's a choice (pybind11's selection + is disabled if ``CMAKE_INTERPROCEDURAL_OPTIMIZATIONS`` is set). +``WITHOUT_SOABI`` + Disable the SOABI component (``PYBIND11_NEWPYTHON`` mode only). +``NO_EXTRAS`` + Disable all extras, exit immediately after making the module. + +pybind11_strip +^^^^^^^^^^^^^^ + +.. code-block:: cmake + + pybind11_strip() + +Strip a target after building it (linux/macOS), called by ``pybind11_add_module``. + +pybind11_extension +^^^^^^^^^^^^^^^^^^ + +.. code-block:: cmake + + pybind11_extension() + +Sets the Python extension name correctly for Python on your platform, called by +``pybind11_add_module``. + +pybind11_find_import(module) +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. code-block:: cmake + + pybind11_find_import( [VERSION ] [REQUIRED] [QUIET]) + +See if a module is installed. Use the registered name (the one on PyPI). You +can specify a ``VERSION``, and you can specify ``REQUIRED`` or ``QUIET``. Only available if +``NOPYTHON`` mode is not active. Sets ``module_VERSION`` and ``module_FOUND``. Caches the +result once a valid install is found. + +Suggested usage +=============== + +Using ``find_package`` with version info is not recommended except for release versions. + +.. code-block:: cmake + + find_package(pybind11 CONFIG) + find_package(pybind11 2.0 EXACT CONFIG REQUIRED) + +#]=============================================================================] +@PACKAGE_INIT@ + +# Location of pybind11/pybind11.h +set(pybind11_INCLUDE_DIR "${PACKAGE_PREFIX_DIR}/@CMAKE_INSTALL_INCLUDEDIR@") + +set(pybind11_LIBRARY "") +set(pybind11_DEFINITIONS USING_pybind11) +set(pybind11_VERSION_TYPE "@pybind11_VERSION_TYPE@") + +check_required_components(pybind11) + +if(TARGET pybind11::python_link_helper) + # This has already been setup elsewhere, such as with a previous call or + # add_subdirectory + return() +endif() + +include("${CMAKE_CURRENT_LIST_DIR}/pybind11Targets.cmake") + +# Easier to use / remember +add_library(pybind11::headers IMPORTED INTERFACE) +set_target_properties(pybind11::headers PROPERTIES INTERFACE_LINK_LIBRARIES + pybind11::pybind11_headers) + +include("${CMAKE_CURRENT_LIST_DIR}/pybind11Common.cmake") + +if(NOT pybind11_FIND_QUIETLY) + message( + STATUS + "Found pybind11: ${pybind11_INCLUDE_DIR} (found version \"${pybind11_VERSION}\" ${pybind11_VERSION_TYPE})" + ) +endif() diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pybind11NewTools.cmake b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pybind11NewTools.cmake new file mode 100644 index 0000000000000000000000000000000000000000..18da8be1701f37e5b9ebc94b7825d2230ca4bcc4 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pybind11NewTools.cmake @@ -0,0 +1,267 @@ +# tools/pybind11NewTools.cmake -- Build system for the pybind11 modules +# +# Copyright (c) 2020 Wenzel Jakob and Henry Schreiner +# +# All rights reserved. Use of this source code is governed by a +# BSD-style license that can be found in the LICENSE file. + +get_property( + is_config + TARGET pybind11::headers + PROPERTY IMPORTED) + +if(pybind11_FIND_QUIETLY) + set(_pybind11_quiet QUIET) +else() + set(_pybind11_quiet "") +endif() + +if(CMAKE_VERSION VERSION_LESS 3.12) + message(FATAL_ERROR "You cannot use the new FindPython module with CMake < 3.12") +endif() + +if(NOT Python_FOUND + AND NOT Python3_FOUND + AND NOT Python2_FOUND) + if(NOT DEFINED Python_FIND_IMPLEMENTATIONS) + set(Python_FIND_IMPLEMENTATIONS CPython PyPy) + endif() + + # GitHub Actions like activation + if(NOT DEFINED Python_ROOT_DIR AND DEFINED ENV{pythonLocation}) + set(Python_ROOT_DIR "$ENV{pythonLocation}") + endif() + + find_package(Python REQUIRED COMPONENTS Interpreter Development ${_pybind11_quiet}) + + # If we are in submodule mode, export the Python targets to global targets. + # If this behavior is not desired, FindPython _before_ pybind11. + if(NOT is_config) + set_property(TARGET Python::Python PROPERTY IMPORTED_GLOBAL TRUE) + set_property(TARGET Python::Interpreter PROPERTY IMPORTED_GLOBAL TRUE) + if(TARGET Python::Module) + set_property(TARGET Python::Module PROPERTY IMPORTED_GLOBAL TRUE) + endif() + endif() +endif() + +if(Python_FOUND) + set(_Python + Python + CACHE INTERNAL "" FORCE) +elseif(Python3_FOUND AND NOT Python2_FOUND) + set(_Python + Python3 + CACHE INTERNAL "" FORCE) +elseif(Python2_FOUND AND NOT Python3_FOUND) + set(_Python + Python2 + CACHE INTERNAL "" FORCE) +else() + message(AUTHOR_WARNING "Python2 and Python3 both present, pybind11 in " + "PYBIND11_NOPYTHON mode (manually activate to silence warning)") + set(_pybind11_nopython ON) + return() +endif() + +if(PYBIND11_MASTER_PROJECT) + if(${_Python}_INTERPRETER_ID MATCHES "PyPy") + message(STATUS "PyPy ${${_Python}_PyPy_VERSION} (Py ${${_Python}_VERSION})") + else() + message(STATUS "${_Python} ${${_Python}_VERSION}") + endif() +endif() + +# If a user finds Python, they may forget to include the Interpreter component +# and the following two steps require it. It is highly recommended by CMake +# when finding development libraries anyway, so we will require it. +if(NOT DEFINED ${_Python}_EXECUTABLE) + message( + FATAL_ERROR + "${_Python} was found without the Interpreter component. Pybind11 requires this component.") + +endif() + +if(NOT DEFINED PYTHON_IS_DEBUG) + # Debug check - see https://stackoverflow.com/questions/646518/python-how-to-detect-debug-Interpreter + execute_process( + COMMAND "${${_Python}_EXECUTABLE}" "-c" + "import sys; sys.exit(hasattr(sys, 'gettotalrefcount'))" + RESULT_VARIABLE _PYTHON_IS_DEBUG) + set(PYTHON_IS_DEBUG + "${_PYTHON_IS_DEBUG}" + CACHE INTERNAL "Python debug status") +endif() + +# Get the suffix - SO is deprecated, should use EXT_SUFFIX, but this is +# required for PyPy3 (as of 7.3.1) +if(NOT DEFINED PYTHON_MODULE_EXTENSION) + execute_process( + COMMAND + "${${_Python}_EXECUTABLE}" "-c" + "from distutils import sysconfig as s;print(s.get_config_var('EXT_SUFFIX') or s.get_config_var('SO'))" + OUTPUT_VARIABLE _PYTHON_MODULE_EXTENSION + ERROR_VARIABLE _PYTHON_MODULE_EXTENSION_ERR + OUTPUT_STRIP_TRAILING_WHITESPACE) + + if(_PYTHON_MODULE_EXTENSION STREQUAL "") + message( + FATAL_ERROR "pybind11 could not query the module file extension, likely the 'distutils'" + "package is not installed. Full error message:\n${_PYTHON_MODULE_EXTENSION_ERR}") + endif() + + # This needs to be available for the pybind11_extension function + set(PYTHON_MODULE_EXTENSION + "${_PYTHON_MODULE_EXTENSION}" + CACHE INTERNAL "") +endif() + +# Python debug libraries expose slightly different objects before 3.8 +# https://docs.python.org/3.6/c-api/intro.html#debugging-builds +# https://stackoverflow.com/questions/39161202/how-to-work-around-missing-pymodule-create2-in-amd64-win-python35-d-lib +if(PYTHON_IS_DEBUG) + set_property( + TARGET pybind11::pybind11 + APPEND + PROPERTY INTERFACE_COMPILE_DEFINITIONS Py_DEBUG) +endif() + +# Check on every access - since Python2 and Python3 could have been used - do nothing in that case. + +if(DEFINED ${_Python}_INCLUDE_DIRS) + # Only add Python for build - must be added during the import for config + # since it has to be re-discovered. + # + # This needs to be a target to be included after the local pybind11 + # directory, just in case there there is an installed pybind11 sitting + # next to Python's includes. It also ensures Python is a SYSTEM library. + add_library(pybind11::python_headers INTERFACE IMPORTED) + set_property( + TARGET pybind11::python_headers PROPERTY INTERFACE_INCLUDE_DIRECTORIES + "$") + set_property( + TARGET pybind11::pybind11 + APPEND + PROPERTY INTERFACE_LINK_LIBRARIES pybind11::python_headers) + set(pybind11_INCLUDE_DIRS + "${pybind11_INCLUDE_DIR}" "${${_Python}_INCLUDE_DIRS}" + CACHE INTERNAL "Directories where pybind11 and possibly Python headers are located") +endif() + +if(DEFINED ${_Python}_VERSION AND ${_Python}_VERSION VERSION_LESS 3) + set_property( + TARGET pybind11::pybind11 + APPEND + PROPERTY INTERFACE_LINK_LIBRARIES pybind11::python2_no_register) +endif() + +# In CMake 3.18+, you can find these separately, so include an if +if(TARGET ${_Python}::Python) + set_property( + TARGET pybind11::embed + APPEND + PROPERTY INTERFACE_LINK_LIBRARIES ${_Python}::Python) +endif() + +# CMake 3.15+ has this +if(TARGET ${_Python}::Module) + set_property( + TARGET pybind11::module + APPEND + PROPERTY INTERFACE_LINK_LIBRARIES ${_Python}::Module) +else() + set_property( + TARGET pybind11::module + APPEND + PROPERTY INTERFACE_LINK_LIBRARIES pybind11::python_link_helper) +endif() + +# WITHOUT_SOABI and WITH_SOABI will disable the custom extension handling used by pybind11. +# WITH_SOABI is passed on to python_add_library. +function(pybind11_add_module target_name) + cmake_parse_arguments(PARSE_ARGV 1 ARG + "STATIC;SHARED;MODULE;THIN_LTO;OPT_SIZE;NO_EXTRAS;WITHOUT_SOABI" "" "") + + if(ARG_STATIC) + set(lib_type STATIC) + elseif(ARG_SHARED) + set(lib_type SHARED) + else() + set(lib_type MODULE) + endif() + + if("${_Python}" STREQUAL "Python") + python_add_library(${target_name} ${lib_type} ${ARG_UNPARSED_ARGUMENTS}) + elseif("${_Python}" STREQUAL "Python3") + python3_add_library(${target_name} ${lib_type} ${ARG_UNPARSED_ARGUMENTS}) + elseif("${_Python}" STREQUAL "Python2") + python2_add_library(${target_name} ${lib_type} ${ARG_UNPARSED_ARGUMENTS}) + else() + message(FATAL_ERROR "Cannot detect FindPython version: ${_Python}") + endif() + + target_link_libraries(${target_name} PRIVATE pybind11::headers) + + if(lib_type STREQUAL "MODULE") + target_link_libraries(${target_name} PRIVATE pybind11::module) + else() + target_link_libraries(${target_name} PRIVATE pybind11::embed) + endif() + + if(MSVC) + target_link_libraries(${target_name} PRIVATE pybind11::windows_extras) + endif() + + if(DEFINED ${_Python}_VERSION AND ${_Python}_VERSION VERSION_LESS 3) + target_link_libraries(${target_name} PRIVATE pybind11::python2_no_register) + endif() + + # -fvisibility=hidden is required to allow multiple modules compiled against + # different pybind versions to work properly, and for some features (e.g. + # py::module_local). We force it on everything inside the `pybind11` + # namespace; also turning it on for a pybind module compilation here avoids + # potential warnings or issues from having mixed hidden/non-hidden types. + if(NOT DEFINED CMAKE_CXX_VISIBILITY_PRESET) + set_target_properties(${target_name} PROPERTIES CXX_VISIBILITY_PRESET "hidden") + endif() + + if(NOT DEFINED CMAKE_CUDA_VISIBILITY_PRESET) + set_target_properties(${target_name} PROPERTIES CUDA_VISIBILITY_PRESET "hidden") + endif() + + # If we don't pass a WITH_SOABI or WITHOUT_SOABI, use our own default handling of extensions + if(NOT ARG_WITHOUT_SOABI OR NOT "WITH_SOABI" IN_LIST ARG_UNPARSED_ARGUMENTS) + pybind11_extension(${target_name}) + endif() + + if(ARG_NO_EXTRAS) + return() + endif() + + if(NOT DEFINED CMAKE_INTERPROCEDURAL_OPTIMIZATION) + if(ARG_THIN_LTO) + target_link_libraries(${target_name} PRIVATE pybind11::thin_lto) + else() + target_link_libraries(${target_name} PRIVATE pybind11::lto) + endif() + endif() + + if(NOT MSVC AND NOT ${CMAKE_BUILD_TYPE} MATCHES Debug|RelWithDebInfo) + # Strip unnecessary sections of the binary on Linux/macOS + pybind11_strip(${target_name}) + endif() + + if(MSVC) + target_link_libraries(${target_name} PRIVATE pybind11::windows_extras) + endif() + + if(ARG_OPT_SIZE) + target_link_libraries(${target_name} PRIVATE pybind11::opt_size) + endif() +endfunction() + +function(pybind11_extension name) + # The extension is precomputed + set_target_properties(${name} PROPERTIES PREFIX "" SUFFIX "${PYTHON_MODULE_EXTENSION}") + +endfunction() diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pybind11Tools.cmake b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pybind11Tools.cmake new file mode 100644 index 0000000000000000000000000000000000000000..323135399810958931390e811cebf135f3ee27a9 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pybind11Tools.cmake @@ -0,0 +1,220 @@ +# tools/pybind11Tools.cmake -- Build system for the pybind11 modules +# +# Copyright (c) 2020 Wenzel Jakob +# +# All rights reserved. Use of this source code is governed by a +# BSD-style license that can be found in the LICENSE file. + +# Built-in in CMake 3.5+ +include(CMakeParseArguments) + +if(pybind11_FIND_QUIETLY) + set(_pybind11_quiet QUIET) +else() + set(_pybind11_quiet "") +endif() + +# If this is the first run, PYTHON_VERSION can stand in for PYBIND11_PYTHON_VERSION +if(NOT DEFINED PYBIND11_PYTHON_VERSION AND DEFINED PYTHON_VERSION) + message(WARNING "Set PYBIND11_PYTHON_VERSION to search for a specific version, not " + "PYTHON_VERSION (which is an output). Assuming that is what you " + "meant to do and continuing anyway.") + set(PYBIND11_PYTHON_VERSION + "${PYTHON_VERSION}" + CACHE STRING "Python version to use for compiling modules") + unset(PYTHON_VERSION) + unset(PYTHON_VERSION CACHE) +elseif(DEFINED PYBIND11_PYTHON_VERSION) + # If this is set as a normal variable, promote it + set(PYBIND11_PYTHON_VERSION + "${PYBIND11_PYTHON_VERSION}" + CACHE STRING "Python version to use for compiling modules") +else() + # Make an empty cache variable. + set(PYBIND11_PYTHON_VERSION + "" + CACHE STRING "Python version to use for compiling modules") +endif() + +# A user can set versions manually too +set(Python_ADDITIONAL_VERSIONS + "3.10;3.9;3.8;3.7;3.6;3.5;3.4" + CACHE INTERNAL "") + +list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}") +find_package(PythonLibsNew ${PYBIND11_PYTHON_VERSION} MODULE REQUIRED ${_pybind11_quiet}) +list(REMOVE_AT CMAKE_MODULE_PATH -1) + +# Cache variables so pybind11_add_module can be used in parent projects +set(PYTHON_INCLUDE_DIRS + ${PYTHON_INCLUDE_DIRS} + CACHE INTERNAL "") +set(PYTHON_LIBRARIES + ${PYTHON_LIBRARIES} + CACHE INTERNAL "") +set(PYTHON_MODULE_PREFIX + ${PYTHON_MODULE_PREFIX} + CACHE INTERNAL "") +set(PYTHON_MODULE_EXTENSION + ${PYTHON_MODULE_EXTENSION} + CACHE INTERNAL "") +set(PYTHON_VERSION_MAJOR + ${PYTHON_VERSION_MAJOR} + CACHE INTERNAL "") +set(PYTHON_VERSION_MINOR + ${PYTHON_VERSION_MINOR} + CACHE INTERNAL "") +set(PYTHON_VERSION + ${PYTHON_VERSION} + CACHE INTERNAL "") +set(PYTHON_IS_DEBUG + "${PYTHON_IS_DEBUG}" + CACHE INTERNAL "") + +if(PYBIND11_MASTER_PROJECT) + if(PYTHON_MODULE_EXTENSION MATCHES "pypy") + if(NOT DEFINED PYPY_VERSION) + execute_process( + COMMAND ${PYTHON_EXECUTABLE} -c + [=[import sys; sys.stdout.write(".".join(map(str, sys.pypy_version_info[:3])))]=] + OUTPUT_VARIABLE pypy_version) + set(PYPY_VERSION + ${pypy_version} + CACHE INTERNAL "") + endif() + message(STATUS "PYPY ${PYPY_VERSION} (Py ${PYTHON_VERSION})") + else() + message(STATUS "PYTHON ${PYTHON_VERSION}") + endif() +endif() + +# Only add Python for build - must be added during the import for config since +# it has to be re-discovered. +# +# This needs to be an target to it is included after the local pybind11 +# directory, just in case there are multiple versions of pybind11, we want the +# one we expect. +add_library(pybind11::python_headers INTERFACE IMPORTED) +set_property(TARGET pybind11::python_headers PROPERTY INTERFACE_INCLUDE_DIRECTORIES + "$") +set_property( + TARGET pybind11::pybind11 + APPEND + PROPERTY INTERFACE_LINK_LIBRARIES pybind11::python_headers) + +set(pybind11_INCLUDE_DIRS + "${pybind11_INCLUDE_DIR}" "${PYTHON_INCLUDE_DIRS}" + CACHE INTERNAL "Directories where pybind11 and possibly Python headers are located") + +# Python debug libraries expose slightly different objects before 3.8 +# https://docs.python.org/3.6/c-api/intro.html#debugging-builds +# https://stackoverflow.com/questions/39161202/how-to-work-around-missing-pymodule-create2-in-amd64-win-python35-d-lib +if(PYTHON_IS_DEBUG) + set_property( + TARGET pybind11::pybind11 + APPEND + PROPERTY INTERFACE_COMPILE_DEFINITIONS Py_DEBUG) +endif() + +set_property( + TARGET pybind11::module + APPEND + PROPERTY + INTERFACE_LINK_LIBRARIES pybind11::python_link_helper + "$<$,$>:$>") + +if(PYTHON_VERSION VERSION_LESS 3) + set_property( + TARGET pybind11::pybind11 + APPEND + PROPERTY INTERFACE_LINK_LIBRARIES pybind11::python2_no_register) +endif() + +set_property( + TARGET pybind11::embed + APPEND + PROPERTY INTERFACE_LINK_LIBRARIES pybind11::pybind11 $) + +function(pybind11_extension name) + # The prefix and extension are provided by FindPythonLibsNew.cmake + set_target_properties(${name} PROPERTIES PREFIX "${PYTHON_MODULE_PREFIX}" + SUFFIX "${PYTHON_MODULE_EXTENSION}") +endfunction() + +# Build a Python extension module: +# pybind11_add_module( [MODULE | SHARED] [EXCLUDE_FROM_ALL] +# [NO_EXTRAS] [THIN_LTO] [OPT_SIZE] source1 [source2 ...]) +# +function(pybind11_add_module target_name) + set(options "MODULE;SHARED;EXCLUDE_FROM_ALL;NO_EXTRAS;SYSTEM;THIN_LTO;OPT_SIZE") + cmake_parse_arguments(ARG "${options}" "" "" ${ARGN}) + + if(ARG_MODULE AND ARG_SHARED) + message(FATAL_ERROR "Can't be both MODULE and SHARED") + elseif(ARG_SHARED) + set(lib_type SHARED) + else() + set(lib_type MODULE) + endif() + + if(ARG_EXCLUDE_FROM_ALL) + set(exclude_from_all EXCLUDE_FROM_ALL) + else() + set(exclude_from_all "") + endif() + + add_library(${target_name} ${lib_type} ${exclude_from_all} ${ARG_UNPARSED_ARGUMENTS}) + + target_link_libraries(${target_name} PRIVATE pybind11::module) + + if(ARG_SYSTEM) + message( + STATUS + "Warning: this does not have an effect - use NO_SYSTEM_FROM_IMPORTED if using imported targets" + ) + endif() + + pybind11_extension(${target_name}) + + # -fvisibility=hidden is required to allow multiple modules compiled against + # different pybind versions to work properly, and for some features (e.g. + # py::module_local). We force it on everything inside the `pybind11` + # namespace; also turning it on for a pybind module compilation here avoids + # potential warnings or issues from having mixed hidden/non-hidden types. + if(NOT DEFINED CMAKE_CXX_VISIBILITY_PRESET) + set_target_properties(${target_name} PROPERTIES CXX_VISIBILITY_PRESET "hidden") + endif() + + if(NOT DEFINED CMAKE_CUDA_VISIBILITY_PRESET) + set_target_properties(${target_name} PROPERTIES CUDA_VISIBILITY_PRESET "hidden") + endif() + + if(ARG_NO_EXTRAS) + return() + endif() + + if(NOT DEFINED CMAKE_INTERPROCEDURAL_OPTIMIZATION) + if(ARG_THIN_LTO) + target_link_libraries(${target_name} PRIVATE pybind11::thin_lto) + else() + target_link_libraries(${target_name} PRIVATE pybind11::lto) + endif() + endif() + + if(NOT MSVC AND NOT ${CMAKE_BUILD_TYPE} MATCHES Debug|RelWithDebInfo) + pybind11_strip(${target_name}) + endif() + + if(MSVC) + target_link_libraries(${target_name} PRIVATE pybind11::windows_extras) + endif() + + if(ARG_OPT_SIZE) + target_link_libraries(${target_name} PRIVATE pybind11::opt_size) + endif() +endfunction() + +# Provide general way to call common Python commands in "common" file. +set(_Python + PYTHON + CACHE INTERNAL "" FORCE) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pyproject.toml b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pyproject.toml new file mode 100644 index 0000000000000000000000000000000000000000..8fe2f47af9a18ad9f272357023d09f78aefebe2d --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/pyproject.toml @@ -0,0 +1,3 @@ +[build-system] +requires = ["setuptools>=42", "wheel"] +build-backend = "setuptools.build_meta" diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/setup_global.py.in b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/setup_global.py.in new file mode 100644 index 0000000000000000000000000000000000000000..4cf040b2d8102bc9220f4858114b217750173923 --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/setup_global.py.in @@ -0,0 +1,63 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +# Setup script for pybind11-global (in the sdist or in tools/setup_global.py in the repository) +# This package is targeted for easy use from CMake. + +import contextlib +import glob +import os +import re +import shutil +import subprocess +import sys +import tempfile + +# Setuptools has to be before distutils +from setuptools import setup + +from distutils.command.install_headers import install_headers + +class InstallHeadersNested(install_headers): + def run(self): + headers = self.distribution.headers or [] + for header in headers: + # Remove pybind11/include/ + short_header = header.split("/", 2)[-1] + + dst = os.path.join(self.install_dir, os.path.dirname(short_header)) + self.mkpath(dst) + (out, _) = self.copy_file(header, dst) + self.outfiles.append(out) + + +main_headers = glob.glob("pybind11/include/pybind11/*.h") +detail_headers = glob.glob("pybind11/include/pybind11/detail/*.h") +cmake_files = glob.glob("pybind11/share/cmake/pybind11/*.cmake") +headers = main_headers + detail_headers + +cmdclass = {"install_headers": InstallHeadersNested} +$extra_cmd + +# This will _not_ affect installing from wheels, +# only building wheels or installing from SDist. +# Primarily intended on Windows, where this is sometimes +# customized (for example, conda-forge uses Library/) +base = os.environ.get("PYBIND11_GLOBAL_PREFIX", "") + +# Must have a separator +if base and not base.endswith("/"): + base += "/" + +setup( + name="pybind11_global", + version="$version", + packages=[], + headers=headers, + data_files=[ + (base + "share/cmake/pybind11", cmake_files), + (base + "include/pybind11", main_headers), + (base + "include/pybind11/detail", detail_headers), + ], + cmdclass=cmdclass, +) diff --git a/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/setup_main.py.in b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/setup_main.py.in new file mode 100644 index 0000000000000000000000000000000000000000..2231a08fdc1d4f0c9a0241e744d99bef486270bf --- /dev/null +++ b/methods/ring/utils/fast_gicp/thirdparty/pybind11/tools/setup_main.py.in @@ -0,0 +1,36 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +# Setup script (in the sdist or in tools/setup_main.py in the repository) + +from setuptools import setup + +cmdclass = {} +$extra_cmd + +setup( + name="pybind11", + version="$version", + download_url='https://github.com/pybind/pybind11/tarball/v$version', + packages=[ + "pybind11", + "pybind11.include.pybind11", + "pybind11.include.pybind11.detail", + "pybind11.share.cmake.pybind11", + ], + package_data={ + "pybind11": ["py.typed", "*.pyi"], + "pybind11.include.pybind11": ["*.h"], + "pybind11.include.pybind11.detail": ["*.h"], + "pybind11.share.cmake.pybind11": ["*.cmake"], + }, + extras_require={ + "global": ["pybind11_global==$version"] + }, + entry_points={ + "console_scripts": [ + "pybind11-config = pybind11.__main__:main", + ] + }, + cmdclass=cmdclass +)